@article {pmid40273693, year = {2025}, author = {Yan, X and Xin, Y and Zhu, L and Tang, Q and Chen, M and Wei, Y and Zhang, J and Richnow, HH}, title = {Neglected role of virus-host interactions driving antibiotic resistance genes reduction in an urban river receiving treated wastewater.}, journal = {Water research}, volume = {282}, number = {}, pages = {123627}, doi = {10.1016/j.watres.2025.123627}, pmid = {40273693}, issn = {1879-2448}, abstract = {Treated wastewater from wastewater treatment plants (WWTPs) is a major contributor to the transfer of antibiotic resistance genes (ARGs) into urban rivers. However, the role of viral communities in this process remains poorly understood. This study focused on North Canal in Beijing, China, which receives over 80 % of its water from treated wastewater, to investigate the impact of viral communities on ARGs transfer. Results showed significant seasonal variation in the abundance and composition of ARGs, with 30 high-risk ARGs detected, accounting for 1.50 % ± 1.28 % of total ARGs. The assembly of ARGs in North Canal followed a stochastic process of homogenizing dispersal, with conjugative mobility playing a key role in horizontal gene transfer with Pseudomonas as primary host for HGT. The potential conjugative mobility of ARGs is significantly higher in wet season (69.4 % ± 17.3 %) compared to dry season (42.9 % ± 17.1 %), with conjugation frequencies ranging from 1.18 × 10[-6] to 2.26 × 10[-4]. Viral species accumulation curves approaching saturation indicated the well captured viral diversity, and no phages carrying ARGs were found among 27,523 non-redundant viral operational taxonomic units. Most of the phages (89.2 % ± 3.8 %) were lytic in North Canal, which were observed to contribute to ARGs reduction by lysing their host bacteria, reflected by higher virus-host ratio and demonstrated by the phage lysis assays in treated wastewater and receiving river. We provided compelling evidence that phage-host interactions can reduce ARGs through host lysis, highlighting their potential role in mitigating ARG transmission in urban rivers receiving treated wastewater.}, } @article {pmid40273602, year = {2025}, author = {Hu, C and Lu, JN and Chen, Z and Tian, L and Yin, Y and Jiang, G and Fei, YH and Tang, YT and Wang, S and Jin, C and Qiu, R and Chao, Y}, title = {Viral diversity and auxiliary metabolic genes in rare earth element mine drainage in South China.}, journal = {Water research}, volume = {281}, number = {}, pages = {123666}, doi = {10.1016/j.watres.2025.123666}, pmid = {40273602}, issn = {1879-2448}, abstract = {In extreme environments, viruses play a crucial role in regulating the structure and metabolic activities of microbial communities, thereby impacting the overall biogeochemical cycles. Previous research found that rare earth element acid mine drainage (REE-AMD) harbors a wide array of microbial species. However, our understanding of the viruses that infect these microorganisms remains limited. In this study, we utilized metagenomic analysis to explore the viral diversity, interactions between viruses and their hosts, as well as the viruses encoded auxiliary metabolic genes (AMGs) within REE-AMD. The results demonstrated that viral communities showed increased diversity with REEs pollution. Furthermore, AMGs exhibited habitat and host specificity. Viruses in water samples contaminated with REEs tended to encode AMGs related to cellular metabolic processes and stress responses to protect their hosts. In contrast, viruses in sediment samples were more likely to encode AMGs associated with nutrient competition, thereby expanding the ecological niches of hosts and viruses. Viruses would carry more AMGs from the dominant prokaryotes. Additionally, under REEs stress, viruses encode a greater number of carbon- and sulfur-related AMGs, influencing the carbon and sulfur cycles of microorganisms in REE-AMD. Overall, our study provides a first systematic characterization of the viral community in REE-AMD, which is crucial for understanding the intricate interactions among viruses, their hosts, and the surrounding environment.}, } @article {pmid40273394, year = {2025}, author = {Chen, CC and Chiu, JY and Tan, AH and Toh, TS and Lim, SY and Tan, EK and Pettersson, S and Hsu, CC and Liou, JM and Wu, MS and Hsu, CL and Lin, CH}, title = {Investigating Plasma Metabolomics and Gut Microbiota Changes Associated With Parkinson Disease: A Focus on Caffeine Metabolism.}, journal = {Neurology}, volume = {104}, number = {10}, pages = {e213592}, doi = {10.1212/WNL.0000000000213592}, pmid = {40273394}, issn = {1526-632X}, abstract = {BACKGROUND AND OBJECTIVES: Coffee intake is linked to a reduced risk of Parkinson disease (PD), but whether this effect is mediated by gut microbiota and metabolomic changes remains unclear. This study examines PD-associated metabolomic shifts, caffeine metabolism, and their connection to gut microbiome alterations in a multicenter study.

METHODS: We conducted an untargeted serum metabolomic assay using liquid chromatography with high-resolution mass spectrometry on an exploratory cohort recruited from National Taiwan University Hospital (NTUH). A targeted metabolomic assay focusing on caffeine and its 12 downstream metabolites was conducted and validated in an independent cohort from University Malaya Medical Centre (UMMC). In the exploratory cohort, the association of each caffeine metabolite with gut microbiota changes was investigated by metagenomic shotgun sequencing. A clustering-based approach was used to correlate microbiome changes with plasma caffeine metabolite level and clinical severity. Body mass index, antiparkinsonism medication use, and dietary habits (including coffee and tea intake) were recorded.

RESULTS: Sixty-three patients with PD and 54 controls from NTUH formed the exploratory cohort while 36 patients with PD and 20 controls from UMMC served as an validation cohort to replicate the plasma caffeine findings. A total of 5,158 metabolites were detected from untargeted metabolomic analysis, with 3,131 having high confidence for analysis. Compared with controls, the abundance of 56 metabolites was significantly higher and that of 7 metabolites was significantly lower (adjusted p < 0.05 and log2 fold change >1) in patients with PD. Caffeine metabolism was significantly lower in patients with PD (p = 0.0013), and serum levels of caffeine and its metabolites negatively correlated with motor severity (p < 0.01). Targeted metabolomic analysis confirmed reduced levels of caffeine and its metabolites, including theophylline, paraxanthine, 1,7-dimethyluric acid, and 5-acetylamino-6-amino-3-methyluracil, in patients with PD; these findings were replicated in the validation cohort (p < 0.05). A clustering approach found that 56 microbiome species enriched in patients with PD negatively correlated with caffeine and its metabolites paraxanthine and theophylline (both p < 0.05), notably Clostridium sp000435655, Acetatifactor sp900066565, Oliverpabstia intestinalis, and Ruminiclostridium siraeum.

DISCUSSION: This study identifies PD-related changes in microbial-caffeine metabolism compared with controls. Our findings offer insights for future functional research on caffeine-microbiome interactions in PD.}, } @article {pmid40272442, year = {2025}, author = {Diao, Z and Zhao, Z and Han, Y and Chen, Y and Huang, T and Feng, L and Ma, Y and Li, J and Zhang, R}, title = {A Comprehensive Assessment of Metagenomic cfDNA Sequencing for Microbe Detection.}, journal = {Clinical chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1093/clinchem/hvaf044}, pmid = {40272442}, issn = {1530-8561}, support = {2024-2-40510//Capital's Funds for Health Improvement and Research/ ; 2022YFC2603800//National Key R&D Program of China/ ; }, abstract = {BACKGROUND: Metagenomic cell-free DNA (cfDNA) sequencing provides a new avenue for diagnosing infectious diseases. Owing to the low concentration and highly fragmented nature of microbial cfDNA in plasma, coupled with methodological complexity, ensuring accurate and comparable metagenomic cfDNA sequencing results has proved challenging. This study aims to evaluate the performance of metagenomic cfDNA sequencing for detecting microorganisms in plasma across various laboratories and to examine factors affecting accuracy.

METHODS: A reference panel consisting of 18 microbial cfDNA communities was designed and used to investigate the performance of metagenomic cfDNA sequencing across 130 laboratories. We comprehensively assessed the accuracy, repeatability, anti-interference, limit of detection (LoD), and linear correlation.

RESULTS: The results showed that the performance of most laboratories was excellent, with an average F1 score of 0.98. Most contamination in metagenomic cfDNA sequencing originated from "wet labs," as 68.25% (475/696) of the false-positive sequences matched reported microorganisms. The chief cause (74.24%, 49/66) of false-negative errors in metagenomic cfDNA sequencing was from "dry labs." Laboratories showed favorable reproducibility, LoD, and linearity. Interference from elevated human cfDNA concentrations was minimal, whereas interference from genetically similar microorganisms was more pronounced. Overall, viral cfDNA detection showed weaker performance compared to bacterial and fungal detection.

CONCLUSIONS: This study presented the performance of metagenomic cfDNA sequencing in real-world settings, identifying key factors critical for its development and optimization. These findings provide valuable guidance for accurate pathogen detection in infectious diseases and promote the adoption of metagenomic cfDNA sequencing in diagnostics.}, } @article {pmid40272326, year = {2025}, author = {Adi, A and Lebrun, S and Kondo, M and Alvarez Villela, M and Fontes, JD}, title = {Culture-Negative Subacute Lactobacillus Endocarditis Diagnosed by Microbial Cell-Free DNA Sequencing.}, journal = {JACC. Case reports}, volume = {}, number = {}, pages = {103505}, doi = {10.1016/j.jaccas.2025.103505}, pmid = {40272326}, issn = {2666-0849}, abstract = {BACKGROUND: Lactobacillus endocarditis is a rare infection generally occurring in patients with heart disease and immunosuppression. Although Lactobacillus is typically a benign part of the gastrointestinal and genitourinary flora, it can cause invasive infections.

CASE SUMMARY: We present a case of a 74-year-old patient with low-grade fever and a nonproductive cough following recent cardiac surgery. Transesophageal echocardiography revealed vegetations, suggestive of endocarditis, despite negative blood cultures. Due to high suspicion for endocarditis, advanced genetic testing identified Lactobacillus fermentum as the causative pathogen. The patient disclosed daily probiotic use, likely the infection source. Treatment with intravenous ampicillin resulted in significant symptom improvement.

DISCUSSION: This case underscores the importance of considering probiotics as a potential source of bacteremia in patients with negative cultures after surgery and highlights how metagenomic sequencing can identify pathogens and guide effective therapy in challenging cases.}, } @article {pmid40272234, year = {2025}, author = {Wang, X and Zhang, J and Yang, B and Mao, H and Yu, Q and Zhang, Y}, title = {Intermittent Microaeration Enhanced Anaerobic Digestion: The Key Role of Fe(III)/Fe(II) Cycle and Reactive Oxygen Species.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c04187}, pmid = {40272234}, issn = {1520-5851}, abstract = {Microaeration has been reported to improve anaerobic digestion, which is generally attributed to increased microbial diversity, but a thorough explanation is lacking. In this study, it was found that intermittent microaeration (IMA) supplied to an anaerobic digester could oxidize Fe(II) produced by dissimilatory iron reduction (DIR) to form a Fe(III)/Fe(II) cycle and generate extracellular reactive oxygen species (ROS) to improve anaerobic treatment of phenol-containing wastewater. The results showed that compared to the control group without IMA, the removal rates of COD and phenol increased by 29.54 and 49.68 percentage points, respectively, and daily average methane production increased by 85.44%. The Fe(III)/Fe(II) cycle slowed down the loss of iron (13.97%) released from sludge due to the lower solubility of Fe(III) and facilitated [•]OH generation (1.22 ± 0.04 μM) via Fenton-like reactions. The DIR and the generation of [•]OH accelerated phenol degradation. Metagenomic analysis revealed that the abundance of methanogens and antioxidant enzymes-encoding genes in response to oxidative stress significantly increased in the IMA group compared to the control, enabling methanogenesis to proceed smoothly under microaeration. This study investigated the extracellular ROS generation induced by microaeration during anaerobic digestion and their roles in promoting anaerobic performance, thereby providing a new perspective for optimizing anaerobic systems with microaeration.}, } @article {pmid40272147, year = {2025}, author = {Dai, X and Cao, Y and Li, L and Gao, Y-X and Wang, J-X and Liu, Y-J and Ma, T-T and Zheng, J-M and Zhan, P-P and Shen, Z-Y}, title = {Gut microbiome and metabolome profiles in renal allograft rejection from multiomics integration.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0162624}, doi = {10.1128/msystems.01626-24}, pmid = {40272147}, issn = {2379-5077}, abstract = {UNLABELLED: The gut microbiome and metabolome play crucial roles in renal allograft rejection progression. Integrated multiomics analyses may provide a comprehensive understanding of specific underlying mechanisms, which remain elusive. This study aimed to identify new approaches for clinical renal allograft rejection diagnosis and treatment. Thirty-five patients were divided into three groups: the rejection (n = 16), dysfunction (n = 7), and control (n = 12) groups. Metagenomic sequencing and nontargeted metabolomics were used to analyze stool and plasma samples. Significant microbiota, metabolites, and signaling pathways were identified. LASSO regression was used to construct a diagnostic model, and its diagnostic value was assessed via receiver operating characteristic curves. The microbiota composition and the related genes in the rejection group significantly differed from that in the dysfunction and control groups at the phylum, genus, and species levels (P < 0.001). The core species in the rejection group networks were Escherichia coli and Ruminococcus gnavus, while core species in the dysfunction group networks were Faecalibacterium prausnitzii and Bacteroides ovatus. The balance of specific microbial species was associated with kidney function in rejection patients. Spearman analysis revealed that specific differential species like Agathobaculum butyriciproducens and Gemmiger qucibialis were closely linked to the levels of serum 4-pyridoxic acid, 4-acetamidobutanoate, and fecal tryptamine from specific differential pathways. Finally, we constructed four clinical models to distinguish the rejection and dysfunction groups, and the model had excellent diagnostic performance. Altered gut microbiota may contribute to changes in metabolic pathway activity and metabolite abundance in rejection and dysfunction patients, which are strongly correlated with host immunological rejection. The diagnostic model, developed based on the gut microbiota and metabolites, has high clinical value for diagnosing renal rejection.

IMPORTANCE: This study aimed to screen new markers for non-invasive diagnosis by the gut microbiome and metabolome analysis, providing new insights into rejection mechanisms and identifying new approaches for clinical renal allograft rejection diagnosis.}, } @article {pmid40271228, year = {2025}, author = {Liu, J and Wu, X}, title = {Rare Bloodstream Infection of Rhodococcus rhodochrous as the Prodromal Signal for Malignancy.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {1951-1959}, doi = {10.2147/IDR.S512213}, pmid = {40271228}, issn = {1178-6973}, abstract = {Rhodococcus-associated infections are extremely rare, and previous publications have indicated that such infections are primarily observed among individuals with HIV. Limited information is available regarding therapy, and no clear consensus has been reached to guide treatment. Here, we report the first case of bloodstream infection with Rhodococcus rhodochrous in a non-HIV patient with a viral intracranial infection. During follow-up, lymph node biopsy and bone marrow aspiration were performed because superficial lymphadenectasis had failed to regress as expected within 3 months. The patient was newly diagnosed with nodal T-follicular helper cell lymphoma, angioimmunoblastic-type. For cases of rare infection or co-infection, screening for pathogenic microorganisms is the priority, and several methods should be employed, such as microorganism culture, antigen and antibody detection, and metagenomic next-generation sequencing. In retrospect to integrated case management, our case indicated that early malignancy screening is significant for early diagnosis and treatment of occult cancer during patients with rare opportunistic infections.}, } @article {pmid40270817, year = {2025}, author = {Onohuean, H and Olot, H and Onohuean, FE and Bukke, SPN and Akinsuyi, OS and Kade, A}, title = {A scoping review of the prevalence of antimicrobial-resistant pathogens and signatures in ready-to-eat street foods in Africa: implications for public health.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1525564}, doi = {10.3389/fmicb.2025.1525564}, pmid = {40270817}, issn = {1664-302X}, abstract = {BACKGROUND AND OBJECTIVE: Despite its critical role in individual and societal health, food hygiene remains underexplored. Antibiotic-resistant pathogenic bacteria in ready-to-eat (RTE) food threaten public health. This scoping review collected data on the epidemiological prevalence of RTE food-contaminated pathogens resistant to antimicrobial drugs and resistance genes in Africa.

METHOD: Using electronic databases, such as PubMed, Scopus, and Web of Science (WoS), handpicked from references, pre-reviewed published articles were retrieved and analyzed according to the PRISMA-ScR guidelines.

RESULTS: The findings indicate 40 previewed published articles qualified for meta-synthesis in the scoping review with a population/case ratio of 11,653/5,338 (45.80%). The most frequently reported RTE foods were meat or beef/beef-soup, chicken or poultry products, salads, vegetable salads, and sandwiches, which harboured pathogens such as E. coli, Salmonella, and Staphylococcus. Antibiotic susceptibility tests revealed the use of 48 antibiotics to manage infections, following CLSI (Clinical and Laboratory Standards Institute) protocols. Moreover, 10 authors reported 54 resistance genes associated with pathogenic resistant bacteria. In addition, only 15 studies received funding or financial support.

CONCLUSION: These findings from several researchers indicate that RTE street foods in African and resource-limited nations harbour enteric pathogens and are a significant concern to the public health system and reservoir of the spread of antibiotic resistance. This underscores the necessity of implementing effective control strategies to address challenges and limit the spread of resistant bacteria in RTE foods. The antimicrobial resistance surveillance system in the region is a significant concern. Notably, Africa needs to strengthen the national and international regulatory bodies and a health surveillance system on antimicrobial resistance, particularly among developing nations.}, } @article {pmid40270812, year = {2025}, author = {Fagerlund, A and Møretrø, T and Jensen, MR and Langsrud, S and Moen, B}, title = {Early detection and population dynamics of Listeria monocytogenes in naturally contaminated drains from a meat processing plant.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1541481}, doi = {10.3389/fmicb.2025.1541481}, pmid = {40270812}, issn = {1664-302X}, abstract = {Listeria monocytogenes, a significant foodborne pathogen, often contaminates ready-to-eat foods through cross-contamination in food processing environments, and floor drains represent one of the most common sites of persistence. Subtyping of L. monocytogenes from food processing plants for the purpose of source tracking is usually performed on a single colony obtained after selective enrichment. This study investigates the temporal variation and population dynamics of L. monocytogenes in drains, focusing on the diversity of L. monocytogenes and the impact of the resident microbiota. Six different drains in a meat processing plant were each sampled four times over a period of 8 weeks and subjected to two-step selective enrichment in Half Fraser and Full Fraser broths. The clonal complexes (CCs) of at least 20 individual L. monocytogenes isolates from each positive sample (460 isolates in total) were determined using either the GenoListeria Multiplex qPCR assay or whole genome sequencing (WGS). The microbiota in drains and enrichment cultures was analyzed by 16S rRNA gene amplicon sequencing and metagenomic or quasimetagenomic sequencing. L. monocytogenes was detected in the majority of samples and four different CCs were identified - CC9, CC11 (ST451), CC121 and CC8 - with up to three CCs in the same sample and with different CCs dominating in different drains. The same clones of CC9, CC11, and CC121 had persisted in the facility for 3-5 years. The composition of the drain microbiota remained relatively stable over time, with Pseudomonas, Acinetobacter, Janthinobacterium, Chryseobacterium, Staphylococcus, and Sphingomonas as the most commonly identified genera. There were no apparent differences in the microbial genera present in L. monocytogenes positive and negative drains or samples. The study highlights the use of techniques such as qPCR and quasimetagenomics for monitoring and controlling the risk of L. monocytogenes contamination in processing environments.}, } @article {pmid40270585, year = {2025}, author = {Zheng, Z and Gong, Z and Zhang, R and Lin, X and Hong, W and Song, L}, title = {Potential pathogens drive ARGs enrichment during biofilms formation on environmental surfaces.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf057}, doi = {10.1093/ismeco/ycaf057}, pmid = {40270585}, issn = {2730-6151}, abstract = {The enrichment of antibiotic resistance genes (ARGs) on environmental surfaces is a fundamental question in microbial ecology. Understanding the processes driving ARG variations can provide clues into their transfer mechanisms between phases and offer insights for public health management. In this study, we examined microbiota, potential pathogen, and ARG dynamics on two common environment surfaces-polyvinyl chloride (PVC) and carbon steel (CS)-under environmental stress (induced by landfill leachate flow) in a Center for Disease Control and Prevention Biofilm Reactor using metagenomics and quantitative polymerase chain reaction-Chip techniques. Contrary to the expected changes in biofilms morphology and physiochemical properties, microbiota, potential pathogens, and ARGs exhibited a divergence-convergence pattern, primarily shaped by attachment surface properties and, subsequently, biofilm maturity during biofilms formation. During this process, ARG levels in biofilms gradually increased to and exceeded the levels in the surrounding environment, but with a distinct structure (P < .05). Furthermore, 1.93- and 3.05-fold increases in the concentrations of mobile genetic elements intI-1 in PVC and CS biofilms, respectively, suggested their important role in the transfer and spread of ARGs within the biofilm matrix. Although potential pathogens were less abundant (3.48%-5.63%) in the biofilms microbiota, they accounted for 18.28%-45.16% of the ARG hosts and harbored multiple ARGs. Pathogens significantly impacted ARG enrichment (Procrustes analysis: P = .0136, M[2] = 0.34) although microbiota development also influenced this process (P = .0385, M[2] = 0.67). These results suggest that pathogens are key in shaping ARG enrichment in biofilms. Our findings provide dynamic insights into resistome enrichment on environmental surfaces.}, } @article {pmid40270483, year = {2025}, author = {McElwee-Adame, A and Esplin-Stout, R and Mugoya, T and Vourlitis, G and Welch, N and Henning, J and Afram, K and Jeshvaghane, MA and Bingham, N and Dockter, A and Eslava, J and Gil, G and Mergens, J and Mohamed, A and Nguyen, T and Noor, F and Salcedo, N and Sethuraman, A}, title = {Evolutionary History and Rhizosphere Microbial Community Composition in Domesticated Hops (Humulus lupulus L.).}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {e17769}, doi = {10.1111/mec.17769}, pmid = {40270483}, issn = {1365-294X}, support = {2017-06423//USDA; National Institute of Food and Agriculture/ ; 2022-77040-38529//USDA; National Institute of Food and Agriculture/ ; 1564659//NSF; Division of Biological Infrastructure/ ; 2147812//NSF; Division of Biological Infrastructure/ ; }, abstract = {Humulus lupulus L., commonly known as hop, is a perennial crop grown worldwide and is well known for its pharmacological, commercial, and most importantly brewing applications. For hundreds of years, hop has undergone intense artificial selection, with over 250 cultivated varieties being developed worldwide, all displaying differences in key characteristics such as bitter acid concentrations, flavour and aroma profiles, changes in photoperiod, growth, and pathogen/pest resistances. Previous studies have individually explored differences between cultivars, aiming to identify markers that can quickly and cost-effectively differentiate between cultivars. However, little is known about their evolutionary history and the variability in their associated rhizospheric microbial communities. Coupling phenotypic, genomic, and soil metagenomic data, our study explores the global population structure and domestication history of 98 hop cultivars. We assessed differences in growth rates, rates of viral infection, usage of dissolvable nitrogen, and soil microbial community compositions between US and non-US based cultivars. Our study revealed that worldwide hop cultivars cluster into four subpopulations: Central European, English, and American ancestry as previously reported, and one new group, the Nobles, revealing further substructure amongst Central European cultivars. Modelling the evolutionary history of domesticated hop reveals divergence of the common ancestors of modern US cultivars around 2800 years before present (ybp), and more recent divergences with gene flow across English, Central European, and Noble cultivars, reconciled with key events in human history and migrations. Furthermore, cultivars of US origin were shown to overall outperform non-US cultivars in both growth rates and usage of dissolvable nitrogen and display novel microbial composition under common-garden settings in the United States.}, } @article {pmid40270118, year = {2025}, author = {Murtaza, N and Collins, L and Yao, CK and Thwaites, PA and Veitch, P and Varney, JE and Gill, PA and Gibson, PR and Morrison, M and Muir, JG}, title = {Effects of dietary FODMAP content on the faecal microbiome and gastrointestinal physiology in healthy adults: a randomised, controlled cross-over feeding study.}, journal = {The British journal of nutrition}, volume = {}, number = {}, pages = {1-39}, doi = {10.1017/S0007114525000868}, pmid = {40270118}, issn = {1475-2662}, abstract = {The effect dietary FODMAPs (fermentable oligo-, di- and mono-saccharides and polyols) in healthy adults is poorly documented. This study compared specific effects of low and moderate FODMAP intake (relative to typical intake) on the faecal microbiome, participant-reported outcomes and gastrointestinal physiology. In a single-blind cross-over study, 25 healthy participants were randomised to one of two provided diets, 'low' (LFD) <4 g/d or 'moderate' (MFD) 14-18 g/d, for 3 weeks each, with ≥2-week washout between. Endpoints were assessed in the last week of each diet. The faecal bacterial/archaeal and fungal communities were characterised in 18 participants in whom high quality DNA was extracted by 16S rRNA and ITS2 profiling, and by metagenomic sequencing. There were no differences in gastrointestinal or behavioural symptoms (fatigue, depression, anxiety), or in faecal characteristics and biochemistry (including short-chain fatty acids). Mean colonic transit time (telemetry) was 23 (95% confidence interval: 15, 30) h with the MFD compared with 34 (24, 44) h with LFD (n=12; p=0.009). Fungal diversity (richness) increased in response to MFD, but bacterial richness was reduced, coincident with expansion of the relative abundances of Bifidobacterium, Anaerostipes, and Eubacterium. Metagenomic analysis showed expansion of polyol-utilising Bifidobacteria, and Anaerostipes with MFD. In conclusion, short-term alterations of FODMAP intake are not associated with symptomatic, stool or behavioural manifestations in healthy adults, but remarkable shifts within the bacterial and mycobiome populations were observed. These findings emphasise the need to quantitatively assess all microbial Domains and their interrelationships to improve understanding of consequences of diet on gut function.}, } @article {pmid40270064, year = {2025}, author = {Basu, A and Chalasani, D and Sarma, PVSRN and Uikey, S and Chenna, VR and Choudhari, PL and Podile, AR}, title = {Influence of genotype, nodule position, and edaphic factors on microbial diversity and assembly of pigeonpea (Cajanus cajan) root nodules in Indian soils.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {41}, pmid = {40270064}, issn = {2524-6372}, abstract = {BACKGROUND: Pigeonpea (Cajanus cajan) is an important legume crop in semi-arid regions with multiple uses. The microbial diversity within its root nodules in Indian soils remains poorly explored. We investigated the bacterial diversity of pigeonpea root nodules across different genotypes and soil types to identify the factors driving their assembly. Using a metagenomic approach and high-throughput sequencing of the 16S rRNA gene, we analyzed the nodule microbiomes of three pigeonpea genotypes (Asha, Durga, and Mannem Konda Kandi) grown in three different soil types (Alfisol, Vertisol, and Inceptisol) and wild pigeonpea (C. scarabaeoides) in its native soil.

RESULTS: Our results indicated that pigeonpea nodules harbor diverse rhizobial and non-rhizobial endophytes and that host genotype, nodule position, soil type, and other edaphic factors influence significant variation in the microbial community structure. The core nodule microbiome was dominated by Proteobacteria and Bacteroidetes. Bradyrhizobium and Ensifer were predominant among the rhizobial taxa, and non-rhizobial genera such as Pseudomonas, Chitinophaga, and Limnobacter were also abundant. Edaphic factors, particularly soil type, pH, and nutrient availability, had a stronger influence on the nodule bacterial community composition than the host genotype. Although bulk soil exhibited higher bacterial diversity, nodule microbiomes were less diverse but more specialized, indicating host-mediated selection. A comparison of the nodule microbiomes of wild and cultivated pigeonpea revealed distinct differences, with the core nodule microbiome of wild pigeonpea dominated by Bradyrhizobium, while that of cultivated pigeonpea exhibited a diverse bacterial community.

CONCLUSIONS: These findings demonstrate that soil properties play a more critical role than host genetics in shaping the pigeonpea nodule microbiome, emphasizing the importance of environmental conditions in symbiotic interactions. The differences between wild and cultivated genotypes suggest that domestication has altered microbial recruitment strategies. This study provides foundational insights into the factors driving microbial assembly in pigeonpea nodules, with implications for improving crop productivity through targeted microbial management. Future research should explore the functional roles of these microbial communities to optimize their use in sustainable agriculture.}, } @article {pmid40269715, year = {2025}, author = {Poopedi, E and Pierneef, R and Singh, T and Gomba, A}, title = {Antibiotic resistance profiles and mutations that might affect drug susceptibility in metagenome-assembled genomes of Legionella pneumophila and Aeromonas species from municipal wastewater.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {237}, pmid = {40269715}, issn = {1471-2180}, support = {121333//National Research Foundation/ ; K5/2885//3//Water Research Commission/ ; }, mesh = {*Wastewater/microbiology ; *Aeromonas/genetics/drug effects/isolation & purification ; *Anti-Bacterial Agents/pharmacology ; *Legionella pneumophila/genetics/drug effects/isolation & purification ; Genome, Bacterial ; Mutation ; *Metagenome ; *Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests ; }, abstract = {Antibiotic resistance (AR) has emerged as a significant global health issue. Wastewater treatment plants (WWTPs) contain diverse bacterial communities, including pathogens, and have been identified as crucial reservoirs for the emergence and dissemination of AR. The present study aimed to identify antibiotic resistance genes (ARGs) and screen for the presence of mutations associated with AR in Legionella pneumophila and Aeromonas spp. from municipal wastewater. Metagenome-assembled genomes (MAGs) of L. pneumophila and Aeromonas spp. were reconstructed to investigate the molecular mechanisms of AR in these organisms. A total of 138 nonsynonymous single nucleotide variants (SNVs) in seven genes associated with AR and one deletion mutation in the lpeB gene were identified in L. pneumophila. In Aeromonas spp., two (aph(6)-Id and aph(3'')-Ib) and five (blaMOX-4, blaOXA-1143, blaOXA-724, cepH, and imiH) ARGs conferring resistance to aminoglycosides and β-lactams were identified, respectively. Moreover, this study presents β-lactam resistance genes, blaOXA-1143 and blaOXA-724, for the first time in Aeromonas spp. from a municipal WWTP. In conclusion, these findings shed light on the molecular mechanisms through which clinically relevant pathogenic bacteria such as L. pneumophila and Aeromonas spp. found in natural environments like municipal wastewater acquire AR.}, } @article {pmid40269516, year = {2025}, author = {Cumbo, F and Truglia, S and Weitschek, E and Blankenberg, D}, title = {Feature selection with vector-symbolic architectures: a case study on microbial profiles of shotgun metagenomic samples of colorectal cancer.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {2}, pages = {}, doi = {10.1093/bib/bbaf177}, pmid = {40269516}, issn = {1477-4054}, support = {U24HG006620/NH/NIH HHS/United States ; }, mesh = {Humans ; *Colorectal Neoplasms/microbiology/genetics ; *Metagenomics/methods ; *Metagenome ; *Microbiota ; *Gastrointestinal Microbiome ; Computational Biology/methods ; Algorithms ; }, abstract = {UNLABELLED: The continuously decreasing cost of next-generation sequencing has recently led to a significant increase in the number of microbiome-related studies, providing invaluable information for understanding host-microbiome interactions and their relation to diseases. A common approach in metagenomics consists of determining the composition of samples in terms of the amount and types of microbial species that populate them, with the goal of identifying microbes whose profiles are able to differentiate samples under different conditions with advanced feature selection techniques. Here, we propose a novel backward variable selection method based on the hyperdimensional computing (HDC) paradigm, which takes inspiration from how the human brain works in the classification of concepts by encoding features into vectors in a high-dimensional space. We validated our method on public metagenomic samples collected from patients affected by colorectal cancer in a case/control scenario, by performing a comparative analysis with other state-of-the-art feature selection methods, obtaining promising results.

AUTHOR SUMMARY: Characterizing the microbial composition of metagenomic samples is crucial for identifying potential biomarkers that can distinguish between healthy and diseased states. However, the high dimensionality and complexity of metagenomic data present significant challenges in the context of accurately selecting features. Our backward variable selection method, based on the HDC paradigm, offers a promising approach to overcoming these challenges. By effectively reducing the feature space while preserving essential information, this method enhances the ability to detect critical microbial signatures associated with diseases like colorectal cancer, leading to more precise diagnostic tools.}, } @article {pmid40269515, year = {2025}, author = {Sirasani, JP and Gardner, C and Jung, G and Lee, H and Ahn, TH}, title = {Bioinformatic approaches to blood and tissue microbiome analyses: challenges and perspectives.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {2}, pages = {}, doi = {10.1093/bib/bbaf176}, pmid = {40269515}, issn = {1477-4054}, support = {2430236//National Science Foundation/ ; }, mesh = {Humans ; *Microbiota/genetics ; *Computational Biology/methods ; High-Throughput Nucleotide Sequencing ; Machine Learning ; Biomarkers/blood ; }, abstract = {Advances in next-generation sequencing have resulted in a growing understanding of the microbiome and its role in human health. Unlike traditional microbiome analysis, blood and tissue microbiome analyses focus on the detection and characterization of microbial DNA in blood and tissue, previously considered a sterile environment. In this review, we discuss the challenges and methodologies associated with analyzing these samples, particularly emphasizing blood and tissue microbiome research. Key preprocessing steps-including the removal of ribosomal RNA, host DNA, and other contaminants-are critical to reducing noise and accurately capturing microbial evidence. We also explore how taxonomic profiling tools, machine learning, and advanced normalization techniques address contamination and low microbial biomass, thereby improving reliability. While it offers the potential for identifying microbial involvement in systemic diseases previously undetectable by traditional methods, this methodology also carries risks and lacks universal acceptance due to concerns over reliability and interpretation errors. This paper critically reviews these factors, highlighting both the promise and pitfalls of using blood and tissue microbiome analyses as a tool for biomarker discovery.}, } @article {pmid40269473, year = {2025}, author = {Khan, MAW and Bohannan, BJM and Meyer, KM and Womack, AM and Nüsslein, K and Grover, JP and Mazza Rodrigues, JL}, title = {Community-Level Metabolic Shifts Following Land Use Change in the Amazon Rainforest Identified by a Supervised Machine Leaning Approach.}, journal = {Environmental microbiology reports}, volume = {17}, number = {2}, pages = {e70088}, doi = {10.1111/1758-2229.70088}, pmid = {40269473}, issn = {1758-2229}, support = {DE-AC02-05CH11231//U.S. Department of Energy/ ; DEB 14422214//National Science Foundation/ ; }, mesh = {*Rainforest ; *Soil Microbiology ; *Bacteria/genetics/metabolism/classification/isolation & purification ; *Microbiota ; Metagenomics/methods ; Metagenome ; *Archaea/genetics/metabolism/classification/isolation & purification ; Soil/chemistry ; Viruses/genetics/classification/metabolism/isolation & purification ; Machine Learning ; Brazil ; }, abstract = {The Amazon rainforest has been subjected to high rates of deforestation, mostly for pasturelands, over the last few decades. This change in plant cover is known to alter the soil microbiome and the functions it mediates, but the genomic changes underlying this response are still unresolved. In this study, we used a combination of deep shotgun metagenomics complemented by a supervised machine learning approach to compare the metabolic strategies of tropical soil microbial communities in pristine forests and long-term established pastures in the Amazon. Machine learning-derived metagenome analysis indicated that microbial community structures (bacteria, archaea and viruses) and the composition of protein-coding genes were distinct in each plant cover type environment. Forest and pasture soils had different genomic diversities for the above three taxonomic groups, characterised by their protein-coding genes. These differences in metagenome profiles in soils under forests and pastures suggest that metabolic strategies related to carbohydrate and energy metabolisms were altered at community level. Changes were also consistent with known modifications to the C and N cycles caused by long-term shifts in aboveground vegetation and were also associated with several soil physicochemical properties known to change with land use, such as the C/N ratio, soil temperature and exchangeable acidity. In addition, our analysis reveals that these alterations in land use can also result in changes to the composition and diversity of the soil DNA virome. Collectively, our study indicates that soil microbial communities shift their overall metabolic strategies, driven by genomic alterations observed in pristine forests and long-term established pastures with implications for the C and N cycles.}, } @article {pmid40269059, year = {2025}, author = {Aljutaily, T and Aladhadh, M and Alsaleem, KA and Alharbi, HF and Barakat, H and Aljumayi, H and Moustafa, MMA and Rehan, M}, title = {Gut microbiota diversity in obese rats treated with intermittent fasting, probiotic-fermented camel milk with or without dates and their combinations.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {14204}, pmid = {40269059}, issn = {2045-2322}, support = {QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Camelus ; Rats ; *Obesity/microbiology/diet therapy ; *Probiotics/administration & dosage ; *Fasting ; *Milk ; Male ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; Biodiversity ; Cultured Milk Products ; Intermittent Fasting ; }, abstract = {Dietary alternatives help effectively in obesity management. The present study examines the gut microbiota diversity in obesity-induced rats treated with intermittent fasting, fermented camel milk (FCM), and FCM-incorporated Sukkari date or their combinations. The metagenomic analysis of the gut microbiome through 16 S rRNA revealed 226 families, 499 genera, and 879 bacterial species. In the taxonomy distributions and heatmap analysis, Bacteroidota (i.e., Prevotella) had the uppermost relative abundance in groups before treatments (Before_Groups, most samples clustered in one sub-cluster) reached 80.50% in sample S11 (Before_G2), whereas Firmicutes (i.e., Lactobacillus) presented the dominant in groups after treatments (After_Groups, generality samples grouped in another sub-cluster) and counted 70.86% in sample S88 (After_G6), reflecting potential short-chain fatty acids production. The alpha and beta diversity explored by Shannon and PCoA indices presented high diversity in most groups after treatment. Deferribacterota and Fusobacteriota, in addition to Stenotrophomonas and Listeria, were the key phylotypes in the treated groups at the Phylum and genus levels, respectively. The proposed functional pathways involving mannan, rhamnose I, glucose, and xylose degradation were the most supported pathways in After_Groups with potential carbohydrate degradation. Eventually, intermittent fasting and probiotic fermented camel milk increased microbiome diversity and accelerated weight loss, preventing health issues.}, } @article {pmid40268958, year = {2025}, author = {Luo, Q and Gao, H and Xiang, Y and Li, J and Dong, L and Wang, X and Liu, F and Guo, Y and Shen, C and Ding, Q and Qin, C and Liang, G and Wen, L}, title = {The dynamics of microbiome and virome in migratory birds of southwest China.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {64}, pmid = {40268958}, issn = {2055-5008}, mesh = {Animals ; China ; *Virome ; Feces/microbiology/virology ; *Gastrointestinal Microbiome ; *Charadriiformes/microbiology/virology ; Animal Migration ; *Bacteria/classification/genetics/isolation & purification ; *Viruses/classification/genetics/isolation & purification ; *Birds/microbiology/virology ; Metagenomics ; Phylogeny ; }, abstract = {Migratory birds carry pathogens, posing a significant threat to environmental and human health. We documented the metatranscriptome and RNA virome of 896 stool samples from migratory birds and environmental samples over four consecutive years in southwest China. Our analysis identified Catellicoccus marimammalium as the predominant bacterium in the gut of black-headed gulls, with an average relative abundance of 79.3%. Strain-level analysis of C. marimammalium revealed a dominant population with some longitudinal diversity over the four years. Additionally, the gut of black-headed gulls was found to harbor numerous viruses, including a novel hepatovirus. Lysates of cells of C. marimammalium but not other bacteria derived from black-headed gulls could inhibit the replication of human hepatovirus, suggesting a potential regulatory role for gut commensal bacteria in modulating viral carriage. These findings enhance our understanding of the microbiome and RNA virome diversity in migratory birds and provide insights into the modulation of asymptomatic infections.}, } @article {pmid40268922, year = {2025}, author = {Patsis, AC and Schuler, CJ and Toner, BM and Santelli, CM and Sheik, CS}, title = {The potential for coupled organic and inorganic sulfur cycles across the terrestrial deep subsurface biosphere.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {3827}, pmid = {40268922}, issn = {2041-1723}, support = {EAR-1813526//National Science Foundation (NSF)/ ; EAR-1813526//National Science Foundation (NSF)/ ; }, mesh = {*Sulfur/metabolism ; Ecosystem ; *Sulfur Compounds/metabolism ; *Bacteria/metabolism/genetics/classification ; Metagenome ; Sulfides/metabolism ; Metagenomics ; Sulfites/metabolism ; Soil Microbiology ; Sulfonium Compounds ; }, abstract = {Organosulfur compounds (OrgS) are fundamental components of life's biomass, yet the cycling of these compounds in the terrestrial deep subsurface, one of Earth's largest ecosystems, has gone relatively unexplored. Here, we show that all subsurface microbial genomes reconstructed from Soudan Underground Mine State Park have the capacity to cycle organic sulfur species. Our findings suggest that OrgS degradation may be an integral link between the organic and inorganic sulfur cycle via the production of sulfite and sulfide. Furthermore, despite isolation from surface ecosystems, most Soudan microorganisms retained genes for dimethylsulfoniopropionate and taurine biosynthesis. Metagenomic analyses of an additional 54 deep subsurface sites spanning diverse lithologies revealed the capacity for OrgS cycling to be widespread, occurring in 89% of assembled metagenomes. Our results indicate that consideration of OrgS cycling may be necessary to accurately constrain sulfur fluxes, discern the energetic limits of deep life, and determine the impact of deep subsurface biogeochemical sulfur cycling on greater Earth system processes.}, } @article {pmid40268850, year = {2025}, author = {Zhao, J and Zhuge, R and Hu, B and Wang, Y and Wang, X and Zhang, Y and Yuan, L and Qiu, C and Yan, Y and Zhang, X and Hua, Z and Tang, J and Guo, K and Sun, Y and Wang, K and Qiu, L and Luo, J and Zhang, W and Zhuge, J and Fang, H}, title = {Clinical impact of bronchoalveolar lavage fluid metagenomic next-generation sequencing in immunocompromised patients with severe community-acquired pneumonia in ICU: a multicenter retrospective study.}, journal = {Infection}, volume = {}, number = {}, pages = {}, pmid = {40268850}, issn = {1439-0973}, support = {2023KY1296//The Project of Zhejiang Provincial Department of Health/ ; 2022K71//Quzhou Bureau of Science and Technology/ ; }, abstract = {BACKGROUND: An increasing number of critically ill patients are immunocompromised. These patients are at high risk of intensive care unit (ICU) admission because of numerous complications. Acute respiratory failure due to severe community-acquired pneumonia (SCAP) is one of the leading causes of admission. Early targeted antibiotic therapy is crucial for improving the prognosis of these patients. Metagenomic next-generation sequencing (mNGS) in bronchoalveolar lavage fluid (BALF) has shown significant value in pathogen detection in recent years. However, there are few studies on summarizing pathogen profiles of SCAP in immunocompromised patients.

METHODS: We performed a multicenter retrospective analysis of patients with SCAP in the ICU diagnosed between May 2021 to October 2024. Bronchoalveolar lavage fluid (BALF), blood, and sputum samples were collected and subjected to mNGS and conventional microbiological tests (CMTs). The pathogen profiles detected by the two methods were compared.

RESULTS: In our study, compared to CMTs, mNGS increased the detection rates of mixed infections in the immunocompromised group (58.82% vs 17.96%, P < 0.05) and immunocompetent group (44.58% vs 18.72%, P < 0.05), while also reducing the rate of no pathogen detected (4.90% vs 38.73%, P < 0.05; 8.37% vs 32.76%, P < 0.05). In both groups, the proportion of positive clinical impacts (diagnosis) resulting from mNGS results exceeded 90% (96.57% vs 93.84%), and the treatment effectiveness rate in the immunocompromised group was higher than in the immunocompetent group (65.69% vs 56.40%, P < 0.05). Further analysis showed that when mNGS-guided treatment was effective, the 28-day mortality rate significantly improved in both the immunocompromised group (31.34% vs 74.29%, P < 0.05) and the immunocompetent group (42.36% vs 40.68%, P < 0.05) compared to when the treatment was ineffective.

CONCLUSION: This study indicates that ICU patients with SCAP, particularly those who are immunocompromised, are more likely to have polymicrobial infections. mNGS in BALF provides rapid and comprehensive pathogen profiling of pulmonary infections, thereby having a positive impact on both the diagnosis, treatment and prognosis of immunocompromised patients with SCAP.}, } @article {pmid40268777, year = {2025}, author = {Claverie, JM and Legendre, M and Rigou, S and Abergel, C}, title = {Refining the taxonomy of pithovirus-related giant DNA viruses within the order Pimascovirales.}, journal = {Archives of virology}, volume = {170}, number = {5}, pages = {111}, pmid = {40268777}, issn = {1432-8798}, mesh = {Genome, Viral ; Phylogeny ; *DNA Viruses/classification/genetics/ultrastructure ; *Giant Viruses/classification/genetics/ultrastructure ; DNA, Viral/genetics ; }, abstract = {The first member of the family Pithoviridae (Pithovirus sibericum) was isolated from ancient Siberian permafrost and characterized in 2014. Since then, many relatives have been isolated, characterized, and classified as members of the genera Alphapithovirus, Alphacedratvirus, and Alphaorpheovirus. In addition, one complete circular genome sequence was assembled from metagenomic data (hydrivirus). All of these viruses form distinctive giant elongated ovoid particles, up to 2 µm in length, but they differ significantly in the size of their genome, their nucleotide composition, and their gene content. Based on their shared ovoid virion shape, common replication strategy, and core gene similarity, we recently proposed to update their taxonomic status by classifying them in three distinct families (Pithoviridae, Orpheoviridae, and Hydriviridae) within a new suborder, the Ocovirineae, to separate them clearly from the other more distant families (Marseilleviridae, Ascoviridae, Iridoviridae) of the order Pimascovirales. This new taxonomy, validated by the last ICTV Ratification vote held in March 2025, extends the previous partition from three clades to four (to include hydrivirus) while keeping the genera Alphacedratvirus and Alphapithovirus in the same family, Pithoviridae (but split into two subfamilies), due to their much greater similarity to each other than to orpheovirus and hydrivirus.}, } @article {pmid40268631, year = {2025}, author = {Pemán, J and Ruiz-Gaitán, A}, title = {Diagnosing invasive fungal infections in the laboratory today: It's all good news?.}, journal = {Revista iberoamericana de micologia}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.riam.2025.01.004}, pmid = {40268631}, issn = {2173-9188}, abstract = {Despite the advances in medical science, invasive fungal infections (IFI) remain a diagnostic challenge. The increasing prevalence of IFI, driven by immunosuppressive therapies, advances in intensive care and emerging pathogens, underscores the need for early and accurate diagnosis. This review evaluates current laboratory methods for the diagnosis of IFI, highlighting their strengths and limitations. Conventional techniques, including fungal culture, direct microscopy, and histopathology, remain the gold standard for the diagnosis of proven IFIs. These methods allow pathogen isolation, species identification and antifungal susceptibility testing. However, these techniques have limitations in terms of sensitivity and turnaround times. Although microscopy is a rapid technique, its sensitivity and species discrimination profile are limited. Modern serological assays, such as β-d-glucan and galactomannan detection, have improved the diagnostic accuracy of probable IFI cases. Integration of these assays with clinical and radiological findings, enables earlier intervention, although this is accompanied by an increased risk of false positives and necessitates careful clinical correlation. Molecular diagnostics, particularly polymerase chain reaction (PCR), allow rapid, species-specific identification directly from clinical samples. The advent of MALDI-TOF mass spectrometry has further improved diagnostic efficiency, particularly for yeast identification, although challenges remain for filamentous fungi. Innovative techniques, such as metagenomic sequencing, lateral-flow assays, and loop-mediated isothermal amplification, offer the potential for rapid and precise detection, even in resource-limited settings. The combination of conventional and innovative methods provides a comprehensive diagnostic framework. The continuous refinement of these tools, in conjunction with multidisciplinary collaboration, is imperative to improve the early diagnostic and targeted treatment of patients with IFI.}, } @article {pmid40268236, year = {2025}, author = {Emon, MI and Cheung, YF and Stoll, J and Rumi, MA and Brown, C and Choi, JM and Moumi, NA and Ahmed, S and Song, H and Sein, J and Yao, S and Khan, A and Gupta, S and Kulkarni, R and Butt, A and Vikesland, P and Pruden, A and Zhang, L}, title = {CIWARS: a web server for antibiotic resistance surveillance using longitudinal metagenomic data.}, journal = {Journal of molecular biology}, volume = {}, number = {}, pages = {169159}, doi = {10.1016/j.jmb.2025.169159}, pmid = {40268236}, issn = {1089-8638}, abstract = {The rise of antibiotic resistance (AR) poses a substantial threat to human and animal health, food security, and economic stability. Wastewater-based surveillance (WBS) has emerged as a powerful strategy for population-level AR monitoring, providing valuable data to guide public health and policy decisions. Metagenomic sequencing is especially promising, as it can yield comprehensive profiles of antibiotic resistance genes (ARGs) and other genes relevant to AR in a single run. However, online analytical platforms to facilitate analysis of longitudinal metagenomic data are lacking. To address this, we introduce CyberInfrastructure for Waterborne Antibiotic Resistance Surveillance (CIWARS), a web server configured for characterizing key AR trends from longitudinal metagenomic WBS data. CIWARS offers comprehensive profiling of ARGs and taxonomic profiling of pathogen-associated bacterial taxonomic groups, identifies potential associations of ARGs with mobile genetic elements (MGEs) and pathogen-containing taxa, and assesses resistome risk based on the co-occurrence of ARGs, MGEs, and pathogen-like sequences. Additionally, it detects anomalous AR indicators over time, aiding in identifying potential events of concern, such as the emergence of resistant strains or outbreaks. Through interactive temporal data visualization, CIWARS enables AR monitoring and can serve as a tool to inform effective and timely interventions to mitigate the spread and transmission of AR. Here, CIWARS is demonstrated using longitudinal metagenomic data from a wastewater treatment plant (WWTP) influent and effluent, but it can be extended to any environment. CIWARS provides a valuable tool to support global efforts to combat the evolution and spread of AR, while also guiding agricultural and public health efforts aimed at optimizing antibiotic use. The web server is freely available at https://ciwars.cs.vt.edu/.}, } @article {pmid40271438, year = {2017}, author = {Lu, J and Breitwieser, FP and Thielen, P and Salzberg, SL}, title = {Bracken: estimating species abundance in metagenomics data.}, journal = {PeerJ. Computer science}, volume = {3}, number = {}, pages = {}, doi = {10.7717/peerj-cs.104}, pmid = {40271438}, issn = {2376-5992}, abstract = {Metagenomic experiments attempt to characterize microbial communities using high-throughput DNA sequencing. Identification of the microorganisms in a sample provides information about the genetic profile, population structure, and role of microorganisms within an environment. Until recently, most metagenomics studies focused on high-level characterization at the level of phyla, or alternatively sequenced the 16S ribosomal RNA gene that is present in bacterial species. As the cost of sequencing has fallen, though, metagenomics experiments have increasingly used unbiased shotgun sequencing to capture all the organisms in a sample. This approach requires a method for estimating abundance directly from the raw read data. Here we describe a fast, accurate new method that computes the abundance at the species level using the reads collected in a metagenomics experiment. Bracken (Bayesian Reestimation of Abundance after Classification with KrakEN) uses the taxonomic assignments made by Kraken, a very fast read-level classifier, along with information about the genomes themselves to estimate abundance at the species level, the genus level, or above. We demonstrate that Bracken can produce accurate species- and genus-level abundance estimates even when a sample contains multiple near-identical species.}, } @article {pmid40268215, year = {2025}, author = {Sun, X and Hu, P and Xiao, M and Zhang, S and Shi, J and Cai, D and Wang, D and Xu, L and Liu, L and Liu, Y}, title = {Synergy of Multi-Enzyme Pretreatment and Paraclostridium benzoelyticum Bioaugmentation: A Dual Strategy for Enhancing Methane Production in Dry Anaerobic Digestion of Kitchen Waste.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121671}, doi = {10.1016/j.envres.2025.121671}, pmid = {40268215}, issn = {1096-0953}, abstract = {Dry anaerobic digestion (DAD) of kitchen waste (KW) has low methane production due to the poor mass transfer and the low abundance of functional microorganisms. This study employed multi-enzyme pretreatment (PRE), bioaugmentation with Paraclostridium benzoelyticum (BIO), and their combination (COM) to enhance methane production. Interestingly, the COM group had the highest methane production, which was increased by 18.51%, 9.91% and 12.39% compared with the control, PRE and BIO groups, respectively, which indicated that there was a synergy between multi-enzyme pretreatment and bioaugmentation. Further analysis of microbial community and metagenome was conducted to reveal the synergistic mechanism. The results showed that in COM group, the enrichment of the Rikenellaceae, Methanobacteriaceae and Methanosaetaceae was the directly reason for enhancing methane production. Additionally, key metabolic functions including biosynthesis of cofactors, methane metabolism and oxidative phosphorylation also played a pivotal role in boosting methane production. Furthermore, the enhancement of the hydrogenotrophic methanogenesis pathway has been demonstrated to be a critical factor in the synergistic effects. It provided a reliable theoretical basis for the practical application of the multi-enzyme pretreatment combined with Paraclostridium benzoelyticum bioaugmentation for DAD.}, } @article {pmid40268122, year = {2025}, author = {Highmore, C and Cooper, K and Parker, J and Robinson, J and Castangia, R and Webb, JS}, title = {Real-time detection of Foodborne Pathogens and Biofilm in the food processing environment with Bactiscan, a macro-scale fluorescence device.}, journal = {Journal of food protection}, volume = {}, number = {}, pages = {100511}, doi = {10.1016/j.jfp.2025.100511}, pmid = {40268122}, issn = {1944-9097}, abstract = {Food safety relies on rapid detection methods and rigorous sampling of the food processing environment, and is challenged by recurrent biofilm contamination and by sub-lethally injured bacteria that can evade detection. Bactiscan is investigated as an alternative detection approach, a macro-scale and reagentless device that detects microbial contamination through activating green fluorescence of glycoproteins in the bacterial cell wall. The detection capability of Bactiscan was tested on foodborne pathogens Escherichia coli, Listeria monocytogenes, Salmonella enterica, and Staphylococcus aureus. Detection by Bactiscan was assessed using 3 independent observers viewing bacterial samples dried on stainless steel, using 3 biological repeats and 5 technical repeats. Detection by Bactiscan was possible to 1.20*10[6] colony forming units (CFU), compared to 1.36*10[4] CFU by ATP swab testing, where Bactiscan detection limits were defined by the concentration at which 50% of the samples were observed under illumination of the device. Heat-killed and chlorine stressed E. coli and S. enterica caused a 2-log reduction in detection by ATP swab tests (p≤0.05), while detection by Bactiscan was unaffected (p≥0.05). Pathogen biofilms were detectable via Bactiscan with >80% accuracy at 4 days of growth; E. coli and L. monocytogenes biofilms were visible at 2 days of growth. In situ contamination studies determined that Bactiscan can detect microbial contamination on chicken, salmon, and yoghurt samples with stronger fluorescence than a competitor UV torch. The presence of one of the pathogens on the food samples was confirmed by metagenome sequencing, determining that S. aureus was present in 7 samples out of 9 with a relative abundance of >0.5%. These data demonstrate that Bactiscan can effectively detect bacteria present in the food processing environment and can complement existing technologies to improve food industry cleaning practices and infection prevention.}, } @article {pmid40267797, year = {2025}, author = {Sun, X and Sun, Y and Li, P and Gao, Y and Han, M and Zhang, P}, title = {Intensive oyster farming alters the microbial-regulated blue carbon storage in sediment.}, journal = {Marine pollution bulletin}, volume = {216}, number = {}, pages = {118016}, doi = {10.1016/j.marpolbul.2025.118016}, pmid = {40267797}, issn = {1879-3363}, abstract = {Intensive oyster farming enhances the organic matter coupling from water to sediment through biodeposition, potentially contributing to carbon storage. Microbes play a key role in regulating biogeochemical cycling in the coastal sediment. However, their specific contributions to carbon storage under oyster farming remain poorly understood. This study investigates microbial necromass and associated biogeochemical processes in sediments from an intensive oyster farm in Sanggou Bay, China, and compares these indicators with adjacent seagrass beds and bare zones. Additionally, carbon use efficiency (CUE) was employed to indicate microbial-regulated carbon cycling and storage in sediment. The results demonstrate that oyster farming promotes organic carbon accumulation in surface sediments but reduces its stability. Microbial necromass was identified as a critical driver of sedimentary organic carbon in oyster farm sediments, supported by enhanced nitrogen and sulfur cycling pathways. Notably, contrasting relationships between CUE and organic carbon were observed between the seagrass bed and the oyster farm. Functional metagenomic analysis further revealed distinct microbial metabolic pathways across habitats, highlighting the role of biodeposition in shaping microbial functions. These findings enhance our understanding of microbial contributions to blue carbon storage in aquaculture systems and provide new insights into coastal carbon storage beyond vegetated ecosystems.}, } @article {pmid40267563, year = {2025}, author = {Jian, Z and Wu, H and Yan, S and Li, T and Zhao, R and Zhao, J and Zi, X and Wang, K and Huang, Y and Gu, D and Zhao, S and Ge, C and Jia, J and Liu, L and Xu, Z and Dou, T}, title = {Species and functional composition of cecal microbiota and resistance gene diversity in different Yunnan native chicken breeds: A metagenomic analysis.}, journal = {Poultry science}, volume = {104}, number = {7}, pages = {105138}, doi = {10.1016/j.psj.2025.105138}, pmid = {40267563}, issn = {1525-3171}, abstract = {The gut microbiota of chickens not only modulates host immune function and production performance through nutrient metabolism but also serves as a reservoir for antibiotic resistance genes (ARGs), whose accumulation exacerbates bacterial resistance. This study integrated 108 cecal microbiome samples from six Yunnan native chicken breeds under free-range and caged farming systems, constructing a comprehensive catalog comprising 12,715 microbial genomes. We systematically revealed the dual mechanisms by which the gut microbiota regulates host phenotypes and ARG dissemination. Metagenomic analysis demonstrated that Alistipes, Prevotella, and Spirochaeta synergistically regulate body weight and immune indices through metabolic networks, which are linked to the significant enrichment of carbohydrate-active enzymes. GH23 and GT2 presented the greatest abundance, highlighting their pivotal role in dietary fiber metabolism. A total of 1327 ARGs were identified, spanning seven resistance mechanisms dominated by antibiotic efflux and target alteration. Alistipes_sp._CAG:831 presented the highest ARG abundance and diversity, with ARG levels strongly correlated with host bacterial abundance. Metagenomic-phenotype association networks further revealed that environmental stress drives disparities in ARG enrichment by altering the microbial community structure. This study elucidates the gut microbiota-host interaction network in Yunnan native chickens and provides critical insights into ARG transmission dynamics, offering a theoretical foundation for antibiotic resistance risk assessment and sustainable poultry farming strategies.}, } @article {pmid40266944, year = {2025}, author = {Herzog, F and Crissman, KR and Beckers, KF and Zhou, G and Liu, CC and Sones, JL}, title = {Lactobacillus Genus Complex Probiotic-Induced Changes on the Equine Clitoral Microbiome.}, journal = {Veterinary sciences}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/vetsci12030232}, pmid = {40266944}, issn = {2306-7381}, support = {2022//Louisiana State University Charles V. Cusimano/ ; }, abstract = {Dysbiosis of the lower reproductive tract (LRT) in mares may play a role in clinical diseases, including endometritis and placentitis. Metagenomic/metagenetic analysis of bacterial DNA can identify organisms that are not readily cultured and, thus, may go undetected. In this study, we tested the following hypotheses: (1) the clitoris of estrual mares harbors a unique resident microbiome, (2) topical Lactobacillus genus complex (LGC)-containing probiotic will alter the equine clitoral microbiome, and (3) early pregnancy rates following clitoral LGC application will not differ significantly from industry standards. Mares (n = 12) in estrus had sterile clitoral swabs collected (0) prior to daily topical LGC for 4 days. Second (12 h) and third clitoral swabs (48 h) were collected following final LGC application. During the next estrus, the mares were bred by artificial insemination. Genomic DNA was extracted and used for 16S rRNA sequencing via the Illumina Miseq platform. Abundance was evaluated via Friedman test with pairwise Dunn's post hoc comparisons. Statistical significance was set at p < 0.05. Compared to time 0, Desulfobacterota decreased and Corynebacterium spp. increased at 12 h and 48 h compared to 0, while Actinobacillus and Fusobacterium spp. increased in a time-dependent manner. Furthermore, Mobiluncus spp. and Christensenellacea_R-7_group decreased at 12 h and 48 h compared to 0. LGC changed the beta but not alpha diversity at both 12 h and 48 h. Mares with LGC application achieved an 85% pregnancy rate in the subsequent estrus. Future investigations are needed to understand the role of the LRT microbiome and probiotics in equine breeding.}, } @article {pmid40266232, year = {2025}, author = {Zhang, M and Shi, S and Feng, Y and Zhang, F and Xiao, Y and Li, X and Pan, X and Feng, Y and Liu, D and Guo, Y and Hu, Y}, title = {Synthetic microbial community improves chicken intestinal homeostasis and provokes anti-Salmonella immunity mediated by segmented filamentous bacteria.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf076}, pmid = {40266232}, issn = {1751-7370}, support = {2024TZXD026//Shandong Provincial Key Research and Development Program of China/ ; 2022YFA1304201//National Key Research and Development Program of China/ ; }, abstract = {Applying synthetic microbial communities to manipulate the gut microbiota is a promising manner for reshaping the chicken gut microbial community. However, it remains elusive the role of a designed microbial community in chicken physiological metabolism and immune responses. In this study, we constructed a ten-member synthetic microbial community (SynComBac10) that recapitulated the phylogenetic diversity and functional capability of adult chicken intestinal microbiota. We found that early life SynComBac10 exposure significantly enhanced chicken growth performance and facilitated the maturation of both the intestinal epithelial barrier function and the gut microbiota. Additionally, SynComBac10 promoted the pre-colonization and growth of segmented filamentous bacteria, which in turn induced Th17 cell-mediated immune responses, thereby conferring resistance to Salmonella infection. Through metagenomic sequencing, we assembled the genomes of two distinct species of segmented filamentous bacteria from the chicken gut microbiota, which displayed common metabolic deficiency with segmented filamentous bacteria of other host origins. In silico analyses indicated that the SynComBac10-stimulated early establishment of segmented filamentous bacteria in the chicken intestine was likely through SynComBac10-derived metabolite cross-feeding. Our study demonstrated the pivotal role of a designed microbial consortium in promoting chicken gut homeostasis and anti-infection immunity, providing a new avenue for engineering chicken gut microbiota.}, } @article {pmid40265464, year = {2025}, author = {Yan, X and Xie, F and Yang, S and Sun, Y and Lei, Y and Ren, Q and Si, H and Li, Z and Qiu, Q}, title = {Metagenomic Insights into the Rumen Microbiome in Solid and Liquid Fractions of Yaks and their Differences Compared to Other Ruminants.}, journal = {Integrative zoology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1749-4877.12984}, pmid = {40265464}, issn = {1749-4877}, support = {32225009//National Natural Science Foundation of China/ ; 32122083//National Natural Science Foundation of China/ ; 32402780//National Natural Science Foundation of China/ ; XDA26040301//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; }, abstract = {The rumen microbiome plays a critical role in nutrient metabolism and adaptation of the yak (Bos grunniens), an import livestock animal of the Qinghai-Tibet Plateau renowned for their superior plant fiber degradation capacity. However, the microbiome among the different ecological niches within yak's rumen remains unelucidated. Through shotgun sequencing of rumen solid and liquid fractions from five yaks, we identified significant differences in the microbial communities and their genetic functions between the solid and liquid fractions. Solid fractions exhibited dominance by Ruminococcus, Succiniclasticum, and Aspergillus, while Prevotella, Paludibacter, Parabacteroides, and Bacteroides prevailed in liquid fractions. Comparative CAZyme profiling revealed solid fractions were significantly enriched in cellulose/hemicellulose-targeting enzymes (GH5, GH11, and CBM63), implicating their specialization in breaking down the fibrous grasses. In contrast, liquid fractions showed higher abundances of starch-degrading enzymes (GH13, CBM48) and host-glycan utilizers (GH92), suggesting roles in soluble nutrient extraction and host-microbe interactions. Comparative analysis of 574 metagenome-assembled genomes suggested that Methanomethylophilaceae_UBA71 and nitrate-respiring Ruminococcaceae_Firm-04 preferentially colonized in the solids, whereas propionate-producing Quinella and animal glycan-degrading Bacteroides were more prevalent in the liquids. Moreover, compared to Hu sheep, yak's rumen microbiome showed significantly enhanced utilization of plant polysaccharide capacity. Comparative analysis across 10 ruminant species further highlighted host phylogeny as a key driver of rumen microbiome variation. These findings advance our understanding of niche differentiation and functional specialization within the unique yak rumen ecosystem.}, } @article {pmid40265338, year = {2025}, author = {Venkatraman, K and Lipp, NF and Budin, I}, title = {Origin and evolution of mitochondrial inner membrane composition.}, journal = {Journal of cell science}, volume = {138}, number = {9}, pages = {}, doi = {10.1242/jcs.263780}, pmid = {40265338}, issn = {1477-9137}, support = {GM142960/NH/NIH HHS/United States ; GBMF9734//Gordon and Betty Moore Foundation/ ; //University of California/ ; }, mesh = {*Mitochondrial Membranes/metabolism/chemistry ; *Mitochondria/metabolism/genetics ; Humans ; Animals ; Mitochondrial Proteins/metabolism ; *Evolution, Molecular ; }, abstract = {Unique membrane architectures and lipid building blocks underlie the metabolic and non-metabolic functions of mitochondria. During eukaryogenesis, mitochondria likely arose from an alphaproteobacterial symbiont of an Asgard archaea-related host cell. Subsequently, mitochondria evolved inner membrane folds known as cristae alongside a specialized lipid composition supported by metabolic and transport machinery. Advancements in phylogenetic methods and genomic and metagenomic data have suggested potential origins for cristae-shaping protein complexes, such as the mitochondrial contact site and cristae-organizing system (MICOS). MICOS protein homologs function in the formation of cristae-like intracytoplasmic membranes (ICMs) in diverse extant alphaproteobacteria. The machinery responsible for synthesizing key mitochondrial phospholipids - which cooperate with cristae-shaping proteins to establish inner membrane architecture - could have also evolved from a bacterial ancestor, but its origins have been less explored. In this Review, we examine the current understanding of mitochondrial membrane evolution, highlighting distinctions between prokaryotic and eukaryotic mitochondrial-specific proteins and lipids and their differing roles in shaping cristae and ICM architecture, and propose a model explaining the concurrent specialization of the mitochondrial lipidome and inner membrane structure in eukaryogenesis. We discuss how advancements across a range of disciplines are shedding light on how multiple membrane components co-evolved to support the central functions of eukaryotic mitochondria.}, } @article {pmid40265160, year = {2025}, author = {Fässler, D and Heinken, A and Hertel, J}, title = {Characterising functional redundancy in microbiome communities via relative entropy.}, journal = {Computational and structural biotechnology journal}, volume = {27}, number = {}, pages = {1482-1497}, pmid = {40265160}, issn = {2001-0370}, abstract = {Functional redundancy has been hypothesised to be at the core of the well-evidenced relation between high ecological microbiome diversity and human health. Here, we conceptualise and operationalise functional redundancy on a single-trait level for functionally annotated microbial communities, utilising an information-theoretic approach based on relative entropy that also allows for the quantification of functional interdependency across species. Via constraint-based microbiome community modelling of a public faecal metagenomic dataset, we demonstrate that the strength of the relation between species diversity and functional redundancy is dependent on specific attributes of the function under consideration such as the rarity and the occurring functional interdependencies. Moreover, by integrating faecal metabolome data, we highlight that measures of functional redundancy have correlates in the host's metabolome. We further demonstrate that microbiomes sampled from colorectal cancer patients display higher levels of species-species functional interdependencies than those of healthy controls. By analysing microbiome community models from an inflammatory bowel disease (IBD) study, we show that although species diversity decreased in IBD subjects, functional redundancy increased for certain metabolites, notably hydrogen sulphide. This finding highlights their potential to provide valuable insights beyond species diversity. Here, we formalise the concept of functional redundancy in microbial communities and demonstrate its usefulness in real microbiome data, providing a foundation for a deeper understanding of how microbiome diversity shapes the functional capacities of a microbiome.}, } @article {pmid40264979, year = {2025}, author = {Zhong, Y and Chi, H and Wu, T and Fan, W and Su, H and Li, R and Jiang, W and Du, X and Ma, Z}, title = {Diversity of rhizosphere microbial communities in different rice varieties and their diverse adaptive responses to saline and alkaline stress.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1537846}, pmid = {40264979}, issn = {1664-302X}, abstract = {Rice rhizosphere microbiota plays a crucial role in crop yield and abiotic stress tolerance. However, little is known about how the composition and function of rhizosphere soil microbial communities respond to soil salinity, alkalinity, and rice variety in rice paddy ecosystems. In this study, we analyzed the composition and function of rhizosphere soil microbial communities associated with two rice varieties (Jida177 and Tongxi933) cultivated in soils with different levels of salinity-alkalinity in Northeast China using a metagenomics approach. Our results indicate that the rhizospheres of Jida177 and Tongxi933 rice varieties harbor distinct microbial communities, and these microbial communities are differentiated based on both soil salinity-alkalinity and rice varieties. Furthermore, the observed differences in rice yield and grain quality between the Jida177 and Tongxi933 rice varieties suggest that these changes may be attributed to alterations in the rhizosphere microbiome under varying salinity conditions. These findings may pave the way for more efficient soil management and deeper understanding of the potential effects of soil salinization on the rice rhizosphere system.}, } @article {pmid40264936, year = {2025}, author = {Hou, F and Qiao, Y and Qiao, Y and Shi, Y and Chen, M and Kong, M and Hu, X and Jiang, L and Liu, X}, title = {A retrospective analysis comparing metagenomic next-generation sequencing with conventional microbiology testing for the identification of pathogens in patients with severe infections.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1530486}, pmid = {40264936}, issn = {2235-2988}, abstract = {INTRODUCTION: The application value of metagenomic next-generation sequencing (mNGS) in detecting pathogenic bacteria was evaluated to promote the rational and accurate use of antibiotics. A total of 180 patients with severe infections were included in this study.

METHODS: Based on their different symptoms, bronchoalveolar lavage fluid (BALF) or blood samples were collected for conventional microbiological testing (CMT) and mNGS.

RESULTS: The results indicated that the etiological diagnosis rate of mNGS (78.89%) was significantly higher than that of CMT (20%) (p<0.001). Notably, mNGS exhibited greater sensitivity towards rare pathogens such as Chlamydia pneumoniae, Mycobacterium tuberculosis complex, and Legionella pneumophila, which were undetectable by CMT. Additionally, 64 cases underwent blood culture, BALF culture, and mNGS testing. Analysis revealed that the positive rate of blood culture (3.1%) was lower than that of BALF (25%), and the positive rate of CMT from both types was significantly lower than that of mNGS (89.1%) (p<0.001). In this study, 168 mNGS results were accepted, and 116 patients had their antibiotic therapy adjustment based on mNGS. Paired analysis indicated that white blood cell count (WBC), procalcitonin (PCT), C-reactive protein (CRP), and neutrophil (NEU) percentage provided valuable therapeutic guidance. The survival rate of patients was 55.36%, influenced by patient physical condition and age.

DISCUSSION: Our data indicated that mNGS had significant auxiliary value in the clinical diagnosis and treatment for critically ill patients, especially for those with negative CMT results and clinically undefined infections. mNGS could broaden the detection scope, especially for special pathogens, and improve the detection rate, providing powerful assistance for early clinical diagnosis and treatment.}, } @article {pmid40263874, year = {2025}, author = {Huang, X and Li, R and Xu, J and Kang, J and Chen, X and Han, B and Xue, Y}, title = {Integrated multi-omics uncover viruses, active fermenting microbes and their metabolic profiles in the Daqu microbiome.}, journal = {Food research international (Ottawa, Ont.)}, volume = {208}, number = {}, pages = {116061}, doi = {10.1016/j.foodres.2025.116061}, pmid = {40263874}, issn = {1873-7145}, mesh = {*Fermentation ; *Microbiota ; Fungi/metabolism/genetics ; *Bacteria/metabolism/genetics ; *Viruses/genetics/classification ; Metagenomics ; Food Microbiology ; *Fermented Foods/microbiology/virology ; Bacteriophages/genetics ; *Metabolome ; Multiomics ; }, abstract = {The coexistence and coevolution of viruses and fermenting microbes have a significant impact on the structure and function of microbial communities. Although the presence of viruses in Daqu, the fermentation starter for Chinese Baijiu, has been documented, their specific effects on the community composition and metabolic functions of low, medium, and high-temperature Daqu remain unclear. In this study, we employed multi-omics technology to explore the distribution of viruses and active bacteria and fungi in various Daqu and their potential metabolic roles. Viral metagenomic sequencing showed a predominance of Parvoviridae in High-Temperature Daqu (HTQ), while Genomoviridae were dominant in Medium-Temperature Daqu (MTQ) and Low- Temperature Daqu (LTQ). Phages belonging to the Siphoviridae, Podoviridae, Herelleviridae, and Myoviridae families showed significantly different abundances across three Daqu groups. Metatranscriptomic analysis showed that fungal communities were most active in LTQ, whereas bacterial communities were dominant in MTQ and HTQ. By employing the CRISPR-Cas spacer, a higher predicted number of phage-host linkages was identified in LTQ, particularly with hosts including Lactobacillus, Staphylococcus, Acinetobacter, Enterobacter, and Bacillus. Correlation analysis showed that bacteria like Acinetobacter, Lactobacillus, and Streptococcus exhibited the strongest associations with metabolites, particularly amino acids and organic acids. The potential phage-induced metabolic differences in the three Daqu groups were mainly linked to pathways involved in the metabolism of amino acids, sugars, and organic acids. Overall, our study elucidates the impact of viruses on shaping microbial composition and influencing metabolic functions in Daqu. These results improve our comprehension of viruses and microbes in Daqu microbial communities and provide valuable insights for enhancing quality control in Daqu production.}, } @article {pmid40263747, year = {2025}, author = {Liu, CG and Lin, MX and Xin, Y and Sun, M and Cui, J and Liu, D and Zang, D and Chen, J}, title = {Metagenomics and Non-Targeted Metabolomics Reveal the Role of Gut Microbiota and Its Metabolites in Brain Metastasis of Non-Small Cell Lung Cancer.}, journal = {Thoracic cancer}, volume = {16}, number = {8}, pages = {e70068}, doi = {10.1111/1759-7714.70068}, pmid = {40263747}, issn = {1759-7714}, support = {2022RQ091//Science and Technology Talent Innovation Support Plan of Dalian/ ; 82203056//National Natural Science Foundation of China/ ; 2022LCYJYB01//The "1+X" program for Clinical Competency enhancement-Clinical Research Incubation Project of the Second Hospital of Dalian Medical University/ ; 2023-BS-167//Natural Science Foundation of Liaoning Province/ ; }, mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/pathology/metabolism/microbiology ; *Gastrointestinal Microbiome ; *Brain Neoplasms/secondary/metabolism ; *Lung Neoplasms/pathology/metabolism/microbiology ; *Metabolomics/methods ; Female ; Male ; *Metagenomics/methods ; Middle Aged ; Aged ; Prognosis ; }, abstract = {BACKGROUND: Brain metastasis is a common and severe complication in non-small cell lung cancer (NSCLC) patients, significantly affecting prognosis. However, the role of gut microbiota and its metabolites in NSCLC brain metastasis remains poorly understood. This study aims to explore the relationship between gut microbiota, metabolites, and the development of brain metastasis in NSCLC.

METHODS: We conducted an integrative analysis combining metagenomics and non-targeted metabolomics on baseline fecal samples from NSCLC patients with brain metastasis (n = 18) and those without distant metastasis (n = 12). Gut microbiota composition and metabolite profiles were detected and analyzed, and statistical methods, including machine learning models, were applied to identify differences and potential biomarkers.

RESULTS: Significant differences in gut microbiota composition were found between the two groups, with higher microbial diversity observed in patients with brain metastasis. Specific genera, such as Paenibacillus, Fournierella, and Adlercreutzia, were enriched in the brain metastasis group. Metabolomic analysis revealed altered levels of short-chain fatty acids and other metabolites associated with immune modulation and vascular permeability, including angiotensin (1-7). These changes were linked to the metastatic process and may influence brain metastasis development. Furthermore, machine learning models identified key biomarkers, such as Raoultibacter, Mobilibacterium, and N-acetyl-L-glutamic acid, which could serve as valuable indicators for brain metastasis.

CONCLUSIONS: Our findings suggest that gut microbiota dysbiosis and its metabolic products may contribute to the development of brain metastasis in NSCLC. The identification of microbiota-derived biomarkers holds potential for early detection and therapeutic intervention in NSCLC brain metastasis.}, } @article {pmid40263712, year = {2025}, author = {Hör, J}, title = {Advancing RNA phage biology through meta-omics.}, journal = {Nucleic acids research}, volume = {53}, number = {8}, pages = {}, doi = {10.1093/nar/gkaf314}, pmid = {40263712}, issn = {1362-4962}, mesh = {*Bacteria/virology/genetics ; *RNA Phages/genetics/physiology/classification ; Genome, Viral ; *Metagenomics/methods ; *Genomics/methods ; Transcriptome ; Bacteriophages/genetics ; }, abstract = {Bacteriophages with RNA genomes are among the simplest biological entities on Earth. Since their discovery in the 1960s, they have been used as important models to understand the principal processes of life, including translation and the genetic code. While RNA phages were generally thought of as rare oddities in nature, meta-omics methods are rapidly changing this simplistic view by studying diverse biomes with unprecedented resolution. Metatranscriptomics dramatically expanded the number of known RNA phages from tens to tens of thousands, revealed their widespread abundance, and discovered several new families of potential RNA phages with largely unknown hosts, biology, and environmental impact. At the same time, (meta)genomic analyses of bacterial hosts are discovering an arsenal of defense systems bacteria employ to protect themselves from predation, whose functions in immunity against RNA phages we are only beginning to understand. Here, I review how meta-omics approaches are advancing the field of RNA phage biology with a focus on the discovery of new RNA phages and how bacteria might fight them.}, } @article {pmid40263502, year = {2025}, author = {Canderan, J and Ye, Y}, title = {Identification of microbial species and proteins associated with colorectal cancer by reanalyzing CPTAC proteomic datasets.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {13926}, pmid = {40263502}, issn = {2045-2322}, support = {R01AI143254//U.S. Department of Health & Human Services | NIH | Center for Information Technology (Center for Information Technology, National Institutes of Health)/ ; EF-202545//National Science Foundation (NSF)/ ; }, mesh = {*Colorectal Neoplasms/microbiology/metabolism ; Humans ; *Proteomics/methods ; *Bacterial Proteins/metabolism ; Aspergillus/metabolism ; }, abstract = {Microbiome research has revealed associations between microbial species and colorectal cancer (CRC). Most of the existing research relied on metagenomic data. We leveraged a tool that we recently developed for detecting human and microbial peptides from (meta)proteomics data to reanalyze Clinical Proteomic Tumor Analysis Consortium CRC proteomics datasets. Our analyses revealed potential microbial species and proteins that are associated with CRC, especially when analyzing multiplexed proteomics data consisting of cancerous and healthy tissue taken from the same individuals. Many of the identified proteins are associated with species with known links to CRC, such as the fungi Aspergillus kawachii, but many are unstudied or their specific roles unknown. Proteins from other microbial species, such as Paenibacillus cellulosilyticus, were also identified in the samples. We showed that Aspergillus kawachii and others are depleted overall in cancer samples, which is consistent with a previous genomic-based multi-cohort study. Our analysis also revealed that some proteins belonging to this species are more abundantly detected, while others in this and other species are not. Further, we showed that microbial identifications could be used to build predictive models for tumor detection, but caution needs to be taken when applying such models trained on one dataset to another due to the substantial impacts of different experimental techniques on peptide detection profiles.}, } @article {pmid40263397, year = {2025}, author = {Li, C and Zhu, J and Wang, Y and Jiang, W and Lin, Y}, title = {Metagenomic NGS reveals determinants of polymicrobial spinal infection pathogenesis.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {13959}, pmid = {40263397}, issn = {2045-2322}, support = {20230135-9-9//Guilin City Scientific Research and Technology Development Plan project/ ; 20230135-9-9//Guilin City Scientific Research and Technology Development Plan project/ ; 20230135-9-9//Guilin City Scientific Research and Technology Development Plan project/ ; 20230135-9-9//Guilin City Scientific Research and Technology Development Plan project/ ; 20230135-9-9//Guilin City Scientific Research and Technology Development Plan project/ ; }, mesh = {Humans ; Male ; Female ; Middle Aged ; Retrospective Studies ; Aged ; Risk Factors ; *Coinfection/microbiology ; *Metagenomics/methods ; ROC Curve ; Adult ; *Spinal Diseases/microbiology ; }, abstract = {To explore the influencing factors of spinal mixed infection under mNGS-assisted detection. A retrospective analysis was conducted on the general clinical data of patients diagnosed with spinal infections at Guilin People's Hospital, covering the period from October 2022 to October 2024, to evaluate the effectiveness of different treatment modalities including conservative, pharmacological, and surgical interventions. In the end, a total of 45 cases were included, including 18 cases of mixed infection and 27 cases of single infection. The receiver operating characteristic (ROC) curve was utilized to evaluate the predictive efficacy of various indices for the occurrence of mixed infection in patients with spinal infections, with the curve's proximity to the top left corner indicating higher diagnostic accuracy. Multivariate Logistic regression was used to analyze the independent risk factors affecting the development of mixed infection in patients with spinal infection. No significant differences were found between the two groups regarding gender, smoking, alcohol consumption, hypertension, albumin levels, liver function, malignancy, or rheumatic immune disease history (P > 0.05). However, the mixed infection group had significantly higher proportions of patients aged > 60 years (78% (14/18) vs. 48% (13/27)), diabetes mellitus (44% (8/18) vs. 15% (4/27)), chronic kidney disease (17% (3/18) vs. 0.00 (0/27)), and previous spinal surgery (39% (7/18) vs. 11% (3/27)), along with lower BMI (20.70 ± 2.15 vs. 24.04 ± 3.76) and hemoglobin levels (105.17 ± 14.05 g/L vs. 117.48 ± 18.08 g/L). The results of the ROC curve analysis showed that the area under the curve for BMI and hemoglobin in predicting the occurrence of mixed infection in patients was 0.787 and 0.704, respectively, with optimal cutoff values of 21.12 kg/m[2] and 119 g/L. Multivariate logistic regression identified BMI < 21.12 kg/m[2], hemoglobin < 119 g/L, and diabetes as independent risk factors. Lower BMI, diabetes and hemoglobin are independent risk factors for spinal mixed infection. Increasing BMI, effectively controlling blood glucose and improving anemia are helpful to reduce the occurrence of spinal mixed infection.}, } @article {pmid40263287, year = {2025}, author = {Gao, D and Zhuang, Y and Liu, S and Ma, B and Xu, Y and Zhang, H and Nuermaimaiti, Y and Chen, T and Hou, G and Guo, W and You, J and Huang, Z and Xiao, J and Wang, W and Li, M and Li, S and Cao, Z}, title = {Multi-omics profiling of dairy cattle oxidative stress identifies hindgut-derived Phascolarctobacterium succinatutens exhibiting antioxidant activity.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {61}, pmid = {40263287}, issn = {2055-5008}, support = {2024BBF01006//Key Research and Development Program of Ningxia/ ; 2023YFD1300904//National Key Research and Development Program of China/ ; 2024-KFKT-026//National Center of Technology Innovation for Dairy/ ; PC2023B02002//Pinduoduo-China Agricultural University Research Fund/ ; }, mesh = {Animals ; Cattle ; *Oxidative Stress ; *Antioxidants/metabolism ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Female ; Mice ; Fatty Acids, Volatile/metabolism ; Metabolomics ; Metagenomics ; *Clostridiales/genetics/metabolism/isolation & purification ; Multiomics ; }, abstract = {An imbalance between oxidative and antioxidant processes in the host can lead to excessive oxidation, a condition known as oxidative stress (OS). Although changes in the hindgut microbiota have been frequently linked to OS, the specific microbial and metabolic underpinnings of this association remain unclear. In this study, we enrolled 81 postpartum Holstein cows and stratified them into high oxidative stress (HOS, n = 9) and low oxidative stress (LOS, n = 9) groups based on the oxidative stress index (OSi). Using a multi-omics approach, we performed 16S rRNA gene sequencing to evaluate microbial diversity, conducted metagenomic analysis to identify functional bacteria, and utilized untargeted metabolomics to profile serum metabolites. Our analyses revealed elevated levels of kynurenine, formyl-5-hydroxykynurenamine, and 5-hydroxyindole-3-acetic acid in LOS dairy cows. Additionally, the LOS cows had a higher abundance of short-chain fatty acids (SCFAs)-producing bacteria, including Bacteroidetes bacterium, Paludibacter propionicigenes, and Phascolarctobacterium succinatutens (P. succinatutens), which were negatively correlated with OSi. To explore the potential role of these bacteria in mitigating OS, we administered P. succinatutens (10[8] cfu/day for 14 days) to C57BL/6 J mice (n = 10). Oral administration of P. succinatutens significantly increased serum total antioxidant capacity, decreased total oxidants, and reduced OSi in mice. Moreover, this treatment promoted activation of the Nrf2-Keap1 antioxidant pathway, significantly enhancing the enzymatic activities of GSH-Px and SOD, as well as the concentrations of acetate and propionate in the colon. In conclusion, our findings suggest that systemic tryptophan metabolism and disordered SCFAs production are concurrent factors influenced by hindgut microbiota and associated with OS development. Modulating the hindgut microbiota, particularly by introducing specific SCFAs-producing bacteria, could be a promising strategy for combating OS.}, } @article {pmid40263159, year = {2025}, author = {Pandey, A and Israr, J and Pandey, J and Misra, S}, title = {Current Approaches and Implications in Discovery of Novel Bioactive Products from Microbial Sources.}, journal = {Current microbiology}, volume = {82}, number = {6}, pages = {258}, pmid = {40263159}, issn = {1432-0991}, mesh = {*Biological Products/metabolism/pharmacology/isolation & purification/chemistry ; *Drug Discovery/methods ; *Bacteria/metabolism/genetics ; Multigene Family ; Biosynthetic Pathways/genetics ; Microbiota ; }, abstract = {Bioactive Natural Products (BNPs) are in high demand due to their disease-preventive capabilities and resistance to pathogens. However, our understanding of BNP-producing microbes is limited, because many microbial populations remain uncultivated. Various approaches have been employed to explore the potential of these hidden microbes for new bioactive therapeutic compounds. Nevertheless, the possibility of discovering BNPs from microbial communities is largely cryptic due to their unculturable nature and the absence of triggers to activate the dormant Biosynthetic Gene Clusters (BGCs). Metagenome sequencing, followed by mining and characterization, is an effective approach for discovering new therapeutic BNPs. The inactive state of BGCs can be activated through the combinatorial interaction of different microbial communities within a common niche, overcoming programmable co-evolutionary stress and producing new BNPs. The present review discusses and explores the potential of hidden, uncultivated microbes for discovering novel Bioactive Natural Products (BNPs). Moreover, it provides insights into optimizing microbial production systems and fostering sustainable drug discovery and development practices by integrating multidisciplinary strategies. This review also emphasizes the critical role of microbial sources in the ongoing search for new bioactive products that can meet the demands of modern healthcare and environmental sustainability.}, } @article {pmid40262434, year = {2025}, author = {Lima, RAT and Garay, AV and Frederico, TD and de Oliveira, GM and Quirino, BF and Barbosa, JARG and Freitas, SM and Krüger, RH}, title = {Biochemical and structural characterization of a family-9 glycoside hydrolase bioprospected from the termite Syntermes wheeleri gut bacteria metagenome.}, journal = {Enzyme and microbial technology}, volume = {189}, number = {}, pages = {110654}, doi = {10.1016/j.enzmictec.2025.110654}, pmid = {40262434}, issn = {1879-0909}, abstract = {Glycosyl hydrolases (GH) are enzymes involved in the degradation of plant biomass. They are important for biorefineries that aim at the sustainable utilization of lignocellulosic residues to generate value-added products. The termite Syntermes wheeleri gut microbiota showed an abundance of bacteria from the phylum Firmicutes, a phylum with enzymes capable of breaking down cellulose and degrading lignin, facilitating the use of plant materials as a food source for termites. Using bioinformatics techniques, cellobiohydrolases were searched for in the gut metagenome of the termite Syntermes wheeleri, endemic to the Cerrado. After selecting sequences of the target enzymes, termite gut microbiome metatranscriptome data were used as the criteria to choose the GH9 enzyme sequence Exo8574. Here we present the biochemical and structural characterization of Exo8574, a GH9 enzyme that showed activity with the substrate p-nitrophenyl-D-cellobioside (pNPC), consistent with cellobiohydrolase activity. Bioinformatics tools were used to perform phylogeny studies of Exo8574 and to identify conserved families and domains. Exo8574 showed 48.8 % homology to a protein from a bacterium belonging to the phylum Firmicutes. The high-quality three-dimensional (3D) model of Exo8574 was obtained by protein structure prediction AlphaFold 2, a neural network-based method. After the heterologous expression of Exo8574 and its purification, biochemical experiments showed that the optimal activity of the enzyme was at a temperature of 55 ºC and pH 6.0, which was enhanced in the presence of metal ions, especially Fe[2 +]. The estimated kinetic parameters of Exo8574 using the synthetic substrate p-nithrophenyl-beta-D-cellobioside (pNPC) were: Vmax = 9.14 ± 0.2 x10[-5] μmol/min and Km = 248.27 ± 26.35 μmol/L. The thermostability test showed a 50 % loss of activity after 1 h incubation at 55 °C. The secondary structure contents of Exo8574 evaluated by Circular Dichroism were pH dependent, with greater structuring of protein in β-antiparallel and α-helices at pH 6.0. The similarity between the CD results and the Ramachandran plot of the 3D model suggests that a reliable model has been obtained. Altogether, the results of the biochemical and structural characterization showed that Exo8574 is capable of acting on p-nithrophenyl-beta-D-cellobioside (pNPC), a substrate that mimics bonds cleaved by cellobiohydrolases. These findings have significant implications for advancing in the field of biomass conversion while also contributing to efforts aimed at overcoming challenges in developing more efficient cellulase cocktails.}, } @article {pmid40262432, year = {2025}, author = {Wu, G and Zhang, H and Huang, T and Song, Y and Liu, X and Liu, X and Wang, X and Pei, T and Xu, G and Wang, Z}, title = {Hydraulic and thermal performance trigger the deterministic assembly of water microbiomes: From biogeographical homogenization to machine learning model.}, journal = {Water research}, volume = {282}, number = {}, pages = {123626}, doi = {10.1016/j.watres.2025.123626}, pmid = {40262432}, issn = {1879-2448}, abstract = {Water quality at the point of consumption has long been a health issue because of the potential for microbial ecology. However, research on water hydraulic performance remains in its infancy, and in particular, little is known about the effects of thermal performance during winter. This study explored the effects of stagnation and municipal heating on microbial communities in tap water, focusing on spatial and temporal variations in microbial community composition. The results revealed that stagnation significantly alters the microbial community, especially in heating areas, where the temperature exacerbates microbial growth. Furthermore, hydraulic and thermal performance drive deterministic assembly processes in microbial communities, as evidenced by the reductions in β-diversity, normalized stochasticity ratio (NST), and neutral community model (NCM) fit. Machine learning models revealed that stagnation time greater than 8 h results in increased community abundance because of longer exposure to organic matter and nutrients. The study finding illustrate the importance of environmental influences on microbial community dynamics, and provide valuable insights into the water microbial community, particularly in areas with prolonged stagnation.}, } @article {pmid40261735, year = {2025}, author = {Rogers, AB and Kale, V and Baldi, G and Alberdi, A and Gilbert, MTP and Gupta, D and Limborg, MT and Li, S and Payne, T and Petersen, B and Rasmussen, JA and Richardson, L and Finn, RD}, title = {HoloFood Data Portal: holo-omic datasets for analysing host-microbiota interactions in animal production.}, journal = {Database : the journal of biological databases and curation}, volume = {2025}, number = {}, pages = {}, doi = {10.1093/database/baae112}, pmid = {40261735}, issn = {1758-0463}, mesh = {Animals ; *Chickens/microbiology ; *Microbiota ; *Salmon/microbiology ; *Databases, Genetic ; *Host Microbial Interactions ; Metadata ; *Gastrointestinal Microbiome ; }, abstract = {The HoloFood project used a hologenomic approach to understand the impact of host-microbiota interactions on salmon and chicken production by analysing multiomic data, phenotypic characteristics, and associated metadata in response to novel feeds. The project's raw data, derived analyses, and metadata are deposited in public, open archives (BioSamples, European Nucleotide Archive, MetaboLights, and MGnify), so making use of these diverse data types may require access to multiple resources. This is especially complex where analysis pipelines produce derived outputs such as functional profiles or genome catalogues. The HoloFood Data Portal is a web resource that simplifies access to the project datasets. For example, users can conveniently access multiomic datasets derived from the same individual or retrieve host phenotypic data with a linked gut microbiome sample. Project-specific metagenome-assembled genome and viral catalogues are also provided, linking to broader datasets in MGnify. The portal stores only data necessary to provide these relationships, with possible linking to the underlying repositories. The portal showcases a model approach for how future multiomics datasets can be made available. Database URL: https://www.holofooddata.org.}, } @article {pmid40261409, year = {2025}, author = {Zhao, S and Guo, H and Wang, Z and Zhang, B and Chen, H and Klitzsch, N and Yue, L and Xia, D}, title = {Clay mineral content modulates biogenic gas production in coal: divergent microbial responses in low- and medium-rank coals revealed by multi-omics.}, journal = {Bioprocess and biosystems engineering}, volume = {}, number = {}, pages = {}, pmid = {40261409}, issn = {1615-7605}, support = {23ZX015//Key Scientific Research Project of Colleges and Universities in Henan Province/ ; 42172195//National Natural Science Foundation of China/ ; 42172199//National Natural Science Foundation of China/ ; AQ20240302//Double First-Class Initiative for Safety Discipline Construction Project/ ; 2024B03002//Xinjiang Key R & D Task Project/ ; }, abstract = {The influence of clay mineral content on biogenic gas production in coal seams remains insufficiently understood. This study systematically investigated the mechanisms by which clay minerals affect biogas production in low- and medium-rank coals by integrating simulated biogas production experiments with multidimensional analytical techniques, including infrared spectroscopy, X-ray diffraction, scanning electron microscopy, gas chromatography-mass spectrometry, fluorescence spectroscopy, and metagenomic analysis. The results demonstrated that in low-rank coal, increasing the clay content from 2.78 to 4.75 g per 20 g of coal reduced the biogas yield from 6.30 to 3.47 mL/g. Conversely, in medium-rank coal, increasing the clay content from 1.66 to 2.65 g per 20 g of coal enhanced the biogas yield from 3.45 to 5.28 mL/g. These contrasting outcomes are primarily attributed to the distinct mechanistic roles of clay minerals across coal ranks. In low-rank coal, the hydration-induced swelling of clay minerals intensified pore blockage, impeded gas diffusion, decreased the abundance of genes involved in propionate degradation, and suppressed microbial metabolic activity, ultimately limiting methane production. In contrast, in medium-rank coal, clay minerals facilitated the enrichment of key functional microbial taxa, such as Acetobacteroides and Methanoculleus, promoted the degradation of fatty acids, hydroxyls, and amines, and enhanced the activity of acidogenic and methanogenic pathways, thereby increasing methane yield. This study elucidates the microbial mechanisms underlying the regulatory role of clay minerals in biogas production, offering new theoretical insights into the origin of coalbed methane (CBM) and providing a scientific foundation for optimizing biogenic CBM recovery.}, } @article {pmid40261207, year = {2025}, author = {Liao, X and Li, Y and Wu, Y and Li, X and Shang, X}, title = {Deep Learning-Based Classification of CRISPR Loci Using Repeat Sequences.}, journal = {ACS synthetic biology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acssynbio.5c00174}, pmid = {40261207}, issn = {2161-5063}, abstract = {With the widespread application of the CRISPR-Cas system in gene editing and related fields, along with the increasing availability of metagenomic data, the demand for detecting and classifying CRISPR-Cas systems in metagenomic data sets has grown significantly. Traditional classification methods for CRISPR-Cas systems primarily rely on identifying cas genes near CRISPR arrays. However, in cases where cas gene information is absent, such as in metagenomes or fragmented genome assemblies, traditional methods may fail. Here, we present a deep learning-based method, CRISPRclassify-CNN-Att, which classifies CRISPR loci solely based on repeat sequences. CRISPRclassify-CNN-Att utilizes convolutional neural networks (CNNs) and self-attention mechanisms to extract features from repeat sequences. It employs a stacking strategy to address the imbalance of samples across different subtypes and uses transfer learning to improve classification accuracy for subtypes with fewer samples. CRISPRclassify-CNN-Att demonstrates outstanding performance in classifying multiple subtypes, particularly those with larger sample sizes. Although CRISPR loci classification traditionally depends on cas genes, CRISPRclassify-CNN-Att offers a novel approach that serves as a significant complement to cas-based methods, enabling the classification of orphan or distant CRISPR loci. The proposed tool is freely accessible via https://github.com/Xingyu-Liao/CRISPRclassify-CNN-Att.}, } @article {pmid40261064, year = {2025}, author = {Žuštra, A and Leonard, VR and Holland, LA and Hu, JC and Mu, T and Holland, SC and Wu, LI and Begnel, ER and Ojee, E and Chohan, BH and Richardson, BA and Kinuthia, J and Wamalwa, D and Slyker, J and Lehman, DA and Gantt, S and Lim, ES}, title = {Longitudinal dynamics of the nasopharyngeal microbiome in response to SARS-CoV-2 Omicron variant and HIV infection in Kenyan women and their children.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0156824}, doi = {10.1128/msystems.01568-24}, pmid = {40261064}, issn = {2379-5077}, abstract = {UNLABELLED: The nasopharynx and its microbiota are implicated in respiratory health and disease. The interplay between viral infection and the nasopharyngeal microbiome is an area of increased interest. The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of the coronavirus disease 2019 pandemic, on the nasopharyngeal microbiome among individuals living with HIV is not fully characterized. Here, we describe the nasopharyngeal microbiome before, during, and after SARS-CoV-2 infection in a longitudinal cohort of Kenyan women (21 living with HIV and 14 HIV-uninfected) and their children (18 HIV-exposed, uninfected and 7 HIV-unexposed, uninfected) between September 2021 and March 2022. We show using genomic epidemiology that mother and child dyads were infected with the same strain of the SARS-CoV-2 Omicron variant that spread rapidly across Kenya. We used metagenomic sequencing to characterize the nasopharyngeal microbiome of 20 women and children infected with SARS-CoV-2, six children negative for SARS-CoV-2 but experiencing respiratory symptoms, and 34 timepoint-matched SARS-CoV-2-negative mothers and children. Since individuals were sampled longitudinally before and after SARS-CoV-2 infection, we could characterize the short- (within a week of infection) and longer- (average of 38 days post-infection) term impact of SARS-CoV-2 infection on the nasopharyngeal microbiome. We found that mothers and children had significantly different microbiome composition and bacterial load (P-values < 0.0001). In both mothers and children, the nasopharyngeal microbiome did not differ before and after SARS-CoV-2 infection, regardless of HIV exposure status. Our results indicate that the nasopharyngeal microbiome is resilient to SARS-CoV-2 infection and was not significantly modified by HIV.

IMPORTANCE: The nasopharyngeal microbiome plays an important role in human health. The degree of impact that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has on the nasopharyngeal microbiome varies among studies and may be influenced by diverse SARS-CoV-2 variants and variations in the microbiome between individuals. Our results show that the nasopharyngeal microbiome was not altered substantially by SARS-CoV-2 infection nor by HIV infection in mothers or HIV exposure in children. Our findings highlight the resilience of the nasopharyngeal microbiome after SARS-CoV-2 infection. These findings advance our understanding of the nasopharyngeal microbiome and its interactions with viral infections.}, } @article {pmid40261045, year = {2025}, author = {Doing, G and Shanbhag, P and Bell, I and Cassidy, S and Motakis, E and Aiken, E and Oh, J and Adams, MD}, title = {TEAL-Seq: targeted expression analysis sequencing.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0098424}, doi = {10.1128/msphere.00984-24}, pmid = {40261045}, issn = {2379-5042}, abstract = {Metagenome sequencing enables the genetic characterization of complex microbial communities. However, determining the activity of isolates within a community presents several challenges, including the wide range of organismal and gene expression abundances, the presence of host RNA, and low microbial biomass at many sites. To address these limitations, we developed "targeted expression analysis sequencing" or TEAL-seq, enabling sensitive species-specific analyses of gene expression using highly multiplexed custom probe pools. For proof of concept, we targeted about 1,700 core and accessory genes of Staphylococcus aureus and S. epidermidis, two key species of the skin microbiome. Two targeting methods were applied to laboratory cultures and human nasal swab specimens. Both methods showed a high degree of specificity, with >90% reads on target, even in the presence of complex microbial or human background DNA/RNA. Targeting using molecular inversion probes demonstrated excellent correlation in inferred expression levels with bulk RNA-seq. Furthermore, we show that a linear pre-amplification step to increase the number of nucleic acids for analysis yielded consistent and predictable results when applied to complex samples and enabled profiling of expression from as little as 1 ng of total RNA. TEAL-seq is much less expensive than bulk metatranscriptomic profiling, enables detection across a greater dynamic range, and uses a strategy that is readily configurable for determining the transcriptional status of organisms in any microbial community.IMPORTANCEThe gene expression patterns of bacteria in microbial communities reflect their activity and interactions with other community members. Measuring gene expression in complex microbiome contexts is challenging, however, due to the large dynamic range of microbial abundances and transcript levels. Here we describe an approach to assessing gene expression for specific species of interest using highly multiplexed pools of targeting probes. We show that an isothermal amplification step enables the profiling of low biomass samples. TEAL-seq should be widely adaptable to the study of microbial activity in natural environments.}, } @article {pmid40260991, year = {2025}, author = {López-Gálvez, R and Orenes-Piñero, E and Rivera-Caravaca, JM and Pérez-Sanz, F and Ramos-Bratos, MP and Roca, MI and Mandaglio-Collados, D and López-García, C and Gil-Pérez, P and Esteve-Pastor, MA and Marín, F}, title = {Microbial Insights: The Role of Diet in Modulating Gut Microbiota and Metabolites After Acute Coronary Syndrome.}, journal = {Molecular nutrition & food research}, volume = {}, number = {}, pages = {e70046}, doi = {10.1002/mnfr.70046}, pmid = {40260991}, issn = {1613-4133}, support = {//Instituto de Salud Carlos III/ ; //Centro de investigación Biomédica en Red/ ; }, abstract = {Acute coronary syndrome (ACS) is a leading cause of global mortality, largely due to atherosclerosis influenced by lifestyle factors like diet. Gut microbiota impacts lipid metabolism, inflammation, and endothelial function, all vital in atherosclerosis. Dysbiosis increases intestinal permeability, causing inflammation and plaque instability, elevating cardiac event risk. This study investigates the impact of dietary improvements on gut microbiota and metabolite release in recent ACS patients versus healthy individuals. A cohort of 29 recent ACS patients receiving lipid-lowering therapy and dietary advice was analyzed alongside 56 healthy controls. Dietary habits, serum, and stool samples were collected at admission and after 3 months. Metagenomic analysis of stool and metabolomic analysis of serum were conducted. The results showed bacterial dysbiosis in ACS patients, characterized by a reduction in beneficial genera and an increase in potentially pro-inflammatory bacteria. After 3 months of dietary improvements, three metabolites with anti-inflammatory properties were significantly upregulated. The findings highlight the association between gut microbiota dysbiosis, fatty diets, and inflammation in ACS patients. The observed increase in anti-inflammatory metabolites following dietary changes underscore the following dietary interventions in modulating gut microbiota and improving cardiovascular and metabolic health.}, } @article {pmid40260089, year = {2025}, author = {Xu, P and Pan, C and Yuan, M and Zhu, Y and Wei, S and Lu, H and Zhang, W}, title = {Viral metagenomics reveals diverse viruses in the fecal samples of children with acute respiratory infection.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1564755}, pmid = {40260089}, issn = {1664-302X}, abstract = {INTRODUCTION: Changes in the gut microbiome have been associated with the development of acute respiratory infection (ARI). However, due to methodological limitations, our knowledge of the gut virome in patients with ARIs remains limited.

METHODS: In this study, fecal samples from children with ARI were investigated using viral metagenomics.

RESULTS: The fecal virome was analyzed, and several suspected disease-causing viruses were identified. The five viral families with the highest abundance of sequence reads were Podoviridae, Virgaviridae, Siphoviridae, Microviridae, and Myoviridae. Additionally, human adenovirus, human bocavirus, human astrovirus, norovirus, and human rhinovirus were detected. The genome sequences of these viruses were respectively described, and phylogenetic trees were constructed using the gene sequences of the viruses.

DISCUSSION: We characterized the composition of gut virome in children with acute respiratory infections. However, further research is required to elucidate the relationship between acute respiratory infection and gut viruses.}, } @article {pmid40260085, year = {2025}, author = {Perez, LJ and Perez-Restrepo, LS and Ciuoderis, K and Usuga, J and Moreno, I and Vargas, V and Arévalo-Arbelaez, AJ and Berg, MG and Cloherty, GA and Hernández-Ortiz, JP and Osorio, JE}, title = {Emergence, persistence, and positive selection of yellow fever virus in Colombia.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1548556}, pmid = {40260085}, issn = {1664-302X}, abstract = {Yellow fever virus (YFV) is an arbovirus that causes acute febrile illness (AFI), in tropical areas of South America and Africa. Through a 2020-2023 AFI study in Leticia, Colombia, leveraging metagenomic next-generation sequencing (mNGS), we identified and isolated YFV (LET1450). Phylogenetic analysis showed this strain belongs to South American genotype II (SamII), linked to Peruvian and Bolivian sequences emerging around 1989. Phylodynamic analysis indicates these strains, with a unique genetic makeup, could have reduced vaccine susceptibility, and due to positive Darwinian selection have an enhanced adaptive capacity. Antigenic analysis identified additional immune-evasive traits and this strain's potential for wider Latin American spread. Phylogeographic reconstruction demonstrated the persistence of YFV in Colombia is not due to repeated external introductions, but results from continuous, cryptic internal circulation. This study highlights the crucial role of mNGS in monitoring emerging strains and underscores the need for genomic surveillance of YFV and other arboviral infections.}, } @article {pmid40260047, year = {2025}, author = {Guo, L and Wu, X and Cao, L}, title = {Clinical Characteristics of Miliary Pulmonary Tuberculosis in Pregnancy After In Vitro Fertilization-Embryo Transfer: A Retrospective Clinical Study.}, journal = {Health science reports}, volume = {8}, number = {4}, pages = {e70705}, pmid = {40260047}, issn = {2398-8835}, abstract = {BACKGROUND AND AIMS: Miliary pulmonary tuberculosis (MPTB) is rare in patients treated with In Vitro fertilization-embryo transfer (IVF-ET), and can be life-threatening to pregnant women and fetuses. We aimed to describe the clinical characteristics of MPTB after IVF-ET and pregnancy outcomes to provide reference for early diagnosis and treatment.

METHODS: Clinical data from patients who developed MPTB after IVF-ET from January 2018-December 2021 were retrospectively and statistically analyzed.

RESULTS: Ultimately, 21 patients (mean age: 29.81 ± 3.79 years) were included. Three patients had a history of pulmonary or extrapulmonary tuberculosis (TB), and were cured or showed no suggestive TB activity before pregnancy. Patients presented with atypical early symptoms, fever (39.16 ± 0.74°C), and vaginal bleeding, and lung imaging changes. Patients became febrile 78.90 ± 26.04 days after IVF-ET; the time from fever to diagnosis was 17.76 ± 9.05 days. Patients were admitted 96.05 ± 25.33 days after IVF-ET. Sputum Mycobacterium tuberculosis smear and culture, purified protein derivative, TB polymerase chain reaction, and other routine TB examinations had low positivity rates; the erythrocyte sedimentation rate was generally within normal limits. Chest imaging during pregnancy is limited, further increasing the diagnosis time. Two critically ill patients were diagnosed by metagenomic next-generation sequencing. Seven patients had TB meningitis or encephalitis. Pregnancy was terminated in all but three patients. All patients received anti-TB therapy; however, two patients died during hospitalization (mean hospitalization: 58.29 ± 33.40 days).

CONCLUSIONS: Comprehensive TB screening before IVF-ET is necessary for infertile patients. MPTB develops after IVF-ET with atypical symptoms and poor pregnancy outcomes. Clinicians should use multiple methods to confirm TB diagnoses early on, without delaying chest imaging.}, } @article {pmid40259990, year = {2025}, author = {Chen, Y and Liu, Y and Ji, M and Zhang, Z and Xing, T and Pan, H and Liu, K and Li, Y and Liu, P}, title = {Metabolic diversity and adaptation of carbon-fixing microorganisms in extreme glacial cryoconite.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf056}, pmid = {40259990}, issn = {2730-6151}, abstract = {Understanding the diversity and functionality of carbon-fixing microorganisms in glacial ecosystems is crucial for elucidating carbon cycling processes in extreme environments. This study investigates the composition, diversity, and metabolic potential of carbon-fixing microorganisms in Tibetan cryoconite. Through metagenomic sequencing, we identified 13 carbon-fixing metagenome-assembled genomes spanning ten known and three unclassified genera. Deoxyribonucleic acid -stable isotope probing experiments with [13]C-labeled sodium bicarbonate confirmed the metabolic activity of key genera, including Cyanobacteria (Microcoleus and Phormidesmis) and Proteobacteria (Rhizobacter and Rhodoferax). Our results reveal a diverse array of carbon fixation pathways, with the Calvin-Benson-Bassham cycle and 3-hydroxypropionate bicycle being the most prominent. In addition to photoautotrophic microorganisms, chemoautotrophic microorganisms also contribute to carbon fixation through mechanisms such as sulfur oxidation and atmospheric reducing gas utilization. The study highlights the adaptability of microbial communities to varying environmental conditions, including fluctuations in oxygen, light, and substrate availability. The findings underscore the complex interplay between carbon fixation pathways and environmental factors in cryoconite ecosystems. It also emphasizes the importance of exploring alternative carbon fixation pathways to gain a more comprehensive understanding of carbon cycling in these harsh and dynamic ecosystems.}, } @article {pmid40259731, year = {2025}, author = {Sun, YS and Zhao, L and Zheng, CL and Yan, XT and Li, Y and Gao, XL and Xue, TF and Zhang, YM and Li, ZP and Heller, R and Feng, CG and Xu, C and Wang, K and Qiu, Q}, title = {Convergent musk biosynthesis across host and microbiota in musk deer and muskrat.}, journal = {Zoological research}, volume = {46}, number = {3}, pages = {505-517}, doi = {10.24272/j.issn.2095-8137.2025.094}, pmid = {40259731}, issn = {2095-8137}, mesh = {Animals ; *Deer/microbiology/metabolism ; *Fatty Acids, Monounsaturated/metabolism ; *Microbiota ; Scent Glands/metabolism ; *Arvicolinae/microbiology/metabolism ; }, abstract = {Mammalian scent glands mediate species-specific chemical communication, yet the mechanistic basis for convergent musk production remain incompletely understood. Forest musk deer and muskrat have independently evolved specialized musk-secreting glands, representing a striking case of convergent evolution. Through an integrated multi-omics approach, this study identified cyclopentadecanone as a shared key metabolic precursor in musk from both forest musk deer and muskrat, although downstream metabolite profiles diverged between the two lineages. Single-cell RNA sequencing revealed that these specialized apocrine glands possessed unique secretory architecture and exhibited transcriptional profiles associated with periodic musk production, distinct from those in conventional apocrine glands. Convergent features were evident at the cellular level, where acinar, ductal, and basal epithelial subtypes showed parallel molecular signatures across both taxa. Notably, acinar cells in both species expressed common genes involved in fatty acid and glycerolipid metabolism (e.g., ACSBG1, HSD17B12, HACD2, and HADHA), suggesting a conserved molecular framework for musk precursor biosynthesis. Metagenomic analysis of musk samples further revealed parallel microbial community structures dominated by Corynebacterium and enriched in lipid metabolic pathways. These findings suggest multi-level convergence in musk biosynthesis, from molecular pathways to microbial communities, providing novel insights into mammalian chemical signaling and artificial musk production.}, } @article {pmid40259344, year = {2025}, author = {Zhang, Q and Hutchison, ER and Pan, C and Warren, MF and Keller, MP and Attie, AD and Lusis, AJ and Rey, FE}, title = {Systems genetics uncovers associations among host amylase locus, gut microbiome, and metabolic traits in mice.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {101}, pmid = {40259344}, issn = {2049-2618}, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome/genetics ; *Amylases/genetics/metabolism ; Genome-Wide Association Study ; Metagenomics/methods ; Male ; Bacteroidetes/genetics/classification/isolation & purification ; Mendelian Randomization Analysis ; Firmicutes/genetics/classification/isolation & purification ; Cecum/microbiology ; }, abstract = {BACKGROUND: Population studies have revealed associations between host genetic and gut microbiome in humans and mice. However, the molecular bases for how host genetic variation impacts the gut microbial community and bacterial metabolic niches remain largely unknown.

RESULTS: We leveraged 90 inbred hyperlipidemic mouse strains from the hybrid mouse diversity panel (HMDP), previously studied for a variety of cardio-metabolic traits. Metagenomic analysis of cecal DNA followed by genome-wide association analysis identified genomic loci that were associated with microbial enterotypes in the gut. Among these, we detected a genetic locus surrounding multiple amylase genes that were associated with abundances of Firmicutes (Lachnospiraceae family) and Bacteroidetes (Muribaculaceae family) taxa encoding distinct starch and sugar degrading capabilities. The genetic variants at the amylase gene locus were associated with distinct gut microbial communities (enterotypes) with different predicted metabolic capacities for carbohydrate degradation. Mendelian randomization analysis revealed host phenotypes, including liver fibrosis and plasma HDL-cholesterol levels, that were associated with gut microbiome enterotypes.

CONCLUSIONS: This work reveals novel relationships among host genetic variation, gut microbial enterotypes, and host metabolic traits and supports the notion that variation of host amylase may represent a key determinant of gut microbiome in mice. Video Abstract.}, } @article {pmid40258842, year = {2025}, author = {Duru, IC and Lecomte, A and Laine, P and Shishido, TK and Suppula, J and Paulin, L and Scheperjans, F and Pereira, PAB and Auvinen, P}, title = {Comparison of phage and plasmid populations in the gut microbiota between Parkinson's disease patients and controls.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {13723}, pmid = {40258842}, issn = {2045-2322}, support = {NNF22OC0080109//Novo Nordisk Foundation/ ; }, mesh = {Humans ; *Parkinson Disease/microbiology/virology ; *Gastrointestinal Microbiome/genetics ; *Bacteriophages/genetics/isolation & purification ; Aged ; *Plasmids/genetics ; Male ; Female ; Middle Aged ; Feces/microbiology/virology ; Case-Control Studies ; Metagenomics/methods ; Machine Learning ; }, abstract = {The aging population worldwide is on the rise, leading to a higher number of Parkinson's disease (PD) cases each year. PD is presently the second most prevalent neurodegenerative disease, affecting an estimated 7-10 million individuals globally. This research aimed to identify mobile genetic elements in human fecal samples using a shotgun metagenomics approach. We identified over 44,000 plasmid contigs and compared plasmid populations between PD patients (n = 68) and controls (n = 68). Significant associations emerged between groups (control vs PD) based on plasmid alpha and beta diversity. Moreover, the gene populations present on plasmids displayed marked differences in alpha and beta diversity between PD patients and controls. We identified a considerable number of phage contigs that were differentially abundant in the two groups. We also developed a predictive machine learning model based on phage abundance data, achieving a mean Area Under the Curve (AUC) of 0.74 with a standard deviation of 0.105 and a mean F1 score of 0.68 with a standard deviation of 0.14 across cross-validation folds, indicating moderate discriminatory power. Additionally, when tested on external data, the model yielded an AUC of 0.74 and an F1 score of 0.8, further demonstrating the predictive potential of phage populations in Parkinson's disease. Further, we improved the continuity and identification of the protein coding regions of the phage contigs by implementing alternative genetic codes.}, } @article {pmid40258509, year = {2025}, author = {Fang, C and Zhu, J and Xu, H and Qian, M and Jin, Y}, title = {Polystyrene microplastics and cypermethrin exposure interfered the complexity of antibiotic resistance genes and induced metabolic dysfunction in the gut of adult zebrafish.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {374}, number = {}, pages = {126288}, doi = {10.1016/j.envpol.2025.126288}, pmid = {40258509}, issn = {1873-6424}, abstract = {Environmental pollutants such as microplastics (MPs) and pesticides are becoming prevalent in aquatic ecosystems, posing risks to wildlife and human health. This study investigated the toxicological effects of polystyrene microplastics (PS-MPs) and cypermethrin (CYP) on adult female zebrafish (Danio rerio), focusing on intestinal microenvironment. Adsorption kinetics experimental results showed that PS-MPs can adsorb a certain amount of CYP on its surface, thereby forming a new type of composite pollutant. After exposure to red fluorescent PS-MPs for 4 days, it was found that the PS-MPs could enter the zebrafish and accumulate in the intestines. Five-month-old female zebrafish were exposed to PS-MPs, CYP, and a mixture of both for 21 days. After exposure, feces were collected and analyzed using metagenomic sequencing to determine microbial composition and functional changes. Metagenomic sequencing of naturally excreted feces showed that co-exposure synergistically reduced α-diversity and shifted community structure, with marked losses of beneficial Fusobacteriota, Firmicutes and Cetobacterium somerae and enrichment of pathogenic Preplasmiviricota. Functional annotation indicated that PS-MPs alone up-regulated glycoside hydrolases and glycosyl-transferases, whereas CYP and the co-exposure group suppressed a great number of the top 50 carbohydrate-active enzymes and decreased secondary metabolic pathways linked to amino-acid, lipid and carbohydrate metabolism pathways. Antibiotic-resistance gene (ARGs) profiling identified 57 ARG types (such as sul1, adeF, lnuC and mphA) after co-exposure. Finally, key genes related to amino acid metabolism, carbohydrate metabolism, and lipid metabolism in intestinal tissue were significantly altered. Collectively, our data demonstrated that PS-MPs and CYP exposure amplified gut dysbiosis, metabolic dysfunction and ARG complexity in zebrafish. Overall, the study highlighted the potential risks of combined environmental pollutants on intestinal microbiota, with implications for ecosystem health.}, } @article {pmid40258462, year = {2025}, author = {He, R and Li, X and Zhang, X}, title = {Methane enhancing nitrous oxide consumption in microaerobic sludge systems.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121658}, doi = {10.1016/j.envres.2025.121658}, pmid = {40258462}, issn = {1096-0953}, abstract = {Nitrous oxide (N2O) reduction is traditionally known to be active under extremely low oxygen concentrations and hypoxic conditions. Herein, microaerobic sludge systems (∼38.2 and ∼12.1 μM dissolved oxygen) were conducted to investigate the performance of simultaneous methane (CH4) oxidation and N2O consumption compared with hypoxic conditions. During the whole experiment, the average N2O consumption rate in the high dissolved oxygen sludge system with CH4 was 3.4-4.9 times that of the others. A positively linear correlation was observed between the CH4 oxidation rate and the N2O consumption rate in the sludge systems. Compared to the treatment without CH4, the N2O consumption rate was higher in the treatment with CH4, indicating that aerobic CH4 oxidation might be related with the N2O consumption in the systems. The N2O consumption in the microaerobic system was influenced by the O2, CH4 and NH4[+]-N concentrations and was regulated by the microbial species. Type I methane-oxidizing bacteria (MOB) including Methylococcus, Methylocaldum, Methylomagnum, Methylosarcina, Methylobacter and Methylogaea, type II MOB Methylocystis and NC10 phylum Candidatus Methylomirabilis were the main methanotrophs in the systems. Compared with type II MOB, type I MOB were more abundant in the system. Anaerolinea and Lautropia were the main denitrifying bacteria in the microaerobic system with CH4 and N2O. Clad I nosZ and clad II nosZ were both rich in the microaerobic system. These findings suggest that an appropriate oxygen concentration would be favorable for simultaneous mitigation of CH4 and N2O emission in the sludge systems.}, } @article {pmid40257249, year = {2025}, author = {Maggiori, C and John, Z and Bower, DM and Millan, M and Hahn, AS and McAdam, A and Johnson, SS}, title = {Draft genome sequence of a member of a putatively novel Rubrobacteraceae genus from lava tubes in Lava Beds National Monument.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0133524}, doi = {10.1128/mra.01335-24}, pmid = {40257249}, issn = {2576-098X}, abstract = {We report the draft genome sequence of a member of a potentially novel genus of Rubrobacteraceae isolated from Golden Dome Cave in Lava Beds National Monument. Members of this family are known to inhabit thermophilic environments. The metagenome-assembled genome presented here helps illuminate the genetic capacity of basaltic lava tube environments.}, } @article {pmid40257199, year = {2025}, author = {Wang, X and Wang, M and Zhang, W and Li, H and Tiedje, JM and Zhou, J and Topp, E and Luo, Y and Chen, Z}, title = {Treatment of antibiotic-manufacturing wastewater enriches for Aeromonas veronii, a zoonotic antibiotic-resistant emerging pathogen.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf077}, pmid = {40257199}, issn = {1751-7370}, abstract = {Antibiotic-manufacturing wastewater treatment plants primarily target chemical pollutants, but their processes may select for antibiotic-resistant pathogens and antibiotic resistance genes. Here, leveraging the combined strengths of deep metagenomic sequencing, 16S rRNA gene sequencing, qPCR, and bacterial culturing, we investigated bacterial communities and antibiotic resistomes across eleven treatment units in a full-scale antibiotic-manufacturing wastewater treatment plant processing wastewater from a β-lactam manufacturing facility. We demonstrated that both bacterial communities and antibiotic resistance gene compositions varied across the treatment units, but were associated. Certain antibiotic resistance gene persisted through treatment, either carried by identical bacterial species, or linked to mobile genetic elements in different species. Despite the satisfactory performance in chemical removal, the antibiotic-manufacturing wastewater treatment plant continuously enriched zoonotic antibiotic-resistant Aeromonas veronii (an emerging pathogen responsible for substantial economic losses in aquaculture and human health) from influent to effluent, probably due to prolonged β-lactam selection pressure and aquatic nature of A. veronii. This enrichment resulted in a significantly higher abundance of A. veronii in the antibiotic-manufacturing wastewater treatment plant compared to other aquatic samples worldwide. Furthermore, the closest evolutionary relative to the antibiotic-manufacturing wastewater treatment plant derived A. veronii was an isolate obtained from the stool of a local diarrhea patient. These findings highlighted a substantial public health risk posed by antibiotic-manufacturing wastewater treatment plants, underlining their potential role in enriching and disseminating zoonotic antibiotic-resistant pathogens. Beyond chemical monitoring, enhanced surveillance of antibiotic-resistant pathogens and antibiotic resistance genes is needed in antibiotic-manufacturing wastewater treatment plants to avoid creating environmental hotspots of antibiotic resistant pathogens from discharging wastewater effluents.}, } @article {pmid40256453, year = {2025}, author = {Shen, D and Ju, H and Wang, H and Wang, X and Li, G}, title = {The clinic application of mNGS and ENA-78 assays to identify intra-amniotic infection/inflammation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1510671}, pmid = {40256453}, issn = {2235-2988}, mesh = {Humans ; Female ; Pregnancy ; *Amniotic Fluid/microbiology/chemistry ; Adult ; *Chorioamnionitis/diagnosis ; *Inflammation/diagnosis ; *Pregnancy Complications, Infectious/diagnosis ; Biomarkers/analysis ; High-Throughput Nucleotide Sequencing ; Obstetric Labor, Premature/diagnosis ; Pregnancy Outcome ; Cerclage, Cervical ; Young Adult ; *Chemokine CXCL5/analysis ; }, abstract = {OBJECTIVE: The objective of this study is to explore whether metagenomic next-generation sequencing (mNGS) and Epithelial Neutrophil Activating Peptide-78 (ENA-78) assays in the amniotic fluid (AF) of patients with preterm labor (PTL) could be employed for diagnosing intra-amniotic infection/inflammation (IAI/I) and predict the outcomes of emergency cerclage in women with cervical insufficiency(CI).

METHODS: AF samples from 40 patients were subjected to PTL were subjected to mNGS and microbial culture to diagnose intra-amniotic infection known as microbial invasion of the amniotic cavity (MIAC); ELISA was used to analyze ENA-78 levels for prediction of intra-amniotic inflammation (IAI). Pregnancy outcomes were compared, the predictive performance of mNGS and ENA-78 were assessed to evaluate the efficacy of emergency cervical cerclage.

RESULTS: The diagnosis rate of MIAC was higher with mNGS (17.5%) compared to microbial culture (2.5%). AF ENA-78 levels were significantly higher in IAI patients than in non-IAI/I patients. ENA-78 demonstrated certain accuracy in identifying IAI, with sensitivity and specificity of 73.3% and 100%, respectively. Compared with non-IAI/I patients, patients with MIAC or IAI exhibited poor pregnancy outcomes after cervical cerclage.

CONCLUSIONS: mNGS and ENA-78 assays are valuable means for assessing the state of infection/inflammation in the amniotic cavity and predicting the outcomes of emergency cerclage.}, } @article {pmid40255248, year = {2025}, author = {Favale, N and Costa, S and Summa, D and Sabbioni, S and Mamolini, E and Tamburini, E and Scapoli, C}, title = {Comparison of microbiome community structure and dynamics during anaerobic digestion of different renewable solid wastes.}, journal = {Current research in microbial sciences}, volume = {8}, number = {}, pages = {100383}, pmid = {40255248}, issn = {2666-5174}, abstract = {This study analysed the effect of the different lignocellulose composition of two crop substrates on the structure and dynamics of bacterial communities during anaerobic digestion (AD) processes for biogas production. To this end, cereal grains and grape pomace biomasses were analysed in parallel in an experimental AD bench-scale system to define and compare their metagenomic profiles for different experimental time intervals. The bacterial community structure and dynamics during the AD process were detected and characterised using high-resolution whole metagenomic shotgun analyses. Statistical evaluation identified 15 strains as specific to two substrates. Some strains, like Clostridium isatidis, Methanothermobacter wolfeii, and Methanobacter sp. MB1 in cereal grains, and Acetomicrobium hydrogeniformans and Acetomicrobium thermoterrenum in grape pomace, were never before detected in biogas reactors. The presence of bacteria such as Acetomicrobium sp. and Petrimonas mucosa, which degrade lipids and protein-rich substrates, along with Methanosarcina sp. and Peptococcaceae bacterium 1109, which tolerate high hydrogen pressures and ammonia concentrations, suggests a complex syntrophic community in lignin-cellulose-enriched substrates. This finding could help develop new strategies for the production of a tailor-made microbial consortium to be inoculated from the beginning of the digestion process of specific lignocellulosic biomass.}, } @article {pmid40255076, year = {2025}, author = {Buttler, L and Velázquez-Ramírez, DA and Tiede, A and Conradi, AM and Woltemate, S and Geffers, R and Bremer, B and Spielmann, V and Kahlhöfer, J and Kraft, ARM and Schlüter, D and Wedemeyer, H and Cornberg, M and Falk, C and Vital, M and Maasoumy, B}, title = {Distinct clusters of bacterial and fungal microbiota in end-stage liver cirrhosis correlate with antibiotic treatment, intestinal barrier impairment, and systemic inflammation.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2487209}, doi = {10.1080/19490976.2025.2487209}, pmid = {40255076}, issn = {1949-0984}, mesh = {Humans ; Male ; Female ; Middle Aged ; *Gastrointestinal Microbiome/drug effects ; *Bacteria/classification/genetics/isolation & purification/drug effects ; *Anti-Bacterial Agents/therapeutic use/adverse effects ; Aged ; Dysbiosis/microbiology ; *Fungi/classification/isolation & purification/genetics ; *Inflammation/microbiology ; *Liver Cirrhosis/microbiology ; *Mycobiome ; Prospective Studies ; Metagenomics ; Intestinal Mucosa/microbiology ; *End Stage Liver Disease/microbiology/drug therapy ; Adult ; }, abstract = {Decompensated liver cirrhosis (dLC) is associated with intestinal dysbiosis, however, underlying reasons and clinical consequences remain largely unexplored. We investigated bacterial and fungal microbiota, their relation with gut barrier integrity, inflammation, and cirrhosis-specific complications in dLC-patients. Competing-risk analyses were performed to investigate clinical outcomes within 90 days. Samples were prospectively collected from 95 dLC-patients between 2017 and 2022. Quantitative metagenomic analyses clustered patients into three groups (G1-G3) showing distinct microbial patterns. G1 (n = 39) displayed lowest diversity and highest Enterococcus abundance, G2 (n = 24) was dominated by Bifidobacteria, G3 (n = 29) was most diverse and clustered most closely with healthy controls (HC). Of note, bacterial concentrations were significantly lower in cirrhosis compared with HC, especially for G1 that also showed the lowest capacity to produce short chain fatty acids and secondary bile acids. Consequently, fungal overgrowth, dominated by Candida spp. (51.63%), was observed in G1. Moreover, G1-patients most frequently received antibiotics (n = 33; 86.8%), had highest plasma-levels of Zonulin (p = 0.044) and a proinflammatory cytokine profile along with numerically higher incidences of subsequent infections (p = 0.09). In conclusion, distinct bacterial clusters were observed at qualitative and quantitative levels and correlated with fungal abundances. Antibiotic treatment significantly contributed to dysbiosis, which translated into intestinal barrier impairment and systemic inflammation.}, } @article {pmid40254830, year = {2025}, author = {Pham, CM and Rankin, TJ and Stinear, TP and Walsh, CJ and Ryan, FJ}, title = {TaxSEA: rapid interpretation of microbiome alterations using taxon set enrichment analysis and public databases.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {2}, pages = {}, doi = {10.1093/bib/bbaf173}, pmid = {40254830}, issn = {1477-4054}, support = {GNT1194325//National Health and Medical Research Council of Australia/ ; }, mesh = {*Microbiota ; Humans ; *Software ; *Metagenomics/methods ; Diabetes Mellitus, Type 2/microbiology/genetics ; *Databases, Genetic ; *Computational Biology/methods ; Inflammatory Bowel Diseases/microbiology/genetics ; Metagenome ; }, abstract = {Microbial communities are essential regulators of ecosystem function, with their composition commonly assessed through DNA sequencing. Most current tools focus on detecting changes among individual taxa (e.g. species or genera), however in other omics fields, such as transcriptomics, enrichment analyses like gene set enrichment analysis are commonly used to uncover patterns not seen with individual features. Here, we introduce TaxSEA, a taxon set enrichment analysis tool available as an R package, a web portal (https://shiny.taxsea.app), and a Python package. TaxSEA integrates taxon sets from five public microbiota databases (BugSigDB, MiMeDB, GutMGene, mBodyMap, and GMRepoV2) while also allowing users to incorporate custom sets such as taxonomic groupings. In silico assessments show TaxSEA is accurate across a range of set sizes. When applied to differential abundance analysis output from inflammatory bowel disease and type 2 diabetes metagenomic data, TaxSEA can rapidly identify changes in functional groups corresponding to known associations. We also show that TaxSEA is robust to the choice of differential abundance analysis package. In summary, TaxSEA enables researchers to efficiently contextualize their findings within the broader microbiome literature, facilitating rapid interpretation, and advancing understanding of microbiome-host and environmental interactions.}, } @article {pmid40254787, year = {2025}, author = {Dame-Teixeira, N and Lynch, J and Yu, X and Cena, JA and Do, T}, title = {The Caries and Caries-Free Archaeome.}, journal = {Journal of dental research}, volume = {}, number = {}, pages = {220345251329343}, doi = {10.1177/00220345251329343}, pmid = {40254787}, issn = {1544-0591}, abstract = {The difficulty of establishing a relationship between archaea and oral diseases such as dental caries stems from the challenges of detecting, identifying, and isolating these microorganisms. This study aimed to detect archaea in publicly available datasets comprising caries and caries-free saliva and dental plaque by using a tailored bioinformatic pipeline for shotgun sequencing analysis. A systematic search was performed to identify studies using shotgun metagenomics or metatranscriptomics on samples obtained from individuals with dental caries. Two reviewers selected studies based on eligibility criteria. Sequencing and metadata from each study were retrieved from the SRA Bioproject. A count table was generated for each database by mapping reads against an archaea genome database, specifically tailored for this study, using stringent filtering parameters of greater than 97% similarity and 90% query coverage. Archaeal prevalence was determined using an arbitrary cutoff point (>500 reads). An effect size meta-analysis was performed to determine the overall prevalence. Phyloseq and DESeq2 packages were used to determine alpha and beta diversities, differential abundance in different taxonomic levels, and differential expression comparing caries and caries-free samples. Spearman correlation was performed with the bacteriome. The search yielded 154 titles, from which a collection of 7 datasets from 8 studies was obtained. Of 397 samples, N = 63 were positive for archaea using postfiltering, comprising a putative prevalence of 20% (confidence interval = 0%-40%) and identifying Euryarchaeota, Thermoplasmatota, and Nitrosphaeria. Methanogens were present in both the caries and caries-free groups (Methanobrevibacter spp., Methanosarcina, and Methanosphaera) and positively correlated with Stenotrophomonas, Streptococcus, Actinomyces, Abiotrophia, Gemella, and Corynebacterium. Several methanogenesis genes, including methyl-coenzyme M reductase, which catalyzes the final step of methane production in methanogens, were underexpressed in caries-active samples compared with caries-free samples. Saliva and dental plaque emerged as sites of low-abundance archaea, with methanogenesis genes underexpressed in caries-active samples.}, } @article {pmid40254701, year = {2025}, author = {Zaharuddin, AM and Muslim, A and Aazmi, S and Idorus, MY and Almabhouh, FA and Lim, SY and Loganathan, AL and Ayub, Q and Chong, CW and Khalil, KA and Ghani, NA and Lim, SM and Ramasamy, K}, title = {Probiotic Lactobacillus rhamnosus GG Alleviates Prehypertension and Restores Gut Health and Microbiota in NaCl-Induced Prehypertensive Rats.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {40254701}, issn = {1867-1314}, abstract = {Probiotics could be used as adjuvant treatments in prehypertension management to restore gut microbiota dysbiosis caused by a high-salt diet. This study investigated the antihypertensive effects of the probiotic Lactobacillus rhamnosus strain GG (LGG) on high-salt diet-induced prehypertensive rats. Eighteen Sprague-Dawley rats were assigned equally into three groups: normotensive fed on a normal diet (ND), prehypertensive induced on a 4% NaCl high-salt diet (HSD), and prehypertensive induced on an HSD treated with LGG at 1 × 10[9] CFU daily for 8 weeks (LGG). Weekly changes in water, food, body weight, diastolic blood pressure (DBP), systolic blood pressure (SBP), and mean arterial pressure (MAP) were monitored. Serum levels of Na, K, Cl, ALB, Ca, and TP were measured at the end of treatment, along with morphological and histomorphometric changes in the small intestine. Stool samples collected before (W0) and 8 weeks after treatment (W8) were sequenced for bacterial 16S rDNA metagenomics. Probiotic LGG significantly reduces average DBP, SBP, and MAP while improving gut integrity through intact intestine morphology, higher villus heights, and a V/C ratio. At the genus level, the LGG group's gut microbiota composition is more similar to the HSD profile at W0 but shifts to the ND profile after treatment at W8. Thus, probiotic LGG lowers blood pressure indices, improves serum biochemistry profile, restores small intestinal integrity barrier, and modulates gut microbiota profile, indicating its potential as an adjuvant treatment for prehypertension and the significance of gut health in blood pressure regulation.}, } @article {pmid40254251, year = {2025}, author = {Chang, FM and Chen, YH and Hsu, PS and Wu, TH and Sung, IH and Wu, MC and Nai, YS}, title = {RNA metagenomics revealed insights into the viromes of honey bees (Apis mellifera) and Varroa mites (Varroa destructor) in Taiwan.}, journal = {Journal of invertebrate pathology}, volume = {}, number = {}, pages = {108341}, doi = {10.1016/j.jip.2025.108341}, pmid = {40254251}, issn = {1096-0805}, abstract = {The honey bee (Apis mellifera) is a vital pollinator for crops. However, they are infested by a worldwide spread ecto-parasite, Varroa mite (Varroa destructor). The Varroa mite is a vector of various western honey bee viruses. In this study, the prevalence of seven honey bee viruses (Deformed wing virus, Lake Sinai virus, Acute bee paralysis virus, Sacbrood virus, Kashmir bee virus, Black queen cell virus, Israeli acute paralysis virus), was screened with the honey bees, which were collected from fourteen apiaries from March 2023 to January 2024, and the Varroa mites, which were collected from two apiaries from July to October 2023 by using RT-PCR. Subsequently, metagenomic analyses were conducted on seven honey bee samples and two Varroa mite samples using next-generation sequencing with poly-A capture and rRNA depletion library construction methods. The results showed that 50% to 85.7% of honey bee viruses in each sample were detected by both methods, with up to three additional viruses identified when combining the two approaches. These findings underscore the importance of integrating both methods for comprehensive virome analysis. According to the virome analysis, 28 honey bee viruses were identified in honey bees and 11 in Varroa mites. Among these, 23 viruses were newly recorded in Taiwanese honey bee populations. Notably, three of the newly recorded viruses, Acute bee paralysis virus, Israeli acute paralysis virus, and Apis mellifera filamentous virus, are known to cause symptoms in honey bees, posing potential risks to their health. Six of these viruses were also detected in Varroa mites, highlighting their role in viral transmission. This study represents the first virome analysis of honey bees and Varroa mites in Taiwan, providing critical insights into honey bee health and establishing a foundation for future health assessment indices and mitigation strategies.}, } @article {pmid40253770, year = {2025}, author = {Zhu, Y and Tian, Q and Huang, Q and Wang, J}, title = {Bile-processed Rhizoma Coptidis alleviates type 2 diabetes mellitus through modulating the gut microbiota and short-chain fatty acid metabolism.}, journal = {International immunopharmacology}, volume = {156}, number = {}, pages = {114645}, doi = {10.1016/j.intimp.2025.114645}, pmid = {40253770}, issn = {1878-1705}, abstract = {BACKGROUND: Bile-Processed Rhizoma Coptidis (BPRC) is a processed products of Rhizoma Coptidis (RC) commonly used to treat type 2 diabetes mellitus (T2DM). However, the synergistic mechanism of its processing remains unknown. Current research indicates that the gut microbiota and its metabolites, such as short-chain fatty acids (SCFAs), are closely associated with the progression of T2DM.

PURPOSE: This study aims to investigate the effects of BPRC on the gut microbiota and its metabolite SCFAs in T2DM rats.

METHODS: T2DM rat model was induced by a high-fat diet (HFD) combined with streptozotocin (STZ), followed by a 4-week treatment with BPRC to observe its therapeutic effects. The impact of BPRC on the gut microbiota was studied through metagenomic sequencing. Quantitative analysis of SCFAs was conducted using GC-MS. Western blot and quantitative real-time PCR (qRT-PCR) were conducted to investigate the potential mechanisms of BPRC.

RESULTS: BPRC significantly improved insulin resistance in T2DM rats, downregulated levels of pancreatic cell apoptosis factors, and upregulated the abundance of Bacteroides uniformis, Bacteroides sp A1C1, Anaerostipes caccae, Alistipes finegoldii and Blautia sp.N6H1-15 in T2DM rats. Additionally, BPRC increased the levels of seven SCFAs in the intestines of T2DM rats. It activated intestinal TGR5, GPR41, GPR43, and GPR109a receptors, collectively upregulating GLP-1 protein expression, and exerted therapeutic effects on T2DM.

CONCLUSION: The results indicate that the synergistic mechanism of BPRC in treating T2DM is associated with modulating the gut microbiota, increasing SCFAs content in the intestines, and regulating intestinal GLP-1 production.}, } @article {pmid40253436, year = {2025}, author = {Huang, J and Zheng, X and Yu, T and Ali, M and Wiese, J and Hu, S and Huang, L and Huang, Y}, title = {Diverse lifestyles and adaptive evolution of uncultured UBA5794 actinobacteria, a sister order of "Candidatus actinomarinales".}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {39}, pmid = {40253436}, issn = {2524-6372}, support = {92351301, 32470005, 42376238, and 32393970//National Natural Science Foundation of China/ ; 91751000//Major Research Plan of the National Natural Science Foundation of China/ ; GML20240002//the PI Project of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; }, abstract = {Uncultured UBA5794 actinobacteria are frequently found in marine and inland water environments by using metagenomic approaches. However, knowledge about these actinobacteria is limited, hindering their isolation and cultivation, and they are always confused with "Candidatus Actinomarinales" based on 16S rRNA gene classification. Here, to conduct genomic characterization of them, we obtained three high-quality UBA5794 metagenome-assembled genomes (MAGs) from a hydrothermal sediment on the Carlsberg Ridge (CR) and retrieved 131 high-quality UBA5794 genomes from public datasets. Phylogenomic analysis confirms UBA5794 as an independent order within the class Acidimicrobiia. Genome-based metabolic predictions reveal that flexible metabolism and diversified energy acquisition, as well as heavy metal(loid) detoxification capacity, are crucial for the ability of UBA5794 to thrive in diverse environments. Moreover, there is separation between sponge-associated and free-living UBA5794 groups in phylogeny and functional potential, which can be attributed to the symbiotic nature of the sponge-associated group and the extensive horizontal gene transfer (HGT) events observed in these bacteria. Ancestral state reconstruction suggests that the UBA5794 clade may have originated from a free-living environment and then some members gradually migrated to the sponge host. Overall, our study sheds light on the ecological adaptation and evolutionary history of the ubiquitous but poorly understood UBA5794 actinobacteria.}, } @article {pmid40253169, year = {2025}, author = {Aryal, A and Nwachukwu, ID and Aryee, ANA}, title = {Examining the impact of crops and foods biofortified with micronutrients on the gut microbiome.}, journal = {Food research international (Ottawa, Ont.)}, volume = {209}, number = {}, pages = {116189}, doi = {10.1016/j.foodres.2025.116189}, pmid = {40253169}, issn = {1873-7145}, mesh = {*Gastrointestinal Microbiome/physiology ; *Micronutrients ; Humans ; *Crops, Agricultural ; *Biofortification ; *Food, Fortified ; Animals ; }, abstract = {Micronutrient deficiencies (MNDs) impact more than three billion individuals worldwide, particularly those in impoverished and marginalized communities, leading to adverse long-term health consequences. Biofortification, which focusses on enhancing the nutrient density of food crops, presents a promising strategy to address this challenge. Recent studies involving both model organisms and human subjects have demonstrated that, beyond remedying common dietary insufficiencies, micronutrients can modulate the composition and functionality of the gut microbiome. The microbiota, in turn, utilize these micronutrients, facilitating digestion, synthesizing essential nutrients, and modulating immune responses, thereby establishing a bidirectional relationship known as the micronutrient-microbiome axis. Numerous studies have also documented significant variations in these interactions, highlighting the complex dynamics of the micronutrient-microbiome relationship. The composition and interactions of the microbiota have been investigated using various methodologies, including 16S rRNA gene sequencing, RT-PCR, metagenomics, and metabolomics. This review explores recent advancements in understanding the reciprocal relationship between micronutrient levels and the gut microbiome, emphasizing key findings that provide critical insights for the development of targeted dietary strategies aimed at alleviating MNDs and improving overall health.}, } @article {pmid40252922, year = {2025}, author = {Charya, AV and Jang, MK and Kong, H and Park, W and Tian, X and Keller, M and Phipps, K and Sanders, A and Shah, P and Mathew, J and Aryal, S and Berry, GJ and Marboe, C and Orens, JB and Nathan, SD and Agbor-Enoh, S}, title = {Donor-derived cell-free DNA is associated with the degree of immunosuppression in lung transplantation.}, journal = {American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ajt.2025.04.011}, pmid = {40252922}, issn = {1600-6143}, abstract = {Donor-derived cell-free DNA is increasingly used in clinical practice to monitor lung transplant patients for acute rejection. However, its association with conventional approaches to monitor immunosuppression remains unclear. This multicenter observational cohort study examines the association of donor-derived cell free DNA with surrogate measures of immunosuppression. Serial plasma samples were collected for quantification of donor-derived cell-free DNA and anellovirus abundance via shotgun and metagenomic sequencing. Adjudication committees reviewed clinical data to define acute cellular and antibody-mediated rejection. The association between ddcfDNA, anellovirus abundance, and serum tacrolimus trough concentrations over the study period and during episodes of acute rejection were examined via linear mixed effects modeling. Donor-derived cell-free DNA demonstrated a significant inverse association with tacrolimus troughs (p=0.027) and anellovirus abundance (p<0.001) over time. Acute rejection episodes were associated with significantly decreased anellovirus abundance (median, 0.042 vs. 0.708, p<0.001) and higher ddcfDNA levels (1.49% vs. 0.26%, p<0.001) compared to stable control timepoints. However, tacrolimus levels were similar between acute rejection and controls (10.1 ng/ml vs 10.3 ng/ml, p = 0.13). Our findings suggest donor-derived cell-free DNA correlates with measures of immunosuppression in lung transplant patients. Additional studies are needed to assess the utility of donor-derived cell-free DNA to assess immunosuppression adequacy.}, } @article {pmid40252793, year = {2025}, author = {Yang, R and Guo, S and Huo, L and Yang, G and Tian, S}, title = {Impact of Watershed-Scale Land Restoration on Soil Microbial Communities and Their Functions: Insights from Metagenomic Analysis.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121609}, doi = {10.1016/j.envres.2025.121609}, pmid = {40252793}, issn = {1096-0953}, abstract = {Land restoration in the gully regions of China's Loess Plateau has significantly altered soil conditions and farming practices, yet its impact on soil microbes remains unclear. This study applied metagenomic sequencing and correlation analysis to examine microbial community shifts and key genes involved in carbon, nitrogen, and phosphorus cycling. Results show increased biodiversity and microbial activity, especially downstream, enhancing carbon metabolism and ecosystem resilience. Phosphorus activation improved, with related gene abundance rising by 27.45%-52.57%, facilitating phosphorus availability. Nitrogen cycling showed enhanced nitrification and nitrogen fixation, with reduced denitrification, promoting nitrogen retention. Soil organic carbon, total nitrogen, ammonium nitrogen, and available phosphorus (AP), particularly AP, strongly influenced microbial dynamics. These findings highlight the positive role of land restoration in improving soil health and nutrient cycling, supporting sustainable agriculture.}, } @article {pmid40252750, year = {2025}, author = {Yang, M and Peng, L and Mu, M and Yang, F and Li, Z and Han, B and Zhang, K}, title = {Significant effects of earthworm species on antibiotic resistome in livestock manure as revealed by metagenomic analysis.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {126277}, doi = {10.1016/j.envpol.2025.126277}, pmid = {40252750}, issn = {1873-6424}, abstract = {Animal-derived antibiotic resistance genes (ARGs) have emerged as a critical threat, while vermicomposting has been recognized as an effective strategy for reducing ARGs. However, the efficacy of different earthworm species in reducing ARGs remains poorly understood. In this study, 72 vermicompost and earthworm gut samples were collected from various earthworm farms to evaluate the impact of vermicomposting with different earthworm species on ARGs via metagenomic analysis. Approximately 28 ARG types were detected in gut and vermicompost samples. There were significant differences in ARGs among the four species of earthworm composting systems (p < 0.05), and each species possessed its dominant ARGs and microbes. Proteobacteria represented the predominant bacterial phylum within the gut microbiota of Pheretima guillelmi (46.89%) and Eisenia fetida (48.42%), whereas Euryarchaeota (36.71%) and Actinobacteria (39.42%) were the most abundant in Perionyx excavatus and Eudrilus eugeniae, respectively. The overall abundance of ARGs in vermicompost processed by Eisenia fetida (0.18 copies16S rRNA gene copies) was lower than that observed in other earthworm species (0.23-0.39 copies/16S rRNA gene copies), with gut microbial identified as a key determinant of variations in ARG reduction. These findings provide valuable insights into selecting suitable earthworm species to promote ARG degradation, thus contributing to the decrease in ARG dissemination risks in agricultural ecosystems.}, } @article {pmid40252553, year = {2025}, author = {Bariod, L and Fuentes, E and Millet, M and White, J and Jacquiod, S and Moreau, J and Monceau, K}, title = {Exposure to pesticides is correlated with gut microbiota alterations in a farmland raptor.}, journal = {Environment international}, volume = {199}, number = {}, pages = {109436}, doi = {10.1016/j.envint.2025.109436}, pmid = {40252553}, issn = {1873-6750}, abstract = {The gut microbiota is crucial for host health and can be impacted by various environmental disruptions, yet the effects of multiple pesticide exposures on farmland organisms' microbiomes remain largely unexplored. We assessed microbiota changes in a wild apex predator exposed to multiple pesticides in agricultural landscapes. Pesticides, including acetochlor and quinoxyfen, which are supposed to be banned, were significantly positively correlated with certain key bacteria from Actinobacteria, Alphaproteobacteria and Gammaproteobacteria classes. Our results light up the potential collateral effect of pesticides on gut bacterial assemblages through unknown mechanisms. These effects could result in dysbiosis and the promotion of potential pathogens and/or the selection of bacteria that might allow the organism to detoxify the organism. Although formal metagenomic analyses would be required soon, these microbial shifts underline the broader ecological consequences of pesticide exposure, emphasising the need for integrated biodiversity conservation and ecosystem management to protect environmental and public health.}, } @article {pmid40252419, year = {2025}, author = {Ciuchcinski, K and Kaczorowska, AK and Biernacka, D and Dorawa, S and Kaczorowski, T and Park, Y and Piekarski, K and Stanowski, M and Ishikawa, T and Stokke, R and Steen, IH and Dziewit, L}, title = {Computational pipeline for sustainable enzyme discovery through (re)use of metagenomic data.}, journal = {Journal of environmental management}, volume = {382}, number = {}, pages = {125381}, doi = {10.1016/j.jenvman.2025.125381}, pmid = {40252419}, issn = {1095-8630}, abstract = {Enzymes derived from extremophilic organisms, also known as extremozymes, offer sustainable and efficient solutions for industrial applications. Valued for their resilience and low environmental impact, extremozymes have found use as catalysts in various processes, ranging from dairy production to pharmaceutical manufacturing. However, discovery of novel extremozymes is often hindered by challenges such as culturing difficulties, underrepresentation of extreme environments in reference databases, and limitations of traditional sequence-based screening methods. In this work, we present a computational pipeline designed to discover novel enzymes from metagenomic data derived from extreme environments. This pipeline represents a versatile and sustainable approach that promotes reuse and recycling of existing datasets and minimises the need for additional environmental sampling. In its core, the algorithm integrates both traditional bioinformatic techniques and recent advances in structural prediction, enabling rapid and accurate identification of enzymes. However, due to its design, the algorithm relies heavily on existing databases, which can limit its effectiveness in situations where reference data is scarce or when encountering novel protein families. As a proof-of-concept, we applied the pipeline to metagenomic data from deep-sea hydrothermal vents, with a focus on β-galactosidases. The pipeline identified 11 potential candidate proteins, out of which 10 showed in vitro activity. One of the selected enzymes, βGal_UW07, showed strong potential for industrial applications. The enzyme exhibited optimal activity at 70 °C and was exceptionally resistant to high pH and the presence of metal ions and reducing agents. Overall, our results indicate that the pipeline is highly accurate and can play a key role in sustainable bioprospecting, leveraging existing metagenomic datasets and minimising in situ interventions in pristine regions.}, } @article {pmid40252413, year = {2025}, author = {Okamura, T and Hasegawa, Y and Ohno, Y and Saijo, Y and Nakanishi, N and Honda, A and Hamaguchi, M and Takano, H and Fukui, M}, title = {Oral exposure to nanoplastics and food allergy in mice fed a normal or high-fat diet.}, journal = {Chemosphere}, volume = {379}, number = {}, pages = {144401}, doi = {10.1016/j.chemosphere.2025.144401}, pmid = {40252413}, issn = {1879-1298}, abstract = {The global prevalence of food allergies, particularly IgE-mediated responses, is increasing at an alarming rate. This trend is likely driven by environmental factors such as nanoplastics (NPs) ingestion and the westernization of dietary and lifestyle habits. This study examines the impact of polystyrene nanoplastics (PS-NPs) on ovalbumin (OVA)-induced food allergies in mice subjected to either a normal diet (ND) or a high-fat diet (HFD). BALB/c mice were stratified into eight groups based on dietary regimen, NP exposure, and OVA sensitization. Food allergy was induced via OVA administration, and multiple physiological and immunological parameters were evaluated, including body weight, intestinal permeability, cytokine profiles, gut microbiota composition, and small intestinal gene expression. Mice in the HFD + OVA + NP group exhibited significant increases in intestinal permeability, diarrhea severity, and serum OVA-specific IgE levels compared to other groups. Flow cytometric analysis revealed an expansion of innate lymphoid cells (ILC2 and ILC1) within the lamina propria of the small intestine. Shotgun metagenomic sequencing demonstrated gut microbiota dysbiosis, characterized by a reduction in beneficial bacterial populations in the HFD + OVA + NP cohort. Weighted Gene Co-Expression Network Analysis (WGCNA) identified a negative correlation between NPs exposure or OVA sensitization and the expression of Slc1a1, Slc5a8, and Mep1a, while a positive correlation was observed with Aa467197 expression. These findings indicate that oral exposure to PS-NPs exacerbates OVA-induced food allergies, particularly in the context of an HFD, through mechanisms involving increased intestinal permeability, gut microbial dysbiosis, and gene expression modulation. This study highlights the potential health hazards posed by environmental microplastic contamination and its possible contribution to the escalating incidence of food allergies.}, } @article {pmid40252307, year = {2025}, author = {Qian, L and Jiang, J and Zhang, Y and Huang, X and Che, Z and Chen, G and Liu, S}, title = {Sublethal exposure to boscalid induced respiratory abnormalities and gut microbiota dysbiosis in adult zebrafish.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {283}, number = {}, pages = {107370}, doi = {10.1016/j.aquatox.2025.107370}, pmid = {40252307}, issn = {1879-1514}, abstract = {Boscalid (BO), one of the frequently detected fungicides of succinate dehydrogenase inhibitor in water environments, has unknown effects on the respiratory function and gut health of aquatic organisms. Therefore, zebrafish were exposed to BO solutions (0.01-1.0 mg/L) for 21 days to assess its effects on zebrafish respiration and intestinal microbiota in this study. The results showed that exposure to 0.1 and 1.0 mg/L BO for 21 days resulted in zebrafish exhibiting aggregation of gill filaments, reduction of mucous cells, and significantly decreased opercular movement, linked to a marked decline in the activity of respiratory chain complex II. 16S rRNA gene sequencing revealed significant changes in the intestinal microbiota composition of zebrafish exposed to 1.0 mg/L BO. Specifically, the relative abundance of beneficial bacteria (Cetobacterium) was markedly reduced, while pathogenic bacteria (such as Ralstonia, Legionella, Acinetobacter, Escherichia/Shigella) associated with energy metabolism and immune pathways in zebrafish showed a significant increase in relative abundance. Accordingly, metagenomic functional prediction analysis further revealed the potential impact of BO-induced gut microbiota changes on energy metabolism and immune pathways in zebrafish. Furthermore, histopathological analysis of intestinal tissues revealed that exposure to BO resulted in necrosis and shedding of epithelial cells, as well as a decrease in goblet cell count, which exacerbated adverse effects on intestinal health. In conclusion, sublethal exposure to BO affects the respiratory function and intestinal health of zebrafish. Therefore, the impact of BO in aquatic environments on fish health warrants attention.}, } @article {pmid40252261, year = {2025}, author = {Li, B and Liang, C and Xu, B and Song, P and Liu, D and Zhang, J and Gu, H and Jiang, F and Gao, H and Cai, Z and Zhang, T}, title = {Extreme winter environment dominates gut microbiota and metabolome of white-lipped deer.}, journal = {Microbiological research}, volume = {297}, number = {}, pages = {128182}, doi = {10.1016/j.micres.2025.128182}, pmid = {40252261}, issn = {1618-0623}, abstract = {Qinghai-Tibet Plateau (QTP) is marked by harsh environments that drive the evolution of unique nutrient metabolism mechanism in indigenous animal gut microbiotas. Yet, responses of these microbiotas to different extreme environments remain poorly understood. White-lipped deer (Przewalskium albirostris), a native endangered species in the QTP, serves as an ideal model to study how gut microbiotas adapt to season and human disturbances. Here, a multi-omics integrated analysis of 16S rRNA, metagenomics, and untargeted metabolomics was performed to investigate the composition, function, and metabolic characteristics of gut microbiota in White-lipped deer across different seasons and living environments. Our results revealed that extreme winter environment dominated the composition, function, and metabolism of gut microbiota in white-lipped deer. The white-lipped deer exhibited an enriched gut microbiota associated with producing short-chain fatty acids in winter, with core feature genera including norank_o_Rhodospirillales, Rikenellaceae_RC9_gut_group, and unclassified_c_Clostridia. However, potential pathogenic bacteria and few short-chain fatty acid producers, with core feature genera including norank_f_p-2534-18B5_gut_group, Cellulosilyticum, and Paeniclostridium, showed enrichment in captivity. Pathways associated with carbohydrate metabolism, amino acid metabolism, and immune regulation showed enrichment in winter group as an adaptation to the cold and food scarcity. Among these, Rikenellaceae_RC9_gut_group and unclassified_c_Clostridia contributed significantly to these metabolic pathways. The gut microbiota of white-lipped deer exhibited enrichment in pathways related to intestinal inflammation and enhanced immune regulation to alleviate the stress of captivity. Among these, norank_f_p-2534-18B5_gut_group contributed the most to these pathways. Butyric, valeric, and valproic acids were significantly more abundant in the winter group, while 3-hydroxybutyric and (S)-beta-aminoisobutyric acids were higher in the captive group. Furthermore, enriched metabolites and associated pathways in both groups further supported the inferences on metagenomic functions. This study confirms the key role of specific gut microbiota in adapting to high-altitude winters and anthropogenic disturbances, emphasizing its importance for environmental resilience in wild, high-altitude mammals.}, } @article {pmid40251489, year = {2025}, author = {Bini, F and Soffritti, I and D'Accolti, M and Mazziga, E and Caballero, JD and David, S and Argimon, S and Aanensen, DM and Volta, A and Bisi, M and Mazzacane, S and Caselli, E}, title = {Profiling the resistome and virulome of Bacillus strains used for probiotic-based sanitation: a multicenter WGS analysis.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {382}, pmid = {40251489}, issn = {1471-2164}, support = {INV-004891/GATES/Gates Foundation/United States ; }, mesh = {*Bacillus/genetics/isolation & purification/drug effects/classification/pathogenicity ; *Probiotics ; *Whole Genome Sequencing ; *Genome, Bacterial ; Polymorphism, Single Nucleotide ; *Sanitation ; Humans ; *Drug Resistance, Bacterial/genetics ; }, abstract = {BACKGROUND: Healthcare-associated infections (HAIs) caused by microbes that acquire antimicrobial resistance (AMR) represent an increasing threat to human health worldwide. The high use of chemical disinfectants aimed at reducing the presence of pathogens in the hospital environment can simultaneously favor the selection of resistant strains, potentially worsening AMR concerns. In the search for sustainable ways to control bioburden without affecting this aspect, probiotic-based sanitation (PBS) using Bacillus spp. was proposed to achieve stable reduction of pathogens, AMR, and associated HAIs. Although Bacillus probiotics are classified as nonpathogenic, comprehensive data about the potential genetic alterations of these probiotics following prolonged contact with surrounding pathogens are not yet available. This study aimed to assess in depth the genetic content of PBS-Bacillus isolates to evaluate any eventual variations that occurred during their usage.

RESULTS: WGS analysis was used for the precise identification of PBS-Bacillus species and detailed profiling of their SNPs, resistome, virulome, and mobilome. Analyses were conducted on both the original PBS detergent and 172 environmental isolates from eight hospitals sanitized with PBS over a 30-month period. The two species B. subtilis and B. velezensis were identified in both the original product and the hospital environment, and SNP analysis revealed the presence of two clusters in each species. No virulence/resistance genes or mobile conjugative plasmids were detected in either the original PBS-Bacillus strain or any of the analyzed environmental isolates, confirming their high genetic stability and their low/no tendency to be involved in horizontal gene transfer events.

CONCLUSIONS: The data obtained by metagenomic analysis revealed the absence of genetic sequences associated with PBS-Bacillus and the lack of alterations in all the environmental isolates analyzed, despite their continuous contact with surrounding pathogens. These results support the safety of the Bacillus species analyzed. Further metagenomic studies aimed at profiling the whole genomes of these and other species of Bacillus, possibly during longer periods and under stress conditions, would be of interest since they may provide further confirmation of their stability and safety.}, } @article {pmid40251030, year = {2025}, author = {Chen, J and Zhang, S and Wang, M and Kang, G and Lu, L and Chang, N and Wang, N and Xie, Z and Liu, Y and Zhang, H and Shen, W}, title = {Investigating the Impact of Landfill Age and Season on the Occurrence and Dissemination of Antibiotic Resistance Genes in Leachate and the Underlying Mechanisms Using Metagenomics.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxaf091}, pmid = {40251030}, issn = {1365-2672}, abstract = {AIMS: Antibiotic resistance genes (ARGs) pose a critical public health concern, with landfill leachate serving as a significant environmental reservoir. While ARG dynamics in leachate have been investigated in various contexts, their occurrence and influence factors in semi-arid regions remain poorly understood. This study investigated the occurrence and influence factors of ARG profiles, their potential hosts, and underlying mechanisms driving their proliferation.

METHODS AND RESULTS: Comprehensive metagenomic analysis of leachate samples collected from landfills of varying landfill ages (5, 10, and 20 years) in Hohhot, Inner Mongolia-a representative semi-arid region of northern China-across three seasons (autumn, spring, and summer). Metagenomic analysis revealed distinct patterns in core ARG abundances modulated by both landfill age and seasonal variations. Notably, landfill age predominantly influenced tetracycline- and glycopeptide- ARGs, while seasonal fluctuations primarily affected glycopeptide- and multidrug- ARGs. Taxonomic analysis identified Pseudomonas aeruginosa and Pseudomonas fluorescens as the predominant resistant pathogens, with elevated prevalence during spring and winter compared to summer. Network analysis and metabolic pathway reconstruction demonstrated that landfill age maybe impacted ARG dissemination through modulation of carbohydrate and nitrogen metabolic pathways. This novel finding suggests a previously unrecognized mechanism linking waste decomposition stages to ARG proliferation.

CONCLUSIONS: Our study provides the first systematic characterization of ARG dynamics in semi-arid landfill leachate, offering crucial insights for developing targeted strategies to mitigate ARG dissemination in these distinct ecological contexts. These findings establish a theoretical framework for understanding ARG transmission in semi-arid environments while providing empirical evidence to inform environmental management practices.}, } @article {pmid40251011, year = {2025}, author = {Dawson, SJT and Shibu, P and Garnett, S and Newberry, F and Brook, TC and Tijani, T and Kujawska, M and Hall, LJ and McCartney, AL and Negus, D and Hoyles, L}, title = {Weberviruses are gut-associated phages that infect Klebsiella spp.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaf043}, pmid = {40251011}, issn = {1574-6941}, abstract = {Weberviruses are bacteriophages (phages) that can infect and lyse clinically relevant, multidrug-resistant (MDR) strains of Klebsiella. They are an attractive therapeutic option to tackle Klebsiella infections due to their high burst sizes, long shelf life and associated depolymerases. In this study we isolated and characterized seven new lytic phages and compared their genomes with those of their closest relatives. Gene-sharing network, ViPTree proteome and terL gene-sequence-based analyses incorporating all publicly available webervirus genomes [n=258 from isolates, n=65 from metagenome-assembled genome (MAG) datasets] confirmed the seven phages as members of the genus Webervirus and identified a novel genus (Defiantjazzvirus) within the family Drexlerviridae. Using our curated database of 265 isolated phage genomes and 65 MAGs (n=330 total), we found that weberviruses are distributed globally and primarily associated with samples originating from the gut: sewage (154/330, 47%), wastewater (83/330, 25%) and human faeces (66/330, 20%). We identified three distinct clusters of potential depolymerases encoded within the 330 genomes. Due to their global distribution, frequency of isolation and lytic activity against the MDR clinical Klebsiella strains used in this study, we conclude that weberviruses and their depolymerases show promise for development as therapeutic agents against Klebsiella spp.}, } @article {pmid40250773, year = {2025}, author = {Wu, X and Li, Y and Li, P and Lu, G and Wu, J and Wang, Z and Wen, Q and Cui, B and Wang, J and Zhang, F}, title = {Structural variations in ulcerative colitis-associated E. coli reduce fructose utilization and aggravate inflammation under high fructose diet.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2025.03.039}, pmid = {40250773}, issn = {1528-0012}, abstract = {BACKGROUND AND AIMS: Structural variations (SVs) have significant effects on the microbial phenotypes. The underlying mechanism of functional changes caused by gut microbial SVs in the development of ulcerative colitis (UC) need further investigation.

METHODS: We performed long-read (ONT-based) and short-read (Illumina-based) metagenomic sequencing on stool samples from 93 UC patients and 100 healthy controls (HCs), and analyzed microbial SVs. A total of 648 Escherichia coli (E. coli) strains from fecal samples of UC patients (UC-strains) and HCs (HC-strains) were isolated. SV-associated scrK gene deletion was verified via whole-genome sequencing or targeted PCR. Then, representative UC-strains, HC-strains, and scrK-knockout E. coli were used for the in vitro and in vivo experiments to investigate the effects of specific SV in E. coli on fructose utilization ability and colitis.

RESULTS: E. coli in UC with the highest fold change had SVs-affected functional differences on fructose metabolism to that of HCs. The fructose utilization genes deletion was common in UC-strains, ostensibly reducing fructose utilization in vitro and leading to fructose-dependent aggravation of colitis in murine models. UC-strains and HC-strains induced comparable colitis under low fructose. However, high fructose exacerbated colitis severity exclusively in UC-strain-colonized mice, with elevated intestinal fructose residues, significant microbiome/metabolome changes, increased inflammation, and gut barrier disruption. These changes were mechanistically depended on the deletion of fructose utilization gene scrK.

CONCLUSIONS: SV-caused difference in fructose utilization and proinflammatory properties in E. coli from UC patients influence the development of UC, emphasizing the importance of fine-scale metagenomic studies in disease.}, } @article {pmid40250459, year = {2025}, author = {Munroe, ES and Spicer, A and Castellvi-Font, A and Zalucky, A and Dianti, J and Graham Linck, E and Talisa, V and Urner, M and Angus, DC and Baedorf-Kassis, E and Blette, B and Bos, LD and Buell, KG and Casey, JD and Calfee, CS and Del Sorbo, L and Estenssoro, E and Ferguson, ND and Giblon, R and Granholm, A and Harhay, MO and Heath, A and Hodgson, C and Houle, T and Jiang, C and Kramer, L and Lawler, PR and Leligdowicz, A and Li, F and Liu, K and Maiga, A and Maslove, D and McArthur, C and McAuley, DF and Serpa Neto, A and Oosthuysen, C and Perner, A and Prescott, HC and Rochwerg, B and Sahetya, S and Samoilenko, M and Schnitzer, ME and Seitz, KP and Shah, F and Shankar-Hari, M and Sinha, P and Slutsky, AS and Qian, ET and Webb, SA and Young, PJ and Zampieri, FG and Zarychanski, R and Fan, E and Semler, MW and Churpek, M and Goligher, EC and , and , }, title = {Evidence-based personalised medicine in critical care: a framework for quantifying and applying individualised treatment effects in patients who are critically ill.}, journal = {The Lancet. Respiratory medicine}, volume = {}, number = {}, pages = {}, doi = {10.1016/S2213-2600(25)00054-2}, pmid = {40250459}, issn = {2213-2619}, abstract = {Clinicians aim to provide treatments that will result in the best outcome for each patient. Ideally, treatment decisions are based on evidence from randomised clinical trials. Randomised trials conventionally report an aggregated difference in outcomes between patients in each group, known as an average treatment effect. However, the actual effect of treatment on outcomes (treatment response) can vary considerably between individuals, and can differ substantially from the average treatment effect. This variation in response to treatment between patients-heterogeneity of treatment effect-is particularly important in critical care because common critical care syndromes (eg, sepsis and acute respiratory distress syndrome) are clinically and biologically heterogeneous. Statistical approaches have been developed to analyse heterogeneity of treatment effect and predict individualised treatment effects for each patient. In this Review, we outline a framework for deriving and validating individualised treatment effects and identify challenges to applying individualised treatment effect estimates to inform treatment decisions in clinical care.}, } @article {pmid40250281, year = {2025}, author = {Chen, Y and Hu, S and Hu, B and Li, Y and Chen, Z}, title = {Functional insights into microbial community dynamics and resilience in mycorrhizal associated constructed wetlands under pesticide stress.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138315}, doi = {10.1016/j.jhazmat.2025.138315}, pmid = {40250281}, issn = {1873-3336}, abstract = {Arbuscular mycorrhizal fungi (AMF) are critical mutualistic symbionts in most terrestrial ecosystems, where they facilitate nutrient acquisition, enhance plant resilience to environmental stressors, and shape the surrounding microbiome. However, its contributions (especially for microorganisms) to constructed wetlands (CWs) under pesticide stress remain poorly understood. This study investigated the effects of AMF on microbial community composition, diversity, metabolic pathways, and functional genes by metagenomics in CWs exposed to pesticides stress. Using comparative analyses of AMF-colonized and non-colonized CWs, we found that AMF enhanced overall microbial diversity, as evidenced by increases of 2.22 % (Chao1) and 2.83 % (observed species). Under fungicide stress, nitrogen-cycling microorganisms (e.g., Nitrososphaerota and Mucoromycota) increased in relative abundance, while carbon cycle-related microorganisms (e.g., Pseudomonadota and Bacteroidota) generally declined. AMF colonization improved microbial resilience, demonstrated by a 312 % rise in Rhizophagus abundance and significant increases in phosphorus-cycling microorganisms (e.g., Bradyrhizobium and Mesorhizobium). Functional gene analysis further revealed that AMF helped mitigate fungicide-induced reductions in genes related to nitrogen and carbon cycling, lowering the average decline rates to 4.02 % and 1.44 %, respectively, compared to higher rates in non-AMF treatments. In summary, these findings highlight the crucial role of AMF in enhancing pesticide stress resilience, maintaining microbial community stability, and improving the bioremediation capacity of CWs.}, } @article {pmid40250270, year = {2025}, author = {Yang, C and Xu, Y and Yu, T and Li, Y and Zeng, XC}, title = {Microbial reductive mobilization of As(V) in solid phase coupled with the oxidation of sulfur compounds: An overlooked biogeochemical reaction affecting the formation of arsenic-contaminated groundwater.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138234}, doi = {10.1016/j.jhazmat.2025.138234}, pmid = {40250270}, issn = {1873-3336}, abstract = {Dissimilatory As(V)-respiring prokaryotes (DARPs) are recognized as having a crucial role in the formation of arsenic-contaminated groundwater. DARPs use small-molecule organic acids as electron donor to directly reduce As(V) in solid phase to more mobile As(III). Therefore, DARPs are considered to be heterotrophic bacteria. However, these cannot explain why high concentrations of As(III) are produced in environments lacking soluble organic carbon. We thus propose that reduced sulfur compounds may also be utilized by DARPs and affect the DARPs-mediated arsenic mobilization. This study sought to confirm this hypothesis. Metagenomic investigations on the DARP population derived from As-contaminated soil indicated that approximately 84 % of DARP MAGs possess the enzymes potentially catalyzing the oxidation of S[2-], S[0], SO3[2-], or S2O3[2-]. Functional analysis of DARP population and a cultivable strain suggested that DARPs, in addition to small-molecule organic carbon, can effectively use sulfur compounds as electron donor to reduce As(V) to mobile As(III). Arsenic release experiments using DARP population and a cultivable DARP strain showed that DARPs indeed utilized sulfur compounds as the sole electron donors under autotrophic and anaerobic conditions to directly reduce adsorbed As(V) in the soils to mobile As(III). These findings provide new insights into the microbial mechanism responsible for the variation of As(III) concentrations in contaminated groundwater.}, } @article {pmid40250268, year = {2025}, author = {Yang, JH and Huang, DQ and Wu, GG and Han, NN and Fan, NS and Jin, RC}, title = {Quorum sensing-mediated microecological homeostasis in anammox consortia.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138285}, doi = {10.1016/j.jhazmat.2025.138285}, pmid = {40250268}, issn = {1873-3336}, abstract = {Quorum sensing (QS) mediated by signal molecules regulates bacterial communication and further affects the performance and microbial physiological characteristics of anaerobic ammonium oxidation (anammox) process. The potential application of low concentrations of typical exogenous signal molecules into maintaining the long-term homeostasis of anammox consortia were evaluated in this study. The results of 150-d continuous-flow experiment showed that 30 μg L[-1]N-hexanoyl-homoserine lactone (C6-HSL) and diffusible signaling factor (DSF) could maintain the stable nitrogen removal efficiency of anammox systems (90.3 ± 3.6 % and 90.2 ± 3.8 %). C6-HSL and DSF also significantly promoted the anammox activity and the production of extracellular polymeric substances (EPS). Microbial community analysis indicated that the relative abundance of Candidatus Kuenenia fluctuated and finally maintained at 27.0 % and 39.3 %, which was still significantly higher than that of initial phase. Meanwhile, the abundances of functional genes related to anammox process (hzsA, hdh and nirS) increased significantly. Metagenomic analysis revealed that the abundances of main functional genes involved in nitrogen metabolism, amino acid metabolism and QS were significantly upregulated. The interspecies interactions were also enhanced through QS-mediated intercellular communication, which was beneficial to microecological homeostasis in anammox systems. In contrast, DSF exhibited the more significant and longer-lasting promotion impact, while the effect of C6-HSL was rapid. These findings reveal the potential regulatory mechanism of exogenous signaling molecules on anammox consortia and drive the potential application of signaling molecules in the anammox process to treat real wastewater.}, } @article {pmid40250228, year = {2025}, author = {Wang, H and Yang, Q and Wang, S}, title = {Metagenomic insights into the impact of tillage practices on soil nutrient cycling and wheat yield.}, journal = {The Science of the total environment}, volume = {978}, number = {}, pages = {179427}, doi = {10.1016/j.scitotenv.2025.179427}, pmid = {40250228}, issn = {1879-1026}, abstract = {Decreasing tillage intensity (DT) are beneficial for soil health and crop yield; however, the relationship between microbial nutrient cycling function and crop yield remains poorly understood.The objective of this study was to investigate the impact of tillage practices of conventional tillage with rotary tillage (RT) and decreasing tillage intensity (DT) on the soil microbial community and the functions of carbon, nitrogen, and phosphorus cycles of wheat and examine the relationship between soil microbes and yield based on a four year field experiment. An increased maize yield of 9.3 % and 8.5 % in DT compared with that in RT in 2023 and 2024, respectively. Further analysis reveals that DT influences the availability of soil carbon, nitrogen, and phosphorus by altering microbial communities and their functions. Microbial function analysis indicates that DT leads to higher abundances of genes associated with glgP (starch degradation) and xynB (hemicellulose degradation), which play a crucial role in elevating POC levels (11.6 %-23.4 %). Additionally, DT shows increased abundances of genes related to organic nitrogen metabolism (glnA), nitrification (amoB), and nitrogen fixation (nifK), contributing to the rise in NO3[-]- N content (19.1 %-31.1 %). Furthermore, DT exhibits a high abundance of the organic phosphorus mineralization gene phnM, resulting in enhanced AP content (4.7 %-25.4 %). Moreover, among the microbial genera significantly influenced by DT, ten genera-Lysobacter, Luteimonas, Bradyrhizobium, Aromatoleum, Acidibacter, Variovorax, Polaromonas, Pseudorhodoplanes, Piscinibacter, and Ramlibacter-show increased abundance, positively impacting wheat yield. Our study offers a novel framework for comprehending the enhancement of wheat yield through the lens of microbial nutrient cycling functionality and mining of beneficial bacteria for wheat yield.}, } @article {pmid40250042, year = {2025}, author = {Menichini, D and Seta, F and Mastrolia, SA and Cetin, I and Carafa, A and Santagni, S and Foschi, C and Cerboneschi, M and Smeazzetto, S and Neri, I and Facchinetti, F}, title = {Probiotics in pregnancy and group B streptococcus colonization: A multicentric, randomized, placebo-controlled, double-blind study with a focus on vaginal microbioma.}, journal = {European journal of obstetrics, gynecology, and reproductive biology}, volume = {310}, number = {}, pages = {113976}, doi = {10.1016/j.ejogrb.2025.113976}, pmid = {40250042}, issn = {1872-7654}, abstract = {OBJECTIVE: To evaluate the feasibility and effects of the use of probiotics in pregnancy, starting in the third trimester, on rectovaginal colonization of group B streptococcus (GBS) in women at low obstetric risk.

METHODS: A multicentre, randomized, placebo-controlled, double-blind, parallel-group study was conducted in three tertiary hospitals in northern Italy and included low-risk pregnant women. The intervention consisted of oral administration of two capsules of probiotics or placebo from 30 weeks of pregnancy until 37 weeks of pregnancy. The primary outcome was GBS colonization, evaluated with rectovaginal swabs. In a subgroup, selected at random, changes in the vaginal microbiome after treatment administration were evaluated using 16S Metagenomic Sequencing Library Preparation sequencing and analysis.

RESULTS: In total, 267 pregnant women were randomized to receive probiotics (n = 133) or placebo (n = 134). The two groups were similar at baseline. After treatment, no differences were found in the rates of positive rectovaginal swabs (p = 0.24) and antibiotic administration (p = 0.27). Only one case of postpartum fever (>38 °C) was found in the placebo group. Labour and delivery outcomes and neonatal outcomes were similar in both groups. Analysis of the vaginal microbiota showed that the relative abundance of Lactobacillus spp. was not modified significantly by the probiotics, but the relative abundance of Gardnerella spp. decreased significantly (3.6 ± 7.9 vs 5.5 ± 10.2; p = 0.03). Interestingly, the relative abundance of Lactobacillus spp. reduced significantly in women who subsequently presented with partial rupture of membranes (46.9 ± 43.6 vs 77.7 ± 24.9; p = 0.02).

CONCLUSION: Although the clinical outcomes were unaffected, administration of probiotics led to favourable changes in vaginal microbiota. It remains to be established how this effect could be translated into clinical advantage.}, } @article {pmid40249976, year = {2025}, author = {Zhang, WG and Liang, S and Liao, Y and Ran, G and Ji, S and Gao, Y and Lei, Z}, title = {Insights into the impact of different phytoremediation strategies on antibiotic resistance genes at the metagenomic level in real scenarios.}, journal = {Ecotoxicology and environmental safety}, volume = {296}, number = {}, pages = {118211}, doi = {10.1016/j.ecoenv.2025.118211}, pmid = {40249976}, issn = {1090-2414}, abstract = {Engineered phytoremediation strategies provide cost effective options for eliminating antibiotics and antibiotic resistance genes (ARGs) from wastewater. However, there is a knowledge gap in understanding the impact of these phytoremediation strategies on the on the diversity and composition of ARGs as well as the key driving biotic and biological factors of ARGs at the metagenomic level in real scenarios. Through metagenomic sequencing, this study demonstrates that phytoremediation with Iris pseudacorus L., Myriophyllum verticillatum L., Eichhornia crassipes (Mart.) Solms and Oenanthe javanica (Bl. DC) significantly alters the pattern of antibiotic resistome. This study is the first to reveal, at the omics level, that phytoremediation enhances the diversity of ARGs (3.2 %∼11.6 % improvement), despite reducing their absolute abundances. Furthermore, this study highlights that plant varieties have a significant impact on the performance of phytoremediation in mitigating ARGs. The non-dominant bacterial taxa, specifically Verrucomicrobia, Planctomycetes, and Actinobacteria, play a crucial role in shaping the pattern of the antibiotic resistome during the wastewater treatment. The changes in the total organic carbon, total nitrogen and antibiotics robustly influence the environmental behaviors of antibiotic resistome and microbiome. In summary, this study gives insight into the impact of different phytoremediation strategies on mitigating ARGs at the omics level in real scenarios.}, } @article {pmid40249811, year = {2025}, author = {Huss, P and Kieft, K and Meger, A and Nishikawa, K and Anantharaman, K and Raman, S}, title = {Engineering bacteriophages through deep mining of metagenomic motifs.}, journal = {Science advances}, volume = {11}, number = {16}, pages = {eadt6432}, doi = {10.1126/sciadv.adt6432}, pmid = {40249811}, issn = {2375-2548}, mesh = {*Metagenomics/methods ; *Bacteriophage T7/genetics ; *Metagenome ; *Bacteriophages/genetics ; *Genetic Engineering ; }, abstract = {Bacteriophages can adapt to new hosts by altering sequence motifs through recombination or convergent evolution. Where these motifs exist and what fitness advantage they confer remains largely unknown. We report a new method, Metagenomic Sequence Informed Functional Scoring (Meta-SIFT), to find sequence motifs in metagenomic datasets to engineer phage activity. Meta-SIFT uses experimental deep mutational scanning data to create sequence profiles to mine metagenomes for functional motifs invisible to other searches. We experimentally tested ~17,000 Meta-SIFT-derived sequence motifs in the receptor binding protein of the T7 phage. The screen revealed thousands of T7 variants with novel host specificity with motifs sourced from distant families. Position, substitution, and location preferences dictated specificity across a panel of 20 hosts and conditions. To demonstrate therapeutic utility, we engineered active T7 variants against foodborne pathogen Escherichia coli O121. Meta-SIFT is a powerful tool to unlock the potential encoded in phage metagenomes to engineer bacteriophages.}, } @article {pmid40249033, year = {2025}, author = {Wei, Q and Chen, L and Yin, Y and Pai, M and Duan, H and Zeng, W and Hu, X and Xu, M and Li, S}, title = {Analysis of Blood Microbiome From People Living With HIV and Donors by 16S rRNA Metagenomic Sequencing.}, journal = {Journal of medical virology}, volume = {97}, number = {4}, pages = {e70341}, doi = {10.1002/jmv.70341}, pmid = {40249033}, issn = {1096-9071}, support = {//This work was supported by the Chinese Society of Blood Transfusion Weigao Research Fund Project (CSBT-MWG-2020-02) and the Chinese Academy of Medical Sciences Medical and Health Science and Technology Innovation Project (CAMS-2021-I2M-1-060)./ ; }, mesh = {Humans ; *RNA, Ribosomal, 16S/genetics ; *HIV Infections/microbiology/blood/drug therapy ; *Microbiota ; Metagenomics ; *Blood Donors ; *Bacteria/genetics/classification/isolation & purification ; Male ; Adult ; Female ; Middle Aged ; Sequence Analysis, DNA ; *Blood/microbiology ; DNA, Bacterial/genetics/chemistry ; DNA, Ribosomal/genetics/chemistry ; }, abstract = {Utilize 16S rRNA sequencing technology to characterize bacterial species susceptible to people living with HIV (PLWH) across different stages. This mapping aims to establish a foundational framework for preventing secondary HIV infections, prolonging patient survival, enhancing quality of life, and advancing the diagnosis, treatment, and research of bacterial co-infections. In this study, we classified the participants into three groups: The blood of donors living with HIV (DI group), AIDS patients who have received ART treatment (PI group), and healthy blood donors as the control group (DH group). Each group was divided into three parallel subgroups, with 30 samples pooled from each parallel group for plasma extraction. As initial processing steps, the nine parallel subgroups were subjected to nucleic acid extraction and PCR amplification targeting the 16SV34 region. The resulting amplified products were subsequently forwarded to a sequencing company. It can be seen from the Venn diagram that the DI groups showed significantly higher bacterial diversity than the PI group and the DH group. The PI group had lower bacterial relative abundance and diversity compared to the DI group, with a community structure more similar to the control group. The DI group is particularly susceptible to several significant pathogens, including Ralstonia, Pseudomonas, Acinetobacter, Methyloversatilis, and Vibrio. The study revealed a greater quantity and diversity of bacteria in the DI blood compared to the PI and DH groups. This observation may be attributed to PI group patients in this study being hospitalized and receiving treatment.}, } @article {pmid40248366, year = {2025}, author = {Lu, X and Lu, Q and Zhu, R and Sun, M and Chen, H and Ge, Z and Jiang, Y and Wang, Z and Zhang, L and Zhang, W and Dai, Z}, title = {Metagenomic analysis reveals the diversity of the vaginal virome and its association with vaginitis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1582553}, pmid = {40248366}, issn = {2235-2988}, mesh = {Female ; Humans ; *Virome/genetics ; *Vagina/virology/microbiology ; *Metagenomics ; Phylogeny ; *Vaginitis/virology/microbiology ; Adult ; Microbiota ; Bacteriophages/genetics/classification ; *Viruses/classification/genetics/isolation & purification ; Middle Aged ; Biodiversity ; Young Adult ; Bacteria/classification/genetics ; }, abstract = {INTRODUCTION: The human vaginal virome is an essential yet understudied component of the vaginal microbiome. Its diversity and potential contributions to health and disease, particularly vaginitis, remain poorly understood.

METHODS: We conducted metagenomic sequencing on 24 pooled vaginal swab libraries collected from 267 women, including both healthy individuals and those diagnosed with vaginitis. Viral community composition, diversity indices (Shannon, Richness, and Pielou), and phylogenetic characteristics were analyzed. Virus-host associations were also investigated.

RESULTS: DNA viruses dominated the vaginal virome. Anelloviridae and Papillomaviridae were the most prevalent eukaryotic viruses, while Siphoviridae and Microviridae were the leading bacteriophages. Compared to healthy controls, the vaginitis group exhibited significantly reduced alpha diversity and greater beta diversity dispersion, indicating altered viral community structure. Anelloviruses, detected in both groups, showed extensive lineage diversity, frequent recombination, and pronounced phylogenetic divergence. HPV diversity and richness were significantly elevated in the vaginitis group, alongside an unbalanced distribution of viral lineages. Novel phage-bacterial associations were also identified, suggesting a potential role for bacteriophages in shaping the vaginal microbiome.

DISCUSSION: These findings provide new insights into the composition and structure of the vaginal virome and its potential association with vaginal dysbiosis. The distinct virome characteristics observed in women with vaginitis highlight the relevance of viral communities in reproductive health. Future studies incorporating individual-level sequencing and metatranscriptomics are warranted to explore intra-host viral dynamics, assess viral activity, and clarify the functional roles of vaginal viruses in host-microbiome interactions.}, } @article {pmid40247828, year = {2025}, author = {Doorenspleet, K and Mailli, AA and van der Hoorn, BB and Beentjes, KK and De Backer, A and Derycke, S and Murk, AJ and Reiss, H and Nijland, R}, title = {Advancing molecular macrobenthos biodiversity monitoring: a comparison between Oxford Nanopore and Illumina based metabarcoding and metagenomics.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19158}, pmid = {40247828}, issn = {2167-8359}, mesh = {*Biodiversity ; *Metagenomics/methods ; *DNA Barcoding, Taxonomic/methods ; North Sea ; Nanopores ; Belgium ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {DNA-based methods and developments of sequencing technologies are integral to macrobenthos biodiversity studies, and their implementation as standardized monitoring methods is approaching. Evaluating the efficacy and reliability of these technological developments is crucial for macrobenthos biodiversity assessments. In this study, we compared three DNA-based techniques for assessing the diversity of bulk macrobenthos samples from the Belgian North Sea. Specifically, we compared amplicon sequencing using Illumina MiSeq and portable real-time sequencing of Oxford Nanopore versus shotgun sequencing using Illumina NovaSeq sequencing. The 313 bp mitochondrial cytochrome c oxidase subunit I (COI) metabarcoding fragment served as the target region for the metabarcoding analysis. Our results indicate that Oxford Nanopore and MiSeq metabarcoding had similar performances in terms of alpha and beta diversity, revealing highly similar location-specific community compositions. The NovaSeq metagenomics method also resulted in similar alpha diversity, but slightly different community compositions compared to the metabarcoding approach. Despite these differences, location-specific community compositions were maintained across all platforms. Notably, read counts from the NovaSeq metagenomic analysis showed the weakest correlation to size corrected morphological abundance and there were mismatches between morphological identification and all DNA based findings which are likely caused by a combination of factors such as primer efficiency and an incomplete reference database. Our findings underscore the critical importance of database completeness prior to implementing DNA-based techniques as standardized monitoring method, especially for metagenomics. Nevertheless, our findings emphasize that Oxford Nanopore metabarcoding proves to be a viable alternative to the conventional Illumina MiSeq metabarcoding platform for macrobenthos biodiversity monitoring.}, } @article {pmid40247824, year = {2025}, author = {Chen, P and Yu, Q and Wang, C and Montoya, L and West, PT and Xu, L and Varoquaux, N and Cole, B and Hixson, KK and Kim, YM and Liu, L and Zhang, B and Zhang, J and Li, B and Purdom, E and Vogel, J and Jansson, C and Hutmacher, RB and Dahlberg, JA and Coleman-Derr, D and Lemaux, PG and Taylor, JW and Gao, C}, title = {Holo-omics disentangle drought response and biotic interactions among plant, endophyte and pathogen.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.70155}, pmid = {40247824}, issn = {1469-8137}, support = {32022002//National Natural Science Foundation of China/ ; 32101286//National Natural Science Foundation of China/ ; 32170129//National Natural Science Foundation of China/ ; 32322053//National Natural Science Foundation of China/ ; 2022YFC2303100//National Key Research and Development Program of China/ ; XDA28030401//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; }, abstract = {Holo-omics provide a novel opportunity to study the interactions among fungi from different functional guilds in host plants in field conditions. We address the entangled responses of plant pathogenic and endophytic fungi associated with sorghum when droughted through the assembly of the most abundant fungal, endophyte genome from rhizospheric metagenomic sequences followed by a comparison of its metatranscriptome with the host plant metabolome and transcriptome. The rise in relative abundance of endophytic Acremonium persicinum (operational taxonomic unit 5 (OTU5)) in drought co-occurs with a rise in fungal membrane dynamics and plant metabolites, led by ethanolamine, a key phospholipid membrane component. The negative association between endophytic A. persicinum (OTU5) and plant pathogenic fungi co-occurs with a rise in expression of the endophyte's biosynthetic gene clusters coding for secondary compounds. Endophytic A. persicinum (OTU5) and plant pathogenic fungi are negatively associated under preflowering drought but not under postflowering drought, likely a consequence of variation in fungal fitness responses to changes in the availability of water and niche space caused by plant maturation over the growing season. Our findings suggest that the dynamic biotic interactions among host, beneficial and harmful microbiota in a changing environment can be disentangled by a blending of field observation, laboratory validation, holo-omics and ecological modelling.}, } @article {pmid40247698, year = {2025}, author = {Zhao, J and Pachiadaki, M and Conrad, RE and Hatt, JK and Bristow, LA and Rodriguez-R, LM and Rossello-Mora, R and Stewart, FJ and Konstantinidis, KT}, title = {Promiscuous and genome-wide recombination underlies the sequence-discrete species of the SAR11 lineage in the deep ocean.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf072}, pmid = {40247698}, issn = {1751-7370}, abstract = {Surveys of microbial communities (metagenomics) or isolate genomes have revealed sequence-discrete species. That is, members of the same species show >95% Average Nucleotide Identity (ANI) of shared genes among themselves vs. <83% ANI to members of other species while genome pairs showing between 83-95% ANI are comparatively rare. In these surveys, aquatic bacteria of the ubiquitous SAR11 clade (Class Alphaproteobacteria) are an outlier and often do not exhibit discrete species boundaries, suggesting the potential for alternate modes of genetic differentiation. To explore evolution in SAR11, we analyzed high-quality, single-cell amplified genomes (SAGs) and companion metagenomes from an oxygen minimum zone (OMZ) in the Eastern Tropical Pacific Ocean, where the SAR11 make up ~20% of the total microbial community. Our results show that SAR11 do form several sequence-discrete species, but their ANI range of discreteness is shifted to lower identities between 86-91%, with intra-species ANI ranging between 91-100%. Measuring recent gene exchange among these genomes based on a recently developed methodology revealed higher frequency of homologous recombination within compared to between species that affects sequence evolution at least twice as much as diversifying point mutation across the genome. Recombination in SAR11 appears to be more promiscuous compared to other prokaryotic species, likely due to the deletion of universal genes involved in the mismatch repair, and has facilitated the spreading of adaptive mutations within the species (gene sweeps), further promoting the high intra-species diversity observed. Collectively, these results implicate rampant, genome-wide homologous recombination as the mechanism of cohesion for distinct SAR11 species.}, } @article {pmid40247632, year = {2025}, author = {Lee, JS and Kao, DJ and Worledge, CS and Villamaria, ZF and Wang, RX and Welch, NM and Kostelecky, RE and Colgan, SP}, title = {E. coli genetically modified for purine nucleobase release promotes butyrate generation and colonic wound healing during DSS insult.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2490211}, doi = {10.1080/19490976.2025.2490211}, pmid = {40247632}, issn = {1949-0984}, mesh = {Animals ; *Escherichia coli/genetics/metabolism ; *Wound Healing ; Gastrointestinal Microbiome ; Mice ; *Purines/metabolism ; *Colon/microbiology/metabolism/pathology ; *Butyrates/metabolism ; Mice, Inbred C57BL ; Disease Models, Animal ; *Colitis/chemically induced/microbiology ; Intestinal Mucosa/metabolism/microbiology ; Male ; }, abstract = {The gut microbiota transforms energy stored as undigestible carbohydrates into a remarkable number of metabolites that fuel intestinal bacterial communities and the host tissue. Colonic epithelial cells at the microbiota-host interface depend upon such microbiota-derived metabolites (MDMs) to satisfy their energy requisite. Microbial dysbiosis eliciting MDM loss contributes to barrier dysfunction and mucosal disease. Recent work has identified a role for microbiota-sourced purines (MSPs), notably hypoxanthine, as an MDM salvaged by the colonic epithelium for nucleotide biogenesis and energy balance. Here, we investigated the role of MSPs in mice during disease-modeled colonic energetic stress using a strain of E. coli genetically modified for enhanced purine nucleobase release (E. coli Mutant). E. coli Mutant colonization protected against DSS-induced tissue damage and permeability while promoting proliferation for wound healing. Metabolite and metagenomic analyses suggested a colonic butyrate-purine nucleobase metabolic axis, wherein the E. coli Mutant provided purine substrate for Clostridia butyrate production and host purine salvage, altogether supplying the host substrate for efficient nucleotide biogenesis and energy balance.}, } @article {pmid40246700, year = {2025}, author = {Iguchi, H and Watanabe, A}, title = {Honey flavors formed via yeast fermentation in honey from Japanese honeybees.}, journal = {Bioscience, biotechnology, and biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1093/bbb/zbaf057}, pmid = {40246700}, issn = {1347-6947}, abstract = {Honey is formed from floral nectar through bee-derived substances, dehydration, and chemical reactions during storage in beehives. While bacteria and fungi inhabit honey and beehives, their roles in honey maturation remain unclear. In this study, we characterized the fermentation process of honey from Apis cerana japonica (Japanese honeybee) with respect to its microbial and flavor compound profiles. Metagenomic analysis revealed that the fungi in Japanese honeybee honey are dominated by Zygosaccharomyces siamensis, with minor members of Talaromyces, Oidiodendron, Starmerella, and Priceomyces. Fermentation of diluted raw honey increased the population of Z. siamensis. Inoculating honey with Z. siamensis produced aromatic compounds, including isoamyl alcohol, hotrienol, 2-phenylethanol, and 2-phenylethyl acetate, as well as the organic acid succinate. These results indicate that fermentation by Z. siamensis can generate favorable flavor compounds, offering the potential for enhancing honey's sensory qualities and applications in the food industry.}, } @article {pmid40246602, year = {2025}, author = {Zeng, S and Wang, S and Mu, D}, title = {Metagenomics for IgA-coated gut microbiota: from taxonomy to function.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2025.04.001}, pmid = {40246602}, issn = {1878-4380}, abstract = {Immunoglobulin A (IgA) establishes intricate interactions with human gut microbiota, thereby forming IgA-coated microbiota. This forum first explores state-of-the-art metagenomic techniques for characterizing IgA-coated microbiota. Thereafter, metagenomic insights into its taxonomic diversity and microbial genomic functions that mediate IgA coating are provided. Finally, clinical implications for human health are highlighted.}, } @article {pmid40246210, year = {2025}, author = {Wani, AK and Qadir, F and Elboughdiri, N and Rahayu, F and Saefudin, and Pranowo, D and Martasari, C and Kosmiatin, M and Suhara, C and Sudaryono, T and Prayogo, Y and Yadav, KK and Muzammil, K and Eltayeb, LB and Alreshidi, MA and Singh, R}, title = {Metagenomics and plant-microbe symbioses: Microbial community dynamics, functional roles in carbon sequestration, nitrogen transformation, sulfur and phosphorus mobilization for sustainable soil health.}, journal = {Biotechnology advances}, volume = {}, number = {}, pages = {108580}, doi = {10.1016/j.biotechadv.2025.108580}, pmid = {40246210}, issn = {1873-1899}, abstract = {Biogeochemical cycles are fundamental processes that regulate the flow of essential elements such as carbon, nitrogen, and phosphorus, sustaining ecosystem productivity and global biogeochemical equilibrium. These cycles are intricately influenced by plant-microbe symbioses, which facilitate nutrient acquisition, organic matter decomposition, and the transformation of soil nutrients. Through mutualistic interactions, plants and microbes co-regulate nutrient availability and promote ecosystem resilience, especially under environmental stress. Metagenomics has emerged as a transformative tool for deciphering the complex microbial communities and functional genes driving these cycles. By enabling the high-throughput sequencing and annotation of microbial genomes, metagenomics provides unparalleled insights into the taxonomic diversity, metabolic potential, and functional pathways underlying microbial contributions to biogeochemical processes. Unlike previous reviews, this work integrates recent advancements in metagenomics with complementary omics approaches to provide a comprehensive perspective on how plant-microbe interactions modulate biogeochemical cycles at molecular, genetic, and ecosystem levels. By highlighting novel microbial processes and potential biotechnological applications, this review aims to guide future research in leveraging plant-microbe symbioses for sustainable agriculture, ecosystem restoration, and climate change mitigation.}, } @article {pmid40245994, year = {2025}, author = {Yang, R and Liu, Z and Liu, Y and Yang, Z and Zhang, Y and Lei, J and Wang, J and Zhang, A and Li, Z}, title = {High-throughput community and metagenomic elucidate systematic performance variation and functional transition mechanisms during morphological evolution of aerobic sludge.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132550}, doi = {10.1016/j.biortech.2025.132550}, pmid = {40245994}, issn = {1873-2976}, abstract = {In this study, high-throughput sequencing and metagenomics were used to investigate the microbial succession and functional gene dynamics during aerobic sludge granulation from activated sludge (AS) to aerobic granular sludge (AGS) to algal-bacterial granular sludge (ABGS). It was found that the settleability and pollutant removal efficiency of the sludge system increased with the sludge morphology evolution. Extracellular polymeric substances (EPS) analysis showed a rise in protein from 2.1 to 17.4 mg/gSS during stage of AGS and polysaccharides from 3.3 to 5.9 mg/gSS during stage of ABGS. Microbial community analysis revealed that the sludge evolution reduced species richness but enriched functional bacteria for nitrogen/phosphorus removal, while increasing the complexity of community structure and close interactions between species. Key genes involved in the tricarboxylic acid cycle, nitrogen/phosphorus and EPS metabolism were also upregulated. This study revealed the continuity mechanism and stage dependence of the functional transition during sludge morphology evolution.}, } @article {pmid40245993, year = {2025}, author = {Zhang, J and Zhang, B and Duan, F and Xuan, Z and Sun, T and Lu, L}, title = {Metagenomic exploration of novel β-galactosidases for glycosylation engineering.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132546}, doi = {10.1016/j.biortech.2025.132546}, pmid = {40245993}, issn = {1873-2976}, abstract = {β-Galactosidases are important enzymatic tools for glycosylation, but their properties vary greatly with the source. Here, ten putative β-galactosidase genes, designated as bga1 to bga10, encoding proteins Bga1 to Bga10, were mined from an environmental metagenomic dataset comprising 119,152 sequences. Five of the encoded enzyme proteins exhibited less than 80% sequence similarity to known enzymes, but displayed conserved catalytic sites in their predicted three-dimensional models. After heterologous expression and characterization, two recombinant enzymes showed specific hydrolysis activity toward o-nitrophenyl-β-d-galactopyranoside. One of them, Bga4R, exhibited remarkable activity at pH 7.4 and 50℃, with excellent alkaline stability. Notably, Bga4R tolerated a wide range of acceptors for transglycosylation. It catalyzed galactosyl transfer to various monosaccharides and sugar alcohols, and enabling the synthesis of diverse glycosylated derivatives. This study identifies a novel GH 1 β-galactosidase as a powerful tool for glycosylation engineering, with promising potential for synthesizing galactosides valuable to food and pharmaceutical industries.}, } @article {pmid40245807, year = {2025}, author = {Wang, J and Zhang, Y and Meng, Q and Hu, Z and Fu, J and Dang, C}, title = {New perspectives on bacterial chlorine resistance: Phages encoding chlorine resistance genes improve bacterial adaptation.}, journal = {Water research}, volume = {282}, number = {}, pages = {123607}, doi = {10.1016/j.watres.2025.123607}, pmid = {40245807}, issn = {1879-2448}, abstract = {Bacterial resistance to chlorine disinfectant reduces its effectiveness in killing pathogenic bacteria and poses a severe threat to environmental and health safety. The interaction between bacteria and phages is the most frequent biological activity in Earth's biosphere, but little is known about what role and mechanism phages play in the resistance of bacterial communities to chlorine disinfectants. Here, we investigated the changes in the abundance, activity and function of the bacterial-phage community under the effect of chlorine disinfectants in a 92-day running anaerobic-anoxic-oxic system, using metagenomics and metatranscriptomics sequencing. We found that transcriptional activities of both bacteria and phage are highly sensitive to chlorine disinfectants, although their relative abundance was not obviously altered. The increase in both phage diversity and the ratio of temperate to lytic phages' average activity indicated phages, especially temperate, could play a crucial role in the response to chlorine disinfectants. Interestingly, the phages that carry chlorine resistance genes (CRGs) were the drivers of the phage and microbial community when chlorine disinfectants were present, but they followed the dynamics of community in the absence of chlorine disinfectants. Based on the association bipartite network, we further found that phages directly mediated the horizontal transfer of CRGs among bacteria, facilitating the spread of CRGs in the bacterial community. Moreover, the 4 CRGs related to cell wall repair, redox balance regulation, and efflux pumps that were carried by the phages but lacking in the hosts suggest the potential compensatory effects of the phage for the chlorine resistance of their hosts. Our findings reveal the important role of phages in improving the resistance of bacterial communities to chlorine disinfectants, providing a new perspective on the co-evolution of phages and bacteria to adapt to environments.}, } @article {pmid40245806, year = {2025}, author = {Li, J and Zuo, X and Chen, Q and Lin, Y and Meng, F}, title = {Genome-resolved metagenomic analysis reveals a novel denitrifier with truncated nitrite reduction pathway from the genus SC-I-84.}, journal = {Water research}, volume = {282}, number = {}, pages = {123598}, doi = {10.1016/j.watres.2025.123598}, pmid = {40245806}, issn = {1879-2448}, abstract = {Understanding the genomic and ecological traits of partial denitrification (PD) bacteria is of high importance for developing wastewater treatment technologies. In this study, a PD-based bioreactor was operated, resulting in a mixed culture dominated by a potentially novel PD functional bacterium (SC-I-84). Progressively increased activity in both nitrate reduction and nitrite production were observed in the SC-I-84 enrichment system, whereas the nitrite reduction activity was always negligible. The phylogenetic analysis indicated that SC-I-84 was closely related to an uncultured beta-proteobacterium (99 %), whereas its denitrification functional genes (napA, napB, narV, and narY) exhibited evidence of co-evolution with chromosomal genes from the genus Cupriavidus, order Burkholderiales. In the genetic sketch of SC-I-84, only nitrate-reduction genes (nar and nap) were identified, whereas nitrite-reduction genes (nir) were absent. Notably, nitrate reduction genes were adjacent to carbon metabolism genes (sucB/C, mdh, idh) and a high abundance of tricarboxylic acid (TCA) cycling genes were found. This can promote the utilization efficiency of electron donors by nitrate reduction genes in SC-I-84, thus enhancing the denitrification activity. Furthermore, SC-I-84 positively cooperated with some bacteria that participate in nitrogen and carbon metabolism and other PD bacteria, but negatively interacted with full-denitrification bacteria. These results indicate that the enrichment of SC-I-84 restricted the growth of full-denitrification bacteria, aiding in the maintenance of a stable PD process. Taken together, the meta-genomic analysis of the novel PD functional bacterium is expected to enhance our understanding of PD processes and aid in the development of PD-based wastewater treatment processes.}, } @article {pmid40245686, year = {2025}, author = {Simó, C and Mamani-Huanca, M and Hernández-Hernández, O and Redondo-Río, Á and Muñoz, S and García-Cañas, V}, title = {Application of nanopore long-read sequencing and metabolomics in an in vitro dynamic intestinal digestion model: A genome-centric metatranscriptomic approach to investigating microbial TMA and SCFA metabolism.}, journal = {Journal of pharmaceutical and biomedical analysis}, volume = {262}, number = {}, pages = {116896}, doi = {10.1016/j.jpba.2025.116896}, pmid = {40245686}, issn = {1873-264X}, abstract = {The gut microbiota plays a relevant role in human health by metabolizing dietary components into bioactive molecules, including short-chain fatty acids and trimethylamine. Understanding how dietary interventions modulate microbial metabolism is key to developing strategies for reducing harmful metabolites such as TMA, a precursor of the pro-atherogenic trimethylamine-N-oxide. In this study, we integrated a dynamic in vitro gastrointestinal model (simgi®) with nanopore sequencing technology and metabolomics to investigate the impact of red thyme extract on microbial trimethylamine metabolism from L-carnitine. Metabarcoding, metagenomic, and metatranscriptomic analyses were performed alongside targeted metabolite quantification. Our results showed that microbial trimethylamine production primarily occurred in the transverse and descending colon compartments, coinciding with increased transcriptional activity of taxa harboring gbu cluster, associated with trimethylamine production. The administration of red thyme extract transiently reduced L-carnitine utilization but had a limited effect on overall trimethylamine levels. In parallel, short-chain fatty acids analysis revealed a shift in microbial fermentation patterns, with Acidaminococcus emerging as a dominant butyrate producer. Carbohydrate-active enzyme profiling identified Bacteroides and Parabacteroides genera as key mucin utilizers under the simulation conditions. These findings highlight the metabolic plasticity of the gut microbiota in response to the presence of L-carnitine and reduced complex carbohydrates availability, and provide new insights into microbial functional responses to dietary interventions targeting trimethylamine metabolism. Additionally, this study represents the first integration of nanopore-based metagenomics and genome-centric metatranscriptomics with targeted metabolomics in a dynamic in vitro gastrointestinal model. This multi-omics approach enabled a detailed reconstruction of the microbial metabolic network involved in L-carnitine utilization and trimethylamine formation, offering a powerful tool for mechanistic studies of gut microbiota-diet interactions.}, } @article {pmid40245533, year = {2025}, author = {Zhao, J and Wang, Y and Zhang, D and Du, J and Gao, Y and Lu, MY and Guo, JY and Su, HT and Chen, XF and Wen, DH and Jia, SY and Xu, YC and Chen, J and Yang, QW}, title = {Uncovering the unseen: Metagenomic next-generation sequencing improves liver abscess diagnostics.}, journal = {Journal of infection and public health}, volume = {18}, number = {7}, pages = {102708}, doi = {10.1016/j.jiph.2025.102708}, pmid = {40245533}, issn = {1876-035X}, abstract = {BACKGROUND: This study retrospectively analyzed the metagenomic next-generation sequencing (mNGS) results and clinical data from patients with liver abscess (LA) to investigate the clinical value of mNGS in the diagnosis of LA.

METHODS: This retrospective observational study included patients with LA who were admitted to Peking Union Medical College Hospital (PUMCH) between April 2022 and July 2024. We comprehensively analyzed the final clinical etiological diagnosis, traditional pathogen detection through conventional microbiological testing (CMT), and mNGS results in terms of pathogen type and specimen turnaround time.

RESULTS: Among 60 patients with LA, 19 types of pathogens were identified. Using clinical etiological diagnosis as the standard, mNGS identified all pathogens, whereas CMT identified only 42.11 % of pathogens. The true-positivity rate of mNGS (86.67 %) was significantly higher than that of CMT (58.33 %; P < 0.001). The average specimen turnaround time for mNGS (57.66 h) was shorter than that for CMT (86.54 hours, P < 0.001).

CONCLUSIONS: Compared with existing CMT, mNGS offers higher true-positive rates, broader pathogen coverage, and shorter specimen turnaround time. These advantages contribute to more accurate clinical diagnosis and treatment.}, } @article {pmid40245502, year = {2025}, author = {Zhong, Y and Teo, JQ and Guo, S and Schlundt, J and Kwa, AL and Ong, RT}, title = {Characterization of mobile resistance elements in extended-spectrum β-lactamase producing gram-negative bacteria from aquatic environment.}, journal = {The Science of the total environment}, volume = {978}, number = {}, pages = {179353}, doi = {10.1016/j.scitotenv.2025.179353}, pmid = {40245502}, issn = {1879-1026}, abstract = {Extended-spectrum β-lactamase producing (ESBL) bacteria from aquatic environments can pose potential threats to public health due to their capability of spreading antimicrobial resistance (AMR) genes through mobile genetic elements (MGEs), such as plasmids, insertion sequences (ISs), transposons, and integrons. Currently, there is no policy for routine monitoring of AMR genes in aquatic environments and their roles in transmission are therefore unknown. Previous metagenomic and PCR-based culture-independent approaches are limited in recovering AMR resistant aquatic bacteria isolates and the data resolution generated are not able to provide detailed genetic comparison with known human pathogens particularly for determining genetic islands harbouring AMR genes. To address these gaps, we thus investigated the genetic profiles of ESBL-producing gram-negative aquatic bacteria found from water body sites within Singapore, examining the AMR genes carried and their associated MGEs. In total, 16 ESBL-producing gram-negative bacteria were identified, of which 8 were Escherichia coli, 3 Klebsiella pneumoniae, and 5 Aeromonas spp. Whole genome sequencing (WGS) analysis revealed the presence of 12 distinct classes of AMR genes, including 16 distinct variants of β-lactamase, of which blaCTX-M was the dominant beta-lactamase genotype in all 11 Enterobacterales. The AMR genetic islands in the aquatic bacteria were also found to share similar genetic structures similar to those of circulating ESBL bacteria causing human infections. These findings underscore the potential role of aquatic ESBL bacteria as AMR reservoirs for human pathogens, suggesting that aquatic bacteria may facilitate the hidden transmission of AMR mediated by MGEs through horizontal gene transfer across different sources and species, highlighting the importance of integrating environmental AMR monitoring into local surveillance strategies.}, } @article {pmid40244604, year = {2025}, author = {Koyanagi, Y and Sajiki, AF and Yuki, K and Ushida, H and Kawano, K and Fujita, K and Shimizu, H and Okuda, D and Kosaka, M and Yamada, K and Suzumura, A and Kachi, S and Kaneko, H and Komatsu, H and Usui, Y and Goto, H and Nishiguchi, KM}, title = {Application of Metagenomic Long-Read Sequencing for the Diagnosis of Herpetic Uveitis.}, journal = {Investigative ophthalmology & visual science}, volume = {66}, number = {4}, pages = {50}, doi = {10.1167/iovs.66.4.50}, pmid = {40244604}, issn = {1552-5783}, mesh = {Humans ; *Aqueous Humor/virology ; Female ; Male ; *Uveitis/diagnosis/virology ; Middle Aged ; *Metagenomics/methods ; *DNA, Viral/analysis/genetics ; *Eye Infections, Viral/diagnosis/virology ; Adult ; Sensitivity and Specificity ; Aged ; Multiplex Polymerase Chain Reaction ; *Herpesviridae/genetics/isolation & purification ; Young Adult ; }, abstract = {PURPOSE: To investigate the sensitivity and specificity of herpes virus detection by nanopore metagenomic analysis (NMA) compared with multiplex polymerase chain reaction (mPCR)-positive and -negative controls.

METHODS: This study included 43 patients with uveitis who had been screened for intraocular herpes virus infection using mPCR from aqueous humor samples. Aqueous humor samples stored after mPCR were subjected to whole-genome amplification, long-read sequencing, and analysis of the phylogenetic microorganism composition using a Flongle flow cell on the Oxford Nanopore MinION platform. For samples that tested positive with mPCR and negative with the Flongle flow cell, additional long-read sequencing was performed using a MinION flow cell, which enabled acquisition of more sequence data. The sensitivity and specificity of herpes virus detection by NMA were compared with the mPCR-positive and -negative controls.

RESULTS: NMA using a Flongle flow cell detected the pathogenic virus in 60.0% of those who tested positive by mPCR (12/20). Further analysis using the MinION flow cell successfully identified viral DNA fragments in three out of the eight initially undetected samples, yielding a collective sensitivity of 75.0% (15/20). All of the virus detected with the long-read sequencing were identical to those diagnosed by mPCR testing, and none of the samples that tested negative by mPCR revealed herpes viral DNA with the use of long-read sequencing.

CONCLUSIONS: For the detection of etiologic herpes virus DNA fragments, NMA revealed a reasonable sensitivity and high specificity. Our study highlights the potential of nanopore sequencing to facilitate further advances in uveitis diagnosis.}, } @article {pmid40244481, year = {2025}, author = {Klangnurak, W and Hinthong, W and Aue-Umneoy, D and Yomla, R}, title = {Assessment of Bacterial Community and Other Microorganism Along the Lam Takhong Watercourse, Nakhon Ratchasima, Thailand.}, journal = {Current microbiology}, volume = {82}, number = {6}, pages = {248}, pmid = {40244481}, issn = {1432-0991}, support = {grant number FRB650039/0240 project number 165430//Chulabhorn Royal Academy (Fundamental Fund: fiscal year 2022 by National Science Research and Innovation Fund (NSRF))/ ; contract number FF-65/008//Chulabhorn Royal Academy (Fundamental Fund: fiscal year 2022 by National Science Research and Innovation Fund (NSRF))/ ; }, mesh = {Thailand ; *Bacteria/classification/genetics/isolation & purification ; *Water Microbiology ; *Rivers/microbiology ; Metagenomics ; *Microbiota ; Water Quality ; Environmental Monitoring ; }, abstract = {Lam Takhong, a vital watercourse in Nakhon Ratchasima province, Thailand, supports agricultural, recreational, and urban activities. Originating in a national park, it flows through urban areas before discharging into a dam and running off via the sluice gate. While water quality monitoring is routine, microbial community data have never been reported. This study assesses the microorganism diversity and functional genes in Lam Takhong watercourse using a shotgun sequencing metagenomics approach. Water samples were collected from the upstream, midstream, and downstream sections. The midstream area exhibited the highest abundance of fecal coliform bacteria, plankton, and benthos, suggesting elevated pollution levels. Genes related to metabolism, particularly carbohydrate and amino acid pathways, were predominant. Proteobacteria was the most abundant phylum found in the water, with Limnohabitans as the dominant planktonic bacteria. Bacteria such as Staphylococcus, Mycobacterium, Escherichia, Pseudomonas, Enterococcus, Neisseria, Streptomyces, and Salmonella were detected, along with antibiotic resistance genes, raising public health concerns. These findings emphasize the need for microbial monitoring in the Lam Takhong to determine the potential water quality bioindicator and prevent potential disease spread through the water system.}, } @article {pmid40244477, year = {2025}, author = {Li, J and Zhang, Y and He, L}, title = {The role of urine microbiota in culture-negative patients with pyuria.}, journal = {World journal of urology}, volume = {43}, number = {1}, pages = {227}, pmid = {40244477}, issn = {1433-8726}, mesh = {Humans ; *Pyuria/microbiology/virology/urine ; Retrospective Studies ; Male ; Female ; *Microbiota ; Middle Aged ; *Urine/microbiology/virology ; Aged ; Adult ; }, abstract = {BACKGROUND: Pyuria is usually caused by bacteria and usually results in antibiotic prescriptions. However, traditional urine culture is time-consuming and has a high false negative possibility. Additionally, the role of urine viruses in pyuria is unclear. Metagenomics can enhance the precision and efficiency of diagnosis by directly sequencing the microbiota in urine. We aimed to determine the association of urine microbiota in patients with or without pyuria and culture negative.

METHODS: In this retrospective study, we screened urine samples from patients who received whole genome sequencing (WGS) and had a negative urine culture from October 2021 to May 2024. We compared differences in the top 10 detected genera of urine microbiota between the pyuria group and the non-pyuria group. Multivariable analysis was used for correlation analysis and performed to odds ratio (OR) and OR with 95% confidence interval (CI). The receiver operating characteristic (ROC) curve analyses tested the predictive ability of associated microbiota to pyuria.

RESULTS: We found 29 microbial genera including 2 viral genera. Escherichia [OR 11.688 (95%CI 2.190-62.362), p = 0.004], Gardnerella [OR 9.904 (95%CI 2.180-45.005), p = 0.003] or Polyomavirus [OR 5.205 (95%CI 1.295-20.919), p = 0.020] was associated with the independent risk factors of pyuria, while Lactobacillus was associated with a decreased risk of pyuria [OR 17.273 (95%CI 1.297-230.061), p = 0.031]. An integrated logistic regression model of Escherichia, Gardnerella, Polyomavirus, and Lactobacillus exhibited a predictive power for pyuria with the area under curve (AUC) of 0.8132 [95%CI (0.7098-0.9167), p < 0.001].

CONCLUSION: Urine microbiota is diverse. Escherichia, Gardnerella, or Polyomavirus are independently associated with pyuria, while Lactobacillus is a positive factor against pyuria.}, } @article {pmid40244062, year = {2025}, author = {Stevens, EJ and Li, JD and Hector, TE and Drew, GC and Hoang, K and Greenrod, STE and Paterson, S and King, KC}, title = {Within-host competition causes pathogen molecular evolution and perpetual microbiota dysbiosis.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf071}, pmid = {40244062}, issn = {1751-7370}, support = {COEVOPRO 802242//European Research Council Starting/ ; }, abstract = {Pathogens newly invading a host must compete with resident microbiota. This. within-host microbial warfare could lead to more severe disease outcomes or constrain the evolution of virulence. By passaging a widespread pathogen (Staphylococcus aureus) and a native microbiota community across populations of nematode hosts, we show that the pathogen displaced microbiota and reduced species richness, but maintained its virulence across generations. Conversely, pathogen populations and microbiota passaged in isolation caused more host harm relative to their respective no-host controls. For the evolved pathogens, this increase in virulence was partly mediated by enhanced biofilm formation and expression of the global virulence regulator agr. Whole genome sequencing revealed shifts in the mode of selection from directional (on pathogens evolving in isolation) to fluctuating (on pathogens evolving in host microbiota). This approach also revealed that competitive interactions with the microbiota drove early pathogen genomic diversification. Metagenome sequencing of the passaged microbiota shows that evolution in pathogen-infected hosts caused a significant reduction in community stability (dysbiosis), along with restrictions on the co-existence of some species based on nutrient competition. Our study reveals how microbial competition during novel infection could determine the patterns and processes of evolution with major consequences for host health.}, } @article {pmid40243577, year = {2025}, author = {Paradzik Simunovic, M and Degoricija, M and Korac-Prlic, J and Lesin, M and Stanic, R and Puljak, L and Olujic, I and Marin Lovric, J and Vucinovic, A and Ljubic, Z and Thissen, J and Reen Kok, C and Jaing, C and Bucan, K and Terzic, J}, title = {Potential Role of Malassezia restricta in Pterygium Development.}, journal = {International journal of molecular sciences}, volume = {26}, number = {7}, pages = {}, doi = {10.3390/ijms26072976}, pmid = {40243577}, issn = {1422-0067}, support = {IP-2020-02-8921//Croatian Science Foundation/ ; }, mesh = {Humans ; *Pterygium/microbiology/pathology/genetics ; *Malassezia/genetics/isolation & purification ; Male ; Female ; Middle Aged ; Conjunctiva/microbiology/pathology ; Microbiota ; Aged ; Gene Expression Profiling ; }, abstract = {Pterygium is a condition affecting the ocular surface, marked by a triangular-shaped growth of fibrotic tissue extending from the nasal conjunctiva toward the corneal center, potentially causing visual impairment. While ultraviolet (UV)light exposure is the primary risk factor for pterygium, its underlying cause remains unclear. In order to better understand the true genesis of pterygium development, we investigated pterygium tissue and compared it with healthy conjunctiva controls. Given the eye's direct environmental exposure, we analyzed the microbiota composition using metagenomic sequencing of pterygium tissue to identify microbes potentially associated with this condition. Metagenomic sequencing revealed a higher prevalence of the fungus Malassezia restricta in five pterygium samples, confirmed by in situ hybridization. The CHIT1 gene, which plays a role in antifungal defenses, displayed the highest expression in five pterygium tissue samples compared to healthy conjunctiva controls, suggesting the potential involvement of Malassezia restricta in pterygium development. Gene expression profiling of pterygium highlighted an IL-33 and IL-4 gene expression signature, along with an increased presence of M2 macrophages, emphasizing their role in promoting fibrosis-a hallmark feature of pterygium. The detection of Malassezia restricta in the pterygium samples and associated molecular changes provides novel insights into the ocular microbiome and raises the possibility of Malassezia's involvement in pterygium pathology.}, } @article {pmid40243351, year = {2025}, author = {Li, Y and Liu, S and Han, P and Lei, J and Wang, H and Zhu, W and Dong, Z and Zhang, Y and Jiang, Z and Zheng, B and Rao, G and Yu, Z and Li, A}, title = {Performance and hypothetical clinical impact of an mNGS-based machine learning model for antimicrobial susceptibility prediction of five ESKAPEE bacteria.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0259224}, doi = {10.1128/spectrum.02592-24}, pmid = {40243351}, issn = {2165-0497}, abstract = {UNLABELLED: Antimicrobial resistance is an escalating global health crisis, underscoring the urgent need for timely and targeted therapies to ensure effective clinical treatment. We developed a machine learning model based on metagenomic next-generation sequencing (mNGS) for rapid antimicrobial susceptibility prediction (mNGS-based AST), which was tailored to five ESKAPEE bacteria: Acinetobacter baumannii, Klebsiella pneumoniae, Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus. However, the clinical utility remained unvalidated. Assuming that mNGS-based AST results were obtained during clinical management, we assessed its clinical utility using data from a previous observational cohort study of clinical mNGS applications. We collected the data from 114 patients infected with five ESKAPEE bacteria from 07/2021 to 03/2023 and incorporated the sequencing data into the model. We evaluated the performance and hypothetical impact of the method by comparing its results and therapy recommendations with those based on traditional culture-based AST. The primary outcome was the performance of mNGS-based AST (n = 113 strains). mNGS-based AST displayed an overall accuracy of 93.84% and shorter turnaround time (1.12 ± 0.33 days vs 2.81 ± 0.57 days for culture-based AST, t = -27.31, P < 0.05). The secondary outcomes included the proportion of patients who could benefit from mNGS-based AST. It could allow earlier and suitable antibacterial adjustments in 32.05% of culture-positive patients (25/78) and offer actionable antimicrobial susceptibility results in 16.67% of culture-negative cases (6/36). mNGS-based AST offers a promising approach for individualized antibacterial therapy.

IMPORTANCE: Metagenomic next-generation sequencing (mNGS)-based antimicrobial susceptibility prediction (AST) is a novel method for predicting the antimicrobial susceptibility of ESKAPEE bacteria using a machine learning approach and short-read sequencing data. Assuming that mNGS-based AST results were obtained during clinical management, it could significantly reduce turnaround time while maintaining a high level of accuracy, allowing for earlier therapeutic adjustments for patients. Furthermore, mNGS-based AST can be integrated with clinical mNGS to maximize the utility of short-read data without substantial cost increases. This study demonstrates the potential of mNGS-based AST for precise, individualized antibacterial selection and highlights its broader applicability in enhancing clinical antimicrobial use for various infections.}, } @article {pmid40243342, year = {2025}, author = {Gruninger, RJ and McCormack, ML and Chomistek, NC and Zaheer, R and McAllister, TA}, title = {Unraveling the microbial diversity of bovine liver abscesses: isolation, identification, and genomic characterization of the Bacteroides found in hepatic lesions.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0042325}, doi = {10.1128/spectrum.00423-25}, pmid = {40243342}, issn = {2165-0497}, abstract = {UNLABELLED: Liver abscesses in cattle reduce animal performance, increase the environmental footprint of beef production, and cause significant economic losses. The low pH of the rumen resulting from the consumption of high grain diets damages the rumen epithelium and facilitates the translocation of opportunistic pathogens from the gastrointestinal tract into the bloodstream where they can colonize the liver, causing infection. Recently, 16s rRNA sequencing has revealed that 25%-50% of liver abscess microbiomes have prominent levels of Bacteroides. Due to the inability to reliably classify amplicon sequences beyond the genus level, the identity of these microbes remains unknown. We have employed a combination of culture-independent and culture-based methods to isolate and identify the Bacteroides associated with liver abscesses in cattle. Shotgun metagenomic sequencing and assembly of metagenome-assembled genomes generated four high-quality genomes, two of which were putatively identified as Bacteroides. These microbes were subsequently isolated from the purulent material of liver abscesses. Whole-genome sequencing conclusively identified these isolates as Bacteroides pyogenes and a previously unknown species of Bacteroides, revealing distinct differences from Bacteroides typically found in the gut. Carbohydrate utilization assays revealed that both organisms metabolize glycogen and glycosaminoglycans found in the extracellular matrix of the liver but display differences in substrate specificity. These data not only identify Bacteroides found in bovine liver abscesses but also provide new insights into the potential role that these organisms may play in this production-limiting disease.

IMPORTANCE: Liver abscesses (LAs) are commonly found in cattle raised in feedlots and result from a bacterial infection of the liver. Not only are LAs a concern for animal health, but they also impact growth efficiency, animal welfare, and cost the North American beef industry upwards of $120 million per annum. Recently, it has been found that 25%-50% of liver abscess microbiomes have prominent levels of Bacteroides; however, to date, the biological relevance in LA pathogenesis and the identity of these bacteria are unknown. This research describes the isolation, identification, and genomic characterization of the Bacteroides found in bovine liver abscesses. These data provide a critical foundation for expanding our knowledge of the potential role Bacteroides play in liver abscess development and could contribute to the identification of novel targets for developing treatments to prevent this important production-limiting disease.}, } @article {pmid40243306, year = {2025}, author = {Wang, Z and Sun, Y and Wang, H and Yun, J and Du, W}, title = {Metagenome-assembled genome of a novel Pseudoalteromonas species from South Mid-Atlantic Ridge deep-sea water suggests potential for chitin degradation.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0018925}, doi = {10.1128/mra.00189-25}, pmid = {40243306}, issn = {2576-098X}, abstract = {We report a high-quality metagenome-assembled genome (MAG) of a novel Pseudoalteromonas species recovered from deep-sea water of the South Mid-Atlantic Ridge. This MAG encodes key chitinase-related genes, suggesting potential involvement in chitin degradation and organic matter remineralization in the deep sea.}, } @article {pmid40242593, year = {2025}, author = {Sun, S and He, R and Chen, S and Ren, J and Ma, X and Yang, J}, title = {Odontogenic brain abscess caused by Porphyromonas gingivalis and Streptococcus constellatus: a case report and review article.}, journal = {Journal of oral microbiology}, volume = {17}, number = {1}, pages = {2485197}, pmid = {40242593}, issn = {2000-2297}, abstract = {BACKGROUND: Odontogenic brain abscess is a rare, but potentially fatal, central nervous system infection, with insidious onset and unclear etiology.

METHODS: This case reports a 70-year-old male patient who developed an odontogenic brain abscess secondary to periodontal infection and underwent neurological surgery. Extract pus during surgery for the metagenomic next-generation sequencing (mNGS).

RESULTS: The mNGS of pus samples obtained from brain abscess aspiration identified the periodontal pathogens Porphyromonas gingivalis and Streptococcus constellatus. Consequently, he was referred to the department of stomatology for further examination and treatment.

CONCLUSIONS: Our study found that major periodontal pathogens including P. gingivalis and S. constellatus were essential in the development of odontogenic brain abscesses; thus, timely intervention and preventive measures are important for treatment.}, } @article {pmid40242244, year = {2025}, author = {Kang, Z and Zhang, R and Li, S and Wang, J and Huang, M and Li, W}, title = {Preliminary investigation of gut microbiota and associated metabolic pathways in the pathogenesis of primary central nervous system lymphoma.}, journal = {Frontiers in oncology}, volume = {15}, number = {}, pages = {1548146}, pmid = {40242244}, issn = {2234-943X}, abstract = {BACKGROUND: Primary central nervous system lymphoma (PCNSL) is a rare and highly aggressive form of non-Hodgkin lymphoma, primarily confined to the central nervous system. In recent years, growing evidence has indicated that dysbiosis of the gut microbiota is closely associated with the development of various malignancies. This study aims to systematically explore the potential role of gut microbiota and their metabolic pathways in the pathogenesis of PCNSL by integrating metagenomic and metabolomic approaches.

MATERIALS AND METHODS: A total of 33 PCNSL patients and 32 healthy controls were enrolled in this study, and fecal samples were collected from each participant. The fecal samples were analyzed using metagenomic and metabolomic techniques, followed by KEGG pathway enrichment analysis to investigate the biological pathways enriched by the differential gut microbiota and metabolites.

RESULTS: Significant differences were observed in the composition of gut microbiota and metabolites between PCNSL patients and healthy controls. In the gut microbiota of PCNSL patients, the abundance of the phylum Proteobacteria was markedly increased, while the Firmicutes/Bacteroidetes (F/B) ratio was significantly elevated. Metabolomic analysis revealed that the abundance of oleamide was significantly reduced in the PCNSL group, while the relative abundance of deoxycholic acid was significantly elevated. KEGG pathway analysis indicated that the differential gut microbiota and metabolites were primarily involved in key metabolic pathways such as nitrogen metabolism, phenylalanine metabolism, purine metabolism, and pyrimidine metabolism, with these pathways being more active in PCNSL patients.

CONCLUSION: This study is the first to systematically investigate the differences in gut microbiota and their metabolites between PCNSL patients and healthy individuals, highlighting the potential role of gut microbiota alterations in the pathogenesis of PCNSL.}, } @article {pmid40241899, year = {2025}, author = {Chen, L and Weng, W and Li, D and Xie, W and Lu, L and Li, S}, title = {Case Report: A clinically relevant isolation of Gardnerella leopoldii guided by morphological and molecular evidence from a urinary tract infection case.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1548067}, pmid = {40241899}, issn = {2296-858X}, abstract = {BACKGROUND: The genus Gardnerella is commonly found in the vaginal ecosystem and is considered a covert pathogen of the urinary tract. However, Gardnerella vaginalis had been the only recognized species of the genus Gardnerella for decades. Cases regarding the clinical relevance of Gardnerella leopoldii have rarely been reported, which is crucial for fully understanding the various species within the genus Gardnerella.

CASE PRESENTATION: A 72-year-old female patient was admitted to the hospital with gross hematuria and complaints of waist soreness. Physical examinations, including those of the head, chest, and abdomen, along with routine laboratory tests such as white blood cell (WBC) count and proportion, liver function, and renal function, yielded normal results. However, the patient also exhibited significantly elevated levels of serum C-reactive protein (CRP) and abnormal urinary test findings, which revealed positive results for occult blood and leukocyte esterase, and increased counts of erythrocyte and leukocyte. To further evaluate the urinary system, computerized tomography urography (CTU) was performed. The CTU results revealed multiple weakly enhanced foci in the right kidney and thickening of the right ureter, renal pelvis, calyces, and bladder walls. Based on the above findings, the initial diagnosis included hematuria, hydronephrosis, and urinary tract infection (UTI). To identify the causative pathogens, we employed a comprehensive approach that included microscopic morphology, Sanger sequencing, and metagenomic next-generation sequencing (mNGS). Finally, both Mycobacterium tuberculosis and G. leopoldii were identified as the co-infecting etiological agents responsible for the patient's urinary tract infection.

CONCLUSION: This case represents the first documented isolation of clinically relevant G. leopoldii, guided by morphological and molecular evidence from a clinical urine sample. It highlights the potential of mNGS as a promising tool for identifying previously unrecognized species and offers valuable insights to enhance the understanding of clinically relevant microorganisms.}, } @article {pmid40241768, year = {2025}, author = {Yao, XQ and Bao, H and La, NT and Jiang, GS and Zhai, PH and Liu, CB and Yu, L}, title = {Gut microbiota contribute to cold adaptation in mammals-primates and ungulates.}, journal = {iScience}, volume = {28}, number = {4}, pages = {112245}, pmid = {40241768}, issn = {2589-0042}, abstract = {Gut microbiota play an influential role in how animals adapt to extreme environments. Two phylogenetically distant mammals, Yunnan snub-nosed monkey and reindeer both adapted to frigid environments. Metagenomic analyses revealed they developed similar cold adaptation strategies in response to food scarcity (enhanced fiber degradation and nitrogen balance maintenance), energy shortages (increased short-chain fatty acid [SCFA] synthesis), and a constant body temperature sustainment (stimulation of non-shivering thermogenesis [NST]). Moreover, they evolved distinct adaptation strategies to cope with different cold ecosystems. Yunnan snub-nosed monkey adapt to high-altitude hypoxia environment through enhancing ability to synthesize lactate and metabolize purine, while reindeer adapt to extreme cold environment through increasing blood flow, strengthening urea cycling, and enriching fat storage associated bacteria. Notably, reindeer microbiota uniquely enriched cholesterol-degrading bacteria, potentially mitigating cardiovascular risks from lipid storage. Our study expands the knowledge of how gut microbiome promotes cold adaptation through shared and specialized mechanisms shaped by different phylogenetic and ecological contexts.}, } @article {pmid40241748, year = {2025}, author = {Liu, T and Kress, AM and Debelius, J and Zhao, N and Smirnova, E and Bandyopadhyay, S and Bonham, K and Comstock, SS and Gill, S and Gern, JE and Koinis-Mitchell, D and Klepac-Ceraj, V and Lee-Sarwar, K and Litonjua, AA and McKee, K and McCauley, K and O'Connor, TG and Rosas-Salazar, C and Scheible, K and Stanford, JB and Moore, B and Jacobson, LP and Mueller, NT and , }, title = {Maternal vaginal and fecal microbiota in later pregnancy contribute to child fecal microbiota development in the ECHO cohort.}, journal = {iScience}, volume = {28}, number = {4}, pages = {112211}, pmid = {40241748}, issn = {2589-0042}, abstract = {There is growing interest in the use of microbial-seeding interventions to mitigate the impacts of prenatal antibiotics, C-section, and lack of breastfeeding on mother-child microbe sharing. However, the relative importance of maternal vaginal vs. fecal microbiota in this process is unclear. Analyzing 16S rRNA sequences from five US birth cohorts, we found that maternal vaginal and fecal microbiota became more similar as pregnancy progressed, and both niches influenced the child's fecal microbiota. The relative contribution of maternal vaginal microbiota increased when vaginal sampling occurred later in gestation. As children aged from birth to 5 years, their fecal microbiota increasingly resembled their mother's fecal microbiota as compared to vaginal microbiota. Patterns of sharing appeared to differ by prenatal antibiotic use, birth mode (C-section vs. vaginal), and breastfeeding. Our findings enhance understanding of niche-specific mother-child microbe sharing and may inform microbial-seeding interventions. Metagenomic studies are needed to identify specific shared strains.}, } @article {pmid40241728, year = {2025}, author = {Xie, L and Wang, X and Wang, X and Liu, X}, title = {Changes in microbial community succession and volatile compounds during the natural fermentation of bangcai.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1581378}, pmid = {40241728}, issn = {1664-302X}, abstract = {INTRODUCTION: Fermented bangcai (Brassica juncea var. crassicaulis) is a traditional Chinese food with unique flavor. However, the formation mechanism of flavor compounds related to the fermentation process of bangcai has not been thoroughly studied.

METHODS: Gas chromatography-ion mobility spectrometry technology combined with metagenomics was used to analyze the characteristic volatile flavor compounds and microbial community structure of bangcai before and after fermentation in this study.

RESULTS: A total of 91 types of volatile organic compounds were detected in this study. The pungent odor brought by allyl isothiocyanate, 1-butene isothiocyanate, and other substances in the raw materials was removed through fermentation. This process led to the formation of flavor substances such as propyl acetate, ethyl acetate, and 2-methyl-3-furanthiol, which imparted bangcai with flavors of flower and fruit, roast meat, and fried coffee. In addition, our study found that after air drying, bangcai mainly contained γ-butyrolactone, nonanal and other flavor compounds, giving the bangcai products a richer floral and fruity flavor profile. Citrobacter, Lactobacillus, and Leuconostoc were the dominant bacteria in the fermentation process of bangcai. They were significantly related to the formation of differential flavor compounds such as γ-butyrolactone, ethyl 2-methylpropanoat, and benzaldehyde-D.

DISCUSSION: These results provide a theoretical basis for improving the flavor quality of fermented vegetable products.}, } @article {pmid40241696, year = {2025}, author = {Yang, Z and Xie, Y and Zhu, Y and Lei, M and Chen, X and Jin, W and Fu, C and Yu, L}, title = {Unraveling the flavor formation process of mellow and thick-type ripened Pu-erh tea through non-targeted metabolomics and metagenomics.}, journal = {Food chemistry: X}, volume = {27}, number = {}, pages = {102424}, pmid = {40241696}, issn = {2590-1575}, abstract = {Ripened Pu-erh tea (RPT) is renowned for its distinctive flavor and health benefits. However, its complex fermentation process poses challenges in ensuring consistency in production. This study investigated RPT flavor formation through sensory evaluation, multi-omics analysis, and multivariate statistical approaches. By day 24, the tea exhibited a reddish-brown infusion and a mellow, thick taste (MT_RPT), achieving the highest sensory score (94.0, P < 0.05). Sixteen flavor-related chemical components exhibited significant changes (P < 0.05). The contents of free amino acids, L-theanine, tea polyphenols, flavonoids, catechins, and thearubigins decreased. In contrast, the contents of total soluble sugars, caffeine, theobromine, epicatechin, and theabrownins (TBs) increased, reaching 74.1 mg/g, 65.38 mg/g, 3.13 mg/g, 3.33 mg/g, and 134.84 mg/g, respectively. Additionally, 33 nonvolatile metabolites (e.g., pelargonidin 3-O-glucoside, dihydroisorhamnetin, and puerarin) were significantly correlated with MT_RPT flavor (VIP > 1, |r| ≥ 0.8, P < 0.05) and influenced by key functional microbes, including Pantoea, Aspergillus, Brachybacterium, and Staphylococcus. By day 30, the infusion darkened, and sensory scores declined (81.4, P < 0.05), attributed to the dominance of Brevibacterium. This microbial shift reduced water-soluble pectin, free amino acids, and 11 metabolites while increasing TBs and theophylline (219.33 mg/g and 0.09 mg/g, respectively). Therefore, TBs were identified as a crucial indicator of optimal fermentation. Moreover, redundancy analysis indicated that the tea pile's central temperature, moisture content, and pH were essential fermentation parameters (P < 0.05). These findings deepen our understanding of MT_RPT flavor development mechanisms and provide valuable insights into precise fermentation control.}, } @article {pmid40241220, year = {2025}, author = {Yang, K and Li, G and Li, Q and Wang, W and Zhao, X and Shao, N and Qiu, H and Liu, J and Xu, L and Zhao, J}, title = {Distribution of gut microbiota across intestinal segments and their impact on human physiological and pathological processes.}, journal = {Cell & bioscience}, volume = {15}, number = {1}, pages = {47}, pmid = {40241220}, issn = {2045-3701}, support = {82272812//National Natural Science Foundation of China/ ; 82360018//National Natural Science Foundation of China/ ; }, abstract = {In recent years, advancements in metagenomics, metabolomics, and single-cell sequencing have enhanced our understanding of the intricate relationships between gut microbiota and their hosts. Gut microbiota colonize humans from birth, with their initial composition significantly influenced by the mode of delivery and feeding method. During the transition from infancy to early childhood, exposure to a diverse diet and the maturation of the immune system lead to the gradual stabilization of gut microbiota's composition and distribution. Numerous studies have demonstrated that gut microbiota can influence a wide range of physiological functions and pathological processes by interacting with various tissues and organs through the gut-organ axis. Different intestinal segments exhibit unique physical and chemical conditions, which leads to the formation of vertical gradients along the intestinal tract: aerobes and facultative aerobes mainly live in the small intestine and anaerobic bacteria mainly live in the large intestine, and horizontal gradients: mucosa-associated microbiota and lumen-associated microbiota. In this review, we systematically summarize the distribution characteristics of gut microbiota across six intestinal segments: duodenum, jejunum, ileum, cecum, colon, and rectum. We also draw a conclusion that gut microbiota distributed in different intestinal segments affect the progression of different diseases. We hope to elucidate the role of microbiota at specific anatomic sites within the gut in precisely regulating the processes of particular diseases, thereby providing a solid foundation for developing novel diagnostic and therapeutic strategies for related diseases.}, } @article {pmid40240641, year = {2025}, author = {Muñoz-Rivera, MP and Martínez-Morales, F and Guzmán-Morales, D and Rivera-Ramírez, A and Sánchez-Reyes, A and Trejo-Hernández, MR}, title = {Population dynamics of a bacterial consortium from a marine sediment of the Gulf of Mexico during biodegradation of the aromatic fraction of heavy crude oil.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {40240641}, issn = {1618-1905}, abstract = {In the marine environment, uncontained crude oil is dispersed and degraded by abiotic or biotic processes; native bacterial populations gradually adapt to integrate interspecific and intraspecific metabolic networks for efficient and dynamic utilization of xenobiotic substrates as carbon source. Aromatic compounds accumulate in marine sediments and bacterial populations at these sites play a crucial role in the mobilization of those complex molecules into the global geochemical cycles. The aim of this work was to use native bacteria from a marine sediment sample in the Gulf of Mexico to enhance the biodegradation of the aromatic fraction from a heavy crude oil, as the sole carbon source, during a 200-day microcosm experiment. This process involved the gradual increase of the aromatic fraction into the culture to promote bacterial enrichment; the increase in viable cells correlated well with a biodegradation pattern of the aromatic fraction at some points. Bacterial biodiversity, as revealed by metagenomic and microbiological approaches, indicates that bacterial groups are present at all fraction concentrations, but with changes in abundance, richness and dominance. Population dynamics revealed the presence of bacteria that modify emulsification and surface tension reduction values, which could promote the incorporation of the highly hydrophobic polyaromatic compounds into the culture aqueous phase for their biodegradation by hydrocarbonoclastic bacteria present. On the other hand, the presence of non-hydrocarbonoclastic bacteria probably is sustained by cross-feeding events involving sugars, amino acids, short carbon compounds, lipids produced by the former bacteria by co-metabolism of complex aromatic substrates, which are transformed into diverse biomolecules for biofilm development to promote a bacterial population dynamics adapted to this environment.}, } @article {pmid40240456, year = {2025}, author = {Bahetjan, K and Yu-Xia, and Lin, S and Aili, N and Yang, H and Du, S}, title = {Analysis of the bronchoalveolar lavage fluid microbial flora in COPD patients at different lung function during acute exacerbation.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {13179}, pmid = {40240456}, issn = {2045-2322}, mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/physiopathology ; *Bronchoalveolar Lavage Fluid/microbiology ; Male ; Female ; Aged ; Middle Aged ; *Microbiota ; Bacteria/classification/genetics/isolation & purification ; *Lung/microbiology/physiopathology ; Dysbiosis/microbiology ; }, abstract = {There is a correlation between the dysbiosis of the respiratory microbiota and the occurrence, severity, frequency, and mortality of Chronic Obstructive Pulmonary Disease (COPD). However, it is not unclear if there are differences in the bronchoalveolar lavage fluid (BALF) microbiota among patients at differente lung function. In this study, BALF samples were collected from 70 COPD patients experiencing acute exacerbations (AECOPD). The patients were divided into a mild group (FEV1/pre ≥ 50; PFT I, n = 50) and a severe group (FEV1/pre < 50; PFT II, n = 20) according to the lung function: or a frequent exacerbation (FE, n = 41) group and a non-frequent exacerbation (NFE, n = 29) group according to their exacerbation history. Microbiota analysis of BALF samples was conducted using mNGS and bioinfromatic analysis. Compared to PFT I group, PFT II group exhibited a significant decrease in species diversity (Shannon index), as well as a significant reduction in total species count and richness (Chao1, ACE indices). NFE group demonstrated diversity similar to that of FE group. Conversely, the microbial diversity of NFE group was comparable to that of FE group. The most abundant bacterial genera were Streptococcus, Prevotella, Veillonella, Rod-shaped Bacillus, and Rothia. Aspergillus was the most dominant fungal genus in AECOPD. Lymphocryptovirus was the most prevalent virus in AECOPD.Compared to the PFT I group, Corynebacterium's abundance significantly increased in PFT II group. Furthermore, FE group showed a notable increase in Streptococcus mitis abundance relative to NFE group. Bubble plot analysis revealed a significant increase in Moraxella, Fusobacterium, Haemophilus, Pseudomonas, Streptomyces, and Klebsiella in PFT II group, including a notable increase in typical Veillonella, Actinomyces, and Gordonia. The NFE group exhibited a significant increase in Bacteroides and Prevotella's relative abundance. Spearman correlation analysis revealed strong positive correlations among certain microbial communities. There exists a significant variation in microbial composition across groups of AECOPD patients at different lung function. Specifically, patients with severe airflow limitations exhibit a significant reduction in microbial diversity. Additionally, distinct bacterial taxa are enriched in patients characterized by varying levels of airflow limitation and exacerbation frequency. These observations offer vital insights into the pathogenesis of AECOPD, suggesting a potentially crucial role for the microbiota in its development. Such findings pave the way for identifying potential therapeutic targets and intervention strategies, ultimately aiming to improve treatment outcomes for AECOPD patients.}, } @article {pmid40240384, year = {2025}, author = {Pinto, OHB and Biazotti, BB and de Souza, RSC and Yassitepe, JÉCT and Arruda, P and Dante, RA and Gerhardt, IR}, title = {Seasonal bacterial profiles of Vellozia with distinct drought adaptations in the megadiverse campos rupestres.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {636}, pmid = {40240384}, issn = {2052-4463}, support = {2022/08797-4//Fundação de Amparo à Pesquisa do Estado de São Paulo (São Paulo Research Foundation)/ ; 2022/08797-4//Fundação de Amparo à Pesquisa do Estado de São Paulo (São Paulo Research Foundation)/ ; }, mesh = {*Droughts ; Seasons ; *Soil Microbiology ; Brazil ; RNA, Ribosomal, 16S/genetics ; Adaptation, Physiological ; *Microbiota ; Bacteria/genetics/classification ; }, abstract = {Microbial communities can vary as a function of seasonal precipitation and the phenotypic characteristics of the prevailing plant species in an ecosystem. The Brazilian campos rupestres (CRs) host a unique flora adapted to harsh conditions, including severe droughts and nutrient-poor soils. Velloziaceae, a dominant angiosperm family in CRs, exhibit contrasting drought adaptive strategies, prominently desiccation tolerance and dehydration avoidance. Here, we created a comprehensive dataset of microbial composition and dynamics of bulk soil and distinct plant compartments (leaf blade, dry sheath, aerial root, and underground root) from two desiccation-tolerant and two dehydration-avoiding, non-desiccation-tolerant Vellozia species, across four seasons (beginning and end of rainy and dry seasons) through 16S rRNA gene sequencing of 374 samples. This dataset also includes 38 soil metagenomes encompassing dry and rainy seasons from both drought adaptive strategies. Exploring an overlooked aspect of CRs biology offers significant potential for understanding plant-microbial associations and adaptations to water availability in tropical regions. The genetic data and metadata support further research for hypothesis testing and cross-study comparisons.}, } @article {pmid40240311, year = {2025}, author = {Liu, D and Abdellah, YAY and Dou, T and Keiblinger, KM and Zhou, Z and Bhople, P and Jiang, J and Shi, X and Zhang, F and Yu, F and Xing, B}, title = {Livestock-Crop-Mushroom (LCM) Circular System: An Eco-Friendly Approach for Enhancing Plant Performance and Mitigating Microbiological Risks.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c12517}, pmid = {40240311}, issn = {1520-5851}, abstract = {Mushroom production using agroforestry biowaste is a great green cycling agriculture alternative. Therefore, the current study explored the Livestock-Crop-Mushroom (LCM) circular production model, starting with co-composting of straw and cow manure as a'St' biofertilizer further used for mushroom cultivation that ultimately produced a'StM' biofertilizer. The two biofertilizers were tested for their impacts on plant growth and potential microbial risks. The results show significant growth of oats stimulated by biofertiliser use. Both'St' and'StM' increased plant biomass, while with the latter, the crude protein content (+5.1%) and root biomass were also higher. Reduced abundances of resistome genes (30%) and pathogens (25%) were observed during the oat growth. Further, metagenomics analysis also indicated a reduction in antibiotic-resistance genes by -20% in soils with oats treated by'St' and -46% in'StM' biofertilizer treatment. The'StM' had a three-fold stronger inhibitory effect on oat rhizosphere soil pathogens than'St'. Moreover, compared to'St','StM' suppressed pathogens in seeds and stems, with specific beneficial biomarker microbes in different plant parts. Overall, the antibiotic resistance gene related to oxytetracycline decreased more than three-fold in the LCM system. This study demonstrates the substantial potential and scalability of the LCM circular system within the agricultural domain.}, } @article {pmid40239498, year = {2025}, author = {Chen, M and Grégoire, DS and St-Germain, P and Berdugo-Clavijo, C and Hug, LA}, title = {Microbial diversity and capacity for arsenic biogeochemical cycling in aquifers associated with thermal mobilization.}, journal = {The Science of the total environment}, volume = {977}, number = {}, pages = {179357}, doi = {10.1016/j.scitotenv.2025.179357}, pmid = {40239498}, issn = {1879-1026}, abstract = {Thermal recovery technologies for in-situ bitumen extraction can result in the heating of surrounding aquifers, potentially mobilizing arsenic naturally present in the sediments to the groundwater. The relative toxicity of dissolved arsenic is related to its speciation, with As(V) being less toxic than As(III). Microorganisms have various mechanisms of arsenic detoxification and metabolism, which include genes for efflux, methylation, and reduction/oxidation of As(V)/As(III). We characterized the microbial communities along two aquifer transects associated with thermally mobilized arsenic near Northeastern Alberta oil sands deposits. 16S rRNA amplicons and metagenomic sequencing data of biomass from filtered groundwater indicated major changes in the dominant taxa between wells, especially those currently experiencing elevated arsenic concentrations. Annotation of arsenic-related genes indicated that efflux pumps (arsB, acr3), intracellular reduction (arsC) and methylation (arsM) genes were widespread among community members but comparatively few organisms encoded genes for arsenic respiratory reductases (arrA) and oxidases (arxA, aioA). While this indicates that microbes have the capacity to exacerbate arsenic toxicity by increasing the relative concentration of As(III), some populations of iron oxidizing and sulfate reducing bacteria (including novel Gallionella and Thermodesulfovibrionia populations) show potential for indirect bioremediation through formation of insoluble iron/sulfide minerals which adsorb or coprecipitate arsenic. An unusually high proportional abundance of a single Paceibacteria population that lacked arsenic resistance genes was identified in one high‑arsenic well, and we discuss hypotheses for its ability to persist. Overall, this study describes how aquifer microbial communities respond to thermal and arsenic plumes, and predicts potential contributions of microbes to arsenic biogeochemical cycling under this disturbance.}, } @article {pmid40238917, year = {2025}, author = {Trepka, KR and Kidder, WA and Kyaw, TS and Halsey, T and Olson, CA and Ortega, EF and Noecker, C and Upadhyay, V and Stanfield, D and Steiding, P and Guthrie, BGH and Spanogiannopoulos, P and Dumlao, D and Turnbaugh, JA and Stachler, MD and Van Blarigan, EL and Venook, AP and Atreya, CE and Turnbaugh, PJ}, title = {Expansion of a bacterial operon during cancer treatment ameliorates fluoropyrimidine toxicity.}, journal = {Science translational medicine}, volume = {17}, number = {794}, pages = {eadq8870}, doi = {10.1126/scitranslmed.adq8870}, pmid = {40238917}, issn = {1946-6242}, mesh = {Animals ; Humans ; *Operon/genetics ; *Fluorouracil/therapeutic use/toxicity/adverse effects ; Gastrointestinal Microbiome/drug effects/genetics ; Mice ; *Colorectal Neoplasms/drug therapy/microbiology ; *Pyrimidines/toxicity ; *Bacteria/genetics/drug effects ; RNA, Ribosomal, 16S/genetics ; Female ; Male ; }, abstract = {Dose-limiting toxicities remain a major barrier to drug development and therapy, revealing the limited predictive power of human genetics. Here, we demonstrate the utility of a more comprehensive approach to studying drug toxicity through longitudinal profiling of the human gut microbiome during colorectal cancer (CRC) treatment (NCT04054908) coupled to cell culture and mouse experiments. Substantial shifts in gut microbial community structure during oral fluoropyrimidine treatment across multiple patient cohorts, in mouse small and large intestinal contents, and in patient-derived ex vivo communities were revealed by 16S rRNA gene sequencing. Metagenomic sequencing revealed marked shifts in pyrimidine-related gene abundance during oral fluoropyrimidine treatment, including enrichment of the preTA operon, which was sufficient for the inactivation of active metabolite 5-fluorouracil (5-FU). preTA[+] bacteria depleted 5-FU in gut microbiota grown ex vivo and in the mouse distal gut. Germ-free and antibiotic-treated mice experienced increased fluoropyrimidine toxicity, which was rescued by colonization with the mouse gut microbiota, preTA[+] Escherichia coli, or preTA-high stool from patients with CRC. Last, preTA abundance was negatively associated with fluoropyrimidine toxicity in patients. Together, these data support a causal, clinically relevant interaction between a human gut bacterial operon and the dose-limiting side effects of cancer treatment. Our approach may be generalizable to other drugs, including cancer immunotherapies, and provides valuable insights into host-microbiome interactions in the context of disease.}, } @article {pmid40238748, year = {2025}, author = {da Silva-Álvarez, E and Gómez-Arrones, V and Correa-Fiz, F and Martín-Cano, FE and Gaitskell-Phillips, G and Carrasco, JJ and Rey, J and Aparicio, IM and Peña, FJ and Alonso, JM and Ortega-Ferrusola, C}, title = {Metagenomic and proteomic analyses reveal similar reproductive microbial profiles and shared functional pathways in uterine immune regulation in mares and jennies.}, journal = {PloS one}, volume = {20}, number = {4}, pages = {e0321389}, doi = {10.1371/journal.pone.0321389}, pmid = {40238748}, issn = {1932-6203}, mesh = {Animals ; Female ; Horses/microbiology/immunology ; *Uterus/microbiology/immunology/metabolism ; Proteomics/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Metagenomics ; Vagina/microbiology/immunology ; Bacteria/genetics/classification ; Proteome ; }, abstract = {This study aims to unveil potential differences in the vaginal and uterine microbiomes in mares and jennies, and to identify possible mechanisms involved in uterine immune homeostasis. The microbiota was characterized using 16S rRNA sequencing, and the uterine proteome was analyzed using UHPLC/MS/MS in 18 samples from healthy mares and 14 from jennies. While taxonomic analysis revealed high interspecies similarities, β-diversity analysis showed distinct clustering, with only two vaginal taxa and five uterine taxa differing between species. Despite compositional differences, PICRUSt analysis suggested minimal variations in predicted functional pathways across species. Comparing vaginal and uterine microbiota within the same species revealed overlapping bacterial taxa, but significant differences in α- and β-diversity and functional pathways. The uterine microbiota of both species was dominated by Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, with abundant taxa like Streptococcus, Pseudomonas, Bacillus, Corynebacterium, and Staphylococcus, many of which are frequently associated with endometritis. The presence of Lactobacillus in the equine reproductive tract was minimal or non-existent. KEGG functional pathway analysis predicted that uterine microbiota of both species utilize metabolic pathways with potential immunomodulatory effects. Proteomic enrichment analysis showed that numerous overexpressed uterine proteins in both species are linked to adaptive and innate immune regulation and defense mechanisms against symbionts. Gene enrichment analysis identified several enriched Gene Ontology terms, including response to bacterial stimuli, humoral immune regulation, and TGF-beta receptor signaling, underscoring microbial-host interactions. The uterine microbiota may play a vital role in maintaining immune balance. Further research is required to confirm its interaction with the uterine immune system and clarify the mechanisms involved.}, } @article {pmid40238740, year = {2025}, author = {Wang, J and Yin, J and Liu, X and Liu, Y and Jin, X}, title = {Gut commensal bacterium Bacteroides vulgatus exacerbates helminth-induced cardiac fibrosis through succinate accumulation.}, journal = {PLoS pathogens}, volume = {21}, number = {4}, pages = {e1013069}, doi = {10.1371/journal.ppat.1013069}, pmid = {40238740}, issn = {1553-7374}, mesh = {Animals ; *Succinic Acid/metabolism ; Mice ; Fibrosis ; *Gastrointestinal Microbiome/physiology ; *Trichinellosis/complications/metabolism/pathology ; *Trichinella spiralis ; *Bacteroides/metabolism ; Mice, Inbred C57BL ; Receptors, G-Protein-Coupled/metabolism ; Myocardium/pathology/metabolism ; Male ; }, abstract = {Trichinella spiralis (Ts) is known to cause cardiac fibrosis, which is a critical precursor to various heart diseases, and its progression is influenced by metabolic changes. However, the metabolic mechanisms remain unclear. Here, we observed that Ts-infected mice exhibited cardiac fibrosis along with elevated succinate levels in the heart using metabolomic analysis. Administration of succinate exacerbated fibrosis during Ts infection, while deficiency in succinate receptor 1 (Sucnr1) alleviated the condition, highlighting the role of the succinate-Sucnr1 axis in fibrosis development. Furthermore, metagenomics sequencing showed that Ts-infected mice had a higher abundance ratio of succinate-producing bacteria to succinate-consuming bacteria in the intestines. Notably, the succinate-producer Bacteroides vulgatus was enriched in Ts group. Oral supplementation with B. vulgatus aggravated Ts-induced cardiac fibrosis. In summary, our findings underscore the succinate-Sucnr1 axis as a critical pathway in helminth-induced cardiac fibrosis and highlight the potential of targeting this axis for therapeutic interventions. This study presents novel insights into the gut-heart axis, revealing innovative strategies for managing cardiovascular complications associated with helminth infections.}, } @article {pmid40238414, year = {2025}, author = {Magnano San Lio, R and Maugeri, A and Barchitta, M and Favara, G and La Rosa, MC and La Mastra, C and Agodi, A}, title = {Monitoring Antibiotic Resistance in Wastewater: Findings from Three Treatment Plants in Sicily, Italy.}, journal = {International journal of environmental research and public health}, volume = {22}, number = {3}, pages = {}, doi = {10.3390/ijerph22030351}, pmid = {40238414}, issn = {1660-4601}, support = {MUR-PNRR project SAMOTHRACE (ECS00000022)//European Union (NextGeneration EU)/ ; }, mesh = {*Wastewater/microbiology ; Sicily ; *Drug Resistance, Microbial/genetics ; *Environmental Monitoring ; *Drug Resistance, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; }, abstract = {Antimicrobial resistance (AMR) poses a global public health threat. Wastewater analysis provides valuable insights into antimicrobial resistance genes (ARGs), identifying sources and trends and evaluating AMR control measures. Between February 2022 and March 2023, pre-treatment urban wastewater samples were collected weekly from treatment plants in Pantano D'Arci, Siracusa, and Giarre (Sicily, Italy). Monthly composite DNA extracts were prepared by combining weekly subsamples from each site, yielding 42 composite samples-14 from each treatment plant. Real-time PCR analysis targeted specific ARGs, including blaSHV, erm(A), erm(B), blaOXA, blaNDM, blaVIM, blaTEM, and blaCTX-M. The preliminary findings revealed that blaERM-B, blaOXA, blaTEM, and blaCTX-M were present in all samples, with erm(B) (median value: 8.51; range: 1.67-30.93), blaSHV (0.78; 0.00-6.36), and blaTEM (0.72; 0.34-4.30) showing the highest relative abundance. These results underscore the importance of integrating ARG data with broader research to understand the persistence and proliferation mechanisms of ARGs in wastewater environments. Future studies should employ metagenomic analyses to profile resistomes in urban, hospital, agricultural, and farm wastewater. Comparing these profiles will help identify contamination pathways and inform the development of targeted ARG surveillance programs. Monitoring shifts in ARG abundance could signal cross-sectoral contamination, enabling more effective AMR control strategies.}, } @article {pmid40238256, year = {2025}, author = {Rueangsri, N and Roytrakul, S and Muangnoi, C and Tongkhao, K and Sae-Tan, S and Treesuwan, K and Sirivarasai, J}, title = {Metaproteomic Analysis of Fermented Vegetable Formulations with Lactic Acid Bacteria: A Comparative Study from Initial Stage to 15 Days of Production.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {7}, pages = {}, doi = {10.3390/foods14071148}, pmid = {40238256}, issn = {2304-8158}, support = {C02F660008//Mahidol University and the Office of National Higher Education Science Research and Innova-tion Policy Council through the Program Management Unit for Competitiveness, Thailand/ ; }, abstract = {Research in metagenomics and metaproteomics can reveal how microbiological interactions in fermented foods contribute to their health benefits. This study examined three types of fermented vegetables: a standard formulation, a probiotic formulation with Lacticaseibacillus rhamnosus GG, and a polyphenol formulation with vitexin from Mung bean seed coat. Measurements were taken at day 0 (after 36 h of fermentation at room temperature) and after 15 days. We applied 16S rRNA sequencing to evaluate microbial diversity and utilized LC-MS/MS to investigate the proteomic profiles of specific genera (Lactobacillus and Weissella) and species (Lacticaseibacillus rhamnosus and Levilactobacillus brevis) of lactic acid bacteria (LAB). All of these taxa demonstrated significant relative abundance between 0 and 15 days of fermentation in our metagenomic analysis. Our findings from principal component analysis and clustering analysis categorically distinguished protein expression patterns at various stages of fermentation. By comparing samples from day 0 to day 15, we identified proteins associated with DNA replication and repair mechanisms, including transcription elongation factor GreA, tRNA pseudouridine synthase B, and helicases. We also observed their roles in protein synthesis, which encompasses oxidoreductases and aspartokinase. Furthermore, we identified strong correlations of specific proteins across the three formulations with antioxidant markers. In conclusion, the results of this study decisively enhance our understanding of the role of the proteins related to specific LAB in fermented foods, highlighting their potential to improve texture, flavor, nutritional quality, and health benefits.}, } @article {pmid40238219, year = {2025}, author = {Cadamuro, RD and Elois, MA and Pilati, GVT and Savi, BP and Pessi, L and Jempierre, YFSH and Rodríguez-Lázaro, D and Fongaro, G}, title = {Role of Lysogenic Phages in the Dissemination of Antibiotic Resistance Genes Applied in the Food Chain.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {7}, pages = {}, doi = {10.3390/foods14071082}, pmid = {40238219}, issn = {2304-8158}, abstract = {Bacteriophages, first discovered in 1915, have re-emerged as critical players in microbial ecosystems, particularly in food production. Their ability to lysogenize bacterial hosts raises concerns about their role in the horizontal transfer of antibiotic resistance genes (ARGs) and virulence factors, contributing to the global challenge of antimicrobial resistance. Key studies reveal that ARG-carrying phages are prevalent across various stages of the food chain, including soil, vegetables, meat, dairy, and wastewater associated with food production. These findings demonstrate the potential for lysogenic phages to act as vectors for resistance gene dissemination, posing risks to public health. The review also explores emerging genetic elements, such as phage-inducible chromosomal islands and gene transfer agents, that further enhance the mobility of resistance and virulence genes. Advancements in metagenomic tools have improved our understanding of phage-mediated gene transfer, but significant knowledge gaps remain. Future research should aim to quantify these processes in real-world settings and develop strategies to mitigate the risks associated with lysogenic phages in food systems.}, } @article {pmid40238218, year = {2025}, author = {Zhadyra, S and Tao, F and Xu, P}, title = {Exploring the Microbiome and Functional Metabolism of Fermented Camel Milk (Shubat) Using Metagenomics.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {7}, pages = {}, doi = {10.3390/foods14071102}, pmid = {40238218}, issn = {2304-8158}, abstract = {Shubat is a traditional fermented camel milk drink that originated in Central Asia, with especially deep cultural roots in Kazakhstan. However, systematic studies on the microbial ecology and functional genes of Shubat remain scarce. As a distinctive fer-mented food, its microbial diversity and functional properties have not been fully ex-plored. This study investigates the microbial diversity and functional potential of Shubat by using advanced metagenomic techniques. Its microbial community is mainly composed of bacteria (96.6%), with Lactobacillus, Lactococcus, and Streptococcus being the dominant genera. Functional annotations through EggNOG, KEGG, and CAZy databases highlighted the metabolic versatility of Shubat's microbiota. Key pathways included amino acid and carbohydrate metabolism, vitamin biosynthesis, and central carbon metabolism, emphasizing their roles in fermentation and nutritional enhancement. The identification of various enzymes related to chemical synthesis further emphasizes the contribution of the microbiota to Shubat's unique flavor and texture. This study not only provides an important basis for the scientific understanding of Shubat but also expands the application possibilities of fermented food in the field of health and nutrition and confers modern value and significance to traditional food. This integration of science and tradition has not only facilitated the development of food microbiology but also paved new pathways for the global dissemination of traditional foods and the development of functional foods.}, } @article {pmid40238191, year = {2025}, author = {Ren, C and Zhao, M and Xue, T and Geng, T and Nie, X and Han, C and Wen, Y and Jia, L}, title = {Metagenomic and Physicochemical Analyses Reveal Microbial Community and Functional Differences Between Three Different Grades of Hongxin Low-Temperature Daqu.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {7}, pages = {}, doi = {10.3390/foods14071104}, pmid = {40238191}, issn = {2304-8158}, support = {202302140601016//Key R&D Program of Shanxi Province/ ; }, abstract = {Hongxin (HX) is an indispensable Daqu in the production of light-flavor Baijiu (LFB). However, the classification method of HX is highly subjective, and the classification and functional differences in microorganisms in different grades of HX are still unclear. In this study, metagenomics and physiochemical analysis were used to compare three grades of HX (top, first, second) and clarify their brewing functions in LFB. The results showed that a total of 1556 genera and 5367 species were detected in all samples. Bacteria and fungi are the main microorganisms in HX, and the relative abundance of bacteria and fungi is above 4.5:1. Kroppenstedtia (11.43%), Leuconostoc (10.52%), Fructilactobacillus (9.00%) were the top three genera in HX. Although the microbial community composition of the three grades of HX is highly similar, each HX has a specific microbial community structure and macrogene functional characteristics, indicating that they have different brewing functions. The dominant microorganisms in top-grade HX and first-grade HX were mainly positively correlated with energy metabolism and lipid metabolism, while the dominant microorganisms in second-grade HX were mainly positively correlated with carbohydrate metabolism and amino acid metabolism. This study revealed the different fermentation effects of different grades of HX in LFB and provided suggestions for the scientific classification and quality control of HX.}, } @article {pmid40238188, year = {2025}, author = {Ugarcina Perovic, S and Ramji, V and Chong, H and Duan, Y and Maguire, F and Coelho, LP}, title = {argNorm: normalization of antibiotic resistance gene annotations to the Antibiotic Resistance Ontology (ARO).}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btaf173}, pmid = {40238188}, issn = {1367-4811}, abstract = {SUMMARY: Currently available and frequently used tools for annotating antimicrobial resistance genes (ARGs) in genomes and metagenomes provide results using inconsistent nomenclature. This makes the comparison of different ARG annotation outputs challenging. The comparability of ARG annotation outputs can be improved by mapping gene names and their categories to a common controlled vocabulary such as the Antibiotic Resistance Ontology (ARO). We developed argNorm, a command line tool and Python library, to normalize all detected genes across 6 ARG annotation tools (8 databases) to the ARO. argNorm also adds information to the outputs using the same ARG categorization so that they are comparable across tools.

argNorm is available as an open-source tool at: https://github.com/BigDataBiology/argNorm. It can also be downloaded as a PyPI package and is available on Bioconda and as an nf-core module.}, } @article {pmid40237937, year = {2025}, author = {Maimaris, J and Payne, J and Roa-Bautista, A and Breuer, J and Storey, N and Morfopoulou, S and Bamford, A and D'Arco, F and Gilmour, K and Aquilina, K and Hassell, J and Hacohen, Y and Silva, AHD and Merve, A and Jacques, TS and Rao, K and Chiesa, R and Amrolia, P and Silva, J and Braggins, H and Xu-Bayford, J and Goldblatt, D and Worth, A and Booth, C and Ip, W and Qasim, W and Kusters, M and Kaliakatsos, M and Brown, JR and Elfeky, R}, title = {Safety and Diagnostic Utility of Brain Biopsy and Metagenomics in Decision-Making for Patients with Inborn Errors of Immunity (IEI) and Unexplained Neurological Manifestations.}, journal = {Journal of clinical immunology}, volume = {45}, number = {1}, pages = {86}, pmid = {40237937}, issn = {1573-2592}, support = {GN-000707//Brain Tumour Charity/ ; }, mesh = {Humans ; *Metagenomics/methods ; *Brain/pathology ; Male ; Biopsy ; Female ; Child, Preschool ; Infant ; Child ; Retrospective Studies ; *Nervous System Diseases/diagnosis/etiology ; Clinical Decision-Making ; Adolescent ; High-Throughput Nucleotide Sequencing ; }, abstract = {Unexplained neurological symptoms can pose a diagnostic challenge in patients with inborn errors of immunity (IEI) where the aetiology can be varied, and diverse pathologies may require contrasting treatments. Brain biopsy, the process of sampling brain tissue directly, has historically provided histological and microbiological information and can now be exploited for deep metagenomic next generation analysis (mNGS). We conducted a retrospective analysis of clinical and diagnostic data on paediatric patients with IEI who had a brain biopsy between 2010 and 2022 at a UK tertiary centre where 14 patients fulfilled our search criteria. We report on clinical characteristics, adverse events and the additional impact of mNGS of brain biopsies, where these were conducted. We found that brain biopsy enabled diagnostics with manageable complications in most cases, either by tissue or metagenomics analysis (n = 11/14, 79%). We found that mNGS analysis improved the diagnostic yield of brain biopsy in 29% of IEI cases (n = 4/14). Brain biopsy enabled a change in management in 71% of cases (n = 10/14). This series provides compelling evidence for the safe and purposeful use of brain biopsy in children with IEI.}, } @article {pmid40237802, year = {2025}, author = {Lei, W and Huang, R and Qu, L and Ma, K and Li, J}, title = {Exogenous Mogroside V Drove Microbial Carbohydrate Metabolism and Consequently Enhanced Fruity Aroma in Greengage Wine.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.4c10783}, pmid = {40237802}, issn = {1520-5118}, abstract = {The microbial community is essential for the formation of aroma development in high-acidity greengage wine fermentation. Recent observations also highlight positive effects of mogroside V (MG V) on microorganisms in fermented foods, but the underlying chemical and biological mechanisms remain inadequate. The results indicated differences in the physicochemical properties among greengage wines, particularly a 50% increase in the ethanol conversion rate. Concurrently, GC-MS and sensory analyses demonstrated that MG V augmented carbohydrate conversion into ethyl esters (twice as much as in the control group), exhibiting tropical fruit and floral aroma profiles. The perceived intensity of these aromatic compounds increased by over 30%, thereby enriching the overall aromatic harmony of the wine. Integrated analysis of KEGG pathways and CAZymes annotations demonstrated that the enhancement of ethyl ester formation by MG V depends on improvement of the transport of carbohydrates and MG V, as well as accelerating the flux of pyruvate to acetyl-CoA in yeast. In conclusion, our study presents a targeted strategy for the high-acidity fruit wine industry of modulating this metabolic node in yeast, thereby achieving a focused enhancement of tropical fruit aroma characteristics in fruit wines.}, } @article {pmid40237492, year = {2025}, author = {Hu, T and Meng, Y and Zhao, C and Sheng, D and Yang, S and Dai, J and Wei, T and Zhang, Y and Zhao, G and Liu, Y and Wang, Q and Zhang, L}, title = {Genome-scale metabolic modeling reveals specific vaginal Lactobacillus strains and their metabolites as key inhibitors of Candida albicans.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0298424}, doi = {10.1128/spectrum.02984-24}, pmid = {40237492}, issn = {2165-0497}, abstract = {As the predominant constituents of the vaginal microbiome in healthy women, Lactobacillus species are considered essential in maintaining a homeostatic vaginal microbiome. Specific Lactobacillus species can produce beneficial metabolites to support their persistence within the host environment and inhibit Candida albicans colonization. Due to the extensive diversity of Lactobacillus species and their metabolites, comprehensively investigating all possible interactions remains challenging. This study employed an integrative approach combining genome-scale metabolic modeling, metagenomic sequencing, and in vitro validation to explore Lactobacillus and C. albicans interactions. Pairwise simulations of 159 Lactobacillus strains with C. albicans revealed that most strains exhibit inhibitory effects, altering fungal amino acid and carbohydrate metabolism. Key inhibitory metabolites identified included formate, L-lactate, and L-malate. Metagenomic analysis of vaginal swabs from 20 vulvovaginal candidiasis (VVC) patients and 20 healthy women showed a correlation between Lactobacillus species abundance and reduced C. albicans colonization. In vitro experiments confirmed the inhibitory effects of these metabolites and the selected Lactobacillus strains on C. albicans growth, thereby validating our computational predictions. These findings provide insights into the metabolic interactions within the vaginal microbiome and pave the way for targeted microbial or metabolite-based therapeutic strategies to manage VVC.IMPORTANCEVulvovaginal candidiasis is a prevalent fungal infection with significant implications for women's health, caused primarily by Candida albicans. Although the protective role of a Lactobacillus-dominated vaginal microbiome is well established, the metabolic mechanisms underlying the interactions between Lactobacillus species and C. albicans remain inadequately understood. Specifically, the Lactobacillus species that effectively inhibit C. albicans and the metabolic pathways involved warrant further investigation. This study offers novel insights into the metabolic mechanisms underlying Lactobacillus antagonism against C. albicans. By identifying critical metabolic pathways and inhibitory metabolites, this study enhances our understanding of vaginal microbiome dynamics and host-microbe interactions. The findings suggest that key Lactobacillus strains and their metabolites could significantly reduce harmful levels of C. albicans, paving the way for future therapeutic strategies that leverage these microbial characteristics to promote vaginal health.}, } @article {pmid40237489, year = {2025}, author = {Rybicka, I and Kaźmierczak, Z}, title = {The human phageome: niche-specific distribution of bacteriophages and their clinical implications.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0178824}, doi = {10.1128/aem.01788-24}, pmid = {40237489}, issn = {1098-5336}, abstract = {Bacteriophages (phages) play a crucial role in shaping the composition and diversity of the human microbiome across various body niches. Recent advancements in high-throughput sequencing technologies have enabled comprehensive analysis of the human phageome in different body sites. This review comprehensively analyzes phage populations across major human body niches, examining their distribution and dynamics through recent metagenomic discoveries. We explore how phage-bacteria interactions within different body sites contribute to homeostasis and disease development. Emerging evidence demonstrates that phageome perturbations can serve as early indicators of various disorders, particularly in the gut microbiome. Understanding these complex microbial interactions offers promising opportunities for developing novel diagnostic markers and therapeutic approaches. However, the causal relationship between phages, bacteria, and disease development remains unclear. Further research is needed to elucidate the role of phages in human health and disease and to explore their potential as diagnostic or therapeutic tools. Understanding the intricate interactions between phages, bacteria, and the human host is crucial for unraveling the complexities of the human microbiome and its impact on health and disease.}, } @article {pmid40237482, year = {2025}, author = {Zhang, C and Bosma, TNP and Atashgahi, S and Smidt, H}, title = {Genome-resolved transcriptomics reveals novel PCE-dehalogenating bacteria from Aarhus Bay sediments.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0150324}, doi = {10.1128/msystems.01503-24}, pmid = {40237482}, issn = {2379-5077}, abstract = {Organohalide-respiring bacteria (OHRB) are keystone microbes in bioremediation of sites contaminated with organohalides and in natural halogen cycling. Known OHRB belong to distinct genera within the phyla Chloroflexota, Proteobacteria, and Firmicutes, whereas information about novel OHRB mediating natural halogen cycling remains scarce. In this study, we applied a genome-resolved transcriptomic approach to characterize the identity and activity of OHRB from tetrachloroethene respiring cultures previously enriched from sediments of Aarhus Bay. Combining short- and long-read sequencing approaches, we assembled 37 medium-quality bins with over 75% completeness and less than 5% contamination. Sixteen bins harbored RDase genes and were affiliated taxonomically to the class of Bacilli and phyla of Bacteroidota, Synergistota, and Spirochaetota, which have not been reported to catalyze reductive dehalogenation. Among the 16 bins, bin.26, phylogenetically close to the genus Vulcanibacillus (phylum Firmicutes), contained an unprecedented 97 reductive dehalogenase (RDase) genes. Of these, 84 RDase genes of bin.26 were transcribed during tetrachloroethene dechlorination in addition to RDase genes from the members of Synergistales (bin.5 and bin.32) and Bacteroidales (bin.18 and bin.24). Moreover, metatranscriptome analysis suggested that the RDase genes were likely under the regulation of transcriptional regulators not previously associated with organohalide respiration, such as HrcA and SigW, which are known to respond to abiotic environmental stresses, such as temperature changes. Combined application of genomic methods enabled us to pinpoint novel OHRB from pristine environments not previously known to mediate reductive dechlorination and to add to the current knowledge of the diversity, activity, and regulation of RDase genes.IMPORTANCEPristine marine environment is the major reservoir for naturally produced organohalides, in which reductive dehalogenation underneath plays an important role in the overall cycling of these compounds. Here, we obtain some novel OHRB genomes from Aarhus Bay marine sediments, which are phylogenetically distant to the well-documented OHRB and widely distributed across the bacterial phyla, such as Bacteroidota, Synergistota, and Spirochaetota. Furthermore, transcriptional profiles unravel that these RDase genes are induced differently, and their activity is controlled by diverse regulatory systems. Accordingly, elucidating the reductive dehalogenation of pristine marine environments substantially advances our understanding of the diversity, phylogeny, and regulatory variety of dehalogenating bacteria contributing to the global halogen cycle.}, } @article {pmid40237336, year = {2025}, author = {Naspolini, NF and Schüroff, PA and Vanzele, PAR and Pereira-Santos, D and Valim, TA and Bonham, KS and Fujita, A and Passos-Bueno, MR and Beltrão-Braga, PCB and Carvalho, ACPLF and Klepac-Ceraj, V and Polanczyk, GV and Campos, AC and Taddei, CR}, title = {Exclusive breastfeeding is associated with the gut microbiome maturation in infants according to delivery mode.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2493900}, doi = {10.1080/19490976.2025.2493900}, pmid = {40237336}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; Infant ; *Breast Feeding ; Female ; *Bacteria/classification/genetics/isolation & purification ; Male ; Brazil ; Feces/microbiology ; Metagenomics ; *Delivery, Obstetric/methods ; Cohort Studies ; Infant, Newborn ; }, abstract = {Exclusive breastfeeding (EBF) plays a crucial role in infant gut microbiome assembly and development. However, few studies have investigated the effects of EBF in restoring a perturbed microbiome. In this study, we applied whole metagenomic sequencing to assess the gut microbiome assembly in 525 Brazilian infants from 3 to 9 months of age of the Germina Cohort, demonstrating the early determinants of microbial taxonomy and function modulation. Our analysis shows that EBF alters the relative abundance of genes related to the microbiome taxonomy and function, with effects varying by delivery mode. EBF alters the pattern of carbohydrates, lipid metabolism, and cell structure pathways depending on the delivery mode. The microbiome age is closer to chronological infant age in EBF than in non-EBF infants, meaning a lower microbiome maturation index (MMI). Using a complementary machine learning approach, we show that Escherichia coli, Ruminococcus gnavus, and Clostridium neonatale, as well as vitamin K and o-antigen pathways contribute strongly to EBF prediction. Moreover, EBF influences the microbiome maturation in early life, toward a microbiome age more similar to the chronological infant's age.}, } @article {pmid40236771, year = {2025}, author = {Liu, W and Lau, HCH and Ding, X and Yin, X and Wu, WKK and Wong, SH and Sung, JJY and Zhang, T and Yu, J}, title = {Transmission of antimicrobial resistance genes from the environment to human gut is more pronounced in colorectal cancer patients than in healthy subjects.}, journal = {iMeta}, volume = {4}, number = {2}, pages = {e70008}, pmid = {40236771}, issn = {2770-596X}, abstract = {Antimicrobial resistance is a major global health concern. However, the source of gut resistome remains unsolved. We aimed to analyze the contribution of environmental antimicrobial resistance genes (ARGs) to colorectal cancer (CRC) patients. Here, we collected metagenomic data from 1,605 human stool samples (CRC = 748; healthy = 857) and 1,035 city-matched environmental samples, in which 110 CRC, 112 healthy, and 56 environmental samples were newly collected. Compared to healthy subjects, CRC patients had significantly higher ARG burden (p < 0.01) with increased levels of multidrug-resistant ARGs. Gut ARGs in CRC also had a closer similarity to environmental ARGs (p < 0.001). By comparing environmental and gut ARGs, 28 environmental ARGs were identified as CRC-specific ARGs, including SUL2 and MEXE, which were not identified in healthy subjects. Meanwhile, more mobile ARGs (mARGs) from the environment were observed in CRC patients compared to healthy subjects (p < 0.05). The hosts of mARGs were mainly pathogenic bacteria (e.g., Escherichia coli (E. coli) and Clostridium symbiosum (C. symbiosum)). Compared to healthy subjects, CRC patients showed elevated horizontal gene transfer efficiency from the environment to gut. Consistently, the abundance of pathobionts carrying specific mARGs (e.g., E. coli-SUL2 and C. symbiosum-SUL2) were significantly increased in CRC patients compared to healthy subjects (p < 0.05). We thus reveal a route of ARG dissemination from the environment into the gut of CRC patients.}, } @article {pmid40236770, year = {2025}, author = {Zhang, C and Chen, Y and Duan, R and Zhang, Y and Zheng, H and Zhang, J and Zhang, T and Xu, J and Li, K and Pei, F and Duan, L}, title = {Preconception maternal gut dysbiosis affects enteric nervous system development and disease susceptibility in offspring via the GPR41-GDNF/RET/SOX10 signaling pathway.}, journal = {iMeta}, volume = {4}, number = {2}, pages = {e70012}, pmid = {40236770}, issn = {2770-596X}, abstract = {Maternal health, specifically changes in the gut microbiota, can profoundly impact offspring health; however, our understanding of how gut microbiota alterations during the preconception period influence the offspring remains limited. In this study, we investigated the impact and mechanisms of preconception maternal gut dysbiosis on the development of the enteric nervous system (ENS) in mice. We found that preconception maternal exposure to antibiotics led to the abnormal development of the ENS in offspring, increasing their susceptibility to water avoidance stress at the adult stage. Metagenomic, targeted metabolomic, and transcriptomic analyses revealed that preconception antibiotic exposure disrupted the expression of genes crucial for embryonic ENS development by altering maternal gut microbiota composition. Multi-omics analysis combined with Limosilactobacillus reuteri and propionate gestational supplementation demonstrated that the maternal gut microbiota and metabolites may influence embryonic ENS development via the GPR41-GDNF/RET/SOX10 signaling pathway. Our findings highlight the critical importance of maintaining a healthy maternal gut microbiota before conception to support normal ENS development in offspring.}, } @article {pmid40236767, year = {2025}, author = {Huang, L and Wang, P and Liu, S and Deng, G and Qi, X and Sun, G and Gao, X and Zhang, L and Zhang, Y and Xiao, Y and Gao, T and Maitiabula, G and Wang, X}, title = {Gut microbiota-derived tryptophan metabolites improve total parenteral nutrition-associated infections by regulating Group 3 innate lymphoid cells.}, journal = {iMeta}, volume = {4}, number = {2}, pages = {e70007}, pmid = {40236767}, issn = {2770-596X}, abstract = {Clinical nutritional support is recognized by Klinefner's Surgery as one of the four pivotal advancements in surgical practice during the 20th century. Surgeons regard clinical nutrition as a "life-saving" discipline, pivotal in preserving the lives of numerous critically ill patients and facilitating the success of many surgical procedures. Parenteral nutrition (PN) support serves as a crucial component of clinical nutritional therapy, while a range of complications associated with total parenteral nutrition (TPN) can significantly undermine the efficacy of patient treatment. Impaired intestinal homeostasis is strongly associated with the occurrence and progression of TPN-related infections, yet the underlying mechanisms remain poorly understood. In this study, RNA sequencing and single-cell RNA sequencing (scRNA-Seq) revealed that reduced secretion of interleukin-22 (IL-22) by intestinal Group 3 innate lymphoid cells (ILC3s) is a significant factor contributing to the onset of TPN-related infections. Additionally, through 16S ribosomal RNA (16S rRNA) gene sequencing of the gut microbiota from patients with chronic intestinal failure and metagenomic sequencing analysis of the gut microbiota from mice, we observed that TPN reduced the abundance of Lactobacillus murinus (L. murinus), while supplementation with L. murinus could promote IL-22 secretion by ILC3s. Mechanistically, L. murinus upregulates indole-3-carboxylic acid, which activates the nuclear receptor Rorγt to stimulate IL-22 secretion by ILC3s. This pathway strengthens gut barrier integrity and reduces infection susceptibility. Our findings enhance our understanding of the mechanisms driving the onset of TPN-related infections, highlighting the critical role of gut microbiota in maintaining immune homeostasis and improving clinical outcomes.}, } @article {pmid40236616, year = {2025}, author = {Lu, Y and Zhang, C and Wu, J and Xu, X and Lu, A and Huang, H and Chen, M}, title = {Explore the Application Value of Metagenomic Next-Generation Sequencing of Bronchoalveolar Lavage Fluid in the Early Diagnosis of Pulmonary Tuberculosis.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {1837-1845}, pmid = {40236616}, issn = {1178-6973}, abstract = {OBJECTIVE: Compare the diagnostic efficacy of bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) with that of four traditional methods in the diagnosis of pulmonary tuberculosis (PTB), and explore the application value of BALF mNGS in the early diagnosis of PTB.

METHODS: A retrospective analysis was performed on 102 patients with suspected PTB in Wuming Hospital Affiliated with Guangxi Medical University from January 2021 to August 2024, among which 61 cases were PTB and 41 cases were non - PTB. Diagnostic performance metrics (sensitivity, specificity, positive/negative predictive value [PPV/NPV], accuracy) were calculated for BALF mNGS, sputum TB-DNA, sputum acid-fast bacilli (AFB) smear, BALF AFB smear, and BALF TB-DNA, using clinical diagnosis as the reference standard.

RESULTS: BALF mNGS demonstrated a sensitivity of 75.41% (46/61), specificity of 87.80% (36/41), PPV of 90.20% (46/51), NPV of 70.59% (36/51), and accuracy of 80.39% (82/102). Its accuracy was significantly higher than sputum-based methods (53.03-58.82%, P < 0.0125) and second only to BALF TB-DNA (84.13%, P > 0.0125). BALF mNGS exhibited superior sensitivity compared to sputum TB-DNA (38.00%), sputum AFB smear (41.67%), and BALF AFB smear (41.50%) (P < 0.0125). While specificity and PPV showed no significant differences among methods, BALF mNGS had a higher NPV than sputum-based assays (53.03-54.17%) but lower than BALF TB-DNA (82.53%, P < 0.0125). Both BALF mNGS (Kappa = 0.608, P < 0.001) and BALF TB-DNA (Kappa = 0.670, P < 0.001) showed strong concordance with clinical diagnosis.

CONCLUSION: BALF mNGS demonstrates high sensitivity and accuracy for PTB diagnosis, outperforming conventional sputum-based methods. Although BALF TB-DNA achieved the highest specificity and NPV, BALF mNGS serves as a robust supplementary tool, particularly for early-stage or paucibacillary PTB. Integration of these molecular techniques may optimize diagnostic workflows in high-TB-burden settings.}, } @article {pmid40236150, year = {2025}, author = {Bommana, S and Olagoke, S and Hu, Y and Wang, R and Kama, M and Dehdashti, M and Kodimerla, R and Read, T and Dean, D}, title = {Effect of Azithromycin treatment on the microbial composition, functional dynamics and resistomes of endocervical, vaginal and rectal microbiomes of women in Fiji with Chlamydia trachomatis infection.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.04.02.646699}, pmid = {40236150}, issn = {2692-8205}, abstract = {Antibiotics disrupt mucosal microbial communities, yet the effects on microbiomes with Chlamydia trachomatis (Ct) infection remain poorly understood. Some data exist on vaginal microbiomes pre- and post-treatment, but none are available for the endocervix or rectum that are primary sites of infection. We applied metagenomic shotgun sequencing to vaginal, endocervical and rectal samples from women who, overtime, had Ct persistence, clearance, or no infection to evaluate azithromycin-induced changes in microbial composition, function, and the resistome. Our results show a shift in composition and function that support Ct post-treatment with azithromycin resistance mutations in the Ct rplV gene and significant endocervical enrichment of azithromycin resistance genes in Lactobacillus iners and Gardnerella vaginalis, the strains of which have moderate/high potential for biofilm formation. These findings highlight the unintended ecological consequences of azithromycin, including resistance gene propagation and microbiome shifts that support persistent/recurrent Ct, emphasizing the need for novel treatment and microbiome-preserving strategies.}, } @article {pmid40235649, year = {2025}, author = {Mohamed, AYA and Gill, L and Monleon, A and Pronk, M and van Loosdrecht, M and Saikaly, PE and Ali, M}, title = {Genome-resolved metatranscriptomics unveils distinct microbial functionalities across aggregate sizes in aerobic granular sludge.}, journal = {Environmental science and ecotechnology}, volume = {25}, number = {}, pages = {100560}, pmid = {40235649}, issn = {2666-4984}, abstract = {Microbial aggregates of different sizes in aerobic granular sludge (AGS) systems have been shown to exhibit distinct microbial community compositions. However, studies comparing the microbial activities of different-sized aggregates in AGS systems remain limited. In this study, genome-resolved metatranscriptomics was used to investigate microbial activity patterns within differently sized aggregates in a full-scale AGS plant. Our analysis revealed a weak correlation between the relative abundance of metagenome-assembled genomes (MAGs) and their transcriptomic activity, indicating that microbial abundance does not directly correspond to metabolic activity within the system. Flocculent sludge (FL; <0.2 mm) predominantly featured active nitrifiers and fermentative polyphosphate-accumulating organisms (PAOs) from Candidatus Phosphoribacter, while small granules (SG; 0.2-1.0 mm) and large granules (LG; >1.0 mm) hosted more metabolically active PAOs affiliated with Ca. Accumulibacter. Differential gene expression analysis further supported these findings, demonstrating significantly higher expression levels of key phosphorus uptake genes associated with Ca. Accumulibacter in granular sludge (SG and LG) compared to flocculent sludge. Conversely, Ca. Phosphoribacter showed higher expression of these genes in the FL fraction. This study highlights distinct functional roles and metabolic activities of crucial microbial communities depending on aggregate size within AGS systems, offering new insights into optimizing wastewater treatment processes.}, } @article {pmid40234711, year = {2025}, author = {Wu, M and Liu, X and Musat, F and Guo, J}, title = {Microbial oxidation of short-chain gaseous alkanes.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {40234711}, issn = {2058-5276}, abstract = {Short-chain gaseous alkanes (SCGAs), including ethane, propane and butane, are major components of natural gas and their atmospheric emissions impact global air quality and tropospheric chemistry. Many microbial taxa can degrade SCGAs aerobically and anaerobically to CO2, acting as the major biological sink of these compounds and reducing their negative impacts on climate. Environmental metagenomics and cultivation efforts have expanded our understanding of SCGA-oxidizing microorganisms. In this Review, we discuss recent discoveries in the diversity, physiology and metabolism of aerobic and anaerobic SCGA-oxidizing microorganisms, highlight their climate implications and discuss how knowledge of these processes can help develop biotechnologies for environmental remediation and value-added chemical production.}, } @article {pmid40234093, year = {2025}, author = {Block, MS and Nelson, GD and Chen, J and Johnson, S and Yang, L and Flotte, TJ and Grewal, EP and McWilliams, RR and Kottschade, LA and Domingo-Musibay, E and Markovic, SN and Dimou, A and Montane, HN and Piltin, MA and Price, DL and Khariwala, SS and Hui, JYC and Erskine, CL and Strand, CA and Zahrieh, D and Dong, H and Hieken, TJ}, title = {Neoadjuvant cobimetinib and atezolizumab with or without vemurafenib for stage III melanoma: outcomes and the impact of the microbiome from the NeoACTIVATE trial.}, journal = {Journal for immunotherapy of cancer}, volume = {13}, number = {4}, pages = {}, doi = {10.1136/jitc-2025-011706}, pmid = {40234093}, issn = {2051-1426}, mesh = {Humans ; *Melanoma/drug therapy/pathology/mortality ; Female ; Male ; *Azetidines/therapeutic use/pharmacology ; *Antibodies, Monoclonal, Humanized/pharmacology/therapeutic use ; Middle Aged ; *Antineoplastic Combined Chemotherapy Protocols/therapeutic use/pharmacology ; *Neoadjuvant Therapy/methods ; *Piperidines/pharmacology/therapeutic use ; *Vemurafenib/pharmacology/therapeutic use ; Aged ; Neoplasm Staging ; Adult ; Gastrointestinal Microbiome ; Treatment Outcome ; *Skin Neoplasms/drug therapy ; }, abstract = {BACKGROUND: Neoadjuvant treatment has become standard for patients with high-risk operable stage III melanoma, but the optimal regimen is unknown. Targeted therapy approaches yield high pathological response rates, while immunotherapy regimens show favorable recurrence-free survival (RFS). NeoACTIVATE was designed to address whether a neoadjuvant combination of both targeted therapy and immunotherapy might leverage the benefits of each.

METHODS: We tested neoadjuvant treatment with 12 weeks of vemurafenib, cobimetinib, and atezolizumab for patients with BRAF-mutated (BRAFm) melanoma (cohort A) and cobimetinib and atezolizumab for patients with BRAF-wild-type (BRAFwt) melanoma (cohort B), regimens which we have shown generate a substantial major pathological response. After therapeutic lymph node dissection, patients received 24 weeks of adjuvant atezolizumab. Here, we report survival outcomes and their association with biomarkers assayed among the gut microbiome and peripheral blood immune subsets.

RESULTS: With 49 months median follow-up, the median RFS was not reached for cohort A and was 40.8 months for cohort B. At 24 months after operation, 2 of 14 cohort A patients and 4 of 13 cohort B patients had experienced distant relapse. Key findings from correlative analyses included diversity, taxonomic and functional metagenomic gut microbiome signals associated with distant metastasis-free survival at 2 years. Notably, we observed a strong correlation between low microbial arginine biosynthesis (required for T-cell activation and effector function) and early distant recurrence (p=0.0005), which correlated with taxonomic differential abundance findings. Peripheral blood immune monitoring revealed increased double-positive (CD4+CD8+) T cells in patients with early recurrence.

CONCLUSIONS: Neoadjuvant treatment with cobimetinib and atezolizumab±vemurafenib was associated with a low rate of distant metastasis in patients with high-risk stage III melanoma. Freedom from early distant metastasis was highly associated with taxonomic differences in gut microbiome structure and with functional pathway alterations known to modulate T cell immunity. Identification of predictive biomarkers will permit optimization of neoadjuvant therapy regimens for individual patients.

TRIAL REGISTRATION NUMBER: NCT03554083.}, } @article {pmid40233994, year = {2025}, author = {Jenkins, R and Samec, M and Arment, C and Warrington, KJ and Davis, JM and Koster, MJ}, title = {Use of Metagenomic Microbial Plasma Cell-Free DNA Next-Generation Sequencing Assay in Outpatient Rheumatology Practice.}, journal = {The Journal of rheumatology}, volume = {}, number = {}, pages = {}, doi = {10.3899/jrheum.2024-1211}, pmid = {40233994}, issn = {1499-2752}, abstract = {OBJECTIVE: To assess the utility of a metagenomic microbial plasma cell-free DNA next-generation sequencing assay (Karius TestTM; KT) in the evaluation of patients in an outpatient rheumatology practice.

METHODS: All patients with a KT ordered and obtained by a rheumatology provider in the outpatient setting from 1 January 2020 through 31 December 2022 were retrospectively identified. Demographic, clinical, laboratory, radiologic, histopathology, and microbial studies were abstracted. Indication for KT testing was categorized. KT results were defined based on positive result and clinical relevance regarding the symptoms under investigation at the time of the rheumatologic investigation. Review of cases three months after KT was undertaken to determine clinical outcome.

RESULTS: 150 patients with a KT were included (52.7% female, mean age 52 years). The reason for KT was evaluation of atypical presentation of rheumatic disease (80.0%), assessing flare versus infection in patient on immunosuppression (16.7%), and fever of unknown origin (3.3%). 24 (16.0%) KTs were positive, six of which were considered clinically relevant and altered the final diagnosis and treatment. Of the 126 negative KTs, 5 (4.0%) were found to have a clinically relevant infection by conventional testing methodologies.

CONCLUSION: In this large retrospective cohort study, the most frequent reason for KT utilization was an atypical presentation of rheumatic disease. Twenty-five percent of positive KTs altered the final diagnosis and treatment, whereas a false-negative rate of 4.0% was observed. KT has utility in the outpatient rheumatology assessment. Further delineation of which patients are best suited for KT testing remains to be defined.}, } @article {pmid40233938, year = {2025}, author = {Kolokotronis, SO and Bhattacharya, C and Panja, R and Quate, I and Seibert, M and Jorgensen, E and Mason, CE and Hénaff, EM}, title = {Metagenomic interrogation of urban Superfund site reveals antimicrobial resistance reservoir and bioremediation potential.}, journal = {Journal of applied microbiology}, volume = {136}, number = {4}, pages = {}, doi = {10.1093/jambio/lxaf076}, pmid = {40233938}, issn = {1365-2672}, support = {80NSSC24K0728/NASA/NASA/United States ; R01AI125416/NH/NIH HHS/United States ; 1758800//National Science Foundation/ ; }, mesh = {Biodegradation, Environmental ; Metagenomics ; *Microbiota/genetics ; Metals, Heavy/metabolism ; *Geologic Sediments/microbiology ; *Bacteria/genetics/metabolism/drug effects/isolation & purification/classification ; Water Pollutants, Chemical/metabolism ; Polychlorinated Biphenyls/metabolism ; *Drug Resistance, Bacterial/genetics ; Metagenome ; }, abstract = {AIMS: We investigate the bioremediation potential of the microbiome of the Gowanus Canal, a contaminated waterway in Brooklyn, NY, USA, designated a Superfund site by the US Environmental Protection Agency due to high concentrations of contaminants, including polychlorinated biphenyls, petrochemicals, and heavy metals.

METHODS AND RESULTS: We present a metagenomic analysis of the Gowanus Canal sediment, consisting of a longitudinal study of surface sediment and a depth-based study of sediment core samples. We demonstrate that the resident microbiome includes 455 species, including extremophiles across a range of saltwater and freshwater species, which collectively encode 64 metabolic pathways related to organic contaminant degradation and 1171 genes related to heavy metal utilization and detoxification. Furthermore, our genetic screening reveals an environmental reservoir of antimicrobial resistance markers falling within 8 different classes of resistance, as well as de-novo characterization of 2319 biosynthetic gene clusters and diverse groups of secondary metabolites with biomining potential.

CONCLUSION: The microbiome of the Gowanus Canal is a biotechnological resource of novel metabolic functions that could aid in efforts for bioremediation, AMR reservoir mapping, and heavy metal mitigation.}, } @article {pmid40037519, year = {2025}, author = {Jawale, N and Shenberger, JS and Rodriguez, RJ and Shetty, AK and Garg, PM}, title = {The Nonbacterial Infant Microbiome and Necrotizing Enterocolitis.}, journal = {American journal of perinatology}, volume = {}, number = {}, pages = {}, doi = {10.1055/a-2549-6551}, pmid = {40037519}, issn = {1098-8785}, support = {U54GM115428/GM/NIGMS NIH HHS/United States ; U54GM115428//NIGMS of the NIH/ ; }, abstract = {Necrotizing enterocolitis (NEC) is among the most devastating neonatal illnesses of premature infants. Although it is a disease of multifactorial etiology associated with bacterial dysbiosis, several reports of viral and some fungal infections associated with NEC have been published. Despite the abundance of viruses-primarily bacteriophages, and "virus-like particles" in the normal infant gut flora, there is limited understanding of the contribution of these elements to newborn gut health and disease. This study aims to review existing evidence on normal newborn virome and mycobiome development and present insights into the complex inter-kingdom interactions between gut bacteria, viruses, and fungi in the intestinal ecosystem, exploring their potential role in predisposing the preterm infant to NEC. · We have reviewed a number of viral and fungal infections reported in association with NEC-like illnesses.. · Bacteriophages play a crucial role in the gut microbiome development, but their role in pathogenesis of NEC and potential for therapeutic use is unknown.. · Development of next-gen metagenomic tools are needed to enhance our understanding of viral diversity, bacteriophages, and the gut virome in the context of neonatal health and disease..}, } @article {pmid40233768, year = {2025}, author = {Tinker, KA and Anthony, W and Brandi, M and Flett, S and Bagwell, CE and Smallwood, C and Davis, R and Gulliver, D}, title = {Identifying Potential Geochemical and Microbial Impacts of Hydrogen Storage in a Deep Saline Aquifer.}, journal = {Environmental microbiology reports}, volume = {17}, number = {2}, pages = {e70076}, doi = {10.1111/1758-2229.70076}, pmid = {40233768}, issn = {1758-2229}, support = {//U.S. Department of Energy's (DOE) Office of Fossil Energy and Carbon Management's Hydrogen with Carbon Management Program and executed through the National Energy Technology Laboratory (NETL) Research & Innovation Center's Natural Gas Decarbonization and Hydrogen Technologies Multi-Year Research Plan/ ; }, mesh = {*Hydrogen/metabolism ; *Groundwater/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Illinois ; Methane/metabolism ; Microbiota ; Metagenomics ; }, abstract = {Hydrogen is valuable commodity and a promising energy carrier for variable energy production. Storage of hydrogen may occur through injection of hydrogen or a hydrogen/methane gas blend in subsurface reservoirs. However, the geochemical and biological reactions that may impact the stored hydrogen are not yet understood. Therefore, we collected samples from a deep storage aquifer located in the St. Peter Formation in southern Illinois. The reservoir material was primarily quartz with sulphur and iron deposits, while the major constituents of the fluid were chloride and sulphate. 16S rRNA gene amplicon sequencing revealed a low biomass microbial community that contained no obvious hydrogen-consuming bacteria. Next, we enriched a field sample to increase the biomass and completed a metagenomic analysis, finding a low number of genes present that are associated with hydrogen consumption. Then, we completed a series of reactor experiments under reservoir conditions with 15% H2/85% CH4 gas simulating a short-term hydrogen storage, high withdrawal scenario. We found minimal changes in the geochemistry or microbiology for the reactor experiments. This work suggests that short-term storage may be highly successful, although significant additional work needs to be completed in order to accurately evaluate the risks associated with long-term hydrogen storage scenarios. It is essential we continue to expand our understanding of the dynamics present in saline aquifers and provide new insights into how hydrogen storage may impact underground geological storage environments.}, } @article {pmid40233618, year = {2025}, author = {Fan, C and Hou, D and Zhang, L and Li, C and Chen, L and Zhang, P and Wu, Y and Zou, J}, title = {Bioaugmentation using HN-AD consortia for high salinity wastewater treatment: Synergistic effects of halotolerant bacteria and nitrogen removal bacteria.}, journal = {Journal of environmental management}, volume = {381}, number = {}, pages = {125355}, doi = {10.1016/j.jenvman.2025.125355}, pmid = {40233618}, issn = {1095-8630}, abstract = {Bioaugmentation shows promise in enhancing nitrogen removal efficiency of high-salt wastewater, yet the impact of microbial associations on ecosystem function and community stability remains unclear. This study innovatively introduced a novel heterotrophic nitrification-aerobic denitrification bacterial consortium to improve the performance of SBR reactor for removing nitrogen from saline wastewater. The results revealed that the bioaugmented reactor (R2) exhibited superior removal performance, achieving maximum removal efficiencies of 87.8 % for COD and 97.8 % for NH4[+]-N. Moreover, proper salinity (2 % and 4 %) promoted the secretion of EPS and ectoine, further enhancing the resistance and stability of bacterial consortia. 16S rRNA gene sequencing and metagenomics analysis revealed the key denitrifying bacteria Pseudomonas and salt-tolerant bacteria Halomonas were successfully coexistence and the relative abundances of crucial genes (napB, nirS, norB, norC and nosZ) were increased obviously, which were benefit for the excellent nitrogen removal performance in R2. These findings elucidate microbial interactions in response to salinity in bioaugmentation, providing a valuable reference for the efficient treatment of high-saline wastewater.}, } @article {pmid40233040, year = {2025}, author = {Pomej, K and Frick, A and Scheiner, B and Balcar, L and Pajancic, L and Klotz, A and Kreuter, A and Lampichler, K and Regnat, K and Zinober, K and Trauner, M and Tamandl, D and Gasche, C and Pinter, M}, title = {Study protocol: Fecal Microbiota Transplant combined with Atezolizumab/Bevacizumab in Patients with Hepatocellular Carcinoma who failed to achieve or maintain objective response to Atezolizumab/Bevacizumab - the FAB-HCC pilot study.}, journal = {PloS one}, volume = {20}, number = {4}, pages = {e0321189}, doi = {10.1371/journal.pone.0321189}, pmid = {40233040}, issn = {1932-6203}, mesh = {Humans ; *Liver Neoplasms/therapy/drug therapy ; *Carcinoma, Hepatocellular/therapy/drug therapy ; Pilot Projects ; *Fecal Microbiota Transplantation/methods ; *Bevacizumab/therapeutic use/administration & dosage ; *Antibodies, Monoclonal, Humanized/therapeutic use/administration & dosage ; Male ; Female ; Gastrointestinal Microbiome ; Middle Aged ; *Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; Aged ; }, abstract = {BACKGROUND: The gut microbiota is often altered in chronic liver diseases and hepatocellular carcinoma (HCC), and increasing evidence suggests that it may influence response to cancer immunotherapy. Strategies to modulate the gut microbiome (i.e., fecal microbiota transplant (FMT)) may help to improve efficacy of immune checkpoint inhibitors (ICIs) or even overcome resistance to ICIs. Here, we describe the design and rationale of FAB-HCC, a single-center, single-arm, phase II pilot study to assess safety, feasibility, and efficacy of FMT from patients with HCC who responded to PD-(L)1-based immunotherapy or from healthy donors to patients with HCC who failed to achieve or maintain a response to atezolizumab plus bevacizumab.

METHODS: In this single-center, single-arm, phase II pilot study (ClinicalTrials.gov identifier: NCT05750030), we plan to include 12 patients with advanced HCC who failed to achieve or maintain a response to atezolizumab/bevacizumab. Patients will receive a single FMT via colonoscopy from donors with HCC who responded to PD-(L)1-based immunotherapy or from healthy individuals, followed by atezolizumab/bevacizumab every 3 weeks. The primary endpoint is safety, measured by incidence and severity of treatment-related adverse events. The main secondary endpoint is efficacy, as assessed by best radiological response according to RECISTv1.1 and mRECIST. Additional exploratory endpoints include data on the effect of FMT on recipient gut microbiota, as well as metagenomic analysis of stool samples, analyses of circulating immune cells and serum and stool proteomic, metabolomic and lipidomic signatures.

DISCUSSION: The results of this study will help to define the potential of FMT as add-on intervention in the systemic treatment of advanced HCC, with the potential to improve efficacy of immunotherapy or even overcome resistance.

TRIAL REGISTRATION: EudraCT Number: 2022-000234-42 Clinical trial registry & ID: ClinicalTrials.gov identifier: NCT05750030 (Registration date: 16.01.2023).}, } @article {pmid40232948, year = {2025}, author = {Leech, SM and Barrett, HL and Dorey, ES and Mullins, T and Laurie, J and Nitert, MD}, title = {Consensus approach to differential abundance analysis detects few differences in the oral microbiome of pregnant women due to pre-existing type 2 diabetes mellitus.}, journal = {Microbial genomics}, volume = {11}, number = {4}, pages = {}, doi = {10.1099/mgen.0.001385}, pmid = {40232948}, issn = {2057-5858}, mesh = {Humans ; Female ; Pregnancy ; *Diabetes Mellitus, Type 2/microbiology/complications ; *Microbiota/genetics ; Adult ; *Diabetes, Gestational/microbiology ; Saliva/microbiology ; *Mouth/microbiology ; Metagenomics/methods ; Dysbiosis/microbiology ; *Bacteria/classification/genetics/isolation & purification ; }, abstract = {Oral microbiome dysbiosis has been proposed as a potential contributing factor to rising rates of diabetes in pregnancy, with oral health previously associated with an increased risk of numerous chronic diseases and complications in pregnancy, including gestational diabetes mellitus (GDM). However, whilst most studies examining the relationship between GDM and the oral microbiome identify significant differences, these differences are highly variable between studies. Additionally, no previous research has examined the oral microbiome of women with pre-existing type 2 diabetes mellitus (T2DM), which has greater risks of complications to both mother and baby. In this study, we compared the oral microbiome of 11 pregnant women with pre-existing T2DM with 28 pregnant normoglycaemic controls. We used shotgun metagenomic sequencing to examine buccal swab and saliva rinse samples at two time points between 26 and 38 weeks of gestation. To reduce variation caused by the choice of differential abundance analysis tool, we employed a consensus approach to identify differential taxa and pathways due to diabetes status. Differences were identified at the late time point only. In swab samples, there was increased Flavobacteriaceae, Capnocytophaga, Capnocytophaga gingivalis SGB2479, Capnocytophaga leadbetteri SGB2492 and Neisseria elongata SGB9447 abundance in T2DM as well as increased Shannon diversity and richness. In rinse samples, there was an increased abundance of Haemophilus, Pasteurellaceae, Pasteurellales and Proteobacteria. In contrast to studies of the oral microbiome in T2DM or GDM that use a single differential abundance analysis tool, our consensus approach identified few differences between pregnant women with and without T2DM.}, } @article {pmid40232107, year = {2025}, author = {Ravizza, T and Volpedo, G and Riva, A and Striano, P and Vezzani, A}, title = {Intestinal microbiome alterations in pediatric epilepsy: Implications for seizures and therapeutic approaches.}, journal = {Epilepsia open}, volume = {}, number = {}, pages = {}, doi = {10.1002/epi4.70037}, pmid = {40232107}, issn = {2470-9239}, support = {PE0000006/DN.1553//National Recovery and Resilience Plan (NRRP)/ ; //AICE-FIRE/ ; }, abstract = {The intestinal microbiome plays a pivotal role in maintaining host health through its involvement in gastrointestinal, immune, and central nervous system (CNS) functions. Recent evidence underscores the bidirectional communication between the microbiota, the gut, and the brain and the impact of this axis on neurological diseases, including epilepsy. In pediatric patients, alterations in gut microbiota composition-called intestinal dysbiosis-have been linked to seizure susceptibility. Preclinical models revealed that gut dysbiosis may exacerbate seizures, while microbiome-targeted therapies, including fecal microbiota transplantation, pre/pro-biotics, and ketogenic diets, show promise in reducing seizures. Focusing on clinical and preclinical studies, this review examines the role of the gut microbiota in pediatric epilepsy with the aim of exploring its implications for seizure control and management of epilepsy. We also discuss mechanisms that may underlie mutual gut-brain communication and emerging therapeutic strategies targeting the gut microbiome as a novel approach to improve outcomes in pediatric epilepsy. PLAIN LANGUAGE SUMMARY: Reciprocal communication between the brain and the gut appears to be dysfunctional in pediatric epilepsy. The composition of bacteria in the intestine -known as microbiota- and the gastrointestinal functions are altered in children with drug-resistant epilepsy and animal models of pediatric epilepsies. Microbiota-targeted interventions, such as ketogenic diets, pre-/post-biotics administration, and fecal microbiota transplantation, improve both gastrointestinal dysfunctions and seizures in pediatric epilepsy. These findings suggest that the gut and its microbiota represent potential therapeutic targets for reducing drug-resistant seizures in pediatric epilepsy.}, } @article {pmid40232020, year = {2025}, author = {Zhang, X and Chi, H and Peng, D and Jiang, M and Wang, C and Zhang, H and Kang, W and Li, L}, title = {Integrated Metagenomic and LC-MS/MS Analysis Reveals the Biogenic Amine-Producing Strains of Two Typical Chinese Traditional Fish Products: Fermented Mandarin Fish (Siniperca chuatsi) and Semi-Dried Yellow Croaker (Larimichthys crocea).}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/foods14061016}, pmid = {40232020}, issn = {2304-8158}, support = {2022TD02//Central Public-interest Scientific Institution Basal Research Fund, ECSFR, CAFS/ ; }, abstract = {Two typical fish products-fermented mandarin fish and semi-dried yellow croaker-are associated with biogenic amines (BAs), which are harmful to human health. The objective of this study was to investigate the bacterial ecology of the two fish products and to determine their capacity for producing BAs. Putrescine and cadaverine were major BAs detected in the fish products. Concentrations of BAs were significantly corrected with microbial count (p < 0.05). BA-producing isolates (33) in the two fish products were all multiple BA producers. Several of them, including Lactobacillus sakei, Bacillus cereus and Hafnia alvei isolated from fermented mandarin fish, as well as Shewanella baltica, Aeromonas veronii, and Photobacterium phosphoreum isolated from semi-dried yellow croaker, showed remarkable BA-producing capacity. Hafnia alvei produced the greatest abundance of putrescine, cadaverine, tyramine and 2-phenylethylamine. Lactobacillus sakei mainly produced tryptamine and putrescine. Photobacterium phosphoreum showed the strongest histamine-producing capacity.}, } @article {pmid40231916, year = {2025}, author = {A'yuni, Q and Mok, K and Nakphaichit, M and Jangchud, K and Pirak, T}, title = {Thai Cannabis sativa Leaves as a Functional Ingredient for Quality Improvement and Lactic Acid Bacterial Growth Enhancement in Kombucha.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/foods14060942}, pmid = {40231916}, issn = {2304-8158}, support = {FF(KU)25.66//Fundamental fund of Kasetsart University/ ; //Kasetsart's Agro-Industry Scholarship from Department of Product Development, Faculty of Agro-Industry, Kasetsart University/ ; }, abstract = {Kombucha is a well-known fermented drink that gained interest due to its gut health benefits. However, it has a harsh taste of acetic acid and is hard to consume. Thai Cannabis leaves (Cannabis sativa sp. Hang Kra Rog Phu phan ST1) contain high protein and phytochemicals which can improve the growth of lactic acid bacteria (LAB) and enhance the organoleptic quality of the Kombucha. This study revealed the effect of infusing assam green tea leaves with cannabis leaves on the fermentation rate, microbial communities, volatile compounds, and overall quality and taste of the kombucha. The high protein content (23.10%) of Cannabis leaves was found. Phytonutrients and phytochemicals found in the leaves promotes LAB growth, which resulted in the higher number of LAB in the treatment with cannabis leaves. At the end of fermentation (day 7), the highest LAB count (5.53 log CFU mL[-1]) was presented in kombucha infused with 30% cannabis leaves. Kombucha with better quality, higher pH, and less acidity was obtained in a dose manner. The change in microbial communities was detected using metagenomic analysis. The prominence of Dekkera and Komagataeibacter, with low abundance of Zygosaccharomyces and Weissella were identified. These microorganisms improved flavor by lessening strong fermented odor and harsh acidic taste. From volatile compounds, HS-SPME-GCMS revealed that kombucha infused with 30% cannabis leaves possessed less acetic acid, ethanol, and carbon dioxide and gave a better odor and taste. Hence, cannabis leaves was the novel substrate for kombucha fermentation by enhancing LAB growth and improving the overall qualities.}, } @article {pmid40231684, year = {2025}, author = {Glenna, S and Birkeland, EE and Orr, RJ and Gilfillan, GD and Dalland, M and Økstad, OA and Voie, ØA and Rounge, TB}, title = {Skin bacterial community dynamics of hands and forearms before and after military field exercise.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0295324}, doi = {10.1128/spectrum.02953-24}, pmid = {40231684}, issn = {2165-0497}, abstract = {The human skin microbiome is crucial for health and immunity, especially under the extreme conditions military personnel face. Soldiers often encounter unique stressors and hygienic challenges that can alter their skin's microbial composition, particularly in field environments. In this study, we aimed to investigate the impact of military field exercises on the diversity and composition of the skin bacterial microbiota using 16S rRNA sequencing. We conducted a longitudinal study of Norwegian soldiers (n = 19) participating in outdoor training operations during the NATO winter exercise Cold Response 2022. Skin swabs were taken from soldiers' hands and forearms before and after the 10-day military exercise, and following a 3-week post-exercise leave. Our results reveal hand- and forearm-specific shifts in bacterial populations associated with the exercise, likely influenced by environmental exposure, reduced hygiene, and heightened social contact. Alpha diversity increased on forearms while remaining stable on hands, which appeared more resilient to perturbations. Both sites exhibited temporal changes in composition, with soil- and water-associated bacteria enriched post-exercise; most being transient on hands but more sustained on forearms. The soldiers' microbiomes converged during the exercise, then diverged in the post-exercise leave period, and neither skin site returned to baseline composition at follow-up. Our findings highlight the impact of collaborative outdoor activities on microbial communities and suggest that resilience and stability differ between skin sites.IMPORTANCEOptimizing soldier health and resilience is critical for maintaining military readiness and operational effectiveness. The skin, as the body's first line of defense, is subjected to numerous challenges in military environments. Unique environmental and hygiene challenges can disrupt the skin microbiome and increase susceptibility to skin and soft tissue infections. This longitudinal research provides valuable insights into the effects of military service on the bacterial dynamics of the skin microbiome but can also inform hygiene management and disease prevention in comparable situations.}, } @article {pmid40230845, year = {2025}, author = {Gao, Q and Li, Z and Geng, J and Han, B and Yang, T and Feng, S and Zhao, L and Teng, Y and Li, Y and Zhao, R and Zhang, W and Wang, Y and Wang, Y}, title = {The type of pathogen is associated with organ failure and legacy dysfunction in patients with sepsis.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1541634}, pmid = {40230845}, issn = {1664-3224}, mesh = {Humans ; *Sepsis/mortality/microbiology/complications ; Male ; Female ; *Multiple Organ Failure/mortality/microbiology/etiology ; Middle Aged ; Aged ; High-Throughput Nucleotide Sequencing ; Adult ; Retrospective Studies ; }, abstract = {INTRODUCTION: Is there a difference in pathogen infection among sepsis patients with different organ dysfunction and Post-sepsis persistent organ dysfunction? Is this related to survival? It is currently unclear.

METHODS: This study reviewed 1982 sepsis patients between December 2019 and September 2023, and included 619 patients after removing patients with missing data. Of these, 332 were tested for metagenomic next-generation sequencing (mNGS). First, the pathogens distribution was assessed in all NGS-positive patients, followed by patients with different organ dysfunction (excluding those who died during hospitalization). Lastly, the survival analysis was conducted on patients infected with different pathogens.

RESULTS: The results showed that the mortality rate in our cohort was 27.63% in patients with sepsis, and patients with Respiratory, Liver, Circulatory, Hematologic, Neurological, and Renal dysfunction had poor survival. And patients with post-sepsis persistent organ dysfunction after sepsis have worse survival rates. In addition, we found the infection rates of Legionella and Betapapillomavirus were higher in patients with liver dysfunction. The infection rates of Mastadenovirus, Enterococcus, and Candida were higher in patients with neurological dysfunction. The infection rates of Candida were higher in patients with renal dysfunction and hematologic dysfunction. The infection rates of Moraxella were higher in patients with circulatory dysfunction. The infection rates of Enterococcus, Pneumocystis, and Acinetobacter were higher in patients with Post-sepsis cardiac dysfunction.The infection rates of Enterococcus, Acinetobacter, and Morganella were higher in patients with Post-sepsis liver dysfunction. The infection rates of Enterococcus, Acinetobacter, and Staphylococcus were higher in patients with Post-sepsis respiratory dysfunction. The infection rates of Enterococcus, Candida, Pneumocystis, Staphylococcus, and Listeria were higher in patients with Post-sepsis renal dysfunction. In addition, we found that patients with Escherichia infection in sepsis had the lowest survival rate. The survival rate of patients with Enterococcus infection combined with post-sepsis persistent respiratory dysfunction is also worse.

DISCUSSION: In conclusion, there are differences in the types and proportions of pathogens infected in patients with different organ dysfunction and Post-sepsis persistent organ dysfunction. The combination of Escherichia infection and Enterococcus infection with post-sepsis persistent respiratory dysfunction can affect the survival of patients. We should strengthen the management of sepsis patients, especially those with Post-sepsis persistent organ dysfunction.}, } @article {pmid40230330, year = {2025}, author = {Cui, T and Kushmaro, A and Barak, H and Poehlein, A and Daniel, R and Mägert, HJ}, title = {Enhanced discovery of bacterial laccase-like multicopper oxidase through computer simulation and metagenomic analysis of industrial wastewater.}, journal = {FEBS open bio}, volume = {}, number = {}, pages = {}, doi = {10.1002/2211-5463.70037}, pmid = {40230330}, issn = {2211-5463}, abstract = {Laccases belong to the superfamily of multicopper oxidases (MCO), a group of enzymes with the ability to reduce oxygen to water in a reaction without producing harmful byproducts. Laccase activity is influenced by many factors, such as structure; the number, location and binding status of copper ions; and the substrate-binding status. A large number of sequences that have not been experimentally characterized yet have been annotated as laccases. However, the biological functions of the characterized MCOs are considered to vary, and the substrate spectrum overlaps with that of other MCOs. Here, we identified 34 putative bacterial laccase sequences from metagenome data for industrial wastewater. We used machine-learning tools to screen enzymes with laccase activity by combining the T1 copper-binding capacity, the overall copper-binding capacity and the substrate-binding capacity. We also used the software comparisons to remove sequences with large discrepancies between different software applications. Three-dimensional structures of identified enzymes were predicted using alphafold, the positions of metal ions within the proteins were predicted by metal3d and autodock-vina, and their docking with ABTS [i.e. 2,2'-azinobis(3‑ethylbenzo-6‑thiazolinesulfonic acid)] as a substrate was predicted by rosetta and autodock-vina. Based on the docking results, we selected 10 high-scoring proteins, two low-scoring proteins and one composite protein for expression using the pET-21d (+) vector. In line with our predictions, all selected high-scoring proteins exhibited activity towards ABTS. Overall, we describe a method for discovering and designing novel bacterial laccase-like multicopper oxidases, offering increased possibilities for the degradation of various harmful components derived from environmental pollution.}, } @article {pmid40230307, year = {2025}, author = {Liu, B and He, N and Li, H and Yang, Z and Lin, Y and Wu, X and Zhang, H and Zhang, Z and Zhang, Z and Tian, Y and Wu, Z and Zou, Y and Peng, J and Li, S}, title = {3-Fucosyllactose Prevents Nonalcoholic Fatty Liver Disease by Modulating the Gut Microbiota-Derived Pantothenate in Mice.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.5c00079}, pmid = {40230307}, issn = {1520-5118}, abstract = {Nonalcoholic fatty liver disease (NAFLD) is a growing global health threat. Human milk oligosaccharides (HMOs) exhibit prebiotic properties that may alleviate NAFLD progression. Herein, our study demonstrates that 3-fucosyllactose (3-FL), a distinctive and crucial HMO, significantly attenuates body weight gain, enhances hepatic lipid metabolism, and reduces inflammation in a high-fat diet (HFD)-induced NAFLD mouse model. These findings suggest its potential as a dietary supplement for preventing and alleviating NAFLD progression. Subsequently, fecal metagenomic and nontargeted metabolomics analyses revealed that 3-FL treatment significantly alleviated HFD-induced gut microbiota dysbiosis, with a specific enhancement of the pantothenate (vitamin B5) metabolic pathways. Our targeted metabolite analysis further revealed a significant increase in both hepatic and fecal pantothenate concentrations, which contributed to the enhancement of the coenzyme A (CoA)-mediated lipid metabolism pathway. Furthermore, the subsequent population cohort analyses revealed a significant correlation between serum pantothenate levels and the progression of NAFLD, thereby reinforcing its candidacy as a noninvasive diagnostic biomarker. These findings show that 3-FL acts as an effective prebiotic to alleviate NAFLD symptoms, in part by enhancing the gut microbiota-mediated pantothenate/CoA metabolic pathway.}, } @article {pmid40230133, year = {2025}, author = {Chen, HD and Gao, S and Wang, LJ and Zhao, B and Lu, MQ and Song, YM and Cui, JS and Zhang, LL}, title = {[Spatial and Temporal Differences and Influencing Factors of Mobile Genetic Elements in Urban and Suburban River Sediments in Shijiazhuang City].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {46}, number = {4}, pages = {2250-2262}, doi = {10.13227/j.hjkx.202403034}, pmid = {40230133}, issn = {0250-3301}, mesh = {*Rivers ; China ; *Geologic Sediments/microbiology ; *Interspersed Repetitive Sequences/genetics ; Cities ; Drug Resistance, Microbial/genetics ; Environmental Monitoring ; Spatio-Temporal Analysis ; }, abstract = {With the widespread use of antibiotics in medicine and agriculture, the spread of antibiotic resistance genes （ARGs） in the environment has become a serious threat to ecological balance and human health, particularly for its role in facilitating the emergence of multidrug-resistant pathogens. The study of riverine environments as a major transmission route for ARGs and closely related mobile genetic elements （MGEs） is of great importance. MGEs exacerbate the spread of resistance genes by facilitating the horizontal transfer of ARGs in bacterial populations. Although studies have been conducted to explore the interactions between MGEs and ARGs, there is still a relative lack of research on the spatial and temporal differences in the distribution of MGEs in rivers and their drivers. This study selected two rural rivers （with a total of six sampling points） and three urban rivers （with a total of nine sampling points） within Shijiazhuang as research subjects, and sediment samples were collected in December 2020 and April 2021. By employing metagenomic sequencing technology, this study comprehensively compared and analyzed the spatiotemporal distribution characteristics and influencing factors of MGEs in the sediment of urban and rural rivers. The results showed that： ① In December, 1 738 types of MGEs （60572 RPKM） and 1 604 types of MGEs （26916 RPKM） were detected in urban and rural rivers, respectively. In April, 1 790 types of MGEs （74354 RPKM） and 1 631 types of MGEs （32062 RPKM） were detected in urban and rural rivers, respectively. ② The types and abundance of MGEs in urban rivers were greater than those in rural rivers, and the types and abundance of MGEs in April were greater than those in December. ③ ISPa38, IS26, and tnpA were the most significantly different typical MGEs among the rivers in urban and suburban Shijiazhuang. ④ PCoA and NMDS analyses showed significant spatiotemporal differences in MGEs between urban and rural rivers. ⑤ Correlation analysis and co-occurrence results indicated that the abundance of MGEs in urban rivers was significantly positively correlated with antibiotic concentration, industrial enterprises, sewage treatment plants, total population, livestock farming, and aquaculture. In suburban rivers, the abundance of MGEs was mainly significantly positively correlated with antibiotic concentration, livestock farming, aquaculture, and total population. Overall, by comparing the spatiotemporal heterogeneity of MGEs in urban and rural rivers and identifying the main driving factors of MGEs in urban and suburban rivers, this study provides data support for subsequent risk management and control of antibiotic resistance in different rivers.}, } @article {pmid40229213, year = {2025}, author = {Hoops, SL and Moutsoglou, D and Vaughn, BP and Khoruts, A and Knights, D}, title = {Metagenomic source tracking after microbiota transplant therapy.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2487840}, doi = {10.1080/19490976.2025.2487840}, pmid = {40229213}, issn = {1949-0984}, mesh = {Humans ; *Metagenomics/methods ; *Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome/genetics ; Colitis, Ulcerative/therapy/microbiology ; *Bacteria/genetics/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Metagenome ; Bayes Theorem ; Feces/microbiology ; }, abstract = {Reliable engraftment assessment of donor microbial communities and individual strains is an essential component of characterizing the pharmacokinetics of microbiota transplant therapies (MTTs). Recent methods for measuring donor engraftment use whole-genome sequencing and reference databases or metagenome-assembled genomes (MAGs) to track individual bacterial strains but lack the ability to disambiguate DNA that matches both donor and patient microbiota. Here, we describe a new, cost-efficient analytic pipeline, MAGEnTa, which compares post-MTT samples to a database comprised MAGs derived directly from donor and pre-treatment metagenomic data, without relying on an external database. The pipeline uses Bayesian statistics to determine the likely sources of ambiguous reads that align with both the donor and pre-treatment samples. MAGEnTa recovers engrafted strains with minimal type II error in a simulated dataset and is robust to shallow sequencing depths in a downsampled dataset. Applying MAGEnTa to a dataset from a recent MTT clinical trial for ulcerative colitis, we found the results to be consistent with 16S rRNA gene SourceTracker analysis but with added MAG-level specificity. MAGEnTa is a powerful tool to study community and strain engraftment dynamics in the development of MTT-based treatments that can be integrated into frameworks for functional and taxonomic analysis.}, } @article {pmid40228816, year = {2025}, author = {Chen, J and Liu, X and Bai, Y and Tang, X and Xue, K and Zhu, Z and Liu, W and Wang, J and Wang, C and Qiao, H and Dang, E and Yin, W and Wang, G and Shao, S}, title = {Tonsillar Microbiota Alterations Contribute to Immune Responses in Psoriasis by Skewing Aged Neutrophils.}, journal = {The British journal of dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1093/bjd/ljaf134}, pmid = {40228816}, issn = {1365-2133}, abstract = {BACKGROUND: The interplay between microbiota and the onset of immune-mediated diseases is increasingly coming to light. However, the role of tonsillar microbiota in cutaneous inflammation remains largely unknown.

OBJECTIVE: We aimed to determine how tonsillar microbiota influence skin inflammation in psoriasis and to uncover the underlying molecular mechanisms.

METHODS: Tonsillar microbiota samples were collected from 24 healthy controls and 28 psoriasis patients. Microbial community composition was analyzed using 16S rRNA sequencing and metagenomic sequencing. Serum levels of short-chain fatty acids (SCFAs) were measured via liquid chromatography-mass spectrometry in 10 healthy controls and 14 psoriasis patients. Peripheral blood neutrophils from both groups were then exposed to a representative microbial metabolite, and key pro-inflammatory markers were evaluated using functional immune assays.

RESULTS: We found significant alterations in the diversity and composition of the tonsillar microbial community in psoriasis group, with an increased prevalence of Bacteroidales and a decreased prevalence of Burkholderiales, Micrococcales, and Pasteurellales relative to healthy controls. Notably, a marked reduction in Rothia mucilaginosa correlated inversely with systemic inflammation (neutrophil-to-lymphocyte ratio) and disease severity (psoriasis area and severity index). Metagenomic analysis revealed disruptions in pathways critical for SCFAs production, including propanoate, pyruvate, and butanoate metabolism, which was supported by significantly lower serum SCFAs levels in psoriasis patients. Functional assays demonstrated that SCFAs inhibited neutrophil aging, pro-inflammatory cytokine secretion, and neutrophil extracellular traps (NETs) formation.

CONCLUSION: Our findings reveal that changes in tonsillar microbiota and their metabolic outputs contribute to psoriasis by modulating immune responses, highlighting potential clinical implications.}, } @article {pmid40228693, year = {2025}, author = {Ma, JY and Liu, JH and Chen, CZ and Zhang, YZ and Guo, ZS and Song, MP and Jiang, F and Chai, ZT and Li, Z and Lv, SX and Zhen, YJ and Wang, L and Liang, ZL and Jiang, ZY}, title = {Characteristics of microbial carbon pump in the sediment of kelp aquaculture zone and its contribution to recalcitrant dissolved organic carbon turnover: insights into metabolic patterns and ecological functions.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121559}, doi = {10.1016/j.envres.2025.121559}, pmid = {40228693}, issn = {1096-0953}, abstract = {The study delves into the microbial carbon pump (MCP) within the sediments of kelp aquaculture zones, focusing on its influence on the turnover of recalcitrant dissolved organic carbon (RDOC). Following kelp harvest, significant alterations in the microbial community structure were noted, with a decrease in complexity and heterogeneity within co-occurrence networks potentially impacting RDOC production efficiency. Metabolic models constructed identified four key microbial lineages crucial for RDOC turnover, with their abundance observed to decrease post-harvest. Analysis of metabolic complementarity revealed that RDOC-degrading microorganisms exhibit broad substrate diversity and are engaged in specific resource exchange patterns, with cross-feeding interactions possibly enhancing the ecological efficiency of the MCP. Notably, the degradation of RDOC was found not to deplete the RDOC pool; as aromatic compounds break down, new ones are released into the environment, thus supporting the renewal of the RDOC pool. The research highlights the pivotal role of microbial communities in RDOC turnover and offers fresh insights into their cross-feeding behavior related to RDOC cycling, providing valuable data to support the future development and application of MCP theory.}, } @article {pmid40228470, year = {2025}, author = {Zhang, Y and Ye, Y and Fang, M and Xiang, Y and Chen, J and Tang, X and Yang, Z and Qian, Q}, title = {Biogas production enhancement from anaerobic digestion with magnetic biochar: Insights into the functional microbes and DIET.}, journal = {Journal of environmental management}, volume = {381}, number = {}, pages = {125347}, doi = {10.1016/j.jenvman.2025.125347}, pmid = {40228470}, issn = {1095-8630}, abstract = {The application of magnetic biochar in anaerobic digestion (AD) has gained increasing attention. However, the underlying mechanisms remain insufficiently understood. This study systematically investigated the effects of magnetic biochar on functional microbial communities involved in methanogenesis and elucidated its role in promoting direct interspecies electron transfer (DIET) within AD systems. The addition of 40 mg g[-1] TSadded of magnetic biochar significantly enhanced methane production by 42.21 %, reaching 223.08 mL g[-1] TS with highest organic matter degradation efficiency. Microbial community analysis showed that magnetic biochar significantly enriched microorganisms associated with hydrolysis, acidogenesis, and methanogenesis, as well as electroactive microorganisms' abundance such as Geobacter spp., Syntrophus spp., P. aestuarii, and M. harundinacea, providing direct evidence for the DIET process of AD with magnetic biochar. Furthermore, the abundance of key genes involved in the DIET, including pilA, Fpo, and the genes encoded outer-membrane c-type cytochromes, was respectively upregulated by 44.49 %, 22.04 %, and 37.6 % in the presence of magnetic biochar. These findings suggest that magnetic biochar enhances the production of conductive pili and cytochrome c, facilitating extracellular electron transfer between syntrophic microorganisms. This accelerated electron transfer promotes CO2 reduction to CH4, ultimately improving methane production efficiency in the AD system. Moreover, the enhancement of hydrogenotrophic methanogenesis was particularly pronounced with magnetic biochar, further contributing to the improved AD performance. This study provides novel mechanistic insights into biochar-mediated DIET, offering a theoretical basis for optimizing biochar applications in AD.}, } @article {pmid40226917, year = {2025}, author = {Lai, Q and Yao, S and Zha, Y and Zhang, H and Zhang, H and Ye, Y and Zhang, Y and Bai, H and Ning, K}, title = {Deciphering the biosynthetic potential of microbial genomes using a BGC language processing neural network model.}, journal = {Nucleic acids research}, volume = {53}, number = {7}, pages = {}, doi = {10.1093/nar/gkaf305}, pmid = {40226917}, issn = {1362-4962}, support = {2021YFA0910500//National Key R&D Program of China/ ; 32071465//National Natural Science Foundation of China/ ; }, mesh = {*Multigene Family ; *Biosynthetic Pathways/genetics ; *Neural Networks, Computer ; *Genome, Microbial ; Phylogeny ; Metagenome ; Secondary Metabolism/genetics ; Genome, Bacterial ; }, abstract = {Biosynthetic gene clusters (BGCs), key in synthesizing microbial secondary metabolites, are mostly hidden in microbial genomes and metagenomes. To unearth this vast potential, we present BGC-Prophet, a transformer-based language model for BGC prediction and classification. Leveraging the transformer encoder, BGC-Prophet captures location-dependent relationships between genes. As one of the pioneering ultrahigh-throughput tools, BGC-Prophet significantly surpasses existing methods in efficiency and fidelity, enabling comprehensive pan-phylogenetic and whole-metagenome BGC screening. Through the analysis of 85 203 genomes and 9428 metagenomes, BGC-Prophet has profiled an extensive array of sub-million BGCs. It highlights notable enrichment in phyla like Actinomycetota and the widespread distribution of polyketide, NRP, and RiPP BGCs across diverse lineages. It reveals enrichment patterns of BGCs following important geological events, suggesting environmental influences on BGC evolution. BGC-Prophet's capabilities in detection of BGCs and evolutionary patterns offer contributions to deeper understanding of microbial secondary metabolites and application in synthetic biology.}, } @article {pmid40226542, year = {2025}, author = {Cao, J and Wang, S and Ding, R and Liu, Y and Yuan, B}, title = {Comparative analyses of the gut microbiome of two sympatric rodent species, Myodes rufocanus and Apodemus peninsulae, in northeast China based on metagenome sequencing.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19260}, pmid = {40226542}, issn = {2167-8359}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; China ; *Arvicolinae/microbiology ; *Murinae/microbiology ; *Metagenome ; Metagenomics ; High-Throughput Nucleotide Sequencing ; Proteobacteria/genetics/isolation & purification ; Firmicutes/genetics/isolation & purification ; Sympatry ; Bacteroidetes/genetics/isolation & purification ; }, abstract = {The gut microbiota is integral to an animal's physiology, influencing nutritional metabolism, immune function, and environmental adaptation. Despite the significance of gut microbiota in wild rodents, the Korean field mouse (Apodemus peninsulae) and the gray red-backed vole (Myodes rufocanus) remain understudied. To address this, a metagenomic sequencing analysis of the gut microbiome of these sympatric rodents in northeast China's temperate forests was conducted. Intestinal contents were collected from A. peninsulae and M. rufocanus within the Mudanfeng National Nature Reserve. High-throughput sequencing elucidated the gut microbiome's composition, diversity, and functional pathways. Firmicutes, Bacteroidetes, and Proteobacteria were identified as the dominant phyla, with M. rufocanus showing greater microbiome diversity. Key findings indicated distinct gut bacterial communities between the species, with M. rufocanus having a higher abundance of Proteobacteria. The gut microbiota of A. peninsulae and M. rufocanus differed marginally in functional profiles, specifically in the breakdown of complex carbohydrates, which might reflect their distinct food preferences albeit both being herbivores with a substantial dietary overlap. The investigation further elucidated gut microbiota's contributions to energy metabolism and environmental adaptation mechanisms. This study aligns with information on rodent gut microbiota in literature and highlights the two understudied rodent species, providing comparative data for future studies investigating the role of gut microbiota in wildlife health and ecosystem functioning.}, } @article {pmid40226095, year = {2025}, author = {Ho, JY and Koh, XQ and Kang, DY and Low, A and Hu, D and Haryono, MAS and Williams, RBH and Case, RJ and Boucher, YF}, title = {Discovery of a phylogenetically novel tropical marine Gammaproteobacteria elucidated from assembled genomes and the proposed transfer of the genus Umboniibacter from the family Cellvibrionaceae to Umboniibacteraceae fam. nov.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1437936}, pmid = {40226095}, issn = {1664-302X}, abstract = {Marine heterotrophic bacteria in coastal waters respond to the influx of carbon from natural and anthropogenic sources. We identified two nearly identical, (99.9% average nucleotide identity; 100% amino acid identity; same DNA G + C content of 52.3 mol%) high-quality (≥99% CheckM completeness and ≤ 1.3% contamination) draft metagenome-assembled genomes (MAGs; SJ0813 and SJ0972) from seawater microbiomes of a southern island of Singapore that is in a protected marine park. The MAGs were only assigned to the Cellvibrionaceae family according to Genome Taxonomy Database. Overall genome related indices to Pseudomaricurvus alkylphenolicus KU41G[T] as the closest phylogenetic relative revealed no more than 70.45% average nucleotide identity (ANIcutoff < 95%), below the 50% percentage of conserved proteins (POCPcutoff = 43.54%) for genera cutoff and low digital DNA-DNA hybridization values (DDH = 20.6 and 20.8%). The major respiratory quinone is predicted to be ubiquinone-9 from the annotation of 3-demethylubiquinone-9 3-methyltransferase (ubiG, K00568) involved in the last step of the ubiquinone biosynthesis pathway (M00117), which differed from the ubiquinone-8 utilized by known members of Cellvibrionaceae. Both MAGs contained a complete pathway for dissimilatory nitrate reduction to ammonia, which increases bioavailability of nitrogen in seawater. An identical choline dehydrogenase found in both MAGs have a low amino-acid identity (≤64.47%) compared to existing GMC family oxidoreductases, expanding on the diversity of this family of enzymes. The MAGs meet nearly all the minimum requirements but lack a 16S rRNA gene of sufficient length required for the proposed novel genus and species under SeqCode. Nevertheless, phylogenetic trees based on core-genome and RpoB as an alternative phylogenetic marker are congruent with the taxon standing as a monophyletic clade to other taxa of the order Cellvibrionales. Taken together, the MAGs (SJ0813 and SJ0972) represent an uncultured, undescribed genus and species in which we tentatively propose the name Candidatus Pelagadaptatus aseana gen. nov., sp. nov. and strain SJ0813[TS] (=BAABNI000000000.1[TS]) as type sequence. Phylogenetic inference from core-genome and RpoB phylogenetic trees placed Umboniibacter marinipuniceus KMM 3891[T] outside Cellvibrionaceae. We, therefore, propose the transfer of the genus Umboniibacter from the family Cellvibrionaceae to a new family Umboniibacteraceae according to the International Code of Nomenclature of Prokaryotes.}, } @article {pmid40225905, year = {2025}, author = {Lambisia, AW and Mwita Morobe, J and Moraa, E and Mwarumba, S and K N Korir, F and Seif Athman, R and Kiptui, R and Mbee, M and Mugo, N and Amoth, P and Muange, P and J Houldcroft, C and Barasa, E and Mwangangi, J and Githinji, G and C Holmes, E and Isabella Ochola-Oyier, L and N Agoti, C}, title = {Identification of coxsackievirus A24 variant during an acute hemorrhagic conjunctivitis outbreak in coastal Kenya, 2024.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {28}, pmid = {40225905}, issn = {2398-502X}, abstract = {BACKGROUND: In early 2024, a surge in acute hemorrhagic conjunctivitis (AHC), also referred as "red eye" disease, was observed in coastal Kenya, prompting the Ministry of Health to issue an outbreak alert. Herein, we investigated the etiology of this outbreak.

METHODS: Ocular swabs were obtained from 13 individuals presenting with AHC at a Mombasa clinic in early February 2024. Ten of these were analyzed using bacterial cultures, and all 13 using a pan-adenovirus quantitative PCR (qPCR) and metagenomic sequencing. Potential viral etiology was confirmed by a specific qPCR, amplicon sequencing and phylogenetic analysis.

RESULTS: Bacterial cultures yielded no growth except in three samples where non-pathogenic bacteria were detected. All 13 samples were adenovirus qPCR negative. Metagenomic sequencing detected coxsackievirus A24 variant (CA24v) in three of the 13 samples. CV-A24v detections were confirmed by both CV-A24v specific qPCR and amplicon sequencing of an approximately 450 nucleotide long VP4/2 junction genomic region. Phylogenetic analysis of the VP4/2 sequences showed that they were closely related to CV-A24v genotype IV.

CONCLUSION: The AHC epidemic in coastal Kenya in early 2024 was likely caused by CA24v. Metagenomic sequencing is a powerful tool for identifying potential causative agents of new disease outbreaks.}, } @article {pmid40225898, year = {2025}, author = {Liu, H and Wang, H and Sun, J and Yang, T and Mo, Z and Huang, H and Pan, Y}, title = {High-Altitude Open-Pit Coal Mining has Changed the Sulfur Cycle and Ecological Network of Plant Rhizosphere Microorganisms.}, journal = {Ecology and evolution}, volume = {15}, number = {4}, pages = {e71183}, pmid = {40225898}, issn = {2045-7758}, abstract = {Ecological restoration of mining sites has a considerable effect on microbial community dynamics; however, its impact on sulfur cycling is unclear. This study explored the changes in functional genes related to sulfur cycling and microbial diversity during different stages of succession following the ecological restoration of a mining site in a cold arid area. A total of three succession stages were selected-natural, secondary, and artificial. The expression of sulfur cycle-related genes and associated microbial drivers was investigated using metagenomics and network analysis. The dominant bacteria in the secondary succession were found to be r-strategy-adopting Proteobacteria and Cyanobacteria. Natural succession primarily comprised Aspergillus and Thermus, whereas artificial succession comprised Proteobacteria, Chlorophyta, and Actinobacteria. Mining disturbances were determined to significantly reduce the abundance of sulfur-cycling archaea. Secondary succession was primarily influenced by soil total phosphorus in the sulfur-cycle gene network. The key bacteria and archaea involved in the sulfur cycle were found to be Bradyrhizobium and Nitrosopumilus, respectively. The abundance of Streptomyces was significantly higher in natural succession than in artificial or secondary succession. Burkholderia, which has biological control and bioremediation effects, was abundant during artificial succession. These results provide a theoretical basis for restoring the sulfur cycle and promoting a positive succession of ecosystems in mining areas.}, } @article {pmid40225105, year = {2025}, author = {He, W and Wang, S and Xiong, X and Dai, W}, title = {[18]F-FDG PET/CT Imaging of Talaromyces marneffei Infection with Bone Destruction in an HIV-Negative Patient: Case Report and Review.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {1745-1752}, pmid = {40225105}, issn = {1178-6973}, abstract = {BACKGROUND: Talaromycosis is an opportunistic fungal infection caused by Talaromyces marneffei (T. marneffei), commonly occurs in HIV-positive individuals. While less common, it can also affect HIV-negative individuals. We reported a T. marneffei infection in an HIV-negative patient, whose imaging findings and diagnostic process offer valuable clinical insights.

CASE PRESENTATION: An HIV-negative male adult patient with an intermittent cough for more than two years and worsened for more than one month. Enhanced CT scan indicated lung cancer with rib and lymph nodes metastasis. The lower respiratory tract and bronchial lavage fluid culture of the patient were negative. He received two bronchoscopies, two biopsies and two metagenomic next-generation sequencing (mNGS) tests, which failed to find the malignant cell but sequentially identified the presence of Pasteurella multocida and the Epstein-Barr virus. His condition did not improve after anti-infective treatment for 2weeks. An 18-fluorodeoxy glucose ([18]F-FDG) PET/CT scan revealed increased radioactivity in right supraclavicular lymph node, left lung and the right tenth rib. Ultimately, a biopsy at the hypermetabolic lesion of left lung, and a third mNGS test confirmed the presence of Talaromyces marneffei. Subsequently, the patient started antifungal therapy with amphotericin B and itraconazole and showed a favorable response.

CONCLUSION: We reviewed all reported PET/CT findings of T. marneffei infection patients, suggesting that fungus T. marneffei should be considered in patients identified as infection and exhibited bone destruction and also highlight the role of PET/CT in guiding the biopsy site.}, } @article {pmid40224142, year = {2025}, author = {Caille, A and Connan, C and Lyon Belgy, N and Borezée, E and Cherbuy, C and Meunier, N and Meslier, V}, title = {Positive nutritional selection of adults with healthy lifestyle and high daily fiber consumption for the isolation of beneficial intestinal bacteria: The iTARGET cohort study protocol.}, journal = {MethodsX}, volume = {14}, number = {}, pages = {103268}, pmid = {40224142}, issn = {2215-0161}, abstract = {Recent advances in the study of the gut microbiota has pointed to its under-utilized source of potentially beneficial bacteria, known as next generation probiotics, offering a promising avenue to restore or compensate impaired gut microbiota toward a healthy state. Aside from the difficulties to achieve in-lab adequate culture conditions, the use of beneficial bacterial isolates is also limited by their bioavailability in the donor itself. In the iTARGET study, we positively selected donors based on their diet enriched in fiber, that has been shown to increase the prevalence of bacterial species associated with health. The iTARGET study is a monocenter, prospective, observational study of adults with healthy lifestyle and high daily fiber consumption. We aim to recruit individuals in two phases, the first one for all individuals that will permit the identification of carriers for bacteria of interest and the second phase for a subset of individuals to allow for culture and isolation of previously identified potentially beneficial bacteria. Our primary outcome is the isolation and culture of at least one potentially beneficial isolate. The secondary outcomes comprised the high throughput metagenomic profiles of the intestinal microbiota and the characterization of the cultured isolates. The study was approved by the French Research Ethics Committees (Comité de Protection des Personnes Sud-Est I) under the National reference ID 2023-A01677-38. Study findings and results will be published in peer-reviewed Open Access journals. (Trial registration number on ClinicalTrials.gov: NCT06166810).}, } @article {pmid40223813, year = {2025}, author = {Alp-Baltakesmez, D and Ertürkmen, P and Bulantekin, Ö}, title = {Diversity and Functional Roles of Microorganisms in Anatolian Black Pine Cone Vinegar Fermentation.}, journal = {Food science & nutrition}, volume = {13}, number = {4}, pages = {e70155}, pmid = {40223813}, issn = {2048-7177}, abstract = {The parts of some pine species are a rich source of bioactive compounds that can be used in various food products. The current work, the physicochemical, bioactive, antimicrobial, sensory, and aromatic properties of traditional vinegar produced from Anatolian Black Pine Cones from different provinces of Turkey were determined, as well as the cultivable microbial diversity and metagenomic analysis. The total phenolic content of the vinegars ranged from 163.88 to 174.79 mg GAE/L. Antioxidant activity, measured via DPPH and ABTS assays, varied among the samples. CnB vinegar, made from Burdur province cones, stood out for its bioactive compounds, including terpenes, acetic acid, ascorbic acid, and the highest α-terpineol content (3.13%). CnB also exhibited the strongest antimicrobial activity, with the largest inhibition zone (44.91 mm) against E. coli type A, while CnM showed the lowest activity. Sensory evaluations favored CnB for its balanced flavor, while CnV was criticized for excessive sharpness, and CnM was deemed too mild. The bacterial microbiome of CnB was predominantly composed of acetic acid bacteria, with an average concentration of 7.36 log CFU/mL in the enumeration of culturable microorganisms. The dominant bacterial taxa at the phyla level included Proteobacteria (72.296%), Firmicutes (22.062%), Bacteroidota (3.665%), followed by Acetobacteraceae (71.47%), Clostridia (13.187%), Bacilli (5.066%), Bacteroidetes (3.665%), and C. negativicutes (3.737%) at the phylum level. The fungal microbiome was mainly represented by Ascomycota (78.717%) and Eukaryota Incertae sedis (15.840%). The findings demonstrate that pine cone vinegar can be employed in a multitude of applications, including food preservation and health promotion.}, } @article {pmid40223739, year = {2025}, author = {El Mouzan, M and Savidge, TC and Al Sarkhy, A and Badu, S and Alsaleem, B and Al Mofarreh, M and Almasood, A and Assiri, A}, title = {Gut virome profile in new onset treatment naïve Saudi children with ulcerative colitis.}, journal = {Saudi journal of gastroenterology : official journal of the Saudi Gastroenterology Association}, volume = {}, number = {}, pages = {}, doi = {10.4103/sjg.sjg_24_25}, pmid = {40223739}, issn = {1998-4049}, abstract = {BACKGROUND: Gut microbiome imbalance is well established in ulcerative colitis (UC) in Western populations. Significantly less is known about the gut virome and whether geography impacts the UC-associated microbiome. The aim of this study was to characterize gut bacteriophage changes, as well as to identify phage-bacterial associations that can serve as potential biomarkers of UC.

METHODS: Twenty children with UC and 20 healthy controls were enrolled in the study. Inclusion criteria included newly diagnosed treatment-naïve children with UC with no antibiotic exposure for at least six months prior to sample collection. Deoxyribonucleic acid (DNA) was extracted from stool and rectal biopsies and was processed for shotgun metagenomic sequencing. Bioinformatics and statistical analyses were performed to assess phage diversity and their associations with gut bacteria. Candidate biomarkers were identified using the random forest classifier.

RESULTS: In fecal samples, bacteriophage diversity was not significantly altered, but 72 species were significantly altered in UC, five of which (Salmonella_phage_SEN4, uncultured_crAssphage, Staphylococcus_phage_SPbeta-like, Streptococcus_phage_YMC-2011 and Siphoviridae_u_s) were identified as candidate biomarker signatures.

CONCLUSIONS: We found a significantly altered bacteriophage signature in children with new onset, treatment naïve UC in Saudi children, a Middle Eastern population. These changes differed from previously reported Western UC cases, indicating that demographic bias needs to be considered when developing microbiota-based diagnostics and therapeutic applications for non-Western populations.}, } @article {pmid40223703, year = {2025}, author = {Gao, M and Zhang, Q and Chen, B and Lei, C and Xia, Q and Sun, L and Li, T and Zhou, NY and Lu, T and Qian, H}, title = {Global Geographic Patterns of Soil Microbial Degradation Potential for Polycyclic Aromatic Hydrocarbons.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c00306}, pmid = {40223703}, issn = {1520-5851}, abstract = {Polycyclic aromatic hydrocarbons (PAHs) are toxic and persistent pollutants that are widely distributed in the environment. PAHs are toxic to microorganisms and pose ecological risks. Bacteria encode enzymes for PAH degradation through specific genes, thereby mitigating PAH pollution. However, due to PAHs' complexity, information on the global degradation potential, diversity, and associated risks of PAH-degrading microbes in soils is lacking. In this study, we analyzed 121 PAH-degrading genes and selected 33 as marker genes to predict the degradation potential within the soil microbiome. By constructing a Hidden Markov Model, we identified 4990 species carrying PAH-degrading genes in 40,039 soil metagenomic assembly genomes, with Burkholderiaceae and Stellaceae emerging as high-potential degraders. We demonstrated that the candidate PAH degraders predominantly emerged in artificial soil and farmland, with significantly fewer present in extreme environments, driven by factors such as average annual rainfall, organic carbon, and human modification of terrestrial systems. Furthermore, we comprehensively quantified the potential risks of each potential host in future practical applications using three indicators (antibiotic resistance genes, virulence factors, and pathogenic bacteria). We found that the degrader Stellaceae has significant application prospects. Our research will help determine the biosynthetic potential of PAH-degrading enzymes globally and further identify potential PAH-degrading bacteria at lower risk.}, } @article {pmid40223273, year = {2025}, author = {Yang, SY and Han, SM and Lee, JY and Kim, KS and Lee, JE and Lee, DW}, title = {Advancing Gut Microbiome Research: The Shift from Metagenomics to Multi-Omics and Future Perspectives.}, journal = {Journal of microbiology and biotechnology}, volume = {35}, number = {}, pages = {e2412001}, doi = {10.4014/jmb.2412.12001}, pmid = {40223273}, issn = {1738-8872}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods/trends ; *Metabolomics/methods ; *Genomics/methods ; Proteomics/methods ; Precision Medicine ; Host Microbial Interactions ; Multiomics ; }, abstract = {The gut microbiome, a dynamic and integral component of human health, has co-evolved with its host, playing essential roles in metabolism, immunity, and disease prevention. Traditional microbiome studies, primarily focused on microbial composition, have provided limited insights into the functional and mechanistic interactions between microbiota and their host. The advent of multi-omics technologies has transformed microbiome research by integrating genomics, transcriptomics, proteomics, and metabolomics, offering a comprehensive, systems-level understanding of microbial ecology and host-microbiome interactions. These advances have propelled innovations in personalized medicine, enabling more precise diagnostics and targeted therapeutic strategies. This review highlights recent breakthroughs in microbiome research, demonstrating how these approaches have elucidated microbial functions and their implications for health and disease. Additionally, it underscores the necessity of standardizing multi-omics methodologies, conducting large-scale cohort studies, and developing novel platforms for mechanistic studies, which are critical steps toward translating microbiome research into clinical applications and advancing precision medicine.}, } @article {pmid40223231, year = {2025}, author = {Lin, H and Chen, Y and Zhou, M and Wang, H and Chen, L and Zheng, L and Wang, Z and Zheng, X and Lu, S}, title = {Comprehensive analysis of faecal metagenomic and serum metabolism revealed the role of gut microbes and related metabolites in detecting colorectal lateral spreading tumours.}, journal = {Virulence}, volume = {16}, number = {1}, pages = {2489154}, doi = {10.1080/21505594.2025.2489154}, pmid = {40223231}, issn = {2150-5608}, mesh = {Humans ; *Colorectal Neoplasms/diagnosis/microbiology/pathology/metabolism/blood ; *Gastrointestinal Microbiome ; *Feces/microbiology/chemistry ; Male ; Female ; Middle Aged ; Metagenomics ; Aged ; Metabolomics ; Dysbiosis/microbiology ; Bacteria/classification/genetics/metabolism/isolation & purification ; Metabolic Networks and Pathways ; Case-Control Studies ; Adult ; }, abstract = {Colorectal lateral spreading tumours (LST), early-stage lesions of colorectal cancer (CRC), are associated with gut microbiota dysbiosis. However, the functional alterations in gut microbiota and their metabolic pathways remain inadequately understood. This study employed propensity score matching to compare 35 LST patients with 35 healthy controls. Metagenomic and metabolomic analyses revealed notable differences in gut microbiota composition and metabolic pathways. LST patients exhibited a marked reduction in short-chain fatty acid (SCFA)-producing probiotics, such as Roseburia, Clostridium, and Butyricicoccus sp-OF13-6, alongside anti-inflammatory metabolites. In contrast, potential intestinal pathogens linked to inflammatory bowel disease (IBD), including Escherichia and Citrobacter amalonaticus, were significantly enriched. Orthogonal partial least squares discriminant analysis (OPLS-DA) highlighted significant metabolic disparities between the groups, with enrichment in pathways associated with cholesterol metabolism, choline metabolism in cancer, and amino acid metabolism - all relevant to cancer progression. Key biomarkers identified for LST included fumarate, succinate, glutamic acid, glycine, and L-aspartic acid, which were closely linked to these pathways. Functional studies demonstrated that these metabolites promoted the proliferation and invasion of HCT-116 and SW480 human colorectal cancer cells in vitro. Metagenomic and metabolomic analysis revealed a strong positive correlation between Escherichia and Ruminococcus sp-AM41-2AC abundance and the enriched pathways, whereas reductions in Roseburia species, including Roseburia-OF03-24 and Roseburia intestinalis_CAG13-exhibited negative correlations. These results suggest that gut microbiota and metabolite alterations in LST contribute to intestinal inflammation and CRC development, underscoring their potential as biomarkers for early detection and therapeutic targets.}, } @article {pmid40223096, year = {2025}, author = {Yang, Z and Zhou, Y and Lin, J and Wang, X and Huang, C and Gao, J and Wang, G and Yang, B and Liu, G and Duan, H and Cui, J and Zhao, J and Luo, W and Cheng, S and Liu, Y}, title = {Identification and characterization of pigeon adenovirus 1 as an emerging pathogen in pigeons from Northern and Northwest China.}, journal = {BMC veterinary research}, volume = {21}, number = {1}, pages = {266}, pmid = {40223096}, issn = {1746-6148}, support = {BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; BAIC06-2024-G10//Beijing Innovation Consortium of Agriculture Research System/ ; KJCX20230213//Beijing Academy of Agricultural and Forestry Sciences/ ; KJCX20230213//Beijing Academy of Agricultural and Forestry Sciences/ ; KJCX20230213//Beijing Academy of Agricultural and Forestry Sciences/ ; KJCX20230213//Beijing Academy of Agricultural and Forestry Sciences/ ; QNJJ202234//Beijing Academy of Agricultural and Forestry Sciences/ ; KJCX20230213//Beijing Academy of Agricultural and Forestry Sciences/ ; QNJJ202234//Beijing Academy of Agricultural and Forestry Sciences/ ; KJCX20230213//Beijing Academy of Agricultural and Forestry Sciences/ ; KJCX20230213//Beijing Academy of Agricultural and Forestry Sciences/ ; KJCX20230213//Beijing Academy of Agricultural and Forestry Sciences/ ; }, mesh = {Animals ; *Columbidae/virology ; China/epidemiology ; *Adenoviridae Infections/veterinary/virology/epidemiology/pathology ; *Bird Diseases/virology/epidemiology/pathology ; *Aviadenovirus/genetics/isolation & purification ; Phylogeny ; Genome, Viral ; *Communicable Diseases, Emerging/veterinary/virology/epidemiology ; }, abstract = {BACKGROUND: In 2022, a new infectious disease characterized by severe acute hepatitis, sudden death, and high mortality among breeding pigeons, was reported in China.

RESULTS: In naturally infected pigeons, key necropsy findings comprised hepatic swelling with patchy hemorrhage and pericardial effusion. Histopathological examination further revealed degeneration, necrosis, and basophilic intranuclear inclusion bodies affecting hepatocytes, cardiomyocytes, and vascular endothelial cells. Transmission electron microscopy revealed a typical icosahedral virus structure and crystal-like arrangement of viral particles in the nucleus. Metagenomic next-generation sequencing (mNGS) of pericardial effusion samples revealed the presence of pigeon adenovirus. Sequencing analysis of the hexon and fiber-2 genes suggested that it constituted pigeon adenovirus 1 (PiAdV-1). The complete genome of CH/BJ/1/2022 was determined to be 48,071 nucleotides in length, with a 10-amino acid deletion in the fiber-2 gene at residues 627-636 and a 95-animo acid insertion in the 100 K gene at residue 75. The same disease was reproduced in pigeons by experimental infection.

CONCLUSION: Collectively, our analyses confirmed that the etiological agent was PiAdV-1, an emerging pathogen that causes severe acute hepatitis and high mortality in pigeons. This virus merits close attention because it could be catastrophic for the pigeon industry.}, } @article {pmid40222673, year = {2025}, author = {Fu, CM and Luo, SQ and Tang, DR and Zhang, YM and Xu, JW and Lin, LB and Zhang, QL}, title = {Effect of bacteriocin RSQ01 on milk microbiota during pasteurized milk preservation.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2025-26395}, pmid = {40222673}, issn = {1525-3198}, abstract = {Milk has high risk for microbial contamination. RSQ01, a bacteriocin, previously has shown potentiality for pasteurized milk preservation. This study analyzed the effects of RSQ01 on milk microbiota by comparison of bacterial number and composition in 3 pasteurized milk groups: controls without RSQ01, treatment group with the addition of 2 × MIC (low concentration) and 4 × MIC RSQ01 (high concentration). Integrated 16S rDNA sequencing and metagenomics of these groups after 3 d of storage showed inhibition of RSQ01 on microbiota diversity. Pathogenic bacteria such as Salmonella showed a decrease in relative abundance after RSQ01 treatment, while probiotic bacteria such as Lactococcus showed an increase, indicating that RSQ01 contributed to milk preservation by maintaining a low abundance of pathogens and a relatively high abundance of probiotics. Further investigations revealed that milk preservation was primarily attributed to the ability of RSQ01 to decrease the relative abundance of genes related to metabolism of energy and nutrients (e.g., vitamins, lipids, and amino acids) of microbiota, with change of genetic, environmental, and cellular processes. Interestingly, RSQ01 generally reduced the relative abundance of virulence factors- and quorum-sensing-related genes in microbiota, likely reducing virulence and resistance. The findings provided insights into microbiomics mechanisms regarding pasteurized milk preservation of bacteriocins.}, } @article {pmid40222492, year = {2025}, author = {Xia, Y and Chen, X and Jiang, X and Shen, J}, title = {Enhanced denitrification under saline Conditions: Glycine betaine as a key osmoprotectant.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132517}, doi = {10.1016/j.biortech.2025.132517}, pmid = {40222492}, issn = {1873-2976}, abstract = {Biological denitrification is significantly inhibited by salinity, which adversely affects microbial activity and reduces efficiency. This study aimed to evaluate the impact of salinity on denitrification performance and assess the potential of glycine betaine (GB) as an osmotic pressure regulator and protective agent. Results indicated that under the optimal conditions, including an influent nitrate concentration of 51.03 mg L[-1], C/N ratio of 5.42, pH value of 8.95, and salinity of 1.05 %, the nitrate removal efficiency was predicted to reach 100 %. However, a sharp decline (56.09 ± 4.52 %) in nitrate removal efficiency occurred when salinity increased from 0 % to 3 % within the initial 6 h. This inhibition was mitigated by adding 25 mg L[-1] GB, which enhanced nitrate removal efficiency by 2.19 times. GB promoted the secretion of extracellular polymeric substances (EPS), especially polymeric protein, a critical contributor to salinity resistance. Metagenomics analysis revealed that GB improved denitrification process by upregulating key genes involved in nitrogen and carbon metabolism. Furthermore, the relative abundance of Na[+] transporter genes, K[+] transporter genes, and GB absorption and synthesis genes rose with GB addition, underscoring the indispensable role of GB in alleviating osmotic stress and accelerating microbial metabolism. These findings emphasize the detrimental effects of salinity on denitrification and demonstrate the potential of GB as an osmoprotectant, enabling efficient nitrogen removal under saline conditions.}, } @article {pmid40222473, year = {2025}, author = {Jing, K and Li, Y and Li, Y and Meng, Q and Guan, Q}, title = {The treated wastewater enhances the biodegradation of sulfonamide antibiotics in biofilm-sediment downstream of the receiving river outlet.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121600}, doi = {10.1016/j.envres.2025.121600}, pmid = {40222473}, issn = {1096-0953}, abstract = {Although the treated wastewater meets the discharge standards, it can still become a potential transmitted stressor that affects aquatic organisms in receiving rivers. Biofilms and sediments as the main solid-phase substances in natural aquatic environments can biodegrade micropollutants. However, most of the current studies have selected a single solid-phase material, and there are relatively few studies that comprehensively consider the effect of treated wastewater on the dissipation of micropollutants in a composite biofilm-sediment system. Therefore, this study investigated the dissipation pathways of six sulfonamide antibiotics (SAs) in biofilm-sediment and the effect of treated wastewater on SAs dissipation. The results showed that biodegradation was the main pathway for SAs dissipation in biofilm-sediment. The input of treated wastewater increased the abundance of dominant degradation bacteria Burkholderiales and Pseudomonadale, thereby improving the biodegradation rate of SAs (approximately 1.5 times higher than upstream degradation rate). These genera could also be further integrated into downstream communities to continuously mediate the biodegradation of SAs. Through mass spectrometry and metagenomic sequencing analysis, it was found that the common degradation pathways of SAs in biofilm-sediment affected by treated wastewater are acetylation, formylation, hydroxylation, and bond cleavage. Acetyltransferase played an important role in the biodegradation of SAs. In addition, the enrichment of antibiotic resistant genes during biodegradation increased the risk of their spread in the aquatic environment. These findings provide new insights into the fate of antibiotics in aquatic environments and the impact of treated wastewater on downstream bacterial communities.}, } @article {pmid40222470, year = {2025}, author = {Yang, X and Yu, X and Ming, Y and Liu, H and Zhu, W and Yan, B and Huang, H and Ding, L and Qian, X and Wang, Y and Wu, K and Niu, M and Yan, Q and Huang, X and Wang, C and Wang, Y and He, Z}, title = {The vertical distribution and metabolic versatility of complete ammonia oxidizing communities in mangrove sediments.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121602}, doi = {10.1016/j.envres.2025.121602}, pmid = {40222470}, issn = {1096-0953}, abstract = {Recently discovered complete ammonia-oxidizing (comammox) microorganisms can completely oxidize ammonia to nitrate and play an important role in the nitrogen (N) cycle across various ecosystems. However, little is known about the vertical distribution and metabolic versatility of comammox communities in mangrove ecosystems. Here we profiled comammox communities from deep sediments (up to 5 m) in a mangrove wetland by combining metagenome sequencing and physicochemical properties analysis. Our results showed that the relative abundance of comammox bacteria (23.2%) was higher than ammonia-oxidizing bacteria (AOB, 12.0%), but lower than ammonia-oxidizing archaea (AOA, 64.8%). The abundance of comammox communities significantly (p < 0.01) decreased with the sediment depth, and dissolved organic carbon and total sulfur appeared to be major environmental factors influencing the nitrifying microbial community structure. We also recovered a high-quality metagenome-assembled genome (MAG) of comammox bacteria (Nitrospira sp. bin2030) affiliated with comammox clade A. Nitrospira sp. bin2030 possessed diverse metabolic processes, not only the key genes for ammonia oxidation and urea utilization in the N cycle, but also key genes involved in carbon and energy metabolisms, sulfur metabolism, and environmental adaptation (e.g., oxidative stress, salinity, temperature, heavy metal tolerance). The findings advance our understanding of vertical distribution and metabolic versatility of comammox communities in mangrove sediments, having important implications for quantifying their contribution to nitrification processes in mangrove ecosystems.}, } @article {pmid40222255, year = {2025}, author = {Bobrovska, S and Newcomer, E and Gottlieb, M and McSorley, VE and Kittner, A and Hayden, MK and Green, S and Barbian, HJ}, title = {Hospital air sampling enables surveillance of respiratory virus infections and genomes.}, journal = {The Science of the total environment}, volume = {977}, number = {}, pages = {179346}, doi = {10.1016/j.scitotenv.2025.179346}, pmid = {40222255}, issn = {1879-1026}, abstract = {There is an urgent need for early detection and comprehensive surveillance of respiratory pathogens. Environmental surveillance may be key to timely responses for newly emerging pathogens and infections that are unreported or underreported. Here, we employed air sampling in a large urban hospital. Air samples (n = 358) were collected weekly at five locations, including two in the emergency department, two in hospital common areas and one in a storage room, for two respiratory virus seasons (November 2022 to June 2024). Air samples were tested for eight respiratory pathogens by qPCR, including RNA and DNA viruses and a bacterium. Air samples had an average of four detected pathogens per sample and 97 % samples contained SARS-CoV-2. Air sample pathogen positivity and quantity were strongly correlated with clinical surveillance for four seasonal respiratory pathogens: influenza A and B, respiratory syncytial virus, and human metapneumovirus. Targeted amplicon sequencing of SARS-CoV-2 showed that lineages detected in air samples reflected those in contemporaneous regional clinical specimens. Metagenomic sequencing with viral capture enrichment detected myriad human pathogens, including respiratory-associated viruses with recovery of full viral genomes. Detection of viral pathogens correlated well between virus capture sequencing and qPCR. Overall, this suggests air sampling can be an agile and effective tool for pathogen early warning, surveillance and genome characterization.}, } @article {pmid40222247, year = {2025}, author = {Suzuki, M and Hayashi, T and Takahashi, K and Nozaki, K and Kasuya, KI}, title = {Exploring biodegradation limits of n-alkanes as polyethylene models using multi-omics approaches.}, journal = {The Science of the total environment}, volume = {977}, number = {}, pages = {179365}, doi = {10.1016/j.scitotenv.2025.179365}, pmid = {40222247}, issn = {1879-1026}, abstract = {Polyethylene (PE) is widely regarded as non-biodegradable in natural environments, despite reports suggesting partial biotic degradation. Using multi-omics analysis, this study investigated the biodegradation mechanisms of n-alkanes-structural analogs of PE-to determine the threshold carbon number in PE that allows for environmental biodegradation. n-Alkanes with 6-40 carbons (C6-C40) were biodegraded in the soil, whereas C44 and PE were not. 16S rRNA gene amplicon sequence analysis identified distinct microbial communities associated with non-degradable compounds (PEs and C44) and biodegradable alkanes (C6-C40). Notably, the microbial community composition for C40 differed from those associated with biodegradable alkanes below C36. Multi-omics analysis identified the genera Aeromicrobium, Nocardia, Nocardioides, Rhodococcus, Acinetobacter, and Fontimonas as key degraders of n-alkanes at C36 and below, utilizing alkane hydroxylases such as alkane monooxygenase (AlkB), LC-alkane monooxygenase from Acinetobacter (AlmA), and cytochrome P450 (CYP153). Conversely, the biodegradation of C40 was facilitated by taxa, including the order Acidimicrobiales and the genera, Acidovorax, Sphingorhabdus, Prosthecobacter, and Roseimicrobium using AlmA and CYP153-type hydroxylases. This difference in key degraders and alkane hydroxylases may explain the reduced biodegradability of n-alkanes above C40, including PE.}, } @article {pmid40222078, year = {2025}, author = {Xu, A and Gao, D and Wu, WM and Gong, X and Liang, H}, title = {Enhanced denitrification using iron modified biochar under low carbon source condition: Modulating community assembly, allocating carbon metabolism and facilitating electron transfer.}, journal = {Journal of environmental management}, volume = {381}, number = {}, pages = {125354}, doi = {10.1016/j.jenvman.2025.125354}, pmid = {40222078}, issn = {1095-8630}, abstract = {Biochar can modulate microbial community structure to enhance denitrification but the activity is still restricted by the availability of electron transfer (ETS) under metabolic imbalance conditions. Here we developed iron (Ⅲ) modified biochar (FeBC) to substantially mitigate this electron limitation, enhance ETS and accelerate denitrification reaction via intracellular metabolism and community interaction. The results demonstrated that FeBC could significantly improve the denitrification performance, the nitrate removal rate was significantly increased by 30 % at C/N ratio of 3 (W/W) with little nitrite and nitrous oxide accumulation, attributing to the enhanced activities of the ETS and denitrifying reductases and complex microbial interactions via increased abundance of microorganisms involved in carbon and nitrogen transformations. Biochemical quantification and electrochemical analysis, revealed that FeBC activated the acceleration of the ETS process. Comparative metagenome analyses indicated that upregulating key enzymes in the tricarboxylic acid cycle was the potential respiratory enzyme associated with FeBC-mediated ETS. NADH/NAD[+] circulation stimulate the startup of carbon metabolism. This energy-linked mechanism could provide ATP for denitrification. This study revealed the functional roles of FeBC in mediating ETS and regulating the bacterial community to achieve enhanced denitrification.}, } @article {pmid40221653, year = {2025}, author = {Babalola, OO and Adebayo, AA and Enagbonma, BJ}, title = {Shotgun metagenomics dataset of the core rhizo-microbiome of monoculture and soybean-precedent carrot.}, journal = {BMC genomic data}, volume = {26}, number = {1}, pages = {26}, pmid = {40221653}, issn = {2730-6844}, mesh = {*Daucus carota/microbiology ; *Metagenomics/methods ; *Rhizosphere ; *Glycine max/microbiology/growth & development ; *Microbiota ; Soil Microbiology ; High-Throughput Nucleotide Sequencing ; }, abstract = {OBJECTIVES: Carrot is a significant vegetable crop contributing to agricultural diversity and food security, but less is known about the core microbiome associated with its rhizosphere. More so, the effect of preceding crop and cropping history on the composition and diversity of carrot rhizo-microbiome remains largely unknown. With shotgun metagenomics, the study unveils how cropping systems direct rhizo-microbiome structure and functions, previously limited by other methods.

DATA DESCRIPTION: Metagenomic-DNA molecule was extracted from four replicates each (12 samples) of a distant bulk soil and the rhizosphere soils from monoculture and soybean-precedent carrots, with the Power soil® DNA Isolation kit. The DNA samples were subjected to Next Generation Sequencing using the Illumina Novaseq X Plus (PE 150) platform. Raw sequencing reads were assembled and annotated with MEGAHIT and LCA algorithms in MEGAN software respectively, before a quality control check was done with FASTP. CD-Hit was used to de-replicate the sequences and the removal of host genomic-DNA and contaminant sequences was done with Bowtie2. The clean sequence data, in FastQ files, were analyzed for taxonomic classification and functional diversity of the rhizosphere microbiome using the Micro_NR and KEGG database respectively. The findings provide insights into microbiome dynamics, with potential implications for sustainable agricultural practices.}, } @article {pmid40221647, year = {2025}, author = {Zhang, N and Dou, H and Guo, P and Sun, J and Zhang, F and Chen, T and Gao, C and Wang, Z}, title = {Concurrent invasive disseminated Nocardia farcinica and Candida infections in a patient undergoing long-term glucocorticoid therapy for autoimmune thrombocytopenia: a case report.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {520}, pmid = {40221647}, issn = {1471-2334}, support = {gxgnfx2022035//Domestic Visiting Training Program for Outstanding Young Backbone Teachers/ ; 2023SYKFZ05//Open project of Anhui Biochemical Drug Engineering Technology Research Center in 2023/ ; }, mesh = {Humans ; Female ; *Nocardia Infections/drug therapy/diagnosis/microbiology/complications ; Middle Aged ; *Nocardia/isolation & purification ; *Candidiasis/drug therapy/diagnosis/microbiology/complications ; *Purpura, Thrombocytopenic, Idiopathic/drug therapy/complications ; *Glucocorticoids/therapeutic use/adverse effects ; Antifungal Agents/therapeutic use ; Candida albicans/isolation & purification ; Anti-Bacterial Agents/therapeutic use ; *Coinfection/microbiology ; Prednisone/therapeutic use/adverse effects ; Immunocompromised Host ; }, abstract = {BACKGROUND: Nocardia farcinica is a virulent organism known for its high resistance to many antibiotics and its ability to cause disseminated life-threatening infections, particularly in immunocompromised patients or those undergoing organ transplantation. Candida albicans can cause disseminated candidiasis with a mortality rate ranging from 30% to 60%. Cases involving concurrent disseminated N. farcinica and C. albicans, particularly in patients with autoimmune thrombocytopenia, are extremely rare. The presence of two disseminated pathogens complicates both diagnosis and treatment, creating substantial challenges for healthcare providers.

CASE PRESENTATION: A 50-year-old woman who had a history of autoimmune thrombocytopenia and was being treated with prednisone (60 mg qd). She presented with a 40-day history of high-grade fevers (40℃), cough, headache, and multiple abscesses in the skin structure. N. farcinica was found in her skin structure, cerebrospinal fluid, and blood, and C. albicans was cultured in cerebrospinal fluid, sputum, and urine. She was diagnosed with disseminated nocardiosis and disseminated candidiasis. The patient received a prolonged course of multiple anti-bacterial and anti-fungal medications and eventually recovered.

CONCLUSIONS: Due to the atypical clinical presentations, the diagnosis of concurrent invasive disseminated N. farcinica and C. albicans infections might be delayed. A variety of diagnostic testing, including metagenomics next-generation sequencing, can help to identify the pathogen rapidly. Drug susceptibility test can guide the selection and adjustment of antibiotics, which should be in companion with surgical interventions to save lives in affected patients.}, } @article {pmid40221512, year = {2025}, author = {Yong, Y and Zhou, L and Zhang, X and Ran, X and Guo, Y and Gai, W and Chen, Y}, title = {The clinical value of metagenomic next-generation sequencing in the diagnosis of pulmonary tuberculosis and the exploration of lung microbiota characteristics.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {12568}, pmid = {40221512}, issn = {2045-2322}, support = {82104236//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Tuberculosis, Pulmonary/diagnosis/microbiology ; Male ; Female ; Middle Aged ; *Lung/microbiology ; *Microbiota/genetics ; Adult ; *Mycobacterium tuberculosis/genetics/isolation & purification ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; *Metagenomics/methods ; Bronchoalveolar Lavage Fluid/microbiology ; Aged ; }, abstract = {The lung microbiota plays a critical role in many important physiological processes and is linked with various pulmonary infectious diseases. The present study aimed to characterize the lung microbiota in patients with pulmonary tuberculosis (PTB), and to explore the association between the abundance of Mycobacterium tuberculosis complex (MTBC) and the lung microbiota. This retrospective study included 190 patients with MTBC infection. The enrolled patients were classified into three groups based on the abundance results of bronchoalveolar lavage fluid (BALF) mNGS: low [reads per ten million (RPTM) = 1 ~ 1000], medium (RPTM = 1001 ~ 10000) and high (RPTM > 10000). In the high-abundance group, there were more bilateral lobar involvement and symptoms of cavitation. In addition to mNGS, the highest positivity rates were T-spot (92.36%), GeneXpert (71.58%), culture (68.95%) and AFB smear (17.84%). The positive rates of culture, AFB smear and GeneXpert increased with the increase of MTBC abundance, and the positive rates were highest in the high-abundance MTBC group. Both the alpha and beta diversity showed significant difference between the three groups, with the high-abundance MTBC groups showed lowest alpha diversity. The increased abundance of MTBC positively associated with the longer time of hospital stay. To sum up, the lung microbiota of patients with PTB were significantly distinct between groups with different abundant levels of MTBC. Combined with imaging features, a high abundance of MTBC suggests the patient is more severely ill and has a poorer prognosis.}, } @article {pmid40221485, year = {2025}, author = {Wu, Q and Gao, J and Sa, B and Cong, H and Deng, W and Zhang, Y and Zhong, X and Zhang, J and Wang, L and Liu, H and Yan, Y and Zhang, Y and Liu, D and Yan, W}, title = {Genomes of Prochlorococcus, Synechococcus, bacteria, and viruses recovered from marine picocyanobacteria cultures based on Illumina and Qitan nanopore sequencing.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {612}, pmid = {40221485}, issn = {2052-4463}, support = {42188102//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42293292//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Prochlorococcus/genetics ; *Synechococcus/genetics ; *Genome, Bacterial ; Nanopore Sequencing ; *Genome, Viral ; Metagenome ; Pacific Ocean ; Indian Ocean ; Seawater/microbiology ; High-Throughput Nucleotide Sequencing ; }, abstract = {Prochlorococcus and Synechococcus are key contributors to marine primary production and play essential roles in global biogeochemical cycles. Despite the ecological importance of these two picocyanobacterial genera, current genomic datasets still lack comprehensive representation of under-sampled ocean regions, associated bacteria and viruses. To address this gap, we used a combination of second- and third-generation sequencing technologies to assemble comprehensive genomic data from 105 Picocyanobacterial enrichment cultures isolated from the Indian Ocean, the South China Sea, and the western Pacific Ocean. This dataset includes 55 Prochlorococcus and 50 Synechococcus genomes with high completeness (>98%) and low contamination (<2%), along with 308 non-redundant associated bacterial genomes derived from 1,457 medium- and high-quality non-cyanobacteria metagenome-assembled genomes (MAGs, completeness ≥50% and contamination ≤10%). Additionally, 2,113 non-redundant viral operational taxonomic units (vOTUs) were derived from a total of 7632 qualified viral contigs. This dataset provides a valuable resource for improving our understanding of the complex interactions among Prochlorococcus, Synechococcus, and their associated bacteria and viruses in marine ecosystems, offering a foundation to study their ecological roles and evolutionary dynamics.}, } @article {pmid40221450, year = {2025}, author = {Kim, KS and Noh, J and Kim, BS and Koh, H and Lee, DW}, title = {Refining microbiome diversity analysis by concatenating and integrating dual 16S rRNA amplicon reads.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {57}, pmid = {40221450}, issn = {2055-5008}, support = {RS-2021-NR056579//National Research Foundation of Korea (NRF)/ ; RS-2023-KH141436//Ministry of Health and Welfare (Ministry of Health, Welfare and Family Affairs)/ ; 200118770//Ministry of Trade, Industry and Energy (Ministry of Trade, Industry and Energy, Korea)/ ; }, mesh = {*RNA, Ribosomal, 16S/genetics ; Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteria/classification/genetics/isolation & purification ; *Metagenomics/methods ; Sequence Analysis, DNA/methods ; Metagenome ; Colitis, Ulcerative/microbiology ; DNA, Bacterial/genetics ; Republic of Korea ; Phylogeny ; Feces/microbiology ; Biodiversity ; High-Throughput Nucleotide Sequencing ; }, abstract = {Understanding the role of human gut microbiota in health and disease requires insights into its taxonomic composition and functional capabilities. This study evaluates whether concatenating paired-end reads enhances data output for gut microbiome analysis compared to the merging approach across various regions of the 16S rRNA gene. We assessed this approach in both mock communities and Korean cohorts with or without ulcerative colitis. Our results indicate that using the direct joining method for the V1-V3 or V6-V8 regions improves taxonomic resolution compared to merging paired-end reads (ME) in post-sequencing data. While predicting microbial function based on 16S rRNA sequencing has inherent limitations, integrating sequencing reads from both the V1-V3 and V6-V8 regions enhanced functional predictions. This was confirmed by whole metagenome sequencing (WMS) of Korean cohorts, where our approach improved taxa detection that was lost using the ME method. Thus, we propose that the integrated dual 16S rRNA sequencing technique serves as a valuable tool for microbiome research by bridging the gap between amplicon sequencing and WMS.}, } @article {pmid40220806, year = {2025}, author = {Ye, G and Li, M and Huang, H and Avellán-Llaguno, RD and Chen, J and Chen, G and Huang, Q}, title = {Polystyrene microplastic exposure induces selective accumulation of antibiotic resistance genes in gut microbiota and its potential health risks.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {142983}, doi = {10.1016/j.ijbiomac.2025.142983}, pmid = {40220806}, issn = {1879-0003}, abstract = {As emerging pollutants, antibiotic resistance genes (ARGs) and microplastics threaten the environment and human health. Gut microbiota is a hotspot for ARG emergence and spread. However, effects of microplastic exposure on the emergence and spread of gut microbial ARGs are unclear. Therefore, metagenomics was used to characterize polystyrene microplastics (PS)-induced ARG alterations in rat gut microbiota and their health risks, and to identify key ARG hosts and pathways as intervention targets. We found that PS exposure not only induced selective accumulation of glycopeptide and aminoglycoside ARGs, but also promoted mobility risks of glycopeptide and macrolide-lincosamide-streptogramin ARGs in gut microbiota. Metagenomic reassembly identified microbes belonging to Firmicutes (particularly order Clostridiales, such as speices Lachnospiraceae bacterium 3-1 and MD335) as major ARG hosts. Meanwhile, genera Enterococcus, Clostridioides and Streptococcus were main ARG hosts among human pathogens. Furthermore, glycopeptide and aminoglycoside ARGs were highly correlated with VanS/VanR signaling and its regulatory pathways of vancomycin resistance and peptidoglycan metabolism, amino sugar and nucleotide sugar metabolism, and CpxR signaling and its regulatory remodeling of cell envelope peptidoglycans and proteins in gut microbiota upon PS exposure. This study provides novel insights and intervention targets involved in PS-induced changes in gut microbial ARGs and their health risks.}, } @article {pmid40220770, year = {2025}, author = {Venkatesan, P}, title = {UK launch metagenomic pathogen surveillance programme.}, journal = {The Lancet. Microbe}, volume = {}, number = {}, pages = {101143}, doi = {10.1016/j.lanmic.2025.101143}, pmid = {40220770}, issn = {2666-5247}, } @article {pmid40220715, year = {2025}, author = {Chen, Y and Chen, Z and Liang, L and Li, J and Meng, L and Yuan, W and Xie, B and Zhang, X and Feng, L and Jia, Y and Fu, Z and Su, P and Tong, Z and Zhong, J and Liu, X}, title = {Multi-kingdom gut microbiota dysbiosis is associated with the development of pulmonary arterial hypertension.}, journal = {EBioMedicine}, volume = {115}, number = {}, pages = {105686}, doi = {10.1016/j.ebiom.2025.105686}, pmid = {40220715}, issn = {2352-3964}, abstract = {BACKGROUND: Gut microbiota dysbiosis has been implicated in pulmonary arterial hypertension (PAH). However, the exact roles and underlying mechanisms of multi-kingdom gut microbiota, including bacteria, archaea, and fungi, in PAH remain largely unclear.

METHODS: The shotgun metagenomics was used to analyse multi-kingdom gut microbial communities in patients with idiopathic PAH (IPAH) and healthy controls. Furthermore, fecal microbiota transplantation (FMT) was performed to transfer gut microbiota from IPAH patients or monocrotaline (MCT)-PAH rats to normal rats and from normal rats to MCT-PAH rats.

FINDINGS: Gut microbiota analysis revealed substantial alterations in the bacterial, archaeal, and fungal communities in patients with IPAH compared with healthy controls. Notably, FMT from IPAH patients or MCT-PAH rats induced PAH phenotypes in recipient rats. More intriguingly, FMT from normal rats to MCT-PAH rats significantly ameliorated PAH symptoms; restored gut bacteria, archaea, and fungi composition; and shifted the plasma metabolite profiles of MCT-PAH rats toward those of normal rats. In parallel, RNA-sequencing analysis demonstrated the expression of genes involved in key signalling pathways related to PAH. A panel of multi-kingdom markers exhibited superior diagnostic accuracy compared with single-kingdom panels for IPAH.

INTERPRETATION: Our findings established an association between multi-kingdom gut microbiota dysbiosis and PAH, thereby indicating the therapeutic potential of FMT in PAH. More importantly, apart from gut bacteria, gut archaea and fungi were also significantly associated with PAH pathogenesis, highlighting their indispensable role in PAH.

FUNDING: This work was supported by Noncommunicable Chronic Diseases-National Science and Technology Major Projects No. 2024ZD0531200, No. 2024ZD0531201 (Research on Prevention and Treatment of Cancer, Cardiovascular and Cerebrovascular Diseases, Respiratory Diseases, and Metabolic Diseases), the National Natural Science Foundation of China of China (No. 82170302, 82370432), Financial Budgeting Project of Beijing Institute of Respiratory Medicine (Ysbz2025004, Ysbz2025007), National clinical key speciality construction project Cardiovascular Surgery, Reform and Development Program of Beijing Institute of Respiratory Medicine (Ggyfz202417, Ggyfz202501), Clinical Research Incubation Program of Beijing Chaoyang Hospital Affiliated to Capital Medical University (CYFH202209).}, } @article {pmid40220662, year = {2025}, author = {Yuan, Q and Ng, C and Goh, SG and Khor, WC and Ong, GHM and Aung, KT and Gin, KY}, title = {Evaluation of public health impact risks associated with bacterial antimicrobial resistome in tropical coastal environments.}, journal = {Water research}, volume = {282}, number = {}, pages = {123621}, doi = {10.1016/j.watres.2025.123621}, pmid = {40220662}, issn = {1879-2448}, abstract = {This study investigated antimicrobial resistance genes (ARGs) and microbial communities in Singapore's tropical coastal environments, comparing natural marine waters with aquaculture sites using metagenomic analysis. Results show consistently low ARG levels in natural ecosystems, whereas aquaculture sites exhibit elevated ARG concentrations, particularly those relevant to human pathogens, with considerably temporal fluctuations likely driven by human activities and seasonal factors. Additionally, aquaculture sites were found to host mobile genetic elements (MGEs) that may facilitate ARG spread, identifying aquaculture as a key reservoir of resistance genes with potential public health implications. These findings underscore distinct prevalence of ARG between natural and managed marine environments and highlight the need for continued surveillance to monitor ARG dynamics in coastal areas. By elucidating the potential for ARGs to transfer from aquaculture environments to the human food chain, this research emphasizes the importance of sustainable aquaculture practices and proactive ARG management strategies to mitigate antimicrobial resistance risks posed by tropical coastal ecosystem.}, } @article {pmid40220550, year = {2025}, author = {Silva, CJFD and Silva, CVFD and Cardoso, AM and de Oliveira Santos, E}, title = {Exploring clinical parameters and salivary microbiome profiles associated with metabolic syndrome in a population of Rio de Janeiro, Brazil.}, journal = {Archives of oral biology}, volume = {175}, number = {}, pages = {106251}, doi = {10.1016/j.archoralbio.2025.106251}, pmid = {40220550}, issn = {1879-1506}, abstract = {OBJECTIVES: This study investigates for the first time the association between metabolic syndrome and oral microbial profiles in a population-based sample from Rio de Janeiro, Brazil.

DESIGN: We assessed 66 volunteers, collecting detailed sociodemographic, anthropometric, and clinical data alongside salivary samples for metagenomic analysis.

RESULTS: Our findings reveal significant differences in anthropometric parameters, including waist circumference, glycemia, High-Density Lipoprotein (HDL), and triglycerides between the metabolic syndrome and control groups. Increased abundance of Bacteroidetes and Bacteroidia was observed in the metabolic syndrome group, suggesting a potential link between these phyla and metabolic dysregulation. While no significant differences in alpha diversity were found between the overall groups, stratification by body mass index (BMI) indicated that the normal weight subgroup without Metabolic Syndrome exhibited notable variations compared to overweight and obese individuals.

CONCLUSIONS: This study identifies specific shifts in oral microbiota composition that are associated with metabolic syndrome, highlighting their potential as microbial biomarkers for this condition. These findings suggest a link between oral dysbiosis and metabolic dysregulation, providing new insights into the pathophysiology of metabolic syndrome. Additionally, the results pave the way for the development of non-invasive diagnostics tools and targeted therapies that leverage the oral microbiome's role in systemic health.}, } @article {pmid40220395, year = {2025}, author = {Zhu, Y and Zhang, X and Tao, W and Yang, S and Qi, H and Zhou, Q and Su, W and Zhang, Y and Dong, Y and Gan, Y and Lei, C and Zhang, A}, title = {Mitigating the risk of antibiotic resistance and pathogenic bacteria in swine waste: The role of ectopic fermentation beds.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138221}, doi = {10.1016/j.jhazmat.2025.138221}, pmid = {40220395}, issn = {1873-3336}, abstract = {The ectopic fermentation bed (EFB) is used to recycle animal waste, but the fate and dynamic change of antibiotic resistance genes (ARGs) with biocide or heavy metal resistance genes (B/MRGs) and pathogens remain unclear. We performed metagenomic sequencing on 129 samples to study the resistome and bacteriome in pig feces from 24 farms, comparing these profiles with EFBs from five farms, and one farm's EFB was monitored for 154 days. Results showed pig feces from different cities (Chengdu, Meishan, and Chongqing) shared 284 of 311 ARG subtypes, with over 70 % being high-risk ARGs, and 106 of 114 pathogenic bacteria. Swine farms were heavily contaminated with co-occurrences of risky ARGs, B/MRGs, and pathogenic hosts, particularly Escherichia coli and Streptococcus suis being hosts of multidrug ARGs. The application of EFBs markedly mitigated these risks in feces, showing a 3.09-fold decrease in high-risk ARGs, a 72.22 % reduction in B/MRGs, a 3.95-fold drop in prioritized pathogens, an 89.09 % decline in the relative abundance of pig pathogens, and a simplification of their correlation networks and co-occurrence patterns. A mantel analysis revealed that metal contents (Fe, Mn, and Cu) and time influenced pathogen and ARG profiles. Pathogens, ARGs, and risk ARGs exhibited periodic variations, peaking at days 14, 84, and 154, with 70-day intervals. This study provides a comprehensive assessment of the risks associated with pig feces and EFBs and demonstrates that EFBs reduce ARG risks by inhibiting their associations with B/MRGs and pathogens. These findings can help guide and improve the management of antimicrobial resistance and pathogenic contaminants in EFB applications to reduce environmental pollution.}, } @article {pmid40219113, year = {2025}, author = {Vinskienė, J and Tamošiūnė, I and Andriūnaitė, E and Gelvonauskienė, D and Rugienius, R and Hakim, MF and Stanys, V and Buzaitė, O and Baniulis, D}, title = {Inoculum of Endophytic Bacillus spp. Stimulates Growth of Ex Vitro Acclimatised Apple Plantlets.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {7}, pages = {}, doi = {10.3390/plants14071045}, pmid = {40219113}, issn = {2223-7747}, support = {S-MIP-22-54//Lietuvos Mokslo Taryba/ ; }, abstract = {In vitro shoot culture and cryopreservation (CP) are techniques essential for the ex situ preservation of genetic resources and the production of plant propagation material of clonally propagated horticultural crops. Changes in plant-associated microbiota diversity and composition induced by in vitro cultivation and CP treatment could have a negative effect on the growth and ex vitro adaptation of the in vitro propagated shoots. Therefore, the aim of the present study was to assess changes in endophytic bacteria diversity in domestic apple tissues induced by in vitro cultivation and CP treatment and to investigate the potential of the bacterial inoculum to improve the rooting and ex vitro acclimatisation of the propagated shoots. Metataxonomic analysis revealed a variation in the endophytic bacteria diversity and taxonomic composition between the field-grown tree dormant bud and the in vitro propagated or CP-treated shoot samples of apple cv. Gala. Whereas Sphingobacteriaceae, Sphingomonadaceae, Pseudomonadaceae, and Beijerinckiaceae families were the most prevalent families in the bud samples, Enterobacteriaceae, Bacillaceae, and Lactobacillaceae were dominant in the in vitro shoots. The bacterial inoculum effect on rooting and ex vitro acclimatisation was assessed using four isolates selected by screening the endophytic isolate collection. Bacillus sp. L3.4, B. toyonensis Nt18, or a combined inoculum resulted in a 21%, 36%, and 59% increase in cumulative root length and a 41%, 46%, and 35% increase in the biomass accumulation of ex vitro acclimatised plantlets, respectively. Root zone microbiota functional diversity analysis implied that growth stimulation was not related to improved nutrient uptake but could involve a pathogen-suppressing effect. The results demonstrate that the application of plant growth-promoting bacteria can potentially improve the performance of the in vitro propagated germplasm.}, } @article {pmid40219101, year = {2025}, author = {Fouad, N and El-Zayat, EM and Amr, D and El-Khishin, DA and Abd-Elhalim, HM and Hafez, A and Radwan, KH and Hamwieh, A and Tadesse, W}, title = {Characterizing Wheat Rhizosphere Bacterial Microbiome Dynamics Under Salinity Stress: Insights from 16S rRNA Metagenomics for Enhancing Stress Tolerance.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {7}, pages = {}, doi = {10.3390/plants14071033}, pmid = {40219101}, issn = {2223-7747}, abstract = {Salinity is one of the most important abiotic stress factors affecting wheat production. Salt in the soil is a major environmental stressor that can affect the bacterial community in the rhizosphere of wheat. The bacteria in the plant's rhizosphere promote growth and stress tolerance, which vary by variety and location. Nevertheless, the soil harbors some of the most diverse microbial communities, while the rhizosphere selectively recruits according to the needs of plants in a complex harmonic regulation. The microbial composition and diversity under normal and saline conditions were assessed by comparing the rhizosphere of wheat with soil using 16S rRNA gene amplicon sequencing, highlighting the number of operational taxonomic units (OTUs). Taxonomic analyzes showed that the bacterial community was predominantly and characteristically composed of the phyla Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Verrucomicrobia, and Fibrobacteres, representing the usual microbial profile for the rhizosphere of wheat. Idiomarinaceae, Rheinheimera, Halomonas, and Pseudomonas (a strain of Proteobacteria), together with Gracilibacillus (a strain of Firmicutes Bacilli), were recognized as microbial signatures for the rhizosphere microbiome under saline conditions. This was observed even with unchanged soil type and genotype. These patterns occurred despite the same soil type and genotype, with salinity being the only variable. The collective action of these bacterial phyla in the rhizosphere not only improves nutrient availability but also induces systemic resistance in the plants. This synergistic effect improves plant resistance to salt stress and supports the development of salt-tolerant wheat varieties. These microbial signatures could improve our understanding of plant-microbe interactions and support the development of microbiome-based solutions for salt stress.}, } @article {pmid40218354, year = {2025}, author = {Zhu, F and Ma, J and Xue, M and Xu, W and Liu, W and Zhou, Y and Liu, M and Fan, Y}, title = {Seasonal and Regional Dynamics of the Intestinal Microbiota in Schizothorax nukiangensis from the Nujiang River.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {7}, pages = {}, doi = {10.3390/ani15070961}, pmid = {40218354}, issn = {2076-2615}, support = {2023TD46, 2023TD09//Central Public-interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences (CAFS)/ ; }, abstract = {The dynamic alterations in intestinal microbiota can provide insights into the adaptive relationships between these microorganisms and their hosts in response to environmental changes. Schizothorax nukiangensis is widely distributed throughout the Nujiang River and exhibits numerous unique adaptations. In this study, we collected samples of S. nukiangensis across different seasons and regions within the Nujiang River to comprehensively elucidate the diversity and composition of its intestinal microbiota using metagenomic technology. The results indicated that Firmicutes and Proteobacteria predominated at the phylum level, while Priestia, Bacillus, and Aeromonas were the most abundant genera identified. Notably, the relative abundance of these microorganisms varied significantly across different seasons and regions. From autumn through spring and into summer, the predominant microorganisms shifted from Firmicutes to Proteobacteria. Biomarker analysis revealed that Firmicutes (including the class bacilli and the genera Priestia and Bacillus) exhibited a higher relative abundance within the upstream group, where categories related to amino acid metabolism and carbohydrate metabolism were significantly enriched. Conversely, Proteobacteria (including several potential pathogens, such as Saezia, Pantoea, Lelliotia, and Aeromonas genera) showed an increased relative abundance within downstream groups, where disease-related categories exhibited significant enrichment. Our findings significantly enhance our understanding of how S. nukiangensis adapts to its environment, providing valuable data support for the conservation of S. nukiangensis and for ecological security assessment of the Nujiang River.}, } @article {pmid40218343, year = {2025}, author = {Ajmi, N and Duman, M and Coskun, B and Esen, C and Sonmez, O and Tasci, G and Coskuner-Weber, O and Ay, H and Yoyen-Ermis, D and Yibar, A and Desbois, AP and Saticioglu, IB}, title = {Unraveling Genomic and Pathogenic Features of Aeromonas ichthyocola sp. nov., Aeromonas mytilicola sp. nov., and Aeromonas mytilicola subsp. aquatica subsp. nov.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {7}, pages = {}, doi = {10.3390/ani15070948}, pmid = {40218343}, issn = {2076-2615}, support = {TGA-2024-1797 and 124Z735//The Research Fund of Bursa Uludag University and TÜBİTAK/ ; }, abstract = {The Gram-negative genus Aeromonas contains diverse bacterial species that are prevalent in aquatic environments. This present study describes three novel Aeromonas strains: A. ichthyocola sp. nov. A-5[T] and A. mytilicola subsp. aquatica subsp. nov. A-8[T] isolated from rainbow trout (Oncorhynchus mykiss), and A. mytilicola sp. nov. A-7[T] isolated from mussels (Mytilus galloprovincialis), respectively. Genomic analyses revealed that strains A-5[T] and A-7[T] shared the highest 16S rRNA gene sequence similarity with A. rivipollensis P2G1[T] (99.7% and 99.8%, respectively), while strain A-8[T] exhibited 99.7% identity with A. media RM[T]. Together with morphological, physiological, and biochemical data, genome-based analyses provided additional evidence for species differentiation. Digital DNA-DNA hybridization (dDDH; 56.8-65.9%) and average nucleotide identity (ANI; 94.2-95.7%) values fell below the species delineation thresholds, confirming that these isolates represent distinct taxa. Pathogenicity assays using greater wax moth (Galleria mellonella) larvae demonstrated strain-specific virulence profiles. Further genomic analyses identified biosynthetic gene clusters for nonribosomal peptides (NRPs) and ribosomally synthesized and post-translationally modified peptides (RiPPs), which often have roles in secondary metabolite production. Ecological analyses, based on genomic comparisons and metagenomic database searches, revealed the adaptability of the strains to diverse habitats, including freshwater, wastewater, and activated sludge. Based on the genetic and phenotypic data, the novel taxa Aeromonas ichthyocola sp. nov. A-5ᵀ (LMG 33534ᵀ = DSM 117488ᵀ), Aeromonas mytilicola sp. nov. A-7ᵀ (LMG 33536ᵀ = DSM 117490ᵀ), and Aeromonas mytilicola subsp. aquatica subsp. nov. A-8ᵀ (LMG 33537ᵀ = DSM 117493ᵀ) are proposed.}, } @article {pmid40217586, year = {2025}, author = {Komoróczy, B and Váncsa, S and Váradi, A and Hegyi, P and Vágási, V and Baradács, I and Szabó, A and Nyirády, P and Benkő, Z and Ács, N}, title = {Optimal Aspirin Dosage for the Prevention of Preeclampsia and Other Adverse Pregnancy Outcomes: A Systematic Review and Meta-Analysis of Randomized Controlled Trials.}, journal = {Journal of clinical medicine}, volume = {14}, number = {7}, pages = {}, doi = {10.3390/jcm14072134}, pmid = {40217586}, issn = {2077-0383}, abstract = {Background/Objectives: This systematic review and meta-analysis aimed to determine the effectiveness of different aspirin dosages in preventing preeclampsia and its effect on other pregnancy-associated conditions. Methods: A comprehensive search of three databases (Pubmed, Embase, and Cochrane Library) was conducted for randomized controlled trials without time interval criteria, comparing aspirin at various doses with placebo or no specific preeclampsia prophylaxis. Eligible randomized controlled trials (RCTs) examined pregnant women receiving aspirin at any dose and time during their pregnancy, while the control group received a placebo, or placebo and a different dose of aspirin, or no specific preeclampsia prevention. No exclusion criteria were established regarding the population, study size, study site, or length of aspirin prophylaxis. Studies examining additional preventive medication (such as low-molecular-weight heparin) compared to aspirin without a placebo group were excluded. For all outcomes, the risk ratios (RRs) and mean differences (MDs) with 95% confidence intervals (CIs) were calculated. Meta-regression was performed to examine the relation between aspirin dosage and preeclampsia. Results: Based on the analysis of 31 studies involving 28,318 pregnancies and 20 studies involving 26,551 pregnancies, the early initiation of aspirin significantly reduced the overall incidence of preeclampsia (RR = 0.63, CI: 0.47-0.84) and perinatal death risk (RR = 0.82, CI: 0.72-0.93), respectively. Based on our meta-regression model, we could not establish a dose-dependent correlation between aspirin dosage and the risk of preeclampsia. Conclusions: Early-initiated aspirin prophylaxis is effective in preventing preeclampsia, without raising the incidence of placental abruption or increasing the amount of peripartum bleeding. No specific dose was superior to others; thus, further research should explore higher doses and focus on preterm preeclampsia, maternal-fetal complications, and bleeding.}, } @article {pmid40217292, year = {2025}, author = {Diop, K and Mbaye, B and Nili, S and Filin, A and Benlaifaoui, M and Malo, J and Renaud, AS and Belkaid, W and Hunter, S and Messaoudene, M and Lee, KA and Elkrief, A and Routy, B}, title = {Coupling culturomics and metagenomics sequencing to characterize the gut microbiome of patients with cancer treated with immune checkpoint inhibitors.}, journal = {Gut pathogens}, volume = {17}, number = {1}, pages = {21}, pmid = {40217292}, issn = {1757-4749}, abstract = {BACKGROUND: The gut microbiome represents a novel biomarker for melanoma and non-small cell lung cancer (NSCLC) patients treated with immune checkpoint inhibitors (ICI). Gut microbiome metagenomics profiling studies of patients treated with immunotherapy identified bacteria associated with ICI efficacy, while others have been linked to resistance. However, limitations of metagenomics sequencing, such as complex bioinformatic processing requirements, necessity of a threshold for positive detection, and the inability to detect live organisms, have hindered our ability to fully characterize the gut microbiome. Therefore, combining metagenomics with high-throughput culture-based techniques (culturomics) represents an ideal strategy to fully characterize microbiome composition to more robustly position the microbiome as a biomarker of response to ICI.

METHODS: We performed culturomics using fecal samples from 22 patients from two academic centres in Canada and the United Kingdom with NSCLC and cutaneous melanoma treated with ICI (cancer group), comparing their microbiome composition to that of 7 healthy volunteers (HV), along with matching shotgun metagenomics sequencing.

RESULTS: For culturomics results, 221 distinct species were isolated. Among these 221 distinct species, 182 were identified in the cancer group and 110 in the HV group. In the HV group, the mean species richness was higher compared to the cancer group (34 vs. 18, respectively, p = 0.002). Beta diversity revealed separate clusters between groups (p = 0.004). Bifidobacterium spp. and Bacteroides spp. were enriched in HV, while cancer patients showed an overrepresentation of Enterocloster species, as well as Veillonella parvula. Next, comparing cancer patients' clinical outcomes to ICI, we observed that among the 20 most abundant bacteria present in non-responder patients, 2 belonged to the genus Enterocloster, along with an enrichment of Hungatella hathewayi and Cutibacterium acnes. In contrast, responders to ICI exhibited a predominance of Bacteroides spp. In NSCLC patients, metagenomics analysis revealed that of the 154 bacteria species isolated through culturomics, 61/154 (39%) were also identified by metagenomics sequencing. Importantly, 94 individual species were uniquely detected by culturomics.

CONCLUSION: These findings highlight that culturomics and metagenomics can serve as complementary tools to characterize the microbiome in patients with cancer. This integrated approach uncovers specific microbiome signatures that differentiate HV from cancer patients, and identifies specific species associated with therapy response and resistance.}, } @article {pmid40216789, year = {2025}, author = {Shekarriz, S and Szamosi, JC and Whelan, FJ and Lau, JT and Libertucci, J and Rossi, L and Fontes, ME and Wolfe, M and Lee, CH and Moayyedi, P and Surette, MG}, title = {Detecting microbial engraftment after FMT using placebo sequencing and culture enriched metagenomics to sort signals from noise.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {3469}, pmid = {40216789}, issn = {2041-1723}, mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Metagenomics/methods ; *Colitis, Ulcerative/therapy/microbiology ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Male ; Female ; Placebos ; Adult ; Middle Aged ; }, abstract = {Fecal microbiota transplantation (FMT) has shown efficacy for the treatment of ulcerative colitis but with variable response between patients and trials. The mechanisms underlying FMT's therapeutic effects remains poorly understood but is generally assumed to involve engraftment of donor microbiota into the recipient's microbiome. Reports of microbial engraftment following FMT have been inconsistent between studies. Here, we investigate microbial engraftment in a previous randomized controlled trial (NCT01545908), in which FMT was sourced from a single donor, using amplicon-based profiling, shotgun metagenomics, and culture-enriched metagenomics. Placebo samples were included to estimate engraftment noise, and a significant level of false-positive engraftment was observed which confounds the prediction of true engraftment. We show that analyzing engraftment across multiple patients from a single donor enhances the accuracy of detection. We identified a unique set of genes engrafted in responders to FMT which supports strain displacement as the primary mechanism of engraftment in our cohort.}, } @article {pmid40216686, year = {2025}, author = {Fan, Q and Zhang, Y and Lian, J and Liang, D and Yu, J and Liu, X and Zhang, N}, title = {Screening and community succession and functional prediction of high-efficiency degradation microbial communities for rice straw at low-temperature.}, journal = {Extremophiles : life under extreme conditions}, volume = {29}, number = {2}, pages = {20}, pmid = {40216686}, issn = {1433-4909}, support = {2023YFD2100803//National Key R&D Programme Project of China/ ; }, mesh = {*Oryza/microbiology/metabolism ; *Microbiota ; *Cold Temperature ; Lignin/metabolism ; }, abstract = {Traditional straw return relies on microbial degradation, but cold winters delay it, risking crops. Therefore, a microbial community adapted to rice straw degradation in cold regions was constructed by restrictive consecutively sub-cultured under low-temperature limitations. The capabilities of the microbial community, such as adaptability, stability, and degradation power, were evaluated by analyzing straw degradation features, Characterization experiments and lignocellulose enzyme activities across multiple generations. 16S amplicon sequencing was used to monitor the changes in its structure over generations. Metagenomic sequencing uses CAZy and KEGG to classify gene functions. The results showed that the highest degradation efficiencies and enzyme activities were observed in the E and F generations, dominated by Proteobacteria, Bacteroidetes, and Fungi The stable microbial community was designated as LJ-7. Metagenomic analysis showed that functional genes of LJ-7 were mainly concentrated in glycoside hydrolase (GHs) and glycosyl transferase (GTs) related genes which contained many fiber and lignin-degrading enzyme genes. It is speculated that microbial enzymes degrade straw by breaking down its complex structure into monosaccharides or metabolizing quinone compounds for energy. This experiment successfully screened a microbial community capable of degrading rice straw at low temperatures, thus offering novel research insights and pathways for straw degradation in cold conditions.}, } @article {pmid40216167, year = {2025}, author = {Sangfuang, N and Xie, Y and McCoubrey, LE and Taub, M and Favaron, A and Mai, Y and Gaisford, S and Basit, AW}, title = {Investigating the bidirectional interactions between senotherepeutic agents and human gut microbiota.}, journal = {European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences}, volume = {}, number = {}, pages = {107098}, doi = {10.1016/j.ejps.2025.107098}, pmid = {40216167}, issn = {1879-0720}, abstract = {Biological ageing is a time-dependent process that has implications for health and disease. Cellular senescence is a key driver in ageing and age-related diseases. Senotherapeutic agents have been shown to slow biological ageing by eliminating senescent mammalian cells. Given the increasing awareness of the gut microbiome in regulating human health, this study aimed to investigate the effects of senotherapeutic agents as pharmacological interventions on the human gut microbiota. In this study, the bidirectional effects of four senotherapeutic agents, quercetin, fisetin, dasatinib, and sirolimus, with the gut microbiota sourced from healthy human donors were investigated. The results revealed that quercetin was completely biotransformed by the gut microbiota within six hours, while dasatinib was the most stable of the four compounds. Additionally, metagenomic analysis confirmed that all four compounds increased the abundance of bacterial species associated with healthy ageing (e.g., Bacteroides fragilis, Bifidobacterium longum, and Veillonella parvula), and decreased the abundance of pathogenic bacteria primarily associated with age-related diseases (e.g., Enterococcus faecalis and Streptococcus spp.). The findings from this study provide a comprehensive understanding of the pharmacobiomics of senotherapeutic interventions, highlighting the potential of microbiome-targeted senolytics in promoting healthy ageing.}, } @article {pmid40216056, year = {2025}, author = {Liu, S and Li, J and Zhang, Z and Tuo, J and Zhang, Q and Zhou, J and Liu, P and Zhang, XX}, title = {Exploring phylogenetic diversity of antibiotic resistance genes in activated sludge: A host and genomic location perspective.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121588}, doi = {10.1016/j.envres.2025.121588}, pmid = {40216056}, issn = {1096-0953}, abstract = {Antibiotic resistance has emerged as a significant global public health issue. The environmental behaviors of antibiotic resistance genes (ARGs), such as their persistence and horizontal transfer, have been extensively investigated. However, the genetic diversity characteristics of ARGs remain underexplored, which limits a comprehensive analysis of their roles in the environment. In this study, we examined the genetic diversity of ARGs in activated sludge from 44 wastewater treatment plants in five countries. Most ARGs detected in activated sludge possessed multiple variants, with a median of 48. The number of variants of gd-ARGs varied among different resistance mechanisms and ARG types. The number of potential variants of ARGs was strongly correlated with host diversity. Pseudomonas spp. and Klebsiella pneumoniae, identified as pathogenic bacteria, harbored multiple ARGs and had the most variants. Most ARG subtypes on plasmids and chromosomes showed divergent evolution. Molecular docking of AdeH proteins revealed that genomic location affects tetracycline binding energy. The findings underscore the intricate interplay between genetic variation and environmental adaptation in ARGs, offering a novel perspective on the spread of antibiotic resistance.}, } @article {pmid40215877, year = {2025}, author = {Saeed, M and Al-Khalaifah, H and Al-Nasser, A and Al-Surrayai, T}, title = {Feeding the future: A new potential nutritional impact of Lactiplantibacillus plantarum and its promising interventions in future for poultry industry.}, journal = {Poultry science}, volume = {104}, number = {6}, pages = {105130}, doi = {10.1016/j.psj.2025.105130}, pmid = {40215877}, issn = {1525-3171}, abstract = {The increasing demand for sustainable and efficient chicken production has intensified the interest in functional feed additives such as probiotics. Lactiplantibacillus plantarum (formerly known as Lactobacillus plantarum) is an important probiotic bacterium that has become an essential component in poultry nutrition owing to its diverse advantages. This bacterium improves gut health by regulating the intestinal microbiota, increasing food absorption, and strengthening the immune system. It also alleviates the detrimental impacts of pathogenic bacteria, thereby reducing the reliance on antibiotics and promoting antibiotic-free poultry production. Additionally, Lactobacillus plantarum enhances growth performance, feed conversion efficiency, and total flock productivity. Adding Lactobacillus plantarum to chicken feed helps the gut microbiota by encouraging good bacterial communities (e.g., Eubacterium, Faecalibacterium, Ligilactobacillus, Limosilactobacillus, Blautia and Clostridium). This leads to increased growth in chickens and helps maintain the balance of their gut flora. Lactobacillus plantarum has been extensively investigated as a potential feed additive to replace in-feed antibiotics. Published literature have revealed that a dietary additive of Lactobacillus plantarum improved the health and growth of broilers by improving the balance of bacteria and the metabolism of nutrients in the gut. This study explores the incorporation of Lactobacillus plantarum into poultry diets and its importance in sustainable and healthy poultry production. This study will encourage poultry scientists to investigate further before encapsulation. Innovations in Lactiplantibacillus plantarum, including its intestine colonization methods and novel strategies to improve its colonization, have the potential to transform the industry. Rapid development of tools and techniques (microencapsulated, nanotechnology, metagenomics, and transcriptome for L. plantarum) could help cover research and application shortages.}, } @article {pmid40215446, year = {2025}, author = {Allioni, GA and de Souza, GSM and Labello, JH and Torres, GSA and da Costa, DL and Casal, YR and Duarte-Neto, AN and Dorlass, EG and Amgarten, D and Malta, FM and Doi, AM and Peres Fernandes, GB and Rebello Pinho, JR and Vieira, GT and Castro, LH and Guedes, BF}, title = {Chronic Dengue Virus Encephalitis: A Case Study and Metagenomic Analysis.}, journal = {Neurology(R) neuroimmunology & neuroinflammation}, volume = {12}, number = {3}, pages = {e200394}, doi = {10.1212/NXI.0000000000200394}, pmid = {40215446}, issn = {2332-7812}, mesh = {Humans ; Male ; *Dengue/complications/diagnosis ; Young Adult ; Metagenomics ; *Dengue Virus/genetics ; *Encephalitis, Viral/virology/pathology/diagnosis/complications ; Chronic Disease ; }, abstract = {BACKGROUND AND OBJECTIVES: Dengue virus (DENV) infection can cause acute encephalitis. Chronic encephalitis with progressive dementia is rarely reported.

METHODS: We present a case of chronic encephalitis with rapidly progressive dementia, in which a potential DENV brain infection was identified with brain tissue metagenomic next-generation sequencing. Brain pathology and molecular diagnosis are also presented.

RESULTS: A 20-year-old man from SP, Brazil, presented with rapidly progressive dementia, speech apraxia, and apathy in June 2022. By January 2023, cognitive testing showed severe global impairment (MMSE score of 18/30). MRI revealed white matter abnormalities and atrophy; CSF analysis disclosed a mild lymphocytic pleocytosis, mildly elevated protein levels, and positive CSF oligoclonal bands. Despite extensive testing ruling out common infectious and inflammatory causes, the patient's condition worsened with executive dysfunction, language impairment, tremors, and myoclonus. In August 2023, a brain biopsy and next-generation sequencing identified DENV-1 genotype V, linked to Brazilian sequences from 2000 to 2022.

DISCUSSION: This case highlights a challenging instance of encephalitis with unknown etiology, where metagenomic analysis detected DENV-1 RNA in brain tissue, suggesting a possible cause.}, } @article {pmid40215391, year = {2025}, author = {Gómez, Á and Rodríguez-Largo, A and Pérez, E and García Freire, S and Hundehege, C and Berberich, E and Luján, L and Cortés, D}, title = {Clinicopathological progression and molecular characterization of intestinal dilatation syndrome in commercial brown layers.}, journal = {Veterinary pathology}, volume = {}, number = {}, pages = {3009858251331106}, doi = {10.1177/03009858251331106}, pmid = {40215391}, issn = {1544-2217}, abstract = {Intestinal dilatation syndrome (IDS) is a poorly described condition affecting layers and breeder hens globally. Its prevalence is increasing, particularly in free-range systems, but the cause remains unknown. This retrospective study examined 35 hens from 3 flocks: free-range flock A (n = 20) and enriched-caged flock B (n = 5), both affected by IDS, and enriched-caged flock C (n = 10), with no history of IDS. Clinicopathological studies were performed on these hens, and metagenomic analysis was conducted on the proventriculus and jejunum of hens from flock A (n = 2) and flock C (n = 2). Based on clinical signs and lesions, 3 progressive stages of IDS were identified. In the first stage, although hens were without clinical signs, proventricular dilatation and lymphoplasmacytic and heterophilic jejunitis and duodenitis were observed. The second stage was marked by cachexia, pale and small combs and wattles, and severe egg production drop. Jejunal dilatation was observed, with microscopic evidence of necrotic, lymphoplasmacytic and heterophilic jejunitis; ganglioneuritis; and mineralization of the jejunal nervous plexuses and subserosal ganglia. In the third stage, spontaneous death occurred due to jejunal volvulus and vascular involvement. Affected hens (stage 2) also exhibited elevated cloacal temperatures (>0.9°C) and marked heterophilia. Metagenomic analysis identified sequences consistent with Megrivirus C in IDS-affected hens and a disruption of the gut microbiota, with increased abundance of Fusobacterium mortiferum and Megamonas funiformis. In conclusion, this study describes in detail the clinicopathological progression of the IDS and suggests that Megrivirus C, in combination with opportunistic intestinal bacteria, could play a role in the pathogenesis of this disease.}, } @article {pmid40214404, year = {2025}, author = {Nilsen, T and Pettersen, R and Keeley, NB and Ray, JL and Majaneva, S and Stokkan, M and Hervik, A and Angell, IL and Snipen, LG and Sundt, MØ and Rudi, K}, title = {Association of Microbial Networks with the Coastal Seafloor Macrofauna Ecological State.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c12464}, pmid = {40214404}, issn = {1520-5851}, abstract = {Recent evidence suggests that there is a major switch in coastal seafloor microbial ecology already at a mildly deteriorated macrofaunal state. This knowledge is of critical value in the management and conservation of the coastal seafloor. We therefore aimed to determine the relationships between seafloor microbiota and macrofauna on a regional scale. We compared prokaryote, macrofauna, chemical, and geographical data from 1546 seafloor samples, which varied in their exposure to aquaculture activities along the Norwegian and Icelandic coasts. We found that the seafloor samples contained either a network centralized by a sulfur oxidizer (42.4% of samples, n = 656) or a network centralized by an archaeal ammonium oxidizer (44.0% of samples, n = 681). Very few samples contained neither network (9.8% of samples, n = 151) or both (3.8% of samples, n = 58). Samples with a sulfur oxidizer network had a 10-fold higher risk of macrofauna loss (odds ratios, 95% CI: 9.5 to 15.6), while those with an ammonium oxidizer network had a 10-fold lower risk (95% CI: 0.068 to 0.11). The sulfur oxidizer network was negatively correlated to distance from Norwegian aquaculture sites (Spearman rho = -0.42, p < 0.01) and was present in all Icelandic samples (n = 274). The ammonium oxidizer network was absent from Icelandic samples and positively correlated to distance from Norwegian aquaculture sites (Spearman rho = 0.67, p < 0.01). Based on 356 high-quality metagenome-assembled genomes (MAGs), we found that bicarbonate-dependent carbon fixation and low-affinity oxygen respiration were associated with the ammonium oxidizer network, while the sulfur oxidizer network was associated with ammonium retention, sulfur metabolism, and high-affinity oxygen respiration. In conclusion, our findings highlight the critical roles of microbial networks centralized by sulfur and ammonium oxidizers in mild macrofauna deterioration, which should be included as an essential part of seafloor surveillance.}, } @article {pmid40214102, year = {2025}, author = {Cernooka, E and Zrelovs, N and Kazaks, A}, title = {C-terminal anchor endolysins-proposing a third class of tailed bacteriophage endolysins.}, journal = {FEBS letters}, volume = {}, number = {}, pages = {}, doi = {10.1002/1873-3468.70042}, pmid = {40214102}, issn = {1873-3468}, support = {lzp-2021/1-0050//Latvijas Zinātnes Padome/ ; }, abstract = {Endolysins-enzymes produced by tailed bacteriophages to degrade bacterial cell walls-have traditionally been classified as canonical or signal-anchor-release (SAR) endolysins. However, analysis of expanding viral (meta)genomic data has revealed a third class, which we designate as C-terminal anchor (CTA) endolysins. These enzymes feature an N-terminal enzymatic domain, a C-terminal transmembrane domain, and typically lack signal sequences, distinguishing them from SAR endolysins. CTA endolysins span all known enzymatic activities and exhibit diverse architectures, though most have a single transmembrane helix and an N-out, C-in topology, consistent with periplasmic activity. While their functional mechanisms remain to be elucidated, our findings suggest that CTA endolysins are nearly as prevalent as SAR endolysins and represent a distinct, previously unrecognized branch of the endolysin world.}, } @article {pmid40213331, year = {2025}, author = {Wang, X and Zhao, Z and Zhao, F and Li, Y and Liang, Y and Zhou, R and Shen, S and Yu, J and Liu, W and Menghe, B}, title = {Dual-omics strategy for selecting optimal fermentation strains in traditional koumiss production.}, journal = {Food chemistry: X}, volume = {27}, number = {}, pages = {102407}, pmid = {40213331}, issn = {2590-1575}, abstract = {Koumiss is a fermented mare's milk beverage with a long history. However, due to the current lack of specialized starters, the product quality is unstable. Therefore, we used dual-omics combined with pure culture technology to screen out strains with excellent fermentation performance for koumiss. The results showed that: (1) The dominant species in koumiss were mainly Lactobacillus and Lactococcus, and metabolites such as arachidonic acid and ascorbic acid were significantly enriched in koumiss. (2) There was a significant correlation between specific microbial species and metabolites. (3) Through preliminary screening using experiments such as milk-based curdling experiments and acid resistance tests, and then rescreening through fermentation tests, five strains with excellent fermentation characteristics were screened out. They are Lacticaseibacillus paracasei SXM-5, Lactobacillus kefianofaciens MGE42-8, Lactobacillus helveticus CFS12-11-1, Saccharomyces cerevisiae PFD-2, and Kluyveromyces marxianus PYM-1. The screened strains supply microbial resources for koumiss products and boost the development of milk beverages.}, } @article {pmid40212922, year = {2025}, author = {Wang, C and Li, C and You, F and Zhou, Y and Tu, G and Liu, R and Yi, P and Wu, X and Nie, H}, title = {Multi-Omics Analysis of Gut Microbiome and Host Metabolism in Different Populations of Chinese Alligators (alligator sinensis) During Various Reintroduction Phases.}, journal = {Ecology and evolution}, volume = {15}, number = {4}, pages = {e71221}, pmid = {40212922}, issn = {2045-7758}, abstract = {Reintroduction plays a significant role in the self-maintenance and reconstruction of wild animal populations, serving as a communication bridge between captive and wild animals. The Chinese alligator (Alligator sinensis) is a distinct and endangered reptile species found in China. The mechanisms by which artificially bred Chinese alligators adapt following their release into the wild remain poorly understood. This study aims to elucidate the alterations in gut microbiomes and metabolic phenotypes of Chinese alligators during their reintroduction. During the Chinese alligator's reintroduction, Fusobacterium and Cetobacterium became more abundant, while typical pathogens declined significantly. The gut type of the Chinese alligator changed from Acinetobacter to Cetobacterium. The construction of the gut microbial community was dominated by neutral (random) processes and shifted towards deterministic processes with the progression of reintroduction. In terms of species function, reintroduction significantly upregulated the expression of host immune-related genes and significantly decreased the expression of gut bacterial pathogenic genes and antibiotic resistance genes. Metagenomic and metabolomic KEGG enrichment analyses indicate that glucoside hydrolase families 13 and 23-alongside glycolysis and gluconeogenesis pathways-may play pivotal roles in energy metabolism, host-pathogen interactions, and homeostasis maintenance for Chinese alligators. Differential metabolite analysis identified significant upregulation of metabolites related to neuroendocrine immune modulation and significant down-regulation of anti-inflammatory metabolites during Chinese alligator reintroduction. Association analysis showed that there were significant co-metabolic effects between microorganisms and metabolites, which coordinated host adaptive interaction. This study provides insights into the synergistic mechanisms of host adaptation and wild environment adaptation for Chinese alligators.}, } @article {pmid40212663, year = {2025}, author = {Natasha, A and Pye, SE and Park, K and Rajoriya, S and Yang, I and Park, J and Pangestu, HS and Kim, J and Oh, Y and López, CB and Song, JW and Kim, WK}, title = {Detection and characterization of Langya virus in Crocidura lasiura (the Ussuri white-toothed shrew), Republic of Korea.}, journal = {One health (Amsterdam, Netherlands)}, volume = {20}, number = {}, pages = {101017}, pmid = {40212663}, issn = {2352-7714}, abstract = {Langya virus (LayV) is the only documented zoonotic agent within the shrew borne Parahenipavirus genus. Other Parahenipavirus species, including Gamak virus and Daeryeong virus, have been discovered in the Republic of Korea, highlighting the prevalence of this genus in the region. We retrospectively analyzed metagenomic next-generation sequencing of two Crocidura lasiura (the Ussuri white-toothed shrew) kidney samples from 2017, followed by paramyxovirus screening of 24 kidney samples from the same species collected in 2023. The LayV positivity rate was 12.5 % (3 of 24). Amplicon-based sequencing was subsequently developed to obtain the complete viral sequences. Five complete genomes of Langya virus Korea (LayV KOR) were identified: two from 2017 samples and three from 2023 samples. LayV KOR exhibited approximately 80 % and 95.5 % homology at the nucleotide and amino acid levels, respectively. Phylogenetic analysis underscored the close relationship between LayV KOR and LayV from China. This study represents the first detection of LayV complete sequences in shrews outside of China.}, } @article {pmid40212081, year = {2024}, author = {Tuerhongjiang, G and Guo, M and Qiao, X and Liu, J and Xi, W and Wei, Y and Liu, P and Lou, B and Wang, C and Sun, L and Yuan, X and Liu, H and Xiong, Y and Ma, Y and Li, H and Zhou, B and Li, L and Yuan, Z and Wu, Y and She, J}, title = {Gut Microbiota Regulate Saturated Free Fatty Acid Metabolism in Heart Failure.}, journal = {Small science}, volume = {4}, number = {9}, pages = {2300337}, pmid = {40212081}, issn = {2688-4046}, abstract = {AIMS: Heart failure (HF) is associated with profound changes in cardiac metabolism. At present, there is still a lack of relevant research to explore the key microbiome and their metabolites affecting the progression of HF. Herein, the interaction of gut microbiota and circulating free fatty acid (FFA) in HF patients and mice is investigated.

METHODS AND RESULTS: In HF patients, by applying metagenomics analysis and targeted FFA metabolomics, enriched abundance of Clostridium sporogenes (C.sp) in early and late stage of HF patients, which negatively correlated to saturated free fatty acid (SFA) levels, is identified. KEGG analysis further indicates microbiota gene enrichment in FFA degradation in early HF, and decreased gene expression in FFA synthesis in late HF. In HF mice (C57BL/6J) induced by isoproterenol (ISO), impaired intestinal permeability is observed, and decreased fecal C.sp and increased SFA are further validated. At last, by supplementing C.sp to ISO-induced HF mice, the cardiac function, fibrosis, and myocardial size are partially rescued, together with decreased circulating SFA levels.

CONCLUSIONS: Clostridium abundance is increased in HF, compensating cardiac function deterioration via downregulation of circulating SFA levels. The results demonstrate that the gut microbiota-SFA axis plays an important role in HF protection, which may provide a strategic advantage for the probiotic therapy development in HF.}, } @article {pmid40211978, year = {2025}, author = {Duan, C and Zang, Z and Xu, Y and He, H and Li, S and Liu, Z and Lei, Z and Zheng, JS and Li, SZ}, title = {FGeneBERT: function-driven pre-trained gene language model for metagenomics.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {2}, pages = {}, doi = {10.1093/bib/bbaf149}, pmid = {40211978}, issn = {1477-4054}, support = {2022ZD0115101//National Science and Technology Major Project/ ; U21A20427//National Natural Science Foundation of China Project/ ; WU2023C019//Center of Synthetic Biology and Integrated Bioengineering of Westlake University/ ; //Westlake University Industries of the Future Research Funding/ ; }, mesh = {*Metagenomics/methods ; Humans ; *Models, Genetic ; Metagenome ; Algorithms ; }, abstract = {Metagenomic data, comprising mixed multi-species genomes, are prevalent in diverse environments like oceans and soils, significantly impacting human health and ecological functions. However, current research relies on K-mer, which limits the capture of structurally and functionally relevant gene contexts. Moreover, these approaches struggle with encoding biologically meaningful genes and fail to address the one-to-many and many-to-one relationships inherent in metagenomic data. To overcome these challenges, we introduce FGeneBERT, a novel metagenomic pre-trained model that employs a protein-based gene representation as a context-aware and structure-relevant tokenizer. FGeneBERT incorporates masked gene modeling to enhance the understanding of inter-gene contextual relationships and triplet enhanced metagenomic contrastive learning to elucidate gene sequence-function relationships. Pre-trained on over 100 million metagenomic sequences, FGeneBERT demonstrates superior performance on metagenomic datasets at four levels, spanning gene, functional, bacterial, and environmental levels and ranging from 1 to 213 k input sequences. Case studies of ATP synthase and gene operons highlight FGeneBERT's capability for functional recognition and its biological relevance in metagenomic research.}, } @article {pmid40211688, year = {2025}, author = {Ge, SX and Niu, YM and Ren, LL and Zong, SX}, title = {Inheritance or Recruitment? The Assembly Mechanisms and Functional Dynamics of Microbial Communities in the Life Cycle of a Wood-Feeding Beetle.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {e17751}, doi = {10.1111/mec.17751}, pmid = {40211688}, issn = {1365-294X}, support = {2021YFD1400900//National Key R&D Program of China/ ; }, abstract = {Microbial partners enhance the metabolic capabilities of insects, enabling their adaptation to diverse ecological niches. Xylophagous insects have larvae that can digest lignocellulose and cope with plant secondary metabolites (PSMs). However, there is little information in terms of microbiome sources, dynamics and species contributions. This limits our understanding of the interaction between xylophagous insects and the microbiome. Monochamus saltuarius (Cerambycidae) is a significant borer of conifers. We used combined qPCR, host genomic and microbiome metagenomic datasets, as well as in vitro validation experiments to study the dynamics of the associated microbiome and its interactions with M. saltuarius. We evaluated microbial metabolic/biosynthetic contributions and validated their related functions. Our findings revealed that insect growth and development altered the quantity and community composition of associated bacteria and fungi. The egg microbiome was particularly susceptible to alteration due to oviposition pits. Bacterial transmission largely persisted between developmental stages, while fungal re-acquisition primarily originated from the external environment. By reconstructing community pathway maps, we identified the cooperative interactions between the insect and its gut microbiome. As larvae transitioned from phloem to xylem feeding, the functional role of the gut microbiome in various pathways was weakened. Remarkably, high-contribution bacterial species largely overlapped across different functional roles, and these species also showed considerable overlap between phloem and xylem feeding periods. Overall, our study highlights the unique interaction between xylophagous insects and their microbiome, which enhances their ability in lignocellulose digestion, PSMs degradation and the acquisition of essential amino acids, as well as vitamins.}, } @article {pmid40211685, year = {2025}, author = {Kim, JW and Choi, EC and Lee, KJ}, title = {Standardizing the approach to clinical-based human microbiome research: from clinical information collection to microbiome profiling and human resource utilization.}, journal = {Osong public health and research perspectives}, volume = {}, number = {}, pages = {}, doi = {10.24171/j.phrp.2024.0319}, pmid = {40211685}, issn = {2210-9099}, abstract = {OBJECTIVES: This study presents the standardized protocols developed by the Clinical-Based Human Microbiome Research and Development Project (cHMP) in the Republic of Korea.

METHODS: It addresses clinical metadata collection, specimen handling, DNA extraction, sequencing methods, and quality control measures for microbiome research.

RESULTS: The cHMP involves collecting samples from healthy individuals and patients across various body sites, including the gastrointestinal tract, oral cavity, respiratory system, urogenital tract, and skin. These standardized procedures ensure consistent data quality through controlled specimen collection, storage, transportation, DNA extraction, and sequencing. Sequencing encompasses both amplicon and whole metagenome methods, followed by stringent quality checks. The protocols conform to international guidelines, ensuring that the data generated are both reliable and comparable across microbiome studies.

CONCLUSION: The cHMP underscores the importance of methodological standardization in enhancing data integrity, reproducibility, and advancing microbiome-based research with potential applications for improving human health outcomes.}, } @article {pmid40211121, year = {2025}, author = {Polizel, GHG and Diniz, WJS and Cesar, ASM and Ramírez-Zamudio, GD and Cánovas, A and Dias, EFF and Fernandes, AC and Prati, BCT and Furlan, É and Pombo, GDV and Santana, MHA}, title = {Impacts of prenatal nutrition on metabolic pathways in beef cattle: an integrative approach using metabolomics and metagenomics.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {359}, pmid = {40211121}, issn = {1471-2164}, support = {2021/03265-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2017/12105-2//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 307593/2021-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; }, mesh = {Animals ; Cattle ; Female ; *Metabolomics/methods ; Pregnancy ; *Metabolic Networks and Pathways ; *Metagenomics/methods ; Male ; Metabolome ; Rumen/microbiology ; Microbiota ; *Prenatal Nutritional Physiological Phenomena ; *Animal Nutritional Physiological Phenomena ; Gastrointestinal Microbiome ; }, abstract = {BACKGROUND: This study assessed the long-term metabolic effects of prenatal nutrition in Nelore bulls through an integrated analysis of metabolome and microbiome data to elucidate the interconnected host-microbe metabolic pathways. To this end, a total of 126 cows were assigned to three supplementation strategies during pregnancy: NP (control)- only mineral supplementation; PP- protein-energy supplementation during the last trimester; and FP- protein-energy supplementation throughout pregnancy. At the end of the finishing phase, blood, fecal, and ruminal fluid samples were collected from 63 male offspring. The plasma underwent targeted metabolomics analysis, and fecal and ruminal fluid samples were used to perform 16 S rRNA gene sequencing. Metabolite and ASV (amplicon sequence variant) co-abundance networks were constructed for each treatment using the weighted gene correlation network analysis (WGCNA) framework. Significant modules (p ≤ 0.1) were selected for over-representation analyses to assess the metabolic pathways underlying the metabolome (MetaboAnalyst 6.0) and the microbiome (MicrobiomeProfiler). To explore the metabolome-metagenome interplay, correlation analyses between host metabolome and microbiome were performed. Additionally, a holistic integration of metabolic pathways was performed (MicrobiomeAnalyst 2.0).

RESULTS: A total of one and two metabolite modules associated with the NP and FP were identified, respectively. Regarding fecal microbiome, three, one, and two modules for the NP, PP, and FP were identified, respectively. The rumen microbiome demonstrated two modules correlated with each of the groups under study. Metabolite and microbiome enrichment analyses revealed the main metabolic pathways associated with lipid and protein metabolism, and regulatory mechanisms. The correlation analyses performed between the host metabolome and fecal ASVs revealed 13 and 12 significant correlations for NP and FP, respectively. Regarding the rumen, 16 and 17 significant correlations were found for NP and FP, respectively. The NP holistic analysis was mainly associated with amino acid and methane metabolism. Glycerophospholipid and polyunsaturated fatty acid metabolism were over-represented in the FP group.

CONCLUSIONS: Prenatal nutrition significantly affected the plasma metabolome, fecal microbiome, and ruminal fluid microbiome of Nelore bulls, providing insights into key pathways in protein, lipid, and methane metabolism. These findings offer novel discoveries about the molecular mechanisms underlying the effects of prenatal nutrition.

CLINICAL TRIAL NUMBER: Not applicable.}, } @article {pmid40210868, year = {2025}, author = {Fu, Y and Guzior, DV and Okros, M and Bridges, C and Rosset, SL and González, CT and Martin, C and Karunarathne, H and Watson, VE and Quinn, RA}, title = {Balance between bile acid conjugation and hydrolysis activity can alter outcomes of gut inflammation.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {3434}, pmid = {40210868}, issn = {2041-1723}, support = {1R01DK140854//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; }, mesh = {Animals ; *Bile Acids and Salts/metabolism ; Humans ; Gastrointestinal Microbiome/genetics ; Mice, Knockout ; Mice ; Amidohydrolases/metabolism/genetics ; Hydrolysis ; Acyltransferases/genetics/metabolism ; Taurocholic Acid/pharmacology/metabolism ; Disease Models, Animal ; *Colitis/metabolism/pathology/microbiology ; Male ; Inflammatory Bowel Diseases/metabolism/microbiology ; Female ; Mice, Inbred C57BL ; Clostridiales/metabolism/genetics ; Crohn Disease/metabolism/microbiology/genetics ; }, abstract = {Conjugated bile acids (BAs) are multi-functional detergents in the gastrointestinal (GI) tract produced by the liver enzyme bile acid-CoA:amino acid N-acyltransferase (BAAT) and by the microbiome from the acyltransferase activity of bile salt hydrolase (BSH). Humans with inflammatory bowel disease (IBD) have an enrichment in both host and microbially conjugated BAs (MCBAs), but their impacts on GI inflammation are not well understood. We investigated the role of host-conjugated BAs in a mouse model of colitis using a BAAT knockout background. Baat[-/-] KO mice have severe phenotypes in the colitis model that were rescued by supplementation with taurocholate (TCA). Gene expression and histology showed that this rescue was due to an improved epithelial barrier integrity and goblet cell function. However, metabolomics also showed that TCA supplementation resulted in extensive metabolism to secondary BAs. We therefore investigated the BSH activity of diverse gut bacteria on a panel of conjugated BAs and found broad hydrolytic capacity depending on the bacterium and the amino acid conjugate. The complexity of this microbial BA hydrolysis led to the exploration of bsh genes in metagenomic data from human IBD patients. Certain bsh sequences were enriched in people with Crohn's disease particularly that from Ruminococcus gnavus. This study shows that both host and microbially conjugated BAs may provide benefits to those with IBD, but this is dictated by a delicate balance between BA conjugation/deconjugation based on the bsh genes present.}, } @article {pmid40210629, year = {2025}, author = {Park, JW and Yun, YE and Cho, JA and Yoon, SI and In, SA and Park, EJ and Kim, MS}, title = {Characterization of the phyllosphere virome of fresh vegetables and potential transfer to the human gut.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {3427}, pmid = {40210629}, issn = {2041-1723}, support = {2020R1A5A8017671//National Research Foundation of Korea (NRF)/ ; 2019R1C1C1009664//National Research Foundation of Korea (NRF)/ ; 2018R1D1A3B07050366//National Research Foundation of Korea (NRF)/ ; 2021R1F1A1064222//National Research Foundation of Korea (NRF)/ ; }, mesh = {Humans ; *Virome/genetics ; *Vegetables/virology ; *Gastrointestinal Microbiome/genetics ; Feces/virology ; *Plant Leaves/virology ; Metagenome ; Bacteriophages/genetics/classification/isolation & purification ; Phylogeny ; Metagenomics ; }, abstract = {Fresh vegetables harbor diverse microorganisms on leaf surfaces, yet their viral communities remain unexplored. We investigate the diversity and ecology of phyllosphere viromes of six leafy green vegetables using virus-like particle (VLP) enrichment and shotgun metagenome sequencing. On average, 9.2 × 10[7] viruses are present per gram of leaf tissue. The majority (93.1 ± 6.2%) of these viruses are taxonomically unclassified. Virome compositions are distinct among vegetable types and exhibit temporal variations. Virulent phages with replication-enhancing auxiliary metabolic genes (AMGs) are more dominant than temperate phages with host fitness-benefiting AMGs. Analysis of 1498 human fecal VLP metagenomes reveals that approximately 10% of vegetable viruses are present in the human gut virome, including viruses commonly observed in multiple studies. These gut-associated vegetable viruses are enriched with short-term vegetable intake, and depleted in individuals with metabolic and immunologic disorders. Overall, this study elucidates the ecological contribution of the fresh vegetable virome to human gut virome diversity.}, } @article {pmid40210439, year = {2025}, author = {Smith, BJ and Zhao, C and Dubinkina, V and Jin, X and Zahavi, L and Shoer, S and Moltzau-Anderson, J and Segal, E and Pollard, KS}, title = {Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC.}, journal = {Genome research}, volume = {}, number = {}, pages = {}, doi = {10.1101/gr.279543.124}, pmid = {40210439}, issn = {1549-5469}, abstract = {Metagenomics has greatly expanded our understanding of the human gut microbiome by revealing a vast diversity of bacterial species within and across individuals. Even within a single species, different strains can have highly divergent gene content, affecting traits such as antibiotic resistance, metabolism, and virulence. Methods that harness metagenomic data to resolve strain-level differences in functional potential are crucial for understanding the causes and consequences of this intraspecific diversity. The enormous size of pangenome references, strain mixing within samples, and inconsistent sequencing depth present challenges for existing tools that analyze samples one at a time. To address this gap, we updated the MIDAS pangenome profiler, now released as version 3, and developed StrainPGC, an approach to strain-specific gene content estimation that combines strain tracking and correlations across multiple samples. We validate our integrated analysis using a complex synthetic community of strains from the human gut and find that StrainPGC outperforms existing approaches. Analyzing a large, publicly available metagenome collection from inflammatory bowel disease patients and healthy controls, we catalog the functional repertoires of thousands of strains across hundreds of species, capturing extensive diversity missing from reference databases. Finally, we apply StrainPGC to metagenomes from a clinical trial of fecal microbiota transplantation for the treatment of ulcerative colitis. We identify two Escherichia coli strains, from two different donors, that are both frequently transmitted to patients but have notable differences in functional potential. StrainPGC and MIDAS v3 together enable precise, intraspecific pangenomic investigations using large collections of metagenomic data without microbial isolation or de novo assembly.}, } @article {pmid40210403, year = {2025}, author = {Africa, AJ and Setati, ME and Hitzeroth, AC and Blancquaert, EH}, title = {Exploring the evolution of microbial communities from the phyllosphere and carposphere to the grape must of Vitis vinifera L. cv's Chardonnay and Pinot noir.}, journal = {Food microbiology}, volume = {130}, number = {}, pages = {104780}, doi = {10.1016/j.fm.2025.104780}, pmid = {40210403}, issn = {1095-9998}, mesh = {*Vitis/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota ; *Fungi/classification/genetics/isolation & purification ; *Plant Leaves/microbiology ; *Fruit/microbiology ; Wine/microbiology/analysis ; South Africa ; }, abstract = {Microbial communities associated with the grapevine phyllosphere and carposhere are a fundamental determinant of grape and wine quality. High throughput amplicon sequencing was used to profile the fungal and bacterial communities on the associated phylloplane and carposphere of Vitis vinifera L. cv's Chardonnay and Pinot noir in the Elgin and Hemel-en-Aarde wine districts of South Africa in the 2021-2022 growing season. The subsequent grape must was analysed to determine the prevalent microbiome. The most abundant bacterial and fungal genera found in both the phylloplane and carposphere of Chardonnay and Pinot noir were Pseudomonas and Filobasidium. The LEfSe (Linear discriminant analysis Effect Size) revealed significant differences in fungal and bacterial biomarkers from leaf, berry and grape must samples; however, no biomarkers were identified for cultivar nor location. Fungal β-diversity was significantly similar at different phenological stages, whereas bacterial β-diversity was significantly similar regardless of the site of colonisation. However, skin integrity of the grapes was may have influenced the microbial diversity.}, } @article {pmid40210162, year = {2025}, author = {Gao, X and Yuan, S and Li, X and Xing, W}, title = {Non-synergistic effects of microplastics and submerged macrophytes on sediment microorganisms involved in carbon and nitrogen cycling.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {126213}, doi = {10.1016/j.envpol.2025.126213}, pmid = {40210162}, issn = {1873-6424}, abstract = {Submerged macrophyte communities play a crucial role in regulating sediment carbon and nitrogen cycling in lake ecosystems. However, their interactions with emerging pollutants such as polystyrene microplastics (PS-MPs) remain poorly understood. In this study, we employed metagenomic analysis to examine the combined effects of submerged macrophyte communities and PS-MPs on sediment microbial communities, focusing on microbial populations, functional genes, and metabolic pathways involved in carbon and nitrogen cycling. Our results revealed a non-synergistic interaction between macrophyte communities and PS-MPs in shaping sediment biogeochemical processes. While increasing PS-MPs concentrations (from 0.5 to 2.5% w/w) significantly enhanced microbial diversity (species richness increased from 533 to 1,301), the presence of macrophytes moderated this response. Notably, we observed differential selective pressures on functional genes involved in key carbon and nitrogen cycling steps, particularly amoAB and amoC, nirS, and nirK, indicating distinct shifts in microbial functional groups. Furthermore, we identified complex substrate-pathway interactions: nitrate and ammonium differentially influenced fermentation and methanogenesis, while inorganic carbon positively regulated nitrate dissimilatory reduction. These findings provide novel insights into the regulatory mechanisms of submerged macrophytes in sediment biogeochemical cycling under microplastic stress, highlighting their potential role in maintaining ecosystem functions in contaminated aquatic environments.}, } @article {pmid40210157, year = {2025}, author = {Li, C and Zhu, YX and Shen, XX and Gao, Y and Xu, M and Chen, MK and An, MY}, title = {Exploring the distribution and transmission mechanism of ARGs in crab aquaculture ponds and ditches using metagenomics.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {126209}, doi = {10.1016/j.envpol.2025.126209}, pmid = {40210157}, issn = {1873-6424}, abstract = {Aquaculture provides notable economic benefits; however, the excessive use of antibiotics has resulted in the production and spread of antibiotic resistance genes (ARGs). The intricate pollution dynamics in aquaculture areas complicate the comprehension of the distribution and transmission of ARGs in aquaculture systems. Using metagenomic sequencing technology, this study used eight ponds and four ditches in a large crab aquaculture area in Taizhou City, where Proteobacteria (61.58%) and Acidobacteria (6.04%) were identified as the dominant phyla and Thiobacillus (1.84%) and Lysobacter (0.99%) were the dominant genera. Network and linear discriminant analysis effect size (LEfse) analyses showed that Proteobacteria and Lysobacter were the main host phyla of ARGs, and Lysobacter, which are key host bacteria in ponds, played an important role in determining the abundance of ARGs in ponds. Co-occurrence network analysis (spearman r>0.7, p<0.01) revealed that prophages can dominate the spread of ARGs by carrying several ARG subtypes (rsmA, OXA-21, THIN-B and lnuF). Analysis of variance demonstrated that functions related to the horizontal gene transfer (HGT) of ARGs, such as EPS synthesis (lptF), oxidative stress (gor and ompR), ATP synthesis (lapB and vcaM), and cell membrane permeability (yajC and gspJ), were significantly expressed in the pond (p<0.05), confirming that ARGs had stronger transmission potential in the pond. The Mantel test and partial least squares path modeling (PLS-PM) analysis showed that ARGs exist in bacteria and spread among them through mobile genetic elements and HGT. This study revealed the distribution and transmission mechanism of ARGs in the ponds and ditches of a crab aquaculture system and provided a theoretical basis for controlling the spread of ARGs in crab aquaculture in this area.}, } @article {pmid40209695, year = {2025}, author = {Yamane, T and Masaoka, T and Ishii, C and Masuoka, H and Suda, W and Kurokawa, S and Kishimoto, T and Mikami, Y and Fukuda, S and Kanai, T}, title = {Factors contributing to the efficacy of fecal microbiota transplantation for diarrhea-dominant functional bowel disorders.}, journal = {Digestion}, volume = {}, number = {}, pages = {1-22}, doi = {10.1159/000545183}, pmid = {40209695}, issn = {1421-9867}, abstract = {INTRODUCTION: In cases of effective fecal microbiota transplantation (FMT) for irritable bowel syndrome (IBS), donor feces have been observed to be enriched in Bifidobacterium spp., and FMT for functional bowel disease improved psychiatric symptoms. Although intestinal dysbiosis has received attention as one of the pathophysiologies of IBS, the efficacy of FMT for IBS has not yet been established. In this study, we performed a post-hoc analysis of the efficacy of FMT, focusing on metabolites in donor feces.

METHODS: FMT was performed in 12 patients, 8 with refractory diarrhea-predominant IBS and 4 with functional diarrhea (FDr), who were refractory to medical therapy. The donors were family members within the second degree of kinship and were different for each transplant. Fecal characteristics were evaluated before and 12 weeks after transplantation using the Bristol stool scale (BS). BS scores of 3-5 at 12 weeks after transplantation were considered indicative of responders, while BS scores of 6 and 7 were indicative of non-responders. Metagenomic and metabolomic analyses of all 12 donor fecal samples were performed to compare the responder and non-responder groups.

RESULTS: Before transplantation, all 12 patients had BS scores of 6-7, but 12 weeks after transplantation, 6 were in the responder group and 6 were in the non-responder group. Metagenomic analysis showed that effective donor feces contained significantly higher levels of Prevotella than ineffective donor feces. Metabolomic analysis showed that effective donor feces contained significantly higher levels of propionate and butyrate and significantly lower lactate levels than ineffective donor feces.

CONCLUSION: Propionate-, butyrate-, or Prevotella-rich donor feces may contribute to successful FMT in patients with diarrhea-dominant functional gastrointestinal disorders.}, } @article {pmid40209677, year = {2025}, author = {Lin, Y and Lau, HC and Liu, C and Ding, X and Sun, Y and Rong, J and Zhang, X and Wang, L and Yuan, K and Miao, Y and Wu, WK and Wong, SH and Sung, JJ and Yu, J}, title = {Multi-cohort analysis reveals colorectal cancer tumor location-associated fecal microbiota and their clinical impact.}, journal = {Cell host & microbe}, volume = {33}, number = {4}, pages = {589-601.e3}, doi = {10.1016/j.chom.2025.03.012}, pmid = {40209677}, issn = {1934-6069}, mesh = {Humans ; *Feces/microbiology ; *Colorectal Neoplasms/microbiology/pathology/diagnosis ; *Gastrointestinal Microbiome ; Cohort Studies ; Metagenome ; Male ; Female ; *Bacteria/classification/genetics/isolation & purification ; Middle Aged ; Aged ; Fusobacterium nucleatum/isolation & purification ; Biomarkers, Tumor ; ROC Curve ; }, abstract = {Microbial alterations in different tumor locations of colorectal cancer (CRC) remain unclear. Here, 1,375 fecal metagenomes from six in-house and published datasets were analyzed, including 128 right-sided CRC (rCRC), 168 left-sided CRC (lCRC), 250 rectal cancer (RC), and 829 controls. Firmicutes progressively increase from rCRC, lCRC, to RC, in contrast to the gradual decrease of Bacteroidetes. Tumor location-associated fecal microbes are identified, including Veillonella parvula for rCRC, Streptococcus angionosus for lCRC, and Peptostreptococcus anaerobius for RC, while Fusobacterium nucleatum is enriched in all tumor locations. Tumor location-associated bacteria correlate with patient survival. Clinically, we establish a microbial biomarker panel for each tumor location that accurately diagnoses rCRC (area under the receiver operating characteristic curve [AUC] = 91.59%), lCRC (AUC = 91.69%), or RC (AUC = 90.53%) from controls. Tumor location-specific biomarkers also have higher diagnostic accuracy (AUC = 91.38%) than location-non-specific biomarkers (AUC = 82.92%). Overall, we characterize fecal microbes associated with different CRC tumor locations, highlighting that tumor location should be considered in non-invasive diagnosis.}, } @article {pmid40209409, year = {2025}, author = {Cheng, Y and Zheng, X and Jiang, Y and Xiao, Q and Luo, Q and Ding, Y}, title = {Key genes and microbial ecological clusters involved in organophosphate ester degradation in agricultural fields of a typical watershed in southwest China.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138076}, doi = {10.1016/j.jhazmat.2025.138076}, pmid = {40209409}, issn = {1873-3336}, abstract = {Organophosphate esters (OPEs) are widely used as flame retardants and plasticizers, and they have raised global concern due to their persistence, bioaccumulation, and potential toxicity. However, OPE contamination characteristics and microbial degradation mechanisms in agricultural soils remain poorly understood. This study investigated agricultural soils from the riparian zone of the Anning River Basin in southwest China. The concentrations of 12 OPEs were determined using gas chromatography-tandem mass spectrometry. The results revealed that the total OPE concentration was moderate, with triethyl phosphate being the most abundant compound. Metagenomic techniques and Bayesian linear regression analysis were employed in combination with the Kyoto Encyclopedia of Genes and Genomes database to identify potential degradation pathways for triethyl phosphate and tris (2-chloroethyl) phosphate. The phoA, phoB, phoD, and glpQ genes, which encode phosphatases, catalyze ester bond cleavage, thereby facilitating the degradation of OPEs. Further microbial interaction network analysis identified core OPE-degrading microorganisms, including Pimelobacter simplex, Nocardioides sp. JS614, Nocardioides daphniae, and Methylocystis heyeri. Additionally, neutral community models indicated that environmental selection drives microbial community structure. In conclusion, this study provides an in-depth understanding of OPE contamination and its microbial degradation mechanisms in agricultural soils, offering theoretical insights for pollution management and remediation strategies.}, } @article {pmid40209382, year = {2025}, author = {Su, C and Kang, J and Liu, S and Li, C}, title = {Exploring the influence of fruit ripeness on the microbiome, bioactive components, and flavor profiles of naturally fermented noni (Morinda citrifolia L.) juice.}, journal = {Food chemistry}, volume = {482}, number = {}, pages = {144192}, doi = {10.1016/j.foodchem.2025.144192}, pmid = {40209382}, issn = {1873-7072}, abstract = {Raw fruit ripeness is an important factor affecting fermented noni fruit juice (FNJ). This study investigated the physicochemical properties, active and volatile components, microbiota, and functional characteristics of FNJ prepared from noni fruits at varying ripening stages. The results showed that deacetylasperulosidic acid (203.54-805.89 mg/L) and asperulosidic acid (102.78-393.41 mg/L) were detected across in all FNJs during fermentation. As noni fruit ripens, the levels of octanoic acid and hexanoic acid in FNJs gradually decreased, while the content of esters significantly increased, particularly during the final stage of ripeness. Metagenomic analysis revealed that Acetobacter sp. and Gluconobacter sp. were core microbes responsible for FNJs, primarily contributing to fatty acid metabolism. Correlation analysis further indicated that the fruit's ripeness significantly influenced its functional properties and volatile components of FNJs. This study offered new insights into selecting the optimal ripeness of noni fruits for the preparation of FNJ and its potential industrial applications.}, } @article {pmid40209373, year = {2025}, author = {Wang, L and Pei, H and Xing, T and Chen, D and Chen, Y and Hao, Z and Tian, Y and Ding, J}, title = {Gut bacteria and host metabolism: The keys to sea cucumber (Apostichopus japonicus) quality traits.}, journal = {Food chemistry}, volume = {482}, number = {}, pages = {144178}, doi = {10.1016/j.foodchem.2025.144178}, pmid = {40209373}, issn = {1873-7072}, abstract = {Gut bacteria have a significant impact on modern genetics and contribute to the improvement of aquatic germplasm, which is a key focus for breeders. However, the effects of complex interactions between gut bacteria community and phenotypic trait of aquatic products remain largely unknown. Here, we unravel the association between phenotypic trait, gut microbiota and host metabolic variables of 216 sea cucumbers (Apostichopus japonicus) by Metagenome-wide association studies (MWAS) and Weighted correlation network analysis (WGCNA) methods. Our findings reveal that a total of 14 microbial biomarkers and 201 metabolic markers considered being associated with polysaccharide and collagen content. Among them, Desulfobacterota has the capacity to facilitate the synthesis of octopamine within the neuroactive ligand-receptor metabolic pathway, subsequently influencing polysaccharide content. Additionally, the Lachnospiraceae_NK4A136_group was shown to enhance collagen content through the facilitation of glycine synthesis. In conclusion, this research indicating that precision microbiome management could be a strategy for develop strategies for cultivating high-quality aquatic germplasm.}, } @article {pmid40209228, year = {2025}, author = {Den Uyl, PA and Kiledal, EA and Errera, RM and Chaganti, SR and Godwin, CM and Raymond, HA and Dick, GJ}, title = {Genomic Identification and Characterization of Saxitoxin Producing Cyanobacteria in Western Lake Erie Harmful Algal Blooms.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c10888}, pmid = {40209228}, issn = {1520-5851}, abstract = {Saxitoxins (STXs), a group of closely related neurotoxins, are among the most potent natural toxins known. While genes encoding STX biosynthesis have been observed in Lake Erie, the organism(s) responsible for producing STXs in the Laurentian Great Lakes have not been identified. We identified a full suite of STX biosynthesis genes in a Dolichospermum metagenome-assembled genome (MAG). The content of sxt genes suggest that this organism can produce STX, decarbamoyl and deoxy-decarbamoyl saxitoxins, and other congeners. The absence of sxtX indicates this organism is unable to produce neosaxitoxin, a potent congener. However, a distinct, lower abundance sxt operon from an unidentified organism did contain sxtX, indicating neosaxitoxin biosynthesis potential. Metatranscriptomic data confirmed STX biosynthesis gene expression. We also recovered highly similar Dolichospermum MAGs lacking sxt genes, implying gene loss or horizontal gene transfer. sxtA was detected by quantitative polymerase chain reaction during 47 of 76 sampling dates between 2015 and 2019, demonstrating higher sensitivity than metagenomic approaches. sxtA gene abundance was positively correlated with temperature and particulate nitrogen:phosphorus ratio and negatively correlated with ammonium concentration. All Dolichospermum MAGs had genes required for nitrogen fixation. Collectively, this study provides a foundation for understanding potential new threats to Lake Erie water quality.}, } @article {pmid40208400, year = {2025}, author = {Bourgon, N and Padioleau, I and Guibon, J and Fourgeaud, J and Lermine, A and Meurice, G and Guilleminot, T and Bussieres, L and Leruez-Ville, M and Dupont, JM and Ville, Y}, title = {Metagenomic analysis of NIPT raw data suggests high negative predictive value for congenital cytomegalovirus infection screening.}, journal = {Ultrasound in obstetrics & gynecology : the official journal of the International Society of Ultrasound in Obstetrics and Gynecology}, volume = {}, number = {}, pages = {}, doi = {10.1002/uog.29221}, pmid = {40208400}, issn = {1469-0705}, } @article {pmid40207985, year = {2025}, author = {Zhang, Q and Wang, Q and Zhang, F and Li, X and Sun, Y and Wang, L and Zhang, Z}, title = {Diagnostic value of metagenomic next-generation sequencing in patients with osteoarticular infections: a prospective study.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0106424}, doi = {10.1128/spectrum.01064-24}, pmid = {40207985}, issn = {2165-0497}, abstract = {Due to the limits of traditional microbiological methods and the complexity of osteoarthritis pathogens, only a few pathogens can be detected. We evaluated metagenomic next-generation sequencing (mNGS) for detecting pathogens in osteoarthritis infection samples. We prospectively included 150 patients with osteoarthritis infection who visited the Orthopedics Department of Shandong Provincial Public Health Center from 2023 to 2024, including 124 cases of primary osteoarthritis (POI) and 26 cases of invasive osteoarthritis (IOI). The most common pathogenic bacteria were Mycobacterium tuberculosis complex, Staphylococcus aureus, and Brucella melitensis. mNGS (75.33%) significantly improved the detection of pathogens in osteoarticular infections compared to conventional tests (CT) methods (36.67%). mNGS could detect a wider spectrum of pathogens compared to CT methods, especially for mixed and rare pathogens. The treatment strategies for patients with osteoarthritis infection could be adjusted based on the results obtained from mNGS testing. Furthermore, the abundance of M. tuberculosis complex, B. melitensis, and Staphylococcus epidermidis was significantly correlated with clinical indicators.IMPORTANCEIdentifying the microorganisms responsible for osteoarthritis infection could help with early diagnosis and treatment. In this study, we compared the pathogen detection rate of metagenomic next-generation sequencing (mNGS) and CT methods in patients with osteoarthritis infection and found that mNGS had a higher microbial detection rate and a broader spectrum of pathogens (especially for mixed pathogens). This study demonstrates that mNGS is an ideal tool for detecting pathogens in patients with osteoarticular infections.}, } @article {pmid40207938, year = {2025}, author = {Zhao, D and Salas-Leiva, DE and Williams, SK and Dunn, KA and Shao, JD and Roger, AJ}, title = {Eukfinder: a pipeline to retrieve microbial eukaryote genome sequences from metagenomic data.}, journal = {mBio}, volume = {}, number = {}, pages = {e0069925}, doi = {10.1128/mbio.00699-25}, pmid = {40207938}, issn = {2150-7511}, abstract = {UNLABELLED: Whole-genome shotgun (WGS) metagenomic sequencing of microbial communities enables the discovery of the functions, physiologies, and evolutionary histories of prokaryotic and eukaryotic microbes. However, metagenomic studies of microbial eukaryotes lag due to challenges in identifying and assembling high-quality genomes from WGS data. To address this problem, we developed Eukfinder, a bioinformatics pipeline that identifies potential eukaryotic sequences from WGS metagenomic data, with a complementary binning workflow for recovering nuclear and mitochondrial genomes. Eukfinder uses two specialized databases for read/contig classification, customizable to specific data sets or environments. We tested Eukfinder on simulated gut microbiome data sets which included varying numbers of reads from the protist Blastocystis, a human gut commensal. We also applied Eukfinder to previously published human gut microbiome WGS metagenomic data to recover new genomes of Blastocystis. Compared to other workflows, Eukfinder offers the potential to recover high-quality, near-complete genomes of diverse eukaryotes, including different Blastocystis subtypes, without relying on a reference genome. With sufficient sequencing depth, Eukfinder outperforms similar tools for recovering eukaryotic genomes from metagenomic data. Eukfinder is a valuable tool for reference-independent and cultivation-free studies of eukaryotic microbial genomes from environmental WGS metagenomic samples.

IMPORTANCE: Advancements in next-generation sequencing have made whole-genome shotgun (WGS) metagenomic sequencing an efficient method for de novo reconstruction of microbial genomes from various environments. Thousands of new prokaryotic genomes have been characterized; however, the large size and complexity of protistan genomes have hindered the use of WGS metagenomics to sample microbial eukaryotic diversity. Eukfinder enables the recovery of eukaryotic microbial genomes from environmental WGS metagenomic samples. Retrieval of high-quality protistan genomes from diverse metagenomic samples increases the number of reference genomes available. This aids future metagenomic investigations into the functions, physiologies, and evolutionary histories of eukaryotic microbes in the gut microbiome and other ecosystems.}, } @article {pmid40207877, year = {2025}, author = {Huang, L and Chen, C and Meng, J and Yan, Q and Luo, G and Sha, S and Xing, Y and Liu, C and Xu, M and Zhao, L and Guo, S and Wu, X and Chen, H and Ma, J and You, W and Zhang, Y and Guo, R and Li, S and Yao, X and Ma, W and Kong, X and Zhou, P and Sun, W}, title = {Metagenome-Based Characterization of the Gut Virome Signatures in Patients With Gout.}, journal = {Journal of medical virology}, volume = {97}, number = {4}, pages = {e70336}, doi = {10.1002/jmv.70336}, pmid = {40207877}, issn = {1096-9071}, support = {//This study was supported by 2024 High-quality Development Project of Shenzhen Bao'an Public Hospital (BAGZL2024138 and BAGZL2024130), National Natural Science Foundation of China (82370563), Dalian Medical University Interdisciplinary Research Cooperation Project Team Funding (JCH22023017), the Key Laboratory of Guizhou Provincial Education Department (Guizhou Education Technology [2023] No. 017), National and Provincial Science and Technology Innovation Talent Team Cultivation Program of Guizhou University of Traditional Chinese Medicine (GZUTCM-TD[2022]004)./ ; }, mesh = {Humans ; *Virome ; *Gastrointestinal Microbiome ; *Gout/virology ; Male ; Middle Aged ; Feces/virology ; Female ; *Metagenome ; Metagenomics ; *Viruses/classification/genetics/isolation & purification ; Adult ; Aged ; Longitudinal Studies ; }, abstract = {The gut microbiome has been implicated in the development of autoimmune diseases, including gout. However, the role of the gut virome in gout pathogenesis remains underexplored. We employed a reference-dependent virome approach to analyze fecal metagenomic data from 102 gout patients (77 in the discovery cohort and 25 in the validation cohort) and 86 healthy controls (HCs) (63 and 23 in each cohort). A subset of gout patients in the discovery cohort provided longitudinal samples at Weeks 2, 4, and 24. Our analysis revealed significant alterations in the gut virome of gout patients, including reduced viral richness and shifts in viral family composition. Notably, Siphoviridae, Myoviridae, and Podoviridae were depleted, while Quimbyviridae, Retroviridae, and Schitoviridae were enriched in gout patients. We identified 359 viral operational taxonomic units (vOTUs) associated with gout. Enriched vOTUs in gout patients predominantly consisted of Fusobacteriaceae, Bacteroidaceae, and Selenomonadaceae phages, while control-enriched vOTUs included Ruminococcaceae, Oscillospiraceae, and Enterobacteriaceae phages. Longitudinal analysis revealed that a substantial proportion of these virome signatures remained stable over 6 months. Functional profiling highlighted the enrichment of viral auxiliary metabolic genes, suggesting potential metabolic interactions between viruses and host bacteria. Notably, gut virome signatures effectively discriminated gout patients from HCs, with high classification performance in the validation cohort. This study provides the first comprehensive characterization of the gut virome in gout, revealing its potential role in disease pathogenesis and highlighting virome-based signatures as promising biomarkers for gout diagnosis and future therapeutic strategies.}, } @article {pmid40207279, year = {2025}, author = {Teng, NM and Malfettone, A and Dalby, MJ and Kiu, R and Seki, D and Robinson, T and Gion, M and Bermejo, B and Pérez-García, JM and Prat, A and Vázquez, RM and Llombart-Cussac, A and Curigliano, G and Schmid, P and Barroso-Sousa, R and Mancino, M and Shimizu, E and Rodríguez-Morató, J and Mina, L and Hall, LJ and Robinson, SD and Cortés, J}, title = {Profiling the gut and oral microbiota of hormone receptor-positive, HER2-negative metastatic breast cancer patients receiving pembrolizumab and eribulin.}, journal = {Microbiome research reports}, volume = {4}, number = {1}, pages = {4}, pmid = {40207279}, issn = {2771-5965}, abstract = {Aim: Changes in host-associated microbial communities (i.e., the microbiota) may modulate responses to checkpoint blockade immunotherapy. In the KELLY phase II study (NCT03222856), we previously demonstrated that pembrolizumab [anti-programmed cell death protein 1 (PD-1)] combined with eribulin (plus microtubule-targeting chemotherapy) showed encouraging antitumor activity in patients with hormone receptor (HR)-positive/human epidermal growth factor receptor 2 (HER2)-negative metastatic breast cancer (mBC) who had received prior treatments. Methods: A total of 58 fecal and 67 saliva samples were prospectively collected from a subset of 28 patients at baseline (BL), after three treatment cycles, and end of treatment. Shotgun metagenomics, 16S rRNA gene amplicon sequencing, and bioinformatics and statistical approaches were used to characterize fecal and oral microbiota profiles. Results: Treatment caused no substantial perturbations in gut or oral microbiota, suggesting minimal drug-related microbial toxicity. Bacteroides and Faecalibacterium were the dominant gut microbiota genera, while Prevotella and Streptococcus were present in both oral and gut samples, highlighting potential gut-oral microbial interactions. Additionally, clinical benefit (CB) appeared to be associated with gut-associated Bacteroides fragilis (B. fragilis) and a BL oral abundance of Streptococcus ≥ 30%. Notably, B. fragilis NCTC 9343 supernatant induced dose-dependent lactate dehydrogenase (LDH) release from the MCF-7 (HR-positive/HER2-negative) BC cell line. Conclusion: These findings suggest that specific gut and oral microbiota may modulate the effectiveness of combinatory anti-BC therapies, potentially through the action of microbial metabolites.}, } @article {pmid40207161, year = {2025}, author = {Helmi, NR}, title = {Exploring the diversity and antimicrobial potential of actinomycetes isolated from different environments in Saudi Arabia: a systematic review.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1568899}, pmid = {40207161}, issn = {1664-302X}, abstract = {The increasing prevalence of antimicrobial resistance (AMR) presents a significant global health challenge, underscoring the urgent need for novel antimicrobial agents. Actinomycetes, particularly Streptomyces species, are well known for synthesizing bioactive compounds with antibacterial, antifungal, and antiviral properties. This review explores the diversity and antimicrobial potential of actinomycetes from Saudi Arabia's unique ecosystems, including terrestrial (soil, rhizosphere), aquatic (marine, freshwater), extreme (deserts, caves, hot springs, mountains, and mangroves), and other unique environments. The adaptation of these microorganisms to harsh environmental conditions has driven the evolution of unique strains with enhanced biosynthetic capacities. Several studies have demonstrated their antimicrobial efficacy against multidrug-resistant pathogens, including methicillin-resistant Staphylococcus aureus (MRSA), extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae, Pseudomonas aeruginosa, and Candida albicans. However, challenges in actinomycete research persist, including difficulties in culturing rare strains, limited genomic characterization, and high production costs. Recent advancements, such as genome mining, metagenomics, AI-driven bioinformatics, and CRISPR-based gene activation, offer promising avenues for unlocking novel antimicrobial compounds. Additionally, synthetic biology, advanced fermentation technologies, and nanotechnology-based drug delivery systems are enhancing the industrial scalability of actinomycete-derived antibiotics. Beyond antimicrobials, actinomycete-derived compounds show potential applications in oncology, immunotherapy, and agriculture. Alternative therapeutic strategies, including quorum sensing inhibitors, phage therapy, and combination therapies, are being explored to combat AMR. Cutting-edge analytical techniques, such as mass spectrometry, liquid chromatography, and nuclear magnetic resonance spectroscopy (NMR), are essential for structural elucidation and mechanism characterization of new bioactive compounds. To harness Saudi Arabia's microbial biodiversity effectively, interdisciplinary collaborations between microbiologists, biotechnologists, and pharmaceutical industries are crucial. Sustainable bioprospecting and advanced bioprocessing strategies will facilitate the translation of actinomycete-derived bioactive compounds into clinically viable therapeutics. Expanding research efforts into underexplored Saudi ecosystems can lead to groundbreaking discoveries in antibiotic development and beyond.}, } @article {pmid40207154, year = {2025}, author = {Ahn, JS and Han, EJ and Chung, HJ}, title = {Comparison of metagenomic analysis of fecal and gastrointestinal tract samples for identifying beneficial gut microorganisms.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1533580}, pmid = {40207154}, issn = {1664-302X}, abstract = {INTRODUCTION: Previous research on the gut microbiome has primarily focused on fecal microbiota, raising concerns about whether fecal samples accurately represent the entire intestinal microbiota. Studies have shown that microbial communities across the gastrointestinal (GI) tract are more diverse than those in feces, suggesting that microbial composition may vary depending on the sampling method. Additionally, analyzing the broader diversity of microbial communities in the GI tract may enhance the identification of potentially beneficial microbiota.

METHODS: In this study, we compare gut microbiome datasets obtained from fecal samples and GI samples (collected by pooling luminal contents and mucosal scrapings from the stomach to the end of the colon) of 6-month-old mice using 16S rRNA sequencing. We further investigate the associations between gut microbiota and motor, cognitive, and emotional functions in mice, examining differences between the two sample types. To assess these variations, we apply DESeq2 analysis to identify microbial species enriched in high-functioning groups and evaluate how their selection may differ depending on the sampling approach.

RESULTS: Our findings reveal notable differences in microbial composition between fecal and GI samples, suggesting that sampling methods may influence the identification of beneficial bacteria.

DISCUSSION: These results highlight the importance of selecting an appropriate sampling approach in microbiome research to ensure a comprehensive understanding of gut microbiota-host interactions.}, } @article {pmid40207150, year = {2025}, author = {Zhao, C and Yang, Y and Zhao, P and Bai, L}, title = {Comparative analysis of the fecal microbiota in Père David's deer and five other captive deer species.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1547348}, pmid = {40207150}, issn = {1664-302X}, abstract = {INTRODUCTION: Gut microbes are essential for host nutrition, immunity, and development. Various factors influence the composition and function of the gut microbial community. However, there is limited knowledge regarding the comparison of gut microbiota across different deer species, particularly those in the World Deer Park of Baotou (Inner Mongolia, China).

METHODS: This study utilized 16S rRNA gene amplicon sequencing to analyze the fecal microbiota and potential microbial function in Père David's Deer (Elaphurus davidianus), Sika deer (Cervus nippon), American Wapiti (Cervus canadensis), Red Deer (Cervuselaphus), Fallow Deer (Dama dama), and Reindeer (Rangifer tarandus).

RESULTS AND DISCUSSION: The findings indicated no significant differences in alpha diversity, yet there was a noteworthy distinction in beta diversity among the six deer groups. At the phylum level, the predominant bacteria in the deer populations were Firmicutes, Bacteroidetes, and Proteobacteria. At the genus level, 54 core bacterial microbiota were identified. The top four genera in AW, FD, PD, and SD were Ruminococcaceae UCG-005, Rikenellaceae RC9 gut group, RuminococcaceaeUCG-010 and Christensenellaceae R-7 group. The results of the neutral model revealed that neutral processes predominantly governed the gut microbiota community assembly in different deer species, particularly in Père David's deer. PICRUSt2 predictions showed significant enrichment of fecal bacterial functions related to fatty acid, lipid, metabolic regulator, and amino acid biosynthesis. This comparative analysis sheds light on the microbial community structure, community assembly, and potential functions, offering improved insights into the management and conservation of deer species, especially Père David's deer. Future research might focus on exploring metagenomic functions and dynamics in wild settings or across different seasons using metagenomics or metatranscriptomics.}, } @article {pmid40206877, year = {2025}, author = {Shi, M and Qin, T and Pu, Z and Yang, Z and Lim, KJ and Yang, M and Wang, Z}, title = {Salt stress alters the selectivity of mature pecan for the rhizosphere community and its associated functional traits.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1473473}, pmid = {40206877}, issn = {1664-462X}, abstract = {INTRODUCTION: Salt stress is a major global environmental factor limiting plant growth. Rhizosphere bacteria, recruited from bulk soil, play a pivotal role in enhancing salt stress resistance in herbaceous and crop species. However, whether the rhizosphere bacterial community of a mature tree can respond to salt stress, particularly in saline-alkalitolerant trees, remains unexplored. Pecan (Carya illinoinensis), an important commercially cultivated nut tree, is considered saline-alkali tolerant.

METHODS: Pecan trees (12 years) were subjected to different NaCl concentrations for 12 weeks. Collected samples included bulk soil, rhizosphere soil, roots, leaves, and fruit. Amplicon sequencing data and shotgun metagenomic sequencing data obtained from the samples were investigated: 1) microbial communities in various ecological niches of mature pecan trees; 2) the characteristic of the rhizosphere bacteria community and the associated functional traits when pecan suffered from salt stress.

RESULTS AND DISCUSSION: We characterized the mature pecan-associated microbiome (i.e., fruit, leaf, root, and rhizosphere soil) for the first time. These findings suggest that niche-based processes, such as habitat selection, drive bacterial and fungal community assembly in pecan tissues. Salt stress reduced bacterial diversity, altered community composition, and shifted pecan's selective pressure on Proteobacteria and Actinobacteria. Shotgun metagenomic sequencing further revealed functional traits of the rhizosphere microbiome in response to salt stress. This study enhances our understanding of mature tree-associated microbiomes and supports the theory that shaping the rhizosphere microbiome may be a strategy for saline-alkali-tolerant mature trees to resist salt stress. These findings provide insights into salt tolerance in mature trees and suggest potential applications, such as the development of bio-inoculants, for managing saline environments in agricultural and ecological contexts.}, } @article {pmid40206699, year = {2025}, author = {Connors, E and Gallagher, KL and Dutta, A and Oliver, M and Bowman, JS}, title = {Suspended detrital particles support a distinct microbial ecosystem in Palmer Canyon, Antarctica, a coastal biological hotspot.}, journal = {Polar biology}, volume = {48}, number = {2}, pages = {62}, pmid = {40206699}, issn = {0722-4060}, abstract = {UNLABELLED: The coastal region of the Western Antarctic Peninsula is considered a biological hotspot with high levels of phytoplankton productivity and krill biomass. Recent in situ observations and particle modeling studies of Palmer Canyon, a deep bathymetric feature in the region, demonstrated the presence of a recirculating eddy that traps particles, retaining a distinct particle layer over the summer season. We applied metagenomic sequencing and Imaging Flow Cytobot (IFCB) analysis to characterize the microbial community in the particle layer. We sampled across the upper water column (< 200 m) along a transect to identify the locations of increased particle density, categorizing particles into either living cells or cellular detritus via IFCB. An indicator species analysis of community composition demonstrated the diatom Corethron and the bacteria Sulfitobacter were significantly highly abundant in samples with high levels of living cells, while the mixotrophic dinoflagellate Prorocentrum texanum and prokaryotes Methanomassiliicoccales and Fluviicola taffensis were significantly more abundant in samples with high detritus within the particle layer. From our metagenomic analysis, the significantly differentially abundant metabolic pathway genes in the particle layer of Palmer Canyon included pathways for anaerobic metabolism, such as methanogenesis and sulfate reduction. Overall, our results indicate that distinct microbial species and metabolic pathway genes are present in the retained particle layer of Palmer Canyon.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00300-025-03380-y.}, } @article {pmid40206488, year = {2025}, author = {He, J and Chen, Y and Jiang, Z and Li, F and Zhu, M and Xu, Z and Wang, M and Tang, M and Wu, Y and Li, Y}, title = {Diagnostic value of metagenomic next-generation sequencing in detecting Pneumocystis jirovecii pneumonia in HIV-infected patients.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1567484}, pmid = {40206488}, issn = {2296-858X}, abstract = {INTRODUCTION: Accurate diagnosis of Pneumocystis jirovecii pneumonia (PJP) in HIV patients remains challenging. This study compares metagenomic next-generation sequencing (mNGS) with PCR, GMS staining, and serum β-D-glucan (BG) assays for PJP detection and co-infection identification.

METHODS: BALF samples from 34 HIV-positive PJP patients and 50 non-PJP controls were analyzed. Diagnostic performance metrics (sensitivity, specificity, NPV, AUC) and co-pathogen profiles were evaluated for mNGS versus conventional methods.

RESULTS: mNGS and PCR both achieved 100% sensitivity. mNGS showed higher specificity (91.3% vs. 88%) and AUC (0.898 vs. 0.940 for PCR). Co-infections were detected in 67.6% of PJP cases by mNGS, including cytomegalovirus (41.2%), Epstein-Barr virus (29.4%), and non-tuberculous mycobacteria (14.7%). GMS and BG assays exhibited lower sensitivity (64.7% and 76.5%, respectively).

DISCUSSION: mNGS offers superior specificity, accuracy, and co-infection detection compared to traditional methods. Its high NPV (100%) supports clinical utility in ruling out PJP. While resource-intensive, mNGS is a promising first-line diagnostic tool for HIV-associated PJP, particularly in polymicrobial infection settings.}, } @article {pmid40206430, year = {2025}, author = {Zhou, Z and Sun, L and Zhou, W and Gao, W and Yuan, X and Zhou, H and Ren, Y and Li, B and Wu, Y and She, J}, title = {Probiotic Bifidobacterium reduces serum TMAO in unstable angina patients via the gut to liver to heart axis.}, journal = {Liver research (Beijing, China)}, volume = {9}, number = {1}, pages = {57-65}, pmid = {40206430}, issn = {2542-5684}, abstract = {BACKGROUND AND AIMS: Studies indicate that the gut microbiota and its metabolites are involved in the progression of cardiovascular diseases, and enterohepatic circulation plays an important role in this progression. This study aims to identify potential probiotics for the treatment of unstable angina (UA) and elucidate their mechanisms of action.

METHODS: Initially, the gut microbiota from patients with UA and control was analyzed. To directly assess the effects of Bifidobacterium supplementation, 10 patients with UA were enrolled and administered Bifidobacterium (630 mg per intake twice a day for 1 month). The fecal metagenome, serum trimethylamine N-oxide (TMAO) levels, and other laboratory parameters were evaluated before and after Bifidobacterium supplementation.

RESULTS: After supplementing with Bifidobacterium for 1 month, there were statistically significant differences (P < 0.05) in TMAO, aspartate aminotransferase, total cholesterol, and low-density lipoprotein compared to before. Additionally, the abundance of Bifidobacterium longum increased significantly, although the overall abundance of Bifidobacterium did not reach statistical significance. The gut microbiota, metabolites, and gut-liver axis are involved in the progression of UA, and potential mechanisms should be further studied.

CONCLUSIONS: Metagenomic analysis demonstrated a reduced abundance of Bifidobacterium in patients with UA. Supplementation with Bifidobacterium restored gut dysbiosis and decreased circulating TMAO levels in patients with UA. This study provides evidence that Bifidobacterium may exert cardiovascular-protective effects through the gut-liver-heart axis.

CLINICAL TRIAL NUMBER: ChiCTR2400093946.}, } @article {pmid40205852, year = {2025}, author = {Nowicki, M and Mroczek, M and Mukhedkar, D and Bała, P and Nikolai Pimenoff, V and Arroyo Mühr, LS}, title = {HPV-KITE: sequence analysis software for rapid HPV genotype detection.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {2}, pages = {}, doi = {10.1093/bib/bbaf155}, pmid = {40205852}, issn = {1477-4054}, mesh = {Humans ; Genotype ; Algorithms ; *Software ; *Papillomaviridae/genetics/classification ; *Papillomavirus Infections/virology/diagnosis ; High-Throughput Nucleotide Sequencing ; DNA, Viral/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Human papillomaviruses (HPVs) are among the most diverse viral families that infect humans. Fortunately, only a small number of closely related HPV types affect human health, most notably by causing nearly all cervical cancers, as well as some oral and other anogenital cancers, particularly when infections with high-risk HPV types become persistent. Numerous viral polymerase chain reaction-based diagnostic methods as well as sequencing protocols have been developed for accurate, rapid, and efficient HPV genotyping. However, due to the large number of closely related HPV genotypes and the abundance of nonviral DNA in human derived biological samples, it can be challenging to correctly detect HPV genotypes using high throughput deep sequencing. Here, we introduce a novel HPV detection algorithm, HPV-KITE (HPV K-mer Index Tversky Estimator), which leverages k-mer data analysis and utilizes Tversky indexing for DNA and RNA sequence data. This method offers a rapid and sensitive alternative for detecting HPV from both metagenomic and transcriptomic datasets. We assessed HPV-KITE using three previously analyzed HPV infection-related datasets, comprising a total of 1430 sequenced human samples. For benchmarking, we compared our method's performance with standard HPV sequencing analysis algorithms, including general sequence-based mapping, and k-mer-based classification methods. Parallelization demonstrated fast processing times achieved through shingling, and scalability analysis revealed optimal performance when employing multiple nodes. Our results showed that HPV-KITE is one of the fastest, most accurate, and easiest ways to detect HPV genotypes from virtually any next-generation sequencing data. Moreover, the method is also highly scalable and available to be optimized for any microorganism other than HPV.}, } @article {pmid40205718, year = {2025}, author = {Zhang, H and Yang, M and Ying, W and Hou, J and Zhou, Q and Sun, B and Wang, Y and Hui, X and Liu, L and Yao, H and Sun, J and Wang, W and Wang, X}, title = {Invasive fungal disease in a large cohort of hospitalized children with inborn errors of immunity in China.}, journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology}, volume = {36}, number = {4}, pages = {e70074}, doi = {10.1111/pai.70074}, pmid = {40205718}, issn = {1399-3038}, support = {ZD2021CY001//the Shanghai Municipal Science and Technology Major Project/ ; }, mesh = {Humans ; China/epidemiology ; Male ; Female ; Retrospective Studies ; *Invasive Fungal Infections/epidemiology/drug therapy ; Child, Preschool ; Child ; Infant ; Prevalence ; *Immunologic Deficiency Syndromes/epidemiology/complications ; Adolescent ; Hospitalization ; Infant, Newborn ; }, abstract = {BACKGROUND: Invasive fungal disease (IFD) is a common complication observed in inborn errors of immunodeficiency (IEI) patients, and little is known about the overall prevalence of IFD in IEI patients. We aimed to summarize the fungal spectrum and outcomes of IFDs in a Chinese cohort of hospitalized patients with IEI.

METHODS: In this retrospective study, 607 IEI patients hospitalized from January 2018 to June 2022 were included. Demographic, clinical, and fungal infection data and IEI patient characteristics were collected and analyzed according to the IEI classification.

RESULTS: One hundred and two IEI patients were diagnosed with proven or probable IFD. The overall prevalence of IFD was 17% (102/607). There were 29 different genotypes, among which CYBB (25%), CD40LG (9%), and RAG1 (7%) mutations were the most common. Most IFD infections (87/102) were caused by one fungus. Invasive Aspergillus, Pneumocystis jirovecii pneumonia, and Penicillium infections were more commonly observed in patients with congenital defects in phagocytes, immunodeficiencies affecting cellular and humoral immunity, and defects in innate immunity, respectively. Most IFDs observed in IEI patients were single-site infections, most of which were lung infections (74%). Seventeen patients were diagnosed with disseminated IFDs, nine of which were caused by Penicillium. All patients received antifungal treatments. Eight patients (8%) died within 3 months of IFD diagnosis.

CONCLUSIONS: IFD occurrence suggests the presence of immunity impairment. The IFD fungal profile may indicate different types of IEI. Early recognition of immunodeficiency and optimal timing of antifungal therapy can reduce fatality in IEI patients.}, } @article {pmid40205678, year = {2025}, author = {He, Y and Zhao, G and Ouyang, X and Wang, S and Chen, Y and Li, C and He, Y and Gao, J and Han, S and Zhao, J and Wang, J and Wang, C}, title = {Creatine-mediated ferroptosis inhibition is involved in the intestinal radioprotection of daytime-restricted feeding.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2489072}, doi = {10.1080/19490976.2025.2489072}, pmid = {40205678}, issn = {1949-0984}, mesh = {Animals ; Mice ; Gastrointestinal Microbiome/drug effects/radiation effects ; *Creatine/metabolism/pharmacology/administration & dosage ; *Ferroptosis/drug effects/radiation effects ; Mice, Inbred C57BL ; Male ; *Intestines/radiation effects/microbiology ; *Radiation-Protective Agents/metabolism/administration & dosage ; Radiation, Ionizing ; Feces/microbiology ; Enterocytes/radiation effects/metabolism ; }, abstract = {Ionizing radiation-induced intestinal injury (IRIII) is a catastrophic disease lack of sufficient medical countermeasures currently. Regulation of the gut microbiota through dietary adjustments is a potential strategy to mitigate IRIII. Time-restricted feeding (TRF) is an emerging behavioral nutrition intervention with pleiotropic health benefits. Whether this dietary pattern influences the pathogenesis of IRIII remains vague. We evaluated the impact of TRF on intestinal radiosensitivity in this study and discovered that only daytime TRF (DTRF), not nighttime TRF, could ameliorate intestinal damage in mice that received a high dose of IR. Faecal metagenomic and metabolomic studies revealed that the intestinal creatine level was increased by approximate 9 times by DTRF, to which the Bifidobacterium pseudolongum enrichment contribute. Further investigations showed that creatine could activate the energy sensor AMP-activated protein kinase in irradiated enterocytes and induce phosphorylation of acetyl-CoA carboxylase, resulting in reduced production of polyunsaturated fatty acids and reduced ferroptosis after IR. The administration of creatine mitigated IRIII and reduced bacteremia and proinflammatory responses. Blockade of creatine import compromised the ferroptosis inhibition and mitigation of DTRF on IRIII. Our study demonstrates a radioprotective dietary mode that can reshape the gut microbiota and increase intestinal creatine, which can suppress IR-induced ferroptosis, thereby providing effective countermeasures for IRIII prevention.}, } @article {pmid40205588, year = {2025}, author = {Li, M and Wang, Z and Ma, Z and Wang, Y and Jia, H and Zhang, L and Chen, P and Mao, Y and Yang, Z}, title = {Metagenomic analysis reveals microbial drivers of heat resistance in dairy cattle.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {35}, pmid = {40205588}, issn = {2524-4671}, support = {2022YFF1001200//National Key Research and Development Program of China/ ; }, abstract = {Heat stress poses a significant challenge to dairy cattle, leading to adverse physiological effects, reduced milk yield, impaired reproduction performance and economic losses. This study investigates the role of the rumen microbiome in mediating heat resistance in dairy cows. Using the entropy-weighted TOPSIS method, we classified 120 dairy cows into heat-resistant (HR) and heat-sensitive (HS) groups based on physiological and biochemical markers, including rectal temperature (RT), respiratory rate (RR), salivation index (SI) and serum levels of potassium ion (K[+]), heat shock protein 70 (HSP70) and cortisol. Metagenomic sequencing of rumen fluid samples revealed distinct microbial compositions and functional profiles between the two groups. HR cows exhibited a more cohesive and functionally stable microbiome, dominated by taxa such as Ruminococcus flavefaciens and Succiniclasticum, which are key players in fiber degradation and short-chain fatty acid production. Functional analysis highlighted the enrichment of the pentose phosphate pathway (PPP) in HR cows, suggesting a metabolic adaptation that enhances oxidative stress management. In contrast, HS cows showed increased activity in the tricarboxylic acid (TCA) cycle, pyruvate metabolism and other energy-intensive pathways, indicating a higher metabolic burden under heat stress. These findings underscore the critical role of the rumen microbiome in modulating heat resistance and suggest potential microbiome-based strategies for improving dairy cattle resilience to climate change.}, } @article {pmid40205543, year = {2025}, author = {Zou, Z and Zhao, W and Chen, Y and Liu, Z and He, G and Zhang, H}, title = {Extracorporeal membrane oxygenation in the treatment of critical Pneumocystis jirovecii pneumonia in a child with Langerhans cell histiocytosis: a case report and literature review.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {492}, pmid = {40205543}, issn = {1471-2334}, mesh = {Humans ; *Extracorporeal Membrane Oxygenation/methods ; Female ; *Pneumonia, Pneumocystis/therapy/complications/microbiology ; Child, Preschool ; *Pneumocystis carinii/genetics/isolation & purification ; *Histiocytosis, Langerhans-Cell/complications/drug therapy ; Treatment Outcome ; }, abstract = {BACKGROUND: Children with Langerhans cell histiocytosis (LCH) are particularly susceptible to infections such as Pneumocystis jirovecii pneumonia (PJP) due to the immunosuppressive effects of chemotherapy, which can progress to acute respiratory distress syndrome (ARDS) and respiratory failure. The use of Extracorporeal Membrane Oxygenation (ECMO) to manage hypoxemia secondary to PJP in LCH presents unique challenges, including the prevention of catheter-related bloodstream infections associated with arterial and venous access. This study explores a case wherein ECMO was crucial in treating severe PJP-induced respiratory failure in a pediatric patient with LCH.

CASE PRESENTATION: A 3-year-old female with a history of LCH, undergoing long-term chemotherapy and corticosteroid treatment, was admitted with fever, dyspnea, and lethargy. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid confirmed Pneumocystis jirovecii (PJ). Despite aggressive management with invasive high-frequency ventilation, inhaled nitric oxide, and prone positioning, the patient's oxygenation remained critically low, with severe hypercapnia and resultant severe respiratory acidosis, necessitating vasopressor support for hemodynamic stability and venoarterial (VA) ECMO intervention. Early initiation of VA ECMO facilitated ultraprotective lung ventilation and circulatory support, effectively preventing hemodynamic collapse. The patient was successfully decannulated after 13 days of ECMO support.

CONCLUSION: While PJP is a rare and extremely serious opportunistic infection, the VA ECMO support in this pediatric case effectively managed severe PJP without ECMO-related complications. This highlights ECMO as a potentially viable, relatively effective, and safe adjunctive therapy in the management of severe PJP infections in children.}, } @article {pmid40205497, year = {2025}, author = {Grønbæk, IMB and Halkjær, SI and Mollerup, S and Hansen, EH and Paulsen, SJ and Engel, S and Theede, K and Wilkens, R and Boysen, T and Petersen, AM}, title = {The effects of probiotic treatment with Bifidobacterium breve, Bif195 for small intestinal Crohn's disease and the gut microbiome: results from a randomised, double-blind, placebo-controlled trial.}, journal = {Gut pathogens}, volume = {17}, number = {1}, pages = {19}, pmid = {40205497}, issn = {1757-4749}, support = {A6876//The Capital Region's Research Foundation for Health Research/ ; }, abstract = {BACKGROUND: The aetiology of Crohn's disease, a chronic inflammatory bowel disease, is multifactorial and not completely understood. However, the association with gut dysbiosis is well-established, and manipulation of the gut microbiota has gained interest as a treatment strategy. This study aimed to investigate the effects of the probiotic strain Bifidobacterium breve, Bif195™ (Bif195) on intestinal inflammation, symptoms, and the gut microbiome composition in patients with small intestinal Crohn's disease.

METHODS: This was a randomised, double-blind, placebo-controlled trial. Thirty-three patients with small intestinal Crohn's disease were assigned to eight weeks of treatment with Bif195 or placebo (1:1). The primary outcome was changes in bowel wall thickness measured by intestinal ultrasonography. Other outcomes were changes in symptom severity, quality of life, faecal calprotectin, fatigue, and specific inflammatory parameters on ultrasonography. Changes in the microbiome composition were also examined.

RESULTS: Bif195 did not affect the bowel wall thickness in the small intestine compared to placebo. Nor did we observe effects on secondary or clinical explorative outcomes. Analysis of the gut microbiome showed that the relative abundance of B. breve rose during the intervention in the Bif195 group, but the result was statistically non-significant. Surprisingly, we observed a clustering of baseline microbiome data into two groups that differed in several aspects including a statistically significant difference in the incidence of previous bowel resections among the participants. Furthermore, changes in symptom scores after eight weeks of intervention were significantly different across the two microbiome groups, with an interaction effect of p = 0.04.

CONCLUSIONS: Eight weeks of treatment with Bif195 did not affect clinical outcomes for Crohn's disease. However, variations in baseline microbiome data influenced the results. This underscores the importance of assessing baseline microbiome data in intervention studies in Crohn's disease.

CLINICALTRIALS: gov NCT04842149.}, } @article {pmid40205473, year = {2025}, author = {Rodriguez-Cruz, UE and Ochoa-Sánchez, M and Eguiarte, LE and Souza, V}, title = {Running against the clock: Exploring microbial diversity in an extremely endangered microbial oasis in the Chihuahuan Desert.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaf033}, pmid = {40205473}, issn = {1574-6941}, abstract = {The Cuatro Ciénegas Basin is a biodiversity hotspot known for its unique biodiversity. However, this ecosystem is facing severe anthropogenic threats that are drying its aquatic systems. We investigated microbial communities at three sites with different physicochemical and environmental characteristics (Pozas Rojas, Archean Domes, and the Churince system) within the basin to explore potential connections to deep aquifers and determine if the sites shared microorganisms. Utilizing 16S rRNA gene data, we identified a core microbiota between Pozas Rojas and Archean Domes. Sulfur reduction appears to shape the microbial connectivity among sites, since sulfur-reducing bacteria has the highest prevalence between samples from Pozas Rojas and Archean Domes: Halanaerobium sp. (88.46%) and Desulfovermiculus halophilus (65%); and between the Churince system and Archean Domes: Halanaerobium sp. (63%) and Desulfovermiculus halophilus (60%). Furthermore, metagenome assembled genomes from Ectothiorhodospira genus were found in both Archean Domes and Churince, suggesting microbial dispersal. An important finding is that microbial diversity in the Archean Domes system declined, from 2016 to 2023 the ecosystem lost 29 microbial phyla. If this trend continues, the basin will lose most of its water, resulting in the loss of various prokaryotic lineages and potential biotechnological solutions, such as enzymes or novel antibiotics. Our findings highlighting the need for water extraction regulations to preserve the basin's biodiversity.}, } @article {pmid40205381, year = {2025}, author = {Chen, G and Yin, L and Zhang, H}, title = {Isolation and characterization of goose astrovirus genotype 1 causing enteritis in goslings from Sichuan Province, China.}, journal = {BMC veterinary research}, volume = {21}, number = {1}, pages = {259}, pmid = {40205381}, issn = {1746-6148}, support = {ZYN2024087//Central University Basic Scientific Research Business Expenses Special Funds/ ; }, abstract = {Since 2017, goose astrovirus (GoAstV) has been widely prevalent in various provinces of China, causing economic losses in the goose industry, with outbreak mortality rates ranging from 10 to 60%. Notably, a goose farm in Sichuan Province has faced an outbreak of infectious disease in 1-3 weeks old goslings, with a mortality rate of approximately 30%. Viral metagenomic analysis of fecal samples identified Goose astrovirus genotype 1 (GoAstV-1), and PCR analysis confirmed the presence of GoAstV-1. Furthermore, we successfully isolated a GoAstV-C1 strain using goose embryos named AAstV/Goose/CHN/2023/C1 (GenBank No. PP108251), and its viral titer was calculated as 10^4.834 ELD50/0.5 mL using the Reed-Muench method. The genome size of GoAstV-C1 was about 7,261 nucleotides through amplifying with Sanger sequencing and assembling with SeqMan software. Phylogenetic analysis revealed that GoAstV-1 strains are classified into three major subtypes: A, B, and C, with the GoAstV-C1 strain identified as a unique variant within subtype B, characterized by distinct genetic divergence features. Experimental inoculation of one-day-old goslings with the virus resulted in a mortality rate of 5 out of 15 (p-value = 0.0421) and a significant reduction in weight gain compared to controls (p-value = 0.005). Pathological examination revealed that GoAstV-C1 infection caused severe damage to the liver, spleen, and kidneys. Interestingly, unlike most GoAstV, which leads to characteristic gout symptoms, our isolates GoAstV-C1 caused obvious intestinal damage characterized by necrosis, inflammatory infiltration, and crypt architectural disruption. We indicated that GoAstV-C1 displays a unique intestinal tropism rather than characteristic gout symptoms and elucidated genomic features and evolutionary relationships of GoAstV strains. These findings help advance our knowledge of the epidemiology and pathogenicity of GoAstV-1, and the predicted structure of capsid protein could serve as a potential target for designing novel antiviral drugs or vaccines against GoAstV-1.}, } @article {pmid40204977, year = {2025}, author = {Deng, Z and Poulsen, JS and Nielsen, JL and Weissbrodt, DG and Spanjers, H and van Lier, JB}, title = {Identification of protein-degraders in an anaerobic digester by protein stable isotope probing and metagenomics.}, journal = {Applied microbiology and biotechnology}, volume = {109}, number = {1}, pages = {87}, pmid = {40204977}, issn = {1432-0614}, support = {201708450043//China Scholarship Council/ ; }, mesh = {Anaerobiosis ; *Metagenomics ; *Acinetobacter/metabolism/genetics ; Carbon Isotopes/metabolism ; Bacterial Proteins/metabolism/genetics ; Isotope Labeling ; Metabolic Networks and Pathways ; Proteomics ; *Bioreactors/microbiology ; Proteolysis ; Glucose/metabolism ; *Proteins/metabolism ; }, abstract = {Presence of carbohydrates hampers protein degradation in anaerobic digesters. To understand this phenomenon, we used proteogenomics to identify the active protein-degraders in the presence of low and high carbohydrates concentrations. Active metabolic pathways of the identified protein-degraders were investigated using proteomics with [13]C-protein substrates (protein stable isotope probing). Results showed that 1) Acinetobacter was the active protein-degraders under both protein-fed and protein-glucose mixture-fed conditions, 2) the relative abundance of Acinetobacter was not affected by the presence of carbohydrates, 3) the incorporation of the [13]C-labelled protein substrate was predominantly observed in outer membrane-bound proteins and porin proteins, which are associated with proteinases or the transportation of amino acids across the cell wall. The Acinetobacter metabolic model and the incubation conditions suggested that glucose and proteins were degraded through anaerobic respiration. The negative impact of carbohydrates on protein biodegradation was attributed to Acinetobacter's preference for carbohydrates. This work highlights that efficient degradation of protein and carbohydrate mixtures in anaerobic digesters requires a staged or time-phased approach and enrichment of active protein-degraders, offering a new direction for process optimization in anaerobic digestion systems. KEY POINTS: • Acinetobacter identified for the first time as main anaerobic protein-degrader • Metabolic model revealed protein degradation via anaerobic respiration • Metabolic pathway analysis indicated SO4[2-] or Fe[3+] as terminal electron acceptors.}, } @article {pmid40204761, year = {2025}, author = {Li, F and Hooi, SL and Choo, YM and Teh, CSJ and Toh, KY and Lim, LWZ and Lee, YQ and Chong, CW and Ahmad Kamar, A}, title = {Progression of gut microbiome in preterm infants during the first three months.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {12104}, pmid = {40204761}, issn = {2045-2322}, support = {IF047-2021//International Funding/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Infant, Premature ; Infant, Newborn ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Female ; Male ; Prospective Studies ; *Bacteria/genetics/classification ; Infant ; Gestational Age ; Bifidobacterium/genetics/isolation & purification ; Meconium/microbiology ; Metagenomics ; }, abstract = {The colonization and evolution of gut microbiota early in life play a vital role in shaping a healthy, robust immune system for infant health, whether in combating short-term illness or improving long-term health outcomes. Early-life clinical practices may interrupt or disrupt the normal colonization process of the infant gut microbiota, thereby increasing disease susceptibility. In this prospective cohort study, we analyzed the gut microbiota of 46 term and 23 preterm infants using 16S rRNA gene metagenomic sequencing. Fecal samples were collected at six timepoints during the first three months of life. Notably, gestational age was the main factor contributing to differences in the meconium microbial composition. Intriguingly, our study unveiled a more homogeneous microbial composition in preterm infants with more abundant Bifidobacterium from the postnatal age (PNA) of one month. Concurrently, the beneficial bacteria Bifidobacterium and Lactobacillus gradually increased, and the potentially pathogenic bacteria Clostridium, Enterobacter, Enterococcus, Klebsiella, and Pseudomonas gradually decreased. Furthermore, our study underscored a link between decreased microbial diversity of preterm infants and exclusive breastfeeding and antibiotic exposure. Moreover, preterm infants with patent ductus arteriosus (PDA) exhibited reduced microbial diversity but higher abundances of Streptococcus oralis and Streptococcus mitis.}, } @article {pmid40204742, year = {2025}, author = {Napit, R and Gurung, A and Poudel, A and Chaudhary, A and Manandhar, P and Sharma, AN and Raut, S and Pradhan, SM and Joshi, J and Poyet, M and Groussin, M and Rajbhandari, RM and Karmacharya, DB}, title = {Metagenomic analysis of human, animal, and environmental samples identifies potential emerging pathogens, profiles antibiotic resistance genes, and reveals horizontal gene transfer dynamics.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {12156}, pmid = {40204742}, issn = {2045-2322}, mesh = {*Gene Transfer, Horizontal ; Animals ; Humans ; *Metagenomics/methods ; Feces/microbiology ; *Bacteria/genetics/drug effects ; Nepal ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; Virulence Factors/genetics ; Birds/microbiology ; Metagenome ; }, abstract = {Antimicrobial resistance (AMR) poses a significant threat to global health. The indiscriminate use of antibiotics has accelerated the emergence and spread of drug-resistant bacteria, compromising our ability to treat infectious diseases. A One Health approach is essential to address this urgent issue, recognizing the interconnectedness of human, animal, and environmental health. This study investigated the prevalence and transmission of AMR in a temporary settlement in Kathmandu, Nepal. By employing shotgun metagenomics, we analyzed a diverse range of samples, including human fecal samples, avian fecal samples, and environmental samples. Our analysis revealed a complex interplay of pathogenic bacteria, virulence factors (VF), and antimicrobial resistance genes (ARGs) across these different domains. We identified a diverse range of bacterial species, including potential pathogens, in both human and animal samples. Notably, Prevotella spp. was the dominant gut bacterium in human samples. Additionally, we detected a wide range of phages and viruses, including Stx-2 converting phages, which can contribute to the virulence of Shiga toxin-producing E. coli (STEC) strains. Our analysis revealed the presence of 72 virulence factor genes and 53 ARG subtypes across the studied samples. Poultry samples exhibited the highest number of ARG subtypes, suggesting that the intensive use of antibiotics in poultry production may contribute to the dissemination of AMR. Furthermore, we observed frequent horizontal gene transfer (HGT) events, with gut microbiomes serving as key reservoirs for ARGs. This study underscores the critical role of a One Health approach in addressing AMR. By integrating human, animal, and environmental health perspectives, we can better understand the complex dynamics of AMR and develop effective strategies for prevention and control. Our findings highlight the urgent need for robust surveillance systems, judicious antibiotic use, and improved hygiene practices to mitigate the impact of AMR on public health.}, } @article {pmid40204671, year = {2025}, author = {Luo, G and Fan, L and Liang, B and Guo, J and Gao, SH}, title = {Determining Antimicrobial Resistance in the Plastisphere: Lower Risks of Nonbiodegradable vs Higher Risks of Biodegradable Microplastics.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c00246}, pmid = {40204671}, issn = {1520-5851}, abstract = {The plastisphere is a potential contributor to global antimicrobial resistance (AMR), posing potential threats to public and environmental health. However, comprehensively quantifying the contribution of microplastics with different biodegradability to AMR is lacking. In this study, we systematically quantified AMR risk mediated by biodegradable and nonbiodegradable microplastics using abundance-based methods and a custom AMR risk ranking framework that includes antimicrobial resistance genes (ARGs) abundance, mobility, and host pathogenicity. Our results demonstrated that biodegradable microplastics exhibited higher AMR risk compared to that of nonbiodegradable plastics. Key resistance genes, including those for multidrug, bacitracin, and aminoglycoside resistance, were predominant. Machine learning analysis identified cell motility as the most significant signature associated with AMR risk, highlighting its potential role in promoting ARGs dissemination. In addition, biodegradable microplastics promoted oxidative stress and SOS responses, which likely enhanced horizontal gene transfer (HGT) and AMR. Metagenome-assembled genomes (MAGs) analysis uncovered the colocalization of microplastic degradation genes, ARGs, and virulence factors (VFs), further supporting the elevated risk in biodegradable plastisphere. The proximity of ARGs to mobile genetic elements (MGEs) suggests that microplastic degradation processes might favor ARGs mobility. These findings would contribute critical insights into AMR dissemination in the plastisphere, emphasizing the need for integrated environmental and public health strategies under the context of One Health.}, } @article {pmid40204030, year = {2025}, author = {Bao, Y and Feng, S and Yu, F and Ye, W and Xing, H and Zhu, X and Bao, W and Huang, M}, title = {Self-Regulating pH Pyrite-Construction waste Biofilter: Denitrification Performance, metabolic Pathways, and clogging Alleviation.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132500}, doi = {10.1016/j.biortech.2025.132500}, pmid = {40204030}, issn = {1873-2976}, abstract = {Waste-based denitrification filters face challenges like alkalinity accumulation, low efficiency, and clogging. This study proposes a novel denitrification filter using construction waste and pyrite (WPDF) to address these issues. WPDF's performance, safety, and mechanisms were evaluated by measuring effluent, filler characteristics and metagenomics. Results demonstrated a high total nitrogen removal load (88.65 g N m[-3]d[-1]) with minimal biofilm (13 %) and filler accumulation (39 %), effectively mitigating clogging. Phosphorus removal relied on chemical precipitation in construction waste. WPDF was pH self-regulating and promoted the formation and release of fulvic acid. Pyrite promotes bio-metabolism, making WPDF enriched in energy metabolism (6 %) and transporter capacity (6 %). Functional prediction indicated that WPDF was more abundant in genes related to denitrification, glycolysis, and electron transport, which promoted the heterotrophic denitrification process. This study provides a novel, efficient, and eco-friendly possible solution for wastewater and offers new insights into the molecular mechanisms of carbon and nitrogen metabolism.}, } @article {pmid40203979, year = {2025}, author = {Genitsaris, S and Stefanidou, N and Kourkoutmani, P and Michaloudi, E and Gros, M and García-Gómez, E and Petrović, M and Ntziachristos, L and Moustaka-Gouni, M}, title = {Do coastal bacterioplankton communities hold the molecular key to the rapid biodegradation of Polycyclic Aromatic Hydrocarbons (PAHs) from shipping scrubber effluent?.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121563}, doi = {10.1016/j.envres.2025.121563}, pmid = {40203979}, issn = {1096-0953}, abstract = {Shipping scrubber effluents, containing a cocktail of Polycyclic Aromatic Hydrocarbons (PAHs), show undisputed effects at single-species experiments while PAHs fate in the marine environment after effluent discharge is still investigated. Bacterioplankton, composed of abundant diverse taxa with xenobiotic-degrading capabilities, are the first responders to scrubber emissions and can affect PAHs impacts on marine life. This work aims to examine the fate of scrubber effluent PAHs and alkyl-PAHs in mesocosms of coastal bacterioplankton communities from a pristine (phytoplankton carbon biomass was 8.16 μg C L[-1]) and a eutrophic (105.35 μg C L[-1]) coastal site. High-throughput 16S rRNA metabarcoding revealed differential responses of the bacterioplankton linked to their initial community structure and population abundances. Taxa known for their PAHs-degrading capacity were retrieved, including the genera Roseobacter, Porticoccus, Marinomonas, Arcobacter, Lentibacter, Lacinutrix, Pseudospirillum, Glaciecola, Vibrio, Marivita, and Mycobacterium, and were found to have increased roles in shifted communities by increasing their relative abundances at least 5-fold in treatments with high scrubber effluent additions. Additionally, metagenomic analysis of shotgun sequencing, indicated an increase on the number of Clusters of Orthologous Genes (COGs) associated with pathways involved in PAHs degradation. Up to 198 more COGs involved in signal transduction were retrieved in scrubber effluent enriched mesocosms compared to controls, while 15, 86, and 136 more COGs associated with naphthalene, aromatic compound, and benzoate degradation, respectively, were detected in the pristine mesocosms after effluent additions. In both experiments, bacterioplankton responses towards xenobiotic degradation under increased PAHs and alkyl-PAHs were coupled with a drop in their concentrations, below the limit of detection by Day 3 of the experiment in the eutrophic community, and by half in Day 6 in the pristine environment's community. Our findings indicate that PAHs and alkyl-PAHs impacts can be rapidly reduced in natural systems of high bacterial activity.}, } @article {pmid40203710, year = {2025}, author = {Qv, M and Wu, Q and Wang, W and Wang, H and Zhu, L}, title = {Metagenomic insights into the response of microbial metabolic function and extracellular polymeric substances from microalgae-bacteria consortia to fluoroquinolone antibiotics.}, journal = {Journal of environmental management}, volume = {381}, number = {}, pages = {125283}, doi = {10.1016/j.jenvman.2025.125283}, pmid = {40203710}, issn = {1095-8630}, abstract = {Microalgae-bacteria consortia (MBC) are considered a promising bioremediation technology for removing pollutants from swine wastewater. However, the overuse of antibiotics poses challenges to the effective functioning of MBC. In this study, the removal efficiency of nutrients in wastewater by MBC under different antibiotic concentrations (0, 1, 5, 10 and 50 mg/L) was evaluated. The changes of functional microbial abundance were elucidated and the response mechanism of MBC against antibiotics was investigated. Antibiotics inhibited the accumulation of MBC biomass and reduced the removal efficiency of ammonia nitrogen and total phosphorus in wastewater by 8.39 % and 8.74 % respectively. In addition, antibiotics affected the relative abundance of microorganisms (Raineyella, from 30.72 % to 15.96 %) and functional genes (glnA, gudB, NirK, NirBD, NarB, NapAB, NorBC and NosZEPS) involved in N metabolism. MBC could defend against the adverse effects of antibiotics by regulating the content of proteins in the extracellular polymeric substances.}, } @article {pmid40203094, year = {2025}, author = {Isobe, N and Tanaka, K and Ishii, S and Shimane, Y and Okada, S and Daicho, K and Sakuma, W and Uetani, K and Yoshimura, T and Kimoto, K and Kimura, S and Saito, T and Nakajima, R and Tsuchiya, M and Ikuta, T and Kawagucci, S and Iwata, T and Nomaki, H}, title = {Fully circular shapable transparent paperboard with closed-loop recyclability and marine biodegradability across shallow to deep sea.}, journal = {Science advances}, volume = {11}, number = {15}, pages = {eads2426}, doi = {10.1126/sciadv.ads2426}, pmid = {40203094}, issn = {2375-2548}, abstract = {To mitigate marine pollution from single-use plastics, it is crucial to transition to next-generation commodity materials that are derived from biomass and are recyclable and marine biodegradable even at abyssal depths in case of the accidental release to the ocean. Here, we develop an optically transparent millimeter-thick paperboard called transparent paperboard (tPB) through dissolution and coagulation of cellulose. The tPB is made entirely of pristine cellulose and compositionally identical to paper. A cup-shaped tPB can hold just-boiled water without an internal film coating because of its high wet tensile properties and anisotropic thermal properties. In addition, the spent tPB is material recyclable in a closed system, where all chemicals and water are also recyclable. Furthermore, the marine biodegradability of tPB across shallow to abyssal depths is confirmed by on-site degradation tests and metagenomic analyses. Hence, tPB is expected to serve as a key fully circular commodity material in sustainable societies of the future.}, } @article {pmid40202861, year = {2025}, author = {Singh, AK and Sathaye, SB and Rai, AK and Singh, SP}, title = {Novel Cellobiose 2-Epimerase from Thermal Aquatic Metagenome for the Production of Epilactose.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.4c09753}, pmid = {40202861}, issn = {1520-5118}, abstract = {Epilactose is a prebiotic molecule that exerts a bifidogenic effect and increases calcium and iron absorption in the small intestine. This study identifies a novel cellobiose 2-epimerase gene (ceM) by investigating metagenomic data generated from a thermal aquatic habitat. The computation of secondary and tertiary structure analysis, molecular docking, and MD simulation analysis indicated the protein CEM to be a novel cellobiose 2-epimerase. The gene was expressed in Escherichia coli, followed by biochemical characterization of the purified protein. CEM is capable of transforming lactose into the high-value rare sugar, epilactose, in a wide range of temperatures (4-70 °C) and pH (6.0-10.0). The enzyme was exposed to 50 °C, and hardly a 10% loss in activity was recorded after 32 h of heat treatment, suggesting that CEM is a thermostable protein. CEM is a kinetically highly efficient enzyme, with a turnover number of 9832 ± 490 s[-1] for lactose to epilactose epimerization. The maximum conversion yield of 26% epilactose was obtained in 15 min of catalytic reaction. Further, the enzyme was successfully tested to transform lactose in milk and whey samples.}, } @article {pmid40202719, year = {2025}, author = {Huang, Z and Liu, C and Zhao, X and Guo, Y}, title = {The effect of elevated levels of the gut metabolite TMAO on glucose metabolism after sleeve gastrectomy.}, journal = {Archives of physiology and biochemistry}, volume = {}, number = {}, pages = {1-10}, doi = {10.1080/13813455.2025.2489721}, pmid = {40202719}, issn = {1744-4160}, abstract = {Purpose：Bariatric surgery can effectively alleviate obesity and diabetes by regulation of the gut microbiota. This study aimed to investigate the change in the gut microbiota metabolite TMAO and to explore its effect on glucose metabolism after sleeve gastrectomy (SG). Materials and methods：Diet-induced obesity mouse models were established, and the mice were randomly divided into four groups: an SG group, a sham-operated group pair-fed with the SG group (PF), a sham-operated group fed ad libitum (AL), and a lean control group (C). At 10 weeks post-surgery, the changes in glycogen content of liver, gut microbiota and the level of FMO3 in the liver were evaluated, and their correlation with TMAO production was analysed. The expression levels of the TMAO/PERK/FOXO1 pathway and the gluconeogenic genes G6PC and PCK1 were measured. Results：At 10 weeks post-surgery, hepatocyte glycogen levels were restored, and serum TMA and TMAO levels were significantly increased. Faecal metagenomic sequencing results showed that the abundances of Ruminococcaceae and Lachnospiraceae, which were positively correlated with TMAO production, were significantly increased after surgery. While the changes in FMO3, the key enzyme producing TMAO in the liver was found decreased significantly after SG. The expression levels of the TMAO/PERK/FOXO1 pathway and the gluconeogenic genes G6PC and PCK1 were measured. Inconsistent with the changing trend of TMAO, the expression of PERK, FOXO1, PCK, and G6PC significantly decreased after SG. Conclusions：SG can significantly reduce obesity and restore glucose metabolism. After surgery, TMAO metabolites increased in a microbiota-dependent manner.}, } @article {pmid40202375, year = {2025}, author = {Pan, C and Xu, P and Yuan, M and Wei, S and Lu, Y and Lu, H and Zhang, W}, title = {Effects of Different Feeding Patterns on the Gut Virome of 6-Month-Old Infants.}, journal = {Journal of medical virology}, volume = {97}, number = {4}, pages = {e70344}, doi = {10.1002/jmv.70344}, pmid = {40202375}, issn = {1096-9071}, support = {//This study was supported by the Zhenjiang Science and Technology Innovation Funds-Clinical Medicine Key Laboratory and Scientific Research Project of Health Commission of Jiangsu Province./ ; }, mesh = {Humans ; Infant ; *Gastrointestinal Microbiome ; *Virome ; Feces/virology ; *Breast Feeding ; Female ; Male ; *Viruses/classification/genetics/isolation & purification ; Metagenomics ; *Feeding Behavior ; Bacteriophages/genetics/classification/isolation & purification ; Milk, Human/virology ; *Gastrointestinal Tract/virology ; }, abstract = {The gut microbiome is essential for infant health, and in recent years, the impact of enteroviruses on infant health and disease has received increasing attention. The transmission of breast milk phages to the infant gastrointestinal tract contributes to the shaping of the infant gut virome, while breastfeeding regulates the colonization of the infant gut virome. In this study, we collected fecal samples from healthy infants and analyzed the distribution characteristics of infant viral communities by viral metagenomic analysis, and analyzed the differences in infant viral communities under different feeding practices. Our results indicate that the infant intestinal virome consists of phages and eukaryotic viruses. Caudovirales and Microviridae dominated the phage composition, and except for Siphoviridae, which was more predominant in the intestines of formula-fed infants, there were no significant differences in the overall abundance of other Caudovirales and Microviridae in the intestines of infants with different feeding patterns. Breastfeeding can lead to a higher diversity of infant gut viruses through vertical transmission, and a highly diverse gut virome helps maintain the maturation of the gut microbiome. This study informs the shaping of gut virome in healthy infants by breastfeeding and contributes to further research on infant gut virome characteristics and formation processes.}, } @article {pmid40202358, year = {2025}, author = {Alexandre, A and Gerard, À and Sergio, I and Whim, T and Isabelle, L and Maria José, C and Lorena, I and Enrique, H and Gerardo, MA and Carolina, M and José, N and Vanessa, B and Rubén, L}, title = {Geographic Influence on Subgingival Microbiota in Health and Periodontitis: A Multinational Shotgun Metagenomic Study.}, journal = {Journal of periodontal research}, volume = {}, number = {}, pages = {}, doi = {10.1111/jre.13406}, pmid = {40202358}, issn = {1600-0765}, abstract = {AIMS: To assess the differences in the taxonomical and functional profile of the subgingival microbiota isolated from healthy subjects (HS) and patients with periodontitis (PP) from four different countries.

METHODS: In this study, 80 subgingival samples from HS and PP from four different countries (Belgium, Chile, Peru, and Spain) were analyzed using shotgun metagenomic sequencing.

RESULTS: The results indicated significant variation in α-diversity between HS and PP, segregated by country, with PP from Peru clearly standing out from the rest. In terms of composition, β-diversity was explained more by the country of origin (6.8%) than by the diagnosis (4.1%). In addition, more than 75 different taxa, 63 of which were identified at the species level, showed significantly different relative abundances when comparing the country of origin, diagnosis, and both variables combined. Moreover, 85 metabolic pathways showed significantly different relative abundances between HS and PP, with species commonly associated with periodontitis, such as Porphyromonas gingivalis and Tannerella forsythia, strongly contributing to the reinforcement of periodontitis-associated pathways. On the other hand, differences in functional profiles based on the country of origin were almost nonexistent, suggesting that variability in taxonomic profiles does not have a direct impact on healthy or periodontitis-associated functional profiles.

CONCLUSION: These findings suggest that microbial analysis should take into account the geographic origin of samples in order to provide a more accurate description of the subgingival microbiota. Moreover, they lay the groundwork for larger and more comprehensive studies that might analyze this phenomenon in the future.}, } @article {pmid40202322, year = {2025}, author = {Scheffer, G and Chakraborty, A and Amundson, KK and Khan, R and Wilkins, MJ and Evans, P and Hubert, CRJ}, title = {Polymer biodegradation by Halanaerobium promotes reservoir souring during hydraulic fracturing.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0225324}, doi = {10.1128/aem.02253-24}, pmid = {40202322}, issn = {1098-5336}, abstract = {UNLABELLED: Hydraulically fractured shale reservoirs have facilitated studies of unexplored niches in the continental deep biosphere. In high-salinity North American shale systems, members of the genus Halanaerobium seem to be ubiquitous. Polymers like guar gum used as gelling agents in hydraulic fracturing fluids are known to be fermentable substrates, but metabolic pathways encoding these processes have not been characterized. To explore this, produced water samples from the Permian Basin were incubated both at 30°C to simulate above-ground storage conditions and at 60°C to simulate subsurface reservoir conditions. Guar metabolism coincided with Halanaerobium growing only at 30°C, revealing genes for polymer biodegradation through the mixed-acid fermentation pathway in different metagenome-assembled genomes (MAGs). Whereas thiosulfate reduction to sulfide is often invoked to explain the dominance of Halanaerobium in these settings, genes for thiosulfate metabolism were lacking in Halanaerobium genomes with high estimated completeness. Sulfide production was observed in 60°C incubations, with corresponding enrichment of Desulfohalobium and Desulfovibrionaceae that possess complete pathways for coupling mannose and acetate oxidation to sulfate reduction. These findings outline how production of fermentation intermediates (mannose and acetate) by Halanaerobium in topside settings can result in reservoir souring when these metabolites are introduced into the subsurface through produced water reuse.

IMPORTANCE: Hydraulically fractured shale oil reservoirs are ideal for studying extremophiles such as thermohalophiles. During hydraulic fracturing, reservoir production water is stored in surface ponds prior to reuse. Microorganisms in these systems therefore need to withstand various environmental changes such as the swing between warm downhole oil reservoir temperatures and cooler surface conditions. While most studies on hydraulically fractured oil reservoirs mimic the environmental conditions found in oil wells, this study follows this water cycle during fracking and the associated microbial metabolic potential during topside-produced water storage and subsurface oil reservoir conditions. Of particular interest are members of the genus Halanaerobium that have been reported to reduce thiosulfate contributing to souring of oil reservoirs. Here, we show that some Halanaerobium strains were unable to grow at hotter temperatures reflective of oil reservoir conditions and lack genes for thiosulfate reduction, despite the proposed importance of this metabolism in other studies. Rather, it is likely that these organisms metabolize complex organics in fracking fluids at lower temperatures, thereby generating substrates that support reservoir souring by thermophilic sulfate-reducing bacteria at higher temperatures. In this way, Halanaerobium promotes souring indirectly by feeding sulfate-reducing microorganisms fermentation products (e.g., acetate and hydrogen) rather than via direct sulfidogenesis via thiosulfate reduction. Therefore, the novelty of this research is not within the detection of known oil reservoir colonizing bacteria but rather in the relationship between bacteria and the indirect involvement of Halanaerobium, promoting souring throughout the produced water reuse cycle.}, } @article {pmid40202301, year = {2025}, author = {Mahillon, M and Debonneville, C and Groux, R and Roquis, D and Brodard, J and Faoro, F and Foissac, X and Schumpp, O and Dittmer, J}, title = {From insect endosymbiont to phloem colonizer: comparative genomics unveils the lifestyle transition of phytopathogenic Arsenophonus strains.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0149624}, doi = {10.1128/msystems.01496-24}, pmid = {40202301}, issn = {2379-5077}, abstract = {UNLABELLED: Bacteria infecting the plant phloem represent a growing threat worldwide. While these organisms often resist in vitro culture, they multiply both in plant sieve elements and hemipteran vectors. Such cross-kingdom parasitic lifestyle has emerged in diverse taxa via distinct ecological routes. In the genus Arsenophonus, the phloem pathogens "Candidatus Arsenophonus phytopathogenicus" (Ap) and "Ca. Phlomobacter fragariae" (Pf) have evolved from insect endosymbionts, but the genetic mechanisms underlying this transition have not been explored. To fill this gap, we obtained the genomes of both strains from insect host metagenomes. The resulting assemblies are highly similar in size and functional repertoire, rich in viral sequences, and closely resemble the genomes of several facultative endosymbiotic Arsenophonus strains of sap-sucking hemipterans. However, a phylogenomic analysis demonstrated distinct origins, as Ap belongs to the "Triatominarum" clade, whereas Pf represents a distant species. We identified a set of orthologs encoded only by Ap and Pf in the genus, including hydrolytic enzymes likely targeting plant substrates. In particular, both bacteria encode putative plant cell wall-degrading enzymes and cysteine peptidases related to xylellain, a papain-like peptidase from Xylella fastidiosa, for which close homologs are found in diverse Pseudomonadota infecting the plant vasculature. In silico predictions and gene expression analyses further support a role during phloem colonization for several of the shared orthologs. We conclude that the double emergence of phytopathogenicity in Arsenophonus may have been mediated by a few horizontal gene transfer events, involving genes acquired from other Pseudomonadota, including phytopathogens.

IMPORTANCE: We investigate the genetic mechanisms of a transition in bacterial lifestyle. We focus on two phloem pathogens belonging to the genus Arsenophonus: "Candidatus Arsenophonus phytopathogenicus" and "Ca. Phlomobacter fragariae." Both bacteria cause economically significant pathologies, and they have likely emerged among facultative insect endosymbionts. Our genomic analyses show that both strains are highly similar to other strains of the genus associated with sap-sucking hemipterans, suggesting a recent lifestyle shift. Importantly, although the phytopathogenic Arsenophonus strains belong to distant clades, they share a small set of orthologs unique in the genus pangenome. We provide evidence that several of these genes produce hydrolytic enzymes that are secreted and may target plant substrates. The acquisition and exchange of these genes may thus have played a pivotal role in the lifestyle transition of the phytopathogenic Arsenophonus strains.}, } @article {pmid40201781, year = {2025}, author = {Belkina, D and Stepanov, I and Makarkina, M and Porotikova, E and Lifanov, I and Kozhevnikov, E and Gorislavets, S and Vinogradova, S}, title = {In-depth population genetic study of Vitis vinifera ssp. sylvestris from the Black Sea region and its virome.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1536862}, pmid = {40201781}, issn = {1664-462X}, abstract = {The spread of cultivated grapevine from primary centers of origin is inevitably accompanied by the range expansion of its pathogens, including viruses. A limited number of wild Vitis vinifera L. ssp. sylvestris (Gmelin) Hegi populations have survived in the centers of grapevine domestication and can be used for comprehensive studies. We analyzed 50 grapevines collected in protected areas of the Black Sea region, which belong to the Caucasian domestication center. Based on genotyping of grapevines using simple sequence repeats as DNA markers, we determined the phylogenetic placement of V. vinifera ssp. sylvestris from the Black Sea region compared to cultivated and wild grapevines of the world. Using high-throughput sequencing of total RNA, we obtained the viromes of these grapevines. Ten viruses and one viroid were identified. The most common viruses detected were Vitis cryptic virus, grapevine rupestris stem pitting-associated virus, grapevine Pinot gris virus, and grapevine virus T. Among the economically significant viruses, we identified grapevine leafroll-associated virus 1 and grapevine virus A. A total of 91 complete or nearly complete virus genomes and one viroid genome were assembled, and phylogenetic analysis was performed. Two novel (+) ssRNA viruses were discovered, tentatively named Abrau grapevine-associated virus in the order Hepelivirales and Taurida grapevine-associated virus in the order Picornavirales. It is important to comprehensively consider the phylogeography of both viruses and their plant hosts. This is the first study that simultaneously addresses the population genetics of V. vinifera ssp. sylvestris from the Caucasian domestication center and its viruses.}, } @article {pmid40201723, year = {2025}, author = {Luo, H and Jiang, Y and He, Y and Zhou, H}, title = {Clinical Value of Metagenomic Next-Generation Sequencing From Blood Samples to Identify Pneumocystis jirovecii Pneumonia in Patients With Human Immunodeficiency Virus.}, journal = {Open forum infectious diseases}, volume = {12}, number = {4}, pages = {ofaf170}, pmid = {40201723}, issn = {2328-8957}, abstract = {BACKGROUND: The aim of this study was to evaluate the clinical value of metagenomic next-generation sequencing (mNGS) of blood samples for identifying Pneumocystis jirovecii pneumonia (PJP) in patients with human immunodeficiency virus (HIV).

METHODS: A total of 76 people with HIV (PWH) with suspected lung infections were enrolled in the study. The patients were divided into two groups: the PJP group and the non-PJP group.All patients underwent pulmonary computed tomography scans, and blood or respiratory tract specimens were subjected to mNGS and conventional microbiological tests. Patient characteristics were collected from their medical records.

RESULTS: Thirty patients were diagnosed with PJP and 46 were confirmed to have non-P jirovecii (Pj) infectious pneumonia. mNGS was conducted on bronchoalveolar lavage fluid samples from 25 patients and on blood samples from 59 patients. Twenty-one of 22 (95.5%) blood samples from the PIP group contained sequences of Pi, with the number of specific reads for circulating Pj sequences ranging from 2 to 2035. In the non-PJP group, 4 blood samples exhibited low Pj sequences, ranging from 1 to 2 reads. The sensitivity and specificity for blood samples were 95.5% (95% confidence interval [CI], 91.2%-98.4%) and 90.0% (95% Cl, 89.5%-100%), respectively.

CONCLUSIONS: Our study indicates that mNGS of blood samples exhibits high sensitivity and specificity for diagnosing PJP in PWH. Caution should be exercised when interpreting low Pj mNGS read counts in blood samples; the definitive diagnosis of PJP relies on the synthesis of clinical data with Pj mNGS results. Further studies are necessary to validate this finding.}, } @article {pmid40201438, year = {2025}, author = {Lu, W and Yi, X and Ge, Y and Zhang, X and Shen, K and Zhuang, H and Deng, Z and Liu, D and Cao, J and Ma, C}, title = {Effects of dietary fiber on the composition, function, and symbiotic interactions of intestinal microbiota in pre-weaned calves.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1554484}, pmid = {40201438}, issn = {1664-302X}, abstract = {INTRODUCTION: Dietary fiber plays a crucial role in maintaining gastrointestinal health. However, its protective effects on the intestinal health of calves remain to be fully elucidated. This study aimed to investigate the impact of dietary fiber supplementation on the intestinal microbiota of pre-weaned calves and its potential role in modulating microbial metabolic pathways.

METHODS: A randomized controlled trial was conducted, enrolling 135 calves that were randomly assigned into three groups: (1) inulin supplementation, (2) psyllium husk powder (PHP) supplementation, and (3) a control group receiving no dietary fiber. Fecal microbiota samples were collected from calves without diarrhea at five time points (0, 7, 14, 28, and 56 days of age). Metagenomic sequencing was performed to analyze microbial composition and functional pathways. Additionally, a differential analysis of carbohydrate-active enzymes (CAZymes) was performed to evaluate the effect of dietary fiber on carbohydrate metabolism enzyme activity within the intestinal microbiota.

RESULTS: Calves supplemented with dietary fiber exhibited a significant increase in the abundance of Bifidobacterium and Prevotella compared to the control group. These bacterial genera contributed to intestinal protection by modulating secondary bile acid metabolism and flavonoid metabolism pathways. CAZymes differential analysis revealed an increased abundance of carbohydrate metabolism enzymes in response to dietary fiber supplementation, with distinct microbial community compositions observed among different fiber treatments. Notably, at 56 days of age, calves fed PHP harbored intergeneric symbiotic clusters comprising Clostridium, Prevotella, and Bacteroides, suggesting a cooperative microbial network that may contribute to intestinal homeostasis.

DISCUSSION: The findings of this study highlight the beneficial effects of dietary fiber on calf intestinal microbiota, particularly in enhancing microbial diversity and enzymatic activity related to carbohydrate metabolism. The observed microbial symbiosis in PHP-fed calves suggests a potential role in maintaining intestinal homeostasis. These insights provide a theoretical foundation for optimizing dietary interventions to promote gut health in calves during the transition period. Further research is warranted to explore the mechanistic interactions between dietary fiber, gut microbiota, and host health outcomes.}, } @article {pmid40201435, year = {2025}, author = {Tang, J and Li, P and Xu, H and Han, J}, title = {Clinical application of metagenomic next-generation sequencing in rapid diagnosis and prognostic assessment of herpes simplex encephalitis.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1534513}, pmid = {40201435}, issn = {1664-302X}, abstract = {PURPOSE: Herpes simplex encephalitis (HSE) ranks among the most common causes of severe viral encephalitis. It leads to meningitis or encephalitis, with patients frequently encountering adverse outcomes. In this study, we utilized metagenomic next-generation sequencing (mNGS) to rapidly and accurately detect and identify the HSV pathogen directly from cerebrospinal fluid (CSF) samples, aiming to achieve a definitive diagnosis for encephalitis patients.

METHODS: From 2018 to 2023, we prospectively identified and enrolled 28 patients diagnosed with HSE at Hengshui People's Hospital. CSF samples were subjected to mNGS to facilitate the diagnosis and characterization of HSE in this cohort. We compiled the clinical characteristics, supplementary examinations, and outcomes of HSE patients, with prognosis assessed using the Glasgow Outcome Scale (GOS) scores at discharge, 1 month post-discharge, and 3 months thereafter.

RESULTS: In this cohort of 28 patients, 12 were females and 16 males, with a mean age of 41.82 ± 18.23. HSE manifested with a variety of clinical symptoms, the most prevalent being headaches (67.9%), fever exceeding 38°C (60.7%), and altered consciousness (60.7%). Seizures (42.9%), vomiting (35.7%), and speech deficits (35.7%) were frequently observed, with a minority of patients displaying personality changes (28.6%). CSF analysis revealed pleocytosis and a mild increase in protein levels. Magnetic resonance imaging (MRI) abnormalities (28.6%) were primarily confined to the frontal and temporal lobes as well as limbic regions, with no indications of cerebral hemorrhage. Half of the patients exhibited Electroencephalogram (EEG) changes suggestive of encephalitis. HSE was confirmed through mNGS analysis of CSF within 3 days of admission. All patients received empirical treatment with ganciclovir, with 46.4% undergoing hormonotherapy and 32.1% receiving immunoglobulin therapy. At the three-month follow-up, 32.1% had GOS scores <5.

CONCLUSION: HSE often presents with nonspecific signs of encephalitis, and it's not easy for traditional CNS examinations to confirm the diagnosis. mNGS serves as a cutting-edge diagnostic tool for the rapid and precise identification of HSE, facilitating timely clinical diagnosis and intervention to prevent the progression of the disease.}, } @article {pmid40201423, year = {2025}, author = {Boden, L and Bludau, D and Sieber, G and Deep, A and Baikova, D and David, GM and Hadžiomerović, U and Stach, TL and Boenigk, J}, title = {The impact of elevated temperature and salinity on microbial communities and food selectivity in heterotrophic nanoflagellates in the Boye River.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf049}, pmid = {40201423}, issn = {2730-6151}, abstract = {Microbial predator-prey interactions play a crucial role in aquatic food webs. Bacterivorous protists not only regulate the quantity and biomass of bacterial populations but also profoundly influence the structure of bacterial communities. Consequently, alterations in both the quantity and quality of protist bacterivory can influence the overall structure of aquatic food webs. While it is well-documented that changes in environmental conditions or the occurrence of abiotic stressors can lead to shifts in microbial community compositions, the impact of such disturbances on food selection remains unknown. Here, we investigated the effects of elevated temperature and salinization on food selectivity of heterotrophic nanoflagellates by monitoring the uptake of preselected target bacteria via catalyzed reporter deposition fluorescence in situ hybridization and fluorescence microscopy. Our results indicate that salinization, but not increased temperature, significantly increased the flagellates' selection against Microbacterium lacusdiani (Actinomycetota). However, the effect of the reduced grazing pressure was counterbalanced by the negative effect of increased salinity on the growth of Actinomycetota. Our results suggest that the effect of stressors on the feeding behavior of protistan predators may strongly affect the composition of their prey community, when bacterial taxa are concerned that are less sensitive to the particular stressor.}, } @article {pmid40201367, year = {2025}, author = {Wen, Y and Zhang, W and Li, Y and Liao, X and Xu, J and Zhen, R and Qin, P}, title = {Epidemiological characteristics of human psittacosis in Guangzhou, China, January 2021 to June 2024.}, journal = {Frontiers in public health}, volume = {13}, number = {}, pages = {1526990}, pmid = {40201367}, issn = {2296-2565}, mesh = {Humans ; China/epidemiology ; Male ; Middle Aged ; Adult ; *Psittacosis/epidemiology ; Female ; Aged ; Animals ; Seasons ; Zoonoses/epidemiology ; Adolescent ; Young Adult ; Prevalence ; Child ; }, abstract = {BACKGROUND: Psittacosis is a global and underappreciated zoonosis, with increasing reported cases in many countries. There have been several outbreaks and even deaths of psittacosis reported in China. Understanding its epidemiological characteristics and dimensions is crucial for formulating precise prevention and control strategies. This study aimed to analyze the epidemiological characteristics of human psittacosis in Guangzhou, China.

METHODS: The demographic characteristics, clinical manifestations, temporal patterns, geographic distribution and potential exposures of psittacosis in Guangzhou were analyzed based on the surveillance data and epidemiological investigation conducted between January 2021 and June 2024. Seasonal and trend decomposition using LOESS was applied to decompose the number of psittacosis cases into trend, seasonal and remainder component.

RESULTS: A total of 148 cases were reported, with a significant increase in the number of psittacosis cases over the study period. Most of cases were sporadic and detected by metagenomic next-generation sequencing (mNGS). Psittacosis was predominant males aged 40-79 years. Fever and pneumonia were the most commonly observed clinical manifestations. A seasonal trend was observed in the number of psittacosis cases with a high prevalence of cases in December and March. A total of 108 local cases (87%) occurred in rural regions. Among local cases, 67.7% reported a history of contact with birds or poultry, and 17.7% had been exposed to a related environment. The suspected source of infection differed between urban and rural areas, with parrots being the primary source in urban areas and poultry in rural areas.

CONCLUSION: Increasing clinicians' awareness, enhancing epidemiological surveillance, paying close attention to the epidemic in rural areas, and implementing measures against avian influenza, will be conducive to preventing and controlling psittacosis.}, } @article {pmid40200351, year = {2025}, author = {Zhang, Z and Huang, Z and Fang, X and Bai, G and Li, W and Zhang, W and Zhang, C}, title = {Diagnosis and surgical treatment of chronic destructive septic hip arthritis.}, journal = {Arthroplasty (London, England)}, volume = {7}, number = {1}, pages = {19}, pmid = {40200351}, issn = {2524-7948}, support = {2023Y9092//Joint Funds for the Innovation of Science and Technology, Fujian province/ ; 2022Y4003//University-Industry Research Cooperation Project of Science and Technology, Fujian province/ ; YXRQN-ZCF2023//The First Affiliated Hospital of Fujian Medical University Excellent Talent Program/ ; YJCRC-B-ZWM2024//The First Affiliated Hospital of Fujian Medical University Excellent Talent Program/ ; }, abstract = {Septic hip arthritis (SHA) is a relatively rare but hazardous disease. Much controversy exists regarding the definition, diagnosis and treatment of chronic destructive SHAs. This review aims to provide an overview of the diagnostic and therapeutic approaches for chronic, destructive SHA and suggest possible research directions for this disease's future diagnosis and treatment. There is no unified naming or classification standard for SHAs. Chronic destructive SHA still requires a comprehensive diagnosis combining history, signs, bacterial culture, histopathological examination, inflammation and other indicators, of which metagenomic next-generation sequencing is a promising diagnostic tool. Previous treatment options for this disease include debridement, debridement + Girdlestone femoral head and neck resection, and debridement + Girdlestone femoral head and neck resection + two-stage arthroplasty. Among them, one-stage spacer implantation + two-stage arthroplasty is the current standard surgical option with a high success rate and low reinfection rate, while one-stage arthroplasty is a new treatment option proposed in recent years with unique advantages but limitations in terms of surgical indications. In the future, more high-quality studies are needed to provide the latest evidence to support clinical decision-making.}, } @article {pmid40200155, year = {2025}, author = {Zhou, Z and Hu, X and Wang, J and Wang, N}, title = {Invasive cerebral aspergillosis in a pregnant woman: a rare case of intracranial giant granuloma.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {478}, pmid = {40200155}, issn = {1471-2334}, mesh = {Humans ; Female ; Pregnancy ; Adult ; Antifungal Agents/therapeutic use ; *Neuroaspergillosis/diagnosis/drug therapy/pathology/surgery/microbiology ; *Granuloma/microbiology/pathology/diagnosis/surgery ; *Pregnancy Complications, Infectious/diagnosis/microbiology/drug therapy/pathology ; High-Throughput Nucleotide Sequencing ; Polymerase Chain Reaction ; Brain/pathology/diagnostic imaging/microbiology ; }, abstract = {BACKGROUND: Invasive Cerebral Aspergillosis (ICA) is a rare fungal infection affecting the brain, primarily seen in individuals with compromised immune systems. Despite various treatment options, substantial cerebral granulomas caused by ICA still result in high mortality and recurrence rates.

CASE PRESENTATION: We report a rare instance of ICA in a 30-year-old pregnant woman. The infection initiated in the nasal cavity and progressed to form a large intracranial granuloma, leading to brain herniation. Diagnosis was confirmed through histopathology, Polymerase Chain Reaction (PCR), and metagenomic next-generation sequencing (mNGS) following decompressive craniotomy and sinus window drainage surgery. Prompt administration of antifungal medication resulted in a favorable prognosis.

CONCLUSION: This case highlights the critical roles of mNGS and PCR in the early diagnosis of ICA, as well as the pivotal importance of surgical interventions and prompt initiation of antifungal therapy in enhancing patient outcomes.}, } @article {pmid40199830, year = {2025}, author = {Singh, P and Haldhar, P and Das, T and Chaubey, G and Gupta, MK and Kumar, B}, title = {Thermal Stress and Its Effects on the Gut Microbiome of Parthenium Beetles.}, journal = {Archives of insect biochemistry and physiology}, volume = {118}, number = {4}, pages = {e70058}, doi = {10.1002/arch.70058}, pmid = {40199830}, issn = {1520-6327}, support = {//The authors received no specific funding for this work./ ; }, mesh = {Animals ; *Coleoptera/microbiology/physiology ; *Gastrointestinal Microbiome ; *Stress, Physiological ; Bacteria/classification/isolation & purification/genetics ; Hot Temperature ; RNA, Ribosomal, 16S/analysis ; }, abstract = {The gut microbiota plays a vital role in nutrient and energy utilization, as well as in the host's ability to adapt its immune system to environmental changes. As a biological control agent for the invasive Parthenium weed, the Parthenium beetle Zygogramma bicolorata (Z. bicolorata) Pallister is often exposed to fluctuating temperatures, which may induce stress in its natural habitat. This study utilized 16S amplicon sequencing to explore the impact of temperature stress on the gut microbiome of Z. bicolorata under cold (15°C), control (27°C), and hot (35°C) conditions. A total of 11 bacterial phyla and 149 genera were identified, with Firmicutes, Proteobacteria, and Cyanobacteria being the most abundant. Temperature treatments significantly influenced the diversity of the gut microbiota, as evidenced by alpha diversity measures. Principal coordinate analysis further revealed substantial variations in microbiome composition across the different temperature conditions. Additionally, PICRUSt2 analysis suggested that the gut microbiota is linked to metagenomic functions related to amino acid and carbohydrate transport, inorganic ion metabolism, and cellular processes. Our findings suggest that thermal stress alters the gut microbiome of Parthenium beetles, offering new insights into how these beetles may have ecologically adapted to temperature fluctuations, while also highlighting the potential role of gut microbes in maintaining beetle health under environmental stress.}, } @article {pmid40199391, year = {2025}, author = {Tan, Y and Li, L and Zhao, Z and Li, Y and Li, T and Li, Y and Sheng, X and Shen, L and Xu, Z and Song, S and Zhang, P}, title = {Simultaneous pollutant removal and organic matter sequestration by coral sand-pyrite-based electroactive constructed wetlands.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132498}, doi = {10.1016/j.biortech.2025.132498}, pmid = {40199391}, issn = {1873-2976}, abstract = {The development of integrated solutions for sewage treatment and soil restoration in remote regions remains a challenge. This study innovatively designed coral sand-pyrite-based electroactive constructed wetlands (E-CWs) to synchronize wastewater purification and organic matter (OM) enrichment. Metagenomic analyses revealed that the addition of pyrite increased the abundance of iron redox-related genes, whereas coral sand salinity promoted the enrichment of functional bacteria for OM decomposition. Furthermore, the combined substrate comprising coral sand and pyrite facilitated the adsorption and sequestration of OM, while providing a stable environment for microorganisms. This achieved dual objectives: efficient chemical oxygen demand removal (90.6 ± 2.4 %) from sewage and substantial OM sequestration in substrates (total organic carbon: 2.9-4.8 %). This study achieved sewage treatment through the combination of coral sand and pyrite as substrates of E-CWs and enhanced the OM content of the substrates, contributing to the improvement of local soil infertility.}, } @article {pmid40198556, year = {2025}, author = {Holden, S and Kim, SH and Chen, W and Li, X and Bakkeren, G and Brar, GS}, title = {Identification of Rust Fungi Using High-Throughput Sequencing Data from Environmental Samples.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2898}, number = {}, pages = {151-188}, pmid = {40198556}, issn = {1940-6029}, mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Basidiomycota/genetics/isolation & purification/classification ; *Plant Diseases/microbiology ; *Fungi/genetics ; DNA, Fungal/genetics ; }, abstract = {Working with any plant-associated microbe comes with the inherent challenge that no environment is sterile, and a plant's metabiome is teeming with life. When collecting field samples outside of the laboratory, this issue is compounded further. Rust fungi, being obligate plant pathogens, are challenging to maintain, and strict protocols must be adhered to in the laboratory to prevent cross-contamination. In this era of big data and easy access to next generation sequencing (NGS), it is increasingly common for scientists to work with large sequencing datasets, which must first be evaluated for quality and filtered for potentially nontarget reads. Sequencing data files from environmental samples often contain genetic material from organisms not targeted by the experimental design. This situation can lead to issues if researchers assume the presence of only their intended subjects. Additionally, the origin of some samples may be inherently unknown, making the main objective of certain sequencing experiments to identify all organisms present, not just the expected ones.This chapter details common in silico approaches for identifying and classifying samples from sequencing data, drawing on experiences with cereal rust samples collected in the field. While the concepts are broadly applicable, they may require some tailoring for your species of interest. The chapter does not cover population-genomics level approaches to sample classification; instead, it describes essential quality control steps that researchers should implement before conducting downstream analyses to ensure that their data is appropriate for the intended tests.}, } @article {pmid40198136, year = {2025}, author = {Fishman, JA and Denner, J and Scobie, L}, title = {International Xenotransplantation Association (IXA) Position Paper on Infectious Disease Considerations in Xenotransplantation.}, journal = {Transplantation}, volume = {}, number = {}, pages = {}, pmid = {40198136}, issn = {1534-6080}, abstract = {Clinical xenotransplantation has the potential to address shortages of human organs for patients with end-stage organ failure. Advances in genetic engineering, immunosuppressive regimens, and infectious disease diagnostics have improved prospects for clinical xenotransplantation. Management of the infectious risks posed by clinical xenotransplantation requires biosecure breeding and validated methods for microbiological surveillance of source animals and recipients. Novel infection control protocols may complement biosafety requirements. Infectious risks in xenotransplantation include both known human pathogens common to immunosuppressed organ recipients and from porcine organisms or xenozoonoses for which the clinical manifestations are less well defined and for which microbial assays and therapies are more limited. Some pig-specific organisms do not infect human cells but have systemic manifestations when active within the xenograft. The human risk posed by porcine endogenous retroviruses (PERV) is uncertain. There are no documented transmissions of PERV in humans and swine are available with inactivated genomic PERV loci. Metagenomic sequencing will complement more traditional diagnostic tools in the detection of any unknown pathogens in xenotransplantation recipients. Such data are required for the development of protocols for donor and recipient microbiological surveillance, infection control, and antimicrobial therapies that will enhance the safety of clinical xenotransplantation.}, } @article {pmid40197807, year = {2025}, author = {Fishman, JA and Denner, J and Scobie, L}, title = {International Xenotransplantation Association (IXA) Position Paper on Infectious Disease Considerations in Xenotransplantation.}, journal = {Xenotransplantation}, volume = {32}, number = {2}, pages = {e70001}, doi = {10.1111/xen.70001}, pmid = {40197807}, issn = {1399-3089}, mesh = {*Transplantation, Heterologous/adverse effects/methods ; Animals ; Humans ; Swine ; *Heterografts/microbiology/virology ; Endogenous Retroviruses ; *Communicable Diseases/transmission ; }, abstract = {Clinical xenotransplantation has the potential to address shortages of human organs for patients with end-stage organ failure. Advances in genetic engineering, immunosuppressive regimens, and infectious disease diagnostics have improved prospects for clinical xenotransplantation. Management of the infectious risks posed by clinical xenotransplantation requires biosecure breeding and validated methods for microbiological surveillance of source animals and recipients. Novel infection control protocols may complement biosafety requirements. Infectious risks in xenotransplantation include both known human pathogens common to immunosuppressed organ recipients and from porcine organisms or xenozoonoses for which the clinical manifestations are less well defined and for which microbial assays and therapies are more limited. Some pig-specific organisms do not infect human cells but have systemic manifestations when active within the xenograft. The human risk posed by porcine endogenous retroviruses (PERV) is uncertain. There are no documented transmissions of PERV in humans and swine are available with inactivated genomic PERV loci. Metagenomic sequencing will complement more traditional diagnostic tools in the detection of any unknown pathogens in xenotransplantation recipients. Such data are required for the development of protocols for donor and recipient microbiological surveillance, infection control, and antimicrobial therapies that will enhance the safety of clinical xenotransplantation.}, } @article {pmid40197788, year = {2025}, author = {Arenas-Montes, J and Alcala-Diaz, JF and Garcia-Fernandez, H and Gutierrez-Mariscal, FM and Lopez-Moreno, A and Luque-Cordoba, D and Arenas-de Larriva, AP and Torres-Peña, JD and Luque, RM and Prodam, F and Priego-Capote, F and Delgado-Lista, J and Lopez-Miranda, J and Camargo, A}, title = {A microbiota pattern associated with cardiovascular events in secondary prevention: the CORDIOPREV study.}, journal = {European heart journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/eurheartj/ehaf181}, pmid = {40197788}, issn = {1522-9645}, support = {//Fundacion Patrimonio Comunal Olivarero/ ; //CEAS/ ; //Centro de Excelencia en Investigacion sobre Aceite de Oliva/ ; CVI-7450//Junta de Andalucia/ ; //Diputaciones de Jaen y Córdoba/ ; //Ministerio de Medio Ambiente, Medio Rural y Marino/ ; //Spanish Government/ ; AGL2012/39615//Ministerio de Ciencia e Innovación, Spain/ ; //MCIN/AEI/10.13039/501100011033/ ; CP14/00114//Instituto de Salud Carlos III/ ; PI-0055-2021//Consejería de Salud y Familias, Junta de Andalucía/ ; //Consejeria de Innovación, Ciencia y Empresa, Proyectos de Investigación de Excelencia/ ; //European Union/ ; CP14/00114//Programa Miguel-Servet/ ; //Servicio Andaluz de Salud-Junta de Andalucia/ ; C1-0001-2022//Nicolas Monardes Programme Contract/ ; }, abstract = {BACKGROUND AND AIMS: Preventing new cardiovascular events in patients with established cardiovascular disease (CVD) is a daunting task for clinicians. Intestinal microbiota may help identify patients at risk, thus improving the strategies of secondary prevention. The aim of this study was to evaluate the baseline differences between the gut microbiota from coronary heart disease (CHD) patients suffering new major adverse cardiovascular events (MACEs) in the following 7 years, compared with CHD patients who did not undergo new MACE in this period, and to build a score associated with the risk of suffering new MACE.

METHODS: Within the framework of the CORDIOPREV study, a clinical trial that involved 1002 patients with CHD, intestinal microbiota was examined in patients with available faecal samples (n = 679, 132 MACE), through 16S metagenomics on the Illumina MiSeq and Quiime2 software. Lipopolysaccharide (LPS) was measured using limulus amoebocyte lysate test.

RESULTS: Random survival forest identified 10 bacterial taxa with a higher predictive power for MACE incidence. Receiver operating characteristic curves yielded an area under the curve of 65.2% (59.1%-71.3%) in the training set and 68.6% (59.3%-77.9%) in the validation set. The intestinal microbiota risk score was associated with a MACE incidence hazard ratio of 2.01 (95% confidence interval 1.37-3.22). Lipopolysaccharide analysis showed a greater LPS post-prandial fold change in the MACE group (P = .005).

CONCLUSIONS: These results reinforce the relationship between intestinal microbiota and CVD and suggest that a microbiota profile is associated with MACE in CHD patients, in addition to higher endotoxaemia.}, } @article {pmid40197742, year = {2025}, author = {He, C and Gonsior, M and Liu, J and Jiao, N and Chen, F}, title = {Genome-streamlined SAR202 bacteria are widely present and active in the euphotic ocean.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf049}, pmid = {40197742}, issn = {1751-7370}, abstract = {SAR202 bacteria are a diverse group of bacteria in the ocean. The SAR202 lineages dominate the bacterial community and evolve specialized metabolisms for oxidizing recalcitrant organic compounds in the dark ocean. SAR202 bacteria are also present in the euphotic oceans; however, their ecological roles and metabolic potential remain poorly understood. In this study, we collected 392 non-redundant metagenome-assembled genomes from different oceans, with 18% of these SAR202 genomes characterized by small genome sizes (< 2 Mbp), low GC content (< 40%), and high gene density. The 70 genome-streamlined SAR202 bacteria constitute more than an average of 90% of SAR202 in the euphotic zone and exhibit streamlined metabolic features compared to the dark ocean SAR202. Genome-streamlined SAR202 are distributed in many major SAR202 lineages (i.e. I, II, III, and VI). Phylogenomic analysis shows that the genome-streamlined SAR202 clades diverged from the non-genome-streamlined SAR202 lineages and evolved independently within the same clades. Certain genes are enriched in genome-streamlined SAR202, such as proteorhodopsin genes and the coding genes of major facilitator superfamily transporters, nucleoside transporters, and deoxyribodipyrimidine photo-lyase, indicating their adaptation to sunlit oligotrophic water. A detailed comparison between genome-streamlined SAR202 and non-genome-streamlined SAR202 was made to illustrate their distinct niche distribution and metabolic buildup. In addition, the metatranscriptomic analysis supports that genome-streamlined SAR202 bacteria are active in the upper ocean. This study represents a systematic study of streamlined SAR202 bacteria that occupy the euphotic ocean and provides a comprehensive view of the ecological roles of SAR202 bacteria in the ocean.}, } @article {pmid40197145, year = {2025}, author = {Feng, KH and Qi, YH and Ye, ZX and Li, T and Jiao, GY and Zhang, CX and Chen, JP and Lu, G and Li, JM}, title = {Diversity and evolution analysis of RNA viruses in three wheat aphid species.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {353}, doi = {10.1186/s12864-025-11512-1}, pmid = {40197145}, issn = {1471-2164}, support = {2024YFD1400400//National Key Research and Development Program of China/ ; LY24C140001//Natural Science Foundation of Zhejiang Province/ ; 2024J016//Ningbo Natural Science Foundation/ ; 2023S029//Ningbo Commonweal Project/ ; }, mesh = {*Aphids/virology/genetics ; Animals ; }, abstract = {BACKGROUND: Although advances in metagenomics, viral diversity and non-retroviral endogenous viral elements (EVEs) in wheat aphids remain underexplored. By analyzing 470 publicly available datasets and one laboratory-generated transcriptome, the RNA virome and EVEs in the genomes of Sitobion avenae, Schizaphis graminum, and Rhopalosiphum padi were systematically investigated.

RESULTS: We identified 43 RNA viruses, including 12 novel and 31 known RNA viruses. These viruses were widely distributed and abundant in different geographic populations of three wheat aphid species. +ssRNA viruses were the dominant type of aphid viruses. Besides, 90 EVEs were discovered in the genomes of three aphid species. In addition, the EVEs exhibit potential domestication and novel functional roles within aphid genomes.

CONCLUSIONS: This study expands the understanding of RNA virus diversity in aphids and provides valuable insights into the potential functions of EVEs in virus-host coevolution.}, } @article {pmid40197113, year = {2025}, author = {Karabekmez, ME}, title = {Harnessing Human Holobiome and Meta-Multi-Omics Analyses for Medical Applications.}, journal = {Omics : a journal of integrative biology}, volume = {}, number = {}, pages = {}, doi = {10.1089/omi.2025.0024}, pmid = {40197113}, issn = {1557-8100}, abstract = {Next-generation sequencing technology has revolutionized all fields of living systems, and its applications almost reinvented some research areas including metagenomics. The microbiotas in our body, including those of the oral, nasal, ocular, alveolar, skin regions, and particularly gut microbiota, have close linkages with our health status. Maturation of experimental techniques for metagenomics has been followed by other related omics platforms, for example, metatranscriptomics, metaproteomics, and all possible metacounterparts of multiomics studies. Now, we are on the eve of a meta-multi-omics era for the analysis of human holobiome in medical research. This era will help buttress the current efforts for systems medicine by illuminating the relationships between human holobiome and health or all human diseases including not only cancers but also infectious diseases, autoimmune diseases, obesity, aging, genetic disorders, and psychiatric conditions. Equally important, meta-multi-omics era is also poised to inform the determinants of human health and, by extension, help build individually tailored precision medicine interventions.}, } @article {pmid40197060, year = {2025}, author = {Giacomini, JJ and Torres-Morales, J and Dewhirst, FE and Borisy, GG and Mark Welch, JL}, title = {Spatial ecology of the Neisseriaceae family in the human oral cavity.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0327524}, doi = {10.1128/spectrum.03275-24}, pmid = {40197060}, issn = {2165-0497}, abstract = {The human oral microbiome is a diverse ecosystem in which bacterial species have evolved to occupy specific niches within the oral cavity. The Neisseriaceae family, which includes human oral species in the genera Neisseria, Eikenella, Kingella, and Simonsiella, plays a significant role in both commensal and pathogenic relationships. In this study, we investigate the distribution and functional adaptations of Neisseriaceae species across oral habitats, focusing on their site tropisms and ecological roles. We employed a metapangenomic approach in which a curated set of reference genomes representing Neisseriaceae diversity was used for competitive mapping of metagenomic reads. Our analysis revealed distinct habitat preferences among Neisseriaceae species, with Kingella oralis, Neisseria elongata, and Neisseria mucosa primarily found in dental plaque; Neisseria subflava on the tongue dorsum; and Neisseria cinerea in the keratinized gingiva. Functional enrichment analyses identified genes and pathways underpinning habitat-specific adaptations. Plaque specialists showed metabolic versatility, with adaptations in nitrogen metabolism, including nitrate reduction and denitrification, lysine degradation, and galactose metabolism. Tongue dorsum specialists exhibited adaptations including enhanced capabilities for amino acid biosynthesis, short-chain fatty acid and glycerol transport, as well as lipopolysaccharide glycosylation, which may aid in resisting antimicrobial peptides and maintaining membrane integrity. These findings provide insights into the ecological roles and adaptive strategies of Neisseriaceae species within the human oral microbiome and establish a foundation for exploring functional specialization and microbial interactions in these niches.IMPORTANCEUnraveling the distribution and functional adaptations of Neisseriaceae within the human oral microbiome is essential for understanding the roles of these abundant and prevalent commensals in both health and disease. Through a metapangenomic approach, we uncovered distinct habitat preferences of various Neisseriaceae taxa across the oral cavity and identified key genetic traits that may drive their habitat specialization and role in host-microbe interactions. These insights enhance our understanding of the microbial dynamics that shape oral microbial ecology, offering potential pathways for advancing oral health research.}, } @article {pmid40197053, year = {2025}, author = {Langsiri, N and Meyer, W and Irinyi, L and Worasilchai, N and Pombubpa, N and Wongsurawat, T and Jenjaroenpun, P and Luangsa-Ard, JJ and Chindamporn, A}, title = {Optimizing fungal DNA extraction and purification for Oxford Nanopore untargeted shotgun metagenomic sequencing from simulated hemoculture specimens.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0116624}, doi = {10.1128/msystems.01166-24}, pmid = {40197053}, issn = {2379-5077}, abstract = {UNLABELLED: Long-read metagenomics provides a promising alternative approach to fungal identification, circumventing methodological biases, associated with DNA amplification, which is a prerequisite for DNA barcoding/metabarcoding based on the primary fungal DNA barcode (Internal Transcribed Spacer (ITS) region). However, DNA extraction for long-read sequencing-based fungal identification poses a significant challenge, as obtaining long and intact fungal DNA is imperative. Comparing different lysis methods showed that chemical lysis with CTAB/SDS generated DNA from pure fungal cultures with high yields (ranging from 11.20 ± 0.17 µg to 22.99 ± 2.22 µg depending on the species) while preserving integrity. Evaluating the efficacy of human DNA depletion protocols demonstrated an 88.73% reduction in human reads and a 99.53% increase in fungal reads compared to the untreated yeast-spiked human blood control. Evaluation of the developed DNA extraction protocol on simulated clinical hemocultures revealed that the obtained DNA sequences exceed 10 kb in length, enabling a highly efficient sequencing run with over 80% active pores. The quality of the DNA, as indicated by the 260/280 and 260/230 ratios obtained from NanoDrop spectrophotometer readings, exceeded 1.8 and 2.0, respectively. This demonstrated the great potential of the herein optimized protocol to extract high-quality fungal DNA from clinical specimens enabling long-read metagenomics sequencing.

IMPORTANCE: A novel streamlined DNA extraction protocol was developed to efficiently isolate high molecular weight fungal DNA from hemoculture samples, which is crucial for long-read sequencing applications. By eliminating the need for labor-intensive and shear-force-inducing steps, such as liquid nitrogen grinding or bead beating, the protocol is more user-friendly and better suited for clinical laboratory settings. The automation of cleanup and extraction steps further shortens the overall turnaround time to under 6 hours. Although not specifically designed for ultra-long DNA extraction, this protocol effectively supports fungal identification through Oxford Nanopore Technology (ONT) sequencing. It yields high molecular weight DNA, resulting in longer sequence fragments that improve the number of fungal reads over human reads. Future improvements, including adaptive sampling technology, could further simplify the process by reducing the need for human DNA depletion, paving the way for more automated, bioinformatics-driven workflows.}, } @article {pmid40197051, year = {2025}, author = {Shamash, M and Sinha, A and Maurice, CF}, title = {Improving gut virome comparisons using predicted phage host information.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0136424}, doi = {10.1128/msystems.01364-24}, pmid = {40197051}, issn = {2379-5077}, abstract = {UNLABELLED: The human gut virome is predominantly made up of bacteriophages (phages), viruses that infect bacteria. Metagenomic studies have revealed that phages in the gut are highly individual specific and dynamic. These features make it challenging to perform meaningful cross-study comparisons. While several taxonomy frameworks exist to group phages and improve these comparisons, these strategies provide little insight into the potential effects phages have on their bacterial hosts. Here, we propose the use of predicted phage host families (PHFs) as a functionally relevant, qualitative unit of phage classification to improve these cross-study analyses. We first show that bioinformatic predictions of phage hosts are accurate at the host family level by measuring their concordance to Hi-C sequencing-based predictions in human and mouse fecal samples. Next, using phage host family predictions, we determined that PHFs reduce intra- and interindividual ecological distances compared to viral contigs in a previously published cohort of 10 healthy individuals, while simultaneously improving longitudinal virome stability. Lastly, by reanalyzing a previously published metagenomics data set with >1,000 samples, we determined that PHFs are prevalent across individuals and can aid in the detection of inflammatory bowel disease-specific virome signatures. Overall, our analyses support the use of predicted phage hosts in reducing between-sample distances and providing a biologically relevant framework for making between-sample virome comparisons.

IMPORTANCE: The human gut virome consists mainly of bacteriophages (phages), which infect bacteria and show high individual specificity and variability, complicating cross-study comparisons. Furthermore, existing taxonomic frameworks offer limited insight into their interactions with bacterial hosts. In this study, we propose using predicted phage host families (PHFs) as a higher-level classification unit to enhance functional cross-study comparisons. We demonstrate that bioinformatic predictions of phage hosts align with Hi-C sequencing results at the host family level in human and mouse fecal samples. We further show that PHFs reduce ecological distances and improve virome stability over time. Additionally, reanalysis of a large metagenomics data set revealed that PHFs are widespread and can help identify disease-specific virome patterns, such as those linked to inflammatory bowel disease.}, } @article {pmid40196042, year = {2025}, author = {Wang, H and Zhu, W and Lei, J and Liu, Z and Cai, Y and Wang, S and Li, A}, title = {Gut microbiome differences and disease risk in colorectal cancer relatives and healthy individuals.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1573216}, pmid = {40196042}, issn = {2235-2988}, mesh = {Humans ; Feces/microbiology ; Male ; Female ; Middle Aged ; Aged ; *Bacteria/classification/genetics/isolation & purification ; Adult ; Family ; }, abstract = {Given the heightened focus on high-risk populations, this study aimed to provide insights into early susceptibility and preventive strategies for colorectal cancer (CRC) by focusing on high-risk populations. In this research, fecal samples from 1,647 individuals across three discovery cohorts and nine external validation cohorts were sequenced using whole-genome metagenomic sequencing. A prediction model based on random forest was constructed using the nine external cohorts and independently validated with the three discovery cohorts. A disease probability (POD) model based on microbial biomarkers was developed to assess CRC risk. We found that the gut microbiome composition of CRC relatives differed from that of controls, with enrichment of species such as Fusobacterium and Bacteroides and a reduction in beneficial genera like Coprococcus and Roseburia. Additionally, dietary red meat intake emerged as a risk factor. The POD model indicated an elevated risk of CRC in unaffected relatives. The findings suggest that the POD for CRC may be increased in unaffected relatives or individuals living in shared environments, although this difference did not reach statistical significance. Our study introduces a novel framework for assessing the risk of colorectal cancer in ostensibly healthy individuals.}, } @article {pmid40196035, year = {2025}, author = {Decadt, H and Díaz-Muñoz, C and Vermote, L and Pradal, I and De Vuyst, L and Weckx, S}, title = {Long-read metagenomics gives a more accurate insight into the microbiota of long-ripened gouda cheeses.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1543079}, pmid = {40196035}, issn = {1664-302X}, abstract = {Metagenomic studies of the Gouda cheese microbiota and starter cultures are scarce. During the present study, short-read metagenomic sequencing (Illumina) was applied on 89 Gouda cheese and processed milk samples, which have been investigated before concerning their metabolite and taxonomic composition, the latter applying amplicon-based, high-throughput sequencing (HTS) of the full-length 16S rRNA gene. Selected samples were additionally investigated using long-read metagenomic sequencing (Oxford Nanopore Technologies, ONT). Whereas the species identified by amplicon-based HTS and metagenomic sequencing were identical, the relative abundances of the major species differed significantly. Lactococcus cremoris was more abundant in the metagenomics-based taxonomic analysis compared to the amplicon-based one, whereas the opposite was true for the non-starter lactic acid bacteria (NSLAB). This discrepancy was related to a higher fragmentation of the lactococcal DNA compared with the DNA of other species when applying ONT. Possibly, a higher fragmentation was linked with a higher percentage of dead or metabolically inactive cells, suggesting that full-length 16S rRNA gene amplicon-based HTS might give a more accurate view on active cells. Further, fungi were not abundantly present in the Gouda cheeses examined, whereas about 2% of the metagenomic sequence reads was related to phages, with higher relative abundances in the cheese rinds and long-ripened cheeses. Intraspecies differences found by short-read metagenomic sequencing were in agreement with the amplicon sequence variants obtained previously, confirming the ability of full-length 16S rRNA gene amplicon-based HTS to reach a taxonomic assignment below species level. Metagenome-assembled genomes (MAGs) were retrieved for 15 species, among which the starter cultures Lc. cremoris and Lactococcus lactis and the NSLAB Lacticaseibacillus paracasei, Loigolactobacillus rennini, and Tetragenococcus halophilus, although obtaining MAGs from Lc. cremoris and Lc. lactis was more challenging because of a high intraspecies diversity and high similarity between these species. Long-read metagenomic sequencing could not improve the retrieval of lactococcal MAGs, but, overall, MAGs obtained by long-read metagenomic sequencing solely were superior compared with those obtained by short-read metagenomic sequencing solely, reaching a high-quality draft status of the genomes.}, } @article {pmid40195635, year = {2025}, author = {Lv, H and Zhou, J and Guo, Y and Liao, S and Chen, H and Luo, F and Xu, J and Zhang, Z and Zhang, Z}, title = {Uniportal endoscopic decompression and debridement for infectious diseases of spine with neurological deficits: a retrospective study in China.}, journal = {Asian spine journal}, volume = {}, number = {}, pages = {}, doi = {10.31616/asj.2025.0020}, pmid = {40195635}, issn = {1976-1902}, abstract = {STUDY DESIGN: A retrospective study.

PURPOSE: To evaluate the clinical efficacy of uniportal endoscopic decompression and debridement (UEDD) in treating infectious diseases of the spine (IDS) with neurological deficits.

OVERVIEW OF LITERATURE: IDS patients with neurological deficits often require urgent surgical decompression. However, the efficacy of UEDD in this complex patient population is not well-characterized.

METHODS: This retrospective study analyzed 32 consecutive IDS patients who underwent UEDD surgery. Clinical features, laboratory data (erythrocyte sedimentation rate and C-reactive protein), and treatment outcomes were analyzed.

RESULTS: Definite microorganisms were identified in 27 patients (84.3%), with 24 (88.9%) meeting cure criteria. The cure rate was significantly higher in the detected pathogen group compared to the undetected pathogen group (88.9% vs. 80%; χ²=19.36, p<0.0001). Metagenomic next generation sequencing (mNGS) provided faster diagnosis (41.72±6.81 hours) compared to tissue culture (95.74±35.47 hours, p<0.05). The predominant causative pathogen was Mycobacterium tuberculosis, followed by Staphylococcus aureus. Significant improvements were observed in Visual Analog Scale pain scores, from a mean of 7.9 preoperatively to 1.06 at 1 year postoperatively. The Oswestry Disability Index revealed a similar trend, showing significant improvement (p<0.05).

CONCLUSIONS: UEDD is a viable alternative to traditional open surgery for managing IDS in high-risk patients. UEDD offers a dual therapeutic-diagnostic advantage during the initial admission phase, enabling simultaneous debridement, neurological decompression, and targeted biopsy in a single intervention. Compared with traditional tissue culture, mNGS enables rapid microbiological diagnosis and extensive pathogen coverage.}, } @article {pmid40195460, year = {2025}, author = {Bhagat, NR and Bharti, VK and Shukla, G and Rishi, P and Chaurasia, OP}, title = {Gut bacteriome dynamics in high altitude-adapted chicken lines: a key to future poultry therapeutics.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {11910}, pmid = {40195460}, issn = {2045-2322}, mesh = {Animals ; *Chickens/microbiology ; *Gastrointestinal Microbiome ; *Altitude ; Metagenomics/methods ; *Bacteria/genetics/classification ; *Adaptation, Physiological ; Metagenome ; }, abstract = {High-altitude-adapted chickens harbor a unique gut bacteriome essential for their survival under extremely cold and hypoxic environment, however, little is known about their population and functional dynamics, limiting their application in poultry production. Hence, this study employed amplicon-based metagenomics to examine the gut bacterial diversity and their functional profile in two high-altitude-adapted chicken lines, e.g. LEHBRO-1 and LEHBRO-3. The results revealed significant variations in taxonomic abundance at the phylum level, with Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria predominating in LEHBRO-1, whereas Firmicutes, Proteobacteria, Bacteroidetes, Planctomycetes, and Actinobacteria predominated in LEHBRO-3. Genus-level diversity and Linear Discriminant Analysis Effect Size (LEfSe) biomarker analysis also substantiated the differences in the gut bacterial communities between the two chicken lines. Furthermore, functional profiling revealed enrichment of carbohydrate, nucleotide, lipid, amino acid, fatty acid, energy, and glycan metabolic pathways in the gut bacteriomes of these high-altitude chicken lines. The Statistical Analysis of Metagenomic Profiles (STAMP) for metabolic profiling identified a significant difference in purine and protein metabolism between these two chicken lines. These findings indicate the unique gut bacteriome and their functional diversity in high-altitude-adapted chickens, which would provide a foundation for future research on gut therapeutics to improve chicken health and productivity in high-altitude areas.}, } @article {pmid40195156, year = {2025}, author = {Sefrji, FO and Abulfaraj, AA and Alshehrei, FM and Al-Andal, A and Alnahari, AA and Tashkandi, M and Baz, L and Barqawi, AA and Almutrafy, AM and Alshareef, SA and Alkhatib, SN and Abuauf, HW and Jalal, RS and Aloufi, AS}, title = {Comprehensive analysis of orthologous genes reveals functional dynamics and energy metabolism in the rhizospheric microbiome of Moringa oleifera.}, journal = {Functional & integrative genomics}, volume = {25}, number = {1}, pages = {82}, pmid = {40195156}, issn = {1438-7948}, mesh = {*Moringa oleifera/microbiology/genetics/metabolism ; *Rhizosphere ; *Microbiota/genetics ; *Energy Metabolism/genetics ; Soil Microbiology ; Bacteria/genetics/classification ; Adenosine Triphosphate/metabolism ; Metagenome ; }, abstract = {Moringa oleifera, known for its nutritional and therapeutic properties, exhibits a complex relationship with its rhizospheric soil microbiome. This study aimed to elucidate the microbiome's structural composition, molecular functions, and its role in plant growth by integrating Clusters of Orthologous Genes (COG) analysis with enzymatic functions previously identified through KEGG, CAZy, and CARD databases. Metagenomic sequencing and bioinformatics analysis were performed from the rhizospheric soil microbiome of M. oleifera collected from the Mecca district in Saudi Arabia. The analysis revealed a role for the rhizospheric microbiome in energy production, storage, and regulation, with glucose serving as a crucial precursor for NADH synthesis and subsequent ATP production via oxidative phosphorylation. Key orthologous genes (OGs) implicated in this process include NuoD, NuoH, NuoM, NuoN, NuoL, atpA, QcrB/PetB, and AccC. Additionally, OGs involved in ATP hydrolysis, such as ClpP, EntF, YopO, and AtoC, were identified. Taxonomic analysis highlighted Actinobacteria and Proteobacteria as the predominant phyla, with enriched genera including Blastococcus, Nocardioides, Streptomyces, Microvirga, Sphingomonas, and Massilia, correlating with specific OGs involved in ATP hydrolysis. This study provides insights into the molecular mechanisms underpinning plant-microbe interactions and highlights the multifaceted roles of ATP-dependent processes in the rhizosphere. Further research is recommended to explore the potential applications of these findings in sustainable agriculture and ecosystem management.}, } @article {pmid40194944, year = {2025}, author = {Wilson, I and Perry, T and Eisenhofer, R and Rismiller, P and Shaw, M and Grutzner, F}, title = {Microbiota changes in lactation in the short-beaked echidna (Tachyglossus aculeatus).}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaf036}, pmid = {40194944}, issn = {1574-6941}, abstract = {Monotreme and marsupial development is characterised by a short gestation, with young exposed to the environment at an early developmental stage and supported by a long lactation in the pouch, pseudo-pouch, or burrow. The lack of a functional adaptive immune system in these altricial young raises questions about how they survive in a microbe-rich environment. Previous studies on marsupial pouches have revealed changes to pouch microbe composition during lactation, but no information is available in monotremes. We investigated changes in the echidna pseudo-pouch microbiota (n = 22) during different stages of the reproductive cycle and whether this differs between wild and zoo-managed animals. Metataxonomic profiling using 16S rRNA gene sequencing revealed that pseudo-pouch microbial communities undergo dramatic changes during lactation, with significant differences in taxonomic composition compared with samples taken outside of breeding season or during courtship and mating. This suggests that the echidna pseudo-pouch environment changes during lactation to accommodate young that lack a functional adaptive immune system. Furthermore, captivity was not found to have a significant effect on pseudo-pouch microbiota. This study pioneers pouch microbiota research in monotremes, provides new biological information on echidna reproduction, and may also provide information about the effects of captive management to inform breeding programs in the future.}, } @article {pmid40194477, year = {2025}, author = {Zhang, H and Zhang, X and Sun, H and Ling, H and Xie, R and Fang, L and Guo, M and Wu, X}, title = {Polyvinyl chloride microplastic triggers bidirectional transmission of antibiotic resistance genes in soil-earthworm systems.}, journal = {Environment international}, volume = {198}, number = {}, pages = {109414}, doi = {10.1016/j.envint.2025.109414}, pmid = {40194477}, issn = {1873-6750}, abstract = {The diffusion and distribution of ubiquitous microplastics and antibiotic resistance genes (ARGs) in soil ecosystems are easily influenced by earthworm activity. However, minimal research exists on the bidirectional dissemination of ARGs in the soil-earthworm ecosystems under microplastic stress. Focusing on the typical microplastic polyvinyl chloride (PVC) microspheres in simulated soil-earthworm (Eisenia fetida) systems, we characterized the PVC-triggered interactive transmission of ARGs between earthworm guts and their dwelling soils using shotgun metagenomics and qPCR methodologies. PVC exposure did not alter the diversity and relative abundance of ARGs in earthworm-uninoculated soils but significantly increased those in earthworm-inoculated soils. Meanwhile, the abundance of ARGs increased in the earthworm gut under PVC stress. Source tracking analysis showed a higher source proportion of soil-borne ARGs into earthworm gut under PVC treatments. Mechanistically, PVC-triggered increasing prevalence of ARGs was significantly related to both the bacterial community and mobile genetic elements-mediated horizontal transfer in the soils, whereas the bacterial community predominated the process in the earthworm guts. Overall, our findings reveal a PVC-triggered bidirectional transmission pattern of ARGs between earthworm guts and their dwelling soils and highlight the overlooked ecotoxicological risk of microplastics in soil-earthworm systems.}, } @article {pmid40193404, year = {2025}, author = {Aroney, STN and Newell, RJP and Nissen, JN and Camargo, AP and Tyson, GW and Woodcroft, BJ}, title = {CoverM: Read alignment statistics for metagenomics.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btaf147}, pmid = {40193404}, issn = {1367-4811}, abstract = {SUMMARY: Genome-centric analysis of metagenomic samples is a powerful method for understanding the function of microbial communities. Calculating read coverage is a central part of analysis, enabling differential coverage binning for recovery of genomes and estimation of microbial community composition. Coverage is determined by processing read alignments to reference sequences of either contigs or genomes. Per-reference coverage is typically calculated in an ad-hoc manner, with each software package providing its own implementation and specific definition of coverage. Here we present a unified software package CoverM which calculates several coverage statistics for contigs and genomes in an ergonomic and flexible manner. It uses 'Mosdepth arrays' for computational efficiency and avoids unnecessary I/O overhead by calculating coverage statistics from streamed read alignment results.

CoverM is free software available at https://github.com/wwood/coverm. CoverM is implemented in Rust, with Python (https://github.com/apcamargo/pycoverm) and Julia (https://github.com/JuliaBinaryWrappers/CoverM_jll.jl) interfaces.}, } @article {pmid40193328, year = {2025}, author = {Jagadesan, S and Guda, C}, title = {MetaDAVis: An R shiny application for metagenomic data analysis and visualization.}, journal = {PloS one}, volume = {20}, number = {4}, pages = {e0319949}, doi = {10.1371/journal.pone.0319949}, pmid = {40193328}, issn = {1932-6203}, mesh = {*Metagenomics/methods ; Humans ; RNA, Ribosomal, 16S/genetics ; *Software ; *Metagenome ; Microbiota/genetics ; High-Throughput Nucleotide Sequencing ; }, abstract = {The human microbiome exerts tremendous influence on maintaining a balance between human health and disease. High-throughput sequencing has enabled the study of microbial communities at an unprecedented resolution. Generation of massive amounts of sequencing data has also presented novel challenges to analyzing and visualizing data to make biologically relevant interpretations. We have developed an interactive Metagenome Data Analysis and Visualization (MetaDAVis) tool for 16S rRNA as well as the whole genome sequencing data analysis and visualization to address these challenges using an R Shiny application. MetaDAVis can perform six different types of analyses that include: i) Taxonomic abundance distribution; ii) Alpha and beta diversity analyses; iii) Dimension reduction tasks using PCA, t-SNE, and UMAP; iv) Correlation analysis using taxa- or sample-based data; v) Heatmap generation; and vi) Differential abundance analysis. MetaDAVis creates interactive and dynamic figures and tables from multiple methods enabling users to easily understand their data using different variables. Our program is user-friendly and easily customizable allowing those without any programming background to perform comprehensive data analyses using a standalone or web-based interface.}, } @article {pmid40193099, year = {2025}, author = {Chiu, CY and López-Labrador, FX and Wilson, MR and de Vries, JJC}, title = {The Regulatory Landscape for Clinical Metagenomic Testing.}, journal = {JAMA neurology}, volume = {}, number = {}, pages = {}, doi = {10.1001/jamaneurol.2025.0461}, pmid = {40193099}, issn = {2168-6157}, } @article {pmid40193036, year = {2025}, author = {Kim, SY and Seol, D and Jung, M and Kwak, W and Kim, H and Cho, S and Kim, TH}, title = {Assessing the Efficacy of Ligilactobacillus salivarius CLS0420 and Lacticaseibacillus paracasei CLPC0603 on Vaginal Well-Being in Healthy Women: A Pilot, Randomized, Double-Blind, Placebo-Controlled Trial.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {40193036}, issn = {1867-1314}, abstract = {Despite the growing development of probiotics for preventing bacterial vaginosis (BV), their effectiveness in women without BV has not been thoroughly investigated. This pilot, randomized, double-blind, placebo-controlled study aims to assess the impact of orally administered probiotic strains, exhibiting in vitro antimicrobial activity against Gardnerella vaginalis and Candida albicans, on vaginal well-being in women without preexisting health conditions. Healthy women (n = 30, aged 19-50) were enrolled and randomly assigned using simple randomization to receive either probiotic or placebo capsules. After excluding dropouts, 26 participants (15 in the probiotic group, 11 in the placebo group) completed the study, undergoing a 3-week intervention. Vaginal well-being was assessed before and after the intervention using self-assessed health on a 5-point Likert scale, along with analysis of the vaginal microbiome by targeting the 16S-ITS-23S rRNA operon region with the Nanopore sequencing platform and MIrROR database. Notably, only the probiotic group exhibited a significant improvement in self-assessed overall gut and vaginal health following the intervention (p = 0.009 and p = 0.003, respectively). Nevertheless, no significant changes were observed in the vaginal bacterial community following the intervention and confirming the vaginal colonization of orally ingested probiotic strains through metagenome sequencing proved challenging. In summary, these findings suggest that while oral probiotics may improve perceived vaginal well-being, their role in modulating the vaginal microbiome in healthy women remains inconclusive. Additional research with a larger sample size is necessary to substantiate the endorsement of oral probiotic consumption for preventing BV or maintaining vaginal health in healthy women. This study was retrospectively registered at Clinical Research Information Service (CRIS) (KCT0008957, November 15, 2023).}, } @article {pmid40192235, year = {2025}, author = {Jiao, Y and Ren, J and Xie, S and Yuan, N and Shen, J and Yin, H and Wang, J and Guo, H and Cao, J and Wang, X and Wu, D and Zhou, Z and Qi, X}, title = {Raffinose-metabolizing bacteria impair radiation-associated hematopoietic recovery via the bile acid/FXR/NF-κB signaling pathway.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2488105}, doi = {10.1080/19490976.2025.2488105}, pmid = {40192235}, issn = {1949-0984}, mesh = {Animals ; *Gastrointestinal Microbiome/radiation effects ; *Bile Acids and Salts/metabolism ; Mice ; *NF-kappa B/metabolism/genetics ; Signal Transduction/radiation effects ; *Raffinose/metabolism ; Mice, Inbred C57BL ; Whole-Body Irradiation/adverse effects ; *Receptors, Cytoplasmic and Nuclear/metabolism/genetics ; Fecal Microbiota Transplantation ; Male ; *Acute Radiation Syndrome/microbiology/metabolism ; *Hematopoiesis/radiation effects ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Dysbiosis/microbiology ; }, abstract = {Radiation-associated hematopoietic recovery (RAHR) is critical for mitigating lethal complications of acute radiation syndrome (ARS), yet therapeutic strategies remain limited. Through integrated multi-omics analysis of a total body irradiation (TBI) mouse model, we identify Bacteroides acidifaciens-dominated gut microbiota as key mediators of RAHR impairment. 16S ribosomal rRNA sequencing revealed TBI-induced dysbiosis characterized by Bacteroidaceae enrichment, while functional metagenomics identified raffinose metabolism as the most significantly perturbed pathway. Notably, raffinose supplementation (10% w/v) recapitulated radiation-induced microbiota shifts and delayed bone marrow recovery. Fecal microbiota transplantation (FMT) revealed a causative role for raffinose-metabolizing microbiota, particularly Bacteroides acidifaciens, in delaying RAHR progression. Mechanistically, B. acidifaciens-mediated bile acid deconjugation activated FXR, subsequently suppressing NF-κB-dependent hematopoietic recovery. Therapeutic FXR inhibition via ursodeoxycholic acid (UDCA) had been shown to be a viable method for rescuing RAHR. Our results delineated a microbiome-bile acid-FXR axis as a master regulator of post-irradiation hematopoiesis. Targeting B. acidifaciens or its metabolic derivatives could represent a translatable strategy to mitigate radiation-induced hematopoietic injury.}, } @article {pmid40191975, year = {2025}, author = {Okechukwu Paul-Chima, U and Chinyere Nkemjika, A and Melvin Nnaemeka, U and Onohuean, H}, title = {Harnessing plant metabolic pathways for innovative diabetes management: unlocking the therapeutic potential of medicinal plants.}, journal = {Plant signaling & behavior}, volume = {20}, number = {1}, pages = {2486076}, doi = {10.1080/15592324.2025.2486076}, pmid = {40191975}, issn = {1559-2324}, mesh = {*Plants, Medicinal/metabolism ; Humans ; *Diabetes Mellitus/drug therapy/metabolism ; *Metabolic Networks and Pathways ; }, abstract = {The exploration of plant signaling pathways is transforming the way diabetes is managed, providing new, multi-target strategies for controlling this complex metabolic disorder. Medicinal plants are rich in bioactive compounds like phytohormones, flavonoids and polyphenols, which regulate key pathways including oxidative stress, inflammation, insulin resistance, and gut microbiota modulation. Research is emerging on the therapeutic potential of Momordica charantia, Cinnamomum verum and Trigonella foenum-graecum, which enhance insulin secretion, sensitivity and glucose homeostasis. These plant derived compounds, resveratrol and plant based insulin mimetics, not only address metabolic dysfunction but also offer holistic treatment for long term complications such as neuropathy and retinopathy. The development of precision medicine advances the tailoring of plant based therapies to individual metabolic responses, increasing efficacy and decreasing reliance on synthetic drugs with adverse side effects. Despite challenges of standardization, regulatory barriers, and limited clinical trials, incorporating medicinal plants into national diabetes management guidelines represents a cost effective and accessible option, particularly in resource limited settings. In this review, we highlight the importance of collaborative work across disciplines and the use of technologies such as artificial intelligence to speed research and optimize patient specific applications. The therapeutic power of plant signaling pathways is harnessed to develop sustainable, inclusive, and effective diabetes management strategies.}, } @article {pmid40191290, year = {2025}, author = {Kurt, H and Sever Kaya, D and Akçok, İ and Sarı, C and Albayrak, E and Velioğlu, HM and Şamlı, HE and Özdüven, ML and Sürmeli, Y}, title = {Discovery and In Silico Characterization of Anatolian Water Buffalo Rumen-Derived Bacterial Thermostable Xylanases: A Sequence-Based Metagenomic Approach.}, journal = {ACS omega}, volume = {10}, number = {12}, pages = {12679-12698}, pmid = {40191290}, issn = {2470-1343}, abstract = {This study involved shotgun sequencing of rumen metagenomes from three Anatolian water buffalos, an exploration of the relationship between microbial flora and xylanases, and in silico analyses of thermostable xylanases, focusing on their sequence, structure, and dynamic properties. For this purpose, the rumen metagenome of three Anatolian water buffalos was sequenced and bioinformatically analyzed to determine microbial diversity and full-length xylanases. Analyses of BLAST, biophysicochemical characteristics, phylogenetic tree, and multiple sequence alignment were performed with Blastp, ProtParam, MEGA11 software, and Clustal Omega, respectively. Three-dimensional homology models of three xylanases (AWBRMetXyn5, AWBRMetXyn10, and AWBRMetXyn19) were constructed by SWISS-MODEL and validated by ProSA, ProCheck, and Verify3D. Also, their 3D models were structurally analyzed by PyMOL, BANΔIT, thermostability predictor, What If, and Protein Interaction Calculator (PIC) software. Protein-ligand interactions were examined by docking and MD simulation. Shotgun sequence and Blastp analyses showed that Clostridium (Clostridiales bacterial order), Ruminococcus (Oscillospiraceae bacterial family), Prevotella (Bacteroidales bacterial order), and Butyrivibrio (Lachnospiraceae bacterial family) were found as dominant potential xylanase-producer genera in three rumen samples. Furthermore, the biophysicochemical analysis indicated that three xylanases exhibited an aliphatic index above 80, an instability index below 40, and melting temperatures (T m) surpassing 65 °C. Phylogenetic analysis placed three xylanases within the GH10 family, clustering them with thermophilic xylanases, while homology modeling identified the optimal template as a xylanase from a thermophilic bacterium. The structural analysis indicated that three xylanases possessed the number of salt bridges, hydrophobic interactions, and T m score higher than 50, 165, and 70 °C, respectively; however, the reference thermophilic XynAS9 had 43, 145, and 54.41 °C, respectively. BANΔIT analysis revealed that three xylanases exhibited lower B'-factor values in the β3-α1 loop/short-helix at the N-terminal site compared to the reference thermophilic XynAS9. In contrast, six residues (G79, M123, D150, T199, A329, and G377) possessed higher B'-factor values in AWBRMetXyn5 and their aligned positions in AWBRMetXyn10 and AWBRMetXyn19, relative to XynAS9 including Gln, Glu, Ile, Lys, Ser, and Val at these positions, respectively. MD simulation results showed that the β9-η5 loop including catalytic nucleophile glutamic acid in the RMSF plot of three xylanases had a higher fluctuation than the aligned region in XynAS9. The distance analysis from the MD simulation showed that the nucleophile residue in AWBRMetXyn5 and AWBRMetXyn10 remained closer to the ligand throughout the simulation compared with XynAS9 and AWBRMetXyn19. The most notable difference between AWBRMetXyn5 and AWBRMetXyn10 was the increased amino acid fluctuations in two specific regions, the η3 short-helix and the η3-α3 loop, despite a minimal sequence difference of only 1.24%, which included three key amino acid variations (N345, N396, and T397 in AWBRMetXyn5; D345, K396, and A397 in AWBRMetXyn10). Thus, this study provided computational insights into xylanase function and thermostability, which could inform future protein engineering efforts. Additionally, three xylanases, especially AWBRMetXyn5, are promising candidates for various high-temperature industrial applications. In a forthcoming study, three xylanases will be experimentally characterized and considered for potential industrial applications. In addition, the amino acid substitutions (G79Q, M123E, D150I, T199K, A329S, and G377V) and the residues in the β3-α1 loop will be targeted for thermostability improvement of AWBRMetXyn5. The amino acids (N345, N396, and T397) and the residues on the β9-η5 loop, η3 short-helix, and η3-α3 loop will also be focused on development of the catalytic efficiency.}, } @article {pmid40190795, year = {2025}, author = {Zhang, Y and Dai, Y and Li, J and Cong, W and Zhang, Y and Nie, X and Wu, Q and Xue, Y}, title = {Climate Change and Human Pressure: Assessing the Vulnerability of Snow Leopard (Panthera uncia) Habitat Integrated With Prey Distribution on the Qinghai-Tibet Plateau.}, journal = {Ecology and evolution}, volume = {15}, number = {4}, pages = {e71232}, pmid = {40190795}, issn = {2045-7758}, abstract = {Climate change is significantly altering the distribution of large carnivores and their primary prey species, with particular emphasis on the changing prey distribution in high-altitude regions. The Qinghai-Tibet Plateau, known for its rich biodiversity, is highly sensitive to climate change, affecting the habitats of snow leopards (Panthera uncia) and blue sheep (Pseudois nayaur). Our study identified blue sheep as the primary prey of snow leopards through metagenomic analysis and used bioclimatic data and Land Use/Cover Change (LUCC) information to model habitat suitability under three climate scenarios (RCP 2.6, RCP 4.5, and RCP 8.5). Projections showed that under RCP 4.5 and RCP 8.5, snow leopard habitats will decrease by 13.0% and 23.4%, while blue sheep habitats will decrease by 38.3% and 49.7%, respectively. These habitats are expected to shift to higher altitudes, with snow leopards experiencing a more significant shift. Based on these findings, we recommend adjusting protected area boundaries for S1 (Ideal distribution range), establishing ecological corridors for S2 (stepping stone), and implementing targeted measures to mitigate human-wildlife conflicts in S3 (potential conflict area). To protect these species, international efforts to reduce carbon emissions, cross-administrative cooperation, and community-based conservation strategies are essential.}, } @article {pmid40190731, year = {2025}, author = {Atencio, B and Malavin, S and Rubin-Blum, M and Ram, R and Adar, E and Ronen, Z}, title = {Site-specific incubations reveal biofilm diversity and functional adaptations in deep, ancient desert aquifers.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1533115}, pmid = {40190731}, issn = {1664-302X}, abstract = {Deep pristine aquifers are ecological hotspots with diverse microbial life, where microorganisms exist either attached (sessile) to solid substrates or suspended in groundwater (planktonic). Characterizing the attached microbial communities is of paramount importance, especially in the context of biofouling. However, obtaining samples of attached microbes that thrive under natural (undisturbed) conditions is challenging. Our study addresses this by retrieving sessile microbes on-site. We installed columns filled with site-specific rock cuttings at the wellhead, allowing fresh groundwater to flow continuously for approximately 60 days. We hypothesized that the attached microbial communities would differ structurally from planktonic microbes due to the aquifer's lithological and mineralogical composition. This study involved an exploratory examination of the microbial communities in different aquifers with distinct mineralogies, including quartzitic sandstone, calcareous, chert, and highly heterogeneous (clastic) aquifers in Israel's Negev Desert. Metagenomic analysis revealed both shared and distinct microbial communities among attached and planktonic forms in the various environments, likely shaped by the aquifers' physical, lithological, and mineralogical properties. A wealth of carbon-fixation pathways and energy-conservation strategies in the attached microbiome provide evidence for the potential productivity of these biofilms. We identified widespread genetic potential for biofilm formation (e.g., via pili, flagella, and extracellular polymeric substance production) and the interactome (e.g., quorum-sensing genes). Our assessment of these functions provides a genomic framework for groundwater management and biofouling treatment.}, } @article {pmid40190171, year = {2025}, author = {Milev, M and Roglev, B and Kondeva Rogleva, M and Georgieva, M and Miloshev, G and Ruskovska, T}, title = {Impact of (poly)phenol-rich dietary sources on DNA damage: Insights from human intervention studies using the Comet assay - a review and perspective.}, journal = {The British journal of nutrition}, volume = {}, number = {}, pages = {1-40}, doi = {10.1017/S000711452500073X}, pmid = {40190171}, issn = {1475-2662}, abstract = {(Poly)phenols are plant-derived food bioactives abundantly present in human diet. They exert positive effects on various aspects of human health, and in particular in reducing the risk of chronic non-communicable diseases. Dietary (poly)phenols have been reported to improve vascular function, blood lipids, insulin sensitivity, and to decrease systemic inflammation. Evidence also suggests that (poly)phenols may exert protective effects on DNA, by reducing the extent of its damage. In recent years, advanced analytical methods, including transcriptomics, metabolomics, proteomics, and metagenomics, have been employed to unravel the complex impact of (poly)phenols in health and disease. Advances in bioinformatics enable an integrated multi-omics approach to data analysis, opening avenues for discovering new, previously unknown molecular mechanisms of action. Innovative solutions and automation of the Comet assay offer new opportunities for more in-depth analysis of the impact of (poly)phenols on DNA damage and its inclusion in integrative bioinformatic models. Such an approach has the potential to uncover new multi-level interactions and to reveal previously unknown factors underlying inter-individual variabilities in health-promoting effects of (poly)phenols. This review provides an insight into the application of the Comet assay in human intervention studies using (poly)phenol-rich dietary sources. Recent advancements in the Comet assay technology, and the prospects for more extensive use of this method in future human intervention studies with (poly)phenols could contribute to the development of personalized dietary recommendations for these plant-derived food bioactives.}, } @article {pmid40190120, year = {2025}, author = {Aboulalazm, FA and Kazen, AB and deLeon, O and Müller, S and Saravia, FL and Lozada-Fernandez, V and Hadiono, MA and Keyes, RF and Smith, BC and Kellogg, SL and Grobe, JL and Kindel, TL and Kirby, JR}, title = {Reutericyclin, a specialized metabolite of Limosilactobacillus reuteri, mitigates risperidone-induced weight gain in mice.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2477819}, doi = {10.1080/19490976.2025.2477819}, pmid = {40190120}, issn = {1949-0984}, mesh = {Animals ; *Risperidone/adverse effects ; *Limosilactobacillus reuteri/metabolism ; *Weight Gain/drug effects ; Female ; Gastrointestinal Microbiome/drug effects ; Mice ; Mice, Inbred C57BL ; *Antipsychotic Agents/adverse effects ; Probiotics/administration & dosage ; Feces/microbiology ; Energy Metabolism/drug effects ; Bacteria/classification/genetics/isolation & purification/metabolism ; }, abstract = {The role of xenobiotic disruption of microbiota, corresponding dysbiosis, and potential links to host metabolic diseases are of critical importance. In this study, we used a widely prescribed antipsychotic drug, risperidone, known to influence weight gain in humans, to induce weight gain in C57BL/6J female mice. We hypothesized that microbes essential for maintaining gut homeostasis and energy balance would be depleted following treatment with risperidone, leading to enhanced weight gain relative to controls. Thus, we performed metagenomic analyses on stool samples to identify microbes that were excluded in risperidone-treated animals but remained present in controls. We identified multiple taxa including Limosilactobacillus reuteri as a candidate for further study. Oral supplementation with L. reuteri protected against risperidone-induced weight gain (RIWG) and was dependent on cellular production of a specialized metabolite, reutericyclin. Further, synthetic reutericyclin was sufficient to mitigate RIWG. Both synthetic reutericyclin and L. reuteri restored energy balance in the presence of risperidone to mitigate excess weight gain and induce shifts in the microbiome associated with leanness. In total, our results identify reutericyclin production by L. reuteri as a potential probiotic to restore energy balance induced by risperidone and to promote leanness.}, } @article {pmid40189999, year = {2025}, author = {Peng, K and Gao, Y and Li, C and Wang, Q and Yin, Y and Hameed, MF and Feil, E and Chen, S and Wang, Z and Liu, YX and Li, R}, title = {Benchmarking of analysis tools and pipeline development for nanopore long-read metagenomics.}, journal = {Science bulletin}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.scib.2025.03.044}, pmid = {40189999}, issn = {2095-9281}, } @article {pmid40189749, year = {2025}, author = {Birebent, R and Drubay, D and Alves Costa Silva, C and Marmorino, F and Vitali, G and Piccinno, G and Hurtado, Y and Bonato, A and Belluomini, L and Messaoudene, M and Routy, B and Fidelle, M and Zalcman, G and Mazieres, J and Audigier-Valette, C and Moro-Sibilot, D and Goldwasser, F and Scherpereel, A and Pegliasco, H and Ghiringhelli, F and Reni, A and Barlesi, F and Albiges, L and Planchard, D and Martinez, S and Besse, B and Segata, N and Cremolini, C and Zitvogel, L and Iebba, V and Derosa, L}, title = {Surrogate markers of intestinal dysfunction associated with survival in advanced cancers.}, journal = {Oncoimmunology}, volume = {14}, number = {1}, pages = {2484880}, doi = {10.1080/2162402X.2025.2484880}, pmid = {40189749}, issn = {2162-402X}, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; *Dysbiosis/microbiology ; Middle Aged ; *Colorectal Neoplasms/mortality/microbiology/pathology ; Aged ; Prognosis ; *Carcinoma, Non-Small-Cell Lung/mortality/microbiology/pathology ; *Lung Neoplasms/mortality/microbiology/pathology ; Akkermansia/isolation & purification ; *Urogenital Neoplasms/mortality/microbiology/pathology ; }, abstract = {Deviations in the diversity and composition of the gut microbiota are called "gut dysbiosis". They have been linked to various chronic diseases including cancers and resistance to immunotherapy. Stool shotgun based-metagenomics informs on the ecological composition of the gut microbiota and the prevalence of homeostatic bacteria such as Akkermansia muciniphila (Akk), while determination of the serum addressin MAdCAM-1 instructs on endothelial gut barrier dysfunction. Here we examined patient survival during chemo-immuno-therapy in 955 cancer patients across four independent cohorts of non-small cell lung (NSCLC), genitourinary (GU) and colorectal (CRC) cancers, according to hallmarks of gut dysbiosis. We show that Akk prevalence represents a stable and favorable phenotype in NSCLC and CRC cancer patients. Over-dominance of Akk above the healthy threshold was observed in dismal prognosis in NSCLC and GU and mirrored an immunosuppressive gut ecosystem and excessive intestinal epithelial exfoliation in NSCLC. In CRC, the combination of a lack of Akk and low sMAdCAM-1 levels identified a subset comprising 28% of patients with reduced survival, independent of the immunoscore. We conclude that gut dysbiosis hallmarks deserve integration within the diagnosis toolbox in oncological practice.}, } @article {pmid40189708, year = {2025}, author = {Gen-Jiménez, A and Flores-Félix, JD and Rincón-Molina, CI and Manzano-Gómez, LA and Villalobos-Maldonado, JJ and Ruiz-Lau, N and Roca-Couso, R and Ruíz-Valdiviezo, VM and Rincón-Rosales, R}, title = {Native Rhizobium biofertilization enhances yield and quality in Solanum lycopersicum under field conditions.}, journal = {World journal of microbiology & biotechnology}, volume = {41}, number = {4}, pages = {126}, pmid = {40189708}, issn = {1573-0972}, support = {19337.24-P//Tecnológico Nacional de México/ ; }, mesh = {*Solanum lycopersicum/growth & development/microbiology ; *Rhizobium/physiology ; Soil Microbiology ; *Fertilizers ; Soil/chemistry ; Fruit/growth & development ; Nitrogen/analysis/metabolism ; Microbiota ; Agriculture/methods ; }, abstract = {In response to growing concerns about the environmental and economic impacts of chemical fertilizers, this study explores the potential of biofertilization using native Rhizobium strains to enhance the growth, yield, and quality of Solanum lycopersicum (tomato) under field conditions. The experiment assessed the effects of Rhizobium biofertilization on plant performance and soil microbial communities by applying R. calliandrae, R. jaguaris, R. mayense, and a bacterial consortium, in comparison to conventional chemical fertilization. Key parameters such as plant height, fruit yield, macronutrient and micronutrient content, and fruit quality (lycopene and β-carotene levels) were measured. Results showed that R. calliandrae and R. jaguaris significantly enhanced fruit yield, nitrogen, potassium, manganese, and boron levels, while also improving fruit quality compared to the control. The impact of strain inoculation on the structure of the microbial community was also examined. Metataxonomic analysis of rhizospheric soils revealed no significant changes in microbial diversity, indicating that biofertilization with Rhizobium strains promotes plant growth without disrupting the composition of the soil microbiome. These findings suggest that Rhizobium biofertilization is a viable and sustainable alternative to chemical fertilizers, providing benefits to both crop productivity and soil health while minimizing the environmental footprint associated with conventional agricultural practices. The study underscores the importance of carefully selecting bacterial species with complementary functions to maximize the effectiveness of biofertilization strategies.}, } @article {pmid40189564, year = {2025}, author = {He, Y and Zhuo, S and Li, M and Pan, J and Jiang, Y and Hu, Y and Sanford, RA and Lin, Q and Sun, W and Wei, N and Peng, S and Jiang, Z and Li, S and Li, Y and Dong, Y and Shi, L}, title = {Candidate Phyla Radiation (CPR) bacteria from hyperalkaline ecosystems provide novel insight into their symbiotic lifestyle and ecological implications.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {94}, pmid = {40189564}, issn = {2049-2618}, support = {42472366, 92051111 and 42272353//National Natural Science Foundation of China/ ; 122-G1323522144//Fundamental Research Funds for the Chinese Central Government via China University of Geosciences (Wuhan)/ ; }, mesh = {*Symbiosis ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Metagenomics/methods ; Metagenome ; Folic Acid/biosynthesis ; Ecosystem ; Phylogeny ; Genome, Bacterial ; *Microbiota ; }, abstract = {BACKGROUND: Candidate Phyla Radiation (CPR) represents a unique superphylum characterized by ultra-small cell size and symbiotic lifestyle. Although CPR bacteria have been identified in varied environments, their broader distribution, associations with hosts, and ecological roles remain largely unexplored. To address these knowledge gaps, a serpentinite-like environment was selected as a simplified model system to investigate the CPR communities in hyperalkaline environments and their association with hosts in extreme conditions. Additionally, the enzymatic activity, global distribution, and evolution of the CPR-derived genes encoding essential metabolites (e.g., folate or vitamin B9) were analyzed and assessed.

RESULTS: In the highly alkaline serpentinite-like ecosystem (pH = 10.9-12.4), metagenomic analyses of the water and sediment samples revealed that CPR bacteria constituted 1.93-34.8% of the microbial communities. Metabolic reconstruction of 12 high-quality CPR metagenome-assembled genomes (MAGs) affiliated to the novel taxa from orders UBA6257, UBA9973, and Paceibacterales suggests that these bacteria lack the complete biosynthetic pathways for amino acids, lipids, and nucleotides. Notably, the CPR bacteria commonly harbored the genes associated with essential folate cofactor biosynthesis and metabolism, including dihydrofolate reductase (folA), serine hydroxymethyltransferase (glyA), and methylenetetrahydrofolate reductase (folD). Additionally, two presumed auxotrophic hosts, incapable of forming tetrahydrofolate (THF) due to the absence of folA, were identified as potential hosts for some CPR bacteria harboring folA genes. The functionality of these CPR-derived folA genes was experimentally verified by heterologous expression in the folA-deletion mutant Escherichia coli MG1655 ΔfolA. Further assessment of the available CPR genomes (n = 4,581) revealed that the genes encoding the proteins for the synthesis of bioactive folate derivatives (e.g., folA, glyA, and/or folD genes) were present in 90.8% of the genomes examined. It suggests potential widespread metabolic complementarity in folate biosynthesis between CPR and their hosts.

CONCLUSIONS: This finding deepens our understanding of the mechanisms of CPR-host symbiosis, providing novel insight into essential cofactor-dependent mutualistic CPR-host interactions. Our observations suggest that CPR bacteria may contribute to auxotrophic organisms and indirectly influence biogeochemical processes. Video Abstract.}, } @article {pmid40189545, year = {2025}, author = {Serrana, JM and Nascimento, FJA and Dessirier, B and Broman, E and Posselt, M}, title = {Environmental drivers of the resistome across the Baltic Sea.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {92}, pmid = {40189545}, issn = {2049-2618}, mesh = {*Bacteria/genetics/drug effects/classification/isolation & purification ; *Microbiota/genetics ; *Seawater/microbiology ; Oceans and Seas ; *Geologic Sediments/microbiology ; Metagenome ; Salinity ; Anti-Bacterial Agents/pharmacology ; Temperature ; }, abstract = {BACKGROUND: Antimicrobial resistance is a major global health concern, with the environment playing a key role in its emergence and spread. Understanding the relationships between environmental factors, microbial communities, and resistance mechanisms is vital for elucidating environmental resistome dynamics. In this study, we characterized the environmental resistome of the Baltic Sea and evaluated how environmental gradients and spatial variability, alongside its microbial communities and associated functional genes, influence resistome diversity and composition across geographic regions.

RESULTS: We analyzed the metagenomes of benthic sediments from 59 monitoring stations across a 1,150 km distance of the Baltic Sea, revealing an environmental resistome comprised of predicted antimicrobial resistance genes (ARGs) associated with resistance against 26 antibiotic classes. We observed spatial variation in its resistance profile, with higher resistome diversity in the northern regions and a decline in the dead zones and the southern areas. The combined effects of salinity and temperature gradients, alongside nutrient availability, created a complex environmental landscape that shaped the diversity and distribution of the predicted ARGs. Salinity predominantly influenced microbial communities and predicted ARG composition, leading to clear distinctions between high-saline regions and those with lower to mid-level salinity. Furthermore, our analysis suggests that microbial community composition and mobile genetic elements might be crucial in shaping ARG diversity and composition.

CONCLUSIONS: We presented that salinity and temperature were identified as the primary environmental factors influencing resistome diversity and distribution across geographic regions, with nutrient availability further shaping these patterns in the Baltic Sea. Our study also highlighted the interplay between microbial communities, resistance, and associated functional genes in the benthic ecosystem, underscoring the potential role of microbial and mobile genetic element composition in ARG distribution. Understanding how environmental factors and microbial communities modulate environmental resistomes will help predict the impact of future environmental changes on resistance mechanisms in complex aquatic ecosystems. Video Abstract.}, } @article {pmid40189243, year = {2025}, author = {Chitcharoen, S and Sawaswong, V and Klomkliew, P and Chanchaem, P and Payungporn, S}, title = {Comparative analysis of human gut bacterial microbiota between shallow shotgun metagenomic sequencing and full-length 16S rDNA amplicon sequencing.}, journal = {Bioscience trends}, volume = {}, number = {}, pages = {}, doi = {10.5582/bst.2024.01393}, pmid = {40189243}, issn = {1881-7823}, abstract = {The human gut microbiome is increasingly recognized as important to health and disease, influencing immune function, metabolism, mental health, and chronic illnesses. Two widely used, cost-effective, and fast approaches for analyzing gut microbial communities are shallow shotgun metagenomic sequencing (SSMS) and full-length 16S rDNA sequencing. This study compares these methods across 43 stool samples, revealing notable differences in taxonomic and species-level detection. At the genus level, Bacteroides was most abundant in both methods, with Faecalibacterium showing similar trends but Prevotella was more abundant in full-length 16S rDNA. Genera such as Alistipes and Akkermansia were more frequently detected by full-length 16S rDNA, whereas Eubacterium and Roseburia were more prevalent in SSMS. At the species level, Faecalibacterium prausnitzii, a key indicator of gut health, was abundant across both datasets, while Bacteroides vulgatus was more frequently detected by SSMS. Species within Parabacteroides and Bacteroides were primarily detected by 16S rDNA, contrasting with higher SSMS detection of Prevotella copri and Oscillibacter valericigenes. LEfSe analysis identified 18 species (9 species in each method) with significantly different detection between methods, underscoring the impact of methodological choice on microbial diversity and abundance. Differences in classification databases, such as Ribosomal Database Project (RDP) for 16S rDNA and Kraken2 for SSMS, further highlight the influence of database selection on outcomes. These findings emphasize the importance of carefully selecting sequencing methods and bioinformatics tools in microbiome research, as each approach demonstrates unique strengths and limitations in capturing microbial diversity and relative abundances.}, } @article {pmid40188788, year = {2025}, author = {Lu, H and Miao, J and Zhang, N and Ji, J and Zhang, R and Zhu, S and Wei, X}, title = {Targeting regulation of nitrate removal and chlorophenol degradation through hydrogen/oxygen switching.}, journal = {Water research}, volume = {281}, number = {}, pages = {123581}, doi = {10.1016/j.watres.2025.123581}, pmid = {40188788}, issn = {1879-2448}, abstract = {Nitrate is a common co-contaminant with 2,4-dichlorophenol (2,4-DCP) in water, presenting a challenge for environmental remediation. Under anaerobic conditions, the ring cleavage of chlorophenol is inefficient, while under aerobic conditions, nitrate removal is hindered. In this study, a microbial consortium capable of hydrogenotrophic denitrification and 2,4-DCP degradation was cultured, aiming to achieve efficient nitrate removal and 2,4-DCP degradation by alternately switching between hydrogen (H2) and oxygen (O2). Under H2 conditions, nitrate removal exceeded 90 %, while under O2 conditions, 2,4-DCP degradation reached 100 %. Under H2 conditions, the abundance of the Nar gene which was involved in nitrate reduction was higher than that under O2 conditions, promoting hydrogenotrophic denitrification. In contrast, under O2 conditions, 2,4-DCP degradation occurred via hydroxylation, ring-cleavage, dechlorination, and mineralization through the TCA cycle. Metagenomic and metabolomic analysis was performed to explore microbial metabolic pathways and potential synergistic mechanisms involved in hydrogenotrophic denitrification and 2,4-DCP biodegradation. In the H2-atmosphere, microbes (Methylobacillus and Chromobacterium), genes (E3.1.1.45 and speG), and metabolites (Cytosine and Uridine) may play a crucial role in hydrogenotrophic denitrification. In the O2-atmosphere, the functional genus of Paracoccus and Aquamicrobium associated with genes (tfdB and tfdC) may contribute to 2,4-DCP and its metabolites 2-Chloromaleylacetate degradation. These findings confirmed the role of functional microbial communities through H2/O2 regulation. This work provides a promising technological reference for treating industrial wastewater containing phenols and nitrogen.}, } @article {pmid40188743, year = {2025}, author = {Deng, K and Wang, L and Nguyen, SM and Shrubsole, MJ and Cai, Q and Lipworth, L and Gupta, DK and Zheng, W and Shu, XO and Yu, D}, title = {A dietary pattern promoting gut sulfur metabolism is associated with increased mortality and altered circulating metabolites in low-income American adults.}, journal = {EBioMedicine}, volume = {115}, number = {}, pages = {105690}, doi = {10.1016/j.ebiom.2025.105690}, pmid = {40188743}, issn = {2352-3964}, abstract = {BACKGROUND: Excessive hydrogen sulfide in the gut, generated by sulfur-metabolising bacteria from foods, has been linked to intestinal inflammation and human diseases. We aim to investigate the interplay between diet and sulphur-metabolising bacteria in relation to mortality and circulating metabolites in understudied populations.

METHODS: In the Southern Community Cohort Study (SCCS), a prospective cohort of primarily low-income American adults, habitual diets were assessed using a food frequency questionnaire at baseline (2002-2009). A sulfur microbial diet score (SMDS) was developed among 514 Black/African American participants by linking habitual dietary intakes with the abundance of sulfur-metabolising bacteria profiled by faecal shotgun metagenomics. The SMDS was then constructed among all eligible SCCS participants (50,114 Black/African American and 23,923 non-Hispanic White adults), and its associations with mortality outcomes were examined by Cox proportional hazards model and Fine-Grey subdistribution hazard model. The association between SMDS and 1110 circulating metabolites was examined by linear regression among 1688 SCCS participants with untargeted metabolomic profiling of baseline plasma samples.

FINDINGS: Over an average 13.9-year follow-up, SMDS was associated with increased all-cause mortality (HR [95% CI] for the highest vs. lowest quartiles: 1.21 [1.15-1.27]) and cardiovascular disease (1.18 [1.08-1.29]), cancer (1.13 [1.02-1.25]), and gastrointestinal cancer-specific (1.22 [1.00-1.49]) mortality among Black/African American participants (all P-trend<0.05). The associations were largely consistent across participant subgroups. Similar results were observed among non-Hispanic White participants. The SMDS was associated with 112 circulating metabolites, which mediated 36.15% of the SMDS-mortality association (P = 0.002).

INTERPRETATION: A dietary pattern promoting sulfur-metabolising gut bacteria may contribute to increased total and disease mortality in low-income American adults.

FUNDING: This study was funded by the National Institutes of Health, United States, to Vanderbilt University Medical Center, United States, and Anne Potter Wilson Chair endowment to Vanderbilt University, United States.}, } @article {pmid40188549, year = {2025}, author = {Sun, J and Yang, W and Li, M and Zhang, S and Sun, Y and Wang, F}, title = {Metagenomic analysis reveals soil microbiome responses to microplastics and ZnO nanoparticles in an agricultural soil.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138164}, doi = {10.1016/j.jhazmat.2025.138164}, pmid = {40188549}, issn = {1873-3336}, abstract = {Both microplastics (MPs) and engineered nanoparticles are pervasive emerging contaminants that can produce combined toxicity to terrestrial ecosystems, yet their effects on soil microbiomes remain inadequately understood. Here, metagenomic analysis was employed to investigate the impacts of three common MPs [i.e., polyethylene (PE), polystyrene (PS), and polylactic acid (PLA)] and zinc oxide nanoparticles (nZnO) on soil microbiomes. Both MPs and nZnO significantly altered the taxonomic, genetic, and functional diversity of soil microbes, with distinct effects depending on dosage or type. Archaea, fungi, and viruses exhibited more pronounced responses compared to bacteria. Higher doses of MPs and nZnO reduced gene abundance for nutrient cycles like C degradation and N cycling, but enhanced CO2 fixation and S metabolism. nZnO consistently decreased the complexity, connectivity, and modularity of microbial networks; however, these negative effects could be mitigated by co-existing MPs, particularly at elevated doses. Notably, PLA (10 %, w/w) exhibited greater harm to fungal communities and increased negative interactions between microbes and nutrient-cycling genes, posing unique risks compared to PE and PS. These findings demonstrate that MPs and nZnO interact synergistically, complicating ecological predictions and emphasizing the need to consider pollutant interactions in ecological risk assessments, particularly for biodegradable MPs.}, } @article {pmid40188455, year = {2025}, author = {Li, Z and Xu, H and Zhang, L and Zhou, Y}, title = {Genome-Resolved Metagenomic and Metatranscriptomics Reveal Feammox Metabolism of Anaerobic Ammonia Oxidation Bacteria in Microaerobic Granular Sludge.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c13580}, pmid = {40188455}, issn = {1520-5851}, abstract = {Anammox is an energy-efficient nitrogen removal process in which anammox bacteria (AnAOB) oxidize NH4[+]-N to N2 using NO2[-]-N as the electron acceptor. Recent evidence suggests that AnAOB can perform extracellular electron transfer (EET), potentially coupling Fe(III) reduction with NH4[+]-N oxidation (Feammox). However, whether AnAOB directly participate in Feammox within complex wastewater treatment systems remains unclear. Here, we investigated the iron-mediated nitrogen metabolism pathways in a microaerobic granular sludge (MGS) reactor by integrating enzyme inhibition assays with analyses of gene dynamics and co-occurrence patterns of nitrogen- and iron-cycling genes. Results demonstrate that AnAOB contributed to Feammox activity. The iron reduction gene CT573071, coding a porin-cytochrome c protein complex associated with EET, co-occurred with hao, hzsABC, and hdh genes in Candidatus Kuenenia, suggesting its role in Feammox. Furthermore, four high-quality metagenome-assembled genomes (MAGs) affiliated with Kuenenia stuttgartiensis_A harbored CT573071, hao-like, hzsABC, and hdh genes, along with the hao-cluster, which catalyzes the oxidation of NH4[+]-N to hydroxylamine. This genomic evidence further supports their dual metabolic capacity. Metatranscriptomic analysis confirmed CT573071 upregulation and its coexpression with the hao, hzsABC, and hdh genes. These findings establish the potential role of K. stuttgartiensis_A in Feammox, providing novel insights into nitrogen removal in low-strength wastewater treatment systems.}, } @article {pmid40187695, year = {2025}, author = {Palumbo, S and Lucarelli, G and Lasorsa, F and Damiano, R and Autorino, R and Aveta, A and Spena, G and Perdonà, S and Russo, P and Giulioni, C and Cafarelli, A and Finati, M and Siracusano, S and Pandolfo, SD}, title = {Urobiome and Inflammation: A Systematic Review on Microbial Imbalances and Diagnostic Tools for Urinary Disorders.}, journal = {Urology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.urology.2025.03.050}, pmid = {40187695}, issn = {1527-9995}, abstract = {OBJECTIVE: To synthesize current knowledge on urobiome alterations, innovative diagnostic advancements, and emerging therapeutic strategies targeting urobiome dysbiosis in inflammatory urinary tract disorders, including urinary tract infections (UTIs), non-gonococcal urethritis (NGU), and interstitial cystitis.

METHODS: A systematic review was conducted by screening the most important scientific databases. The search included the keywords: (microbiome) OR (microbial) OR (bacteria) OR (bacterial profile) AND (urine) OR (urinary) AND (first-morning sample) OR (first void). Only original studies in English involving human specimens were considered.

RESULTS: Of the 760 articles initially identified, a final sample of 20 original studies met the inclusion criteria. Disruptions in the urobiome composition were associated with increased colonization by pathogens such as Escherichia coli and Mycoplasma genitalium, resulting in inflammation and recurrent urinary conditions. Advanced diagnostic techniques, including metaproteomics, metagenomics, and point-of-care assays like NG-LFA, demonstrated enhanced capabilities for rapid pathogen detection and differentiation of inflammatory conditions. Therapeutic interventions targeting urobiome dysbiosis, particularly probiotics (Lactobacillus rhamnosus, L. reuteri, L. crispatus), showed promising efficacy in reducing recurrence and inflammation in clinical trials.

CONCLUSIONS: Urobiome dysbiosis plays a critical role in inflammatory urinary tract disorders. Innovative diagnostic methods and targeted therapeutic approaches, especially probiotics, offer substantial potential to improve patient outcomes. Further research is warranted to refine these strategies and validate their clinical applicability.}, } @article {pmid40187301, year = {2025}, author = {Peng, Q and Wu, Z and Qian, D and Ren, H and Xie, G}, title = {Comprehensive multi-omics analysis of secondary distillate from fermented Huangjiu residue: Insights into flavor formation and microbial dynamics.}, journal = {Food chemistry}, volume = {482}, number = {}, pages = {144145}, doi = {10.1016/j.foodchem.2025.144145}, pmid = {40187301}, issn = {1873-7072}, abstract = {Huangjiu residue distillate, or Zaoshao, is a traditional Chinese liquor produced from the fermentation and distillation of Huangjiu lees. This study investigates the fermentation mechanisms and flavor formation of secondary Zaoshao, derived from the second round of Huangjiu lees fermentation, using flavoromics, amino acid and organic acid profiling, and metagenomics. Flavoromics identified ethyl octanoate, ethyl decanoate, ethyl dodecanoate, ethyl hexadecanoate, and ethyl (Z)-octadec-9-enoate as key flavor compounds. Amino acid and organic acid profiling showed continuous increases in amino acid content and significant changes in organic acids during fermentation. Metagenomics identified 9 dominant genera and 10 key species, with Saccharomyces, Saccharopolyspora, Aspergillus, Streptomyces, and Bacillus playing crucial roles in fermentation and flavor formation. These findings provide insights into microbial community functions and offer a foundation for regulating microbial consortia to enhance the flavor quality of secondary Zaoshao.}, } @article {pmid40187295, year = {2025}, author = {Coskuner-Weber, O and Alpsoy, S and Yolcu, O and Teber, E and de Marco, A and Shumka, S}, title = {Metagenomics studies in aquaculture systems: Big data analysis, bioinformatics, machine learning and quantum computing.}, journal = {Computational biology and chemistry}, volume = {118}, number = {}, pages = {108444}, doi = {10.1016/j.compbiolchem.2025.108444}, pmid = {40187295}, issn = {1476-928X}, abstract = {The burgeoning field of aquaculture has become a pivotal contributor to global food security and economic growth, presently surpassing capture fisheries in aquatic animal production as evidenced by recent statistics. However, the dense fish populations inherent in aquaculture systems exacerbate abiotic stressors and promote pathogenic spread, posing a risk to sustainability and yield. This study delves into the transformative potential of metagenomics, a method that directly retrieves genetic material from environmental samples, in elucidating microbial dynamics within aquaculture ecosystems. Our findings affirm that metagenomics, bolstered by tools in big data analytics, bioinformatics, and machine learning, can significantly enhance the precision of microbial assessment and pathogen detection. Furthermore, we explore quantum computing's emergent role, which promises unparalleled efficiency in data processing and model construction, poised to address the limitations of conventional computational techniques. Distinct from metabarcoding, metagenomics offers an expansive, unbiased profile of microbial biodiversity, revolutionizing our capacity to monitor, predict, and manage aquaculture systems with high accuracy and adaptability. Despite the challenges of computational demands and variability in data standardization, this study advocates for continued technological integration, thereby fostering resilient and sustainable aquaculture practices in a climate of escalating global food requirements.}, } @article {pmid40187264, year = {2025}, author = {Kwon, H and Li, B and Xu, M and Wang, Q and Maqbool, T and Lu, H and Winkler, M and Jiang, D}, title = {Minimizing byproduct formation in bioelectrochemical denitrification with anammox bacteria.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138110}, doi = {10.1016/j.jhazmat.2025.138110}, pmid = {40187264}, issn = {1873-3336}, abstract = {Autotrophic bioelectrochemical denitrification (BED) holds promise for nitrate remediation. However, the accumulation of byproducts such as NO2[-], N2O, and NH4[+], poses a significant challenge to effluent quality and climate adaptation. This study hypothesized that introducing anaerobic ammonium oxidation bacteria (anammox) to BED could alleviate this issue through synergy: a) anammox can utilize NH4[+] and NO2[-] from BED without producing N2O, as seen in canonical denitrification, and b) BED can recycle NO3[-] from the anammox anabolic pathway. Results showed that Anammox_BED reduced NO2[-] accumulation by two-thirds, lowered the relative abundance of N2O by 80 %, and eliminated NO. Metagenomic analysis revealed that the anammox species Ca. Brocadia sapporoensis tripled in abundance in the bulk sludge. Meanwhile, Pseudomonas stutzeri and Bosea robiniae, species capable of reducing nitrate via extracellular electron transfer (EET) and supplying NO2[-] to anammox, halved in relative abundance, while the abundance of Stenotrophomonas acidaminiphila, a non-EET, ammonia assimilation species, doubled following anammox introduction. Metatranscriptomic analysis found upregulation of denitrification-related functional genes in Anammox_BED biofilm and survival- and motility- related genes in bulk sludge, possibly due to insufficient substrate. Overall, BED-Anammox successfully diverted the rate-limiting EET nitrite reduction towards anammox-driven nitrite utilization thereby mitigating the generation of unwanted intermediates.}, } @article {pmid40187012, year = {2025}, author = {Khan, MM and Mushtaq, MA and Suleman, M and Ahmed, U and Ashraf, MF and Aslam, R and Mohsin, M and Rödiger, S and Sarwar, Y and Schierack, P and Ali, A}, title = {Fecal microbiota landscape of commercial poultry farms in Faisalabad, Pakistan: A 16S rRNA gene-based metagenomics study.}, journal = {Poultry science}, volume = {104}, number = {6}, pages = {105089}, doi = {10.1016/j.psj.2025.105089}, pmid = {40187012}, issn = {1525-3171}, abstract = {This study explores the microbiota of broiler and layer farms, aiming to understand how genetic breed, age, and farm type influence microbial communities in commercial settings. Fecal samples from 18 poultry farms (twelve layers and six broilers) in Faisalabad, Pakistan were analyzed using 16S rRNA gene sequencing of the V3-V4 region to evaluate bacterial composition. The dominant phylum, Firmicutes, accounted for 58.72 % of the microbial population, with Lactobacillus being the most abundant genus in both broilers and layers. The total abundance of potentially pathogenic genera was also assessed with Enterococcus and Corynebacterium being the most prevalent across all farms, regardless of bird type. Layers exhibited greater microbial richness and diversity than broilers, while the Karachi cage system (KCS) farm type showed higher richness than Floor system (FS). Although the breed significantly influenced microbial diversity, age was not a determining factor. Co-occurrence analyses revealed close interactions among phyla (Actinobacteriota, Proteobacteria, Firmicutes, Fusobacteriota, and Bacteroidota) and genera (Lactobacillus, Brevibacterium, Enterococcus), suggesting their pivotal roles within the microbial community. Additionally, functional analysis detected important metabolic pathways and traced microbial signatures of key pathogenic bacteria, enhancing our understanding of microbial contributions to poultry health. Despite limitations such as the need for broader geographic sampling and accounting for diet and medication, this study advances microbiome research in Pakistan's poultry sector, emphasizing consistent taxa and opening avenues for future investigations into microbiome manipulations for improved food safety and achieve better sustainable practices.}, } @article {pmid40186063, year = {2025}, author = {Saveetha, K and Somala, CS and Anand, T and Balamurugan, D and Vasudevan, V and Saravanan, KM and Senthil, R}, title = {Impact of Soil Microbiomes on Mung Bean Cultivation: Insights from 16S rRNA Metagenomics.}, journal = {Molecular biotechnology}, volume = {}, number = {}, pages = {}, pmid = {40186063}, issn = {1559-0305}, abstract = {Cyclic nutrient processes, soil health maintenance, and plant development are contingent upon soil microbiomes. The microbial makeup of the soil of Maruthupandiyar College, Thanjavur, is assessed using 16S rRNA gene sequencing. QIIME2, in conjunction with the SILVA database, analyzed the sequencing data to examine microbial diversity and composition. The experimental results revealed a diverse array of bacteria in soil physicochemical properties. The alpha and beta diversity assessment revealed significant microbial community complexity and distribution patterns disparities. The research revealed bacterial groups associated with biological nitrogen fixing, suggesting their potential to enhance mung bean growth. The current study illustrates the significance of microbial interactions in soil for sustaining soil fertility and enhancing crop output. Research findings provide essential insights into improving the sustainability of tropical agriculture through intentional microbial management to create sustainable soil health systems.}, } @article {pmid40185904, year = {2025}, author = {Wang, D and Gui, S and Pu, J and Zhong, X and Yan, L and Li, Z and Tao, X and Yang, D and Zhou, H and Qiao, R and Zhang, H and Cheng, X and Ren, Y and Chen, W and Chen, X and Tao, W and Chen, Y and Chen, X and Liu, Y and Xie, P}, title = {PsycGM: a comprehensive database for associations between gut microbiota and psychiatric disorders.}, journal = {Molecular psychiatry}, volume = {}, number = {}, pages = {}, pmid = {40185904}, issn = {1476-5578}, support = {CSTB2024NSCQ-MSX1027//Natural Science Foundation of Chongqing (Natural Science Foundation of Chongqing Municipality)/ ; CSTB2024NSCQ-QCXMX0033//Natural Science Foundation of Chongqing (Natural Science Foundation of Chongqing Municipality)/ ; 82371526//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Psychiatric disorders pose substantial global burdens on public health, yet therapeutic options remain limited. Recently, gut microbiota is in the spotlight of new research on psychiatric disorders, as emerging discoveries have highlighted the importance of gut microbiome in the regulation of central nervous system via mediating the gut-brain-axis bidirectional communication. While metagenomics studies have accumulated for psychiatric disorders, few systematic efforts were dedicated to integrating these high-throughput data across diverse phenotypes, interventions, geographical regions, and biological species. To present a panoramic view of global data and provide a comprehensive resource for investigating the gut microbiota dysbiosis in psychiatric disorders, we developed the PsycGM, a manually curated and well-annotated database that provides the literature-supported associations between gut microbiota and psychiatric disorders or intervention measures. In total, PsycGM incorporated 559 studies from 31 countries worldwide, encompassing research involving humans, rats, mice, and non-human primates. PsycGM documented 8907 curated associations between 1514 gut microbial taxa and 11 psychiatric disorders, as well as 4050 associations between 869 taxa and 232 microbiota-based and non-microbiota-based interventions. Moreover, PsycGM provided a user-friendly web interface with comprehensive information, enabling browsing, retrieving and downloading of all entries. In the application of PsycGM, we panoramically depicted the intestinal microecological imbalance in depression. Additionally, we identified 9 microbial taxa consistently altered in patients with depression, with the most common dysregulations observed for Parabacteroides, Alistipes, and Faecalibacterium; in animal models of depression, consistent changes were observed in 21 microbial taxa, most frequently reported as Helicobacter, Lactobacillus, Roseburia, and the ratio of Firmicutes/Bacteroidetes. PsycGM is a comprehensive resource for future investigations on the role of gut microbiota in mental and brain health, and for therapeutic target innovations based on modifications of gut microbiota. PsycGM is freely accessed at http://psycgmomics.info .}, } @article {pmid40185827, year = {2025}, author = {Chornchoem, P and Tandhavanant, S and Saiprom, N and Preechanukul, A and Thongchompoo, N and Sensorn, I and Chantratita, W and Chantratita, N}, title = {Metagenomic evaluation, antimicrobial activities, and immune stimulation of probiotics from dietary supplements and dairy products.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {11537}, pmid = {40185827}, issn = {2045-2322}, support = {220211/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Probiotics/pharmacology ; *Dietary Supplements/microbiology ; *Dairy Products/microbiology ; *Metagenomics/methods ; Humans ; Lactobacillus/genetics ; Killer Cells, Natural/immunology/drug effects ; Bifidobacterium/genetics ; Animals ; Macrophages/immunology/drug effects ; Anti-Bacterial Agents/pharmacology ; Cytokines/metabolism ; Mice ; }, abstract = {Probiotics are widely marketed as dietary supplements and dairy products for their purported antimicrobial and immunomodulatory activities, often with limited supporting evidence. We identified and isolated probiotics from commercial dietary supplements and dairy products using metagenomics and cultured-based methods. We assessed their anti-bacterial activity against diverse pathogens and investigated their immunomodulatory effects on phagocytes and natural killer (NK) cells. Metagenomic analysis revealed that Lactobacillus and Bifidobacterium were the predominant genera in dietary supplements, while Streptococcus spp. was dominated in dairy products. However, only 37% of the predominant microorganisms identified by metagenomics were accurately listed on product labels. Among 70 representative probiotic strains, 4.3-17.1% probiotic strains demonstrated strong antibacterial-effects against pathogenic bacteria. Notably, specific strains of Bifidobacterium longum and Lactobacillus plantarum exhibited strong antagonistic activity against extended-spectrum beta-lactamase-producing and carbapenem-resistant Escherichia coli. Some strains of Lactobacillus spp. significantly enhanced phagocytic activity in monocytes and increased IFN-γ production in NK cells, while members of Lactobacillus rhamnosus significantly suppressed TNF-α, IL-6, and IL-8 production in lipopolysaccharide-stimulated macrophages. In contrast, Bifidobacterium animalis stimulated the production of anti-inflammatory cytokines. This study highlights discrepancies in probiotic labeling and demonstrates the antimicrobial and immunomodulatory potential of specific probiotic strains, suggesting their utility in enhancing health and wellness.}, } @article {pmid40185819, year = {2025}, author = {Manzoor, M and Leskelä, J and Pietiäinen, M and Martinez-Majander, N and Könönen, E and Sinisalo, J and Putaala, J and Pussinen, PJ and Paju, S}, title = {Oral microbiome dysbiosis in cryptogenic ischemic stroke patients with high-risk patent foramen ovale.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {11535}, pmid = {40185819}, issn = {2045-2322}, support = {286246//Research Council of Finland/ ; 340750//Research Council of Finland/ ; 355532//Research Council of Finland/ ; TYH2014407//Helsinki and Uusimaa Hospital District/ ; TYH2018318//Helsinki and Uusimaa Hospital District/ ; }, mesh = {Humans ; *Foramen Ovale, Patent/complications/microbiology ; Female ; Male ; *Ischemic Stroke/microbiology/etiology/complications ; *Dysbiosis/microbiology/complications ; *Microbiota ; Adult ; Middle Aged ; Saliva/microbiology ; Case-Control Studies ; *Mouth/microbiology ; Risk Factors ; }, abstract = {Patent foramen ovale (PFO) is the most common congenital heart abnormality of foetal origin and has been associated with cryptogenic ischemic stroke (CIS) through several mechanisms, with most theories supporting paradoxical embolism. Other possible but unknown contributing factors, such as the role of the microbiome in PFO-associated strokes, remain unclear. We analysed saliva metagenomes to study the differences in the oral microbiome between young-onset CIS patients with clinically relevant high-risk PFO (n = 52) and those without PFO (n = 52). Age- and sex-matched stroke-free controls (n = 16) with high-risk PFO were included for the comparison. Beta diversity was significantly different between patients and controls with high-risk PFO, but not between patients with and without high-risk PFO. The phylum Ascomycota and class Saccharomycetes were significantly more abundant in patients with high-risk PFO than in those without high-risk PFO. Additionally, the abundance of Lactococcus, including Lactococcus raffinolactis and L. cremoris, was higher in controls with high-risk PFO than in patients with high-risk PFO. These findings highlight that oral dysbiosis and high-risk PFO may form a critical but under-recognized combination in the aetiology of CIS. Future research should focus on elucidating the precise mechanisms of these interactions and developing targeted interventions.}, } @article {pmid40185271, year = {2025}, author = {Guajardo-Leiva, S and Díez, B and Rojas-Fuentes, C and Chnaiderman, J and Castro-Nallar, E and Catril, V and Ampuero, M and Gaggero, A}, title = {From sewage to genomes: expanding our understanding of the urban and semi-urban wastewater RNA virome.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121509}, doi = {10.1016/j.envres.2025.121509}, pmid = {40185271}, issn = {1096-0953}, abstract = {Wastewater is a hotspot for viral diversity, harboring various microbial, plant, and animal viruses, including those that infect humans. However, the dynamics, resilience, and ecological roles of viral communities during treatment are largely unknown. In this study, we explored RNA virus ecogenomics using metagenomics from influent and effluent samples across three wastewater catchment areas in Chile, with a population of 7.05 million equivalent inhabitants. We identified 14,212 RNA-dependent RNA polymerase (RdRP)-coding sequences from the Orthornavirae kingdom, clustering into 4,989 viral species. Using extensive databases of 14,150 family-level representative sequences, we classified 90% of our sequences at the family level. Our analysis revealed that treatment reduced viral richness and evenness (Shannon index), but phylogenetic diversity remained unchanged. Effluents showed lower richness and evenness than influents with similar phylogenetic diversity. Species turnover, influenced by catchment area and treatment, accounted for 54% of sample dissimilarities (Weighted Unifrac). Biomarker analysis indicated that families like Astroviridae and Fiersviridae were more abundant in influents, while Reoviridae and Virgaviridae dominated effluents. This suggests that viral resistance to treatment varies and cannot be solely attributed to genome type, size, or morphology. We traced viral genomes through time and space, identifying sequences like the Pepper Mild Mottle Virus (PMMoV) from the Virgaviridae family over large distances and periods, highlighting its wastewater marker potential. High concentrations of human pathogens, such as Rotavirus (Reoviridae) and Human Astrovirus (Astroviridae), were found in both influents and effluents, stressing the need for continuous monitoring, especially for treated wastewater reuse.}, } @article {pmid40185197, year = {2025}, author = {Jiang, Y and Yang, J and Liu, Y and Liu, Y and Zhou, W and Yang, B and Hu, B and Wu, H}, title = {A Neonate with Meningitis Caused by probiotic-related Clostridium butyricum.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {107900}, doi = {10.1016/j.ijid.2025.107900}, pmid = {40185197}, issn = {1878-3511}, abstract = {Clostridium butyricum (C. butyricum), a normal gut bacterium in humans, is commonly used as a probiotic. We described a 26-day-old premature neonate who was diagnosed with probiotic-related C. butyricum meningitis. Upon the admission, suppurative meningitis was considered based on cerebrospinal fluid (CSF) biochemical test and neuroimaging examination, and C. butyricum was subsequently identified by CSF metagenomic next-generation sequencing. Given the history of administrating living C. butyricum products before admission, probiotics-associated suppurative meningitis was considered a high possibility, leading to the confirmation of anti-infection treatment including vancomycin and meropenem. Following this therapy, the infant's CSF profiles demonstrated improvement. Additionally, further phylogenetic analysis confirmed the high homologous of C. butyricum from CSF with probiotics. This is the first report of C. butyricum infection in neonates, highlighting the importance for prudence in administrating probiotics for neonates, particularly in high-risk groups such as preterm infants, those with central venous catheters and intestinal diseases.}, } @article {pmid40185186, year = {2025}, author = {Liu, Y and Pei, Y and Wang, H and Yang, Z}, title = {Lead promoted bile acid deconjugation by modulating gut bacteria encoding bile salt hydrolase (BSH) in Rana chensinensis tadpoles.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {126187}, doi = {10.1016/j.envpol.2025.126187}, pmid = {40185186}, issn = {1873-6424}, abstract = {Bile salt hydrolase (BSH) is produced by gut bacteria and is responsible for deconjugating amino acids from the aliphatic side chains of conjugated bile acids (BAs), initiating the critical first step in BAs metabolism. Lead (Pb) is known to cause gut microbial dysbiosis, but whether it affects BAs profiles by reshaping the gut microbiota remains elusive. Here, using targeted BAs metabolomics and metagenomics sequencing, we found that 200 μg/L Pb treatment led to a significant increase in the abundance of BSH-producing microbiota (e.g., Eubacterium and Yersinia), thus promoting the deconjugation of taurocholic acid (TCA) and taurochenodeoxycholic acid (TCDCA). Consequently, the accumulation of relatively hydrophobic BAs cholic acid (CA) and chenodeoxycholic acid (CDCA) may cause damage to enterocytes (e.g., reduced microvilli and enterocyte heights), which attenuated tadpole digestion and ultimately led to significant reductions in morphological parameters. The inhibition of tadpole growth by Pb toxicity may negatively affect their survival and even increase their risk of death. Overall, these results revealed for the first time the toxicological mechanism by which Pb reshapes the gut microbiota and thus disrupts the BAs profile, shedding new insights into the detrimental effects of Pb toxicity on amphibian growth.}, } @article {pmid40185016, year = {2025}, author = {Yang, M and Yang, H and Wang, W and Fang, H and Huang, L and Li, D and Fu, L and Ding, S and Li, XD and Liu, CQ and Wei, G and Li, D and Cui, G and Fan, Z and Zeng, F}, title = {Impact of particle-attached microbial denitrification on N2O production in an agricultural-urban watershed.}, journal = {Journal of environmental management}, volume = {381}, number = {}, pages = {125223}, doi = {10.1016/j.jenvman.2025.125223}, pmid = {40185016}, issn = {1095-8630}, abstract = {Anthropogenically influenced rivers are key hotspots for nitrous oxide (N2O) emissions. However, the seasonal and spatial heterogeneity of N2O emissions in subtropical riverine systems, particularly the role of particle-attached microbes (PAM) in regulating N2O production, remains poorly understood, contributing to uncertainties in global N2O estimates. This study investigates the potential impacts of PAM-driven nitrogen transformations on N2O production in the Dongjiang River under agricultural and urban influences. Water samples collected during the wet and dry seasons were analyzed for N2O concentrations, dual nitrogen-oxygen isotopes (δ[15]N-NO3[-], δ[18]O-NO3[-]), and metagenomic sequencing of PAM. All samples exhibited N2O supersaturation, with emissions significantly higher in the dry season than in the wet season. A linearly positive δ[15]N-δ[18]O correlation, accompanied by lower NO3[-] in the bottom layers than the surface layers in the dry season indicates active denitrification, leading to elevated N2O concentrations. PAM-driven denitrification was identified as the dominant nitrogen transformation process, supported by higher abundances of denitrification genes (nirKS, norBC, nosZ) relative to nitrification genes (amoABC). Despite aerobic water column conditions, low-oxygen microhabitats around suspended particles facilitated N2O production. A significantly positive correlation (p < 0.05, R[2] = 0.42) between N2O concentrations and the nirK/nosZ gene ratio suggests that gene expression imbalances contributed to net N2O accumulation. Additionally, the downstream urban area exhibited lower DO and higher DOC levels, enhancing denitrification and increasing N2O production by 4.7 % compared to the upstream agricultural region. Seasonal differences further influenced N2O dynamics: higher DOC/NO3[-] ratios in the dry season promoted heterotrophic denitrification, while elevated temperatures in the wet season favored complete denitrification, reducing N2O emissions. These findings provide critical insights into PAM-driven nitrogen cycling, informing strategies for mitigating N2O emissions and managing nitrogen pollution in subtropical riverine systems.}, } @article {pmid40184966, year = {2025}, author = {Tu, M and Lin, H and Zhang, X and Zhang, X and Yan, J}, title = {Elemental sulfur facilitates co-metabolism of Cr(VI) and nitrate by autotrophic denitrifiers in constructed wetlands.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138153}, doi = {10.1016/j.jhazmat.2025.138153}, pmid = {40184966}, issn = {1873-3336}, abstract = {The antagonistic microbial reduction of chromate and nitrate poses significant challenges for their simultaneous removal in autotrophic denitrifying systems. This study explored the treatment performance and mechanisms for the simultaneous removal of chromate (0, 2, and 10 mg·L[-1]) and nitrate (20 mg·L[-1]) in constructed wetland (CW) microcosms with elemental sulfur additions at 0-, 5-, and 25-times background levels. Results showed that sulfur-amended microcosms achieved chromate and nitrate removal up to 76.46 % and 28.12 % higher, respectively, than 0S groups. Notably, the nitrate removal rate constant was higher in the presence of chromate than its absence, exclusively in the 25S groups. In a sediment core assay, the 25S groups also exhibited substantially facilitating effect of chromate removal potential in the presence of nitrate. Metagenomic analyses revealed upregulations of denitrification and sulfur oxidation-related functional genes along with sulfur supplementation. Autotrophic denitrifiers including Dechloromonas, Thiobacillus, Sulfuricella, and Sulfuritalea made significant contributions to chromate and nitrate removal rates, as well as functional genes encoding sulfur, nitrogen, and chromium transformation, in response to sulfur addition. These findings shed first light on the co-metabolism of chromate and nitrate by sulfur-based autotrophic denitrifiers, emphasizing their pivotal role in denitrification systems, e.g., CWs, with chromate inputs.}, } @article {pmid40184824, year = {2025}, author = {Zhu, H and Mao, X and Sajnani, S and Yang, H and Li, T and Tan, S}, title = {Psychrophilic insights into petroleum degradation: Gene abundance dynamics.}, journal = {Enzyme and microbial technology}, volume = {188}, number = {}, pages = {110642}, doi = {10.1016/j.enzmictec.2025.110642}, pmid = {40184824}, issn = {1879-0909}, abstract = {Petroleum degradation by psychrophiles can be enhanced on the basis of omics analyses, which offer better sensitivity than traditional biochemical methods do. A metagenomic analysis focusing on gene abundance comparisons may provide new guidance to optimize soil decontamination under cold environmental conditions. The soil used in this study was sampled from Dalian, from which an indigenous consortium was isolated. The degradative soil systems, initially categorized into control (DLC) and experimental (DLD) groups, were kept at room temperature (20 ± 5 °C) for six weeks. The DLD group was subsequently transferred to a low-temperature environment (5-10 °C) for 90 days and renamed DDL. A petroleum removal rate of 74.59 % was achieved in the process from DLD to DDL groups. Each soil sample was subjected to analysis and metagenomic sequencing. The abundance of genes of interest was compared between pathways to determine trends. The findings demonstrate that psychrophilic degradation is more effective than natural remediation is. The soil microbial community structure displayed site specificity, with 802 genes in DDL associated with 249 pathways, indicating greater abundance of psychrophilic genes in DDL than in DLC. The abundance of key genes was at different orders of magnitude but showed similar trends. The abundance of genes associated with hydrocarbon-related metabolism surpassed that of genes associated with sphingolipid, fatty acid, or benzene metabolism. This study provides valuable insights into psychrophilic microbe-driven petroleum degradation and indicates the need for precise supplementation of biosurfactants to improve remediation efficiency.}, } @article {pmid40184708, year = {2025}, author = {He, D and Nong, Y and He, Y and Luo, Y and Li, C and Gao, J and Dang, C and Fu, J}, title = {Effect of pre-chlorination on bioelectricity production and stabilization of excess sludge by microbial fuel cell.}, journal = {Water research}, volume = {281}, number = {}, pages = {123564}, doi = {10.1016/j.watres.2025.123564}, pmid = {40184708}, issn = {1879-2448}, abstract = {Microbial fuel cell (MFC) is a technology that can generate electricity while degrading excess sludge. However, the complex components, intricate biological structures, and inhibitory compounds in sludge limit the application of MFC. Therefore, this study utilized chlorination as a sludge pretreatment method to improve the comprehensive performance of MFC in sludge treatment. Results showed that pre-chlorination at a dose of 0.2 mg/L increased output voltage of MFC by 500 % from approximately 100 mV to around 600 mV, and power density by 15.60 % from 3.15 W/m[3] to 3.64 W/m[3], and simultaneously increased the degradation of sludge MLSS (mixed liquor suspended solids), MLVSS (mixed liquor volatile suspended solids), EPS (extracellular polymeric substances) polysaccharide and protein by 9.64 %, 47.07 %, 18.63 % and 16.26 %, respectively. Molecular composition analysis of EPS in sludge by three-dimensional excitation emission matrix fluorescence spectroscopy (3D-EEM), Fourier transform infrared spectroscopy (FTIR) and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) indicated pre-chlorination significantly promoted the molecular transformation in MFC. The microbiome analysis of anode biofilm in MFC by scanning electron microscopy (SEM), confocal laser scanning microscopy (CLSM), metagenomics and metametabolomics revealed that pre-chlorination facilitated the development of biomass, enrichment of electricity-producing bacteria (EPB), enhancement of electricity-producing activity and metabolic activity. Moreover, the sludge EPS was the importance source for the microbial metabolites in MFC was validated by the joint analysis of FT-ICR-MS and metametabolomics.}, } @article {pmid40184705, year = {2025}, author = {Barrantes-Jiménez, K and Lejzerowicz, F and Tran, T and Calderón-Osorno, M and Rivera-Montero, L and Rodríguez-Sánchez, C and Wikmark, OG and Eiler, A and Grossart, HP and Arias-Andrés, M and Rojas-Jiménez, K}, title = {Anthropogenic imprint on riverine plasmidome diversity and proliferation of antibiotic resistance genes following pollution and urbanization.}, journal = {Water research}, volume = {281}, number = {}, pages = {123553}, doi = {10.1016/j.watres.2025.123553}, pmid = {40184705}, issn = {1879-2448}, abstract = {Plasmids are key determinants in microbial ecology and evolution, facilitating the dissemination of adaptive traits and antibiotic resistance genes (ARGs). Although the molecular mechanisms governing plasmid replication, maintenance, and transfer have been extensively studied, the specific impacts of urbanization-induced pollution on plasmid ecology, diversity, and associated ARGs in tropical regions remain underexplored. This study investigates these dynamics in a tropical aquatic ecosystem, providing novel insights into how pollution shapes plasmid composition and function. In contrast to the observed decrease in chromosomal diversity, we demonstrate that pollution associated with urbanization increases the diversity and taxonomic composition of plasmids within a bacterial community (plasmidome). We analyzed eighteen water and sediment metagenomes, capturing a gradient of pollution and ARG contamination along a tropical urban river. Plasmid and chromosomal diversity profiles were found to be anti-correlated. Plasmid species enrichment along the pollution gradient led to significant compositional differences in water samples, where differentially abundant species suggest plasmid maintenance within specific taxonomic classes. Additionally, the diversity and abundance of ARGs related to the plasmidome increased concomitantly with the intensity of fecal and chemical pollution. These findings highlight the critical need for targeted plasmidome studies to better understand plasmids' environmental spread, as their dynamics are independent of chromosomal patterns. This research is crucial for understanding the consequences of bacterial evolution, particularly in the context of environmental and public health.}, } @article {pmid40184632, year = {2025}, author = {Huang, Y and Mao, X and Zheng, X and Zhao, Y and Wang, D and Wang, M and Chen, Y and Liu, L and Wang, Y and Polz, MF and Zhang, T}, title = {Longitudinal dynamics and cross-domain interactions of eukaryotic populations in wastewater treatment plants.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf058}, pmid = {40184632}, issn = {1751-7370}, abstract = {Activated sludge is a large reservoir of novel microorganisms and microbial genetic diversity. While much attention has been given to the profile and functions of prokaryotes, the eukaryotic diversity remains largely unexplored. In this study, we analyzed longitudinal activated sludge samples spanning 13 years from the largest secondary wastewater treatment plants in Hong Kong, unveiling a wealth of eukaryotic taxa and 681 856 non-redundant protein-coding genes, the majority (416044) of which appeared novel. Ciliophora was the most dominant phylum with a significant increase after a transient intervention (bleaching event). Our metagenomic analysis reveals close linkage and covariation of eukaryotes, prokaryotes, and prokaryotic viruses (phages), indicating common responses to environmental changes such as transient intervention and intermittent fluctuations. Furthermore, high-resolution cross-domain relationships were interpreted by S-map, demonstrating a predatory role of Arthropoda, Ascomycota, Mucoromycota, and Rotifera. This high-resolution profile of microbial dynamics expands our knowledge on yet-to-be-cultured populations and their cross-domain interactions and highlights the ecological importance of eukaryotes in the activated sludge ecosystem.}, } @article {pmid40184383, year = {2025}, author = {Shen, C and Wedell, E and Pop, M and Warnow, T}, title = {TIPP3 and TIPP3-fast: Improved abundance profiling in metagenomics.}, journal = {PLoS computational biology}, volume = {21}, number = {4}, pages = {e1012593}, doi = {10.1371/journal.pcbi.1012593}, pmid = {40184383}, issn = {1553-7358}, mesh = {*Metagenomics/methods ; Algorithms ; *Software ; Computational Biology/methods ; Databases, Genetic ; Likelihood Functions ; Sequence Analysis, DNA/methods ; }, abstract = {We present TIPP3 and TIPP3-fast, new tools for abundance profiling in metagenomic datasets. Like its predecessor, TIPP2, the TIPP3 pipeline uses a maximum likelihood approach to place reads into labeled taxonomies using marker genes, but it achieves superior accuracy to TIPP2 by enabling the use of much larger taxonomies through improved algorithmic techniques. We show that TIPP3 is generally more accurate than leading methods for abundance profiling in two important contexts: when reads come from genomes not already in a public database (i.e., novel genomes) and when reads contain sequencing errors. We also show that TIPP3-fast has slightly lower accuracy than TIPP3, but is also generally more accurate than other leading methods and uses a small fraction of TIPP3's runtime. Additionally, we highlight the potential benefits of restricting abundance profiling methods to those reads that map to marker genes (i.e., using a filtered marker-gene based analysis), which we show typically improves accuracy. TIPP3 is freely available at https://github.com/c5shen/TIPP3.}, } @article {pmid40183829, year = {2025}, author = {Moscona, R and Wagner, T and Geva, M and Bucris, E and Erster, O and Zuckerman, NS and Mor, O}, title = {Newly designed amplicons-based method for near-full-length genome (NFLG) sequencing of HIV-1 group M recombinant forms.}, journal = {Molecular biology reports}, volume = {52}, number = {1}, pages = {362}, pmid = {40183829}, issn = {1573-4978}, mesh = {*HIV-1/genetics ; Humans ; *Genome, Viral/genetics ; Phylogeny ; HIV Infections/virology/genetics ; Recombination, Genetic/genetics ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Whole Genome Sequencing/methods ; Genotype ; }, abstract = {BACKGROUND: Over the years the spread of HIV-1 across the globe resulted in the creation of multiple subtypes and new recombinant forms (RFs). While the pol gene region of the HIV-1 genome is used for resistance mutations analysis and initial detection of RFs, whole genome sequencing analysis is required to determine recombination events across the viral genome. Here, we present a newly designed robust near-full length genome (NFLG) sequencing approach for the sequencing of HIV-1 genomes, out of clinical whole blood samples. This method has been successfully tested for various HIV-1 subtypes and RFs.

METHODS AND RESULTS: The method is based on an in-house developed set of 32 pan-genotypic primer pairs, divided into two pools, each containing 16 primer pairs covering the entire HIV-1 genome. Two parallel multiplex PCR reactions were used to generate 32 overlapping DNA fragments spanning the HIV-1 genome. Nextera XT protocol was used to obtain barcoded DNA libraries, which were sequenced with the Illumina Miseq platform using a V3 kit. A consensus sequence was determined for each sample and was used to define recombination events across the genome. For this aim, a combined analysis of several computational tools including HIV BLAST, phylogenetic analysis, RIP, SimPlot +  + and jpHMM were employed. Overall, plasma samples from 33 patients suspected to carry RFs and 2 different, known pure subtypes controls, were included in this study. Genome coverage varied between RFs, while the gag and pol genes were nearly fully covered, the highly variable env gene region was not. Yet, these NFLG analyses enabled the identification of recombination events genome wide.

CONCLUSIONS: In summary, we describe a methodology for HIV-1 NFLG sequencing, which is based on partially overlapping, multiple PCR fragments, spanning the HIV-1 genome. Additionally, this newly refined method was compared to HIV-1 NFLG results of PCR-free metagenomic sequencing and proved to obtain greater coverage of the HXB2 reference genome. Yet, further testing and validation on a larger cohort is required. Still, this method enables sequencing of 20 different patient samples in a single MiSeq sequencing run and was used for the characterization of different HIV-1 RFs and pure subtypes circulating in Israel.}, } @article {pmid40183042, year = {2025}, author = {Li, T and Shafiul Alam, M and Yang, Y and Mohammad Al-Amin, H and Rahman, M and Islam, F and Conte, MA and Price, DC and Hang, J}, title = {Metagenome analysis of viruses associated with Anopheles mosquitoes from Ramu Upazila, Cox's Bazar District, Bangladesh.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19180}, pmid = {40183042}, issn = {2167-8359}, mesh = {*Anopheles/virology ; Animals ; Bangladesh ; Phylogeny ; *Mosquito Vectors/virology ; *Metagenome ; Male ; Female ; High-Throughput Nucleotide Sequencing ; }, abstract = {Bangladesh has a warm climate and landscapes favourable for the proliferation of mosquitoes. Mosquito-borne pathogens including malaria and arthropod-borne viruses (arboviruses) remain a serious threat to the public health requiring constant vector control and disease surveillance. From November 2018 to April 2019, Anopheles mosquitoes were collected in three unions in the Ramu Upazila (sub-district) of Cox's Bazar District, Bangladesh. The mosquito specimens were combined into pools based on date of collection, household ID, and sex. Metagenome next-generation sequencing was conducted to elucidate diversity of virus sequences in each pool. Homology-based taxonomic classification and phylogenetic analyses identified a broad diversity of putative viruses from 12 known families, with additional unclassified viruses also likely present. Analysis of male mosquitoes showed some of these viruses are likely capable of being vertically transmitted. Moreover, many of the assembled virus sequences share homology and phylogenetic affinity with segments in sequenced Anopheles genomes, and may represent endogenous viral elements derived from a past evolutionary relationship between these putative viruses and their mosquito hosts.}, } @article {pmid40182804, year = {2025}, author = {Sarwar, A and Aslam, B and Mahmood, S and Muzammil, S and Siddique, AB and Sarwar, F and Khurshid, M and Rasool, MH and Sasanya, J and Aljasir, SF}, title = {Distribution of multidrug-resistant Proteus mirabilis in poultry, livestock, fish, and the related environment: One Health heed.}, journal = {Veterinary world}, volume = {18}, number = {2}, pages = {446-454}, doi = {10.14202/vetworld.2025.446-454}, pmid = {40182804}, issn = {0972-8988}, abstract = {BACKGROUND AND AIM: The emergence of multidrug-resistant (MDR) Proteus mirabilis in food-producing animals and their associated environments is a growing public health concern. The indiscriminate use of antimicrobials in animal husbandry exacerbates resistance development, posing significant threats to food safety and sustainability. This study investigates the distribution, antibiotic resistance patterns, and virulence-associated genes (VAGs) of P. mirabilis isolated from poultry, livestock, fish, and their environments in Pakistan under a One Health perspective.

MATERIALS AND METHODS: A total of 225 samples were collected from poultry (n = 100), livestock (n = 75), and aquatic sources (n = 50) from March 2023 to September 2024. Standard microbiological methods were employed for the isolation and identification of P. mirabilis. Polymerase chain reaction (PCR)-based detection of antibiotic resistance genes and VAGs was performed using specific primers. Antibiotic susceptibility was assessed through the disk diffusion method following Clinical and Laboratory Standards Institute 2022 guidelines. Statistical analyses, including analysis of variance and correlation models, were applied to assess the relationships between variables.

RESULTS: P. mirabilis was detected in 28.44% (64/225) of the total samples, with the highest occurrence observed in poultry (38%), followed by livestock (22.67%) and aquatic sources (18%). Resistance to ampicillin (100%), chloramphenicol (82%), cefepime (75%), and ciprofloxacin (75%) was widespread. PCR analysis revealed a high occurrence of extended-spectrum beta-lactamase-producing P. mirabilis carrying bla CTX-M (49%), bla OXA (54%), and bla TEM (25.67%) genes. In addition, VAGs such as zapA (39.53%), ucaA (34.88%), and hpmA (32.55%) were frequently identified. The presence of MDR P. mirabilis in fish and related environments (18%) is alarming, highlighting potential zoonotic and foodborne transmission risks.

CONCLUSION: The study underscores the widespread distribution of MDR P. mirabilis in animal-based food sources, raising significant concerns regarding food safety and antimicrobial resistance. The findings reinforce the need for stringent monitoring and regulatory policies to mitigate MDR bacterial dissemination across the food supply chain. Future research should employ metagenomic approaches for comprehensive surveillance and risk assessment.}, } @article {pmid40182766, year = {2025}, author = {Lazarevic, V and Gaïa, N and Pham, TT and de Lorenzi-Tognon, M and Girard, M and Mauffrey, F and Charretier, Y and Renzi, G and Huber, C and Schrenzel, J}, title = {Identification of causative agents of infective endocarditis by metagenomic next-generation sequencing of resected valves.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1532257}, doi = {10.3389/fcimb.2025.1532257}, pmid = {40182766}, issn = {2235-2988}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Male ; Middle Aged ; Female ; *Heart Valves/microbiology/surgery ; Sensitivity and Specificity ; Aged ; *Endocarditis/microbiology/diagnosis/surgery ; Prospective Studies ; *Bacteria/genetics/classification/isolation & purification ; DNA, Bacterial/genetics ; Adult ; Aged, 80 and over ; }, abstract = {BACKGROUND: Infective endocarditis (IE) is a rare and life-threatening condition with considerable mortality rates. Diagnosis is often complicated by negative blood culture results, limiting the accurate identification of causative pathogens. This study aimed to evaluate the effectiveness of metagenomic next-generation sequencing (mNGS) of cardiac valve specimens compared to conventional clinical laboratory methods for identifying pathogens in IE.

METHODS: Nineteen patients with suspected IE who were scheduled for surgical valve removal were prospectively enrolled. The metagenomic workflow included bacterial DNA enrichment from resected valves using the Molzym Ultra-Deep Microbiome Prep, sequencing of metagenomic libraries using the Illumina MiSeq platform, and Kraken 2 taxonomic assignments based on read data.

RESULTS: Valve mNGS achieved a sensitivity of 82.4% and a specificity of 100% relative to the final adjudicated pathogen diagnosis. Blood culture, considered the reference standard, exhibited slightly higher sensitivity (88.2%) with comparable specificity (100%). In comparison, valve culture (sensitivity: 29.4%, specificity: 50.0%) and microscopy (sensitivity: 35.3%, specificity: 100%) showed lower diagnostic performance. Delays between blood culture negativization and valve resection impacted mNGS sensitivity, likely due to pathogen clearance. Notably, valves resected within 12 days from blood culture negativization achieved 100% diagnostic accuracy, emphasizing the importance of timing for optimal mNGS results.

CONCLUSION: This study underscores mNGS as a valuable diagnostic tool for detecting IE pathogens, complementing traditional diagnostic methods. The detection of antibiotic resistance genes and multi-locus sequence typing profiles in some samples further demonstrated its utility.}, } @article {pmid40182295, year = {2025}, author = {Hou, J and Yin, H and Wang, D and Luo, J and Yang, W and Kang, T}, title = {The influence of rhizosphere soil microorganisms and environmental factors on gentiopicroside content in the roots and rhizomes of Gentiana scabra Bunge from Liaoning Province.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1554981}, doi = {10.3389/fmicb.2025.1554981}, pmid = {40182295}, issn = {1664-302X}, abstract = {BACKGROUND: Rhizosphere soil microorganisms, as the second genome of plants, play an important role in the formation of secondary metabolites of medicinal plants and are one of the key factors in the formation of the authenticity of medicinal materials.

METHODS: In this paper, the rhizosphere soils of Gentiana scabra Bunge from six producing areas in Liaoning Province were taken as the research objects. Through high-throughput sequencing technology, and with the help of PLS-DA and RDA, the impacts of rhizosphere soil microorganisms and environmental factors on the quality of G. scabra were explored in depth.

RESULTS: Alpha diversity shows that the diversity of bacterial communities varies significantly, while the regularity of fungi is weak; beta diversity shows that samples from different producing areas can be effectively grouped according to community structure. LDA effect shows that the differential species of bacteria and fungi vary among different producing areas. Indicator and random forest analysis show that Sphingomonas and Subgroup_2 are the main indicator species of the bacterial communities in the high-content group, which can increase the evenness of microbial communities and maintain or enhance species diversity. The regularity of fungal communities is relatively weak. Functional metagenomic analysis shows that the functions of soil microorganisms in the six producing areas are similar but the relative abundances are different. The main functions of bacteria are closely related to microbial metabolism in diverse environments, biosynthesis of secondary metabolites, metabolic pathways, etc.; fungi are mainly lichen parasite, plant saprotroph, and ericoid mycorrhizal. PLS-DA and RDA analysis show that properly adjusting the key environmental factors of Ca, pH, and rapidly available potassium, which have a great influence on G. scabra, can affect the abundances of microorganisms such as Subgroup_2, Burkholderia-Caballeronia-Paraburkholderia, Metarhizium, Bryobacter, Fusarium, Rhodanobacter, Cladophialophora, Sphingomonas and Trichoderma, and then regulate the content of gentiopicroside.

DISCUSSION: This study provides practical microbial approaches and strategies for improving gentiopicroside content in the roots and rhizomes of G. scabra, and lays a solid scientific foundation for ensuring the quality and safety of genuine medicinal materials and the stable and sustainable development of the G. scabra planting industry.}, } @article {pmid40182288, year = {2025}, author = {Lin, TS and Zhu, Z and Lin, X and Huang, HY and Li, LP and Li, J and Ni, J and Li, P and Chen, L and Tang, W and Liu, H and Se, X and Xie, M and Long, C and Chiu, CM and Fang, SH and Zhao, J and Lin, YC and Yu, X and Huang, HD}, title = {Enhancing bloodstream infection diagnostics: a novel filtration and targeted next-generation sequencing approach for precise pathogen identification.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1538265}, doi = {10.3389/fmicb.2025.1538265}, pmid = {40182288}, issn = {1664-302X}, abstract = {Bloodstream infections (BSIs) pose a significant diagnostic challenge, largely due to the limitations of traditional methods such as blood cultures. These methods often yield low positive rates, have lengthy processing times that delay treatment, and are limited in detecting only a narrow range of pathogens. Such delays and inaccuracies can critically impede timely clinical interventions, potentially compromising patient outcomes. Next-generation sequencing (NGS) is a powerful tool for rapid, precise pathogen identification. While metagenomic NGS (mNGS) offers broad pathogen coverage, it is often costly and complex. Targeted NGS (tNGS), however, focuses on key regions of clinically relevant pathogens, reducing costs and simplifying workflows while maintaining high sensitivity, making it more practical for routine diagnostics. In this study, we introduce a novel approach combining a human cell-specific filtration membrane with a multiplex tNGS panel to overcome these challenges. The filtration membrane, designed with surface charge properties to be electrostatically attractive to leukocytes for the selective capture of specific cells, demonstrated high efficiency in removing host cells and nucleic acids, achieving over a 98% reduction in host DNA and thereby minimizing background interference in pathogen detection. Additionally, we developed an effective multiplex tNGS panel targeting over 330 clinically relevant pathogens and verified its consistency with mNGS and blood culture results, demonstrating a significant improvement in detection sensitivity. By integrating these two methods, we achieved a synergistic enhancement in diagnostic capability, boosting pathogen reads by 6- to 8-fold, which enabled reliable identification even in cases of low-abundance pathogens. This approach provides faster, more accurate, and more sensitive detection of BSIs, enabling earlier identification of infections. This facilitates timely and targeted treatment, ultimately improving patient outcomes in critical care settings. Given the unique properties of the filtration membrane and the strengths of the tNGS panel, this approach shows promising applications in prenatal and genetic health support, as well as in advancing early cancer screening strategies.}, } @article {pmid40182062, year = {2025}, author = {Simon, SA and Soares, AR and Bornemann, TLV and Lange, A and Griesdorn, L and Fuentes, A and Dieckmann, M and Krok, BA and Ruff, SE and Hügler, M and Moraru, C and Probst, AJ}, title = {Inferring replication states of bacteria and viruses in enrichment cultures via long-read sequencing.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf041}, doi = {10.1093/ismeco/ycaf041}, pmid = {40182062}, issn = {2730-6151}, abstract = {Most microorganisms cannot be cultured in isolation, necessitating sophisticated methods for studying their (eco)physiology. While numerous approaches can probe the activity of given microbes in enrichment cultures, no single technique can render simultaneous data on both metabolic capacities and mobile genetic elements. Here, we apply long-read sequencing to monitor the incorporation of non-canonical bases in genome-resolved metagenomic datasets and elucidate the replication patterns of both bacteria and phages. This technology enables the simultaneous reconstruction of both prokaryotic and viral genomes (alongside genomics downstream analyses like metabolic predictions), in addition to providing information regarding their replication in enrichment cultures. By spiking the base analog 5-bromo-2'-deoxyuridine (BrdU) into activated sludge microcosms, we determined that 114 of the 118 high-quality genomes recovered were actively replicating in enrichment cultures from activated sludge and identified both slow (low BrdU incorporation and change in abundance) and rapidly replicating organisms (high BrdU incorporation and change in abundance). Some of the genomes detected exhibited regions rich in BrdU that were predicted to represent prophages in their lytic cycle. Ultimately, this novel means of monitoring the replication responses of microbes, and deciphering their genomes and active mobile genetic elements will advance and empower strategies aimed at isolating previously uncultivated microbes in pure culture.}, } @article {pmid40182061, year = {2025}, author = {Cheung, S and Morando, M and Magasin, J and Cornejo-Castillo, FM and Zehr, JP and Turk-Kubo, KA}, title = {NifH gene amplicon sequencing and metagenomic approaches are complementary in assessing diazotroph diversity.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf038}, doi = {10.1093/ismeco/ycaf038}, pmid = {40182061}, issn = {2730-6151}, abstract = {Exploring the diversity of diazotrophs is key to understanding their role in supplying fixed nitrogen that supports marine productivity. A nested PCR assay using the universal primer set nifH1-nifH4, which targets the nitrogenase (nifH) gene, is a widely used approach for studying marine diazotrophs by amplicon sequencing. Metagenomics, direct sequencing of DNA without PCR, has provided complementary views of the diversity of marine diazotrophs. A significant fraction of the metagenome-derived nifH sequences (e.g. Planctomycete- and Proteobacteria-affiliated) were reported to have nucleotide mismatches with the nifH1-nifH4 primers, leading to the suggestion that nifH amplicon sequencing does not detect specific diazotrophic taxa and underrepresents diazotroph diversity. Here, we report that these mismatches are mostly located in a single-base at the 5'-end of the nifH4 primer, which does not impact detection of the nifH genes. This is demonstrated by the presence of nifH genes that contain the nucleotide mismatches in a recent compilation of global ocean nifH amplicon datasets, with high relative abundances detected in a variety of samples. While the metagenome- and metatranscriptome-derived nifH genes accounted for 4.4% of the total amplicon sequence variants from the global ocean nifH amplicon database, the corresponding amplicon sequence variants can have high relative abundances (accounting for 47% of the reads in the database). These analyses underscore that nifH amplicon sequencing using the nifH1-nifH4 primers is an important tool for studying diversity of marine diazotrophs, particularly as a complement to metagenomics which can provide taxonomic and metabolic information for some dominant groups.}, } @article {pmid40181528, year = {2025}, author = {Sun, Q and Teng, R and Shi, Q and Liu, Y and Cai, X and Yang, B and Cao, Q and Shu, C and Mei, X and Zeng, W and Hu, B and Zhang, J and Qiu, H and Liu, L}, title = {Clinical implement of Probe-Capture Metagenomics in sepsis patients: A multicentre and prospective study.}, journal = {Clinical and translational medicine}, volume = {15}, number = {4}, pages = {e70297}, doi = {10.1002/ctm2.70297}, pmid = {40181528}, issn = {2001-1326}, support = {2022YFC2504405//National Key Research and Development Program of China/ ; 82341032//National Natural Science Foundation of China/ ; 81930058//National Natural Science Foundation of China/ ; 82270083//National Natural Science Foundation of China/ ; LGY2022025//Second Level Talents of the '333 High Level Talents Training Project' in the sixth phase in Jiangsu/ ; ZDXYS202205//Jiangsu Provincial Medical Key Laboratory/ ; HMJH-2020-0005//Hongmian Plan' Project of Guangzhou/ ; }, mesh = {Humans ; *Sepsis/diagnosis/microbiology/blood/drug therapy ; *Metagenomics/methods ; Male ; Female ; Prospective Studies ; Aged ; Middle Aged ; Blood Culture/methods ; }, abstract = {BACKGROUND: Accurate pathogen identification is critical for managing sepsis. However, traditional microbiological methods are time-consuming and exhibit limited sensitivity, particularly with blood samples. Metagenomic sequencing of plasma or whole blood was highly affected by the proportion of host nucleic acid.

METHODS: We developed a Probe-Capture Metagenomic assay and established a multicentre prospective cohort to assess its clinical utility. In this study, 184 blood samples from patients suspected of sepsis were sent for blood culture and Probe-Capture Metagenomic sequencing before using antibiotics. The pathogen-positive rate and auxiliary abilities in diagnosis were compared among Probe-Capture Metagenomics, blood culture and real-time PCR (RT-PCR). Antibiotic therapy adjustments were based on the identification of pathogens, and changes in the Sequential Organ Failure Assessment (SOFA) score were monitored on days 0, 3 and 7 of admission.

RESULTS: A total of 184 sepsis patients were enrolled, with a mean age of 66 years (range 56-74). The Probe-Capture Metagenomics method, confirmed by RT-PCR, demonstrated a significantly higher pathogen detection rate than blood culture alone (51.6% vs. 17.4%, p < .001). When combining the results of blood culture and RT-PCR, Probe-Capture Metagenomics achieved a concordance rate of 91.8% (169/184), with a sensitivity of 100% and specificity of 87.1%. In terms of clinical impact, antibiotic therapy was adjusted for 64 patients (34.8%) based on the results from Probe-Capture Metagenomics, and 41 patients (22.3%) showed a > 2-point decrease in SOFA score following antibiotic adjustments.

CONCLUSION: Probe-Capture Metagenomics significantly enhances the ability of pathogen detection compared with traditional metagenomics. Compared to blood culture and RT-PCR in sepsis patients, it leads to improved antibiotic treatment and better patient outcomes. This study, for the first time, evaluates the clinical impact of metagenomic sequencing by integrating antibiotic adjustments and SOFA score changes, indicating that approximately one-fifth of sepsis patients benefit from this advanced diagnostic approach.

TRIAL REGISTRATION: This study has been registered in clinical trials (clinicaltrials.gov) on 30 November 2018, and the registration number is NCT03760315.

KEY POINTS: Probe-Capture Metagenome had a significantly higher positive rate than blood culture (51.6% vs. 17.4%, p < .001). Combining blood culture and RT-PCR results, Probe-Capture Metagenome achieved a consistency rate of 91.8%. Antibiotics were adjusted in 34.8% of patients based on Probe-Capture Metagenome results, and 22.3% of patients experienced a more than 2-point decrease in SOFA score.}, } @article {pmid40181443, year = {2025}, author = {Xu, F and Chen, C and Lu, S and Xue, M and Ding, H and Song, Y and Zhang, Y and Sun, K and Tang, L and Wang, W and Wang, M and Tang, Y and Tan, D and Yao, C and Shi, D and Mao, E and Shao, M and Ying, Y and Zhou, C and Huang, L and Peng, H and Kuang, Z and Wang, S and Ma, Q and Sun, S and Guo, D and Gu, T and Yang, B and Ma, L and Gao, C and Lu, X and Zhang, H and Wang, R and Tong, C and Song, Z}, title = {Impact of metagenomics next-generation sequencing on etiological diagnosis and early outcomes in sepsis.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {394}, pmid = {40181443}, issn = {1479-5876}, support = {2021YFC2501800//Key Technologies Research and Development Program/ ; 2023YFC0872500//Key Technologies Research and Development Program/ ; 2023YFC3043507//Key Technologies Research and Development Program/ ; 82072214//National Natural Science Foundation of China/ ; 23Y31900100//Science and Technology Commission of Shanghai Municipality/ ; 21MC1930400//Science and Technology Commission of Shanghai Municipality/ ; PWYts2021-17//Shanghai Pudong New Area Health Commission/ ; }, mesh = {Humans ; *Sepsis/diagnosis/microbiology/etiology/mortality ; Male ; Female ; *Metagenomics/methods ; Middle Aged ; *High-Throughput Nucleotide Sequencing ; Aged ; Treatment Outcome ; Prognosis ; Prospective Studies ; Adult ; }, abstract = {BACKGROUND: Clinical implications of metagenomics next-generation sequencing (mNGS) in sepsis have not been fully evaluated. This study aimed to determine the diagnostic, therapeutic, and prognostic impacts of mNGS in sepsis.

METHODS: This multicenter prospective study was conducted at 19 sites in China from 2020 to 2021, and 859 adult patients hospitalized with sepsis were enrolled. The advantages, challenges, knowledge gaps and privacy risks of mNGS were carefully introduced to all participants, and participants chose on their own to either receive conventional microbiological test (CMT) alone (conventional-test-only group, n = 394) or receive mNGS test along with CMT (combined test group, n = 465). For prognostic analysis, the primary endpoint was 28-day mortality. Secondary endpoints included 7-day mortality and average per-day hospital cost. Inverse probability of treatment weighting was used to balance covariates between groups. Concurrent CMT and mNGS results from patients in the combined test group were used for diagnostic analyses. Therapeutic impact of mNGS was evaluated based on subsequent antibiotic adjustment.

RESULTS: Compared with composite reference standard, the positive percent agreement of mNGS among infected site samples was significantly higher than that of CMT (92.0% [95% CI, 88.7 to 94.5] vs. 51.1% [95% CI, 45.9 to 56.2], p < 0.001), while the negative percent agreement of mNGS was inferior to that of CMT (39.6% [95% CI, 29.5 to 50.4] vs. 69.2% [95% CI, 58.7 to 78.5], p < 0.001). The mNGS test identified causal microbes in 344 (74.0%) patients, and concomitant antibiotic changes occurred in 136 patients (29.2%). Death by day 7 occurred in 24 of 465 (5.2%) patients in the combined test group and in 34 of 394 (8.6%) patients in the conventional-test-only group (hazard ratio, 0.44 [95% CI, 0.26 to 0.77], p = 0.004). However, no significant difference in 28-day mortality was observed between two study groups (hazard ratio, 0.82 [0.56 to 1.20], p = 0.300).

CONCLUSIONS: The mNGS test of infected site samples exhibited 40% higher pathogen detection rate than CMT in patients with sepsis, which led to improved etiological diagnosis and tailored antibiotic therapy. Additional use of mNGS halved the risk of early death in 7 days, but did not improve 28-day survival in patients with sepsis.

TRIAL REGISTRATION: chictr.org.cn Identifier: ChiCTR2000031113. Registered 22 March 2020.}, } @article {pmid40181255, year = {2025}, author = {Mohammadzadeh, R and Mahnert, A and Shinde, T and Kumpitsch, C and Weinberger, V and Schmidt, H and Moissl-Eichinger, C}, title = {Age-related dynamics of predominant methanogenic archaea in the human gut microbiome.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {193}, pmid = {40181255}, issn = {1471-2180}, support = {P 32697//Austrian Science Fund/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Middle Aged ; Adult ; Aged ; *Archaea/classification/genetics/metabolism/isolation & purification ; *Methane/metabolism ; Feces/microbiology ; Aged, 80 and over ; Young Adult ; Female ; Male ; *Aging ; Age Factors ; Methanobrevibacter/genetics ; Metagenomics ; Phylogeny ; Bacteria/classification/genetics/metabolism ; }, abstract = {BACKGROUND: The reciprocal relationship between aging and alterations in the gut microbiota is a subject of ongoing research. While the role of bacteria in the gut microbiome is well-documented, specific changes in the composition of methanogens during extreme aging and the impact of high methane production in general on health remain unclear. This study was designed to explore the association of predominant methanogenic archaea within the human gut and aging.

METHODS: Shotgun metagenomic data from the stool samples of young adults (n = 127, Age: 19-59 y), older adults (n = 86, Age: 60-99 y), and centenarians (n = 34, age: 100-109 years) were analyzed.

RESULTS: Our findings reveal a compelling link between age and the prevalence of high methanogen phenotype, while overall archaeal diversity diminishes. Surprisingly, the archaeal composition of methanogens in the microbiome of centenarians appears more akin to that of younger adults, showing an increase in Methanobrevibacter smithii, rather than Candidatus Methanobrevibacter intestini. Remarkably, Ca. M. intestini emerged as a central player in the stability of the archaea-bacteria network in adults, paving the way for M. smithii in older adults and centenarians. Notably, centenarians exhibit a highly complex and stable network of these two methanogens with other bacteria. The mutual exclusion between Lachnospiraceae and these methanogens throughout all age groups suggests that these archaeal communities may compensate for the age-related drop in Lachnospiraceae by co-occurring with Oscillospiraceae.

CONCLUSIONS: This study underscores the dynamics of archaeal microbiome in human physiology and aging. It highlights age-related shifts in methanogen composition, emphasizing the significance of both M. smithii and Ca. M. intestini and their partnership with butyrate-producing bacteria for potential enhanced health.}, } @article {pmid40180917, year = {2025}, author = {Schmitz, MA and Dimonaco, NJ and Clavel, T and Hitch, TCA}, title = {Lineage-specific microbial protein prediction enables large-scale exploration of protein ecology within the human gut.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {3204}, pmid = {40180917}, issn = {2041-1723}, support = {460129525//Massachusetts Department of Fish and Game (DFG)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Metagenome/genetics ; *Metagenomics/methods ; *Bacterial Proteins/genetics/metabolism ; *Bacteria/genetics/classification/metabolism ; Phylogeny ; Computational Biology/methods ; }, abstract = {Microbes use a range of genetic codes and gene structures, yet these are often ignored during metagenomic analysis. This causes spurious protein predictions, preventing functional assignment which limits our understanding of ecosystems. To resolve this, we developed a lineage-specific gene prediction approach that uses the correct genetic code based on the taxonomic assignment of genetic fragments, removes incomplete protein predictions, and optimises prediction of small proteins. Applied to 9634 metagenomes and 3594 genomes from the human gut, this approach increased the landscape of captured expressed microbial proteins by 78.9%, including previously hidden functional groups. Optimised small protein prediction captured 3,772,658 small protein clusters, which form an improved microbial protein catalogue of the human gut (MiProGut). To enable the ecological study of a protein's prevalence and association with host parameters, we developed InvestiGUT, a tool which integrates both the protein sequences and sample metadata. Accurate prediction of proteins is critical to providing a functional understanding of microbiomes, enhancing our ability to study interactions between microbes and hosts.}, } @article {pmid40180909, year = {2025}, author = {Bedarf, JR and Romano, S and Heinzmann, SS and Duncan, A and Traka, MH and Ng, D and Segovia-Lizano, D and Simon, MC and Narbad, A and Wüllner, U and Hildebrand, F}, title = {A prebiotic dietary pilot intervention restores faecal metabolites and may be neuroprotective in Parkinson's Disease.}, journal = {NPJ Parkinson's disease}, volume = {11}, number = {1}, pages = {66}, pmid = {40180909}, issn = {2373-8057}, support = {BB/CCG2260/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, abstract = {Current treatment of Parkinson's Disease (PD) remains symptomatic, and disease-modifying approaches are urgently required. A promising approach is to modify intestinal microbiota and key metabolites of bacterial fermentation: short-chain fatty acids (SCFA), which are decreased in PD. A prospective, controlled pilot study (DRKS00034528) was conducted on 11 couples (PD patient plus healthy spouse as control (CO)). Participants followed a 4-week diet rich in dietary fibre, including intake of the prebiotic Lactulose. Gut metagenomes, faecal and urinary metabolites, and clinical characteristics were assessed. The dietary intervention significantly augmented faecal SCFA and increased Bifidobacteria spp., reducing PD-related gastrointestinal symptoms. The pre-existing bacterial dysbiosis in PD (depletion of Blautia, Dorea, Erysipelatoclostridium) persisted. Bacterial metabolite composition in faeces and urine positively changed with the intervention: Brain-relevant gut metabolic functions involved in neuroprotective and antioxidant pathways, including S-adenosyl methionine, glutathione, and inositol, improved in PD. These promising results warrant further investigation in larger cohorts.}, } @article {pmid40180580, year = {2025}, author = {Chiu, CY and Servellita, V and de Lorenzi-Tognon, M and Benoit, P and Sumimoto, N and Foresythe, A and Cerqueira, FM and Williams-Bouyer, N and Ren, P and Herrera, LNS and Gaston, DC and Sayyad, L and Whitmer, SL and Klena, J and Vikram, HR and Gold, JAW and Gade, L and Parnell, L and Misas, E and Chiller, TM and Griffin, IS and Basavaraju, SV and Smith, DJ and Litvintseva, AP and Chow, NA}, title = {Metagenomic Identification of Fusarium solani Strain as Cause of US Fungal Meningitis Outbreak Associated with Surgical Procedures in Mexico, 2023.}, journal = {Emerging infectious diseases}, volume = {31}, number = {5}, pages = {}, doi = {10.3201/eid3105.241657}, pmid = {40180580}, issn = {1080-6059}, abstract = {We used metagenomic next-generation sequencing (mNGS) to investigate an outbreak of Fusarium solani meningitis in US patients who had surgical procedures under spinal anesthesia in Matamoros, Mexico, during 2023. Using a novel method called metaMELT (metagenomic multiple extended locus typing), we performed phylogenetic analysis of concatenated mNGS reads from 4 patients (P1-P4) in parallel with reads from 28 fungal reference genomes. Fungal strains from the 4 patients were most closely related to each other and to 2 cultured isolates from P1 and an additional case (P5), suggesting that all cases arose from a point source exposure. Our findings support epidemiologic data implicating a contaminated drug or device used for epidural anesthesia as the likely cause of the outbreak. In addition, our findings show that the benefits of mNGS extend beyond diagnosis of infections to public health outbreak investigation.}, } @article {pmid40180222, year = {2025}, author = {Yang, Y and Wang, D and Li, L and Song, J and Yang, X and Li, J}, title = {Evolution of enteric viruses in the progression of colorectal cancer via the adenoma-carcinoma sequence pathway.}, journal = {Virus research}, volume = {}, number = {}, pages = {199569}, doi = {10.1016/j.virusres.2025.199569}, pmid = {40180222}, issn = {1872-7492}, abstract = {The global incidence of colorectal cancer (CRC) is increasing. In the majority of CRC cases, colon cancer develops from alterations in the adenoma-carcinoma sequence pathway. Currently, there are few studies regarding the effects of enteric viruses on the adenoma-carcinoma sequence pathway, and subsequently, the progression and development of the CRC. Here, fecal and tissue samples from a normal control group, an adenomatous polyp group, and a colorectal adenocarcinoma group were collected to gain a deeper understanding of the variations in enteric viruses in CRC patients and to analyze their significance. With the progression of CRC from adenoma to adenocarcinoma, the number of DNA viruses in the virus-like particles (VLPs) of fecal and tissue samples gradually increased, and there were distinct differences in the composition of enteric viruses among the different groups. Multiple species correlation analysis revealed extensive interactions among viruses, bacteria, and fungi in fecal and tissue samples. Functional analysis also revealed that the functional pathways in fecal and tissue samples also underwent significant changes. In conclusion, the changes in the composition and function of enteric viruses in the progression of CRC via adenoma-carcinoma sequence pathway were analyzed in this study, and these changes hold certain importance for exploring the role of enteric viruses in the occurrence of this disease; however, their mode of action and specific mechanisms require further investigation.}, } @article {pmid39930907, year = {2025}, author = {Doorenspleet, K and Jansen, L and Oosterbroek, S and Kamermans, P and Bos, O and Wurz, E and Murk, A and Nijland, R}, title = {The Long and the Short of It: Nanopore-Based eDNA Metabarcoding of Marine Vertebrates Works; Sensitivity and Species-Level Assignment Depend on Amplicon Lengths.}, journal = {Molecular ecology resources}, volume = {25}, number = {4}, pages = {e14079}, doi = {10.1111/1755-0998.14079}, pmid = {39930907}, issn = {1755-0998}, support = {//European Regional Development Fund Interreg North Sea region GEANS/ ; TEWZ118017//Rijksdienst voor Ondernemend Nederland/ ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; North Sea ; *Vertebrates/classification/genetics ; *Aquatic Organisms/classification/genetics ; DNA Primers/genetics ; Biodiversity ; *Nanopore Sequencing/methods ; *Metagenomics/methods ; *DNA, Environmental/genetics ; Fishes/genetics/classification ; Sequence Analysis, DNA ; DNA, Mitochondrial/genetics ; }, abstract = {To monitor the effect of nature restoration projects in North Sea ecosystems, accurate and intensive biodiversity assessments are vital. DNA-based techniques and especially environmental (e)DNA metabarcoding is becoming a powerful monitoring tool. However, current approaches rely on genetic target regions under 500 bp, offering limited taxonomic resolution. We developed a method for long-read eDNA metabarcoding, using Nanopore sequencing of a longer amplicon and present DECONA, a read processing pipeline to enable improved identification of marine vertebrate species. We designed a universal primer pair targeting a 2 kb region of fish mitochondrial DNA and compared it to the commonly used MiFish primer pair targeting a ~ 170 bp region. In silico testing showed that 2 kb fragments improved accurate identification of closely related species. Analysing eDNA from a North Sea aquarium showed that sequences from both primer pairs could be assigned to most species, and additional species level assignments could be made through the 2 kb primer pair. Interestingly, this difference was opposite in eDNA from the North Sea, where not the 2 kb but the MiFish primer pair detected more species. This study demonstrates the feasibility of using long-read metabarcoding for eDNA vertebrate biodiversity assessments. However, our findings suggests that longer fragments are less abundant in environmental settings, but not in aquarium settings, suggesting that longer fragments may provide a more recent snapshot of the community. Thus, long-read metabarcoding can expand the molecular toolbox for biodiversity assessments by improving species-level identification and may be especially useful when the temporal origin of the eDNA signal is better understood.}, } @article {pmid40180172, year = {2025}, author = {Li, VW and Dong, TS and Funes, D and Hernandez, L and Kushnir, NR and Nair, D and Jacobs, JP and Reddy, ST and Mayer, EA and Chang, L and Meriwether, D}, title = {Mass spectrometric profiling of primary estrogens and estrogen metabolites in human stool and plasma partially elucidates the role of the gut microbiome in estrogen recycling.}, journal = {Molecular and cellular endocrinology}, volume = {}, number = {}, pages = {112534}, doi = {10.1016/j.mce.2025.112534}, pmid = {40180172}, issn = {1872-8057}, abstract = {Primary estrogens and estrogen metabolites are commonly measured in human plasma and serum, but there exist almost no recent reports for human stool. This knowledge gap limits our understanding of the relationships between systemic and gut estrogens. We developed a highly sensitive liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) method to determine, in human plasma and stool, the free and conjugated levels of estrone, estradiol, and estriol together with their additional hydroxyestrogen and methoxyestrogen metabolites. We investigated human stool and plasma estrogens in healthy control men; in follicular and luteal phase premenopausal women; and in postmenopausal women. Most estrogens were present in plasma and stool of all groups, while the plasma and stool levels of hydroxyestrogen and methoxyestrogen metabolites but not estrone were correlated. In stool, estrogens were higher in premenopausal women, with estrogens increasing across the menstrual cycle. We combined these LC-MS/MS measures with shotgun metagenomic sequencing of the stool microbiomes. Estrogen deconjugation enzyme gene copy numbers (β-glucuronidase and arylsulfatase) were higher in premenopausal women; while the gene copy number of β-glucuronidase + arylsulfatase, but not β-glucuronidase alone, correlated with deconjugated stool estrogens in all groups. Moreover, β-glucuronidase + arylsulfatase gene copy numbers correlated with combined plasma estrogens in men and with individual plasma estrogen metabolites in men and premenopausal women. These results support the hypothesis that gut microbial β-glucuronidase and arylsulfatase control the deconjugation of gut estrogens while modulating systemic levels through the uptake and recirculation of these deconjugated estrogens. The intestine may thus constitute an important additional compartment in estrogen physiology.}, } @article {pmid40179782, year = {2025}, author = {Chen, S and Xin, X and Wang, Z and Wang, H and Yan, W}, title = {Enhancing tetramethylammonium hydroxide degradation in anaerobic digestion: Neglected role of iron-based conductive materials in regulating degradation pathway.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138115}, doi = {10.1016/j.jhazmat.2025.138115}, pmid = {40179782}, issn = {1873-3336}, abstract = {The rapid expansion of TFT-LCD industry led to significant environmental challenges due to the highly corrosive and ecotoxic tetramethylammonium hydroxide (TMAH). This study explores a previously unrecognized role of iron-based conductive materials - nano magnetite (Fe3O4) and nano zero-valent iron (ZVI) - in enhancing TMAH degradation and regulating degradation pathways in anaerobic digestion systems. Results show these materials significantly enhance degradation efficiency as TMAH concentration increases. At the highest TMAH level (10 g/L), while the control group achieved only 78.41 % degradation efficiency, Fe3O4 and ZVI groups reached efficiencies of 97.36 % and 94.96 %, with methane yields increased by 89.00 % and 97.21 %. Mechanistic exploration revealed these materials promoted secretion of charged functional groups into extracellular polymeric substances that effectively shielded microbes from TMAH toxicity. Additionally, they stimulated flavin and riboflavin production, enhancing interspecies electron transfer rates by up to 46.14-fold for Fe3O4 and 9.00-fold for ZVI. Microbial and metagenomic analyses further uncovered these materials induced a shift in TMAH degradation from methylotrophic methanogenesis to syntrophic metabolism, facilitating a more efficient breakdown of TMAH through direct interspecies electron transfer. These findings unravel the effects of iron-based conductive materials in regulating degradation pathways, offering a promising approach to addressing environmental challenges posed by TFT-LCD industry.}, } @article {pmid40179570, year = {2025}, author = {Zhang, P and Liu, Y and Xu, M and Zhang, J and Xia, J and Shi, Y and Wang, J and Han, B and Feng, G}, title = {Gut microbiota characteristics and prognostic value in patients with aneurysmal subarachnoid hemorrhage: A clinical study.}, journal = {Journal of clinical neuroscience : official journal of the Neurosurgical Society of Australasia}, volume = {136}, number = {}, pages = {111200}, doi = {10.1016/j.jocn.2025.111200}, pmid = {40179570}, issn = {1532-2653}, abstract = {BACKGROUND: This study aims to explore the characteristics of gut microbiota in the aneurysmal subarachnoid hemorrhage (aSAH) group and the healthy control group, as well as in the good prognosis group and the poor prognosis group. It also investigates the relationship between the severity of aSAH and gut microbiota, and the predictive value of gut microbiota for the prognosis outcome of patients with aSAH.

METHODS: Stool samples from 22 patients with aSAH and 11 healthy controls were subjected to metagenomic sequencing, and species annotations were obtained through the taxonomic information database corresponding to the NR database. The characteristics of the gut microbiota in the aSAH group versus the healthy control group, and the good prognosis group versus the poor prognosis group were analyzed.The correlations between differential microbiota and clinical hematology markers between the aSAH and control groups and between gut microbiota and aSAH severity were analyzed. The prognosis of patients with aSAH after three months was assessed. Finally, gut microbiota with significant effects were screened for potential as biomarkers, and the predictive value of gut microbiota for different prognostic outcomes in patients with aSAH was explored.

RESULTS: Gut microbiota composition, diversity, and abundance differed significantly between patients in the aSAH group and the control group. Additionally, the composition, diversity, and abundance differed between patients with good and poor prognosis. Five dominant genera--Bacillus, Eggerthia, Hominisplanchenecus, Carnobacterium, and Bifidobacterium were identified as potential biomarkers for predicting aSAH outcomes.

CONCLUSION: Patients with aSAH have altered gut microbiota composition, structure, and diversity compared with the healthy population. These alterations may be potential biomarkers for aSAH diagnosis and outcome prediction.}, } @article {pmid40178790, year = {2025}, author = {Yuan, J and Yang, J and Sun, Y and Meng, Y and He, Z and Zhang, W and Dang, L and Song, Y and Xu, K and Lv, N and Zhang, Z and Guo, P and Yin, H and Shi, W}, title = {An early microbial landscape: inspiring endeavor from the China Space Station Habitation Area Microbiome Program (CHAMP).}, journal = {Science China. Life sciences}, volume = {}, number = {}, pages = {}, pmid = {40178790}, issn = {1869-1889}, abstract = {China's progressing space program, as evidenced by the formal operation of the China Space Station (CSS), has provided great opportunities for various space missions. Since microbes can present potential risks to human health and the normal operation of spacecraft, the study on space-microorganisms in the CSS is always a matter of urgency. In addition, the knowledge on the interactions between microorganisms, astronauts, and spacecraft equipment will shed light on our understanding of life activities in space and a closed environment. Here, we present the first comprehensive report on the microbial communities aboard the CSS based on the results of the first two survey missions of the CSS Habitation Area Microbiome Program (CHAMP). By combining metagenomic and cultivation methods, we have discovered that, in the early stage of the CSS, microbial communities are dominated by human-associated microbes, with strikingly large differences in both composition and functional diversity compared to those found on the International Space Station (ISS). While the samples from two missions of CHAMP possessed substantial differences in microbial composition, no significant difference in functional diversity was found, although signs of accumulating antibiotic resistance were evident. Meanwhile, strong bacteria co-occurrence was noted within the station's microbiota. At the strain level, environmental isolates from the CSS exhibited numerous genomic mutations compared to those from the Assembly, Integration, and Test (AIT) center, potentially linked to the adaptation to the unique conditions of space. Besides, the intraspecies variation within four high-abundance species suggests possible propagation and residency effects between sampling sites. In summary, this study offers critical insights that not only advance our understanding of space microbiology but also lay the groundwork for effective microbial management in future long-term human space missions.}, } @article {pmid40178526, year = {2025}, author = {Contreras-de la Rosa, PA and De la Torre-Zavala, S and O Connor-Sánchez, A and Prieto-Davó, A and Góngora-Castillo, EB}, title = {Exploring the microbial communities in coastal cenote and their hidden biotechnological potential.}, journal = {Microbial genomics}, volume = {11}, number = {4}, pages = {}, doi = {10.1099/mgen.0.001382}, pmid = {40178526}, issn = {2057-5858}, mesh = {*Archaea/genetics/classification/metabolism/isolation & purification ; *Bacteria/genetics/classification/metabolism ; Biotechnology ; Secondary Metabolism/genetics ; Metagenomics/methods ; *Geologic Sediments/microbiology ; Multigene Family ; Polyketide Synthases/genetics ; *Microbiota/genetics ; Phylogeny ; }, abstract = {Bacterial secondary metabolites are crucial bioactive compounds with significant therapeutic potential, playing key roles in ecological processes and the discovery of novel antimicrobial agents and natural products. Cenotes, as extreme environments, harbour untapped microbial diversity and hold an interesting potential as sources of novel secondary metabolites. While research has focused on the fauna and flora of cenotes, the study of their microbial communities and their biosynthetic capabilities remains limited. Advances in metagenomics and genome sequencing have greatly improved the capacity to explore these communities and their metabolites. In this study, we analysed the microbial diversity and biotechnological potential of micro-organisms inhabiting sediments from a coastal cenote. Metagenomic analyses revealed a rich diversity of bacterial and archaeal communities, containing several novel biosynthetic gene clusters (BGCs) linked to secondary metabolite production. Notably, polyketide synthase BGCs, including those encoding ladderanes and aryl-polyenes, were identified. Bioinformatics analyses of these pathways suggest the presence of compounds with potential industrial and pharmaceutical applications. These findings highlight the biotechnological value of cenotes as reservoirs of secondary metabolites. The study and conservation of these ecosystems are essential to facilitate the discovery of new bioactive compounds that could benefit various industries.}, } @article {pmid40178319, year = {2025}, author = {Herzog, E and Ishida, K and Scherlach, K and Chen, X and Bartels, B and Niehs, SP and Cheaib, B and Panagiotou, G and Hertweck, C}, title = {Antibacterial Siderophores of Pandoraea Pathogens and their Impact on the Diseased Lung Microbiota.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {}, number = {}, pages = {e202505714}, doi = {10.1002/anie.202505714}, pmid = {40178319}, issn = {1521-3773}, abstract = {Antibiotic-resistant bacteria of the genus Pandoraea, frequently acquired from the environment, are an emerging cause of opportunistic respiratory infections, especially in cystic fibrosis (CF) patients. However, their specialized metabolites, including niche and virulence factors, remained unknown. Through genome mining of environmental and clinical isolates of diverse Pandoraea species, we identified a highly conserved biosynthesis gene cluster (pan) that codes for a non-ribosomal peptide synthetase (NRPS) assembling a new siderophore. Using bioinformatics-guided metabolic profiling of wild type and a targeted null mutant, we discovered the corresponding metabolites, pandorabactin A and B. Their structures and chelate (gallium) complexes were elucidated by a combination of chemical degradation, derivatization, NMR, and MS analysis. Metagenomics and bioinformatics of sputum samples of CF patients indicated that the presence of the pan gene locus correlates with the prevalence of specific bacteria in the lung microbiome. Bioassays and mass spectrometry imaging showed that pandorabactins have antibacterial activities against various lung pathogens (Pseudomonas, Mycobacterium, and Stenotrophomonas) through depleting iron in the competitors. Taken together, these findings offer first insight into niche factors of Pandoraea and indicate that pandorabactins shape the diseased lung microbiota through the competition for iron.}, } @article {pmid40177842, year = {2025}, author = {Larnder, AH and Manges, AR and Murphy, RA}, title = {The estrobolome: Estrogen-metabolizing pathways of the gut microbiome and their relation to breast cancer.}, journal = {International journal of cancer}, volume = {}, number = {}, pages = {}, doi = {10.1002/ijc.35427}, pmid = {40177842}, issn = {1097-0215}, support = {/CAPMC/CIHR/Canada ; //Weston Family Foundation/ ; }, abstract = {Increasing evidence links the gut microbiome to carcinogenesis. Disruptions in estrogen regulation by the estrobolome-gut microbiota with estrogen-related functions-may promote breast cancer. However, precise information on estrobolome targets and their underlying mechanisms is limited. This review identifies relevant targets for measuring the estrobolome, focusing on enzymes and microbial taxa involved in processing estrogens, precursors, metabolites, and phytoestrogens, to facilitate the exploration of potential links to breast cancer. Evidence from breast cancer case-control studies is synthesized to assess alignment with these targets, highlight gaps in the evidence, and suggest new paths forward. Findings from case-control studies were heterogeneous and showed limited alignment with estrobolome targets, with only Escherichia coli and Roseburia inulinivorans identified as differentially abundant and functionally relevant between cases and controls. The lack of compelling evidence for estrobolome-specific mechanisms may reflect measurement challenges or may suggest that broader ecological changes in the microbiome, which influence a network of interacting mechanisms, are more influential for carcinogenesis. To clarify the estrobolome's role in breast cancer, future research should use advanced sequencing techniques and methods such as metabolomics and transcriptomics, while considering clinical and behavioral factors that may modify estrobolome mechanisms.}, } @article {pmid40177486, year = {2025}, author = {Yang, S and Chen, J and Zheng, J and Mao, H and Deng, F and Wu, D and Chai, J}, title = {Feeding systems influence the rumen resistome in yaks by changing the microbiome.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1505938}, doi = {10.3389/fmicb.2025.1505938}, pmid = {40177486}, issn = {1664-302X}, abstract = {The rumen microbiome serves as a reservoir of antibiotic-resistance genes (ARGs) with significant implications for public health. This study aimed to investigate the effects of different feeding systems on the rumen resistome in yaks. Yaks that grazed naturally on pasture were used as controls, while the experimental yaks were housed in a high-density pen environment and fed a specially designed diet to optimally meet their nutritional requirements, with increased interactions with farm workers. Metagenomic analysis was performed to assess changes in the rumen microbiome and resistome. Dietary factors influencing changes in the rumen microbiome and resistome were identified. A greater variety of microbiomes associated with carbohydrate digestion was found in yaks under a house-feeding system, such as Stomatobaculum longum and Succiniclasticum ruminis. Although grazing yaks exhibited various dominant antibiotic resistance genes (ARGs) at the class level, house-fed yaks were mainly enriched with tetracycline-resistant genes. A random forest model identified specific ARG signatures for each group, such as Sent_cmlA and Sliv_cmlR (Phenicol) and vanHD (Glycopeptide) prevalent in grazing yaks, while tet44, tetW, tetW/N/W, and tet40 were abundant in house-fed yaks. ARG interactions varied by feeding system, with signature ARGs in each group showing distinct correlations. Nevertheless, strong correlations among ARGs existed regardless of the treatments, such as the positive correlation between tetW and tetW/N/W in both groups. The rumen microbiome was strongly associated with the resistome, especially regarding abundant microbiomes and ARGs. Proteobacteria carrying ARGs were observed in grazing yaks, while Firmicutes served as hosts for ARGs in yaks under a housed feeding system. The specific bacteria contributing to the distinct ARGs in each group were identified. For instance, members of Firmicutes (Clostridium tepidiprofundi) carried their ARG signatures, such as tet44. These findings emphasized that diet, along with environmental factors and farmworker interactions, contributed to changes in the rumen resistome of yaks. This study is the first to discuss how multiple factors within a feeding regime influence the gut resistome, highlighting the drawbacks of intensive feedings with respect to the gut resistome.}, } @article {pmid40177475, year = {2025}, author = {Tenea, GN and Reyes, P and Flores, C}, title = {Crosslinking bacterial postbiotics for microbial and quality control of strawberries postharvest: bacteriological and 16S amplicon metagenome evidence.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1570312}, doi = {10.3389/fmicb.2025.1570312}, pmid = {40177475}, issn = {1664-302X}, abstract = {INTRODUCTION: Strawberries are renowned for their exceptional flavor and nutritional properties but have a short shelf life due to rapid ripening and a high vulnerability to postharvest microbial decay. Postbiotic formulations (PBFs) derived from lactic acid bacteria (LAB) can be developed into effective preservation products, extending postharvest shelf life while maintaining fruit quality.

METHODS: This study aimed to assess the effects of postbiotic-based formulations (PBFs) consisting of two key components: (1) a precipitated peptide-protein extract (PP) from Weissella cibaria UTNGt21O, serving as the antimicrobial agent, and (2) an exopolysaccharide (EPS) from W. confusa UTNCys2-2, functioning as the biopolymer carrier. These formulations were tested against a multidrug-resistant Serratia liquefaciens P4StpC1 strain, isolated from ready-to-eat strawberries, and their potential mode of action was analyzed in vitro. Time-kill assays and electron microscopy were used to evaluate their impact on the target cells. Furthermore, the performance of PBFs was compared to a commercial disinfectant (C1) in terms of their effects on strawberry microbiota and fruit quality, employing bacteriological techniques and 16S amplicon metagenomic analysis.

RESULTS: The selected PBFs showed bacteriolytic effect on Serratia in vitro. The target cell viability was significantly reduced upon 1 h co-cultivation by inducing several morphological and ultrastructural modifications. Dipping strawberries at the ripe stage four in PBFs indicated no increase in total cell counts, thus the microorganisms colonization was retained during storage with refrigeration. The 16S metagenome analysis showed that the treatment impacted the fruit microbiota, significantly increasing Lactobacillus abundance (p < 0.001) by day eight compared to the disinfectant control. This suggests the formulation supports beneficial microbes, enhancing antimicrobial effects. Additionally, the postbiotic coating improved shelf-life, preserved fruit quality, and delayed deterioration in strawberries. The strawberries quality attributes were not affected by the treatment. Principal Component Analysis (PCA) revealed clear sample separation based on maturity stage, independent of the treatment.

CONCLUSION: The results highlight the potential of crosslinking of a peptide-protein fraction with EPS to prevent the colonization of undesirable microorganisms on postharvest strawberries while enhancing their safety and quality.}, } @article {pmid40177465, year = {2025}, author = {Krause, SMB and van den Berg, NI and Brenzinger, K and Zweers, H and Bodelier, PLE}, title = {Beyond methane consumption: exploring the potential of methanotrophic bacteria to produce secondary metabolites.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf030}, doi = {10.1093/ismeco/ycaf030}, pmid = {40177465}, issn = {2730-6151}, abstract = {Microbial methane-consuming communities significantly impact biogeochemical processes and greenhouse gas emissions. In this study, we explored secondary metabolites produced by methane-oxidizing bacteria (MOB) and their ecological roles. We analyzed the volatile profiles of four MOB strains under controlled conditions and conducted a meta-analysis using high-quality genomes from 62 cultured MOB strains and 289 metagenome-assembled genomes to investigate their potential for producing secondary metabolites. Results show species-specific volatile production, such as germacrene by Methylobacter luteus, which may play a role in the regulation of environmental methane consumption. The meta-analysis revealed that biosynthetic gene clusters (BGCs) for terpenes and β-lactones were more prevalent in the Methylocystaceae and/or Beijerinckiaceae families, while aryl polyene BGCs were dominant in the Methylococcaceae family, reflecting habitat-specific adaptations. These findings advance our understanding of the metabolic capabilities of MOB and underscore the importance of integrating experimental data with genomic and metabolomic analyses to elucidate their ecology, environmental interactions, and contributions to methane cycling.}, } @article {pmid40177421, year = {2025}, author = {Tian, Y and Yang, X and Yang, Y and Lin, T and Wang, G and Zhang, Y and Wu, H and Wang, J}, title = {Aeromonas veronii-induced septic arthritis of the hip in a child with acute lymphoblastic leukemia.}, journal = {Open life sciences}, volume = {20}, number = {1}, pages = {20221042}, doi = {10.1515/biol-2022-1042}, pmid = {40177421}, issn = {2391-5412}, abstract = {Septic arthritis of the hip (SAH) is a prevalent form of infectious arthritis in children that can lead to serious complications if not promptly diagnosed and treated. A 6-year 4-month-old female child with a 1-year history of acute lymphoblastic leukemia chemotherapy was admitted to our hospital due to a 1-day fever. After 1 week, the child experienced right inguinal pain and exhibited severe restriction in the flexion of the right lower limb and hip. Consequently, edema was observed in the right lower extremity and foot. SAH was initially diagnosed using computed tomography and magnetic resonance imaging examinations of both hip joints. Subsequently, incision and irrigation procedure were performed on the hip joint. Following the surgery, pus metagenomic next-generation sequencing (mNGS) were conducted promptly, and the mNGS analysis indicated an Aeromonas veronii infection. The diagnosis of A. veronii SAH was subsequently confirmed through polymerase chain reaction. The child's condition was successfully treated with a combination of amikacin and imipenem-cilastatin, leading to improvement and subsequent discharge in a satisfactory state. SAH caused by A. veronii is a rare occurrence, and the utilization of mNGS holds significant potential for the early detection of uncommon infections in immunosuppressed children.}, } @article {pmid40177267, year = {2025}, author = {Yan, Z and Sun, C and Tang, W and Cao, W and Lv, J and Liang, Z and Wei, S and Zhong, W and Zhao, Z and Zhao, Z and Li, Y}, title = {Application of the metagenomic next-generation sequencing technology to identify the causes of pleural effusion.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1525100}, doi = {10.3389/fmed.2025.1525100}, pmid = {40177267}, issn = {2296-858X}, abstract = {BACKGROUND: Pleural effusion (PE), frequently encountered in clinical practice, can arise from a variety of underlying conditions. Accurate differential diagnosis of PE is crucial, as treatment and prognosis are heavily dependent on the underlying etiology. However, diagnosing the cause of PE remains challenging, relying on mycobacteriological methods that lack sensitivity and are time-consuming, or on histological examinations that require invasive biopsies. The recent advancements in metagenomic next-generation sequencing (mNGS) have shown promising applications in the diagnosis of infectious diseases. Despite this, there is limited research on the utility of mNGS as a comprehensive diagnostic tool for simultaneously identifying the causes of PE, particularly in cases of tuberculosis or malignancy.

METHODS: This study aimed to assess the efficacy of mNGS in detecting tuberculous pleural effusion (TPE) and malignant pleural effusion (MPE). A total of 35 patients with PE were included, and their PE samples were analyzed using mNGS.

RESULTS: Among the participants, 8 were ultimately diagnosed with TPE, and 10 were diagnosed with MPE, with lung adenocarcinoma being the most prevalent pathological type (50%, 5/10), according to established diagnostic criteria. Additionally, 7 patients were diagnosed with non-infectious PE. However, mNGS identified only 2 cases of TPE and 8 cases of MPE. The sensitivity of mNGS for detecting Mycobacterium tuberculosis was 25% (2/8), while the specificity was 100%. For tumor detection, mNGS demonstrated a sensitivity of 80%, a specificity of 92.6%, and an AUC of 0.882.

CONCLUSION: mNGS is effective in distinguishing MPE from non-MPE, but is not suitable for diagnosing TPE.}, } @article {pmid40177264, year = {2025}, author = {Kananen, K and Veseli, I and Quiles Pérez, CJ and Miller, SE and Eren, AM and Bradley, PH}, title = {Adaptive adjustment of profile HMM significance thresholds improves functional and metabolic insights into microbial genomes.}, journal = {Bioinformatics advances}, volume = {5}, number = {1}, pages = {vbaf039}, doi = {10.1093/bioadv/vbaf039}, pmid = {40177264}, issn = {2635-0041}, abstract = {MOTIVATION: Gene function annotation in microbial genomes and metagenomes is a fundamental in silico first step toward understanding metabolic potential and determinants of fitness. The Kyoto Encyclopedia of Genes and Genomes publishes a curated list of profile hidden Markov models to identify orthologous gene families (KOfams) with roles in metabolism. However, the computational tools that rely upon KOfams yield different annotations for the same set of genomes, leading to different downstream biological inferences.

RESULTS: Here, we apply three open-source software tools that can annotate KOfams to genomes of phylogenetically diverse bacterial families from host-associated and free-living biomes. We use multiple computational approaches to benchmark these methods and investigate individual case studies where they differ. Our results show that despite their fundamental similarities, these methods have different annotation rates and quality. In particular, a method that adaptively tunes sequence similarity thresholds substantially improves sensitivity while maintaining high accuracy. We observe particularly large improvements for protein families with few reference sequences, or when annotating genomes from nonmodel organisms (such as gut-dwelling Lachnospiraceae). Our findings show that small improvements in annotation workflows can maximize the utility of existing databases and meaningfully improve in silico characterizations of microbial metabolism.

Anvi'o is available at https://anvio.org under the GNU GPL license. Scripts and workflow are available at https://github.com/pbradleylab/2023-anvio-comparison under the MIT license.}, } @article {pmid40176261, year = {2025}, author = {Sim, BZ and Mah, JK and Heldman, MR and Stanly, KL and Hanson, KE and Caliendo, AM and Andes, D and Ostroskly-Zeichner, L and Wingard, JR and Alexander, BD}, title = {Plasma microbial cell-free DNA Metagenomic Sequencing for Diagnosis of Invasive Fungal Diseases Among High Risk Outpatient and Inpatient Immunocompromised Hosts.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {}, number = {}, pages = {}, doi = {10.1093/cid/ciaf170}, pmid = {40176261}, issn = {1537-6591}, abstract = {BACKGROUND: New and minimally-invasive tools to aid the diagnosis of invasive fungal diseases (IFD) are urgently needed as the immunocompromised population at highest risk increases. Advancements in molecular technology have rendered new diagnostics more readily available for clinical use.

METHODS: This case-control study utilized prospectively collected, archived plasma specimens and data from the Aspergillus Technology Consortium (AsTeC) Repository to investigate the diagnostic performance of microbial cell free DNA (mcfDNA) sequencing as a minimally-invasive diagnostic for IFDs in a population of high-risk immunocompromised hosts including hematologic malignancy, stem cell and solid organ transplants patients. The 2008 Mycoses Study Group/European Organization for the Research and Treatment of Cancer diagnostic criteria served as the gold standard for test performance.

RESULTS: Sixty-five adult subjects with proven or probable IFD and 65 controls without IFD were included. Among IFD episodes Aspergillus was the most common pathogen (70.8%, 46/65), followed by Mucorales (10.8%, 7/65). Overall, sensitivity was 47.7% and specificity was 100%. Sensitivity varied based on disease certainty and pathogen; sensitivity was higher in proven versus probable IFD (60.0% vs 37.1%, respectively) and higher for subjects with invasive mucormycosis (100%) compared with aspergillosis (45.7%).

CONCLUSIONS: A positive result by mcfDNA sequencing may reduce the need for invasive sampling in patients with suspected IFD. In this exploratory analysis, its high sensitivity and specificity for invasive mucormycosis suggests it could be useful for early treatment and intervention of this IFD. Future studies should focus on understanding how specific factors impact the sensitivity of mcfDNA sequencing for invasive aspergillosis.}, } @article {pmid40176190, year = {2025}, author = {Xing, J and Niu, T and Yu, T and Zou, B and Shi, C and Wang, Y and Fan, S and Li, M and Bao, M and Sun, Y and Gao, K and Qiu, J and Zhang, D and Wang, N and Jiang, Y and Huang, H and Cao, X and Zeng, Y and Wang, J and Zhang, S and Hu, J and Zhang, D and Sun, W and Yang, G and Yang, W and Wang, C}, title = {Faecalibacterium prausnitzii-derived outer membrane vesicles reprogram gut microbiota metabolism to alleviate Porcine Epidemic Diarrhea Virus infection.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {90}, pmid = {40176190}, issn = {2049-2618}, support = {U21A20261//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Swine ; *Porcine epidemic diarrhea virus/physiology ; *Gastrointestinal Microbiome ; *Swine Diseases/virology/microbiology ; *Faecalibacterium prausnitzii/metabolism/physiology ; *Coronavirus Infections/veterinary/virology/microbiology ; Probiotics/administration & dosage ; Feces/microbiology ; *Bacterial Outer Membrane/metabolism ; }, abstract = {BACKGROUND: The Porcine Epidemic Diarrhea Virus (PEDV) is one of the major challenges facing the global pig farming industry, and vaccines and treatments have proven difficult in controlling its spread. Faecalibacterium prausnitzii (F.prausnitzii), a key commensal bacterium in the gut, has been recognized as a promising candidate for next-generation probiotics due to its potential wide-ranging health benefits. A decrease in F.prausnitzii abundance has been associated with certain viral infections, suggesting its potential application in preventing intestinal viral infections. In this study, we utilized a piglet model to examine the potential role of F.prausnitzii in PEDV infections.

RESULTS: A piglet model of PEDV infection was established and supplemented with F.prausnitzii, revealing that F.prausnitzii mitigated PEDV infection. Further studies found that outer membrane vesicles (OMVs) are the main functional components of F.prausnitzii, and proteomics, untargeted metabolomics, and small RNA-seq were used to analyze the composition of OMVs. Exhaustion of the gut microbiota demonstrated that the function of Fp. OMVs relies on the presence of the gut microbiota. Additionally, metagenomic analysis indicated that Fp. OMVs altered the gut microbiota composition, enhancing the abundance of Faecalibacterium prausnitzii, Prevotellamassilia timonensis, and Limosilactobacillus reuteri. Untargeted metabolomics analysis showed that Fp. OMVs increased phosphatidylcholine (PC) levels, with PC identified as a key metabolite in alleviating PEDV infection. Single-cell sequencing revealed that PC altered the relative abundance of intestinal cells, increased the number of intestinal epithelial cells, and reduced necroptosis in target cells. PC treatment in infected IPEC-J2 and Vero cells alleviated necroptosis and reduced the activation of the RIPK1-RIPK3-MLKL signaling axis, thereby improving PEDV infection.

CONCLUSION: F.prausnitzii and its OMVs play a critical role in mitigating PEDV infections. These findings provide a promising strategy to ameliorate PEDV infection in piglets. Video Abstract.}, } @article {pmid40176137, year = {2025}, author = {Sommer, F and Bernardes, JP and Best, L and Sommer, N and Hamm, J and Messner, B and López-Agudelo, VA and Fazio, A and Marinos, G and Kadibalban, AS and Ito, G and Falk-Paulsen, M and Kaleta, C and Rosenstiel, P}, title = {Life-long microbiome rejuvenation improves intestinal barrier function and inflammaging in mice.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {91}, pmid = {40176137}, issn = {2049-2618}, support = {SO1141/10-1//Deutsche Forschungsgemeinschaft/ ; CRC1182//Deutsche Forschungsgemeinschaft/ ; miTARGET//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Mice ; RNA, Ribosomal, 16S/genetics ; *Fecal Microbiota Transplantation ; *Aging/physiology ; Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Male ; *Intestinal Mucosa/microbiology/metabolism ; *Inflammation/microbiology ; Mice, Inbred C57BL ; *Rejuvenation ; Permeability ; *Intestines/microbiology ; Metagenomics ; Intestinal Barrier Function ; }, abstract = {BACKGROUND: Alterations in the composition and function of the intestinal microbiota have been observed in organismal aging across a broad spectrum of animal phyla. Recent findings, which have been derived mostly in simple animal models, have even established a causal relationship between age-related microbial shifts and lifespan, suggesting microbiota-directed interventions as a potential tool to decelerate aging processes. To test whether a life-long microbiome rejuvenation strategy could delay or even prevent aging in non-ruminant mammals, we performed recurrent fecal microbial transfer (FMT) in mice throughout life. Transfer material was either derived from 8-week-old mice (young microbiome, yMB) or from animals of the same age as the recipients (isochronic microbiome, iMB) as control. Motor coordination and strength were analyzed by rotarod and grip strength tests, intestinal barrier function by serum LAL assay, transcriptional responses by single-cell RNA sequencing, and fecal microbial community properties by 16S rRNA gene profiling and metagenomics.

RESULTS: Colonization with yMB improved coordination and intestinal permeability compared to iMB. yMB encoded fewer pro-inflammatory factors and altered metabolic pathways favoring oxidative phosphorylation. Ecological interactions among bacteria in yMB were more antagonistic than in iMB implying more stable microbiome communities. Single-cell RNA sequencing analysis of intestinal mucosa revealed a salient shift of cellular phenotypes in the yMB group with markedly increased ATP synthesis and mitochondrial pathways as well as a decrease of age-dependent mesenchymal hallmark transcripts in enterocytes and TA cells, but reduced inflammatory signaling in macrophages.

CONCLUSIONS: Taken together, we demonstrate that life-long and repeated transfer of microbiota material from young mice improved age-related processes including coordinative ability (rotarod), intestinal permeability, and both metabolic and inflammatory profiles mainly of macrophages but also of other immune cells. Video Abstract.}, } @article {pmid40175903, year = {2025}, author = {Cao, L and Sun, H and Xu, Z and Xu, X and Shi, G and Zhang, J and Liang, C and Li, T and Liu, C and Wang, M and Tian, S and Li, E}, title = {Metagenomic and physicochemical profiling reveal microbial functions in pit mud for Jiang-Nong Jianxiang Baijiu fermentation.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {190}, pmid = {40175903}, issn = {1471-2180}, mesh = {*Fermentation ; *Metagenomics/methods ; *Bacteria/genetics/classification/metabolism/isolation & purification ; China ; Food Microbiology ; *Metagenome ; Microbiota ; *Alcoholic Beverages/microbiology ; }, abstract = {BACKGROUND: The unique flavour and quality of Baijiu, a treasure of traditional Chinese culture, has attracted increasing attention. The pit mud is a key component for forming the unique flavour styles of different Baijiu brands. Hence, conducting in-depth research on the microbial colonies present in pit mud is paramount for enhancing the intricate bouquets of Baijiu flavours.

RESULTS: This study conducts a comprehensive metagenomic examination of the microbial ecosystem within Chinese Jiang-Nong Jianxiang Baijiu fermentation pit mud. Within the pit mud walls, six prominent species, each accounting for more than 1% of the average relative abundance, emerged as key contributors: Lentilactobacillus buchneri, Secundilactobacillus silagincola, Clostridium tyrobutyricum, Lentilactobacillus parafarraginis, Ligilactobacillus acidipiscis, and Lactobacillus acetotolerans. Conversely, at the pit mud bases, four species surpassed this threshold: Petrimonas sp. IBARAKI, Methanosarcina barkeri, Methanofollis ethanolicus, and Proteiniphilum propionicum. Notably, the abundance of Clostridium in the pit mud walls impart superior saccharifying capabilities compared with those at the bases. The consistently high relative abundance of enzymes belonging to the glycoside hydrolases (GHs), glycosyltransferases (GTs), and carbohydrate-binding modules (CBMs) across both the pit mud walls and the bases highlight their importance in fermentation.

CONCLUSIONS: The microbial composition analysis results underscore the important role of pit mud microorganisms in facilitating starch saccharification, ethyl caproate and ethyl butyrate production, among other aromatic compounds. Microbes residing in the pit mud walls may be exhibited a heightened propensity for lactic acid generation, whereas those inhabiting the bases may be displayed a stronger inclination towards caproic acid production. This research serves as a valuable reference for future endeavours aimed at harnessing microbial resources to refine and optimize Baijiu fermentation methodologies.}, } @article {pmid40175854, year = {2025}, author = {Abuzahrah, SS}, title = {Exploring the microorganisms biodiversity associated with sponge species in the red sea through 18S ribosomal RNA gene sequencing.}, journal = {AMB Express}, volume = {15}, number = {1}, pages = {60}, pmid = {40175854}, issn = {2191-0855}, abstract = {Around the world, sponges play a significant role in marine ecosystems, and a wide variety of sponge species can be found in the coast of Red Sea of Saudi Arabia. The unique environmental conditions of the Red Sea, including warm, oligotrophic water and high salinity, have encouraged the growth of abundant sponge fauna. Our study aims to investigate the biodiversity, taxonomic composition, and phylogenetic relationships of eukaryotic organisms linked with sponges in the Red Sea off the coast of Saudi Arabia and infer the possible ecological roles and functional contributions of the identified eukaryotic taxa to sponge health and ecosystem functioning. The study investigated the microbial diversity, focusing on the genera Hyalosynedra sp., Navicula sp., Papiliocellulus sp., Psammodictyon sp., Pynococcus sp., Ostreococcus sp., Micromonas sp., and other unclassified species. Our metagenomic analysis and phylogenetic evaluation revealed a deep and diverse microbial community, with each genus performing significant ecological roles, including nutrient cycling, primary production, and contributing to marine food networks. Moreover, these genera display promising biotechnological prospects, including uses in bioremediation, biofuel production, and the synthesis of high-value biomolecules. Comparative analysis with other marine regions has focused on both the similarities and unique aspects of the Red Sea microbial community, which are influenced by its distinct environmental conditions. The gained findings contribute to a deeper understanding of the ecological dynamics in the Red Sea and open new avenues for biotechnological exploration in marine ecosystems.}, } @article {pmid40175821, year = {2025}, author = {Takagi, K and Tamura, Y and Narita, N and Komatsu, S and Yamazaki, S and Matsumura, A and Kubota, K and Matsumiya, T and Sawada, K and Nakaji, S and Mikami, T and Kobayashi, W}, title = {Involvement of Megasphaera in the oral microbiome and dyslipidemia onset: evidence from a community-based study in Japan.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, pmid = {40175821}, issn = {1874-9356}, support = {21K10202//Japan Society for the Promotion of Science/ ; 22K17281//Japan Society for the Promotion of Science/ ; 24K13233//Japan Society for the Promotion of Science/ ; JPMJCE 1302//Japan Science and Technology Agency/ ; JPMJCA　2201//Japan Science and Technology Agency/ ; JPMJPE 2210//Japan Science and Technology Agency/ ; }, abstract = {Dyslipidemia is a major risk factor for cardiovascular diseases and is influenced by genetic and environmental factors, including diet. Emerging research suggests a link between the gut microbiome and metabolic disorders. While the connection between the gut microbiota and dyslipidemia is well documented, the specific relationship between oral bacteria and dyslipidemia has not been thoroughly investigated. This study aimed to identify oral bacterial species associated with dyslipidemia in a community-based Japanese population. We conducted a metagenomic analysis on tongue coating samples from 763 participants in the Iwaki Health Promotion Project, which were collected during health checkups in 2017 and 2019. Dyslipidemia was diagnosed using standard lipid level criteria. The oral microbiome was analyzed via 16S rDNA amplicon sequencing. Statistical analyses included multiple regression and β diversity assessments. Our analysis revealed that the abundances of several bacterial genera, including Veillonella, Atopobium, Stomatobaculum, Tanneralla, and Megasphaera, are significantly associated with dyslipidemia. A higher relative abundance of Megasphaera was specifically observed in individuals with dyslipidemia. Moreover, Megasphaera abundance was closely associated with the onset of dyslipidemia (P = 0.038, odds ratio: 1.005, 95% confidence interval: 1.000-1.009), suggesting its role in metabolic regulation. This study revealed a significant association between the abundance of specific oral bacteria and dyslipidemia, suggesting the potential of using the oral microbiota as a biomarker for the early detection and management of dyslipidemia. Future research should explore the mechanisms through which oral bacteria influence lipid metabolism and the potential for microbioma-based therapies.}, } @article {pmid40175737, year = {2025}, author = {Sawhney, SS and Thänert, R and Thänert, A and Hall-Moore, C and Ndao, IM and Mahmud, B and Warner, BB and Tarr, PI and Dantas, G}, title = {Gut microbiome evolution from infancy to 8 years of age.}, journal = {Nature medicine}, volume = {}, number = {}, pages = {}, pmid = {40175737}, issn = {1546-170X}, support = {R01AI155893//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01HD092414//U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; R01HD092414//U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; T32GM007067//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; MD-FR-2013-292//Children's Discovery Institute (CDI)/ ; 5P30 DK052574//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; }, abstract = {The human gut microbiome is most dynamic in early life. Although sweeping changes in taxonomic architecture are well described, it remains unknown how, and to what extent, individual strains colonize and persist and how selective pressures define their genomic architecture. In this study, we combined shotgun sequencing of 1,203 stool samples from 26 mothers and their twins (52 infants), sampled from childbirth to 8 years after birth, with culture-enhanced, deep short-read and long-read stool sequencing from a subset of 10 twins (20 infants) to define transmission, persistence and evolutionary trajectories of gut species from infancy to middle childhood. We constructed 3,995 strain-resolved metagenome-assembled genomes across 399 taxa, and we found that 27.4% persist within individuals. We identified 726 strains shared within families, with Bacteroidales, Oscillospiraceae and Lachnospiraceae, but not Bifidobacteriaceae, vertically transferred. Lastly, we identified weaning as a critical inflection point that accelerates bacterial mutation rates and separates functional profiles of genes accruing mutations.}, } @article {pmid40175647, year = {2025}, author = {Ahn, JS and Kim, S and Han, EJ and Hong, ST and Chung, HJ}, title = {Increasing spatial working memory in mice with Akkermansia muciniphila.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {546}, pmid = {40175647}, issn = {2399-3642}, support = {C512230//Korea Basic Science Institute (KBSI)/ ; RS-2023-00224099//National Research Foundation of Korea (NRF)/ ; }, abstract = {Recent research has shown the gut microbiome's impact on memory, yet limitations hinder the identification of specific microbes linked to cognitive function. We measured spatial working memory in individual mice before and after fecal microbiota transplantation (FMT) to develop a targeted analysis that identifies memory-associated strains while minimizing host genetic effects. Transplantation of human fecal into C57BL/6 mice yielded varied outcomes: some mice showed significant improvements while others had negligible changes, indicating that these changes are due to differences in FMT colonization. Metagenomic analysis, stratified by memory performance, revealed a positive correlation between the abundance of Akkermansia muciniphila and improved memory. Moreover, administering two A. muciniphila strains, GMB 0476 and GMB 2066, to wild-type mice elevated spatial working memory via BDNF activation. Our findings indicate that specific gut microbes, particularly A. muciniphila, may modulate memory and represent potential targets for therapeutic intervention in cognitive enhancement.}, } @article {pmid40175554, year = {2025}, author = {Ryan, FJ and Clarke, M and Lynn, MA and Benson, SC and McAlister, S and Giles, LC and Choo, JM and Rossouw, C and Ng, YY and Semchenko, EA and Richard, A and Leong, LEX and Taylor, SL and Blake, SJ and Mugabushaka, JI and Walker, M and Wesselingh, SL and Licciardi, PV and Seib, KL and Tumes, DJ and Richmond, P and Rogers, GB and Marshall, HS and Lynn, DJ}, title = {Bifidobacteria support optimal infant vaccine responses.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {40175554}, issn = {1476-4687}, abstract = {Accumulating evidence indicates that antibiotic exposure may lead to impaired vaccine responses[1-4]; however, the mechanisms underlying this association remain poorly understood. Here we prospectively followed 191 healthy, vaginally born, term infants from birth to 15 months, using a systems vaccinology approach to assess the effects of antibiotic exposure on immune responses to vaccination. Exposure to direct neonatal but not intrapartum antibiotics was associated with significantly lower antibody titres against various polysaccharides in the 13-valent pneumococcal conjugate vaccine and the Haemophilus influenzae type b polyribosylribitol phosphate and diphtheria toxoid antigens in the combined 6-in-1 Infanrix Hexa vaccine at 7 months of age. Blood from infants exposed to neonatal antibiotics had an inflammatory transcriptional profile before vaccination; in addition, faecal metagenomics showed reduced abundance of Bifidobacterium species in these infants at the time of vaccination, which was correlated with reduced vaccine antibody titres 6 months later. In preclinical models, responses to the 13-valent pneumococcal conjugate vaccine were strongly dependent on an intact microbiota but could be restored in germ-free mice by administering a consortium of Bifidobacterium species or a probiotic already widely used in neonatal units. Our data suggest that microbiota-targeted interventions could mitigate the detrimental effects of early-life antibiotics on vaccine immunogenicity.}, } @article {pmid40175522, year = {2025}, author = {Gichuki, BM and Van Camp, AG and Shao, Y}, title = {A new strain of thought in gut metagenomics.}, journal = {Nature reviews. Microbiology}, volume = {}, number = {}, pages = {}, pmid = {40175522}, issn = {1740-1534}, } @article {pmid40175313, year = {2025}, author = {Fortin, SG and Uhlig, K and Hale, RC and Song, B}, title = {Microplastic biofilms as potential hotspots for plastic biodegradation and nitrogen cycling: A metagenomic perspective.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaf035}, pmid = {40175313}, issn = {1574-6941}, abstract = {Microplastics are an emerging contaminant worldwide, with the potential to impact organisms and facilitate the sorption and release of chemicals. Additionally, they create a novel habitat for microbial communities, forming biofilms known as the plastisphere. While the plastisphere has been studied in select aquatic environments, those in estuarine ecosystems merit additional attention due to their proximity to plastic debris sources. Additionally, the role plastisphere communities play in nutrient cycling has rarely been examined. This study used metagenomic analysis to investigate the taxonomic composition and functional genes of developing plastisphere communities living on petroleum-based (polyethylene and polyvinyl chloride) and biopolymer-based (polylactic acid) substrates. Isolated metagenome assembled genomes (MAGs) showed plastisphere communities have the genes necessary to perform nitrification and denitrification and degrade petroleum and biopolymer-based plastics. The functions of these plastispheres have implications for estuarine nitrogen cycling and provide a possible explanation for the plastisphere microbes' competitiveness in biofilm environments. Overall, microplastics in the estuarine system provide a novel habitat for microbial communities and associated nitrogen cycling, facilitating the growth of microbes with plastic degrading capabilities.}, } @article {pmid40174744, year = {2025}, author = {Liu, M and Wang, S and Zhou, H and Liu, H and Huang, D and Liu, L and Li, Q and Chen, H and Lei, Y and Jin, LN and Zhang, W}, title = {Thermal Environment Driving Specific Microbial Species to Form the Visible Biofilms on the UNESCO World Heritage Dazu Rock Carvings.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121510}, doi = {10.1016/j.envres.2025.121510}, pmid = {40174744}, issn = {1096-0953}, abstract = {The Dazu Rock Carvings, a UNESCO World Heritage site with over a millennium of history, are facing significant deterioration from microbial biofilms. However, the key microbial species responsible and the environmental factors driving their growth remain unclear. To address this gap, we conducted metagenomic sequencing to characterize the microbial community on the carvings, followed by correlation analyses with a variety of environmental factors in the surrounding air and within the rocks. Bacterial communities exhibited significantly higher richness and diversity than eukaryotic communities, though diversity metrics showed no significant differences between visibly colonized and uncolonized surfaces. We identified a distinctive consortium of 64 bacterial species, 35 fungal species, and 1 algal species specifically associated with visible biofilms, occurring at 9.56-fold higher relative abundance in colonized areas. These microorganisms contribute to characteristic green, brown-black, and white coloration on the carvings. Statistical analysis revealed absolute humidity and dew point temperature as key environmental factors influencing biofilm visibility, with thresholds of 21.00 g/m[3] and 23.4°C respectively, above which biofilms became visible. This study provides precise targets for conservation efforts and establishes critical environmental parameters to guide preservation strategies for this irreplaceable cultural heritage.}, } @article {pmid40174653, year = {2025}, author = {Balasundaram, G and Gahlot, P and Hafyan, RH and Tyagi, VK and Gadkari, S and Sahu, A and Barber, B and Mutiyar, PK and Kazmi, AA and Kleiven, H}, title = {Anaerobic digestion of thermal hydrolysis pretreated sludge: Process performance, metagenomic analysis, techno-economic and life cycle assessment.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132470}, doi = {10.1016/j.biortech.2025.132470}, pmid = {40174653}, issn = {1873-2976}, abstract = {This study assessed the potential of thermal hydrolysis process (THP) combined with anaerobic digestion (AD) for high solids sewage sludge treatment across various hydraulic retention times (HRTs). Optimal performance was achieved at a 10-day HRT (6 kg VS/m[3]·day), yielding 408 L CH4/kg VS added and 54 % volatile solids (VS) removal under THP conditions of 160 °C, 30 min, and 6 bar pressure. Microbial analysis revealed predominant acetoclastic and hydrogenotrophic methanogens. Four scenarios were designed and analyzed for environmental and economic performance: Scenario 1 (conventional AD-CHP), Scenario 2 (conventional AD-BioCNG), Scenario 3 (THP AD-BioCNG), and Scenario 4 (THP AD-CHP). The results showed that scenarios with CHP integration achieved better environmental performance by generating sufficient energy to meet demand, with energy consumption as a key factor. Notably, scenario 4 had the lowest global warming potential (GWP) at -0.0185 kg CO2-eq, outperforming conventional AD (Scenario 1) with CHP, which had a GWP of -0.00232 kg CO2-eq. However, profitability analysis showed that Scenario 3 was the most economically viable, with a net present value (NPV) of $4.3 million, an internal rate of return (IRR) of 10.21 %, and a 17-year payback period. Although it had higher capital ($58 million) and operational costs ($12.5 million/year) than Scenario 4 ($45 million and $8.6 million/year), its greater biomethane yield resulted in higher revenue ($20.7 million/year), making it the most profitable option. While Scenario 4 offered the best environmental benefits, Scenario 3 emerged as the most financially sustainable choice. These findings highlight the environmental and economic advantage of utilizing THP-AD process over conventional AD, suggesting that THP-AD optimizes methane production, solids reduction, and environmental impact, making the Bio CNG pathway a sustainable and economically viable option.}, } @article {pmid40174641, year = {2025}, author = {He, T and Zhang, X and Zhang, X}, title = {Thousands-years-old deep-sea DNA viruses reveal the evolution of human pathogenic viruses.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2025.03.057}, pmid = {40174641}, issn = {2090-1224}, abstract = {INTRODUCTION: In the last two decades, outbreaks of pathogenic viruses have led to significant human mortality and economic repercussions. Despite extensive investigations into tracing these viruses in terrestrial environments, their origins remain enigmatic.

OBJECTIVES: The Earth's biosphere encompasses both sunlight-dependent terrestrial and surface ocean ecosystems, as well as the sunlight-independent deep-sea ecosystem. However, the traceability of human pathogenic viruses in the deep sea has not been thoroughly explored. This study aimed to investigate the presence of human pathogenic viruses in the deep sea.

METHODS: In this study, we performed a viral metagenomic analysis using a global deep-sea sediment virome 2.0 dataset which contained 159 deep-sea sediment samples with geologic ages from 2,500 to 7,750 years.

RESULTS: A total of 554,664 viral operational taxonomic units (vOTUs) were identified and further obtained 2,254 potential pathogenic viruses of vertebrates. Among them, 23 vOTUs exhibited high homology with 12 species of human pathogenic viruses which belonged to 4 viral families. Notably, variola virus, the first human pathogenic virus eradicated from humans and now only found in laboratories, was discovered in the ancient deep-sea sediments. The evolution analysis showed that these DNA viruses might represent the ancestors or variants of human pathogenic viruses, suggesting that the deep sea could be a crucial reservoir for human pathogenic viruses.

CONCLUSION: Our findings present all the ancient pathogenic DNA viruses of humans found in the deep sea for the first time, highlighting the source of the future epidemics. It is imperative to implement the stringent virus monitoring and management measures for human activities in marine environments to address the emerging challenges of marine biosecurity and promote sustainable use of oceans.}, } @article {pmid40174574, year = {2025}, author = {Zeng, S and Almeida, A and Mu, D and Wang, S}, title = {Embracing the unknown: Proteomic insights into the human microbiome.}, journal = {Cell metabolism}, volume = {37}, number = {4}, pages = {799-801}, doi = {10.1016/j.cmet.2025.02.003}, pmid = {40174574}, issn = {1932-7420}, abstract = {Protein-level investigations into the human microbiome provide insights into active microbial functions. Recently, Valdés-Mas et al.[1] introduced a metagenome-informed metaproteomics approach to functionally explore species-level microbiome-host interactions and quantify the dietary exposome. Its potential has been implemented in mice and humans to uncover proteomic signatures of health and inflammatory bowel disease.}, } @article {pmid40174565, year = {2025}, author = {Krohn, C and Khudur, L and Biek, SK and Elliott, JA and Tabatabaei, S and Jiang, C and Wood, JL and Dias, DA and Dueholm, MKD and Rees, CA and O'Carroll, D and Stuetz, R and Batstone, DJ and Surapaneni, A and Ball, AS}, title = {Microbial population shifts during disturbance induced foaming in anaerobic digestion of primary and activated sludge.}, journal = {Water research}, volume = {281}, number = {}, pages = {123548}, doi = {10.1016/j.watres.2025.123548}, pmid = {40174565}, issn = {1879-2448}, abstract = {Foaming during anaerobic digestion (AD) of sewage sludge is poorly understood and remains an uncontrollable operational obstacle for sewage treatment systems globally, causing mechanical damage, increased hazards and reduced biogas recovery. Foams during AD commonly occur after process disturbances, such as organic loading shocks. However, it is still unclear whether these foam events are biologically driven and linked to the abundance of organisms like filamentous or hydrophobic bacteria. A time-series study was conducted, comparing digestion performance, microbial community succession, metagenomes, and metabolomes in six anaerobic continuous stirred-tank reactors (CSTRs): a control group fed normally (n = 3), and one treated group inhibited through organic shock loading of more than twice the steady state loading rate with glycerol (treatment, n = 3). As soon as microbial activity and methanogenesis recovered after inhibition, significant volumes of foam accumulated simultaneously in the reactor headspace of the three treated CSTRs. Microbial abundance profiles (16S rRNA, V3-V4) from 165 days of operation showed that filamentous or mycolic acid-producing organisms were not associated with this foam event. Shock loading led to acidification, biomass decline and microbial imbalance, contributing indirectly to the foam event. During that period, metabolomes and functional pathway abundances indicated that the stressed microbial biomass was enriched in long-chain fatty acids prior to foaming. This biomass, combined with pH changes, may have modified the physicochemical properties of sludge, leading to the fractionation of organic mass once gas production resumed. More research is needed to understand how abiotic and biotic interactions contribute to foam formation.}, } @article {pmid40174457, year = {2025}, author = {Han, Q and Wang, Y and Shi, C and Qian, Y and Wang, X and Wang, S and Sun, X and Yu, Q and Li, H}, title = {Urban landscape lakes with backwater hide higher antibiotic resistance risk than living water.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138101}, doi = {10.1016/j.jhazmat.2025.138101}, pmid = {40174457}, issn = {1873-3336}, abstract = {The pollution of antibiotic resistance genes (ARGs) in urban landscape lakes threatens the aquatic ecosystems and public health. However, a comprehensive understanding of the fate of ARGs in different types of park landscape lakes (i.e., backwater and living water) remains deficient. Here, we profiled the distribution, diversity, origin and potential spread risk to human of ARGs in backwater and living water using metagenomics and 16S rRNA gene sequencing. Our results showed higher antibiotic resistance risk presented in backwater due to higher ARG diversity, while higher resistance transfer risk occurred in living water due to higher mobile genetic elements (MGEs) diversity. Source tracking analysis revealed Yellow River water was the main the dominant source of ARGs in both backwater and living water, with an average contribution of 41.06 % and 65.82 %, respectively. Notably, nine high-risk ARGs (such as mdtM and msrA) significantly enriched in human feces, implying possible spread risk from environment to human. Metagenomics binning revealed that MAGs carrying ARGs mainly belong to Actinobacteria, while MAGs carrying MGEs belong to Proteobacteria. Our study highlights the significance of healthy management of park landscape lakes to prevent the spread of resistomes to the public.}, } @article {pmid40174456, year = {2025}, author = {Long, M and Zheng, CW and Zhou, C and Rittmann, BE}, title = {Mitigating chromate toxicity through concurrent denitrification in the H2-based membrane biofilm reactor.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138073}, doi = {10.1016/j.jhazmat.2025.138073}, pmid = {40174456}, issn = {1873-3336}, abstract = {High concentrations of hexavalent chromium (Cr(VI)) in industrial wastewaters pose significant environmental and health hazards. Biotranformation is a viable means to lower Cr(VI) toxicity, but research to date has focused on wastewaters with low concentrations (e.g., 2-5 mg/L Cr(VI)). This study evaluated the dynamics of biosorption and biotransformation of higher-concentration Cr(VI) by biofilms in the H2-based membrane biofilm reactor (MBfR). While the biofilm in an MBfR receiving Cr(VI) alone had limited capacity to remove Cr(VI) and Cr(VI) removal ceased in 30 days, an autotrophic denitrifying biofilms achieved 99 % reduction of over 20 mg/L Cr(VI) to less-toxic trivalent chromium (Cr(III)) in continuous long-term operation system over 4 months. Increasing the H2 pressure from 3 psig to 10 psig improved Cr(VI) removal from 87 % to 99 %, which occurred in parallel with over 95 % NO3[-] reduction to N2. Metagenomic analyses revealed the mechanisms of Cr(VI) bioreduction and highlighted the beneficial role of nitrate (NO3[-]) as the primary electron acceptor. For example, nitrite reductase NrfA could reduce Cr(VI), which lowered Cr(VI) caused oxidative stress. This research demonstrates the MBfR's effectiveness in reducing elevated levels of Cr(VI) and provides mechanistic understanding of the roles of denitrification in accelerating Cr(VI) reduction and detoxification.}, } @article {pmid40174424, year = {2025}, author = {Dai, Z and Li, Y and Zhang, Y and Xiang, T and Peng, J and Mao, X and Fan, Y and Wang, F and Yang, S and Cao, W}, title = {Nutrient enrichment by high aquaculture effluent input exacerbates imbalances between methane production and oxidation in mangrove sediments.}, journal = {Water research}, volume = {280}, number = {}, pages = {123552}, doi = {10.1016/j.watres.2025.123552}, pmid = {40174424}, issn = {1879-2448}, abstract = {Frequent aquaculture activities introduce substantial nutrients into mangrove ecosystems; however, the impact of this nutrient enrichment on methane (CH4) emissions and the associated microbial communities remains largely unexplored. In this study, we used the static chamber method, combined with 16S rRNA-based, metagenomic sequencing and binning techniques, to investigate the emission patterns of greenhouse gases (GHGs), with a particular focus on CH4, in mangroves subjected to different levels of effluents. The results showed that the effluent input decreased the mineral protection of sediment carbon (C) pools and increased C loss by more than double. In particular, high effluent input increased CH4 emissions by 243.3 %. Random forest analysis revealed that changes in methanogens were an important factor in explaining the variation of CH4 emissions. Amplicon data showed that the proportion of methylotrophic methanogens increased after effluent input, and metagenomic binning further attributed this change to the adaptability of methylotrophic methanogens to the substances transporting by the effluent. The enhanced hypoxia in sediments resulting from effluent input promoted the transition of methanotrophic communities from aerobic to anaerobic types and made anaerobic oxidation of CH4 more reliant on sulfur reduction rather than nitrate reduction. The PLS model further revealed that the nutrients brought by effluent input stimulated an increase in DOC content which induced an imbalance between CH4 production and oxidation in sediments by facilitating methanogens but inhibiting methanotrophs, ultimately resulting in an increase in CH4 fluxes. These findings underscore the significance of mangroves receiving effluent input as critical consequent reactors, highlighting the necessity to consider effects of high nutrient enrichment by aquaculture effluent input on GHG emissions and blue C potential in mangroves.}, } @article {pmid40172536, year = {2025}, author = {Madison, JD and Osborne, OG and Ellison, A and Garvey Griffith, CN and Gentry, L and Gross, H and Gratwicke, B and Grayfer, L and Muletz-Wolz, CR}, title = {Probiotic colonization of Xenopus laevis skin causes short-term changes in skin microbiomes and gene expression.}, journal = {Infection and immunity}, volume = {}, number = {}, pages = {e0056924}, doi = {10.1128/iai.00569-24}, pmid = {40172536}, issn = {1098-5522}, abstract = {Probiotic therapies have been suggested for amelioration efforts of wildlife disease such as chytridiomycosis caused by Batrachochytrium spp. in amphibians. However, there is a lack of information on how probiotic application affects resident microbial communities and immune responses. To better understand these interactions, we hypothesized that probiotic application would alter microbial community composition and host immune expression in Xenopus laevis. Accordingly, we applied three amphibian-derived and anti-Batrachochytrium bacteria strains (two Pseudomonas spp. and one Stenotrophomonas sp.) to X. laevis in monoculture and also as a cocktail. We quantified microbial community structure using 16S rRNA gene sequencing. We also quantified genes involved in X. laevis immune responses using quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) and skin transcriptomics over 1 and 3-week periods. All probiotic treatments successfully colonized X. laevis skin for 3 weeks, but with differential amplicon sequence variant (ASV) sequence counts over time. Bacterial community and immune gene effects were most pronounced at week 1 post-probiotic exposure and decreased thereafter. All probiotic treatments caused initial changes to bacterial community alpha and beta diversity, including reduction in diversity from pre-exposure anti-Batrachochytrium bacterial ASV relative abundance. Probiotic colonization by Pseudomonas probiotic strain RSB5.4 reduced expression of regulatory T cell marker (FOXP3, measured with RT-qPCR) and caused the greatest gene expression changes detected by transcriptomics. Single bacterial strains and mixed cultures, therefore, altered amphibian microbiome-immune interactions. This work will help to improve our understanding of the role of the microbiome-immune interface underlying both disease dynamics and emergent eco-evolutionary processes.IMPORTANCEAmphibian skin microbial communities have an important role in determining disease outcomes, in part through complex yet poorly understood interactions with host immune systems. Here we report that probiotic-induced changes to the Xenopus laevis frog skin microbial communities also result in significant alterations to these animals' immune gene expression. These findings underscore the interdependence of amphibian skin immune-microbiome interactions.}, } @article {pmid40172519, year = {2025}, author = {Chaves-Sierra, C and Botero-Rozo, D and Rodriguez-Cruz, MC and Montoya, C and Romero, HM}, title = {Detection and molecular characterization of 'Candidatus Liberibacter' in Colombian oil palms affected by Lethal Wilt Disease.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-10-24-2079-RE}, pmid = {40172519}, issn = {0191-2917}, abstract = {Lethal wilt (LW), also known as "Marchitez Letal (ML)" in Colombia, is an endemic disease affecting oil palms (Elaeis guineensis Jacq.) and is a leading cause of crop loss. The disease is characterized by the drying of leaflets from the tip to the base, primarily impacting the lower third of the plant and progressively moving upward. This progression leads to physiological disturbances, including necrosis at the tips of immature inflorescence bracts (spines) and the detachment of bunch fruits, ultimately causing wilting. As a phytosanitary measure, infected palms are eradicated to prevent further spread of the disease. The primary goal of this research was to identify the bacteria associated with LW and to validate a molecular detection method. A 16S amplicon-based analysis was employed to identify and compare the microbial diversity in LW-affected palm tissues with those of healthy plants. Among the 16 OTUs corresponding to different bacterial genera found in all LW samples, taxonomic classification and symptomatology suggested that the bacteria closely associated with LW belong to the genus Candidatus Liberibacter. Further phylogenetic analysis indicated that these bacteria are part of the Rhizobiaceae family, grouping closely with other species of the genus Candidatus. Liberibacter. The concentration of the pathogen in different oil palm tissues was determined using droplet digital PCR (ddPCR) and quantitative PCR (qPCR), expressed in copies/µL in the LW samples. This study represents the first report of 'Candidatus Liberibacter sp'. being associated with lethal wilt in oil palms of the Arecaceae family in Colombia. The findings from this research have the potential to contribute significantly to the development of effective management strategies to prevent crop losses.}, } @article {pmid40172478, year = {2025}, author = {Wang, H and Zhao, X and Li, D and Meng, L and Liu, S and Zhang, Y and Huo, L}, title = {Marine Metagenome Mining Reveals Lanthipeptides Colwesin A-C, Exhibiting Novel Ring Topology and Anti-inflammatory Activity.}, journal = {ACS synthetic biology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acssynbio.5c00057}, pmid = {40172478}, issn = {2161-5063}, abstract = {Marine natural products are promising sources for drug discovery due to their unique structures and diverse biological activities. The establishment of the Global Marine Microbiome Genome Catalogue (GOMC) has significantly expanded the repository of natural products derived from marine-associated bacteria. In this study, we identified the Class I lanthipeptide biosynthetic gene cluster col from Colwellia_A sp. based on the GOMC database. Through heterologous expression in Escherichia coli and subsequent structural analysis, we characterized three novel lanthipeptides, colwesins A-C, which possess unique cyclic structures characterized by an exceptionally large number of thioether rings. To the best of our knowledge, colwesin C is the first lanthipeptide simultaneously containing locked, nonoverlapped, and nested ring topologies. These findings highlight the robust ring-forming capacity of Class I lanthipeptide synthetases. Colwesins A-C were found to exhibit anti-inflammatory activity in lipopolysaccharide-induced mouse macrophage RAW264.7 cell lines without detectable cytotoxicity. Overall, our results broaden our understanding of the structural diversity of marine-derived lanthipeptides.}, } @article {pmid40172215, year = {2025}, author = {Brito Rodrigues, P and de Rezende Rodovalho, V and Sencio, V and Benech, N and Creskey, M and Silva Angulo, F and Delval, L and Robil, C and Gosset, P and Machelart, A and Haas, J and Descat, A and Goosens, JF and Beury, D and Maurier, F and Hot, D and Wolowczuk, I and Sokol, H and Zhang, X and Ramirez Vinolo, MA and Trottein, F}, title = {Integrative metagenomics and metabolomics reveal age-associated gut microbiota and metabolite alterations in a hamster model of COVID-19.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2486511}, doi = {10.1080/19490976.2025.2486511}, pmid = {40172215}, issn = {1949-0984}, mesh = {Animals ; *Gastrointestinal Microbiome ; *COVID-19/microbiology/virology/metabolism ; *Metagenomics ; *Metabolomics ; *Disease Models, Animal ; Cricetinae ; *SARS-CoV-2/genetics ; Aging ; Age Factors ; Dysbiosis/microbiology ; Male ; Bacteria/classification/genetics/metabolism/isolation & purification ; Mesocricetus ; Metabolome ; }, abstract = {Aging is a key contributor of morbidity and mortality during acute viral pneumonia. The potential role of age-associated dysbiosis on disease outcomes is still elusive. In the current study, we used high-resolution shotgun metagenomics and targeted metabolomics to characterize SARS-CoV-2-associated changes in the gut microbiota from young (2-month-old) and aged (22-month-old) hamsters, a valuable model of COVID-19. We show that age-related dysfunctions in the gut microbiota are linked to disease severity and long-term sequelae in older hamsters. Our data also reveal age-specific changes in the composition and metabolic activity of the gut microbiota during both the acute phase (day 7 post-infection, D7) and the recovery phase (D22) of infection. Aged hamsters exhibited the most notable shifts in gut microbiota composition and plasma metabolic profiles. Through an integrative analysis of metagenomics, metabolomics, and clinical data, we identified significant associations between bacterial taxa, metabolites and disease markers in the aged group. On D7 (high viral load and lung epithelial damage) and D22 (body weight loss and fibrosis), numerous amino acids, amino acid-related molecules, and indole derivatives were found to correlate with disease markers. In particular, a persistent decrease in phenylalanine, tryptophan, glutamic acid, and indoleacetic acid in aged animals positively correlated with poor recovery of body weight and/or lung fibrosis by D22. In younger hamsters, several bacterial taxa (Eubacterium, Oscillospiraceae, Lawsonibacter) and plasma metabolites (carnosine and cis-aconitic acid) were associated with mild disease outcomes. These findings support the need for age-specific microbiome-targeting strategies to more effectively manage acute viral pneumonia and long-term disease outcomes.}, } @article {pmid40172109, year = {2025}, author = {Tarracchini, C and Lordan, C and Milani, C and Moreira, LPD and Alabedallat, QM and de Moreno de LeBlanc, A and Turroni, F and Lugli, GA and Mancabelli, L and Longhi, G and Brennan, L and Mahony, J and LeBlanc, JG and Nilaweera, KN and Cotter, PD and van Sinderen, D and Ventura, M}, title = {Vitamin biosynthesis in the gut: interplay between mammalian host and its resident microbiota.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {}, number = {}, pages = {e0018423}, doi = {10.1128/mmbr.00184-23}, pmid = {40172109}, issn = {1098-5557}, abstract = {SUMMARYIn recent years, exhaustive efforts have been made to dissect the composition of gut-associated microbial communities and associated interactions with their human host, which are thought to play a crucial role in host development, physiology, and metabolic functions. Although such studies were initially focused on the description of the compositional shifts in the microbiota that occur between different health conditions, more recently, they have provided key insights into the functional and metabolic contributions of the gut microbiota to overall host physiology. In this context, an important metabolic activity of the human gut microbiota is believed to be represented by the synthesis of various vitamins that may elicit considerable benefits to human health. A growing body of scientific literature is now available relating to (predicted) bacterial vitamin biosynthetic abilities, with ever-growing information concerning the prevalence of these biosynthetic abilities among members of the human microbiota. This review is aimed at disentangling if and how cooperative trophic interactions of human microbiota members contribute to vitamin production, and if such, gut microbiota-mediated vitamin production varies according to different life stages. Moreover, it offers a brief exploration of how different diets may influence vitamin production by shaping the overall composition and metabolic activity of the human gut microbiota while also providing preliminary insights into potential correlations between human microbiota-associated vitamin production and the occurrence of human diseases and/or metabolic disorders.}, } @article {pmid40171165, year = {2025}, author = {Shi, H and Li, J}, title = {MAGs-based genomic comparison of gut significantly enriched microbes in obese individuals pre- and post-bariatric surgery across diverse locations.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1485048}, pmid = {40171165}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Obesity/microbiology ; *Bariatric Surgery ; Metagenome ; Metagenomics/methods ; Genomics ; Bacteria/classification/genetics/isolation & purification/metabolism ; Gastric Bypass ; Computational Biology/methods ; Adult ; }, abstract = {INTRODUCTION: Obesity, a pressing global health issue, is intricately associated with distinct gut microbiota profiles. Bariatric surgeries, such as Laparoscopic Sleeve Gastrectomy (LSG), Sleeve Gastrectomy (SG), and Roux-en-Y Gastric Bypass (RYGB), induce substantial weight loss and reshape gut microbiota composition and functionality, yet their comparative impacts remain underexplored.

METHODS: This study integrated four published metagenomic datasets, encompassing 500 samples, and employed a unified bioinformatics workflow for analysis. We assessed gut microbiota α-diversity, identified species biomarkers using three differential analysis approaches, and constructed high-quality Metagenome-Assembled Genomes (MAGs). Comparative genomic, functional profiling and KEGG pathway analyses were performed, alongside estimation of microbial growth rates via Peak-to-Trough Ratios (PTRs).

RESULTS: RYGB exhibited the most pronounced enhancement of gut microbiota α-diversity compared to LSG and SG. Cross-cohort analysis identified 39 species biomarkers: 27 enriched in the non-obesity group (NonOB_Enrich) and 12 in the obesity group (OB_Enrich). Among the MAGs, 177 were NonOB_Enrich and 14 were OB_Enrich. NonOB_Enrich MAGs displayed enriched carbohydrate degradation profiles (e.g., GH105, GH2, GH23, GH43, and GT0 families) and higher gene diversity in fatty acid biosynthesis and secondary metabolite pathways, alongside significant enrichment in amino acid metabolism (KEGG analysis). Post-surgery, Akkermansia muciniphila and Bacteroides uniformis showed elevated growth rates based on PTRs.

DISCUSSION: These findings underscore RYGB's superior impact on gut microbiota diversity and highlight distinct microbial functional adaptations linked to weight loss, offering insights for targeted therapeutic strategies.}, } @article {pmid40170926, year = {2025}, author = {Zhai, R and Zhao, C and Chang, L and Liu, J and Zhao, T and Jiang, J and Zhu, W}, title = {Diets shape thermal responses in Chinese giant salamanders by altering liver metabolism.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1546912}, pmid = {40170926}, issn = {1664-302X}, abstract = {Diet can influence the thermal performance of ectotherms, providing potential strategies for biological conservation in the context of global warming. The endangered Andrias davidianus is susceptible to heat stress due to energy deficiency in the liver when fed a worm-based diet rich in carbohydrates. A fish-based diet, rich in protein and lipids, improves their thermal performance, but the underlying physiological mechanisms remain unclear. In this study, we used metabolomics and metagenomics to examine the combined effects of temperature (15, 20, and 25°C) and diet (fish-based and worm-based) on liver metabolism and gut microbiota. Our results show that both temperature and diet shape liver metabolism, with several vital metabolic pathways (e.g., TCA cycle and sulfate metabolism) regulated by their combined effects. Notably, diet-dependent thermal responses in energy metabolism were observed, with fish-fed salamanders exhibiting a marked upregulation of the TCA cycle intermediates under heat stress, a response absent in worm-fed individuals. Given the role of TCA cycle in heat susceptibility of A. davidianus, these findings suggest that the TCA cycle likely mediates the interactive effects of temperature and diet on thermal performance. We then examined whether the gut microbiota is also a target of interactive effects or a mediator of the diet's influence on liver metabolism. While both temperature and diet shape microbiota composition, functional shifts occur only in response to temperature, indicating that the microbiota is not a major link between diet and liver metabolism. However, several bacterial groups (e.g., Thiosulfatimonas and Alcanivorax), jointly regulated by temperature and diet, correlate with liver metabolites, suggesting alternative, function-independent pathways through which dietary-related microbial changes may influence liver metabolism and even thermal tolerance. Overall, this study provides molecular insights into the dietary modulation of thermal performance in A. davidianus and highlight the potential of dietary microbial management strategies for amphibian conservation.}, } @article {pmid40170918, year = {2025}, author = {Hager, K and Luo, ZH and Montserrat-Diez, M and Ponce-Toledo, RI and Baur, P and Dahlke, S and Andrei, AS and Bulzu, PA and Ghai, R and Urich, T and Glatzel, S and Schleper, C and Rodrigues-Oliveira, T}, title = {Diversity and environmental distribution of Asgard archaea in shallow saline sediments.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1549128}, pmid = {40170918}, issn = {1664-302X}, abstract = {In recent years, our understanding of archaeal diversity has greatly expanded, especially with the discovery of new groups like the Asgard archaea. These archaea show diverse phylogenetic and genomic traits, enabling them to thrive in various environments. Due to their close relationship to eukaryotes, a large number of metagenomic studies have been performed on Asgard archaea. Research on the fine scale distribution, diversity and quantification in saline aquatic sediments where they mostly occur, has, however, remained scarce. In this study, we investigated depths of shallow saline sediment cores from three distinct European environments: the Baltic Sea near Hiddensee, the coastal Lake Techirghiol in Romania, and an estuarine canal in Piran, Slovenia. Based on 16S rDNA amplicon sequencing, we observe variation in the relative abundance and occurrence of at least seven different Asgard groups that are distinct between the three environments and in their depth distribution. Lokiarchaeia and Thorarchaeia emerge as dominant Asgard groups across all sites, reaching maximal relative abundances of 2.28 and 2.68% of the total microbial communities respectively, with a maximal abundance of all Asgard reaching approx. 5.21% in Hiddensee. Quantitative PCR assays provide insights into the absolute abundance of Lokiarchaeia, supporting distinct patterns of distribution across depths in different sediments. Co-occurrence network analysis indicates distinct potential microbial partners across different Asgard groups. Overall, our study shows that Asgard archaea are found as a stable component in shallow sediment layers and have considerably diversified on macro- and microscales.}, } @article {pmid40170844, year = {2025}, author = {Zhou, Y and Han, W and Feng, Y and Wang, Y and Liu, X and Sun, T and Xu, J}, title = {Revealing gut microbiota biomarkers associated with melanoma immunotherapy response and key bacteria-fungi interaction relationships: evidence from metagenomics, machine learning, and SHAP methodology.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1539653}, pmid = {40170844}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Melanoma/therapy/immunology/microbiology ; *Metagenomics/methods ; *Immunotherapy/methods ; *Machine Learning ; Male ; *Bacteria/genetics/classification/immunology ; Female ; Fungi/immunology ; Middle Aged ; Skin Neoplasms/immunology/therapy/microbiology ; Biomarkers ; Aged ; Adult ; Treatment Outcome ; }, abstract = {INTRODUCTION: The gut microbiota is associated with the response to immunotherapy in cutaneous melanoma (CM). However, gut fungal biomarkers and bacterial-fungal interactions have yet to be determined.

METHODS: Metagenomic sequencing data of stool samples collected before immunotherapy from three independent groups of European ancestry CM patients were collected. After characterizing the relative abundances of bacteria and fungi, Linear Discriminant Analysis Effect Size (LEfSe) analysis, Random Forest (RF) model construction, and SHapley Additive exPlanations (SHAP) methodology were applied to identify biomarkers and key bacterial-fungal interactions associated with immunotherapy responders in CM.

RESULTS: Diversity analysis revealed significant differences in the bacterial and fungal composition between CM immunotherapy responders and non-responders. LEfSe analysis identified 45 bacterial and 4 fungal taxa as potential biomarkers. After constructing the RF model, the AUC of models built using bacterial and fungal data separately were 0.64 and 0.65, respectively. However, when bacterial and fungal data were combined, the AUC of the merged model increased to 0.71. In the merged model, the following taxa were identified as important biomarkers: Romboutsia, Endomicrobium, Aggregatilinea, Candidatus Moduliflexus, Colwellia, Akkermansia, Mucispirillum, and Rutstroemia, which were associated with responders, whereas Zancudomyces was associated with non-responders. Moreover, the positive correlation interaction between Akkermansia and Rutstroemia is considered a key bacterial-fungal interaction associated with CM immunotherapy response.

CONCLUSION: Our results provide valuable insights for the enrichment of responders to immunotherapy in CM patients. Moreover, this study highlights the critical role of bacterial-fungal interactions in CM immunotherapy.}, } @article {pmid40170341, year = {2025}, author = {Sorn, S and Matsuura, N and Honda, R}, title = {Metagenome-Assembled Genomes and Metatranscriptome Analysis of Perfluorooctane Sulfonate-Reducing Bacteria Enriched From Activated Sludge.}, journal = {Environmental microbiology}, volume = {27}, number = {4}, pages = {e70087}, doi = {10.1111/1462-2920.70087}, pmid = {40170341}, issn = {1462-2920}, support = {19K22925//Japan Society for the Promotion of Science/ ; 22K19865//Japan Society for the Promotion of Science/ ; //Steel Foundation for Environmental Protection Technology/ ; }, mesh = {*Fluorocarbons/metabolism ; *Alkanesulfonic Acids/metabolism ; *Sewage/microbiology ; *Bacteria/genetics/metabolism/classification/isolation & purification ; *Biodegradation, Environmental ; *Metagenome ; *RNA, Ribosomal, 16S/genetics ; Genome, Bacterial ; Transcriptome ; Biotransformation ; Phylogeny ; }, abstract = {Per- and polyfluoroalkyl substances (PFAS) exhibit a widespread distribution across diverse global ecosystems throughout their lifecycle, posing substantial risks to human health. The persistence of PFAS makes biodegradation a challenging yet environmentally friendly solution for their treatment. In the authors' previous study, a bacterial consortium capable of reducing perfluorooctane sulfonate (PFOS) was successfully enriched from activated sludge. This study aimed to investigate the array of genes associated with PFOS reduction via biosorption and biotransformation to elucidate the metabolic pathways. Two metagenome-assembled genomes (MAGs) based on 16S rRNA sequences that share 99.86% and 97.88% similarity with Hyphomicrobium denitrificans and Paracoccus yeei, respectively were obtained. They were found to contain several genes encoding enzymes that potentially regulate biofilm formation of biosorption and facilitate the desulfonation and defluorination processes of biotransformation. Transcriptomic analysis demonstrated the high expression levels of these genes, including alkanesulfonate monooxygenase, catechol dioxygenase, (S)-2-haloacid dehalogenase and putative cytochrome P450, suggesting their involvement in PFOS biotransformation. The expression of these genes supports the presence of candidate metabolites of PFOS biotransformation detected in the previous study. These findings emphasise the significant potential of bacterial consortia and the crucial role played by genes encoding enzymes in facilitating the remediation of PFOS contaminants.}, } @article {pmid40170118, year = {2025}, author = {Li, J and Sun, W and Cao, Y and Wu, J and Duan, L and Zhang, M and Luo, X and Deng, Q and Peng, Z and Mou, X and Li, W and Wang, P}, title = {Increased temperature enhances microbial-mediated lignin decomposition in river sediment.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {89}, pmid = {40170118}, issn = {2049-2618}, support = {32200090//National Natural Science Foundation of China/ ; 91951205//National Natural Science Foundation of China/ ; 2023A1515012270//Guangdong Basic and Applied Basic Research Foundation, China/ ; }, mesh = {*Lignin/metabolism ; *Geologic Sediments/microbiology ; *Rivers/microbiology/chemistry ; *Temperature ; *RNA, Ribosomal, 16S/genetics ; Bacteria/metabolism/classification/genetics ; Carbon Dioxide/metabolism ; Carbon Cycle ; Metagenomics ; }, abstract = {BACKGROUND: Lignin, as the most abundant recalcitrant organic carbon in terrestrial ecosystems, plays a crucial role in the Earth's carbon cycle. After lignin entering aquatic environments, portion of it tends to accumulate in sediments, forming a stable carbon relatively reservoir. However, the increasing temperature caused by human activities may impact microbial-mediated lignin decomposition, thereby affecting sedimentary carbon reservoirs. Therefore, revealing how temperature affects microbial-mediated lignin decomposition in river sediment, a topic that remains elusive, is essential for comprehending the feedbacks between river carbon reservoirs and climate. To address this, we conducted stable isotope probing of river surface sediment using [13]C-lignin and [13]C-vanillin, and utilized a series of techniques, including CO2 production analysis, 16S rRNA gene amplicon sequencing, metagenomics, and metatranscriptomics, to identify the lignin-decomposing microbes and the effects of temperature on microbial-mediated lignin decomposition.

RESULTS: We found that elevated temperatures not only increased the total sediment respiration (total CO2) and the CO2 emissions from lignin/vanillin decomposition, but also enhanced priming effects. The [13]C-labled taxa, including Burkholderiales, Sphingomonadales, and Pseudomonadales, were identified as the main potential lignin/vanillin decomposers, and their abundances and activity significantly increased as temperature increased. Furthermore, we observed that increasing temperature significantly increased the activity of lignin decomposing pathways, including β-aryl ether fragments and 4,5-PDOG pathway. Additionally, as temperature increases, the transcriptional abundances of other carbon cycling related genes, such as pulA (starch decomposition) and xyla (hemicellulose decomposition), also exhibited increasing trends. Overall, our study elucidated the potential lignin-decomposing microbes and pathways in river sediment and their responses to temperature increasing.

CONCLUSIONS: Our study demonstrated that the temperature increasing can increase the rate of lignin/vanillin decomposition via affecting the activity of lignin-decomposing microbes. This finding indicates that the ongoing intensification of global warming may enhance the decomposition of recalcitrant organic carbon in river sediment, thereby impacting global carbon cycling. Video Abstract.}, } @article {pmid40169660, year = {2025}, author = {Legrand, TPRA and Alexandre, PA and Wilson, A and Farr, RJ and Reverter, A and Denman, SE}, title = {Genome-centric metagenomics reveals uncharacterised microbiomes in Angus cattle.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {547}, pmid = {40169660}, issn = {2052-4463}, mesh = {Animals ; Cattle/microbiology ; *Metagenomics ; *Microbiota ; *Feces/microbiology ; Metagenome ; Saliva/microbiology ; Mouth/microbiology ; }, abstract = {Understanding the intricate nexus between cattle health and microbiome dynamics holds profound implications for enhancing animal productivity and welfare. However, our understanding of the role of these microbial communities is limited in beef cattle, especially in understudied body sites such as the oral and nasal microbiome. Here, using a genome-centric metagenomics approach, we recovered substantial metagenome-assembled genomes (MAGs) from the faecal, oral and nasal microbiome of Australian Angus cattle from different herds and life stages. The MAGs recovered from faecal samples were dominated by Bacillota and Bacteroidota, while the MAGs from saliva and nasal mucus samples were mainly associated with Pseudomonadota, Actinomycetota and Bacteroidota. Functional annotation of the MAGs revealed enriched pathways involved in the production of some amino acids, nucleic acids and short chain fatty acids (SCFA). The metabolic capacities of the MAGs were correlated with their taxonomy, notably at the phylum level. Overall, this study provides a comprehensive catalogue of MAGs to further our understanding of their role in the health and fitness of beef cattle.}, } @article {pmid40169555, year = {2025}, author = {Li, H and Liu, P and Sun, T and Li, Y and Wu, J and Huang, Y and Yang, J and Yuan, M and Zhang, J and Yang, J and Wong, ML and Licinio, J and Zheng, P}, title = {Dynamic alterations of depressive-like behaviors, gut microbiome, and fecal metabolome in social defeat stress mice.}, journal = {Translational psychiatry}, volume = {15}, number = {1}, pages = {115}, pmid = {40169555}, issn = {2158-3188}, mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; *Stress, Psychological/metabolism/microbiology ; *Feces/microbiology/chemistry ; Male ; *Social Defeat ; *Metabolome ; *Disease Models, Animal ; *Depressive Disorder, Major/metabolism/microbiology ; *Behavior, Animal ; *Anhedonia ; Humans ; Mice, Inbred C57BL ; Female ; RNA, Ribosomal, 16S/genetics ; Depression/metabolism/microbiology ; }, abstract = {Gut microbiome is implicated in the onset and progression of major depressive disorder (MDD), but the dynamic alterations of depressive symptoms, gut microbiome, and fecal metabolome across different stages of stress exposure remain unclear. Here, we modified the chronic social defeat stress (CSDS) model to evaluate mice subjected to social defeat stress for 1, 4, 7, and 10 days. Behavioral tests, 16S rRNA, metagenomics, and fecal metabolomics were conducted to investigate the impact of stress exposure on behaviors, gut microbiota and fecal metabolites. We observed that depressive-like behaviors, such as anhedonia and social avoidance, worsened significantly as stress exposure increased. The microbial composition, function, and fecal metabolites exhibited distinct separations across the different social defeat stress groups. Mediation analysis identified key bacteria, such as Lachnospiraceae_UCG-001 and Bacteroidetes, and fecal metabolites like valeric acid and N-acetylaspartate. In our clinical depression cohort, we confirmed that fecal valeric acid levels, were significantly lower in depressive-like mice and MDD patients, correlating closely with stress exposure and anhedonia in mice. Further analysis of serum and brain metabolites in mice revealed sustained changes of N-acetylaspartate abundance in fecal, serum, and cortical samples following increasing stress exposure. Together, this study elucidated the characteristics of depressive-like behaviors, gut microbiome, and fecal metabolome across various social defeat stress exposure, and identified key bacteria and fecal metabolites potentially involved in modulating social defeat stress response and depressive-like behaviors, providing new insights into the pathogenesis and intervention of depression.}, } @article {pmid40169141, year = {2025}, author = {Zhang, J and Ying, X and Hu, R and Huang, Y and Wang, R and Wu, L and Han, D and Ma, R and He, K}, title = {Metagenomic and metabolomic analysis of gut microbiome's role in spinal cord injury recovery in rats.}, journal = {Biomolecules & biomedicine}, volume = {}, number = {}, pages = {}, doi = {10.17305/bb.2025.12164}, pmid = {40169141}, issn = {2831-090X}, abstract = {Spinal cord injury (SCI) induces profound systemic changes, including disruptions in gut microbiome composition and host metabolism. This study aimed to investigate the impact of SCI on gut microbial diversity and serum metabolites in rats, and to explore potential microbiome-metabolite interactions that may influence recovery. Male Sprague-Dawley (SD) rats were assigned to either SCI or sham-operated groups. Fecal samples were collected for whole-genome metagenomic sequencing, and serum samples were analyzed using untargeted metabolomics. Gut microbial composition and diversity were assessed using α- and β-diversity indices, while Linear discriminant analysis effect size (LEfSe) identified differentially abundant taxa. Metabolomic pathway analysis was performed to detect significant changes in serum metabolites, and Spearman's correlation was used to evaluate associations between gut microbes and metabolites. SCI significantly altered gut microbiota composition, with increased proportions of Ligilactobacillus and Staphylococcus, and decreased proportions of Lactobacillus and Limosilactobacillus. Metabolomic analysis revealed disrupted energy metabolism and elevated oxidative stress in SCI rats, as indicated by increased serum levels of pyruvate and lactic acid. Correlation analysis further identified significant associations between specific gut bacteria and key metabolites, suggesting microbiome-driven metabolic dysregulation following SCI. These findings highlight significant interactions between the gut microbiota and host metabolism after SCI and suggest that microbiome-targeted interventions may hold therapeutic potential for improving recovery by modulating metabolic function and oxidative stress responses.}, } @article {pmid40156868, year = {2025}, author = {Yang, W and Luyten, Y and Reister, E and Mangelson, H and Sisson, Z and Auch, B and Liachko, I and Roberts, RJ and Ettwiller, L}, title = {Proxi-RIMS-seq2 applied to native microbiomes uncovers hundreds of known and novel m5C methyltransferase specificities.}, journal = {Nucleic acids research}, volume = {53}, number = {6}, pages = {}, pmid = {40156868}, issn = {1362-4962}, support = {//New England Biolabs, Inc./ ; R44AI172703/GF/NIH HHS/United States ; //Bill & Melinda Gates Foundation/ ; }, mesh = {*Methyltransferases/metabolism/genetics ; *Microbiota/genetics ; DNA Methylation ; Bacteriophages/genetics/enzymology ; High-Throughput Nucleotide Sequencing ; Bacteria/genetics/enzymology ; Substrate Specificity ; Bacterial Proteins/metabolism/genetics ; Sequence Analysis, DNA/methods ; DNA, Viral/genetics/metabolism ; }, abstract = {Methylation patterns in bacteria can be used to study restriction-modification or other defense systems with novel properties. While m4C and m6A methylation are well characterized mainly through PacBio sequencing, the landscape of m5C methylation is under-characterized. To bridge this gap, we performed RIMS-seq2 (rapid identification of methyltransferase specificity sequencing) on microbiomes composed of resolved assemblies of distinct genomes through proximity ligation. This high-throughput approach enables the identification of m5C methylated motifs and links them to cognate methyltransferases directly on native microbiomes without the need to isolate bacterial strains. Methylation patterns can also be identified on bacteriophage DNA and compared with host DNA, strengthening evidence for phage-host interactions. Applied to three different microbiomes, the method unveiled over 1900 motifs that were deposited in REBASE. The motifs include a novel eight-base recognition site (CATm5CGATG) that was experimentally validated by characterizing its cognate methyltransferase. Our findings suggest that microbiomes harbor arrays of untapped m5C methyltransferase specificities, providing insights into bacterial biology and biotechnological applications.}, } @article {pmid40169073, year = {2025}, author = {Sun, L and Yin, Y and Guo, Y and Chen, H and Wang, H}, title = {Metagenomic Next-Generation Sequencing Enhances the Diagnosis of Q Fever: A Retrospective Observational Study.}, journal = {Travel medicine and infectious disease}, volume = {}, number = {}, pages = {102845}, doi = {10.1016/j.tmaid.2025.102845}, pmid = {40169073}, issn = {1873-0442}, abstract = {BACKGROUND: Q fever, a global zoonosis, poses a significant challenge for public health due to its varied and nonspecific clinical presentations, making diagnosis difficult. Metagenomic next-generation sequencing (mNGS) is a potential tool for diagnosing Q fever.

METHODS: This retrospective observational study was conducted on patients with Q fever admitted to Peking University People's Hospital, from May 2023 to November 2024. mNGS was performed using the patient's peripheral blood, and the qPCR of Coxiella burnetii was also adopted. Subsequently, the clinical data of patients diagnosed with Q fever were systematically evaluated.

RESULTS: Twelve peripheral blood samples of 12 patients were detected Coxiella burnetii positive by mNGS. Most patients were male (10, 83.33%). Fever (12, 100%), muscle soreness (8, 66.7%), and headache (4, 33.3%) were the most common clinical manifestations. Specific qPCR of Coxiella burnetii was detected positive in 8 patients. Chronic Q fever was diagnosed in two patients, who had aortic valve replacement, and their immunological markers, like anti-nuclear were elevated. Once the diagnosis was clear, proper antibiotics were used, and all patients were discharged in better health.

CONCLUSION: Metagenomic next-generation sequencing enhances the diagnosis of Q fever, especially for patients displaying atypical and various clinical symptoms and having unclear epidemiological data or histories of antibiotic use.}, } @article {pmid40169018, year = {2025}, author = {Wallace, MA and Wille, M and Geoghegan, J and Imrie, RM and Holmes, EC and Harrison, XA and Longdon, B}, title = {Making sense of the virome in light of evolution and ecology.}, journal = {Proceedings. Biological sciences}, volume = {292}, number = {2044}, pages = {20250389}, doi = {10.1098/rspb.2025.0389}, pmid = {40169018}, issn = {1471-2954}, support = {//Leverhulme Trust/ ; //National Health and Medical Research Council (NHMRC)/ ; //Royal Society/ ; /WT_/Wellcome Trust/United Kingdom ; //Webster Family Chair in Viral Pathogenesis/ ; //New Zealand Royal Society Rutherford Discovery Fellowship/ ; //Innovation and Technology Commission, Hong Kong Special Administrative Region, China/ ; }, mesh = {*Virome ; *Viruses/genetics ; Biological Evolution ; Metagenomics ; Ecology ; Ecosystem ; Phylogeny ; }, abstract = {Understanding the patterns and drivers of viral prevalence and abundance is of key importance for understanding pathogen emergence. Over the last decade, metagenomic sequencing has exponentially expanded our knowledge of the diversity and evolution of viruses associated with all domains of life. However, as most of these 'virome' studies are primarily descriptive, our understanding of the predictors of virus prevalence, abundance and diversity, and their variation in space and time, remains limited. For example, we do not yet understand the relative importance of ecological predictors (e.g. seasonality and habitat) versus evolutionary predictors (e.g. host and virus phylogenies) in driving virus prevalence and diversity. Few studies are set up to reveal the factors that predict the virome composition of individual hosts, populations or species. In addition, most studies of virus ecology represent a snapshot of single species viromes at a single point in time and space. Fortunately, recent studies have begun to use metagenomic data to directly test hypotheses about the evolutionary and ecological factors which drive virus prevalence, sharing and diversity. By synthesizing evidence across studies, we present some over-arching ecological and evolutionary patterns in virome composition, and illustrate the need for additional work to quantify the drivers of virus prevalence and diversity.}, } @article {pmid40168930, year = {2025}, author = {Tang, GX and Huang, YH and Feng, LW and Hu, YC and Wei, JL and Lü, H and Liu, LH and Zhao, HM and Xiang, L and Li, H and Mo, CH and Li, YW and Cai, QY}, title = {New insights into rhizosphere bacterial community shaped by lettuce genotypes for divergent degradation efficiencies of phthalates.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138077}, doi = {10.1016/j.jhazmat.2025.138077}, pmid = {40168930}, issn = {1873-3336}, abstract = {Rhizosphere dissipation of organic pollutants benefits safe utilization of the polluted agricultural soil. Nevertheless, dissipation variation of phthalates (PAEs) in rhizosphere among different vegetable genotypes and the related microbial mechanisms remain unknown. Here, twelve lettuce cultivars with different genetic relationships identified by 18S rRNA gene sequencing were cultivated in soil spiked with di-(2-ethylhexyl) phthalate (DEHP). Bacterial communities and function genes in rhizosphere of lettuce were analyzed by 16S rRNA gene and metagenomic sequencing. Results showed significant variations in DEHP concentrations of roots (2.8-15.3 mg/kg) and shoots (0.70-1.8 mg/kg) among 12 cultivars. Notably, cultivars L11 and L12 showed the lowest DEHP accumulation in roots and shoots, being lower by 82 % and 58 % than the highest accumulators (cultivars L5 and L6), respectively. This accumulation variation was closely connected with their genetic relationships and exhibited genotype-dependent trait. The significantly different bacterial community diversities and structures were recorded in rhizosphere among 12 cultivars. Especially, bacterial communities in rhizosphere of cultivars L11 and L12 (low-DEHP accumulators with high DEHP dissipation) strengthened their adaptation by enriching pollutant-resistant taxa, increasing extracellular polymeric substance contents and biofilm formation, as well as constructing complex ecological networks under DEHP pollution. Moreover, PAE-degrading bacteria and genes (e.g., hydrolase65, phtAb, and pcaI) in rhizosphere were enriched by low-DEHP accumulators, which benefited DEHP removal and subsequently safe agricultural products. This study provides new insights into microbial mechanisms on rhizosphere DEHP degradation and its correlation with accumulation variation among different crop genotypes.}, } @article {pmid40168814, year = {2025}, author = {Harish, J and Prasannakumar, MK and Venkateshbabu, G and Karan, R and Mahesh, HB and Devanna, P and Sarangi, AN and Patil, SS and Tejashwini, V and Lohithaswa, HC and Kagale, S}, title = {Molecular and genomic insights into the pathogenicity of Sarocladium zeae causing maize stalk rot disease.}, journal = {Microbiological research}, volume = {296}, number = {}, pages = {128146}, doi = {10.1016/j.micres.2025.128146}, pmid = {40168814}, issn = {1618-0623}, abstract = {Post-flowering stalk rot (PFSR) of maize has been traditionally associated with Fusarium verticillioides. Conversely, this study reveals Sarocladium zeae as a new phytopathogen responsible for the disease. This research was conducted to gain a comprehensive understanding of S. zeae by investigating its pathogenic mechanisms, profiling its metabolome, and deciphering its genomic characteristics. Maize stalks displaying stalk rot symptoms were collected from various regions of India. S. zeae was isolated and characterized using ITS and TEF-1α sequencing. Cultures of S. zeae exhibited slower growth on PDA medium compared to F. verticillioides, which dominated due to its rapid growth rate. Pathogenicity was confirmed through a toothpick inoculation assay. The symptoms induced by S. zeae was characterized by powdery, dry, pale brown-black discoloration, were distinct from the typical dark-brown lesions of Fusarium stalk rot. Enzymatic assays revealed increased activity of β-glucosidase, cellulase, and pectate lyase in infected stalks, while qPCR analysis showed the upregulation of endoglucanase and β-glucosidase genes in infected stalks underscored the critical roles of cellulase and β-glucosidase in pathogenicity Metagenomic analysis identified S. zeae as the predominant species in infected stalk samples. Genome assembly revealed the pathogen's complete genetic repertoire, including genes encoding effector proteins and CAZymes involved in cell wall degradation. Moreover, we have demonstrated that the S. zeae as a causal agent of maize stalk rot and further shedding light on its transition from an endophytic to a pathogenic lifestyle. Taken together, this research represents the first report to attribute maize stalk rot to S. zeae and to present its complete genome assembly, significantly advancing the understanding of its biology and pathogenic potential.}, } @article {pmid40168753, year = {2025}, author = {Ji, X and Yu, X and Xu, Y and Wu, Q and Madadi, M and Khaneghah, AM}, title = {Initial acidity regulates microbial sulfur metabolism in the spontaneous fermentation of sesame flavor-type baijiu.}, journal = {International journal of food microbiology}, volume = {435}, number = {}, pages = {111182}, doi = {10.1016/j.ijfoodmicro.2025.111182}, pmid = {40168753}, issn = {1879-3460}, abstract = {Volatile sulfur compounds play a crucial role in fermented foods, however, their metabolism during spontaneous food fermentation remains underexplored. With 3-(methylthio)-1-propanal as a case, we revealed the effect of initial acidity on the sulfur metabolism during sesame flavor-type baijiu fermentation. Results showed that the content of 3-(methylthio)-1-propanal reached 383.29 μg/kg with 1.8 mmol/10 g of the initial acidity, and it decreased to 320.54 μg/kg when the initial acidity increased to 2.4 mmol/10 g. Metagenomic analysis identified 11 core microbes associated with sulfur metabolism, characterized by gene abundance (> 0.5 %) and catalytic enzyme distribution frequency (> 10 %). Saccharomyces was the main producer of sulfur compounds. Lactobacillus was an important player in the methyl cycle pathway of sulfur metabolism. Low initial acidity increased the abundance of Lactobacillus and the content of genes associated with the methyl cycle pathway (P < 0.05). This resulted in a significant increase of methionine (253.26 mg/kg) (P < 0.05) and 3-(methylthio)-1-propanal contents (383.29 μg/kg) (P < 0.05). In simulated fermentation, the content of 3-(methylthio)-1-propanal significantly increased by 2.91 folds when Saccharomyces cerevisiae was cocultured with Lactobacillus acetotolerans (P < 0.05), and the transcription of genes related to sulfur metabolism significantly increased by 33.71 folds (P < 0.05). Results indicated that low initial acidity increased the abundance of Lactobacillus, which mediates the methyl cycle pathway in the sulfur metabolism, thereby increasing the contents of methionine and volatile sulfur compounds. This work provided insight into the regulation of metabolic mechanisms of volatile sulfur compounds in baijiu fermentation.}, } @article {pmid40168325, year = {2025}, author = {Yun, H and Seo, JH and Kim, YK and Yang, J}, title = {Examining the bacterial diversity including extracellular vesicles in air and soil: implications for human health.}, journal = {PloS one}, volume = {20}, number = {4}, pages = {e0320916}, doi = {10.1371/journal.pone.0320916}, pmid = {40168325}, issn = {1932-6203}, mesh = {*Extracellular Vesicles/metabolism ; *Soil Microbiology ; Humans ; *Bacteria/genetics/classification/metabolism ; *RNA, Ribosomal, 16S/genetics ; Air Microbiology ; Microbiota ; Biodiversity ; Metagenomics/methods ; }, abstract = {As the significance of human health continues to rise, the microbiome has shifted its focus from microbial composition to the functional roles it plays. In parallel, interest in ultrafine particles associated with clinically important impact has been increasing. Bacterial extracellular vesicles (BEVs), involved in systemic microbiome activity, are nano-sized spherical vesicles (20 - 100 nm in diameter) containing DNA, RNA, proteins, and lipids. They are known to be absorbed into the body potentially through air and soil, circulate in the blood, and directly impact diseases by affecting organs. Therefore, the aim of this study is to examine the biodiversity of bacteria and BEVs and predicted functional pathways. We sampled air and soil samples in Seoul, Korea and analyzed metagenomics based on 16S rRNA sequencing. At the phylum levels, Firmicutes in BEVs from soil and air were significantly higher than in bacteria, and Acidobacteria in both bacteria and BEVs from soil were significantly higher than from air (p < 0.05). The most dominant genera were Pseudomonas in bacteria from air and soil; and Escherichia-Shigella in BEVs from air and soil. In addition, Two-component system (ko02020) and ATP-binding cassette transporters (ko02010) were dominant functional pathways in both air and soil. The most functional pathways and orthologous groups were significantly different between air and soil (p < 0.05). In conclusion, human health can be affected differently depending on type of environment. Future study is necessary to have a better understanding of human health effects from environmental microbiota.}, } @article {pmid40167463, year = {2025}, author = {Sun, C and Liu, H and Teng, J and Feng, W and Wang, D and Wang, X and Zhao, J and Wang, Q}, title = {Impact of Microplastic Exposure on Sand Crab Scopimera globosa Behavior: Implications for Microplastic Transport and Sulfur Cycling through Bioturbation.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c01192}, pmid = {40167463}, issn = {1520-5851}, abstract = {The accumulation of microplastics (MPs) in estuarine regions and their ecological consequences have become global environmental concerns. Estuarine sediments function as major sinks for MPs and hotspots for critical biogeochemical processes, which are significantly influenced by benthic bioturbation. However, the impacts of MPs on the behavior of highly mobile benthic organisms and the ecological effects of bioturbation activities remain poorly understood. This study utilized laboratory simulation experiments, AI-based behavioral tracking, and metagenomic sequencing to systematically examine the effects of sand crab bioturbation on MPs migration, sediment physicochemical properties and sulfur cycling processes. Results demonstrated that sand crab bioturbation substantially enhanced the vertical migration of MPs, with fluxes to surface layers and the overlying water increasing by 27-fold compared to undisturbed conditions. Exposure to PE-MPs reduced sand crabs' surface foraging intensity and induced behavioral abnormalities. The crabs actively avoided MPs, exhibiting a preference for burrowing and residing in deeper sediment layers. This behavioral shift significantly altered microbial community distributions, with an increase of Pseudomonadota abundance and a decline of sulfate-reducing bacteria Thermodesulfobacteriota abundance. Furthermore, bioturbation accelerated sulfate oxidation in deeper sediments while inhibited dissimilatory sulfate reduction. This study is the first to identify the role of bioturbation in promoting the upward migration of MPs in sediments. Altered sand crab bioturbation will impact sediment biogeochemistry, estuarine function, and coastal resilience.}, } @article {pmid40167332, year = {2025}, author = {Curto, M and Veríssimo, A and Riccioni, G and Santos, CD and Ribeiro, F and Jentoft, S and Alves, MJ and Gante, HF}, title = {Improving Whole Biodiversity Monitoring and Discovery With Environmental DNA Metagenomics.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e14105}, doi = {10.1111/1755-0998.14105}, pmid = {40167332}, issn = {1755-0998}, support = {CEEC/0482/2020//Fundação para a Ciência e a Tecnologia/ ; DL 57/2016/CP1440/CP1646/CT0001//Fundação para a Ciência e a Tecnologia/ ; LA/P/0069/2020//Fundação para a Ciência e a Tecnologia/ ; PTDC/BIA-CBI/31644/2017//Fundação para a Ciência e a Tecnologia/ ; UID/04292/2020//Fundação para a Ciência e a Tecnologia/ ; UID/BIA/00329/2020//Fundação para a Ciência e a Tecnologia/ ; UIDP/50027/2020//Fundação para a Ciência e a Tecnologia/ ; LA/P/0048/2020//Fundação para a Ciência e a Tecnologia/ ; 857251//Horizon 2020 Framework Programme/ ; STG/21/044//KU Leuven/ ; }, abstract = {Environmental DNA (eDNA) metagenomics sequences all DNA molecules present in environmental samples and has the potential of identifying virtually any organism from which they are derived. However, due to unacceptable levels of false positives and negatives, this approach is underexplored as a tool for biodiversity monitoring across the tree of life, particularly for non-microscopic eukaryotes. We present SeqIDist, a framework that combines multilocus BLAST matches against several reference databases followed by an analysis of sequence identity distribution patterns to disentangle false positives while revealing new biodiversity and increasing the accuracy of metagenomic approaches. We tested SeqIDist on an eDNA metagenomic dataset from a riverine site and compared the results to those obtained with an eDNA metabarcoding approach for benchmarking purposes. We start by characterising the biological community (~2000 taxa) across the tree of life at low taxonomic levels and show that eDNA metagenomics has a higher sensitivity than eDNA metabarcoding in discovering new diversity. We show that limited representation of whole genome sequences in reference databases can lead to false positives. For non-microscopic eukaryotes, eDNA metagenomic data often consist of a few sparse, anonymous sequences scattered across the genome, making metagenome assembly methods unfeasible. Finally, we infer eDNA source and residency time using read length distributions as a measure of decay status. The higher accuracy of SeqIDist opens the discussion of the potential of eDNA metagenomics for archived samples and its implementation in long-term biodiversity monitoring at a planetary scale.}, } @article {pmid40166061, year = {2025}, author = {Zhang, L and Guo, Y and Wang, X and Gai, W and Liu, L}, title = {Severe adenovirus pneumonia complicated by acute respiratory distress syndrome in immunocompetent patients: a case report and literature review.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1524783}, pmid = {40166061}, issn = {2296-858X}, abstract = {BACKGROUND: Human adenovirus (HAdV) is one of the most important pathogens detected in acute respiratory illness in pediatric and immunocompromised patients, but it is relatively rare to develop severe pneumonia in immunocompetent patients. We analyzed the clinical features, as well as the diagnosis and treatment processes, to provide a reference for clinical practice.

CASE PRESENTATION: We report a case of severe pneumonia caused by HAdV, complicated by acute respiratory distress syndrome (ARDS), in an immunocompetent patient with no underlying conditions. Chest computed tomography (CT) revealed consolidation in the right lower lung. Conventional microbial tests were negative, but metagenomic next-generation sequencing (mNGS) identified a large number of HAdV sequences in blood and sputum. Together with the clinical symptoms, this confirmed the diagnosis of severe pneumonia caused by HAdV. The patient was discharged after timely treatment with cidofovir.

CONCLUSION: In our study, we described a rare case of severe pneumonia caused by HAdV, complicated by ARDS, in an immunocompetent patient. mNGS proves to be an effective diagnostic tool for guiding treatment decisions.}, } @article {pmid40165946, year = {2025}, author = {Guo, Z and Wang, X and Li, Y and Zhang, Y and Guo, P and Zhang, J and Zhang, Z and Ma, X}, title = {Evaluation of the therapeutic effect of pomegranate peel ginger ultrafine powder on chronic enteritis in mice by regulating intestinal microbiota.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1563225}, pmid = {40165946}, issn = {1664-3224}, mesh = {Animals ; Mice ; *Pomegranate/chemistry ; *Zingiber officinale ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; *Enteritis/drug therapy/microbiology/veterinary ; *Aquaporins/metabolism/genetics ; Cytokines/metabolism ; Chronic Disease ; Disease Models, Animal ; Powders ; Plant Extracts/pharmacology/administration & dosage ; Aquaporin 3 ; Aquaporin 4 ; }, abstract = {To explore the efficacy and mechanism of Pomegranate peel Ginger ultrafine powder (PG) in treating chronic enteritis in mice. Sixty SPF-grade mice were randomly divided into a blank group, a model group, loperamide hydrochloride group (5 mg/kg), a high-dose PG group (100 mg/kg), a medium-dose group (50 mg/kg), and a low-dose group (25 mg/kg), with 10 mice in each group and an equal number of males and females. A chronic enteritis mouse model was established using a multifactorial method of low temperature + ice water + castor oil. The blank group was given an equal amount of physiological saline intragastrically, while the other groups were intervened with corresponding drugs for 7 consecutive days. After 7 days, samples were collected, and Enzyme-linked immunosorbent assay (ELISA) was used to detect the levels of interleuckin 1β (IL-1β), IL-6, and Tumor necrosis factorα(TNF-α) in mouse serum. HE staining was used to examine the pathological changes in the small intestine. oxidative reagent kits were used to detect the content of total superoxide dismutase(T-SOD) and Malondialdehyde (MDA) in the small intestine. Western blot was used to detect the expression of Aquaporin 8(AQP8) proteins in the small intestine. Real time quantitative reverse transcription polymerase chain reaction (RT-qPCR) was used to detect the expression of AQP3, AQP4, AQP8, and Sodium/hydrogen exchanger 8 (NHE8) genes in the small intestine. metagenomics was used to detect the gut microbiota in mouse feces. Compared with the model group, all doses of PG groups reduced the levels of IL-1β, IL-6, and TNF-α in mouse serum (P<0.05), improved pathological changes in the small intestine, increased the content of T-SOD in the small intestine tissue, reduced the content of MDA, increased the expression of AQP4 and AQP8 mRNA, and decreased the expression of AQP3 and NHE8 mRNA (P<0.05), increased the expression of AQP8 protein. PG could improve the pathological changes of chronic enteritis in mice, enhance antioxidant capacity, and alleviate diarrhea caused by chronic enteritis by downregulating the expression of intestinal epithelial transport proteins and acute-phase proteins, and altering gut microbiota.}, } @article {pmid40165815, year = {2025}, author = {Battur, M and Aaqil, M and Zheng, J and Lin, HX and Chuluunotgon, B and Zorigtbaatar, T and Zhao, C and Tian, Y}, title = {Exploring the effects of milk-enriched walnut soy sauce: Insights from GC-IMS and metagenomics approach to flavor and microbial shifts.}, journal = {Food chemistry: X}, volume = {27}, number = {}, pages = {102364}, pmid = {40165815}, issn = {2590-1575}, abstract = {This study investigates the impact of milk addition on the fermentation of walnut soy sauce, using Gas Chromatography-Ion Mobility Spectrometry (GC-IMS) and metagenomics to analyze flavor profiles and microbial dynamics. GC-IMS analysis showed significant increases in volatile compounds such as esters (ethyl acetate), aldehydes (hexanal), and alcohols (isoamyl alcohol), enhancing the aroma and taste. Metagenomic analysis revealed that milk increased microbial diversity, with Weissella and Lactobacillus dominating early fermentation. The milk-enriched soy sauce (SYM) exhibited higher amino acid nitrogen (2.67 g/L), and total nitrogen (7.18 g/L) compared to the control, indicating improved nutritional quality. Protease activity peaked at 2438.5 U/g for neutral protease, supporting efficient protein hydrolysis. Relative Odor Activity Value (ROAV) analysis identified 29 key flavor compounds, including 3-methyl butanol and ethyl 2-methyl butyrate, which contributed fruity and buttery notes to SYM. These results suggest that milk enhances microbial growth and improves both flavor and nutritional quality of walnut soy sauce.}, } @article {pmid40165787, year = {2025}, author = {Huang, Z and Wang, J and He, X and Zhang, M and Ren, X and Yu, W and Yao, S and Ji, K}, title = {Divergent profiles of rhizosphere soil carbon and nitrogen cycling in Pinus massoniana provenances with different types of carbon storage.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1537173}, pmid = {40165787}, issn = {1664-302X}, abstract = {INTRODUCTION: In subtropical China, P. massoniana is a timber tree species which have a great potential for carbon sequestration. However, few studies have investigated how varying levels of carbon storage in P. massoniana provenances affect the soil microbial functional potential related to nutrient cycling within the rhizosphere.

METHODS: In this investigation, metagenomic sequencing was employed to explore the differences in carbon and nitrogen cycling capabilities among rhizosphere microbial communities within P. massoniana provenances, categorized by high, medium, and low levels of carbon storage.

RESULTS: Our findings revealed a significant increase in the relative abundance of Acidobacteriota and Ascomycota by 23 and 61%, respectively, whereas Basidiomycota significantly decreased by 8% in the rhizosphere of P. massoniana provenances with high carbon storage compared with those with low carbon storage. The variability in carbon storage among P. massoniana provenances was linked to marked disparities in the presence of key genes essential for carbon and nitrogen cycling within their rhizosphere soils.

DISCUSSION: Notably, in P. massoniana provenances characterized by high carbon storage, the rhizosphere presented a significantly elevated presence of genes associated with carbon decomposition, carbon assimilation, methane generation, and denitrification, in stark contrast to provenances with medium and low carbon storage. Furthermore, P. massoniana provenances with high carbon storage rates presented increased transformation and availability of soil carbon and nitrogen, along with increased potential for ecological restoration. Moreover, the rhizosphere soil nitrification of P. massoniana provenances with low carbon storage surpassed that of other provenances, leading to increased available nitrogen content and elevated nitrate leaching risk. In the P. massoniana rhizosphere, critical soil factors, including soil organic carbon (SOC), total nitrogen (TN), pH, and nitrate nitrogen (NO3 [-]-N) content, significantly shape the functionality of genes associated with carbon and nitrogen cycling. In conclusion, our study lays a scientific foundation for establishing P. massoniana plantations and identifying P. massoniana provenances with superior ecological value and potential.}, } @article {pmid40165255, year = {2025}, author = {Xie, B and Dong, C and Zhao, X and Qu, L and Lv, Y and Liu, H and Xu, J and Yu, Z and Shen, H and Shang, Y and Zhao, X and Zhang, J}, title = {Structural and functional alteration of the gut microbiomes in ICU staff: a cross-sectional analysis.}, journal = {Critical care (London, England)}, volume = {29}, number = {1}, pages = {141}, pmid = {40165255}, issn = {1466-609X}, support = {82402568//National Natural Science Foundation of China/ ; 82472223//National Natural Science Foundation of China/ ; }, mesh = {Humans ; Cross-Sectional Studies ; *Gastrointestinal Microbiome/physiology ; *Intensive Care Units/organization & administration/statistics & numerical data ; Male ; Female ; Prospective Studies ; Adult ; Middle Aged ; RNA, Ribosomal, 16S/analysis/genetics ; Cohort Studies ; Feces/microbiology ; Health Personnel/statistics & numerical data ; }, abstract = {BACKGROUND: 16S rRNA sequencing has revealed structural alterations in the gut microbiomes of medical workers, particularly those working in intensive care unit (ICU). This study aims to further compare the taxonomic and functional characteristics of gut microbiomes between ICU staff and non-medical individuals using metagenomic sequencing.

METHODS: A prospective cross-sectional cohort study was conducted, fecal samples from 39 individuals in each group-ICU staff and non-medical subjects were analyzed using metagenomic sequencing. PERMANOVA (using the adonis function) was employed to analyze the genus-level profiles and assess the impact of individual parameters on the gut microbiome. Multiple databases were utilized to annotate and compare the functional differences in gut microbiomes between the two groups.

RESULTS: We observed that ICU staff exhibited a significant decrease in gut microbiome diversity, characterized by a marked decline in Actinobacteria and a substantial increase in Bacteroides and Bacteroidaceae. CAZy annotation revealed a notable increase in carbohydrate-active enzymes within the ICU staff cohort. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis further indicated an elevated risk of endocrine and metabolic disorders, along with enhanced glycan biosynthesis and metabolism. Additionally, KEGG pathway enrichment analysis highlighted significant enrichment in cancer-related pathways. Analysis using the Virulence Factor Database (VFDB) showed a higher abundance of virulence factors associated with immune modulation, invasion, and antimicrobial activity/competitive advantage among ICU staff. Notably, no discernible difference in the presence of antibiotic resistance genes within the gut microbiomes was observed between the two groups. Importantly, all aforementioned differences demonstrated clear gender disparities.

CONCLUSIONS: Our findings indicated that ICU staff exhibited a reduction in gut microbiome diversity which was associated with an increase in virulence factors and carbohydrate-active enzymes, as well as with a heightened susceptibility to endocrine and metabolic diseases and cancers.}, } @article {pmid40165201, year = {2025}, author = {Lin, L and Peng, X and Chen, L and Dong, L and Zhong, L}, title = {Case report: novel NFKB2 variant associated with pediatric eosinophilic granulomatosis with polyangiitis (EGPA) in the COVID-19 pandemic.}, journal = {Pediatric rheumatology online journal}, volume = {23}, number = {1}, pages = {35}, pmid = {40165201}, issn = {1546-0096}, mesh = {Humans ; Female ; *COVID-19/complications ; Child ; *NF-kappa B p52 Subunit/genetics ; SARS-CoV-2 ; Churg-Strauss Syndrome/genetics/diagnosis ; Granulomatosis with Polyangiitis/genetics/diagnosis ; }, abstract = {BACKGROUND: Childhood-onset eosinophilic granulomatosis with polyangiitis (cEGPA) is a rare type of systemic autoimmune disorder. Variants in the NFKB2 gene can manifest as common variable immunodeficiency or combined immunodeficiency, often accompanied by autoimmunity and ectodermal dysplasia. Here, we report a case of a Chinese patient who carries NFKB2 variants that coexist with cEGPA, a novel combination which, to our knowledge, has not been previously published.

CASE PRESENTATION: We reported a 9-year and 10-month-old girl who presented with cough, wheezing, dyspnea, hypereosinophilia, and vasculitis. Notably, she had significant bilateral pulmonary interstitial lesions. We performed metagenomic next-generation sequencing (mNGS), bronchoscopy and immunological analysis. She was considered to have refractory cEGPA after six months of corticosteroid and immunosuppressive treatment. Tapering off corticosteroids posed a challenge, and multiple immunosuppressive agents were ineffective. Our patient suffered from recurrent fever, wheezing, dyspnea and perianal abscess, along with life-threatening infections, including pneumocystis jirovecii pneumonia (PJP) and severe coronavirus disease 2019 (COVID-19) pneumonia during the pandemic. Her cytokines and inflammatory markers showed a profound collapse. She developed significant hypoxemia, which necessitated mechanical ventilation. Primary immunodeficiency gene panel testing revealed a novel de novo variant in NFKB2 (c.2578 + 2 dup) that was classified as pathogenic. Despite treatment with antibacterial, antiviral, and antifungal agents, biologics, and plasma exchange, she ultimately succumbed to respiratory failure.

CONCLUSIONS: This case report establishes a novel link between NFKB2 variants and EGPA, particularly in the context of the COVID-19 pandemic. This study expands the spectrum of NFKB2 variants and vividly illustrates the complex interrelationships among autoimmunity, infection, and immunodeficiency.}, } @article {pmid40165140, year = {2025}, author = {Trivett, H and Darby, AC and Oyebode, O}, title = {Academic and clinical perspectives of metagenome sequencing as a diagnostic tool for infectious disease: an interpretive phenomenological study.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {448}, pmid = {40165140}, issn = {1471-2334}, mesh = {Humans ; *Metagenome ; *Communicable Diseases/diagnosis ; *COVID-19/diagnosis ; Metagenomics/methods ; SARS-CoV-2/genetics ; England ; }, abstract = {BACKGROUND: Effective infectious disease diagnostics (IDD) are vital for informing clinical decision-making regarding the treatment and patient management of disease and infections. In England, conventional clinical methods rely upon culture-dependent techniques, and there has been little shift in the acceptance and integration of culture-independent sequencing methods into routine clinical IDD. This study explored stakeholders' experiences within IDD, including those working in clinical settings and those conducting research at the forefront of microbial genomics. From the participants' experiences, the study aimed to identify barriers and facilitators driving the development and implementation of metagenome sequencing as a routine diagnostic.

METHODS: Virtual semi-structured interviews were conducted with purposively selected individuals involved in IDD. The interviews explored the experiences of implementing metagenome sequencing as a diagnostic tool and decisions about which diagnostics are used for identifying bacteria-causing infections. Thematic analysis was used to analyse the data, and an Interpretive Phenomenological approach was used throughout.

RESULTS: Ten individuals were interviewed between July 2021 and October 2021, including clinical scientists, consultants, and professors in academia. Their experience ranged from limited knowledge of metagenome sequencing to an expert understanding of the phenomenon. The thoughts and perspectives of participants of the study could be grouped into five themes: Availability of diagnostics for infectious diseases; Clinical laboratory infrastructure; Ethical Data Sharing: Enhancing metagenomics through Open Access; Case study in action: COVID-19; and The importance of communication to improve developments of new diagnostics. Participants recognised the need for new diagnostics to be implemented to overcome the limitations of current diagnostic approaches but highlighted the barriers to integrating new diagnostics into clinical settings, such as the impact on clinical decision-making, accreditation, and cost. Further, participants felt that lessons could be learnt from using metagenomics in COVID-19 and how other diagnostic platforms have been integrated into clinical settings over the last 20 years.

CONCLUSIONS: The study provided insights into stakeholders' perspectives and opinions to address the knowledge gap in current literature and identified barriers and facilitators which drive the implementation of metagenome sequencing as a routine IDD in clinical settings. Knowledge of new and upcoming genomic diagnostic testing is not equally distributed throughout the UK, impacting the understanding and drive to integrate metagenome sequencing into routine clinical diagnostics. Improvements in access to new diagnostics could improve patient treatment and management and positively impact population health.}, } @article {pmid40165002, year = {2025}, author = {Wang, H and Su, Q and Sun, H and Meng, Y and Xing, X and Zheng, H and Li, Y}, title = {Unexpected Microbial and Genetic Diversity in the Gut of Chinese Giant Salamander.}, journal = {Integrative zoology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1749-4877.12976}, pmid = {40165002}, issn = {1749-4877}, abstract = {The gut microbiome is crucial for animal health, yet the diversity of the critically endangered Chinese giant salamander's gut microbiota remains largely uncharacterized. In this study, we first conducted a comprehensive landscape survey of the gut microbiome of the Chinese giant salamander using 16S rRNA sequencing across a wide geographic range, identifying a distinct microbial cluster within its habitat. Subsequently, using shotgun metagenomes, we recovered 1518 metagenome-assembled genomes. Notably, 85% of the newly identified genomes could not be assigned to any known bacterial species, indicating a significant presence of novel taxa in Chinese giant salamander intestines. We observed substantial species-level variations in the gut microbiome across different age groups, with some novel species uniquely enriched in specific age populations. From the gut symbionts, we established a gene catalog comprising 3 278 107 non-redundant protein-coding genes, of which 7733 were annotated into recognized KEGG orthology groups. Additionally, we found that the gut microbiota of the Chinese giant salamander exhibits enhanced functional capacities explicitly in lipid metabolism and assimilatory sulfate reduction. Significant variations in the abundance of related enzyme-encoding genes across age groups suggest the unique roles of microbial metabolism in salamander health. By identifying microbial genomes and constructing an integrated gene catalog from metagenomic data, we significantly expand the resources available for research on the gut microbiome of the Chinese giant salamander, paving the way for further investigations into its ecological and health-related implications.}, } @article {pmid40164980, year = {2025}, author = {Otani, S and Louise Jespersen, M and Brinch, C and Duus Møller, F and Pilgaard, B and Egholm Bruun Jensen, E and Leekitcharoenphon, P and Aaby Svendsen, C and Aarestrup, AH and Sonda, T and Sylvina, TJ and Leach, J and Piel, A and Stewart, F and Sapountzis, P and Kazyoba, PE and Kumburu, H and Aarestrup, FM}, title = {Genomic and functional co-diversification imprint African Hominidae microbiomes to signal dietary and lifestyle adaptations.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2484385}, doi = {10.1080/19490976.2025.2484385}, pmid = {40164980}, issn = {1949-0984}, mesh = {Animals ; *Diet ; *Hominidae/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Gastrointestinal Microbiome ; *Life Style ; Humans ; Adaptation, Physiological ; Pan troglodytes/microbiology ; Metagenome ; Phylogeny ; Africa ; }, abstract = {In the diverse landscape of African hominids, the obligate relationship between the host and its microbiome narrates signals of adaptation and co-evolution. Sequencing 546 African hominid metagenomes, including those from indigenous Hadza and wild chimpanzees, identified similar bacterial richness and diversity surpassing those of westernized populations. While hominids share core bacterial communities, they also harbor distinct, population-specific bacterial taxa tailored to specific diets, ecology and lifestyles, differentiating non-indigenous and indigenous humans and chimpanzees. Even amongst shared bacterial communities, several core bacteria have co-diversified to fulfil unique dietary degradation functions within their host populations. These co-evolutionary trends extend to non-bacterial elements, such as mitochondrial DNA, antimicrobial resistance, and parasites. Our findings indicate that microbiome-host co-adaptations have led to both taxonomic and within taxa functional displacements to meet host physiological demands. The microbiome, in turn, transcends its taxonomic interchangeable role, reflecting the lifestyle, ecology and dietary history of its host.}, } @article {pmid40164860, year = {2025}, author = {Adawiah, A and Meryandini, A and Ridwan, R and Fidriyanto, R and Sarwono, KA and Wiryawan, KG}, title = {The rumen microbiome and metabolome profile of Ongole crossbreed cattle fed probiotics and protected amino acids.}, journal = {Tropical animal health and production}, volume = {57}, number = {3}, pages = {148}, pmid = {40164860}, issn = {1573-7438}, mesh = {Animals ; *Rumen/microbiology/metabolism ; Cattle ; *Amino Acids/metabolism ; *Animal Feed/analysis ; Male ; *Metabolome ; *Diet/veterinary ; *Gastrointestinal Microbiome/drug effects ; *Probiotics/administration & dosage/pharmacology ; Cross-Over Studies ; Dietary Supplements/analysis ; Bacteria/classification/metabolism/genetics ; }, abstract = {This study aimed to investigate the microbial population dynamics and metabolite profiles of Ongole crossbreed cattle (OCC) fed a combination of feed additives using metagenomic and metabolomic analyses. A crossover design was employed, involving four 3-year-old fistulated OCC bulls, each receiving four distinct dietary treatments per experimental period, followed by a washout phase with a basal diet. The treatments consisted of a basal diet (G1) as control, and the addition of feed additives as follows: G2: probiotics (Lactiplantibacillus plantarum); G3: premix; G4: G2 + G3 + amino acids lysine and methionine; and G5: G2 + G3 + amino acids protected with tannin. Rumen fluid was collected for the analysis of microbiome dynamics and metabolite profiles. The bacterial communities in diets G1, G2, G3, and G5 exhibited similar compositions, dominated by Bacteroidota, particularly the genus Prevotella. The G5 diet successfully suppressed the population of archaea, notably Methanosarcinales and Methanobacteriales, which are associated with methane production. A total of 28 significant metabolites (VIP > 1) was identified in rumen fluid, including lipid prenols, phenolic compounds, indoles and derivatives, saturated and unsaturated hydrocarbons, fatty acyls, benzene derivatives, and organooxygen compounds. The volatile compounds profile of rumen fluid showed a marked increase in prenol lipid compounds, especially in the G5 diet. Additionally, Methanosarcinales and Methanobacteriales were negatively correlated with prenol lipid levels. The inclusion of probiotics and protected amino acids alters the microbiome community structure and metabolites, positively affecting ruminant productivity.}, } @article {pmid40164832, year = {2025}, author = {Litichevskiy, L and Considine, M and Gill, J and Shandar, V and Cox, TO and Descamps, HC and Wright, KM and Amses, KR and Dohnalová, L and Liou, MJ and Tetlak, M and Galindo-Fiallos, MR and Wong, AC and Lundgren, P and Kim, J and Uhr, GT and Rahman, RJ and Mason, S and Merenstein, C and Bushman, FD and Raj, A and Harding, F and Chen, Z and Prateek, GV and Mullis, M and Deighan, AG and Robinson, L and Tanes, C and Bittinger, K and Chakraborty, M and Bhatt, AS and Li, H and Barnett, I and Davenport, ER and Broman, KW and Levy, M and Cohen, RL and Botstein, D and Freund, A and Di Francesco, A and Churchill, GA and Li, M and Thaiss, CA}, title = {Gut metagenomes reveal interactions between dietary restriction, ageing and the microbiome in genetically diverse mice.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {40164832}, issn = {2058-5276}, abstract = {The gut microbiome changes with age and has been proposed to mediate the benefit of lifespan-extending interventions such as dietary restriction. However, the causes and consequences of microbiome ageing and the potential of such interventions remain unclear. Here we analysed 2,997 metagenomes collected longitudinally from 913 deeply phenotyped, genetically diverse mice to investigate interactions between the microbiome, ageing, dietary restriction (caloric restriction and fasting), host genetics and a range of health parameters. Among the numerous age-associated microbiome changes that we find in this cohort, increased microbiome uniqueness is the most consistent parameter across a second longitudinal mouse experiment that we performed on inbred mice and a compendium of 4,101 human metagenomes. Furthermore, cohousing experiments show that age-associated microbiome changes may be caused by an accumulation of stochastic environmental exposures (neutral theory) rather than by the influence of an ageing host (selection theory). Unexpectedly, the majority of taxonomic and functional microbiome features show small but significant heritability, and the amount of variation explained by host genetics is similar to ageing and dietary restriction. We also find that more intense dietary interventions lead to larger microbiome changes and that dietary restriction does not rejuvenate the microbiome. Lastly, we find that the microbiome is associated with multiple health parameters, including body composition, immune components and frailty, but not lifespan. Overall, this study sheds light on the factors influencing microbiome ageing and aspects of host physiology modulated by the microbiome.}, } @article {pmid40164697, year = {2025}, author = {Jia, L and Ke, Y and Zhao, S and Liu, J and Luo, X and Cao, J and Liu, Y and Guo, Q and Chen, WH and Chen, F and , and Wang, J and Wu, H and Ding, J and Zhao, XM}, title = {Metagenomic analysis characterizes stage-specific gut microbiota in Alzheimer's disease.}, journal = {Molecular psychiatry}, volume = {}, number = {}, pages = {}, pmid = {40164697}, issn = {1476-5578}, abstract = {Alzheimer's disease (AD) is a progressive neurodegenerative disorder with a decade-long preclinical pathological period that can be divided into several stages. Emerging evidence has revealed that the microbiota-gut-brain axis plays an important role in AD pathology. However, the role of gut microbiota in different AD stages has not been well characterized. In this study, we performed fecal shotgun metagenomic analysis on a Chinese cohort with 476 participants across five stages of AD pathology to characterize stage-specific alterations in gut microbiota and evaluate their diagnostic potential. We discovered extensive gut dysbiosis that is associated with neuroinflammation and neurotransmitter dysregulation, with over 10% of microbial species and gene families showing significant alterations during AD progression. Furthermore, we demonstrated that microbial gene families exhibited strong diagnostic capabilities, evidenced by an average AUC of 0.80 in cross-validation and 0.75 in independent external validation. In the optimal model, the most discriminant gene families are primarily involved in the metabolism of carbohydrates, amino acids, energy, glycan and vitamins. We found that stage-specific microbial gene families in AD pathology could be validated by an in vitro gut simulator and were associated with specific genera. We also observed that the gut microbiota could affect the progression of cognitive decline in 5xFAD mice through fecal microbiota transplantation, which could be used for early intervention of AD. Our multi-stage large cohort metagenomic analysis demonstrates that alterations in gut microbiota occur from the very early stages of AD pathology, offering important etiological and diagnostic insights.}, } @article {pmid40164638, year = {2025}, author = {Mills, S and Ijaz, UZ and Lens, PNL}, title = {Environmental instability reduces shock resistance by enriching specialist taxa with distinct two component regulatory systems.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {54}, pmid = {40164638}, issn = {2055-5008}, support = {15/RP/2763//Science Foundation Ireland (SFI)/ ; 16/RI/3401//Science Foundation Ireland (SFI)/ ; 15/RP/2763//Science Foundation Ireland (SFI)/ ; 16/RI/3401//Science Foundation Ireland (SFI)/ ; EP/P029329/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; EP/V030515/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; }, mesh = {*RNA, Ribosomal, 16S/genetics ; *Bioreactors/microbiology ; *Metagenomics/methods ; Bacteria/genetics/classification/isolation & purification ; Microbiota ; High-Throughput Nucleotide Sequencing ; Microbial Consortia/genetics ; Methane/metabolism ; Metagenome ; Phylogeny ; }, abstract = {Different microbial communities are impacted disproportionately by environmental disturbances. The degree to which a community can remain unchanged under a disturbance is referred to as resistance[1]. However, the contributing ecological factors, which infer a community's resistance are unknown. In this study, the impact of historical environmental stability on ecological phenomena and microbial community resistance to shocks was investigated. Three separate methanogenic bioreactor consortia, which were subjected to varying degrees of historical environmental stability, and displayed different levels of resistance to an organic loading rate (OLR) shock were sampled. Their community composition was assessed using high throughput sequencing of 16S rRNA genes and assembly based metagenomics. The effect environmental instability on ecological phenomena such as microbial community assembly, microbial niche breadth and the rare biosphere were assessed in the context of each reactor's demonstrated resistance to an OLR shock. Additionally, metagenome assembled genomes were analysed for functional effects of prolonged stability/instability. The system which was subjected to more environmental instability experienced more temporal variation in community beta diversity and a proliferation of specialists, with more abundant two component regulatory systems. This community was more susceptible to deterministic community assembly and demonstrated a lower degree of resistance, indicating that microbial communities experiencing longer term environmental instability (e.g. variations in pH or temperature) are less able to resist a large disturbance.}, } @article {pmid39812462, year = {2025}, author = {Kamel, K and Sardo Infirri, S and Riddell, A and Chowdary, P and Batty, P}, title = {Factor VIII Antibodies Demonstrate Type I or Type II Kinetics in Acquired Haemophilia A.}, journal = {Haemophilia : the official journal of the World Federation of Hemophilia}, volume = {31}, number = {2}, pages = {313-318}, pmid = {39812462}, issn = {1365-2516}, mesh = {*Hemophilia A/immunology/blood ; Humans ; *Factor VIII/immunology ; Kinetics ; Male ; Retrospective Studies ; *Autoantibodies/immunology/blood ; Aged ; Middle Aged ; Female ; Adult ; Aged, 80 and over ; }, abstract = {BACKGROUND: Acquired haemophilia A (AHA) is an acquired bleeding disorder resulting from autoantibodies against Factor VIII (FVIII). Previous studies have reported differences in FVIII inhibitor kinetics (type I or type II) in AHA compared to severe haemophilia A.

AIM: To characterise inhibitor kinetics in AHA and evaluate the proportions displaying type I, II or indeterminate kinetics.

METHODS: Single-centre retrospective study of inhibitor kinetics in adults with AHA. Type I kinetics were defined as linear FVIII inhibition with ≥ 97% FVIII inactivation. Type II kinetics were defined as non-linear kinetics and inability to completely neutralise FVIII. Inhibitor titres were calculated using two methods outlined by the International Council for Standardisation in Haematology.

RESULTS: Baseline samples from 34 patients were included. Fifteen samples (44.1%) exhibited type I kinetics, 16 samples (47.1%) exhibited type II kinetics and 3 (8.8%) were indeterminate. Plateau mean residual FVIII:C was higher for inhibitors displaying type II compared to type I kinetics (18.6 vs. 2.9 IU/dL, p < 0.0001). Non-linear regression using a dose-response curve without categorisation for kinetics type yielded a poor fit (R[2] = 38%), which improved with refitting using categories of type I or II kinetics that explained 87% and 85% of the variability. The median difference in inhibitor titre between the two reporting methods was 5% and 15% in the type I and II kinetics groups, respectively.

CONCLUSION: FVIII autoantibodies demonstrate either type I or type II kinetics. Greater discrepancy in reported inhibitor titres depending on the method used is seen for inhibitors with type II kinetics.}, } @article {pmid40164558, year = {2025}, author = {Zhou, HY and Zhang, J and Weng, DD}, title = {[One case of recurrent infection with chlamydia psittaci pneumonia].}, journal = {Zhonghua lao dong wei sheng zhi ye bing za zhi = Zhonghua laodong weisheng zhiyebing zazhi = Chinese journal of industrial hygiene and occupational diseases}, volume = {43}, number = {3}, pages = {237-240}, doi = {10.3760/cma.j.cn121094-20240109-00008}, pmid = {40164558}, issn = {1001-9391}, mesh = {Humans ; *Chlamydophila psittaci/isolation & purification ; Male ; Bronchoalveolar Lavage Fluid/microbiology ; Psittacosis/microbiology ; Recurrence ; Middle Aged ; High-Throughput Nucleotide Sequencing ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {This paper analyzed the clinical data of a patient with recurrent infection of chlamydia psittaci pneumonia within 7 months. The patient had a clear history of contact with live poultry, and the clinical manifestations were dry cough, persistent fever, and respiratory failure. Chest CT imaging changes showed lobar consolidation of infected lung lobes, ground-glass shadows, bronchial air-filling signs, and pleural effusion. The two infections were detected in bronchoalveolar lavage fluid by metagenomic next-generation sequencing (mNGS) and pathogen targeted next-generation sequencing (tNGS), respectively, to achieve early diagnosis of chlamydia psittaci pneumonia. New tetracycline drugs were used as the core of treatment for both infections, and rapid improvement was achieved after anti-infection treatment.}, } @article {pmid40163992, year = {2025}, author = {Lei, H and Zhou, N and Zhang, J and Lin, R and Chen, T and Wu, J and Su, L and Liu, S and Liu, T}, title = {Salinity as a key factor affects viral structure, function, and life strategies in lakes from arid and semi-arid regions.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138075}, doi = {10.1016/j.jhazmat.2025.138075}, pmid = {40163992}, issn = {1873-3336}, abstract = {Salinity impacts lake microorganisms in arid and semiarid zones, affecting climate change. Viruses regulate community structure, facilitate gene transfer, and mediate nutrient cycling. However, studies on the diversity and functional differences of viruses in lakes of varying salinity are limited. Thus, we investigated metagenomic data from 20 lakes in Xinjiang Province, China, to determine viral distribution, virus-host linkage, function, and drivers in lakes of varying salinity. The results showed that salinity shaped the distribution of viral community composition, and Hafunaviridae was the dominant virus in high-salinity lakes. All the metagenome-assembled genomes (MAGs) belonging to Halobacteriota were predicted as hosts, with a lysogenic lifestyle predominating the life strategy, implying their potential protection in salt lakes. Moreover, some auxiliary metabolic genes (AMGs), such as cpeT and PTOX, were related to antioxidant and stress responses, which might help the host survive high salinity stress-induced peroxidation. Notably, the main antibiotic resistance genes (ARGs) carried by viruses, which conferred resistance to polymyxin and trimethoprim, related to the local use of veterinary antibiotics, suggesting that they are potential vehicles for the transmission of ARGs. Overall, these findings suggest that lake systems include unique viral varieties that may influence microbial ecosystems and host metabolism related to environmental adaptability.}, } @article {pmid40163955, year = {2025}, author = {Du, R and Cui, L and Feng, Y and Lv, X and Gao, Y and Li, A and Wang, Q and Ma, Y}, title = {Enhancing the decomposition and composting of food waste by in situ directional enzymatic hydrolysis: performance, ARGs removal and engineering application.}, journal = {Waste management (New York, N.Y.)}, volume = {200}, number = {}, pages = {114774}, doi = {10.1016/j.wasman.2025.114774}, pmid = {40163955}, issn = {1879-2456}, abstract = {This research utilized food waste (FW) as substrate, innovatively developed a directional multienzyme applied for accelerating FW hydrolysis and composting, and an in situ enzymatic hydrolysis combining in composting has been developed to manage FW. Results showed that the composting was achieved at 4 days and the humification index was increased by 2.60 compared with that of without enzymatic hydrolysis. FTIR analysis revealed that following multienzyme pretreatment, the primary constituents of FW, including protein, starch and lipid, underwent structural breakdown, among which protein exhibited the higher susceptibility to multienzyme action and was the first to disintegrated, and the structure also became looser. Moreover, the total antibiotic resistance gene (ARGs) was reduced more than 90 % in the proposed composting process. Analysis of microbial communities and metagenomes showed that multienzyme pretreatment reshaped microbial communities towards favoring FW hydrolysis and humification. The engineering application analysis further implied that the proposed composting approach is scale flexible, engineering applicable, economic viability and environmentally sustainability. It was anticipated that this study has the potential to trigger a paradigm shift in future in-situ treatment of FW to achieve full resource recovery towards zero solid discharge.}, } @article {pmid40163458, year = {2025}, author = {Vendrell-Fernández, S and Beamud, B and Abou Haydar, Y and Am de Sousa, J and Burlaud-Gaillard, J and Kornobis, E and Raynal, B and Vinh, J and Bikard, D and Ghigo, JM}, title = {Incomplete lytic cycle of a widespread Bacteroides bacteriophage leads to the formation of defective viral particles.}, journal = {PLoS biology}, volume = {23}, number = {3}, pages = {e3002787}, doi = {10.1371/journal.pbio.3002787}, pmid = {40163458}, issn = {1545-7885}, mesh = {*Bacteriophages/physiology/genetics ; *Virion/ultrastructure ; *Bacteroides/virology/genetics ; *Lysogeny ; Phylogeny ; Retroelements/genetics ; DNA, Viral/genetics ; Genome, Viral ; }, abstract = {Advances in metagenomics have led to the identification of new intestinal temperate bacteriophages. However, their experimental characterization remains challenging due to a limited understanding of their lysogenic-lytic cycle and the common lack of plaque formation in vitro. In this study, we investigated the hankyphage, a widespread transposable phage of prominent Bacteroides symbionts. Hankyphages spontaneously produced virions in laboratory conditions even in the absence of inducer, but virions did not show any evidence of infectivity. To increase virion production and raise the chances of observing infection events, we identified a master repressor of the hankyphage lytic cycle, RepCHP, whose silencing amplified hankyphage gene expression, and enhanced replicative transposition and virion production. However, attempts to infect or lysogenize new host cells with different capsular types remained unsuccessful. Transmission electron microscopy and capsid DNA sequencing revealed an abnormal virion morphology and incomplete DNA packaging of the hankyphage, suggesting that it cannot complete its assembly in laboratory conditions for reasons that are yet to be identified. Still, metavirome and phylogenetic analyses were suggestive of hankyphage horizontal transmission. We could also detect the activity of diversity-generating retroelements (DGRs) that mutagenize the hankyphage tail fiber, and likely contribute to its broad host range. This study sheds light on the life cycle of this abundant intestinal bacteriophage and highlights important gaps in our understanding of the factors required for the completion of its life cycle. Elucidating this puzzle will be critical to gain a better understanding of the hankyphage biology and ecological role.}, } @article {pmid40163416, year = {2025}, author = {Tordoff, J and Alfonse, LE and Makarova, KS and Ornstein, A and Garrity, AJ and Yan, WX and Scott, DA and Koonin, EV and Cheng, DR}, title = {Initial Characterization of 12 New Subtypes and Variants of Type V CRISPR Systems.}, journal = {The CRISPR journal}, volume = {}, number = {}, pages = {}, doi = {10.1089/crispr.2024.0100}, pmid = {40163416}, issn = {2573-1602}, abstract = {Type V CRISPR systems are highly diverse in sequence, mechanism, and function. Although recent efforts have greatly expanded our understanding of their evolution, the diversity of type V systems remains to be completely explored, and many clades have not been experimentally characterized. In this work, we mined metagenomic databases to identify three new subtypes and nine new variants of Cas12, the effector of Type V systems, and provide experimental and computational characterization of their Protospacer-Adjacent Motif (PAM), interference activity, loci architecture, and tracrRNA dependence. Half of the new Cas12s are found in phages or prophages. New subtypes Cas12o and Cas12p lack the canonical RuvC catalytic residues, suggesting they interfere with the target without cleavage, possibly by blocking transcription or replication. One variant, Cas12f10, displays substantial activity on PAM-less targets. Our work expands the diversity of the functionally characterized Cas12 effectors and provides some promising candidates for genome engineering tools.}, } @article {pmid40162776, year = {2025}, author = {Haft, DH and Tolstoy, I}, title = {Novel selenoprotein neighborhoods suggest specialized biochemical processes.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0141724}, doi = {10.1128/msystems.01417-24}, pmid = {40162776}, issn = {2379-5077}, abstract = {UNLABELLED: Prokaryotic genomes encode selenoproteins sparsely, roughly one protein per 5,000. Finding novel selenoprotein families can expose unknown biological processes that are enabled, or at least enhanced, by having a selenium atom replace a sulfur atom in some cysteine residues. Here, we report the discovery of 18 novel selenoprotein families or second selenocysteine sites in previously unrecognized extensions of protein translations. Most of these families had some confounding factors-too small a family, too few selenoproteins in the family, selenocysteine (U) too close to one end, a skew toward understudied or uncultured lineages, and consequently were missed previously. Discoveries were triggered by observations during the ongoing construction of protein family models for the National Center for Biotechnology Information's RefSeq and Prokaryotic Gene Annotation Pipeline or made by targeted searches for novel selenoproteins in the vicinity of known ones, rather than by any broadly applied genome mining method. Unrelated families TsoA, TsoB, TsoC, and TsoX are adjacent in tso (three selenoprotein operon) loci in the bacterial phylum Thermodesulfobacteriota. TrsS (third radical SAM selenoprotein) occurs strictly in the context of a molybdopterin-dependent aldehyde oxidoreductase. A short carboxy-terminal motif, U-X-X-stop (UXX-star), occurs in selenoproteins with various architectures, usually providing the second U in the protein. The multiple new selenocysteine insertion sites, selenoprotein families, and selenium-dependent operons we curated manually suggest that many more proteins and pathways remain to be discovered; once improved computational methods are applied comprehensively to the latest collections of microbial genomes and metagenomes, they may reveal surprising new biochemical processes.

IMPORTANCE: Next-generation DNA sequencing and assembly of metagenome-assembled genomes (MAGs) for uncultured species of various microbiomes adds a vast "dark matter" of hard-to-decipher protein sequences. Selenoproteins, optimized by natural selection to encode selenocysteine where cysteine might have been encoded much more easily, carry a strong clue to their function-some specialized aspect of binding or catalysis. Operons with multiple adjacent, but otherwise unrelated, selenoproteins should provide even more vivid information. In this study, efforts in protein family construction and curation, aimed at improving the PGAP genome annotation pipeline, generated multiple novel selenoprotein-containing genomic contexts that may lead to the future characterization of several systems of proteins. Past observations suggest roles in the metabolic handling of trace elements (mercury, tungsten, arsenic, etc.) or of organic compounds refractory to simpler enzymatic pathways. In addition, the work significantly expands the truth set of validated selenoproteins, which should aid future, more automated genome mining efforts.}, } @article {pmid40162769, year = {2025}, author = {Dickter, JK and Zhao, Y and Parekh, V and Ma, H and Modi, BG and Li, W-Y and Armenian, SH and Wu, X and Abdulla, FR}, title = {Mining metagenomes and metatranscriptomes unveils viruses associated with cutaneous squamous cell carcinoma in hematopoietic stem cell transplant recipients.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0005325}, doi = {10.1128/spectrum.00053-25}, pmid = {40162769}, issn = {2165-0497}, abstract = {UNLABELLED: We investigated the presence of viral DNA and RNA in cutaneous squamous cell carcinoma (cSCC) tumor and normal tissues from nine individuals with a history of hematopoietic stem cell transplantation (HCT). Microbiome quantification through DNA and RNA sequencing (RNA-seq) revealed the presence of 18 viruses in both tumor and normal tissues. DNA sequencing (DNA-seq) identified Torque teno virus, Saimiriine herpesvirus 1, Merkel cell polyomavirus, Human parvovirus B19, Human gammaherpesvirus-4, Human herpesvirus-6, and others. RNA-seq revealed additional viruses such as Tobamovirus, Pinus nigra virus, Orthohepadnavirus, Human papillomavirus-5, Human herpesvirus-7, Human gammaherpesvirus-4, Gammaretrovirus, and others. Notably, DNA-seq indicated that tumor samples exhibited low levels of Escherichia virus in three out of nine subjects and elevated levels of Human gammaherpesvirus-4 in one subject, while normal samples frequently contained Gammaretrovirus and occasionally Escherichia virus. A comparative analysis using both DNA- and RNA-seq captured three common viruses: Abelson murine leukemia virus, Murine type C retrovirus, and Human gammaherpesvirus-4. These findings were corroborated by an independent data set, supporting the reliability of the viral detection methods utilized. The study provides insights into the viral landscape in post-HCT patients, emphasizing the need for comprehensive viral monitoring in this vulnerable population.

IMPORTANCE: This study is important because it explores the potential role of viruses in the development of cSCC in individuals who have undergone allogeneic HCT. cSCC is common in this population, particularly in those with chronic graft-versus-host disease on long-term immunosuppression. By using advanced metagenomic and metatranscriptomic next-generation sequencing, we aimed to identify viral pathogens present in tumor and adjacent normal tissue. The results could lead to targeted preventive or therapeutic interventions for these high-risk people, potentially improving their outcomes and management of cSCC.}, } @article {pmid40162572, year = {2025}, author = {Wu, H and Zhang, H and Dong, T and Li, Z and Guo, X and Chen, H and Yao, Y}, title = {Overcoming Extreme Ammonia Inhibition on Methanogenesis by Artificially Constructing a Synergistically Community with Acidogenic Bacteria and Hydrogenotrophic Archaea.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e2502743}, doi = {10.1002/advs.202502743}, pmid = {40162572}, issn = {2198-3844}, support = {2024YFD1700500//National Key R&D Program of China/ ; A279021901//Shaanxi Youth Thousand Talents/ ; 2024CY2-GJHX-74//Shaanxi Key R&D Program of China/ ; 2452021112//Chinese Universities Scientific Fund/ ; JCYJ20220530161408019//Shenzhen Natural Science Foundation/ ; 2023KCXTD038//Guangdong Provincial University Innovation Team Project/ ; 2022-K32//Foundation of State Key Laboratory of High-efficiency Utilization of Coal and Green Chemical Engineering/ ; Z111021902//Northwest A&F University Young Talent Project/ ; }, abstract = {High total ammonia nitrogen (TAN) inhibits anaerobic digestion (AD) and cannot be completely eliminated by merely enhancing a stage of AD. This study incorporates TAN-tolerant inoculum into substrates hydrolyzed by Rhizopus mixed agents to simultaneously enhance hydrolysis-acidogenesis-methanogenesis. The results show a 16.46-fold increase in CH4 production under TAN-inhibited (6870.97 mg L-1) conditions, even exceeding the AD without TAN by 21.10%. Model substrates sodium acetate and mixed H2 confirm hydrogenotrophic methanogenesis is the main pathway, with reduced TAN inhibition. Furthermore, a synergistic metabolic microbial community dominated by hydrolytic bacteria JAAYGG01 sp. and DTU014 sp., acidogenic bacteria DTU015 sp., DTU013 sp., and JAAYLO01 sp., and methanogens Methanosarcina mazei and an unclassified species in the Methanoculleus is reconstructed to resist TAN inhibition. Metagenomic combined with metatranscriptomic sequencing identifies that this microbial community carries xynD and bglB to regulate substrate hydrolysis, leading to acetate production through glycolysis, butyrate, and pyruvate metabolism with high acetate kinase activity, thereby CH4 produced primarily via hydrogenotrophic methanogenesis with high coenzyme F420 activity, facilitated by efficient mass transfer processes and quorum sensing regulation. This cleaner strategy obtains higher economic benefit (US$149.02) than conventional AD and can increase 154.64-fold energy production of a 24 000 m3 biogas plant, guided by machine learning.}, } @article {pmid40162034, year = {2025}, author = {Huang, L and Zheng, D and Li, T and Li, X and Kong, J and Wang, K and Wang, S and Cao, C}, title = {Disseminated Histoplasmosis Due to Anti-IFN-γ Autoantibodies-Associated Immunodeficiency.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {1605-1609}, doi = {10.2147/IDR.S513750}, pmid = {40162034}, issn = {1178-6973}, abstract = {BACKGROUND: Disseminated histoplasmosis caused by the temperature-dependent dimorphic fungus Histoplasma capsulatum is an invasive fungal disease rarely reported in southern China. Here, we report a case of disseminated histoplasmosis due to anti-IFN-γ autoantibodies (AIGA)- associated immunodeficiency.

CASE PRESENTATION: We present the case of a 57-year-old HIV-negative female patient with disseminated histoplasmosis in southern China. The patient showed progressively enlarging multiple clavicular, neck, and upper chest skin nodules and dyspnea, which led to the initial suspicion of pulmonary tuberculosis or lung cancer. Bacterial cultures results were negative. Histopathology of a skin tissue showed infectious granulomas. Disseminated histoplasmosis was diagnosed via next-generation sequencing (mNGS) and fungal culture. Furthermore, enzyme-linked immunosorbent assay results from a peripheral blood confirmed that the patient had a high-titer of AIGA.

CONCLUSION: This case prompts clinicians to consider histoplasmosis an important differential diagnosis in a region where talaromycosis is highly endemic. This case report emphasizes that clinicians should be vigilant for immunodeficiency and consider testing for AIGA in HIV-negative patients who are suspected of having complex opportunistic infections.}, } @article {pmid40161798, year = {2025}, author = {Zeamer, AL and Lai, Y and Sanborn, V and Loew, E and Tracy, M and Jo, C and Ward, DV and Bhattarai, SK and Drake, J and McCormick, BA and Bucci, V and Haran, JP}, title = {Microbiome functional gene pathways predict cognitive performance in older adults with Alzheimer's disease.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.03.06.641911}, pmid = {40161798}, issn = {2692-8205}, abstract = {Disturbances in the gut microbiome is increasing correlated with neurodegenerative disorders, including Alzheimer's Disease. The microbiome may in fact influence disease pathology in AD by triggering or potentiating systemic and neuroinflammation, thereby driving disease pathology along the "microbiota-gut-brain-axis". Currently, drivers of cognitive decline and symptomatic progression in AD remain unknown and understudied. Changes in gut microbiome composition may offer clues to potential systemic physiologic and neuropathologic changes that contribute to cognitive decline. Here, we recruited a cohort of 260 older adults (age 60+) living in the community and followed them over time, tracking objective measures of cognition, clinical information, and gut microbiomes. Subjects were classified as healthy controls or as having mild cognitive impairment based on cognitive performance. Those with a diagnosis of Alzheimer's Diseases with confirmed using serum biomarkers. Using metagenomic sequencing, we found that relative species abundances correlated well with cognition status (MCI or AD). Furthermore, gene pathways analyses suggest certain microbial metabolic pathways to either be correlated with cognitive decline or maintaining cognitive function. Specifically, genes involved in the urea cycle or production of methionine and cysteine predicted worse cognitive performance. Our study suggests that gut microbiome composition may predict AD cognitive performance.}, } @article {pmid40161742, year = {2025}, author = {Wong, MK and Armstrong, E and Heirali, AA and Schneeberger, PHH and Chen, H and Cochrane, K and Sherriff, K and Allen-Vercoe, E and Siu, LL and Spreafico, A and Coburn, B}, title = {Assessment of ecological fidelity of human microbiome-associated mice in observational studies and an interventional trial.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.03.11.642547}, pmid = {40161742}, issn = {2692-8205}, abstract = {UNLABELLED: Composition and function of the gut microbiome is associated with diverse health conditions and treatment responses. Human microbiota-associated (HMA) mouse models are used to establish causal links for these associations but have important limitations. We assessed the fidelity of HMA mouse models to recapitulate ecological responses to a microbial consortium using stools collected from a human clinical trial. HMA mice were generated using different routes of consortium exposure and their ecological features were compared to human donors by metagenomic sequencing. HMA mice were more similar in gut composition to other mice than their respective human donors, with taxa including Akkermansia muciniphila and Bacteroides species enriched in mouse recipients. A limited repertoire of microbes was able to engraft into HMA mice regardless of route of consortium exposure. In publicly available HMA mouse datasets from four distinct health conditions, we confirmed our observation that a taxonomically restricted set of microbes reproducibly engrafts in HMA mice and observed that stool microbiome composition of HMA mice were more like other mice than their human donor. Our data suggest that HMA mice are limited models to assess the ecological impact of microbial consortia, with ecological effects in HMA mice being more strongly associated with host species than donor stool ecology or ecological responses to treatment in humans. Comparisons to published studies suggest this may be due to comparatively large host-species effects that overwhelm ecological effects of treatment in humans that HMA models aim to recapitulate.

IMPORTANCE: Human microbiota-associated (HMA) mice are models that better represent human gut ecology compared to conventional laboratory mice and are commonly used to test the effect of the gut microbiome on disease or treatment response. We evaluated the fidelity of using HMA mice as avatars of ecological response to a human microbial consortium, MET4. Our results show that HMA mice in our cohort and across other published studies are more similar to each other than the human donors or inoculum they are derived from and harbour a taxonomically restricted gut microbiome. These findings highlight the limitations of HMA mice in evaluating the ecological effects of complex human microbiome-targeting interventions, such as microbial consortia.}, } @article {pmid40161675, year = {2025}, author = {Secaira-Morocho, H and Jiang, X and Zhu, Q}, title = {Augmenting microbial phylogenomic signal with tailored marker gene sets.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.03.13.643052}, pmid = {40161675}, issn = {2692-8205}, abstract = {Phylogenetic marker genes are traditionally selected from a fixed collection of whole genomes evenly distributed across major microbial phyla, covering only a small fraction of gene families. And yet, most microbial diversity is found in metagenome-assembled genomes that are unevenly distributed and harbor gene families that do not fit the criteria of universal orthologous genes. To address these limitations, we systematically evaluate the phylogenetic signal of gene families annotated from KEGG and EggNOG functional databases for deep microbial phylogenomics. We show that markers selected from an expanded pool of gene families and tailored to the input genomes improve the accuracy of phylogenetic trees across simulated and real-world datasets of whole genomes and metagenome-assembled genomes. The improved accuracy of trees compared to previous markers persists even when metagenome-assembled genomes lack a fraction of open reading frames. The selected markers have functional annotations related to metabolism, cellular processes, and environmental information processing, in addition to replication, translation, and transcription. We introduce TMarSel, a software tool for automated, systematic, free-from-expert opinion, and tailored marker selection that provides flexibility in the number of markers and annotation databases while remaining robust against uneven taxon sampling and incomplete genomic data.}, } @article {pmid40161639, year = {2025}, author = {Williams, A and Ravel, J and Kaul, R and Armstrong, E and Huibner, S and Holm, JB}, title = {Temporal Dynamics of the Vaginal Microbiome and Host Immune Markers Before, During, and After Metronidazole Treatment for Bacterial Vaginosis.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.03.13.643085}, pmid = {40161639}, issn = {2692-8205}, abstract = {UNLABELLED: This study analyzed metagenomic and immune marker profiles of seven individuals before, during, and after a 7-day course of metronidazole treatment for bacterial vaginosis (BV). Treatment reduced BV-associated bacteria and immune marker levels, with distinct early (days 1-4) and late (days 5-7) phases. Post-treatment, variability in microbial and immune marker profiles demonstrated a rapid resurgence of certain BV associated bacteria, highlighting the need for additional strategies like probiotics to maintain a healthy vaginal microbiome. The study found significant host and microbial influences on immune response variance, with IP-10 and sEcad highly correlated with the vaginal microbiome. The findings identify optimal timing for administering live biotherapeutics to restore D-lactic acid-producing Lactobacillus species dominance and underscore the complexity of BV infection and treatment response among different people.

IMPORTANCE: Bacterial vaginosis (BV), a common condition associated with an increased risk of preterm birth and sexually transmitted infections among others, is characterized by a dysbiotic vaginal microbiome associated with dominance of a diverse assortment of anaerobic bacterial species. Metronidazole is the first-line treatment recommended by the CDC for BV when patients report symptoms. Despite treatment, BV recurrence is common. There is limited data regarding the effects of oral metronidazole on the vaginal microbiome starting at initiation of treatment as most studies have compared measurements taken before and after treatment completion. This study utilized metagenomic sequencing, pan-bacterial qPCR, and immune marker measurements to analyze the longitudinal dynamics of the vaginal microbiome and host immune response before, during and after metronidazole treatment.}, } @article {pmid40160274, year = {2025}, author = {Naushad, S and Gao, R and Duceppe, MO and Dupras, AA and Reiling, SJ and Merks, H and Dixon, B and Ogunremi, D}, title = {Metagenomic detection of protozoan parasites on leafy greens aided by a rapid and efficient DNA extraction protocol.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1566579}, doi = {10.3389/fmicb.2025.1566579}, pmid = {40160274}, issn = {1664-302X}, abstract = {INTRODUCTION: Infections with protozoan parasites associated with the consumption of fresh produce is an on-going issue in developed countries but mitigating the risk is hampered by the lack of adequate methods for their detection and identification.

MATERIALS AND METHODS: We developed a metagenomic next-generation sequencing (mNGS) assay using a MinION sequencer for the identification of parasites in intentionally contaminated lettuce to achieve a more accurate and rapid method than the traditional molecular and microscopy methods commonly used for regulatory purposes. Lettuce (25 g) was spiked with varying numbers of Cryptosporidium parvum oocysts, and microbes washed from the surface of the lettuce were lysed using the OmniLyse device. DNA was then extracted by acetate precipitation, followed by whole genome amplification. The amplified DNA was sequenced by nanopore technology and validated with the Ion Gene Studio S5, and the generated fastq files raw reads were uploaded to the CosmosID webserver for the bioinformatic identification of microbes in the metagenome. To demonstrate the ability of the procedure to distinguish other common food and waterborne protozoan parasites, lettuce was also spiked with C. hominis, C. muris, Giardia duodenalis and Toxoplasma gondii individually or together.

RESULTS: The efficient lysis of oocysts and cysts was a prerequisite for the sensitive detection of parasite DNA and was rapidly achieved within 3 min. Amplification of extracted DNA led to the generation of 0.16-8.25 μg of DNA (median = 4.10 μg), sufficient to perform mNGS. Nanopore sequencing followed by bioinformatic analysis led to the consistent identification of as few as 100 oocysts of C. parvum in 25 g of fresh lettuce. Similar results were obtained using the Ion S5 sequencing platform. The assay proved useful for the simultaneous detection of C. parvum, C. hominis, C. muris, G. duodenalis and T. gondii.

DISCUSSION: Our metagenomic procedure led to the identification of C. parvum present on lettuce at low numbers and successfully identified and differentiated other protozoa either of the same genus or of different genera. This novel mNGS assay has the potential for application as a single universal test for the detection of foodborne parasites, and the subtyping of parasites for foodborne outbreak investigations and surveillance studies.}, } @article {pmid40160273, year = {2025}, author = {Liu, Y and Ying, Y and Li, Y and Zhang, W and Shu, J}, title = {Symbiotic bacteria associated with different species of Curculio (Coleoptera: Curculionidae) and their host plants.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1531847}, doi = {10.3389/fmicb.2025.1531847}, pmid = {40160273}, issn = {1664-302X}, abstract = {Bacteria often play important roles in the host adaptation of phytophagous insects. Beetles of the genus Curculio (Coleoptera: Curculionidae) include pest species that bore into the seeds of trees in the family Fagaceae and damage the cotyledons. At present, there are few studies of the taxonomic diversity and functional effects of symbiotic bacteria involved in changes in host ranges and host adaptation of Curculio. Here, we used 16S rRNA gene Illumina and metagenomic sequencing to compare the composition and functions of the bacterial communities of three species of host plants and several Curculio species combinations: Curculio bimaculatus feeding on Castanopsis sclerophylla, C. bimaculatus feeding on Castanopsis tibetana, and Curculio davidi feeding on Ca. tibetana. The host plants influenced the diversity of symbiotic bacteria, while the Curculio species influenced the community structure of the symbiotic bacteria. Functional predictions showed that symbiotic bacteria contributed to the metabolism of the hosts. However, consistent with the variation in bacteria, the major metabolism-related bacterial genera varied among the treatment groups. Comparisons of metabolic enzymes based on KEGG (Kyoto Encyclopedia of Genes and Genomes) annotation revealed differences in the enzymes involved in insect development and detoxification of plant secondary compounds among the three groups, and the patterns were influenced by the dominance of the Curculio species on the host plants. This study provides valuable insights into the possible role of symbiotic bacteria in Curculio as host insects.}, } @article {pmid40160271, year = {2025}, author = {Yang, B and Feng, C and Jiang, H and Chen, Y and Ding, M and Dai, H and Zhai, Z and Yang, M and Liang, T and Zhang, Y}, title = {Effects of long-term continuous cropping on microbial community structure and function in tobacco rhizosphere soil.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1496385}, doi = {10.3389/fmicb.2025.1496385}, pmid = {40160271}, issn = {1664-302X}, abstract = {As is well known, continuous cropping can lead to a decrease in crop yield and quality. Despite this, continuous cropping remains prevalent in practical agricultural production, particularly in the case of tobacco cultivation, owing to its high economic value. The samples for this study were collected from a flue-cured tobacco planting base located in Huili County, Liangshan Yi Autonomous Prefecture, Sichuan Province, China. After years of continuous planting, the yield of tobacco in this base has significantly decreased. In order to explain the microecological causes of this phenomenon, we collected non-continuous cropping, continuous cropping for 5 years, and continuous cropping for 10 years of tobacco rhizosphere soil, and analyzed the effects of long-term continuous cropping on nutrients, enzyme activities, microbial community structure, and function of tobacco rhizosphere soil. The results showed that with the continuous cropping, the majority nutrients (except for phosphorus and manganese) in rhizosphere soil decreased significantly, and the rhizosphere microbial community structure changed significantly. Correlation network analysis results showed that changes in the rhizosphere microbial community of tobacco were closely related to soil urease, active organic carbon, and available iron content. The results of functional analysis based on microorganisms and genes showed that the rhizosphere microbiota may change the content of soil nutrients through iron_respiration, sulfur_respiration, and Carbon fixation in prokaryotes pathways. The results of the correlation network analysis and the functional analysis mutually confirmed each other, both emphasizing the important role of soil carbon and iron in shaping the structure of the tobacco rhizosphere microbial community. Based on the results of this study, we propose to improve the microbial community structure of tobacco rhizosphere soil by increasing the levels of readily oxidizable organic carbon, available iron, and soil urease activity in the future, so as to alleviate the negative impact of continuous cropping on crop yield. The results of this study provide theoretical support for modifying the rhizosphere microbial environment through nutrient regulation, thereby enhancing plant growth in the context of continuous tobacco cropping.}, } @article {pmid40160267, year = {2025}, author = {Kragh, ML and Scheel, NH and Leekitcharoenphon, P and Truelstrup Hansen, L}, title = {Repeated biocide treatments cause changes to the microbiome of a food industry floor drain biofilm model.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1542193}, doi = {10.3389/fmicb.2025.1542193}, pmid = {40160267}, issn = {1664-302X}, abstract = {There is a concern about the development of microbial tolerance and resistance to biocides due to their repeated use within the food industry. This study aimed to develop a floor drain biofilm model and test whether repeated biocide treatment would result in increased tolerance to biocides. Culturomics and shotgun metagenomic analysis of 14 drains and 214 bacterial isolates from three industrial food production environments revealed microbiomes with great diversity and complexity, but with the dominance of a few highly abundant taxa, including Pseudomonas. A representative drain biofilm was created (3 days, 15°C) using 31 whole genome sequenced bacterial isolates from 24 genera. The biofilm model represented 47-58% and 76-81% of the microbial abundance observed in the metagenome and viable microbiota, respectively. The biofilm model was exposed on days 3 and 6 to water or different industrial concentrations of benzalkonium chloride (BC), peracetic acid (PAA), or sodium hypochlorite (SH). Analysis of the viable survivors using MALDI-TOF MS and the regrowing biofilms using 16S rRNA amplicon sequencing showed how the diversity of the biofilm decreased but without any change in biocide tolerance as seen in log reductions (CFU/cm[2]). The use of different biocides did, however, exert significantly different selective pressures on the microbiomes as Citrobacter, Acinetobacter, Aeromonas, and Pseudomonas dominated the biofilm after treatments with SH or PAA, while Serratia and Moraxella dominated after treatments with BC. The dominance of Serratia marcescens could be explained by the carriage of a BC efflux pump (oqxB) and the highest (20 mg/L BC) minimum inhibitory concentration (MIC) result of the drain isolates. In contrast, despite carrying a BC efflux pump (qacH), Listeria monocytogenes ST121 did not show increased survival or presence in the biofilm after BC treatments. Only the highest tested concentration of PAA was able to completely eradicate L. monocytogenes. The developed biofilm model and the repeated biocide treatments enabled a better understanding of how biocides affect the biofilm microbiome. Future research should involve testing biocide rotation strategies to control biofilm regrowth and inactivation of persistent foodborne pathogens in floor drains.}, } @article {pmid40159059, year = {2025}, author = {Shang, SY and Li, XP and Xu, J and Li, Y and Cao, LQ and Ye, H}, title = {[A case of acute pseudomembranous necrotizing tracheobronchitis in an adult].}, journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases}, volume = {48}, number = {4}, pages = {385-388}, doi = {10.3760/cma.j.cn112147-20240828-00510}, pmid = {40159059}, issn = {1001-0939}, mesh = {Humans ; *Tracheitis/diagnosis/microbiology ; *Bronchitis/microbiology/diagnosis ; *Staphylococcal Infections/diagnosis ; Male ; Staphylococcus aureus/isolation & purification ; Bronchoscopy ; Influenza B virus/isolation & purification ; Adult ; Necrosis ; Influenza, Human/complications ; Middle Aged ; Linezolid/therapeutic use ; }, abstract = {This study presented a rare case of secondary Staphylococcus aureus (S. aureus) infection following influenza B virus infection, resulting in diffuse airway injury and hemorrhagic pneumonia. The patient initially underwent bronchial artery embolization (BAE) due to persistent hemoptysis refractory to conventional hemostatic therapy. Although the hemoptysis was resolved postoperatively, severe hypoxemia persisted. Bronchoscopy revealed diffuse yellow plaques with mucosal erosion and necrosis in the airways. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid identified S. aureus harboring the Panton-Valentine leukocidin (PVL) genes. Histopathological examination revealed severe acute inflammatory changes consistent with necrotizing airway pathology. A diagnosis of IBV-associated S. aureus infection leading to acute pseudomembranous necrotizing tracheobronchitis and hemorrhagic pneumonia was made. The patient responded favorably to linezolid therapy. Follow-up bronchoscopy revealed multiple granulation tissues in the airways, which were subsequently removed under endoscopic guidance. After ruling out persistent infection, the patient was treated with low-dose oral prednisone, which resulted in significant clinical improvement.}, } @article {pmid40158829, year = {2025}, author = {Liu, Y and Zhang, Q and Lu, L and Qian, Y and Wu, Y and Hu, D and Xu, Y and Xu, H and Ji, G}, title = {Huang-qin Decoction alleviates Deoxycholic Acid-induced Colorectal Cancer in Mice by Regulating Gut Microbiota.}, journal = {Journal of ethnopharmacology}, volume = {}, number = {}, pages = {119715}, doi = {10.1016/j.jep.2025.119715}, pmid = {40158829}, issn = {1872-7573}, abstract = {Huangqin Decoction (HQD), a traditional Chinese medicine (TCM) formula documented in Shang Han Lun, has demonstrated safety and efficacy in the treatment of ulcerative colitis (UC). Recent studies also suggest that HQD exerts therapeutic effects on colorectal cancer (CRC). However, the underlying mechanisms remain unclear.

AIMS OF THE STUDY: This study aimed to investigate the therapeutic effects of HQD on CRC and explore its potential mechanisms of action.

METHODS: The active ingredients and potential targets of HQD were identified through network pharmacology-based analyses. The CRC-related targets were compared with those of HQD. Shared targets were subjected to Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, and a protein-protein interaction (PPI) network was constructed. Additionally, APC[min/+] mice were treated with 0.2% deoxycholic acid (DCA) and gavaged with low or high doses of HQD. Tumor morphology was assessed using hematoxylin and eosin (HE) staining. Immunohistochemical staining was performed to evaluate the expression of Ki-67, Caspase-3, and MUC2 in the intestine. Periodic acid-Schiff (PAS) and PAS-alcian blue (PAS-AB) staining were utilized to detect mucin distribution and the number of goblet cells in the intestines of the mice. The mRNA expression levels of interleukin 6 (IL-6), mitogen-activated protein kinase 8 (MAPK8), vascular endothelial growth factor A (VEGFA), epidermal growth factor receptor (EGFR), albumin (ALB), and Caspase 3 (CASP3) were quantified using quantitative reverse-transcription PCR (qRT-PCR). Immunofluorescence was employed to assess the degree of apoptosis. Additionally, 16S ribosomal RNA gene sequencing, sequence curation and annotation, and metagenomic sequencing were performed to analyze changes in the composition of the mouse intestinal microbiota and related functions and signaling pathways.

RESULTS: The active ingredients of HQD were identified. GO and KEGG pathway enrichment analyses indicated that the shared targets were primarily involved in tumor suppression. HQD effectively treated DCA-induced CRC in mice. Furthermore, positive PAS and PAS-AB staining was significantly increased in the intestines of mice treated with HQD. HQD enhanced the abundance of Lachnospiraceae, Firmicutes, Fusobacteria, and Clostridium, while reducing the abundance of Eggerthellales. Additionally, HQD modulated secondary bile acid metabolism, carbohydrate synthesis, and other energy metabolism pathways, which may underlie its therapeutic effects.

CONCLUSION: HQD effectively treated CRC in mice, and its mechanisms of action may be related to the regulation of the gut microbiota.}, } @article {pmid40158299, year = {2025}, author = {Borkakoti, N and Ribeiro, AJM and Thornton, JM}, title = {A structural perspective on enzymes and their catalytic mechanisms.}, journal = {Current opinion in structural biology}, volume = {92}, number = {}, pages = {103040}, doi = {10.1016/j.sbi.2025.103040}, pmid = {40158299}, issn = {1879-033X}, abstract = {In this perspective, we analyse the progress made in our knowledge of enzyme sequences, structures and functions in the last 2 years. We review how much new enzyme data have been garnered and annotated, derived from the study of proteins using structural and computational approaches. Recent advances towards capturing 'Catalysis in silico' are described, including knowledge and predictions of enzyme structures, their interactions and mechanisms. We highlight the flood of enzyme data, driven by metagenomic sequencing, the improved enzyme data resources, the high coverage in Protein Data Bank of E.C. classes and the AI-driven structure prediction techniques that facilitate the accurate prediction of protein structures. We note the focus on disordered regions in the context of enzyme regulation and specificity and comment on emerging bioinformatic approaches that capture reaction mechanisms computationally for comparing and predicting enzyme mechanisms. We also consider the drivers of progress in this field in the next five years.}, } @article {pmid40158160, year = {2025}, author = {Zhu, M and Wang, Q and Yang, Y and Liu, X and Zhang, J and Li, G and Liu, W and Xiang, X and Chen, J}, title = {Multiomics approach reveals the comprehensive interactions between nutrition and children's gut microbiota, and microbial and host metabolomes.}, journal = {Nutrition journal}, volume = {24}, number = {1}, pages = {50}, pmid = {40158160}, issn = {1475-2891}, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Child ; Male ; Cross-Sectional Studies ; *Metabolome/physiology ; Female ; Child, Preschool ; *Feces/microbiology ; China ; *Diet/methods ; Metabolomics/methods ; Nutritional Status ; Multiomics ; }, abstract = {The gut microbiome can modulate nutrient metabolism to produce many metabolites interacting with the host. However, the intricate interactions among dietary intake, the gut microbiome and metabolites, and host metabolites need to be further explored although some studies have been devoted to it. Here, in a cross-sectional studies, 88 children aged 2-12 years were enrolled from northwestern China. The dietary intake data were collected via a designed food frequency questionnaire to calculate plant-based diet indices (PDIs). Stool and plasma samples were collected for metagenomic and broad-targeted metabolomic analysis. Spearman's rank correlation was used to describe the associations between nutrients/PDIs and the gut microbiota and metabolites. PDI was significantly positively associated with Bilophila wadsworthia, Bacteroides thetaiotaomicron, and Alistipes indistinctus, etc., but was obviously negatively correlated with Roseburia intestinalis, Faecalibacterium prausnitzii, etc. However, these species showed no significant associations with either healthy PDI (hPDI) or unhealthy PDI (uPDI). Interestingly, hPDI was significantly positively related to species, including Ruminococcus bicirculans, and was significantly negatively associated with uPDI, and vice versa. The above correlation trends were also observed between PDIs and predicted gut microbial functional pathways, microbial metabolites and the host metabolome. Notably, the significantly related pathways were focused mainly on substances and energy metabolism. PDI was significantly positively associated with the fecal contents of P-aminobenzoate, chenodeoxycholic acid, 4,6-dihydroxyquinoline, quinoline-4,8-diol, etc., but was significantly negatively associated with those of TMAO, FFA, creatine phosphate, etc. In plasma, PDI was significantly positively associated with sarcosine, ornithine, L-histidine, etc., but was distinctly negatively correlated with FFAs, carnitine C2:0, etc. Strikingly, the healthy plant-based diet index (hPDI) is correlated with increased levels of metabolites related to tryptophan metabolism, whereas the unhealthy PDI (uPDI) is linked to increased levels of metabolites associated with tyrosine and sphingolipid metabolism, which are pathways commonly associated with Western diets. Our studies provide reliable data support and a comprehensive understanding of the effects of dietary intake on the gut microbiome and microbial and host metabolites and lay a foundation for further studies of the diet-gut microbiota-microbial metabolites and host metabolism.}, } @article {pmid40158141, year = {2025}, author = {Jiang, Y and Aton, M and Zhu, Q and Lu, YY}, title = {Modeling microbiome-trait associations with taxonomy-adaptive neural networks.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {87}, pmid = {40158141}, issn = {2049-2618}, support = {RGPIN-03270-2023//Canadian NSERC Discovery Grant/ ; RGPIN-03270-2023//Canadian NSERC Discovery Grant/ ; }, mesh = {Humans ; *Neural Networks, Computer ; *Microbiota ; Metagenomics/methods ; Bacteria/classification/genetics ; Computer Simulation ; }, abstract = {The human microbiome, a complex ecosystem of microorganisms inhabiting the body, plays a critical role in human health. Investigating its association with host traits is essential for understanding its impact on various diseases. Although shotgun metagenomic sequencing technologies have produced vast amounts of microbiome data, analyzing such data is highly challenging due to its sparsity, noisiness, and high feature dimensionality. Here, we develop MIOSTONE, an accurate and interpretable neural network model for microbiome-disease association that simulates a real taxonomy by encoding the relationships among microbial features. The taxonomy-encoding architecture provides a natural bridge from variations in microbial taxa abundance to variations in traits, encompassing increasingly coarse scales from species to domains. MIOSTONE has the ability to determine whether taxa within the corresponding taxonomic group provide a better explanation in a data-driven manner. MIOSTONE serves as an effective predictive model, as it not only accurately predicts microbiome-trait associations across extensive simulated and real datasets but also offers interpretability for scientific discovery. Both attributes are crucial for facilitating in silico investigations into the biological mechanisms underlying such associations among microbial taxa. Video Abstract.}, } @article {pmid40157594, year = {2025}, author = {Wang, C and Fan, S and Li, M and Ye, Y and Li, Z and Long, W and Li, Y and Huang, Z and Jiang, Q and Yang, W and Yang, R and Tang, D}, title = {A 7-year feed study on the long-term effects of genetically modified maize containing cry1Ab/cry2Aj and EPSPS genes on gut microbiota and metabolite profiles across two generations of cynomolgus macaques.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {}, number = {}, pages = {115419}, doi = {10.1016/j.fct.2025.115419}, pmid = {40157594}, issn = {1873-6351}, abstract = {The health implications of genetically modified (GM) crops remain controversial relative to their non-GM counterparts, particularly regarding long-term dietary exposure. Although the gut microbiome is a key health indicator, studies investigating the impact of GM crop consumption on intestinal microbiota remain limited. This study presents a comprehensive 7-year evaluation of GM maize expressing cry1Ab/cry2Aj and G10evo-EPSPS proteins through metagenomic and metabolomic analyses. We assessed the effects of GM maize consumption on gut microbiota diversity and metabolite profiles in cynomolgus macaques (Macaca fascicularis) compared with non-GM maize. Three diet regimens were implemented: a conventional compound feed (CK group), diet formulation containing 70% non-GM maize (Corn group), and diet formulation containing 70% GM maize (Tg group). The results demonstrated that feeding GM maize to the first (F0) and second (F1) generations of monkeys did not substantially affect the composition, community structure, or function of the intestinal microbiome, as indicated by species composition and diversity analyses. Minor differences in intestinal metabolites were observed but were not directly linked to transgenic maize consumption. Collectively, long-term intake of maize with cry1Ab/cry2Aj and g10evo-epsps genes had no adverse effects on macaques or their offspring.}, } @article {pmid40157532, year = {2025}, author = {Pienaar, RD and Herrero, S and Cerqueira de Araujo, A and Krupa, F and Abd-Alla, AMM and Herniou, EA}, title = {High-throughput screening reveals high diversity and widespread distribution of viruses in black soldier flies (Hermetia illucens).}, journal = {Journal of invertebrate pathology}, volume = {}, number = {}, pages = {108322}, doi = {10.1016/j.jip.2025.108322}, pmid = {40157532}, issn = {1096-0805}, abstract = {Virus discovery in mass-reared insects is a growing topic of interest due to outbreak risks and for insect welfare concerns. In the case of black soldier flies (Hermetia illucens, BSF), pioneering bioinformatic studies have uncovered exogenous viruses from the orders Ghabrivirales and Bunyavirales, as well as endogenous viral elements from five virus families. This prompted further virome investigation of BSF metagenomes and metatranscriptomes, including from BSF individuals displaying signs and symptoms of disease. A high-throughput pipeline allowed the simultaneous investigation of 203 next generation sequencing datasets. This revealed the presence of seven viruses belonging to the families Dicistroviridae, Iflaviridae, Rhabdoviridae, Solinviviridae, Inseviridae, Lebotiviridae, and an unclassified Bunyavirales. Here we describe five viruses, which were detected in BSF from multiple origins, outlining the diversity of naturally occurring viruses associated with BSF colonies. As this viral community may also include BSF pathogens, we developed molecular detection tools which could be used for viral surveillance, both in mass-reared and wild populations of BSF.}, } @article {pmid40157487, year = {2025}, author = {Li, J and Zhu, L and Li, X and Han, X and Yi, J and Wu, Y and Wang, M}, title = {Characterization and Risk-quantification of Antibiotic Resistome in Grain-based and Non-grain Cropping Soils.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {126147}, doi = {10.1016/j.envpol.2025.126147}, pmid = {40157487}, issn = {1873-6424}, abstract = {Microbial contamination in soils, encompassing human bacterial pathogens (HBPs), antibiotic resistance genes (ARGs), and virulence factor genes (VFGs), poses a significant threat to human health via the food chain. Currently, there is a lack of comprehensive assessments of microbial contamination and associated health risks of ARGs in agricultural soils. In this study, metagenomic sequencing was used to evaluate microbial contamination in grain-based cropping soils (rice cultivation) and non-grain cropping soils (vegetable cultivation and aquaculture). The results showed that the diversity and abundance of HBPs and VFGs were significantly higher in non-grain soils. Further resistome analysis revealed higher abundances of high-risk (from 0.014 to 0.018 - 0.023) and "last-resort" ARGs (from 0.007 to 0.034 - 0.046) in non-grain soils. Besides ARGs abundance, health risk quantification revealed that non-grain soils exhibited 1.49 to 2.14-fold greater ARG-related risks than grain-based soils. Additionally, stronger network associations were found between HBPs, ARGs, and mobile genetic elements (MGEs) in non-grain soils. This study indicated that the non-grain cropping pattern of soils elevated the risk of microbial contamination and ARGs health risk, which provided an important basis for accurately quantifying the risk of microbial contamination in different agricultural soils.}, } @article {pmid40157184, year = {2025}, author = {Qiao, X and Kong, X and Zhou, H and Fan, X and Yuan, J and Zhang, Y}, title = {Deciphering the inhibitory mechanisms of polystyrene microplastics on thermophilic methanogens from the insights of microbial metabolite profiling and metagenomic analyses.}, journal = {Journal of hazardous materials}, volume = {492}, number = {}, pages = {138054}, doi = {10.1016/j.jhazmat.2025.138054}, pmid = {40157184}, issn = {1873-3336}, abstract = {Due to the utilization of food packaging bags, a substantial amount of polystyrene microplastics (PS MPs) are introduced into the food waste (FW) treatment system during the pre-treatment process, potentially impacting the subsequent biochemical treatment system. In order to investigate the mechanism by which PS MPs affect anaerobic methanogenesis metabolism in thermophilic condition, this study analyzed the characteristics of methanogenesis in thermophilic anaerobic digestion (AD) of FW under different concentrations of PS MPs (100 μm, 10-200 mg/L). The results revealed a negative correlation between PS MPs concentration and methane (CH4) yield from FW. When the concentration of PS MPs reached 200 mg/L, CH4 yield decreased by 47.8 %. Further mechanistic investigations revealed that while the presence of PS MPs at lower concentrations could alleviate its adverse impact on methanogenesis by enhancing EPS content, the accumulation of reactive oxygen species (ROS) persisted with increasing PS MPs concentration, thereby inhibiting the activities of key enzymes involved in solubilization and acidification metabolisms (e.g., acetate kinase and F420). Metagenomics analysis indicated that the presence of PS MPs down-regulate abundance of genes for quorum sensing and CH4 metabolism pathways. These findings not only unveil potential detrimental effects of PS MPs on AD systems but also provide novel insights into comprehending and controlling the impact of MPs pollution on environmental preservation and energy recovery processes.}, } @article {pmid40157173, year = {2025}, author = {Weiting, S and Chen, W and Xiao, L and Yanqiu, H}, title = {Enhanced acid reduction in lactic acid bacteria: Breeding through irradiation-induced mutation and functional assessment.}, journal = {International journal of food microbiology}, volume = {435}, number = {}, pages = {111161}, doi = {10.1016/j.ijfoodmicro.2025.111161}, pmid = {40157173}, issn = {1879-3460}, abstract = {High concentrations of citric acid (CA), malic acid (MA), and tartaric acids (TA) are the primary contributors to the sour taste of fruit and fruit products. However, lactic acid bacteria that are capable of efficiently degrading these organic acids are scarce. Here, three brands of sauerkraut (Xinxi, X; Yuyuan, Y; and Zou Youcai, Z) with various doses of [60]Co γ-irradiation could be treated to induce mutations in their associated lactic acid bacteria and then the abilities of the resulting microbial communities to degrade CA, MA, and TA were evaluated. Sauerkraut X treated with 0.4 kGy irradiation demonstrated the greatest ability of acid reduction. Metagenomic analyses of irradiated (0.4 kGy) and non-irradiated bacterial communities from sauerkraut X revealed a slight decrease in microbial diversity due to irradiation, with a substantial decline in the relative abundance of Lactiplantibacillus xiangfangensis. Concurrently, the relative abundance of dominant acid-reducing lactic acid bacteria such as Levilactobacillus brevis, Pediococcus ethanolidurans, and Lentilactobacillus parafarraginis increased. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed an increase in metabolism-related genes after irradiation, indicating that fatty acid synthesis and aspartate metabolism might be key pathways involved in the enhanced degradation of CA, MA, and TA. Analysis using the Carbohydrate-Active enzymes Database (CAZy) database revealed that glycoside hydrolase (GH) and glycosyltransferase (GT) genes were the most abundant carbohydrate-associated enzyme genes in the bacterial community of sauerkraut X. This finding proved that the oligosaccharides and monosaccharides produced by GH and GT might indirectly affect rates of organic acid degradation. Three highly effective acid-reducing lactic acid bacteria from the microbial community of irradiated sauerkraut X a were isolated and identified via 16S rRNA sequencing as Pediococcus ethanolidurans, Levilactobacillus brevis, and Loigolactobacillus coryniformis. The individual strains showed degradation rates as high as 92.02 % for citric acid (Pediococcus ethanolidurans), 83.04 % for malic acid (Levilactobacillus brevis), and 90.33 % for TA (Loigolactobacillus coryniformis). This study provides a theoretical basis and technical support for the development of enhanced microbial strains that can reduce the acid content of fruit materials.}, } @article {pmid40156973, year = {2025}, author = {Zhong, S and Li, B and Chen, Q and Zhang, J and Cai, H and An, R and Liu, G and Zhou, S}, title = {Identifying groundwater anthropogenic disturbances and their predominant impact on microbial nitrogen cycling at a former contamination site adjacent to Baiyangdian Lake.}, journal = {Water research}, volume = {280}, number = {}, pages = {123544}, doi = {10.1016/j.watres.2025.123544}, pmid = {40156973}, issn = {1879-2448}, abstract = {Groundwater ecosystems face increasing threat from declining water quality due to intensified urbanization, agricultural, and industrial activities. Accurately identifying anthropogenic disturbances remains challenging, and their effects on microbial nitrogen cycling are still largely unknown. Here, by collecting 64 groundwater samples from an aquifer beneath the Tanghe sewage reservoir in the North China Plain, we conducted a full-spectrum screening of 228 physiochemical indices, 47 nitrogen cycling genes (NCGs) and 2182 metagenome-assembled genomes (MAGs) harboring NCGs. Unmix model identified antibiotic usage, industrial manufacturing, and agricultural practices as the predominant pollution sources, explaining 49.6-92.2 % (averaged 81.0 %) of the variations in aquifer attributes. These activities were primary drivers governing distributions of groundwater NCGs and NCG-hosts, with fragmented denitrification processes being prevalent. Antibiotic usage and industrial activities were probably associated with suppressed nitrogen cycling, while agriculture had a positive effect. Notably, we observed enhanced mutualistic interactions within NCG-hosts and increased enrichment of NCG-antibiotic resistance gene (ARG), NCG-mental resistance gene (MRG), and NCG-ARG-MRG co-hosts under high anthropogenic stresses, suggesting microbial adaptation to optimize nutrient and energy metabolism. This study provided new insight into how groundwater nitrogen cycling responds to anthropogenic disturbances, offering valuable information for developing groundwater management and pollution control strategies.}, } @article {pmid40156579, year = {2025}, author = {Sanghani, A and Antaliya, K and Patel, R and Dave, S and Tipre, D}, title = {Revealing Microbial Functionalities and Ecological Roles in Rajpardi Lignite Mine: Insights from Metagenomics Analysis.}, journal = {Letters in applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/lambio/ovaf048}, pmid = {40156579}, issn = {1472-765X}, abstract = {The present study employs a metagenomics approach to evaluate microbial communities' ecological functions and potential within the Rajpardi lignite mine of Gujarat, India. Through whole genome shotgun sequencing on the Illumina Miseq platform, we obtained 10,071,318 sequences, which unveiled a diverse and abundant microbial community primarily composed of Proteobacteria, Acidobacteria, and Nitrospirae. Comprehensive taxonomic profiling and gene prediction was carried out using the SqueezeMeta pipline, which highlighted significant contributions to carbohydrate, amino acid, and energy metabolism. The detection of antimicrobial resistance (AMR) and stress resistance genes, such as blaTEM and merA, suggests that these microbes possess the ability to adapt to harsh environmental conditions. Genome binning revealed species such as Acidiphilum sp. 20-67-58, emphasising the nature of these communities as they adapted to an acidic environment. This finding highlights the crucial role of microbes in biogeochemical cycles, emphasizing their potential in bioremediation, pollutant degradation, and ecosystem restoration.}, } @article {pmid40156577, year = {2025}, author = {Kop, LFM and Koch, H and Martins, PD and Suarez, C and Karačić, S and Persson, F and Wilén, BM and Hagelia, P and Jetten, MSM and Lücker, S}, title = {High diversity of nitrifying bacteria and archaea in biofilms from a subsea tunnel.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaf032}, pmid = {40156577}, issn = {1574-6941}, abstract = {Microbial biofilm formation can contribute to the accelerated deterioration of steel-reinforced concrete structures and significantly impact their service life, making it critical to understand the diversity of the biofilm community and prevailing processes in these habitats. Here, we analyzed 16S rRNA gene amplicon and metagenomics sequencing data to study the abundance and diversity of nitrifiers within biofilms on the concrete surface of the Oslofjord subsea road tunnel in Norway. We showed that the abundance of nitrifiers varied greatly in time and space, with a mean abundance of 24.7±15% but a wide range between 1.2-61.4%. We hypothesize that niche differentiation allows the coexistence of several nitrifier groups and that their high diversity increases the resilience to fluctuating environmental conditions. Strong correlations were observed between the nitrifying families Nitrosomonadaceae and Nitrospinaceae, and the iron-oxidizing family Mariprofundaceae. Metagenome-assembled genome (MAG) analyses suggested that early Mariprofundaceae colonizers may provide a protected environment for nitrifiers in exchange for nitrogen compounds and vitamin B12, but further studies are needed to elucidate the spatial organization of the biofilms and the cooperative and competitive interactions in this environment. Together, this research provides novel insights into the diverse communities of nitrifiers living within biofilms on concrete surfaces and establishes a foundation for future experimental studies of concrete biofilms.}, } @article {pmid40156536, year = {2025}, author = {Sarker, S and Klukowski, N and Talukder, S and Athukorala, A and Uddin, MJ}, title = {Opportunistic sampling from the near-threatened Alexandrine parakeet uncovers genomes of a novel parvovirus and beak and feather disease virus.}, journal = {Australian veterinary journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/avj.13442}, pmid = {40156536}, issn = {1751-0813}, support = {DE200100367//Australian Research Council/ ; }, abstract = {Birds are known to harbour a wide range of pathogenic viruses, including the beak and feather disease virus (BFDV; species, Circovirus parrot), which poses a significant threat to the conservation of endangered avian species. This study reports the genomic identification and characterisation of a novel psittaciform chaphamaparvovirus (PsChPV-6) and BFDV, sequenced from the faecal samples of healthy Alexandrine parakeets (Psittacula eupatria). PsChPV-6 is a linear, single-stranded DNA virus consisting of 4232 nucleotides (nt) with a high A + T content and five predicted open reading frames (ORFs). Key proteins encoded by PsChPV-6, such as the nonstructural protein 1 (NS1) and major capsid protein VP1, demonstrate strong sequence similarities to other avian parvoviruses, with conserved motifs in NS1 crucial for viral replication. The presence of a previously uncharacterised ORF1 region suggests strain-specific viral features that warrant further exploration. BFDV is a circular single-stranded DNA virus in the Circoviridae family and was also identified in the samples. Phylogenetic analysis positioned PsChPV-6 within the Chaphamaparvovirus genus, closely related to parvoviruses from diverse avian species, whereas BFDV was grouped with strains from Australian cockatoos and other nonpsittacine birds, suggesting potential cross-species transmission. These findings contribute to a deeper understanding of the genetic diversity and evolutionary dynamics of these viral pathogens in bird populations, underscoring the importance of ongoing surveillance to evaluate their ecological and veterinary impacts.}, } @article {pmid40156205, year = {2025}, author = {Huyghe, CET and Fages, A and Ronco, F and Indermaur, A and Schedel, FDB and Kimirei, I and Makasa, L and Tschopp, P and Salzburger, W}, title = {Metagenomic Insights Into the Dietary Diversity of the Adaptive Radiation of Cichlid Fishes in Lake Tanganyika.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {e17743}, doi = {10.1111/mec.17743}, pmid = {40156205}, issn = {1365-294X}, support = {189970//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; }, abstract = {Diet specialisation is a main driver of diversification in many adaptive radiations. Therefore, identifying diet items is essential to characterise trophic specialisations and to understand the dynamics of dietary adaptations. In this study, we explored the trophic niches of 56 species from the adaptive radiation of cichlid fishes in Lake Tanganyika, encompassing all major phylogenetic lineages and feeding specialisations. We employed a metagenomic sequencing approach to identify the food sources of the investigated species at high taxonomic resolution, sequencing over 400 digestive content samples from wild-caught individuals at around 50 million paired-end read depth per sample. Our analyses revealed Arthropoda, Chordata (fishes), Bacillariophyta and Streptophyta as the primary diet phyla of the Tanganyikan cichlids. Moreover, we confirmed the presence of other food sources and identified taxa not previously documented to be part of the cichlids' diet. Based on their dietary compositions, the Tanganyikan cichlids can be grouped into herbivores, invertivores, piscivores and mixed feeders. Further, we showed that trophic disparity in the radiation is shaped by rapid divergence and documented cases of dietary niche convergence. Diet composition correlated with carbon and nitrogen stable isotope values, gut length, and body morphology. Differences in diet-such as the consumption of diatoms, streptophytes and chlorophytes versus fish and arthropods-were associated with changes in body, upper oral jaw and lower pharyngeal jaw shape. Collectively, this study presents a comprehensive and detailed diet classification of the Tanganyikan cichlids, highlighting the power of metagenomic approaches in delineating dietary adaptations.}, } @article {pmid40155949, year = {2025}, author = {Song, J and Lin, LA and Tang, C and Chen, C and Yang, Q and Zhang, D and Zhao, Y and Wei, HC and Linghu, K and Xu, Z and Chen, T and He, Z and Liu, D and Zhong, Y and Zhu, W and Zeng, W and Chen, L and Song, G and Chen, M and Jiang, J and Zhou, J and Wang, J and Chen, B and Ying, B and Wang, Y and Geng, J and Lin, JW and Chen, L}, title = {DEMINERS enables clinical metagenomics and comparative transcriptomic analysis by increasing throughput and accuracy of nanopore direct RNA sequencing.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {76}, pmid = {40155949}, issn = {1474-760X}, mesh = {*Metagenomics/methods ; Humans ; *Nanopore Sequencing/methods ; *Sequence Analysis, RNA/methods ; COVID-19/virology/genetics ; Gene Expression Profiling/methods ; Transcriptome ; Glioma/genetics ; High-Throughput Nucleotide Sequencing/methods ; SARS-CoV-2/genetics ; Software ; Malaria ; }, abstract = {Nanopore direct RNA sequencing (DRS) is a powerful tool for RNA biology but suffers from low basecalling accuracy, low throughput, and high input requirements. We present DEMINERS, a novel DRS toolkit combining an RNA multiplexing workflow, a Random Forest-based barcode classifier, and an optimized convolutional neural network basecaller with species-specific training. DEMINERS enables accurate demultiplexing of up to 24 samples, reducing RNA input and runtime. Applications include clinical metagenomics, cancer transcriptomics, and parallel transcriptomic comparisons, uncovering microbial diversity in COVID-19 and m[6]A's role in malaria and glioma. DEMINERS offers a robust, high-throughput solution for precise transcript and RNA modification analysis.}, } @article {pmid40155846, year = {2025}, author = {Zhang, Z and Tian, L}, title = {Validation of mNGS results using extensive lab and clinical data.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {173}, pmid = {40155846}, issn = {1471-2180}, mesh = {Humans ; Retrospective Studies ; *Mycobacterium tuberculosis/genetics/isolation & purification ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Mycoplasma pneumoniae/genetics/isolation & purification ; Male ; Adult ; Middle Aged ; Female ; Tuberculosis/microbiology/diagnosis ; Aged ; Adolescent ; Young Adult ; Child ; }, abstract = {PURPOSE: Interpreting the results of metagenomic next-generation sequencing (mNGS) presents a significant challenge in both clinical and laboratory contexts.

METHODS: A retrospective analysis was conducted to validate mNGS findings, with a particular emphasis on Mycobacterium tuberculosis, Mycoplasma pneumoniae, and Pneumocystis jirovecii as representative pathogens, examined from both clinical and laboratory perspectives.

RESULTS: Based on a comprehensive clinical analysis, the mNGS demonstrated detection accuracies for M. tuberculosis, M. pneumoniae, and P. jirovecii of 87.0% (60 out of 69; 95% confidence interval [CI], 77.04%-92.99%), 97.6% (81 out of 83; 95% CI, 91.63%-99.34%), and 78.9% (45 out of 57; 95% CI, 66.72%-87.53%), respectively. Conversely, when incorporating laboratory confirmation from a variety of detection methodologies, the accuracy rates for mNGS in identifying M. tuberculosis, M. pneumoniae, and P. jirovecii were 92.7% (51 out of 55; 95% CI, 82.74%-97.14%), 82.3% (51 out of 62; 95% CI, 70.96%-89.80%), and 83.9% (26 out of 31; 95% CI, 67.36%-92.91%), respectively. Additionally, our analysis revealed no statistically significant difference in read counts and relative abundances between mNGS results deemed clinically as false positives and those considered true positives (P < 0.05).

CONCLUSION: In contemporary clinical practice, the detection of positive results from mNGS is notably high from both laboratory and clinical standpoints. Nonetheless, the interpretation of results with low read counts presents significant challenges for both clinical and laboratory environments under current conditions.}, } @article {pmid40155693, year = {2025}, author = {Refahi, M and Sokhansanj, BA and Mell, JC and Brown, JR and Yoo, H and Hearne, G and Rosen, GL}, title = {Enhancing nucleotide sequence representations in genomic analysis with contrastive optimization.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {517}, pmid = {40155693}, issn = {2399-3642}, support = {1936791//National Science Foundation (NSF)/ ; 1919691//National Science Foundation (NSF)/ ; 2107108//National Science Foundation (NSF)/ ; }, mesh = {*Genomics/methods ; Sequence Analysis, DNA/methods ; Base Sequence ; Algorithms ; Metagenomics/methods ; }, abstract = {Analysis of genomic and metagenomic sequences is inherently more challenging than that of amino acid sequences due to the higher divergence among evolutionarily related nucleotide sequences, variable k-mer and codon usage within and among genomes of diverse species, and poorly understood selective constraints. We introduce Scorpio (Sequence Contrastive Optimization for Representation and Predictive Inference on DNA), a versatile framework designed for nucleotide sequences that employ contrastive learning to improve embeddings. By leveraging pre-trained genomic language models and k-mer frequency embeddings, Scorpio demonstrates competitive performance in diverse applications, including taxonomic and gene classification, antimicrobial resistance (AMR) gene identification, and promoter detection. A key strength of Scorpio is its ability to generalize to novel DNA sequences and taxa, addressing a significant limitation of alignment-based methods. Scorpio has been tested on multiple datasets with DNA sequences of varying lengths (long and short) and shows robust inference capabilities. Additionally, we provide an analysis of the biological information underlying this representation, including correlations between codon adaptation index as a gene expression factor, sequence similarity, and taxonomy, as well as the functional and structural information of genes.}, } @article {pmid40155620, year = {2025}, author = {Kazarina, A and Wiechman, H and Sarkar, S and Richie, T and Lee, STM}, title = {Recovery of 679 metagenome-assembled genomes from different soil depths along a precipitation gradient.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {521}, pmid = {40155620}, issn = {2052-4463}, support = {2020-67019-31803//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; 2238633//National Science Foundation (NSF)/ ; OIA-1656006//National Science Foundation (NSF)/ ; }, mesh = {*Soil Microbiology ; *Metagenome ; Metagenomics ; Bacteria/genetics/classification ; Kansas ; Soil/chemistry ; Archaea/genetics ; }, abstract = {Soil contains a diverse community of organisms; these can include archaea, fungi, viruses, and bacteria. In situ identification of soil microorganisms is challenging. The use of genome-centric metagenomics enables the assembly and identification of microbial populations, allowing the categorization and exploration of potential functions living in the complex soil environment. However, the heterogeneity of the soil-inhabiting microbes poses a tremendous challenge, with their functions left unknown, and difficult to culture in lab settings. In this study, using genome assembling strategies from both field core samples and enriched monolith samples, we assembled 679 highly complete metagenome-assembled genomes (MAGs). The ability to identify these MAGs from samples across a precipitation gradient in the state of Kansas (USA) provided insights into the impact of precipitation levels on soil microbial populations. Metabolite modeling of the MAGs revealed that more than 80% of the microbial populations possessed carbohydrate-active enzymes, capable of breaking down chitin and starch.}, } @article {pmid40155586, year = {2025}, author = {Bebawy, AS and Saad, BT and Saad, MT and Mosaad, GS and Gomaa, FAM and Alshahrani, MY and Aboshanab, KM}, title = {Evaluation of the taxonomic classification tools and visualizers for metagenomic analysis using the Oxford nanopore sequence database.}, journal = {Journal of applied genetics}, volume = {}, number = {}, pages = {}, pmid = {40155586}, issn = {2190-3883}, abstract = {Microbial metagenomic identification is generally attributed to the specificity and type of the bioinformatic tools, including classifiers and visualizers. In this study, the performance of two major classifiers, Centrifuge and Kraken2, and two visualizers (Recentrifuge and Krona) has been thoroughly investigated for their efficiency in the identification of the microorganisms using the Whole-Genome Sequence (WGS) database and four targeted databases including NCBI, Silva, Greengenes, and Ribosomal Database Project (RDP). Two standard DNA metagenomic library replicates, Zymo and Zymo-1, were used as quality control. Results showed that Centrifuge gave a higher percentage of Pseudomonas aeruginosa, Escherichia coli, and Salmonella enterica identification than Kraken2. Compared to Recentrifuge, Kraken2 was more accurate in identifying Staphylococcus aureus, Listeria monocytogenes, Bacillus subtilis, and Cryptococcus neoformans. The results of the rest of the detected microorganisms were generally consistent with the two classifiers. Regarding visualizers, both Recentrifuge and Krona provided similar results regarding the abundance of each microbial species regardless of the classifier used. The differences in results between the two mentioned classifiers may be attributed to the specific algorithms each method uses and the sequencing depth. Centrifuge uses a read mapping approach, while Kraken2 uses a k-mer-based system to classify the sequencing reads into taxonomic groups. In conclusion, both Centrifuge and Kraken2 are effective tools for microbial classification. However, the choice of classifier can influence the accuracy of microbial classification and, therefore, should be made carefully, depending on the desired application, even when the same reference database is used.}, } @article {pmid40154870, year = {2025}, author = {Yang, JT and Zhang, Y and Xiong, SY and Wei, HJ and Zhang, WT and Lian, XL and Xu, XL and Jiang, HX and Sun, J}, title = {Microplastics Reduced the Natural Attenuation of Antibiotic Resistance Genes in Fertilized Soils.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {126144}, doi = {10.1016/j.envpol.2025.126144}, pmid = {40154870}, issn = {1873-6424}, abstract = {The prolonged application of mulch and manure in agriculture has led to significant microplastic (MP) pollution in fertilized soils, raising global concerns about its potential impacts on soil health and ecosystem function. However, the effects of MP exposure on antibiotic resistance genes (ARGs) and microbial communities in fertilized soils are unknown. Therefore, we comprehensively explored the trends and drivers of ARGs during their natural abatement under the stress of conventional and biodegradable MP addition in fertilized soils using a soil microcosm experiment and metagenomic. The findings indicated that the presence of polybutylene succinate MPs (PBS-MPs) reduced the natural attenuation rate of ARGs in fertilized soils while increasing the fraction of high-risk ARGs in soils. Microbial communities and mobile genetic elements (MGEs) mainly drove the inhibitory effect of MPs on ARG abatement. Interestingly, most potential hosts for the coexistence of ARGs, metal resistance genes (MRGs), and MGEs were annotated as pathogens, such as Escherichia spp., Salmonella spp., and Klebsiella spp. In addition, MP stress in fertilized soil may lead to long-term contamination by highly virulent and antibiotic-resistant Escherichia coli. MPs influence the distribution of carbon sources, which in turn reduces the diversity and stability of soil microbial communities, while simultaneously promoting the colonization of crucial ARG hosts, like Dyella spp. This ultimately prolonged the high-risk state for ARG proliferation in the soil. This study highlights the significant risk posed by MPs to the persistence and spread of ARGs in fertilized soils. These results provide valuable insights for managing MP contamination in agricultural systems, emphasizing the need for sustainable practices to mitigate the long-term environmental risks associated with MP pollution.}, } @article {pmid40154751, year = {2025}, author = {Jiang, X and Zhao, Y and Zhang, W and Zheng, Q and Li, D and Zhang, G and Zhou, T}, title = {Chlorotetracycline-driven modulation of substrate utilization and metabolic traits in sludge anaerobic fermentation for optimized methane production.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132449}, doi = {10.1016/j.biortech.2025.132449}, pmid = {40154751}, issn = {1873-2976}, abstract = {Anaerobic digestion (AD) is a highly efficient and promising method for treating waste activated sludge (WAS). Nevertheless, the presence of chlortetracycline (CTC) in WAS introduced uncertainty into the AD process. This study revealed thatthe cumulative methane yield was increased by 27.5 % with the CTC concentration at 50 mg/kg dry sludge by enhancing hydrolysis, acidification and methanogenesis during which specific microbial communities were enriched and related functional genes were enhanced. Subsequent investigations foundthe accumulation of extracellular polymeric substances (EPS) was improved and methane-producing microorganisms (e.g., Bacteroidetes and Euryarchaeota) were also enriched under CTC exposure. Metagenomic analysis further elucidated thatCTC significantly increased functional genes related to bacterial secretion system and metabolism of organic matter for methane production (e.g., pyruvate metabolism and methane metabolism). This study shed light on the substantial impact of CTC on the AD of WAS and provided a promising strategy for improvements in anaerobic fermentation.}, } @article {pmid40154110, year = {2025}, author = {Alameer, RM and Tayeb, H and Magrashi, A and Alqasabi, A and Nazmi, A and Yamani, A and Almaghrabi, RS}, title = {Diagnosis of donor-derived Malassezia restricta &Aspergillus species invasive fungal infection in renal transplant recipient using next generation sequencing - A report of 2 cases and literature review.}, journal = {Journal of infection and public health}, volume = {18}, number = {5}, pages = {102742}, doi = {10.1016/j.jiph.2025.102742}, pmid = {40154110}, issn = {1876-035X}, abstract = {Diagnosing donor-derived fungal infection in solid organ transplant recipients can be particularly challenging and is associated with high mortality. Here, we report two cases of Malassezia restricta and Aspergillus spp donor-derived fungal infection in renal transplant recipients leading to graft loss. Fortunately, both patients achieved full recovery with the administration of antifungal therapy.}, } @article {pmid40154057, year = {2025}, author = {Chen, H and Zhong, S and Liu, Z and Hu, Z and Wang, C and Zhou, Y and Xu, N and Zhao, F and Li, D and Hu, Y}, title = {Microbiome-metabolomic insights into the systemic regulation in Fangxian Huangjiu fermentation.}, journal = {Food chemistry}, volume = {481}, number = {}, pages = {143980}, doi = {10.1016/j.foodchem.2025.143980}, pmid = {40154057}, issn = {1873-7072}, abstract = {Metabolic forces drive microecological succession in Huangjiu fermentation. This study investigates the dynamic metabolic-microbial interplay during Fangxian Huangjiu fermentation. Temporal changes of metabolome and microbiome revealed a syntropic relationship that purified the microbial community with convergent metabolic patterns. With species turnover driving microbial community structure, early-stage microbiomes exhibited great functional diversity. Functions related to energy and molecular building blocks were enriched at the end of early stage, and contributed greatly to microbial adaptation, highlighting the importance of metabolic forces in shaping community structure. Proteobacteria were identified as key facilitators of diverse metabolic activities, and Enterobacter emerged as a fundamental microbial community particularly for materials transformation. Correlation analysis enriched amino acid metabolism pathways. Further, Pantoea ananatis and Wickerhamomyces anomalus were isolated to enhance sphingosine-1-phosphate, γ-aminobutyric acid, and creatine levels without altering physicochemical properties. The study offers insights into the regulation of Huangjiu fermentation, and suggested potential micobiome manipulation to optimize characteristics.}, } @article {pmid40154039, year = {2025}, author = {Li, J and Huang, Z and Zhang, R}, title = {Unmasking Prototheca wickerhamii: A rare case of cutaneous infection and its implications for clinical practice.}, journal = {The Brazilian journal of infectious diseases : an official publication of the Brazilian Society of Infectious Diseases}, volume = {29}, number = {3}, pages = {104525}, doi = {10.1016/j.bjid.2025.104525}, pmid = {40154039}, issn = {1678-4391}, abstract = {Prototheca, an opportunistic pathogenic algae widely found in nature, has emerged as a potential public health concern. Most cases occur in immunocompromised individuals, with infections in immunocompetent patients being relatively rare. Due to their non-specific clinical presentation and limited awareness among clinicians, Prototheca infections are often misdiagnosed, resulting in delayed treatment. Recent advances in species identification and antifungal susceptibility testing have provided important tools for diagnosis and therapy. Here, we report a case of recurrent facial infection in a 76-year-old immunocompetent man. Skin biopsy revealed an infectious granuloma, and fungal culture identified yeast-like colonies. Fluorescence staining and scanning electron microscopy revealed abundant spores, while metagenomic sequencing confirmed the infection as Prototheca wickerhamii. The patient was successfully treated with long-term itraconazole and dipotassium glycyrrhizinate capsules. This case highlights the importance of early and accurate diagnosis in the management of Prototheca skin infections and reviews the therapeutic strategies used.}, } @article {pmid40153957, year = {2025}, author = {Huang, M and Mu, G and Mai, F and Zhou, Y and Li, X and Yang, Q and Shao, B and Wang, J and Tong, Y}, title = {Methane cycling in typical emerging proglacial lakes on the Tibetan Plateau: Insights into the metabolic mechanisms mediated by microorganisms.}, journal = {Water research}, volume = {280}, number = {}, pages = {123533}, doi = {10.1016/j.watres.2025.123533}, pmid = {40153957}, issn = {1879-2448}, abstract = {A large number of high-latitude emerging proglacial lakes have formed on the Tibetan Plateau (TP) due to the global warming and deglaciation. These lakes have the potential to emit methane (CH4) because of the exposure of cryopreserved organic carbon, leading to their significance in regional carbon turnover and cycling. However, previous studies have focused more on human-impacted lakes (e.g., eutrophic lakes), resulting in limited research on the mechanisms of CH4 cycling in the proglacial lakes. In this study, we demonstrated that three typical emerging high-latitude proglacial lakes (∼5500 m a.s.l.) on the TP exhibited a diffusive emission flux of 32.39 ± 11.66 μmol/m[2]/d during the summer. The δ[13]C-CH4 values (-50.10 ± 0.56‰) suggested a biogenic origin of CH4 through the acetoclastic pathway in the lakes. Metagenome sequencing further showed that microbes involved in methanogenesis were dominated by Methanosarcina (36.74 ± 0.07 % of total methanogens). Significant CH4 consumption was observed in the proglacial lakes. The microbes involved in the CH4 consumption were dominated by Methylobacter (48.50 ± 0.17 % of total methanotrophs). A Mantel test demonstrated that dissolved iron (Fe) was a key factor controlling the structure of the CH4 cycling microbial communities. Functional gene and co-occurrence network analyses indicated that members of Pseudomonadota, Bacteroidota, and Actinomycetota may be involved in CH4 cycling by providing methanogenic substrates (i.e., acetyl coenzyme A) and consuming CH4 oxidative intermediates (i.e., methanol, formaldehyde, and formic acid). This study emphasized the ecological significance of emerging proglacial lakes in CH4 releases. It broadened the current understanding of cryophilic CH4 cycling microbes and their mechanisms, that enhances our knowledge of the carbon cycle on the TP.}, } @article {pmid40153355, year = {2025}, author = {Klištincová, N and Koreňová, J and Rešková, Z and Čaplová, Z and Burdová, A and Farkas, Z and Polovka, M and Drahovská, H and Pangallo, D and Kuchta, T}, title = {Bacterial consortia of ewes´ whey in the production of bryndza cheese in Slovakia.}, journal = {Letters in applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/lambio/ovaf047}, pmid = {40153355}, issn = {1472-765X}, abstract = {Whey from previous production is often used as a natural starter in the technology of traditional cheeses, including bryndza-cheese in Slovakia. Therefore, studying its bacterial community and isolating new potential natural starters is important for improving the characterisitics of final product. Composition of bacterial consortia of fresh and fermented whey in the production of raw ewes´ milk-based bryndza-cheese from 8 small or medium-sized producers was analysed. Culture-based microbiological analysis and culture-independent analysis based on 16S rRNA gene sequencing by MiSeq and MinION were used. Results showed the dominance of lactococci or streptococci, with 3 - 8 log CFU ml-[1] of Lactobacillus sensu lato in all whey samples. Potential natural starters comprising Lacticaseibacillus paracasei/casei, Lactiplantibacillus plantarum, Lentilactobacillus parabuchneri, Lactobacillus helveticus, Lactobacillus diolivorans, Levilactobacillus brevis, Limosilactobacillus fermentum, Lactobacillus delbrueckii, Lactobacillus gasseri and Lentilactobacillus otakiensis were isolated. Coliforms were also present in all samples, with no consistently lower values in fermented whey samples. Some samples contained pseudomonads and/or acinetobacters. Coagulase positive staphylococci were present at relevant levels in samples from 4 producers. The results revealed that whey is a source of natural starters due to the presence of lactobacilli.}, } @article {pmid40153196, year = {2025}, author = {Erickson, I and Davidson, S and Choi, H and Rho, S and Guignet, M and Peagler, K and Thummel, K and Ericsson, A and Barker-Haliski, M}, title = {Intestinal dysbiosis alters acute seizure burden and antiseizure medicine activity in Theiler's virus model of encephalitis.}, journal = {Epilepsia}, volume = {}, number = {}, pages = {}, doi = {10.1111/epi.18395}, pmid = {40153196}, issn = {1528-1167}, support = {//University of Washington/ ; }, abstract = {OBJECTIVE: Brain infection with Theiler's murine encephalomyelitis virus (TMEV) in C57BL/6J mice produces an etiologically relevant model of acquired seizures. Dietary changes can modify seizure presentation following TMEV brain infection and influence intestinal microbiome diversity and composition. Intestinal dysbiosis may thus similarly affect seizure burden and antiseizure medicine (ASM) activity in this model, independent of pharmacokinetic effects. We thus sought to define the influence of antibiotic (ABX)-induced gut dysbiosis on acute seizure presentation, anticonvulsant activity of carbamazepine (CBZ), and CBZ pharmacokinetics with TMEV infection.

METHODS: Male C57BL/6J mice (4-5 weeks old) received oral ABX or saline (SAL) once daily beginning on arrival through day 7 after TMEV infection (postinfection [p.i.]). Mice were infected with TMEV or phosphate-buffered saline on day 0. Mice received intraperitoneal (20 mg/kg) CBZ or vehicle (VEH) twice daily on days 3-7 p.i. and were assessed for handling-induced seizures 30 min after treatment. Plasma was collected on day 7 p.i. at 15 and 60 min after CBZ administration for bioanalysis.

RESULTS: TMEV infection induced acute seizures, but ABX-induced gut dysbiosis altered seizure presentation. There were 75% SAL-VEH, 35% SAL-CBZ, 35% ABX-VEH, and 72% ABX-CBZ mice with seizures during the 7-day monitoring period. There was a significant pretreatment × ASM interaction (p = .0001), with differences in seizure burden in SAL- versus ABX-pretreated mice (p = .004). CBZ significantly increased latency to seizure presentation, an effect absent in ABX-CBZ mice. Plasma CBZ concentrations did not differ between SAL and ABX pretreatment groups, suggesting that ABX did not influence CBZ pharmacokinetics.

SIGNIFICANCE: ABX-induced gut dysbiosis markedly altered acute disease trajectory with TMEV-induced encephalitis, reflecting a novel contribution of the gut microbiome to seizure presentation. ABX-induced gut dysbiosis also significantly changed acute seizure control by CBZ, but did not influence plasma CBZ concentrations. The gut-brain axis is thus an underrecognized contributor to TMEV infection-induced seizures, ASM activity, and disease burden.}, } @article {pmid40152616, year = {2025}, author = {Yao, J and Zeng, Y and Hong, X and Wang, M and Zhang, Q and Chen, Y and Gou, M and Xia, Z-Y and Tang, Y-Q}, title = {Phages-bacteria interactions underlying the dynamics of polyhydroxyalkanoate-producing mixed microbial cultures via meta-omics study.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0020025}, doi = {10.1128/msystems.00200-25}, pmid = {40152616}, issn = {2379-5077}, abstract = {The dynamics of the structure of polyhydroxyalkanoate-producing mixed microbial cultures (PHA-MMCs) during enrichment and maintenance is an unsolved problem. The effect of phages has been proposed as a cause of dynamic changes in community structure, but evidence is lacking. To address this question, five PHA-MMCs were enriched, and biological samples were sampled temporally to study the interactions between phage and bacterial members by combining metagenomics and metatranscriptomics. A total of 963 metagenome-assembled genomes (MAGs) and 4,294 phage operational taxonomic units (pOTUs) were assembled from bulk metagenomic data. The dynamic changes in the structure of phage and bacterial communities were remarkably consistent. Structural equation modeling analysis showed that phages could infect and lyse dominant species to vacate ecological niches for other species, resulting in a community succession state in which dominant species alternated. Seven key auxiliary metabolic genes (AMGs), phaC, fadJ, acs, ackA, phbB, acdAB, and fadD, potentially contributing to PHA synthesis were identified from phage sequences. Importantly, these AMGs were transcribed, indicating that they were in an active expression state. The meta-analysis provides the first catalog of phages in PHA-MMCs and the AMGs they carry, as well as how they affect the dynamic changes in bacterial communities. This study provides a reference for subsequent studies on understanding and regulating the microbial community structure of open microbial systems.IMPORTANCEThe synthesis of biodegradable plastic PHA from organic waste through mixed microbial cultures (PHA-MMCs), at extremely low cost, has the potential for expanded production. However, the dynamics of dominant species in PHA-MMCs are poorly understood. Our results demonstrate for the first time the impact of phages on the structure of bacterial communities in the PHA-MMCs. There are complex interactions between the PHA producers (e.g., Azomonas, Paracoccus, and Thauera) and phages (e.g., Casadabanvirus and unclassified Hendrixvirinae). Phage communities can regulate the activity and structure of bacterial communities. In addition, the AMGs related to PHA synthesis may hitchhike during phage-host infection cycles, enabling their dissemination across bacterial communities, and phages may act as a critical genetic reservoir for bacterial members, facilitating access to PHA synthesis-related functional traits. This study highlights the impact of phages on bacterial community structure, suggesting that phages have the potential to be used as a tool for better controlling the microbial community structure of PHA-MMCs.}, } @article {pmid40152185, year = {2025}, author = {Allos, H and Hasbun, R}, title = {Aseptic meningitis: a foundation review.}, journal = {Current opinion in infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1097/QCO.0000000000001105}, pmid = {40152185}, issn = {1473-6527}, abstract = {PURPOSE OF REVIEW: This review addresses the multifaceted nature of aseptic meningitis, a condition with diverse infectious and noninfectious etiologies. Despite its common presentation in clinical settings, over half of the cases remain without an identified cause, necessitating a comprehensive examination of diagnostic and management strategies. The increasing availability of advanced molecular diagnostics and the challenge of distinguishing bacterial from nonbacterial cases make this an opportune time to explore its implications for clinical practice.

RECENT FINDINGS: The literature highlights the pivotal role of advanced molecular diagnostics, such as multiplex PCR and metagenomic sequencing, in improving the identification of pathogens in aseptic meningitis. Enteroviruses remain the leading cause, but pathogens like Herpesviridae, arboviruses, and nonviral agents such as fungi and spirochetes also contribute significantly. New diagnostic algorithms and clinical models are emerging to distinguish bacterial from viral meningitis, reducing unnecessary treatments.

SUMMARY: Aseptic meningitis management is evolving with advancements in diagnostic technologies that allow for earlier pathogen identification, improving patient outcomes and minimizing healthcare costs. These findings underscore the importance of timely and accurate diagnostics and tailored therapeutic strategies in both clinical and research settings. Enhanced awareness of noninfectious causes is also crucial for comprehensive care.}, } @article {pmid40152095, year = {2025}, author = {Wu, S and Luo, Y and Wei, F and Li, Y and Fan, J and Chen, Y and Zhang, W and Li, X and Xu, Y and Chen, Z and Xia, C and Hu, M and Li, P and Gu, Q}, title = {Lactic acid bacteria target NF-κB signaling to alleviate gastric inflammation.}, journal = {Food & function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d4fo06308b}, pmid = {40152095}, issn = {2042-650X}, abstract = {Helicobacter pylori (H. pylori) infection and the resulting gastric inflammation are major contributors to gastric cancer development. Probiotics, particularly Lactobacillus, are promising for their anti-inflammatory potential, yet their exact mechanisms in inhibiting H. pylori-induced inflammation are unclear. In our previous study, Lactiplantibacillus plantarum ZJ316 (L. plantarum ZJ316) demonstrated strong anti-inflammatory effects against H. pylori infection in vivo, but its precise mechanisms were not fully understood. Here, we aimed to investigate how L. plantarum ZJ316 inhibits the inflammatory response to H. pylori infection. Our results demonstrated that L. plantarum ZJ316 effectively reduced the expression of pro-inflammatory cytokines in H. pylori-infected AGS cells. Mechanistically, L. plantarum ZJ316 inhibited the NF-κB signaling pathway by preventing the degradation of IκBα, suppressing p65 phosphorylation, and blocking the nuclear translocation of phosphorylated p65. Treatment with the NF-κB inhibitor BAY 11-7082 further decreased tumor necrosis factor-α (TNF-α), interleukin-8 (IL-8), and interleukin-1β (IL-1β) levels, confirming the inhibitory effect of L. plantarum ZJ316 on the NF-κB pathway. In H. pylori-infected mice, oral administration of L. plantarum ZJ316 significantly alleviated inflammatory cell infiltration, reduced TNF-α and pepsinogen II (PGII) levels, and increased interleukin-10 (IL-10) levels in serum. A comparative metagenomic analysis of the gastric microbiota revealed a decrease in Prevotella and Desulfovibrio, alongside an increase in Ligilactobacillus and Akkermansia, supporting the protective effects of L. plantarum ZJ316 and correlating with their decreased inflammatory response. In summary, administration of L. plantarum ZJ316 demonstrated robust anti-inflammatory effects against H. pylori infection by suppressing NF-κB signaling and promoting favorable changes in the gastric microbiota composition. Therefore, L. plantarum ZJ316 holds promise as a novel functional food for protecting the body against H. pylori infection.}, } @article {pmid40151642, year = {2025}, author = {Cai, X and Cho, JY and Chen, L and Liu, Y and Ji, F and Salgado, K and Ge, S and Yang, D and Yu, H and Shao, J and Futreal, PA and Sepesi, B and Gibbons, D and Chen, Y and Wang, G and Cheng, C and Wu, M and Zhang, J and Hsiao, A and Xia, T}, title = {Enriched pathways in gut microbiome predict response to immune checkpoint inhibitor treatment across demographic regions and various cancer types.}, journal = {iScience}, volume = {28}, number = {4}, pages = {112162}, pmid = {40151642}, issn = {2589-0042}, abstract = {Understanding the effect of gut microbiota function on immune checkpoint inhibitor (ICI) responses is urgently needed. Here, we integrated 821 fecal metagenomes from 12 datasets to identify differentially abundant genes and construct random forest models to predict ICI response. Gene markers demonstrated excellent predictive performance, with an average area under the curve (AUC) of 0.810. Pathway analyses revealed that quorum sensing (QS), ABC transporters, flagellar assembly, and amino acid biosynthesis pathways were enriched between responders (R) and non-responders (NRs) across 12 datasets. Furthermore, luxS, manA, fliC, and trpB exhibited consistent changes between R and NR across 12 datasets. Follow-up microbiota transplant experiments showed that inter-species signaling by different QS autoinducer-2 (AI-2) molecules (synthesized by luxS) can act on overall community function to promote the colonization of Akkermansia muciniphila, which is associated with superior ICI responses. Together, our data highlight the role of gut microbiota function in modulating the microbiome and antitumor immunity.}, } @article {pmid40151403, year = {2025}, author = {Otsuki, A and Inoue, R and Imai, T and Miura, H and Nishida, A and Inatomi, O and Andoh, A}, title = {Characterization of the gut phageome of Japanese patients with ulcerative colitis under endoscopic remission.}, journal = {Journal of clinical biochemistry and nutrition}, volume = {76}, number = {2}, pages = {202-209}, pmid = {40151403}, issn = {0912-0009}, abstract = {This study aimed to analyze the gut phageome in Japanese patients with ulcerative colitis (UC) in endoscopic remission. Fecal samples were collected from 35 UC patients and 22 healthy controls. The gut microbiome was analyzed using 16S rRNA amplicon sequencing, and the phageome was profiled through shotgun metagenomic sequencing. Compared to healthy controls, UC patients showed a significant reduction in phageome richness (observed species and Chao1 index). Principal coordinate analysis revealed a significant difference in beta-diversity between UC and healthy controls (p = 0.001). The abundance of temperate phages was higher in UC (15.2%) compared to healthy controls (5.9%), although this was not statistically significant (p = 0.088). Temperate phages associated with Coprococcus sp., Bacteroides sp. KFT8, and Faecalibacterium prausnitzii, as well as virulent phages associated with Ruminococcus gnavus and Lactobacillus farciminis, were increased in UC patients. Conversely, phages associated with Thermosipho affectus, Bacteroides sp. OF03-11BH, and Odoribacter splanchnicus were decreased in UC patients. Phages associated with the genera Odoribacter (p = 0.0004), Ruminococcus (p = 0.009), and Veillonella (p = 0.013) were significantly reduced in UC patients. The gut phageome of inactive UC patients exhibited notable alterations in viral composition compared to healthy controls. These results suggest that changes in the gut phageome might be involved in the pathogenesis of UC.}, } @article {pmid40151093, year = {2025}, author = {Liu, D and Zhang, W and Zhu, L and Gong, J and Huang, Y and Li, Z and He, J}, title = {Autoinducer-2 Quorum Sensing Is an Active Universal Signaling System in Sociomicrobiology.}, journal = {Journal of basic microbiology}, volume = {}, number = {}, pages = {e024}, doi = {10.1002/jobm.70024}, pmid = {40151093}, issn = {1521-4028}, support = {//This study was supported by National Natural Science Foundation of China (grants 32371495 and 32171424), Hubei Province Technology Innovation Plan Project (2024BCB028), and Wuhan Science and Technology Major Project (grant 2023020302020708)./ ; }, abstract = {Autoinducer-2 (AI-2) is a bacterial quorum sensing (QS) signaling molecule that regulates inter-specific and intraspecific bacterial communication in complex ecological environments. Here, we systematically analyzed the distribution of AI-2 QS-related proteins (synthases and receptors) in the domain bacteria, explored the evolution and development of AI-2 receptors, and analyzed the AI-2 regulatory networks using human intestinal metagenomic data. The results show that AI-2 QS-related proteins are distributed in 17 bacterial phyla, accounting for approximately 36.80% of the total genomes. Based on the ability of bacteria to synthesize and receive AI-2 signals, we divided bacteria into four major categories, namely Prosumer, Producer, Monitor, and Immunizer. The Gram-positive bacteria are mainly responsible for producing the AI-2 signals, while Gram-negative bacteria are more likely to respond to AI-2. Evolutionary analysis shows that the AI-2 receptor CahR is mainly derived from the methyl-accepting chemotaxis protein (MCP). Based on the length difference of the ligand-binding domains, we further speculate that AI-2 binding activates CahR through either allostery or aggregation mode. Using human intestinal metagenomic data, we found a strong correlation between AI-2 signaling and c-di-GMP signaling. These findings will have an important impact on the AI-2 QS research and accelerate its development.}, } @article {pmid40150979, year = {2025}, author = {Yildirim, EA and Laptev, GY and Ilina, LA and Ponomareva, ES and Brazhnik, EA and Smetannikova, TS and Novikova, NI and Turina, DG and Filippova, VA and Dubrovin, AV and Dubrovina, AS and Kalitkina, KA and Klyuchnikova, IA and Zaikin, VA and Griffin, DK and Romanov, MN}, title = {Metagenomic Composition and Predicted Metabolic Pathway Analyses of the Endometrial and Rectal Microbiota in Dairy Cows Following the Introduction of a Complex Feed Additive.}, journal = {Frontiers in bioscience (Elite edition)}, volume = {17}, number = {1}, pages = {25725}, doi = {10.31083/FBE25725}, pmid = {40150979}, issn = {1945-0508}, support = {24-16-00131//Russian Science Foundation/ ; }, mesh = {Animals ; Cattle/microbiology ; Female ; *Animal Feed ; *Rectum/microbiology ; *Endometrium/microbiology/metabolism ; *Microbiota ; Metabolic Networks and Pathways ; Metagenomics ; Dairying ; }, abstract = {BACKGROUND: The microbiome composition in dairy cows (Bos taurus) directly impacts on health and reproductive performance. This study aimed to determine the metagenomic composition and predicted microbial community functions in the endometrium and rectal chyme of cows fed a complex feed additive (CFA). The latter included the Bacillus mucilaginosus 159 strain, a short-chain fatty acid, plus essential oils.

METHODS: Clinically healthy cows were divided into two groups (n = 15 in each): (I) a control group fed the standard diet, and (II) an experimental group. CFA was introduced into the diet of Group II during the entire transit period at a dose of 50 g per animal per day; moreover, all animals received Pen-Strep 400 antibiotics to prevent endometritis and other pathologies. The microbial community composition from the endometrium and rectal chyme biotopes was assessed using targeted next-generation sequencing.

RESULTS: Significant changes were observed in the composition and predicted metabolic pathways due to the CFA administration, with the endometrial microbiota being more responsive to CFA than the intestinal chyme microbiome. Remarkably, the Actinobacteriota representatives disappeared in the endometrium of Group II animals compared to controls, whose content ranged from 0.34 to 3.3%. The use of CFA also resulted in a less pronounced effect in four predicted metabolic pathways for microbial degradation of catechol in the endometrium compared to controls (p < 0.05).

CONCLUSIONS: Our findings support the concept of a relationship between the gut microbiome and the reproductive system microflora of cows, as we observed changes in the composition and predicted metabolic pathways of the endometrial microbiota after orally administering CFA. This emphasizes the need for an integrated approach combining the correction of microecological disorders in the intestines and the reproductive system simultaneously.}, } @article {pmid40150359, year = {2025}, author = {Liu, Y and Dong, X and Sun, L and Cui, H and Kang, J and Bu, N and Zhang, Y and Qi, Z and Li, Z and Zhang, Z and Zhao, L}, title = {Analysis of the Microbial Community Structure of Ixodes persulcatus at Each Developmental Stage.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/ani15060830}, pmid = {40150359}, issn = {2076-2615}, support = {32260887//National Natural Science Foundation of China/ ; }, abstract = {Ticks are the second most significant vector of pathogens worldwide. Ixodes persulcatus is one of the dominant tick species in Inner Mongolia that can carry and transmit various pathogenic microorganisms. However, only one specific pathogen has been detected in a particular developmental stage of I. persulcatus, moreover metagenomic analysis has been conducted only in the adult tick stage. In this study, we used I. persulcatus at different developmental stages (first-generation female adult ticks, eggs, larval ticks, engorged larval ticks, nymphal ticks, engorged nymphal ticks, and second-generation adult ticks) from Inner Mongolia as materials for nucleic acid extraction. Subsequently, we constructed Illumina PE250 and Illumina PE150 libraries and sequenced them on the Illumina NovaSeq 6000 platform. Finally, we used molecular biology software and sequence analysis platform to analyze microbial community structures. Illumina PE250 sequencing revealed that the seven developmental stages of I. persulcatus were annotated to 21 phyla, 43 classes, 104 orders, 188 families, 391 genera, and 556 species of bacteria. Among them, 4 phyla and 14 genera were present at all developmental stages, with Proteobacteria being the dominant phylum and Rickettsia spp. being the dominant genus. In addition, Rickettsia had the highest relative abundance in the seven developmental stages. All developmental stages were annotated to a certain abundance of Brucella spp. Illumina PE150 sequencing revealed that the three samples (X-I-YDCP: first-generation adult ticks; X-I-MIX: mixed samples of eggs, larval ticks, and nymphal ticks; X-I-EDCP: second-generation adult ticks) of I. persulcatus were annotated to six orders, 28 families, 72 genera, and 158 species of viruses, of which 46 genera and 80 species were found in all three sample species. To the best of our knowledge, this is the first study that comprehensively analyzed the microbial community composition of I. persulcatus at different developmental stages. Based on the study outcomes, certain abundance of Rickettsia japonica, bovine viral diarrhea virus, and African swine fever virus were annotated to I. persulcatus.}, } @article {pmid40149936, year = {2025}, author = {Zhan, J and Cheng, J and Chang, W and Su, Y and Yue, X and Wu, C}, title = {Absolute Quantitative Metagenomic Analysis Provides More Accurate Insights for the Anti-Colitis Effect of Berberine via Modulation of Gut Microbiota.}, journal = {Biomolecules}, volume = {15}, number = {3}, pages = {}, doi = {10.3390/biom15030400}, pmid = {40149936}, issn = {2218-273X}, mesh = {*Berberine/pharmacology ; *Gastrointestinal Microbiome/drug effects/genetics ; Animals ; *Metagenomics/methods ; Colitis, Ulcerative/microbiology/drug therapy ; Mice ; Bacteria/drug effects/genetics/classification ; Male ; Butyric Acid/pharmacology ; Disease Models, Animal ; }, abstract = {Current gut microbiota studies often rely on relative quantitative sequencing. However, under certain circumstances, while the relative quantitative abundance of these bacteria may remain stable, the absolute quantities of specific bacteria can vary considerably. Since the function of bacteria is directly linked to their total numbers, absolute quantification is crucial. This study aims to identify the optimal method for microbiome analysis by comparing relative and absolute quantitative sequencing. Using ulcerative colitis, which is closely associated with gut microbiota, as a disease model and berberine (which affects microbiota) versus sodium butyrate (which does not) as drugs, relative and absolute quantitative methods were used to evaluate the varying effects of the different drugs on the regulation of gut microbiota in UC-affected animals. The regulatory effects of BBR on gut microbiota were further synthesized as identified in earlier studies using an individual-based meta-analysis, and we compared these findings with our absolute sequencing results. The results from absolute sequencing were more consistent with the actual microbial community, suggesting that relative abundance measurements might not accurately reflect the true abundance of microbial species. Moreover, meta-analysis results were only partially consistent with absolute quantitative sequencing and sometimes directly opposed, suggesting that relative quantitative sequencing analyses are prone to misinterpretation and incorrect correlation of results. This study underscores the importance of absolute quantitative analysis in accurately representing the true microbial counts in a sample and evaluating the modulatory effects of drugs on the microbiome, which plays a vital role in the study of the microbiome.}, } @article {pmid40149684, year = {2025}, author = {Zhao, X and Xu, J and Wu, D and Chen, N and Liu, Y}, title = {Gut Microbiota in Different Treatment Response Types of Crohn's Disease Patients Treated with Biologics over a Long Disease Course.}, journal = {Biomedicines}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/biomedicines13030708}, pmid = {40149684}, issn = {2227-9059}, support = {(No. RDJP2022-15 to X.Z., No. RDJP2023-22 to J.X.)//Scientific Research Development Funds of Peking University 401 People's Hospital/ ; No. CFH2024-4-4089 to J.X.//the Capital Health Research and Development of Special/ ; (82370555 to J.X., 400 No. 82370537, 82341228 to Y.L.)//the National Natural Science Foundation of China/ ; (No. XZ2024ZR-ZY012(Z) to X.Z.//the Xizang Autono- 402 mous Region Natural Science Foundation Group Medical Aid Project/ ; }, abstract = {Background and Aims: Crohn's disease (CD) is a chronic inflammatory bowel disease (IBD) with a globally increasing prevalence, partially driven by alterations in gut microbiota. Although biological therapy is the first-line treatment for CD, a significant proportion of patients experience a primary non-response or secondary loss of response over time. This study aimed to explore the differences in gut microbiota among CD patients with divergent long-term responses to biological therapy, focusing on a long disease course. Methods: Sixteen CD patients who applied the biological agents for a while were enrolled in this study and were followed for one year, during which fecal specimens were collected monthly. Metagenomic analysis was used to determine the microbiota profiles in fecal samples. The response to biological therapy was evaluated both endoscopically and clinically. Patients were categorized into three groups based on their response: R (long-term remission), mA (mild active), and R2A group (remission to active). The differences in the gut microbiota among the groups were analyzed. Results: Significant differences in fecal bacterial composition were observed between the groups. The R2A group exhibited a notable decline in gut microbial diversity compared to the other two groups (p < 0.05). Patients in the R group had higher abundances of Akkermansia muciniphila, Bifidobacterium adolescentis, and Megasphaera elsdenii. In contrast, Veillonella parvula, Veillonella atypica, and Klebsiella pneumoniae were higher in the R2A group. Conclusions: Gut microbial diversity and specific bacterial significantly differed among groups, reflecting distinct characteristics between responders and non-responders.}, } @article {pmid40149628, year = {2025}, author = {Kaczka, A and Błońska, A and Chojnacki, C and Gąsiorowska, A and Błasiak, J and Popławski, T and Chojnacki, J}, title = {Periodic Changes in the Gut Microbiome in Women with the Mixed Type of Irritable Bowel Syndrome.}, journal = {Biomedicines}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/biomedicines13030652}, pmid = {40149628}, issn = {2227-9059}, abstract = {Background: The mixed type of irritable bowel syndrome (IBS-M) is characterized by recurrent constipation and diarrhea. The cause of the variability of these symptoms is not sufficiently understood. The aim of this study was to perform metagenomic and metabolic assessment of the gut microbiome in constipation and diarrheal period of IBS-M. Methods: This study included 30 women, aged 28-47 years old, with the symptoms which aligned with those of IBS-M, according to the Rome IV Criteria. Results: In both periods of the disease, the dysbiosis index (DI), the Shannon diversity index (SDI), the hydrogen-methane and ammonia breath tests, as well as the selected bacterial metabolites (-p-hydroxyphenyl acetic acid (HPA), 3-indoxyl sulfate (Indican, 3-IS)), and hippuric acid (A) in urine, were determined. The dysbiosis index (DI) in the period of constipation was 3.73 ± 0.90 points, and in the diarrheal period it did not change significantly 3.93 ± 0.75 points (p > 0.05). During the diarrheal period, the diversity of bacteria increases from 2.16 ± 0.59 to 2.74 ± 0.50 points on the Shannon dietary index (p < 0.001). The gut microbiome profile also changed, especially during the diarrheal period where an abundance of Bifidobacterium spp. and Lactobacillus spp. decreased significantly. In addition, during this period, the levels of hydrogen and ammonia in breath air increased, while the methane level decreased. The differences also concern the results of urinary metabolites, especially related to hippuric acid and indican. During the diarrheal period, the levels of hydrogen and ammonia ions increased, while the methane level decreased. The differences also concern the results of urinary metabolites, especially related to hippuric acid and indican. Conclusions: In patients with IBS-M, periodic changes in the profile and metabolism of the gut microbiome occur, which coexist with recurrent symptoms such as constipation and diarrhea.}, } @article {pmid40149502, year = {2025}, author = {Hailu, G and Legesse, M and Mulu, A and Medhin, G and Tsegaye, MM and Alemayehu, DH and Ayele, A and Gebreegziabxier, A and Tayachew, A and Aguine, A and Dejene, H and Tessema, SK and Onywera, H and Stanislas, AE and Abate, E and Marcello, A and Bitew, M}, title = {SARS-CoV-2 Genetic Variants Identified in Selected Regions of Ethiopia Through Whole Genome Sequencing: Insights from the Fifth Wave of COVID-19.}, journal = {Genes}, volume = {16}, number = {3}, pages = {}, doi = {10.3390/genes16030351}, pmid = {40149502}, issn = {2073-4425}, mesh = {Humans ; Ethiopia/epidemiology ; *COVID-19/virology/epidemiology/transmission ; *SARS-CoV-2/genetics/pathogenicity ; Male ; Female ; Adult ; *Whole Genome Sequencing/methods ; *Genome, Viral ; Middle Aged ; Phylogeny ; Genetic Variation ; Young Adult ; Adolescent ; }, abstract = {BACKGROUND: The COVID-19 pandemic highlighted SARS-CoV-2 variants with increased transmissibility and immune evasion. In Ethiopia, where cases surged, the understanding of the virus's dynamics was limited. This study analyzed SARS-CoV-2 variants during the fifth wave, crucial for guiding vaccines, therapeutics, diagnostics, and understanding disease severity.

METHOD: From June to August 2022, 150 SARS-CoV-2-positive samples were randomly selected from the Ethiopian Public Health Institute repository. Sixty-three high-quality genome sequences were analyzed.

RESULTS: Of the 63 sequences, 70% were from males and 30% from females, with a median age of 34. Omicron dominated (97%, 61/63), primarily clade 22A (64%, 40/63), followed by 22B (18%, 11/63) and 21K (14%, 9/63). Delta accounted for 3.2% (2/63). Omicron was identified in all (25) vaccinated study participants. Ethiopian sequences showed limited evolutionary divergence and lower genetic diversity compared to global sequences.

CONCLUSION: Omicron was the predominant variant during Ethiopia's fifth wave, indicating recent community transmission. Despite minor genetic diversity differences, ongoing surveillance remains critical for tracking variants and informing public health interventions.}, } @article {pmid40149437, year = {2025}, author = {Alharbi, SM and Al-Sulami, N and Al-Amrah, H and Anwar, Y and Gadah, OA and Bahamdain, LA and Al-Matary, M and Alamri, AM and Bahieldin, A}, title = {Metagenomic Characterization of the Maerua crassifolia Soil Rhizosphere: Uncovering Microbial Networks for Nutrient Acquisition and Plant Resilience in Arid Ecosystems.}, journal = {Genes}, volume = {16}, number = {3}, pages = {}, doi = {10.3390/genes16030285}, pmid = {40149437}, issn = {2073-4425}, mesh = {*Rhizosphere ; *Soil Microbiology ; Mycorrhizae/genetics/classification ; Bacteria/genetics/classification/metabolism/isolation & purification ; Metagenomics/methods ; Metagenome ; Ecosystem ; Microbiota/genetics ; Plant Roots/microbiology ; Fungi/genetics/classification ; }, abstract = {Background/Objectives:Maerua crassifolia, a threatened medicinal species endemic to drylands, exhibits a pronounced drought sensitivity. Despite the critical role of microorganisms, particularly bacteria and fungi, the microbial consortia in M. crassifolia's rhizosphere remain underexplored. Methods: Metagenomic whole genome shotgun sequencing (WGS) was employed to elucidate the taxonomic composition of bacterial and fungal communities inhabiting the soil rhizosphere of M. crassifolia. Results: The data revealed a marked predominance of bacterial genomes relative to fungal communities, as evidenced by non-redundant gene analysis. Notably, arbuscular mycorrhizal fungi (AMF), specifically Rhizophagus clarus, Rhizophagus irregularis and Funneliformis geosporum, are key rhizosphere colonizers. This study confirmed the presence of phosphate-solubilizing bacteria (PSB), such as Sphingomonas spp., Cyanobacteria and Pseudomonadota, underscoring the critical role of these microorganisms in the phosphorus cycle. Additionally, the study uncovered the presence of previously uncharacterized species within the phylum Actinobacteria, as well as unidentified taxa from the Betaproteobacteria, Gemmatimonadota and Chloroflexota phyla, which may represent novel microbial taxa with potential plant growth-promoting properties. Conclusions: Findings suggest a complex, symbiotic network where AMF facilitate phosphorus uptake through plant-root interactions. In a tripartite symbiosis, PSB enhance inorganic phosphorus solubilization, increasing bioavailability, which AMF assimilate and deliver to plant roots, optimizing nutrition. This bacterial-fungal interplay is essential for plant resilience in arid environments. Future investigations should prioritize the isolation and characterization of underexplored microbial taxa residing in the rhizosphere of M. crassifolia, with particular emphasis on members of the Actinobacteria, Betaproteobacteria, Gemmatimonadota and Chloroflexota phyla to uncover their roles in nutrient acquisition and sustainability.}, } @article {pmid40149106, year = {2025}, author = {Olsen, NS and Riber, L}, title = {Metagenomics as a Transformative Tool for Antibiotic Resistance Surveillance: Highlighting the Impact of Mobile Genetic Elements with a Focus on the Complex Role of Phages.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/antibiotics14030296}, pmid = {40149106}, issn = {2079-6382}, support = {NNF23OC0086264//Novo Nordisk Foundation/ ; }, abstract = {Extensive use of antibiotics in human healthcare as well as in agricultural and environmental settings has led to the emergence and spread of antibiotic-resistant bacteria, rendering many infections increasingly difficult to treat. Coupled with the limited development of new antibiotics, the rise of antimicrobial resistance (AMR) has caused a major health crisis worldwide, which calls for immediate action. Strengthening AMR surveillance systems is, therefore, crucial to global and national efforts in combating this escalating threat. This review explores the potential of metagenomics, a sequenced-based approach to analyze entire microbial communities without the need for cultivation, as a transformative and rapid tool for improving AMR surveillance strategies as compared to traditional cultivation-based methods. We emphasize the importance of monitoring mobile genetic elements (MGEs), such as integrons, transposons, plasmids, and bacteriophages (phages), in relation to their critical role in facilitating the dissemination of genetic resistance determinants via horizontal gene transfer (HGT) across diverse environments and clinical settings. In this context, the strengths and limitations of current bioinformatic tools designed to detect AMR-associated MGEs in metagenomic datasets, including the emerging potential of predictive machine learning models, are evaluated. Moreover, the controversial role of phages in AMR transmission is discussed alongside the potential of phage therapy as a promising alternative to conventional antibiotic treatment.}, } @article {pmid40148934, year = {2025}, author = {de Campos, GM and Clemente, LG and Lima, ARJ and Cella, E and Fonseca, V and Ximenez, JPB and Nishiyama, MY and de Carvalho, E and Sampaio, SC and Giovanetti, M and Elias, MC and Slavov, SN}, title = {Anellovirus abundance as an indicator for viral metagenomic classifier utility in plasma samples.}, journal = {Virology journal}, volume = {22}, number = {1}, pages = {88}, pmid = {40148934}, issn = {1743-422X}, support = {2022/00910-6//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2021/11944-6//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2021/11944-6//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2021/11944-6//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2017/23205-8//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 403075/2023-8//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, mesh = {*Metagenomics/methods ; Humans ; *Anelloviridae/genetics/classification/isolation & purification ; *Torque teno virus/genetics/classification/isolation & purification ; High-Throughput Nucleotide Sequencing/methods ; DNA Virus Infections/virology/blood ; Plasma/virology ; Algorithms ; Metagenome ; Genome, Viral/genetics ; }, abstract = {BACKGROUND: Viral metagenomics has expanded significantly in recent years due to advancements in next-generation sequencing, establishing it as the leading method for identifying emerging viruses. A crucial step in metagenomics is taxonomic classification, where sequence data is assigned to specific taxa, thereby enabling the characterization of species composition within a sample. Various taxonomic classifiers have been developed in recent years, each employing distinct classification approaches that produce varying results and abundance profiles, even when analyzing the same sample.

METHODS: In this study, we propose using the identification of Torque Teno Viruses (TTVs), from the Anelloviridae family, as indicators to evaluate the performance of four short-read-based metagenomic classifiers: Kraken2, Kaiju, CLARK and DIAMOND, when evaluating human plasma samples.

RESULTS: Our results show that each classifier assigns TTV species at different abundance levels, potentially influencing the interpretation of diversity within samples. Specifically, nucleotide-based classifiers tend to detect a broader range of TTV species, indicating higher sensitivity, while amino acid-based classifiers like DIAMOND and CLARK display lower abundance indices. Interestingly, despite employing different algorithms and data types (protein-based vs. nucleotide-based), Kaiju and Kraken2 performed similarly.

CONCLUSION: Our study underscores the critical impact of classifier selection on diversity indices in metagenomic analyses. Kaiju effectively assigned a wide variety of TTV species, demonstrating it did not require a high volume of reads to capture diversity. Nucleotide-based classifiers like CLARK and Kraken2 showed superior sensitivity, which is valuable for detecting emerging or rare viruses. At the same time, protein-based approaches such as DIAMOND and Kaiju proved robust for identifying known species with low variability.}, } @article {pmid40148927, year = {2025}, author = {Feng, Z and Lorenc, N and O'Brien, B and Sun, G and Li, Z and Jung, D and Ronholm, J}, title = {Deep culturing the fecal microbiota of healthy laying hens.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {32}, pmid = {40148927}, issn = {2524-4671}, abstract = {BACKGROUND: The microbiota is implicated in several aspects of livestock health and disease. Understanding the structure and function of the poultry microbiota would be a valuable tool for improving their health and productivity since the microbiota can likely be optimized for metrics that are important to the industry such as improved feed conversion ratio, lower greenhouse gas emissions, and higher levels of competitive exclusion against pathogens. Most research into understanding the poultry microbiota has relied on culture-independent methods; however, the pure culture of bacteria is essential to elucidating the roles of individual bacteria in the microbiota and developing novel probiotic products for poultry production.

RESULTS: In this study, we have used a deep culturing approach consisting of 76 culture conditions to generate a culture collection of 1,240 bacterial isolates from healthy chickens. We then compared the taxonomy of cultured isolates to the taxonomic results of metagenomic sequencing to estimate what proportion of the microbiota was cultured. Metagenomic sequencing detected DNA from 545 bacterial species while deep culturing was able to produce isolates for 128 bacterial species. Some bacterial families, such as Comamonadaceae and Neisseriaceae were only detected via culturing - indicating that metagenomic analysis may not provide a complete taxonomic census of the microbiota. To further examine sub-species diversity in the poultry bacteriome, we whole genome sequenced 114 Escherichia coli isolates from 6 fecal samples and observed a great deal of diversity.

CONCLUSIONS: Deep culturing and metagenomic sequencing approaches to examine the diversity of the microbiota within an individual will yield different results. In this project we generated a culture collection of enteric bacteria from healthy laying hens that can be used to further understand the role of specific commensals within the broader microbiota context and have made this collection available to the community. Isolates from this collection can be requested by contacting the corresponding author and will be provided at cost.}, } @article {pmid40148567, year = {2025}, author = {Austin, GI and Brown Kav, A and ElNaggar, S and Park, H and Biermann, J and Uhlemann, AC and Pe'er, I and Korem, T}, title = {Processing-bias correction with DEBIAS-M improves cross-study generalization of microbiome-based prediction models.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {40148567}, issn = {2058-5276}, support = {R01HD106017//U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; R01HD114715//U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; T15LM007079//U.S. Department of Health & Human Services | NIH | U.S. National Library of Medicine (NLM)/ ; U54DK104309//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; }, abstract = {Every step in common microbiome profiling protocols has variable efficiency for each microbe, for example, different DNA extraction efficiency for Gram-positive bacteria. These processing biases impede the identification of signals that are biologically interpretable and generalizable across studies. 'Batch-correction' methods have been used to address these issues computationally with some success, but they are largely non-interpretable and often require the use of an outcome variable in a manner that risks overfitting. We present DEBIAS-M (domain adaptation with phenotype estimation and batch integration across studies of the microbiome), an interpretable framework for inference and correction of processing bias, which facilitates domain adaptation in microbiome studies. DEBIAS-M learns bias-correction factors for each microbe in each batch that simultaneously minimize batch effects and maximize cross-study associations with phenotypes. Using diverse benchmarks including 16S rRNA and metagenomic sequencing, classification and regression, and a variety of clinical and molecular targets, we demonstrate that using DEBIAS-M improves cross-study prediction accuracy compared with commonly used batch-correction methods. Notably, we show that the inferred bias-correction factors are stable, interpretable and strongly associated with specific experimental protocols. Overall, we show that DEBIAS-M facilitates improved modelling of microbiome data and identification of interpretable signals that generalize across studies.}, } @article {pmid40147547, year = {2025}, author = {Liu, H and Sun, R and Wu, Y and Feng, J and Fan, G and Chen, S and Li, L}, title = {Molecular detection and identification of goose astrovirus in GuangDong Province, China.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {}, number = {}, pages = {105745}, doi = {10.1016/j.meegid.2025.105745}, pmid = {40147547}, issn = {1567-7257}, abstract = {In recent years, Goose Astrovirus (GAstV) has become a major pathogen in China, afflicting geese with significant clinical manifestations like gout and urate deposits in organs. Notably, similar symptoms have emerged in ducks. From 2023 to 2024, 126 liver samples were collected from ducks in Guangdong Province, where farms reported emaciation, paralysis, and deaths. Metagenomic analysis pinpointed GAstV as the primary pathogen, with a 43.65 % confirmed positive rate via qPCR. A new strain, GD2406, was identified, showing 97.5 %-98.8 % similarity to 30 GAstV-2 strains in GenBank. GD2406 displayed 98.3 % and 97.7 % identity with the duck strains HNNY0620 and SDTA, and 98.3 % and 98.4 % identity with highly virulent GAstV strains HNKF-1 and HNSQ-6. Phylogenetic analysis indicated a genetic closeness between GD2406 and the goose strain HB01. There were 13 amino acid mutations, mainly within ORF2, and a single mutation differing from HNKF-1 and HNSQ-6, hinting at significant pathogenic potential for both ducks and geese. This study is the first to report GAstV causing severe symptoms and mortality in Muscovy ducks in Guangdong Province, suggesting ducks could be key hosts and underscoring the risk of cross-species transmission.}, } @article {pmid40147421, year = {2025}, author = {Goswami, P and Ji, R and Shen, J and Roberts, AP and Lin, W}, title = {Genomic and metabolic characterisation of a novel species Magnetominusculus dajiuhuensis DJH-1[Ts] sp. nov. from an acidic peatland.}, journal = {Systematic and applied microbiology}, volume = {48}, number = {3}, pages = {126605}, doi = {10.1016/j.syapm.2025.126605}, pmid = {40147421}, issn = {1618-0984}, abstract = {Magnetotactic bacteria (MTB) are recognised widely for their ability to synthesise intracellular magnetite (Fe3O4) and/or greigite (Fe3S4) nanocrystals and align with Earth's magnetic field. They are crucial for understanding prokaryotic organelle biogenesis. MTB members of the Nitrospirota phylum (previously known as the Nitrospirae phylum) are of interest due to their important ecological roles in the biogeochemical cycling of iron and sulphur. Here, we introduce Magnetominusculus dajiuhuensis DJH-1[Ts], a newly discovered Nitrospirota MTB species that thrives in the acidic Dajiuhu Peatland of central China. By combining electron microscopy, 16S rRNA gene-based analysis and genome-resolved metagenomics, we elucidate its distinctive morphology, genomic features, and metabolic functions. The metagenome-assembled genome, assigned to the genus Magnetominusculus, family Magnetobacteriaceae, order Thermodesulfovibrionales, class Thermodesulfovibrionia according to the GTDB taxonomy, reveals an obligate anaerobe that lives in central China's largest wetland. We propose the formal name Magnetominusculus dajiuhuensis DJH-1[Ts] sp. nov., following the SeqCode system. Genomic and metabolic characterisation of this novel species suggests its potential role in nitrogen, sulphur, and carbon metabolism in aquatic biogeochemistry, particularly in peatlands. The genome of this novel strain indicates that it harnesses the Wood-Ljungdahl pathway for carbon fixation and acetate metabolism in anaerobic conditions, while its potential role in nitrogen cycling is characterised by denitrification and nitrogen fixation. It also participates in reduction of sulphate to sulphide, indicating a role in sulphur cycling in its ecological niche. Taken together, the discovery and characterisation of Magnetominusculus dajiuhuensis DJH-1[Ts] provide new insights into MTB diversity and ecological functions, particularly in peatland biogeochemistry.}, } @article {pmid40147302, year = {2025}, author = {Keneally, C and Chilton, D and Dornan, TN and Kidd, SP and Gaget, V and Toomes, A and Lassaline, C and Petrovski, R and Wood, L and Brookes, JD}, title = {Multi-omics reveal microbial succession and metabolomic adaptations to flood in a hypersaline coastal lagoon.}, journal = {Water research}, volume = {280}, number = {}, pages = {123511}, doi = {10.1016/j.watres.2025.123511}, pmid = {40147302}, issn = {1879-2448}, abstract = {Microorganisms drive essential biogeochemical processes in aquatic ecosystems and are sensitive to both salinity and hydrological changes. As climate change and anthropogenic activities alter hydrology and salinity worldwide, understanding microbial ecology and metabolism becomes increasingly important for managing aquatic ecosystems. Biogeochemical processes were investigated on sediment microbial communities during a significant flood event in the hypersaline Coorong lagoon, South Australia (the largest in the Murray-Darling Basin since 1956). Samples from six sites across a salinity gradient were collected before and during flooding in 2022. To assess changes in microbial taxonomy and metabolic function, 16S rRNA amplicon sequencing was employed alongside untargeted liquid chromatography-mass spectrometry (LC-MS) to assess changes in microbial taxonomy and metabolic function. Results showed a decrease in microbial richness and diversity during flooding, especially in hypersaline conditions. Pre-flood communities were enriched with osmolyte-degrading and methanogenic taxa, alongside osmoprotectant metabolites, such as glycine betaine and choline. Flood conditions favored taxa such as Halanaerobiaceae and Beggiatoaceae, inducing inferred metagenomic shifts indicative of sulfur cycling and nitrogen reduction pathways, while also enriching a greater diversity of metabolites including Gly-Phe dipeptides and guanine. This study demonstrates that integrating metabolomics with microbial community analysis enhances understanding of ecosystem responses to disturbance. These findings suggest microbial communities rapidly change in response to salinity reductions while maintaining key biogeochemical functions. Such insights are valuable for ecosystem management and predictive modelling under environmental stressors such as flooding.}, } @article {pmid40147232, year = {2025}, author = {Wang, J and Ge, Y}, title = {Unveiling the latitudinal dependency of global patterns in soil prokaryotic gene content.}, journal = {The Science of the total environment}, volume = {974}, number = {}, pages = {179224}, doi = {10.1016/j.scitotenv.2025.179224}, pmid = {40147232}, issn = {1879-1026}, abstract = {Prokaryotic genomic traits offer insights into their functional roles, evolutionary processes, and ecological interactions, but global patterns in soil microbial genomes remain poorly understood. In this study, we examined 6436 metagenome-assembled genomes (MAGs) from global soil environments to explore the driving factors of prokaryotic gene content. Through random forest analysis, we found that, among numerous potential influencing factors such as climate, soil physicochemical properties, and human activities, geographic latitude was the primary factor affecting prokaryotic gene content. Our results showed a marked decrease in gene content from the tropics to the poles, with polar MAGs containing 10.4 % and 13.3 % fewer genes than those in tropical and temperate zones, respectively. This decline correlates with shifts in key metabolic processes, such as nitrogen fixation and energy conversion. Furthermore, we assessed interspecies metabolic interactions using Metabolic Resource Overlap (MRO) and Metabolic Interaction Potential (MIP) metrics. Our analysis revealed significantly lower MRO in high-latitude microbial communities, yet comparable MIP values to those in lower latitudes, indicating that reduced competition may contribute to genomic streamlining. These findings highlight the significant influence of latitude and interspecies interactions on microbial genomic characteristics, advancing our comprehension of microbial ecological adaptations.}, } @article {pmid38630846, year = {2024}, author = {Phan, HV and Tsitsiklis, A and Maguire, CP and Haddad, EK and Becker, PM and Kim-Schulze, S and Lee, B and Chen, J and Hoch, A and Pickering, H and van Zalm, P and Altman, MC and Augustine, AD and Calfee, CS and Bosinger, S and Cairns, CB and Eckalbar, W and Guan, L and Jayavelu, ND and Kleinstein, SH and Krammer, F and Maecker, HT and Ozonoff, A and Peters, B and Rouphael, N and , and Montgomery, RR and Reed, E and Schaenman, J and Steen, H and Levy, O and Diray-Arce, J and Langelier, CR}, title = {Host-microbe multiomic profiling reveals age-dependent immune dysregulation associated with COVID-19 immunopathology.}, journal = {Science translational medicine}, volume = {16}, number = {743}, pages = {eadj5154}, pmid = {38630846}, issn = {1946-6242}, support = {U19 AI090023/AI/NIAID NIH HHS/United States ; U19 AI118608/AI/NIAID NIH HHS/United States ; U19 AI057229/AI/NIAID NIH HHS/United States ; S10 OD026880/OD/NIH HHS/United States ; U19 AI077439/AI/NIAID NIH HHS/United States ; U19 AI118610/AI/NIAID NIH HHS/United States ; U19 AI167891/AI/NIAID NIH HHS/United States ; U19 AI167903/AI/NIAID NIH HHS/United States ; U19 AI128913/AI/NIAID NIH HHS/United States ; R01 AI132774/AI/NIAID NIH HHS/United States ; S10 OD030463/OD/NIH HHS/United States ; R01 AI135803/AI/NIAID NIH HHS/United States ; U19 AI089992/AI/NIAID NIH HHS/United States ; R01 HL155418/HL/NHLBI NIH HHS/United States ; U19 AI128910/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Aged ; Adolescent ; Young Adult ; Adult ; Middle Aged ; Aged, 80 and over ; *COVID-19 ; SARS-CoV-2 ; Prospective Studies ; Multiomics ; Chemokines ; }, abstract = {Age is a major risk factor for severe coronavirus disease 2019 (COVID-19), yet the mechanisms behind this relationship have remained incompletely understood. To address this, we evaluated the impact of aging on host immune response in the blood and the upper airway, as well as the nasal microbiome in a prospective, multicenter cohort of 1031 vaccine-naïve patients hospitalized for COVID-19 between 18 and 96 years old. We performed mass cytometry, serum protein profiling, anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody assays, and blood and nasal transcriptomics. We found that older age correlated with increased SARS-CoV-2 viral abundance upon hospital admission, delayed viral clearance, and increased type I interferon gene expression in both the blood and upper airway. We also observed age-dependent up-regulation of innate immune signaling pathways and down-regulation of adaptive immune signaling pathways. Older adults had lower naïve T and B cell populations and higher monocyte populations. Over time, older adults demonstrated a sustained induction of pro-inflammatory genes and serum chemokines compared with younger individuals, suggesting an age-dependent impairment in inflammation resolution. Transcriptional and protein biomarkers of disease severity differed with age, with the oldest adults exhibiting greater expression of pro-inflammatory genes and proteins in severe disease. Together, our study finds that aging is associated with impaired viral clearance, dysregulated immune signaling, and persistent and potentially pathologic activation of pro-inflammatory genes and proteins.}, } @article {pmid40146796, year = {2025}, author = {Li, J and Zhu, Y and Chang, Q and Gong, Y and Wan, J and Xu, S}, title = {Comparative Analysis of Microbiological Profiles and Antibiotic Resistance Genes in Subjects with Colorectal Cancer and Healthy Individuals.}, journal = {Polish journal of microbiology}, volume = {74}, number = {1}, pages = {71-81}, doi = {10.33073/pjm-2025-006}, pmid = {40146796}, issn = {2544-4646}, mesh = {Humans ; *Colorectal Neoplasms/microbiology ; Male ; Middle Aged ; Female ; *Bacteria/genetics/classification/isolation & purification ; *Gastrointestinal Microbiome ; Feces/microbiology ; Aged ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Adult ; }, abstract = {Alteration of the gut microbiota (GM) is associated with various diseases, including colorectal cancer (CRC). With the development of next-generation sequencing techniques, metagenomic sequencing, along with metabolic function and antibiotic-resistant gene analyses, has been used to investigate differences in GM between CRC patients and healthy controls. Fecal samples were obtained from seven CRC patients and six healthy subjects, and the sequencing data were analyzed for similarity, a-diversity, principal component analysis (PCA), and linear discriminant analyses (LDA). Regarding Actinobacteria, 3 orders, 5 families, 9 genera, and 19 species were identified with no differences between the CRC and control groups, while the levels of Bifidobacterium bifidum and Bifidobacterium dentium were higher, and the level of Bifidobacterium breve was lower in the CRC group compared to the healthy controls (p = 0.053). Otherwise, 2 genera (Leuco-nostoc and Salmonella) and 7 species of bacteria (Parabacteroides merdae, Alistipes shahii, Alistipes finegoldii, Clostridium nexile, Salmonella enterica, unclassified Salmonella, Enterobacter cloacae) were found to be significantly differently distributed between CRC patients and healthy controls. PCA-LDA successfully classified these 2 groups with satisfactory accuracy (84.52% for metabolic function and 77.38% for resistant genes). These findings underscore the potential of GM as a diagnostic tool for CRC, offering a promising avenue for non-invasive screening and risk assessment. The identification of specific microbial signatures, particularly those linked to metabolic functions and resistance traits, could open new doors for understanding the role of the microbiome in CRC progression and treatment resistance.}, } @article {pmid40146759, year = {2025}, author = {Guan, Y and Guo, H and Xia, D and Liu, Y and Wang, X}, title = {Migration of heavy metals and microbial metabolic regulation mechanisms in the co-fermentation of coal slime and sawdust.}, journal = {Environmental technology}, volume = {}, number = {}, pages = {1-15}, doi = {10.1080/09593330.2025.2482966}, pmid = {40146759}, issn = {1479-487X}, abstract = {Heavy metals (HMs) significantly affect the anaerobic fermentation of coal slime (CS), while sawdust serves as a promising substrate for methane bioconversion and an effective adsorbent for HMs. To explore the migration of HMs and improve the conversion efficiency of CS and sawdust to biomethane, experiments were conducted on the co-fermentation of CS and sawdust with different mass ratios. FT-IR, ICP-MS, SEM-EDS, and metagenomic sequencing were employed to elucidate the regulation mechanism of microorganisms after adding sawdust in altering the toxicological environment. The results revealed that the optimum mass ratio of CS to sawdust was 2:1. Oxygen-containing functional groups in CS were removed, and the fatty structure was degraded. Addition of sawdust promoted the further degradation of CS and migration of various HMs. Metal elements such as Fe, Mg, Co, and Cd had also been detected on its surface. Bacillota (39.05%) was significantly enriched, which effectively improved the microbial community structure. The abundance of species with metal detoxification functions increased. The types and abundance of transporters related to toxic metal ions increased in families such as ATP-binding Cassette Superfamily (ABC) and Resistance-Nodulation-Cell Division Superfamily (RND), which would further aid in cellular homeostasis. Moreover, the addition of sawdust promoted the expression of metal resistance genes (MRGs). Multi-MRGs were primarily linked to Cu, As, and Zn, with an increased abundance of bacterial species contributing to key MRGs such as copA, ziaA, and actP. These findings offer valuable insights that support the clean and efficient utilization of CS and sawdust.}, } @article {pmid40145240, year = {2025}, author = {Zhou, Y and Oba, K and Xu, T and Kuroiwa, M and Hori, T and Terada, A}, title = {Actively N2O-Reducing Oxygen-Tolerant Microbial Consortium Attained by Using a High-Dilution-Rate Chemostat Fed with Methanol.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c12732}, pmid = {40145240}, issn = {1520-5851}, abstract = {Nitrous oxide-reducing bacteria (N2ORB) are generally considered the only biological sink for the potent greenhouse gas N2O. Although N2O consumption activities by diverse heterotrophic N2ORB have been detected, knowledge gaps remain about the phylogenies, physiologies, and activities of N2ORB. Here, we successfully enriched a methylotrophic N2ORB consortium under intermittent oxygen and N2O supplies. [15]N tracer analysis showed that the N2O consumption activity of the enriched consortium was higher than its N2O production activity in the presence of either a single or multiple electron acceptors (i.e., nitrogen oxides). The observed maximum N2O consumption was 80.7 μmol·g-biomass[-1]·h[-1]. Quantitative PCR results showed that clade I nosZ bacteria overwhelmed clade II nosZ bacteria at high (0.41 mmol·min[-1]) and low (0.08 mmol·min[-1]) N2O loading rates. The dilution rate and N2O loading rate affected the microbial community composition and activity. A higher N2O loading rate stimulated active and oxygen-tolerant N2ORB that boosted N2O consumption by approximately 50% in the presence of oxygen. Metagenomic analysis unraveled the predominance of a novel methylotrophic N2ORB, possessing entire denitrifying genes and high-affinity terminal oxidase genes, from the reactor with a high N2O loading rate. The unique physiological traits of the consortium enriched by methanol shed light on a novel function─aerobic N2O consumption by N2ORB─and pave the way for innovative N2O mitigation strategies applying powerful N2O sinks in engineered systems.}, } @article {pmid40144527, year = {2025}, author = {Wang, J and Ren, W and Sun, Z and Liu, S and Han, Z and Wang, Y and Zeng, Y and Meng, J and Yao, X}, title = {Impact of intragastric administration of donkey milk on mouse immunity utilizing gut microbiomics and plasma metabolomics.}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1486406}, pmid = {40144527}, issn = {2297-1769}, abstract = {INTRODUCTION: Donkey milk demonstrates closer compositional resemblance to human milk compared to bovine milk, positioning it as an optimal nutritional substitute for infants with cow's milk allergy. Furthermore, its rich profile of bioactive compounds suggests potential immunomodulatory properties. This study systematically investigated the effects of donkey milk supplementation on murine immune function and gut microbiome dynamics, thereby providing mechanistic insights to support its clinical development in functional food applications.

METHODS: Following daily intragastric administration of 10 mL/kg of body weight of donkey milk (DM) or distilled water (DW) to the mice for 28 consecutive days, liver tissues were harvested for immunological profiling, with concurrent collection of blood samples for plasma metabolomic analysis and fecal specimens for gut microbiome characterization. Subsequently, the modulatory effects of donkey milk supplementation on immune parameters, intestinal microbiota composition, and plasma metabolic profiles were systematically evaluated.

RESULTS: Immunity analysis revealed that intragastric administration of DM raised the levels of IL-6 and TNF-α cytokines in mouse liver. In addition, DM modulated the composition of both the murine gut microbiome and plasma metabolites. One-hundred and forty-five differentially-produced metabolites were identified, most prominently nicotinamide, L-valine, and β-estradiol, that are primarily associated with valine, leucine, and isoleucine biosynthesis and degradation, nicotinate and nicotinamide metabolism, and unsaturated fatty acid biosynthesis. Alterations at phylum, genus, and species levels were evident in the fecal microbiota of mice after intragastric administration of DM. In particular, an increased abundance of the Lactobacillus bacterium was observed. Correlation analysis of differential metabolites and microbiomes indicated a correspondence between Falsiroseomonas and Salipiger species and the antioxidant coenzyme Q that has the potential to activate the immune system.

CONCLUSION: The data collectively suggest that DM may adjust the murine gut microbiome and plasma metabolites thereby potentially improving immunity in mice.}, } @article {pmid40144403, year = {2025}, author = {Li, Z and Zou, D and Liu, R and Pan, J and Huang, J and Ma, J and Huang, L and He, J and Fu, L and Zheng, X and Wang, M and Fang, J and Dong, H and Li, M and Huang, L and Dai, X}, title = {A hunting ground for predatory bacteria at the Zhenbei seamount in the South China Sea.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf042}, pmid = {40144403}, issn = {2730-6151}, abstract = {Seamounts are critical marine biodiversity hot spots, while the metabolic activity of their microbial community remains largely unknown. In this study, we investigated the diversity and activity of free-living and particle-attached microorganisms in the surface, middle, and bottom layers of seawater at the Zhenbei seamount in the South China Sea using omics approaches, including 16S ribosomal RNA (rRNA)/16S rDNA ratio analysis. Over 20 phyla were detected, with Proteobacteria, Actinobacteriota, Cyanobacteria, Bacteroidota, Thaumarchaeota, and Planctomycetota being predominant. Surprisingly, Bdellovibrionota and Myxococcota, the two well-known predatory bacteria, exhibited exceptionally higher rRNA/rDNA ratios than the other phyla, with rRNA abundances being 10- or even 200-fold higher than their rDNA abundances. These metabolically active predatory bacteria are mainly uncultured species. A total of 23 Myxococcota metagenome-assembled genomes (MAGs) and 12 Bdellovibrionota MAGs were assembled. The most highly overexpressed genes frequently detected in these MAGs were those that encode flagellum and pilus proteins as well as T4-like virus tail tube protein, indicating that these predator bacteria were likely active in hunting. Our results suggest that seamounts may serve as hunting grounds for predatory bacteria, which may be involved in controlling the flows of elements and energy in the seamount microbial communities and, thus, in shaping the seamount ecosystems.}, } @article {pmid40143870, year = {2025}, author = {Hu, Y and Zhou, J and Lin, X}, title = {Akkermansia muciniphila helps in the recovery of lipopolysaccharide-fed mice with mild intestinal dysfunction.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1523742}, pmid = {40143870}, issn = {1664-302X}, abstract = {BACKGROUND: Mild intestinal dysfunction, linked to subtle yet significant health issues, can be induced by lipopolysaccharide (LPS), a Gram-negative bacterial component that disrupts gut function and triggers inflammation. Akkermansia muciniphila has shown promise as a probiotic for gut health due to its roles in mucin degradation and short-chain fatty acid production. This study explores the therapeutic effects of Akkermansia muciniphila on LPS-induced mild intestinal dysfunction in mice.

METHODS: Thirty-eight 6-week-old C57BL/6 mice were split into control (n = 19) and LPS-treated (n = 19) groups. LPS-treated mice received 300 μg/kg/day of LPS for 4 weeks, followed by Akkermansia muciniphila supplementation at 41 mg/kg/day (Akk1) or 82 mg/kg/day (Akk2) for another 4 weeks. Gut microbiota was analyzed via metagenomic sequencing, and gene expression was evaluated through transcriptomics.

RESULTS: LPS significantly altered gut microbiota, reducing diversity and increasing pathogenic genera like Lachnoclostridium. Akkermansia muciniphila supplementation, particularly at higher doses, partially restored gut microbiota by increasing beneficial genera such as Muribaculum. Transcriptomics showed that LPS induced immune and inflammatory responses, while Akkermansia muciniphila reduced these effects by modulating pathways like TNF and NF-kappa B signaling.

CONCLUSION: Akkermansia muciniphila mitigates LPS-induced gut dysfunction by restoring microbiota balance and modulating immune responses, highlighting its potential as a therapeutic agent for gut health.}, } @article {pmid40143862, year = {2025}, author = {Sujatha, S and Sindhura, KAV and Koti, PS and Hiremath, S and Muttappagol, M and Vinay Kumar, HD and Shankarappa, KS and Venkataravanappa, V and Reddy, KMS and Reddy, CNL}, title = {Influence of weather and seasonal factors on whitefly dynamics, associated endosymbiotic microbiomes, and Begomovirus transmission causing tomato leaf curl disease: insights from a metagenomic perspective.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1555058}, pmid = {40143862}, issn = {1664-302X}, abstract = {INTRODUCTION: Bemisia tabaci (Gennadius) is a globally significant agricultural pest, responsible for transmitting over 120 plant viruses, including those from the Begomovirus genus, which contribute to considerable crop losses. The species complex comprises cryptic species, associated with a diverse array of bacterial endosymbionts that play essential roles in host nutrition, virus transmission, and overall host adaptability. These endosymbionts are classified into primary and secondary categories, with primary endosymbionts forming obligatory, long-term associations, and secondary endosymbionts influencing factors such as biotype differentiation and vector competency. Notably, these microbial communities enhance B. tabaci's capacity to transmit viruses, including the tomato leaf curl virus (ToLCuV), which poses a significant threat to tomato production.

METHODS: In this study, we examined the population dynamics of B. tabaci across three major tomato-growing regions in Karnataka, South India, focusing on their seasonal associations with endosymbionts and the incidence of tomato leaf curl disease (ToLCuD). Multiple regression analysis was employed to assess the influence of weather parameters on whitefly populations and disease prevalence. Additionally, we constructed a metagenomic profile to evaluate the effects of geographical location, seasonality, environmental factors, and agricultural practices on the bacterial communities associated with B. tabaci. Species-specific primers were used to validate the presence and diversity of these bacterial communities.

RESULTS: Meteorological data revealed a positive correlation between temperature and B. tabaci populations, which corresponded with an increased incidence of ToLCuD. Genetic characterization of the whitefly identified Asia II-5 and Asia II-7 cryptic species as the dominant forms in the surveyed regions, with Portiera emerging as the most prevalent endosymbiont. A more in-depth analysis of the microbial communities associated with B. tabaci, utilizing 16S rRNA metagenomic sequencing, revealed a dominance of the Proteobacteria phylum. The endosymbiotic bacterial consortium was primarily composed of Candidatus Portiera, Candidatus Hamiltonella, Candidatus Rickettsia, and Candidatus Arsenophonus.

DISCUSSION: The metagenomic analysis revealed a highly diverse array of bacterial communities, with 92% of sequences classified under Proteobacteria, representing a spectrum of microbial types associated with B. tabaci ranging from parasitic and pathogenic to mutualistic. Within this phylum, Alphaproteobacteria were predominant, known for their role as facultative symbionts, while Gammaproteobacteria provided essential nutrients to arthropods, enhancing their survival and fitness. The interplay of continuous and intensive tomato cultivation, elevated temperatures, favorable host plants, and abundant viral inoculum creates an ideal environment for the proliferation of B. tabaci and the widespread transmission of ToLCuD. The presence of diverse cryptic species of B. tabaci, which are efficient viral vectors, further complicates the situation. These findings underscore the urgent need for integrated management strategies globally to control both whitefly populations and ToLCuD, ensuring the protection of tomato crops and the sustainability of farmer livelihoods.}, } @article {pmid40143285, year = {2025}, author = {Popov, N and Sonets, I and Evdokimova, A and Molchanova, M and Panova, V and Korneenko, E and Manolov, A and Ilina, E}, title = {AliMarko: A Pipeline for Virus Identification Using an Expert-Guided Approach.}, journal = {Viruses}, volume = {17}, number = {3}, pages = {}, doi = {10.3390/v17030355}, pmid = {40143285}, issn = {1999-4915}, support = {122030900069-4//Russian State/ ; }, mesh = {*Phylogeny ; *Metagenomics/methods ; *Viruses/genetics/classification/isolation & purification ; *Feces/virology ; Animals ; *Genome, Viral ; Humans ; Metagenome ; Chiroptera/virology ; Computational Biology/methods ; Software ; Sequence Analysis, RNA/methods ; }, abstract = {Viruses are ubiquitous across all kingdoms of cellular life, posing a significant threat to human health, and analyzing viral communities is challenging due to their genetic diversity and lack of a single, universally conserved marker gene. To address this challenge, we developed the AliMarko pipeline, a tool designed to streamline virus identification in metagenomic data. Our pipeline uses a dual approach, combining mapping reads with reference genomes and a de novo assembly-based approach involving an HMM-based homology search and phylogenetic analysis, to enable comprehensive detection of viral sequences, including low-coverage and divergent sequences. We applied our pipeline to total RNA sequencing of bat feces and identified a range of viruses, quickly validating viral sequences and assessing their phylogenetic relationships. We hope that the AliMarko pipeline will be a useful resource for the scientific community, facilitating the interpretation of viral communities and advancing our understanding of viral diversity and its impact on human health.}, } @article {pmid40143275, year = {2025}, author = {Sarana da Silva, A and de Campos, GM and Altizani, GM and de Carvalho, E and Barros, AC and Cella, E and Kashima, S and Sampaio, SC and Elias, MC and Giovanetti, M and Scrideli, CA and Slavov, SN}, title = {Utilizing Viral Metagenomics to Characterize Pathogenic and Commensal Viruses in Pediatric Patients with Febrile Neutropenia.}, journal = {Viruses}, volume = {17}, number = {3}, pages = {}, doi = {10.3390/v17030345}, pmid = {40143275}, issn = {1999-4915}, support = {17/23205-8; 21/11944-6; 2022/10278-5//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 403075/2023-8; 305111/2022-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, mesh = {Humans ; *Metagenomics/methods ; Child ; Male ; Female ; Child, Preschool ; *Febrile Neutropenia/virology ; Adolescent ; Viruses/classification/genetics/isolation & purification ; Infant ; Herpesviridae/genetics/classification/isolation & purification ; Oropharynx/virology ; Neoplasms/virology/complications ; Metagenome ; }, abstract = {Febrile neutropenia (FN) is one of the most common complications in pediatric oncology patients. It has a complex etiologic nature, which in the majority of cases remains unclear. Intervention often follows empirical treatment protocols, mainly using broad-spectrum antibiotics. To evaluate potential viral etiologic agents, this study applied viral metagenomics to paired plasma and oropharyngeal samples obtained from pediatric patients with oncological diseases diagnosed with FN. Metagenomic sequencing was performed on 15 pediatric patients with oncological diseases and FN at the outpatient clinic of Pediatric Oncology at the University Hospital of the Faculty of Medicine of Ribeirão Preto, University of São Paulo. As a control group, we included 15 pediatric patients with oncological diseases in remission or undergoing treatment. Clinically relevant viruses identified by metagenomics in FN patients predominantly included herpesviruses and viruses found in the respiratory tract, like adenoviruses. Direct molecular confirmation was performed on all of them. Anelloviruses, represented by various genera and species in all groups, were also highly prevalent. The data obtained in this study show that viruses might also have possible implications for the etiology of FN. However, due to the complex nature of this disease, more studies are necessary to evaluate their causal relationship. The results obtained in our study may serve to improve patient treatment and ensure adequate management.}, } @article {pmid40142589, year = {2025}, author = {Chen, X and Gao, L and Kou, Y and Wang, X and Li, X and He, H and Wang, M}, title = {Composition, Distribution and Mobility Potential of the Antibiotic Resistome in Sediments from the East China Sea Revealed by Metagenomic Analysis.}, journal = {Microorganisms}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/microorganisms13030697}, pmid = {40142589}, issn = {2076-2607}, support = {41806131//National Natural Science Foundation of China/ ; 42120104006//National Natural Science Foundation of China/ ; ZR2024QD036//Natural Science Foundation of Shandong Province/ ; }, abstract = {Marine sediments are recognized as crucial reservoirs of antibiotic resistance genes (ARGs). However, the antibiotic resistome in sediments of the East China Sea, an area heavily impacted by human activities, has not been thoroughly studied. Here, we conducted a systematic investigation into the antibiotic resistome in these sediments using metagenomic analysis. Overall, we detected eighty ARG subtypes and nineteen ARG types. Beta-lactams were the dominant ARG type, and Gammaproteobacteria was the main ARG host in this study. Mobile genetic elements (MGEs) were not major drivers of ARG profiles. Although the ARG host communities significantly differed between the spring and autumn (p < 0.05), the antibiotic resistome remained stable across the two seasons. The assembly of ARGs and their hosts was governed by stochastic processes, and a high ratio of stochastic processes implied its crucial role in the assembly and stabilization of the antibiotic resistome. Co-occurrence network analysis revealed an important role of Deltaproteobacteria in the stabilization of ARG profiles across seasons. Environmental parameters (e.g., temperature and density) played certain roles in the stabilization of the antibiotic resistome between spring and autumn. Moreover, nine human pathogen bacteria (HPB) were detected in this study. We also found that the health risks caused by ARGs were relatively higher in the spring. Our results will provide a strong foundation for the development of targeted management strategies to mitigate the further dissemination and spread of ARGs in marine sediments.}, } @article {pmid40142582, year = {2025}, author = {Peng, Y and Jiang, L and Wu, J and Yang, J and Guo, Z and Miao, M and Peng, Z and Chang, M and Miao, B and Liu, H and Liang, Y and Yin, H and He, Q and Liu, X}, title = {Red Mud Potentially Alleviates Ammonia Nitrogen Inhibition in Swine Manure Anaerobic Digestion by Enhancing Phage-Mediated Ammonia Assimilation.}, journal = {Microorganisms}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/microorganisms13030690}, pmid = {40142582}, issn = {2076-2607}, support = {Grant No. 2018YFC1800400//the National Key Research and Development Program of China/ ; Grant No. 51909282//the National Natural Science Foundation of China/ ; Grant No. 2022JJ40583//the Natural Science Foundation of Hunan Province of China/ ; Grant No. 2022WK2017//the Hunan Provincial Key Research and Development Plan/ ; Grant No. 2023NK2030//the Hunan Provincial Key Research and Development Plan/ ; }, abstract = {Red mud has been demonstrated to improve the methane production performance of anaerobic digestion (AD). However, the influence of red mud on ammonia nitrogen inhibition during AD through the mediating role of bacteria-phages interactions in this process remains poorly understood. Thus, this study investigated the impact of red mud on nitrogen metabolism in AD and characterized the phage and prokaryotic communities through a metagenomic analysis. The results showed that red mud significantly increased methane production by 23.1% and promoted the conversion of ammonia nitrogen into organic nitrogen, resulting in a 4.8% increase in total nitrogen. Simultaneously, it enriched the key microbial genera Methanothrix, Proteinophilum, and Petrimonas by 0.5%, 0.8%, and 2.7%, respectively, suggesting an enhancement in syntrophic acetate oxidation with greater ammonia tolerance. A viral metagenomic analysis identified seven nitrogen-metabolism-related auxiliary metabolic genes (AMGs), with glnA (encoding glutamine synthetase) being the most abundant. Compared to the control treatments, the red mud treatments led to a higher abundance of temperate phages and an increased number of AMGs. Furthermore, two new hosts carrying glnA (Mycolicibacteria smegmatis and Kitasatopola aureofaciens) were predicted, indicating that red mud expanded the host range of phages and promoted the spread of AMGs. Overall, our findings highlight the importance of phages in alleviating ammonia nitrogen inhibition and provide a novel understanding of the role of red mud in the AD of swine manure.}, } @article {pmid40142572, year = {2025}, author = {Yi, Q and Zhang, G and Wang, T and Li, J and Kang, W and Zhang, J and Liu, Y and Xu, Y}, title = {Comparative Analysis of Metagenomic Next-Generation Sequencing, Sanger Sequencing, and Conventional Culture for Detecting Common Pathogens Causing Lower Respiratory Tract Infections in Clinical Samples.}, journal = {Microorganisms}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/microorganisms13030682}, pmid = {40142572}, issn = {2076-2607}, support = {2022-PUMCH-B-074//National High Level Hospital Clinical Research Funding/ ; }, abstract = {Metagenomic next-generation sequencing (mNGS) has emerged as a revolutionary tool for infectious disease diagnostics. The necessity of mNGS in real-world clinical practice for common Lower Respiratory Tract Infections (LRTI) needs further evaluation. A total of 184 bronchoalveolar lavage fluid (BALF) samples and 322 sputa associated with LRTI were fully examined. The detection performance was compared between mNGS and standard microbiology culture, using Sanger sequencing as the reference method. 52.05% (165/317) of sputa showed identical results for all three methods. Compared to Sanger sequencing, the same results obtained by mNGS were 88.20% (284/322). In 2.80% (9/322) of cases, Sanger sequencing detected more microorganisms, while mNGS detected more in 9% (29/322) of cases. For BALF, 49.41% (85/172) of cases showed identical results for all three methods. In 91.30% (168/184) of cases, identical results were produced by both mNGS and Sanger sequencing. mNGS detected more species in 7.61% (14/184) of cases, whereas in 2.80% (2/184) instances, the Sanger sequencing detected more microorganisms than mNGS. In the 184 BALF samples, 66 samples were identified as having co-infections by mNGS, Sanger sequencing identified 64 samples, and cultures identified 22 samples. Our study demonstrates that mNGS offers a significant advantage over conventional culture methods in detecting co-infections. For common bacterial pathogens, conventional culture methods are sufficient for detection. However, mNGS provides comprehensive pathogen detection and is particularly useful for identifying rare and difficult-to-culture pathogens.}, } @article {pmid40142491, year = {2025}, author = {Kioukis, A and Camargo, AP and Pavlidis, P and Iliopoulos, I and Kyrpides, NC and Lagkouvardos, I}, title = {Global Archaeal Diversity Revealed Through Massive Data Integration: Uncovering Just Tip of Iceberg.}, journal = {Microorganisms}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/microorganisms13030598}, pmid = {40142491}, issn = {2076-2607}, support = {710//Hellenic Foundation for Research and Innovation/ ; DE-AC02-05CH11231//Joint Genome Institute/ ; }, abstract = {The domain of Archaea has gathered significant interest for its ecological and biotechnological potential and its role in helping us to understand the evolutionary history of Eukaryotes. In comparison to the bacterial domain, the number of adequately described members in Archaea is relatively low, with less than 1000 species described. It is not clear whether this is solely due to the cultivation difficulty of its members or, indeed, the domain is characterized by evolutionary constraints that keep the number of species relatively low. Based on molecular evidence that bypasses the difficulties of formal cultivation and characterization, several novel clades have been proposed, enabling insights into their metabolism and physiology. Given the extent of global sampling and sequencing efforts, it is now possible and meaningful to question the magnitude of global archaeal diversity based on molecular evidence. To do so, we extracted all sequences classified as Archaea from 500 thousand amplicon samples available in public repositories. After processing through our highly conservative pipeline, we named this comprehensive resource the 'Global Archaea Diversity' (GAD), which encompassed nearly 3 million molecular species clusters at 97% similarity, and organized it into over 500 thousand genera and nearly 100 thousand families. Saline environments have contributed the most to the novel taxa of this previously unseen diversity. The majority of those 16S rRNA gene sequence fragments were verified by matches in metagenomic datasets from IMG/M. These findings reveal a vast and previously overlooked diversity within the Archaea, offering insights into their ecological roles and evolutionary importance while establishing a foundation for the future study and characterization of this intriguing domain of life.}, } @article {pmid40142462, year = {2025}, author = {Hadian, S and Smith, DL and Supronienė, S}, title = {Modulating the Plant Microbiome: Effects of Seed Inoculation with Endophytic Bacteria on Microbial Diversity and Growth Enhancement in Pea Plants.}, journal = {Microorganisms}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/microorganisms13030570}, pmid = {40142462}, issn = {2076-2607}, abstract = {Understanding plant microbe interactions is crucial for achieving sustainable agriculture. This study investigated the effects of inoculating pea plants (Pisum sativum) with two endophytic Bacillus strains, AR11 and AR32, isolated from Artemisia species and characterized by phosphate solubilization, nitrogen fixation, and pathogen antagonism. Utilizing cutting-edge methods such as rarefaction curves, rank abundance modeling, and metagenomic analysis, this research provides a detailed understanding of how these bacterial strains influence plant associated microbiomes. AR11 significantly enhanced microbial diversity, while AR32 showed a moderate effect. Beta diversity analyses revealed distinct shifts in microbial community composition, with AR11-treated samples enriched with beneficial taxa such as Paenibacillus, Flavobacterium, and Methylotenera, known for their roles in nutrient cycling, pathogen suppression, and plant health promotion. This innovative methodological framework surpasses traditional approaches by offering a comprehensive view of ecological and functional microbiome shifts. The study highlights the potential of nonhost bacteria as biostimulants and their role in developing microbiome engineering strategies to enhance plant resilience. These findings contribute to sustainable agriculture by demonstrating how microbial inoculants can be employed to enhance crop productivity and environmental resilience in diverse agricultural systems.}, } @article {pmid40142456, year = {2025}, author = {Zhu, S and Guo, Z and Liu, L and Gao, Y and Bai, L and Chen, Y and Zha, M}, title = {Complex Probiotics Relieve Constipation Through Regulation of the Intestinal Microbiota in Kittens.}, journal = {Microorganisms}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/microorganisms13030563}, pmid = {40142456}, issn = {2076-2607}, support = {2024LHMS03043//The Natural Science Foundation of Inner Mongolia, China/ ; 2022 - Science and Technology Xing Meng - Quality improvement - 02//Science and Technology Xing Meng action focus project of Inner Mongolia Autonomous Region/ ; SPYQ202001//The Cultivation Project for Excellent Youth of Inner Mongolia Agricultural University/ ; }, abstract = {The early developmental phase is a critical window for feline growth, during which immature digestive systems are susceptible to microbiome imbalances caused by environmental stressors. Our research employed macrogenomic analysis to evaluate how complex probiotic formulations influence growth metrics and gastrointestinal flora in juvenile felines. Two dozen healthy kittens were equally divided into the control group and the probiotics group following a 5-day environmental adaptation phase. Fecal scores were recorded daily for all kittens. Fresh fecal samples were collected on days 1 and 14 for macrogenomic analysis. The results showed a significantly lower rate of constipation in the probiotics group compared to the control group (p < 0.05). However, no significant differences were observed in intestinal microbial diversity or structure between the two groups. Metagenomic analysis revealed a higher relative abundance of Bifidobacterium animalis in the probiotics group compared to the control group (p < 0.05). Additionally, the probiotics group exhibited lower relative abundances of Lachnospiraceae bacterium 2 1 58FAA, Lachnospiraceae bacterium 1 1 57FAA, and Acidaminococcus intestini compared to the control group (p < 0.05). These results suggest that complex probiotics can regulate the intestinal microbiota, improve constipation, and promote intestinal health in kittens.}, } @article {pmid40142431, year = {2025}, author = {Aires, C and Maioto, R and Inês, A and Dias, AA and Rodrigues, P and Egas, C and Sampaio, A}, title = {Microbiome and Microbiota Within Wineries: A Review.}, journal = {Microorganisms}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/microorganisms13030538}, pmid = {40142431}, issn = {2076-2607}, abstract = {The main goal of this work is to review the winery's microbiota, from the grape to the winery's microbial niches (fermentation tanks, surfaces, air), and their risks to wine and human health. The impact of climate change on the winery microbiome and related challenges are also discussed. Microbial diversity in wineries depends on several factors, such as the grape variety and its ripeness, temperature, relative humidity and the diverse activities of the winemaking process. Winery surfaces and equipment allow the establishment of a microbial community that can impact wine quality, the health of winery workers and visitors and even wine consumers. In the context of climate change, changes in the sugar content, phenolic compounds and the profile of hexoses and amino acids are already evident. These changes interfere with the fermentation microbiota and the quality of the wines, which are more alcoholic and less acidic. Furthermore, periods of drought or heavy rain favor species associated with berry diseases, including some capable of producing mycotoxins or harmful biogenic amines. In order to understand the impact of these changes on microbial communities, the use of various techniques will be discussed, such as flow cytometry, fluorescence in situ hybridization (FISH), quantitative polymerase chain reaction (qPCR) and metagenomic methods.}, } @article {pmid40142426, year = {2025}, author = {Needle, DB and Reboul, G and Mitchell, PK and Rothenheber, D and Marra, NJ and Cronk, BD and Patel, NG and Goodman, LB}, title = {Application of Amplicon Metagenomics to Identify Fungal Pathogens in Formalin-Fixed Paraffin-Embedded Samples: Proof of Concept in Animals with Fungal Pathologies.}, journal = {Microorganisms}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/microorganisms13030533}, pmid = {40142426}, issn = {2076-2607}, support = {1U18FD006716//US Food and Drug Administration's Veterinary Laboratory Investigation and Response Network (FDA Vet-LIRN)/ ; 1R03DE033304-01A1/NH/NIH HHS/United States ; }, abstract = {The identification of fungal pathogens in formalin-fixed paraffin-embedded (FFPE) tissues is an unmet need in human and animal medicine, and sequence-agnostic approaches are needed to identify emerging pathogens. Eleven FFPE biopsy specimens with etiologic diagnoses of fungal disease based on standard testing of paired fresh tissue samples were utilized here to evaluate metabarcoding approaches. The cases included tissues from three dogs, three cats, one box turtle, one goat, one common loon, and one gray tree frog. The diagnoses from the fresh tissues in these cases were Microsporum canis, Penicillium sp., Exophiala sp. (likely E. jeanselmei), Verticillium sp., Rhizopus sp., atypical Cryptococcus neoformans, Conidiobolus spp., Aspergillus fumigatus, Cryptococcus neoformans var grubii, Batrachochytrium dendrobatidis, Fusarium solani, Blastomyces dermatitidis, Coccidiodes immitis, and Histoplasma capsulatum. We compared the ITS1 and 28S D1 rRNA gene genetic markers in combination with several bioinformatic strategies to identify fungal pathogens in the FFPE tissue samples, with a success rate of 9/11. These methods could allow diagnosticians who receive only FFPE tissues and see fungal pathogens to speciate the pathogens and could be of value in retrospective studies wherein FFPE tissue is the only archived tissue. Furthermore, these techniques could be of use to researchers investigating polymicrobial communities where DNA preservation is suboptimal.}, } @article {pmid40142417, year = {2025}, author = {Chao, S and Chen, Y and Wu, J and Zhang, Y and Song, L and Li, P and Sun, Y and Hu, Y and Wang, H and Jiang, Y and Lv, B}, title = {Exserohilum turcicum Alters Phyllosphere Microbiome Diversity and Functions-Implications for Plant Health Management.}, journal = {Microorganisms}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/microorganisms13030524}, pmid = {40142417}, issn = {2076-2607}, support = {2024-02-08-00-12-F00021//Shanghai Agriculture Applied Technology Development Program, China/ ; 32302635//National Natural Science Foundation of China/ ; 22ZR1442500//Natural Science Foundation of Shanghai/ ; SAAS Application Basic Study 2025(08)//2025 SAAS Project on Agricultural Science and Technology Innovation Supporting Area/ ; 016//Shanghai Academy of Agricultural Sciences 2022/ ; 20DZ2255300//Shanghai Engineering Research Center of Specialty Maize/ ; 2023ZD04062//the Science and Technology Innovation 2030 Biological Breeding-Major Projects/ ; 23DZ2290700//Shanghai "Science and Technology Innovation Action Plan" Professional Technical Service Platform Project/ ; }, abstract = {The phyllosphere represents the largest biological surface on Earth and serves as an untapped reservoir of functional microbiota. The phyllosphere microbiome has the potential to mitigate plant diseases; however, limited information exists regarding its role in maintaining plant health. In this study, metagenomic sequencing was employed to analyze the microbiomes of the adaxial and abaxial leaf surfaces of healthy (CKWT) and diseased (EWT) maize, with the aim of dissecting the influence of Exserohilum turcicum on phyllosphere microbiome function. E. turcicum altered the alpha and beta diversity of the phyllosphere microbiome, with the Shannon diversity and Chao1 index values significantly reduced in EWT. More beneficial microbes accumulated in the CKWT phyllosphere, whereas pathogenic microbes decreased. E. turcicum may have altered the balance between commensal and pathogenic microorganisms. The species and abundances of microorganisms on the two sets of leaf surfaces were also altered after inoculation with E. turcicum. Further analysis of disease-resistance-related metabolic pathways and abundances of antibiotic-resistance genes revealed that E. turcicum altered the abundance of the functional microbiome and modified the microbiome differences between adaxial and abaxial leaf surfaces. In conclusion, the results reveal that microbial diversity in the maize phyllosphere can influence the microbiome and regulate microbial functions to support plant health. These findings enhance our understanding of how E. turcicum affects the phyllosphere microbiome and provide a theoretical basis for biological control of E. turcicum.}, } @article {pmid40142410, year = {2025}, author = {Hassen, AI and Muema, EK and Diale, MO and Mpai, T and Bopape, FL}, title = {Non-Rhizobial Endophytes (NREs) of the Nodule Microbiome Have Synergistic Roles in Beneficial Tripartite Plant-Microbe Interactions.}, journal = {Microorganisms}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/microorganisms13030518}, pmid = {40142410}, issn = {2076-2607}, support = {A-089//Department of Agriculture Land Reform and Rural Development/ ; }, abstract = {Microbial symbioses deal with the symbiotic interactions between a given microorganism and another host. The most widely known and investigated microbial symbiosis is the association between leguminous plants and nitrogen-fixing rhizobia. It is one of the best-studied plant-microbe interactions that occur in the soil rhizosphere and one of the oldest plant-microbe interactions extensively studied for the past several decades globally. Until recently, it used to be a common understanding among scientists in the field of rhizobia and microbial ecology that the root nodules of thousands of leguminous species only contain nitrogen-fixing symbiotic rhizobia. With the advancement of molecular microbiology and the coming into being of state-of-the-art biotechnology innovations, including next-generation sequencing, it has now been revealed that rhizobia living in the root nodules of legumes are not alone. Microbiome studies such as metagenomics of the root nodule microbial community showed that, in addition to symbiotic rhizobia, other bacteria referred to as non-rhizobial endophytes (NREs) exist in the nodules. This review provides an insight into the occurrence of non-rhizobial endophytes in the root nodules of several legume species and the beneficial roles of the tripartite interactions between the legumes, the rhizobia and the non-rhizobial endophytes (NREs).}, } @article {pmid40141768, year = {2025}, author = {Ghobashy, MOI and Al-Otaibi, AS and Alharbi, BM and Alshehri, D and Ghabban, H and Albalawi, DA and Alenzi, AM and Alatawy, M and Alatawi, FA and Algammal, AM and Mir, R and Mahrous, YM}, title = {Metagenomic Characterization of Microbiome Taxa Associated with Coral Reef Communities in North Area of Tabuk Region, Saudia Arabia.}, journal = {Life (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, doi = {10.3390/life15030423}, pmid = {40141768}, issn = {2075-1729}, support = {Research no.0144-1444-S//Deanship of Research and Graduate Studies at University of Tabuk/ ; }, abstract = {The coral microbiome is highly related to the overall health and the survival and proliferation of coral reefs. The Red Sea's unique physiochemical characteristics, such a significant north-south temperature and salinity gradient, make it a very intriguing research system. However, the Red Sea is rather isolated, with a very diversified ecosystem rich in coral communities, and the makeup of the coral-associated microbiome remains little understood. Therefore, comprehending the makeup and dispersion of the endogenous microbiome associated with coral is crucial for understanding how the coral microbiome coexists and interacts, as well as its contribution to temperature tolerance and resistance against possible pathogens. Here, we investigate metagenomic sequencing targeting 16S rRNA using DNAs from the sediment samples to identify the coral microbiome and to understand the dynamics of microbial taxa and genes in the surface mucous layer (SML) microbiome of the coral communities in three distinct areas close to and far from coral communities in the Red Sea. These findings highlight the genomic array of the microbiome in three areas around and beneath the coral communities and revealed distinct bacterial communities in each group, where Pseudoalteromonas agarivorans (30%), Vibrio owensii (11%), and Pseudoalteromonas sp. Xi13 (10%) were the most predominant species in samples closer to coral (a coral-associated microbiome), with the domination of Pseudoalteromonas_agarivorans and Vibrio_owensii in Alshreah samples distant from coral, while Pseudoalteromonas_sp._Xi13 was more abundant in closer samples. Moreover, Proteobacteria such as Pseudoalteromonas, Pseudomonas and Cyanobacteria were the most prevalent phyla of the coral microbiome. Further, Saweehal showed the highest diversity far from corals (52.8%) and in Alshreah (7.35%) compared to Marwan (1.75%). The microbial community was less diversified in the samples from Alshreah Far (5.99%) and Marwan Far (1.75%), which had comparatively lower values for all indices. Also, Vibrio species were the most prevalent microorganisms in the coral mucus, and the prevalence of these bacteria is significantly higher than those found in the surrounding saltwater. These findings reveal that there is a notable difference in microbial diversity across the various settings and locales, revealing that geographic variables and coral closeness affect the diversity of microbial communities. There were significant differences in microbial community composition regarding the proximity to coral. In addition, there were strong positive correlations between genera Pseudoalteromonas and Vibrio in close-to-coral environments, suggesting that these bacteria may play a synergistic role in Immunizing coral, raising its tolerance towards environmental stress and overall coral health.}, } @article {pmid40140988, year = {2025}, author = {Yan, Q and Huang, L and Li, S and Zhang, Y and Guo, R and Zhang, P and Lei, Z and Lv, Q and Chen, F and Li, Z and Meng, J and Li, J and Wang, G and Chen, C and Ullah, H and Cheng, L and Fan, S and You, W and Zhang, Y and Ma, J and Sha, S and Sun, W}, title = {The Chinese gut virus catalogue reveals gut virome diversity and disease-related viral signatures.}, journal = {Genome medicine}, volume = {17}, number = {1}, pages = {30}, pmid = {40140988}, issn = {1756-994X}, mesh = {Humans ; *Virome/genetics ; *Viruses/genetics/classification ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; China ; Female ; Feces/virology ; Male ; Metagenomics/methods ; Genome, Viral ; Asian People/genetics ; East Asian People ; }, abstract = {BACKGROUND: The gut viral community has been increasingly recognized for its role in human physiology and health; however, our understanding of its genetic makeup, functional potential, and disease associations remains incomplete.

METHODS: In this study, we collected 11,286 bulk or viral metagenomes from fecal samples across large-scale Chinese populations to establish a Chinese Gut Virus Catalogue (cnGVC) using a de novo virus identification approach. We then examined the diversity and compositional patterns of the gut virome in relation to common diseases by analyzing 6311 bulk metagenomes representing 28 disease or unhealthy states.

RESULTS: The cnGVC contains 93,462 nonredundant viral genomes, with over 70% of these being novel viruses not included in existing gut viral databases. This resource enabled us to characterize the functional diversity and specificity of the gut virome. Using cnGVC, we profiled the gut virome in large-scale populations, assessed sex- and age-related variations, and identified 4238 universal viral signatures of diseases. A random forest classifier based on these signatures achieved high accuracy in distinguishing diseased individuals from controls (AUC = 0.698) and high-risk patients from controls (AUC = 0.761), and its predictive ability was also validated in external cohorts.

CONCLUSIONS: Our resources and findings significantly expand the current understanding of the human gut virome and provide a comprehensive view of the associations between gut viruses and common diseases. This will pave the way for novel strategies in the treatment and prevention of these diseases.}, } @article {pmid40140753, year = {2025}, author = {Yan, Z and Wang, Y and Zeng, W and Hui, J and Yang, B and Xu, J and Miao, Y and Xia, R}, title = {Antibiotic-driven pathogen replacement events in a kidney transplant recipient with ADPKD: a case report.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {423}, pmid = {40140753}, issn = {1471-2334}, support = {82270784//National Natural Science Foundation of China/ ; 2023A1515012276//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2024CL-GX03//Clinical High-tech and Major Technology Projects in Guangzhou Area/ ; }, mesh = {Humans ; *Kidney Transplantation/adverse effects ; *Polycystic Kidney, Autosomal Dominant/complications/surgery ; *Anti-Bacterial Agents/therapeutic use ; Male ; Transplant Recipients ; Middle Aged ; Nephrectomy ; Enterococcus faecium/isolation & purification/drug effects ; }, abstract = {BACKGROUND: Retaining the native bilateral kidneys after transplantation is a common treatment for patients with end-stage autosomal dominant polycystic kidney disease. However, this strategy poses the risks of potential complications from polycystic kidney infection. The efficiency of antibiotic therapy and the optimal time for native nephrectomy in managing these infections remain uncertain.

CASE PRESENTATION: We report a case of a kidney transplant recipient with retained bilateral polycystic kidneys who experienced recurrent cyst and bloodstream infections, accompanied by antibiotic-driven pathogen replacement. After multiple failed attempts at antibiotic therapy, the patient subsequently underwent unilateral polycystic kidney resection. Subsequently, a new infection episode occurred, leading to the other native nephrectomy. Cystic tissue and fluid samples were collected from both shallow and deep layers of the polycystic kidneys, along with peripheral blood and urine samples. These samples were analyzed using microbial culture, metagenome sequencing, and digital polymerase chain reaction to identify infectious pathogens. Pathogen replacement occurred across different infection episodes, with the dominant bacterial species being Escherichia coli, Klebsiella aerogenes, and Enterococcus faecium, in succession.

CONCLUSIONS: This case highlights the replacement of dominant pathogens under antibiotic selection pressure in polycystic kidney infections, primarily involving gram-negative bacilli. When initial and subsequent antibiotic therapy fail, re-evaluation of the cyst infection definition is necessary, and preemptive native nephrectomy should be considered.}, } @article {pmid40140741, year = {2025}, author = {Zhao, X and Liu, X and Wang, Z and Wei, S and Wu, Z}, title = {Metagenomic next-generation sequencing for the diagnosis of Corynebacterium striatum meningitis: case report and literature review.}, journal = {BMC neurology}, volume = {25}, number = {1}, pages = {127}, pmid = {40140741}, issn = {1471-2377}, support = {20230058//Shanxi Provincial Department of Human Resources and Social Security/ ; 20230058//Shanxi Provincial Department of Human Resources and Social Security/ ; 20230058//Shanxi Provincial Department of Human Resources and Social Security/ ; [2023]14-73//Shanxi Provincial Department of Education/ ; }, mesh = {Humans ; Male ; Aged ; *Corynebacterium/isolation & purification/genetics ; *Corynebacterium Infections/diagnosis/microbiology/drug therapy ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Meningitis, Bacterial/diagnosis/drug therapy/microbiology ; }, abstract = {OBJECTIVE: To report a case of Corynebacterium striatum meningitis and conduct a comprehensive literature review to determine the clinical presentation, microbiology, and treatment approaches for these patients.

MATERIALS AND METHODS: A 75-year-old male patient presented with headache and fever; however, bacterial cultures of cerebrospinal fluid (CSF) yielded negative results. Metagenomic next-generation sequencing (mNGS) of CSF subsequently identified Corynebacterium striatum meningitis as the causative agent for meningitis. A systematic search was performed across various databases encompassing systematic reviews, cohort studies, case series, and case reports involving patients diagnosed with Corynebacterium striatum meningitis regardless of age. Clinical presentation characteristics and the most frequently employed diagnostic technologies were obtained. A narrative summary of the findings is presented.

RESULTS: Corynebacterium striatum meningitis patients do not exhibit any specific age or sex predisposition or distinctive symptoms or signs. In patients with Corynebacterium striatum meningitis, CSF tests typically reveal an increased number of white blood cells (predominantly polymorphonuclear cells), elevated protein levels, and decreased glucose levels. Notably, the prevalence of antibiotic-resistant strains of Corynebacterium striatum has increased in recent years, leading to a gradual rise in antibiotic treatment failure rates. It is predicted that by 2030, vancomycin may be the sole effective drug available.

CONCLUSION: The possibility of Corynebacterium striatum infection should be considered during clinical diagnosis and laboratory testing procedures for bacterial meningitis. mNGS can serve as a supplementary gold standard in the diagnosis of bacterial meningitis, effectively enhancing the detection rate of rare pathogens.}, } @article {pmid40140706, year = {2025}, author = {Best, L and Dost, T and Esser, D and Flor, S and Gamarra, AM and Haase, M and Kadibalban, AS and Marinos, G and Walker, A and Zimmermann, J and Simon, R and Schmidt, S and Taubenheim, J and Künzel, S and Häsler, R and Franzenburg, S and Groth, M and Waschina, S and Rosenstiel, P and Sommer, F and Witte, OW and Schmitt-Kopplin, P and Baines, JF and Frahm, C and Kaleta, C}, title = {Metabolic modelling reveals the aging-associated decline of host-microbiome metabolic interactions in mice.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {40140706}, issn = {2058-5276}, support = {859890//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 859890//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 859890//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; FOR5042//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC2167//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 416 418087534//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC2167//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, abstract = {Aging is accompanied by considerable changes in the gut microbiome, yet the molecular mechanisms driving aging and the role of the microbiome remain unclear. Here we combined metagenomics, transcriptomics and metabolomics from aging mice with metabolic modelling to characterize host-microbiome interactions during aging. Reconstructing integrated metabolic models of host and 181 mouse gut microorganisms, we show a complex dependency of host metabolism on known and previously undescribed microbial interactions. We observed a pronounced reduction in metabolic activity within the aging microbiome accompanied by reduced beneficial interactions between bacterial species. These changes coincided with increased systemic inflammation and the downregulation of essential host pathways, particularly in nucleotide metabolism, predicted to rely on the microbiota and critical for preserving intestinal barrier function, cellular replication and homeostasis. Our results elucidate microbiome-host interactions that potentially influence host aging processes. These pathways could serve as future targets for the development of microbiome-based anti-aging therapies.}, } @article {pmid40140705, year = {2025}, author = {Garrido-Sanz, D and Keel, C}, title = {Seed-borne bacteria drive wheat rhizosphere microbiome assembly via niche partitioning and facilitation.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {40140705}, issn = {2058-5276}, abstract = {Microbial communities play a crucial role in supporting plant health and productivity. Reproducible, natural plant-associated microbiomes can help disentangle microbial dynamics across time and space. Here, using a sequential propagation strategy, we generated a complex and reproducible wheat rhizosphere microbiome (RhizCom) to study successional dynamics and interactions between the soil and heritable seed-borne rhizosphere microbiomes (SbRB) in a microcosm. Using 16S rRNA sequencing and genome-resolved shotgun metagenomics, we find that SbRB surpassed native soil microbes as the dominant rhizosphere-associated microbiome source. SbRB genomes were enriched in host-associated traits including degradation of key saccharide (niche partitioning) and cross-feeding interactions that supported partner strains (niche facilitation). In vitro co-culture experiments confirmed that helper SbRB strains facilitated the growth of partner bacteria on disaccharides as sole carbon source. These results reveal the importance of seed microbiota dynamics in microbial succession and community assembly, which could inform strategies for crop microbiome manipulation.}, } @article {pmid40140473, year = {2025}, author = {Brown, AA and Widdowson, M and Brandt, S and Mohammadzadeh, P and Rosenberg, JB and Jepsen, JRM and Ebdrup, BH and Hernández-Lorca, M and Bønnelykke, K and Chawes, B and Stokholm, J and Thorsen, J and Ibrahimi, P and Li, X and Sørensen, SJ and Rasmussen, MA}, title = {Associations of the gut microbiome and inflammatory markers with mental health symptoms: a cross-sectional study on Danish adolescents.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {10378}, pmid = {40140473}, issn = {2045-2322}, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Adolescent ; Cross-Sectional Studies ; Female ; Denmark/epidemiology ; *Inflammation/metabolism ; *Attention Deficit Disorder with Hyperactivity/metabolism/microbiology ; *Biomarkers ; *Depression/metabolism ; Anxiety/microbiology ; Mental Health ; Stress, Psychological/metabolism ; Feces/microbiology ; }, abstract = {Attention-deficit/hyperactivity disorder (ADHD) is a common neurodevelopmental disorder that often persists into adulthood and is accompanied by comorbid mental health problems. This cross-sectional cohort study analyzed 411 18-year-olds from the Danish COPSAC2000 birth cohort to investigate the relationship between the gut microbiome, fasting and postprandial systemic inflammation, ADHD symptoms, and symptoms of anxiety, stress, and depression. ADHD was assessed using the Adult ADHD Self-Report Scale (ASRS), while depression, stress, and anxiety were evaluated with the Depression, Anxiety, and Stress Scale 21 (DASS-21). Fecal metagenomic data and inflammation levels, measured as glycosylated protein A (GlycA), were analyzed following a standardized meal challenge. In males, higher ADHD symptom scores correlated significantly with increased abundance of a tryptophan biosynthesis pathway (MetaCyc Metabolic Pathways Database) and elevated fasting and postprandial GlycA levels (p < 0.05). While the severity of depression, anxiety, and stress symptoms showed weak associations with GlycA and the gut microbiome, our findings indicate a significant link between ADHD symptoms and postprandial inflammation, warranting further investigation into underlying mechanisms.}, } @article {pmid40140149, year = {2025}, author = {Ananda, A and Brigiyanti, LN and Widhiastuty, MP and Haryati, T and Suharti, and Ma'ruf, IF and Akhmaloka, }, title = {Characterization and molecular dynamics simulation of Lk2 lipase expressed in Pichia pastoris.}, journal = {Molecular biology reports}, volume = {52}, number = {1}, pages = {342}, pmid = {40140149}, issn = {1573-4978}, support = {12/II.7/HK/2023//RIIM Research Project Program, National Research and Innovation/ ; }, mesh = {*Lipase/genetics/metabolism/chemistry/isolation & purification ; *Molecular Dynamics Simulation ; Substrate Specificity ; Pichia/genetics/metabolism ; Hydrogen-Ion Concentration ; Fungal Proteins/genetics/metabolism/chemistry ; Recombinant Proteins/metabolism/genetics/isolation & purification/chemistry ; Molecular Docking Simulation ; Hydrolysis ; Saccharomycetales ; }, abstract = {BACKGROUND: Lipase is a versatile enzyme that serves as a biocatalyst in various industries. lk2 was successfully isolated from household waste compost through a metagenomic approach.

MATERIALS AND METHODS: lk2 from plasmid pPICZαA- lk2 was integrated into chromosomes of Pichia. pastoris GS115 using the electroporation method. Lk2 was expressed on Pichia. pastoris by methanol induction. The enzyme was purified through Ion Metal Affinity Chromatography Ni-NTA. The purified enzyme was characterized based on hydrolytic activity and in silico analysis.

RESULTS: Lk2 was successfully expressed as an extracellular protein in Pichia pastoris. The cell-free supernatant exhibited hydrolysis activity to para-nitro phenyl laurate. The purified protein showed 15 times activity compared to cell-free supernatant and the size at around 35 kDa following gel electrophoresis. The enzyme showed optimum activity at 60[o]C and pH 8. Lk2 preferred para nitro phenyl laurate as substrate. The enzyme's preference for medium-long carbon chains was corroborated by in silico analysis, which revealed favorable interactions between the enzyme and substrate, including affinity binding energy and optimal orientation of catalytic pocket to the substrate. Furthermore, the radius of gyration analysis of the Lk2 showed that the best structural compactness of Lk2 was at 60[o]C. This is in line with the optimal temperature of Lk2 activity. In addition, docking analysis found important substrate binding residues, including Tyr30, Ser85, Leu121, Leu163, Leu166, Leu 233, and Leu254 beside Ser85, Asp231, and His253 as triad catalytic.

CONCLUSION: Lk2 belongs to a thermotolerant and alkaline lipase, prefers a medium-length carbon chain as substrate and is confirmed by in silico analysis. Several amino acid residues were probed to be important for substrate binding residues. The data give valuable information to develop the possibility of Lk2 as an industry's enzyme.}, } @article {pmid40139349, year = {2025}, author = {Bilton, TP and Hickey, SM and Jonker, A and McRae, K and Hess, MK and Perry, BJ and Bryson, B and Henry, H and Bain, W and Booker, F and Veenvliet, B and Peers-Adams, J and Pile, G and Waller, E and Janssen, PH and Tiplady, KM and Reid, P and Muetzel, S and Agnew, M and Dodds, KG and McEwan, JC and Rowe, SJ}, title = {Milk fatty acids and rumen composition as proxy measures of enteric methane.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2024-25876}, pmid = {40139349}, issn = {1525-3198}, abstract = {Genomic selection is a powerful tool to reduce methane emissions in ruminants. However, it requires large-scale on-farm phenotypic measures of methane. Current technologies to measure methane emissions have several limitations and may not be suitable for lactating animals. Because enteric methane is closely linked to the fermentation process in the rumen, which in turn affects milk composition, breeding for low-methane ruminants may change the rumen microbial and milk composition. Consequently, these compositions may provide proxy measures of methane for use in selective breeding of low-methane ruminants. We investigated the effect on rumen and milk composition in sheep bred for divergent methane yield and the potential for generating proxy measures of methane emissions from rumen or milk samples in lactating ewes. Four hundred genotyped lactating ewes from a sheep research flock bred specifically for high and low-methane emissions had methane measured and rumen and milk samples collected approximately 6 wk post-lambing across 4 lactation years. Rumen samples were processed to generate VFA and metagenomic profiles of the rumen microbial community, and fatty acid profiles and mid-infrared spectra were generated for the milk samples. Although no differences in total fat, protein, and lactose percentages in the milk were found, the milk fatty acid profiles differed between methane selection lines, with higher PUFA and branched-chain fatty acids levels, and lower total SFA contents in ewes from the low-methane line. Higher proportions of acetate relative to propionate were found in the rumen samples from the low-methane ewes. Predictions of methane were obtained from the rumen VFA and metagenomic profiles and the fatty acid profiles and mid-infrared spectra from milk. These predictions formed the proxy methane measures and were heritable (between 0.12 to 0.36) and correlated (between 0.29 and 0.42) with the measured methane values. The genetic correlation between proxies and measured methane was between 0.52 and 0.71. The estimated efficiency of indirect selection for methane was higher for the milk sample proxies (49%-75%) than the rumen metagenomic profiles (45%-47%) and rumen VFA profiles (12%-38%). These results suggest that milk fatty acid, MIR spectroscopic, and rumen microbial composition phenotypes have the potential to be used as proxy measures of methane in lactating ruminants, with the milk-based proxies showing greater promise. Results show that the number of animals with methane proxy measures could be increased substantially and will enable access to breeding technology in countries with limited methane measurement infrastructure.}, } @article {pmid40139294, year = {2025}, author = {Hou, Y and Jia, R and Zhou, L and Zhang, L and Sun, W and Li, B and Zhu, J}, title = {Integrated rice-fish farming dynamically altered the metal resistances and microbial-mediated iron, arsenic, and mercury biotransformation in paddy soil.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {126107}, doi = {10.1016/j.envpol.2025.126107}, pmid = {40139294}, issn = {1873-6424}, abstract = {Given the global concern over heavy metal contamination in agricultural soil, comprehensive and in-depth investigations into the microbial ecological impacts of different agricultural practices on soil heavy metals and their biotransformation processes are both urgent and necessary. We employed metagenomic sequencing to investigate the impacts of integrated rice-fish farming on metal concentrations, metal resistance genes (MRGs), and microbial-mediated Fe, As, and Hg biotransformation processes within rice field. Our findings revealed that integrated rice-fish farming significantly reduced both the diversity and total abundance of MRGs. It also reduced the soil Al, Cd, Cu, Fe, Hg, Ni, Se, V, and Zn levels, with a marked correlation observed between metal concentration and MRGs profiles. Furthermore, integrated rice-fish farming markedly altered the microbial-mediated biotransformation processes for Fe, As, and Hg. It notably upregulated the abundance of Fe biotransformation genes, particularly those involved in the Fe gene regulation, oxidation, reduction, and storage. Biotransformation genes responsible for the As (III) oxidation and As methylation also exhibited increased abundances, along with mercury methylation and demethylation genes. Through metagenome assembled genomes (MAGs), we identified the Mycobacterium aubagnese from paddy soil which contained As oxidation genes and other multiple MRGs, exhibiting strong As remediation potential. Our findings demonstrated the potential of integrated rice-fish farming to reduce soil metal concentrations and mitigate soil metal pollution.}, } @article {pmid40139249, year = {2025}, author = {Taylor, JT and Lee, V and Dearlove, T and Jolly, M and Wierenga, JR and Dubrulle, J and Hodgkinson-Bean, J and Hunter, S and Gartrell, B and Morgan, K and McInnes, K and French, N and Holmes, EC and Geoghegan, JL}, title = {A Metagenomic Investigation into Apteryx rowi Dermatosis Identifies Multiple Novel Viruses and a Highly Abundant Nematode.}, journal = {Journal of wildlife diseases}, volume = {}, number = {}, pages = {}, doi = {10.7589/JWD-D-24-00115}, pmid = {40139249}, issn = {1943-3700}, abstract = {Sporadic cases of dermatosis have been reported in wild Ōkārito Rowi (Apteryx rowi), a species of brown kiwi, for over a decade. The disease exhibits distinctive features, including lesions, lichenification, and feather loss. Swab samples and full-thickness skin biopsies were collected during a survey of affected kiwi in 2023 for a metatranscriptome-based, total infectome investigation to identify any possible microbial agents associated with the disease. Our approach identified novel viruses as well as a species of nematode in high relative abundance. We found a highly abundant hepacivirus within the Flaviviridae, but only in some mild cases of dermatitis across all sample types, and in both active and chronic infections. In addition, we found a significant shift in the taxonomic composition of the nonviral microbiome within severe chronic dermatitis cases, particularly an increased abundance of transcripts from a Eucoleus sp. parasitic. Although determining the primary cause of disease in critically endangered wildlife such as Rowi remains challenging, our detection of novel and highly abundant microorganisms opens new lines of inquiry to investigate their potential association with dermatosis in this nationally iconic species.}, } @article {pmid40139192, year = {2025}, author = {Munneke, MJ and Yuan, Y and Preisner, EC and Shelton, CD and Carroll, DT and Kirchoff, NS and Dickson, KP and Cantu, JO and Douglass, MV and Calcutt, MW and Gibson-Corley, KN and Nicholson, MR and Byndloss, MX and Britton, RA and de Crécy-Lagard, V and Skaar, EP}, title = {A thiouracil desulfurase protects Clostridioides difficile RNA from 4-thiouracil incorporation, providing a competitive advantage in the gut.}, journal = {Cell host & microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2025.03.001}, pmid = {40139192}, issn = {1934-6069}, abstract = {Nucleotides are essential building blocks for major cellular macromolecules and are critical for life. Consequently, bacterial pathogens must acquire or synthesize nucleotides during infection. Clostridioides difficile is the most common hospital-acquired gastrointestinal infection, and nutrient acquisition is critical for pathogenesis. However, the impact of nucleotide metabolism on C. difficile infection remains unclear. Here, we discover that 4-thiouracil (4-TU), a pyrimidine analog present in the human gut, is toxic to commensal bacteria. 4-TU hijacks the uracil salvage pathway for incorporation into RNA through the uracil phosphoribosyltransferase activity encoded by PyrR and Upp. C. difficile can salvage 4-TU as a pyrimidine source through the enzymatic action of a thiouracil desulfurase (TudS), thereby contributing to C. difficile fitness in mice fed 4-TU or MiniBioreactor models of infection containing exogenous 4-TU. Collectively, these results reveal a molecular mechanism for C. difficile to utilize a poisonous pyrimidine analog in the vertebrate gut to outcompete commensal microbes.}, } @article {pmid40138989, year = {2025}, author = {Uprety, T and Swan, M and Kennedy, L and Bryant, U and Cassone, L and Loynachan, A and Janes, J and Evely, MM and Calvaruso, FC and Quick, M and Morgan, J and Abdelrazek, S and Lahmers, K and Carter, C and Erol, E}, title = {Retrospective investigation of 43 necropsy cases of Tyzzer disease in foals and partial genome sequence of Clostridium piliforme by shotgun metagenomics.}, journal = {Veterinary microbiology}, volume = {304}, number = {}, pages = {110489}, doi = {10.1016/j.vetmic.2025.110489}, pmid = {40138989}, issn = {1873-2542}, abstract = {Clostridium piliforme is an obligate intracellular filamentous bacterium that causes Tyzzer disease (TD) in many animals. The disease manifests as severe, multifocal necrotizing hepatitis, with a high fatality rate in foals. Through retrospective investigation, we detected C. piliforme in 43 equine necropsy cases from 2012 to 2024. Positive cases were diagnosed from February to July, peaking in May. The age of affected foals ranged from 4 days to 2 months. Histologically, all cases had necrotizing hepatitis with multifocal, coalescing pinpoint, tan or reddish foci. Since only a partial 16S rRNA gene sequence was available for the horse strain of C. piliforme, we used shotgun metagenomics to obtain its genome sequence from the liver of a necropsied foal with TD. The sequences obtained were compared against the NCBI NT/NR database with the highest number of reads and contigs aligning to Clostridium species. A complete 16S rRNA gene was obtained, showing the highest identity to a 16S rRNA gene of the horse strain of C. piliforme (99.05 %), followed by 98.02-96.71 % identities to rabbit and rodent strains of C. piliforme, indicating cross-species variation. Additional identified genes included alveolysin, exo-α-sialidase, flagellar and spore formation/vegetation, providing the first genetic evidence of virulence factors for C. piliforme. Furthermore, presence of genes encoding multidrug export and multidrug resistance proteins suggested C. piliforme could develop resistance to beta-lactams and fluoroquinolones. This study provides the first partial genome sequence of C. piliforme using a shotgun metagenomics hepatic sampling approach on a foal with TD.}, } @article {pmid40138908, year = {2025}, author = {Díaz-García, C and Sánchez-Osuna, M and Serra-Compte, A and Karakatsanidou, I and Gómez-Sánchez, I and Fidalgo, B and Barbuzana-Armas, C and Fittipaldi, M and Rosselli, R and Vinyoles, J and González, S and Pich, OQ and Espasa, M and Yáñez, MA}, title = {Mapping antimicrobial resistance landscape at a city scale sewage network.}, journal = {The Science of the total environment}, volume = {974}, number = {}, pages = {179127}, doi = {10.1016/j.scitotenv.2025.179127}, pmid = {40138908}, issn = {1879-1026}, abstract = {Wastewater is a valuable source for monitoring contaminants of biotic or abiotic origin. Antimicrobial resistance (AMR) has emerged as a public health threat that consists of the ability of microorganisms to resist the effects of antimicrobial compounds, rendering them very difficult or impossible to eradicate in case of infection. Considering the dissemination of antimicrobial resistance genes (ARGs) to a wide number of ecosystems, there is a need for the identification of hotspots that concentrate antimicrobial resistance determinants. A comprehensive investigation conducted at a city-scale in Sabadell (Barcelona, Spain) has integrated both phenotypic and genotypic methodologies, including metagenomics and culture-based techniques coupled with whole-genome sequencing (WGS), to monitor ARG presence in seven different spots of the sewage system. Metagenomics approach identified 262 ARG variants across analyzed sampling sites, grouped into 15 resistance categories. The most prevalent ARGs were macrolides-lincosamides-class B streptogramins (MLSB) (35.1 %) and beta-lactams (28.7 %), including carbapenems (5.9 %) and cephalosporins (5.3 %). MLSB resistance featured dominant msr(E) and mph(E) genes, the most abundant ARGs in our study. ARGs conferring resistance to beta-lactam were dominated by blaOXA-464, blaOXA-491, and blaNPS. Key genes for carbapenem (blaOXA-372, blaKPC-2) and cephalosporin (blaOXA-10, blaOXA-1) resistance were identified. The hospital sector exhibited the highest relative abundance of ARGs, dominated by beta-lactams, MLSB, and aminoglycosides. Wastewater treatment plant (WWTP) entrance points and residential areas displayed similar ARG profiles, while WWTP effluent and industrial zones had the lowest ARG levels. WWTP significantly reduced ARG presence (93.3 %). The characterization of antibiotic-resistant bacterial isolates found that most abundant ARGs were predominantly plasmid-borne, favoring ARG spread across bacterial genera. This finding confirmed the significant role of plasmids in ARG dissemination, increasing both diversity and prevalence within waterborne bacterial communities. City-scale surveillance programs can play a pivotal role in guiding effective measures to reduce the dissemination of AMR and mitigate their environmental impact.}, } @article {pmid40138872, year = {2025}, author = {Liang, T and Jiang, T and Liang, Z and Li, L and Chen, Y and Chen, T and Yang, L and Zhang, N and Dong, B and Xie, X and Gu, B and Wu, Q}, title = {Gut microbiota-driven BCAA biosynthesis via Staphylococcus aureus -expressed acetolactate synthase impairs glycemic control in type 2 diabetes in South China.}, journal = {Microbiological research}, volume = {296}, number = {}, pages = {128145}, doi = {10.1016/j.micres.2025.128145}, pmid = {40138872}, issn = {1618-0623}, abstract = {An increase in branched-chain amino acid (BCAA) levels can result in insulin resistance at different stages of type 2 diabetes (T2D), however, the causes of this increase are unclear. We performed metagenomics and metabolomics profiling in patients with prediabetes (PDM), newly diagnosed diabetes (NDDM), and post-medication type 2 diabetes (P2DM) to investigate whether altered gut microbes and metabolites could explain the specific clinical characteristics of different disease stages of T2D. Here we identify acetolactate synthase (ALS) a BCAA biosynthesis enzyme in Staphylococcus aureus as a cause of T2D insulin resistance. Compared with healthy peoples, patients with PDM, NDDM, and P2DM groups, especially in P2DM group, have increased faecal numbers of S. aureus. We also demonstrated that insulin administration may be a risk factor for S. aureus infection in T2D. The presence of ALS-positive S. aureus correlated with the levels of BCAAs and was associated with an increased fasting blood glucose (FBG) and insulin resistance. Humanized microbiota transplantation experiment indicated that ALS contributes to disordered insulin resistance mediated by S. aureus. We also found that S. aureus phage can reduced the FBG levels and insulin resistance in db/db mice. The ALS-positive S. aureus are associated with insulin resistance in T2D, opening a new therapeutic avenue for the prevention or treatment of diabetes.}, } @article {pmid40138860, year = {2025}, author = {Li, G and Srinivasan, V and Tooker, NB and Wang, D and Onnis-Hayden, A and Bott, C and Dombrowski, P and Pinto, A and Gu, AZ}, title = {Metagenomic analysis revealed community-level metabolic differences between full-scale EBPR and S2EBPR systems.}, journal = {Water research}, volume = {280}, number = {}, pages = {123509}, doi = {10.1016/j.watres.2025.123509}, pmid = {40138860}, issn = {1879-2448}, abstract = {Side-Stream Enhanced Biological Phosphorus Removal (S2EBPR) has emerged as a promising technology addressing certain challenges of conventional Enhanced Biological Phosphorus Removal (EBPR), notably stability in phosphorus removal, yet the underlying mechanisms are not fully understood. Metagenomic analysis presents a powerful approach to elucidate community-level metabolic differences between EBPR and S2EBPR configurations. In this study, we compared three EBPR and three S2EBPR activated sludge communities using metagenomic analysis at taxonomy, key functional pathways/genes, and polyphosphate-metabolism marker genes. Our analysis revealed larger genus-level diversity variance in S2EBPR communities, indicating distinct microbial community compositions influenced by different operational configurations. A higher diversity index in the S2EBPR than the EBPR was observed, and a higher Ca. Accumulibacter abundance was detected in EBPRs, whereas the fermentative candidate PAOs genera, including Ca. Phosphoribacter and Ca. Promineifilum, were more abundant in S2EBPR systems. EBPR and S2EBPR groups displayed similar gene and pathway abundance patterns related to core metabolisms essential for carbon and nitrogen metabolism. PolyP-metabolism marker gene phylogeny analysis suggested that exopolyphosphatase gene (ppx) showed better distinctions between EBPR and S2EBPR communities than polyphosphate kinase gene (ppk). This also highlighted the needs in fine-cale microdiversity analysis and finding novel Ca. Accumulibacter clades and species as resolved using the ppk gene. These findings provide valuable insights into AS community dynamics and metabolic functionalities, paving the way for further research into optimizing phosphorus removal processes in wastewater treatment systems.}, } @article {pmid40138725, year = {2025}, author = {Stachler, E and Gnirke, A and McMahon, K and Gomez, M and Stenson, L and Guevara-Reyes, C and Knoll, H and Hill, T and Hill, S and Messer, KS and Arizti-Sanz, J and Albeez, F and Curtis, E and Samani, P and Wewior, N and O'Connor, DH and Vuyk, W and Khoury, SE and Schnizlein, MK and Rockey, NC and Broemmel, Z and Mina, M and Madoff, LC and Wohl, S and O'Connor, L and Brown, CM and Ozonoff, A and Park, DJ and MacInnis, BL and Sabeti, PC}, title = {Establishing Methods to Monitor Influenza (A)H5N1 Virus in Dairy Cattle Milk, Massachusetts, USA.}, journal = {Emerging infectious diseases}, volume = {31}, number = {13}, pages = {}, doi = {10.3201/eid3113.250087}, pmid = {40138725}, issn = {1080-6059}, abstract = {Highly pathogenic avian influenza A(H5N1) virus has caused a multistate outbreak among US dairy cattle, spreading across 16 states and infecting hundreds of herds since its onset. We rapidly developed and optimized PCR-based detection assays and sequencing protocols to support H5N1 molecular surveillance. Using 214 retail milk samples from 20 states for methods development, we found that H5N1 virus concentrations by digital PCR strongly correlated with quantitative PCR cycle threshold values; digital PCR exhibited greater sensitivity. Metagenomic sequencing after hybrid selection was best for higher concentration samples, whereas amplicon sequencing performed best for lower concentrations. By establishing these methods, we were able to support the creation of a statewide surveillance program to perform monthly testing of bulk milk samples from all dairy cattle farms in Massachusetts, USA, which remain negative to date. The methods, workflow, and recommendations described provide a framework for others aiming to conduct H5N1 surveillance efforts.}, } @article {pmid40138143, year = {2025}, author = {Ali, KA and He, LX and Gao, F and Xia, ZA and Huang, H and Zeng, H and Hu, WH}, title = {Pathogen Detection in Spinal Infections: Next-Generation Sequencing Versus Conventional Microbiological Methods.}, journal = {Current medical science}, volume = {}, number = {}, pages = {}, pmid = {40138143}, issn = {2523-899X}, support = {(2023AFB646)//Hubei Provincial Natural Science Foundation of China/ ; (No. 2023020201010155)//Innovation Program of Wuhan Basic Research/ ; (2022135)//Educational Research Program of Huazhong University of Science and Technology/ ; }, abstract = {OBJECTIVE AND BACKGROUND: Early and accurate diagnosis of spinal infections, including spinal tuberculosis, is pivotal for effective treatment but remains challenging. This study aims to assess the diagnostic yield of metagenomic next-generation sequencing (mNGS) compared with that of conventional microbiological tests (CMTs) in identifying pathogens associated with spinal pathologies, with a special focus on infections leading to surgical interventions.

METHODS: We enrolled 85 patients who underwent spinal surgery, comprising 63 patients with clinically diagnosed spinal infections, including patients with spinal tuberculosis, and 22 patients with noninfectious spinal conditions. The procedures involved irrigation and debridement for persistent wound drainage, with subsequent DNA extraction from plasma and joint fluid for mNGS and CMT analysis.

RESULTS: Significantly increased C-reactive protein (CRP) levels were observed in patients with infections. The mNGS approach showed greater diagnostic sensitivity (92.06%) for detecting pathogens, including Mycobacterium tuberculosis, than did CMTs (36.51%). Despite its low specificity, mNGS had considerable negative predictive value (70.59%), underscoring its utility in ruling out infections.

CONCLUSIONS: The mNGS offers superior sensitivity over CMTs in the diagnosis of a variety of spinal infections, notably spinal tuberculosis. This study highlights the potential of mNGS in enhancing the diagnosis of complex spinal infections, thereby informing targeted treatment strategies.}, } @article {pmid40138008, year = {2025}, author = {Davasaz Tabrizi, E and Sevil, M and Arican, E}, title = {Bioinformatic strategies in metagenomics of chronic prostatitis.}, journal = {World journal of urology}, volume = {43}, number = {1}, pages = {188}, pmid = {40138008}, issn = {1433-8726}, mesh = {Male ; *Prostatitis/microbiology ; Humans ; Adult ; *Metagenomics ; *Computational Biology ; Chronic Disease ; Young Adult ; Middle Aged ; Microbiota/genetics ; }, abstract = {PURPOSE: Chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) is a prevalent urological condition in young men, significantly affecting quality of life due to persistent discomfort and neuropsychological symptoms. Despite its high prevalence, the etiology of CP/CPPS remains poorly understood. This study investigated urinary microbiota differences between CP/CPPS patients and healthy controls to identify microbial contributors, antibiotic resistance genes (ARGs), and virulence factors of dominant bacteria, as well as to explore potential therapeutic targets.

METHODS: Urine samples were collected from 58 CP/CPPS patients and 25 controls. Symptom severity was assessed by a specialist urologist using the NIH Chronic Prostatitis Symptom Index and UPOINT classification. Bacterial-specific 16 S rRNA sequencing was performed using nanopore technology, with bioinformatics analyses conducted via ONT guppy 5.0.11, NCBI and SLV 16 S bacterial taxonomic databases, UPGMA hierarchical clustering, and the Bacterial and Viral Bioinformatics Resource Center (BV-BRC). Pairwise comparisons were analyzed using the Mann-Whitney U test.

RESULTS: Distinct microbial diversity patterns were observed between patients and controls. Bacillus species were significantly enriched in CP/CPPS patients, while Enterococcus species predominated in controls. Younger patients exhibited unique microbiome profiles compared to older groups. Bioinformatics analyses identified ARGs and virulence factors associated with Bacillus species, implicating them in localized inflammation. Antibiotics like pleuromutilin or vancomycin were identified as potential therapeutic options, though experimental validation was beyond the study's scope.

CONCLUSION: These findings highlight microbial imbalances and provide a foundation for microbiome-targeted therapeutic strategies for CP/CPPS management in the future. Additionally, the identification of bacterial virulence factors and ARG provides insights into the potential mechanisms driving persistent symptoms. Future research with larger cohorts and experimental validation of the suggested therapeutic options may contribute to more effective treatment for CP/CPPS.}, } @article {pmid40137749, year = {2025}, author = {Mao, W and Wang, J and Li, T and Wu, J and Wang, J and Wen, S and Huang, J and Shi, Y and Zheng, K and Zhai, Y and Li, X and Long, Y and Lu, J and Guo, C}, title = {Hybrid Capture-Based Sequencing Enables Highly Sensitive Zoonotic Virus Detection Within the One Health Framework.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/pathogens14030264}, pmid = {40137749}, issn = {2076-0817}, support = {2023YFVA1005//National Natural Science Foundation of China International (Regional) Cooperation and Ex-change Project/ ; 51000-12240016//Startup Fund for Young Researchers of Sun Yat-sen University/ ; z1-2023005//Discipline Cluster of Oncology, Wenzhou Medical University/ ; }, mesh = {Animals ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; *One Health ; *SARS-CoV-2/genetics/isolation & purification ; Cattle ; Metagenomics/methods ; Genome, Viral/genetics ; Zoonoses/virology/diagnosis ; COVID-19/diagnosis/virology ; Viruses/genetics/isolation & purification ; Sensitivity and Specificity ; Limit of Detection ; }, abstract = {Hybrid capture-based target enrichment prior to sequencing has been shown to significantly improve the sensitivity of detection for genetic regions of interest. In the context of One Health relevant pathogen detection, we present a hybrid capture-based sequencing method that employs an optimized probe set consisting of 149,990 probes, targeting 663 viruses associated with humans and animals. The detection performance was initially assessed using viral reference materials in a background of human nucleic acids. Compared to standard metagenomic next-generation sequencing (mNGS), our method achieved substantial read enrichment, with increases ranging from 143- to 1126-fold, and enhanced detection sensitivity by lowering the limit of detection (LoD) from 10[3]-10[4] copies to as few as 10 copies based on whole genomes. This method was further validated using infectious samples from both animals and humans, including bovine rectal swabs and throat swabs from SARS-CoV-2 patients across various concentration gradients. In both sample types, our hybrid capture-based sequencing method exhibited heightened sensitivity, increased viral genome coverage, and more comprehensive viral identification and characterization. Our method bridges a critical divide between diagnostic detection and genomic surveillance. These findings illustrate that our hybrid capture-based sequencing method can effectively enhance sensitivity to as few as 10 viral copies and genome coverage to >99% in medium-to-high viral loads. This dual capability is particularly impactful for emerging pathogens like SARS-CoV-2, where early detection and genomic characterization are equally vital, thereby addressing the limitations of metagenomics in the surveillance of emerging infectious diseases in complex samples.}, } @article {pmid40137713, year = {2025}, author = {Shaw, CA and Soltero-Rivera, M and Profeta, R and Weimer, BC}, title = {Case Report: Shift from Aggressive Periodontitis to Feline Chronic Gingivostomatitis Is Linked to Increased Microbial Diversity.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/pathogens14030228}, pmid = {40137713}, issn = {2076-0817}, support = {UL1 TR001860/NH/NIH HHS/United States ; }, mesh = {Animals ; Cats ; *Microbiota/genetics ; *Cat Diseases/microbiology/diagnosis ; *Aggressive Periodontitis/microbiology ; Stomatitis/microbiology/veterinary ; Bacteria/genetics/classification/isolation & purification ; Disease Progression ; Mouth/microbiology ; Metagenomics ; Male ; }, abstract = {Aggressive Periodontitis (AP) and Feline Chronic Gingivostomatitis (FCGS) are two oral inflammatory diseases in cats with unknown etiology. Both conditions present with severe inflammation of the oral cavity and in FCGS it is found with additional deterioration of the non-keratinized mucosa. The oral microbiome is increasingly implicated in disease progression, but little is known about shifts in the microbial community during the AP and FCGS progression. To that end, we used deep metagenomic sequencing with total RNA on three longitudinal samples of the oral microbiome in a cat first diagnosed with AP that progressed to FCGS. This deep sequencing approach revealed that increased diversity at both the genus and species levels marked the shift from AP to FCGS, including increases in Porphyromonas and Treponema species, and decreased Streptobacillus species. The metatranscriptomes were then probed for expression of antimicrobial resistance genes and virulence factors. Disease-related genes that include cheY, and ompP5 were expressed in early AP and FCGS, while others like galU were only expressed in one or the other disease state. Both genus and species-level shifts were observed along the longitudinal microbiome samples with a noted increase in species diversity in the FCGS-associated microbiome. Corroborating that functional shifts accompany taxonomic changes, the AMR and virulence factor expression similarly changed between the sampling points. Together, these taxonomic and functional shifts indicate that AP and FCGS are potentially linked and may be marked by changes in the oral microbiome, which supports the development of microbial-based clinical diagnostics and therapeutics.}, } @article {pmid40137232, year = {2025}, author = {Krivonos, DV and Fedorov, DE and Klimina, KM and Veselovsky, VA and Kovalchuk, SN and Pavlenko, AV and Yanushevich, OO and Andreev, DN and Sokolov, FS and Fomenko, AK and Devkota, MK and Andreev, NG and Zaborovsky, AV and Tsaregorodtsev, SV and Evdokimov, VV and Krikheli, NI and Bely, PA and Levchenko, OV and Maev, IV and Govorun, VM and Ilina, EN}, title = {Gut Mycobiome Changes During COVID-19 Disease.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {11}, number = {3}, pages = {}, pmid = {40137232}, issn = {2309-608X}, support = {№ 122030900064-9//The government task/ ; №056-00108-22-01//The government task/ ; }, abstract = {The majority of metagenomic studies are based on the study of bacterial biota. At the same time, the COVID-19 pandemic has prompted interest in the study of both individual fungal pathogens and fungal communities (i.e., the mycobiome) as a whole. Here, in this work, we investigated the human gut mycobiome during COVID-19. Stool samples were collected from patients at two time points: at the time of admission to the hospital (the first time point) and at the time of discharge from the hospital (the second time point). The results of this study revealed that Geotrichum sp. is more represented in a group of patients with COVID-19. Therefore, Geotrichum sp. is elevated in patients at the time of admission to the hospital and underestimated at the time of discharge. Additionally, the influence of factors associated with the diversity of fungal gut microbiota was separately studied, including disease severity and age factors.}, } @article {pmid40136572, year = {2025}, author = {Malik, Y and Ali, I and Sajjad, A and Jing, L and Iqbal, I and Rehman, AU and Azam, T and Chen, X}, title = {Bacterial Diversity at Himalayan Pink Salt Extraction Site.}, journal = {Biology}, volume = {14}, number = {3}, pages = {}, pmid = {40136572}, issn = {2079-7737}, abstract = {Table salt, or sodium chloride, is extensively utilized in the culinary business as a flavoring agent, texture garnishing [...].}, } @article {pmid40136549, year = {2025}, author = {Pizzi, S and Conti, A and Di Canito, A and Casagrande Pierantoni, D and Foschino, R and Setati, ME and Vigentini, I}, title = {Endophytic Diversity in Vitis vinifera with Different Vineyard Managements and Vitis sylvestris Populations from Northern Italy: A Comparative Study of Culture-Dependent and Amplicon Sequencing Methods.}, journal = {Biology}, volume = {14}, number = {3}, pages = {}, pmid = {40136549}, issn = {2079-7737}, support = {150549//Italy/South Africa Joint Research Programme (ISARP) 2023-2025/ ; }, abstract = {This study aimed to investigate the endophytic microbial populations associated with wild and domesticated grapevines using both culture-based and culture-independent methods. Through culture-based methods, 148 endophytes were identified. The dominant fungal species included Aureobasidium pullulans, Alternaria alternata, and Cladosporium allicinum, while predominant bacterial species were Ralstonia pikettii, Nocardia niigatensis, and Sphingomonas echinoides. Culture-independent methods employed metagenomic techniques to explore microbial biodiversity, focusing on targeted amplification of bacterial 16S rRNA as well as fungal ITS and 26S rRNA gene regions. The main bacterial species identified included Halomonas sp., Sphingomonas sp. and Massilia sp., whereas the fungal population was dominated by Cladosporium sp., Malassezia sp. and Mucor sp. The findings revealed that vineyard management practices did not lead to statistically significant variations in microbial communities. The consistent presence of these genera across all samples suggests that they are stable components of the grapevine endophytic microbiota, remaining relatively unaffected by external environmental factors.}, } @article {pmid40136543, year = {2025}, author = {Claros, MG and Bullones, A and Castro, AJ and Lima-Cabello, E and Viruel, MÁ and Suárez, MF and Romero-Aranda, R and Fernández-Pozo, N and Veredas, FJ and Belver, A and Alché, JD}, title = {Multi-Omic Advances in Olive Tree (Olea europaea subsp. europaea L.) Under Salinity: Stepping Towards 'Smart Oliviculture'.}, journal = {Biology}, volume = {14}, number = {3}, pages = {}, pmid = {40136543}, issn = {2079-7737}, support = {TED2021-130015B-C21//Agencia Estatal de Investigación/ ; TED2021-130015B-C22//Agencia Estatal de Investigación/ ; PID2020-113324GB-I00//Agencia Estatal de Investigación/ ; PID2020-115853RR-C33//Agencia Estatal de Investigación/ ; PID2021-125805OA-I00//Agencia Estatal de Investigación/ ; RED2022-134072-T//Agencia Estatal de Investigación/ ; RYC2020-030219-I//Agencia Estatal de Investigación/ ; EMERGIA20_00286//Consejería de Economía, Conocimiento, Empresas y Universidad, Junta de Andalucía/ERDF-UE/ ; UMA20-FEDERJA-029//Consejería de Economía, Conocimiento, Empresas y Universidad, Junta de Andalucía/ERDF-UE/ ; PYC20 RE 009 CSIC EEZ//Consejería de Economía, Conocimiento, Empresas y Universidad, Junta de Andalucía/ERDF-UE/ ; }, abstract = {Soil salinisation is threatening crop sustainability worldwide, mainly due to anthropogenic climate change. Molecular mechanisms developed to counteract salinity have been intensely studied in model plants. Nevertheless, the economically relevant olive tree (Olea europaea subsp. europaea L.), being highly exposed to soil salinisation, deserves a specific review to extract the recent genomic advances that support the known morphological and biochemical mechanisms that make it a relative salt-tolerant crop. A comprehensive list of 98 olive cultivars classified by salt tolerance is provided, together with the list of available olive tree genomes and genes known to be involved in salt response. Na[+] and Cl[-] exclusion in leaves and retention in roots seem to be the most prominent adaptations, but cell wall thickening and antioxidant changes are also required for a tolerant response. Several post-translational modifications of proteins are emerging as key factors, together with microbiota amendments, making treatments with biostimulants and chemical compounds a promising approach to enable cultivation in already salinised soils. Low and high-throughput transcriptomics and metagenomics results obtained from salt-sensitive and -tolerant cultivars, and the future advantages of engineering specific metacaspases involved in programmed cell death and autophagy pathways to rapidly raise salt-tolerant cultivars or rootstocks are also discussed. The overview of bioinformatic tools focused on olive tree, combined with machine learning approaches for studying plant stress from a multi-omics perspective, indicates that the development of salt-tolerant cultivars or rootstocks adapted to soil salinisation is progressing. This could pave the way for 'smart oliviculture', promoting more productive and sustainable practices under salt stress.}, } @article {pmid40134914, year = {2025}, author = {Xu, J and Zeng, H and Li, H and Lin, X and Lin, T}, title = {Severe pneumonia caused by Chlamydia abortus complicated by hemophagocytic syndrome: a case report.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1547766}, pmid = {40134914}, issn = {2296-858X}, abstract = {BACKGROUND: Pneumonia caused by Chlamydia abortus (C. abortus) is uncommon, particularly when complicated by severe acute respiratory distress syndrome (ARDS) and multiple organ dysfunction syndrome (MODS). Hemophagocytic lymphohistiocytosis (HLH) is a rare and potentially fatal disease characterized by the uncontrolled activation and non-malignant expansion of macrophages and T lymphocytes. This report describes a case of severe pneumonia complicated by hemophagocytic lymphohistiocytosis, caused by Chlamydia abortus.

CASE INTRODUCTION: A 42-year-old female with no history of underlying medical conditions, no known exposure to poultry or avian animals, and no consumption of undercooked sheep or ewes contaminated with infected placenta, presented to the respiratory medicine department with a 3-day history of fever, cough, and sputum production. Initially diagnosed with community-acquired pneumonia, she was treated with piperacillin-tazobactam for 5 days. However, despite 12 h of high-flow oxygen therapy, her oxygenation did not improve, and she was transferred to the ICU, where she received additional treatments, including moxifloxacin and methylprednisolone. Her condition worsened further, prompting the initiation of veno-venous extracorporeal membrane oxygenation (VV-ECMO) and bronchoalveolar lavage for metagenomic next-generation sequencing (mNGS) analysis. The mNGS results identified Chlamydia abortus with a count of 180,791, leading to the cessation of moxifloxacin and the addition of omadacycline to her regimen. After 13 days of ECMO therapy, her condition improved, and the ECMO was discontinued. The endotracheal tube was successfully removed 15 days after intubation. However, 3 days later, the patient developed recurrent fever, pancytopenia, elevated ferritin, blood lipids, soluble CD25, and decreased natural killer cell activity, leading to a diagnosis of hemophagocytic lymphohistiocytosis (HLH). She was treated with ruxolitinib, etoposide, and other supportive medications. Despite treatment, her condition continued to deteriorate. Three days later, the family opted to discontinue therapy due to financial constraints. She passed away 12 h later.

CONCLUSION: Chlamydia abortus infection can result in severe acute respiratory distress syndrome (ARDS), necessitating prompt diagnosis and active clinical intervention. This case is unique due to the rare occurrence of HLH following Chlamydia abortus infection, a pathogen not commonly associated with this condition. Metagenomic next-generation sequencing (mNGS) offers a distinct advantage in rapidly and accurately identifying rare pathogen infections, while extracorporeal membrane oxygenation (ECMO) can be an effective treatment for severe pneumonia caused by Chlamydia abortus. It highlights the importance of early recognition and management of HLH in patients with severe, unexplained infections, particularly in those with unusual pathogens. Additionally, Chlamydia abortus infection may be complicated by HLH. Clinicians should remain vigilant for patients presenting with unexplained high fever, hepatosplenomegaly, and pancytopenia, and HLH screening should be initiated promptly. Early intervention can significantly improve patient survival rates.}, } @article {pmid40134637, year = {2025}, author = {Armstrong, E and Kulikova, M and Yee, N and Rishu, A and Muscedere, J and Sibley, S and Maslove, D and Boyd, JG and Evans, G and Detsky, M and Marshall, J and Taggart, LR and Friedrich, JO and Tsang, JLY and Duan, E and Ali Firdous, K and McCullagh, D and Findlater, A and Fowler, R and Daneman, N and Coburn, B}, title = {Impact of Antibiotic Duration on Gut Microbiome Composition and Antimicrobial Resistance: A Substudy of the BALANCE Randomized Controlled Trial.}, journal = {Open forum infectious diseases}, volume = {12}, number = {3}, pages = {ofaf137}, pmid = {40134637}, issn = {2328-8957}, abstract = {BACKGROUND: Maintaining a diverse gut microbiome and minimizing antimicrobial resistance gene (ARG) carriage through reduced antibiotic utilization may decrease antimicrobial resistance. We compared gut microbiome disruption and ARG carriage following 7 or 14 days of antibiotics for treatment of bacteremia in a substudy of the BALANCE randomized controlled trial.

METHODS: The BALANCE randomized controlled trial enrolled 3631 participants with bacteremia, who were randomized 1:1 to receive 7 or 14 days of antibiotics. Rectal swabs were collected from 131 participants and analyzed with metagenomic sequencing to characterize the gut microbiome and ARGs. The primary outcome was change in gut microbiome diversity at day 7 vs 14.

RESULTS: Forty-one participants (n = 28 in the 14-day group, n = 13 in the 7-day group) had samples available for the primary analysis, with an imbalance in piperacillin-tazobactam exposure between groups. Change in gut microbiome diversity at day 7 vs 14 was comparable between the 14-day group (median, 0.07; IQR, -0.46 to +0.51) and 7-day group (median, 0.19; IQR, -0.77 to +0.22; P = .49). Change in ARG abundance at day 7 vs 14 did not differ by treatment duration, nor did the abundance of individual ARGs. We did not observe any change in gut microbiome diversity or ARG carriage at enrollment vs day 7.

CONCLUSIONS: In this subset of patients from the BALANCE randomized controlled trial, we did not detect greater gut microbiome disruption or ARG carriage among participants who received 14 vs 7 days of antibiotics, but we were limited by small sample size and imbalances between groups.}, } @article {pmid40134271, year = {2025}, author = {Orme, W and Grimm, SL and Vella, DSN and Fowler, JC and Frueh, BC and Weinstein, BL and Petrosino, J and Coarfa, C and Madan, A}, title = {Relationships of Personality Traits With the Taxonomic Composition of the Gut Microbiome Among Psychiatric Inpatients.}, journal = {The Journal of neuropsychiatry and clinical neurosciences}, volume = {}, number = {}, pages = {appineuropsych20240126}, doi = {10.1176/appi.neuropsych.20240126}, pmid = {40134271}, issn = {1545-7222}, abstract = {OBJECTIVE: Through the brain-gut-microbiome axis, myriad psychological functions that affect behavior share a dynamic, bidirectional relationship with the intestinal microbiome. Little is known about the relationship between personality-a stable construct that influences social- and health-related behaviors-and the bacterial ecosystem. The authors of this exploratory study examined the relationship between general and maladaptive personality traits and the composition of the gut microbiome.

METHODS: In total, 105 psychiatric inpatients provided clinical data and fecal samples. Personality traits were measured with the five-factor model of personality, the Structured Clinical Interview for DSM-IV Axis II Personality Disorders, and the Personality Inventory for DSM-5; 16S ribosomal DNA sequencing and whole-genome shotgun sequencing methods were used on fecal samples. Machine learning (ML) was used to identify personality traits associated with bacterial variability and specific taxa.

RESULTS: Supervised ML techniques were used to classify traits of social detachment (maximum area under the receiver operating characteristic curve [AUROC]=0.944, R[2]>0.20), perceptual disturbance (maximum AUROC=0.763, R[2]=0.301), and hoarding behaviors (maximum AUROC=0.722) by using limited sets of discriminant bacterial species or genera. Established bacterial genera associated with psychosis (e.g., Peptococcus and Coprococcus) were associated with traits of perceptual disturbance. Hoarding behaviors were associated with a defined gut microbial composition that included Streptococcus, a known contributor to the development of pediatric autoimmune neuropsychiatric disorders.

CONCLUSIONS: Observations from this study are consistent with recent findings demonstrating person-to-person interactions as a mode of gut microbiome transmission. This study adds to the emerging literature on the intricate connections between brain and gut function, expanding the interdisciplinary field of psychiatric microbiology.}, } @article {pmid40133835, year = {2025}, author = {Gao, N and Feng, S and Yu, X and Zhao, J and Wan, Y and Yao, Z and Li, D}, title = {Diagnostic value of metagenomic next-generation sequencing combined by medical thoracoscopy surgery among infectious pleural effusion patients.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {407}, pmid = {40133835}, issn = {1471-2334}, support = {ZR2014HQ050//Natural Science Foundation of Shandong province/ ; }, mesh = {Humans ; Male ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; Female ; Middle Aged ; *Metagenomics/methods ; *Pleural Effusion/microbiology/diagnosis ; Aged ; *Thoracoscopy/methods ; Adult ; Bacteria/isolation & purification/genetics/classification ; Aged, 80 and over ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is a novel method for identifying pathogens in infectious diseases. This study aimed to explored the application value of mNGS in diagnosing pulmonary infections with pleural effusion, confirmed by medical thoracoscopy.

METHODS: We retrospectively reviewed 25 patients with pulmonary infections and pleural effusion between July 2020 and December 2021. All patients had their diagnosis confirmed by medical thoracoscopy to obtain tissue samples for both traditional testing and mNGS. Samples included pleural effusion, successive sputum, and tissue obtained through medical thoracoscopy. We wanted to assess how effective mNGS was in accurately diagnosing these infections.

RESULTS: This study found that the positive predictive value of mNGS (76% (19/25)) was significantly higher than that of traditional testing (32% (8/25)). The most commonly identified pathogens were Mycobacterium tuberculosis (n = 5), followed by Fusobacterium nucleatum (n = 4), Torque teno virus (n = 4), Streptococcus intermedius (n = 3), Peptostreptococcus stomatis (n = 2), Porphyromonas endodontalis (n = 2), and Campylobacter rectus (n = 2). The percentage of mNGS-positive cases was significantly higher than that from traditional testing for bacteria, but the superiority of mNGS for tuberculosis detection was insignificant. Ten cases were identified with mixed infections by mNGS, while no mixed infections were found by traditional testing.

CONCLUSIONS: Our study showed that using mNGS in combination with biopsy samples obtained through medical thoracoscopy resulted in higher positive rates compared to traditional tests and provided more evidence of pathogens for patients with infectious pleural effusion.}, } @article {pmid40133828, year = {2025}, author = {Lei, H and Liao, J and Lin, Y and Liu, T and Lei, W and Gao, W}, title = {Application of metagenomic next-generation sequencing in treatment guidance for deep neck space abscess.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {166}, pmid = {40133828}, issn = {1471-2180}, support = {82000950, 81972528, 82273053, 82203783//National Natural Science Foundation of China/ ; 82000950, 81972528, 82273053, 82203783//National Natural Science Foundation of China/ ; 2020YFC1316903//National Key Research and Development Program of China/ ; 2017004//Sun Yat-sen University/ ; 202201011050//Guangzhou Science, Technology and Innovation Commission/ ; 24QNPY345//Young Teacher Foundation of Sun Yat-sen University/ ; }, mesh = {Humans ; Male ; Female ; *High-Throughput Nucleotide Sequencing/methods ; *Neck/microbiology ; Middle Aged ; *Metagenomics/methods ; Retrospective Studies ; *Abscess/microbiology/drug therapy ; Adult ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Aged ; Bacteria/genetics/isolation & purification/classification/drug effects ; Treatment Outcome ; }, abstract = {BACKGROUND: Infectious etiologies of deep neck space abscess (DNSA) by conventional culture tests can be challenging, which also leads to frequent irrational antibiotic usage. Metagenomic next-generation sequencing (mNGS), as a novel method for analyzing the complex microbial ecosystem from clinical samples, has been utilized in clinical research and practice of various infectious diseases but deep neck space abscess. We here aimed to explore the clinical value of mNGS for pathogen detection and treatment guidance in DNSA patients compared with conventional culture tests.

METHODS: One hundred six patients diagnosed with DNSA were retrospectively enrolled and allocated into mNGS group and culture group according to whether mNGS was conducted. The pathogen detection effectiveness was of mNGS was compared with conventional culture. Effectiveness of mNGS-modified antimicrobial therapy was evaluated by comparing the treatment outcomes between two groups.

RESULTS: mNGS showed a significantly higher detection rate than conventional culture (p < 0.05) with faster result acquisition. Treatment success rate of patients in the mNGS group was significantly higher than in the culture group (RR: 1.22, 95%CI: 1.07-1.82, p = 0.033). Besides, patients in the mNGS group had shorter duration of irrational antimicrobial therapy, shorter hospital stay and less medical costs (p < 0.05).

CONCLUSIONS: mNGS is an effective technology for facilitating pathogen detection and improving treatment outcomes of DNSA patients.}, } @article {pmid40133298, year = {2025}, author = {Bhanu, P and Buchke, S and Hemandhar-Kumar, N and Varsha, P and Kiran, SKR and Vikneswaran, G and Alva, A and Basavaraj, GS and Kumar, J}, title = {Comparative metagenomic analysis of the oral microbiome in COVID-19 patients and healthy individuals.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {10303}, pmid = {40133298}, issn = {2045-2322}, support = {20210001//Bangalore Bioinnovation Centre/ ; }, mesh = {Humans ; *COVID-19/microbiology/virology ; *Mouth/microbiology/virology ; *Microbiota/genetics ; *Metagenomics/methods ; *SARS-CoV-2/genetics/isolation & purification ; Male ; Female ; Adult ; Middle Aged ; Metagenome ; Aged ; }, abstract = {COVID-19, caused by SARS-CoV-2, affects multiple body systems, including the oral cavity, where it may disrupt the oral microbiome in ways that contribute to disease pathology. Understanding the long-term interaction between SARS-CoV-2 and the oral microbiome is crucial, as it may reveal microbial markers valuable for diagnosing or monitoring persistent health issues in COVID-19 survivors. Metagenomic sequencing revealed significant microbial shifts in the oral microbiome of COVID-19 patients, showing reduced microbial diversity and increased prevalence of opportunistic pathogens compared to healthy individuals. Alpha diversity measures indicated lower microbial diversity and evenness, while beta diversity analyses demonstrated distinct microbial community compositions. Core microbiome analysis identified unique taxa in COVID-19 patients that may contribute to disease pathology, while differential abundance analysis highlighted specific taxa shifts, including an increase in potential pathogens. Our findings advance the understanding of microbial changes in the oral microbiome associated with COVID-19 and suggest potential targets for microbiome-based interventions. While these results indicate associations with possible health impacts, further research is needed to determine causative links and long-term implications for COVID-19 survivors. This foundational research highlights the potential for microbiome science to inform diagnostic tools, such as microbial markers for disease progression, and therapeutic approaches, including targeted probiotics, which could ultimately support better patient outcomes and public health strategies.}, } @article {pmid40132505, year = {2025}, author = {Wang, L and Zhang, W and Yao, J and Qi, Z and Liu, Y and Li, Z and Qu, J and Ma, Y and Zhang, Y}, title = {Effect of freeze-thaw cycle aging on biochar application in DEHP contaminated Mollisols: Insights from soil properties and microbial community.}, journal = {Ecotoxicology and environmental safety}, volume = {294}, number = {}, pages = {118082}, doi = {10.1016/j.ecoenv.2025.118082}, pmid = {40132505}, issn = {1090-2414}, abstract = {Biochar holds significant promise for remediation of organic pollutants. However, the impact of biochar on di-(2-ethylhexyl) phthalate (DEHP)-contaminated Mollisols after freeze-thaw cycles is largely unknown, according to the seasonal traits observed at high latitudes. In this study, fresh biochar (BC) was produced from corn straw, and freeze-thaw aging biochar (FBC) was prepared by simulating winter temperatures in the Mollisol region of Northeast China using BC as a precursor. Pot experiments were conducted to evaluate the effects of freeze-thaw aging on the detoxification efficiency of biochar, the improvement of soil physical and chemical properties, and the regulation of soil microbial community structure and functional genes. The results indicated that biochar after freeze-thaw cycling significantly improved the physical and chemical properties of Mollisols compared with the control, reducing DEHP content by 99.08 % after 28 days. Metagenomic sequencing further revealed the presence of microorganisms and genetic elements potentially involved in DEHP degradation in the soil. The treatment group with freeze-thaw aging biochar exhibited higher microbial diversity and abundance, particularly in Proteobacteria, Bacteroides, and Firmicutes. Analysis of the DEHP degradation pathway via benzoic acid route revealed an increase in the abundance of degraded functional genes/enzymes (benC-xylZ, pacL, catB, pcaG, mhpE, and mhpF). The up-regulation of nitrogen fixation genes and nitrification genes (amoB, hao, narG, nifD, and vnfH) along with a 49.19 % increase in soil microbial biomass nitrogen suggested that freeze-thaw aging biochar benefited nitrogen cycling. Furthermore, the feasibility of applying biochar to high-latitude agricultural settings was validated using pakchoi (Brassica rapa L. ssp. chinensis) as a test crop. These findings suggest that the freeze-thaw aging process enhances the effectiveness of biochar in remediating DEHP-contaminated Mollisols. This study offers a novel perspective on the restoration and improvement of Mollisol productivity in high-latitude regions through biochar application.}, } @article {pmid40132340, year = {2025}, author = {Roselli, WR and de Oliveira Miraglia, FF and de Mello Malta, F and Fernandes, GBP and Ribas, GC and de Oliveira Godeiro Júnior, C and Amgarten, DE and Nunes, FCG and Trindade, M and de Almeida Junior, JN and Martino, MDV and Santana, RAF and Pinho, JRR and Doi, AM}, title = {Diagnosis of Cladophialophora bantiana cerebral infection by clinical metagenomics.}, journal = {Diagnostic microbiology and infectious disease}, volume = {112}, number = {3}, pages = {116822}, doi = {10.1016/j.diagmicrobio.2025.116822}, pmid = {40132340}, issn = {1879-0070}, abstract = {PURPOSE: Cladophialophora bantiana is a rare cause of severe central nervous system phaeohyphomycosis.

RESULTS: A 44-year-old woman from Northeastern Brazil with a history of scotomas, mental confusion, and impaired coordination presented Magnetic Resonance Imaging with vasogenic edema and nodular enhancement in the left occipital lobe. Brain biopsy showed neutrophilic exudate with eosinophils, macrophages, giant multinucleated cells, and septate hyphae with a brown-colored birefringent wall and acute angle branching. Metagenomic analysis of the biopsy's total RNA revealed the presence of RNA sequences highly similari to C. bantiana. Culture confirmed the presence of olivaceous-gray suede-like to floccose colonies, with septate dematiaceous hyphae and long conidia chains from undifferentiated conidiophores, consistent with C. bantiana.

CONCLUSIONS: This case highlights the potential of metagenomic testing as a tool for early diagnosis of infections caused by uncommon fungal pathogens. To our knowledge, this is the first report of C. bantiana central nervous system infection in Brazil.}, } @article {pmid40135889, year = {2025}, author = {Nielsen, ME and Søgaard, KK and Karst, SM and Krarup, AL and Albertsen, M and Nielsen, HL}, title = {Application of rapid Nanopore metagenomic cell-free DNA sequencing to diagnose bloodstream infections: a prospective observational study.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0329524}, doi = {10.1128/spectrum.03295-24}, pmid = {40135889}, issn = {2165-0497}, abstract = {Bloodstream infections are a major cause of mortality, often leading to sepsis or septic shock. Rapid initiation of effective antimicrobial therapy is essential for survival; however, the current gold standard for identifying pathogens in bloodstream infections, blood culturing, has limitations with long turnaround time and poor sensitivity. This delay in refining empirical broad-spectrum antimicrobial treatments contributes to increased mortality and the development of antimicrobial resistance. In this study, we developed a metagenomic next-generation sequencing assay utilizing the Oxford Nanopore Technologies platform to sequence microbial cell-free DNA from blood plasma. We demonstrated proof of concept in a prospective observational clinical study including patients (n = 40) admitted to the emergency ward on suspicion of bloodstream infection. Study samples were drawn from the same venipuncture as a blood culture sample from the included patients. Nanopore metagenomic sequencing confirmed all microbiological findings in patients with positive blood cultures (n = 11) and identified pathogens relevant to the acute infection in an additional 11 patients with negative blood cultures. This proof-of-concept study demonstrates that culture-independent Nanopore metagenomic sequencing directly on blood plasma could be a feasible supplementary test for infection diagnostics in patients admitted with severe infections or sepsis. These findings support further studies on Nanopore metagenomic sequencing for sepsis diagnostics in larger cohorts to validate and expand the results from this study.IMPORTANCEThis study demonstrates the potential of Nanopore metagenomic sequencing as a rapid, culture-independent diagnostic tool for bloodstream infections, identifying pathogens missed by conventional blood cultures. The study highlights the method's promise in improving pathogen detection and warrants further validation in larger clinical studies.}, } @article {pmid40135776, year = {2025}, author = {Wang, J and Liu, Q and Jin, S and Yang, B and Wang, C and Tan, Y and Feng, W and Tao, J and Wang, H and Wang, Y and Yang, S and Cui, L}, title = {Characterization of bile microbiota in patients with obstructive jaundice associated with biliary tract diseases.}, journal = {Clinical and translational gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.14309/ctg.0000000000000841}, pmid = {40135776}, issn = {2155-384X}, abstract = {BACKGROUND: Cholangiocarcinoma (CHOL), a malignant tumor of the biliary system, is particularly concerning due to its high malignancy and poor prognosis, often leading to obstructive jaundice. The advent of metagenomic sequencing(mNGS) technology has expanded diagnostic capabilities, including the identification of microbes within tumors and their potential role in cancer progression.

OBJECTIVE: This study aims to explore the bacterial composition in bile from patients with obstructive jaundice of different etiologies and to investigate the association between bile microbiota and biochemical analytes, as well as their potential as biomarkers for diagnosis of obstructive jaundice diseases.

METHODS: Bile samples from patients with obstructive jaundice admitted to Beijing Friendship Hospital were collected and subjected to 16S rRNA and metagenomic sequencing. The study included patients diagnosed with benign biliary stricture, gallstone, and cholangiocarcinoma. Clinical data and bile chemical components were analyzed. The potential functional roles of the identified microbiota were predicted using bioinformatics tools.

RESULTS: The study enrolled 13 patients with benign biliary stricture, 19 with gallstones, and 10 with cholangiocarcinoma. Significant differences in bile chemical components and microbial diversity were observed among the groups. The bile microbiota was dominated by distinct phyla and genera across the groups, with Proteobacteria and Fusobacteriota enriched in benign biliary stricture, Firmicutes and Desulfobacterota in cholangiocarcinoma, and Synergistota in gallstone patients. Functional analysis revealed differences in gene functions related to metabolism and other biological processes. A correlation between bile microbiota and biochemical markers was established, and the combination of differential microbiota showed potential as a diagnostic marker for obstructive jaundice of different etiologies.

CONCLUSION: Bile microbiota varies significantly among patients with obstructive jaundice of different etiologies. The identified microbial signatures and their functional roles could serve as novel diagnostic markers and provide insights into the pathogenesis of biliary diseases.}, } @article {pmid40135668, year = {2025}, author = {Nassar, R and Nassar, M and Mohamed, L and Senok, A and Williams, D}, title = {Characterization and ex vivo modelling of endodontic infections from the Arabian Gulf region.}, journal = {International endodontic journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/iej.14227}, pmid = {40135668}, issn = {1365-2591}, support = {MBRU-CMRG2020-11//Mohammed Bin Rashid University of Medicine and Health Sciences/ ; 2201100262//University of Sharjah/ ; }, abstract = {AIM: The microbiota of endodontic infections in patients from the Arabian Gulf region (AGR) is largely unexplored. While research in different global regions has investigated the microbial composition of such infections, studies using shotgun metagenomic sequencing (SMS) alongside culture-dependent techniques (CDT) are limited. There are also few in vitro biofilm models that reflect the microbial profiles of endodontic infections. Therefore, by employing SMS and CDT, this research aimed to explore compositional and functional microbial profiles of endodontic infections from the AGR. The research also sought to develop ex vivo biofilms directly from endodontic infection samples.

METHODOLOGY: SMS and CDT were used to analyze 32 root canal samples from necrotic pulp. Patients' samples were categorized into two cohorts: symptomatic (n = 19) and asymptomatic (n = 13). Samples underwent sequencing followed by bioinformatic analysis to investigate microbial composition, resistome, virulome, and functional differences. Two representative samples (8R, 15R) were selected to develop ex vivo biofilms on hydroxyapatite coupons. Similarity between inoculum and developed biofilms was assessed using SMS and CDT. The reproducibility of developed biofilms was assessed based on microbial composition and relative abundance at the species level using correlation coefficient analysis.

RESULTS: Endodontic samples had high bacterial diversity, with a total of 366 bacterial species detected across the two cohorts. Several antibiotic resistance (n = 59) and virulence (n = 82) genes were identified, with no significant differences between the cohorts. CDT identified 28 bacterial species, with 71.4% of the isolated bacteria having phenotypic resistance to clinically relevant antibiotics. SMS showed that the ex vivo biofilms were polymicrobial. Biofilm derived from sample 15R had 9 species and was dominated by Enterococcus faecalis, while sample 8R had 12 species and was dominated by Streptococcus mutans. Pearson correlation analysis demonstrated a significant positive correlation between biological biofilm replicates, confirming the reproducibility of biofilm formation.

CONCLUSIONS: There was high bacterial diversity in root canal samples from necrotic pulp. Samples were shown to contain antibiotic resistance and virulence genes, with no differences evident between symptomatic and asymptomatic infections. A high number of isolated bacteria were resistant to clinically used antibiotics. Ex vivo biofilm models from clinical samples were successfully developed and reproducibly reflected a polymicrobial composition.}, } @article {pmid40135504, year = {2025}, author = {Pelto, J and Auranen, K and Kujala, JV and Lahti, L}, title = {Elementary methods provide more replicable results in microbial differential abundance analysis.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {2}, pages = {}, doi = {10.1093/bib/bbaf130}, pmid = {40135504}, issn = {1477-4054}, support = {952914//European Union's Horizon 2020 research and innovation programme/ ; }, mesh = {*Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; Humans ; Reproducibility of Results ; Computational Biology/methods ; Bacteria/genetics/classification ; }, abstract = {Differential abundance analysis (DAA) is a key component of microbiome studies. Although dozens of methods exist, there is currently no consensus on the preferred methods. While the correctness of results in DAA is an ambiguous concept and cannot be fully evaluated without setting the ground truth and employing simulated data, we argue that a well-performing method should be effective in producing highly reproducible results. We compared the performance of 14 DAA methods by employing datasets from 53 taxonomic profiling studies based on 16S rRNA gene or shotgun metagenomic sequencing. For each method, we examined how the results replicated between random partitions of each dataset and between datasets from separate studies. While certain methods showed good consistency, some widely used methods were observed to produce a substantial number of conflicting findings. Overall, when considering consistency together with sensitivity, the best performance was attained by analyzing relative abundances with a nonparametric method (Wilcoxon test or ordinal regression model) or linear regression/t-test. Moreover, a comparable performance was obtained by analyzing presence/absence of taxa with logistic regression.}, } @article {pmid40132013, year = {2025}, author = {Halo, BA and Aljabri, YAS and Yaish, MW}, title = {Drought-induced microbial dynamics in cowpea rhizosphere: Exploring bacterial diversity and bioinoculant prospects.}, journal = {PloS one}, volume = {20}, number = {3}, pages = {e0320197}, doi = {10.1371/journal.pone.0320197}, pmid = {40132013}, issn = {1932-6203}, mesh = {*Rhizosphere ; *Vigna/microbiology/genetics ; *Droughts ; *Soil Microbiology ; *Bacteria/genetics/classification/isolation & purification ; *Biodiversity ; *RNA, Ribosomal, 16S/genetics ; *Phylogeny ; Microbiota ; Plant Roots/microbiology ; }, abstract = {Rhizospheric bacterial communities in plants contribute to drought resilience by promoting plant-soil interactions, yet their biodiversity and ecological impacts are not fully characterized. In cowpeas, these interactions may be crucial in enhancing tolerance to drought conditions. In this study, cowpea plants were subjected to drought treatment, the soil attached to the roots was collected, environmental DNA (e-DNA) was extracted, and the bacterial communities were identified as amplicon sequence variants (ASVs) by metagenomics analysis of the 16S rRNA gene. Microbial communities under drought and control conditions were analyzed using taxonomy and diversity metrics. The sequencing results revealed 5,571 ASVs, and taxonomic analysis identified 1,752 bacterial species. Alpha and beta diversity analyses showed less conserved microbial community structures and compositions among the samples isolated from the rhizosphere under drought conditions compared to untreated samples, implying the enhancement effect of drought on species' biodiversity and richness. The differential accumulation analysis of the bacterial community identified 75 species that accumulated significantly (P ≤ 0.05) in response to drought, including 13 species exclusively present, seven absent, and 46 forming a high-abundance cluster within the hierarchical heatmap. These species were also grouped into specific clades in the phylogenetic tree, suggesting common genetic ancestry and potentially shared traits associated with drought tolerance. The differentially accumulated bacterial list included previously characterized species from drought and saline habitats. These findings suggest that drought stress significantly alters the composition and abundance of epiphytic bacterial communities, potentially impacting the rhizosphere's ecological balance and interactions with cowpeas. The results highlight microbial adaptations that enhance plant resilience through improved stress mitigation, providing meaningful understandings for advancing sustainable agriculture and developing microbial-based strategies to boost crop productivity in drought-prone regions.}, } @article {pmid40131885, year = {2025}, author = {Elsakhawy, OK and Roozitalab, A and Abouelkhair, MA}, title = {Genome sequence of a Tetraparvovirus ungulate 1 strain from a cow in Tennessee, USA.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0129124}, doi = {10.1128/mra.01291-24}, pmid = {40131885}, issn = {2576-098X}, abstract = {We report the genome sequence of a strain belonging to the species Tetraparvovirus ungulate 1 (hereafter referred to as UTPV1-1882), identified in a 4-month-old cow with respiratory disease in Tennessee, USA. The sequence data will improve the existing genomic database, which currently lacks information on these viruses in the United States.}, } @article {pmid40131631, year = {2025}, author = {Pavan, E and Pavón, JAR and Nunes, MRT and Carrasco, MM and Dos Santos, MAM and Slhessarenko, RD}, title = {Anellovirus species in the serum of acute febrile patients from Mato Grosso, central Western Brazil, 2019.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, pmid = {40131631}, issn = {1678-4405}, support = {FAPEMAT.0290384/2018//Fundação de Amparo à Pesquisa do Estado de Mato Grosso/ ; 88887.838336/2023-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 309750/2020-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 304781/2019-3//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 144451/2023-9 (PIBIC)//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, abstract = {The Anelloviridae family is one of the most diverse group of viruses within human virome, comprising 155 species distributed across 30 genera, four of which infect humans. Using a metagenomic approach to examine the frequency and diversity of viruses in the serum of patients with acute febrile illness in Mato Grosso during 2019, we identified and characterized two complete, three nearly complete and nine partial anellovirus genomes, including eleven putatively new species. Alphatorquevirus was the most prevalent genus (50%; n = 7), followed by Gammatorquevirus (35.7%; n = 5) and Betatorquevirus (14.3%; n = 2), consistent with global reports showing its dominance within Anelloviridae. Additionally, 65% of genomes were recovered from children, supporting higher anellovirus diversity and load in younger individuals.}, } @article {pmid40131463, year = {2025}, author = {Liu, H and Gan, Y and He, B and Liu, H and Zhuo, H and Tang, J and Xie, B and Shen, G and Ren, H and Jiang, X}, title = {mNGS technique was used to analyze the microbiome structure of intervertebral disc tissue in 99 patients with degenerative disc disease.}, journal = {European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society}, volume = {}, number = {}, pages = {}, pmid = {40131463}, issn = {1432-0932}, abstract = {OBJECTIVE: Whether bacterial hypotoxic infection in the intervertebral disc is the cause of disc degenerative disease (DDD) is controversial. The mNGS technique can provide valuable insights by obtaining more comprehensive evidence of the presence of bacteria in the intervertebral disc. This study was designed to analyze the characteristics of intervertebral microbiome structure in patients with lumbar disc degenerative disease and its correlation with clinical indicators.

METHODS: A total of 104 patients with lumbar disc degenerative diseases were included in this study. The surgically removed lumbar intervertebral disc tissues were collected for clinical culture and metagenomic second-generation sequencing (mNGS), and the consistency of the two microbial detection methods was compared.According to the collected clinical information, patients were grouped according to the modified Pfirrmann grading, Modic typing and age, and the differences of microbial communities detected by mNGS among different groups were compared, including α diversity analysis, β diversity analysis, species abundance difference analysis, etc. Spearman correlation between clinical features and generic relative abundance was calculated.

RESULTS: The effective culture results of 104 intervertebral disc tissue samples were only 19 cases positive, with a positive rate of 18.3% (19/104), and the mNGS detection results were positive in 99 cases, with a positive rate of 95.2% (99/104). According to the 19 samples with positive culture, nearly half 47.4% (9/19) of staphylococcus species were positive, and all the positive species were basically epidermal common colonization species or environmental common bacteria. At the same time, we conducted two times of mNGS sequencing for these 19 samples, and the consistency rate between the two sequencing results and the culture results was 84.2% (16/19). According to the results of mNGS detection, 250 species from 110 genera were detected in 99 positive samples. The results of group analysis showed that patients with lower degree of disc degeneration (modified Pfirrmann ≤ 4) and young patients (age < 45 years) had more abundant microbial communities in disc tissue (P < 0.05). Correlation analysis showed that there was a positive correlation between Arcobacter skirrowii and improved Pfirrmann classification at the species level (P < 0.01). There was a negative correlation between pseudomonas thermotolerans and modified Pfirrmann classification (P < 0.05). There was a positive correlation between Staphylococcus hominis and Modic typing scores (P < 0.05). Staphylococcus arlettae was negatively correlated with age (P < 0.05). At the genus level, Arcobacter had a significant positive correlation with the modified Pfirrmann grade and Modic classification (P < 0.05), Corynebacterium had a significant negative correlation with the modified Pfirrmann grade (P < 0.05), and Pseudomonas had a significant negative correlation with age (P < 0.05). After our follow-up of six months to one year, two of the patients included in this study eventually developed severe lumbar disc infection, and the rest did not develop infection.

CONCLUSIONS: This study proves that hypotoxic infection may be involved in the degeneration of intervertebral disc, and the bacterial species that cause this occult infection may be more abundant than previously thought. In addition, there was a significant correlation between the biome structure of these bacteria and clinical indicators. The hypothesis of the cause of this insidious infection has the potential to change the way the disease is treated.}, } @article {pmid40131352, year = {2025}, author = {Lu, W and Ji, R and Li, W}, title = {Invasive pulmonary and central nervous system aspergillosis: A case report and literature review.}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {}, number = {}, pages = {}, doi = {10.1556/030.2025.02528}, pmid = {40131352}, issn = {1588-2640}, abstract = {Invasive aspergillosis primarily affects individuals with compromised immune systems. This study endeavors to suggest the importance of early diagnosis and treatment related to central nervous system (CNS) aspergillosis. Recognizing the typical and atypical imaging characteristics of CNS aspergillosis enables the early and aggressive treatment of an otherwise rapidly fatal infection. We reported a case of an elderly patient with a history of non-Hodgkin lymphoma and prostate cancer who underwent repeated chemotherapy and subsequently experienced a sudden disturbance of consciousness. The diagnosis was affirmed through metagenomic next-generation sequencing (mNGS) of sputum and cerebrospinal fluid. The treatment encompassed systemic antifungal agents and intrathecal injection of amphotericin B. Metagenomic sequencing of sputum and cerebrospinal fluid detected Aspergillus fumigatus and Aspergillus flavus, leading to a diagnosis of invasive pulmonary and CNS aspergillosis. Although the patient actively received combined systemic antifungal drugs (voriconazole and amphoteric B liposome) and intrathecal injection of amphotericin B, he ultimately succumbed to the infection. A review of similar cases from PubMed and Medline from 2014 to 2024, encompassing 64 patients, showed that while early diagnosis and combination therapy have improved survival rates, outcomes remain suboptimal. Invasive aspergillosis has a high mortality rate and requires early diagnosis and treatment. Metagenomic sequencing of pathogenic microorganisms constitutes a convenient approach to facilitate the early diagnosis of aspergillosis. Voriconazole is the preferred treatment for invasive aspergillosis. When CNS aspergillosis emerges, it might be necessary to combine other systemic antifungal agents with intrathecal injection of amphotericin B.}, } @article {pmid40131312, year = {2025}, author = {Herazo-Álvarez, J and Mora, M and Cuadros-Orellana, S and Vilches-Ponce, K and Hernández-García, R}, title = {A review of neural networks for metagenomic binning.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {2}, pages = {}, doi = {10.1093/bib/bbaf065}, pmid = {40131312}, issn = {1477-4054}, support = {2022-21221825//National Agency for Research and Development/ ; EQM210185//Fondequip/ ; }, mesh = {*Metagenomics/methods ; *Neural Networks, Computer ; Humans ; Machine Learning ; Metagenome ; Deep Learning ; }, abstract = {One of the main goals of metagenomic studies is to describe the taxonomic diversity of microbial communities. A crucial step in metagenomic analysis is metagenomic binning, which involves the (supervised) classification or (unsupervised) clustering of metagenomic sequences. Various machine learning models have been applied to address this task. In this review, the contributions of artificial neural networks (ANN) in the context of metagenomic binning are detailed, addressing both supervised, unsupervised, and semi-supervised approaches. 34 ANN-based binning tools are systematically compared, detailing their architectures, input features, datasets, advantages, disadvantages, and other relevant aspects. The findings reveal that deep learning approaches, such as convolutional neural networks and autoencoders, achieve higher accuracy and scalability than traditional methods. Gaps in benchmarking practices are highlighted, and future directions are proposed, including standardized datasets and optimization of architectures, for third-generation sequencing. This review provides support to researchers in identifying trends and selecting suitable tools for the metagenomic binning problem.}, } @article {pmid40130931, year = {2025}, author = {Xia, T and Yang, J and Chen, S and Li, H and Xu, S and Guo, K and Hou, S}, title = {Recovery of 26 metagenome-assembled genomes from the phycosphere of the marine diatom Skeletonema tropicum.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0101324}, doi = {10.1128/mra.01013-24}, pmid = {40130931}, issn = {2576-098X}, abstract = {Metagenome-assembled genomes (MAGs) were recovered from the phycosphere of marine diatom Skeletonema tropicum, which has been long-term maintained in artificial seawater. Most MAGs were found to be highly complete (>90%) with minimum contaminations (<5%), which could serve as reference genomes to investigate the interactions between Skeletonema and their phycosphere microbiota.}, } @article {pmid40130924, year = {2025}, author = {Fuchsman, CA and Cram, JA and Huntemann, M and Riley, R and Foster, B and Foster, B and Roux, S and Palaniappan, K and Mukherjee, S and Reddy, T and Daum, C and Copeland, A and Chen, I-MA and Ivanova, NN and Kyrpides, NC and Graham, D and Eloe-Fadrosh, EA and Malkin, SY}, title = {Size-fractionated metagenomic depth profiles from two sulfidic stations in the Chesapeake Bay.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0008425}, doi = {10.1128/mra.00084-25}, pmid = {40130924}, issn = {2576-098X}, abstract = {We present 45 size-fractionated metagenomes collected from two stratified Chesapeake Bay mainstem stations during bottom water sulfidic conditions. This data set enables investigations into shifts in community structure and genomic potential across redox gradients and particle associations (free-living [0.2-3 µm], small [3-30 µm], medium [30-180 µm], and large [>180 µm] fractions).}, } @article {pmid40130858, year = {2025}, author = {Vaccaro, M and Pilat, AM and Gusmano, L and Pham, MTN and Barich, D and Gibson, A and Epalle, M and Frost, DJ and Volin, E and Slimak, ZC and Menke, CC and Fennessy, MS and Slonczewski, JL}, title = {Pond water microbiome antibiotic resistance genes vary seasonally with environmental pH and tannins.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0303424}, doi = {10.1128/spectrum.03034-24}, pmid = {40130858}, issn = {2165-0497}, abstract = {UNLABELLED: Microbial communities of small freshwater bodies interact dynamically with environmental factors in unknown ways. Longitudinal sampling of four ponds in Knox County, Ohio, revealed relationships among antibiotic resistance genes (ARGs) and environmental factors such as pH and tannin concentrations. For each site, microbial communities were collected by filtration, and metagenomes were analyzed by short-read sequencing. ARGs were quantified using the ShortBRED pipeline to detect and quantify hits to a marker set derived from the Comprehensive Antibiotic Resistance Database. The top 30 ARGs showed increased abundance at the end of the growing season. The top two ARGs with the largest marker hits encode components of a Stenotrophomonas drug efflux pump powered by proton-motive force (smeABC) and a mycobacterial global regulator that activates a drug pump and acid stress response (mtrA). The smeABC and mtrA prevalence showed a modest correlation with acidifying conditions (low pH and high tannic acids). Acidity amplifies the transmembrane pH difference component of the proton-motive force, thus increasing the cell's energy available for pump function and ARG expression. Association with microbial taxa was tested by the Kraken2/Bracken predictor of taxa profiles. The ARG profiles showed the strongest acid dependence in ponds with a high proportion of Proteobacteria, whereas a pond with high Cyanobacteria showed the lowest ARG counts. Efflux pumps such as SmeABC and transcriptional activation by MtrA incur large energy expenditures whose function may be favored at low external pH, where the cell's proton-motive force is maximal.

IMPORTANCE: Compared to rivers and lakes, pond microbial ecosystems are understudied despite close contact with agriculture and recreation. Environmental microbes offer health benefits as well as hazards for human contact. Small water bodies may act as reservoirs for drug-resistant organisms and transfer of antibiotic resistance genes (ARGs). Yet, the public is rarely aware of the potential for exposure to ARG-carrying organisms in recreational water bodies. Little is known about the capacity of freshwater microbial communities to remediate drug pollution and which biochemical factors may select against antibiotic resistance genes. This study analyzes how aquatic ARG prevalence may depend on environmental factors such as pH and tannic acid levels.}, } @article {pmid40130853, year = {2025}, author = {Lisha, W and Jiao, Q and Mengyuan, C and Jiajia, Q and Tianbin, T and Yilan, W and Linjie, H and Sufei, Y}, title = {Clinical evaluation of negative mNGS reports in sterile body fluids and tissues.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0201324}, doi = {10.1128/spectrum.02013-24}, pmid = {40130853}, issn = {2165-0497}, abstract = {Regarding metagenomics next-generation sequencing (mNGS) negative literature, there have been much discussions about methodology; thus, we collected clinical and laboratory information for retrospective evidence-based research. We retrospectively analyzed 150 negative mNGS results of patients suspected of having aseptic body fluid infections and divided them into a plasma group, cerebrospinal fluid (CSF) group, and others group according to the sample types. Based on the final laboratory and clinical diagnoses, the diagnostic accuracy of excluding infections in the plasma, CSF, and others groups of negative mNGS results were 72.0%, 40.4%, and 30.2%, respectively. The false-negative rates of the CSF and others group were relatively high. The positive impact rates of clinical application in the plasma, CSF, and others groups were 68.0%, 40.4%, and 25.6%, respectively. Three factors, including patient department distribution, admission symptoms, and doctors' judgment of patient infection were used to analyze the reasons for uncertain negative or false-negative results in mNGS. The clinical information analysis of false-negative patients' aims were to reduce the false-negative rate and improve the diagnostic accuracy of mNGS. On the selection of sampling timing in mNGS, within half a month after a patient develops suspected symptoms of infection, the earlier the mNGS test, the higher the true-negative rate.IMPORTANCEThere has been little research carried out on the diagnostic value of negative metagenomics next-generation sequencing (mNGS) results in clinical practice, especially for sterile body fluids. In the present study, plasma negative mNGS results showed the highest diagnostic accuracy for excluding infection. However, the cerebrospinal fluid and other mNGS false-negative rates were 59.6% and 69.8%, respectively. Our findings emphasized the role of negative mNGS results in practical clinical applications and clarified that patients, mNGS sampling time, and doctor's decision making were the key factors for the diagnosis of clinical infections. More attention should be paid to the diagnostic role of mNGS true negatives, the analysis of clinical patterns of false negatives, and improving the diagnostic accuracy of mNGS.}, } @article {pmid40130725, year = {2025}, author = {Filis, G and Bezantakou, D and Rigkos, K and Noti, D and Saridis, P and Zarafeta, D and Skretas, G}, title = {ProteoSeeker: A Feature-Rich Metagenomic Analysis Tool for Accessible and Comprehensive Metagenomic Exploration.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e2414877}, doi = {10.1002/advs.202414877}, pmid = {40130725}, issn = {2198-3844}, support = {T2EDK-02899//Operational Program Competitiveness, Entrepreneurship, and Innovation of the NSRF 2014-2020/ ; ATTP4-0340328//Operational Program "Attica 2014-2020" of the NSRF 2014-2020/ ; 101 079 363//Horizon Europe Programme/ ; 101 087 471//Horizon Europe Programme/ ; 101087471//HORIZON EUROPE Widening participation and spreading excellence/ ; }, abstract = {The vast majority of microbial diversity remains unculturable, limiting access to novel biotechnological resources. Advances in metagenomics have expanded the understanding of microbial communities, yet targeted protein discovery remains challenging. This study introduces ProteoSeeker, a command-line tool for streamlined metagenomic protein identification and annotation. ProteoSeeker operates in two primary modes: i) Seek mode, which screens the proteins according to user-defined protein families, and ii) Taxonomy mode, which uncovers the taxonomy of the host organisms. By automating key steps, ProteoSeeker reduces computational complexity, enabling time-efficient and comprehensive metagenomic analysis for both specialized and nonspecialized users. The efficiency of ProteoSeeker to achieve targeted enzyme discovery is demonstrated by identifying extremophilic enzymes with desired biochemical features, such as amylases for starch hydrolysis and carbonic anhydrases for CO2 capture applications. By democratizing functional metagenomics, ProteoSeeker is anticipated to accelerate biotechnology, synthetic biology, and biomedical research and innovation.}, } @article {pmid40130207, year = {2025}, author = {Lewin, S and Wehrhan, M and Wende, S and Sommer, M and Kolb, S}, title = {Variation of N cycle guilds of the rye rhizosphere microbiome is driven by crop productivity along a tillage erosion catena.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf020}, doi = {10.1093/ismeco/ycaf020}, pmid = {40130207}, issn = {2730-6151}, abstract = {Tillage erosion poses threats to crop yields. A transition towards more sustainable agricultural practices may be advanced by harnessing ecosystem services provided by plant microbiomes. However, targeting microbiomes at the agroecosystem scale necessitates bridging the gap to microscale structures of microbiomes. We hypothesized that differences of microbial nitrogen (N) cycle guilds in the rhizosphere of rye align with a soil catena that has been formed by tillage erosion. The rhizosphere was sampled at four sites, which captured a complete tillage erosion gradient from extremely eroded to depositional soils. The gene abundances characteristic of microbial N cycle guilds were assessed via metagenomics. The eroded sites showed the lowest plant productivity and soil mineral N availability, which was associated with an enrichment of glnA in the rhizosphere. Genes associated with dissimilatory nitrate-to-ammonium reducers and diazotrophy prevailed in the eroded soil profiles. The strongest correlations of the biomasses of rye plants along the catena with N cycle functions were observed for norBC. Thus, tillage erosion as a legacy of agricultural management aligns with substantial differences in rhizosphere microbiome functionality in N cycling. These microbiome differences were linked to plant shoot properties. Thus, the dynamics of the microbiome can be indirectly assessed by remote sensing.}, } @article {pmid40130011, year = {2025}, author = {Keenum, I and Jackson, SA and Eloe-Fadrosh, E and Schriml, LM}, title = {A standards perspective on genomic data reusability and reproducibility.}, journal = {Frontiers in bioinformatics}, volume = {5}, number = {}, pages = {1572937}, doi = {10.3389/fbinf.2025.1572937}, pmid = {40130011}, issn = {2673-7647}, abstract = {Genomic and metagenomic sequence data provides an unprecedented ability to re-examine findings, offering a transformative potential for advancing research, developing computational tools, enhancing clinical applications, and fostering scientific collaboration. However, effective and ethical reuse of genomics data is hampered by numerous technical and social challenges. The International Microbiome and Multi'Omics Standards Alliance (IMMSA, https://www.microbialstandards.org/) and the Genomic Standards Consortium (GSC, https://gensc.org) hosted a 5-part seminar series "A Year of Data Reuse" in 2024 to explore challenges and opportunities of data reuse and reproducibility across disparate domains of the genomic sciences. Addressing these challenges will require a multifaceted approach, including common metadata reporting, clear communication, standardized protocols, improved data management infrastructure, ethical guidelines, and collaborative policies that prioritize transparency and accessibility. We offer strategies to enable responsible and technically feasible data reuse, recognition of data reproducibility challenges, and emphasizing the importance of cross-disciplinary efforts in the pursuit of open science and data-driven innovation.}, } @article {pmid40129931, year = {2025}, author = {Lee, G and Rosa, BA and Fernandez-Baca, MV and Martin, J and Ore, RA and Ortiz, P and Cabada, MM and Mitreva, M}, title = {Distinct gut microbiome features characterize Fasciola hepatica infection and predict triclabendazole treatment outcomes in Peruvian patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1555171}, doi = {10.3389/fcimb.2025.1555171}, pmid = {40129931}, issn = {2235-2988}, mesh = {*Gastrointestinal Microbiome/drug effects/genetics ; Humans ; Peru ; Animals ; *Fasciola hepatica/drug effects/genetics ; *Fascioliasis/drug therapy/microbiology ; *Triclabendazole/therapeutic use ; Treatment Outcome ; *Anthelmintics/pharmacology/therapeutic use ; Female ; Male ; Adult ; Middle Aged ; Bacteria/classification/genetics/drug effects/isolation & purification ; Metagenomics ; Young Adult ; Feces/microbiology/parasitology ; }, abstract = {BACKGROUND: Fasciola hepatica, a globally distributed helminth, causes fasciolosis, a disease with significant health and economic impacts. Variability in triclabendazole (TCBZ) efficacy and emerging resistance are remaining challenges. Evidence suggests that the gut microbiome influences host-helminth interactions and is associated with anthelmintic effects, but its association with human F. hepatica infection and TCBZ efficacy is not well understood.

METHODS: In this study, we investigated the relationship between Fasciola hepatica infection and the gut microbiome through metagenomic shotgun sequencing of 30 infected and 60 age- and sex-matched uninfected individuals from Peru. Additionally, we performed a longitudinal analysis to evaluate microbiome dynamics in relation to TCBZ treatment response.

RESULTS AND DISCUSSION: Infection was associated with specific microbial taxonomic and functional features, including higher abundance of Negativibacillus sp900547015, Blautia A sp000285855, and Prevotella sp002299635 species, and enrichment of microbial pathways linked to survival under stress and depletion of pathways for microbial growth. Unexpectedly, we identified that responders to TCBZ treatment (who cleared infection) harbored many microbiome features significantly different relative to non-responders, both before and after treatment. Specifically, the microbiomes of responders had a higher abundance Firmicutes A and Bacteroides species as well as phospholipid synthesis and glucuronidation pathways, while non-responders had higher abundance of Actinobacteria species including several from the Parolsenella and Bifidobacterium genera, and Bifidobacterium shunt and amino acid biosynthesis pathways.

CONCLUSIONS: Our findings underscore the impact of helminth infection on gut microbiome and suggest a potential role of gut microbiota in modulating TCBZ efficacy, offering novel insights into F. hepatica-microbiome interactions and paving the way for microbiome-informed treatment approaches.}, } @article {pmid40129370, year = {2025}, author = {Lázaro, Á and Gómez-Ramírez, P and Vila-Donat, P and Cimbalo, A and Manyes, L}, title = {Effects of pumpkin and fermented whey on fecal microbiota profile against AFB1 and OTA exposure in Wistar rats.}, journal = {Toxicology mechanisms and methods}, volume = {}, number = {}, pages = {1-18}, doi = {10.1080/15376516.2025.2484636}, pmid = {40129370}, issn = {1537-6524}, abstract = {Mycotoxins perturb the gut microbiota performance. Bioactive compounds have been recently used as a new food strategy to diminish mycotoxins bioaccessibility and prevent their toxic effects on human and animal health. Male and female Wistar rats were exposed orally to twelve different diets containing aflatoxin B1 (AFB1) and/or ochratoxin A (OTA) with or without fermented whey (FW) and pumpkin (P) for 28 days. Fecal microbiota using 16S rRNA gene sequencing and subsequent metagenomics analysis were analyzed to study the effect of 28 day-exposure through diet of contaminated and enriched feed. QIIME 2 microbiome analysis package (version 2024.5) was used to analyze the demultiplexed data. Mycotoxins-functional ingredients combination contributed more to microbial phylogenetic faith α-diversity rather than the functional ingredients alone, while the same combination reported a microbial α-diversity enhancement in comparison to the mycotoxins alone. Proteobacteria phylum was reduced in rat samples fed with contaminated diets (AFB1, OTA and AFB1 + OTA), while there was an increase - although not in all groups - when adding the functional ingredients. The main difference between the sexes was found in FW + AFB1 + OTA group, with males (25%) showing higher % of Proteobacteria than females (1.86%). Phylogenetic diversity faith only focuses on microbial genetic (dis)similarity, not considering the biological function. Morganella morganii, a Proteobacteria found in some groups presents anticancer activity, but it is also related to inflammatory bowel disease and colorectal cancer. To sum up, both mycotoxins and functional ingredients trigger changes in the microbiota profile of Wistar rats in a sex-specific manner.}, } @article {pmid40129261, year = {2025}, author = {Boden, JS and Som, SM and Brazelton, WJ and Anderson, RE and Stüeken, EE}, title = {Evaluating Serpentinization as a Source of Phosphite to Microbial Communities in Hydrothermal Vents.}, journal = {Geobiology}, volume = {23}, number = {2}, pages = {e70016}, doi = {10.1111/gbi.70016}, pmid = {40129261}, issn = {1472-4669}, support = {NE/V010824/1//Natural Environment Research Council/ ; 80NSSC19K1427//NASA Planetary Science Division ISFM Program/ ; OCE-1536405//National Science Foundation/ ; 80NSSC18K0829//NASA Astrobiology Program/ ; 80NSSC19K1427//NASA Astrobiology Program/ ; }, mesh = {*Hydrothermal Vents/microbiology ; *Phosphites/chemistry/metabolism ; Microbiota ; Bacteria/genetics/metabolism/classification ; Phosphorus/metabolism/analysis ; }, abstract = {Previous studies have documented the presence of phosphite, a reduced and highly soluble form of phosphorus, in serpentinites, which has led to the hypothesis that serpentinizing hydrothermal vents could have been an important source of bioavailable phosphorus for early microbial communities in the Archean. Here, we test this hypothesis by evaluating the genomic hallmarks of phosphorus usage in microbial communities living in modern hydrothermal vents with and without influence from serpentinization. These genomic analyses are combined with results from a geochemical model that calculates phosphorus speciation during serpentinization as a function of temperature, water:rock ratio, and lithology at thermodynamic equilibrium. We find little to no genomic evidence of phosphite use in serpentinizing environments at the Voltri Massif or the Von Damm hydrothermal field at the Mid Cayman Rise, but relatively more in the Lost City hydrothermal field, Coast Range Ophiolite Microbial Observatory, The Cedars, and chimney samples from Old City hydrothermal field and Prony Bay hydrothermal field, as well as in the non-serpentinizing hydrothermal vents at Axial Seamount. Geochemical modeling shows that phosphite production is favored at ca 275°C-325°C and low water:rock ratios, which may explain previous observations of phosphite in serpentinite rocks; however, most of the initial phosphate is trapped in apatite during serpentinization, suppressing the absolute phosphite yield. As a result, phosphite from serpentinizing vents could have supported microbial growth around olivine minerals in chimney walls and suspended aggregates, but it is unlikely to have fueled substantial primary productivity in diffusely venting fluids during life's origin and evolution in the Archean unless substrates equivalent to dunites (composed of > 90 wt% olivine) were more common.}, } @article {pmid40128855, year = {2025}, author = {DeVeaux, AL and Hall-Moore, C and Shaikh, N and Wallace, M and Burnham, CD and Schnadower, D and Kuppermann, N and Mahajan, P and Ramilo, O and Tarr, PI and Dantas, G and Schwartz, DJ}, title = {Metagenomic signatures of extraintestinal bacterial infection in the febrile term infant gut microbiome.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {82}, pmid = {40128855}, issn = {2049-2618}, support = {R01AI155893//National Institute of Allergy and Infectious Diseases/ ; R01AI155893//National Institute of Allergy and Infectious Diseases/ ; R01AI155893//National Institute of Allergy and Infectious Diseases/ ; R01AI155893//National Institute of Allergy and Infectious Diseases/ ; R01AI155893//National Institute of Allergy and Infectious Diseases/ ; R01AI155893//National Institute of Allergy and Infectious Diseases/ ; T32GM139774/GM/NIGMS NIH HHS/United States ; P30DK052574/DK/NIDDK NIH HHS/United States ; P30DK052574/DK/NIDDK NIH HHS/United States ; P30DK052574/DK/NIDDK NIH HHS/United States ; R01HD062477//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; R01HD062477//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; R01HD062477//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; R01HD062477//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; U03MC00007/HRSA/HRSA HHS/United States ; U03MC00007/HRSA/HRSA HHS/United States ; U03MC00007/HRSA/HRSA HHS/United States ; U03MC00007/HRSA/HRSA HHS/United States ; 2021081/DDCF/Doris Duke Charitable Foundation/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Infant ; Female ; Male ; *Metagenomics/methods ; Infant, Newborn ; *Fever/microbiology ; *Feces/microbiology ; Bacteria/classification/genetics/isolation & purification ; Urinary Tract Infections/microbiology ; Case-Control Studies ; Bacterial Infections/microbiology ; Metagenome ; }, abstract = {BACKGROUND: Extraintestinal bacterial infections (EBIs), e.g., urinary tract infection, bacteremia, and meningitis, occur in approximately 10% of febrile infants younger than 60 days. Although many EBI-causing species commonly reside in the infant gut, proof that the digestive system is a pre-infection habitat remains unestablished.

RESULTS: We studied a cohort of febrile term infants < 60 days old who presented to one of thirteen US emergency departments in the Pediatric Emergency Care Applied Research Network from 2016 to 2019. Forty EBI cases and 74 febrile controls matched for age, sex, and race without documented EBIs were selected for analysis. Shotgun sequencing was performed of the gut microbiome and of strains cultured from the gut and extraintestinal site(s) of EBI cases, including blood, urine, and/or cerebrospinal fluid. Using a combination of EBI isolate genomics and fecal metagenomics, we detected an intestinal strain presumptively isogenic to the EBI pathogen (> 99.999% average nucleotide identity) in 63% of infants with EBIs. Although there was no difference in gut microbiome diversity between cases and controls, we observed significantly increased Escherichia coli relative abundance in the gut microbiome of infants with EBIs caused by E. coli. Infants with E. coli infections who were colonized by the putatively isogenic pathogen strain had significantly higher E. coli phylogroup B2 abundance in their gut, and their microbiome was more likely to contain virulence factor loci associated with adherence, exotoxin production, and nutritional/metabolic function.

CONCLUSIONS: The intestine plausibly serves as a reservoir for EBI pathogens in a subset of febrile term infants, prompting consideration of new opportunities for surveillance and EBI prevention among colonized, pre-symptomatic infants. Video Abstract.}, } @article {pmid40128848, year = {2025}, author = {Byrne, SR and DeMott, MS and Yuan, Y and Ghanegolmohammadi, F and Kaiser, S and Fox, JG and Alm, EJ and Dedon, PC}, title = {Temporal dynamics and metagenomics of phosphorothioate epigenomes in the human gut microbiome.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {81}, pmid = {40128848}, issn = {2049-2618}, support = {T32-ES007020//NIEHS Training Grant in Environmental Toxicology/ ; R01-OD028099-01//NIH Transformative Award/ ; R01-OD028099-01//NIH Transformative Award/ ; P30-ES002109//NIEHS Core Center Grant/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Feces/microbiology ; *Bacteria/genetics/classification/metabolism ; Mice ; Animals ; Epigenesis, Genetic ; Epigenome ; Female ; Male ; Phosphates/metabolism ; }, abstract = {BACKGROUND: Epigenetic regulation of gene expression and host defense is well established in microbial communities, with dozens of DNA modifications comprising the epigenomes of prokaryotes and bacteriophage. Phosphorothioation (PT) of DNA, in which a chemically reactive sulfur atom replaces a non-bridging oxygen in the sugar-phosphate backbone, is catalyzed by dnd and ssp gene families widespread in bacteria and archaea. However, little is known about the role of PTs or other microbial epigenetic modifications in the human microbiome. Here we optimized and applied fecal DNA extraction, mass spectrometric, and metagenomics technologies to characterize the landscape and temporal dynamics of gut microbes possessing PT modifications.

RESULTS: Exploiting the nuclease-resistance of PTs, mass spectrometric analysis of limit digests of PT-containing DNA reveals PT dinucleotides as part of genomic consensus sequences, with 16 possible dinucleotide combinations. Analysis of mouse fecal DNA revealed a highly uniform spectrum of 11 PT dinucleotides in all littermates, with PTs estimated to occur in 5-10% of gut microbes. Though at similar levels, PT dinucleotides in fecal DNA from 11 healthy humans possessed signature combinations and levels of individual PTs. Comparison with a widely distributed microbial epigenetic mark, m[6]dA, suggested temporal dynamics consistent with expectations for gut microbial communities based on Taylor's Power Law. Application of PT-seq for site-specific metagenomic analysis of PT-containing bacteria in one fecal donor revealed the larger consensus sequences for the PT dinucleotides in Bacteroidota, Bacillota (formerly Firmicutes), Actinomycetota (formerly Actinobacteria), and Pseudomonadota (formerly Proteobacteria), which differed from unbiased metagenomics and suggested that the abundance of PT-containing bacteria did not simply mirror the spectrum of gut bacteria. PT-seq further revealed low abundance PT sites not detected as dinucleotides by mass spectrometry, attesting to the complementarity of the technologies. Video Abstract CONCLUSIONS: The results of our studies provide a benchmark for understanding the behavior of an abundant and chemically reactive epigenetic mark in the human gut microbiome, with implications for inflammatory conditions of the gut.}, } @article {pmid40128686, year = {2025}, author = {Sun, N and Zhang, J and Guo, W and Cao, J and Chen, Y and Gao, D and Xia, X}, title = {Comparative analysis of metagenomic next-generation sequencing for pathogenic identification in clinical body fluid samples.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {165}, pmid = {40128686}, issn = {1471-2180}, support = {SY202214//Suqian Sci&Tech Program/ ; SY202214//Suqian Sci&Tech Program/ ; 81601857//National Natural Science Foundation of China/ ; YKK18216//Health Technology Development Special Foundation of Nanjing City/ ; YKK18216//Health Technology Development Special Foundation of Nanjing City/ ; }, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Body Fluids/microbiology/virology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/isolation & purification/classification ; Male ; Middle Aged ; Female ; Adult ; Aged ; Sensitivity and Specificity ; Young Adult ; Adolescent ; Cell-Free Nucleic Acids/genetics ; DNA, Bacterial/genetics ; Child ; Aged, 80 and over ; Child, Preschool ; }, abstract = {OBJECTIVES: This study aims to evaluate and compare the effectiveness of metagenomic next-generation sequencing (mNGS) in identifying pathogens from clinical body fluid samples, with a specific focus on the application of microbial cell-free DNA (cfDNA) mNGS.

METHODS: A total of 125 clinical body fluid samples were collected. All samples underwent mNGS targeting whole-cell DNA (wcDNA), with 30 samples also analyzed for cfDNA mNGS and 41 subjected to 16S rRNA NGS for comparative analysis. Patient clinical data, including culture results, were obtained from electronic medical records.

RESULTS: In comparison to cfDNA mNGS, the mean proportion of host DNA in wcDNA mNGS was 84%, significantly lower than the 95% observed in cfDNA mNGS (p < 0.05). Using culture results as a reference, concordance rates were 63.33% (19/30) for wcDNA mNGS and 46.67% (14/30) for cfDNA mNGS. Additionally, wcDNA mNGS showed greater consistency in bacterial detection with culture results, achieving a rate of 70.7% (29/41) compared to 58.54% (24/41) for 16S rRNA NGS. The sensitivity and specificity of wcDNA mNGS for pathogen detection in body fluid samples were 74.07% and 56.34%, respectively, when compared to culture results.

CONCLUSION: Whole-cell DNA mNGS demonstrates significantly higher sensitivity for pathogen detection and identification compared to both cfDNA mNGS and 16S rRNA NGS in clinical body fluid samples, particularly those associated with abdominal infections. However, the compromised specificity of wcDNA mNGS highlights the necessity for careful interpretation in clinical practice.}, } @article {pmid40128614, year = {2025}, author = {Diener, C and Holscher, HD and Filek, K and Corbin, KD and Moissl-Eichinger, C and Gibbons, SM}, title = {Author Correction: Metagenomic estimation of dietary intake from human stool.}, journal = {Nature metabolism}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42255-025-01284-z}, pmid = {40128614}, issn = {2522-5812}, } @article {pmid40128575, year = {2025}, author = {Yun, H and Seo, JH and Kim, YG and Yang, J}, title = {Impact of scented candle use on indoor air quality and airborne microbiome.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {10181}, pmid = {40128575}, issn = {2045-2322}, support = {RS-2023-00244833//National Research Foundation of Korea/ ; }, mesh = {*Air Pollution, Indoor/analysis ; *Microbiota ; *Particulate Matter/analysis ; *Air Microbiology ; Humans ; Bacteria/classification/isolation & purification ; Environmental Monitoring/methods ; Extracellular Vesicles ; }, abstract = {Indoor air quality has become a growing concern worldwide due to its significant impact on human health, particularly in residential environments where people spend most of their time. Many studies have examined particulate matter (PM) in indoor air and indoor bioaerosols. However, there is a significant lack of research on airborne micro-sized bacteria (m-AB) and nano-sized bacterial extracellular vesicles (n-ABE), particularly those produced by common household activities, such as burning scented candles. This study investigates changes in PM concentrations and indoor microbiome composition resulting from candle use. Air samples were collected from three locations in residential homes: at the candle-lit spot (CL), 3 m away (3m_CL), and 6 m away (6m_CL). PM10 concentrations peaked at 1.52 times the baseline at the source after 5 min of burning, while PM2.5 and PM1 remained elevated at 3m_CL and 6m_CL over time. Before burning, dominant m-AB genera included Phyllobacterium and Pseudomonas, while post-burning, Phyllobacterium myrsinacearum in n-ABE significantly increased, marking its first detection in indoor air. This suggests that existing airborne bacteria may undergo growth or apoptosis due to combustion byproducts. These findings highlight the importance of improving ventilation in indoor spaces to minimize health risks from prolonged exposure to airborne particles and bacterial vesicles.}, } @article {pmid40128554, year = {2025}, author = {Toma, R and Hu, L and Banavar, G and Vuyisich, M}, title = {Preparation of robust synthetic control samples and their use in a metatranscriptomic clinical test.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {10101}, pmid = {40128554}, issn = {2045-2322}, mesh = {Humans ; Reproducibility of Results ; *Transcriptome ; Metagenomics/methods ; Gene Expression Profiling/methods ; }, abstract = {Metatranscriptomics (MT) has the potential to revolutionize the field of molecular diagnostics. Due to the complexity of MT diagnostic models, positive and negative control materials for specific disease indications can be difficult to obtain. Controls must often be sourced directly from patients. This introduces logistical burdens, assay variability, and limits high throughput clinical laboratory operations. To overcome this limitation, we developed a method for generating Synthetic Control (SC) samples, which duplicate the nucleic acid signature of complex clinical specimens and produce the desired test outcome. SCs can be easily and cost-effectively produced in large quantities (> 100,000 SCs per amplification cycle), enabling high throughput diagnostic testing. Here, we report the generation of Synthetic Positive Control (SPC) samples. SPCs were validated and implemented in a clinical laboratory. The SPCs produced robust positive signals (average OC risk score of 0.996) and high levels of reproducibility (%CV of 0.29%) in a high throughput automated CLIA laboratory. SCs are a novel and useful method for the generation of high quality controls for MT-based diagnostic tests, and their adoption could herald the widespread use of MT tests in molecular diagnostics.}, } @article {pmid40128535, year = {2025}, author = {Han, H and Wang, Z and Zhu, S}, title = {Benchmarking metagenomic binning tools on real datasets across sequencing platforms and binning modes.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {2865}, pmid = {40128535}, issn = {2041-1723}, support = {62272105//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Metagenomics/methods ; *Benchmarking ; *Metagenome/genetics ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Software ; }, abstract = {Metagenomic binning is a culture-free approach that facilitates the recovery of metagenome-assembled genomes by grouping genomic fragments. However, there remains a lack of a comprehensive benchmark to evaluate the performance of metagenomic binning tools across various combinations of data types and binning modes. In this study, we benchmark 13 metagenomic binning tools using short-read, long-read, and hybrid data under co-assembly, single-sample, and multi-sample binning, respectively. The benchmark results demonstrate that multi-sample binning exhibits optimal performance across short-read, long-read, and hybrid data. Moreover, multi-sample binning outperforms other binning modes in identifying potential antibiotic resistance gene hosts and near-complete strains containing potential biosynthetic gene clusters across diverse data types. This study also recommends three efficient binners across all data-binning combinations, as well as high-performance binners for each combination.}, } @article {pmid40128181, year = {2025}, author = {Yan, W and Shi, X and Zhao, Y and Liu, X and Jia, X and Gao, L and Yuan, J and Liao, A and Yasui, H and Wang, X and Wang, X and Zhang, R and Wang, H}, title = {Microbiota-reprogrammed phosphatidylcholine inactivates cytotoxic CD8 T cells through UFMylation via exosomal SerpinB9 in multiple myeloma.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {2863}, pmid = {40128181}, issn = {2041-1723}, support = {2022-YGJC-61;2022-MS-219//Natural Science Foundation of Liaoning Province (Liaoning Provincial Natural Science Foundation)/ ; }, mesh = {Female ; Animals ; Mice ; Humans ; Cell Line ; *T-Lymphocytes, Cytotoxic/immunology ; *Gastrointestinal Microbiome ; *Phosphatidylcholines/immunology/metabolism ; *Multiple Myeloma/genetics/immunology/metabolism/pathology ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; *Exosomes/immunology/metabolism ; *Serpins/genetics/immunology/metabolism ; *Membrane Proteins/genetics/immunology/metabolism ; }, abstract = {Gut microbiome influences tumorigenesis and tumor progression through regulating the tumor microenvironment (TME) and modifying blood metabolites. However, the mechanisms by which gut microbiome and blood metabolites regulate the TME in multiple myeloma (MM) remain unclear. By employing16S rRNA gene sequencing coupled with metagenomics and ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry, we find that Lachnospiraceae are high and phosphatidylcholine (PC) are low in MM patients. We further show that Lachnospiraceae inhibits PC production from MM cells and enhances cytotoxic CD8 T cell function. Mechanistically, PC promotes Sb9 mRNA maturation in MM cells by LIN28A/B via lysophosphatidic acid, thus enhances exosamal Sb9 production. Exosamal Sb9 then reduces GZMB expression by suppressing tumor protein p53 (TP53) UFMylation via the competitive binding of TP53 with the ubiquitin-fold modifier conjugating enzyme 1 in CD8 T cells. We thus show that Lachnospiraceae and PC may be potential therapeutic targets for MM treatment.}, } @article {pmid40128138, year = {2025}, author = {Bai, M and Zhou, Z and Yin, M and Wang, M and Gao, X and Zhao, J}, title = {Corrigendum to "The use of metagenomic and untargeted metabolomics in the analysis of the effects of the Lycium barbarum glycopeptide on allergic airway inflammation induced by Artemesia annua pollen" [J. Ethnopharmacol. (2025) 337(Pt 1) 118816].}, journal = {Journal of ethnopharmacology}, volume = {}, number = {}, pages = {119657}, doi = {10.1016/j.jep.2025.119657}, pmid = {40128138}, issn = {1872-7573}, } @article {pmid40127879, year = {2025}, author = {Mirsalami, SM and Mirsalami, M}, title = {Assessing microbial ecology and antibiotic resistance genes in river sediments.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {}, number = {}, pages = {105738}, doi = {10.1016/j.meegid.2025.105738}, pmid = {40127879}, issn = {1567-7257}, abstract = {Anthropogenic activities greatly affect the Karon River leading to deterioration of water quality. This investigation utilizes environmental genomic techniques to delineate microbial populations, examine functional genomics, and evaluate the occurrence of virulence determinants and antibiotic resistance genes (ARGs) in fluvial sediment. Taxonomic assessment identified that Firmicutes were the predominant phyla, with Bacillus being the most abundant genus across samples. Functional analysis revealed the metabolic capabilities of sediment-associated bacteria, linking them to biogeochemical processes and potential health impacts. The S2 samples exhibited the highest virulence factor genes, while the S3 samples had the most ARGs (30), highlighting concerns about pathogenicity. Analyzing ARGs provides critical insights into environmental data collected, such as water quality parameters (e.g., nutrient concentrations, pH) or pollution levels, prevalence, and distribution of these resistance factors within the sediment samples, helping to identify potential hotspots of antibiotic resistance in the Karon River ecosystem. The study identified similar operational taxonomic units (OTUs) across sampling sites at the phylogenetic level, indicating a consistent presence of certain microbial taxa. However, the lack of variation in functional classification suggests that while these taxa may be present, they are not exhibiting significant differences in metabolic capabilities or functional roles. These findings emphasize the significance of metagenomic methods in understanding microbial ecology and antibiotic resistance in aquatic environments, suggesting a need for further research into the restoration of microbial functions related to ARGs and virulence factors.}, } @article {pmid40127846, year = {2025}, author = {Brito, J and Frade-González, C and Almenglo, F and González-Cortés, JJ and Valle, A and Durán-Ruiz, MC and Ramírez, M}, title = {Anoxic desulfurization of biogas rich in hydrogen sulfide through feedback control using biotrickling filters: Operational limits and multi-omics analysis.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132439}, doi = {10.1016/j.biortech.2025.132439}, pmid = {40127846}, issn = {1873-2976}, abstract = {Biodesulfurization is crucial for sustainable biogas purification from hydrogen sulfide (H2S). This study investigates the operational limits of anoxic biotrickling filters (BTFs) for treating biogas with high H2S concentrations (up to 20,000 ppmv) using nitrite, along with simulated interruptions in H2S supply. The BTF achieved a maximum elimination capacity of 312 g S-H2S m[-3] h[-1] with an H2S removal efficiency of 98 % at an empty bed residence time of 284 s. A proportional-integral-derivative (PID) feedback control system was successfully employed to maintain an H2S outlet concentration close to the requisite setpoint (100 and 500 ppmv) by adjusting the nitrite flow rate, thereby minimizing its accumulation. Continuous nitrite feeding after interruptions in H2S supply was essential to avoid H2S release due to sulfate-reducing bacteria. Multi-omics analyses, combining metagenomics and proteomics, revealed Sulfurimonas as the dominant sulfur-oxidizing bacteria, which downregulates most enzyme genes involved in nitrogen and sulfur metabolism in response to substrate starvation. These findings underscore the resilience of BTFs under extreme conditions and the value of multi-omics approaches in understanding microbial population dynamics, positioning BTFs as a robust solution for large-scale biogas purification.}, } @article {pmid40127751, year = {2025}, author = {Lim, TW and Huang, S and Burrow, MF and McGrath, C}, title = {A randomised crossover clinical trial of the efficacy of an ultrasonic cleaner combined with a denture cleanser on the microbiome on removable dentures among community-dwelling older adults.}, journal = {Journal of dentistry}, volume = {}, number = {}, pages = {105709}, doi = {10.1016/j.jdent.2025.105709}, pmid = {40127751}, issn = {1879-176X}, abstract = {OBJECTIVE: To evaluate and characterise the microbial compositional changes of removable dentures after interventions by comparing the efficacy of the test arm (a portable self-operated ultrasonic cleaner combined with an enzymatic peroxide-based denture cleanser solution) to the control arm (immersion of the denture in the same cleanser solution followed by conventional brushing).

MATERIALS AND METHODS: A prospective, single-blind, block-randomised, two-period crossover, controlled clinical trial was conducted, involving 56 community-dwelling older adults wearing removable acrylic dentures. They were block-randomized into the test/control or control/test denture cleaning sequence. Type IIB Restriction-site Associated DNA for Microbiome metagenomic sequencing was adopted to characterize the species-resolved microbial composition for denture biofilm.

RESULTS: For the intervention effect, the overall microbial richness in both arms was not significantly different based on the Chao 1 index (P=0.343). However, Beta diversity analysis (Jaccard qualitative distance matrix) demonstrated significant differences in the microbial community structures between the Test and Control arms after interventions, confirmed by the Permanova test (R[2]=0.01118, P=0.034). Among the opportunistic pathogenic bacteria, Pseudomonas aeruginosa was detected as one of the top 30 species by relative abundance at the end of the clinical trial, and Enterobacter kobei was significantly enriched in the control arm, as determined by LEfSe analysis.

CONCLUSIONS: The microbial community of denture biofilm samples after both interventions were significantly 'shifted' and had limited numbers of opportunistic pathogens, suggesting the interventions equally effective in mitigating the overall number of pathogenic bacteria.

CLINICAL SIGNIFICANCE: Denture cleaning intervention using ultrasonic cleaner combined with immersion in denture cleanser solution appears to be effective in shifting the denture microbiome with reduced pathogenic bacteria among community-dwelling denture wearers.}, } @article {pmid40127491, year = {2025}, author = {Penner, M and Klein, OJ and Gantz, M and Nintzel, FEH and Prowald, AC and Boss, S and Barker, P and Dupree, P and Hollfelder, F}, title = {Fluorogenic, Subsingle-Turnover Monitoring of Enzymatic Reactions Involving NAD(P)H Provides a Generalized Platform for Directed Ultrahigh-Throughput Evolution of Biocatalysts in Microdroplets.}, journal = {Journal of the American Chemical Society}, volume = {}, number = {}, pages = {}, doi = {10.1021/jacs.4c11804}, pmid = {40127491}, issn = {1520-5126}, abstract = {Enzyme engineering and discovery are crucial for a sustainable future bioeconomy. Harvesting new biocatalysts from large libraries through directed evolution or functional metagenomics requires accessible, rapid assays. Ultrahigh-throughput screening formats often require optical readouts, leading to the use of model substrates that may misreport target activity and necessitate bespoke synthesis. This is a particular challenge when screening glycosyl hydrolases, which leverage molecular recognition beyond the target glycosidic bond, so that complex chemical synthesis would have to be deployed to build a fluoro- or chromogenic substrate. In contrast, coupled assays represent a modular "plug-and-play" system: any enzyme-substrate pairing can be investigated, provided the reaction can produce a common intermediate which links the catalytic reaction to a detection cascade readout. Here, we establish a detection cascade producing a fluorescent readout in response to NAD(P)H via glutathione reductase and a subsequent thiol-mediated uncaging reaction, with a low nanomolar detection limit in plates. Further scaling down to microfluidic droplet screening is possible: the fluorophore is leakage-free and we report 3 orders of magnitude-improved sensitivity compared to absorbance-based systems, with a resolution of 361,000 product molecules per droplet. Our approach enables the use of nonfluorogenic substrates in droplet-based enrichments, with applicability in screening for glycosyl hydrolases and imine reductases (IREDs). To demonstrate the assay's readiness for combinatorial experiments, one round of directed evolution was performed to select a glycosidase processing a natural substrate, beechwood xylan, with improved kinetic parameters from a pool of >10[6] mutagenized sequences.}, } @article {pmid40127066, year = {2025}, author = {Pankovics, P and Takáts, K and Urbán, P and Mátics, R and Reuter, G and Boros, Á}, title = {Identification of a potential interspecies reassortant rotavirus G and avastrovirus 2 co-infection from black-headed gull (Chroicocephalus ridibundus) in Hungary.}, journal = {PloS one}, volume = {20}, number = {3}, pages = {e0317400}, doi = {10.1371/journal.pone.0317400}, pmid = {40127066}, issn = {1932-6203}, mesh = {*Rotavirus/genetics/isolation & purification ; Animals ; Hungary ; *Reassortant Viruses/genetics/isolation & purification ; *Charadriiformes/virology ; *Phylogeny ; *Genome, Viral ; Avastrovirus/genetics/isolation & purification/classification ; Coinfection/virology ; Rotavirus Infections/virology/veterinary ; Bird Diseases/virology/epidemiology ; Feces/virology ; Astroviridae Infections/virology/veterinary ; }, abstract = {The black-headed gull is the most common nesting gull species in Hungary. Based on the lifestyle and feeding habits of the black-headed gull, which is highly adapted to the human environment, they can be carriers and spreaders of potential human and other animal pathogens. Between 2014 and 2018 within the framework of the "Life Bird Ringing program" a total of 7 faecal samples were collected from gulls and one sample (MR04) was randomly selected for viral metagenomics and mass sequencing. 95.4% and 4% of the reads were classified into family Seadornaviridae and Astroviridae, respectively, and then were verified by RT-PCR method. In this study, the complete genome of a potential interspecies reassortant rotavirus (RV) strain gull/MR04_RV/HUN/2014 (PP239049-PP239059) and the partial ORF1ab, complete ORF2 of a novel avian nephritis virus strain gull/MR04_AAstV/HUN/2014 (PP239060) was discussed. The strain gull/MR04_RV/HUN/2014 was closely related to rotavirus G (RVG) viruses based on the proteins VP1-VP3, VP6, NSP2, NSP3, and NSP5, but it was more related to the human rotavirus B (RVB) strain Bang373 based on the NSP1, NSP4 and VP7, VP4 proteins, which is assumed to be the result of reassortment between different RVG-RVB rotavirus species. The strain gull/MR04_AAstV/HUN/2014 belonged to the genus Avastrovirus species avastrovirus 2 (AAstV-2) and is related to members of group 6 of avian nephritis viruses (ANVs), but based on the genetic distances it may be the first representative of a separate group. Additional gull samples were found to be negative by RT-PCR. Gulls, which are well adapted to the human environment, could potentially spread enterically transmitted viral pathogens like interspecies reassortant rotaviruses (RVG/RVB), but further molecular surveillance is needed to explore more deeply the viral communities of gulls or other related species adapted to human environments.}, } @article {pmid40127030, year = {2025}, author = {Abraham, A and Green, A and Ferrolino, J and Flerlage, T and Gowen, A and Allison, KJ and Suliman, AY and Bhakta, N and McArthur, J and Srinivasan, S and Hayden, RT and Hijano, DR}, title = {Utility and Safety of Bronchoalveolar Lavage for Diagnosis and Management of Respiratory Illnesses in Immunocompromised Children.}, journal = {Journal of the Pediatric Infectious Diseases Society}, volume = {14}, number = {3}, pages = {}, doi = {10.1093/jpids/piaf015}, pmid = {40127030}, issn = {2048-7207}, support = {//American Lebanese Syrian Associated Charities/ ; }, mesh = {Humans ; *Immunocompromised Host ; Retrospective Studies ; *Bronchoalveolar Lavage ; Child ; Child, Preschool ; Female ; Male ; *Respiratory Tract Infections/diagnosis/drug therapy ; Infant ; Adolescent ; Bronchoalveolar Lavage Fluid/microbiology ; }, abstract = {BACKGROUND: Acute respiratory illnesses (ARIs) in immunocompromised children have diverse causes, which can obscure accurate diagnosis and lead to unnecessary antimicrobial use. The risk-benefit ratio of bronchoalveolar lavage (BAL) in these patients is debated. This study aimed to evaluate the safety, yield, and utility of BAL in managing ARIs in immunocompromised children.

METHODS: This retrospective review examined BALs performed on immunocompromised children with ARI at St. Jude Children's Research Hospital between 2016 and 2021. Microbiological and molecular test results were reviewed from BAL, respiratory tract, and blood within 7 days of the BAL. The final ARI diagnosis was determined by the primary team, changes in antimicrobial management and adverse events were assessed.

RESULTS: BAL identified a potential pathogen in 84/137 (61.3%) of ARI episodes. BAL results contributed to changes in antimicrobial management in 120 (87.6%) cases and contributed to the ARI diagnosis in 106 (77.3%) cases. In 81 (59.1%) cases, ARI diagnosis was established solely from BAL results (infectious [33.3%], noninfectious [63%], multifactorial [3.7%]). BAL results usually agreed with the ARI diagnosis, but 31/137 (22.6%) were not concordant. Post-BAL, only 5 (3.6%) had increased supplemental oxygen > 24 hours, and 3 (3.4%) required new, persistent intubation. Consolidative or nodular pulmonary lesions and post-hematopoietic cell transplant had the highest BAL yields, with no significant differences based on the diffuseness of lesions.

CONCLUSIONS: BAL is a safe, high-yield diagnostic procedure in immunocompromised children, with results leading to changes in clinical management of ARI. Prospective studies are needed to generate BAL guidelines for ARI in this population.}, } @article {pmid40126889, year = {2025}, author = {Cheng, GB and Bongcam-Rudloff, E and Schnürer, A}, title = {Metagenomic Exploration Uncovers Several Novel 'Candidatus' Species Involved in Acetate Metabolism in High-Ammonia Thermophilic Biogas Processes.}, journal = {Microbial biotechnology}, volume = {18}, number = {3}, pages = {e70133}, doi = {10.1111/1751-7915.70133}, pmid = {40126889}, issn = {1751-7915}, support = {2018-01341//Svenska Forskningsrådet Formas/ ; }, mesh = {*Ammonia/metabolism ; *Biofuels ; *Acetates/metabolism ; *Bioreactors/microbiology ; Bacteria/metabolism/genetics/classification/isolation & purification ; Metagenomics ; Archaea/metabolism/genetics/classification ; Anaerobiosis ; Hot Temperature ; Metabolic Networks and Pathways/genetics ; Metagenome ; Methane/metabolism ; }, abstract = {Biogas reactors operating at elevated ammonia levels are commonly susceptible to process disturbances, further augmented at thermophilic temperatures. The major cause is assumed to be linked to inhibition followed by an imbalance between different functional microbial groups, centred around the last two steps of the anaerobic digestion, involving acetogens, syntrophic acetate oxidisers (SAOB) and methanogens. Acetogens are key contributors to reactor efficiency, acting as the crucial link between the hydrolysis and fermentation steps and the final methanogenesis step. Their major product is acetate, at high ammonia levels further converted by SAOB and hydrogenotrophic methanogens to biogas. Even though these functionally different processes are well recognised, less is known about the responsible organism at elevated temperature and ammonia conditions. The main aim of this study was to garner insights into the penultimate stages in three thermophilic reactors (52°C) operated under high ammonia levels (FAN 0.7-1.0 g/L; TAN 3.6-4.4 g/L). The primary objective was to identify potential acetogens and SAOBs. Metagenomic data from the three reactors were analysed for the reductive acetyl-CoA pathway (Wood-Ljungdahl Pathway) and glycine synthase reductase pathway. The results revealed a lack of true acetogens but uncovered three potential SAOB candidates that harbour the WLP, 'Candidatus Thermodarwinisyntropha acetovorans', 'Candidatus Thermosyntrophaceticus schinkii', 'Candidatus Thermotepidanaerobacter aceticum', and a potential lipid-degrader 'Candidatus Thermosyntrophomonas ammoiaca'.}, } @article {pmid40126871, year = {2025}, author = {Yang, S}, title = {The Economics of Cell-Free DNA Metagenomic Next-Generation Sequencing for Pathogen Detection.}, journal = {Clinical chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1093/clinchem/hvaf027}, pmid = {40126871}, issn = {1530-8561}, } @article {pmid40126624, year = {2025}, author = {Orellana, E and Zampieri, G and De Bernardini, N and Guerrero, LD and Erijman, L and Campanaro, S and Treu, L}, title = {Sustainable Food Waste Management in Anaerobic Digesters: Prediction of the Organic Load Impact by Metagenome-Scale Metabolic Modeling.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c11180}, pmid = {40126624}, issn = {1520-5851}, abstract = {The increasing urbanization has led to rising waste and energy demands, necessitating innovative solutions. A sustainable food waste management approach involves anaerobic codigestion with sewage sludge, enhancing biogas production while managing waste. Although this technology has been successfully tested, the biological mechanisms determining its efficiency are still poorly understood. This study leverages genome-scale metabolic modeling of 138 metagenome-assembled genomes to explore species interactions in lab-scale anaerobic reactors fed with sewage sludge to increasing proportions of food waste. The models showed positive correlations with experimental biogas production (CH4: r = 0.54, CO2: r = 0.66), validating their reliability. The dominant methanogen, Methanothrix sp., adapted its metabolism based on feedstock, affecting methane yields, which ranged from 2.5 to 3 mmol/g of volatile solids·h with sewage sludge to 10-14 mmol/g of VS·h with high food waste. The integration of extracellular enzymes into the models highlighted the role in methane production of pectin degradation, protein hydrolysis, and lipid metabolism, mediated by Proteiniphilum sp., Kiritimatiellae sp., and Olb16 sp. The study identified 475 mutualistic interactions involving amino acid, hydrogen, acetate, and phosphate exchange and 44 competitive interactions in hydrolytic and fermentative processes. These insights can help optimize anaerobic digestion and sustainable waste management in urban settings.}, } @article {pmid40126388, year = {2025}, author = {Zhang, Q and Su, T and Pan, Y and Wang, X and Zhang, C and Qin, H and Li, M and Li, Q and Li, X and Guo, J and Wu, L and Qin, L and Liu, T}, title = {Malus hupehensis leaves: a functional beverage for alleviating hepatic inflammation and modulating gut microbiota in diabetic mice.}, journal = {Food & function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d4fo05325g}, pmid = {40126388}, issn = {2042-650X}, abstract = {Malus hupehensis leaves (MHL), consumed as a daily beverage in Chinese folk tradition and recently recognized as a new food material, are abundant in polyphenols and bioactive compounds that demonstrate hypoglycemic, lipid-lowering, and anti-inflammatory effects. However, the antidiabetic mechanisms have not been fully elucidated. This study aimed to investigate the protective mechanisms of Malus hupehensis leaves' extract (MHLE) against type 2 diabetes mellitus (T2DM). The results showed that MHLE effectively ameliorated glucose and lipid metabolic abnormalities in db/db mice, and attenuated hepatic macrophage activation. Transcriptomic analysis of the liver revealed that MHLE primarily affects genes involved in inflammatory responses and inhibited the TLR4/MAPK pathway to reduce hepatic inflammation. Metagenomic sequencing identified changes in gut microbiota composition and showed that MHLE restored the abundance of Lachnospiraceae bacterium, Oscillospiraceae bacterium, and Clostridia bacterium while reducing the abundance of Escherichia coli, thereby ameliorating gut dysbiosis. The integrated regulation of metabolism, immune response, and the microbial environment by MHLE significantly alleviated symptoms of T2DM. This study offers strong scientific evidence for the potential use of MHL as a functional food.}, } @article {pmid40125310, year = {2025}, author = {Xiao, Y and Jing, D and Xiao, H and Mao, M and Kuang, Y and Shen, M and Lv, C and Jian, X and Peng, C and Chen, X}, title = {Metagenomics Analysis of Altered Gut Microbiome in Psoriasis and the Mediation Analysis: A Case-Control Study.}, journal = {Psoriasis (Auckland, N.Z.)}, volume = {15}, number = {}, pages = {45-54}, doi = {10.2147/PTT.S505283}, pmid = {40125310}, issn = {2230-326X}, abstract = {PURPOSE: Psoriasis is an inflammatory disease linked to gut microbiome dysbiosis. However, the mechanisms underlying gut microbiome changes caused by dietary habits in psoriasis remain unclear.

PATIENTS AND METHODS: We performed a case-control study including 64 psoriasis patients and 64 age-, sex-, and body mass index (BMI)-matched controls. Stool samples were collected for metagenomics sequencing. The differential abundance analysis was performed to identify differentially abundant taxa between psoriasis and control groups. The dietary intake frequency information of each included subject was obtained through face-to-face interviews. Mediation analysis was used to identify potential mediators of the gut microbiome alterations in psoriasis.

RESULTS: The gut microbiome of psoriasis patients was significantly alterated when compared to controls. Anaerostipes Hadrus, Blautia Wexlerae, and the other six species may be beneficial to psoriasis. However, Prevotella Copri and Eggerthellaceae could be pathogenic bacteria. The study also identified correlations between specific dietary habits and psoriasis, with the largest correlation observed between poultry consumption and psoriasis (OR=0.735, P=0.001), followed by red meat (OR=0.784, P=0.007) and fresh vegetables (OR=0.794, P=0.028). Mediation analysis revealed that Anaerostipes hadrus, Dorea longicatena, and Eggerthella lenta mediated the association between poultry and psoriasis.

CONCLUSION: The characteristics of intestinal flora in psoriasis patients were significantly different from controls. Intestinal flora mediated the association between diet and psoriasis to some extent. This study provides new insights for adjuvant treatments of psoriasis through dietary and intestinal microbiota interventions.}, } @article {pmid40125276, year = {2025}, author = {Zhu, X and Angelidaki, I and Zhang, T and Ju, F}, title = {Metagenomics Disentangles Differential Resistome Traits and Risks in Full-Scale Anaerobic Digestion Plants under Ambient, Mesophilic, and Thermophilic Conditions.}, journal = {ACS environmental Au}, volume = {5}, number = {2}, pages = {183-196}, doi = {10.1021/acsenvironau.4c00071}, pmid = {40125276}, issn = {2694-2518}, abstract = {Anaerobic digestion (AD) systems are vital for converting organic waste to green bioenergy but also serve as a non-negligible environmental reservoir for antibiotic-resistance genes (ARGs) and resistant bacteria of environmental and human health concerns. This study profiles the antibiotic resistome of 90 full-scale biogas reactors and reveals that AD microbiomes harbor at least 30 types and 1257 subtypes of ARGs, of which 16% are located on plasmids showing potential mobility. The total abundance of AD-ARGs ranges widely from 0.13 to 7.81 copies per cell and is distributed into 42-739 subtypes, significantly influenced (P < 0.05) by operational conditions like digestion temperature and substrate types. Compared with the ambient and mesophilic digesters, the thermophilic digesters harbor a significantly lower abundance and diversity as well as greatly reduced mobility and host pathogenicity levels (all P < 0.05) of ARGs, revealing that a higher digestion temperature mitigates the overall resistome risks. The comprehensive analysis of basic traits and key traits of the AD resistome is demonstrated to provide crucial quantitative and qualitative insights into the diversity, distribution pattern, and health risks of ARGs in full-scale AD systems. The revealed knowledge offers new guidance for improving environmental resistome management and developing oriented mitigation strategies to minimize the unwanted spread of clinically important antimicrobial resistance from AD systems.}, } @article {pmid40124740, year = {2025}, author = {Brucato, N and Lisant, V and Kinipi, C and Kik, A and Besnard, G and Leavesley, M and Ricaut, FX}, title = {Influence of betel nut chewing on oral microbiome in Papua New Guinea.}, journal = {Evolution, medicine, and public health}, volume = {13}, number = {1}, pages = {36-44}, doi = {10.1093/emph/eoae030}, pmid = {40124740}, issn = {2050-6201}, abstract = {BACKGROUND AND OBJECTIVES: For thousands of years, betel nut has been used as a psychoactive agent in Asian and Oceanian populations. Betel nut chewing was associated with the alteration of human oral microbiome and with diseases such as oral cancer and periodontitis, but only in populations of Asian cultural background. We studied the influence of betel nut chewing on the oral microbiome in Papua New Guinea, where half of the population uses betel nut and the prevalence of these diseases is one of the highest in the world.

METHODOLOGY: We characterized the oral microbiomes of 100 Papua New Guineans. We defined two cohorts of betel chewers (n = 50) and non-chewers (n = 50) based on a genetic approach to identify the presence of betel nut in saliva. We statistically compared the alpha and beta microbial diversities between the two cohorts. We performed linear discriminant analyses to identify bacterial species more prevalent in each cohort.

RESULTS: We found that oral microbial diversity is significantly different between betel chewers and non-chewers. The dysbiosis observed in betel chewers, led to an increase of pathogenic bacterial species including Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia, known to be in the aetiology of periodontal diseases.

CONCLUSIONS AND IMPLICATIONS: Our study strongly supports the alteration of human oral microbiome by betel nut use, potentially leading to periodontal diseases. It also shows the need to consider local specificities (e.g. different habits, betel nut types, and oral microbial diversities) to better characterize the impact of betel nut chewing on health.}, } @article {pmid40124696, year = {2025}, author = {Li, S and Zhang, S and Zhou, T and Ge, Z and Li, Y and Zhang, J and Zhu, Y and Li, S}, title = {The second generation metagenomic sequencing of cerebrospinal fluid for diagnosis of non-eschar scrub typhus.}, journal = {Oxford medical case reports}, volume = {2025}, number = {3}, pages = {omae198}, doi = {10.1093/omcr/omae198}, pmid = {40124696}, issn = {2053-8855}, abstract = {Tsutsugamushi disease, is an infectious disease transmitted by ticks and caused by the rickettsiella. It is characterized by eschar, fever, rash, and flu-like symptoms. However, diagnosing atypical cases without an eschar and with negative Weil-Felix test results poses a significant diagnostic challenge. This study presents a noteworthy case of non-eschar typhus which was effectively diagnosed using advanced next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) samples.}, } @article {pmid40124394, year = {2025}, author = {Ma, CM and Zhang, FS and Zhao, XH and Yang, Y and Wang, B and Wang, Y and Liu, XF and Bian, X and Xu, ZX and Zhang, G and Qu, LZ and Zhang, N}, title = {Genistein improves depression-like behavior in rats by regulating intestinal flora and altering glutamate gene expression.}, journal = {Current research in food science}, volume = {10}, number = {}, pages = {101020}, doi = {10.1016/j.crfs.2025.101020}, pmid = {40124394}, issn = {2665-9271}, abstract = {Depression is a mental disorder, and genistein is known to have antidepressant effects, but its mechanism of action is still unclear. Here, the mechanism of genistein improving depression based on gut microbiota was explored using classic behavioral indicators of depression combined with genomic technology. The behavioral evaluation showed that rats gavaged with 20-40 mg/kg genistein showed an increase in body weight, glucose preference, absenteeism score, body temperature, and 5-hydroxytryptamine (5-HT) content, while a decrease in adrenocorticotropic hormone (ACTH) and corticosterone (CORT) content compared to the depression rat model group, but there was no significant difference compared to the positive control (fluoxetine). The results of high-throughput sequencing showed that genistein increased the relative abundance of Firmicutes and Actinobacteriota and decreased the relative abundance of Bacteroidota at the phylum level. At the genus level, the abundance of Bifidobacterium, a short-chain fatty acid producing bacterium, was increased. Furthermore, metagenome results revealed that the antidepressant effect of genistein can be achieved by promoting glutamate metabolism, increasing glutamic acid decarboxylase (GAD) expression levels, promoting γ-aminobutyric acid (GABA) synthesis, and indirectly increasing 5-HT levels.}, } @article {pmid40124227, year = {2025}, author = {Sun, C and Dong, Q and An, H and Liu, Y and Lv, W and Liu, W and Ji, H and Yang, X}, title = {Responses of Soil Microbial Communities and Functions in an Alpine Grassland of the Qinghai Lake Basin With Grazing Disturbance.}, journal = {Ecology and evolution}, volume = {15}, number = {3}, pages = {e71082}, doi = {10.1002/ece3.71082}, pmid = {40124227}, issn = {2045-7758}, abstract = {Soil ecosystems host diverse microbial communities, which are influenced by various environmental factors, soil properties, vegetation characteristics, and anthropogenic activities, such as livestock grazing. Grazing serves as a critical management practice in the alpine grasslands of the Qinghai-Tibet Plateau, affecting soil microbial communities and their functions through processes such as forage consumption, trampling, and the deposition of feces and urine. In this study, we utilized the scientific and technological platform "Alpine Grassland-Livestock Adaptive Management Technology Platform" in Qinghai Province to examine the effects of grazing intensity on soil microbial communities and functions. Experimental treatments included different grazing intensities (light grazing, moderate grazing, and heavy grazing), along with a no-grazing control. Metagenomic sequencing technology was employed to investigate the impact of these grazing intensities on the microbial community composition and functional attributes in alpine grasslands. The results indicated that: (1) Actinobacteria, Proteobacteria, and Chloroflexi were the dominant bacterial communities in the soil, while Ascomycota, Mucoromycota, and Basidiomycota represented the primary fungal communities. (2) Grazing had a greater impact on soil fungal communities than on bacterial communities, altering the Shannon diversity index and Simpson index of soil fungal communities. (3) Soil pH and soil moisture were important factors influencing changes in soil microbial communities. (4) Functional analysis focusing on the "nitrogen metabolism" pathway indicated that under light grazing conditions, the relative abundance of multiple functional genes, particularly those involved in denitrification, decreased.}, } @article {pmid40123920, year = {2025}, author = {Jimenez, K and Kong, Y and Zhang, Y and Ferketic, D and Nagori, SK and Yang, J and Yulo, AA and Kramer, B and Prado, OG and Cason, T and Chowdhry, R and Kemsley, A and Espinosa, LM and Steele, JA and Griffith, J and Jay, JA}, title = {Evaluation of a modified IDEXX method for antimicrobial resistance monitoring of extended Beta-lactamases-producing Escherichia coli in impacted waters near the U.S.-Mexico border.}, journal = {One health (Amsterdam, Netherlands)}, volume = {20}, number = {}, pages = {100997}, pmid = {40123920}, issn = {2352-7714}, abstract = {As part of a One Health approach, the World Health Organization (WHO) has deemed extended beta-lactamases-producing Escherichia coli (ESBL-Ec) as an appropriate proxy for antimicrobial resistance (AMR) in human, animal, and environmental samples. Traditional methods for ESBL-Ec quantification involve a labor-intensive process of membrane filtration, culturing in the presence and absence of antibiotics, and colony confirmation. The emerging modified IDEXX method utilizes IDEXX Colilert-18 test kits, recognized by the USEPA for the enumeration of total coliforms and E. coli in water samples, modified with cefotaxime for measurement of ESBL-Ec in environmental samples. However, this method has yet to be validated for ocean or sewage-contaminated water and has not been compared against the plate-based method with mTEC for surface water. In this study, ESBL-Ec in ocean and river waters of the Tijuana River Estuary were analyzed by three methods: membrane filtration using mTEC plates (as outlined in USEPA Method 1603), membrane filtration using TBX plates (as outlined in the WHO Tricycle Protocol), and Colilert-18 spiked with cefotaxime (Hornsby et al., 2023). Levels of ESBL-Ec were elevated in the Tijuana River Estuary and nearby ocean samples, as high as 2.2 × 10[6] CFU/100 mL. The modified IDEXX method correlated with membrane filtration methods using selective mTEC (r = 0.967, p < 0.001, n = 14) and TBX (r = 0.95, p < 0.001, n = 14) agars. These results indicate that the modified IDEXX method can be used as a more accessible alternative to the traditional culturing methods as a screening tool for antibiotic resistance in urban aquatic environments. Advantages of the IDEXX-based method including portability, lower Biosafety Level requirements, fewer dilutions to stay within the dynamic range, greater ease of maintaining sterility during analysis, and less required staff training are discussed. Future studies into the validity of the modified IDEXX method compared to qPCR and metagenomic sequencing are needed.}, } @article {pmid40123796, year = {2025}, author = {Kim, SH and Kwak, MJ and Hwang, JK and Keum, J and Jin, HY and Lee, CY and Tanpure, RS and Kim, YJ and Hoh, JK and Park, JY and Chung, W and Jeon, BH and Park, HK}, title = {Altered heme metabolism and hemoglobin concentration due to empirical antibiotics-induced gut dysbiosis in preterm infants.}, journal = {Computational and structural biotechnology journal}, volume = {27}, number = {}, pages = {937-945}, pmid = {40123796}, issn = {2001-0370}, abstract = {BACKGROUND: High-risk infants are usually treated with empirical antibiotics after birth, regardless of the evidence of infection; however, their gut microbiome and metabolome have seldom been studied. This study investigated the influence of antibiotic exposure on the gut microbiome and associated metabolic pathways in term and preterm infants.

METHODS: Thirty-six infants within 10 days of birth who were admitted to a neonatal intensive care unit/newborn nursery unit were divided into four groups based on maturity (gestational age) and use of empirical antibiotics. Genomic DNA was extracted from the fecal samples and underwent high-throughput 16S rRNA amplicon sequencing using the Illumina platforms. Taxonomic classification, diversity analysis, and metagenomic function prediction were performed.

RESULTS: Preterm infants with empirical antibiotics showed a significantly decreased population of Firmicutes (p = 0.003) and an increased population of Proteobacteria (p < 0.001) compared to other groups. At the genus level, the populations of Raoultella (p = 0.065) and Escherichia (p = 0.052) showed an increased trend. The change in microbial composition was correlated with increased heme biosynthesis and decreased hemoglobin levels.

CONCLUSION: Collectively, our finding suggested that empirical antibiotic exposure in preterm infants alters the gut microbiome, potentially leading to adverse health outcomes. This dysbiosis may affect heme metabolism, increasing the risk of anemia in these vulnerable infants. Therefore, antibiotic use should be carefully tailored to minimize potential harm.}, } @article {pmid40123706, year = {2025}, author = {Min, S and Lu, Q and Zhang, Y}, title = {A Case of Severe Community-Acquired Pneumonia Caused by Coinfection of Five Pathogens.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {1515-1519}, pmid = {40123706}, issn = {1178-6973}, abstract = {INTRODUCTION: Severe pneumonia is a serious pulmonary infection, and its high morbidity and mortality are associated with underlying diseases, treatment-induced immunodeficiency, co-infection of multiple pathogens, and increase of multi-resistant pathogens; For severe community-acquired pneumonia (SCAP) in immunocompromised patients, most of which are infected with rare atypical pathogens, mNGS as an unbiased and hypothesis-free approach to rapidly detect potential infectious agents in pulmonary mixed infections. The cases of simultaneous co-infection of five non-respiratory core pathogens represented by Nocardia farcinica have not been reported.

CASE PRESENTATION: This article will elaborate on a case of immunocompromised patient with nephrotic syndrome after corticosteroid treatment, who was diagnosed as SCAP after hospital admission and relevant laboratory examination. Bronchoalveolar lavage fluid (BALF) metagenome next-generation sequencing (mNGS) method identified as Nocardia farcinica, Aspergillus fumigatus, Pneumocystis jirovecii, cytomegalovirus and human coronavirus OC43 five pathogens co-infection, the patient improved and he was discharged after receiving the combination treatment of imipenem, ganciclovir, compound sulfamethoxazole, and fluconazole.

CONCLUSION: For SCAP patients with immunocompromised, there may be possible co-infection of multiple rare pathogens, low positive rate of conventional laboratory tests, mNGS can quickly and accurately identify pathogens, which can be used for targeted drug treatment, promote the early recovery of patients and reduce the abuse of broad-spectrum antibiotics.}, } @article {pmid40122890, year = {2025}, author = {Nori, SRC and Walsh, CJ and McAuliffe, FM and Moore, RL and Van Sinderen, D and Feehily, C and Cotter, PD}, title = {Strain-level variation among vaginal Lactobacillus crispatus and Lactobacillus iners as identified by comparative metagenomics.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {49}, pmid = {40122890}, issn = {2055-5008}, support = {H2020-MSCA-COFUND-2019-945385//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)/ ; 18/CRT/6214//Science Foundation Ireland (SFI)/ ; }, mesh = {Female ; *Vagina/microbiology ; Humans ; *Lactobacillus/genetics/classification/isolation & purification ; *Metagenomics/methods ; *Lactobacillus crispatus/genetics/isolation & purification ; Pregnancy ; Microbiota ; Ireland ; Host Microbial Interactions ; Metagenome ; Genome, Bacterial ; Gardnerella vaginalis/genetics/isolation & purification/classification ; }, abstract = {The vaginal microbiome, a relatively simple, low diversity ecosystem crucial for female health, is often dominated by Lactobacillus spp. Detailed strain-level data, facilitated by shotgun sequencing, can provide a greater understanding of the mechanisms of colonization and host-microbe interactions. We analysed 354 vaginal metagenomes from pregnant women in Ireland to investigate metagenomic community state types and strain-level variation, focusing on cell surface interfaces. Our analysis revealed multiple subspecies, with Lactobacillus crispatus and Lactobacillus iners being the most dominant. We found genes, including putative mucin-binding genes, distinct to L. crispatus subspecies. Using 337 metagenome-assembled genomes, we observed a higher number of strain-specific genes in L. crispatus related to cell wall biogenesis, carbohydrate and amino acid metabolism, many under positive selection. A cell surface glycan gene cluster was predominantly found in L. crispatus but absent in L. iners and Gardnerella vaginalis. These findings highlight strain-specific factors associated with colonisation and host-microbe interactions.}, } @article {pmid40122843, year = {2025}, author = {Ashraf, S and Jerome, H and Bugembe, DL and Ssemwanga, D and Byaruhanga, T and Kayiwa, JT and Downing, R and Salazar-Gonzalez, JF and Salazar, MG and Shepherd, JG and Wilkie, C and Davis, C and Logan, N and Vattipally, SB and Wilkie, GS and da Silva Filipe, A and Ssekagiri, A and Namuwulya, P and Bukenya, H and Kigozi, BK and McConnell, WW and Willett, BJ and Balinandi, S and Lutwama, J and Kaleebu, P and Bwogi, J and Thomson, EC}, title = {Uncovering the viral aetiology of undiagnosed acute febrile illness in Uganda using metagenomic sequencing.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {2844}, pmid = {40122843}, issn = {2041-1723}, support = {MC_UU_00034/6//RCUK | Medical Research Council (MRC)/ ; MC_PC_ MR/Y002814/1//RCUK | Medical Research Council (MRC)/ ; 102789/Z/13/A//Wellcome Trust (Wellcome)/ ; }, mesh = {Humans ; Uganda/epidemiology ; *Metagenomics/methods ; Female ; Male ; Adult ; Adolescent ; Middle Aged ; Child ; Young Adult ; Child, Preschool ; Fever/virology/diagnosis ; Prospective Studies ; Viruses/genetics/isolation & purification/classification ; Virus Diseases/epidemiology/virology/diagnosis ; Disease Outbreaks ; Aged ; Acute Disease ; Yellow Fever/epidemiology/virology/diagnosis ; Dengue/epidemiology/virology/diagnosis ; Infant ; Rift Valley Fever/epidemiology/diagnosis/virology ; Hemorrhagic Fever, Crimean/epidemiology/diagnosis/virology ; }, abstract = {Viruses associated with acute febrile illness in Africa cause a spectrum of clinical disease from mild to life-threatening. Routine diagnostic methods are insufficient to identify all viral pathogens in this region. In this study, 1281 febrile Ugandan patients were prospectively recruited as part of the CDC-UVRI Acute Febrile Illness Study and pre-screened for common pathogens. 210/1281 undiagnosed samples, and 20 additional samples from viral outbreaks were subjected to metagenomic sequencing. Viral pathogens were identified in 44/230 (19%), including respiratory, hepatitis, blood-borne, gastrointestinal and vector-borne viruses. Importantly, one case of Crimean-Congo haemorrhagic fever and two cases each of Rift Valley fever, dengue and yellow fever were detected in 7/230 (3%) of cases. Le Dantec virus, last reported in 1969, was also identified in one patient. The presence of high-consequence and (re-)emerging viruses of public health concern highlights the need for enhanced population-based diagnostic surveillance in the African region.}, } @article {pmid40122128, year = {2025}, author = {Zhang, D and Wang, Q and Li, D and Chen, S and Chen, J and Zhu, X and Bai, F}, title = {Gut microbiome composition and metabolic activity in metabolic associated fatty liver disease.}, journal = {Virulence}, volume = {}, number = {}, pages = {2482158}, doi = {10.1080/21505594.2025.2482158}, pmid = {40122128}, issn = {2150-5608}, abstract = {OBJECTIVE: Metabolic Associated Fatty Liver Disease (MAFLD) impacts approximately 25% of the global population. The objective of our study was to elucidate the characteristics of the gut microbiome and alterations in plasma metabolites among MAFLD patients.

METHODS: Between April 2023 and July 2023, 60 patients with MAFLD, along with 60 age, ethnicity, and sex-matched healthy controls (HCs), were enrolled from Inner Mongolia Autonomous Region, China. Analysis of gut microbiota composition and plasma metabolic profiles was conducted using metagenome sequencing and LC-MS.

RESULTS: LEfSe analysis identified five pivotal species: Eubacterium rectale, Dialister invisus, Pseudoruminococcus massiliensis, GGB3278 SGB4328, and Ruminococcaceae bacteria. In subgroup analysis, Eubacterium rectale tended to be increased by more than 2 times and more than double in the non-obese MAFLD group, and MAFLD with moderate hepatic steatosis（HS）respectively. Combinations of phenomics and metabolomics yielded the highest accuracy (AUC = 0.97) in the MAFLD diagnosis. Combinations of phenomics and metagenomics yielded the highest accuracy (AUC = 0.94) in the prediction of the MAFLD HS progress. Plasma samples identified 172 metabolites mainly composed of fatty acid metabolites such as propionic acid and butyric acid analogues. Ruminococcaceae bacteria have a strong positive correlation with β-Alanine, Uric acid and L-Valine. Pseudoruminococcus massiliensis have a strong positive correlation with β-Alanine.

CONCLUSION: Increases in Eubacterium rectale and decreases in Dialister invisus seem to be indicative of MAFLD patients. Eubacterium rectale may predicts HS degree of MAFLD and play an important role in the development of non-obese MAFLD. Eubacterium rectale can generate more propionic acid and butyric acid analogues to absorb energy and increase lipid synthesis, and ultimately cause MAFLD. The observed association between Ruminococcaceae bacteria and β-Alanine or Uric acid in these patients could offer fresh insights into the disease mechanism.}, } @article {pmid40122011, year = {2025}, author = {Yin, M and Li, P and Chen, C and Jia, R and Xia, B and Liu, Y and Liu, A and Liu, L and Li, ZH}, title = {Bioremediation potential of sulfadiazine-degrading bacteria: Impacts on ryegrass growth and soil functionality.}, journal = {Journal of hazardous materials}, volume = {491}, number = {}, pages = {138012}, doi = {10.1016/j.jhazmat.2025.138012}, pmid = {40122011}, issn = {1873-3336}, abstract = {The extensive use of antibiotics, particularly sulfadiazine (SDZ), has led to significant environmental contamination and the proliferation of antibiotic resistance genes (ARGs). This study investigates the bioremediation potential of two SDZ-degrading bacterial strains, Acinetobacter sp. M9 and Enterobacter sp. H1, and their impact on ryegrass (Lolium perenne) growth and the inter-root microenvironment in SDZ-contaminated soils. A pot experiment combined with amplicon and metagenomic sequencing revealed that inoculation with M9 and H1 significantly enhanced ryegrass growth by alleviating oxidative stress, increasing chlorophyll content, and improving soil nutrient availability. The strains also promoted SDZ degradation efficiency and improved carbon and nitrogen cycling through the upregulation of key functional genes. Furthermore, microbial community analysis demonstrated increased alpha diversity, shifts in dominant taxa, and functional enrichment in pollutant degradation pathways. The dynamics of ARGs revealed a decrease in aminoglycoside, rifamycin, and streptomycin resistance genes, while sulfonamide resistance genes increased due to the residual SDZ stress. These findings highlight the potential of M9 and H1 as sustainable bioremediation agents to mitigate antibiotic contamination, improve soil health, and support plant growth in polluted environments.}, } @article {pmid40121909, year = {2025}, author = {Thomson, R and Le, C and Wang, L and Batstone, DJ and Zhou, Y and Oehmen, A}, title = {Higher order volatile fatty acid metabolism and atypical polyhydroxyalkanoate production in fermentation-enhanced biological phosphorus removal.}, journal = {Water research}, volume = {280}, number = {}, pages = {123503}, doi = {10.1016/j.watres.2025.123503}, pmid = {40121909}, issn = {1879-2448}, abstract = {Enhanced biological phosphorus removal (EBPR) is an established wastewater treatment process, but its wider implementation has been limited by factors like high temperature and low carbon availability. Fermentation-enhanced EBPR (F-EBPR) processes have shown promise in addressing these limitations, but the underlying mechanisms are not fully understood. This study investigates the metabolism of higher order (C4-5) volatile fatty acids (VFAs) in F-EBPR systems using a combination of carbon isotope labelling and shotgun metagenomic sequencing analyses. Results show that butyrate (HBu) uptake leads to the formation of both typical (C4-5) and atypical (C6+) polyhydroxyalkanoates (PHAs) through a combination ofβ-oxidation and standard condensation pathways, while the putative role of HBu oxidisers were identified relative to substrate composition in F-EBPR processes. Metagenomic analysis reveals the presence of genes required for higher order VFA metabolism in both polyphosphate accumulating organisms (PAOs) and glycogen accumulating organisms (GAOs). This study also highlights the limitations of current models in describing F-EBPR processes and emphasises the need for improved models that account for higher order VFA metabolism and microbial community dynamics.}, } @article {pmid40121477, year = {2025}, author = {Zhang, Q and Feng, Y and Xia, Y and Shao, Q and Zhao, M and Xu, P and Tang, T and Liu, J and Jin, B and Liu, S and Jiang, C}, title = {Clinical efficacy of metagenomic next-generation sequencing for the detection of pathogens in peritoneal dialysis-related peritonitis: a prospective cohort study.}, journal = {European journal of medical research}, volume = {30}, number = {1}, pages = {198}, pmid = {40121477}, issn = {2047-783X}, support = {2021- LCYJ- PY- 12//Fundings for Clinical Trials from the Affiliated Drum Tower Hospital, Medical School of Nanjing University/ ; YKK21090//Nanjing Healthcare Science and Technology Development Special Fund Project/ ; }, mesh = {Humans ; *Peritonitis/microbiology/diagnosis ; *Peritoneal Dialysis/adverse effects ; Male ; *High-Throughput Nucleotide Sequencing/methods ; Female ; Middle Aged ; Prospective Studies ; *Metagenomics/methods ; Aged ; Adult ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) has been reported to improve pathogen identification in infectious diseases. This prospective cohort study aimed to explore the etiological diagnostic value of mNGS in peritoneal dialysis (PD)-related peritonitis.

METHODS: Patients with PD-related peritonitis were consecutively recruited at the Nephrology Department of Nanjing Drum Tower Hospital. PD effluent samples for mNGS and culture were collected simultaneously. The positive rate, detection time, and consistency of mNGS and culture were compared.

RESULTS: From August 1, 2021 to August 31, 2022, 38 patients with 41 episodes of PD-related peritonitis were enrolled. The positive rate of mNGS was higher than that of culture, although not statistically significant (92.7% vs 78.0%, P = 0.109). The average reporting time of mNGS was significantly shorter than that of culture (30.4 ± 10.5 vs 86.9 ± 22.2 h, P < 0.001). mNGS identified more co-pathogens and unusual pathogens than culture, with multiple pathogens being detected in nearly half of the samples. Among the 30 samples that tested positive by both methods, 27 (90%) showed completely (13 cases) or partly (14 cases) matched results between mNGS and culture. Fourteen patients (with 14 episodes of peritonitis) had used antibiotics within 2 weeks before specimen collection. Antibiotic usage led to a significant decrease in the culture-positive rate (57.1% vs 88.9%, P = 0.042), while the mNGS-positive rate remained unaffected (92.9% vs 92.6%, P = 1.000).

CONCLUSIONS: This study revealed that mNGS exhibited higher sensitivity and shorter reporting time compared to culture in detecting pathogens in PD-related peritonitis. For samples that yielded positive results by both methods, the consistency between mNGS and culture was substantial. mNGS may offer a novel approach for the etiological diagnosis of PD-associated peritonitis, particularly in cases involving prior antibiotic use and unusual pathogens.}, } @article {pmid40121075, year = {2025}, author = {Omura, SN and Nureki, O}, title = {General and robust sample preparation strategies for cryo-EM studies of CRISPR-Cas9 and Cas12 enzymes.}, journal = {Methods in enzymology}, volume = {712}, number = {}, pages = {23-39}, doi = {10.1016/bs.mie.2025.01.052}, pmid = {40121075}, issn = {1557-7988}, mesh = {*Cryoelectron Microscopy/methods ; *CRISPR-Cas Systems ; *CRISPR-Associated Proteins/genetics/chemistry/metabolism ; Gene Editing/methods ; CRISPR-Associated Protein 9/genetics/chemistry/metabolism ; Bacterial Proteins/genetics/chemistry/metabolism ; Endodeoxyribonucleases ; }, abstract = {Cas9 and Cas12 are RNA-guided DNA endonucleases derived from prokaryotic CRISPR-Cas adaptive immune systems that have been repurposed as versatile genome-engineering tools. Computational mining of genomes and metagenomes has expanded the diversity of Cas9 and Cas12 enzymes that can be used to develop versatile, orthogonal molecular toolboxes. Structural information is pivotal to uncovering the precise molecular mechanisms of newly discovered Cas enzymes and providing a foundation for their application in genome editing. In this chapter, we describe detailed protocols for the preparation of Cas9 and Cas12 enzymes for cryo-electron microscopy. These methods will enable fast and robust structural determination of newly discovered Cas9 and Cas12 enzymes, which will enhance the understanding of diverse CRISPR-Cas effectors and provide a molecular framework for expanding CRISPR-based genome-editing technologies.}, } @article {pmid40121033, year = {2025}, author = {Wong, MK and Boukhaled, GM and Armstrong, E and Liu, R and Heirali, AA and Yee, NR and Tsang, J and Spiliopoulou, P and Schneeberger, PHH and Wang, BX and Cochrane, K and Sherriff, K and Allen-Vercoe, E and Siu, LL and Spreafico, A and Coburn, B}, title = {Microbial Ecosystem Therapeutics 4 (MET4) elicits treatment-specific IgG responses associated with changes in gut microbiota in immune checkpoint inhibitor recipients with advanced solid tumors.}, journal = {Journal for immunotherapy of cancer}, volume = {13}, number = {3}, pages = {}, doi = {10.1136/jitc-2024-010681}, pmid = {40121033}, issn = {2051-1426}, mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Neoplasms/immunology/drug therapy/therapy ; *Immunoglobulin G/blood/immunology ; Male ; Female ; Middle Aged ; Aged ; }, abstract = {BACKGROUND: Gut microbiome modulation has shown promise in its potential to treat cancer in combination with immunotherapy. Mechanistically, the pathways and routes by which gut microbiota may influence systemic and antitumor immunity remain uncertain. Here, we used blood and stool samples from Microbial Ecosystem Therapeutic 4 (MET4)-IO, an early-phase trial testing the safety and engraftment of the MET4 bacterial consortium in immune checkpoint inhibitor recipients, to assess how MET4 may affect systemic immunity.

METHODS: Circulating antibody responses induced by MET4 were assessed using an antimicrobial antibody flow cytometry assay on pretreatment and post-treatment plasma. Antibody responses were associated with taxonomic changes in stool identified by metagenomic sequencing. Mass cytometry was performed on peripheral blood mononuclear cells to identify shifts in circulating immune subsets associated with antibody responses.

RESULTS: Increases in circulating anti-MET4 immunoglobulin G (IgG) responses were measured by flow cytometry post-consortium treatment in MET4 recipients, but not untreated control participants, with five individuals displaying notably higher antibody responses. Stronger IgG responses were associated with greater increases in multiple taxa, including MET4 microbe Collinsella aerofaciens, which was previously linked with immune checkpoint response. However, these taxa were not enriched in the IgG-bound fraction post-MET4 treatment. Greater increases in circulating B cells and FoxP3[+] CD4[+] T cells post-MET4 treatment were observed in the blood of high IgG responders, while CD14[+] and CD16[+] monocyte populations were decreased in these individuals.

CONCLUSION: These results demonstrate the induction of treatment-specific circulating humoral immunity by a bacterial consortium and suggest potential mechanisms by which gut microbes may contribute to antitumor immunity.}, } @article {pmid40120232, year = {2025}, author = {Ebmeyer, S and Kristiansson, E and Larsson, DGJ}, title = {Unraveling the origins of mobile antibiotic resistance genes using random forest classification of large-scale genomic data.}, journal = {Environment international}, volume = {198}, number = {}, pages = {109374}, doi = {10.1016/j.envint.2025.109374}, pmid = {40120232}, issn = {1873-6750}, abstract = {Understanding in which environments and under what conditions chromosomal antibiotic resistance genes (ARGs) acquire increased mobility is crucial to effectively mitigate their emergence in and dissemination among pathogens. In order to identify the conditions and environments facilitating these processes, it is valuable to know from which bacterial species mobile ARGs were mobilized initially, before their dissemination to other species. In this study, we used data generated from > 1.5 million publicly available bacterial genome assemblies to train a random forest classifier to identify the origins of mobile genes. Analysis of the models' predictions revealed the previously unknown origins of 12 mobile ARG groups, which confer resistance to 4 different classes of antibiotics. This included ARGs conferring resistance to tetracyclines, an antibiotic class for which, to the best of our knowledge, no recent origins of ARGs have previously been convincingly demonstrated. All identified origin species in this study are known opportunistic pathogens, and some are the origin of multiple mobile ARGs. An analysis of public metagenomes from different sources indicates that most of the origin species are particularly abundant in municipal wastewaters, a few were highly abundant in animal feces and three were most common in environments polluted with waste from antibiotic manufacturing. This study highlights environments where these origin species thrive and where there is a need for limiting antibiotic selection pressures.}, } @article {pmid40120189, year = {2025}, author = {Sun, Q and Li, D and He, Y and Ping, Q and Wang, L and Li, Y}, title = {Improved anaerobic digestion of waste activated sludge under ammonia stress by nanoscale zero-valent iron/peracetic acid pretreatment and hydrochar regulation: Insights from multi-omics analyses.}, journal = {Water research}, volume = {279}, number = {}, pages = {123497}, doi = {10.1016/j.watres.2025.123497}, pmid = {40120189}, issn = {1879-2448}, abstract = {This study developed a novel strategy combining a nanoscale zero-valent iron (nZVI)/peracetic acid (PAA) pretreatment and hydrochar regulation to enhance anaerobic digestion of waste activated sludge (WAS) under ammonia-stressed conditions. The strategy significantly enhanced methane production at ammonia concentrations below 3000 mg/L, with the regulation groups (AN3000/REG) achieving a 50.1 % increase in cumulative methane yield. Metagenomic analysis demonstrated a 14.2 % enrichment of key functional microorganisms, including syntrophic fatty acid-oxidizing bacteria and hydrogenotrophic methanogens, in the AN3000/REG groups. Some of them promote the conversion of butyrate and valerate to acetate through the upregulation of key genes in the fatty acid β-oxidation pathway, thereby supplying sufficient substrates for acetoclastic methanogenesis. Beyond enhancing acetoclastic methanogenesis, the AN3000/REG groups exhibited significant upregulation of other metabolic pathways, with a 34.2 % increase in syntrophic acetate oxidation-hydrogenotrophic methanogenesis genes and a 17.1 % increase in methanol/methylotrophic methanogenesis-related genes. These findings were further validated by the metatranscriptomic and metaproteomic combination analyses. Furthermore, the AN3000/REG groups exhibited a significant enhancement in direct interspecies electron transfer, with functional microbes (e.g., Geobacter, Methanosarcina, and Methanobacterium), pili, and cytochrome c showing significant increases of 1.38-fold, 12.7-fold, and 5.6-fold, respectively. This might be due to the synergistic effects of nZVI and hydrochar in the regulation groups. Additionally, metabolomic analyses revealed that the regulation strategy improved the microbial adaptability to ammonia stress by modulating metabolic products, such as alkaloids. Our study not only provides a promising strategy for alleviating ammonia inhibition during the anaerobic digestion of WAS but also provides a strong basis for understanding the underlying mechanism under ammonia-stressed conditions.}, } @article {pmid40119849, year = {2025}, author = {Riva, A and Sahin, E and Volpedo, G and Catania, NT and Venara, I and Biagioli, V and Balagura, G and Amadori, E and De Caro, C and Cerulli Irelli, E and Di Bonaventura, C and Zara, F and Sezerman, OU and Russo, E and Striano, P}, title = {Medication-resistant epilepsy is associated with a unique gut microbiota signature.}, journal = {Epilepsia}, volume = {}, number = {}, pages = {}, doi = {10.1111/epi.18367}, pmid = {40119849}, issn = {1528-1167}, support = {MDBR-23-004-STXBP1//Fingerprinting a multiomics biomarker profile in patients with STXBP1-RD/ ; PNRR-MUR-M4C2 PE0000006//MNESYS/ ; }, abstract = {OBJECTIVE: Dysfunction of the microbiota-gut-brain axis is emerging as a new pathogenic mechanism in epilepsy, potentially impacting on medication response and disease outcome. We investigated the composition of the gut microbiota in a cohort of medication-resistant (MR) and medication-sensitive (MS) pediatric patients with epilepsy.

METHODS: Children with epilepsy of genetic and presumed genetic etiologies were evaluated clinically and subgrouped into MR and MS. Age-matched healthy controls (HCs) were also recruited. A food diary was used to evaluate nutritional habits, and the Rome IV questionnaire was used to record gastrointestinal symptoms. The microbiota composition was assessed in stool samples through 16S rRNA. α-Diversity (AD) and β-diversity (BD) were calculated, and differential abundance analysis was performed using linear multivariable models (significance: p.adj < .05).

RESULTS: Forty-one patients (MR:MS = 20:21) with a mean age of 7.2 years (±4.6 SD) and 27 age-matched HCs were recruited. No significant differences in AD were found when comparing patients and HCs. Significant positive correlation was found between AD and age (Chao1 p.adj = .0004, Shannon p.adj = .0004, Simpson p.adj = .0028). BD depicted a different bacterial profile in the epilepsy groups compared to HCs (MS vs. HC: Bray-Curtis F = 1.783, p = .001; Jaccard F = 1.24, p = .001; MR vs. HC: Bray-Curtis F = 2.24, p = .001; Jaccard F = 1.364, p = .001). At the genus level, the epilepsy groups were characterized by a significant increase in Hungatella (MS vs. HC: +4.95 log2 change; MR vs. HC: +6.72 log2 change); the [Eubacterium] siraeum group changed between the MR and MS subgroups.

SIGNIFICANCE: Epileptic patients display unique gut metagenomic signatures compared to HCs. Moreover, a different ratio of the butyrate-producing [Eubacterium] siraeum group suggests dissimilarities between patients based on the response to antiseizure medications.}, } @article {pmid40119394, year = {2025}, author = {Guo, R and Chang, Y and Wang, D and Sun, H and Gu, T and Zong, Y and Zhou, S and Huang, Z and Chen, L and Tian, Y and Xu, W and Lu, L and Zeng, T}, title = {Interaction between cecal microbiota and liver genes of laying ducks with different residual feed intake.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {30}, pmid = {40119394}, issn = {2524-4671}, support = {CARS-42//China Agriculture Research System of MOF and MARA/ ; 2021C02068//Zhejiang Province Agricultural New Breeding Major Science and Technology Special Project/ ; LZ23C170001//Zhejiang Provincial Natural Science Foundation of China/ ; 32472892//National Natural Science Foundation of China/ ; 2022YFD1300100//National Key Research and Development Program of China/ ; }, abstract = {BACKGROUND: The gut microbiota exerts a critical influence on energy metabolism homeostasis and productive performance in avian species. Given the diminishing availability of arable land and intensifying competition for finite resources between livestock production and human populations, the agricultural sector faces dual imperatives to enhance productive efficiency while mitigating ecological footprints. Within this paradigm, optimizing nutrient assimilation efficiency in commercial waterfowl operations emerges as a strategic priority. This investigation employs an integrated multi-omics approach framework (metagenomic, metabolomic, and transcriptomic analyses) to elucidate the mechanistic relationships between cecal microbial consortia and feed conversion ratios in Shan Partridge ducks.

RESULTS: Based on the analysis of metagenome data, a total of 34 phyla, 1033 genera and 3262 species of bacteria were identified by metagenomic sequencing analysis. At the phylum level, 31 phylums had higher mean abundance in the low residual feed intake (LRFI) group than in the high residual feed intake (HRFI) group. Among them, the expression of microbiome Elusimicrobiota was significantly higher in the LRFI group than in the HRFI group (P < 0.05). And we also found a significant differences in secondary metabolites biosynthesis, transport, and catabolism pathways between the two groups in microbial function (P < 0.05). Based on metabolomic analysis, 17 different metabolites were found. Among them, Lipids and lipid molecules accounted for the highest proportion. Whereas the liver is very closely related to lipid metabolism, we are close to understanding whether an individual's energy utilization efficiency is related to gene expression in the liver. We selected six ducks from each group of six ducks each for liver transcriptome analysis. A total of 322 differential genes were identified in the transcriptome analysis results, and 319 genes were significantly down-regulated. Among them, we found that prostaglandin endoperoxide synthase 2 (PTGS2) might be a key hub gene regulating RFI by co-occurrence network analysis. Interestingly, the differential gene PTGS2 was enriched in the arachidonic acid pathway at the same time as the differential metabolite 15-deoxy-delta12,14-prostaglandin J2 (15d-PGJ2). In addition, the results of the association analysis of differential metabolites with microorganisms also revealed a significant negative correlation between 15d-PGJ2 and Elusimicrobiota.

CONCLUSION: Based on comprehensive analysis of the research results, we speculate that the Elusimicrobiota may affect the feed utilization efficiency in ducks by regulating the expression of the PTGS2 gene.}, } @article {pmid40119266, year = {2025}, author = {Zhou, Y and Ren, D and Li, Y and Gui, S}, title = {A case of septic shock caused by drug-resistant Edwardsiella tarda and literature review.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {393}, pmid = {40119266}, issn = {1471-2334}, support = {SZSM202211016//Sanming Project of Medicine in Shenzhen/ ; SZSM202211016//Sanming Project of Medicine in Shenzhen/ ; SZSM202211016//Sanming Project of Medicine in Shenzhen/ ; SZSM202211016//Sanming Project of Medicine in Shenzhen/ ; SZGSP006//the Shenzhen Fund for Guangdong Provincial High-level Clinical Key Specialties/ ; SZGSP006//the Shenzhen Fund for Guangdong Provincial High-level Clinical Key Specialties/ ; SZGSP006//the Shenzhen Fund for Guangdong Provincial High-level Clinical Key Specialties/ ; SZGSP006//the Shenzhen Fund for Guangdong Provincial High-level Clinical Key Specialties/ ; Grant No. 20223357008//the Shenzhen Second People's Hospital Clinical Research Fund of Shenzhen High-level Hospital Construction Project/ ; Grant No. 20223357008//the Shenzhen Second People's Hospital Clinical Research Fund of Shenzhen High-level Hospital Construction Project/ ; Grant No. 20223357008//the Shenzhen Second People's Hospital Clinical Research Fund of Shenzhen High-level Hospital Construction Project/ ; Grant No. 20223357008//the Shenzhen Second People's Hospital Clinical Research Fund of Shenzhen High-level Hospital Construction Project/ ; No. 20213357020//the Shenzhen Second People's Hospital Clinical Research Fund of Guangdong Province High-level Hospital Construction Project/ ; No. 20213357020//the Shenzhen Second People's Hospital Clinical Research Fund of Guangdong Province High-level Hospital Construction Project/ ; No. 20213357020//the Shenzhen Second People's Hospital Clinical Research Fund of Guangdong Province High-level Hospital Construction Project/ ; No. 20213357020//the Shenzhen Second People's Hospital Clinical Research Fund of Guangdong Province High-level Hospital Construction Project/ ; }, mesh = {Humans ; *Shock, Septic/microbiology/drug therapy ; *Edwardsiella tarda/drug effects/isolation & purification/genetics ; Female ; Adult ; *Enterobacteriaceae Infections/microbiology/drug therapy ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Piperacillin, Tazobactam Drug Combination/therapeutic use ; Microbial Sensitivity Tests ; }, abstract = {BACKGROUND: Edwardsiella tarda (E. tarda) causes highly mortality, which is rare in septic patients. We herein reported a case of septic shock caused by drug-resistant E. tarda.

CASE PRESENTATION: We herein describe a 32-year-old female with septic shock who had the medical history of abortion 1 month ago and "systemic lupus erythematosus and rheumatoid arthritis" presented abdominal pain, diarrhea, and dyspnea as the primary symptoms and rapidly deteriorated to MODS following breakfast (undercooked fish porridge) in the ICU. Sepsis surviving bundle was initiated by collecting pathogen culture (sputum, urine and blood samples), empirically broad-spectrum antibiotics administration (Meropenem), along with fluid resuscitation, vasopressor use. E. tarda was confirmed both in blood culture and mNGS (metagenomics next generation sequencing). Thus, the antibiotics were switched to piperacillin-tazobactam according to the susceptibility test that was susceptible to piperacillin-tazobactam and resistant to ampicillin, quinolones and gentamicin. The patient finally recovered and discharged after 18 days of ICU treatment.

CONCLUSIONS: Empiric antibiotics should be selected with piperacillin-tazobactam and amikacin, and avoid ampicillin, quinolones and gentamicin for suspecting E. tarda infection in southern China. Bacteremia complicated with septic shock caused by E. tarda requires intensive care to improve survival rates.}, } @article {pmid40119088, year = {2025}, author = {Santos, CA and Morais, MAB and Mandelli, F and Lima, EA and Miyamoto, RY and Higasi, PMR and Araujo, EA and Paixão, DAA and Junior, JM and Motta, ML and Streit, RSA and Morão, LG and Silva, CBC and Wolf, LD and Terrasan, CRF and Bulka, NR and Diogo, JA and Fuzita, FJ and Colombari, FM and Santos, CR and Rodrigues, PT and Silva, DB and Grisel, S and Bernardes, JS and Terrapon, N and Lombard, V and Filho, AJC and Henrissat, B and Bissaro, B and Berrin, JG and Persinoti, GF and Murakami, MT}, title = {Publisher Correction: A metagenomic 'dark matter' enzyme catalyses oxidative cellulose conversion.}, journal = {Nature}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41586-025-08872-9}, pmid = {40119088}, issn = {1476-4687}, } @article {pmid40118380, year = {2025}, author = {Guo, D and Fan, J and Zhang, X and Chen, S and Du, X}, title = {Next-generation Sequencing assistance in the diagnosis of Active Tuberculosis following Allogeneic Hematopoietic Stem Cell Transplantation: A Case Series.}, journal = {Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy}, volume = {}, number = {}, pages = {102683}, doi = {10.1016/j.jiac.2025.102683}, pmid = {40118380}, issn = {1437-7780}, abstract = {Tuberculosis poses a rare but life-threatening complication for patients undergoing hematopoietic stem cell transplantation. In a case series spanning January 2020 to January 2024, we evaluated the application of metagenomic Next-Generation Sequencing in the early diagnosis of tuberculosis in patients following allogeneic hematopoietic stem cell transplantation. We identified 9 cases of post-transplant tuberculosis, predominantly pulmonary, with 1 case of disseminated disease. In early fluid samples from patients with post-transplant active tuberculosis, metagenomic next-generation sequencing detected Mycobacterium tuberculosis complex earlier than conventional tests, enabling rapid diagnosis. In this study, metagenomic next-generation sequencing showed a sensitivity of 66.6% and specificity of 100%, higher than TB-DNA and Xpert (55.6%). Concurrently, among mNGS-positive samples, 4 (44.4%) were from peripheral blood and 3 (33.3%) from bronchoalveolar lavage fluid. The combination of metagenomic Next-Generation sequencing and Xpert may enhance the capacity for detecting Mycobacterium tuberculosis complex in extrapulmonary specimens from post-transplant patients. The time from symptom onset to Next-Generation Sequencing positivity was 2 to 76 days, and from transplantation to TB diagnosis was 30 to 485 days. Despite some fatalities, the majority of patients completed extended anti-tuberculosis treatment and are under regular follow-up, highlighting the value of Next-Generation Sequencing in diagnosing tuberculosis in this high-risk population.}, } @article {pmid40118224, year = {2025}, author = {Bai, M and Wang, B and Zhao, W and Qiu, H and Su, S and Wang, Y and Qin, Y and Wang, C and Zhao, Z and Gao, Z and Yang, C}, title = {Novel anammox-enhanced A-B wastewater treatment process based on carbon capture concept.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132431}, doi = {10.1016/j.biortech.2025.132431}, pmid = {40118224}, issn = {1873-2976}, abstract = {The high energy consumption and high carbon footprint of sewage treatment are technical shortcomings of the conventional activated sludge process. To address the emergency issue, this research demonstrated the viability of a pre-anammox enhanced A-B process to treat municipal wastewater while achieving an energy-efficient operation. In the proposed A-B process, an anaerobic moving bed biofilm reactor (A-MBBR) functions as the A-stage for COD capture, while a nitrification MBBR functions as the B-stage. The results show that during the 210-days of operation, 83.3 % of the influent COD was converted in the A-stage, and 93.1 % NH4[+]-N removal was achieved, resulting in an effluent NH4[+]-N concentration of 0.9 mg/L. The metagenomic sequencing results show that, in the B-stage MBBR, Nitrosomonas was the main ammonia-oxidizing bacterium (4.9 % relative abundance) and Nitrospira was the main nitrite-oxidizing bacterium (18.0 % relative abundance). In the A-stage MBBR, Thauera was the dominant denitrification bacterium (9.2 % relative abundance) and Candidatus Brocadia was the dominant anammox bacterium. Finally, hdh and hzs were key anammox genes detected in this system. This study clearly demonstrates a novel pre-anammox enhanced A-B process with an energy-efficient operation.}, } @article {pmid40118220, year = {2025}, author = {Rozera, T and Pasolli, E and Segata, N and Ianiro, G}, title = {Machine learning and artificial intelligence in the multi-omics approach to gut microbiota.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2025.02.035}, pmid = {40118220}, issn = {1528-0012}, abstract = {The gut microbiome is involved in human health and disease, and its comprehensive understanding is necessary to exploit it as a diagnostic or therapeutic tool. Multi-omics approaches, including metagenomics, metatranscriptomics, metabolomics, and metaproteomics, enable depicting the complexity of the gut microbial ecosystem. However, these tools generate a large data stream, which integration is needed to produce clinically useful readouts but, in turn, might be difficult to carry out with conventional statistical methods. Artificial intelligence and machine learning have been increasingly applied to multi-omics datasets in several conditions associated with microbiome disruption, from chronic disorders to cancer. Such tools show potential for clinical implementation, including the discovery of microbial biomarkers for disease classification or prediction, the prediction of response to specific treatments, the fine-tuning of microbiome-modulating therapies. Here we discuss the state of the art, potential, and limits, of artificial intelligence and machine learning in the multi-omics approach to gut microbiome.}, } @article {pmid40118219, year = {2025}, author = {Yan, R and Zhang, L and Chen, Y and Zheng, Y and Xu, P and Xu, Z}, title = {Therapeutic potential of gut microbiota modulation in epilepsy: A focus on short-chain fatty acids.}, journal = {Neurobiology of disease}, volume = {}, number = {}, pages = {106880}, doi = {10.1016/j.nbd.2025.106880}, pmid = {40118219}, issn = {1095-953X}, abstract = {According to the criteria established by the International League Against Epilepsy (ILAE), epilepsy is defined as a disorder characterized by at least two unprovoked seizures occurring more than 24 h apart. Its pathogenesis is closely related to various physiological and pathological factors. Advances in high-throughput metagenomic sequencing have increasingly highlighted the role of gut microbiota dysbiosis in epilepsy. Short-chain fatty acids (SCFAs), the major metabolites of the gut microbiota and key regulators of the gut-brain axis, support physiological homeostasis through multiple mechanisms. Recent studies have indicated that SCFAs not only regulate seizures by maintaining intestinal barrier integrity and modulating intestinal immune responses, but also affect the structure and function of the blood-brain barrier (BBB) and regulate neuroinflammation. This review, based on current literatures, explores the relationship between SCFAs and epilepsy, emphasizing how SCFAs affect epilepsy by modulating the intestinal barrier and BBB. In-depth studies on SCFAs may reveal their therapeutic potential and inform the development of gut microbiota-targeted epilepsy treatments.}, } @article {pmid40117915, year = {2025}, author = {Ghemrawi, M and Ramírez Torres, A and Netherland, M and Wang, Y and Hasan, NA and El-Fahmawi, B and Duncan, G and McCord, B}, title = {Forensic insights from shotgun metagenomics: Tracing microbial exchange during sexual intercourse.}, journal = {Forensic science international. Genetics}, volume = {78}, number = {}, pages = {103266}, doi = {10.1016/j.fsigen.2025.103266}, pmid = {40117915}, issn = {1878-0326}, abstract = {The microbiome is becoming an emerging field of interest within forensic science with high potential for individualization; however, little is known about bacterial species specific to the genital area or their ability to transfer between individuals during sexual contact. In this proof-of-concept study, we investigated microbial transfer dynamics in seven monogamous, heterosexual couples by collecting pre- and post-sexual intercourse samples from their genital areas, including penile, vaginal, and labial locations. Utilizing Shotgun Metagenomic Sequencing, we sequenced the microbial profiles of these samples. Our findings reveal significant transfer from the vaginal microbiome onto the penile microbiome, predominantly originating from the labial genitalia. Moreover, strain analysis unveiled distinct differentiation between the same species of bacteria across individuals, underscoring the potential for microbial forensics to distinguish individuals. This study contributes to our understanding of microbial transfer during sexual contact and highlights the forensic implications of the genital microbiome.}, } @article {pmid40117911, year = {2025}, author = {Wang, J and Feng, Y and Cheng, H and Qian, K and Wan, B and Liu, S and Liu, Y and Hu, J}, title = {Management strategies and outcomes for fracture-related infection of patellar fractures.}, journal = {Injury}, volume = {56}, number = {4}, pages = {112272}, doi = {10.1016/j.injury.2025.112272}, pmid = {40117911}, issn = {1879-0267}, abstract = {INTRODUCTION: Fracture-related infection (FRI) poses a substantial challenge in orthopaedic trauma surgery, potentially leading to permanent functional impairment or necessitating amputation in patients who are expected to recover fully. Data on the incidence, pathogen detection rates, outcomes, and optimal management strategies for patellar FRI are limited. Therefore, this study aimed to identify the most common pathogens associated with patellar fixation-related infections, evaluate the functional outcome associated with FRI of the patella, and develop a management algorithm for addressing these severe complications.

METHODS: This retrospective review analyzed a prospectively maintained database to identify all patients with FRI of the patella treated at our institution between January 2015 and August 2023. Data on demographics, fracture characteristics, surgical details, and outcomes were collected. Descriptive statistical analyses were performed using SPSS software.

RESULTS: Over the 9-year period, 32 cases of patellar fractures complicated by infection following surgical treatment were identified, with complete follow-up data available (mean age, 56.5 ± 15.8 years). Infection occurred in 13 patients within 2 weeks of fixation and in 19 patients between 2 and 10 weeks postoperatively. Following debridement, nine patients retained their original fixation, eight underwent hardware removal, and 15 underwent hardware replacement. Seven patients developed septic arthritis and were managed with arthroscopic knee lavage. Metagenomic next-generation sequencing demonstrated a sensitivity of 93.8 % (30/32), which was significantly higher than that of traditional microbiological culture (53.1 %; P < 0.01). All surgical incisions achieved primary healing within 2 weeks post-closure with no recurrence of infection, skin necrosis, osteomyelitis, or nonunion. At the final follow-up, all fractures had united, with the Böstman patellar fracture functional scores ranging from 24 to 29, resulting in a 100 % excellent/good rate.

CONCLUSIONS: Comprehensive and multidisciplinary management approaches can achieve successful bone union and favourable long-term outcomes in patients with patellar FRI. However, further validation through large-scale studies is necessary to confirm these findings.}, } @article {pmid40117769, year = {2025}, author = {Jiang, Z and Fang, W and Jiang, Y and Hu, Y and Dong, Y and Li, P and Shi, L}, title = {Arsenic mobilization by Bathyarchaeia in subsurface sediments at the Jianghan Plain, China.}, journal = {Journal of hazardous materials}, volume = {491}, number = {}, pages = {138002}, doi = {10.1016/j.jhazmat.2025.138002}, pmid = {40117769}, issn = {1873-3336}, abstract = {As one of the most abundant microorganisms on Earth, Bathyarchaeia with diverse abilities to degrade complex organic carbon play a vital role in the global carbon cycle. However, the role of Bathyarchaeia in arsenic (As) metabolism and their contribution to As mobilization in aquifers remain unclear. In this study, we recovered 15 Bathyarchaeota metagenome-assembled genomes (MAGs) from metagenomes of borehole sediments in the Jianghan Plain (JHP), China. Together with 374 representative Bathyarchaeia MAGs from public databases, six As metabolism genes i.e. arrA, arsR, arsA, arsB, arsC (Trx) and arsM were identified, accounting for 4.4, 47.6, 20.3, 38.3, 37.5 and 49.4 % of total Bathyarchaeia MAGs, respectively. Heterologous expression of multiple arsC and arsM genes of Bathyarchaeia MAGs obtained from JHP sediments validated their abilities for As(V) reduction and As(III) methylation at environmentally relevant As concentration. These results indicate that in addition to providing bioavailable carbon sources for other microbial functional populations, Bathyarchaeia directly participate in As mobilization in the JHP aquifer via As(V) reduction and As(III) methylation. The diversified distribution of arsC and arsM in the class Bathyarchaeia suggests that Bathyarchaeia may contribute to As cycling in other As-rich environments, such as hot spring, saline lakes, marine hydrothermal sediments and soils.}, } @article {pmid40117176, year = {2025}, author = {Zielińska, K and Udekwu, KI and Rudnicki, W and Frolova, A and Łabaj, PP}, title = {Healthy microbiome-moving towards functional interpretation.}, journal = {GigaScience}, volume = {14}, number = {}, pages = {}, doi = {10.1093/gigascience/giaf015}, pmid = {40117176}, issn = {2047-217X}, support = {2020/38/E/NZ2/00598//NCN/ ; PLG/2023/016234//Jagiellonian University in Krakow/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Inflammatory Bowel Diseases/microbiology ; *Metagenomics/methods ; Metagenome ; Phylogeny ; Dysbiosis/microbiology ; Principal Component Analysis ; COVID-19/virology ; }, abstract = {BACKGROUND: Microbiome-based disease prediction has significant potential as an early, noninvasive marker of multiple health conditions linked to dysbiosis of the human gut microbiota, thanks in part to decreasing sequencing and analysis costs. Microbiome health indices and other computational tools currently proposed in the field often are based on a microbiome's species richness and are completely reliant on taxonomic classification. A resurgent interest in a metabolism-centric, ecological approach has led to an increased understanding of microbiome metabolic and phenotypic complexity, revealing substantial restrictions of taxonomy-reliant approaches.

FINDINGS: In this study, we introduce a new metagenomic health index developed as an answer to recent developments in microbiome definitions, in an effort to distinguish between healthy and unhealthy microbiomes, here in focus, inflammatory bowel disease (IBD). The novelty of our approach is a shift from a traditional Linnean phylogenetic classification toward a more holistic consideration of the metabolic functional potential underlining ecological interactions between species. Based on well-explored data cohorts, we compare our method and its performance with the most comprehensive indices to date, the taxonomy-based Gut Microbiome Health Index (GMHI), and the high-dimensional principal component analysis (hiPCA) methods, as well as to the standard taxon- and function-based Shannon entropy scoring. After demonstrating better performance on the initially targeted IBD cohorts, in comparison with other methods, we retrain our index on an additional 27 datasets obtained from different clinical conditions and validate our index's ability to distinguish between healthy and disease states using a variety of complementary benchmarking approaches. Finally, we demonstrate its superiority over the GMHI and the hiPCA on a longitudinal COVID-19 cohort and highlight the distinct robustness of our method to sequencing depth.

CONCLUSIONS: Overall, we emphasize the potential of this metagenomic approach and advocate a shift toward functional approaches to better understand and assess microbiome health as well as provide directions for future index enhancements. Our method, q2-predict-dysbiosis (Q2PD), is freely available (https://github.com/Kizielins/q2-predict-dysbiosis).}, } @article {pmid40116459, year = {2025}, author = {Blakeley-Ruiz, JA and Bartlett, A and McMillan, AS and Awan, A and Walsh, MV and Meyerhoffer, AK and Vintila, S and Maier, JL and Richie, TG and Theriot, CM and Kleiner, M}, title = {Dietary protein source alters gut microbiota composition and function.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf048}, pmid = {40116459}, issn = {1751-7370}, support = {7002782//USDA National Institute of Food and Agriculture, Hatch/ ; P30 DK034987/NH/NIH HHS/United States ; }, abstract = {The source of protein in a person's diet affects their total life expectancy. However, the mechanisms by which dietary protein sources differentially impact human health and life expectancy are poorly understood. Dietary choices impact the composition and function of the intestinal microbiota that ultimately modulate host health. This raises the possibility that health outcomes based on dietary protein sources might be driven by interactions between dietary protein and the gut microbiota. In this study, we determined the effects of seven different sources of dietary protein on the gut microbiota of mice using an integrated metagenomics-metaproteomics approach. The protein abundances measured by metaproteomics can provide microbial species abundances, and evidence for the molecular phenotype of microbiota members because measured proteins indicate the metabolic and physiological processes used by a microbial community. We showed that dietary protein source significantly altered the species composition and overall function of the gut microbiota. Different dietary protein sources led to changes in the abundance of microbial proteins involved in the degradation of amino acids and the degradation of glycosylations conjugated to dietary protein. In particular, brown rice and egg white protein increased the abundance of amino acid degrading enzymes. Egg white protein increased the abundance of bacteria and proteins usually associated with the degradation of the intestinal mucus barrier. These results show that dietary protein sources can change the gut microbiota's metabolism, which could have major implications in the context of gut microbiota mediated diseases.}, } @article {pmid40116405, year = {2025}, author = {Shekhawat, N}, title = {Precision Medicine for Diagnosis of Microbial Keratitis.}, journal = {International ophthalmology clinics}, volume = {65}, number = {2}, pages = {20-25}, doi = {10.1097/IIO.0000000000000562}, pmid = {40116405}, issn = {1536-9617}, mesh = {Humans ; *Precision Medicine/methods ; *Eye Infections, Bacterial/diagnosis/microbiology ; *Keratitis/diagnosis/microbiology ; Eye Infections, Fungal/diagnosis/microbiology ; Cornea/microbiology ; Bacteria/genetics/isolation & purification ; Proteomics/methods ; }, abstract = {Microbial keratitis (MK) is the leading cause of corneal blindness and can be caused by several species of bacteria, fungi, or parasites. Accurate and timely identification of the causative microbe is critical for initiating targeted antimicrobial and anti-inflammatory treatment and preventing vision loss. MK diagnosis currently relies on corneal culture or microscopy, which have suboptimal yield and can produce inconclusive results. MK requires immediate treatment with empiric antimicrobials, followed by targeted treatment after the microbe is identified. The clinical utility of anti-inflammatory therapy in MK remains controversial and likely differs due to host- and microbe-specific factors. Newer diagnostic techniques such as whole genome sequencing, metagenomic deep sequencing, transcriptomics, and proteomics have the potential to greatly improve timeliness, accuracy, and precision when diagnosing and treating MK. Metagenomic deep sequencing can identify pathogenic microbes with comparable or superior accuracy to traditional microbiology techniques, enabling faster and more accurate diagnosis and initiation of appropriate treatment. Whole genome sequencing of corneal culture isolates has the potential to provide patient-specific insights about microbial phylogenetics, antimicrobial resistance genes, and virulence factors to enable more targeted antimicrobial therapy. Characterization of the host immune response using RNA sequencing or tear proteomics could help inform the use of tailored anti-inflammatory therapies to prevent corneal damage. Although most of these precision medicine approaches are in the research phase, they show the potential to customize MK treatment based on host and microbial factors and improve clinical outcomes.}, } @article {pmid40115744, year = {2025}, author = {Kimmel, M and Tong, B and Devall, AE and Björvang, RD and Schuppe-Koistinen, I and Engstrand, L and Fransson, E and Skalkidou, A and Hugerth, LW}, title = {Investigating the Microbiome in Relation to Mental Distress Across Two Points During Pregnancy: Data From U.S. and Swedish Cohorts.}, journal = {Biological psychiatry global open science}, volume = {5}, number = {3}, pages = {100453}, pmid = {40115744}, issn = {2667-1743}, abstract = {BACKGROUND: In this study, we aimed to characterize the gut microbiome and its potential functioning in 2 populations at 2 time points during pregnancy in relation to mental distress.

METHODS: During the second and third trimester, individuals from the United States and Sweden completed the Edinburgh Postnatal Depression Scale and provided fecal samples for whole-genome metagenomics. A total of 832 and 161 samples were sequenced and analyzed from the Swedish cohort and the U.S. cohort, respectively. Multiple characterizations of the microbial community were analyzed in relation to distress measured using the Edinburgh Postnatal Depression Scale. Principal coordinate analysis and distance-based redundancy analysis assessed variation in functional gut-brain modules. For the U.S. cohort, the Trier Social Stress Test was administered 8 weeks postpartum while collecting salivary cortisol.

RESULTS: Principal coordinate analysis identified 4 sample clusters based on the gut-brain modules distinguished by functions such as short-chain fatty acid synthesis and cortisol degradation. While with distance-based redundancy analysis, mental distress subtypes did not significantly contribute to variation in gut-brain modules (p = .085 for Sweden, p = .23 for the U.S.), a U.S. sample cluster distinguished by lower cortisol degradation from another cluster with higher gut microbial cortisol degradation abundance had significantly higher odds of being associated with depression (p = .024). The U.S. sample cluster with lower gut microbial cortisol degradation abundance also had significantly higher cortisol levels after a postpartum social stressor.

CONCLUSIONS: Further studies are warranted to investigate the potential for the gut microbiome to serve as biomarkers of gut-brain axis health during pregnancy across disparate populations.}, } @article {pmid40115680, year = {2025}, author = {Patankar, C and Kulsum, U and Mahajan, S and Kumar, S and Kale, D and Sharma, VK and Nema, S and Biswas, D}, title = {Mapping Viral Landscapes: Genomic Surveillance of Aedes Mosquitoes From Central India.}, journal = {Cureus}, volume = {17}, number = {2}, pages = {e79206}, pmid = {40115680}, issn = {2168-8184}, abstract = {BACKGROUND: Mosquito-borne viral diseases pose a significant impact on human health, with the potential to cause widespread outbreaks of diseases. Monitoring viral genomes in mosquito populations can lead to informed risk assessment and promote early diagnosis. However, a standardized methodology is lacking to decipher circulating viral sequences in mosquito populations collected from human habitats. Our study aims to establish and evaluate a system of viral metagenomic analysis in the Aedes mosquito population.

METHODS: Mosquitoes were collected using CDC-approved BG-Sentinel version 2 traps (Biogents AG, Regensburg, Germany) and battery-operated vacuum aspirators from different locations in the Bhopal region, India. They were sorted based on genus, gender, location, and collection date. The RNA was extracted from the homogenized mosquito pools and reverse transcribed. Complementary DNA (cDNA) was amplified using sequence-independent, single-prime amplification (SISPA). Further, polymerase chain reaction (PCR) products were sequenced using the Illumina NovaSeq 6000 platform (Illumina, Inc., San Diego, CA). Bioinformatic analysis of the reads was performed using Trimmomatic (Bolger AM, Lohse M, Usadel B (2014). Trimmomatic: A flexible trimmer for Illumina Sequence Data (Bioinformatics, btu170) for trimming low-quality raw reads. Later, Kraken2 and Bracken (Johns Hopkins University, Baltimore, MD) were used for the identification of viral sequences.

RESULTS: The study examined virus diversity and seasonal distribution in mosquito populations collected from 13 sites in Bhopal, India, over 15 months. A total of 31 mosquito pools of female Aedes mosquitoes were analyzed. Metagenomic analysis revealed viruses encompassing plant, animal, insect, fungal, and bacteriophage hosts. The highest mosquito catch was during the post-monsoon period, while virus diversity peaked during the monsoon. Seasonal variations showed a higher frequency and diversity of viruses during the monsoon than during pre- and post-monsoon periods. The findings highlight the importance of temporal and ecological factors in viral surveillance and mosquito-borne disease management.

CONCLUSIONS: Our findings demonstrate the potential of combining entomological and genomic surveillance for monitoring virus circulation in mosquito populations, which may be implemented as a routine surveillance tool for the timely detection of spikes in viruses with human pathogenic potential and thus inform targeted vector control measures to avert potential outbreaks in the future.}, } @article {pmid40115125, year = {2025}, author = {Pavloudi, C and Santi, I and Azua, I and Baña, Z and Bastianini, M and Belser, C and Bilbao, J and Bitz-Thorsen, J and Broudin, C and Camusat, M and Cancio, I and Caray-Counil, L and Casotti, R and Castel, J and Comtet, T and Cox, CJ and Daguin, C and Díaz de Cerio, O and Exter, K and Fauvelot, C and Frada, MJ and Galand, PE and Garczarek, L and González Fernández, J and Guillou, L and Hablützel, PI and Heynderickx, H and Houbin, C and Kervella, AE and Krystallas, A and Lagaisse, R and Laroquette, A and Lescure, L and Lopes, E and Loulakaki, M and Louro, B and Magalhaes, C and Maidanou, M and Margiotta, F and Montresor, M and Not, F and Paredes, E and Percopo, I and Péru, E and Poulain, J and Præbel, K and Rigaut-Jalabert, F and Romac, S and Stavroulaki, M and Souza Troncoso, J and Thiébaut, E and Thomas, W and Tkacz, A and Trano, AC and Wincker, P and Pade, N}, title = {First release of the European marine omics biodiversity observation network (EMO BON) shotgun metagenomics data from water and sediment samples.}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e143585}, pmid = {40115125}, issn = {1314-2828}, abstract = {The European Marine Omics Biodiversity Observation Network (EMO BON) is an initiative of the European Marine Biological Resource Centre (EMBRC) to establish a persistent genomic observatory amongst designated European coastal marine sites, sharing the same protocols for sampling and data curation. Environmental samples are collected from the water column and, at some sites, soft sediments and hard substrates (Autonomous Reef Monitoring Structures - ARMS), together with a set of mandatory and discretionary metadata (including Essential Ocean Variables - EOVs). Samples are collected following standardised protocols at regular and specified intervals and sequenced in large six-monthly batches at a centralised sequencing facility. The use of standard operating procedures (SOPs) during data collection, library preparation and sequencing aims to provide uniformity amongst the data collected from the sites. Coupled with strict adherence to open and FAIR (Findable, Accessible, Interoperable, Reusable) data principles, this ensures maximum comparability amongst samples and enhances reusability and interoperability of the data with other data sources. The observatory network was launched in June 2021, when the first sampling campaign took place.}, } @article {pmid40115072, year = {2025}, author = {Li, J and Hu, X and Tao, X and Li, Y and Jiang, W and Zhao, M and Ma, Z and Chen, B and Sheng, S and Tong, J and Zhang, H and Shen, B and Gao, X}, title = {Deconstruct the link between gut microbiota and neurological diseases: application of Mendelian randomization analysis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1433131}, pmid = {40115072}, issn = {2235-2988}, mesh = {Humans ; *Mendelian Randomization Analysis ; *Gastrointestinal Microbiome/genetics ; *Nervous System Diseases/genetics/microbiology ; Brain-Gut Axis ; Genome-Wide Association Study ; }, abstract = {BACKGROUND: Recent research on the gut-brain axis has deepened our understanding of the correlation between gut bacteria and the neurological system. The inflammatory response triggered by gut microbiota may be associated with neurodegenerative diseases. Additionally, the impact of gut microbiota on emotional state, known as the "Gut-mood" relationship, could play a role in depression and anxiety disorders.

RESULTS: This review summarizes recent data on the role of gut-brain axis in the pathophysiology of neuropsychiatric and neurological disorders including epilepsy, schizophrenia, Alzheimer's disease, brain cancer, Parkinson's disease, bipolar disorder and stroke. Also, we conducted a Mendelian randomization study on seven neurological disorders (Epilepsy, schizophrenia, Alzheimer's disease, brain cancer, Parkinson's disease, bipolar disorder and stroke). MR-Egger and MR-PRESSO tests confirmed the robustness of analysis against horizontal pleiotropy.

CONCLUSIONS: By comparing the protective and risk factors for neurological disorders found in our research and other researches, we can furtherly determine valuable indicators for disease evolution tracking and potential treatment targets. Future research should explore extensive microbiome genome-wide association study datasets using metagenomics sequencing techniques to deepen our understanding of connections and causality between neurological disorders.}, } @article {pmid40114670, year = {2025}, author = {Hu, W and Teng, Y and Wang, X and Xu, Y and Sun, Y and Wang, H and Li, Y and Dai, S and Zhong, M and Luo, Y}, title = {Mixotrophic cyanobacteria are critical active diazotrophs in polychlorinated biphenyl-contaminated paddy soil.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycae160}, pmid = {40114670}, issn = {2730-6151}, abstract = {Biological nitrogen fixation by diazotrophs is a crucial biogeochemical process in global terrestrial ecosystems, especially in nitrogen-limited, organic-contaminated soils. The metabolic activities of diazotrophs and their ability to supply fixed nitrogen may facilitate the transformation of organic pollutants. However, the active diazotrophic communities in organic-contaminated soils and their potential metabolic functions have received little attention. In the current study, the relationship between biological nitrogen fixation and polychlorinated biphenyl (PCB) metabolism was analyzed in situ in paddy soil contaminated with a representative tetrachlorobiphenyl (PCB52). [15]N-DNA stable isotope probing was combined with high-throughput sequencing to identify active diazotrophs, which were distributed in 14 phyla, predominantly Cyanobacteria (23.40%). Subsequent metagenome binning and functional gene mining revealed that some mixotrophic cyanobacteria (e.g. FACHB-36 and Cylindrospermum) contain essential genes for nitrogen fixation, PCB metabolism, and photosynthesis. The bifunctionality of Cylindrospermum sp. in nitrogen fixation and PCB metabolism was further confirmed by metabolite analyses of Cylindrospermum sp. from a culture collection as a representative species, which showed that Cylindrospermum sp. metabolized PCB and produced 2-chlorobiphenyl and 2,5-dihydroxybenzonic acid. Collectively, these findings indicate that active diazotrophs, particularly mixotrophic cyanobacteria, have important ecological remediation functions and are a promising nature-based in situ remediation solution for organic-contaminated environments.}, } @article {pmid40114290, year = {2025}, author = {Demina, T and Marttila, H and Pessi, IS and Männistö, MK and Dutilh, BE and Roux, S and Hultman, J}, title = {Tunturi virus isolates and metagenome-assembled viral genomes provide insights into the virome of Acidobacteriota in Arctic tundra soils.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {79}, pmid = {40114290}, issn = {2049-2618}, mesh = {*Soil Microbiology ; *Genome, Viral ; *Virome ; *Tundra ; *Phylogeny ; *Metagenome ; Arctic Regions ; Finland ; Bacteriophages/genetics/classification/isolation & purification ; Acidobacteria/genetics/classification/isolation & purification ; Soil ; DNA, Viral/genetics ; }, abstract = {BACKGROUND: Arctic soils are climate-critical areas, where microorganisms play crucial roles in nutrient cycling processes. Acidobacteriota are phylogenetically and physiologically diverse bacteria that are abundant and active in Arctic tundra soils. Still, surprisingly little is known about acidobacterial viruses in general and those residing in the Arctic in particular. Here, we applied both culture-dependent and -independent methods to study the virome of Acidobacteriota in Arctic soils.

RESULTS: Five virus isolates, Tunturi 1-5, were obtained from Arctic tundra soils, Kilpisjärvi, Finland (69°N), using Tunturiibacter spp. strains originating from the same area as hosts. The new virus isolates have tailed particles with podo- (Tunturi 1, 2, 3), sipho- (Tunturi 4), or myovirus-like (Tunturi 5) morphologies. The dsDNA genomes of the viral isolates are 63-98 kbp long, except Tunturi 5, which is a jumbo phage with a 309-kbp genome. Tunturi 1 and Tunturi 2 share 88% overall nucleotide identity, while the other three are not related to one another. For over half of the open reading frames in Tunturi genomes, no functions could be predicted. To further assess the Acidobacteriota-associated viral diversity in Kilpisjärvi soils, bulk metagenomes from the same soils were explored and a total of 1881 viral operational taxonomic units (vOTUs) were bioinformatically predicted. Almost all vOTUs (98%) were assigned to the class Caudoviricetes. For 125 vOTUs, including five (near-)complete ones, Acidobacteriota hosts were predicted. Acidobacteriota-linked vOTUs were abundant across sites, especially in fens. Terriglobia-associated proviruses were observed in Kilpisjärvi soils, being related to proviruses from distant soils and other biomes. Approximately genus- or higher-level similarities were found between the Tunturi viruses, Kilpisjärvi vOTUs, and other soil vOTUs, suggesting some shared groups of Acidobacteriota viruses across soils.

CONCLUSIONS: This study provides acidobacterial virus isolates as laboratory models for future research and adds insights into the diversity of viral communities associated with Acidobacteriota in tundra soils. Predicted virus-host links and viral gene functions suggest various interactions between viruses and their host microorganisms. Largely unknown sequences in the isolates and metagenome-assembled viral genomes highlight a need for more extensive sampling of Arctic soils to better understand viral functions and contributions to ecosystem-wide cycling processes in the Arctic. Video Abstract.}, } @article {pmid40114168, year = {2025}, author = {Wu, Y and Qu, Z and Wu, Z and Zhuang, J and Wang, Y and Wang, Z and Chu, J and Qi, Q and Han, S}, title = {Multiple primary malignancies and gut microbiome.}, journal = {BMC cancer}, volume = {25}, number = {1}, pages = {516}, pmid = {40114168}, issn = {1471-2407}, support = {2022E50008, 2024ZY01056//Zhejiang Provincial Clinical Research Center for CANCER/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; Male ; Middle Aged ; *Metagenomics/methods ; *Neoplasms, Multiple Primary/microbiology/virology ; Colorectal Neoplasms/microbiology/virology ; Adult ; Aged ; Bacteria/classification/genetics/isolation & purification ; Enterovirus/isolation & purification/genetics ; Case-Control Studies ; Feces/microbiology/virology ; }, abstract = {BACKGROUND: Multiple primary malignancies (MPM) are two or more independent primary malignancies. Recently, the relationship between microbiome and various tumors has been gradually focused on.

OBJECTIVE: To describe the relationship between MPM patients (MPMs) and gut microbiome.

METHODS: A total of 27 MPMs, 30 colorectal cancer patients (CRCs), and 30 healthy individuals were included to obtain metagenomic sequencing data. The knowledge graphs of gut bacteria and enteroviruses were plotted based on metagenomics. Wilcoxon rank-sum test was used to screen the characteristic gut microbiome.

RESULTS: The knowledge graph of gut microbiome in MPM patients was plotted. A total of 26 different gut bacteria, including Dialister, Fecalibacterium and Mediterraneibacter, were found between MPMs and healthy individuals. Twenty gut bacteria, including Parvimonas, Dialister and Mediterraneibacter, were more abundant in MPM complicated by CRC compared with CRCs. Twenty-one different enterovirus, including Triavirus, Punavirus and Lilyvirus, were screened between MPMs and healthy individuals. Triavirus, Punavirus and Lilyvirus were less abundant in MPM than healthy individuals. The abundance of Triavirus, Punavirus and Lilyvirus in CRC patients were also lower than MPM complicated by CRC patients.

CONCLUSION: The knowledge graph of gut microbiome in MPM patients was plotted. It may provide basic data support for future research of MPM.}, } @article {pmid40113957, year = {2025}, author = {Lai, Y and Chen, B and Chen, S and Shen, Y}, title = {Experience of implementing metagenomic next-generation sequencing in patients with suspected pulmonary infection in clinical practice.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {9579}, pmid = {40113957}, issn = {2045-2322}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Male ; *Metagenomics/methods ; Female ; Aged ; Middle Aged ; Retrospective Studies ; Adult ; Aged, 80 and over ; Respiratory Tract Infections/microbiology/diagnosis/drug therapy ; Bacteria/genetics/isolation & purification/classification ; Metagenome ; }, abstract = {Pulmonary infections remain a leading cause of infectious disease-related hospitalizations. Metagenomic next-generation sequencing (mNGS) has emerged as a promising diagnostic tool for identifying pathogens responsible for pulmonary infections. However, implementing mNGS in clinical practice presents several challenges. We conducted a retrospective analysis of 97 patients with suspected pulmonary infections who were admitted to our hospital and underwent mNGS alongside conventional microbiologic tests (CMT) over the past three years. We compared the diagnostic efficacy of mNGS versus CMT and assessed the clinical applications and challenges associated with mNGS in managing pulmonary infections. mNGS detected pathogens in 63.9% of cases, outperforming CMT (27.8%) and showing notable improvements in identifying Mycobacterium, fungal species, and rare pathogens. Antibiotic regimens were adjusted for 77.4% of patients with positive mNGS results, with clinical improvement observed in 93.5%. Of the 138 microbial strains initially identified by mNGS as possible pathogens, 65 (47.1%) were reclassified as colonizing organisms upon further clinical evaluation, including bacteria and fungi commonly associated with pulmonary infections. Notably, one patient was diagnosed with aspiration pneumonia due to oral anaerobes, which mNGS had categorized as normal microbial flora. In conclusion, mNGS serves as a valuable diagnostic approach for pulmonary infections, enhancing etiologic precision and informing patient management. Nevertheless, a comprehensive clinical interpretation of mNGS-identified microorganisms is essential to achieve accurate diagnosis.}, } @article {pmid40113286, year = {2025}, author = {Li, F and Qiu, CS and Wang, CC and Xu, F and Wang, D and Liu, NN and Chen, X and Wang, SP}, title = {[Distribution Characteristics and Influencing Factors of Antibiotic Resistance Genes in Surface Sediments of Regulating Pond in South-to-North Water Transfer Pumping Station].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {46}, number = {3}, pages = {1435-1442}, doi = {10.13227/j.hjkx.202312226}, pmid = {40113286}, issn = {0250-3301}, mesh = {*Geologic Sediments/microbiology ; China ; *Drug Resistance, Microbial/genetics ; Ponds/microbiology ; Genes, Bacterial ; Environmental Monitoring ; Water Supply ; Bacteria/genetics/classification ; Rivers/microbiology ; Water Microbiology ; }, abstract = {As an important facility to ensure the safety of the water supply, the regulating pond of a raw water pumping station in the Tianjin Section of the middle route of the South-to-North Water Transfer Project linked the raw water from the Hanjiang River with the urban water plants. Surface sediment samples from different regions of the regulator pond were collected in summer, autumn, and winter of 2022 and spring of 2023, respectively. Metagenomic sequencing technology was used to analyze the distribution characteristics and influencing factors of antibiotic resistance genes （ARGs）, and the correlation between sediment ARGs and physicochemical indices, microbial community structure, and mobile genetic elements （MGEs） was also analyzed. The results showed that 20 antibiotic resistance types and 921 ARGs subtypes were detected in the surface sediment samples of the regulator pond. The dominant ARGs in the samples at different sampling times and sampling points were multidrug resistance, MLS, tetracycline, and glycopeptides, and the main resistance mechanism was efflux pump. Correlation analysis showed that TN, NO3[-]-N, TP, and OM of sediments were significantly correlated （P<0.05） with various ARGs of the top 20 ARGs. Among the top 20 microbial genera, 19 species were significantly correlated （P<0.05） with ARGs. The MGEs types of conjugate transfer protein, recombinase, and transposase were significantly positively correlated （P<0.05） with the top 20 ARGs.}, } @article {pmid40113151, year = {2025}, author = {Zhang, W and Wen, L and Xin, Z and Wang, G and Lin, H and Wang, H and Wei, B and Yan, X and Wang, W and Guo, B}, title = {Research on the histopathology of Larimichthys crocea affected by white gill disease and analysis of its bacterial and viral community characteristics.}, journal = {Fish & shellfish immunology}, volume = {}, number = {}, pages = {110287}, doi = {10.1016/j.fsi.2025.110287}, pmid = {40113151}, issn = {1095-9947}, abstract = {White gill disease (WGD) is one of the major diseases affecting Larimichthys crocea, although its etiology remains unclear. To investigate the causes of WGD, this study selected WGD-affected Larimichthys crocea (WG) and healthy Larimichthys crocea (NH) from multiple aquaculture regions for pathological analysis and analysis of bacterial and viral community characteristics. The results indicated severe tissue damage and significant inflammatory responses, as evidenced by clinical manifestations and electron microscopy. Two bacterial species, Photobacterium damselae and Vibrio campbellii, were isolated from all lesion tissues. Additionally, 16S full-length sequencing results showed that Photobacterium damselae and Vibrio campbellii dominated in the tissues of Larimichthys crocea, with a combined relative abundance of approximately 90%. There were no significant differences in α-diversity and β-diversity between the NH group and WG group from the three aquaculture regions, and no significant biomarkers were identified. The diversity of DNA and RNA viruses did not show significant differences between the NH and WG groups, although both types of viruses exhibited notable synergistic and antagonistic relationships. Analyses from 16S full-length sequencing, metagenomics, and metatranscriptomics revealed that the related functional genes were primarily enriched in various metabolic pathways, including glycine biosynthesis, membrane transport, and energy metabolism. The metatranscriptomic analysis indicated that the expression levels of genes related to antibiotic resistance, biosynthesis, transport, and degradation processes were significantly downregulated in the WG group. Finally, through PCR, qPCR, and metagenomic sequencing, we were unable to detect iridovirus in Larimichthys crocea, further suggesting that the causes of WGD may differ across aquaculture regions compared to previous reports. This study indicates that the etiology of WGD may involve complex ecological and metabolic mechanisms, rather than being merely the result of a single pathogen infection. This research provides a comprehensive analysis of the microbial communities in WGD-affected Larimichthys crocea from multiple aquaculture regions for the first time, providing a theoretical basis for further elucidating the causes of WGD and developing preventive measures.}, } @article {pmid40113108, year = {2025}, author = {Ruan, Z and Shi, H and Chang, L and Zhang, J and Fu, M and Li, R and Zeng, D and Yang, Y and Li, R and Ai, L and Wang, Y and Hai, B}, title = {The Diagnostic Efficacy of Metagenomic Next-Generation Sequencing (mNGS) in Pathogen Identification of Pediatric Pneumonia using Bronchoalveolar Lavage Fluid (BALF): A Systematic Review and Meta-Analysis.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {107492}, doi = {10.1016/j.micpath.2025.107492}, pmid = {40113108}, issn = {1096-1208}, abstract = {OBJECTIVE: This meta-analysis evaluates and compares the diagnostic efficacy of metagenomic next-generation sequencing (mNGS) with conventional microbiological tests (CMTs) in diagnosing pediatric pneumonia using bronchoalveolar lavage fluid (BALF).

METHODS: Data were sourced from Embase, Medline (via PubMed), Web of Science, and the Cochrane Library. The pooled positive detection rate (PDR) of pathogens was estimated using fixed-effects or random-effects models. Subgroup analyses explored factors influencing mNGS diagnostic performance. Data analysis was conducted using Review Manager (RevMan) 5.4 and Stata version 16.0.

RESULTS: The pooled PDR of mNGS was 85.83%, which is higher than the pooled PDR of 49.97% for CMTs. A random-effects model indicated that, compared to CMTs, mNGS has a significantly higher PDR in pediatric pneumonia (OR=3.99, 95%CI: 2.12-7.50, P<0.0001, I[2]=81%). Subgroup analysis indicated that mNGS exhibited greater advantages in the group using the QIAamp kit (OR=5.55, 95% CI: 3.03-10.16, P<0.00001), the group using the Illumina Nextseq platform (OR=4.87, 95% CI: 2.97-7.99, P<0.00001), the DNA-only mNGS group (OR=4.54, 95% CI: 2.73-7.54, P<0.00001), and the non-severe pneumonia group (OR=4.76, 95% CI: 3.51-6.46, P<0.00001). However, when the subgroups were categorized as mixed infections or single-pathogen infections, no statistically significant differences were observed (Mixed: OR=1.77, 95% CI: 0.30-10.56, P=0.53; Single: OR=3.97, 95% CI: 0.42-37.87, P=0.23) CONCLUSION: mNGS demonstrates high diagnostic efficacy in detecting pathogens in BALF from pediatric patients with pneumonia. The diagnostic stability of mNGS is influenced by sample extraction, sequencing platforms, positive interpretation criteria, and disease status. Standardized procedures and technologies can enhance mNGS diagnostic performance.}, } @article {pmid40112621, year = {2025}, author = {Ma, C and Zhao, Y and Ma, B and Li, X and Li, X and Chen, X}, title = {Co-critical golden-flower fungus (Eurotium repens) contributed to characteristic flavor formation of two Yunnan jinhua teas through jinhua formation during the storage.}, journal = {Food chemistry}, volume = {479}, number = {}, pages = {143765}, doi = {10.1016/j.foodchem.2025.143765}, pmid = {40112621}, issn = {1873-7072}, abstract = {Jinhua formation during the storage (JFDS) was found in two Yunnan teas that were defined as jinhua ripened Pu-erh tea (JRIPT) and jinhua white tea (JWT), respectively. Integrated multi-omics of metagenomics, volatilomics and metabolomics was developed to elucidate JFDS mechanism. Overall, JFDS caused significant differences in characteristic flavor, microbial community structure and volatile organic compounds (VOCs) profile. Among 14 co-critical fungi, Eurotium repens was regarded as the golden-flower fungus for JFDS, and had higher relative abundance in Yunnan jinhua teas over 50 %. Based on 291 VOCs and 83 odor-active compounds, E. repens directly promoted glycoside hydrolysis and carotene degradation to formulate β-linalool, β-ionone and 3,4-dehydro-β-ionone for jinhua fungus aroma of JWT. With Arxula adeninivorans synergy, E. repens activity contributed to Chinese medicine-like smell of JRIPT through sesquiterpenes and methoxybenzenes accumulation. Additionally, E. repens activity in the JFDS accelerated catechins oxidative polymerization, and other flavonoids conversion to enhance mellow taste.}, } @article {pmid40111891, year = {2025}, author = {Díez-Madueño, K and Montero, I and Fernández-Gosende, M and Martínez-Álvarez, N and Hidalgo-Cantabrana, C and de la Cueva Dobao, P and Coto-Segura, P}, title = {Compositional and Functional Profile of Gut Microbiota in a Cohort of Adult Spanish Patients with Atopic Dermatitis Using Metagenomics: A Cross-Sectional Study.}, journal = {Dermatitis : contact, atopic, occupational, drug}, volume = {}, number = {}, pages = {}, doi = {10.1089/derm.2024.0536}, pmid = {40111891}, issn = {2162-5220}, abstract = {Background: The role of gut dysbiosis in the pathophysiology of atopic dermatitis (AD) through immune system (IS) imbalance is a novel line of investigation currently under discussion. This study aimed to characterize compare the composition and functional profile of the gut microbiota (GM) between adults with AD and healthy individuals. Methods: Observational cross-sectional study, where fecal samples from 70 adults (38 patients and 32 controls) were analyzed using metagenomics and bioinformatics. Results: Differences between the GM of patients with AD and healthy individuals were demonstrated. Reduced microbial diversity was found in subjects with AD. Bacterial species with lower abundance primarily belonged to the families Ruminococcaceae, Akkermansiaceae, and Methanobacteriaceae. Several microbial metabolic pathways were found to be decreased in patients with AD, including amino acid biosynthesis, vitamin biosynthesis, fatty acids and lipids biosynthesis, and energy metabolism. Conclusion: Adults with AD exhibited a distinct GM compared to healthy individuals. Changes were demonstrated both compositionally and functionally. Further investigation is mandatory to elucidate the potential link and causal relationship between gut dysbiosis and AD, which may be crucial for a deeper understanding of the disease's pathophysiology and the development of novel therapeutic approaches.}, } @article {pmid40111684, year = {2025}, author = {de Barros Santos, HS and Pagnussatti, MEL and Arthur, RA}, title = {Symbiosis Between the Oral Microbiome and the Human Host: Microbial Homeostasis and Stability of the Host.}, journal = {Advances in experimental medicine and biology}, volume = {1472}, number = {}, pages = {31-51}, pmid = {40111684}, issn = {0065-2598}, mesh = {Humans ; *Symbiosis ; *Mouth/microbiology ; *Microbiota/physiology ; *Homeostasis ; *Host Microbial Interactions ; Bacteria/metabolism/genetics/classification ; Metagenomics/methods ; Oral Health ; }, abstract = {The oral cavity presents a highly diverse microbial composition. All the three domains of life, Bacteria, Eukarya, and Archaea, as well as viruses constitute the oral microbiome. Bacteria are among the most abundant microorganisms in the oral cavity, followed by viruses, fungi, and Archaea. These microorganisms tend to live in harmony with each other and with the host by preventing the colonization of oral sites by exogenous microorganisms. Interactions between the host and its microbiota are crucial for keeping ecological stability in the oral cavity and a condition compatible with oral health. This chapter focuses on describing the oral microbiota in healthy individuals based on both targeted and nontargeted genome sequencing methods and the functional activity played by those microorganisms based on metagenomic, metatranscriptomic, metaproteomic, and metabolomic analyses. Additionally, this chapter explores mutualistic and antagonistic microbe-microbe relationships. These interactions are mediated by complex mechanisms like cross-feeding networks, production of bacteriocins and secondary metabolites, synthesis of pH-buffering compounds, and the use of universal signaling molecules. At last, the role played by host-microbe interactions on colonization resistance and immune tolerance will help provide a better understanding about the harmonious and peaceful coexistence among host and microbial cells under oral health-related conditions.}, } @article {pmid40111141, year = {2025}, author = {Yang, F and Zhang, Y and Qi, B and Chen, L and Lin, F and Wu, J and Gong, S and Cao, L and Zeng, M and Cheng, Q and Jiang, D and Tang, S and He, J and Xu, Z and Li, T and Ni, Z and Li, Y and Huang, X and Pan, C and Liu, R and Lan, Y}, title = {Clinical Manifestations and Prognosis of Patients With Mucormycosis in Intensive Care Units in Western China: A Multi-Center Retrospective Study.}, journal = {Mycoses}, volume = {68}, number = {3}, pages = {e70042}, doi = {10.1111/myc.70042}, pmid = {40111141}, issn = {1439-0507}, support = {2023QN02//Research Fund of Sichuan Academy of Medical Science and Sichuan Provincial People's Hospital/ ; 2025ZNSFSC1542//Sichuan Science and Technology Program/ ; }, mesh = {Humans ; *Mucormycosis/mortality/diagnosis/drug therapy/epidemiology/microbiology ; Female ; Male ; Middle Aged ; Retrospective Studies ; *Intensive Care Units ; China/epidemiology ; Aged ; *Antifungal Agents/therapeutic use ; Adult ; Prognosis ; Critical Illness ; Amphotericin B/therapeutic use ; }, abstract = {BACKGROUND: Mucormycosis is a life-threatening fungal infection with high mortality in critically ill patients. Clinical manifestations and outcomes of mucormycosis in intensive care units (ICUs) remain poorly investigated.

METHODS: We conducted a multicenter retrospective study including 43 adult patients with confirmed mucormycosis admitted to 14 tertiary ICUs between January 2014 and May 2022. Clinical characteristics, diagnostic approaches, treatment strategies, and outcomes were analysed.

RESULTS: The mean age was 56.8 ± 16.2 years, with 16/43 (37.2%) female patients. The 28-day survival rate was 46.5% (20/43). Lung involvement was predominant (29/43, 67.4%), and 29/43 (67.4%) patients received amphotericin B therapy. Survivors showed significantly better treatment response compared to non-survivors (16/20, 80% vs. 4/23, 17.4%, p < 0.001). Non-survivors demonstrated significantly higher levels of aspartate aminotransferase, C-reactive protein, and white blood cells, along with lower albumin levels. Metagenomic next-generation sequencing (mNGS) was associated with a shorter time to diagnosis. Multivariate analysis identified age, respiratory failure, time from symptom onset to diagnosis, and antifungal treatment response as independent predictors of 28-day mortality (AUC = 0.852).

CONCLUSION: In critically ill patients with mucormycosis, early diagnosis and prompt targeted therapy are crucial determinants of survival, with our newly developed prediction model providing a practical tool for risk stratification, while mNGS shows promise in expediting diagnosis.}, } @article {pmid40111052, year = {2025}, author = {Martí, JM and Kok, CR and Thissen, JB and Mulakken, NJ and Avila-Herrera, A and Jaing, CJ and Allen, JE and Be, NA}, title = {Addressing the dynamic nature of reference data: a new nucleotide database for robust metagenomic classification.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0123924}, doi = {10.1128/msystems.01239-24}, pmid = {40111052}, issn = {2379-5077}, abstract = {UNLABELLED: Accurate metagenomic classification relies on comprehensive, up-to-date, and validated reference databases. While the NCBI BLAST Nucleotide (nt) database, encompassing a vast collection of sequences from all domains of life, represents an invaluable resource, its massive size-currently exceeding 10[12] nucleotides-and exponential growth pose significant challenges for researchers seeking to maintain current nt-based indices for metagenomic classification. Recognizing that no current nt-based indices exist for the widely used Centrifuge classifier, and the last public version currently available was released in 2018, we addressed this critical gap by leveraging advanced high-performance computing resources. We present new Centrifuge-compatible nt databases, meticulously constructed using a novel pipeline incorporating different quality control measures, including reference decontamination and filtering. These measures demonstrably reduce spurious classifications, as shown through our reanalysis of published metagenomic data where Plasmodium annotations were dramatically reduced using our decontaminated database, highlighting how database quality can significantly impact research conclusions. Through temporal comparisons, we also reveal how our approach minimizes inconsistencies in taxonomic assignments stemming from asynchronous updates between public sequence and taxonomy databases. These discrepancies are particularly evident in taxa such as Listeria monocytogenes and Naegleria fowleri, where classification accuracy varied significantly across database versions. These new databases, made available as pre-built Centrifuge indexes, respond to the need for an open, robust, nt-based pipeline for taxonomic classification in metagenomics. Applications such as environmental metagenomics, forensics, and clinical metagenomics, which require comprehensive taxonomic coverage, will benefit from this resource. Our work highlights the importance of treating reference databases as dynamic entities, subject to ongoing quality control and validation akin to software development best practices. This approach is crucial for ensuring accuracy and reliability of metagenomic analysis, especially as databases continue to expand in size and complexity.

IMPORTANCE: Accurately identifying the diverse microbes present in a sample, whether from the human gut, a soil sample, or a crime scene, is crucial for fields ranging from medicine to environmental science. Researchers rely on comprehensive DNA databases to match sequenced DNA fragments to known microbial species. However, the widely used NCBI nt database, while vast, poses significant challenges. Its massive size makes it difficult for many researchers to use effectively with taxonomic classifiers, and inconsistencies and contamination within the database can impact the accuracy of microbial identification. This work addresses these challenges by providing cleaned, updated, and validated nt-based databases specifically optimized for the widely used Centrifuge classification tool. This new resource demonstrably reduces errors and improves the reliability of microbial identification across diverse taxonomic groups. Moreover, by providing readily usable indexes, we overcome the size barrier, enabling researchers to leverage the full potential of the nt database for metagenomic analysis. Our findings underscore the need to treat reference databases as dynamic entities, emphasizing continuous quality control and versioning as essential practices for robust and reproducible metagenomics research.}, } @article {pmid40111022, year = {2025}, author = {Lim, SJ and Rogers, A and Rosario, K and Kerr, M and Garrett, M and Koester, J and Hubbard, K and Breitbart, M}, title = {Diverse ssRNA viruses associated with Karenia brevis harmful algal blooms in southwest Florida.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0109024}, doi = {10.1128/msphere.01090-24}, pmid = {40111022}, issn = {2379-5042}, abstract = {Harmful algal blooms (HABs) caused by the dinoflagellate Karenia brevis frequently occur in the eastern Gulf of Mexico, where they negatively impact the environment, human health, and economy. Very little is known about viruses associated with K. brevis blooms, although viral infection of other HAB-forming phytoplankton species can play an important role in bloom dynamics. We used viral metagenomics to identify viruses in 11 pooled seawater samples collected from southwest Florida, USA, in 2021 during a severe, spatiotemporally dynamic K. brevis bloom. Assembled viral genomes were similar to published genomes from the order Picornavirales, family Marnaviridae, and genera Sogarnavirus, Bacillarnavirus, and Marnavirus. Several of the cultured viruses from these groups infect bloom-forming diatoms (Chaetoceros sp. and Rhizosolenia setigera) and the raphidophyte Heterosigma akashiwo. We also recovered unclassified Riboviria genomes related to a Symbiodinium positive-sense ssRNA virus sequenced from coral dinoflagellate symbionts. Reverse-transcriptase PCR assays were performed to monitor the occurrence of seven representative virus genomes in these samples from 2021 and 43 seawater samples collected during a subsequent, typical bloom between November 2022 and May 2023. Over half of the samples contained multiple viruses, and at least one viral genome was detected in 44 of the 54 samples collected across seasons and years, highlighting the ubiquity of these viruses in this region. Alpha diversity was highest in the summer months and positively correlated with K. brevis cell counts. Multiple regression revealed month and the presence of unclassified Riboviria sequences most similar to dinoflagellate viruses as significant predictors of K. brevis cellular abundance.IMPORTANCEHarmful algal blooms caused by the dinoflagellate Karenia brevis negatively impact the tourism, fisheries, and public health sectors. Anticipated impacts of climate change, nutrient pollution, and ocean acidification may sustain and/or exacerbate K. brevis blooms in the future, underscoring the need for proactive monitoring, communication, and mitigation strategies. This study represents a pioneering effort in monitoring viruses associated with K. brevis blooms. The findings lay the groundwork for studying the effects of environmental drivers on K. brevis blooms and their associated viruses, as well as for exploring the roles of viruses in bloom dynamics and potential applications of viruses as biocontrol agents for K. brevis blooms. Furthermore, the comparison of viral dynamics relative to local and regional bloom dynamics in this study helps inform future monitoring and modeling needs.}, } @article {pmid40110701, year = {2025}, author = {Liang, H and Li, T and Chen, Y and Wang, J and Aslam, M and Qin, H and Fan, W and Du, H and Kao, SJ and Lin, S}, title = {Urea Amidolyase as an Enzyme for Urea Utilisation in Phytoplankton: Functional Display in Chlamydomonas reinhardtii.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {e17734}, doi = {10.1111/mec.17734}, pmid = {40110701}, issn = {1365-294X}, support = {42206116//Natural Science Foundation of China/ ; 2024A1515011467；2025A1515010095//Natural Science Foundation of Guangdong Province, China/ ; 2021B1212050025//Science and Technology Plan Projects of Guangdong Province/ ; 2022KCXTD008//Program for University Innovation Team of Guangdong Province/ ; 2024-MRB-00-001//Research on Breeding Technology of Candidate Species for Guangdong Modern Marine Ranching/ ; }, abstract = {Urea is an important source of nitrogen for many phytoplankton with the potential to stimulate harmful algal blooms, but the molecular machinery underpinning urea uptake and assimilation by algae is not fully understood. Urease (URE) is commonly regarded as the responsible enzyme, but urea amidolyase (UAL), albeit known to exist, has hardly been studied. Here, the species distribution, expression patterns and functional roles of UAL are examined. We found a widespread occurrence of UAL across six major phytoplankton lineages, along with evidence of a potential URE-independent evolutionary trajectory and lineage-specific losses. Quantitative analyses based on marine planktonic metagenomes and metatranscriptomes revealed that UAL is as prevalent as URE, but exhibits higher expression levels in phytoplankton than in bacteria, suggesting that UAL plays a crucial role in nitrogen nutrition in marine phytoplankton. Furthermore, using the CRISPR/Cas9 genome editing method and Chlamydomonas reinhardtii as the algal model, we showed that DUR2 in UAL is essential for urea utilisation, as its knockout completely abolishes the ability of algae to grow under urea as the sole nitrogen source. This study unveils an unappreciated mechanism in algae for utilising urea as a nutrient, underscores the need to consider both URE and UAL enzyme systems to model urea utilisation by algae and provides a crucial gene (DUR2) as a potential genetic marker for detecting the contribution of UAL to urea utilisation in phytoplankton.}, } @article {pmid40110433, year = {2025}, author = {Cheng, C and Zheng, Y and Wang, X and Tao, J and Cheng, D}, title = {Research in etiology of Floppy Kid Syndrome.}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1557951}, pmid = {40110433}, issn = {2297-1769}, abstract = {Floppy Kid Syndrome (FKS) is a common and serious disease in goats, with incidence rates ranging from 10 to 50% and mortality rates between 20 and 60%. This study aimed to investigate the etiology of FKS through blood biochemical analysis and metagenomic sequencing. Blood biochemical analysis revealed metabolic disorders in FKS-affected goats, including acidosis and hypoglycemia. Metagenomic analysis showed marked gastric and gut dysbacteriosis, characterized by an increase in pathogenic bacteria such as Escherichia coli and Staphylococcus aureus, alongside a significant reduction in probiotic like Lactobacillus amylovorus. Furthermore, species diversity and richness were notably lower in FKS-affected goats compared to healthy goats. Based on these findings, we infer that FKS is a multifactorial disease caused by gastric and gut dysbacteriosis. The immaturity of the digestive system in newborn goats, combined with environmental stressors (such as sudden changes in weather), leads to gastric and gut dysbacteriosis, with a significant reduction in probiotic and an overgrowth of pathogenic bacteria. The dysbacteriosis, along with the inability to properly digest excessive milk intake, contributes to the accumulation of undigested milk in the digestive tract, creating an environment conducive to pathogenic bacteria growth. The fermentation of milk and the production of excessive lactic acid by pathogenic bacteria are absorbed into the bloodstream, causing acidosis and hypoglycemia. These metabolic disorders, in conjunction with the dysbacteriosis and systemic dysfunction, lead to the onset of FKS. These results underscore the critical role of gastric and gut dysbacteriosis in the pathogenesis of FKS, highlighting the need for targeted preventive and therapeutic strategies.}, } @article {pmid40109965, year = {2025}, author = {Zou, Z and Tang, F and Qiao, L and Wang, S and Zhang, H}, title = {Integrating sequencing methods with machine learning for antimicrobial susceptibility testing in pediatric infections: current advances and future insights.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1528696}, pmid = {40109965}, issn = {1664-302X}, abstract = {Antimicrobial resistance (AMR) presents a critical challenge in clinical settings, particularly among pediatric patients with life-threatening conditions such as sepsis, meningitis, and neonatal infections. The increasing prevalence of multi- and pan-resistant pathogens is strongly associated with adverse clinical outcomes. Recent technological advances in sequencing methods, including metagenomic next-generation sequencing (mNGS), Oxford Nanopore Technologies (ONT), and targeted sequencing (TS), have significantly enhanced the detection of both pathogens and their associated resistance genes. However, discrepancies between resistance gene detection and antimicrobial susceptibility testing (AST) often hinder the direct clinical application of sequencing results. These inconsistencies may arise from factors such as genetic mutations or variants in resistance genes, differences in the phenotypic expression of resistance, and the influence of environmental conditions on resistance levels, which can lead to variations in the observed resistance patterns. Machine learning (ML) provides a promising solution by integrating large-scale resistance data with sequencing outcomes, enabling more accurate predictions of pathogen drug susceptibility. This review explores the application of sequencing technologies and ML in the context of pediatric infections, with a focus on their potential to track the evolution of resistance genes and predict antibiotic susceptibility. The goal of this review is to promote the incorporation of ML-based predictions into clinical practice, thereby improving the management of AMR in pediatric populations.}, } @article {pmid40109771, year = {2025}, author = {Chen, HB and Liu, J and Zhang, Y and Huang, H and Wang, LN}, title = {Application of metagenomic next-generation sequencing in the diagnosis of pathogens in patients with diabetes complicated by community-acquired pneumonia.}, journal = {Open life sciences}, volume = {20}, number = {1}, pages = {20221048}, pmid = {40109771}, issn = {2391-5412}, abstract = {To explore the clinical utility and optimal timing of metagenomic next-generation sequencing (mNGS) in diagnosing pathogens in patients with diabetes complicated by community-acquired pneumonia (CAP). The study included 50 hospitalized patients diagnosed with diabetes complicated by CAP who underwent conventional microbiological testing (CMT) and mNGS using bronchoalveolar lavage fluid. Among the 50 cases, 16% presented no respiratory symptoms. There were significant increases in inflammatory markers such as C-reactive protein, erythrocyte sedimentation rate, and interleukin-6, with patchy imaging changes being the most prevalent. The positive rates for pathogen detection by mNGS and CMTs were 78 and 21% (P < 0.05). The mNGS was significantly better than the CMTs in the detection of rare pathogens such as Anaerobes, Chlamydia psittaci, Legionella pneumophila, Mycobacterium bovis, Aspergillus fumigatus, and Pneumocystis japonicus (P < 0.05). After clinical interpretation, 85% (22/26) of viruses, 24% (9/37) of bacteria, and 25% (2/8) of fungi were non-pathogen organisms by mNGS. There was a significant difference in the rates of adjustment in anti-infection treatment strategies based on the pathogen detection results from CMTs and mNGS, which were 2 and 46%, respectively (P < 0.05). We found that mNGS was superior to CMTs in terms of the positive rate of pathogen detection, detecting mixed infection incidence, rare pathogen detection rates, and the adjustment of treatment strategies. However, mNGS results need to be interpreted in the context of the clinic.}, } @article {pmid40109467, year = {2025}, author = {Han, Y and Shen, S and Fu, J and Ren, Q}, title = {[Mechanisms of Wandai Decoction in Improving Vaginal Flora of Vulvovaginal Candidiasis of the Spleen Deficiency and Excessive Dampness Type: A Study Based on Metagenomics and Metabolomics].}, journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition}, volume = {56}, number = {1}, pages = {68-73}, pmid = {40109467}, issn = {1672-173X}, mesh = {Female ; Humans ; *Vagina/microbiology ; *Candidiasis, Vulvovaginal/drug therapy/microbiology ; *Metabolomics ; *Drugs, Chinese Herbal/therapeutic use/administration & dosage ; *Fluconazole/pharmacology/therapeutic use ; Metagenomics ; Antifungal Agents/therapeutic use ; Adult ; Spleen/metabolism/microbiology ; }, abstract = {OBJECTIVE: To explore the mechanism by which Wandai Decoction prevents and treats vulvovaginal candidiasis (VVC) of the spleen deficiency and excessive dampness type and restores the vaginal flora structure, and to identify the potential metabolic pathways involved using metagenomics and metabolomics.

METHODS: Twenty VVC patients who met the inclusion criteria were randomly assigned to a Wandai Decoction group and a fluconazole group (n = 10 in each group). Subjects in the fluconazole group were given a single oral dose of 150 mg fluconazole, while those in the Wandai Decoction group took the Wandai Decoction orally for 14 days. The vulvovaginal signs and symptoms (VSS) scores of both patient groups were evaluated before and after treatment. Vaginal secretions were collected before and after treatment. The Illumina sequencing and the liquid chromatography with tandem mass spectrometry (LC-MS/MS) platform were used to conduct metagenomic and metabolomics analyses of the vaginal secretions, respectively.

RESULTS: The VSS score results showed that the VSS scores of both groups decreased after treatment compared with those before treatment (P < 0.01), and there was no statistically significant difference in the VSS scores between the two groups after treatment. Metagenomics results showed that, after treatment, the vaginal microbial communities in the Wandai Decoction group were of CST Ⅱ and Ⅴ types (predominated by Lactobacillus gasseri and Lactobacillus jensenii), while those in the fluconazole group were Lactobacillus_intestinalis and Streptococcus_sp._oral_ taxon_431. KEGG functional enrichment analysis results showed that, in terms of the cell cycle and meiosis functions of Candida albicans, statistically significant differences between the Wandai Decoction and fluconazole groups were observed (P < 0.05). Metabolomic analysis identified 120 differential metabolites between the two groups after treatment. The results of KEGG metabolic pathway enrichment analysis of differential metabolites showed that the Wandai Decoction might be significantly superior to fluconazole in improving local vaginal metabolic pathways of α-linolenic acid, glycerophospholipid metabolism, pentose and glucuronic acid interconversion, and arachidonic acid.

CONCLUSION: The Wandai Decoction can improve the vaginal flora of VVC patients. It may be superior to fluconazole in the signaling pathways of the cell cycle and meiosis. The improvement of the vaginal flora by the Wandai Decoction may be associated with its effect on metabolic pathways of glycerophospholipid metabolism, pentose and glucuronic acid interconversion, and others in the vagina.}, } @article {pmid40109356, year = {2025}, author = {Kantor, RS and Kennedy, LC and Miller, SE and Favere, J and Nelson, KL}, title = {Reverse Osmosis in an Advanced Water Treatment Train Produces a Simple, Consistent Microbial Community.}, journal = {ACS ES&T engineering}, volume = {5}, number = {3}, pages = {772-781}, pmid = {40109356}, issn = {2690-0645}, abstract = {Potable water reuse has become a key component of water sustainability planning in arid regions. Many advanced water purification facilities use reverse osmosis (RO) as part of treatment, including as a barrier for microorganisms; however, regrowth after RO treatment has been observed. Questions remain about the identity, source, and survival mechanisms of microorganisms in RO permeate, but the extremely low biomass of this water is a limitation for common microbiological methods. Here, we performed high-throughput sequencing on samples collected throughout a potable reuse train, including samples collected by filtering large volumes of RO permeate and biomass collected from RO membranes during an autopsy. We observed a stable, consistent microbial community across three months and in two parallel RO trains. RO permeate samples contained Burkholderiaceae at high relative abundance, including one Aquabacterium sp. that accounted for 29% of the community, on average. Like most other RO permeate microorganisms, this sequence was not seen in upstream samples and we suggest that biofilm growing on unit process infrastructure, rather than active treatment breakthrough, was the primary source. A metagenome-assembled genome corresponding to Aquabacterium sp. from RO permeate was found to lack most sugar-utilization pathways and to be able to consume low molecular weight organic molecules, potentially those that pass through RO.}, } @article {pmid40108525, year = {2025}, author = {Liu, G and Chen, T and Tian, X and Ai, Y and Chen, Z and Liu, J and Sun, Z}, title = {Brain abscess due to clostridium celerecrescens: first report and literature review.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {386}, pmid = {40108525}, issn = {1471-2334}, support = {82371407//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Brain Abscess/microbiology/diagnostic imaging/drug therapy ; Female ; *Clostridium Infections/microbiology/diagnosis/drug therapy ; *Anti-Bacterial Agents/therapeutic use ; Adolescent ; *Clostridium/isolation & purification/genetics ; Foreign Bodies/complications/surgery ; Debridement ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Brain abscess caused by atypical pathogens presents significant diagnostic and therapeutic challenges. The unusual clinical presentations, coupled with incomplete or inaccurate patient histories, often result in misdiagnosis and inappropriate treatment.

CASE PRESENTATION: We report a case of a retained intracranial bamboo foreign body resulting in a brain abscess. A female adolescent presented with a newly developed mass on the eyelid. Medical imaging identified a foreign body that had penetrated the frontal lobes via the transorbital route, leading to the formation of a brain abscess. The foreign body was successfully removed through transnasal endoscopy. Inflamed tissue adherent to the foreign body was cultured and analyzed using metagenomic next-generation sequencing (mNGS), which identified Clostridium celerecrescens as the causative pathogen. The patient fully recovered after surgical debridement and two weeks of antibiotic therapy.

CONCLUSIONS: Infections caused by C. celerecrescens are exceedingly rare in clinical practice. This case highlights the bacterium's ability to adhere to a bamboo foreign body, leading to the formation of a rare brain abscess. mNGS proves to be a valuable diagnostic tool for identifying uncommon infectious agents.}, } @article {pmid40108202, year = {2025}, author = {Redgwell, TA and Thorsen, J and Petit, MA and Deng, L and Vestergaard, G and Russel, J and Chawes, B and Bønnelykke, K and Bisgaard, H and Nielsen, DS and Sørensen, S and Stokholm, J and Shah, SA}, title = {Prophages in the infant gut are pervasively induced and may modulate the functionality of their hosts.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {46}, pmid = {40108202}, issn = {2055-5008}, mesh = {*Gastrointestinal Microbiome ; *Prophages/genetics/physiology ; Humans ; Infant ; *Metagenome ; Virome ; Female ; Feces/microbiology/virology ; Bacteria/genetics/classification/virology ; Bacteroides/genetics/virology ; }, abstract = {Gut microbiome (GM) composition and function is pivotal for human health and disease, of which the virome's importance is increasingly recognised. However, prophages and their induction patterns in the infant gut remain understudied. Here, we identified 10645 putative prophages in 662 metagenomes from 1-year-old children in the COPSAC2010 mother-child cohort and investigated their potential functions. No core provirome was found as the most prevalent vOTU was identified in only ~70% of the samples. The most dominant cluster of vOTUs in the cohort was related to Bacteroides phage Hanky p00', and it carried both diversity generating retroelements and genes involved in capsular polysaccharide synthesis. Paired analysis of viromes and metagenomes from the same samples revealed that most prophages within the infant gut were induced and that induction was unaffected by a range of environmental perturbers. In summary, prophages are major components of the infant gut that may have far reaching influences on the microbiome and its host.}, } @article {pmid40108151, year = {2025}, author = {Krueger, ME and Boles, JS and Simon, ZD and Alvarez, SD and McFarland, NR and Okun, MS and Zimmermann, EM and Forsmark, CE and Tansey, MG}, title = {Comparative analysis of Parkinson's and inflammatory bowel disease gut microbiomes reveals shared butyrate-producing bacteria depletion.}, journal = {NPJ Parkinson's disease}, volume = {11}, number = {1}, pages = {50}, pmid = {40108151}, issn = {2373-8057}, support = {PF-RCE-1945//Parkinson's Foundation (Parkinson's Foundation, Inc.)/ ; PF-RCE-1945//Parkinson's Foundation (Parkinson's Foundation, Inc.)/ ; PF-RCE-1945//Parkinson's Foundation (Parkinson's Foundation, Inc.)/ ; }, abstract = {Epidemiological studies reveal that inflammatory bowel disease (IBD) is associated with an increased risk of Parkinson's disease (PD). Gut dysbiosis has been documented in both PD and IBD, however it is currently unknown whether gut dysbiosis underlies the epidemiological association between both diseases. To identify shared and distinct features of the PD and IBD microbiome, we recruited 54 PD, 26 IBD, and 16 healthy control individuals and performed the first joint analysis of gut metagenomes. Larger, publicly available PD and IBD metagenomic datasets were also analyzed to validate and extend our findings. Depletions in short-chain fatty acid (SCFA)-producing bacteria, including Roseburia intestinalis, Faecalibacterium prausnitzii, Anaerostipes hadrus, and Eubacterium rectale, as well depletion in SCFA-synthesis pathways were detected across PD and IBD datasets, suggesting that depletion of these microbes in IBD may influence the risk for PD development.}, } @article {pmid40107220, year = {2025}, author = {Zhang, T and Zhou, S and Cheng, C and Yang, Y and Yang, D and Shi, D and Li, H and Yang, Z and Chen, T and Li, J and Jin, M}, title = {Metagenomic assembled genomes profile potential pathogens and antibiotic-resistant pathogens in an urban river.}, journal = {Ecotoxicology and environmental safety}, volume = {294}, number = {}, pages = {118063}, doi = {10.1016/j.ecoenv.2025.118063}, pmid = {40107220}, issn = {1090-2414}, abstract = {The microbiological safety of urban rivers that flow through cities is crucial to local public health. However, detailed insights into the key characteristics of pathogens in urban rivers remain limited due to the lack of efficient high-throughput analysis tools. In this study, a comprehensive profiling of potential pathogens, antibiotic-resistant pathogens (ARPs), and multidrug-resistant pathogens (MDRPs) in the Hai River, which runs through the central city of Tianjin, was conducted using metagenomic assembled genome (MAG) analysis. Of the 436 recovered MAGs assigned to 430 species, 110 MAGs were identified as potential pathogens due to the presence of virulence factors (VFs), whereas 19 MAGs containing both antibiotic resistance genes (ARGs) and VFs, were classified as potential ARPs, predominantly belonging to the genera Kluyvera, Enterobacter, and Klebsiella. Notably, nine species of MDRPs, including Enterobacter kobei, Klebsiella pneumoniae, Morganella morganii, Kluyvera intermedia, Aeromonas salmonicida, Rahnella aceris, Hafnia paralvei, the unidentified species Sep. D_bin46, and Vibrio cholerae, exhibited resistance to multidrug, beta-lactam, polymyxin, bacitracin, tetracycline, other peptide antibiotics, macrolide-lincosamide-streptogramin, aminoglycoside, and chloramphenicol. The unknown pathogen Sep. D_bin46, classified under Aeromonas, showed resistance to both carbapenems and polymyxins. The strong co-occurrence of ARGs, VFs, and mobile genetic elements suggests a significant risk of ARGs and VFs transfers among MDRPs with last-resort ARGs (r > 0.8; p < 0.05). Interestingly, the sampling location significantly influenced the presence of pathogens, ARPs, and MDRPs carrying last-resort ARGs in the water. Notably, their abundance was lower downstream of the Hai River compared to upstream. This observation suggests that urban environmental sanitation facilities may be more effective in reducing contaminants as the river flows from upstream to downstream. Nevertheless, the presence of pathogens, ARPs, and MDRPs with last-resort ARGs in the water underscores the ongoing microbiological risks associated with urban surface water.}, } @article {pmid40107213, year = {2025}, author = {Lu, W and Guo, X and Wu, Y and Sun, S and Wang, Q and Guo, J and Zhao, HP and Lai, CY}, title = {Particulate methane monooxygenase and cytochrome P450-induced reactive oxygen species facilitate 17β-estradiol biodegradation in a methane-fed biofilm.}, journal = {Water research}, volume = {280}, number = {}, pages = {123501}, doi = {10.1016/j.watres.2025.123501}, pmid = {40107213}, issn = {1879-2448}, abstract = {Methane-fed biosystems have shown great potential for degrading various organic micropollutants, yet underlying molecular degradation mechanisms remain largely unexplored. In this study, we uncover the critical role of biogenic reactive oxygen species (ROS) in driving the degradation of 17β-estradiol (E2) within a methane-fed biofilm reactor. Metagenomic analyses confirm that aerobic methanotrophs, specifically Methylococcus and Methylomonas, are responsible for the efficient degradation of E2, achieving a degradation rate of 367.7 ± 8.3 μg/L/d. ROS scavenging in conjunction with enzyme inhibition experiments indicate that particulate methane monooxygenase (pMMO) and cytochrome P450 monooxygenase (CYP450) could generate hydroxyl radicals (•OH), which are the primary ROS involved in E2 degradation. Molecular dynamics simulations suggest that E2 can enter the active catalytic site of pMMO through electrostatic attraction. Four amino acid residues are found to form stable hydrogen bonds with E2, with a high binding free energy, indicating a high affinity for the substrate. Additionally, density functional theory calculations combined with transformation product analysis reveal that •OH targets carbon atoms on the benzene ring and the hydroxyl group attaches to the cyclopentane ring, primarily through hydrogen abstraction and hydroxylation reactions. This work provides critical insights into the mechanisms of E2 biodegradation in methane-fed systems and highlights the potential for optimizing microbial pathways to enhance the degradation of organic micropollutants from contaminated water.}, } @article {pmid40107211, year = {2025}, author = {Gong, Q and Zeng, W and Hao, X and Wang, Y and Peng, Y}, title = {DNA stable isotope probing and metagenomics reveal temperature responses of sulfur-driven autotrophic partial denitrification coupled with anammox (SPDA) system.}, journal = {Water research}, volume = {280}, number = {}, pages = {123494}, doi = {10.1016/j.watres.2025.123494}, pmid = {40107211}, issn = {1879-2448}, abstract = {The sulfur-driven autotrophic partial denitrification coupled with anammox (SPDA) process showed significant advantages in energy conservation and resource recovery in municipal wastewater treatment. However, its application in regions with seasonal temperature fluctuations and high latitudes is challenged by low temperatures. In this study, the feasibility of the SPDA process for treating low-strength municipal wastewater across a wide temperature range (30-10 °C) was systematically investigated. The results demonstrated that thiosulfate-driven autotrophic partial denitrification maintained an efficient nitrate removal rate of 7.82 mg NO3[-]-N/gVSS/h and a nitrate to nitrite transformation rate of 62.7 % even at temperatures as low as 10 °C. Molecular ecological network and DNA-SIP revealed that dominant sulfur-oxidizing bacteria (SOB) shifted from norank_f_Hydrogenophilaceae and Thiobacillus at higher temperatures (30-20 °C) to Thiobacillus and Sulfurimonas as temperature decreased, thus ensuring the performance of autotrophic partial denitrification and consistent nitrite supply for anammox. Metagenomic analysis showed that the abundance of functional genes related to sulfur conversion increased almost universally, ensuring a stable electron supply for nitrate reduction through sulfur oxidation at low temperatures. The functional genes responsible for nitrate reduction changed from nar genes at higher temperatures to nap genes at lower temperatures, while a decrease in the abundance of hzs and hdh genes corresponding to reduced anammox performance. This study highlights the stable performance of the sulfur-driven autotrophic denitrification at low temperatures and the reliability of coupling with anammox, extending the applicability of SPDA to a broader geographical range.}, } @article {pmid40107206, year = {2025}, author = {Tang, H and Chen, Y and Tang, X and Wei, M and Hu, J and Zhang, X and Xiang, D and Yang, Q and Han, D}, title = {Corrigendum to "Yield of clinical metagenomics: insights from real-world practice for tissue infections" [eBioMedicine 111(2025), 105536].}, journal = {EBioMedicine}, volume = {114}, number = {}, pages = {105574}, doi = {10.1016/j.ebiom.2025.105574}, pmid = {40107206}, issn = {2352-3964}, } @article {pmid40107015, year = {2025}, author = {Xia, Z and Luo, G and Gou, LY and Zhang, W and Ji, EG and Li, S and Gao, T and Abi, KM and Yang, F}, title = {Metaviromic and metagenomic study of the pathogens in unexplained pneumonia cases in goats.}, journal = {Veterinary microbiology}, volume = {304}, number = {}, pages = {110469}, doi = {10.1016/j.vetmic.2025.110469}, pmid = {40107015}, issn = {1873-2542}, abstract = {Goats are an economically important livestock species in China. However, the high mortality rate due to pneumonia represents a significant challenge to the development of intensive goat farms. 10 goat lung tissue samples were collected in this study, and all samples exhibited pneumonia of different severity as determined by lung lesion scoring and histopathological examination. Subsequently, this study employed qRT-PCR to measure the relative expression level of pro-inflammatory cytokines in lung tissue, and conducted metaviromic and metagenomic analyses to elucidate the structure and composition of the pulmonary microbiota, the correlation between the abundance of specific microbes and inflammatory factors, and between microbial abundance and the expression of virulence genes. Metaviromic results indicated that Ungulate tetraparvovirus 4 (83.3 %) had the highest relative abundance in the viral composition. Metagenomic data showed that Mycoplasma (28.2 %) and Streptococcus (24.8 %) are the primary dominant genus in goat pneumonia. Notably, a total of 8 pathogens associated with pneumonia in humans or animals were identified across all samples, including Mycoplasma ovipneumoniae, Streptococcus agalactiae, Streptococcus pneumoniae, Escherichia coli, Bordetella hinzii, Bibersteinia trehalosi, Bordetella pertussis, and Pasteurella multocida, with mixed infections with multiple pathogens are very common in this study. Correlation analysis indicates a significant association between the degree of pathogen co-infection and the severity of pulmonary lesions. Furthermore, Pasteurella multocida showed a significant positive correlation with the expression of IL-6 (P< 0.01). The pneumonia samples also revealed a multitude of virulence factors associated with bacterial pathogenicity including those related to biofilm formation, endotoxin production, bacterial invasion and evasion of host immunity. In conclusion, the present study can provide a reference for clinical pathogen diagnosis of unexplained pneumonia in goats.}, } @article {pmid40105325, year = {2025}, author = {Zhang, H and Lu, T and Guo, S and He, T and Shin, M-K and Luo, C and Tong, J and Zhang, Y}, title = {Rumen microbes affect the somatic cell counts of dairy cows by modulating glutathione metabolism.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0109324}, doi = {10.1128/msystems.01093-24}, pmid = {40105325}, issn = {2379-5077}, abstract = {Healthy mammary glands are essential for high-quality milk production in the dairy industry. The relationship between somatic cell counts (SCCs), rumen fermentation, and microbiota interactions remains unclear. This study integrated physiological indicators, high-throughput 16S rRNA gene sequencing, and metagenomics data analysis to investigate the mechanisms linking rumen microbes and mastitis and to evaluate the changes in milk production and serum cytokine levels in cows with low (L-SCC) and high (H-SCC) somatic cell counts. Compared with the L-SCC group, the H-SCC group exhibited significantly lower lactose and fat contents in milk, reduced rumen fermentation product levels, and increased abundances of Bacteroidetes, Firmicutes, Lachnospiraceae, Prevotella, and Rumiclostridium. Elevated serum levels of IgG2, IgM, IL-1β, IL-6, and TNF-ɑ in the H-SCC group indicated inflammation and rumen microbiota dysbiosis. Functional analysis of microbial communities revealed significant enrichment in pathways related to glutathione metabolism, thyroid hormone synthesis, hypertrophic cardiomyopathy (HCM), the phosphotransferase system (PTS), the P53 signaling pathway, and the Jak-STAT signaling pathway. Correlation network analysis showed that changes in bacterial families, such as Rikenellaceae, Muribaculaceae, and Prevotellaceae, were associated with cytokines, rumen fermentation, and milk quality. The study highlights the interaction between rumen microbiota homeostasis and mammary gland health, indicating that rumen fermentation status influences serum inflammation and milk quality. Modulating rumen fermentation to enhance mammary gland immune function presents a viable strategy for sustainable dairy industry development with long-lived, highly productive cows.IMPORTANCEHigh somatic cell counts (SCCs) are a key biomarker of mastitis and are associated with decreased milk production and significant economic losses in dairy farming. This study systematically examines the relationship between elevated SCCs, rumen microbial dysbiosis, and host inflammatory responses, shedding light on the intricate interplay between microbial ecosystems and host physiology. The findings highlight the potential for microbiota-targeted interventions to reduce inflammation, improve milk composition, and enhance dairy cow productivity. Rather than presuming a direct causative link between SCC-associated dysbiosis and inflammation, this research focuses on their interdependent dynamics, offering a nuanced understanding of the complex biological mechanisms involved. This work advances knowledge of host-microbiota interactions in livestock, providing practical insights for the development of innovative strategies to manage mastitis and improve overall herd health. By adhering to One Health principles, this study underscores the significance of sustainable agricultural practices that prioritize animal welfare, environmental stewardship, and food security. These findings establish a robust foundation for future research into microbiota-driven solutions aimed at enhancing the health and productivity of dairy cattle.}, } @article {pmid40104686, year = {2025}, author = {Lin, X and Zhang, R and Cui, FQ and Hong, W and Yang, S and Ju, F and Xi, C and Sun, X and Song, L}, title = {Natural-selected plastics biodegradation species and enzymes in landfills.}, journal = {PNAS nexus}, volume = {4}, number = {3}, pages = {pgaf066}, pmid = {40104686}, issn = {2752-6542}, abstract = {Biodegradation is a promising and environmentally friendly strategy for plastic pollution management. Landfills decompose municipal solid waste, including almost 50% of global plastic debris and even some of the oldest synthetic plastics, fostering naturally selected plastic biodegradation. Herein, we present a global collection of plastic biocatalytic enzymes from landfills using metagenomics and machine learning. Metagenomic analysis identified 117 plastic-degrading genes, with 39 incorporated in 22 prokaryotic metagenome-assembled genomes (MAGs). A machine-learning approach predicted 978,107 candidate plastic-degrading genes, 712 of which were encoded respectively by 150 MAGs. Our results highlight landfills as reservoirs of diverse, naturally selected plastic-degrading microbes and enzymes, serving as references and/or models for biocatalysis engineering and in situ bioremediation of plastic pollution.}, } @article {pmid40104674, year = {2025}, author = {Nawrocki, EP and Petrov, AI and Williams, KP}, title = {Expansion of the tmRNA sequence database and new tools for search and visualization.}, journal = {NAR genomics and bioinformatics}, volume = {7}, number = {1}, pages = {lqaf019}, pmid = {40104674}, issn = {2631-9268}, mesh = {*RNA, Bacterial/genetics/chemistry ; Databases, Nucleic Acid ; Nucleic Acid Conformation ; Databases, Genetic ; Introns/genetics ; Sequence Analysis, RNA/methods ; }, abstract = {Transfer-messenger RNA (tmRNA) contributes essential tRNA-like and mRNA-like functions during the process of trans-translation, a mechanism of quality control for the translating bacterial ribosome. Proper tmRNA identification benefits the study of trans-translation and also the study of genomic islands, which frequently use the tmRNA gene as an integration site. Automated tmRNA gene identification tools are available, but manual inspection is still important for eliminating false positives. We have increased our database of precisely mapped tmRNA sequences over 50-fold to 97 179 unique sequences. Group I introns had previously been found integrated within a single subsite within the TψC-loop; they have now been identified at four distinct subsites, suggesting multiple founding events of invasion of tmRNA genes by group I introns, all in the same vicinity. tmRNA genes were found in metagenomic archaeal genomes, perhaps a result of misbinning of bacterial sequences during genome assembly. With the expanded database, we have produced new covariance models for improved tmRNA sequence search and new secondary structure visualization tools.}, } @article {pmid40104595, year = {2025}, author = {Galanis, A and Papadimitriou, K and Moloney, GM}, title = {Editorial: Omics technologies and bioinformatic tools in probiotic research.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1577852}, pmid = {40104595}, issn = {1664-302X}, } @article {pmid40104149, year = {2025}, author = {Wu, W and Xu, J and Ruan, J and Tian, B and Xuan, N}, title = {Metagenomic next-generation sequencing identifies native valve Aspergillus fumigatus endocarditis with cerebral involvement: a case report.}, journal = {Frontiers in cardiovascular medicine}, volume = {12}, number = {}, pages = {1487543}, pmid = {40104149}, issn = {2297-055X}, abstract = {Aspergillus endocarditis is a rare but highly fatal condition, particularly in immunocompromised patients. This case report describes a 74-year-old male with native valve Aspergillus fumigatus endocarditis and intracranial infection. Diagnosis was complicated by atypical presentation and negative blood cultures, but metagenomic next-generation sequencing (mNGS) enabled rapid identification of the pathogen. This case is notable for being the first to document Aspergillus fumigatus endocarditis with cerebral involvement confirmed by mNGS, highlighting the importance of early diagnosis and advanced diagnostic tools in improving outcomes.}, } @article {pmid40103993, year = {2025}, author = {Rai, A and Sirotiya, V and Ahirwar, A and Singh, G and Kawatra, R and Sharma, AK and Harish, and Vinayak, V}, title = {Textile dye removal using diatomite nanocomposites: a metagenomic study in photosynthetic microalgae-assisted microbial fuel cells.}, journal = {RSC advances}, volume = {15}, number = {11}, pages = {8300-8314}, pmid = {40103993}, issn = {2046-2069}, abstract = {In this study, Coomassie brilliant blue (CBB), brilliant green (BG), and rhodamine (Rh) dyes were used to simulate dye-rich wastewater. Adsorption and degradation of these dyes (2 μM, 10 μM, and 30 μM) on diatomite (DE) were evaluated under light (L) and dark (D) conditions. The adsorption of dye-DE composites followed pseudo-second-order kinetics at all concentrations and conditions had R [2] > 0.99, thus showing a good fit. The calculated equilibrium adsorption amount q e,(cal) was coherent with the value of experimental q e,(exp). The poorest adsorption and photocatalysis occurred at 30 μM, prompting the functionalization of dyes with TiO2 and Fe3O4 nanoparticles (NP(s)). The highest dye degradation efficiencies (DGeff) for 30 μM dyes were 86.79% (CBB-DE-Fe3O4, 72 h), 96.10% (BG-DE-TiO2, 52 h), and 81.74% (Rh-DE-TiO2, 48 h), with Rh-DE-TiO2 showing the fastest degradation. Functionalized DE-dye (30 μM) nanocomposites were further tested in a photosynthetic microalgae-assisted microbial fuel cell with dye-simulated wastewater at the anode (PMA-MFC-1 with CBB-DE-Fe3O4, PMA-MFC-2 with BG-DE-TiO2 and PMA-MFC-3 with Rh-DE-TiO2) and Asterarcys sp. GA4 microalgae at the cathode. In dark anode chambers, PMA-MFC-3 achieved the highest DGeff value of Rh dye as 88.23% and a polarization density of 30.06 mW m[-2], outperforming PMA-MFC-2 with BG dye and PMA-MFC-1 with CBB dye. The molecular identifier analysis of microbes in wastewater at the anode showed the dominance of Sphingobacteria and Proteobacteria in PMA-MFC-3 (Rh-DE-TiO2) and COD removal of 61.36%, highlighting its potential for efficient dye degradation and bioelectricity generation. Furthermore, PMA-MFC-3 simultaneously demonstrated a superior microalgal lipid yield of 3.42 μg g[-1] and an algal growth of 8.19 μg g[-1] at the cathode.}, } @article {pmid40103786, year = {2025}, author = {Wang, KM and Mu, N and Wang, HB}, title = {Intracranial infection in an adult caused by Mycoplasma hominis, diagnosed using mNGS technology: a case report.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1560635}, pmid = {40103786}, issn = {2296-858X}, abstract = {Mycoplasma hominis is a rare cause of adult central nervous system infections, posing significant diagnostic challenges due to its fastidious growth requirements and high false-negative rate in conventional cultures. We report a case of Mycoplasma hominis meningoencephalitis in a postpartum female, diagnosed via metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF). The patient presented with fever, headache, and progressive neurological deficits following a cesarean section. Neuroimaging revealed a subdural hematoma, and CSF analysis demonstrated an inflammatory response. mNGS identified Mycoplasma hominis, prompting targeted antimicrobial therapy with moxifloxacin and doxycycline, which led to significant clinical improvement. This case underscores the utility of mNGS in detecting rare intracranial infections and highlights the critical role of early pathogen identification in optimizing treatment outcomes.}, } @article {pmid40103293, year = {2025}, author = {Rasmussen, AN and Tolar, BB and Bargar, JR and Boye, K and Francis, CA}, title = {Metagenome-Assembled Genomes for Oligotrophic Nitrifiers From a Mountainous Gravelbed Floodplain.}, journal = {Environmental microbiology}, volume = {27}, number = {3}, pages = {e70060}, doi = {10.1111/1462-2920.70060}, pmid = {40103293}, issn = {1462-2920}, support = {DE- AC02-76SF00515//SLAC Accelerator Laboratory, U.S. Department of Energy, Biological and Environmental Research/ ; //Watershed Function Science Focus Area/ ; }, mesh = {*Archaea/genetics/classification/metabolism ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Geologic Sediments/microbiology ; *Nitrification ; *Metagenome ; *Ammonia/metabolism ; *Phylogeny ; Rivers/microbiology ; Oxidation-Reduction ; Nitrites/metabolism ; Genome, Bacterial ; }, abstract = {Riparian floodplains are important regions for biogeochemical cycling, including nitrogen. Here, we present MAGs from nitrifying microorganisms, including ammonia-oxidising archaea (AOA) and comammox bacteria from Slate River (SR) floodplain sediments (Crested Butte, CO, US). Additionally, we explore MAGs from potential nitrite-oxidising bacteria (NOB) from the Nitrospirales. AOA diversity in SR is lower than observed in other western US floodplain sediments and Nitrosotalea-like lineages such as the genus TA-20 are the dominant AOA. No ammonia-oxidising bacteria (AOB) MAGs were recovered. Microorganisms from the Palsa-1315 genus (clade B comammox) are the most abundant ammonia-oxidizers in SR floodplain sediments. Established NOB are conspicuously absent; however, we recovered MAGs from uncultured lineages of the NS-4 family (Nitrospirales) and Nitrospiraceae that we propose as putative NOB. Nitrite oxidation may be carried out by organisms sister to established Nitrospira NOB lineages based on the genomic content of uncultured Nitrospirales clades. Nitrifier MAGs recovered from SR floodplain sediments harbour genes for using alternative sources of ammonia, such as urea, cyanate, biuret, triuret and nitriles. The SR floodplain therefore appears to be a low ammonia flux environment that selects for oligotrophic nitrifiers.}, } @article {pmid40102971, year = {2025}, author = {Luo, Z and Ou, H and Tan, Z and Jiao, J}, title = {Rumen-protected methionine and lysine supplementation to the low protein diet improves animal growth through modulating colonic microbiome in lambs.}, journal = {Journal of animal science and biotechnology}, volume = {16}, number = {1}, pages = {46}, pmid = {40102971}, issn = {1674-9782}, abstract = {BACKGROUND: Dietary protein level and amino acid (AA) balance are crucial determinants of animal health and productivity. Supplementing rumen-protected AAs in low-protein diets was considered as an efficient strategy to improve the growth performance of ruminants. The colon serves as a crucial conduit for nutrient metabolism during rumen-protected methionine (RPMet) and rumen-protected lysine (RPLys) supplementation, however, it has been challenging to clarify which specific microbiota and their metabolites play a pivotal role in this process. Here, we applied metagenomic and metabolomic approaches to compare the characteristic microbiome and metabolic strategies in the colon of lambs fed a control diet (CON), a low-protein diet (LP) or a LP diet supplemented with RPMet and RPLys (LR).

RESULTS: The LP treatment decreased the average daily weight gain (ADG) in lambs, while the LR treatment tended to elicit a remission in ADG. The butyrate molar concentration was greater (P < 0.05), while acetate molar concentration (P < 0.05) was lower for lambs fed the LP and LR diets compared to those fed the CON diet. Moreover, the LP treatment remarkably decreased total AA concentration (P < 0.05), while LR treatment showed an improvement in the concentrations of methionine, lysine, leucine, glutamate, and tryptophan. Metagenomic insights proved that the microbial metabolic potentials referring to biosynthesis of volatile fatty acids (VFAs) and AAs in the colon were remarkably altered by three dietary treatments. Metagenomic binning identified distinct microbial markers for the CON group (Alistipes spp., Phocaeicola spp., and Ruminococcus spp.), LP group (Fibrobacter spp., Prevotella spp., Ruminococcus spp., and Escherichia coli), and LR group (Akkermansia muciniphila and RUG099 spp.).

CONCLUSIONS: Our findings suggest that RPMet and RPLys supplementation to the low-protein diet could enhance the microbial biosynthesis of butyrate and amino acids, enriche the beneficial bacteria in the colon, and thereby improve the growth performance of lambs.}, } @article {pmid40102641, year = {2025}, author = {Kalvapalle, PB and Staubus, A and Dysart, MJ and Gambill, L and Reyes Gamas, K and Lu, LC and Silberg, JJ and Stadler, LB and Chappell, J}, title = {Information storage across a microbial community using universal RNA barcoding.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {40102641}, issn = {1546-1696}, support = {2021-33522-35356//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; W911NF-24-2-0073//United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (ARO)/ ; 1805901//National Science Foundation (NSF)/ ; 1828869//National Science Foundation (NSF)/ ; 2227526//National Science Foundation (NSF)/ ; 2237052//National Science Foundation (NSF)/ ; 2237512//National Science Foundation (NSF)/ ; FWP 78814//U.S. Department of Energy (DOE)/ ; A23-0202-004//Robert J. Kleberg, Jr. and Helen C. Kleberg Foundation/ ; }, abstract = {Gene transfer can be studied using genetically encoded reporters or metagenomic sequencing but these methods are limited by sensitivity when used to monitor the mobile DNA host range in microbial communities. To record information about gene transfer across a wastewater microbiome, a synthetic catalytic RNA was used to barcode a highly conserved segment of ribosomal RNA (rRNA). By writing information into rRNA using a ribozyme and reading out native and modified rRNA using amplicon sequencing, we find that microbial community members from 20 taxonomic orders participate in plasmid conjugation with an Escherichia coli donor strain and observe differences in 16S rRNA barcode signal across amplicon sequence variants. Multiplexed rRNA barcoding using plasmids with pBBR1 or ColE1 origins of replication reveals differences in host range. This autonomous RNA-addressable modification provides information about gene transfer without requiring translation and will enable microbiome engineering across diverse ecological settings and studies of environmental controls on gene transfer and cellular uptake of extracellular materials.}, } @article {pmid40102546, year = {2025}, author = {Lechleiter, N and Wedemeyer, J and Schütz, A and Sehl-Ewert, J and Schaufler, K and Homeier-Bachmann, T}, title = {Metagenomic analysis of the faecal microbiota and AMR in roe deer in Western Pomerania.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {9288}, pmid = {40102546}, issn = {2045-2322}, mesh = {Animals ; *Deer/microbiology ; *Feces/microbiology ; *Metagenomics/methods ; Escherichia coli/genetics/isolation & purification ; Microbiota/genetics ; Drug Resistance, Bacterial/genetics ; Germany ; Metagenome ; Gastrointestinal Microbiome/genetics ; Bacteria/genetics/classification ; Anti-Bacterial Agents/pharmacology ; }, abstract = {As an integral part of the global wellbeing, the health of wild animals should be regarded just as important as that of humans and livestock. The investigation of wildlife health, however, is limited by the availability of samples. In an attempt to implement a method with little invasiveness and broad areas of application, shotgun metagenomics were utilised to investigate the faecal microbiome and its antimicrobial resistance genes (AMRG) in roe deer. These genes can facilitate antimicrobial resistances (AMR) in bacteria and are therefore of increasing importance in global health. Accordingly, the abundance in potential vectors like wildlife needs to be assessed. The samples were additionally investigated for ESBL-E. coli, an antibiotic resistant pathogen of global concern, via cultivation. Twenty-seven hunt-harvested animals in Western Pomerania were sampled. This study is the first to our knowledge to describe the faecal microbiome of the European roe deer (Capreolus capreolus), providing insights into the bacterial and archaeal composition. Among the animals, the microbiome was mostly similar and showed a comparable composition to what has been reported in related species, with a ratio of 1.76 between Bacillota and Bacteroidota. The normalised abundance of AMR genes was found to be 0.035 on average, which is similar to other investigations on wild ruminants. Selective cultivation found no ESBL-E. coli in the animals. The prevalence of AMRG in roe deer of Western Pomerania was found to be in line with previous results. The use of shotgun metagenomics allowed for the simultaneous investigation of composition and AMR genes in the faecal microbiome of roe deer, which suggests it as a promising method for the health monitoring of wildlife. This study is the first to describe the prokaryotic assemblage in the faeces of roe deer and its differences to the microbiomes published on other cervids were discussed.}, } @article {pmid40102379, year = {2025}, author = {Deng, L and Taelman, S and Olm, MR and Toe, LC and Balini, E and Ouédraogo, LO and Bastos-Moreira, Y and Argaw, A and Tesfamariam, K and Sonnenburg, ED and Hanley-Cook, GT and Ouédraogo, M and Ganaba, R and Van Criekinge, W and Huybregts, L and Stock, M and Kolsteren, P and Sonnenburg, JL and Lachat, C and Dailey-Chwalibóg, T}, title = {Maternal balanced energy-protein supplementation reshapes the maternal gut microbiome and enhances carbohydrate metabolism in infants: a randomized controlled trial.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {2683}, pmid = {40102379}, issn = {2041-1723}, support = {OPP1175213//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Female ; *Dietary Supplements ; Infant ; Pregnancy ; Adult ; Burkina Faso ; *Carbohydrate Metabolism ; Infant, Newborn ; Feces/microbiology ; Dietary Proteins/metabolism ; Male ; Lactation ; }, abstract = {Balanced energy-protein (BEP) supplementation during pregnancy and lactation can improve birth outcomes and infant growth, with the gut microbiome as a potential mediator. The MISAME-III randomized controlled trial (ClinicalTrial.gov: NCT03533712) assessed the effect of BEP supplementation, provided during pregnancy and the first six months of lactation, on small-for-gestational age prevalence and length-for-age Z-scores at six months in rural Burkina Faso. Nested within MISAME-III, this sub-study examines the impact of BEP supplementation on maternal and infant gut microbiomes and their mediating role in birth outcomes and infant growth. A total of 152 mother-infant dyads (n = 71 intervention, n = 81 control) were included for metagenomic sequencing, with stool samples collected at the second and third trimesters, and at 1-2 and 5-6 months postpartum. BEP supplementation significantly altered maternal gut microbiome diversity, composition, and function, particularly those with immune-modulatory properties. Pathways linked to lipopolysaccharide biosynthesis were depleted and the species Bacteroides fragilis was enriched in BEP-supplemented mothers. Maternal BEP supplementation also accelerated infant microbiome changes and enhanced carbohydrate metabolism. Causal mediation analyses identified specific taxa mediating the effect of BEP on birth outcomes and infant growth. These findings suggest that maternal supplementation modulates gut microbiome composition and influences early-life development in resource-limited settings.}, } @article {pmid40101714, year = {2025}, author = {Lynn, HM and Gordon, JI}, title = {Sequential co-assembly reduces computational resources and errors in metagenome-assembled genomes.}, journal = {Cell reports methods}, volume = {}, number = {}, pages = {101005}, doi = {10.1016/j.crmeth.2025.101005}, pmid = {40101714}, issn = {2667-2375}, abstract = {Generating metagenome-assembled genomes from DNA shotgun sequencing datasets can demand considerable computational resources. Here, we describe a sequential co-assembly method that reduces the assembly of duplicate reads through successive application of single-node computing tools for read assembly and mapping. Using a simulated mouse microbiome DNA shotgun sequencing dataset, we demonstrated that this approach shortens assembly time, uses less memory than traditional co-assembly, and produces significantly fewer assembly errors. Applying sequential co-assembly to shotgun sequencing reads from (1) a longitudinal study of gut microbiomes from undernourished Bangladeshi children and (2) a 2.3-terabyte dataset generated from gnotobiotic mice colonized with pooled microbiomes from these children that was too large to be handled by a traditional co-assembly approach also demonstrated significant reductions in assembly time and memory requirements. These results suggest that this approach should be useful in resource-constrained settings, including in low- and middle-income countries.}, } @article {pmid40101514, year = {2025}, author = {Zhang, X and Wu, L and Gu, L and Jiang, Q and He, Z and Qi, Y and Zheng, X and Xu, T}, title = {Dietary areca nut extract supplementation modulates the growth performance and immunity of Jiaji ducks (Cairina moschata).}, journal = {Poultry science}, volume = {104}, number = {5}, pages = {104971}, doi = {10.1016/j.psj.2025.104971}, pmid = {40101514}, issn = {1525-3171}, abstract = {Areca nut extract (ANE) has a variety of pharmacological effects on animals. Here, we investigated the influence of ANE on the slaughter performance and immune function of Jiaji ducks. One hundred and fifty 42-day-old healthy Jiaji ducks were randomly divided into 2 groups (5 replicates of 15 ducks each), named DCK group (control) and DNT group (treatment), respectively. Ducks in the DCK group were fed a basal diet and ducks in the DNT group were fed a basal food supplemented with 0.08 g ANE per kg of basal diet. Additionally, using proteomics, untargeted metabolomics, and metagenomics, we analyzed the impact of ANE on the protein profile of the spleen, the composition of plasma metabolites, and the structure of the cecal microbiota. The results showed that the dietary inclusion of ANE significantly increased the slaughter rate of Jiaji ducks. Proteomic analysis revealed 78 differentially expressed proteins in the spleens of ANE-treated birds, including 54 proteins up-regulated and 24 proteins down-regulated in the DNT group, mainly enriched in cell adhesion molecules and glutathione metabolic pathways. Untargeted metabolomic analysis revealed that 117 serum metabolites were differentially regulated between the ANE and DCK groups; meanwhile, KEGG pathway analysis indicated that these metabolites were mainly involved in arachidonic acid metabolism, phospholipase D signaling pathway and eicosanoids. Furthermore, a metagenomic analysis showed that the genus Methanobrevibacter was significantly downregulated in the ANE supplementation group. Combined, the results of the metagenomic and metabolomic analyses showed that the relative abundance of Prevotella was significantly lower in the ANE group than in the DCK group and that Prevotella was negatively correlated with the levels of the anti-inflammatory compound hydrocinnamic acid and the lipid metabolism regulator ganoderic acid A. This study provides a reference for the application of ANE as a supplement in the diet of Jiaji ducks.}, } @article {pmid40101486, year = {2025}, author = {Sun, J and Geng, L and Zhou, D and Teng, X and Chen, M}, title = {Gut microbiota participates in polystyrene microplastics-induced defective implantation through impairing uterine receptivity.}, journal = {Journal of environmental management}, volume = {380}, number = {}, pages = {124997}, doi = {10.1016/j.jenvman.2025.124997}, pmid = {40101486}, issn = {1095-8630}, abstract = {Microplastics (MPs) are widespread in global ecosystems and could pose risks to human health. However, crucial information on the impact of MP exposure on female reproductive health remains insufficient. In this study, we constructed an MP-exposure mice model through oral administration of polystyrene microplastics (PS-MPs) and found that it resulted in impaired uterine receptivity and defective implantation. An accumulation of plastic particles was detected in MP mice intestines. Metagenomic sequencing of feces samples indicated a structural and functional alteration of gut microbiota. Alistipes played a prominent role in MP biodegradation, while among the biodegradable functional genes, ACSL made the greatest contribution. Both had a significant increase in MP group, suggesting a potential occurrence of ferroptosis. Ferroptosis, a form of programmed cell death, is closely associated with uterine receptivity impairment and defective implantation. We detected MDA contents and ferroptosis-related proteins, and the results indicated the activation of ferroptosis in the process. Our research is the first to elucidate that exposure to MPs impairs uterine receptivity and results in deficient implantation, while also providing initial evidence that gut microbiota plays a critical role in this process.}, } @article {pmid40100955, year = {2025}, author = {Davis, BC and Vikesland, PJ and Pruden, A}, title = {Evaluating Quantitative Metagenomics for Environmental Monitoring of Antibiotic Resistance and Establishing Detection Limits.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c08284}, pmid = {40100955}, issn = {1520-5851}, abstract = {Metagenomics holds promise as a comprehensive, nontargeted tool for environmental monitoring. However, one key limitation is that the quantitative capacity of metagenomics is not well-defined. Here, we demonstrated a quantitative metagenomic technique and benchmarked the approach for wastewater-based surveillance of antibiotic resistance genes. To assess the variability of low-abundance oligonucleotide detection across sample matrices, we spiked DNA reference standards (meta sequins) into replicate wastewater DNA extracts at logarithmically decreasing mass-to-mass percentages (m/m%). Meta sequin ladders exhibited strong linearity at input concentrations as low as 2 × 10[-3] m/m% (R[2] > 0.95), with little to no reference length or GC bias. At a mean sequencing depth of 94 Gb, the limits of quantification (LoQ) and detection were calculated to be 1.3 × 10[3] and 1 gene copy per μL DNA extract, respectively. In wastewater influent, activated sludge, and secondary effluent samples, 27.3, 47.7, and 44.3% of detected genes were ≤LoQ, respectively. Volumetric gene concentrations and log removal values were statistically equivalent between quantitative metagenomics and ddPCR for 16S rRNA, intI1, sul1, CTX-M-1, and vanA. The quantitative metagenomics benchmark here is a key step toward establishing metagenomics for high-throughput, nontargeted, and quantitative environmental monitoring.}, } @article {pmid40100697, year = {2025}, author = {Sun, J and Hirai, M and Takaki, Y and Evans, PN and Nunoura, T and Rinke, C}, title = {Metagenomic insights into taxonomic and functional patterns in shallow coastal and deep subseafloor sediments in the Western Pacific.}, journal = {Microbial genomics}, volume = {11}, number = {3}, pages = {}, doi = {10.1099/mgen.0.001351}, pmid = {40100697}, issn = {2057-5858}, mesh = {*Geologic Sediments/microbiology ; *Archaea/genetics/classification ; *Metagenomics/methods ; *Bacteria/genetics/classification ; *Metagenome ; Phylogeny ; Pacific Ocean ; Microbiota/genetics ; }, abstract = {Marine sediments are vast, underexplored habitats and represent one of the largest carbon deposits on our planet. Microbial communities drive nutrient cycling in these sediments, but the full extent of their taxonomic and metabolic diversity remains to be explored. Here, we analysed shallow coastal and deep subseafloor sediment cores from 0.01 to nearly 600 metres below the seafloor, in the Western Pacific Region. Applying metagenomics, we identified several taxonomic clusters across all samples, which mainly aligned with depth and sediment type. Inferring functional patterns provided insights into possible ecological roles of the main microbial taxa. These included Chloroflexota, the most abundant phylum across all samples, whereby the classes Dehalococcoida and Anaerolineae dominated deep-subsurface and most shallow coastal sediments, respectively. Thermoproteota and Asgardarchaeota were the most abundant phyla among Archaea, contributing to high relative abundances of Archaea reaching over 50% in some samples. We recovered high-quality metagenome-assembled genomes for all main prokaryotic lineages and proposed names for three phyla, i.e. Tangaroaeota phyl. nov. (former RBG-13-66-14), Ryujiniota phyl. nov. (former UBA6262) and Spongiamicota phyl. nov. (former UBA8248). Metabolic capabilities across all samples ranged from aerobic respiration and photosynthesis in the shallowest sediment layers to heterotrophic carbon utilization, sulphate reduction and methanogenesis in deeper anoxic sediments. We also identified taxa with the potential to be involved in nitrogen and sulphur cycling and heterotrophic carbon utilization. In summary, this study contributes to our understanding of the taxonomic and functional diversity in benthic prokaryotic communities across marine sediments in the Western Pacific Region.}, } @article {pmid40099977, year = {2025}, author = {López-Sánchez, R and Aguilar-Vera, A and Castillo-Ramírez, S}, title = {Metagenome-assembled genomes reveal novel diversity and atypical sources of a superbug.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0010625}, doi = {10.1128/spectrum.00106-25}, pmid = {40099977}, issn = {2165-0497}, abstract = {The genomic epidemiology of Acinetobacter baumannii has been based on culture-dependent whole-genome sequencing. However, this approach neglects sources that are not amenable to microbial culture. Here, we show that metagenome-assembled genomes (MAGs) are useful in appraising the neglected diversity of A. baumannii from unconventional sources. We analyzed 22 MAGs in the context of genomes from the main human international clones and some animal and plant isolates. Given the known ecology of the species, some of these MAGs came from unexpected sources, such as the New York City subway or a kitchen counter. Our global phylogeny, with 240 genomes, demonstrated that although some MAGs were associated with some human international clones, most of them were not and were distantly related to the human clones. Furthermore, we found that these MAGs have antibiotic-resistance genes. Our results show that many MAGs represent novel lineages with some important resistance genes coming from unexpected sources. Our work illustrates a powerful approach to studying the neglected diversity of this superbug from uncommon sources. We anticipate that in the coming years, MAGs will be employed to analyze unconventional sources for other important superbugs.IMPORTANCEThe genomic epidemiology of Acinetobacter baumannii has been based on cultivated bacterial isolates. This disregards A. baumannii diversity from sources not amenable to microbial culture. In this study, we demonstrate that metagenome-assembled genomes (MAGs) are very helpful in assessing the understudied diversity of A. baumannii from atypical sources. Our results show that many MAGs represent novel lineages with important resistance genes coming from unexpected sources. We anticipate that in the coming years, approaches similar to ours will be employed to delve into different sources for other important superbugs.}, } @article {pmid40099899, year = {2025}, author = {Nakao, R and Yamaguchi, T and Shibasaki, H and Saeki, J and Takahashi, A and Tominaga, R and Abe, K and Akeda, Y and Nakagawa-Nakamura, T and Nishino, T and Ishihara, K and Jinno-Oue, A and Inoue, S}, title = {Assessment of periodontitis vaccine using three different bacterial outer membrane vesicles in canine model.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0103324}, doi = {10.1128/msphere.01033-24}, pmid = {40099899}, issn = {2379-5042}, abstract = {UNLABELLED: Canines frequently develop periodontitis, which is similar and relevant to immunopathology and microbiology of human periodontitis. The aim of this study was to investigate whether bacterial outer membrane vesicle (OMV)-based periodontal vaccines induced humoral immune response in canines from a human vaccine development perspective. Porphyromonas gingivalis (Pg) and Treponema denticola (Td), two major periodontal pathobionts, were chosen as vaccine targets. Intranasal (IN) immunization with Pg OMVs and Td OMVs strongly elicited humoral immune responses against the two respective species in preparative mouse experiments, particularly when adjuvanted with a probiotic Escherichia coli derivative (EcNΔflhD)-derived OMVs. However, in beagles, intranasal immunization with the same Pg/Td/EcNΔflhD OMV vaccine insufficiently elicits humoral immune responses. Nevertheless, the subcutaneous booster with the same OMVs dramatically improved antibody responses in both systemic blood circulation and mucosal sites such as eyes, oral cavity, and upper and lower respiratory tracts. Metagenomic analysis of salivary microbiota revealed that the OMV vaccine might change the microbial composition, while not reducing the number of any periodontal pathobionts at least during the timeframe of the present beagle study. In in vitro Pg growth inhibition assay, serum samples from OMV-immunized beagles significantly inhibited growth of the gingipain-deficient strain but not the gingipain-expressing wild-type strain. Taken together, our data offer the trivalent OMV vaccine strategy by IN-prime/SC-boost regimen, which could elicit robust mucosal immune responses, while suggesting the requirement of revised periodontal vaccine regimen toward achievement of sterilizing immunity in the oral cavity.

IMPORTANCE: Bacterial outer-membrane vesicles (OMVs) are attractive for use as novel nanoparticle adjuvants, as well as delivery platforms. Periodontal diseases are the most prevalent oral diseases in humans and have serious health and economic burdens, greatly reducing quality of life. The aim of this study is to investigate the humoral immune responses to an OMV-based periodontal disease vaccine in beagles. The vaccine elicited strong mucosal immune responses when administered to beagles by a four-dose heterologous immunization (IN-IN-IN prime and subcutaneous [SC] boost). The OMV vaccine significantly altered the composition of the microbial community in the oral cavity. These findings suggest the utility of the intranasal (IN) prime followed by the SC boost regimen as a rational option to elicit robust humoral immune responses in canines, and most probably in humans as well. We here discuss the outcomes of beagle experiments, the mechanism behind immunological escape of Pg from host immunity, and a rational perspective toward sterilizing immunity in the oral cavity.}, } @article {pmid40099881, year = {2025}, author = {de Kleine, RH and Carbo, EC and Lexmond, WS and Zhou, XW and de Kroon, A and Mei, H and Bontemps, STH and Hennevelt, R and Gard, L and Sidorov, IA and Boers, SA and van den Heuvel, MC and Buddingh, EP and Kroes, ACM and de Meijer, VE and Schölvinck, EH and von Eije, KJ and Jochems, SP and de Vries, JJC}, title = {Metagenomic and transcriptomic investigation of pediatric acute liver failure cases reveals a common pathway predominated by monocytes.}, journal = {mBio}, volume = {}, number = {}, pages = {e0391324}, doi = {10.1128/mbio.03913-24}, pmid = {40099881}, issn = {2150-7511}, abstract = {UNLABELLED: In 2022, a cluster of severe childhood hepatitis was detected primarily in Europe and North America, leading to a global alert by the World Health Organization. An association with adeno-associated virus 2 (AAV2) in conjunction with human adenoviruses was found. Five percent of the cases progressed to acute liver failure, necessitating transplantation. The mechanism of disease that accounts for fulminant liver failure in these patients remains incompletely described. An upsurge was observed of in the five total cases of acute liver failure that presented to the Dutch national referral center for pediatric liver transplantation in the spring of 2022. An in-depth molecular analysis of the mechanism of pediatric acute liver failure was performed using targeted transcriptomics and metagenomics to identify any virus present in the cases, immune profile haplotypes, and differentially expressed gene groups. Explanted liver tissue and plasma samples (n = 15) were subjected to viral metagenomic and human transcriptomic profiling, targeting >600 inflammatory genes. Liver transcriptomic signatures of transplanted cases were compared with those of pediatric controls from a liver biobank (n = 6). AAV2, adenoviruses, and herpesviruses were detected in liver explant tissue and plasma samples of the cases. Epstein-Barr virus and varicella zoster virus infection with pathognomonic clinical symptomatology preceded liver failure in two respective cases. AAV2 was detected in one-third of control livers. Excessive activation of monocyte pathways was detected in liver explants from cases compared with controls. Remarkably, this signature was comparable for AAV2, adenoviruses, and/or herpesviruses-positive transplant cases. Our multi-omic findings suggest a common transcriptomic profile, with an upregulation of monocyte pathways in the presented transplanted cases, which had similar severe clinical outcomes. In the cohort presented, AAV2 was not exclusively associated with acute liver failure, suggesting that other processes may have contributed to a uniform cascade of irreversible pathology.

IMPORTANCE: Since the appearance of the cluster of pediatric hepatitis of unknown origin in 2022, several groups have reported an association of adenoviruses and AAV2 in a high number of cases in contrast to controls. The adenoviruses detected were heterogeneous in both species-adenovirus C and F-and sequences. The mechanisms of disease that accounts for fulminant liver failure, occurring in 5% of pediatric hepatitis cases, remain incompletely described. The current study adds to previous data by including pediatric acute liver failure cases during the upsurge, enabling the analyses of inflammation expression profiles in cases with different viruses in relation to pediatric controls. This led to the discovery of transcriptome upregulation of monocyte pathways in liver explants from the cases. This inflammatory transcriptomic signature was comparable for AAV2, adenoviruses, and/or herpesviruses-positive transplant cases.}, } @article {pmid40099113, year = {2025}, author = {Tomasella, F and Pizzi, C}, title = {MetaComBin: combining abundances and overlaps for binning metagenomics reads.}, journal = {Frontiers in bioinformatics}, volume = {5}, number = {}, pages = {1504728}, pmid = {40099113}, issn = {2673-7647}, abstract = {INTRODUCTION: Metagenomics is the discipline that studies heterogeneous microbial samples extracted directly from their natural environment, for example, from soil, water, or the human body. The detection and quantification of species that populate microbial communities have been the subject of many recent studies based on classification and clustering, motivated by being the first step in more complex pipelines (e.g., for functional analysis, de novo assembly, or comparison of metagenomes). Metagenomics has an impact on both environmental studies and precision medicine; thus, it is crucial to improve the quality of species identification through computational tools.

METHODS: In this paper, we explore the idea of improving the overall quality of metagenomics binning at the read level by proposing a computational framework that sequentially combines two complementary read-binning approaches: one based on species abundance determination and another one relying on read overlap in order to cluster reads together. We called this approach MetaComBin (metagenomics combined binning).

RESULTS AND DISCUSSION: The results of our experiments with the MetaComBin approach showed that the combination of two tools, based on different approaches, can improve the clustering quality in realistic conditions where the number of species is not known beforehand.}, } @article {pmid40098591, year = {2025}, author = {Hernández-Trujillo, PN and Lopez-Barón, CA and Arévalo-Pinzón, G and Trujillo-Güiza, ML and González-Duque, MI and Flórez, AM and Franco, DC and Vanegas, J}, title = {Taxonomic and functional profile of the anorectal microbiota in HIV-positive and HIV-negative men who have sex with men, using a metagenomic approach.}, journal = {HIV medicine}, volume = {}, number = {}, pages = {}, doi = {10.1111/hiv.70014}, pmid = {40098591}, issn = {1468-1293}, support = {2022218//Universidad Antonio Nariño/ ; }, abstract = {INTRODUCTION: The study of bacterial diversity in human samples is crucial for developing biomarkers of health and disease. This research characterized the taxonomic and functional diversity of the anorectal bacterial microbiota in men who hae sex with men (MSM) with HIV compared to men from this group without HIV.

MATERIALS AND METHODS: In July and August 2023, self-collected anorectal swabs were obtained. DNA was extracted from each sample, and metagenomic sequencing was performed. With the obtained data, alpha and beta diversity, bacterial abundance, differential operational taxonomic units, and functional diversity were determined.

RESULTS: Initially, 90 samples were collected, with 20 discarded due to having less than 200 ng of DNA and 15 due to incomplete sequencing, leaving 55 samples analysed (15 HIV-positive and 40 HIV-negative). No significant differences were found between groups in terms of alpha diversity (Shannon index p = 0.45) and beta diversity (PERMANOVA R = -0.03). Prevotella was identified as the most abundant genus in both groups. Twelve genes were found to be more abundant in the anorectal microbiota of the HIV group, which promote bacterial growth, colonization and survival.

CONCLUSION: Alterations in the anorectal microbiota could influence the pathogenesis of HIV and its complications in this population, underscoring the need to investigate these mechanisms and explore interventions to improve health. Longitudinal studies are needed to analyse changes in the anorectal microbiota during HIV infection and its response to treatment, integrating metagenomic, clinical, and immunological data to better understand the interactions between HIV, the microbiota and host health.}, } @article {pmid40098558, year = {2025}, author = {Di Rienzi, SC and Danhof, HA and Forshee, MD and Roberts, A and Britton, RA}, title = {Limosilactobacillus reuteri promotes the expression and secretion of enteroendocrine- and enterocyte-derived hormones.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {39}, number = {6}, pages = {e70408}, doi = {10.1096/fj.202401669R}, pmid = {40098558}, issn = {1530-6860}, support = {T15 LM007093/LM/NLM NIH HHS/United States ; F32 AI136404/AI/NIAID NIH HHS/United States ; //Weston Family Foundation (WFF)/ ; //BioGaia/ ; }, mesh = {*Limosilactobacillus reuteri/metabolism ; *Enteroendocrine Cells/metabolism ; *Enterocytes/metabolism/microbiology ; Humans ; Organoids/metabolism ; Gastrointestinal Hormones/metabolism/genetics ; Gastrointestinal Microbiome ; Animals ; }, abstract = {Intestinal microbes can beneficially impact host physiology, prompting investigations into the therapeutic usage of such microbes in a range of diseases. For example, human intestinal microbe Limosilactobacillus reuteri strains ATCC PTA 6475 and DSM 17938 are being considered for use for intestinal ailments, including colic, infection, and inflammation, as well as for non-intestinal ailments, including osteoporosis, wound healing, and autism spectrum disorder. While many of their beneficial properties are attributed to suppressing inflammatory responses, we postulated that L. reuteri may also regulate intestinal hormones to affect physiology within and outside of the gut. To determine if L. reuteri secreted factors impact the secretion of enteric hormones, we treated an engineered jejunal organoid line, NGN3-HIO, which can be induced to be enriched in enteroendocrine cells, with L. reuteri 6475 or 17938 conditioned medium and performed transcriptomics. Our data suggest that these L. reuteri strains affect the transcription of many gut hormones, including vasopressin and luteinizing hormone subunit beta, which have not been previously recognized as produced in the gut epithelium. Moreover, we find that these hormones appear to be produced in enterocytes, in contrast to canonical gut hormones produced in enteroendocrine cells. Finally, we show that L. reuteri conditioned media promote the secretion of enteric hormones, including serotonin, GIP, PYY, vasopressin, and luteinizing hormone subunit beta, and identify by metabolomics metabolites potentially mediating these effects on hormones. These results support L. reuteri affecting host physiology through intestinal hormone secretion, thereby expanding our understanding of the mechanistic actions of this microbe.}, } @article {pmid40098182, year = {2025}, author = {Rodríguez, V and Bartholomäus, A and Liebner, S and Oses, R and Scholten, T and Wagner, D}, title = {Microbial transcriptome patterns highlight increased pedogenesis-related activity in arid soils under simulated humid conditions.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {31}, pmid = {40098182}, issn = {2524-6372}, support = {72200201//BECAS Chile (ANID)/ ; SCHO 739/17//Deutsche Forschungsgemeinschaft/ ; }, abstract = {BACKGROUND: In arid and semiarid environments, microbial activity is restricted by low water availability and high evapotranspiration rates, and soil development is limited. Under humid conditions, such limitations can be overcome, accelerating pedogenesis by microbial processes. Our study aims to broaden our understanding of soil development under a climate change scenario toward humid conditions and to identify the microorganisms that help transform initial soils from arid and semiarid sites. We characterized pedogenetic microbial processes and how their gene expression differs between soils from arid and semiarid sites under a sixteen-week climate simulation experiment using metagenomic and metatranscriptomic approaches.

RESULTS: We found that an intense functional response is triggered under humid climate conditions in the arid site compared to the semiarid site, which showed greater resilience. The arid site undergoes higher transcription of genes involved in soil aggregate formation, phosphorus metabolism, and weathering, potentially adapting the development of arid sites to climate change. Additionally, a transcriptional reconfiguration linked to soil carbon and nitrogen dynamics suggests that soil microorganisms use available organic resources alongside autotrophy in response to increased moisture. Pseudomonadota and Actinomycetota dominated the overall transcriptional profile and specific functions associated with the early stages of soil development in both sites.

CONCLUSIONS: Our findings highlight the rapid activation of pathways related to pedogenesis under humid conditions in arid sites, potentially driven by their metabolic requirements and environmental stressors, influencing soil development dynamics under global climate change.}, } @article {pmid40098172, year = {2025}, author = {Raziq, MF and Khan, N and Manzoor, H and Tariq, HMA and Rafiq, M and Rasool, S and Kayani, MUR and Huang, L}, title = {Prioritizing gut microbial SNPs linked to immunotherapy outcomes in NSCLC patients by integrative bioinformatics analysis.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {343}, pmid = {40098172}, issn = {1479-5876}, mesh = {Humans ; *Polymorphism, Single Nucleotide/genetics ; *Carcinoma, Non-Small-Cell Lung/genetics/microbiology/drug therapy ; *Computational Biology/methods ; *Gastrointestinal Microbiome/genetics ; *Lung Neoplasms/genetics/drug therapy/microbiology ; *Immunotherapy ; Treatment Outcome ; Male ; Female ; Metagenome/genetics ; }, abstract = {BACKGROUND: The human gut microbiome has emerged as a potential modulator of treatment efficacy for different cancers, including non-small cell lung cancer (NSCLC) patients undergoing immune checkpoint inhibitor (ICI) therapy. In this study, we investigated the association of gut microbial variations with response against ICIs by analyzing the gut metagenomes of NSCLC patients.

METHODS: Strain identification from the publicly available metagenomes of 87 NSCLC patients, treated with nivolumab and collected at three different timepoints (T0, T1, and T2), was performed using StrainPhlAn3. Variant calling and annotations were performed using Snippy and associations between microbial genes and genomic variations with treatment responses were evaluated using MaAsLin2. Supervised machine learning models were developed to prioritize single nucleotide polymorphisms (SNPs) predictive of treatment response. Structural bioinformatics approaches were employed using MUpro, I-Mutant 2.0, CASTp and PyMOL to access the functional impact of prioritized SNPs on protein stability and active site interactions.

RESULTS: Our findings revealed the presence of strains for several microbial species (e.g., Lachnospira eligens) exclusively in Responders (R) or Non-responders (NR) (e.g., Parabacteroides distasonis). Variant calling and annotations for the identified strains from R and NR patients highlighted variations in genes (e.g., ftsA, lpdA, and nadB) that were significantly associated with the NR status of patients. Among the developed models, Logistic Regression performed best (accuracy > 90% and AUC ROC > 95%) in prioritizing SNPs in genes that could distinguish R and NR at T0. These SNPs included Ala168Val (lpdA) in Phocaeicola dorei and Tyr233His (lpdA), Leu330Ser (lpdA), and His233Arg (obgE) in Parabacteroides distasonis. Lastly, structural analyses of these prioritized variants in objE and lpdA revealed their involvement in the substrate binding site and an overall reduction in protein stability. This suggests that these variations might likely disrupt substrate interactions and compromise protein stability, thereby impairing normal protein functionality.

CONCLUSION: The integration of metagenomics, machine learning, and structural bioinformatics provides a robust framework for understanding the association between gut microbial variations and treatment response, paving the way for personalized therapies for NSCLC in the future. These findings emphasize the potential clinical implications of microbiome-based biomarkers in guiding patient-specific treatment strategies and improving immunotherapy outcomes.}, } @article {pmid40097931, year = {2025}, author = {Boutin, S and Käding, N and Belheouane, M and Merker, M and Rupp, J and Nurjadi, D}, title = {Towards unraveling antimicrobial resistance dynamics: a longitudinal exploration of rectal swab metagenomes.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {150}, pmid = {40097931}, issn = {1471-2180}, mesh = {Humans ; *Rectum/microbiology ; *Metagenome ; *Metagenomics/methods ; Bacteria/genetics/drug effects/isolation & purification/classification ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Whole Genome Sequencing ; Longitudinal Studies ; Male ; Microbial Sensitivity Tests ; Female ; Middle Aged ; Microbiota/genetics/drug effects ; Aged ; Genome, Bacterial/genetics ; Adult ; }, abstract = {The increasing prevalence of antimicrobial resistance (AMR) poses significant challenges in clinical settings. In particular, early screening and detection of colonization by multidrug-resistant organisms (MDROs) in patients at admission is crucial. In this context, the clinical use of metagenomics (mNGS) holds promise for fast and untargeted diagnostic methods. Here, we aimed to evaluate the long-term stability of the rectal microbiome and the diagnostic accuracy of mNGS in comparison to culture and whole-genome sequencing (WGS) of MDROs. We analyzed rectal swabs from 26 patients with two consecutive admissions over a four-year period. The detected antimicrobial resistance genes and assembled metagenomes were compared to those obtained via classical culture-based antimicrobial susceptibility testing and WGS of isolated MDROs. Our results showed that the rectal microbiome is variable during the two timepoints, highlighting the variability in the niche. Nevertheless, we also observed strong co-occurrence of taxa, suggesting that the rectal swab microbiome is also a regulated environment with cooperative biotic interactions. In total, we isolated and sequenced 6 MDROs from 6 patients at individual timepoints. Almost all AMR genes from the genomes of the isolates (median: 100%, range: 84.6-100%) could be detected by mNGS of the rectal swabs at the time of isolation of the MDRO but not at the time of culture negativity. In addition, we detected AMR genes and potentially pathogenic species in patients with negative cultures. In conclusion, our study showed that, in principle, mNGS of rectal swabs can detect clinically relevant AMR profiles. However, the cooccurrence of AMR genes and potentially-pathogenic species does not always correlate with culture-based diagnostic results but rather indicates a potential risk of horizontal AMR gene transfer. However, it is unclear whether the observed discrepancies are due to transient or locally confined colonization of MDROs, limits of detection, or variability of the sampling method and specimens.}, } @article {pmid40097230, year = {2025}, author = {Nair, SS and Kutty Narayanan, A and Nair, K and Mallick, S and Zackariah, NM and Biswas, L and Praseedom, R and G Nair, BK and Surendran, S}, title = {Microbiota-directed intervention in living donor liver transplant recipients: protocol for a randomised double-blind placebo-controlled trial.}, journal = {BMJ open}, volume = {15}, number = {3}, pages = {e092984}, doi = {10.1136/bmjopen-2024-092984}, pmid = {40097230}, issn = {2044-6055}, mesh = {Humans ; *Liver Transplantation ; *Living Donors ; Double-Blind Method ; *Synbiotics/administration & dosage ; *Gastrointestinal Microbiome ; Randomized Controlled Trials as Topic ; Acute-On-Chronic Liver Failure/therapy ; Probiotics/therapeutic use ; Adult ; Postoperative Complications/microbiology ; Male ; Female ; }, abstract = {INTRODUCTION: Acute-on-chronic liver failure (ACLF) patients have the highest propensity for post-liver transplantation (LT) infections and mortality. Liver-associated diseases have been one of the primary targets for synbiotic therapy to augment immunity and mitigate infections. However, despite multiple studies showing benefits of synbiotics in liver diseases, data on their use following LT are sparse.

METHODS AND ANALYSIS: This randomised placebo-controlled study aims to assess the impact of synbiotics in ACLF patients undergoing living donor liver transplantation (LDLT). Following randomisation by computer-generated block number sequence, 3 days prior to LDLT, the intervention arm will receive standard medical treatment and synbiotics (VSL#3 a probiotic, and Yogut, prebiotic and probiotic combination) for 6 weeks, while the control arm will receive standard medical treatment with a placebo. The patients will be followed up for 6 months to study the clinical and biochemical outcomes. The primary objective is to compare the difference in the occurrence of infectious complications between the patients who receive synbiotics versus placebo during the 6-month period following LDLT. The secondary objectives include assessing the qualitative and quantitative change in microbiota with synbiotics and LDLT, adverse reactions due to synbiotics, and post-LT morbidity and mortality. The minimum sample size comes to 71 in each group. The first 50 patients in the study protocol will undergo gut microbiome analysis using 16s metagenomic and nanopore sequencing to analyse the microbial composition before starting synbiotics/placebo and at 6 weeks after LDLT.

ETHICS AND DISSEMINATION: The study is approved by the Research Ethics Committee of Amrita Institute of Medical Sciences, Kochi, India (IEC-AIMS-2022-GISUR-203) and registered in the Clinical Trial Registry of India (CTRI) CTRI/2022/10/046327. The results of the trial will be disseminated by presentation at national/international conferences and publication in peer-reviewed journals.

TRIAL REGISTRATION NUMBER: CTRI/2022/10/046327 - Clinical Trial Registry of India.}, } @article {pmid40096869, year = {2025}, author = {Xing, X and Zhu, J and Li, Z and Zhang, G and Li, W and Tan, H and Xie, B and Yang, Y and Zhao, S and Ding, Y and You, H}, title = {Increasing the light-dark ratio enhances nitrogen removal performance by altering the mechanism in photogranules.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132400}, doi = {10.1016/j.biortech.2025.132400}, pmid = {40096869}, issn = {1873-2976}, abstract = {Photogranules provide a cost-effective solution for treating mariculture wastewater. The impact of light: dark ratios on nitrogen removal needs further study. We tested four photogranular reactors with different light: dark ratios and found that higher ratios increased total inorganic nitrogen (TIN) removal rate, achieved 99 ± 0 % every 48 h at a 5.5 h:0.5 h ratio. Kinetic and metagenomic analyses showed that increased TIN removal was mainly due to a significant transformation in the nitrogen removal mechanism of photogranules. At 5.5 h:0.5 h, diatoms replaced the outer cyanobacteria, causing nitrifying bacteria to disappear via direct and indirect inhibition. In addition, the mechanisms by which photogranules remove nitrate nitrogen are diverse. Adjusting the light: dark ratio could change the nitrogen removal mechanism of photogranules in mariculture wastewater treatment and enhance their nitrogen removal performance. This offered insights into controlling light - related parameters of photogranules for practical engineering applications.}, } @article {pmid40096540, year = {2025}, author = {Zhang, Q and Li, J and Tuo, J and Liu, S and Liu, Y and Liu, P and Ye, L and Zhang, XX}, title = {Long-term metagenomic insights into the roles of antiviral defense systems in stabilizing activated sludge bacterial communities.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf051}, pmid = {40096540}, issn = {1751-7370}, abstract = {Bacteria have evolved various antiviral defense systems to protect themselves, but how defense systems respond to the variation of bacteriophages in complex bacterial communities and whether defense systems function effectively in maintaining the stability of bacterial community structure and function remain unknown. Here, we conducted a long-term metagenomic investigation on the composition of bacterial and phage communities of monthly collected activated sludge samples from two full-scale wastewater treatment plants over six years and found that defense systems were widespread in activated sludge, with 91.1% of metagenome-assembled genomes having more than one complete defense system. The stability of the bacterial community was maintained under the fluctuations of the phage community, and defense system abundance and phage abundance were strongly positively correlated; there was a 0-3-month time lag in the responses of defense systems to phage fluctuations. The rapid turnover of CRISPR spacer repertoires further highlighted the dynamic nature of bacterial defense mechanisms. A pan-immunity phenomenon was also observed, with nearly identical metagenome-assembled genomes showing significant differences in defense system composition, which contributed to community stability at the species level. This study provides novel insights into the complexity of phage-bacteria interactions in complex bacterial communities, and reveals the key roles of defense systems in stabilizing bacterial community structure and function.}, } @article {pmid40095061, year = {2025}, author = {Laiho, JE and Oikarinen, S and Morfopoulou, S and Oikarinen, M and Renner, A and Depledge, D and Ross, MC and Gerling, IC and Breuer, J and Petrosino, JF and Plagnol, V and Pugliese, A and Toniolo, A and Lloyd, RE and Hyöty, H and , }, title = {Detection of enterovirus RNA in pancreas and lymphoid tissues of organ donors with type 1 diabetes.}, journal = {Diabetologia}, volume = {}, number = {}, pages = {}, pmid = {40095061}, issn = {1432-0428}, support = {R01-AI50237//National Institutes of Health, USA/ ; personal grant for JEL//Diabetestutkimussäätiö/ ; personal grants for JEL//Yrjö Jahnssonin Säätiö/ ; MO//Yrjö Jahnssonin Säätiö/ ; Grant#2018PG-T1D053//Leona M. and Harry B. Helmsley Charitable Trust/ ; G-2108-04793//Leona M. and Harry B. Helmsley Charitable Trust/ ; 97013//European Foundation for the Study of Diabetes/ ; 25-2012-770//JDRF/United States ; JDRF 25-2012-516//JDRF/United States ; nPOD: 5-SRA-2018-557-Q-R//JDRF/United States ; RRID:SCR_014641//network for Pancreatic Organ donors with Diabetes, nPOD/ ; personal grant for JEL//Pirkanmaan Rahasto/ ; Persistent Virus Infection in Diabetes Network [PE//Seventh Framework Programme/ ; for HH//Sigrid Juséliuksen Säätiö/ ; 288671//Research Council of Finland/ ; personal grants for JEL//Päivikki ja Sakari Sohlbergin Säätiö/ ; MO//Päivikki ja Sakari Sohlbergin Säätiö/ ; }, abstract = {AIMS/HYPOTHESIS: The nPOD-Virus group collaboratively applied innovative technologies to detect and sequence viral RNA in pancreas and other tissues from organ donors with type 1 diabetes. These analyses involved the largest number of pancreas samples collected to date. The aim of the current work was to examine the presence of enterovirus RNA in pancreas and lymphoid tissues of organ donors with and without type 1 diabetes.

METHODS: We analysed pancreas, spleen, pancreatic lymph nodes and duodenum samples from the following groups: (1) donors with type 1 diabetes (n=71) with (n=35) or without (n=36) insulin-containing islets; (2) donors with single or double islet autoantibody positivity without diabetes (n=22); and (3) autoantibody-negative donors without diabetes (control donors) (n=74). Five research laboratories participated in this collaborative effort using approaches for unbiased discovery of RNA viruses (two RNA-Seq platforms), targeted detection of Enterovirus A-D species using RT-PCR, and tests for virus growth in cell culture.

RESULTS: Direct RNA-Seq did not detect virus signal in pancreas samples, whereas RT-PCR detected enterovirus RNA confirmed by sequencing in low amounts in pancreas samples in three of the five donor groups: donors with type 1 diabetes with insulin-containing islets, 16% (5/32) being positive; donors with single islet autoantibody positivity, 53% (8/15) being positive; and non-diabetic donors, 8% (4/49) being positive. Detection of enterovirus RNA was significantly more frequent in single islet autoantibody-positive donors compared with donors with type 1 diabetes with insulin-deficient islets (p<0.001) and control (non-diabetic) donors (p=0.004). In some donors, pancreatic lymph nodes were also positive. RT-PCR detected enterovirus RNA also in the spleen of a small number of donors and virus enrichment in susceptible cell lines before RT-PCR resulted in much higher rate in spleen positivity, particularly in donors with type 1 diabetes. Interestingly, the enterovirus strains detected did not cause a typical lytic infection, possibly reflecting their persistence-prone nature.

CONCLUSIONS/INTERPRETATION: This was the largest coordinated effort to examine the presence of enterovirus RNA in the pancreas of organ donors with type 1 diabetes, using a multitude of assays. These findings are consistent with the notion that donors with type 1 diabetes and donors with islet autoantibodies may carry a low-grade enterovirus infection in the pancreas and lymphoid tissues.}, } @article {pmid40094563, year = {2025}, author = {Cheng, W and Yi, L and Xu, T and Xie, Y and Zhu, J and Guan, X and Li, Q and Huang, Y and Zhao, Y and Zhao, S}, title = {The stems and leaves of Panax notoginseng reduce the abundance of antibiotic resistance genes by regulating intestinal microbiota in Duzang pigs.}, journal = {Animal biotechnology}, volume = {36}, number = {1}, pages = {2471785}, doi = {10.1080/10495398.2025.2471785}, pmid = {40094563}, issn = {1532-2378}, mesh = {Animals ; *Panax notoginseng/microbiology ; Swine ; *Gastrointestinal Microbiome/drug effects ; *Plant Leaves ; *Plant Stems ; Drug Resistance, Microbial/genetics ; Animal Feed/analysis ; Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/genetics/classification ; Genes, Bacterial/genetics ; Cecum/microbiology ; Drug Resistance, Bacterial/genetics ; }, abstract = {In order to study the distribution characteristics of intestinal microbiota and antibiotic resistance genes (ARGs) in Duzang pigs after adding stems and leaves of Panax notoginseng to the feed, the characteristics of intestinal microbiota were explored by metagenomic sequencing, and 14 ARGs and 2 integrase genes were detected by qPCR. The results showed that the addition of stems and leaves of P. notoginseng increased the relative abundance of Firmicutes, Lactobacillus and Pediococcus in the cecum of Duzang pigs. A total of 10 ARGs and 2 integrase genes were detected in the cecal contents of pigs. The addition of stems and leaves of P. notoginseng reduced the relative abundance of total ARGs, ermB, tetO and tetW in the cecum of Duzang pigs. The results of network analysis showed that multiple genera were potential hosts of ARGs. The addition of stems and leaves of P. notoginseng may reduce the relative abundance of ARGs by reducing the relative abundance of genera such as Corynebacterium and Flavonifractor, thereby reducing the risk of ARGs spread. This study provides a theoretical basis for the rational use of stems and leaves of P. notoginseng to control ARGs.}, } @article {pmid40094561, year = {2025}, author = {Gai, Y and Liu, S and Zhang, Z and Wei, J and Wang, H and Liu, L and Bai, Q and Qin, Q and Zhao, C and Zhang, S and Xiang, N and Zhang, X}, title = {Integrative Approaches to Soybean Resilience, Productivity, and Utility: A Review of Genomics, Computational Modeling, and Economic Viability.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/plants14050671}, pmid = {40094561}, issn = {2223-7747}, abstract = {Soybean is a vital crop globally and a key source of food, feed, and biofuel. With advancements in high-throughput technologies, soybeans have become a key target for genetic improvement. This comprehensive review explores advances in multi-omics, artificial intelligence, and economic sustainability to enhance soybean resilience and productivity. Genomics revolution, including marker-assisted selection (MAS), genomic selection (GS), genome-wide association studies (GWAS), QTL mapping, GBS, and CRISPR-Cas9, metagenomics, and metabolomics have boosted the growth and development by creating stress-resilient soybean varieties. The artificial intelligence (AI) and machine learning approaches are improving genetic trait discovery associated with nutritional quality, stresses, and adaptation of soybeans. Additionally, AI-driven technologies like IoT-based disease detection and deep learning are revolutionizing soybean monitoring, early disease identification, yield prediction, disease prevention, and precision farming. Additionally, the economic viability and environmental sustainability of soybean-derived biofuels are critically evaluated, focusing on trade-offs and policy implications. Finally, the potential impact of climate change on soybean growth and productivity is explored through predictive modeling and adaptive strategies. Thus, this study highlights the transformative potential of multidisciplinary approaches in advancing soybean resilience and global utility.}, } @article {pmid40094559, year = {2025}, author = {Gao, S and Wei, G and Chang, Y and Yin, Y and Wei, Q and Shi, Y}, title = {Multiomic Analysis of Environmental Effects and Nitrogen Use Efficiency of Two Potato Varieties Under High Nitrogen Conditions.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/plants14050633}, pmid = {40094559}, issn = {2223-7747}, support = {CARS-09；2022ZXJ06B01；JD2023GJ01-09；LH2021C027//China Agriculture Research Systems；Heilongjiang Province Scientific and Technological Project；Key R&D projects of Heilongjiang Province in 2023；Natural Science Foundation of Heilongjiang Province/ ; }, abstract = {Potato (Solanum tuberosum L.) has high nutritional value and strong adaptability and plays an extremely important role in global food security. Excessive use of nitrogen (N) fertilizer in potato production has increased costs and environmental pollution. In this study, the N use efficiency (NUE) of two potato varieties (DXY and DN310) was determined under high nitrogen conditions. The N use efficiency of DXY was relatively high. The differences between the rhizosphere microbial population groups of the two varieties were determined using the metagenomic sequencing method. The genes related to N efficiency were jointly identified using transcriptome and metabolome analyses. Significant difference was observed between the two varieties of microorganisms, leading to different rhizosphere microorganisms. Compared with DN310, the roots of DXY retained more available N and generated less NO. Additionally, DXY exhibited relatively low disease susceptibility. Combined transcriptome and metabolome analyses indicated that the differentially expressed metabolites in the two different varieties under high N conditions were mainly enriched in amino acid metabolism and sugar metabolism pathways. Using weighted gene co-expression network analysis, two genes associated with N fertilizer response were identified: PGSC0003DMG400025888 and PGSC0003DMG400017276. This study provided valuable insights into breeding potato varieties with high N efficiency.}, } @article {pmid40094201, year = {2025}, author = {Masaadeh, AH and Eletrebi, M and Parajuli, B and De Jager, N and Bosch, DE}, title = {Human colitis-associated colorectal carcinoma progression is accompanied by dysbiosis with enriched pathobionts.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2479774}, doi = {10.1080/19490976.2025.2479774}, pmid = {40094201}, issn = {1949-0984}, mesh = {Humans ; *Dysbiosis/microbiology ; Male ; Female ; Middle Aged ; *Gastrointestinal Microbiome ; Aged ; *Disease Progression ; *Colorectal Neoplasms/microbiology/pathology ; *Bacteria/classification/isolation & purification/genetics ; Inflammatory Bowel Diseases/microbiology/pathology/complications ; Colitis-Associated Neoplasms/microbiology/pathology ; Adult ; RNA, Ribosomal, 16S/genetics ; Colitis/microbiology/pathology ; Metagenomics ; Intestinal Mucosa/microbiology/pathology ; }, abstract = {Dysbiosis and pathobionts contribute to inflammation and the risk of colitis-associated carcinoma (CAC) in animal models, but their roles in humans with this uncommon disease are unknown. We identified microbiome differences in human CAC compared with longstanding inflammatory bowel disease (IBD) and sporadic colorectal carcinoma (CRC). Twenty-four CAC resections were matched with CRC and IBD controls. Methods included histopathology, 16S rDNA metagenomics, and pathobiont-specific qPCR. Beta diversity differed by diagnosis (PERMANOVA p = 0.007). The distinguishing taxa included Akkermansia enriched in CRC, and Bacteroides spp. enriched in IBD. The non-neoplastic mucosae presented distinct beta diversity (p = 0.005), but the CAC/CRC tumor microbiomes were similar (p = 0.7). Within metastases and margins, Enterobacteriaceae were enriched in CAC, and Bacteroidales in CRC. Pathobiont-specific qPCR confirmed a greater frequency of pks+ E. coli and enterotoxigenic Bacteroides fragilis in CAC than IBD. High alpha diversity was associated with active inflammation, advanced cancer stage, and shorter overall survival (log-rank p = 0.008). Mucosal microbiomes distinguish CAC from longstanding IBD, implicating pathobionts as markers for disease progression. Integrating our findings with prior animal model research, pathobionts promote carcinogenesis in IBD patients through genotoxicity and host cell signaling.}, } @article {pmid40093613, year = {2025}, author = {Huang, X and Yuan, T and Huang, Y and Qazi, IH and Liu, J}, title = {Analysis of causal pathogens of mulberry bacterial blight in samples collected from eight provinces of China using culturomics and metagenomic sequencing methods.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1517050}, pmid = {40093613}, issn = {1664-462X}, abstract = {Mulberry bacterial blight (MBB) is a complex and one of the devastating diseases of mulberry that causes serious reduction in the yield and quality of mulberry. In recent years, the transformation of sericulture industry, mulberry production system, and increasing seedling trade have resulted in the spread of MBB to different parts of China, posing a major economic threat to the farmers and industry. This study investigated the occurrence of MBB in eight provinces of China during years 2023 and 2024. The MBB disease samples were collected and the composition of the MBB pathogenic microbiome was analyzed by combining culturomics and metagenomic sequencing methods. A total of 498 bacterial strains were isolated and identified through culturomics, and then 109 suspected pathogen strains were preliminarily screened based on metagenomic sequencing data. Finally, 10 pathogens including, Pseudomonas syringae, P. fulva, P. fluorescens, Pantoea ananatis, Pectobacterium parvum, P. carotovorum, Flavobacterium fluviale, Citrobacter portucalensis, Klebsiella grimontii, Stenotrophomonas maltophilia, were identified through Koch's postulates. Based on the distribution pattern of pathogens and the changes in the microbiome community of mulberry following infection with P. syringae, we infer that P. syringae, and P. fulva are important pathogens of MBB. In addition, based on the analysis of meteorological data, different bacteria showed adaptability to different environments, leading to differences in the pathogens of MBB under different climate conditions and latitudes. The data presented herein provides a foundation for understanding the occurrence, spatial distribution and pathogenic mechanism of MBB and its major pathogens.}, } @article {pmid40093185, year = {2025}, author = {France, MT and Chaudry, I and Rutt, L and Quain, M and Shirtliff, B and McComb, E and Maros, A and Alizadeh, M and Hussain, FA and Elovitz, MA and Relman, DA and Rahman, A and Brotman, RM and Price, J and Kassaro, M and Holm, JB and Ma, B and Ravel, J}, title = {VIRGO2: Unveiling the Functional and Ecological Complexity of the Vaginal Microbiome with an Enhanced Non-Redundant Gene Catalog.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.03.04.641479}, pmid = {40093185}, issn = {2692-8205}, abstract = {Despite the importance of the cervicovaginal microbiome, the mechanisms that govern its composition and drive its impact on host physiology remain poorly understood. This study expands our understanding of the function and ecology of the vaginal microbiome using VIRGO2, an enhanced non-redundant gene catalog comprising over 1.7 million well-annotated genes from body-site specific microbes and viruses. Analyses using VIRGO2 revealed novel insights, including the identification of previously uncharacterized vaginal bacteria, features of the vaginal mycobiome and phageome, and differential expression of bacterial carbohydrate catabolic genes. Constructed from over 2,500 metagenomes and 4,000 bacterial genomes, VIRGO2 broadens geographic representation and microbial diversity compared to its predecessor. This updated catalog enables more precise profiling of taxonomic and functional composition from metagenomic and metatranscriptomic datasets. VIRGO2 is a critical resource for integrative analyses of vaginal microbial communities and their interactions with host tissues, thereby enhancing our mechanistic understanding of vaginal health and disease.}, } @article {pmid40092793, year = {2025}, author = {Abakumov, S and Ruppeka-Rupeika, E and Chen, X and Bouwens, A and Leen, V and Dedecker, P and Hofkens, J}, title = {DeepMAP: Deep CNN Classifiers Applied to Optical Mapping for Fast and Precise Species-Level Metagenomic Analysis.}, journal = {ACS omega}, volume = {10}, number = {9}, pages = {9224-9232}, pmid = {40092793}, issn = {2470-1343}, abstract = {DNA optical mapping is a powerful technique commonly used for structural variant calling and genome assembly verification. Despite being inherently high-throughput, the method has not yet been applied to highly complex settings such as species identification in microbiome analysis due to the lack of alignment algorithms that can both assign large numbers of reads in minutes and handle large database size. In this work, we present a novel genomic classification pipeline based on deep convolutional neural networks for optical mapping data (DeepMAP), which can perform fast and accurate assignment of individual optical maps to their respective genomes. We furthermore achieve a superior performance of DeepMAP in the presence of evolutionary divergent sequences, making it robust to the presence of unknown strains within metagenomic samples. We evaluate DeepMAP on genomic DNA extracted from bacterial mixtures, reaching species-level resolution with true positive rates of around 75% and a false positive rate of less than 1%, with measured classification speeds significantly outpacing those of previously developed approaches for high-density optical mapping data alignment.}, } @article {pmid40092035, year = {2025}, author = {Li, S and Liu, Y and Yang, X and Yang, Y and Peng, J and Xu, Y and Wei, J}, title = {Spatiotemporal composition and diversity of endophyte communities in Dracaena cambodiana on Hainan Island.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1540669}, pmid = {40092035}, issn = {1664-302X}, abstract = {INTRODUCTION: Dracaena cambodiana produces a red resin known as Dragon's blood, which is used worldwide in traditional medicine and as a dye. The role of endophytes in the resin-formation process remains underexplored. Understanding the endophyte communities and their functional roles in resin production could enable the development of efficient induction techniques for resin production.

METHODS: In this study, ITS and metagenomic sequencing analyzed endophyte communities' characteristics and functional traits in different tissues and D. cambodiana across multiple wild populations on Hainan Island.

RESULTS: We identified distinct fungal genera that were dominant in different tissues. Following injury, we observed significant changes in the expression of endophytic fungal genes. These changes indicated that metabolic pathways associated with resin metabolism, sucrose metabolism, signal transduction, and phenylalanine metabolism were likely involved in resin formation. Additionally, several glycosylation gene families were upregulated in the post-injury endophytic communities, which suggests a role in flavonoid transport and the reduction of autotoxic effects.

DISCUSSION: Our results suggest that endophytes play a vital role in the resin-formation process of D. cambodiana. Isolating specific endophytes or using synthetic communities could potentially improve resin yields and avoid pathogenic fungi, ensuring safety. The findings from this study provide a theoretical basis for the development of high-efficiency resin induction techniques by targeting the dynamic changes in endophyte communities across tissues, regions, and resin formation stages.}, } @article {pmid40091996, year = {2025}, author = {Chandra Nayak, S and Latha, PB and Kandanattu, B and Pympallil, U and Kumar, A and Kumar Banga, H}, title = {The Oral Microbiome and Systemic Health: Bridging the Gap Between Dentistry and Medicine.}, journal = {Cureus}, volume = {17}, number = {2}, pages = {e78918}, pmid = {40091996}, issn = {2168-8184}, abstract = {The oral microbiome, consisting of a mixture of bacteria, fungi, and viruses, is an important contributor to oral and systemic health. Microbial balance disruptions are associated with oral pathologies like dental caries and periodontitis as well as systemic diseases such as cardiovascular diseases, adverse pregnancy outcomes, and respiratory diseases. This review explores the mechanistic pathways linking oral dysbiosis to systemic inflammation, endothelial dysfunction, and immune modulation. The roles of key microbial species in health and disease are analyzed, with an emphasis on how hematogenous dissemination leads to systemic pathologies through inflammatory signaling. Also, advances in high throughput sequencing are discussed, as well as microbial diversity and its implications for diagnostics and therapeutics. The review highlights the potential of oral microbiota-targeted interventions to mitigate systemic diseases through dentistry and medicine integration, by throwing light on interdisciplinary strategies. Future work should focus on the evaluation of the mechanisms by which the oral microbiome plays a role in systemic diseases through the integration of multi-omics approaches such as metagenomics, transcriptomics, and metabolomics. Furthermore, clinical trials need to be designed in a way to evaluate the efficacy of microbiome-targeted therapies in the prevention of cardiovascular diseases, adverse pregnancy outcomes, and autoimmune disorders.}, } @article {pmid40091534, year = {2025}, author = {Lu, YM and Lu, JQ and Zhao, Q and Chen, J and Xiong, JB}, title = {Pathogenic mechanisms of Enterocytozoon hepatopenaei through the parasite-gut microbiome-shrimp (Litopenaeus vannamei) physiology axis.}, journal = {Zoological research}, volume = {46}, number = {2}, pages = {401-413}, doi = {10.24272/j.issn.2095-8137.2024.411}, pmid = {40091534}, issn = {2095-8137}, mesh = {Animals ; *Penaeidae/microbiology ; *Gastrointestinal Microbiome/physiology ; *Enterocytozoon/physiology/genetics ; Host-Parasite Interactions ; }, abstract = {The progressive impact of Enterocytozoon hepatopenaei (EHP) infection on gut microbial function in Litopenaeus vannamei remains poorly understood beyond static comparisons between healthy and infected individuals. To close this knowledge gap, metagenomic sequencing was used to characterize the gut microbiomes of normal, long, medium, and short-sized adult shrimp categorized by increasing severity of infection. EHP infection suppressed digestive activity while inducing immune responses compared with healthy shrimp. Increasing infection severity was associated with a gradual decline in gut α-diversity and an expansion of potential pathogens and virulence factors (VFs). In addition, dysbiosis in gut microbiota composition and function, as well as reduced network stability among differential species, intensified with infection severity. Accordingly, we identified 24 EHP-discriminatory species that contributed an overall 83.3% accuracy in diagnosing infection severity without false negatives. Functional pathway analysis revealed significant suppression of metabolic, degradative, and biosynthetic processes in EHP-infected shrimp compared with healthy controls. Among them, map00630 glyoxylate and dicarboxylate metabolism and map00280 valine, leucine and isoleucine degradation were consistently depleted in infected individuals, thereby impairing their digestive function and anti-inflammatory responses. Additionally, EHP infection diversified VFs directly affecting shrimp gut microbiome. These findings support a conceptual model linking EHP pathogenesis to the parasite-gut microbiome-shrimp physiology axis.}, } @article {pmid40091365, year = {2025}, author = {Norgan, AP and Enninga, EAL and Fedyshyn, B and Wolf, M and Goldstein, JA and Shanes, ED}, title = {Enterovirus Placentitis is an Underrecognized Cause of Placental Pathology.}, journal = {The American journal of surgical pathology}, volume = {}, number = {}, pages = {}, doi = {10.1097/PAS.0000000000002378}, pmid = {40091365}, issn = {1532-0979}, abstract = {The placenta is susceptible to infection by a number of viral pathogens, including severe acute respiratory syndrome coronavirus 2, which is associated with poor fetal outcomes. The histologic pattern of injury, termed severe acute respiratory syndrome coronavirus 2 placentitis, is characterized by a triad of increased perivillous fibrin deposition, intervillous histiocytes, and trophoblast necrosis. While the etiology of massive perivillous fibrin deposition (MPVFD) is mostly unknown, previous case reports of MPVFD in association with maternal Enterovirus (ENT) suggest that a subset of these cases are a consequence of undiagnosed viral infection. We evaluated 46 placentas collected between 2011 and 2022 with a diagnosis of MPVFD (n = 41) or chronic histiocytic intervillositis (CHI; n = 4). Combining methods of pan-viral metagenomic sequencing and targeted viral PCR, we detected Enterovirus DNA in 8 of 45 (18%) MPVFD and/or CHI cases. Seven of these positive cases were from MPVFD, and 1 was associated with a CHI diagnosis. Enterovirus A species (n = 7) were commonly identified, whereas one case had Enterovirus B. Histologic evaluation of these cases, including immunohistochemical staining for CD68, demonstrated increased intervillous histiocytes in Enterovirus-positive MPVFD cases in comparison with Enterovirus-negative, as well as evidence of trophoblast necrosis. Thus, we favor the terminology Enterovirus placentitis to describe this pathology. Overall, these findings suggest that Enterovirus is an underrecognized etiology of histologic MPVFD and, possibly, CHI. Further study to evaluate the recurrence risk of Enterovirus placentitis in comparison to MPVFD may help inform future fertility planning in patients with these diagnoses.}, } @article {pmid40091083, year = {2025}, author = {Honda, H and Suzuki, T and Kitajima, M and Kondo, NI and Miyata, K and Utsumi, S and Yamada, M}, title = {The new era shaped by environmental genome monitoring - symposium of the japanese environmental mutagen and genome society (JEMS), 2024.}, journal = {Genes and environment : the official journal of the Japanese Environmental Mutagen Society}, volume = {47}, number = {1}, pages = {6}, pmid = {40091083}, issn = {1880-7046}, abstract = {The symposium "The New Era Shaped by Environmental Genome Monitoring," held in December 2024 by the Japanese Environmental Mutagen and Genome Society (JEMS), aimed to explore the interdisciplinary collaborations that are essential for the development of new scopes in environmental genome monitoring. This event highlighted the necessity of integrating mutagenicity research with ecological assessments to enhance public health and biodiversity conservation. Presentations focused on the evolving landscape of environmental genomics, including metagenomic analyses for antibiotic resistance, viral genomic surveillance in wastewater, and innovations in noninvasive biodiversity and stress monitoring through environmental DNA and RNA. This report summarizes the key discussions and presentations from the symposium, underscoring the critical role of environmental genome monitoring in shaping future safety research.}, } @article {pmid40090954, year = {2025}, author = {Lund, D and Parras-Moltó, M and Inda-Díaz, JS and Ebmeyer, S and Larsson, DGJ and Johnning, A and Kristiansson, E}, title = {Genetic compatibility and ecological connectivity drive the dissemination of antibiotic resistance genes.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {2595}, pmid = {40090954}, issn = {2041-1723}, support = {2018-02835//Vetenskapsrådet (Swedish Research Council)/ ; 2018-05771//Vetenskapsrådet (Swedish Research Council)/ ; 2019-03482//Vetenskapsrådet (Swedish Research Council)/ ; 2022-00945//Vetenskapsrådet (Swedish Research Council)/ ; }, mesh = {*Gene Transfer, Horizontal ; *Bacteria/genetics/drug effects ; Humans ; *Phylogeny ; Wastewater/microbiology ; Genome, Bacterial ; Animals ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Microbiota/genetics/drug effects ; Genes, Bacterial ; Metagenome ; Drug Resistance, Bacterial/genetics ; }, abstract = {The dissemination of mobile antibiotic resistance genes (ARGs) via horizontal gene transfer is a significant threat to public health globally. The flow of ARGs into and between pathogens, however, remains poorly understood, limiting our ability to develop strategies for managing the antibiotic resistance crisis. Therefore, we aim to identify genetic and ecological factors that are fundamental for successful horizontal ARG transfer. We used a phylogenetic method to identify instances of horizontal ARG transfer in ~1 million bacterial genomes. This data was then integrated with >20,000 metagenomes representing animal, human, soil, water, and wastewater microbiomes to develop random forest models that can reliably predict horizontal ARG transfer between bacteria. Our results suggest that genetic incompatibility, measured as nucleotide composition dissimilarity, negatively influences the likelihood of transfer of ARGs between evolutionarily divergent bacteria. Conversely, environmental co-occurrence increases the likelihood, especially in humans and wastewater, in which several environment-specific dissemination patterns are observed. This study provides data-driven ways to predict the spread of ARGs and provides insights into the mechanisms governing this evolutionary process.}, } @article {pmid40090735, year = {2025}, author = {Yabuki, A and Fujii, C and Yazaki, E and Tame, A and Mizuno, K and Obayashi, Y and Takao, Y}, title = {Massive RNA Editing in Ascetosporean Mitochondria.}, journal = {Microbes and environments}, volume = {40}, number = {1}, pages = {}, doi = {10.1264/jsme2.ME24070}, pmid = {40090735}, issn = {1347-4405}, mesh = {*RNA Editing ; *Mitochondria/genetics ; *Genome, Mitochondrial/genetics ; High-Throughput Nucleotide Sequencing ; Eukaryota/genetics/classification ; Phylogeny ; Adenosine Deaminase/genetics/metabolism ; }, abstract = {Ascetosporeans are parasitic protists of invertebrates. A deep sequencing ana-lysis of species within the orders Mikrocytida, Paramyxida, and Haplosporida using metagenomic approaches revealed that their mitochondria were functionally reduced and their organellar genomes were lacking. Ascetosporeans belonging to the order Paradinida have not been sequenced, and the nature of their mitochondria remains unclear. We herein established two cultures of Paradinida and conducted DNA and RNA sequencing ana-lyses. The results obtained indicate that mitochondrial function in paradinids was not reduced and their organellar genomes were retained. In contrast, their mitochondrial genomes were involved in massive A-to-I and C-to-U substitution types of RNA editing. All edits in protein-coding genes were nonsynonymous substitutions, and likely had a restorative function against negative mutations. Furthermore, we detected possible sequences of DYW type of pentatricopeptide repeat (PPR-DYW) protein and a homologue of adenosine deaminase acting on RNA (ADAR-like), which are key enzymes for C-to-U and A-to-I substitutions, respectively. An immunofluorescence ana-lysis showed that ADAR-like of paradinids may specifically localize within mitochondria. These results expand our knowledge of the diversity and complexity of organellar RNA editing phenomena.}, } @article {pmid40090521, year = {2025}, author = {Kitaya, S and Horiba, K and Kabata, T and Iyobe, T and Hashino, M and Yamazaki, H and Takahashi, Y and Zaimoku, Y and Oshima, M and Kanamori, H}, title = {The contribution of metagenomic next-generation sequencing to a diagnosis of gas-producing Fusobacterium-induced septic hip arthritis: A case report.}, journal = {Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy}, volume = {}, number = {}, pages = {102681}, doi = {10.1016/j.jiac.2025.102681}, pmid = {40090521}, issn = {1437-7780}, abstract = {Pyogenic arthritis with gas gangrene triggered by intra-articular steroid injections can occasionally result in fatal complications. Clostridium perfringens is typically the causative pathogen, with infections caused by Fusobacterium sp. being relatively rare. Fusobacterium sp. are known to cause pyogenic infections, but due to their extreme sensitivity to oxygen, they can be difficult to detect with traditional culture methods. Recently, metagenomic next-generation sequencing (mNGS) has gained attention as an alternative diagnostic tool to traditional culture, enabling rapid identification of causative pathogens in infectious diseases, including pyogenic arthritis. Its use is illustrated in the following case report, which demonstrates the diagnostic utility of mNGS in pyogenic arthritis with gas gangrene triggered by an intra-articular steroid injection. Using mNGS as a complement to conventional culture testing allows for a more precise narrowing-down of causative pathogens, enabling targeted therapy and improving patient outcomes. This approach may also help reduce the use of broad-spectrum antibiotics and prevent the emergence of antibiotic-resistant bacteria.}, } @article {pmid40090450, year = {2025}, author = {Wu, H and Chen, S and Deng, Y and Shen, J and Xu, Y and Wen, T and Yuan, J and Shen, Q and Xue, C}, title = {Dynamics of antibiotic resistance genes and the bacterial community after stress from a single Dazomet fumigation.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {126048}, doi = {10.1016/j.envpol.2025.126048}, pmid = {40090450}, issn = {1873-6424}, abstract = {Although chemical fumigants are widely applied in agriculture to control soil-borne diseases, their influence on soil antibiotic resistance genes (ARGs) remains poorly understood. This study employed metagenomic sequencing to investigate the dynamic response and recovery processes of soil bacterial communities and ARGs after the end of fumigation with Dazomet. The results revealed that the effects of Dazomet were both phased and recoverable. Initially, no significant shifts in bacterial community diversity were observed; however, by day 10 of recovery (Dazomet10), diversity had decreased by 3.1%. By contrast, ARG levels surged by 17.3% and 10.9% on days 10 and 20 (Dazomet20), respectively, before reverting to the baseline by day 50 (Dazomet50). These patterns were corroborated by qPCR data, which showed a 90.8% reduction in 16S rRNA gene abundance, alongside a 4.17- to 4.38-fold increase in the relative abundance of ARGs at Dazomet10 and Dazomet20. Approximately 63% of the variation in ARGs was attributed to bacterial community composition and mobile genetic elements (MGEs). Combined with community analysis and host-tracking analysis, it was found that Streptomyces and Nocardioides were identified as key ARGs hosts. Overall, the microbial communities and resistome required at least 50 days after the end of fumigation to recover to their pre-fumigation state. This study sheds light on the dynamic interactions between bacterial communities and ARGs during recovery from Dazomet fumigation and underscores the critical need for the rational use of fumigants in agricultural practices.}, } @article {pmid40090148, year = {2025}, author = {Dong, KY and Yang, CX and Pang, JL and Chang, RR and Chen, KY and Yao, W and Huang, BC and Jin, RC}, title = {Antibiotics shape the core microbial community distribution between floc and biofilm in an endogenous partial denitrification system: Insight from metabolic pathway.}, journal = {Water research}, volume = {280}, number = {}, pages = {123491}, doi = {10.1016/j.watres.2025.123491}, pmid = {40090148}, issn = {1879-2448}, abstract = {The response mechanism of microorganisms in partial denitrification (PD) system under antibiotic stress, particularly microbial energy metabolism and electron transfer, remain inadequately understood. This knowledge gap hinders the establishment of ecological links between microbial dynamics and macro-level reactor performance. To address this, moving bed biofilm reactors were employed to investigate the dynamic changes of microbial community and metabolism under sulfadiazine (SDZ) and ciprofloxacin (CIP) stress. Results showed that dosing 2 mg/L SDZ or CIP accelerated nitrite accumulation, achieving this milestone 15 days earlier than in the control group. At the end of the operational phase, nitrate removal efficiencies reached 90.3 ± 18.3 % (Control), 83.5 ± 16.2 % (SDZ-treated) and 93.9 ± 12.4 % (CIP-treated), with nitrate-to nitrite-transformation rates of 61.3 ± 12.7 %, 65.6 ± 13.1 % and 58.0 ± 21.2 %, respectively. The abundances of energy supply related genes, i.e., sucC and PK were higher in the CIP-treated group, while those in the other two groups were similar. The promoted tricarboxylic acid cycle and glycolysis led to NADH and ATP accumulation, accelerating nitrogen metabolism and benefiting early nitrite accumulation in the antibiotic-stressed system. More importantly, increasing antibiotics concentration from 2 mg/L to 4 mg/L induced selective migration of Thauera from floc to biofilm (abundance in floc reduced to < 2.01 %). Metagenomic sequencing indicated that the higher abundance of narGHI in biofilms, compared to flocs, was crucial for maintaining stable PD performance under antibiotic stress. The electron transport related genes, such as IDH1, DLD and DLAT, were more abundant in biofilms than in flocs after SDZ and CIP addition. These findings provide a theoretical basis for understanding the response mechanism of PD consortia to antibiotic.}, } @article {pmid40090144, year = {2025}, author = {Deng, B and Ren, Z and Li, Q and Zhang, Z and Xu, C and Wang, P and Zhao, H and Yuan, Q}, title = {Black soldier fly larvae mediate Zinc and Chromium transformation through the ZnuCBA and citric acid cycle system.}, journal = {Water research}, volume = {280}, number = {}, pages = {123483}, doi = {10.1016/j.watres.2025.123483}, pmid = {40090144}, issn = {1879-2448}, abstract = {Intestinal microbiota and metal regulatory proteins (MRPs) underlie the transformation of heavy metals (HMs) by the black soldier fly larvae (BSFL), but the mechanisms involved are still not fully defined. Here, using 16S rRNA and metagenomics-assisted tracing, we found that zinc (Zn) and chromium (Cr) stress led to enrichment of Proteobacteria in the BSFL intestine. Support of Proteobacteria also led to increased levels of the Zn transporter proteins ZnuC/B/A and the Zn efflux proteins zntR/A. Meanwhile, the genes MltE, CitT, and SLT, which mediate the citric acid cycle, were also significantly up-regulated and involved in the cellular uptake of Cr. Although Zn and Cr stress affected the expression of antibiotic resistance genes and pathogenic genes, the BSFL intestine tended to form stable microbial communities (MCs) to transform HMs through a mechanism driven by ZupT and chrA. In addition, the expression of SCARB1 and LdcA was significantly down-regulated by acute HMs stimulation, but BSFL were still able to complete the life cycle. Therefore, we determined the protective role of MCs and MRPs on BSFL during the transformation of HMs.}, } @article {pmid40089680, year = {2025}, author = {Wang, S and Niu, W and Lv, T and Xie, K}, title = {Traceability of septic shock caused by phocaeicola vulgatus: a rare case report.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {364}, pmid = {40089680}, issn = {1471-2334}, mesh = {Humans ; *Shock, Septic/microbiology ; Male ; Middle Aged ; High-Throughput Nucleotide Sequencing ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {BACKGROUND: Phocaeicola vulgatus (P.vulgatus) is a member of Bacteroides fragilis Group(BFG). Septic shock caused by P.vulgatus has not been reported yet. In recent years, BFG have attracted much clinical attention. BFG are the commensal microbiota residing in human mucosal sites, most notably the gut, that provide several benefits to healthy hosts. Yet BFG can cause devastating infections when they gain access to normally sterile body compartments following trauma, surgery, or mucosal barrier disruption.

CASE PRESENTATION: We report a case of septic shock event in a middle-aged male who underwent surgical intervention for a gallbladder mass incidentally detected during routine abdominal CT screening. P.vulgatus was isolated and cultured from blood sample and abdominal drainage fluid after surgery. We further performed the Metagenomic Next-Generation Sequencing (mNGS) with pathological slices of colon and hepatobiliary tissue, and result of mNGS also showed P.vulgatus. The patient was treated with comprehensive therapies and had a good outcome.

CONCLUSION: To the best of our knowledge, septic shock secondary to P.vulgatus infection originating from non-gastrointestinal area represents an rare clinical condition. We realized that research on BFG should not only focus on its positive effects on the intestine, but also on its potential pathogenicity, including intra-abdominal infections, abscesses, and bloodstream infection.}, } @article {pmid40089034, year = {2025}, author = {Zhang, Z and Liu, Y and Yang, X and Luo, Q and Huang, W and Zhao, Z}, title = {Impacts of hydraulic retention time on organic removal in treating liquor wastewater via algal-bacterial granular sludge.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132394}, doi = {10.1016/j.biortech.2025.132394}, pmid = {40089034}, issn = {1873-2976}, abstract = {This study optimized hydraulic retention time (HRT) to improve p-cresol and chemical oxygen demand (COD) removal and promote algal-bacterial granular sludge (ABGS) formation in Chinese fermented liquor wastewater treatment. At an HRT of 4 h, no granules formed in the sequential batch reactor, and after 30 days, the removal efficiencies were low for both COD (58.5 %) and p-cresol (21.6 %). In contrast, compact granules developed at HRT 8 and 12 h. The HRT of 8 h achieved the highest removal efficiencies (COD: 96.0 %, p-cresol: 91.3 %), outperforming the HRT of 12 h (COD: 95.1 %, p-cresol: 82.7 %). Microbial analysis identified Rhodobacteraceae and Pseudomonas as key p-cresol degraders. Metagenomic analysis revealed a higher abundance of benzoate degradation genes at an HRT of 8 h compared to 12 h, with Acidovorax predominantly contributing at 8 h and Hydrogenophaga at 12 h. These findings provide insights into the optimization of liquor wastewater treatment.}, } @article {pmid40088533, year = {2025}, author = {Kim, HR and Kim, SH and Le, HD and Kim, JK and Her, M}, title = {The complete genome sequence of quail coronavirus identified in disease surveillance on quail farms in South Korea.}, journal = {Poultry science}, volume = {104}, number = {5}, pages = {105007}, doi = {10.1016/j.psj.2025.105007}, pmid = {40088533}, issn = {1525-3171}, abstract = {Avian carcasses collected from 103 flocks on 14 quail farms in Korea between 2022 and 2023 were diagnosed with viral diseases (22 flocks), bacterial disease (58 flocks), parasitic diseases (28 flocks) and non-infectious diseases (60 flocks). The only viral disease identified was viral enteritis in quails that showed pathological lesions in duodenum and appeared to be caused by quail coronavirus (QcoV) through viral metagenomics and RT-PCR assay. Two complete genomes of QCoV from samples diagnosed as viral enteritis were obtained using amplicon-based whole genome sequencing. The two QcoVs were gammacoronavirus, but were distinct from other avian coronaviruses. The spike genes of QCoV have 86.2 ∼ 87.1 % identity with that of American turkey coronavirus, but other gene sequences of QcoV was found to be similar to those of Korean infectious bronchitis virus. Genetic analysis based on the complete genomic sequences found QCoVs had a genetic structure similar to avian coronaviruses, yet it seems to be a unique pathogen specific to quail. This is the first report about the complete genome and genetic analysis of QCoV and the result of disease surveillance in quail in South Korea.}, } @article {pmid40087960, year = {2025}, author = {Sabba, F and Farmer, M and Dunlap, P and Qin, C and Kozak, J and Barnard, J and Wells, G and Downing, L}, title = {Unlocking the potential of sidestream EBPR: exploring the coexistence of PAO, GAO and DGAO for effective phosphorus and nitrogen removal.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {91}, number = {5}, pages = {469-481}, pmid = {40087960}, issn = {0273-1223}, mesh = {*Phosphorus/metabolism ; *Nitrogen/metabolism ; *Waste Disposal, Fluid/methods ; Bioreactors ; Denitrification ; Anaerobiosis ; Glycogen/metabolism ; Water Pollutants, Chemical/metabolism ; }, abstract = {Wastewater treatment facilities use enhanced biological phosphorus removal (EBPR) to meet discharge quality limits. However, the EBPR process can experience upsets due to a lack of influent carbon or inadequate anaerobic zones. By using a sidestream EBPR (S2EBPR) process, carbon can be generated internally through fermentation processes and a higher anaerobic mass fraction can be attained in smaller volumes. This study investigates nutrient removal and microbial community trends in a full-scale S2EBPR demonstration at the Calumet Water Reclamation Plant. The study aims to improve a process model of the system by better representing the activity of glycogen-accumulating organisms (GAO) and potential competitors of phosphorus-accumulating organisms (PAO), which were found in high abundance in this study. Modifying anaerobic hydrolysis, GAO glycogen storage and ORP activity parameters resulted in model prediction improvements of approximately 5% for nitrate and nitrite and 10-60% for phosphorus. The study also uses shotgun metagenomic sequencing to profile denitrification pathways of PAO and GAO. It shows that denitrifying GAO may contribute to nitric oxide reduction to a greater degree than denitrifying PAO. This study improves process modeling predictions for S2EBPR and highlights the potential role of denitrifying PAO and GAO in combined phosphorus and nitrogen removal in S2EBPR.}, } @article {pmid40087791, year = {2025}, author = {Centeno-Delphia, RE and Glidden, N and Long, E and Ellis, A and Hoffman, S and Mosier, K and Ulloa, N and Cheng, JJ and Davidson, JL and Mohan, S and Kamel, M and Szasz, JI and Schoonmaker, J and Koziol, J and Boerman, JP and Ault, A and Verma, MS and Johnson, TA}, title = {Nasal pathobiont abundance is a moderate feedlot-dependent indicator of bovine respiratory disease in beef cattle.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {27}, pmid = {40087791}, issn = {2524-4671}, support = {2020-68014-31302//National Institute of Food and Agriculture/ ; 2018-006//Purdue University's Colleges of Agriculture and Engineering Collaborative Projects Program/ ; }, abstract = {BACKGROUND: Bovine respiratory disease (BRD) poses a persistent challenge in the beef cattle industry, impacting both animal health and economic aspects. Several risk factors make an animal susceptible to BRD, including bacteria such as Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Mycoplasma bovis. Despite efforts to characterize and quantify these bacteria in the nasal cavity for disease diagnosis, more research is needed to understand if there is a pathobiont abundance threshold for clinical signs of respiratory disease, and if the results are similar across feedlots. This study aims to compare the nasal microbiome community diversity and composition, along with the abundance of four bacterial pathogens and associated serotypes, in apparently healthy and BRD-affected beef cattle. Nasal swabs were collected from four beef feedlots across the US, covering the years 2019 to 2022. The study included post-weaned beef cattle with diverse housing conditions.

RESULTS: Quantification of BRD-associated pathogens effectively distinguished BRD-affected from apparently healthy beef cattle, surpassing the efficacy of 16S rRNA gene sequencing of the nasal microbiome community. Specifically, H. somni, M. bovis, and M. haemolytica had higher abundance in the BRD-affected group. Utilizing the abundance of these pathobionts and analyzing their combined abundance with machine learning models resulted in an accuracy of approximately 63% for sample classification into disease status. Moreover, there were no significant differences in nasal microbiome diversity (alpha and beta) between BRD-affected and apparently healthy cattle; instead, differences were detected between feedlots.

CONCLUSIONS: Notably, this study sheds light on the beef cattle nasal microbiome community composition, revealing specific differences between BRD-affected and apparently healthy cattle. Pathobiont abundance was increased in some, but not all farms. Nonetheless, more research is needed to determine if these differences are consistent across other studies. Additionally, future research should consider bacterial-viral interactions in the beef nasal metagenome.}, } @article {pmid40087775, year = {2025}, author = {Duret, M and Wallner, A and Besaury, L and Aziz, A}, title = {Diversity and functional features of the root-associated bacteriome are dependent on grapevine susceptibility to Plasmopara viticola.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {30}, pmid = {40087775}, issn = {2524-6372}, support = {1564//French National Research Agency through the PRIMA-MiDiVine project/ ; 1564//French National Research Agency through the PRIMA-MiDiVine project/ ; 1564//French National Research Agency through the PRIMA-MiDiVine project/ ; }, abstract = {BACKGROUND: Plant health depends on beneficial interactions between the roots and their microbiomes. Despite recent progress on the role of the grapevine microbiome, the taxonomic identity and functional traits of microbial taxa specific to healthy or Plasmopara viticola-diseased plants, as well as to the susceptible or resistant cultivar are unknown. Using metabarcoding and shotgun metagenomics sequencing, we investigated the effect of downy mildew on the root-associated microbiome (rhizospheric soil, rhizoplane and endosphere) of 41B-grafted susceptible cultivar (Chardonnay) and resistant interspecific hybrid (Voltis) at flowering and veraison stages. The impact of conventional treatment on the rhizomicrobiome assembly of Chardonnay was also evaluated.

RESULTS: Analyses revealed a core bacteriome shared between both susceptible and resistant cultivars. This also highlighted common functional traits between the rhizosphere and rhizoplane bacteriomes in both cultivars. A dysbiosis state was also evidenced by a loss of beneficial communities in the rhizosphere of the P. viticola-infected cultivar. Microbial genome assemblies showed functional differences between healthy and diseased plants, with a loss of Pseudomonas and Phyllobacterium taxa at veraison. This state was mainly characterized by a loss of genes involved in polyamine transport and metabolism in the susceptible cultivar. It was also marked by an increase in population evenness and total bacterial diversity, and the presence of pathogenic species in susceptible plants.

CONCLUSIONS: This study reveals distinct and overlapping bacterial communities and functional genes in the rhizospheric soil, rhizoplane and root endosphere of both susceptible and resistant grapevine cultivars to downy mildew. Microbial diversity and abundant taxa of grapevine roots are influenced by downy mildew and cultivar susceptibility. Common bacterial functions are shared among rhizocompartments of susceptible and resistant cultivars, revealing a dysbiosis state and functional signatures related to plant immunity, especially in the infected-susceptible plants.}, } @article {pmid40087699, year = {2025}, author = {Gu, D and Liu, J and Wang, J and Yi, Y and Chu, Y and Gao, R and Liu, H and She, J and Lu, B}, title = {Integrating DNA and RNA sequencing for enhanced pathogen detection in respiratory infections.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {325}, pmid = {40087699}, issn = {1479-5876}, support = {L222073//Beijing Natural Science Foundation/ ; CFH, 2024-1-4063//Alpha Foundation for the Improvement of Mine Safety and Health/ ; ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; }, mesh = {Humans ; *Respiratory Tract Infections/microbiology/diagnosis/virology ; Male ; Female ; Sequence Analysis, RNA/methods ; Middle Aged ; High-Throughput Nucleotide Sequencing/methods ; Adult ; Sequence Analysis, DNA/methods ; Aged ; Reproducibility of Results ; Retrospective Studies ; Young Adult ; Metagenomics/methods ; Adolescent ; }, abstract = {BACKGROUND: The clinical value of shotgun metagenomic next-generation sequencing (mNGS) in improving the detection rates of respiratory pathogens is well-established. However, mNGS is complex and expensive. This study designed and evaluated the performance of targeted NGS (tNGS) in diagnosing respiratory infections.

METHODS: We retrospectively included samples from 281 patients with lower respiratory tract infections to establish thresholds of pathogens. Subsequently, target pathogens were selected and a probe hybridization system was established. The performance and clinical manifestations of tNGS for 306 pathogens were evaluated using clinical and simulated samples.

RESULTS: The tNGS method took 16 h with sequencing data sizes of 5 M reads. The limit-of-detection of tNGS was 100-200 CFU/mL, respectively. Bioinformatics simulation confirmed the method's high specificity and robustness. In 281 patients of clinical validation cohort, tNGS exhibited a sensitivity of 97.73% and specificity of 75.41% compared to the composite reference standard, which notably surpasses those of culture-based and conventional microbiological methods (CMT). In detecting bacterial and viral infection, tNGS demonstrated superior sensitivity relative to CMT. Notably, 61.40% of target viruses were subtype-resolved with the initial establishment of reliable typing cutoffs, with the subtyping results being completely consistent with the PCR results. tNGS allowed for concurrent identification of antimicrobial resistance (AMR) markers and viral subtyping. 80.56% of AMR markers identified by tNGS were consistent with antimicrobial susceptibility testing.

CONCLUSION: This research established the robust performance of our tailored tNGS assay in the simultaneous detection of DNA and RNA pathogens, underscoring its prospective suitability for widespread use in clinical diagnostics.}, } @article {pmid40087607, year = {2025}, author = {Meng, B and Liu, H and Wu, Q and Qu, L and Mao, C and Yang, F and Lan, T and Fang, J and Hu, Z and Fang, Y}, title = {Antimicrobial strategies of lower respiratory tract infections in immunocompromised patients based on metagenomic next-generation sequencing: a retrospective study.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {360}, pmid = {40087607}, issn = {1471-2334}, support = {2020-55//Wuhan Young and Middle-aged Medical Backbone Talent Project 2020/ ; ZZ20231693//Young Talent Project of General Hospital of Center Theater/ ; JCZRYB202500657//Natural Science Foundation of Hubei Province/ ; }, mesh = {Humans ; *Immunocompromised Host ; *High-Throughput Nucleotide Sequencing ; Male ; Female ; Retrospective Studies ; Middle Aged ; *Metagenomics/methods ; *Respiratory Tract Infections/drug therapy/microbiology ; Aged ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Adult ; Bacteria/genetics/drug effects/isolation & purification/classification ; }, abstract = {BACKGROUND: Immunocompromised patients with Lower Respiratory Tract Infections (LRTI) frequently encounter a diverse range of pathogenic infections, characterized by rapid disease progression and significant mortality rates due to reckless or excessive utilization of antibiotics. Therefore, it is crucial to promptly and accurately identify the causative microorganisms for pathogen diagnosis and clinical decision-making. The objective of this study is to evaluate the clinical applicability of metagenomic next-generation sequencing (mNGS) in the diagnosis and management of LRTI, as well as its impact on empirical antibacterial therapy for patients with varying immune statuses.

METHODS: We conducted a comparative analysis of positivity rate, detection accuracy, pathogen spectrum, duration of treatment (DOT), and antibiotic management in a cohort of 283 patients diagnosed with lower respiratory tract infections.

RESULTS: The positive detection rate was higher in mNGS compared to conventional culture in both immunocompetent group (89.92% vs. 28.57%, P < 0.001) and immunocompromised group (84.44% vs. 33.33%, P < 0.001). The antibiotic escalation in the immunocompromised group was more frequent than that in the immunocompetent group (49.00% vs. 31.00%, P = 0.018), but no difference was observed for antibiotic de-escalation (20.00% vs. 15.00%, P = 0.458).

CONCLUSIONS: The application of mNGS can significantly enhance the pathogen detection rate and optimize antimicrobial drug management in immunocompromised patients with LRTI.}, } @article {pmid40087598, year = {2025}, author = {Lu, S and Li, H and Ma, C and Li, X}, title = {Systemic and localized infections in humans caused by Paenibacillus: a case report and literature review.}, journal = {BMC ophthalmology}, volume = {25}, number = {1}, pages = {133}, pmid = {40087598}, issn = {1471-2415}, support = {LHGJ20220370//Joint Construction Project of Henan Medical Science and Technology/ ; LHGJ20220370//Joint Construction Project of Henan Medical Science and Technology/ ; 232300420237//Natural Science Foundation of Henan/ ; 232300420237//Natural Science Foundation of Henan/ ; }, mesh = {Humans ; Male ; Adult ; *Eye Infections, Bacterial/diagnosis/microbiology/drug therapy ; *Paenibacillus/isolation & purification ; *Gram-Positive Bacterial Infections/diagnosis/microbiology/drug therapy ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {BACKGROUND: As opportunistic pathogens, Paenibacillus organisms rarely induce human infections. This research paper details the clinical manifestations, treatment, and prognosis of an intraocular infection caused by Paenibacillus in a 43-year-old male patient.

CASE PRESENTATION: In this case, the patient initially presented with persistent ocular redness and a sensation of foreign bodies following trauma surgery. Upon admission, we performed intraocular fluid metagenomic next generation sequencing (mNGS) testing and systemic blood sampling for infection-related assessments. The results revealed a localized ocular infection with Paenibacillus organisms. Consequently, the patient received daily levofloxacin injections (500 mg) and clindamycin (300 mg) for systemic anti-infective therapy, along with subconjunctival injections of gentamicin (2 WIU) and dexamethasone (5 mg) for topical application. The infection was effectively managed, and their ocular symptoms showed improvement during the treatment course.

CONCLUSIONS: We conducted a comprehensive review of previously reported cases involving Bacillus-like organisms causing human infections, exploring mechanisms, diagnostic approaches, and treatment strategies.}, } @article {pmid40087549, year = {2025}, author = {Wang, X and Shang, Y and Xing, Y and Chen, Y and Wu, X and Zhang, H}, title = {Captive environments reshape the compositions of carbohydrate active enzymes and virulence factors in wolf gut microbiome.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {142}, pmid = {40087549}, issn = {1471-2180}, support = {2022KJ177//the Youth Innovation Team in Colleges and Universities of Shandong Province/ ; 32001228//the National Natural Science Foundation of China/ ; 32270444//the National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Virulence Factors/genetics ; *Wolves/microbiology ; *Bacteria/classification/genetics/isolation & purification/enzymology ; Dogs ; *Foxes/microbiology ; Animals, Zoo/microbiology ; Animals, Wild/microbiology ; Carbohydrate Metabolism ; Metagenomics ; }, abstract = {Species in the family Canidae occupy different spatial ecological niches, and some (e.g., wolf) can be kept in zoos. The gut microbiome may differ among various wild and captive canids. Therefore, we compared the gut microbiomes of wild canids (wolf, red fox, and corsac fox) in the Hulun Lake area, captive wolves, and domestic dogs in different regions using metagenomic data. A random forest analysis revealed significant enrichment for bacterial species producing short-chain fatty acids and the thermogenesis pathway (ko04714) in the gut microbiome of wild wolf, potentially providing sufficient energy for adaptation to a wide range of spatial ecological niches. The significantly enriched bacterial species and functional pathways in the gut microbiome of corsac foxes were related to physiological stability and adaptation to arid environments. Alpha diversity of carbohydrate-active enzymes in the gut microbiome was higher in the red fox than in the corsac fox and wild wolf, which may be related to the abundance of plant seeds (containing carbohydrates) in their diets (red foxes inhabit seed-rich willow bosk habitats). However, the influence of host genetic factors cannot be excluded, and further experimental studies are needed to verify the study results. In addition, captive environments drove similarity in carbohydrate-active enzymes (CAZymes) and virulence factors (VFs) in the gut microbiomes of captive wolf and domestic dog, and increased the diversity of CAZymes and VFs in the gut microbiome of captive wolf. Increased VFs diversity may increase the pathogenic potential of the gut microbiome in captive wolves. Therefore, it is necessary to continue monitoring the health status of captive wolves and develop appropriate management strategies.}, } @article {pmid40087199, year = {2025}, author = {Zhang, Y and Xu, S and Xu, Y}, title = {Clinical Analyses of 4 Cases of Microsporidial Keratoconjunctivitis.}, journal = {Acta parasitologica}, volume = {70}, number = {2}, pages = {71}, pmid = {40087199}, issn = {1896-1851}, mesh = {Humans ; *Keratoconjunctivitis/microbiology/drug therapy/diagnosis ; Male ; Adult ; Female ; Middle Aged ; China ; Microsporidiosis/diagnosis/drug therapy/microbiology ; Encephalitozoon/isolation & purification/genetics ; Antifungal Agents/therapeutic use ; Eye Infections, Fungal/drug therapy/microbiology/diagnosis ; Encephalitozoonosis/drug therapy/diagnosis ; }, abstract = {OBJECTIVE: To report four cases of microsporidial keratoconjunctivitis (MKC) from The Affiliated Eye Hospital of Nanjing Medical University (from May 2023 to October 2024) and to aid ophthalmologists in diagnosing and treating MKC, as MKC has been increasingly reported in Asian healthy individuals but not much in Mainland China.

METHODS: Four patients with MKC were studied. Demographic information, symptoms, and clinical data were collected. Diagnosis involved ophthalmic examinations, corneal scraping microscopy (including Giemsa staining, modified Ziehl-Neelsen staining, Calcofour white staining), bacterial and fungal cultures, and metagenomic next-generation sequencing (mNGS). Treatment included various topical medications like polyhexamethylene biguanide (PHMB), fluconazole, tacrolimus, sodium hyaluronate, and systemic medication such as albendazole.

RESULTS: Three cases were caused by Encephalitozoon hellem proved by mNGS. Patients had symptoms like eye redness, swelling, pain, foreign body sensation, and vision loss. Risk factors included improper contact lens - wearing habits, contact with birds, or exposure to potentially contaminated environments. All patients showed improvements after treatment, with 3 cases cured and 1 case improved.

CONCLUSION: MKC is a unilateral, acute, non-purulent ocular surface infectious disease. Clinicians should be more aware of it. Diagnosis depends on recognizing clinical signs, exploring risk factors, and laboratory tests. There is no consensus on treatment, but combined topical and systemic anti-protozoal drugs showed good results. Further large-scale validation is needed. Relevant departments should strengthen water source management, and patients should pay attention to personal hygiene.}, } @article {pmid40087044, year = {2025}, author = {Chen, B and Li, Y and Li, Z and Hu, X and Zhen, H and Chen, H and Nie, C and Hou, Y and Zhu, S and Xiao, L and Li, T}, title = {Vitamin E ameliorates blood cholesterol level and alters gut microbiota composition: A randomized controlled trial.}, journal = {Nutrition, metabolism, and cardiovascular diseases : NMCD}, volume = {}, number = {}, pages = {103964}, doi = {10.1016/j.numecd.2025.103964}, pmid = {40087044}, issn = {1590-3729}, abstract = {BACKGROUND AND AIMS: Antioxidants, including vitamin E (VE) and grape seed extract (GSE), as anti-aging supplementation have been widely used to improve human health. The gut microbiota plays a crucial role in health and affects the treatment effect of various interventions. However, the role of gut microbiota in VE remains unclear. This study aimed to assess the longitudinal impact of VE treatment on body health and the gut microbiota.

METHODS AND RESULTS: A randomized controlled trial was conducted with 90 healthy individuals. The participants were randomly assigned to three groups: a treatment group receiving VE, another antioxidant treatment group receiving GSE, and a control group receiving a placebo. We found that VE ameliorated blood cholesterol levels by reducing the levels of low-density lipoprotein cholesterol (LDL-C) in healthy volunteers. After the intervention, there was an increase in the relative abundance of short-chain fatty acid (SCFA)-producing bacteria and bile acid metabolizers. Specifically, the abundances of Lachnospira sp. and Faecalibacterium spp. increased in the VE. Interestingly, the gut microbiota of poor responders harbored a greater proportion of disease-associated bacterial species.

CONCLUSIONS: VE could promote health by lowering LDL-C, partly and indirectly by affecting gut bacteria with the ability to produce SCFAs or metabolize bile acids.

The clinical trial was registered on August 28, 2021. Registration number was ChiCTR2100050567 (https://www.chictr.org.cn).}, } @article {pmid40086988, year = {2025}, author = {Peng, Q and Quan, L and Zheng, H and Li, J and Xie, G}, title = {Analyzing the contribution of top-down and bottom-up methods to the construction of synthetic microbial communities in Jiuyao.}, journal = {Food microbiology}, volume = {129}, number = {}, pages = {104759}, doi = {10.1016/j.fm.2025.104759}, pmid = {40086988}, issn = {1095-9998}, mesh = {*Fermentation ; *Microbiota ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Food Microbiology ; Fermented Foods/microbiology ; Metagenomics ; Fungi/genetics/classification/metabolism/isolation & purification ; Saccharomyces cerevisiae/genetics/metabolism ; Taste ; }, abstract = {The construction of synthetic microbial communities is a crucial strategy for improving the stability of microbial populations and the quality of fermented foods. Jiuyao, an essential saccharification and fermentation starter in Huangjiu production, was the focus of this study. Using metagenomics combined with culture-dependent methods, we identified 11 microbial species involved in Huangjiu fermentation. Through metagenomic analysis and simulated fermentation, Rhizopus delemar, Rhizopus microspores, Rhizopus stolonife, Rhizopus azygosporus, Saccharomycopsis fibuligera, Saccharomyces cerevisiae, Wickerhamomyces anomalus and Pediococcus pentosaceus were determined to be the core microbial species driving the Jiuyao fermentation process. A synthetic microbial community was constructed based on these species, successfully reproducing the flavor and sensory qualities of Huangjiu while enhancing fermentation efficiency. This study provides valuable insights into the functional roles of Jiuyao-associated microbes and offers a framework for improving microbial community stability and fermentation quality in Huangjiu production.}, } @article {pmid40086981, year = {2025}, author = {Kothe, CI and Renault, P}, title = {Metagenomic driven isolation of poorly culturable species in food.}, journal = {Food microbiology}, volume = {129}, number = {}, pages = {104722}, doi = {10.1016/j.fm.2025.104722}, pmid = {40086981}, issn = {1095-9998}, mesh = {*Metagenomics ; *Cheese/microbiology ; *Food Microbiology ; *Bacteria/isolation & purification/classification/genetics ; Microbiota ; Metagenome ; Phylogeny ; }, abstract = {Although isolating microorganisms from food microbiota may appear less challenging than from the gut or environmental sources, recovering all representative species from food remains a difficult task. Here, we showed by metagenomic analysis that several abundant species had escaped isolation in a previous study of ten cheeses, including several previously uncharacterized species. This highlights the ongoing challenge of achieving a comprehensive recovery of microbes from food. To address this gap, we designed a novel strategy integrating metagenomics-based probes targeting the species of interest, coupled with an incremental culturing approach using pooled samples. As proof of concept, we applied this strategy to two cheeses containing species that were not isolated in our previous study, with the objective of isolating all species present at levels above 2% and, in particular, potential novel food species. Through this approach, we successfully performed the targeted isolation of two Psychrobacter and two Vibrio species from the first cheese, and four Halomonas and two Pseudoalteromonas species from the second one. Notably, P. undina and V. litoralis represented, as far as we know, the first cheese isolates characterized for these species. However, we were unable to isolate a novel species of Pseudoalteromonas, with no characterized representative to date, and Marinomonas foliarum, previously isolated from marine environment. Using metagenome-assembled genomes (MAGs) and metagenomic analysis, we discussed the possible reasons for their non-recovery. Finally, this strategy offers a promising approach for isolating a set of strains representative of the microbial diversity present in food ecosystems. These isolates can serve as a basis for investigating their roles in the communities, their impact on product development, safety implications and their potential in the development of starter cultures.}, } @article {pmid40086705, year = {2025}, author = {Ma, G and Chai, Y and Tye, KD and Xie, H and Meng, L and Tang, X and Luo, H and Xiao, X}, title = {Predictive analysis of the impact of probiotic administration during pregnancy on the functional pathways of the gut microbiome in healthy infants based on 16S rRNA gene sequencing.}, journal = {Gene}, volume = {}, number = {}, pages = {149414}, doi = {10.1016/j.gene.2025.149414}, pmid = {40086705}, issn = {1879-0038}, abstract = {Maternal probiotic supplementation altered the microbial composition in infants' gut, yet its effect on the functional pathways of the microbiota remains unclear. This study aimed to explore the potential impact of maternal probiotic intake on the predicted functional pathways of the gut microbiome in healthy infants. A total of 24 pregnant women were randomly allocated to either the control group or the probiotic group. The women in the probiotic group began receiving probiotics at the 32nd week of pregnancy and continued until delivery. Meconium and fecal samples were collected from infants at birth, as well as on the 3rd day, 14th day, and 6th month after birth. The functional characteristics of the microbial community were inferred using 16S rRNA gene analysis, processed with PICRUSt software, and cross-referenced with the KEGG database. The probiotic group had lower levels of Actinobacteria and Bacteroidetes, while Bifidobacterium growth was notably increased in the infant gut microbiota. At day 0 postpartum, the control group exhibited higher levels of Prevotellaceae compared to the probiotic group (P < 0.05). However, no significant differences were found by day 3. At day 14, the control group exhibited higher levels of Bacteroidaceae and Bacteroides, while Bacteroides_thetaiotaomicron was more abundant in the probiotic group (P < 0.05). By 6 months, the control group showed a higher abundance of Firmicutes (P < 0.05). On day 0 postpartum, maternal probiotic consumption increased the Environmental information processing pathway at KEGG Level 1, and increased Energy metabolism, Metabolism of cofactors and vitamins, and Cell growth and death pathways at KEGG Level 2. It also increased Histidine metabolism, One carbon pool by folate, and Folate biosynthesis at KEGG Level 3. No changes were observed in the infant gut microbiota's functional metabolic pathways at 3 days postpartum. At 14 days postpartum, probiotics reduced Lipid metabolism pathways at KEGG Level 2 and the Citrate cycle at KEGG Level 3. At 6 months postpartum, probiotics decreased Carbohydrate metabolism pathways at KEGG Level 2. Our findings suggest that probiotic supplementation during pregnancy affects the functional metabolism of the gut microbiota in healthy infants. This, in turn, may influence the development of the infant's immune system, metabolism, and overall health by modifying the gut microbial environment.}, } @article {pmid40086585, year = {2025}, author = {Rawat, N and Sivanesan, S and Kanade, GS and Bafana, A}, title = {Interaction of environmental fluoride exposure and gut microbes: potential implication in the development of fluorosis in human subjects.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {}, number = {}, pages = {115388}, doi = {10.1016/j.fct.2025.115388}, pmid = {40086585}, issn = {1873-6351}, abstract = {Fluoride exposure primarily occurs through contaminated water and leads to fluorosis, which is a global health concern. After ingestion, fluoride is absorbed via gastrointestinal tract, where it interacts with the gut microbiota. While animal studies have explored fluoride's effects on gut microbiota, no human studies have yet been conducted. Most research emphasizes metagenomic diversity, neglecting isolation and characterization of pure cultures for further applications. Additionally, the association between gut microbiota with fluorosis outcomes in fluoride-exposed populations is unexplored. This study characterizes and compares the cultivable gut microbiota in the fluoride-exposed population with (symptomatic, group II) or without (asymptomatic, group I) signs of skeletal fluorosis along with unexposed control (group III). Group I displayed higher abundance of Firmicutes (58.58%), group II had predominance of Proteobacteria (61.25%) while group III showed similar abundance of Proteobacteria (50.38%) and Firmicutes (49.51%). On analyzing short-chain fatty acid (SCFA) profiles, group I isolates produced higher isobutyric acid (1.31 ± 0.9 mM) than group II (0.71 ± 0.35 mM), while group II produced more isovaleric acid (0.8 ± 0.41 mM) than group I (0.61 ± 0.08 mM) (p < 0.05). These findings suggest that gut microbiota and SCFAs alteration may influence bone metabolism, affecting the fluorosis progression.}, } @article {pmid40086354, year = {2025}, author = {Can Yilmaz, E and Barnes, MA}, title = {Comparative study of rates of environmental DNA (eDNA) accumulation and degradation in water and sediment from model plant (Egeria densa) and animal (Daphnia magna) species.}, journal = {The Science of the total environment}, volume = {971}, number = {}, pages = {179057}, doi = {10.1016/j.scitotenv.2025.179057}, pmid = {40086354}, issn = {1879-1026}, abstract = {Understanding of the ecology of environmental DNA (eDNA)-its origin, state, transport, and fate- is critical for interpreting the results of eDNA applications ranging from single-species presence/absence monitoring to whole-community analysis via metabarcoding and metagenomics. Accumulation and degradation of eDNA can be most accurately measured by conducting systematic manipulative experiments under controlled conditions. We compared eDNA accumulation and degradation in a laboratory setting for two different taxa (Daphnia magna and Egeria densa) across two different substrates (water and sediment). In accumulation experiments, both D. magna and E. densa showed increased eDNA levels in both water and sediment over 24 h. Daphnia magna eDNA concentrations were twice as high in sediment compared to water, whereas E. densa eDNA remained consistent between the two substrates. Degradation kinetic models were applied to our data for the two model organisms to characterize eDNA decay rates, inadvertently introducing an additional nutrient treatment with three different levels. The degradation of D. magna and E. densa eDNA varied based on nutrient concentrations and substrate types, with different models providing the best fit for different scenarios. Overall, we have demonstrated the importance of taxonomic, sample type, and environmental differences in eDNA ecological processes such as accumulation and degradation. These and similar processes require further study to enhance the interpretation of eDNA results in both research and management contexts.}, } @article {pmid40086306, year = {2025}, author = {Russo, A and D'Alessandro, A and Di Paola, M and Cerasuolo, B and Renzi, S and Meriggi, N and Conti, L and Costa, J and Pogni, R and Martellini, T and Cincinelli, A and Ugolini, A and Cavalieri, D}, title = {On the role of bacterial gut microbiota from supralittoral amphipod Talitrus saltator (Montagu, 1808) in bioplastic degradation.}, journal = {The Science of the total environment}, volume = {972}, number = {}, pages = {179109}, doi = {10.1016/j.scitotenv.2025.179109}, pmid = {40086306}, issn = {1879-1026}, abstract = {Despite the promise of a reduced environmental impact, bioplastics are subjected to dispersion and accumulation similarly to traditional plastics, especially in marine and coastal environments. The environmental impact of bioplastics is attracting increasing attention due to the growing market demand. The ability of the supralittoral amphipod Talitrus saltator to ingest and survive on pristine starch-based bioplastic has already been assessed. However, the involvement of the gut microbiota of this key coastal species in making bioplastics a dietary supplement, remains unknown. In this study, we investigated the modification of T. saltator gut microbiota following bioplastic ingestion and the effect of this change on the modification of their chemical composition. Groups of adult amphipods were fed with: 1 - two different kinds of starch-based bioplastic; 2 - a 50 %/50 % chitosan-starch mixture; and 3 - paper and dry-fish-food. Freshly collected, unfed individuals were used as control group. Faecal pellets from the amphipods were collected and characterized using ATR-FTIR spectroscopy. DNA was extracted from gut samples for metagenomic analysis. Spectroscopic investigation suggested a partial digestion of polysaccharide components in the experimental polymeric materials. The analysis of the gut microbiota revealed that bioplastic feeding induced modification of sandhopper's gut microbial communities, shifting the abundance of specific microbial genera already present in the gut, towards bacterial genera associated with plastic/bioplastic degradation, especially in groups fed with starch-based bioplastics. Overall, our results highlight the involvement of T. saltator's gut microbiota in bioplastic modification, providing new insights into the potential role of microbial consortia associated to sandhoppers in bioplastic management.}, } @article {pmid40086246, year = {2025}, author = {Han, NN and Yang, JH and Wu, GG and Yang, JH and Jin, JA and Fan, NS and Jin, RC}, title = {Differential size-dependent response patterns and antibiotic resistance development mechanism in anammox consortia.}, journal = {Journal of hazardous materials}, volume = {491}, number = {}, pages = {137886}, doi = {10.1016/j.jhazmat.2025.137886}, pmid = {40086246}, issn = {1873-3336}, abstract = {Antibiotic resistance is a global threat to human and animal health. Anaerobic ammonia oxidation (anammox) is an efficient and innovative wastewater treatment technology, which can be served as a promising approach to teat antibiotic wastewater. This study systematically investigated effects of sulfamethazine on the performance, microbial community dynamics and the resistome in anammox systems inoculated with different-sized granular sludge. The activity and performance of small (< 0.5 mm) anammox granules were more susceptible to sulfamethazine stress than those of medium (0.5-1.0 mm) and large (1.0-2.0 mm) granules. Sulfamethazine addition greatly increased the diversity and abundance of mobile genetic elements (MGEs) and antibiotic resistance genes (ARGs). Based on the metagenomic analysis, the horizontal transfer of ARGs in the anammox system was upregulated through bacterial oxidative stress, pili synthesis and type IV secretion system. In addition, two strains of sulfamethazine-resistant bacteria (Pseudomonas asiatica sp. nov. and Pseudomonas shirazica sp. nov.) were isolated from the anammox system. Their whole genome sequencing results showed that the most abundant plasmid was pkF7158B, which mediated the horizontal transfer of two main multidrug resistance genes (cpxR and mexB). This work provides a holistic insight into microbial heterogeneity of different-sized anammox granular sludge and their evolution and resistance development mechanism.}, } @article {pmid40086153, year = {2025}, author = {Huang, JN and Liu, ZQ and Wen, B and Wang, ZN and Gao, JZ and Chen, ZZ}, title = {Stocking filter-feeder in fed fish aquaculture pond: Unexpected Aggravation of nitrous oxide emission.}, journal = {Water research}, volume = {280}, number = {}, pages = {123475}, doi = {10.1016/j.watres.2025.123475}, pmid = {40086153}, issn = {1879-2448}, abstract = {Intensive farming of fed fish could produce large amounts of uneaten feed and feces, potentially leading to increased nitrous oxide (N2O) emissions. Filter-feeding fish can ingest residual feed and feces, but it is unclear whether introducing them into fed fish farming ponds could reduce N2O emissions. This study employed monoculture of fed largemouth bass (Micropterus salmoides, LB) and polyculture of LB with filter-feeding silver carp (Hypophthalmichthys molitrix, SC) at density ratios of 18:1, 9:1 and 4.5:1 to compare the N2O emission characteristics. The results showed that silver carp could indeed feed on largemouth bass feces, and isotope mixing model indicated that feces was the second largest contributor to the food of silver carp, reaching 14.75 %-15.56 %. However, polyculture of the two species did not or even increased N2O emission flux at water-air interface and its release potential in sediment. Increased mineralization, nitrification and denitrification rates were observed in polyculture systems, particularly at high stocking densities of silver carp. Also, the higher NH4[+] accumulation were found across sediment-water interface within polyculture systems. Metagenome revealed that polyculture disturbed the microbial community structure and increased the abundance of Burkholderiales and Steroidobacteraceae. Moreover, polyculture increased the abundance of nitrogen-cycling functional genes, including gdhA, hao, nirB and norB, potentially contributing to the elevated N2O emissions. Structural equation model highlighted that polyculture of largemouth bass and silver carp could drive N2O emissions, mainly through increased sedimental NH4[+] concentration and microbial activity. These findings indicate that the introduction of extractive filter-feeding fish into fed fish farming ponds could not reduce N2O emissions, implying the need for optimized management strategies to balance aquaculture productivity with environmental sustainability.}, } @article {pmid40085365, year = {2025}, author = {Makarani, N and Kaushal, RS}, title = {Advances in actinobacteria-based bioremediation: mechanistic insights, genetic regulation, and emerging technologies.}, journal = {Biodegradation}, volume = {36}, number = {2}, pages = {24}, pmid = {40085365}, issn = {1572-9729}, mesh = {*Biodegradation, Environmental ; *Actinobacteria/metabolism/genetics ; *Metals, Heavy/metabolism ; }, abstract = {Untreated wastewater from sewage, industries, and agriculture contaminates ecosystems due to rapid population growth and industrialization. It introduces hazardous pollutants, including pesticides, polycyclic aromatic hydrocarbons (PAHs), and heavy metals, which pose serious health risks such as cancer, lung disorders, and kidney damage, threatening both environmental and human well-being. Using microorganisms for bioremediation is thought to be safer and more effective. Compared to other approaches, bioremediation is the most effective way to absorb heavy metals. Due to the high cost and unreliability of traditional remediation techniques, such as chemical and physical treatments, interest in bioremediation as an environmentally benign substitute has grown. Through the use of microorganisms, bioremediation successfully removes heavy metals and breaks down organic contaminants from contaminated circumstances. Actinobacteria are unique among these microbes because of their flexibility in metabolism and capacity to endure severe environments. They create secondary metabolites, such as enzymes, that help break down a variety of pollutants. Actinobacteria also produce siderophores and extracellular polymeric substances (EPS), which aid in trapping organic contaminants and immobilizing heavy metals. This review explores the diverse applications of actinobacteria in bioremediation, with a focus on their mechanisms for breaking down and neutralizing pollutants. We highlighted the advancements in bioremediation strategies, including the use of mixed microbial cultures, biosurfactants, nanoparticles and immobilized cell technologies which enhance the efficiency and sustainability of pollutant removal. The integration of omics technologies such as metagenomics, meta-transcriptomics, and meta-proteomics provides deeper insights into the genetic and metabolic pathways involved in bioremediation, suggesting the way for the development of genetically optimized strains with enhanced degradation capabilities. By leveraging these emerging technologies and microbial strategies, actinobacteria-mediated bioremediation presents a highly promising approach for mitigating environmental pollution. Ongoing research and technological advancements in this field can further enhance the scalability and applicability of bioremediation techniques, offering sustainable solutions for restoring contaminated ecosystems and protecting human health.}, } @article {pmid40085274, year = {2025}, author = {Rono, JK and Zhang, Q and He, Y and Wang, S and Lyu, Y and Yang, ZM and Feng, Z}, title = {Biochemical characterization of a bilfunctional endoglucanase/glucomannanase derived from mountain soil.}, journal = {Biotechnology letters}, volume = {47}, number = {2}, pages = {33}, pmid = {40085274}, issn = {1573-6776}, support = {32370089//National Natural Science Foundation of China/ ; }, mesh = {*Soil Microbiology ; *Enzyme Stability ; *Cellulase/genetics/metabolism/chemistry ; *Mannans/metabolism ; Hydrogen-Ion Concentration ; Substrate Specificity ; *Recombinant Proteins/genetics/metabolism/chemistry/isolation & purification ; Temperature ; Escherichia coli/genetics ; Carboxymethylcellulose Sodium/metabolism ; Metagenome/genetics ; Kinetics ; Hydrolysis ; Cloning, Molecular ; }, abstract = {Metagenomics is increasingly recognized as a vital technique for exploring uncultured microorganisms, with one key application being the discovery of novel enzymes for industrial use. This study identified an endoglucanase gene from soil metagenome, termed ZFEG1801, which was expressed in E. coli BL21, purified, and characterized for its biochemical properties. The 72.8 kDa recombinant protein exhibited hydrolytic activity against sodium carboxymethyl cellulose (CMC) and konjac glucomannan (KG), with activities of 12.1 U/mg and 42.1 U/mg, respectively. The enzyme displayed optimal activity at pH 5 for CMC and pH 6 for KG, with broad pH stability ranging from 5 to 9. The optimal temperature was 40 °C, and it remained thermally stable between 20 and 40 °C, retaining over 60% of its activity. The enzyme activity remained stable in the presence of most metal ions; however, CMCase activity was inhibited by Cu[2+], while glucomannanase activity was inhibited by Mn[2+], Fe[3+], and Ca[2+]. The catalytic efficiency towards both substrates was reduced by addition of SDS, DMSO, ethanol, isopropanol and acetonitrile. The Vmax and Km of the purified recombinant enzyme were 106.4 μmol/L/min and 4.9 mg/mL for CMC, and 833.3 μmol/L/min and 11.1 mg/mL for KG, respectively. The dual catalytic properties of ZFEG1801, broad pH stability and resistance to additives, demonstrate its potential for use in various biomass degradation processes.}, } @article {pmid40084919, year = {2025}, author = {Baalbaki, N and Slob, EMA and Kazer, SW and I Abdel-Aziz, M and Bogaard, HJ and Golebski, K and Maitland-van der Zee, AH}, title = {The Omics Landscape of Long COVID-A Comprehensive Systematic Review to Advance Biomarker, Target and Drug Discovery.}, journal = {Allergy}, volume = {}, number = {}, pages = {}, doi = {10.1111/all.16526}, pmid = {40084919}, issn = {1398-9995}, support = {//Health~Holland/ ; }, abstract = {An estimated 10% of coronavirus disease (COVID-19) survivors suffer from persisting symptoms referred to as long COVID (LC), a condition for which approved treatment options are still lacking. This systematic review (PROSPERO: CRD42024499281) aimed to explore the pathophysiological mechanisms underlying LC and potential treatable traits across symptom-based phenotypes. We included studies with primary data, written in English, focusing on omics analyses of human samples from LC patients with persistent symptoms of at least 3 months. Our search in PubMed and Embase, conducted on January 8, 2024, identified 642 studies, of which 29 met the inclusion criteria after full-text assessment. The risk of bias was evaluated using the Joanna Briggs Institute appraisal tool. The synthesis of omics data, including genomics, transcriptomics, proteomics, metabolomics, and metagenomics, revealed common findings associated with fatigue, cardiovascular, pulmonary, neurological, and gastrointestinal phenotypes. Key findings included mitochondrial dysfunction, dysregulated microRNAs associated with pulmonary dysfunction, tissue impairment, blood-brain barrier disruption, coagulopathy, vascular dysfunction, microbiome disturbances, microbial-derived metabolite production and persistent inflammation. Limitations include cross-study heterogeneity and variability in sampling methods. Our review emphasizes the complexity of LC and the need for further longitudinal omics-integrated studies to advance the development of biomarkers and targeted treatments.}, } @article {pmid40084893, year = {2025}, author = {Yuan, S and Wu, Y and Balcazar, JL and Wang, D and Zhu, D and Ye, M and Sun, M and Hu, F}, title = {Expanding the potential soil carbon sink: unraveling carbon sequestration accessory genes in vermicompost phages.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0029625}, doi = {10.1128/aem.00296-25}, pmid = {40084893}, issn = {1098-5336}, abstract = {The compost microbiome is important in regulating soil carbon sequestration. However, there is limited information concerning phage communities and phage-encoded auxiliary metabolic genes (AMGs) in compost-applied soils. We combined metagenomics and meta-viromes to explore the potential role of bacterial and phage communities in carbon sequestration in the compost microbiome. The experiment comprised swine manure compost (SW) and vermicompost (VE) applied to the soil along with a control treatment (CK). The bacterial community richness decreased after swine manure application and increased after vermicomposting compared to the control treatment. The phage community in the vermicompost-applied soil was dominated (63.1%) by temperate phages. In comparison, the communities of the swine manure compost-applied soil (92.7%) and control treatments (75.4%) were dominated by virulent phages. Phage-encoded carbon sequestration AMGs were detected in all three treatments, with significant enrichment in the vermicompost-applied soil. The average carbon sequestration potential (the coverage ratio of phage AMGs:total genes) of phage AMGs (aceF, GT11, and GT6) in the vermicompost-applied soil (65.18%) was greater than in the swine manure-applied (0) and control soils (50.21%). The results highlight the role of phage-encoded AMGs in improving soil carbon sequestration in vermicompost-applied soil. The findings provide new avenues for increasing soil carbon sequestration.IMPORTANCEThe phage-bacteria interactions have a significant impact on the global carbon cycle. Soil microbial carbon sequestration is a process in combination withcarbon sequestration genes and growth activity. This is the first study aimed at understanding the carbon sequestration potential of phage communities in vermicompost. The results of this study provide variations in carbon sequestration genes in vermicompost microbial communities, and some novel phage auxiliary metabolic genes were revealed to assist bacterial communities to increase soil carbon sequestration potential. Our results highlight the importance of phages in soil carbon sequestration from the perspective of phage-bacterial community interactions.}, } @article {pmid40084890, year = {2025}, author = {Sarkar, P and Beebe, M and Bhandari, G and Wielinski, J and Lowry, GV and Gulliver, D}, title = {Novel anaerobic selenium oxyanion reducers native to FGD wastewater for enhanced selenium removal.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0122224}, doi = {10.1128/aem.01222-24}, pmid = {40084890}, issn = {1098-5336}, abstract = {Biological treatment is a recognized approach for removing selenate and selenite oxyanions present in flue gas desulfurization (FGD) wastewater. However, the knowledge of the specific microbial species or communities responsible for reducing water-soluble selenium oxyanions to insoluble elemental selenium remains limited. In addition, the selenium oxyanion reduction genes and pathways have yet to be understood in these wastewaters. This study characterizes selenium oxyanion-reducing bacteria (SeRB) native to FGD wastewater, and the resulting elemental selenium particles formed. By selecting native SeRB microbes in a defined media, a novel resolution of these organisms has been achieved. This research identifies previously unrecognized selenium oxyanion-reducing capabilities in Anaerosolibacter, alongside predominant SeRB from Mesobacillus and Tepidibacillus genera. This work encompasses both 16S and metagenomic techniques to recover novel metagenome-assembled genomes, distinct to this environment. The biogenic selenium produced by these organisms was predominantly of elemental selenium, either amorphous or with a hexagonal structure. This study identifies the SeRB present in FGD wastewater and characterizes their selenium products, offering crucial insights to enhance the efficiency of biological treatment strategies and the potential of selenium recovery from this industrial waste.IMPORTANCEThis is the first report on the culturability and recovery of taxonomic and metabolic information of the anaerobic selenium oxyanion-reducing bacteria (SeRB) in flue gas desulfurization (FGD) wastewater. Selenium is a regulated contaminant in FGD wastewater found on average to be 3,130 µg/L that must be removed to meet EPA discharge limits of 16 µg/L (D. B. Gingerich, E. Grol, and M. S. Mauter, Environ Sci Water Res Technol 4:909-925, 2018, https://doi.org/10.1039/C8EW00264A; also see U.S. EPA EPA-821-R-20-001, 2020). Better understanding of anaerobic SeRB and the microbial community in FGD wastewater is needed to harness their full potential for the bioremediation and recovery of selenium from FGD wastewater. Optimizing the biotreatment strategies for these wastewaters promises to yield cleaner and healthier waterways and ecosystems, even as the United States undergoes a shift in its energy landscape.}, } @article {pmid40084855, year = {2025}, author = {Brock, ML and Tavares-Reager, JF and Dong, J and Larkin, AA and Lam, T and Pineda, N and Olivares, CI and Mackey, KRM and Martiny, AC}, title = {Bacterial response to the 2021 Orange County, California, oil spill was episodic but subtle relative to natural fluctuations.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0226724}, doi = {10.1128/spectrum.02267-24}, pmid = {40084855}, issn = {2165-0497}, abstract = {An oil spill began in October 2021 off the coast of Orange County, California, releasing 24,696 gallons of crude oil into coastal environments. Although oil spills, such as this one, are recurrent accidents along the California coast, no prior studies have been performed to examine the severity of the local bacterial response. A coastal 10-year time series of short-read metagenomes located within the impacted area allowed us to quantify the magnitude and duration of the disturbance relative to natural fluctuations. We found that the largest change in bacterial beta-diversity occurred at the end of October. The change in taxonomic beta-diversity corresponded with an increase in the sulfur-oxidizing clade Candidatus Thioglobus, an increase in the total relative abundance of potential hydrocarbon-degrading bacteria, and an anomalous decline in the picocyanobacteria Synechococcus. Similarly, changes in function were related to anomalous declines in photosynthetic pathways and anomalous increases in sulfur metabolism pathways as well as aromatic degradation pathways. There was a lagged response in taxonomy and function to peaks in total PAHs. One week after peaks in total PAH concentrations, the largest shifts in taxonomy were observed, and 1 week after the taxonomy shifts were observed, unique functional changes were seen. This response pattern was observed twice during our sampling period, corresponding with the combined effect of resuspended PAHs and increased nutrient concentrations due to physical transport events. Thus, the impact of the spill on bacterial communities was temporally extended and demonstrates the need for continued monitoring for longer than 3 months after initial oil exposure.IMPORTANCEOil spills are common occurrences in waterways, releasing contaminants into the aquatic environment that persist for long periods of time. Bacterial communities are rapid responders to environmental disturbances, such as oil spills. Within bacterial communities, some members will be susceptible to the disturbance caused by crude oil components and will decline in abundance, whereas others will be opportunistic and will be able to use crude oil components for their metabolism. In many cases, when an oil spill occurs, it is difficult to assess the oil spill's impact because no samples were collected prior to the accident. Here, we examined the bacterial response to the 2021 Orange County oil spill using a 10-year time series that lies within the impacted area. The results presented here are significant because (i) susceptible and opportunistic taxa to oil spills within the coastal California environment are identified and (ii) the magnitude and duration of the in situ bacterial response is quantified for the first time.}, } @article {pmid40083791, year = {2025}, author = {, }, title = {Erratum: Integrative analysis of intestinal flora and untargeted metabolomics in attention-deficit/hyperactivity disorder.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1576969}, doi = {10.3389/fmicb.2025.1576969}, pmid = {40083791}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2025.1452423.].}, } @article {pmid40083784, year = {2025}, author = {Yang, D and Wuyunsiqin, and YanNiu, and Hashentuya, and Tana, and Anna, and Ma, M and Zhao, W and Menggenduxi, and Wang, M}, title = {Traditional Mongolian Medicine Qiqirigan-8 alleviates non-alcoholic fatty liver disease via restoring gut microbiota and metabolism.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1517082}, pmid = {40083784}, issn = {1664-302X}, abstract = {BACKGROUND: Mongolian Medicine Qiqirigan-8 (MMQ-8) is a traditional Mongolian medicine formula used to treat fatty liver disease. However, the material basis and in vivo metabolic process of the therapeutic effect of MMQ-8 on non-alcoholic fatty liver disease (NAFLD) remain unclear.

METHODS: The chemical composition of MMQ-8 was determined using Ultra-high-performance liquid chromatography-quadrupole Exactive Mass spectrometry analysis (UHPLC-QE-MS). C57BL/6J mice were fed a choline-deficient diet for 12 weeks to induce a NAFLD model. Hematoxylin and Eosin (H&E)-staining, combined with serum biochemical indexes, was used to observe liver appearance and characterize the pathological changes and functions of the liver. HE staining and Alcian Blue-Phosphoric Acid Schiff (AB-PAS) staining of the colon, along with ZO-1 immunofluorescence expression in the colon were used to reveal the effect of MMQ-8 on the disruption of the intestinal epithelial mucosal barrier in the NAFLD. The expression of intestinal tight junction genes was analyzed by qRT-PCR to observe the protective effect of MMQ-8 against intestinal epithelial mucosal barrier disruption. Fecal metagenomics and serum non-targeted metabolomics were used to reveal the effects of MMQ-8 on the gut microbiota and metabolism in mice with NAFLD. Finally, we emphasize the interaction between gut microbiota and metabolites through Spearman correlation coefficient analysis.

RESULTS: Mongolian Medicine Qiqirigan-8 contains 17 active ingredients, which can reduce hepatic steatosis and lobular inflammation in mice with NAFLD, and have protective effects against liver injury. MMQ-8 reduced the infiltration of inflammatory cells in the colon epithelium of model mice while restoring the number of goblet cells. MMQ-8 significantly enhanced ZO-1 protein expression in the colon, as well as the mRNA expression of both ZO-1 and Occludin. Fecal metagenomics results showed that MMQ-8 reduced the Bacillota/Bacteroidota ratio in NAFLD mice. Increased the abundance of beneficial bacteria such as Porphyromonadaceae, Prevotella, and Bacteroidota. and suppressed the abundance of dysfunctional bacteria, such as Bacillota, Acetatifactor, and Erysipelotrichaceae. Furthermore, metabolomics studies revealed that MMQ-8 intervention significantly regulated the expression of metabolites related to glutathione metabolism, butyric acid metabolism, sphingolipid metabolism, and glycerophospholipid metabolism in NAFLD mice compared to the model group. These metabolic pathways play key roles in NAFLD. According to Spearman's correlation coefficient analysis, up-regulation of Porphyromonadaceae, Prevotella, and Bacteroidota after MMQ-8 intervention was negatively correlated with LPC levels in glycerophospholipid metabolic pathways, while positively correlated with PC levels. In contrast, the relationship between Bacillota and Acetatifactor, which were down-regulated after MMQ-8 intervention, was the opposite. In addition, the up-regulation of Porphyromonadaceae, Prevotella, and Bacteroidota after MMQ-8 intervention was positively correlated with fumaric acid, 2-oxoglutaric acid, adenosine, and L-glutathione levels, while those down-regulated after MMQ-8 intervention were positively correlated with the levels of Bacillota, Acetatifactor were negatively correlated with all the above metabolites. Thus, glutathione metabolism, butyric acid metabolism, sphingolipid metabolism, glycerophospholipid metabolism and gut microbial ecosystem are tightly intertwined in this process.

CONCLUSION: In summary, these findings indicate that MMQ-8 has a synergistic anti-NAFLD effect through its multi-component, multi-target, gut microbiota-modulating and multi metabolic pathway characteristics. The host's regulation of specific gut microbiota and involvement in multiple metabolic pathways may be one of the important mechanisms by which MMQ-8 exerts its therapeutic effects on NAFLD. It is worth noting that metabolic pathways such as glutathione metabolism, butyric acid metabolism, sphingolipid metabolism, glycerophospholipid metabolism, and the gut microbiota ecosystem are closely intertwined in this process.}, } @article {pmid40083550, year = {2025}, author = {Ng, HY and Liao, Y and Cheung, CL and Zhang, R and Chan, KH and Seto, WK and Leung, WK and Hung, IFN and Lam, TTY and Cheung, KS}, title = {Gut microbiota is associated with persistence of longer-term BNT162b2 vaccine immunogenicity.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1534787}, pmid = {40083550}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Male ; Female ; Middle Aged ; Adult ; *BNT162 Vaccine/immunology ; *SARS-CoV-2/immunology ; *COVID-19/immunology ; Antibodies, Neutralizing/blood/immunology ; Immunogenicity, Vaccine ; Prospective Studies ; Antibodies, Viral/blood/immunology ; Hong Kong ; Feces/microbiology ; }, abstract = {INTRODUCTION: BNT162b2 immunogenicity wanes with time and we investigated association between gut microbiota and longer-term immunogenicity.

METHODS: This cohort study prospectively recruited adult BNT162b2 two-dose recipients from three vaccination centers in Hong Kong. Blood samples were collected at baseline and day 180 after first dose, and tested for neutralizing antibodies (NAb) against receptor-binding domain (RBD) of wild type SARS-CoV-2 virus using chemiluminescence immunoassay. Shotgun DNA metagenomic sequencing was performed to characterize baseline stool microbiome. Baseline metabolites were measured by gas and liquid chromatography-tandem mass spectrometry (GC-MS/MS and LC-MS/MS). Primary outcome was persistent high NAb response (defined as top 25% of NAb level) at day 180. Putative bacterial species and metabolic pathways were identified using linear discriminant analysis [LDA] effect size analysis. Multivariable logistic regression adjusting for clinical factors was used to derive adjusted odds ratio (aOR) of outcome with bacterial species and metabolites.

RESULTS: Of 242 subjects (median age: 50.2 years [IQR:42.5-55.6]; male:85 [35.1%]), 61 (25.2%) were high-responders while 33 (13.6%) were extreme-high responders (defined as NAb≥200AU/mL). None had COVID-19 at end of study. Ruminococcus bicirculans (log10LDA score=3.65), Parasutterella excrementihominis (score=2.82) and Streptococcus salivarius (score=2.31) were enriched in high-responders, while Bacteroides thetaiotaomicron was enriched in low-responders (score=-3.70). On multivariable analysis, bacterial species (R. bicirculans-aOR: 1.87, 95% CI: 1.02-3.51; P. excrementihominis-aOR: 2.2, 95% CI: 1.18-4.18; S. salivarius-aOR: 2.09, 95% CI: 1.13-3.94) but not clinical factors associated with high response. R. bicirculans positively correlated with most metabolic pathways enriched in high-responders, including superpathway of L-cysteine biosynthesis (score=2.25) and L-isoleucine biosynthesis I pathway (score=2.16) known to benefit immune system. Baseline serum butyrate (aOR:10.00, 95% CI:1.81-107.2) and isoleucine (aOR:1.17, 95% CI:1.04-1.35) significantly associated with extreme-high vaccine response.

CONCLUSION: Certain gut bacterial species, metabolic pathways and metabolites associate with longer-term COVID-19 vaccine immunogenicity.}, } @article {pmid40083506, year = {2025}, author = {Zhou, Y and Ren, D and Chen, Y and Wen, S and Zhang, Y and Song, F and Yang, M and Eisenhut, M and O'Rourke, J and Li, Y and Gui, S}, title = {Presepsin, procalcitonin, interleukin-6, and high-sensitivity C-reactive protein for predicting bacterial DNAaemia among patients with sepsis.}, journal = {Journal of thoracic disease}, volume = {17}, number = {2}, pages = {991-1001}, pmid = {40083506}, issn = {2072-1439}, abstract = {BACKGROUND: Anti-infective therapy against pathogens is the key to treatment of sepsis. Metagenomic next-generation sequencing (mNGS) has higher sensitivity than blood culture. The aim of this study was to use mNGS to identify DNAaemia of pathogens and to assess the diagnostic accuracy of presepsin (PSEP), procalcitonin (PCT), interleukin-6 (IL-6), and high-sensitivity C-reactive protein (hsCRP) in differentiating between bacterial and nonbacterial infections in patients with sepsis.

METHODS: This retrospective study included patients with sepsis from November 2020 to September 2022 in the Shenzhen Second People's Hospital. Blood samples were sent for blood culture and mNGS when the patients were diagnosed with sepsis. Plasma PSEP, PCT, and IL-6 levels were measured using whole blood specimens that were collected and analyzed after a diagnosis of sepsis. Area under the receiver operating characteristic curve (AUC) was used to evaluate the accuracy of PSEP, PCT, IL-6, and hsCRP for prediction of bacterial DNAaemia detected by mNGS in patients with sepsis.

RESULTS: This study included 230 patients with sepsis. The bacterial DNAaemia rate was 53.0% [Gram-positive DNAaemia (GPD), Gram-negative DNAaemia (GND), and fungi DNAaemia rate was 18.2%, 37.8%, and 10.9%, respectively]. Among GND, Klebsiella was the most common, followed by Escherichia coli; meanwhile, the GPD were mainly Enterococcus, and Aspergillus was identified in 5 patients with sepsis. The PSEP median values were significantly higher in GND than in non-GND [GND: 1,291 pg/mL, interquartile range (IQR) 456-3,502 pg/mL; non-GND: 707 pg/mL, IQR 332-2,417 pg/mL; P=0.035]. There was no significant difference in PSEP values between GPD and non-GPD groups, or between fungi DNAaemia and non-fungi DNAaemia groups. Receiver operating characteristics analysis indicated that the best cutoff values for PSEP, PCT, IL-6, and hsCRP were 869 pg/mL, 1.14 ng/mL, 85.5 pg/mL, and hsCRP 96.2 mg/L, respectively. Logistic regression indicated that PSEP, PCT, IL-6, and hsCRP had significant predictive value for GND in patients with sepsis. The levels of PCT and IL-6 were different between patients with GPD and those with non-GPD. Only PCT levels differed significantly between fungal DNAaemia and nonfungal DNAaemia.

CONCLUSIONS: Bacterial-DNAaemia was detected in half of the patients with sepsis. PSEP, PCT, IL-6, and hsCRP demonstrated significant predictive value for GND, PCT and IL-6 levels demonstrated significant predictive value for GPD. Meanwhile, only PCT demonstrated significant predictive value for fungal DNAaemia.}, } @article {pmid40083031, year = {2025}, author = {Wang, H and Li, Y and You, J and Feng, N and Wang, D and Su, Y and Feng, X}, title = {Diurnal oscillations of amino acids dynamically associate with microbiota and resistome in the colon of pigs.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {26}, pmid = {40083031}, issn = {2524-4671}, support = {2023YFD1301304//National Key R&D Program of China/ ; 32072688//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Nutrients are one of the key determinants of gut microbiota variation. However, the intricate associations between the amino acid (AA) profile and the dynamic fluctuations in the gut microbiota and resistome remain incompletely elucidated. Herein, we investigated the temporal dynamics of AA profile and gut microbiota in the colon of pigs over a 24-hour period, and further explored the dynamic interrelationships among AA profile, microbiota, and resistome using metagenomics and metabolomics approaches.

RESULTS: JTK_circle analysis revealed that both the AA profile and the gut microbiota exhibited rhythmic fluctuations. With respect to the feed intake, all AAs except L-homoserine (PAdj = 0.553) demonstrated significant fluctuations. Over 50% of Lactobacillaceae, Ruminococcaceae, Clostridiaceae, and Eubacteriaceae species reached their peaks during T15 ∼ T21 when 50% of Lachnospiraceae species experienced a trough. The eLSA results showed that most AAs positively correlated with Prevotellaceae species but negatively correlated with Lactobacillaceae and Lachnospiraceae species. Moreover, most of the AAs negatively correlated with the mobile genetic elements Tn916 and istA group but positively correlated with plasmids. Further partial least squares structural equation model analysis indicated that AAs affected the antibiotic resistance gene dynamics through mobile genetic elements and the gut microbiota.

CONCLUSIONS: Taken together, the AA profile and the gut microbiota exhibit robust fluctuations over a day. The AA profile can affect the gut microbiota and resistome in a direct or indirect manner. These findings may provide new insights into a potential strategy for manipulating the gut microbiota and resistome.}, } @article {pmid40082992, year = {2025}, author = {Edminster, SY and Rebbe, RW and Khatchadourian, C and Hurth, KM and Mathew, AJ and Huss-Bawab, J and Shiroishi, MS and Clark, D and Norgan, AP and Butler-Wu, SM and Hiniker, A}, title = {The role of plasma metagenomic sequencing in identification of Balamuthia mandrillaris encephalitis.}, journal = {Acta neuropathologica communications}, volume = {13}, number = {1}, pages = {60}, pmid = {40082992}, issn = {2051-5960}, mesh = {Humans ; Female ; *Balamuthia mandrillaris/genetics/isolation & purification ; Middle Aged ; *Amebiasis/diagnosis/cerebrospinal fluid ; *Metagenomics/methods ; Encephalitis/diagnosis/parasitology/cerebrospinal fluid ; High-Throughput Nucleotide Sequencing ; Infectious Encephalitis/diagnosis/cerebrospinal fluid ; Central Nervous System Protozoal Infections/diagnosis/parasitology ; Brain/pathology/parasitology ; }, abstract = {Balamuthia mandrillaris is a rare, free-living amoeba (FLA) that causes granulomatous amoebic encephalitis, a disease with close to 90% mortality. The geographical ranges of many FLA are expanding, potentially increasing human exposure to B. mandrillaris. Here, we report a case of a 58-year-old woman with progressive neurological symptoms, ultimately diagnosed postmortem with B. mandrillaris encephalitis through plasma metagenomic next-generation sequencing (mNGS) despite negative results on both cerebrospinal fluid (CSF) mNGS and CSF PCR testing. Histologic analysis and real-time PCR (qPCR) studies on postmortem brain tissue confirmed B. mandrillaris infection with significant vascular clustering of trophozoites. Retrospective analysis of CSF mNGS data demonstrated subthreshold reads for B. mandrillaris, emphasizing the challenges of interpreting low-level pathogen signals. A systematic review of 159 published B. mandrillaris cases revealed only two reports of B. mandrillaris diagnosed using plasma mNGS, both of which also had diagnostic CSF studies. This case demonstrates the diagnostic challenges of B. mandrillaris infections, highlights its vascular tropism, and suggests that plasma mNGS may warrant evaluation as a diagnostic tool for B. mandrillaris.}, } @article {pmid40082612, year = {2025}, author = {Đokić, J and Dinić, M and Soković Bajić, S and Bisenić, A and Mitrović, H and Jakovljević, S and Radojević, D and Brdarić, E and Lukić, J and Živković, M and Tolinački, M and Terzić-Vidojević, A and Golić, N}, title = {High-throughput workflow for cultivation and characterization of gut microbiota strains with anti-inflammatory properties and metabolite signature associated with gut-brain communication.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {8741}, pmid = {40082612}, issn = {2045-2322}, support = {Grant IDEAS No. 7744507, NextGenBiotics//Science Fund of the Republic of Serbia/ ; Grant No. 451-03-66/2024-03/200042//Ministry of Science, Technological Development and Innovations of the Republic of Serbia/ ; }, mesh = {*Gastrointestinal Microbiome ; Humans ; *Brain-Gut Axis ; Anti-Inflammatory Agents/metabolism/pharmacology ; Workflow ; Bacteria/metabolism/classification/genetics ; Brain/metabolism ; Probiotics ; Metagenome ; }, abstract = {The gut microbiota is deeply interconnected with the brain, a phenomenon often referred to as the gut-brain axis. Dysfunction in the microbiota-gut-brain axis can cause various neurological and psychiatric disorders associated with chronic inflammation and gut microbiota dysbiosis. Therefore, cultivation of anaerobic human gut microbiota strains, and characterization of their safety status and immunomodulatory potential could contribute to deciphering the molecular mechanisms underlying the microbiota-gut-brain communication and revealed their biotherapeutic potential. However, poor cultivability of gut microbiota members, makes research into their physiological role challenging. Hence, we report a high-throughput workflow based on targeted cultivation linked to metagenome sequencing, combined with the bioinformatic search for gut members with anti-inflammatory properties which produce the most important microbial metabolites that affect brain function. With this approach, we isolated 147 bacterial strains, and 41 were characterized for their immunomodulatory status with 12 strains showing immunosuppressive features with ability of producing brain important metabolites. Through this workflow we established the best growing conditions essential for cultivation, archiving, phenotyping, and characterization of anaerobic gut bacteria important for microbiota-gut-brain-axis research, and characterized the safety and probiotic potential of 7 extremely oxygen-sensitive strains.}, } @article {pmid40082593, year = {2025}, author = {Cardona, ST and Rahman, ASMZ and Novomisky Nechcoff, J}, title = {Innovative perspectives on the discovery of small molecule antibiotics.}, journal = {npj antimicrobials and resistance}, volume = {3}, number = {1}, pages = {19}, pmid = {40082593}, issn = {2731-8745}, support = {169121//Canadian Institutes of Health Research (CIHR)/ ; }, abstract = {Antibiotics are essential to modern medicine, but multidrug-resistant (MDR) bacterial infections threaten their efficacy. Resistance evolution shortens antibiotic lifespans, limiting investment returns and slowing new approvals. Consequently, the WHO defines four innovation criteria: new chemical class, target, mode of action (MoA), and lack of cross-resistance. This review explores innovative discovery approaches, including AI-driven screening, metagenomics, and target-based strategies, to develop novel antibiotics that meet these criteria and combat MDR infections.}, } @article {pmid40082238, year = {2025}, author = {Yong-Chun, R and Yi-Qing, Z and Hai-Wang, Z and Jie, Z and Jin-Nan, D and Xiao-Jing, Z and Ming-Hui, LI}, title = {Metagenomic Next-Generation Sequencing-Assisted Diagnosis of Japanese Spotted Fever: Report of One Case.}, journal = {Zhongguo yi xue ke xue yuan xue bao. Acta Academiae Medicinae Sinicae}, volume = {47}, number = {1}, pages = {146-149}, doi = {10.3881/j.issn.1000-503X.15997}, pmid = {40082238}, issn = {1000-503X}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Rickettsia/genetics/isolation & purification ; *Metagenomics/methods ; Spotted Fever Group Rickettsiosis/diagnosis/microbiology ; Male ; Doxycycline/therapeutic use ; }, abstract = {Japanese spotted fever(JSF)is an infectious disease caused by Rickettsia japonica,with nonspecific clinical symptoms and a high risk of misdiagnosis.We reported a case of JSF,in which Rickettsia japonica was detected in blood cells by metagenomic next-generation sequencing.The patient recovered after treatment with doxycycline.This report provides a reference for the clinical diagnosis and treatment of JSF.}, } @article {pmid40082172, year = {2025}, author = {Wang, ZJ and Zhang, J and Shi, YY}, title = {Successful Oral Isavuconazole Monotherapy for Invasive Pulmonary Mucormycosis in Kidney Transplant Recipients: Case Reports and Literature Review.}, journal = {Transplantation proceedings}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.transproceed.2025.02.047}, pmid = {40082172}, issn = {1873-2623}, abstract = {This study represents 2 cases of kidney transplant recipients (KTRs) with invasive pulmonary Rhizopus infection, successfully treated with oral isavuconazole monotherapy without lobectomy. The rapid detection via mNGS of bronchoalveolar lavage fluid enabled early diagnosis and timely intervention, resulting in complete recovery and stable graft function. The literature review revealed a 16.7% mortality rate among 13 cases, with a higher mortality rate of 66.7% among patients receiving antifungal treatment without surgical intervention. Our findings underscore the efficacy of isavuconazole as a first-line monotherapy, characterized by lower nephrotoxicity and fewer interactions with immunosuppressants, and emphasize the crucial role of metagenome next-generation sequencing (mNGS) in early diagnosis of invasive mucormycosis in high-risk population.}, } @article {pmid40082024, year = {2025}, author = {Yin, F and Ge, T and Zalucki, MP and Xiao, Y and Peng, Z and Li, Z}, title = {Gut symbionts affect Plutella xylostella (L.) susceptibility to chlorantraniliprole.}, journal = {Pesticide biochemistry and physiology}, volume = {209}, number = {}, pages = {106327}, doi = {10.1016/j.pestbp.2025.106327}, pmid = {40082024}, issn = {1095-9939}, mesh = {Animals ; *ortho-Aminobenzoates/pharmacology ; *Moths/drug effects/microbiology ; *Insecticides/pharmacology ; *Insecticide Resistance/genetics ; *Gastrointestinal Microbiome/drug effects ; *Symbiosis ; Bacteria/drug effects/genetics/metabolism ; Larva/drug effects/microbiology ; }, abstract = {Plutella xylostella, a globally economically important pest of cruciferous crops, has varying degrees of resistance to almost all insecticides. Insect gut microbiotas have a variety of physiological functions, and recent studies have shown that they have some potential connection with insecticide resistance. Here, we use metagenomics to analyze the differences in gut microbiota among 5 different populations of P. xylostella resistant to chlorantraniliprole. Differential gene expression was enriched in various metabolic pathways including carbohydrate metabolism, amino acid metabolism, energy metabolism, metabolism of cofactors and vitamins, nucleotide metabolism and so on. Proteobacteria was the dominate phyla, and the relative abundance of common dominant genera in the treated group (CL, Bt, and BtCL) was higher than that in susceptible controls. We successfully isolated 15 species of bacteria, in which the Enterobacter hormaechei was associated with enhanced insecticide resistance. The population we isolated can metabolize chlorantraniliprole in vitro, with a metabolic rate of 34.8 % within 4 days. Our work advances understanding of the evolution of insecticide resistance and lays a foundation for the further exploration of symbiotic microbial associations of lepidopteran insects and their ecological consequences.}, } @article {pmid40082000, year = {2025}, author = {Massaro, CA and Meade, S and Lemarié, FL and Kaur, G and Bressler, B and Rosenfeld, G and Leung, Y and Williams, AJ and Lunken, G}, title = {Gut microbiome predictors of advanced therapy response in Crohn's disease: protocol for the OPTIMIST prospective, longitudinal, observational pilot study in Canada.}, journal = {BMJ open}, volume = {15}, number = {3}, pages = {e094280}, doi = {10.1136/bmjopen-2024-094280}, pmid = {40082000}, issn = {2044-6055}, mesh = {Humans ; *Crohn Disease/microbiology/therapy ; *Gastrointestinal Microbiome ; Pilot Projects ; Prospective Studies ; Longitudinal Studies ; Observational Studies as Topic ; Feces/microbiology ; British Columbia/epidemiology ; Canada ; }, abstract = {INTRODUCTION: Inflammatory bowel disease (IBD), including Crohn's disease (CD) and ulcerative colitis, is characterised by chronic and relapsing inflammation of the gastrointestinal tract, leading to significant morbidity and reduced quality of life. The global rise in IBD incidence is driven by a complex interplay of genetic, environmental, dietary and microbiome-related factors. Despite advancements in treatment, such as biologics, response rates remain variable, highlighting the need for personalised approaches. Recent research suggests that specific microbiome signatures may serve as biomarkers for predicting therapeutic efficacy, offering a potential tool for optimising treatment strategies in CD. The aim of the Optimising IBD Patient Treatment with Integrated Microbiome Investigation for Specialised Therapeutics (OPTIMIST) study is to evaluate microbiome profiles across various sample types in a Canadian CD cohort starting or already on advanced therapy, with the goal of developing predictive models for personalised therapeutics.

METHODS AND ANALYSIS: This study is a two-phase, longitudinal, prospective observational pilot study conducted in British Columbia, Canada, involving both CD patients and non-IBD controls. Phase 1 focuses on baseline microbiome differences across participant cohorts through cross-sectional analysis. Phase 2 follows participants over 12 months to assess microbiome changes and their association with treatment response. Stool samples, intestinal biopsies from the left colon, right colon and ileum, as well as mucosal wash samples from the proximal part of the distal colon, will undergo metagenomics, metaproteomics and metabolomics analyses to explore compositional and functional differences. Data will be analysed using alpha and beta diversity metrics, differential abundance analyses and multivariate analyses to identify microbiome-based predictors of therapeutic response.

ETHICS AND DISSEMINATION: Ethical approval was received by the Research Ethics Board (REB) of University of British Columbia-Providence Healthcare (UBC-PHC) with a REB number H23-02927. All amendments to the protocol are reported and adapted based on the requirements of the REB. The results of this study will be submitted to peer-reviewed journals and will be communicated in editorials/articles by the IBD Centre of BC and BC Children's Hospital Research Institute.

TRIAL REGISTRATION NUMBER: NCT06453720.

PROTOCOL VERSION: 2024-06-21, version 3.0.}, } @article {pmid40081757, year = {2025}, author = {Armengaud, J}, title = {The dawn of the revolution that will allow us to precisely describe how microbiomes function.}, journal = {Journal of proteomics}, volume = {}, number = {}, pages = {105430}, doi = {10.1016/j.jprot.2025.105430}, pmid = {40081757}, issn = {1876-7737}, abstract = {The community of microorganisms inhabiting a specific environment, such as the human gut - including bacteria, fungi, archaea, viruses, protozoa, and others - is known as the microbiota. A holobiont, in turn, refers to an integrated ecological unit where microbial communities function and interact with their host, thus is a more integrative concept. To understand the processes involved, the diversity of microorganisms present must be identified and their molecular components quantified, especially proteins. Indeed, proteins - through their roles as catalytic units, structural components, and signaling molecules - are the main drivers of biological processes. Metagenomics has significantly expanded what we know about the genetic material present in microbiota, revealing their functional potential; metabolomics delivers an overall snapshot of the metabolites produced by the community. But metaproteomics offers a complementary approach to explore microbiome and holobiont functionality by focusing on the active proteins and functional pathways from each taxon. Significant recent advances in high-resolution tandem mass spectrometry have greatly expanded the catalog of peptide sequences accessible in each sample, creating the conditions for unprecedented taxonomical profiling, while also providing more accurate biomass quantification, more detailed protein characterization, and a greater capacity to monitor abundance and distinguish host biomarkers. By integrating artificial intelligence into the metaproteomics pipeline, extended datasets can now be efficiently mined to gain a more comprehensive functional view of complex biological systems, paving the way for next-generation metaproteomics. In this perspective, I discuss the transformative potential of this methodology. We are on the cusp of a remarkable omic revolution that promises to uncover the intricate workings of microbiomes by producing a vast array of new knowledge with multiple applications. SIGNIFICANCE: Metaproteomics provides a powerful lens to investigate microbiome and holobiont functionality by identifying and quantifying active proteins and functional pathways within each taxon. Recent breakthroughs in high-resolution tandem mass spectrometry have dramatically expanded the repertoire of peptide sequences detectable per sample. This progress enables unprecedented taxonomic resolution for microbial identification, more precise biomass quantification, comprehensive protein characterization, abundance monitoring, and the unique identification of host biomarkers. In this commentary, I delve into the distinctive features that make metaproteomics a transformative tool. I discuss the recent advancements in tandem mass spectrometry and argue that the primary challenge in analyzing complex samples is shifting from data acquisition to data interpretation. With the integration of artificial intelligence, I believe next-generation metaproteomics is poised to become the next Big Thing in microbiome research, unlocking profound insights into microbial functionality and ecosystem dynamics.}, } @article {pmid40081368, year = {2025}, author = {Dai, R and Zhang, J and Liu, F and Xu, H and Qian, JM and Cheskis, S and Liu, W and Wang, B and Zhu, H and Pronk, LJU and Medema, MH and de Jonge, R and Pieterse, CMJ and Levy, A and Schlaeppi, K and Bai, Y}, title = {Crop root bacterial and viral genomes reveal unexplored species and microbiome patterns.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2025.02.013}, pmid = {40081368}, issn = {1097-4172}, abstract = {Reference genomes of root microbes are essential for metagenomic analyses and mechanistic studies of crop root microbiomes. By combining high-throughput bacterial cultivation with metagenomic sequencing, we constructed comprehensive bacterial and viral genome collections from the roots of wheat, rice, maize, and Medicago. The crop root bacterial genome collection (CRBC) significantly expands the quantity and phylogenetic diversity of publicly available crop root bacterial genomes, with 6,699 bacterial genomes (68.9% from isolates) and 1,817 undefined species, expanding crop root bacterial diversity by 290.6%. The crop root viral genome collection (CRVC) contains 9,736 non-redundant viral genomes, with 1,572 previously unreported genus-level clusters in crop root microbiomes. From these, we identified conserved bacterial functions enriched in root microbiomes across soils and host species and uncovered previously unexplored bacteria-virus connections in crop root ecosystems. Together, the CRBC and CRVC serve as valuable resources for investigating microbial mechanisms and applications, supporting sustainable agriculture.}, } @article {pmid40081359, year = {2025}, author = {Ali, MJ}, title = {Metagenomic Profile of the Lacrimal Sac Microbial Communities in Congenital Nasolacrimal Duct Obstruction: The Lacriome Paper 7.}, journal = {Ophthalmic plastic and reconstructive surgery}, volume = {}, number = {}, pages = {}, doi = {10.1097/IOP.0000000000002931}, pmid = {40081359}, issn = {1537-2677}, abstract = {PURPOSE: To study the metagenomics of microbes isolated from the lacrimal sacs of patients with congenital nasolacrimal duct obstruction (CNLDO).

METHODS: A prospective study was performed on 10 consecutive lacrimal sac samples obtained for the metagenomic analysis from the patients with CNLDO who underwent endoscopic dacryocystorhinostomy at a tertiary care dacryology service. Immediately after a full-length lacrimal sac marsupialization, the samples were collected and transported on ice to the laboratory. A whole shotgun metagenome sequencing was performed on the Illumina platform following DNA extraction and library preparation. The downstream processing and bioinformatics of the samples were performed using multiple software packaged in the SqueezeMeta pipeline, and the functional annotation was performed using the MetaCerberus, v1.3.1.

RESULTS: The taxonomic hit distribution across the samples showed that bacteria were the most common isolates, followed by fungi and viruses. The major bacterial phyla identified across the samples of CNLDO were proteobacteria, firmicutes, actinobacteria, and bacteroidetes. The prevalent organisms include Haemophilus influenzae, Streptococcus pneumoniae, Stenotrophomonas maltophilia, Achromobacter xylosoxidans, Staphylococcus aureus, and Ochrobactrum anthropi, among others. The predominant fungal species identified include Botrytis cinerea, Aspergillus oryzae, and Fusarium fujikuroi. Several species of pandoravirus were the common viruses recognized.

CONCLUSIONS: This is the first whole metagenome sequencing of the lacrimal sac contents from patients with CNLDO, which showed that the sacs harbored diverse microbial communities of bacteria, fungi, and viruses. Further work is needed to decipher the polymicrobial interactions and their relationship with CNLDO.}, } @article {pmid40081035, year = {2025}, author = {Qv, M and Dai, D and Wu, Q and Wang, W and Li, L and Zhu, L}, title = {Metagenomic insight into the horizontal transfer mechanism of fluoroquinolone antibiotic resistance genes mediated by mobile genetic element in microalgae-bacteria consortia.}, journal = {Journal of environmental management}, volume = {380}, number = {}, pages = {124946}, doi = {10.1016/j.jenvman.2025.124946}, pmid = {40081035}, issn = {1095-8630}, abstract = {Antibiotics could accumulate in the environment with the discharge of wastewater from families, hospitals and livestock farms, which intensifies the spread of resistance genes around the world. Although microalgae-bacteria consortia (MBC) can efficiently remove antibiotics, the horizontal transfer mechanism of antibiotics resistance genes in MBC is still rarely reported. In this study, the removal efficiency of ofloxacin, norfloxacin and enrofloxacin by MBC under different antibiotic concentrations was investigated, while resistance genes in the MBC were identified and the mechanism of horizontal transfer was disclosed. The results showed that norfloxacin removal efficiency (up to 56.35 %) surpassed that of ofloxacin and enrofloxacin. The abundance of the fluoroquinolone resistance gene QnrS8 was the highest at 1331. The horizontal transfer of resistance gene QnrS8 and QnrS11 were mainly mediated by transposons. Fluoroquinolones increased the abundance of Brevundimonas (<0.10 % up to 9.63 %) and Bosea (0.96 % up to 17.67 %) involved in antibiotic removal. Arthrobacter and Acidovorax might be potential hosts which carried fluoroquinolone resistance genes. Structural equation model indicated that the key factor influencing the fluoroquinolone resistance genes abundance in MBC was transposons. These findings drew an insightful understanding of MBC application for fluoroquinolone antibiotics removal and the horizontal transfer mechanism of fluoroquinolone resistance genes.}, } @article {pmid40080648, year = {2025}, author = {Starcevic, A and Figueredo, RTA and Naldoni, J and Corrêa, LL and Okamura, B and Adriano, EA and Long, PF}, title = {Long-read metagenomic sequencing negates inferred loss of cytosine methylation in Myxosporea (Cnidaria: Myxozoa).}, journal = {GigaScience}, volume = {14}, number = {}, pages = {}, doi = {10.1093/gigascience/giaf014}, pmid = {40080648}, issn = {2047-217X}, support = {2019/17427-3//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 307485/2023-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, mesh = {*DNA Methylation ; *Myxozoa/genetics ; Animals ; *Cytosine/metabolism ; Metagenomics/methods ; Sequence Analysis, DNA/methods ; Metagenome ; }, abstract = {Oxford-Nanopore PromethION sequencing is a PCR-free method that retains epigenetic markers and provides direct quantitative information about DNA methylation. Using this long-read sequencing technology, we successfully assembled 5 myxozoan genomes free from discernible host DNA contamination, surpassing previous studies in both quality and completeness. Genome assembly revealed DNA methylation patterns within myxozoan genomes, particularly in GC-rich regions within gene bodies. The findings not only refute the notion of myxozoans lacking DNA methylation capability but also offer a new perspective on gene regulation in these parasites. The high-quality genome assemblies lay a solid foundation for future research on myxozoans, including new strategies to control these commercially significant fish pathogens.}, } @article {pmid40080343, year = {2025}, author = {Birkeland, KW and Mostert, L and Claas, ECJ and Aamot, HV and Demuyser, T}, title = {The added value of metagenomic next-generation sequencing in central nervous system infections: a systematic review of case reports.}, journal = {Infection}, volume = {}, number = {}, pages = {}, pmid = {40080343}, issn = {1439-0973}, abstract = {BACKGROUND: The diversity of pathogens causing central nervous system (CNS) infections presents a diagnostic challenge. Patient demographics and geographical location affect the likelihood of certain pathogens causing infection. Current diagnostic methods rely on labour-intensive cultivation or targeted detection. Metagenomic next-generation sequencing (mNGS) is a promising tool for detecting pathogens in CNS infections, offering an unbiased approach. To enhance our understanding of patient demographics and the range of pathogens identified through mNGS, we conducted a systematic review of case reports.

METHODS: The PubMed database was searched in March 2024. Case reports on CNS infections and mNGS published from January 2014 through February 2024 were included based on predefined criteria.

RESULTS: The search yielded 649 articles, of which 76 were included, encompassing 104 patients. Most patients were male (75%), the median age was 31,5 years [0-75] and 28% were immunocompromised. The most common diagnosis was encephalitis (36%), followed by meningitis (23%) and meningoencephalitis (22%). 53 unique pathogens were identified, comprising 27 different viruses, 19 bacteria, 5 parasites, and 2 fungi. Syndromic encephalitis/meningitis panels would only have detected four of the viruses and five of the bacteria. Additionally, 14 of the bacterial species are considered slow-growing or fastidious and could be challenging to detect by culture.

CONCLUSION: The application of mNGS in diagnosing CNS infections reveals the diversity of pathogens responsible for these severe infections, thereby improving diagnostics and facilitating targeted treatment. While case reports may be subjected to bias, they provide valuable insights into the use of mNGS in this clinical context.}, } @article {pmid40079640, year = {2025}, author = {Passos, GS and Pellegrinetti, TA and Fiore, MF}, title = {Metagenome-assembled bacterial genomes from long accurate reads associated with Capilliphycus salinus ALCB114379.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0080724}, doi = {10.1128/mra.00807-24}, pmid = {40079640}, issn = {2576-098X}, abstract = {We report the complete genome sequences of five bacteria associated with the marine cyanobacterium Capilliphycus salinus ALCB114379 of the phylum Pseudomonadota. This genetic diversity offers insights into the cyanosphere, shedding light on potential relationships between these microorganisms and their cyanobacterial hosts.}, } @article {pmid40078981, year = {2024}, author = {Hu, T and Cheng, Y and Wan, J and Liu, Y and Zhuang, Y and Zhou, M and Zhang, X and Tan, X and Deng, A and Zhang, M and Wang, P and Li, X and Zong, J and Cheng, L and Kang, M}, title = {Q fever diagnosed using metagenomic next-generation sequencing in Guangdong Province, China.}, journal = {Biosafety and health}, volume = {6}, number = {6}, pages = {337-340}, pmid = {40078981}, issn = {2590-0536}, abstract = {Q fever is a zoonotic disease caused by infection with Coxiella burnetii (C. burnetii). Due to its atypical symptoms and the absence of specific detection methods, Q fever is underdiagnosed commonly. Herein, we report a case of Q fever confirmed by metagenomic next-generation sequencing (mNGS) in March 2024 in Guangdong Province, China. The patient initially experienced fever and was admitted to hospital six days later. Despite a series of laboratory tests conducted at the hospital, the pathogen remained undetermined. Ten days after admission, mNGS revealed that the patient was infected with C. burnetii. The patient subsequently underwent treatment with doxycycline and recovered well. Epidemiological investigation revealed that the patient had been exposed to sheep infected with C. burnetii without any protective measures in Jiangxi Province, China. Based on the comprehensive results of mNGS, exposure history, clinical manifestations and treatment response, the patient was confirmed as a Q fever case. As a neglected and underestimated illness, Q fever necessitates an elevation in awareness among medical staff and the public. The public should be encouraged to take personal protective measures when exposed to livestock. Further research is needed to explore the rational application of mNGS in the diagnosis of uncommon and unknown diseases.}, } @article {pmid40078947, year = {2024}, author = {Fan, Q and Jiang, M and Zhang, J and Tang, G and Gao, M and Wen, Y and Deng, X and Dai, J and Lai, H and Qian, P and Lin, Y and He, R and Li, L and Li, Y and Li, Z and Liu, X and Li, Y and Yu, N and Lan, Y and Hu, F and Li, F}, title = {Prevalence of bacteria, fungi, and virus coinfections with SARS-CoV-2 Omicron variant among patients with severe COVID-19 in Guangzhou, China, winter 2022.}, journal = {Biosafety and health}, volume = {6}, number = {2}, pages = {92-97}, pmid = {40078947}, issn = {2590-0536}, abstract = {The status of coinfection during the national outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron BA.5.2 or BF.7 in China in the winter of 2022, which is suspected to contribute substantially to the overloaded severe cases, needs to be investigated. We analyzed the coinfection status of 385 severe patients infected with the Omicron variant in Guangzhou using metagenomic sequencing. We found that 317 (82.3 %) patients were coinfected with at least one additional pathogen(s), including bacteria (58.7 %), fungi (27.1 %) and viruses (73.5 %). Pseudomonas aeruginosa (P. aeruginosa) (24.2 %), Staphylococcus aureus (S. aureus) (14.0 %), and Klebsiella pneumoniae (K. pneumonia) (13.4 %) ranked as the top three coinfected bacteria. Aspergillus fumigatus (A. fumigatus) (39.5 %), Pneumocystis jirovecii (P. jirovecii) (24.4 %) and Canidia albicans (C. albicans) (22.1 %) were the top three coinfected fungi. Epstein-Barr virus (EBV) (63.1 %), Human herpesvirus 7 (HHV-7) (34.8 %), and Herpes simplex virus 1 (HSV-1) (32.6 %) were the top three coinfected viruses. Of note, the detection of multiple coinfections of potential pathogenic bacteria, fungi, and viruses, despite lacking consistent patterns, highlighted a complicated synergistic contribution to disease severity. Our study presents the most comprehensive spectrum of bacterial, fungal, and viral coinfections in Omicron-associated severe coronavirus disease 2019 (COVID-19), implying that the coinfection of conditional pathogens might synergistically deteriorate the Omicron infection outcomes.}, } @article {pmid40078943, year = {2024}, author = {Wang, Y and Qu, M and Bi, Y and Liu, WJ and Ma, S and Wan, B and Hu, Y and Zhu, B and Zhang, G and Gao, GF}, title = {The multi-kingdom microbiome catalog of the chicken gastrointestinal tract.}, journal = {Biosafety and health}, volume = {6}, number = {2}, pages = {101-115}, doi = {10.1016/j.bsheal.2024.02.006}, pmid = {40078943}, issn = {2590-0536}, abstract = {Chicken is an important food animal worldwide and plays an important role in human life by providing meat and eggs. Despite recent significant advances in gut microbiome studies, a comprehensive study of chicken gut bacterial, archaeal, and viral genomes remains unavailable. In this study, we constructed a chicken multi-kingdom microbiome catalog (CMKMC), including 18,201 bacterial, 225 archaeal, and 33,411 viral genomes, and annotated over 6,076,006 protein-coding genes by integrating 135 chicken gut metagenomes and publicly available metagenome-assembled genomes (MAGs) from ten countries. We found that 812 and 240 MAGs in our dataset were putative novel species and genera, respectively, far beyond what was previously reported. The newly unclassified MAGs were predominant in Phyla Firmicutes_A (n = 263), followed by Firmicutes (n = 126), Bacteroidota (n = 121), and Proteobacteria (n = 87). Most of the classified species-level viral operational taxonomic units belong to Caudovirales. Approximately, 63.24 % of chicken gut viromes are predicted to infect two or more hosts, including complete circular viruses. Moreover, we found that diverse auxiliary metabolic genes and antibiotic resistance genes were carried by viruses. Together, our CMKMC provides the largest integrated MAGs and viral genomes from the chicken gut to date, functional insights into the chicken gastrointestinal tract microbiota, and paves the way for microbial interventions for better chicken health and productivity.}, } @article {pmid40078550, year = {2025}, author = {Wang, G and Haenelt, S and Corrêa, FB and da Rocha, UN and Musat, F and Zhang, J and Müller, JA and Musat, N}, title = {Riverine antibiotic resistome along an anthropogenic gradient.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1516033}, doi = {10.3389/fmicb.2025.1516033}, pmid = {40078550}, issn = {1664-302X}, abstract = {The introduction of antibiotic-resistant bacteria into riverine systems through the discharge of wastewater treatment plant (WWTP) effluent and agricultural waste poses significant health risks. Even when not pathogenic, these bacteria can act as reservoirs for antibiotic resistance genes (ARGs), transferring them to pathogens that infect humans and animals. In this study, we used fluorescence in situ hybridization, qPCR, and metagenomics to investigate how anthropogenic activities affect microbial abundance and the resistome along the Holtemme River, a small river in Germany, from near-pristine to human-impacted sites. Our results showed higher bacterial abundance, a greater absolute and relative abundance of ARGs, and a more diverse ARG profile at the impacted sites. Overall, the ARG profiles at these sites reflected antibiotic usage in Germany, with genes conferring resistance to drug classes such as beta-lactams, aminoglycosides, folate biosynthesis inhibitors, and tetracyclines. There were also variations in the ARG profiles of the impacted sites. Notably, there was a high abundance of the oxacillin resistance gene OXA-4 at the downstream site in the river. In the metagenome assembly, this gene was associated with a contig homologous to small plasmids previously identified in members of the Thiotrichaceae. The likely in-situ host of the putative plasmid was a close relative of Thiolinea (also known as Thiothrix) eikelboomii, a prominent member of WWTP microbiomes worldwide. Our results show that the effluent from WWTPs can introduce bacteria into the environment that act as shuttle systems for clinically relevant ARG.}, } @article {pmid40078542, year = {2025}, author = {Zhang, C and Liu, Z and Yu, H and Shen, Y and Lu, L and Kong, F and Sun, W and Wei, X and Jin, L and Ge, L and Zeng, B}, title = {Dynamic changes in the gut microbiota of SPF Bama piglets during breast and formula feeding.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1537286}, doi = {10.3389/fmicb.2025.1537286}, pmid = {40078542}, issn = {1664-302X}, abstract = {The gut microbiota plays a crucial role in the growth performance, health status, and welfare of pigs. Breast milk is a key factor in the colonization of gut microbiota and the overall health of newborn piglets. With advancements in breeding technology, formula milk has been widely adopted as a substitute for breast milk. This study aims to investigate the effects of sow feeding (natural breastfeeding) and formula milk feeding on the gut microbiota of specific pathogen-free (SPF) Bama pigs. Using metagenomic sequencing technology, we analyzed 114 fecal samples to uncover the impacts of different feeding methods on gut microbial diversity, dominant microbial populations, metabolic functions, carbohydrate-active enzymes (CAZymes), and antibiotic resistance genes (ARGs). The results revealed significant differences in the structure and function of gut microbiota between the breast milk (BM) group and the formula milk (FM) group at day 21. The BM group exhibited higher gut microbial diversity compared to the FM group, along with more extensive metabolic functions at both the gene and species levels. Notably, the FM group demonstrated higher activity in galactose metabolism and glycan metabolism, particularly at day 21. Additionally, the FM group showed significantly higher levels of ARGs against glycopeptide antibiotics at days 21 and 28 compared to the BM group. This study also found that breastfeeding and formula feeding differentially regulate the metabolic activity of gut microbiota and the expression of related enzymes, which may have long-term effects on nutrient absorption and disease resistance in pigs. These findings provide new insights into how different feeding methods shape the gut microbiota of pigs and offer a scientific basis for optimizing feeding strategies and improving breeding efficiency.}, } @article {pmid40078316, year = {2025}, author = {Zhao, C and Escalante, C and Jacobson, AL and Balkcom, KS and Conner, KN and Martin, KM}, title = {Metatranscriptomic and metagenomic analyses of cotton aphids (Aphis gossypii) collected from cotton fields in Alabama, USA.}, journal = {Frontiers in insect science}, volume = {5}, number = {}, pages = {1461588}, doi = {10.3389/finsc.2025.1461588}, pmid = {40078316}, issn = {2673-8600}, } @article {pmid40077957, year = {2025}, author = {Ma, Z and Wen, X and Zhang, Y and Ai, Z and Zhao, X and Dong, N and Dou, X and Shan, A}, title = {Thymol Alleviates Colitis by Modulating Intestinal Barrier Damage, Gut Microbiota, and Amino Acid Metabolic Pathways.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.4c10406}, pmid = {40077957}, issn = {1520-5118}, abstract = {Thymol (THY) is a phenolic monoterpene compound that has garnered attention due to its various biological properties, including antioxidant, anti-inflammatory, and immune-regulatory effects. The purpose of this study was to determine the therapeutic and protective effects of THY in colitic mice, with a particular focus on the mechanisms involving gut microbiota. The results showed that early intervention with THY (40 and 80 mg/kg) not only alleviated the clinical symptoms and colonic damage in mice with dextran sodium sulfate (DSS)-induced colitis but also suppressed the colonic production of inflammatory cytokines (IL-1β, IL-6, and IL-18) and enhanced the expression of mucins (MUC1 and MUC2) and trefoil factor family 3 (TFF3), thereby improving the integrity of the intestinal epithelial barrier. In addition, THY altered the composition of the gut microbiota in colitis mice by increasing the abundance of Bacteroides and reducing the abundance of Proteobacteria. Fecal microbial transplantation (FMT) results demonstrated that FM from THY donor mice significantly improved symptoms of inflammatory bowel disease (IBD), confirming the crucial role of the gut microbiota. Metagenomic and untargeted metabolomic studies found that the characteristic microbiota of THY is Prevotellaceae, and THY significantly upregulated the amino acid metabolic pathways related to arginine and proline metabolism, arginine biosynthesis, and glycerophospholipid metabolism. In summary, THY holds significant potential as a functional additive to enhance host intestinal activity.}, } @article {pmid40077671, year = {2025}, author = {Gao, Y and Borjihan, Q and Zhang, W and Li, L and Wang, D and Bai, L and Zhu, S and Chen, Y}, title = {Complex Probiotics Ameliorate Fecal Microbiota Transplantation-Induced IBS in Mice via Gut Microbiota and Metabolite Modulation.}, journal = {Nutrients}, volume = {17}, number = {5}, pages = {}, doi = {10.3390/nu17050801}, pmid = {40077671}, issn = {2072-6643}, support = {2022-Science and Technology Xing Meng-Quality improvement-02//the Science and Technology Xing Meng action focus project of Inner Mongolia Autonomous Region/ ; 2022-Science and Technology Xing Meng-Quality improvement-02//the Science and Technology Xing Meng action focus project of Inner Mongolia Autonomous Region/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Irritable Bowel Syndrome/therapy/microbiology ; *Fecal Microbiota Transplantation ; *Probiotics/pharmacology ; Mice ; *Feces/microbiology ; *Disease Models, Animal ; Mice, Inbred C57BL ; Male ; Dysbiosis/therapy ; Serotonin/metabolism ; Serotonin Plasma Membrane Transport Proteins/metabolism ; Acetic Acid ; Constipation/therapy/microbiology/metabolism ; Butyric Acid/metabolism ; Tryptophan/metabolism ; }, abstract = {Background/Objectives: Irritable bowel syndrome (IBS) is a highly prevalent functional gastrointestinal disorder. Emerging evidence implicates gut microbiota dysbiosis in IBS pathogenesis, and probiotic interventions targeting microbial modulation hold therapeutic promise. Methods: this study used fecal microbiota transplantation to establish a mouse model of IBS before evaluating the effects of the complex probiotic by using metagenomics and targeted metabolomics to explore the potential mechanism. Results: After 14 days, the probiotic relieved constipation, reduced inflammation and intestinal permeability, lowered 5-HT levels and increased serotonin transporter (SERT) expression in tissues. Metagenomic analysis showed a reduced inflammation-related species abundance. It also decreased fecal butyric acid, acetic acid and tryptophan levels in IBS mice. Conclusions: The probiotic complex effectively alleviated IBS symptoms in mice by modulating gut microbiota and fecal metabolites, providing insights for future IBS research and treatment.}, } @article {pmid40077516, year = {2025}, author = {Li, W and Xu, M and Liu, Y and Zhang, S and Wang, J and Zhang, Z and Xiao, G and Wang, R and Zhang, J and Xue, H}, title = {Lactiplantibacillus plantarum GOLDGUT-HNU082 Alleviates CUMS-Induced Depressive-like Behaviors in Mice by Modulating the Gut Microbiota and Neurotransmitter Levels.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/foods14050813}, pmid = {40077516}, issn = {2304-8158}, support = {No. 32222066//National Natural Science Foundation of China/ ; THAITS-4//Earmarked Fund for Tropical High-efficiency Agricultural Industry Technology System of Hainan University/ ; }, abstract = {Emerging evidence links depressive disorders to the gut microbiota via the gut-brain axis. Probiotics, which are microorganisms that modulate the gut microbiota, have shown promising results in alleviating depression and are increasingly recognized as functional food components with potential health benefits. This study examines the effects of Lactiplantibacillus plantarum GOLDGUT-HNU082 (Lp082), a probiotic strain with potential applications in functional foods, on chronic unpredictable mild stress (CUMS)-induced depression in mice. Behavioral tests, measurements of the neurotransmitters and inflammatory cytokines in the serum and colon tissue, and the metagenomic sequencing of the gut microbiota were used to investigate potential mechanisms. The results demonstrated that Lp082 significantly alleviated depressive-like behaviors in CUMS mice, restored the balance of key neurotransmitters like serotonin (5-HT), reduced the levels of inflammatory cytokines like TNF-α, and enhanced brain neuroplasticity by promoting hippocampal neurogenesis. Additionally, Lp082 altered the composition of the gut microbiota in CUMS mice and promoted the growth of Bifidobacterium, improving metabolic pathways related to neurotransmitter synthesis. These findings indicate that Lp082, as a potential functional food ingredient, alleviates depressive-like behaviors in mice by reshaping the gut microbiota, offering new insights into the use of probiotics in functional foods for mental health management.}, } @article {pmid40077458, year = {2025}, author = {Jing, Y and Wang, Z and Cheng, W and Fan, H and Zheng, K and Zheng, Y and Wu, L}, title = {Structure Characterization and Treatment Effect of Zingiber officinale Polysaccharide on Dextran Sulfate Sodium-Induced Ulcerative Colitis.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/foods14050753}, pmid = {40077458}, issn = {2304-8158}, support = {HBCT2023080201, HBCT2023080205//the Innovation Team of Hebei Province Modern Agricultural Industry Technology System/ ; H2024423098//the Hebei Natural Science Foundation/ ; 2024107//the Science and Technology Program of Hebei Administration of Traditional Chinese Medicine/ ; }, abstract = {BACKGROUND: Ulcerative colitis (UC) is on the rise all over the world. Zingiber officinale polysaccharide (ZOP-1) has good anti-inflammatory and antioxidant effects, but the therapeutic effect and mechanism of ZOP-1 on UC are still unclear.

METHODS: ZOP-1 obtained by water extraction and alcohol precipitation was analyzed by methylation and NMR. At the same time, the mechanism of ZOP-1 in the treatment of UC was clarified by hematoxylin-eosin (HE) staining, metagenomics, immunohistochemistry, and protein blot (Wb).

RESULTS: ZOP-1 was the structure of the by →4,6)-β-Glcp-1→ and →3,6)-α-Galp-(1→ constitute the main chain, there were two branched chain by →4)-β-Glcp(1→, and α-Araf(1→ as the end group. ZOP-1 significantly improved the shortening and thickening of the colon, changed the index of immune organs, inhibited the production of inflammatory factors in mice with ulcerative colitis, changed the intestinal flora of mice, increased the content of short-chain fatty acids (SCFAs) in the intestine, and controlled the TLR4/NF-κB/MAPK signaling pathway, thus preventing and treating DSS-induced ulcerative colitis in mice.

CONCLUSIONS: ZOP-1 alleviated UC by controlling the expression of cytokines, thereby reducing intestinal inflammation and oxidative stress, enhancing intestinal integrity, modulating intestinal flora, and regulating the levels of SCFAs.}, } @article {pmid40076957, year = {2025}, author = {Kumagai, K and Ishikawa, S and Iino, M and Edamatsu, K and Okuyama, N and Yusa, K and Shimizu, Y and Aoki, R and Masuda, C and Ohashi, Y and Horie, A and Hoshi, K and Hamada, Y}, title = {Characterization of Salivary Microbiota in Japanese Patients with Oral Cancer.}, journal = {International journal of molecular sciences}, volume = {26}, number = {5}, pages = {}, doi = {10.3390/ijms26052339}, pmid = {40076957}, issn = {1422-0067}, support = {JP 22K10113//JSPS KAKENHI Grant-in-Aid for Scientific Research (C)/ ; }, mesh = {Humans ; *Saliva/microbiology ; Male ; Female ; *Microbiota/genetics ; Middle Aged ; *RNA, Ribosomal, 16S/genetics ; *Mouth Neoplasms/microbiology ; Aged ; Bacteria/classification/genetics/isolation & purification ; Japan ; Case-Control Studies ; Adult ; Metagenomics/methods ; East Asian People ; }, abstract = {This study aimed to characterize salivary microbiota in patients with oral cancer using 16S rRNA amplicon sequencing. DNA was extracted from saliva samples of 23 patients with oral cancer and 95 age-matched controls. A metagenomic analysis was performed using 16S rRNA amplicon sequencing. Patients with oral cancer exhibited lower α-diversity, as indicated by the Chao-1 index, compared to the control group, and significant differences in β-diversity were observed between the two groups. At the genus level, 25 bacterial species such as Lautropia, Megasphaera, Lactobacillus, Kingella, Gemella, Staphylococcus, and Propionibacterium were identified in patients with oral cancer, with more than half being Gram-positive facultative anaerobes or anaerobes. The reduced bacterial diversity in saliva of patients with oral cancer suggests dysbiosis during oral carcinogenesis may contribute to changes in bacterial distribution within the oral cavity.}, } @article {pmid40076673, year = {2025}, author = {Velazquez-Meza, ME and Galarde-López, M and Cornejo-Juárez, P and Bobadilla-Del-Valle, M and Godoy-Lozano, E and Aguilar-Vera, E and Carrillo-Quiroz, BA and Ponce de León-Garduño, A and Velazquez Acosta, C and Alpuche-Aranda, CM}, title = {Bacterial Communities and Resistance and Virulence Genes in Hospital and Community Wastewater: Metagenomic Analysis.}, journal = {International journal of molecular sciences}, volume = {26}, number = {5}, pages = {}, doi = {10.3390/ijms26052051}, pmid = {40076673}, issn = {1422-0067}, support = {682339//CONAHCYT, México/ ; }, mesh = {*Wastewater/microbiology ; *Metagenomics/methods ; *Virulence Factors/genetics ; *Drug Resistance, Bacterial/genetics ; Hospitals ; Bacteria/genetics/pathogenicity ; Metagenome ; Plasmids/genetics ; Anti-Bacterial Agents/pharmacology ; Virulence/genetics ; Genes, Bacterial ; Humans ; Microbiota/genetics ; }, abstract = {Metagenomic studies have made it possible to deepen the analysis of the abundance of bacterial populations that carry resistance and virulence determinants in the wastewater environment. In this study, a longitudinal collection of samples of community and hospital wastewater from August 2021 to September 2022 was obtained. Shotgun metagenomic sequencing and bioinformatic analysis were performed to characterize the bacterial abundance, antimicrobial resistance genes (ARGs), plasmids, and virulence factor genes (VFGs) contained in the wastewater. The microbial composition of the community and hospital wastewater showed that the most abundant bacterial phyla detected in all samples were: Proteobacteria, Bacteroides, Firmicutes, Campylobacterota, and Actinobacteria. Seasonal differences in the relative abundances of species, ARGs, plasmids, and VFGs were observed. In this study, a total of 270 ARGs were detected, and it was found that the absolute abundance of ARGs only showed a 39% reduction in the treated wastewater. Furthermore, the ARGs detected in this study were found to encode resistance to antibiotics of the last choice. Our results showed that plasmids carrying resistance genes were more abundant in raw wastewater, and 60% more abundant in hospital wastewater compared to community wastewater. Several of the VFGs detected in this study encode for adhesion, motility, and biofilm formation, which likely allows bacteria to remain and persist in the wastewater environment and survive WWTP treatment systems, thus managing to escape into the environment via treated wastewater.}, } @article {pmid40076252, year = {2025}, author = {Gao, Y and Xu, Y and Dong, Z and Guo, Y and Luo, J and Wang, F and Yan, L and Zou, X}, title = {Endophytic Fungal Diversity and Its Interaction Mechanism with Medicinal Plants.}, journal = {Molecules (Basel, Switzerland)}, volume = {30}, number = {5}, pages = {}, doi = {10.3390/molecules30051028}, pmid = {40076252}, issn = {1420-3049}, support = {BS0050//Heilongjiang Province Postdoctoral Research Fund/ ; LH2022H001//Heilongjiang Natural Science Foundation Joint Guidance Project/ ; ZYW2023-073//Heilongjiang Province Traditional Chinese Medicine Research Project/ ; GZ20210110//Key Research and Development Guidance Project of Heilongjiang Province/ ; }, mesh = {*Plants, Medicinal/microbiology/chemistry ; *Endophytes/metabolism ; *Fungi/metabolism ; Biodiversity ; Metabolomics/methods ; Metagenomics/methods ; Proteomics/methods ; }, abstract = {This paper reviewed the diversity of endophytic fungi and their interactions with medicinal plants, along with the research methodologies utilized to investigate these interactions. It mainly includes the diversity of endophytic fungi, as well as distribution diversity, species diversity, and the diversity of their metabolites and functions, including antibacterial, anti-inflammatory, anti-tumor, insecticidal, antioxidant capabilities, and so on. The research methodologies employed to investigate the interactions between endophytic fungi and medicinal plants are categorized into metagenomics, transcriptomics, metatranscriptomics, proteomics, and metabolomics. Furthermore, this study anticipates the potential applications of secondary metabolites derived from endophytic fungi in both medicine and agriculture.}, } @article {pmid40076036, year = {2025}, author = {Bai, X and Gu, Y and Li, D and Li, M}, title = {Gut Metagenome Reveals the Microbiome Signatures in Tibetan and Black Pigs.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {5}, pages = {}, doi = {10.3390/ani15050753}, pmid = {40076036}, issn = {2076-2615}, support = {National Key R & D Program of China (2020YFA0509500 and 2023YFD1301302)//Mingzhou Li/ ; the Biological Breeding-Major Projects in National Science and Technology (2023ZD0404404)//Mingzhou Li/ ; the Sichuan Science and Technology Program (2021ZDZX0008 and 2021YFYZ0009)//Mingzhou Li/ ; the National Natural Science Foundation of China (32421005, 32225046 and 32494802)//Mingzhou Li/ ; }, abstract = {The harsh conditions of the Qinghai-Tibet Plateau pose significant physiological challenges to local fauna, often resulting in gastrointestinal disorders. However, Tibetan pigs have exhibited remarkable adaptability to the high-altitude stress of the Tibetan Plateau, a phenomenon that remains not fully understood in terms of their gastrointestinal microbiota. This study collected 57 gastrointestinal tract samples from Tibetan pigs (n = 6) and plain black pigs (n = 6) with comparable genetic backgrounds. Samples from the stomach, jejunum, cecum, colon, and rectum, underwent comprehensive metagenomic analysis to elucidate the gut microbiota-related adaptive mechanisms in Tibetan pigs to the extreme high-altitude environment. A predominance of Pseudomonadota was observed within gut microbiome of Tibetan pigs. Significant differences in the microbial composition were also identified across the tested gastrointestinal segments, with 18 genera and 141 species exhibiting differential abundance. Genera such as Bifidobacterium, Megasphaera, Fusobacterium, and Mitsuokella were significantly more abundant in Tibetan pigs than in their lowland counterparts, suggesting specialized adaptations. Network analysis found greater complexity and modularity in the microbiota of Tibetan pigs compared to black pigs, indicating enhanced ecological stability and adaptability. Functional analysis revealed that the Tibetan pig microbiota was particularly enriched with bacterial species involved in metabolic pathways for propionate and butyrate, key short-chain fatty acids that support energy provision under low-oxygen conditions. The enzymatic profiles of Tibetan pigs, characterized by elevated levels of 4-hydroxybutyrate dehydrogenase and glutaconyl-CoA decarboxylase, highlighted a robust fatty acid metabolism and enhanced tricarboxylic acid cycle activity. In contrast, the gut microbiome of plain black pigs showed a reliance on the succinate pathway, with a reduced butyrate metabolism and lower metabolic flexibility. Taken together, these results demonstrate the crucial role of the gastrointestinal microbiota in the adaptation of Tibetan pigs to high-altitude environments by optimizing carbohydrate metabolism and short-chain fatty acid production for efficient energy utilization. This study not only highlights the metabolic benefits conferred by the gut microbiota of Tibetan pigs in extreme environments, but also advances our understanding of the adaptive gastrointestinal mechanisms in plateau-dwelling animals. These insights lay the foundation for exploring metabolic interventions to support health and performance in high-altitude conditions.}, } @article {pmid40075266, year = {2025}, author = {Cao, H and Xu, J and Wang, H and Yi, W and Yang, D and Yang, J and Sun, J and Wang, Y and Zhang, F and Yan, J and Li, D}, title = {Fecal microbiota transplantation mitigates postdieting weight regain in mice by modulating the gut-liver axis.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {135}, pmid = {40075266}, issn = {1471-2180}, support = {2023YFF1104305//National Key Research and Development Program of China/ ; 2022YFF1100601//National Key Research and Development Program of China/ ; K2023004//Key Research project of Health Commission of Jiangsu Province/ ; M2021055//Key Research project of Health Commission of Jiangsu Province/ ; Y2021001//Wuxi Science and Technology Bureau, "Taihu Light" Science and Technology Research program/ ; K20221026//Wuxi Science and Technology Bureau, "Taihu Light" Science and Technology Research program/ ; CXTD2021003//Key discipline construction program of Wuxi Commission of Health/ ; KX-23-B050//Soft Science Project of Wuxi Science and Technology Association/ ; KX-23-C196//Soft Science Project of Wuxi Science and Technology Association/ ; YJZ202305//Medical research projects in research-oriented hospitals of Affiliated Hospital of Jiangnan University/ ; HB2023062//"Shuangbai Talents" research program of Wuxi Commission of Health/ ; HB2023063//"Shuangbai Talents" research program of Wuxi Commission of Health/ ; HB2023061//"Shuangbai Talents" research program of Wuxi Commission of Health/ ; LCYJ202347//Clinical Research and translational medicine research program of Affiliated Hospital of Jiangnan University/ ; LCYJ202310//Clinical Research and translational medicine research program of Affiliated Hospital of Jiangnan University/ ; LCYJ202322//Clinical Research and translational medicine research program of Affiliated Hospital of Jiangnan University/ ; LCYJ202303//Clinical Research and translational medicine research program of Affiliated Hospital of Jiangnan University/ ; BK20210468//Natural Science Foundation of Jiangsu Province/ ; BK20210060//Natural Science Foundation of Jiangsu Province/ ; 82370809//National Natural Science Foundation of China/ ; 32101033//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Fecal Microbiota Transplantation/methods ; *Gastrointestinal Microbiome ; Mice ; *Weight Gain ; *Liver/metabolism ; Male ; Bacteria/classification/isolation & purification/genetics/metabolism ; Mice, Inbred C57BL ; Feces/microbiology ; Dysbiosis/therapy/microbiology ; Fatty Acids, Volatile/metabolism ; Lipid Metabolism ; }, abstract = {BACKGROUND: Dysbiosis of the microbiome is strongly associated with weight rebound after dieting. However, the interactions between the host and microbiome and their relevance to the pathogenesis of post-diet weight rebound remain unclear.

PURPOSE: This study aimed to evaluate the effects of fecal microbiota transplantation (FMT) on post-diet weight regain and to investigate the underlying mechanisms by which FMT inhibits weight regain.

METHODS: FMT was administered once daily to mice for 5 weeks. Gas chromatography tandem mass spectrometry was employed to analyze short-chain fatty acid levels in serum, ultrahigh-performance liquid chromatography tandem mass spectrometry was utilized for analyzing hepatic lipid metabolites, and shotgun metagenomic sequencing was applied to examine the intestinal microbiome.

RESULTS: FMT reduced weight regain and prevented lipid accumulation in both liver and adipose tissue while also improving glucose intolerance in mice. Furthermore, FMT increased the abundance of Enterorhabdus caecimuris and decreased the abundances of Burkholderiales, Sutterellaceae, Turicimonas muris, Bacteroides stercorirosoris, and Acetivibrio ethanolgignens within the gut microbiota. Additionally, elevated propionic acid levels and significant alterations in hepatic lipid metabolites were observed following FMT administration.

CONCLUSIONS: Our findings demonstrate that FMT effectively mitigates post-diet weight regain and associated complications. These effects are mediated through interactions between the gut microbiota and the liver via the gut-propionic acid-liver axis.

CLINICAL TRIAL NUMBER: Not applicable.}, } @article {pmid40075219, year = {2025}, author = {Sun, Y and Huang, S and Li, M and Yang, Y and Ma, J and Xie, R and Wang, J and Zhao, Q and Qin, S and He, L and Jiang, J and Zhao, Q and Jin, G and Liu, X and Huang, H and Yang, Y and Wei, J and Liu, W and Wang, B and Yang, R and Su, X and Cao, H}, title = {Maternal high-fat diet disrupts intestinal mucus barrier of offspring by regulating gut immune receptor LRRC19.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {420}, pmid = {40075219}, issn = {2399-3642}, support = {82270574//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82070545//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82400632//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81970488//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; *Diet, High-Fat/adverse effects ; *Gastrointestinal Microbiome ; Female ; Mice ; *Intestinal Mucosa/metabolism/immunology/microbiology ; Mice, Inbred C57BL ; Pregnancy ; Mice, Knockout ; Male ; Interleukin-22 ; Receptors, Immunologic/metabolism/genetics ; }, abstract = {Maternal high fat diet (MHFD) increased colitis susceptibility in adulthood. However, the mechanism remains unclear. We sought to explore whether novel gut immune receptor leucine-rich repeat C19 (LRRC19) contributed to the impaired mucus barrier of offspring exposed to MHFD via gut immune response and microbiota. The results showed that MHFD significantly impaired the intestinal mucus barrier of offspring, and up-regulated the expression of LRRC19. Lrrc19 deletion alleviated the mucus barrier disruption. Mechanistically, metagenome sequencing revealed that the MHFD-induced gut microbiota alteration was partly restored in Lrrc19[-/-] offspring. Muc2-associated bacteria were decreased in the MHFD group, such as Akkermansia_muciniphila_CAG_154, which increased in the Lrrc19-deficient offspring. Moreover, Lrrc19[-/-] offspring had a higher rate of indole-3-acetic acid (IAA)-producing bacterium, such as Lactobacillus reuteri. A targeted metabolomics analysis revealed that IAA emerged as the top candidate that might mediate the protective effects. IAA was found to improve the mucus barrier function by increasing the ratio of interleukin-22 (IL-22)[+] ILC3 cells in an aryl hydrocarbon receptor (AhR)-dependent manner. These results suggest that MHFD disrupts the intestinal mucus barrier of offspring through regulating gut immune receptor LRRC19 and inducing an imbalance of gut microbiota and microbiota-derived metabolites.}, } @article {pmid40074067, year = {2025}, author = {Pragasam, AK and Maurya, S and Jain, K and Pal, S and Raja, C and Yadav, R and Kumar, S and Purohit, A and Pradhan, D and Kajal, K and Talukdar, D and Singh, AN and Verma, J and Jana, P and Rawat, S and Kshetrapal, P and Krishna, A and Kumar, S and Bansal, VK and Das, B and Srikanth, CV and Garg, PK}, title = {Invasive Salmonella Typhimurium Colonizes Gallbladder and Contributes to Gallbladder Carcinogenesis through Activation of Host Epigenetic Modulator KDM6B.}, journal = {Cancer letters}, volume = {}, number = {}, pages = {217621}, doi = {10.1016/j.canlet.2025.217621}, pmid = {40074067}, issn = {1872-7980}, abstract = {Gallbladder stones alone do not explain the risk of gallbladder cancer (GBC) as the sole etiological factor. Chronic microbial infection, particularly Salmonella, has been implicated in GB carcinogenesis, but its causative role and the underlying mechanisms are largely unknown. We studied gut and gallbladder tissue microbiome through targeted metagenomics to identify pathogenic bacteria in GBC. Virulence and pathogenicity of identified Salmonella Typhimurium from GBC tissue were studied after culture by whole genome sequencing, phylogenetic analysis, mutational profiling, and pangenome analysis. Mechanistic studies for GBC carcinogenesis were carried out in a mouse model of gallstones and chronic Salmonella infection, a cellular model using GBC (NOZ) cell lines, and a xenograft tumor model. We found an increased abundance of Salmonella in the gut microbiome of patients with GBC and culturable S. Typhimurium from the gallbladder cancer tissue. Comparative genomics of S. Typhimurium isolated from the GBC tissue showed a high invasive index. S. Typhimurium isolates harbored horizontally acquired virulence functions in their accessory genome. Chronic S. Typhimurium infection caused chronic inflammation, pre-malignant changes, and tumor-promoting mechanisms in the mouse model with gallbladder stones with activation of the epigenetic modulator KDM6B both in the mouse model and human GBC. Inhibition of KDM6B reduced engrafted tumor size in SCID mice. Of the differentially regulated genes in human GBC tissue, ADAMTSL5, CX3CR1, and SPSB4 were also significantly dysregulated in NOZ cells infected with Salmonella. Chronic Salmonella infection contributes to gallbladder carcinogenesis through a host epigenetic mechanism involving KDM6B.}, } @article {pmid40073489, year = {2025}, author = {Han, NN and Wang, XP and Jin, JA and Li, WH and Yang, WY and Fan, NS and Jin, RC}, title = {Underrated risk of antibiotic resistance genes dissemination mediated by bioaerosols released from anaerobic biological wastewater treatment system.}, journal = {Water research}, volume = {279}, number = {}, pages = {123463}, doi = {10.1016/j.watres.2025.123463}, pmid = {40073489}, issn = {1879-2448}, abstract = {Antibiotic resistance has been recognized as one of the most prevalent public health problems. The bioaerosol-mediated spread of antibiotic resistance genes (ARGs) is an important but underrated pathway. Therefore, this work investigated the comprehensive resistome and pathogen-induced risk in bioaerosols released from anaerobic ammonium oxidation (anammox) process under antibiotic stress. The results showed that the bioaerosol oxidation potential increased by 2.7 times after the addition of sulfamethoxazole (SMX) into the anammox system. Based on the metagenomic analyses, abundant ARGs were enriched in bioaerosols, especially novA, olec, msbA and patA. There were many antibiotic resistance contigs carrying at least two mobile genetic elements (MGEs) in bioaerosols. Compared to the control, SMX caused the significant increase in ARGs proportion in plasmids from 11.4 % to 19.4 %. Similarly, the abundance of the type IV secretion system protein encoding genes (mtrA and mtrB) increased by 30.2 % and 31.5 %, respectively, which was conducive to gene transfer between bacteria. In addition, SMX stress induced the reactive oxygen species (ROS) production and the upregulation of genes related to membrane protein and DNA replication, further facilitating ARGs transfer. The co-occurrence networks showed that Aquamicrobium and Microbacterium probably were the hosts of most ARGs. Notably, four abundant human pathogens were detected in bioaerosols from the anammox system, which raised concerns on the health risk of resistant bioaerosol diffusion. These findings reveal the potential of horizontal gene transfer through bioaerosols and provide a guidance for systematically assessing the risk of environmental antibiotic resistance and relevant pathogens.}, } @article {pmid40072902, year = {2025}, author = {Varsani, A and Custer, JM and Cobb, IN and Harding, C and Collins, CL and Suazo, C and Schreck, J and Fontenele, RS and Stainton, D and Dayaram, A and Goldstein, S and Kazlauskas, D and Kraberger, S and Krupovic, M}, title = {Bacilladnaviridae: refined taxonomy and new insights into the biology and evolution of diatom-infecting DNA viruses.}, journal = {The Journal of general virology}, volume = {106}, number = {3}, pages = {}, doi = {10.1099/jgv.0.002084}, pmid = {40072902}, issn = {1465-2099}, mesh = {*Diatoms/virology/genetics ; *Phylogeny ; *Genome, Viral ; *DNA Viruses/genetics/classification ; New Zealand ; Metagenomics ; Animals ; Evolution, Molecular ; DNA, Viral/genetics ; Capsid Proteins/genetics ; }, abstract = {Bacilladnaviruses are single-stranded DNA viruses that infect diatoms that, so far, have been primarily identified in marine organisms and environments. Using a viral metagenomics approach, we discovered 13 novel bacilladnaviruses originating from samples of mud-flat snail (Amphibola crenata; n=3 genomes) and benthic sediments (n=10 genomes) collected from the Avon-Heathcote Estuary in New Zealand. Comparative genomics and phylogenetic analysis of the new bacilladnavirus sequences in the context of the previously classified members of the family helped refine and further expand the Bacilladnaviridae taxonomy. Here, based on the replication-associated protein phylogeny and pairwise identities, we established 4 new genera - Aberdnavirus, Keisodnavirus, Puahadnavirus and Seawadnavirus - and 13 new species within the family. Comparison of the bacilladnavirus capsid protein sequences suggests that the positively charged N-terminal region (R-arm) is required for encapsidation of the larger genomes, whereas the smaller bacilladnavirus genomes can be packaged in the absence of the R-arm subdomain. Furthermore, analysis of the bacilladnavirus genomes revealed that members of three genera encode a highly derived variant of a phospholipase A1, which is predicted to be involved in the lysis of the infected diatoms and/or facilitates the entry of the virions into the host cells. Collectively, our results allow refining of the taxonomy of bacilladnaviruses and provide new insights into the biology and evolution of this understudied group of diatom viruses.}, } @article {pmid40078515, year = {2023}, author = {Li, Z and Wu, C and Tang, LA and Liang, Y and A, R and Huang, D and Ning, C and Wang, W and Tan, W}, title = {mNGS-based dynamic pathogen monitoring for accurate diagnosis and treatment of severe pneumonia caused by fungal infections.}, journal = {Biosafety and health}, volume = {5}, number = {3}, pages = {138-143}, doi = {10.1016/j.bsheal.2023.04.004}, pmid = {40078515}, issn = {2590-0536}, abstract = {Metagenomic next-generation sequencing (mNGS) has been widely applied to identify pathogens associated with infectious diseases. However, limited studies have explored the use of mNGS-based dynamic pathogen monitoring in intensive care unit patients with severe pneumonia. Here, we present a clinical case of an 86-year-old male patient with severe pneumonia caused by a fungal infection. During the clinical treatment, four mNGS analyses were performed within two consecutive weeks. Various respiratory fungal pathogens, including Candida orthopsilosis, Candida albicans, and Aspergillus fumigatus were detected by mNGS of bronchoalveolar lavage fluid (BALF). Based on conventional pathogen identification and clinical symptoms, the patient was diagnosed with severe pneumonia caused by a fungal infection. The abundance of fungal species decreased gradually in response to antifungal and empirical therapies, and the fungal infections were effectively controlled. In summary, our results demonstrated that mNGS could effectively identify pathogens in patients with severe pneumonia. Additionally, dynamic pathogen monitoring based on mNGS could assist in the precise diagnosis of complex infections and may facilitate rapid induction of the most appropriate therapy.}, } @article {pmid40072675, year = {2025}, author = {Verma, N and Chavan, N and Aulakh, KS and Sharma, A and Shouche, Y and Ramana, VV}, title = {Temporal Dynamics of Microbial Community Composition and Antimicrobial Resistance in a Mass Gathering Setting Using Culturomics and Metagenomic Approaches.}, journal = {Journal of epidemiology and global health}, volume = {15}, number = {1}, pages = {41}, pmid = {40072675}, issn = {2210-6014}, support = {OLP-805//CSIR - Institute of Microbial Technology/ ; GAP-233//Department of Biotechnology, Ministry of Science and Technology, India/ ; }, mesh = {Humans ; India/epidemiology ; *Metagenomics/methods ; Microbiota/drug effects ; Bacteria/drug effects/genetics/isolation & purification/classification ; Water Microbiology ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; }, abstract = {INTRODUCTION: Antimicrobial resistance (AMR) is one of the major global concerns in the current scenario. Mass-gathering events in fast-developing and densely populated areas may contribute to antibiotic resistance. Despite meticulous planning and infrastructure development, the effect of mass gatherings on microbial ecosystems and antibiotic resistance must be investigated. This study used culture and metagenome-based methods to investigate and compare the bacterial diversity, AMR profile & mechanism of resistance for bacteria in water samples collected from the mass gathering event (2019 Prayagraj Kumbh Mela in Uttar Pradesh, India) with the control samples, collected during no mass gathering.

METHODS: This study analyzed the water samples collected from a mass gathering event held in February 2019. Water samples collected in this study were grouped into "Test" (mass gathering event) and "Control" (no mass gathering event) groups. This study involved methods including culturomics, antibiotyping, phenotypic & genotypic identification methods, and metagenomics.

RESULTS: There is a significant variation observed in the evenness and richness of bacterial diversity and MDR profile, expressed in terms of the relative abundance of the bacterial species between test and control samples. Out of the total multi-drug resistant (MDR) strains identified in the Prayagraj sample, the majority were derived from the test sample. A pathway-based analysis of MDR strains revealed the highest levels of acquired resistance were related to the inhibition of cell wall synthesis primarily in Pseudomonas spp., followed by resistance to protein synthesis and nucleic acid synthesis pathways. Additionally, the overall resistance profile of the test sample demonstrated a significantly elevated resistome for beta-lactams, particularly in the Pseudomonas spp. Additionally, several ESBL (Extended-spectrum beta-lactamase)-associated gene variants were identified. The test sample showed a two-fold increase in the prevalence and diversity of common beta-lactam gene variants in addition to the presence of unique variants. Using the metagenomics approach, we investigated the mechanism of antibiotic resistance, and it revealed a dominant trend in antibiotic efflux and inactivation pathways within both the test and control samples. Overall, the bacterial diversity, abundance (including AMR strains of human origin), and ARGs were relatively higher in the Test sample compared to the control sample which was collected 3 months after the mass gathering event.

CONCLUSION: Our study found significant variations in microbial communities, MDR strains, and ARGs due to environmental and human influences. Pseudomonas spp. was the most abundant MDR strain, primarily resistant to cell wall synthesis inhibitors. The test sample showed an increased resistome for beta-lactams, while the control sample had reduced bacterial species, ARGs, and MDR strains linked to human microflora. This shift could be due to the re-establishment of native bacterial communities in the Ganges River which may be attributed to its bacteriophage activity, biomolecules, and inherent antimicrobial properties. The study highlights the need for surveillance, monitoring AMR emergence to develop new strategies to combat it.}, } @article {pmid40072088, year = {2025}, author = {Świdnicka-Siergiejko, A and Daniluk, J and Miniewska, K and Daniluk, U and Guzińska-Ustymowicz, K and Pryczynicz, A and Dąbrowska, M and Rusak, M and Ciborowski, M and Dąbrowski, A}, title = {Inflammatory Stimuli and Fecal Microbiota Transplantation Accelerate Pancreatic Carcinogenesis in Transgenic Mice, Accompanied by Changes in the Microbiota Composition.}, journal = {Cells}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/cells14050361}, pmid = {40072088}, issn = {2073-4409}, support = {No NCN 2017/27/B/NZ5/02904//National Science Center/ ; }, mesh = {Animals ; *Fecal Microbiota Transplantation ; *Mice, Transgenic ; *Pancreatic Neoplasms/microbiology/genetics/pathology ; Mice ; *Inflammation/pathology/microbiology ; *Gastrointestinal Microbiome/genetics ; *Carcinoma, Pancreatic Ductal/microbiology/genetics/pathology ; Carcinogenesis/genetics/pathology ; Feces/microbiology ; Proto-Oncogene Proteins p21(ras)/genetics ; Pancreas/pathology ; }, abstract = {An association between gut microbiota and the development of pancreatic ductal adenocarcinoma (PDAC) has been previously described. To better understand the bacterial microbiota changes accompanying PDAC promotion and progression stimulated by inflammation and fecal microbiota transplantation (FMT), we investigated stool and pancreatic microbiota by 16s RNA-based metagenomic analysis in mice with inducible acinar transgenic expressions of KrasG12D, and age- and sex-matched control mice that were exposed to inflammatory stimuli and fecal microbiota obtained from mice with PDAC. Time- and inflammatory-dependent stool and pancreatic bacterial composition alterations and stool alpha microbiota diversity reduction were observed only in mice with a Kras mutation that developed advanced pancreatic changes. Stool Actinobacteriota abundance and pancreatic Actinobacteriota and Bifidobacterium abundances increased. In contrast, stool abundance of Firmicutes, Verrucomicrobiota, Spirochaetota, Desulfobacterota, Butyricicoccus, Roseburia, Lachnospiraceae A2, Lachnospiraceae unclassified, and Oscillospiraceae unclassified decreased, and pancreatic detection of Alloprevotella and Oscillospiraceae uncultured was not observed. Furthermore, FMT accelerated tumorigenesis, gradually decreased the stool alpha diversity, and changed the pancreatic and stool microbial composition in mice with a Kras mutation. Specifically, the abundance of Actinobacteriota, Bifidobacterium and Faecalibaculum increased, while the abundance of genera such as Lachnospiraceace A2 and ASF356, Desulfovibrionaceace uncultured, and Roseburia has decreased. In conclusion, pancreatic carcinogenesis in the presence of an oncogenic Kras mutation stimulated by chronic inflammation and FMT dynamically changes the stool and pancreas microbiota. In particular, a decrease in stool microbiota diversity and abundance of bacteria known to be involved in short-fatty acids production were observed. PDAC mouse model can be used for further research on microbiota-PDAC interactions and towards more personalized and effective cancer therapies.}, } @article {pmid40072031, year = {2025}, author = {Huang, YJ}, title = {The Microbiome in Asthma Heterogeneity: The Role of Multi-Omic Investigations.}, journal = {Immunological reviews}, volume = {330}, number = {1}, pages = {e70015}, doi = {10.1111/imr.70015}, pmid = {40072031}, issn = {1600-065X}, support = {U01TR004066/TR/NCATS NIH HHS/United States ; 75N92024D00012-0-759202400001-1/HL/NHLBI NIH HHS/United States ; }, mesh = {*Asthma/microbiology/immunology/etiology ; Humans ; *Microbiota/immunology ; Animals ; Biomarkers ; Genomics/methods ; Proteomics ; Metabolomics/methods ; Disease Susceptibility ; Metagenomics/methods ; Multiomics ; }, abstract = {Asthma is one of the most prevalent and extensively studied chronic respiratory conditions, yet the heterogeneity of asthma remains biologically puzzling. Established factors like exogenous exposures and treatment adherence contribute to variability in asthma risk and clinical outcomes. It is also clear that the endogenous factors of genetics and immune system response patterns play key roles in asthma. Despite significant existing knowledge in the above, divergent clinical trajectories and outcomes are still observed, even among individuals with similar risk profiles, biomarkers, and optimal medical management. This suggests uncaptured biological interactions that contribute to asthma's heterogeneity, for which the role of host microbiota has lately attracted much research attention. This review will highlight recent evidence in this area, focusing on bedside-to-bench investigations that have leveraged omic technologies to uncover microbiome links to asthma outcomes and immunobiology. Studies centered on the respiratory system and the use of multi-omics are noted in particular. These represent a new generation of reverse-translational investigations revealing potential functional crosstalk in host microbiomes that may drive phenotypic heterogeneity in chronic diseases like asthma. Multi-omic data offer a wide lens into ecosystem interactions within a host. This informs new hypotheses and experimental work to elucidate mechanistic pathways for unresolved asthma endotypes. Further incorporation of multi-omics into patient-centered investigations can yield new insights that hopefully lead to even more precise, microbiome-informed strategies to reduce asthma burden.}, } @article {pmid40071918, year = {2025}, author = {Foysal, MJ and Neilan, BA and Timms, V}, title = {The impact of anthropogenic activities on antimicrobial and heavy metal resistance in aquatic environments.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0231724}, doi = {10.1128/aem.02317-24}, pmid = {40071918}, issn = {1098-5336}, abstract = {UNLABELLED: This study investigated the prevalence and co-occurrence of antimicrobial (AMR) and metal resistance (MR) in aquatic environments with different human impacts. Metagenomes from pristine, rural and urban sites in Australia were analyzed with AMR ++ and customized binning pipelines. AMR was present in all environments, while MR was mainly in rural and urban samples. AMR gene diversity was higher in rural and urban sites, exhibiting resistance to more antibiotic classes (n = 10) than the pristine site (n = 4). Metal and multicompound resistance was more frequent in rural (14%) compared to urban samples (5%). Pristine samples lacked multidrug and multicompound resistance and had lower resistance to aminoglycosides and the MLS group. Multiresistance was evidenced by copper and aminocoumarin resistance in rural samples and aminoglycoside and mercury resistance in Pseudomonas in all environments. These findings highlight the impact of human activities on AMR and MR spread, emphasizing the need for environmental monitoring and management.

IMPORTANCE: Antimicrobial resistance (AMR) and metal resistance (MR) are critical global health concerns exacerbated by anthropogenic activities. The intricate mechanism underlying the interaction among anthropogenic activities, microbial communities, and resistance remains enigmatic. We developed novel bioinformatic pipelines to unveil this interaction in three aquatic environments. Our findings demonstrate the presence of specific bacterial communities that drive AMR and MR in rural and urban environments. This study underscores the significance of proper agricultural practices, comprehensive monitoring, and management strategies to reduce anthropogenic impacts on environmental resistance.}, } @article {pmid40071515, year = {2025}, author = {Medina, JS and Zhang, S and Narayanasamy, S and Wang, C and Al-Gashgari, B and Hong, PY}, title = {Metagenomic Insights in Antimicrobial Resistance Threats in Sludge from Aerobic and Anaerobic Membrane Bioreactors.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c10879}, pmid = {40071515}, issn = {1520-5851}, abstract = {Sludge is a biohazardous solid waste that is produced during wastewater treatment. It contains antibiotic resistance genes (ARGs) that pose significant antimicrobial resistance (AMR) threats. Herein, aerobic and anaerobic membrane bioreactors (AeMBRs and AnMBRs, respectively) were compared in terms of the volume of waste sludge generated by them, the presence of ARGs in the sludge, and the potential for horizontal gene transfer (HGT) events using metagenomics to determine which treatment process can better address AMR concerns associated with the generation of waste sludge. The estimated abundance of ARGs in the suspended sludge generated by the AnMBR per treated volume is, on average, 5-55 times lower than that of sludge generated by the AeMBR. Additionally, the ratio of potential HGT in the two independent runs was lower in the anaerobic sludge (0.6 and 0.9) compared with that in the aerobic sludge (2.4 and 1.6). The AnMBR sludge exhibited reduced HGT of ARGs involving potential opportunistic pathogens (0.09) compared with the AeMBR sludge (0.27). Conversely, the AeMBR sludge displayed higher diversity and more transfer events, encompassing genes that confer resistance to quinolones, rifamycin, multidrug, aminoglycosides, and tetracycline. A significant portion of these ARGs were transferred to Burkholderia sp. By contrast, the AnMBR showed a lower abundance of mobile genetic elements associated with conjugation and exhibited less favorable conditions for natural transformation. Our findings suggest that the risk of potential HGT to opportunistic pathogens is greater in the AeMBR sludge than in AnMBR sludge.}, } @article {pmid40071205, year = {2025}, author = {Park, J and Park, T}, title = {Composite quantile regression approach to batch effect correction in microbiome data.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1484183}, doi = {10.3389/fmicb.2025.1484183}, pmid = {40071205}, issn = {1664-302X}, abstract = {BACKGROUND: Batch effects refer to data variations that arise from non-biological factors such as experimental conditions, equipment, and external factors. These effects are considered significant issues in the analysis of biological data since they can compromise data consistency and distort actual biological differences, which can severely skew the results of downstream analyses.

METHOD: In this study, we introduce a new approach that comprehensively addresses two types of batch effects: "systematic batch effects" which are consistent across all samples in a batch, and "nonsystematic batch effects" which vary depending on the variability of operational taxonomic units (OTUs) within each sample in the same batch. To address systematic batch effects, we apply a negative binomial regression model and correct for consistent batch influences by excluding fixed batch effects. Additionally, to handle nonsystematic batch effects, we employ composite quantile regression. By adjusting the distribution of OTUs to be similar based on a reference batch selected using the Kruskal-Walis test method, we consider the variability at the OTU level.

RESULTS: The performance of the model is evaluated and compared with existing methods using PERMANOVA R-squared values, Principal Coordinates Analysis (PCoA) plots and Average Silhouette Coefficient calculated with diverse distance-based metrics. The model is applied to three real microbiome datasets: Metagenomic urine control data, Human Immunodeficiency Virus Re-analysis Consortium data, and Men and Women Offering Understanding of Throat HPV study data. The results demonstrate that the model effectively corrects for batch effects across all datasets.}, } @article {pmid40070462, year = {2025}, author = {Amevor, FK and Uyanga, VA and Wu, L and Xu, D and Shu, G and Wang, Y and Zhao, X}, title = {Enhancing poultry health and productivity through the liver-gut axis with integrated nutritional and immunological approaches: a mini-review.}, journal = {Frontiers in physiology}, volume = {16}, number = {}, pages = {1537099}, doi = {10.3389/fphys.2025.1537099}, pmid = {40070462}, issn = {1664-042X}, abstract = {The liver-gut axis plays a central role in maintaining the health and productivity of poultry. In addition, the liver-gut axis serves as a key regulator of digestion, metabolism, immunity, and detoxification. The gut, with its diverse microbiota, is the primary site for nutrient absorption and immune modulation, while the liver metabolizes nutrients, detoxifies harmful substances, and acts as a frontline defense against pathogens translocated from the gut. Disruptions in this interconnected system, including gut dysbiosis or liver inflammation, can lead to compromised immunity and reduced productivity. This mini-review explores integrated nutritional and immunological strategies aimed at optimizing the liver-gut axis to enhance poultry performance. Nutritional interventions, such as the use of flavonoids, vitamins, amino acids, micronutrients, probiotics, prebiotics, and synbiotics, have demonstrated their potential to support liver and gut health. Dietary components such as phytogenic additives, fiber, and fatty acids further contribute to immune modulation and systemic health. Immunological approaches, such as beta-glucans and in ovo stimulation, and molecular approaches, including advanced genetic techniques, offer additional avenues for improving disease resistance and organ function. Despite notable advancements, challenges including antibiotic resistance, environmental stressors, and implementation costs persist. Emerging technologies like metagenomics, metabolomics, and precision breeding offer innovative solutions to enhance liver-gut interactions. This review underscores recent advancements in understanding the liver-gut axis and calls for holistic strategies to improve sustainable poultry production. Future research should integrate these approaches to enhance resilience, productivity, and sustainability in the poultry industry.}, } @article {pmid40069804, year = {2025}, author = {Ye, X and Sahana, G and Lund, MS and Li, B and Cai, Z}, title = {Network analyses unraveled the complex interactions in the rumen microbiota associated with methane emission in dairy cattle.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {24}, pmid = {40069804}, issn = {2524-4671}, abstract = {BACKGROUND: Methane emissions from livestock, particularly from dairy cattle, represent a significant source of greenhouse gas, contributing to the global climate crisis. Understanding the complex interactions within the rumen microbiota that influence methane emissions is crucial for developing effective mitigation strategies.

RESULTS: This study employed Weighted Gene Co-expression Network Analysis to investigate the complex interactions within the rumen microbiota that influence methane emissions. By integrating extensive rumen microbiota sequencing data with precise methane emission measurements in 750 Holstein dairy cattle, our research identified distinct microbial communities and their associations with methane production. Key findings revealed that the blue module from network analysis was significantly correlated (0.45) with methane emissions. In this module, taxa included the genera Prevotella and Methanobrevibactor, along with species such as Prevotella brevis, Prevotella ruminicola, Prevotella baroniae, Prevotella bryantii, Lachnobacterium bovis, and Methanomassiliicoccus luminyensis are the key components to drive the complex networks. However, the absence of metagenomics sequencing is difficult to reveal the deeper taxa level and functional profiles.

CONCLUSIONS: The application of Weighted Gene Co-expression Network Analysis provided a comprehensive understanding of the microbiota-methane emission relationship, serving as an innovative approach for microbiota-phenotype association studies in cattle. Our findings underscore the importance of microbiota-trait and microbiota-microbiota associations related to methane emission in dairy cattle, contributing to a systematic understanding of methane production in cattle. This research offers key information on microbial management for mitigating environmental impact on the cattle population.}, } @article {pmid40069605, year = {2025}, author = {Zhang, H and Wang, Y and Luo, Z and Zhang, B and Lan, X and Xu, L and Li, X and Huang, Z and Bai, J and Hu, D}, title = {Gut microbiome reveals the trophic variation and significant adaption of three sympatric forest-dwelling ungulates on the eastern Qinghai-Xizang Plateau.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {128}, pmid = {40069605}, issn = {1471-2180}, support = {YC-20018//Zhangzhou Pientzehuang Pharmaceutical Co., Ltd./ ; 2023I0046//Supported by Science and Technology Planning Project of Fujian Province, China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *RNA, Ribosomal, 16S/genetics ; China ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Phylogeny ; Forests ; Metagenomics ; Sympatry ; Adaptation, Physiological ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; Ruminants/microbiology ; }, abstract = {BACKGROUND: The gut microbiome of herbivorous mammals regulates numerous physiological processes, including digestion and energy metabolism. The complex stomach architecture of ruminants, in conjunction with the metabolic capabilities of their microbiota, confers a considerable adaptive advantage to these animals. Nevertheless, a significant gap persists in comparative studies on the variations in the gut microbiome among sympatric ruminants and their potential adaptive implications. Accordingly, in this study, 16S rRNA gene sequencing and metagenomic approaches were used to analyse the composition and functional attributes of the gut microbiome of sympatric Moschus chrysogaster, Capricornis sumatraensis, and Cervus albirostris inhabiting the eastern periphery of the Qinghai-Xizang Plateau.

RESULTS: The gut microbiome of C. albirostris exhibited a higher diversity than that of M. chrysogaster and C. sumatraensis, whereas those of M. chrysogaster and C. sumatraensis were similar. Although species-specific variations existed among the three mammalian microbiomes, the microbiomes of C. albirostris and C. sumatraensis were more similar, whereas that of M. chrysogaster was markedly distinct. Metagenomic analysis revealed a pattern of functional convergence in the gut microbiome of the three species, with the gut microbiome of C. albirostris exhibiting a pronounced emphasis on carbohydrate metabolism, significantly surpassing that of M. chrysogaster and C. sumatraensis. Compared to the other two species, the gut microbiome of C. sumatraensis presented significantly elevated levels of amino acids and energy metabolism, whereas that of M. chrysogaster presented an increased capacity for 3-hydroxyacyl- [acyl carrier protein]-dehydratase production.

CONCLUSION: These findings suggest that the gut microbiome of sympatric M. chrysogaster, C. sumatraensis, and C. albirostris tend to converge. Metabolic variations within their gut microbiome may result in differential food resource utilisation, potentially indicating significant nutritional and ecological trait characteristics for stable coexistence.}, } @article {pmid40069560, year = {2025}, author = {Breselge, S and Skibinska, I and Yin, X and Brennan, L and Kilcawley, K and Cotter, PD}, title = {The core microbiomes and associated metabolic potential of water kefir as revealed by pan multi-omics.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {415}, pmid = {40069560}, issn = {2399-3642}, support = {818368//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; SFI/12/RC/2273_P2//Science Foundation Ireland (SFI)/ ; USIRL-2019-1//Science Foundation Ireland (SFI)/ ; SFI/16/RC/3835//Department of Agriculture, Food and the Marine (DAFM)/ ; TC/2018/0025//Enterprise Ireland/ ; }, mesh = {*Fermentation ; *Kefir/microbiology ; *Microbiota/genetics ; Metagenomics/methods ; Bacteria/metabolism/genetics/classification ; Metabolomics/methods ; Food Microbiology ; Water/metabolism ; Multiomics ; }, abstract = {Water kefir (WK) is an artisanal fermented beverage made from sugary water, optional fruits and WK grains. WK grains can be reused to start new fermentations. Here we investigate the microbial composition and function of 69 WK grains and their ferments by shotgun metagenomics. A subset of samples was subjected to metabolomic, including volatilomic, analysis. The impact of different fermentation practices on microbial composition and fermentation characteristics was analysed and it was noted that, for example, the common practice of drying water kefir grains significantly reduces microbial diversity and negatively impacts subsequent grain growth. Metagenomic analysis allowed the detection of 96 species within WK, the definition of core genera and the detection of different community states after 48 h of fermentation. A total of 485 bacterial metagenome assembled genomes were obtained and 18 putatively novel species were predicted. Metabolite and volatile analysis show associations between key species with flavour compounds. We show the complex microbial composition of WK and links between fermentation practices, microbes and the fermented product. The results can be used as a foundation for the selection of species for large scale WK production with desired flavour profiles and to guide the regulatory framework for commercial WK production.}, } @article {pmid40068786, year = {2025}, author = {Wang, L and Zhao, G and Guo, W and Li, Y and Chen, J and Niu, L}, title = {Microbial transformation of sulfur-containing dissolved organic matter in the intertidal zone of a mountainous river estuary responding to tidal fluctuation.}, journal = {Environmental research}, volume = {274}, number = {}, pages = {121363}, doi = {10.1016/j.envres.2025.121363}, pmid = {40068786}, issn = {1096-0953}, abstract = {Tidal fluctuation disturbances and amplified anthropogenic activities are defining characteristics of the intertidal zones of mountainous river estuaries. The accumulation and degradation of organic matter and nutrients in the sediments result in a complex element migration and transformation dynamics. Nonetheless, microbial transformation of dissolved organic sulfur (DOS) in the intertidal sediments upon tidal fluctuation remains poorly understood. Here, by taking a representative small mountainous river estuary in southeast China as an example, we synthesize evidence describing the composition of dissolved organic matter (DOM), microbial community structure and metabolic functions in sediments of variable depths (0-80 cm) at both high and low tide via FT-ICR-MS and metagenomic approach. Labile DOM, e.g., aliphatic and proteins were more inclined to be enriched in shallow sediments (0-30 cm). Upon tidal inundation, Thaumarchaeota was verified to facilitate the accumulation of recalcitrant organic matter through the mevalonate pathway, elevating the proportion of carboxyl-rich alicyclic molecules (CRAMs) and lignins in sediments. Whereas during ebb period, the microbial production of DOS through assimilated sulfate reduction (ASR) was signally intensified, contributing to the accumulation of sulfur-containing organic matter in deeper sediments. Based on the associations between Kyoto encyclopedia of Genes and Genomes modules and DOM formulas, cobalamin biosynthesis, ASR, and cysteine biosynthesis were observed positively correlated with the accumulation of sulfur-containing organic matter. Microbial community exhibited obvious taxonomic and functional variations between flood and ebb states. Nitrososphaerta in shallow sediments (0∼30 cm) was beneficial for the production of nitrogen-containing organic matter, while Bathyarchaeota and Chloroflexota in deep sediments (70-80 cm) predominantly governed the mineralization of organic matter. We firstly provided metagenomic evidence for the microbial transformation of sulfur-containing dissolved organic matter in the intertidal zone of a mountainous river estuary, which will be key to predicting coastal carbon storage and offer an important scientific basis for formulating intertidal ecosystem management and restoration strategies.}, } @article {pmid40068396, year = {2025}, author = {Guo, M and Wu, Y and Huang, H and Li, S and Zhao, L and Cao, J and Wang, C}, title = {Revealing the critical role of rare bacterial communities in shaping antibiotic resistance genes in saline soils through metagenomic analysis.}, journal = {Journal of hazardous materials}, volume = {491}, number = {}, pages = {137848}, doi = {10.1016/j.jhazmat.2025.137848}, pmid = {40068396}, issn = {1873-3336}, abstract = {Salinity is considered one of the basic abiotic factors influencing the diversity and distribution of antibiotic resistance genes (ARGs) in soils, yet little is known about the distribution and driving factors of ARGs in naturally saline soils. In this study, metagenomic analysis was conducted to explore the intricate dynamics among soil salinity, microbial community structure and ARGs propagation, with a particular focus on the key contribution of rare potential-hosts of ARGs in light and heavy saline soils. The findings revealed that salinity was significantly negatively correlated with the abundance of ARGs, light saline soils hosted a greater abundance of ARGs than high saline soils, with particularly significant enrichment in genes conferring resistance to multidrug, vancomycin, bacitracin and tetracenomycin C. Proteobacteria and Actinobacteria were identified as primary hosts for ARGs. Notably, rare potential hosts of ARGs play a crucial role in shaping the abundance of ARGs despite their low relative abundance (0.85 %), significantly influencing the relative abundance of ARGs in light and heavy saline soils. The average degree of rare potential-hosts of ARGs was found to be higher in light saline soils (average degree = 45.729 and 25.923 in light and heavy saline soils, respectively), and there was stronger interaction connected between microorganisms (edges = 35,760 and 20,259 in light and heavy saline soils, respectively). Also, microbial community niche width and niche overlap of rare potential-hosts of ARGs in light saline soils were significantly greater than that in heavy saline soils. This work emphasizes the importance of bacterial communities of rare potential-hosts of ARGs on antibiotic resistome, and provides advanced insights into the fate and dissemination of ARGs in saline soils.}, } @article {pmid40068378, year = {2025}, author = {Weng, YT and Huang, CK and Cheng, A and Ruan, SY and Wang, JT}, title = {Next-generation sequencing for rapid etiologic diagnosis of acute respiratory distress syndrome: A case of life-threatening leptospirosis.}, journal = {Journal of infection and public health}, volume = {18}, number = {6}, pages = {102727}, doi = {10.1016/j.jiph.2025.102727}, pmid = {40068378}, issn = {1876-035X}, abstract = {Leptospirosis is a zoonotic infection with public health implications and diverse clinical presentations, ranging from mild symptoms to severe, life-threatening disease. In critical cases, it can cause multiorgan failure and death. Diagnosis is typically based on clinical suspicion and confirmed by laboratory testing. However, in acute, life-threatening cases, obtaining a history of exposure and recognizing early symptoms may be challenging. Traditional diagnostic methods for identifying causative pathogens are time-consuming and limited. Next-generation sequencing (NGS) has emerged as a novel diagnostic tool that identifies pathogens using DNA or RNA from bodily fluids, offering more timely, unbiased results, especially for fastidious or non-culturable organisms.}, } @article {pmid40068343, year = {2025}, author = {Almarhabi, H and Sarhan, A and Alharbi, A and Al-Amri, A and Ahamed, MF and Hala, S}, title = {Multifocal osteolytic lesions as an initial presentation of mycobacterium riyadhense: Case report and literature review.}, journal = {Journal of infection and public health}, volume = {18}, number = {5}, pages = {102741}, doi = {10.1016/j.jiph.2025.102741}, pmid = {40068343}, issn = {1876-035X}, abstract = {Mycobacterium riyadhense is a newly discovered, slow-growing nontuberculous mycobacterium with an emerging global distribution. We report a case of multifocal osteolytic lesions as the first sign of infection in a previously healthy 39-year-old female. M. riyadhense was detected in this case using next-generation metagenomic sequencing after it failed to be identified with conventional methods. The patient received 12 months of therapy with isoniazid, rifampin, and ethambutol, with the addition of moxifloxacin and clarithromycin in the first four months, and had a full return to health with no detectable disease at the last follow-up.}, } @article {pmid40068342, year = {2025}, author = {Song, R and Lv, B and He, Z and Li, H and Wang, H}, title = {Rhizosphere metabolite dynamics in continuous cropping of vineyards: Impact on microflora diversity and co-occurrence networks.}, journal = {Microbiological research}, volume = {296}, number = {}, pages = {128134}, doi = {10.1016/j.micres.2025.128134}, pmid = {40068342}, issn = {1618-0623}, abstract = {The metabolism of the crop rhizosphere affects microflora diversity and nutrient cycling. However, understanding rhizosphere metabolism in suitable crops within arid desert environments and its impact on microflora interactions remains limited. Through metagenomic and non-targeted metabolomic sequencing of rhizosphere soils from one uncultivated land and four vineyards with cropping years of 5, 10, 15 and 20 years, the critical importance of rhizosphere metabolites in maintaining bacterial and fungal diversity was elucidated. The results revealed that Nocardioides, Streptomyces, and Solirubrobacter were the relatively abundant bacterial genera in rhizosphere soils, while Rhizophagus, Glomus, and Pseudogymnoascus were the relatively abundant fungal genera. The composition of rhizosphere metabolic changed significantly during the continuous cropping of grapevines. Dimethylglycine, Formononetin, and Dehydroepiandrosterone were the most important metabolites. Enrichment analysis revealed significant involvement of metabolic pathways such as biosynthesis of amino acids, unsaturated fatty acids, and linoleic acid metabolism. Procrustes analysis highlighted stronger correlations between rhizosphere metabolites and bacterial community compared to those of fungal community. This suggests distinct responses of microflora to crop-released chemical elements across different soil habitats. Co-occurrence network analysis demonstrated complex associations between rhizosphere metabolites and soil microflora, the positive correlations between rhizosphere metabolites and microflora networks predominated over negative correlations. Partial least squares path model indicated that the effect of cropping years on rhizosphere metabolites was greater than that on bacterial microflora diversity. Futhermore, pH, total phosphorus, and alkali-hydrolyzed nitrogen were the key environmental factors affecting rhizosphere metabolites and microbial diversity. These results deepen our valuable insights into the complex biological processes that rhizosphere metabolites influence on microorganisms, and provide strong support for maintaining microbial diversity in farmland soils in arid regions.}, } @article {pmid40068284, year = {2025}, author = {Corbera-Rubio, F and Boersma, AS and de Vet, W and Pabst, M and van der Wielen, PWJJ and van Kessel, MAHJ and van Loosdrecht, MCM and van Halem, D and Lücker, S and Laureni, M}, title = {Biological methane removal by groundwater trickling biofiltration for emissions reduction.}, journal = {Water research}, volume = {279}, number = {}, pages = {123450}, doi = {10.1016/j.watres.2025.123450}, pmid = {40068284}, issn = {1879-2448}, abstract = {Methane removal is an essential step in drinking water production from methane-rich groundwaters. Conventional aeration-based stripping results in significant direct methane emissions, contributing up to one-third of a treatment plant's total carbon footprint. To address this, a full-scale trickling filter was operated for biological methane oxidation upstream of a submerged sand filter, and its performance was compared to a conventional aeration-submerged sand filtration set-up. Full-scale data were combined with ex-situ batch assays and metagenome-resolved metaproteomics to quantify the individual contribution of the main (a)biotic processes and characterize the enriched microbial communities. Both treatment setups fully removed methane, iron, ammonium, and manganese, yet the underlying mechanisms differed significantly. Methane was completely removed from the effluent after trickling filtration, with stripping and biological oxidation each accounting for half of the removal, thereby halving overall methane emissions. Methane-oxidizing bacteria not only outcompeted nitrifiers in the trickling filter, but also likely contributed directly to ammonia oxidation. In contrast to the submerged filter preceded by methane stripping, signatures of biological iron oxidation were almost completely absent in the trickling filter, suggesting that the presence of methane directly or indirectly promotes chemical iron oxidation. All systems had similar ex-situ manganese oxidation capacities, yet removal occurred only in the submerged filters but not the trickling filter. Ultimately, our results demonstrate that trickling filtration is effective in promoting biological methane oxidation at comparable produced drinking water quality, highlighting its potential for advancing sustainable drinking water production.}, } @article {pmid40067770, year = {2025}, author = {Dominguez, EG and McDonald, BR and Zhang, H and Stephens, MD and Dietmann, EC and Nedden, M and Byington, N and Thompson, S and Junak, M and Pepperell, CS and Kisat, MT}, title = {Enrichment of Microbial DNA in Plasma to Improve Pathogen Detection in Sepsis: A Pilot Study.}, journal = {Clinical chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1093/clinchem/hvaf011}, pmid = {40067770}, issn = {1530-8561}, support = {//the American Association for Surgery of Trauma Research and Education Fund Trauma Critical Care Scholarship/ ; K08GM148858/GF/NIH HHS/United States ; R01-AI113287//NIH/NIAID/ ; }, abstract = {BACKGROUND: Diagnosis of sepsis and timely identification of pathogens in critically ill patients remains challenging. Plasma metagenomic sequencing to detect microbial cell-free DNA (mDNA) has shown promise, but low abundance of mDNA in plasma limits sensitivity and necessitates high sequencing depth. mDNA is shorter and more fragmented than human cell-free DNA. Here, we evaluated whether combining single-stranded DNA (ssDNA) sequencing library preparation and size selection can enrich mDNA and improve pathogen detection.

METHODS: We prospectively enrolled 48 trauma patients and collected daily blood samples during the first 10 days of intensive care unit (ICU) admission. For patients with culture-proven infections, we extracted plasma DNA, prepared double-stranded DNA (dsDNA) and ssDNA sequencing libraries, and applied size selection to exclude fragments >110 bp. Following sequencing, we performed taxonomic classification, and evaluated differences in mDNA fractions and in sensitivity for pathogen detection (compared to background noise).

RESULTS: We analyzed 46 plasma samples from 5 patients who developed culture-proven infections, including 17 samples coincident with positive microbial cultures. Size-selected ssDNA libraries showed the total mDNA fraction 204-fold higher on average than conventional dsDNA libraries (P < 0.0001). However, for pathogen-specific DNA (at the genus level), the highest sensitivity was observed in size-selected dsDNA (82%), compared to dsDNA (41%), ssDNA (71%), and size-selected ssDNA (35%) library preparations.

CONCLUSIONS: Our results demonstrate that combining ssDNA library preparation together with fragment size selection improves mDNA yield, potentially reducing sequencing requirements. However, at the genus level, this combination also increases background noise, which limits sensitivity for pathogen detection.}, } @article {pmid40067020, year = {2025}, author = {Kaminsky, LM and Burghardt, L and Bell, TH}, title = {Evolving a plant-beneficial bacterium in soil vs. nutrient-rich liquid culture has contrasting effects on in-soil fitness.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0208524}, doi = {10.1128/aem.02085-24}, pmid = {40067020}, issn = {1098-5336}, abstract = {UNLABELLED: Inoculation of plant-beneficial microbes into agricultural soils can improve crop growth, but such outcomes depend on microbial survival. Here, we assessed how exposure to prior environmental conditions impacts microbial in-soil fitness, particularly focusing on incubation in liquid culture as an unavoidable phase of inoculant production and on pre-incubation in target soils as a potential method to improve performance. We conducted experimental evolution on a phosphorus-solubilizing bacterial species, Priestia megaterium, in (i) soil only, (ii) liquid media only, and (iii) soil followed by liquid media, using population metagenomic sequencing to track mutations over time. Several typical in vitro evolutionary phenomena were observed in liquid media-incubated populations, including clonal interference, genetic hitchhiking, and mutation parallelism between replicate populations, particularly in the sporulation transcription factor spo0A. Liquid media-incubated populations also developed a clear fitness reduction in soil compared to the ancestral isolate. However, soil-incubated populations grew slowly, experienced far fewer generations despite longer absolute time, and accumulated minimal mutational changes. Correspondingly, soil-incubated populations did not display improved survival compared to the ancestral isolate in their target soils, though there did appear to be minor fitness reductions in unfamiliar soil. This work demonstrates that adaptation to liquid media and/or a native soil can impact bacterial fitness in new soil and that bacterial evolution in more complex real-world habitats does not closely resemble bacterial evolution in liquid media.

IMPORTANCE: Innovative solutions are needed to address emerging challenges in agriculture while reducing its environmental footprint. Management of soil microbiomes could contribute to this effort, as plant growth-promoting microorganisms provide key ecosystem services that support crops. Yet, inoculating beneficial microbes into farm soils yields unreliable results. We require a greater knowledge of the ecology of these taxa to improve their functioning in sustainable agroecosystems. In this report, we demonstrate that exposure to laboratory media and lingering adaptation to another soil can negatively impact the in-soil survival of a phosphorus-solubilizing bacterial species. We go further to highlight the underlying mutations that give rise to these patterns. These insights can be leveraged to improve our understanding of how soil-dwelling beneficial microorganisms adapt to different evolutionary pressures.}, } @article {pmid40066816, year = {2025}, author = {Karchmer, AW and Kaufman, NJ and Park, SY and Modi, RM and Abdul-Azim, A and van den Berg, P and Matos, JD and Kramer, DB and Zimetbaum, PJ}, title = {Quantitative Microbial Cell-Free DNA Sequencing from Plasma: A Potential Biomarker for the Diagnosis of Staphylococcal Infection of Cardiac Implantable Electronic Devices.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {}, number = {}, pages = {}, doi = {10.1093/cid/ciaf113}, pmid = {40066816}, issn = {1537-6591}, abstract = {BACKGROUND: Staphylococcus aureus bacteremia in patients with cardiac implantable electronic devices (CIED) is often associated with infective endocarditis (CIED-IE). The CIED-IE diagnosis is syndromic. Diagnostic uncertainty is common. Frequently, these patients are classified possible CIED-IE, resulting in guideline non-compliant treatment and heterogeneous outcomes. Improved outcomes require accurate diagnoses. In these patients, we evaluated whether metagenomic sequencing of microbial cell-free DNA (mcfDNA) in serial plasma specimens could improve diagnostic precision.

METHODS: We studied 16 patients with staphylococcal bacteremia who were classified definite or possible CIED-IE and recommended for device removal, if there was a positive blood culture within 7 days and no concurrent deep infection. Plasma specimens obtained at consent, before extraction, and during 96 hours after extraction underwent metagenomic sequencing and quantification of staphylococcal mcfDNA.

RESULTS: In 10 of 11 definite CIED-IE patients, mcfDNA persisted during antibiotic therapy for prolonged durations (median 11 days, IQR 7.5 days [7.5,15]). In these cases, mcfDNA concentration in plasma obtained early after lead extraction increased significantly and thereafter decreased rapidly. In 5 cases of possible CIED-IE, mcfDNA was undetectable after 6 days (IQR 2 days [5.5,7.5]) of antibiotic therapy and remained undetectable after CIED extraction. These mcfDNA patterns differ significantly (p=0.001), suggesting two distinct patient populations: one with definite CIED-IE and one without lead infection.

CONCLUSIONS: If confirmed, these mcfDNA patterns can serve as biomarkers, together with clinical features, to improve precision in diagnosing or rejecting S. aureus CIED-IE. Strategically timed mcfDNA testing before and after CIED extraction may aid in planning therapy.}, } @article {pmid40066307, year = {2025}, author = {Ci, X and Zhang, J and Lu, J and Qi, X and Ma, Y and Liu, W and Shi, J}, title = {Clinical characteristics of varicella-zoster virus central nervous system infection in 108 unimmunocompromised patients.}, journal = {Frontiers in neurology}, volume = {16}, number = {}, pages = {1554954}, pmid = {40066307}, issn = {1664-2295}, abstract = {BACKGROUND: Varicella-zoster virus (VZV) central nervous system infection is typically observed in immunocompromised patients, and there is a lack of studies involving large samples of non-immunocompromised individuals. In this study, we retrospectively analyzed 108 non-immunocompromised patients diagnosed with VZV central nervous system infection.

METHODS: This retrospective study was conducted in the Department of Neurology, Affiliated Nanjing Brain Hospital, Nanjing Medical University, China. Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) revealed a positive result for VZV with a sequence number greater than 3, leading to a clinical diagnosis of VZV central nervous system infection. We analyzed the patients' age, gender, clinical manifestations, blood routine, erythrocyte sedimentation rate (ESR), CSF examination, magnetic resonance imaging (MRI), electroencephalogram (EEG), and Activities of Daily Living (ADL) scale scores (Barthel Index) on the day of admission and 3 month post-discharge.

RESULTS: The study involved 108 patients, average age was 47.58 ± 2.91 years old (16 to 80), 33 were female (30.60%) and 75 were male (69.40%). Clinical manifestations were fever (63.9%), headache (88.9%), nausea (50%), vomiting (27.8%), fatigue (50%), dizziness (25.0%), herpes zoster (47.2%), chickenpox (0.9%), peripheral facial paralysis (19.4%), encephalopathy (5.6%), and myelitis (2.8%). The average white blood cell (WBC) count was 7.40 ± 0.48*10[9]/l, the average CRP was 6.58 ± 0.69 mg/L, and the average ESR was 7.79 ± 0.53 mm/h. 28.1% of patients exhibited elevated lumbar puncture pressure, the average lumbar puncture pressure was 155.41 ± 2.38 mmH2O; the average CSF WBC count was 196.60 ± 3.98*10^6/l, the average CSF protein was 1.35 ± 0.03 g/L, the average CSF glucose was 3.41 ± 0.03 mmoL/L, the average CSF chloride was 116.62 ± 0.15 mmoL/L, the average CSF IgG index was 0.66 ± 0.01, the average mNGS examination of VZV sequence count was 626.25 ± 5402.17. Head MRI scans revealed no new lesions; three patients' spinal cord MRI displayed short-segment, non-transverse, and non-continuous patchy long T1 and long T2 signals in the thoracic or cervical spinal cord. On the first day of admission, 41.7% of the patients achieved ADL score of 100 points, 19.4% scored between 41 and 99 points, and 38.9% of the patients scored less than 40 points. All patients received intravenous infusions of acyclovir with low-dose corticosteroids. An outpatient review conducted 3 months after discharge indicated 98.15% of the patients recovered well without any sequelae.

CONCLUSION: VZV encephalitis in immunocompetent individuals typically presents with mild clinical symptoms and has a favorable prognosis. VZV should be considered the common pathogen in the management of patients without immunocompeted condition with encephalitis.}, } @article {pmid40066275, year = {2025}, author = {Negrete-Méndez, H and Valencia-Toxqui, G and Sepúlveda-Robles, OA and Ríos-Castro, E and Hurtado-Cortés, JC and Flores, V and Cázares, A and Kameyama, L and Martínez-Peñafiel, E and Fernández-Ramírez, F}, title = {Genomic and proteomic analyses of Nus-dependent non-lambdoid phages reveal a novel coliphage group prevalent in gut: mEpimmI.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1480411}, pmid = {40066275}, issn = {1664-302X}, abstract = {INTRODUCTION: Nus-dependent Mexican Escherichia coli phages (mEp) were previously isolated from clinical samples of human feces. Approximately 50% corresponded to non-lambdoid temperate phages integrating a single immunity group, namely immunity I (mEpimmI), and these were as prevalent as the lambdoid phages identified in such collection.

METHODS: In this work, we present the structural and functional characterization of six representative mEpimmI phages (mEp010, mEp013, mEp021, mEp044, mEp515, and mEp554). In addition, we searched for homologous phages and prophages in the GenBank sequence database, and performed extensive phylogenetic analyses on the compiled genomes.

RESULTS: A biological feature-based characterization of these phages was carried out, focusing on proteins relevant to phage biological activities. This included mass spectrometry analysis of mEp021 virion structural proteins, and a series of infection assays to characterize the function of the main repressor protein and the lipoproteins associated with superinfection-exclusion; to identify the main host receptor proteins recognized by these phages and the prophage insertion sites within the host genome, which were associated with specific integrase sequence-types present in the viral genomes. Further, we compiled 42 complete homologous genomes corresponding to 38 prophages from E. coli strains and 4 phages from metagenomes, displaying a wide geographical distribution. Intergenomic distance analyses revealed that these phages differ from previously established phage clades, and whole-proteome similarity analyses yielded a cohesive and monophyletic branch, when compared to >5,600 phages with dsDNA genomes.

DISCUSSION: According to current taxonomic criteria, our results are consistent with a novel family demarcation, and the studied genomes correspond to 9 genera and 45 distinct species. Further, we identified 50 core genes displaying high synteny among the mEpimmI genomes, and these genes were found arranged in functional clusters. Furthermore, a biological feature-based characterization of these phages was carried out, with experiments focusing on proteins relevant to phage biological activities, revealing common traits as well as diversity within the group. With the integration of all these experimental and bioinformatics findings, our results indicate that the mEpimmI phages constitute a novel branch of Caudoviricetes distinct to other known siphovirus, contributing to the current knowledge on the diversity of phages infecting Escherichia coli.}, } @article {pmid40065594, year = {2025}, author = {Sun, Y and Yu, YT and Castillo, XO and Anderson, R and Wang, M and Sun, Q and Tallmadge, R and Sams, K and Reboul, G and Zehr, J and Brown, J and Wang, X and Marra, N and Stanhope, B and Grenier, J and Pusterla, N and Divers, T and Mittel, L and Goodman, LB}, title = {Investigation of the Blood Microbiome in Horses With Fever of Unknown Origin.}, journal = {Veterinary medicine and science}, volume = {11}, number = {2}, pages = {e70272}, doi = {10.1002/vms3.70272}, pmid = {40065594}, issn = {2053-1095}, support = {//Harry M. Zweig Memorial Fund for Equine Research/ ; 1U18FD006993//US Food and Drug Administration's Veterinary Laboratory Investigation and Response Network/ ; 1U18FD006716//US Food and Drug Administration's Veterinary Laboratory Investigation and Response Network/ ; W81XWH-22-1-0891//Department of Defense/ ; }, mesh = {Horses ; Animals ; *Horse Diseases/microbiology/virology/blood/epidemiology ; Case-Control Studies ; *Fever of Unknown Origin/veterinary/microbiology/etiology ; Microbiota ; Male ; Female ; }, abstract = {BACKGROUND: Fever of unknown origin (FUO) without a respiratory component is a frequent clinical presentation in horses. Multiple pathogens, both tick-borne and enteric, can be involved as etiologic agents. An additional potential mechanism is intestinal barrier dysfunction.

OBJECTIVES: This case-control study aimed to detect and associate microbial taxa in blood with disease state.

STUDY DESIGN: Areas known for a high prevalence of tick-borne diseases in humans were chosen to survey horses with FUO, which was defined as fever of 101.5°F or higher with no signs of respiratory illness or other recognisable diseases. Blood samples and clinical parameters were obtained from 52 FUO cases and also from matched controls from the same farms. An additional 23 febrile horses without matched controls were included.

METHODS: Broadly targeted polymerase chain reaction (PCR) amplification directed at conserved sequence regions of bacterial 16S rRNA, parasite 18S rRNA, coronavirus RdRp and parvovirus NS1 was performed, followed by deep sequencing. To control for contamination and identify taxa unique to the cases, metagenomic sequences from the controls were subtracted from those of the cases, and additional targeted molecular testing was performed. Sera were also tested for antibodies to equine coronavirus.

RESULTS: Over 60% of cases had intestinal microbial DNA circulating in the blood. Nineteen percent of cases were attributed to infection with Anaplasma phagocytophilum, of which two were subtyped as human-associated strains. A novel Erythroparvovirus was detected in two cases and two controls. Serum titres for equine coronavirus were elevated in some cases but not statistically different overall between the cases and controls.

MAIN LIMITATIONS: Not all pathogens are expected to circulate in blood, which was the sole focus of this study.

CONCLUSIONS: The presence of commensal gut microbes in blood of equine FUO cases is consistent with a compromised intestinal barrier, which is highlighted as a direction for future study.}, } @article {pmid40064809, year = {2025}, author = {Ouarabi, L and Taminiau, B and Daube, G and Barache, N and Bendali, F and Drider, D and Lucau-Danila, A}, title = {Insights into fungal diversity and dynamics of vaginal mycobiota.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, pmid = {40064809}, issn = {1678-4405}, support = {Alibiotech CPER/FEDER 2016-2021//Région Hauts-de-France/ ; }, abstract = {Although less studied than its bacterial counterpart, the fungal component of the vaginal microbiota plays a critical role in maintaining vaginal homeostasis. Most research on the composition of the vaginal mycobiota has focused on pathological conditions, with relatively few studies involving healthy women. To gain comprehensive insights into the vaginal mycobiota of Algerian women in two different age groups, we performed a targeted metagenomic analysis using ITS2 region sequencing data from 14 vaginal samples collected from healthy women in reproductive and postmenopausal stages. A single dominant fungal species per individual was observed in both young and postmenopausal women, with differences in fungal community composition between the two groups being related to hormone levels. Our results show that Candida and Saccharomyces were the dominant genera in both young and postmenopausal women. Notably, the postmenopausal group had twice as many species, along with the presence of uncommon taxa such as Dipodascus and Fusarium, indicating greater taxonomic diversity. These findings suggest that menopause is associated with increased microbial variability, likely due to hormonal changes that disrupt the vaginal environment. This study paves the way for more extensive analyses involving diverse age groups and ethnic backgrounds.}, } @article {pmid40064789, year = {2025}, author = {Wang, H and Ma, H and Yan, H and Pei, Z and Zhao, J and Zhang, H and Zhang, Z and Lu, W}, title = {Study on the Effect of Bifidobacterium adolescentis CCFM1066 on Exercise Performance, Gut Microbiota, and Its Metabolites in Mice.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {40064789}, issn = {1867-1314}, support = {32172212, 32394052//National Natural Science Foundation of China/ ; 2022YFF1100403//National Key Research and Development Program of China/ ; WMCC202403//Cohort and Clinical Research Program of Wuxi Medical Center, Nanjing Medical University/ ; }, abstract = {Prolonged high-intensity exercise consumes significant energy, leading to fatigue and decreased performance. This study explores the effects of Bifidobacterium adolescentis CCFM1066 on exercise performance, gut microbiota, and its metabolites in mice. The results of the mouse experiments showed the mice which were intervened by Bifidobacterium adolescentis CCFM1066 have a significant increase in exercise performance, including forceful swimming time, fatigue baton turning time, and forelimb grip strength. Through metagenomic sequencing and differential metabolites, analysis indicated that the intervention of CCFM1066 increased Lachnospiraceae bacterium, Parabacteroides goldsteinii, Bacteroides xylanisolvens, and Bifidobacterium adolescentis and altered the key metabolic pathways including protein digestion and absorption and biosynthesis of amino acids. Supplementation with CCFM1066 modulates the production of short-chain fatty acids (SCFAs) and fatty acid amides (FAAs) by gut microbiota, decreasing levels of lactic acid (LA), blood urea nitrogen (BUN), lactate dehydrogenase (LDH), and creatine kinase (CK) while increasing muscle and hepatic glycogen content, thus reducing central nervous system fatigue and thereby improving exercise endurance and performance. These findings provide new insights into nutritional interventions for sports performance.}, } @article {pmid40064739, year = {2025}, author = {Thakur, SS and González, SS and Suravajhala, P and Jain, SK and Yadav, S and Narayan, KS and Esack, E and Kuzyakov, Y and Ratnasari, A}, title = {Metagenomic insights of microbial functions under conventional and conservation agriculture.}, journal = {World journal of microbiology & biotechnology}, volume = {41}, number = {3}, pages = {100}, pmid = {40064739}, issn = {1573-0972}, support = {Grant ID: 3203/SKMCCC/EPCO/2021//Environmental Planning & Coordination Organisation (EPCO), Ministry of Environment, Government of Madhya Pradesh, India/ ; }, mesh = {*Soil Microbiology ; *Bacteria/genetics/classification/isolation & purification ; *Metagenomics ; *Agriculture ; *Archaea/genetics/classification ; *Soil/chemistry ; Metagenome ; Phylogeny ; Biodiversity ; Carbon/metabolism ; Nitrogen/metabolism ; }, abstract = {Agricultural practices such as conventional (CN) and conservation agriculture (CA) influence the composition and structure of soil microorganisms. We used short reads and genome-resolved metagenomic-based dual sequencing approaches to create a profile of bacterial and archaeal communities in hyperthermic Typic Haplustepts soil after seven years of CA and CN. The most differences in the physico-chemical and biological properties of soil were higher pH, organics carbon, available nitrogen and microbial biomass contents, activities of dehydrogenase, β-glucosidase, and arylsulfatase, found in CA soil. The dominant bacterial taxa under both management types were Pseudomonadota (46-48%), Acidobacteriota (12-13%), Planctomycetota (8-10%), Bacteroidota (7-8%), and Actinomycetota (6-7%). Nitrososphaerota (1.1-1.5%) was the predominant archaeal phyla in CA and CN soils. The alpha diversity was 1.5 times higher in CA compared to CN soils. Fourteen high-quality (HQ) metagenomic-assembled genomes (MAGs) were recovered from both groups. Four HQ metagenome-assembled genomes (MAGs) from the Pseudomonadota phylum were exclusively recovered from the CA soil. The dominance of this phylum in the CA soil might be correlated with its nutrient richness, as certain classes of Pseudomonadota, such as Alpha, Beta-, Gamma-, and Deltaproteobacteria, are known to be copiotrophic. Copiotrophic organisms thrive in nutrient-rich environments, which could explain their prevalence in the CA soil. CAZyme gene analysis showed that Glycoside Hydrolases (GH) and GlycosylTransferases (GT) classes are dominant in the CA group, possibly due to higher substrate availability from the application of crop residues, which provide a rich source of complex carbohydrates. Several biogeochemical gene families related to C1 compounds, hydrogen, oxygen, and sulfur metabolism were enriched in CA soils, suggesting these practices may contribute to a soil environment with increased organic matter content, microbial diversity, and nutrient availability. Overall, CA practices seemed to improve soil health by supporting soil microbial communities abundance.}, } @article {pmid40064231, year = {2025}, author = {Jia, Y and Huang, D and Lan, X and Sun, X and Lin, W and Sun, W and Wang, Y}, title = {Community structure and metabolic potentials of keystone taxa and their associated bacteriophages within rice root endophytic microbiome in response to metal(loid)s contamination.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {126028}, doi = {10.1016/j.envpol.2025.126028}, pmid = {40064231}, issn = {1873-6424}, abstract = {Heavy metal (HM) contamination of agricultural products is of global environmental concern as it directly threatened the food safety. Plant-associated microbiome, particularly endophytic microbiome, hold the potential for mitigating HM stress as well as promoting plant growth. The metabolic potentials of the endophytes, especially those under the HM stresses, have not been well addressed. Rice, a major staple food worldwide, is more vulnerable to HM contamination compared to other crops and therefore requires special attentions. Therefore, this study selected rice as the target plants. Geochemical analysis and amplicon sequencing were combined to characterize the rice root endophytic bacterial communities and identify keystone taxa in two HM-contaminated rice fields. Metagenomic analysis was employed to investigate the metabolic potentials of these keystone taxa. Burkholderiales and Rhizobiales were identified as predominant keystone taxa. The metagenome-assembled genome (MAG)s associated with these keystone populations suggested that they possessed diverse genetic potentials related to metal resistance and transformation (e.g., As resistance and cycling, V reduction, Cr efflux and reduction), and plant growth promotion (nitrogen fixation, phosphate solubilization, oxidative stress resistance, indole-3-acetic acid, and siderophore production). Moreover, bacteriophages encoding auxiliary metabolism genes (AMGs) associated with the HM resistance as well as nitrogen and phosphate acquisition were identified, suggesting that these phages may contribute to these crucial biogeochemical processes within rice roots. The current findings revealed the beneficial roles of rice endophytic keystone taxa and their associated bacteriophages within HM-contaminated rice root endophytic microbiome, which may provide valuable insights on future applications of employing root microbiome for safety management of agriculture productions.}, } @article {pmid40064141, year = {2025}, author = {She, Y and Wu, L and Qi, X and Sun, S and Li, Z}, title = {Aging behaviors intensify the impacts of microplastics on nitrate bioreduction-driven nitrogen cycling in freshwater sediments.}, journal = {Water research}, volume = {279}, number = {}, pages = {123448}, doi = {10.1016/j.watres.2025.123448}, pmid = {40064141}, issn = {1879-2448}, abstract = {Microplastics (MPs) inevitably undergo aging processes in natural environments; however, how aging behaviors influence the interactions between MPs exposures and nitrate bioreduction in freshwater sediments remains poorly understood. Here, we explored the distinct impacts of virgin and aged MPs (polystyrene (PS) and polylactic acid (PLA)) on nitrate bioreduction processes in lake sediments through a long-term microcosm experiment utilizing the [15]N isotope tracing technique and molecular analysis. Compared to virgin MPs, aged PLA significantly increased the rates of denitrification, anaerobic ammonium oxidation (anammox), and dissimilatory nitrate reduction to ammonium (DNRA) (p < 0.05), facilitating sediment nitrogen loss, while aged PS only significantly improved the rates of DNRA by 272-297 % and contributed to nitrogen retention in sediments. Metagenomic sequencing demonstrated that a more significant enrichment of functional genes responsible for nitrate bioreduction pathways occurred with aged MPs exposures than with virgin MPs. By combining analyses of MPs aging traits and the key drivers of nitrate bioreduction, we revealed that aging behaviors directly regulated sediment nutrient status (e.g., DOC/NOx[-] ratio) and microbiological properties (from genes to bacteria), thereby further determining the activity of nitrate bioreduction. This work provides new insights into the impacts of aged MPs on sediment nitrate reduction and highlights the role of MPs aging in future assessments of long-term MPs pollution in freshwater ecosystems.}, } @article {pmid40063888, year = {2025}, author = {Saraphol, B and Hinthong, W and Chienwichai, P and Pumipuntu, N and Reamtong, O and Srisook, T and Premsuriya, J}, title = {Analysis of the fecal microbiome and metabolome in dairy cows with different body condition scores.}, journal = {PloS one}, volume = {20}, number = {3}, pages = {e0319461}, pmid = {40063888}, issn = {1932-6203}, mesh = {Animals ; Cattle ; *Feces/microbiology ; *Metabolome ; Female ; *RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; }, abstract = {Holstein Friesian is the most popular breed of dairy cows worldwide due to its exceptional milk production capabilities. In dairy cow management, the body condition score (BCS) is a useful tool, serving as a reliable indicator of a cow's nutritional status and overall health. It is determined via a subjective visual and tactile assessment of fat cover and muscle mass. A low BCS is associated with decreased milk production and fertility. While genetic and nutritional factors have previously been associated with BCS, their effects are often moderate. In this study, we compared the fecal microbiome and the untargeted fecal metabolome of normal (BCS ≥ 3, n = 16) and thin (BCS < 3, n = 16) Holstein Friesian dairy cows. The 16S rRNA gene-based metagenomic analysis revealed that thin cows had significantly higher levels of Clostridiaceae, Erysipelotrichales, Erysipelotrichaceae, and Turicibacter, while normal cows had higher levels of Clostridiales_vadinBB60_group, UCG-010, Bacteroidaceae, Ruminococcaceae, Paludibacteraceae, Alistipes, and Bacteroides. The fecal metabolomic analysis showed that key signaling pathways, including the mechanistic target of rapamycin (mTOR), phosphatidylinositol 3-kinase (PI3K)-Akt, and AMP-activated protein kinase (AMPK) pathways, were enriched in thin cows. In addition, a significant correlation was observed between differential microbial taxa and metabolites. Notably, Clostridiaceae and Erysipelotrichaceae species are linked to inflammation, infectious diseases, and conditions such as ruminal acidosis. Additionally, the mTOR, PI3K-Akt, and AMPK pathways are known to be activated by both nutrient deficiencies and inflammation. We propose that, in addition to genetic and nutritional factors, gut microbiome dysbiosis may contribute to subclinical health conditions, such as chronic inflammation and acidosis, which indirectly affect the cow's BCS. These findings are guiding our ongoing research on the underlying health conditions in thin cows to better understand the role that the gut microbiome plays in the regulation of the body condition.}, } @article {pmid40063675, year = {2025}, author = {Chavarria, X and Park, HS and Oh, S and Kang, D and Choi, JH and Kim, M and Cho, YH and Yi, MH and Kim, JY}, title = {Using gut microbiome metagenomic hypervariable features for diabetes screening and typing through supervised machine learning.}, journal = {Microbial genomics}, volume = {11}, number = {3}, pages = {}, doi = {10.1099/mgen.0.001365}, pmid = {40063675}, issn = {2057-5858}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Diabetes Mellitus, Type 2/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Supervised Machine Learning ; *Diabetes Mellitus, Type 1/microbiology ; *Metagenomics/methods ; Male ; Female ; Middle Aged ; Adult ; Bacteria/genetics/classification/isolation & purification ; Metagenome ; Support Vector Machine ; Aged ; Algorithms ; }, abstract = {Diabetes mellitus is a complex metabolic disorder and one of the fastest-growing global public health concerns. The gut microbiota is implicated in the pathophysiology of various diseases, including diabetes. This study utilized 16S rRNA metagenomic data from a volunteer citizen science initiative to investigate microbial markers associated with diabetes status (positive or negative) and type (type 1 or type 2 diabetes mellitus) using supervised machine learning (ML) models. The diversity of the microbiome varied according to diabetes status and type. Differential microbial signatures between diabetes types and negative group revealed an increased presence of Brucellaceae, Ruminococcaceae, Clostridiaceae, Micrococcaceae, Barnesiellaceae and Fusobacteriaceae in subjects with diabetes type 1, and Veillonellaceae, Streptococcaceae and the order Gammaproteobacteria in subjects with diabetes type 2. The decision tree, elastic net, random forest (RF) and support vector machine with radial kernel ML algorithms were trained to screen and type diabetes based on microbial profiles of 76 subjects with type 1 diabetes, 366 subjects with type 2 diabetes and 250 subjects without diabetes. Using the 1000 most variable features, tree-based models were the highest-performing algorithms. The RF screening models achieved the best performance, with an average area under the receiver operating characteristic curve (AUC) of 0.76, although all models lacked sensitivity. Reducing the dataset to 500 features produced an AUC of 0.77 with sensitivity increasing by 74% from 0.46 to 0.80. Model performance improved for the classification of negative-status and type 2 diabetes. Diabetes type models performed best with 500 features, but the metric performed poorly across all model iterations. ML has the potential to facilitate early diagnosis of diabetes based on microbial profiles of the gut microbiome.}, } @article {pmid40063348, year = {2025}, author = {Koul, M and Kaushik, S and Singh, K and Sharma, D}, title = {VITALdb: to select the best viroinformatics tools for a desired virus or application.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {2}, pages = {}, doi = {10.1093/bib/bbaf084}, pmid = {40063348}, issn = {1477-4054}, support = {BT/2014-15/Plan/P-955//MHRD/ ; R.11013/51/2021-GIA/HR//DHR/ ; }, mesh = {Humans ; *Computational Biology/methods ; Antiviral Agents/therapeutic use ; COVID-19/virology/epidemiology ; SARS-CoV-2/genetics ; Viruses/genetics/classification ; Virus Diseases/virology ; Algorithms ; Software ; }, abstract = {The recent pandemics of viral diseases, COVID-19/mpox (humans) and lumpy skin disease (cattle), have kept us glued to viral research. These pandemics along with the recent human metapneumovirus outbreak have exposed the urgency for early diagnosis of viral infections, vaccine development, and discovery of novel antiviral drugs and therapeutics. To support this, there is an armamentarium of virus-specific computational tools that are currently available. VITALdb (VIroinformatics Tools and ALgorithms database) is a resource of ~360 viroinformatics tools encompassing all major viruses (SARS-CoV-2, influenza virus, human immunodeficiency virus, papillomavirus, herpes simplex virus, hepatitis virus, dengue virus, Ebola virus, Zika virus, etc.) and several diverse applications [structural and functional annotation, antiviral peptides development, subspecies characterization, recognition of viral recombination, inhibitors identification, phylogenetic analysis, virus-host prediction, viral metagenomics, detection of mutation(s), primer designing, etc.]. Resources, tools, and other utilities mentioned in this article will not only facilitate further developments in the realm of viroinformatics but also provide tremendous fillip to translate fundamental knowledge into applied research. Most importantly, VITALdb is an inevitable tool for selecting the best tool(s) to carry out a desired task and hence will prove to be a vital database (VITALdb) for the scientific community. Database URL: https://compbio.iitr.ac.in/vitaldb.}, } @article {pmid40062866, year = {2025}, author = {Ingle, DJ and Walsh, CJ and Samuel, GR and Wick, RR and Davidovich, N and Fiocchi, E and Judd, LM and Elliman, J and Owens, L and Stinear, TP and Basso, A and Pretto, T and Newton, HJ}, title = {The complete genome sequence of the crayfish pathogen Candidatus Paracoxiella cheracis n.g. n.sp. provides insight into pathogenesis and the phylogeny of the Coxiellaceae family.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0100224}, doi = {10.1128/msphere.01002-24}, pmid = {40062866}, issn = {2379-5042}, abstract = {The Coxiellaceae bacterial family, within the order Legionellales, is defined by a collection of poorly characterized obligate intracellular bacteria. The zoonotic pathogen and causative agent of human Q fever, Coxiella burnetii, represents the best-characterized member of this family. Coxiellaceae establish replicative niches within diverse host cells and rely on their host for survival, making them challenging to isolate and cultivate within a laboratory setting. Here, we describe a new genus within the Coxiellaceae family that has been previously shown to infect economically significant freshwater crayfish. Using culture-independent long-read metagenomics, we reconstructed the complete genome of this novel organism and demonstrate that the species previously referred to as Candidatus Coxiella cheraxi represents a novel genus within this family, herein denoted Candidatus Paracoxiella cheracis. Interestingly, we demonstrate that Candidatus P. cheracis encodes a complete, putatively functional Dot/Icm type 4 secretion system that likely mediates the intracellular success of this pathogen. In silico analysis defined a unique repertoire of Dot/Icm effector proteins and highlighted homologs of several important C. burnetii effectors, including a homolog of CpeB that was demonstrated to be a Dot/Icm substrate in C. burnetii.IMPORTANCEUsing long-read sequencing technology, we have uncovered the full genome sequence of Candidatus Paracoxiella cheracis, a pathogen of economic importance in aquaculture. Analysis of this sequence has revealed new insights into this novel member of the Coxiellaceae family, demonstrating that it represents a new genus within this poorly characterized family of intracellular organisms. Importantly, the genome sequence reveals invaluable information that will support diagnostics and potentially both preventative and treatment strategies within crayfish breeding facilities. Candidatus P. cheracis also represents a new member of Dot/Icm pathogens that rely on this system to establish an intracellular niche. Candidatus P. cheracis possesses a unique cohort of putative Dot/Icm substrates that constitute a collection of new eukaryotic cell biology-manipulating effector proteins.}, } @article {pmid40062856, year = {2025}, author = {Kralj, JG and Servetas, SL and Forry, SP and Hunter, ME and Dootz, JN and Jackson, SA}, title = {Analytical assessment of metagenomic workflows for pathogen detection with NIST RM 8376 and two sample matrices.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0280624}, doi = {10.1128/spectrum.02806-24}, pmid = {40062856}, issn = {2165-0497}, abstract = {We assessed the analytical performance of metagenomic workflows using NIST Reference Material (RM) 8376 DNA from bacterial pathogens spiked into two simulated clinical samples: cerebrospinal fluid (CSF) and stool. Sequencing and taxonomic classification were used to generate signals for each sample and taxa of interest and to estimate the limit of detection (LOD), the linearity of response, and linear dynamic range. We found that the LODs for taxa spiked into CSF ranged from approximately 100 to 300 copy/mL, with a linearity of 0.96 to 0.99. For stool, the LODs ranged from 10 to 221 kcopy/mL, with a linearity of 0.99 to 1.01. Furthermore, discriminating different E. coli strains proved to be workflow-dependent as only one classifier:database combination of the three tested showed the ability to differentiate the two pathogenic and commensal strains. Surprisingly, when we compared the linear response of the same taxa in the two different sample types, we found those functions to be the same, despite large differences in LODs. This suggests that the "agnostic diagnostic" theory for metagenomics (i.e., any organism can be identified because DNA is the measurand) may apply to different target organisms and different sample types. Because we are using RMs, we were able to generate quantitative analytical performance metrics for each workflow and sample set, enabling relatively rapid workflow screening before employing clinical samples. This makes these RMs a useful tool that will generate data needed to support the translation of metagenomics into regulated use.IMPORTANCEAssessing the analytical performance of metagenomic workflows, especially when developing clinical diagnostics, is foundational for ensuring that the measurements underlying a diagnosis are supported by rigorous characterization. To facilitate the translation of metagenomics into clinical practice, workflows must be tested using control samples designed to probe the analytical limitations (e.g., limit of detection). Spike-ins allow developers to generate fit-for-purpose control samples for initial workflow assessments and inform decisions about further development. However, clinical sample types include a wide range of compositions and concentrations, each presenting different detection challenges. In this work, we demonstrate how spike-ins elucidate workflow performance in two highly dissimilar sample types (stool and CSF), and we provide evidence that detection of individual organisms is unaffected by background sample composition, making detection sample-agnostic within a workflow. These demonstrations and performance insights will facilitate the translation of the technology to the clinic.}, } @article {pmid40062854, year = {2025}, author = {Zhang, F and Luan, J and Suo, L and Wang, H and Zhao, Y and Sun, T and Ni, Y and Cao, H and Zou, X and Liu, B}, title = {Altered gut microbiota and metabolite profiles in community-acquired pneumonia: a metagenomic and metabolomic study.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0263924}, doi = {10.1128/spectrum.02639-24}, pmid = {40062854}, issn = {2165-0497}, abstract = {UNLABELLED: Emerging evidence suggests that altered gut microbiota is linked to community-acquired pneumonia (CAP), but the potential mechanisms by which gut microbiota and its metabolites contribute to the development of CAP remain unclear. Fecal samples from 32 CAP patients and 36 healthy controls were analyzed through metagenomic sequencing and metabolomic profiling. The gut microbiota composition in CAP patients showed significant differences and lower diversity compared to healthy controls. Genera involved in short-chain fatty acid (SCFA) production, such as Faecalibacterium, Ruminococcus, and Eubacterium, as well as species like Faecalibacterium prausnitzii, Bifidobacterium adolescentis, Eubacterium rectale, Prevotella copri, and Ruminococcus bromii, were significantly depleted in CAP patients. Bacterial co-occurrence network analysis revealed an over-representation of pro-inflammatory bacteria, which contributed to the core gut microbiome in CAP patients. Metabolomic analysis of fecal samples identified a distinct metabolic profile, with a notable increase in arachidonic acid, but a decrease in secondary bile acids, such as deoxycholic acid, lithocholic acid, and ursodeoxycholic acid, compared to healthy controls. Spearman correlation analysis between differential microbiota and bile acids showed that Faecalibacterium prausnitzii, Bifidobacterium adolescentis, Eubacterium rectale, and Prevotella copri were positively correlated with ursocholic acid, lithocholic acid, and ursodeoxycholic acid, respectively. Our results suggest that the reduction in secondary bile acids, insufficient production of SCFAs, and an overabundance of pro-inflammatory bacteria may contribute to metabolic inflammation in the body. These factors could play a key role in the pathogenesis of CAP, driven by gut microbiota alterations.

IMPORTANCE: This study presents a comprehensive metagenomic and metabolomic analysis of fecal samples from community-acquired pneumonia (CAP) patients, identifying key characteristics, such as decreased secondary bile acids, imbalanced short-chain fatty acid production, and increased pro-inflammatory bacteria. These findings provide valuable insights into the mechanisms linking gut microbiota alterations to CAP pathogenesis and suggest that targeting the gut microbiota could be a promising strategy for intervening in CAP.}, } @article {pmid40062772, year = {2025}, author = {Connolly, JP and Kelly, L}, title = {The physical biogeography of Fusobacterium nucleatum in health and disease.}, journal = {mBio}, volume = {}, number = {}, pages = {e0298924}, doi = {10.1128/mbio.02989-24}, pmid = {40062772}, issn = {2150-7511}, abstract = {UNLABELLED: Fusobacterium nucleatum (Fn) is an oral commensal inhabiting the human gingival plaque that is rarely found in the gut. However, in colorectal cancer (CRC), Fn can be isolated from stool samples and detected in metagenomes. We hypothesized that ecological characteristics of the gut are altered by disease, enabling Fn to colonize. Multiple genomically distinct populations of Fn exist, but their ecological preferences are unstudied. We identified six well-separated populations in 133 Fn genomes and used simulated metagenomes to demonstrate sensitive detection of populations in human oral and gut metagenomes. In 9,560 samples from 11 studies, Fn population C2 animalis is elevated in gut metagenomes from CRC and Crohn's disease patients and is observed more frequently in CRC stool samples than in the gingiva. Polymorphum, the most prevalent gingival Fn population, is significantly increased in Crohn's stool samples; this effect was significantly stronger in male hosts than in female. We find polymorphum genomes are enriched for biosynthetic gene clusters and fluoride exporters, while C2 animalis are high in iron transporters. Fn populations thus associate with specific clinical and demographic phenotypes and harbor distinct functional features. Ecological differences in closely related groups of bacteria inform microbiome impacts on human health.

IMPORTANCE: Fusobacterium nucleatum is a bacterium normally found in the gingiva. F. nucleatum generally does not colonize the healthy gut, but is observed in approximately a third of colorectal cancer (CRC) patient guts. F. nucleatum's presence in the gut during CRC has been linked to worse prognosis and increased tumor proliferation. Here, we describe the population structure of F. nucleatum in oral and gut microbiomes. We report substantial diversity in gene carriage among six distinct populations of F. nucleatum and identify population disease and body-site preferences. We find the C2 animalis population is more common in the CRC gut than in the gingiva and is enriched for iron transporters, which support gut colonization in known pathogens. We find that C2 animalis is also enriched in Crohn's disease and type 2 diabetes, suggesting ecological commonalities between the three diseases. Our work shows that closely related bacteria can have different associations with human physiology.}, } @article {pmid40062294, year = {2025}, author = {Kuzudisli, C and Bakir-Gungor, B and Qaqish, B and Yousef, M}, title = {RCE-IFE: recursive cluster elimination with intra-cluster feature elimination.}, journal = {PeerJ. Computer science}, volume = {11}, number = {}, pages = {e2528}, pmid = {40062294}, issn = {2376-5992}, abstract = {The computational and interpretational difficulties caused by the ever-increasing dimensionality of biological data generated by new technologies pose a significant challenge. Feature selection (FS) methods aim to reduce the dimension, and feature grouping has emerged as a foundation for FS techniques that seek to detect strong correlations among features and identify irrelevant features. In this work, we propose the Recursive Cluster Elimination with Intra-Cluster Feature Elimination (RCE-IFE) method that utilizes feature grouping and iterates grouping and elimination steps in a supervised context. We assess dimensionality reduction and discriminatory capabilities of RCE-IFE on various high-dimensional datasets from different biological domains. For a set of gene expression, microRNA (miRNA) expression, and methylation datasets, the performance of RCE-IFE is comparatively evaluated with RCE-IFE-SVM (the SVM-adapted version of RCE-IFE) and SVM-RCE. On average, RCE-IFE attains an area under the curve (AUC) of 0.85 among tested expression datasets with the fewest features and the shortest running time, while RCE-IFE-SVM (the SVM-adapted version of RCE-IFE) and SVM-RCE achieve similar AUCs of 0.84 and 0.83, respectively. RCE-IFE and SVM-RCE yield AUCs of 0.79 and 0.68, respectively when averaged over seven different metagenomics datasets, with RCE-IFE significantly reducing feature subsets. Furthermore, RCE-IFE surpasses several state-of-the-art FS methods, such as Minimum Redundancy Maximum Relevance (MRMR), Fast Correlation-Based Filter (FCBF), Information Gain (IG), Conditional Mutual Information Maximization (CMIM), SelectKBest (SKB), and eXtreme Gradient Boosting (XGBoost), obtaining an average AUC of 0.76 on five gene expression datasets. Compared with a similar tool, Multi-stage, RCE-IFE gives a similar average accuracy rate of 89.27% using fewer features on four cancer-related datasets. The comparability of RCE-IFE is also verified with other biological domain knowledge-based Grouping-Scoring-Modeling (G-S-M) tools, including mirGediNET, 3Mint, and miRcorrNet. Additionally, the biological relevance of the selected features by RCE-IFE is evaluated. The proposed method also exhibits high consistency in terms of the selected features across multiple runs. Our experimental findings imply that RCE-IFE provides robust classifier performance and significantly reduces feature size while maintaining feature relevance and consistency.}, } @article {pmid40061332, year = {2025}, author = {Moore, CM and Secor, EA and Fairbanks-Mahnke, A and Everman, JL and Elhawary, JR and Witonsky, JI and Pruesse, E and Chang, CH and Contreras, MG and Eng, C and Canales, K and Rosado, T and Hu, D and Huntsman, S and Jackson, ND and Li, Y and Lopez, N and Valentin, AM and Medina, V and Montanez-Lopez, CA and Morin, A and Nieves, NA and Oh, SS and Otero, RA and Colon, R and Rodriguez, L and Sajuthi, SP and Salazar, S and Serrano, G and Morales, EV and Vazquez, G and Morales, NV and Williams, BJM and Zhang, P and Sheppard, D and Rodriguez Santana, JR and Seibold, MA}, title = {Independent and interactive effects of viral species on risk for lower respiratory tract illnesses in early life.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.02.25.25322678}, pmid = {40061332}, abstract = {IMPORTANCE: All children experience upper respiratory tract illnesses (URI) caused by viral infections. However, some of these illnesses progress to the lower airways. Although studies have found infection with certain viral species are more likely to trigger lower respiratory illnesses (LRIs), a comprehensive analysis of viruses underlying early-life LRIs is lacking.

OBJECTIVE: Determine the incidence of URIs, mild and severe LRIs (mLRI, sLRI) during the first 2 years of life and the association between viral respiratory pathogens and odds of LRIs versus URIs in Puerto Rican children, a population at high risk for respiratory disease.

Healthy mother-infant pairs were enrolled in the Puerto Rican Infant Metagenomic and Epidemiologic Study of Respiratory Outcomes birth cohort, in Caguas, Puerto Rico. Infants (n=2,061) were surveilled for respiratory illnesses during the first two years of life (March 2020 to April 2024). Nasal swabs from a subset of 1,363 illnesses from 774 participants were screened for 21 pathogens.

EXPOSURES: Infection with respiratory pathogens.

MAIN OUTCOMES AND MEASURES: URI, mLRI, and sLRI in the first two years of life.

RESULTS: RSV infections occurred in 23% of sLRIs and were associated with dramatically increased odds of sLRI vs URI (OR=9.28; 95% CI, 5.43-15.85). Metapneumovirus, parainfluenza, and non-SARS-CoV-2 coronavirus infections also increased odds of sLRIs. SARS-CoV-2 was associated with lower risk of sLRIs vs. URIs (OR=0.33; 95% CI, 0.16-0.68). Though rhinovirus (43%) and bocavirus (16.1%) were commonly detected in sLRIs, neither was associated with increased sLRI risk. Infection with multiple viral species (i.e. co-infection) occurred in one-third of sLRIs and was associated with 2.92-fold greater odds of sLRI (95% CI, 2.05-4.16) compared to single viral species infections. Rhinovirus-bocavirus was the most common co-infection (32.4%), and interaction between these viral infections was associated with increased sLRI risk (OR=2.21; 95% CI, 1.20-4.09) relative to illnesses that were negative for rhinovirus and bocavirus.

CONCLUSIONS AND RELEVANCE: A diversity of viral pathogens drive early-life sLRIs. Some viral pathogens (e.g. RSV and metapneumovirus) have intrinsic propensity to cause sLRIs, whereas many sLRIs are caused by viruses whose lower airway pathogenicity is dependent on other factors, including co-infection.

KEY POINTS: Question: How do common respiratory viruses differ in their prevalence and risk of causing severe lower respiratory illnesses (LRIs) during early childhood?Findings: RSV, metapneumovirus, and parainfluenza are independent risk factors for early childhood severe LRIs. While rhinovirus and bocavirus infections alone do not increase the risk of severe LRIs, these two viruses significantly elevate risk when they occur as co-infections.Meaning: Our findings highlight significant variability in viruses that drive severe early-life LRIs. Some viral species appear to inherently predispose individuals to lower airway disease, while for others, the development of disease likely depends on co-infections and/or host susceptibility.}, } @article {pmid40060957, year = {2025}, author = {Zhao, JH and Li, WJ and Jiao, J and Wang, MX and Zhang, XM and Yin, JY and Hu, WZ and Song, Q and Liu, J}, title = {Treatment of a rare and severe infection of central nervous system by Angiostrongylus cantonensis: A case report.}, journal = {World journal of radiology}, volume = {17}, number = {2}, pages = {105059}, pmid = {40060957}, issn = {1949-8470}, abstract = {BACKGROUND: Angiostrongylus cantonensis-induced acute parasitic infection is a rare food-borne disease in clinical practice. Lack of its specific laboratory markers and subsequent difficulty in detecting pathogens cause high misdiagnosis and missed diagnosis rates.

CASE SUMMARY: A 20-year-old male developed persistent neck and back pain after consuming raw snail meat, followed by urinary retention and low fever. After admission, the patient was misdiagnosed as viral infection and Mycobacterium tuberculosis in central nervous system. After detection of Angiostrongylus cantonensis in blood and cerebrospinal fluid by metagenomics next generation sequencing, albendazole was administered with ceftriaxone and methylprednisolone treatment simultaneously. With effective antiparasitic treatment, the patient weaned from mechanical ventilation successfully and transferred out of intensive care unit for hyperbaric oxygen and rehabilitation treatment.

CONCLUSION: This case highlights the diagnostic challenges of Angiostrongylus cantonensis infection and the importance of advanced sequencing techniques in identifying rare pathogens.}, } @article {pmid40060808, year = {2025}, author = {Gao, B and Shi, X and Zhao, M and Ren, F and Xu, W and Gao, N and Shan, J and Shen, W}, title = {Mixture Effects of Polystyrene Microplastics on the Gut Microbiota in C57BL/6 Mice.}, journal = {ACS omega}, volume = {10}, number = {8}, pages = {7597-7608}, pmid = {40060808}, issn = {2470-1343}, abstract = {Microplastics are plastic particles with sizes of less than 5 mm. The ubiquity of microplastics in the environment has raised serious public health concerns. Microplastics could disturb the composition of the gut microbiota due to both chemical composition and physical interactions, which might further influence the metabolism and immune function of the host. However, most of the exposure studies chose microplastics of specific sizes. In the natural environment, living organisms are exposed to a mixture of microplastics of various sizes. In this study, male C57BL/6 mice were exposed to polystyrene (PS) microplastics with different sizes, including microplastics with diameters of 0.05-0.1 μm (PS0.1 group, 100 ppb), 9-10 μm (PS10 group, 100 ppb), and microplastic mixtures of both 0.05-0.1 and 9-10 μm (PSMix group) at a total concentration of 100 ppb (50 ppb for each size). Mixture effects of microplastics were investigated on the composition of bacteria and fungi as well as functional metagenome and microbial genes encoding antibiotic resistance and virulence factors. We found that some bacteria, fungi, and microbial metabolic pathways were only altered in the PSMix group, not in the PS0.1 or PS10 group, suggesting the toxic effects of the microplastic mixture on the composition of fungi and bacteria, and the functional metagenome is different from the effects of microplastics at specific sizes. Meanwhile, altered genes encoding antibiotic resistance and virulence factors in the PSMix group were shared with the PS0.1 and PS10 groups, possibly due to functional redundancy. Our findings help improve the understanding of the toxic effects of the microplastic mixture on the gut microbiome.}, } @article {pmid40060671, year = {2025}, author = {Trunfio, M and Scutari, R and Fox, V and Vuaran, E and Dastgheyb, RM and Fini, V and Granaglia, A and Balbo, F and Tortarolo, D and Bonora, S and Perno, CF and Di Perri, G and Alteri, C and Calcagno, A}, title = {The cerebrospinal fluid virome in people with HIV: links to neuroinflammation and cognition.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.02.28.640732}, pmid = {40060671}, issn = {2692-8205}, abstract = {UNLABELLED: Despite effective HIV suppression, neuroinflammation and neurocognitive issues are prevalent in people with HIV (PWH) yet poorly understood. HIV infection alters the human virome, and virome perturbations have been linked to neurocognitive issues in people without HIV. Once thought to be sterile, the cerebrospinal fluid (CSF) hosts a recently discovered virome, presenting an unexplored avenue for understanding brain and mental health in PWH. This cross-sectional study analyzed 85 CSF samples (74 from PWH on suppressive antiretroviral therapy, and 11 from controls without HIV, CWH) through shotgun metagenomics for DNA/RNA viruses. Taxonomic composition (reads and contigs), α and β diversity, and relative abundance (RA) of prokaryotic (PV), human eukaryotic (hEV), and non-human eukaryotic viruses (nhEV) were evaluated in relation to HIV infection, markers of neuroinflammation and neurodegeneration, cognitive functions, and depressive symptoms. Sensitivity analyses and post-hoc cluster analysis on the RA of viral groups and blood-brain barrier permeability were also performed. Of 46 read-positive CSF samples, 93.5% contained PV sequences, 47.8% hEV, and 45.6% nhEV. Alpha diversity was lower in PWH versus CWH, although p>0.05. At β diversity analysis, HIV status explained 3.3% of the variation in viral composition (p=0.016). Contigs retained 13 samples positive for 8 hEV, 2 nhEV, and 6 PV. Higher RA of PV was correlated with higher CSF S100β (p=0.002) and β-Amyloid 1-42 fragment (βA-42, p=0.026), while higher RA of nhEV with poorer cognitive performance (p=0.022). Conversely, higher RA of hEV correlated with better cognition (p=0.003) and lower βA-42 (p=0.012). Sensitivity analyses in virome-positive samples only confirmed these findings. Three CSF clusters were identified and showed differences in astrocytosis, βA-42, tau protein, and cognitive functions. Participants with hEV-enriched CSF showed better cognitive performance compared to those with virus-devoid and nhEV-enriched CSF (models'p<0.05). This study provides the first comprehensive description of the CSF virome in PWH, revealing associations with neuroinflammation and cognition. These findings highlight the potential involvement of the CSF virome in brain health and inform about its composition, origin, and potential clinical implications in people with and without HIV.

AUTHOR SUMMARY: HIV can affect brain health and mental well-being, even in people on successful antiretroviral therapy. The reasons behind this are still unclear. HIV also influences the communities of microbes and viruses living in the human body, and recent research suggests that the human virome, the collection of all viruses within the body, may play a role in cognitive functions, mood, and brain health. For a long time, scientists believed that the cerebrospinal fluid (CSF), which surrounds the brain, was sterile, while robust evidence has shown that the CSF hosts its own unique virome. Via advanced genetic sequencing (shotgun metagenomics), we analyzed the CSF virome in people with and without HIV looking for possible links to neuroinflammation, cognitive performance, and depression. We found that while HIV infection does affect the composition of CSF viral communities, there were no remarkable differences in the CSF virome of individuals with and without HIV. Most viral sequences appeared to come outside the brain. A higher abundance of non-human viral sequences, such as viruses of bacteria, plants, fungi, and animals, was associated with neuroinflammation and poorer cognitive performance. On the other hand, a higher abundance of human viruses correlated with better cognitive function and healthier signature of neuromarkers. These findings provide new insights into the presence and characteristics of the human CSF virome and how it might influence brain health. They also suggest new potential mechanisms of HIV-associated neuropathology.}, } @article {pmid40060627, year = {2025}, author = {Rodriguez-Rodriguez, L and Pfister, J and Schuck, L and Martin, AE and Mercado-Santiago, LM and Tagliabracci, VS and Forsberg, KJ}, title = {Metagenomic selections reveal diverse antiphage defenses in human and environmental microbiomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.02.28.640651}, pmid = {40060627}, issn = {2692-8205}, abstract = {To prevent phage infection, bacteria have developed an arsenal of antiphage defense systems. Using functional metagenomic selections, we identified new examples of these systems from human fecal, human oral, and grassland soil microbiomes. Our antiphage selections in Escherichia coli revealed over 200 putative defenses from 14 diverse bacterial phyla, highlighting the broad phylogenetic interoperability of these systems. Many defense systems were unrecognizable based on sequence or predicted structure, so could only be identified via functional assays. In mechanistic studies, we show that some defense systems encode nucleases that only degrade covalently modified phage DNA, but which accommodate diverse chemical modifications. We also identify outer membrane proteins that prevent phage adsorption and a set of previously unknown defense systems with diverse antiphage profiles and modalities. Most defenses acted against at least two phages, indicating that broadly acting systems are widely distributed among non-model bacteria.}, } @article {pmid40060500, year = {2025}, author = {Depuydt, L and Ahmed, OY and Fostier, J and Langmead, B and Gagie, T}, title = {Run-length compressed metagenomic read classification with SMEM-finding and tagging.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.02.25.640119}, pmid = {40060500}, issn = {2692-8205}, abstract = {Metagenomic read classification is a fundamental task in computational biology, yet it remains challenging due to the scale, diversity, and complexity of sequencing datasets. We propose a novel, lossless, run-length compressed index that enables efficient multi-class metagenomic classification in O (r) space, based on the move structure. Our method identifies all super-maximal exact matches (SMEMs) of length at least L between a read and the reference dataset and associates each SMEM with one class identifier using a sampled tag array. A consensus algorithm then compacts these SMEMs with their class identifier into a single classification per read. We are the first to perform run-length compressed read classification based on full SMEMs instead of semi-SMEMs. We evaluate our approach on both long and short reads in two conceptually distinct datasets: a large bacterial pan-genome with few metagenomic classes and a smaller 16S rRNA gene database spanning thousands of genera or classes. Our method consistently outperforms SPUMONI 2 in accuracy and runtime, with only a modest memory overhead. Compared to Cliffy, we demonstrate better memory efficiency while achieving superior accuracy on the simpler dataset and comparable performance on the more complex one. Overall, our implementation carefully balances accuracy, runtime, and memory usage, offering a versatile solution for metagenomic classification across diverse datasets. The open-source C++11 implementation is available at https://github.com/biointec/tagger under the AGPL-3.0 license.}, } @article {pmid40060387, year = {2025}, author = {Kim, M and Wang, J and Pilley, SE and Lu, RJ and Xu, A and Kim, Y and Liu, M and Fu, X and Booth, SL and Mullen, PJ and Benayoun, BA}, title = {Estropausal gut microbiota transplant improves measures of ovarian function in adult mice.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.05.03.592475}, pmid = {40060387}, issn = {2692-8205}, abstract = {Decline in ovarian function with age not only affects fertility but is also linked to a higher risk of age-related diseases in women (e.g . osteoporosis, dementia). Intriguingly, earlier menopause is linked to shorter lifespan; however, the underlying molecular mechanisms of ovarian aging are not well understood. Recent evidence suggests the gut microbiota may influence ovarian health. In this study, we characterized ovarian aging associated microbial profiles in mice and investigated the effect of the gut microbiome from young and estropausal female mice on ovarian health through fecal microbiota transplantation. We demonstrate that the ovarian transcriptome can be broadly remodeled after heterochronic microbiota transplantation, with a reduction in inflammation-related gene expression and trends consistent with transcriptional rejuvenation. Consistently, these mice exhibited enhanced ovarian health and increased fertility. Using metagenomics-based causal mediation analyses and serum untargeted metabolomics, we identified candidate microbial species and metabolites that may contribute to the observed effects of fecal microbiota transplantation. Our findings reveal a direct link between the gut microbiota and ovarian health.}, } @article {pmid40060187, year = {2025}, author = {Cao, J and Ma, Y and Fu, J and Wang, Z and Zhao, Y and Zhong, N and Zhao, P}, title = {Bacillus atrophaeus DX-9 biocontrol against potato common scab involves significant changes in the soil microbiome and metabolome.}, journal = {aBIOTECH}, volume = {6}, number = {1}, pages = {33-49}, pmid = {40060187}, issn = {2662-1738}, abstract = {UNLABELLED: Potato common scab (CS) is a worldwide disease, caused by Streptomyces spp., and its presence reduces the market value of potatoes. A nontoxic and potentially effective approach in many control strategies is the use of antagonistic microbes as biocontrol agents. In this study, Bacillus atrophaeus DX-9 was isolated and assessed for its ability to protect against CS. Through integrated metagenomic and metabolomic analyses, changes in the soil microbial community structure and soil properties were analyzed to understand the effects of Bacillus atrophaeus DX-9 on CS. These studies revealed that DX-9 inoculation could significantly decrease CS disease rate, disease index, and the number of CS pathogens, along with an increase in soil N and P content. Our metagenomic assays identified 102 phyla and 1154 genera, and DX-9 inoculation increased the relative abundances of the phyla Pseudomonadota, Chloroflexota and Gemmatimonadota. Additionally, an increase in the relative abundance of genera, such as Bradyrhizobium, Agrobacterium, and Nitrobacter, were significantly and positively correlated with soil N and P. Metabolomic analysis revealed that DX-9 inoculation significantly increased the soil levels of phytolaccoside A, 7,8-dihydropteroic acid, novobiocin, and azafrin. These compounds were enriched in microbe pathway metabolites, including xenobiotic biodegradation and metabolism, biosynthesis of other secondary metabolites, and metabolism of cofactors and vitamins. In summary, the use of Bacillus atrophaeus DX-9 against potato CS offers an alternative biocontrol method that can improve both soil microbial community and properties. This study provides insight into the potential mechanisms by which microbial inoculants can control CS disease.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42994-025-00199-3.}, } @article {pmid40060112, year = {2024}, author = {Wei, B and Xu, Q and Kong, J and Su, X and Chen, K and Wang, H}, title = {Metagenomics-based study of rhizospheric microorganisms of Poa alpigena L. in Qinghai Lake, Ganzi River Plateau.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1518637}, pmid = {40060112}, issn = {1664-462X}, abstract = {INTRODUCTION: Poa alpigena Lindm., a dominant forage grass on the Tibetan Plateau, plays a critical role in livestock production and grassland restoration. This study investigates the rhizospheric and non-rhizospheric soil microorganisms of Poa alpigena L. in the Ganzi River area of the Qinghai Lake basin using metagenomic sequencing to understand their diversity and potential ecological functions.

METHODS: Soil samples were collected from rhizospheric and non-rhizospheric areas of Poa alpigena L. using the S-type five-point sampling method. DNA was extracted, and metagenomic sequencing was performed using the BGISEQ-500 platform. Alpha and Beta diversity analyses were conducted, and LEfSe analysis was used to identify differentially abundant microbial taxa and metabolic pathways.

RESULTS: A total of 5,681 microbial species across 1,606 genera, 521 families, 61 phyla, and 246 orders were identified. Non-rhizospheric soils exhibited higher species richness than rhizospheric soils. Proteobacteria was the most abundant phylum in both soil types. Rhizospheric soils showed significant enrichment in pathways related to antibiotic biosynthesis, carbon metabolism, and methane metabolism, while non-rhizospheric soils were enriched in quorum sensing and drug-metabolizing pathways.

DISCUSSION: The findings highlight the selective influence of Poa alpigena L. on soil microbial communities and their potential role in mitigating methane emissions. The study provides a foundation for understanding the ecological functions of soil microorganisms in alpine meadows and supports sustainable grassland management practices.}, } @article {pmid40059905, year = {2025}, author = {Su, Z and Gu, AZ and Wen, D and Li, F and Huang, B and Mu, Q and Chen, L}, title = {Rapid identification of antibiotic resistance gene hosts by prescreening ARG-like reads.}, journal = {Environmental science and ecotechnology}, volume = {23}, number = {}, pages = {100502}, pmid = {40059905}, issn = {2666-4984}, abstract = {Effective risk assessment and control of environmental antibiotic resistance depend on comprehensive information about antibiotic resistance genes (ARGs) and their microbial hosts. Advances in sequencing technologies and bioinformatics have enabled the identification of ARG hosts using metagenome-assembled contigs and genomes. However, these approaches often suffer from information loss and require extensive computational resources. Here we introduce a bioinformatic strategy that identifies ARG hosts by prescreening ARG-like reads (ALRs) directly from total metagenomic datasets. This ALR-based method offers several advantages: (1) it enables the detection of low-abundance ARG hosts with higher accuracy in complex environments; (2) it establishes a direct relationship between the abundance of ARGs and their hosts; and (3) it reduces computation time by approximately 44-96% compared to strategies relying on assembled contigs and genomes. We applied our ALR-based strategy alongside two traditional methods to investigate a typical human-impacted environment. The results were consistent across all methods, revealing that ARGs are predominantly carried by Gammaproteobacteria and Bacilli, and their distribution patterns may indicate the impact of wastewater discharge on coastal resistome. Our strategy provides rapid and accurate identification of antibiotic-resistant bacteria, offering valuable insights for the high-throughput surveillance of environmental antibiotic resistance. This study further expands our knowledge of ARG-related risk management in future.}, } @article {pmid40059755, year = {2025}, author = {Munk, P and Brinch, C and Aarestrup, FM}, title = {Resistance genes are not like chemical pollutants and surveillance of them should reflect that.}, journal = {Future microbiology}, volume = {}, number = {}, pages = {1-3}, doi = {10.1080/17460913.2025.2476880}, pmid = {40059755}, issn = {1746-0921}, } @article {pmid40059174, year = {2025}, author = {Jin, X and Cheng, AG and Chanin, RB and Yu, FB and Dimas, A and Jasper, M and Weakley, A and Yan, J and Bhatt, AS and Pollard, KS}, title = {Comprehensive profiling of genomic invertons in defined gut microbial community reveals associations with intestinal colonization and surface adhesion.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {71}, pmid = {40059174}, issn = {2049-2618}, support = {1563159//National Science Foundation/ ; HL160862/HL/NHLBI NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Bacteria/genetics/classification/isolation & purification ; *Bacterial Adhesion/genetics ; *Metagenomics/methods ; Computational Biology/methods ; Animals ; Metagenome ; Mice ; Promoter Regions, Genetic ; Intestines/microbiology ; }, abstract = {BACKGROUND: Bacteria use invertible genetic elements known as invertons to generate heterogeneity among a population and adapt to new and changing environments. In human gut bacteria, invertons are often found near genes associated with cell surface modifications, suggesting key roles in modulating dynamic processes such as surface adhesion and intestinal colonization. However, comprehensive testing of this hypothesis across complex bacterial communities like the human gut microbiome remains challenging. Metagenomic sequencing holds promise for detecting inversions without isolation and culturing, but ambiguity in read alignment limits the accuracy of the resulting inverton predictions.

RESULTS: Here, we developed a customized bioinformatic workflow-PhaseFinderDC-to identify and track invertons in metagenomic data. Applying this method to a defined yet complex gut community (hCom2) across different growth environments over time using both in vitro and in vivo metagenomic samples, we detected invertons in most hCom2 strains. These include invertons whose orientation probabilities change over time and are statistically associated with environmental conditions. We used motif enrichment to identify putative inverton promoters and predict genes regulated by inverton flipping during intestinal colonization and surface adhesion. Analysis of inverton-proximal genes also revealed candidate invertases that may regulate flipping of specific invertons.

CONCLUSIONS: Collectively, these findings suggest that surface adhesion and intestinal colonization in complex gut communities directly modulate inverton dynamics, offering new insights into the genetic mechanisms underlying these processes. Video Abstract.}, } @article {pmid40058902, year = {2025}, author = {Revelo-Romo, DM and Hurtado Gutiérrez, NH and Hidalgo Troya, A and Amaya-Gómez, CV and Flórez-Martínez, DH and Overmann, J and Villegas Torres, MF and González Barrios, AF}, title = {Omics approaches to explore the coffee fermentation microecosystem and its effects on cup quality.}, journal = {Food research international (Ottawa, Ont.)}, volume = {206}, number = {}, pages = {116035}, doi = {10.1016/j.foodres.2025.116035}, pmid = {40058902}, issn = {1873-7145}, mesh = {*Fermentation ; *Coffee/microbiology ; *Coffea/microbiology/chemistry/metabolism ; Microbiota ; Metagenomics/methods ; Seeds/microbiology/metabolism ; Food Handling/methods ; }, abstract = {The cultivation and postharvest processing of coffee constitute the basis of the subsistence and traditional culture for rural family-owned farms, as well as for the economic success of commercial enterprises in many coffee-producing countries worldwide. The quality of the final beverage is determined by a multitude of variables. A key post-harvest factor is the spontaneous fermentation of the coffee beans, conducted directly on the farm, to remove the mucilage that firmly adheres to the beans. The effect of this fermentation step on the aromatic profile of the coffee is not yet sufficiently understood. All of the above have drawn the attention of researchers on the application of various omics approaches to elucidate fermentation processes in more detail. These approaches have been used to study the fermentation of Arabica (Coffea arabica) beans, as this species is economically most important worldwide. It is known that Arabica mild coffee is obtained through the wet method, which involves fermenting depulped coffee beans using various strategies and then washing the fermented coffee with clean water. In contrast, the fermentation of Canephora coffee beans has been much less studied using omics technologies. This review highlights the trends and future research in coffee fermentation based on a scientometric analysis, supplemented by a traditional systematic literature review. It highlights the composition of the coffee fermentation microbiome, as elucidated by metagenomics applications, in light of several factors that can influence its structure. Additionally, it considers the metabolites associated with microbial metabolism that can influence the chemical composition of coffee beans and, consequently, the cup quality. In this way, this review evidences the promising path in understanding microbial functions in coffee fermentation and in particular in the development of microbial inocula and in the refinement of fermentation processes to improve coffee quality.}, } @article {pmid40058900, year = {2025}, author = {Wang, X and Li, Q and Li, W and Cai, G and Wu, D and Xie, G and Lu, J}, title = {Metagenomics unveils the roles of microbes in the metabolic network of purine formation during Huangjiu fermentation.}, journal = {Food research international (Ottawa, Ont.)}, volume = {206}, number = {}, pages = {116031}, doi = {10.1016/j.foodres.2025.116031}, pmid = {40058900}, issn = {1873-7145}, mesh = {*Fermentation ; *Purines/metabolism ; *Metagenomics ; Metabolic Networks and Pathways ; Bacteria/metabolism/genetics/classification ; Microbiota/physiology ; Fermented Foods/microbiology ; }, abstract = {Purine is a major factor contributing to the development of hyperuricemia and gout, and it is found in large quantities in Huangjiu as free bases. Purine production in Huangjiu is strongly associated with microbial metabolism. However, to the best of our knowledge the microorganisms responsible for and the mechanisms of purine formation during Huangjiu fermentation are yet to be evaluated. Herein, changes in purine levels during Huangjiu fermentation were analyzed. Further, the microbes responsible for purine production were identified and their gene abundance was studied. Results revealed that adenine, guanine, hypoxanthine, and xanthine are produced during Huangjiu fermentation. The total purines content on day 0 (27.99 mg/L) was found to be considerably lower than that produced on day 24 (122.15 mg/L) during Huangjiu fermentation. Metagenomics showed that the composition of the microbial community fluctuates sharply during five fermentation periods of Huangjiu, with the microbial community richness and diversity being the most prominent on day 3. At the genus level, Klebsiella, Lactobacillus, Staphylococcus, Saccharopolyspora, and Saccharomyces were abundant during Huangjiu fermentation and were involved in purine metabolism. Relationships between the dominant microorganisms and key enzyme genes of the purine pathways were also established based on the Kyoto Encyclopedia of Genes and Genomes database. Correlation analysis showed that Lactobacillus and Saccharomyces were the main genera involved in purine formation. Saccharomyces cerevisiae, Lactobacillus paralimentarius, and Lactiplantibacillus plantarum were involved in purine formation during Huangjiu fermentation. Overall, this study improves our understanding of the purine formation mechanism during Huangjiu fermentation and provides valuable insights into the regulation of purine formation by microorganisms.}, } @article {pmid40058503, year = {2025}, author = {Chang, Z and Deng, J and Zhang, J and Wu, H and Wu, Y and Bin, L and Li, D and Liu, J and Yu, R and Lin, H and An, L and Sun, B}, title = {Rapid and Accurate Diagnosis of Urinary Tract Infections Using Targeted Next-Generation Sequencing: A Multicenter Comparative Study with Metagenomic Sequencing and Traditional Culture Methods.}, journal = {The Journal of infection}, volume = {}, number = {}, pages = {106459}, doi = {10.1016/j.jinf.2025.106459}, pmid = {40058503}, issn = {1532-2742}, abstract = {BACKGROUND: Urinary tract infections (UTIs) rank among the most prevalent bacterial infections globally. Traditional urine culture methods have significant limitations in detection time and sensitivity, prompting the need to evaluate targeted next-generation sequencing (tNGS) as a potential diagnostic tool.

METHODS: The study included a discovery cohort of 400 suspected UTI patients (202 analyzed) and a validation cohort of 200 patients (110 analyzed). The study assessed detection time, concordance rates, ability to identify polymicrobial infections, and antibiotic resistance genes (ARGs). Both clear and turbid urine samples were evaluated across different clinical settings.

RESULTS: In the discovery cohort, tNGS demonstrated 96.5% concordance with culture-positive samples, while showing superior specificity in culture-negative specimens (53.1% vs 28.1% for mNGS). Detection time for tNGS (12.89h) was notably shorter than mNGS (17.38h) and traditional culture (61.48h). tNGS exhibited remarkable capability in identifying polymicrobial infections (55.4% of samples), significantly outperforming both mNGS (27.7%) and traditional culture methods, which failed to detect any co-infections. The method showed particular strength in detecting fastidious organisms like Ureaplasma parvum and fungal species such as Candida tropicalis. For antibiotic resistance prediction, tNGS detected more ARGs (52.67% vs 41.22% for mNGS) and achieved 100% sensitivity for vancomycin and methicillin resistance in Gram-positive pathogens. The validation cohort confirmed tNGS's robust performance, maintaining high concordance rates for both culture-positive (90.00%) and culture-negative samples (55.00%), demonstrating consistent reliability across different clinical settings CONCLUSIONS: tNGS demonstrates advantages in rapid and accurate UTI diagnosis, particularly in detecting polymicrobial infections and analyzing antibiotic resistance genes. It shows promise as an effective complementary tool for UTI diagnostics.}, } @article {pmid40058443, year = {2025}, author = {Zhou, Y and Li, MY and Li, CY and Sheng, YJ and Ye, QT and Chen, RY and Zhou, KY and Zhang, Y and Shen, LF and Shou, D}, title = {Effective mechanism of polysaccharides from Erxian herbal pair in promoting bone repair in traumatic osteomyelitis by activating osteoblast GPR41 and inhibiting the MEK/ERK/MAPK signalling axis.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {141858}, doi = {10.1016/j.ijbiomac.2025.141858}, pmid = {40058443}, issn = {1879-0003}, abstract = {Polysaccharides are the key components of natural products; however, their effects on bone repair haven't been fully evaluated. This study aimed to assess the efficacy and mechanism of polysaccharides in promoting bone repair. The Erxian herb pair polysaccharide (EHP) was isolated and purified using water extraction (1:20 (w/v); 100 ± 2 °C; 5 h) and alcohol precipitation (80 ± 2 %). A traumatic osteomyelitis (TO) rat model was established using lipopolysaccharide (LPS). The gut microbiota was analysed through intestinal flora and metagenomic sequencing. The results revealed that the yields of crude polysaccharide and purified polysaccharide EHP were 3.73 ± 0.34 % and 0.48 ± 0.06 %, respectively. The total sugar content of EHP was 83.53 ± 0.16 %. The EHP, with a molecular weight of 31.964 kDa, was primarily composed of mannose, rhamnose, glucose, galactose, and arabinose. In vivo experiments demonstrated that EHP intervention (300 mg/kg/day) significantly augmented bone density and enhanced the activity of alkaline phosphatase (ALP) (P < 0.01). EHP upregulated the abundance of probiotics and increased the production of butyric acid (P < 0.05). In vitro experiments revealed that butyric acid (500-1000 μM) enhanced osteoblast activity and inhibited the expression of mitogen-activated protein kinase kinase (MEK) and extracellular signal-regulated kinase (ERK) (P < 0.01). These findings indicate that polysaccharides may represent a promising therapeutic agent for bone-healing.}, } @article {pmid40058279, year = {2025}, author = {Chen, H and Zeng, Z and Lal, R and Wu, J and Chen, J and Li, M and Cao, L and Liu, X and Zhang, R and Gong, C}, title = {Acetic acid production from corn straw via enzymatic degradation using putative acetyl esterase from the metagenome assembled genome.}, journal = {Enzyme and microbial technology}, volume = {187}, number = {}, pages = {110619}, doi = {10.1016/j.enzmictec.2025.110619}, pmid = {40058279}, issn = {1879-0909}, abstract = {Acetic acid production from corn straw by enzyme catalysis shows its application value in food industry. In this study, a gene encoding for a putative acetyl esterase derived from Sphingobacterium soilsilvae Em02 was discovered in metagenome assembled genome. The gene was expressed in Escherichia coli BL21 to obtain enzyme with a molecular mass of 38.8 kDa. P-Nitrophenyl acetate was used as a substrate to determine the enzyme activity. The enzyme demonstrated optimal activity under conditions of 40 °C and a neutral pH of 7.0. Under optimal conditions, 17.58 mg of acetic acid was obtained using the enzyme from 50 mg corn straw pretreated with amylase. The acetyl esterase derived from Sphingobacterium soilsilvae Em02, demonstrates significant potential for biotechnological applications, particularly in biomass degradation.}, } @article {pmid40058278, year = {2025}, author = {Neri, LCM and Guðmundsson, H and Meurrens, G and Robert, A and Fridjonsson, OH and Hreggvidsson, GO and Adalsteinsson, BT}, title = {Identification and characterization of endo-xylanases from families GH10 and GH11 sourced from marine thermal environments.}, journal = {Enzyme and microbial technology}, volume = {187}, number = {}, pages = {110592}, doi = {10.1016/j.enzmictec.2025.110592}, pmid = {40058278}, issn = {1879-0909}, abstract = {Seaweed biomass is an underutilized resource that is rich in polysaccharides, including xylan. Seaweed polysaccharides could be used as a feedstock in industrial microbiology and and for production of prebiotic oligosaccharides and rare monosaccharides - processes that would benefit from the availability of robust enzymes that break down the seaweed polysaccharides. The present study aimed to identify genes encoding endo-xylanases in bacterial genomes and metagenomes sourced from marine thermal environments, and to characterize the respective enzymes. Twelve endo-xylanases were studied which displayed 59 % median maximal sequence similarity to characterized GH10 or GH11 enzymes. Overall, most of the enzymes functioned optimally at high temperatures, in the presence of salt, and at circumneutral pH. Eight enzymes functioned optimally at temperatures of 50°C or higher, and in the most extreme cases at 85°C to 95°C. Six enzymes retained activity after three-hour incubation at 60°C or higher. Ten enzymes displayed improved catalytic function in the presence of salt, and several retained high catalytic function at 10 % NaCl concentration. All the enzymes hydrolyzed xylan from diverse sources, including crude biomass. The study contributes to an increased understanding of the structural diversity of xylanases; it expands the availability of thermostable xylanases of marine origin; and contributes to increased valorization of seaweed biomass.}, } @article {pmid40058228, year = {2025}, author = {Tromas, N and Simon, DF and Fortin, N and Hernández-Zamora, M and Pereira, A and Mazza, A and Pacheco, SM and Levesque, MJ and Martínez-Jerónimo, L and Antuna-González, P and Munoz, G and Shapiro, BJ and Sauvé, S and Martínez-Jerónimo, F}, title = {Metagenomic insights into cyanotoxin dynamics in a Mexican subtropical lake.}, journal = {Chemosphere}, volume = {376}, number = {}, pages = {144285}, doi = {10.1016/j.chemosphere.2025.144285}, pmid = {40058228}, issn = {1879-1298}, abstract = {Valle de Bravo is a vital water supply for part of the metropolitan area of the Valle de Mexico megacity, providing 30% of Mexico City's water demand. This water body has experienced an acceleration in its trophic status, going from oligotrophic to eutrophic in just a few years. This temperate lake (at a tropical latitude) is in a persistent bloom dominated by a variety of co-occurring cyanobacteria, many of which have toxigenic potential based on microscopic identification, that makes it difficult or even impractical to identify the cyanotoxin producers. To unravel this complexity and directly identify the toxigenic genera, we showed that integrating classical approaches with metagenomic is required. We first characterized, from genes to metagenomes assembled genomes, the toxigenic Cyanobacteria. We found that Microcystis was the most dominant cyanobacterial genus and the sole carrier of the mcy operon, making it the only microcystin producer. We then quantified twenty-one different cyanopeptides, including twelve microcystin congeners using a high-performance liquid chromatography-high-resolution. Nine microcystins (MCs) and the emerging cyanotoxin anabaenopeptin-A and -B were found at varying concentrations throughout the year, with MC-LA being the most common and abundant. Our findings, constrained by our sampling strategy, indicate that conventional cyanotoxin biomarkers (e.g., toxin mcy genes) were not consistently reliable indicators of cyanotoxin concentrations in this freshwater system. In this study, we followed the dynamics of the cyanobacterial community and the associated cyanopeptides with unprecedented resolution. Our results have implications for better management of toxic blooms in this freshwater system, which supplies drinking water to more than 7 million people in the megalopolis of Valle de México.}, } @article {pmid40058051, year = {2025}, author = {Castellano-Hinojosa, A and Gallardo-Altamirano, MJ and Pozo, C and González-Martínez, A and González-López, J and Marshall, IPG}, title = {Salinity levels influence treatment performance and the activity of electroactive microorganisms in a microbial fuel cell system for wastewater treatment.}, journal = {Journal of environmental management}, volume = {379}, number = {}, pages = {124858}, doi = {10.1016/j.jenvman.2025.124858}, pmid = {40058051}, issn = {1095-8630}, abstract = {There is growing interest in developing effective treatment technologies to mitigate the environmental impact of saline wastewater while also potentially recovering valuable resources from it. However, it remains largely unknown how different salinity levels impact treatment performance, energy generation, and the diversity and composition of electroactive microorganisms in MFCs treating real effluents such as urban wastewater. This study explores the impact of three salinity levels (3.5, 7, and 15 g/L NaCl) on current production, organic removal rates, and bacterial community dynamics in a continuous-flow microbial fuel cell (MFC) fed with urban wastewater. Using metagenomics and metatranscriptomics, we explored variations in the abundance and expression of extracellular electron transfer (EET) genes and those involved in other general metabolisms. We found that low salinity (3.5 g/L NaCl) enhanced both current production and organic removal efficiency compared to higher salinity levels. This improvement was linked to an increased abundance and activity of electroactive microorganisms, particularly taxa within the Ignavibacteria class, which possess genes coding for outer membrane cytochromes and porin cytochromes. Additionally, salinity influenced general metabolic genes and microbial community composition, with higher salinity levels limiting bacterial growth and diversity. This research provides valuable insights into the interplay between salinity stress and microbial adaptation, contributing to the optimization of MFC technologies for enhanced environmental and bioengineering applications.}, } @article {pmid40057978, year = {2025}, author = {Jeevannavar, A and Florenza, J and Divne, AM and Tamminen, M and Bertilsson, S}, title = {Cellular heterogeneity in metabolism and associated microbiome of a non-model phytoflagellate.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf046}, pmid = {40057978}, issn = {1751-7370}, abstract = {Single-cell transcriptomics is a key tool for unravelling metabolism and tissue diversity in model organisms. Its potential for elucidating the ecological roles of microeukaryotes, especially non-model ones, remains largely unexplored. This study employed the Smart-seq2 protocol on Ochromonas triangulata, a microeukaryote lacking a reference genome, showcasing how transcriptional states align with two distinct growth phases: a fast-growing phase and a slow-growing phase. Besides the two expected expression clusters, each corresponding to either growth phase, a third transcriptional state was identified across both growth phases. Metabolic mapping revealed a boost of photosynthetic activity in the fast growth over the slow growth stage, as well as down-regulation trend in pathways associated with ribosome functioning, CO2 fixation, and carbohydrate catabolism characteristic of the third transcriptional state. In addition, carry-over rRNA reads recapitulated the taxonomic identity of the target while revealing distinct bacterial communities, in co-culture with the eukaryote, each associated with distinct transcriptional states. This study underscores single-cell transcriptomics as a powerful tool for characterizing metabolic states in microeukaryotes without a reference genome, offering insights into unknown physiological states and individual-level interactions with different bacterial taxa. This approach holds broad applicability to describe the ecological roles of environmental microeukaryotes, culture-free and reference-free, surpassing alternative methods like metagenomics or metatranscriptomics.}, } @article {pmid40057571, year = {2025}, author = {Adams, SE and Cawley, AK and Arnold, D and Hoptroff, MJ and Slomka, V and Matheson, JR and Marriott, RE and Gemmell, MR and Marsh, PD}, title = {A randomised, double-blind clinical study into the effect of zinc citrate trihydrate toothpaste on oral plaque microbiome ecology and function.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {8136}, pmid = {40057571}, issn = {2045-2322}, mesh = {Humans ; *Toothpastes/pharmacology/therapeutic use ; *Dental Plaque/microbiology ; Male ; Female ; Adult ; *Microbiota/drug effects ; Double-Blind Method ; Middle Aged ; Zinc Compounds/pharmacology/therapeutic use/administration & dosage ; Young Adult ; Bacteria/classification/drug effects/genetics/isolation & purification ; }, abstract = {The oral microbiome is a diverse community of microbes residing on all oral surfaces. A balanced oral microbiome is associated with good oral health, and disruption can result in imbalance associated with diseases including gingivitis and dental caries. It is important, therefore, to understand how daily use of oral hygiene products impacts the microbiome. Composition and activity of dental plaque microbiome from 115 participants was analysed after brushing with one of two toothpastes, one containing zinc citrate trihydrate and the other a control toothpaste, in a parallel design. Each participant brushed twice daily for 6-weeks, with samples collected at baseline, 2 and 6-weeks. Metataxonomic analysis demonstrated changes in bacterial communities with use of the zinc toothpaste compared to the control product at community and species level. Increases at the species level were observed for taxa from the genus Veillonella with decrease in a taxon from the genus Fusobacterium for the zinc toothpaste. Analysis of microbiome function based on predicted metagenomic and metatranscriptomic analysis show that use of the zinc toothpaste is associated with an in-vivo reduction in glycolysis, consistent with the mode of action of zinc and, increases in processes linked to gum-health (lysine biosynthesis), and to whole-body health (nitrate reduction). Our findings provide the first understanding of the beneficial modulation of microbiome composition and function by zinc-containing toothpaste in-vivo for oral care benefits.}, } @article {pmid40057258, year = {2025}, author = {Ragone, P and Parodi, C and Tomasini, N and Ramos, F and Uncos, A and Brandán, CP}, title = {The interplay between Trypanosoma cruzi and the microbiome of Triatoma infestans: Implications for the host's immune response.}, journal = {Acta tropica}, volume = {}, number = {}, pages = {107577}, doi = {10.1016/j.actatropica.2025.107577}, pmid = {40057258}, issn = {1873-6254}, abstract = {The infection dynamics of Trypanosoma cruzi is shaped by the parasite's genetics and interactions with host and vector factors. While most studies in the area use axenic parasite cultures devoid of insect fecal components, this study is focused on the immune response and the parasite loads generated after the interaction of T. cruzi with feces from Triatoma infestans in a murine model. First, using metagenomics, we analyzed the microbiota of infected and uninfected feces. Illumina sequencing of the 16S rRNA gene (V3-V4 region) revealed a predominance of the genus Arsenophonus in infected feces and of Enterococcus in uninfected ones. C57BL/6J mice inoculated with T. cruzi infected feces, displayed distinct immune responses compared to those inoculated with culture-derived metacyclic trypomastigotes alone, with lower levels of pro-inflammatory cytokines (IFN-ɣ, TNF-α) and higher amounts of IL-10, suggesting a regulatory response. Besides, total anti-T. cruzi IgG levels remained similar among groups, but IgG1 and IgG2c were reduced in the T. cruzi infected feces group, indicating a balanced Th1/Th2 response. Notably, mice inoculated with T. cruzi infected feces demonstrated significantly reduced blood and muscle parasite loads, potentially limiting inflammation and parasite dissemination. These findings highlight the possible role of vector fecal microbiota in shaping immune responses and influencing disease outcomes during natural T. cruzi infections.}, } @article {pmid40057163, year = {2025}, author = {Leonard, AFC and Higgins, SL and Hui, M and Gaze, WH}, title = {Investigating landscape-scale variables impacting human exposure to antibiotic resistant bacteria using a targeted metagenome approach.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {126015}, doi = {10.1016/j.envpol.2025.126015}, pmid = {40057163}, issn = {1873-6424}, abstract = {Research has shown that exposure to coastal waters containing antibiotic resistant bacteria (ARB) is associated with higher likelihood of gut colonisation by ARB. The aim was to identify landscape-scale processes contributing to the spread of ARB in Hong Kong's coastal waters and to estimate the scale of bathers' exposure to ARB. Twelve recreational water locations were sampled in 2017 for Escherichia coli. A targeted metagenomic approach was used to quantify the abundance and diversity of antibiotic resistance genes (ARGs) harboured by viable E. coli. Data on environmental variables related to ARB distribution in the environment were modelled to identify processes driving the abundance and diversity of ARG-bearing E. coli in coastal waters. These data were combined with data about Hong Kong residents' use of blue space to quantify human exposure to E. coli borne ARG. Several meteorological variables, like rainfall and temperature, were associated with E. coli-borne ARG profiles. Yet when rigorous statistical methods were applied, these relationships were not significant. Meropenem-resistant bacteria were also isolated from samples, most of which were taken from western beaches. Additionally, there was some evidence of elevated abundances of several ARGs, including blaCTX-M, in western beaches. The average E. coli harboured 6.09 ARGs. Over 1.16 million exposure events occurred in 2017 that involved ingestion of E. coli harbouring at least one ARG. This study used robust methods to quantify and explain the abundance and diversity of ARB in Hong Kong's coastal waters. We detected elevated levels of several E. coli-borne ARGs and meropenem-resistant pathogens at western beaches, indicating an influence of the Pearl River on Hong Kong's water quality. Despite updates to wastewater treatment in Hong Kong, recreational use of natural surface waters remains a significant risk of exposure to ARB capable of human gut colonisation.}, } @article {pmid40056814, year = {2025}, author = {Yasemi, M and Jalali, A and Asadzadeh, M and Komijani, M}, title = {Organophosphate pesticides and their potential in the change of microbial population and frequency of antibiotic resistance genes in aquatic environments.}, journal = {Chemosphere}, volume = {376}, number = {}, pages = {144296}, doi = {10.1016/j.chemosphere.2025.144296}, pmid = {40056814}, issn = {1879-1298}, abstract = {Heavy metals (HMs) and pesticides disrupt aquatic biodiversity and microbial communities, contributing to antibiotic resistance via cross-resistance and co-selection mechanisms. This study investigates the relationship between organophosphorus pesticides (OPs), HMs, microbial diversity, and antibiotic resistance genes (ARGs) in eight lakes and wetlands. Microbial communities were analyzed via metagenomics methods, and data were processed using CLC Genomics Workbench 22. ARGs, including tetA, tetB, qnrA, qnrS, CIT, Fox, KPC, CTX-M1, DHA, GES, OXA, IMP, VEB, NDM1, SHV, TEM, CTX-M, PER, and MOX, were identified through polymerase chain reaction (PCR). Element concentrations and pesticide were quantified using inductively coupled plasma mass spectrometry and gas chromatography-mass spectrometry, respectively. The results indicate that environmental elements and pesticides significantly influence microbial diversity. Proteobacteria (Gamma, Beta, Alpha) dominate over other bacteria in all locations. β-Lactamase resistance genes have a significant positive correlations with the concentrations of boron, iron, lithium, magnesium, sodium, and phosphorus (P-value<0.05). Positive correlations between phosphorus, iron, and beta-lactamase genes suggest that higher concentrations of these elements may increase resistance likelihood by promoting resistant bacterial growth or facilitating gene transfer. Additionally, tetA and tetB exhibited a significant positive correlation with parathion concentration. The results showed that OPs and HMs increase antibiotic resistance by causing gene mutations, altering gene expression, and promoting horizontal gene transfer, resulting in multidrug-resistant strains. This highlights the need for monitoring these pollutants as they affect microbial diversity and accelerate antibiotic resistance. Targeted measures, such as bioremediation and pollution control, are essential to mitigate risks to the environment and public health.}, } @article {pmid40056517, year = {2025}, author = {Choonut, A and Wongfaed, N and Wongthong, L and Poolpol, A and Chaikitkaew, S and Sittijunda, S and Reungsang, A}, title = {Microbial degradation of polypropylene microplastics and concomitant polyhydroxybutyrate production: An integrated bioremediation approach with metagenomic insights.}, journal = {Journal of hazardous materials}, volume = {490}, number = {}, pages = {137806}, doi = {10.1016/j.jhazmat.2025.137806}, pmid = {40056517}, issn = {1873-3336}, abstract = {The persistence of plastics, particularly polypropylene (PP), and their conversion into microplastics (MPs), specifically PP-MPs, have emerged as serious ecological threats to soil and aquatic environments. In the present study, we aimed to isolate a microbial consortium capable of degrading PP-MPs. The results revealed that three microbial consortia (CPP-KKU1, CPP-KKU2, and CPP-KKU3) exhibited the ability to degrade PP-MPs, achieving weight losses ranging from 11.6 ± 0.2 % to 17.8 ± 0.5 % after 30 days. Fourier transform infrared (FTIR) spectroscopy analysis confirmed the degradation through oxidation, as evidenced by the presence of new functional groups (-OH and -C=O). In particular, CPP-KKU3 showed the highest degradation efficiency, with scanning electron microscopy (SEM) analysis revealing surface cracking after treatment. Additionally, gas chromatography-mass spectrometry (GC-MS) analysis identified various intermediate compounds, including heterocyclic aromatic compounds, phenyl groups, methylthio derivatives, and ethoxycarbonyl derivatives, indicating complex biochemical processes that were likely mediated by microbial enzymes. Furthermore, polyhydroxybutyrate (PHB) production by these consortia was also investigated. The result showed that both CPP-KKU2 and CPP-KKU3 successfully produced PHB, with CPP-KKU3 demonstrating superior performance in terms of PP-MP degradation and PHB production. Metagenomic analysis of CPP-KKU3 revealed abundant carbohydrate-active enzymes (CAZymes), particularly glycosyl transferases and glycoside hydrolases, which are associated with MP digestion. This study presents a promising bioremediation approach that addresses plastic waste degradation and sustainable bioplastic production, offering a potential solution for environmental plastic pollution.}, } @article {pmid40056474, year = {2025}, author = {Wang, H and Zhong, Y and Yang, Q and Li, J and Li, D and Wu, J and Yang, S and Liu, J and Deng, Y and Song, J and Peng, P}, title = {Coupling of sulfate reduction and dissolved organic carbon degradation accelerated by microplastics in blue carbon ecosystems.}, journal = {Water research}, volume = {279}, number = {}, pages = {123414}, doi = {10.1016/j.watres.2025.123414}, pmid = {40056474}, issn = {1879-2448}, abstract = {Microplastics have increasingly accumulated in sulfate- and organic matter-rich mangrove ecosystems, yet their effects on microbially mediated carbon and sulfur cycling in sediments remains poorly understood. In this study, we performed a 70-day anaerobic microcosm experiment to examine the effects of polylactic acid (PLA) microplastics with different sizes on sulfate reduction and dissolved organic carbon (DOC) degradation in mangrove sediments. Our results demonstrated that millimeter-scale PLA (mm-PLA) more effectively enhanced sulfate reduction, sulfur isotope fractionation, reduced sulfide production, and carbon dioxide (CO2) emission compared to micrometer-scale PLA (m-PLA). These results suggested that mm-PLA had a more pronounced impact on the carbon and sulfur cycles. Integrated 16S rRNA gene amplicon sequencing and metagenomic analyses revealed that mm-PLA preferentially enriched key functional microorganisms, including acetate-producing bacteria (e.g., Acetobacteroides), completely oxidizing sulfate-reducing bacteria (e.g., Desulfobacter), and incompletely oxidizing sulfate-reducing bacteria (e.g., Desulfobulbus). These microorganisms exhibited higher abundances and greater genetic potential for carbon metabolism and sulfate reduction under mm-PLA treatment. Their relative abundances showed positive correlations with sulfate reduction rates, sulfur isotope fractionation, and CO2 emission, identifying them as crucial drivers of coupled carbon-sulfur cycling. Furthermore, the synergistic interactions among Acetobacteroides, Desulfobacter, and Desulfobulbus facilitated the oxidation of sediment-derived DOC, highlighting significant implications for carbon sequestration in blue carbon ecosystems.}, } @article {pmid40056186, year = {2025}, author = {Chen, XX and Ju, Q and Qiu, D and Zhou, Y and Wang, Y and Zhang, XX and Li, JG and Wang, M and Chang, N and Xu, XR and Zhang, YB and Zhao, T and Wang, K and Zhang, Y and Zhang, J}, title = {Microbial dysbiosis with tryptophan metabolites alteration in lower respiratory tract is associated with clinical responses to anti-PD-1 immunotherapy in advanced non-small cell lung cancer.}, journal = {Cancer immunology, immunotherapy : CII}, volume = {74}, number = {4}, pages = {140}, pmid = {40056186}, issn = {1432-0851}, support = {82103446//National Natural Science Foundation of China/ ; 82273226//National Natural Science Foundation of China/ ; 82473215//National Natural Science Foundation of China/ ; 2020QNRC001//China Association for Science and Technology/ ; 2021LC2115//Fourth Military Medical University/ ; }, mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/immunology/drug therapy/metabolism/therapy ; *Tryptophan/metabolism ; *Lung Neoplasms/immunology/drug therapy/therapy/metabolism ; *Dysbiosis/immunology ; Female ; Male ; Middle Aged ; Aged ; *Immunotherapy/methods ; *Immune Checkpoint Inhibitors/therapeutic use ; Microbiota/drug effects/immunology ; Programmed Cell Death 1 Receptor/antagonists & inhibitors/metabolism ; Respiratory System/immunology/metabolism/microbiology ; Adult ; }, abstract = {Lower respiratory tract microbiome constitutes a unique immune microenvironment for advanced non-small cell lung cancer as one of dominant localized microbial components. However, there exists little knowledge on the associations between this regional microbiome and clinical responses to anti-PD-1 immunotherapy from clinical perspectives. Here, we equivalently collected bronchoalveolar lavage fluids from 56 advanced NSCLC participants treated with none (untreated, n = 28) or anti-PD-1 immunotherapy (treated, n = 28), which was further divided into responder (n = 17) and non-responder (n = 11) subgroups according to clinical responses, aiming to compare their microbial discrepancy by performing metagenomic sequencing and targeted metabolic alterations by tryptophan sequencing. Correspondingly, microbial diversities transformed significantly after receiving immunotherapeutic agents, where Gammaproteobacteria and Campylobacter enriched, but Escherichia, Streptococcus, Chlamydia, and Staphylococcus reduced at the genus level, differences of which failed to be achieved among subgroups with various clinical responses (responder or non-responder; LDA > 2, P < 0.05[*]). And the relative abundance of Staphylococcus and Streptomyces was escalated in response subgroup to anti-PD-1 immunotherapy by microbial compositional analysis (as relative abundance ≥ 3%, P < 0.05[*]), no significance of which was achieved among treated and untreated groups. In addition, relative abundances of bacterial tryptophan metabolites and its derivatives were also higher in the responder subgroup, distinctively being associated with divergent genera (VIP > 1, P < 0.05[*]). Our study revealed predictive performance of lower respiratory tract microbiome to antitumoral immunotherapy and further suggested that anti-PD-1 immunotherapy may alter lower respiratory tract microbiome composition and interact with its tryptophan metabolites to regulate therapeutic efficacy in advanced NSCLC, performing as potential biomarkers to prognosis and interventional strategies.}, } @article {pmid40055840, year = {2025}, author = {Rannon, E and Shaashua, S and Burstein, D}, title = {DRAMMA: a multifaceted machine learning approach for novel antimicrobial resistance gene detection in metagenomic data.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {67}, pmid = {40055840}, issn = {2049-2618}, mesh = {*Machine Learning ; *Metagenomics/methods ; Humans ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/drug effects/classification ; Computational Biology/methods ; Metagenome ; }, abstract = {BACKGROUND: Antibiotics are essential for medical procedures, food security, and public health. However, ill-advised usage leads to increased pathogen resistance to antimicrobial substances, posing a threat of fatal infections and limiting the benefits of antibiotics. Therefore, early detection of antimicrobial resistance genes (ARGs), especially in pathogens, is crucial for human health. Most computational methods for ARG detection rely on homology to a predefined gene database and therefore are limited in their ability to discover novel genes.

RESULTS: We introduce DRAMMA, a machine learning method for predicting new ARGs with no sequence similarity to known ARGs or any annotated gene. DRAMMA utilizes various features, including protein properties, genomic context, and evolutionary patterns. The model demonstrated robust predictive performance both in cross-validation and an external validation set annotated by an empirical ARG database. Analyses of the high-ranking model-generated candidates revealed a significant enrichment of candidates within the Bacteroidetes/Chlorobi and Betaproteobacteria taxonomic groups.

CONCLUSIONS: DRAMMA enables rapid ARG identification for global-scale genomic and metagenomic samples, thus holding promise for the discovery of novel ARGs that lack sequence similarity to any known resistance genes. Further, our model has the potential to facilitate early detection of specific ARGs, potentially influencing the selection of antibiotics administered to patients. Video Abstract.}, } @article {pmid40055835, year = {2025}, author = {Yin, CF and Pan, P and Li, T and Song, X and Xu, Y and Zhou, NY}, title = {The universal accumulation of p-aminophenol during the microbial degradation of analgesic and antipyretic acetaminophen in WWTPs: a novel metagenomic perspective.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {68}, pmid = {40055835}, issn = {2049-2618}, support = {32400079//the National Natural Science Foundation of China/ ; 2024YFA0919000//the National Key R&D Program of China/ ; 2024YFA0919000//the National Key R&D Program of China/ ; }, mesh = {*Acetaminophen/metabolism ; *Metagenomics ; *Biodegradation, Environmental ; *Aminophenols/metabolism ; *Antipyretics ; Wastewater/microbiology ; Water Pollutants, Chemical/metabolism ; China ; Bacteria/genetics/classification/metabolism/isolation & purification ; Humans ; Microbiota ; Analgesics ; Metagenome ; }, abstract = {BACKGROUND: Acetaminophen, a widely used analgesic and antipyretic drug, has become a significant aquatic micro-pollutant due to its extensive global production and increased consumption, particularly during the COVID-19 pandemic. Its high-water solubility leads to its pervasive presence in wastewater treatment plants (WWTPs), posing substantial risks to the environment and human health. Biological treatment is one of the promising approaches to remove such pollutants. Although previous studies have isolated acetaminophen-degrading pure cultures and proposed catabolic pathways, the interactions between microbiotas and acetaminophen, the distribution feature of acetaminophen degradation genes, and the gene-driven fate of acetaminophen in the real-world environment remain largely unexplored.

RESULTS: Among the water samples from 20 WWTPs across China, acetaminophen was detected from 19 samples at concentrations ranging from 0.06 to 29.20 nM. However, p-aminophenol, a more toxic metabolite, was detected in all samples at significantly higher concentrations (23.93 to 108.68 nM), indicating the presence of a catabolic bottleneck in WWTPs. Metagenomic analysis from both the above 20 samples and global datasets revealed a consistently higher abundance of initial acetaminophen amidases compared to downstream enzymes, potentially having explained the reason for the bottleneck. Meanwhile, a close correlation between initial amidases and Actinomycetota revealed by genome-based taxonomy suggests a species-dependent degradation pattern. Additionally, a distinct amidase ApaA was characterized by newly isolated Rhodococcus sp. NyZ502 (Actinomycetota), represents a predominant category of amidase in WWTPs. Significant phylogenetic and structural diversity observed among putative amidases suggest versatile acetaminophen hydrolysis potential in WWTPs.

CONCLUSIONS: This study enhances our understanding of acetaminophen's environmental fate and highlights the possible occurrence of ecological risks driven by imbalanced genes in the process of acetaminophen degradation in global WWTPs. Video Abstract.}, } @article {pmid40055808, year = {2025}, author = {Avershina, E and Qureshi, AI and Winther-Larsen, HC and Rounge, TB}, title = {Challenges in capturing the mycobiome from shotgun metagenome data: lack of software and databases.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {66}, pmid = {40055808}, issn = {2049-2618}, support = {2022067//Helse Sør-Øst RHF/ ; }, mesh = {*Software ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; Humans ; *Mycobiome ; *Fungi/genetics/classification/isolation & purification ; *Metagenomics/methods ; Computational Biology/methods ; Ascomycota/genetics/classification/isolation & purification ; Basidiomycota/genetics/isolation & purification/classification ; Databases, Genetic ; }, abstract = {BACKGROUND: The mycobiome, representing the fungal component of microbial communities, is increasingly acknowledged as an integral part of the gut microbiome. However, research in this area remains relatively limited. The characterization of mycobiome taxa from metagenomic data is heavily reliant on the quality of the software and databases. In this study, we evaluated the feasibility of mycobiome profiling using existing bioinformatics tools on simulated fungal metagenomic data.

RESULTS: We identified seven tools claiming to perform taxonomic assignment of fungal shotgun metagenomic sequences. One of these was outdated and required substantial modifications of the code to be functional and was thus excluded. To evaluate the accuracy of identification and relative abundance of the remaining tools (Kraken2, MetaPhlAn4, EukDetect, FunOMIC, MiCoP, and HumanMycobiomeScan), we constructed 18 mock communities of varying species richness and abundance levels. The mock communities comprised up to 165 fungal species belonging to the phyla Ascomycota and Basidiomycota, commonly found in gut microbiomes. Of the tools, FunOMIC and HumanMycobiomeScan needed source code modifications to run. Notably, only one species, Candida orthopsilosis, was consistently identified by all tools across all communities where it was included. Increasing community richness improved precision of Kraken2 and the relative abundance accuracy of all tools on species, genus, and family levels. MetaPhlAn4 accurately identified all genera present in the communities and FunOMIC identified most species. The top three tools for overall accuracy in both identification and relative abundance estimation were EukDetect, MiCoP, and FunOMIC, respectively. Adding 90% and 99% bacterial background did not significantly impact these tools' performance. Among the whole genome reference tools (Kraken2, HMS, and MiCoP), MiCoP exhibited the highest accuracy when the same reference database was used.

CONCLUSION: Our survey of mycobiome-specific software revealed a very limited selection of such tools and their poor robustness due to error-prone software, along with a significant lack of comprehensive databases enabling characterization of the mycobiome. None of the implemented tools fully agreed on the mock community profiles. FunOMIC recognized most of the species, but EukDetect and MiCoP provided predictions that were closest to the correct compositions. The bacterial background did not impact these tools' performance. Video Abstract.}, } @article {pmid40054447, year = {2025}, author = {Xiao, X and Zhao, W and Song, Z and Qi, Q and Wang, B and Zhu, J and Lin, J and Wang, J and Hu, A and Huang, S and Wang, Y and Chen, J and Fang, C and Ji, Q and Zhang, N and Meng, L and Wei, X and Chen, C and Cai, S and Chen, S and Ding, K and Li, D and Liu, S and Song, T and Tian, L and Zhang, H and Zhang, Y and Xu, S and Chen, J and Chen, H and Cen, Q and Jiang, F and Hu, G and Tang, C and Guo, W and Wang, X and Zhan, L and Fan, J and Wang, J and Zhou, C and Li, L and Lv, Z and Hu, Y and Lin, X and Mai, G and Luo, L and Yang, T and Wang, W and Kristiansen, K and Chen, L and Yang, H and Ni, M and Gu, Y and Mu, F and Yang, Y and Zhou, J and Wang, J and Zhang, WJ and Han, M and Xu, X and Liu, S}, title = {Microbial ecosystems and ecological driving forces in the deepest ocean sediments.}, journal = {Cell}, volume = {188}, number = {5}, pages = {1363-1377.e9}, doi = {10.1016/j.cell.2024.12.036}, pmid = {40054447}, issn = {1097-4172}, mesh = {*Geologic Sediments/microbiology/chemistry ; *Oceans and Seas ; *RNA, Ribosomal, 16S/genetics ; *Ecosystem ; Phylogeny ; Bacteria/genetics/classification/metabolism ; Microbiota/genetics ; Metagenome ; Metagenomics ; }, abstract = {Systematic exploration of the hadal zone, Earth's deepest oceanic realm, has historically faced technical limitations. Here, we collected 1,648 sediment samples at 6-11 km in the Mariana Trench, Yap Trench, and Philippine Basin for the Mariana Trench Environment and Ecology Research (MEER) project. Metagenomic and 16S rRNA gene amplicon sequencing generated the 92-Tbp MEER dataset, comprising 7,564 species (89.4% unreported), indicating high taxonomic novelty. Unlike in reported environments, neutral drift played a minimal role, while homogeneous selection (HoS, 50.5%) and dispersal limitation (DL, 43.8%) emerged as dominant ecological drivers. HoS favored streamlined genomes with key functions for hadal adaptation, e.g., aromatic compound utilization (oligotrophic adaptation) and antioxidation (high-pressure adaptation). Conversely, DL promoted versatile metabolism with larger genomes. These findings indicated that environmental factors drive the high taxonomic novelty in the hadal zone, advancing our understanding of the ecological mechanisms governing microbial ecosystems in such an extreme oceanic environment.}, } @article {pmid40054445, year = {2025}, author = {Turjeman, S and Rozera, T and Elinav, E and Ianiro, G and Koren, O}, title = {From big data and experimental models to clinical trials: Iterative strategies in microbiome research.}, journal = {Cell}, volume = {188}, number = {5}, pages = {1178-1197}, doi = {10.1016/j.cell.2025.01.038}, pmid = {40054445}, issn = {1097-4172}, mesh = {*Microbiota ; Humans ; *Big Data ; Animals ; Clinical Trials as Topic ; Metagenomics/methods ; Metabolomics/methods ; }, abstract = {Microbiome research has expanded significantly in the last two decades, yet translating findings into clinical applications remains challenging. This perspective discusses the persistent issue of correlational studies in microbiome research and proposes an iterative method leveraging in silico, in vitro, ex vivo, and in vivo studies toward successful preclinical and clinical trials. The evolution of research methodologies, including the shift from small cohort studies to large-scale, multi-cohort, and even "meta-cohort" analyses, has been facilitated by advancements in sequencing technologies, providing researchers with tools to examine multiple health phenotypes within a single study. The integration of multi-omics approaches-such as metagenomics, metatranscriptomics, metaproteomics, and metabolomics-provides a comprehensive understanding of host-microbe interactions and serves as a robust hypothesis generator for downstream in vitro and in vivo research. These hypotheses must then be rigorously tested, first with proof-of-concept experiments to clarify the causative effects of the microbiota, and then with the goal of deep mechanistic understanding. Only following these two phases can preclinical studies be conducted with the goal of translation into the clinic. We highlight the importance of combining traditional microbiological techniques with big-data approaches, underscoring the necessity of iterative experiments in diverse model systems to enhance the translational potential of microbiome research.}, } @article {pmid40054329, year = {2025}, author = {Saticioglu, IB and Ajmi, N and Coskuner-Weber, O and Alpsoy, S and Ay, H and Aydin, F and Abay, S and Karakaya, E and Kayman, T and Dalyan, C and Koca, FD and Tasci, G and Yarim, D and Morick, D and Yibar, A and Erdogan, S and Altun, S and Duman, M}, title = {Three new Microbacterium species isolated from the Marmara Sea mucilage event: Microbacterium istanbulense sp. nov., Microbacterium bandirmense sp. nov., Microbacterium marmarense sp. nov.}, journal = {Systematic and applied microbiology}, volume = {48}, number = {3}, pages = {126600}, doi = {10.1016/j.syapm.2025.126600}, pmid = {40054329}, issn = {1618-0984}, abstract = {Three bacterial strains, Mu-43[T], Mu-80[T], and Mu-86[T], were isolated from the 2021 and 2022 mucilage event in the Marmara Sea and were taxonomically characterized. 16S rRNA gene sequence analysis confirmed that these strains belong to the genus Microbacterium. A polyphasic approach involving genomic and phenotypic analysis was employed to determine their taxonomic positions. A polyphasic approach integrating genomic and phenotypic analyses established their taxonomic positions. M. istanbulense Mu-43[T] showed 99.0 % 16S rRNA similarity to M. bandirmense Mu-80[T], with digital DNA-DNA hybridization (dDDH) and average nucleotide identity using BLAST (ANIb) values of 22.3 % and 78.3 %, respectively. M. bandirmense Mu-80[T] exhibited 99.2 % similarity to M. esteraromaticum DSM 8609[T], with dDDH and ANIb values of 23.6 % and 80 %. M. marmarense Mu-86[T] showed 97.4 % similarity to M. arthrosphaerae JCM 30492[T], with dDDH and ANIb values of 20.1 % and 74.2 %. Metagenomic analysis highlighted their ecological relevance, with relative abundances of 1.43 %, 1.15 %, and 0.95 %, respectively. Further genomic analysis identified biosynthetic gene clusters associated with secondary metabolite production, including non-ribosomal peptide synthetases and terpenoid biosynthesis pathways, suggesting potential antimicrobial activity. Additionally, antibiotic resistance genes, such as ABC efflux pumps and Erm23S_rRNA methyltransferase, indicate adaptation to environmental stress. These findings indicate that these species contribute to nutrient cycling and organic matter decomposition in mucilage-affected environments. Based on genomic and phenotypic data, these strains are proposed as novel species: M. istanbulense sp. nov. Mu-43[T] (LMG 33297[T] = DSM 117065[T]), M. bandirmense sp. nov. Mu-80[T] (LMG 33295[T] = DSM 117210[T]), and M. marmarense sp. nov. Mu-86[T] (LMG 33293[T] = DSM 117066[T]).}, } @article {pmid40054170, year = {2025}, author = {Aalam, J and Ahmad Shah, SN and Parveen, R}, title = {An extensive review on infectious disease diagnosis using machine learning techniques and next generation sequencing: State-of-the-art and perspectives.}, journal = {Computers in biology and medicine}, volume = {189}, number = {}, pages = {109962}, doi = {10.1016/j.compbiomed.2025.109962}, pmid = {40054170}, issn = {1879-0534}, abstract = {UNLABELLED: Infectious diseases, including tuberculosis (TB), HIV/AIDS, and emerging pathogens like COVID-19 pose severe global health challenges due to their rapid spread and significant morbidity and mortality rates. Next-generation sequencing (NGS) and machine learning (ML) have emerged as transformative technologies for enhancing disease diagnosis and management.

OBJECTIVE: This review aims to explore integrating ML techniques with NGS for diagnosing infectious diseases, highlighting their effectiveness and identifying existing challenges.

METHODS: A comprehensive literature review spanning the past decade was conducted using reputable databases, including IEEE Xplore, PubMed, Scopus, SpringerLink, and Science Direct. Research papers, articles, and conference proceedings meeting stringent quality criteria were analysed to assess the performance of ML algorithms applied to NGS and metagenomic NGS (mNGS) data.

RESULTS: The findings reveal that ML algorithms, such as deep neural networks (DNNs), support vector machines (SVM), and K-nearest neighbours (KNN), achieve high accuracy rates, often exceeding 95 %, in diagnosing infectious diseases. Deep learning methods excel in genomic and metagenomic data analysis, while traditional algorithms like Gaussian mixture models (GMM) also demonstrate robust classification capabilities. Challenges include reliance on single data types and difficulty distinguishing closely related pathogens.

CONCLUSION: The integration of ML and NGS significantly advances infectious disease diagnosis, offering rapid and precise detection capabilities. Addressing current limitations can further enhance the effectiveness of these technologies, ultimately improving global public health outcomes.}, } @article {pmid40056781, year = {2025}, author = {Chen, H and Li, J and Wu, Y and Li, Y and Zheng, S and Wu, Y and Xuan, R and Wu, L and Miao, J and Wang, Y and Tan, H and Zhou, J and Huang, J and Yan, X}, title = {Structural characteristics of intestinal microbiota of domestic ducks with different body sizes.}, journal = {Poultry science}, volume = {104}, number = {4}, pages = {104930}, doi = {10.1016/j.psj.2025.104930}, pmid = {40056781}, issn = {1525-3171}, abstract = {Domestic ducks are economically important agricultural animals, and their body size is a crucial economic trait. The intestinal flora plays a pivotal role in influencing body metabolism, growth, and development. Currently, no literature is available on the potential effect of the intestinal flora of domestic ducks on body size. This study used 16S rRNA sequencing technology to investigate the fecal microbiota of 229 individuals reared under identical feeding conditions. The findings revealed that partridge ducks with large body sizes (LBS) exhibited a higher level of intestinal microbial diversity than ducks with small body sizes (SBS). Notably, the gut microbiota composition of SBS displayed significantly elevated proportions of Streptococcus, Rothia, and Psychrobacter compared to their counterparts with LBS. Conversely, Lactobacillus was significantly more abundant in LBS. Jeotgalibaca and Psychrobacter were identified as key biomarkers of SBS, whereas Lactobacillus and Bacteroides were predominant biomarkers of LBS. Functional predictions based on intestinal microbiota indicated discernible differences among different body types, particularly evident in non- partridge ducks. The present study investigated the correlation between the intestinal microbiota and body size of domestic ducks, aiming to provide practical insights for the production management of domestic duck farming.}, } @article {pmid40056745, year = {2025}, author = {Zhu, S and Mao, H and Yang, X and Zhao, W and Sheng, L and Sun, S and Du, X}, title = {Resilience mechanisms of rhizosphere microorganisms in lead-zinc tailings: Metagenomic insights into heavy metal resistance.}, journal = {Ecotoxicology and environmental safety}, volume = {292}, number = {}, pages = {117956}, doi = {10.1016/j.ecoenv.2025.117956}, pmid = {40056745}, issn = {1090-2414}, abstract = {This study investigates the impact of heavy metal contamination in lead-zinc tailings on plant and soil microbial communities, focusing on the resilience mechanisms of rhizosphere microorganisms in these extreme environments. Utilizing metagenomic techniques, we identified a significant association between Coriaria nepalensis Wall. rhizosphere microbial communities and metal(loid) resistance genes. Our results reveal a notable diversity and abundance of bacteria within the rhizosphere of tailings, primarily consisting of Proteobacteria, Actinobacteria, and Chloroflexi. The presence of metal-resistant bacterial taxa, including Afipia, Bradyrhizobium, Sphingomonas, and Miltoncostaea, indicates specific evolutionary adaptations to metal-rich, nutrient-deficient environments. Elevated expression of resistance genes such as znuD, zntA, pbrB, and pbrT underscores the microorganisms' ability to endure these harsh conditions. These resistance genes are crucial for maintaining biodiversity, ecosystem stability, and adaptability. Our findings enhance the understanding of interactions between heavy metal contamination, microbial community structure, and resistance gene dynamics in lead-zinc tailings. Additionally, this research provides a theoretical and practical foundation for employing plant-microbial synergies in the in-situ remediation of contaminated sites.}, } @article {pmid40056594, year = {2025}, author = {Zhang, H and Zhang, Y and Li, L and Huang, S and Ma, W and Xu, B and Ng, HY and Kim, DH and Kang, S and Shi, X}, title = {An innovative high-rate biofilm-based process: Biopolymer production and recovery from wastewater organic pollutants.}, journal = {Journal of environmental management}, volume = {379}, number = {}, pages = {124800}, doi = {10.1016/j.jenvman.2025.124800}, pmid = {40056594}, issn = {1095-8630}, abstract = {In this study, a novel high-rate moving bed biofilm reactor (MBBR) was constructed to enhance wastewater COD bio-conversion and biopolymer recovery with a hydraulic retention time (HRT) of 1.0 h and an organic loading rate (OLR) of 4.8 kg COD·m[-3]·d[-1]. A superior specific COD reduction rate of 4.1 kg COD·m[-3]·d[-1] was obtained. The settleability analyses showed that within a settling time of 30 min, a low effluent suspended solids (SS) concentration (40.6 mg/L) with a high biomass recovery rate (83.3%) was achieved. From the recovered biomass, a remarkably higher alginate-like exopolymer (ALE) yield (274.2-385.1 mg/g VSS) was extracted as compared with seeding sludge (148.3 mg/g VSS). In addition, high protein/polysaccharide ratios of 8.5-12.4 were revealed owing to the short HRT condition. Moreover, key functional genes involving classic ALE synthesis were fully detected in such mixed-cultured bioprocess through metagenomic sequencing. Overall, this study offers a proof of concept that bio-refinery of organics into value-added biopolymers could provide a promising direction for the transformation of wastewater treatment plants from energy/resource-consuming factories to resource-recovery factories.}, } @article {pmid40056581, year = {2025}, author = {Wu, Y and Xu, L and He, F and Song, X and Ding, J and Ma, J}, title = {Effects of micro-magnetite on anaerobic co-digestion of waste activated sludge and slaughterhouse waste: Microbial community and metabolism analyses.}, journal = {Journal of environmental management}, volume = {379}, number = {}, pages = {124896}, doi = {10.1016/j.jenvman.2025.124896}, pmid = {40056581}, issn = {1095-8630}, abstract = {Micro-magnetite has been widely applied to improve anaerobic digestion (AD) performance, while comprehensive investigation of microbial community succession, metabolic pathway and magnetite fate remains unclear. In the current study, the effects of micro-magnetite (Fe3O4) on anaerobic co-digestion (AcD) of waste activated sludge and slaughterhouse waste were investigated. Experimental results indicated that the cumulative methane production was significantly increased from 484.6 mL/g VS to 524.4 mL/g VS with 0.8 g/L Fe3O4 addition. Recycled magnetite remained the initial physicochemical properties, including morphology, particle size and crystal structure, as evidenced by various characterization methods. Microbial community analysis indicated that magnetite addition enriched syntrophic bacteria (Armatimonadota, Syntrophomonas and Petrimonas) and methanogens (Methanosarcina). Metagenomic sequencing analysis demonstrated that hydrolysis and acidogenesis metabolic pathways were reinforced by magnetite addition. Meanwhile, the magnetite stimulated the direct interspecies electron transfer via enriching syntrophic microbes (Syntrophomonas and Methanosarcina) and conductive pili functional genes (pilA, mshA and mshC), finally achieving higher cumulative methane yield. This study provided in-depth investigation of the methane production facilitated by micro-magnetite addition and the magnetite fate during the AcD process.}, } @article {pmid40056523, year = {2025}, author = {Zhang, Q and Fan, Y and Qian, X and Zhang, Y}, title = {Unraveling the role of microplastics in antibiotic resistance: Insights from long-read metagenomics on ARG mobility and host dynamics.}, journal = {Journal of hazardous materials}, volume = {490}, number = {}, pages = {137804}, doi = {10.1016/j.jhazmat.2025.137804}, pmid = {40056523}, issn = {1873-3336}, abstract = {As two emerging pollutants, microplastics (MPs) potentially serve as vectors for antibiotic resistance genes (ARGs) in aquatic environments, but the mechanisms driving ARG enrichment remain unclear. This study used long-read metagenomics to investigate ARG mobility and hosts dynamics within the biofilms of MPs and rocks in different water environments. We identified distinct enrichment patterns for microbial communities and ARGs, highlighting the significant role of horizontal gene transfer in ARG enrichment. Specifically, plasmid-encoded ARGs varied significantly among MP biofilms, rock biofilms, and water samples, while chromosome-encoded ARGs remained consistent across these environments, emphasizing the impact of plasmids on ARG enrichment. Despite this, 55.1 % of ARGs were on chromosomes, indicating that host organisms also play a crucial role. The related mechanisms driving ARG enrichment included enhanced cell adhesion, increased transmembrane transporter activity, and responses to environmental stressors, which led to an increased presence of plasmid-encoded ARGs on MP biofilms, facilitating more frequent horizontal gene transfer. Additionally, the diversity of hosts on MPs was notably lower compared to the water column, with specific bacteria, including Herbaspirillu, Limnohabitans, Polaromonas, Variovorax, Rubrivivax, and Thauera significantly driving ARG enrichment. This study highlights key mechanisms and bacterial taxa involved in ARG dynamics on MPs.}, } @article {pmid40056518, year = {2025}, author = {Zhu, Y and Li, R and Yan, S and Li, Y and Xie, S}, title = {Copper contamination determined the impact of phages on microbially-driven nitrogen cycling in coastal wetland sediments.}, journal = {Journal of hazardous materials}, volume = {490}, number = {}, pages = {137870}, doi = {10.1016/j.jhazmat.2025.137870}, pmid = {40056518}, issn = {1873-3336}, abstract = {Phages have garnered increasing attention due to their potential roles in biogeochemical cycling. However, their impacts on nitrogen cycling have primarily been inferred from the presence of putative auxiliary metabolic genes (AMGs) and the virus-host linkage, despite of very limited direct experimental evidence. In this study, a series of microcosms were established with the inoculation of either native or non-native phages to simulate coastal wetlands with different phage sources and different levels of copper (Cu) contamination. Metagenomics and metatranscriptomics were combined to reveal phages' regulation on microbially-driven nitrogen cycling and to explore how the effects were mediated by Cu stress. Phages significantly impacted denitrification-related genes, with their effects depending on Cu level. Phages inhibited nirK-type denitrification under Cu stress but led to up-regulation of nirS gene in the treatments without Cu addition. Non-native phages also promoted the transcription of genes related to nitrogen assimilation and organic nitrogen transformation. Detection of viral AMGs involved in glutamate synthesis suggested that horizontal gene transfer may be a crucial pathway for phages to facilitate microbial nitrogen uptake. Overall, these findings enhance the understanding of phages' impact on biogeochemical metabolism in coastal wetland, offering novel insights into the links of phages' regulation on microbial nitrogen cycling with Cu stress.}, } @article {pmid40054748, year = {2025}, author = {Wine, E}, title = {Metagenome-informed metaproteomics: a new frontier in gut host-microbe-diet analysis.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2025.02.024}, pmid = {40054748}, issn = {1528-0012}, } @article {pmid40054424, year = {2025}, author = {Ding, C and Sun, J}, title = {The potential contribution of microbial communities to carbon fixation and nitrogen cycle in the Eastern Indian Ocean.}, journal = {Marine environmental research}, volume = {207}, number = {}, pages = {107056}, doi = {10.1016/j.marenvres.2025.107056}, pmid = {40054424}, issn = {1879-0291}, abstract = {This study investigated the diversity and metabolic potential of microbial communities in the Eastern Indian Ocean (EIO) through 16S rDNA gene sequencing and metagenomics analyses. Water samples were collected from the surface waters (5 m depth) and 150 m depth layer in the EIO between March 20th and June 6th, 2019. This study reveals microbial-driven biogeochemical dynamics in the oligotrophic Eastern Indian Ocean, where vertically stratified communities (Cyanobacteria/Proteobacteria-dominated surface vs. diversified Proteobacteria at 150 m) and latitudinal diversity gradients reflect nutrient limitations. Metagenomics identified four carbon fixation strategies: the Calvin cycle dominated epipelagic CO2 assimilation, while the 3-hydroxypropionate bicycle showed elevated surface activity, alongside reductive citrate and Wood-Ljungdahl pathways involving novel Actinobacteria. Nitrogen cycling exhibited spatial heterogeneity: nifH-dominated nitrogen fixation in the surface waters, prevalent narGHI nitrate reduction, and divergent nirS/nirK/nosZ distributions tied to nutrient gradients. Proteobacteria and Actinobacteria were key nitrogen fixers, with novel Actinobacteriota diazotrophs expanding known diversity. Elevated nosZ abundance in the Bay of Bengal underscored regional nitrous oxide consumption hotspots. These findings underscore microbial mediation of carbon-nitrogen fluxes in oligotrophic systems, providing genomic insights into ecosystem responses to climate-driven ocean changes.}, } @article {pmid40054356, year = {2025}, author = {Yu, Y and Wu, J and Tang, Z and Wan, S and Hu, J and Li, B and Wang, J and Li, F}, title = {Unveiling the nitrogen metabolism mechanism for nitrogen retention in compost via in-situ ammonia recycling strategy.}, journal = {Journal of environmental management}, volume = {379}, number = {}, pages = {124863}, doi = {10.1016/j.jenvman.2025.124863}, pmid = {40054356}, issn = {1095-8630}, abstract = {A large amount of ammonia volatilization in compost causes environmental pollution and reduces the quality of compost. Ammonia recycling composting strategy (ARCS) is new strategy for reducing ammonia volatilization by absorbing with backfilling ammonia into the compost. This study revealed the mechanism of ARCS on ammonia volatilization and nitrogen retention during chicken manure composting. The results showed that the adsorption layer containing wood vinegar had an obvious inhibition effect on ammonia volatilization. Compared to CK, ARCS treatment could reduce ammonia emissions and nitrogen loss by 20.65% and 39.6% with T3 (12d), respectively. Different adsorption time would affect the occurrence of various nitrogen components in the adsorption layer, especially the change of inorganic nitrogen content. Metagenomic analysis showed that ARCS treatment resulted in significant changes in bacterial communities, and different backfilling times had significant effects on nitrogen metabolism pathways in compost. Glutamate dehydrogenase and glutamate synthase were the key nitrogen metabolism processes during composting, which played an important role in ammonia volatilization and nitrogen retention. The suitable backfilling time (12d) promoted the acceleration of ammonia nitrogen metabolism in the early stage of composting and enhanced the ammonia assimilation and dissimilatory nitrate reduction function in the maturation stage to achieve nitrogen retention. This study provided valuable insights into the effects of in-situ ammonia absorption and backfilling on nitrogen metabolism pathways during composting.}, } @article {pmid40054196, year = {2025}, author = {Wang, S and Li, T and Yuan, X and Yu, J and Luan, Z and Guo, Z and Yu, Y and Liu, C and Duan, C}, title = {Biotic and abiotic drivers of soil carbon, nitrogen and phosphorus and metal dynamic changes during spontaneous restoration of Pb-Zn mining wastelands.}, journal = {Journal of hazardous materials}, volume = {490}, number = {}, pages = {137818}, doi = {10.1016/j.jhazmat.2025.137818}, pmid = {40054196}, issn = {1873-3336}, abstract = {The biotic and abiotic mechanisms that drive important biogeochemical processes (carbon, nitrogen, phosphorus and metals dynamics) in metal mine revegetation remains elusive. Metagenomic sequencing was used to explored vegetation, soil properties, microbial communities, functional genes and their impacts on soil processes during vegetation restoration in a typical Pb-Zn mine. The results showed a clear niche differentiation between bacteria, fungi and archaea. Compared to bacteria and fungi, the archaea richness were more tightly coupled with natural restoration changes. The relative abundances of CAZyme-related, denitrification-related and metal resistance genes reduced, while nitrification, urease, inorganic phosphorus solubilisation, phosphorus transport, and phosphorus regulation -related genes increased. Redundancy analysis, hierarchical partitioning analysis, relative-importance analysis and partial least squares path modelling, indicated that archaea diversity, primarily influenced by available lead, directly impacts carbon dynamics. Functional genes, significantly affected by available cadmium, directly alter nitrogen dynamics. Additionally, pH affects phosphorus dynamics through changes in bacterial diversity, while metal dynamics are directly influenced by vegetation. These insights elucidate natural restoration mechanisms in mine and highlight the importance of archaea in soil processes.}, } @article {pmid40053579, year = {2025}, author = {Wöhlbrand, L and Dörries, M and Siani, R and Medrano-Soto, A and Schnaars, V and Schumacher, J and Hilbers, C and Thies, D and Kube, M and Reinhardt, R and Schloter, M and Saier, MH and Winklhofer, M and Rabus, R}, title = {Key role of Desulfobacteraceae in C/S cycles of marine sediments is based on congeneric catabolic-regulatory networks.}, journal = {Science advances}, volume = {11}, number = {10}, pages = {eads5631}, pmid = {40053579}, issn = {2375-2548}, support = {R01 GM077402/GM/NIGMS NIH HHS/United States ; }, mesh = {*Geologic Sediments/microbiology ; *Deltaproteobacteria/metabolism/genetics ; *Carbon Cycle ; Sulfur/metabolism ; Gene Regulatory Networks ; Phylogeny ; Metagenome ; Carbon/metabolism ; Proteome/metabolism ; Oxidation-Reduction ; Metabolic Networks and Pathways ; }, abstract = {Marine sediments are highly bioactive habitats, where sulfate-reducing bacteria contribute substantially to seabed carbon cycling by oxidizing ~77 Tmol Corg year[-1]. This remarkable activity is largely attributable to the deltaproteobacterial family Desulfobacteraceae of complete oxidizers (to CO2), which our biogeography focused meta-analysis verified as cosmopolitan. However, the catabolic/regulatory networks underlying this ecophysiological feat at the thermodynamic limit are essentially unknown. Integrating cultivation-based (80 conditions) proteogenomics of six representative Desulfobacteraceae spp., we identify molecular commonalities explaining the family's environmental relevance and success. Desulfobacteraceae genomes are specifically enriched in substrate uptake, degradation capacities, and regulatory functions including fine-tuned sulfate uptake. Conserved gene arrangements and shared regulatory patterns translate into strikingly similar (sub-)proteome profiles. From 319 proteins, we constructed a meta-network for catabolizing 35 substrates. Therefrom, we defined a Desulfobacteraceae characteristic gene subset, which we found prevalent in metagenomes of organic-rich, marine sediments. These genes are promising targets to advance our mechanistic understanding of Desulfobacteraceae-driven biogeochemical processes in marine sediments and beyond.}, } @article {pmid40053318, year = {2025}, author = {Nihalani, R and Zola, J and Aluru, S}, title = {Disambiguating a Soft Metagenomic Clustering.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {}, number = {}, pages = {}, doi = {10.1089/cmb.2024.0825}, pmid = {40053318}, issn = {1557-8666}, abstract = {Clustering is a popular technique used for analyzing amplicon sequencing data in metagenomics. Specifically, it is used to assign sequences (reads) to clusters, each cluster representing a species or a higher level taxonomic unit. Reads from multiple species often sharing subsequences, combined with lack of a perfect similarity measure, make it difficult to correctly assign reads to clusters. Thus, metagenomic clustering methods must either resort to ambiguity, or make the best available choice at each read assignment stage, which could lead to incorrect clusters and potentially cascading errors. In this article, we argue for first generating an ambiguous clustering and then resolving the ambiguities collectively by analyzing the ambiguous clusters. We propose a rigorous formulation of this problem and show that it is NP-Hard. We then propose an efficient heuristic to solve it in practice. We validate our approach on several synthetically generated datasets and two datasets consisting of 16S rDNA sequences from the microbiome of rat guts.}, } @article {pmid40053297, year = {2025}, author = {Scholand, KK and Schaefer, L and Govindarajan, G and Yu, Z and Galletti, JG and de Paiva, CS}, title = {Aged regulatory T cells fail to control autoimmune lacrimal gland pathogenic CD4[+] T cells.}, journal = {GeroScience}, volume = {}, number = {}, pages = {}, pmid = {40053297}, issn = {2509-2723}, support = {R01EY030447/EY/NEI NIH HHS/United States ; EY-002520/EY/NEI NIH HHS/United States ; EY021725/EY/NEI NIH HHS/United States ; EY007001/EY/NEI NIH HHS/United States ; R01EY035333/EY/NEI NIH HHS/United States ; P30CA125123/CA/NCI NIH HHS/United States ; CPRIT-RP180672//CPRIT/ ; CA125123//National Institutes of Health (US)/ ; RR024574//National Institutes of Health (US)/ ; 221859/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; PICT 2020-00138//Agencia Nacional de Promoción Científica y Tecnológica/ ; PICT 2021-00109//Agencia Nacional de Promoción Científica y Tecnológica/ ; }, abstract = {CD25KO mice are a model of Sjögren disease. CD25KO mice have severe inflammation and infiltrating lymphocytes to the lacrimal glands (LG). Whether the pathogenicity of CD25KO CD4[+] T cells can be controlled in vivo by Tregs is unknown. Eight-week-old B6 and CD25KO mice LGs were submitted for RNA bulk sequencing. A total of 3481 genes were differentially expressed in CD25KO LG compared to B6. Tear washing analysis identified CD25KO mice had elevated protein levels of TNF, IFN-γ, and CCL5 and decreased protein levels of IL-12p40 and VEGF-A. Co-adoptive transfer of CD25KO CD4[+] T cells with either young or aged B6 Tregs was performed in RAG1KO mice. Recipients of CD25KO CD4[+] T cells alone had higher LG inflammation than naive mice. However, in recipients of young B6 Tregs plus CD25KO CD4[+] T cells, LGs had significantly reduced inflammation. Recipients of CD25KO CD4[+] T cells with aged B6 Tregs had more inflamed LGs than young Tregs, suggesting aged Tregs have less suppressive capacity in vivo. Altogether, CD25KO mice have phenotypic and genetic changes resulting in increased inflammation and severe lymphocytic infiltration in the LGs. However, this autoimmunity can be controlled by the addition of young, but not aged, Tregs, suggesting that aging Tregs have dysfunctional suppression.}, } @article {pmid40052570, year = {2025}, author = {Shen, M and Gao, S and Zhu, R and Wang, W and Gao, W and Tao, L and Chen, W and Zhu, X and Yang, Y and Xu, T and Zhao, T and Jiao, N and Zhi, M and Zhu, L}, title = {Multimodal Metagenomic Analysis Reveals Microbial InDels as Superior Biomarkers for Pediatric Crohn's Disease.}, journal = {Journal of Crohn's & colitis}, volume = {}, number = {}, pages = {}, doi = {10.1093/ecco-jcc/jjaf039}, pmid = {40052570}, issn = {1876-4479}, abstract = {BACKGROUND AND AIMS: The gut microbiome is closely associated with pediatric Crohn's disease (CD), while the multidimensional microbial signature and their capabilities for distinguishing pediatric CD are underexplored. This study aims to characterize the microbial alterations in pediatric CD and develop a robust classification model.

METHODS: A total of 1,175 fecal metagenomic sequencing samples, predominantly from three cohorts of pediatric CD patients, were re-analyzed from raw sequencing data using uniform process pipelines to obtain multidimensional microbial alterations in pediatric CD, including taxonomic profiles, functional profiles, and multi-type genetic variants. Random forest algorithms were used to construct classification models after comparing multiple machine learning algorithms.

RESULTS: We found pediatric CD samples exhibited reduced microbial diversity and unique microbial characteristics. Pronounced abundance differences in 45 species and 1,357 KO genes. Particularly, Enterocloster bolteae emerged as a pivotal pediatric CD-associated species. Additionally, we identified a vast amount of microbial genetic variants linked to pediatric CD, including 192 structural variants, 1,256 insertions/deletions (InDels), and 3,567 single nucleotide variants, with a considerable portion of these variants occurred in non-genic regions. The InDel-based model outperformed other predictive models against multidimensional microbial signatures, achieving an AUC of 0.982. The robustness and disease specificity were further confirmed in an independent CD cohort (AUC=0.996) and five other microbiome-associated pediatric cohorts.

CONCLUSIONS: Our study provided a comprehensive landscape of microbial alterations in pediatric CD and introduced a highly effective diagnostic model rooted in microbial InDels, which contributes to the development of the non-invasive diagnostic tools and targeted therapies.}, } @article {pmid40052474, year = {2025}, author = {Bamigbade, GB and Abdin, M and Subhash, A and Arachchi, MP and Ullah, N and Gan, RY and Ali, A and Kamal-Eldin, A and Ayyash, M}, title = {Plant polysaccharide-capped nanoparticles: A sustainable approach to modulate gut microbiota and advance functional food applications.}, journal = {Comprehensive reviews in food science and food safety}, volume = {24}, number = {2}, pages = {e70156}, doi = {10.1111/1541-4337.70156}, pmid = {40052474}, issn = {1541-4337}, support = {//United Arab Emirates University/ ; }, mesh = {*Gastrointestinal Microbiome/drug effects ; *Nanoparticles/chemistry ; *Polysaccharides/chemistry ; *Functional Food ; Humans ; Plants/chemistry ; }, abstract = {Plant-derived polysaccharides have emerged as sustainable biopolymers for fabricating nanoparticles (polysaccharide-based nanomaterials [PS-NPs]), presenting unique opportunities to enhance food functionality and human health. PS-NPs exhibit exceptional biocompatibility, biodegradability, and structural versatility, enabling their integration into functional foods to positively influence gut microbiota. This review explores the mechanisms of PS-NPs interaction with gut microbiota, highlighting their ability to promote beneficial microbial populations, such as Lactobacilli and Bifidobacteria, and stimulate the production of short-chain fatty acids. Key synthesis and stabilization methods of PS-NPs are discussed, focusing on their role in improving bioavailability, stability, and gastrointestinal delivery of bioactive compounds in food systems. The potential of PS-NPs to address challenges in food science, including enhancing nutrient absorption, mitigating intestinal dysbiosis, and supporting sustainable food production through innovative nanotechnology, is critically evaluated. Barriers such as enzymatic degradation and physicochemical stability are analyzed, alongside strategies to optimize their functionality within complex food matrices. The integration of PS-NPs in food systems offers a novel approach to modulate gut microbiota, improve intestinal health, and drive the development of next-generation functional foods. Future research should focus on bridging knowledge gaps in metagenomic and metabolomic profiling of PS-NPs, optimizing their design for diverse applications, and advancing their role in sustainable and health-promoting food innovations.}, } @article {pmid40052450, year = {2025}, author = {Qian, Z and Chen, S and Liao, X and Xie, J and Xu, Y and Zhong, H and Ou, L and Zuo, X and Xu, X and Peng, J and Wu, J and Cai, S}, title = {Decreased intestinal abundance of Akkermansia muciniphila is associated with metabolic disorders among people living with HIV.}, journal = {Annals of medicine}, volume = {57}, number = {1}, pages = {2474730}, doi = {10.1080/07853890.2025.2474730}, pmid = {40052450}, issn = {1365-2060}, mesh = {Humans ; Male ; *HIV Infections/complications/microbiology ; Female ; *Gastrointestinal Microbiome ; Middle Aged ; Adult ; *Akkermansia ; *Non-alcoholic Fatty Liver Disease/microbiology/metabolism ; Prospective Studies ; Feces/microbiology ; Metagenomics/methods ; Hyperlipidemias/microbiology ; Metabolic Diseases/microbiology/epidemiology ; Verrucomicrobia/isolation & purification ; Overweight/microbiology/complications ; }, abstract = {BACKGROUND: Previous studies have shown changes in gut microbiota after human immunodeficiency virus (HIV) infection, but there is limited research linking the gut microbiota of people living with HIV (PLWHIV) to metabolic diseases.

METHODS: A total of 103 PLWHIV were followed for 48 weeks of anti-retroviral therapy (ART), with demographic and clinical data collected. Gut microbiome analysis was conducted using metagenomic sequencing of fecal samples from 12 individuals. Nonalcoholic fatty liver disease (NAFLD) was diagnosed based on controlled attenuation parameter (CAP) values of 238 dB/m from liver fibro-scans. Participants were divided based on the presence of metabolic disorders, including NAFLD, overweight, and hyperlipidemia. Akkermansia abundance in stool samples was measured using RT-qPCR, and Pearson correlation and logistic regression were applied for analysis.

RESULTS: Metagenomic sequencing revealed a significant decline in gut Akkermansia abundance in PLWHIV with NAFLD. STAMP analysis of public datasets confirmed this decline after HIV infection, while KEGG pathway analysis identified enrichment of metabolism-related genes. A prospective cohort study with 103 PLWHIV followed for 48 weeks validated these findings. Akkermansia abundance was significantly lower in participants with NAFLD, overweight, and hyperlipidemia at baseline, and it emerged as an independent predictor of NAFLD and overweight. Negative correlations were observed between Akkermansia abundance and both CAP values and body mass index (BMI) at baseline and at week 48. At the 48-week follow-up, Akkermansia remained a predictive marker for NAFLD.

CONCLUSIONS: Akkermansia abundance was reduced in PLWHIV with metabolic disorders and served as a predictive biomarker for NAFLD progression over 48 weeks of ART.}, } @article {pmid40052378, year = {2025}, author = {Mise, K and Masuda, Y and Senoo, K and Itoh, H}, title = {Betaproteobacterial clade II nosZ activated under high N2O concentrations in paddy soil microcosms.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxaf055}, pmid = {40052378}, issn = {1365-2672}, abstract = {AIMS: Microbial communities in paddy soils act as potential sinks of nitrous oxide (N2O), a notorious greenhouse gas, but their potential to reduce external N2O is unclear. The direct observation of N2O reduction in submerged field soils is technically difficult. Here, we aimed to identify soil microbial clades that underpin the strong N2O mitigation capacity.

METHODS AND RESULTS: We constructed paddy soil microcosms with external N2O amendment that enabled the simultaneous evaluation of N2O reductase gene (nosZ) transcripts and N2O consumption. Although the amount of N2O amended was large, it was mostly consumed after 6-8 days of microcosm incubation. Metatranscriptomic sequencing revealed that betaproteobacterial nosZ, especially those classified as clade II nosZ belonging to the orders Rhodocyclales or Nitrosomonadales, occupied > 50% of the nosZ transcripts in three of the five paddy soils used. On the other hand, publicly available shotgun metagenomic sequences of 46 paddy soils were not dominated by betaproteobacterial clade II nosZ sequences, although they were ubiquitous. The same applied to the 16S rRNA sequences of Rhodocyclales or Nitrosomonadales.

CONCLUSIONS: The results indicated that betaproteobacterial N2O reducers potentially serve as powerful N2O sinks. Betaproteobacteria holding clade II nosZ can be targets of biostimulation, although further studies are required to understand their ecophysiology.}, } @article {pmid40052334, year = {2025}, author = {Lu, Y and Dong, Y and Zhang, M and Mao, L}, title = {Genome and Metagenome Skimming: Future Sequencing Methods for Environmental DNA (eDNA) Studies.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e14095}, doi = {10.1111/1755-0998.14095}, pmid = {40052334}, issn = {1755-0998}, support = {2023YFF0805800//the National Key Research and Development Program of China/ ; BE2022792//Jiangsu Social Development Program/ ; }, abstract = {Genome skimming (GS), also referred to as low-coverage shotgun sequencing, is an efficient and cost-effective sequencing method that targets high-copy regions in genomes. It is most commonly used for species identification, phylogenetic analysis and expansion of reference libraries. GS can be applied to single species or composite DNA samples representing multiple species; the latter is termed metagenome skimming (MGS). GS/MGS shows promise as an effective approach for environmental DNA (eDNA) studies, but it is currently limited to ancient sedimentary samples. There is the potential to expand this methodology to other eDNA sources, including water, soil and airborne samples. In this paper, we introduce GS/MGS and briefly review its current applications. We also discuss the potential benefits and challenges of using GS/MGS to assay eDNA. eDNA GS/MGS is a promising technology that could broaden eDNA studies if some methodological challenges can be addressed.}, } @article {pmid40052063, year = {2025}, author = {Zheng, H and Peng, P and Wang, S and Zhang, B and Yang, L and Wang, Y and Li, L and Pang, G}, title = {Microbiological Diagnostic Performance and Clinical Effect of Metagenomic Next-Generation Sequencing for the Detection of Immunocompromised Patients With Community-Acquired Pneumonia.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {1223-1236}, pmid = {40052063}, issn = {1178-6973}, abstract = {OBJECTIVE: Community-acquired pneumonia (CAP) presents a significant public health concern, necessitating timely and precise diagnosis. Metagenomic next-generation sequencing (mNGS) has shown promise as a powerful tool for pathogen identification in infectious diseases. This study aimed to evaluate the diagnostic efficacy and clinical applicability of mNGS for immunocompromised patients with CAP compared to the culture method.

METHODS: This study included 168 patients. We used both mNGS and conventional culture methods to identify the pathogen spectrum and evaluate diagnostic performance. Treatment regimens and clinical outcomes were meticulously documented.

RESULTS: The sensitivity of mNGS was greater than that of the culture method across all samples (79.05% vs 16.03%; p < 0.001). mNGS identified pathogens missed by culture in 59.52% of patients and detected polymicrobial infections that were not detected by culture in 47.62% of patients. Streptococcus pneumoniae, Candida albicans, and Human herpesvirus 4 at classification level emerged as the predominant pathogens identified in CAP patients through mNGS. When examining the mNGS results between groups, the proportions of immunocompromised patients with bacterial (p < 0.001), fungal (p < 0.001), viral (p < 0.05), and mixed infections (p < 0.001) were all significantly higher than those in immunocompetent patients. Treatment adjustments guided by mNGS were observed in 73.21% of patients. Specifically, a beneficial clinical effect was observed in 50.60% (85/168) of patients, treatment confirmation in 22.62% (38/168) of patients, and no clinical benefit in 26.80% (45/168) of patients based on mNGS-guided antibiotic treatment adjustments.

CONCLUSION: These findings highlight the diagnostic performance of mNGS for identifying pathogens, particularly in immunocompromised patients vulnerable to infections, offering valuable insights for clinical decision-making.}, } @article {pmid40051621, year = {2025}, author = {Chen, Y and Liang, S and Lu, Y and Zhou, X and Zheng, R and Chen, Y}, title = {Case Report: First report of Legionella micdadei pneumonia and organizing pneumonia in a patient with myelodysplastic and Sweet syndromes.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1510948}, pmid = {40051621}, issn = {1664-3224}, mesh = {Humans ; *Myelodysplastic Syndromes/complications ; *Sweet Syndrome/diagnosis/drug therapy ; Male ; Legionella ; Pneumonia, Bacterial/diagnosis/drug therapy/microbiology/immunology ; Immunocompromised Host ; Legionellosis/diagnosis/drug therapy/microbiology ; Aged ; Middle Aged ; Anti-Bacterial Agents/therapeutic use ; Glucocorticoids/therapeutic use ; Female ; Legionnaires' Disease/diagnosis/drug therapy/complications/immunology ; Organizing Pneumonia ; }, abstract = {The immunocompromised population is susceptible to Legionella pneumonia. The diagnosis and treatment of Legionella pneumonia in immunocompromised individuals are challenging clinical endeavors. Previous studies have identified Legionella pneumonia as a potential cause of organizing pneumonia (OP), however, the association between Legionella pneumonia and OP has not received enough clinical attention. We retrospectively evaluated a case involving Legionella micdadei infection and OP in a patient with myelodysplastic syndrome and concurrent Sweet syndrome. The diagnosis of Legionella micdadei pneumonia was confirmed through various methods: metagenomic next generation sequencing (mNGS), Giemsa-staining and fluorescence in situ hybridization of lung tissue, as well as serum immunofluorescence antibody testing. Histopathological analysis of lung tissue revealed OP. The patient was successfully treated with a combination of antibiotics and low-dose glucocorticoids. In immunocompromised individuals, mNGS was capable of detection non-Legionella pneumophila serogroup 1. The pathological examination is important for identifying secondary OP and provides the evidence for treatment with glucocorticoids.}, } @article {pmid40051412, year = {2025}, author = {Houttu, V and Boulund, U and Troelstra, M and Csader, S and Stols-Gonçalves, D and Mak, AL and Dijk, AV and Bouts, J and Winkelmeijer, M and Verdoes, X and van den Berg-Faay, S and Lek, D and Ronteltap, T and de Haan, F and Jorstad, H and Männistö, V and Savonen, K and Pentikäinen, H and Hanhineva, K and Babu, AF and Panagiotou, G and van Delden, O and Verheij, J and Doukas, M and Nederveen, A and Schwab, U and Grefhorst, A and Nieuwdorp, M and Holleboom, AG}, title = {Deep phenotyping of patients with MASLD upon high-intensity interval training.}, journal = {JHEP reports : innovation in hepatology}, volume = {7}, number = {3}, pages = {101289}, pmid = {40051412}, issn = {2589-5559}, abstract = {BACKGROUND & AIMS: Exercise is a key component of lifestyle management in patients with metabolic dysfunction-associated steatotic liver disease (MASLD), but neither its therapeutic effect on the active stage of the disease, that is metabolic dysfunction-associated steatohepatitis (MASH) nor the mediating mechanisms have been characterized. Therefore, we performed multi-omic phenotyping of patients with MASLD-MASH on an exercise program.

METHODS: Fifteen patients with MASLD conducted high-intensity interval training (HIIT) combined with home-based training for 12 weeks. MASLD was evaluated using histology, transient elastography, and multiparametric magnetic resonance imaging (MRI) before and after the intervention. Change in maximal oxygen consumption (VO2max) and MRI-determined liver fat were compared with a control group of patients with MASLD (n = 22). RNA sequencing was performed on liver, muscle, and fat biopsies of patients in the exercise group. Stool was analyzed by shotgun metagenomics and untargeted metabolomics was performed on plasma, urine, adipose, and stool.

RESULTS: HIIT increased VO2max by 10.1% and improved mitochondrial metabolism in skeletal muscle, indicating improved cardiorespiratory fitness and adherence. VO2max increased significantly in the exercise group compared with controls. Histologically, no reduction in steatosis, MASH, or liver fibrosis was observed; however, transient elastography tended to improve. MRI-determined liver fat did not change in the exercise group compared with controls. HIIT induced changes in mRNA expression of genes related to beiging of adipose tissue and fibrogenesis in liver. In addition, specific gut microbial taxa and metabolites changed.

CONCLUSIONS: HIIT increased cardiorespiratory fitness and induced beneficial gene expression changes in muscle, adipose tissue, and liver, but without translation into histological improvement of MASLD. Longer exercise intervention trials are warranted to validate or refute current recommendations for exercise as a cornerstone treatment for MASLD-MASH.

IMPACT AND IMPLICATIONS: Despite exercise being considered as a key component of lifestyle management for steatotic liver disease, neither the clinical effects nor the mechanisms involved are completely understood. We show that a high-intensity interval training (HIIT) program in 15 patients with metabolic dysfunction-associated steatotic liver disease (MASLD) improved cardiorespiratory fitness, compared with 22 control patients with MASLD who did not participate in an exercise program, however, it did not improve MASLD. HIIT induced a positive effect on fat tissue and muscle metabolism which was accompanied with changes in certain gut bacteria and metabolites in blood and urine. These findings improve our understanding of the effects of exercise on the whole-body metabolism in relation to steatotic liver disease. As such, this study provides a basis for future exercise interventions in patients with MASLD, required to thoroughly test current guideline advice for exercise as a cornerstone treatment for MASLD of all stages.

CLINICAL TRIAL REGISTRY: Dutch Trial Register (registration number NL7932).}, } @article {pmid40050994, year = {2025}, author = {Talat, A and Bashir, Y and Khalil, N and Brown, CL and Gupta, D and Khan, AU}, title = {Antimicrobial resistance transmission in the environmental settings through traditional and UV-enabled advanced wastewater treatment plants: a metagenomic insight.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {27}, pmid = {40050994}, issn = {2524-6372}, support = {BT/PR40148/BTIS/137/20/2021//Department of Biotechnology, Ministry of Science and Technology, India/ ; }, abstract = {BACKGROUND: Municipal wastewater treatment plants (WWTPs) are pivotal reservoirs for antibiotic-resistance genes (ARGs) and antibiotic-resistant bacteria (ARB). Selective pressures from antibiotic residues, co-selection by heavy metals, and conducive environments sustain ARGs, fostering the emergence of ARB. While advancements in WWTP technology have enhanced the removal of inorganic and organic pollutants, assessing ARG and ARB content in treated water remains a gap. This metagenomic study meticulously examines the filtration efficiency of two distinct WWTPs-conventional (WWTPC) and advanced (WWTPA), operating on the same influent characteristics and located at Aligarh, India.

RESULTS: The dominance of Proteobacteria or Pseudomonadota, characterized the samples from both WWTPs and carried most ARGs. Acinetobacter johnsonii, a prevailing species, exhibited a diminishing trend with wastewater treatment, yet its persistence and association with antibiotic resistance underscore its adaptive resilience. The total ARG count was reduced in effluents, from 58 ARGs, representing 14 distinct classes of antibiotics in the influent to 46 and 21 in the effluents of WWTPC and WWTPA respectively. However, an overall surge in abundance, particularly influenced by genes such as qacL, blaOXA-900, and rsmA was observed. Numerous clinically significant ARGs, including those against aminoglycosides (AAC(6')-Ib9, APH(3'')-Ib, APH(6)-Id), macrolides (EreD, mphE, mphF, mphG, mphN, msrE), lincosamide (lnuG), sulfonamides (sul1, sul2), and beta-lactamases (blaNDM-1), persisted across both conventional and advanced treatment processes. The prevalence of mobile genetic elements and virulence factors in the effluents possess a high risk for ARG dissemination.

CONCLUSIONS: Advanced technologies are essential for effective ARG and ARB removal. A multidisciplinary approach focused on investigating the intricate association between ARGs, microbiome dynamics, MGEs, and VFs is required to identify robust indicators for filtration efficacy, contributing to optimized WWTP operations and combating ARG proliferation across sectors.}, } @article {pmid40050500, year = {2025}, author = {Dave, M and Tattar, R}, title = {Antimicrobial resistance genes in the oral microbiome.}, journal = {Evidence-based dentistry}, volume = {}, number = {}, pages = {}, pmid = {40050500}, issn = {1476-5446}, abstract = {A COMMENTARY ON: Sukumar S, Rahmanyar Z, El Jurf H Q et al. Mapping the oral resistome: a systematic review. J Med Microbiol 2024; https://doi.org/10.1099/jmm.0.001866 .

DESIGN: This systematic review, without meta-analysis, aimed to map the oral resistome by analysing clinical studies that detected bacterial antimicrobial resistance genes (ARGs) in the oral cavity using molecular techniques.

DATA SOURCES: The researchers used Medline, Embase, Web of Science, CINAHL and Scopus databases from January 2015 to August 2023.

STUDY SELECTION: This systematic review included cross-sectional or longitudinal clinical studies that detected ARGs using molecular techniques; specifically polymerase chain reaction (PCR) or next-generation sequencing (NGS) metagenomics for samples from the oral cavity (saliva, gingival biofilm, pulp, or oral mucosa). Studies were excluded if they were in vitro or animal studies, literature reviews and not focused on ARG detection.

DATA EXTRACTION AND SYNTHESIS: Five reviewers independently screened titles and abstracts based on inclusion criteria. Full-text reports were then independently assessed for eligibility by three reviewers. Extracted data encompassed publication details, sample size, country, molecular methods used, number of ARGs detected, participants' health status, antibiotic exposure, and sample location within the oral cavity.

RESULTS: Out of 580 initially identified studies, 15 met the inclusion criteria. These studies, published between 2015 and 2023 from 12 different countries, employed either PCR (n = 10) or NGS metagenomics (n = 5) to detect ARGs from a pool of 1486 participants (1 study did not report on the number of participants). PCR-based studies identified an average of 7 ARGs (range 1-20), while NGS studies identified an average of 34 ARGs (range 7-70). In total, 159 unique ARGs conferring resistance to 22 antibiotic classes were identified across six regions of the oral cavity. The supragingival biofilm and saliva exhibited the highest richness of ARGs, defined by the number of unique ARGs detected. Genes conferring resistance to 19 antibiotic classes were present in the supragingival biofilm. Notably, 49 ARGs, including tetracycline and macrolide resistance genes, were found across all sampled locations, indicating a widespread distribution within the oral cavity. Thirteen studies reported on bacterial species associated with ARGs. NGS studies identified a mean of 65 ARG-carrying bacterial species, compared to a mean of 4 species in PCR studies. Specifically, 25 ARG-carrying species were identified in PCR studies, while NGS studies identified 177 species. Four studies reported ARGs associated with streptococcal species implicated in distant-site infections such as infective endocarditis. ESKAPE pathogens (group of highly virulent multidrug-resistant bacteria) were detected with ARGs in various oral sites using both PCR and NGS methods. Comparisons between healthy and diseased states revealed that a healthy oral microbiome harbours a more diverse resistome at the antibiotic class level. The supragingival resistome demonstrated the richest composition in both health and disease, with tetracycline ARGs predominating in the supragingival and saliva resistomes in cases of dental caries.

CONCLUSIONS: The analysis of the oral resistome from these 15 studies identified three ARGs present in all sites of the oral cavity, suggesting the presence of a core resistome. NGS studies provided greater insights compared to PCR studies; however, the overall research base is limited. Further comprehensive studies are necessary to fully map the oral resistome.}, } @article {pmid39726137, year = {2025}, author = {Schwesig, K and Zizka, V and Scherber, C and Hölzel, N}, title = {Comparing eDNA and Transect Methods for Aquatic Biodiversity Assessment in Lakes and Ponds.}, journal = {Molecular ecology resources}, volume = {25}, number = {3}, pages = {e14060}, doi = {10.1111/1755-0998.14060}, pmid = {39726137}, issn = {1755-0998}, support = {01UT2101C//Bundesministerium für Bildung und Forschung/ ; 01UT2101B//Bundesministerium für Bildung und Forschung/ ; }, mesh = {*Biodiversity ; Animals ; *Amphibians/genetics/classification ; *Ponds ; Germany ; *DNA Barcoding, Taxonomic/methods ; *Lakes ; Odonata/genetics/classification ; Metagenomics/methods ; DNA, Environmental/genetics ; Aquatic Organisms/genetics/classification ; }, abstract = {Biodiversity monitoring increasingly relies on molecular methods such as eDNA metabarcoding. However, sound applications have so far been only established for a limited number of taxonomic groups. More information on the strengths and weaknesses of eDNA methods, especially for poorly covered groups, is essential for practical applications to achieve the highest possible reliability. We compared amphibian and Odonata data from eDNA metabarcoding and traditional transect walks on N = 56 plots in 38 water bodies distributed over six extraction sites for building materials in Northwest Germany. The traditional amphibian assessment included visual encounters, dip netting and acoustic detection, while Odonata were assessed through exuviae. In total, both methods detected 8 out of 11 amphibian species, while the remaining three species were detected by eDNA only. We did not find differences in amphibian species numbers per plot, but mean detection probabilities were higher with metabarcoding. In contrast, both methods detected 10 out of 29 Odonata species, while the remaining 19 species were detected by exuviae only. Species numbers per plot were higher for exuviae and only 30% of species were detected with metabarcoding. The species identified by eDNA were those with high abundance, and their detection probabilities were similar to transect walks. The results for amphibians show equal suitability and high complementarity of the compared methods. Metabarcoding detected species more efficiently and therefore offers a suitable protocol for biodiversity monitoring. For Odonata, eDNA metabarcoding showed considerable gaps, implying the need for protocol evaluation and improvement in assessment of ecological communities based on eDNA.}, } @article {pmid40050382, year = {2025}, author = {Liu, C and Wang, H and Wang, Z and Liang, L and Li, Y and Liu, D and Lu, Q}, title = {Distinct assembly processes of intestinal and non-intestinal microbes of bark beetles from clues of metagenomic insights.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {7910}, pmid = {40050382}, issn = {2045-2322}, support = {32230071//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Coleoptera/microbiology/genetics ; Metagenome ; Bacteria/genetics/classification/metabolism ; Microbiota ; Symbiosis ; Weevils/microbiology/genetics ; Phylogeny ; }, abstract = {Ips (Curculionidae: Scolytinae) bark beetles (BBs) are ecologically and economically devastating coniferous pests in the Northern Hemisphere. Although the microbial diversity associated with these beetles has been well studied, mechanisms of community assembly and the functional roles of key microbes remain poorly understood. This study investigates the microbial community structures and functions in both intestinal and non-intestinal environments of five Ips BBs using a metagenomic approach. The findings reveal similar microbial community compositions, though the α-diversity of dominant taxa differs between intestinal and non-intestinal environments due to the variability in bark beetle species, host trees, and habitats. Intestinal microbial communities are predominantly shaped homogenizing dispersal (HD) and undominated processes (UP), whereas non-intestinal microbial communities are primarily driven by heterogeneous selection (HS). Functional analysis shows that genes and enzymes associated with steroid biosynthesis and oxidative phosphorylation are primarily found in non-intestinal fungal symbionts Ogataea, Wickerhamomyce, Ophiostoma, and Ceratocystis of Ips species. Genes and enzymes involved in degrading terpenoids, phenolic compounds, and polysaccharides are predominately found in the intestinal Acinetobacter, Erwinia, and Serratia. This study provides valuable and in-depth insights into the symbiotic relationships between Ips BBs and their microbial partners, enhancing our understanding of insect-microbe coevolution and suggesting new strategies for pest management.}, } @article {pmid40050078, year = {2025}, author = {Zheng, YJ and Hou, JY and Zhong, J and Ye, XW}, title = {[A case of COVID-19-associated pulmonary aspergillosis combined with COVID-19-associated pulmonary mucormycosis].}, journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases}, volume = {48}, number = {3}, pages = {267-271}, doi = {10.3760/cma.j.cn112147-20240809-00476}, pmid = {40050078}, issn = {1001-0939}, support = {82460015//National Natural Science Foundation of China/ ; 2019PT320003//Special Fund for Basic Scientific Research Operations of the Chinese Academy of Medical Sciences/ ; }, mesh = {Humans ; *Mucormycosis/diagnosis/complications ; *COVID-19/complications ; *Pulmonary Aspergillosis/complications/diagnosis ; Male ; Tomography, X-Ray Computed ; SARS-CoV-2/isolation & purification ; Lung Diseases, Fungal/diagnosis/complications ; Middle Aged ; Bronchoalveolar Lavage Fluid/microbiology ; Lung/pathology/diagnostic imaging/microbiology ; Antifungal Agents/therapeutic use ; }, abstract = {COVID-19-associated invasive fungal infections are fungal infections that develop during COVID-19, including pulmonary aspergillosis (CAPA) and pulmonary mucormycosis (CAPM). This report presents a case of a patient with recurrent COVID-19 infections who showed pulmonary cavities and pleural effusion on chest CT. A mixed diagnosis of CAPA and CAPM was confirmed by histopathological analysis of bronchoalveolar lavage fluid and metagenomic next-generation sequencing. This study highlights the importance of suspecting CAPA and CAPM in diabetic COVID-19 patients with unexplained radiological findings that cannot be attributed to common infections or pulmonary tumors. Prompt and thorough diagnostic investigations, including histopathology, microbiology, and molecular techniques, are essential for accurate diagnosis. Early and effective antifungal treatment can significantly improve patient outcomes.}, } @article {pmid40049907, year = {2025}, author = {Jia, Z and Li, C and Zhang, S and Tang, Y and Ma, S and Liu, X and Zhang, J}, title = {Microbial inoculants modify the functions of soil microbes to optimize plant growth at abandoned mine sites.}, journal = {Journal of environmental sciences (China)}, volume = {154}, number = {}, pages = {678-690}, doi = {10.1016/j.jes.2024.10.002}, pmid = {40049907}, issn = {1001-0742}, mesh = {*Soil Microbiology ; *Mining ; *Plant Development ; *Soil/chemistry ; Phosphorus/metabolism ; Carbon/metabolism ; Biodegradation, Environmental ; Nitrogen/metabolism ; Microbiota ; Bacillus thuringiensis ; }, abstract = {Mining activities have caused significant land degradation globally, emphasizing the need for effective restoration. Microbial inoculants offer a promising solution for sustainable remediation by enhancing soil nutrients, enzyme activities, and microbial communities to support plant growth. However, the mechanisms by which inoculants influence soil microbes and their relationship with plant growth require further investigation. Metagenomic sequencing was employed for this study, based on a one-year greenhouse experiment, to elucidate the effects of Bacillus thuringiensis NL-11 on the microbial functions of abandoned mine soils. Our findings revealed that the application of microbial inoculants significantly enhanced the soil total carbon (TC), total sulfur (TS), organic carbon (SOC), available phosphorus (AP), ammonium (NH4[+]), urease, arylsulfatase, phosphatase, β-1,4-glucosidase (BG), β-1,4-N-acetylglucosaminidase (NAG). Moreover, this led to substantial improvements in plant height, as well as aboveground and belowground biomass. Microbial inoculants impacted functional gene structures without altering diversity. The normalized abundance of genes related to the degradation of carbon and nitrogen, methane metabolism, and nitrogen fixation were observed to increase, as well as the functional genes related to phosphorus cycling. Significant correlations were found between nutrient cycling gene abundance and plant biomass. Partial Least Squares Path Model analysis showed that microbial inoculants not only directly influenced plant biomass but also indirectly affected the plant biomass through C cycle modifications. This study highlights the role of microbial inoculants in promoting plant growth and soil restoration by improving soil properties and enhancing normalized abundance of nutrient cycling gene, making them essential for the recovery of abandoned mine sites.}, } @article {pmid40049896, year = {2025}, author = {Yu, Q and Hu, X and Qian, Y and Wang, Y and Shi, C and Qi, R and Heděnec, P and Nan, Z and Li, H}, title = {Virus communities rather than bacterial communities contribute more on nutrient pool in polluted aquatic environment.}, journal = {Journal of environmental sciences (China)}, volume = {154}, number = {}, pages = {550-562}, doi = {10.1016/j.jes.2024.08.026}, pmid = {40049896}, issn = {1001-0742}, mesh = {*Bacteria/metabolism/classification/genetics ; *Viruses ; Phosphorus/analysis ; RNA, Ribosomal, 16S/genetics ; Nitrogen/analysis ; Carbon/metabolism ; Water Microbiology ; Water Pollutants, Chemical/analysis ; Nutrients/analysis ; }, abstract = {The degradation of animal carcasses can lead to rapid waste release (e.g., pathogenic bacteria, viruses, prions, or parasites) and also result in nutrient accumulation in the surrounding environment. However, how viral profile responds and influences nutrient pool (carbon (C), nitrogen (N), phosphorus (P) and sulfur (S)) in polluted water caused by animal carcass decomposition had not been explored. Here, we combined metagenomic analysis, 16S rRNA gene sequencing and water physicochemical assessment to explore the response of viral communities under different temperatures (23 °C, 26 °C, 29 °C, 32 °C, and 35 °C) in water polluted by cadaver, as well as compare the contribution of viral/bacterial communities on water nutrient pool. We found that a total of 15,240 viral species were classified and mainly consisted of Siphoviridae. Both temperature and carrion reduced the viral diversity and abundance. Only a small portion of the viruses (∼8.8 %) had significant negative correlations with temperature, while most were not sensitive. Our results revealed that the viruses had lager contribution on nutrient pool than bacteria. Besides, viral-related functional genes involved in C, N, P and S cycling. These functional genes declined during carcass decomposition and covered part of the central nutrient cycle metabolism (including carbon sugar transformation, denitrification, P mineralization and extracelluar sulfate transfer, etc.). Our result implies that human regulation of virus communities may be more important than bacterial communities in regulating and managing polluted water quality and nutrition.}, } @article {pmid40049874, year = {2025}, author = {Yao, W and Chang, R and Chen, K and Yang, C and Lu, Y and Wang, S and Dong, K and Huang, B and Jin, R}, title = {Performance and mechanism of enhanced phosphorus release and volatile fatty acid production from Fe-P sludge via co-fermenting with agricultural wastes.}, journal = {Journal of environmental sciences (China)}, volume = {154}, number = {}, pages = {290-299}, doi = {10.1016/j.jes.2024.07.019}, pmid = {40049874}, issn = {1001-0742}, mesh = {*Phosphorus/metabolism ; *Fatty Acids, Volatile/metabolism ; *Sewage ; *Fermentation ; *Agriculture/methods ; *Waste Disposal, Fluid/methods ; Iron/metabolism ; }, abstract = {Anaerobic fermentation is an efficient method to extract phosphorus from excess sludge, thereby facilitating its recovery and mitigating the phosphorus resource shortage. However, the prevalent metal-bound phosphorus species within sludge was difficult to release into the fermentation liquor. To address this, this study evaluated the enhanced phosphorus release performance from sludge containing iron-phosphorus compounds (Fe-P) via co-fermenting it with agriculture wastes. Specifically, protein-rich feather (Feather Group) and polysaccharide-rich tea residue (Tea Group) was respectively dosed into batch-scale fermentation jar. Results showed that the Feather Group exhibited significantly higher levels of released soluble phosphorus (2.1 folds) and volatile fatty acids (41.4 folds) compared to the Control Group, with concentrations reaching up to 280 mg/L and 9366 mg chemical oxygen demand /L, respectively. The activities of α-glucosidase, neutral protease and acetate kinase in the Feather group were increased by 11.1 %, 92.3 % and 37.6 %, respectively, compared with the Control group. Methanogen abundance decreased while hydrolytic acid-producing bacteria and iron-reducing bacteria increased significantly after supplying agricultural wastes. Metagenomic analysis demonstrated a significant increase in genes related to acetic acid synthesis. Mechanism elucidation suggested that increased iron-reducing bacteria abundance promoted Fe[3+] reduction into Fe[2+], thus enhancing phosphorus release from Fe-P compounds. This work may provide valuable information for developing effective strategy to extract phosphorus resource from complex environmental wastes.}, } @article {pmid40049354, year = {2025}, author = {Sun, RZ and Pan, Y and Wang, J and Gao, T and Yu, HQ and Wang, J}, title = {Metabolic and Ecological Responses of Denitrifying Consortia to Different Carbon Source Strategies Under Fluctuating C/N Conditions.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121292}, doi = {10.1016/j.envres.2025.121292}, pmid = {40049354}, issn = {1096-0953}, abstract = {Frequent fluctuations in the carbon-to-nitrogen (C/N) ratio of urban wastewater influent can undermine denitrification performance, posing challenges for stable nitrogen removal. Although supplying additional carbon sources is a recognized strategy to mitigate these issues, the underlying microbial interactions and metabolic reconfigurations triggered by changing C/N ratios remain incompletely understood. Here, we employed methanol, glycerol, sodium acetate, and glucose in long-term denitrification reactors and integrated denitrification kinetics, 16S rRNA gene amplicon sequencing, metagenomic binning, and metabolic modeling to elucidate how these systems respond to a declining C/N ratio. Our results show that lower C/N ratios diminished denitrification efficiency in all treatments, with each carbon source eliciting distinct shifts in microbial assemblages. Fluctuations in the C/N ratio determine the extent of directional selection of microbial communities based on carbon source metabolism and induce significant changes in non-dominant microorganisms. Throughout the process, the synthesis potential of PHA is closely linked to the system's ability to withstand fluctuations. Notably, metabolic modeling indicated that heightened tricarboxylic acid (TCA) cycle activity in the methanol- and glucose-fed communities was associated with suboptimal nitrogen removal. These findings offer novel insights into the metabolic and ecological mechanisms governing carbon source-driven denitrification under fluctuating C/N conditions, providing a valuable framework for optimizing nitrogen removal in urban wastewater treatment systems.}, } @article {pmid40049094, year = {2025}, author = {Yu, C and He, Q and Nie, WB and Zhang, T and Wu, H and Yang, Y and Fu, S and Tan, X and Chen, Y}, title = {Effluent organic matter facilitates anaerobic methane oxidation coupled with nitrous oxide reduction in river sediments.}, journal = {Water research}, volume = {278}, number = {}, pages = {123415}, doi = {10.1016/j.watres.2025.123415}, pmid = {40049094}, issn = {1879-2448}, abstract = {Effluent organic matter (EfOM) from wastewater treatment plants (WWTPs) contains humic-like substances that function as electron shuttles, thereby facilitating microbially-mediated redox reactions. However, the mechanisms governing the coupled processes of anaerobic oxidation of methane (CH4) (AOM) and nitrous oxide (N2O) reduction in river sediments, which receive WWTPs effluents, remain poorly understood. In this study, an incubation experiment with anoxic river sediments was conducted to assess the impacts of EfOM on AOM and nitrous oxide reduction using different effluent dilution ratios. The results showed that EfOM significantly enhanced both processes. Specifically, the AOM rate increased from 8.1 to 14.3 μg gdw[-1] d[-1], while the N2O reduction rate increased from 29.2 to 56.5 μg gdw[-1] d[-1]. The results of batch tests demonstrated that AOM process enhanced N2O reduction in the presence of EfOM, highlighting the critical role of EfOM in linking these processes. Nitrate-dependent anaerobic methane oxidation (n-DAMO) archaea and denitrifying bacteria dominated the sediment incubated with EfOM. Metagenomic and metatranscriptomic analyses revealed that the denitrifying bacteria exclusively reduce N2O, confirming the role of EfOM in facilitating electron transfer between n-DAMO archaea and N2O reducers. This indicates that effluent discharge could be a potential factor driving the concurrent sinks of methane and nitrous oxide, offering a perspective for investigating the impacts of WWTPs effluent on greenhouse gas sinks in freshwater ecosystems.}, } @article {pmid40048953, year = {2025}, author = {Tamai, S and Okuno, M and Ogura, Y and Suzuki, Y}, title = {Genetic diversity of dissolved free extracellular DNA compared to intracellular DNA in wastewater treatment plants.}, journal = {The Science of the total environment}, volume = {970}, number = {}, pages = {178989}, doi = {10.1016/j.scitotenv.2025.178989}, pmid = {40048953}, issn = {1879-1026}, abstract = {Dissolved free extracellular DNA (free-exDNA) coexists with intracellular DNA (inDNA) in aquatic environments. Free-exDNA can be taken up by bacteria through transformation, and wastewater treatment plants (WWTPs) are positioned as potential hot spots for genetic contamination. However, studies comparing the composition of free-exDNA and inDNA is limited. This study employed colloidal adsorption and foam concentration method to recover free-exDNA from different WWTP stages and compared its diversity with inDNA via metagenomic analysis. Free-exDNA concentrations were observed to increase after chlorination. Genetic analysis revealed a higher abundance of specific genes following chlorination, suggesting that free-exDNA in effluent originated from bacterial death in secondary treated water. This result indicates that free-exDNA, which increases due to chlorination, is subsequently released into the catchment. Additionally, several high-risk antibiotic-resistance genes (ARGs) were detected that colocalized with mobile genetic elements. These ARGs were expected to have a high potential for gene transfer via transformation, and the risk was highlighted. Overall, these findings deepen our understanding of horizontal gene transfer risks in WWTPs.}, } @article {pmid40048849, year = {2025}, author = {Bargheet, A and Noordzij, HT and Ponsero, AJ and Jian, C and Korpela, K and Valles-Colomer, M and Debelius, J and Kurilshikov, A and Pettersen, VK}, title = {Dynamics of gut resistome and mobilome in early life: a meta-analysis.}, journal = {EBioMedicine}, volume = {114}, number = {}, pages = {105630}, doi = {10.1016/j.ebiom.2025.105630}, pmid = {40048849}, issn = {2352-3964}, abstract = {BACKGROUND: The gut microbiota of infants harbours a higher proportion of antibiotic resistance genes (ARGs) compared to adults, even in infants never exposed to antibiotics. Our study aims to elucidate this phenomenon by analysing how different perinatal factors influence the presence of ARGs, mobile genetic elements (MGEs), and their bacterial hosts in the infant gut.

METHODS: We searched MEDLINE and Embase up to April 3rd, 2023, for studies reporting infant cohorts with shotgun metagenomic sequencing of stool samples. The systematic search identified 14 longitudinal infant cohorts from 10 countries across three continents, featuring publicly available sequencing data with corresponding metadata. For subsequent integrative bioinformatic analyses, we used 3981 high-quality metagenomic samples from 1270 infants and 415 mothers.

FINDINGS: We identified distinct trajectories of the resistome and mobilome associated with birth mode, gestational age, antibiotic use, and geographical location. Geographical variation was exemplified by differences between cohorts from Europe, Southern Africa, and Northern America, which showed variation in both diversity and abundance of ARGs. On the other hand, we did not detect a significant impact of breastfeeding on the infants' gut resistome. More than half of detected ARGs co-localised with plasmids in key bacterial hosts, such as Escherichia coli and Enterococcus faecalis. These ARG-associated plasmids were gradually lost during infancy. We also demonstrate that E. coli role as a primary modulator of the infant gut resistome and mobilome is facilitated by its increased abundance and strain diversity compared to adults.

INTERPRETATION: Birth mode, gestational age, antibiotic exposure, and geographical location significantly influence the development of the infant gut resistome and mobilome. A reduction in E. coli relative abundance over time appears as a key factor driving the decrease in both resistome and plasmid relative abundance as infants grow.

FUNDING: Centre for Advanced Study in Oslo, Norway. Centre for New Antibacterial Strategies through the Tromsø Research Foundation, Norway.}, } @article {pmid40048707, year = {2025}, author = {Hernández-Verdin, I and Kirasic, E and Mokhtari, K and Barillot, N and Rincón de la Rosa, L and Sourdeau, E and Abada, Y and Le Tarff-Tavernier, M and Nichelli, L and Rozenblum, L and Kas, A and Mathon, B and Choquet, S and Houillier, C and Hoang-Xuan, K and Alentorn, A}, title = {Gut microbiome modulates the outcome in primary central nervous system lymphoma patients undergoing chemotherapy: an ancillary study from the BLOCAGE trial.}, journal = {Neuro-oncology}, volume = {}, number = {}, pages = {}, doi = {10.1093/neuonc/noaf059}, pmid = {40048707}, issn = {1523-5866}, abstract = {BACKGROUND: Primary central nervous system lymphoma (PCNSL) treatment relies on a high-dose methotrexate based chemotherapy (HD-MTX-based CT) regimen; however, whether there is a specific microbiota composition association with treatment response and clinical outcomes remains incompletely understood.

METHODS: We conducted a prospective study of PCNSL patients, included in the clinical trial NCT02313389 and the ancillary study NCT04253496 from 2020 to 2023, where patients were treated with first line HD-MTX-based polychemotherapy without a consolidation treatment. Stool (n=52), cerebrospinal fluid (CSF, n=52), and plasma samples (n=35) were collected before and/or after therapy initiation to perform metagenomic, flow cytometry, and metabolomic analyses. Plasma metabolomic data of 90 patients also included in the BLOCAGE clinical trial was subsequently used as a validation cohort.

RESULTS: Unsupervised clustering of microbial data identified two distinct gut microbial communities, differing in Parabacteroides distasonis abundance, which correlated with progression-free survival and overall survival in both uni- and multivariate analyses. Higher P. distasonis levels were linked to increased plasma betaine/valine metabolites and enhanced CD8 T cell infiltration in the CSF, suggesting a connection between gut microbiota and immune regulation. Stratifying the validation cohort by betaine/valine content confirmed these clinical associations.

CONCLUSIONS: Our findings suggest that gut microbiome communities modulate clinical outcomes in PCNSL patients undergoing standard treatment. Moreover, after future validation in external cohorts, the quantification of Parabacteroides distasonis could potentially provide a basis for patient stratification and guide personalized therapeutic strategies in the near future.}, } @article {pmid40047424, year = {2025}, author = {Li, N and Li, M and Zhang, H and Bai, Z and Fei, Z and Dong, Y and Zhang, X and Xiao, P and Sun, X and Zhou, D}, title = {Effects of post-adulthood environmental hygiene improvement on gut microbiota and immune tolerance in mice.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0247724}, doi = {10.1128/aem.02477-24}, pmid = {40047424}, issn = {1098-5336}, abstract = {UNLABELLED: Changes in diet, cleanliness, stress, and exercise patterns may contribute to the disappearance of various gut microbes in humans who relocate to developed countries from developing countries. To explore the impact of environmental cleanliness on the gut microbiota, adult mice housed in a general animal room were divided into three groups. The control group was subjected to an unchanged living environment, SPF mice were moved to a specific pathogen-free (SPF) animal room with higher environmental cleanliness, and SPFL (specific pathogen-free specific with a fecal leakage grid) mice were moved to the SPF animal room and reared in cages with the function of preventing mice from eating feces as much as possible. Metagenome sequencing results showed that the gut microbial diversity decreased after the environmental change, accompanied by a substantial loss in gut microbiota, including genera known to have protective effects against allergies and those involved in short-chain fatty acid production. Additionally, the abundance of functional genes involved in short-chain fatty acid metabolism, amino acid synthesis, vitamin metabolism, flagellar assembly, and bacterial chemotaxis decreased. The environmental hygiene improvement also resulted in significant increases in total serum IgE, IL-4, IL-5, and IL-13 levels in mice with artificially induced chronic inflammatory dermatosis. Compared with SPF mice, preventing mice from eating feces as much as possible decreased the gut microbial diversity but did not markedly change functional gene expression or total serum cytokine levels.

IMPORTANCE: Research has indicated that the human gut microbial diversity gradually decreases, while the prevalence of allergic diseases increases after movement from developing countries to developed countries. A healthy gut microbiota is necessary for proper human immune function. Movement from undeveloped to developed regions is often accompanied by an increase in environmental cleanliness. However, whether changes in environmental cleanliness are an important factor contributing to the decreased gut microbial diversity and increased prevalence of allergic diseases has not been reported. This study demonstrates the impact of increased environmental cleanliness on gut microbiota and susceptibility to allergic diseases and contributes to a better understanding of the increased incidence rate of various chronic diseases.}, } @article {pmid40047330, year = {2025}, author = {Gong, S and Li, M and Gao, J and Huang, S and Song, W and Sun, L}, title = {Cucumaria frondosa intestines and ovum hydrolysates intervention ameliorates the symptoms of dextran sulfate sodium-induced colitis by modulating gut microbiota and its metabolites.}, journal = {Journal of food science}, volume = {90}, number = {3}, pages = {e70106}, doi = {10.1111/1750-3841.70106}, pmid = {40047330}, issn = {1750-3841}, support = {42106111//National Natural Science Foundation of China/ ; ZR2021QD030//Natural Science Foundation of Shandong Province/ ; NYJG202303//Fund of Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, China/ ; 2023KJ241//Program for Scientific Research Innovation Team of Young Scholar in Colleges and Universities of Shandong Province/ ; R20076//Doctoral Startup Project of Guangdong Ocean University funded by W.S/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Colitis/chemically induced ; *Dextran Sulfate ; Mice ; Male ; Disease Models, Animal ; Mice, Inbred C57BL ; Colon/metabolism/microbiology/drug effects ; Cytokines/metabolism ; Intestines/microbiology/drug effects ; }, abstract = {Colitis, a troublesome inflammatory disease that significantly impacts daily life, has garnered considerable attention in recent times. Protolysates play a crucial role in the treatment of colitis, and the intestines and ovum of Cucumaria frondosa represent a readily available source of these hydrolysates. However, the effects of C. frondosa intestines and ovum hydrolysates (CFHs) on colitis have not been thoroughly investigated. We initially examined the molecular weight distribution of CFHs and found that the fraction of molecules with a weight less than 1000 Da accounted for 86.98%, indicating that the hydrolysis primarily produced oligopeptides. Subsequently, we employed a dextran sulfate sodium-induced experimental colitis model to assess the therapeutic potential of CFHs. The findings indicated that preventive administration of CFHs dramatically attenuated the pathological manifestations associated with colitis in mice, including weight loss, colon shortening, and tissue damage. Furthermore, CFHs suppressed the secretion of pro-inflammatory cytokines IL-6, TNF-α, and IL-1β, as well as MPO in colon tissue. Metagenomic sequencing demonstrated that CFHs could restore balance to the dysregulated gut microbiota by reinforcing Bacteroidota and suppressing Verrucomicrobia populations, impacting various microbial functions. Metabolomic analyses further revealed that CFHs exhibited a more efficacious modulatory effect on DSS-induced metabolic abnormalities, including amino acid biosynthesis, linoleic acid metabolism, and dopaminergic synapses. In conclusion, CFHs showed promise in alleviating colitis, laying the groundwork for the development and application of CFHs as functional food for colitis relief.}, } @article {pmid40047235, year = {2025}, author = {Garg, RK}, title = {Tuberculosis of the central nervous system: current concepts in diagnosis and treatment.}, journal = {Current opinion in neurology}, volume = {}, number = {}, pages = {}, pmid = {40047235}, issn = {1473-6551}, abstract = {PURPOSE OF REVIEW: The outcome of central nervous system (CNS) tuberculosis has shown little improvement over several decades, with diagnosis remaining unconfirmed in nearly half of the cases. This review highlights current insights and advancements in the diagnosis and treatment of CNS tuberculosis.

RECENT FINDINGS: Miliary pulmonary tuberculosis is often linked to CNS tuberculosis and is associated with a worse prognosis. Complications, such as, optochiasmatic arachnoiditis, strokes, and transverse myelitis severely affect prognosis and quality of life. Nearly half of tuberculous meningitis patients exhibited impaired cognition. Diagnosing CNS tuberculosis is challenging because of the low accuracy of standard tests. Advanced techniques like metagenomic and nanopore sequencing enhance detection but are hindered by high costs and limited access. Treatment outcomes remain suboptimal but approaches such as higher drug doses, novel medications, and host-directed therapies are being explored. Drug-resistant tuberculous meningitis is increasingly recognized, posing significant challenges to both diagnosis and treatment. Artificial intelligence (AI) enhances care by enabling early diagnosis, disease monitoring, and personalized treatments, improving outcomes.

SUMMARY: CNS tuberculosis diagnosis faces challenges due to limited sensitivity and delayed results of available tests. Treatments remain suboptimal, with multidrug-resistant cases posing high mortality risks. AI aids in early diagnosis and personalized care.}, } @article {pmid40046986, year = {2025}, author = {Zhang, D and Deng, M and Li, F and Shen, R}, title = {A Report of Primary Pyogenic Ventriculitis Caused by Streptococcus Constellatus Diagnosed by Metagenomic Next-Generation Sequencing.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {1209-1214}, pmid = {40046986}, issn = {1178-6973}, abstract = {BACKGROUND: Primary ventriculitis is a rare but serious brain infection characterized by inflammation of the ependyma and purulence within the ventricular system. Due to the challenges in early diagnosis and the potential for suboptimal treatment, this condition carries a significant risk of complications such as recurrence, hydrocephalus, and death. Metagenomic next-generation sequencing (mNGS) enables the rapid and broad-spectrum identification of pathogens, facilitating timely and precise diagnosis.

CASE REPORT: This study presents the first reported case of primary ventriculitis caused by Streptococcus constellatus. An 81-year-old female patient with hydrocephalus and clinical signs of central nervous system infection was diagnosed with primary ventriculitis based on brain magnetic resonance imaging (MRI) and cerebrospinal fluid (CSF) analysis using mNGS. The patient underwent external ventricular drainage (EVD) and received a five-week course of ceftriaxone and linezolid. Following timely and targeted therapy, she demonstrated significant clinical improvement and was discharged without residual symptoms.

CONCLUSION: Key insights from this case include: 1) mNGS is an invaluable tool for the early and accurate diagnosis of primary ventriculitis; 2) MRI is indispensable for identifying characteristic radiological features of the condition; 3) prompt initiation and completion of appropriate antibiotic regimens significantly improve clinical outcomes.}, } @article {pmid40046887, year = {2025}, author = {Kim, M and Damronglerd, P and Molina Garcia, S and Yetmar, ZA and Razi, S and Ranganath, N and Mahmood, M and Abu Saleh, OM}, title = {Illuminating the Challenges and Diagnostic Utility of Plasma Microbial Cell-Free DNA Sequencing in Suspected Infective Endocarditis: A Retrospective Observational Cohort Study.}, journal = {Open forum infectious diseases}, volume = {12}, number = {3}, pages = {ofaf099}, pmid = {40046887}, issn = {2328-8957}, abstract = {BACKGROUND: Infective endocarditis (IE) is a life-threatening infection often challenging to diagnose, particularly in culture-negative cases. Plasma microbial cell-free DNA (mcfDNA) sequencing has shown potential for detecting pathogens in IE. However, its clinical utility, diagnostic impact, and limitations remain debated. This study evaluates its use in diagnosing and managing IE in a tertiary care setting.

METHODS: This single-center retrospective cohort study included adult patients (≥18 years) who underwent mcfDNA sequencing via the Karius test for suspected IE at Mayo Clinic Rochester between December 2019 and February 2024. Diagnostic classification followed the 2023 Duke-International Society of Cardiovascular Infectious Diseases criteria. Data on demographics, clinical features, routine microbiologic workup, and mcfDNA sequencing results were collected. Statistical analysis was conducted to evaluate diagnostic utility and treatment impact.

RESULTS: Among 141 patients, 66 had a diagnosis of IE, with mcfDNA sequencing identifying pathogens in 60.6% of them, compared with 39.4% with routine workup. mcfDNA sequencing was the sole microbiologic test with positive results in 33.3% of patients, leading to antimicrobial adjustments in 50.0% of that group. Clinically insignificant mcfDNA sequence detection occurred in 28.6% of patients without a diagnosis of IE.

CONCLUSIONS: mcfDNA sequencing is a valuable adjunctive tool for diagnosing culture-negative IE and guiding antimicrobial therapy when clinical suspicion is high. However, its utility depends on appropriate clinical context, highlighting the need for careful test interpretation and further prospective studies to assess patient-centered outcomes and cost-effectiveness.}, } @article {pmid40046856, year = {2025}, author = {Tan, L and He, Z and Liang, Y and Wang, K and Chen, X}, title = {Correlation analysis between the severity of respiratory syncytial virus pneumonia and the expression levels of inflammatory cytokines in bronchoalveolar lavage fluid among infants and young children.}, journal = {Frontiers in pediatrics}, volume = {13}, number = {}, pages = {1482029}, pmid = {40046856}, issn = {2296-2360}, abstract = {PURPOSE: RSV is the primary cause of lower respiratory tract infections in infants and young children. Current study aims to investigate the correlation between the severity of respiratory syncytial virus pneumonia (RSVP) in infants and young children and the number of RSV infection sequences as well as the levels of cytokines in bronchoalveolar lavage fluid (BALF).

METHODS: Metagenomics next-generation sequencing (mNGS) and enzyme-linked immunosorbent assay (ELISA) were used to detect the number of RSV infection sequences and the levels of related inflammatory cytokines in BALF samples. Comparisons between groups and Logistic regression analysis were performed to examine the differences in RSV infection sequences and inflammatory cytokine levels between the sRSVP and nsRSVP groups. Spearman's correlation coefficient was used to analyze the correlations among PCIS, RSV infection sequences, and inflammatory cytokines. Finally, ROC curve analysis was conducted to assess the diagnostic performance of inflammatory cytokines as biomarkers in determining the severity of RSVP.

RESULTS: A total of 49 infants and young children diagnosed with RSV infection were enrolled and divided into severe RSVP (sRSVP) and non-severe RSVP (nsRSVP) groups based on the pediatric critical illness score (PCIS) scale. The levels of Interleukin (IL)-6, IL-8, IL-10, tumor necrosis factor α (TNF-α), IL-17A, and monocyte chemotactic protein 1 (MCP-1) as well as the number of RSV sequences in BALF were significantly higher in the sRSVP group than in the nsRSVP group. Additionally, elevated levels of IL-6, IL-10, TNF-α, IL-17A, and the number of RSV sequences were identified as risk factors for the severity of RSVP. Spearman's correlation analysis revealed significant negative correlations between the levels of IL-6, IL-10, TNF-α, IL-17A, and MCP-1 in BALF with PCIS, and significant positive correlations with the number of RSV sequences. Furthermore, a significant negative correlation was observed between RSV sequence count and PCIS. ROC curve analysis showed that the levels of IL-6, IL-10, TNF-α, IL-17A, and MCP-1, as well as their combined diagnostic approach, exhibited high diagnostic performance in determining the severity of RSVP.

CONCLUSION: The levels of inflammatory cytokines and RSV sequences in BALF are significantly correlated with the severity of RSVP in infants and young children. The levels of IL-6, IL-10, TNF-α, IL-17A, and MCP-1 can serve as potential biomarkers for diagnosing the severity of RSVP.}, } @article {pmid40046438, year = {2025}, author = {Lin, K and Lin, W and Guo, Z and Chen, C and Chen, L and Cai, X}, title = {Plasma exosomal miRNA expression and gut microbiota dysbiosis are associated with cognitive impairment in Alzheimer's disease.}, journal = {Frontiers in neuroscience}, volume = {19}, number = {}, pages = {1545690}, pmid = {40046438}, issn = {1662-4548}, abstract = {INTRODUCTION: The gut microbiota composition and the expression profiles of microRNAs (miRNAs) in the brain tissue, cerebrospinal fluid, and blood of patients with Alzheimer's disease (AD) differ significantly from those with normal cognition function. The study aimed to initially explore the relationship between plasma exosomal microRNAs, gut microbiota, and cognitive impairment, providing insights into the pathogenesis and treatment of AD.

METHODS: The study enrolled 8 participants with AD and 8 participants with normal cognition. The Mini-Mental State Examination (MMSE) was utilized to evaluate cognitive function. High-throughput sequencing was used to identify differentially expressed miRNAs in plasma exosomes, while metagenomic sequencing was employed to detect differences in the abundance of gut microbiota. Furthermore, the associations among them were analyzed.

RESULTS: Four exosomal miRNAs and 14 microbiota taxa, which exhibited differential expression and abundance, respectively, in comparison between AD group and normal cognition group, were identified to be significantly associated with MMSE scores. Notably, the abundance of potential probiotics, including Faecalibacterium prausnitzii, Roseburia intestinalis and Roseburia inulinivorans, which was decreased in AD patients, exhibited positive correlations with specific exosomal miRNAs: Roseburia intestinalis correlated with miR-3120-3p and miR-6529-5p; Roseburia inulinivorans correlated with miR-3120-3p, miR-6529-5p and miR-124-3p; Faecalibacterium prausnitzii correlated with miR-3120-3p.

DISCUSSION: The study revealed a close association among gut microbiota, plasma exosomal miRNAs, and cognitive impairment in AD, and suggested that specific components of gut microbiota and exosomal miRNAs may serve as potential biomarkers and therapeutic targets for AD on the microbiota-gut-brain axis.}, } @article {pmid40046298, year = {2025}, author = {Sun, W and Li, M and Zhu, X}, title = {Bordetella pertussis bacteremia in infants co-infected with cytomegalovirus and respiratory syncytial virus.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1544935}, pmid = {40046298}, issn = {1664-302X}, abstract = {INTRODUCTION: Hematogenous infections caused by Bordetella pertussis are rare. This study aimed to increase clinicians' knowledge of B. pertussis bacteremia.

METHODS: We described a case of an infant with B. pertussis bacteremia, searched and reviewed for B. pertussis bacteremia-related literatures published in the PubMed database between 1946 to 2022.

RESULTS: A 3-month-old male infant was admitted to the hospital with a respiratory tract infection. Respiratory pathogen testing indicated the presence of B. pertussis, cytomegalovirus, and respiratory syncytial viruses. Blood metagenomic next-generation sequencing (mNGS) confirmed B. pertussis bacteremia. After 32 days of anti-infective treatment and supportive therapy, the patient's condition improved, and he was discharged. The literature review found that B. pertussis bacteremia is rare, often with fever as the first symptom, and is most common in individuals with underlying diseases or prolonged immunosuppressive therapy.

DISCUSSION: In infants lacking specific protective antibodies against B. pertussis, B. pertussis bacteremia should be considered when bacteremia-associated clinical manifestations are present and the causative organism remains undetected. Timely refinement of mNGS can help clarify the diagnosis.}, } @article {pmid40046038, year = {2025}, author = {Bird, E and Pickens, V and Molik, D and Silver, K and Nayduch, D}, title = {BALROG-MON: a high-throughput pipeline for Bacterial AntimicrobiaL Resistance annOtation of Genomes-Metagenomic Oxford Nanopore.}, journal = {microPublication biology}, volume = {2025}, number = {}, pages = {}, pmid = {40046038}, issn = {2578-9430}, abstract = {BALROG-MON is a Nextflow pipeline for automated analysis of metagenomic long-read data to detect pathogens, annotate antimicrobial resistance genes (ARGs), link ARGs to specific pathogens, predict ARG origin (e.g., plasmid, chromosomal) and optionally perform steps like community analysis. With both assembly-based and assembly-free workflows, BALROG-MON is applicable to a wide range of sample types with low or high coverage, varying complexities and origins. Optional genome binning provides a comprehensive overview of ARGs within the dataset. BALROG-MON additionally presents results in summarized reports, overall serving as a flexible analysis tool for exploring diverse metagenomic samples for pathogens and antibiotic resistance.}, } @article {pmid40045326, year = {2025}, author = {Zhang, R and Yu, J and Shang, X and Wang, Z and Li, H and Cao, B}, title = {Heterogeneity in clinical patterns of adult lung abscess patients: an 8-year retrospective study in a tertiary hospital.}, journal = {BMC pulmonary medicine}, volume = {25}, number = {1}, pages = {101}, pmid = {40045326}, issn = {1471-2466}, support = {NO. 82030002/H0102//National Natural Science Foundation of China/ ; NO.20220484049//Beijing Nova Program of Science and Technology under grant/ ; No. ZRJY2021-QM09//National High Level Hospital Clinical Research Funding, the Elite Medical Professionals Project of China-Japan Friendship Hospital/ ; }, mesh = {Humans ; *Lung Abscess/microbiology ; Male ; Retrospective Studies ; Female ; Middle Aged ; China/epidemiology ; *Tertiary Care Centers ; Aged ; *Tomography, X-Ray Computed ; Adult ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Hospital Mortality ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {BACKGROUND: The widespread use of broad-spectrum antibiotics has led to changes in both the microbiological and clinical characteristics of lung abscesses. It is necessary to re-evaluate the bacterial spectrum associated with these infections. As a novel method for pathogen detection, metagenomic next-generation sequencing (mNGS) is increasingly being applied in clinical practice. There is limited research evaluating the use of mNGS in patients with lung abscesses.

METHODS: A retrospective analysis was conducted on patients with lung abscess who were hospitalized between July 2015 and July 2023 at a teaching hospital in China. Patients who underwent both computerized tomography (CT) imaging and conventional pathogen testing were included in the study. The efficacy of pathogen detection using conventional methods was compared with that of mNGS. Additionally, the clinical and radiological features were analyzed to provide a comprehensive understanding of the disease patterns.

RESULTS: A total of 782 patients with lung abscess were included in the study and hematogenous abscess accounting for 7.16% (56/782) of cases. The overall hospital mortality rate was 1.53%. The mean age of the patients with lung abscess was 60 years, with a male predominance (80.2%). A significant proportion of patients had comorbid conditions, including diabetes (29.7%) and cardiovascular disease (18.2%). Lung abscesses were predominantly located in the right lung, and pleural effusion was more commonly observed in the deceased group. The detection rate of pathogen via conventional test was lower at 41.8% (327/782). Among patients with positive mNGS results, only 51.9% had pathogens identified through conventional testing methods. Klebsiella pneumoniae was the most frequently detected pathogen by conventional culture, while mNGS identified was Parvimonas micra. Infections caused solely by anaerobic bacteria or facultative anaerobes were associated with shorter hospital stays. Patient infected with Gram-negative bacilli (GNB) had a higher proportion of liver abscesses (11.8%).

CONCLUSION: Compared to conventional testing methods, mNGS demonstrates superior performance in detecting anaerobic and facultative anaerobic bacteria. The low detection rate of conventional tests may result in an underestimation of the clinical significance of anaerobic bacteria infections. In patients with lung abscess caused by GNB, hematogenous dissemination, liver abscess and diabetes were more commonly observed and these patients tended to have longer hospital stays.}, } @article {pmid40045185, year = {2025}, author = {Freund, L and Hung, C and Topacio, TM and Diamond, C and Fresquez, A and Lyons, TW and Aronson, EL}, title = {Diversity of sulfur cycling halophiles within the Salton Sea, California's largest lake.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {120}, pmid = {40045185}, issn = {1471-2180}, support = {NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; }, mesh = {California ; *Sulfur/metabolism ; *Microbiota ; *Lakes/microbiology ; *Seawater/microbiology/chemistry ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Seasons ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Biodiversity ; }, abstract = {BACKGROUND: Microorganisms are the biotic foundation for nutrient cycling across ecosystems, and their assembly is often based on the nutrient availability of their environment. Though previous research has explored the seasonal lake turnover and geochemical cycling within the Salton Sea, California's largest lake, the microbial community of this declining ecosystem has been largely overlooked. We collected seawater from a single location within the Salton Sea at 0 m, 3 m, 4 m, 5 m, 7 m, 9 m, 10 m, and 10.5 m depths in August 2021, December 2021, and April 2022.

RESULTS: We observed that the water column microbiome significantly varied by season (R[2] = 0.59, P = 0.003). Temperature (R[2] = 0.27, P = 0.004), dissolved organic matter (R[2] = 0.13, P = 0.004), and dissolved oxygen (R[2] = 0.089, P = 0.004) were significant drivers of seasonal changes in microbial composition. In addition, several halophilic mixotrophs and other extremotolerant bacteria were consistently identified in samples across depths and time points, though their relative abundances fluctuated by season. We found that while sulfur cycling genes were present in all metagenomes, their relative coverages fluctuated by pathway and season throughout the water column. Sulfur oxidation and incomplete sulfur oxidation pathways were conserved in the microbiome across seasons.

CONCLUSIONS: Our work demonstrates that the microbiome within the Salton Seawater has the capacity to metabolize sulfur species and utilize multiple trophic strategies, such as alternating between chemorganotrophy and chemolithoautrophy, to survive this harsh, fluctuating environment. Together, these results suggest that the Salton Sea microbiome is integral in the geochemical cycling of this ever-changing ecosystem and thus contributes to the seasonal dynamics of the Salton Sea. Further work is required to understand how these environmental bacteria are implicated relationship between the Salton Sea's sulfur cycle, dust proliferation, and respiratory distress experienced by the local population.}, } @article {pmid40045177, year = {2025}, author = {Torshizi Esfahani, A and Zafarjafarzadeh, N and Vakili, F and Bizhanpour, A and Mashaollahi, A and Karimi Kordestani, B and Baratinamin, M and Mohammadpour, S}, title = {Gut Microbiome in Colorectal Cancer: Metagenomics from Bench to Bedside.}, journal = {JNCI cancer spectrum}, volume = {}, number = {}, pages = {}, doi = {10.1093/jncics/pkaf026}, pmid = {40045177}, issn = {2515-5091}, abstract = {Colorectal cancer (CRC) is a major global health challenge. Emerging research highlights the pivotal role of the gut microbiota in influencing CRC risk, progression, and treatment response. Metagenomic approaches, especially high-throughput shotgun sequencing, have provided unprecedented insights into the intricate connections between the gut microbiome and CRC. By enabling comprehensive taxonomic and functional profiling, metagenomics has revealed microbial signatures, activities, and biomarkers associated with colorectal tumorigenesis. Furthermore, metagenomics has shown a potential to guide patient stratification, predict treatment outcomes, and inform microbiome-targeted interventions. Despite remaining challenges in multi-omics data integration, taxonomic gaps, and validation across diverse cohorts, metagenomics has propelled our comprehension of the intricate gut microbiome-CRC interplay. This review underscores the clinical relevance of microbial signatures as potential diagnostic and prognostic tools in CRC. Furthermore, it discusses personalized treatment strategies guided by this omics' approaches.}, } @article {pmid40044917, year = {2025}, author = {Štůsková, K and Vavřiník, A and Hakalová, E and Čechová, J and Gramaje, D and Eichmeier, A}, title = {Arbuscular mycorrhizal fungi strongly influence the endorhizosphere of grapevine rootstock with soil type as a key factor.}, journal = {Mycorrhiza}, volume = {35}, number = {2}, pages = {17}, pmid = {40044917}, issn = {1432-1890}, support = {CZ.02.1.01/0.0/0.0/16_025/0007314//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; CZ.02.1.01/0.0/0.0/16_025/0007314//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; CZ.02.1.01/0.0/0.0/16_025/0007314//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; CZ.02.1.01/0.0/0.0/16_025/0007314//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; IGA-ZF/2022-ST2-004//Internal Grant Agency, Mendel university in Brno/ ; IGA-ZF/2022-ST2-004//Internal Grant Agency, Mendel university in Brno/ ; }, mesh = {*Mycorrhizae/physiology ; *Vitis/microbiology ; *Soil Microbiology ; *Soil/chemistry ; Czech Republic ; Plant Roots/microbiology ; Mycobiome ; Basidiomycota/genetics/physiology ; Rhizosphere ; Phosphorus/metabolism/analysis ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) play a crucial role in enhancing the health and productivity of host plants, including grapevine. By forming symbiotic relationships with plant roots, AMF significantly improve water uptake and nutrient absorption, particularly phosphorus (P) and nitrogen (N). This study evaluated the microbiome composition and AMF colonization in the grapevine endorhizosphere across five wine-growing sub-regions in the Czech Republic. In all five sub-regions, in terms of composition of the fungal microbiome, the phyla Ascomycetes and Basidiomycetes were most numerous. Additionally, the study confirmed that LSU primers are more sensitive than ITS primers for AMF sequencing. While the representation of the phylum Glomeromycetes ranged from 0.07% to 5.65% in the ITS library, it was significantly higher, ranging from 83.74% to 98.71%, in the LSU library. The most significant difference compared to other sub-regions was observed in the Slovácko sub-region, where the soil had a low pH, a different texture (sandy loam), reduced micronutrient concentration, and low organic matter. The application of chemical plant protection products to grapevines also could have played a significant role, with 49 applications recorded in the Slovácko sub-region during the three years preceding sample collection. In other sub-regions, chemical treatments were conducted only 19-26 times. These factors resulted in only trace amounts of AMF being detected in Slovácko. Furthermore, it was demonstrated that AMF positively influenced the phosphorus concentration in the soil and reduced the presence of certain fungal pathogens.}, } @article {pmid40044690, year = {2025}, author = {Zheng, K and Sun, J and Liang, Y and Kong, L and Paez-Espino, D and Mcminn, A and Wang, M}, title = {VITAP: a high precision tool for DNA and RNA viral classification based on meta-omic data.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {2226}, pmid = {40044690}, issn = {2041-1723}, support = {41976117//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42176111//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*RNA, Viral/genetics ; *RNA Viruses/genetics/classification/isolation & purification ; *DNA Viruses/genetics/classification ; *DNA, Viral/genetics ; Software ; Phylogeny ; Genome, Viral/genetics ; Metagenomics/methods ; Virome/genetics ; Computational Biology/methods ; }, abstract = {The rapid growth in the number of newly identified DNA and RNA viral sequences underscores the need for an accurate and comprehensive classification system for all viral realms at different taxonomic levels. Here, we establish the Viral Taxonomic Assignment Pipeline (VITAP), which addresses classification challenges by integrating alignment-based techniques with graphs, offering high precision in classifying both DNA and RNA viral sequences and providing confidence level for each taxonomic unit. This tool automatically updates its database in sync with the latest references from the International Committee on Taxonomy of Viruses (ICTV), efficiently classifying viral sequences as short as 1,000 base pairs to genus level. VITAP possesses good generalization capabilities, maintaining accuracy comparable to other pipelines while achieving higher annotation rates across most DNA and RNA viral phyla. Its application in deep-sea viromes has led to significant taxonomic updates, providing comprehensive diversity information of viruses from deep-sea. VITAP is available at https://github.com/DrKaiyangZheng/VITAP .}, } @article {pmid40044673, year = {2025}, author = {Wood, JR and Zhou, C and Cole, TL and Coleman, M and Anderson, DP and Lyver, PO and Tan, S and Xiang, X and Long, X and Luo, S and Lou, M and Southon, JR and Li, Q and Zhang, G}, title = {Sedimentary DNA insights into Holocene Adélie penguin (Pygoscelis adeliae) populations and ecology in the Ross Sea, Antarctica.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {1798}, pmid = {40044673}, issn = {2041-1723}, mesh = {Animals ; Antarctic Regions ; *Spheniscidae/genetics ; *DNA, Mitochondrial/genetics ; *Geologic Sediments ; Phylogeny ; Seals, Earless ; Metagenome ; Ecosystem ; Diet ; }, abstract = {We report 156 sediment metagenomes from Adélie penguin (Pygoscelis adeliae) colonies dating back 6000 years along the Ross Sea coast, Antarctica, and identify marine and terrestrial eukaryotes, including locally occurring bird and seal species. The data reveal spatiotemporal patterns of Adélie penguin diet, including spatial patterns in consumption of cnidarians, a historically overlooked component of Adélie penguin diets. Relative proportions of Adélie penguin mitochondrial lineages detected at each colony are comparable to those previously reported from bones. Elevated levels of Adélie penguin mitochondrial nucleotide diversity in upper stratigraphic samples of several active colonies are consistent with recent population growth. Moreover, the highest levels of Adélie penguin mitochondrial nucleotide diversity recovered from surface sediment layers are from the two largest colonies, indicating that sedaDNA could provide estimates for the former size of abandoned colonies. SedaDNA also reveals prior occupation of the Cape Hallett Adélie penguin colony site by southern elephant seal (Mirounga leonina), demonstrating how terrestrial sedaDNA can detect faunal turnover events in Antarctica driven by past climate or sea ice conditions. Low rates of cytosine deamination indicate exceptional sedaDNA preservation within the region, suggesting there is high potential for recovering much older sedaDNA records from local Pleistocene terrestrial sediments.}, } @article {pmid40043990, year = {2025}, author = {Lou, D and Xiao, S and Cui, J and Duan, J and Duan, H and Cao, Y and Wang, D and Zhou, B and Tan, J}, title = {Discovery and characterization of the first hyperthermophilic 3-quinuclidinone reductase from hot-spring metagenomes.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {141706}, doi = {10.1016/j.ijbiomac.2025.141706}, pmid = {40043990}, issn = {1879-0003}, abstract = {Extremozymes play an essential part in the biosynthesis of pharmaceuticals (intermediates). In this study, a mixed assembly was performed for five metagenomes from hot springs. Via a series of procedures, including homology analysis, heterologous expression, and catalytic property characterization, the first hyperthermophilic 3-quinuclidinone reductase (SbQR) was successfully identified. The SbQR exhibits an optimal temperature of ≥95 °C and demonstrates remarkable thermal stability, with over 80 % of its activity retained following a 48-hour incubation at 50 °C. At particular concentrations, Mg[2+], Na[+], and Mn[2+] can substantially enhance the enzymatic activity. However, no significant influence of K[+] on the activity of SbQR was detected within the concentration range of 0-400 mM. Employing AlphaFold2, the three-dimensional structure of SbQR was predicted, which presents the typical traits of the Rossmann fold and is classified as a member of the short-chain dehydrogenases/reductases (SDR) superfamily. Molecular dynamics simulations were carried out and the results showed that when the temperature was increased to 390 K, the flexibility of residues 90-104 and the C-terminal increased significantly. This increase might lead to the destruction of the three-dimensional structure of the enzyme. In conclusion, this study identified the first hyperthermophilic 3-quinuclidinone reductase, providing a potential biocatalyst for the biopreparation of (R)-3-quinuclidinol.}, } @article {pmid40043973, year = {2025}, author = {Liu, N and Dai, S and Fan, X and Li, B and Chen, M and Gong, P and Chen, X}, title = {In vitro fermentation of Auricularia auricula polysaccharides and their regulation of human gut microbiota and metabolism.}, journal = {International journal of biological macromolecules}, volume = {306}, number = {Pt 4}, pages = {141714}, doi = {10.1016/j.ijbiomac.2025.141714}, pmid = {40043973}, issn = {1879-0003}, abstract = {Auricularia auricula is abundant in polysaccharides that received increasing attention due to their variety biological activities and prebiotic potential. In order to explore the role of A. auricula polysaccharides (AAP) in regulating human gut microbiota and metabolic health, this study employed metagenomic and metabolomic analyses to examine the impact of AAP on the gut microbiota via in vitro fecal fermentation experiments. After in vitro fermentation, the data indicated that gut microbiota utilized AAP to produce rich short-chain fatty acids (SCFAs) including acetic acid, propionic acid, butyric acid and modulate gut microbiota structure, such as increasing the proportion of Bacteroidetes to Firmicutes, elevating the abundance of beneficial bacteria, including Bacteroides, especially the Parabacteroides, and inhibiting the abundance of harmful bacteria such as Bilophila, Morganella, and Escherichia-Shigella. Furthermore, the metabolomic analysis indicated that AAP utilization by gut microbes substantially alters the metabolic profile, in which 26 potential biological biomarkers were found and affects tryptophan, bile acids, purines, and butyric acid pathways to promote host health. In conclusion, this research indicated that AAP has a prebiotic potential, which can regulate the gut microbiota and promote host health. Moreover, this study provided scientific evidence for using AAP as a functional food with prebiotic effect.}, } @article {pmid40043931, year = {2025}, author = {Li, HQ and Wang, WL and Shen, YJ and Su, JQ}, title = {Mangrove Plastisphere as a Hotspot for High-Risk Antibiotic Resistance Genes and Pathogens.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121282}, doi = {10.1016/j.envres.2025.121282}, pmid = {40043931}, issn = {1096-0953}, abstract = {Microplastics (MPs) are critical vectors for the dissemination of antibiotic resistance genes (ARGs); however, the prevalence and ecological risks of high-risk ARGs in mangrove ecosystems-globally vital yet understudied coastal habitats-remain poorly understood. To address this gap, this study investigated polyethylene, polystyrene, and polyvinyl chloride incubated in mangrove sediments for one month, focusing on high-risk ARGs, virulence gene (VGs), and pathogenic antibiotic-resistant bacteria within the mangrove plastisphere. High-throughput PCR and metagenomic analyses revealed that high-risk ARGs, VGs, and mobile genetic elements (MGEs) were significantly enriched on MPs compared to surrounding sediments. Pathogenic bacteria and MGEs were also more abundant in the plastisphere, highlighting its role as a hotspot for ARG dispersal. Metagenome-assembled genome analysis identified Pseudomonas and Bacillus as key hosts for ARGs, MGEs, and VGs, particularly multidrug resistance genes, integrase genes, and adherence factors. Notably, polystyrene harbored the highest abundance of pathogenic bacteria carrying ARGs, MGEs, and VGs, and mangrove root exudates were found to amplify horizontal gene transfer on MPs, uncovering a previously overlooked mechanism driving antibiotic resistance in coastal ecosystems. These findings not only elucidate how MPs accelerate the spread of ARGs, but also underscore the urgent need for targeted mitigation strategies to address the adverse impacts microplastic pollution on human, animal, and environmental health.}, } @article {pmid40043916, year = {2025}, author = {Yang, H and Zhu, X and Zhan, Z and Wu, X and Mou, S and Zhou, P and Peng, Q and Wang, W and Teng, H and Tang, H}, title = {Metagenomic Analysis of Pathogenic Microorganisms in Bloodstream Infections Following Venomous Snakebites.}, journal = {Toxicon : official journal of the International Society on Toxinology}, volume = {}, number = {}, pages = {108304}, doi = {10.1016/j.toxicon.2025.108304}, pmid = {40043916}, issn = {1879-3150}, abstract = {PURPOSE: This study aimed to investigate the biometric characterization of pathogenic microorganisms associated with bloodstream infections in patients bitten by venomous snakes, and to determine whether the composition of these microorganisms influences the effects of snake venom.

METHODS: The composition and relative abundance of microorganisms were statistically analyzed using metagenomic next-generation sequencing (mNGS) on blood samples from patients with varying degrees of snakebite injuries. These patients were admitted to the our study.

RESULTS: In the light injury group (group L), the dominant phylum and genus were Pseudomonadota (73.31%) and Pseudomonas (35.32%). In the moderate injury group (group M), the predominant phylum was Bacillota (56.74%) and Aerococcus (45.45%). There was no statistically significant difference in the microbial composition between group L and group M based on α- and β- diversity analyses. LEfSe differential analysis revealed that the absolute abundances of Actinomycetota and Actinomycetes were higher in group L, while Pseudomonas aeruginosa emerged as a significantly differential species in Group M.

CONCLUSION: The study found that differences in bacterial bloodstream infections due to venomous snakebite may enhance the effects of snake venom, leading to more severe injuries. The mNGS technique can rapidly detect pathogens related to venomous snakebites and has the potential for broader clinical use.}, } @article {pmid40043765, year = {2025}, author = {Yang, Y and Wu, X and Xu, Y and Shuang, Q and Xia, YN}, title = {Influence of Feeding Systems on the Microbial Community and Flavor Characteristics of Raw Milk: A Comparative Analysis.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2024-25959}, pmid = {40043765}, issn = {1525-3198}, abstract = {This study analyzed the composition of the microbial community in raw milk and its effects on flavor compounds by comparing samples from cows raised on pasture (PXN) and in housing (HXN). In August 2023, 9 raw milk samples from Holstein cows were collected from a pasture in the Xilin Gol League, Inner Mongolia, China, and labeled as the PXN group. Simultaneously, 9 raw milk samples were collected from Holstein cows raised by individual farmers in the region and labeled as the HXN group. Metagenomic sequencing technology was used to detect and analyze the dynamics of microbial community in milk samples. At the same time, headspace solid phase microextraction, electronic nose and electronic tongue technology were used to monitor the flavor characteristics of raw milk under the 2 feeding conditions and to analyze the correlations between them. The results showed that raw milk protein (PXN 3.43%; HXN 3.36%) and fat (PXN 4.01%; HXN 3.79%) content in pasture group were higher than that in the housed group, while lactose content (PXN 4.98%; HXN 5.12%) and total solid content (PXN 4.98%; HXN 5.12%) were lower than that under the housed system. However, there was no significant difference between non-milk fat solid contents of the 2 groups. W1C, W5C, W5S, W2S sensors of electronic nose played an important role in distinguishing the 2 groups of samples. The sour taste of raw milk in pasture group was different from that in house feeding group. There were significant differences in the microbial communities of the 2 groups, with Macrococcus caseolyticus (39.85%) in PXN group and Lactococcus lactis (49.59%) in HXN group being the dominant bacteria. The volatile compounds of raw milk in PXN and HXN groups were detected by headspace solid phase microextraction method. A total of 62 and 53 flavor compounds were detected in PXN and HXN groups, respectively. Terpenoids, esters and aldehydes were dominant in PXN group, while acids were dominant in HXN group. The saturated fatty acid (SFA) content in HXN group (76.13%) was higher than that in PXN group (72.47%). The gamma-linolenic acid (GLA) content in PXN group (3.56 g/100g) was higher than that in HXN group (1.32 g/100g). The dominant strains, i.e., Macrococcus caseolyticus, Lactococcus lactis and Lactococcus cremoris, in both PXN and HXN groups exhibited positive effects on the formation of alcohols, esters, phenols and unsaturated fatty acids. In addition, Macrococcus caseolyticus in PXN group showed significant positive correlation with calcium lactate (CAL). This study comprehensively elaborates the microbial community structure and flavor quality of raw milk under different feeding methods, which may serve as a reference to control the quality of raw milk.}, } @article {pmid40043731, year = {2025}, author = {Wang, M and Liu, YB and Tong, WM and Leung, WK and He, LL and Xu, X and Xu, D and Zhou, Q}, title = {Periodontitis History Shapes the Early Peri-Implant Microbiome Formation: A Metagenomic Analysis.}, journal = {Journal of clinical periodontology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jcpe.14147}, pmid = {40043731}, issn = {1600-051X}, support = {32270188//National Natural Science Foundation of China/ ; 32070134//National Natural Science Foundation of China/ ; 2023-YBSF-162//Key Research and Development Program of Shaanxi Province, China/ ; //National Training Program of Innovation and Entrepreneurship for Undergraduates/ ; }, abstract = {AIM: This study aims to investigate the early alterations in microbiome construction and succession around dental implants in both periodontally healthy individuals and patients with a history of periodontitis during the first month after implant-crown placement.

MATERIALS AND METHODS: Ninety-five subgingival plaque samples were collected from 10 periodontally compromised patients (PCP) and nine periodontally healthy patients (PHP) at four time points with a 1-week interval and analysed using dynamic metagenomic analysis. The study compared the formation and temporal change in the peri-implant microbiome in the PCP and PHP groups during the first month after the implant crown placement. A two-year follow-up examination was conducted to assess the clinical outcomes of early peri-implant dysbiosis.

RESULTS: The results showed that PCP groups exhibited distinctively dysbiotic features in their peri-implant microbiome upon initial establishment, with an earlier and elevated emergence of periodontopathogens. This dysbiosis in the PCP group was associated with significantly higher modified sulcus bleeding index (mBI) scores compared with the PHP group. Neisseria was identified as a key driver of early peri-implant dysbiosis in patients with a periodontitis history.

CONCLUSIONS: This study established the first microbial link between periodontitis history and early peri-implant dysbiosis, highlighting the importance of early prevention strategies against peri-implant diseases in patients with a periodontitis history.}, } @article {pmid40043574, year = {2025}, author = {Wang, B and Chen, X and Wen, G and Duan, Z and Xue, P and Gao, H}, title = {Treating nitrobenzene (NB) wastewater via an enhanced iron‒manganese oxides electron transfer strategy: Methods and mechanisms.}, journal = {Water research}, volume = {278}, number = {}, pages = {123407}, doi = {10.1016/j.watres.2025.123407}, pmid = {40043574}, issn = {1879-2448}, abstract = {Nitrobenzene (NB) is widely used in the fine chemical, pharmaceutical, and textile industries, but its toxicity and resistance to degradation present challenges, and traditional treatment methods are limited due to costs and a lack of efficiency. In this study, using a three-dimensional biofilm electrode reactor (3D-BER) enhanced with iron-manganese oxide catalysts was explored for the treatment of NB wastewater. Modifying polyurethane (PU) sponge fillers with Fe3O4 and Mn3O4 improved the conductivity and microbial electron transfer of the 3D-BER, significantly enhancing organic compound degradation, nitrogen and phosphorus removal. At the optimal voltage of 6 V and hydraulic retention time (HRT) of 24 h, the reactor achieved CODCr and ammonia nitrogen removal rates of 93.04 % and 86.25 %, respectively, which were more than 20 % higher than those in the control group. The iron and manganese present facilitated increased microbial activity and electron transfer efficiency, and metagenomic sequencing revealed shifts in the microbial communities and the enrichment of specific functional genes related to NB degradation. This integrated bioelectrochemical approach offers an effective and low-cost solution for treating NB wastewater, with broader implications for organic chemical wastewater management.}, } @article {pmid40043404, year = {2025}, author = {Pang, L and Chen, J and Li, W and Chatzisymeon, E and Xu, K and Yang, P}, title = {Particle size of zero-valent iron affects the risks from antibiotic resistance genes in waste activated sludge during anaerobic digestion.}, journal = {Journal of hazardous materials}, volume = {490}, number = {}, pages = {137785}, doi = {10.1016/j.jhazmat.2025.137785}, pmid = {40043404}, issn = {1873-3336}, abstract = {Zero-valent iron (ZVI) is the promising enhancer for sludge anaerobic digestion (AD) performance and for mitigating the proliferation of antibiotic resistance genes (ARGs). However, concerns about its size effects in shifting the behavior and risk of ARGs in sludge, during the AD process. Here, the metagenomics-based profile of ARGs, along with their potential (pathogenic) hosts in sludge were investigated, during mesophilic AD enhanced by ZVI with three different sizes. Results showed that the size of ZVI affected the profiles of ARGs, with nano-ZVI (nZVI, 50 nm) demonstrating the most significant reduction in abundance (by 45.0 %) and diversity (by 8.6 %) of total ARGs, followed by micron-ZVI (150 μm) and iron scrap (1 mm). Similar trends were also observed for high-risk ARGs, pathogens, and potential pathogenic hosts for ARGs. Notably, nZVI achieved the greatest reductions in the abundance of risk ARGs and potential pathogenic hosts (superbugs) by 58.8 % and 53.9 %, respectively. Correlation and redundancy analyses revealed that, the size of ZVI induced concentration differences in ammonium nitrogen, pH, carbonaceous matters, iron, and potential microbial hosts were the main reasons for the variation in the risk of ARGs. Moreover, the down-regulation of genes involved in oxidative stress contributed to the lower risk of ARGs in the three ZVI groups, especially in nZVI. This study provides insights into AD processes of solid wastes using ZVI enhancers.}, } @article {pmid40043390, year = {2025}, author = {Li, F and Zeng, Z and Wu, Y and Wang, Y and Shen, L and Huang, X and Wang, X and Sun, Y}, title = {Characteristics of microplastics in typical poultry farms and the association of environment microplastics colonized-microbiota, waterfowl gut microbiota, and antibiotic resistance genes.}, journal = {Journal of hazardous materials}, volume = {490}, number = {}, pages = {137808}, doi = {10.1016/j.jhazmat.2025.137808}, pmid = {40043390}, issn = {1873-3336}, abstract = {Microplastics (MPs) pollution is a growing global environmental concern. MPs serve as ecological niches for microbial communities, which may accelerate the spread of antibiotic resistance genes (ARGs), posing risks to the breeding industry. While studies on MPs in aquatic organisms are common, research on farmed poultry is limited. This study investigates MPs in poultry farm environments and waterfowl intestines for the first time. MPs were isolated via density separation and analyzed for characterization in soil, pond water, and waterfowl intestines. Metagenomics was used to investigate the association between environment MPs colonized-microbiota and waterfowl gut microbiota. Our findings reveal that MPs are abundant in soil (6.75 ± 2.78 items/g d.w.), pond water (0.94 ± 0.28 items/g w.w.), and poultry intestines (45.35 ± 19.52 items/g w.w.), primarily appearing as fragmented particles sized 20-50 μm. MPs abundance in intestines correlates with environmental levels. Colonized-microbiota on MPs are linked to poultry intestinal microbiota, with greater diversity and microbial functions. Network analysis reveals that Corynebacterium plays a key role in MPs and poultry intestinal. Polymyxin resistance exhibits high clustering. Procrustes analysis reveals correlations between MPs, bacteria, and ARGs in the farming environment. Overall, MPs in poultry farms may facilitate pathogen and ARGs transmission, posing risks to animal gut health.}, } @article {pmid40043057, year = {2025}, author = {Mercado-Juárez, RA and Valdespino-Castillo, PM and Merino Ibarra, M and Batista, S and Mac Cormack, W and Ruberto, L and Carpenter, EJ and Capone, DG and Falcón, LI}, title = {What defines a photosynthetic microbial mat in western Antarctica?.}, journal = {PloS one}, volume = {20}, number = {3}, pages = {e0315919}, pmid = {40043057}, issn = {1932-6203}, mesh = {Antarctic Regions ; *Bacteria/genetics/classification/isolation & purification ; Photosynthesis ; Archaea/genetics/classification/isolation & purification ; Biodiversity ; Phylogeny ; Microbiota ; }, abstract = {Antarctic microbial mats, with their significant biodiversity and key role in biogeochemical cycling, were the focus of our study. We employed a metagenomic approach to analyze 14 microbial mats from meltwater streams of western Antarctica, covering the Maritime, Peninsula, and Dry Valleys regions. Our findings revealed that the taxonomic compositional level of the microbial mat communities is characterized by similar bacterial groups, with diatoms being the main distinguishing factor between the rapidly warming Maritime Antarctica and the other mats. Bacteria were found to be the predominant component of all microbial mats (>90%), followed by Eukarya (>3%), Archaea (<1%), and Viruses (<0.1%). The average abundance of the main phyla composing Antarctic microbial mats included Bacteroidota (35%), Pseudomonadota (29%), Cyanobacteriota (19%), Verrucomicrobiota (3%), Bacillariophyta (2%), Planctomycetota (2%), Acidobacteriota (2%), Actinomycetota (2%), Bacillota (1%), and Chloroflexota (1%). We also identified some microeukaryotes that could play essential roles in the functioning of Antarctic microbial mats. Notably, all mats were found in sites with varied environmental characteristics, showed N-limitation, and shared functional patterns.}, } @article {pmid40042766, year = {2025}, author = {Kumar, A and Saini, S and Anvikar, A and Mishra, N and Misra, G}, title = {Evolving Landscape of Emerging Virus Diagnosis: Challenges and Innovations.}, journal = {Molecular biotechnology}, volume = {}, number = {}, pages = {}, pmid = {40042766}, issn = {1559-0305}, abstract = {Emerging and re-emerging viruses (like Spanish flu, SARS-CoV-2, etc.) have substantially impacted global public health since the early twentieth century. These outbreaks are unpredictable and novel viruses are difficult to understand due to emerging variations. Advanced virology and diagnostic technologies have revolutionized viral diagnostics, enabling accurate early identification and successful treatment and containment. Next-generation sequencing (NGS) technologies, such as metagenomics and whole-genome sequencing, have played a crucial role in the detection and monitoring of emerging viruses, such as SARS-CoV-2 and its variants. Advanced diagnostic methods, such as digital PCR, CRISPR-based tools, and serological techniques like ELISA, enhance viral detection's sensitivity, specificity, and speed. Research has shown that innovations such as lateral flow immunoassays, biosensors, and aptamers have the potential to significantly enhance diagnostic accuracy in various fields. The integration of AI in diagnostics aids researchers in understanding viral evolution and outbreak management, offering new avenues for rapid response. This review aims to examine the latest advancements in virus diagnosis technologies, identify unresolved accuracy and detection issues, and discuss emerging ideas that are transforming the future of viral diagnostics. It is important to improve early identification, rendering the system more cost-effective and adaptable to new viral threats.}, } @article {pmid39902625, year = {2025}, author = {Pelosi, JA and Sorojsrisom, ES and Barbazuk, WB and Sessa, EB}, title = {Population genomics of the gametophyte-only fern Vittaria appalachiana provides insights into clonal plant evolution.}, journal = {The New phytologist}, volume = {246}, number = {1}, pages = {349-364}, doi = {10.1111/nph.20433}, pmid = {39902625}, issn = {1469-8137}, support = {2024-67012-43394//National Institute of Food and Agriculture/ ; 1701708//Division of Environmental Biology/ ; 1754911/2310485//Division of Integrative Organismal Systems/ ; //Department of Biology, University of Florida/ ; //Southern Appalachian Botanical Society/ ; }, mesh = {*Germ Cells, Plant/physiology ; *Ferns/genetics/physiology ; *Genetic Variation ; *Biological Evolution ; Reproduction, Asexual/genetics ; Genome, Plant ; Metagenomics ; Genetics, Population ; Mutation/genetics ; Clone Cells ; }, abstract = {How asexually reproducing organisms maintain genetic diversity and adaptive potential is a long-standing question in evolutionary biology. Asexual lineages have historically been thought of as evolutionary dead ends, yet some exhibit remarkable persistence through time. The gametophyte-only fern Vittaria appalachiana is a clonal eukaryote, the focus of extensive study due to its peculiar habit and life history, and is an excellent system to explore the consequences of asexuality. Using reduced representation sequencing and life cycle simulations, we assess theoretical expectations for genomic consequences of long-term asexual reproduction and test hypotheses about its origin and demographic history. We show that V. appalachiana colonies are not patches of single genotypes but are mosaics of genetic diversity, and the accumulation of mutations in the absence of recombination plays an important role in driving this diversity. We identify increased genomic variation, excess heterozygosity, decreased population differentiation, and increased effective population size, all of which are consistent with the expectations for prolonged clonality. Our analyses support the hypothesis that the loss of sexual reproduction in V. appalachiana occurred during the Last Glacial Maximum. Our results from empirical and simulation-based analyses illuminate how an asexual eukaryote generates, retains, and partitions genomic diversity.}, } @article {pmid40042720, year = {2025}, author = {Zhang, H and Zhang, H and Du, H and Zhang, Y and Zhang, M and Yu, X and Xu, Y}, title = {Unraveling the multiple interactions between phages, microbes and flavor in the fermentation of strong-flavor Baijiu.}, journal = {Bioresources and bioprocessing}, volume = {12}, number = {1}, pages = {14}, pmid = {40042720}, issn = {2197-4365}, abstract = {The fermentation process of strong-flavor Baijiu represents a complex and unique ecosystem, characterized by the involvement of various microorganisms that drive intricate biochemical reactions, ultimately contributing to the distinct flavor profile of the Baijiu. Viruses may affect the succession of microorganisms and thus affect the style and quality of the product. However, the interaction between viruses and microorganisms during the fermentation of Baijiu is still unclear. Here we combined viral metagenomics and amplicon sequencing, physicochemical analysis, and GC-MS detection with temporal sampling to study the dynamics of viral and microbial communities, physicochemical properties, and flavor compounds during strong-flavor Baijiu fermentation. Viral metagenomic analysis revealed 513 viral operational taxonomic units (vOTUs), encompassing 34 viral families. Principal coordinates analysis (PCoA) demonstrated significant differences in vOTUs at different fermentation stages. Notably, the microbial community exhibited distinct succession patterns at various fermentation stages; it changed rapidly during the initial five days, with similarities observed between days 10 and 20. Volatile profile analysis identified 38 flavor components in fermented grains, comprising 16 ester compounds, 11 alcohols, and 8 acids, with the majority formed between days 10 and 30. The Spearman's rank correlation analysis revealed that Peduoviridae exhibited a negative correlation with Gluconobacter. Genomoviridae showed a negative correlation with Issatchenkia, Penicillium, and Monascus. These findings highlight the potential for complex interactions between viruses and microbial communities during Baijiu fermentation, underscoring the importance of considering viral communities in studies of the microbial ecology of fermented foods.}, } @article {pmid40042334, year = {2025}, author = {Venturini, AM and Gontijo, JB and Berrios, L and Rodrigues, JLM and Peay, KG and Tsai, SM}, title = {Linking soil microbial genomic features to forest-to-pasture conversion in the Amazon.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0156124}, doi = {10.1128/spectrum.01561-24}, pmid = {40042334}, issn = {2165-0497}, abstract = {Amazonian soil microbial communities are known to be altered by land-use change. However, attempts to understand these impacts have focused on broader community alterations or the response of specific microbial groups. Here, we recovered and characterized 69 soil bacterial and archaeal metagenome-assembled genomes (MAGs) from three forests and three pastures of the Eastern Brazilian Amazon and evaluated the impacts of land conversion on their genomic features. Pasture MAGs had significantly higher GC content (64.9% vs 60.2%), genome size (4.0 vs 3.1 Mbp), and number of coding sequences (4,058 vs 3,306) compared to forest genomes. Taxonomically, MAGs belonged to eight phyla; however, most (90%) had low similarity to previously known species, indicating potentially novel taxa at multiple levels. We also observed that the functional profiles associated with biogeochemical cycling and carbohydrate-active enzyme genes were impacted by forest conversion, with pasture MAGs exhibiting a notably higher number of both gene groups. Together, these data constitute the largest single-sourced genomic data set from upland soils of the Brazilian Amazon to date and increase the known MAG richness in these soils by 78%. Our data, therefore, not only add to a neglected yet emerging field but, importantly, highlight that land-use change has drastic impacts on the genomic characteristics and functional traits of dominant soil microbes.IMPORTANCEThe Brazilian Amazon is facing unprecedented threats, including increasing deforestation and degradation, which together impact half of the original forest area. Soil microorganisms are sensitive indicators of land-use change, linked to a rise in microbial methane emissions and antibiotic-resistance genes in the Amazon. However, most Amazonian soil microbes remain unknown, and little attention has been given to their genomes. Using sequencing and bioinformatics, we recovered and characterized 69 soil bacterial and archaeal genomes (metagenome-assembled genomes). These abundant members of the microbial communities diverged across forests and pastures in terms of taxonomic and functional traits. Forest conversion favors organisms with specific genomic features - increased GC content, genome size, and gene number - selecting for microorganisms that can thrive under altered conditions. Our paper helps us understand the intricate relationships between microbes and the environment, which are crucial pieces of information for comprehensive soil health assessments and future policy formulation.}, } @article {pmid40042126, year = {2025}, author = {Hayden, HS and Nelson, MT and Ross, SE and Verster, AJ and Bouzek, DC and Eng, A and Waalkes, A and Penewit, K and Kopp, BT and Siracusa, C and Rock, MJ and Salipante, SJ and Hoffman, LR and Sanders, DB}, title = {Effects of Therapeutic Antibiotic Exposure on the Oropharyngeal and Fecal Microbiota in Infants With Cystic Fibrosis.}, journal = {Pediatric pulmonology}, volume = {60}, number = {3}, pages = {e71024}, doi = {10.1002/ppul.71024}, pmid = {40042126}, issn = {1099-0496}, support = {//This work was supported by the Cystic Fibrosis Foundation (CFF; SANDER16Y5, SANDER18A0-I) and the National Institutes of Health (NIH; NIH NHLBI K24HL141669)./ ; }, mesh = {Humans ; *Cystic Fibrosis/microbiology/drug therapy ; *Feces/microbiology ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Infant ; *Oropharynx/microbiology ; Male ; Female ; *Microbiota/drug effects ; beta-Lactams/pharmacology/therapeutic use ; Bacterial Load/drug effects ; Longitudinal Studies ; }, abstract = {BACKGROUND: Systemic antibiotics can impact all microbes inhabiting patients, regardless of the intended target organism(s). We studied the simultaneous effects on respiratory and fecal microbiomes of β-lactam antibiotics administered for respiratory symptoms in infants with cystic fibrosis (IWCF).

OBJECTIVE: To compare the magnitude and duration of intended (respiratory) and unintended (fecal) antimicrobial action by analyzing oropharyngeal (OP) and fecal microbiota in IWCF.

DESIGN: Shotgun metagenomic sequencing and qPCR were performed on OP and fecal samples collected longitudinally from 14 IWCF (ages 1-17 months) during ("On Antibiotics") and after ("Off Antibiotics") β-lactam therapy, and from 5 IWCF (3-16 months) never treated with antibiotics.

RESULTS: Total bacterial loads (TBL) for On Antibiotics samples were lower than for both Never (OP and fecal) and Off Antibiotics samples (fecal only). α-diversities (within-sample) for OP On Antibiotics samples were lower than for Never and Off Antibiotics samples but did not differ between fecal sample groups. β-diversity (between-sample) differed between all OP sample groups and between fecal On and Never Antibiotics and Off and Never antibiotics samples; however, fecal On and Off Antibiotics sample β-diversities did not differ. Patterns of change in antibiotic resistance gene abundances reflected shifts in microbial community composition.

CONCLUSIONS: β-lactam antibiotic exposure was followed by marked alterations in both OP and fecal microbiota. While microbiota appeared to rebound after treatment in both sample types, our results suggest that fecal microbiota recovered less than OP. The clinical consequences of these findings should be studied in IWCF and other populations frequently treated with antibiotics.}, } @article {pmid40041876, year = {2025}, author = {Zhang, Y and Peng, J and Wang, Z and Zhou, F and Yu, J and Chi, R and Xiao, C}, title = {Metagenomic analysis revealed the bioremediation mechanism of lead and cadmium contamination by modified biochar synergized with Bacillus cereus PSB-2 in phosphate mining wasteland.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1529784}, pmid = {40041876}, issn = {1664-302X}, abstract = {INTRODUCTION: Phosphate mining wasteland is contaminated with heavy metals, such as lead (Pb) and cadmium (Cd), which pose significant environmental risks. Ecological restoration of these lands is crucial, but limited research has focused on the remediation of heavy metal-contaminated soils using modified biochar and functional microorganisms.

METHODS: In this study, we investigated the bioremediation of phosphate mining wasteland soil using modified biochar in combination with the phosphate-solubilizing bacterium Bacillus cereus. The effects of this synergistic approach on soil nutrient content, heavy metal immobilization, and microbial community structure were assessed.

RESULTS AND DISCUSSION: The results indicated that the available phosphate content in the soil increased by 59.32%. The content of extractable state Pb[2 +] and Cd[2 +] decreased by 65.06 and 71.26%, respectively. And the soil nutrient conditions were significantly improved. Synergistic remediation can significantly increase the diversity and abundance of soil microbial communities (p < 0.05). Janibacter, Lysobacter, Ornithinimicrobium, Bacillus, and Salinimicrobium were the main functional flora during soil remediation, with significant correlations for the promotion of Pb[2 +] and Cd[2 +] immobilization and the increase of available phosphate and organic matter. ZitB, czcD, zntA, and cmtR are the major heavy metal resistance genes and regulate metabolic pathways to make microbial community function more stable after soil remediation in phosphate mining wasteland.}, } @article {pmid40041864, year = {2025}, author = {Brick, S and Niggemann, J and Reckhardt, A and Könneke, M and Engelen, B}, title = {Interstitial microbial communities of coastal sediments are dominated by Nanoarchaeota.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1532193}, pmid = {40041864}, issn = {1664-302X}, abstract = {Microbial communities in subsurface coastal sediments are highly diverse and play an important role in nutrient cycling. While the major fraction of microorganisms in sandy sediments lives as epipsammon (attached to sand grains), only a small fraction thrives in the interstitial porewaters. So far, little is known about the composition of these free-living microbial communities. In the subsurface of the sandy beach, investigated in this study, we compared the archaeal and bacterial community structures within sediments and corresponding porewaters applying 16S rRNA gene sequencing. We found that the free-living prokaryotes only had a proportion of about 0.2-2.3% of the bulk communities, depending on the pore space. The interstitial microbial communities showed a small overlap with the attached fraction of 4-7% ASVs, and comprised a unique composition of 75-81% ASVs found exclusively in the porewaters. They were more diverse than the respective sediment-attached fraction and showed a much higher archaea-to-bacteria ratio. The archaea were mainly affiliated to Nanoarchaeota of the DPANN superphylum, with a relative abundance up to 50% of the interstitial communities. The bacterial fraction included several species related to the Candidate Phyla Radiation (CPR). Both prokaryotic lineages are known to have small cell sizes, comprising not-yet cultured species with unidentified metabolic functions. Our findings were supported by the investigation of an adjacent tidal flat, showing a similar trend. Thus, our results indicate the presence of distinct interstitial microbial communities in the subsurface of coastal sediments. This natural enrichment of not-yet cultured Nanoarchaeota and members of the CPR provides the opportunity for targeted metagenomic analyses or even isolating members of these groups for further metabolic characterization.}, } @article {pmid40041703, year = {2025}, author = {Sato, Y}, title = {Rumen DNA virome in beef cattle reveals an unexplored diverse community with potential links to carcass traits.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf021}, pmid = {40041703}, issn = {2730-6151}, abstract = {Rumen deoxyribonucleic acid viruses that infect and replicate within bacteria and archaea are key modulators of the prokaryotic community. These viruses influence prokaryotic community abundance, composition, and function impacting host productivity and methane production. In this study, viral genomes were assembled from the rumen of 37 Japanese Black cattle using virus-like particle metagenome sequencing, providing insights into viral diversity, functional potential, and virus-host interactions. The relationship between the rumen deoxyribonucleic acid virome and carcass traits, particularly carcass weight and marbling, was also investigated. A total of 22 942 viral operational taxonomic units of medium-quality or higher (≥5 kb length and ≥ 50% completeness), referred to as Japanese Black Rumen Viral genomes, were reconstructed. Among these, 5973 putative novel genera were identified, significantly expanding the catalog of rumen viral genomes. Hosts were predicted for 2364 viral operational taxonomic units, including carbohydrate-degrading bacteria and methanogens. Additionally, 27 auxiliary metabolic genes were categorized as glycosyl hydrolases which are responsible for the degradation of cellulose, hemicellulose, and oligosaccharides, suggesting that rumen viruses may enhance the breakdown of complex carbohydrates during infection. Furthermore, the rumen virome differed considerably between high vs low carcass weight cattle and high vs low marbling cattle. Viruses associated with Methanobrevibacter were linked to higher carcass weight. This database and the insights from this study provide primary information for the development and improvement of beef production.}, } @article {pmid40041700, year = {2025}, author = {Wang, X and Cao, D and Zhang, H and Chen, W and Sun, J and Hu, H}, title = {Utilizing metagenomic profiling and machine learning model to identify bacterial biomarkers for major depressive disorder.}, journal = {Frontiers in psychiatry}, volume = {16}, number = {}, pages = {1539596}, pmid = {40041700}, issn = {1664-0640}, abstract = {BACKGROUND: Major depressive disorder (MDD) is highly heterogeneous, which provides a significant challenge in the management of this disorder. However, the pathogenesis of major depressive disorder is not fully understood. Studies have shown that depression is highly correlated with gut flora. The objective of this study was to explore the potential of microbial biomarkers in the diagnosis of major depressive disorder.

METHODS: In this study, we used a metagenomic approach to analyze the composition and differences of gut bacterial communities in 36 patients with major depressive disorder and 36 healthy individuals. We then applied a Support Vector Machine Recursive Feature Elimination (SVM-RFE) machine learning model to find potential microbial markers.

RESULTS: Our results showed that the alpha diversity of the intestinal flora did not differ significantly in major depressive disorder compared to healthy populations. However, the beta diversity was significantly altered. Machine learning identified 8 MDD-specific bacterial biomarkers, with Alistipes, Dysosmobacter, Actinomyces, Ruthenibacterium, and Thomasclavelia being significantly enriched, while Faecalibacterium, Pseudobutyrivibrio, and Roseburia were significantly reduced, demonstrating superior diagnostic accuracy (area under the curve, AUC = 0.919). In addition, the gut bacteria performed satisfactorily in the validation cohort with an AUC of 0.800 (95% CI: 0.6334-0.9143).

CONCLUSION: This study reveals the complex relationship between gut microbiota and major depressive disorder and provides a scientific basis for the development of a microbiota-based diagnostic tool for depression.}, } @article {pmid40041441, year = {2025}, author = {Xu, C and Shen, Y and Chen, S and Liu, T and Chen, X and Yu, Y and Liu, L and Ma, R and Zhang, L and Liu, X and Zhou, L and Zhu, G and Feng, S}, title = {Effect of Interpretation of Positive Metagenomic Next-Generation Sequencing Reports on the Infection Diagnosis in Patients With Hematological Disorders.}, journal = {Open forum infectious diseases}, volume = {12}, number = {2}, pages = {ofaf076}, pmid = {40041441}, issn = {2328-8957}, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) has become a crucial diagnostic tool for infectious diseases in patients with hematological disorders. However, despite the abundant microbial information provided by positive mNGS reports, interpreting these results remains challenging due to the lack of standardized criteria.

METHODS: We surveyed 92 clinicians to identify common challenges in understanding mNGS reports. Microbiologists then provided additional "report interpretation cards" (RICs) for positive mNGS results alongside original reports. The aim of using RICs was to determine whether each detected microorganism was likely cause of infection. After a 3-month period, a panel of clinical experts retrospectively reviewed 281 cases, involving 728 detected microorganisms, to assess RIC accuracy.

RESULTS: In total, 82.6% of clinicians (76 of 92) experienced difficulties in interpreting mNGS reports. After receiving RICs, 97.8% of clinicians (90 of 92) reported satisfaction. The overall concordance rates between interpretation and adjudication in the 281 cases was 79.0% (222 of 281). In 203 cases in which multiple microorganisms were detected, 37.9% (77 of 203) and 37.4% (76 of 203) were interpreted and adjudicated as mixed infections. Among the 728 microorganisms, interpretation and adjudication revealed concordance rates of 93.9% (154 of 164), 95.7% (88 of 92), and 72.3% (339 of 469) for bacterial, fungal, and viral infections, respectively. In 68.7% of the cases (193 of 281), mNGS positively influenced pathogen diagnosis.

CONCLUSIONS: Not all microorganisms detected by mNGS are responsible for infection, and appropriate interpretation is essential. The provision of interpretations by microbiologists aids clinicians in accurately using mNGS for infection diagnosis.}, } @article {pmid40040800, year = {2025}, author = {He, J and Ye, L and Xu, H and Yang, H and Shen, J and Li, M and Weng, S and Jiao, D and Chu, C and Liao, Q and Zou, H and Zhu, J and Wang, C and Xu, X}, title = {Multi-omics analysis reveals a novel NFE2L3 variant impairing choroidal vasculature development in high myopia and myopic maculopathy.}, journal = {National science review}, volume = {12}, number = {2}, pages = {nwae291}, pmid = {40040800}, issn = {2053-714X}, } @article {pmid40040609, year = {2025}, author = {Liu, FQ and An, ZY and Cui, LJ and Xiao, MY and Wu, YJ and Li, W and Zhang, BS and Yu, L and Feng, J and Liu, ZG and Feng, R and Jiang, ZX and Huang, RB and Jing, HM and Ren, JH and Zhu, XY and Cheng, YF and Li, YH and Zhou, HB and Gao, D and Liu, Y and Yu, F and Wang, X and Qiao, JL and Hu, DH and Wang, LL and Zang, MT and Chen, Q and Qu, QY and Zhou, JY and Li, ML and Chen, YX and Huang, QS and Fu, HX and Li, YY and Wang, QF and Huang, XJ and Zhang, XH and , }, title = {Correlation Between Fecal Microbiota and Corticosteroid Responsiveness in Primary Immune Thrombocytopenia: an Exploratory Study.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e2410417}, doi = {10.1002/advs.202410417}, pmid = {40040609}, issn = {2198-3844}, support = {2023YFC2507803//Key Technologies Research and Development Program/ ; 82300149//National Natural Science Foundation of China/ ; 82130008//National Natural Science Foundation of China/ ; 82230004//National Natural Science Foundation of China/ ; 82350004//National Natural Science Foundation of China/ ; 82430006//National Natural Science Foundation of China/ ; 2024M761208//China Postdoctoral Science Foundation/ ; 2023ZB182//Department of Human Resources and Social Security of Jiangsu Province/ ; 2022-1-4082//Capital Health Research and Development of Special Fund/ ; 7242154//Natural Science Foundation of Beijing Municipality/ ; 7232188//Natural Science Foundation of Beijing Municipality/ ; 71003Y3035//Peking University Medicine/ ; }, abstract = {Corticosteroids (CSs) are the initial therapy for immune thrombocytopenia (ITP); however, their efficacy is not adequately predicted. As a novel biomarker, the composition of the gut microbiota is non-invasively tested and altered in patients with ITP. This study aims to develop a predictive model that leverages gut microbiome data to predict the CS response in patients with ITP within the initial four weeks of treatment. Metagenomic sequencing is performed on fecal samples from 212 patients with ITP, 152 of whom underwent CS treatment and follow-up. Predictive models are trained using six machine-learning algorithms, integrating clinical indices and gut microbiome data. The support vector machine (SVM) algorithm-based model has the highest accuracy (AUC = 0.80). This model utilized a comprehensive feature set that combined clinical data (including sex, age, duration, platelet count, and bleeding scales) with selected microbial species (including Bacteroides ovatus, Bacteroides xylanisolvens, and Parabacteroides gordonii), alpha diversities, KEGG pathways, and microbial modules. This study will provide new ideas for the prediction of clinical CS efficacy, enabling informed decision-making regarding the initiation of CS or personalized treatment in patients with ITP.}, } @article {pmid40040342, year = {2025}, author = {Ren, M and Hu, A and Zhao, Z and Yao, X and Kimirei, IA and Zhang, L and Wang, J}, title = {Trait-environmental relationships reveal microbial strategies of environmental adaptation.}, journal = {Ecology}, volume = {106}, number = {3}, pages = {e70047}, doi = {10.1002/ecy.70047}, pmid = {40040342}, issn = {1939-9170}, support = {BK20240111//Basic Research Program of Jiangsu/ ; 067GJHZ2023034MI//the International Collaboration Program of Chinese Academy of Sciences/ ; 151542KYSB20210007//the International Collaboration Program of Chinese Academy of Sciences/ ; SAJC202403//the International Collaboration Program of Chinese Academy of Sciences/ ; 42002304//National Natural Science Foundation of China/ ; 42107445//National Natural Science Foundation of China/ ; 42225708//National Natural Science Foundation of China/ ; 42372353//National Natural Science Foundation of China/ ; 92251304//National Natural Science Foundation of China/ ; 92351303//National Natural Science Foundation of China/ ; }, mesh = {*Lakes/microbiology ; *Adaptation, Physiological ; *Bacteria/classification/genetics ; Bacterial Physiological Phenomena ; Microbiota ; Hydrogen-Ion Concentration ; }, abstract = {Microbial trait variation along environmental gradients is crucial to understanding their ecological adaptation mechanisms. With the increasing availability of microbial genomes, making full use of the genome-based traits to decipher their adaptation strategies becomes promising and urgent. Here, we examined microbial communities in water and sediments of 20 East African lakes with pH values ranging from 7.2 to 10.1 through taxonomic profiling and genome-centric metagenomics. We identified functional traits important for microbial adaptation to the stresses of alkalinity and salinity based on the significant trait-environment relationships (TERs), including those involved in cytoplasmic pH homeostasis, compatible solute accumulation, cell envelope modification, and energy requisition. By integrating these significant traits, we further developed an environmental adaptation index to quantify the species-level adaptive capacity for environmental stresses, such as high pH environments. The adaptation index of pH showed consistently significant positive relationships with species pH optima across regional and global genomic datasets from freshwater, marine, and soda lake ecosystems. The generality of the index for quantifying environmental adaptation was demonstrated by showing significant relationships with the species niche optima for the gradients of soil temperature and seawater salinity. These results highlight the importance of TERs in facilitating the inference of microbial genomic-based adaptation mechanisms and expand our understanding of ecological adaptive strategies along environmental gradients.}, } @article {pmid40038896, year = {2025}, author = {Zhang, H and Ruan, Y and Kuzyakov, Y and Sun, H and Huang, Q and Guo, S and Shen, Q and Ling, N}, title = {Viruses Facilitate Energy Acquisition Potential by Their Bacterial Hosts in Rhizosphere of Grafted Plants.}, journal = {Plant, cell & environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.15458}, pmid = {40038896}, issn = {1365-3040}, support = {//This study was supported by the National Nature Science Foundation of China (32302670) and Nanjing Agricultural University (XUEKEN2023039)./ ; }, abstract = {Viruses alter the ecological and evolutionary trajectories of bacterial host communities. Plant grafting is a technique that integrates two species or varietiies and have consequences on the rhizosphere functioning. The grafting effects on the taxonomic and functional assembly of viruses and their bacterial host in the plant rhizosphere remain largely elusive. Using shotgun metagenome sequencing, we recover a total of 1441 viral operational taxonomic units from the rhizosphere of grafted and ungrafted plants after 8-year continuous monoculture. In the grafted and ungrafted rhizosphere, the Myoviridae, Zobellviridae and Kyanoviridae emerged as the predominant viral families, collectively representing around 40% of the viral community in each respective environment. Grafting enriched the members in viral family Kyanoviridae, Tectiviridae, Peduoviridae and Suoliviridae, and auxiliary metabolic genes related to pyruvate metabolism and energy acquisition (e.g., gloB, DNMT1 and dcyD). The virus-bacterial interactions increased the rapid growth potential of bacteria, which explains the strong increase in abundance of specific bacterial hosts (i.e., Chitinophagaceae, Cyclobacteriaceae and Spirosomaceae) in the grafted-plant rhizosphere. Overall, these results deepen our understanding of microbial community assembly and ecological services from the perspective of virus-host interactions.}, } @article {pmid40038838, year = {2025}, author = {Thiruppathy, D and Moyne, O and Marotz, C and Williams, M and Navarro, P and Zaramela, L and Zengler, K}, title = {Absolute quantification of the living skin microbiome overcomes relic-DNA bias and reveals specific patterns across volunteers.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {65}, pmid = {40038838}, issn = {2049-2618}, support = {S10 OD026929/NH/NIH HHS/United States ; S10 OD026929/NH/NIH HHS/United States ; }, mesh = {Humans ; *Skin/microbiology ; *Microbiota/genetics ; *DNA, Bacterial/genetics ; *Bacteria/classification/genetics/isolation & purification ; *Metagenomics/methods ; Sequence Analysis, DNA/methods ; Bacterial Load ; Healthy Volunteers ; Adult ; Female ; Male ; }, abstract = {BACKGROUND: As the first line of defense against external pathogens, the skin and its resident microbiota are responsible for protection and eubiosis. Innovations in DNA sequencing have significantly increased our knowledge of the skin microbiome. However, current characterizations do not discriminate between DNA from live cells and remnant DNA from dead organisms (relic DNA), resulting in a combined readout of all microorganisms that were and are currently present on the skin rather than the actual living population of the microbiome. Additionally, most methods lack the capability for absolute quantification of the microbial load on the skin, complicating the extrapolation of clinically relevant information.

RESULTS: Here, we integrated relic-DNA depletion with shotgun metagenomics and bacterial load determination to quantify live bacterial cell abundances across different skin sites. Though we discovered up to 90% of microbial DNA from the skin to be relic DNA, we saw no significant effect of this on the relative abundances of taxa determined by shotgun sequencing. Relic-DNA depletion prior to sequencing strengthened underlying patterns between microbiomes across volunteers and reduced intraindividual similarity. We determined the absolute abundance and the fraction of population alive for several common skin taxa across body sites and found taxa-specific differential abundance of live bacteria across regions to be different from estimates generated by total DNA (live + dead) sequencing.

CONCLUSIONS: Our results reveal the significant bias relic DNA has on the quantification of low biomass samples like the skin. The reduced intraindividual similarity across samples following relic-DNA depletion highlights the bias introduced by traditional (total DNA) sequencing in diversity comparisons across samples. The divergent levels of cell viability measured across different skin sites, along with the inconsistencies in taxa differential abundance determined by total vs live cell DNA sequencing, suggest an important hypothesis for certain sites being susceptible to pathogen infection. Overall, our study demonstrates a characterization of the skin microbiome that overcomes relic-DNA bias to provide a baseline for live microbiota that will further improve mechanistic studies of infection, disease progression, and the design of therapies for the skin. Video Abstract.}, } @article {pmid40038823, year = {2025}, author = {Liu, F and Yang, J and Shen, W and Fu, J and Meng, J and Zhang, Y and Li, J and Yuan, Z}, title = {Effects of drainage and long-term tillage on greenhouse gas fluxes in a natural wetland: insights from microbial mechanisms.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {26}, pmid = {40038823}, issn = {2524-6372}, support = {No. ES202308//Open Project of State Key Laboratory of Urban Water Resource and Environment/ ; No. 2024M763244//China Postdoctoral Science Foundation/ ; No. 242300421652//Natural Science Foundation of Henan Province/ ; No. 30501300//Top Talent Foundation of Henan Agricultural University/ ; }, abstract = {BACKGROUND: The conversion of natural wetlands to agricultural land through drainage contributes to 62% of the global wetland loss. Such conversion significantly alters greenhouse gas (GHG) fluxes, yet the underlying mechanisms of GHG fluxes resulting from drainage and long-term tillage practices remain highly uncertain. In this study, we measured GHG fluxes of a natural reed wetland (referred to as "Wetland") and a drained wetland that used as farmland (referred to as "Dryland").

RESULTS: The results demonstrated that annual cumulative N2O and CO2 fluxes in Dryland were 282.77% and 53.79% higher than those in Wetland, respectively. However, CH4 annual cumulative fluxes decreased from 12,669.45 ± 564.69 kg·ha[- 1] to 8,238.40 ± 207.72 kg·ha[- 1] in Dryland compared to Wetland. The global warming potential (GWP) showed no significant difference between Dryland and Wetland, with comparable average rates of 427.50 ± 48.83 and 422.21 ± 73.59 mg·CO2-eq·m[- 2]·h[- 1], respectively. Metagenomic analysis showed a decrease in the abundance of acetoclastic methanogens and their functional genes responsible for CH4 production. Functional genes related to CH4 oxidation (pmoA) and gene related to N2O reduction (nosZ) exhibited a substantial sensitivity to variations in TOC concentration (p < 0.05). Candidatus Methylomirabilis, belonging to the NC10 phylum, was identified as the dominant methanotroph and accounted for 49.26% of the methanotrophs. Its relative abundance was significantly higher in Dryland than in Wetland, as the nitrogenous fertilizer applied in Dryland acted as an electron acceptor, with the nearby Wetland produced CH4 serving as an electron donor. This suggests that Dryland may act as a CH4 sink, despite the significant enhancement in CO2 and N2O fluxes.

CONCLUSIONS: In conclusion, this study provides insights into the influence of drainage and long-term tillage on GHG fluxes in wetlands and their contribution to global warming.}, } @article {pmid40038809, year = {2025}, author = {Reyes, G and Betancourt, I and Andrade, B and Pozo, Y and Sorroza, L and Trujillo, LE and Bayot, B}, title = {Genomic sequence data of Thiohalocapsa marina: a sulfur-oxidizing bacterium prevalent in treated municipal wastewater and commercial shrimp hatchery effluents.}, journal = {BMC research notes}, volume = {18}, number = {1}, pages = {97}, pmid = {40038809}, issn = {1756-0500}, mesh = {*Wastewater/microbiology ; Animals ; *Genome, Bacterial ; *Sulfur/metabolism ; Oxidation-Reduction ; Biodegradation, Environmental ; Chlorobi/genetics/metabolism ; Aquaculture ; Penaeidae/microbiology ; Phylogeny ; }, abstract = {OBJECTIVES: This study highlighted the gap in the genetic characterization of marine bacteria, specifically within the genus Thiohalocapsa. This genus thrives in contaminated environments with high concentrations of sulfide, such as treated municipal wastewater. Thc. marina is a phototrophic purple bacterium known for its role in sulfur oxidation and bioremediation in marine aquaculture systems. To date, only one Thc. marina genome has been published in the GenBank database. This study enhances the understanding of the ecological adaptation and bioremediation capabilities of Thc. marina in treated municipal wastewater effluents.

DATA DESCRIPTION: We present a draft genome of Thc. marina LNA26 recovered from treated municipal wastewater effluents using shotgun metagenomic sequencing. The genome of Thc. marina LNA26 harbors 4,356,720 bp and contains 4,032 genes (3,936 CDSs, 50 RNA genes, and 46 pseudogenes), some of them involved in sporulation, siderophores biosynthesis, arsenate bioremediation, sulfide metabolism, capacity for nitrogen fixation, the biosynthesis of PHA, and NHPL bacteriocins. Thc. marina LNA26 exhibits 3 CRISPR Arrays and a high abundance of COGs in signal transduction, energy production, and cell wall biogenesis, indicating advanced environmental responsiveness, energy efficiency, and cellular robustness.}, } @article {pmid40038603, year = {2025}, author = {Gao, M and Zhong, S and Han, G and Kuang, D and Yun, C and Fu, C}, title = {Atypical rat bite fever associated with knee joint infection in a Chinese patient: a case report.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {312}, pmid = {40038603}, issn = {1471-2334}, mesh = {*Rat-Bite Fever/microbiology/diagnosis/drug therapy ; Humans ; *Streptobacillus/isolation & purification/genetics ; *Knee Joint/microbiology/pathology ; Animals ; Male ; *Anti-Bacterial Agents/therapeutic use ; *RNA, Ribosomal, 16S/genetics ; Synovial Fluid/microbiology ; Arthroscopy ; China ; Middle Aged ; Rats ; East Asian People ; }, abstract = {BACKGROUND: Rat bite fever (RBF) is a rare zoonosis transmitted from rodents to humans through bites and scratches. However, diagnosis and treatment of atypical clinical cases can be challenging.

CASE PRESENTATION: Herein, we report an atypical case of RBF with unilateral knee joint infection caused by Streptobacillus moniliformis. Streptobacillus moniliformis was isolated from the knee synovial fluid of the patient via microbiological culture and metagenomic next-generation sequencing (mNGS). After treatment with antibiotics and arthroscopic surgery, the patient reported symptom alleviation and was subsequently discharged home. This is the first reported detection of intraarticular histopathological changes caused by Streptobacillus moniliformis during knee arthroscopy.

CONCLUSIONS: In atypical cases, importantly, clinical healthcare professionals should promptly obtain microbiological culture results. When culture is negative, 16S ribosomal RNA gene polymerase chain reaction (16S rRNA PCR) or mNGS can be considered for identification, with inquiring about the patient's disease history, including any contact with rodents. Surgical interventions, such as arthroscopy, may be included in treatment. Streptobacillus moniliformis infection should be considered when considerable fibrous connective tissue and capillary proliferation are observed under arthroscopic guidance.}, } @article {pmid40038315, year = {2025}, author = {Chen, Y and Chen, S and Tao, J and Li, M and Wang, W and Chen, M and Fang, X and Kong, L and Wang, Y and Pereira, O and Zhang, C}, title = {Multi-omic stock of surface ocean microbiome built by monthly, weekly and daily sampling in Dapeng Bay, China.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {378}, pmid = {40038315}, issn = {2052-4463}, support = {32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; RCBS20221008093229035//Shenzhen Science and Technology Innovation Commission/ ; 92351301//École Nationale d'Ingénieurs de Saint-Etienne (National Engineering School of Saint-Étienne)/ ; }, mesh = {China ; *Microbiota ; *Archaea/genetics ; *Bacteria/genetics/classification ; *Bays ; Seawater/microbiology ; Metagenome ; Multiomics ; }, abstract = {The coastal ocean is the dynamic interface where terrestrial, atmospheric, and marine systems converge, acting as a hotspot for microbial activity, which underpins the intricate web of carbon and nitrogen cycling. Dapeng Bay, a typical semi-enclosed bay along the southern coastline of China, is strongly influenced by monsoon climates and human activities. Despite its ecological importance, long-term observations and investigations into the microbial community structure in this region are notably lacking. To address this gap, we conducted a two-year continuous sampling from May 2021 to June 2023 to explore shifts in nearshore surface microbial communities and assess the long-term effects of environmental stressors. This study presents comprehensive amplicon, metagenomic, and metatranscriptomic information. We identified 3,600 amplicon sequence variants and recovered 1,216 high-quality metagenome-assembled MAGs, representing 17 bacterial and 3 archaeal phyla. Additionally, 587 MAGs were correlated with transcriptional activity, comprising 539 bacterial and 48 archaeal populations. This dataset is anticipated to provide a multi-dimensional perspective, enhancing our understanding of the complexity, dynamics, and adaptability of microbial communities in coastal environments.}, } @article {pmid38892504, year = {2024}, author = {Duysburgh, C and Govaert, M and Guillemet, D and Marzorati, M}, title = {Co-Supplementation of Baobab Fiber and Arabic Gum Synergistically Modulates the In Vitro Human Gut Microbiome Revealing Complementary and Promising Prebiotic Properties.}, journal = {Nutrients}, volume = {16}, number = {11}, pages = {}, pmid = {38892504}, issn = {2072-6643}, mesh = {*Gastrointestinal Microbiome ; *Prebiotics ; *Gum Arabic/therapeutic use ; *Adansonia ; *Plant Preparations/therapeutic use ; Metabolome ; Metagenome ; Colon/microbiology ; }, abstract = {Arabic gum, a high molecular weight heteropolysaccharide, is a promising prebiotic candidate as its fermentation occurs more distally in the colon, which is the region where most chronic colonic diseases originate. Baobab fiber could be complementary due to its relatively simple structure, facilitating breakdown in the proximal colon. Therefore, the current study aimed to gain insight into how the human gut microbiota was affected in response to long-term baobab fiber and Arabic gum supplementation when tested individually or as a combination of both, allowing the identification of potential complementary and/or synergetic effects. The validated Simulator of the Human Intestinal Microbial Ecosystem (SHIME[®]), an in vitro gut model simulating the entire human gastrointestinal tract, was used. The microbial metabolic activity was examined, and quantitative 16S-targeted Illumina sequencing was used to monitor the gut microbial composition. Moreover, the effect on the gut microbial metabolome was quantitatively analyzed. Repeated administration of baobab fiber, Arabic gum, and their combination had a significant effect on the metabolic activity, diversity index, and community composition of the microbiome present in the simulated proximal and distal colon with specific impacts on Bifidobacteriaceae and Faecalibacterium prausnitzii. Despite the lower dosage strategy (2.5 g/day), co-supplementation of both compounds resulted in some specific synergistic prebiotic effects, including a biological activity throughout the entire colon, SCFA synthesis including a synergy on propionate, specifically increasing abundance of Akkermansiaceae and Christensenellaceae in the distal colon region, and enhancing levels of spermidine and other metabolites of interest (such as serotonin and ProBetaine).}, } @article {pmid40038282, year = {2025}, author = {Li, Z and Riley, WJ and Marschmann, GL and Karaoz, U and Shirley, IA and Wu, Q and Bouskill, NJ and Chang, KY and Crill, PM and Grant, RF and King, E and Saleska, SR and Sullivan, MB and Tang, J and Varner, RK and Woodcroft, BJ and Wrighton, KC and , and Brodie, EL}, title = {A framework for integrating genomics, microbial traits, and ecosystem biogeochemistry.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {2186}, pmid = {40038282}, issn = {2041-1723}, support = {DE-AC02-05CH11231//DOE | Office of Science (SC)/ ; SCW1746//DOE | Office of Science (SC)/ ; DE-AC02-05CH11231//DOE | Office of Science (SC)/ ; (#FP00005182//DOE | Office of Science (SC)/ ; 2022070//National Science Foundation (NSF)/ ; }, mesh = {*Ecosystem ; *Methane/metabolism ; *Genomics/methods ; *Microbiota/genetics ; Arctic Regions ; Metagenomics/methods ; Wetlands ; Greenhouse Gases/metabolism ; Climate Change ; Bacteria/genetics/metabolism/classification ; }, abstract = {Microbes drive the biogeochemical cycles of earth systems, yet the long-standing goal of linking emerging genomic information, microbial traits, mechanistic ecosystem models, and projections under climate change has remained elusive despite a wealth of emerging genomic information. Here we developed a general genome-to-ecosystem (G2E) framework for integrating genome-inferred microbial kinetic traits into mechanistic models of terrestrial ecosystems and applied it at a well-studied Arctic wetland by benchmarking predictions against observed greenhouse gas emissions. We found variation in genome-inferred microbial kinetic traits resulted in large differences in simulated annual methane emissions, quantitatively demonstrating that the genomically observable variations in microbial capacity are consequential for ecosystem functioning. Applying microbial community-aggregated traits via genome relative-abundance-weighting gave better methane emissions predictions (i.e., up to 54% decrease in bias) compared to ignoring the observed abundances, highlighting the value of combined trait inferences and abundances. This work provides an example of integrating microbial functional trait-based genomics, mechanistic and pragmatic trait parameterizations of diverse microbial metabolisms, and mechanistic ecosystem modeling. The generalizable G2E framework will enable the use of abundant microbial metagenomics data to improve predictions of microbial interactions in many complex systems, including oceanic microbiomes.}, } @article {pmid40038255, year = {2025}, author = {Cui, B and Luo, H and He, B and Liu, X and Lv, D and Zhang, X and Su, K and Zheng, S and Lu, J and Wang, C and Yang, Y and Zhao, Z and Liu, X and Wang, X and Zhao, Y and Nie, X and Jiang, Y and Zhang, Z and Liu, C and Chen, X and Cai, A and Lv, Z and Liu, Z and An, F and Zhang, Y and Yan, Q and Kelley, KW and Xu, G and Xu, L and Liu, Q and Peng, F}, title = {Gut dysbiosis conveys psychological stress to activate LRP5/β-catenin pathway promoting cancer stemness.}, journal = {Signal transduction and targeted therapy}, volume = {10}, number = {1}, pages = {79}, pmid = {40038255}, issn = {2059-3635}, support = {82373096//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 82273480//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 82273480//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 82273480//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82473131//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82273480//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Low Density Lipoprotein Receptor-Related Protein-5/genetics/metabolism ; Animals ; Mice ; *Gastrointestinal Microbiome ; Humans ; *Dysbiosis/genetics/microbiology/metabolism ; Female ; *beta Catenin/genetics/metabolism ; *Stress, Psychological/genetics/microbiology/metabolism ; Neoplastic Stem Cells/metabolism/pathology ; Wnt Signaling Pathway/genetics ; Breast Neoplasms/genetics/metabolism/pathology/microbiology ; }, abstract = {Psychological stress causes gut microbial dysbiosis and cancer progression, yet how gut microbiota determines psychological stress-induced tumor development remains unclear. Here we showed that psychological stress promotes breast tumor growth and cancer stemness, an outcome that depends on gut microbiota in germ-free and antibiotic-treated mice. Metagenomic and metabolomic analyses revealed that psychological stress markedly alters the composition and abundance of gut microbiota, especially Akkermansia muciniphila (A. muciniphila), and decreases short-chain fatty acid butyrate. Supplement of active A. muciniphila, butyrate or a butyrate-producing high fiber diet dramatically reversed the oncogenic property and anxiety-like behavior of psychological stress in a murine spontaneous tumor model or an orthotopic tumor model. Mechanistically, RNA sequencing analysis screened out that butyrate decreases LRP5 expression to block the activation of Wnt/β-catenin signaling pathway, dampening breast cancer stemness. Moreover, butyrate as a HDAC inhibitor elevated histone H3K9 acetylation level to transcriptionally activate ZFP36, which further accelerates LRP5 mRNA decay by binding adenine uridine-rich (AU-rich) elements of LRP5 transcript. Clinically, fecal A. muciniphila and serum butyrate were inversely correlated with tumoral LRP5/β-catenin expression, poor prognosis and negative mood in breast cancer patients. Altogether, our findings uncover a microbiota-dependent mechanism of psychological stress-triggered cancer stemness, and provide both clinical biomarkers and potential therapeutic avenues for cancer patients undergoing psychological stress.}, } @article {pmid40038232, year = {2025}, author = {Gohar, M and Shaheen, N and Goyal, SM and Mor, SK and Rodriguez-R, LM and Imran, M}, title = {Probiotic Potential of Yeast, Mold, and Intermediate Morphotypes of Geotrichum candidum in Modulating Gut Microbiota and Body Physiology in Mice.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {40038232}, issn = {1867-1314}, support = {No: 1-8/HEC/HRD/2020/10594//Higher Education Commission (HEC), Pakistan/ ; No: 1-8/HEC/HRD/2020/10594//Higher Education Commission (HEC), Pakistan/ ; No: 1-8/HEC/HRD/2020/10594//Higher Education Commission (HEC), Pakistan/ ; MPC-2022-02167//OeAD-GmbH, Austria ́s Agency for Education and Internationalization/ ; MPC-2022-02167//OeAD-GmbH, Austria ́s Agency for Education and Internationalization/ ; No. PSF/CRP/C-QU/T-Helix (70)//Pakistan Science Foundation (PSF) Research/ ; }, abstract = {Geotrichum candidum, a polymorphic fungus, exists in yeast, mold, and intermediate morphotypes, each with varying genome sizes and phenotypic traits. While G. candidum has been studied as a probiotic in dairy cattle and aquaculture, the differential probiotic potential of its morphotypes has not been fully investigated; therefore, the current study was designed to investigate their impact on the modulation of physiological and gut microbial diversity in BALB/c male mice. In this study, four strains of G. candidum were used, comprising two yeast morphotypes (QAUGC01 and UCMA3730), one mold morphotype (UCMA103), and one intermediate morphotype (UCMA91). BALB/c male mice were administered G. candidum yeast, intermediate, and mold morphotypes via drinking water for 4 weeks. After 4 weeks of experimentation, the yeast morphotype (QAUGC01) notably facilitated healthy weight gain compared to other groups. This was accompanied by significant increases in red blood cell count (p = 0.01). Importantly, QAUGC01 showed no detrimental effects on kidney function, as evidenced by significantly reduced CPK levels (77.25 ± 4.87 U/L) and low cholesterol levels (64.75 ± 0.83 mg/dL). Metagenomic analysis revealed that Firmicutes, Bacteroidetes, and Proteobacteria were predominant bacterial phyla, while Ascomycota and Basidiomycota dominated the fungal populations. Lactobacillus and Bifidobacterium were prominent in the gastrointestinal tract of QAUGC01-treated mice, while Lactococcus correlated with intermediate and mold morphotypes. Predictive functional annotation (PICRUSt2) has revealed the maximum relative abundance of metabolic pathways in mold and intermediate-supplemented mice gut. In contrast, the yeast morphotype (UCMA3730) exhibited a higher metabolic pathway activity in the large intestine. Conclusively, yeast morphotypes increase beneficial bacterial diversity, including Brevibacillus and Bacillus, particularly lactic acid bacteria throughout the gastrointestinal tract. These findings suggest that different G. candidum morphotypes have distinct probiotic potentials, with implications for enhancing gut health in food and feed applications.}, } @article {pmid40038088, year = {2025}, author = {Leung, MBW and Chan, DYL and Fok, EKL and Yim, HCH and Jiang, X and Li, TC}, title = {Semen metagenomics and spent culture media in patients undergoing conventional in vitro fertilisation: abridged secondary publication.}, journal = {Hong Kong medical journal = Xianggang yi xue za zhi}, volume = {31 Suppl 1}, number = {1}, pages = {45-47}, pmid = {40038088}, issn = {1024-2708}, } @article {pmid40037896, year = {2025}, author = {Chen, N and Kishida, K and Stari, L and Moriuchi, R and Ohtsubo, Y and Damborsky, J and Nagata, Y}, title = {Haloalkane dehalogenases other than LinB can contribute to the γ-hexachlorocyclohexane utilization.}, journal = {Bioscience, biotechnology, and biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1093/bbb/zbaf022}, pmid = {40037896}, issn = {1347-6947}, abstract = {Haloalkane dehalogenases (HLDs) convert halogenated compounds to corresponding alcohols by a simple hydrolytic mechanism. Although many bacterial strains possess HLDs or HLD homologues, LinB is the only HLD known to be involved in the utilization of γ-hexachlorocyclohexane (γ-HCH), a man-made chlorinated pesticide. In this study, to gain insight into the functional evolution of HLDs toward the γ-HCH utilization, the linB gene in γ-HCH-degrading Sphingobium japonicum strain UT26 was replaced by 7 other HLD or HLD homologous genes, including 3 putative ancestral enzymes. Interestingly, strains carrying genes for DmmA from marine metagenome or Rluc_anc, an ancestor of Renilla-luciferin 2-monooxygenase (Rluc) and LinB, produced 2,5-dichlorophenol and 2,5-dichlorohydroquinone from γ-HCH, which are indicators of LinB activity, and grew in minimal medium supplied with γ-HCH as a sole carbon source. These results indicated that other HLDs in addition to LinB can play roles in the γ-HCH utilization.}, } @article {pmid40037607, year = {2025}, author = {Antaliya, K and Godhaniya, M and Galawala, J and Vansia, A and Mangrola, A and Ghelani, A and Patel, R}, title = {Microbial community transition in Surti buffalo-based fermented formulations sustainably enhances soil fertility and plant growth.}, journal = {Letters in applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/lambio/ovaf030}, pmid = {40037607}, issn = {1472-765X}, abstract = {This study investigates the role of microbial dynamics during the fermentation of Buffalo dung and urine-fermented plant growth-promoting formulation, a natural biofertilizer, and its impact on plant growth and soil health. This formulation was prepared using Surti buffalo dung, urine, jaggery, gram flour, and soil and fermented for up to 14 days. Metagenomic analysis revealed microbial succession from a diverse initial community to a Bacillus-dominated population, especially the Lactic Acid Bacteria, after eight days of fermentation. The changes were accompanied by increases in the plant growth-promoting genes related to nutrient acquisition, phytohormone production, and stress resistance. The pot experiment revealed a significant increase in mung bean growth, with the maximum effect obtained from the 8th-day fermented formulation. The experiment showed considerable improvement in the physicochemical properties of soil, including increased organic carbon and nutrient availability. These findings underscore the ecological importance of microbial input preparation in enhancing soil fertility and plant growth sustainably. Future research should delve deeper into the specific mechanisms these microbes facilitate nutrient cycling and resilience in various agroclimatic conditions.}, } @article {pmid40037564, year = {2025}, author = {Miller, SJ and Zhang, F and Taylor, S and Woodman, R and Shoubridge, AP and Papanicolas, LE and Rogers, GB}, title = {Oropharyngeal Staphylococcus aureus is linked to higher mortality in long-term aged care residents.}, journal = {Age and ageing}, volume = {54}, number = {3}, pages = {}, doi = {10.1093/ageing/afaf042}, pmid = {40037564}, issn = {1468-2834}, support = {//Australian Medical Research Future Fund/ ; GNT1152268//Australian Department of Health/ ; //Australian Department of Health/ ; GNT119378//National Health and Medical Research Council/ ; //Matthew Flinders Professorial Fellowship/ ; GNT2008625//NHMRC Emerging Leadership/ ; }, mesh = {Humans ; Male ; Female ; *Staphylococcal Infections/mortality/microbiology/diagnosis ; Aged, 80 and over ; Aged ; *Staphylococcus aureus/isolation & purification ; *Oropharynx/microbiology ; *Homes for the Aged/statistics & numerical data ; Risk Factors ; South Australia/epidemiology ; Nursing Homes/statistics & numerical data ; Age Factors ; Long-Term Care/statistics & numerical data ; Carrier State/microbiology/diagnosis ; Time Factors ; Metagenomics ; Microbiota ; Comorbidity ; Cause of Death ; Risk Assessment ; Methicillin-Resistant Staphylococcus aureus/isolation & purification ; }, abstract = {BACKGROUND: Biological ageing, healthcare interactions, and pharmaceutical and environmental exposures in later life alter the characteristics of the oropharyngeal (OP) microbiome. These changes, including an increased susceptibility to colonisation by pathobiont species, have been linked with diverse health outcomes.

OBJECTIVES: To investigate the relationship between OP microbiome characteristics and all-cause mortality in long-term aged care residents.

METHODS: OP swabs were collected from 190 residents of five aged care facilities in South Australia. Microbiota composition was assessed by shotgun metagenomics and related to health outcomes during a 12-month follow-up period. OP carriage of Staphylococcus aureus and methicillin resistance was confirmed by qPCR.

RESULTS: OP carriage of S. aureus was identified in 13 (6.8%) residents. Detection of S. aureus was significantly associated with an increased risk of mortality (adjusted HR [95% CI]: 9.7 [3.8-24.9], P < .0001), compared with non-carriers, independent of methicillin resistance. Staphylococcus aureus carriage demonstrated a stronger association with mortality risk than the total number of comorbidities at the univariate level (S. aureus HR [95% CI]: 7.2 [3.4-15.5], P < .0001 vs. comorbidity count HR [95% CI]: 1.1 [1.0-1.3], P = .03), and remained significant after multivariable adjustment. Staphylococcus aureus detection was significantly associated with total number of comorbidities (adjusted OR [95% CI]: 1.4 [1.0-2.0], P = .04).

CONCLUSION: OP S. aureus carriage predicts all-cause mortality in long-term aged care. We speculate that S. aureus carriage represents a marker of general health, including prior healthcare exposures. OP S. aureus carriage could contribute to estimations of general health in older individuals and thereby inform care strategies.}, } @article {pmid40037293, year = {2025}, author = {Delherbe, NA and Gomez, O and Plominsky, AM and Oliver, A and Manzanera, M and Kalyuzhnaya, MG}, title = {Atmospheric methane consumption in arid ecosystems acts as a reverse chimney and is accelerated by plant-methanotroph biomes.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf026}, pmid = {40037293}, issn = {1751-7370}, abstract = {Drylands cover one-third of the Earth's surface and are one of the largest terrestrial sinks for methane. Understanding the structure-function interplay between members of arid biomes can provide critical insights into mechanisms of resilience toward anthropogenic and climate-change-driven environmental stressors-water scarcity, heatwaves, and increased atmospheric greenhouse gases. This study integrates in situ measurements with culture-independent and enrichment-based investigations of methane-consuming microbiomes inhabiting soil in the Anza-Borrego Desert, a model arid ecosystem in Southern California, United States. The atmospheric methane consumption ranged between 2.26 to 12.73 μmol m2 h-1, peaking during the daytime at vegetated sites. Metagenomic studies revealed similar soil-microbiome compositions at vegetated and unvegetated sites, with Methylocaldum being the major methanotrophic clade. Eighty-four metagenome-assembled genomes were recovered, six represented by methanotrophic bacteria (three Methylocaldum, two Methylobacter, and uncultivated Methylococcaceae). The prevalence of copper-containing methane monooxygenases in metagenomic datasets suggests a diverse potential for methane oxidation in canonical methanotrophs and uncultivated Gammaproteobacteria. Five pure cultures of methanotrophic bacteria were obtained, including four Methylocaldum. Genomic analysis of Methylocaldum isolates and metagenome-assembled genomes revealed the presence of multiple stand-alone methane monooxygenase subunit C paralogs, which may have functions beyond methane oxidation. Furthermore, these methanotrophs have genetic signatures typically linked to symbiotic interactions with plants, including tryptophan synthesis and indole-3-acetic acid production. Based on in situ fluxes and soil microbiome compositions, we propose the existence of arid-soil reverse chimneys, an empowered methane sink represented by yet-to-be-defined cooperation between desert vegetation and methane-consuming microbiomes.}, } @article {pmid40037072, year = {2025}, author = {Meng, JX and Li, MH and Wang, XY and Li, S and Zhang, Y and Ni, HB and Ma, H and Liu, R and Yan, JC and Li, XM and Sun, YZ and Yang, X and Zhang, XX}, title = {Temporal variability in the diversity, function and resistome landscapes in the gut microbiome of broilers.}, journal = {Ecotoxicology and environmental safety}, volume = {292}, number = {}, pages = {117976}, doi = {10.1016/j.ecoenv.2025.117976}, pmid = {40037072}, issn = {1090-2414}, abstract = {Understanding the dynamic and stability of gut microbiota over the course of production cycle of broiler chicken can help identify microbial features that associate with better health and productivity. In the present study, we profile the changes in the composition and stability of gut microbiota of commercially raised broilers at nine distinct time points using shotgun metagenomics and culturomics approaches. We demonstrate, within the first week post-hatching, a rapid decline in relative abundance of 122 pioneer microbial species including Bacteroides fragilis, Lachnospira eligens and Ruminococcus gnavus, accompanied by a substantial decrease in both microbial richness and diversity. This was followed by a gradual increase and stabilization in the microbial diversity and population structure that persisted until the broilers reached the marketing age. Throughout the production cycle, key bacterial families such as Lachnospiraceae, Bacteroidaceae, and Ruminococcaceae were identified. However, significant shifts at the lower taxonomic levels occurred at different production stages, influencing the functional capacities and resistance profiles of the microbiota. During the rapid growth phase, enzymes crucial to vitamin and amino acid metabolism dominated, whereas enzymes associated with carbohydrate and energy metabolism were notably more abundant during the fattening stage. Many predicted antibiotic resistance genes were detected in association with typical commensal bacterial species in the gut microbiota, indicating a sustained resistance of the gut microbiota to antibiotic classes such as aminoglycosides and tetracyclines, which persist even in the absence of antibiotic selection pressure. Our research carries important implications for the management and health surveillance of broiler production.}, } @article {pmid40036691, year = {2025}, author = {Gao, Y and Luo, H and Lyu, H and Yang, H and Yousuf, S and Huang, S and Liu, YX}, title = {Benchmarking short-read metagenomics tools for removing host contamination.}, journal = {GigaScience}, volume = {14}, number = {}, pages = {}, doi = {10.1093/gigascience/giaf004}, pmid = {40036691}, issn = {2047-217X}, support = {2024M753580//China Postdoctoral Science Foundation/ ; U23A20148//National Natural Science Foundation of China/ ; CAAS-ZDRW202308//Agricultural Science and Technology Innovation Program/ ; }, mesh = {*Metagenomics/methods ; *Benchmarking ; Microbiota/genetics ; Humans ; DNA Contamination ; Metagenome ; Software ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing/methods ; Reproducibility of Results ; }, abstract = {BACKGROUND: The rapid evolution of metagenomic sequencing technology offers remarkable opportunities to explore the intricate roles of microbiome in host health and disease, as well as to uncover the unknown structure and functions of microbial communities. However, the swift accumulation of metagenomic data poses substantial challenges for data analysis. Contamination from host DNA can substantially compromise result accuracy and increase additional computational resources by including nontarget sequences.

RESULTS: In this study, we assessed the impact of computational host DNA decontamination on downstream analyses, highlighting its importance in producing accurate results efficiently. We also evaluated the performance of conventional tools like KneadData, Bowtie2, BWA, KMCP, Kraken2, and KrakenUniq, each offering unique advantages for different applications. Furthermore, we highlighted the importance of an accurate host reference genome, noting that its absence negatively affected the decontamination performance across all tools.

CONCLUSIONS: Our findings underscore the need for careful selection of decontamination tools and reference genomes to enhance the accuracy of metagenomic analyses. These insights provide valuable guidance for improving the reliability and reproducibility of microbiome research.}, } @article {pmid40036505, year = {2025}, author = {Langenfeld, K and Hegarty, B and Vidaurri, S and Crossette, E and Duhaime, MB and Wigginton, KR}, title = {Development of a quantitative metagenomic approach to establish quantitative limits and its application to viruses.}, journal = {Nucleic acids research}, volume = {53}, number = {5}, pages = {}, doi = {10.1093/nar/gkaf118}, pmid = {40036505}, issn = {1362-4962}, support = {1 545 756//NSF/ ; //University of Michigan Integrated Training in Microbial Systems (ITiMS)/ ; //University of Michigan/ ; //NSF/ ; //ITiMS/ ; //Burroughs Wellcome Fund/ ; }, mesh = {*Metagenomics/methods ; *Metagenome/genetics ; Humans ; Wastewater/virology/microbiology ; DNA Viruses/genetics ; DNA, Viral/genetics ; Bacteriophages/genetics ; Genome, Viral/genetics ; Viruses/genetics ; }, abstract = {Quantitative metagenomic methods are maturing but continue to lack clearly-defined analytical limits. Here, we developed a computational tool, QuantMeta, to determine the absolute abundance of targets in metagenomes spiked with synthetic DNA standards. The tool establishes (i) entropy-based detection thresholds to confidently determine the presence of targets, and (ii) an approach to identify and correct read mapping or assembly errors and thus improve the quantification accuracy. Together this allows for an approach to confidently quantify absolute abundance of targets, be they microbial populations, genes, contigs, or metagenome-assembled genomes. We applied the approach to quantify single- and double-stranded DNA viruses in wastewater viral metagenomes, including pathogens and bacteriophages. Concentrations of total DNA viruses in wastewater influent and effluent were >108 copies/ml using QuantMeta. Human-associated DNA viruses were detected and quantifiable with QuantMeta thresholds, including polyomavirus, papillomavirus, and crAss-like phages, at concentrations similar to previous reports that utilized quantitative polymerase chain reaction (PCR)-based assays. Our results highlight the higher detection thresholds of quantitative metagenomics (approximately 500 copies/μl) as compared to PCR-based quantification (approximately 10 copies/μl) despite a sequencing depth of 200 million reads per sample. The QuantMeta approach, applicable to both viral and cellular metagenomes, advances quantitative metagenomics by improving the accuracy of measured target absolute abundances.}, } @article {pmid40036345, year = {2025}, author = {Hemeda, AA and Zahran, SA and Tammam, MA and Ewida, MA and Kashef, MT and Yassin, AS and Mitra, A and Youssef, NH and Elshahed, MS}, title = {Metagenomic mining unveils a novel GH130 enzyme with exclusive xylanase activity over a wide temperature and pH ranges.}, journal = {Journal of industrial microbiology & biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jimb/kuaf006}, pmid = {40036345}, issn = {1476-5535}, abstract = {The equine gut harbours a diverse microbial community and represents a rich source of carbohydrate-active enzymes (CAZymes). To identify and characterize potentially novel CAZymes from a horse's hindgut metagenome, shotgun metagenomic sequencing was performed on DNA extracted from a stool sample of a male horse followed by CAZyme annotation. Here, we report on the characterization of a novel enzyme (AH2) that was identified, synthesized, cloned and characterized from the obtained CAZyme dataset. AH2 was identified as a GH130 family member and displayed an exclusive xylanase activity, a trait hitherto unreported in prior characterization of GH130 CAZymes. AH2 displayed an optimal activity at a pH of 5.6 and a temperature of 50°C. AH2 maintained significant activity across a pH range of 4 to 10 (62 -72%) and temperatures of 30 to 70°C (77-86%). The enzyme had remarkable stability, with minimal reductions in activity across a temperature range of 4 to 70°C and pH levels of 3, 7, and 9. Docking studies identified AH2's amino acids (Glu90 and Glu149) to be involved in substrate binding. Molecular dynamics simulation confirmed the structural stability of AH2 at pH 5.6 and 50°C, further supporting its resilience under these conditions. Our results expand on the known activities associated with the GH130 CAZyme family and demonstrate that the horse gut metagenome represents an unexplored source of novel CAZymes.}, } @article {pmid40035787, year = {2025}, author = {Tappauf, N and Lamers, Y and Sham, HP and Piper, HG}, title = {Multiomics profiling and parenteral nutrition weaning in pediatric patients with intestinal failure: A longitudinal cohort study.}, journal = {JPEN. Journal of parenteral and enteral nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1002/jpen.2742}, pmid = {40035787}, issn = {1941-2444}, support = {//This study was funded through a 2021-2022 Healthy Starts Catalyst Grant, awarded by the BC Children's Hospital Research Institute in Vancouver, Canada./ ; }, abstract = {BACKGROUND: Intestinal failure (IF) is a life-limiting condition that includes a variety of intestinal pathologies. Currently, there are few clinical biomarkers that reflect intestinal function or a patient's potential to wean off parenteral nutrition (PN), making it difficult to predict the clinical trajectory. By associating gut microbiome taxonomic and functional features and blood analytes with the proportion of daily energy delivered via PN-a proxy for intestinal function-our study aimed to discover potential predictors of intestinal function and PN weaning potential.

METHODS: In this longitudinal multiomics cohort study, we followed 18 pediatric patients with IF and PN support for ≤1.5 years. Fecal and stoma samples were analyzed using metagenomic shotgun sequencing to assess bacterial taxonomy and function and internal transcribed spacer 2 ribosomal RNA sequencing to characterize the fungal community. Targeted metabolomics was used to quantify 257 blood analytes. Linear mixed models were used to analyze the associations of PN dependence with microbiome features and blood analytes.

RESULTS: The bacterial and fungal taxonomic composition exhibited substantial interpatient and intrapatient variability, with no link to PN dependence. In contrast, bacterial functional analysis revealed 63 MetaCyc pathways significantly associated with PN dependence. Additionally, 32 blood analytes were associated with PN dependence.

CONCLUSION: In this exploratory study, we found that functional microbiome features and blood metabolomic profiles-particularly urea cycle metabolites, creatinine, asparagine, and tryptophan-derived metabolites-show promise for predicting intestinal function. Furthermore, they may have therapeutic implications for promoting intestinal adaptation. Confirmatory trials with larger sample sizes are needed to validate these findings.}, } @article {pmid40034816, year = {2024}, author = {Liu, Z and Jiang, A and Ma, D and Liu, D and Han, X and Zhao, M and Zhou, C and Tan, Z}, title = {The impact of rumen microbial composition on apparent digestibility, rumen fermentation and metabolism in Sanhe cows and Holstein cows of different parities under identical dietary conditions.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1463209}, pmid = {40034816}, issn = {2297-1769}, abstract = {Previous studies have discussed the association between serum metabolism and lactation performance among Sanhe and Holstein cows of different parities and found that the metabolic profiles of these two breeds vary differently with parity. Since the rumen is the central organ for nutrient absorption and production transformation in dairy cows, it remains unknown whether the differences observed under the same dietary conditions are related to the structure of the rumen microbiome. This study measured the apparent digestibility and rumen fermentation parameters of Sanhe cows (S1/S2/S3/S4) and Holstein cows (H1/H2/H3/H4) across four parities and generated a comprehensive rumen microbiome dataset using high-throughput sequencing technology. Significant differences in dry matter digestibility (p = 0.001) and ammonia nitrogen (p = 0.024) were observed among the S groups, with higher trends of various VFA contents in S1 (0.05 < p < 0.1). The H group showed significant differences in crude protein digestibility (p = 0.001), higher isovaleric acid content in H1 (p = 0.002), and the lowest acetate to propionate ratio (p = 0.002) in H3. Metagenomic sequencing results indicated consistency between rumen microbiome patterns and metabolic changes, with S1 distinctly different from S2/S3/S4, and H1 and H2 different from H3 and H4. The species composition of the rumen microbiome was similar between Sanhe and Holstein cows, but differences in abundance were noted. Rhizophagus , Neocallimastix, and Piromyces were more abundant in S1, H1, and H2, and pathways such as autophagy-animal, plant-pathogen interaction, and endocytosis were significantly enriched in these parities. Multiparous Sanhe cows had higher abundances of ATP-binding cassette transporters pathways. Additionally, CAZymes such as GH84 and GH37 were significantly associated with differential physiological indicators and milk traits. In conclusion, this study reveals the complex relationship between rumen microbiota and metabolic characteristics in Sanhe and Holstein cows of different parities, indicating that changes in the structure of the rumen microbiome may be key factors affecting lactation performance and metabolic differences in dairy cows.}, } @article {pmid40034572, year = {2025}, author = {Phillips, R and Fisher, BT and Ladas, EJ and Patel, P and Robinson, PD and Dupuis, LL and Ammann, RA and Beauchemin, MP and Carlesse, F and Castagnola, E and Davis, BL and Efremov, K and Elgarten, CW and Groll, AH and Haeusler, GM and Koenig, C and Morris, A and Santolaya, ME and Spinelli, D and Tissing, WJE and Wolf, J and Sung, L and Lehrnbecher, T}, title = {Use of food restrictions to prevent infections in paediatric patients with cancer and haematopoietic cell transplantation recipients: a systematic review and clinical practice guideline.}, journal = {EClinicalMedicine}, volume = {81}, number = {}, pages = {103093}, pmid = {40034572}, issn = {2589-5370}, abstract = {BACKGROUND: Food restrictions during periods of neutropenia have been widely used in oncology settings to prevent infections. As there is a lack of clearly demonstrated effectiveness, this strategy is being increasingly questioned.

METHODS: A multi-national panel of 23 individuals was convened to develop a clinical practice guideline (CPG) on the use of food restrictions to prevent infections in paediatric patients with cancer and haematopoietic cell transplantation (HCT) recipients. It included representation from persons with lived experience and physicians, dieticians, nurses, pharmacists and guideline methodologists working in paediatric oncology/HCT or infectious diseases. Panel members (female n = 15; 65%) were from North America (12, 52%), Europe (8, 35%), South America (2, 9%) and Australia (1, 4%). The Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach was used to formulate the CPG recommendations based on a systematic review of randomised controlled trials (RCTs). MEDLINE, MEDLINE in-Process and Embase databases were searched from January 1, 1980, to May 7, 2024, with a broad strategy which combined subject headings and text words relating to neutropenia, infection and diet.

FINDINGS: The systematic review, which provided the evidence base for the CPG recommendations, identified 4312 unique citations, of which 52 were retrieved for full-text evaluation. Eight RCTs met the eligibility criteria and informed panel deliberations. Although there was clinical heterogeneity in the food restrictions evaluated, data were consistent in suggesting that food restrictions lack clinically significant benefit in preventing infections. The panel made two conditional recommendations against the use of food restrictions in a) paediatric patients with cancer receiving chemotherapy and b) in the setting of allogeneic and autologous HCT. The panel developed a good practice statement to emphasise the importance of health care organisations and families adhering to local food safety practices.

INTERPRETATION: This CPG provides the first evidence-based recommendations on use of food restrictions to prevent infections in children and adolescents undergoing chemotherapy and paediatric haematopoietic cell transplant recipients.

FUNDING: This CPG was funded and developed through the POGO Guidelines Program.}, } @article {pmid40034495, year = {2025}, author = {Zhao, SY and Meng, YL and Yang, ZH and Li, BL and Li, YY and Han, H and Liu, L and Duan, PF and Chen, ZJ}, title = {Rhizosphere microbiome metagenomics in PGPR-mediated alleviation of combined stress from polypropylene microplastics and Cd in hybrid Pennisetum.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1549043}, pmid = {40034495}, issn = {1664-302X}, abstract = {The simultaneous presence of microplastics (MPs) and heavy metals in soil may result in heightened toxicity, causing more significant adverse effects on plant growth. Plant growth-promoting rhizobacteria (PGPR) have demonstrated significant capacities in alleviating the toxic stress caused by the combined pollution of heavy metals and other contaminants. However, research on the impacts and processes of PGPR in alleviating stress induced by the combined pollution from MPs and heavy metals is still insufficient. This study involved a pot experiment to evaluate the ability of PGPR to mitigate stress induced by the combined pollution from polypropylene microplastic (PP MPs) particles of different sizes (6.5 μm and 830 μm) and the heavy metal cadmium (Cd) in the bioenergy plant hybrid Pennisetum. Moreover, metagenomic analysis was used to examine the effects of PGPR on the rhizospheric microbial community and function. The cocontamination of PP and Cd affected the growth of the hybrid Pennisetum differently depending on the size of the MPs particles, with the aboveground and underground lengths of the 6.5 μm PP + Cd experimental group being smaller than those of the 830 μm PP + Cd group. The PGPRs (Bacillus sp. Y-35, Bacillus sp. Y-62, Bacillus sp. Y-S, and Enterobacter sp. Y-V) successfully alleviated the stress caused by the combined pollution of PP and Cd, resulting in increases of 8.24 and 42.21% in the plant height and dry weight, respectively. The metagenomic studies indicated that the cocontamination of PP and Cd, along with PGPR inoculation, altered the composition of the rhizospheric bacterial community, leading to changes in microbial diversity indices and the composition of dominant groups such as Pseudomonadota, Actinomycetota, and Acidobacteriota. The functional analysis revealed that the main functional groups involved glucose metabolism, energy metabolism, signal transduction, and nucleotide metabolism. The MPs particle size and different PGPR significantly affected functions such as the pentose phosphate pathway, benzoate degradation, and amide biosynthesis. This study provides essential data and scientific evidence on the ecotoxicological effects of simultaneous contamination by MPs and heavy metals, as well as insights into potential bioremediation methods.}, } @article {pmid40033444, year = {2025}, author = {Dias, BDC and Lamarca, AP and Machado, DT and Kloh, VP and de Carvalho, FM and Vasconcelos, ATR}, title = {Metabolic pathways associated with Firmicutes prevalence in the gut of multiple livestock animals and humans.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {20}, pmid = {40033444}, issn = {2524-4671}, support = {88887.508687/2020-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 88887.677436/2022-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; E-26/200.200/2024//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; E-26/201.046/2022//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; 302023/2024-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 307145/2021-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, abstract = {Dynamic interspecific interactions and environmental factors deeply impact the composition of microbiotic communities in the gut. These factors intertwined with the host's genetic background and social habits cooperate synergistically as a hidden force modulating the host's physiological and health determinants, with certain bacterial species being maintained from generation to generation. Firmicutes, one of the dominant bacterial phyla present across vertebrate classes, exhibits a wide range of functional capabilities and colonization strategies. While ecological scenarios involving microbial specialization and metabolic functions have been hypothesized, the specific mechanisms that sustain the persistence of its microbial taxa in a high diversity of hosts remain elusive. This study fills this gap by investigating the Firmicutes metabolic mechanisms contributing to their prevalence and heritability in the host gut on metagenomes-assembled bacterial genomes collected from 351 vertebrate samples, covering 18 food-producing animals and humans, specific breeds and closely-related species. We observed that taxa belonging to Acetivibrionaceae, Clostridiaceae, Lachnospiraceae, Ruminococcaceae, and the not well understood CAG-74 family were evolutionarily shared across all hosts. These prevalent taxa exhibit metabolic pathways significantly correlated with extra-host survival mechanisms, cell adhesion, colonization and host transmission, highlighted by sporulation, glycan biosynthesis, bile acid metabolism, and short-chain fatty acid encoded genes. Our findings provide a deeper understanding of the ecological foundations governing distinct transmission modes, effective colonization establishment, and maintenance of Firmicutes, offering new perspectives on both well-known and poorly characterized species.}, } @article {pmid40032396, year = {2025}, author = {Zimmermann, P and Kurth, S and Giannoukos, S and Stocker, M and Bokulich, NA}, title = {NapBiome trial: Targeting gut microbiota to improve sleep rhythm and developmental and behavioural outcomes in early childhood in a birth cohort in Switzerland - a study protocol.}, journal = {BMJ open}, volume = {15}, number = {3}, pages = {e092938}, doi = {10.1136/bmjopen-2024-092938}, pmid = {40032396}, issn = {2044-6055}, mesh = {Humans ; *Gastrointestinal Microbiome ; Switzerland ; Infant ; Infant, Newborn ; *Sleep/physiology ; Double-Blind Method ; Child Development ; Infant, Premature ; Child, Preschool ; Brain-Gut Axis ; Female ; Randomized Controlled Trials as Topic ; Male ; Probiotics/therapeutic use ; Multicenter Studies as Topic ; }, abstract = {INTRODUCTION: The gut-brain axis plays a crucial role in the regulation and development of psychological and physical processes. The first year of life is a critical period for the development of the gut microbiome, which parallels important milestones in establishing sleep rhythm and brain development. Growing evidence suggests that the gut microbiome influences sleep, cognition and early neurodevelopment. For term-born and preterm-born infants, difficulties in sleep regulation may have consequences on health. Identifying effective interventions on the gut-brain axis in early life is likely to have long-term implications for the health and development of at-risk infants.

METHODS AND ANALYSES: In this multicentre, four-group, double-blinded, placebo (PLC)-controlled randomised trial with a factorial design, 120 preterm-born and 260 term-born infants will be included. The study will investigate whether the administration of daily synbiotics or PLC for a duration of 3 months improves sleep patterns and neurodevelopmental outcomes up to 2 years of age. The trial will also: (1) determine the association between gut microbiota, sleep patterns and health outcomes in children up to 2 years of age; and (2) leverage the interactions between gut microbiota, brain and sleep to develop new intervention strategies for at-risk infants.

ETHICS AND DISSEMINATION: The NapBiome trial has received ethical approval by the Committee of Northwestern and Central Switzerland and Canton Vaud, Switzerland (#2024-01681). Outcomes will be disseminated through publication and will be presented at scientific conferences. Metagenomic data will be shared through the European Nucleotide Archive.

TRIAL REGISTRATION NUMBER: The US National Institutes of Health NCT06396689.}, } @article {pmid40032028, year = {2025}, author = {Ismaiah, MJ and Kwan Lo, EK and Chen, C and Shing-Jie Tsui, J and Johnson-Hill, WA and Felicianna, and Zhang, F and Matthew Leung, HK and Oger, C and Durand, T and Chung-Yung Lee, J and El-Nezami, H}, title = {Alpha-aminobutyric acid administration suppressed visceral obesity and modulated hepatic oxidized PUFA metabolism via gut microbiota modulation.}, journal = {Free radical biology & medicine}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.freeradbiomed.2025.02.029}, pmid = {40032028}, issn = {1873-4596}, abstract = {BACKGROUND: High-fat diet (HFD) is associated with visceral obesity due to disruption in the lipid metabolism and gut dysbiosis. These symptoms may contribute to hepatic steatosis and the formation of oxidized polyunsaturated fatty acids (PUFAs). Alpha-aminobutyric acid (ABA) is an amino-acid derived metabolite, and its concentration has been correlated with several metabolic conditions and gut microbiome diversity while its direct effects on visceral obesity, lipid metabolism and the gut microbiota are not well understood. This study was designed to investigate the effect of physiological dose of ABA on diet-induced visceral obesity and lipid metabolism dysregulation by examining the fatty acids and oxidized PUFAs profile in the liver as well as the gut microbiota.

RESULTS: ABA administration reduced visceral obesity by 28% and lessened adipocyte hypertrophy. The expression of liver Cd36 was lowered by more than 50% as well as the saturated and monounsaturated FA concentration. Notably, the desaturation index for C16 and C18 FAs that are correlated with adiposity were reduced. The concentration of several DHA-derived oxidized PUFAs were also enhanced. Faecal metagenomics sequencing revealed enriched abundance of Leptogranulimonas caecicola and Bacteroides sp. ZJ-18 and were positively correlated with several DHA- and ALA-derived oxidized PUFAs in ABA group.

CONCLUSION: Our study revealed the modulatory effect of physiological dose of ABA on attenuating visceral obesity, reducing hepatic steatosis, and promoting the production of anti-inflammatory oxidized PUFAs that were potentially mediated by the gut microbiota.}, } @article {pmid40030240, year = {2024}, author = {Xiao, Z and Sun, H and Wei, A and Zhao, W and Jiang, X}, title = {A Novel Framework for Predicting Phage-Host Interactions Via Host Specificity-Aware Graph Autoencoder.}, journal = {IEEE journal of biomedical and health informatics}, volume = {PP}, number = {}, pages = {}, doi = {10.1109/JBHI.2024.3500137}, pmid = {40030240}, issn = {2168-2208}, abstract = {Due to the abuse of antibiotics, some pathogenic bacteria have developed resistance to most antibiotics, leading to the emergence of antibiotic-resistant superbugs. Therefore, researchers resort to phage therapy for bacterial infections. For phage therapy, the fundamental step is to accurately identify phage-host interactions. Although various methods have been proposed, the existing methods suffer from the following two shortcomings: 1) they fail to make full use of genetic information including both genome and protein sequence of phages; 2) host specificity of phages is not explicitly utilized when learning representations of phages and bacteria. In this paper, we present an efficient computational method called PHISGAE for predicting phage-host interactions, in which the host specificity is explicitly employed. Firstly, initial phage-phage connections are efficiently constructed via utilizing phage genome and protein sequence. Then, the refined heterogeneous network is derived by applying K-nearest neighbor strategy, keeping relatively more meaningful local semantics among phages and bacteria. Finally, a host specificity-aware graph autoencoder is proposed to learn high-quality representations of phages and bacteria for predicting phage-host interactions. Experimental results show that PHISGAE outperforms the state-of-the-art methods on predicting phage-host interactions at both species level and genus level (AUC values of 94.73% and 96.32%, respectively). Moreover, results of case study demonstrate that PHISGAE is able to identify candidate hosts with high probability for previously unseen phages identified from metagenomics, effectively predicting potential phage-host interactions in real-world applications.}, } @article {pmid40030030, year = {2025}, author = {Ghimire, S and Lehman, PC and Aguilar Meza, LS and Shahi, SK and Hoang, J and Olalde, H and Paullus, M and Cherwin, C and Wang, K and Gill, C and Cho, T and Mangalam, AK}, title = {Specific microbial ratio in the gut microbiome is associated with multiple sclerosis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {10}, pages = {e2413953122}, doi = {10.1073/pnas.2413953122}, pmid = {40030030}, issn = {1091-6490}, support = {R01AI137075//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 1I01CX002212//U.S. Department of Veterans Affairs (VA)/ ; P30 ES005605/ES/NIEHS NIH HHS/United States ; T32AI007260//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; }, mesh = {*Gastrointestinal Microbiome ; *Multiple Sclerosis/microbiology ; Animals ; Humans ; Mice ; Female ; *Dysbiosis/microbiology ; *Feces/microbiology ; Male ; Akkermansia ; Adult ; Encephalomyelitis, Autoimmune, Experimental/microbiology ; Middle Aged ; Bifidobacterium ; Prevotella/isolation & purification ; Mice, Inbred C57BL ; Case-Control Studies ; }, abstract = {Gut microbiota dysbiosis is associated with multiple sclerosis (MS), but the causal relationship between specific gut bacteria and MS pathogenesis remains poorly understood. Therefore, we profiled the stool microbiome of people with MS (PwMS) and healthy controls (HC) using shotgun metagenomic sequencing. PwMS showed a distinct microbiome compared to HC, with Prevotella copri (PC) and Blautia species as drivers of microbial communities in HC and PwMS, respectively. Administration of MS-driving Blautia species (Blautia wexlerae; BW) to mice resulted in increased levels of gut inflammatory markers and altered microbiota with increased capacity to induce proinflammatory cytokines. Utilizing experimental autoimmune encephalomyelitis (EAE), an animal model of MS, we identified a lower gut Bifidobacterium to Akkermansia ratio as a hallmark of the disease. BW-administered mice also showed a lower Bifidobacterium to Akkermansia ratio pre-EAE induction which correlated with increased disease severity post-EAE induction. The importance of the Bifidobacterium to Akkermansia ratio at the species level, lower Bifidobacterium adolescentis to Akkermansia muciniphila (BA:AM), was validated in our MS cohort and a large International Multiple Sclerosis Microbiome Study. Thus, our findings highlight the BA:AM ratio as a potential gut microbial marker in PwMS, opening avenues for microbiome-based diagnosis, prognosis, and therapy in MS.}, } @article {pmid39882942, year = {2025}, author = {Tran Lu Y, A and Ruault, S and Daguin-Thiebaut, C and Le Port, AS and Ballenghien, M and Castel, J and Gagnaire, PA and Bierne, N and Arnaud-Haond, S and Poitrimol, C and Thiebaut, E and Lallier, F and Broquet, T and Jollivet, D and Bonhomme, F and Hourdez, S}, title = {Comparative Population Genomics Unveils Congruent Secondary Suture Zone in Southwest Pacific Hydrothermal Vents.}, journal = {Molecular biology and evolution}, volume = {42}, number = {2}, pages = {}, doi = {10.1093/molbev/msaf024}, pmid = {39882942}, issn = {1537-1719}, support = {ANR-17-CE02-0003//ANR CERBERUS project/ ; }, mesh = {*Hydrothermal Vents ; *Phylogeography ; Pacific Ocean ; Gene Flow ; Genetic Variation ; Metagenomics ; }, abstract = {How the interplay of biotic and abiotic factors shapes current genetic diversity at the community level remains an open question, particularly in the deep sea. Comparative phylogeography of multiple species can reveal the influence of past climatic events, geographic barriers, and species life history traits on spatial patterns of genetic structure across lineages. To shed light on the factors that shape community-level genetic variation and to improve our understanding of deep-sea biogeographic patterns, we conducted a comparative population genomics study on seven hydrothermal vent species co-distributed in the Back-Arc Basins of the Southwest Pacific region. Using ddRAD-seq, we compared the range-wide distribution of genomic diversity across species and discovered a shared phylogeographic break. Demogenetic inference revealed shared histories of lineage divergence and a secondary contact. Low levels of asymmetric gene flow probably occurred in most species between the Woodlark and North Fiji basins, but the exact location of contact zones varied from species to species. For two species, we found individuals from the two lineages co-occurring in sympatry in Woodlark Basin. Although species exhibit congruent patterns of spatial structure (Eastern vs. Western sites), they also show variation in the degree of divergence among lineages across the suture zone. Our results also show heterogeneous gene flow across the genome, indicating possible partial reproductive isolation between lineages and early speciation. Our comparative study highlights the pivotal role of historical and contemporary factors, underscoring the need for a comprehensive approach-especially in addressing knowledge gaps on the life history traits of deep-sea species.}, } @article {pmid40028749, year = {2025}, author = {Salahi, A and Abd El-Ghany, WA}, title = {A Spotlight on Archaea in Humans, Livestock and Poultry: A Review.}, journal = {Veterinary medicine and science}, volume = {11}, number = {2}, pages = {e70263}, doi = {10.1002/vms3.70263}, pmid = {40028749}, issn = {2053-1095}, mesh = {Animals ; *Archaea/physiology ; Humans ; *Poultry ; Livestock ; Gastrointestinal Microbiome ; }, abstract = {The microbiota includes prokaryotes (archaea and bacteria) and eukaryotes. Archaea are single-celled prokaryotes and essential part of gut microbiome. Researches on archaea in ruminants and humans are more than mono-gastric. The low abundance of archaea in the gut depends on the method used (metagenomics or meta-transcriptomic) and age of people or poultry. The lack of complete recognition of archaea is due to their small number and method of identifying them (16S rRNA gene primers). The uses of archaea include analytical kit, reduce oil pollution, archaeosomes or drugs production, vaccines agents, lipid carriers in the pharmaceutical industry and molybdenum extraction in the nuclear industry. The nutritional functions of methanogenic archaea including feed utilization (ruminants) and efficiency, hydrogen reducing (human), fat deposition and enhancement of energy harvesting in mice, CAZymes genes, cecal fermentation, syntrophic potential, carotenoid source and improved transit time and appetite and SCFAs production. Archaea acting as antibiotics (produce archaeocins, sulfolobicins and halocin KPS1) and as probiotics (archaeobiotics) can reduce TMAU (trimethylaminuria) disease, cardiovascular diseases (CVDs), and atherosclerosis, brain abscess, cancer, colorectal cancer, inflammatory bowel disease (IBD), constipation, obesity, food allergies, asthma and anti-inflammation which can be prevented by using archaea, and other functions include energy homeostasis, heat shock protein (HSP) production and reducing aging.}, } @article {pmid40028600, year = {2025}, author = {Lu, K and Wang, Y and Wang, Y and Zhang, Q and Zhu, Y and Yu, X and Niu, G}, title = {Chijiahe virus, a novel mosquito-associated virus of the Iflaviridae family found in Shandong Province, China.}, journal = {Heliyon}, volume = {11}, number = {4}, pages = {e42532}, pmid = {40028600}, issn = {2405-8440}, abstract = {Climate change is increasing the threat of arboviruses globally, amplifying their geographic distribution and virulence. This poses a grave risk to public health as mosquito-transmitted viral infections resurge and spread. Unbiased metagenomics plays a crucial role in identifying unknown pathogens and monitoring significant ones. Using this approach, a novel mosquito-associated virus, named Chijiahe virus, was discovered. We collected 2910 mosquitoes and divided them into 65 pools based on species and collection site. To ascertain the existence of Chijiahe virus, we utilized nested PCR alongside real-time quantitative reverse transcription PCR (RT-qPCR). Further analysis of the virus's genomic characteristics and phylogenetic relationships revealed its detection in 10 out of 65 mosquito pools, yielding a minimum infection rate (MIR) of 0.34 %. The virus genome consists of a 9654-nucleotide single-stranded RNA, containing an open reading frame (ORF) that encodes essential proteins, including the capsid protein, RNA helicase, and RNA-dependent RNA polymerase (RdRp). Pairwise distance analysis revealed high nucleotide identity among all obtained sequences. Phylogenetic analysis demonstrated Chijiahe virus's close relationship to Arthropod iflavirus, a member of the family Iflaviridae. Additional analyses confirmed Chijiahe virus as a novel member of Iflaviridae.}, } @article {pmid40028274, year = {2025}, author = {Veluz, JT and Mallari, LAN and Gloria, PCT and Siringan, MAT}, title = {Exploring the taxonomical and functional profiles of marine microorganisms in Submarine Groundwater Discharge vent water from Mabini, Batangas, Philippines through metagenome-assembled genomes.}, journal = {Frontiers in genetics}, volume = {16}, number = {}, pages = {1522253}, pmid = {40028274}, issn = {1664-8021}, } @article {pmid40027914, year = {2025}, author = {Huang, M and Wang, Y and Lu, Y and Qu, W and Zou, Q and Zhang, D and Shen, Y and Han, D and Yu, F and Zheng, S}, title = {Clinical Characteristics and Predicting Disease Severity in Chlamydia psittaci Infection Based on Metagenomic Next-Generation Sequencing.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {1171-1181}, pmid = {40027914}, issn = {1178-6973}, abstract = {INTRODUCTION: Psittacosis pneumonia, as a zoonotic infection, is induced by the pathogen Chlamydia psittaci. In the present study, we sought to characterize the clinical manifestations and prognosticate the severity of psittacosis pneumonia.

METHODS: We retrospectively verified instances of psittacosis pneumonia in Zhejiang province, China, from January 2021 to April 2024. Relevant data pertaining to epidemiological, clinical, and laboratory aspects were compiled and evaluated.

RESULTS: Among a total of 110 individuals enrolled who were diagnosed with psittacosis pneumonia, the median age being 62.0 years (IQR, 53-69 years). The most common comorbidities were hypertension (36.4%) and diabetes mellitus (17.3%). Patients categorized as having severe disease (n=68) were significantly older than those with mild disease (n=42). Most patients had notable elevations in aspartate aminotransferase (AST), creatine kinase (CK), creatine kinase-MB (CK-MB), lactate dehydrogenase (LDH), D-dimer, C-reactive protein (CRP), procalcitonin, total bilirubin (TBil), and interleukin-6, as along with significant reductions in lymphocytes, monocytes, albumin, and interleukin-4. Chest CT scans showed bilateral lung involvement in 70 cases. In the cohort of patients having received empirical antibiotic therapy, 57.3% had their antibacterial medication adjusted in light of the mNGS findings. mNGS results indicated that 31.8% (35/110) had suspected coinfections. The random forest classifiers based upon the clinical and laboratory characteristics attained AUC values of 0.822.

DISCUSSION: The study underscores the efficacy of mNGS as a robust diagnostic tool for detecting Chlamydia psittaci, which can simultaneously detect other pathogens and guide clinical treatment. Severe patients exhibit significant inflammatory imbalances and lymphocyte depletion. A predictive model based on clinical and laboratory data at admission can effectively guide early clinical intervention.}, } @article {pmid40027489, year = {2025}, author = {Bai, D and Chen, T and Xun, J and Ma, C and Luo, H and Yang, H and Cao, C and Cao, X and Cui, J and Deng, YP and Deng, Z and Dong, W and Dong, W and Du, J and Fang, Q and Fang, W and Fang, Y and Fu, F and Fu, M and Fu, YT and Gao, H and Ge, J and Gong, Q and Gu, L and Guo, P and Guo, Y and Hai, T and Liu, H and He, J and He, ZY and Hou, H and Huang, C and Ji, S and Jiang, C and Jiang, GL and Jiang, L and Jin, LN and Kan, Y and Kang, D and Kou, J and Lam, KL and Li, C and Li, C and Li, F and Li, L and Li, M and Li, X and Li, Y and Li, ZT and Liang, J and Lin, Y and Liu, C and Liu, D and Liu, F and Liu, J and Liu, T and Liu, T and Liu, X and Liu, Y and Liu, B and Liu, M and Lou, W and Luan, Y and Luo, Y and Lv, H and Ma, T and Mai, Z and Mo, J and Niu, D and Pan, Z and Qi, H and Shi, Z and Song, C and Sun, F and Sun, Y and Tian, S and Wan, X and Wang, G and Wang, H and Wang, H and Wang, H and Wang, J and Wang, J and Wang, K and Wang, L and Wang, SK and Wang, X and Wang, Y and Xiao, Z and Xing, H and Xu, Y and Yan, SY and Yang, L and Yang, S and Yang, Y and Yao, X and Yousuf, S and Yu, H and Lei, Y and Yuan, Z and Zeng, M and Zhang, C and Zhang, C and Zhang, H and Zhang, J and Zhang, N and Zhang, T and Zhang, YB and Zhang, Y and Zhang, Z and Zhou, M and Zhou, Y and Zhu, C and Zhu, L and Zhu, Y and Zhu, Z and Zou, H and Zuo, A and Dong, W and Wen, T and Chen, S and Li, G and Gao, Y and Liu, YX}, title = {EasyMetagenome: A user-friendly and flexible pipeline for shotgun metagenomic analysis in microbiome research.}, journal = {iMeta}, volume = {4}, number = {1}, pages = {e70001}, pmid = {40027489}, issn = {2770-596X}, abstract = {Shotgun metagenomics has become a pivotal technology in microbiome research, enabling in-depth analysis of microbial communities at both the high-resolution taxonomic and functional levels. This approach provides valuable insights of microbial diversity, interactions, and their roles in health and disease. However, the complexity of data processing and the need for reproducibility pose significant challenges to researchers. To address these challenges, we developed EasyMetagenome, a user-friendly pipeline that supports multiple analysis methods, including quality control and host removal, read-based, assembly-based, and binning, along with advanced genome analysis. The pipeline also features customizable settings, comprehensive data visualizations, and detailed parameter explanations, ensuring its adaptability across a wide range of data scenarios. Looking forward, we aim to refine the pipeline by addressing host contamination issues, optimizing workflows for third-generation sequencing data, and integrating emerging technologies like deep learning and network analysis, to further enhance microbiome insights and data accuracy. EasyMetageonome is freely available at https://github.com/YongxinLiu/EasyMetagenome.}, } @article {pmid40027486, year = {2025}, author = {Zhao, Y and Hu, J and Wang, J and Yao, X and Zhang, T and Hu, B}, title = {Comammox Nitrospira act as key bacteria in weakly acidic soil via potential cobalamin sharing.}, journal = {iMeta}, volume = {4}, number = {1}, pages = {e271}, pmid = {40027486}, issn = {2770-596X}, abstract = {The discovery of comammox Nitrospira in low pH environments has reshaped the ammonia oxidation process in acidic settings, providing a plausible explanation for the higher nitrification rates observed in weakly acidic soils. However, the response of comammox Nitrospira to varying pH levels and its ecological role in these environments remains unclear. Here, a survey across soils with varying pH values (ranging from 4.4 to 9.7) was conducted to assess how comammox Nitrospira perform under different pH conditions. Results showed that comammox Nitrospira dominate ammonia oxidation in weakly acidic soils, functioning as a K-strategy species characterized by slow growth and stress tolerance. As a key species in this environment, comammox Nitrospira may promote bacterial cooperation under low pH conditions. Genomic evidence suggested that cobalamin sharing is a potential mechanism, as comammox Nitrospira uniquely encode a metabolic pathway that compensates for cobalamin imbalance in weakly acidic soils, where 86.8% of metagenome-assembled genomes (MAGs) encode cobalamin-dependent genes. Additionally, we used DNA stable-isotope probing (DNA-SIP) to demonstrate its response to pH fluctuations to reflect how it responds to the decrease in pH. Results confirmed that comammox Nitrospira became dominant ammonia oxidizers in the soil after the decrease in pH. We suggested that comammox Nitrospira will become increasingly important in global soils, under the trend of soil acidification. Overall, our work provides insights that how comammox Nitrospira perform in weakly acidic soil and its response to pH changes.}, } @article {pmid40027485, year = {2025}, author = {Liu, Y and Li, H and Sun, T and Sun, G and Jiang, B and Liu, M and Wang, Q and Li, T and Cao, J and Zhao, L and Xiao, F and Zhao, F and Cui, H}, title = {Gut microbiome and metabolome characteristics of patients with cholesterol gallstones suggest the preventive potential of prebiotics.}, journal = {iMeta}, volume = {4}, number = {1}, pages = {e70000}, pmid = {40027485}, issn = {2770-596X}, abstract = {Cholesterol gallstones (CGS) still lack effective noninvasive treatment. The etiology of experimentally proven cholesterol stones remains underexplored. This cross-sectional study aims to comprehensively evaluate potential biomarkers in patients with gallstones and assess the effects of microbiome-targeted interventions in mice. Microbiome taxonomic profiling was conducted on 191 samples via V3-V4 16S rRNA sequencing. Next, 60 samples (30 age- and sex-matched CGS patients and 30 controls) were selected for metagenomic sequencing and fecal metabolite profiling via liquid chromatography-mass spectrometry. Microbiome and metabolite characterizations were performed to identify potential biomarkers for CGS. Eight-week-old male C57BL/6J mice were given a lithogenic diet for 8 weeks to promote gallstone development. The causal relationship was examined through monocolonization in antibiotics-treated mice. The effects of short-chain fatty acids such as sodium butyrate, sodium acetate (NaA), sodium propionate, and fructooligosaccharides (FOS) on lithogenic diet-induced gallstones were investigated in mice. Gut microbiota and metabolites exhibited distinct characteristics, and selected biomarkers demonstrated good diagnostic performance in distinguishing CGS patients from healthy controls. Multi-omics data indicated associations between CGS and pathways involving butanoate and propanoate metabolism, fatty acid biosynthesis and degradation pathways, taurine and hypotaurine metabolism, and glyoxylate and dicarboxylate metabolism. The incidence of gallstones was significantly higher in the Clostridium glycyrrhizinilyticum group compared to the control group in mice. The grade of experimental gallstones in control mice was significantly higher than in mice treated with NaA and FOS. FOS could completely inhibit the formation of gallstones in mice. This study characterized gut microbiome and metabolome alterations in CGS. C. glycyrrhizinilyticum contributed to gallstone formation in mice. Supplementing with FOS could serve as a potential approach for managing CGS by altering the composition and functionality of gut microbiota.}, } @article {pmid40026814, year = {2025}, author = {Zhang, X and Yin, H and Yang, X and Kang, J and Sui, N}, title = {Therapeutic Mechanism of Zhuyang Tongbian Decoction in Treating Functional Constipation: Insights from a Pilot Study Utilizing 16S rRNA Sequencing, Metagenomics, and Metabolomics.}, journal = {International journal of general medicine}, volume = {18}, number = {}, pages = {1007-1022}, pmid = {40026814}, issn = {1178-7074}, abstract = {PURPOSE: To explore the mechanism of Zhuyang Tongbian Decoction (ZTD) in treating functional constipation (FC) by observing its effects on intestinal flora composition, the metabolic function of gut microbiota, fecal short-chain fatty acid (SCFA) levels, and serum concentrations of TLR4, NF-κB, TNF-α, and IL-6 in patients with FC.

PATIENTS AND METHODS: 40 patients with FC were randomly divided into the control group and the treatment group, 20 cases in each group. And 20 healthy volunteers were recruited during the same period. The control group was administered lactulose, while the treatment group was treated with ZTD. 16s RNA sequencing technology was used to compare the changes in the structure and diversity of the intestinal flora of patients before and after treatment. Changes in the levels of SCFAs in faeces and the levels of TLR4, NF-κB, TNF-α and IL-6 in serum were analysed. Metagenomics sequencing assessed microbiota metabolic functions.

RESULTS: The treatment group showed a significant increase in the relative abundance of beneficial bacteria, including Bifidobacterium, Lactobacillus, and Faecalibacterium_prausnitzii (P < 0.05), whereas Desulfobacterota and Ruminococcus were significantly reduced (P < 0.05). Notably, fecal acetic and propionic acid levels were significantly higher in the treatment group (P < 0.05). Serum biomarkers TLR4, NF-κB, TNF-α, and IL-6 decreased significantly (P < 0.05). Metagenomics sequencing showed that Carbohydrate metabolism, Metabolism of cofactors and vitamins, and C5- Branched dibasic acid metabolism were significantly increased in functional abundance (P < 0.05).

CONCLUSION: ZTD notably improves intestinal flora composition and gut microbiota metabolic function, regulates SCFA levels, and reduces inflammation markers in FC patients. The strain Faecalibacterium_prausnitzii shows significant potential in regulation of intestinal inflammation and may play a crucial role in the treatment efficacy of ZTD for FC.}, } @article {pmid40026575, year = {2025}, author = {Shen, W and Wang, D and Li, J and Liu, Y and Wang, Y and Yang, X and Peng, X and Xie, B and Su, L and Wei, Z and He, Q and Wang, Z and Feng, K and Du, W and Deng, Y}, title = {Developing a microfluidic-based epicPCR reveals diverse potential hosts of the mcrA gene in marine cold seep.}, journal = {mLife}, volume = {4}, number = {1}, pages = {70-82}, pmid = {40026575}, issn = {2770-100X}, abstract = {Anaerobic methanotrophic (ANME) microbes play a crucial role in the bioprocess of anaerobic oxidation of methane (AOM). However, due to their unculturable status, their diversity is poorly understood. In this study, we established a microfluidics-based epicPCR (Emulsion, Paired Isolation, and Concatenation PCR) to fuse the 16S rRNA gene and mcrA gene to reveal the diversity of ANME microbes (mcrA gene hosts) in three sampling push-cores from the marine cold seep. A total of 3725 16S amplicon sequence variants (ASVs) of the mcrA gene hosts were detected, and classified into 78 genera across 23 phyla. Across all samples, the dominant phyla with high relative abundance (>10%) were the well-known Euryarchaeota, and some bacterial phyla such as Campylobacterota, Proteobacteria, and Chloroflexi; however, the specificity of these associations was not verified. In addition, the compositions of the mcrA gene hosts were significantly different in different layers, where the archaeal hosts increased with the depths of sediments, indicating the carriers of AOM were divergent in depth. Furthermore, the consensus phylogenetic trees of the mcrA gene and the 16S rRNA gene showed congruence in archaea not in bacteria, suggesting the horizontal transfer of the mcrA gene may occur among host members. Finally, some bacterial metagenomes were found to contain the mcrA gene as well as other genes that encode enzymes in the AOM pathway, which prospectively propose the existence of ANME bacteria. This study describes improvements for a potential method for studying the diversity of uncultured functional microbes and broadens our understanding of the diversity of ANMEs.}, } @article {pmid40026326, year = {2024}, author = {Laço, J and Martorell, S and Gallegos, MDC and Gomila, M}, title = {Yearlong analysis of bacterial diversity in hospital sink drains: culturomics, antibiotic resistance and implications for infection control.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1501170}, pmid = {40026326}, issn = {1664-302X}, abstract = {Hospitals can carry high levels of bacterial diversity from all types of origins, such as human skin, outside environment and medical equipment. Sink drains in clinical settings are considered reservoirs for pathogenic bacteria and potential sources of hospital-acquired infections (HAI's) and antibiotic resistance genes (ARGs). Therefore, infection control measures are crucial to minimizing the risks associated with these reservoirs. Recent research has focused primarily on intensive care units (ICUs) and known pathogens, often employing metagenomic approaches that do not include bacterial isolation. This study aims to evaluate bacterial diversity using culturomics, extending the investigation beyond the ICU to identify antibiotic-resistant bacteria. A total of four samplings were conducted over 1 year (March 2022 to March 2023) in five different hospital wards [ICU, General Medicine (GM), Hematology (H), Short stay unit (UCE), and Microbiology laboratory (MS)]. All samples were cultured on selective and non-selective culture media, resulting in 1,058 isolates identified using MALDI-TOF MS, with a subset confirmed through 16S rRNA gene sequencing. Isolates retrieved from antibiotic supplemented agar were subjected to antibiotic susceptibility testing. The highest bacterial diversity, as measured by the Shannon index, was observed in the ICU and GM wards, posing significant risks to patients in these areas. While bacterial genera were largely similar across wards and sampling times, with Pseudomonas and Stenotrophomonas being the most prevalent, different species were detected in each sampling, indicating no loss of diversity. This suggests that these environments undergo dynamic changes over time, influenced by their surroundings. The results also indicate a relationship between human activity and drain usage and the presence of Pseudomonas aeruginosa, the most commonly found species across most wards. Antibiotic susceptibility testing revealed that all tested isolates, except for one, were multi-resistant, including clinically relevant species, such as P. aeruginosa and K. pneumoniae. Hospital drains may serve as reservoirs for both known and emerging pathogens exhibiting high antibiotic resistance phenotypes. Their dynamic nature may provide insights into strategies for preventing the colonization of these environments by such species.}, } @article {pmid40025421, year = {2025}, author = {Sun, J and Ru, J and Cribbs, AP and Xiong, D}, title = {PyPropel: a Python-based tool for efficiently processing and characterising protein data.}, journal = {BMC bioinformatics}, volume = {26}, number = {1}, pages = {70}, pmid = {40025421}, issn = {1471-2105}, support = {MR/V010182/1//UKRI Medical Research Council (MRC) career development fellowship/ ; MR/V010182/1//UKRI Medical Research Council (MRC) career development fellowship/ ; }, mesh = {*Software ; *Proteins/chemistry/metabolism ; *Computational Biology/methods ; Databases, Protein ; Machine Learning ; Sequence Analysis, Protein/methods ; }, abstract = {BACKGROUND: The volume of protein sequence data has grown exponentially in recent years, driven by advancements in metagenomics. Despite this, a substantial proportion of these sequences remain poorly annotated, underscoring the need for robust bioinformatics tools to facilitate efficient characterisation and annotation for functional studies.

RESULTS: We present PyPropel, a Python-based computational tool developed to streamline the large-scale analysis of protein data, with a particular focus on applications in machine learning. PyPropel integrates sequence and structural data pre-processing, feature generation, and post-processing for model performance evaluation and visualisation, offering a comprehensive solution for handling complex protein datasets.

CONCLUSION: PyPropel provides added value over existing tools by offering a unified workflow that encompasses the full spectrum of protein research, from raw data pre-processing to functional annotation and model performance analysis, thereby supporting efficient protein function studies.}, } @article {pmid40025420, year = {2025}, author = {Zhao, J and Zhang, W and Luo, J and Fang, H and Wang, K}, title = {Clinical application of acute Q fever -induced systemic capillary leak syndrome in a patient by using metagenomic next-generation sequencing: a case report and literature review.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {300}, pmid = {40025420}, issn = {1471-2334}, support = {No. 2023KY1296//Medical and Health Research Program of Zhejiang Province/ ; }, mesh = {Humans ; Male ; Middle Aged ; *Q Fever/diagnosis/complications/microbiology/drug therapy ; *High-Throughput Nucleotide Sequencing ; *Capillary Leak Syndrome/diagnosis ; *Metagenomics ; Anti-Bacterial Agents/therapeutic use ; Coxiella burnetii/genetics/isolation & purification ; }, abstract = {INTRODUCTION: Query fever (Q fever), a zoonotic disease, caused by Coxiella burnetii, is an infectious disease that has long been considered a rare and regionally restricted disease. It can be responsible for endocarditis and endovascular infections. Systemic capillary leak syndrome (SCLS), a rare disease of unknown etiology that most commonly develops in adults 50-70 years of age, is diagnosed clinically based on a characteristic symptomatic triad of hypotension, hemoconcentration (elevated hemoglobin or hematocrit), and serum hypoalbuminemia resulting from fluid extravasation. Although Q fever has increasingly been recognized and reported in recent years, the treatment of Q fever complicated by SCLS, with an etiological diagnosis aided by metagenomic next-generation sequencing (mNGS), remains uncommon.

CASE PRESENTATION: This report describes a case of acute Q fever with concurrent SCLS in a 54-year-old male who worked in a slaughterhouse. The patient presented with fever, chest tightness, and shortness of breath, accompanied by severe headache. His condition rapidly deteriorated, leading to acute fever, generalized weakness, and hypotension. Due to respiratory failure and shock, he was admitted to the intensive care unit (ICU) for treatment. Despite empirical antibiotic therapy along with fluid resuscitation, his blood pressure continued to decline, and metabolic acidosis and respiratory distress worsened. As his condition failed to improve, tracheal intubation was performed. mNGS detected both Coxiella burnetii in his BALF and blood samples. Based on the mNGS results, he was started on doxycycline, alongside penicillin antibiotics, vasopressors, and continuous renal replacement therapy (CRRT). The patient's condition gradually improved, and he was discharged home after 12 days of treatment. At his 90-day follow-up, he had nearly fully recovered to his pre-illness status.

CONCLUSIONS: mNGS plays a crucial role in assisting the diagnosis of Q fever, which enables the timely treatment of the underlying disease triggering SCLS. This, combined with restrictive fluid resuscitation strategies, is essential for improving patient outcomes.}, } @article {pmid40023822, year = {2025}, author = {Gooskens, J and van Essen, EHR and Kraakman, MEM and Wörz, P and Heddema, ER and Boers, SA}, title = {Community-Acquired Pneumonia Caused by Avian Chlamydia abortus, the Netherlands.}, journal = {Emerging infectious diseases}, volume = {31}, number = {3}, pages = {630-633}, doi = {10.3201/eid3103.241406}, pmid = {40023822}, issn = {1080-6059}, mesh = {Netherlands/epidemiology ; Humans ; Animals ; *Chlamydia/isolation & purification ; *Community-Acquired Infections/microbiology/epidemiology ; *Chlamydia Infections/veterinary/microbiology/epidemiology ; *Birds/microbiology ; Aged ; Male ; Bird Diseases/microbiology/epidemiology ; Pneumonia, Bacterial/veterinary/microbiology/epidemiology ; Chlamydial Pneumonia/microbiology/epidemiology ; }, abstract = {We report avian Chlamydia abortus pneumonia in an immunocompetent elderly patient in the Netherlands after environmental exposure to wild aquatic birds, including seabirds. New molecular surveillance studies are needed in wild and captive birds, as well as increased awareness to establish occurrence, clinical manifestations, and geographic distribution of this rare zoonotic disease.}, } @article {pmid40023383, year = {2025}, author = {Zhang, Y and Zhang, H and Zhang, B}, title = {Biological and terrestrial influences on dissolved organic matter in Antarctic surface waters: insights from mass spectrometry and metagenomic analysis.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121252}, doi = {10.1016/j.envres.2025.121252}, pmid = {40023383}, issn = {1096-0953}, abstract = {Global warming increases the surface waters and biodiversity in polar regions. However, the intrinsic biological sources of dissolved organic matter (DOM) in Antarctic surface waters remain poorly understood. This work evaluated the sources and driving mechanisms of DOM in Antarctic lakes systematically, based on fluorescence excitation-emission matrices, ultrahigh-resolution mass spectra, biological detection, and metagenomic analyses. The most abundant DOM in the water was peptides (37.02%), which differed from those in soil (lignins: 26.33%) and penguin guano (lipids: 50.71%). The relative abundance of CHON and CHOP compounds in water was significantly correlated with the distance from the penguin colony (p < 0.05). Both the fluorescence and mass spectrum fingerprints of water and soil/faeces showed low similarities using end-member source tracking methods. This could be attributed to the facilitation of guano-derived nutrients and organic carbon to phytoplankton proliferation, whereas the concentrations of NH4[+]-N, NO3[-]-N, total phosphorus, and total organic carbon were significantly higher in the penguin-intensive area than in the other areas. Algae had significant positive effects on carbohydrates and amino sugars and positive effects on lignins, compared to zooplankton and bacteria. Zooplankton had significantly more positive effects on peptides than phytoplankton. Secondary bacterial metabolic activity can be positively linked with CHO compounds. Carbohydrates and amino sugars co-occurred with carbohydrate-active enzyme genes and nitrogen cycling genes in one module of the co-occurrence network, whereas the other module was characterised by the co-occurrence patterns of condensed aromatic structures with carbohydrate-active enzyme genes and nitrogen cycling genes. These results emphasise the roles of secondary metabolites from algae and bacteria in species-specific sources of DOM, shedding light on the driving mechanisms of the biogeochemical cycling of DOM in the Antarctic water environment.}, } @article {pmid40023333, year = {2025}, author = {Liu, H and Zhou, Z and Long, C and Qing, T and Feng, B and Zhang, P and Chen, YP}, title = {Light/dark synergy enhances cyanophycin accumulation in algal-bacterial consortia: Boosted strategy for nitrogen recovery from wastewater.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132309}, doi = {10.1016/j.biortech.2025.132309}, pmid = {40023333}, issn = {1873-2976}, abstract = {Recovering the nitrogen-rich biopolymer cyanophycin [(β-Asp-Arg)n] from algal-bacterial consortia enhances the reclamation of value-added chemicals from wastewater. However, the modulation of light/dark conditions on cyanophycin accumulation remain unknown. In this study, the trends and mechanisms of cyanophycin synthesis in algal-bacterial consortia under light/dark conditions were investigated. The results showed that cyanophycin production during the dark periods ranged from 137-150 mg/g MLSS (mixed liquid suspended solids), which was 32 %-38 % higher than those during the light period (p < 0.001). Metatranscriptomics results demonstrated that 50 metagenome-assembled genomes contribute to cyanophycin production, with the Planktothrix genus being the dominant contributor. Metabolomics findings suggested that algal-bacterial consortia produce higher level of arginine for cyanophycin synthesis under light conditions. This study demonstrates the feasibility of increasing cyanophycin production by merging light/dark cycles, and offers a novel strategy for high yield of valuable biopolymers from wastewater substrate.}, } @article {pmid40023316, year = {2025}, author = {Olearo, F and Zein, SE and Eugenia, PM and Zapf, A and Rohde, H and Berbari, EF and Wouthuyzen-Bakker, M and , }, title = {Diagnostic accuracy of 16S rDNA PCR, Multiplex PCR and Metagenomic Next-Generation Sequencing in Periprosthetic Joint Infections: A Systematic Review and Meta-Analysis.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmi.2025.02.022}, pmid = {40023316}, issn = {1469-0691}, abstract = {BACKGROUND: The diagnostic accuracy of 16S rDNA PCR, multiplex PCR (mPCR), and metagenomic next-generation sequencing (mNGS) in periprosthetic joint infections (PJIs) remains unclear.

OBJECTIVES: To evaluate the diagnostic accuracy of 16S rDNA PCR, mPCR, and mNGS in PJI.

DATA SOURCES: PubMed and EMBASE (January 1, 2000-March 1, 2024), with no language restrictions.

STUDY ELIGIBILITY CRITERIA: Studies containing sufficient data to construct a 2×2 contingency table allowing for sensitivity and specificity calculation were considered.

PARTICIPANTS: Adults (≥18 years) with PJI and appropriate control groups.

TESTS: 16S rDNA PCR, mPCR, and mNGS.

REFERENCE STANDARD: Diagnosis required adherence to Musculoskeletal Infection Society, Infectious Diseases Society of America (IDSA), International Consensus Meeting, European Bone and Joint Infection Society criteria. Studies employing alternative author-defined criteria were included only if they did not rely solely on positive cultures to define PJI.

ASSESSMENT OF RISK OF BIAS: QUADAS-2 was used.

METHODS OF DATA SYNTHESIS: A bivariate model calculated pooled diagnostic odds ratios (DORs), sensitivities, and specificities, each with 95% confidence intervals (CIs).

RESULTS: Seventy-nine studies were included, comprising 3,940 PJI cases and 4,700 uninfected controls. Pooled sensitivity/specificity were 80.0% (95% CI: 75.4-84.3%)/94.0% (95% CI: 91-96%) for 16S rDNA PCR; 62.2% (52.5-70.9%)/96.2% (93.2-97.9%) for mPCR; and 88.6% (83.3-92.4%)/93.2% (89.5-95.6%) for mNGS. Notably, mNGS had the highest DOR (105.9; 95% CI: 60-186.9). A sensitivity analysis excluding lower-quality studies resulted in increased DORs for all methods.

DISCUSSION: These molecular techniques display strong diagnostic accuracy for identifying PJI. Although mNGS yielded the highest DOR, numerous technical and practical challenges preclude its routine use for PJI diagnosis. Significant heterogeneity across studies warrants cautious interpretation and underscores the need for future comparative research.}, } @article {pmid40022926, year = {2025}, author = {Xu, Y and Wang, J and Chi, Q and Zheng, P and Lv, H and Mu, Y and Shen, J}, title = {Mechanistic insights into substituent-induced hydrolytic debromination and electron flow of bromophenols under nitrate-reducing conditions.}, journal = {Journal of hazardous materials}, volume = {490}, number = {}, pages = {137767}, doi = {10.1016/j.jhazmat.2025.137767}, pmid = {40022926}, issn = {1873-3336}, abstract = {Exogenous electron acceptors, such as nitrate, hold great potential for the bioremediation of wastewater contaminated with bromophenols (BPs). However, research into the mechanisms underlying BPs biodegradation remains in its early stages, particularly regarding the molecular structure and bioremediation performance. This study provides a comprehensive analysis of the mechanisms involved in BPs within a nitrate-reducing system, focusing on the molecular structure of BPs. Therefore, three up-flow bioreactors were operated for 187 days, achieving removal efficiencies of 100 %, 90.4 ± 0.6 % and 50.2 ± 2.8 % for ortho-bromophenol (2-BP), para-bromophenol (4-BP) and meta-bromophenol (3-BP), respectively. Hydrolytic dehalogenase (LinB) was found to play a critical role in BP metabolism. Molecular docking and density functional theory calculations revealed that the geometric structure and electronic effects of the Br-substituent significantly influenced LinB activity and BP reactivity, thereby affecting removal efficiencies. Notably, 2-BP, with a shorter orientation distance, was more readily catalyzed by LinB, as evidenced by metagenomic analyses showing significant increases in the abundance of N-transforming and BP-degrading genes. Furthermore, 2-BP and 4-BP stimulated more robust microbial responses, including dehalogenation (Thauera), denitrification (Delftia), and electron transport (Xanthomonadales). These results provide valuable insights into the environmental fate of BPs at the molecular level and how the Br-substituent influences microbial metabolism.}, } @article {pmid38392845, year = {2024}, author = {Lamichhane, B and Brockway, C and Evasco, K and Nicholson, J and Neville, PJ and Levy, A and Smith, D and Imrie, A}, title = {Metatranscriptomic Sequencing of Medically Important Mosquitoes Reveals Extensive Diversity of RNA Viruses and Other Microbial Communities in Western Australia.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {2}, pages = {}, pmid = {38392845}, issn = {2076-0817}, mesh = {Animals ; Western Australia ; *RNA Viruses/genetics/isolation & purification ; Microbiota/genetics ; Virome/genetics ; Mosquito Vectors/microbiology/virology ; Culicidae/virology/microbiology ; Aedes/microbiology/virology ; Biodiversity ; Culex/virology/microbiology ; Transcriptome ; Metagenomics/methods ; Phylogeny ; }, abstract = {Mosquitoes harbor a wide diversity of microorganisms, including viruses that are human pathogens, or that are insect specific. We used metatranscriptomics, an unbiased high-throughput molecular approach, to describe the composition of viral and other microbial communities in six medically important mosquito species from across Western Australia: Aedes vigilax, Culex annulirostris, Cx. australicus, Cx. globocoxitus, Cx. pipiens biotype molestus, and Cx. quinquefasciatus. We identified 42 viral species, including 13 novel viruses, from 19 families. Culex mosquitoes exhibited a significantly higher diversity of viruses than Aedes mosquitoes, and no virus was shared between the two genera. Comparison of mosquito populations revealed a heterogenous distribution of viruses between geographical regions and between closely related species, suggesting that geography and host species may play a role in shaping virome composition. We also detected bacterial and parasitic microorganisms, among which Wolbachia bacteria were detected in three members of the Cx. pipiens complex, Cx. australicus, Cx. pipiens biotype molestus, and Cx. quinquefasciatus. In summary, our unbiased metatranscriptomics approach provides important insights into viral and other microbial diversity in Western Australian mosquitoes that vector medically important viruses.}, } @article {pmid40025414, year = {2025}, author = {Izhar, MZ and Nawaz, M and Yaqub, T and Avais, M}, title = {Effect of probiotic Lactobacillus plantarum CM49 on microbial profile and lactobacilli counts in milk of mastitic cattle.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {109}, pmid = {40025414}, issn = {1471-2180}, support = {PHEC/ARA/PIRCA/20211/9//Punjab Higher Education Commission, Pakistan/ ; }, abstract = {BACKGROUND: Bovine mastitis is a common udder disease in cattle, mainly caused by bacteria and other infectious agents. Traditionally antibiotics are used for their treatment, but the development of antibiotic resistance has increased the importance of using non antibiotic alternative such as probiotic. In current study a previously in vitro characterized isolate Lactobacillus plantarum CM49 infused into two groups of cattle suffering from clinical mastitis (n = 5) and sub-clinical mastitis (n = 5).

RESULTS: The bacterial composition and diversity analysis of milk samples before and after probiotic administration was analyzed using 16S rRNA gene base metagenomic analysis and lactobacillus counts were also evaluated using Real time PCR. The results show that there was an increase in abundance of Proteobacteria and decrease in Firmicutes at phylum level in both groups while major mastitogens genera Staphylococcus and Streptococcus abundance was reduced after treatment in sub-clinical mastitis group (SCMG) and clinical mastitis group (CMG) respectively. Lactobacilli counts evaluated through Real time PCR showed an increase in number, furthermore diversity indices showed an increase in diversity after treatment with probiotic.

CONCLUSION: It is concluded from the results that Lactobacillus plantarum CM49 may serve as promising candidate for improving dysbiosis resulting from mastitis and improving microbial diversity.}, } @article {pmid40025399, year = {2025}, author = {Liu, A and Wu, J and Li, J and Li, Q and Zhao, N and Hu, K and Liu, S and Blaiotta, G and Zhou, J}, title = {Uncovering the microbial community dynamics and metabolic pathways of primary organic acids in Sichuan Baoning vinegar through metagenomics.}, journal = {World journal of microbiology & biotechnology}, volume = {41}, number = {3}, pages = {91}, pmid = {40025399}, issn = {1573-0972}, support = {No. 2024NSFSC2079//Science and Technology Department of Sichuan Province/ ; }, abstract = {Sichuan Baoning vinegar, a renowned traditional vinegar in China, exhibits a higher lactic acid content compared to acetic acid. The microbiota plays a crucial role in shaping the unique flavor of vinegar, but the species-level succession of key microorganisms and metabolic pathways of major organic acids in this vinegar are still unclear. This study utilized metagenomic sequencing to elucidate microbial succession during fermentation and the functional roles of the microbial community, as well as explore the metabolic network of lactic acid and acetic acid. Our findings revealed that bacteria dominated the fermentation process, with Acetilactobacillus jinshanensis, Lactobacillus amylovorus, and Limosilactobacillus sp. emerging as the top three species. Notably, Acetilactobacillus jinshanensis, Limosilactobacillus sp., Lactobacillus amylovorus, and Limosilactobacillus pontis were key players in lactic acid production, while acetic acid synthesis might be primarily driven by Lactobacillus amylovorus, Limosilactobacillus sp., Lactobacillus acetotolerans, and Acetobacter pasteurianus. This study enhances our understanding of the key microorganisms and organic acids metabolism in vinegar, shedding light on the fermentation mechanism of cereal vinegar.}, } @article {pmid40025082, year = {2025}, author = {Regmi, R and Anderson, J and Burgess, L and Mangelson, H and Liachko, I and Vadakattu, G}, title = {Shotgun and Hi-C Sequencing Datasets for Binning Wheat Rhizosphere Microbiome.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {367}, pmid = {40025082}, issn = {2052-4463}, mesh = {*Triticum/microbiology ; *Rhizosphere ; *Microbiota ; *Soil Microbiology ; Metagenome ; Metagenomics ; Bacteria/genetics/classification ; High-Throughput Nucleotide Sequencing ; Archaea/genetics ; South Australia ; }, abstract = {Binning is a crucial process in metagenomics studies, where sequenced reads are combined to form longer contigs and assigned to individual genomes. Conventional methods, such as shotgun binning, rely on similarity measurements and abundance profiles across multiple samples. However, cost constraints for sequencing and limited sample collection capacity hinder their effectiveness. High-throughput chromosome conformation capture (Hi-C), a DNA proximity ligation technique, has been adapted to accurately bin metagenome-assembled genomes (MAGs) from a single sample, addressing challenges like chimeric MAGs. In this study, we generated over 190 Gb of metagenomic data from wheat rhizospheres grown in two highly calcareous soils of South Australian region and compared conventional and Hi-C binning methods. Two shotgun metagenomes and Hi-C libraries were generated, assembling 1089 shotgun MAGs across 39 bacterial and one archaeal taxon, including 94 Hi-C based bins. Binning performed using only short read sequences was prone to high contamination, while the addition of Hi-C binning improved MAG quality and identified mobile element-host-infection interaction. This dataset provides important tools for studying microbial communities in wheat rhizosphere soils.}, } @article {pmid40024121, year = {2025}, author = {Woo, SY and Park, SB and Lee, SY and Sul, WJ and Chun, HS}, title = {Mycotoxin and microbiome profiling for aflatoxin control in the Korean traditional fermented soybean paste Doenjang.}, journal = {Journal of hazardous materials}, volume = {490}, number = {}, pages = {137777}, doi = {10.1016/j.jhazmat.2025.137777}, pmid = {40024121}, issn = {1873-3336}, abstract = {Mycotoxin contamination is an important concern in producing traditional fermented soybean paste, though no effective control strategy has been developed. This study investigated the mycotoxin profiles of the intermediate (fermented soybean brick, known as "Meju" in South Korea) and final soybean paste products ("Doenjang") to identify major contaminants and describe microbial diversity with the mycotoxins. Profiling of 323 Meju and Doenjang samples revealed severe aflatoxin (AF) contamination. Metagenomic analysis revealed that the species richness and phylogenetic diversity were significantly higher in AF-free than in AF-contaminated Meju and Doenjang. Certain Aspergillus and Penicillium species were more abundant in AF-free than in AF-contaminated Meju and Doenjang. To control AF levels, we developed a novel mycotoxin-reduction approach that preserves the indigenous microbiome by backslopping fermentation of Meju in both Aspergillus-dominant and Penicillium-dominant modes. Both treatments reduced AF levels by > 95 % at a backslopping rate of > 2.5 %. Our results suggested that backslopping fermentation can effectively reduce AF contamination in traditional soybean fermentation, maintaining food safety standards and artisanal practices.}, } @article {pmid40023235, year = {2025}, author = {Fang, J and Yin, B and Wang, X and Pan, K and Wang, WX}, title = {Clamworm bioturbation reduces mercury methylation through alteration of methylator composition in sediment.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {371}, number = {}, pages = {125947}, doi = {10.1016/j.envpol.2025.125947}, pmid = {40023235}, issn = {1873-6424}, abstract = {Coastal sediment has been recognized as a hotspot of mercury (Hg) methylation and acts as an important reservoir for Hg-methylating microbes. The bioturbation behaviors of benthic organisms can significantly influence sediment properties and potentially affect the mobility and availability of contaminants within the sediment. However, the effects of bioturbation on Hg speciation and disposition in sediment have not been well addressed. This study investigated the influence of clamworm activities on the Hg-methylation process and the composition of methylators in sediment. The results showed that the presence of clamworms greatly suppressed the growth of Hg-methylators and led to a significant decrease in the production rate of methylmercury (MeHg) (from 0.61 to 0.36 ng g[-1] dw d[-1]). Metagenomic results indicate that bioturbation significantly decreased the abundance and diversity of putative Hg methylators and altered the dominant contributors to Hg methylation process. Furthermore, clamworm activities influenced the metabolic traits of Hg methylators and shifted the community toward greater oxygen tolerance. Overall, bioturbation by clamworms suppressed the Hg methylation process and increased the abundance of eco-friendly microbiome, which ultimately contributed to making the sedimentary ecosystem more diverse and resilient. These findings highlight the vital role of bioturbation in mitigating MeHg contamination in sediment and provide a deeper understanding of Hg-methylating microbes and the Hg cycling processes in coastal environments.}, } @article {pmid40022370, year = {2025}, author = {Li, X and You, Y and Xue, B and Chen, J and Du, M and Ibrahim, A and Suo, H and Zhang, F and Zheng, J}, title = {Decoding microbiota and metabolite transformation in inoculated fermented suansun using metagenomics, GC-MS, non-targeted metabolomics, and metatranscriptomics:Impacts of different Lactobacillus plantarum strains.}, journal = {Food research international (Ottawa, Ont.)}, volume = {203}, number = {}, pages = {115847}, doi = {10.1016/j.foodres.2025.115847}, pmid = {40022370}, issn = {1873-7145}, mesh = {*Lactobacillus plantarum/metabolism/genetics ; *Metabolomics/methods ; *Fermentation ; *Gas Chromatography-Mass Spectrometry ; *Metagenomics/methods ; *Microbiota/physiology/genetics ; Flavoring Agents/metabolism ; Transcriptome ; Gene Expression Profiling ; Fermented Foods/microbiology ; Food Microbiology ; }, abstract = {Using metagenomics, GC-MS, non-targeted metabolomics, and metatranscriptomics, we investigated the microbial communities and metabolites in two different Lactobacillus plantarum fermentations. Metagenomics revealed Weissella cibaria dominantly contributed to the DACN766-fermented suansun (LPS1) and Lactiplantibacillus pentosus to the DACN760-fermented suansun (LPS2). GC-MS identified 38 and 40 flavor compounds in LPS1 and LPS2, respectively, with p-cresol, 4-hydroxybenzaldehyde, acetic acid, hexanal, and propionic acid crucial for aroma development. LPS2 exhibited higher levels of p-cresol and acetic acid, contributing to its stronger sour and pungent flavors, which was achieved by regulating many metabolisms like glycolysis and tyrosine metabolism. In contrast, Weissella cibaria plays a role in mitigating off-flavors, resulting in a milder flavor profile in LPS1. Non-targeted metabolomics indicated 70.78% of differential metabolites were upregulated in LPS1. Conversely, the elevated expression of tryptophan and tyrosine underscores the more pronounced sour and odor-producing characteristics observed in LPS2. Metatranscriptomics highlighted the regulation of genes like XFA, XFT, and XFM, which inhibit the formation of the precursors of p-cresol and indole in LPS2. This integrated multi-omics analysis provides deep insights into the fermentation dynamics, facilitating the targeted selection of Lactobacillus plantarum strains with flavor-regulating capabilities.}, } @article {pmid40022356, year = {2025}, author = {Li, Y and Wu, Y and Chen, S and Zhao, Y and Li, C and Xiang, H and Wang, D and Wang, Y}, title = {Decoding the aroma landscape of fermented golden pompano: The interplay of ester compounds and symbiotic microbiota as revealed by metagenomics and two-dimensional flavoromics.}, journal = {Food research international (Ottawa, Ont.)}, volume = {203}, number = {}, pages = {115832}, doi = {10.1016/j.foodres.2025.115832}, pmid = {40022356}, issn = {1873-7145}, mesh = {*Metagenomics/methods ; *Fermentation ; *Volatile Organic Compounds/analysis/metabolism ; *Esters/metabolism/analysis ; *Microbiota ; Odorants/analysis ; Taste ; Seafood/microbiology ; Flavoring Agents/metabolism ; Animals ; Fermented Foods/microbiology ; Symbiosis ; }, abstract = {Fermented pompano (Trachinotus ovatus) is a traditionally popular fermented seafood throughout Asia. Its distinctive flavor profile is primarily attributed to the microbial metabolic conversion of nutrients, which produces specific volatile compounds. Two-dimensional flavoromics of mature pompano revealed that various volatile flavor compounds accumulate throughout fermentation, with fruity (predominantly esters) and oleogustus (primarily ketones) being key flavor markers. S-curve analysis further demonstrated synergistic and additive interactions between these compounds, which enhance flavor release. Metagenomics and Kyoto Encyclopedia of Genes and Genome analysis revealed that amino acid metabolism was the pivotal pathway for ethyl ester synthesis, with Staphylococcus equorum being positively correlated with esters such as ethyl isobutyrate and ethyl enanthate. This study elucidated the interrelationship between flavor compounds and the microbial community in fermented pompano, which is expected to provide insights into flavor modulation and guide the selection of strains that produce key esters in fermented seafood products.}, } @article {pmid40022320, year = {2025}, author = {Cámara-Martos, F and Bolívar, A and Rabasco-Vílchez, L and Lafont-Déniz, F and Luque-Ojeda, JL and Pérez-Rodríguez, F}, title = {Exploring the bioaccessibility, in vitro colonic fermentation, and the impact on the intestinal microbiota of allyl-and benzyl-isothiocyanate from white and Ethiopian mustard.}, journal = {Food research international (Ottawa, Ont.)}, volume = {203}, number = {}, pages = {115781}, doi = {10.1016/j.foodres.2025.115781}, pmid = {40022320}, issn = {1873-7145}, mesh = {*Gastrointestinal Microbiome ; *Mustard Plant/microbiology/chemistry ; *Colon/microbiology/metabolism ; *Fermentation ; *Isothiocyanates/metabolism ; Humans ; Biological Availability ; Digestion ; Glucosinolates/metabolism/analysis ; Gas Chromatography-Mass Spectrometry ; }, abstract = {The aim of this research was to study the formation and bioaccessibility of allyl- and benzyl-isothiocyanate (ITC) resulting from the gastrointestinal digestion (small and large intestine) of green parts from Ethiopian and white mustard. In addition, a GC-MS methodology was validated to determine these compounds in bioaccessible and non-bioaccessible fraction. Plant clumps were divided into two batches: fresh and freeze-dried samples. ITC bioaccessibility was low in the small intestine, with values ranged between 11 and 53 % and mean values of 26 %. These results are in agreement with the fact that ITCs are poorly water-soluble compounds. Bioaccessibility values for lyophilised samples were lower than those obtained in fresh samples. This could be due to the degradation of the precursor glucosinolates (sinigrin and glucotropaeolin respectively). The simulation of the colonic fermentation reduced allyl - and benzyl - ITC levels from the non-bioaccessible fraction of Ethiopian and white mustard (values between 0.009 and 0.087 mg/g). In both cases, ITCs concentration dropped dramatically, i.e. with a ten-fold reduction. Nevertheless, this result does not necessarily indicate that ITCs have not been produced in the large intestine. Bacterial microbiota plays a key role in generating ITCs; however, ITCs are not always the final products of this process. The metagenomic analysis of colonic samples revealed that ITCs and cruciferous matrix significantly influenced the composition of gut microbiota, inhibiting potentially pathogenic bacteria such as Enterobacter and Klebsiella, while promoting beneficial bacteria such as Bifidobacterium, Faecalibacterium, Blautia, and Ruminococcus. Interestingly, ITCs-rich environments selected bacterial species (i.e. Enterobacter ludwigii) and promoted metabolic pathways involved in glucosinolate/ITCs metabolism.}, } @article {pmid40022097, year = {2025}, author = {Ferneyhough, B and Roddis, M and Millington, S and Quirk, J and Clements, C and West, S and Schilizzi, R and Fischer, MD and Parkinson, NJ}, title = {A highly accurate nanopore-based sequencing workflow for culture and PCR-free microbial metagenomic profiling of urogenital samples.}, journal = {BMC urology}, volume = {25}, number = {1}, pages = {41}, pmid = {40022097}, issn = {1471-2490}, mesh = {Humans ; Female ; Male ; *Metagenomics/methods ; *Microbiota/genetics ; Nanopore Sequencing/methods ; Vagina/microbiology ; Workflow ; Urogenital System/microbiology ; }, abstract = {BACKGROUND: The application of molecular sequencing methods for microbiome profiling of biological samples are largely restricted to research use. However, they require significant resources such as time and cost and can suffer from amplification biases that may hamper interpretation of complex systems. These issues are also a barrier to adoption as standard clinical tools in, for example, diagnosis of urogenital infections. We report a new method that utilises third generation long-read nanopore sequencing to produce fast, accurate and fully quantitated metagenomic microbiome profiles. Here, as proof of principle, we apply this methodology to reassess the healthy urogenital microbiomes of asymptomatic female and male samples.

RESULTS: We show that our method is capable of accurately and reproducibly detecting both levels and composition of a synthetic mixture of ten species comprising known amounts of hard to lyse gram-positive bacteria, gram-negative bacteria and yeast. When applied to urogenital samples, we confirm previous observations that the female asymptomatic vaginal and urinary microbiomes are predominated by Gardnerella spp. or one of several Lactobacillus species (L. crispatus, L. gasseri, L. iners or L. jensenii) that conform to previously defined community state types. We show the tight relationship between vaginal and urinary populations of the same individual at both species and strain level, provide evidence for the previously observed dynamic nature of these microbiomes over a menstrual cycle and compare biomass and complexity of male and female urobiomes.

CONCLUSIONS: We set out to develop an unbiased, amplification and culture-free, fully quantitative metagenomic microbiome profiling tool. Our initial observations suggest our method represents a viable alternative to existing molecular research tools employed in the analysis of complex microbiomes.}, } @article {pmid40020351, year = {2025}, author = {Manna, B and Zhou, X and Singhal, N}, title = {ROS-induced stress promotes enrichment and emergence of antibiotic resistance in conventional activated sludge processes.}, journal = {Water research}, volume = {277}, number = {}, pages = {123366}, doi = {10.1016/j.watres.2025.123366}, pmid = {40020351}, issn = {1879-2448}, abstract = {Since the Great Oxidation Event 2.4 billion years ago, microorganisms have evolved sophisticated responses to oxidative stress. These ancient adaptations remain relevant in modern engineered systems, particularly in conventional activated sludge (CAS) processes, which serve as significant reservoirs of antibiotic resistance genes (ARGs). While ROS-induced stress responses are known to promote ARG enrichment/emergence in pure cultures, their impact on ARG dynamics in wastewater treatment processes remains unexplored. Shotgun-metagenomics analysis of two hospital wastewater treatment plants showed that only 35-53 % of hospital effluent resistome was retained in final effluent. Despite this reduction, approximately 29-36 % of ARGs in CAS showed higher abundance than upstream stages, of which 20-22 % emerged de novo. Beta-lactamases and efflux pumps constituted nearly 47-53 % of these enriched ARGs. These ARGs exhibited significant correlations (p < 0.05) with ROS stress response genes (oxyR, soxR, sodAB, katG and ahpCF). The CAS resistome determined 58-75 % of the effluent ARG profiles, indicating treatment processes outweigh influent composition in shaping final resistome. Proof-of-concept batch reactor experiments confirmed increased ROS and ARG levels under high dissolved oxygen (8 mg/L) compared to low oxygen (2 mg/L) concentrations. Untargeted metaproteomics revealed higher expression of resistant proteins (e.g., OXA-184, OXA-576, PME-1, RpoB2, Tet(W/32/O)) under elevated ROS levels. Our findings demonstrate that CAS processes actively shape effluent resistome through ROS-mediated selection, indicating that treatment processes, rather than initial wastewater composition, determine final ARG profiles. This study indicates that the emergence of ARGs needs to be considered as an integral aspect of wastewater treatment design and operation to prevent antibiotic resistance dissemination.}, } @article {pmid40020294, year = {2025}, author = {Zhao, Y and Li, L and Tan, J and Zhao, H and Wang, Y and Zhang, A and Jiang, L}, title = {Metagenomic insights into the inhibitory effect of phytochemical supplementation on antibiotic resistance genes and virulence factors in the rumen of transition dairy cows.}, journal = {Journal of hazardous materials}, volume = {490}, number = {}, pages = {137717}, doi = {10.1016/j.jhazmat.2025.137717}, pmid = {40020294}, issn = {1873-3336}, abstract = {Antimicrobial resistance (AMR) is a major global health concern, with the rumen microbiota of dairy cows serving as an important reservoir for antibiotic resistance genes (ARGs) and virulence factors (VFs). This study explores the impact of dietary phytochemical supplementation on the rumen resistome and virulome of transition dairy cows using metagenomic sequencing. Naringin supplementation reduced the abundance of ARGs by up to 9.0 % and VFs by up to 7.2 % during the transition period, as indicated by metagenomic analysis (P < 0.05). Clinically high-risk ARGs, including those conferring resistance to beta-lactams (mecA), tetracyclines (tetM, tetO), and aminoglycosides (rmtF), were notably downregulated (P < 0.05). Virulence factors associated with adherence, secretion systems, and toxins were also significantly decreased (P < 0.05). Naringin altered the microbial community structure, particularly reducing the abundance of Proteobacteria, a key phylum harboring ARGs and VFs. Despite inducing increased ARG-VF network complexity, naringin supplementation promoted a less pathogenic microbiome with reduced resistance potential. These findings demonstrate the potential of naringin as a natural dietary strategy to mitigate AMR by reducing the risk of ARG and VF dissemination into the environment, while supporting rumen microbiota stability in transition dairy cows.}, } @article {pmid40022204, year = {2025}, author = {Debray, R and Dickson, CC and Webb, SE and Archie, EA and Tung, J}, title = {Shared environments complicate the use of strain-resolved metagenomics to infer microbiome transmission.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {59}, pmid = {40022204}, issn = {2049-2618}, support = {R01AG071684/NH/NIH HHS/United States ; R01AG071684/NH/NIH HHS/United States ; R61AG078470//National Science Foundation/ ; R61AG078470//National Science Foundation/ ; }, mesh = {Animals ; *Metagenomics/methods ; *Gastrointestinal Microbiome ; *Fecal Microbiota Transplantation ; Humans ; Papio/microbiology ; Feces/microbiology ; Bacteria/classification/genetics/isolation & purification ; Metagenome ; }, abstract = {BACKGROUND: In humans and other social animals, social partners have more similar microbiomes than expected by chance, suggesting that social contact transfers microorganisms. Yet, social microbiome transmission can be difficult to identify based on compositional data alone. To overcome this challenge, recent studies have used information about microbial strain sharing (i.e., the shared presence of highly similar microbial sequences) to infer transmission. However, the degree to which strain sharing is influenced by shared traits and environments among social partners, rather than transmission per se, is not well understood.

RESULTS: Here, we first use a fecal microbiota transplant dataset to show that strain sharing can recapitulate true transmission networks under ideal settings when donor-recipient pairs are unambiguous and recipients are sampled shortly after transmission. In contrast, in gut metagenomes from a wild baboon population, we find that demographic and environmental factors can override signals of strain sharing among social partners.

CONCLUSIONS: We conclude that strain-level analyses provide useful information about microbiome similarity, but other facets of study design, especially longitudinal sampling and careful consideration of host characteristics, are essential for inferring the underlying mechanisms of strain sharing and resolving true social transmission network. Video Abstract.}, } @article {pmid40021978, year = {2025}, author = {Lv, Y and Zhang, L and Wang, X and Zhang, Y}, title = {Genomic evidence on the distribution and ecological function of Pseudomonas in hadal zone.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {100}, pmid = {40021978}, issn = {1471-2180}, support = {42306104//National Natural Science Foundation of China/ ; 42188102//National Natural Science Foundation of China/ ; 2023M742237//China Postdoctoral Science Foundation/ ; 21TQ1400201//Shanghai Pilot Program for Basic Research of Shanghai Jiao Tong University/ ; HRSJ-ZSZX-008//Project of Hainan Research Institute, Shanghai Jiao Tong University/ ; 2023YFC2812800//National Key Research and Development Program of China/ ; }, mesh = {*Pseudomonas/genetics/metabolism/classification ; *Seawater/microbiology ; *Genome, Bacterial/genetics ; *Geologic Sediments/microbiology ; *Phylogeny ; Metagenome ; Genomics ; Carbon/metabolism ; }, abstract = {The hadal zone is the deepest region on Earth. It serves as a depositional zone for the sinking matter from surface ocean and continental margin, aided by its unique V-shaped structure. Due to extreme depth (over 6000 m), normally only organic matter with low degradability typically reaches the bottom of the trench. Concurrently, reports have indicated highly active carbon turnover and dense bacterial cells in the Mariana Trench. There remains a cognitive gap in understanding the connection between this phenomenon and the microbial taxa along with their metabolic activities. Here, we surveyed the Pseudomonas, one of the most widely distributed bacterial genera on Earth. The result revealed widespread distribution of Pseudomonas in the hadal zones. We obtained 21 metagenome-assembled genomes (MAGs) from seawater and sediment samples of the Mariana Trench, including three novel species. Comparative genomic analysis showed that hadal Pseudomonas possess more unique ortholog groups of genes related to energy generation and substances transport, distinct from those in other marine zones. These bacteria exhibit the ability to utilize diverse electron acceptors and accumulate compatible solutes, indicating two key strategies for adaptation for high hydrostatic pressure conditions. Furthermore, predicted genomic capabilities suggest that Pseudomonas could decompose various components of organic matter, particularly aromatics, as supported by metatranscriptomic datasets. These findings significantly enhance our understanding of Pseudomonas diversity and metabolic potential, providing valuable insights into the carbon and nitrogen cycles in hadal trench ecosystems.}, } @article {pmid40021694, year = {2025}, author = {Gambardella, N and Costa, J and Martins, BM and Folhas, D and Ribeiro, AP and Hintelmann, H and Canário, J and Magalhães, C}, title = {The role of prokaryotic mercury methylators and demethylators in Canadian Arctic thermokarst lakes.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {7173}, pmid = {40021694}, issn = {2045-2322}, support = {PTDC/CTA-AMB/4744/2020//Fundação para a Ciência e a Tecnologia/ ; PTDC/CTA-AMB/4744/2020//Fundação para a Ciência e a Tecnologia/ ; PTDC/CTA-AMB/4744/2020//Fundação para a Ciência e a Tecnologia/ ; PTDC/CTA-AMB/4744/2020//Fundação para a Ciência e a Tecnologia/ ; PTDC/CTA-AMB/4744/2020//Fundação para a Ciência e a Tecnologia/ ; PTDC/CTA-AMB/4744/2020//Fundação para a Ciência e a Tecnologia/ ; PTDC/CTA-AMB/4744/2020//Fundação para a Ciência e a Tecnologia/ ; }, mesh = {Arctic Regions ; Canada ; *Lakes/microbiology ; *Mercury/metabolism ; Methylation ; Methylmercury Compounds/metabolism/analysis ; Microbiota ; Geologic Sediments/microbiology ; Bacteria/genetics/metabolism/classification ; Permafrost/microbiology ; Seasons ; Metagenomics/methods ; Water Pollutants, Chemical/metabolism ; Environmental Monitoring/methods ; }, abstract = {Permafrost soils are critical reservoirs for mercury (Hg), with the thawing process leading to the release of this element into the environment, posing significant environmental risks. Of particular concern is the methylated form of mercury, monomethylmercury (MMHg), known for its adverse effects on Human health. Microbial communities play a pivotal role in the formation of MMHg by facilitating Hg methylation and in the demethylation of MMHg, slowing the crossing of toxic threshold concentration in the environment. However, the specific microbes involved still need to be understood. This study aimed to identify the microbial drivers behind changes in Hg speciation (MMHg and Hg) in permafrost thaw lakes and assess the significance of the biotic component in Hg biogeochemistry. Sediment samples from two thermokarst lakes in the Canadian sub-Arctic were collected during the winter and summer of 2022. Gene-centric metagenomics using whole-genome sequencing (WGS) was employed to identify key genes involved in mercury methylation (hgcA and hgcB) and demethylation (merA and merB), supported by qPCR analyses. A seasonal decline in microbial diversity, involved in the Hg methylation, and hgcA gene coverage was observed from winter to summer, mirroring patterns in mercury methylation rates. Notably, hgcA sequences were significantly more abundant than merAB sequences, with contrasting seasonal trends. These results indicate a seasonal shift in the microbial community, transitioning from a dominance of mercury methylation in winter to a predominance of mercury demethylation in summer. Environmental drivers of these dynamics were integrated into a conceptual model. This study provide new insights on the microbial processes influencing the Hg cycle in Arctic permafrost undergoing degradation.}, } @article {pmid40021498, year = {2025}, author = {Urrea, V and Páez-Triana, L and Velásquez-Ortiz, N and Camargo, M and Patiño, LH and Vega, L and Ballesteros, N and Hidalgo-Troya, A and Galeano, LA and Ramírez, JD and Muñoz, M}, title = {Metagenomic Analysis of Surface Waters and Wastewater in the Colombian Andean Highlands: Implications for Health and Disease.}, journal = {Current microbiology}, volume = {82}, number = {4}, pages = {162}, pmid = {40021498}, issn = {1432-0991}, support = {BPIN: 2020000100770//Colombian Fund for Science, Technology, and Innovation of Sistema General de Regalías/ ; }, mesh = {*Wastewater/microbiology/parasitology ; *Metagenomics ; Colombia ; *Cryptosporidium/genetics/isolation & purification/classification ; Giardia/genetics/isolation & purification/classification ; Bacteria/genetics/classification/isolation & purification ; Humans ; Rivers/microbiology/parasitology ; Water Microbiology ; }, abstract = {Urban water bodies serve as critical reservoirs of microbial diversity, with major implications for public health and environmental quality. This study aimed to characterize the microbial diversity of surface waters and wastewater from the Pasto River in the Colombian Andean Highlands, offering insights that may support water quality monitoring efforts. Sampling was conducted at three river sites and one wastewater location. Standard physicochemical and microbiological analyses were performed, including real-time PCR to detect protozoan pathogens Giardia spp. and Cryptosporidium spp. Metagenomic sequencing provided an in-depth taxonomic and functional profile of microbial communities through two complementary approaches: (i) read-based analysis to identify abundant families and species, both pathogenic and beneficial, and (ii) detection of health-related molecular markers, including antimicrobial resistance markers and virulence factors. Physicochemical analyses showed distinct profiles between wastewater and surface water, with wastewater exhibiting elevated levels of suspended solids (113.6 mg/L), biochemical oxygen demand (BOD, 311.2 mg/L), and chemical oxygen demand (COD, 426.7 mg/L). Real-time PCR detected Giardia spp. DNA in 75% (76/102) of the samples and Cryptosporidium spp. DNA in 94% (96/102) of samples. The metagenomic read-based profiling identified Aeromonas media as a prevalent pathogen and Polaromonas naphthalenivorans as a potential biodegradative agent. The metagenomic assembly produced 270 high-quality genomes, revealing 16 bacterial species (e. g., Acinetobacter johnsonii and Megamonas funiformis) that provided insights into fecal contaminants and native aquatic microbes. Functional profiling further revealed a high prevalence of antimicrobial resistance markers, particularly for tetracyclines, aminoglycosides, and macrolides, with the highest abundance found in wastewater samples. Additionally, virulence factors were notably present in Zoogloea ramigera. The findings underscore the value of metagenomic profiling as a comprehensive tool for water quality monitoring, facilitating the detection of pathogens, beneficial species, and molecular markers indicative of potential health risks. This approach supports continuous monitoring efforts, offering actionable data for water management strategies to safeguard public health and maintain ecological integrity.}, } @article {pmid40020898, year = {2025}, author = {Chen, F and Chen, J and Chen, Y and He, Y and Li, H and Li, J and Tian, YS}, title = {Mechanistic insight into degradation of dibutyl phthalate by microorganism in sediment-water environment: metabolic pathway, community succession, keystone phylotypes and functional genes.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {125932}, doi = {10.1016/j.envpol.2025.125932}, pmid = {40020898}, issn = {1873-6424}, abstract = {Despite extensive studies on dibutyl phthalate (DBP) degradation in isolated bacterial cultures, the primary degraders, community dynamics, and metabolic pathways involved in its biotransformation within complex sediment microbial communities remain poorly understood. In this study, we aimed to investigate the biotransformation mechanism of DBP by microorganisms in a sediment-water system by employing gas chromatography-mass spectrometry, 16S rRNA gene sequencing, metagenomic analysis, and bacterial isolation techniques. We observed that DBP biotransformation has three distinct phases: lag, degradative, and stationary. During the degradative phase, DBP gets progressively degraded by microorganisms, resulting in a microbial community with reduced stability and ambiguous boundaries. DBP, primarily metabolised by key phylotypes into monobutyl phthalate (MBP), phthalic acid (PA), and protocatechuic acid, subsequently enters the tricarboxylic acid (TCA) cycle. Through metagenomic analysis, ten functional genes from five genera were identified as crucial for DBP metabolism. Firstly, Arthrobacter degrades DBP into MBP and PA using pheA. Subsequently, Acinetobacter, Massilia, and Arthrobacter convert PA into TCA cycle intermediates using phtBAaAbAcAd and pcaCH. Concurrently, Hydrogenophaga and Acidovorax degrade PA to TCA cycle intermediates through pht1234 and ligAB. Genes related to amino acid synthesis, ABC transporters, and two-component regulatory systems also contribute significantly. Thus, the listed key bacteria, along with their diverse functional genes, collectively exhibit a high capacity for DBP degradation. This study provides insights into the bacterial responses to DBP degradation and offers a theoretical basis for the prevention and control of this pollutant.}, } @article {pmid40020468, year = {2025}, author = {Huang, Y and Li, XT and Jiang, Z and Liang, ZL and Liu, W and Liu, ZH and Li, LZ and Yang, ZN and Zhang, GQ and Yin, HQ and Liang, JL and Zhou, N and Liu, SJ and Jiang, CY}, title = {Mineral types dominate microbiomes and biogeochemical cycling in acid mine drainage.}, journal = {Water research}, volume = {278}, number = {}, pages = {123367}, doi = {10.1016/j.watres.2025.123367}, pmid = {40020468}, issn = {1879-2448}, abstract = {Acid mine drainage (AMD) environments are typically used as models to study the crucial roles of acidophilic microbes in aquatic environments. Nevertheless, knowledge regarding microbial-driven biogeochemical cycling across mining regions remains limited. In this study, a metagenomics-based approach was employed to explore the diversity, composition, and ecological functions of microbiomes in global AMD environments with different mineral types. A total of 226 metagenomes, covering 12 mineral types of AMD, were analyzed. As a result, 2114 microbial metagenome-assembled genomes (MAGs) were obtained, representing members from 33 bacterial phyla and 8 archaeal phyla. The core taxa and functional groups in AMDs were identified. Additionally, twelve bacterial and two archaeal lineages were discovered for the first time in AMD environments. The specific metabolic potentials of these genomes were also determined. Our results revealed a high level of specialization in the diversity structures and ecological functions of AMD microbial communities based on mineral-type conditions. Mineral type significantly contributed to the dissimilarity in the AMD microbiomes, especially in water environments, underscoring the pivotal role of mineral types in shaping the microbial community in the AMD environment. Collectively, these findings provide novel perspectives on the ecology and metabolism of microbiomes in extreme AMD environments globally.}, } @article {pmid40020369, year = {2025}, author = {Tang, Z and Xu, H and Zhu, R and Li, D and Zhao, Z and Xiao, H and Li, H}, title = {Long-term effects of food waste on erosion resistance and production of methane and sulfide in sewer sediments: New insights into extracellular polymeric substances and genetic response mechanisms.}, journal = {Journal of environmental management}, volume = {377}, number = {}, pages = {124700}, doi = {10.1016/j.jenvman.2025.124700}, pmid = {40020369}, issn = {1095-8630}, abstract = {Discharge of food waste (FW) into sewer systems causes environmental issues, such as sewer blockage and odour problems. This study investigated the long-term effects of FW addition on sediment properties, microbial communities, and metabolic pathways using laboratory-scale reactors for 160-day incubation. The addition of 2 g/L FW increased the critical erosion shear stress of sediments by 40.63% and reduced their self-cleaning capacity by 39.46%. This was attributed to the fact that FW discharge increased extracellular polymeric substances (EPS) in sediments by 82.94%, especially aromatic protein with high hydrophobicity and high content of intermolecular hydrogen bonds, which was supported by the increased genes encoding aminoacyl-tRNA biosynthesis. The denser biofilm on the sediment surface hindered oxygen transfer to deeper sediment zones, and lowered oxidation-reduction potential below -400 mV. Microbial and metagenomic analysis revealed an enrichment of methanogenic archaea (e.g., Methanothrix) and sulfate-reducing bacteria (e.g., Desulforhabdus), along with increased genes for dissimilatory sulfate reduction and methanogenesis pathways of acetate and CO2/H2. These microbial and metabolic shifts led to a 95.49% and 34.99% increase methane and sulfide production in the FW-2 group. Overall, the negative effects of FW discharge into sewers emphasizes the need for more rational policies to manage this issue.}, } @article {pmid40020131, year = {2025}, author = {Onohuean, H and Nwodo, UU}, title = {Global systematic mapping of Vibrio species pathogenicity: A PRISMA-guided cluster-based analysis.}, journal = {Medicine}, volume = {104}, number = {9}, pages = {e41664}, doi = {10.1097/MD.0000000000041664}, pmid = {40020131}, issn = {1536-5964}, mesh = {*Vibrio/pathogenicity/genetics ; *Virulence Factors/genetics ; Virulence ; Humans ; Cluster Analysis ; Vibrio Infections/microbiology ; }, abstract = {BACKGROUND: A systematic global map on toxigenesis and genomic virulence of Vibrio spp. was analyzed for research progress to identify the emerging research patterns for establishing a database for designing future interventions.

METHOD: The databases (Web of Science and Scopus) were analyzed with Voxviewer software to map the global scale of Vibrio spp. or virulence toxin/genes publications and standardized using Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) strategies.

RESULTS: The results identified 1162 (Web of Science n = 620, Scopus n = 542), while 314 studies qualified for inclusion and were significantly analyzed on virulence toxin/genes. By co-citation analysis, 4-thematic clusters were developed from 6420 citations and a total reference of 9062. Cluster #1 (pathogenesis & virulence factors) and cluster #4 (host response factors) generated the utmost publications and citations (n = 40, 643) and the least (n = 7, 85) interest by the researcher. Whereas 8-thematic clusters were developed by bibliographic coupling technique analysis, cluster#1 and cluster#8 generated the utmost (n = 78, 1684) and least (n = 7, 81) publications and citations interest by the researcher.

CONCLUSIONS: Our findings suggest that Vibrio toxigenesis and virulence factors are a complex field requiring an interdisciplinary approach consisting of interconnected perspectives that have important consequences for academics and policymakers.}, } @article {pmid40020117, year = {2025}, author = {Zheng, X and Fan, J and Yin, J and Chu, Y}, title = {The role of gut microbiota and plasma metabolites in ulcerative colitis: Insights from Mendelian randomization analysis.}, journal = {Medicine}, volume = {104}, number = {9}, pages = {e41710}, pmid = {40020117}, issn = {1536-5964}, mesh = {Humans ; *Mendelian Randomization Analysis ; *Gastrointestinal Microbiome ; *Colitis, Ulcerative/blood/microbiology ; *Genome-Wide Association Study ; }, abstract = {Emerging research suggests that alterations in gut microbiota composition may play a significant role in the pathogenesis of ulcerative colitis (UC). Plasma metabolites, which are influenced by gut microbiota, have also been implicated, but their role in UC remains unclear. This study aims to determine whether specific plasma metabolites mediate the causal relationship between gut microbiota and UC using Mendelian randomization (MR) analysis. This study employed publicly available summary-level data from genome-wide association studies and metagenomic datasets. Gut microbiota data were derived from the FINRISK cohort (5959 participants), plasma metabolite data from the Canadian Longitudinal Study on Aging (8299 individuals), and UC data from multiple consortia (17,030 cases and 883,787 controls). Forward and reverse MR analyses, supplemented by linkage disequilibrium score regression (LDSC), were conducted to assess causal relationships. Mediation effects of plasma metabolites between gut microbiota and UC were analyzed using the product of coefficients method. Various sensitivity analyses, including MR-Egger and MR-PRESSO, were applied to detect pleiotropy and ensure robust results. The study identified 20 bacterial taxa and 93 plasma metabolites linked to UC. Forward MR analysis showed that Clostridium S felsineum increased UC risk via reduced carnitine levels, with a mediation proportion of 39.77%. Eubacterium callanderi was associated with decreased UC risk through the tryptophan to pyruvate ratio (16.02% mediation). Additionally, species CAG-590 sp000431135 increased UC risk through elevated mannitol/sorbitol levels, mediating 28.38% of the effect. Sensitivity analyses confirmed the robustness of these findings, with minimal heterogeneity and pleiotropy detected. This study highlights the significant role of gut microbiota and their associated plasma metabolites in the pathogenesis of UC. Specific microbial species influence UC through metabolites, suggesting potential therapeutic targets. Modulating carnitine, tryptophan metabolism, or sugar alcohols could offer promising avenues for UC management.}, } @article {pmid40020100, year = {2025}, author = {Zheng, H and Li, S and Liang, ZY and Feng, RL and Lu, JX and Dong, YJ and Chen, XP}, title = {M1 enrichment facilitates virus detection in patients with allogeneic hematopoietic stemcell transplantation.}, journal = {Medicine}, volume = {104}, number = {9}, pages = {e41683}, doi = {10.1097/MD.0000000000041683}, pmid = {40020100}, issn = {1536-5964}, support = {0104335//National Institute for Communicable Disease Control and Prevention/ ; }, mesh = {Humans ; *Hematopoietic Stem Cell Transplantation/adverse effects ; *Real-Time Polymerase Chain Reaction ; Male ; Female ; Middle Aged ; Adult ; *High-Throughput Nucleotide Sequencing ; Transplantation, Homologous/adverse effects ; Hematologic Neoplasms/therapy/virology ; Viremia/virology/diagnosis ; Virus Diseases/diagnosis/virology ; Viruses/isolation & purification/genetics/classification ; Young Adult ; }, abstract = {Due to the severe consequences of viral infection in allogeneic hematopoietic stem cell transplantation (allo-HSCT) patients, the routine use of polymerase chain reaction (PCR) screening of viruses is common in clinic, while the sensitivities of molecular methods are not always sufficient for blood samples. We aimed to increase the detection efficiency of viremia in allo-HSCT patients with M1 bead enrichment. Blood samples of allo-HSCT patients with fever were collected. Simultaneously with analyses of real-time PCR without enrichment, M1 bead enrichment followed by real-time PCR was applied to detect possible viruses in these samples, and metagenomic next-generation sequencing analyses were also applied in 10 samples negative with real-time PCR without enrichment. Various species of viruses were detected with M1 enrichment method. Significantly, some viruses that had not been found by real-time PCR without M1 enrichment were also detected by those with M1 enrichment and verified by metagenomic next-generation sequencing analyses. Furthermore, blood samples enriched with M1 beads had lower Ct values of real-time PCR assay than those that had not been treated. In conclusion, M1 bead enrichment increased the detection efficiency of most viruses in hematological malignancy patients.}, } @article {pmid40019273, year = {2025}, author = {Hackenberger, D and Imtiaz, H and Raphenya, AR and Alcock, BP and Poinar, HN and Wright, GD and McArthur, AG}, title = {CARPDM: cost-effective antibiotic resistome profiling of metagenomic samples using targeted enrichment.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0187624}, doi = {10.1128/aem.01876-24}, pmid = {40019273}, issn = {1098-5336}, abstract = {Better interrogation of antimicrobial resistance requires new approaches to detect the associated genes in metagenomic samples. Targeted enrichment is an ideal method for their sequencing and characterization. However, no open-source, up-to-date hybridization probe set targeting antimicrobial resistance genes exists. Here, we describe the Comprehensive Antibiotic Resistance Probe Design Machine (CARPDM), a probe design software package made to run alongside all future Comprehensive Antibiotic Resistance Database releases. To test its efficacy, we have created and tested two separate probe sets: allCARD, which enriches all genes encoded in the Comprehensive Antibiotic Resistance Database's protein homolog models (n = 4,661), and clinicalCARD, which focuses on a clinically relevant subset of resistance genes (n = 323). We demonstrate that allCARD increases the number of reads mapping to resistance genes by up to 594-fold. clinicalCARD performs similarly when clinically relevant genes are present, increasing the number of resistance-gene mapping reads by up to 598-fold. In parallel with this development, we have established a protocol to synthesize any probe set in-house, saving up to 350 dollars per reaction. Together, these probe sets, their associated design program CARPDM, and the protocol for in-house synthesis will democratize metagenomic resistome analyses, allowing researchers access to a cost-effective and efficient means to explore the antibiotic resistome.IMPORTANCEAntimicrobial resistance threatens to undermine all modern medicine and is driven by the spread of antimicrobial resistance genes among pathogens, environments, patients, and animals. DNA sequencing of complex samples, such as wastewater, shows considerable promise for tracking these genes and making risk assessments. However, these methods suffer from high costs and low detection limits, plus a requirement for frequent redesign due to the constantly evolving diversity of resistance genes. Building upon our Comprehensive Antibiotic Resistance Database, our research provides software for on-demand renewal, based on the latest knowledge of resistance gene diversity, of our novel bait-capture hybridization platform that simultaneously reduces cost and increases detection levels for DNA sequencing of complex samples. The significance of our research is in the development of new software tools, reagent synthesis protocols, and hybridization enrichment protocols to provide affordable, high-resolution metagenomics DNA sequencing, which we test using environmental and wastewater samples.}, } @article {pmid40019271, year = {2025}, author = {Milani, C and Longhi, G and Alessandri, G and Fontana, F and Viglioli, M and Tarracchini, C and Mancabelli, L and Lugli, GA and Petraro, S and Argentini, C and Anzalone, R and Viappiani, A and Carli, E and Vacondio, F and van Sinderen, D and Turroni, F and Mor, M and Ventura, M}, title = {Functional modulation of the human gut microbiome by bacteria vehicled by cheese.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0018025}, doi = {10.1128/aem.00180-25}, pmid = {40019271}, issn = {1098-5336}, abstract = {Since cheese is one of the most commonly and globally consumed fermented foods, scientific investigations in recent decades have focused on determining the impact of this dairy product on human health and well-being. However, the modulatory effect exerted by the autochthonous cheese microbial community on the taxonomic composition and associated functional potential of the gut microbiota of human is still far from being fully dissected or understood. Here, through the use of an in vitro human gut-simulating cultivation model in combination with multi-omics approaches, we have shown that minor rather than dominant bacterial players of the cheese microbiota are responsible for gut microbiota modulation of cheese consumers. These include taxa from the genera Enterococcus, Bacillus, Clostridium, and Hafnia. Indeed, they contribute to expand the functional potential of the intestinal microbial ecosystem by introducing genes responsible for the production of metabolites with relevant biological activity, including genes involved in the synthesis of vitamins, short-chain fatty acids, and amino acids. Furthermore, tracing of cheese microbiota-associated bacterial strains in fecal samples from cheese consumers provided evidence of horizontal transmission events, enabling the detection of particular bacterial strains transferred from cheese to humans. Moreover, transcriptomic and metabolomic analyses of a horizontally transmitted (cheese-to-consumer) bacterial strain, i.e., Hafnia paralvei T10, cultivated in a human gut environment-simulating medium, confirmed the concept that cheese-derived bacteria may expand the functional arsenal of the consumer's gut microbiota. This highlights the functional and biologically relevant contributions of food microbes acquired through cheese consumption on the human health.IMPORTANCEDiet is universally recognized as the primary factor influencing and modulating the human intestinal microbiota both taxonomically and functionally. In this context, cheese, being a fermented food with its own microbiota, serves not only as a source of nourishment for humans, but also as a source of nutrients for the consumer's gut microbiota. Additionally, it may act as a vehicle for autochthonous food-associated microorganisms which undergo transfer from cheese to the consumer, potentially influencing host gut health. The current study highlights not only that cheese microbiota-associated bacteria can be traced in the human gut microbiota, but also that they may expand the functional repertoire of the human gut microbiota, with potentially significant implications for human health.}, } @article {pmid40018976, year = {2025}, author = {Yu, T and Gao, J and Yuan, J and Yin, Z and Chen, X and Wu, Y and Dai, R and Yan, D and Chen, H and Wu, Y}, title = {Dietary methionine restriction restores wheat gluten-induced celiac-associated small intestine damage in association with affecting butyric acid production by intestinal flora.}, journal = {Food & function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d4fo05757k}, pmid = {40018976}, issn = {2042-650X}, abstract = {Methionine restriction has received some attention in recent years as a novel mode of dietary intervention. Our previous study found that methionine restriction could inhibit the celiac toxic effects of wheat gluten in an in vitro model. However, the role of methionine restriction in gluten-induced celiac intestinal damage remains unclear. The aim of this study was to explore whether dietary methionine restriction could suppress the celiac toxic effects of gluten in an in vivo model, thereby mitigating intestine damage. This study systematically investigated the effects of dietary methionine restriction on celiac characteristic indicators such as symptoms, small intestine damage, and intestinal TG2 and IL-15 expression in a gluten-induced C57BL/6 mouse model. The availability of dietary methionine restriction in different ages (adolescent and adult) was also evaluated. Moreover, mouse cecum contents were assayed and co-analyzed for the metagenome of intestinal flora and target short-chain fatty acid metabolomics, with the goal of further exploring and elucidating critical pathways by which dietary methionine restriction plays a role. We discovered that dietary methionine restriction could effectively ameliorate the gluten-induced celiac-associated small intestine damage by modulating intestinal flora to inhibit butyric acid production. Specifically, dietary methionine restriction could inhibit butyric acid production with the help of s_CAG-485 sp002493045 and s_CAG-475 sp910577815, which in turn affected the mitochondrial function within the intestinal epithelial cells to assist in the repair of intestine damage. This study might provide new insights into modulating dietary patterns to mitigate intestinal damage in celiac disease and the production of novel gluten-free products.}, } @article {pmid40018750, year = {2025}, author = {Zhu, X and Deng, H and Yu, M and Yang, S and Cao, Q and Zhao, C and Wang, Y and Jiang, J and Zhang, Y}, title = {Middle Ear Cholesteatoma Complicated By Lemierre's Syndrome: A Case Report and Literature Review.}, journal = {Ear, nose, & throat journal}, volume = {}, number = {}, pages = {1455613251323992}, doi = {10.1177/01455613251323992}, pmid = {40018750}, issn = {1942-7522}, abstract = {Septic thrombophlebitis of the internal jugular vein (IJV), known as Lemierre's syndrome, is a rare complication secondary to infections in the head and neck. Cholesteatoma of the middle ear complicated with Lemierre's syndrome is rarely observed in clinical practice. Currently, the treatment controversy centers on whether anticoagulation therapy is necessary for IJV and distant metastatic emboli induced by Lemierre's syndrome. A 46-year-old female patient with middle ear cholesteatoma underwent modified radical mastoidectomy and tympanoplasty surgery and complicated with Lemierre's syndrome, presenting with intermittent high fever, chills, headache, and left lateral neck pain. Computed tomography (CT) revealed thrombosis and internal gas in the left IJV, while blood culture and blood pathogenic microorganism metagenomic detection were negative. We administered sodium ceftriaxone (1 g every 12 hours) for 3 days. According to the secretion culture results showing 90% Actinomyces europaeus and 10% Corynebacterium without mycolic acid, penicillin (2.4 million IU) was added intravenously every 6 hours. The patient's infection worsened on the first day after surgery. We adjusted to upgrade anti-infection vancomycin 1 g every 12 hours, combined with meropenem (1 g every 8 hours) and metronidazole (0.5 g) every 8 hours for 4 weeks, and subcutaneous injection of enoxaparin 0.4 mL every 12 hours for 1 week, then adjusted to rivaroxaban tablets (15 mg bid). Amoxicillin-clavulanate for 2 weeks and rivaroxaban 10 mg were administered orally for 3 months after discharge. A follow-up neck CT scan with intravenous contrast suggested that the gas in the left IJV had disappeared, but the thrombus persisted. During the 3 month follow-up, the patient's vital signs, blood routine, and D-dimer levels were within the normal range. The surgical area healed well, and the patient reported no discomfort. Lemierre's syndrome represents a potentially-fatal complication that results in considerable mortality and must be identified early and aggressively treated.}, } @article {pmid40018491, year = {2025}, author = {Shaikh, RG and Dey, A and Singh, VP and Khandagle, A and M, B and Naik, S and Hasan, A}, title = {Understanding the Impact of the Gut Microbiome on Mental Health: A Systematic Review.}, journal = {Cureus}, volume = {17}, number = {1}, pages = {e78100}, pmid = {40018491}, issn = {2168-8184}, abstract = {Mental health is a serious issue, with mental health disorders affecting millions of people globally. Gut microbiota has received considerable attention because of its potential role in the pathogenesis of mental health disorders. This systematic review synthesized 15 studies exploring the effects of the gut microbiome on depression, anxiety, schizophrenia, and bipolar disorder, with qualitative and quantitative insights. The studies were conducted in different countries and employed various methods including 16S rRNA sequencing and metagenomic analysis with sample sizes varying from 50 to 600. Some of the key findings were that depression was associated with reduced microbial diversity and high levels of Firmicutes, and anxiety was associated with low levels of short-chain fatty acid (SCFA)-producing bacteria and high levels of Proteobacteria. Schizophrenia was related to endotoxemia and a reduction in the Lactobacillus count whereas bipolar disorder displayed a shift in the Firmicutes/Bacteroidetes ratio. Of interest, probiotics and dietary changes were as effective as drug treatment leading to symptom alleviation in many patients. It was found that depression was linked to less diverse gut bacteria while anxiety was associated with an increase in inflammatory bacteria. People with bipolar disorder were also found to have different gut bacteria patterns. This review also emphasizes the importance of the gut microbiota in the pathophysiology of mental disorders and the promising value of targeting microbiomes in pharmacological treatment approaches.}, } @article {pmid40018346, year = {2025}, author = {Sun, C and Zhang, Z}, title = {SARS-CoV-2 detection via metagenomic next-generation sequencing of bronchoalveolar lavage fluid/sputum in lymphoma patients receiving B-cell-depleting therapy: a case report of two cases.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1434340}, pmid = {40018346}, issn = {2296-858X}, abstract = {We describe two cases of coronavirus disease 2019 (COVID-19) infection in patients with lymphoma receiving B-cell-depleting therapy. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF)/sputum showed ongoing viral replication, despite repeated nasopharyngeal swabs being negative for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA. The patients failed to develop seroconversion of IgG antibodies for SARS-CoV-2. However, they showed favorable clinical outcomes after treatment with nirmatrelvir/ritonavir or molnupiravir, despite the antiviral therapies being initiated later in the clinical course. Our case highlights that in immunocompromised hosts, viral clearance of SARS-CoV-2 in lung tissue may lag behind that in the upper respiratory tract. Thus, alternative diagnostic criteria are necessary, and clinical decisions and interventions should be tailored to each individual case.}, } @article {pmid40018345, year = {2025}, author = {Fan, Z and Mei, M and Chen, C}, title = {Pyogenic liver abscess and sepsis caused by mixed anaerobic bacteria in an immunocompetent adult: a case report.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1486256}, pmid = {40018345}, issn = {2296-858X}, abstract = {BACKGROUND: Anaerobic bacterial communities in the digestive tract play an important role in digestive tract infections and aspiration pneumonia. However, ectopic infections originating from these communities are uncommon.

CASE REPORT: We present a rare case of a 64-year-old immunocompetent female was admitted with no significant medical history who developed a pyogenic liver abscess and sepsis caused by multiple anaerobic bacteria of digestive tract origin. Metagenomic next-generation sequencing (mNGS) detected four types of anaerobic bacteria in both peripheral blood and abscess puncture fluid. Culture confirmed the presence of three of these microorganisms. Treatment with a combination of meropenem and metronidazole resulted in the patient's subsequent recovery and discharge.

CONCLUSION: This report highlights the occurrence of ectopic infections caused by multiple anaerobic bacteria leading to pyogenic liver abscess and sepsis, underscoring the importance of considering anaerobic bacteria and conducting rapid comprehensive pathogen detection in clinical practice.}, } @article {pmid40017465, year = {2024}, author = {Mishra, AK and Yadav, P and Sharma, S and Maurya, P}, title = {Comparison of microbial diversity and community structure in soils managed with organic and chemical fertilization strategies using amplicon sequencing of 16 s and ITS regions.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1444903}, pmid = {40017465}, issn = {1664-302X}, abstract = {Soil microbial species diversity and distribution of microbial communities are vital for soil and crop health, nutrient cycling, availability, and subsequent plant growth. These soil dynamics are highly influenced and altered by various soil management practices, inputs, and agricultural techniques. In the present study, the effects of chemical and organic management practices on soil microbial diversity and community structure were examined and compared using amplicon sequencing of the 16S and ITS regions. Two contrasting soil samples were selected from each crop fields at the International Rice Research Institute-South Asia Regional Centre (IRRI-SARC) in Varanasi: one field followed conventional chemical fertilizer inputs, while the other implemented natural farming practices, including tillage, on-farm crop residue management, and water management. Soil samples from each field were analyzed for bacterial and fungal diversity. Our findings showed that the two differently managed soils exhibited distinct microbial community compositions, with the organically managed soil exhibiting a higher diversity of decomposer bacteria and fungi, showing 40 unique elements in organic soil samples and 19 in chemically managed soil. Natural farming practices also demonstrated a higher relative abundance of bacterial and fungal phyla. Our results emphasize the significance of sustainable soil management techniques, suggesting that organic inputs can increase soil microbial diversity and richness. The functional roles of these microbial communities in soil ecosystems and their potential impact on crop yield and nutrient cycling warrant further study.}, } @article {pmid40017391, year = {2025}, author = {Orru', S and Reissinger, A and Filomena, A and Heitmann, A and Funk, MB and Schmidt-Chanasit, J and Kreß, J and Scheiblauer, H and Cadar, D and Fiedler, SA}, title = {Assessment of the effectiveness of West Nile virus screening by analysing suspected positive donations among blood donors, Germany, 2020 to 2023.}, journal = {Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin}, volume = {30}, number = {8}, pages = {}, doi = {10.2807/1560-7917.ES.2025.30.8.2400373}, pmid = {40017391}, issn = {1560-7917}, mesh = {Humans ; *Blood Donors ; *West Nile virus/isolation & purification/genetics/immunology ; *West Nile Fever/diagnosis ; Germany ; *Mass Screening/methods ; *Nucleic Acid Amplification Techniques ; Male ; Female ; Middle Aged ; Adult ; High-Throughput Nucleotide Sequencing ; Antibodies, Viral/blood ; Donor Selection/methods ; Viral Load ; RNA, Viral/genetics ; }, abstract = {BackgroundThe first autochthonous human West Nile virus (WNV)-positive cases in Germany were confirmed in 2019. Risk minimisation measures (RMM) were introduced in 2020; no WNV transfusion-transmitted infections have been reported to date.AimTo analyse German suspected WNV-positive blood donations during annual seasons 2020-23 to review donor testing requirements.MethodsWNV look-back procedures were initiated as per German regulations and additional donor data were collected. Blood samples were analysed by metagenomic next-generation sequencing (mNGS), individual donor nucleic acid amplification technique (ID-NAT)-based testing and antibody (Ab) testing.ResultsSeventy-four cases were followed up after WNV-positive donor mini-pool screening. Forty-five (83%) of 54 samples tested with the cobas WNV assay and 14 (29%) of 49 samples tested with the RealStar WNV assay showed a reactive ID-NAT-based result; the viral load ranged between 70,251 IU/mL and values below quantification limits. Fifteen (23%) of 64 samples serologically tested were reactive with at least one of the three Ab tests performed; the previous WNV-negative donation was nearly always documented > 28 days before. Of 73 samples sequenced, mNGS detected WNV in 26 (36%) and other flaviviruses in 14 (19%) cases.ConclusionIn some suspected cases where a WNV infection was not confirmed, mNGS demonstrated a cross-reaction with other flaviviruses. Ab testing could only detect WNV in late stages of infection. A NAT-based WNV donor screening with a detection limit of at least 120 IU/mL seems to be a sufficiently effective RMM at present. However, a continuous re-evaluation of test strategy is always required.}, } @article {pmid40017220, year = {2025}, author = {Zheng, JS and Ye, ZL and Liu, LL}, title = {[Observational Study on the Diagnostic Efficacy of Metagenomic Next-Generation Sequencing for Bloodstream Infections Secondary to Hematologic Diseases in Children].}, journal = {Zhongguo shi yan xue ye xue za zhi}, volume = {33}, number = {1}, pages = {280-285}, doi = {10.19746/j.cnki.issn.1009-2137.2025.01.042}, pmid = {40017220}, issn = {1009-2137}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing ; *Hematologic Diseases/complications ; Retrospective Studies ; Child ; *Metagenomics/methods ; Precursor Cell Lymphoblastic Leukemia-Lymphoma/complications ; Anemia, Aplastic/complications ; Leukemia, Myeloid, Acute/complications ; Lymphohistiocytosis, Hemophagocytic/diagnosis ; Male ; }, abstract = {OBJECTIVE: To explore the clinical application value of metagenomic next-generation sequencing (mNGS) in pathogen detection of bloodstream infection secondary to hematologic diseases in children.

METHODS: 42 children with bloodstream infections secondary to hematologic diseases admitted to the Children's Hematology and Tumor Center of the Affiliated Hospital of Guangdong Medical University from November 2021 to May 2023 were included in the study, and their clinical data, results of peripheral blood mNGS and traditional blood culture, pathogen distribution characteristics, and diagnostic efficacy of mNGS were retrospectively analyzed.

RESULTS: Among the 42 children included, there were 2 cases (4.8%) of aplastic anemia (AA), 27 cases (64.3%) of acute lymphoblastic leukemia (ALL), 7 cases (16.7%) of acute myeloid leukemia (AML), 1 case (2.4%) of chronic myeloid leukemia (CML), 2 cases (4.8%) of hemophagocytic lymphohistiocytosis (HLH), 2 cases (4.8%) of non-Hodgkin lymphoma (NHL), and 1 case (2.4%) of Wiskott-Aldrich syndrome (WAS). In mNGS testing, pathogens were detected in 31 peripheral blood samples, with a positive rate of 73.8% (31/42), significantly higher than the pathogen positive rate of 16.7% (7/42) detected by traditional blood culture, and the difference was statistically significant (P < 0.05). Among the pathogen-positive cases detected by mNGS, 23 cases (74.2%) were positive for bacteria, 12 cases (38.7%) were positive for viruses, and 9 cases (29.0%) were positive for fungi. 32.2% (10/31) of the pathogen-positive samples detected by mNGS were mixed pathogens, which could not be effectively detected by traditional blood culture.

CONCLUSION: Peripheral blood mNGS has advantages in the detection of pathogens of bloodstream infection secondary to hematologic diseases, with a higher detection rate of pathogen positivity than traditional blood cultures. It can detect viruses, rare pathogens and mixed pathogens, and has good clinical application value.}, } @article {pmid40016914, year = {2025}, author = {Lu, X and Xu, Y and Liu, Y and Li, F and Feng, Q and Gao, C and Liu, D and Zhou, L and Yang, H and Zhang, J and Cui, F and Chen, Q}, title = {Neutrophil Depletion Reduced the Relative Abundance of Unsaturated Long-Chain Fatty Acid Synthesis Microbiota and Intestinal Lipid Absorption.}, journal = {Cell biochemistry and function}, volume = {43}, number = {3}, pages = {e70060}, doi = {10.1002/cbf.70060}, pmid = {40016914}, issn = {1099-0844}, support = {//This work was supported by the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), Suzhou Fundamental Research Project (SJC2023001), and Key Laboratory of Radiation Damage and Treatment of Jiangsu Provincial Universities and Colleges. It was funded by the National Natural Science Foundation of China (Grant No. 81773355)./ ; }, mesh = {Animals ; Mice ; *Neutrophils/metabolism ; *Intestinal Absorption ; Male ; Gastrointestinal Microbiome ; Lipid Metabolism ; Mice, Inbred C57BL ; Fatty Acids, Unsaturated/metabolism ; Rats ; }, abstract = {As immune cells, neutrophils serve as the first line of defense against infections; however, the mechanism by which neutrophils regulate lipid metabolism is unknown. The neutrophil depletion group was treated with 100 μg InVivoMAb anti-mouse Ly6G 6 times, whereas the control group mice were intraperitoneally injected with the same quantity of InVivoMAb rat IgG2a. Body fat content, triglycerides (TGs), total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C) in the jejunum and ileum, as well as 9 long-chain fatty acids (LCFAs) in the intestinal contents were significantly decreased. Furthermore, genes involved in the absorption of lipids in each segment of the intestine also showed decreased expression. Neutrophil-depletion and control models were administered 25 μCi of [3]H-cholesterol by gavage. The distribution of [3]H cholesterol in the intestinal segment, heart, liver, serum, and feces was not altered by anti-Ly6G antibodies. Metagenomics was applied to investigate uncultured microorganisms in the intestinal contents to identify bacteria containing lipid metabolism genes. At the species level, 12 bacteria were involved in unsaturated LCFA synthesis, among which 2 increased and 10 decreased. The overall relative abundance of these bacteria decreased from 3.102% to 0.734%. Many genes involved in lipid metabolism were also reduced as a result, such as fatty acid synthase and peroxisome proliferator-activated receptor γ. In conclusion, neutrophil depletion does not affect intestinal lipid absorption in the diet but leads to a decrease in the overall relative abundance of gut bacteria involved in unsaturated LCFA synthesis. Consequently, intestinal lipid synthesis and absorption are reduced.}, } @article {pmid40016913, year = {2025}, author = {Boukhchtaber, DC and von Meijenfeldt, FAB and Sahonero Canavesi, DX and Dorhout, D and Bale, NJ and Hopmans, EC and Villanueva, L}, title = {Discovering Hidden Archaeal and Bacterial Lipid Producers in a Euxinic Marine System.}, journal = {Environmental microbiology}, volume = {27}, number = {3}, pages = {e70054}, doi = {10.1111/1462-2920.70054}, pmid = {40016913}, issn = {1462-2920}, support = {024.002.002//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; ALWOP.256//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; //Spinoza prize 2004| NWO/ ; }, mesh = {*Archaea/metabolism/genetics/classification ; *Bacteria/metabolism/genetics/classification ; Seawater/microbiology ; Membrane Lipids/metabolism ; Black Sea ; Metagenome ; Biosynthetic Pathways/genetics ; }, abstract = {Bacterial membrane lipids are typically characterised by fatty acid bilayers linked through ester bonds, whereas those of Archaea are characterised by ether-linked isoprenoids forming bilayers or monolayers of membrane-spanning lipids known as isoprenoidal glycerol dialkyl glycerol tetraethers (isoGDGTs). However, this understanding has been reconsidered with the identification of branched GDGTs (brGDGTs), which are membrane-spanning ether-bound branched alkyl fatty acids of bacterial origin, though their producers are often unidentified. The limited availability of microbial cultures constrains the understanding of the biological sources of these membrane lipids, thus limiting their use as biomarkers. To address this issue, we identified membrane lipids in the Black Sea using high-resolution accurate mass/mass spectrometry and inferred their potential producers by targeting lipid biosynthetic pathways encoded on the metagenome, in metagenome-assembled genomes and unbinned scaffolds. We also identified brGDGTs and highly branched GDGTs in the suboxic and euxinic waters, potentially attributed to Planctomycetota, Cloacimonadota, Desulfobacterota, Chloroflexota, Actinobacteria and Myxococcota-based on their lipid biosynthetic genomic potential. These findings introduce new possibilities for using specific brGDGTs as biomarkers of anoxic conditions in marine environments and highlight the role of these membrane lipids in microbial adaptation.}, } @article {pmid40016544, year = {2025}, author = {Zaminhan-Hassemer, M and Zagolin, GB and Aráujo, BC and Perazza, CA and Barbosa, DA and Menegidio, FB and Coutinho, LL and Tizioto, P and Hilsdorf, AWS}, title = {Effect of green propolis crude extract on the modulation of intestinal microbiota and on the productive performance of juvenile Nile tilapia.}, journal = {Veterinary research communications}, volume = {49}, number = {2}, pages = {120}, pmid = {40016544}, issn = {1573-7446}, mesh = {Animals ; *Propolis/pharmacology/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; *Cichlids/microbiology ; *Animal Feed/analysis ; *Diet/veterinary ; Dietary Supplements/analysis ; }, abstract = {The study aimed to investigate the impact of dietary supplementation with green propolis crude extract on juvenile tilapia's growth and intestinal microbiota. The experiment was conducted in raceway tanks with a volume of 19m[3], comprising two treatments with three replicates each. Fish were assigned to either a control diet or a diet supplemented with 0.67% green propolis crude extract. Each experimental unit consisted of 30 fish, initially averaging 22.38 g ± 0.32 in weight, and which were fed ad libitum for 60 days. Results demonstrated that dietary supplementation with green propolis crude extract significantly improved the growth of juvenile tilapia compared to the control group. Firmicutes, Proteobacteria, Verrucomicrobia, Bacteroidetes, and Cyanobacteria were identified as the predominant bacterial phyla in the intestinal microbiota of both groups. The genera Candidatus xiphinematobacter (Verrucomicrobia) and Somerae (Firmicutes) were consistently abundant across treatments, with Somerae and Dispar as the most prevalent species. Significant differences in alpha diversity were observed between treatments at the genus and species levels according to the Chao 1 index. However, no significant differences were detected in Shannon index diversity between the control and green propolis crude extract groups. Beta diversity analysis revealed distinct clustering between treatments. Linear discriminant analysis Effect Size (LEfSe) highlighted significant differences in bacterial abundance between the control and green propolis crude extract groups. In conclusion, dietary supplementation with green propolis crude extract improved growth. It also modulated the intestinal microbiota of juvenile Thai tilapia.}, } @article {pmid40016305, year = {2025}, author = {Oba, M and Sakaguchi, S and Teshima, N and Yokota, T and Takemae, H and Tohei, M and Shimokawa, F and Murakami, M and Mizuno, S and Ishida, H and Murakami, H and Takano, T and Mizutani, T and Tsukada, H and Nagai, M}, title = {Metatranscriptomic identification of novel RNA viruses from raccoon dog (Nyctereutes procyonoides) feces in Japan.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {7100}, pmid = {40016305}, issn = {2045-2322}, support = {21K05947//JSPS KAKENHI/ ; }, mesh = {Animals ; *Raccoon Dogs/virology ; *Feces/virology ; Japan ; *RNA Viruses/genetics/isolation & purification/classification ; *Phylogeny ; *Genome, Viral ; Transcriptome ; Metagenomics/methods ; }, abstract = {The raccoon dog (Nyctereutes procyonoides), classified in the order Carnivora within the family Canidae, is native to East Asia and widely distributed throughout Japan due to its adaptability to various environments. Despite the close relationship between raccoon dogs and other animals, viruses infecting raccoon dogs have not been thoroughly investigated in Japan. In this study, we performed metatranscriptomic analyses using fecal samples collected from latrines of wild raccoon dogs in two locations on mainland Japan. Nearly complete viral genomes were identified, including viruses belonging to the genus Kobuvirus (CaKoV), an unclassified canine sapelovirus within the subfamily Ensavirinae (CaSaV), the Genius Mamastrovirus (CaAstV), unclassified hepe-astro-like virus (bastrovirus-like) (Bast-like V), and an unclassified dicistrovirus (DiciV) within the family Dicistroviridae. Phylogenetic analyses revealed that raccoon dog CaKoV, CaSaV, and CaAstV are related to canine strains but form independent clusters specific to raccoon dogs, suggesting they have evolved within this host population. Bast-like V, detected for the first time in raccoon dogs, showed high sequence identity with viruses previously identified in Chinese shrews. The shared insectivorous nature of these hosts and in silico host range predictions suggest that Bast-like Vs may originate from arthropod viruses. Although DiciV is likely of dietary origin due to its arthropod hosts, the large number of sequence reads detected and the phylogenetic clustering of raccoon dog DiciVs with mammalian DiciVs indicate the need to assess their potential infectivity in mammals and the risk of spillover. These findings suggest that raccoon dogs harbor endemic viruses within the canine population and may act as potential vectors for viruses with unknown infectivity in mammals but with spillover risk.}, } @article {pmid40016229, year = {2025}, author = {Chang, J and Costa, OYA and Sun, Y and Wang, J and Tian, L and Shi, S and Wang, E and Ji, L and Wang, C and Pang, Y and Yao, Z and Ye, L and Zhang, J and Chen, H and Cai, Y and Chen, D and Song, Z and Rong, J and Raaijmakers, JM and Tian, C and Kuramae, EE}, title = {Domesticated rice alters the rhizosphere microbiome, reducing nitrogen fixation and increasing nitrous oxide emissions.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {2038}, pmid = {40016229}, issn = {2041-1723}, mesh = {*Oryza/microbiology/metabolism ; *Nitrous Oxide/metabolism ; *Rhizosphere ; *Microbiota/genetics ; *Soil Microbiology ; *Nitrogen Fixation ; *Plant Roots/microbiology/metabolism ; Domestication ; Metagenomics ; Soil/chemistry ; Nitrogenase/metabolism/genetics ; Nitrogen/metabolism ; Bacteria/genetics/metabolism/classification/isolation & purification ; Agriculture/methods ; }, abstract = {Crop domestication has revolutionized food production but increased agriculture's reliance on fertilizers and pesticides. We investigate differences in the rhizosphere microbiome functions of wild and domesticated rice, focusing on nitrogen (N) cycling genes. Shotgun metagenomics and real-time PCR reveal a higher abundance of N-fixing genes in the wild rice rhizosphere microbiomes. Validation through transplanting rhizosphere microbiome suspensions shows the highest nitrogenase activity in soils with wild rice suspensions, regardless of planted rice type. Domesticated rice, however, exhibits an increased number of genes associated with nitrous oxide (N2O) production. Measurements of N2O emissions in soils with wild and domesticated rice are significantly higher in soil with domesticated rice compared to wild rice. Comparative root metabolomics between wild and domesticated rice further show that wild rice root exudates positively correlate with the frequency and abundance of microbial N-fixing genes, as indicated by metagenomic and qPCR, respectively. To confirm, we add wild and domesticated rice root metabolites to black soil, and qPCR shows that wild rice exudates maximize microbial N-fixing gene abundances and nitrogenase activity. Collectively, these findings suggest that rice domestication negatively impacts N-fixing bacteria and enriches bacteria that produce the greenhouse gas N2O, highlighting the environmental trade-offs associated with crop domestication.}, } @article {pmid40015949, year = {2025}, author = {Hu, M and Xu, Y and Wang, Y and Huang, Z and Wang, L and Zeng, F and Qiu, B and Liu, Z and Yuan, P and Wan, Y and Ge, S and Zhong, D and Xiao, S and Luo, R and He, J and Sun, M and Zhuang, X and Guo, N and Cui, C and Gao, J and Zhou, H and He, X}, title = {Gut microbial-derived N-acetylmuramic acid alleviates colorectal cancer via the AKT1 pathway.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2024-332891}, pmid = {40015949}, issn = {1468-3288}, abstract = {BACKGROUND: Gut microbial metabolites are recognised as critical effector molecules that influence the development of colorectal cancer (CRC). Peptidoglycan fragments (PGFs) produced by microbiota play a crucial role in maintaining intestinal homeostasis, but their role in CRC remains unclear.

OBJECTIVE: Here, we aimed to explore the potential contribution of PGFs in intestinal tumourigenesis.

DESIGN: The relative abundance of peptidoglycan synthase and hydrolase genes was assessed by metagenomic analysis. Specific PGFs in the faeces and serum of CRC patients were quantified using targeted mass spectrometry. The effects of PGF on intestinal tumourigenesis were systematically evaluated using various murine models of CRC and organoids derived from CRC patients. Downstream molecular targets were screened and evaluated using proteome microarray, transcriptome sequencing and rescue assays.

RESULTS: Metagenomic analysis across seven independent cohorts (n=1121) revealed a comprehensive reduction in peptidoglycan synthase gene relative abundance in CRC patients. Targeted mass spectrometry identified significant depletion of a specific PGF, N-acetylmuramic acid (NAM) in CRC patients, which decreased as tumours progressed (p<0.001). NAM significantly inhibits intestinal tumourigenesis in various models, including Apc [Min/+], AOM/DSS-treated and MC38 tumour-bearing mice. Additionally, NAM inhibits the growth of patient-derived CRC organoids in a concentration-dependent manner. Mechanistically, NAM inhibits the activation of AKT1 by directly binding to it and blocking its phosphorylation, which is a partial mediator of NAM's anticancer effects.

CONCLUSION: The PGF NAM protects against intestinal tumourigenesis by targeting the AKT1 signalling pathway. NAM may serve as a novel potential preventive and therapeutic biomarker against CRC.}, } @article {pmid40015896, year = {2025}, author = {Zheng, R and Peng, J and Li, Q and Liu, Y and Huang, D and Sheng, Y and Liu, C and Qi, L and Keyhani, NO and Tang, Q}, title = {Alterations in microbial community structures and metabolic function in soil treated with biological and chemical insecticides.}, journal = {Pesticide biochemistry and physiology}, volume = {208}, number = {}, pages = {106304}, doi = {10.1016/j.pestbp.2025.106304}, pmid = {40015896}, issn = {1095-9939}, mesh = {*Insecticides/pharmacology ; *Soil Microbiology ; *Metarhizium/genetics ; *Ivermectin/analogs & derivatives/pharmacology ; *Neonicotinoids/pharmacology ; Nitro Compounds/pharmacology ; Soil/chemistry ; Microbiota/drug effects ; }, abstract = {Entomopathogenic fungi show significant promise as effective and ecological friendly alternatives to chemical insecticides for insect pest control. However, little is known concerning their effects on soil ecosystems, especially in comparison to application of chemical insecticides. Here, we examined the effects of one biological and two chemical insecticides, Metarhizium anisopliae, imidacloprid (IMI) and emamectin benzoate (EMB) on microbial community structure, metabolic functioning, and soil biochemistry. Treatment with EMB and IMI, reduced Actinobacteriota populations, while increasing that of Acidobacteriota. However, these populations were not significantly altered under M. anisopliae treatment. Chemical pesticides also altered fungal communities including potential pathogens. Activities of soil beneficial nitrogen-cycling-related enzymes were reduced after application of IMI and EMB, but were increased after treatment with M. anisopliae. Metagenomics analysis showed that IMI treatment reduced levels of carbon and nitrogen-related metabolic pathways. However, M. anisopliae treatment increased representation of key enzymes involved in the carbon, nitrogen, and sulfur cycling important for maintenance of soil fertility. Insecticides treatments altered the abundance of a number antibiotic resistance genes (ARGs) but not virulence factors (VFs), whereas application of M. anisopliae resulted had only minimal effects. These findings highlight the consequences of use of biological vs. chemical pesticides on soil microbiology can affect plant and ecosystem health indicating that the fungal biological control agent, M. anisopliae likely has far less detrimental and potentially beneficial effects on soil ecology as compared to chemical pesticides.}, } @article {pmid40015523, year = {2025}, author = {Ma, WJ and Zhang, HM}, title = {Metagenomics deciphers the function of biochar in alleviating zinc ion stress during sulfur autotrophic denitrification process.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132303}, doi = {10.1016/j.biortech.2025.132303}, pmid = {40015523}, issn = {1873-2976}, abstract = {Sulfur autotrophic denitrification (SAD) process has significant potential in treating low carbon/nitrogen ratio wastewater. However, the presence of zinc ions (Zn[2+]) adversely affects the denitrification performance. This study investigated the effect of biochar prepared at 300 °C (BC300) and 600 °C (BC600), as well as dosing strategy, on denitrification performance in the SAD process under Zn[2+] inhibition. Firstly, BC600 had a higher maximum adsorption capacity for Zn[2+] than BC300 in nitrogen-containing wastewater. Surface complexation was mainly adsorption mechanism. BC300 exhibited a greater ability in enhancing denitrification ability than BC600. The strategy of synchronous addition is more effective than pre-adsorption. Firstly, BC300 enhancing humic-like component secretion. BC300 enriched higher abundance of sulfur-oxidizing bacteria. More importantly, BC300 counteracted the negative effect of Zn[2+] by enhancing glycan biosynthesis and metabolism, enriching functional genes, and increased the level of quorum sensing. The study presents a sustainable approach for maintaining denitrification performance under environmental stress.}, } @article {pmid40015429, year = {2025}, author = {Wani, SM and Chesti, A and Rehman, S and Chandra Nautiyal, V and Bhat, IA and Ahmad, I}, title = {Repurposing and reusing aquaculture wastes through a biosecure microfloc technology.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121214}, doi = {10.1016/j.envres.2025.121214}, pmid = {40015429}, issn = {1096-0953}, abstract = {Intensive aquaculture waste management is a significant challenge in the aquaculture industry, often contributing to environmental issues. Intensive aquacultural techniques demand new strategies and alternatives aimed to achieving sustainability. Repurposing and reusing wastes through innovative technologies can mitigate their negative impact. Biofloc technology (BFT) or bio-colloidal technology is based on the concept of aquaculture waste utilization by heterotrophic microbial biomass and presents a biosecure and sustainable solution. The dynamics of BFT are shaped by ecological interactions like commensalism, competition, and predation, forming a trophic micro-network consisting of rotifers, ciliates, heterotrophic bacteria, and microalgae. Metagenomic studies showed dominance of microbial communities within the biofloc, such as Cyanobacteria, Nitrosomonas, Proteobacteria, Bacteroidetes, Pseudomonadota, Rhodobacteraceae and Bacillus species that play a crucial role in the mineralization and bioremediation of waste. These microbes also help to break down hazardous toxic compounds into non-toxic, beneficial nutrients, which are subsequently utilized as food by fish and shellfish. Also by recycling waste reduces pollution, improves water quality, and enhances the efficiency of aquaculture system. With increasing incidences of microbial diseases and growing expenses for energy, biosecurity with BFT seems, by all means a sustainable production method for aquaculture. The incorporation of biosecure biofloc technology into aquaculture practices enhances environmental sustainability while optimizing resource use, creating more eco-friendly and cost-effective systems. This review highlights key aspects such as the microbial dynamics, role of metagenomics in identifying the bacterial communities, bioremediation of aquaculture waste, biosecurity concerns, and the biocontrol of pathogenic microbes across various biofloc systems.}, } @article {pmid40015361, year = {2025}, author = {Liu, W and Geng, Y and Wang, Y and Zhao, J and Fan, Y and Zhang, X and Xie, W and Zhang, L and Zhang, Z}, title = {Evolution of gut microbiota in psoriatic arthritis treated with IL-17 inhibitor revealed by metagenomics.}, journal = {Joint bone spine}, volume = {}, number = {}, pages = {105868}, doi = {10.1016/j.jbspin.2025.105868}, pmid = {40015361}, issn = {1778-7254}, abstract = {OBJECTIVES: To explore the evolution of gut microbiota in taxonomy and function in PsA patients during IL-17i treatment.

METHODS: Twenty PsA patients treated with secukizumab were included. Fecal samples were collected before treatment (0 mo.), first month (1 mo.) and third month (3mo.) after treatment, and a total of 60 samples were collected. Shotgun metagenomic sequencing was used to detect all fecal samples.

RESULTS: In the 1 mo. and 3 mo. after IL-17i treatment, the disease activity in PsA patients decreased significantly. Compared with 0 mo., α-diversity calculated by Shannon index and Pielou index increased significantly at 1 mo. and 3 mo. after treatment. Microbial genes encoding Carbohydrate Active enZymes (CAZy) tended to be upregulated after treatment. After treatment, Bacteroidota phylum expanded, especially the abundance of Phocaeicola genus increased gradually with the treatment time (P<0.05). The abundance of Phocaeicola genus was positively correlated with the α-diversity. The Polysaccharide Lyases and Carbohydrate Esterases in CAZy were significantly positively correlated with most of species in Phocaeicola genus.

CONCLUSIONS: Treatment with IL-17i induces gut microbiota evolution in PsA patients. The key features of this evolution include increased α-diversity, expansion of the Phocaeicola genus, and upregulation of CAZy. Species within the Phocaeicola genus may be the critical bacteria driving this evolution.}, } @article {pmid40015321, year = {2025}, author = {Valadez-Cano, C and Tromas, N and Reyes-Prieto, A and Johnston, L and Huang, Y and Morris, H and Zamlynny, L and Beach, DG and Jamieson, RC and Lawrence, J}, title = {Genetic Diversity and Anatoxin Profiles of Freshwater Benthic Cyanobacteria From Nova Scotia (Canada).}, journal = {Environmental microbiology}, volume = {27}, number = {3}, pages = {e70067}, doi = {10.1111/1462-2920.70067}, pmid = {40015321}, issn = {1462-2920}, support = {ALLRP 576532-22//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Nova Scotia ; *Cyanobacteria/genetics/metabolism/classification ; *Fresh Water/microbiology ; *Genetic Variation ; *Cyanobacteria Toxins ; *Tropanes/metabolism ; Phylogeny ; Multigene Family ; Bacterial Toxins/genetics/metabolism ; }, abstract = {Some mat-forming cyanobacteria produce harmful cyanotoxins, yet benthic species remain understudied compared to planktonic counterparts. This study assesses the diversity, distribution and toxin production of mat-forming cyanobacteria across lentic and lotic systems in Nova Scotia, Canada. We documented greater cyanobacterial species richness in lentic environments, with six dominant species distributed into two major Microcoleus clades, five of which represent putative novel taxa. Two Microcoleus species with the genetic repertoire to produce anatoxins were prevalent. One has been previously reported in Canada, while the second represents a novel species found exclusively in an environment impacted by discharge from a water treatment plant. We observed variability in the gene clusters responsible for the biosynthesis of anatoxin-a and associated analogues (ATXs), including the discovery of a novel anaG variant with a ~ 1.7 kb insertion in a Microcoleus strain dominating homoanatoxin-producing mats. This extended anaG, encoding a polyketide synthase with an additional methyltransferase domain, coexists with shorter variants, leading to the production of a mixture of ATXs. These findings highlight the genetic diversity of benthic cyanobacteria in freshwater environments, with Microcoleus as the primary contributor to the production of ATXs in both lentic and lotic systems, underscoring their potential to produce harmful toxins.}, } @article {pmid40015021, year = {2025}, author = {Velásquez-Reyes, D and García-Alamilla, P and Kirchmayr, MR and Lugo-Cervantes, E and Gschaedler, A}, title = {Contribution of post-harvest processing in cocoa bean: Chemometric and metagenomic analysis in fermentation step.}, journal = {Food chemistry}, volume = {477}, number = {}, pages = {143458}, doi = {10.1016/j.foodchem.2025.143458}, pmid = {40015021}, issn = {1873-7072}, abstract = {Cocoa fermentation is a heterogeneous process, exhibiting a high degree of diversity of flavor, aroma, and microbial communities. A study was conducted to examine cocoa fermentations in five municipalities of a region in Mexico, with the objective of associating post-harvest practices, geographic area, and chemical and microbiological profiles. Through the application of high-performance DNA sequencing, the microbial diversity was identified, and the non-volatile and volatile compounds were identified and quantified by UHPLC-RID/PDA and HS-SPME/GC-MS, respectively. Using PCA, PLS regression and Pearson correlation, post-harvest practices, geographical factors, microbial communities, and volatile and non-volatile compounds were made. The absence of control in cocoa fermentation was associated to Aspergillus, Escherichia, and Bacillus, and reduced the production of essential acids for aroma. This study provides data on the diversity of post-harvest practices and their impact on cocoa quality.}, } @article {pmid40014853, year = {2025}, author = {Lee, C and Zaheer, R and Thomas, K and Poulin-Laprade, D and Talbot, G and Diarra, M and Van Domselaar, G and Zovoilis, A and McAllister, TA}, title = {Comparative Metagenomics Reveals Limited Differences in Antimicrobial Resistance Gene Abundance Across Conventional and Natural Livestock Production Systems.}, journal = {Canadian journal of microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1139/cjm-2024-0191}, pmid = {40014853}, issn = {1480-3275}, abstract = {The livestock industry has been a source of concern in terms of antimicrobial resistance (AMR) development and spread, especially from a One Health perspective. Raising livestock without antimicrobials, so called natural (NAT) production is an increasingly popular practice. This study used metagenomics to compare this practice to conventional (CONV) antimicrobial use (AMU) on the microbiome and resistome in the feces of beef cattle and swine and the cecal contents of broiler chickens. In cattle, Bacteroidetes, Euryarchaeota, and Spirochaetes were more abundant (q < 0.01) in CONV than NAT systems, with no differences (q > 0.05) in bacterial profiles in either swine or chickens. Classes of antimicrobial resistant genes (ARG) were not impacted regardless of AMU in any of the livestock species. However, many tetracycline resistance genes were more abundant in CONV as compared to NAT swine (q < 0.05), but this difference was not observed in cattle or chickens. This study confirmed that elimination of AMU does not necessarily result in an immediate decline in the abundance or diversity of ARGs within a single livestock production cycle.}, } @article {pmid40014144, year = {2025}, author = {Bhure, M and Savaliya, K and Patil, S and Nehra, C and Pandit, R and Shah, T and Patil, NV and Patel, AK and Kachhawaha, S and Kumawat, RN and Joshi, M and Joshi, CG}, title = {Bioprospecting of 101 facultative rumen bacterial isolates through comprehensive genome analysis.}, journal = {Molecular biology reports}, volume = {52}, number = {1}, pages = {265}, pmid = {40014144}, issn = {1573-4978}, support = {BT/AQ/1/SP41105/2020//Department of Biotechnology (DBT), Government of India/ ; }, mesh = {*Rumen/microbiology ; Animals ; *Genome, Bacterial/genetics ; Phylogeny ; Bioprospecting/methods ; Bacteria, Anaerobic/genetics/metabolism/isolation & purification ; Bacteria/genetics/metabolism/classification/isolation & purification ; Metagenomics/methods ; }, abstract = {BACKGROUND: Microbes within the rumen play a pivotal role in the digestion of feed ingested by the ruminants. Researchers have been investigating microbes within rumen to assess its genetic capabilities, which hold immense potential across various fields including agro-industrial advantages. Since rumen is preliminary an anaerobic sac, numerous anaerobic bacteria and fungi have been isolated and characterized, however facultative anaerobic bacteria yet not fully investigated.

METHODS AND RESULTS: In present study, we isolated, characterized and performed whole genome analysis of 101 facultative anaerobic bacteria from rumen, offering a unique perspective compared to metagenomic approaches. All assembled genomes were of high quality, i.e. completeness 100% (only seven were between 92 and 99.5%) and only two had contamination > 5%. We identified 9,542 sequences of Carbohydrate-Active Enzymes (CAZymes). Over 8,136 of these CAZymes were full-length sequences, with 2,048 harbouring signal peptides also. Xylan (n = 634), pectin (n = 604), and starch (n = 312) degrading enzyme sequences were dominant. Several isolates also harbour secondary metabolite biosynthesis gene clusters for various metabolites, including fengycin, lichenysin, bacillibactins, bacilysin etc. All the isolates have metabolic versatility, encompassing pathways such as carbohydrate, amino acid, lipid, and vitamin and cofactor metabolism. Intriguingly, lipoic acid metabolism was absent in most of these facultative bacterial isolates.

CONCLUSION: This comprehensive study sheds light on the genetic potential of culturable facultative rumen bacteria, emphasizing their pivotal roles in carbohydrate degradation, secondary metabolite production, and metabolic diversity. These findings hold promise for enhancing ruminant nutrition, advancing eco-friendly biomass conversion, and bolstering bioprospecting of industrially important biocules and enzymes biofuel production.}, } @article {pmid40013924, year = {2025}, author = {Johnson, T and Jamrozik, E and Ramachandran, P and Johnson, S}, title = {Clinical metagenomics: ethical issues.}, journal = {Journal of medical microbiology}, volume = {74}, number = {2}, pages = {}, doi = {10.1099/jmm.0.001967}, pmid = {40013924}, issn = {1473-5644}, mesh = {Humans ; *Metagenomics/ethics ; Male ; Klebsiella pneumoniae/genetics/isolation & purification ; Klebsiella Infections/diagnosis/microbiology ; Encephalitis/diagnosis/microbiology ; Female ; Hepatitis/microbiology/diagnosis ; Child ; Coinfection/diagnosis/microbiology ; }, abstract = {Metagenomics is increasingly used for diagnosis in hospital settings. It is useful particularly in cases of unknown aetiology, where novel or difficult-to-diagnose pathogens are suspected, and/or following unexplained disease outbreaks. In this paper, we present three use cases that draw on existing reports: one involving a patient in intensive care with encephalitis of unknown aetiology; a second case with likely infection with drug-resistant Klebsiella pneumoniae and an incidental finding of unknown relevance; and a third case situated in an unexplained outbreak of acute hepatitis in children, with severe outcomes due to co-infection. We examine each case in turn, highlighting ethical questions arising in relation to clinical issues including: disclosure to patients of untreatable disease, cost-effectiveness, the value of resistance testing, sensitivity and specificity, uncertain or unexpected findings, patient consent and data sharing. We conclude by proposing recommendations for further research and developing particular pieces of guidance to improve clinical uses of metagenomics for diagnosis.}, } @article {pmid40013797, year = {2025}, author = {Bai, Y and Hu, Y and Chen, X and Hu, L and Wu, K and Liang, S and Zheng, J and Gänzle, MG and Chen, C}, title = {Comparative metagenome-associated analysis of gut microbiota and antibiotic resistance genes in acute gastrointestinal injury patients with the risk of in-hospital mortality.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0144424}, doi = {10.1128/msystems.01444-24}, pmid = {40013797}, issn = {2379-5077}, abstract = {UNLABELLED: Acute gastrointestinal injury (AGI) is known for its poor long-term prognosis and the associated increase in mortality among intensive care unit (ICU) patients. As the role of the gut microbiome and resistome in AGI remains unclear, the present study aimed to explore the possible associations between dysbacteriosis and in-hospital mortality in ICU patients with gastrointestinal dysfunction. Fecal samples were collected from a prospective cohort of 210 ICU patients with AGI, and shotgun metagenomic sequencing was used to determine the taxonomic composition of gut microbiota and the differences of antibiotic resistance genes (ARGs) between the Death and Survival groups. Compared to the Survival group, patients in the Death group shifted from strict anaerobes to facultative anaerobes in the fecal microbial community, with more Klebsiella but less Prevotella. The co-occurrence patterns revealed that more ARG subtypes were enriched in microbial taxa in the Death group, especially for Clostridium and Methanobrevibacter. Furthermore, the ARG type had large area under the curve (AUCs) in receiver operating characteristic for predicting the disease severity, and a combined gut microbiota-ARG subtype classifiers showed better performance than either of them. Thus, comparative metagenome-associated analysis can help to obtain valuable information about gut microbiota and gene coding for antibiotic resistance in AGI patients.

IMPORTANCE: A metagenomic-related strategy was conducted to obtain a highly valuable resource to improve understanding of intestinal microbiota dysbiosis and antibiotic resistance genes (ARGs) profiles. The results indicate that intestinal microbiota, including Klebsiella and Prevotella, changed dramatically in intensive care unit (ICU) patients with acute gastrointestinal injury (AGI). Due to longer ICU stays and receiving more antibiotic treatment, the types and correlations of ARGs in the Death group were significantly higher than those in the Survival group. The findings of this study are expected to expand our knowledge of gut microbiota and resistome profiles reflecting gastrointestinal status, accelerate the identification of disease biomarkers, and provide new insights into the prevention and treatment of AGI-related diseases.}, } @article {pmid40013792, year = {2025}, author = {Qin, Y and Wang, Q and Lin, Q and Liu, F and Pan, X and Wei, C and Chen, J and Huang, T and Fang, M and Yang, W and Pan, L}, title = {Multi-omics analysis reveals associations between gut microbiota and host transcriptome in colon cancer patients.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0080524}, doi = {10.1128/msystems.00805-24}, pmid = {40013792}, issn = {2379-5077}, abstract = {UNLABELLED: Colon cancer (CC) is one of the most common cancers globally, which is associated with the gut microbiota intimately. In current research, exploring the complex interaction between microbiomes and CC is a hotspot. However, the information on microbiomes in most previous studies is based on fecal, which does not fully display the microbial environment of CC. Herein, we collected mucosal and tissue samples from both the tumor and normal regions of 19 CC patients and clarified the composition of mucosal microbiota by 16S rRNA and metagenomic sequencing. Additionally, RNA-Seq was also conducted to identify the different expression genes between tumor and normal tissue samples. We revealed significantly different microbial community structures and expression profiles to CC. Depending on correlation analysis, we demonstrated that 1,472 genes were significantly correlated with CC tumor microbiota. Our study reveals a significant enrichment of Campylobacter jejuni in the mucosa of CC, which correlates with bile secretion. Additionally, we observe a negative correlation between C. jejuni and immune cells CD4+ Tem and mast cells. Finally, we discovered that metabolic bacterial endosymbiont of Bathymodiolus sp., Bacillus wiedmannii, and Mycobacterium tuberculosis had a significant survival value for CC, which was ignored by previous research. Overall, our study expands the understanding of the complex interplay between microbiota and CC and provides new targets for the treatment of CC.

IMPORTANCE: This study contributes to our understanding of the interaction between microbiota and colon cancer (CC). By examining mucosal and tissue samples rather than solely relying on fecal samples, we have uncovered previously unknown aspects of CC-associated microbiota. Our findings reveal distinct microbial community structures and gene expression profiles correlated with CC progression. Notably, the enrichment of Campylobacter jejuni in CC mucosa, linked to bile secretion, underscores potential mechanisms in CC pathogenesis. Additionally, observed correlations between microbial taxa and immune cell populations offer new avenues for immunotherapy research in CC. Importantly, this study introduces CC-associated microbiota with survival implications for CC, expanding therapeutic targets beyond conventional strategies. By elucidating these correlations, our study not only contributes to uncovering the potential role of gut microbiota in colon cancer but also establishes a foundation for mechanistic studies of gut microbiota in colon cancer, emphasizing the broader impact of microbiota research on cancer biology.}, } @article {pmid40013791, year = {2025}, author = {Walter, JM and Greses, S and Hagen, LH and Schiml, VC and Pope, PB and González-Fernández, C and Arntzen, M}, title = {Anaerobic digestion of microalgae: microbial response and recovery after organic loading disturbances.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0167424}, doi = {10.1128/msystems.01674-24}, pmid = {40013791}, issn = {2379-5077}, abstract = {UNLABELLED: Industrial anaerobic digestion (AD) represents a relevant energy source beyond today's fossil fuels, wherein organic matter is recycled to methane gas via an intricate and complex microbial food web. Despite its potential, anaerobic reactors often undergo process instability over time, which is frequently caused by substrate composition perturbations, making the system unreliable for stable energy production. To ensure the reliability of AD technologies, it is crucial to identify microbial and system responses to better understand the effect of such perturbations and ultimately detect signatures indicative of process failure. Here, we investigate the effect of the microalgal organic loading rate (OLR) on the fermentation product profile, microbiome dynamics, and disruption/recovery of major microbial metabolisms. Reactors subjected to low- and high-OLR disturbances were operated and monitored for fermentation products and biogas production over time, while microbial responses were investigated via 16S rRNA gene amplicon data, shotgun metagenomics, and metagenome-centric metaproteomics. Both low- and high-ORL fed systems encountered a sudden decline in methane production during OLR disturbances, followed by a recovery of the methanogenic activity within the microbiome. In the high-OLR disturbances, system failure triggered an upregulation of hydrolytic enzymes, an accumulation of fermentation products, and a shift in the methanogenic population from hydrogenotrophic to acetoclastic methanogens, with the latter being essential for recovery of the system after collapse.

IMPORTANCE: Anaerobic digestion (AD) with microalgae holds great potential for sustainable energy production, but process instability caused by substrate disturbances remains a significant barrier. This study highlights the importance of understanding the microbial dynamics and system responses during organic loading rate perturbations. By identifying key shifts in microbial populations and enzyme activity, particularly the transition from hydrogenotrophic to acetoclastic methanogens during recovery, this research provides critical insights for improving AD system stability and can contribute to optimizing microalgae-based AD processes for more reliable and efficient methane production.}, } @article {pmid40013784, year = {2025}, author = {Midani, FS and Danhof, HA and Mathew, N and Ardis, CK and Garey, KW and Spinler, JK and Britton, RA}, title = {Emerging Clostridioides difficile ribotypes have divergent metabolic phenotypes.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0107524}, doi = {10.1128/msystems.01075-24}, pmid = {40013784}, issn = {2379-5077}, abstract = {Clostridioides difficile is a gram-positive spore-forming pathogen that commonly causes diarrheal infections in the developed world. Although C. difficile is a genetically diverse species, certain ribotypes are overrepresented in human infections, and it is unclear if metabolic adaptations are essential for the emergence of these epidemic ribotypes. To identify ribotype-specific metabolic differences, we therefore tested carbon substrate utilization by 88 C. difficile isolates and looked for differences in growth between 22 ribotypes. As expected, C. difficile was capable of growing on a variety of carbon substrates. Further, C. difficile strains clustered by phylogenetic relationship and displayed ribotype-specific and clade-specific metabolic capabilities. Surprisingly, we observed that two emerging lineages, ribotypes 023 and 255, have divergent metabolic phenotypes. In addition, although C. difficile Clade 5 is the most evolutionary distant clade and often detected in animals, it displayed robust growth on simple sugars similar to Clades 1-4. Altogether, our results corroborate the generalist metabolic strategy of C. difficile but also demonstrate lineage-specific metabolic capabilities.IMPORTANCEThe gut pathogen Clostridioides difficile utilizes a wide range of carbon sources. Microbial communities can be rationally designed to combat C. difficile by depleting its preferred nutrients in the gut. However, C. difficile is genetically diverse with hundreds of identified ribotypes, and most of its metabolic studies were performed with lab-adapted strains. To identify ribotype-specific metabolic differences, we profiled carbon metabolism by a myriad of C. difficile clinical isolates. While the metabolic capabilities of these isolates clustered by their genetic lineage, we observed surprising metabolic divergence between two emerging lineages. We also found that genetically newer and older clades grew to a similar level on simple sugars, which contrasts with recent findings that newer clades experienced positive selection on genes involved in simple sugar metabolism. Altogether, our results underscore the importance of considering the metabolic diversity of pathogens in the study of their evolution and the rational design of therapeutic interventions.}, } @article {pmid40013331, year = {2025}, author = {Standley, JM and Marcelino, J and Yu, F and Ellis, JD}, title = {A Meta-Omics Approach Using eDNA and eRNA for the Assessment of Biotic Communities Associated With Royal Jelly Produced by the Western Honey Bee (Apis mellifera L.).}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e14090}, doi = {10.1111/1755-0998.14090}, pmid = {40013331}, issn = {1755-0998}, support = {//University of Florida Entomology and Nematology Gahan Endowment/ ; //Clay County Beekeepers Association/ ; 1019945//USDA/NIFA Multi-State Project/ ; AP22PPQS&T00C189//USDA/APHIS Cooperative Agreement/ ; }, abstract = {Royal jelly (RJ) is a glandular secretion fed to developing honey bee larvae by adult worker bees. It is also a potential source of disease transmission in and between honey bee colonies. We endeavored to characterize the microbiome, virome, and other biota present in RJ via an integrated meta-omics approach. Using a magnetic beads-based extraction protocol, we identified eDNA and eRNA fragments from organisms of interest in RJ using high-throughput metagenomics (DNA-seq), metatranscriptomics (total RNA-seq), and parallel sequencing. This allowed us to enhance the detection of Operational Taxonomic Units (OTUs) undetectable by standard 'omics or amplicon protocols'. Using this integrated approach, we detected OTUs present in RJ from honey bee pests and pathogens, including Melissococcus plutonius, Paenibacillus larvae, Varroa destructor, V. jacobsoni, Aethina tumida, Galleria mellonella, Vairimorpha ceranae, Apis mellifera filamentous virus, Black queen cell virus, Acute bee paralysis virus, Sacbrood virus, Deformed wing virus, Israeli acute bee paralysis virus, Kashmir bee virus, and Slow bee paralysis virus, as well as multiple beneficial gut bacteria from the genera Lactobacillus, Actinobacteria, and Gluconobacter. The presence of DNA and RNA from these organisms does not conclusively indicate the presence of live organisms in the RJ, but it does suggest some exposure of the RJ to these organisms. The results present a comprehensive eDNA and eRNA microbial profile of RJ, demonstrating that our novel method is an effective and sensitive molecular tool for high-resolution metagenomic and metatranscriptomic profiling, and is of value for detection of pathogens of concern for the beekeeping industry.}, } @article {pmid40012972, year = {2025}, author = {Hu, M and Qiao, X and Zhang, J and Qin, D and Guo, S and Zhao, W and Wang, C}, title = {Case report: Clinical characteristics of anthrax meningoencephalitis: two cases diagnosed using metagenomic next-generation sequencing and literature review.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1539314}, pmid = {40012972}, issn = {2296-858X}, abstract = {PURPOSE: To explore the clinical features, diagnosis, treatment, and prognosis of anthrax meningoencephalitis.

METHODS: The clinical data of two cases of anthrax meningoencephalitis were summarized and the relevant literature was reviewed.

RESULTS: Both patients, who were farmers, had cutaneous lesions prior to the onset of meningoencephalitis. The clinical manifestations included fever (2/2), headache (2/2), stupor (2/2), meningeal signs (2/2), and lymph node enlargement (2/2). The CSF analysis showed erythrocytes, increased neutrophils, low glucose levels and high protein levels. CSF cytology revealed rod-shaped bacilli. Metagenomic next-generation sequencing of the CSF from both patients detected Bacillus anthracis. Additionally, cultures confirmed the presence of endogenous spores of macrobacteria. Brain imaging revealed subarachnoid hemorrhages and minimal cerebral edema. Despite aggressive antibiotic treatment, both patients died. Fifty-seven articles of the past 70 years were reviewed. There were 59 patients of anthrax meningoencephalitis in total, including 46 patients died. Stupor (42/46, 91.3% vs. 3/13, 46.2%, p = 0.001), agitation (15/46, 32.6% vs. 0/13, 0.0%, p = 0.043) and intracranial hemorrhage (37/46, 80.4% vs. 4/13, 30.8%, p = 0.002) were more common in the deceased group. Two types of bactericidal drugs or intrathecal injection drugs presented more often in the surviving group (10/13, 76.9% vs. 13/46, 28.3%, p = 0.001), whereas penicillin monotherapy presented more often in the deceased group (23/46, 50.0% vs. 2/13, 15.4%, p = 0.026).

CONCLUSION: Anthrax meningoencephalitis typically presents as a rapidly progressive bacterial meningoencephalitis. The occurrence of stupor, agitation and intracranial hemorrhage is possibly correlated with poor outcome. Two types of bactericidal drugs or intrathecal injection drugs are associated with better prognosis. Metagenomic next-generation sequencing can quickly and accurately detect B. anthracis in CSF.}, } @article {pmid40012786, year = {2025}, author = {Stein, M and Brinks, E and Habermann, D and Cho, GS and Franz, CMAP}, title = {Exogenous plasmid capture to characterize tetracycline-resistance plasmids in sprouts obtained from retail in Germany.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1538973}, pmid = {40012786}, issn = {1664-302X}, abstract = {This study aimed to characterize antibiotic-resistance plasmids present in microorganisms from sprout samples using exogenous plasmid capture. Fresh mung bean sprouts were predominantly colonized by bacteria from the phyla Proteobacteria and Bacteroidetes. To capture plasmids, a plasmid-free Escherichia (E.) coli CV601 strain, containing a green fluorescent protein gene for selection, was used as the recipient strain in exogenous plasmid capture experiments. Transconjugants were selected on media containing cefotaxime or tetracycline antibiotics. While no cefotaxime-resistant transconjugants were obtained, 40 tetracycline-resistant isolates were obtained and sequenced by Illumina NextSeq short read and Nanopore MinION long read sequencing. Sequences were assembled using Unicycler hybrid assembly. Most of the captured long plasmids carried either the tet(A) or tet(D) resistance gene, belonged to the IncFI or IncFII replicon types, and were predicted as conjugative. While the smaller plasmids contained the tet(A) tetracycline resistance gene as well as additional quinolone (qnrS1), sulfonamide (sul1) and trimethoprim (dfrA1) resistance genes, the larger plasmids only contained the tet(D) resistance gene. An exception was the largest 192 kbp plasmid isolated, which contained the tet(D), as well as sulfonamide (sul1) and streptomycin (aadA1) resistance genes. The smaller plasmid was isolated from different sprout samples more often and showed a 100% identity in size (71,155 bp), while the 180 kbp plasmids showed some smaller or larger differences (in size between 157,683 to 192,360 bp). This suggested that the plasmids obtained from the similar sprout production batches could be clonally related. Nanopore MinION based 16S metagenomics showed the presence of Enterobacter (En.) cloacae, En. ludwigii, En. kobei, Citrobacter (C.) werkmanii, C. freundii, Klebsiella (K.) oxytoca and K. pneumonia, which have previously been isolated from fresh produce in Germany. These bacteria may harbor antibiotic resistance genes on plasmids that could potentially be transferred to similar genera. This study demonstrated that bacteria present in sprouts may act as the donors of antibiotic resistance plasmids which can transfer resistance to other bacteria on this product via conjugation.}, } @article {pmid40012781, year = {2025}, author = {Zhao, B and Zhang, R and Jin, B and Yu, Z and Wen, W and Zhao, T and Quan, Y and Zhou, J}, title = {Sludge water: a potential pathway for the spread of antibiotic resistance and pathogenic bacteria from hospitals to the environment.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1492128}, pmid = {40012781}, issn = {1664-302X}, abstract = {Hospitals play an important role in the spread of antibiotic resistance genes (ARGs) and antimicrobial resistance (AMR). The ARGs present in hospital wastewater tend to accumulate in activated sludge, with different ARGs exhibiting varying migration rates. As a result, sludge water produced during the activated sludge treatment process may be a significant source of ARGs entering the environment. Despite this, research into the behavior of ARGs during sludge concentration and dewatering remains limited. This study hypothesizes that ARGs might exhibit new behaviors in sludge water during sludge concentration. Using metagenomic analysis, we explored the distribution and migration risks of ARGs and human pathogenic bacteria (HPB) in sludge water, comparing them with those in hospital wastewater. The findings reveal a strong correlation between ARGs in sludge water and hospital wastewater, with subtypes such as arlR, efpA, and tetR showing higher abundance in sludge water. Although the horizontal gene transfer potential of ARGs is greater in hospital wastewater than in sludge water, the resistance mechanisms and migration pathways are similar even when their HPB host associations differ. ARGs in both environments are primarily transmitted through coexisting mobile genetic elements (MGEs). This suggests that sludge water serves as a critical route for the release of hospital-derived ARGs into the environment, posing potential threats to public health and ecological safety.}, } @article {pmid40012777, year = {2025}, author = {Li, Y and Zhao, J}, title = {Xiaohua Funing decoction ameliorates non-alcoholic fatty liver disease by modulating the gut microbiota and bile acids.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1511885}, pmid = {40012777}, issn = {1664-302X}, abstract = {INTRODUCTION: The gut microbiota and bile acids (BAs) have emerged as factors involved in the development of non-alcoholic fatty liver disease (NAFLD). Xiaohua Funing decoction (XFD) is a traditional Chinese medicine formula used for the treatment of NAFLD. Previous studies have indicated that XFD protects liver function, but the underlying mechanism remains unclear.

METHODS: In this study, a Wistar rat model of NAFLD (Mod) was established via a high-fat diet. The effects of obeticholic acid (OCA) and XFD on Mod rats were subsequently evaluated. Wistar rats in the control (Con) group were fed a standard diet. There were eight rats in each group, and the treatment lasted for 12 weeks. Furthermore, metagenomic sequencing and BA metabolomic analyses were performed.

RESULTS: Compared to the Con group, the Mod group presented significant differences in body and liver weights; serum total cholesterol (TC) and triglyceride (TG) levels; and liver TG, TC, and bile salt hydrolase levels (p < 0.05 or p < 0.01). Importantly, OCA and XFD administration normalized these indicators (p < 0.05 or p < 0.01). Pathology of the liver and white fat steatosis was observed in the Mod group, but steatosis was significantly alleviated in the OCA and XFD groups (p < 0.05 or p < 0.01). The abundances of Bacteroidales_bacterium, Prevotella_sp., bacterium_0.1xD8-71, and unclassified_g_Turicibacter in the Mod group were significantly different from those in the Con group (p < 0.05 or p < 0.01), whereas the abundance of Bacteroidales_bacterium was greater in the XFD group. A total of 17, 24, and 24 differentially abundant BAs were detected in the feces, liver, and serum samples from the Mod and Con groups, respectively (p < 0.05 or p < 0.01). In the feces, liver, and serum, XFD normalized the levels of 16, 23, and 14 BAs, respectively, including glycochenodeoxycholic acid, deoxycholic acid, murideoxycholic acid, lithocholic acid, 23-nordeoxycholic acid, and 3β-ursodeoxycholic acid. In addition, glycochenodeoxycholic acid was identified as a potential biomarker of NAFLD.

DISCUSSION: In summary, our experiments revealed that XFD regulates the gut microbiota and BAs, providing beneficial effects on liver lipid accumulation in NAFLD.}, } @article {pmid40012717, year = {2025}, author = {Li, YI and Pagulayan, K and Rau, H and Hendrickson, R and Schindler, AG}, title = {Gut Microbial Composition Is Associated with Symptom Self-Report in Trauma-Exposed Iraq and Afghanistan Veterans.}, journal = {Neurotrauma reports}, volume = {6}, number = {1}, pages = {1-12}, pmid = {40012717}, issn = {2689-288X}, abstract = {Iraq and Afghanistan War-era Veterans are at elevated risk for physical injuries and psychiatric illnesses, in particular the polytrauma triad of mild traumatic brain injury (mTBI), post-traumatic stress disorder (PTSD), and chronic pain. The gut microbiome has been implicated in modulation of critical processes beyond digestion, including immune system functioning and stress responsivity, and may be an important factor in understanding physical and mental health outcomes following deployment and trauma exposure. However, minimal research to date has sought to characterize gut microbiome composition in this population. Male Veterans of the conflicts in Iraq and Afghanistan who previously completed a Veterans Affairs' comprehensive TBI evaluation were enrolled in the current study. Participants completed self-report measures of PTSD symptom severity, pain intensity and interference, fatigue, cognitive symptoms, substance use, and sleep quality. They also submitted fecal samples, and metagenomic sequencing was used to calculate alpha and beta diversity and taxonomic microbial composition. Associations between microbiome data and clinical variables were then examined. Alpha and beta diversity measures were not significantly correlated with clinical outcomes. Fatigue, post-concussive symptoms, executive function symptoms, and cannabis use were associated with differences in gut microbial composition, specifically Verrucomicrobiota. Together, results suggest that altered gut microbiome composition is associated with psychiatric and cognitive symptoms in Veterans and highlight a potential new therapeutic target of interest. Future research is needed to examine whether probiotic treatment is effective for reducing symptoms common in this clinical population.}, } @article {pmid40011862, year = {2025}, author = {Blomström, AL and Källse, A and Riihimäki, M}, title = {Detection and genetic characterization of equine viruses in Sweden using viral metagenomics.}, journal = {BMC veterinary research}, volume = {21}, number = {1}, pages = {119}, pmid = {40011862}, issn = {1746-6148}, support = {H-20-47-555//The Swedish-Norwegian Foundation for Equine Research/ ; H-20-47-555//The Swedish-Norwegian Foundation for Equine Research/ ; }, mesh = {Animals ; Horses ; Sweden/epidemiology ; *Horse Diseases/virology/epidemiology ; *Metagenomics ; *Virus Diseases/veterinary/virology/epidemiology ; Viruses/classification/isolation & purification/genetics ; Genome, Viral ; }, abstract = {BACKGROUND: Viral infections pose a significant challenge to the equine population, compromising welfare and causing substantial economic losses for the global equine industry. While numerous equine viral pathogens have been identified, many suspected viral infections remain undiagnosed. This highlights the need for further identification and characterization of viruses circulating within the equine population. In this study, we utilized viral metagenomics to investigate viruses present in serum samples and nasal swabs collected from horses in Sweden. The primary focus was on horses presenting with fever, although control horses were also included for comparison.

RESULT: The viral metagenomic analysis identified several viruses in the investigated samples. Among nasal swabs, the majority of the viral reads were classified as various equine herpesvirues (EHVs), mainly EHV-2 and EHV-5. Other viruses in nasal swabs include but are not limited to EHV-4, Torque teno equus virus 1 (TTeqV1) and equine copiparvovirus (eqCopV). Both TTeqV1 and eqCopV were also detected in the serum samples together with equine circovirus and equine pegivirus. A number of the detected viruses were further genetically characterized and were shown to display high sequence similarity to viruses from the US and/or China. qPCR screening of a selected number of the detected viruses revealed a rather low detection rate (1.6%-9.4%) in individual horses.

CONCLUSION: This study identified several viruses that circulate in the horse population in Sweden, some of which have not been previously detected in Sweden or Europe. Furthermore, the complete or nearly complete genomes of several of these viruses have been genetically characterized. These new data provide a valuable foundation for developing improved detection assays and conducting larger prevalence studies to assess the potential impact of these viruses on the equine population. Such efforts could ultimately contribute to enhanced equine welfare.}, } @article {pmid40011766, year = {2025}, author = {Proctor, DM and Sansom, SE and Deming, C and Conlan, S and Blaustein, RA and Atkins, TK and , and Dangana, T and Fukuda, C and Thotapalli, L and Kong, HH and Lin, MY and Hayden, MK and Segre, JA}, title = {Clonal Candida auris and ESKAPE pathogens on the skin of residents of nursing homes.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {40011766}, issn = {1476-4687}, abstract = {Antimicrobial resistance is a public health threat associated with increased morbidity, mortality and financial burden in nursing homes and other healthcare settings[1]. Residents of nursing homes are at increased risk of pathogen colonization and infection owing to antimicrobial-resistant bacteria and fungi. Nursing homes act as reservoirs, amplifiers and disseminators of antimicrobial resistance in healthcare networks and across geographical regions[2]. Here we investigate the genomic epidemiology of the emerging, multidrug-resistant human fungal pathogen Candida auris in a ventilator-capable nursing home. Coupling strain-resolved metagenomics with isolate sequencing, we report skin colonization and clonal spread of C. auris on the skin of nursing home residents and throughout a metropolitan region. We also report that most Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Entobacter species (ESKAPE) pathogens and other high-priority pathogens (including Escherichia coli, Providencia stuartii, Proteus mirabilis and Morganella morganii) are shared in a nursing home. Integrating microbiome and clinical microbiology data, we detect carbapenemase genes at multiple skin sites on residents identified as carriers of these genes. We analyse publicly available shotgun metagenomic samples (stool and skin) collected from residents with varying medical conditions living in seven other nursing homes and provide additional evidence of previously unappreciated bacterial strain sharing. Taken together, our data suggest that skin is a reservoir for colonization by C. auris and ESKAPE pathogens and their associated antimicrobial-resistance genes.}, } @article {pmid40011381, year = {2025}, author = {Esquivel-López, A and Rocha-Mendoza, D and Serrano-Maldonado, CE and Escobar-Zepeda, A and Quirasco, M}, title = {Heterologous Expression of Bacteriocins from the Metagenome Mining of Cotija Cheese.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {40011381}, issn = {1867-1314}, support = {IN222717//Universidad Nacional Autónoma de México-Programa de Apoyo a Proyectos de Investigación e Innovación Tecnológica (UNAM-PAPIIT)/ ; IN222717//Universidad Nacional Autónoma de México-Programa de Apoyo a Proyectos de Investigación e Innovación Tecnológica (UNAM-PAPIIT)/ ; }, abstract = {Bacteriocins are a heterologous group of ribosomal peptides with antibacterial activity. They are of interest to the pharmaceutical and food industries due to their potential to fight antibiotic-resistant pathogens and improve microbial food safety, respectively. Metagenomic data mining for antibacterial activity is valuable for the information it provides from unstudied genomic sequences. Furthermore, the higher biosynthetic yield obtained by the heterologous expression of putative bacteriocins allows their subsequent purification and characterization. This work aimed to express antilisterial bacteriocins in Escherichia coli after obtaining their gene sequences by in silico mining the bacterial metagenome of Cotija cheese. This artisanal Mexican cheese is manufactured with unpasteurized milk and ripens for at least 3 months. Analyzing the Cotija cheese bacterial shotgun metagenome allowed us to select two sequences (QC1 and QC2) encoding novel Class IId bacteriocins belonging to the lactococcin family. These genes were expressed as (His)6-fusion proteins in E. coli BL21 (DE3) and showed high antimicrobial activity against Listeria monocytogenes, with a minimum inhibitory concentration of 78 µg/mL. QC1 and QC2 were tested against several pathogenic bacteria and showed activity exclusively against L. monocytogenes. QC2 has a novel sequence that showed no matches against the UniProt database. It was purified by Ni[2+] affinity chromatography and retained its activity after heating at 70 °C for 30 min. As the sequences were obtained by genomic mining on a fermented food metagenome, QC1 and QC2 have potential applications as sanitizers in industrial food facilities where L. monocytogenes contamination is the most prevalent.}, } @article {pmid40010603, year = {2025}, author = {Han, B and Shi, Y and Zhang, P and Liu, Y and Xu, M and Xia, J and Li, J and Li, Y and Zhang, M and Wang, J and Ren, Z and Yang, F and Chen, Y and Feng, G}, title = {Clinical Application Value of Metagenomic Next-generation Sequencing at Perioperative Period in Patients with Central Nervous System Infections in Neurosurgical Intensive Care Unit.}, journal = {World neurosurgery}, volume = {}, number = {}, pages = {123824}, doi = {10.1016/j.wneu.2025.123824}, pmid = {40010603}, issn = {1878-8769}, abstract = {OBJECTIVE: This study aims to evaluate the clinical utility of metagenomic next-generation sequencing (mNGS) for diagnosing central nervous system infections (CNSIs) during the perioperative period in neurosurgical intensive care unit (ICU) patients.

METHODS: In this prospective study, we included patients suspected of CNSIs during the perioperative period who were admitted to the Neurosurgical-ICU at Henan Provincial People's Hospital. Clinical samples were tested using both mNGS and conventional pathogen culture methods. Based on comprehensive clinical diagnoses, patients were categorized into the CNSIs and non-CNSIs groups. The diagnostic performance of mNGS was compared with traditional methods, including time to pathogen detection and evaluation of optimal testing conditions. Additionally, the study assessed whether antibiotic resistance genes detected by mNGS could predict drug resistance phenotypes.

RESULTS: Between January 2022 and December 2023, 116 patients were enrolled, including 48 in the CNSIs group and 30 in the non-CNSIs group. mNGS identified a greater variety and quantity of pathogens compared to conventional methods. First, mNGS results were consistent with traditional culture in five cases. mNGS exhibited superior sensitivity (85.42% vs. 10.42%) and a higher negative predictive value (80.00% vs. 40.10%) compared to traditional cultures. Second, only 8.33% of CNSIs patients showed identical pathogens in both cerebrospinal fluid (CSF) and blood samples. Third, 28.6% of CSF samples with an mNGS detection interval of over seven days showed complete pathogen consistency, while 60% of samples with a detection interval of less than three days were consistent. Moreover, the antibiotic resistance genes detected by mNGS largely corresponded with the resistance phenotypes identified by antibiotic susceptibility testing.

CONCLUSION: To sum up, mNGS offers excellent diagnostic accuracy and significant clinical value in CNSIs diagnosis during the perioperative period in the neurosurgical-ICU, complementing traditional culture methods effectively.}, } @article {pmid40010597, year = {2025}, author = {Wang, X and Lin, Y and Li, S and Wang, J and Li, X and Zhang, D and Duan, D and Shao, Z}, title = {Metagenomic analysis reveals the composition and sources of antibiotic resistance genes in coastal water ecosystems of the Yellow Sea and Yangtze River Delta.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {125923}, doi = {10.1016/j.envpol.2025.125923}, pmid = {40010597}, issn = {1873-6424}, abstract = {The rapid development of coastal areas has raised concerns about marine environmental pollution. In this study, metagenomics was employed to investigate antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and bacterial communities in the Yellow Sea and Yangtze River Delta in China. Multidrug resistance genes were the most abundant ARGs in these regions. Transposons and insertion_element_IS91 were the dominant MGEs, closely related to the horizontal gene transfer of ARGs. Temperature, dissolved oxygen, pH, and depth were identified as important environmental factors influencing the distribution of ARGs in seawater. Oil, agriculture, animal husbandry, and wastewater treatment plants are likely the primary sources of ARGs. From the perspective of ARG control, bacterial communities contributed the most to the development of the resistome and may carry ARGs, spreading from the Yangtze River Delta to the Yellow Sea along ocean currents. A comparison with Tara Oceans datasets revealed that the dominant ARG types and bacterial genera in coastal waters were consistent with global characteristics, with variations in ARG subtypes. This study expands knowledge on the distribution patterns of ARGs at an offshore scale and provides a reference for the prevention and control of resistant gene pollution in the Yellow Sea and Yangtze River Delta.}, } @article {pmid40010587, year = {2025}, author = {Lai, Y and Qu, Y and Liu, H and Yue, Y and Cui, X and Wang, X and Wang, C and Zhang, L and Shi, Y and Huo, M}, title = {Anomalous reduced sequence: Potential hazards of disinfection byproduct chlorate in reclaimed water.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {125924}, doi = {10.1016/j.envpol.2025.125924}, pmid = {40010587}, issn = {1873-6424}, abstract = {Chlorine dioxide is used in reclaimed water treatment technologies and generates the inorganic disinfection byproduct (DBP) chlorate (ClO3[-]) during disinfection. Currently, water quality standards for reclaimed water do not specify concentration limits for ClO3[-]. This DBP can infiltrate the soil along with reclaimed water. Ion concentrations are determined by ion chromatography. Metagenomics is used to measure and analyze the genomes of all microorganisms in soil. Results indicate that ClO3[-] remains stable in groundwater, and despite its higher redox potential (+1.21 V), it is not biologically reduced. Instead, NO3[-] with a lower redox potential (+0.94 V), undergoes significant biological reduction. Concurrently, microbial oxidative stress levels increase markedly by 133.77%, significantly stimulating the production of extracellular proteins by over 20.13% and polysaccharides by over 9.68%. Additionally, slight changes in microbial community structure are observed, including the elimination of microorganisms such as Chloroflexota, a slight decrease in species richness, and a minor increase in the regulation of genes related to amino acid metabolism by 2.56%. In terms of microbial ecological risks, ClO3[-] significantly upregulates microbial resistance gene levels by 16.15%, with microorganisms adopting two main strategies to mitigate ClO3[-] toxicity: altering target proteins or nucleic acids (51.70%) and efflux (43.41%). The relative abundance of efflux-related genes increases by 44.72%. Pathogenic bacteria show significant changes in relative abundance (over 156.52%) and community structure, with Acinetobacter junii increasing by 222.22% and Acinetobacter baumannii decreasing by 63.20%. In summary, ClO3[-] infiltrating with reclaimed water may potentially contaminate the groundwater environment. This study provides a comprehensive understanding of the interactions between ClO3[-] and soil microorganisms.}, } @article {pmid38961050, year = {2025}, author = {Bandeira, L and Faria, C and Cavalcante, F and Mesquita, A and Martins, C and Martins, S}, title = {Metabarcoding expands knowledge on diversity and ecology of rare actinobacteria in the Brazilian Cerrado.}, journal = {Folia microbiologica}, volume = {70}, number = {1}, pages = {159-175}, pmid = {38961050}, issn = {1874-9356}, support = {421350/2017-2//Instituto Chico Mendes de Conservação da Biodiversidade/ ; 18/2017//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, mesh = {*Actinobacteria/chemistry/classification/genetics/isolation & purification ; DNA Barcoding, Taxonomic ; RNA, Ribosomal, 16S/analysis ; Parks, Recreational ; Brazil ; *Soil Microbiology ; Biodiversity ; Soil/chemistry ; Metagenome ; }, abstract = {Rare and unknown actinobacteria from unexplored environments have the potential to produce new bioactive molecules. This study aimed to use 16 s rRNA metabarcoding to determine the composition of the actinobacterial community, particularly focusing on rare and undescribed species, in a nature reserve within the Brazilian Cerrado called Sete Cidades National Park. Since this is an inaccessible area without due legal authorization, it is understudied, and, therefore, its diversity and biotechnological potential are not yet fully understood, and it may harbor species with groundbreaking genetic potential. In total, 543 operational taxonomic units (OTUs) across 14 phyla were detected, with Actinobacteria (41.2%), Proteobacteria (26.5%), and Acidobacteria (14.3%) being the most abundant. Within Actinobacteria, 107 OTUs were found, primarily from the families Mycobacteriaceae, Pseudonocardiaceae, and Streptomycetaceae. Mycobacterium and Streptomyces were the predominant genera across all samples. Seventeen rare OTUs with relative abundance < 0.1% were identified, with 82.3% found in only one sample yet 25.5% detected in all units. Notable rare and transient genera included Salinibacterium, Nocardia, Actinomycetospora_01, Saccharopolyspora, Sporichthya, and Nonomuraea. The high diversity and distribution of Actinobacteria OTUs indicate the area's potential for discovering new rare species. Intensified prospection on underexplored environments and characterization of their actinobacterial diversity could lead to the discovery of new species capable of generating innovative natural products.}, } @article {pmid40008244, year = {2025}, author = {Xu, LL and McIlroy, SE and Ni, Y and Guibert, I and Chen, J and Rocha, U and Baker, DM and Panagiotou, G}, title = {Chemical pollution drives taxonomic and functional shifts in marine sediment microbiome, influencing benthic metazoans.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycae141}, pmid = {40008244}, issn = {2730-6151}, abstract = {Microbial communities in marine sediments contribute significantly to the overall health and resiliency of marine ecosystems. However, increased human disturbance undermines biodiversity and, hence, natural functionality provided by marine sediments. Here, through a deep shotgun metagenomics sequencing of the sediment microbiome and COI metabarcoding of benthic metazoans, we demonstrate that >50% of the microorganisms' and metazoan's taxonomic variation can be explained by specific chemical pollution indices. Interestingly, there was a significant correlation between the similarity in microbiome communities' taxonomical and functional attributes and the similarity of benthic metazoans community composition. Furthermore, mediation analysis was conducted to evaluate the microbiome-mediated indirect effect, suggesting that microbial species and functions accounted for 36% and 26%, respectively, of the total effect of pollution on the benthic metazoans. Our study introduces a multi-level perspective for future studies in urbanized coastal areas to explore marine ecosystems, revealing the impact of pollution stress on microbiome communities and their critical biogeochemical functions, which in turn may influence macrofaunal composition.}, } @article {pmid40007957, year = {2025}, author = {Wang, J and Lv, G and Yang, J and He, X and Wang, H and Li, W}, title = {Impacts of plant root traits and microbial functional attributes on soil respiration components in the desert-oasis ecotone.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1511277}, pmid = {40007957}, issn = {1664-462X}, abstract = {Dividing soil respiration (Rs) into autotrophic respiration (Ra) and heterotrophic respiration (Rh) represents a pivotal step in deciphering how Rs responds to environmental perturbations. Nevertheless, in arid ecosystems beset by environmental stress, the partitioning of Rs and the underlying mechanisms through which microbial and root traits govern the distinct components remain poorly understood. This study was strategically designed to investigate Rs and its components (Ra and Rh), soil properties, and root traits within the desert-oasis ecotone (encompassing the river bank, transitional zone, and desert margin) of northwest China. Employing metagenomics, we quantitatively characterized microbial taxonomic attributes (i.e., taxonomic composition) and functional attributes (specifically, functional genes implicated in microbial carbon metabolism). Field measurements during the growing season of 2019 unveiled a pronounced decline in soil respiration rates along the environmental gradient from the river bank to the desert margin. The mean soil respiration rate was recorded as 1.82 ± 0.41 μmol m[-2] s[-1] at the river bank, 0.49 ± 0.15 μmol m[-2] s[-1] in the transitional zone, and a meager 0.45 ± 0.12 μmol m[-2] s[-1] in the desert margin. Concomitantly, the Ra and Rh components exhibited a similar trend throughout the study period, with Rh emerging as the dominant driver of Rs. Utilizing random forest modeling, we unearthed significant associations between microbial taxonomic and functional features and Rs components. Notably, both Ra and Rh displayed robust positive correlations with the abundance of phosphatidylinositol glycan A, a key player in microbial carbon metabolism. Partial least squares path modeling further elucidated that soil properties and microbial functions exerted direct and positive influences on both Ra and Rh, whereas taxonomic features failed to register a significant impact. When considering the combined effects of biotic and abiotic factors, microbial functional attributes emerged as the linchpin in dictating Rs composition. Collectively, these findings suggest that a trait-based approach holds great promise in more effectively revealing the response mechanisms of Rs composition to environmental changes, thereby offering novel vistas for future investigations into carbon cycling in terrestrial soils.}, } @article {pmid40007795, year = {2025}, author = {Li, J and Shi, Y and Hu, L and He, W and Li, Y}, title = {Assessing Gut Microbiome Alterations in Children With Allergic Rhinitis: Associations With Allergen-Specific IgE Levels and Sensitization Patterns.}, journal = {Journal of asthma and allergy}, volume = {18}, number = {}, pages = {269-281}, pmid = {40007795}, issn = {1178-6965}, abstract = {BACKGROUND: The relationship between gut microbiota composition and allergen exposure in children with allergic rhinitis (AR) remains insufficiently explored, particularly concerning variations in gut microbiota at different allergen-specific IgE (sIgE) levels and the distinction between monosensitization and polysensitization to allergens.

METHODS: We employed metagenomic shotgun sequencing to compare the fecal microbiota of 50 healthy controls (HC) to 88 children with AR induced by house dust mites (HDM-AR). We further examined differences in gut microbiota among HDM-AR subgroups with extremely high house dust mite-sIgE (EH-HDM), high HDM-sIgE (H-HDM), as well as between monosensitized (mono-HDM) and polysensitized (poly-HDM) individuals.

RESULTS: While no significant differences in overall gut microbiome diversity were observed between the HC and HDM-AR groups, a notable increase in the relative abundance of Streptococcus sanguinis within the genus was identified in children with AR. Further analysis revealed a significant enrichment of the Streptococcus genus in the EH-HDM group, particularly highlighting an increased relative abundance of the Streptococcus salivarius. Functional gene analysis via KEGG pathways indicated substantial enrichment in the salivary secretion pathway. Additionally, in comparisons among the HC, mono-HDM, and poly-HDM groups, Streptococcus salivarius emerged as the key differential species, showing a marked increase in the mono-HDM group.

CONCLUSION: Our study suggests that specific bacterial strains, particularly Streptococcus salivarius, may be potential biomarkers for assessing varying degrees and patterns of HDM sensitization. These findings open the avenues for developing targeted interventions aimed at mitigating the pathophysiology of AR.}, } @article {pmid40007605, year = {2025}, author = {Buffet-Bataillon, S and Durão, G and Le Huërou-Luron, I and Rué, O and Le Cunff, Y and Cattoir, V and Bouguen, G}, title = {Gut microbiota dysfunction in Crohn's disease.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1540352}, pmid = {40007605}, issn = {2235-2988}, mesh = {*Crohn Disease/microbiology ; Humans ; *Gastrointestinal Microbiome ; *RNA, Ribosomal, 16S/genetics ; *Metagenomics ; *Feces/microbiology ; Adult ; Female ; Male ; Virulence Factors/genetics ; Bacteria/classification/genetics/isolation & purification ; Oxidative Stress ; Dysbiosis/microbiology ; Middle Aged ; Young Adult ; }, abstract = {INTRODUCTION: Crohn's disease (CD) results from alterations in the gut microbiota and the immune system. However, the exact metabolic dysfunctions of the gut microbiota during CD are still unclear. Here, we investigated metagenomic functions using PICRUSt2 during the course of CD to better understand microbiota-related disease mechanisms and provide new insights for novel therapeutic strategies.

METHODS: We performed 16S rRNA-based microbial profiling of 567 faecal samples collected from a cohort of 383 CD patients, including 291 remissions (CR), 177 mild-moderate (CM) and 99 severe (CS) disease states. Gene and pathway composition was assessed using PICRUSt2 analyses of 16S data.

RESULTS: As expected, changes in alpha and beta diversity, in interaction networks and increases in Proteobacteria abundance were associated with disease severity. However, microbial function was more consistently disrupted than composition from CR, to CM and then to CS. Major shifts in oxidative stress pathways and reduced carbohydrate and amino acid metabolism in favour of nutrient transport were identified in CS compared to CR. Virulence factors involved in host invasion, host evasion and inflammation were also increased in CS.

CONCLUSIONS: This functional metagenomic information provides new insights into community-wide microbial processes and pathways associated with CD pathogenesis. This study paves the way for new advanced strategies to rebalance gut microbiota and/or eliminate oxidative stress, and biofilm to downregulate gut inflammation.}, } @article {pmid40007035, year = {2025}, author = {De Koch, MD and Sweeney, N and Taylor, JE and Lucas, F and Ratheesh, NK and Lamb, SK and Miller, J and Kraberger, S and Varsani, A}, title = {Diverse Anelloviruses Identified in Leporids from Arizona (USA).}, journal = {Viruses}, volume = {17}, number = {2}, pages = {}, doi = {10.3390/v17020280}, pmid = {40007035}, issn = {1999-4915}, mesh = {Animals ; Arizona ; *Genome, Viral ; *Phylogeny ; *Anelloviridae/genetics/classification/isolation & purification ; Host Specificity ; Metagenomics ; Hares/virology ; Genome, Mitochondrial ; Ticks/virology ; Open Reading Frames ; }, abstract = {The communities of viruses studied in rabbits and hares (family Leporidae) have largely been those with clinical significance. Consequently, less is known broadly about other leporid viruses. Anelloviruses (family Anelloviridae) are likely commensal members of the single-stranded DNA virome in mammals. Here, we employ a viral metagenomic approach to identify DNA viruses of leporids and the ticks feeding on them in Arizona, USA. We characterize five complete anellovirus genomes from four leporids belonging to the black-tailed jackrabbit (Lepus californicus, n = 3) and the desert cottontail (Sylvilagus audubonii, n = 1). All five anellovirus genomes share > 69% orf1 gene pairwise nucleotide identity with those found in Iberian hares and thus belong to the species Aleptorquevirus lepor1. Accordingly, we expand the known host range of this anellovirus species to include Iberian hares in Europe and black-tailed jackrabbit and desert cottontail in the USA. We also sequenced the complete mitochondrial genomes of the four leporid hosts (Sylvilagus audubonii, n = 1; Lepus californicus, n = 3) and two ticks (Dermacentor parumapertus, n = 2) found feeding on two black-tailed jackrabbits. These results expand the diversity of anelloviruses in leporids while giving insight into the host genetics of leporids and ticks in Arizona, USA.}, } @article {pmid40006931, year = {2025}, author = {Sarker, S and Talukder, S and Athukorala, A and Whiteley, PL}, title = {The Spleen Virome of Australia's Endemic Platypus Is Dominated by Highly Diverse Papillomaviruses.}, journal = {Viruses}, volume = {17}, number = {2}, pages = {}, doi = {10.3390/v17020176}, pmid = {40006931}, issn = {1999-4915}, mesh = {Animals ; *Phylogeny ; *Platypus/virology ; *Virome ; *Genome, Viral ; Australia ; *Papillomaviridae/genetics/classification/isolation & purification ; *Spleen/virology ; High-Throughput Nucleotide Sequencing ; DNA, Viral/genetics ; Genetic Variation ; }, abstract = {The platypus (Ornithorhynchus anatinus), a unique monotreme, represents a pivotal point in mammalian evolution with its distinctive traits, such as electroreception and venom production. Despite its evolutionary significance, the viral diversity within platypuses remains poorly understood. This study employed next-generation sequencing to investigate the virome of the dead platypuses, uncovering a range of novel and divergent viruses. Among the identified viruses were four complete genomes of papillomaviruses (OaPV1-4) exhibiting substantial divergence from known strains, suggesting a novel genus within the subfamily Secondpapillomavirinae. Additionally, five novel parvoviruses were detected, including two with complete genomes, highlighting the complex viral ecosystem of the platypus. Phylogenetic analysis placed these viruses in unique evolutionary branches, further demonstrating the platypus's evolutionary significance. A circular DNA virus, a tombus-like virus, and a nodamuvirus were also identified, expanding the understanding of viral diversity in monotremes. These findings offer crucial insights into viral evolution in one of the most unique mammalian lineages, emphasising the need for further exploration to assess ecological and pathological impacts on platypus populations.}, } @article {pmid40006910, year = {2025}, author = {Haagmans, R and Charity, OJ and Baker, D and Telatin, A and Savva, GM and Adriaenssens, EM and Powell, PP and Carding, SR}, title = {Assessing Bias and Reproducibility of Viral Metagenomics Methods for the Combined Detection of Faecal RNA and DNA Viruses.}, journal = {Viruses}, volume = {17}, number = {2}, pages = {}, doi = {10.3390/v17020155}, pmid = {40006910}, issn = {1999-4915}, support = {BB/R012490/1//BBSRC/ ; BB/X011054/1//BBSRC/ ; BB/X011054/1//BBSRC/ ; BB/X011011/1//BBSRC/ ; BB/CCG1860/1//BBSRC/ ; Project Grant//ME Research UK/ ; PhD studentship//Invest in ME Research/ ; PhD studentship//UEA Faculty Medicine and Health/ ; }, mesh = {*Metagenomics/methods ; *Feces/virology ; Humans ; *DNA Viruses/genetics/classification/isolation & purification ; Reproducibility of Results ; *RNA Viruses/genetics/isolation & purification/classification ; *Computational Biology/methods ; High-Throughput Nucleotide Sequencing/methods ; RNA, Viral/genetics ; Nucleic Acid Amplification Techniques/methods ; Genome, Viral ; }, abstract = {Whole transcriptome amplification (WTA2) and sequence-independent single primer amplification (SISPA) are two widely used methods for combined metagenomic sequencing of RNA and DNA viruses. However, information on the reproducibility and bias of these methods on diverse viruses in faecal samples is currently lacking. A mock community (MC) of diverse viruses was developed and used to spike faecal samples at different concentrations. Virus-like particles (VLPs) were extracted, nucleic acid isolated, reverse-transcribed, and PCR amplified using either WTA2 or SISPA and sequenced for metagenomic analysis. A bioinformatics pipeline measured the recovery of MC viruses in replicates of faecal samples from three human donors, analysing the consistency of viral abundance measures and taxonomy. Viruses had different recovery levels with VLP extraction introducing variability between replicates, while WTA2 and SISPA produced comparable results. In comparing WTA2- and SISPA-generated libraries, WTA2 gave more uniform coverage depth profiles and improved assembly quality and virus identification. SISPA produced more consistent abundance, with a 50% difference between replicates occurring in ~20% and ~10% of sequences for WTA2 and SISPA, respectively. In conclusion, a bioinformatics pipeline has been developed to assess the methodological variability and bias of WTA2 and SISPA, demonstrating higher sensitivity with WTA2 and higher consistency with SISPA.}, } @article {pmid40005922, year = {2025}, author = {Chrzastek, K and Seal, BS and Kulkarni, A and Kapczynski, DR}, title = {Whole-Genome Shotgun Sequencing from Chicken Clinical Tracheal Samples for Bacterial and Novel Bacteriophage Identification.}, journal = {Veterinary sciences}, volume = {12}, number = {2}, pages = {}, doi = {10.3390/vetsci12020162}, pmid = {40005922}, issn = {2306-7381}, abstract = {A whole-genome shotgun sequencing (sWGS) approach was applied to chicken clinical tracheal swab samples during metagenomics investigations to identify possible microorganisms among poultry with respiratory diseases. After applying shotgun sequencing, Ornithobacterium rhinotracheale (ORT) and a putative prophage candidate were found in one of the swab samples. A multi-locus sequence typing (MLST) scheme of the ORT genome involved the adk, aroE, fumC, gdhA, pgi, and pmi genes. Antibiotic resistant analysis demonstrated tetracycline-resistan t ribosomal protection protein, tetQ, the aminoglycoside-(3)-acetyltransferase IV gene, aminoglycoside antibiotic inactivation and macrolide resistance, and the ermX gene in the ORT genome. A putative prophage candidate was predicted using Prophage Hunter and PHAST, while BLAST analyses were utilized to identify genes encoding bacteriophage proteins. Interestingly, genes encoding endolysins were detected in bacteriophage genomes. The gene products encoded in the prophage sequence were most closely related to bacteriophages in the N4-like family among the Authographiviridae in the Caudovirales. This study demonstrates the potential of sWGS for the rapid detection and characterization of etiologic agents found in clinical samples.}, } @article {pmid40005859, year = {2025}, author = {Chen, H and Qing, Y and Xu, L and Zhu, L and Yin, W and Li, S and Kuang, S and Zhou, Y and Xu, Z}, title = {Prevalence and Molecular Characterization of Porcine Parvovirus 2 in Southwest China During 2020-2023.}, journal = {Veterinary sciences}, volume = {12}, number = {2}, pages = {}, doi = {10.3390/vetsci12020099}, pmid = {40005859}, issn = {2306-7381}, abstract = {Porcine parvovirus (PPV) is a non-enveloped, single-stranded linear DNA virus that induces reproductive disorders in sows, particularly abortions in primiparous sows. This study investigated the prevalence of PPV in the southwestern region and conducted molecular characterization of PPV strains. An epidemiological survey was conducted on 1534 aborted fetuses from the southwestern region between 2020 and 2023, revealing an abortion rate of 3.00% due to PPV2, with the highest rate of 3.77% in Sichuan. Additionally, 2973 blood samples from sows were tested using ELISA, showing a PPV2 antibody positivity rate of 73.03% to 90%. Through shotgun metagenomics, PPV2 SC2020 was identified in aborted fetal samples from a pig farm in Pengzhou, Sichuan. PCR sequencing analysis yielded seven PPV2 genomic sequences, and the phylogenetic analysis of eight PPV2 strains with thirty reference strains showed distinct evolutionary branches. The virus was successfully isolated from PPV2-positive samples, and the phylogenetic analysis of PPV2 SC2020 revealed ORF1 gene homology of 94.9% to 99.3% and the ORF2 gene homology of 93.1% to 98.0%, with 34 reference strains. Homologous recombination analysis indicated that SC2020 is a recombinant strain of HeB03 and S1.}, } @article {pmid40005817, year = {2025}, author = {Tavano, F and Napoli, A and Gioffreda, D and Palmieri, O and Latiano, T and Tardio, M and di Mola, FF and Grottola, T and Büchler, MW and Gentile, M and Latiano, A and Mazza, T and Perri, F}, title = {Could the Microbial Profiling of Normal Pancreatic Tissue from Healthy Organ Donors Contribute to Understanding the Intratumoral Microbiota Signature in Pancreatic Ductal Adenocarcinoma?.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020452}, pmid = {40005817}, issn = {2076-2607}, support = {Ricerca Corrente program 2022-2024//Italian Minister of Health/ ; }, abstract = {Pancreatic ductal adenocarcinoma (PDAC) is associated with intratumoral microbiota changes. However, defining the normal pancreatic microbial composition remains a challenge. Herein, we tested the hypothesis that the microbial profiling of normal pancreatic tissue from healthy organ donors (HC) could help in determining the signature of microbiota in PDAC. Matched pairs of tumor and normal tissues from PDAC patients (n = 32) and normal pancreatic tissues from HC (n = 17) were analyzed by 16S rRNA gene sequencing. Dissimilarities in all the beta metrics emerged in both normal samples and tumor samples, compared to HC (Bray-Curtis dissimilarity and Jaccard distance: p = 0.002; weighted UniFrac distances: p = 0.42 and p = 0.012, respectively; unweighted UniFrac distance: p = 0.009); a trend toward a lower Faith's phylogenetic distance was found at the tumor level vs. HC (p = 0.08). Within PDAC, a lower Faith's phylogenetic distance (p = 0.003) and a significant unweighted UniFrac distance (p = 0.024) were observed in tumor samples vs. normal samples. We noted the presence of a decreased abundance of bacteria with potential beneficial effects (Jeotgalicoccus) and anticancer activity (Acinetobacter_guillouiae) in PDAC vs. HC; bacteria involved in immune homeostasis and suppression of tumor progression (Streptococcus_salivarius, Sphingomonas) were reduced, and those implicated in tumor initiation and development (Methylobacterium-Methylorubrum, g_Delftia) were enhanced in tumor samples vs. normal samples. Metagenomic functions involved in fatty acid synthesis were reduced in normal samples compared to HC, while peptidoglycan biosynthesis IV and L-rhamnose degradation were more abundant in tumor samples vs. normal samples. Future prospective studies on larger populations, also including patients in advanced tumor stages and considering all potential existing confounding factors, as well as further functional investigations, are needed to prove the role of microbiota-mediated pathogenicity in PDAC.}, } @article {pmid40005798, year = {2025}, author = {Di, H and Zhang, M and Ning, Z and Liu, C and He, Z and Wang, S and Kong, S and Gan, S and Sun, W and Xu, Z and Ti, J}, title = {Metagenomic Insights into the Abundance of Iron-Reducing Microorganisms in a Petroleum-Contaminated Iron-Rich Aquifer.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020433}, pmid = {40005798}, issn = {2076-2607}, abstract = {In petroleum-contaminated aquifers, iron (III) serves as an electron acceptor, enabling microbial degradation of organic matter. While previous studies have focused on iron reduction and organic matter degradation under laboratory conditions, research on iron-associated microorganisms in petroleum-contaminated aquifers is limited. To explore the diversity and distribution of such microorganisms in natural settings, this study used metagenomic analysis of an iron-rich, petroleum-contaminated aquifer. Sixteen groundwater samples from both pollution source and background areas were collected for species annotation and functional gene identification. Results show more than 7000 species were identified as iron-reducing microorganisms (IRMs), including several previously well-characterized iron-reducing species (e.g., Geobacter luticola and Geobacter sulfurreducens). However, the majority of IRMs were not found in existing iron-reducing microbial databases. Some of them, such as Sulfurospirillum sp. and Extensimonas perlucida, could be taxonomically classified at the species level, while most were only annotated as unclassified bacteria. In the contamination source zone, these microorganisms proliferated extensively, which led to hydrocarbon degradation predominantly driven by iron reduction in the aquifer. This study enhances our understanding of hydrocarbon-degrading microorganisms and supports the management of petroleum-contaminated sites.}, } @article {pmid40005739, year = {2025}, author = {Fu, Z and Zhang, H and Yang, Z and Liu, Y and Wang, P and Zhang, J and Chi, H}, title = {Metagenomic and Metabolomic Analyses Reveal the Role of a Bacteriocin-Producing Strain of Enterococcus faecalis DH9003 in Regulating Gut Microbiota in Mice.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020372}, pmid = {40005739}, issn = {2076-2607}, abstract = {To investigate the regulatory effect of a bacteriocin-producing strain of Enterococcus faecalis DH9003 on the gut microbiota of mice, 15 healthy C57 male mice were randomly administered an equal volume of sterile normal saline (HD, control group, n = 7) and E. faecalis DH9003 (YD, treatment group, n = 8) via gavage. Metagenomic and metabolomic analyses were performed to determine the composition and metabolic function of the intestinal microbiota in mice. The results showed that the relative abundance of Firmicutes continuously increased over time in YD compared to HD. The number of E. faecalis DH9003 increased slowly and remained steady from days 7 to 28, indicating that E. faecalis DH9003 could colonize a considerable number of mouse guts via intragastric administration. Supplementation with E. faecalis DH9003 demonstrated a regulatory effect on the intestinal microbiota composition of mice, causing a shift in the relative abundance of Bacteroidetes and Firmicutes at the phylum level. In addition, a total of 2426 different metabolites were found in mouse feces, including 1286 and 1140 metabolites in positive and negative modes, respectively. Vitamin B6 and succinate were the most regulated and downregulated metabolites in negative ion mode, and the most upregulated and downregulated metabolites in positive ion mode were N-methyl-glutamic acid and N-octanoyl sphingosine. In conclusion, E. faecalis DH9003 can colonize mice gut, affecting the gut microbiota and metabolic competence. This strain therefore offers considerable potential for application as a probiotic.}, } @article {pmid40005729, year = {2025}, author = {Chao, S and Zhang, Y and Hu, Y and Chen, Y and Li, P and Sun, Y and Song, L and Hu, Y and Wang, H and Wu, J and Lv, B}, title = {Transgenic Maize of ZmMYB3R Shapes Microbiome on Adaxial and Abaxial Surface of Leaves to Promote Disease Resistance.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020362}, pmid = {40005729}, issn = {2076-2607}, support = {2024-02-08-00-12-F00021//Shanghai Agriculture Applied Technology Development Program, China/ ; 32302635//National Natural Science Foundation of China/ ; 22ZR1442500//Natural Science Foundation of Shanghai/ ; SAAS Application Basic Study 2025(08)//2025 SAAS Project on Agricultural Science and Technology Innovation Supporting Area/ ; 016//Shanghai Academy of Agricultural Sciences 2022/ ; 20DZ2255300//Shanghai Engineering Research Center of Specialty Maize/ ; 2023ZD04062//the Science and Technology Innovation 2030 Biological Breeding-Major Projects/ ; 23DZ2290700//Shanghai "Science and Technology Innovation Action Plan" Professional Technical Service Platform Project/ ; }, abstract = {The phyllosphere is one of the largest habitats for microorganisms, and host genetic factors play an important role during the interaction between microorganisms and the phyllosphere. Therefore, the transgene may also lead to changes in the maize phyllosphere. ZmMYB3R was identified as a drought-tolerant gene in Arabisopsis. Here, we employed metagenomic sequencing to analyze the microbiome of the adaxial and abaxial leaf surfaces on ZmMYB3R-overexpressing (OE) and wild-type (WT)·maize, aiming to dissect the possible associations between ZmMYB3R and changes in phyllosphere microbiome functioning. Our results revealed that overexpressing ZmMYB3R altered the alpha and beta diversity of the phyllosphere microbiome. In OE plants, more beneficial microbes accumulated on the phyllosphere, while pathogenic ones diminished, especially on the abaxial surface of ZmMYB3R leaves. Further analysis of disease resistance-related metabolic pathways and abundances of disease resistance genes revealed significant differences between OE and WT. The inoculation experiment between OE and WT proved that ZmMYB3R increased the disease resistance of maize. In conclusion, the results reveal that transgenes affect the phyllosphere microbiome, and ZmMYB3R might alter leaf disease resistance by reshaping the phyllosphere microbiome structure. These findings help us understand how ZmMYB3R regulates leaf disease resistance and may facilitate the development of disease control by harnessing beneficial microbial communities.}, } @article {pmid40005715, year = {2025}, author = {Wu, H and Shi, C and Xu, T and Dai, X and Zhao, D}, title = {Characterization and Optimization of Cellulose-Degrading Bacteria Isolated from Fecal Samples of Elaphurus davidianus Through Response Surface Methodology.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020348}, pmid = {40005715}, issn = {2076-2607}, support = {23YFYSHZ00080//Chinese Academy of Sciences - Tianjin cooperation project/ ; Tianjin Bureau of Planning and Natural Resources//Tianjin Bureau of Planning and Natural Resources/ ; }, abstract = {The screening of cellulose-degrading microorganisms from herbivores and the optimization of fermentation conditions are of great significance for the utilization of cellulose resources. In this study, we initially employed a metagenomic analysis to investigate the fecal microbiota of both captive and semi-free-ranging Père David's deer (Elaphurus davidianus) under varying environmental conditions. Subsequently, we isolated and cultured cellulase-degrading microorganisms from the fecal samples using Congo red medium. There was consistency in the dominant phyla and genera of gut microorganisms between the two groups, with only differences in abundance. Then, a cellulose-degrading strain identified as Bacillus pumilus XM was isolated after a morphological analysis and molecular identification by 16S rRNA amplicon. In addition, a series of single factor experiments and response surface analysis were conducted to determine the optimal conditions for best cellulase activity. The optimum temperature, culture time, and shaking speed for the reaction of cellulase produced by the strain Bacillus pumilus XM were 34 °C, 28 h, and 154 r/min, respectively. Under these conditions, the cellulase activity reached a maximum of 10.96 U/mL, which was relatively close to the predicted value of 10.975 U/mL. The results have enriched the existing bacterial resources and laid a foundation for the development of new enzymes, providing a theoretical basis for the rational utilization of cellulase from wild animal resources.}, } @article {pmid40005661, year = {2025}, author = {Van Poelvoorde, LAE and Karlsson, EA and Dupont-Rouzeyrol, M and Roosens, NHCJ}, title = {Can Wastewater Surveillance Enhance Genomic Tracking of Climate-Driven Pathogens?.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020294}, pmid = {40005661}, issn = {2076-2607}, support = {ACIP 648-2023//Institut Pasteur/ ; }, abstract = {Climate change heightens the threat of infectious diseases in Europe, necessitating innovative surveillance methods. Based on 390 scientific papers, for the first time, this review associates climate-related pathogens, data related to their presence in wastewater, and associated available genomic detection methods. This deep analysis reveals a wide range of pathogens that can be tracked through methods such as quantitative and digital PCR, as well as genomic pathogen enrichment in combination with sequencing and metagenomics. Nevertheless, significant gaps remain in the development of methods, particularly for vector-borne pathogens, and in their general harmonization relating to performance criteria. By offering an overview of recent advancements while identifying critical gaps, we advocate for collaborative research and validation to integrate detection techniques into surveillance frameworks. This will enhance public health resilience against emerging infectious diseases driven by climate change.}, } @article {pmid40005646, year = {2025}, author = {Choi, Y and Jeong, J and Han, Y and Han, M and Yu, B and Han, K}, title = {Exploring Competitive Relationship Between Haemophilus parainfluenzae and Mitis Streptococci via Co-Culture-Based Molecular Diagnosis and Metabolomic Assay.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020279}, pmid = {40005646}, issn = {2076-2607}, support = {RS-2024-00355393//the Ministry of Education of the Republic of Korea and the National Research Foundation of Korea/ ; }, abstract = {Various bacterial strains with nitrate-reducing capacity (NRC), such as Haemophilus, Actinomyces, and Neisseria, are known to promote NH3 production, control pH in the oral cavity, and inhibit the growth of aciduric bacteria. However, experimental evidence on various estimated bacterial networks within the salivary microbiome is insufficient. This study aims to explore potential bacterial compositional competition observed within saliva samples from dental caries patients through a co-culture assay of mitis Streptococci, which is a primary colonizer in the salivary microbiome, and nitrate-reducing bacteria Haemophilus parainfluenzae. We investigated bacterial growth efficiency change by co-culture time using the qRT-PCR method. In addition, we applied LC/Q-TOF-based metabolites screening to confirm metabolic interactions between oral bacterial species and their association with dental caries from a metabolomics perspective. As a result, we first found that the nitrate reduction ability of H. parainfluenzae is maintained even in a co-culture environment with the mitis Streptococci group through a nitrate reduction test. However, nitrate reduction efficiency was hindered when compared with monoculture-based nitrate reduction test results. Next, we designed species-specific primers, and we confirmed by qRT-PCR that there is an obvious competitive relationship in growth efficiency between H. parainfluenzae and two mitis Streptococci (S. australis and S. sanguinis). Furthermore, although direct effects of nitrate reduction on competition have not been identified, we have potentially confirmed through LC/Q-TOF-based metabolite screening analysis that the interaction of various metabolic compounds synthesized from mitis Streptococci is driving inter-strain competition. In particular, we constructed a basic reference core-metabolites list to understand the metabolic network between each target bacterial species (H. parainfluenzae and mitis Streptococci) within the salivary microbiome, which still lacks accumulated research data. Ultimately, we suggest that our data have potential value to be referenced in further metagenomics and metabolomics-based studies related to oral health care.}, } @article {pmid40005640, year = {2025}, author = {Cao, X and Cui, Q and Li, D and Liu, Y and Liu, K and Li, Z}, title = {Characteristics of Soil Microbial Community Structure in Different Land Use Types of the Huanghe Alluvial Plain.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020273}, pmid = {40005640}, issn = {2076-2607}, support = {2022YSKY-57//Integrated analysis of soil hydrologic function of returning farmland to forest (grass) in Basic Scientific Research Youth Exploration Project of Central public welfare research Institute of Chinese Research Academy of Environmental Sciences, China/ ; }, abstract = {The Huanghe alluvial plain plays a crucial role in biodiversity conservation. However, its ecosystem has become sensitive and fragile due to long-term human disturbances. Enhancing the resilience of this ecosystem and promoting the sustainable use of land resources are key to addressing its ecological challenges. Soil microbial communities are vital to ecosystem functioning, and land use is a major human factor influencing their structure and diversity. Existing research on the Huanghe alluvial plain primarily focuses on soil physicochemical properties and moisture content, with relatively limited attention given to soil microorganisms. Therefore, this study, using the Wudi Tanyang Forest Farm in the Huanghe alluvial plain as a case study, employs high-throughput metagenomic sequencing to analyze the composition and diversity of soil bacteria, eukaryota, archaea, and virus communities in five different land use types (Tamarix chinensis forest, Fraxinus chinensis forest, farmland, wetland, and grassland). The results indicate that: (1) At the phylum level, the top three bacteria communities were Pseudomonadota, Acidobacteriota, and Actinomycetota; the top three in the eukaryota communities were Ascomycota, Mucoromycota, and Basidiomycotina; the top three in the archaea communities were Nitrososphaerota, Euryarchaeota, and Candidatus Thermoplasmatota; and the virus communities were dominated by Uroviricota; (2) The microbial community structure of the Tamarix chinensis forest and the Fraxinus chinensis forest was similar, and was significantly different from the other three land use types; (3) The land use type had a significant effect on the diversity of the soil microbial communities, with a higher diversity in the wetland and grassland soils; (4) The dominant species of the soil microbial communities under different land use types showed significant differences. This study provides theoretical support for land use optimization and sustainable soil management in the Huanghe alluvial plain region.}, } @article {pmid40005630, year = {2025}, author = {Song, X and Chen, G and Zheng, L and Shen, J and Xue, C and Chang, Y}, title = {Microbiota Involved in the Degradation of Tremella fuciformis Polysaccharide and Microbial Enzymatic Potential Revealed by Microbiome and Metagenome.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020263}, pmid = {40005630}, issn = {2076-2607}, support = {2023YFD2100605//the National Key R&D Program of China/ ; }, abstract = {Tremella fuciformis, as a traditional edible fungus in Asian countries, is rich in polysaccharides with a variety of bioactivities. Nevertheless, its high molecular weight and complex structure have caused limitations in its application and structural analysis. In this study, we successfully screened a Tremella fuciformis polysaccharide-degrading bacterium from the soil by enriching and screening. The mixed bacterium consisted mainly of Verrucomicrobium (55.4%) and Lysobacter (43.8%), which released extracellular enzymes that enabled the degradation of Tremella fuciformis polysaccharides. The functional annotation using microbiome and metagenome combined with bioinformatics revealed its active carbohydrate metabolism, binding, and catalysis. It exposed the enzymatic potential of the bacterium and provided a basis for the exploration of hydrolytic enzymes for hardly degradable polysaccharides in fungi.}, } @article {pmid40005614, year = {2025}, author = {Lee, JL and Yourek, G}, title = {The Microbiome of Catfish (Ictalurus punctatus) Treated with Natural Preservatives During Refrigerated Storage.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020244}, pmid = {40005614}, issn = {2076-2607}, abstract = {Fish is an essential lean protein source worldwide. Unfortunately, fresh fish food products deteriorate rapidly due to microbial spoilage. With consumers' growing concerns about using chemical preservatives, we propose using natural preservatives as safer alternatives to prevent microbial spoilage. In this study, we used Next-Generation Sequencing (NGS) metagenomics to study microbiomes on catfish fillets at early (day one for all samples), middle (day seven for control store-bought and aquaculture-raised samples, day nine for other treatment store-bought samples, and day eleven for other treatment aquaculture-raised samples), and late (day fifteen for all store-bought, day eleven for control aquaculture-raised samples, and day twenty-seven for other treatment aquaculture-raised samples) points. Store-bought and aquaculture-raised catfish were treated individually with natural preservatives (vinegar, lemon, and grapefruit seed [GSE]). We observed bacterial populations and sequenced 16S NGS libraries of catfish microbes. Vinegar treatment showed the greatest suppression of bacterial growth in both groups, and GSE and lemon treatment had similar levels of suppression in the mid and late points (-4 to -5 Log CFU/g vinegar and -0.1 to -4 Log CFU/g other treatments in aquaculture and -1 to -2 Log CFU/g vinegar and -0.2 to -0.5 Log CFU/g other treatments in store-bought). Aquaculture-raised vinegar treatment samples had similar proportional taxonomy abundance values through storage duration. Pseudomonas, Janthinobacterium, and Camobacteriaceae were the dominant bacteria species in the early point for store-bought fish. Still, Pseudomonas was suppressed by vinegar treatment in the middle point, which allowed for less biased relative abundance compared to other treatments. Chryseobacterium, CK-1C4-19, and Cetobacterium were the dominant bacteria species for early point treatments in aquaculture-raised fish. Still, they remained the predominant bacteria for only aquaculture-raised vinegar samples in the middle and late points, which allowed for a similar relative abundance to fresh catfish. Meanwhile, Pseudomonas in most lemon and GSE samples became the dominant species at a later point. This study provides a better understanding of bacterial spoilage of catfish during storage. Additionally, we showed that natural preservative treatments can effectively extend the shelf-life of fishery products.}, } @article {pmid40005601, year = {2025}, author = {Goel, A and Ncho, CM and Jeong, CM and Gupta, V and Jung, JY and Ha, SY and Yang, JK and Choi, YH}, title = {Alleviation of Acute Heat Stress in Broiler Chickens by Dietary Supplementation of Polyphenols from Shredded, Steam-Exploded Pine Particles.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020235}, pmid = {40005601}, issn = {2076-2607}, support = {2020193C10-2022-BA01//Korea Forest Service/ ; No. RS-2024-00350745//Ministry of Science and ICT/ ; }, abstract = {Reducing the detrimental effects of heat stress (HS) in poultry is essential to minimize production losses. The present study evaluates the effects of dietary polyphenols prepared from underutilized wood byproducts on the growth, gut health, and cecal microbiota in broilers subjected to acute heat stress (AHS). One hundred eight one-day-old Indian River broilers were fed with 0%, 0.5%, or 1% polyphenols from shredded, steam-exploded pine particles (PSPP) in their diet. On the 37th day, forty birds were equally distributed among four groups containing either a control diet at thermoneutral temperatures (NT0%) or AHS temperatures with 0% (AHS0%), 0.5% (AHS0.5%), and 1% (AHS1%) PSPP-supplemented diets. The temperature in the NT room was maintained at 21.0 °C, while, in the AHS room, it was increased to 31 °C. AHS negatively influenced performance parameters and increased rectal temperature (RT) in broilers. The AHS0% group showed a higher expression of NOX4, HSP-70, and HSP-90 genes, while the expression was lower in PSPP-supplemented birds. In the jejunum, mRNA expression of SOD was increased in all the birds under AHS compared to NT. The expression of the CLDN1 and ZO2 genes was increased in AHS0%, while that of the ZO1 and MUC2 genes was increased in PSPP-supplemented birds. HS tends to increase TLR2 and TLR4 gene expression in chickens. The significantly modified genera were Bariatricus, Sporobacter, Sporanaerobacter, and Natranaerovirga. Concludingly, AHS negatively influences the performance parameters, RT, stress, gut-health-related genes, and pathogenic penetration, but PSPP supplementation reduces its bad impact by overcoming the stress and gut-health-related genes, increasing favorable bacterial abundance and reducing pathogenic penetration in chickens.}, } @article {pmid40005600, year = {2025}, author = {Misu, IJ and Kayess, MO and Siddiqui, MN and Gupta, DR and Islam, MN and Islam, T}, title = {Microbiome Engineering for Sustainable Rice Production: Strategies for Biofertilization, Stress Tolerance, and Climate Resilience.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020233}, pmid = {40005600}, issn = {2076-2607}, abstract = {The plant microbiome, found in the rhizosphere, phyllosphere, and endosphere, is essential for nutrient acquisition, stress tolerance, and the overall health of plants. This review aims to update our knowledge of and critically discuss the diversity and functional roles of the rice microbiome, as well as microbiome engineering strategies to enhance biofertilization and stress resilience. Rice hosts various microorganisms that affect nutrient cycling, growth promotion, and resistance to stresses. Microorganisms carry out these functions through nitrogen fixation, phytohormone and metabolite production, enhanced nutrient solubilization and uptake, and regulation of host gene expression. Recent research on molecular biology has elucidated the complex interactions within rice microbiomes and the signalling mechanisms that establish beneficial microbial communities, which are crucial for sustainable rice production and environmental health. Crucial factors for the successful commercialization of microbial agents in rice production include soil properties, practical environmental field conditions, and plant genotype. Advances in microbiome engineering, from traditional inoculants to synthetic biology, optimize nutrient availability and enhance resilience to abiotic stresses like drought. Climate change intensifies these challenges, but microbiome innovations and microbiome-shaping genes (M genes) offer promising solutions for crop resilience. This review also discusses the environmental and agronomic implications of microbiome engineering, emphasizing the need for further exploration of M genes for breeding disease resistance traits. Ultimately, we provide an update to the current findings on microbiome engineering in rice, highlighting pathways to enhance crop productivity sustainably while minimizing environmental impacts.}, } @article {pmid40005589, year = {2025}, author = {Warkhade, Y and Schaerer, LG and Bigcraft, I and Hazen, TC and Techtmann, SM}, title = {Diversity and Distribution of Hydrocarbon-Degrading Genes in the Cold Seeps from the Mediterranean and Caspian Seas.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020222}, pmid = {40005589}, issn = {2076-2607}, support = {Merck Future Insight Prize//Merck KGaA/ ; }, abstract = {Marine cold seeps are unique ecological niches characterized by the emergence of hydrocarbons, including methane, which fosters diverse microbial communities. This study investigates the diversity and distribution of hydrocarbon-degrading genes and organisms in sediments from the Caspian and Mediterranean Seas, utilizing 16S rRNA and metagenomic sequencing to elucidate microbial community structure and functional potential. Our findings reveal distinct differences in hydrocarbon degrading gene profiles between the two seas, with pathways for aerobic and anaerobic hydrocarbon degradation co-existing in sediments from both basins. Aerobic pathways predominate in the surface sediments of the Mediterranean Sea, while anaerobic pathways are favored in the surface sediments of the anoxic Caspian Sea. Additionally, sediment depths significantly influence microbial diversity, with variations in gene abundance and community composition observed at different depths. Aerobic hydrocarbon-degrading genes decrease in diversity with depth in the Mediterranean Sea, whereas the diversity of aerobic hydrocarbon-degrading genes increases with depth in the Caspian Sea. These results enhance our understanding of microbial ecology in cold seep environments and have implications for bioremediation practices targeting hydrocarbon pollutants in marine ecosystems.}, } @article {pmid40005401, year = {2025}, author = {Straume, Z and Krūmiņa, N and Elbere, I and Rozenberga, M and Erts, R and Rudzīte, D and Proskurina, A and Krumina, A}, title = {Impact of Vitamins, Antibiotics, Probiotics, and History of COVID-19 on the Gut Microbiome in Ulcerative Colitis Patients: A Cross-Sectional Study.}, journal = {Medicina (Kaunas, Lithuania)}, volume = {61}, number = {2}, pages = {}, doi = {10.3390/medicina61020284}, pmid = {40005401}, issn = {1648-9144}, support = {1.1.1.1/21/A/029//the European Regional Development Fund (ERDF)/ ; }, mesh = {Humans ; Cross-Sectional Studies ; Female ; *Colitis, Ulcerative/drug therapy/microbiology ; Male ; *Gastrointestinal Microbiome/drug effects ; *COVID-19 ; *Vitamins/therapeutic use ; Adult ; Middle Aged ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; *Probiotics/therapeutic use ; *SARS-CoV-2 ; Aged ; }, abstract = {Background and Objectives: The human gut microbiome is essential for the health of the host and is affected by antibiotics and coronavirus disease 2019 (COVID-19). The gut microbiome is recognized as a contributing factor in the development of ulcerative colitis. Specific vitamins and probiotics have been demonstrated to positively influence the microbiome by enhancing the prevalence of expected beneficial microorganisms. Materials and Methods: Forty-nine ulcerative colitis (UC) outpatients from Riga East Clinical University Hospital were enrolled in this cross-sectional study from June 2021 to December 2021. All patients were divided into groups based on history of COVID-19 (COVID-19 positive vs. COVID-19 negative) in the last six months. Information about antibiotic, probiotic, and vitamin intake were outlined, and faecal samples were collected. The MetaPhlAn v.2.6.0 tool was used for the taxonomic classification of the gut microbiome metagenome data. Statistical analysis was performed using R 4.2.1. Results: Of the 49 patients enrolled, 31 (63%) were male and 18 (37%) were female. Coronavirus disease 2019 was found in 14 (28.6%) patients in the last 6 months. Verrucomicrobia was statistically significantly lower in the COVID-19 positive group (M = 0.05; SD = 0.11) compared to the COVID-19 negative group (M = 0.5; SD = 1.22), p = 0.03. Antibiotic non-users had more Firmicutes in their microbiome than antibiotic users (p = 0.008). The most used vitamin supplement was vitamin D (N = 18), fifteen (42.9%) of the patients were COVID-19 negative and 3 (21.4%) were COVID-19 positive over the last six months (p > 0.05). Vitamin C users had more Firmicutes in their gut microbiome compared to non-users (Md = 72.8 [IQR: 66.6; 78.7] vs. Md = 60.1 [IQR: 42.4; 67.7]), p = 0.01. Conclusions: Antibiotic non-users had more Firmicutes than antibiotic users in their gut microbiome. Only vitamin C had statistically significant results; in users, more Firmicutes were observed. A mild course of COVID-19 may not influence ulcerative colitis patients' gut microbiome.}, } @article {pmid40005052, year = {2025}, author = {Zang, P and Chen, P and Chen, J and Sun, J and Lan, H and Dong, H and Liu, W and Xu, N and Wang, W and Hou, L and Sun, B and Zhang, L and Huang, J and Wang, P and Ren, F and Liu, S}, title = {Alteration of Gastrointestinal Function and the Ameliorative Effects of Hericium erinaceus Polysaccharides in Tail Suspension Rats.}, journal = {Nutrients}, volume = {17}, number = {4}, pages = {}, doi = {10.3390/nu17040724}, pmid = {40005052}, issn = {2072-6643}, support = {242300421105//Henan Natural Science Foundation of Excellent Young Scholars/ ; }, mesh = {Animals ; *Rats, Sprague-Dawley ; *Gastrointestinal Microbiome/drug effects ; *Hericium ; Rats ; Male ; *Polysaccharides/pharmacology ; Hindlimb Suspension ; Dysbiosis ; Dietary Supplements ; Gastrointestinal Tract/drug effects ; Gastrointestinal Diseases/drug therapy/prevention & control ; Weightlessness Simulation ; }, abstract = {Background/Objectives: Long-term spaceflight in a microgravity environment frequently results in gastrointestinal dysfunction, presenting substantial challenges to astronauts' health. Hericium erinaceus, a plant recognized for its dual use as food and medicine, contains a key functional component called Hericium erinaceus polysaccharide (HEP), which is purported to promote gastrointestinal health. This study aims to investigate the protective effects of HEP against gastrointestinal disturbances induced by simulated weightlessness and to elucidate its regulatory mechanisms. Methods: Sprague Dawley rats subjected to a tail suspension model were administered either a standard diet or a diet supplemented with 0.125% HEP over a period of 4 weeks (the intake of HEP is approximately 157.5 mg/kg bw/d, n = 8), metagenomics and targeted metabolomics to investigate the effects of HEP on gastrointestinal hormone secretion disorders, gut microbiota dysbiosis, and intestinal barrier damage induced by simulated weightlessness. Results: Dietary supplementation with HEP was observed to significantly alleviate weightlessness-induced gastrointestinal hormone disruptions, enhancing motility and intestinal barrier function while reducing inflammation. In addition, HEP improved gut microbiota by boosting beneficial bacteria as Oscillibacter sp.1-3, Firmicutes bacterium ASF500, and Lactobacillus reuteri, while reducing harmful bacteria like Escherichia coli and Mucispirillum schaedleri at the species level. Furthermore, HEP altered the serum metabolic profile of the rats, reducing inflammation by upregulating the tryptophan metabolism pathway and enhancing the production of short-chain fatty acids. Conclusions: HEP effectively protects against gastrointestinal dysfunction induced by simulated weightlessness by regulating hormone secretion and maintaining intestinal homeostasis.}, } @article {pmid40004244, year = {2025}, author = {Blankestijn, JM and Baalbaki, N and Beijers, RJHCG and Cornelissen, MEB and Wiersinga, WJ and Abdel-Aziz, MI and Maitland-van der Zee, AH and , }, title = {Exploring Heterogeneity of Fecal Microbiome in Long COVID Patients at 3 to 6 Months After Infection.}, journal = {International journal of molecular sciences}, volume = {26}, number = {4}, pages = {}, doi = {10.3390/ijms26041781}, pmid = {40004244}, issn = {1422-0067}, support = {LSHM20104; LSHM20068//Health Holland/ ; }, mesh = {Humans ; *COVID-19/microbiology/virology ; *Feces/microbiology/virology ; Male ; Female ; *Gastrointestinal Microbiome/genetics ; Middle Aged ; Aged ; *SARS-CoV-2/isolation & purification ; Adult ; Metagenome ; Bacteria/classification/genetics/isolation & purification ; }, abstract = {An estimated 10% of COVID-19 survivors have been reported to suffer from complaints after at least three months. The intestinal microbiome has been shown to impact long COVID through the gut-lung axis and impact the severity. We aimed to investigate the relationship between the gut microbiome and clinical characteristics, exploring microbiome heterogeneity through clustering. Seventy-nine patients with long COVID evaluated at 3 to 6 months after infection were sampled for fecal metagenome analysis. Patients were divided into two distinct hierarchical clusters, based solely on the microbiome composition. Compared to cluster 1 (n = 67), patients in cluster 2 (n = 12) showed a significantly reduced lung function (FEV1, FVC, and DLCO) and during acute COVID-19 showed a longer duration of hospital admissions (48 compared to 7 days) and higher rates of ICU admissions (92% compared to 22%). Additionally, the microbiome composition showed a reduced alpha diversity and lower proportion of butyrate-producing bacteria in cluster 2 together with higher abundances of Ruminococcus gnavus, Escherichia coli, Veillonella spp. and Streptococcus spp. and reduced abundances of Faecalibacterium prausnitzii and Eubacteria spp. Further research could explore the effect of pre- and pro-biotic supplementation and its impact on lung function and societal participation in long COVID.}, } @article {pmid40004174, year = {2025}, author = {Cui, Y and Guan, H and Okyere, SK and Hua, Z and Deng, Y and Deng, H and Ren, Z and Deng, J}, title = {Microbial Guardians or Foes? Metagenomics Reveal Association of Gut Microbiota in Intestinal Toxicity Caused by DON in Mice.}, journal = {International journal of molecular sciences}, volume = {26}, number = {4}, pages = {}, doi = {10.3390/ijms26041712}, pmid = {40004174}, issn = {1422-0067}, support = {. 32273072//This research was supported by National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Trichothecenes/toxicity ; *Metagenomics/methods ; Cytokines/metabolism ; Intestinal Mucosa/metabolism/microbiology/pathology ; Zonula Occludens-1 Protein/metabolism/genetics ; Male ; Colon/microbiology/metabolism/pathology/drug effects ; Jejunum/microbiology/pathology/metabolism/drug effects ; Occludin/metabolism/genetics ; Intestines/microbiology/pathology/drug effects ; }, abstract = {The role of gut microbiota has become a research hotspot in recent years; however, whether the gut microbiota are involved in the alleviation or exacerbation of Deoxynivalenol (DON) toxicity has not been fully studied. Therefore, the objective of this study was to investigate whether the gut microbiota are involved in reducing or aggravating the intestinal damage induced by DON in mice. Mice that received or did not receive antibiotic-induced intestinal flora clearance were orally given DON (5 mg kg/bw/day) for 14 days. At the end of the experiment, serum, intestinal tissue samples and colon contents were collected for further analysis. DON caused development of severe histopathological damage, such as necrosis and inflammation of the jejunum and colon in mice without gut microbiota clearance. The levels of tight junction proteins ZO-1 and occludin were reduced in the jejunum and colon of mice without gut microbiota clearance. In addition, the mRNA and protein levels of pro-inflammatory cytokines (IL-1β, IL-6, and TNF-α) were increased in mice without gut microbiota clearance. The presence of microbiota exacerbate the intestinal damage induced by DON via changes in gut microbiota abundance and production of gut damaging metabolites.}, } @article {pmid40003915, year = {2025}, author = {Chao, X and Fan, Z and Wu, J and Ye, C and Wang, X and Li, R and Chen, S and Zhang, X and Fang, C and Luo, Q}, title = {Application of mRNA-Seq and Metagenomic Sequencing to Study Salmonella pullorum Infections in Chickens.}, journal = {International journal of molecular sciences}, volume = {26}, number = {4}, pages = {}, doi = {10.3390/ijms26041448}, pmid = {40003915}, issn = {1422-0067}, support = {2022B0202100002//Key-Area Research and Development Program of Guangdong Province/ ; 2024B03J1353//Science and Technology Program of Guangzhou City/ ; 2023ZD04064//STI2030-Major Projects/ ; }, mesh = {Animals ; *Chickens/microbiology ; *Poultry Diseases/microbiology/genetics ; *Metagenomics/methods ; *Salmonella Infections, Animal/microbiology/genetics ; Cecum/microbiology ; RNA, Messenger/genetics/metabolism ; Gastrointestinal Microbiome/genetics ; Alternative Splicing ; Salmonella/genetics/pathogenicity ; RNA-Seq/methods ; Gene Expression Profiling ; Metagenome ; Gene Expression Regulation ; }, abstract = {The disease caused by Salmonella pullorum has been demonstrated to exert a deleterious effect on the performance of poultry, giving rise to elevated mortality and considerable economic losses within the breeding industry. However, there is a paucity of research investigating the relationship between cecal gene expression and different isomer and Salmonella pullorum infection, and research on the relationship between intestinal microbiota and Salmonella pullorum infection is also limited. In this study, mRNA-Seq and metagenomic sequencing were performed on the cecal tissues and fresh feces of individuals who tested positive (n = 4) and negative (n = 4) for Salmonella pullorum, with the aim of exploring the chickens infected with Salmonella pullorum from two perspectives: the gene transcription level and the microbial level. The mRNA sequencing results revealed 1560 differentially expressed genes (DEGs), of which 380 genes were found to be up-regulated and 1180 genes were down-regulated. A number of genes were reported to be associated with immunity, including AQP8, SLC26A3, CBS, IFI6, DDX60, IL8L1 and IL8L2. Furthermore, a total of 1047 differentially expressed alternative splicings (DEASs) were identified through alternative splicing analysis, including CBS, SLC6A9, ILDR2, OCRL, etc. The joint analysis of DEGs and DEASs revealed 70 genes that exhibited both differentially expressed alternative splicings and differential expression, including CTNND1, TPM1, SPPL2A, etc. The results of metagenomic sequencing demonstrated that the abundances of Bacteroides, Firmicutes, and Verrucobacteria underwent a significant alteration subsequent to the infection of Salmonella pullorum. In summary, the present study conducted a preliminary exploration of the genetic basis of chickens infected with Salmonella pullorum. TPM1 and SPPL2A were found to be differentially expressed by mRNA-Seq, and differences in alternative splicing events. Furthermore, metagenomic sequencing revealed significant changes in the microbial communities of Bacteroidetes, Firmicutes, and Verrucobacteria during infection with Salmonella pullorum.}, } @article {pmid40003912, year = {2025}, author = {Chatzokou, D and Tsarna, E and Davouti, E and Siristatidis, CS and Christopoulou, S and Spanakis, N and Tsakris, A and Christopoulos, P}, title = {Semen Microbiome, Male Infertility, and Reproductive Health.}, journal = {International journal of molecular sciences}, volume = {26}, number = {4}, pages = {}, doi = {10.3390/ijms26041446}, pmid = {40003912}, issn = {1422-0067}, mesh = {Male ; Humans ; *Microbiota ; *Semen/microbiology ; *Infertility, Male/microbiology ; *Reproductive Health ; Female ; Reproductive Techniques, Assisted ; Spermatozoa/microbiology ; Fertility ; Pregnancy ; }, abstract = {The semen microbiome, once believed to be sterile, is now recognized as a dynamic ecosystem containing a diverse range of microorganisms with potential implications for male fertility and reproductive health. We aimed to examine the relationship between the semen microbiome, male infertility, and reproductive outcomes, highlighting the transformative role of next generation sequencing techniques and bioinformatics in exploring this intricate interaction, and we present a critical review of the published literature on this issue. Current evidence suggests a complex association between the composition of the semen microbiome and male fertility, with certain bacterial genera, such as Lactobacillus and Prevotella that exert opposing effects on sperm quality and DNA integrity. In addition, the influence of the semen microbiome extends beyond natural fertility, affecting assisted reproductive technologies and pregnancy outcomes. Despite considerable progress, challenges remain in standardizing methodologies and interpreting findings. In conclusion, we identify the lack of a definitive management proposal for couples presenting with this phenomenon, and we underline the need for an algorithm and indicate the questions raised that point toward our goal for a strategy. Continued research is essential to clarify the role of the semen microbiome in male reproductive health and to advance the development of personalized fertility management approaches.}, } @article {pmid40003742, year = {2025}, author = {Castillo, D and Abella, E and Sinpoo, C and Phokasem, P and Chantaphanwattana, T and Yongsawas, R and Cervancia, C and Baroga-Barbecho, J and Attasopa, K and Noirungsee, N and Disayathanoowat, T}, title = {Gut Microbiome Diversity in European Honeybees (Apis mellifera L.) from La Union, Northern Luzon, Philippines.}, journal = {Insects}, volume = {16}, number = {2}, pages = {}, doi = {10.3390/insects16020112}, pmid = {40003742}, issn = {2075-4450}, support = {2022//Mekong - Lancang Special Fund/ ; }, abstract = {Insects often rely on symbiotic bacteria and fungi for various physiological processes, developmental stages, and defenses against parasites and diseases. Despite their significance, the associations between bacterial and fungal symbionts in Apis mellifera are not well studied, particularly in the Philippines. In this study, we collected A. mellifera from two different sites in the Municipality of Bacnotan, La Union, Philippines. A gut microbiome analysis was conducted using next-generation sequencing with the Illumina MiSeq platform. Bacterial and fungal community compositions were assessed using 16S rRNA and ITS gene sequences, respectively. Our findings confirm that adult worker bees of A. mellifera from the two locations possess distinct but comparably proportioned bacterial and fungal microbiomes. Key bacterial symbionts, including Lactobacillus, Bombilactobacillus, Bifidobacterium, Gilliamella, Snodgrassella, and Frischella, were identified. The fungal community was dominated by the yeasts Zygosaccharomyces and Priceomyces. Using the ENZYME nomenclature database and PICRUSt2 software version 2.5.2, a predicted functional enzyme analysis revealed the presence of β-glucosidase, catalase, glucose-6-phosphate dehydrogenase, glutathione transferase, and superoxide dismutase, which are involved in host defense, carbohydrate metabolism, and energy support. Additionally, we identified notable bacterial enzymes, including acetyl-CoA carboxylase and AMPs nucleosidase. Interestingly, the key bee symbionts were observed to have a negative correlation with other microbiota. These results provide a detailed characterization of the gut microbiota associated with A. mellifera in the Philippines and lay a foundation for further metagenomic studies of microbiomes in native or indigenous bee species in the region.}, } @article {pmid40002888, year = {2025}, author = {Fu, Z and Jia, Y and Zhao, J and Guo, Y and Xie, B and An, K and Yuan, W and Chen, Y and Zhong, J and Tong, Z and Liu, X and Su, P}, title = {Perioperative Multi-Kingdom Gut Microbiota Alters in Coronary Artery Bypass Grafting.}, journal = {Biomedicines}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/biomedicines13020475}, pmid = {40002888}, issn = {2227-9059}, support = {(Cardiovascular Surgery)//National clinical key specialty construction project/ ; }, abstract = {Background: Coronary artery bypass grafting (CABG) is one of the main treatments for coronary heart disease (CHD). Gut microbiota, including bacteria, fungi, archaea, and virus, has been reported to be associated with CHD. However, the changes in the multi-kingdom gut microbiota after CABG are not yet clear. This study aimed to explore the changes in multi-kingdom gut microbiota during the early postoperative period of CABG. Methods: We collected fecal samples from 40 patients before and 1 week after CABG surgery. Metagenomic sequencing was used to detect the microbial spectrum and gene functions in the patients' fecal samples. Results: Post-CABG patients exhibited significant changes in the composition of multi-kingdom gut microbiota and gene functions. Among bacteria, beneficial species such as Bifidobacterium, Bacteroides, and Blautia were significantly reduced after CABG, while the harmful species Enterococcus was significantly increased. In fungi, Schizosaccharomyces pombe was significantly decreased in the postoperative group, while Saccharomyces cerevisiae and Aspergillus chevalieri were significantly increased postoperatively. Spearman correlation analysis indicated that Schizosaccharomyces pombe had positive interactions with beneficial bacteria such as Lachnospiraceae, Ruminococcus, and Blautia. Among archaea, the preoperatively enriched Methanomethylovorans-SGB40959 was significantly reduced postoperatively, and Spearman correlation analysis showed a significant positive interaction with probiotics Ruminococcus and Dorea. In viruses, the phage Enterococcus virus EFP01, which infects Enterococcus, was significantly increased postoperatively and showed a significant positive interaction with Enterococcus. Additionally, postoperative dysregulation of gene functions such as the Phosphoenolpyruvate-dependent Sugar Phosphotransferase System (PTS), Transposition, DNA-mediated, and Transposase Activity was observed, and Spearman correlation analysis indicated significant correlations between the dysregulated gene functions and the microbial communities. Conclusions: This study comprehensively revealed the changes in multi-kingdom species post-CABG. The reduction of beneficial microorganisms and the increase of harmful microorganisms after surgery are of significant clinical importance for understanding the overall health status of post-CABG patients and for optimizing postoperative treatment plans. Future research needs to further explore how to improve the prognosis of post-CABG patients by modulating the gut microbiota.}, } @article {pmid40002576, year = {2025}, author = {Pais, RJ and Botelho, J and Machado, V and Alcoforado, G and Mendes, JJ and Alves, R and Bessa, LJ}, title = {Exploring AI-Driven Machine Learning Approaches for Optimal Classification of Peri-Implantitis Based on Oral Microbiome Data: A Feasibility Study.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {15}, number = {4}, pages = {}, doi = {10.3390/diagnostics15040425}, pmid = {40002576}, issn = {2075-4418}, support = {2022.01430.PTDC//Fundação para a Ciência e Tecnologia/ ; }, abstract = {Background: Machine learning (ML) techniques have been recently proposed as a solution for aiding in the prevention and diagnosis of microbiome-related diseases. Here, we applied auto-ML approaches on real-case metagenomic datasets from saliva and subgingival peri-implant biofilm microbiomes to explore a wide range of ML algorithms to benchmark best-performing algorithms for predicting peri-implantitis (PI). Methods: A total of 100 metagenomes from the NCBI SRA database (PRJNA1163384) were used in this study to construct biofilm and saliva metagenomes datasets. Two AI-driven auto-ML approaches were used on constructed datasets to generate 100 ML-based models for the prediction of PI. These were compared with statistically significant single-microorganism-based models. Results: Several ML algorithms were pinpointed as suitable bespoke predictive approaches to apply to metagenomic data, outperforming the single-microorganism-based classification. Auto-ML approaches rendered high-performing models with Receiver Operating Characteristic-Area Under the Curve, sensitivities and specificities between 80% and 100%. Among these, classifiers based on ML-driven scoring of combinations of 2-4 microorganisms presented top-ranked performances and can be suitable for clinical application. Moreover, models generated based on the saliva microbiome showed higher predictive performance than those from the biofilm microbiome. Conclusions: This feasibility study bridges complex AI research with practical dental applications by benchmarking ML algorithms and exploring oral microbiomes as foundations for developing intuitive, cost-effective, and clinically relevant diagnostic platforms.}, } @article {pmid40002490, year = {2025}, author = {Thirupathi, K and Ghozy, S and Reda, A and Ranatunga, WK and Ruben, MA and Armin, Z and Mereuta, OM and Prabhjot, S and Dai, D and Brinjikji, W and Kallmes, DF and Kadirvel, R}, title = {Metagenomic Insights into Microbial Signatures in Thrombi from Acute Ischemic Stroke Patients Undergoing Endovascular Treatment.}, journal = {Brain sciences}, volume = {15}, number = {2}, pages = {}, doi = {10.3390/brainsci15020157}, pmid = {40002490}, issn = {2076-3425}, abstract = {Background: Variability in recanalization success during endovascular treatment for acute ischemic stroke (AIS) has led to increased interests in thrombus composition and associated cellular materials. While evidence suggests that bacteria may influence thrombus characteristics, limited data exist on microbiological profiles of thrombi in stroke patients. Objectives: Characterization of bacterial communities present in thrombi of AIS patients undergoing mechanical thrombectomy, providing insights into microbial contributions to stroke pathogenesis and treatment outcomes. Methods: Thrombi were collected from 20 AIS patients. After extracting metagenome, 16S rDNA sequencing was performed. Bioinformatic analysis included taxonomy and diversity assessments. The presence of bacterial DNA and viable bacteria in thrombi was validated using polymerase chain reaction (PCR) and bacterial culturing followed by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) analysis, respectively. Results: 16S rDNA was amplified in 19/20 thrombi (95%). Analysis identified a diverse microbial community, with Corynebacterium spp. as the most prevalent genus, followed by Staphylococcus spp., Bifidobacterium spp., Methylobacterium spp., and Anaerococcus spp. Alpha diversity analyses (Shannon index: 4.0-6.0 and Simpson index: 0.8-1.0) revealed moderate to high microbial diversity across samples; beta diversity demonstrated distinct clustering, indicating inter-patient variability in microbial profiles. PCR confirmed the presence of DNA specific to dominant bacterial taxa identified through sequencing. Culturing showed the presence of Staphylococcus epidermidis and Enterococcus faecalis in some clots as identified through MALDI analysis. Conclusions: This study shows bacterial communities present in AIS patients' thrombi, suggesting a potential link between microbial signatures and thrombus characteristics.}, } @article {pmid40002376, year = {2025}, author = {Smirnova, YD and Hanetseder, D and Derigo, L and Gasser, AS and Vaglio-Garro, A and Sperger, S and Brunauer, R and Korneeva, OS and Duvigneau, JC and Marolt Presen, D and Kozlov, AV}, title = {Osteosarcoma Cells and Undifferentiated Human Mesenchymal Stromal Cells Are More Susceptible to Ferroptosis than Differentiated Human Mesenchymal Stromal Cells.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/antiox14020189}, pmid = {40002376}, issn = {2076-3921}, support = {ICM-2020-00212//OeAD-GmbH/ ; MPC-2022-00040//OeAD-GmbH/ ; 953134//European Union's Horizon 2020; H2020-NMBP-TR-IND-2020/ ; 877452//Austrian Research Promotion Agency (FFG)/ ; P-33799//Austrian Science Fund (FWF)/ ; }, abstract = {Current research suggests that promoting ferroptosis, a non-apoptotic form of cell death, may be an effective therapy for osteosarcoma, while its inhibition could facilitate bone regeneration and prevent osteoporosis. Our objective was to investigate whether the susceptibility to and regulation of ferroptosis differ between undifferentiated (UBC) and differentiated (DBC) human bone marrow stromal cells, as well as human osteosarcoma cells (MG63). Ferroptosis was induced by either inhibiting glutathione peroxidase 4 (GPX4) using RSL3 or blocking all glutathione-dependent enzymes through inhibition of the glutamate/cysteine antiporter with Erastin. Lipid peroxidation was assessed using the fluorescent probe BODIPY™581/591C11, while Ferrostatin-1 was used to inhibit ferroptosis. We demonstrate that neither Erastin nor RSL3 induces ferroptosis in DBC. However, both RSL3 and Erastin induce ferroptosis in UBC, while Erastin predominantly induces ferroptosis in MG63 cells. Our data suggest that ferroptosis induction in undifferentiated hBMSCs is primarily regulated by GPX4, whereas glutathione S-Transferase P1 (GSTP1) plays a key role in controlling ferroptosis in osteosarcoma cells. In conclusion, targeting the key pathways involved in ferroptosis across different bone cell types may improve the efficacy of cancer treatments while minimizing collateral damage and supporting regenerative processes, with minimal impact on cancer therapy.}, } @article {pmid40002058, year = {2025}, author = {Tenea, GN and Cifuentes, V and Reyes, P and Cevallos-Vallejos, M}, title = {Unveiling the Microbial Signatures of Arabica Coffee Cherries: Insights into Ripeness Specific Diversity, Functional Traits, and Implications for Quality and Safety.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {4}, pages = {}, doi = {10.3390/foods14040614}, pmid = {40002058}, issn = {2304-8158}, support = {7874/2023//Universidad Técnica del Norte/ ; }, abstract = {Arabica coffee, one of the most valuable crop commodities, harbors diverse microbial communities with unique genetic and functional traits that influence bean safety and final coffee quality. In Ecuador, coffee production faces challenges due to the spread of pathogenic organisms across cultivars, leading to reduced yields and compromised quality. This study employed a shotgun metagenomic approach to characterize the indigenous microbial diversity present in the cell biomass of fermented coffee cherries from three Coffea arabica varieties: Typica (Group A), Yellow Caturra (Group B), and Red Caturra (Group C), originating from the Intag Valley in northern Ecuador, at two ripe stages: green (immature fruits) and ripe (red/yellow mature fruits). Gene prediction and functional annotation were performed using multiple databases, including EggNOG, COG, KEGG, CAZy, CARD, and BacMet, to explore the potential impact of microbial communities on bean quality and safety. Metagenomic sequencing generated over 416 million high-quality reads, averaging 66 million clean reads per sample and yielding a total of 47 Gbps of data. Analysis revealed distinct differences in species abundance based on the coffee variety and ripening stage. A total of 799,658 protein-coding sequences (CDSs) were predicted, of which 205,937 genes were annotated with EggNOG, 181,723 with COG, 155,220 with KEGG, and 10,473 with CAZy. Additionally, 432 antibiotic resistance genes (ARGs) were identified using CARD, and 8974 biocide and metal resistance genes (BMRGs) were annotated with BacMet. Immature cherries exhibited enriched pathways associated with resistance to antibiotics such as fluoroquinolones, penams, rifamycin, macrolides, carbapenems, and cephalosporins. The abundance of these pathways varied with the ripening stage and variety. Furthermore, green cherries showed a significant increase in BMRGs associated with resistance to substances including hydrochloric acid, copper, nickel, hydrogen peroxide, arsenic, and zinc. Among mature cherries, Typica and Red Caturra shared similar profiles, while Yellow Caturra displayed a divergent microbial and functional profile. These study findings emphasize the interplay between microbial diversity, ripening stages, and coffee varieties, providing a foundation for innovative approaches to enhance coffee quality through microbiome management.}, } @article {pmid40002014, year = {2025}, author = {Yan, C and Huang, Z and Tu, R and Zhang, L and Wu, C and Wang, S and Huang, P and Zeng, Y and Shi, B}, title = {Revealing the Differences in Microbial Community and Quality of High-Temperature Daqu in the Southern Sichuan-Northern Guizhou Region.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {4}, pages = {}, doi = {10.3390/foods14040570}, pmid = {40002014}, issn = {2304-8158}, support = {KY202301//Scientific Research Cooperation Project of Sichuan University - Luzhou Laojiao Culture and Technology Innovation Research Center/ ; }, abstract = {High-temperature Daqu is crucial to Jiang-flavor Baijiu production in the Southern Sichuan-Northern Guizhou region of China. However, the complex interplay among microorganisms, enzymes, and metabolites in the Daqu from this region requires further investigation. This study compared four high-temperature Daqu samples from this region, analyzing their physicochemical properties, enzyme activities, volatile compounds, and microbial community composition and function, and exploring the influence of microorganisms on the saccharification and aroma-formation function of Daqu in combination with correlation analysis. The microbial communities in the Daqu samples exhibited functional redundancy, with Desmospora sp. 8437 being consistently dominant (3.6-7.3%). Members of the family Bacillaceae were the principal factors contributing to the differences in starch degradation capacity, protein degradation capacity, and pyrazine content among the Daqu samples, mainly through the amylases and proteases they produce. Kroppenstedtia spp. were principal factors causing the differences in aldehyde and ketone contents, primarily via the lipid degradation enzymes they synthesize. Overall, the bacterial community composition of Daqu greatly influenced its characteristics. This study provided a theoretical basis for understanding the diversity of high-temperature Daqu in the Southern Sichuan-Northern Guizhou region.}, } @article {pmid40001366, year = {2025}, author = {Ortiz-Severín, J and Hojas, I and Redin, F and Serón, E and Santana, J and Maass, A and Cambiazo, V}, title = {From Metagenomes to Functional Expression of Resistance: floR Gene Diversity in Bacteria from Salmon Farms.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/antibiotics14020122}, pmid = {40001366}, issn = {2079-6382}, support = {Convocatoria Nacional Subvención a Instalación en la Academia Convocatoria año 2021 Folio SA77210027//Agencia Nacional de Investigación y Desarrollo/ ; Fondecyt 1211893//Agencia Nacional de Investigación y Desarrollo/ ; Exploración number 13220002//Agencia Nacional de Investigación y Desarrollo/ ; Basal Center grant FB210005//Agencia Nacional de Investigación y Desarrollo/ ; ANID-MILENIO-ICN2021_044//Agencia Nacional de Investigación y Desarrollo/ ; }, abstract = {Background. The increase in antibiotic resistance in human-impacted environments, such as coastal waters with aquaculture activity, is related to the widespread use of antibiotics, even at sub-lethal concentrations. In Chile, the world's second largest producer of salmon, aquaculture is considered the main source of antibiotics in coastal waters. In this work, we aimed to characterize the genetic and phenotypic profiles of antibiotic resistance in bacterial communities from salmon farms. Methods. Bacterial metagenomes from an intensive aquaculture zone in southern Chile were sequenced, and the composition, abundance and sequence of antibiotic resistance genes (ARGs) were analyzed using assembled and raw read data. Total DNA from bacterial communities was used as a template to recover floR gene variants, which were tested by heterologous expression and functional characterization of phenicol resistance. Results. Prediction of ARGs in salmon farm metagenomes using more permissive parameters yielded significantly more results than the default Resistance Gene Identifier (RGI) software. ARGs grouped into drug classes showed similar abundance profiles to global ocean bacteria. The floR gene was the most abundant phenicol-resistance gene with the lowest gene counts, showing a conserved sequence although with variations from the reference floR. These differences were recovered by RGI prediction and, in greater depth, by mapping reads to the floR sequence using SNP base-calling. These variants were analyzed by heterologous expression, revealing the co-existence of high- and low-resistance sequences in the environmental bacteria. Conclusions. This study highlights the importance of combining metagenomic and phenotypic approaches to study the genetic variability in and evolution of antibiotic-resistant bacteria associated with salmon farms.}, } @article {pmid40001165, year = {2025}, author = {Awasthi, S and Hiremath, VM and Nain, S and Malik, S and Srinivasan, V and Rose, P and Choudhury, A and Grover, R and Sharma, R}, title = {Microbial landscape of Indian homes: the microbial diversity, pathogens and antimicrobial resistome in urban residential spaces.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {25}, pmid = {40001165}, issn = {2524-6372}, support = {CLP0030, CNP0011//Reckitt (India) Ltd, India/ ; JRF//CSIR/ ; }, abstract = {BACKGROUND: Urban dwellings serve as complex and diverse microbial community niches. Interactions and impact of house microbiome on the health of the inhabitants need to be clearly defined. Therefore, it is critical to understand the diversity of the house microbiota, the presence and abundance of potential pathogens, and antimicrobial resistance.

RESULTS: Shotgun metagenomics was used to analyze the samples collected from 9 locations in 10 houses in New Delhi, India. The microbiota includes more than 1409 bacterial, 5 fungal, and 474 viral species en masse. The most prevalent bacterial species were Moraxella osloensis, Paracoccus marcusii, Microbacterium aurum, Qipengyuania sp YIMB01966, and Paracoccus sphaerophysae, which were detected in at least 80 samples. The location was the primary factor influencing the microbiome diversity in the Indian houses. The overall diversity of different houses did not differ significantly from each other. The surface type influenced the microbial community, but the microbial diversity on the cemented and tiled floors did not vary significantly. A substantial fraction of the bacterial species were potentially pathogenic or opportunistic pathogens, including the ESKAPE pathogens. Escherichia coli was relatively more abundant in bedroom, foyer, and drawing room locations. Analysis of the house microbiome antimicrobial resistome revealed 669 subtypes representing 22 categories of antimicrobial resistance genes, with multidrug resistance genes being the most abundant, followed by aminoglycoside genes.

CONCLUSIONS: This study provides the first insight into the microbiomes of houses in New Delhi, showing that these houses have diverse microbiomes and that the location within the house significantly influences the microbiota. The presence of potential pathogens and a repertoire of antimicrobial resistance genes reflect possible health risks, as these could lead to infectious disease transmission. This study builds a framework for understanding the microbial diversity of houses in terms of geographical location, environment, building design, cleaning habits, and impact on the health of occupants.}, } @article {pmid40001114, year = {2025}, author = {Feng, X and Cheng, J and Jiang, L and Lin, J and Ye, Z and Pang, Q and Liu, J}, title = {The application of endoscopic debridement combined with metagenomic next-generation sequencing technology in primary spinal infections: a retrospective study.}, journal = {Journal of orthopaedic surgery and research}, volume = {20}, number = {1}, pages = {195}, pmid = {40001114}, issn = {1749-799X}, support = {2024HMZD05//the Key Research Foundation of Ningbo No.2 Hospital/ ; 2024021//Zhejiang provincial key clinical specialty/ ; 2022-F15//the project of Ningbo leading medical & Health Discipline/ ; 2023HMJQ03//the Distinguished Young Scholars of Ningbo No.2 Hospital/ ; }, mesh = {Humans ; Retrospective Studies ; *Debridement/methods ; Male ; Female ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Aged ; *Endoscopy/methods ; Adult ; Spinal Diseases/surgery/microbiology ; Bacterial Infections/microbiology/diagnosis ; }, abstract = {PURPOSE: Spinal endoscopy is a novel minimally invasive spinal surgery technique used in recent years to treat various degenerative spinal diseases. Metagenomic next-generation sequencing (mNGS) is a new method for identifying infectious microorganisms in infectious diseases. We aim to evaluate the application effect of combining spinal endoscopy with mNGS in diagnosing and treating spinal infections.

METHODS: The clinical data of 62 patients with suspected spinal infectious diseases admitted from January 2020 to December 2023 were retrospectively analyzed. All patients underwent spinal endoscopy to obtain tissue specimens, histopathological examination, routine bacterial culture, and mNGS sequencing. Describe the pathogenic microbial spectrum of spinal infection, and compare the differences in sensitivity (true positive rate) and specificity (true negative rate) between the two detection methods. White blood cell (WBC) erythrocyte deposition rate (ESR), C-reactive protein (CRP), visual analog scale (VAS), Japanese Orthopaedic Association (JOA) score, Oswestry Disability Index (ODI), and other clinical results were analyzed.

RESULTS: In 62 cases, mNGS, microbiological culture, serologic testing, and pathologic examination results were obtained. 49 cases of spinal infections and 13 cases of non-spinal infections were finally diagnosed clinically. Among the 49 patients with spinal infections, there were 31 cases of purulent bacterial infections, 8 cases of tuberculosis infections, and 10 cases of infections with unspecified etiological microorganisms. Among the 13 cases of non-spinal infections, there were 3 cases of spinal tumors, 6 cases of Modic changes of the endplates, and 4 cases of endplate fracture. The positive rate of microbial culture was 36.73% (18/49), and the positive rate of the mNGS test was 71.43% (35/49), which was statistically different from each other (P < 0.01). The sensitivity of the mNGS test was 71.43%, and the specificity of the mNGS test was 84.62%. At the 3-month follow-up, WBC, ESR, and CRP levels were normalized. The VAS, JOA score, and ODI of the lower back and legs at each follow-up point after surgery were significantly improved compared with those before surgery, and the difference was statistically significant (P < 0.01).

CONCLUSION: Metagenomic sequencing technology is fast, efficient, and accurate in detecting pathogenic microorganisms, and has high diagnostic value in the diagnosis and treatment of spinal infections. Spinal endoscopic debridement combined with mNGS can achieve good clinical results.}, } @article {pmid40000989, year = {2025}, author = {Zhao, M and Zhang, Y and Liu, S and Wang, F and Zhang, P}, title = {Eradication of Helicobacter pylori reshapes gut microbiota and facilitates the evolution of antimicrobial resistance through gene transfer and genomic mutations in the gut.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {90}, pmid = {40000989}, issn = {1471-2180}, support = {32201393//National Natural Science Foundation of China/ ; }, abstract = {Treating Helicobacter pylori (H. pylori) infection requires large quantities of antibiotics, thus dramatically promoting the enrichment and dissemination of antimicrobial resistance (AMR) in feces. However, the influence of H. pylori eradication on the AMR mobility and the gut microbiota evolution has yet to be thoroughly investigated. Here, a study involving 12 H. pylori-positive participants was conducted, and the pre- and post- eradication fecal samples were sequenced. Metagenomic analysis revealed that the eradication treatment drastically altered the gut microbiome, with the Escherichia and Klebsiella genera emerging as the predominant bacteria. Interestingly, the eradication treatment significantly increased the relative abundance and diversity of resistome and mobilome in gut microbiota. Eradication of H. pylori also enriched AMR genes (ARGs) conferring resistance to antibiotics not administered because of the co-location with other ARGs or mobile genetic elements (MGEs). Additionally, the Escherichia and Klebsiella genera were identified as the primary bacterial hosts of these highly transferable ARGs. Furthermore, the genomic variations associated with ARGs in Escherichia coli (E. coli) caused by the eradication treatment were profiled, including the parC, parE, and gyrA genes. These findings revealed that H. pylori eradication promoted the enrichment of ARGs and MGEs in the Escherichia and Klebsiella genera, and further facilitated bacterial evolution through the horizontal transfer of ARGs and genomic variations.}, } @article {pmid39999861, year = {2025}, author = {Mejia, G and Jara-Servin, A and Hernández-Álvarez, C and Romero-Chora, L and Peimbert, M and Cruz-Ortega, R and Alcaraz, LD}, title = {Rhizosphere Microbiome Influence on Tomato Growth under Low-Nutrient Settings.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaf019}, pmid = {39999861}, issn = {1574-6941}, abstract = {Studies have suggested that reduced nutrient availability enhances microbial diversity around plant roots, positively impacting plant productivity. However, the specific contributions of rhizosphere microbiomes in nutrient-poor environments still need to be better understood. This study investigates tomato (Solanum lycopersicum L.) root microbiome under low-nutrient conditions. Plants were grown in hydroponics with soil-derived microbial community inoculations. We hypothesised that nutrient limitation would increase the selection of beneficial bacterial communities, compensating for nutrient deficiencies. We identified 12 294 OTUs across treatments and controls using 16S rRNA gene sequencing. Increased plant biomass was observed in treatments compared to controls, suggesting a role for the microbiome in mitigating nutrient limitations. The relative abundance of genera such as Luteolibacter and Sphingopyxis relative abundance correlated with plant phenotypic traits (p ≤ 0.05), and their presence was further validated using shotgun metagenomics. We annotated 722 677 protein families and calculated a core set of 48 116 protein families shared across all treatments and assigned them into Bacteria (93.7%) and Eukaryota (6.2%). Within the core bacterial metagenome, we identified protein families associated with pathways involved in positive plant interactions like the nitrogen fixation. Limited nutrient availability enhanced plant productivity under controlled conditions, offering a path to reduce fertiliser use in agriculture.}, } @article {pmid39999781, year = {2025}, author = {Chrismas, N and Yahr, R}, title = {Genomics: A window into the molecular mystery box of lichen symbiosis.}, journal = {Current biology : CB}, volume = {35}, number = {4}, pages = {R139-R141}, doi = {10.1016/j.cub.2025.01.034}, pmid = {39999781}, issn = {1879-0445}, mesh = {*Lichens/genetics/physiology/microbiology ; *Symbiosis/genetics ; *Genomics ; Metagenomics ; }, abstract = {How is a symbiosis built? Lichen metagenomic and metatranscriptomic surveys comparing growth stages, experimental treatments and environmental settings identify a catalogue of candidate genes - and microbial partners - in a developing model system.}, } @article {pmid39999355, year = {2025}, author = {Ahmed, AA and Park, SY and Smollin, MJ and Lindner, MS and Sarmiento Clemente, A and Del Valle Penella, A and Laufer, PM and Sanchez-Vegas, C and Cotilla, MR and Melish, ME and Trieu, C and Kabani, NA and Cooper, J and Lloyd, AR and Kimberlin, DW and Arnold, JC and Jordan-Villegas, A and Patterson, LE and Foster, CE and Yagupsky, P}, title = {Plasma Microbial Cell-free DNA Sequencing for the Detection of Kingella kingae Pediatric Spinal Infections.}, journal = {The Pediatric infectious disease journal}, volume = {}, number = {}, pages = {}, doi = {10.1097/INF.0000000000004743}, pmid = {39999355}, issn = {1532-0987}, abstract = {BACKGROUND: Diagnosis of Kingella kingae skeletal system infections is made challenging by the microbe's fastidious nature. Detection and quantification of circulating microbial cell-free DNA (mcfDNA) in plasma by the Karius Test, a commercial metagenomic sequencing test, may offer promise in diagnosing pediatric spinal infections caused by difficult-to-culture organisms such as K. kingae.

METHODS: Plasma mcfDNA sequencing detections of K. kingae from April 2018 to December 2020 were reviewed to identify pediatric (age <18 years) patients. Medical charts of those with spinal infections were reviewed, and mcfDNA sequencing diagnostic performance was compared with usual care tests (ie, cultures, polymerase chain reaction).

RESULTS: Ten children with K. kingae spinal infections were identified across 7 institutions. The median age was 16.5 months (range 11-23 months). All case-patients had vertebral osteomyelitis with 9 having spondylodiscitis. Compared with usual care tests, mcfDNA sequencing was significantly more sensitive (McNemar's test 6.25, 2-tailed P = 0.0133). It was the only method of microbiological diagnosis in 9 patients, providing results in a median of 2.5 days (range 2-5 days) from sample collection. K. kingae mcfDNA was detected despite antibiotic pretreatment in 5/5 case-patients. Pathogen-tailoring of antimicrobial coverage was undertaken in 9 children.

CONCLUSION: Plasma mcfDNA sequencing offers a rapid, noninvasive method of detecting K. kingae causing pediatric spinal infections. This culture-independent approach may facilitate diagnosis, despite antibiotic pretreatment and subsequently targeted therapy and potentially obviate the need for biopsy.}, } @article {pmid39999339, year = {2025}, author = {Hohmann, M and Iliasov, D and Larralde, M and Johannes, W and Janßen, KP and Zeller, G and Mascher, T and Gulder, TAM}, title = {Heterologous Expression of a Cryptic BGC from Bilophila sp. Provides Access to a Novel Family of Antibacterial Thiazoles.}, journal = {ACS synthetic biology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acssynbio.5c00042}, pmid = {39999339}, issn = {2161-5063}, abstract = {Human health is greatly influenced by the gut microbiota and microbiota imbalance can lead to the development of diseases. It is widely acknowledged that the interaction of bacteria within competitive ecosystems is influenced by their specialized metabolites, which act, e.g., as antibacterials or siderophores. However, our understanding of the occurrence and impact of such natural products in the human gut microbiome remains very limited. As arylthiazole siderophores are an emerging family of growth-promoting molecules in pathogenic bacteria, we analyzed a metagenomic data set from the human microbiome and thereby identified the bil-BGC, which originates from an uncultured Bilophila strain. Through gene synthesis and BGC assembly, heterologous expression and mutasynthetic experiments, we discovered the arylthiazole natural products bilothiazoles A-F. While established activities of related molecules indicate their involvement in metal-binding and -uptake, which could promote the growth of pathogenic strains, we also found antibiotic activity for some bilothiazoles. This is supported by biosensor-experiments, where bilothiazoles C and E show PrecA-suppressing activity, while bilothiazole F induces PblaZ, a biosensor characteristic for β-lactam antibiotics. These findings serve as a starting point for investigating the role of bilothiazoles in the pathogenicity of Bilophila species in the gut.}, } @article {pmid39998665, year = {2025}, author = {Szóstak, N and Budnik, M and Tomela, K and Handschuh, L and Samelak-Czajka, A and Pietrzak, B and Schmidt, M and Kaczmarek, M and Galus, Ł and Mackiewicz, J and Mackiewicz, A and Kozlowski, P and Philips, A}, title = {Exploring correlations between gut mycobiome and lymphocytes in melanoma patients undergoing anti-PD-1 therapy.}, journal = {Cancer immunology, immunotherapy : CII}, volume = {74}, number = {4}, pages = {110}, pmid = {39998665}, issn = {1432-0851}, support = {2017/25/B/NZ5/01949//Narodowe Centrum Nauki/ ; POIR.04.01.02-00-0025/17-00//Narodowe Centrum Badań i Rozwoju/ ; }, mesh = {Humans ; *Melanoma/drug therapy/immunology ; *Gastrointestinal Microbiome/immunology/drug effects ; Male ; Female ; Middle Aged ; *Lymphocytes/immunology ; *Immune Checkpoint Inhibitors/therapeutic use ; *Mycobiome ; Aged ; Programmed Cell Death 1 Receptor/antagonists & inhibitors ; Adult ; Skin Neoplasms/immunology/drug therapy/microbiology ; Fungi/immunology ; }, abstract = {Research has shown that the microbiome can influence how the immune system responds to melanoma cells, affecting the course of the disease and the outcome of the therapy. Here, we used the metagenomic approach and flow cytometry analyses of blood cells to discover correlations between gut fungi of metastatic melanoma patients enrolled in anti-PD-1 therapy and lymphocytes in their blood.We analyzed the patterns of associations before the first administration of anti-PD-1 therapy (BT, n = 61) and in the third month of the therapy (T3, n = 37), allowing us to track changes during treatment. To understand the possible impact of gut fungi on the efficacy of anti-PD-1 therapy, we analyzed the associations in clinical beneficiaries (CB, n = 37) and non-beneficiaries (NB, n = 24), as well as responders (R, n = 28) and non-responders (NR, n = 33).Patients with LDH < 338 units/L, overall survival (OS) > 12, CB, as well as R, had lower levels of Shannon diversity (p = 0.02, p = 0.05, p = 0.05, and p = 0.03, respectively). We found that the correlation pattern between intestinal fungi and lymphocytes was specific to the type of response, positive or negative. When comparing CB and NB groups, correlations with opposite directions were detected for C. albicans, suggesting a response-specific immune reaction. For CB, M. restricta exhibited a set of correlations with different types of lymphocytes, with prevalent positive correlations, suggesting a robust immune response in the CB group. This result extends our former research, where M. restricta and C. albicans were associated with an increased risk of melanoma progression and a poorer response to anti-PD-1 treatment.}, } @article {pmid39998261, year = {2025}, author = {Woh, PY and Chen, Y and Kumpitsch, C and Mohammadzadeh, R and Schmidt, L and Moissl-Eichinger, C}, title = {Reevaluation of the gastrointestinal methanogenic archaeome in multiple sclerosis and its association with treatment.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0218324}, doi = {10.1128/spectrum.02183-24}, pmid = {39998261}, issn = {2165-0497}, abstract = {The role of the gut archaeal microbiome (archaeome) in health and disease remains poorly understood. Methanogenic archaea have been linked to multiple sclerosis (MS), but prior studies were limited by small cohorts and inconsistent methodologies. To address this, we re-evaluated the association between methanogenic archaea and MS using metagenomic data from the International Multiple Sclerosis Microbiome Study. We analyzed gut microbiome profiles from 115 MS patients and 115 healthy household controls across Buenos Aires (27.8%), Edinburgh (33.9%), New York (10.4%), and San Francisco (27.8%). Metagenomic sequences were taxonomically classified using kraken2/bracken and a curated profiling database to detect archaea, specifically Methanobrevibacter species. Most MS patients were female (80/115), aged 25-72 years (median: 44.5), and 70% were undergoing treatment, including dimethyl fumarate (n = 21), fingolimod (n = 20), glatiramer acetate (n = 14), interferon (n = 18), natalizumab (n = 6), or ocrelizumab/rituximab (n = 1). We found no significant differences in overall archaeome profiles between MS patients and controls. However, treated MS patients exhibited higher abundances of Methanobrevibacter smithii and M. sp900766745 compared to untreated patients. Notably, M. sp900766745 abundance correlated with lower disease severity scores in treated patients. Our results suggest that gut methanogens are not directly associated with MS onset or progression but may reflect microbiome health during treatment. These findings highlight potential roles for M. smithii and M. sp900766745 in modulating treatment outcomes, warranting further investigation into their relevance to gut microbiome function and MS management.IMPORTANCEMultiple sclerosis (MS) is a chronic neuroinflammatory disease affecting the central nervous system, with approximately 2.8 million people diagnosed worldwide, mainly young adults aged 20-30 years. While recent studies have focused on bacterial changes in the MS microbiome, the role of gut archaea has been less explored. Previous research suggested a potential link between methanogenic archaea and MS disease status, but these findings remained inconclusive. Our study addresses this gap by investigating the gut archaeal composition in MS patients and examining how it changes in response to treatment. By focusing on methanogens, we aim to uncover novel insights into their role in MS, potentially revealing new biomarkers or therapeutic targets. This research is crucial for enhancing our understanding of the gut microbiome's impact on MS and improving patient management.}, } @article {pmid39998243, year = {2025}, author = {Brochu, HN and Zhang, Q and Song, K and Wang, L and Deare, EA and Williams, JD and Icenhour, CR and Iyer, LK}, title = {Characterization of vaginal microbiomes in clinician-collected bacterial vaginosis diagnosed samples.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0258224}, doi = {10.1128/spectrum.02582-24}, pmid = {39998243}, issn = {2165-0497}, abstract = {Bacterial vaginosis (BV) is a type of vaginal inflammation caused by bacterial overgrowth, upsetting the healthy microbiome of the vagina. Existing clinical testing for BV is primarily based upon physical and microscopic examination of vaginal secretions. Modern PCR-based clinical tests target panels of BV-associated microbes, such as the Labcorp NuSwab test that targets Atopobium (Fannyhessea) vaginae, Megasphaera-1, and Bacterial Vaginosis Associated Bacterium (BVAB)-2. Remnant clinician-collected NuSwab vaginal swabs underwent DNA extraction and 16S V3-V4 rRNA gene sequencing to profile microbes in addition to those included in the Labcorp NuSwab test. Community state types (CSTs) were determined using the most abundant taxon detected in each sample. PCR results for NuSwab panel microbial targets were compared against the corresponding microbiome profiles. Metabolic pathway abundances were characterized via metagenomic prediction from amplicon sequence variants (ASVs). 16S V3-V4 rRNA gene sequencing of 75 remnant vaginal swabs yielded 492 unique 16S V3-V4 ASVs, identifying 83 unique genera. NuSwab microbe quantification was strongly concordant with quantification by sequencing (P < 0.01). Samples in CST-I (18 of 18, 100%), CST-II (three of three, 100%), CST-III (15 of 17, 88%), and CST-V (one of one, 100%) were largely categorized as BV-negative via the NuSwab panel, while most CST-IV samples (28 of 36, 78%) were BV-positive or BV-indeterminate. BV-associated microbial and predicted metabolic signatures were shared across multiple CSTs. These findings highlight robust sequencing-based quantification of Labcorp NuSwab BV microbes, accurate discrimination of vaginal microbiome CSTs dominated by distinct Lactobacilli, and expanded the identification of BV-associated bacterial and metabolic biomarkers.IMPORTANCEBacterial vaginosis (BV) poses a significant health burden for women during reproductive years and onward. Current BV diagnostics rely on either panels of select microbes or on physical and microscopic evaluations by technicians. Here, we sequenced the microbiome profiles of samples previously diagnosed by the Labcorp NuSwab test to better understand disruptions to the vaginal microbiome during BV. We show that microbial sequencing can faithfully reproduce targeted PCR diagnostic results and can improve our knowledge of healthy and BV-associated microbial and metabolic biomarkers. This work highlights a robust, agnostic BV classification scheme with potential for future development of sequencing-based BV diagnostic tools.}, } @article {pmid39998226, year = {2025}, author = {Martino, C and Kellman, BP and Sandoval, DR and Clausen, TM and Cooper, R and Benjdia, A and Soualmia, F and Clark, AE and Garretson, AF and Marotz, CA and Song, SJ and Wandro, S and Zaramela, LS and Salido, RA and Zhu, Q and Armingol, E and Vázquez-Baeza, Y and McDonald, D and Sorrentino, JT and Taylor, B and Belda-Ferre, P and Das, P and Ali, F and Liang, C and Zhang, Y and Schifanella, L and Covizzi, A and Lai, A and Riva, A and Basting, C and Broedlow, CA and Havulinna, AS and Jousilahti, P and Estaki, M and Kosciolek, T and Kuplicki, R and Victor, TA and Paulus, MP and Savage, KE and Benbow, JL and Spielfogel, ES and Anderson, CAM and Martinez, ME and Lacey, JV and Huang, S and Haiminen, N and Parida, L and Kim, H-C and Gilbert, JA and Sweeney, DA and Allard, SM and Swafford, AD and Cheng, S and Inoyue, M and Niiranen, T and Jain, M and Salomaa, V and Zengler, K and Klatt, NR and Hasty, J and Berteau, O and Carlin, AF and Esko, JD and Lewis, NE and Knight, R}, title = {SARS-CoV-2 infectivity can be modulated through bacterial grooming of the glycocalyx.}, journal = {mBio}, volume = {}, number = {}, pages = {e0401524}, doi = {10.1128/mbio.04015-24}, pmid = {39998226}, issn = {2150-7511}, abstract = {The gastrointestinal (GI) tract is a site of replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and GI symptoms are often reported by patients. SARS-CoV-2 cell entry depends upon heparan sulfate (HS) proteoglycans, which commensal bacteria that bathe the human mucosa are known to modify. To explore human gut HS-modifying bacterial abundances and how their presence may impact SARS-CoV-2 infection, we developed a task-based analysis of proteoglycan degradation on large-scale shotgun metagenomic data. We observed that gut bacteria with high predicted catabolic capacity for HS differ by age and sex, factors associated with coronavirus disease 2019 (COVID-19) severity, and directly by disease severity during/after infection, but do not vary between subjects with COVID-19 comorbidities or by diet. Gut commensal bacterial HS-modifying enzymes reduce spike protein binding and infection of authentic SARS-CoV-2, suggesting that bacterial grooming of the GI mucosa may impact viral susceptibility.IMPORTANCESevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for coronavirus disease 2019, can infect the gastrointestinal (GI) tract, and individuals who exhibit GI symptoms often have more severe disease. The GI tract's glycocalyx, a component of the mucosa covering the large intestine, plays a key role in viral entry by binding SARS-CoV-2's spike protein via heparan sulfate (HS). Here, using metabolic task analysis of multiple large microbiome sequencing data sets of the human gut microbiome, we identify a key commensal human intestinal bacteria capable of grooming glycocalyx HS and modulating SARS-CoV-2 infectivity in vitro. Moreover, we engineered the common probiotic Escherichia coli Nissle 1917 (EcN) to effectively block SARS-CoV-2 binding and infection of human cell cultures. Understanding these microbial interactions could lead to better risk assessments and novel therapies targeting viral entry mechanisms.}, } @article {pmid39998220, year = {2025}, author = {Kwak, Y and Argandona, JA and Miao, S and Son, TJ and Hansen, AK}, title = {A dual insect symbiont and plant pathogen improves insect host fitness under arginine limitation.}, journal = {mBio}, volume = {}, number = {}, pages = {e0358824}, doi = {10.1128/mbio.03588-24}, pmid = {39998220}, issn = {2150-7511}, abstract = {Some facultative bacterial symbionts are known to benefit insects, but nutritional advantages are rare among these non-obligate symbionts. Here, we demonstrate that the facultative symbiont Candidatus Liberibacter psyllaurous enhances the fitness of its psyllid insect host, Bactericera cockerelli, by providing nutritional benefits. L. psyllaurous, an unculturable pathogen of solanaceous crops, also establishes a close relationship with its insect vector, B. cockerelli, increasing in titer during insect development, vertically transmitting through eggs, and colonizing various tissues, including the bacteriome, which houses the obligate nutritional symbiont, Carsonella. Carsonella supplies essential amino acids to its insect host but has gaps in some of its essential amino acid pathways that the psyllid complements with its own genes, many of which have been acquired through horizontal gene transfer (HGT) from bacteria. Our findings reveal that L. psyllaurous increases psyllid fitness on plants by reducing developmental time and increasing adult weight. In addition, through metagenomic sequencing, we reveal that L. psyllaurous maintains complete pathways for synthesizing the essential amino acids arginine, lysine, and threonine, unlike the psyllid's other resident microbiota, Carsonella, and two co-occurring Wolbachia strains. RNA sequencing reveals the downregulation of a HGT collaborative psyllid gene (ASL), which indicates a reduced demand for arginine supplied by Carsonella when the psyllid is infected with L. psyllaurous. Notably, artificial diet assays show that L. psyllaurous enhances psyllid fitness on an arginine-deplete diet. These results corroborate the role of L. psyllaurous as a beneficial insect symbiont, contributing to the nutrition of its insect host.IMPORTANCEUnlike obligate symbionts that are permanently associated with their hosts, facultative symbionts rarely show direct nutritional contributions, especially under nutrient-limited conditions. This study demonstrates, for the first time, that Candidatus Liberibacter psyllaurous, a facultative symbiont and a plant pathogen, enhances the fitness of its Bactericera cockerelli host by supplying an essential nutrient arginine that is lacking in the plant sap diet. Our findings reveal how facultative symbionts can play a vital role in helping their insect hosts adapt to nutrient-limited environments. This work provides new insights into the dynamic interactions between insect hosts, their symbiotic microbes, and their shared ecological niches, broadening our understanding of symbiosis and its role in shaping adaptation and survival.}, } @article {pmid39998197, year = {2025}, author = {Sahu, RP and Sar, P}, title = {Metagenome-assembled genomes of acetogenic enrichment obtained from deep subsurface archean granitoids of Koyna Seismogenic Zone, Koyna, India.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0092224}, doi = {10.1128/mra.00922-24}, pmid = {39998197}, issn = {2576-098X}, abstract = {We report 14 metagenome-assembled genomes (MAGs) of acetogenic bacteria (acetogens) enriched from deep (1,679-2,912 m below surface), hot (55°C-74 °C) granitoids of the Koyna Seismogenic Zone, India. These MAGs include Thermoanaerobacter pseudethanolicus, Exiguobacterium alkaliphilum, Moorella humiferrea, Caldanaerobacter subterraneus, etc. The study allowed access to the genomes of deep biosphere acetogens.}, } @article {pmid39998193, year = {2025}, author = {Tobun, OA and Adebusoye, SA and Ilori, MO}, title = {Comparative metagenomic analysis of 16S RNA amplicon sequencing of bacterial population of an industrial site contaminated with halogenated anilines.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0085624}, doi = {10.1128/mra.00856-24}, pmid = {39998193}, issn = {2576-098X}, abstract = {Here, we use 16S rRNA gene sequencing to identify bacterial communities in three soil samples from contaminated soils with halogenated anilines and empty soil (serving as control) in Lagos state, Nigeria. BNE, BLB, and BLC had unique operational taxonomic units (OTUs) of 160, 1,797, and 4,815, respectively. Proteobacteria were the dominant phyla across all samples.}, } @article {pmid39998179, year = {2025}, author = {Lu, C and Wu, Y and Zhang, Z and Mao, L and Ge, X and Wu, A and Sun, F and Jiang, Y and Peng, Y}, title = {Estimated size of the total genome and protein space of viruses.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0068324}, doi = {10.1128/msphere.00683-24}, pmid = {39998179}, issn = {2379-5042}, abstract = {Recent metagenomic studies have identified a vast number of viruses. However, the systematic assessment of the true genetic diversity of the whole virus community on our planet remains to be investigated. Here, we explored the genome and protein space of viruses by simulating the process of virus discovery in viral metagenomic studies. Among multiple functions, the power function was found to best fit the increasing trends of virus diversity and was, therefore, used to predict the genetic space of viruses. The estimate suggests that there are at least 8.23e+08 viral operational taxonomic units and 1.62e+09 viral protein clusters on Earth when assuming the saturation of the virus genetic space, taking into account the balance of costs and the identification of novel viruses. It is noteworthy that less than 3% of the viral genetic diversity has been uncovered thus far, emphasizing the vastness of the unexplored viral landscape. To saturate the genetic space, a total of 3.08e+08 samples would be required. Analysis of viral genetic diversity by ecosystem yielded estimates consistent with those mentioned above. Furthermore, the estimate of the virus genetic space remained robust when accounting for the redundancy of sampling, sampling time, sequencing platform, and parameters used for protein clustering. This study provides a guide for future sequencing efforts in virus discovery and contributes to a better understanding of viral diversity in nature.IMPORTANCEViruses are the most abundant and diverse biological entities on Earth. In recent years, a large number of viruses have been discovered based on sequencing technology. However, it is not clear how many kinds of viruses exist on Earth. This study estimates that there are at least 823 million types of viruses and 1.62 billion types of viral proteins. Remarkably, less than 3% of this large diversity has been uncovered to date. These findings highlight the enormous potential for discovering new viruses and reveal a significant gap in our current understanding of the viral world. This study calls for increased attention and resources to be directed toward viral discovery and metagenomics and provides a guide for future sequencing efforts, enhancing our knowledge of viral diversity in nature for ecology, biology, and public health.}, } @article {pmid39998061, year = {2025}, author = {Zhang, S and Zhao, C and Liu, G and Guo, L and Zhang, R and Yan, J and He, J and Guo, C}, title = {Monitoring of Pathogens Carried by Imported Flies and Cockroaches at Shenzhen Ports.}, journal = {Tropical medicine and infectious disease}, volume = {10}, number = {2}, pages = {}, doi = {10.3390/tropicalmed10020057}, pmid = {39998061}, issn = {2414-6366}, support = {2022YFC2302804//National Health Commission Medical Science and Technology development research center/ ; }, abstract = {This study tested the efficacy of xenomonitoring using contaminated flies and cockroaches at ports in Shenzhen by analysing sample data from imported flies and cockroaches from October 2023 to April 2024 to identify the pathogens they carried. Among all the samples of flies and cockroaches collected, Musca domestica vicina and Blattella germanica accounted for the highest proportion, 27.59% and 66.47%, respectively. Their positive rates for carrying Staphylococcus aureus were also the most significant, reaching 4.35% and 6.47%, respectively. The imported flies and cockroaches mainly came from Asia, with the highest proportion coming from Hong Kong, at 97.71% and 92.11%, respectively. Metagenomic sequencing indicated that the pathogens carried by the flies and cockroaches from different regions of Asia were generally similar but showed some differences. Flies from Southeast Asia, East Asia, South Asia, and West Asia and cockroaches from Southeast Asia, East Asia, and West Asia harboured unique opportunistic pathogens capable of causing gastrointestinal and respiratory infections in humans. Specifically, flies carried pathogens such as Campylobacter jejuni, Bacillus anthracis, Bacteroides fragilis, and Bordetella bronchiseptica, while cockroaches carried B. fragilis, Clostridium tetani, and Bacillus cereus. Our findings provide data support for future risk assessments of pathogens carried by imported vectors.}, } @article {pmid39997957, year = {2025}, author = {Muhie, S and Gautam, A and Mylroie, J and Sowe, B and Campbell, R and Perkins, EJ and Hammamieh, R and Garcia-Reyero, N}, title = {Effects of Environmental Chemical Pollutants on Microbiome Diversity: Insights from Shotgun Metagenomics.}, journal = {Toxics}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/toxics13020142}, pmid = {39997957}, issn = {2305-6304}, abstract = {Chemical exposure in the environment can adversely affect the biodiversity of living organisms, particularly when persistent chemicals accumulate over time and disrupt the balance of microbial populations. In this study, we examined how chemical contaminants influence microorganisms in sediment and overlaying water samples collected from the Kinnickinnic, Milwaukee, and Menomonee Rivers near Milwaukee, Wisconsin, USA. We characterized these samples using shotgun metagenomic sequencing to assess microbiome diversity and employed chemical analyses to quantify more than 200 compounds spanning 16 broad classes, including pesticides, industrial products, personal care products, and pharmaceuticals. Integrative and differential comparative analyses of the combined datasets revealed that microbial density, approximated by adjusted total sequence reads, declined with increasing total chemical concentrations. Protozoan, metazoan, and fungal populations were negatively correlated with higher chemical concentrations, whereas certain bacterial (particularly Proteobacteria) and archaeal populations showed positive correlations. As expected, sediment samples exhibited higher concentrations and a wider dynamic range of chemicals compared to water samples. Varying levels of chemical contamination appeared to shape the distribution of microbial taxa, with some bacterial, metazoan, and protozoan populations present only at certain sites or in specific sample types (sediment versus water). These findings suggest that microbial diversity may be linked to both the type and concentration of chemicals present. Additionally, this study demonstrates the potential roles of multiple microbial kingdoms in degrading environmental pollutants, emphasizing the metabolic versatility of bacteria and archaea in processing complex contaminants such as polyaromatic hydrocarbons and bisphenols. Through functional and resistance gene profiling, we observed that multi-kingdom microbial consortia-including bacteria, fungi, and protozoa-can contribute to bioremediation strategies and help restore ecological balance in contaminated ecosystems. This approach may also serve as a valuable proxy for assessing the types and levels of chemical pollutants, as well as their effects on biodiversity.}, } @article {pmid39997213, year = {2025}, author = {Calado, R and Leal, MC and Silva, RXG and Borba, M and Ferro, A and Almeida, M and Madeira, D and Vieira, H}, title = {Living Coral Displays, Research Laboratories, and Biobanks as Important Reservoirs of Chemodiversity with Potential for Biodiscovery.}, journal = {Marine drugs}, volume = {23}, number = {2}, pages = {}, doi = {10.3390/md23020089}, pmid = {39997213}, issn = {1660-3397}, support = {UIDB/50017/2020 + UIDP/50017/2020 + LA/P/0094/2020//Fundação para a Ciência e Tecnologia/ ; (Project Nº. C644915664-00000026)//"BLUE BIOECONOMY PACT", co-funded by the Next Gen-eration EU European Fund, under the incentive line "Agendas for Business Innovation" within Component 5-Capitalization and Business Innovation of the Portuguese Recovery and Resili-ence Plan (RRP), specifi/ ; }, mesh = {*Anthozoa/metabolism ; Animals ; *Coral Reefs ; *Biological Specimen Banks ; Bioprospecting ; Laboratories ; Humans ; Biological Products ; }, abstract = {Over the last decades, bioprospecting of tropical corals has revealed numerous bioactive compounds with potential for biotechnological applications. However, this search involves sampling in natural reefs, and this is currently hampered by multiple ethical and technological constraints. Living coral displays, research laboratories, and biobanks currently offer an opportunity to continue to unravel coral chemodiversity, acting as "Noah's Arks" that may continue to support the bioprospecting of molecules of interest. This issue is even more relevant if one considers that tropical coral reefs currently face unprecedent threats and irreversible losses that may impair the biodiscovery of molecules with potential for new products, processes, and services. Living coral displays provide controlled environments for studying corals and producing both known and new metabolites under varied conditions, and they are not prone to common bottlenecks associated with bioprospecting in natural coral reefs, such as loss of the source and replicability. Research laboratories may focus on a particular coral species or bioactive compound using corals that were cultured ex situ, although they may differ from wild conspecifics in metabolite production both in quantitative and qualitative terms. Biobanks collect and preserve coral specimens, tissues, cells, and/or information (e.g., genes, associated microorganisms), which offers a plethora of data to support the study of bioactive compounds' mode of action without having to cope with issues related to access, standardization, and regulatory compliance. Bioprospecting in these settings faces several challenges and opportunities. On one hand, it is difficult to ensure the complexity of highly biodiverse ecosystems that shape the production and chemodiversity of corals. On the other hand, it is possible to maximize biomass production and fine tune the synthesis of metabolites of interest under highly controlled environments. Collaborative efforts are needed to overcome barriers and foster opportunities to fully harness the chemodiversity of tropical corals before in-depth knowledge of this pool of metabolites is irreversibly lost due to tropical coral reefs' degradation.}, } @article {pmid39995421, year = {2025}, author = {Freyria, NJ and de Oliveira, TC and Meng, A and Pelletier, E and Lovejoy, C}, title = {Shotgun metagenomics reveals the flexibility and diversity of Arctic marine microbiomes.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf007}, pmid = {39995421}, issn = {2730-6151}, abstract = {Polar oceanographic regions are exposed to rapid changes in temperature, salinity, and light fields that determine microbial species distributions, but resilience to an increasingly unstable climate is unknown. To unravel microbial genomic potential of the Northern Baffin Bay's polynya, we constructed eight metagenomes from the same latitude but targeting two sides of Pikialasorsuaq (The North Water) that differ by current systems, stratification, and temperature regimes. Samples from the surface and subsurface chlorophyll maximum (SCM) of both sides were collected 13 months apart. Details of metabolic pathways were determined for 18 bacteria and 10 microbial eukaryote metagenome-assembled genomes (MAGs). The microbial eukaryotic MAGs were associated with the dominant green algae in the Mamiellales and diatoms in the Mediophyceae, which tended to respectively dominate the eastern and western sides of Pikialasorsuaq. We show that microbial community taxonomic and functional signatures were ca. 80% similar at the latitude sampled with only 20% of genes associated with local conditions. From the metagenomes we found genes involved in osmotic regulation, antifreeze proteins, and photosystem protection, with hydrocarbon biodegradation and methane oxidation potential detected. The shared genomic compliment was consistent with adaptation to the Arctic's extreme fluctuating conditions, with implications for their evolutionary history and the long-term survival of a pan-arctic microbiome. In particular, previously unrecognized genetic capabilities for methane bio-attenuation and hydrocarbon metabolism in eukaryotic phytoplankton suggest adaptation to dark conditions that will remain, despite climate warming, in the high latitude offshore waters of a future Arctic.}, } @article {pmid39995022, year = {2025}, author = {Thangavel, M and Sneha, MJX and Mani, I and Surendrababu, A and Rajapriya, P and Arulselvan, P and Alarfaj, AA and Thangavelu, I and Pandi, M}, title = {Diversity of Endophytic Fungi in Plant Species: Traditional vs. Metagenomic Approaches.}, journal = {Chemistry & biodiversity}, volume = {}, number = {}, pages = {e202402792}, doi = {10.1002/cbdv.202402792}, pmid = {39995022}, issn = {1612-1880}, abstract = {Plant microbiomes impact plant life, with fungi's unique characteristics influencing classification. Cultivation technologies influence fungal classification, and research links soil fungi with plant hosts. This study utilizes morphological and phylogenetic methods, along with NGS data from ITS2 secondary structure predicted endophytes, to identify plant leaves using both traditional and high-resolution techniques. Various topology of the study site was examined. Recent ecological studies highlight unculturable taxa, or dark taxa, where many species cannot sporulate or be cultured emphasizing the need for metagenomics approaches. The study gathered 68,791 reads from S. auriculata with 101 OTU's, 58,620 from C. spinosa with 219 OTU'S, and 66,087 from Z. mauritiana with 193 OTU's, with the majority of OTUs were related to Colletotrichum (69%) and a minimum of Ustilago (16%). A total of 49 fungal isolates were obtained from traditional methods, while 513 fungal OTU's were retrieved through metagenomic methods, confirming the presence of a highly abundant fungus population in plant samples. The study reveals that using the ITS short amplicon sequencing technique provides distinct insights into endophytic fungal communities in three plant samples. In conclusion, analysing plant fungal components using a combination of culture dependent and culture independent techniques may be a novel strategy.}, } @article {pmid39994640, year = {2025}, author = {Wu, J and Qi, Y and Zhang, W and Liu, L and Chen, J and Yang, Y and Zhang, X and Liu, X and Shi, Y}, title = {Metagenomic next-generation sequencing for etiological diagnosis of an unexpected rabies case with unclear exposure history.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {258}, pmid = {39994640}, issn = {1471-2334}, abstract = {BACKGROUND: Rabies is an acute and lethal zoonotic disease caused by the rabies virus (RABV). After onset, there are no effective drugs or treatment methods.

CASE PRESENTATION: A 49-year-old female from Hefei, Anhui Province, China, presented to a local hospital with fever, pruritus, chest distress, and shortness of breath. During the consultation, the patient exhibited agitation and was later admitted to the intensive care unit (ICU) in the local hospital for endotracheal intubation and mechanical ventilation due to worsened agitation and dyspnea. Cerebrospinal fluid (CSF) and blood samples were collected and pathogenic microorganism identification was performed by culture and mNGS. However, all results were negative. In addition, the patient did not display typical rabies-specific symptoms such as aerophobia, hydrophobia or photophobia from onset to admission. Subsequently, saliva samples were collected for mNGS detection following consultation with experts at our hospital. Nucleic acid sequences uniquely aligned to the rabies virus (RABV) were identified in these samples. The result was further confirmed by local Center for Disease Control and Prevention (CDC) through RT-qPCR which detected part of the N gene of RABV in the saliva sample. The patient was then transferred to the ICU for isolation. Unfortunately, the patient died on the 10th day of admission due to multiple organ failure. The detection of human rabies virus IgG antibodies reported positive during the advanced stage of the disease during the hospitalization. We consistently verified with the patient's family member that there was no clear history of animal bites and no history of RABV vaccination. Furthermore, we performed phylogenetic analysis of partial L and G gene sequences of RABV obtained by mNGS (designated HFG23-L and HFG23-G, respectively), the results showed that both HFG23-L and HFG23-G belonged to the China I lineage, and shared 99.7% similarity with the Fengtai strain isolated from dogs in Beijing.

CONCLUSIONS: The identification of unique RABV sequence through mNGS in the patient's saliva sample suggested that mNGS could serve as a valuable screening tool for the etiological diagnosis of rabies, especially when timely laboratory testing was unavailable or when patients lacked non-specific prodromal symptom and clear exposure history.}, } @article {pmid39993154, year = {2025}, author = {Yang, K and Zhang, L and Ruiz-Valencia, A and Song, X and Vogel, TM and Zhang, X}, title = {Heterogeneity in the Composition and Catabolism of Indigenous Microbiomes in Subsurface Soils Cocontaminated with BTEX and Chlorinated Aliphatic Hydrocarbons.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c10071}, pmid = {39993154}, issn = {1520-5851}, abstract = {The effectiveness of in situ bioremediation can be affected by an insufficient understanding of high site/soil heterogeneity, especially in cocontaminated soils and sediments. In this study, samples from multiple locations within a relatively small area (20 × 20 m[2]) contaminated with benzene, toluene, ethylbenzene, and xylene (BTEX) and chlorinated aliphatic hydrocarbons (CAHs) were compared to examine their physicochemical and microbial properties. Unsupervised clustering analysis of 16S rRNA gene amplicon and metagenome shotgun sequencing data indicates that the indigenous community differentiated into three distinct patterns. In Cluster 1, Pseudomonas, with multiple monooxygenases and glutathione S-transferase (GST), was enriched in samples contaminated with high concentrations of BTEX and CAHs. Cluster 2 contained a high fraction of cometabolic degraders. Cluster 3 was dominated by Ralstonia and organohalide-respiring bacteria (OHRBs) mediating the reductive dechlorination of CAHs. Significant differences in composition and function among microbiomes were attributed to the differential distribution of organic pollutants, even in such a small area. Incorporating genomic features with physicochemical data can significantly enhance the understanding of the heterogeneities in soil and their impacts on microbial communities, thereby providing valuable information for the optimization of bioremediation strategies.}, } @article {pmid39992229, year = {2025}, author = {Bai, Z and Zhang, YZ and Pang, Y and Imoto, S}, title = {PharaCon: A new framework for identifying bacteriophages via conditional representation learning.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btaf085}, pmid = {39992229}, issn = {1367-4811}, abstract = {MOTIVATION: Identifying bacteriophages (phages) within metagenomic sequences is essential for understanding microbial community dynamics. Transformer-based foundation models have been successfully employed to address various biological challenges. However, these models are typically pre-trained with self-supervised tasks that do not consider label variance in the pre-training data. This presents a challenge for phage identification as pre-training on mixed bacterial and phage data may lead to information bias due to the imbalance between bacterial and phage samples.

RESULTS: To overcome this limitation, we proposed a novel conditional BERT framework that incorporates label classes as special tokens during pre-training. Specifically, our conditional BERT model attaches labels directly during tokenization, introducing label constraints into the model's input. Additionally, we introduced a new fine-tuning scheme that enables the conditional BERT to be effectively utilized for classification tasks. This framework allows the BERT model to acquire label-specific contextual representations from mixed sequence data during pre-training and applies the conditional BERT as a classifier during fine-tuning and we named the fine-tuned model as PharaCon. We evaluated PharaCon against several existing methods on both simulated sequence datasets and real metagenomic contig datasets. The results demonstrate PharaCon's effectiveness and efficiency in phage identification, highlighting the advantages of incorporating label information during both pre-training and fine-tuning.

AVAILABILITY: The codes of PharaCon are now available in: https://github.com/Celestial-Bai/PharaCon.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid39992148, year = {2025}, author = {Fang, J and Chen, H and Hamal, K and Liu, D}, title = {CD86 immunohistochemical staining for the detection of Talaromyces marneffei in lesions.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0206324}, doi = {10.1128/spectrum.02063-24}, pmid = {39992148}, issn = {2165-0497}, abstract = {Talaromycosis is an invasive fungal disease caused by the pathogenic thermodimorphic fungus Talaromyces marneffei (TM), which is often overlooked in tropical and subtropical regions of Asia. In view of the diversity of clinical manifestations in patients with TM infection, early diagnosis remains challenging. We assessed the sensitivity and specificity of a novel immunohistochemical staining by performing CD86 immunohistochemical staining on 56 tissue sections from patients with talaromycosis who had fungal culture or metagenomic next-generation sequencing confirmed to exist in clinical specimens, as well as 26 patients with other fungi that had been culture-proven. Hematoxylin and eosin and periodic acid Schiff (PAS) stains were also applied to each specimen. We found that anti-CD86 antibody can label TM pathogens in 38 HIV-negative specimens (38/42) and 14 HIV-positive specimens (14/14); conversely, PAS staining yielded positive results in seven cases of HIV-negative specimens (7/42) and 13 cases of HIV-positive specimens (13/14). Additionally, CD86 immunohistochemical staining was negative in other fungi. Importantly, CD86 immunohistochemical staining significantly outperformed PAS staining in terms of localizing and highlighting TM yeasts, as well as demonstrating the specificity of 100% and a significantly higher sensitivity compared to PAS staining at 92.9% versus 35.7% (P < 0.05, McNemar test). Our findings suggest that CD86 immunohistochemical staining has the potential for the rapid diagnosis of talaromycosis.IMPORTANCETalaromycosis is an opportunistic endemic disease without typical clinical manifestations that has emerged as a fungal disease impacting the survival and mortality of immunocompromised individuals and HIV-positive individuals in endemic regions. Nonetheless, talaromycosis is completely curable if it is accurately diagnosed and treated effectively at an early stage. Rapid pathological diagnosis relies on the unique morphological features of Talaromyces marneffei observed under the microscope. This study introduces a novel pathological diagnostic approach, CD86 immunohistochemical staining, to enhance the early detection of TM-infected lesions.}, } @article {pmid39992132, year = {2025}, author = {Rodríguez-Ramos, J and Sadler, N and Zegeye, EK and Farris, Y and Purvine, S and Couvillion, S and Nelson, WC and Hofmockel, KS}, title = {Environmental matrix and moisture influence soil microbial phenotypes in a simplified porous media incubation.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0161624}, doi = {10.1128/msystems.01616-24}, pmid = {39992132}, issn = {2379-5077}, abstract = {Soil moisture and porosity regulate microbial metabolism by influencing factors, such as system chemistry, substrate availability, and soil connectivity. However, accurately representing the soil environment and establishing a tractable microbial community that limits confounding variables is difficult. Here, we use a reduced-complexity microbial consortium grown in a glass bead porous media amended with chitin to test the effects of moisture and a structural matrix on microbial phenotypes. Leveraging metagenomes, metatranscriptomes, metaproteomes, and metabolomes, we saw that our porous media system significantly altered microbial phenotypes compared with the liquid incubations, denoting the importance of incorporating pores and surfaces for understanding microbial phenotypes in soils. These phenotypic shifts were mainly driven by differences in expression of Streptomyces and Ensifer, which included a significant decrease in overall chitin degradation between porous media and liquid. Our findings suggest that the success of Ensifer in porous media is likely related to its ability to repurpose carbon via the glyoxylate shunt amidst a lack of chitin degradation byproducts while potentially using polyhydroxyalkanoate granules as a C source. We also identified traits expressed by Ensifer and others, including motility, stress resistance, and carbon conservation, that likely influence the metabolic profiles observed across treatments. Together, these results demonstrate that porous media incubations promote structure-induced microbial phenotypes and are likely a better proxy for soil conditions than liquid culture systems. Furthermore, they emphasize that microbial phenotypes encompass not only the multi-enzyme pathways involved in metabolism but also include the complex interactions with the environment and other community members.IMPORTANCESoil moisture and porosity are critical in shaping microbial metabolism. However, accurately representing the soil environment in tractable laboratory experiments remains a challenging frontier. Through our reduced complexity microbial consortium experiment in porous media, we reveal that predicting microbial metabolism from gene-based pathways alone often falls short of capturing the intricate phenotypes driven by cellular interactions. Our findings highlight that porosity and moisture significantly affect chitin decomposition, with environmental matrix (i.e., glass beads) shifting community metabolism towards stress tolerance, reduced resource acquisition, and increased carbon conservation, ultimately invoking unique microbial strategies not evident in liquid cultures. Moreover, we find evidence that changes in moisture relate to community shifts regarding motility, transporters, and biofilm formation, which likely influence chitin degradation. Ultimately, our incubations showcase how reduced complexity communities can be informative of microbial metabolism and present a useful alternative to liquid cultures for studying soil microbial phenotypes.}, } @article {pmid39992097, year = {2025}, author = {Salamzade, R and Kalan, LR}, title = {Context matters: assessing the impacts of genomic background and ecology on microbial biosynthetic gene cluster evolution.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0153824}, doi = {10.1128/msystems.01538-24}, pmid = {39992097}, issn = {2379-5077}, abstract = {Encoded within many microbial genomes, biosynthetic gene clusters (BGCs) underlie the synthesis of various secondary metabolites that often mediate ecologically important functions. Several studies and bioinformatics methods developed over the past decade have advanced our understanding of both microbial pangenomes and BGC evolution. In this minireview, we first highlight challenges in broad evolutionary analysis of BGCs, including delineation of BGC boundaries and clustering of BGCs across genomes. We further summarize key findings from microbial comparative genomics studies on BGC conservation across taxa and habitats and discuss the potential fitness effects of BGCs in different settings. Afterward, recent research showing the importance of genomic context on the production of secondary metabolites and the evolution of BGCs is highlighted. These studies draw parallels to recent, broader, investigations on gene-to-gene associations within microbial pangenomes. Finally, we describe mechanisms by which microbial pangenomes and BGCs evolve, ranging from the acquisition or origination of entire BGCs to micro-evolutionary trends of individual biosynthetic genes. An outlook on how expansions in the biosynthetic capabilities of some taxa might support theories that open pangenomes are the result of adaptive evolution is also discussed. We conclude with remarks about how future work leveraging longitudinal metagenomics across diverse ecosystems is likely to significantly improve our understanding on the evolution of microbial genomes and BGCs.}, } @article {pmid39991711, year = {2025}, author = {Lin, T}, title = {Editorial: New techniques in microbiome research - volume II: Host-microbiome interactions using 'meta-omics' techniques.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1541881}, pmid = {39991711}, issn = {2235-2988}, } @article {pmid39991687, year = {2025}, author = {Pan, Y and Jiao, FY}, title = {Helicobacter pylori infection and gastric microbiota: Insights into gastric and duodenal ulcer development.}, journal = {World journal of gastroenterology}, volume = {31}, number = {7}, pages = {100044}, pmid = {39991687}, issn = {2219-2840}, mesh = {Humans ; *Helicobacter Infections/microbiology ; *Helicobacter pylori/isolation & purification/genetics/pathogenicity ; *Duodenal Ulcer/microbiology ; *Gastrointestinal Microbiome ; *Stomach Ulcer/microbiology ; *Gastric Mucosa/microbiology/pathology ; Metagenomics/methods ; Stomach/microbiology/pathology ; Dysbiosis/microbiology ; }, abstract = {Helicobacter pylori (H. pylori) infection plays a critical role in gastric diseases, impacting the microbiota structure in gastric and duodenal ulcers. In their study, Jin et al utilized metagenomic sequencing to analyze mucosal samples from patients with ulcers and healthy controls, revealing significant changes in microbial diversity and composition. This article reviews their findings, emphasizing H. pylori's role in gastric ulcers and the need for further research on its impact on duodenal ulcers. We evaluate the study's strengths and limitations, suggesting future research directions to enhance our understanding of H. pylori's contribution to ulcerative diseases.}, } @article {pmid39991683, year = {2025}, author = {Darnindro, N and Abdullah, M and Sukartini, N and Rumende, CM and Pitarini, A and Nursyirwan, SA and Fauzi, A and Makmun, D and Nelwan, EJ and Shatri, H and Rinaldi, I and Tanadi, C}, title = {Differences in diversity and composition of mucosa-associated colonic microbiota in colorectal cancer and non-colorectal cancer in Indonesia.}, journal = {World journal of gastroenterology}, volume = {31}, number = {7}, pages = {100051}, pmid = {39991683}, issn = {2219-2840}, mesh = {Humans ; Indonesia/epidemiology ; *Colorectal Neoplasms/microbiology ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; Case-Control Studies ; *Colonoscopy ; *Colon/microbiology ; *Intestinal Mucosa/microbiology ; *RNA, Ribosomal, 16S/genetics ; Aged ; Adult ; Metagenomics/methods ; Bacteria/isolation & purification/genetics/classification ; }, abstract = {BACKGROUND: Colorectal cancer is the third most common malignancy and the fourth leading cause of cancer-related deaths worldwide. Several studies have shown an association between gut microbiota and colorectal cancer. Gut microbiota is unique and can be influenced by geographic factors and habits. This study aimed to determine the diversity and composition of colonic mucosal microbiota in patients with and without colorectal cancer.

AIM: To determine the diversity and composition of colonic mucosal microbiota in patients with and without colorectal cancer in Indonesia.

METHODS: This case-control study included 59 subjects (35 colorectal cancer patients and 24 non-colorectal cancer patients indicated for colonoscopy at Dr. Cipto Mangunkusumo Gastrointestinal Endoscopy Center and Fatmawati Hospital. Microbiota examination was performed using 16S rRNA sequencing. Bioinformatics analysis was performed using the wf-metagenomics pipeline from EPI2Me-Labs (Oxford Nanopore Technologies platform).

RESULTS: Patients with colorectal cancer had a higher median index value on the Shannon index (3.28 vs 2.82, P > 0.05) and a lower value on the Simpson index (0.050 vs 0.060, P > 0.05). Significant differences in beta diversity were observed at the genus (P = 0.002) and species levels (P = 0.001). Firmicutes, Proteobacteria, Bacteroidetes, and Fusobacteria were the dominant phyla. The genera Bacteroides, Campylobacter, Peptostreptococcus, and Parvimonas were found more frequently in colorectal cancer, while Faecalibacterium, Haemophilus, and Phocaeicola were more frequently found in non-colorectal cancer. The relative abundance of Fusobacterium nucleatum, Bacteroides fragilis, Enterococcus faecalis, Campylobacter hominis, and Enterococcus faecalis species was significantly elevated in patients with colorectal cancer. Meanwhile, Faecalibacterium prausnitzii, Faecalibacterium duncaniae, and Prevotella copri were more commonly found in non-colorectal cancer.

CONCLUSION: Patients with colorectal cancer exhibit distinct differences in the composition and diversity of their colonic mucosal microbiota compared to those with non-colorectal cancer. This study was reviewed and approved by the Ethics Committee of Faculty of Medicine, Universitas Indonesia (No. KET-1517/UN2.F1/ETIK/PPM.00.02/2023).}, } @article {pmid39991100, year = {2025}, author = {Bajinka, O and Ouedraogo, SY and Li, N and Zhan, X}, title = {Multiomics as instrument to promote 3P medical approaches for the overall management of respiratory syncytial viral infections.}, journal = {The EPMA journal}, volume = {16}, number = {1}, pages = {217-238}, pmid = {39991100}, issn = {1878-5077}, abstract = {Respiratory syncytial viral (RSV) infection is a leading persisting pulmonary disease-causing agent. It causes loss of lives especially among infants, old ages, and adults immunocompromised individuals. This viral pathogen infects children more especially those under the age of 2 and may lead to death. It causes 3 million hospitalizations and up to 60,000 deaths annually for under the age of 5. The most vulnerable are immunocompromised individuals and asthmatic children with suboptimal antiviral defenses. It is associated with bronchiolitis, pneumonia, and bronchopneumonia. Despite all the current interventions and clinical trials, the only available therapeutic strategies for this viral infection are palliative care. Therefore, it is imperative to understand the pathogenicity of RSV and the corresponding host immune response to depict a sort of a targeted intervention. With the increasingly cutting-edge methods in harnessing the pathogenicity of this viral infection, high throughput systems including omics technological advances are at the spotlight. For instance, the associated genes with RSV complications for the host, the set of microbiome identified as operational taxonomic unit, the upregulated or downregulated metabolites, the protein subtypes, and the small molecules can help explain the viral microenvironment. Moreover, these big data will lead to RSV patients' stratification through individualized patient profiles that will bring in targeted prevention and treatment algorithms tailored to individualized patients' profiles. Through this, the virus and host interactions based on the pathogenicity of infection will provide a strong ground for depicting the prevention, prediction, and personalized medicine (3PM) for RSV. The 3PM approach brought cutting edge functional medicine to the healthcare givers, thus conferring targeted prevention and precision medicine while observing personalized treatment as well as preventive regularities. The viral replication mechanisms against the host defense mechanisms are crucial for the development of safe and effective therapy. Integrative personal omics profiles, whose analysis is based on the combined proteomics, transcriptomics, genomics, proteoformics, metabolomics, and autoantibody profiles, are very robust for predicting the risk of RSV infection. The targeted prevention will emerge from the patient stratification when the diagnosis is accurately predicted. In addition, the personalized medical services will give an effective prognostic assessment for RSV complications.}, } @article {pmid39990777, year = {2025}, author = {Zhu, X and Cao, L and Wang, J and Lu, X and Huang, Z and Wen, X and Bian, L and Wu, C and Zou, M}, title = {Identification of Pathogens in HIV-Infected Patients Using Metagenomic Next-Generation Sequencing (mNGS) as Compared to Conventional Microbiological Tests (CMTs).}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {929-940}, pmid = {39990777}, issn = {1178-6973}, abstract = {BACKGROUND: The rapid and accurate identification of infectious pathogens in HIV-infected patients remains a challenge. Metagenomic next-generation sequencing (mNGS) is a panpathogen assay for rapid diagnosis of infectious diseases. Here, the diagnostic value of mNGS was evaluated in HIV-infected patients and compared with conventional microbiological tests (CMTs).

METHODS: This study was conducted on 216 hIV-infected patients with suspected opportunistic infections. Infectious pathogen detection was done by mNGS and conventional microbiological tests, respectively.

RESULTS: A total of 195 patients (90.2%) were positive for microbial pathogens by mNGS, while 135 patients (62.5%) were positive for microbial pathogens by CMTs. Mixed infection was identified in 92 patients by mNGS, and 41 patients were detected with mixed infection by CMTs. Fungi and virus mixed infection was the most frequent pattern detected by mNGS (32, 14.8%) and CMTs (22, 10.2%). The CD4+ T cell count in patients with mixed pathogens was significantly lower than that in patients infected with a single pathogen. Pathogens were quickly identified by mNGS in 151 patients (69.9%), and appropriate treatments were initiated. In 47 patients antibacterial agents were adjusted based on mNGS results, in 39 patients antifungal agents were changed, and 35 patients had antiviral agents added.

CONCLUSION: mNGS is a valuable tool and enhances rapid microbiological identification in HIV-infected patients. Combined with CMTs, mNGS may facilitate personalized antimicrobial treatment strategies and increase survival.}, } @article {pmid39990197, year = {2025}, author = {Cheng, H and Li, H and Zhao, Y and Yang, K and Wang, J and Tan, B and Ma, X}, title = {Transcriptome analysis reveals modulations in glycosylation profiles of the mucosal barrier and their potential interaction with gut microbiota in weaned piglets.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {20}, number = {}, pages = {226-238}, pmid = {39990197}, issn = {2405-6383}, abstract = {The current study aims to investigate the potential interaction between glycosylation profiles of the Ningxiang breed (NX) and Western Duroc × Landrace × Yorkshire breed (DLY) weaned piglets, and their characteristic microbes, employing integrated analyses of transcriptomics and metagenomics. Twenty-four (12 NX and 12 DLY) at 28 days of age were transported into an experimental house and fed the same weaned piglet diet. The trail period was 7 days. Results revealed that the NX piglets had a higher growth-to-feed ratio, body weight gain scale, and lower pathological score of intestinal injury compared with the DLY piglets (P < 0.01). DLY piglets displayed elevated mRNA expression levels of MUC2 and MUC5AC in colonic mucosal tissue than NX piglets (P < 0.05). Within the O-linked glycosylated differentially expressed genes (DEGs), FNTA, GALNT18, POMGNT1, POMGNT2, and POMT1 were significantly upregulated in DLY piglets relative to NX piglets (P < 0.05). Conversely, C1GALT2, GALNT1, KMT2C, and OGT were significantly downregulated in DLY piglets compared to NX piglets (P < 0.05). The KMT2C gene was hardly expressed in the transcriptome of DLY piglets. At the phylum taxonomic level, NX piglets had a higher abundance of Firmicutes, while DLY piglets had a higher abundance of Proteobacteria. At the genus taxonomic level, NX piglets had a higher abundance of Lactobacillus, whereas DLY piglets had a higher abundance of Collinsella, Enterococcus and Escherichia. The results of the correlation between intestinal differential bacteria and O-chain glycosylated DEG showed that C1GALT2, GALNT1 and KMT2 were associated with Lactobacillus_pontis showed a positive correlation (R = 0.67). Through comparative analysis of differentially glycosylated genes and their associated functions, this study highlights the potential role of reduced expression of GALNT1 and KMT2C genes, involved in O-linked protein and glycan reactions, in impairing the intestinal barrier function of DLY piglets. Furthermore, members of the Lactobacillus and Prevotella genera may actively contribute to the regulation of piglet colon glycosylation profiles.}, } @article {pmid39990142, year = {2025}, author = {Rodriguez, P and Berg, JS and Deng, L and Vogel, H and Okoniewski, M and Lever, MA and Magnabosco, C}, title = {Persistent functional and taxonomic groups dominate an 8,000-year sedimentary sequence from Lake Cadagno, Switzerland.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1504355}, pmid = {39990142}, issn = {1664-302X}, abstract = {Most of our knowledge of deep sedimentary life comes from marine environments; however, despite their relatively small volume, lacustrine sediments constitute one of the largest global carbon sinks and their deep sediments are largely unexplored. Here, we reconstruct the microbial functional and taxonomic composition of an 8,000-year Holocene sedimentary succession from meromictic Lake Cadagno (Switzerland) using shotgun metagenomics and 16S rRNA gene amplicon sequencing. While younger sediments (<1,000 years) are dominated by typical anaerobic surface sedimentary bacterial taxa (Deltaproteobacteria, Acidobacteria, and Firmicutes), older layers with lower organic matter concentrations and reduced terminal electron acceptor availability are dominated by taxa previously identified as "persistent populations" within deep anoxic marine sediments (Candidatus Bathyarchaeia, Chloroflexi, and Atribacteria). Despite these dramatic changes in taxonomic community composition and sediment geochemistry throughout the sediment core, higher-order functional categories and metabolic marker gene abundances remain relatively consistent and indicate a microbial community capable of carbon fixation, fermentation, dissimilatory sulfate reduction and dissimilatory nitrate reduction to ammonium. As the conservation of these metabolic pathways through changes in microbial community compositions helps preserve the metabolic pathway connectivity required for nutrient cycling, we hypothesize that the persistence of these functional groups helps enable the Lake Cadagno sedimentary communities persist amidst changing environmental conditions.}, } @article {pmid39990124, year = {2025}, author = {Carpenter, RE and Almas, S and Tamrakar, VK and Sharma, R}, title = {Dataset for comparative analysis of precision metagenomics and traditional methods in urinary tract infection diagnostics.}, journal = {Data in brief}, volume = {59}, number = {}, pages = {111339}, pmid = {39990124}, issn = {2352-3409}, abstract = {This study presents a comprehensive dataset comparing three diagnostic methodologies-microbial culture, polymerase chain reaction (PCR), and precision metagenomics (precision metagenomics)-for the detection and classification of uropathogens in urine samples from patients with suspected urinary tract infections (UTIs). While microbial culture remains the gold standard for UTI diagnosis, it has limitations in sensitivity, particularly for fastidious or non-culturable microorganisms. PCR offers higher sensitivity but is restricted to pre-targeted organisms, limiting its diagnostic range. Precision Metagenomics, a target-agnostic sequencing method, provides a more inclusive approach by enabling the identification of a broad spectrum of pathogens, including bacteria, viruses, fungi, and parasites, without prior knowledge of the organisms. The dataset includes 47 urine samples, each analyzed by microbial culture, PCR, and precision metagenomics, followed by bioinformatic classification using the Explify® platform. precision metagenomics identified significantly more uropathogens (62 distinct organisms) compared to PCR (19 organisms) and microbial culture (13 organisms), with 98 % of samples testing positive for polymicrobial infections via precision metagenomics. The precision metagenomics method demonstrated superior diagnostic yield by detecting pathogens that were missed by both microbial culture and PCR, particularly in culture-negative and PCR-negative cases. This dataset holds substantial reuse potential for further research into the microbiome of urinary tract infections, pathogen discovery, antimicrobial resistance studies, and the development of more accurate diagnostic models for UTI management. By offering insights into both polymicrobial infections and rare pathogens, this dataset supports the advancement of diagnostic strategies for complex and chronic UTIs.}, } @article {pmid39989955, year = {2025}, author = {Cronin, P and Siegers, J and Heang, V and Tok, S and Sin, S and Sievers, B and Omondi, V and Nuon, S and Chhel, K and Nouhin, J and Chim, V and Seng, B and Hak, M and San, S and Tum, S and Claes, F and Firth, C and Su, Y and Smith, G and Karlsson, E}, title = {Air sampling accurately captures circulating zoonotic viral diversity emerging from poultry live-animal markets.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-5682962/v1}, pmid = {39989955}, issn = {2693-5015}, abstract = {Environmental surveillance has emerged as a pivotal strategy for early detection of pathogens that pose threats to humans (1) but has not been utilized for zoonotic agents. In Asia, live-bird markets (LBMs) are key human-animal interfaces for zoonotic virus transmission (2). Traditional sampling strategies are time-consuming, expensive, threaten animal welfare and have significant occupational biosafety risks. In this study, we assessed the performance of metagenomics on environmental samples (ES) compared to traditional poultry swabs for detecting avian viral pathogens in LBMs in Cambodia. ES, including air, cage swabs, and carcass wash water, were collected alongside throat and cloacal swabs from domestic chickens and ducks across twelve sampling visits in two LBMs over a 15-month period. Viral nucleic acids were extracted and sequenced using a capture probe-based metagenomics approach. Our results show that metagenomics on ES outperformed traditional poultry samples in detecting the highly pathogenic Influenza A/H5N1, including circulating clades 2.3.4.4b and 2.3.2.1c, which were found in the environment but missed by poultry swabs on multiple occasions. Environmental metagenomics was also highly sensitive in the detection of over 40 other viruses from key pathogen families such as Astroviridae , Coronaviridae , Picornaviridae , and Retroviridae . Viral contigs from ES showed high similarity to those from poultry swabs further highlighting the accuracy of this approach. Our findings highlight metagenomics on ES can precisely and effectively replicate metagenomic results from traditional surveillance samples, offering broader coverage and enhanced detection of avian pathogens. This robust approach could be pivotal for mitigating zoonotic spillover, controlling pathogen transmission at LBMs, and enhancing pandemic preparedness strategies.}, } @article {pmid39988326, year = {2025}, author = {Zheng, X and Zou, W and Zou, S and Ye, J and Bao, Z and Song, Y}, title = {Diagnostic Significance of Metagenomic Next-Generation Sequencing in Immunocompromised Patients With Suspected Pulmonary Infection.}, journal = {Immunology}, volume = {}, number = {}, pages = {}, doi = {10.1111/imm.13911}, pmid = {39988326}, issn = {1365-2567}, support = {2020J11134//Science and Technology Projects of Fujian Province/ ; }, abstract = {Immunocompromised hosts are highly vulnerable to lung infections, but the efficacy of traditional diagnosis is unsatisfactory. Metagenomic next-generation sequencing (mNGS) has high throughput and broad coverage. Its value in different types of immunocompromised patients has yet to be fully explored. Therefore, the study aims to evaluate the value of mNGS in immunocompromised patients. Clinical data from immunocompromised patients with suspected pulmonary infection (PI) (September 2018-2021) were retrospectively analysed. Patients were categorised into PI (87 cases) and non-pulmonary infection (NPI, 14 cases) groups. The diagnostic performance between mNGS and conventional microbiological tests (CMTs) was compared. Subgroup analyses were also conducted based on whether the patients received organ transplantation, including the comparison of the diagnostic performance of mNGS and culture and the spectrum of characteristics among them. mNGS demonstrated significantly elevated diagnostic sensitivity (p < 0.001) over traditional methods, with a pronounced advantage in identifying mixed PIs (p < 0.05). Among immunocompromised cohorts, mNGS outperformed cultures, showing higher positivity rates in both organ transplant (p < 0.001) and non-transplant patients (p < 0.001). Mixed infections, predominantly bacterial-fungal, were more prevalent in transplant recipients with reduced lymphocytes and CD4[+] T cells. Pathogen profiles differed, with Pneumocystis jirovecii, Cytomegalovirus, and Pseudomonas aeruginosa predominating in organ transplant recipients, and P. jirovecii, P. aeruginosa, Streptococcus pneumoniae and Streptococcus pallidum in non-transplant individuals. mNGS is valuable in diagnosing PI and mixed infections in immunocompromised patients, which may be particularly suitable for identifying mixed infections in patients with organ transplants and low lymphocyte and CD4[+] T lymphocyte counts.}, } @article {pmid39988254, year = {2025}, author = {Hou, W and Yu, J and Shi, H and Xu, J and Chen, SS and Shaban, SS and Kim, Y and Bai, J}, title = {As a reservoir of antibiotic resistance genes and pathogens, the hydrodynamic characteristics drive their distribution patterns in Lake Victoria.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {125903}, doi = {10.1016/j.envpol.2025.125903}, pmid = {39988254}, issn = {1873-6424}, abstract = {Antibiotic resistance genes (ARGs) and pathogenic bacteria pose significant challenges to human health, and hydrodynamic processes complicate their transmission mechanisms in lake ecosystems, particularly in tropical regions. Lake Victoria supports abundant water resources and provides livelihoods for millions of people, yet the environmental behavior of ARGs and pathogenic bacteria remains unclear. Herein, the novel insights into the co-occurrence patterns and transmission mechanisms of ARGs and pathogenic bacteria in Lake Victoria was investigated via molecular techniques and a hydrodynamic model. The results showed that as a large reservoir of ARGs and pathogenic bacteria, a total of 172 ARG subtypes and 93 pathogenic bacteria were identified in Lake Victoria. ARGs were spread through mobile genetic elements (tnpA4 and int2), enhancing the antibiotic resistance and virulence factors (secretion systems, regulatory factors, and toxins) of various pathogenic bacteria. The hydrodynamic model indicated that surface wind-driven currents and bottom compensatory flows shaped the outward dispersion of ARGs and pathogenic bacteria from the gulf. The NCM model suggested that water exchange accelerated the diffusion of antibiotics and pathogens, likely enhancing the deterministic assembly process of ARGs and the stochastic assembly process of pathogens. The PLS-PM model revealed that hydrodynamics directly influenced the accumulation of ARGs and pathogenic bacteria, and subsequently affected the diffusion and distribution patterns of ARGs and pathogens by facilitating the propagation of MGEs. Our study overcomes the limitations associated with lake and microenvironmental scale, providing insights and understanding into the transmission mechanisms of ARGs and pathogenic bacteria.}, } @article {pmid39987875, year = {2025}, author = {Pourrostami Niavol, K and Andaluri, G and Achary, MP and Suri, RPS}, title = {How does carbon to nitrogen ratio and carrier type affect moving bed biofilm reactor (MBBR): Performance evaluation and the fate of antibiotic resistance genes.}, journal = {Journal of environmental management}, volume = {377}, number = {}, pages = {124619}, doi = {10.1016/j.jenvman.2025.124619}, pmid = {39987875}, issn = {1095-8630}, abstract = {With the spread of antibiotic resistance genes (ARGs) in the environment, monitoring and controlling ARGs have become an emerging issue of concern in biological processes. Moving bed biofilm reactors (MBBR) have been gaining attention for application in wastewater treatment. Since the performance of MBBR depends on operational parameters and biocarriers, selection of suitable biocarriers and start-up conditions are vital for efficiency of MBBRs. This study investigates the effects of different carbon-to-nitrogen (C/N) ratios and carrier types on the fate of selected ARGs and microbial communities in four MBBR systems using two conventional (K3 and sponge biocarrier (SB)) and two modified carriers (Fe-Ca@SB and Ze-AC@SB). Results showed that the modified biocarriers achieved higher NH4-N removal and better simultaneous nitrification and denitrification (SND) performance (90%) at C/N of 20. However, as the C/N ratio decreased to 10 and 7, the performance of all bioreactors was approximately similar. Moreover, COD removal of 90% was achieved in all reactors regardless of C/N ratio and carrier type. Further studies on the fate of selected ARGs (tetA, blaTEM, ampR) showed that the C/N ratio could affect the abundance of target ARGs, especially for K3 biocarrier, with tetA being the most abundant gene. Also, as the C/N ratio decreased, intl1 was enriched using K3 and SB. However, for Ze-AC@SB, the increase in the abundance of ARGs and intl1 was the lowest making it a reliable carrier not only in MBBR performance but in the control of ARGs. Metagenomic studies showed that the C/N ratio and carrier type could alter the diversity and structure of the bacterial communities in different MBBR systems, with Proteobacteria being the most abundant phylum in all four systems.}, } @article {pmid39987826, year = {2025}, author = {Liu, Y and Chen, H and Liu, C and Wang, R and Zhang, Z}, title = {Effects and mechanisms of reclaimed water irrigation and tillage treatment on the propagation of antibiotic resistome in soil.}, journal = {The Science of the total environment}, volume = {968}, number = {}, pages = {178935}, doi = {10.1016/j.scitotenv.2025.178935}, pmid = {39987826}, issn = {1879-1026}, abstract = {Reclaimed water irrigation can alleviate water resource pressure, while soil tillage is a common agricultural practice to increase crop yield. However, both of these practices may lead to the propagation of antibiotic resistance genes (ARGs). To date, there has been little research that has systematically investigated this issue. To fill this gap, this study has conducted microcosmic experiments to reveal the effect and mechanisms of using reclaimed water for irrigation and tillage treatment on the propagation of ARGs in soil, by utilizing high-throughput sequencing-based metagenomic assembly analysis approaches. The results showed irrigation significantly enhanced the abundance and diversity of ARGs in the soil. Compared to the initial soil, the total coverage of ARGs in the irrigated soil increased by 14.0 % (without tillage) to 22.7 % (with tillage). In particular, tillage treatment facilitated the enhancement of antibiotic resistome in the environment. The analysis with null model suggested soil tillage enabled ecological drift (52.4 %-66.7 %) to dominate the ARGs. Quantitative source apportionment using a machine learning-based microbial source tracking tool showed the irrigation exhibited considerable effect on the ARGs in the soil, with an average contribution of about 13.3 %-17.0 %. Network analysis revealed a close association of ARGs with mobile genetic elements (MGEs) and virulence factors, indicating potential dissemination risk of ARGs in the soil. Microbial communities, MGEs, and environmental factors collectively shaped the ARGs in the environment. Relatively, soil tillage enhanced the complex and stability of network structure and led to the colonization of ARGs in modular manner, resulting in higher contribution of ecological drift to soil resistome. Findings of this study will contribute to the management of resistome risks in reclaimed water utilization and agricultural activities for protecting soil ecosystem safety and public health.}, } @article {pmid39987648, year = {2025}, author = {Zampieri, A and Carraro, L and Mohammadpour, H and Rovere, GD and Milan, M and Fasolato, L and Cardazzo, B}, title = {Presence and characterization of the human pathogenic Vibrio species in the microbiota of Manila clams using cultural and molecular methods.}, journal = {International journal of food microbiology}, volume = {433}, number = {}, pages = {111113}, doi = {10.1016/j.ijfoodmicro.2025.111113}, pmid = {39987648}, issn = {1879-3460}, abstract = {The North Adriatic lagoons and the Po River Delta are important areas for farming Manila clams (Ruditapes philippinarum). These areas have been heavily impacted by climate change, reducing livestock numbers and increasing pathogen spread. Shellfish, particularly clams, are primary vectors for Vibrio pathogens affecting humans. In this study, the occurrence of human pathogenic Vibrio species on Manila clams was investigated using an integrated approach that combined culture-dependent and culture-independent techniques. Samples were collected over three years from farming areas in the northeastern Adriatic lagoons and the Po River Delta, regions seriously impacted by climate change and pollution. In this study, species of the human pathogen Vibrio were analyzed in the clam microbiota and characterized using recA-pyrH metabarcoding and shotgun metagenomics. Human pathogenic Vibrio species were widespread in the clam microbiota, especially in summer, demonstrating that the environmental conditions on the northern Adriatic coasts allowed the growth of these bacteria. V. parahaemolyticus and V. vulnificus were also quantified using qPCR in <50 % of summer samples Shotgun metagenomics revealed the similarity of V. parahaemolyticus strains to other worldwide genomes, enabling improved pathogen identification and tracking. In the future, climate change could cause these conditions to become even more favorable to these bacteria, potentially increasing pathogen spread. Consequently, enhanced monitoring and control of both the environment and seafood products should be planned to ensure food safety.}, } @article {pmid39987284, year = {2025}, author = {Barcan, AS and Humble, JL and Kasaragod, S and Sajib, MSI and Barcan, RA and McGinnity, P and Welch, TJ and Robertson, B and Vamanu, E and Bacigalupo, A and Llewellyn, MS and Samsing, F}, title = {Understanding the transfer and persistence of antimicrobial resistance in aquaculture using a model teleost gut system.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {18}, pmid = {39987284}, issn = {2524-4671}, support = {H.G. no. 118/2023.//Agency for Student Loans and Scholarships/ ; H.G. no. 118/2023.//Agency for Student Loans and Scholarships/ ; BB/T016280/1//BBSRC/ ; }, abstract = {BACKGROUND: The development, progression, and dissemination of antimicrobial resistance (AMR) are determined by interlinked human, animal, and environmental drivers, which pose severe risks to human and livestock health. Conjugative plasmid transfer drives the rapid dissemination of AMR among bacteria. In addition to the judicious use and implementation of stewardship programs, mitigating the spread of antibiotic resistance requires an understanding of the dynamics of AMR transfer among microbial communities, as well as the role of various microbial taxa as potential reservoirs that promote long-term AMR persistence. Here, we employed Hi-C, a high-throughput, culture-free technique, combined with qPCR, to monitor carriage and transfer of a multidrug-resistent (MDR) plasmid within an Atlantic salmon in vitro gut model during florfenicol treatment, a benzenesulfonyl antibiotic widely deployed in fin-fish aquaculture.

RESULTS: Microbial communities from the pyloric ceaca of three healthy adult farmed salmon were inoculated into three bioreactors simulating the teleost gut, which were developed for the SalmoSim gut system. The model system was then inoculated with the Escherichia coli strain ATCC 25922 carrying the plasmid pM07-1 and treated with florfenicol at a concentration of 150 mg/L in fish feed media for 5 days prior to the washout/recovery phase. Hi-C and metagenomic sequencing identified numerous transfer events, including those involving gram-negative and gram-positive taxa, and, crucially, the transfer and persistence of the plasmid continued once florfenicol treatment was withdrawn.

CONCLUSIONS: Our findings highlight the role of the commensal teleost gut flora as a reservoir for AMR even once antimicrobial selective pressure has been withdrawn. Our system also provides a model to study how different treatment regimens and interventions may be deployed to mitigate AMR persistence.}, } @article {pmid39986751, year = {2025}, author = {Wang, C and Zhao, J and Zhao, W and Xue, L and Chen, Y and Tian, J and Wang, H and Ji, X and Tian, X and Zhang, J and Gu, Y}, title = {A comparative study of the composition of microorganisms and metabolites in different β-casein genetic types of dairy cows based on metagenomics and non-targeted metabolomics.}, journal = {Food research international (Ottawa, Ont.)}, volume = {204}, number = {}, pages = {115859}, doi = {10.1016/j.foodres.2025.115859}, pmid = {39986751}, issn = {1873-7145}, mesh = {Animals ; Cattle ; *Caseins/metabolism ; *Metabolomics ; *Metagenomics ; Female ; Rumen/microbiology/metabolism ; Gastrointestinal Microbiome ; Milk/microbiology ; Bacteria/metabolism/classification/genetics ; Genotype ; }, abstract = {β-Casein is the main component of cow's milk protein, with A1 and A2 β-casein being the most common. Of these, A1 β-casein hydrolysate produces BCM-7, which can cause lactose intolerance, while A2 β-casein milk is more gentle on the gut. However, there is limited research on the composition of rumen microbiota, metabolites, and host metabolites in different genotype cows using metagenomics and metabolomics. In this study, we used multi-omics analysis techniques to perform enrichment analysis of differential metabolites, identifying three key metabolic pathways in all three groups: Arachidonic acid metabolism and Tryptophan metabolism. The metabolites in these pathways exhibited unique metabolic characteristics within each group. We then used random forests and ROC to predict key metabolites in these pathways, identifying that the signature metabolites in the A2A2 group were predominantly anti-inflammatory substances, including 12-HETE, PGD2-4d, and Arachidonic Acid. The signature metabolites in the A1A2 group and A2A2 group were Indoleacetaldehyde. The AUC of these signature metabolites was greater than 0.85. Macrogenic linear discriminant analysis (LDA > 2.5) found that the microorganisms with greater contribution were concentrated in the A2A2 group. Compared with the other two groups, g_Bacteroides and g_Parabacteroides were mainly enriched in the A1A2 group. In group A2A2, g_Xanthomonas and g_Acetobacter are mainly enriched. Then, the key microorganisms in A1A2 group were identified by correlation analysis as g_Bacteroides and g_Parabacteroides. The key microorganisms in group A2A2 were g_Acetobacter, g_Xanthomonas and g_Mannheimia, which were consistent with the results of LEfSe analysis. These microorganisms mainly affect the degradation of fiber in the diet, host metabolism and the occurrence of inflammation. In conclusion, our results provide theoretical basis and data support for the study of dairy cows with different genotypes of β-casein, and help to determine the potential biological functions of different genotypes of casein in dairy products and their effects on human health.}, } @article {pmid39986631, year = {2025}, author = {Trueba-Santiso, A and Wimmer, R and Eskildsen, M and Cubero-Cardoso, J and Lema, JM and Nielsen, JL}, title = {Reliable methodology to determine biotransformation of PBAT in anaerobic conditions.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132242}, doi = {10.1016/j.biortech.2025.132242}, pmid = {39986631}, issn = {1873-2976}, abstract = {Biodegradable plastics can enhance food waste utilization in anaerobic digestion (AD) units, but their fate under thermophilic conditions remains unclear. Previous studies using methane production, calorimetry, or spectroscopic analyses often report inconsistent results. This study tracks the biotransformation of polybutylene adipate co-terephthalate (PBAT) in thermophilic AD (55 °C) using [1]H NMR to quantify monomers. While 1,4-butanediol degraded quickly, adipic (AA) and terephthalic acid (TPA) accumulated over time. Monomer analysis estimated PBAT biotransformation at 11.1 ± 1.9 % (TPA) and 10.1 ± 2.3 % (AA). The core microbial community remained stable, indicating intrinsic hydrolytic capacities, which were stable despite TPA and AA accumulation. This workflow provides a robust methodology to evaluate the biotransformation of plastics.}, } @article {pmid39986132, year = {2025}, author = {Ren, L and Liu, Z and Wang, J and Su, Y}, title = {Mixed fungal infection of Actinomucor elegans and Aspergillus fumigatus in a person with severe fever with thrombocytopenia syndrome.}, journal = {Diagnostic microbiology and infectious disease}, volume = {112}, number = {1}, pages = {116750}, doi = {10.1016/j.diagmicrobio.2025.116750}, pmid = {39986132}, issn = {1879-0070}, abstract = {In this report, a 69-year-old man with fever, thrombocytopenia, and hepatic and renal dysfunction presented to our hospital. His disease progression was rapid, and he became unconscious. The patient was diagnosed with severe fever with thrombocytopenia syndrome (SFTS). However, his inflammation markers continued to rise until a mixed fungal infection was detected. Metagenomic next-generation sequencing of blood detected elevated sequence numbers for Actinomucor elegans and Aspergillus fumigatus. The culture of the bronchoalveolar lavage fluid were positive for Aspergillus fumigatus and Escherichia coli. Infection was controlled after adjusting the antifungal regimens against Actinomucor elegans. The patient's condition gradually improved. This patient was diagnosed with possible mucormycosis. Reports of Mucorales infection associated with SFTS are rare. We hope that this case report will draw the attention of physicians in the area where SFTS occurs to figure out if patients with SFTS are susceptible to mucormycosis.}, } @article {pmid39986099, year = {2025}, author = {Li, M and Wang, Z and Feng, Z and Lu, J and Chen, D and Chen, C and He, H and Zhang, Q and Chen, X and Morel, JL and Baker, AJM and Chao, Y and Tang, Y and Jiang, F and Qiu, R and Wang, S}, title = {New insights into efficient iron sulfide oxidation for arsenic immobilization by microaerophilic and acidophilic Fe(II)-oxidizing bacteria under micro-oxygen and acidic conditions.}, journal = {Journal of hazardous materials}, volume = {489}, number = {}, pages = {137695}, doi = {10.1016/j.jhazmat.2025.137695}, pmid = {39986099}, issn = {1873-3336}, abstract = {Microbial-mediated FeS oxidation to Fe(Ⅲ) minerals via chemolithoautotrophic Fe(Ⅱ) oxidizers under pH/O2 limitations engages As immobilization. However, this process is constrained under the dual stress of micro-oxygen and acidic conditions due to the critically diminished Fe(Ⅱ) oxidation capacity. Therefore, the interplay between Fe(Ⅱ) oxidation, carbon metabolism, and As immobilization in Fe(Ⅱ)-oxidizing bacteria under micro-oxygen and acidic conditions remains unclear. This study presents the first successful enrichment of microaerophilic and acidophilic Fe(II)-oxidizing bacteria (MAFeOB). These bacteria are capable of oxidizing FeS to Fe(III) minerals and immobilizing up to 27,835 mg/kg of As(Ⅴ) under micro-oxygen content (below 3.2 mg/L) and acidic pH (4.5-6.2). Through comprehensive metagenomic analysis, it was speculated that MAFeOB harbor a suite of genes potentially participating in critical processes, including carbon fixation, Fe(II) oxidation, and arsenic detoxification. Notably, a potential electron transfer pathway from Cyc2_repCluster2 to Cytochrome cbb3-type oxidases facilitates Fe(II) oxidation. Furthermore, As(Ⅲ) efflux pump (arsA, arsB, acr3) and As(Ⅲ) oxidase (aioA) genes indicate MAFeOB's potential for As immobilization. Our findings underscore the pivotal role of MAFeOB in overcoming limitations associated with Fe(III) mineral formation, thereby enhancing arsenic immobilization under micro-oxygen and acidic water.}, } @article {pmid39986042, year = {2025}, author = {Bacha, LF and Oliveira, MAP and Landuci, F and Vicente, AC and Paz, PH and Lima, M and Hilário, M and Campos, LS and Thompson, M and Chueke, C and Tschoeke, D and Ottoni, A and Teixera, LM and Cosenza, C and de Souza, W and de Rezende, C and Thompson, C and Thompson, F}, title = {Antibiotic-resistance genes and metals increase in polluted tropical rivers of the Baia da Ilha Grande, Rio de Janeiro, Brazil.}, journal = {The Science of the total environment}, volume = {968}, number = {}, pages = {178778}, doi = {10.1016/j.scitotenv.2025.178778}, pmid = {39986042}, issn = {1879-1026}, abstract = {Baia da Ilha Grande (BIG), Rio de Janeiro, Brazil, is one of the largest bays in the world. BIG is important because it serves as a route for the mining and oil industries and plays a vital role in mariculture activities. However, BIG has suffered significant impacts in recent years due to increased pollution and climate change, culminating in a local mariculture collapse. We examined the pollution levels of the bay. Biogeochemical, microbiological, and metagenomics analyses were conducted in ten rivers during the 2022 dry and rainy seasons. Combined data analyses showed that the bay's ten most significant rivers are polluted and classified into three decreasing levels of pollution groups (P1-P3). The P1 group (Centro, Japuíba, Jacuecanga) had the worst-case scenario for all pollution types, and the highest number of the nearby populations, nautical workshops and hospitals. Whereas the P2 (Jacarei, Perequeaçu and Taquari) and P3 (Frade, Bracuí, Mambucaba, São Roque) had relatively reduced pollution, as shown mainly by fecal bacteria. Metals, such as Al (>0.3 mg/L), Fe (>1.4 mg/L), Pb (>0.15 mg/L), and resistance genes (∼2 % metagenomic profile) were also more abundant in P1. High levels of metals and antibiotic resistance genes were a strong indication of pollution. The results from this study shed light on the health status of BIG rivers for further conservation programs and public policies to prevent rivers and marine biodiversity losses, and they serves as a warning on the urgent need to treat effluents in the region.}, } @article {pmid39985994, year = {2025}, author = {Song, C and Wang, S and Zhang, Q and Li, M and Zhang, B}, title = {Natural mackinawite-based elimination of vanadium and ammonium from wastewater in autotrophic biosystem.}, journal = {Water research}, volume = {277}, number = {}, pages = {123333}, doi = {10.1016/j.watres.2025.123333}, pmid = {39985994}, issn = {1879-2448}, abstract = {Vanadium (V) production results in significant amounts of wastewater, which often co-contains considerable ammonium (NH4[+]) after being used as precipitants. Both pentavalent V [V(V)] and NH4[+] can be removed independently through biological process. However, internal interactive biotechnology for one-step elimination of V(V) and NH4[+] remains an enigma. In this study, we proposed biologically removing V(V) and NH4[+] simultaneously with natural mineral mackinawite as electron donor and its oxidation products as electron acceptors. Our bioreactor achieved a V(V) removal efficiency of 99.5 ± 0.22 % and an NH4[+]-N removal capacity of 49.5 ± 0.40 g/m[3]·d. V(V) was reduced to tetravalent V precipitates, while mackinawite was bio-oxidized to Fe(III) and sulfate. Metagenomic binning analysis indicated Sulfurivermis sp. mediated mackinawite oxidation and V(V) reduction. Putative Pseudomonas sp. conducted NH4[+] assimilation, anaerobic ammonium oxidation coupled to Fe(III) reduction (Feammox), and denitrification, achieving complete NH4[+]-N removal. Real-time qPCR validated the upregulation of functional genes involved in V(V) reduction and nitrogen metabolisms, with improved functional enzyme activities. Cytochrome c, nicotinamide adenine dinucleotide, and extracellular polymeric substances promoted electron transfer, facilitating the elimination of both V(V) and NH4[+]-N from wastewater. This study offers a novel and sustainable biological strategy for one-step treating V industrial wastewater.}, } @article {pmid39985639, year = {2025}, author = {Zhang, N and Tran, S and Moskatel, LS}, title = {The Gut Microbiome and Migraine: Updates in Understanding.}, journal = {Current neurology and neuroscience reports}, volume = {25}, number = {1}, pages = {20}, pmid = {39985639}, issn = {1534-6293}, mesh = {Humans ; *Migraine Disorders/microbiology ; *Gastrointestinal Microbiome/physiology ; Animals ; *Brain-Gut Axis/physiology ; Dysbiosis/microbiology ; Probiotics/therapeutic use ; }, abstract = {PURPOSE OF REVIEW: We provide an overview of the field of microbiome research, the current understanding of the microbiome-gut-brain axis, and the most recent updates on the interplay between migraine and the gut microbiome.

RECENT FINDINGS: Pre-clinical studies suggest that gut microbiota is required for normal pain sensation. There is also evidence in rodent models that there is potential application of food, herbal medicines, probiotics, and short chain fatty acids (SCFAs) as novel therapies for migraine. Evidence from human cohorts suggests that there is altered gut microbiota in people with migraine, and that the microbiome dysbiosis is from both compositional and functional aspects. Recent metagenome-wide association studies (MWAS) that employ Mendelian Randomization support the causal association between gut microbiota and migraine. The connection between migraine and the gut microbiome remains underexplored, but recent preclinical and clinical studies support the association between gut microbiota and the development of migraine.}, } @article {pmid39985228, year = {2025}, author = {Song, MJ and Freund, F and Tribble, CM and Toffelmier, E and Miller, C and Bradley Shaffer, H and Li, FW and Rothfels, CJ}, title = {The nitrogen-fixing fern Azolla has a complex microbiome characterized by varying degrees of cophylogenetic signal.}, journal = {American journal of botany}, volume = {}, number = {}, pages = {e70010}, doi = {10.1002/ajb2.70010}, pmid = {39985228}, issn = {1537-2197}, support = {//California Conservation Genomics Project, with funding provided to the University of California by the State of California, State Budget Act of 2019 [UC Award ID RSI-19-690224]./ ; }, abstract = {PREMISE: Azolla is a genus of floating ferns that has closely evolved with a vertically transmitted obligate cyanobacterium endosymbiont-Anabaena azollae-that fixes nitrogen. There are also other lesser-known Azolla symbionts whose role and mode of transmission are unknown.

METHODS: We sequenced 112 Azolla specimens collected across the state of California and characterized their metagenomes to identify the common bacterial endosymbionts and assess their patterns of interaction.

RESULTS: Four genera were found across all samples, establishing that multiple Azolla endosymbionts were consistently present. We found varying degrees of cophylogenetic signal across these taxa as well as varying degrees of isolation by distance and of pseudogenation, which demonstrates that multiple processes underlie how this endosymbiotic community is constituted. We also characterized the entire Azolla leaf pocket microbiome.

CONCLUSIONS: These results show that the Azolla symbiotic community is complex and features members at potentially different stages of symbiosis evolution, further supporting the utility of the Azolla microcosm as a system for studying the evolution of symbioses.}, } @article {pmid39984934, year = {2025}, author = {Chen, X and Wei, J and Zhang, L and Wang, H and Zhang, Y and Li, Z and Wang, X and Liu, L and Zhang, Y and Zhang, T}, title = {Association between plasma short-chain fatty acids and inflammation in human immunodeficiency virus-associated neurocognitive disorder: a pilot study.}, journal = {Lipids in health and disease}, volume = {24}, number = {1}, pages = {66}, pmid = {39984934}, issn = {1476-511X}, support = {7222091//Natural Science Foundation of Beijing Municipality/ ; 81873761//National Natural Science Foundation of China/ ; 82241072, 82072271//National Natural Science Foundation of China/ ; 7222095//Beijing Natural Science Foundation/ ; }, abstract = {BACKGROUND AND AIMS: Short-chain fatty acids (SCFAs), key metabolites produced by gut microbiota, have neuroprotective effects in neurodegenerative diseases by modulating immune responses. However, their role in human immunodeficiency virus (HIV)-associated neurocognitive disorder (HAND) remains largely unexplored.

METHODS: We recruited HAND patients, HIV Control, and healthy controls (HC). Plasma SCFAs and SCFA-producing gut microbiota were quantified via gas chromatography-mass spectrometry and fecal metagenomic analysis. Inflammatory cytokine levels were measured using liquid chromatography. Receiver operating characteristic (ROC) curves were generated to evaluate the predictive accuracy of SCFAs for HAND.

RESULTS: Plasma SCFAs were significantly reduced in HAND patients, correlating with a decrease in SCFA-producing gut bacteria, such as Prevotella and its related species. Reduced SCFAs were positively correlated with pro-inflammatory cytokines and cognitive impairment, while being negatively correlated with anti-inflammatory cytokines. ROC curve analysis demonstrated that several SCFAs exhibited strong predictive accuracy for HAND status.

CONCLUSIONS: SCFAs may influence cognitive function by modulating inflammatory responses, and identifies plasma SCFAs as potential biomarkers and therapeutic targets for HAND. Further investigation is needed to delineate the mechanisms that SCFAs influence HAND pathology.}, } @article {pmid39984857, year = {2025}, author = {Zhang, L and Hu, J and Xin, Y and Cheng, H and Yan, Y and Wang, Q}, title = {Capnocytophaga ochracea detected in cerebrospinal fluid of a meningioma patient: a case report.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {249}, pmid = {39984857}, issn = {1471-2334}, support = {81972349//National Natural Science Foundation of China/ ; }, abstract = {Capnocytophaga ochracea (C. ochracea) is a species of Gram-negative and facultative anaerobic bacterium. It was first reported in 1979 and isolated from both healthy and diseased sites in the oral flora. The bacteria can cause septicemia, endocarditis, endometritis, blepharoconjunctivitis and other infections. Herein, we present the first cerebrospinal fluid (CSF) infection case caused by C. ochracea in humans. Gram-negative fusiform, non-spore forming rods were detected in an anaerobic bottle of CSF culture obtained from a 50-year-old man who had been hospitalized for meningioma in Tianjin Huanhu Hospital. Although the organism could not be identified using a conventional method, it was finally identified as C. ochracea based on the results of metagenomics next generation sequencing, matrix-assisted laser desorption ionization time-of-flight mass spectrometry and 16 S rDNA sequencing analysis. Subsequently, Streptococcus oralis was also detected in the CSF of the patient. The patient was treated with meropenem and vancomycin, and the infection was well controlled. The clinically rare C. ochracea can be pathogenic in central nervous system of humans.}, } @article {pmid39984459, year = {2025}, author = {Maharramov, E and Czikkely, MS and Szili, P and Farkas, Z and Grézal, G and Daruka, L and Kurkó, E and Mészáros, L and Daraba, A and Kovács, T and Bognár, B and Juhász, S and Papp, B and Lázár, V and Pál, C}, title = {Exploring the principles behind antibiotics with limited resistance.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {1842}, pmid = {39984459}, issn = {2041-1723}, mesh = {*Anti-Bacterial Agents/pharmacology ; Humans ; Drug Resistance, Bacterial/genetics/drug effects ; Mutation ; Microbial Sensitivity Tests ; Bacteria/drug effects/genetics ; Acinetobacter baumannii/drug effects/genetics ; Pseudomonas aeruginosa/drug effects/genetics ; Metagenomics/methods ; Escherichia coli/drug effects/genetics ; Klebsiella pneumoniae/drug effects/genetics ; }, abstract = {Antibiotics that target multiple cellular functions are anticipated to be less prone to bacterial resistance. Here we hypothesize that while dual targeting is crucial, it is not sufficient in preventing resistance. Only those antibiotics that simultaneously target membrane integrity and block another cellular pathway display reduced resistance development. To test the hypothesis, we focus on three antibiotic candidates, POL7306, Tridecaptin M152-P3 and SCH79797, all of which fulfill the above criteria. Here we show that resistance evolution against these antibiotics is limited in ESKAPE pathogens, including Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa, while dual-target topoisomerase antibiotics are prone to resistance. We discover several mechanisms restricting resistance. First, de novo mutations result in only a limited elevation in resistance, including those affecting the molecular targets and efflux pumps. Second, resistance is inaccessible through gene amplification. Third, functional metagenomics reveal that mobile resistance genes are rare in human gut, soil and clinical microbiomes. Finally, we detect rapid eradication of bacterial populations upon toxic exposure to membrane targeting antibiotics. We conclude that resistance mechanisms commonly found in natural bacterial pathogens provide only limited protection to these antibiotics. Our work provides guidelines for the future development of antibiotics.}, } @article {pmid39984074, year = {2025}, author = {OuYang, M and Liu, C and Shengping, and Qiu, Q and OuYang, K and Li, Y and Zang, Y and Zhao, X}, title = {Characterization of acidophilic cellulase with β-glucanase and xylanase activity from the rumen metagenome and in vitro evaluation of barley digestibility.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {141141}, doi = {10.1016/j.ijbiomac.2025.141141}, pmid = {39984074}, issn = {1879-0003}, abstract = {In this study, RuCel143, an acidophilic GH5 cellulase endowed with β-glucanase and xylanase activity was identified from the rumen metagenome. Its hydrolytic efficacy was evaluated using barley in an in vitro simulation of monogastric digestion. Optimal activity for RuCel143's cellulase was observed at pH 3.5 and 40 °C, while for xylanase it was pH 4.0 and 50 °C. The cellulase exhibited strong pH tolerance, retaining 94.3 % of its initial activity after 4 h at pH 2.5. In contrast, xylanase activity increased by 80.7 % after 4 h at pH 8.0. RuCel143 exhibited good resistance to various ions and common inhibitors, with Cu[2+] and Mn[2+] enhancing the cellulase activity by 26.9 % and 95.6 % at 1 mM concentration, respectively. Mutation analysis involving Tyr162Ala, His235Ala, and Glu285Ala showed reduced activities to 67.4 %, 29.3 %, and 19.5 % of the wild type, respectively. Hydrolysis product analysis revealed that RuCel143 primarily produced cellobiose and xylopentaose from carboxymethyl cellulose sodium and wheat straw xylan. Comparative tests on barley, wheat, and wheat bran demonstrated RuCel143's superior performance on barley. Simulation results of in vitro monogastric digestion indicated that RuCel143 can increase the digestibility of barley from 52.6 % to 60.8 % and reduce the viscosity coefficient from 1.41 to 1.38. In summary, RuCel143 is an exceptionally acid-tolerant cellulase with both β-glucanase and xylanase activities, demonstrating unique enzymatic properties that could potentially be leveraged to improve the degradation of barley in monogastric animals.}, } @article {pmid39983954, year = {2025}, author = {Guo, J and Guan, A and Chen, M and Chen, Y and Qi, W and Cao, X and Peng, J and Liu, H and Qu, J and Jia, Z and Hu, H}, title = {Spatial Distribution of Potential Nitrogen Reduction Rates and Associated Microbial Communities Revealed by Metagenomic Analysis in Yangtze River Sediments.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121170}, doi = {10.1016/j.envres.2025.121170}, pmid = {39983954}, issn = {1096-0953}, abstract = {Understanding the intricacies of nitrogen reduction processes and the composition of associated microbial communities is crucial for illuminating the reactions of ecosystems and their functions to persistent nitrogen inputs. To enhance research on the nitrogen reduction process, we determined the potential rates, quantified the relevant genes, and analyzed the macro factors in the sediments of the Yangtze River. The results showed that dissimilatory reduction of nitrate to ammonium (DNRA) dominated the N-reduction processes in the Yangtze River sediment, with average rates of 0.89±0.71 nmol N g[-1]·h[-1]. Meanwhile, denitrification and anammox rates were 0.73±0.74 and 0.07±0.07 nmol N g[-1]·h[-1], respectively. The Three Gorges Dam (TGD) caused higher potential rates (nmol N g[-1]·h[-1]) of denitrification (1.38), anammox (0.12), DNRA (1.48), and N2O depletion (1.49 nmol g[-1]·h[-1]) in the Three Gorges Reservoir (TGR) compared to other river reaches. The average copy numbers (copies·g[-1]) of nrfA (2.96×10[6]), narG (8.17×10[5]), nirS (6.10×10[6]), nosZ (2.77×10[6]), and hzsB (3.68×10[5]) in TGR sediments were higher than those in the other reaches. The TGD's interception of fine sediments and nutrients enhanced microbial gene abundance, thereby favoring N-reduction processes and resulting in N2O depletion in reservoir sediments. Moreover, the TGD caused a decreased contribution gap between DNRA and denitrification in the TGR (2%) compared with the upper (35%) and lower (18%) reaches, while causing predominant anammox (50%) in the middle reach. Metagenomic results suggested that sediment particle size, along with organic carbon and inorganic nitrogen concentrations, influenced N reduction rates by affecting narG, norB and C, nrfA and H, and hzsB and C. This study reveals the spatial pattern of the N-reduction rate in the Yangtze River sediments and quantitatively defines the intensity of dam effects on sediment N-reduction rate.}, } @article {pmid39983731, year = {2025}, author = {Saha, S and Kalathera, J and Sumi, TS and Mane, V and Zimmermann, S and Waschina, S and Pande, S}, title = {Mass lysis of predatory bacteria drives the enrichment of antibiotic resistance in soil microbial communities.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2025.01.068}, pmid = {39983731}, issn = {1879-0445}, abstract = {Numerous studies have investigated the effects of antibiotics on the evolution and maintenance of antimicrobial resistance (AMR). However, the impact of microbial interactions in antibiotic-free environments on resistance within complex communities remains unclear. We investigated whether the predatory bacterium M. xanthus, which can produce antimicrobials and employ various contact-dependent and -independent prey-killing mechanisms, influences the abundance of antibiotic-resistant bacteria in its local environment simply through its presence, regardless of active predation. We observed an association between the presence of M. xanthus in soil and the frequency of antibiotic-resistant bacteria. Additionally, culture-based and metagenomic analysis showed that coculturing M. xanthus with soil-derived communities in liquid cultures enriched AMR among non-myxobacterial isolates. This is because the lysis of M. xanthus, triggered during the starvation phase of the coculture experiments, releases diffusible growth-inhibitory compounds that enrich pre-existing resistant bacteria. Furthermore, our results show that death during multicellular fruiting body formation-a starvation-induced stress response in M. xanthus that results in over 90% cell death-also releases growth-inhibitory molecules that enrich resistant bacteria. Hence, the higher abundance of resistant bacteria in soil communities, where M. xanthus can be detected, was because of the diffusible growth-inhibitory substances that were released due to the death of M. xanthus cells during fruiting body formation. Together, our findings demonstrate how the death of M. xanthus, an important aspect of its life cycle, can impact antibiotic resistomes in natural soil communities without the anthropogenic influx of antibiotics.}, } @article {pmid39983710, year = {2025}, author = {Chiu, CY and Godasi, RR and Hughes, HR and Servellita, V and Foresythe, K and Tubati, A and Zorn, K and Sidhu, S and Wilson, MR and Bethina, SV and Abenroth, D and Cheng, Y and Grams, R and Reese, C and Isada, C and Thottempudi, N}, title = {Two Human Cases of Fatal Meningoencephalitis Associated with Potosi and Lone Star Virus Infections, United States, 2020-2023.}, journal = {Emerging infectious diseases}, volume = {31}, number = {2}, pages = {215-221}, doi = {10.3201/eid3102.240831}, pmid = {39983710}, issn = {1080-6059}, mesh = {Humans ; *Meningoencephalitis/virology/diagnosis/epidemiology ; United States/epidemiology ; Fatal Outcome ; Male ; Animals ; Female ; Middle Aged ; Phylogeny ; Bunyaviridae Infections/virology/epidemiology/diagnosis ; Immunocompromised Host ; High-Throughput Nucleotide Sequencing ; Metagenomics/methods ; Aged ; History, 21st Century ; }, abstract = {We used clinical metagenomic next-generation sequencing of cerebrospinal fluid to investigate bunyavirus infections in 2 immunocompromised patients in the United States who had fatal meningoencephalitis. Potosi virus has been isolated from mosquito vectors and Lone Star virus from tick vectors. These findings highlight the power of metagenomic next-generation sequencing in broad-based, agnostic detection of emerging viral infections that test negative using conventional targeted diagnostic methods.}, } @article {pmid39983689, year = {2025}, author = {Parry, RH and Yamada, KYH and Hood, WR and Zhao, Y and Lu, JY and Seluanov, A and Gorbunova, V and Modhiran, N and Watterson, D and Isaacs, A}, title = {Henipavirus in Northern Short-Tailed Shrew, Alabama, USA.}, journal = {Emerging infectious diseases}, volume = {31}, number = {2}, pages = {392-394}, doi = {10.3201/eid3102.241155}, pmid = {39983689}, issn = {1080-6059}, mesh = {Animals ; Alabama/epidemiology ; *Phylogeny ; *Shrews/virology ; *Henipavirus/genetics/classification ; Genome, Viral ; Metagenomics/methods ; Paramyxoviridae Infections/epidemiology/virology/veterinary ; }, abstract = {RNA metagenomic analysis of tissues from 4 wild-caught northern short-tailed shrews in Alabama, USA, revealed a novel henipavirus (family Paramyxoviridae). Phylogenetic analysis supported the placement of the virus within the shrew henipavirus clade, related to human-infecting shrewborne henipaviruses. Our study results highlight the presence of henipavirus infections in North America.}, } @article {pmid39983489, year = {2025}, author = {Karlsson, M and Jönsson, HL and Hultberg, M}, title = {Inclusion of biochar in mushroom substrate influences microbial community composition of the substrate and elemental composition of the fruiting bodies.}, journal = {The Science of the total environment}, volume = {968}, number = {}, pages = {178914}, doi = {10.1016/j.scitotenv.2025.178914}, pmid = {39983489}, issn = {1879-1026}, abstract = {Due to its structure, biochar makes the soil porous and oxygen-rich, enhancing the water-holding capacity and increasing the cation exchange capacity for a longer duration. These aspects could also be favourable for mushroom production. However, biochar has been considerably less investigated within this context. This study investigated the impact of biochar on mushroom production, quality, and the microbial communities of the substrates. Two different biochar's produced from local feedstocks, plant- or sludge based, were evaluated in the production of oyster mushrooms (Pleurotus ostreatus) at two different concentrations (5 % and 10 %). The results showed that inclusion of biochar in the substrate negatively impacted fruiting body production. The elemental composition of the fruiting body was also affected by inclusion of biochar and partly reflected the elemental composition of the biochar. The metagenomics revealed that inclusion of biochar in the substrate altered the microbial community structure. The bacterial diversity based on Shannon indices was higher in the substrate wherein no biochar was added. Bacterial community richness (Chao 1) was higher in samples with biochar compared to the control with no added biochar. Fungal community richness based on Chao 1 indices displayed an increase in samples with an inclusion of biochar. Overall, this study provides novel insights into the impact of biochar in mushroom production regarding its concentration and the effect of the origin material of the biochar.}, } @article {pmid39983413, year = {2025}, author = {Li, Q and Li, H and Tian, L and Wang, Y and Ouyang, Z and Li, L and Mao, Y}, title = {Genomic insights and metabolic pathways of an enriched bacterial community capable of degrading polyethylene.}, journal = {Environment international}, volume = {197}, number = {}, pages = {109334}, doi = {10.1016/j.envint.2025.109334}, pmid = {39983413}, issn = {1873-6750}, abstract = {In the face of mounting global plastic pollution, especially concerning microplastics, biodegradation must be a sustainable solution. The key factor driving this technology is to explore efficient plastic-biodegraders from different habitats, among which activated sludge (AS) may be an important option since it holds diverse microorganisms occupying various ecological niches. Here we intend to enrich the plastic-degrading microorganisms from AS by using polyethylene (PE) plastic as the carbon and energy source. After a 28-day incubation, the weight loss of PE films reached 3% and the hydrophobicity decreased, indicating physical biodegradation. Moreover, Fourier-transform infrared spectroscopy (FTIR) results showed the formation of several new oxygen-containing functional groups on PE. Microbial analysis extracted 26 metagenome-assembled genomes (MAGs) from the enriched microbial communities. Among them MAG10, MAG21 and MAG26 displayed the increased abundance upon PE addition and harbored abundant genes related to carbohydrate transport and metabolism, suggesting their potential to degrade PE. Additionally, functional analysis revealed 14 plastic degradation-related genes, including oxidase, laccase, and lipase, indicating the significant potential in plastic degradation. Furthermore, a pathway for synergistic biodegradation of PE was proposed based on the potential PE degradation genes retrieved from MAGs. This work offers a promising and sustainable solution to plastic pollution by enriching the potential biodegraders from AS.}, } @article {pmid39983259, year = {2025}, author = {Lyte, JM and Jia, X and Caputi, V and Zhang, D and Daniels, KM and Phillips, GJ and Lyte, M}, title = {Heat stress in chickens induces temporal changes in the cecal microbiome concomitant with host enteric serotonin responses.}, journal = {Poultry science}, volume = {104}, number = {3}, pages = {104886}, doi = {10.1016/j.psj.2025.104886}, pmid = {39983259}, issn = {1525-3171}, abstract = {Heat stress is a potent modulator of the avian neuroendocrine system with concomitant impact on the gut microbiome. As an interkingdom signaling molecule, serotonin is largely derived from the gut and found in large concentrations in the avian gut lumen. Despite the role of serotonin in animal stress physiology and related host-microbe interactions, whether heat stress alters avian enteric concentrations of serotonin is unknown. As such, the present study sought to determine whether acute or chronic exposure to moderate heat stress alters both enteric serotonin concentrations and the microbiome in the chicken gut. Chickens were, or were not, subjected to an acute (1 day), repeated acute (2 days) or chronic (6 days) moderate ambient cyclic heat stress (12h per day, 31°C). Enteric concentrations of serotonin were significantly decreased in the acute heat stress group (P < 0.05), and rebounded to become elevated in the chronic heat stress group (P < 0.05). Shotgun metagenomic sequencing revealed heat stress caused both functional and taxonomic changes in the cecal microbiome. Abundances of bacterial taxa that are known to interact with the host via the serotonergic system, including Lactobacillus spp., and Bifidobacterium spp., were significantly (P < 0.05) altered by heat stress. As these findings demonstrate that heat stress can alter serotonin concentrations in the chicken intestinal tract, with distinct outcomes depending on duration of the stressor, serotonergic signaling may serve as potential leverageable point of intervention in host-microbe interactions including foodborne pathogen colonization in the chicken gut. In addition, this study provides novel insight into the impact of acute and chronic heat stress on the avian microbiome, and its relationship to stress-driven changes in the enteric serotonergic system.}, } @article {pmid39983257, year = {2025}, author = {Wang, Y and Cao, J and Liu, Q and Huang, J and Zhang, P and Zhang, Z and Li, B and Liu, Y and Xiao, B and Song, X and De Clercq, E and Li, G and Zheng, F}, title = {Association between respiratory pathogens and severe clinical outcomes in people living with HIV-1 and pulmonary infections: A 180-day longitudinal cohort study.}, journal = {Journal of infection and public health}, volume = {18}, number = {4}, pages = {102694}, doi = {10.1016/j.jiph.2025.102694}, pmid = {39983257}, issn = {1876-035X}, abstract = {BACKGROUND: Many respiratory pathogens have been identified in people living with HIV-1 and pulmonary infection, but their impact on clinical outcomes remains largely unclear.

METHODS: Metagenomic sequencing and traditional laboratory diagnostics were applied to identify bacterial, viral, and fungal respiratory pathogens. Clinical outcomes were assessed by (i) mortality or ICU transfer during hospitalization, and (ii) 30-day re-hospitalization and 180-day mortality after hospital discharge.

RESULTS: Microbiological analyses of bacterial, viral and fungal pathogens in 237 in-patients with HIV-1 and pulmonary infections revealed Pneumocystis jirovecii (58 %) as the most prevalent respiratory pathogen, followed by Cytomegalovirus (39 %), Mycobacterium tuberculosis (22 %), Talaromyces marneffei (17 %), and Epstein-Barr virus (16 %). Fifty-six patients (24 %) were coinfected with bacterial, viral and fungal pathogens, referred to as bacterial+fungal+viral coinfections. Risk factors for bacterial+fungal+viral coinfections (RR=8.41, 95 %CI: 4.2-14.3), severe pneumonia (RR=13.6, 95 %CI: 8.14-19.3), and elevated C-reactive protein levels (RR=6.42, 95 %CI: 1.58-10.13) were significantly associated with mortality or ICU transfer during hospitalization. After hospital discharge, 38 patients (16 %) were rehospitalized within 30 days. Antiretroviral therapy reduced the risk of 30-day rehospitalization (HR=0.21, p = 0.01). During the 180-day follow-up, 13 patients (5.5 %) died. Survival analyses identified severe pneumonia and age ≥ 60 years as risk factors for 180-day mortality.

CONCLUSIONS: Multiple pulmonary coinfections are associated with severe outcomes in in-patients with HIV-1 infection. Effective management of both HIV-1 and pulmonary infections is crucial to reduce hospitalization rates and mortality risk.}, } @article {pmid39982899, year = {2025}, author = {Gittrich, MR and Sanderson, CM and Wainaina, JM and Noel, CM and Leopold, JE and Babusci, E and Selbes, SC and Farinas, OR and Caine, J and Davis Ii, J and Mutalik, VK and Hyman, P and Sullivan, MB}, title = {Isolation and characterization of 24 phages infecting the plant growth-promoting rhizobacterium Klebsiella sp. M5al.}, journal = {PloS one}, volume = {20}, number = {2}, pages = {e0313947}, doi = {10.1371/journal.pone.0313947}, pmid = {39982899}, issn = {1932-6203}, mesh = {*Klebsiella/virology/genetics ; *Bacteriophages/genetics/isolation & purification/physiology ; *Genome, Viral ; Rhizosphere ; Phylogeny ; Plant Development ; Soil Microbiology ; Host Specificity ; }, abstract = {Bacteriophages largely impact bacterial communities via lysis, gene transfer, and metabolic reprogramming and thus are increasingly thought to alter nutrient and energy cycling across many of Earth's ecosystems. However, there are few model systems to mechanistically and quantitatively study phage-bacteria interactions, especially in soil systems. Here, we isolated, sequenced, and genomically characterized 24 novel phages infecting Klebsiella sp. M5al, a plant growth-promoting, nonencapsulated rhizosphere-associated bacterium, and compared many of their features against all 565 sequenced, dsDNA Klebsiella phage genomes. Taxonomic analyses revealed that these Klebsiella phages belong to three known phage families (Autographiviridae, Drexlerviridae, and Straboviridae) and two newly proposed phage families (Candidatus Mavericviridae and Ca. Rivulusviridae). At the phage family level, we found that core genes were often phage-centric proteins, such as structural proteins for the phage head and tail and DNA packaging proteins. In contrast, genes involved in transcription, translation, or hypothetical proteins were commonly not shared or flexible genes. Ecologically, we assessed the phages' ubiquity in recent large-scale metagenomic datasets, which revealed they were not widespread, as well as a possible direct role in reprogramming specific metabolisms during infection by screening their genomes for phage-encoded auxiliary metabolic genes (AMGs). Even though AMGs are common in the environmental literature, only one of our phage families, Straboviridae, contained AMGs, and the types of AMGs were correlated at the genus level. Host range phenotyping revealed the phages had a wide range of infectivity, infecting between 1-14 of our 22 bacterial strain panel that included pathogenic Klebsiella and Raoultella strains. This indicates that not all capsule-independent Klebsiella phages have broad host ranges. Together, these isolates, with corresponding genome, AMG, and host range analyses, help build the Klebsiella model system for studying phage-host interactions of rhizosphere-associated bacteria.}, } @article {pmid39982611, year = {2025}, author = {Wang, X and Liu, Q and Wu, B and Zhao, H and Hu, J and Li, N}, title = {Successful treatment of carbapenem-resistant Acinetobacter baumannii meningitis and purulent ventriculitis using cefiderocol combination therapy: a case report and literature review.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {}, number = {}, pages = {}, pmid = {39982611}, issn = {1435-4373}, abstract = {The application of cefiderocol in treating carbapenem-resistant Acinetobacter baumannii (CRAB) central nervous system (CNS) infections is rarely reported. Here we presented the case of a 66-year-old man with CRAB meningitis and purulent ventriculitis successfully treated with a combination antibiotic therapy including cefiderocol. Cerebrospinal fluid (CSF) analysis revealed normalization of glucose, chloride, protein, and lactate levels. CRAB cultures turned negative by Day 7, and metagenomics next generation sequencing (mNGS) results were negative by Day 25. The cefiderocol-contained regimen was continued for 41 days, with no recurrence of CRAB infection and no cefiderocol-associated adverse effects were observed. This case highlighted the potential of cefiderocol as a promising therapeutic option in treating CRAB CNS infections.}, } @article {pmid39982015, year = {2025}, author = {Cao, X and Ma, H and Li, SA and Huang, H and Cui, F and Tanentzap, AJ}, title = {Enhanced Release and Reactivity of Soil Water-Extractable Organic Matter Following Wildfire in a Subtropical Forest.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c13557}, pmid = {39982015}, issn = {1520-5851}, abstract = {Climate-driven increases in wildfire frequency may disrupt soil carbon dynamics, potentially creating positive feedback within global carbon cycle. However, the release and lability of soil carbon following wildfire remain unclear, limiting our ability to predict fire impacts on carbon cycling. Here, we investigated chemical alterations in soil water-extractable organic matter (WEOM) following a subtropical forest wildfire by comparing burned soils to an adjacent unburned site. The consensus is that fire-altered DOM is aromatic and less reactive. However, we found that 10 months postfire, burned soils contained nearly three times more water-extractable organic carbon (WEOC) than the control site. Reactomics analysis further revealed an overall 8-fold increase in potential reactivity of this carbon, identified by higher abundances of molecular formulas involved in identified microbial reaction pathways. Specifically, burned soils exhibited elevated potential oxidative enzyme reactions, linked to a higher nominal oxidation state of carbon (NOSC) in WEOM. Metagenomic analysis revealed an enrichment of microbial taxa specialized in degrading aromatic compounds in burned areas, supporting the occurrence of potential microbial reaction pathways acting on WEOM in postfire soils. These findings highlight that wildfires may accelerate soil carbon loss through reactive WEOM mobilization and microbial response, with implications for long-term carbon-climate projections.}, } @article {pmid39981802, year = {2025}, author = {Bartlett, A and Blakeley-Ruiz, JA and Richie, T and Theriot, CM and Kleiner, M}, title = {Large Quantities of Bacterial DNA and Protein in Common Dietary Protein Source Used in Microbiome Studies.}, journal = {Proteomics}, volume = {}, number = {}, pages = {e202400149}, doi = {10.1002/pmic.202400149}, pmid = {39981802}, issn = {1615-9861}, support = {593607//Foundation for Food and Agriculture Research/ ; R35GM138362//National Institute of General Medical Sciences of the National Institutes of Health/ ; }, abstract = {Diet has been shown to greatly impact the intestinal microbiota. To understand the role of individual dietary components, defined diets with purified components are frequently used in diet-microbiota studies. Defined diets frequently use purified casein as the protein source. Previous work indicated that casein contains microbial DNA potentially impacting results of microbiome studies. Other diet-based microbially derived molecules that may impact microbiome measurements, such as proteins detected by metaproteomics, have not been determined for casein. Additionally, other protein sources used in microbiome studies have not been characterized for their microbial content. We used metagenomics and metaproteomics to identify and quantify microbial DNA and protein in a casein-based defined diet to better understand potential impacts on metagenomic and metaproteomic microbiome studies. We further tested six additional defined diets with purified protein sources with an integrated metagenomic-metaproteomic approach and found that contaminating microbial protein is unique to casein within the tested set as microbial protein was not identified in diets with other protein sources. We also illustrate the contribution of diet-derived microbial protein in diet-microbiota studies by metaproteomic analysis of stool samples from germ-free mice (GF) and mice with a conventional microbiota (CV) following consumption of diets with casein and non-casein protein. This study highlights a potentially confounding factor in diet-microbiota studies that must be considered through evaluation of the diet itself within a given study.}, } @article {pmid39981377, year = {2025}, author = {Zhao, R and He, G and Xiang, L and Ji, M and He, R and Wei, X}, title = {Metagenomic next-generation sequencing assists in the diagnosis of visceral leishmaniasis in non-endemic areas of China.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1517046}, pmid = {39981377}, issn = {2235-2988}, mesh = {*Leishmaniasis, Visceral/diagnosis/parasitology ; Humans ; China ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Male ; Molecular Diagnostic Techniques/methods ; Leishmania/genetics/isolation & purification/classification ; Female ; Adult ; DNA, Protozoan/genetics ; }, abstract = {INTRODUCTION: Leishmaniasis, a protozoan disease caused by infection by Leishmania, is a critical issue in Asia, South America, East Africa, and North Africa. With 12 million cases globally, leishmaniasis is one of the most serious neglected tropical diseases worldwide. Direct identification of infected tissues is currently the primary method of diagnosis; however, the low sensitivity and inconvenience of microscopic examination in detecting amastigotes, parasitic manifestations of Leishmania, leads to the possibility of misdiagnosis, delayed diagnosis, and underdiagnosis.

METHODS: With the development of metagenomic nextgeneration sequencing (mNGS) technology for pathogen identification, it is possible to detect specific nucleic acid sequences characteristic of Leishmania parasites, which opens new avenues for the more accurate diagnosis of leishmaniasis. In this study, we report two cases of leishmaniasis from Henan Province, China, in which Leishmania parasites were identified using mNGS technology, massively expediting diagnosis and treatment.

RESULTS: Our report demonstrates that the mNGS method is applicable to peripheral blood samples (PB), which are far more readily available in clinical settings, in addition to bone marrow aspirate samples (BM), which are traditionally used for diagnosis of visceral leishmaniasis.

CONCLUSION: Our report validates the efficacy of mNGS technology as a rapid and accurate method of diagnosis for leishmaniasis.}, } @article {pmid39980208, year = {2025}, author = {Holman, LE and Zampirolo, G and Gyllencreutz, R and Scourse, J and Frøslev, T and Carøe, C and Gopalakrishnan, S and Pedersen, MW and Bohmann, K}, title = {Navigating Past Oceans: Comparing Metabarcoding and Metagenomics of Marine Ancient Sediment Environmental DNA.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e14086}, doi = {10.1111/1755-0998.14086}, pmid = {39980208}, issn = {1755-0998}, support = {856488//H2020 European Research Council/ ; }, abstract = {The condition of ancient marine ecosystems provides context for contemporary biodiversity changes in human-impacted oceans. Sequencing sedimentary ancient DNA (sedaDNA) is an emerging method for generating high-resolution biodiversity time-series data, offering insights into past ecosystems. However, few studies directly compare the two predominant sedaDNA sequencing approaches: metabarcoding and shotgun-metagenomics, and it remains unclear if these methodological differences affect diversity metrics. We compared these methods using sedaDNA from an archived marine sediment record sampled in the Skagerrak, North Sea, spanning almost 8000 years. We performed metabarcoding of a eukaryotic 18S rRNA region (V9) and sequenced 153-229 million metagenomic reads per sample. Our results show limited overlap between metabarcoding and metagenomics, with only three metazoan genera detected by both methods. For overlapping taxa, metabarcoding detections became inconsistent for samples older than 2000 years, while metagenomics detected taxa throughout the time series. We observed divergent patterns of alpha diversity, with metagenomics indicating decreased richness towards the present and metabarcoding showing an increase. However, beta diversity patterns were similar between methods, with discrepancies only in metazoan data comparisons. Our findings demonstrate that the choice of sequencing method significantly impacts detected biodiversity in an ancient marine sediment record. While we stress that studies with limited variation in DNA degradation among samples may not be strongly affected, researchers should exonerate methodological explanations for observed biodiversity changes in marine sediment cores, particularly when considering alpha diversity, before making ecological interpretations.}, } @article {pmid39979617, year = {2025}, author = {Ohlsson, C and Lawenius, L and Jiang, Y and Horkeby, K and Wu, J and Nilsson, KH and Koskela, A and Tuukkanen, J and Movérare-Skrtic, S and Henning, P and Sjögren, K}, title = {The beneficial effects of a probiotic mix on bone and lean mass are dependent on the diet in female mice.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {6182}, doi = {10.1038/s41598-025-91056-2}, pmid = {39979617}, issn = {2045-2322}, mesh = {Animals ; Female ; *Probiotics/pharmacology/administration & dosage ; Mice ; *Bone Density/drug effects ; Diet, High-Fat/adverse effects ; Bone and Bones/drug effects ; Mice, Inbred C57BL ; Ovariectomy ; Gastrointestinal Microbiome/drug effects ; Diet ; }, abstract = {Bone mass and lean mass decrease with age and these changes are associated with increased fracture risk and sarcopenia. Previous studies demonstrated that a probiotic mixture of Lacticaseibacillus paracasei DSM13434, Lactiplantibacillus plantarum DSM 15312 and DSM 15313 (L. Mix) prevents bone loss in ovariectomized (ovx) female mice. The purpose of the present study is to test if the beneficial effect of L. Mix is modified by the diet. Female mice were fed either a high-fat (HFD, 60% kcal from fat) or a low-fat (LFD, 10% kcal from fat) diet and subjected to either sham or ovx surgery and treated with L. Mix for 12 weeks. L. Mix treatment increased total body bone mineral density (p ≤ 0.01), by increasing cortical bone area, and total body lean mass (p = 0.035) in mice on LFD but not in mice on HFD. Metagenome sequencing of cecal content showed that L. Mix treatment increased the relative abundance of Lacticaseibacillus paracasei and, Lactiplantibacillus plantarum, demonstrating successful treatment. In addition, the probiotic treatment affected the overall gut microbiota composition and functionality. These findings demonstrate that the L. Mix in combination with a healthy diet is beneficial for musculoskeletal health in female mice.}, } @article {pmid39979545, year = {2025}, author = {Thompson, S and Wang, J and Schott, T and Nissinen, R and Haapalainen, M}, title = {Genomes of the Bacterial Endosymbionts of Carrot Psyllid Trioza apicalis Suggest Complementary Biosynthetic Capabilities.}, journal = {Current microbiology}, volume = {82}, number = {4}, pages = {145}, pmid = {39979545}, issn = {1432-0991}, mesh = {Animals ; *Hemiptera/microbiology ; *Symbiosis ; *Genome, Bacterial ; *Daucus carota/microbiology ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Bacteria/genetics/classification/metabolism ; Metagenome ; }, abstract = {Carrot psyllid Trioza apicalis is a serious pest of cultivated carrot and also a vector of the plant pathogen 'Candidatus Liberibacter solanacearum' (Lso). To find out whether T. apicalis harbours other species of bacteria that might affect the Lso infection rate, the bacterial communities and metagenome in T. apicalis were studied. Lso haplotype C was detected in a third of the psyllids sampled, at different relative amounts. Surprisingly, T. apicalis was found to harbour only one secondary endosymbiont, a previously unknown species of gamma proteobacterium endosymbiont (Gpe), beside the primary endosymbiont 'Candidatus Carsonella ruddii' (CCr). The relative abundancies of these two endosymbionts were approximately equal. The genomes of CCr, Gpe and Lso were assembled from a T. apicalis metagenome sample. Based on the 16S rRNA gene, the closest relative of Gpe of T. apicalis could be a secondary endosymbiont of Trioza magnoliae. The 253.171 kb Gpe genome contains all the tRNA and rRNA genes and most of the protein-coding genes required for DNA replication, transcription and translation, but it lacks most of the genes for amino acid biosynthesis. Gpe has no genes encoding cell wall peptidoglycan synthesis, suggesting it has no cell wall, and could thus live as an intracellular endosymbiont. Like the CCr of other psyllids, CCr of T. apicalis retains a broad amino acid biosynthetic capacity, whilst lacking many genes required for DNA replication and repair and for transcription and translation. These findings suggest that these two endosymbionts of T. apicalis are complementary in their biosynthetic capabilities.}, } @article {pmid39979340, year = {2025}, author = {Di Costanzo, F and Di Marsico, M and Orefice, I and Kristoffersen, JB and Kasapidis, P and Chaumier, T and Ambrosino, L and Miralto, M and Aiese Cigliano, R and Verret, F and Tirichine, L and Trindade, M and Van Zyl, L and Di Dato, V and Romano, G}, title = {High-quality genome assembly and annotation of Thalassiosira rotula (synonym of Thalassiosira gravida).}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {310}, pmid = {39979340}, issn = {2052-4463}, mesh = {*Diatoms/genetics ; Genome ; Molecular Sequence Annotation ; DNA Methylation ; Transcriptome ; DNA Transposable Elements ; Metagenome ; }, abstract = {Diatoms are unicellular eukaryotic microorganisms thriving in most aquatic environments thanks to the expression of biosynthetic pathways for secondary metabolites involved in defence and adaptation to environmental changes. The sequencing of the transcriptome of the cosmopolitan diatom Thalassiosira rotula Meunier 1910 (synonym of Thalassiosira gravida Cleve 1896) and of the metagenome of its associated microbiome revealed the presence of biosynthetic pathways synthesising molecules and compounds useful for the algae survival and with potential biotechnological applications. Here we present the genome of a Neapolitan T. rotula strain, which is 672 Mbp in size due to a high proportion of repetitive elements (63.59%) and segmental duplications (14%), while the number of predicted genes resulted to be comparable to that of smaller diatom genomes. DNA methylation was predominantly located in transposable elements.}, } @article {pmid39978635, year = {2025}, author = {Esse, J and Träger, J and Steininger, P and Bihlmaier, K and Fürst, J and Bardonicsek-Depnering, Z and Naumann-Bartsch, N and Morhart, P and Castellanos, I and Krause, SW and Herbst, L and Strauß, R and Chada, M and Korn, K and Valenza, G and Teschner, D and Bogdan, C and Held, J}, title = {Metagenomic analysis of microbial cell-free DNA from plasma of patients with suspected infections: performance and therapeutic impact in clinical routine.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmi.2025.02.016}, pmid = {39978635}, issn = {1469-0691}, abstract = {OBJECTIVES: The sensitivity of blood cultures (BC) is limited, especially when antimicrobial therapy already has been administered or when non-culturable pathogens are causing the disease. Metagenomic next-generation sequencing (mNGS) of cell-free DNA (cfDNA) from plasma has the potential to compensate for the disadvantages of BC diagnostics.

METHODS: We conducted a retrospective study in patients with suspected infections over a period of 3 months. cfDNA from plasma was analysed by mNGS (Illumina NextSeq, 25 million reads per sample, read length 75 base pairs) and sequences were analysed with DISQVER®, a CE-IVDD-labelled software algorithm and curated database. The data were compared to findings obtained with simultaneously taken BC and other microbiological results (+/- 7 days).

RESULTS: DISQVER® analysis was performed on 190 samples from 147 patients (124 adult, 23 pediatric). The median time-to-result including transport was two days (IQR 2-3; range 2-8). DISQVER® detected 158 pathogens (103 bacteria, 49 viruses, four fungi, one parasite) in 80 plasma samples (positivity rate 42.1%). The median number of pathogens per positive sample was one (IQR 1-2; range 1-10). The most common bacteria were Enterobacterales (30.1%; 31/103), anaerobic bacteria (18.4%; 19/103) and Enterococcus spp. (15.5%; 16/103), the most frequent viruses were Epstein-Barr virus (28.6%; 14/49), human herpesvirus 6B (18.4%; 9/49) and human cytomegalovirus (18.4%; 9/49). Mycobacterium avium, Legionella pneumophila, Tropheryma whipplei, Rhizomucor pusillus and Leishmania infantum were detected in one sample each. Simultaneous BC were positive in only 10.2% (18/176) of the samples, but were mostly (68.2%; 120/176) collected under antibiotic therapy. DISQVER® analysis resulted in 24 treatment changes in 20 patients (13.6%; 20/147; 9 start/escalation, 10 stop/de-escalation, 2 catheter replacements, 3 other).

CONCLUSIONS: DISQVER® significantly increased the detection rate of pathogens, led to the diagnosis of serious infections that otherwise would have been missed, and possibly improved the treatment of more than 10% of patients.}, } @article {pmid39978531, year = {2025}, author = {Perrotta, BG and Kidd, KA and Marcarelli, AM and Paterson, G and Walters, DM}, title = {Effects of chronic metal exposure and metamorphosis on the microbiomes of larval and adult insects, and riparian spiders through the aquatic-riparian food web.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {125867}, doi = {10.1016/j.envpol.2025.125867}, pmid = {39978531}, issn = {1873-6424}, abstract = {The macroinvertebrate microbiome controls various aspects of the host's physiology, from regulation of environmental contaminants to reproductive output. Aquatic insects provide critical nutritional subsidies linking aquatic and riparian food webs while simultaneously serving as a contaminant pathway for riparian insectivores in polluted ecosystems. Previous studies have characterized the transport and transfer of contaminants from aquatic to riparian ecosystems through insect metamorphosis, but both contaminant exposure and metamorphosis are energetically intensive processes that may cause host microbiomes to undergo radical transformation in structure and function, potentially affecting the host's physiology. We collected arthropods from three sites within Torch Lake, a historical copper mine in the Keweenaw Peninsula, Michigan, USA, and three sites within a nearby reference lake. Our objectives were to: 1) characterize the variation in microbiome communities and predicted metagenomic functions with legacy copper mining activity across space, among host types and family-level host taxonomy, 2) characterize how insect metamorphosis alters the microbiome community, including the degree of endosymbiotic infection, and predicted metagenomic function. We field-collected organisms, extracted their DNA, and sequenced the 16S region of the rRNA gene to characterize microbiome communities, then predicted metagenomic function. Site, lake, and host taxonomy affected the host microbiome community composition. Copper exposure increased the abundance of xenobiotic and lipid metabolism pathways in the Araneidae spider microbiome. Metamorphosis reduced the alpha diversity, altered the community composition, and predicted metagenomic function. We observed a bioconcentration of endosymbiotic bacteria in adult insects, especially holometabolous insects. Through metamorphosis, we observed a transition in function from xenobiotic degradation pathways to carbohydrate metabolism. Overall, contaminant exposure alters the microbiome composition in aquatic insects and riparian spiders and alters the function of the microbiome across the aquatic-riparian interface. Furthermore, metamorphosis is a critical element in shaping the aquatic insect microbiome across its life history.}, } @article {pmid39978335, year = {2025}, author = {Wang, Z and Tian, L and Jiang, Y and Ning, L and Zhu, X and Chen, X and Xuan, B and Zhou, Y and Ding, J and Ma, Y and Zhao, Y and Huang, X and Hu, M and Fang, JY and Shen, N and Cao, Z and Chen, H and Wang, X and Hong, J}, title = {Synergistic role of gut-microbial L-ornithine in enhancing ustekinumab efficacy for Crohn's disease.}, journal = {Cell metabolism}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmet.2025.01.007}, pmid = {39978335}, issn = {1932-7420}, abstract = {The role of the intestinal microbiome in Crohn's disease (CD) treatment remains poorly understood. This study investigates microbe-host interactions in CD patients undergoing ustekinumab (UST) therapy. Fecal metagenome, metabolome, and host transcriptome data from 85 CD patients were analyzed using multi-omics integration and mediation analysis. Our findings reveal significant microbiome-metabolite-host interactions. Specifically, Faecalibacterium prausnitzii was linked to altered L-ornithine biosynthesis, resulting in higher L-ornithine levels in patients before UST therapy. In vivo and in vitro studies demonstrated that microbiome-derived L-ornithine enhances UST treatment sensitivity in CD by disrupting the host IL-23 receptor signaling and inhibiting Th17 cell stabilization through the IL-12RB1/TYK2/STAT3 axis. L-ornithine significantly enhances the therapeutic efficacy of UST in CD patients, as demonstrated in a prospective clinical trial. These findings suggest that targeting specific microbe-host metabolic pathways may improve the efficacy of inflammatory bowel disease (IBD) treatments.}, } @article {pmid39978123, year = {2025}, author = {Jin, G and Wang, X and Cui, R and Yuan, S and Wang, M and Chen, Z}, title = {Comprehensive assessment of antibiotic impacts and risk thresholds on aquatic microbiomes and resistomes.}, journal = {Water research}, volume = {276}, number = {}, pages = {123262}, doi = {10.1016/j.watres.2025.123262}, pmid = {39978123}, issn = {1879-2448}, abstract = {Understanding the impacts of environmentally relevant low-level antibiotics on aquatic microbiomes and resistomes is crucial for risk assessment of anthropogenic antibiotic contamination. Here, we investigated the effects of seven subinhibitory concentrations of trimethoprim and lincomycin (10 ng/L to 10 mg/L), individually and in combination, on surface water microcosms over 1 and 7 days, using unspiked samples as controls. Metagenomic sequencing revealed a decrease in bacterial community α-diversity and an increase in resistome α-diversity with rising antibiotic concentrations upon 7 days of exposure. Notably, the β-diversity of both bacterial communities and resistomes exhibited a biphasic response, decreasing and then increasing with breakpoint concentrations of 2.73 µg/L and 0.68 µg/L, respectively. We also observed concentration-dependent increases in certain metagenome-assembled antibiotic-resistant bacteria (MAARB) and antibiotic resistance genes (ARGs), with minimum selective concentrations (MSCs) of 2.28 µg/L for trimethoprim targeting OXA-21 and 32.4 µg/L for lincomycin targeting erm(F). Among various metrics for identifying risk thresholds that induce significant changes in microbial taxa, resistomes, individual ARGs, and MAARB, the breakpoint concentration derived from resistome β-diversity was the most conservative. We propose integrating this metric into environmental risk assessment frameworks for antibiotics. Our study provides a systematic evaluation of antibiotic impacts on aquatic microbiomes and resistomes, offering key insights for refining risk assessments of antibiotic contamination in aquatic environments.}, } @article {pmid39978085, year = {2025}, author = {Mu, X and Chen, S and He, C and Li, H and Huang, Z}, title = {Bartonella henselae and Aspergillus flavus coinfection in an immunocompromised patient.}, journal = {Diagnostic microbiology and infectious disease}, volume = {112}, number = {1}, pages = {116708}, doi = {10.1016/j.diagmicrobio.2025.116708}, pmid = {39978085}, issn = {1879-0070}, abstract = {OBJECTIVE: This clinical study reports a case of atypical cat scratch disease in a patient undergoing immunosuppressive treatment, who contracted COVID-19 during the treatment period. Despite pharmacological and surgical interventions, Bartonella henselae was not completely cleared, leading to the recurrence of symptoms. The study highlights the challenges of management and the need for thorough immune assessment and precise diagnosis.

METHODS: A case report provides a detailed description of the treatment process for a young female patient with cat scratch disease (CSD), who had been treated with immunosuppressive agents (adalimumab and baricitinib) for ankylosing spondylitis and developed a concurrent COVID-19 infection during the treatment of CSD.The diagnosis was confirmed through macrogenomic second-generation sequencing. Pharmacological and surgical interventions were administered, and clinical outcomes were monitored.

RESULTS: When a patient is infected with Bartonella henselae and remains in a prolonged immunocompromised state, pharmacological or surgical treatment may still fail to completely clear the pathogen, leading to the recurrence of symptoms.

CONCLUSION: This case emphasizes the recurrence of symptoms in a patient undergoing long-term immunosuppressive treatment who contracted COVID-19 during Bartonella henselae infection. It suggests a potential interaction between immunosuppression and infection. It highlights the importance of immune assessment, accurate diagnosis, and vigilant management. Appropriate therapeutic strategies should be considered for patients with prolonged illness and impaired self-healing capability. Further research is warranted to clarify the mechanisms behind these interactions and to optimize management strategies for similar cases.}, } @article {pmid39975892, year = {2025}, author = {AlHilli, MM and Sangwan, N and Myers, A and Tewari, S and Lindner, DJ and Cresci, GAM and Reizes, O}, title = {The effects of dietary fat on gut microbial composition and function in ovarian cancer.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-5904007/v1}, pmid = {39975892}, issn = {2693-5015}, abstract = {Objectives : The gut microbiome (GM) is pivotal in regulating inflammation, immune responses, and cancer progression. This study investigates the effects of a ketogenic diet (KD) and a high-fat/low-carbohydrate (HF/LC) diet on GM alterations and tumor growth in a syngeneic mouse model of high-grade serous ovarian cancer (EOC). Methods : Thirty female C57BL/6J mice injected with KPCA cells were randomized into KD, HF/LC, and low-fat/high-carbohydrate (LF/HC) diet groups. Tumor growth was monitored with live, in vivo imaging. Stool samples were collected at the time of euthanasia and analyzed by 16SrRNA sequencing and shotgun metagenomic sequencing was performed to identify differential microbial taxonomic composition and metabolic function. Results : Our findings revealed that KD and HF/LC diets significantly accelerated EOC tumor growth compared to the LF/HC diet in a xenograft model. GM diversity was markedly reduced in KD and HF/LC-fed mice, correlating with increased tumor growth, whereas LF/HC-fed mice showed higher GM diversity. Metagenomic analyses identified distinct alterations in microbial taxa including Bacteroides , Lachnospiracae bacterium , Bacterium_D16_50, and Enterococcus faecalis predominantly abundant in HF/LC-fed mice, Dubsiella_newyorkensis predominantly abundant in LF/HC-fed, and KD fed mice showing a higher abundance of Akkermansia and Bacteroides . Functional pathways across diet groups indicated polyamine biosynthesis and fatty acid oxidation pathways were enriched in HF/LC-fed mice. Conclusions These results highlight the intricate relationship between diet, the gut microbiome, and tumor metabolism. The potential role of dietary interventions in cancer prevention and treatment warrants further investigation.}, } @article {pmid39975683, year = {2025}, author = {Fang, J and Wang, Z and Shen, Y and Wu, X and Fang, H and Sun, X and Yu, T and Zhang, Q}, title = {Case report: The value of early application of mNGS technology in the diagnosis and treatment of severe Legionnaires' disease: reports of two cases with different outcomes.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1501192}, pmid = {39975683}, issn = {2296-858X}, abstract = {BACKGROUND: Legionnaires' disease has a high clinical mortality rate, and early diagnosis and treatment are critical. Increasing evidence shows that metagenomic next-generation sequencing (mNGS) has excellent potential for the early identification of pathogens. To help clinicians better recognize Legionnaires' disease in its early stage and to illustrate the diagnostic value of mNGS technology, we reviewed and summarized two cases of severe Legionnaires' disease.

METHODS AND ANALYSIS: We selected two patients with severe Legionnaires' disease who were admitted to our department in recent years. We discuss experience with them and the shortcomings in their treatment by summarizing their medical history, disease evolution, tests, and diagnostic and therapeutic processes.

RESULTS: In both patients, the diagnosis of Legionnaires' disease was confirmed through analysis of the bronchoalveolar lavage fluid (BALF). The middle-aged male patient was cured and discharged due to early detection and diagnosis. The elderly immunocompromised patient died due to a delay in diagnosis.

CONCLUSION: This study highlights the importance of the early recognition and diagnosis of severe Legionnaires' disease and the advantages of mNGS in identifying the pathogen.}, } @article {pmid39975405, year = {2025}, author = {Zhou, Z and Riley, R and Kautsar, S and Wu, W and Egan, R and Hofmeyr, S and Goldhaber-Gordon, S and Yu, M and Ho, H and Liu, F and Chen, F and Morgan-Kiss, R and Shi, L and Liu, H and Wang, Z}, title = {GenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.01.30.635558}, pmid = {39975405}, issn = {2692-8205}, abstract = {Genome foundation models hold transformative potential for precision medicine, drug discovery, and understanding complex biological systems. However, existing models are often inefficient, constrained by suboptimal tokenization and architectural design, and biased toward reference genomes, limiting their representation of low-abundance, uncultured microbes in the rare biosphere. To address these challenges, we developed GenomeOcean , a 4-billion-parameter generative genome foundation model trained on over 600 Gbp of high-quality contigs derived from 220 TB of metagenomic datasets collected from diverse habitats across Earth's ecosystems. A key innovation of GenomeOcean is training directly on large-scale co-assemblies of metagenomic samples, enabling enhanced representation of rare microbial species and improving generalizability beyond genome-centric approaches. We implemented a byte-pair encoding (BPE) tokenization strategy for genome sequence generation, alongside architectural optimizations, achieving up to 150× faster sequence generation while maintaining high biological fidelity. GenomeOcean excels in representing microbial species and generating protein-coding genes constrained by evolutionary principles. Additionally, its fine-tuned model demonstrates the ability to discover novel biosynthetic gene clusters (BGCs) in natural genomes and perform zero-shot synthesis of biochemically plausible, complete BGCs. GenomeOcean sets a new benchmark for metagenomic research, natural product discovery, and synthetic biology, offering a robust foundation for advancing these fields.}, } @article {pmid39975011, year = {2025}, author = {Ziemski, M and Gehret, L and Simard, A and Dau, SC and Risch, V and Grabocka, D and Matzoros, C and Wood, C and Cabrera, PM and Hernández-Velázquez, R and Herman, C and Evans, K and Robeson, MS and Bolyen, E and Caporaso, JG and Bokulich, NA}, title = {MOSHPIT: accessible, reproducible metagenome data science on the QIIME 2 framework.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.01.27.635007}, pmid = {39975011}, issn = {2692-8205}, abstract = {Metagenome sequencing has revolutionized functional microbiome analysis across diverse ecosystems, but is fraught with technical hurdles. We introduce MOSHPIT (https://moshpit.readthedocs.io), software built on the QIIME 2 framework (Q2F) that integrates best-in-class CAMI2-validated metagenome tools with robust provenance tracking and multiple user interfaces, enabling streamlined, reproducible metagenome analysis for all expertise levels. By building on Q2F, MOSHPIT enhances scalability, interoperability, and reproducibility in complex workflows, democratizing and accelerating discovery at the frontiers of metagenomics.}, } @article {pmid39974997, year = {2025}, author = {Qu, EB and Baker, JS and Markey, L and Khadka, V and Mancuso, C and Tripp, D and Lieberman, TD}, title = {Intraspecies associations from strain-rich metagenome samples.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.02.07.636498}, pmid = {39974997}, issn = {2692-8205}, abstract = {Genetically distinct strains of a species can vary widely in phenotype, reducing the utility of species-resolved microbiome measurements for detecting associations with health or disease. While metagenomics theoretically provides information on all strains in a sample, current strain-resolved analysis methods face a tradeoff: de novo genotyping approaches can detect novel strains but struggle when applied to strain-rich or low-coverage samples, while reference database methods work robustly across sample types but are insensitive to novel diversity. We present PHLAME, a method that bridges this divide by combining the advantages of reference-based approaches with novelty awareness. PHLAME explicitly defines clades at multiple phylogenetic levels and introduces a probabilistic, mutation-based, framework to accurately quantify novelty from the nearest reference. By applying PHLAME to publicly available human skin and vaginal metagenomes, we uncover previously undetected clade associations with coexisting species, geography, and host age. The ability to characterize intraspecies associations and dynamics in previously inaccessible environments will propel new mechanistic insights from accumulating metagenomic data.}, } @article {pmid39974142, year = {2025}, author = {Dravillas, C and Williams, N and Husain, M and Hoyd, R and Hussein, A and Meara, A and Lynn, M and Bibi, A and Conrad, B and Lepola, N and Gray, S and Bodnar, M and Arya, N and Roberts, S and Hoang, P and Apparicio, J and Merrill, D and Wu, R and Verschraegen, C and Burd, CE and Kendra, K and Spakowicz, D}, title = {The Association of the Microbiome with Melanoma Tumor Response to Immune Checkpoint Inhibitor Treatment and Immune-Related Adverse Events (NCT05102773).}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.01.30.25321413}, pmid = {39974142}, abstract = {Improved understanding of the factors that underlie immune checkpoint inhibitor (ICI) response and toxicity are needed as only half of patients with metastatic melanoma respond, and 10-40% experience immune-related adverse events (irAEs). Modifying the gut microbiome could positively affect response to ICIs and reduce toxicities. Here, we sought to determine if the pre-treatment gut microbiome predicts ICI response or toxicity in the setting of metastatic melanoma. Melanoma patients (n=88) over 18 years of age, planning to receive ICI therapy enrolled in a prospective observational cohort study at The Ohio State University Comprehensive Cancer Center Skin Cancer Clinic. Patients taking corticosteroids for indications other than adrenal physiologic replacement were excluded. Stools were collected at baseline, within 10 days of an irAE as determined by CTCAE v 5.0 criteria, and at 12 weeks. ICI response and progression-free survival (PFS) were evaluated q12 weeks using Response Evaluation Criteria in Solid Tumors (RECIST v1.1). Metagenomic whole-genome shotgun sequencing of the microbiome was classified using MetaPhlAn4/HUMAnN3 and differential abundance analyzed with ANCOM-BC2. Of the 88 patients enrolled, 41 had metastatic disease and complete data. There were 25 participants classified as responders, defined as having complete response or partial response according to RECIST criteria, or stable disease with 6-month PFS. Grade ≥ 1 irAEs were observed in 15/41 participants. The abundance of Intestinimonas butyriciproducens (q-value = 0.002) and Longicatena caecimuris (q-value = 0.003) were enriched in responders, Tenericutes (q-value= 0.001) and Lachnospira sp. NSJ 43 (q-value =0.002) in non-responders. Blautia luti , as well as several other Lachnospiraceae , were associated with response and no irAE (response q-value = 0.02, no irAE q-value = 0.02). The association of response to ICIs with several taxa in the family Lachnospiraceae , a prevalent microbial family in the gut, is consistent with prior research, which has found that this family may influence treatment outcomes through various mechanisms, such as immune regulation, metabolism, and pathogen exclusion. While no statistical relationship was observed between response and irAEs in this cohort, the microbes associated with both could serve as biomarkers. Future studies to assign causal roles for (specific microbes) in response and toxicity could identify mechanisms to improve patient outcomes.}, } @article {pmid39973225, year = {2025}, author = {Chen, C and Yu, Y and Zhu Ma, LZ and Nin, J and Zhang, D and Nong, W and Pan, X}, title = {Visceral leishmaniasis related secondary haemophagocytic syndrome: A case report.}, journal = {The Journal of international medical research}, volume = {53}, number = {2}, pages = {3000605251318204}, doi = {10.1177/03000605251318204}, pmid = {39973225}, issn = {1473-2300}, mesh = {Humans ; *Lymphohistiocytosis, Hemophagocytic/diagnosis/parasitology/complications ; *Leishmaniasis, Visceral/diagnosis/complications ; Male ; Middle Aged ; High-Throughput Nucleotide Sequencing ; Bone Marrow/pathology/parasitology ; }, abstract = {Visceral leishmaniasis (VL) is a parasitic disease that can trigger haemophagocytic syndrome (HPS), making its prompt diagnosis crucial. The application of metagenome next-generation sequencing (mNGS) provides a rapid diagnostic approach, particularly for patients with negative bone marrow aspiration results. We present here, a case of a male patient in his early 50s who presented with fever and abdominal pain. Routine examinations failed to identify its specific cause. However, diagnosis through mNGS helped prevent a potentially fatal outcome.}, } @article {pmid39578945, year = {2025}, author = {Li, D and Zhi, J and Ye, J and Yue, W and Yang, Y}, title = {Influence of different diet categories on gut bacterial diversity in Frankliniella occidentalis.}, journal = {Environmental entomology}, volume = {54}, number = {1}, pages = {119-129}, doi = {10.1093/ee/nvae117}, pmid = {39578945}, issn = {1938-2936}, support = {[2016] 5802//Guizhou International Science and Technology Cooperation Base/ ; }, mesh = {Diet ; Gastrointestinal Microbiome ; Metagenome ; Phaseolus ; Rosa ; Sequence Analysis, DNA ; *Thysanoptera/microbiology ; *Bacteria/classification/genetics/isolation & purification ; }, abstract = {The microbial composition of insect guts is typically influenced by the type of food consumed, and conversely, these microbes influence the food habits of insects. Western flower thrips (WFT; Frankliniella occidentalis) is an invasive pest with a wide range of hosts, including vegetables and horticultural crops. To elucidate variations in gut bacteria among WFT feeding on rose (Rosa rugosa) flowers (FF), kidney bean (Phaseolus vulgaris) pods (PF), and kidney bean leaves (LF), we collected adult guts and extracted DNA for 16S ribosomal RNA gene sequencing of microbial communities. The results revealed that the FF population had the highest number of annotations. Alpha diversity analysis revealed that the Chao and Ace indexes were the greatest in the PF population, indicating a higher abundance of gut bacteria. Moreover, the Simpson index was the highest in the FF population, indicating that gut bacterial diversity was the highest in the FF population. Comparison of species composition demonstrated that Proteobacteria dominated all 3 populations at the phylum level, with Actinobacteria being the subdominant phylum. At the genus level, Stenotrophomonas was the dominant bacteria in the PF and LF populations, whereas Rosenbergiella was dominant in the FF population. KEGG pathway annotation predicted that the gut bacteria of adult WFT were mainly involved in carbohydrate and amino acid metabolism. Our results revealed that the diversity and composition of WFT gut microbiota are influenced by diet, offering evidence for future studies on the ecological adaptability of WFT and the mechanisms underlying the interaction between gut microbiota and host.}, } @article {pmid39971118, year = {2025}, author = {Kong, F and Wang, W and Wang, X and Yang, H and Tang, J and Li, Y and Shi, J and Wang, S}, title = {Performance and mechanism of nano Fe-Al bimetallic oxide enhanced constructed wetlands for the treatment of Cr(VI)-contaminated wastewater.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121154}, doi = {10.1016/j.envres.2025.121154}, pmid = {39971118}, issn = {1096-0953}, abstract = {Enhancing the synergistic interactions between substrates and microorganisms in constructed wetlands (CWs) represents a promising approach for treating heavy metal-contaminated wastewater. Multifunctional nanomaterials may play a significant role in this process. However, their impacts and mechanisms in this context remain unclear. In this study, artificial zeolite spheres loaded with Fe-Al double metal oxide (Fe-Al-NBMO) were synthesized and utilized in the CW to treat Cr(VI)-contaminated wastewater. Adsorption experiments demonstrated that the adsorption capacity of Fe-Al-NBMO loaded substrate for Cr(VI) was 988.43 mg/kg at an initial concentration of 30 mg/L, 361, and 37 times higher than that of gravel and carrier, respectively. The CW experiment indicated that the Cr(VI) effluent concentration in CW-ZL with Fe-Al-NBMO substrate did not exceed the integrated wastewater discharge standard (GB8978-1996) (0.5 mg/L) at an influent concentration of 50 mg/L. The introduction of the Fe-Al-NBMO substrate promoted microbial growth and increase the Extracellular Polymeric Substances (EPS) and other metabolite contents, thereby enhancing the microbial adsorption of Cr(VI). Furthermore, the removal performance of Cr(VI) was enhanced by the increase in resistant microorganisms (Hyphomicrobium and Rhodopseudomonas) and functional genes. Notably, metaproteomic analysis revealed that the elevated abundance of NADH-quinone oxidoreductase (nuoB, nuoC, nuoD, nuoE, nuoF, and nuoG), reductive coenzymes (fbp, ALDO, mcrA, and cdhC), metabolic pathways of sulfur (Cysp), and glutathione transferase (GsiB, frmA, and gfa) contributed to Cr(VI) removal. Our results provide a robust strategy for treating Cr(VI)-contaminated wastewater by CWs with Fe-Al-NBMO loaded substrate.}, } @article {pmid39970657, year = {2025}, author = {Feng, W and Zhang, Q and Li, J and Liu, J and Duan, C and Peng, Y and Peng, Y}, title = {Facilitating multiple nitrite for anammox process directly treating municipal wastewater: Optimized organics utilization and microbial composition.}, journal = {Journal of environmental management}, volume = {376}, number = {}, pages = {124460}, doi = {10.1016/j.jenvman.2025.124460}, pmid = {39970657}, issn = {1095-8630}, abstract = {While direct anammox implementation is attractive when treating wastewater, nitrite (NO2[-]-N) availability and excess organic matter significantly limit its practical application. This study proposed partial nitrification and endogenous partial denitrification/anammox (PN/A-EPD/A) for the treatment of real municipal wastewater (COD/N ratio: 2.8) within a single-stage reactor under anaerobic/aerobic/anoxic mode. Interestingly, with reducing dissolved oxygen concentration (5.0 ± 1.0 → 1.0 ± 0.5 mg-O2/L) during aerobic phase, Comammox Nitrospira clade A became dominated and introduced vast nitrate (NO3[-]-N) into the subsequent anoxic stage. Both in-situ and ex-situ tests confirmed that sufficient NO3[-]-N as electron acceptors were in favor of the EPD/A occurrence with endogenous organics utilization, which was obtained by anaerobic endogenous transformation. Metagenomic results confirmed the role of Thauera in facilitating NO3[-]-N→NO2[-]-N process, and further supporting AnAOB. As a result, Ca. Brocadia gradually enriched on granules (from 0.08% to 3.51%) and contributed up to 51.5 % to total inorganic nitrogen removal through the PN/A-EPD/A process. Optimized carbon utilization pathway promoted the re-cooperative balance of microorganisms and this process achieved efficient nitrogen removal (93.5%) and desirable quality of effluent (3.2 mg-N/L) when treating real municipal wastewater.}, } @article {pmid39970645, year = {2025}, author = {Wang, W and Tao, J and Pang, R and Zhang, L and Zhang, Y and Su, Y and Li, W and Hong, S and Kim, H and Zhan, M and Xie, B}, title = {Effect of alkaline-thermal pretreatment on biodegradable plastics degradation and dissemination of antibiotic resistance genes in co-compost system.}, journal = {Journal of hazardous materials}, volume = {489}, number = {}, pages = {137644}, doi = {10.1016/j.jhazmat.2025.137644}, pmid = {39970645}, issn = {1873-3336}, abstract = {Biodegradable plastics (BDPs) are an eco-friendly alternative to traditional plastics in organic waste, but their microbial degradation and impact on antibiotic resistance genes (ARGs) transmission during co-composting remain poorly understood. This study examines how alkaline-thermal pretreatment enhances BDPs degradation and influences the fate of ARGs and mobile genetic elements (MGEs) in co-composting. Pretreatment with 0.1 mol/L NaOH at 100℃ for 40 minutes increased the surface roughness and hydrophilicity of BDPs while reducing their molecular weight and thermal stability. Incorporating pretreated BDPs film (8 g/kg-TS) into the compost reduced the molecular weight of the BDPs by 59.70 % during the maturation stage, facilitating compost heating and prolonging the thermophilic stage. However, incomplete degradation of BDPs releases numerous smaller-sized microplastics, which can act as carriers for microorganisms, facilitating the dissemination of ARGs across environments and posing significant ecological and public health risks. Metagenomic analysis revealed that pretreatment enriched plastic-degrading bacteria, such as Thermobifida fusca, on BDPs surfaces and accelerated microbial plastic degradation during the thermophilic stage, but also increased ARGs abundance. Although pretreatment significantly reduced MGEs abundance (tnpA, IS19), the risk of ARGs dissemination remained. Three plastic-degrading bacteria (Pigmentiphaga sp002188465, Bacillus clausii, and Bacillus altitudinis) were identified as ARGs hosts, underscoring the need to address the risk of horizontal gene transfer of ARGs associated with pretreatment in organic waste management.}, } @article {pmid39970096, year = {2024}, author = {Begmatov, SA and Beletsky, AV and Rakitin, AL and Lukina, AP and Sokolyanskaya, LO and Rakitin, AV and Glukhova, LB and Mardanov, AV and Karnachuk, OV and Ravin, NV}, title = {[Antibiotic Resistance Genes in Cattle Gut Microbiota: Influence of Housing Conditions].}, journal = {Molekuliarnaia biologiia}, volume = {58}, number = {6}, pages = {996-1006}, pmid = {39970096}, issn = {0026-8984}, mesh = {Animals ; Cattle ; *Gastrointestinal Microbiome/drug effects/genetics ; *Feces/microbiology ; Anti-Bacterial Agents/pharmacology ; Housing, Animal ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics/drug effects ; beta-Lactams/pharmacology ; beta-Lactamases/genetics ; }, abstract = {Resistance to antimicrobial drugs is an urgent problem not only in public health, but also in animal husbandry. The widespread use of antimicrobials in feed additives is one of the main reasons for the rapid spread of antibiotic resistance in the microbiota of the gastrointestinal tract of farm animals. To characterize antibiotic resistance genes (resistome), we performed metagenomic analysis of the feces of 24 cattle from different regions of Russia, including cows of different breeds and yaks. Animals differed in the type of housing: year-round on pastures or in barns of conventional farms, with consumption of feed additives. Although genes of resistance to aminoglycosides, β-lactams, glycopeptides, MLS antibiotics (macrolides, lincosamides, and streptogramins), phenicols, and tetracyclines were detected in samples from both groups of animals, the content of the resistome in the fecal microbiome of stall-bred cattle was about ten times higher than in animals kept on pastures. The resistome of stall cattle was dominated by β-lactamases and tetracycline resistance genes, the content of which in the microbiome was 24 and 60 times higher, respectively, than in animals kept on pastures. Apparently, the spread of resistance to β-lactams and tetracyclines in stall cattle reflects the active use of these antibiotics in livestock production. Metagenomic analysis of livestock feces can be used to quantify antibiotic resistance genes for the purpose of monitoring antimicrobial drugs used in animal husbandry.}, } @article {pmid39969428, year = {2025}, author = {Bloom, PP and Bassis, CM and Crossette, E and Silber, JL and Norman, JM and Young, VB and Lok, ASF}, title = {Safety and efficacy of a defined bacterial consortium, VE303, to treat HE.}, journal = {Hepatology communications}, volume = {9}, number = {3}, pages = {}, doi = {10.1097/HC9.0000000000000650}, pmid = {39969428}, issn = {2471-254X}, mesh = {Humans ; Male ; Middle Aged ; Female ; *Gastrointestinal Microbiome/drug effects ; *Hepatic Encephalopathy/drug therapy ; Aged ; Treatment Outcome ; Vancomycin/therapeutic use/adverse effects ; Anti-Bacterial Agents/therapeutic use/adverse effects/administration & dosage ; Feces/microbiology/chemistry ; Lactulose/therapeutic use ; Rifaximin/therapeutic use ; Adult ; }, abstract = {BACKGROUND: Novel therapies are needed to treat HE, and microbiome modulation is a promising target. VE303 is a defined consortium of 8 purified, clonal bacterial strains, known to produce metabolites that may be beneficial in HE. We evaluated the safety and efficacy of VE303 to treat HE.

METHODS: We performed a single-center, randomized, placebo-controlled trial of VE303 in adult patients with a history of overt HE (NCT04899115). Eligible patients were taking lactulose and rifaximin, had no recent systemic antibiotics, and had MELD ≤20. All patients received 5 days of oral vancomycin followed by randomization to 14 days of VE303 or placebo (2:1). The primary endpoints were incidence of serious adverse events and change in psychometric HE score (PHES) from baseline to 4 weeks after treatment. Stool samples underwent metagenomic sequencing and metabolite quantification.

RESULTS: Eighteen patients completed the trial, 56% men, with a mean age of 59 years and a mean MELD of 11. Patients who received VE303 had a mean change in PHES of +1.5 versus -1.0 in those who received a placebo (p=0.20). Two of the 12 patients who received VE303 had at least 1 serious adverse event (all overt HE hospitalizations), compared with 0/6 patients who received a placebo. In the patients who received VE303, 2 of 8 strains engrafted in >50% of patients. Both VE303 strain engraftment and increased stool butyrate production had a trend toward improved PHES.

CONCLUSIONS: VE303 was well tolerated in patients with cirrhosis and a history of overt HE, leading to the engraftment of certain VE303 strains and a higher percentage of patients with improved PHES.}, } @article {pmid39969320, year = {2024}, author = {Liu, K and Yang, Z and Xie, W and Wang, S and Hu, S}, title = {Revision after knee arthroplasty due to Mycoplasma hominis infection: A case report and literature review.}, journal = {Medicine}, volume = {103}, number = {52}, pages = {e41174}, doi = {10.1097/MD.0000000000041174}, pmid = {39969320}, issn = {1536-5964}, support = {2021MS10//Research on the mechanism of PRMT3 regulating trabecular bone chromatin remodeling and participating in ONFH/ ; 2024RS-CXTD-86//Shaanxi Province Innovation Capacity Support Program/ ; }, mesh = {Humans ; Male ; *Mycoplasma Infections/diagnosis/drug therapy ; Aged ; *Arthroplasty, Replacement, Knee/adverse effects ; *Reoperation ; *Mycoplasma hominis/isolation & purification ; *Anti-Bacterial Agents/therapeutic use/administration & dosage ; Prosthesis-Related Infections/diagnosis/microbiology/drug therapy ; Osteoarthritis, Knee/surgery ; }, abstract = {RATIONALE: Mycoplasma hominis is an opportunistic pathogen commonly found in the human genitourinary system. However, infections caused by Mycoplasma hominis following knee arthroplasty are relatively rare.

PATIENT CONCERNS: A 68-year-old male patient underwent bilateral total knee arthroplasty 2 years ago due to osteoarthritis. Over the past 3 months, he developed persistent swelling and pain in both knees, along with the formation of a mass in the left knee. The patient also has a history of type 2 diabetes and hypoalbuminemia.

DIAGNOSES: Joint fluid samples from both knees were collected for metagenomic sequencing (mNGS), which detected Mycoplasma hominis infection. Histopathological examination confirmed chronic infection.

INTERVENTIONS: The patient underwent 1-stage revision surgery for the left knee, followed by intravenous doxycycline (100 mg, q12h) and intra-articular injections of vancomycin (0.5 g/d) and meropenem (0.5 g/d) for 2 weeks. Afterward, the patient was switched to oral rifampin (450 mg daily) and moxifloxacin (400 mg daily) for six weeks. Following improvement in the left knee symptoms, 1-stage revision surgery was performed on the right knee. The same antibiotic regimen was used postoperatively.

OUTCOMES: The patient experienced significant postoperative improvement, with marked pain relief and no signs of recurrent infection. The knee remained stable, and functional recovery was observed. To date, there have been no signs of infection recurrence during follow-up.

LESSONS: After joint arthroplasty, if a patient has persistent infection symptoms, does not respond to beta-lactam antibiotics, and has negative blood cultures, Mycoplasma infection should be considered. In this instance, the use of mNGS proved highly effective in diagnosing this atypical pathogen. The patient improved significantly after 1-stage revision surgery and targeted antibiotic therapy, though longer follow-up is needed to confirm long-term outcomes. Additionally, limited access to mNGS in some regions may delay diagnosis and treatment.}, } @article {pmid39969192, year = {2025}, author = {Haro-Moreno, JM and López-Pérez, M and Molina-Pardines, C and Rodriguez-Valera, F}, title = {Large diversity in the O-chain biosynthetic cluster within populations of Pelagibacterales.}, journal = {mBio}, volume = {}, number = {}, pages = {e0345524}, doi = {10.1128/mbio.03455-24}, pmid = {39969192}, issn = {2150-7511}, abstract = {Genomic diversity in prokaryotic species is largely due to the existence of extensive pangenomes, allowing different gene complements to be drawn depending on the strain. Here, we have studied the diversity of the O-chain polysaccharide biosynthesis cluster (OBC) in marine bacteria of the Pelagibacterales order as a proxy to measure such genetic diversity in a single population. The study of single-amplified genomes (SAGs) from the whole order found a pattern similar to that of other well-studied microbes, such as the Enterobacteriales or Alteromonas, where distinct OBCs represent strains containing different gene pools. We found that most of the OBC sharing happened among individuals of the same clonal frame (>99% average nucleotide identity). Moreover, given the parsimonious way this cluster changes, the diversity of the OBCs can be extrapolated to the size of the population's pangenome. This assumes that different OBCs correspond to lineages containing unique flexible gene pools, as seen in the aforementioned microbes. Through long-read metagenomics, we could detect 380 different OBCs at a single Mediterranean sampling site. Within a single population (single species and sample) of the endemic Ia.3/VII (gMED) genomospecies, we identified 158 OBCs, of which 130 were unique. These findings suggest that the gene pool within a single population might be substantial (several thousands). While this figure is large, it aligns with the complexity of the dissolved organic matter that these organisms can potentially degrade.IMPORTANCEDifferent strains of the same bacterial species contain very different gene pools. This has been long known by epidemiologists. However, it is unknown what gene pool is present in a single set of environmental conditions, i.e., the same time and place in free-living bacteria. Here, we have leveraged information from SAGs to analyze the diversity of the gene cluster coding for the O-chain polysaccharide, a typical component of the flexible gene pool classically used as a tool to differentiate strains in clinical microbiology. It evolves at a similar rate to the rest of the genome and does not seem to be affected by an arms race with phages. One single species of Pelagibacteriales (gMED) revealed an astounding diversity in one sample studied by long-read metagenomics. Our results point to a large gene pool (local pangenome) present in a single population, which is critical to interpreting the biological meaning of the pangenome, i.e., it provides intrapopulation diversity rather than characterizing strains with different distribution in time and/or space.}, } @article {pmid39968394, year = {2025}, author = {Zhao, N and Bai, J and Li, X and Xu, G and Fu, X and Li, J and Niu, L and Yao, J and Zhou, X}, title = {Correlation study on gut microbiota and myosteatosis in patients with liver cirrhosis.}, journal = {Frontiers in nutrition}, volume = {12}, number = {}, pages = {1513973}, pmid = {39968394}, issn = {2296-861X}, abstract = {OBJECTIVE: To investigate the features of gut microbiota in cirrhotic patients with myosteatosis and identify specific bacterial species that may be involved in the pathogenesis of myosteatosis.

METHODS: 80 patients with liver cirrhosis were categorized into the myosteatosis group (n = 44) and the non-myosteatosis group (n = 36). Metagenomic sequencing was used to analyze the differences in gut microbiota composition between the two groups. Subsequently, the value of meaningful gut microbiota in the diagnosis of myosteatosis in patients with liver cirrhosis was analyzed.

RESULTS: At the species level, however, 15 bacterial species exhibited significant differences in relative abundance between these two groups. The relative abundance of Roseburia hominis and Subdoligranulum unclassified was inversely associated with mean muscle attenuation density at the L3 level (p < 0.05). Assessement of the diagnostic potential of Roseburia hominis and Subdoligranulum unclassified for the development of myosteatosis showed that the areas under the ROC curves (AUCs) was 0.869 [95% confidence interval (CI): 0.709-1.029; p < 0.05] for Roseburia hominis and 0.828 (95% CI: 0.6472-1.009; p < 0.05) for Subdoligranulum unclassified.

CONCLUSION: Our study establishes compositional alterations of gut microbiota in patients with liver cirrhosis combined with myosteatosis and suggests the diagnostic potential for using gut microbiota as noninvasive biomarkers.}, } @article {pmid39968350, year = {2025}, author = {Lee, CZ and Worsley, SF and Davies, CS and Silan, E and Burke, T and Komdeur, J and Hildebrand, F and Dugdale, HL and Richardson, DS}, title = {Metagenomic analyses of gut microbiome composition and function with age in a wild bird; little change, except increased transposase gene abundance.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf008}, pmid = {39968350}, issn = {2730-6151}, abstract = {Studies on wild animals, mostly undertaken using 16S metabarcoding, have yielded ambiguous evidence regarding changes in the gut microbiome (GM) with age and senescence. Furthermore, variation in GM function has rarely been studied in such wild populations, despite GM metabolic characteristics potentially being associated with host senescent declines. Here, we used 7 years of repeated sampling of individuals and shotgun metagenomic sequencing to investigate taxonomic and functional changes in the GM of Seychelles warblers (Acrocephalus sechellensis) with age. Our results suggest that taxonomic GM species richness declines with age and in the terminal year, with this terminal decline occurring consistently across all ages. Taxonomic and functional GM composition also shifted with host age. However, the changes we identified occurred linearly with age (or even mainly during early years prior to the onset of senescence in this species) with little evidence of accelerated change in later life or during their terminal year. Therefore, the results suggest that changes in the GM with age are not linked to senescence. Interestingly, we found a significant increase in the abundance of a group of transposase genes with age, which may accumulate passively or due to increased transposition induced as a result of stressors that arise with age. These findings reveal taxonomic and functional GM changes with age, but not senescence, in a wild vertebrate and provide a blueprint for future wild functional GM studies linked to age and senescence.}, } @article {pmid39968349, year = {2025}, author = {Bhandari, R and Robbins, CJ and Arora, AK and Chaston, JM and Kang, DS}, title = {Motility genes are associated with the occurrence of Drosophila melanogaster-associated gut microbes.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf013}, pmid = {39968349}, issn = {2730-6151}, abstract = {Recent work highlighted the role of motility genes in dispersing fly-associated microbes and their spread between hosts. We investigated whether bacterial genes encoding motility are associated with the occurrence of bacteria above passive dispersal levels in the gut of wild Drosophila melanogaster. We revisited 16S amplicon and shotgun metagenome data of wild flies and correlated four genera of bacteria (Commensalibacter, Gluconobacter, Lactobacillus, and Tatumella) with motility genes. We plotted the microbes against neutral models of ecological drift and passive dispersal. Microbes with positive correlations to motility were exclusively found at or above neutral model predictions, suggesting motility genes are crucial for fly microbiota spread and colonization. This information is crucial for understanding how specific gene functions contribute to microbial community dispersal and colonization within the fly host. Moreover, this study's findings serve as a proof of concept for using the neutral model to predict microbial functions essential for survival and dissemination in diverse hosts.}, } @article {pmid39968048, year = {2024}, author = {Nene, M and Kunene, NW and Pierneef, R and Hadebe, K}, title = {Profiling the diversity of the village chicken faecal microbiota using 16S rRNA gene and metagenomic sequencing data to reveal patterns of gut microbiome signatures.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1487595}, pmid = {39968048}, issn = {1664-302X}, abstract = {INTRODUCTION: The production environment of extensively raised village chickens necessitates their adaptability to low-resource systems. The gut microbiome plays a critical role in supporting this adaptability by influencing health and productivity. This study aimed to investigate the diversity and functional capacities of the faecal microbiome in village chickens from Limpopo and KwaZulu-Natal provinces of South Africa.

METHODS: Using a combination of 16S rRNA gene sequencing and shotgun metagenomic sequencing technologies, we analysed 98 16S rRNA and 72 metagenomic datasets. Taxonomic profiles and functional gene annotations were derived, focusing on microbial diversity, antibiotic resistance genes (ARGs), and potential zoonotic pathogens.

RESULTS: Taxonomic analysis showed that the predominant phyla in both provinces were Firmicutes, Bacteroidota, Proteobacteria, and Actinobacteria. At the genus level, Escherichia and Shigella were prevalent, with Escherichia coli and Shigella dysenteriae identified as major contributors to the gut microbiome. ARGs were identified, with MarA, PmrF, and AcrE detected in KwaZulu-Natal, and cpxA, mdtG, and TolA in Limpopo. These genes primarily mediate antibiotic efflux and alteration.

DISCUSSION: The detection of zoonotic bacteria such as Escherichia coli and Streptococcus spp. highlights potential health risks to humans through the food chain, emphasizing the importance of improved household hygiene practices. This study underscores the role of the gut microbiome in village chicken health and adaptability, linking microbial diversity to production efficiency in low-resource settings. Targeted interventions and further research are crucial for mitigating zoonotic risks and enhancing sustainability in village chicken farming.}, } @article {pmid39968047, year = {2024}, author = {Ling, M and Szarvas, J and Kurmauskaitė, V and Kiseliovas, V and Žilionis, R and Avot, B and Munk, P and Aarestrup, FM}, title = {High throughput single cell metagenomic sequencing with semi-permeable capsules: unraveling microbial diversity at the single-cell level in sewage and fecal microbiomes.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1516656}, pmid = {39968047}, issn = {1664-302X}, abstract = {Single-cell sequencing may serve as a powerful complementary technique to shotgun metagenomics to study microbiomes. This emerging technology allows the separation of complex microbial communities into individual bacterial cells, enabling high-throughput sequencing of genetic material from thousands of singular bacterial cells in parallel. Here, we validated the use of microfluidics and semi-permeable capsules (SPCs) technology (Atrandi) to isolate individual bacterial cells from sewage and pig fecal samples. Our method involves extracting and amplifying single bacterial DNA within individual SPCs, followed by combinatorial split-and-pool single-amplified genome (SAG) barcoding and short-read sequencing. We tested two different sequencing approaches with different numbers of SPCs from the same sample for each sequencing run. Using a deep sequencing approach, we detected 1,796 and 1,220 SAGs, of which 576 and 599 were used for further analysis from one sewage and one fecal sample, respectively. In shallow sequencing data, we aimed for 10-times more cells and detected 12,731 and 17,909 SAGs, of which we used 2,456 and 1,599 for further analysis for sewage and fecal samples, respectively. Additionally, we identified the top 10 antimicrobial resistance genes (ARGs) in both sewage and feces samples and linked them to their individual host bacterial species.}, } @article {pmid39967836, year = {2025}, author = {Álvarez-Narváez, S and Harrell, TL and Nour, I and Mohanty, SK and Conrad, SJ}, title = {Choosing the most suitable NGS technology to combine with a standardized viral enrichment protocol for obtaining complete avian orthoreovirus genomes from metagenomic samples.}, journal = {Frontiers in bioinformatics}, volume = {5}, number = {}, pages = {1498921}, pmid = {39967836}, issn = {2673-7647}, abstract = {Since viruses are obligate intracellular pathogens, sequencing their genomes results in metagenomic data from both the virus and the host. Virology researchers are constantly seeking new, cost-effective strategies and bioinformatic pipelines for the retrieval of complete viral genomes from these metagenomic samples. Avian orthoreoviruses (ARVs) pose a significant and growing threat to the poultry industry and frequently cause economic losses associated with disease in production birds. Currently available commercial vaccines are ineffective against new ARV variants and ARV outbreaks are increasing worldwide, requiring whole genome sequencing (WGS) to characterize strains that evade vaccines. This study compares the effectiveness of long-read and short-read sequencing technologies for obtaining ARV complete genomes. We used eight clinical isolates of ARV, each previously processed using our published viral genome enrichment protocol. Additionally, we evaluate three assembly methods to determine which provided the most complete and reliable whole genomes: De novo, reference-guided or hybrid. The results suggest that our ARV genome enrichment protocol caused some fragmentation of the viral cDNA that impacted the length of the long reads (but not the short reads) and, as a result, caused a failure to produce complete genomes via de novo assembly. Overall, we observed that regardless of the sequencing technology, the best quality assemblies were generated by mapping quality-trimmed reads to a custom reference genome. The custom reference genomes were in turn constructed with the publicly available ARV genomic segments that shared the highest sequence similarity with the contigs from short-read de novo assemblies. Hence, we conclude that short-read sequencing is the most suitable technology to combine with our ARV genome enrichment protocol.}, } @article {pmid39967182, year = {2025}, author = {Mu, Y and Yao, S and Huang, Y and Zhu, Z and Li, D and Song, Y and Liu, Z and Zhang, C and Yu, S}, title = {Unveiling the metabolic heterogeneity and formation mechanism in Chinese typical Daqu based on Qu-omics.}, journal = {Food research international (Ottawa, Ont.)}, volume = {202}, number = {}, pages = {115735}, doi = {10.1016/j.foodres.2025.115735}, pmid = {39967182}, issn = {1873-7145}, mesh = {*Metabolomics ; Alcoholic Beverages/analysis ; Volatile Organic Compounds/analysis/metabolism ; Odorants/analysis ; Taste ; Bacteria/classification/metabolism/genetics ; Pyrazines/metabolism/analysis ; Metabolome ; Humans ; China ; East Asian People ; }, abstract = {The metabolic characteristics of Daqu are crucial factors affecting the sensory attributes of Baijiu. However, the mechanisms underlying the development of Daqu's metabolic profile, particularly the relationship with functional species, remain insufficiently understood. Therefore, we employed Qu-omics to comprehensively analyze the metabolic profiles of the three typical types of Daqu, namely high-, medium-, and low-temperature Daqu (HTD, MTD, and LTD). Flavoromics and metabolomics analyses revealed that the concentrations of both volatile and non-volatile compounds were highest in MTD, followed by those in LTD, which were characterized by elevated levels of esters, alcohols, and organic acids. In contrast, HTD exhibited a distinct metabolic profile, with a significantly higher abundance of aldehydes, ketones, pyrazines, amino acids, and small peptides. Additionally, 47 volatiles and 26 non-volatiles were identified as differential markers among three types of Daqu, including aroma-active compounds such as 2,5-dimethylpyrazine and phenethyl alcohol. The metabolic pathways associated with these metabolites were reconstructed by integrating metagenomic datasets, which highlighted the potential role of functional bacteria in shaping Daqu's metabolic profiles. Specifically, Staphylococcus gallinarum, Brevibacterium intestinavium, and Kroppenstedtia eburnean may play essential roles in HTD, while Bacillus velezensis/Weissella cibaria and Kosakonia cowanii/Pantoea agglomerans in MTD and LTD, respectively. These findings enhance our understanding of the metabolic diversity of Chinese Daqu and provide valuable insights for flavor regulation.}, } @article {pmid39967175, year = {2025}, author = {Aragão, MOP and Lima, FR and Passamani, FRF and Santos, MAA and Rezende, JP and Batista, LR}, title = {Fungal and bacterial diversity present on the rind and core of Natural Bloomy Rind Artisanal Minas Cheese from the Canastra region, Brazil.}, journal = {Food research international (Ottawa, Ont.)}, volume = {202}, number = {}, pages = {115724}, doi = {10.1016/j.foodres.2025.115724}, pmid = {39967175}, issn = {1873-7145}, mesh = {*Cheese/microbiology ; Brazil ; *Food Microbiology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; *Fungi/genetics/classification/isolation & purification ; Animals ; Microbiota/genetics ; Geotrichum/genetics ; Milk/microbiology ; Biodiversity ; Cattle ; Lactococcus/genetics/isolation & purification/classification ; }, abstract = {Globally recognized for its unique sensory attributes, Natural Bloomy Rind Artisanal Minas Cheese (NBRAMC) from the Canastra microregion is made from raw cow's milk using a natural starter culture derived from the local environment. During ripening process, microorganisms, predominantly Geotrichum candidum, develop on the surface, with the microbial community playing a crucial role in shaping the cheese's distinctive characteristics. This study aimed to characterize the microbial community, including filamentous fungi, yeasts, and bacteria, present in the rind and core of NBRAMC. Amplicon sequencing of the ITS and 16S rRNA gene regions was performed on rind and core samples from cheeses produced at six distinct producers. Results indicated that G. candidum and Diutina catenulata were the most prevalent fungal species, and Candida intermedia being more abundant exclusively in the interior of the cheeses. The bacterial community displayed greater diversity in the rind, with genera such as Lactococcus, Brevibacterium, and Corynebacterium variabile, while Lactococcus and Streptococcus dominated the core. An inverse relationship between D. catenulata and G. candidum abundance was noted. Significant variations in microbial community profiles were found among producers, despite their geographical proximity. While low levels of undesirable fungi were detected, some samples showed a notable presence of undesirable bacteria, indicating potential hygiene issues during cheese handling. These findings provide valuable insights into the microbial dynamics of NBRAMC, supporting the implementation of strategies that can enhance the quality and safety of the product.}, } @article {pmid39967137, year = {2025}, author = {Espí-Malillos, A and López-Almela, I and Ruiz-García, P and López-Mendoza, MC and Carrón, N and González-Torres, P and Quereda, JJ}, title = {Raw milk at refrigeration temperature displays an independent microbiota dynamic regardless Listeria monocytogenes contamination.}, journal = {Food research international (Ottawa, Ont.)}, volume = {202}, number = {}, pages = {115637}, doi = {10.1016/j.foodres.2024.115637}, pmid = {39967137}, issn = {1873-7145}, mesh = {*Listeria monocytogenes/growth & development/genetics/isolation & purification ; *Milk/microbiology ; Animals ; *Refrigeration ; *Microbiota ; *Food Microbiology ; RNA, Ribosomal, 16S/genetics ; Food Contamination/analysis ; Cold Temperature ; }, abstract = {Dairy products made of raw milk are associated with hypervirulent L. monocytogenes clonal complexes (CCs) CC1, CC4, and CC6, and cause half of the reported listeriosis outbreaks in Europe. However, it is currently unknown whether the overrepresentation of L. monocytogenes hypervirulent clones in dairy products made of raw milk is conditioned by an alteration in the native raw milk microbiota growth and/or composition. In this study, the lag phase, maximal growth rate, and the final maximal concentration of mesophilic aerobic bacteria from native raw milk bacteria were measured at refrigerated temperature (4 °C) in the presence and absence of L. monocytogenes contamination. The raw milk microbiota composition and dynamics were evaluated in the presence and absence of L. monocytogenes hypervirulent (CC1, CC4, CC6), and hypovirulent (CC9 and CC121) clones at 4 °C by using 16S rRNA high-throughput sequencing. Our results showed that the growth and composition of the microbial communities naturally present in raw milk are independent of the contamination with hyper- or hypovirulent L. monocytogenes CCs at refrigeration temperature. Pseudomonas was the most abundant genus in raw milk on days 11 and 21, while Carnobacterium was the second most abundant genus regardless of the contaminant L. monocytogenes CCs. Altogether these results suggest that the overrepresentation of hypervirulent L. monocytogenes CC1, CC4, and CC6 in dairy products is not the consequence of a differential alteration in the native composition of the raw milk microbiota.}, } @article {pmid39967058, year = {2025}, author = {Zhang, L and Zhong, Y and Fan, Q and Li, S and Zhu, J and Ma, X and Zhu, Y and Wu, R and Zhang, Z and Zhou, F and Wu, Y and Cai, M and Ma, Y}, title = {Coupled Physical-Biogeochemical Dynamics of Polycyclic Aromatic Compounds in the East China Sea.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c11906}, pmid = {39967058}, issn = {1520-5851}, abstract = {Polycyclic aromatic compounds (PACs), including harmful polycyclic aromatic hydrocarbons (PAHs) and more toxic derivatives, are continuously released contaminants. Their provenance and dynamics in coastal oceans remain poorly understood. This study presents the first comprehensive assessment of PACs in coastal oceans by combining their presence with key hydrological and biogeochemical indicators, and potential microbial degradation. High concentrations of Σ92PACs (48-660 ng/L) were observed in the East China Sea, influenced vertically by upwelling and related sediment resuspension during winter. Spatial heterogeneity reveals distinct distribution patterns: PAHs and alkyl-PAHs were mainly influenced by riverine inputs, horizontal transport via coastal currents, and fronts acting as barriers, in contrast, oxygen-PAHs and nitro-PAHs were primarily shaped by secondary transformations within warm water masses rich in nutrients. The relationship between dissolved PACs and chlorophyll a underscores the dominance of biodegradation over the marginal biological pump effect during wintertime low primary productivity. Metagenomic analysis further highlights microbial degradation as a crucial PAC removal pathway, with enhanced microbial diversity driven by terrigenous advection and upwelling. The methodologies and findings of this research provide valuable insights into PAC cycling in coastal oceans.}, } @article {pmid39966722, year = {2025}, author = {Wang, J and Song, M and Yao, L and Li, P and Si, E and Li, B and Meng, Y and Ma, X and Yang, K and Zhang, H and Shang, X and Wang, H}, title = {Metagenomic analysis reveal the phytoremediation effects of monocropping and intercropping of halophytes Halogeton glomeratus and Suaeda glauca in saline soil of Northwestern China.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {213}, pmid = {39966722}, issn = {1471-2229}, support = {32001514//National Natural Science Foundation of China/ ; 31960072//National Natural Science Foundation of China/ ; 20JR10RA507//Key Projects of Natural Science Foundation of Gansu Province/ ; 22JR5RA880//Key Projects of Natural Science Foundation of Gansu Province/ ; Ganfx-03Y06//Fuxi Talent Project of Gansu Agricultural University/ ; GAUfx-04Y011//Fuxi Talent Project of Gansu Agricultural University/ ; 2021CYZC-12//Industrial Support Project of Colleges and Universities in Gansu Province/ ; Grant CARS-05-04B-2//China Agriculture Research System/ ; }, abstract = {AIMS: Planting halophytes is a widely used method of phytoremediation for saline soils. The succulent halophytes Halogeton glomeratus and Suaeda glauca are widely used for remediation of saline soil in the arid region of Northwestern China. However, whether intercropping of H. glomeratus and S. glauca can increase the improvement effect for saline soil is yet to be proved.

MATERIALS AND METHODS: Therefore, this study analyzed three phytoremediation planting modes: monocropping of H. glomeratus (Hg), monocropping of S. glauca (Sg), and H. glomeratus and S. glauca intercropping (Hg||Sg). These were applied in field experiments, with biomass and soil physicochemical properties measured for each treatment, and the mechanism was analyzed using macrogenomics.

RESULTS: After harvesting the halophytes after one season, the Hg treatment had the highest dry biomass and soil total dissolved salt content was reduced; correspondingly, soil pH were decreased and soil organic matter content were increased. The results showed that Actinobacteria, Acidobacteria and Proteobacteria were the dominant phylum under the four treatments. This suggests that Hg treatment was more capable of producing microorganisms favorable to saline soil remediation.

CONCLUSIONS: Thus, H. glomeratus monocropping is a more effective phytoremediation strategy for saline soil in the dry zone of Northwestern China.}, } @article {pmid39966546, year = {2025}, author = {Pietrasanta, C and Ronchi, A and Carlosama, C and Lizier, M and Silvestri, A and Fornasa, G and Melacarne, A and D'Ambrosi, F and Lutterotti, M and Carbone, E and Cetin, I and Fumagalli, M and Ferrazzi, E and Penna, G and Mosca, F and Pugni, L and Rescigno, M}, title = {Effect of prenatal antibiotics on breast milk and neonatal IgA and microbiome: a case-control translational study protocol.}, journal = {Pediatric research}, volume = {}, number = {}, pages = {}, pmid = {39966546}, issn = {1530-0447}, abstract = {BACKGROUND: Up to 25-35% of women receive antibiotics (ABX) during pregnancy, but little is known about the consequences on a key mucosal interface such as the mammary gland, and on the development of the neonatal gut's microbiota and IgA. We hypothesize that prenatal ABX negatively affect the immune functionality of mammary gland, the composition of breast milk microbiota, the development of neonatal fecal microbiota and the abundance of neonatal fecal IgA.

METHODS: Case-control translational cohort study on women and neonates in the presence or absence (N = 41 + 41 pairs) of exposure to prenatal ABX for at least 7 consecutive days after 32 weeks of gestation.

RESULTS: We will evaluate IgA concentration in breast milk and in neonatal feces up to one year after delivery. We will also evaluate clinical parameters, neurodevelopment and the composition of the IgA-coated and uncoated fractions of breast milk and fecal microbiota by means of magnetic-activated cell sorting (MACS) coupled with shotgun metagenomics. Finally, we will measure the concentration of the chemokine CCL28 on maternal serum and breast milk, as a marker of activity of the entero-mammary pathway.

CONCLUSIONS: Our results might support a data-driven evaluation of breast milk immune function in women exposed to prenatal ABX.

IMPACT: Breast milk IgA and microbiota are critical to determine the positive effects of breastfeeding in infants. This research protocol will investigate breast milk IgA, microbiota, and the IgA[+] / IgA[-] fractions of neonatal fecal microbiota upon exposure to prenatal antibiotics. Fecal IgA and microbiota in infants exposed or not exposed to prenatal antibiotics will be analyzed up to 1 year after birth. This research will clarify the impact of prenatal antibiotics on the immune function of breast milk. This, in turn, might support the selective evaluation of breast milk IgA/microbiota in mothers exposed to prenatal antibiotics, or in donor human milk.}, } @article {pmid39966520, year = {2025}, author = {Diener, C and Holscher, HD and Filek, K and Corbin, KD and Moissl-Eichinger, C and Gibbons, SM}, title = {Metagenomic estimation of dietary intake from human stool.}, journal = {Nature metabolism}, volume = {}, number = {}, pages = {}, pmid = {39966520}, issn = {2522-5812}, support = {R01DK133468//U.S. Department of Health & Human Services | NIH | Office of Extramural Research, National Institutes of Health (OER)/ ; Cluster of Excellence COE7//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; Cluster of Excellence COE7//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; }, abstract = {Dietary intake is tightly coupled to gut microbiota composition, human metabolism and the incidence of virtually all major chronic diseases. Dietary and nutrient intake are usually assessed using self-reporting methods, including dietary questionnaires and food records, which suffer from reporting biases and require strong compliance from study participants. Here, we present Metagenomic Estimation of Dietary Intake (MEDI): a method for quantifying food-derived DNA in human faecal metagenomes. We show that DNA-containing food components can be reliably detected in stool-derived metagenomic data, even when present at low abundances (more than ten reads). We show how MEDI dietary intake profiles can be converted into detailed metabolic representations of nutrient intake. MEDI identifies the onset of solid food consumption in infants, shows significant agreement with food frequency questionnaire responses in an adult population and shows agreement with food and nutrient intake in two controlled-feeding studies. Finally, we identify specific dietary features associated with metabolic syndrome in a large clinical cohort without dietary records, providing a proof-of-concept for detailed tracking of individual-specific, health-relevant dietary patterns without the need for questionnaires.}, } @article {pmid39966439, year = {2025}, author = {Chen, X and Yin, X and Xu, X and Zhang, T}, title = {Species-resolved profiling of antibiotic resistance genes in complex metagenomes through long-read overlapping with Argo.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {1744}, pmid = {39966439}, issn = {2041-1723}, support = {T21-705/20-N//University Grants Committee (UGC)/ ; }, mesh = {*Metagenome/genetics ; Humans ; Animals ; *Metagenomics/methods ; *Drug Resistance, Microbial/genetics ; *Feces/microbiology ; Anti-Bacterial Agents/pharmacology ; Primates/genetics ; Genes, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; }, abstract = {Environmental surveillance of antibiotic resistance genes (ARGs) is critical for understanding and mitigating the spread of antimicrobial resistance. Current short-read-based ARG profiling methods are limited in their ability to provide detailed host information, which is indispensable for tracking the transmission and assessing the risk of ARGs. Here, we present Argo, a novel approach that leverages long-read overlapping to rapidly identify and quantify ARGs in complex environmental metagenomes at the species level. Argo significantly enhances the resolution of ARG detection by assigning taxonomic labels collectively to clusters of reads, rather than to individual reads. By benchmarking the performance in host identification using simulation, we confirm the advantage of long-read overlapping over existing metagenomic profiling strategies in terms of accuracy. Using sequenced mock communities with varying quality scores and read lengths, along with a global fecal dataset comprising 329 human and non-human primate samples, we demonstrate Argo's capability to deliver comprehensive and species-resolved ARG profiles in real settings.}, } @article {pmid39966419, year = {2025}, author = {Heidrich, V and Fackelmann, G and Malesevic, M and Armanini, F and Dey, H and Mengoni, C and Stanisavljevic, N and Vukotic, G and Segata, N}, title = {Newly identified species from the dog dental plaque microbiome highlight little overlap with humans.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {30}, pmid = {39966419}, issn = {2055-5008}, abstract = {Understudied pet-associated microbiomes represent a rich source for the discovery of microbial taxa important for pet and human health. From a cohort of 23 dogs, we sampled and metagenomically sequenced 64 dental plaque microbiomes, generating 1945 metagenome-assembled genomes spanning 347 microbial species, including 277 undercharacterized species without cultivated representatives. Integration with human microbiome data revealed the dog plaque microbiome is more diverse than - and shows little overlap (5.9% species in common) with - the human plaque microbiome, even though some shared periodontal pathobionts arise as a potential concern.}, } @article {pmid39965710, year = {2025}, author = {Qiu, H and Zhao, W and Qin, Y and Wang, Y and Bai, M and Su, S and Wang, C and Zhao, Z}, title = {Ammonia-oxidizing activity and microbial structure of ammonia-oxidizing bacteria, ammonia-oxidizing archaea and complete ammonia oxidizers in biofilm systems with different salinities.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132248}, doi = {10.1016/j.biortech.2025.132248}, pmid = {39965710}, issn = {1873-2976}, abstract = {Ammonia-oxidizing activity of different ammonia-oxidizing microorganisms (AOMs), such as ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and complete ammonia oxidizers (comammoxs), were investigated by adding the inhibitors such as 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide, octyne, and KCLO3 in biofilm systems with different salinities. It was found that the ammonia-oxidizing activity of all AOMs gradually decreased with increasing salinity. The ammonia-oxidizing activity of AOB was consistently higher than those of AOA and comammox at different salinities. Moreover, nitrite-oxidizing bacteria (NOB) were more sensitive to changes in salinity than AOMs. Metagenomic analysis revealed that nitrifiers were detected at high level, with the AOB Nitrosomonas sp. comprising 24.9 % and the NOB Nitrospira sp. comprising 47.2% of all nitrifiers. The main functional genes involved in the nitrification reaction were amoABC, hao, and nxrAB. This study demonstrates that higher abundance of functional microorganisms and genes is related to the ammonia-oxidizing activity and ammonia removal contribution rate.}, } @article {pmid39965493, year = {2025}, author = {Zhang, H and Pan, F and Wen, Z and Chen, W and Zhou, C}, title = {Impacts of successive Chinese fir plantations on soil carbon and nitrogen dynamics: Conclusive insights from metagenomic analysis.}, journal = {Journal of environmental management}, volume = {376}, number = {}, pages = {124510}, doi = {10.1016/j.jenvman.2025.124510}, pmid = {39965493}, issn = {1095-8630}, abstract = {Chinese fir forests play a significant role both economically and ecologically, contributing to soil and water conservation while also serving as an efficient timber-producing species that brings economic benefits. However, the issue of soil degradation due to continuous Chinese fir planting cannot be overlooked. Continuous planting leads to a decrease in soil nutrients, a reduction in microbial diversity, and changes in microbial community composition, which in turn affect the abundance of carbon and nitrogen cycle functional genes in Chinese fir forest soils. We utilized metagenomic sequencing technology to investigate the dynamics of microbial community composition and carbon and nitrogen-related functional genes in the soils of Chinese fir forests across different plantation generations, exploring their relationship with soil carbon and nitrogen nutrients. We found that the relative abundance of bacterial communities is dominant in both phylum and genus levels within microbial communities. The partial least squares path models (PLS-PM) indicated that planting generations had a negative effect on dissolved organic carbon (DOC), nitrate nitrogen (NO3[-]-N), and microbial biomass nitrogen (MBN), with a significant negative impact on microbial residual carbon (MRC). Easily utilizable carbon nutrient (DOC) in Chinese fir forest soil showed a significant positive effect on the abundance of carbon fixation functional genes (direct effect = 0.91, p < 0.01), and on the abundance of methane metabolism functional genes (direct effect = 1.27, p < 0.01). Nitrogen nutrients (NO3[-]-N, MBN) in the soil also had a significant positive effect on the abundance of carbon fixation functional genes (direct effect = 0.90, p < 0.01). Bacterial communities (Acidobacteria and Verrucomicrobia) had significant negative effects on carbon and nitrogen cycling processes. The abundance of nasA and nirA genes generally showed a decreasing trend with increasing plantation generations. The decrease in available nitrogen nutrients with increased plantation generations was influenced by Assimilatory nitrogen reduction to ammonia (ANRA), an energy-consuming process. In summary, the continuous planting of Chinese fir had significant impacts on the carbon and nitrogen nutrient cycling processes, and it influenced the composition of microbial communities and the spatial distribution of functional genes. Clarifying the changes in carbon and nitrogen nutrient cycling processes in Chinese fir continuous planting provides a reference for maintaining the productivity of Chinese fir plantations.}, } @article {pmid39965412, year = {2025}, author = {Secomandi, E and De Gregorio, MA and Garcia-Perez, P and Vaccari, F and Puglisi, E and Lucini, L}, title = {Waterlogging alone and combined with other abiotic stresses provides unique metabolic signatures at the plant-rhizosphere interface: A multi-omics perspective on root metabolome, root exudation and rhizomicrobiome.}, journal = {Plant physiology and biochemistry : PPB}, volume = {221}, number = {}, pages = {109646}, doi = {10.1016/j.plaphy.2025.109646}, pmid = {39965412}, issn = {1873-2690}, abstract = {Despite the growing evidence on unique and unpredictable impact of stress combination over plants, waterlogging-combined stresses effects are still underexplored. Under those conditions, besides the impairment of plant aerial parts, the root system is particularly vulnerable, leading to consequences on plant survival. Here, we report on the short-term exposure of soil-grown Arabidopsis thaliana L. to waterlogging alone and combined with cold, heat, and salinity to inspect their antagonistic, additive or synergistic effects in the rhizosphere. To this aim, root metabolic changes, exudation profiles, and microbial diversity were investigated using a combination of metabolomics and metagenomics, and their interaction was analysed through multi-omics data integration. In roots, waterlogging strongly affected metabolism compared to other single stresses, causing a down-accumulation of targeted classes of compounds including, phenylpropanoids, sterols, terpenoids, and alkaloids. Additive and synergistic effects were reported in roots under waterlogging combined with heat and cold stresses, respectively. Regarding root exudates, flavonoids, terpenoids, and alkaloids were the main classes of compounds affected. Waterlogging caused a down-accumulation of all classes except for coumarins, and mixed trends were observed in waterlogging-combined stresses, with waterlogging-salinity stresses resulting in an ameliorating effect. Even though microbial communities' alpha- and beta-diversity remained stable, suggesting their resilience under short-term exposure, specific taxa modulation was recorded under each condition. Overall, these results contribute to understanding the hierarchical impact of waterlogging on root metabolism and exudation, influencing rhizosphere interactions. This multi-omics approach advances our understanding of plant stress responses and microbial dynamics, paving the way for future studies on adaptive mechanisms.}, } @article {pmid39965343, year = {2025}, author = {Šaula, T and Cigić, B and Jamnik, P and Kralj Cigić, I and Poklar Ulrih, N and Požrl, T and Marolt, G}, title = {Enrichment of the nutritional value of pea flour milling fractions through fermentation.}, journal = {Food chemistry}, volume = {476}, number = {}, pages = {143303}, doi = {10.1016/j.foodchem.2025.143303}, pmid = {39965343}, issn = {1873-7072}, abstract = {In this work, pea flour and two milling fractions obtained by industrial-scale air classification were characterized and fermented by Lactiplantibacillus plantarum to increase their nutritional value. Scanning electron microscopy and chemical analysis revealed major differences in the morphology and composition of the flours. Protein-rich (43.7 %) fraction exhibits a few-fold higher mineral, spermidine (290 μg/g), but also a higher phytate (20.4 mg/g) content compared to starch-rich fraction. Flour type and inoculum majorly influenced the composition of the fermented product. In spontaneously fermented flours, biogenic amines accumulated up to 6.6 mg/g, which was the main drawback besides the large variations between batches, as confirmed by metagenomic analysis. Higher contents of lactic acid, free amino groups formed by proteolysis and gamma-aminobutyric acid were determined in inoculated fermentations of protein rich fraction, whereas a higher relative bioavailability of minerals was found in the inoculated starch-rich fraction, as the phytate content was reduced by 42 %.}, } @article {pmid39965334, year = {2025}, author = {Zhang, J and Lei, H and Huang, J and Wong, JWC and Li, B}, title = {Co-occurrence and co-expression of antibiotic, biocide, and metal resistance genes with mobile genetic elements in microbial communities subjected to long-term antibiotic pressure: Novel insights from metagenomics and metatranscriptomics.}, journal = {Journal of hazardous materials}, volume = {489}, number = {}, pages = {137559}, doi = {10.1016/j.jhazmat.2025.137559}, pmid = {39965334}, issn = {1873-3336}, abstract = {The burgeoning of antibiotic resistance has emerged as a pressing global challenge. To gain a deeper understanding of the interactions between antibiotic resistance genes (ARGs), biocide and metal resistance genes (BRGs&MRGs), and mobile genetic elements (MGEs), this study utilized metagenomics and metatranscriptomics to investigate their co-occurrence and co-expression in two consortia subjected to long-term exposure to chloramphenicol and lincomycin. Long-term exposure to these antibiotics resulted in significant disparities in resistance profiles: ConsortiumCAP harbored 130 ARGs and 150 BRGs&MRGs, while ConsortiumLIN contained 57 ARGs and 32 BRGs&MRGs. Horizontal gene transfer (HGT) events were predicted at 125 and 300 instances in ConsortiumCAP and ConsortiumLIN, respectively, facilitating the emergence of multidrug-resistant bacteria, such as Caballeronia (10 ARGs, 2 BRGs&MRGs), Cupriavidus (2 ARGs, 10 BRGs&MRGs), and Bacillus (14 ARGs, 21 BRGs&MRGs). Chloramphenicol exposure significantly enriched genes linked to phenicol resistance (floR, capO) and co-expressed ARGs and BRGs&MRGs, while lincomycin exerted narrower effects on resistance genes. Additionally, both antibiotics modulated the expression of degradation genes and virulence factors, highlighting their role in altering bacterial substrate utilization and pathogenic traits. This study provides quantitative insights into the impact of antibiotics on microbial resistance profiles and functions at both DNA and RNA levels, highlighting the importance of reducing antibiotic pollution and limiting the spread of resistance genes in the environment.}, } @article {pmid39964655, year = {2025}, author = {Pitt, A and Lienbacher, S and Schmidt, J and Neumann-Schaal, M and Wolf, J and Wenng, H and Oren, A and Huber, Z and Hahn, MW}, title = {Biodiversity of strains belonging to the freshwater genus Aquirufa in a riparian forest restoration area in Salzburg, Austria, with a focus on the description of Aquirufa salirivi sp. nov. and Aquirufa novilacunae sp. nov.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {39964655}, issn = {1618-1905}, abstract = {During a citizen science project, four freshwater habitats in a riparian forest restoration area in Salzburg, Austria, were sampled. The primary aim was to obtain bacterial strains of the genus Aquirufa, a group of typical and widespread freshwater bacteria. Numerous pure cultures of Aquirufa strains could be obtained, three of them originating from the river Salzach, a newly created pond and the lake Ausee represented new species. Strain 1-SAACH-A3[T] was characterized by a genome size of 3.2 Mbp and a G + C value of 38.4 mol% and encoded genes predicted for nitrate uptake and nitrous oxide utilization. Strains BAHN-186B[T] and 2-AUSEE-184A6 were characterized by a genome size of 2.4 Mbp and a G + C value of 42.4 and 42.2 mol%, respectively, and encoded genes predicted for the light-harvesting rhodopsin system. Calculated whole-genome average nucleotide identity values with Aquirufa type strains resulted in a maximum value of 93.65% for comparison of strain 1-SAACH[T] with the type strain of Aquirufa ecclesiirivi, which is slightly under the proposed threshold of species demarcation. The calculated gANI value comparing strains BAHN-186B[T] and 2-AUSEE-184A6 revealed 95.76%, thus a value slightly above the threshold. Further analyses revealed that the three new strains represent two new species, proposed here as Aquirufa salirivi sp. nov. with type strain 1-SAACH-A3[T] (= DSM 117800[ T] = JCM 37097[ T]) and Aquirufa novilacunae sp. nov. with type strain BAHN-186B[T] (= DSM 118143[ T] = JCM 37099[ T]). Analyses of 123 publicly available metagenomes and a metagenome of the lake Ausee resulted in no detection of A. salirivi sp. nov. In contrast, A. novilacunae sp. nov. could be detected in 15 water samples of rivers, mainly from Asia, but also from North America and Australia. The analyses suggested that the species occurs in most of these samples in low relative abundance, detections derived from metagenomes of water samples from the river Yangtze in the subtropical zone could be interpreted as occurrence in higher abundances.}, } @article {pmid39964161, year = {2025}, author = {Babalola, OO and Adedayo, AA and Akinola, SA}, title = {Microbiome insights from a South African cultural and natural landmark cave using metagenomics next-generation sequencing.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0118324}, doi = {10.1128/mra.01183-24}, pmid = {39964161}, issn = {2576-098X}, abstract = {The microbiome study of Sterkfontein Cave (a natural and cultural cave) revealed fascinating insights into its metagenome study and functional annotation. The largely unexplored cave soil microbiota showcases intricate survival adaptations with promising potential for various human applications. Here, we report the microbial diversity and functions associated with Sterkfontein Cave soil.}, } @article {pmid39963501, year = {2024}, author = {Nelson, AR and Rhoades, CC and Fegel, TS and Roth, HK and Caiafa, MV and Glassman, SI and Borch, T and Wilkins, MJ}, title = {Wildfire impact on soil microbiome life history traits and roles in ecosystem carbon cycling.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae108}, pmid = {39963501}, issn = {2730-6151}, abstract = {Wildfires, which are increasing in frequency and severity with climate change, reduce soil microbial biomass and alter microbial community composition and function. The soil microbiome plays a vital role in carbon (C) and nitrogen (N) cycling, but its complexity makes it challenging to predict post-wildfire soil microbial dynamics and resulting impacts on ecosystem biogeochemistry. The application of biogeochemically relevant conceptual trait-based frameworks to the soil microbiome can distill this complexity, enabling enhanced predictability of soil microbiome recovery following wildfire and subsequent impacts to biogeochemical cycles. Conceptual frameworks that have direct links to soil C and N cycling have been developed for the soil microbiome; the Y-A-S framework overviews soil microbiome life history strategies that have tradeoffs with one another and others have proposed frameworks specific to wildfire. Here, we aimed to delineate post-wildfire changes of bacterial traits in western US coniferous forests to inform how severe wildfire influences soil microbiome recovery and resultant biogeochemical cycling. We utilized a comprehensive metagenome-assembled genome catalog from post-wildfire soils representing 1 to 11 years following low- and high-severity burning to identify traits that enable the persistence of microbial taxa in burned soils and influence ecosystem C and N cycling. We found that high-severity wildfire initially selects for fast growers and, up to a decade post-fire, taxa that invest in genes for acquiring diverse resources from the external environment, which in combination could increase soil C losses. This work begins to disentangle how climate change-induced shifts in wildfire behavior might alter microbially mediated soil biogeochemical cycling.}, } @article {pmid39963497, year = {2025}, author = {Van Laere, Y and Fraiture, MA and Gobbo, A and De Keersmaecker, SCJ and Marchal, K and Roosens, NHC and Vanneste, K}, title = {Assessing the authenticity and purity of a commercial Bacillus thuringiensis bioinsecticide through whole genome sequencing and metagenomics approaches.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1532788}, pmid = {39963497}, issn = {1664-302X}, abstract = {Biopesticides, biological agents for pest control in plants, are becoming increasingly prevalent in agricultural practices. However, no established methodology currently exists to assess their quality, and there are currently no publicly available authenticity and purity evaluations of commercial products. This lack of data may represent risks because of their widespread dispersal in the environment. We evaluated the potential of whole genome sequencing (WGS) and metagenomics approaches, including nanopore long-read sequencing, to verify both authenticity (i.e., the labeled strain) and biological purity (i.e., the absence of any undesired genetic material) of commercial Bacillus thuringiensis bioinsecticides. Four commercially available bioinsecticidal products containing Bacillus thuringiensis serovar kurstaki strain HD-1 were collected from the European market as a case study. Two sequencing approaches were employed: WGS of isolates and metagenomics sequencing of all genetic material in a product. To assess authenticity, isolate WGS data were compared against the publicly available reference genome of the expected strain. Antimicrobial resistance gene content, insecticidal gene content, and single nucleotide polymorphism differences were characterized to evaluate similarity to the reference genome. To assess purity, metagenomic sequencing data were analyzed using read classification and strain differentiation methods. Additionally, long- and short-read data were used to assess potential large-scale structural variations. Our results confirmed all investigated products to be authentic and pure. With the increasing usage of biopesticides, it is crucial to have adequate quality control methods. Our proposed approach could be adapted for other biopesticides, and similar products, providing a standardized and robust approach to contribute to biopesticide safety.}, } @article {pmid39963423, year = {2024}, author = {Kelliher, JM and Xu, Y and Flynn, MC and Babinski, M and Canon, S and Cavanna, E and Clum, A and Corilo, YE and Fujimoto, G and Giberson, C and Johnson, LYD and Li, KJ and Li, PE and Li, V and Lo, CC and Lynch, W and Piehowski, P and Prime, K and Purvine, S and Rodriguez, F and Roux, S and Shakya, M and Smith, M and Sarrafan, S and Cholia, S and McCue, LA and Mungall, C and Hu, B and Eloe-Fadrosh, EA and Chain, PSG}, title = {Standardized and accessible multi-omics bioinformatics workflows through the NMDC EDGE resource.}, journal = {Computational and structural biotechnology journal}, volume = {23}, number = {}, pages = {3575-3583}, pmid = {39963423}, issn = {2001-0370}, abstract = {Accessible and easy-to-use standardized bioinformatics workflows are necessary to advance microbiome research from observational studies to large-scale, data-driven approaches. Standardized multi-omics data enables comparative studies, data reuse, and applications of machine learning to model biological processes. To advance broad accessibility of standardized multi-omics bioinformatics workflows, the National Microbiome Data Collaborative (NMDC) has developed the Empowering the Development of Genomics Expertise (NMDC EDGE) resource, a user-friendly, open-source web application (https://nmdc-edge.org). Here, we describe the design and main functionality of the NMDC EDGE resource for processing metagenome, metatranscriptome, natural organic matter, and metaproteome data. The architecture relies on three main layers (web application, orchestration, and execution) to ensure flexibility and expansion to future workflows. The orchestration and execution layers leverage best practices in software containers and accommodate high-performance computing and cloud computing services. Further, we have adopted a robust user research process to collect feedback for continuous improvement of the resource. NMDC EDGE provides an accessible interface for researchers to process multi-omics microbiome data using production-quality workflows to facilitate improved data standardization and interoperability.}, } @article {pmid39962786, year = {2025}, author = {Li, Y and Zhou, XH and Wang, XD and Wang, CJ and Cao, K and Liu, SX}, title = {[Diagnosis of mucormycosis in three children following hematopoietic stem cell transplantation using metagenomic next-generation sequencing].}, journal = {Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics}, volume = {27}, number = {2}, pages = {219-224}, pmid = {39962786}, issn = {1008-8830}, mesh = {Humans ; *Mucormycosis/diagnosis/etiology ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Male ; *High-Throughput Nucleotide Sequencing ; Female ; Child ; Child, Preschool ; Metagenomics/methods ; }, abstract = {This article reports the clinical characteristics and treatment processes of three cases of mucormycosis occurring after hematopoietic stem cell transplantation in children, along with a review of relevant literature. All three patients presented with chest pain as the initial symptom, and metagenomic next-generation sequencing (mNGS) confirmed the mucycete infection early in all cases. Two patients recovered after treatment, while one succumbed to disseminated infection. mNGS has facilitated early diagnosis and treatment, reducing mortality rates. Additionally, surgical intervention is an important strategy for improving the prognosis of this condition.}, } @article {pmid39962733, year = {2025}, author = {Chen, N and Liu, L and Wang, J and Mao, D and Lu, H and Shishido, TK and Zhi, S and Chen, H and He, S}, title = {Novel Gene Clusters for Secondary Metabolite Synthesis in Mesophotic Sponge-Associated Bacteria.}, journal = {Microbial biotechnology}, volume = {18}, number = {2}, pages = {e70107}, doi = {10.1111/1751-7915.70107}, pmid = {39962733}, issn = {1751-7915}, support = {422010882//Startup Foundation of Ningbo University/ ; 422110473//Startup Foundation of Ningbo University/ ; 422207513//Startup Foundation of Ningbo University/ ; 31600016//National Natural Science Foundation of China/ ; 41776168//National Natural Science Foundation of China/ ; 2021Z04//Ningbo Natural Science Foundation/ ; D16013//National 111 Project of China/ ; NNF22OC0080109//Novo Nordisk Fonden/ ; }, mesh = {*Multigene Family ; *Porifera/microbiology ; *Secondary Metabolism/genetics ; *Bacteria/genetics/metabolism/classification ; Animals ; Polyketide Synthases/genetics/metabolism ; Biosynthetic Pathways/genetics ; Metagenome ; Peptide Synthases/genetics/metabolism ; Terpenes/metabolism ; Phylogeny ; }, abstract = {Mesophotic coral ecosystems (MCEs) host a diverse array of sponge species, which represent a promising source of bioactive compounds. Increasing evidence suggests that sponge-associated bacteria may be the primary producers of these compounds. However, cultivating these bacteria under laboratory conditions remains a significant challenge. To investigate the rich resource of bioactive compounds synthesised by mesophotic sponge-associated bacteria, we retrieved 429 metagenome-assembled genomes (MAGs) from 15 mesophotic sponges, revealing a strong correlation between bacterial diversity and sponge species. Furthermore, we identified 1637 secondary metabolite biosynthetic gene clusters (BGCs) within these MAGs. Among the identified BGCs, terpenes were the most abundant (495), followed by 369 polyketide synthases (PKSs), 293 ribosomally synthesised and post-translationally modified peptides (RiPPs) and 135 nonribosomal peptide synthetases (NRPSs). The BGCs were classified into 1086 gene cluster families (GCFs) based on sequence similarity. Notably, only five GCFs included experimentally validated reference BGCs from the Minimum Information about a Biosynthetic Gene cluster database (MIBiG). Additionally, an unusual abundance of BGCs was detected in Entotheonella sp. (s191209.Bin93) from the Tectomicrobia phylum. In contrast, members of Proteobacteria and Acidobacteriota harboured fewer BGCs (6-7 on average), yet their high abundance in MCE sponges suggests a potentially rich reservoir of BGCs. Analysis of the BGC distribution patterns revealed that a subset of BGCs, including terpene GCFs (FAM_00447 and FAM_01046), PKS GCF (FAM_00235), and RiPPs GCF (FAM_01143), were widespread across mesophotic sponges. Furthermore, 32 GCFs were consistently present in the same MAGs across different sponges, highlighting their potential key biological roles and capacity to yield novel bioactive compounds. This study not only underscores the untapped potential of mesophotic sponge-associated bacteria as a source of bioactive compounds but also provides valuable insights into the intricate interactions between sponges and their symbiotic microbial communities.}, } @article {pmid39962698, year = {2025}, author = {Ye, Y and Guo, XW and Yang, MQ and Min, W and Guo, HJ}, title = {[Microbial Community Structure and Functional Genes of Phosphorus Cycling in Cotton Field Soil Under Long-term Saline Drip Irrigation].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {46}, number = {2}, pages = {1225-1235}, doi = {10.13227/j.hjkx.202402036}, pmid = {39962698}, issn = {0250-3301}, mesh = {*Phosphorus/metabolism ; *Gossypium/growth & development/genetics ; *Agricultural Irrigation/methods ; *Soil Microbiology ; *Soil/chemistry ; Microbiota ; Salinity ; Saline Waters ; Bacteria/genetics/classification/metabolism/growth & development ; }, abstract = {Freshwater resources are scarce in arid regions, and the rational use of brackish water resources can alleviate local freshwater shortages, but long-term brackish drip irrigation increases the risk of soil salinization, which in turn affects soil nutrient transformation and microbial diversity. Soil phosphorus availability is critical for crop growth, yet it is unclear how long-term brackish drip irrigation will affect soil phosphorus transformation. Therefore, to investigate the effects of long-term brackish drip irrigation on soil phosphorus-transforming microorganisms and their functional genes in cotton fields, the experiment was set up with two irrigation water salinities, freshwater （0.35 dS·m[-1], FW） and brackish water （8.04 dS·m[-1], SW）. The results showed that long-term brackish drip irrigation significantly decreased cotton dry matter weight, phosphorus uptake, yield, soil pH, and Ca2-P and Ca10-P contents but significantly increased cotton phosphorus content and soil water content； electrical conductivity； quick phosphorus； and Ca8-P, Al-P, Fe-P, and O-P contents. The dominant species in each treatment at the phylum level were Ascomycetes, Actinobacteria, Acidobacteria, Bacillus, and Greenscapes； and at the phylum level, the dominant species were α-Ascomycetes, Actinobacteria, β-Ascomycetes, Oleococcus thermophilus, and γ-Ascomycetes. including Proteobacteria, Actinobacteria, Acidobacteria, Gemmatimonadetes, and Chloroflexi. Select dominant species at the class level included Alphaproteobacteria, Actinomycetia, Betaproteobacteria, Thermoleophilia, and Gammaproteobacteria. Long-term saline drip irrigation significantly reduced the relative abundance of Actinobacteria, Acidobacteria, and Nitrospirae but significantly increased the relative abundance of Proteobacteria, Gemmatimonadetes, and Bacteroidetes and significantly reduced the expression levels of the organic phosphorus mineralization gene phnA, transport gene pit, and polyphosphate synthesis gene ppaC. Moreover, it significantly increased the expression levels of the polyphosphate degradation gene HDDC3； organic phosphorus mineralization genes phnG, phoA, phnH, phnL, phnM, phnN, phnP, and phnW； transport genes phnK, phnE, phnC, and phnD； and the regulatory gene phoB. Correlation analysis showed that soil phosphorus-cycling microorganisms and functional genes were closely related to soil physicochemical properties and soil inorganic phosphorus content. Therefore, long-term saline drip irrigation changes the composition of soil phosphorus-cycling microorganisms by affecting soil physical and chemical properties and inorganic phosphorus content, which in turn drives the expression of phosphorus-cycling-related functional genes to regulate and adapt to salt stress.}, } @article {pmid39962619, year = {2025}, author = {Foucault, P and Halary, S and Duval, C and Goto, M and Marie, B and Hamlaoui, S and Jardillier, L and Lamy, D and Lance, E and Raimbault, E and Allouti, F and Troussellier, M and Bernard, C and Leloup, J and Duperron, S}, title = {A summer in the greater Paris: trophic status of peri-urban lakes shapes prokaryotic community structure and functional potential.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {24}, pmid = {39962619}, issn = {2524-6372}, support = {COM2LIFE (ANR-20-CE32-0006)//Agence Nationale de la Recherche/ ; COM2LIFE (ANR-20-CE32-0006)//Agence Nationale de la Recherche/ ; }, abstract = {With more than 12 million inhabitants, the Greater Paris offers a "natural laboratory" to explore the effects of eutrophication on freshwater lake's microbiomes within a relative restricted area (~ 70 km radius). Here, a 4-months survey was carried out during summertime to monitor planktonic microbial communities of nine lakes located around Paris (Île-de-France, France) of comparable morphologies, yet distinct trophic statuses from mesotrophic to hypereutrophic. By thus minimizing the confounding factors, we investigated how trophic status could influence prokaryotic community structures (16S rRNA gene sequencing) and functions (shotgun metagenomics). These freshwater lakes harbored highly distinct and diverse prokaryotic communities, and their trophic status appears as the main driver explaining both differences in community structure and functional potential. Although their gene pool was quite stable and shared among lakes, taxonomical and functional changes were correlated. According to trophic status, differences in phosphorus metabolism-related genes were highlighted among the relevant functions involved in the biogeochemical cycles. Overall, hypereutrophic lakes microbiomes displayed the highest contrast and heterogeneity over time, suggesting a specific microbial regime shift compared to eutrophic and mesotrophic lakes.}, } @article {pmid39962548, year = {2025}, author = {Yuan, J and Ma, L and Du, J and Sun, H and Li, S and Zhou, G and Rao, G and Sun, F and Chen, W and Miao, H and Tian, D and Cheng, C and Wang, Y and Li, L and Li, L and Pang, Y}, title = {Host DNA depletion assisted metagenomic sequencing of bronchoalveolar lavage fluids for diagnosis of pulmonary tuberculosis.}, journal = {Annals of clinical microbiology and antimicrobials}, volume = {24}, number = {1}, pages = {13}, pmid = {39962548}, issn = {1476-0711}, support = {2024-4-1042//Capital's Funds for Health Improvement and Research/ ; 2024-1-1041//Capital's Funds for Health Improvement and Research/ ; }, mesh = {Humans ; *Bronchoalveolar Lavage Fluid/microbiology ; *Tuberculosis, Pulmonary/diagnosis/microbiology ; *Mycobacterium tuberculosis/genetics/isolation & purification ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Sensitivity and Specificity ; DNA, Bacterial/genetics ; Male ; Female ; Adult ; Middle Aged ; Nanopore Sequencing/methods ; Genome, Bacterial ; }, abstract = {Metagenomic next-generation sequencing (mNGS) has greatly improved our understanding of pathogens in infectious diseases such as pulmonary tuberculosis (PTB). However, high human DNA background (> 95%) impedes the detection sensitivity of mNGS in identifying intracellular Mycobacterium tuberculosis (MTB), posing a pressing challenge for MTB diagnosis. Therefore, there is an urgent need to improve MTB diagnosis performance in PTB patients. In this study, we optimized mNGS method for diagnosis of PTB. This led to the development of the host DNA depletion assisted mNGS (HDA-mNGS) technique, which we compared with conventional mNGS and the host DNA depletion-assisted Nanopore sequencing (HDA-Nanopore) in diagnostic performance. We collected 105 bronchoalveolar lavage fluid (BALF) samples from suspected PTB patients across three medical centers to assess the clinical performance of these methods. The results of our study showed that HDA-mNGS had the highest sensitivity (72.0%) and accuracy (74.5%) in PTB detection. This was significantly higher compared to mNGS (51.2%, 58.2%) and HDA-Nanopore (58.5%, 62.2%). Furthermore, HDA-mNGS provided an increased coverage of the MTB genome by up to 16-fold. Antibiotic resistance gene analysis indicated that HDA-mNGS could provide increased depth to the detection of Antimicrobial resistance (AMR) locus more effectively. These findings indicate that HDA-mNGS can significantly improve the clinical performance of PTB diagnosis for BALF samples, offering great potential in managing antibiotic resistance in PTB patients.}, } @article {pmid39961991, year = {2025}, author = {Booth, ME and Wood, HM and Travis, MA and , and Quirke, P and Grabsch, HI}, title = {The relationship between the gastric cancer microbiome and clinicopathological factors: a metagenomic investigation from the 100,000 genomes project and The Cancer Genome Atlas.}, journal = {Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association}, volume = {}, number = {}, pages = {}, pmid = {39961991}, issn = {1436-3305}, abstract = {BACKGROUND: Findings from previous gastric cancer microbiome studies have been conflicting, potentially due to patient and/or tumor heterogeneity. The intratumoral gastric cancer microbiome and its relationship with clinicopathological variables have not yet been characterized in detail. We hypothesized that variation in gastric cancer microbial abundance, alpha diversity, and composition is related to clinicopathological characteristics.

METHODS: Metagenomic analysis of 529 GC samples was performed, including whole exome sequencing data from The Cancer Genome Atlas (TCGA) and whole genome sequencing data from the 100,000 Genomes Project. Microbial abundance, alpha diversity, and composition were compared across patient age, sex, tumor location, geographic origin, pathological depth of invasion, pathological lymph node status, histological phenotype, microsatellite instability status, and TCGA molecular subtype.

RESULTS: Gastric cancer microbiomes resembled previous results, with Prevotella, Selenomonas, Stomatobaculum, Streptococcus, Lactobacillus, and Lachnospiraceae commonly seen across both cohorts. Within the TCGA cohort, microbial abundance and alpha diversity were greater in gastric cancers with microsatellite instability, lower pathological depth of invasion, intestinal-type histology, and those originating from Asia. Microsatellite instability status was associated with microbiome composition in both cohorts. Sex and pathological depth of invasion were associated with microbiome composition in the TCGA cohort.

CONCLUSION: The intratumoral gastric cancer microbiome appears to differ according to clinicopathological factors. Certain clinicopathological factors associated with favourable outcomes in gastric cancer were observed to be associated with greater microbial abundance and diversity. This highlights the need for further work to understand the underlying biological mechanisms behind the observed microbiome differences and their potential clinical and therapeutic impact.}, } @article {pmid39961944, year = {2025}, author = {Andraskar, J and Khan, D and Yadav, S and Kapley, A}, title = {Metagenomic Analysis of Microbial Community Associated with Food Waste Composting.}, journal = {Applied biochemistry and biotechnology}, volume = {}, number = {}, pages = {}, pmid = {39961944}, issn = {1559-0291}, support = {DBT/JRF/BET-18/1/2018/AL/23//Department of Biotechnology, Ministry of Science and Technology, India/ ; }, abstract = {Food waste is an increasing cause of concern in India. Its management through composting plays a vital role in managing the biodegradable fraction of municipal solid waste. However, the existing composting process has many challenges, such as the lack of optimum microenvironment and microbiome knowledge, which limits efficient outcomes. Therefore, the present study aims to bridge the gap by applying metagenomics to study microbial community dynamicity during different stages of composting. The bacterial community analysis showed that genus Marionobacter (9.4%) and Halomonas (7.4%) were prevalent during the mesophilic stage, whereas the Bacillus (12.2%) and Cellulomonas (0.1%) were prevalent during the thermophilic and maturation stage of composting. The functional profiling of metagenome indicated the abundance of genes involved in degradation of polymeric compounds such as carbohydrates, lipids, and proteins. The relative abundance of arginine and proline metabolisms increased during the thermophilic stage. Whereas the relative abundance of genes involved in fatty acid, tryptophan, galactose, and propanoate metabolisms declined. Similarly, the CAZyme tool predicted that the genes encoding for glycoside hydrolase (GH) families were higher during the mesophilic and thermophilic stages of composting. These enzymes play an important role in degradation of complex polysaccharides such as cellulose and hemicellulose. The data obtained from the present study could be utilized for the optimization and improving the composting process.}, } @article {pmid39961017, year = {2025}, author = {Colman, DR and Templeton, AS and Spear, JR and Boyd, ES}, title = {Microbial ecology of Serpentinite-hosted ecosystems.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf029}, pmid = {39961017}, issn = {1751-7370}, abstract = {Serpentinization, the collective set of geochemical reactions initiated by the hydration of ultramafic rock, has occurred throughout Earth history and is inferred to occur on several planets and moons in our solar system. These reactions generate highly reducing conditions that can drive organic synthesis reactions potentially conducive to the emergence of life, while concomitantly generating fluids that challenge life owing to hyperalkalinity and limited inorganic carbon (and oxidant) availability. Consequently, the serpentinite-hosted biosphere offers insights into the earliest life, the habitable limits for life, and the potential for life on other planets. However, the support of abundant microbial communities by serpentinites was only recognized ~20 years ago with the discovery of deep-sea hydrothermal vents emanating serpentinized fluids. Here, we review the microbial ecology of both marine and continental serpentinization-influenced ecosystems in conjunction with a comparison of publicly available metagenomic sequence data from these communities to provide a global perspective of serpentinite microbial ecology. Synthesis of observations across global systems reveal consistent themes in the diversity, ecology, and functioning of communities. Nevertheless, individual systems exhibit nuances due to local geology, hydrology, and input of oxidized, near-surface/seawater fluids. Further, several new (and old) questions remain including the provenance of carbon to support biomass synthesis, the physical and chemical limits of life in serpentinites, the mode and tempo of in situ evolution, and the extent that modern serpentinites serve as analogs for those on early Earth. These topics are explored from a microbial perspective to outline key knowledge-gaps for future research.}, } @article {pmid39960952, year = {2025}, author = {Liu, H and Li, Q and Ouyang, X and Li, Q and Min, Y and Dai, L}, title = {Diagnosis of early neurobrucellosis using metagenomic next-generation sequencing of the cerebrospinal fluid in nonepidemic zone: Case report and lecture review.}, journal = {Medicine}, volume = {104}, number = {7}, pages = {e41481}, doi = {10.1097/MD.0000000000041481}, pmid = {39960952}, issn = {1536-5964}, mesh = {Humans ; *Brucellosis/diagnosis/cerebrospinal fluid/drug therapy ; *High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Anti-Bacterial Agents/therapeutic use ; Female ; Central Nervous System Bacterial Infections/diagnosis/cerebrospinal fluid/drug therapy/microbiology ; Doxycycline/therapeutic use ; Male ; Early Diagnosis ; Brucella/isolation & purification ; Adult ; }, abstract = {RATIONALE: Brucella neuropathy is a rare clinical condition, particularly in nonendemic areas, where it often presents with nonspecific symptoms such as fever and headaches, leading to frequent misdiagnoses. In these regions, Brucella antibodies are not routinely tested, and the positive rate of blood cultures is relatively low during the early stage of the disease. In addition, the low culture-positive rate of cerebrospinal fluid (CSF) means that many neurobrucellosis diagnoses rely on peripheral blood cultures or Brucella antibodies, which is not rigorous. This is problematic because the treatment of central nervous system brucellosis differs significantly from that of other types of brucellosis. The purpose of this study is to provide a method for the early diagnosis of Brucella neuropathy in nonendemic areas. We present a case of early-stage neurobrucellosis diagnosed using metagenomic next-generation sequencing (mNGS) of CSF. This approach helps avoid delaying diagnosis in the early stage in nonepidemic areas, potentially reducing the duration before diagnosis, which is of great significance for timely and appropriate treatment.

PATIENT CONCERNS: The patient had fever, mild headache, and a slight increase in CSF leukocytes.

DIAGNOSES: CSF mNGS detected Brucella, which was later confirmed by serum Brucella antibody testing.

INTERVENTIONS: The patient was treated with rifampicin, doxycycline, and ceftriaxone.

OUTCOMES: The patient experienced significant relief from the headache, and the fever did not recur. Subsequent examinations revealed no abnormalities in the CSF leukocytes or mNGS results.

LESSONS: We reviewed 10 articles on brucellosis diagnosed using mNGS, including 7 articles on neurobrucellosis (10 cases). Our review highlights the sensitivity of mNGS as a powerful tool for early detection of neurobrucellosis in the CSF. The common symptoms include fever and headache, with brain magnetic resonance imaging detecting lesions in most cases. CSF mNGS results varied, with only a few positive Brucella cultures or antibody tests.}, } @article {pmid39960906, year = {2025}, author = {Dong, H and Feng, J and Wu, S and Liang, F and Li, H and Liang, X and Liao, W and Pan, Y and Tang, G and Li, D and Zhou, W and Cao, Z and Wang, W and Hu, J}, title = {First case report of long-term latent infection paracoccidioidomycosis in China.}, journal = {Medicine}, volume = {104}, number = {7}, pages = {e41409}, doi = {10.1097/MD.0000000000041409}, pmid = {39960906}, issn = {1536-5964}, support = {2021-2023//Guangzhou Medical Key Discipline/ ; 202002030152, 202201010744 and 2023A03J0539//Science and Technology Program of Guangzhou/ ; 2023A03J0539//Science and Technology Program of Guangzhou/ ; B2021038//Medical Science Research Foundation of Guangdong Province/ ; }, mesh = {Humans ; *Paracoccidioidomycosis/diagnosis/drug therapy/epidemiology ; Male ; China/epidemiology ; *Antifungal Agents/therapeutic use ; *Paracoccidioides/isolation & purification ; *Latent Infection/diagnosis/drug therapy ; Voriconazole/therapeutic use/administration & dosage ; Middle Aged ; }, abstract = {RATIONALE: Although paracoccidioidomycosis is one of the most prevalent endemic mycoses in Latin American countries, where at least 10 million people are infected, the prevalence of paracoccidioidomycosis in China remains unknown because no related case has been reported, and its diagnosis is extremely challenging for local clinicians because of the complexity of disease progression and lack of specific evidence.

PATIENT CONCERNS: Here, we report the first case of PCM in a male patient with a long-term latent infection in China.

DIAGNOSIS: The results of special staining, immunohistochemistry, lymph node biopsy pathology, and metagenomic second-generation sequencing indicated that the patient was infected with Paracoccidioides brasiliensis.

INTERVENTIONS: In this case, the patient was administered voriconazole 200 mg twice daily.

OUTCOMES: After continuous treatment for 6 months, the patient's symptoms improved significantly, and the medication was discontinued. The outpatient follow-up revealed no discomfort.

LESSONS: This case is of great value for the early diagnosis, treatment, and prevention of the spread of this emerging infectious disease in China.}, } @article {pmid39960726, year = {2025}, author = {Kenyon, AL and Solomon, IH}, title = {What every neuropathologist needs to know: Update on neuro infectious disease workups and consultation resources.}, journal = {Journal of neuropathology and experimental neurology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jnen/nlaf009}, pmid = {39960726}, issn = {1554-6578}, abstract = {Efficient histopathological diagnosis of central nervous system infections can be challenging but is critical for therapeutic decision making in cases for which less invasive blood or cerebrospinal fluid testing has been unrevealing. A wide variety of bacteria, fungi, viruses, and parasites can cause infections, particularly in immunocompromised individuals. Histological findings may be nonspecific or overlap with noninfectious inflammatory conditions. To minimize wasted tissue and time, a systematic approach is recommended in which: (1) relevant patient history (eg, comorbidities, travel and other exposures, and immune status) and radiological findings are reviewed, (2) a preliminary differential diagnosis based on this information and on inflammatory patterns and visualization of potential microorganisms on hematoxylin and eosin stains is generated, (3) special stains, immunohistochemistry, in situ hybridization, or molecular testing (pathogen-specific or broad-spectrum) are used for confirmation and further classification, and (4) correlation with culture results and other laboratory testing is performed to arrive at a final integrated diagnosis. Discrepancies between molecular and histological findings are often due to contamination and require careful evaluation to avoid treatment of false positives. Consultation with infectious disease pathologists or public health reference laboratories may be needed to confirm diagnoses of unusual organisms or when specialized testing is required.}, } @article {pmid39958980, year = {2025}, author = {Huang, X and Qiu, J and Pan, L and Wang, C and Tang, C}, title = {Acute Necrotizing Fasciitis Caused by Rhizopus Infection in a Patient with Diabetes and Pulmonary Tuberculosis: A Case Report.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {775-782}, pmid = {39958980}, issn = {1178-6973}, abstract = {BACKGROUND: Zygomycosis, also termed mucormycosis, is a rare yet highly fatal fungal infection caused by Mucorales species, notably Rhizopus spp.

CASE PRESENTATION: This case study details a 72-year-old man with diabetes, pulmonary tuberculosis, and nephrotic syndrome who developed acute necrotizing fasciitis attributable to R. oryzae. Despite initial empirical antibiotic therapy, the infection progressed rapidly. Metagenomic next-generation sequencing (mNGS) facilitated a swift diagnosis, identifying R. oryzae in blood and drainage samples. The treatment included amphotericin B and isavuconazole, along with aggressive surgical debridement. The patient exhibited substantial improvement, and he was discharged after stabilization.

CONCLUSION: This case highlights the critical role of early diagnosis through mNGS and the need for a multidisciplinary approach to manage severe mucormycosis in immunocompromised patients.}, } @article {pmid39958933, year = {2025}, author = {Kuźmycz, O and Kowalczyk, A and Bolanowska, A and Drozdzowska, A and Lach, J and Wierzbińska, W and Kluz, T and Stączek, P}, title = {A comprehensive analysis of the uterine microbiome in endometrial cancer patients - identification of Anaerococcus as a potential biomarker and carcinogenic cofactor.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1511625}, pmid = {39958933}, issn = {2235-2988}, mesh = {Humans ; Female ; *Endometrial Neoplasms/microbiology/genetics ; *Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; Uterus/microbiology ; Middle Aged ; Phylogeny ; Biomarkers ; Adult ; Aged ; Reactive Oxygen Species/metabolism ; Carcinogenesis ; Fibroblasts/microbiology ; Biomarkers, Tumor/genetics ; Computational Biology/methods ; Oxidative Stress ; }, abstract = {INTRODUCTION: Endometrial cancer (EC) is a significant gynecological malignancy with increasing incidence worldwide. Emerging evidence highlights the role of the uterine microbiome in the pathogenesis of EC. This study aims to characterize the uterine microbiome in EC patients and identify potential microbial biomarkers, with a focus on Anaerococcus as a differentiating taxon.

METHODS: The endocervical canal swabs from patients with EC (n=16) and non-cancerous patients (EM, n=13) were collected. The V3-V4 region of the 16S rRNA gene was sequenced using the Illumina platform. Bioinformatic analyses were performed with QIIME2, and statistical comparisons were conducted to assess differences in microbial composition and diversity. In vitro experiments were conducted to assess the functional impact of Anaerococcus on human uterine fibroblasts, including its ability to adhere to the human cells and induce oxidative stress.

RESULTS: The α-diversity metrics, including Shannon entropy and observed amplicon sequence variants (ASVs), revealed significantly higher microbial diversity in EC samples compared to EM. Anaerococcus was identified as a key taxon differentiating EC from EM groups, showing a higher relative abundance in EC samples. Functional predictions and in vitro assays indicated that Anaerococcus may contribute to carcinogenesis by inducing reactive oxygen species (ROS) production, and has the high ability to adhere to the human endometrial fibroblasts.

DISCUSSION: The study provides evidence of distinct microbial signatures in EC, with Anaerococcus emerging as a potential biomarker. The in vitro findings suggest its role in endometrial carcinogenesis, underscoring its potential as a target for future diagnostic and therapeutic applications.}, } @article {pmid39957783, year = {2024}, author = {Chattaraj, S and Mitra, D and Chattaraj, M and Ganguly, A and Thatoi, H and Mohapatra, PKD}, title = {Brewers' spent grain as fish feed ingredient: Evaluation of bio-safety and analysis of its impact on gut bacteria of Cirrhinus reba by 16S Metagenomic sequencing.}, journal = {Current research in microbial sciences}, volume = {7}, number = {}, pages = {100286}, pmid = {39957783}, issn = {2666-5174}, abstract = {A comprehensive eight week feeding trial was conducted to investigate the potential of brewers' spent grain (BSG) as a sustainable fish feed ingredient. The study assessed both the biosafety of BSG and its impact on the gut microbiome of Cirrhinus reba, utilizing advanced 16S metagenomic sequencing techniques to analyze the composition and diversity of gut bacteria. A total of 90 healthy C. reba juveniles (average weight: 12 ± 1 g) were divided into two dietary groups [for control (C), for BSG meal (tB)] in triplicates. Feed prepared with conventional ingredients was used to feed the control group (C). The group tB was fed with BSG meal. After the feeding trial, the fish in tB group showed significantly higher (p < 0.05) growth parameters as compared to the control group. The results of bio-safety assessment indicated the absence of any pathological symptoms in the BSG meal fed carps. The fish in tB group didn't show any histopathological abnormality. Fish fed the Brewers' Spent Grain exhibited significantly elevated serum biochemical parameters, including alanine transaminase (ALT) and aspartate transaminase (AST), compared to the control group (p < 0.05). 16S Metagenomic sequencing of the fish gut microbiota provides insights into how BSG inclusion affects microbial diversity and composition within the digestive tract of C. reba. The analysis revealed the existence of 240 and 250 diverse bacterial genera in the gastrointestinal tract (GIT) of C. reba in dietary groups C and tB respectively. Importantly, the study found the gut of fish in tB group to be dominated by different beneficial genus including Bacillus, Lactobacillus, Bifidobacterium, Paenibacillus, and Lysinibacillus. Feeding C. reba with BSG meal significantly increased the alpha diversity of the gastrointestinal microbiota, as evidenced by elevated Chao 1 estimator and Shannon index values compared to the control diet (p < 0.05). This study provides comprehensive evidence for the bio-safety of BSG as a sustainable feed ingredient in aquaculture, demonstrating its potential to support healthy fish growth and development. Moreover, the prebiotic potential of BSG in fish has also been highlighted.}, } @article {pmid39956369, year = {2025}, author = {Abe, M and Sekizuka, T and Miyazaki, Y}, title = {Gastrointestinal anaerobes and Enterococcus faecalis promote Candida glabrata gastrointestinal colonization and organ dissemination.}, journal = {Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy}, volume = {}, number = {}, pages = {102658}, doi = {10.1016/j.jiac.2025.102658}, pmid = {39956369}, issn = {1437-7780}, abstract = {BACKGROUND: Candida glabrata is a common causative pathogen of endogenous candidiasis. It is assumed that the gastrointestinal flora affects C. glabrata gastrointestinal colonization and organ dissemination in the gastrointestinal tract (GIT). However, no reports have yet described the relationships between C. glabrata and bacteria in the GIT. This study aimed to clarify these relationships using a mouse endogenous candidiasis model with cortisone acetate immunosuppression.

METHODS: Dysbiosis was induced in the GIT by several antibiotic combinations, and then C. glabrata gastrointestinal colonization and organ dissemination were evaluated. Next, metagenomic sequencing analysis of the gastrointestinal flora was performed to identify bacteria associated with C. glabrata organ dissemination. Finally, coinfection experiments were performed using bacteria isolated from the mouse GIT.

RESULTS: C. glabrata organ dissemination was significantly promoted using specific antibiotics regardless of the amount of colonization in the GIT. Metagenomic sequencing analysis of the gastrointestinal flora showed that Enterococcus species and anaerobes were significantly associated with enhanced organ dissemination, whereas Enterobacterales, such as Escherichia species and Klebsiella species, were associated with the suppression of organ dissemination. In coinfection experiments, Enterococcus faecalis and Faecalibaculum rodentium inoculation, but not either of them, increased C. glabrata organ dissemination without affecting gastrointestinal colonization.

CONCLUSIONS: Coinfection with gastrointestinal bacteria promoted C. glabrata organ dissemination, which would indicate that gastrointestinal flora could affect C. glabrata dissemination. Therefore, the gastrointestinal flora could be a target for intervention or treatment in clinical settings. Insights from this study would lead to better control of endogenous candidiasis focusing on the gastrointestinal flora.}, } @article {pmid39956110, year = {2025}, author = {Echeveste Medrano, MJ and Smith, GJ and Sánchez-Andrea, I and Jetten, MSM and Welte, CU}, title = {Contrasting Methane, Sulfide and Nitrogen-Loading Regimes in Bioreactors Shape Microbial Communities Originating From Methane-Rich Coastal Sediment of the Stockholm Archipelago.}, journal = {Environmental microbiology}, volume = {27}, number = {2}, pages = {e70056}, doi = {10.1111/1462-2920.70056}, pmid = {39956110}, issn = {1462-2920}, support = {854088//European Commission/ ; 024.002.002//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; VI.Vidi.223.012//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; }, mesh = {*Methane/metabolism ; *Geologic Sediments/microbiology ; *Bioreactors/microbiology ; *Sulfides/metabolism ; Sweden ; *Nitrogen/metabolism ; *Microbiota ; *RNA, Ribosomal, 16S/genetics ; *Archaea/metabolism/genetics/classification ; Seawater/microbiology ; Bacteria/classification/genetics/metabolism ; Oxidation-Reduction ; Denitrification ; Nitrates/metabolism ; Phylogeny ; Ecosystem ; }, abstract = {Coastal ecosystems are increasingly exposed to high nutrient loads and salinity intrusions due to rising seawater levels. Microbial communities, key drivers of elemental cycles in these ecosystems, consequently, experience fluctuations. This study investigates how the methane-rich coastal sediment microbiome from the Stockholm Archipelago copes with high and low nitrogen and sulfide loading by simulating coastal conditions in two methane-saturated anoxic brackish bioreactors. Over a year, the bioreactors were subjected to the same ratio of nitrate, ammonium and sulfide (2:1:1) under eutrophic or oligotrophic conditions and monitored using 16S rRNA gene amplicon and metagenomic sequencing. Sulfide was depleted in both conditions. Sulfide-dependent denitrification was the predominant process in eutrophic conditions, whereas dissimilatory nitrate reduction to ammonium dominated under oligotrophic conditions. Methane oxidation was driven by Methylobacter and Methylomonas in eutrophic conditions, whereas a more diverse methane-oxidising microbial community developed under oligotrophic conditions, which likely competed for nitrate with anaerobic methanotrophic archaea and the gammaproteobacterial MBAE14. Novel putative copper-dependent membrane-bound monooxygenases (Cu-MMOs) were identified in MBAE14 and co-enriched Rugosibacter genomes, suggesting the need for further physiological and genetic characterisation. This study highlights the importance of understanding coastal anoxic microbiomes under fluctuating conditions, revealing complex interactions and novel pathways crucial for ecosystem functioning.}, } @article {pmid39955557, year = {2025}, author = {Hernández, M and Langa, J and Aizpurua, O and Navarro-Noya, YE and Alberdi, A}, title = {Contrasting recovery of metagenome‑assembled genomes and derived bacterial communities and functional profiles from lizard fecal and cloacal samples.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {15}, pmid = {39955557}, issn = {2524-4671}, support = {POS_2022_1_0011//Hezkuntza, Hizkuntza Politika Eta Kultura Saila, Eusko Jaurlaritza/ ; DNRF143//Danmarks Grundforskningsfond/ ; }, abstract = {Genome-resolved metagenomics, based on shotgun sequencing, has become a powerful strategy for investigating animal-associated bacterial communities, due its heightened capability for delivering detailed taxonomic, phylogenetic, and functional insights compared to amplicon sequencing-based approaches. While genome-resolved metagenomics holds promise across various non-lethal sample types, their effectiveness in yielding high-quality metagenome-assembled genomes remains largely unexplored. Our investigation of fecal and cloacal microbiota of the mesquite lizards (Sceloporus grammicus) using genome-resolved metagenomics revealed that fecal samples contributed 97% of the 127 reconstructed bacterial genomes, whereas only 3% were recovered from cloacal swabs, which were largely enriched with host DNA. Taxonomic, phylogenetic and functional alpha bacterial diversity was greater in fecal samples than in cloacal swabs. We also observed significant differences in bacterial community composition between sampling methods, and higher inter-individual variation in cloacal swabs. Bacteroides, Phocaeicola and Parabacteroides (all Bacteroidota) were more abundant in the feces, whereas Hafnia and Salmonella (both Pseudomonadota) increased in the cloaca. Functional analyses showed that metabolic capacities of the microbiota to degrade polysaccharides, sugars and nitrogen compounds were enriched in fecal samples, likely reflecting the role of intestinal bacteria in nutrient metabolism. Overall, our results indicate that fecal samples outperform cloacal swabs in characterizing bacterial assemblages within lizards using genome-resolved metagenomics.}, } @article {pmid39955324, year = {2025}, author = {O' Donovan, CM and Nori, SRC and Shanahan, F and Celentano, G and Murphy, TB and Cotter, PD and Sullivan, OO}, title = {Temporal stability and lack of variance in microbiome composition and functionality in fit recreational athletes.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {5619}, pmid = {39955324}, issn = {2045-2322}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Male ; Adult ; *Athletes ; Female ; *Feces/microbiology ; Metagenomics/methods ; Prevotella/genetics/isolation & purification ; Young Adult ; Running ; Faecalibacterium prausnitzii/genetics ; }, abstract = {Human gut microbiome composition and function is influenced by environmental and lifestyle factors, including exercise and fitness. We studied the composition and functionality of the faecal microbiome of recreational (non-elite) runners (n = 62) with serial shotgun metagenomics, at 4 time points over a 7-week period. Gut microbiome composition and function was stable over time. Grouping of samples on the basis of their fitness level (fair, good, excellent, and superior) or habitual training (low (4-6 h/week), medium (7-9 h/week), high (10-12 h/week), and extreme (13 + hours/week)) revealed no significant microbiome-related differences. Overall, the species Faecalibacterium prausnitzii, Blautia wexlerae, and Prevotella copri were the most abundant members of the gut microbiome. Analysis of co-abundance groups (CAGs) revealed no significant relationship between CAGs and fitness levels or training subgroups. Functional pathways were similar across all samples and timepoints with no clustering based on associated metadata. The most abundant genes identified within samples corresponded to pathways for nucleoside and nucleotide biosynthesis, amino acid biosynthesis, and cell wall biosynthesis. Collectively, these results describe the microbiome of active recreational runners and note temporal stability amongst participants.}, } @article {pmid39954816, year = {2025}, author = {Ladyhina, V and Rajala, E and Sternberg-Lewerin, S and Nazirzadeh, L and Bongcam-Rudloff, E and Dicksved, J}, title = {Methodological aspects of investigating the resistome in pig farm environments.}, journal = {Journal of microbiological methods}, volume = {}, number = {}, pages = {107103}, doi = {10.1016/j.mimet.2025.107103}, pmid = {39954816}, issn = {1872-8359}, abstract = {A typical One Health issue, antimicrobial resistance (AMR) development and its spread among people, animals, and the environment attracts significant research attention. The animal sector is one of the major contributors to the development and dissemination of AMR and accounts for more than 50 % of global antibiotics usage. The use of antibiotics exerts a selective pressure for resistant bacteria in the exposed microbiome, but many questions about the epidemiology of AMR in farm environments remain unanswered. This is connected to several methodological challenges and limitations, such as inconsistent sampling methods, complexity of farm environment samples and the lack of standardized protocols for sample collection, processing and bioinformatical analysis. In this project, we combined metagenomics and bioinformatics to optimise the methodology for reproducible research on the resistome in complex samples from the indoor farm environment. The work included optimizing sample collection, transportation, and storage, as well as DNA extraction, sequencing, and bioinformatic analysis, such as metagenome assembly and antibiotic resistance gene (ARG) detection. Our studies suggest that the current most optimal and cost-effective pipeline for ARG search should be based on Illumina sequencing of sock sample material at high depth (at least 25 M 250 bp PE for AMR gene families and 43 M for gene variants). We present a computational analysis utilizing MEGAHIT assembly to balance the identification of bacteria carrying ARGs with the potential loss of diversity and abundance of resistance genes. Our findings indicate that searching against multiple ARG databases is essential for detecting the highest diversity of ARGs.}, } @article {pmid39954481, year = {2025}, author = {El Houari, A and Carpenter, M and Chaplin, D and Golyshin, P and McDonald, JE}, title = {Taxonomic description and genome sequence of Anaerorudis cellulosivorans gen. Nov. sp. nov., a novel cellulose- and Xylan-degrading bacterium of the Bacteroidota phylum isolated from a lab-scale methanogenic landfill bioreactor digesting municipal solid waste.}, journal = {Systematic and applied microbiology}, volume = {48}, number = {2}, pages = {126590}, doi = {10.1016/j.syapm.2025.126590}, pmid = {39954481}, issn = {1618-0984}, abstract = {Bacteria responsible for the anaerobic decomposition of lignocellulosic waste biomass play key roles in the global carbon cycle and possess enzymes with potential industrial application. Here, a novel anaerobic, thermophilic, non-spore-forming bacterium, strain m5[T], was isolated from methanogenic enrichment cultures obtained from a lab-scale methanogenic landfill bioreactor digesting anaerobic municipal solid waste. Cells were Gram-stain-negative, catalase-negative, oxidase-negative, rod-shaped, and non-motile. The genomic DNA G + C content was 40.92 mol%. The optimal NaCl concentration, temperature and pH for growth were 0.5-1 g.L[-1], 45 °C, and at pH 7.0, respectively. The major fatty acids were C14:0, C16:0, C18:0, C18:1ω9c, and anteisoC15:0. Strain m5[T] was able to grow in the absence of yeast extract on glucose, fructose, arabinose, cellobiose, galactose, maltose, raffinose, sucrose, lactose, and pyruvate. In the presence of 0.2 % yeast extract, strain m5[T] grew on wide range of carbohydrates and amino acids, and was able to use complex substrates such cellulose and xylan. Major end products from cellulose and xylan degradation were valerate and propionate. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the new isolate was most closely related to Seramator thermalis SYSU GA16112[T] (94.42 % 16S rRNA gene sequence identity). Genome-based relatedness as well as both Average Nucleotide Identity (ANI), and Average Amino Acid Identity (AAI) strongly supported that strain m5[T] belongs to the Dysgonomonadaceae family. Metagenomic analysis of the landfill bioreactor community revealed that the Dysgonomonadaceae family was the most abundant in the constructed bioreactors. Based on its unique genomic features, strain m5[T] is considered to represent a novel genus, for which the name Anaerorudis is proposed. Moreover, several phenotypic, biochemical, and physiological properties differentiated the novel bacterial strain from related species, indicating that the strain represents a new species for which the name Anaerorudis cellulosivorans sp. nov. is proposed, with strain m5[T] (= DSM 112743[T] = ATCC TSD-267[T]) being the type of strain. This study highlights the biotechnological potential of strain m5[T], specifically in the bioconversion of cellulose and xylan, a recalcitrant substrate within lignocellulosic plant biomass, to enhance biogas production.}, } @article {pmid39954461, year = {2025}, author = {Schacksen, PS and Macêdo, WV and Rellegadla, S and Vergeynst, L and Nielsen, JL}, title = {Dynamics of nitrogen-transforming microbial populations in wastewater treatment during recirculation of hydrothermal liquefaction process-water.}, journal = {Water research}, volume = {276}, number = {}, pages = {123254}, doi = {10.1016/j.watres.2025.123254}, pmid = {39954461}, issn = {1879-2448}, abstract = {The global reliance on non-renewable fossil fuels highlights the urgent need for sustainable alternative energy sources. Hydrothermal liquefaction (HTL) offers a promising solution by converting biomass, such as sewage sludge, into biocrude oil. However, the integration of excess HTL-process water (HTL-PW), a by-product of this process, into conventional wastewater treatment requires careful evaluation. This study investigates the effects of recirculating HTL-PW in sequencing batch reactors (SBRs) using synthetic wastewater. Two SBRs were operated in parallel: one fed 0.15 % (v/v) HTL-PW and the other with only synthetic feed. The reactor receiving HTL-PW demonstrated superior stability, effective nitrification, and consistent denitrification with no adverse effects on nitrogen species turnover. A comprehensive approach combining 16S rRNA gene amplicon sequencing for relative abundance and metagenomic analysis, for enhanced resolution of nitrogen-transforming populations, revealed the genetic repertoire and potential of 58±4 % and 65±4 % of the genus-level annotations from the HTL-PW and control reactors, respectively. The HTL-PW-fed reactor maintained robust performance, with microbial community analysis revealing a strong association between nitrogen transformations and specific microbial taxa, thereby explaining the observed reactor stability and efficiency in nitrogen conversion. These findings demonstrate the feasibility of integrating HTL-PW into wastewater treatment systems, showing that recirculating HTL-PW at the tested concentrations does not adversely affect nitrogen transformations, supports stable nitrification and denitrification, ensures complete ammonium utilisation, and promotes diverse and dynamic microbial communities similar to those in full-scale wastewater treatment plants.}, } @article {pmid39954460, year = {2025}, author = {Luo, S and Yuan, J and Song, Y and Ren, J and Qi, J and Zhu, M and Feng, Y and Li, M and Wang, B and Li, X and Song, C}, title = {Elevated salinity decreases microbial communities complexity and carbon, nitrogen and phosphorus metabolism in the Songnen Plain wetlands of China.}, journal = {Water research}, volume = {276}, number = {}, pages = {123285}, doi = {10.1016/j.watres.2025.123285}, pmid = {39954460}, issn = {1879-2448}, abstract = {Salinity can induce changes in the structure and function of soil microbial communities, which plays an important role in soil carbon (C), nitrogen (N) and phosphorus (P) cycling. However, there are few studies on the relationship between microbial communities and functional properties of wetland soil under elevated salinity. In this study, soil samples from Zhalong, Momoge, Niuxintaobao, and Xianghai wetlands in the Songnen Plain of China were cultured with different salinity and analyzed by metagenomic sequencing to assess the overall impact of salinity on microorganisms. The results showed that increasing soil salinity decreased soil microbial diversity and significantly changed its composition. Elevated salinity led to the replacement of core species (Sphingomonas) by halophilic species (Halomonadaceae, Halomohas campaniensis), reducing the stability of microbial ecological networks. C fixation, denitrification and purine metabolism were the key ways for the maintenance of C, N and P functions in Songnen plain wetlands, and these processes were significantly reduced with increasing salinity. Key genes involved in C, N and P metabolism include EC1.1.1.42, EC4.1.1.31, EC6.4.1.1, nosZ, nirK, purB, purC, adk, purM, and purQ. They were all effectively suppressed due to increased salinity. In summary, elevated salinity reduced the complexity of microorganisms and inhibited the related functions of C, N and P cycling, and affected the stability of wetland ecosystems. Wetland protection should be strengthened to prevent the aggravation of salinization. This study provides a new scientific framework for the restoration and management of salinized wetland ecosystems in the face of upcoming global changes.}, } @article {pmid39954395, year = {2025}, author = {Xiao, H and Zhou, C and Xiao, Z and Cai, F and Zhang, S and Sheng, S and Jin, C and Fu, Y}, title = {Metagenomic next-generation sequencing of bronchoalveolar lavage fluid samples offers diagnostic utility in bacteriologically negative pulmonary tuberculosis.}, journal = {Diagnostic microbiology and infectious disease}, volume = {111}, number = {4}, pages = {116725}, doi = {10.1016/j.diagmicrobio.2025.116725}, pmid = {39954395}, issn = {1879-0070}, abstract = {Rapid diagnosing Mycobacterium tuberculosis (M. tb) in patients with pulmonary tuberculosis (PTB) cases is critical, particularly in cases without bacteriologically confirmed disease, as it enables timely treatment initiation and can thus interrupt further disease transmission. In this study, the utility of metagenomic next-generation sequencing (mNGS) as a diagnostic tool was evaluated using samples of bronchoalveolar lavage fluid (BALF) samples from 300 bacteriologically negative PTB (BN-PTB) patients hospitalized from January 2020 through December 2023. The diagnostic performance of mNGS was compared to that of acid-fast staining (AFS), conventional Roche culture, and the Xpert method among these BN-PTB patients, using clinical diagnosis as the gold standard. The final analyses enrolled 112 PTB patients and 188 non-PTB cases. These analyses revealed that mNGS-based M. tb detection yields a sensitivity of 94.64 % (106/112), a specificity of 98.94 % (186/188), a positive predictive value (PPV) of 98.15 % (106/108), and a negative predictive value (NPV) of 96.88 % (186/192). This mNGS approach outperformed the AFS, Roche culture, and Xpert methods in terms of sensitivity, specificity, PPV, and NPV (p < 0.05). The superior diagnostic performance of this approach was further supported by its area under the curve and corresponding confidence intervals. Together, these data demonstrate that mNGS can improve the detection of M. tb in BALF samples from BN-PTB patients with high levels of speed, sensitivity, and specificity. This mNGS approach may thus be a valuable diagnostic tool for the rapid detection of M. tb in BN-PTB, providing a foundation for the precision diagnosis and treatment of PTB in the future.}, } @article {pmid39954350, year = {2025}, author = {Dong, Y and Liu, H and Habimana, O}, title = {High risk of Vibrio pathogen and antibiotic resistance transfer in live seafood wet markets of Shantou, China.}, journal = {International journal of food microbiology}, volume = {432}, number = {}, pages = {111098}, doi = {10.1016/j.ijfoodmicro.2025.111098}, pmid = {39954350}, issn = {1879-3460}, abstract = {The global demand for seafood necessitates robust food safety practices, particularly within traditional wet markets. This study investigated the microbiomes of live Japanese mantis shrimp (JMS) and their associated environments (water and biofilm) in local wet markets to assess the risk of pathogen and antibiotic resistance gene (ARG) transfer. Metagenomic analysis showed a significant link between microbiome composition and the type of sample (shrimp, biofilm, and water). While several known human pathogens were associated with shrimp samples, water and biofilm samples exhibited higher abundances of ARGs, suggesting a high risk of pathogen and ARG transfer from the market environment. Notably, this study focused on the diversity and characterization of poorly understood Vibrio species associated with JMS. The prevalence of β-lactam resistance genes in Vibrio isolates, combined with a comparative genomic analysis of several species, highlights this concern. Our study emphasizes the need to improve hygiene practices in wet markets to reduce foodborne illness risks and address antibiotic resistance. This work represents, to our knowledge, the first comparative genomic analysis of Vibrio species in the context of JMS and wet market seafood safety.}, } @article {pmid39954080, year = {2025}, author = {Liang, Y and Zhao, Y and Yin, Z and Zeng, X and Han, X and Wen, M}, title = {Functional and structural insights into α-L-Rhamnosidase: cloning, characterization, and decoding evolutionary constraints through structural motif.}, journal = {Archives of microbiology}, volume = {207}, number = {3}, pages = {61}, pmid = {39954080}, issn = {1432-072X}, support = {2023KF005//Yunnan University/ ; 2023KF005//Yunnan University/ ; }, mesh = {*Glycoside Hydrolases/genetics/chemistry/metabolism ; *Cloning, Molecular ; Catalytic Domain ; Substrate Specificity ; Amino Acid Sequence ; Amino Acid Motifs ; Evolution, Molecular ; Bacterial Proteins/genetics/chemistry/metabolism ; Binding Sites ; Phylogeny ; Models, Molecular ; Bacteria/enzymology/genetics ; }, abstract = {α-L-rhamnosidase [E.C. 3.2.1.40] is important in various industrial and biotechnological applications. However, limited knowledge of the structural features of its active site residues and their local geometric arrangements during substrate interaction hinders further application development. In this study, we examined functionally characterized microbial α-L-rhamnosidases. Despite considerable differences in their global structures, the local structures of the substrate-binding sites and key residues were highly conserved. Using the local structural motif, we characterized α-L-rhamnosidase genes from metagenomic samples of traditional fermentation starters. To comprehensively understand the distribution of α-L-rhamnosidases with this motif in the AlphaFold database, we screened 26,858 α-L-rhamnosidase structures. Our findings showed that only 5678 out of 26,858 structures contain the specific conserved motifs, emphasizing their potential significance in mining enzyme function. Moreover, the analysis of structural diversity among representative enzymes demonstrated variation in the number and types of domains within this enzyme family. Further investigation of representative α-L-rhamnosidase sequences with this structural motif confirmed the evolutionary constraints of 15 key residues, indicating strong selective pressures to maintain these elements essential for enzyme functionality. These residues were consistently present across ancestral sequences, underscoring their importance throughout the enzyme's evolutionary history. This study suggests that structure-guided approaches are valuable for discovering functional enzymes. Identifying conserved motif across diverse microbial taxa not only aids in predicting enzyme functionality but also offers opportunities for enzyme engineering and biotechnological applications.}, } @article {pmid39953827, year = {2025}, author = {Reed, GM and Strickland, AK and Mutchler, CT and Ochoa, AR and Asin, SN and Blackburn, AN}, title = {Evaluating Nanopore Sequencing as a Respiratory Virus Diagnostic Tool for the Prehospital Setting.}, journal = {Military medicine}, volume = {}, number = {}, pages = {}, doi = {10.1093/milmed/usaf046}, pmid = {39953827}, issn = {1930-613X}, support = {DS21RES11//Defense Health Agency/ ; DS21RES11//Defense Health Agency/ ; }, abstract = {INTRODUCTION: Upper respiratory tract infections are a strain on military that results in lost duty days and an overall reduced readiness of the force. Improved diagnostic testing would enable better force health protection measures and earlier treatment of illness. Lightweight portable devices are preferred for diagnostic testing in austere environments where they are sometimes needed during military deployment. Current diagnostic testing is targeted to specific pathogens despite multiple pathogens that present with similar symptoms. In practice the pathogens that cause upper respiratory tract infections often go unidentified, which could be improved using agnostic or semi-agnostic diagnostic testing. Here, we performed an evaluation of shotgun metagenomic sequencing using the Oxford Nanopore Technologies (ONT) Rapid Sequencing Kit as a method for diagnostic testing of upper respiratory tract infections. This sequencing library preparation kit was chosen because of its ease of use and compatibility with the ONT MinION, a lightweight portable sequencer.

MATERIALS AND METHODS: Samples from patients with symptoms of upper respiratory tract infections were collected at Wilford Hall Ambulatory Surgical Center under an approved IRB protocol. Nasal rinse samples from 59 study participants were tested using the BioFire FilmArray Respiratory 2.1 Panel as well as shotgun metagenomic sequencing using ONT Rapid Sequencing Kit and ONT R9.4.1 flow cells.

RESULTS: A mixture of various viral pathogens was present among the 59 samples used in this study. We observed high specificity and modest sensitivity to detect the identified pathogens using shotgun metagenomic sequencing. Shotgun metagenomic sequencing detected additional pathogens that were missed by the BioFire FilmArray Respiratory 2.1 Panel, which are discussed. Lastly, we observe modest evidence of nonuniformity of the proportion of reads belonging to the pathogen during the duration of sequencing runs, which has implications for improving sensitivity by increasing the amount of sequencing performed.

CONCLUSIONS: Overall, ONT Rapid Sequencing Kit combined with alignment to a known panel of pathogens has shown great potential utility in our hands for quickly and accurately identifying viral respiratory pathogens. This, combined with its ease of use and portability, makes it a great candidate for further research and development toward a deployable agnostic diagnostic testing platform.}, } @article {pmid39953749, year = {2025}, author = {Aizpurua, O and Botnen, AB and Eisenhofer, R and Odriozola, I and Santos-Bay, L and Bjørnsen, MB and Gilbert, MTP and Alberdi, A}, title = {Functional Insights Into the Effect of Feralisation on the Gut Microbiota of Cats Worldwide.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {e17695}, doi = {10.1111/mec.17695}, pmid = {39953749}, issn = {1365-294X}, support = {CF20-0460//Carlsbergfondet/ ; 17417//Villum Fonden/ ; DNRF143//Danmarks Grundforskningsfond/ ; }, abstract = {Successfully adapting to a feral lifestyle with different access to food, shelter and other resources requires rapid physiological and behavioural changes, which could potentially be facilitated by gut microbiota plasticity. To investigate whether alterations in gut microbiota support this transition to a feral lifestyle, we analysed the gut microbiomes of domestic and feral cats from six geographically diverse locations using genome-resolved metagenomics. By reconstructing 229 non-redundant metagenome-assembled genomes from 92 cats, we identified a typical carnivore microbiome structure, with notable diversity and taxonomic differences across regions. While overall diversity metrics did not differ significantly between domestic and feral cats, hierarchical modelling of species communities, accounting for geographic and sex covariates, revealed significantly larger microbial functional capacities among feral cats. The increased capacity for amino acid and lipid degradation corresponds to feral cats' dietary reliance on crude protein and fat. A second modelling analysis, using behavioural phenotype as the main predictor, unveiled a positive association between microbial production of short-chain fatty acids, neurotransmitters and vitamins and cat aggressiveness, suggesting that gut microbes might contribute to heightened aggression and elusiveness observed in feral cats. Functional microbiome shifts may therefore play a significant role in the development of physiological and behavioural traits advantageous for a feral lifestyle, a hypothesis that warrants validation through microbiota manipulation experiments.}, } @article {pmid39953591, year = {2025}, author = {Chen, H and Yao, X and Yang, C and Zhang, Y and Dong, H and Zhai, J and Fan, D and Zhou, Q}, title = {Distinctive circulating microbial metagenomic signatures in the plasma of patients with lung cancer and their potential value as molecular biomarkers.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {186}, pmid = {39953591}, issn = {1479-5876}, support = {YCZYPT [2018]06//National Human Genetic Resource Sharing Service Platform/ ; }, mesh = {Humans ; *Lung Neoplasms/blood/microbiology/genetics ; *Metagenomics/methods ; *Biomarkers, Tumor/blood ; Female ; Male ; Middle Aged ; Metagenome/genetics ; Aged ; Case-Control Studies ; ROC Curve ; }, abstract = {Lung cancer (LC) remains the leading cause of cancer death globally. Recent reports have suggested that circulating microbial nucleic acids have potential as promising biomarkers for cancer liquid biopsies. However, circulating microbial profiles and their potential clinical value in LC patients remained unexplored. In this study, plasma samples from 76 LC patients, 9 liver cancer patients, 11 pancreatic cancer patients, and 53 healthy controls (HCs) were collected and underwent metagenomic analyses by whole genome sequencing. The composition and relative abundance of the microbial profiles were significantly different between the LC patients and HCs. A distinct plasma-based microbial profile was observed in LC patients. By differential analysis using MaAslin, 40 significant species between LC patients and HCs were identified. Five species were selected as optimal circulating microbial biomarkers for LC. The constructed classifier based on these five species showed an AUC of 0.9592, 0.9131, and 0.8077 in the discovery, validation, and additional validation cohorts, respectively. Furthermore, metagenomic profiles of 25 lung tumor tissue and plasma paired samples were analyzed and compared. The microbial diversity was significantly increased in plasma compared with the tumor tissue. Among the 13 shared core microbial species, 10 had no difference between the tumor tissue and paired plasma. In conclusion, circulating microbial nucleic acids in the plasma have potential as biomarkers for LC liquid biopsies. The microbiome in the tumor tissue was one of the possible sources of circulating microbial nucleic acids.}, } @article {pmid39953490, year = {2025}, author = {Zhan, X and Tian, X and Zhang, C and Ye, J}, title = {A case of explosive community-acquired pneumonia and septic shock caused by Acinetobacter pittii.}, journal = {BMC pulmonary medicine}, volume = {25}, number = {1}, pages = {80}, doi = {10.1186/s12890-024-03457-0}, pmid = {39953490}, issn = {1471-2466}, mesh = {Humans ; *Shock, Septic/microbiology ; *Community-Acquired Infections/microbiology ; *Acinetobacter Infections/diagnosis/drug therapy/microbiology/complications ; *Acinetobacter/isolation & purification ; *Anti-Bacterial Agents/therapeutic use ; Male ; Pneumonia, Bacterial/microbiology/complications/diagnosis ; Middle Aged ; Female ; Aged ; Retrospective Studies ; }, abstract = {BACKGROUND: Acinetobacter pittii, belongs to the genus Acinetobacter, has a special pathogenesis and is commonly known as nosocomial pathogen; community infections are rare.

OBJECTIVE: To present a case study of community-acquired pneumonia and septic shock resulting from infection with Acinetobacter pittii and to investigate the diagnosis, clinical features and treatment of Acinetobacter pittii infection.

METHODS: The clinical features and prognosis of patients with Acinetobacter pittii, infection were analyzed retrospectively.

RESULTS: The sepsis caused by Acinetobacter pittii, was improved after treatment.

DISCUSSION AND CONCLUSION: Pneumonia caused by fully sensitive hypervirulent Acinetobacter pittii is rare, usually with acute course, severe illness and high mortality. It is necessary to identify the infectious agent as soon as possible, and early treatment can improve the success rate of treatment.}, } @article {pmid39952920, year = {2025}, author = {Jiang, Q and Cao, L and Han, Y and Li, S and Zhao, R and Zhang, X and Ruff, SE and Zhao, Z and Peng, J and Liao, J and Zhu, B and Wang, M and Lin, X and Dong, X}, title = {Cold seeps are potential hotspots of deep-sea nitrogen loss driven by microorganisms across 21 phyla.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {1646}, pmid = {39952920}, issn = {2041-1723}, mesh = {*Geologic Sediments/microbiology ; *Nitrogen/metabolism ; *Bacteria/genetics/metabolism/classification ; Seawater/microbiology ; Cold Temperature ; Metagenomics/methods ; Nitrogen Cycle/genetics ; Metagenome/genetics ; Ammonium Compounds/metabolism ; Phylogeny ; Oceans and Seas ; }, abstract = {Nitrogen bioavailability, governed by fixation and loss processes, is crucial for oceanic productivity and global biogeochemical cycles. The key nitrogen loss organisms-denitrifiers and anaerobic ammonium-oxidizing (anammox) bacteria-remain poorly understood in deep-sea cold seeps. This study combined geochemical measurements, [15]N stable isotope tracer analysis, metagenomics, metatranscriptomics, and three-dimensional protein structural simulations to explore cold-seeps nitrogen loss processes. Geochemical evidence from 359 sediment samples shows significantly higher nitrogen loss rates in cold seeps compared to typical deep-sea sediments, with nitrogen loss flux from surface sediments estimated at 4.96-7.63 Tg N yr[-1] (1.65-2.54% of global marine sediment). Examination of 147 million non-redundant genes indicates a high prevalence of nitrogen loss genes, including nitrous-oxide reductase (NosZ; 6.88 genes per million reads, GPM), nitric oxide dismutase (Nod; 1.29 GPM), and hydrazine synthase (HzsA; 3.35 GPM) in surface sediments. Analysis of 3,164 metagenome-assembled genomes expands the nitrous-oxide reducers by three phyla, nitric oxide-dismutating organisms by one phylum and two orders, and anammox bacteria by ten phyla going beyond Planctomycetota. These microbes exhibit structural adaptations and complex gene cluster enabling survival in cold seeps. Cold seeps likely are previously underestimated nitrogen loss hotspots, potentially contributing notably to the global nitrogen cycle.}, } @article {pmid39952771, year = {2025}, author = {Cantuti Gendre, J and Le Marrec, C and Chaillou, S and Omhover-Fougy, L and Landaud, S and Dugat-Bony, E}, title = {Exploring viral diversity in fermented vegetables through viral metagenomics.}, journal = {Food microbiology}, volume = {128}, number = {}, pages = {104733}, doi = {10.1016/j.fm.2025.104733}, pmid = {39952771}, issn = {1095-9998}, mesh = {*Metagenomics ; *Vegetables/virology/microbiology ; *Fermentation ; *Bacteriophages/genetics/isolation & purification/classification ; Microbiota ; Brassica/microbiology/virology ; Fermented Foods/microbiology/virology ; Bacteria/genetics/classification/isolation & purification/virology ; Biodiversity ; Daucus carota/microbiology/virology ; Food Microbiology ; Viruses/isolation & purification/classification/genetics ; Enterobacteriaceae/isolation & purification/genetics/virology/classification ; Metagenome ; Lactobacillaceae/isolation & purification/genetics/classification ; }, abstract = {Fermented vegetables are traditionally produced using the endogenous microorganisms present in raw ingredients. While the diversity of bacteria and fungi in fermented vegetables has been relatively well studied, phage communities remain largely unexplored. In this study, we collected twelve samples of fermented cabbage, carrot, and turnip after fermentation and analyzed the microbial and viral communities using shotgun and viral metagenomic approaches. Assessment of the viral diversity also benefited from epifluorescence microscopy to estimate viral load. The viral metagenomics approach targeted dsDNA, ssDNA, and RNA viruses. The microbiome of fermented vegetables was dominated by lactic acid bacteria and varied according to the type of vegetable used as raw material. The analysis of metagenome-assembled-genomes allowed the detection of 22 prophages of which 8 were present as free particles and therefore detected in the metaviromes. The viral community, estimated to range from 5.28 to 7.57 log virus-like particles per gram of fermented vegetables depending on the sample, was mainly composed of dsDNA viruses, although ssDNA and non-bacterial RNA viruses, possibly originating from the phyllosphere, were also detected. The dsDNA viral community, primarily comprising bacteriophages, varied depending on the type of vegetable used for fermentation. The bacterial hosts predicted for these phages mainly belonged to Lactobacillaceae and Enterobacteriaceae families. These results highlighted the complex microbial and viral composition of fermented vegetables, which varied depending on the three types of vegetables used as raw material. Further research is needed to deepen our understanding of the impact of these viruses on the microbial ecology of fermented vegetables and on the quality of the final products.}, } @article {pmid39952762, year = {2025}, author = {Li, Z and Liao, Y and Huang, C and Liu, J and Kong, X and Li, L and Li, Z and Gui, Y}, title = {Analyzing fungal community succession and its correlation to flavor compounds in the Cupei fermentation process of Sichuan shai vinegar.}, journal = {Food microbiology}, volume = {128}, number = {}, pages = {104718}, doi = {10.1016/j.fm.2024.104718}, pmid = {39952762}, issn = {1095-9998}, mesh = {*Fermentation ; *Acetic Acid/metabolism/analysis ; *Volatile Organic Compounds/metabolism/analysis/chemistry ; *Flavoring Agents/metabolism/chemistry ; *Fungi/classification/metabolism/genetics/isolation & purification ; China ; Gas Chromatography-Mass Spectrometry ; Amino Acids/metabolism/analysis ; Solid Phase Microextraction ; Food Microbiology ; Mycobiome ; Chromatography, High Pressure Liquid ; Condiments/microbiology/analysis ; }, abstract = {Sichuan Shai vinegar, a distinctive condiment from Southwest China, is produced through open-air solid-state fermentation, employing a unique Chinese herbal medicine mixture (Yaoqu) as the fermentation starter. Despite its culinary significance, the dynamics and roles of fungal communities within the Cupei fermentation phase remain understudied. This study employed high-performance liquid chromatography (HPLC) to quantify 11 organic acids and 17 amino acids, revealing a significant increase in organic acid content from 2.56 g/100 g-17.47 g/100 g dry weight and a gradual elevation in free amino acid content from 0.53 g/100 g-5.59 g/100 g throughout the fermentation process. Headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME/GC-MS) identified 85 volatile flavor compounds, predominantly consisting of 2 alcohols, 10 acids, 29 esters, 4 ketones, 6 aldehydes, and 14 other types. High-throughput sequencing facilitated the identification of key microorganisms, with Lichtheimia, Brettanomyces, Pichia, Saccharomyces, Kazachstania, and Syncephalastrum emerging as the most abundant fungal genera. Correlation analysis revealed significant positive correlations between 20 fungi and 11 organic acids, 24 fungi and 16 amino acids, and 50 fungi and 76 volatile flavor compounds. Notably, Lichtheimia, Pichia, and Brettanomyces were identified as the most influential in flavor metabolism. These findings elucidate the microbial metabolic mechanisms during Sichuan Shai vinegar fermentation, laying a foundation for further research and potential applications in vinegar production.}, } @article {pmid39952751, year = {2025}, author = {Sequino, G and Cobo-Diaz, JF and Valentino, V and Tassou, C and Volpe, S and Torrieri, E and Nychas, GJ and Álvarez Ordóñez, A and Ercolini, D and De Filippis, F}, title = {Environmental microbiome mapping in poultry processing chain and assessment of microbial dynamics in response to different storage conditions.}, journal = {Food microbiology}, volume = {128}, number = {}, pages = {104734}, doi = {10.1016/j.fm.2025.104734}, pmid = {39952751}, issn = {1095-9998}, mesh = {Animals ; *Microbiota ; *Bacteria/genetics/classification/isolation & purification ; *Chickens/microbiology ; *Food Storage ; Poultry Products/microbiology ; Food Packaging/methods ; Food Microbiology ; Poultry/microbiology ; Drug Resistance, Bacterial ; Temperature ; Meat/microbiology ; Brochothrix/genetics/isolation & purification ; Anti-Bacterial Agents/pharmacology ; Environmental Microbiology ; Metagenomics ; }, abstract = {Poultry production chain comprises a complex network involving various stages from rearing to the final distribution of poultry products. This study explores the intricate dynamics within this chain, using shotgun metagenomics, particularly focusing on taxonomic and functional composition of the microbiome, antibiotic resistance and virulence potential. Moreover, the study of the impact of different packaging and storage conditions provides insights into how diverse packaging strategies and storage temperature can impact the shelf-life of chicken meat. Microbiome mapping in poultry processing facility revealed the dominance of Brochothrix thermosphacta, Pseudomonas fragi and Psychrobacter immobilis on poultry-based products and industrial surfaces. Indeed, surfaces of equipment and tools have a significant impact on the microbial composition of the final food products. Furthermore, the study of the microbiome dynamics in chicken meat stored in different packaging (air, modified atmosphere, under vacuum) and temperatures (0, 4 and 10 °C) revealed temperature-dependent microbiota shifts in chicken meat, highlighting specific spoilage organisms (SSOs) in the different packaging methods. Additionally, our results showed that poultry-based products and industrial surfaces belonging to carcasses processing area hosted elevated levels of Antibiotic Resistance Genes, mainly associated with resistance to aminoglycosides, β-lactams, MLSPs (which includes macrolides, lincosamides, streptogramins and pleuromutilins) amphenicols and tetracyclines classes and several Virulence-associated genes related to adherence, biofilm, effector delivery system, motility, nutritional/metabolic factors and regulation. Finally, our findings underscored a notably mobile resistome, showing multiple AR class correlated with mobile elements. This poses a considerable risk, emphasizing the urgent need for proactive measures in addressing potential antibiotic resistance genes dissemination in the poultry chain.}, } @article {pmid39952592, year = {2025}, author = {Sun, T and Delaplace, P and Li, G and James, A and Pan, J and Zhang, J}, title = {Novel insights into the effect of arbuscular mycorrhizal fungi inoculation in soils under long-term biosolids application: emphasis on antibiotic and metal resistance genes, and mobile genetic elements.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {125846}, doi = {10.1016/j.envpol.2025.125846}, pmid = {39952592}, issn = {1873-6424}, abstract = {The application of biosolids can improve soil fertility and crop productivity but also accompanies risks of heavy metals and antibiotics introduction. In the presence of heavy metals contamination, using arbuscular mycorrhizal fungi (AMF) is a promising strategy to enhance soil microbial community stability and plant tolerance resistance to heavy metals, and to reduce the spread of antibiotic resistance genes (ARGs). The present study investigated the impacts of AMF inoculation on soil and plant heavy metal contents, and soil microbial communities by pot experiments. The results showed that AMF inoculation significantly enhanced plant biomass, and reduced soil and plant heavy metals contents. While AMF inoculation did not alter bacterial and fungal community compositions, it increased bacterial diversity at higher biosolids concentrations. Notably, AMF inoculation enhanced microbial network complexity and increased keystone taxa abundance. Furthermore, several beneficial microorganisms with high resistance to heavy metals were enriched in AMF-inoculated soils. Metagenomic analysis revealed a reduction in the mobile genetic element (MGE) gene IS91 in AMF-inoculated soils and an increase in heavy metal resistance genes compared to soils without AMF. The possibility of reduction in MGE-mediated spread of ARGs is one of the key findings of this study. As a caution, this study also detected enrichment of few ARGs in high biosolids-amended soils with AMF inoculation. Overall, AMF inoculation could be a valuable strategy in agriculture for mitigating the environmental risks associated with biosolids, heavy metals and antibiotic resistance, thereby promoting sustainable soil management and health.}, } @article {pmid39951448, year = {2025}, author = {Li, Q and Wu, X and Niu, X and Yu, Z and Fang, S and Chu, X and Zhu, J and Song, Q and Hou, C and Wei, X}, title = {Integrated metagenomic and metabolomic analyses of the effects of total flavonoids of Rhizoma Drynariae on reducing ovariectomized-induced osteoporosis by regulating gut microbiota and related metabolites.}, journal = {PloS one}, volume = {20}, number = {2}, pages = {e0317832}, doi = {10.1371/journal.pone.0317832}, pmid = {39951448}, issn = {1932-6203}, mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; Female ; *Ovariectomy ; *Osteoporosis/drug therapy/metabolism ; *Metabolomics ; Rats ; *Flavonoids/pharmacology ; *Bone Density/drug effects ; *Polypodiaceae ; Metagenomics ; Rats, Sprague-Dawley ; Drugs, Chinese Herbal/pharmacology ; Rhizome ; }, abstract = {TFRD has been widely used in China to treat osteoporosis (OP). However, the specific molecular mechanism of TFRD against OP has not been fully clarified. Our previous studies have also proved that TFRD could attenuate OP and the clinical equivalent dose of 67.5mg/kg/d is the effective dose for TFRD treating OP. Therefore, this study used 67.5mg/kg as the dosage of TFRD in combination with multi omics to investigate the mechanism of action of TFRD in the treatment of OP. The aim of this study was to further elucidate molecular mechanism of TFRD for treating OP based on metagenomic and metabolomic analyses. In this study, hematoxylin-eosin (H&E) staining, micro computed tomography (micro-CT) and bone mineral density (BMD) analysis were used to observe pharmacological effects of TFRD against ovariectomized (OVX)-induced OP. Subsequently, multiomics analysis including metagenomics, untargeted and short chain fatty acids (SCFAs) metabolomics were carried out to identify whether the anti-osteoporosis mechanism of TFRD correlated with gut microbiota and related metabolites. Our results indicate that TFRD could improve the microstructure and density of trabecular bone in OVX rats. 17 differential species, which mainly from Akkermansia, Bacteroides, and Phascolarctobacterium genus, 14 related differential metabolites and acetic acid in SCFAs were significantly altered by OVX and reversed by TFRD. Furthermore, according to results of untargeted metabolomics analysis, it was found that several metabolic pathways such as phenylalanine metabolism, phenylalanine, tyrosine and tryptophan biosynthesis and so on might play an important role in TFRD against OP. In order to further study the relationship between gut microbiota and related metabolites, spearman correlation analysis was used, and showed that gut microbiota such as Akkermansia muciniphila might be closely related to several metabolites and metabolic pathways. These findings suggest that TFRD treatment could reduce the effects of OVX-induced OP by altering community composition and abundance of gut microbiota, regulating metabolites and SCFAs. It was speculated that the gut microbiota especially Akkermansia muciniphila and related metabolites might play an important role in TFRD against OP, and deserve further study by follow-up experiment. This conclusion provides new theoretical support for mechanism research of TFRD against OP.}, } @article {pmid39951402, year = {2025}, author = {Reiss, RA and Guerra, PA and Makhnin, O and Kellom, M}, title = {Whole metagenome sequencing and 16S rRNA gene amplicon analyses reveal the complex microbiome responsible for the success of enhanced in-situ reductive dechlorination (ERD) of a tetrachloroethene-contaminated Superfund site.}, journal = {PloS one}, volume = {20}, number = {2}, pages = {e0306503}, doi = {10.1371/journal.pone.0306503}, pmid = {39951402}, issn = {1932-6203}, mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Biodegradation, Environmental ; *Groundwater/microbiology ; *Metagenome ; *Tetrachloroethylene/metabolism ; Water Pollutants, Chemical/metabolism ; Halogenation ; Metagenomics/methods ; Bacteria/genetics/metabolism/classification ; New Mexico ; }, abstract = {The North Railroad Avenue Plume (NRAP) Superfund site in New Mexico, USA exemplifies successful chlorinated solvent bioremediation. NRAP was the result of leakage from a dry-cleaning that operated for 37 years. The presence of tetrachloroethene biodegradation byproducts, organohalide respiring genera (OHRG), and reductive dehalogenase (rdh) genes detected in groundwater samples indicated that enhanced reductive dechlorination (ERD) was the remedy of choice. This was achieved through biostimulation by mixing emulsified vegetable oil into the contaminated aquifer. This report combines metagenomic techniques with site monitoring metadata to reveal new details of ERD. DNA extracts from groundwater samples collected prior to and at four, 23 and 39 months after remedy implementation were subjected to whole metagenome sequencing (WMS) and 16S rRNA gene amplicon (16S) analyses. The response of the indigenous NRAP microbiome to ERD protocols is consistent with results obtained from microcosms, dechlorinating consortia, and observations at other contaminated sites. WMS detects three times as many phyla and six times as many genera as 16S. Both techniques reveal abundance changes in Dehalococcoides and Dehalobacter that reflect organohalide form and availability. Methane was not detected before biostimulation but appeared afterwards, corresponding to an increase in methanogenic Archaea. Assembly of WMS reads produced scaffolds containing rdh genes from Dehalococcoides, Dehalobacter, Dehalogenimonas, Desulfocarbo, and Desulfobacula. Anaerobic and aerobic cometabolic organohalide degrading microbes that increase in abundance include methanogenic Archaea, methanotrophs, Dechloromonas, and Xanthobacter, some of which contain hydrolytic dehalogenase genes. Aerobic cometabolism may be supported by oxygen gradients existing in aquifer microenvironments or by microbes that produce O2 via microbial dismutation. The NRAP model for successful ERD is consistent with the established pathway and identifies new taxa and processes that support this syntrophic process. This project explores the potential of metagenomic tools (MGT) as the next advancement in bioremediation.}, } @article {pmid39951352, year = {2025}, author = {Li, Q and Tan, D and Xiong, S and Yu, K and Su, Y and Zhu, W}, title = {Time-restricted feeding promotes glucagon-like peptide-1 secretion and regulates appetite via tryptophan metabolism of gut Lactobacillus in pigs.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2467185}, doi = {10.1080/19490976.2025.2467185}, pmid = {39951352}, issn = {1949-0984}, mesh = {Animals ; *Glucagon-Like Peptide 1/metabolism/blood ; *Gastrointestinal Microbiome ; Swine ; *Tryptophan/metabolism ; *Lactobacillus/metabolism ; *Appetite/physiology ; Enteroendocrine Cells/metabolism ; Feeding Behavior ; Hypothalamus/metabolism ; }, abstract = {Previous clinical trials have shown that time-restricted feeding can be involved in regulating the metabolic health of humans and animals. However, the underlying mechanism has not been fully explored. In this study, the pig model was employed to simulate four prevalent human eating habits, with the aim of investigating the impact of gut microbiota and microbial metabolites on gut hormone secretion and appetite regulation. Compared to the ad libitum feeding (ALF) pattern, three time-restricted feeding patterns reduced total food intake and eating time. Meanwhile, three time-restricted feeding patterns induced elevated levels of serum and hypothalamic glucagon-like peptide-1 (GLP-1), while suppressing reward-related circuits in the hypothalamus. It is noteworthy that the early time-restricted feeding (eTRF) pattern increased the number of intestinal enteroendocrine cells (EECs) compared to ALF. Metagenomic and metabonomic analyses revealed that three time-restricted feeding patterns induced colonization of Lactobacillus and significantly increased the levels of its metabolite, indole-3-lactic acid (ILA). Dietary supplementation with ILA exhibited an increasing trend in fasting serum GLP-1 level of piglets. In vitro studies with pig intestinal organoids showed the Lactobacillus metabolite ILA enhanced GLP-1 secretion through the promotion of intestinal stem cell differentiation into EECs, rather than activating the ability of EECs to secrete GLP-1. Overall, time-restricted feeding promoted GLP-1 secretion and affected long-term appetite regulation by promoting the colonization of Lactobacillus and modulating microbial tryptophan metabolism.}, } @article {pmid39950859, year = {2025}, author = {Ma, Y and Zhang, M and Wang, Z and Cao, L and Li, Y and Wan, Z and Kane, Y and Wang, G and Li, X and Zhang, C}, title = {Short-term antiretroviral therapy may not correct the dysregulations of plasma virome and cytokines induced by HIV-1 infection.}, journal = {Virulence}, volume = {}, number = {}, pages = {2467168}, doi = {10.1080/21505594.2025.2467168}, pmid = {39950859}, issn = {2150-5608}, abstract = {An expansion of plasma anelloviruses and dysregulation of inflammation was associated with HIV-1 infection. However, how antiretroviral therapy (ART) affects the dynamics of plasma virome and cytokine profile remains largely unknown. To characterize the dynamics of plasma virome and cytokines in HIV-1-infected individuals before and during the first year of ART, a cohort of 26 HIV-1-infected individuals and 19 healthy controls was recruited. Blood samples were collected and subjected to metagenomic analysis and the measurement of 27 cytokines. Metagenomic analysis revealed an increased abundance and prevalence of human pegivirus type 1 (HPgV-1) and a slightly decreased diversity and abundance of anellovirus in plasma of HIV-1-infected individuals after ART. No obvious impact was observed on other plasma commensal viruses. Increased abundance and prevalence of HPgV-1 were further confirmed by RT-qPCR assay in a larger cohort of 114 HIV-1-infected individuals. Notably, most dysregulated cytokines were not fully restored by ART, with extremely abnormal levels of IL-10, GM-CSF, VEGF, and eotaxin, and a significantly increased level of plasma I-FABP. Anelloviruses showed significantly negative correlations with other commensal viruses except HPgV-1, but had positive corrections with several anti-inflammatory and Th1 cytokines. These results suggest that short-term ART may not significantly correct the virome and cytokine dysregulations induced by HIV-1 infection. The results highlight a need for further investigation into the long-term effect of ART on virome and cytokine profile in HIV-1-infected individuals.}, } @article {pmid39950834, year = {2025}, author = {Ng, HY and Zhang, L and Tan, JT and Hui, RWH and Yuen, MF and Seto, WK and Leung, WK and Cheung, KS}, title = {Gut Microbiota Predicts Treatment Response to Empagliflozin Among MASLD Patients Without Diabetes Mellitus.}, journal = {Liver international : official journal of the International Association for the Study of the Liver}, volume = {45}, number = {3}, pages = {e70023}, doi = {10.1111/liv.70023}, pmid = {39950834}, issn = {1478-3231}, support = {//General Research Fund, Research Grant Council, The Government of the Hong Kong Special Administrative Region/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; *Glucosides/therapeutic use ; Middle Aged ; Prospective Studies ; *Benzhydryl Compounds/therapeutic use ; Non-alcoholic Fatty Liver Disease/drug therapy/microbiology ; Treatment Outcome ; Magnetic Resonance Imaging ; Feces/microbiology ; Sodium-Glucose Transporter 2 Inhibitors/therapeutic use ; Logistic Models ; }, abstract = {BACKGROUND AND AIM: We aimed to investigate whether gut microbiota could predict the treatment response to pharmacological agents among metabolic dysfunction-associated steatotic liver disease (MASLD) patients without diabetes mellitus (DM), as data are lacking.

METHODS: We prospectively followed up non-diabetic MASLD patients who used empagliflozin. Clinical, anthropometric, laboratory assessments and magnetic resonance imaging-proton density fat fraction (MRI-PDFF) were performed from baseline to week 52 (EOT). Baseline stool samples were collected, and shotgun DNA metagenomic sequencing was performed to profile microbiome. The primary outcome was treatment response to empagliflozin at EOT, defined as MRI-PDFF decline ≥ 30% at EOT from baseline. Linear discriminant analysis [LDA] effect size was used to identify putative bacterial species. Multivariable logistic regression was used to derive adjusted odds ratio (aOR) of outcome with bacterial species by adjusting for clinical factors.

RESULTS: Twenty-two (48.9%) of 45 patients (median age: 56.9 years [IQR: 51.0-63.2]; male: 23 [51.1%]) achieved treatment response at EOT. There was difference in alpha diversity (Shannon index: p < 0.001; Simpson index: p = 0.001) and beta diversity (p = 0.048) in baseline microbiome between treatment response and non-response groups. Faecalibacterium prausnitzii (log10LDAscore = 4.27), Lachnospira pectinoschiza (log10LDAscore = 3.99), Anaerostipes hadrus (log10LDAscore = 3.98), Roseburia faecis (log10LDAscore = 3.97), Roseburia inulinivorans (log10LDAscore = 3.58) and Agathobaculum butyriciproducens (log10LDAscore = 2.77) were enriched in the treatment response group. L. pectinoschiza (aOR: 34.1; p = 0.015), A. hadrus (aOR:35.0; p = 0.032) and A. butyriciproducens (aOR:22.3; p = 0.023) independently predicted treatment response but not clinical factors. These three species collectively predicted treatment response with AUROC of 0.89 (95% CI: 0.80-0.99).

CONCLUSIONS: Certain gut bacterial species, particularly the combination of A. hadrus, L. pectinoschiza and A. butyriciproducens, may predict treatment response to empagliflozin in MAFLD patients without DM.}, } @article {pmid39950813, year = {2025}, author = {Seguel Suazo, K and Nierychlo, M and Kondrotaite, Z and Petriglieri, F and Peces, M and Singleton, C and Dries, J and Nielsen, PH}, title = {Diversity and abundance of filamentous and non-filamentous "Leptothrix" in global wastewater treatment plants.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0148524}, doi = {10.1128/aem.01485-24}, pmid = {39950813}, issn = {1098-5336}, abstract = {Species belonging to the genus Leptothrix are widely distributed in the environment and in activated sludge (AS) wastewater treatment plants (WWTPs). They are commonly found in iron-rich environments and reported to cause filamentous bulking in WWTPs. In this study, the diversity, distribution, and metabolic potential of the most prevalent Leptothrix spp. found in AS worldwide were studied. Our 16S rRNA amplicon survey showed that Leptothrix belongs to the general core community of AS worldwide, comprising 32 species with four species being most commonly found. Their taxonomic classification was re-evaluated based on both 16S rRNA gene and genome-based phylogenetic analysis showing that three of the most abundant "Leptothrix" species represented species in three other genera, Rubrivivax, Ideonella, and the novel genus, Ca. Intricatilinea. New fluorescence in situ hybridization (FISH) probes revealed rod-shaped morphology for the novel Ca. Rubrivivax defluviihabitans and Ca. Ideonella esbjergensis, while filamentous morphology was found only for Ca. Intricatilinea gracilis. Analysis of high-quality metagenome-assembled genomes revealed metabolic potential for aerobic growth, fermentation, storage of intracellular polymers, partial denitrification, photosynthesis, and iron reduction. FISH in combination with Raman microspectroscopy confirmed the in situ presence of chlorophyll and carotenoids in Ca. Rubrivivax defluviihabitans and Ca. Intricatilinea gracilis. This study resolves the taxonomy of abundant but poorly classified "Leptothrix" species, providing important insights into their diversity, morphology, and function in global AS wastewater treatment systems.IMPORTANCEThe genus Leptothrix has been extensively studied and described since the 1880s, with six species currently described but with the majority uncultured and undescribed. Some species are assumed to have a filamentous morphology and can cause settling problems in wastewater treatment plants (WWTPs). Here, we revised the classification of the most abundant Leptothrix spp. present in WWTPs across the world, showing that most belong to other genera, such as Rubrivivax and Ideonella. Furthermore, most do not have a filamentous morphology and are not problematic in WWTPs as previously believed. Metabolic reconstruction, including some traits validated in situ by the application of new fluorescence in situ hybridization probes and Raman microspectroscopy, provided additional insights into their metabolism. The study has contributed to a better understanding of the diversity, morphology, and function of "Leptothrix," which belong to the abundant core community across global activated sludge WWTPs.}, } @article {pmid39950811, year = {2025}, author = {Kwon, J and Tanner, W and Kong, Y and Wade, M and Bitler, C and Chiavegato, MB and Pettigrew, MM}, title = {Prospective comparison of the digestive tract resistome and microbiota in cattle raised in grass-fed versus grain-fed production systems.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0073824}, doi = {10.1128/msphere.00738-24}, pmid = {39950811}, issn = {2379-5042}, abstract = {Most antimicrobials sold in the United States are used in food animals. Farm management practices contribute to antibacterial resistance (AR). Controversially, grass-fed diets have been recommended over grain-fed diets to reduce AR in beef cattle. Ionophore feed additives (non-therapeutic antibiotics that enhance feed efficiency) may contribute to AR development. We used shotgun metagenomic sequencing of fecal swabs to prospectively compare the cattle gastrointestinal resistome and microbiota in two different production systems over five periods from pre-weaning to pre-harvest. Cattle were grass-fed and pasture-raised (system A, n = 33) or grain-fed with ionophore additives in feedlots (system B, n = 34). System A cattle averaged 639 lb and 22.8 months of age, and system B cattle averaged 1,173 lb and 12.4 months of age preharvest. In total, 367 antibiotic resistance genes (ARGs) and 329 bacterial species were identified. The resistome of system A cattle had higher alpha diversity than system B cattle over their lifespan (P = 0.008). Beta-diversity estimates indicated overlap in the pre-weaning resistome and microbiota in both systems, which diverged post-weaning, with increases in several medically important ARGs when system B cattle transitioned to a grain diet. Analysis of compositions of microbiomes with bias correction indicated that levels of tetracycline, macrolide, aminoglycoside, beta-lactam, and bacitracin ARGs were significantly higher in system B cattle pre-harvest. Resistome changes were highly correlated with bacterial community changes (Procrustes, M[2] = 0.958; P = 0.001). Potentially modifiable farm management strategies, including diet and ionophores, may influence abundance and diversity of ARGs in fecal samples from cattle.IMPORTANCEAntibiotic resistance is a One Health threat. More antibiotics are used in agriculture than in human medicine. We compared the relative abundance of antibiotic resistance genes (ARGs) and bacterial species in cattle raised in two different cattle production systems (grass- and grain-fed). Fecal swab samples were collected at five time points spanning pre-weaning and prior to harvest. The antibiotic resistance gene and bacterial communities were relatively similar in the pre-weaning period when cattle in both systems were milking and on pasture. Resistance genes and bacterial communities diverged post-weaning when system B cattle were given a grain diet with feed additives for growth promotion containing non-medically important antibiotics (i.e., ionophores). The levels of medically important ARGs (e.g., macrolides) increased in system B grain-fed cattle post-weaning and were higher than in system A just prior to slaughter. These data provide additional evidence that farm management strategies impact the level of antibiotic resistance.}, } @article {pmid39950541, year = {2025}, author = {Akter, MS and Punom, NJ and Eshik, MME and Ahmmed, S and Rabbane, MG and Rahman, MS}, title = {Investigation of Tilapia (Oreochromis niloticus) Mortality Events Targeting Tilapia Lake Virus Disease (TiLVD) in Bangladesh.}, journal = {Veterinary medicine and science}, volume = {11}, number = {2}, pages = {e70262}, doi = {10.1002/vms3.70262}, pmid = {39950541}, issn = {2053-1095}, support = {//Grant for Advanced Research in Education (GARE)/ ; //Ministry of Education/ ; 37.20.0000.004.033.020.2016.673//Government of the People's Republic of Bangladesh/ ; }, mesh = {Animals ; Bangladesh/epidemiology ; *Fish Diseases/virology/mortality/epidemiology ; *Cichlids ; DNA Virus Infections/veterinary/virology/mortality/epidemiology ; Aquaculture ; }, abstract = {BACKGROUND: Tilapia lake virus (TiLV) is an emerging threat to the global tilapia industry. In early 2017, FAO declared that Bangladesh was in a high-risk zone of TiLV disease (TiLVD) spread.

OBJECTIVES: Considering the current scenario, the present work was designed to investigate the occurrence of TiLV in cultured Nile tilapia (Oreochromis niloticus) causing TiLVD in Bangladesh.

METHODS: In this study, several unusual tilapia mortality incidences were investigated. A total of 102 pooled organ samples of 102 tilapia fish were collected from 34 ponds of 25 farms in the regions of 12 Upazilas in Bangladesh from May to October 2019. As a part of the classical approach, histopathological analysis was performed. For molecular identification, both conventional and real-time PCR were used as diagnostic tools to identify TiLV in farm-raised Nile tilapia.

RESULTS: A total of 12 representative organ samples did not show any pathognomonic lesions related to TiLV infection in histopathological analysis. Conventional and real-time PCR assays yielded negative results for TiLV.

CONCLUSIONS: In our investigation, no trace of TiLV was detected in the studied samples. A large-scale study involving a broader range of samples collected across Bangladesh, along with the application of a viral metagenomics approach, could provide valuable insights into the unusual mortalities of tilapia in the country.}, } @article {pmid39949721, year = {2025}, author = {Neidhöfer, C and Klein, N and Yürüktümen, A and Hattenhauer, T and Mispelbaum, R and Bode, C and Holderried, TAW and Hoerauf, A and Parčina, M}, title = {Retrospective analysis of 300 microbial cell-free DNA sequencing results in routine blood stream infection diagnostics.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1504262}, pmid = {39949721}, issn = {2235-2988}, mesh = {Humans ; Retrospective Studies ; *Bacteremia/diagnosis/microbiology ; Male ; Female ; *Cell-Free Nucleic Acids/blood ; *Metagenomics/methods ; Middle Aged ; Aged ; Adult ; Bacteria/genetics/isolation & purification/classification ; Aged, 80 and over ; Sequence Analysis, DNA ; Young Adult ; DNA, Bacterial/genetics ; }, abstract = {INTRODUCTION: Bloodstream infections are a critical challenge worldwide due to the slow turnaround time of conventional microbiological tests for detecting bacteremia in septic patients. Noscendo GmbH (Duisburg, Germany) has developed the CE/IVD pipeline DISQVER for clinical metagenomics testing based on cell-free DNA (cfDNA) from blood samples to address this issue.

METHODS: We conducted a retrospective study to evaluate the diagnostic utility of this methodological setup in improving treatment decisions since it was introduced into our clinical setting. Between January 2021 and June 2022, the first 300 cases in which DISQVER was applied at our university hospital were collected and analyzed. The results were compared with routine microbiology test results, clinical picture, associated treatment decisions, and clinical course.

RESULTS: Our findings demonstrate that DISQVER results where no pathogen was reported effectively ruled out bacterial bloodstream infections, whereas positive results varied in their usefulness. While the metagenomic approach proved highly valuable for detecting non-culturable and rare pathogens, its utility was limited in cases where detected microorganisms were commonly associated with the microbiota.

DISCUSSION: Performing on-site analysis might mitigate delays resulting from logistical challenges and might help optimizing antibiotic stewardship. Once prompt results can be obtained, the relevance of incorporating molecular resistograms will become more pronounced. Further, the specific patient subgroups that most benefit from this analysis must be worked out. Guiding clinicians in identifying the infection focus based on the detected bacteria would significantly improve patient care. Lastly, evidence of filamentous fungi must be diligently followed up.}, } @article {pmid39948721, year = {2025}, author = {Douillard, FP and Lanzoni, O and Duplouy, A and Lindström, M}, title = {Insects as Natural Hosts, Vectors and Reservoirs of Botulinum Neurotoxin-Producing Clostridia and Their Non-Toxinogenic Counterparts: Preliminary Evidence.}, journal = {Environmental microbiology}, volume = {27}, number = {2}, pages = {e70053}, doi = {10.1111/1462-2920.70053}, pmid = {39948721}, issn = {1462-2920}, support = {328944//Academy of Finland/ ; 340705//Academy of Finland/ ; 683099/ERC_/European Research Council/International ; }, mesh = {Animals ; *Phylogeny ; *Clostridium/genetics/metabolism/classification ; *Botulinum Toxins/genetics/metabolism ; *Botulism/microbiology ; RNA, Ribosomal, 16S/genetics ; Insecta/microbiology ; Insect Vectors/microbiology ; Butterflies/microbiology ; }, abstract = {Insects play a significant role in the transmission and spread of bacterial pathogens that cause various diseases in humans and animals. The relationship among insects, bacterial pathogens and diseases is complex and depends on the specificity of the pathogens. Some clostridial species produce botulinum neurotoxin (BoNT), which is responsible for paralytic botulism. However, the ecology of these bacterial species and their non-toxinogenic phylogenetic counterparts remains unclear. This study specifically explored in silico evidence of the interconnection between BoNT-producing Clostridia and their non-toxinogenic counterparts with insects. Based on literature meta-analysis, the mining of 16S rRNA amplicon and metagenomic sequencing datasets and a pilot feeding experiment in the Glanville fritillary butterfly, Melitaea cinxia, we propose that BoNT-producing Clostridia and their non-toxinogenic phylogenetic counterparts are carried internally and/or externally in different insect orders. While previous case studies have indicated associations between Clostridia and insects, this work provides a more comprehensive view of their occurrence. It also highlights the need for further multidisciplinary investigations to characterise the natural ecology of BoNT-producing Clostridia and their non-toxinogenic counterparts in insects.}, } @article {pmid39948426, year = {2025}, author = {Zang, T and Zhang, Z and Liu, W and Yin, L and Zhao, S and Liu, B and Ma, L and Li, Z and Tang, X}, title = {Structural and functional changes in the oral microbiome of patients with craniofacial microsomia.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {5400}, pmid = {39948426}, issn = {2045-2322}, support = {2021-I2M-1-068//Chinese Academy of Medical Science Innovation Fund for Medical Sciences/ ; }, mesh = {Humans ; Male ; *Microbiota ; Female ; *Mouth/microbiology ; *Saliva/microbiology/metabolism ; RNA, Ribosomal, 16S/genetics ; Child ; Goldenhar Syndrome/microbiology ; Dysbiosis/microbiology ; Adolescent ; Adult ; Bacteria/classification/genetics/isolation & purification/metabolism ; Young Adult ; Metagenomics/methods ; Child, Preschool ; Case-Control Studies ; }, abstract = {Craniofacial microsomia (CFM) is the second most common congenital craniofacial deformity, presenting diverse clinical manifestations and treatments that may influence oral bacteria dysbiosis (OBD). However, research linking CFM to OBD is limited. Saliva samples were collected from 20 patients with CFM and 24 controls. We compared oral microflora and gene function using 16 S ribosomal RNA sequencing and metagenomics. We also evaluated the correlation between CFM clinical phenotypes and microbiota community structure. Patients with CFM demonstrated greater richness and evenness in their oral microflora. The dominant genera included several pathogenic species, such as Actinomyces, Fusobacterium, and Prevotella. Notably, the severity of CFM correlated positively with the abundance of Neisseria and Porphyromonas. Upregulated pathways were primarily linked to biotin and amino acid metabolism, such as Tryptophan metabolism and Lysine degradation, and further underscored the need for focused oral health interventions in this population. This study is the first to indicate that CFM patients exhibit unique oral bacterial dysbiosis, marked by a higher presence of opportunistic pathogens and increased pathways related to oral and systemic health. These findings highlight the importance of monitoring oral health in patients with CFM.}, } @article {pmid39948184, year = {2025}, author = {Chen, A and Yu, Q and Zheng, L and Yi, J and Tang, Z and Ge, H and Ning, Y and Yin, N and Xie, Y and Chen, S and Shi, W and She, X and Xiang, J and Tang, J}, title = {Dose-dependent M2 macrophage polarization induced by Talaromyces marneffei promotes lung cancer cell growth via arginine-ornithine-cycle activation.}, journal = {Medical microbiology and immunology}, volume = {214}, number = {1}, pages = {11}, pmid = {39948184}, issn = {1432-1831}, support = {81972198, 81773147//National Natural Science Foundation of China/ ; 2019SK2253//Key Research and Development Program of Hunan Province of China/ ; ZLXD2017004//Central South University/ ; ZLXD2017004//Central South University/ ; kq2208299//National Natural Science Foundation of Changsha/ ; }, mesh = {*Talaromyces ; Humans ; Animals ; *Macrophages/microbiology/immunology ; *Lung Neoplasms/microbiology ; Mice ; *Arginine/metabolism ; *Ornithine/metabolism/analogs & derivatives/pharmacology ; Carcinoma, Non-Small-Cell Lung/microbiology/pathology ; Cell Proliferation ; Macrophage Activation ; Female ; Male ; Metagenomics ; Disease Models, Animal ; Cell Line, Tumor ; Mycobiome ; Lung/microbiology/pathology ; }, abstract = {It is now widely accepted that lungs are colonized by diverse microbes. Dysbiosis of the lung microbiota has been found to affect the progression of lung cancer. Fungi are a major component of the lung microbiota. However, the causal links between the mycobiome or specific species and lung cancer remain unclear. To address this, we conducted a study examining the composition of lung mycobiota in Non-Small-Cell Lung Cancer (NSCLC) patients using shotgun metagenomics. The differential taxa between NSCLC patients and non-cancer controls were defined by the Wilcoxon rank-sum test. Nested PCR was used to measure the abundance of specific fungal species. Metabolomics analysis was performed to investigate the metabolic reprogramming of macrophages triggered by intracellular infection of specific fungal species. In vitro and in vivo assays were conducted to examine the effect of the specific fungus on cancer cell growth. Our findings showed that Ascomycota, Microsporidia and Mucoromycota were the dominant fungal taxa in the lungs. Talaromyces marneffei (T.marneffei) was the most significantly differential fungus between lung cancer patients and non-cancer controls, with its abundance positively correlated with lung cancer. The lung cancer animal model demonstrated that T.marneffei promotes lung cancer growth. Our study also demonstrated that T.marneffei promotes lung cancer cell growth by inducing dose-dependent M2 macrophage polarization through arginine-ornithine-cycle activation. Furthermore, inhibition of arginase can reduce M2 polarization of macrophages and the survival of T. marneffei inside macrophages. In summary, our study reveals that the increased abundance of T. marneffei in the lungs affects lung cancer cell growth by triggering arginine-induced M2 polarization of macrophages. These findings provide potential drug targets for the development of therapies aimed at targeting the survival of fungi inside macrophages in the fight against cancer.}, } @article {pmid39947845, year = {2025}, author = {Jeon, Y and Struewing, I and Clauson, K and Reetz, N and Fairchild, N and Goeres-Priest, L and Dreher, TW and Labiosa, R and Carpenter, KD and Rosen, BH and Villegas, EN and Lu, J}, title = {Dominant Dolichospermum and microcystin production in Detroit Lake (Oregon, USA).}, journal = {Harmful algae}, volume = {142}, number = {}, pages = {102802}, doi = {10.1016/j.hal.2025.102802}, pmid = {39947845}, issn = {1878-1470}, mesh = {*Lakes/microbiology/chemistry ; *Microcystins/metabolism ; Cyanobacteria/metabolism/genetics ; Harmful Algal Bloom ; }, abstract = {The excessive growth of harmful cyanobacteria, including Dolichospermum (formerly known as Anabaena), in freshwater bodies has become a pressing global concern. However, detailed information about the role of Dolichospermum in shaping bloom dynamics and producing cyanotoxins is limited. In this study, a bloom event dominated by Dolichospermum spp. at Detroit Lake (Oregon, USA) was examined from 2019 to 2021. In 2019, early summer cyanobacterial community succession reached up to 8.7 % of total phytoplankton abundance. Dolichospermum was the major microcystin (MC)-producing genus, with peak MC levels of 7.34 μg L[-1]. The presence of MCs was strongly correlated with the abundance of Dolichospermum (r = 0.84, p < 0.05) and MC synthetase gene, mcyE-Ana (r = 0.63, p < 0.05). Metabolic analyses further showed that the presence of nif/pst genes linked to nitrogen and phosphorus metabolism was dominated by Dolichospermum from the bloom onset until September. In addition, the abundance of Dolichospermum was significantly correlated with the abundance of nitrogen-fixing nif-Ana gene (r = 0.62, p < 0.05). As the lake experienced a longer N and P scarcity period (May to September), the N2-fixing Dolichospermum was able to dominate over other non-fixing cyanobacteria present, including Microcystis and Planktothrix. Overall, our results facilitate a better understanding of the organism and will help working toward managing/predicting future blooms.}, } @article {pmid39947314, year = {2025}, author = {Zhang, X and Chen, Y and Xia, Y and Lin, S and Zhou, X and Pang, X and Yu, J and Sun, L}, title = {Oral microbiota in colorectal cancer: Unraveling mechanisms and application potential.}, journal = {Life sciences}, volume = {}, number = {}, pages = {123462}, doi = {10.1016/j.lfs.2025.123462}, pmid = {39947314}, issn = {1879-0631}, abstract = {Colorectal cancer (CRC), with a rising prevalence, is the third most commonly diagnosed cancer and the third leading cause of cancer-related death. Studies have shown that a complex interplay between the development of CRC and alterations in the oral microbiome. Recent advancements in genomics and metagenomics have highlighted the significant roles of certain oral microbes, particularly Porphyromonas gingivalis (P. gingivalis) and Fusobacterium nucleatum (F. nucleatum), in the progression of CRC. However, the detailed mechanisms by which the oral microbiota influence CRC development remain unclear. This review aims to elucidate the role of oral microbiota in CRC progression, evaluate their potential as biomarkers, and explore therapeutic strategies targeting these microbes. This review offers insights into the mechanisms underlying the interaction between oral microbiota and CRC, underscoring the potential of oral microbes as diagnostic and prognostic biomarkers, as well as therapeutic targets. Future research should focus on clarifying the exact pathways and developing innovative therapeutic strategies to enhance the diagnosis and treatment.}, } @article {pmid39947201, year = {2025}, author = {Yang, SNN and Kertesz, MA and Coleman, NV}, title = {Phylogenetic and Functional Diversity of Soluble Di-Iron Monooxygenases.}, journal = {Environmental microbiology}, volume = {27}, number = {2}, pages = {e70050}, doi = {10.1111/1462-2920.70050}, pmid = {39947201}, issn = {1462-2920}, support = {//University of Sydney/ ; }, mesh = {*Phylogeny ; *Mixed Function Oxygenases/genetics/metabolism/chemistry ; *Bacteria/enzymology/genetics/classification ; Biodegradation, Environmental ; Gene Transfer, Horizontal ; Substrate Specificity ; Oxidation-Reduction ; Oxygenases/genetics/metabolism ; Bacterial Proteins/genetics/metabolism/chemistry ; Iron/metabolism ; }, abstract = {Monooxygenase (MO) enzymes are responsible for the oxidation of hydrocarbons and other compounds in the carbon and nitrogen cycles, are important for the biodegradation of pollutants and can act as biocatalysts for chemical manufacture. The soluble di-iron monooxygenases (SDIMOs) are of interest due to their broad substrate range, high enantioselectivity and ability to oxidise inert substrates such as methane. Here, we re-examine the phylogeny and functions of these enzymes, using recent advances in the field and expansions in sequence diversity in databases to highlight relationships between SDIMOs and revisit their classification. We discuss the impact of horizontal gene transfer on SDIMO phylogeny, the potential of SDIMOs for the biodegradation of pollutants and the importance of heterologous expression as a tool for understanding SDIMO functions and enabling their use as biocatalysts. Our analysis highlights current knowledge gaps, most notably, the unknown substrate ranges and physiological roles of enzymes that have so far only been detected via genome or metagenome sequencing. Enhanced understanding of the diversity and functions of the SDIMO enzymes will enable better prediction and management of biogeochemical processes and also enable new applications of these enzymes for biocatalysis and bioremediation.}, } @article {pmid39947184, year = {2025}, author = {Heinken, A and Hulshof, TO and Nap, B and Martinelli, F and Basile, A and O'Brolchain, A and O'Sullivan, NF and Gallagher, C and Magee, E and McDonagh, F and Lalor, I and Bergin, M and Evans, P and Daly, R and Farrell, R and Delaney, RM and Hill, S and McAuliffe, SR and Kilgannon, T and Fleming, RMT and Thinnes, CC and Thiele, I}, title = {A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites.}, journal = {Cell systems}, volume = {}, number = {}, pages = {101196}, doi = {10.1016/j.cels.2025.101196}, pmid = {39947184}, issn = {2405-4720}, abstract = {Genome-scale modeling of microbiome metabolism enables the simulation of diet-host-microbiome-disease interactions. However, current genome-scale reconstruction resources are limited in scope by computational challenges. We developed an optimized and highly parallelized reconstruction and analysis pipeline to build a resource of 247,092 microbial genome-scale metabolic reconstructions, deemed APOLLO. APOLLO spans 19 phyla, contains >60% of uncharacterized strains, and accounts for strains from 34 countries, all age groups, and multiple body sites. Using machine learning, we predicted with high accuracy the taxonomic assignment of strains based on the computed metabolic features. We then built 14,451 metagenomic sample-specific microbiome community models to systematically interrogate their community-level metabolic capabilities. We show that sample-specific metabolic pathways accurately stratify microbiomes by body site, age, and disease state. APOLLO is freely available, enables the systematic interrogation of the metabolic capabilities of largely still uncultured and unclassified species, and provides unprecedented opportunities for systems-level modeling of personalized host-microbiome co-metabolism.}, } @article {pmid39947133, year = {2025}, author = {Elmassry, MM and Sugihara, K and Chankhamjon, P and Kim, Y and Camacho, FR and Wang, S and Sugimoto, Y and Chatterjee, S and Chen, LA and Kamada, N and Donia, MS}, title = {A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules.}, journal = {Cell host & microbe}, volume = {33}, number = {2}, pages = {218-234.e12}, doi = {10.1016/j.chom.2025.01.002}, pmid = {39947133}, issn = {1934-6069}, mesh = {*Gastrointestinal Microbiome ; Humans ; Mice ; Animals ; *Inflammatory Bowel Diseases/microbiology ; Feces/microbiology ; Crohn Disease/microbiology ; Disease Models, Animal ; Multigene Family ; Colitis/microbiology ; Metagenomics ; Clostridium/genetics ; Mice, Inbred C57BL ; Female ; }, abstract = {Gut microbiome changes have been associated with several human diseases, but the molecular and functional details underlying these associations remain largely unknown. Here, we performed a meta-analysis of small molecule biosynthetic gene clusters (BGCs) in metagenomic samples of the gut microbiome from inflammatory bowel disease (IBD) patients and matched healthy subjects and identified two Clostridia-derived BGCs that are significantly associated with Crohn's disease (CD), a main IBD type. Using synthetic biology, we discovered and solved the structures of six fatty acid amides as the products of the CD-enriched BGCs, which we subsequently detected in fecal samples from IBD patients. Finally, we show that the discovered molecules disrupt gut permeability and exacerbate disease in chemically or genetically susceptible mouse models of colitis. These findings suggest that microbiome-derived small molecules may play a role in the etiology of IBD and represent a generalizable approach for discovering molecular mediators of disease-relevant microbiome-host interactions.}, } @article {pmid39946947, year = {2025}, author = {Yu, J and Usman, M and Liu, F and Schäfer, F and Shen, Y and Zheng, Z and Cai, Y}, title = {CO2 agitation combined with magnetized biochar to alleviate "ammonia inhibited steady-state": Exploring the mechanism by combining metagenomics with macroscopic indicators.}, journal = {Water research}, volume = {276}, number = {}, pages = {123250}, doi = {10.1016/j.watres.2025.123250}, pmid = {39946947}, issn = {1879-2448}, abstract = {The "ammonia inhibited steady-state" phenomenon is frequently observed in the anaerobic digestion (AD) process of nitrogen-rich substrates. Reconfiguring microbial ecosystems has proven to be an effective strategy for mitigating ammonia inhibition. In the current study, biochars were screened and targeted for modification. CO2 agitation combined with magnetized biochar was used to aid the semi-continuous AD systems with "ammonia inhibited steady-state." The results indicated that coconut shell biochar had the best stimulating effect on AD performance. The content of oxygen-containing functional groups (OCFGs), which had a positive correlation with the electron donating capacity (EDC), was targeted to be regulated. This strategy significantly increased the CH4 yield by 31.7 % (from 344 to 278 mL/g VS) (p < 0.05). Isotope tracing and KEGG gene annotation indicated that this strategy stimulated the efficiency of the hydrogenotrophic pathway. Simultaneously, it accelerated the attachment of microorganisms, which made the DIET pathway between bacteria and archaea efficient. Under CO2 agitation, the attachment of functional microorganisms to the biochar accelerated. Biochar weakened the synthesis of bioelectronic carriers (Cyt-c and chemosensory pili), while the electroactivity of the AD system was enhanced. This means that biochar replaced bioelectronic carriers and improved the DIET efficiency. In addition, the strategy had a positive effect on the colonization of simultaneous nitrification-denitrifying bacteria (Georgenia), which led to a decrease in ammonia nitrogen concentrations. This study revealed the mechanism by which this strategy alleviates ammonia inhibition and provided a promising strategy for the efficient AD of nitrogen-rich substrates.}, } @article {pmid39946886, year = {2025}, author = {Shi, J and Zhang, Q and Sun, Y and Peng, Y and Wang, J and Wang, X}, title = {Microplastic induces microbial nitrogen limitation further alters microbial nitrogentransformation: Insights from metagenomic analysis.}, journal = {The Science of the total environment}, volume = {967}, number = {}, pages = {178825}, doi = {10.1016/j.scitotenv.2025.178825}, pmid = {39946886}, issn = {1879-1026}, abstract = {Microplastic has a significant impact on soil microbial communities, which play crucial roles in soil nitrogen (N) cycles. However, there is a limited understanding of their influences on genes associated with the entire N cycling pathways. Through a 120-day soil incubation using conventional (PE and PET) and biodegradable microplastics (PLA and PBAT), coupled with 16S rRNA and metagenomic sequencing, we investigated the responses of N-cycling genes to microplastics in two contrasting soils (i.e. black soil and loess soil). We found that biodegradable microplastics strongly altered microbial N functional profiles, and enhanced the abundance of numerous key genes involved in N fixation, organic N mineralization, N reduction, and denitrification. Furthermore, biodegradable microplastics significantly decreased net N mineralization (Nm) compared to control and conventional microplastic treatments, suggesting microbial N immobilization outweighed N mineralization. Analysis of the function-taxon bipartite network showed that the Nm was well predicted for the abundances and diversity of bacteria within specific modules, with Nm decreasing, the abundances of specific taxa in a given network modules increasing. These results indicated that biodegradable microplastics act as a carbon source to select specific taxa involved in enhancing N bioavailability (e.g., N fixation and organic N mineralization) to meet microbial N demand, which in turn filtered the bacterial community (decreased diversity but increased abundances) and gradually formed specific function-taxon modules. Comparing the two soils, microbes in the less fertile alkaline loess soil were more sensitive to biodegradable microplastics than those in the nutrient-rich acid black soil. Our study indicated that increasing usage of biodegradable plastics in the future may lead to accelerated soil microbial N limitation and transformation.}, } @article {pmid39946873, year = {2025}, author = {Feng, Y and Li, L and Ma, Q and Liu, S and Wang, P and Li, X and Ma, J}, title = {Effect of microcystin-LR on intestinal microbiota, metabolism, and health of zebrafish (Danio rerio).}, journal = {The Science of the total environment}, volume = {967}, number = {}, pages = {178838}, doi = {10.1016/j.scitotenv.2025.178838}, pmid = {39946873}, issn = {1879-1026}, abstract = {Microcystin-LR (MC-LR) is typically produced along with the occurrence of cyanobacterial blooms, potentially exerting deleterious effects on intestinal microbiota and health in aquatic animals. To date, the underlying mechanism by which MC-LR affects intestinal health remains elusive. In this study, adult male zebrafish were exposed to MC-LR to assess its impact on the microbiome and metabolome. Histopathological and biochemical results indicated that MC-LR damaged intestinal villi and epithelial cells, induced intestinal barrier injury and inflammatory response. Metabolomics results revealed that MC-LR induced amino acid, carbohydrate, lipid, energy metabolisms dysbiosis, and specifically promoted glycine, serine and threonine metabolism. Metagenomics results demonstrated that MC-LR altered the composition of intestinal microbiota, and microbial function prediction suggested that MC-LR promoted the functions associated with amino acid, lipid, carbohydrate and energy metabolisms. Multiomics and Metorigin analyses jointly confirmed that glycine, serine and threonine metabolism was predominantly regulated by dominant Proteobacteria, Firmicutes, Fusobacteriota and Bacteroidota under MC-LR stress. This study offers a comprehensive perspective on the toxicity of microbiota and microbiota-derived metabolism in fish intestines induced by MC-LR and deepens our comprehension of the disruptive influence of MC-LR on intestinal homeostasis in organisms.}, } @article {pmid39946816, year = {2025}, author = {Laredo-Tiscareño, SV and Garza-Hernandez, JA and Tangudu, CS and Dankaona, W and Rodríguez-Alarcón, CA and Gonzalez-Peña, R and Adame-Gallegos, JR and Beristain-Ruiz, DM and Barajas-López, IN and Hargett, AM and Munderloh, UG and Blitvich, BJ}, title = {Detection of multiple novel viruses in argasid and ixodid ticks in Mexico.}, journal = {Ticks and tick-borne diseases}, volume = {16}, number = {2}, pages = {102455}, doi = {10.1016/j.ttbdis.2025.102455}, pmid = {39946816}, issn = {1877-9603}, abstract = {We examined ticks from Mexico using viral metagenomics to increase our understanding of the composition and diversity of the tick virome. The analysis was performed using 3,127 ticks of four Ixodidae spp. and one Argasidae spp. collected in 2019 to 2021 from domestic animals in four states of Mexico (Chiapas, Chihuahua, Guerrero, and Michoacán). All ticks were homogenized and tested for viruses using two approaches. In the first approach, an aliquot of each homogenate underwent two blind passages in Ixodes scapularis (ISE6) cells. Supernatants from all second passage cultures were subjected to polyethylene glycol (PEG) precipitation to enrich for virions then RNAs were extracted from the precipitates and analyzed by unbiased high-throughput sequencing (UHTS). In the second approach, an aliquot of every homogenate was subjected to PEG precipitation then RNAs were extracted and analyzed by UHTS, allowing for the detection of viruses unable to replicate in ISE6 cells. We identified seven novel species of viruses from multiple taxonomic groups (Bunyavirales, Flaviviridae, Nodaviridae, Nyamivirdae, Rhabdoviridae, Solemoviridae, and Totiviridae), some of which are highly divergent from all classified viruses and cannot be assigned to any established genus. Twelve recognized species of viruses were also identified. In summary, multiple novel and recognized viruses were detected in ticks from Mexico, highlighting the remarkable diversity of the tick virome.}, } @article {pmid39946360, year = {2025}, author = {Scaketti, M and Sujii, PS and Alves-Pereira, A and Schwarcz, KD and Francisconi, AF and Moro, MS and Moreno Martins, KK and de Jesus, TA and de Souza, GBF and Zucchi, MI}, title = {Sample Size Impact (SaSii): An R script for estimating optimal sample sizes in population genetics and population genomics studies.}, journal = {PloS one}, volume = {20}, number = {2}, pages = {e0316634}, doi = {10.1371/journal.pone.0316634}, pmid = {39946360}, issn = {1932-6203}, mesh = {Sample Size ; *Genetics, Population ; *Polymorphism, Single Nucleotide ; Humans ; Genomics/methods ; Software ; Microsatellite Repeats/genetics ; Genotype ; Animals ; Metagenomics/methods ; }, abstract = {Obtaining large sample sizes for genetic studies can be challenging, time-consuming, and expensive, and small sample sizes may generate biased or imprecise results. Many studies have suggested the minimum sample size necessary to obtain robust and reliable results, but it is not possible to define one ideal minimum sample size that fits all studies. Here, we present SaSii (Sample Size Impact), an R script to help researchers define the minimum sample size. Based on empirical and simulated data analysis using SaSii, we present patterns and suggest minimum sample sizes for experiment design. The patterns were obtained by analyzing previously published genotype datasets with SaSii and can be used as a starting point for the sample design of population genetics and genomic studies. Our results showed that it is possible to estimate an adequate sample size that accurately represents the real population without requiring the scientist to write any program code, extract and sequence samples, or use population genetics programs, thus simplifying the process. We also confirmed that the minimum sample sizes for SNP (single-nucleotide polymorphism) analysis are usually smaller than for SSR (simple sequence repeat) analysis and discussed other patterns observed from empirical plant and animal datasets.}, } @article {pmid39946339, year = {2025}, author = {Long, C and Wang, P and Wu, J and Liu, J and Tan, Z and Li, W}, title = {Structure and diversity of intestinal methanogens in black carp (Mylopharyngodon piceus), grass carp (Ctenopharyngodon idella) and water samples.}, journal = {PloS one}, volume = {20}, number = {2}, pages = {e0316456}, doi = {10.1371/journal.pone.0316456}, pmid = {39946339}, issn = {1932-6203}, mesh = {*Carps/microbiology ; Animals ; *Gastrointestinal Microbiome/genetics ; Methane/metabolism ; Intestines/microbiology ; Bacteria/genetics/classification/isolation & purification ; Water Microbiology ; Methanosarcina/genetics/metabolism ; }, abstract = {The present research investigation aims to examine the community features of methanogens in the intestinal tract of black and grass carp, as well as their association with methanogens in water samples. Samples of black carp, grass carp and water in a pond were gathered in Spring 2021. Using the Illumina HiSeq 2500 high-throughput sequencing platform, the metagenomic mcrA gene sequences of black carp, grass carp and cultured water specimens were determined and analyzed. The outcomes indicate that the richness and diversity of methanogens in the intestinal tract of black and carp grass carp were highly correlated with the cultured water. Five bacterial genera were found in the three sets of samples, Methanosarcina, Methanocorpusculum, Methanospirillum, Methanobacterium and Methanofollis, in which Methanosarcina and Methanocorpusculum were the dominant genera. In addition, Methanosarcina had the greatest amount in grass carp and Methanocorpusculum had the greatest quantity in black carp. In conclusion, Methanosarcina and Methanocorpusculum were the main methanogens in the digestive tract of black and grass carp and culture water, and hydrolytic fermentative bacteria were its main metabolic substrate, hydrotrophic was its main metabolic pathway. The results will provide a reference for the relationship between intestinal methanogens and aquaculture and the greenhouse effect.}, } @article {pmid39945663, year = {2025}, author = {Park, K and Shin, M and Natasha, A and Kim, J and Noh, J and Kim, SG and Kim, B and Park, J and Seo, YR and Cho, HK and Byun, KS and Kim, JH and Lee, YS and Shim, JO and Kim, WK and Song, JW}, title = {Novel human coronavirus in an infant patient with pneumonia, Republic of Korea.}, journal = {Emerging microbes & infections}, volume = {}, number = {}, pages = {2466705}, doi = {10.1080/22221751.2025.2466705}, pmid = {39945663}, issn = {2222-1751}, abstract = {Coronaviruses (CoVs) pose a significant threat to public health, causing a wide spectrum of clinical manifestations and outcomes. Beyond precipitating global outbreaks, Human CoVs (HCoVs) are frequently found among patients with respiratory infections. To date, limited attention has been directed towards alphacoronaviruses due to their low prevalence and fatality rates. Nasal swab and serum samples were collected from a paediatric patient, and an epidemiological survey was conducted. Retrospective surveillance investigated the molecular prevalence of CoV in 880 rodents collected in the Republic of Korea (ROK) from 2018 to 2022. Next-generation sequencing (NGS) and phylogenetic analyses characterised the novel HCoV and closely related CoVs harboured by Apodemus spp. On 15 December 2022, a 103-day-old infant was admitted with fever, cough, sputum production, and rhinorrhea, diagnosed with human parainfluenza virus 1 (HPIV-1) and rhinovirus co-infection. Elevated AST/ALT levels indicated transient liver dysfunction on the fourth day of hospitalisation. Metagenomic NGS (mNGS) identified a novel HCoV in nasal swab and serum samples. Retrospective rodent surveillance and phylogenetic analyses showed the novel HCoV was closely related to alphacoronaviruses carried by Apodemus spp. in the ROK and China. This case highlights the potential of mNGS to identify emerging pathogens and raises awareness of possible extra-respiratory manifestations, such as transient liver dysfunction, associated with novel HCoVs. While the liver injury in this case may be attributable to the novel HCoV, further research is necessary to elucidate its clinical significance, epidemiological prevalence, and zoonotic origins.}, } @article {pmid39945545, year = {2025}, author = {Verster, AJ and Salerno, P and Valls, R and Barrack, K and Price, CE and McClure, EA and Madan, JC and O'Toole, GA and Sanville, JL and Ross, BD}, title = {Persistent delay in maturation of the developing gut microbiota in infants with cystic fibrosis.}, journal = {mBio}, volume = {}, number = {}, pages = {e0342024}, doi = {10.1128/mbio.03420-24}, pmid = {39945545}, issn = {2150-7511}, abstract = {The healthy human infant gut microbiome undergoes stereotypical changes in taxonomic composition between birth and maturation to an adult-like stable state. During this time, extensive communication between microbiota and the host immune system contributes to health status later in life. Although there are many reported associations between microbiota compositional alterations and disease in adults, less is known about how microbiome development is altered in pediatric diseases. One pediatric disease linked to altered gut microbiota composition is cystic fibrosis (CF), a multi-organ genetic disease involving impaired chloride secretion across epithelia and heightened inflammation both in the gut and at other body sites. Here, we use shotgun metagenomics to profile the strain-level composition and developmental dynamics of the infant fecal microbiota from several CF and non-CF longitudinal cohorts spanning from birth to greater than 36 months of life. We identify a set of keystone species that define microbiota development in early life in non-CF infants but are missing or decreased in relative abundance in infants with CF, resulting in a delayed pattern of microbiota maturation, persistent entrenchment in a transitional developmental phase, and subsequent failure to attain an adult-like stable microbiota. Delayed maturation is strongly associated with cumulative antibiotic treatments, and we also detect the increased relative abundance of oral-derived bacteria and higher levels of fungi in infants with CF, features that are associated with decreased gut bacterial density. These findings suggest the potential for future directed therapies targeted at overcoming developmental delays in microbiota maturation for infants with CF.IMPORTANCEThe human gastrointestinal tract harbors a diversity of microbes that colonize upon birth and collectively contribute to host health throughout life. Infants with the disease cystic fibrosis (CF) harbor altered gut microbiota compared to non-CF counterparts, with lower levels of beneficial bacteria. How this altered population is established in infants with CF and how it develops over the first years of life is not well understood. By leveraging multiple large non-CF infant fecal metagenomic data sets and samples from a CF cohort collected prior to highly effective modulator therapy, we define microbiome maturation in infants up to 3 years of age. Our findings identify conserved age-diagnostic species in the non-CF infant microbiome that are diminished in abundance in CF counterparts that instead exhibit an enrichment of oral-derived bacteria and fungi associated with antibiotic exposure. Together, our study builds toward microbiota-targeted therapy to restore healthy microbiota dynamics in infants with CF.}, } @article {pmid39945541, year = {2025}, author = {Lapid, R and Motro, Y and Craddock, H and Salah, I and King, R and Winner, K and Kahila Bar-Gal, G and Moran-Gilad, J}, title = {Abundance of clinically relevant antimicrobial resistance genes in the golden jackal (Canis aureus) gut.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0081924}, doi = {10.1128/msphere.00819-24}, pmid = {39945541}, issn = {2379-5042}, abstract = {UNLABELLED: The spread of antimicrobial resistance (AMR) is a critical One Health issue. Wildlife could act as reservoirs or vehicles of AMR bacteria (ARBs) and AMR genes (ARGs) but are relatively understudied. We sought to investigate clinically relevant ARGs in golden jackals (Canis aureus) thriving near human settlements in Israel. Fecal samples were collected from 111 jackals across four regions over a 10-month period. Various animal and spatio-temporal metadata were collected. Samples were analyzed by quantitative PCR (qPCR) for beta-lactamases (blaTEM, blaCTX-M15, and blaSHV), qnrS and int1. A subset of samples was subject to shotgun metagenomic sequencing followed by resistome and microbiome analyses. qPCR detected a high prevalence of ARGs, including beta-lactamases (blaTEM-1, 96.4%; blaCTX-M-15, 51.4%, blaSHV, 15.3%), fluoroquinolone resistance (qnrS, 87.4%), and class 1 integrons (Int1, 94.6%). The blaTEM-1 gene was found to be more prevalent in adult jackals compared to younger ones. Metagenomic analysis of a subset of samples revealed a diverse gut microbiome harboring a rich resistome with tetracycline resistance genes being the most prevalent. Metagenome-assembled genome analysis further identified several ARGs associated with clinically relevant bacteria. These findings highlight the potential role of golden jackals as reservoirs for AMR and emphasize the need for ongoing surveillance to better understand AMR transmission dynamics at the wildlife-human interface.

IMPORTANCE: The research highlights the potential role of the golden jackals as reservoirs for antimicrobial resistance (AMR). The high prevalence of clinically relevant AMR genes in these jackals emphasizes the need for ongoing surveillance and monitoring to better understand AMR transmission dynamics at the wildlife-human interface.}, } @article {pmid39945538, year = {2025}, author = {Zhang, L and Zhang, T and Xu, Y-R and Sun, J-M and Pan, X-R and Gu, K-Z and Zhang, K-Q and Zhang, Z-G and Liang, L-M}, title = {Induction of conidial traps in the nematode-trapping fungus Drechslerella dactyloides by soil microbes.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0129124}, doi = {10.1128/msystems.01291-24}, pmid = {39945538}, issn = {2379-5077}, abstract = {UNLABELLED: Nematode-trapping fungi, renowned for their specialized predatory structures that ensnare nematodes, offer a promising biological approach to managing plant-parasitic nematodes. However, the efficacy of these fungi is frequently hampered by biotic and abiotic factors within the soil, which can significantly impede fungal germination (fungistasis). To counteract these environmental challenges, certain nematode-trapping fungi have evolved to produce traps from their conidia, referred to as conidial traps. This adaptation allows them to bypass the inhibitory effects of their surroundings, enhancing their predatory capabilities. In this study, we explored how soil affects conidial trap formation in Drechslerella dactyloides. Our findings revealed that Acinetobacter spp. and Pantoea spp. present in soil extracts play pivotal roles in triggering the development of these traps. Using metagenomic sequencing, we mapped the shifts in bacterial communities and their relative abundances before and after incubation for up to 24 hours to optimize soil induction effects. This analysis highlighted the enrichment of specific functional genes in soil microbes and provided insights into the mechanisms driving conidial trap formation, based on changes in soil characteristics. Furthermore, through bacterial isolation procedures, we successfully cultured and characterized the bacteria responsible for this phenomenon, confirming their potent ability to stimulate the production of conidial traps in nematode-trapping fungi. This study not only underscores the critical role of bacterial diversity in modulating the life cycle transitions of nematode-trapping fungi but also sets the stage for the development of more effective and sustainable strategies to harness these fungi in the battle against pathogenic nematodes.

IMPORTANCE: Predatory nematode-trapping fungi are important microbial antagonists of nematodes and can be developed into biocontrol agents. However, microbial biocontrol agents often suffer from inconsistent efficacy, primarily due to biotic and abiotic stresses in the rhizosphere soil. Drechslerella dactyloides, a nematode-trapping fungus, produces conidial traps in soil, serving as a survival strategy to overcome these stresses. In this study, we optimized soil suspensions to efficiently induce the formation of conidial traps. We found that bacteria in the soil directly trigger this formation. Metagenomic sequencing revealed bacterial enrichment during optimization, and we isolated and purified these bacteria with inducible activity. Our research deepens the understanding of this survival strategy of nematode-trapping fungi in nature, laying the foundation for enhancing the effectiveness of nematode biocontrol using this mechanism.}, } @article {pmid39944722, year = {2025}, author = {Saravanan, C and Gopinath, NK and Ganesan, R and Thirumurugan, D}, title = {Challenges and limitations in using bacterial metabolites as immunomodulators.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1535394}, pmid = {39944722}, issn = {2235-2988}, mesh = {Humans ; *Bacteria/metabolism ; *Immunologic Factors/metabolism ; *Gastrointestinal Microbiome ; Animals ; Metabolomics ; Immunomodulating Agents/metabolism ; Metagenomics ; }, abstract = {Harnessing the immunomodulatory potential of bacterial metabolites opens up exciting possibilities for treating various immune-related disorders. However, turning this potential into a reality presents significant challenges. This review investigates these challenges, focusing on discovery, production, characterization, stability, formulation, safety, and individual variability limitations. The limited bioavailability of many metabolites, as well as potential improvements along with the potential for off-target effects and the importance of precise targeting, are emphasized. Furthermore, the complex interactions between gut bacterial metabolites and the microbiome are investigated, highlighting the importance of personalized approaches. We conclude by discussing promising advances in metagenomics, metabolomics, synthetic biology, and targeted delivery systems, which hold out hope for overcoming these limitations and paving the way for the clinical translation of bacterial metabolites as effective immunomodulators.}, } @article {pmid39944653, year = {2025}, author = {Ma, W and Zhao, Y and Liu, Y and Wang, Y and Yu, S and Huang, L}, title = {Bifidobacterium animalis subsp. lactis TG11 ameliorates loperamide-induced constipation in mice by modulating gut microbiota.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1525887}, pmid = {39944653}, issn = {1664-302X}, abstract = {INTRODUCTION: Constipation is a common gastrointestinal disorder that can affect quality of life. Probiotics have garnered substantial attention for their potential to alleviate constipation. This study investigates the preventive effects of Bifidobacterium animalis subsp. lactis TG11 on loperamide-induced constipation in mice.

METHODS: Mice were randomly assigned to normal control (NC), constipation model (CM), and low, medium, and high-dose TG11 treatment groups (LG, MG, HG). From days 1-14, LG, MG, and HG groups received 10[6], 10[7], and 10[8] CFU/mouse of TG11, respectively, while NC and CM groups received saline. On day 14, all groups except NC were administered loperamide (4 mg/kg) orally to induce constipation. Fecal samples were collected for short-chain fatty acid and gut microbiota analyses. Following a 16-hour fasting period, various parameters were assessed on day 15, including intestinal motility, fecal water content, defecation status, gut peptide levels in blood, and mRNA expression levels of SCF and c-kit in colonic tissue.

RESULTS: TG11 significantly enhanced intestinal motility and maintained fecal water content. It normalized blood levels of MTL, SP, SS, ET-1, Gas, and VIP in constipated mice, promoted short-chain fatty acid production, and improved microbial metabolism. TG11 markedly upregulated mRNA expression of SCF and c-kit in colonic tissue. Metagenomic sequencing revealed that TG11 modulated gut microbiota composition, increasing the abundance of beneficial bacteria, particularly Muribaculum_sp. and uncultured_Duncaniella.

DISCUSSION: Bifidobacterium animalis subsp. lactis TG11 demonstrates efficacy in ameliorating constipation, potentially through modulation of the gut microbiota composition.}, } @article {pmid39944638, year = {2025}, author = {Sarsaiya, S and Jain, A and Singh, R and Gong, Q and Wu, Q and Chen, J and Shi, J}, title = {Unveiling the rhizosphere microbiome of Dendrobium: mechanisms, microbial interactions, and implications for sustainable agriculture.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1531900}, pmid = {39944638}, issn = {1664-302X}, abstract = {The rhizosphere microbiome plays a critical role in plant health and productivity by fostering beneficial microbial interactions that support nutrient cycling, stress tolerance, and disease suppression. In the context of Dendrobium, understanding its interactions is essential for optimizing cultivation and promoting sustainable agricultural practices. This review explores the rhizosphere microbiome of Dendrobium, focusing on the mechanisms and microbial interactions that contribute to plant health, stress tolerance, and growth and their implications for sustainable agriculture. This study highlights the diverse composition of microbial communities in the Dendrobium rhizosphere, including key bacteria (e.g., Pseudomonas fluorescens and Bacillus subtilis), fungi (e.g., Glomus spp.), and biocontrol agents (Trichoderma spp.), and discusses their roles in nutrient cycling, disease suppression, and plant growth promotion. This review emphasizes the significance of plant-microbe signaling, such as the production of flavonoids, phytohormones, and strigolactones, in shaping the microbial environment and enhancing plant resilience. Additionally, it addresses modern techniques for analyzing microbial communities, including metagenomics and next-generation sequencing, and their applications in advancing precision agriculture. Future research should focus on bridging knowledge gaps related to genotype-microbiome interactions, exploring emerging microbial consortia and enhancing the integration of microbiome management in precision agriculture systems to improve plant health and productivity.}, } @article {pmid39944596, year = {2025}, author = {Brizola Toscan, R and Lesiński, W and Stomma, P and Subramanian, B and Łabaj, PP and Rudnicki, WR}, title = {Antimicrobial resistance in diverse urban microbiomes: uncovering patterns and predictive markers.}, journal = {Frontiers in genetics}, volume = {16}, number = {}, pages = {1460508}, pmid = {39944596}, issn = {1664-8021}, abstract = {Antimicrobial resistance (AMR) is a growing global health concern, driven by urbanization and anthropogenic activities. This study investigated AMR distribution and dynamics across microbiomes from six U.S. cities, focusing on resistomes, viromes, and mobile genetic elements (MGEs). Using metagenomic data from the CAMDA 2023 challenge, we applied tools such as AMR++, Bowtie, AMRFinderPlus, and RGI for resistome profiling, along with clustering, normalization, and machine learning techniques to identify predictive markers. AMR++ and Bowtie outperformed other tools in detecting diverse AMR markers, with binary normalization improving classification accuracy. MGEs were found to play a critical role in AMR dissemination, with 394 genes shared across all cities. Removal of MGE-associated AMR genes altered resistome profiles and reduced model performance. The findings reveal a heterogeneous AMR landscape in urban microbiomes, particularly in New York City, which showed the highest resistome diversity. These results underscore the importance of MGEs in AMR profiling and provide valuable insights for designing targeted strategies to address AMR in urban settings.}, } @article {pmid39943872, year = {2025}, author = {Büttner, KA and Bregy, V and Wegner, F and Purushothaman, S and Imkamp, F and Roloff Handschin, T and Puolakkainen, MH and Hiltunen-Back, E and Braun, D and Kisakesen, I and Schreiber, A and Entrocassi, AC and Gallo Vaulet, ML and López Aquino, D and Svidler López, L and La Rosa, L and Egli, A and Rodríguez Fermepin, M and Seth-Smith, HM and On Behalf Of The Escmid Study Group For Mycoplasma And Chlamydia Infections Esgmac, }, title = {Evaluating methods for genome sequencing of Chlamydia trachomatis and other sexually transmitted bacteria directly from clinical swabs.}, journal = {Microbial genomics}, volume = {11}, number = {2}, pages = {}, doi = {10.1099/mgen.0.001353}, pmid = {39943872}, issn = {2057-5858}, mesh = {Humans ; *Chlamydia trachomatis/genetics/isolation & purification ; *Whole Genome Sequencing/methods ; *Genome, Bacterial ; Neisseria gonorrhoeae/genetics/isolation & purification/classification ; High-Throughput Nucleotide Sequencing ; Treponema pallidum/genetics/isolation & purification ; Sexually Transmitted Diseases, Bacterial/microbiology ; Switzerland ; DNA, Bacterial/genetics ; Mycoplasma genitalium/genetics/isolation & purification ; Chlamydia Infections/microbiology ; }, abstract = {Rates of bacterial sexually transmitted infections (STIs) are rising, and accessing their genomes provides information on strain evolution, circulating strains and encoded antimicrobial resistance (AMR). Notable pathogens include Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG) and Treponema pallidum (TP), globally the most common bacterial STIs. Mycoplasmoides (formerly Mycoplasma) genitalium (MG) is also a bacterial STI that is of concern due to AMR development. These bacteria are also fastidious or hard to culture, and standard sampling methods lyse bacteria, completely preventing pathogen culture. Clinical samples contain large amounts of human and other microbiota DNA. These factors hinder the sequencing of bacterial STI genomes. We aimed to overcome these challenges in obtaining whole-genome sequences and evaluated four approaches using clinical samples from Argentina (39), and Switzerland (14), and cultured samples from Finland (2) and Argentina (1). First, direct genome sequencing from swab samples was attempted through Illumina deep metagenomic sequencing, showing extremely low levels of target DNA, with under 0.01% of the sequenced reads being from the target pathogens. Second, host DNA depletion followed by Illumina sequencing was not found to produce enrichment in these very low-load samples. Third, we tried a selective long-read approach with the new adaptive sequencing from Oxford Nanopore Technologies, which also did not improve enrichment sufficiently to provide genomic information. Finally, target enrichment using a novel pan-genome set of custom SureSelect probes targeting CT, NG, TP and MG followed by Illumina sequencing was successful. We produced whole genomes from 64% of CT-positive samples, from 36% of NG-positive samples and 60% of TP-positive samples. Additionally, we enriched MG DNA to gain partial genomes from 60% of samples. This is the first publication to date to utilize a pan-genome STI panel in target enrichment. Target enrichment, though costly, proved essential for obtaining genomic data from clinical samples. These data can be utilized to examine circulating strains and genotypic resistance and guide public health strategies.}, } @article {pmid39941945, year = {2025}, author = {Quek, JJW and Wong, JL and Tan, JL and Yeo, CC and Saw, SH}, title = {Integrating Metagenomic and Culture-Based Techniques to Detect Foodborne Pathogens and Antimicrobial Resistance Genes in Malaysian Produce.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/foods14030352}, pmid = {39941945}, issn = {2304-8158}, support = {FRGS/1/2022/SKK06/UTAR/02/1//Ministry of Higher Education/ ; }, abstract = {Foodborne illnesses pose a significant global health threat, often caused by pathogens like Escherichia coli, Listeria monocytogenes, and Salmonella spp. The emergence of antibiotic-resistant strains further exacerbates food safety challenges. This study combines shotgun metagenomics and culture-based approaches to detect foodborne pathogens and antimicrobial resistance genes (ARGs) in Malaysian produce and meats from the Kinta Valley region. A total of 27 samples comprising vegetables, meats, and fruits were analyzed. Metagenomics provided comprehensive microbial profiles, revealing diverse bacterial communities with species-level taxonomic resolution. Culture-based methods complemented these findings by identifying viable pathogens. Key foodborne pathogens were detected, with Listeria monocytogenes identified in meats and vegetables and Shigella flexneri detected inconsistently between the methods. ARGs analysis highlighted significant resistance to cephalosporins and penams, particularly in raw chicken and vegetable samples, underscoring the potential public health risks. While deli meats and fruits exhibited a lower antimicrobial resistance prevalence, resistant genes linked to E. coli and Salmonella strains were identified. Discrepancies between the methods suggest the need for integrated approaches to improve the pathogen detection accuracy. This study demonstrates the potential of metagenomics in advancing food safety research and supports its adoption as a complementary tool alongside culture-based methods for comprehensive foodborne pathogen surveillance and ARG profiling in Malaysian food systems.}, } @article {pmid39941602, year = {2025}, author = {Bessa, LJ and Egas, C and Botelho, J and Machado, V and Alcoforado, G and Mendes, JJ and Alves, R}, title = {Unveiling the Resistome Landscape in Peri-Implant Health and Disease.}, journal = {Journal of clinical medicine}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/jcm14030931}, pmid = {39941602}, issn = {2077-0383}, support = {2022.01430.PTDC//Fundação para a Ciência e Tecnologia/ ; }, abstract = {Background: The human oral microbiome is a critical reservoir for antibiotic resistance; however, subgingival peri-implant biofilms remain underexplored in this context. We aimed to explore the prevalence and distribution of antibiotic resistance genes (ARGs) in metagenomes derived from saliva and subgingival peri-implant biofilms. Methods: A total of 100 metagenome datasets from 40 individuals were retrieved from the Sequence Read Archive (SRA) database. Of these, 20 individuals had exclusively healthy implants and 20 had both healthy and affected implants with peri-implantitis. ARGs and their taxonomic assignments were identified using the ABRicate tool, and plasmid detection was performed with PlasmidFinder. Results: Four plasmid replicons were identified in 72 metagenomes, and 55 distinct ARGs from 13 antibiotic classes were detected in 89 metagenomes. ARGs conferring resistance to macrolides-lincosamides-streptogramins, tetracyclines, beta-lactams, and fluoroquinolones were the most prevalent. The msr(D) and mef(A) genes showed the highest prevalence, except in saliva samples from individuals with healthy implants, where mef(A) ranked fourth. A pairwise PERMANOVA of principal coordinate analysis based on Jaccard distances revealed that saliva samples exhibited significantly greater ARG diversity than subgingival biofilm samples (p < 0.05). However, no significant differences were observed between healthy and peri-implantitis-affected subgingival biofilm groups (p > 0.05). The taxonomic origins of ARGs were also analyzed to understand their distribution and potential impact on oral microbial communities. Conclusions: Resistome profiles associated with both peri-implant health and disease showed no significant differences and higher salivary abundance of ARGs compared to subgingival biofilm samples.}, } @article {pmid39939775, year = {2025}, author = {Santos, CA and Morais, MAB and Mandelli, F and Lima, EA and Miyamoto, RY and Higasi, PMR and Araujo, EA and Paixão, DAA and Junior, JM and Motta, ML and Streit, RSA and Morão, LG and Silva, CBC and Wolf, LD and Terrasan, CRF and Bulka, NR and Diogo, JA and Fuzita, FJ and Colombari, FM and Santos, CR and Rodrigues, PT and Silva, DB and Grisel, S and Bernardes, JS and Terrapon, N and Lombard, V and Filho, AJC and Henrissat, B and Bissaro, B and Berrin, JG and Persinoti, GF and Murakami, MT}, title = {A metagenomic 'dark matter' enzyme catalyses oxidative cellulose conversion.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {39939775}, issn = {1476-4687}, abstract = {The breakdown of cellulose is one of the most important reactions in nature[1,2] and is central to biomass conversion to fuels and chemicals[3]. However, the microfibrillar organization of cellulose and its complex interactions with other components of the plant cell wall poses a major challenge for enzymatic conversion[4]. Here, by mining the metagenomic 'dark matter' (unclassified DNA with unknown function) of a microbial community specialized in lignocellulose degradation, we discovered a metalloenzyme that oxidatively cleaves cellulose. This metalloenzyme acts on cellulose through an exo-type mechanism with C1 regioselectivity, resulting exclusively in cellobionic acid as a product. The crystal structure reveals a catalytic copper buried in a compact jelly-roll scaffold that features a flattened cellulose binding site. This metalloenzyme exhibits a homodimeric configuration that enables in situ hydrogen peroxide generation by one subunit while the other is productively interacting with cellulose. The secretome of an engineered strain of the fungus Trichoderma reesei expressing this metalloenzyme boosted the glucose release from pretreated lignocellulosic biomass under industrially relevant conditions, demonstrating its biotechnological potential. This discovery modifies the current understanding of bacterial redox enzymatic systems devoted to overcoming biomass recalcitrance[5-7]. Furthermore, it enables the conversion of agro-industrial residues into value-added bioproducts, thereby contributing to the transition to a sustainable and bio-based economy.}, } @article {pmid39938404, year = {2025}, author = {d'Humières, C and Haviari, S and Petitjean, M and Deconinck, L and Gueye, S and Peiffer-Smadja, N and Chalal, L and Beldjoudi, N and Rossi, G and Nguyen, Y and Burdet, C and Perrineau, S and Le Pluart, D and Rahli, R and Thy, M and Szychowiak, P and Lescure, X and Leflon-Guibout, V and de Lastours, V and Ruppé, E}, title = {Comparison of clinical metagenomics with 16S rDNA Sanger sequencing for the bacteriological diagnosis of culture-negative samples.}, journal = {International journal of medical microbiology : IJMM}, volume = {318}, number = {}, pages = {151650}, doi = {10.1016/j.ijmm.2025.151650}, pmid = {39938404}, issn = {1618-0607}, abstract = {BACKGROUND: Currently, diagnosis of bacterial infections is based on culture, possibly followed by the amplification and sequencing (Sanger method) of the 16S rDNA - encoding gene when cultures are negative. Clinical metagenomics (CMg), i.e. the sequencing of a sample's entire nucleic acids, may allow for the identification of bacteria not detected by conventional methods. Here, we tested the performance of CMg compared to 16S rDNA sequencing (Sanger) in 50 patients with suspected bacterial infection but negative cultures.

METHODS: This is a prospective cohort study. Fifty patients (73 samples) with negative culture and a 16S rDNA sequencing demand (Sanger) were recruited from two sites. On the same samples, CMg (Illumina NextSeq) was also performed and compared to 16S rDNA Sanger sequencing. Bacteria were identified using MetaPhlAn4.

RESULTS: Among the 73 samples, 20 (27 %, 17 patients) had a clinically relevant 16S rDNA Sanger sequencing result (used for patient management) while 11 (15 %, 9 patients) were considered contaminants. At the patient level, the sensitivity of CMg was 70 % (12/17) compared to 16S rDNA. In samples negative for 16S rDNA Sanger sequencing (n = 53), CMg identified clinically-relevant bacteria in 10 samples (19 %, 10 patients) with 14 additional bacteria.

CONCLUSIONS: CMg was not 100 % sensitive when compared to 16S, supporting that it may not be a suitable replacement. However, CMg did find additional bacteria in samples negative for 16S rDNA Sanger. CMg could therefore be positioned as a complementary to 16S rDNA Sanger sequencing.}, } @article {pmid39938372, year = {2025}, author = {Guo, Y and Zhao, Y and Lin, K and Zheng, Q and Zhou, T}, title = {Metagenomic analysis of viral community during different municipal solid waste collection and treatment processes: Fate, hosts, and antibiotic resistance genes.}, journal = {Journal of hazardous materials}, volume = {489}, number = {}, pages = {137520}, doi = {10.1016/j.jhazmat.2025.137520}, pmid = {39938372}, issn = {1873-3336}, abstract = {Municipal solid waste (MSW) serves as effective reservoirs of viruses and virus-associated antibiotic resistance genes (vir_ARGs), posing potential risks to human health. However, the composition of viral communities in different MSW collection and treatment processes remains unclear. Here, we profiled the viral communities and vir_ARGs in MSW leachate and aerosol samples from different MSW facilities based on metagenomic and virus enrichment-based viromic sequencings. Results showed that Microviridae and Caudoviricetes_Unclassified were the dominant viral families. Viral hosts were mainly distributed in the specific functional taxa of Bacillota. Additionally, the leachate properties and bacterial community structures significantly correlated with the viral community structures, implying that these environmental factors were the important drivers for viral distribution. The co-occurrence network analysis revealed the complex relationships between vir_ARGs and bacteria, suggesting that certain vir_ARGs have a broad host spectrum. Significant differences of viruses and vir_ARGs were observed between different sample types, but the viruses and vir_ARGs showed no significant differences across three sampling sites. Overall, this study highlights novel perspectives on the changes in viruses and vir_ARGs across the whole MSW collection and treatment processes, and provides valuable insights about the environmental factors affecting the profile of viral communities. These findings are crucial for elucidating the potential risks linked to the transmission of both viruses and ARGs.}, } @article {pmid39944648, year = {2025}, author = {Lu, J and Jiang, M and Chai, D and Sun, Y and Wu, L}, title = {Integrative analysis of intestinal flora and untargeted metabolomics in attention-deficit/hyperactivity disorder.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1452423}, doi = {10.3389/fmicb.2025.1452423}, pmid = {39944648}, issn = {1664-302X}, abstract = {Attention Deficit Hyperactivity Disorder (ADHD) is a clinically common neurodevelopmental disorder of the brain. In addition to genetic factors, an imbalance in gut flora may also play a role in the development of ADHD. Currently, it is critical to investigate the function of gut flora and related metabolites, which may form the fundamental basis of bidirectional cross-linking between the brain and the gut, in addition to focusing on the changed gut flora in ADHD. This study aimed to investigate the possible relationship between changes in gut flora and metabolites and ADHD by analyzing metagenome and untargeted metabolomics of fecal samples from ADHD patients. Specifically, we attempted to identify key metabolites and the metabolic pathways they are involved in, as well as analyze in detail the structure and composition of the gut flora of ADHD patients. In order to further investigate the relationship between gut flora and ADHD symptoms, some behavioral studies were conducted following the transplantation of gut flora from ADHD patients into rats. The results of the metagenome analysis revealed several distinct strains, including Bacteroides cellulosilyticus, which could be important for diagnosing ADHD. Additionally, the ADHD group showed modifications in several metabolic pathways and metabolites, including the nicotinamide and nicotinic acid metabolic pathways and the metabolite nicotinamide in this pathway. The behavioral results demonstrated that rats with ADHD gut flora transplants displayed increased locomotor activity and interest, indicating that the onset of behaviors such as ADHD could be facilitated by the flora associated with ADHD. This research verified the alterations in gut flora and metabolism observed in ADHD patients and provided a list of metabolites and flora that were significantly altered in ADHD. Simultaneously, our findings revealed that modifications to the microbiome could potentially trigger behavioral changes in animals, providing an experimental basis for comprehending the function and influence of gut flora on ADHD. These results might provide new perspectives for the development of novel treatment strategies.}, } @article {pmid39944485, year = {2025}, author = {Zhang, F and Wang, JL and Zhu, J and Si, S and Guo, H and Yue, X and Wen, W}, title = {When a sore throat turns into deadly multiple serous cavity effusions: the role of Prevotella oris in rapidly progressing infection-a case report.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1517389}, doi = {10.3389/fmed.2025.1517389}, pmid = {39944485}, issn = {2296-858X}, abstract = {Severe infections that develop rapidly from ordinary symptoms not only increase patient misunderstandings but also lead to excessive detection of these symptoms by physicians. This case study describes a 19-year-old male individual who initially presented with a sore throat and subsequently developed multiple serous cavity effusions that lead to septic pulmonary embolism and septic shock. After multiple cultures of the patient's sputum yielded no identifiable pathogenic bacteria, the metagenomic next-generation sequencing (mNGS) revealed Prevotella oris as the predominant pathogen present in both the patient's peripheral blood and the pericardial drainage fluid. The subsequent antibiotic treatment, guided by the mNGS results, along with surgical drainage and mediastinal irrigation, effectively controlled and ultimately cured the patient's condition. This case is unique because it is the first to show that normally colonizing Prevotella can also cause fatal multiorgan infection as an opportunistic pathogen in a previously healthy young person with no immune-related diseases. The aim of this study is to expand clinical awareness of this common symptom and its potentially fatal outcome.}, } @article {pmid39943733, year = {2025}, author = {Tizabi, D and Hill, RT and Bachvaroff, T}, title = {Nanopore Sequencing of Amoebophrya sp. Reveals Novel Collection of Bacteria Putatively Associated with Karlodinium veneficum.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evaf022}, pmid = {39943733}, issn = {1759-6653}, abstract = {The dinoflagellate parasite Amoebophrya sp. ex Karlodinium veneficum plays a major role in controlling populations of the toxic bloom-forming dinoflagellate Karlodinium veneficum and is one of the few cultured representatives of Marine Alveolate Group II. The obligate parasitic nature of this Amoebophrya spp. precludes isolation in culture, and therefore, genomic characterization of this parasite relies on metagenomic sequencing. Whole genome sequencing of an Amoebophrya sp. ex Karlodinium veneficum-infected culture using Nanopore long reads revealed a diverse community of novel bacteria as well as several species previously reported to be associated with algae. In sum, 39 metagenome-assembled genomes (MAG) were assembled, and less than half of these required binning of multiple contigs. Seven were abundant but of unknown genera, thirteen were identifiable at the generic level by BLAST (eight of which were apparently complete single-contig genomes), and the remaining 19 comprised less abundant (individually accounting for < 2% of the total bacterial reads in the culture) and often rarer and/or novel species. Attempts to culture strains identified through sequencing revealed that only two of these bacterial isolates were readily amenable to cultivation, stressing the importance of a dual culture- and sequencing-based approach for robust community analysis. Functional annotations of MAGs are presented here to support the characterization of a microbial community associated with K. veneficum and/or Amoebophrya sp. ex K. veneficum cultured from the Chesapeake Bay and give preliminary insights into the nature of the associations these bacteria have with this parasite-host complex.}, } @article {pmid39941991, year = {2025}, author = {Wu, J and Zhao, N and Li, Q and Zhao, K and Tu, M and Li, J and Hu, K and Chen, S and Liu, S and Liu, A}, title = {Metagenomics and Metagenome-Assembled Genomes: Analysis of Cupei from Sichuan Baoning Vinegar, One of the Four Traditional Renowned Vinegars in China.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/foods14030398}, pmid = {39941991}, issn = {2304-8158}, abstract = {The microbial community in vinegar has primarily been investigated by analyzing short reads to determine operational taxonomic units, but it is also crucial to identify metagenome-assembled genomes (MAGs). In this study, the microbial diversity and functionality in Sichuan Baoning vinegar were examined through deep metagenomic sequencing and metagenomic binning. Results revealed that the most prevalent phylum was Firmicutes, followed by Proteobacteria and unclassified Bacteria. The most abundant bacterial species was Acetilactobacillus jinshanensis, while Saccharomyces cerevisiae was the most prevalent fungal species. The predominant viral species were Hopescreekvirus LfeInf, Myoviridae sp., and Siphoviridae sp. A total of 1395 MAGs were reconstructed, with 660 of them annotated. The majority of MAGs resolved at the species level were attributed to Firmicutes (n = 308), with Acetilactobacillus jinshanensis being the most abundant. According to the average nucleotide identity values, 223 out of the 660 MAGs might represent novel species. The recovered MAGs exhibited biomarker genes indicative of the genetic potential to encode several important secondary metabolites. This study helps to uncover the microbial composition and functional potential of microbial genomes in Sichuan Baoning vinegar.}, } @article {pmid39941194, year = {2025}, author = {Bustos, IG and Martinez-Lemus, LF and Reyes, LF and Martin-Loeches, I}, title = {Transforming Microbiological Diagnostics in Nosocomial Lower Respiratory Tract Infections: Innovations Shaping the Future.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, doi = {10.3390/diagnostics15030265}, pmid = {39941194}, issn = {2075-4418}, abstract = {Introduction: Nosocomial lower respiratory tract infections (nLRTIs), including hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP), remain significant challenges due to high mortality, morbidity, and healthcare costs. Implementing accurate and timely diagnostic strategies is pivotal for guiding optimized antimicrobial therapy and addressing the growing threat of antimicrobial resistance. Areas Covered: This review examines emerging microbiological diagnostic methods for nLRTIs. Although widely utilized, traditional culture-based techniques are hindered by prolonged processing times, limiting their clinical utility in timely decision-making. Advanced molecular tools, such as real-time PCR and multiplex PCR, allow rapid pathogen identification but are constrained by predefined panels. Metagenomic next-generation sequencing (mNGS) provides comprehensive pathogen detection and resistance profiling yet faces cost, complexity, and interpretation challenges. Non-invasive methods, including exhaled breath analysis using electronic nose (e-nose) technology, gene expression profiling, and biomarker detection, hold promise for rapid and bedside diagnostics but require further validation to establish clinical applicability. Expert Opinion: Integrating molecular, metagenomic, biomarker-associated, and traditional diagnostics is essential for overcoming limitations. Continued technological refinements and cost reductions will enable broader clinical implementation. These innovations promise to enhance diagnostic accuracy, facilitate targeted therapy, and improve patient outcomes while contributing to global efforts to mitigate antimicrobial resistance.}, } @article {pmid39940952, year = {2025}, author = {Parra, M and Izquierdo, K and Rubio, M and de la Fuente, A and Tello, M and Modak, B}, title = {Quercetin and Silybin Decrease Intracellular Replication of Piscirickettsia salmonis in SHK-1 Cell.}, journal = {International journal of molecular sciences}, volume = {26}, number = {3}, pages = {}, doi = {10.3390/ijms26031184}, pmid = {39940952}, issn = {1422-0067}, support = {21212170//ANID/ ; 022341MC//DICYT/ ; }, mesh = {Animals ; *Quercetin/pharmacology ; *Silybin/pharmacology ; *Piscirickettsia/drug effects ; Cell Line ; Salmon/microbiology ; Fish Diseases/microbiology ; Oncorhynchus mykiss/microbiology ; Epithelial Cells/drug effects/microbiology/metabolism ; Piscirickettsiaceae Infections/microbiology ; Phagocytosis/drug effects ; Head Kidney/cytology ; }, abstract = {Piscirickettsia salmonis is the pathogen that has most affected the Chilean salmon industry for over 30 years. Considering the problems of excessive use of antibiotics, it is necessary to find new strategies to control this pathogen. Antivirulence therapy is an alternative to reduce the virulence of pathogens without affecting their growth. Polyphenolic compounds have been studied for their antiviral capacity. In this study, the capacity of quercetin and silybin to reduce the intracellular replication of P. salmonis in SHK-1 cells was evaluated. For this, three different infection protocols in Salmon Head Kidney-1(SHK-1) cells were used: co-incubation for 24 h, pre-incubation for 24 h prior to infection, and post-incubation for 24 h after infection. In addition, the effect of co-incubation in rainbow trout intestinal epithelial cells (RTgutGC) and the effect on the phagocytic capacity of SHK-1 cells were evaluated. The results obtained showed that quercetin and silybin decreased the intracellular replication of P. salmonis in SHK-1 cells when they were co-incubated for 24 h; however, they did not have the same effect in RTgutGC cells. On the other hand, both compounds decreased the phagocytosis of SHK-1 cells during co-incubation. These results are promising for the study of new treatments against P. salmonis.}, } @article {pmid39940425, year = {2025}, author = {Chen, E and Ajami, NJ and White, DL and Liu, Y and Gurwara, S and Hoffman, K and Graham, DY and El-Serag, HB and Petrosino, JF and Jiao, L}, title = {Dairy Consumption and the Colonic Mucosa-Associated Gut Microbiota in Humans-A Preliminary Investigation.}, journal = {Nutrients}, volume = {17}, number = {3}, pages = {}, doi = {10.3390/nu17030567}, pmid = {39940425}, issn = {2072-6643}, support = {RP#140767//Cancer Prevention and Research Institute of Texas/ ; DK56338/DK/NIDDK NIH HHS/United States ; 001//Gillson Longenbaugh Foundation/ ; 001//Gillson Longenbaugh Foundation/ ; CX001430//U.S. Department of Veterans Affairs/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; Cross-Sectional Studies ; *Dairy Products/microbiology ; Middle Aged ; *Colon/microbiology ; *Intestinal Mucosa/microbiology ; Adult ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation & purification ; Diet ; Aged ; Yogurt/microbiology ; }, abstract = {BACKGROUND: Dairy consumption has been associated with various health outcomes that may be mediated by changes in gut microbiota.

METHODS: This cross-sectional study investigated the association between the colonic mucosa-associated gut microbiota and the self-reported intake of total dairy, milk, cheese, and yogurt. A total of 97 colonic mucosal biopsies collected from 34 polyp-free individuals were analyzed. Dairy consumption in the past year was assessed using a food frequency questionnaire. The 16S rRNA gene V4 region was amplified and sequenced. Operational taxonomic unit (OTU) classification was performed using the UPARSE and SILVA databases. OTU diversity and relative abundance were compared between lower vs. higher dairy consumption groups. Multivariable negative binomial regression models for panel data were used to estimate the incidence rate ratio and 95% confidence interval for bacterial counts and dairy consumption. False discovery rate-adjusted p values (q value) < 0.05 indicated statistical significance.

RESULTS: Higher total dairy and milk consumption and lower cheese consumption were associated with higher alpha microbial diversity (adjusted p values < 0.05). Higher total dairy and milk consumption was also associated with higher relative abundance of Faecalibacterium. Higher milk consumption was associated with higher relative abundance of Akkermansia. Higher total dairy and cheese consumption was associated with lower relative abundance of Bacteroides.

CONCLUSIONS: Dairy consumption may influence host health by modulating the structure and composition of the colonic adherent gut microbiota.}, } @article {pmid39940254, year = {2025}, author = {Barata, P and Oliveira, A and Soares, R and Fernandes, A}, title = {Gut Microbiota Is Not Significantly Altered by Radioiodine Therapy.}, journal = {Nutrients}, volume = {17}, number = {3}, pages = {}, doi = {10.3390/nu17030395}, pmid = {39940254}, issn = {2072-6643}, mesh = {Humans ; *Gastrointestinal Microbiome/radiation effects ; Female ; Middle Aged ; Male ; *Feces/microbiology ; *Iodine Radioisotopes ; *Hyperthyroidism/radiotherapy/microbiology ; Adult ; Prospective Studies ; Thyroid Neoplasms/radiotherapy/microbiology ; Aged ; Bacteria/classification/radiation effects/genetics/isolation & purification ; Metagenomics/methods ; }, abstract = {Purpose: Radiotherapy treatments are known to alter the gut microbiota. However, little is known regarding the effect of nuclear medicine treatments on gut microbiota, and it is established that nuclear medicine is inherently different from radiotherapy. To address this knowledge gap, we conducted a prospective study to identify changes in the gut microbiota of patients treated with [[131]I]NaI by comparing fecal samples before and after RAIT. Methods: Fecal samples of 64 patients (37 with thyroid cancer and 27 with hyperthyroidism) with indication for RAIT were collected 2 to 3 days before treatment and 8 to 10 days post-treatment. After DNA extraction, the gut microbiota's richness, diversity, and composition were analyzed by shotgun metagenomics. In addition, LEfSe was performed to compare compositional changes in specific bacteria. Results: Gut microbiome richness and diversity remained unchanged after RAIT, with few changes in its composition identified, especially in patients with hyperthyroidism. Conclusions: This study provides a conceptual and analytical basis for increasing our understanding of the effects of radiopharmaceuticals on gut microbiota. Our preliminary results indicate that RAIT, contrary to radiotherapy, does not cause major disruptions to the human gut microbiota.}, } @article {pmid39940045, year = {2025}, author = {Schropp, N and Bauer, A and Stanislas, V and Huang, KD and Lesker, TR and Bielecka, AA and Strowig, T and Michels, KB}, title = {The impact of regular sauerkraut consumption on the human gut microbiota: a crossover intervention trial.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {52}, pmid = {39940045}, issn = {2049-2618}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Cross-Over Studies ; Male ; Female ; Adult ; *Bacteria/classification/genetics/isolation & purification ; *Fatty Acids, Volatile/metabolism ; *Fermented Foods/microbiology ; Middle Aged ; Feces/microbiology ; Metagenomics/methods ; Young Adult ; Metabolome ; Healthy Volunteers ; }, abstract = {BACKGROUND: Sauerkraut is a fermented food that has been suspected to have a beneficial impact on the gut microbiome, but scientific evidence is sparse. In this crossover intervention trial with 87 participants (DRKS00027007), we investigated the impact of daily consumption of fresh or pasteurized sauerkraut for 4 weeks on gut microbial composition and the metabolome in a healthy study population.

RESULTS: Using shotgun metagenomic sequencing, we observed changes in single bacterial species following fresh and pasteurized sauerkraut consumption. More pronounced changes were observed in the pasteurized sauerkraut intervention arm. Only pasteurized sauerkraut consumption increased serum short-chain fatty acids (SCFAs).

CONCLUSIONS: The gut microbiome of healthy individuals is rather resilient to short-term dietary interventions even though single species might be affected by sauerkraut consumption. Video Abstract.}, } @article {pmid39939365, year = {2025}, author = {Soares, KO and Da Rocha, TF and Hale, VL and Vasconcelos, PC and do Nascimento, LJ and da Silva, NMV and Rodrigues, AE and de Oliveira, CJB}, title = {Comparing the impact of landscape on the gut microbiome of Apis mellifera in Atlantic Forest and Caatinga Biomes.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {5293}, pmid = {39939365}, issn = {2045-2322}, support = {001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 88881.311776/2018-01//CAPES-PrInt Project "Omic sciences applied to the prevention of antimicrobial resistance at the human-animal-environment interface-a one health approach/ ; 88881.311776/2018-01//CAPES-PrInt Project "Omic sciences applied to the prevention of antimicrobial resistance at the human-animal-environment interface-a one health approach/ ; 3136678/2020-0//Conselho Nacional de Pesquisa e Desenvolvimento/ ; 3136678/2020-0//Conselho Nacional de Pesquisa e Desenvolvimento/ ; }, mesh = {Animals ; Bees/microbiology ; *Gastrointestinal Microbiome ; *Forests ; Brazil ; *RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation & purification ; Ecosystem ; }, abstract = {The composition of the gut microbiota in animals can be influenced by a variety of intrinsic and extrinsic factors in the host, such as diet, physiological state, and genetics. This study aimed to compare the structural composition of the gut microbiota of Apis mellifera bees from two distinct Brazilian biomes, the Atlantic Forest and the Caatinga, using high throughput 16 S rRNA sequencing. We identified a core microbiota composed of seven genera present in all samples: Lactobacillus, Commensalibacter, Rhizobiaceae, Snodgrassella, Gilliamella, Orbaceae and Bifidobacterium. These taxa accounted for 63% of all bacterial genera in the dataset. Interestingly, we observed a significantly differential abundance of the genus Apibacter between bees from the two biomes, with a marked increase in bees from Atlantic Forest. However, the overall variance in the gut structural composition attributable to landscape type, while significant, was relatively low. Notably, none of the members of the core microbiota were differently abundant between the biomes. Understanding the magnitude of landscape-associated effects on the microbiota of bees in different biomes is crucial for the accurate assessment of the impact of anthropogenic factors. These findings provide important insights into the resilience and adaptability of the honey bee gut microbiome across contrasting environments, contributing to the development of conservation and sustainable management strategies for these essential pollinators.}, } @article {pmid39939047, year = {2025}, author = {Wu, BG and Zinter, MS}, title = {Metagenomic Sequencing for Personalized Treatment in Pneumonia: Does Better Detection Lead to Better Outcomes?.}, journal = {Chest}, volume = {167}, number = {2}, pages = {300-302}, doi = {10.1016/j.chest.2024.08.031}, pmid = {39939047}, issn = {1931-3543}, } @article {pmid39938754, year = {2025}, author = {Fernandes, M and Palmieri, O and Castellana, S and Spanetta, M and Latiano, T and Lupo, C and Masi, C and Cardile, C and Calvello, C and Izzi, F and Placidi, F and Mazza, T and Mercuri, NB and Latiano, A and Liguori, C}, title = {Gut microbiome composition changes in obstructive sleep apnoea syndrome also in relation to excessive daytime sleepiness.}, journal = {Brain research bulletin}, volume = {}, number = {}, pages = {111251}, doi = {10.1016/j.brainresbull.2025.111251}, pmid = {39938754}, issn = {1873-2747}, abstract = {INTRODUCTION: Obstructive sleep apnoea syndrome (OSAS) is considered a risk factor for several comorbidities. Alteration in gut microbiome was documented in OSAS animal models and in paediatric patients. This study analysed gut microbiome composition in adult patients with OSAS and compared to controls. Further, the effect of excessive daytime sleepiness (EDS) on gut microbiome was evaluated.

METHODS: Adult patients with OSAS underwent polysomnographic recording and completed the Epworth Sleepiness Scale (ESS) to assess EDS. Faecal samples were collected and compared between patients and healthy controls. Composition, community diversity, differences in taxa abundance profiles and sample dysbiosis were evaluated through 16S metagenomics and multiple bioinformatics algorithms. OSAS patients were distributed in two groups according to EDS (ESS score≥10) to assess differences in clinical, polysomnographic and faecal data.

RESULTS: Twenty-three OSAS patients were compared to 44 controls. Patients presented significant differences of gut microbiome biodiversity, specifically in qualitative alpha diversity metrics (Faith's PD Kruskal-Wallis test, p-value=0.003; Number_of_Observed_Features, p value =0.001). OSAS patients tend to cluster together, at least for Jaccard and Unweighted UniFrac distance-based PERMANOVA tests (q-values=0.02 and =0.003, respectively). Several taxa were detected as different in abundance between OSAS patients and controls, although, globally, OSAS patients cannot be considered as "dysbiotic". Differences in bacteria composition were evident between OSAS patients with and those without EDS.

CONCLUSIONS: OSAS is associated with gut microbiome alteration in adult patients. EDS in OSAS seems to characterize a different gut microbiome composition, although it can be only hypothesized a gut-mediated effect on EDS in OSAS.}, } @article {pmid39938727, year = {2025}, author = {Braga, CM and da Silva, SP and Neto, JPN and Medeiros, DBA and Cruz, ACR and Sena do Nascimento, BL and Pinheiro, LRS and Martins, LC}, title = {Viral Metagenomics of Hematophagous Insects Collected in the Carajas Mining Complex, Pará State, Brazil.}, journal = {Acta tropica}, volume = {}, number = {}, pages = {107551}, doi = {10.1016/j.actatropica.2025.107551}, pmid = {39938727}, issn = {1873-6254}, abstract = {Hematophagous insects are vectors of viruses that cause diseases in humans and animals worldwide. Mosquitoes (Culicidae), biting midges (Ceratopogonidae), and sandflies (Psychodidae) were collected in three municipalities (Marabá, Canaã dos Carajás, and Curionópolis) in the state of Pará, Brazil, in 2019. Morphological keys were used for the taxonomic identification of insect species. High-throughput sequencing and metagenomic analysis were employed to characterize the viromes of the hematophagous insects. We characterized the virome of 839 insects grouped into 14 pools. A total of 729 million paired reads were generated, with 12 million viral sequences (3% of the reads). The families Reoviridae, Myoviridae, Retroviridae, and Poxviridae were found in all samples of this study. Phylogenies of RNA-dependent RNA polymerase (RdRp) from viruses of the families Chuviridae, Dicistroviridae, Flaviviridae, Iflaviridae, Mesoniviridae, Phenuiviridae, and Rhabdoviridae were performed. In this study, the first isolation of the Guaico Culex Virus (GCXV) in the northern region of Brazil was obtained from a pool of Culex (Melanoconion) spp. mosquitoes collected in Curionópolis. The data obtained in this study demonstrate that the Carajás region has an ecosystem rich in viruses. Additional studies are needed to understand the dynamics of viruses in vectors, vertebrates, and the human population in the region.}, } @article {pmid39938449, year = {2025}, author = {Ye, L and Yao, Z and Xuan, Q and Liu, Q and Bo, T}, title = {The impact of sleeve gastrectomy on MASH development by regulating the composition of gut microbiota and metabolic homeostasis.}, journal = {Biochemical and biophysical research communications}, volume = {752}, number = {}, pages = {151466}, doi = {10.1016/j.bbrc.2025.151466}, pmid = {39938449}, issn = {1090-2104}, abstract = {The prevalence of metabolic dysfunction-associated steatohepatitis (MASH) is increasing annually, which is a global public health issue. Although clinical trials are lacking, observational studies indicate that bariatric surgery can alleviate the progression of MASH. Here, we performed sleeve gastrectomy (SG) and Sham surgery on 8-week-old mice, and then fed a AMLN diet for 24 weeks to construct a diet-inducted MASH mice model after 4-week post-surgery recovery. Applying a multi-omics approach combining metagenomics, metabolomics, and transcriptomics, we found that SG prevents the development of hepatic steatosis, inflammation, and fibrosis in MASH mice not only by significantly altering the structure of gut microbiota including s_Akkermansia muciniphila, s_Alistiples dispar, g_Helicobacter and s_uc_Oscillospiraceae, but also by modulating the levels of serum metabolites including l-arginine and taurocholic acid (TCA). These results suggest that SG and the alteration of gut microbiota and its related serum metabolites can be served as the effective therapeutic strategies for MASH.}, } @article {pmid39938296, year = {2025}, author = {Tan, L and Liang, J and Qin, Z and Ning, T and Wei, X and Yang, B and Wang, Q and Xu, Y and Shen, F}, title = {Unveiling the sustained effects of plant root exudates on soil microbiome and resistome and the related functional traits.}, journal = {Journal of environmental management}, volume = {376}, number = {}, pages = {124485}, doi = {10.1016/j.jenvman.2025.124485}, pmid = {39938296}, issn = {1095-8630}, abstract = {Investigating the transmission mechanisms and influencing factors of antibiotic resistance genes (ARGs) in the soil-plant continuum is vital for mitigating ARG contamination and safeguarding plant and human health. Rhizosphere soil serves as a crucial interface for ARG propagation and transmission; however, it is unclear whether and how plant involved in regulating ARGs in their rhizosphere environment. Root exudates acting as vital links in the plant-soil-microbe interaction. Here, we examined the fluctuating patterns of the resistome and mobile genetic elements (MGEs) following exposure to four types of common root exudates: amino acids (AAs), sugars, long-chain organic acids (LCOAs), and short-chain organic acids (SCOAs). AAs exerted a rapid and pronounced effect, leading to a significant elevation in total ARG and MGE abundance by 3.18-fold and 21.06-fold, respectively, compared to the control group by day 7. Conversely, the impact of sugars manifested gradually over time. The influence of AAs and sugars persisted beyond 240 days post-treatment cessation. Importantly, the proliferation of ARGs was closely linked to the enrichment of plant growth-promoting bacteria (PGPBs) such as Pseudomonas, Cupriavidus, Azospirillum, Variovorax, and Ensifer. Functional analysis revealed that the potential features of ARGs and MGEs were associated with cell wall/membrane/envelope biogenesis, cell motility, and inorganic ion transport. This study offers novel insights into the factors influencing the dynamics of ARGs in the plant rhizosphere and may contribute to ecologically sustainable agricultural practices.}, } @article {pmid39937671, year = {2025}, author = {Su, Z and Liu, T and Guo, J and Zheng, M}, title = {Kinetic and Physiological Characterization of Acidophilic Nitrobacter spp. in a Nitrite-Oxidizing Culture.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c10020}, pmid = {39937671}, issn = {1520-5851}, abstract = {Novel acidophilic nitrite-oxidizing Nitrobacter spp. were enriched, with kinetic and physiological features characterized comprehensively. The acidophilic Nitrobacter enrichment culture was cultivated in a membrane bioreactor at pH 4.6-5.5 for 500 days, with a relative abundance of 16S rRNA genes of 17.9 ± 0.5% during the characterization experiments. Metagenomic analysis recovered 2 Nitrobacter genomes, which corresponded to previously unknown species within the Nitrobacter genus with average nucleotide identity (ANI) < 91% compared to the publicly available genomes. In contrast to the known NOB, the acidophilic Nitrobacter enrichment culture exhibited strong tolerance to environmental stress, including low pH and free nitrous acid (FNA), and have low affinity for oxygen. Moreover, the acidophilic Nitrobacter enrichment culture also exhibited a higher nitrite affinity (Km = 0.19 ± 0.03 mg NO2[-]-N/L) than all currently characterized Nitrobacter cultures. These characteristics define acidophilic Nitrobacter as both a K-strategist and an adversity-strategist that tends to flourish in acidic activated sludge, where low pH (<5.5) and low nitrite levels suppress other nitrifiers. This study extends our understanding of nitrifiers growing in acidic environments and also provides a potential to remove nitrogen in acidic wastewater.}, } @article {pmid39936903, year = {2025}, author = {Elena, AX and Orel, N and Fang, P and Herndl, GJ and Berendonk, TU and Tinta, T and Klümper, U}, title = {Jellyfish blooms-an overlooked hotspot and potential vector for the transmission of antimicrobial resistance in marine environments.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0101224}, doi = {10.1128/msystems.01012-24}, pmid = {39936903}, issn = {2379-5077}, abstract = {Gelatinous zooplankton (GZ) represents an important component of marine food webs, capable of generating massive blooms with severe environmental impact. When these blooms collapse, considerable amounts of organic matter (GZ-OM) either sink to the seafloor or can be introduced into the ocean's interior, promoting bacterial growth and providing a colonizable surface for microbial interactions. We hypothesized that GZ-OM is an overlooked marine hotspot for transmitting antimicrobial resistance genes (ARGs). To test this, we first re-analyzed metagenomes from two previous studies that experimentally evolved marine microbial communities in the presence and absence of OM from Aurelia aurita and Mnemiopsis leidyi recovered from bloom events and thereafter performed additional time-resolved GZ-OM degradation experiments to improve sample size and statistical power of our analysis. We analyzed these communities for composition, ARG, and mobile genetic element (MGE) content. Communities exposed to GZ-OM displayed up to fourfold increased relative ARG and up to 10-fold increased MGE abundance per 16S rRNA gene copy compared to the controls. This pattern was consistent across ARG and MGE classes and independent of the GZ species, indicating that nutrient influx and colonizable surfaces drive these changes. Potential ARG carriers included genera containing potential pathogens raising concerns of ARG transfer to pathogenic strains. Vibrio was pinpointed as a key player associated with elevated ARGs and MGEs. Whole-genome sequencing of a Vibrio isolate revealed the genetic capability for ARG mobilization and transfer. This study establishes the first link between two emerging issues of marine coastal zones, jellyfish blooms and ARG spread, both likely increasing with future ocean change. Hence, jellyfish blooms are a quintessential "One Health" issue where decreasing environmental health directly impacts human health.IMPORTANCEJellyfish blooms are, in the context of human health, often seen as mainly problematic for oceanic bathing. Here we demonstrate that they may also play a critical role as marine environmental hotspots for the transmission of antimicrobial resistance (AMR). This study employed (re-)analyses of microcosm experiments to investigate how particulate organic matter introduced to the ocean from collapsed jellyfish blooms, specifically Aurelia aurita and Mnemiopsis leidyi, can significantly increase the presence of antimicrobial resistance genes and mobile genetic elements in marine microbial communities by up to one order of magnitude. By providing abundant nutrients and surfaces for bacterial colonization, organic matter from these blooms enhances ARG proliferation, including transfer to and mobility in potentially pathogenic bacteria like Vibrio. Understanding this connection highlights the importance of monitoring jellyfish blooms as part of marine health assessments and developing strategies to mitigate the spread of AMR in coastal ecosystems.}, } @article {pmid39936895, year = {2025}, author = {Paez-Diaz, JA and Nieves-Morales, R and Melendez-Martinez, G and Rivera-Lopez, EO and Rodríguez-Ramos, J and Rios-Velazquez, C}, title = {Characterization of intestinal fungal communities through ITS amplicon from metagenomic libraries of sea cucumber (Holothuria glaberrima).}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0132024}, doi = {10.1128/mra.01320-24}, pmid = {39936895}, issn = {2576-098X}, abstract = {The brown rock sea cucumber (Holothuria glaberrima) microbiome is vital for understanding its ecological dynamics. This study focuses on the microbial composition and abundance of fungi across different intestinal regions of H. glaberrima, giving insights into host-microbe interactions and supporting future ecological and comparative studies on their regeneration capabilities.}, } @article {pmid39935633, year = {2025}, author = {Wang, Y and Li, R and Wang, C and Sun, T and Zhang, H and Zhao, F and Liu, J and Hao, Y and Xie, X}, title = {The intestinal microbial community and function of Riptortus pedestris at different developmental stages and its effects on development.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1517280}, pmid = {39935633}, issn = {1664-302X}, abstract = {INTRODUCTION: Riptortus pedestris is a destructive pest that threatens multiple leguminous crops in China. The intestinal microbiota plays a crucial role in the growth and reproduction of host insects. However, the composition and function of the gut microbiota at different developmental stages remain unclear.

METHODS: Here, metagenomic sequencing was performed to clarify the gut microbial diversity and function in 2nd-, 3rd-, 4th-, and 5th- instar nymphs (2 N-5 N) and female adults (FAs) of R. pedestris and the effects of vital gut bacteria on development was detected. The gut bacteria have the stage specificity, indicating their function in the development of R. pedestris.

RESULTS: Enterococcus and Caballerronia were the predominant bacteria present during the development of the 2 N-FAs. In addition, the microbial abundances in the 3 N and 4 N guts were significantly greater than those in the others guts. Furthermore, 5 N harbored the abundant microbiota Burkholderia-Paraburkholderia-Caballeronia. The metabolic pathways were significantly enriched from 2 N to FAs. Carbohydrate metabolism, including glycoside hydrolases (GHs) and glycosyl transferases (GTs), occurs throughout the entire developmental stage. Many antibiotic resistance genes (ARGs) were detected from 2 N to FAs. The bacteria from Pseudomonadota and Bacillota presented a broad spectrum of antibiotic resistance. Excitingly, Burkholderia bacteria eliminated by antibiotic treatment were unable to molt normally, and their lifespan was shortened in nymphs, indicating that the gut microbiota had a significant effect on nymph development.

CONCLUSION: In summary, our results, for the first time, systematically illustrate the abundance and function across the gut microbiota from the different developmental stages of R. pedestris and demonstrate that the genera Burkholderia are crucial during the development of R. pedestris. This study provides the basis for stinkbug management strategies that focus on the pivotal gut microbiota.}, } @article {pmid39935632, year = {2025}, author = {Tang, Y and Wang, L and Fu, J and Zhou, F and Wei, H and Wu, X and Fan, S and Zhang, X}, title = {Unraveling the microecological mechanisms of phosphate-solubilizing Pseudomonas asiatica JP233 through metagenomics: insights into the roles of rhizosphere microbiota and predatory bacteria.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1538117}, pmid = {39935632}, issn = {1664-302X}, abstract = {The effects of phosphate-solubilizing bacteria (PSB) on plant productivity are high variable under field conditions. Soil phosphorus (P) levels are proposed to impact PSB performance. Furthermore, the effect of exogenous PSB on rhizosphere microbial community and their functions are largely unexplored. Our study examined how different P background and fertilization affected the performance of PSB Pseudomonas asiatica JP233. We further conducted metagenomic sequencing to assess its impact on rhizosphere microbiota and functions, with a focus on genes related to soil P cycling. We found that JP233 could enhance P solubilization and tomato growth to different extent in both high and low P soils, irrespective of P fertilization. It was particularly effective in high P soil without extra fertilization. JP233 altered the rhizosphere microbial community, boosting taxa known for plant growth promotion. It also changed soil gene profiling, enriching pathways related to secondary metabolite biosynthesis, amino acids, carbon metabolism, and other key processes. Particularly, JP233 increased the abundance of most P cycle genes and strengthened their interconnections. Populations of certain predatory bacteria increased after JP233 inoculation. Our findings provide valuable insights into PSB's mechanisms for P solubilization and plant growth promotion, as well as potential adverse impacts of resident microbes on bioinoculants.}, } @article {pmid39935631, year = {2025}, author = {Redondo-Río, Á and Mundy, CJ and Tamames, J and Pedrós-Alió, C}, title = {Corrigendum: Specialized Bacteroidetes dominate the Arctic Ocean during marine spring blooms.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1534826}, doi = {10.3389/fmicb.2025.1534826}, pmid = {39935631}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2024.1481702.].}, } @article {pmid39935515, year = {2024}, author = {Yao, L and Zhou, X and Jiang, X and Chen, H and Li, Y and Xiong, X and Tang, Y and Zhang, H and Qiao, P}, title = {High-fat diet promotes gestational diabetes mellitus through modulating gut microbiota and bile acid metabolism.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1480446}, pmid = {39935515}, issn = {1664-302X}, abstract = {INTRODUCTION: Gestational diabetes mellitus (GDM) is a condition characterized by glucose intolerance during pregnancy, estimated to affect approximately 20% of the whole pregnancies and is increasing in prevalence globally. However, there is still a big gap in knowledge about the association between gut microbiota associated metabolism alterations and GDM development.

METHODS: All the participants accomplished the validated internet-based dietary questionnaire for Chinese and serum, fecal samples were collected. HFD, control diet or colesevelam intervention was fed to GDM mice models or Fxr-/- mice models, with or without antibiotics cocktail treatment. Fecal microbiota transplantation were used for further validation. Gut microbiota and metabolites were detected by metagenomic sequencing and high-performance liquid chromatography-mass spectrometry, respectively. Bile acids of serum, fecal samples from human and mice were analysised. Body weight, average feed intake, blood glucose, insulin levels and oral glucose tolerance test was performed among each groups. Expression levels of Fxr, Shp and Fgf15 mRNA and protein were detected by quantitative reverse transcription polymerase chain reaction and western blot, respectively.

RESULTS: Our data indicated that high fat diet (HFD) was linked with higher prevalence of GDM, and HFD was positively associated with poor prognosis in GDM patients. Moreover, compared with normal diet (ND) group, GDM patients from HFD group performed a loss of gut microbiota diversity and enrichment of Alistipes onderdonkii, Lachnospiraceae bacterium 1_7_58FAA, and Clostridium aspaaragiforme while ruduction of Akkermansiaceae, Paraprevotell xylaniphila, and Prevotella copri. Additionally, HFD aggravated GDM in mice and gut microbiota depletion by antibiotics crippled the effect of excess fat intake. BAs profile altered in HFD GDM patients and mice models. Fecal microbiota transplantation (FMT) further confirmed that gut microbiota contributed to bile acids (BAs) metabolic dysfunction during HFD-associated GDM development. Mechanically, HFD-FMT administration activated Fxr, Shp, and Fgf15 activity, disturbed the glucose metabolism and aggravated insulin resistance but not in HFD-FMT Fxr-/- mice and ND-FMT Fxr-/- mice. Furthermore, colesevelam intervention alleviated HFD-associated GDM development, improved BAs metabolism, suppressed Fxr, Shp, and Fgf15 activity only in WT mice but not in the Fxr-/- HFD + Colesevelam group and Fxr-/- HFD group. HFD induced GDM and contributed to poor prognosis in GDM parturients through inducing gut microbial dysbiosis and metabolic alteration, especially appeared in BAs profile. Moreover, Fxr pathway participated in regulating HFD-associated gut microbiota disordered BAs metabolites and aggravating GDM in mice.

DISCUSSION: Modulating gut microbiota and BAs metabolites could be a potential therapeutic strategy in the prevention and treatment of HFD-associated GDM.}, } @article {pmid39935055, year = {2025}, author = {Huang, Y and Zheng, X and Zhao, Z and Tao, J and Hu, T and Han, Z and Lin, T}, title = {Integration of manganese ores with activated carbon into constructed wetland for greenhouse gas emissions reduction.}, journal = {Journal of environmental management}, volume = {375}, number = {}, pages = {124205}, doi = {10.1016/j.jenvman.2025.124205}, pmid = {39935055}, issn = {1095-8630}, mesh = {*Wetlands ; *Greenhouse Gases ; *Manganese/metabolism ; Charcoal/chemistry ; Nitrogen/metabolism ; Phosphorus/metabolism ; }, abstract = {Manganese oxide and activated carbon (AC) are widely employed in constructed wetlands (CWs) to remove nutrients and reduce greenhouse gas (GHG) emissions, however, the effect and mechanism of AC combined with manganese ores (MO) on GHG emissions remain unclear. In this study, the mechanisms of nutrient removal and GHG emissions reduction were investigated by three vertical subsurface-flow CWs: gravel (CW-B), manganese ores (MO) uniformly mixing with gravel (CW-M), or activated carbon (CW-MC). The average removal efficiencies of chemical oxygen demand, total nitrogen and total phosphorus in CW-MC were markedly improved compared to CW-B and CW-M, reaching 82.72%, 95.72% and 93.43%, respectively. Moreover, the global warming potential (CO2 equivalent) of CW-MC was reduced by 52.80% and 36.88% relative to CW-B and CW-M, respectively. Mixing of MO with AC reduced the loss of manganese and further enhanced the manganese cycling process by X-ray photoelectron spectroscope and concentration of Mn(Ⅱ) in CWs analysis. The introduction of MO and AC enhanced the PN/PS ratio of extracellular polymeric substances and facilitated extracellular electron transfer (EET). Furthermore, metagenomic analysis showed that the abundances of denitrifying, manganese oxidizing and electroactive bacteria genera were enhanced in the CW-MC, which promoted the transformation of nitrogen and manganese. Meanwhile, high abundances of denitrification and EET related genes were observed in CW-MC, improving denitrification efficiency and reducing N2O emission. This study elucidated the impacts and mechanisms of MO and AC on GHG emissions, providing a new insight to improve manganese-based CW performance.}, } @article {pmid39933522, year = {2025}, author = {Xu, CCY and Fugère, V and Barbosa da Costa, N and Beisner, BE and Bell, G and Cristescu, ME and Fussmann, GF and Gonzalez, A and Shapiro, BJ and Barrett, RDH}, title = {Pre-exposure to stress reduces loss of community and genetic diversity following severe environmental disturbance.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2025.01.037}, pmid = {39933522}, issn = {1879-0445}, abstract = {Environmental stress caused by anthropogenic impacts is increasing worldwide. Understanding the ecological and evolutionary consequences for biodiversity will be crucial for our ability to respond effectively. Historical exposure to environmental stress is expected to select for resistant species, shifting community composition toward more stress-tolerant taxa. Concurrent with this species sorting process, genotypes within resistant taxa that have the highest relative fitness under severe stress are expected to increase in frequency, leading to evolutionary adaptation. However, empirical demonstrations of these dual ecological and evolutionary processes in natural communities are rare. Here, we provide evidence for simultaneous species sorting and evolutionary adaptation across multiple species within a natural freshwater bacterial community. Using a two-phase stressor experimental design (acidification pre-exposure followed by severe acidification) in aquatic mesocosms, we show that pre-exposed communities were more resistant than naive communities to taxonomic loss when faced with severe acid stress. However, after sustained severe acidification, taxonomic richness of both pre-exposed and naive communities eventually converged. All communities experiencing severe acidification became dominated by an acidophilic bacterium, Acidiphilium rubrum, but this species retained greater genetic diversity and followed distinct evolutionary trajectories in pre-exposed relative to naive communities. These patterns were shared across other acidophilic species, providing repeated evidence for the impact of pre-exposure on evolutionary outcomes despite the convergence of community profiles. Our results underscore the need to consider both ecological and evolutionary processes to accurately predict the responses of natural communities to environmental change.}, } @article {pmid39933221, year = {2025}, author = {Cao, Y and Fan, X and Zang, T and Li, Y and Tu, Y and Wei, Y and Bai, J and Liu, Y}, title = {Gut microbiota causes depressive phenotype by modulating glycerophospholipid and sphingolipid metabolism via the gut-brain axis.}, journal = {Psychiatry research}, volume = {346}, number = {}, pages = {116392}, doi = {10.1016/j.psychres.2025.116392}, pmid = {39933221}, issn = {1872-7123}, abstract = {Emerging evidence suggests that changes in the gut microbiota (GM) are related to prenatal depression onset, but the underlying molecular mechanisms remain obscure. This study was conducted to explore how disordered GM is involved in the onset of prenatal depression through the microbiome-gut-brain (MGB) axis. We transplanted fecal microbiota from women with and without prenatal depression into germ-free mice. Fecal metagenomic sequencing and LC-MS untargeted metabolomics analysis were performed to identify the GM composition, function, and metabolites in mice. Lipid metabolomics analysis was then used to characterize the lipid metabolism of brain tissue in mice. We found that mice transplanted with fecal microbiota from women with prenatal depression exhibited depressive-like behaviors as well as characteristic disorders of the phylum Firmicutes. Weighted Gene Correlation Network Analysis identified three microbial and one metabolic module in the gut, alongside two lipid metabolic modules in the brain, as significantly related to all depressive-like behaviors. These modules were enriched for glycerophospholipid and sphingolipid metabolism. In addition, the GM of mice with depressive-like behaviors were enriched and deficient in relevant functions and enzymes in the glycerophospholipid (mainly phosphatidylethanolamine) and sphingolipid (mainly hexosyl-ceramide) metabolic pathways, respectively. Consistently, glycerophospholipid and sphingolipid metabolites in the brains of depressive-like mice were up- and down-regulated. Increased phosphatidylethanolamine and decreased hexosyl-ceramide were significantly related to differential genera in the gut. Collectively, our findings provide a novel microbial and metabolic framework for understanding the role of the MGB axis in prenatal depression, indicating that the GM may be involved in the onset of depressive phenotypes by modulating central glycerophospholipid and sphingolipid metabolic homeostasis.}, } @article {pmid39932999, year = {2025}, author = {Tepekule, B and Barcik, W and Staiger, WI and Bergadà-Pijuan, J and Scheier, T and Brülisauer, L and Hall, AR and Günthard, HF and Hilty, M and Kouyos, RD and Brugger, SD}, title = {Computational and in vitro evaluation of probiotic treatments for nasal Staphylococcus aureus decolonization.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {7}, pages = {e2412742122}, doi = {10.1073/pnas.2412742122}, pmid = {39932999}, issn = {1091-6490}, support = {1449 M//Promedica Stiftung/ ; GRS-09420//Gebert Rüf Stiftung (Gebert Rüf Foundation)/ ; GRS-09420//Gebert Rüf Stiftung (Gebert Rüf Foundation)/ ; BSSGI0_155851//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; K-84804 - 01 - 01//UZH | Foundation for Research in Science and the Humanities (Stiftung für wissenschaftliche Forschung)/ ; }, mesh = {*Probiotics/administration & dosage/pharmacology ; *Staphylococcus aureus/drug effects ; Humans ; *Staphylococcal Infections/microbiology/drug therapy ; *RNA, Ribosomal, 16S/genetics ; Anti-Bacterial Agents/pharmacology ; Microbiota/drug effects ; Nose/microbiology ; Computer Simulation ; Adult ; }, abstract = {Despite the rising challenge of antibiotic resistance, current approaches to eradicate nasal pathobionts Staphylococcus aureus and Streptococcus pneumoniae rely on antibacterials. An alternative is the artificial inoculation of commensal bacteria, i.e., probiotic treatment, supported by the increasing evidence for commensal-mediated inhibition of pathogens. To systematically investigate the potential of this approach, we developed a quantitative framework simulating the nasal microbiome dynamics by combining mathematical modeling with longitudinal microbiota data. By inferring community parameters using 16S ribosomal RNA (rRNA) amplicon sequencing data and simulating the nasal microbial dynamics of patients colonized with S. aureus, we compared the decolonization performance of probiotic and antibiotic treatments under different assumptions on patients' community composition and susceptibility profile. To further compare the robustness of these treatments, we simulated an S. aureus challenge and quantified the recolonization probability. Through in vitro experiments using nasal swabs of adults colonized with S. aureus, we confirmed that after antibiotic treatment, recolonization of S. aureus was inhibited in samples treated with a probiotic mixture compared to the nontreated control. Our results suggest that probiotic treatment outperforms antibiotics in terms of decolonization performance, recolonization robustness, and leads to less collateral reduction in the microbiome diversity. Thus, probiotic treatment may provide a promising alternative to combat antibiotic resistance, with the additional advantage of personalized treatment options via using the patient's own metagenomic data. The combination of an in silico framework with in vitro experiments using clinical samples reported in this work is an important step forward to further investigate this alternative in clinical trials.}, } @article {pmid39932948, year = {2025}, author = {Gao, ZY and Zhao, XD and Chen, C and Zhao, FJ and Zhang, SY}, title = {Paddy Soil Flooding and Nonflooding Affect the Transcriptional Activity of Arsenic Methylation and Demethylation Communities.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c08620}, pmid = {39932948}, issn = {1520-5851}, abstract = {The intermediate product methylarsenite [MMA(III)] of arsenic (As) methylation can be methylated to dimethylarsenate (DMA), which causes rice straighthead disease via the As methylation enzyme (ArsM), demethylated to arsenite via the As demethylation enzyme (ArsI), or excreted from cells via the MMA(III) efflux enzyme (ArsP). Whereas As methylation is commonly reported in flooded soils, As demethylation is mostly mediated by aerobes. We used custom-built ROCker models (accuracies of 99.7-99.9%) to quantify the short-read sequences carrying As genes and investigate the variations in the transcriptional activity of the arsM, arsI, and arsP genes in flooded and nonflooded paddy soils. We revealed significantly (p < 0.05) greater transcriptional activity of the arsM and arsP genes in flooded than nonflooded soils, whereas the transcriptional activity of the arsI genes was comparable. MMA(III) demethylation in flooded soils is possibly coupled with denitrification, as revealed by the significantly (p < 0.05) positively correlated genes in terms of transcriptional activity. Moreover, we showed that microbes coexpressing the arsM and arsI genes were dominated by Actinomycetota and Pseudomonadota. This study sheds light on the active microbial communities involved in As methylation and demethylation in paddy soils and provides insights into the prevention of rice straighthead disease.}, } @article {pmid39932663, year = {2025}, author = {da Silva Pereira, M and Alcantara, LM and de Freitas, LM and de Oliveira Ferreira, AL and Leal, PL}, title = {Microbial Rumen proteome analysis suggests Firmicutes and Bacteroidetes as key producers of lignocellulolytic enzymes and carbohydrate-binding modules.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, pmid = {39932663}, issn = {1678-4405}, support = {Coordenação de Aperfeiçoamento de Pessoal de Nível Superior//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; Fundação de Amparo à Pesquisa do Estado da Bahia//Fundação de Amparo à Pesquisa do Estado da Bahia/ ; Conselho Nacional de Desenvolvimento Científico e Tecnológico//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, abstract = {Lignocellulosic biomass, rich in cellulose, hemicellulose, and lignin, offers a sustainable source for biofuels and and production of other materials such as polymers, paper, fabrics, bioplastics and biofertilizers. However, its complex structure hinders efficient conversion. Chemical, enzymatic, and microbial methods aim to unlock the trapped sugars and phenols. The rumen microbiome, a fascinating ecosystem within ruminant animals, holds particular promise. The Hungate 1000 project sequenced 410 microbial genomes from the rumen, enabling in silico screening for lignocellulolytic enzymes. This approach saves time and resources, supporting the development of sustainable bioconversion technologies aligned with the UN's 2030 agenda goals. Analysis of these 410 predicted proteomes revealed diverse carbohydrate-active enzymes (CAZymes) and carbohydrate-binding modules (CBMs) across various microorganisms. Notably, Firmicutes and Bacteroidetes dominated CAZyme and CBM production, suggesting collaborative efforts among different phyla during degradation. The presence of CBM50 and chitinases hints at the ability to utilize chitin from fungal cell walls. Interestingly, the absence of ligninolytic auxiliary activity enzymes reaffirms the rumen microbiome's incapability of directly degrading lignin. However, enzymes facilitating the loosening of the cell wall by cleaving lignin-hemicellulose linkages were identified. This suggests a strategy for making cellulose more accessible to hydrolytic enzymes. This study highlights the intricate relationship between rumen microbes, contributing necessary enzymes for plant cell wall deconstruction in this unique environment. Additionally, it underlines the power of in silico techniques for analyzing big data, paving the way for advancements in sustainable bioconversion.}, } @article {pmid39932403, year = {2025}, author = {Momo Cabrera, P and Bokulich, NA and Zimmermann, P}, title = {Evaluating stool microbiome integrity after domestic freezer storage using whole-metagenome sequencing, genome assembly, and antimicrobial resistance gene analysis.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0227824}, doi = {10.1128/spectrum.02278-24}, pmid = {39932403}, issn = {2165-0497}, abstract = {UNLABELLED: The gut microbiome is crucial for host health. Early childhood is a critical period for the development of a healthy gut microbiome, but it is particularly sensitive to external influences. Recent research has focused on using advanced techniques like shotgun metagenome sequencing to identify key microbial signatures and disruptions linked to disease. For accurate microbiome analysis, samples need to be collected and stored under specific conditions to preserve microbial integrity and composition, with -80°C storage considered the gold standard for stabilization. This study investigates the effect of domestic freezer storage on the microbial composition of stool samples obtained from 20 children under 4 years of age with the use of shotgun metagenome sequencing. Fresh stool samples were aliquoted into sterile tubes, with one aliquot stored at 4°C and analyzed within 24 hours, while others were frozen in domestic freezers (below -18°C) and analyzed after 1 week, 2 months, and 6 months. Assessments of contig assembly quality, microbial diversity, and antimicrobial resistance genes revealed no significant degradation or variation in microbial composition.

IMPORTANCE: Most prior studies on sample storage have relied on amplicon sequencing, which is less applicable to metagenome sequencing-given considerations of contig quality and functional gene detection-and less reliable in representing microbial composition. Moreover, the effects of domestic freezer storage for at-home stool collection on microbiome profiles, contig quality, and antimicrobial resistance gene profiles have not been previously investigated. Our findings suggest that stool samples stored in domestic freezers for up to 6 months maintain the integrity of metagenomic data. These findings indicate that domestic freezer storage does not compromise the integrity or reproducibility of metagenomic data, offering a reliable and accessible alternative for temporary sample storage. This approach enhances the feasibility of large-scale at-home stool collection and citizen science projects, even those focused on the more easily perturbed early life microbiome. This advancement enables more inclusive research into the gut microbiome, enhancing our understanding of its role in human health.}, } @article {pmid39932299, year = {2025}, author = {Cui, H and Wang, S and Fan, S and Long, H and Lin, J and Ding, W and Zhang, W}, title = {Branched-chain amino acid metabolism supports Roseobacteraceae positive interactions in marine biofilms.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0241124}, doi = {10.1128/aem.02411-24}, pmid = {39932299}, issn = {1098-5336}, abstract = {UNLABELLED: Interspecies interactions are key factors affecting the stability of microbial communities. However, microbial interactions in marine biofilms, which constitute up to 80% of the microbial biomass in certain marine environments, are not well understood. We addressed this knowledge gap by coculturing four marine biofilm-derived Roseobacteraceae strains (Leisingera aquaemixtae M597, Roseibium aggregatum S1616, Alloyangia pacifica T6124, and Sulfitobacter indolifex W002) in 14 single carbon sources. Overall, 140 coculture experiments revealed 39.3% positive interactions compared to 8.3% negative interactions. When the carbon source was consumed by only one strain, the interaction between the strains was more likely to be positive. The interaction between S1616 and M597, when cultured in D-gluconic acid, was further studied as an example. S1616-M597 coculture displayed a higher D-gluconic acid consumption rate than S1616 monoculture, whereas M597 could not use D-gluconic acid as the sole carbon source. The supernatant of S1616 monoculture supported the growth of M597, and branched-chain amino acids in the supernatant were consumed. Transcriptomic analysis suggested that M597 induced the expression of genes for branched-chain amino acid biosynthesis in S1616. Additionally, metagenomic analysis revealed the wide distribution and a strongly correlated co-occurrence of the four strains in global oceanic biofilms. Together, our findings show that interspecies positive interactions are prevalent among marine-biofilm Roseobacteraceae, and the interactions are likely to be mediated by branched-chain amino acids metabolism.

IMPORTANCE: Interspecies interactions are crucial for microbial community structure and function. Despite well-studied social behaviors in model microorganisms, species interactions in natural marine biofilms especially Roseobacteraceae with complex metabolic pathways are not well understood. Our findings suggest that positive microbial interactions, which can be mediated by branched-chain amino acid biosynthesis, are common among marine-biofilm Roseobacteraceae. This study provides new insights into microbial interactions and the ecology of marine biofilms.}, } @article {pmid39931947, year = {2025}, author = {Liu, Y and Zhao, T and Wang, Z and Zhang, Y and Shen, J and Lu, B}, title = {The microbiome- and metabolome-modulating activity of dietary cholesterol: insights from the small and large intestines.}, journal = {Food & function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d4fo03049d}, pmid = {39931947}, issn = {2042-650X}, abstract = {Cholesterol is an important lipid molecule that affects the gut microbiome upon ingestion. We systematically investigated the effects of cholesterol on the microbiota of the large and small intestines using ex vivo and in vivo models, combining flow cytometry, metabolomics, and metagenomics. The results showed that cholesterol directly causes a loss of bacterial membrane polarity and integrity, as well as a reduction in microbial metabolic activity. Cholesterol directly affected the global metabolism of the large and small intestinal microbiota, including amino acid, carbohydrate, and nucleotide metabolism. Ex vivo and in vivo studies shared similar results, showing that cholesterol increased the abundance of the primary bile acid-metabolizing bacteria Clostridium and Dorea in the large intestinal microbiota, confirming the enrichment effect of cholesterol on these bacteria. In the in vivo model, increased conjugated bile acids in the small intestine and decreased abundance of BSH-containing Bifidobacterium were observed due to cholesterol. Only in vivo models have demonstrated that cholesterol increases phosphatidylcholine levels in both the small and large intestines, which may be related to the effects of cholesterol on host metabolism. The pro-inflammatory capacity of the intestinal microbiota was enhanced by cholesterol, as evidenced by the increased levels of IL-1β and TNF-α in THP-1 cells upon stimulation with cholesterol-treated microbiota. This study comprehensively elucidates the effects of cholesterol on the composition and metabolic functions of the microbiota in both the large and small intestines. It offers a novel perspective on the ways in which cholesterol affects host metabolism via the gut microbiome.}, } @article {pmid39931676, year = {2025}, author = {Dutkiewicz, Z and Singleton, CM and Sereika, M and Villada, JC and Mussig, AJ and Chuvochina, M and Albertsen, M and Schulz, F and Woyke, T and Nielsen, PH and Hugenholtz, P and Rinke, C}, title = {Proposal of Patescibacterium danicum gen. nov., sp. nov. in the ubiquitous bacterial phylum Patescibacteriota phyl. nov.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycae147}, pmid = {39931676}, issn = {2730-6151}, abstract = {Candidatus Patescibacteria is a diverse bacterial phylum that is notable for members with ultrasmall cell size, reduced genomes, limited metabolic capabilities, and dependence on other prokaryotic hosts. Despite the prevalence of the name Ca. Patescibacteria in the scientific literature, it is not officially recognized under the International Code of Nomenclature of Prokaryotes and lacks a nomenclatural type. Here, we rectify this situation by describing two closely related circular metagenome-assembled genomes and by proposing one of them (ABY1[TS]) to serve as the nomenclatural type for the species Patescibacterium danicum [TS] gen. nov., sp. nov. according to the rules of the SeqCode. Rank-normalized phylogenomic inference confirmed the stable placement of P. danicum [TS] in the Ca. Patescibacteria class ABY1. Based on these results, we propose Patescibacterium gen. nov. to serve as the type genus for associated higher taxa, including the phylum Patescibacteriota phyl. nov. We complement our proposal with a genomic characterization, metabolic reconstruction, and biogeographical analysis of Patescibacterium. Our results confirm small genome sizes (<1 Mbp), low GC content (>36%), and the occurrence of long gene coding insertions in the 23S rRNA sequences, along with reduced metabolic potential, inferred symbiotic lifestyle, and a global distribution. In summary, our proposal will provide nomenclatural stability to the fourth-largest phylum in the bacterial domain.}, } @article {pmid39931490, year = {2025}, author = {Gong, L and Li, X and Ji, L and Chen, G and Han, Z and Su, L and Wu, D}, title = {Characterization and comparison of gut microbiota in patients with acute pancreatitis by metagenomics and culturomics.}, journal = {Heliyon}, volume = {11}, number = {3}, pages = {e42243}, pmid = {39931490}, issn = {2405-8440}, abstract = {Acute pancreatitis (AP) is a common gastrointestinal disorder with a high mortality rate. This study sought to identify the microbial community structure in patients with AP using metagenomics and culturomics. Compared to healthy controls, patients with AP exhibited a significant decrease in alpha diversity; a higher abundance of unclassified Enterococcus species (sp), Enterococcus faecium, and Enterococcus faecalis; and a lower abundance of Eubacterium rectale. A total of 336 isolates from 25 genera and 44 species were obtained by sample cultivation. The dominant species identified in patients with AP were Enterococcus faecium and Klebsiella grimontii, whereas those in the healthy controls were Enterococcus faecium, Escherichia coli, and Bacteroides faecis. Our research has contributed to the expanded understanding of the genome, diversity, and function of the intestinal microbiota in patients with AP and provided some reference for selecting culture medium and sample processing methods.}, } @article {pmid39931275, year = {2024}, author = {Skoulakis, A and Skoufos, G and Ovsepian, A and Hatzigeorgiou, AG}, title = {Machine learning models reveal microbial signatures in healthy human tissues, challenging the sterility of human organs.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1512304}, pmid = {39931275}, issn = {1664-302X}, abstract = {BACKGROUND: The presence of microbes within healthy human internal organs still remains under question. Our study endeavors to discern microbial signatures within normal human internal tissues using data from the Genotype-Tissue Expression (GTEx) consortium. Machine learning (ML) models were developed to classify each tissue type based solely on microbial profiles, with the identification of tissue-specific microbial signatures suggesting the presence of distinct microbial communities inside tissues.

METHODS: We analyzed 13,871 normal RNA-seq samples from 28 tissues obtained from the GTEx consortium. Unaligned sequencing reads with the human genome were processed using AGAMEMNON, an algorithm for metagenomic microbial quantification, with a reference database comprising bacterial, archaeal, and viral genomes, alongside fungal transcriptomes. Gradient-boosting ML models were trained to classify each tissue against all others based on its microbial profile. To validate the findings, we analyzed 38 healthy living tissue samples (samples from healthy tissues obtained from living individuals, not deceased) from an independent study, as the GTEx samples were derived from post-mortem biopsies.

RESULTS: Tissue-specific microbial signatures were identified in 11 out of the 28 tissues while the signatures for 8 tissues (Muscle, Heart, Stomach, Colon tissue, Testis, Blood, Liver, and Bladder tissue) demonstrated resilience to in silico contamination. The models for Heart, Colon tissue, and Liver displayed high discriminatory performance also in the living dataset, suggesting the presence of a tissue-specific microbiome for these tissues even in a living state. Notably, the most crucial features were the fungus Sporisorium graminicola for the heart, the gram-positive bacterium Flavonifractor plautii for the colon tissue, and the gram-negative bacterium Bartonella machadoae for the liver.

CONCLUSION: The presence of tissue-specific microbial signatures in certain tissues suggests that these organs are not devoid of microorganisms even in healthy conditions and probably they harbor low-biomass microbial communities unique to each tissue. The discoveries presented here confront the enduring dogma positing the sterility of internal tissues, yet further validation through controlled laboratory experiments is imperative to substantiate this hypothesis. Exploring the microbiome of internal tissues holds promise for elucidating the pathophysiology underlying both health and a spectrum of diseases, including sepsis, inflammation, and cancer.}, } @article {pmid39931171, year = {2025}, author = {Yang, X and Pan, Y and Gao, CP and Li, H and Zhang, YH and Huang, CL and Cao, L and Xiao, SY and Zhou, Z}, title = {Prominence of Microbiota to Predict Fibrous Stenosis in Crohn's Disease.}, journal = {Journal of inflammation research}, volume = {18}, number = {}, pages = {1413-1423}, pmid = {39931171}, issn = {1178-7031}, abstract = {PURPOSE: Intestinal fibrous stenosis due to Crohn's disease (CD) is highly prevalent. Although several clinical risk factors for fibrous stenosis have been identified, such as perianal fistulizing disease, small bowel disease location, and deep mucosal ulceration, predicting fibrous stenosis remains challenging. The intestinal microbiota plays a crucial role in the development and progression of CD. However, its role in intestinal fibrous stenosis is poorly understood. Leveraging a single-center cross-sectional study, we aimed to investigate the role of fecal microbiota in CD-associated fibrous stenosis.

METHODS: Using metagenomic analysis, we examined the differences in fecal microbiota between CD patients with intestinal fibrous stenosis and those without stenosis. We identified specific microbiota and assessed their predictive accuracy for intestinal fibrous stenosis. Additionally, we explored functional differences in intestinal microbiota between the two groups.

RESULTS: : Our investigation of fecal samples revealed no significant differences in the gut microbiota structure between patients with fibrous stenosis and those without stenosis in CD. However, taxonomically, we found 70 taxa with significantly different abundance (p < 0.05) between the two groups. Furthermore, LEfSe analysis indicated that g_Bacteroides and g_Enterocloster could predict intestinal fibrous stenosis while p_Actinobacteria, c_Actinomycetia, c_Bacilli, o_Lactobacillales, f_Streptococcaceae and g_Streptococcus could predict CD without stenosis. Functional analysis revealed differential enrichment in five metabolic pathways at the KEGG pathway level in CD patients with fibrous stenosis, including sphingolipid metabolism, lipoic acid metabolism, and biosynthesis of neomycin, kanamycin and gentamicin. In the eggNOG database, we observed differences in four functional categories between the two groups, encompassing cellular process, signaling, and metabolism.

CONCLUSION: Fecal microbiota significantly impacted intestinal fibrous stenosis in CD. Although there were no significant differences in alpha and beta diversities, fibrous stenosis was associated with changes in microbiota composition and function, suggesting the potential of fecal microbiota in predicting CD-associated fibrous stenosis.}, } @article {pmid39931040, year = {2025}, author = {Weng, D and Zhou, H and Huang, G and Cao, Q and Wang, H and Cao, Z and Xie, Q}, title = {Escherichia coli in the T11-12 Thoracic Vertebrae: A Case Report.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {693-702}, pmid = {39931040}, issn = {1178-6973}, abstract = {BACKGROUND: Pyogenic thoracic spondylitis is a rare but severe infection, particularly when complicated by sepsis and acute kidney injury (AKI). Early diagnosis and precise management are essential for improving outcomes, given the limitations of traditional microbiology detection methods in identifying the causative pathogens.

CASE PRESENTATION: A 68-year-old immunocompetent male presented with recurrent fever, fatigue, loss of appetite and initial evidence of sepsis and AKI upon admission. With the prompt computed tomography (CT)-guided percutaneous biopsy of the thoracic vertebrae, Escherichia coli was identified as the causative pathogen using metagenomic next-generation sequencing (mNGS). A diagnosis of pyogenic thoracic spondylitis was then made followed by the treatment of antibiotics optimized by therapeutic drug monitoring (TDM) techniques. With a total effective antibiotic treatment period of 7 weeks, the patient recovered without resorting to surgical interventions.

CONCLUSION: This is a rare case of acute thoracic spondylitis caused by E. coli, successfully treated without surgery. This case highlights the significant challenges in diagnosis and treatment. It underscores the value of mNGS in identifying rare infections and emphasizes the role of TDM in optimizing antibiotic therapy, providing a reference for future cases of rare and critical infections with fever of unknown origin.}, } @article {pmid39930446, year = {2025}, author = {Dong, L and Ji, Z and Hu, J and Jiang, Q and Wei, W}, title = {Oral microbiota shifts following tooth loss affect gut health.}, journal = {BMC oral health}, volume = {25}, number = {1}, pages = {213}, pmid = {39930446}, issn = {1472-6831}, support = {YSP202314//Young Scientist Program of Beijing Stomatological Hospital, Capital Medical University/ ; }, mesh = {Animals ; *Tooth Loss/microbiology ; Mice ; *Gastrointestinal Microbiome ; *Mice, Inbred C57BL ; RNA, Ribosomal, 16S ; Saliva/microbiology ; Feces/microbiology ; Microbiota ; Mouth/microbiology ; Male ; }, abstract = {BACKGROUND: Tooth loss not only impairs oral function but also affects gut health by altering the host microbiota. Understanding the oral-gut axis can provide insights into systemic health implications following tooth loss.

METHODS: Using an animal model, we extracted the molars of C57 mice. Saliva and fecal samples were collected for 16S rRNA and metagenomic sequencing to analyze changes in the oral and gut microbiota. Pearson correlation analysis assessed the relationship between altered microbial communities.

RESULTS: The study found a significant reduction in oral microbiota diversity following tooth loss, with increased Proteobacteria and decreased Muribacter. Gut microbiota showed increased Firmicutes and decreased Bacteroidota. Correlations between oral and gut microbiota changes were observed, indicating a potential link between tooth loss and alterations in intestinal microbial balance.

CONCLUSION: In the mouse model, tooth loss disrupted the balance of the oral-gut microbiota, with potential implications for intestinal health. Although these findings are from a murine model, considering the existence of the oral-gut axis balance in the human body, it is reasonable to postulate that following tooth loss in humans, the health of the intestinal microecology may also warrant attention.}, } @article {pmid39930163, year = {2025}, author = {Kahraman Ilıkkan, Ö}, title = {Lactobacillomics as a new notion in lactic acid bacteria research through omics integration.}, journal = {World journal of microbiology & biotechnology}, volume = {41}, number = {2}, pages = {68}, pmid = {39930163}, issn = {1573-0972}, mesh = {*Lactobacillales/genetics/metabolism ; *Probiotics ; *Metabolomics ; *Genomics/methods ; *Proteomics ; Fermentation ; Metagenomics ; Humans ; Genome, Bacterial ; }, abstract = {Omics technologies are a set of disciplines that analyze large-scale molecular data to understand biological systems in a holistic way. These technologies aim to reveal the structure, functions and interactions of organisms by studying processes at many levels of biomolecules, from the genome to metabolism. Lactobacillomics is introduced as an interdisciplinary field that integrates multiple "omics" technologies-including genomics, transcriptomics, proteomics, metabolomics, and metagenomics- to provide a comprehensive insight into "lactic acid bacteria" species. Lactobacillomics aims to elucidate the genetic, metabolic, and functional characteristics of lactic acid bacteria (LAB) species, providing insights into the mechanisms underlying their probiotic effects and contributions to the host microbiome. By analyzing genomes and metabolic pathways, researchers can identify specific genes responsible for health-promoting functions and desirable fermentation characteristics, which can guide the development of targeted probiotic strains with optimized health benefits. The integration of these omics data allows facilitating the discovery of biomarkers for health and disease states, the development of new probiotics tailored to specific populations or health conditions, and the optimization of fermentation processes to enhance the safety, flavor, and nutritional profile of fermented foods. A comprehensive review and bibliometric analysis were conducted to provide an overview of this promising field between 2005 and 2025 by examining Web of Science Core Collection data. Research results reveal trending topics, future perspectives, and key areas of growth within lactic acid bacteria (LAB) studies, particularly as they intersect with omics technologies.}, } @article {pmid39930064, year = {2025}, author = {Eriksen, AMH and Rodríguez, JA and Seersholm, F and Hollund, HI and Gotfredsen, AB and Collins, MJ and Grønnow, B and Pedersen, MW and Gilbert, MTP and Matthiesen, H}, title = {Exploring DNA degradation in situ and in museum storage through genomics and metagenomics.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {210}, pmid = {39930064}, issn = {2399-3642}, mesh = {*Museums ; *Metagenomics/methods ; *Genomics/methods ; Animals ; *Archaeology ; Greenland ; Bone and Bones ; DNA/genetics ; }, abstract = {Understanding the environmental and microbial processes involved in DNA degradation from archaeological remains is a fundamental part of managing bone specimens. We investigated the state of DNA preservation in 33 archaeozoological caribou (Rangifer tarandus) ribs excavated from the same excavation trench at a former Inuit hunting camp in West Greenland, separated by 43 years: 1978 and 2021. Our findings show that DNA is better preserved in the most recently excavated samples, indicating a detrimental effect of museum storage on DNA integrity. Additionally, our data reveals a diverse microbiome in these bones, encoding genes relevant for bone degradation, such as enzymatic families relating to collagenases, peptidases and glycosidases. Microbes associated with bone degradation were present in both new and historical samples, with museum-stored bones showing significantly more DNA damage. Overall, our research sheds light on the nuanced dynamics governing the preservation of genomic material in archaeological contexts, underscoring the vital importance of careful considerations in museum curation practices for the sustainable conservation of invaluable skeletal records in museum repositories and in situ.}, } @article {pmid39929976, year = {2025}, author = {Sardar, P and Beresford-Jones, BS and Xia, W and Shabana, O and Suyama, S and Ramos, RJF and Soderholm, AT and Tourlomousis, P and Kuo, P and Evans, AC and Imianowski, CJ and Conti, AG and Wesolowski, AJ and Baker, NM and McCord, EAL and Okkenhaug, K and Whiteside, SK and Roychoudhuri, R and Bryant, CE and Cross, JR and Pedicord, VA}, title = {Gut microbiota-derived hexa-acylated lipopolysaccharides enhance cancer immunotherapy responses.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {39929976}, issn = {2058-5276}, support = {206245/Z/17/Z//Wellcome Trust (Wellcome)/ ; 302351/Z/23/Z//Wellcome Trust (Wellcome)/ ; A2194//Rosetrees Trust/ ; EP/X024709/1//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; }, abstract = {The gut microbiome modulates immunotherapy treatment responses, and this may explain why immune checkpoint inhibitors, such as anti-PD-1, are only effective in some patients. Previous studies correlated lipopolysaccharide (LPS)-producing gut microbes with poorer prognosis; however, LPS from diverse bacterial species can range from immunostimulatory to inhibitory. Here, by functionally analysing faecal metagenomes from 112 patients with melanoma, we found that a subset of LPS-producing bacteria encoding immunostimulatory hexa-acylated LPS was enriched in microbiomes of clinical responders. In an implanted tumour mouse model of anti-PD-1 treatment, microbiota-derived hexa-acylated LPS was required for effective anti-tumour immune responses, and LPS-binding antibiotics and a small-molecule TLR4 antagonist abolished anti-PD-1 efficacy. Conversely, oral administration of hexa-acylated LPS to mice significantly augmented anti-PD-1-mediated anti-tumour immunity. Penta-acylated LPS did not improve anti-PD-1 efficacy in vivo and inhibited hexa-acylated LPS-induced immune activation in vitro. Microbiome hexa-acylated LPS therefore represents an accessible predictor and potential enhancer of immunotherapy responses.}, } @article {pmid39929376, year = {2025}, author = {Wu, B and Tang, Y and Zhao, L and Gao, Y and Shen, X and Xiao, S and Yao, S and Qi, H and Shen, F}, title = {Integrated network pharmacological analysis and multi-omics techniques to reveal the mechanism of polydatin in the treatment of silicosis via gut-lung axis.}, journal = {European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences}, volume = {}, number = {}, pages = {107030}, doi = {10.1016/j.ejps.2025.107030}, pmid = {39929376}, issn = {1879-0720}, abstract = {Silicosis is a pulmonary disease characterized by inflammation and progressive fibrosis. Previous studies have shown that polydatin (PD) has potential biological activity in key signaling pathways regulating inflammation and apoptosis. To investigate the effect of PD on rats with silicosis, this study used network pharmacology and molecular docking methods to determine the target of PD treatment for silicosis. The therapeutic effect of PD on silicosis was confirmed by measuring the lung injury score, hydroxyproline content, and mRNA expression levels of key targets. In addition, metagenomic sequencing and gas chromatography-mass spectrometry were used to determine the gut microbiota composition and targeted metabolomics analysis, respectively. The results showed that PD could inhibit the expression of inflammation-related indexes and apoptosis-related indexes at protein and mRNA levels. PD also regulates the diversity of the intestinal flora and the content of short-chain fatty acids. In conclusion, the current data suggest that PD has a protective effect against silica-induced lung injury and plays a protective role in regulating intestinal flora diversity and short-chain fatty acid levels through the gut-lung axis.}, } @article {pmid39929003, year = {2025}, author = {Bakir-Gungor, B and Temiz, M and Canakcimaksutoglu, B and Yousef, M}, title = {Prediction of colorectal cancer based on taxonomic levels of microorganisms and discovery of taxonomic biomarkers using the Grouping-Scoring-Modeling (G-S-M) approach.}, journal = {Computers in biology and medicine}, volume = {187}, number = {}, pages = {109813}, doi = {10.1016/j.compbiomed.2025.109813}, pmid = {39929003}, issn = {1879-0534}, abstract = {Colorectal cancer (CRC) is one of the most prevalent forms of cancer globally. The human gut microbiome plays an important role in the development of CRC and serves as a biomarker for early detection and treatment. This research effort focuses on the identification of potential taxonomic biomarkers of CRC using a grouping-based feature selection method. Additionally, this study investigates the effect of incorporating biological domain knowledge into the feature selection process while identifying CRC-associated microorganisms. Conventional feature selection techniques often fail to leverage existing biological knowledge during metagenomic data analysis. To address this gap, we propose taxonomy-based Grouping Scoring Modeling (G-S-M) method that integrates biological domain knowledge into feature grouping and selection. In this study, using metagenomic data related to CRC, classification is performed at three taxonomic levels (genus, family and order). The MetaPhlAn tool is employed to determine the relative abundance values of species in each sample. Comparative performance analyses involve six feature selection methods and four classification algorithms. When experimented on two CRC associated metagenomics datasets, the highest performance metric, yielding an AUC of 0.90, is observed at the genus taxonomic level. At this level, 7 out of top 10 groups (Parvimonas, Peptostreptococcus, Fusobacterium, Gemella, Streptococcus, Porphyromonas and Solobacterium) were commonly identified for both datasets. Moreover, the identified microorganisms at genus, family, and order levels are thoroughly discussed via refering to CRC-related metagenomic literature. This study not only contributes to our understanding of CRC development, but also highlights the applicability of taxonomy-based G-S-M method in tackling various diseases.}, } @article {pmid39927868, year = {2025}, author = {Zouiouich, S and Wan, Y and Vogtmann, E and Porras, C and Abnet, CC and Shi, J and Sinha, R}, title = {Sample size estimations based on human microbiome temporal stability over six months: a shallow shotgun metagenome sequencing analysis.}, journal = {Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology}, volume = {}, number = {}, pages = {}, doi = {10.1158/1055-9965.EPI-24-0839}, pmid = {39927868}, issn = {1538-7755}, abstract = {BACKGROUND: Biological factors impact the human microbiome, highlighting the need for reasonably estimating sample sizes in future population studies.

METHODS: We assessed the temporal stability of fecal microbiome diversity, species composition, and genes and functional pathways through shallow shotgun metagenome sequencing. Using intraclass correlation coefficients (ICC), we measured biological variability over six months. We estimated case numbers for 1:1 or 1:3 matched case-control studies, considering significance levels of 0.05 and 0.001 with 80% power, based on the collected fecal specimens per participant.

RESULTS: The fecal microbiome's temporal stability over six months varied (ICC <0.6) for most alpha and beta diversity metrics. Heterogeneity was seen in species, genes, and pathways stability (ICC 0.0-0.9). Detecting an odds ratio of 1.5 per standard deviation required 1,000-5,000 cases (0.05 significance for alpha and beta; 0.001 for species, genes, pathways) with equal cases and controls. Low-prevalent species needed 15,102 cases; high-prevalent species required 3,527. Similar needs applied to genes and pathways. In a 1:3 matched case-control study with one fecal specimen, 10,068 cases were needed for low-prevalent species; 2,351 for high-prevalent species. For odds ratios of 1.5 with multiple specimens, cases needed for low-prevalent species were 15,102 (one specimen), 8,267 (two specimens), and 5,989 (three specimens).

CONCLUSIONS: Detecting disease associations requires a large number of cases. Repeating prediagnostic samples and matching cases to more controls could decrease the needed number of cases for such detections.

IMPACT: Our results will help future epidemiologic studies design and implement well-powered microbiome studies.}, } @article {pmid39927795, year = {2025}, author = {Huang, D and Chen, Y and Li, C and Yang, S and Lin, L and Zhang, X and Su, X and Liu, L and Zhao, H and Luo, T and Cai, S and Ren, Q and Dong, H}, title = {Variations in salivary microbiome and metabolites are associated with immunotherapy efficacy in patients with advanced NSCLC.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0111524}, doi = {10.1128/msystems.01115-24}, pmid = {39927795}, issn = {2379-5077}, abstract = {Lung cancer is a leading cause of cancer mortality, with non-small cell lung cancer (NSCLC) comprising the majority of cases. Despite the advent of immune checkpoint inhibitors (ICIs), a significant number of patients fail to achieve a durable response, highlighting the need to understand the factors influencing treatment efficacy. Saliva samples and tumor samples were collected from 20 NSCLC patients. The salivary microbiota was profiled using metagenomic next-generation sequencing, and metabolites were analyzed via liquid chromatography-mass spectrometry to identify correlations among bacteria, metabolites, and immunotherapy responses. Immunohistochemistry (IHC) analysis of tissue samples verified the result. Besides, in vitro experiments and tumor tissue microarray, including 70 NSCLC patients, were utilized to further explore the potential mechanism linking the oral microbiome and immunotherapy efficacy. The study revealed several differential species and distinct metabolite compositions between responders and non-responders to ICI therapy in NSCLC and explored correlations and mechanisms between microbiota metabolites and immunotherapy resistance. Notably, it was found that several Neisseria and Actinomyces species were significantly enriched in responders and identified lipids and lipid-like molecules associated with PD-L1 expression levels and treatment outcomes. Importantly, several differential lipid molecules were associated with differential species. Further, in vitro experiments and IHC experiments indicated that abnormal fat metabolism linked to dysbiosis is correlated with immunotherapy resistance through regulation of CD8[+] T cell activity/infiltration and PD-L1 expression. Specific saliva microbiome and its associated lipids metabolites are significantly associated with the efficacy of ICI-based therapy in lung cancer. Our findings suggest that oral microbiome modulation and targeting lipid metabolism could improve immunotherapy responses, offering new avenues for personalized treatment strategies.IMPORTANCEIn non-small cell lung cancer, our study links specific salivary microbiome profiles and related lipid metabolites to the efficacy of immune checkpoint inhibitor (ICI) therapies. Responders showed enrichment of certain Neisseria and Actinomyces species and distinct lipid compositions. These lipids correlate with PD-L1 expression and CD8[+] T cell activity, affecting treatment outcomes. Our results imply that modulating the oral microbiome and targeting lipid metabolism may enhance ICI effectiveness, suggesting novel personalized therapeutic approaches.}, } @article {pmid39927766, year = {2025}, author = {Li, M and Chen, Z and Zhang, W and Wu, T and Qi, Q and Huo, YX}, title = {Customization of Ethylene Glycol (EG)-Induced BmoR-Based Biosensor for the Directed Evolution of PET Degrading Enzymes.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e2413205}, doi = {10.1002/advs.202413205}, pmid = {39927766}, issn = {2198-3844}, support = {31961133014//National Natural Science Foundation of China/ ; 22278033//National Natural Science Foundation of China/ ; 23130228E//Tangshan Science and Technology Bureau/ ; B2023105008//Natural Science Foundation of Hebei Province/ ; }, abstract = {The immense volume of plastic waste poses continuous threats to the ecosystem and human health. Despite substantial efforts to enhance the catalytic activity, robustness, expression, and tolerance of plastic-degrading enzymes, the lack of high-throughput screening (HTS) tools hinders efficient enzyme engineering for industrial applications. Herein, we develop a novel fluorescence-based HTS tool for evolving polyethylene terephthalate (PET) degrading enzymes by constructing an engineered BmoR-based biosensor targeting the PET breakdown product, ethylene glycol (EG). The EG-responsive biosensors, with notably enhanced dynamic range and operation range, are customized by fluorescence-activated cell sorting (FACS)-assisted transcription factor engineering. The ingeniously designed SUMO-MHETase-FastPETase (SMF) chimera successfully addresses the functional soluble expression of MHETase in Escherichia coli and mitigates the inhibitory effect of mono-(2-hydroxyethyl) terephthalic acid (MHET) intermediate commonly observed with PETase alone. The obtained SM[M3]F mutant demonstrates 1.59-fold higher terephthalic acid (TPA) production, with a 1.18-fold decrease in Km, a 1.29-fold increase in Vmax, and a 1.52-fold increase in kcat/Km, indicating stronger affinity and catalytic activity toward MHET. Furthermore, the SM[M3]F crude extract depolymerizes 5 g L[-1] bis-(2-hydroxyethyl) terephthalic acid (BHET) into TPA completely at 37 °C within 10 h, which is then directedly converted into value-added protocatechuic acid (PCA) (997.16 mg L[-1]) and gallic acid (GA) (411.69 mg L[-1]) at 30 °C, establishing an eco-friendly 'PET-BHET-MHET-TPA-PCA-GA' upcycling route. This study provides a valuable HTS tool for screening large-scale PET and MHET hydrolases candidates or metagenomic libraries, and propels the complete biodegradation and upcycling of PET waste.}, } @article {pmid39927429, year = {2025}, author = {Duan, X and Duan, H and Zhao, C and Feng, L and Zhao, G and Chen, Y}, title = {Genome-Centric Metagenomics and Metaproteomics Profiled the Shared and Unique Taxa in Isomeric Fatty Acid-Differentiated Anaerobic Co-Digestion of Food Waste and Sludge.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c09839}, pmid = {39927429}, issn = {1520-5851}, abstract = {Fatty acids (FAs)-involving structures, widely occurring in production and life, have been increasingly considered as major feedstocks and potential platforms for renewable energy generation. However, the role of isomeric FAs (particularly trans-FAs) in high-concerned energy-reserving technology represented by anaerobic digestion (AD) remains unclear. This study displayed that trans-oleic acid (TOA, 10 mg/L) significantly increased methane production by 56% during the codigestion of food waste and sludge, whereas the same concentration of cis-oleic acid (COA) led to a slight 20% increase. Genome-centric meta-omics and biochemical tests indicated that acidogenic taxa that harbor and express distinct functions in the cell envelopes were primarily responsible for TOA/COA-differentiated AD. Four shared taxa, including three monodermal acidogens and one hydrogenotrophic methanogen, were common drivers of both TOA- and COA-enhanced AD, resulting in stronger acidification and hydrogenotrophic methanogenesis than in the control bioreactor without oleic acid. In addition to four shared species, two unique didermal acidogens were specific drivers of TOA-enhanced AD, demonstrating more robust acidification compared to that of COA-enhanced AD. This study profiled the geometry-dependent effects of isomeric FAs on AD, providing new insights into targeted regulation for energy conservation and decarbonization of FAs-involving feedstocks.}, } @article {pmid39927333, year = {2024}, author = {Safika, S and Indrawati, A and Hidayat, R and Puarada, ARR}, title = {Characterizing the gut microbiome of birds-of-paradise in the northwest lowland of Papua Island.}, journal = {Open veterinary journal}, volume = {14}, number = {12}, pages = {3345-3354}, pmid = {39927333}, issn = {2218-6050}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Bacteria/isolation & purification/classification/genetics ; Indonesia ; Feces/microbiology ; Passeriformes/microbiology ; }, abstract = {BACKGROUND: Birds-of-paradise, renowned for their stunning plumage and intricate mating rituals, have been extensively studied for their external characteristics. However, the microbial communities inhabiting their digestive tracts remain largely unexplored. The gut microbiome plays a vital role in host health and physiology, influencing digestion, nutrient absorption, and immune function. Understanding the microbiome of birds-of-paradise, particularly in their unique tropical rainforest habitats, may offer valuable insights into their adaptation and overall health.

AIM: This study aims to characterize the gut microbiome of birds-of-paradise and to explore the relationship between microbiome and host.

METHODS: Fecal samples were collected from Jayapura Regency, Indonesia, with non-invasive sampling methods. DNA was extracted using the DNeasy PowerSoil Pro Kit. Shotgun metagenomic sequencing was performed on the MGI DNBSEQ-G400 platform to obtain DNA sequences. DNA sequences were analyzed using DIAMOND followed by MEGAN6 to provide insights into the relative abundance of bacterial taxa within the microbiome.

RESULTS: Using Operational Taxonomy Unit analysis we identified 1,398,117 sequences from 5,048,280 initial sequences. Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, and Acidobacteria were the dominant phyla, with other phyla present in smaller amounts. Burkholderiales, Hyphomicrobiales, Sphingobacteriales, and Enterobacterales were dominant orders, each with specific functional roles. Family and Genus-Level Abundance: Flavobacteriaceae, Comamonadaceae, and Sphingobacteriaceae were dominant families, while Flavobacterium, Delftia, and Pedobacter were dominant genera. Delftia sp., Pedobacter sp., Klebsiella pneumoniae, Achromobacter sp., Bacillus pumilus, Rhizobium sp., and Brevundimonas sp. were among the most abundant species.

CONCLUSION: The microbiome in the gut of birds-of-paradise is characterized by a diverse community of bacteria, fungi, and other microorganisms. The abundance of specific orders, families, and genera varies between samples, suggesting that differences in diet, habitat, or host genetics may influence microbiome composition. The findings reveal a diverse and complex microbial community that likely plays a crucial role in host health and physiology.}, } @article {pmid39927261, year = {2025}, author = {Hou, S and Jiang, Y and Zhang, F and Cheng, T and Zhao, D and Yao, J and Wen, P and Jin, L and Huang, S}, title = {Unveiling early-life microbial colonization profile through characterizing low-biomass maternal-infant microbiomes by 2bRAD-M.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1521108}, pmid = {39927261}, issn = {1664-302X}, abstract = {INTRODUCTION: The microbial composition of human breast milk and infant meconium offers critical insights into the early microbial colonization profile, and it greatly contributes to the infant's immune system and long-term health outcomes. However, analyzing these samples often faces technical challenges and limitations of low-resolution using conventional approaches due to their low microbial biomass.

METHODS: Here, we employed the type IIB restriction enzymes site-associated DNA sequencing for microbiome (2bRAD-M) as a reduced metagenomics method to address these issues and profile species-level microbial composition. We collected breast milk samples, maternal feces, and infant meconium, comparing the results from 2bRAD-M with those from both commonly used 16S rRNA amplicon sequencing and the gold-standard whole metagenomics sequencing (WMS).

RESULTS: The accuracy and robustness of 2bRAD-M were demonstrated through its consistently high correlation of microbial individual abundance and low whole-community-level distance with the paired WMS samples. Moreover, 2bRAD-M enabled us to identify clinical variables associated with infant microbiota variations and significant changes in microbial diversity across different lactation stages of breast milk.

DISCUSSION: This study underscores the importance of employing 2bRAD-M in future large-scale and longitudinal studies on maternal and infant microbiomes, thereby enhancing our understanding of microbial colonization in early life stages and demonstrating further translational potential.}, } @article {pmid39927182, year = {2025}, author = {Takeuchi, S and Kawada, JI and Suzuki, A and Sakamoto, K and Fukuda, Y and Horiba, K and Suzuki, T and Torii, Y and Shindo, Y and Ito, Y}, title = {Metagenomic Analysis of Lung Microbiome in Patients With Interstitial Lung Diseases and Sarcoidosis: An Experimental Study.}, journal = {Health science reports}, volume = {8}, number = {2}, pages = {e70328}, pmid = {39927182}, issn = {2398-8835}, abstract = {BACKGROUND AND AIMS: Interactions between the lung microbiome and pulmonary epithelium plays a pivotal role in shaping immunity in the lung. Idiopathic pulmonary fibrosis (IPF) is the most common interstitial lung disease (ILD). Some patients with IPF develop episodic acute exacerbations often associated with microbial dysbiosis in the lungs. This study aimed to investigate etiologic agents as well as the lung microbiome in patients with ILDs and sarcoidosis.

METHODS: This study analyzed 31 patients divided into the IPF (IPF-stable, n = 12), acute exacerbation of ILDs (AE-ILDs, n = 6), and sarcoidosis (n = 13) groups. Bronchoalveolar lavage fluid (BALF) samples were analyzed by RNA-based metagenomic next-generation sequencing (NGS) on an Illumina platform.

RESULTS: In total, 87 pathogens were detected using metagenomic NGS at the genus level. Prevotella, Streptococcus, and Veillonella dominated the BALF microbial communities, and sequence reads of these bacteria were abundant, especially in the sarcoidosis group. Conversely, only a small number of bacterial reads were detected in the AE-ILDs group, and the overall proportion of microbial composition differed from that of the other groups. No significant difference was found in community diversity (α-diversity) among the groups, whereas the structural similarity of the microflora (β-diversity) differed significantly between the AE-ILDs and sarcoidosis groups.

CONCLUSIONS: Bacterial sequence reads in BALF were smaller in both the IPF-stable and AE-ILD groups than in the sarcoidosis group. Dysbiosis in the lung microbiome has been observed in patients with AE-ILD and may be related to the progression of inflammation.}, } @article {pmid39926599, year = {2024}, author = {Guo, M and Gao, M and Gao, J and Zhang, T and Jin, X and Fan, J and Wang, Q and Li, X and Chen, J and Zhu, Z}, title = {Corrigendum: Identifying risk factors for secondary infection post-SARS-COV-2 infection in patients with severe and critical COVID-19.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1548101}, doi = {10.3389/fimmu.2024.1548101}, pmid = {39926599}, issn = {1664-3224}, abstract = {[This corrects the article DOI: 10.3389/fimmu.2021.715023.].}, } @article {pmid39925879, year = {2025}, author = {Gao, Y and Qin, G and Liang, S and Yin, J and Wang, B and Jiang, H and Liu, M and Luo, F and Li, X}, title = {Metagenomic Sequencing Combined with Metabolomics to Explore Gut Microbiota and Metabolic Changes in Mice with Acute Myocardial Infarction and the Potential Mechanism of Allicin.}, journal = {Drug design, development and therapy}, volume = {19}, number = {}, pages = {771-791}, pmid = {39925879}, issn = {1177-8881}, mesh = {Animals ; *Disulfides ; *Gastrointestinal Microbiome/drug effects ; *Sulfinic Acids/pharmacology/administration & dosage ; Mice ; *Myocardial Infarction/drug therapy/metabolism ; Male ; *Metabolomics ; Metagenomics ; Mice, Inbred C57BL ; Administration, Oral ; Disease Models, Animal ; }, abstract = {BACKGROUND: Acute myocardial infarction (AMI) is a significant contributor to global morbidity and mortality. Allicin exhibits promising therapeutic potential in AMI as a primary bioactive component derived from garlic; however, its underlying mechanisms remain incompletely elucidated.

METHODS: Our study induced AMI in mice by ligating the left coronary artery, and administered allicin orally for 28 days. The cardioprotective effects of allicin treatment were comprehensively assessed using echocardiography, histopathological examinations, intestinal barrier function, and serum inflammatory factors. The potential mechanisms of allicin were elucidated through analysis of metagenomics and serum metabolomics. Network pharmacology (NP) was used to further investigate and validate the possible molecular mechanisms of allicin.

RESULTS: Our findings revealed allicin's capacity to ameliorate cardiac impairments, improve intestinal barrier integrity, and reduce serum IL-18 and IL-1β levels after AMI. Further analysis demonstrated that the administration of allicin has the potential to ameliorate intestinal flora disorder following AMI by modulating the abundance of beneficial bacteria, such as g_Lactobacillus, g_Prevotella, g_Alistipes, and g_Limosilactobacillus, while reducing the abundance of harmful bacteria g_Parasutterella. Additionally, it exhibits the ability to enhance myocardial energy metabolism flexibility through modulating metabolites and key enzymes associated with the fatty acid metabolic pathway. Mechanistically, NP and in vivo experiments indicated that allicin might suppress pyroptosis and reduce inflammatory response via blocked activation of the NF-κB-mediated NLRP3/Caspase-1/GSDMD pathway. Moreover, Spearman correlation analysis suggested a significant association between the allicin-induced alterations in microbiota and metabolites with cardiac function and inflammatory cytokines.

CONCLUSION: Our study demonstrated that allicin alleviated myocardial injury and reduced inflammatory response by inhibiting the NF-κB-mediated NLRP3/Caspase-1/GSDMD pathway while remodeling microbiota disturbance, improving serum metabolic disorder, and enhancing the intestinal barrier. These research findings offer a novel perspective on the potential therapeutic value of allicin as an adjunctive dietary supplement to conventional treatments for AMI.}, } @article {pmid39925382, year = {2025}, author = {Mcgonigal, M and Ito, K}, title = {From Soil to Surface: Exploring the Impact of Green Infrastructure on Microbial Communities in the Built Environment.}, journal = {Journal of genomics}, volume = {13}, number = {}, pages = {10-23}, pmid = {39925382}, issn = {1839-9940}, abstract = {High microbial diversity offers extensive benefits to both the environment and human health, contributing to ecosystem stability, nutrient cycling, and pathogen suppression. In built environments, factors such as building design, human activity, and cleaning protocols influence microbial communities. This study investigates the impact of landscape design on microbial diversity and function within the "Visionary Lab" exhibition in Tokyo, Japan, using 16S rRNA gene amplicon sequencing and shallow shotgun sequencing. Despite the limited sample size, the study suggests that the Visionary Lab samples may exhibit higher microbial diversity compared to other museum areas. Potential distinct microbial community structures may be correlated with sampling locations. However, despite this, no consistent patterns were observed in virulence factors or antimicrobial resistance genes across the samples. Metabolic function analysis showed varied profiles, suggesting diverse ecological interactions influenced that may be by the curated landscape. This suggest that the curated landscape design may have the potential to enhance microbial diversity, highlighting a possible avenue to create healthier and more sustainable built environments. However, the lack of consistent patterns in virulence factors and antimicrobial resistance genes underscores the complexity of microbial community dynamics.}, } @article {pmid39925312, year = {2025}, author = {Uçak, S and Yegin, Z and Yurt, MNZ and Altunbas, O and Sudagidan, M and Ozalp, VC}, title = {Bacterial Profiling of Brined Grapevine Leaves Collected from Different Local Markets in Türkiye.}, journal = {Chemistry & biodiversity}, volume = {}, number = {}, pages = {e202403049}, doi = {10.1002/cbdv.202403049}, pmid = {39925312}, issn = {1612-1880}, abstract = {Microorganisms linked to the grapevine, Vitis vinifera, can impact crop quality, plant growth, and human and plant health. This study examined the bacterial community structures of brined grapevine leaves (n=56) taken from seven distinct regions in Türkiye using next-generation sequencing technology. Investigations were also conducted into the samples' chemical properties. Firmicutes was the dominant phylum, followed by Proteobacteria, Actinobacteria, and Bacteroidetes. Bacillaceae was the predominant family in the analyzed samples, followed by Clostridiaceae, Peptostreptococcaceae, and Enterobacteriaceae. Bacillus was the dominant genus, followed by Lysinibacillus and Clostridium sensu stricto. The samples exhibited differences in terms of pH, total acidity, and salt content. The pH values of the brined grapevine leaves ranged from 2.31 to 6.91, the acidity levels ranged from 0.09% to 1.80%, and the salt percentages ranged from 3.39% to 49.14%. This research provides pioneering information for bacterial community analysis of brined grapevine leaves.}, } @article {pmid39924893, year = {2025}, author = {Chen, Y and Fang, H and Chen, H and Liu, X and Zhao, J and Stanton, C and Ross, RP and Chen, W and Yang, B}, title = {Bifidobacterium inhibits the progression of colorectal tumorigenesis in mice through fatty acid isomerization and gut microbiota modulation.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2464945}, pmid = {39924893}, issn = {1949-0984}, mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; *Colorectal Neoplasms/microbiology/metabolism/prevention & control/pathology ; Humans ; *Bifidobacterium/metabolism/physiology ; *Linoleic Acids, Conjugated/metabolism ; Male ; Probiotics/administration & dosage/pharmacology ; Female ; Carcinogenesis ; PPAR gamma/metabolism/genetics ; Fatty Acids/metabolism ; Mice, Inbred C57BL ; NF-kappa B/metabolism ; Middle Aged ; Apoptosis ; Disease Progression ; Butyric Acid/metabolism ; Disease Models, Animal ; }, abstract = {Colorectal cancer (CRC) represents the third most common cancer worldwide. Consequently, there is an urgent need to identify novel preventive and therapeutic strategies for CRC. This study aimed to screen for beneficial bacteria that have a preventive effect on CRC and to elucidate the potential mechanisms. Initially, we compared gut bacteria and bacterial metabolites of healthy volunteers and CRC patients, which demonstrated that intestinal conjugated linoleic acid (CLA), butyric acid, and Bifidobacterium in CRC patients were significantly lower than those in healthy volunteers, and these indicators were significantly negatively correlated with CRC. Next, spontaneous CRC mouse model were conducted to explore the effect of supplemental CLA-producing Bifidobacterium on CRC. Supplementation of mice with CLA-producing Bifidobacterium breve CCFM683 and B. pseudocatenulatum MY40C significantly prevented CRC. Moreover, molecular approaches demonstrated that CLA and the CLA-producing gene, bbi, were the key metabolites and genes for CCFM683 to prevent CRC. Inhibitor intervention results showed that PPAR-γ was the key receptor for preventing CRC. CCFM683 inhibited the NF-κB signaling pathway, up-regulated MUC2, Claudin-1, and ZO-1, and promoted tumor cell apoptosis via the CLA-PPAR-γ axis. Additionally, fecal microbiota transplantation (FMT) and metagenomic analysis showed that CCFM683 up-regulated Odoribacter splanchnicus through CLA production, which then prevented CRC by producing butyric acid, up-regulating TJ proteins, regulating cytokines, and regulating gut microbiota. These results will contribute to the clinical trials of Bifidobacterium and the theoretical research and development of CRC dietary products.}, } @article {pmid39923562, year = {2025}, author = {Solazzo, G and Rovelli, S and Iodice, S and Chung, M and Frimpong, M and Bollati, V and Ferrari, L and Ghedin, E}, title = {The microbiome of Total Suspended Particles and its influence on the respiratory microbiome of healthy office workers.}, journal = {Ecotoxicology and environmental safety}, volume = {291}, number = {}, pages = {117874}, doi = {10.1016/j.ecoenv.2025.117874}, pmid = {39923562}, issn = {1090-2414}, abstract = {Air particulate matter (PM) is widely recognized for its potential to negatively affect human health, including changes in the upper respiratory microbiome. However, research on PM-associated microbiota remains limited and mostly focused on PM (e.g., PM2.5 and PM10). This study aims to characterize for the first time the microbiome of Total Suspended Particles (TSP) and investigate the correlations of indoor TSP with the human upper respiratory microbiome. Biological and environmental samples were collected over three collection periods lasting three weeks each, between May and July 2022 at the University of Milan and the University of Insubria Como. TSP were sampled using a filter-based technique, while respiratory samples from both anterior nares (AN) and the nasopharynx (NP) were collected using swabs. Microbiome analysis of both human (N = 145) and TSP (N = 51) samples was conducted on metagenomic sequencing data. A comparison of indoor and outdoor TSP microbiomes revealed differences in microbial diversity and taxonomic composition. The indoor samples had higher relative abundance of environmental bacteria often associated with opportunistic infections like Paracoccus sp., as well as respiratory bacteria such as Staphylococcus aureus and Klebsiella pneumoniae. Additionally, both indoor and outdoor TSP samples contained broad spectrum antibiotic resistance genes. Indoor TSP exposure was negatively associated with commensal bacteria and positively associated with Staphylococcus aureus relative abundance. Finally, a correlation between the relative abundance of respiratory bacteria identified in the indoor TSP and the upper respiratory microbiome was found, suggesting a potential interaction between TSP and the upper airways.}, } @article {pmid39923519, year = {2025}, author = {Peng, Q and Cheng, S and Lin, J and Zheng, H and Xie, G}, title = {Metabolic and microbial functionality during the fermentation of traditional Amaranth stems: Insights from metagenomics, flavoromics, and metabolomics.}, journal = {Food chemistry}, volume = {474}, number = {}, pages = {143216}, doi = {10.1016/j.foodchem.2025.143216}, pmid = {39923519}, issn = {1873-7072}, abstract = {Fermented Amaranth stems is a traditional Chinese fermented vegetable known for its distinctive aroma, produced through natural microbial fermentation. However, the metabolic processes, flavor compounds, and microbial communities involved in its fermentation are not well understood. This study provides a comprehensive analysis using an integrated approach combining flavoromics, untargeted metabolomics, and metagenomics to examine the dynamic changes in metabolites and microbiota during fermentation. A total of 108 volatile organic compounds were identified, with sugar metabolism peaking on the third day of fermentation. The microbial community analysis revealed that key genera such as Pseudomonas, Acinetobacter, Pectobacterium, and Enterobacter play a significant role in flavor formation. The findings offer critical insights into the fermentation mechanisms and the production of flavor compounds, providing a foundation for optimizing fermentation processes and improving the flavor quality of fermented Amaranth stems. This research holds practical significance for enhancing food safety by controlling microbial communities during fermentation.}, } @article {pmid39923424, year = {2025}, author = {He, M and He, CQ and Ding, NZ}, title = {Human viruses: An ever-increasing list.}, journal = {Virology}, volume = {604}, number = {}, pages = {110445}, doi = {10.1016/j.virol.2025.110445}, pmid = {39923424}, issn = {1096-0341}, abstract = {It has been 124 years since yellow fever was demonstrated to be caused by a 'filterable agent'. While long-standing viral diseases, with the exception of smallpox, continue to be endemic, new ones have been emerging intermittently, primarily from a substantial zoonotic reservoir, leading to significant socioeconomic consequences. Currently, we are contending not only with the ongoing COVID-19 pandemic but with surges of various other viral infections. Recent metagenomic analyses have revealed a variety of novel human viruses whose health implications remain largely unclear. The following questions arise: How many human viruses have been identified? Which of these viruses are etiological agents of human diseases? This review aims to address the two inquiries and highlight the viruses that pose significant public health threats as outlined in the World Health Organization's Fact Sheets. Importantly, many human viruses are preventable; appropriate precautions can be implemented to mitigate the risk of infection.}, } @article {pmid39923290, year = {2025}, author = {Wang, S and Wu, M}, title = {Decoding the link between microbial secondary metabolites and colorectal cancer.}, journal = {Computational biology and chemistry}, volume = {115}, number = {}, pages = {108372}, doi = {10.1016/j.compbiolchem.2025.108372}, pmid = {39923290}, issn = {1476-928X}, abstract = {Colorectal cancer (CRC) is a prevalent form of cancer in humans, with the gut microbiota playing a significant role in its pathogenesis. Although previous research has primarily focused on the role of primary metabolites produced by gut microbes in CRC development, the role of secondary metabolites remains largely unexplored. Secondary metabolites are known to mediate crucial interactions between the microbiota and the host, potentially influencing CRC progression. However, their specific relationship to CRC pathogenesis is poorly understood. To address this gap, we performed a meta-analysis using fecal metagenomic data from a cohort of CRC patients and healthy controls, aiming to identify CRC-associated microbial secondary metabolite biosynthetic gene clusters (BGCs). Our findings not only provide valuable insights into the pathogenicity and carcinogenicity of CRC but also shed light on the potential mechanisms underlying its development.}, } @article {pmid39923117, year = {2025}, author = {Rouzé, T and Martayan, I and Marchet, C and Limasset, A}, title = {Fractional hitting sets for efficient multiset sketching.}, journal = {Algorithms for molecular biology : AMB}, volume = {20}, number = {1}, pages = {1}, pmid = {39923117}, issn = {1748-7188}, support = {IndexThePlanet, 101088572/ERC_/European Research Council/International ; AGATE ANR-21-CE45-0012//Agence Nationale de la Recherche/ ; }, abstract = {The exponential increase in publicly available sequencing data and genomic resources necessitates the development of highly efficient methods for data processing and analysis. Locality-sensitive hashing techniques have successfully transformed large datasets into smaller, more manageable sketches while maintaining comparability using metrics such as Jaccard and containment indices. However, fixed-size sketches encounter difficulties when applied to divergent datasets. Scalable sketching methods, such as sourmash, provide valuable solutions but still lack resource-efficient, tailored indexing. Our objective is to create lighter sketches with comparable results while enhancing efficiency. We introduce the concept of Fractional Hitting Sets, a generalization of Universal Hitting Sets, which cover a specified fraction of the k-mer space. In theory and practice, we demonstrate the feasibility of achieving such coverage with simple but highly efficient schemes. By encoding the covered k-mers as super-k-mers, we provide a space-efficient exact representation that also enables optimized comparisons. Our novel tool, supersampler, implements this scheme, and experimental results with real bacterial collections closely match our theoretical findings. In comparison to sourmash, supersampler achieves similar outcomes while utilizing an order of magnitude less space and memory and operating several times faster. This highlights the potential of our approach in addressing the challenges presented by the ever-expanding landscape of genomic data. supersampler is an open-source software and can be accessed at https://github.com/TimRouze/supersampler . The data required to reproduce the results presented in this manuscript is available at https://github.com/TimRouze/supersampler/experiments .}, } @article {pmid39922935, year = {2025}, author = {Das, BK and Gadnayak, A and Chakraborty, HJ and Pradhan, SP and Raut, SS and Das, SK}, title = {Exploring microbial players for metagenomic profiling of carbon cycling bacteria in sundarban mangrove soils.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {4784}, pmid = {39922935}, issn = {2045-2322}, mesh = {*Wetlands ; *Soil Microbiology ; *Metagenomics/methods ; *Bacteria/genetics/metabolism/classification ; *Carbon Cycle ; Carbon/metabolism ; Microbiota/genetics ; Ecosystem ; Metagenome ; Phylogeny ; }, abstract = {The Sundarbans, the world's largest tidal mangrove forest, acts as a crucial ecosystem for production, conservation, and the cycling of carbon and nitrogen. The study explored the hypothesis that microbial communities in mangrove ecosystems exhibit unique taxonomic and functional traits that play a vital part in carbon cycling and ecosystem resilience. Using metagenomic analysis to evaluate microbial communities in mangrove and non-mangrove environment, evaluating their composition, functional functions, and ecological relevance. The analysis revealed distinct microbial profiles, in mangrove and non-mangrove environments, with bacteria, proteobacteria, and viruses being the most prevalent groups, with varying abundances in each environment. Functional and taxonomical analysis identified genes involved in carbon regulation, including Triacylglycerol lipase, NarG, DsrB, DNA-binding transcriptional dual regulator CRP, Vanillate O-demethylase oxygenase, succinate-CoA ligase, Tetrahydrofolate ligase, Carboxylase, Ribulose-1,5-bisphosphate carboxylase/oxygenase, Glycine hydroxymethyltransferase, MAG: urease, Endosymbiont of Oligobrachia haakonmosbiensis, Ribulose bisphosphate carboxylase, Aconitate hydratase AcnA, and nitrous oxide reductase, suggesting the metabolic versatility of these microbial communities for carbon cycling. The findings emphasize the key role of microbial activity in preserving mangrove ecosystem health and resilience, highlighting the intricate interplay between microbial diversity, functional capabilities, and environmental factors.}, } @article {pmid39922085, year = {2025}, author = {Florio, M and Crudele, L and Sallustio, F and Moschetta, A and Cariello, M and Gadaleta, RM}, title = {Disentangling the nutrition-microbiota liaison in inflammatory bowel disease.}, journal = {Molecular aspects of medicine}, volume = {102}, number = {}, pages = {101349}, doi = {10.1016/j.mam.2025.101349}, pmid = {39922085}, issn = {1872-9452}, abstract = {Inflammatory Bowel Disease (IBD) is a set of chronic intestinal inflammatory disorders affecting the gastrointestinal (GI) tract. Beside compromised intestinal barrier function and immune hyperactivation, a common IBD feature is dysbiosis, characterized by a reduction of some strains of Firmicutes, Bacteroidetes, Actinobacteria and an increase in Proteobacteria and pathobionts. Emerging evidence points to diet and nutrition-dependent gut microbiota (GM) modulation, as etiopathogenetic factors and adjuvant therapies in IBD. Currently, no nutritional regimen shows universal efficacy, and advice are controversial, especially those involving restrictive diets potentially resulting in malnutrition. This review provides an overview of the role of macronutrients, dietary protocols and GM modulation in IBD patients. A Western-like diet contributes to an aberrant mucosal immune response to commensal bacteria and impairment of the intestinal barrier integrity, thereby triggering intestinal inflammation. Conversely, a Mediterranean nutritional pattern appears to be one of the most beneficial dietetic regimens able to restore the host intestinal physiology, by promoting eubiosis and preserving the intestinal barrier and immune function, which in turn create a virtuous cycle improving patient adherence to the pattern. Further clinical studies are warranted, to corroborate current IBD nutritional guidelines, and develop more accurate models to move forward precision nutrition and ameliorate patients' quality of life.}, } @article {pmid39921299, year = {2025}, author = {Li, Z and Han, X and Cong, L and Singh, P and Paiva, P and Branson, Y and Li, W and Chen, Y and Jaradat, DMM and Lennartz, F and Bayer, T and Schmidt, L and Garscha, U and You, S and Fernandes, PA and Ramos, MJ and Bornscheuer, UT and Weber, G and Wei, R and Liu, W}, title = {Structure-Guided Engineering of a Versatile Urethanase Improves Its Polyurethane Depolymerization Activity.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e2416019}, doi = {10.1002/advs.202416019}, pmid = {39921299}, issn = {2198-3844}, support = {2023YFC3905000//National Key Research and Development Program of China/ ; 32371530//National Natural Science Foundation of China/ ; XDC0120400//Strategic Priority Research Program of the Chinese Academy of Science/ ; TSBICIP-PTJJ-008//Tianjin Synthetic Biotechnology Innovation Capacity Improvement Project/ ; TSBICIP-PTJJ-014//Tianjin Synthetic Biotechnology Innovation Capacity Improvement Project/ ; TSBICIP-IJCP-003//Tianjin Synthetic Biotechnology Innovation Capacity Improvement Project/ ; LA/P/0008/2020//FCT/MCTES/ ; UIDP/50006/2020//FCT/MCTES/ ; UIDB/50006/2020//FCT/MCTES/ ; NNF22OC0072891//Novo Nordisk Fonden/ ; EHPC-REG-2023R03-163//European High-Performance Computing Joint Undertaking/ ; KA2-HSC-10//Investment and Networking Fund of the Helmholtz Association/ ; KA-HSC-13//Investment and Networking Fund of the Helmholtz Association/ ; 870294//Horizon 2020 Framework Programme/ ; 953214//Horizon 2020 Framework Programme/ ; }, abstract = {Polyurethane (PUR), the fifth most prevalent synthetic polymer, substantially contributes to the global plastic waste problem. Biotechnology-based recycling methods have recently emerged as innovative solutions to plastic waste disposal and sparked interest among scientific communities and industrial stakeholders in discovering and designing highly active plastic-degrading enzymes. Here, the ligand-free crystal structure of UMG-SP2, a metagenome-derived urethanase with depolymerization activities, at 2.59 Å resolution, as well as its (co-)structures bound to a suicide hydrolase inhibitor and a short-chain carbamate substrate at 2.16 and 2.40 Å resolutions, respectively, is reported. Structural analysis and molecular dynamics simulations reveal that the flexible loop L3 consisting of residues 219-226 is crucial for regulating the hydrolytic activity of UMG-SP2. The semi-rational redesign of UMG-SP2 reveals superior variants, A141G and Q399A, exhibiting over 30.7- and 7.4-fold increased activities on polyester-PUR and a methylene diamine derivative of PUR, respectively, compared to the wild-type enzyme. These findings advance the understanding of the structure-function relationship of PUR-hydrolyzing enzymes, which hold great promise for developing effective industrial PUR recycling processes and mitigating the environmental footprint of plastic waste.}, } @article {pmid39921224, year = {2025}, author = {Vieira, S and Adão, H and Vicente, CSL}, title = {Assessing spatial and temporal patterns of benthic bacterial communities in response to different sediment conditions.}, journal = {Marine environmental research}, volume = {204}, number = {}, pages = {106963}, doi = {10.1016/j.marenvres.2025.106963}, pmid = {39921224}, issn = {1879-0291}, mesh = {*Geologic Sediments/microbiology ; *Bacteria/classification/genetics ; Portugal ; *Estuaries ; *Ecosystem ; Environmental Monitoring ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; Microbiota ; }, abstract = {Benthic bacterial communities are sensitive to habitat condition and present a fast response to environmental stressors, which makes them powerful ecological indicators of estuarine environments. The aim of this work is to study the spatial-temporal patterns of benthic bacterial communities in response to contrasting environmental conditions and assess their potential as ecological indicators of estuarine sediments. We characterized the diversity of bacterial communities in three contrasting sites on Sado Estuary (SW Coast, Portugal) and 4 sampling occasions, using 16S metagenomic approach. Based on previous studies, we hypothesized that diversity patterns of bacterial communities will be distinct between sites and across sampling occasions. Bacterial communities were more influenced by each site conditions than by temporal variations in the sediments. The main drivers of bacterial distribution were sediments' composition, organic contents, and hydrodynamic activity. This work provided an important baseline dataset from Sado estuary to explore bacterial networks concerning benthic ecosystem functioning.}, } @article {pmid39921144, year = {2025}, author = {Cook, D and Kocurek, B and Stonecipher, C and Welch, KD and Gardner, DR and Mammel, M and Reed, E and Ramachandran, P and Erickson, D and Commichaux, S and Ottesen, A}, title = {DNA data (genome skims and metabarcodes) paired with chemical data demonstrate utility for retrospective analysis of forage linked to fatal poisoning of cattle.}, journal = {Toxicon : official journal of the International Society on Toxinology}, volume = {256}, number = {}, pages = {108285}, doi = {10.1016/j.toxicon.2025.108285}, pmid = {39921144}, issn = {1879-3150}, abstract = {Prepared and stored feeds, fodder, silage, and hay may be contaminated by toxic plants resulting in the loss of livestock. Several poisonous plants have played significant roles in livestock deaths from forage consumption in recent years in the Western United States including Salvia reflexa. Metagenomic data, genome skims and metabarcodes, have been used for identification and characterization of plants in complex botanical matrices including diet composition of animals, mixed forages, and herbal products. Here, chemistry, genome skims, and metabarcoding were used to retrospectively describe the composition of contaminated alfalfa hay from a case of Salvia reflexa (lanceleaf sage) poisoning that killed 165 cattle. Genome skims and metabarcoding provided similar estimates of the relative abundance of the Salvia in the hay samples when compared to chemical methods. Additionally, genome skims and metabarcoding provided similar estimates of species composition in the contaminated hay and rumen contents of poisoned animals. The data demonstrate that genome skims and DNA metabarcoding may provide useful tools for plant poisoning investigations.}, } @article {pmid39921114, year = {2025}, author = {Farooq, S and Talat, A and Dhariwal, A and Petersen, FC and Khan, AU}, title = {Transgenerational Gut Dysbiosis: Unveiling the Dynamics of Antibiotic Resistance through Mobile Genetic Elements from Mothers to Infants.}, journal = {International journal of antimicrobial agents}, volume = {}, number = {}, pages = {107458}, doi = {10.1016/j.ijantimicag.2025.107458}, pmid = {39921114}, issn = {1872-7913}, abstract = {The initial microbial colonization of the gut is seeded by microbes transmitted from the mother's gut, skin, and vaginal tract. As the gut microbiome evolves, a few transmitted microbes persist throughout life. Understanding the impact of mother-to-neonate gut microbiome and antibiotic resistance genes (ARGs) transmission is crucial for establishing its role in infants' immunity against pathogens. This study primarily explores mother-neonate ARG transmission through 125 publicly available fecal metagenomes, isolated from eighteen mother-neonate pairs. The core ARGs, detected in both mothers and their respective infants at all stages (birth, 1[st], 2[nd], 3[rd], 4[th], 8[th] and 12[th] months) included aminoglycosidases APH(3')-IIIa, Bifidobacterium adolescentis rpoB mutants conferring resistance to rifampicin, β-lactamases CblA-1, CfxA2, multi-drug resistance gene CRP, diaminopyrimidine resistance gene dfrF, fluoroquinolone-resistance gene emrR, macrolide; lincosamide; streptogramin resistance gene ErmB, ErmG, macrolide resistance gene Mef(En2), nucleosidase SAT-4, and tetracycline-resistance genes tet(O), tet(Q), and tet(W). Most of these infants and mothers were not administered any antibiotics. In infants, ARGs were predominantly carried by Bacillota, Pseudomonadota, and Actinomycetota, similar to the mothers. The dominant ARG-carrying opportunistic pathogens were Escherichia coli, Klebsiella, and Streptococcus, found across all infant cohorts. All the core ARGs were associated with mobile genetic elements, signifying the role of horizontal gene transfer(HGT). We detected 132 virulence determinants, mostly Escherichia coli-specific, including pilus chaperones, general secretion pathway proteins, type III secretion system effectors, and heme-binding proteins. Maternal-neonate transmission of ARGs along with possible nosocomial infections, mode of delivery, breastfeeding versus formula feeding, and gestation period, must be considered for mother-neonate health.}, } @article {pmid39921005, year = {2025}, author = {Wu, X and Wang, S and Zhao, W and Xi, Y and Li, S and Xin, F and Dong, W and Jia, H}, title = {Enhanced methane production through synergistic integration of quorum sensing Signals and microbial electrolysis in anaerobic digestion of low-quality biomass.}, journal = {Bioresource technology}, volume = {421}, number = {}, pages = {132153}, doi = {10.1016/j.biortech.2025.132153}, pmid = {39921005}, issn = {1873-2976}, abstract = {This study explored the synergistic effects of exogenous acyl homoserine lactones (AHLs) and microbial electrolysis (ME) on enhancing anaerobic digestion (AD) of low-quality biomass. The combined AHLs + ME strategy achieved a 79.50 % increase in cumulative methane production compared to the control, outperforming individual treatments. This enhancement was attributed to accelerated substrate degradation, selective enrichment of hydrogenotrophic methanogens (Methanobrevibacter, Methanobacterium, Methanofollis), and strengthened quorum sensing, electron transfer, and methane synthesis pathways. Metagenomic analysis revealed abundance upregulation of key genes involved in AHL synthesis (bjaI, rpaI, braI, rhiI) and sensing (solR, cepR, tofR), direct interspecies electron transfer (pilA, mtrC), and hydrogenotrophic methanogenesis (ftr, mvhD, vhuD, vhcD). This study offers a novel and sustainable strategy to optimize methane production from recalcitrant biomass, advancing AD-based waste-to-energy systems.}, } @article {pmid39920962, year = {2025}, author = {Wang, X and Gao, L and Wang, S and Zhang, X and Feng, R and Jia, S}, title = {Metagenomic insights into the assembly, function, and key taxa of bacterial community in full-scale pesticide wastewater treatment processes.}, journal = {Environmental research}, volume = {271}, number = {}, pages = {121037}, doi = {10.1016/j.envres.2025.121037}, pmid = {39920962}, issn = {1096-0953}, abstract = {Pesticide wastewater emerges as a typical refractory wastewater, characterized by complex composition and high toxicity, posing significant treatment challenges. Bacterial communities are responsible for biological treatment of refractory wastewater in full-scale pesticide wastewater treatment plants (PWWTPs), providing important implications for optimizing system performance and improving management strategies. However, the knowledge of their composition, diversity, function, assembly patterns, and biological interactions remains limited. Therefore, this study applied high-throughput sequencing, machine learning models, and statistical analysis to investigate key features of bacterial communities in eight PWWTPs. We found that Proteobacteria and Bacteroidota were the most abundant phyla, with Pseudomonas, Hyphomicrobium, Comamonas, and Thauera being dominant genera. Bacterial community distribution and diversity varied significantly among influents, sludges, and effluents, with sludges and effluents exhibiting higher diversity, richness, and evenness compared to influents. Deterministic processes primarily shaped the bacterial communities, accounting for 77.12%, 61.44%, and 64.05% of variation in influents, sludges, and effluents, respectively. Homogeneous selection explained 47.71%, 31.37%, and 31.37% of variation across these communities. Key modules (Module 1 in influents, Modules 3 and 4 in sludges, and Module 1 in effluents) were significantly associated with various metabolic and degradative functions (p < 0.05). Core taxa identified by Random Forest analysis were strongly linked to key metabolic and degradation functions, such as the metabolism of cofactors and vitamins, carbohydrates, and amino acids as well as the degradation of benzoate, aminobenzoate, nitrotoluene, chloroalkane, and chloroalkene. This study deepens our understanding of bacterial community dynamics and key features in pesticide wastewater treatment systems, offering scientific guidance for process optimization, efficiency improvement, and system stability assessment.}, } @article {pmid39920864, year = {2025}, author = {Kennedy, EA and Weagley, JS and Kim, AH and Antia, A and DeVeaux, AL and Baldridge, MT}, title = {Bacterial community assembly of specific pathogen-free neonatal mice.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {46}, pmid = {39920864}, issn = {2049-2618}, support = {R01AI139314/NH/NIH HHS/United States ; R01 AI139314/AI/NIAID NIH HHS/United States ; T32AI007163/NH/NIH HHS/United States ; F31AI167499/NH/NIH HHS/United States ; T32AI007172/NH/NIH HHS/United States ; 1065897//Crohn's and Colitis Foundation/ ; DGE-1745038//National Science Foundation/ ; }, mesh = {Animals ; Mice ; *Feces/microbiology ; *Animals, Newborn/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Female ; Specific Pathogen-Free Organisms ; *Mice, Inbred C57BL ; *Mice, Inbred BALB C ; Gastrointestinal Microbiome ; Metagenome ; Metagenomics/methods ; Microbiota ; }, abstract = {BACKGROUND: Neonatal mice are frequently used to model diseases that affect human infants. Microbial community composition has been shown to impact disease progression in these models. Despite this, the maturation of the early-life murine microbiome has not been well-characterized. We address this gap by characterizing the assembly of the bacterial microbiota of C57BL/6 and BALB/c litters from birth to adulthood across multiple independent litters.

RESULTS: The fecal microbiome of young pups is dominated by only a few pioneering bacterial taxa. These taxa are present at low levels in the microbiota of multiple maternal body sites, precluding a clear identification of maternal source. The pup microbiota begins diversifying after 14 days, coinciding with the beginning of coprophagy and the consumption of solid foods. Pup stool bacterial community composition and diversity are not significantly different from dams from day 21 onwards. Short-read shotgun sequencing-based metagenomic profiling of young pups enabled the assembly of metagenome-assembled genomes for strain-level analysis of these pioneer Ligilactobacillus, Streptococcus, and Proteus species.

CONCLUSIONS: Assembly of the murine microbiome occurs over the first weeks of postnatal life and is largely complete by day 21. This detailed view of bacterial community development across multiple commonly employed mouse strains informs experimental design, allowing researchers to better target interventions before, during, or after the maturation of the bacterial microbiota. The source of pioneer bacterial strains appears heterogeneous, as the most abundant taxa identified in young pup stool were found at low levels across multiple maternal body sites, suggesting diverse routes for seeding of the murine microbiome. Video Abstract.}, } @article {pmid39920607, year = {2025}, author = {Mai, G and Chen, J and Zhang, M and Zhang, W and Luo, Y and Dai, Y}, title = {Construction of a pathogenic microorganism detection method based on third-generation nanopore sequencing data.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {189}, pmid = {39920607}, issn = {1471-2334}, support = {24C0330//Project of Hunan Provincial Department of Education/ ; 22C0389//Project of Hunan Provincial Department of Education/ ; 24BSQD04//Hunan University of Arts and Science PhD Boosting Project/ ; E07023009//Hunan University of Arts and Science PhD Boosting Project/ ; 23YB07//Hunan University of Arts and Science Research Projects/ ; 24YB10//Hunan University of Arts and Science Research Projects/ ; }, mesh = {Humans ; *Nanopore Sequencing/methods ; *Metagenomics/methods ; *Bacteria/genetics/isolation & purification/classification ; *Computational Biology/methods ; Respiratory Tract Infections/microbiology/diagnosis ; Female ; Male ; Adult ; Middle Aged ; Aged ; }, abstract = {BACKGROUND: Pathogenic microorganisms can cause infections, allergies, diarrhoea, tumours, other diseases, and even death. Therefore, the detection of pathogenic microorganisms is important.

METHODS: In this study, a bioinformatics pipeline was developed. First, a comprehensive and penetrating reference database of nucleic acids from pathogenic microorganisms was constructed, and sequence alignment analysis was performed via nanopore sequencing of metagenomic data collected from 40 patients with lower respiratory tract infection symptoms. The similarity, abundance, and matching length of the sequences were integrated to obtain a comprehensive parameter, all_ratio, which can be used to identify pathogenic microorganisms effectively.

RESULTS: Compared with two previous methods, i.e., pathogen identification via microbiological culture or a previously reported metagenomic pipeline, pathogens were detected in 23 out of the 40 samples using our method, with the same results as those of the previous two methods. In five samples, pathogens such as Streptococcus pneumoniae and Granulicatella adiacens that had not been detected via the previous two methods were detected using our method. Pathogens such as Streptococcus pneumoniae and Neisseria flavescens were detected in 12 samples via our method, in contrast to the results of the previous two methods. Therefore, it is presumed that the individuals from whom these samples were obtained may have been infected with two or more pathogenic microorganisms.

CONCLUSIONS: This study shows that our method can efficiently identify pathogenic microorganisms and even detect pathogenic microorganisms in samples that cannot be detected via other methods, thus supplementing existing methods.}, } @article {pmid39920574, year = {2025}, author = {Zhao, J and Su, HT and Zhang, D and Li, XT and Lu, MY and Du, J and Guo, JY and Gao, Y and Chen, XF and Wen, DH and Jia, SY and Wang, Y and Yang, QW}, title = {The role of mNGS in the diagnosis of talaromycosis and case series.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {191}, pmid = {39920574}, issn = {1471-2334}, support = {82272380//the National Natural Science Foundation of China/ ; 82272380//the National Natural Science Foundation of China/ ; 2022-PUMCH-B-028//National High Level Hospital Clinical Research Funding/ ; 2022-PUMCH-B-028//National High Level Hospital Clinical Research Funding/ ; 2021YFC2301002//the National Key Research and Development Program of China/ ; 2021YFC2301002//the National Key Research and Development Program of China/ ; 2023-PT330-01//Supported by the Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences/ ; 2023-PT330-01//Supported by the Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences/ ; }, mesh = {Humans ; *Talaromyces/isolation & purification/genetics ; Male ; *Mycoses/diagnosis/drug therapy/microbiology ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing ; Middle Aged ; Adult ; Female ; Metagenomics ; Antifungal Agents/therapeutic use ; HIV Infections/complications ; Voriconazole/therapeutic use ; }, abstract = {BACKGROUND: Talaromycosis is a rare fungal infection characterized by non-specific clinical features, often resulting in misdiagnosis. This study aimed to analyze four classic cases of Talaromyces marneffei infection diagnosed using metagenomic next-generation sequencing (mNGS) to improve understanding of its diagnosis and treatment.

METHODS: This study retrospectively analyzed cases of T. marneffei identified through mNGS at Peking Union Medical College Hospital. Four confirmed cases of talaromycosis were selected based on clinical diagnoses, supplemented by a review of relevant literature. We reviewed and compared the clinical features, laboratory indicators, treatment regimens, and outcomes of these cases, which exhibited varied characteristics.

RESULTS: Among the four patients, two were human immunodeficiency virus (HIV)-positive, and two were HIV-negative. All the participants presented with fever and varying respiratory symptoms, with distinct clinical characteristics aiding diagnosis. Three cases exhibited significant pulmonary infection lesions. Both HIV-positive patients showed T. marneffei bloodstream dissemination and suffered mixed infection with virus. Within them, one case was positive in blood culture, blood mNGS and sputum culture. Another case was positive in blood and bone marrow cultures, brain tissue culture and mNGS. They were both treated with voriconazole and improved. Both HIV-negative patients were T. marneffei positive for BALF mNGS, and only one of them was positive for BALF culture. One of them was mix infected by fungi, bacteria, Mycobacterium tuberculosis and virus, improved by voriconzole and followed by introconaole. The other case was cured by introconazole.

CONCLUSIONS: Traditional diagnostic methods are limited by factors such as the long time and low sensitivity of fungal culture, the effect of prior antibiotic treatment, the invasiveness and complexities of tissue biopsies, and so on. Emerging technologies, particularly mNGS, offer advantages such as rapid processing, high accuracy, and comprehensive pathogen coverage, significantly reducing the risk of missed diagnoses and facilitating timely intervention.}, } @article {pmid39919954, year = {2025}, author = {Lin, T and Yu, Y and Luo, J and Yan, X and Qiu, Y and Tong, J and Wang, Y and Huang, X and Li, D and Zhang, Y and Yang, G}, title = {Clinical value of Metagenomic Next- and Third-Generation Sequencing applied in ultrasound-guided puncture biopsy for diagnosing lymph node tuberculosis.}, journal = {Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jmii.2024.12.011}, pmid = {39919954}, issn = {1995-9133}, abstract = {OBJECTIVES: The aim of this study was to assess the clinical utility of metagenomic next-generation sequencing (mNGS) and metagenomic third-generation sequencing (mTGS) in diagnosing cervical lymph node tuberculosis through analysis of lymph node tissue.

METHODS: This study recruited 101 patients with suspected cervical lymph node tuberculosis and took samples under ultrasound guidance. Parallel culture, X-pert, mNGS and mTGS workflows to each sample were performed. Taking clinical diagnosis as the gold standard, We comparatively compared diagnosis performance of the four methods.

RESULTS: Clinically, 76 cases were diagnosed as lymph node tuberculosis and 20 cases were non-lymph node tuberculosis. Compared with clinical diagnosis, the sensitivities of mNGS and mTGS were 89.47 % and 82.89 %, respectively, significantly higher than those of culture and X-pert which were 43.28 % and 68.42 %, respectively (P < 0.05). The specificity of mNGS and X-pert reached 100 %, while those of culture and mTGS were 93.75 % and 95 %, respectively. And mNGS alone identified 7 species of bacteria, 3 species of viruses, and 5 species of fungi, and identified more mixed infections. Particularly, besides Mycobacterium tuberculosis detection, mNGS may be superior to mTGS for the detection of fungi. Pathogen identification of mNGS and mTGS is less affected by previous anti-tuberculosis drug usage.

CONCLUSION: mNGS and mTGS play a crucial role in the rapid diagnosis and accurate treatment on Cervical lymph node tuberculosis.}, } @article {pmid39919574, year = {2025}, author = {Zhang, L and Luo, Y and Lv, S and Liu, Y and Wang, R and Wang, Y and Lin, K and Liu, L}, title = {Performance of electro-assisted ecological floating bed in antibiotics and conventional pollutants degradation: Mechanisms and microbial response.}, journal = {Journal of environmental management}, volume = {376}, number = {}, pages = {124393}, doi = {10.1016/j.jenvman.2025.124393}, pmid = {39919574}, issn = {1095-8630}, abstract = {Electro-assisted technology is promising for enhancing plant activity, optimizing functional microbial communities, and significantly strengthening pollutant removal efficiency. In this study, four reactors were designed as control group (CG), Hydrocotyle vulgaris L. ecological floating bed (PEFB), microbial fuel cell (MFC), and Hydrocotyle vulgaris L. ecological floating bed-microbial fuel cell (PEFB-MFC) to investigate the efficiency and mechanisms for the synchronous removal of conventional and antibiotic contaminants. Results showed that PEFB-MFC hold superior removal performance for sulfamethoxazole (61%), tetracycline (61%), CODCr (65%), NH4[+]-N (86%), TN (41%), and TP (51%). High-throughput sequencing indicated that Pseudomonadota and Actinomycetota were the predominant phyla in the different reactors. Metagenomic sequencing results showed that pollutant degradation-related metabolic functions, such as those involved in carbohydrate and amino acid metabolism in PEFB-MFC exhibited superior abundance compared to the other reactors. LC-MS analysis revealed sulfamethoxazole degradation occurred through active-site cleavage, and tetracycline underwent demethylation, aldehyde formation, dehydroxylation. This study offers a deeper insight into electro-enhanced PEFB on decontamination performance and functional microbial communities.}, } @article {pmid39919405, year = {2025}, author = {Xing, Y and Li, W and Liao, X and Wang, L and Wang, B and Peng, Y}, title = {Enhanced nitrogen removal from low C/N municipal wastewater in a step-feed integrated fixed-film activated sludge system: Synergizing anammox and partial denitrification with sludge fermentation liquid supplementation.}, journal = {Water research}, volume = {275}, number = {}, pages = {123211}, doi = {10.1016/j.watres.2025.123211}, pmid = {39919405}, issn = {1879-2448}, abstract = {The scarcity of rapidly biodegradable organics, which serve as essential electron donors for the partial denitrification (PD) process, significantly hinders the combined application of PD coupled with anammox (PDA) in municipal wastewater treatment plants. This study innovatively applied, for the first time, a step-feed strategy combined with the use of sludge fermentation liquid (SFL) as an external carbon source in an integrated fixed-film activated sludge (IFAS) system, successfully driving full nitrification and PDA to achieve advanced nitrogen removal from low C/N real municipal wastewater. Moreover, the associated nitrogen removal mechanism of this system was systematically analyzed. By employing second-step SFL feed as a supplementary carbon source, the nitrogen removal efficiency reached 92.26 ± 2.77 % and the effluent total inorganic nitrogen was 6.43 ± 2.23 mg/L, with anammox contributing approximately 70 % to total inorganic nitrogen removal. 16S rRNA gene sequencing and fluorescence in situ hybridization analysis unveiled the extensive cooperation and synergistic interactions among anammox bacteria, denitrifying bacteria, and nitrifying bacteria, with Candidatus Brocadia being highly enriched in biofilms with a relative abundance of 2.21 %. Metagenomic sequencing confirmed that the relative abundance of the narGHI gene was greater than that of the nirS gene, providing stable nitrite accumulation conditions for the anammox process. Overall, this study proposes an innovative synergistic treatment scheme that utilizes a step-feed full nitrification-PDA process driven by SFL to achieve advanced nitrogen removal in municipal wastewater treatment plants. This approach is characterized by low energy consumption, low operational costs and a high nitrogen removal efficiency.}, } @article {pmid39919380, year = {2025}, author = {Prosser, HM and Bortoluzzi, EM and Valeris-Chacin, RJ and Baker, EC and Scott, MA}, title = {Application of artificial intelligence and machine learning in bovine respiratory disease prevention, diagnosis, and classification.}, journal = {American journal of veterinary research}, volume = {}, number = {}, pages = {1-5}, doi = {10.2460/ajvr.24.10.0327}, pmid = {39919380}, issn = {1943-5681}, abstract = {Bovine respiratory disease (BRD) is the leading infectious disease in cattle, resulting in significant economic losses and welfare concerns in beef and dairy production systems. Traditional diagnostic methods for BRD typically rely on clinical observations and diagnostic laboratory tests, which can be time consuming with moderate diagnostic sensitivity. In recent years, machine learning (ML) and AI have emerged as powerful tools in animal health research, offering opportunities for improving BRD diagnostics and management. This review explores the current landscape of published literature on the use of ML and AI in BRD prevention, diagnostics, and classification. First, disease classification and pathogen identification models leveraging supervised models and metagenomic sequencing have identified specific community structure information in classifying specific BRD cases. From epidemiological datasets tracking disease outbreaks and risk factors, user-friendly platforms for producers and veterinarians are capable of being generated and deployed, providing customized scenarios, potential economic impacts, and pathogenic effects as a decision-support tool. Veterinarian-operated technologies, such as computer-aided lung auscultation stethoscopes, can automatically calculate lung scores and associated BRD severity likelihoods. Prediction and detection models used to leverage physical characteristics and feed consumption data provide novel methods of categorizing BRD risk. Finally, sensor technology monitoring behavioral or motion-based information provides continuous data on animal health and can enable early automated detection of BRD symptoms. Through synthesizing research in these key areas, this narrative review highlights the transformative potential of AI and ML in improving the accuracy, speed, and efficiency of BRD diagnostics, enhancing disease control and cattle welfare.}, } @article {pmid39919372, year = {2025}, author = {Swain, S and Sahoo, P and Biswal, S and Sethy, K and Panda, AN and Sahoo, N}, title = {Fecal bacterial microbiota diversity characterized for dogs with atopic dermatitis: its alteration and clinical recovery after meat-exclusion diet.}, journal = {American journal of veterinary research}, volume = {}, number = {}, pages = {1-9}, doi = {10.2460/ajvr.24.09.0274}, pmid = {39919372}, issn = {1943-5681}, abstract = {OBJECTIVE: To achieve clinical recovery in canine atopic dermatitis affected pet dogs via alteration of the gut microbiome, following a meat and egg exclusion diet for 60 days.

METHODS: 24 atopic dermatitis-affected pet dogs, all fed poultry meat and egg, and another 48 apparently healthy controls fed both poultry meat and egg (n = 24) or vegetable diet (24) were included in the study. The study was undertaken in the Bhubaneswar Smart City, Odisha, India, from July to December 2023. Fecal samples were collected at 2 points for DNA analysis, ie, on day 0 and day 60 of the change from a meat/egg-based diet to a vegetable-based diet. Extracted DNA samples were pooled category-wise and subjected to the gut microbiome analysis in the Nanopore sequencer targeting the 16S rRNA gene. Burrows-Wheeler Transform, Ferragina-Manzini index, and Krona charts were used for taxonomical classification and visualization of relative abundances of bacterial species within the metagenome. Alpha- and beta-diversity analyses were performed.

RESULTS: Atopic pets at day 0 showed elevation in the gut microbiome population with an adequate concentration of pathogens like Escherichia coli and Clostridiodes difficile with lower amounts of the beneficial bacteria like Lactobacillus sp, while the pets at 60 days after dietary intervention showed a significant decline in bacterial species like E coli and C difficile with higher amount of Lactobacillus sp. Both control groups showed variations of microbiome between them as well as from the atopic pets.

CONCLUSIONS: We found a close association of poultry meat/egg diet with gut microbiome population and atopic symptoms as well in dogs, and elimination of such diet could be helpful in clinical recovery.

CLINICAL RELEVANCE: Dietary intervention with the exclusion of potential allergens from poultry meat and egg sources can be an effective approach for the management of canine atopic dermatitis.}, } @article {pmid39919360, year = {2025}, author = {Lemons, JMS and Narrowe, AB and Firrman, J and Mahalak, KK and Liu, L and Higgins, S and Moustafa, AM and Baudot, A and Deyaert, S and Van den Abbeele, P}, title = {The food additive butylated hydroxyanisole minimally affects the human gut microbiome ex vivo.}, journal = {Food chemistry}, volume = {473}, number = {}, pages = {143037}, doi = {10.1016/j.foodchem.2025.143037}, pmid = {39919360}, issn = {1873-7072}, abstract = {Butylated hydroxyanisole (BHA) continues to raise consumer concerns. All previous evaluations of this additive have failed to consider its effect on the gut microbiome, even though it enters the colon. An ex vivo model was used to assess the effect of BHA on microbial communities from 24 donors, aged infants to older adults. A dose of 0.35 g/L BHA elicited no statistically significant changes in the functional outputs or community structure for any age group. Although not large enough to affect community diversity, there were some significant decreases at the phylum level. Among the genes most significantly affected by treatment with BHA across age groups are those involved in lipopolysaccharide synthesis and bacterial electron transport encoded by Bacteroidota, Proteobacteria, and Verrucomicrobiota. Given what is known about the intracellular activity of BHA, these genes may hint at a mechanism behind BHA's evident, but minimally detrimental effect on the gut microbiota.}, } @article {pmid39919201, year = {2025}, author = {Liu, C and Chen, Z and Wang, X and Deng, Y and Tao, L and Zhou, X and Deng, J}, title = {Response of Soil Phage Communities and Prokaryote-Phage Interactions to Long-Term Drought.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c08448}, pmid = {39919201}, issn = {1520-5851}, abstract = {Soil moisture is a fundamental factor affecting terrestrial ecosystem functions. In this study, microscopic enumeration and joint metaviromic and metagenomic sequencing were employed together to investigate the impact of prolonged drought on soil phage communities and their interactions with prokaryotes in a subtropical evergreen forest. Our findings revealed a marked reduction in the abundances of prokaryotic and viral-like particles, by 73.1% and 75.2%, respectively, and significantly altered the structure of prokaryotic and phage communities under drought. Meanwhile, drought substantially increased the fraction of prokaryotic communities containing lysogenic phages by 163%, as well as the proportion of temperate phages. Nonetheless, drought likely amplified negative prokaryote-phage interactions given the nearly doubled proportion of negative links in the prokaryote-phage co-occurrence network, as well as the higher frequency and diversity of antiphage defense systems found in prokaryotic genomes. Under drought, soil phages exerted greater top-down control on typical soil k-strategists including Acidobacteria and Chloroflexi. Moreover, phage-encoded auxiliary metabolic genes may impact host metabolism in biosynthesis-related functions. Collectively, the findings of this study underscore the profound impact of drought on soil phages and prokaryote-phage interactions. These results also emphasize the importance of managing soil moisture levels during soil amendment and microbiome manipulation to account for the influence of soil phages.}, } @article {pmid39918326, year = {2025}, author = {Kos, D and Jelinski, M and Ruzzini, A}, title = {Retrospective analysis of antimicrobial resistance associated with bovine respiratory disease.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0190924}, doi = {10.1128/aem.01909-24}, pmid = {39918326}, issn = {1098-5336}, abstract = {The administration and utility of antibiotics to control and treat bovine respiratory disease (BRD) in beef cattle feedlots is a growing concern. Antimicrobial resistance (AMR) among BRD-associated bacterial pathogens has been the subject of cultivation-dependent and cultivation-independent surveillance. Bacterial genome sequencing and metagenomic approaches facilitate the characterization of AMR in the beef industry; however, the current collection of cattle-associated AMR research programs lack connections to each other. A more integrated view of how antimicrobial use (AMU) is related to resistance at a gene level is needed. We sought to establish a catalog of commonly observed AMR genes (ARGs) in opportunistic bacterial pathogens that contribute to BRD using publicly available data sets that were generated by the scientific community with and without AMU in mind. The presence of these clinically relevant ARGs appeared to differ by geography. Greater sampling in North America facilitated the generation of a list of ARGs often encoded by Mannheimia haemolytica and Pasteurella multocida. Detection of clinically relevant ARGs in shotgun metagenomes of cattle-associated and accessible feedlot samples such as water, soil, and feces was possible but limited by relative sequence read abundance. An exception was the tylosin esterase-encoding gene estT, which is among the most frequently observed ARGs in M. haemolytica and feedlot-related metagenomic data sets. Finally, by re-evaluating studies on the impact of AMU on AMR in beef production systems, we show that conventional practices, including in-feed antibiotic use, increase the relative abundance of ARGs in animal-derived samples.IMPORTANCEThis retrospective analysis delivers a list of ARGs found in opportunistic pathogens that contribute to BRD. The high incidence of BRD in North America is linked to the origin and implementation of metaphylaxis to mitigate detrimental animal losses at feedlots. Notably, ARGs commonly observed in these pathogens isolated in North America were not conserved across the globe, underscoring the relationship between regional AMU and AMR. A positive relationship was also observed between the relative abundance of ARGs in cattle-associated metagenomes with greater exposure to antibiotics. Overall, this analysis should help to guide future surveillance efforts and experimental designs to more directly evaluate the impacts of feedlot practices on AMR.}, } @article {pmid39917835, year = {2025}, author = {Hoffbeck, C and Middleton, DMRL and Wallbank, JA and Boey, JS and Taylor, MW}, title = {Culture-Independent Species-Level Taxonomic and Functional Characterisation of Bacteroides, the Core Bacterial Genus Within Reptile Guts.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {e17685}, doi = {10.1111/mec.17685}, pmid = {39917835}, issn = {1365-294X}, support = {//University of Auckland Doctoral Scholarship/ ; }, abstract = {The genus Bacteroides is a widespread and abundant bacterial taxon associated with gut microbiotas. Species within Bacteroides fill many niches, including as mutualists, commensals and pathogens for their hosts. Within many reptiles, Bacteroides is a dominant, 'core' gut bacterium that sometimes exhibits increased abundance in times of food scarcity, such as during hibernation. Here, we take a two-pronged approach to better characterise Bacteroides populations in reptile guts. Firstly, we leverage published 16S rRNA gene sequence datasets to determine the species-level distributions of Bacteroides members in reptile hosts. Secondly, we mine publicly available metagenomes to extract data for Bacteroides from reptiles, birds, amphibians and mammals, to compare the functional potential of Bacteroides in different host taxa. The 16S rRNA gene analyses revealed that B. acidifaciens is the most common Bacteroides species in reptile guts, and that different orders of reptiles differ in which Bacteroides species they harbour. The taxonomy of Bacteroides species recovered from metagenomic assembly did not differ between reptile orders or substantially across birds, amphibians and mammals. Metagenome-assembled genomes for Bacteroides species were marginally more related when their hosts were more closely related, with reptile hosts in particular harbouring markedly more unique Bacteroides MAGs compared to other hosts. Our findings indicate that hosts harbour similar profiles of Bacteroides species across broad comparisons, but with some differences between reptile groups, and that Bacteroides appears to perform largely similar roles in vertebrate host guts regardless of host relatedness.}, } @article {pmid39917570, year = {2025}, author = {Xu, L and Xiong, Y and Fang, C}, title = {Omadacycline for the Treatment of Severe Legionella Pneumonia Complicated with Multiple Organ Failure: A Case Report.}, journal = {International medical case reports journal}, volume = {18}, number = {}, pages = {217-222}, pmid = {39917570}, issn = {1179-142X}, abstract = {BACKGROUND: Fluoroquinolones and macrolides are the preferred antibiotics for treating Legionnaires' disease. However, the limited utility of these antibiotics in cases of organ dysfunction is a major problem. Omadacycline is a novel tetracycline antibiotic with a good safety profile and in vitro antibacterial activity against Legionella, but it lacks validation by clinical data.

CASE DESCRIPTION: Here, we report a case of severe pneumonia caused by Legionella infection. The patient was empirically treated with antibiotics, after admission but had a poor clinical outcome with severe hepatic and renal insufficiency. After Legionella infection was confirmed by metagenomic next-generation sequencing, the patient was switched to omadacycline antibiotic therapy and eventually discharged after recovery.

CONCLUSION: The results of this study suggest that metagenomic next-generation sequencing can facilitate early diagnosis of Legionnaires' disease, and omadacycline can be an alternative antibiotic treatment for severe Legionnaires' disease, especially in patients experiencing multiple organ failure.}, } @article {pmid39917349, year = {2025}, author = {Tigga, A and Mallappa, RH and Muniyappa, SK and Kadyan, S and Pradhan, D and Niharika, ES and Grover, S}, title = {16S metagenomics and metabolomics unveil the microbial compositions and metabolite profiles in Dahi, a traditional Indian fermented milk product prepared by the backslopping method.}, journal = {Journal of food science and technology}, volume = {62}, number = {3}, pages = {584-597}, pmid = {39917349}, issn = {0022-1155}, abstract = {UNLABELLED: Fermentation of milk contributes to an array of organoleptic and nutritional changes, which is largely governed by the metabolic activity of starter cultures. Dahi, a popular traditional fermented milk product of India, varies considerably from its commercial counterparts due to diversity in household production practices and the use of undefined microbial consortia as inoculants. Herein, we investigated the unexplored bacterial signatures and metabolic profiles of traditional Dahi from northern region of India using 16S metagenomics and untargeted gas chromatography-mass spectrophotometry. We found Firmicutes followed by Proteobacteria as the dominant phyla, while Lactobacillus and Streptococcus were the most prevalent lactic acid bacterial genera many species of which also serves as thermophilic starters. Notably, differential abundance of environmental bacteria like Bacilli, Prevotella, Oscillospira, Ruminococcus, and Acinetobacter were also observed in different samples. The study also revealed a total of 62 metabolites belonging to amino acids, fatty acids, sugars, and others metabolic intermediates, which also varied among regions. This highlights different production practices as influenced by milk type, heating methods, container choices and inoculum types leading to distinct microbiota succession and associated metabolites. This study provides valuable insights into the complexities as well as health benefits of indigenous fermented milks particularly Dahi and paves the way for future exploration of novel probiotic strains.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13197-024-06050-9.}, } @article {pmid39917348, year = {2025}, author = {Shuba, AA and Bogdanova, EV and Anokhina, EP and Umarkhanov, RU}, title = {Current trends in the determination of microbiological indicators of dairy products.}, journal = {Journal of food science and technology}, volume = {62}, number = {3}, pages = {453-470}, pmid = {39917348}, issn = {0022-1155}, abstract = {UNLABELLED: Milk and dairy products are the most common and widely consumed foods. At the same time, milk is often contaminated with pathogenic microorganisms by endo- and exogenous ways, which can cause various defects in raw materials and finished products. Recently, new techniques have been developed for monitoring microbiological indicators of milk, which are characterized by simplicity, ease of use and high reliability. In addition, the analysis time using the new techniques is significantly reduced compared to traditional ones. The review considers the microflora of milk and ways of its contamination with pathogenic microorganisms, as well as new methods for monitoring microbiological indicators that will be useful for specialists in the dairy industry.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13197-025-06207-0.}, } @article {pmid39917331, year = {2025}, author = {Ranganath, N and Bisono Garcia, B and Vaillant, J and Katragadda, S and Kerkelis, M and Abu Saleh, O and Fida, M}, title = {From Chart Biopsy to Liquid Biopsy: Evaluating the Diagnostic Yield and Clinical Impact of Plasma Microbial Cell-Free DNA Next-Generation Sequencing in the Management of Fever of Unknown Origin.}, journal = {Open forum infectious diseases}, volume = {12}, number = {2}, pages = {ofaf038}, pmid = {39917331}, issn = {2328-8957}, abstract = {BACKGROUND: The underlying cause of fever of unknown origin (FUO) remains unidentified in up to 51% of cases despite systematic evaluation. Microbial cell-free DNA next-generation sequencing (mcfDNA-NGS) offers an agnostic, noninvasive approach to pathogen identification, but the utility and clinical impact of this assay in FUO remain unknown.

METHODS: This retrospective cohort study evaluated adult patients referred for FUO evaluation at a tertiary medical center between November 2019 and November 2023. Patients underwent both standard microbiologic testing (ST) and mcfDNA-NGS. Diagnostic impact was assessed in 4 domains: new diagnoses, earlier time to diagnosis, avoidance of invasive procedures, and non-hypothesis-driven diagnoses. Logistic regression was used to identify predictors of positive mcfDNA-NGS testing.

RESULTS: Among 176 patients, mcfDNA-NGS was positive in 44.3%, with 49% of these cases considered clinically significant. Infectious cause of FUO was identified in 39% of patients, noninfectious in 35%, and unknown in 26%. mcfDNA-NGS contributed to a positive diagnostic impact in 30% of cases, mainly by earlier diagnosis (16%) and potential for avoidance of invasive procedures (10%). Positive mcfDNA-NGS was significantly associated with higher Charlson comorbidity index score (odds ratio [OR], 1.22; P < .001) and white blood cell (WBC) count ≤4.5 × 10[9] cells/L (OR, 8.61; P < .001). Conversely, FUO without localization was associated with a decreased likelihood of positive mcfNDA testing (OR, 0.18; P < .001).

CONCLUSIONS: mcfDNA-NGS effectively complements ST in diagnosing FUO, providing earlier detection and minimizing invasive testing. Clinical predictors such as high comorbidity and low WBC count may guide the optimal use of mcfDNA-NGS in FUO. Prospective evaluation of optimal timing and use of mcfDNA-NGS and cost-benefit analysis in FUO is needed.}, } @article {pmid39917268, year = {2024}, author = {Zhang, W and Jian, X and Ding, S and Chang, J and Ji, S and Chi, Y}, title = {Insights into the gut microbiota characteristics between the organic and traditional feeding chickens based on amplicon and metagenomic sequencing.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1509461}, pmid = {39917268}, issn = {1664-302X}, abstract = {Intestinal microorganisms play a crucial role in chicken health and production performance, especially in the research of traditional and organic feeding methods. The intestinal contents of organic and feed chickens were analyzed by 16S rRNA gene and metagenome technology. The results showed that the microbial diversity of organic chickens was significantly higher than that of the feed chickens, especially the key microorganisms, such as Enterococcus, were more abundant in organic chickens. The functional analysis of metagenome revealed the significant difference in the metabolic function of intestinal microorganisms between them. The present study provides new insights into the gut microbiota characteristics of the organic and feed chicken based on amplicon and metagenomic sequencing. Our results are helpful to fully illustrate the effects of different feeding methods on intestinal microorganisms in chickens and can offer a more scientific basis for chicken production management.}, } @article {pmid39916977, year = {2025}, author = {Anitua, E and Murias-Freijo, A and Tierno, R and Tejero, R and Hamdan Alkhraisat, M}, title = {Effect of implant abutment surface treatments on bacterial biofilm composition and structure.}, journal = {Journal of oral microbiology}, volume = {17}, number = {1}, pages = {2459922}, pmid = {39916977}, issn = {2000-2297}, abstract = {BACKGROUND: For the long-term success of dental implants, implant abutment surface should promote the attachment of oral epithelial cells and reduce bacterial adhesion. Titanium nitride (TiN) coatings show antimicrobial properties. Nevertheless, there is a lack of clinical trials that assess the biofilm formation on TiN abutments in the context of clinical practice. Thus, the objective of this study was to evaluate the effect of different abutment surfaces (machined, TiN and TiN oxidized) on bacterial biofilm composition and structure.

MATERIALS AND METHODS: Implant abutments were connected to the dental implants. Bacterial communities were sampled at 1 and 60 days later. The relationship between surface, periodontal indices and bacterial community dynamics was assessed using 16S rRNA metagenomics. A total of 17 patients were involved in this study (14 included in final analyses: 15 machined, 16 TiN and 14 TiN oxidized abutments).

RESULTS: No significant differences between surfaces were found considering taxa abundance, most alpha diversity metrics or community structure. Time showed a significant effect on diversity and also on the abundance of several bacterial taxa.

CONCLUSIONS: These results indicate that the effect of the three tested abutment surfaces on biofilm structure and composition was negligible, whereas patient and time exert strong influences on bacterial biofilm formation at different scales.}, } @article {pmid39916938, year = {2024}, author = {Liu, Y and Yang, B and Qi, Q and Liu, S and Du, Y and Ye, L and Zhou, Q}, title = {Metagenomic next-generation sequencing for lung cancer low respiratory tract infections diagnosis and characterizing microbiome features.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1518199}, pmid = {39916938}, issn = {2235-2988}, mesh = {Humans ; *Lung Neoplasms/microbiology/diagnosis ; *Respiratory Tract Infections/microbiology/diagnosis/virology ; *High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; *Microbiota/genetics ; Male ; *Bacteria/genetics/classification/isolation & purification ; Female ; Middle Aged ; Aged ; Sputum/microbiology ; Fungi/isolation & purification/classification/genetics ; Coinfection/microbiology/diagnosis/virology ; Adult ; Metagenome ; Aged, 80 and over ; }, abstract = {BACKGROUND: The capability of mNGS in diagnosing suspected LRTIs and characterizing the respiratory microbiome in lung cancer patients requires further evaluation.

METHODS: This study evaluated mNGS diagnostic performance and utilized background microbial sequences to characterize LRT microbiome in these patients. GSVA was used to analyze the potential functions of identified genera.

RESULTS: Bacteria were the most common pathogens (n=74) in LRTIs of lung cancer patients, and polymicrobial infections predominated compared to monomicrobial infections (p<0.001). In diagnosing LRTIs in lung cancer patients, the pathogen detection rate of mNGS (83.3%, 70/84) was significantly higher than that of sputum culture (34.5%, 29/84) (p<0.001). This result was consistent with that of non-lung cancer patients (p<0.001). Furthermore, in the specific detection of bacteria (95.7% vs. 22.6%) and fungi (96.0% vs. 22.2%), the detection rate of mNGS was also significantly higher than that of CMTs mainly based on culture (p<0.001, p<0.001). However, in the detection of CMV/EBV viruses, there was no significant difference between the detection rate of mNGS and that of viral DNA quantification (p = 1.000 and 0.152). mNGS analysis revealed Prevotella, Streptococcus, Veillonella, Rothia, and Capnocytophaga as the most prevalent genera in the LRT of lung cancer patients. GSVA revealed significant correlations between these genera and tumor metabolic pathways as well as various signaling pathways including PI3K, Hippo, and p53.

CONCLUSION: mNGS showed a higher pathogen detection rate than culture-based CMTs in lung cancer patients with LRTIs, and also characterizing LRT microbiome composition and revealing potential microbial functions linked to lung carcinogenesis.}, } @article {pmid39915809, year = {2025}, author = {Zhang, Y and Li, HZ and Breed, M and Tang, Z and Cui, L and Zhu, YG and Sun, X}, title = {Soil warming increases the active antibiotic resistome in the gut of invasive giant African snails.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {42}, pmid = {39915809}, issn = {2049-2618}, support = {2022T150635//fellowship of China Postdoctoral Science Foundation/ ; 42407166//National Natural Science Foundation of China/ ; 42307165//National Natural Science Foundation of China/ ; 32361143523//National Natural Science Foundation of China/ ; 2021-DST-004//Ningbo S&T project/ ; 2021-DST-004//Ningbo S&T project/ ; 2021-DST-004//Ningbo S&T project/ ; 2023YFF1304601//National Key Research and Development Program of China/ ; 322GJHZ2022028FN//International Partnership Program of Chinese Academy of Sciences/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics/drug effects ; *Snails/microbiology/genetics ; *Global Warming ; *Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/classification/drug effects ; Soil/chemistry ; Soil Microbiology ; beta-Lactamases/genetics ; Metagenomics ; Metagenome ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; }, abstract = {BACKGROUND: Global warming is redrawing the map for invasive species, spotlighting the globally harmful giant African snail as a major ecological disruptor and public health threat. Known for harboring extensive antibiotic resistance genes (ARGs) and human pathogens, it remains uncertain whether global warming exacerbates these associated health risks.

METHODS: We use phenotype-based single-cell Raman with D2O labeling (Raman-D2O) and genotype-based metagenomic sequencing to investigate whether soil warming increases active antibiotic-resistant bacteria (ARBs) in the gut microbiome of giant African snails.

RESULTS: We show a significant increase in beta-lactam phenotypic resistance of active ARBs with rising soil temperatures, mirrored by a surge in beta-lactamase genes such as SHV, TEM, OCH, OKP, and LEN subtypes. Through a correlation analysis between the abundance of phenotypically active ARBs and genotypically ARG-carrying gut microbes, we identify species that contribute to the increased activity of antibiotic resistome under soil warming. Among 299 high-quality ARG-carrying metagenome-assembled genomes (MAGs), we further revealed that the soil warming enhances the abundance of "supercarriers" including human pathogens with multiple ARGs and virulence factors. Furthermore, we identified elevated biosynthetic gene clusters (BGCs) within these ARG-carrying MAGs, with a third encoding at least one BGC. This suggests a link between active ARBs and secondary metabolism, enhancing the environmental adaptability and competitive advantage of these organisms in warmer environments.

CONCLUSIONS: The study underscores the complex interactions between soil warming and antibiotic resistance in the gut microbiome of the giant African snail, highlighting a potential escalation in environmental health risks due to global warming. These findings emphasize the urgent need for integrated environmental and health strategies to manage the rising threat of antibiotic resistance in the context of global climate change. Video Abstract.}, } @article {pmid39915364, year = {2025}, author = {de Castro Oliveira, W and Marques, PH and Erhardt, MM and Felice, AG and Tristão, CLAM and Aburjaile, FF and Oliveira, MBPP and Dos Santos Richards, NSP}, title = {Metagenomic analysis and proteins prediction of emerging pathogens in artisanal cheese.}, journal = {Molecular diversity}, volume = {}, number = {}, pages = {}, pmid = {39915364}, issn = {1573-501X}, abstract = {Currently, reports of the presence of emerging pathogens in cheeses are low and new outbreaks have occurred at an alarming rate, with the Vibrio and Aeromonas genera being the main causes of gastroenteritis in the world. Therefore, Multi-Omics integration has been a strategy to identify and develop detection methods for these pathogens in food. We investigated the presence of emerging pathogens in artisanal cheeses and predicted proteins with immunogenic potential, in silico, for food diagnostics. For this, multiomics integration was used: (a) metagenomics; (b) subtractive genomics; and (c) pan-genomics. Eight species of the genera Vibrio and Aeromonas were identified, the latter being the most abundant (89.7%) and identified in eight regions, with emphasis on the species A. caviae and A. veronii. Pan-genomic analyses revealed intra- and inter-species differences in both genera. Essential, non-cytoplasmic proteins were identified, without homology and with immunological potential for the species researched. Functional annotation of genes present in pan-genomic subsets reveals functionality between the core genome (transcription; amino acid transport and metabolism; and inorganic ion transport and metabolism) and the shared genome (signal transduction and carbohydrate transport and metabolism). A reinterpretation of the genomic plasticity of V. furnissii reveals the presence of mobile genetic elements critical for virulence in human isolates and the RTX toxin, also identified in this species, is present in the pathogenicity islands of V. alginolyticus and V. fluvialis. Collectively, the results provide important information for the development of a diagnostic strategy for emerging pathogens in food using immunoassays.}, } @article {pmid39915243, year = {2025}, author = {Zhao, S and Lin, H and Li, W and Xu, X and Wu, Q and Wang, Z and Shi, J and Chen, Y and Ye, L and Xi, L and Chen, L and Yuan, M and Su, J and Gao, A and Jin, J and Ying, X and Wang, X and Ye, Y and Sun, Y and Zhang, Y and Deng, X and Shen, B and Gu, W and Ning, G and Wang, W and Hong, J and Wang, J and Liu, R}, title = {Post sleeve gastrectomy-enriched gut commensal Clostridia promotes secondary bile acid increase and weight loss.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2462261}, pmid = {39915243}, issn = {1949-0984}, mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Bile Acids and Salts/metabolism ; *Weight Loss ; Mice ; *Gastrectomy ; Humans ; Male ; *Clostridium/metabolism/genetics ; *Mice, Inbred C57BL ; *Obesity/microbiology/metabolism/surgery ; Receptors, G-Protein-Coupled/metabolism/genetics ; Fecal Microbiota Transplantation ; Female ; Adult ; Feces/microbiology ; Symbiosis ; Bariatric Surgery ; Adipose Tissue/metabolism ; }, abstract = {The gut microbiome is altered after bariatric surgery and is associated with weight loss. However, the commensal bacteria involved and the underlying mechanism remain to be determined. We performed shotgun metagenomic sequencing in obese subjects before and longitudinally after sleeve gastrectomy (SG), and found a significant enrichment in microbial species in Clostridia and bile acid metabolizing genes after SG treatment. Bile acid profiling further revealed decreased primary bile acids (PBAs) and increased conjugated secondary bile acids (C-SBAs) after SG. Specifically, glycodeoxycholic acid (GDCA) and taurodeoxycholic acid (TDCA) were increased at different follow-ups after SG, and were associated with the increased abundance of Clostridia and body weight reduction. Fecal microbiome transplantation with post-SG feces increased SBA levels, and alleviated body weight gain in the recipient mice. Furthermore, both Clostridia-enriched spore-forming bacteria and GDCA supplementation increased the expression of genes responsible for lipolysis and fatty acid oxidation in adipose tissue and reduced adiposity via Takeda G-protein-coupled receptor 5 (TGR5) signaling. Our findings reveal post-SG gut microbiome and C-SBAs as contributory to SG-induced weight loss, in part via TGR5 signaling, and suggest SBA-producing gut microbes as a potential therapeutic target for obesity intervention.}, } @article {pmid39914338, year = {2025}, author = {Yang, Y and Li, Q and Xiao, Y and Shen, Y and Wei, R and Zhang, Y and Zhang, W and Lei, N and Pei, X}, title = {Unravelling of the interaction mechanism of PFOA with submerged macrophytes and epiphytic biofilms at gene and molecular level.}, journal = {Journal of hazardous materials}, volume = {488}, number = {}, pages = {137418}, doi = {10.1016/j.jhazmat.2025.137418}, pmid = {39914338}, issn = {1873-3336}, abstract = {Perfluorooctanoic acid (PFOA) is a global concern for the remediation of aquatic environments due to its toxicity, persistence and bioaccumulation. To gain a comprehensive understanding of the effects of PFOA on submerged macrophytes and epiphytic biofilms in eutrophic waters, as well as the mechanisms of PFOA and nutrient removal by submerged macrophyte-biofilm system, plant-attached biofilms were cultured under PFOA stress. Results indicated that PFOA exposure leads to an increase in ROS in plants, seriously damaging cellular systems, activating enzyme antioxidants to protect plant cells from oxidative damage. Additionally, PFOA affects microbial diversity, structure and function in biofilms, with Cyanobacteria and Proteobacteria being the dominant groups. While impacting both plants and biofilms, PFOA will be absorbed by them. PFOA binds to channel proteins (ULX0, VIH9) on plant cells and enters the plant, thus removing it from the environment. Plant co-cultivation has the highest pollutant removal rate of PFOA, reaching to 33.00 %. Furthermore, metagenomics analyses revealed that alterations in genes associated with N (nxrB, nxrA) and P (phoR, pstA) cycling of in the biofilm microorganisms facilitated the removal of N and P, with removal rates of 98.00 % and 99.42 %, respectively. These findings contribute to the ecological assessment of PFOA and provide valuable sights into the mechanisms of PFOA, N and P removal in eutrophic lakes by plants and epiphytic biofilms.}, } @article {pmid39914332, year = {2025}, author = {Rossi, M and Vergara, A and Troisi, R and Alberico, M and Carraturo, F and Salamone, M and Giordano, S and Capozzi, F and Spagnuolo, V and de Magistris, FA and Donadio, C and Scognamiglio, V and Vedi, V and Guida, M}, title = {Microplastics, microfibers and associated microbiota biofilm analysis in seawater, a case study from the Vesuvian Coast, southern Italy.}, journal = {Journal of hazardous materials}, volume = {488}, number = {}, pages = {137468}, doi = {10.1016/j.jhazmat.2025.137468}, pmid = {39914332}, issn = {1873-3336}, abstract = {The growing concerns regarding pollution from microplastics (MPs) and microfibers (MFs) have driven the scientific community to develop new solutions for monitoring ecosystems. However, many of the proposed technologies still include protocols for treating environmental samples that may alter plastic materials, leading to inaccurate results both in observation and in counting. For this reason, we are refining a protocol, based on optical microscopy without the use of pretreatments, applicable to different environmental matrices, which allows not only counting but also a complete morphological characterization of MPs and MFs. Previously, the protocol has successfully been tested on marine sediments from the Vesuvian area of the Gulf of Naples (Italy) with good results. In the present study, we tested the protocol on MPs and MFs in seawater samples collected from the same geographical area to provide a comprehensive overview of their distribution in the marine environments. The protocol enabled not only the morphological characterization of MPs and MFs but also the collection of information on the colonies of microorganisms present on the microparticles. Next Generation Sequencing (NGS) metagenomic technologies enabled us to characterize the microbiota composition of the sampled MPs, the so-called Plastisphere. The analytical approach allowed the characterization of several potentially pathogenic bacteria, which represent a potential threat to the environment and human health. In fact, they may exploit their ability to form biofilms on plastics to proliferate in marine ecosystems.}, } @article {pmid39914322, year = {2025}, author = {SiMa, X and Li, Y and Yu, Z and Gu, H and Liu, J and Liu, J and Fang, R and Hu, X and Liu, X and Wang, G and Tang, C and Franks, A and Wu, J and Miao, S and Qiao, Y and Jin, J}, title = {Long-term warming offsets the beneficial effect of elevated CO2 on mineral associated organic carbon in Mollisols.}, journal = {The Science of the total environment}, volume = {966}, number = {}, pages = {178698}, doi = {10.1016/j.scitotenv.2025.178698}, pmid = {39914322}, issn = {1879-1026}, abstract = {The stability of soil organic carbon (SOC) is fundamentally important to the carbon-climate feedback because soils act as a major carbon source or sink under climate change. The uncertainty of SOC stability in farming soils in response to climate change necessitates mechanistic studies on microbial attributes to the change of SOC. Here, we used open-top chambers to simulate elevated CO2 (eCO2) and warming for 12 years in a soybean-grown Mollisol. We did not find the change of SOC stock under eCO2 or warming. Although eCO2 resulted in the accumulation of mineral-associated organic carbon, this effect diminished under warming. The amplicon sequencing of 16S gene indicated a significant change in microbial community composition under warming or eCO2. The metagenomic sequencing demonstrated that warming increased the abundances of microbial genes related to decomposition of labile carbon such as hemicellulose and pectin. The warming-induced stimulation of microbial catabolic metabolisms on organic carbon decomposition might have accelerated SOC turnover, which may offset the increased mineral-associated organic carbon of the Mollisol under eCO2. Long-term eCO2 and warming might not significantly alter the SOC stock or stability but accelerate carbon cycling in farming Mollisols.}, } @article {pmid39914059, year = {2025}, author = {Lyu, B and Manna, B and Zhou, X and Leung, IKH and Singhal, N}, title = {Microbial metabolic enzymes, pathways and microbial hosts for co-metabolic degradation of organic micropollutants in wastewater.}, journal = {Water research}, volume = {276}, number = {}, pages = {123229}, doi = {10.1016/j.watres.2025.123229}, pmid = {39914059}, issn = {1879-2448}, abstract = {Organic micropollutants (OMPs) in wastewater present significant environmental challenges, but effective removal strategies are hindered by our limited understanding of their co-metabolic biodegradation. We aim to elucidate the microbial enzymes, metabolic pathways, and community members involved in OMP co-metabolic degradation, thereby paving the way for more effective wastewater treatment strategies. We integrated multi-omics (metagenomics, metaproteomics, and metabolomics) and functional group analysis to investigate 24 OMPs under three aeration conditions. Our findings reveal that oxidoreductases, particularly cytochrome P450s and peroxidases, are crucial for recalcitrant OMPs containing halogen groups (-Cl, -F) like fluoxetine and diuron. Hydrolases, including amidases, are instrumental in targeting amide-containing (-CONH2) OMPs such as bezafibrate and carbamazepine. Regarding microbial metabolism involved in OMP co-metabolic degradation, we found that amino acid metabolism is crucial for degrading amine-containing (-NH2) OMPs like metoprolol and citalopram. Lipid metabolism, particularly for fatty acids, contributes to the degradation of carboxylic acid (-COOH) containing OMPs such as bezafibrate and naproxen. Finally, with Actinobacteria, Bacteroidetes, and Proteobacteria emerging as primary contributors to these functionalities, we established connections between OMP functional groups, degradation enzymes, metabolic pathways, and microbial phyla. Our findings provide generalized insights into structure-function relationships in OMP co-metabolic degradation, offering the potential for improved wastewater treatment strategies.}, } @article {pmid39913347, year = {2025}, author = {Phan, HV and Yasuda, S and Oba, K and Tsukamoto, H and Hori, T and Kuroiwa, M and Terada, A}, title = {Active bacteria driving N2O mitigation and dissimilatory nitrate reduction to ammonium in ammonia recovery bioreactors.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf021}, pmid = {39913347}, issn = {1751-7370}, abstract = {Shifting from ammonia removal to recovery is the current strategy in wastewater treatment management. We recently developed a microaerophilic activated sludge system for retaining ammonia whereas removing organic carbon with minimal N2O emissions. A comprehensive understanding of nitrogen metabolisms in the system is essential to optimize system performance. Here, we employed metagenomics and metatranscriptomics analyses to characterize the microbial community structure and activity during the transition from a microoxic to an oxic condition. A hybrid approach combining high-quality short reads and Nanopore long reads reconstructed 98 medium- to high-quality non-redundant metagenome-assembled genomes from the communities. The suppressed bacterial ammonia monooxygenase (amoA) expression was upregulated after shifting from a microoxic to an oxic condition. Seventy-three reconstructed metagenome-assembled genomes (>74% of the total) from 11 bacterial phyla harbored genes encoding proteins involved in nitrate respiration; 39 (~53%) carried N2O reductase (nosZ) genes with the predominance of clade II nosZ (31 metagenome-assembled genomes), and 24 (~33%) possessed nitrite reductase (ammonia-forming) genes (nrfA). Clade II nosZ and nrfA genes exhibited the highest and second-highest expressions among nitrogen metabolism genes, indicating robust N2O consumption and ammonification. Non-denitrifying clade II nosZ bacteria, Cloacibacterium spp., in the most abundant and active phylum Bacteroioda, were likely major N2O sinks. Elevated dissolved oxygen concentration inhibited clade II nosZ expression but not nrfA expression, potentially switching phenotypes from N2O reduction to ammonification. Collectively, the multi-omics analysis illuminated bacteria responsible for N2O reduction and ammonification in microoxic and oxic conditions, facilitating high-performance ammonia recovery.}, } @article {pmid39913343, year = {2025}, author = {Davidovich, C and Erokhina, K and Gupta, CL and Zhu, YG and Su, JQ and Djordjevic, SP and Wyrsch, ER and Blum, SE and Cytryn, E}, title = {Occurrence of "under-the-radar" antibiotic resistance in anthropogenically affected produce.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrae261}, pmid = {39913343}, issn = {1751-7370}, abstract = {With global climate change, treated-wastewater irrigation and manure amendment are becoming increasingly important in sustainable agriculture in water- and nutrient-stressed regions. Yet, these practices can potentially disseminate pathogens and antimicrobial resistance determinants to crops, resulting in serious health risks to humans through the food chain. Previous studies demonstrated that pathogen and antimicrobial resistance indicators from wastewater and manure survive poorly in the environment, suggesting that ecological barriers prevent their dissemination. However, we recently found that these elements can persist below detection levels in low quality treated wastewater-irrigated soil, and potentially proliferate under favorable conditions. This "under-the-radar" phenomenon was further investigated here, in treated wastewater-irrigated and poultry litter-amended lettuce plants, using an enrichment platform that resembles gut conditions, and an analytical approach that combined molecular and cultivation-based techniques. Enrichment uncovered clinically relevant multidrug-resistant pathogen indicators and a myriad of antibiotic resistance genes in the litter amended and treated wastewater-irrigated lettuce that were not detected by direct analyses, or in the enriched freshwater irrigated samples. Selected resistant E. coli isolates were capable of horizontally transferring plasmids carrying multiple resistance genes to a susceptible strain. Overall, our study underlines the hidden risks of under-the-radar pathogen and antimicrobial resistance determinants in anthropogenically affected agroenvironments, providing a platform to improve quantitative microbial risk assessment models in the future.}, } @article {pmid39913342, year = {2025}, author = {Martin, H and Rogers, LA and Moushtaq, L and Brindley, AA and Forbes, P and Quintion, AR and Murphy, ARJ and Hipperson, H and Daniell, TJ and Ndeh, D and Amsbury, S and Hitchcock, A and Lidbury, IDEA}, title = {Metabolism of hemicelluloses by root-associated Bacteroidota species.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf022}, pmid = {39913342}, issn = {1751-7370}, abstract = {Bacteroidota species are enriched in the plant microbiome and provide several beneficial functions for their host, including disease suppression. Determining the mechanisms that enable bacteroidota to colonise plant roots may therefore provide opportunities for enhancing crop production through microbiome engineering. By focusing on nutrient acquisition mechanisms, we discovered Bacteroidota species lack high affinity ATP-binding cassette transporters common in other plant bacteria for capturing simple carbon exudates. Instead, bacteroidota possess TonB-dependent transporters predicted to import glycans produced by plant polysaccharide breakdown. Metatranscriptomics (oat rhizosphere) identified several TonB-dependent transporters genes that were highly expressed in Flavobacterium (phylum Bacteroidota). Using Flavobacterium johnsoniae as the model, we experimentally validated the function of one highly expressed TonB-dependent transporters, identifying a conserved Xyloglucan Utilisation Loci conferring an ability to import xyloglucan, the major hemicellulose secreted from plant roots. Xyloglucan utilisation loci harbour an endoxyloglucanase related to family 5 subfamily 4 subclade 2D glycoside hydrolases carrying a mutation that we demonstrate is required for full activity towards xyloglucan. Based on analysing 700 soil metagenomes, subclade 2D glycoside hydrolases have radiated in soil and are prevalent among plant-associated bacteroidota and certain taxa affiliated with Gammaproteobacteria. In bacteroidota, particularly Flavobacterium species, xyloglucan utilisation loci organisation was highly conserved, which may increase their competitive ability to utilise xyloglucan. Given bacteroidota lack high-affinity nutrient transporters for simple carbon, instead possessing xyloglucan utilisation loci and similar gene clusters, our data suggests hemicellulose exudates provide them with an important carbon source in the rhizosphere.}, } @article {pmid39912643, year = {2025}, author = {Hotchkiss, MZ and Poulain, AJ and Forrest, JRK}, title = {Bumble bee gut microbial community structure differs between species and commercial suppliers, but metabolic potential remains largely consistent.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0203624}, doi = {10.1128/aem.02036-24}, pmid = {39912643}, issn = {1098-5336}, abstract = {Bumble bees are key pollinators for natural and agricultural plant communities. Their health and performance are supported by a core gut microbiota composed of a few bacterial taxa. However, the taxonomic composition and community structure of bumble bee gut microbiotas can vary with bee species, environment, and origin (i.e., whether colonies come from the wild or a commercial rearing facility), and it is unclear whether metabolic capabilities therefore vary as well. Here we used metagenomic sequencing to examine gut microbiota community composition, structure, and metabolic potential across bumble bees from two different commercial Bombus impatiens suppliers, wild B. impatiens, and three other wild bumble bee species sampled from sites within the native range of all four species. We found that the community structure of gut microbiotas varied between bumble bee species, between populations from different origins within species, and between commercial suppliers. Notably, we found that Apibacter is consistently present in some wild bumble bee species-suggesting it may be a previously unrecognized core phylotype of bumble bees-and that commercial B. impatiens colonies can lack core phylotypes consistently found in wild populations. However, despite variation in community structure, the high-level metabolic potential of gut microbiotas was largely consistent across all hosts, including for metabolic capabilities related to host performance, though metabolic activity remains to be investigated.IMPORTANCEOur study is the first to compare genome-level taxonomic structure and metabolic potential of whole bumble bee gut microbiotas between commercial suppliers and between commercial and wild populations. In addition, we profiled the full gut microbiotas of three wild bumble bee species for the first time. Overall, our results provide new insight into bumble bee gut microbiota community structure and function and will help researchers evaluate how well studies conducted in one bumble bee population will translate to other populations and species. Research on taxonomic and metabolic variation in bumble bee gut microbiotas across species and origins is of increasing relevance as we continue to discover new ways that social bee gut microbiotas influence host health, and as some bumble bee species decline in range and abundance.}, } @article {pmid39911714, year = {2024}, author = {Wang, Y and Jiang, X and Xi, Y and Wei, S and Ning, S and Zhang, W}, title = {Novel cycloviruses identified by mining human blood metagenomic data show close relationship to those from animals.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1522416}, pmid = {39911714}, issn = {1664-302X}, abstract = {The family Circoviridae includes the genera Circovirus and Cyclovirus. Cycloviruses have been found in serum samples from chronic HBV, HCV, or HIV-infected individuals as well as asymptomatic blood donors. However, research on cycloviruses is relatively limited. We used viral metagenomics to mine, analyze, and visualize the human blood virome, successfully identifying three new genomes, each encoding Rep and Capsid proteins. These proteins are crucial for viral replication and host-cell interaction: the Rep protein is involved in initiating viral genome replication, while the Capsid protein plays a key role in the assembly of new virions and the virus's ability to interact with host immune systems. Distance matrix and phylogenetic analyses show that these cycloviruses share high sequence similarity with viruses found in both humans and animals across different regions of Africa. This finding not only confirms the presence of previously uncharacterized cycloviruses in human blood, but also provides insight into their potential role in host transmission and their ecological significance. Further research is needed to explore the functional roles of these cycloviruses in viral pathogenesis, particularly how they may influence host immunity and contribute to chronic infections. Additionally, studies investigating the host range and mechanisms of cross-species transmission will be essential to understanding the broader implications of cycloviruses in human and animal health.}, } @article {pmid39911711, year = {2024}, author = {Kimeklis, AK and Gladkov, GV and Orlova, OV and Lisina, TO and Afonin, AM and Aksenova, TS and Kichko, AA and Lapidus, AL and Abakumov, EV and Andronov, EE}, title = {Metagenomic insights into the development of microbial communities of straw and leaf composts.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1485353}, pmid = {39911711}, issn = {1664-302X}, abstract = {INTRODUCTION: Soil microbiome is a major source of physiologically active microorganisms, which can be potentially mobilized by adding various nutrients. To study this process, a long-term experiment was conducted on the decomposition of oat straw and leaf litter using soil as a microbial inoculum.

METHODS: Combined analyses of enzymatic activity and NGS data for 16S rRNA gene amplicon and full metagenome sequencing were applied to study taxonomic, carbohydrate-active enzyme (CAZy), and polysaccharide utilization loci (PULs) composition of microbial communities at different stages of decomposition between substrates.

RESULTS: In straw degradation, the microbial community demonstrated higher amylase, protease, catalase, and cellulase activities, while peroxidase, invertase, and polyphenol oxidase were more active in leaf litter. Consistent with this, the metagenome analysis showed that the microbiome of straw compost was enriched in genes for metabolic pathways of simpler compounds. At the same time, there were more genes for aromatic compound degradation pathways in leaf litter compost. We identified nine metagenome-assembled genomes (MAGs) as the most promising prokaryotic decomposers due to their abnormally high quantity of PULs for their genome sizes, which were confirmed by 16S rRNA gene amplicon sequencing to constitute the bulk of the community at all stages of substrate degradation. MAGs from Bacteroidota (Chitinophaga and Ohtaekwangia) and Actinomycetota (Streptomyces) were found in both composts, while those from Bacillota (Pristimantibacillus) were specific for leaf litter. The most frequently identified PULs were specialized on xylans and pectins, but not cellulose, suggesting that PUL databases may be underrepresented in clusters for complex substrates.

DISCUSSION: Our study explores microbial communities from natural ecosystems, such as soil and lignocellulosic waste, which are capable of decomposing lignocellulosic substrates. Using a comprehensive approach with chemical analyses of the substrates, amplicon, and full metagenome sequencing data, we have shown that such communities may be a source of identifying the highly effective decomposing species with novel PULs.}, } @article {pmid39911706, year = {2024}, author = {Leon-Gomez, P and Romero, VI}, title = {Human papillomavirus, vaginal microbiota and metagenomics: the interplay between development and progression of cervical cancer.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1515258}, pmid = {39911706}, issn = {1664-302X}, abstract = {Persistent infection with oncogenic human papillomavirus (HPV) types, such as HPV 16 or 18, is a major factor in cervical cancer development. However, only a small percentage of infected women develop cancer, indicating that other factors are involved. Emerging evidence links vaginal microbiota with HPV persistence and cancer progression. Alterations in microbial composition, function, and metabolic pathways may contribute to this process. Despite the potential of metagenomics to explore these interactions, studies on the vaginal microbiota's role in cervical cancer are limited. This review systematically examines the relationship between cervical microbiota, HPV, and cervical cancer by analyzing studies from PubMed, EBSCO, and Scopus. We highlight how microbial diversity influences HPV persistence and cancer progression, noting that healthy women typically have lower microbiota diversity and higher Lactobacillus abundance compared to HPV-infected women, who exhibit increased Gardenella, Prevotella, Sneathia, Megasphaera, Streptococcus, and Fusobacterium spp., associated with dysbiosis. We discuss how microbial diversity is associated with HPV persistence and cancer progression, noting that studies suggest healthy women typically have lower microbiota diversity and higher Lactobacillus abundance, while HPV-infected women exhibit increased Gardnerella, Prevotella, Sneathia, Megasphaera, Streptococcus, and Fusobacterium spp., indicative of dysbiosis. Potential markers such as Gardnerella and Prevotella have been identified as potential microbiome biomarkers associated with HPV infection and cervical cancer progression. The review also discusses microbiome-related gene expression changes in cervical cancer patients. However, further research is needed to validate these findings and explore additional microbiome alterations in cancer progression.}, } @article {pmid39911666, year = {2024}, author = {Liu, H and Zhou, K and Zhong, C and Guan, M}, title = {Combination of metagenomic next-generation sequencing and morphology for identifying Coccidioides immitis: a case report.}, journal = {Frontiers in medicine}, volume = {11}, number = {}, pages = {1500014}, pmid = {39911666}, issn = {2296-858X}, abstract = {Coccidioidomycosis is a systemic infection caused by the dimorphic fungus Coccidioides spp., endemic to the Southwestern United States and Central and South America. In this article, we report a case of Coccidioides immitis-induced meningitis in a 27-year-old man who was experiencing recurrent fever and headache. His cerebrospinal fluid (CSF) biochemical markers indicated an infection in the central nervous system. However, repeated routine cultures of the CSF for bacterial detection were all negative. Only metagenomic next-generation sequencing (mNGS) detected low reads of C. immitis. To verify the mNGS results, the Clinical Microbiology Laboratory in Huashan Hospital optimized its culture conditions. Ultimately, 12 days after sampling, the fungal bottle containing the cerebrospinal fluid tested positive. Furthermore, the diagnosis of C. immitis was then confirmed by smear staining combined with morphological characteristics of the colony, which provided an important etiological basis for clinical diagnosis and treatment. As coccidioidomycosis is a rare disease in China, its pathogen-specific diagnostic methods are limited. In this case, we combined two universal methods, mNGS and traditional morphological observation, to confirm the diagnosis. This combined strategy is critical for quick and accurate diagnosis.}, } @article {pmid39911250, year = {2025}, author = {Li, H and Chen, Y and Xia, Z and Zhuang, D and Cong, F and Lian, YX}, title = {Metagenomic investigation of viruses in green sea turtles (Chelonia mydas).}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1492038}, pmid = {39911250}, issn = {1664-302X}, abstract = {Green sea turtles are listed on the International Union for Conservation of Nature's Red List of Threatened Species. Thus, conservation efforts, including investigation of factors affecting the health of green sea turtles, are critical. Viral communities play vital roles in maintaining animal health. In the present study, shotgun metagenomics was used for the first time to survey viruses in the feces of green sea turtles. Most viral contigs were DNA viruses that mainly belonged to Caudoviricetes, followed by Crassvirales. Additionally, most of the viral contigs were not assigned to any known family or genus, implying a large knowledge gap in the taxonomy of green sea turtle gut viruses. Host prediction showed that most viruses were connected to two phyla: Bacteroidetes and Firmicutes. Furthermore, KEGG enrichment analysis showed that the viral genes were mainly involved in phage-associated and metabolic pathways. Phylogenetic tree reconstruction of Caudovirales terminase large-subunit (TerL) protein showed that most of the sequences were phylogenetically distant. This study expands our understanding of the viral diversity in green sea turtles. In particular, analysis of the virome RNA fraction is exceedingly important for investigating intestinal viromes; therefore, future studies could use metatranscriptomics to study RNA viruses.}, } @article {pmid39910644, year = {2025}, author = {Alamoudi, R and Barozzi, A and Michoud, G and Van Goethem, MW and Odobel, C and Chen, Y and Marasco, R and Daffonchio, D}, title = {Metabolic redundancy and specialisation of novel sulfide-oxidizing Sulfurimonas and Sulfurovum along the brine-seawater interface of the Kebrit Deep.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {19}, pmid = {39910644}, issn = {2524-6372}, support = {5569-OFP2023//King Abdullah University of Science and Technology/ ; }, abstract = {BACKGROUND: Members of the Campylobacterota phylum are dominant key players in sulfidic environments, where they make up a stable portion of sulfide-oxidizing bacterial communities. Despite the significance of these bacteria in primary production being well recognised in several ecosystems, their genomic and metabolic traits in sulfidic deep hypersaline anoxic basins (DHABs) remain largely unexplored. This knowledge gap not only hampers our understanding of their adaptation and functional role in DHABs but also their ecological interactions with other microorganisms in these unique ecosystems.

RESULTS: Metabolic reconstructions from metagenome-assembled genomes (MAGs) of sulfide-oxidizing Campylobacterota were conducted at 10 cm spatial resolution within the halocline of the brine-seawater interface (BSI, salinity 91-155 PSU) of the 1466 m deep sulfidic Kebrit Deep in the Red Sea. Fifty-four Campylobacterota MAGs were assembled and dereplicated into three distinct groups, with the highest-quality genome retained as representative. These genomes represent novel sulfide-oxidizing species within the Sulfurimonas and Sulfurovum genera, which differ from those found in mildly saline deep-sea sulfidic pools. They are stratified along the BSI and utilise the reductive tricarboxylic acid cycle to fix carbon dioxide, acting as primary producers. Their energy generation processes include aerobic or anaerobic-nitrate-dependent sulfide oxidation, as well as hydrogen oxidation. In addition to the osmoprotectant pathways commonly observed in Campylobacterota, such as the synthesis and uptake of proline and glutamate, the two Kebrit Deep Sulfurovum species exhibit genomic signatures for ectoine synthesis, further aiding their adaptation to high salinity. This combination of metabolic redundancy and specialisation within the confined spatial boundaries (~1 m) of the BSI is pivotal in governing microbial interactions, including those with sulfate-reducers, heterotrophs, and other primary producers.

CONCLUSIONS: These results show how the selective pressures mediated by the sulfidic and hypersaline conditions of Kebrit Deep have resulted in novel, adapted and metabolically redundant Sulfurimonas and Sulfurovum species that contribute to the energy coupling, nutrient turnover and metabolic continuity along the physico-chemical gradient of the BSI.}, } @article {pmid39910065, year = {2025}, author = {Fumagalli, A and Castells-Nobau, A and Trivedi, D and Garre-Olmo, J and Puig, J and Ramos, R and Ramió-Torrentà, L and Pérez-Brocal, V and Moya, A and Swann, J and Martin-Garcia, E and Maldonado, R and Fernández-Real, JM and Mayneris-Perxachs, J}, title = {Archaea methanogens are associated with cognitive performance through the shaping of gut microbiota, butyrate and histidine metabolism.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2455506}, pmid = {39910065}, issn = {1949-0984}, mesh = {*Gastrointestinal Microbiome/physiology ; *Butyrates/metabolism ; Humans ; *Cognition ; *Histidine/metabolism ; Male ; Female ; Middle Aged ; Aged ; Bacteria/classification/metabolism/genetics/isolation & purification ; Methanobrevibacter/metabolism/genetics ; Metagenomics ; Archaea/metabolism/classification/genetics ; Cohort Studies ; Animals ; Adult ; }, abstract = {The relationship between bacteria, cognitive function and obesity is well established, yet the role of archaeal species remains underexplored. We used shotgun metagenomics and neuropsychological tests to identify microbial species associated with cognition in a discovery cohort (IRONMET, n = 125). Interestingly, methanogen archaeas exhibited the strongest positive associations with cognition, particularly Methanobrevibacter smithii (M. smithii). Stratifying individuals by median-centered log ratios (CLR) of M. smithii (low and high M. smithii groups: LMs and HMs) revealed that HMs exhibited better cognition and distinct gut bacterial profiles (PERMANOVA p = 0.001), characterized by increased levels of Verrucomicrobia, Synergistetes and Lentisphaerae species and reduced levels of Bacteroidetes and Proteobacteria. Several of these species were linked to the cognitive test scores. These findings were replicated in a large-scale validation cohort (Aging Imageomics, n = 942). Functional analyses revealed an enrichment of energy, butyrate, and bile acid metabolism in HMs in both cohorts. Global plasma metabolomics by CIL LC-MS in IRONMET identified an enrichment of methylhistidine, phenylacetate, alpha-linolenic and linoleic acid, and secondary bile acid metabolism associated with increased levels of 3-methylhistidine, phenylacetylgluamine, adrenic acid, and isolithocholic acid in the HMs group. Phenylacetate and linoleic acid metabolism also emerged in the Aging Imageomics cohort performing untargeted HPLC-ESI-MS/MS metabolic profiling, while a targeted bile acid profiling identified again isolithocholic acid as one of the most significant bile acid increased in the HMs. 3-Methylhistidine levels were also associated with intense physical activity in a second validation cohort (IRONMET-CGM, n = 116). Finally, FMT from HMs donors improved cognitive flexibility, reduced weight, and altered SCFAs, histidine-, linoleic acid- and phenylalanine-related metabolites in the dorsal striatum of recipient mice. M. smithii seems to interact with the bacterial ecosystem affecting butyrate, histidine, phenylalanine, and linoleic acid metabolism with a positive impact on cognition, constituting a promising therapeutic target to enhance cognitive performance, especially in subjects with obesity.}, } @article {pmid39910055, year = {2025}, author = {Song, B and Tria, FDK and Skejo, J}, title = {Prokaryotic cellulase gene clusters derived from 2,305 metagenomes.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {218}, pmid = {39910055}, issn = {2052-4463}, mesh = {*Cellulase/genetics/chemistry ; *Metagenome ; *Multigene Family ; Cellulases/genetics/chemistry ; Cellulose ; }, abstract = {Cellulose is a carbon source widespread in nature. However, it is a difficult task for any organism to get carbon atoms from the cellulose as it has a highly complex structure. Only a few taxonomic groups are known to decompose cellulose. They do it by producing cellulases, the various enzymes which break beta-glycosidic bonds in the cellulose. Cellulases were identified in 1,735 metagenomes from 225 bioprojects. The set of 12,837 metagenome-derived cellulases encompass three catalytic functions: exoglucanases (CBH, 1,042), endoglucanases (EG, 5,685), and beta-glucosidases (βG, 6,110). All three enzymatic functions are thought to be necessary for driving cellulase to a cascade of reactions that can make cellulose available as glucose. These metagenome-derived cellulases were clustered into protein families for each EC category individually, resulting in a total of 136 clusters, with the majority observed for EG (97 clusters), followed by βG (19 clusters) and CBH (19 clusters). These clusters provided a useful cellulase dataset for future research on cellulase utilization.}, } @article {pmid39909853, year = {2025}, author = {Hirota, K and Salim, F and Yamada, T}, title = {DeepES: Deep learning-based enzyme screening to identify orphan enzyme genes.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btaf053}, pmid = {39909853}, issn = {1367-4811}, abstract = {MOTIVATION: Progress in sequencing technology has led to determination of large numbers of protein sequences, and large enzyme databases are now available. Although many computational tools for enzyme annotation were developed, sequence information is unavailable for many enzymes, known as orphan enzymes. These orphan enzymes hinder sequence similarity-based functional annotation, leading gaps in understanding the association between sequences and enzymatic reactions.

RESULTS: Therefore, we developed DeepES, a deep learning-based tool for enzyme screening to identify orphan enzyme genes, focusing on biosynthetic gene clusters and reaction class. DeepES uses protein sequences as inputs and evaluates whether the input genes contain biosynthetic gene clusters of interest by integrating the outputs of the binary classifier for each reaction class. The validation results suggested that DeepES can capture functional similarity between protein sequences, and it can be implemented to explore orphan enzyme genes. By applying DeepES to 4744 metagenome-assembled genomes, we identified candidate genes for 236 orphan enzymes, including those involved in short-chain fatty acid production as a characteristic pathway in human gut bacteria.

AVAILABILITY: DeepES is available at https://github.com/yamada-lab/DeepES. Model weights and the candidate genes are available at Zenodo (https://doi.org/10.5281/zenodo.11123900).

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid39909332, year = {2025}, author = {Cheng, Z and He, Y and Wang, N and Wu, L and Xu, J and Shi, J}, title = {Uncovering soil amendment-induced genomic and functional divergence in soybean rhizosphere microbiomes during cadmium-contaminated soil remediation: Novel insights from field multi-omics.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {368}, number = {}, pages = {125787}, doi = {10.1016/j.envpol.2025.125787}, pmid = {39909332}, issn = {1873-6424}, abstract = {Soil amendments exhibit great potential in reducing cadmium (Cd) bioavailability and its accumulation in crop grains, but their practical implications on microbial characteristics (genomic traits and ecological functions) remain unclear. The objective of this study was to combine metagenomics and metatranscriptomics to track the dynamics of bacterial and viral communities in the soybean rhizosphere during the remediation of Cd-contaminated soil using a commercial Mg-Ca-Si conditioner (CMC), applied at low and high (975 kg ha[-1] and 1950 kg ha[-1]) rates under field conditions. Application of CMC increased the average size and decreased the guanine-cytosine (GC) content of microbial genomes, which were strongly shaped by soil pH and available Cd (ACd). Gene and transcript abundances analysis indicated that CMC promoted the enrichment of Alphaproteobacterial metagenome-assembled genomes (MAGs) carrying czcC gene encoding Cd efflux and dsbB gene encoding disulfide bond oxidoreductase. These genes are closely related to Cd resistance and exhibited notable (p < 0.05) increased expression in CMC-treated soils. Additionally, low and high CMC addition significantly increased viral alpha diversity by 5.7% and 9.6%, and viral activity by 3.3% and 7.8%, respectively, in comparison to the control. Temperate viruses were predicted as the major group (64%) and actively linked to the dominant host, and CMC amendment increased host metabolism and adaptability by enhancing (p < 0.05) the abundance and transcriptional activity of virus-encoded auxiliary metabolic genes (AMGs) involved in heavy metal resistance (ABC transport), sulfur cycling (cysH), and host metabolism (galE and queD) through "piggyback-the-winner" strategy. Structural equation modeling further revealed that CMC application influences Cd accumulation in soybean grains through its direct and indirect effects on soil properties and rhizosphere microbiomes, and highlighted the potential role of rhizosphere viruses in agricultural soil remediation.}, } @article {pmid39909254, year = {2025}, author = {Yan, Q and Wang, W and Fan, Z and Wei, Y and Yu, R and Pan, T and Wang, N and Lu, W and Li, B and Fang, Z}, title = {Chickpea-resistant starch exhibits bioactive function for alleviating atopic dermatitis via regulating butyrate production.}, journal = {International journal of biological macromolecules}, volume = {303}, number = {}, pages = {140661}, doi = {10.1016/j.ijbiomac.2025.140661}, pmid = {39909254}, issn = {1879-0003}, abstract = {Resistant starch (RS) is one of the bioactive polysaccharides to produce Short-chain fatty acids (SCFAs) in the colon and contributes to allergic diseases including atopic dermatitis (AD). However, the bioactive mechanism of RS relieving AD needs to be elucidated. In this study, RS was prepared using chickpeas. Its microstructure and crystal structure were thoroughly characterized. Chickpea RS significantly improved the clinical symptoms and restored Th1/Th2 immune balance in mice with AD induced by calcipotriol. These benefits were eliminated by antibiotic cocktail treatment, suggesting that gut microbiota mediated the alleviation effects of chickpea RS on AD. Based on metagenomic sequencing and untargeted metabolomic analysis, chickpea RS treatment significantly increased the proportions of Butyricimonas virosa, Bifidobacterium pseudolongum, and Faecalibaculum rodentium, and a total of 206 differential metabolites were altered, especially the increase in propionate and butyrate production. Furthermore, we found that acylated butyrate, but not propionate, improved the pathological characteristics by activating GPR109A, which inhibit the phosphorylation levels of IκB-α, p50, p65, JNK, and p-JNK. Collectively, chickpea RS exhibited the bioactive function for regulating the communication of the gut-skin axis via regulating butyrate production to activate GPR109A.}, } @article {pmid39909096, year = {2025}, author = {Zhang, Z and Liu, R and Zheng, W and Lan, Y and Li, Y}, title = {Specialized genera and niche partitioning promote the biosynthesis of short-chain fatty acids in anaerobic cofermentation of sewage sludge and protein-rich waste.}, journal = {Environmental research}, volume = {271}, number = {}, pages = {121034}, doi = {10.1016/j.envres.2025.121034}, pmid = {39909096}, issn = {1096-0953}, abstract = {Elucidating the relationships among various microorganisms and their reactions to environmental fluctuations, such as dissolved organic matter (DOM), remains a key objective in the anaerobic cofermentation (ACF) of sewage sludge (SS) and protein-rich waste (PRW); however, this topic is inadequately understood. In this study, the microbial traits associated with the biosynthesis of short-chain fatty acids (SCFAs) were investigated in the ACF of SS in conjunction with four distinct PRWs (pupa, fishmeal, maize gluten, and soybean meal). Compared with those in the SS-only reactor, the first-order rate constants for biosolid dissolution in the SS/PRW reactors were increased by 1.9-4.0-fold. Pupa performed best among the four PRWs in the ACF process, with the solubilization rate increasing from 9.4% (SS-only reactor) to 33.5%. The copious and readily biodegradable DOM created a unique niche for functional microbes, leading to reframing of the microfloral structure. Specialized genera, such as Holophaga, Alistipes, and Geothrix, were responsible for SCFA biosynthesis in the SS/pupa reactor. The highly differentiated, low-redundancy microecosystem constructed in the SS/pupa reactor contributed to the independent functioning of the hydrolyzers and acidogens, resulting in an SCFA yield that was 6.9-fold greater than that in the SS-only reactor. In addition, the ACF of SS/pupa resulted in the genes encoding the NiFe hydrogenase and Wood-Ljungdahl pathway being intact, which promoted the synthesis of SCFAs, especially acetate. These findings offer new insights into the microbiological mechanisms that augment SCFA generation by the ACF of SS/PRW in terms of microorganism fate, metabolic network relationships, and microecosystem niche.}, } @article {pmid39909037, year = {2025}, author = {Lim, B and Xu, J and Wierzbicki, IH and Gonzalez, CG and Chen, Z and Gonzalez, DJ and Gao, X and Goodman, AL}, title = {A human gut bacterium antagonizes neighboring bacteria by altering their protein-folding ability.}, journal = {Cell host & microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2025.01.008}, pmid = {39909037}, issn = {1934-6069}, abstract = {Antagonistic interactions play a key role in determining microbial community dynamics. Here, we report that one of the most widespread contact-dependent effectors in human gut microbiomes, Bte1, directly targets the PpiD-YfgM periplasmic chaperone complex in related microbes. Structural, biochemical, and genetic characterization of this interaction reveals that Bte1 reverses the activity of the chaperone complex, promoting substrate aggregation and toxicity. Using Bacteroides, we show that Bte1 is active in the mammalian gut, conferring a fitness advantage to expressing strains. Recipient cells targeted by Bte1 exhibit sensitivity to membrane-compromising conditions, and human gut microbes can use this effector to exploit pathogen-induced inflammation in the gut. Further, Bte1 allelic variation in gut metagenomes provides evidence for an arms race between Bte1-encoding and immunity-encoding strains in humans. Together, these studies demonstrate that human gut microbes alter the protein-folding capacity of neighboring cells and suggest strategies for manipulating community dynamics.}, } @article {pmid39909032, year = {2025}, author = {Zhu, X and Hu, M and Huang, X and Li, L and Lin, X and Shao, X and Li, J and Du, X and Zhang, X and Sun, R and Tong, T and Ma, Y and Ning, L and Jiang, Y and Zhang, Y and Shao, Y and Wang, Z and Zhou, Y and Ding, J and Zhao, Y and Xuan, B and Zhang, H and Zhang, Y and Hong, J and Fang, JY and Xiao, X and Shen, B and He, S and Chen, H}, title = {Interplay between gut microbial communities and metabolites modulates pan-cancer immunotherapy responses.}, journal = {Cell metabolism}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmet.2024.12.013}, pmid = {39909032}, issn = {1932-7420}, abstract = {Immune checkpoint blockade (ICB) therapy has revolutionized cancer treatment but remains effective in only a subset of patients. Emerging evidence suggests that the gut microbiome and its metabolites critically influence ICB efficacy. In this study, we performed a multi-omics analysis of fecal microbiomes and metabolomes from 165 patients undergoing anti-programmed cell death protein 1 (PD-1)/programmed death ligand 1 (PD-L1) therapy, identifying microbial and metabolic entities associated with treatment response. Integration of data from four public metagenomic datasets (n = 568) uncovered cross-cohort microbial and metabolic signatures, validated in an independent cohort (n = 138). An integrated predictive model incorporating these features demonstrated robust performance. Notably, we characterized five response-associated enterotypes, each linked to specific bacterial taxa and metabolites. Among these, the metabolite phenylacetylglutamine (PAGln) was negatively correlated with response and shown to attenuate anti-PD-1 efficacy in vivo. This study sheds light on the interplay among the gut microbiome, the gut metabolome, and immunotherapy response, identifying potential biomarkers to improve treatment outcomes.}, } @article {pmid39908950, year = {2025}, author = {Alonso-Vásquez, T and Fagorzi, C and Mengoni, A and Oliva, M and Cavalieri, D and Pretti, C and Cangioli, L and Bacci, G and Ugolini, A}, title = {Metagenomic surveys show a widespread diffusion of antibiotic resistance genes in a transect from urbanized to marine protected area.}, journal = {Marine pollution bulletin}, volume = {213}, number = {}, pages = {117640}, doi = {10.1016/j.marpolbul.2025.117640}, pmid = {39908950}, issn = {1879-3363}, abstract = {Ports are hot spots of pollution; they receive pollution from land-based sources, marine traffic and port infrastructures. Marine ecosystems of nearby areas can be strongly affected by pollution from port-related activities. Here, we investigated the microbiomes present in sea floor sediments along a transect from the harbour of Livorno (Central Italy) to a nearby marine protected area. Results of 16S rRNA amplicon sequencing and metagenome assembled genomes (MAGs) analyses indicated the presence of different trends of specific bacterial groups (e.g. phyla NB1-j, Acidobacteriota and Desulfobulbales) along the transect, correlating with the measured pollution levels. Human pathogenic bacteria and antibiotic resistance genes (ARGs) were also found. These results demonstrate a pervasive impact of human port activities and highlight the importance of microbiological surveillance of marine sediments, which may constitute a reservoir of ARGs and pathogenic bacteria.}, } @article {pmid39908754, year = {2025}, author = {Li, Y and Xiao, L and Zeng, XC}, title = {Hydrogen gas oxidation-driven reductive mobilization of arsenic in solid phase contributing to arsenite contamination in groundwater: Insights from metagenomic and microcosm analyses.}, journal = {Journal of hazardous materials}, volume = {488}, number = {}, pages = {137444}, doi = {10.1016/j.jhazmat.2025.137444}, pmid = {39908754}, issn = {1873-3336}, abstract = {Hydrogen gas (H2) is naturally produced by biological and non-biological reactions in various environmental niches. However, the influence of H2 on microbial processes that cause the mobilization and release of arsenic from solid phase into groundwater remains to be resolved. Given that dissimilatory arsenate [As(V)]-respiring prokaryotes (DARPs) have been demonstrated to significantly contribute to the formation of As-contaminated groundwater, our study specifically examined the interactions between H2 and DARPs. We prepared an enriched DARP population from As-contaminated soils. Metagenomic analyses of the DARP population revealed that approximately 46.7 % of the qualified DARPs' MAGs contain at least one type I Ni-Fe hydrogenase. The Ni-Fe hydrogenase proteins in DARPs show unique diversity. Functional assays indicate that the DARP population exhibited notable activity in oxidizing H2 while concurrently reducing As(V) under strictly anaerobic conditions. Arsenic release assays indicate that the DARP population is highly proficient at catalyzing the reductive mobilization of arsenic in scorodite, using hydrogen as the electron donor. These findings offer the initial evidence that H2 can directly promote the formation of arsenic-contaminated groundwater mediated by DARPs, a biogeochemical process that has long been overlooked. Therefore, this study increases our insight into the microbial mechanisms involved in the formation of arsenic-contaminated groundwater.}, } @article {pmid39908679, year = {2025}, author = {Cao, S and Fang, J and Koch, K and Fan, X and Al-Hazmi, HE and Du, R and Wells, GF}, title = {Fluoride-induced stress shapes partial denitrification granules to sustain microbial metabolism.}, journal = {Water research}, volume = {275}, number = {}, pages = {123239}, doi = {10.1016/j.watres.2025.123239}, pmid = {39908679}, issn = {1879-2448}, abstract = {The presence of fluoride ions (F[-]) in nitrogen-rich wastewater from photovoltaic and semiconductor industries introduces a significant challenge to biological treatment processes, particularly for the innovative partial denitrification (PD) process, which supplies nitrite for anaerobic ammonium oxidation (Anammox). This study provides the first comprehensive and systematic investigation of the effects of F[-] stress on the granule-based PD process through batch tests and long-term operation. Results indicate that PD activity remains resilient to F[-] shock up to 1.5 g/L but is markedly impaired at concentrations of 2.0-3.0 g/L, despite maintaining a nitrate-to-nitrite transformation ratio (NTR) of approximately 80 %. Under long-term F[-] stress at 0.5 g/L, NTR gradually reduces to 50 %, but subsequently recovers to and maintains at 70 %. The increased secretion of loosely bound extracellular polymeric substances and proteins likely enhances the resistance of PD granules to F[-] stress, though excessive amounts degrade their settling properties. F[-]-induced microbial community succession shapes a predominance of medium granules (1.0 < d < 2.0 mm of 60.2 %) by enhancing aggregation of smaller granules and disintegration of larger ones. This enhances the mechanical strength and microbial activity of PD granules, aiding in resistance to F[-] stress to sustain microbial metabolism. Thauera is selectively enriched under long-term F[-] stress, with upregulated nirBDS genes contributing to the reduced NTR. Additionally, increased electron metabolism activity and a robust antioxidative response help to maintain higher microbial metabolic activity, mitigating F[-]-induced oxidative stress. These findings advance our understanding of the resilience and adaptability of the PD process under F[-] stress, providing critical insights for optimizing biological wastewater treatment systems in challenging environments.}, } @article {pmid39908385, year = {2025}, author = {Griffiths, ME and Broos, A and Morales, J and Tu, IT and Bergner, L and Behdenna, A and Valderrama Bazan, W and Tello, C and Carrera, JE and Recuenco, S and Streicker, DG and Viana, M}, title = {Dynamics of influenza transmission in vampire bats revealed by longitudinal monitoring and a large-scale anthropogenic perturbation.}, journal = {Science advances}, volume = {11}, number = {6}, pages = {eads1267}, pmid = {39908385}, issn = {2375-2548}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Chiroptera/virology ; Animals ; Orthomyxoviridae Infections/transmission/virology/veterinary ; Humans ; Bayes Theorem ; Peru/epidemiology ; Zoonoses/transmission/virology ; Longitudinal Studies ; }, abstract = {Interrupting pathogen transmission between species is a priority strategy to mitigate zoonotic threats. However, avoiding counterproductive interventions requires knowing animal reservoirs of infection and the dynamics of transmission within them, neither of which are easily ascertained from the cross-sectional surveys that now dominate investigations into newly discovered viruses. We used biobanked sera and metagenomic data to reconstruct the transmission of recently discovered bat-associated influenza virus (BIV; H18N11) over 12 years in three zones of Peru. Mechanistic models fit under a Bayesian framework, which enabled joint inference from serological and molecular data, showed that common vampire bats maintain BIV independently of the now assumed fruit bat reservoir through immune waning and seasonal transmission pulses. A large-scale vampire bat cull targeting rabies incidentally halved BIV transmission, confirming vampire bats as maintenance hosts. Our results show how combining field studies, perturbation responses, and multi-data-type models can elucidate pathogen dynamics in nature and reveal pathogen-dependent effects of interventions.}, } @article {pmid39908317, year = {2025}, author = {Weinheimer, AR and Ha, AD and Aylward, FO}, title = {Towards a unifying phylogenomic framework for tailed phages.}, journal = {PLoS genetics}, volume = {21}, number = {2}, pages = {e1011595}, doi = {10.1371/journal.pgen.1011595}, pmid = {39908317}, issn = {1553-7404}, abstract = {Classifying viruses systematically has remained a key challenge of virology due to the absence of universal genes and vast genetic diversity of viruses. In particular, the most dominant and diverse group of viruses, the tailed double-stranded DNA viruses of prokaryotes belonging to the class Caudoviricetes, lack sufficient homology in the genetic machinery that unifies them to reconstruct inclusive, stable phylogenies of these genes. While previous approaches to organize tailed phage diversity have managed to distinguish various taxonomic levels, these methods are limited in scalability and reproducibility, and they do not include modes of evolution, like gene gains and losses. Here, we present a novel, comprehensive, and reproducible framework for examining evolutionary relationships of tailed phages. In this framework, we compare phage genomes based on presences and absences of a fixed set of gene families which is used as binary trait data that is input into maximum likelihood models and include heterogeneous rates of trait losses and gains. Our resulting phylogeny stably recovers known taxonomic families of tailed phages, with and without the inclusion of metagenomic phages. We also quantify the mosaicism of replication and structural genes among known families. Our results suggest that these exchanges likely underpin the emergence of new families. Additionally, we apply this framework to large phages (>100 kilobases) to map emergences of traits associated with genome expansion. Taken together, this evolutionary framework for charting and organizing tailed phage diversity improves the systemization of phage taxonomy, which can unify phage studies and advance our understanding of their evolution.}, } @article {pmid39908139, year = {2025}, author = {Zhang, Z and Guo, Q and Yang, Z and Sun, Y and Jiang, S and He, Y and Li, J and Zhang, J}, title = {Bifidobacterium adolescentis-derived nicotinic acid improves host skeletal muscle mitochondrial function to ameliorate sarcopenia.}, journal = {Cell reports}, volume = {44}, number = {2}, pages = {115265}, doi = {10.1016/j.celrep.2025.115265}, pmid = {39908139}, issn = {2211-1247}, abstract = {Sarcopenia significantly diminishes quality of life and increases mortality risk in older adults. While the connection between the gut microbiome and muscle health is recognized, the underlying mechanisms are poorly understood. In this study, shotgun metagenomics revealed that Bifidobacterium adolescentis is notably depleted in individuals with sarcopenia, correlating with reduced muscle mass and function. This finding was validated in aged mice. Metabolomics analysis identified nicotinic acid as a key metabolite produced by B. adolescentis, linked to improvements in muscle mass and functionality in individuals with sarcopenia. Mechanistically, nicotinic acid restores nicotinamide adenine dinucleotide (NAD+) levels in muscle, inhibits the FoxO3/Atrogin-1/Murf-1 axis, and promotes satellite cell proliferation, reducing muscle atrophy. Additionally, NAD+ activation enhances the silent-information-regulator 1 (SIRT1)/peroxisome-proliferator-activated-receptor-γ-coactivator 1-alpha (PGC-1α) axis, stimulating mitochondrial biogenesis and promoting oxidative metabolism in slow-twitch fibers, ultimately improving muscle function. Our findings suggest that B. adolescentis-derived nicotinic acid could be a promising therapeutic strategy for individuals with sarcopenia.}, } @article {pmid39907890, year = {2025}, author = {Ramos-Lopez, O}, title = {Personalizing Dietary Polyphenols for Health Maintenance and Disease Management: A Nutrigenetic Approach.}, journal = {Current nutrition reports}, volume = {14}, number = {1}, pages = {29}, pmid = {39907890}, issn = {2161-3311}, mesh = {Humans ; *Polyphenols/pharmacology ; *Nutrigenomics ; *Dietary Supplements ; Polymorphism, Single Nucleotide ; Diet ; Precision Medicine ; Flavonoids/pharmacology ; }, abstract = {PURPOSE OF THE REVIEW: This literature review provides examples of the influence of certain genetic variants on health outcomes after dietary polyphenol consumption or supplementation. Available evidence is organized according to the major classes of polyphenols (flavonoids, phenolic acids, stilbenes, lignans, and tannins) and their derived subgroups.

RECENT FINDINGS: Nutrigenetic studies have identified mainly single nucleotide polymorphisms located within genes involved in the biotransformation of phenolic acids, stilbenes, lignans and several flavonoid molecules. These genetic variants may affect polyphenol metabolism rates and related predisposition to chronic non-communicable diseases. Moreover, differential cardiometabolic outcomes upon polyphenol supplementation as dietary sources or nutraceuticals have been modulated by specific genotypes. Although current evidence is still limited, growing gene-polyphenol interactions are contributing to systematically elucidate the biological functions of polyphenols; determine individual risk phenotypes to specific diseases or particular responses upon polyphenol exposure; and facilitate the prescription of personalized genotype-based doses of dietary polyphenols to optimize related health benefits. Additionally, the integration of genetics with other omics insights (epigenomics, transcriptomics, metagenomics, and metabolomics) trough biological systems and high-dimensional data analyses and interpretation may provide a more comprehensive understanding of polyphenol metabolism for precision nutrition applications in health and disease.}, } @article {pmid39907344, year = {2025}, author = {Cuong, NC and Hung, NV and Linh, TK and Loi, NTT and Tung, QN and Tuyen, DT and Anh, DTN}, title = {Structure of fungal community and culturable fungi on the discolored surfaces of pine storage boxes in the tropical region in Dong Nai, Vietnam.}, journal = {Brazilian journal of biology = Revista brasleira de biologia}, volume = {84}, number = {}, pages = {e289015}, doi = {10.1590/1519-6984.289015}, pmid = {39907344}, issn = {1678-4375}, mesh = {Vietnam ; *Fungi/classification/isolation & purification/genetics ; *Wood/microbiology ; *Pinus/microbiology ; Tropical Climate ; Mycobiome ; }, abstract = {Wood and wood-based materials are commonly used for storage, but their surfaces are prone to biodegradation by microorganisms, especially fungi. This study focuses on the microbial communities on pine wood storage boxes treated with an anti-termite and mold solution in a tropical region in Dong Nai, Vietnam. We isolated 13 fungal strains from these surfaces and classified them into six genera: Rhizopus, Aspergillus, Fusarium, Curvularia, Penicillium, and Trichoderma. Enzyme activity tests revealed that strains Curvularia eragrostidis TD4.2 and Aspergillus sydowii TD5 were the most effective producers of cellulase, amylase, and laccase. Shotgun metagenomics analysis of the biological sample of the discolored surface of pine storage boxes indicated that Ascomycota was the dominant phylum, with Dothideomycetes and Sordariomycetes as the prevalent class. Aureobasidium (0.33%) and Chaetomium (1.1%) were the most abundant genera in the Dothideomycetes and Sordariomycetes, respectively. This research illustrates the complexity of microbial communities on wood surfaces, providing insights into the fungal dynamics affecting wooden storage materials in tropical climates.}, } @article {pmid39907343, year = {2025}, author = {Alifia, L and Zulaika, E and Soeprijanto, S and Hamzah, A and Luqman, A}, title = {Microbial diversity and biotechnological potential of mangrove leaf litter in Kebun Raya Mangrove, Surabaya, Indonesia.}, journal = {Brazilian journal of biology = Revista brasleira de biologia}, volume = {84}, number = {}, pages = {e288968}, doi = {10.1590/1519-6984.288968}, pmid = {39907343}, issn = {1678-4375}, mesh = {Indonesia ; *Plant Leaves/microbiology ; *Rhizophoraceae/microbiology ; *Avicennia/microbiology ; Biodiversity ; Bacteria/classification/genetics/isolation & purification ; Wetlands ; }, abstract = {Mangrove ecosystems play a crucial role in maintaining ecological balance with leaf litter serving as an important substrate for diverse microbial communities. This study investigates the microbial communities inhabiting leaf litter from four different mangrove species: Rhizophora apiculata, Rhizophora stylosa, Sonneratia caseolaris, and Avicennia marina collected from Kebun Raya Mangrove, Surabaya, Indonesia. Using metagenomic sequencing, we revealed that Proteobacteria were predominant, followed by Chlorobi and Actinobacteria in the samples. Interestingly, we detected notable populations of anaerobic bacteria, including genus of Chlorobaculum and Allochromatium. Metagenomic analyses exhibited high levels of adaptation to stressors, evidenced by the prevalence of genes conferring resistance to antibiotics (e.g., beta-lactams, tetracyclines), heavy metals (e.g., chromium, arsenic), and hydrocarbons. Furthermore, the metagenomic analysis revealed the presence of genes involved in the biosynthesis of polyunsaturated fatty acids (PUFAs), antimicrobial compounds, and plant growth-promoting activities. These findings highlight the potential of mangrove leaf litter as a reservoir of beneficial microbes with diverse biotechnological applications, including bioremediation, nutraceuticals, pharmaceuticals, and agriculture.}, } @article {pmid39907107, year = {2025}, author = {Salamzade, R and Tran, PQ and Martin, C and Manson, AL and Gilmore, MS and Earl, AM and Anantharaman, K and Kalan, LR}, title = {zol and fai: large-scale targeted detection and evolutionary investigation of gene clusters.}, journal = {Nucleic acids research}, volume = {53}, number = {3}, pages = {}, pmid = {39907107}, issn = {1362-4962}, support = {R35 GM137828/GM/NIGMS NIH HHS/United States ; U19 AI110818/AI/NIAID NIH HHS/United States ; U19AI110818//Broad Institute/ ; NIAID U19AI142720/NH/NIH HHS/United States ; }, mesh = {*Multigene Family ; *Evolution, Molecular ; Software ; Genomics/methods ; Viruses/genetics/classification ; Metagenome/genetics ; }, abstract = {Many universally and conditionally important genes are genomically aggregated within clusters. Here, we introduce fai and zol, which together enable large-scale comparative analysis of different types of gene clusters and mobile-genetic elements, such as biosynthetic gene clusters (BGCs) or viruses. Fundamentally, they overcome a current bottleneck to reliably perform comprehensive orthology inference at large scale across broad taxonomic contexts and thousands of genomes. First, fai allows the identification of orthologous instances of a query gene cluster of interest amongst a database of target genomes. Subsequently, zol enables reliable, context-specific inference of ortholog groups for individual protein-encoding genes across gene cluster instances. In addition, zol performs functional annotation and computes a variety of evolutionary statistics for each inferred ortholog group. Importantly, in comparison to tools for visual exploration of homologous relationships between gene clusters, zol can scale to handle thousands of gene cluster instances and produce detailed reports that are easy to digest. To showcase fai and zol, we apply them for: (i) longitudinal tracking of a virus in metagenomes, (ii) performing population genetic investigations of BGCs for a fungal species, and (iii) uncovering evolutionary trends for a virulence-associated gene cluster across thousands of genomes from a diverse bacterial genus.}, } @article {pmid39906849, year = {2025}, author = {Vinogradova, E and Jarmukhanov, Z and Nurgaziyev, M and Kossumov, A and Nurgozhina, A and Mukhanbetzhanov, N and Sergazy, S and Chulenabyeva, L and Issilbayeva, A and Askarova, S and Kaiyrlykyzy, A and Rakhimova, S and Kozhamkulov, U and Kairov, U and Khassenbekova, Z and Tarzhanova, D and Akilzhanova, A and Lee, JH and Terwilliger, J and Sailybayeva, A and Bekbossynova, M and Zhumadilov, Z and Kozhakhmetov, S and Kushugulova, A}, title = {Enterococcus dysbiosis as a mediator of vitamin D deficiency-associated memory impairments.}, journal = {Heliyon}, volume = {11}, number = {2}, pages = {e41969}, pmid = {39906849}, issn = {2405-8440}, abstract = {Low vitamin D status is linked to disturbance in cognitive performance. This study explored possible ways how composition and functional capacity of the gut microbiome affects vitamin D metabolism, directing serum vitamin D (VitD) levels and memory impairmets. It was found that gut microbiome composition, characterized by an increase in the relative abundance of Enterococcus and correlated with vitamin D deficiency and, as consequence, with memory impairments. A key mechanism identified in the study was the differential utilization of short-chain fatty acids (SCFAs) produced by gut bacteria as substrates for synthesizing vitamin D3 precursor in the skin. This finding confirms a complex interplay between the gut microbiome, host metabolism, and cognitive health, highlighting the potential significance of targeting Enterococcus dysbiosis in future preventive and therapeutic strategies to address VitD deficiency-related memory impairments. These results underscore the importance of understanding and modulating gut microbiome composition to optimize VitD status and cognitive function.}, } @article {pmid39906540, year = {2024}, author = {Jiang, N and Chen, Z and Ren, Y and Xie, S and Yao, Z and Jiang, D and Zhang, Y and Chen, L}, title = {How do various strategies for returning residues change microbiota modulation: potential implications for soil health.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1495682}, pmid = {39906540}, issn = {1664-302X}, abstract = {INTRODUCTION: Residue incorporation is a crucial aspect of anthropogenic land management practices in agricultural fields. However, the effects of various returning strategies on the soil microbiota, which play an essential vital role in maintaining soil health, remains largely unexplored.

METHODS: In a study conducted, different residue management strategies were implemented, involving the application of chemical fertilizers and residues that had undergone chopping (SD), composting (SC), and pyrolysis (BC) processes, with conventional fertilization serving as the control (CK).

RESULTS AND DISCUSSION: Using metagenomic sequencing, the analysis revealed that while all residue returning strategies had minimal effects on the diversity (both α and β) of microbiota, they did significantly alter microbial functional genes related to carbon (C), nitrogen (N), phosphorus (P), and sulfur (S) cycling, as well as the presence of antibiotic resistance genes (ARGs) and pathogens. Specifically, chopped residues were found to enhance microbial genes associated with C, N, P, and S cycling, while composted residues primarily stimulated C and S cycling. Furthermore, all residue treatments resulted in a disruption of relationships among nutrient cycles, with varying degrees of impact observed across the different management strategies, with the sequence of impact being SD < SC < BC. Moreover, the residue additions resulted in the accumulation of ARGs, while only SC caused an increase in certain pathogens. Finally, through analyzing the correlation network among indices that exhibited active responses to residue additions, potential indicators for functional changes in response to residue additions were identified. This study further offered recommendations for future cropland management practices aimed at enhancing soil health through microbiomes.}, } @article {pmid39906303, year = {2025}, author = {Takada, K and Holmes, EC}, title = {Genome sizes of animal RNA viruses reflect phylogenetic constraints.}, journal = {Virus evolution}, volume = {11}, number = {1}, pages = {veaf005}, pmid = {39906303}, issn = {2057-1577}, abstract = {Animal genomes are characterized by extensive variation in size. RNA viruses similarly exhibit substantial genomic diversity, with genome lengths ranging from 1.7 to ∼64 kb. Despite the myriad of novel viruses discovered by metagenomics, we know little of the factors that shape the evolution of the genome size in RNA viruses. We analyzed the variation in genome sizes across orders and families of animal RNA viruses. We found that RNA viruses can have highly variable genome sizes within and among orders, with the Nidovirales (including the Coronaviridae) exhibiting both significantly larger genomes and a greater range of genome sizes than other orders. In the Bunyavirales, Amarillovirales, Nidovirales, and Picornavirales, the genome sizes of invertebrate-associated RNA viruses were significantly larger than those that infect vertebrates, in contrast to their animal hosts in which vertebrates commonly have larger genomes than invertebrates. However, in the Mononegavirales, vertebrate viruses were significantly larger than those viruses associated with invertebrates. There were similarly complex associations between genome size and patterns of genome segmentation. In the Bunyavirales, Reovirales, and Nidovirales, viruses with segmented genomes, or that possessed a large number of segments, had significantly larger genome sizes than viruses with nonsegmented genomes or a small number of segments, while in Articulavirales, there were no significant differences in genome size among viruses possessing any number of genome segments. More broadly, our analysis revealed that taxonomic position (i.e. RNA virus order) had a greater impact on genome size than whether viruses infected vertebrates or invertebrates or their pattern of genome segmentation. Hence, the phylogenetic constraints on genome size are of sufficient magnitude to shape some other aspects of virus evolution.}, } @article {pmid39906212, year = {2024}, author = {Xi, Z and Chen, J and Wang, L and Lu, A}, title = {Characteristics of lower respiratory microbiota in children's refractory Mycoplasma pneumoniae pneumonia pre- and post-COVID-19 era.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1438777}, pmid = {39906212}, issn = {2235-2988}, mesh = {Humans ; *Microbiota ; *COVID-19/immunology/microbiology ; Male ; Female ; Child ; Child, Preschool ; *Pneumonia, Mycoplasma/microbiology ; Mycoplasma pneumoniae/genetics/isolation & purification ; SARS-CoV-2 ; Infant ; High-Throughput Nucleotide Sequencing ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Drug Resistance, Bacterial ; RNA, Ribosomal, 23S/genetics ; Respiratory System/microbiology/virology ; }, abstract = {INTRODUCTION: Little was known about the characteristics of low respiratory tract (LRT) microbiota of refractory M. pneumoniae pneumonia (RMPP) in children before and after the COVID-19 pandemic.

METHODS: Forty-two children diagnosed with RMPP in 2019 (Y2019 group) and 33 children diagnosed with RMPP in 2023 (Y2023 group), entered into the study. The characteristics of the clinical findings were examined, and the LRT microbiota was analyzed by metagenomic next generation sequencing.

RESULTS: The ratio of consolidate, atelectasis, lung necrosis, and erythema multiforme in Y2023 group was significantly higher than that in Y2019 (P<0.05). Mycoplasmoides pneumoniae was the top species of the LRT microbiota in both groups. The rate of macrolide resistance MP in Y2023 was significantly higher than that in Y2019 (P<0.05), and the mutant site was all 23S rRNA A2063G. There were no significant differences in α-diversity and β-diversity of LRT microbiota between Y2019 and Y2023 group. Trichoderma citrinoviride, Canine mastadenovirus A, Ralstonia pickettii, Lactococcus lactis, Pseudomonas aeruginosa were the biomarkers of LRT microbiota in children with RMPP of Y2023. The abundance of Mycoplasmoides pneumoniae positively correlated with the levels of D-dimer and LDH, negatively correlated with the counts of CD3[+] T cells, CD8[+] T cells, CD19[+] B cells and CD16[+]CD56[+] NK cells.

DISCUSSION: Our study showed that high abundance of MP was correlated with the severity of RMPP and decrease of immune cells. Trichoderma citrinoviride, Canine mastadenovirus A, Ralstonia pickettii, Lactococcus lactis, Pseudomonas aeruginosa were the biomarkers in microbiota of LRT in children with RMPP post COVID-19 era.}, } @article {pmid39906158, year = {2025}, author = {Hunter, B and Cromwell, T and Shim, H}, title = {Nanopore sequencing of protozoa: Decoding biological information on a string of biochemical molecules into human-readable signals.}, journal = {Computational and structural biotechnology journal}, volume = {27}, number = {}, pages = {440-450}, pmid = {39906158}, issn = {2001-0370}, abstract = {Biological information is encoded in a sequence of biochemical molecules such as nucleic acids and amino acids, and nanopore sequencing is a long-read sequencing technology capable of directly decoding these molecules into human-readable signals. The long reads from nanopore sequencing offer the advantage of obtaining contiguous information, which is particularly beneficial for decoding complex or repetitive regions in a genome. In this study, we investigated the efficacy of nanopore sequencing in decoding biological information from distinctive genomes in metagenomic samples, which pose significant challenges for traditional short-read sequencing technologies. Specifically, we sequenced blood and fecal samples from mice infected with Trypanosoma brucei, a unicellular protozoan known for its hypervariable and dynamic regions that help it evade host immunity. Such characteristics are also prevalent in other host-dependent parasites, such as bacteriophages. The taxonomic classification results showed a high proportion of nanopore reads identified as T. brucei in the infected blood samples, with no significant identification in the control blood samples and fecal samples. Furthermore, metagenomic de novo assembly of these nanopore reads yielded contigs that mapped to the reference genome of T. brucei in the infected blood samples with over 96 % accuracy. This exploratory work demonstrates the potential of nanopore sequencing for the challenging task of classifying and assembling hypervariable and dynamic genomes from metagenomic samples.}, } @article {pmid39906131, year = {2025}, author = {Babalola, OO and Enagbonma, BJ}, title = {Dataset of shotgun metagenomic evaluation of Sorghum bicolor rhizosphere microbiome in soils preceded by Glycine max.}, journal = {Data in brief}, volume = {58}, number = {}, pages = {111270}, pmid = {39906131}, issn = {2352-3409}, abstract = {The dataset presents the microbial diversity, community structure, and functional potential of the rhizosphere microbiome associated with Sorghum bicolor in response to crop rotation involving a Glycine max precursor. Soil samples were collected from the rhizospheres of two Sorghum bicolor cultivars, Avenger and NS55, cultivated in soils previously used for Glycine max and cultivated in soils that have not previously been used for Glycine max cultivation, as follows: i) Sorghum bicolor Avenger (SA1, SA2, and SA3) cultivated in soils previously used for Glycine max, ii) Sorghum bicolor NS55 (SN1, SN2, and SN3) grown in soils that had been cultivated with Glycine max, iii) Sorghum bicolor Avenger (RA1, RA2, and RA3) cultivated in soils not previously used for Glycine max, iv) Sorghum bicolor NS55 (RN1, RN2, and RN3) grown in soils not previously cultivated with Glycine max. Thereafter, the shotgun sequencing was done to assess the microbial composition and functional genes from the extracted DNA. The effective metagenome after QC of the twelve samples include SA1 (99.72%), SA2 (99.50%), SA3 (99.68%), SN1 (99.75%), SN2 (99.76%), SN3 (99.70%), RA1 (99.72%), RA2 (99.77%), RN3 (99.72%), RN1 (99.67%), RN2 (99.68%), and RN3 (99.54%). Information from the metagenome sequences is accessible under the bioproject numbers PRJNA1166458 (SA1, SA2, and SA3), PRJNA1166463 (SN1, SN2, and SN3), PRJNA1166623 (RA1, RA2, and RA3), PRJNA1166627 (RN1, RN2 and RN3). Actinomycetota and Function unknown dominated the microbiomes across all cropping systems. The insights gained from this dataset hold promise for advancing sustainable agricultural practices, particularly through optimizing crop rotations, developing microbial bioinoculants, and enhancing soil health. Furthermore, the functional data and the function unknown from this dataset could enrich our understanding of microbial roles in nutrient cycling, plant growth promotion, and stress mitigation, which are critical for addressing challenges in food security and environmental sustainability.}, } @article {pmid39906066, year = {2025}, author = {Zhang, J and Jiao, Y and Liu, K and Situ, W and Menghe, B and Chen, Y and Zha, M}, title = {Characterizing microbial diversity and metabolic pathways in yak milk and fermented yak milk based on metagenomics: A study from Ganzi Tibetan autonomous prefecture.}, journal = {Food chemistry: X}, volume = {25}, number = {}, pages = {102198}, pmid = {39906066}, issn = {2590-1575}, abstract = {Kangding and Litang are the capital and pivotal county respectively within Ganzi. The region's distinctive geographical and climatic environment has endowed yak milk (YM) and its products with unique microbial resources, which play a crucial role in product quality and flavor. Therefore, it is important to understand their microbiota. We analyzed microbiota and metabolic pathways in YM. Results revealed 207 species, with Pseudomonas unclassified, Acinetobacter johnsonii dominant in YM, and Lactobacillus delbrueckii, Streptococcus thermophilus in fermented yak milk (FYM). YM exhibited lower microbial and bacteriophage diversity. Bacteriophage diversity was primarily targeting harmful microbes. Yak and camel milk showed similarities, while koumiss and fermented camel milk shared dominant bacteria. Metabolic pathways in YM were enriched with carbohydrates, amino acids, fats, and purine metabolism. In conclusion, this study provides information on the microbial resources and related metabolic pathways in yak milk and naturally fermented yak milk in the Ganzi region of China.}, } @article {pmid39905573, year = {2025}, author = {Armstrong, E and Liu, R and Pollock, J and Huibner, S and Udayakumar, S and Irungu, E and Ngurukiri, P and Muthoga, P and Adhiambo, W and Yegorov, S and Kimani, J and Beattie, T and Coburn, B and Kaul, R}, title = {Quantitative profiling of the vaginal microbiota improves resolution of the microbiota-immune axis.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {39}, pmid = {39905573}, issn = {2049-2618}, support = {Canada Graduate Scholarship/CAPMC/CIHR/Canada ; Vanier Canada Graduate Scholarship/CAPMC/CIHR/Canada ; PJT-180629/CAPMC/CIHR/Canada ; MR/R023182/1//Medical Research Council and the UK Foreign, Commonwealth and Development Office/ ; }, mesh = {Humans ; Female ; *Vagina/microbiology/immunology ; *Vaginosis, Bacterial/microbiology/immunology ; Kenya ; *Microbiota ; Adult ; *Sex Workers ; *Bacterial Load ; Bacteria/classification/genetics/isolation & purification ; Young Adult ; Interleukin-1alpha/metabolism ; Cytokines/metabolism ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; Lactobacillus/isolation & purification ; }, abstract = {BACKGROUND: The composition of the vaginal microbiota is closely linked to adverse sexual and reproductive health outcomes, due in part to effects on genital immunology. Compositional approaches such as metagenomic sequencing provide a snapshot of all bacteria in a sample and have become the standard for characterizing the vaginal microbiota, but only provide microbial relative abundances. We hypothesized that the addition of absolute abundance data would provide a more complete picture of host-microbe interactions in the female genital tract.

RESULTS: We analyzed cervicovaginal secretions from 196 female sex workers in Kenya and found that bacterial load was elevated among women with diverse, bacterial vaginosis (BV)-type microbiota and lower among women with Lactobacillus predominance. Bacterial load was also positively associated with proinflammatory cytokines, such as IL-1α, and negatively associated with chemokines, such as IP-10. The associations between bacterial load and immune factors differed across bacterial community states, but L. crispatus predominance was the only microbial community where higher bacterial load was not associated with higher proinflammatory cytokines. Total vaginal bacterial load was also a stronger predictor of the genital immune environment than BV by Nugent score, the current clinical standard, in the Kenya-based cohort and in a Uganda-based confirmatory cohort.

CONCLUSIONS: Our results suggest that total vaginal bacterial load is at least as strong a predictor of the genital immune milieu as current BV clinical diagnostic tools, supporting exploration of the vaginal bacterial load as a predictor of adverse reproductive and sexual health outcomes. Video Abstract.}, } @article {pmid39905490, year = {2025}, author = {Molina-Pardines, C and Haro-Moreno, JM and Rodriguez-Valera, F and López-Pérez, M}, title = {Extensive paralogism in the environmental pangenome: a key factor in the ecological success of natural SAR11 populations.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {41}, pmid = {39905490}, issn = {2049-2618}, support = {PRE2021-098122//Ministerio de Economía y Competitividad/ ; PID2020-118052GB-I00//Ministerio de Economía y Competitividad/ ; 2021/PER/00020//Ministerio de Universidades/ ; }, mesh = {*Metagenomics/methods ; Mediterranean Sea ; *Genetic Variation ; Microbiota/genetics ; Genome, Bacterial ; Metagenome ; Phylogeny ; Seawater/microbiology ; }, abstract = {BACKGROUND: The oceanic microbiome is dominated by members of the SAR11 clade. Despite their abundance, challenges in recovering the full genetic diversity of natural populations have hindered our understanding of the eco-evolutionary mechanisms driving intra-species variation. In this study, we employed a combination of single-amplified genomes and long-read metagenomics to recover the genomic diversity of natural populations within the SAR11 genomospecies Ia.3/VII, the dominant group in the Mediterranean Sea.

RESULTS: The reconstruction of the first complete genome within this genomospecies revealed that the core genome represents a significant proportion of the genome (~ 81%), with highly divergent areas that allow for greater strain-dependent metabolic flexibility. The flexible genome was concentrated in small regions, typically containing a single gene, and was located in equivalent regions within the genomospecies. Each variable region was associated with a specific set of genes that, despite exhibiting some divergence, maintained equivalent biological functionality within the population. The environmental pangenome is large and enriched in genes involved in nutrient transport, as well as cell wall synthesis and modification, showing an extremely high degree of functional redundancy in the flexible genome (i.e. paralogisms).

CONCLUSIONS: This genomic architecture promotes polyclonality, preserving genetic variation within the population. This, in turn, mitigates intraspecific competition and enables the population to thrive under variable environmental conditions and selective pressures. Furthermore, this study demonstrates the power of long-read metagenomics in capturing the full genetic diversity of environmental SAR11 populations, overcoming the limitations of second-generation sequencing technologies in genome assembly. Video Abstract.}, } @article {pmid39905469, year = {2025}, author = {Li, S and Zhan, Y and Wang, Y and Li, W and Wang, X and Wang, H and Sun, W and Cao, X and Li, Z and Ye, F}, title = {One-step diagnosis of infection and lung cancer using metagenomic sequencing.}, journal = {Respiratory research}, volume = {26}, number = {1}, pages = {48}, pmid = {39905469}, issn = {1465-993X}, support = {No. 2021YFC2301101//National Key Research and Development Program/ ; No. 82100118//Youth fund of National Natural Science Foundation of China/ ; 92048203//National Natural Science Foundation of China/ ; No. 2022SKLID308//the Science Foundation for the State Key Laboratory for Infectious Disease Prevention and Control of China/ ; }, mesh = {Humans ; *Lung Neoplasms/genetics/diagnosis/microbiology ; Male ; Female ; Middle Aged ; *Metagenomics/methods ; Aged ; Respiratory Tract Infections/diagnosis/microbiology/genetics ; Adult ; }, abstract = {BACKGROUND: Traditional detection methods face challenges in meeting the diverse clinical needs for diagnosing both lung cancer and infections within a single test. Onco-mNGS has emerged as a promising solution capable of accurately identifying infectious pathogens and tumors simultaneously. However, critical evidence is still lacking regarding its diagnostic performance in distinguishing between pulmonary infections, tumors, and non-infectious, non-tumor conditions in real clinical settings.

METHODS: In this study, data were gathered from 223 participants presenting symptoms of lung infection or tumor who underwent Onco-mNGS testing. Patients were categorized into four groups based on clinical diagnoses: infection, tumor, tumor with infection, and non-infection-non-tumor. Comparisons were made across different groups, subtypes, and stages of lung cancer regarding copy number variation (CNV) patterns, microbiome compositions, and clinical detection indices.

RESULTS: Compared to conventional infection testing methods, Onco-mNGS demonstrates superior infection detection performance, boasting a sensitivity of 81.82%, specificity of 72.55%, and an overall accuracy of 77.58%. In lung cancer diagnosis, Onco-mNGS showcases excellent diagnostic capabilities with sensitivity, specificity, accuracy, positive predictive value, and negative predictive value reaching 88.46%, 100%, 91.41%, 100%, and 90.98%, respectively. In bronchoalveolar lavage fluid (BALF) samples, these values stand at 87.5%, 100%, 94.74%, 100%, and 91.67%, respectively. Notably, more abundant CNV mutation types and higher mutation rates were observed in adenocarcinoma (ADC) compared to squamous cell carcinoma (SCC). Concurrently, onco-mNGS data revealed specific enrichment of Capnocytophaga sputigeria in the ADC group and Candida parapsilosis in the SCC group. These species exhibited significant correlations with C reaction protein (CRP) and CA153 values. Furthermore, Haemophilus influenzae was enriched in the early-stage SCC group and significantly associated with CRP values.

CONCLUSIONS: Onco-mNGS has exhibited exceptional efficiencies in the detection and differentiation of infection and lung cancer. This study provides a novel technological option for achieving single-step precise and swift detection of lung cancer.}, } @article {pmid39905327, year = {2025}, author = {Wei, M and Gu, K and Qin, J and Lu, X and Feng, J and Mao, S and Li, M and Li, Z and Wang, C}, title = {Complex and severe infection in a 67-year-old liver transplant recipient due to Cunninghamella elegans, Bordetella bronchiseptica, and Pneumocystis jirovecii.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {164}, pmid = {39905327}, issn = {1471-2334}, support = {23YF1431300//the Yangfan Project of Science and Technology Commission of Shanghai Municipality/ ; GWVI-11.1-11//3-Year Action Plan for Strengthening Public Health System in Shanghai/ ; PW2021D-09//Pudong New Area Joint Project/ ; }, mesh = {Aged ; *Bordetella bronchiseptica/isolation & purification/genetics ; Male ; Humans ; *Cunninghamella/isolation & purification ; *Bordetella Infections/microbiology/diagnosis/drug therapy ; *Coinfection/microbiology ; *Pneumocystis carinii/isolation & purification/genetics ; Mucormycosis/microbiology/drug therapy/diagnosis ; Transplant Recipients ; Bronchoalveolar Lavage Fluid/microbiology ; Pneumonia, Pneumocystis/microbiology/drug therapy/diagnosis ; }, abstract = {INTRODUCTION: Cunninghamella elegans infections cause rare and severe mucormycosis. Bordetella bronchiseptica and Pneumocystis jirovecii relate to pneumonia. They are all clinically uncommon pathogens and no reports of co-infections have been reported.

CASE PRESENTATION: Here we present a case of a 67-year-old male patient who initially presented with fever, chills, and mild cough. B. bronchiseptica, P. jirovecii, Aspergillus fumigatus, and human alphaherpesvirus 1 (HSV1) were detected by clinical metagenomic next-generation sequencing (mNGS) of his bronchoalveolar lavage fluid (BLAF). Despite receiving anti-infective treatment, the patient rapidly developed respiratory failure and was transferred to the intensive care unit. Subsequent mNGS testing further revealed the presence of C. elegans, indicating that different pathogens played dominant roles at various stages of the disease progression. The routine culture also identified several of the above pathogens, but the results were reported much later than those of mNGS. Eventually, imaging findings and symptoms of the patient improved with comprehensive antibiotic coverage, and he was transferred to a lower-level hospital for rehabilitation treatment.

CONCLUSIONS: This is the first detailed report of the combined infection of B. bronchiseptica, P. jirovecii, and C. elegans. During the treatment process, we also observed rare and unusual neurological side effects: visual and auditory hallucinations, restlessness, and aphasia. Also, the case indicates that traditional methods are insufficient for the etiological diagnosis needs of critical and severe patient populations, and timely use of mNGS should be recommended.}, } @article {pmid39905038, year = {2025}, author = {Qu, Q and Dou, Q and Xiang, Z and Yu, B and Chen, L and Fan, Z and Zhao, X and Yang, S and Zeng, P}, title = {Population-level gut microbiome and its associations with environmental factors and metabolic disorders in Southwest China.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {24}, pmid = {39905038}, issn = {2055-5008}, mesh = {*Gastrointestinal Microbiome ; Humans ; China ; *Metabolic Diseases/microbiology/etiology ; *Feces/microbiology ; *Metagenomics/methods ; Female ; Male ; Middle Aged ; Diet ; Adult ; Bacteria/classification/genetics/isolation & purification ; Life Style ; Socioeconomic Factors ; }, abstract = {Gut microbiota affects host health and disease. Large-scale cohorts have explored the interactions between the microbiota, host, and environment to reveal the disease-associated microbiota variation. A population-level gut metagenomic cohort is still rare in China. Here, we performed metagenomic sequencing on fecal samples from the CMEC Microbiome Project in Southwest China. In this study, we identified host socioeconomics, diet, lifestyle, and medical measurements that were significantly associated with microbiome function and composition. We revealed extensive novel associations between the host microbiome and common metabolic disorders. Our results provide new insight into associations of gut microbiota with metabolic disorders so as to support the translation of gut microbiome findings into potential clinical practice.}, } @article {pmid39904998, year = {2025}, author = {Boulton, W and Salamov, A and Grigoriev, IV and Calhoun, S and LaButti, K and Riley, R and Barry, K and Fong, AA and Hoppe, CJM and Metfies, K and Oetjen, K and Eggers, SL and Müller, O and Gardner, J and Granskog, MA and Torstensson, A and Oggier, M and Larsen, A and Bratbak, G and Toseland, A and Leggett, RM and Moulton, V and Mock, T}, title = {Metagenome-assembled-genomes recovered from the Arctic drift expedition MOSAiC.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {204}, pmid = {39904998}, issn = {2052-4463}, mesh = {Arctic Regions ; *Metagenome ; Oceans and Seas ; Expeditions ; Ecosystem ; Ice Cover/microbiology ; }, abstract = {The Multidisciplinary Observatory for Study of the Arctic Climate (MOSAiC) expedition consisted of a year-long drifting survey of the Central Arctic Ocean. The ecosystems component of MOSAiC included the sampling of molecular data, with metagenomes collected from a diverse range of environments. The generation of metagenome-assembled-genomes (MAGs) from metagenomes are a starting point for genome-resolved analyses. This dataset presents a catalogue of MAGs recovered from a set of 73 samples from MOSAiC, including 2407 prokaryotic and 56 eukaryotic MAGs, as well as annotations of a near complete eukaryotic MAG using the Joint Genome Institute (JGI) annotation pipeline. The metagenomic samples are from the surface ocean, chlorophyll maximum, mesopelagic and bathypelagic, within leads and under-ice ocean, as well as melt ponds, ice ridges, and first- and second-year sea ice. This set of MAGs can be used to benchmark microbial biodiversity in the Central Arctic Ocean, compare individual strains across space and time, and to study changes in Arctic microbial communities from the winter to summer, at a genomic level.}, } @article {pmid39904149, year = {2025}, author = {Lang, G and Ye, W and Chen, G and Zhu, T and Li, X and Chen, J and Miao, X and Su, F and Xu, L}, title = {Emerging and stirring Amoebic liver abscess in HIV seropositive men who have sex with men in South-Eastern China.}, journal = {Diagnostic microbiology and infectious disease}, volume = {111}, number = {3}, pages = {116696}, doi = {10.1016/j.diagmicrobio.2025.116696}, pmid = {39904149}, issn = {1879-0070}, abstract = {Amebic liver abscess (ALA) is rare in Chinese population due to dietary habit. Nine Chinese HIV-seropositive men who have sex with men (MSM) with occurrence of amebic liver abscess (ALA) was retrospectively studied. Six participants had concurrent HIV/Syphilis and two had HIV/HCV. Symptoms primarily included fever, abdominal discomfort, and diarrhea. All participants showed intrahepatic abscesses, mainly in liver segments 6, 7, and 8, while two had additional extrahepatic amebic abscesses. Those with CD4 count < 100 cells/μL exhibited multiple and larger liver abscesses. Metagenomic Next-Generation Sequencing (mNGS) conclusively revealed Entamoeba histolytica despite bacterial culture and smear tests' negative results. All affected individuals were treated with percutaneous catheter drainage and metronidazole for at least 10 days. In summary, HIV-positive MSM are prone to develop ALA, and CD4 count < 100 cells/μL is a risk for occurrence of multiple and larger ALA. The optimal ALA treatment course for ALA remains dabatable.}, } @article {pmid39904008, year = {2025}, author = {Bohra, V and Lai, KK and Lam, KL and Tam, NF and Jing-Liang, S and Lee, FW}, title = {Metagenomic surveillance reveals different structure and function of microbial community associated with mangrove pneumatophores and their surrounding matrices.}, journal = {Marine pollution bulletin}, volume = {213}, number = {}, pages = {117614}, doi = {10.1016/j.marpolbul.2025.117614}, pmid = {39904008}, issn = {1879-3363}, abstract = {Present research employed metagenomics to explore the structural and functional diversity of microorganisms in two matrices of pneumatophore: adhered sediments (PS) and epiphytes (PE) of Avicennia marina. These were compared with microorganisms in surrounding environments: tidal water (TW), mudflat sediment (MF) and mangrove sediment (MS). Results revealed that bacteria made up over 95 % of the microbial community across all five matrices, with the dominance of phylum Proteobacteria, because of their metabolic flexibility and ability to survive in harsh mangrove environment. The bacterial community in PS and PE were similar to TW but differed from those in MF and MS, implying their provenance from TW. The high relative abundance of genes involved in nitrate and sulfur reduction pathways in PS and PE indicates pneumatophore bacteria helps in enhancing nitrogen and sulfur availability. This study is the first to explore the functional significance of pneumatophore-adhered prokaryotic communities using metagenomics.}, } @article {pmid39903999, year = {2025}, author = {Mondal, A and Parvez, SS and Majumder, A and Sharma, K and Das, B and Bakshi, U and Alam, M and Banik, A}, title = {Co-inoculation of Trichoderma and tea root-associated bacteria enhance flavonoid production and abundance of mycorrhizal colonization in tea (Camellia sinensis).}, journal = {Microbiological research}, volume = {293}, number = {}, pages = {128084}, doi = {10.1016/j.micres.2025.128084}, pmid = {39903999}, issn = {1618-0623}, abstract = {Tea is one of the most popular nonalcoholic beverages, that contains several medicinally important flavonoids. Due to seasonal variation and various environmental stresses, the overall consistency of tea flavonoids affects the tea quality. To combat stress, plants stimulate symbiotic relationships with root-associated beneficial microbiomes that sustain nutrient allocation. Therefore, a study has been designed to understand the role of the tea root microbiome in sustaining tea leaf flavonoid production. To enumerate the microbiome, tea root and rhizoplane soil were collected from 3 years of healthy plants from Jalpaiguri district, West Bengal, India. A culture-independent approach was adopted to identify root and rhizosphere microbial diversity (BioSample: SAMN31404869; SRA: SRS15503027 [rhizosphere soil metagenome] BioSample: SAMN31404868;SRA:SRS15503030 [root metagenome]. In addition to diverse microbes, four mycorrhiza fungi, i.e., Glomus intraradices, Glomus irregulare, Paraglomus occultum and Scutellospora heterogama were predominant in collected root samples. A culture-dependent approach was also adopted to isolate several plant growth-promoting bacteria [Bacillus sp. D56, Bacillus sp. D42, Bacillus sp. DR15, Rhizobium sp. DR23 (NCBI Accession: OR821747-OR821750)] and one fungal [Trichoderma sp. AM6 (NCBI Accession:OM915414)] strain. A pot experiment was designed to assess the impact of that isolated microbiome on tea seedlings. After six months of microbiome inoculation, tea plants' physicochemical and transcriptional parameters were evaluated. The results confer that the microbiome-treated treatments [(T1-without any microbial inoculation; NCBI Accession: SAMN33591153), Trichoderma sp. AM6 (T2; NCBI Accession: SAMN33591155) and Trichoderma sp. AM6 +VAM containing tea root+synthetic microbial consortia (T5; NCBI Accession: SAMN33591154)] could enhance the total flavonoid content in tea seedlings by upregulating certain transcripts associated with the flavonoid biosynthesis pathway of tea.}, } @article {pmid39903699, year = {2025}, author = {Roothans, N and van Loosdrecht, MCM and Laureni, M}, title = {Metabolic labour division trade-offs in denitrifying microbiomes.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf020}, pmid = {39903699}, issn = {1751-7370}, abstract = {Division of metabolic labour is a defining trait of natural and engineered microbiomes. Denitrification - the stepwise reduction of nitrate and nitrite to nitrogenous gases - is inherently modular, catalysed either by a single microorganism (termed complete denitrifier) or by consortia of partial denitrifiers. Despite the pivotal role of denitrification in biogeochemical cycles and environmental biotechnologies, the ecological factors selecting for complete versus partial denitrifiers remain poorly understood. In this perspective, we critically review over 1500 published metagenome-assembled genomes of denitrifiers from diverse and globally relevant ecosystems. Our findings highlight the widespread occurrence of labour division and the dominance of partial denitrifiers in complex ecosystems, contrasting with the prevalence of complete denitrifiers only in simple laboratory cultures. We challenge current labour division theories centred around catabolic pathways, and discuss their limits in explaining the observed niche partitioning. Instead, we propose that labour division benefits partial denitrifiers by minimising resource allocation to denitrification, enabling broader metabolic adaptability to oligotrophic and dynamic environments. Conversely, stable, nutrient-rich laboratory cultures seem to favour complete denitrifiers, which maximise energy generation through denitrification. To resolve the ecological significance of metabolic trade-offs in denitrifying microbiomes, we advocate for mechanistic studies that integrate mixed-culture enrichments mimicking natural environments, multi-meta-omics, and targeted physiological characterisations. These undertakings will greatly advance our understanding of global nitrogen turnover and nitrogenous greenhouse gases emissions.}, } @article {pmid39903340, year = {2025}, author = {Yan, Z and Zheng, Z and Cao, L and Zhu, Z and Zhou, C and Sun, Q and Tang, B and Zhao, G}, title = {Altered gut microbiome and serum metabolome profiles associated with essential tremor.}, journal = {Metabolic brain disease}, volume = {40}, number = {2}, pages = {118}, pmid = {39903340}, issn = {1573-7365}, support = {U20A20355//National Natural Science Foundation of China/ ; WKJ-ZJ-ZZ08//Major Health Science and Technology Program of Zhejiang Province/ ; LZ23H090004//Key Projects of Zhejiang Provincial Natural Science Fund/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Metabolome ; *Essential Tremor/blood/microbiology ; Male ; Female ; Middle Aged ; Aged ; Dysbiosis/blood ; Lipid Metabolism/physiology ; }, abstract = {The genetic predisposition and environmental factors both trigger the complex neurological dyskinesia of essential tremor (ET). Gut dysbiosis may facilitate the occurrence and development of neurological diseases. Therefore, it is worth exploring the inner connections between gut microbiota and ET. First, the gut microbiota of 19 ET patients and 21 healthy controls (HCs) were analysed with metagenomics approach. Second, the potential linkages between gut microbiome and serum metabolome profiles were explored by integrative analysis. The gut microbiota disorders were present in ET patients. The LEfSe method showed a significant decrease in Bacteroides. The functional analysis revealed that there were differences in gut microbial apoptosis, retinol metabolism, and steroid hormone biosynthesis pathways. The levels of various lipids and lipid-like molecules alter in serum of ET patients, which correlated with altered gut microbial abundance, indicating the alterations in lipid metabolism involved in apoptosis pathway in ET. All of these data point to the gut dysbiosis in ET, and some changed gut microbial species were linked to abnormalities in blood lipid metabolism, which open up new avenues for investigation into the pathophysiology of ET.}, } @article {pmid39902982, year = {2025}, author = {Zhao, M and Shi, Y and Zhang, C and Lu, M and Shen, M and Xie, L and Wang, L and Lu, A}, title = {Diagnostic value of metagenomic next-generation sequencing using bronchoalveolar lavage fluid samples for pathogen detection in children with severe or refractory pneumonia.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0108724}, doi = {10.1128/spectrum.01087-24}, pmid = {39902982}, issn = {2165-0497}, abstract = {UNLABELLED: Pneumonia is the leading cause of morbidity and mortality in children and needs rapid and accurate pathogenic diagnosis. The aim of this study was to evaluate the diagnostic value of bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) and conventional microbiological tests (CMTs) for pathogen detection in children with severe or refractory pneumonia. In this retrospective study, the clinical data of 127 children with severe or refractory pneumonia admitted to the respiratory department from June 2021 to March 2022 were analyzed. BALF mNGS and CMTs were utilized for pathogen diagnosis and comparison of their detection performance for different pathogens. The pathogenic diagnosis rate was 95.28% (121/127) by combining mNGS and CMTs. mNGS had significantly higher overall (96.06% vs 72.44%, P < 0.001), bacterial (69.29% vs 12.60%, P < 0.001), and fungal (11.81% vs 3.15%, P = 0.009) detection rates than CMTs. However, there was no significant difference of detection rates between them for respiratory viruses (33.86% vs 33.75%, P = 0.99) and Mycoplasma pneumoniae (48.03% vs 45.67%, P = 0.71). The sensitivities of mNGS for total pathogens, bacteria, and fungi were 99.17%, 100%, and 87.50%, respectively, which were higher than those of CMTs. CMTs for M. pneumoniae had the highest sensitivity (91.23%) compared with mNGS (89.47%) and multiplex PCR (88.57%). For respiratory viruses, mNGS and mPCR had similar sensitivities (97.67% vs 96.43%). mNGS was superior to CMTs in bacterial and fungal detection, while it was comparable to multiplex PCR for the detection of M. pneumoniae and respiratory viruses. Different detection methods should be rationalized for different pathogens.

IMPORTANCE: This study on 127 patients with severe and refractory pneumonia showed that mNGS was significantly superior to CMTs in terms of bacterial and fungal detection. We also found that multiplex PCR assay was comparable to mNGS for the detection of Mycoplasma pneumoniae and respiratory viruses and may have greater application advantages in combination with CMTs, such as M. pneumoniae IgM. For severe and refractory pneumonia, or when empiric treatment is not effective, collecting BALF for mNGS can help to quickly identify the causative organisms at an early stage. It is also important to choose more appropriate methods or combinations for different pathogens.}, } @article {pmid39902954, year = {2025}, author = {Tran, L and Lansing, L and Cunningham, M and Ho, J and Deckers, T and Newman, T and Wu, L and Gregoris, AS and Zorz, J and Muntz, L and Lee, K and Trépanier-Leroux, D and Conflitti, IM and Pepinelli, M and Walsh, EM and Morfin, N and Powell, JE and Moran, N and Hoover, SE and Pernal, SF and Currie, RW and Giovenazzo, P and Guzman-Novoa, E and Jabbari, H and Foster, LJ and Zayed, A and Ortega Polo, R and Guarna, MM}, title = {Gut microbiome metagenomic sequences of honey bees (Apis mellifera) exposed to crops.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0073124}, doi = {10.1128/mra.00731-24}, pmid = {39902954}, issn = {2576-098X}, abstract = {The gut microbiome of the European honey bee (Apis mellifera) is vital to its health, yet large-scale studies are scarce. We present metagenomic sequencing data from 180 samples collected near and far from eight crops across Canada over 2 years. These data sets will help address various biological and environmental questions.}, } @article {pmid39902937, year = {2025}, author = {Tian, C and Zhang, T and Zhuang, D and Luo, Y and Li, T and Zhao, F and Sang, J and Tang, Z and Jiang, P and Zhang, T and Liu, P and Zhu, L and Zhang, Z}, title = {Industrialization drives the gut microbiome and resistome of the Chinese populations.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0137224}, doi = {10.1128/msystems.01372-24}, pmid = {39902937}, issn = {2379-5077}, abstract = {UNLABELLED: Industrialization has driven lifestyle changes in eastern and western Chinese populations, yet we have a poor understanding of the dynamic changes in their gut microbiome and resistome under industrialization, which is essential for the scientific management of public health. Here, this study employed metagenomics to analyze the gut microbiota of 1,382 healthy individuals from China, including 415 individuals from the eastern region of advanced industrialization and 967 individuals from the western region of developing industrialization. Compared with western populations, eastern populations show a significant increase in interindividual dissimilarity of microbial species composition and metabolic pathways but a significant decrease in intraindividual species and functional diversity. Furthermore, our results found significantly less abundance and richness of antibiotic resistance genes (ARGs) in the gut microbiota of eastern populations, alongside a lower prevalence of unique core ARG subtypes. For the 12 core ARG types shared between eastern and western populations, the mean relative abundance of two types was notably higher in the eastern populations, while eight core ARG types had significantly higher mean relative abundance in the western populations. Based on the reconstruction of metagenomic assembled genomes, we found that Escherichia coli genomes from western populations carried more virulence factor genes (VFGs) and mobile genetic elements (MGEs) compared to those from eastern populations. This large-scale study for the first time revealed industrialization potentially led to unexpected alterations of the gut microbiome and resistome between eastern and western populations that provide a vital implication for Chinese public health and may aid in the development of region-specific strategies for managing pathogenic infections.

IMPORTANCE: As China experiences rapid but uneven industrialization, understanding its effect on people's gut bacteria is critical for public health. This study reveals how industrialization may reshape the health risks related to gut bacteria and antibiotic resistance. This work provides crucial information to help create customized public health policies for different regions.}, } @article {pmid39901928, year = {2025}, author = {Demirci, M and Çubuk, C and Dasdemir, F and Saribas, AS and Balcıoglu, EB and Ozbey, D and Yorulmaz, D and Olmez Hanci, T and Basa, S and Kocazeybek, BS}, title = {Comparative microbial metagenomic analysis of drinking water plants and wastewater treatment plants in Istanbul.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1488268}, pmid = {39901928}, issn = {1664-302X}, abstract = {INTRODUCTION: Wastewater treatment plants (WWTPs) and drinking-water treatment plants (DWTPs) are critical for public health due to the potential risks posed by microorganisms that may persist after treatment. The aim of this study was to detect the microbiome profiles of waters from both DWTPs and WWTPs under the Istanbul Water and Sewerage Administration (ISKI), identify the antimicrobial resistance profiles in all these facilities, and observe the differences in the microbiome between the inlet and outlet of different WWTPs.

METHODS: A total of 52 samples were examined, comprising 18 samples from DWTPs and 34 samples from WWTPs. All water samples underwent pre-isolation filtration. DNA isolation was conducted using filter material, followed by sequencing on a NovaSeq 6000 instrument. Kraken2 tools and R scripts were used for statistical analysis and data visualization.

RESULTS: The microbial metagenomic analysis identified 71 phyla, 113 classes, 217 orders, 480 families, and 1,282 genera across all samples. There were unclassified microbes (53.14% vs. 58.75%), Eukaryota (3.64% vs. 3.5%), Archaea (0.08% vs. 0.03%), bacteria (42% vs. 36.25%), and viruses (0.02% vs. 0.04%) in the raw water and ozonation unit outlet of DWTPs. The inlet and outlet of WWTPs showed unclassified microbes (52.68% vs. 59.62%), Eukaryota (0.6% vs. 1.72%), Archaea (0.26% vs. 0.15%), bacteria (46.43% vs. 38.43%), and viruses (0.05% vs. 0.04%). No statistically significant results were found in the analysis of raw waters collected from DWTPs and samples taken from the ozonation unit outlet-from the phylum level to the genus level (p > 0.05). The inlet and outlet points of WWTPs showed no statistically significant results from the phylum to species levels (p > 0.05). The most detected genera were Desulfobacter (4.82%) in preliminary WWTPs, Thauera (1.93%) in biological WWTPs, Pseudomonas (1.44%) in advanced biological WWTPs, Acidovorax (1.85%) in biological package WWTPs, and Pseudomonas (11.55%) in plant-based WWTPs. No antimicrobial resistance gene markers were detected in water samples from raw water inlets and ozonation unit outlets from DWTPs, membrane wastewater recovery plants, or ultraviolet (UV) recycling facilities. The ANT(3″), Erm, and Sul resistance gene markers were detected in all raw WWTPs samples.

DISCUSSION: There were no significant microbial risk differentiation between biological WWTPs and advanced biological WWTPs. The data could serve as preliminary information for future research. More extensive studies are needed, with multiple sample tracking in these facilities and their feeding basins.}, } @article {pmid39901264, year = {2025}, author = {Liu, C and Song, X and Liu, J and Zong, L and Xu, T and Han, X and Li, F and Li, B and Zhu, H and Shi, D}, title = {Consistency between metagenomic next-generation sequencing versus traditional microbiological tests for infective disease: systemic review and meta-analysis.}, journal = {Critical care (London, England)}, volume = {29}, number = {1}, pages = {55}, pmid = {39901264}, issn = {1466-609X}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Sepsis/diagnosis/microbiology ; }, abstract = {BACKGROUND: Pathogen identification is essential in sepsis and septic shock. Metagenomic next-generation sequencing (mNGS) is a novel pathogen detection method with several advantages over traditional tests. However, the consistency between mNGS and traditional pathogen tests requires further investigation.

OBJECTIVES: We aimed to assess the consistency between mNGS and traditional pathogen tests and to identify the factors influencing this consistency.

METHODS: This systematic review and meta-analysis involved a comprehensive search of mNGS and traditional pathogen tests in PubMed, Embase, Scopus, Web of Science, and the Cochrane Library. Data from included studies were extracted, and kappa consistency between mNGS and traditional tests was calculated. Study quality was evaluated using the QUADAS-2 tool.

RESULTS: The search identified 415 studies, of which 27 were included in the analysis, involving 4112 individuals. Meta-analysis showed a pooled consistency of 0.319 ± 0.013 (p < 0.001), indicating a moderate relationship. In terms of sample type, cerebrospinal fluid showed the highest pooled kappa consistency at 0.500 ± 0.029 (p < 0.001). Immunocompromised patients had a lower pooled kappa consistency of 0.294 ± 0.014 (p < 0.001) compared to 0.321 ± 0.028 (p < 0.001) in immunocompetent patients. Positive percent agreement of mNGS was 83.63% over traditional microbiological test, and negative percent agreement was 54.59%.

CONCLUSION: This review demonstrates a moderate relationship between mNGS and traditional pathogen tests, indicating a complex relationship between these two methods. Sterile samples show higher consistency than non-sterile samples. Immune function deficiency may reduce the consistency between mNGS and traditional tests. Further research is needed on the use of mNGS in sepsis and septic shock.}, } @article {pmid39901058, year = {2025}, author = {Richardson, M and Zhao, S and Lin, L and Sheth, RU and Qu, Y and Lee, J and Moody, T and Ricaurte, D and Huang, Y and Velez-Cortes, F and Urtecho, G and Wang, HH}, title = {SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome.}, journal = {Nature microbiology}, volume = {10}, number = {2}, pages = {527-540}, pmid = {39901058}, issn = {2058-5276}, support = {MCB-2025515//National Science Foundation (NSF)/ ; DGE-1644869//National Science Foundation (NSF)/ ; DGE-1644869//National Science Foundation (NSF)/ ; DGE-1644869//National Science Foundation (NSF)/ ; 2R01AI132403, 1R01DK118044, 1R01EB031935, 1R21AI146817//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; N00014-18-1-2237//United States Department of Defense | United States Navy | ONR | Office of Naval Research Global (ONR Global)/ ; 1016691//Burroughs Wellcome Fund (BWF)/ ; HR0011-23-2-0001//United States Department of Defense | Defense Advanced Research Projects Agency (DARPA)/ ; W911NF-22-2-0210//United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (ARO)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; High-Throughput Nucleotide Sequencing/methods ; Feces/microbiology ; Inulin/metabolism ; RNA, Ribosomal, 16S/genetics ; Metagenome ; }, abstract = {The local arrangement of microbes can profoundly impact community assembly, function and stability. However, our understanding of the spatial organization of the human gut microbiome at the micron scale is limited. Here we describe a high-throughput and streamlined method called Split-And-pool Metagenomic Plot-sampling sequencing (SAMPL-seq) to capture spatial co-localization in a complex microbial consortium. The method obtains microbial composition of micron-scale subcommunities through split-and-pool barcoding. SAMPL-seq analysis of the healthy human gut microbiome identified bacterial taxa pairs that consistently co-occurred both over time and across multiple individuals. These co-localized microbes organize into spatially distinct groups or 'spatial hubs' dominated by Bacteroidaceae, Ruminococcaceae and Lachnospiraceae families. Using inulin as a dietary perturbation, we observed reversible spatial rearrangement of the gut microbiome where specific taxa form new local partnerships. Spatial metagenomics using SAMPL-seq can unlock insights into microbiomes at the micron scale.}, } @article {pmid39900940, year = {2025}, author = {Prabhaharan, D and Go, YW and Kim, H and Kang, S and Sang, BI}, title = {Representative Metagenomes of Mesophilic Biogas Reactor Across South Korea.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {198}, pmid = {39900940}, issn = {2052-4463}, support = {MOE; 2022003480001//MOE | Korea Environmental Industry and Technology Institute (KEITI)/ ; MOE; 2022003480001//MOE | Korea Environmental Industry and Technology Institute (KEITI)/ ; MOE; 2022003480001//MOE | Korea Environmental Industry and Technology Institute (KEITI)/ ; MOE; 2022003480001//MOE | Korea Environmental Industry and Technology Institute (KEITI)/ ; }, mesh = {Republic of Korea ; *Biofuels ; *Metagenome ; *Bioreactors ; Microbiota ; Anaerobiosis ; }, abstract = {Biogas production through the anaerobic digestion (AD) of organic waste plays a crucial role in promoting sustainability and closing the carbon cycle. Over the past decade, this has driven global research on biogas-producing microbiomes, leading to significant advances in our understanding of microbial diversity and metabolic pathways within AD plants. However, substantial knowledge gaps persist, particularly in understanding the specific microbial communities involved in biogas production in countries such as South Korea. The present dataset addresses one of these gaps by providing comprehensive information on the metagenomes of five full-scale mesophilic biogas reactors in South Korea. From 110 GB of raw DNA sequences, 401 metagenome-assembled genomes (MAGs) were created, which include 42,301 annotated genes. Of these, 187 MAGs (46.7%) were classified as high-quality based on Minimum Information about Metagenome-Assembled Genome (MIMAG) standards. The data presented here contribute to a broader understanding of biogas-specific microbial communities and offers a significant resource for future studies and advancements in sustainable biogas production.}, } @article {pmid39900713, year = {2025}, author = {Zhang, L and Zheng, C and Sun, Y and Chen, X and Wang, Y and Xiang, H and Liang, Y and Wei, F and Zhang, Y}, title = {Diagnostic tests performance in detecting Pneumocystis jirovecii: A systematic review and meta-analysis.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {}, number = {}, pages = {}, pmid = {39900713}, issn = {1435-4373}, support = {BRWEP2024W042180101//Beijing Research Ward Excellence Program, BRWEP/ ; }, abstract = {BACKGROUND AND OBJECTIVE: Pneumocystis jirovecii (Pj) pneumonia (PJP) is a life-threatening opportunistic infection primarily affecting immunocompromised individuals. Detecting Pj is challenging, particularly in distinguishing between Pj colonization (PJC) and infection. We aimed to systematically evaluate the diagnostic accuracy of various tests in differentiating Pj colonization from infection.

METHODS: Systematic reviews and meta-analyses were performed. Searches were conducted in PubMed, Embase, and Web of Science. Original clinical studies reporting sensitivity and specificity data for diagnostic tests such as quantitative polymerase chain reaction (qPCR), nested PCR, (1,3)-Beta-D glucan (BDG), metagenomic next-generation sequencing (mNGS), and digital PCR (ddPCR) to differentiate PJC from PJP were included. Quality assessment was performed using QUADAS-2 tool, and data processing followed Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Diagnostic performance was evaluated using either a random-effects or fixed-effects model.

RESULTS: Twenty-eight studies (2,550 patients, 1,445 with PJP) were included, with moderate methodological quality. The pooled sensitivity of these diagnostic tests was 0.80 (95% CI 0.77-0.82) and specificity was 0.83 (95% CI 0.81-0.85), with a diagnostic odds ratio (DOR) of 23.12. Among the individual tests, BDG (5 studies) showed high pooled sensitivity (0.83, 95% CI 0.77-0.88) but lower specificity (0.78, 95% CI 0.69-0.85). mNGS (3 studies) had the highest performance, with pooled sensitivity and specificity both at 0.87 (95% CI 0.80-0.92 and 95% CI 0.77-0.94, respectively), and the highest DOR of 41.57. qPCR (19 studies) demonstrated adequate pooled sensitivity (0.78, 95% CI 0.76-0.81) and high specificity (0.83, 95% CI 0.81-0.86), with a DOR of 20.44.

CONCLUSION: While BDG has low specificity and mNGS is costly with no standardized interpretation, along with the limited number of relevant studies in BDG and mNGS, this meta-analysis concluded that qPCR remains valuable for distinguishing P. jirovecii infection from colonization. A well-designed randomized clinical trial that standardizes the technical aspects of the qPCR protocol is needed to assess its effectiveness and provide a solid basis for clinical diagnosis.}, } @article {pmid39900569, year = {2025}, author = {Priest, T and Oldenburg, E and Popa, O and Dede, B and Metfies, K and von Appen, WJ and Torres-Valdés, S and Bienhold, C and Fuchs, BM and Amann, R and Boetius, A and Wietz, M}, title = {Seasonal recurrence and modular assembly of an Arctic pelagic marine microbiome.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {1326}, pmid = {39900569}, issn = {2041-1723}, mesh = {Arctic Regions ; *Seasons ; *Microbiota/genetics ; *Seawater/microbiology ; *Oceans and Seas ; Metagenomics/methods ; Bacteria/genetics/classification/metabolism ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; DNA Barcoding, Taxonomic ; Metagenome ; Phylogeny ; }, abstract = {Deciphering how microbial communities are shaped by environmental variability is fundamental for understanding the structure and function of ocean ecosystems. While seasonal environmental gradients have been shown to structure the taxonomic dynamics of microbiomes over time, little is known about their impact on functional dynamics and the coupling between taxonomy and function. Here, we demonstrate annually recurrent, seasonal structuring of taxonomic and functional dynamics in a pelagic Arctic Ocean microbiome by combining autonomous samplers and in situ sensors with long-read metagenomics and SSU ribosomal metabarcoding. Specifically, we identified five temporal microbiome modules whose succession within each annual cycle represents a transition across different ecological states. For instance, Cand. Nitrosopumilus, Syndiniales, and the machinery to oxidise ammonia and reduce nitrite are signatures of early polar night, while late summer is characterised by Amylibacter and sulfur compound metabolism. Leveraging metatranscriptomes from Tara Oceans, we also demonstrate the consistency in functional dynamics across the wider Arctic Ocean during similar temporal periods. Furthermore, the structuring of genetic diversity within functions over time indicates that environmental selection pressure acts heterogeneously on microbiomes across seasons. By integrating taxonomic, functional and environmental information, our study provides fundamental insights into how microbiomes are structured under pronounced seasonal changes in understudied, yet rapidly changing polar marine ecosystems.}, } @article {pmid39900484, year = {2025}, author = {Van Etten, J and Stephens, TG and Bhattacharya, D}, title = {Genetic Transfer in Action: Uncovering DNA Flow in an Extremophilic Microbial Community.}, journal = {Environmental microbiology}, volume = {27}, number = {2}, pages = {e70048}, pmid = {39900484}, issn = {1462-2920}, support = {//U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231/ ; 10.46936/10.25585/60000481//Joint Genome Institute/ ; NJ01180//National Institute of Food and Agriculture/ ; 80NSSC19K1542/NASA/NASA/United States ; NASA (80NSSC19K0462)/NASA/NASA/United States ; }, mesh = {*Gene Transfer, Horizontal ; *Bacteria/genetics/classification ; Extremophiles/genetics ; Microbiota/genetics ; DNA, Bacterial/genetics ; Genome, Bacterial ; }, abstract = {Horizontal genetic transfer (HGT) is a significant driver of genomic novelty in all domains of life. HGT has been investigated in many studies however, the focus has been on conspicuous protein-coding DNA transfers that often prove to be adaptive in recipient organisms and are therefore fixed longer-term in lineages. These results comprise a subclass of HGTs and do not represent exhaustive (coding and non-coding) DNA transfer and its impact on ecology. Uncovering exhaustive HGT can provide key insights into the connectivity of genomes in communities and how these transfers may occur. In this study, we use the term frequency-inverse document frequency (TF-IDF) technique, that has been used successfully to mine DNA transfers within real and simulated high-quality prokaryote genomes, to search for exhaustive HGTs within an extremophilic microbial community. We establish a pipeline for validating transfers identified using this approach. We find that most DNA transfers are within-domain and involve non-coding DNA. A relatively high proportion of the predicted protein-coding HGTs appear to encode transposase activity, restriction-modification system components, and biofilm formation functions. Our study demonstrates the utility of the TF-IDF approach for HGT detection and provides insights into the mechanisms of recent DNA transfer.}, } @article {pmid39900123, year = {2025}, author = {Soto-Rodriguez, SA and Quiroz-Guzman, E and Gomez-Gil, B and Lozano-Olvera, R and Aguilar-Rendon, KG and Serrano-Hernández, JM and González-Gómez, JP and Chaidez, C}, title = {Phage cocktail against Vibrio parahaemolyticus causing acute hepatopancreatic necrosis disease (AHPND) in Penaeus vannamei: Genomic, biological, and pathological characterization.}, journal = {Microbial pathogenesis}, volume = {200}, number = {}, pages = {107354}, doi = {10.1016/j.micpath.2025.107354}, pmid = {39900123}, issn = {1096-1208}, abstract = {Phages vB_Pd_PDCC-1, vB_Vc_SrVc9, and vB_Vp_PvVp11 were found to be lytic against Vibrio parahaemolyticus acute hepatopancreatic necrosis disease (AHPND) and other pathogenic vibrios. The complete genomic and biological characterization of phage vB_Vp_PvVp1 was conducted, and a cocktail of these three phages was applied to juvenile Penaeus vannamei infected with V. parahaemolyticus AHPND. Water samples collected during the challenges were analyzed using metagenomics. At the end of the experimental infection, the phage cocktail did not improve shrimp survival compared to the positive control group (infected only with bacteria). This suggests the emergence of phage-resistant V. parahaemolyticus strains. However, a significantly lower mortality rate was observed 12 h post-infection, along with a shortening of the disease course in the phage therapy treatment. A phage-resistant strain of V. parahaemolyticus AHPND was in vitro isolated. For the first time, we report the identification of nucleotide variants in the glycosyltransferase gene of this mutant strain through genome sequencing. Although the phage cocktail was ineffective in controlling AHPND, some protective benefits of phage therapy were noted in P. vannamei during the acute phase-the most critical stage-compared to the positive control. Phage therapy decreased alpha diversity and altered the microbiota composition during the challenge, increasing V. parahaemolyticus. The Vibrio AHPND pathogen produces a potent PirAB toxin, making this disease difficult to manage. Further studies are needed to explore synergistic approaches as effective therapeutic tools.}, } @article {pmid39899931, year = {2025}, author = {Wang, Y and Chen, C and Zhou, B and Zhang, Y and Qin, J and Huang, J and Li, X}, title = {Presence of high-risk ARGs with greater diversity and abundance in the rare resistome in wastewater across China.}, journal = {Journal of hazardous materials}, volume = {488}, number = {}, pages = {137435}, doi = {10.1016/j.jhazmat.2025.137435}, pmid = {39899931}, issn = {1873-3336}, abstract = {Antibiotic resistance genes (ARGs) are widely recognized as hazardous materials that pose risks to public health. The core resistome, with its low ARG diversity yet accounting for the majority of the total ARG abundance, dominating the profile of antibiotic resistance. In this study, nationwide wastewater surveillance in China using metagenomic sequencing also identified a core resistome of 117 ARGs that accounted for 69.6 % of the total abundance. The emphasis of the work was to examine the rare resistome that included 1503 ARGs outside the core resistome. The abundances of clinically relevant ARG types (e.g., β-lactams and quinolones) were significantly higher in the rare resistome compared to the core resistome. Human pathogen-related ARGs were much greater in subtype number (96 vs. 34) and significantly higher in abundance (67.0 % vs. 33.0 %) in the rare relative to the core resistome, indicating that the rare resistome was the major contributor to the human pathogen resistome. The majority of ARG types accounting for the highest proportions of the rare resistome were plasmid-originated (65.5 %-100 %). In addition, human pathogen-related ARGs also had a significantly higher proportion of plasmid sources than non-pathogen ARGs, further highlighting their importance in wastewater-based surveillance.}, } @article {pmid39899597, year = {2024}, author = {Tibiri, EB and Boua, PR and Soulama, I and Dubreuil-Tranchant, C and Tando, N and Tollenaere, C and Brugidou, C and Nanema, RK and Tiendrebeogo, F}, title = {Challenges and opportunities of developing bioinformatics platforms in Africa: the case of BurkinaBioinfo at Joseph Ki-Zerbo University, Burkina Faso.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {1}, pages = {}, pmid = {39899597}, issn = {1477-4054}, support = {2012PASS019//Green Revolution in Africa/ ; }, mesh = {Burkina Faso ; *Computational Biology/methods/education ; Universities ; Humans ; }, abstract = {Bioinformatics, an interdisciplinary field combining biology and computer science, enables meaningful information to be extracted from complex biological data. The exponential growth of biological data, driven by high-throughput omics technologies and advanced sequencing methods, requires robust computational resources. Worldwide, bioinformatics skills and computational clusters are essential for managing and analysing large-scale biological datasets across health, agriculture, and environmental science, which are crucial for the African continent. In Burkina Faso, the establishment of bioinformatics infrastructure has been a gradual process. Initial training initiatives between 2015-2016, including bioinformatics courses and the establishment of the BurkinaBioinfo (BBi) platform, marked significant progress. Over 250 scientists have been trained at diverse levels in bioinformatics, 105 user accounts have been created for high-performance computing access. Operational since 2019, this platform has significantly facilitated training programs for scientists and system administrators in west Africa, covering data production, introductory bioinformatics, phylogenetic analysis, and metagenomics. Financial and technical support from various sources has facilitated the rapid development of the platform to meet the growing need for bioinformatics analysis, particularly in conjunction with local 'wet labs'. Establishing a bioinformatics cluster in Burkina Faso involved identifying the needs of researchers, selecting appropriate hardware and installing the necessary bioinformatics tools. At present, the main challenges for the BBi platform include ongoing staff training in bioinformatics skills and high-level IT infrastructure management in the face of growing infrastructure demands. Despite these challenges, the establishment of a bioinformatics platform in Burkina Faso offers significant opportunities for scientific research and economic development in the country.}, } @article {pmid39898908, year = {2025}, author = {Navia, JC and Alfonso, A and Miller, D and Maestre-Mesa, J and Durkee, H and Sepulveda-Beltran, PA and Echeverri-Tribin, F and Merikansky, S and Martinez, JD and Flynn, HW and Alfonso, EC and Parel, JM and Amescua, G}, title = {Prevalence of HSV Genomic Signatures Among Acanthamoeba Hosts and Contaminated Lens Cases: A Molecular and Clinical Study.}, journal = {Investigative ophthalmology & visual science}, volume = {66}, number = {2}, pages = {4}, pmid = {39898908}, issn = {1552-5783}, support = {P30 EY014801/EY/NEI NIH HHS/United States ; }, mesh = {Humans ; Male ; *Acanthamoeba/genetics/isolation & purification ; Female ; Adult ; *Acanthamoeba Keratitis/epidemiology/diagnosis/parasitology ; Prevalence ; Middle Aged ; DNA, Viral/genetics/analysis ; Young Adult ; Polymerase Chain Reaction ; Genome, Viral/genetics ; Contact Lenses/parasitology ; Keratitis, Herpetic/epidemiology/virology/diagnosis ; Adolescent ; Herpesvirus 1, Human/genetics/isolation & purification ; Visual Acuity ; Metagenomics ; Simplexvirus/genetics ; Aged ; }, abstract = {PURPOSE: To document the presence of herpes simplex virus (HSV) genomic signatures among Acanthamoeba hosts recovered from patients with Acanthamoeba keratitis (AK) and in contaminated lens cases.

METHODS: We used a combination of PCR sequencing and shotgun metagenomics to detect and confirm the presence of HSV genomic signatures in Acanthamoeba hosts and lens cases. Clinical outcomes were correlated with the prevalence of host HSV signatures.

RESULTS: HSV genomic signatures were detected in 26% (n = 6) of Acanthamoeba hosts recovered from patients with culture confirmed AK. HSV-1 and HSV-2 or both were identified in 33%, 50%, and 17% of isolates, respectively. Fifty-two percent of patients (12/23) were misdiagnosed initially as presenting with HSV keratitis. Patients with HSV-positive Acanthamoeba isolates had a mean best-corrected visual acuity of 1.43 LogMAR at diagnosis and 0.53 LogMAR at follow-up, compared with 1.85 and 0.92 LogMAR, respectively, in HSV-negative cases. Contact lens use was identified as a risk factor in 83% of 18 patients. We detected 46,597 viral signatures in 5 of 14 contaminated lens cases (35.7%). Distribution included 33% bacteriophages, 8.2% giant viruses, 4.1% nonhuman Herpesviridae, and 0.39% human Herpesviridae. Among the 184 human Herpesviridae genomic signatures, HSV types 1 or 2 or both were documented in 5.7%, VZV in 39.7%, HHV7 in 38.6%, HHV6 in 15.0%, and Epstein-Barr virus in 0.5%.

CONCLUSIONS: This study is the first to identify HSV-positive genomic signatures in clinical AK isolates and/or contact lens cases. Taken together, the high prevalence of HSV genomic signatures in both amebic hosts and lens cases, might signal an unrecognized Acanthamoeba-HSV association and the need for reassessing current management.}, } @article {pmid39898315, year = {2025}, author = {Walker, JR and Bente, DA and Burch, MT and Cerqueira, FM and Ren, P and Labonté, JM}, title = {Molecular assessment of oyster microbiomes and viromes reveals their potential as pathogen and ecological sentinels.}, journal = {One health (Amsterdam, Netherlands)}, volume = {20}, number = {}, pages = {100973}, pmid = {39898315}, issn = {2352-7714}, support = {UL1 TR001439/TR/NCATS NIH HHS/United States ; }, abstract = {Oyster aquaculture world-wide is a booming industry that can provide many benefits to coastal habitats, including economic, ecosystem-level, and cultural benefits. Oysters present several risks for human consumption, including transmission of parasites, and bacterial and viral pathogens. Oyster microbiomes are well-defined, but their connection to the incidence of pathogens, humans or others, is unclear. Furthermore, viruses associated with oysters are largely unknown, and their connection to humans, animals, and ecosystem health has not been explored. Here, we employed a One Health framework and modern molecular techniques, including 16S rRNA amplicon and metagenomic sequencing, to identify links between changes in the microbial and viral communities associated with oysters and the incidence of pathogens detected in oyster tissues and their surrounding environments. In addition, we adapted the BioFire® FilmArray®, commonly used in hospitals, to determine the presence of human pathogens within the sampled oysters. We detected known human pathogens in 50 % of the oysters tested. Within the genomic datasets, we noted that pathogens of humans, animals, and plants in oysters were shared with the nearby water and sediments, suggesting a sink-source dynamic between the oysters and their surroundings. 16S rRNA gene analysis revealed that while oysters share common microbial constituents with their surrounding environments, they enrich for certain bacteria such as Mycoplasmatales, Fusobacteriales, and Spirochaetales. On the contrary, we found that oyster viromes harbored the same viruses in near equal relative abundances as their surrounding environments. Our results show how oysters could be used not only to determine the risk of human pathogens within coastal estuaries but also how oyster viruses could be used as ecosystem-level sentinels.}, } @article {pmid39897886, year = {2025}, author = {Qayyum, H and Talib, MS and Ali, A and Kayani, MUR}, title = {Evaluating the potential of assembler-binner combinations in recovering low-abundance and strain-resolved genomes from human metagenomes.}, journal = {Heliyon}, volume = {11}, number = {2}, pages = {e41938}, pmid = {39897886}, issn = {2405-8440}, abstract = {Human-associated microbial communities are a complex mixture of bacterial species and diverse strains prevalent at varying abundances. Due to the inherent limitations of metagenomic assemblers and genome binning tools in recovering low-abundance species (<1 %) and strains, we lack comprehensive insight into these communities. Although many bioinformatics approaches are available for recovering metagenome-assembled genomes, their effectiveness in recovering low-abundance species and strains is often questioned. Moreover, each tool has its trade-offs, making selecting the right tools challenging. In this study, we investigated the combinatory effect of various assemblers and binning tools on the recovery of low-abundance species and strain-resolved genomes from real and simulated human metagenomes. We evaluated the performance of nine combinations of metagenome assemblers and genome binning tools for their potential to recover genomes of useable quality. Our results revealed that the metaSPAdes-MetaBAT2 combination is highly effective in recovering low-abundance species, while MEGAHIT-MetaBAT2 excels in recovering strain-resolved genomes. These findings highlight the significant variation in the performance of different combinations, even when aiming for the same objective. This suggests the profound impact of selecting the right assembler-binner combination for metagenome analyses. We believe this study will be a cornerstone for the scientific community, guiding the choice of tools by highlighting their complementary effects. Furthermore, it underscores the potential of existing tools to address the current challenges in the field improving the recovery of information from metagenomes.}, } @article {pmid39897789, year = {2025}, author = {Schmidt, JE and Lewis, CA and Firl, AJ and Umaharan, P}, title = {Microbial bioindicators associated with cadmium uptake in sixteen genotypes of Theobroma cacao.}, journal = {Heliyon}, volume = {11}, number = {2}, pages = {e41890}, pmid = {39897789}, issn = {2405-8440}, abstract = {Recent regulatory limits on concentrations of cadmium (Cd), an element of concern for human health, have made Cd reduction a key issue in the global chocolate industry. Research into Cd minimization has investigated soil management, cacao genetic variation, and postharvest processing, but has overlooked the cacao-associated microbiome despite promising evidence in other crops that root-associated microorganisms could help reduce Cd uptake. A novel approach combining both amplicon and metagenomic sequencing identified microbial bioindicators associated with leaf and stem Cd accumulation in sixteen field-grown genotypes of Theobroma cacao. Sequencing highlighted over 200 amplicon sequence variants (ASVs) whose relative abundance was related to cacao leaf and stem Cd content or concentration. The two highest-accumulating genotypes, PA 32 and TRD 94, showed enrichment of four ASVs belonging to the genus Haliangium, the family Gemmataceae, and the order Polyporales. ASVs whose relative abundance was most negatively associated with plant Cd were identified as Paenibacillus sp. (β = -2.21), Candidatus Koribacter (β = -2.17), and Candidatus Solibacter (β = -2.03) for prokaryotes, and Eurotiomycetes (β = -4.58) and two unidentified ASVs (β = -4.32, β = -3.43) for fungi. Only two ASVs were associated with both leaf and stem Cd, both belonging to the Ktedonobacterales. Of 5543 C d-associated gene families, 478 could be assigned to GO terms, including 68 genes related to binding and transport of divalent heavy metals. Screening for Cd-related bioindicators prior to planting or developing microbial bioamendments could complement existing strategies to minimize the presence of Cd in the global cacao supply.}, } @article {pmid39897560, year = {2025}, author = {Zhang, P and Guo, R and Ma, S and Jiang, H and Yan, Q and Li, S and Wang, K and Deng, J and Zhang, Y and Zhang, Y and Wang, G and Chen, L and Li, L and Guo, X and Zhao, G and Yang, L and Wang, Y and Kang, J and Sha, S and Fan, S and Cheng, L and Meng, J and Yu, H and Chen, F and He, D and Wang, J and Liu, S and Shi, H}, title = {A metagenome-wide study of the gut virome in chronic kidney disease.}, journal = {Theranostics}, volume = {15}, number = {5}, pages = {1642-1661}, pmid = {39897560}, issn = {1838-7640}, mesh = {Humans ; *Renal Insufficiency, Chronic/virology ; *Virome/genetics ; *Gastrointestinal Microbiome/genetics ; *Metagenome/genetics ; *Feces/virology/microbiology ; Middle Aged ; Male ; Female ; Aged ; Dysbiosis/virology/microbiology ; Adult ; Viruses/genetics/classification/isolation & purification ; Bacteria/genetics/classification/isolation & purification ; }, abstract = {Rationale: Chronic kidney disease (CKD) is a progressively debilitating condition leading to kidney dysfunction and severe complications. While dysbiosis of the gut bacteriome has been linked to CKD, the alteration in the gut viral community and its role in CKD remain poorly understood. Methods: Here, we characterize the gut virome in CKD using metagenome-wide analyses of faecal samples from 425 patients and 290 healthy individuals. Results: CKD is associated with a remarkable shift in the gut viral profile that occurs regardless of host properties, disease stage, and underlying diseases. We identify 4,649 differentially abundant viral operational taxonomic units (vOTUs) and reveal that some CKD-enriched viruses are closely related to gut bacterial taxa such as Bacteroides, [Ruminococcus], Erysipelatoclostridium, and Enterocloster spp. In contrast, CKD-depleted viruses include more crAss-like viruses and often target Faecalibacterium, Ruminococcus, and Prevotella species. Functional annotation of the vOTUs reveals numerous viral functional signatures associated with CKD, notably a marked reduction in nicotinamide adenine dinucleotide (NAD[+]) synthesis capacity within the CKD-associated virome. Furthermore, most CKD viral signatures are reproducible in the gut viromes of diabetic kidney disease and several other common diseases, highlighting the considerable universality of disease-associated viromes. Conclusions: This research provides comprehensive resources and novel insights into the CKD-associated gut virome, offering valuable guidance for future mechanistic and therapeutic investigations.}, } @article {pmid39897495, year = {2025}, author = {Solymosi, N and Tóth, AG and Nagy, SÁ and Csabai, I and Feczkó, C and Reibling, T and Németh, T}, title = {Clinical considerations on antimicrobial resistance potential of complex microbiological samples.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e18802}, pmid = {39897495}, issn = {2167-8359}, mesh = {*Escherichia coli/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology ; Humans ; *Drug Resistance, Bacterial/genetics ; *Microbial Sensitivity Tests ; Genotype ; Metagenomics/methods ; Phenotype ; Genes, Bacterial/genetics ; }, abstract = {Antimicrobial resistance (AMR) is one of our greatest public health challenges. Targeted use of antibiotics (ABs) can reduce the occurrence and spread of AMR and boost the effectiveness of treatment. This requires knowledge of the AB susceptibility of the pathogens involved in the disease. Therapeutic recommendations based on classical AB susceptibility testing (AST) are based on the analysis of only a fraction of the bacteria present in the disease process. Next and third generation sequencing technologies allow the identification of antimicrobial resistance genes (ARGs) present in a bacterial community. Using this metagenomic approach, we can map the antimicrobial resistance potential (AMRP) of a complex, multi-bacterial microbial sample. To understand the interpretiveness of AMRP, the concordance between phenotypic AMR properties and ARGs was investigated by analyzing data from 574 Escherichia coli strains of five different studies. The overall results show that for 44% of the studied ABs, phenotypically resistant strains are genotypically associated with a 90% probability of resistance, while for 92% of the ABs, the phenotypically susceptible strains are genotypically susceptible with a 90% probability. ARG detection showed a phenotypic prediction with at least 90% confidence in 67% of ABs. The probability of detecting a phenotypically susceptible strain as resistant based on genotype is below 5% for 92% of ABs. While the probability of detecting a phenotypically resistant strain as susceptible based on genotype is below 5% for 44% of ABs. We can assume that these strain-by-strain concordance results are also true for bacteria in complex microbial samples, and conclude that AMRP obtained from metagenomic ARG analysis can help choose efficient ABs. This is illustrated using AMRP by a canine external otitis sample.}, } @article {pmid39896983, year = {2025}, author = {Sayyad, LE and Smith, KL and Sadigh, KS and Cossaboom, CM and Choi, MJ and Whitmer, S and Cannon, D and Krapiunaya, I and Morales-Betoulle, M and Annambhotla, P and Basavaraju, SV and Ruberto, I and Kretschmer, M and Gutierrez, N and Zabel, K and Austin, C and Sandoval, E and Servellita, V and Foresythe, A and Sumimoto, N and Aqel, BA and Khamash, HA and Jadlowiec, CC and Grys, TE and Jaramillo, A and Grill, MF and Montgomery, JM and Shoemaker, T and Klena, JD and Chiu, CY and Vikram, HR}, title = {Severe Non-Donor-Derived Lymphocytic Choriomeningitis Virus Infection in 2 Solid Organ Transplant Recipients.}, journal = {Open forum infectious diseases}, volume = {12}, number = {2}, pages = {ofaf002}, pmid = {39896983}, issn = {2328-8957}, abstract = {BACKGROUND: Lymphocytic choriomeningitis virus (LCMV) infection in immunocompromised hosts can result in disseminated disease, meningoencephalitis, and death. Published cases in transplant recipients have been traced to transmission from infected donors. We report 2 cases of serious, non-donor-derived LCMV infection in solid organ transplant recipients.

METHODS: Initial identification of LCMV infection was done by using metagenomic next-generation sequencing (mNGS). Subsequent evaluations and confirmatory testing involved molecular diagnostics, serology, and phylogenetic analysis. A detailed epidemiologic investigation was conducted.

RESULTS: LCMV was detected by mNGS in 2 solid organ transplant recipients from distinct donors. A heart transplant recipient (from donor 1) died of progressive, disseminated LCMV infection, while a kidney transplant recipient (from donor 2) with LCMV meningoencephalitis survived. A multistate laboratory and epidemiologic investigation of both donors and all their organ recipients was initiated. Postmortem samples were obtained from both donors, and pretransplant and/or posttransplant samples were obtained from 5 of the 6 organ recipients. mNGS, serologic, and real-time reverse-transcription polymerase chain reaction testing confirmed LCMV infection in both solid organ transplant recipients. Epidemiologic investigation revealed significant pretransplant rodent exposures for both LCMV-infected recipients. Laboratory studies for the other organ recipients from both donors were negative for LCMV infection.

CONCLUSIONS: Our investigations suggest that LCMV infection in 2 solid organ transplant recipients originated from rodent exposure preceding transplantation and were not donor derived. Although uncommon, healthcare providers should be aware of LCMV-associated serious and life-threatening illness in immunocompromised hosts. Diagnostic modalities are limited to reference laboratories.}, } @article {pmid39896720, year = {2024}, author = {Coltro, EP and Cafferati Beltrame, L and da Cunha, CR and Zamparette, CP and Feltrin, C and Benetti Filho, V and Vanny, PA and Beduschi Filho, S and Klein, TCR and Scheffer, MC and Palmeiro, JK and Wagner, G and Sincero, TCM and Zárate-Bladés, CR}, title = {Evaluation of the resistome and gut microbiome composition of hospitalized patients in a health unit of southern Brazil coming from a high animal husbandry production region.}, journal = {Frontiers in antibiotics}, volume = {3}, number = {}, pages = {1489356}, pmid = {39896720}, issn = {2813-2467}, abstract = {INTRODUCTION: Antimicrobial resistance (AMR) poses a significant threat to global public health. The One Health approach, which integrates human, animal, and environmental health, highlights the roles of agricultural and hospital settings in the propagation of AMR. This study aimed to analyze the resistome and gut microbiome composition of individuals from a high-intensity animal husbandry area in the western region of Santa Catarina, Southern Brazil, who were subsequently admitted to the University Hospital in the city of Florianopolis, located in the eastern part of the same state.

METHODS: Rectal swab samples were collected upon admission and discharge. Metagenomic sequencing and resistome analysis were employed to identify antimicrobial resistance genes (ARGs) and their associated bacterial taxa. Additionally, the impact of the hospital environment on the resistome and microbiome profiles of these patients was assessed.

RESULTS: A total of 247 genetic elements related to AMR were identified, with 66.4% of these elements present in both admission and discharge samples. Aminoglycoside resistance genes were the most prevalent, followed by resistance genes for tetracyclines and lincosamides. Notably, unique resistance genes, including dfrF and mutations in gyrB, were identified at discharge. ARGs were associated with 55 bacterial species, with Lactobacillus fermentum, harboring the ermB gene. (MLSB), detected in both admission and discharge samples. The most prevalent bacterial families included Mycobacteriaceae, Enterobacteriaceae, and Bacteroidaceae. Among these, Mycobacteriaceae was the most abundant, with ARGs primarily associated with mutations in the 16S rRNA gene, RNA polymerase subunits, and gyrases.

DISCUSSION: The study revealed a high prevalence of genes related to aminoglycoside and tetracycline resistance, with a notable increase in certain resistance determinants at discharge, likely influenced by extended antimicrobial use. The presence of mcr genes, associated with colistin resistance, in both admission and discharge samples from a single patient highlights a concerning trend in AMR, particularly in relation to animal husbandry. These findings underscore the substantial impact of antimicrobial use on resistance development and the complex dynamics of the resistome in hospital settings. They also emphasize the influence of local factors, such as intensive animal production, on resistance patterns and advocate for ongoing surveillance and policy development to manage multidrug-resistant bacteria eVectively.}, } @article {pmid39896099, year = {2025}, author = {Iwami, N and Komiya, S and Asada, Y and Tatsumi, K and Habara, T and Kuramoto, T and Seki, M and Yoshida, H and Takeuchi, K and Shiotani, M and Mukaida, T and Odawara, Y and Mio, Y and Kamiya, H}, title = {"Shortening time to pregnancy in infertile women by personalizing treatment of microbial imbalance through Emma & Alice: A multicenter prospective study".}, journal = {Reproductive medicine and biology}, volume = {24}, number = {1}, pages = {e12634}, pmid = {39896099}, issn = {1445-5781}, abstract = {PURPOSE: To evaluate the impact of Endometrial Microbiome Metagenomic Analysis and Analysis of Infectious Chronic Endometritis (EMMA & ALICE) on pregnancy outcomes following recommended treatments in women with recurrent implantation failure (RIF) or recurrent pregnancy loss (RPL).

METHODS: This prospective, multicenter cohort study included 527 women under 42 years old with RIF or RPL across 14 IVF centers in Japan. Endometrial samples were analyzed using EMMA & ALICE, and patients received antibiotics, probiotics, or no treatment based on test results. Pregnancy outcomes were assessed using Kaplan-Meier survival analysis and multivariate generalized linear models.

RESULTS: Amongst participants, 43.4% had a normal Lactobacillus-dominated microbiota, 20.9% had dysbiosis, and 35.7% had mild dysbiosis or ultralow biomass. Kaplan-Meier analysis revealed significantly higher ongoing pregnancy rates in the dysbiosis group treated with antibiotics and probiotics compared to other groups (p = 0.031). Post-treatment, ongoing pregnancy rates in the dysbiosis and mild dysbiosis groups were comparable to the normal group.

CONCLUSIONS: EMMA & ALICE-guided antimicrobial and probiotic treatments improved pregnancy outcomes, enabling the dysbiosis group to achieve pregnancy earlier than the normal group. Addressing uterine dysbiosis may reduce the time to pregnancy in patients with RIF and RPL.

TRIAL REGISTRATION: University Hospital Medical Information Network (UMIN), UMIN000036917.}, } @article {pmid39895875, year = {2025}, author = {Esparteiro, D and Fouquet, G and Courtois, A and Naassila, M and Nguyen-Khac, E and Marcq, I}, title = {Shotgun Metagenomics Reveals Bacteroides stercoris as a Fecal Biomarker Depleted in Late-Stage Hepatocellular Carcinoma.}, journal = {Gastro hep advances}, volume = {4}, number = {1}, pages = {100539}, pmid = {39895875}, issn = {2772-5723}, } @article {pmid39895797, year = {2025}, author = {Gao, Y and Zheng, H and Ye, M and Zhou, G and Chen, J and Qiang, X and Bai, J and Lu, X and Tang, Q}, title = {Characteristics and function of the gut microbiota in patients with rectal neuroendocrine tumors.}, journal = {Journal of Cancer}, volume = {16}, number = {4}, pages = {1040-1050}, pmid = {39895797}, issn = {1837-9664}, abstract = {The gut microbiota plays a significant role in the initiation and progression of tumors, but its role in rectal neuroendocrine tumors (rNETs) remains unclear. Fecal samples were collected from 19 healthy individuals and 21 rNET patients,with the rNET cohort further divided into metastatic (rNETs-M) and non-metastatic (rNETs-nM) groups. Using metagenomic high-throughput sequencing, we analyzed the diversity, species composition, and functional characteristics of the gut microbiota. We applied a random forest model to identify potential microbial biomarkers for predicting rNET and specifically distinguishing rNETs-M cases. Alpha diversity analysis revealed that species diversity was lower in the rNETs group than in the control group. In contrast, the rNETs-M group exhibited higher species diversity than the rNETs-nM group. Beta diversity analysis demonstrated significant differences in community structure between the rNETs and control groups between the rNET-M and rNETs-nM groups. Notably, in the rNETs group, the abundance of potential pathogens such as Escherichia coli and Shigella was elevated.Furthermore, the rNETs-M group exhibited an increased abundance of potential pathogens such as Alistipes. KEGG enrichment analysis indicated that these distinct microbiota play a significant role in environmental information processing, genetic information processing, and metabolic pathways. Random forest analysis and ROC curve results identified Lachnospira pectinoschiza (AUC=0.885), Parasutterella muris (AUC=0.862), Sodaliphilus pleomorphus(AUC=0.956), Methylobacterium iners (AUC=0.971) as biomarkers with significant discriminatory value.}, } @article {pmid39895693, year = {2025}, author = {Zhou, CY and Dai, K and Lin, YP and Huang, XC and Hu, YL and Chen, XX and Yang, XF and Sun, QY and Zhang, Y and van Loosdrecht, MCM and Zeng, RJ and Zhang, F}, title = {Elucidating the complex hydrolysis and conversion network of xanthan-like extracellular heteropolysaccharides in waste activated sludge fermentation.}, journal = {Water research X}, volume = {27}, number = {}, pages = {100303}, pmid = {39895693}, issn = {2589-9147}, abstract = {The hydrolysis of structural extracellular polymeric substances (St-EPS) is considered a major limiting step in the anaerobic fermentation of waste activated sludge (WAS). However, the degradation of heteropolysaccharides, characterized by complex monomers of uronic acids and neutral saccharides in St-EPS, has rarely been reported. In this study, microbial-produced xanthan-like heteropolysaccharides, characterized by a blue filamentary film, were identified. The xanthan-producing bacteria comprised ∼7.2% of total genera present in WAS. An xanthan-degrading consortium (XDC) was enriched in an anaerobic batch reactor. This consortium could degrade Xanthan for over 90% and disrupt the gel structure of xanthan while promoting methane production from WAS by 29%. The xanthan degradation network consisting of extracellular enzymes and bacteria was elucidated by combining high-throughput sequencing, metagenomic, and metaproteomic analyses. Five enzymes were identified as responsible for hydrolyzing xanthan to monomers, including xanthan lyase, β-d-glucosidase, β-d-glucanase, α-d-mannosidase, and unsaturated glucuronyl hydrolase. Seven genera, including Paenibacillus (0.2%) and Clostridium (3.1%), were identified as key bacteria excreting one to five of the aforementioned enzymes. This study thus provides insights into the complex conversions in anaerobic digestion of WAS and gives a foundation for future optimization of this process.}, } @article {pmid39895114, year = {2025}, author = {Di Simone, SK and Forster, SC}, title = {Sputum Metagenomics Reveals Multidrug-Resistant Pseudomonas-Dominant Communities in Severe Asthma.}, journal = {Respirology (Carlton, Vic.)}, volume = {}, number = {}, pages = {}, doi = {10.1111/resp.14890}, pmid = {39895114}, issn = {1440-1843}, support = {//CSL Centenary Fellowship/ ; }, } @article {pmid39895074, year = {2025}, author = {Lee, KA and Ul-Haq, A and Seo, H and Jo, S and Kim, S and Song, HY and Kim, HS}, title = {Characteristics of skin microbiome associated with disease severity in systemic sclerosis.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {63}, number = {1}, pages = {e.2409018}, doi = {10.71150/jm.2409018}, pmid = {39895074}, issn = {1976-3794}, support = {//Korea Health Industry Development Institute/ ; HI21C1888//Ministry of Health and Welfare/ ; //National Research Foundation of Korea/ ; RS-2023-00219563//Ministry of Science and ICT/ ; //Soonchunhyang University Research Fund/ ; }, mesh = {Humans ; *Scleroderma, Systemic/microbiology ; *Skin/microbiology/pathology ; *Microbiota ; Female ; Middle Aged ; Male ; *RNA, Ribosomal, 16S/genetics ; Adult ; *Bacteria/classification/genetics/isolation & purification ; Severity of Illness Index ; Aged ; Biomarkers ; Metagenomics ; }, abstract = {Systemic sclerosis (SSc) is a chronic autoimmune disorder characterised by skin fibrosis and internal organ involvement. Disruptions in the microbial communities on the skin may contribute to the onset of autoimmune diseases that affect the skin. However, current research on the skin microbiome in SSc is lacking. This study aimed to investigate skin microbiome associated with disease severity in SSc. Skin swabs were collected from the upper limbs of 46 healthy controls (HCs) and 36 patients with SSc. Metagenomic analysis based on the 16S rRNA gene was conducted and stratified by cutaneous subtype and modified Rodnan skin score (mRSS) severity. Significant differences in skin bacterial communities were observed between the HCs and patients with SSc, with further significant variations based on subtype and mRSS severity. The identified biomarkers were Bacteroides and Faecalibacterium for patients with diffuse cutaneous SSc with high mRSS (≥ 10) and Mycobacterium and Parabacteroides for those with low mRSS (< 10). Gardnerella, Abies, Lactobacillus, and Roseburia were the biomarkers in patients with limited cutaneous SSc (lcSS) and high mRSS, whereas Coprococcus predominated in patients with lcSS and low mRSS. Cutaneous subtype analysis identified Pediococcus as a biomarker in the HCs, whereas mRSS analysis revealed the presence of Pseudomonas in conjunction with Pediococcus. In conclusion, patients with SSc exhibit distinct skin microbiota compared with healthy controls. Bacterial composition varies by systemic sclerosis cutaneous subtype and skin thickness.}, } @article {pmid39894814, year = {2025}, author = {El Leithy, AA and Youssef, ASE and Nassar, A and Aziz, RK and Khaled, NM and Mahrous, MT and Farahat, GN and Mohamed, AH and Bakr, YM}, title = {Long-read 16S rRNA amplicon sequencing reveals microbial characteristics in patients with colorectal adenomas and carcinoma lesions in Egypt.}, journal = {Gut pathogens}, volume = {17}, number = {1}, pages = {8}, pmid = {39894814}, issn = {1757-4749}, abstract = {BACKGROUND: Colorectal cancer (CRC) is among the five leading causes of cancer incidence and mortality. During the past decade, the role of the gut microbiota and its dysbiosis in colorectal tumorigenesis has been emphasized. Metagenomics and amplicon-based microbiome profiling provided insights into the potential role of microbial dysbiosis in the development of CRC.

AIM: To address the scarcity of information on differential microbiome composition of tumor tissue in comparison to adenomas and the lack of such data from Egyptian patients with CRC.

MATERIALS AND METHODS: Long-read nanopore sequencing of 16S rRNA amplicons was used to profile the colonic microbiota from fresh colonoscopic biopsy samples of Egyptian patients with CRC and patients with colonic polyps.

RESULTS: Species richness of CRC lesions was significantly higher than that in colonic polyps (p-value = 0.0078), while evenness of the CRC group was significantly lower than the colonic polyps group (p-value = 0.0055). Both species richness and Shannon diversity index of the late onset CRC samples were significantly higher than those of the early onset ones. The Firmicutes-to-Bacteroidetes (F/B) ratio was significantly higher in the CRC group than in the colonic polyps group (p-value = 0.0054), and significantly higher in samples from early-onset CRC. The Enterococcus spp. were significantly overabundant in patients with rectal cancer and early-onset CRC, while Staphylococcus spp. were significantly higher in patients with sigmoid cancer and late-onset CRC. In addition, the relative abundance of Fusobacterium nucleatum was significantly higher in CRC patients.

CONCLUSION: Differentiating trends were identified at phylum, genus, and species levels, despite the inter-individual differences. In summary, this study addressed the microbial dysbiosis associated with CRC and colonic polyps groups, paving the way for a better understanding of the pathogenesis of early and late-onset CRC in Egyptian patients.}, } @article {pmid39894607, year = {2025}, author = {Gong, JC and Li, BH and Liu, CY and Li, PF and Hu, JW and Yang, GP}, title = {Impact of salinity gradients on nitric oxide emissions and functional microbes in estuarine wetland sediments.}, journal = {Water research}, volume = {273}, number = {}, pages = {123046}, doi = {10.1016/j.watres.2024.123046}, pmid = {39894607}, issn = {1879-2448}, mesh = {*Wetlands ; *Salinity ; *Nitric Oxide/metabolism ; *Geologic Sediments/microbiology ; Estuaries ; China ; }, abstract = {Estuarine wetland sediments are hotspots for nitrogen cycling and critical sources of atmospheric nitric oxide (NO). Yet studies on the impact of sediment salinity gradients on NO emissions and associated functional microbes at the land-ocean interface remain limited. Here, we measured sediment NO emission rates from incubated sediment samples that were collected from an estuarine wetland in Qingdao, China. Our findings indicate that sediment salinity is a pivotal factor shaping NO emission rates, by altering the community composition and gene abundance of functional microbes involved in NO emissions, with rates ranging from 0.04 to 0.25 μg N kg[-1] dry soil h[-1]. Metagenomic analysis of the sediment samples reveals that greater NO emission rates (+486 %) under salinity changes are linked to a higher abundance of the nirS gene (+26 %) responsible for NO formation and a lower abundance of norBC genes (-23 %) responsible for NO consumption. Accordingly, the increase of NO emissions may be attributed to the accumulation of denitrifying NO, which could improve plant salt tolerance through co-evolutionary interactions between plants and sediment-dwelling microbes. Taken together, these findings contribute to a richer understanding of how biochemical NO emissions in estuarine wetland sediments respond to salinity gradients.}, } @article {pmid39894448, year = {2025}, author = {Zhu, Y and Miao, H and Zhang, J and Jiang, Z and Chu, X and Xu, Y and Tian, W and Gao, H and Zhu, Y and Li, L and Yang, Q}, title = {Role of plasma and blood-cell co-metagenomic sequencing in precise diagnosis and severity evaluation of sepsis, a prospective cohort study in sepsis patients.}, journal = {The Journal of infection}, volume = {90}, number = {3}, pages = {106434}, doi = {10.1016/j.jinf.2025.106434}, pmid = {39894448}, issn = {1532-2742}, abstract = {PURPOSES: Sepsis caused great clinical burden all over the world. This study clarified the value of plasma metagenomic next-generation sequencing (p-mNGS) and blood cell mNGS (bc-mNGS) in sepsis diagnosis and evaluation.

METHODS: One hundred and fourty-seven blood samples were collected from sepsis patients who met sepsis 3.0 criteria. Blood culture (BC), qPCR, p-mNGS, bc-mNGS and necessary routine assays were conducted. Taking BC and qPCR as reference, diagnosis performance of p-mNGS and bc-mNGS was analyzed. Blood transcriptome was conducted to evaluate the immunological response of patients in groups with different p/bc-mNGS results. Impact of antibiotic use on different methods was also analyzed.

RESULTS: The p-mNGS demonstrated a sensitivity of 100% for bacteria/fungi and 97% for viruses, which was higher than bc-mNGS (88% for bacteria and fungi, 71% for viruses). However, bc-mNGS showed higher concordance with BC results, which indicated that co-mNGS (p-mNGS plus bc-mNGS) protocol increased sensitivity and was helpful to justify viable blood pathogens in sepsis patients. This study showed that p-mNGS(+) & bc-mNGS(+) samples represented more activated immunity response (low expression of interferon-induced genes and high expression of JAK-STAT pathway genes), poorer clinical laboratory indicators (higher Sequential Organ Failure Assessment, higher procalcitonin and higher C-reactive protein) and lower survival rate. This study also proved that the use of broad-spectrum antibiotics affected much less on p/bc-mNGS diagnostic ability than on BC.

CONCLUSIONS: This research highlighted the potential value of plasma and blood-cell co-metagenomic sequencing in precise diagnosis and severity evaluation of sepsis patients, which will benefit the management of sepsis patients.}, } @article {pmid39894225, year = {2025}, author = {Kim, SY and Woo, SY and Kim, HL and Chang, Y and Ryu, S and Kim, HN}, title = {A shotgun metagenomic study identified short-chain fatty acid-producing species and their functions in the gut microbiome of adults with depressive symptoms: Large-scale shotgun sequencing data of the gut microbiota using a cross-sectional design.}, journal = {Journal of affective disorders}, volume = {376}, number = {}, pages = {26-35}, doi = {10.1016/j.jad.2025.01.149}, pmid = {39894225}, issn = {1573-2517}, abstract = {BACKGROUND: The gut-brain axis is emerging as a novel mechanism to explain depressive disorders.

METHODS: We performed shotgun metagenomic sequencing of stool samples obtained from 133 individuals with depression and 532 without depression. This study examined the taxonomy, functional pathways, and predicted metabolites profiles associated with depressive symptoms, using generalized linear models. To explore links between the taxonomic and functional pathway results, we compared the relative abundance of specific species contributing to pathways significantly associated with depressive symptoms.

RESULTS: Taxonomic composition suggested a disruption in short-chain fatty acid (SCFA)-producing capacity of the gut microbiome in the depressed group. Pathways related to SCFA biosynthesis were also depleted in this group. Faecalibacterium prausnitzii, a well-known SCFA-producing bacterium, was significantly decreased in the depressed group and was identified as a major contributor to the depleted pathways. When inferring the metabolites related to depression from metagenomic data, higher levels of docosapentaenoic acid, stearoyl ethanolamide, putrescine, and bilirubin were more likely to be found in the depressed group.

CONCLUSION: The present findings highlight the altered gut microbiota and associated SCFA-related pathways in individuals with depression. The depletion of F. prausnitzii and its contribution to SCFA production suggest that it is a potential therapeutic target for depression.}, } @article {pmid39894202, year = {2025}, author = {Ladjouzi, R and Taminiau, B and Daube, G and Lucau-Danila, A and Drider, D}, title = {The efficacy of the bacteriocinogenic Enterococcus faecalis 14 in the control of induced necrotic enteritis in broilers.}, journal = {Microbes and infection}, volume = {}, number = {}, pages = {105477}, doi = {10.1016/j.micinf.2025.105477}, pmid = {39894202}, issn = {1769-714X}, abstract = {PURPOSE: To demonstrate the efficacy of the bacteriocinogenic Enterococcus faecalis 14 (E. faecalis 14) in the control of induced necrotic enteritis (NE) in broilers.

METHODS: Six groups of 504 broilers consisting of an infected untreated control (IUC) group, an infected and amoxicillin treated control (ITC) group, and groups receiving prophylactically (2 groups) or therapeutically (2 groups) E. faecalis 14 or its Δbac mutant were used. All groups were challenged with Clostridium perfringens 56 to induce NE. To predispose the boilers to develop subclinical NE, a high protein grower diet containing 15% fishmeal and a coccidial inoculum were administered.

RESULTS: NE lesions were observed on D26 in all groups except ITC and those receiving prophylactically and therapeutically E. faecalis 14. On D27, only ITC and the group prophylactically treated with E. faecalis 14 (T03 T03) were without lesions. Average body weight and daily weight gain remained lower in the treated groups compared to the ITC group, but there was a clear improvement in the period between D21 to D27, especially in the group prophylactically treated with E. faecalis 14. Specifically, the daily weight gain (DWG) in this period for group T03, was second highest after the group ITC. Metataxonomic analyses showed a positive effect of E. faecalis 14 in maintaining the diversity and richness of the intestinal microbiota, in contrast to ITC group and other conditions.

CONCLUSIONS: The results of this in vivo study demonstrated the efficacy of the prophylactic administration of the bacteriocinogenic E. faecalis 14 in preventing of the NE lesions caused by C. perfringens.}, } @article {pmid39893982, year = {2025}, author = {Zhong, YQ and He, XL and Li, YH and Zhu, H and Li, JW and Xu, H and Liu, C and Lin, LC and Wang, JF}, title = {Enhancing antibiotic removal in constructed wetlands: A MgFe-LDHs-based strategy for optimizing microbial communities and metabolic functions.}, journal = {Journal of hazardous materials}, volume = {488}, number = {}, pages = {137412}, doi = {10.1016/j.jhazmat.2025.137412}, pmid = {39893982}, issn = {1873-3336}, abstract = {To efficiently remove antibiotics from domestic and livestock wastewater in southern China, vertical flow constructed wetlands (CWs) were designed with and without magnesium-iron layered double hydroxides (MgFe-LDHs). Their removal efficiencies for three typical antibiotics (tetracycline, oxytetracycline, and ofloxacin) were evaluated. Results showed that MgFe-LDHs significantly improved nitrogen and phosphorus removal (18.7 %-25.6 %) and enhanced the degradation of tetracycline, oxytetracycline, and ofloxacin (13.1 %-17.8 %). High-resolution LC-MS analysis indicated significant biodegradation through various pathways, such as oxidation, hydrolysis, and dealkylation. Analysis of the Shannon diversity index demonstrated that the introduction of novel MgFe-LDHs enhanced microbial diversity and evenness at the phylum, class, and genus levels. The introduction of MgFe-LDHs increased microbial diversity and enriched antibiotic-degrading genera like Xanthobacter, Ochrobactrum, and Stenotrophomonas. Moreover, MgFe-LDHs may have enhanced the metabolic pathways of glycolysis and the tricarboxylic acid cycle, thereby improving the microbial degradation of organic matter. In summary, MgFe-LDHs exhibited a multifaceted role in enhancing antibiotic removal in CWs by inducing the enrichment of antibiotic-degrading bacteria and regulating the metabolic functions of the microbial community, while also ensuring higher nitrogen and phosphorus removal efficiency.}, } @article {pmid39893935, year = {2025}, author = {Luo, Y and Gao, J and Su, X and Li, H and Li, Y and Qi, W and Han, X and Han, J and Zhao, Y and Zhang, A and Zheng, Y and Qian, F and He, H}, title = {Unraveling the immunological landscape and gut microbiome in sepsis: a comprehensive approach to diagnosis and prognosis.}, journal = {EBioMedicine}, volume = {113}, number = {}, pages = {105586}, doi = {10.1016/j.ebiom.2025.105586}, pmid = {39893935}, issn = {2352-3964}, abstract = {BACKGROUND: Comprehensive and in-depth research on the immunophenotype of septic patients remains limited, and effective biomarkers for the diagnosis and treatment of sepsis are urgently needed in clinical practice.

METHODS: Blood samples from 31 septic patients in the Intensive Care Unit (ICU), 25 non-septic ICU patients, and 18 healthy controls were analyzed using flow cytometry for deep immunophenotyping. Metagenomic sequencing was performed in 41 fecal samples, including 13 septic patients, 10 non-septic ICU patients, and 18 healthy controls. Immunophenotype shifts were evaluated using differential expression sliding window analysis, and random forest models were developed for sepsis diagnosis or prognosis prediction.

FINDINGS: Septic patients exhibited decreased proportions of natural killer (NK) cells and plasmacytoid dendritic cells (pDCs) in CD45[+] leukocytes compared with non-septic ICU patients and healthy controls. These changes statistically mediated the association of Bacteroides salyersiae with sepsis, suggesting a potential underlying mechanism. A combined diagnostic model incorporating B.salyersia, NK cells in CD45[+] leukocytes, and C-reactive protein (CRP) demonstrated high accuracy in distinguishing sepsis from non-sepsis (area under the receiver operating characteristic curve, AUC = 0.950, 95% CI: 0.811-1.000). Immunophenotyping and disease severity analysis identified an Acute Physiology and Chronic Health Evaluation (APACHE) II score threshold of 21, effectively distinguishing mild (n = 19) from severe (n = 12) sepsis. A prognostic model based on the proportion of total lymphocytes, Helper T (Th) 17 cells, CD4[+] effector memory T (TEM) cells, and Th1 cells in CD45[+] leukocytes achieved robust outcome prediction (AUC = 0.906, 95% CI: 0.732-1.000), with further accuracy improvement when combined with clinical scores (AUC = 0.938, 95% CI: 0.796-1.000).

INTERPRETATION: NK cell subsets within innate immunity exhibit significant diagnostic value for sepsis, particularly when combined with B. salyersiae and CRP. In addition, T cell phenotypes within adaptive immunity are correlated with sepsis severity and may serve as reliable prognostic markers.

FUNDING: This project was supported by the National Key R&D Program of China (2023YFC2307600, 2021YFA1301000), Shanghai Municipal Science and Technology Major Project (2023SHZDZX02, 2017SHZDZX01), Shanghai Municipal Technology Standards Project (23DZ2202600).}, } @article {pmid39893934, year = {2025}, author = {Zeng, S and Mo, S and Wu, X and Meng, C and Peng, P and Kashif, M and Li, J and He, S and Jiang, C}, title = {Microbial-mediated carbon metabolism in the subtropical marine mangroves affected by shrimp pond discharge.}, journal = {Marine environmental research}, volume = {205}, number = {}, pages = {106980}, doi = {10.1016/j.marenvres.2025.106980}, pmid = {39893934}, issn = {1879-0291}, abstract = {Mangrove ecosystems exhibit high efficiency in carbon (C) sequestering within the global ecosystem. However, the rapid expansion of the shrimp farming industry poses a significant threat to these delicate ecosystems. The microbial mechanisms driving C metabolism in shrimp-affected sediments remain poorly understood. This study investigates the spatiotemporal dynamics of C metabolism-related microbial communities in shrimp pond and natural mangrove sediments in a subtropical region. Shrimp pond discharge altered soil properties, microbial diversity, and microbial stability, driven by factors such as salinity, sulfide, and total organic C (TOC). Metagenomic analyses reveals shifts in C degradation and oxidation, with a reduction in genes for cellulose and hemicellulose degradation. Microbial markers like Prolixibacteraceae and Nitrosopumilaceae reflect these changes. Co-occurrence network analysis indicates higher connectivity within shrimp pond groups, suggesting nutrient-driven changes in symbiotic relationships. PLS-PM analysis further confirms the interplay between microbial composition, nutrient levels, and C metabolism, with higher 16S rRNA operon copy numbers linked to increased C fixation. These findings demonstrate how shrimp pond discharge alters microbial networks and C metabolism, with implications for ecosystem resilience.}, } @article {pmid39893570, year = {2025}, author = {Zampieri, G and Santinello, D and Palù, M and Orellana, E and Costantini, P and Favaro, L and Campanaro, S and Treu, L}, title = {Core cooperative metabolism in low-complexity CO2-fixing anaerobic microbiota.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf017}, pmid = {39893570}, issn = {1751-7370}, abstract = {Biological conversion of carbon dioxide into methane has a crucial role in global carbon cycling and is operated by a specialised set of anaerobic archaea. Although it is known that this conversion is strictly linked with cooperative bacterial activity, such as through syntrophic acetate oxidation, there is also a limited understanding on how this cooperation is regulated and metabolically realised. In this work, we investigate the activity in a microbial community evolved to efficiently convert carbon dioxide into methane and predominantly populated by Methanothermobacter wolfeii. Through multi-omics, biochemical analysis and constraint-based modelling, we identify a potential formate cross-feeding from an uncharacterised Limnochordia species to M. wolfeii, driven by the recently discovered reductive glycine pathway and upregulated when hydrogen and carbon dioxide are limited. The quantitative consistency of this metabolic exchange with experimental data is shown by metagenome-scale metabolic models integrating condition-specific metatranscriptomics, which also indicate a broader three-way interaction involving M. wolfeii, the Limnochordia species, and Sphaerobacter thermophilus. Under limited hydrogen and carbon dioxide, aspartate released by M. wolfeii is fermented by S. thermophilus into acetate, which in turn is convertible into formate by Limnochordia, possibly forming a cooperative loop sustaining hydrogenotrophic methanogenesis. These findings expand our knowledge on the modes of carbon dioxide reduction into methane within natural microbial communities and provide an example of cooperative plasticity surrounding this process.}, } @article {pmid39893166, year = {2025}, author = {Bourquin, M and Peter, H and Michoud, G and Busi, SB and Kohler, TJ and Robison, AL and Styllas, M and Ezzat, L and Geers, AU and Huss, M and Fodelianakis, S and , and Battin, TJ}, title = {Predicting climate-change impacts on the global glacier-fed stream microbiome.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {1264}, pmid = {39893166}, issn = {2041-1723}, mesh = {*Microbiota/genetics ; *Ice Cover/microbiology ; *Climate Change ; *Phylogeny ; *Bacteria/genetics/classification ; *Rivers/microbiology ; Metagenome ; Biodiversity ; Ecosystem ; }, abstract = {The shrinkage of glaciers and the vanishing of glacier-fed streams (GFSs) are emblematic of climate change. However, forecasts of how GFS microbiome structure and function will change under projected climate change scenarios are lacking. Combining 2,333 prokaryotic metagenome-assembled genomes with climatic, glaciological, and environmental data collected by the Vanishing Glaciers project from 164 GFSs draining Earth's major mountain ranges, we here predict the future of the GFS microbiome until the end of the century under various climate change scenarios. Our model framework is rooted in a space-for-time substitution design and leverages statistical learning approaches. We predict that declining environmental selection promotes primary production in GFSs, stimulating both bacterial biomass and biodiversity. Concomitantly, predictions suggest that the phylogenetic structure of the GFS microbiome will change and entire bacterial clades are at risk. Furthermore, genomic projections reveal that microbiome functions will shift, with intensified solar energy acquisition pathways, heterotrophy and algal-bacterial interactions. Altogether, we project a 'greener' future of the world's GFSs accompanied by a loss of clades that have adapted to environmental harshness, with consequences for ecosystem functioning.}, } @article {pmid39893159, year = {2025}, author = {Sampson, TR and Wallen, ZD and Won, WJ and Standaert, DG and Payami, H and Harms, AS}, title = {Alpha synuclein overexpression can drive microbiome dysbiosis in mice.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {4014}, pmid = {39893159}, issn = {2045-2322}, support = {ASAP-020527//Aligning Science Across Parkinson's/ ; ASAP-020527//Aligning Science Across Parkinson's/ ; ASAP-020527//Aligning Science Across Parkinson's/ ; ASAP-000375//Aligning Science Across Parkinson's/ ; }, mesh = {Animals ; *alpha-Synuclein/metabolism/genetics ; *Dysbiosis/microbiology ; *Gastrointestinal Microbiome ; Mice ; *Mice, Transgenic ; *Parkinson Disease/microbiology/metabolism/genetics ; Disease Models, Animal ; Humans ; Aging ; Male ; }, abstract = {Growing evidence indicates that persons with Parkinson disease (PD), have a unique composition of indigenous gut microbes. Given the long prodromal or pre-diagnosed period, longitudinal studies of the human and rodent gut microbiome before symptomatic onset and for the duration of the disease are currently lacking. PD is partially characterized by the accumulation of the protein α-synuclein (α-syn) into insoluble aggregates, in both the central and enteric nervous systems. As such, several experimental rodent and non-human primate models of α-syn overexpression recapitulate some of the hallmark pathophysiologies of PD. These animal models provide an opportunity to assess how the gut microbiome changes with age under disease-relevant conditions. Here, we used a transgenic mouse strain, which overexpress wild-type human α-syn to test how the gut microbiome composition responds in this model of PD pathology during aging. Using shotgun metagenomics, we find significant, age and genotype-dependent bacterial taxa whose abundance becomes altered with age. We reveal that α-syn overexpression can drive alterations to the gut microbiome composition and suggest that it limits diversity through age. Taxa that were most affected by genotype-age interaction were Lactobacillus and Bifidobacteria. In a mouse model, we showed direct link between alpha synuclein geneotype (hallmark of PD), a dysbiotic and low-diversity gut microbiome, and dysbiotic levels of Bifidobacteria and Lactobacillus (most robust features of PD microbiome). Given emerging data on the potential contributions of the gut microbiome to PD pathologies, our data provide an experimental foundation to understand how the PD-associated microbiome may arise as a trigger or co-pathology to disease.}, } @article {pmid39892935, year = {2025}, author = {Hannaford, A and Hernandez-Acosta, RA and Little, JS and Campbell, JI and Weiss, ZF and Sherman, AC}, title = {Molecular Diagnostics for Invasive Molds: From Lab to Bedside.}, journal = {Clinics in laboratory medicine}, volume = {45}, number = {1}, pages = {27-40}, doi = {10.1016/j.cll.2024.10.009}, pmid = {39892935}, issn = {1557-9832}, mesh = {Humans ; *Invasive Fungal Infections/diagnosis ; *Molecular Diagnostic Techniques ; Fungi/isolation & purification ; Immunocompromised Host ; Mycoses/diagnosis ; }, abstract = {This review highlights the current state of molecular diagnostic modalities to detect invasive fungal infections, with a focus on molds in immunocompromised children and adults. Molecular diagnostics may also be utilized to detect antifungal drug resistance. Although both pathogen-specific and pathogen-agnostic assays may be beneficial in more rapidly identifying fungal infection with less invasive sampling in high-risk populations, the clinical implementation and interpretation of these tests must consider several important factors, including anatomic site and type of specimen, host characteristics, use of antifungal prophylaxis, and timing of specimen collection.}, } @article {pmid39892320, year = {2025}, author = {Huang, L and Dai, W and Sun, X and Pu, Y and Feng, J and Jin, L and Sun, K}, title = {Diet-driven diversity of antibiotic resistance genes in wild bats: implications for public health.}, journal = {Microbiological research}, volume = {293}, number = {}, pages = {128086}, doi = {10.1016/j.micres.2025.128086}, pmid = {39892320}, issn = {1618-0623}, abstract = {Wild bats may serve as reservoirs for antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria, potentially contributing to antibiotic resistance and pathogen transmission. However, current assessments of bats' antibiotic resistance potential are limited to culture-dependent bacterial snapshots. In this study, we present metagenomic evidence supporting a strong association between diet, gut microbiota, and the resistome, highlighting bats as significant vectors for ARG propagation. We characterized gut microbiota, ARGs, and mobile genetic elements (MGEs) in bats with five distinct diets: frugivory, insectivory, piscivory, carnivory, and sanguivory. Our analysis revealed high levels of ARGs in bat guts, with limited potential for horizontal transfer, encompassing 1106 ARGs conferring resistance to 26 antibiotics. Multidrug-resistant and polymyxin-resistant genes were particularly prevalent among identified ARG types. The abundance and diversity of ARGs/MGEs varied significantly among bats with different dietary habits, possibly due to diet-related differences in microbial composition. Additionally, genetic linkage between high-risk ARGs and multiple MGEs was observed on the genomes of various zoonotic pathogens, indicating a potential threat to human health from wild bats. Overall, our study provides a comprehensive analysis of the resistome in wild bats and underscores the role of dietary habits in wildlife-associated public health risks.}, } @article {pmid39892190, year = {2025}, author = {Su, R and Shi, L and Wei, Y and Ma, B}, title = {Comammox and AOA responses to ammonia loading rate in oligotrophic environments.}, journal = {Water research}, volume = {275}, number = {}, pages = {123191}, doi = {10.1016/j.watres.2025.123191}, pmid = {39892190}, issn = {1879-2448}, abstract = {Nitrification is a central process in the global nitrogen cycle, yet the ecological niches and growth strategies of ammonia-oxidizing microorganisms in oligotrophic environments remain poorly understood. To investigate the ecological responses of complete ammonia oxidizers (Comammox) and ammonia-oxidizing archaea (AOA), a membrane bioreactor (MBR) system with two distinct ammonia loading rates (ALRs) was employed in this study. Metagenomic and meta-transcriptomic analyses showed that Comammox species-including Candidatus Nitrospira nitrosa and Candidatus Nitrospira inopinata-underwent a pronounced "bloom" only at high ALR, where their DNA and mRNA relative abundances reached 4.7 % and 5.63 %, respectively. Meanwhile, AOA steadily increased under both high and low ALR in oligotrophic environments. Network analysis further indicated stronger cooperative interactions between Comammox and AOA in higher ALR, highlighting distinct ecological strategies that underpin ammonia oxidation in oligotrophic environments. These findings not only support the development of low-carbon nitrogen removal processes in wastewater treatment but also clarify the impact of nitrogen loading on the distribution of ammonia-oxidizing microorganisms in natural ecosystems and provide insights into the origin and evolutionary pathways of these essential microbes.}, } @article {pmid39891257, year = {2025}, author = {Elrashedy, A and Mousa, W and Nayel, M and Salama, A and Zaghawa, A and Elsify, A and Hasan, ME}, title = {Advances in bioinformatics and multi-omics integration: transforming viral infectious disease research in veterinary medicine.}, journal = {Virology journal}, volume = {22}, number = {1}, pages = {22}, pmid = {39891257}, issn = {1743-422X}, mesh = {Animals ; *Computational Biology/methods ; *Veterinary Medicine/methods ; *Virus Diseases/veterinary/virology ; Genomics/methods ; Proteomics ; Multiomics ; }, abstract = {The world is changing due to factors like bioterrorism, massive environmental changes, globalization of trade and commerce, growing urbanization, changing climate, and pollution. Numerous diseases have emerged because of these factors, especially in companion and food-producing animals. Numerous pathogens have established themselves in naïve populations, harming reproduction, productivity, and health. Bioinformatics is considered a valuable tool in infectious disease research, as it provides a comprehensive overview of the identification of pathogens, their genetic makeup, and their evolutionary relationship. Therefore, there is an urgent need for a novel bioinformatics approach to help decipher and model viral epidemiology and informatics on domestic animals and livestock. With significant advancements in bioinformatics and NGS, researchers can now identify contigs, which are contiguous sequences of DNA that are assembled from overlapping fragments, assemble a complete genome, perform phylogenetic analysis to diagnose, investigate the risk of viral diseases in animals, handle and share large biological datasets across various species. Additionally, multi-omics data integration further deepens our understanding of homology, divergence, mutations, and evolutionary relationships, providing a comprehensive perspective on the molecular mechanisms driving animal pathogens infections. This review aims to reveal the importance of utilizing the multidisciplinary areas of bioinformatics, genomics, proteomics, transcriptomics, metabolomics, and metagenomics and their roles in studying viral infectious diseases in veterinary medicine that will eventually improve the health of animals.}, } @article {pmid39891205, year = {2025}, author = {Huang, D and Liao, J and Balcazar, JL and Ye, M and Wu, R and Wang, D and Alvarez, PJJ and Yu, P}, title = {Adaptive modification of antiviral defense systems in microbial community under Cr-induced stress.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {34}, pmid = {39891205}, issn = {2049-2618}, support = {42177113//National Natural Science Foundation of China/ ; 42277418//National Natural Science Foundation of China/ ; Y2022084//the Youth Innovation Promotion Association, Chinese Academy of Sciences/ ; 2022YFC3704700//National Key Research and Development Program of China/ ; }, mesh = {*Chromium/pharmacology ; *Soil Microbiology ; *Stress, Physiological ; *Bacteria/genetics/classification/drug effects ; *Microbiota/drug effects ; Soil Pollutants ; Metagenomics/methods ; Viruses/genetics/drug effects/classification ; Soil/chemistry ; }, abstract = {BACKGROUND: The prokaryotic antiviral defense systems are crucial for mediating prokaryote-virus interactions that influence microbiome functioning and evolutionary dynamics. Despite the prevalence and significance of prokaryotic antiviral defense systems, their responses to abiotic stress and ecological consequences remain poorly understood in soil ecosystems. We established microcosm systems with varying concentrations of hexavalent chromium (Cr(VI)) to investigate the adaptive modifications of prokaryotic antiviral defense systems under abiotic stress.

RESULTS: Utilizing hybrid metagenomic assembly with long-read and short-read sequencing, we discovered that antiviral defense systems were more diverse and prevalent in heavily polluted soils, which was corroborated by meta-analyses of public datasets from various heavy metal-contaminated sites. As the Cr(VI) concentration increased, prokaryotes with defense systems favoring prokaryote-virus mutualism gradually supplanted those with defense systems incurring high adaptive costs. Additionally, as Cr(VI) concentrations increased, enriched antiviral defense systems exhibited synchronization with microbial heavy metal resistance genes. Furthermore, the proportion of antiviral defense systems carried by mobile genetic elements (MGEs), including plasmids and viruses, increased by approximately 43% and 39%, respectively, with rising Cr concentrations. This trend is conducive to strengthening the dissemination and sharing of defense resources within microbial communities.

CONCLUSIONS: Overall, our study reveals the adaptive modification of prokaryotic antiviral defense systems in soil ecosystems under abiotic stress, as well as their positive contributions to establishing prokaryote-virus mutualism and the evolution of microbial heavy metal resistance. These findings advance our understanding of microbial adaptation in stressful environments and may inspire novel approaches for microbiome manipulation and bioremediation. Video Abstract.}, } @article {pmid39891076, year = {2025}, author = {Jia, Q and Sun, J and Wang, D and Xu, J and Li, X and Zhang, S and Wang, L and Liu, S and Tong, X and Fan, H}, title = {Clinical features and prognostic predictors of C. Psittaci Pneumonia: a systematic review and individual patient meta-analysis.}, journal = {BMC pulmonary medicine}, volume = {25}, number = {1}, pages = {55}, pmid = {39891076}, issn = {1471-2466}, mesh = {Humans ; *Psittacosis/diagnosis ; Prognosis ; *Chlamydophila psittaci/isolation & purification ; Risk Factors ; Pneumonia/diagnosis ; Severity of Illness Index ; }, abstract = {BACKGROUND: The clinical presentations and prognostic indicators of C. psittaci pneumonia are inadequately investigated currently. The objective of the study was to assess the clinical presentation of C. psittaci pneumonia and the risk factors for severe pneumonia, within a systematic review and individual patient meta-analysis.

METHODS: We searched PubMed, CNKI, and Wanfang databases for case reports/series of proven/probable psittacosis published between 1st January 2000 and 28th February 2023, including all hospitalized individuals aged ≥ 18 years. Patient demographics, manifestations, diagnostic methods, and outcomes were summarized descriptively. Patients were divided into severe or non-severe pneumonia groups mainly according to the ATS/IDSA 2007 criteria. Prognostic predictors for severe C. psittaci pneumonia were identified using multivariate logistic regression.

RESULTS: 3062 articles of 196 (566 individual patient cases) were included in the final analysis. Patients with chronic cardiovascular disease face a significantly elevated risk of developing severe C. psittaci pneumonia (adjusted odds ratio (aOR) 2.63; 95% confidence interval (CI) 1.05-6.59; P = 0.039). Symptoms including dyspnea (aOR 4.88; 95% CI 3.19-7.46; P < 0.001), neuropsychiatric symptoms (aOR 3.58; 95% CI 2.05-6.28; P < 0.001), gastrointestinal symptoms (aOR 1.76; 95% CI 1.10-2.80; P = 0.018), or the presence of multilobar infiltrates on imaging (aOR 3.27; 95% CI 2.11-5.06; P < 0.001) upon admission frequently serve as indicators of severe pneumonia.

CONCLUSIONS: Chronic cardiovascular disease increases susceptibility to severe C. psittaci pneumonia. The presence of dyspnea, neuropsychiatric symptoms, gastrointestinal symptoms, and multilobar infiltrates upon admission merits clinicians' attention, advocating for timely sample submission for metagenomic next-generation sequencing (mNGS) to ascertain the etiology.}, } @article {pmid39890997, year = {2025}, author = {Marter, P and Freese, HM and Ringel, V and Brinkmann, H and Pradella, S and Rohde, M and Jarek, M and Spröer, C and Wagner-Döbler, I and Overmann, J and Bunk, B and Petersen, J}, title = {Superior Resolution Profiling of the Coleofasciculus Microbiome by Amplicon Sequencing of the Complete 16S rRNA Gene and ITS Region.}, journal = {Environmental microbiology reports}, volume = {17}, number = {1}, pages = {e70066}, pmid = {39890997}, issn = {1758-2229}, support = {34509606-TRR 51//Deutsche Forschungsgemeinschaft/ ; //Collaborative Research Center Roseobacter (TRR51)/ ; }, mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Cyanobacteria/genetics/classification/isolation & purification ; Sequence Analysis, DNA ; Phylogeny ; DNA, Ribosomal Spacer/genetics ; DNA, Bacterial/genetics ; Bacteria/genetics/classification/isolation & purification ; Metagenomics ; }, abstract = {The filamentous cyanobacterium Coleofasciculus chthonoplastes is the key primary producer of marine microbial mats. We elucidated the microbiomes of 32 non-axenic Coleofasciculus isolates using PacBio-based amplicon sequencing of the complete 16S rRNA gene and the internally transcribed spacer (16S-ITS). The length of authentic amplicon sequence variants (ASVs) ranged from 1827 to 3044 nucleotides (median: 2267 nt). The results, which were complemented by metagenome analyses and cultivation approaches, revealed the presence of more than 70 associated heterotrophs in the culture of Coleofasciculus sp. WW12. The great bacterial diversity in the cyanosphere is dominated by Pseudomonadota (59%) and Bacteroidota (23%). Allelic ribosomal operon variants were detected in 18 Coleofasciculus strains and our analyses proposed the presence of at least four different species. A comparative analysis of cyanobacterial microbiomes documented complementary advantages of amplicon sequencing versus metagenomics with an individual strength of the 16S-ITS approach in terms of (i) ribosomal target sequence quality, (ii) contaminant detection and (iii) identification of rare bacteria. The characterisation of the Coleofasciculus microbiome showed that long-read amplicon sequencing of the 16S-ITS region is the method of choice for rapid profiling of non-axenic cyanobacteria. Its superior resolution allows a reliable differentiation of even very closely related strains.}, } @article {pmid39890137, year = {2025}, author = {Kennedy, EC and Ross, FC and O'Shea, CA and Lavelle, A and Ross, P and Dempsey, E and Stanton, C and Hawkes, CP}, title = {Observational study protocol: the faecal microbiome in the acute stage of new-onset paediatric type 1 diabetes in an Irish cohort.}, journal = {BMJ open}, volume = {15}, number = {1}, pages = {e089206}, pmid = {39890137}, issn = {2044-6055}, mesh = {Humans ; *Diabetes Mellitus, Type 1/microbiology ; *Feces/microbiology ; Child ; *Gastrointestinal Microbiome ; Male ; Female ; Prospective Studies ; Ireland ; Child, Preschool ; Adolescent ; Metabolome ; }, abstract = {INTRODUCTION: Type 1 diabetes (T1D) is an autoimmune-mediated disorder caused by the destruction of pancreatic beta cells. Although there is an underlying genetic predisposition to developing T1D, the trigger is multifactorial and likely includes environmental factors. The intestinal microbiome has been identified as one such factor. Previous studies have illustrated differences in the microbiota of people with T1D compared with healthy controls. This study aims to describe the evolution of the microbiome and metabolome during the first year of clinical T1D, or stage 3 T1D diagnosis, and investigate whether there are differences in the microbiome and metabolome of children who present with and without diabetic ketoacidosis. The study will also explore possible associations between the microbiome, metabolome, glycaemic control and beta cell reserve.

METHODS AND ANALYSIS: This prospective cohort study will include children with newly diagnosed T1D and sibling controls (n=100, males and females) and their faecal microbiome will be characterised using shotgun metagenomic sequencing at multiple time points during the first year of diagnosis. We will develop a microbial culture biobank based on culturomic studies of stool samples from the healthy controls that will support future investigation. Metabolomic analysis will aim to identify additional biomarkers which may be involved in disease presentation and progression. Through this initial exploratory study, we aim to identify specific microbial biomarkers which may be used as future interventional targets throughout the various stages of T1D progression.

ETHICS AND DISSEMINATION: This study has been approved by the Clinical Research Ethics Committee of the Cork Teaching Hospitals. Study results will be available to patients with T1D and their families, carers, support networks and microbiome societies and other researchers.

TRIAL REGISTRATION NUMBER: The clinicaltrials.gov registration number for this trial is NCT06157736.}, } @article {pmid39889699, year = {2025}, author = {Tagirdzhanova, G and Scharnagl, K and Sahu, N and Yan, X and Bucknell, A and Bentham, AR and Jégousse, C and Ament-Velásquez, SL and Onuț-Brännström, I and Johannesson, H and MacLean, D and Talbot, NJ}, title = {Complexity of the lichen symbiosis revealed by metagenome and transcriptome analysis of Xanthoria parietina.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2024.12.041}, pmid = {39889699}, issn = {1879-0445}, abstract = {Lichens are composite, symbiotic associations of fungi, algae, and bacteria that result in large, anatomically complex organisms adapted to many of the world's most challenging environments. How such intricate, self-replicating lichen architectures develop from simple microbial components remains unknown because of their recalcitrance to experimental manipulation. Here, we report a metagenomic and metatranscriptomic analysis of the lichen Xanthoria parietina at different developmental stages. We identified 168 genomes of symbionts and lichen-associated microbes across the sampled thalli, including representatives of green algae, three different classes of fungi, and 14 bacterial phyla. By analyzing the occurrence of individual species across lichen thalli from diverse environments, we defined both substrate-specific and core microbial components of the lichen. Metatranscriptomic analysis of the principal fungal symbiont from three different developmental stages of a lichen, compared with axenically grown fungus, revealed differential gene expression profiles indicative of lichen-specific transporter functions, specific cell signaling, transcriptional regulation, and secondary metabolic capacity. Putative immunity-related proteins and lichen-specific structurally conserved secreted proteins resembling fungal pathogen effectors were also identified, consistent with a role for immunity modulation in lichen morphogenesis.}, } @article {pmid39889605, year = {2025}, author = {Gong, X and Peng, Q and Jiang, R and Yang, N and Xing, C and Wang, R}, title = {Mn-oxidizing microalgae and woodchip-denitrifying bioreactor system for recovering manganese and removing nitrogen from electrolytic manganese metal industrial tailwater.}, journal = {Journal of hazardous materials}, volume = {488}, number = {}, pages = {137383}, doi = {10.1016/j.jhazmat.2025.137383}, pmid = {39889605}, issn = {1873-3336}, abstract = {Excess manganese (Mn) and NH4[+]-N emissions from electrolytic manganese metal industrial tailwater may harm the environment. However, previous studies have not combined Mn-oxidizing microalgae to reclaim Mn with woodchip substrates for nitrogen removal from tailwater. Here, a two-stage bioreactor system was constructed to recover Mn by microalgal-mediated bio-oxidation in an algae reactor (AR) and remove nitrogen by denitrification in a woodchip reactor (WR). The results showed that up to 100 % of Mn[2+] in the tailwater was removed after a 3-day incubation period. The maximum amount of biogenerated Mn oxide nanoparticles reached 13.34 mg/L with Mn[4+] as the main Mn valence. Mn recovery reached 65.69 % through precipitate collection, and the NH4[+]-N removal efficiency reached 97 % in the AR. Mn oxidation by algae might promote oxidative removal of NH4[+]-N. NO3[-]-N and total nitrogen removal efficiencies in the WR reached 82-90 % and 65-87 %, respectively, which was attributed to denitrification. The predominance of the denitrification gene narG in the WR may have driven the efficient nitrate removal. Flavobacterium, Acidovora, Massilia, Arcticibacter, and Acinetobacter were the most abundant genera in the WR and represented dominant denitrifying bacteria in the woodchip microbiome, indicating their important contribution to denitrification. Overall, the combined application of Mn-oxidizing algae and woodchip-denitrifying bioreactors may represent an efficient treatment technology for electrolytic manganese wastewater remediation.}, } @article {pmid39889194, year = {2025}, author = {Zhong, Y and Cai, ZY and Wang, JR and Qi, QG and Hao, J}, title = {Peritoneal dialysis-associated peritonitis caused by Coxiella Burnetii: A case report.}, journal = {Medicine}, volume = {104}, number = {5}, pages = {e41407}, pmid = {39889194}, issn = {1536-5964}, support = {2022MS08036//Inner Mongolia Natural Science Foundation/ ; NJYT- 23-068//Program for Young Talents of Science and Technology in Universities of Inner Mongolia Autonomous Region/ ; 202201253//Medical and Health Science and Technology Plan of Health Commission of Inner Mongolia Autonomous Region/ ; YKD2021MS034//Inner Mongolia Medical University General program/ ; }, mesh = {Female ; Humans ; *Peritonitis/microbiology/drug therapy/diagnosis ; Middle Aged ; *Coxiella burnetii/isolation & purification ; *Peritoneal Dialysis/adverse effects ; *Q Fever/diagnosis/drug therapy/microbiology ; *Anti-Bacterial Agents/therapeutic use ; Kidney Failure, Chronic/therapy ; Animals ; China ; }, abstract = {RATIONALE: Peritoneal dialysis (PD)-associated peritonitis (PDAP) is the leading cause of PD failure and discontinuation of PD. Several zoonotic pathogens could lead to the development of PDAP. Coxiella burnetii (C. burnetii) was a zoonotic pathogen and the cause of Q fever. However, reports of PDAP caused by C. burnetii are rare. We herein report the first case of PDAP caused by C. burnetii in mainland China.

PATIENTS CONCERNS: A 45-year-old woman was admitted to our hospital with chief complaint of yellow and cloudy PD effluent for 2 days. She had undergone PD for 5 years due to end-stage renal disease. She was engaged in cattle and sheep breeding. The culture of PD effluent was negative, even for specific species, such as Mycobacteria and fungi.

DIAGNOSES: The culture from the PD effluent tested positive for C. burnetii by adopting metagenomic next-generation sequencing on day 37. We diagnosed her as PDAP caused by C. burnetii.

INTERVENTIONS: Empirical treatment with multiple broad-spectrum antibiotics (including vancomycin, etimicin, piperacillin) was initially adopted. After identifying C. burnetii as the culprint as the PDAP, the regimen was changed to doxycycline (100 mg twice daily) and moxifloxacin (400 mg once daily) orally, leading to clinical improvement.

OUTCOMES: The white blood cell count of the PD effluent decreased to within the normal range and the culture of PD effluent was negative for C. burnetii at the visit of 4 months after discharge. Also, there was no sign for recurrence.

LESSONS: Vigilance should be heightened for PDAP cases with negative culture of PD fluid and poor response to standard broad-spectrum antibiotic treatment, along with a history of cattle and sheep breeding. In such conditions, PD effluent should be tested to detect possible peritonitis caused by C. burnetii, even in patients without symptoms of fever. Prompt pathogen identification and appropriate treatment are crucial for clinical improvement of such cases.}, } @article {pmid39888330, year = {2025}, author = {Thompson, JR and Canto, T and Carr, JP and Pallás, V and Šafářová, D}, title = {ICTV Virus Taxonomy Profile: Bromoviridae 2025.}, journal = {The Journal of general virology}, volume = {106}, number = {1}, pages = {}, pmid = {39888330}, issn = {1465-2099}, mesh = {*Genome, Viral ; *Plant Diseases/virology ; *Bromoviridae/genetics/classification ; RNA, Viral/genetics ; Virion/ultrastructure/genetics ; Phylogeny ; }, abstract = {Bromoviridae is a family of plant viruses with tripartite, positive-sense RNA genomes of about 8 kb in total. Genomic RNAs are packaged in separate virions that may also contain sub-genomic, defective or satellite RNAs. Virions are variable in morphology (spherical or bacilliform) and may be transmitted between hosts mechanically, via pollen, or non-persistently by insect vectors. Members of the family are responsible for major disease epidemics in fruit, vegetable and fodder crops such as tomatoes, cucurbits, bananas, fruit trees, common beans and alfalfa. Since the adoption of metagenomic high-throughput sequencing methodologies, there has been a notable increase in the number of species in the genus Ilarvirus. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Bromoviridae, which is available at ictv.global/report/bromoviridae.}, } @article {pmid39887801, year = {2025}, author = {Tonoli, A and Anselmi, S and Ward, JM and Hailes, HC and Jeffries, J}, title = {Expanding the Enzymatic Toolbox for Carboligation: Increasing the Diversity of the 'Split' Transketolase Sequence Space.}, journal = {Chembiochem : a European journal of chemical biology}, volume = {}, number = {}, pages = {e202401028}, doi = {10.1002/cbic.202401028}, pmid = {39887801}, issn = {1439-7633}, abstract = {Transketolases (TKs) are thiamine diphosphate (ThDP)-dependent enzymes that catalyze the transfer of two-carbon units in a stereoselective manner, making them valuable biocatalysts for sustainable processes. Most known TKs are about 650 amino acids long; however, a second type found in Archaea and many Bacteria consists of two proteins, each of about 300 amino acids. Exploring the unique features and differences of split TKs may help in assessing their potential use in biocatalysis and for uncovering new reactivities. Additionally, it could provide valuable information on how their structure relates to their function, especially compared to full-length TKs. In this study, we significantly expanded the known repertoire of split TKs approximately 14-fold to the best of our knowledge, by identifying and providing accessions of nearly 500 putative split-TK subunit pairs. Moreover, we doubled the number of experimentally produced and tested split TKs by cloning, purifying, and testing ten candidates retrieved from genomes and in-house metagenomes. Interestingly, pQR2809 and pQR2812, derived from hyperthermophilic organisms, showed enhanced thermostability compared to other TK examples in the literature, maintaining partial activity after heating at 90 °C or 100 °C for 1 hour, respectively.}, } @article {pmid39887373, year = {2025}, author = {Byrd, DA and Damerell, V and Gomez Morales, MF and Hogue, SR and Lin, T and Ose, J and Himbert, C and Ilozumba, MN and Kahlert, C and Shibata, D and Toriola, AT and Li, CI and Figueiredo, J and Stephens, WZ and Warby, CA and Hardikar, S and Siegel, EM and Round, J and Ulrich, CM and Gigic, B}, title = {The gut microbiome is associated with disease-free survival in stage I-III colorectal cancer patients.}, journal = {International journal of cancer}, volume = {}, number = {}, pages = {}, doi = {10.1002/ijc.35342}, pmid = {39887373}, issn = {1097-0215}, support = {//ERA-NET on Translational Cancer Research (TRANSCAN)/ ; //Heidelberger Stiftung Chirurgie, Heidelberg University Hospital/ ; //Medizinische Fakultät Heidelberg, Universität Heidelberg/ ; //Matthias-Lackas Foundations/ ; //Stiftung LebensBlicke/ ; R01 CA189184/NH/NIH HHS/United States ; U01 CA206110/NH/NIH HHS/United States ; //Rahel Goitein-Straus-Program/ ; 01KD2101D//German Federal Ministry of Education and Research/ ; 01KT1503//German Federal Ministry of Education and Research/ ; }, abstract = {Colorectal cancer (CRC) is the second overall leading cause of cancer death in the United States, with recurrence being a frequent cause of mortality. Approaches to improve disease-free survival (DFS) are urgently needed. The gut microbiome, reflected in fecal samples, is likely mechanistically linked to CRC progression and may serve as a non-invasive biomarker. Accordingly, we leveraged baseline fecal samples from N = 166 stage I-III CRC patients in the ColoCare Study, a prospective cohort of newly diagnosed CRC patients. We sequenced the V3 and V4 regions of the 16S rRNA gene to characterize fecal bacteria. We calculated estimates of alpha diversity, beta diversity, and a priori- and exploratory-selected bacterial presence/absence and relative abundance. Associations of microbial metrics with DFS were estimated using multivariable Cox proportional hazards models. We found that alpha diversity was strongly associated with improved DFS, most strongly among rectal cancer patients (Shannon HRrectum = 0.40 95% CI = 0.19, 0.87; p = .02). Overall microbiome composition differences (beta diversity), as characterized by principal coordinate axes, were statistically significantly associated with DFS. Peptostreptococcus was statistically significantly associated with worse DFS (HR = 1.62, 95% CI = 1.13, 2.31; p = .01 per 1-SD) and Order Clostridiales was associated with improved DFS (HR = 0.62, 95% CI = 0.43-0.88; p = .01 per 1-SD). In exploratory analyses, Coprococcus and Roseburia were strongly associated with improved DFS. Overall, higher bacterial diversity and multiple bacteria were strongly associated with DFS. Metagenomic sequencing to elucidate species, gene, and functional level details among larger, diverse patient populations are critically needed to support the microbiome as a biomarker of CRC outcomes.}, } @article {pmid39887237, year = {2025}, author = {Stewart, AG and Fishman, JA}, title = {Surveillance and prevention of infection in clinical xenotransplantation.}, journal = {Clinical microbiology reviews}, volume = {}, number = {}, pages = {e0015023}, doi = {10.1128/cmr.00150-23}, pmid = {39887237}, issn = {1098-6618}, abstract = {SUMMARYXenotransplantation, the transplantation of living organs, tissues, or cells between species, carries the potential to address the global shortage of human organs for patients with end-stage organ failure. Recent advances in genetic engineering have improved prospects for clinical xenotransplantation by reducing immune and inflammatory responses to grafts, controlling coagulation on endothelial surfaces, and modifying viral risks, including the porcine endogenous retrovirus (PERV). Management of infectious risks posed by clinical xenotransplantation requires meticulous attention to the biosecure breeding and microbiological surveillance of source animals and recipients and consideration of novel infection control requirements. Infectious risks in xenotransplantation stem from both known human pathogens in immunosuppressed transplant recipients and from porcine organisms for which the clinical manifestations, microbial assays, and therapies are generally limited. Both known and unknown zoonoses may be transmitted from pigs to humans. Some pig-specific pathogens do not infect human cells but have systemic manifestations when active within the xenograft, including porcine cytomegalovirus/porcine roseolovirus (PCMV/PRV), which contributes to graft rejection and consumptive coagulopathy. The role of porcine endogenous retrovirus (PERV) in humans remains uncertain despite the absence of documented transmissions and the availability of swine with inactivated genomic PERV. New technologies, such as metagenomic sequencing and multi-omics approaches, will be essential for detection of novel infections and for understanding interactions between the xenograft, the host's immune system, and potential pathogens. These approaches will allow development of infection control protocols, pathogen surveillance requirements, and tailored antimicrobial therapies to enhance the safety and success of clinical xenotransplantation.}, } @article {pmid39887086, year = {2025}, author = {Breton, J and Tu, V and Tanes, C and Wilson, N and Quinn, R and Kachelries, K and Friedman, ES and Bittinger, K and Baldassano, RN and Compher, C and Albenberg, L}, title = {A pro-inflammatory diet is associated with growth and virulence of Escherichia coli in pediatric Crohn's disease.}, journal = {Journal of Crohn's & colitis}, volume = {}, number = {}, pages = {}, doi = {10.1093/ecco-jcc/jjaf018}, pmid = {39887086}, issn = {1876-4479}, abstract = {BACKGROUND & AIMS: Epidemiological studies have suggested an association between the inflammatory potential of dietary patterns and Crohn's disease (CD). However, relationships of these inflammatory dietary determinants with the microbiome remain largely unknown. In this cross-sectional study, we evaluate the association between the inflammatory potential of habitual diet, as assessed by the modified Children-Dietary Inflammatory Index (mC-DII), and the fecal microbiome and metabolome of children with CD in comparison to healthy children.

METHODS: A cross-sectional study including 51 children with CD between 6 and 18 years of age and 50 healthy controls was conducted. Dietary inflammatory potential was measured using the modified Children-Dietary Inflammatory Index (mC-DII) and diet quality assessed by the Healthy Eating Index (HEI)-2015 and alternate Mediterranean eating index (aMed). Microbiome was analysed using shotgun metagenomic sequencing and untargeted metabolomic analysis.

RESULTS: A poor-quality, pro-inflammatory diet with similar mC-DII, HEI-2015 and aMed scores was found across healthy children and children with CD. In children with active disease, a pro-inflammatory diet was associated with decreased diversity, increased virulence potential and expansion of the Proteobacteria phylum dominated by Escherichia coli (E. coli) spp. Positive correlation between E. coli relative abundance and mC-DII was associated with a low intake of a cluster composed of fibers, vitamins and minerals with anti-inflammatory potential. A negative association between metabolites of fatty acid metabolism and HEI was found.

CONCLUSIONS: In total, our results suggest that a pro-inflammatory diet may potentiate hallmarks of the inflammation-associated dysbiosis in CD and highlight the need for microbiome-targeted dietary interventions optimizing the anti-inflammatory potential of habitual diet in the management of pediatric CD.}, } @article {pmid39886930, year = {2025}, author = {Zhang, W and Feng, J and Tan, K and Jiang, J and Deng, J}, title = {Bordetella pertussis Detected in Blood Samples From Neonatal Twins via Metagenomic Next-generation Sequencing.}, journal = {The Pediatric infectious disease journal}, volume = {44}, number = {2}, pages = {e71-e72}, pmid = {39886930}, issn = {1532-0987}, } @article {pmid39885140, year = {2025}, author = {Shao, B and Xie, YG and Zhang, L and Ruan, Y and Liang, B and Zhang, R and Xu, X and Wang, W and Lin, Z and Pei, X and Wang, X and Zhao, L and Zhou, X and Wu, X and Xing, D and Wang, A and Lee, DJ and Ren, N and Canfield, DE and Hedlund, BP and Hua, ZS and Chen, C}, title = {Versatile nitrate-respiring heterotrophs are previously concealed contributors to sulfur cycle.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {1202}, pmid = {39885140}, issn = {2041-1723}, support = {52076063//National Natural Science Foundation of China (National Science Foundation of China)/ ; 52100035//National Natural Science Foundation of China (National Science Foundation of China)/ ; 52400025//National Natural Science Foundation of China (National Science Foundation of China)/ ; 52300155//National Natural Science Foundation of China (National Science Foundation of China)/ ; 52321005//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32170014//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2023DX04//State Key Laboratory of Urban Water Resource and Environment (SKLUWRE)/ ; 2024M754204//China Postdoctoral Science Foundation/ ; 2023M740917//China Postdoctoral Science Foundation/ ; }, mesh = {*Sulfur/metabolism ; *Nitrates/metabolism ; *Heterotrophic Processes ; *Denitrification ; *Oxidation-Reduction ; Bacteria/metabolism/genetics ; Geologic Sediments/microbiology ; Nitrous Oxide/metabolism ; Microbiota ; Sulfides/metabolism ; Metagenomics ; Greenhouse Gases/metabolism ; }, abstract = {Heterotrophic denitrifiers play crucial roles in global carbon and nitrogen cycling. However, their inability to oxidize sulfide renders them vulnerable to this toxic molecule, which inhibits the key enzymatic reaction responsible for reducing nitrous oxide (N2O), thereby raising greenhouse gas emissions. Here, we applied microcosm incubations, community-isotope-corrected DNA stable-isotope probing, and metagenomics to characterize a cohort of heterotrophic denitrifiers in estuarine sediments that thrive by coupling sulfur oxidation with denitrification through chemolithoheterotrophic metabolism. Remarkably, ecophysiology experiments from enrichments demonstrate that such heterotrophs expedite denitrification with sulfur acting as alternative electron sources and substantially curtail N2O emissions in both organic-rich and organic-limited environments. Their flexible, non-sulfur-dependent physiology may confer competitive advantages over conventional heterotrophic denitrifiers in detoxifying sulfide, adapting to organic matter fluctuations, and mitigating greenhouse gas emissions. Our study provides insights into the ecological role of heterotrophic denitrifiers in microbial communities with implications for sulfur cycling and climate change.}, } @article {pmid39885121, year = {2025}, author = {Nooij, S and Plomp, N and Sanders, IMJG and Schout, L and van der Meulen, AE and Terveer, EM and Norman, JM and Karcher, N and Larralde, MF and Vossen, RHAM and Kloet, SL and Faber, KN and Harmsen, HJM and Zeller, GF and Kuijper, EJ and Smits, WK and Ducarmon, QR}, title = {Metagenomic global survey and in-depth genomic analyses of Ruminococcus gnavus reveal differences across host lifestyle and health status.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {1182}, pmid = {39885121}, issn = {2041-1723}, mesh = {Humans ; *Crohn Disease/microbiology/genetics ; *Metagenomics/methods ; *Genome, Bacterial/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenome/genetics ; Health Status ; Genome-Wide Association Study ; Clostridiales/genetics/isolation & purification ; Life Style ; Phylogeny ; Infant, Newborn ; Genomics ; Female ; Male ; Adult ; Virulence Factors/genetics ; }, abstract = {Ruminococcus gnavus is a gut bacterium found in > 90% of healthy individuals, but its increased abundance is also associated with chronic inflammatory diseases, particularly Crohn's disease. Nevertheless, its global distribution and intraspecies genomic variation remain understudied. By surveying 12,791 gut metagenomes, we recapitulated known associations with metabolic diseases and inflammatory bowel disease. We uncovered a higher prevalence and abundance of R. gnavus in Westernized populations and observed bacterial relative abundances up to 83% in newborns. Next, we built a resource of R. gnavus isolates (N = 45) from healthy individuals and Crohn's disease patients and generated complete R. gnavus genomes using PacBio circular consensus sequencing. Analysis of these genomes and publicly available high-quality draft genomes (N = 333 genomes) revealed multiple clades which separated Crohn's-derived isolates from healthy-derived isolates. Presumed R. gnavus virulence factors could not explain this separation. Bacterial genome-wide association study revealed that Crohn's-derived isolates were enriched in genes related to mobile elements and mucin foraging. Together, we present a large R. gnavus resource that will be available to the scientific community and provide novel biological insights into the global distribution and genomic variation of R. gnavus.}, } @article {pmid39884534, year = {2025}, author = {Zhou, M and Luo, C and Zhang, J and Li, R and Chen, J and Ren, P and Tang, Y and Suo, Z and Chen, K}, title = {Potential risk of microplastics in plateau karst lakes: Insights from metagenomic analysis.}, journal = {Environmental research}, volume = {270}, number = {}, pages = {120984}, doi = {10.1016/j.envres.2025.120984}, pmid = {39884534}, issn = {1096-0953}, abstract = {Microplastic (MP) pollution has become one of global concern. While MP pollution in lakes has been well studied, research on MP sources, distribution, and ecological risks in the Tibetan Plateau is limited. We systematically investigated the MP abundance and distribution in alpine travertine lakes in Jiuzhai nature reserve located in east edge of Qinghai-Tibetan Plateau and assessed the distributions of microbiomes, antibiotic resistance genes (ARGs), and virulence factor genes (VFGs) in water, sediments, and MPs, using macrogenomics. MP abundance was 20.27-58.80 n/L in water and 583.33-996.67 n/kg in sediments. MPs were dominantly fibrous and transparent. The particle size distribution was 0.1-0.5 mm for MPs in water, and 0.5-1 mm in sediments. MPs were mainly composed of polyethylene and polyethylene terephthalate. The microbial community of MP biofilms differed from that in the surrounding environmental medium, and Proteobacteria were more abundant in biofilm than in water and sediment. MP biofilms exhibited more cooperative behavior with microorganisms in water than with those in sediments. MPs were selectively enriched for ARGs and VFGs, and MP biofilms had a higher diversity of ARGs, the most abundant isoform being msbA, which is a multidrug resistance gene. VFGs were more abundant in MP biofilms than in water and sediment. The study results are useful for understanding MP sources and ecological risks in plateau karst lakes and provide a valuable dataset and theoretical basis for studies on MP pollution in other alpine calcareous lakes.}, } @article {pmid39884152, year = {2025}, author = {Maphosa, S and Steyn, M and Lebre, PH and Gokul, JK and Convey, P and Marais, E and Maggs-Kölling, G and Cowan, DA}, title = {Rhizosphere bacterial communities of Namib Desert plant species: Evidence of specialised plant-microbe associations.}, journal = {Microbiological research}, volume = {293}, number = {}, pages = {128076}, doi = {10.1016/j.micres.2025.128076}, pmid = {39884152}, issn = {1618-0623}, abstract = {Rhizosphere microbial communities are intimately associated with plant root surfaces. The rhizosphere microbiome is recruited from the surrounding soil and is known to impact positively on the plant host via enhanced resistance to pathogens, increased nutrient availability, growth stimulation and increased resistance to desiccation. Desert ecosystems harbour a diversity of perennial and annual plant species, generally exhibiting considerable physiological adaptation to the low-water environment. In this study, we explored the rhizosphere bacterial microbiomes associated with selected desert plant species. The rhizosphere bacterial communities of 11 plant species from the central Namib Desert were assessed using 16S rRNA gene-dependent phylogenetic analyses. The rhizosphere microbial community of each host plant species was compared with control soils collected from their immediate vicinity, and with those of all other host plants. Rhizosphere and control soil bacterial communities differed significantly and were influenced by both location and plant species. Rhizosphere-associated genera included 67 known plant growth-promoting taxa, including Rhizobium, Bacillus, Microvirga, Kocuria and Paenibacillus. Other than Kocuria, these genera constituted the 'core' rhizosphere bacterial microbiome, defined as being present in > 90 % of the rhizosphere communities. Nine of the 11 desert plant species harboured varying numbers and proportions of species-specific microbial taxa. Predictive analyses of functional pathways linked to rhizosphere microbial taxa showed that these were significantly enriched in the biosynthesis or degradation of a variety of substances such as sugars, secondary metabolites, phenolic compounds and antimicrobials. Overall, our data suggest that plant species in the Namib Desert recruit unique taxa to their rhizosphere bacterial microbiomes that may contribute to their resilience in this extreme environment.}, } @article {pmid39884010, year = {2025}, author = {Peng, Y and Lu, J and Fan, L and Zhou, J and Dong, W and Jiang, M}, title = {Enzymes offer a promising avenue for enhancing the competitiveness of biodegradable plastics in environmental restoration and the circular economy.}, journal = {Waste management (New York, N.Y.)}, volume = {195}, number = {}, pages = {32-43}, doi = {10.1016/j.wasman.2025.01.040}, pmid = {39884010}, issn = {1879-2456}, abstract = {As a promising alternative to traditional plastics, the widespread application of biodegradable plastic (BP) will help solve worsening environmental problems. Enzymes such as cutinase, lipase, protease and esterase produced by bacteria and fungi in the environment play a crucial role in the degradation, recycling and valorization of BP by degrading them into low-molecular-weight oligomers or small monomers. These enzymes offering advantages such as high efficiency, cleanliness, safety and environmental friendliness, making them more competitive in environmental restoration and circular economy. This review describes in detail the occurrence and distribution of enzymes involved in the degradation of BPs (represented by PHB, PLA and PCL). Omics methods (metagenomic and proteomic) combined with high-throughput platforms can screen out BP-degrading enzymes in different environments, and then use protein engineering to optimize the degrading enzymes to improve enzymatic degradation efficiency. Finally, we focus on the methods and strategies for the commercialization of degrading enzymes, future research prospects and challenges are also discussed. This review highlights the importance of BP-degrading enzymes in the bio-cycling of BP, and expected to drive the widespread use of BP.}, } @article {pmid39883852, year = {2025}, author = {Monpierre, L and Angebault, C and Hua, C and Merio, L and Ortonne, N and Lafont, E and Foulet, F and Botterel, F}, title = {Contribution of shotgun metagenomics in the diagnosis of a subcutaneous phaeohyphomycosis caused by Parathyridaria percutanea.}, journal = {The British journal of dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1093/bjd/ljaf018}, pmid = {39883852}, issn = {1365-2133}, } @article {pmid39883300, year = {2024}, author = {Zhang, D and Yu, H and Yu, X and Yang, Y and Wang, C and Wu, K and Niu, M and He, J and He, Z and Yan, Q}, title = {Mechanisms underlying the interactions and adaptability of nitrogen removal microorganisms in freshwater sediments.}, journal = {Advanced biotechnology}, volume = {2}, number = {3}, pages = {21}, pmid = {39883300}, issn = {2948-2801}, support = {SML2023SP237//Southern Marine Science and Engineering Guangdong Laboratory/ ; SML2021SP203//Southern Marine Science and Engineering Guangdong Laboratory/ ; SML2023SP205//Southern Marine Science and Engineering Guangdong Laboratory/ ; }, abstract = {Microorganisms in eutrophic water play a vital role in nitrogen (N) removal, which contributes significantly to the nutrient cycling and sustainability of eutrophic ecosystems. However, the mechanisms underlying the interactions and adaptation strategies of the N removal microorganisms in eutrophic ecosystems remain unclear. We thus analyzed field sediments collected from a eutrophic freshwater ecosystem, enriched the N removal microorganisms, examined their function and adaptability through amplicon, metagenome and metatranscriptome sequencing. We found that the N removal activities could be affected through potential competition and inhibition among microbial metabolic pathways. High-diversity microbial communities generally increased the abundance and expression of N removal functional genes. Further enrichment experiments showed that the enrichment of N removal microorganisms led to a development of simplified but more stable microbial communities, characterized by similar evolutionary patterns among N removal microorganisms, tighter interactions, and increased adaptability. Notably, the sustained provision of NH4[+] and NO2[-] during the enrichment could potentially strengthen the interconnections among denitrification, anaerobic ammonium oxidation (anammox) and dissimilatory nitrate reduction to ammonium (DNRA) processes. Moreover, the identification of shared metabolic traits among denitrification, anammox and DNRA implies important cooperative associations and adaptability of N removal microorganisms. Our findings highlight the microbial interactions affect the adaptive strategies of key microbial taxa involved in N removal.}, } @article {pmid39882903, year = {2025}, author = {Huang, X and Yao, X and Song, W and Zhao, M and Zhu, Z and Liu, H and Song, X and Huang, J and Chen, Y and Wang, Z and Peng, C and Wu, W and Yang, H and Hua, L and Chen, H and Wu, B and Peng, Z}, title = {Discovery of viruses and bacteria associated with swine respiratory disease on farms at a nationwide scale in China using metatranscriptomic and metagenomic sequencing.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0002525}, doi = {10.1128/msystems.00025-25}, pmid = {39882903}, issn = {2379-5077}, abstract = {Respiratory disease (RD) is a worldwide leading threat to the pig industry, but there is still limited understanding of the pathogens associated with swine RD. In this study, we conducted a nationwide genomic surveillance on identifying viruses, bacteria, and antimicrobial resistance genes (ARGs) from the lungs of pigs with RD in China. By performing metatranscriptomic sequencing combined with metagenomic sequencing, we identified 21 viral species belonging to 12 viral families. Among them, porcine reproductive and respiratory syndrome virus, influenza A virus, herpes virus, adenovirus, and parvovirus were commonly identified. However, emerging viruses, such as Getah virus and porcine respiratory coronaviruses, were also characterized. Apart from viruses, a total of 164 bacterial species were identified, with Streptococcus suis, Mycoplasma hyorhinis, Mycoplasma hyopneumoniae, Glaesserella parasuis, and Pasteurella multocida being frequently detected in high abundances. Notably, Escherichia coli, Enterococcus faecalis, Staphylococcus aureus, and Klebsiella pneumoniae were also highly detected. Our further analysis revealed a complex interaction between the identified pathogens in swine RD. We also conducted retrospectively analyses to demonstrate the prevalent viral genotypes or bacterial serotypes associated with swine RD in China. Finally, we identified 48 ARGs, which conferred resistance to 13 predicted antimicrobial classes, and many of these ARGs were significantly associated with a substantial number of mobile genetic elements, including transposons (e.g., tnpAIS1, tnpA1353, int3, and ISCau1) and plasmids (e.g., Col(BS512), Col(YC)]. These findings will contribute to further understanding the etiology, epidemiology, and microbial interactions in swine RD, and may also shed a light on the development of effective vaccines.IMPORTANCEIn this study, we identified viruses and bacteria from the lungs of pigs with RD in China at a nationwide farm scale by performing metatranscriptomic sequencing combined with metagenomic sequencing. We also demonstrated the complex interactions between different viral and/or bacterial species in swine RD. Our work provides a comprehensive knowledge about the etiology, epidemiology, and microbial interactions in swine RD and data reference for the research and development of effective vaccines against the disease.}, } @article {pmid39882902, year = {2025}, author = {Zhu, D and Wozniak, KJ and Midani, F and Wang, S and Sun, X and Britton, RA}, title = {Control of Clostridioides difficile virulence and physiology by the flagellin homeostasis checkpoint FliC-FliW-CsrA in the absence of motility.}, journal = {mBio}, volume = {}, number = {}, pages = {e0380124}, doi = {10.1128/mbio.03801-24}, pmid = {39882902}, issn = {2150-7511}, abstract = {UNLABELLED: Mutations affecting Clostridioides difficile flagellin (FliC) have been shown to be hypervirulent in animal models and display increased toxin production and alterations in central metabolism. The regulation of flagellin levels in bacteria is governed by a tripartite regulatory network involving fliC, fliW, and csrA, which creates a feedback system to regulate flagella production. Through genomic analysis of C. difficile clade 5 strains (non-motile), we identified they have jettisoned many of the genes required for flagellum biosynthesis yet retain the major flagellin gene fliC and regulatory gene fliW. We therefore investigated the roles of fliC, fliW, and csrA in the clade 5 ribotype 078 strain C. difficile 1015, which lacks flagella and is non-motile. Analysis of mutations in fliC, fliW, and csrA (and all combinations) on C. difficile pathogenesis indicated that FliW plays a central role in C. difficile virulence as animals infected with strains carrying a deletion of fliW showed decreased survival and increased disease severity. These in vivo findings were supported by in vitro studies showing that mutations impacting the activity of FliW showed increased toxin production. We further identified that FliW can interact with the toxin-positive regulator TcdR, indicating that modulation of toxin production via FliW occurs by sequestering TcdR from activating toxin transcription. Furthermore, disruption of the fliC-fliW-csrA network results in significant changes in carbon source utilization and sporulation. This work highlights that key proteins involved in flagellar biosynthesis retain their regulatory roles in C. difficile pathogenesis and physiology independent of their functions in motility.

IMPORTANCE: Clostridioides difficile is a leading cause of nosocomial antibiotic-associated diarrhea in developed countries with many known virulence factors. In several pathogens, motility and virulence are intimately linked by regulatory networks that allow coordination of these processes in pathogenesis and physiology. Regulation of C. difficile toxin production by FliC has been demonstrated in vitro and in vivo and has been proposed to link motility and virulence. Here, we show that clinically important, non-motile C. difficile strains have conserved FliC and regulatory partners FliW and CsrA, despite lacking the rest of the machinery to produce functional flagella. Our work highlights a novel role for flagellin outside of its role in motility and FliW in the pathogenesis and physiology of C. difficile.}, } @article {pmid39882857, year = {2025}, author = {Grettenberger, C and Gold, DA and Brown, CT}, title = {Distribution of early-branching Cyanobacteriia and the potential habitats that gave rise to the earliest oxygenic phototrophs.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0101324}, doi = {10.1128/msphere.01013-24}, pmid = {39882857}, issn = {2379-5042}, abstract = {The evolution of oxygenic photosynthesis in the Cyanobacteria was one of the most transformative events in Earth history, eventually leading to the oxygenation of Earth's atmosphere. However, it is difficult to understand how the earliest Cyanobacteria functioned or evolved on early Earth in part because we do not understand their ecology, including the environments in which they lived. Here, we use a cutting-edge bioinformatics tool to survey nearly 500,000 metagenomes for relatives of the taxa that likely bookended the evolution of oxygenic photosynthesis to identify the modern environments in which these organisms live. Ancestral state reconstruction suggests that the common ancestors of these organisms lived in terrestrial (soil and/or freshwater) environments. This restricted distribution may have increased the lag between the evolution of oxygenic photosynthesis and the oxygenation of Earth's atmosphere.IMPORTANCECyanobacteria generate oxygen as part of their metabolism and are responsible for the rise of oxygen in Earth's atmosphere over two billion years ago. However, we do not know how long this process may have taken. To help constrain how long this process would have taken, it is necessary to understand where the earliest Cyanobacteria may have lived. Here, we use a cutting-edge bioinformatics tool called branch water to examine the environments where modern Cyanobacteria and their relatives live to constrain those inhabited by the earliest Cyanobacteria. We find that these species likely lived in non-marine environments. This indicates that the rise of oxygen may have taken longer than previously believed.}, } @article {pmid39882224, year = {2025}, author = {Takamaru, H and Tsay, C and Shiba, S and Yachida, S and Saito, Y}, title = {Microbiome and Colorectal Cancer in Humans: A Review of Recent Studies.}, journal = {Journal of the anus, rectum and colon}, volume = {9}, number = {1}, pages = {20-24}, pmid = {39882224}, issn = {2432-3853}, abstract = {The tumor microenvironment has recently been well-studied in various gastrointestinal cancers, including colorectal cancer (CRC). The gut microbiota, a collection of microorganisms in the human gastrointestinal tract, is one of the microenvironments associated with colon carcinogenesis. It has been challenging to elucidate the mechanisms by which gut microbiota contributes to carcinogenesis and cancer progression due to complex interactions with the host, including its metabolites and immune and inflammatory responses. Various studies described the influence of diet on reported changes in the composition and microbiota of gut bacteria and its association with CRC. In recent years, metagenomic techniques such as shotgun sequencing and genome-wide association studies focused on understanding the role of the microbiota and the metabolome on early CRCs and colon carcinogenesis to determine if there are modifiable or intervenable targets for CRC. In this review, we will attempt to provide an overview of gut microbiota related to CRC, with particular attention to the findings of recent studies.}, } @article {pmid39881980, year = {2024}, author = {Renk, H and Schoppmeier, U and Müller, J and Kuger, V and Neunhoeffer, F and Gille, C and Peter, S}, title = {Oxygenation and intestinal perfusion and its association with perturbations of the early life gut microbiota composition of children with congenital heart disease.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1468842}, pmid = {39881980}, issn = {1664-302X}, abstract = {BACKGROUND: Early life gut microbiota is known to shape the immune system and has a crucial role in immune homeostasis. Only little is known about composition and dynamics of the intestinal microbiota in infants with congenital heart disease (CHD) and potential influencing factors.

METHODS: We evaluated the intestinal microbial composition of neonates with CHD (n = 13) compared to healthy controls (HC, n = 30). Fecal samples were analyzed by shotgun metagenomics. Different approaches of statistical modeling were applied to assess the impact of influencing factors on variation in species composition. Unsupervised hierarchical clustering of the microbial composition of neonates with CHD was used to detect associations of distinct clusters with intestinal tissue oxygenation and perfusion parameters, obtained by the "oxygen to see" (O2C) method.

RESULTS: Overall, neonates with CHD showed an intestinal core microbiota dominated by the genera Enterococcus (27%) and Staphylococcus (20%). Furthermore, a lower abundance of the genera Bacteroides (8% vs. 14%), Parabacteroides (1% vs. 3%), Bifidobacterium (4% vs. 12%), and Escherichia (8% vs. 23%) was observed in CHD compared to HCs. CHD patients that were born by vaginal delivery showed a lower fraction of the genera Bacteroides (15% vs. 21%) and Bifidobacterium (7% vs. 22%) compared to HCs and in those born by cesarean section, these genera were not found at all. In infants with CHD, we found a significant impact of oxygen saturation (SpO2) on relative abundances of the intestinal core microbiota by multivariate analysis of variance (F[8,2] = 24.9, p = 0.04). Statistical modeling suggested a large proportional shift from a microbiota dominated by the genus Streptococcus (50%) in conditions with low SpO2 towards the genus Enterococcus (61%) in conditions with high SpO2. We identified three distinct compositional microbial clusters, corresponding neonates differed significantly in intestinal blood flow and global gut perfusion.

CONCLUSION: Early life differences in gut microbiota of CHD neonates versus HCs are possibly linked to oxygen levels. Delivery method may affect microbiota stability. However, further studies are needed to assess the effect of potential interventions including probiotics or fecal transplants on early life microbiota perturbations in neonates with CHD.}, } @article {pmid39881594, year = {2025}, author = {Kaur, I and Shaw, B and Multani, A and Pham, C and Malhotra, S and Smith, E and Adachi, K and Allyn, P and Bango, Z and Beaird, OE and Caldera, JR and Chandrasekaran, S and Chan, L and Cheema, R and Daouk, S and Deville, J and Dong, HV and Fan, A and Garner, O and Gaynor, P and Gray, H and Gorin, A and Kalava, S and Kanatani, M and Karnaze, A and Saleh, T and Sharma, Y and Stauber, S and Vargas, M and Veral, M and Winston, D and Yanagimoto-Ogawa, L and Aldrovandi, G and Nielsen-Saines, K and Fuller, T and Jackson, N and Uslan, D and Schaenman, J and Vijayan, T and Sakona, A and Yang, S}, title = {Real-world clinical impact of plasma cell-free DNA metagenomic next-generation sequencing assay.}, journal = {Infection control and hospital epidemiology}, volume = {}, number = {}, pages = {1-8}, doi = {10.1017/ice.2024.242}, pmid = {39881594}, issn = {1559-6834}, abstract = {OBJECTIVE: To describe the real-world clinical impact of a commercially available plasma cell-free DNA metagenomic next-generation sequencing assay, the Karius test (KT).

METHODS: We retrospectively evaluated the clinical impact of KT by clinical panel adjudication. Descriptive statistics were used to study associations of diagnostic indications, host characteristics, and KT-generated microbiologic patterns with the clinical impact of KT. Multivariable logistic regression modeling was used to further characterize predictors of higher positive clinical impact.

RESULTS: We evaluated 1000 unique clinical cases of KT from 941 patients between January 1, 2017-August 31, 2023. The cohort included adult (70%) and pediatric (30%) patients. The overall clinical impact of KT was positive in 16%, negative in 2%, and no clinical impact in 82% of the cases. Among adult patients, multivariable logistic regression modeling showed that culture-negative endocarditis (OR 2.3; 95% CI, 1.11-4.53; P .022) and concern for fastidious/zoonotic/vector-borne pathogens (OR 2.1; 95% CI, 1.11-3.76; P .019) were associated with positive clinical impact of KT. Host immunocompromised status was not reliably associated with a positive clinical impact of KT (OR 1.03; 95% CI, 0.83-1.29; P .7806). No significant predictors of KT clinical impact were found in pediatric patients. Microbiologic result pattern was also a significant predictor of impact.

CONCLUSIONS: Our study highlights that despite the positive clinical impact of KT in select situations, most testing results had no clinical impact. We also confirm diagnostic indications where KT may have the highest yield, thereby generating tools for diagnostic stewardship.}, } @article {pmid39881417, year = {2025}, author = {Ye, GC and Peng, H and Xiang, JC and Miao, LT and Liu, CZ and Wang, SG and Xia, QD}, title = {Comprehensive analysis of the interaction microbiome and prostate cancer: an initial exploration from multi-cohort metagenome and GWAS studies.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {130}, pmid = {39881417}, issn = {1479-5876}, mesh = {Humans ; Male ; *Prostatic Neoplasms/microbiology/genetics/pathology ; *Metagenome/genetics ; *Genome-Wide Association Study ; *Gastrointestinal Microbiome/genetics ; Cohort Studies ; Neoplasm Metastasis ; Mendelian Randomization Analysis ; }, abstract = {INTRODUCTION: Prostate cancer is one of the most common cancers in the United States with a high mortality rate. In recent years, the traditional opinion about prostate microbiome was challenged. Although there still are some arguments, an escalating number of researchers are shifting their focus toward the microbiome within the prostate tumor environment.

METHODS: We mined the data of the microbiome extracted from the metagenome, and it offers a broader taxonomic coverage and accurate functional profiling. We used Kraken2, a mapping tool, to mine the gut microbiota of prostate cancer patients. A two-sample Mendelian Randomization was conducted to reflect the association between gut microbiome and cancer.

RESULTS: In the study, we found the consistency of the special intratumor microbiome of both non-metastatic tumors and metastatic tumors. And we dig the gut microbiome in patients with different treatments. We found that some microbiotas may be associated with prostate cancer progression and a special microbiome in metastatic prostate cancer may exist. The anti-androgen therapy can significantly change both the intratumor and gut microbiome.

CONCLUSION: With the progression and metastasis of prostate cancer, some intratumor microbiome changes. And anti-androgen influences both the intratumor and gut microbiome. Our discovery may help researchers further understand the progression, metastasis, and resistance of prostate cancer from the perspective of microbiome level.}, } @article {pmid39881387, year = {2025}, author = {Pangga, GM and Star-Shirko, B and Psifidi, A and Xia, D and Corcionivoschi, N and Kelly, C and Hughes, C and Lavery, U and Richmond, A and Ijaz, UZ and Gundogdu, O}, title = {Impact of commercial gut health interventions on caecal metagenome and broiler performance.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {30}, pmid = {39881387}, issn = {2049-2618}, support = {BB/T008709/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; EP/V030515/1//Engineering and Physical Sciences Research Council/ ; }, mesh = {Animals ; *Chickens/microbiology ; *Gastrointestinal Microbiome ; *Cecum/microbiology ; *Metagenome ; *Probiotics/administration & dosage ; Prebiotics ; Bacteria/classification/genetics/isolation & purification ; Animal Feed/microbiology ; Vaccination/veterinary ; Dietary Supplements ; }, abstract = {BACKGROUND: Maintaining gut health is a persistent and unresolved challenge in the poultry industry. Given the critical role of gut health in chicken performance and welfare, there is a pressing need to identify effective gut health intervention (GHI) strategies to ensure optimal outcomes in poultry farming. In this study, across three broiler production cycles, we compared the metagenomes and performance of broilers provided with ionophores (as the control group) against birds subjected to five different GHI combinations involving vaccination, probiotics, prebiotics, essential oils, and reduction of ionophore use.

RESULTS: Using a binning strategy, 84 (≥ 75% completeness, ≤ 5% contamination) metagenome-assembled genomes (MAGs) from 118 caecal samples were recovered and annotated for their metabolic potential. The majority of these (n = 52, 61%) had a differential response across all cohorts and are associated with the performance parameter - European poultry efficiency factor (EPEF). The control group exhibited the highest EPEF, followed closely by the cohort where probiotics are used in conjunction with vaccination. The use of probiotics B, a commercial Bacillus strain-based formulation, was determined to contribute to the superior performance of birds. GHI supplementation generally affected the abundance of microbial enzymes relating to carbohydrate and protein digestion and metabolic pathways relating to energy, nucleotide synthesis, short-chain fatty acid synthesis, and drug-transport systems. These shifts are hypothesised to differentiate performance among groups and cycles, highlighting the beneficial role of several bacteria, including Rikenella microfusus and UBA7160 species.

CONCLUSIONS: All GHIs are shown to be effective methods for gut microbial modulation, with varying influences on MAG diversity, composition, and microbial functions. These metagenomic insights greatly enhance our understanding of microbiota-related metabolic pathways, enabling us to devise strategies against enteric pathogens related to poultry products and presenting new opportunities to improve overall poultry performance and health. Video Abstract.}, } @article {pmid39881253, year = {2025}, author = {Garcia, I and Riis, RK and Moen, LV and Rohringer, A and Madslien, EH and Bragstad, K}, title = {Unsupervised detection of novel SARS-CoV-2 mutations and lineages in wastewater samples using long-read sequencing.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {87}, pmid = {39881253}, issn = {1471-2164}, mesh = {*Wastewater/virology ; *SARS-CoV-2/genetics/isolation & purification ; *COVID-19/virology/epidemiology ; Humans ; *Mutation ; *High-Throughput Nucleotide Sequencing/methods ; Spike Glycoprotein, Coronavirus/genetics ; Wastewater-Based Epidemiological Monitoring ; }, abstract = {The COVID-19 pandemic has underscored the importance of virus surveillance in public health and wastewater-based epidemiology (WBE) has emerged as a non-invasive, cost-effective method for monitoring SARS-CoV-2 and its variants at the community level. Unfortunately, current variant surveillance methods depend heavily on updated genomic databases with data derived from clinical samples, which can become less sensitive and representative as clinical testing and sequencing efforts decline.In this paper, we introduce HERCULES (High-throughput Epidemiological Reconstruction and Clustering for Uncovering Lineages from Environmental SARS-CoV-2), an unsupervised method that uses long-read sequencing of a single 1 Kb fragment of the Spike gene. HERCULES identifies and quantifies mutations and lineages without requiring database-guided deconvolution, enhancing the detection of novel variants.We evaluated HERCULES on Norwegian wastewater samples collected from July 2022 to October 2023 as part of a national pilot on WBE of SARS-CoV-2. Strong correlations were observed between wastewater and clinical sample data in terms of prevalence of mutations and lineages. Furthermore, we found that SARS-CoV-2 trends in wastewater samples were identified one week earlier than in clinical data.Our results demonstrate HERCULES' capability to identify new lineages before their detection in clinical samples, providing early warnings of potential outbreaks. The methodology described in this paper is easily adaptable to other pathogens, offering a versatile tool for environmental surveillance of new emerging pathogens.}, } @article {pmid39881163, year = {2025}, author = {Dash, M and Thiyageshwari, S and Selvi, D and Johnson, HKV and Ariyan, M and Rajan, K and Anandham, R}, title = {Unveiling microbial diversity in slightly and moderately magnesium deficient acidic soils.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {3696}, pmid = {39881163}, issn = {2045-2322}, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Magnesium/metabolism/analysis ; *RNA, Ribosomal, 16S/genetics ; India ; Bacteria/genetics/classification/metabolism ; Metagenomics/methods ; Biodiversity ; Magnesium Deficiency/genetics ; Phosphorus/deficiency/metabolism ; Microbiota/genetics ; }, abstract = {Magnesium (Mg) an essential plant nutrient is widespread deficient in the acidic soils of Nilgiris of Tamil nadu, India. The vegetable yield and quality is especially affected due to deficiency of nutrients like Mg. This study investigates soil characteristics and bacterial diversity in the Nilgiris district of Tamil Nadu, India, with respect to Mg deficiency. The soil samples were collected from different vegetable growing regions of the Nilgiris to assess soil physiocochemical parameters, soil enzymes and soil Mg status. 16S rRNA gene-based metagenomic analysis used to investigate the functional potential and structural diversity of the bacterial communities in high Mg and low Mg deficiency soil. Results indicated mildly acidic soils with a sandy loam texture and high organic carbon content. While nitrogen (N), phosphorus (P), and potassium (K) levels were adequate, Mg deficiency was consistent. Soil enzymes such as dehydrogenase, acid phosphatase, urease and aryl sulfatase, varied across the soil samples. Additionally, 16S rRNA gene-based metagenomics analysis revealed the bacterial diversity and functional pathways in soils with high and low Mg deficiency. Low Mg levels were associated with increased bacterial richness, dominated by Proteobacteria, Gemmatimonadetes, Actinobacteria, Bacteroidetes, and Acidobacteria. Functional pathways related to carbon metabolism, amino acid biosynthesis, and various metabolic processes were more abundant in low Mg deficient soils. This research highlights the significant influence of Mg levels on bacterial diversity and functional potentials in acidic soils, providing insights into soil management strategies in Mg-deficient regions.}, } @article {pmid39880958, year = {2025}, author = {Maghini, DG and Oduaran, OH and Olubayo, LAI and Cook, JA and Smyth, N and Mathema, T and Belger, CW and Agongo, G and Boua, PR and Choma, SSR and Gómez-Olivé, FX and Kisiangani, I and Mashaba, GR and Micklesfield, L and Mohamed, SF and Nonterah, EA and Norris, S and Sorgho, H and Tollman, S and Wafawanaka, F and Tluway, F and Ramsay, M and Wirbel, J and , and Bhatt, AS and Hazelhurst, S}, title = {Expanding the human gut microbiome atlas of Africa.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {39880958}, issn = {1476-4687}, support = {R01 AI148623/AI/NIAID NIH HHS/United States ; D43 TW010540/TW/FIC NIH HHS/United States ; R01 AI143757/AI/NIAID NIH HHS/United States ; U54 HG006938/HG/NHGRI NIH HHS/United States ; S10 OD023452/OD/NIH HHS/United States ; }, abstract = {Population studies provide insights into the interplay between the gut microbiome and geographical, lifestyle, genetic and environmental factors. However, low- and middle-income countries, in which approximately 84% of the world's population lives[1], are not equitably represented in large-scale gut microbiome research[2-4]. Here we present the AWI-Gen 2 Microbiome Project, a cross-sectional gut microbiome study sampling 1,801 women from Burkina Faso, Ghana, Kenya and South Africa. By engaging with communities that range from rural and horticultural to post-industrial and urban informal settlements, we capture a far greater breadth of the world's population diversity. Using shotgun metagenomic sequencing, we identify taxa with geographic and lifestyle associations, including Treponema and Cryptobacteroides species loss and Bifidobacterium species gain in urban populations. We uncover 1,005 bacterial metagenome-assembled genomes, and we identify antibiotic susceptibility as a factor that might drive Treponema succinifaciens absence in urban populations. Finally, we find an HIV infection signature defined by several taxa not previously associated with HIV, including Dysosmobacter welbionis and Enterocloster sp. This study represents the largest population-representative survey of gut metagenomes of African individuals so far, and paired with extensive clinical biomarkers and demographic data, provides extensive opportunity for microbiome-related discovery.}, } @article {pmid39880818, year = {2025}, author = {Jiang, ZJ and Hong, JC and Lin, BW and Zhang, WQ and Fan, QC and Yang, BH and Yao, XP}, title = {Comparison of mNGS with conventional methods for diagnosis of cryptococcal meningitis: a retrospective study.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {3656}, pmid = {39880818}, issn = {2045-2322}, support = {2019XQ1079//Startup Fund for Scientific Research of Fujian Medical University/ ; 82171841//National Natural Science Foundation of China/ ; 2020Y93010140//Joint Funds for the Innovation of Science and Technology, Fujian Province/ ; }, mesh = {*Meningitis, Cryptococcal/diagnosis/cerebrospinal fluid/microbiology ; Humans ; Retrospective Studies ; Male ; Female ; Middle Aged ; Adult ; *High-Throughput Nucleotide Sequencing/methods ; Aged ; Sensitivity and Specificity ; Metagenomics/methods ; Antigens, Fungal/cerebrospinal fluid/analysis ; Young Adult ; }, abstract = {The application of metagenomic next-generation sequencing (mNGS) in the diagnosis of cryptococcal meningitis is relatively under characterized. Here, we retrospectively evaluated data from cryptococcal meningitis patients who were tested using mNGS and/or routine testing, including fungal culture, India ink staining, and cryptococcal antigen (CrAg) testing. The performance of mNGS was then assessed. Initial cerebrospinal fluid (CSF) samples were collected from 65 patients with suspected central nervous system (CNS) infection and tested using conventional tests and/or mNGS. mNGS offers a culture-independent approach, facilitating a rapid and unbiased detection of a broad spectrum of pathogens. Patients with bacterial tuberculous or viral meningitis were used as mNGS-positive controls and one autoimmune encephalitis patient was used as an mNGS-negative control. In the 45 patients diagnosed with cryptococcal meningitis, the sensitivity, specificity, positive predictive value, negative predictive value, and concordance rate of mNGS were 92%, 100%, 100%, 90.9%, and 95.6%, respectively. Compared to conventional methods, the sensitivity of mNGS was slightly lower than CrAg tests (96.7%) but higher than India ink (79.5%) and culturing (63.4%). Of the two negative mNGS cases (2/25, 8.0%), one was positive by India ink staining, culture, and CrAg testing, while the other was positive only by CrAg testing. A combination of mNGS and conventional methods enhanced the detection rate to 100%. Our study demonstrates that both CrAg and mNGS offer excellent diagnostic accuracy for cryptococcal meningitis, and utilizing both tests can enhance clinical assessment and patient management.}, } @article {pmid39880110, year = {2025}, author = {Chen, N and Wang, L and Zhao, Z and Zhu, M and Li, Y}, title = {Impacts of aquaculture on nitrogen cycling and microbial community dynamics in coastal tidal flats.}, journal = {Environmental research}, volume = {270}, number = {}, pages = {120973}, doi = {10.1016/j.envres.2025.120973}, pmid = {39880110}, issn = {1096-0953}, abstract = {The expansion of aquaculture areas has encroached upon vast areas of coastal wetlands and introduced excessive nitrogen inputs, disrupting microbial communities and contributing to various environmental issues. However, investigations on how aquaculture affects microbial communities and nitrogen metabolism mechanisms in coastal tidal flats remain scarce. Hence, we explored the composition, diversity, and assembly processes of nitrogen-cycling (N-cycling) microbial communities in tidal flats in Jiangsu using metagenomic assembly methods. Our study further delved into the seasonal variations of these microbial characteristics to better explore the effects of seasonal changes in aquaculture areas on microbial community. Nitrogen metabolism-related processes and functional genes were identified through the KEGG and NCyc databases. The results revealed significant seasonal variation in the relative abundance and composition of microbial communities. Higher diversity was observed in winter, while the co-occurrence network of microbial communities was more complex in summer. Pseudomonadota emerged as the most abundant phylum in the N-cycling community. Furthermore, pH and NO3-N were identified as the primary factors influencing bacterial community composition, whereas NO2-N was more strongly associated with the N-cycling community. Regarding the nitrogen metabolism processes, nitrogen mineralization and nitrification were predominant in the tidal flat regions. NO2-N and NO3-N exhibited significant effects on several N-cycling functional genes (e.g., nirB, hao, and narG). Finally, neutral and null modeling analyses indicated that bacterial communities were predominantly shaped by stochastic processes, whereas N-cycling communities were largely driven by deterministic processes. These findings highlighted the significant role that aquaculture pollution plays in shaping the N-cycling communities in tidal flats. This underscored the importance of understanding microbial community dynamics and nitrogen metabolism in tidal flats to improve environmental management in coastal aquaculture areas.}, } @article {pmid39879767, year = {2025}, author = {Li, S and Bai, Y and Li, Z and Wang, A and Ren, NQ and Ho, SH}, title = {Overlooked role of extracellular polymeric substances in antibiotic-resistance gene transfer within microalgae-bacteria system.}, journal = {Journal of hazardous materials}, volume = {488}, number = {}, pages = {137206}, doi = {10.1016/j.jhazmat.2025.137206}, pmid = {39879767}, issn = {1873-3336}, abstract = {Controlling the spread of antibiotic-resistance genes (ARGs) under antibiotic stress has become an increasingly urgent issue. Microalgae possess the capability to remove antibiotics while concurrently inhibiting ARGs. Microalgae-bacteria systems can produce significant quantities of extracellular polymeric substances (EPS). However, the roles of EPS in the spread of ARGs have not been sufficiently explored, resulting in an insufficient understanding of the contribution of each EPS component and a lack of analysis on the complex interactions between EPS and ARGs. This study systematically explored the overlooked role of EPS in the transmission of ARGs within microalgae-bacteria systems. The current results showed that the potential of the microalgae-bacteria system for treating antibiotic wastewater. The tightly bound-EPS (TB-EPS) can acquire the higher absolute abundances of ARGs compared with the loosely bound-EPS (LB-EPS). The correlation coefficient between polysaccharides and TB-EPS ARGs was higher than that between polysaccharides and LB-EPS ARGs. The gene patterns of LB-EPS closely clustered with those of TB-EPS, while intracellular ARG gene patterns differed from both TB-EPS and LB-EPS. Metagenomic analyses indicated that the relative abundances of sul1 and sul2 were considerably higher at the beginning stage compared to the end stage. The abundance of Achromobacter, increased by the end stage, aligning with its potential to produce exopolysaccharide. Additionally, the absolute abundance of genes encoding exopolysaccharides (nagB and galE) and conjugative transfer transcription regulator (traF), increased over time. These findings enhanced our comprehension of the significance of EPS on the fate of ARGs in microalgae-bacteria systems during the treatment of antibiotic-contaminated wastewater.}, } @article {pmid39879766, year = {2025}, author = {Liu, X and Li, H and Yang, J and Yan, S and Zhou, Y and Jiang, R and Li, R and Wang, M and Ren, P}, title = {Different effects of bio/non-degradable microplastics on sewage sludge compost performance: Focusing on antibiotic resistance genes, virulence factors and key metabolic functions.}, journal = {Journal of hazardous materials}, volume = {488}, number = {}, pages = {137329}, doi = {10.1016/j.jhazmat.2025.137329}, pmid = {39879766}, issn = {1873-3336}, abstract = {Microplastics (MP) have aroused increasing concern due to the negative environmental impact. However, the impact of bio/non-biodegradable MPs on the sludge composting process has not been thoroughly investigated. This study examined antibiotic resistance genes (ARGs), virulence factors (VFs), and microbial community functions in sludge compost with the application of polylactic acid (PLA) and polypropylene (PP), using metagenomic sequencing. The findings indicated that both types of MPs could extend the thermophilic phase, enhance microbial activity, and inhibit the formation of humic acids. Compared to CK, the subtypes of ARGs decreased 4.22 % and 13.11 % in PLA and PP groups, respectively. But new ARGs emerged, particularly in the PLA group. The proportions of ARGs related to efflux and VFs associated with the adhesion system increased 1.62 %-2.27 % and 55.56 %-60.00 %, respectively, in MPs-added composts. The relative abundance of potential bacterial hosts (e.g., Psychrobacter) carrying multiple ARGs and VFs was much higher in PLA-added compost than in the other two. Moreover, PP facilitated denitrification process and PLA enhanced dissimilatory nitrate reduction to ammonium. Both types of MPs inhibited assimilatory nitrate reduction to ammonia but promoted inorganic nitrogen assimilation. This study broadens our understanding of the potential environmental risks posed by biodegradable and non-biodegradable microplastics on sludge compost and offers valuable insights for the management and application of compost products.}, } @article {pmid39879090, year = {2025}, author = {McReynolds, E and Elshahed, MS and Youssef, NH}, title = {An ecological-evolutionary perspective on the genomic diversity and habitat preferences of the Acidobacteriota.}, journal = {Microbial genomics}, volume = {11}, number = {1}, pages = {}, pmid = {39879090}, issn = {2057-5858}, support = {P20 GM152333/GM/NIGMS NIH HHS/United States ; }, mesh = {*Phylogeny ; *Ecosystem ; *Soil Microbiology ; *Acidobacteria/genetics/classification ; Genome, Bacterial ; Evolution, Molecular ; Metagenomics ; Genetic Variation ; }, abstract = {Members of the phylum Acidobacteriota inhabit a wide range of ecosystems including soils. We analysed the global patterns of distribution and habitat preferences of various Acidobacteriota lineages across major ecosystems (soil, engineered, host-associated, marine, non-marine saline and alkaline and terrestrial non-soil ecosystems) in 248 559 publicly available metagenomic datasets. Classes Terriglobia, Vicinamibacteria, Blastocatellia and Thermoanaerobaculia were highly ubiquitous and showed a clear preference to soil over non-soil habitats, while classes Aminicenantia and Holophagae showed preferences to non-soil habitats. However, while specific preferences were observed, most Acidobacteriota lineages were habitat generalists rather than specialists, with genomic and/or metagenomic fragments recovered from soil and non-soil habitats at various levels of taxonomic resolution. Comparative analysis of 1930 genomes strongly indicates that phylogenetic affiliation plays a more important role than the habitat from which the genome was recovered in shaping the genomic characteristics and metabolic capacities of the Acidobacteriota. The observed lack of strong habitat specialization and habitat-transition-driven lineage evolution in the Acidobacteriota suggest ready cross-colonization between soil and non-soil habitats. We posit that such capacity is key to the successful establishment of Acidobacteriota as a major component in soil microbiomes post-ecosystem disturbance events or during pedogenesis.}, } @article {pmid39878481, year = {2025}, author = {Ragupathy, V and Kelley, K and Hewlett, I}, title = {Identification of near full-length human pegivirus type 2 (HPgV-2) genomes in blood donor samples co-infected with hepatitis C virus (HCV).}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0117924}, doi = {10.1128/mra.01179-24}, pmid = {39878481}, issn = {2576-098X}, abstract = {Human pegivirus (HPgV) identified from an HCV-infected plasma sample through nanopore metagenomics. The analysis revealed a nearly complete HPgV-2 genome. Phylogenetic analysis confirmed its classification within the HPgV-2 genotype, providing insights into viral co-infection dynamics. The metagenomics approach advances the understanding of viral diversity and supports the development of accurate diagnostics.}, } @article {pmid39878462, year = {2025}, author = {Ho, JY and Hu, D and Case, RJ and Boucher, YF}, title = {Metagenome-assembled genomes (MAGs) of the emerging pathogen Shewanella algae from enrichment of coastal seawater, sediment, and algae at St. John's Island, Singapore.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0084624}, doi = {10.1128/mra.00846-24}, pmid = {39878462}, issn = {2576-098X}, abstract = {Coastal water, sediment, and algae samples were collected from St. John's Island, Singapore, and enriched in either broth or agar. Metagenomic sequencing was carried out on DNA from these enrichments and analyzed. A total of 29 metagenome-assembled genomes had been successfully asserted to be a close representation of Shewanella algae.}, } @article {pmid39877883, year = {2024}, author = {Takano, Y and Takekoshi, S and Takano, K and Matoba, Y and Mukumoto, M and Sowa, K and Kitazumi, Y and Shirai, O}, title = {A suitable solvent for adsorption of poorly water-soluble substances onto silica gel in a ready biodegradability test.}, journal = {Journal of pesticide science}, volume = {49}, number = {4}, pages = {271-276}, pmid = {39877883}, issn = {1348-589X}, abstract = {When a test substance is poorly water-soluble, it can be adsorbed onto silica gel to facilitate dispersibility in a ready biodegradability test. To uniformly adsorb the test substance onto silica gel, the substance is dissolved in a solvent and then mixed with the silica gel. It is desirable for the solvent to completely evaporate afterward. In this study, we identified n-hexane as a suitable solvent for this purpose. Furthermore, through fluorescence observation, we revealed that the test substance adsorbed onto the silica gel adhered to activated sludge flocs. This is thought to improve contact between the test substance and microorganisms, thereby accelerating biodegradation.}, } @article {pmid39877881, year = {2024}, author = {Takano, Y and Takekoshi, S and Takano, K and Matoba, Y and Mukumoto, M and Sowa, K and Kitazumi, Y and Shirai, O}, title = {Comparative evaluation of trimethylated α-, β-, and γ-cyclodextrins as optimal dispersants for ready biodegradability testing of poorly water-soluble substances.}, journal = {Journal of pesticide science}, volume = {49}, number = {4}, pages = {210-223}, pmid = {39877881}, issn = {1348-589X}, abstract = {We investigated whether various modified cyclodextrins (CDs) and emulsifiers could be applied as dispersing agents in ready biodegradability tests of poorly water-soluble substances. Trimethylated α-, β-, and γ-CDs and partially methylated β-CD were not biodegraded in the test period but accelerated the biodegradation of octabenzone and anthraquinone. The process by which trimethylated α-, β-, and γ-CDs enhance the biodegradation of test substances has been partially uncovered. These CDs create inclusion complexes with the substances, which then coalesce into larger aggregates. These aggregates disperse throughout the testing medium and attach to clusters of activated sludge, known as flocs. This close contact with the sludge speeds up the breakdown of the hydrophobic substances being tested.}, } @article {pmid39877811, year = {2025}, author = {Latif, S and Kousar, R and Fatima, A and Khan, N and Fatimah, H}, title = {Internal transcribed spacer metagenomics data unravelling the core fungal community structure residing the wheat and maize rhizosphere.}, journal = {Data in brief}, volume = {58}, number = {}, pages = {111269}, pmid = {39877811}, issn = {2352-3409}, abstract = {Plants are colonized by a vast array of microorganisms that outstrip plant cell densities and genes, thus referred to as plant's second genome or extended genome. The microbial communities exert a significant influence on the vigor, growth, development and productivity of plants by supporting nutrient acquisition, organic matter decomposition and tolerance against biotic and abiotic stresses such as heat, high salt, drought and disease, by regulating plant defense responses. The rhizosphere is a complex micro-ecological zone in the direct vicinity of plant roots and is considered a hotspot of microbial diversity. The exploration and understanding of the rhizosphere microbes can be valuable in sustainable agriculture. The present dataset aimed to reveal the core fungal community residing in the rhizosphere of wheat (Triticum aestivum L.) and maize (Zea mays L.). The rhizosphere fungal communities were explored via amplicon sequencing of the Internal Transcribed Spacer (ITS) region using the IonS5[TM]XL sequencing platform. The data obtained were filtered and the high-quality reads were clustered into Microbial Operational Taxonomic Units (OTUs) at 97 % similarity. Further, the data were subjected to alpha and beta diversity analysis. The OTUs obtained from the wheat rhizosphere soils of Kallar Syedian (TA.KS), Islamabad (TA.ISB) and Mirpur Azad Kashmir (TA.MAK) were 603, 513 and 424, respectively, whereas 616 OTUs were found in the maize rhizosphere soil of Kallar Syedian (ZM.KS). The major fungal phyla inhabiting the rhizosphere soils were Ascomycota, accounting for 94 %, 97 %, 95 % and 90 % of the fungal community in ZM.KS, TA.KS, TA.MAK and TA.ISB, respectively. Alpha and beta diversity analysis depicted the presence of considerable variations in the relative abundance of fungal groups residing in the rhizosphere soils. The dataset obtained can be employed in meta-analysis studies that will pave the way toward understanding the core fungal community structure and will directly aid in enhancing crop productivity through rhizosphere engineering.}, } @article {pmid39877399, year = {2025}, author = {Park, SY and Goldman, JD and Levine, DJ and Haidar, G}, title = {A Systematic Literature Review to Determine Gaps in Diagnosing Suspected Infection in Solid Organ Transplant Recipients.}, journal = {Open forum infectious diseases}, volume = {12}, number = {1}, pages = {ofaf001}, pmid = {39877399}, issn = {2328-8957}, abstract = {BACKGROUND: Improved diagnostic testing (DT) of infections may optimize outcomes for solid organ transplant recipients (SOTR), but a comprehensive analysis is lacking.

METHODS: We conducted a systematic literature review across multiple databases, including EMBASE and MEDLINE(R), of studies published between 1 January 2012-11 June 2022, to examine the evidence behind DT in SOTR. Eligibility criteria included the use of conventional diagnostic methods (culture, biomarkers, directed-polymerase chain reaction [PCR]) or advanced molecular diagnostics (broad-range PCR, metagenomics) to diagnose infections in hospitalized SOTR. Bias was assessed using tools such as the Cochrane Handbook and PRISMA 2020.

RESULTS: Of 2362 studies, 72 were eligible and evaluated heterogeneous SOT populations, infections, biospecimens, DT, and outcomes. All studies exhibited bias, mainly in reporting quality. Median study sample size was 102 (range, 11-1307). Culture was the most common DT studied (N = 45 studies, 62.5%), with positive results in a median of 27.7% (range, 0%-88.3%). Biomarkers, PCR, and metagenomics were evaluated in 7, 19, and 3 studies, respectively; only 6 reported sensitivity, specificity, and positive/negative predictive values. Directed-PCR performed well for targeted pathogens, but only 1 study evaluated broad-range PCR. Metagenomics approaches detected numerous organisms but required clinical adjudication, with too few studies (N = 3) to draw conclusions. Turnaround time was shorter for PCR/metagenomics than conventional diagnostic methods (N = 4 studies, 5.6%). Only 6 studies reported the impact of DT on outcomes like antimicrobial use and length of stay.

CONCLUSIONS: We identified considerable evidence gaps in infection-related DT among SOT, particularly molecular DT, highlighting the need for further research.}, } @article {pmid39877321, year = {2025}, author = {Ito, E and Ohki, T and Toya, N and Emoto, T and Yamashita, T and Sugiyama, T and Yamada, T and Mori, H and Toyoda, A and Hirata, KI}, title = {Metagenomic Analysis of Gut Microbiota for Abdominal Aortic Aneurysm.}, journal = {Annals of vascular diseases}, volume = {18}, number = {1}, pages = {}, pmid = {39877321}, issn = {1881-641X}, abstract = {Objectives: The pathophysiological mechanism of abdominal aortic aneurysm (AAA) remains unclear. We previously reported that Bifidobacterium adolescentis levels were reduced in the feces of patients with AAA by 16S ribosomal ribonucleic acid (RNA) gene sequencing. In this study, we increased the number of cases and conducted metagenomic analyses to examine bacterial genes associated with the pathophysiology of AAA. Methods: For gut microbiota data, feces from 55 patients with AAA and 52 patients with no history of AAA, lower extremity artery disease, or coronary artery disease (control group) were collected. Metagenomic analysis was performed by collecting raw stool samples from patients. For intestinal microbiota analysis, metagenomic analysis of the fecal samples was performed. Results: Oral bacteria, including Actinomyces oris (p <0.0001), Streptococcus salivarius (p <0.001), Lactobacillus salivarius (p <0.001), and Streptococcus sp. (p <0.001), were increased in the feces of patients with AAA. In addition, bacterial genes related to alpha lipoic acid (ALA) biosynthesis (M00882, M00883, and M00884, p <0.0001) were decreased in patients with AAA. Conclusions: In the feces of patients with AAA, there was an increase in oral bacteria, and the expression of bacterial genes related to ALA biosynthesis was reduced. The results suggest the possibility of developing gut microbial drug treatments for AAA.}, } @article {pmid39877152, year = {2025}, author = {Plewka, J and Alibrandi, A and Bornemann, TLV and Esser, SP and Stach, TL and Sures, K and Becker, J and Moraru, C and Soares, A and di Primio, R and Kallmeyer, J and Probst, AJ}, title = {Metagenomic analysis of pristine oil sheds new light on the global distribution of microbial genetic repertoire in hydrocarbon-associated ecosystems.}, journal = {microLife}, volume = {6}, number = {}, pages = {uqae027}, pmid = {39877152}, issn = {2633-6693}, abstract = {Oil reservoirs are society's primary source of hydrocarbons. While microbial communities in industrially exploited oil reservoirs have been investigated in the past, pristine microbial communities in untapped oil reservoirs are little explored, as are distribution patterns of respective genetic signatures. Here, we show that a pristine oil sample contains a complex community consisting of bacteria and fungi for the degradation of hydrocarbons. We identified microorganisms and their pathways for the degradation of methane, n-alkanes, mono-aromatic, and polycyclic aromatic compounds in a metagenome retrieved from biodegraded petroleum encountered in a subsurface reservoir in the Barents Sea. Capitalizing on marker genes from metagenomes and public data mining, we compared the prokaryotes, putative viruses, and putative plasmids of the sampled site to those from 10 other hydrocarbon-associated sites, revealing a shared network of species and genetic elements across the globe. To test for the potential dispersal of the microbes and predicted elements via seawater, we compared our findings to the Tara Ocean dataset, resulting in a broad distribution of prokaryotic and viral signatures. Although frequently shared between hydrocarbon-associated sites, putative plasmids, however, showed little coverage in the Tara Oceans dataset, suggesting an undiscovered mode of transfer between hydrocarbon-affected ecosystems. Based on our analyses, genetic information is globally shared between oil reservoirs and hydrocarbon-associated sites, and we propose that currents and other physical occurrences within the ocean along with deep aquifers are major distributors of prokaryotes and viruses into these subsurface ecosystems.}, } @article {pmid39876557, year = {2025}, author = {Morsink, MC and van Schaik, EN and Bossers, K and Duijker, DA and Speksnijder, AGCL}, title = {Metagenomics education in a modular CURE format positively affects students' scientific discovery perception and data analytical skills.}, journal = {Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology}, volume = {}, number = {}, pages = {}, doi = {10.1002/bmb.21888}, pmid = {39876557}, issn = {1539-3429}, abstract = {Targeted metagenomics is a rapidly expanding technology to analyze complex biological samples and genetic monitoring of environmental samples. In this research field, data analytical aspects play a crucial role. In order to teach targeted metagenomics data analysis, we developed a 4-week inquiry-driven modular course-based undergraduate research experience (mCURE) using publicly available Australian coral microbiome DNA sequencing data and associated metadata. Since an enormous amount of metadata was provided alongside the DNA sequencing data, groups of students were able to develop their own authentic research questions. Throughout the course, the student groups worked on these research questions and were supported with bioinformatics and statistics lessons. Additionally, practical aspects of data collection and analysis were addressed during hands-on field work on a nearby Dutch beach. Evaluation of the course indicated that the majority of students (1) achieved the intended metagenomics-based learning outcomes and (2) experienced scientific discovery while working on their research projects. In conclusion, the huge amount of data and metadata available in the coral microbiome data set facilitated the development of a strongly inquiry-driven course. Different groups of students were able to develop and conduct their own distinct microbiome research projects and our current mCURE format positively affected students' metagenomics data analytical skills and scientific discovery perception.}, } @article {pmid39876003, year = {2025}, author = {Li, Q and Huo, J and Ni, G and Zhang, F and Zhang, S and Zhang, X and Wang, R and Jiao, J and Yu, Z and Pu, X and Yue, Y and Ungerfeld, EM and Zhang, X and Wu, J and Tan, Z and Greening, C and Wang, M}, title = {Reductive acetogenesis is a dominant process in the ruminant hindgut.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {28}, pmid = {39876003}, issn = {2049-2618}, mesh = {Animals ; *Rumen/microbiology ; *Goats/microbiology ; *Cecum/microbiology ; *Hydrogen/metabolism ; *Bacteria/classification/metabolism/genetics/isolation & purification ; *Gastrointestinal Microbiome ; *Fermentation ; *Acetates/metabolism ; *Fatty Acids, Volatile/metabolism ; Archaea/classification/metabolism/genetics ; Ruminants/microbiology ; Methane/metabolism ; }, abstract = {BACKGROUND: The microbes residing in ruminant gastrointestinal tracts play a crucial role in converting plant biomass to volatile fatty acids, which serve as the primary energy source for ruminants. This gastrointestinal tract comprises a foregut (rumen) and hindgut (cecum and colon), which differ in structures and functions, particularly with respect to feed digestion and fermentation. While the rumen microbiome has been extensively studied, the cecal microbiome remains much less investigated and understood, especially concerning the assembling microbial communities and overriding pathways of hydrogen metabolism.

RESULTS: To address this gap, we comparatively investigated the composition, capabilities, and activities of the rumen and the cecum microbiome using goats as an experimental ruminant model. In situ measurements showed significantly higher levels of dissolved hydrogen and acetate in the cecum than in the rumen. Increased dissolved hydrogen indicated distinct processes and reduced coupling between fermentative H2 production and utilization, whereas higher levels of acetate could be caused by slower VFA absorption through cecal papillae than through the rumen papillae. Microbial profiling indicated that the cecum harbors a greater abundance of mucin-degrading microbes and fermentative hydrogen producers, whereas the rumen contains a higher abundance of fibrolytic fermentative bacteria, hydrogenotrophic respiratory bacteria, and methanogenic archaea. Most strikingly, reductive acetogenic bacteria were 12-fold more abundant in the cecum. Genome-resolved metagenomic analysis unveiled that the cecum acetogens are both phylogenetically and functionally distinct from those found in the rumen. Further supporting these findings, two in vitro experiments demonstrated a marked difference in hydrogen metabolism pathways between the cecum and the rumen, with increased acetate production and reduced methanogenesis in the cecum. Moreover, comparative analysis across multiple ruminant species confirmed a strong enrichment of reductive acetogens in the hindguts, suggesting a conserved functional role.

CONCLUSIONS: These findings highlight an enrichment of acetogenesis in a key region of the gastrointestinal tract and reshape our understanding of ruminant hydrogen metabolism and how the H2 can be managed in accord to livestock methane mitigation efforts. Video Abstract.}, } @article {pmid39875829, year = {2025}, author = {Zhang, Z and Zong, X and Liu, Z and Dong, X and Bai, H and Fan, L and Li, T}, title = {Comprehensive analysis of vaginal microbiota in Chinese women with genital tuberculosis: implications for diagnosis and treatment.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {52}, pmid = {39875829}, issn = {1471-2180}, support = {2024-4-2119//Capital's Funds for Health Improvement and Research/ ; FCYY201916//Special Training Program for Young and Middle-aged Subject Backbone of Beijing Obstetrics and Gynecology Hospital, Capital Medical University/ ; YQRC201906//"Excellent young Talents" project of Beijing Obstetrics and Gynecology Hospital, Capital Medical University/ ; }, mesh = {Humans ; Female ; *Vagina/microbiology ; Adult ; *Tuberculosis, Female Genital/microbiology/diagnosis ; *Microbiota ; China ; Middle Aged ; Young Adult ; Antitubercular Agents/therapeutic use ; Lactobacillus/isolation & purification/genetics ; Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; East Asian People ; }, abstract = {BACKGROUND: Tuberculosis remains an infectious disease of global concern, with potential impacts on respiratory and intestinal microbiota owing to prolonged broad-spectrum antibiotic therapy. Despite its potential to cause infertility, the vaginal microbiota of women with genital tuberculosis remains poorly understood. We comprehensively analyzed the vaginal microbiota in Chinese women with genital tuberculosis.

RESULTS: We recruited women with pelvic (n = 28), endometrial (n = 16), and pulmonary (n = 12) tuberculosis as the research group, and healthy women (n = 11) as the control group. Vaginal discharges were collected for metagenomic analysis of its microbiota. The alpha diversity of the vaginal microbiota in women with genital tuberculosis was slightly higher than that in healthy women, though the difference was not statistically significant (P = 0.23). Similarly, no significant differences in alpha diversity were observed between women with genital and pulmonary tuberculosis (P = 0.82) or between those with pelvic and endometrial tuberculosis (P = 0.82). Notably, the lowest alpha diversity was recorded six months to one year after initiating anti-tuberculosis treatment, with this decline being statistically significant (P = 0.023). The dominance of Lactobacillus iners in the vaginal microbiota was more common in women with genital tuberculosis than that of Lactobacillus crispatus. Furthermore, the abundance of short-chain fatty acid -producing anaerobes, such as Actinomycetes, Streptococcus, and Finegoldia, were significantly increased. Short-chain fatty acid precursor pathways, including the ko03010 ribosome pathway, ko00970 aminoacyl-tRNA synthesis, ko00230 purine metabolism, ko00240 pyrimidine metabolism, and ko00010 glycolysis gluconeogenesis pathway, were significantly upregulated in women with endometrial tuberculosis.

CONCLUSIONS: Extrapulmonary tuberculosis, particularly genital tuberculosis and its associated vaginal dysbiosis impacts female fecundity. Vaginal dysbiosis is more pronounced when M. tuberculosis invades the endometrium. Given the effect of antibiotics on vaginal flora, probiotic combined interventions could be used as a future research direction.

CLINICAL TRIAL NUMBER: Not applicable.}, } @article {pmid39875797, year = {2025}, author = {Sung, YH and Ju, YK and Lee, HJ and Park, SM and Suh, JW and Kim, JY and Sohn, JW and Yoon, YK}, title = {Clinical performance of real-time nanopore metagenomic sequencing for rapid identification of bacterial pathogens in cerebrospinal fluid: a pilot study.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {3493}, pmid = {39875797}, issn = {2045-2322}, support = {Q2021541//Yuhan/ ; HI23C1297//Ministry of Health and Welfare/ ; }, mesh = {Humans ; Pilot Projects ; Female ; Male ; *Meningitis, Bacterial/cerebrospinal fluid/diagnosis/microbiology ; *Metagenomics/methods ; Middle Aged ; *Nanopore Sequencing/methods ; *RNA, Ribosomal, 16S/genetics ; Adult ; *Bacteria/genetics/isolation & purification/classification ; Aged ; Nanopores ; Cerebrospinal Fluid/microbiology ; Young Adult ; Sensitivity and Specificity ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {This study aimed to evaluate the usefulness of amplicon-based real-time metagenomic sequencing applied to cerebrospinal fluid (CSF) for identifying the causative agents of bacterial meningitis. We conducted a 16S rRNA amplicon sequencing using a nanopore-based platform, alongside routine polymerase chain reaction (PCR) testing or bacterial culture, to compare its clinical performance in pathogen detection on CSF samples. Among 17 patients, nanopore-based sequencing, multiplex PCR, and bacterial culture detected potential bacterial pathogens in 47.1%, 0%, and 47.1% samples, respectively. Nanopore-based sequencing demonstrated a sensitivity of 50.0%, specificity of 55.6%, positive predictive value of 50.0%, negative predictive value of 55.6%, and overall accuracy of 47.1%, compared to the gold standard method for bacterial culture. In 44.4% (4/9) of culture-negative cases, nanopore-based sequencing detected potentially causative pathogens, whereas four (23.5%) patients were positive only in culture. Using nanopore-based sequencing alongside bacterial culture increased the positivity rate from 47.1 to 70.6%. However, these values may be overestimated due to challenges in distinguishing significant pathogens from background noise. Meanwhile, the bioinformatics module in EPI2ME reduced the turn-around time to 10 min. Nanopore-based metagenomic sequencing is expected to serve as a complementary tool for pathogen detection in CSF samples by facilitating rapid and accurate diagnosis.}, } @article {pmid39875095, year = {2025}, author = {Moeller, AH}, title = {Partner fidelity, not geography, drives co-diversification of gut microbiota with hominids.}, journal = {Biology letters}, volume = {21}, number = {1}, pages = {20240454}, pmid = {39875095}, issn = {1744-957X}, support = {/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Phylogeny ; Hominidae/microbiology ; Bacteria/classification/genetics/isolation & purification ; Genome, Bacterial ; Geography ; }, abstract = {Bacterial strains that inhabit the gastrointestinal tracts of hominids have diversified in parallel (co-diversified) with their host species. The extent to which co-diversification has been mediated by partner fidelity between strains and hosts or by geographical distance between hosts is not clear due to a lack of strain-level data from clades of hosts with unconfounded phylogenetic relationships and geographical distributions. Here, I tested these competing hypotheses through meta-analyses of 7121 gut bacterial genomes assembled from wild-living ape species and subspecies sampled throughout their ranges in equatorial Africa. Across the gut bacterial phylogeny, strain diversification was more strongly associated with host phylogeny than with geography. In total, approximately 14% of the branch length of the gut bacterial phylogeny showed significant evidence of co-diversification independent of geography, whereas only approximately 4% showed significant evidence of diversification associated with geography independent of host phylogeny. Geographically co-occurring heterospecific hosts (Pan and Gorilla) universally maintained distinct co-diversified bacterial strains. Strains whose diversification was associated with geography independent of host phylogeny included clades of Proteobacteria known to adopt free-living lifestyles (e.g. Escherichia). These results show that co-diversification of gut bacterial strains with hominids has been driven primarily by fidelity of strains to host lineages rather than geography.}, } @article {pmid39875062, year = {2025}, author = {Zhan, M and Li, Z and Chen, J and Zhao, Y and Bai, Z and Lu, B and Chen, H and Liu, Y}, title = {Indoxyl sulfate (IS) mediates pro-inflammatory responses in severe pneumonia in patients with rheumatoid arthritis associated interstitial lung disease.}, journal = {Clinical immunology (Orlando, Fla.)}, volume = {}, number = {}, pages = {110430}, doi = {10.1016/j.clim.2025.110430}, pmid = {39875062}, issn = {1521-7035}, abstract = {OBJECT: Patients with rheumatoid arthritis-associated interstitial lung disease (RA-ILD) have a high risk of serious infection, in particular severe pneumonia. This study aimed to investigate the transcriptional landscape, lower respiratory tract (LRT) microbiome and metabolomic profiles in the lung of RA-ILD patients with pneumonia.

METHOD: A total of 10 RA-ILD with pneumonia were enrolled in this study. In addition, 11 patients with COVID-19-associated pneumonia and 6 patients with non-autoimmune and non-COVID-19-related ILD with pneumonia were included as controls. Bronchoalveolar lavage fluid (BALF) was collected and prepared for metagenomic next-generation sequencing (mNGS), non-targeted metabolomics and bulk RNA-seq.

RESULT: Neutrophil-related genes were shared in the BALF cells of RA-ILD patients with pneumonia and patients with COVID-19-associated pneumonia. Carnobacterium, Wujia, Intestinimonas, Apibacter, Anaerotignum and Parvimonas were enriched in the LRT microbiome of RA-ILD, while Wujia, Apibacter, Pseudocitrobacter, and Thermobacillus were enriched in the LRT microbiome of COVID-19. Metabolomics analysis of BALF revealed significant elevation of indoxyl sulfate (IS) in the BALF of RA-ILD patients in comparison to COVID-19. Mechanistically, IS exerts an pro-inflammatory effect on macrophages and bronchial epithelial cells for pro-inflammatory cytokine production and potentiated neutrophils for neutrophil extracellular traps (NETs) formation.

CONCLUSIONS: Our results demonstrated a significant differences in the LRT microbiome and BALF metabolites between RA-ILD and COVID-19 patients with pneumonia, although they displayed similar local immune responses against lung infection. Alterations of LRT microbiome and related metabolites may be implicated in the pathogenesis of pneumonia in RA-ILD.}, } @article {pmid39874761, year = {2025}, author = {Wang, R and Chen, J and Chen, H}, title = {Metagenomic insights into efficiency and mechanism of antibiotic resistome reduction by electronic mediators-enhanced microbial electrochemical system.}, journal = {Journal of hazardous materials}, volume = {488}, number = {}, pages = {137350}, doi = {10.1016/j.jhazmat.2025.137350}, pmid = {39874761}, issn = {1873-3336}, abstract = {Electronic mediators are an effective means of enhancing the efficiency of microbial electrochemical electron transfer; however, there are still gaps in understanding the strengthening mechanisms and the efficiency of removing antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB). This study systematically elucidates the effects of various electron mediators on bioelectrochemical processes, electron transfer efficiency, and the underlying mechanisms that inhibit ARG propagation within sediment microbial fuel cell systems (SMFCs). The results indicate that the addition of electron mediators significantly increased the output voltage (33.3 %-61.1 %) and maximum power density (14 %-106 %) of SMFCs, while also reducing ARB abundance and transmission risk. The enhancement effect follows the order of biochar, nanoscale zero-valent iron, graphene, and carbon nanotubes, with biochar emerging as the most economical and efficient choice for generating electricity and removing human pathogenic bacteria carrying ARGs. Procrustes analysis revealed that electron mediators facilitated the removal of ARGs by altering the structure of the microbiome, particularly the electricity-generating microorganisms (EGMs). Voltage and mobile genetic elements were the primary drivers of ARGs in the SMFCs. The network analysis results show that multiple carbohydrate-active enzymes, cluster of orthologous groups, and EGMs were negatively correlated with ARGs, indicating that the electron mediator-enhanced SMFCs mainly inhibit the spread of ARGs by promoting cell division, carbohydrate metabolism, and electricity generation. This study provides novel insights into how electron mediators affect ARG removal in microbial electrochemistry, which can inform economically viable strategies for sustainable environmental remediation.}, } @article {pmid39874694, year = {2025}, author = {Wang, H and Dai, H and Jiang, D and Cao, X and Wang, R and Dai, Z and Zhang, W and Abbasi, HN and Li, B and Zhu, G and Wang, X}, title = {Screening, identification, and application of anaerobic ammonia oxidizing bacteria in activated sludge systems: A comprehensive review.}, journal = {Journal of environmental management}, volume = {375}, number = {}, pages = {124272}, doi = {10.1016/j.jenvman.2025.124272}, pmid = {39874694}, issn = {1095-8630}, mesh = {*Sewage/microbiology ; *Ammonia/metabolism ; Oxidation-Reduction ; Anaerobiosis ; RNA, Ribosomal, 16S/genetics ; Bacteria, Anaerobic/metabolism ; Nitrogen/metabolism ; Bacteria/metabolism/genetics ; Waste Disposal, Fluid/methods ; }, abstract = {Anaerobic ammonium oxidation (Anammox) has garnered significant attention due to its ability to eliminate the need for aeration and supplementary carbon sources in biological nitrogen removal process, relying on the capacity of anaerobic ammonium oxidizing bacteria (AnAOB) to directly convert ammonium and nitrite nitrogen into nitrogen gas. This review consolidates the latest advancements in AnAOB research, outlining the mechanisms and enzymatic processes of Anammox, and summarizing the molecular biological techniques used for studying AnAOB, such as 16s rRNA sequencing, qPCR, and metagenomic sequencing. Additionally, it also overviews the currently identified AnAOB species and their distinct metabolic traits, while consolidating strategies to improve their performance. It further delineates coupled processes that utilize Anammox technology, offering practical insights for process selection. Eventually, the review concludes by suggesting future research directions and highlighting critical areas for further investigation. This review serves as a theoretical reference for the enrichment and cultivation of AnAOB, environmental impact management, and the selection of effective treatment processes.}, } @article {pmid39874239, year = {2025}, author = {Zhou, H and Balint, D and Shi, Q and Vartanian, T and Kriegel, MA and Brito, I}, title = {Lupus and inflammatory bowel disease share a common set of microbiome features distinct from other autoimmune disorders.}, journal = {Annals of the rheumatic diseases}, volume = {84}, number = {1}, pages = {93-105}, doi = {10.1136/ard-2024-225829}, pmid = {39874239}, issn = {1468-2060}, mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology/immunology ; *Lupus Erythematosus, Systemic/microbiology/immunology ; *Gastrointestinal Microbiome/genetics ; *Autoimmune Diseases/microbiology/immunology ; Biomarkers ; Female ; Metagenomics/methods ; Metagenome ; Male ; Receptors, Glucocorticoid/genetics ; }, abstract = {OBJECTIVES: This study aims to elucidate the microbial signatures associated with autoimmune diseases, particularly systemic lupus erythematosus (SLE) and inflammatory bowel disease (IBD), compared with colorectal cancer (CRC), to identify unique biomarkers and shared microbial mechanisms that could inform specific treatment protocols.

METHODS: We analysed metagenomic datasets from patient cohorts with six autoimmune conditions-SLE, IBD, multiple sclerosis, myasthenia gravis, Graves' disease and ankylosing spondylitis-contrasting these with CRC metagenomes to delineate disease-specific microbial profiles. The study focused on identifying predictive biomarkers from species profiles and functional genes, integrating protein-protein interaction analyses to explore effector-like proteins and their targets in key signalling pathways.

RESULTS: Distinct microbial signatures were identified across autoimmune disorders, with notable overlaps between SLE and IBD, suggesting shared microbial underpinnings. Significant predictive biomarkers highlighted the diverse microbial influences across these conditions. Protein-protein interaction analyses revealed interactions targeting glucocorticoid signalling, antigen presentation and interleukin-12 signalling pathways, offering insights into possible common disease mechanisms. Experimental validation confirmed interactions between the host protein glucocorticoid receptor (NR3C1) and specific gut bacteria-derived proteins, which may have therapeutic implications for inflammatory disorders like SLE and IBD.

CONCLUSIONS: Our findings underscore the gut microbiome's critical role in autoimmune diseases, offering insights into shared and distinct microbial signatures. The study highlights the potential importance of microbial biomarkers in understanding disease mechanisms and guiding treatment strategies, paving the way for novel therapeutic approaches based on microbial profiles.

TRIAL REGISTRATION NUMBER: NCT02394964.}, } @article {pmid39873828, year = {2025}, author = {Pal, S and Biswas, R and Sar, A and Misra, A and Dam, S and Dam, B}, title = {ABC-type salt tolerance transporter genes are abundant and mutually shared among the microorganisms of the hypersaline Sambhar Lake.}, journal = {Extremophiles : life under extreme conditions}, volume = {29}, number = {1}, pages = {14}, pmid = {39873828}, issn = {1433-4909}, mesh = {*Salt Tolerance ; *Lakes/microbiology ; *ATP-Binding Cassette Transporters/genetics/metabolism ; Metagenome ; India ; Bacterial Proteins/genetics/metabolism ; }, abstract = {To fish-out novel salt-tolerance genes, metagenomic DNA of moderately saline sediments of India's largest hypersaline Sambhar Lake was cloned in fosmid. Two functionally-picked clones helped the Escherichia coli host to tolerate 0.6 M NaCl. Deep sequencing of their fosmid DNA insert revealed 32-37% of genes to encode transporters, mostly belonging to ABC (ATP-Binding Cassette)-type, but none specific to channel Na[+]. The complete metagenome sequence of Sambhar Lake brines, and reanalysed data of twelve other hypersaline metagenome sequences, however, have only around 5% transporter genes, suggesting metagenomic DNA fragments being biasedly-cloned during functional screening. Almost half of the ~ 40 Kb inserts in the two clones was shared, and encode several transporters, and some transposase. This advocates that these transporter-loaded DNA lengths are shuttled among microorganisms of hypersaline environments. Interestingly, one clone showed retarded growth with prominent cell disruptions in scanning electron microscopic images, when fosmid copy number was increased or transporters were NaCl-induced. Its cloned insert exclusively has three genes, encoding a structurally functional ATP-binding protein and its efflux component, whose possible overexpression led to membrane crowding and cell rupture. Thus, microorganisms thriving in hypersaline lakes have plentiful ABC transporters that are mutually shared among themselves. These novel salt tolerance genes have future agricultural biotechnological potential.}, } @article {pmid39873521, year = {2025}, author = {Pu, G and Hou, L and Zhao, Q and Liu, G and Wang, Z and Zhou, W and Niu, P and Wu, C and Li, P and Huang, R}, title = {Interactions between gut microbes and host promote degradation of various fiber components in Meishan pigs.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0150024}, doi = {10.1128/msystems.01500-24}, pmid = {39873521}, issn = {2379-5077}, abstract = {UNLABELLED: Although metagenomic investigations into microbial fiber-degrading capabilities are currently prevalent, there is a notable gap in research concerning the regulatory mechanisms underpinning host-microbiota interactions that confer tolerance to high-fiber diets in pigs. In this study, 28 Meishan (MS) and 28 Large White (LW) pigs were subjected to feeding experiments involving various fiber levels. Subsequently, multi-omics was employed to investigate the influence of host-microbiota interactions on the fiber degradation of pigs. MS exhibited superior fiber digestibility compared with LW, particularly evident when fed a high-fiber diet. In MS, positive interactions among Treponema bryantii, Treponema sp., Rikenellaceae bacterium, and Bacteroidales bacterium WCE2004 facilitated the degradation of both cellulose and pectin. The reduced polymerization of polysaccharides and oligosaccharides observed in MS provides compelling evidence for their superior microbial fiber-degrading capability. The concentrations of propionate and butyrate retained in cecal lumen of MS was unchanged, whereas it was significantly increased in LW, indicating a strong absorption of short-chain fatty acids (SCFAs) in MS intestines. Correlation analysis using RNA-seq data revealed distinct patterns in LW and MS. In LW, microbial profiles along with GPR183 and GPR174 exhibited negative correlations with butyrate and propionate, respectively. Conversely, in MS, GPR174 and SLC2A4 were positively correlated with butyrate. Our findings underscore the dynamic collaboration among microbial species in degrading cellulose and pectin, coupled with the synergistic effects of SCFA transport-related genes, as crucial underpinnings for the heightened fiber digestibility observed in MS. These discoveries offer fresh perspectives into the intricate mechanisms governing host-microbiota interactions that influence fiber digestion in pigs.

IMPORTANCE: Studies on porcine intestinal microbiota have been widely conducted, and some microbial taxa with fiber degradation functions have been identified. However, the mechanisms of division among gut microbes in the degradation of complex fiber components are still unclear. In addition, the regulation of fiber digestion by host through absorption of short-chain fatty acids (SCFAs) needs to be further investigated. Our study used apparent total tract digestibility of dietary fiber to assess the utilization efficiency of dietary fiber between Meishan and Large White pigs. Subsequently, through metagenome sequencing and determination of fiber-degrading products, we found that in Meishan pigs, positive interactions among Treponema bryantii, Treponema sp., Rikenellaceae bacterium, and Bacteroidales bacterium WCE2004 facilitated the degradation of both cellulose and pectin. RNA-seq analysis elucidated breed-specific genes associated with SCFA absorption in cecum. By integrating multi-omics data, we constructed a framework outlining host-microbiota interactions that control dietary fiber utilization in pigs. Our data provide novel insights into host-microbiota interactions regulating fiber degradation and lay some theoretical foundations for improving the utilization efficiency of high-fiber cereal feed in pigs through targeted modulation of gut microbial function.}, } @article {pmid39873074, year = {2025}, author = {Yang, YH and Yu, JJ and Han, HY and Chang, WM and Wang, CW}, title = {Ex-vivo investigation of human salivary microbial growth with lysogeny broth for translational research-A pilot study.}, journal = {Journal of dental sciences}, volume = {20}, number = {1}, pages = {437-443}, pmid = {39873074}, issn = {2213-8862}, abstract = {BACKGROUND/PURPOSE: Salivary microbiome has become a surrogate indicator of oral disease due to its collective reservoirs and convenience in sampling. However, failed clinical trials often lead to wastes of resources, indicating a need for preclinical models. In this pilot study, we aimed to compare the salivary microbiome by metagenomics analysis before and after lysogeny broth culture for prospective translational studies.

MATERIALS AND METHODS: The study cohort included seven patients with severe periodontitis (Stage III/IV, Grade C), from whom unstimulated saliva was collected. The salivary microbiome was sequenced over the 16S rRNA gene V3-V4 hypervariable regions at baseline and after 6 hours of lysogeny broth culture.

RESULTS: The results revealed changes in salivary microbiome and reduced bacterial diversity after culture, mainly due to the expansion of genera Neisseria (Median (Mdn) 15.95% to 37.52%, P < 0.05), Rothia (Mdn 10.21% to 16.32%, P < 0.05), and Haemophilus (Mdn 5.88% to 13.25%, P < 0.05). Periodontitis-related pathogens such as phyla Bacteroidetes, Fusobacteria and Spirochaetes were identified, while genera Porphyromonas, Parvimonas, Peptostreptococcus, and Campylobacter showed a decrease after lysogeny broth culture. Caries-related pathogens, including genera Veillonella, Leptotrichia, and species Haemophilus parainfluenzae and Streptococcus salivarius, were also detected.

CONCLUSION: This pilot study revealed that periodontitis- and caries-related bacteria could be identified in the saliva at baseline and after 6 hours ex-vivo culture with lysogeny broth. Our findings also suggested that lysogeny broth favored the growth of specific genera and may serve as a reference to monitor short-term modulation of these bacteria in salivary microbiome.}, } @article {pmid39872816, year = {2024}, author = {Gu, G and Zeeshan Ul Haq, M and Sun, X and Zhou, J and Liu, Y and Yu, J and Yang, D and Yang, H and Wu, Y}, title = {Continuous cropping of Patchouli alters soil physiochemical properties and rhizosphere microecology revealed by metagenomic sequencing.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1482904}, pmid = {39872816}, issn = {1664-302X}, abstract = {Continuous cropping (CC) profoundly impacts soil ecosystems, including changes in soil factors and the structure and stability of microbial communities. These factors are interrelated and together affect soil health and plant growth. In this research, metagenomic sequencing was used to explore the effects of CC on physicochemical properties, enzyme activities, microbial community composition, and functional genes of the rhizosphere soil of patchouli. We found that this can lead to changes in various soil factors, including the continuous reduction of pH and NH 4 + -N and the unstable changes of many factors. In addition, S-PPO enzyme activity increased significantly with the cropping years, but S-NAG increased in the first 2 years and decreased in the third cropping year. Metagenomic sequencing results showed that CC significantly changed the diversity and composition of rhizosphere microbial communities. The relative abundance of Pseudomonas and Bacteroides decreased substantially from the phylum level. At the genus level, the number of microbial genera specific to the zero-year cropping (CK) and first (T1), second (T2), and third (T3) years decreased significantly, to 1798, 172, 42, and 44, respectively. The abundance of many functional genes changed, among which COG0823, a gene with the cellular process and signaling functions, significantly increased after CC. In addition, NH 4 + -N, S-CAT, S-LAP, and SOC were the main environmental factors affecting rhizosphere-dominant microbial communities at the phylum level, while pH, SOC, and AK were the key environmental factors affecting rhizosphere functional genes of Pogostemon cablin. In summary, this study showed the dynamic changes of soil factors and rhizosphere microorganisms during CC, providing a theoretical basis for understanding the formation mechanism and prevention of CC obstacles and contributing to the formulation of scientific soil management and fertilization strategies.}, } @article {pmid39872134, year = {2025}, author = {Li, Y and Ren, X and Wang, Q and Shen, S and Li, Y and Qian, X and Tang, Y and Jia, J and Zhang, H and Ding, J and Song, Y and Zhang, S and Wang, S and Xu, Y and Jiang, Y and He, X and Dai, M and Zhong, L and Xiong, Y and Pan, Y and Wang, M and Shao, H and Cai, H and Huang, L and Wang, H}, title = {A Predictive Model for Pulmonary Aspergillosis in ICU Patients: A Multicenter Retrospective Cohort Study.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {441-454}, pmid = {39872134}, issn = {1178-6973}, abstract = {BACKGROUND: Several predictive models for invasive pulmonary aspergillosis (IPA) based on clinical characteristics have been reported. Nevertheless, the significance of other concurrently detected microorganisms in IPA patients is equally noteworthy. This study aimed to develop a risk prediction model for IPA by integrating clinical and microbiological characteristics.

METHODS: This retrospective study was conducted in adult intensive care units (ICUs) of 17 medical centers in China. Clinical data were collected from patients with severe pneumonia who underwent clinical metagenomics of bronchoalveolar lavage fluid between January 1, 2019, and June 30, 2023. Subsequently, patients were randomly assigned to training and validation cohorts in a 7:3 ratio. In the training cohort, potential influencing factors were identified through univariate analysis, clinical practice, and existing literature, and a risk prediction model was constructed using multivariate logistic regression analysis. The performance of this model was then assessed and validated in the validation cohort.

RESULTS: Out of 1737 patients initially included in the study, 898 were ultimately analyzed, of which 100 (11%) were diagnosed with IPA. The risk prediction model for IPA, incorporating microbiological characteristics, identified six independent risk factors, namely age, immunosuppression, chronic kidney disease, connective tissue disease, liver failure, and cytomegalovirus positivity. The model demonstrated a superior discriminative ability, with area under the curve (AUC) values of 0.791 and 0.792 in the training and validation cohorts, respectively. Sensitivity and specificity reached 73.1% and 74.9%, respectively, and the model demonstrated good calibration.

CONCLUSION: This study developed a novel risk prediction model for IPA incorporating microbiological characteristics based on clinical metagenomics. The model exhibited good discriminative ability and calibration.}, } @article {pmid39872133, year = {2025}, author = {Liu, B and Bao, Z and Chen, W and Xi, X and Ge, X and Zhou, J and Zheng, X and Zhang, P and Deng, W and Ding, R and Zhou, M and Fang, J}, title = {Targeted Next-Generation Sequencing in Pneumonia: Applications in the Detection of Responsible Pathogens, Antimicrobial Resistance, and Virulence.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {407-418}, pmid = {39872133}, issn = {1178-6973}, abstract = {BACKGROUND: Targeted next-generation sequencing (tNGS) is a high-throughput and cost-effective diagnostic alternative for pneumonia, with the ability to simultaneously detect pathogens, antimicrobial resistance genes, and virulence genes. We aimed to explore the applicability of tNGS in the co-detection of the responsible pathogens, antimicrobial resistance (AMR) genes, and virulence genes in patients with pneumonia.

METHODS: A prospective study was conducted among patients with suspected pneumonia at Ruijin Hospital from March 1 to May 31, 2023. Bronchoalveolar lavage fluid (BALF) or sputum samples were collected and sent for tNGS, metagenomic next-generation sequencing (mNGS), and conventional microbiological tests (CMTs).

RESULTS: In total, 67 BALF and 11 sputum samples from 78 patients were included in the analyses. According to the composite reference standards, the accuracy of tNGS in the detection of responsible pathogens was 0.852 (95% confidence interval 0.786-0.918), which resembled that of mNGS and remarkably exceeded that of CMTs. In addition, 81 AMR genes associated with responsible pathogens were reported, and 75.8% (25/33) priority drug-resistant pathogens could be directly identified. A total of 144 virulence genes were detected for four common pathogens. And patients with virulence genes detected were of higher proportions of severe pneumonia (95.0% vs 42.9%, P = 0.009), acute respiratory distress syndrome (55.0% vs 0%, P = 0.022), and neutrophils (82.3% vs 62.2%, P = 0.026) than those not.

CONCLUSION: In patients with pneumonia, tNGS could detect the responsible pathogens, AMR genes, and virulence genes simultaneously, serving as an efficient and cost-effective tool for the diagnosis, treatment, and severity indication of pneumonia.}, } @article {pmid39872132, year = {2025}, author = {Jia, Q and Wang, L and Tong, X and Sun, J and Fan, H}, title = {Coexistence of Asymptomatic Allergic Bronchopulmonary Aspergillosis and Active Pulmonary Tuberculosis: Case Report.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {401-405}, pmid = {39872132}, issn = {1178-6973}, abstract = {We present a rare case of asymptomatic allergic bronchopulmonary aspergillosis (ABPA) concurrent with active pulmonary tuberculosis. Allergic bronchopulmonary aspergillosis is an immunological pulmonary disorder characterized by hypersensitivity to Aspergillus fumigatus, while pulmonary tuberculosis (PTB) is a complex infection caused by Mycobacterium tuberculosis (MTB). The association between pulmonary tuberculosis infections and Aspergillus infections remains a fascinating area of inquiry. A 26-year-old female patient exhibited no symptoms. However, her initial chest computed tomography revealed bronchiectasis with high-attenuation mucus plugs in the upper lobes, peripheral lung atelectasis, and a tree-in-bud pattern. To obtain a clear diagnosis, she visited multiple hospitals and incurred substantial time and financial costs. Active tuberculosis was initially confirmed using specialized detection methods, including metagenomic next-generation sequencing and Xpert MTB/RIF analysis of bronchoalveolar lavage fluid. Subsequent pathological biopsy and Aspergillus-specific antibody tests further confirmed the diagnosis of allergic bronchopulmonary aspergillosis combined with active tuberculosis. Following twelve months of antituberculosis therapy, an avoidable surgery, and three months of oral glucocorticoid treatment, the patient's lung lesions showed significant resolution. This case provides valuable insights into the clinical diagnosis and management of these two distinct infectious diseases.}, } @article {pmid39871844, year = {2024}, author = {Zhang, Y and Yin, M and Wen, H}, title = {VV-ECMO adjuvant therapy for Leptospira complicated with H1N1 infection: a case report.}, journal = {Frontiers in medicine}, volume = {11}, number = {}, pages = {1495324}, pmid = {39871844}, issn = {2296-858X}, abstract = {BACKGROUND: Leptospirosis is an acute infectious disease that occurs by infection, progresses rapidly, and has a high mortality rate, with an estimated 1.2 million new cases and nearly 59,000 deaths each year. Due to its diverse clinical manifestations, diagnosis is often delayed. Therefore, it is necessary to pay attention to its clinical manifestations, diagnostic techniques, and treatment methods.

CASE REPORT: A 51-year-old male patient from the Han ethnic group experienced fever, chills, headache, and overall fatigue after being exposed to rain, followed by yellowing of the skin and worsening of breathing difficulties. Metagenomic next-generation sequencing (mNGS) indicates infection with leptospirosis and influenza A. After 5 days of treatment with venovenous extracorporeal membrane oxygenation (VV-ECMO), Penicillium, and Oseltamivir, the condition improved.

CONCLUSION: Leptospirosis improves with VV-ECMO support and anti-infective treatment with penicillin and oseltamivir. VV-ECMO provides a therapeutic time window for rescue, and mNGS lays a foundation for early detection of etiology of leptospirosis.}, } @article {pmid39871406, year = {2025}, author = {Noell, SE and Abbaszadeh, J and Richards, H and Labat Saint Vincent, M and Lee, CK and Herbold, CW and Stott, MB and Cary, SC and McDonald, IR}, title = {Antarctic Geothermal Soils Exhibit an Absence of Regional Habitat Generalist Microorganisms.}, journal = {Environmental microbiology}, volume = {27}, number = {1}, pages = {e70032}, pmid = {39871406}, issn = {1462-2920}, support = {18-UOW-028//Marsden Fund/ ; }, mesh = {Antarctic Regions ; *Soil Microbiology ; *Archaea/classification/genetics ; *Bacteria/classification/isolation & purification/genetics ; *Ecosystem ; Microbiota ; Phylogeny ; Hot Springs/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Active geothermal systems are relatively rare in Antarctica and represent metaphorical islands ideal to study microbial dispersal. In this study, we tested the macro-ecological concept that high dispersal rates result in communities being dominated by either habitat generalists or specialists by investigating the microbial communities on four geographically separated geothermal sites on three Antarctic volcanoes (Mts. Erebus, Melbourne, and Rittman). We found that the microbial communities at higher temperature (max 65°C) sites (Tramway Ridge on Erebus and Rittmann) were unique from each other and were dominated by a variety of novel Archaea from class Nitrososphaeria, while lower temperature (max 50°C) sites (Western Crater on Erebus and Melbourne) had characteristically mesophilic communities (Planctomycetes, Acidobacteriota, etc.) that were highly similar. We found that 97% of the detected microbial taxa were regional habitat specialists, with no generalists, with community assembly driven by high dispersal rates and drift (25% and 30% of community assembly, respectively), not environmental selection. Our results indicate that for microbial communities experiencing high dispersal rates between isolated communities, habitat specialists may tend to out-compete habitat generalists.}, } @article {pmid39871128, year = {2025}, author = {Roy, S and Dawson, RA and Bradley, JA and Hernández, M}, title = {Prevalence and dynamics of antimicrobial resistance in pioneer and developing Arctic soils.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {50}, pmid = {39871128}, issn = {1471-2180}, support = {NE/X018180/1//Natural Environment Research Council/ ; NE/X018180/1//Natural Environment Research Council/ ; 730938//HORIZON EUROPE European Research Council/ ; RF\ERE\210050//Royal Society/ ; }, mesh = {*Soil Microbiology ; Arctic Regions ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Soil/chemistry ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Genes, Bacterial/genetics ; Interspersed Repetitive Sequences ; Ecosystem ; }, abstract = {Antimicrobial resistance (AMR) in soil is an ancient phenomenon with widespread spatial presence in terrestrial ecosystems. However, the natural processes shaping the temporal dissemination of AMR in soils are not well understood. We aimed to determine whether, how, and why AMR varies with soil age in recently deglaciated pioneer and developing Arctic soils using a space-for-time approach. Specifically, we assess how the magnitude and spread of AMR changes with soil development stages, including antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and antibiotic-resistant bacteria (ARB). We showed that ARGs, MGEs, and ARB are present, and exhibit a non-uniform distribution in the developing soils. Their abundance generally increases with soil age but at different rates overall and across different glacier forefields. Our analyses suggest a strong positive relationship between soil age and ARGs and ARB, which we attribute to increased competition between microbes in older soils. We also observed a strong negative relationship between soil age and ARG diversity mediated by soil organic matter - suggesting facilitation due to the alleviation of nutrient limitation. These contrasting results suggest that both competition and facilitation can regulate AMR spread through time in the Arctic, but competition might be the stronger determinant of AMR spread.}, } @article {pmid39870396, year = {2025}, author = {Rytter, H and Naimi, S and Wu, G and Lewis, J and Duquesnoy, M and Vigué, L and Tenaillon, O and Belda, E and Vazquez-Gomez, M and Touly, N and Arnone, D and Hao, F and Ley, RE and Clément, K and Peyrin-Biroulet, L and Patterson, AD and Gewirtz, AT and Chassaing, B}, title = {In vitro microbiota model recapitulates and predicts individualised sensitivity to dietary emulsifier.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2024-333925}, pmid = {39870396}, issn = {1468-3288}, abstract = {BACKGROUND: Non-absorbed dietary emulsifiers, including carboxymethylcellulose (CMC), directly disturb intestinal microbiota, thereby promoting chronic intestinal inflammation in mice. A randomised controlled-feeding study (Functional Research on Emulsifiers in Humans, FRESH) found that CMC also detrimentally impacts intestinal microbiota in some, but not all, healthy individuals.

OBJECTIVES: This study aimed to establish an approach for predicting an individual's sensitivity to dietary emulsifiers via their baseline microbiota.

DESIGN: We evaluated the ability of an in vitro microbiota model (MiniBioReactor Arrray, MBRA) to reproduce and predict an individual donor's sensitivity to emulsifiers. Metagenomes were analysed to identify signatures of emulsifier sensitivity.

RESULTS: Exposure of human microbiotas, maintained in the MBRA, to CMC recapitulated the differential CMC sensitivity previously observed in FRESH subjects. Furthermore, select FRESH control subjects (ie, not fed CMC) had microbiotas that were highly perturbed by CMC exposure in the MBRA model. CMC-induced microbiota perturbability was associated with a baseline metagenomic signature, suggesting the possibility of using one's metagenome to predict sensitivity to dietary emulsifiers. Transplant of human microbiotas that the MBRA model deemed CMC-sensitive, but not those deemed insensitive, into IL-10[-/-] germfree mice resulted in overt colitis following CMC feeding.

CONCLUSION: These results suggest that an individual's sensitivity to emulsifier is a consequence of, and can thus be predicted by, examining their baseline microbiota, paving the way to microbiota-based personalised nutrition.}, } @article {pmid39870395, year = {2025}, author = {Nan, K and Zhong, Z and Yue, Y and Shen, Y and Zhang, H and Wang, Z and Zhuma, K and Yu, B and Fu, Y and Wang, L and Sun, X and Qu, M and Chen, Z and Guo, M and Zhang, J and Chu, Y and Liu, R and Miao, C}, title = {Fasting-mimicking diet-enriched Bifidobacterium pseudolongum suppresses colorectal cancer by inducing memory CD8[+] T cells.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2024-333020}, pmid = {39870395}, issn = {1468-3288}, abstract = {BACKGROUND: Fasting-mimicking diet (FMD) boosts the antitumour immune response in patients with colorectal cancer (CRC). The gut microbiota is a key host immunity regulator, affecting physiological homeostasis and disease pathogenesis.

OBJECTIVE: We aimed to investigate how FMD protects against CRC via gut microbiota modulation.

DESIGN: We assessed probiotic species enrichment in FMD-treated CRC mice using faecal metagenomic sequencing. The candidate species were verified in antibiotic-treated conventional and germ-free mouse models. Immune landscape alterations were evaluated using single-cell RNA sequencing and multicolour flow cytometry. The microbiota-derived antitumour metabolites were identified using metabolomic profiling.

RESULTS: Faecal metagenomic profiling revealed Bifidobacterium pseudolongum enrichment in FMD-treated CRC mice. B. pseudolongum mediates the FMD antitumour effects by increasing the tissue-resident memory CD8[+] T-cell (TRM) population in CRC mice. The level of L-arginine, a B. pseudolongum functional metabolite, increased in FMD-treated CRC mice; furthermore, L-arginine induced the TRM phenotype in vivo and in vitro. Mechanistically, L-arginine is transported by the solute carrier family 7-member 1 (SLC7A1) receptor in CD8[+] T cells. Both FMD and B. pseudolongum improved anti-CTLA-4 efficacy in the orthotopic mouse CRC model. In FMD-treated patients with CRC, the CD8[+] TRM cell number increased as B. pseudolongum and L-arginine accumulated. The abundance of CD8[+] TRM cells and B. pseudolongum was associated with a better prognosis in patients with CRC.

CONCLUSION: B. pseudolongum contributes to the FMD antitumour effects in CRC by producing L-arginine. This promotes CD8[+] T-cell differentiation into memory cells. B. pseudolongum administration is a potential CRC therapeutic strategy.}, } @article {pmid39869988, year = {2025}, author = {Pietilä, S and Suomi, T and Paulin, N and Laiho, A and Sclivagnotis, YS and Elo, LL}, title = {Adaptive sequence alignment for metagenomic data analysis.}, journal = {Computers in biology and medicine}, volume = {186}, number = {}, pages = {109743}, doi = {10.1016/j.compbiomed.2025.109743}, pmid = {39869988}, issn = {1879-0534}, abstract = {With advances in sequencing technologies, the use of high-throughput sequencing to characterize microbial communities is becoming increasingly feasible. However, metagenomic assembly poses computational challenges in reconstructing genes and organisms from complex samples. To address this issue, we introduce a new concept called Adaptive Sequence Alignment (ASA) for analyzing metagenomic DNA sequence data. By iteratively adapting a set of partial alignments of reference sequences to match the sample data, the approach can be applied in multiple scenarios, from taxonomic identification to assembly of target regions of interest. To demonstrate the benefits of ASA, we present two application scenarios and compare the results with state-of-the-art methods conventionally used for the same tasks. In the first, ASA accurately detected microorganisms from a sequenced metagenomic sample with a known composition. The second illustrated the utility of ASA in assembling target genetic regions of the microorganisms. An example implementation of the ASA concept is available at https://github.com/elolab/ASA.}, } @article {pmid39869787, year = {2025}, author = {Lin, C and Li, LJ and Yang, K and Xu, JY and Fan, XT and Chen, QL and Zhu, YG}, title = {Protozoa-enhanced conjugation frequency alters the dissemination of soil antibiotic resistance.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf009}, pmid = {39869787}, issn = {1751-7370}, abstract = {Protozoa, as primary predators of soil bacteria, represent an overlooked natural driver in the dissemination of antibiotic resistance genes. However, the effects of protozoan predation on antibiotic resistance genes dissemination at the community level, along with the underlying mechanisms, remain unclear. Here we used fluorescence-activated cell sorting, qPCR, combined with metagenomics and reverse transcription quantitative PCR, to unveil how protozoa (Colpoda steinii and Acanthamoeba castellanii) influence the plasmid-mediated transfer of antibiotic resistance genes to soil microbial communities. Protozoan predation reduced the absolute abundance of plasmids but promoted the expression of conjugation-associated genes, leading to a 5-fold and 4.5-fold increase in conjugation frequency in the presence of C. steinii and A. castellanii, respectively. Excessive oxidative stress, increased membrane permeability, and the provoked SOS response closely associated with the increased conjugative transfer. Protozoan predation also altered the plasmid host range and selected for specific transconjugant taxa along with antibiotic resistance genes and virulence factors carried by transconjugant communities. This study underscores the role of protozoa in the plasmid-mediated conjugative transfer of antibiotic resistance genes, providing new insights into microbial mechanisms that drive the dissemination of environmental antibiotic resistance.}, } @article {pmid39869311, year = {2025}, author = {Li, R and Xu, M and Xu, M and Zhou, Y and Wen, T and Liu, Q and Yi, D and Wang, H and Wei, D}, title = {Semirational Engineering of a Distal Loop Region to Enhance the Catalytic Activity and Stability of Leucine Dehydrogenase.}, journal = {Journal of agricultural and food chemistry}, volume = {73}, number = {5}, pages = {2961-2969}, doi = {10.1021/acs.jafc.4c06915}, pmid = {39869311}, issn = {1520-5118}, mesh = {*Leucine Dehydrogenase/genetics/chemistry/metabolism ; *Protein Engineering ; Enzyme Stability ; Biocatalysis ; Molecular Dynamics Simulation ; Bacterial Proteins/genetics/chemistry/metabolism ; Kinetics ; Substrate Specificity ; Catalysis ; }, abstract = {Enzymatic asymmetric synthesis of l-phenylglycine by amino acid dehydrogenases has potential for industrial applications; however, this is hindered by their low catalytic efficiency toward high-concentration substrates. We identified and characterized a novel leucine dehydrogenase (MsLeuDH) with a high catalytic efficiency for benzoylformic acid via directed metagenomic approaches. Further, we obtained a triple-point mutant MsLeuDH-EER (D332E/G333E/L334R) with improved stability and catalytic efficiency through the rational design of distal loop 13. A coexpression system of MsLeuDH-EER and formate dehydrogenase completely converted a 300 mM substrate within 4 h with >99.9% enantiomeric excess. Molecular dynamics simulations revealed that mutations on loop 13 enhanced the overall structural rigidity of the protein to improve its stability but also stabilized the "closed" conformation through rigidifying the hinge region loop by distant modulation. Our results show that distal loop 13 can serve as a new hotspot region for enhancing the catalytic performance of leucine dehydrogenases.}, } @article {pmid39868792, year = {2025}, author = {Zhou, Z and Yang, M and Fang, H and Niu, Y and Lu, J and Ma, Y and Zhang, B and Zhu, H and Chen, P}, title = {Interspecies interactions mediated by arginine metabolism enhance the stress tolerance of Fusobacterium nucleatum against Bifidobacterium animalis.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0223524}, doi = {10.1128/spectrum.02235-24}, pmid = {39868792}, issn = {2165-0497}, abstract = {Colorectal cancer (CRC) is a common cancer accompanied by microbiome dysbiosis. Exploration of probiotics against oncogenic microorganisms is promising for CRC treatment. Here, differential microorganisms between CRC and healthy control were analyzed. Antibacterial experiments, whole-genome sequencing, and metabolic network reconstruction were combined to reveal the anti-Fusobacterium nucleatum mechanism, which was verified by co-culture assay and mendelian randomization analysis. Sequencing results showed that F. nucleatum was enriched in CRC, yet Bifidobacterium animalis decreased gradually from healthy to CRC. Additionally, F. nucleatum could be inhibited by B. animalis. Whole-genome sequencing of B. animalis showed high phylogenetic similarity with known probiotic strains and highlighted its functions for amino acid and carbohydrate metabolism. Metabolic network reconstruction demonstrated that cross-feeding and specific metabolites (acidic molecules, arginine) had a great influence on the coexistence relationship. Finally, the arginine supplement enhanced the competitive ability of F. nucleatum against B. animalis, and the mendelian randomization and metagenomic sequencing analysis confirmed the positive relationship among F. nucleatum, arginine metabolism, and CRC. Thus, whole-genome sequencing and metabolic network reconstruction are valuable for probiotic mining and patient dietary guidance.IMPORTANCEUsing probiotics to inhibit oncogenic microorganisms (Fusobacterium nucleatum) is promising for colorectal cancer (CRC) treatment. In this study, whole-genome sequencing and metabolic network reconstruction were combined to reveal the anti-F. nucleatum mechanism of Bifidobacterium animalis, which was verified by co-culture assay and mendelian randomization analysis. The result indicated that the arginine supplement enhanced the competitive ability of F. nucleatum, which may be harmful to F. nucleatum-infected CRC patients. B. animalis is a potential probiotic to relieve this dilemma. Thus, using in silico simulation methods based on flux balance analysis, such as genome-scale metabolic reconstruction, provides valuable insights for probiotic mining and dietary guidance for cancer patients.}, } @article {pmid39868304, year = {2025}, author = {Choi, JM and Rumi, MA and Vikesland, PJ and Pruden, A and Zhang, L}, title = {ARGfore: A multivariate framework for forecasting antibiotic resistance gene abundances using time-series metagenomic datasets.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.01.13.632008}, pmid = {39868304}, issn = {2692-8205}, abstract = {BACKGROUND: The global spread of antibiotic resistance presents a significant threat to human, animal, and plant health. Metagenomic sequencing is increasingly being utilized to profile antibiotic resistance genes (ARGs) in various environments, but presently a mechanism for predicting future trends in ARG occurrence patterns is lacking. Capability of forecasting ARG abundance trends could be extremely valuable towards informing policy and practice aimed at mitigating the evolution and spread of ARGs.

RESULTS: Here we propose ARGfore, a multivariate forecasting model for predicting ARG abundances from time-series metagenomic data. ARGfore extracts features that capture inherent relationships among ARGs and is trained to recognize patterns in ARG trends and seasonality.

CONCLUSION: ARGfore outperformed standard time-series forecasting methods, such as N-HiTS, LSTM, and ARIMA, exhibiting the lowest mean absolute percentage error when applied to different wastewater datasets. Additionally, ARGfore demonstrated enhanced computational efficiency, making it a promising candidate for a variety of ARG surveillance applications. The rapid prediction of future trends can facilitate early detection and deployment of mitigation efforts if necessary. ARGfore is publicly available at https://github.com/joungmin-choi/ARGfore .}, } @article {pmid39868213, year = {2025}, author = {Schechter, MS and Trigodet, F and Veseli, IA and Miller, SE and Klein, ML and Sever, M and Maignien, L and Delmont, TO and Light, SH and Eren, AM}, title = {Ribosomal protein phylogeography offers quantitative insights into the efficacy of genome-resolved surveys of microbial communities.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39868213}, issn = {2692-8205}, support = {T32 GM007197/GM/NIGMS NIH HHS/United States ; }, abstract = {The increasing availability of microbial genomes is essential to gain insights into microbial ecology and evolution that can propel biotechnological and biomedical advances. Recent advances in genome recovery have significantly expanded the catalogue of microbial genomes from diverse habitats. However, the ability to explain how well a set of genomes account for the diversity in a given environment remains challenging for individual studies or biome-specific databases. Here we present EcoPhylo, a computational workflow to characterize the phylogeography of any gene family through integrated analyses of genomes and metagenomes, and our application of this approach to ribosomal proteins to quantify phylogeny-aware genome recovery rates across three biomes. Our findings show that genome recovery rates vary widely across taxa and biomes, and that single amplified genomes, metagenome-assembled genomes, and isolate genomes have non-uniform yet quantifiable representation of environmental microbes. EcoPhylo reveals highly resolved, reference-free, multi-domain phylogenies in conjunction with distribution patterns of individual clades across environments, providing a means to assess genome recovery in individual studies and benchmark biome-level genome collections.}, } @article {pmid39868175, year = {2025}, author = {Simmonds, P and Butković, A and Grove, J and Mayne, R and Mifsud, JCO and Beer, M and Bukh, J and Drexler, JF and Kapoor, A and Lohmann, V and Smith, DB and Stapleton, JT and Vasilakis, N and Kuhn, JH}, title = {Integrated analysis of protein sequence and structure redefines viral diversity and the taxonomy of the Flaviviridae.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39868175}, issn = {2692-8205}, support = {/WT_/Wellcome Trust/United Kingdom ; HHSN272201800013C/AI/NIAID NIH HHS/United States ; I01 BX000207/BX/BLRD VA/United States ; U01 AI151807/AI/NIAID NIH HHS/United States ; }, abstract = {The Flaviviridae are a family of non-segmented positive-sense enveloped RNA viruses containing significant pathogens including hepatitis C virus and yellow fever virus. Recent large-scale metagenomic surveys have identified many diverse RNA viruses related to classical orthoflaviviruses and pestiviruses but quite different genome lengths and configurations, and with a hugely expanded host range that spans multiple animal phyla, including molluscs, cnidarians and stramenopiles,, and plants. Grouping of RNA-directed RNA polymerase (RdRP) hallmark gene sequences of flavivirus and 'flavi-like' viruses into four divergent clades and multiple lineages within them was congruent with helicase gene phylogeny, PPHMM profile comparisons, and comparison of RdRP protein structure predicted by AlphFold2. These results support their classification into the established order, Amarillovirales, in three families (Flaviviridae, Pestiviridae, and Hepaciviridae), and 14 genera. This taxonomic framework informed by RdRP hallmark gene evolutionary relationships provides a stable reference from which major genome re-organisational events can be understood.}, } @article {pmid39868118, year = {2025}, author = {Kennedy, EA and Weagley, JS and Kim, AH and Antia, A and DeVeaux, AL and Baldridge, MT}, title = {Microbiota assembly of specific pathogen-free neonatal mice.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39868118}, issn = {2692-8205}, support = {F31 AI167499/AI/NIAID NIH HHS/United States ; R01 AI139314/AI/NIAID NIH HHS/United States ; R01 AI173360/AI/NIAID NIH HHS/United States ; T32 AI007163/AI/NIAID NIH HHS/United States ; T32 AI007172/AI/NIAID NIH HHS/United States ; }, abstract = {BACKGROUND: Neonatal mice are frequently used to model diseases that affect human infants. Microbial community composition has been shown to impact disease progression in these models. Despite this, the maturation of the early-life murine microbiome has not been well-characterized. We address this gap by characterizing the assembly of the bacterial microbiota of C57BL/6 and BALB/c litters from birth to adulthood across multiple independent litters.

RESULTS: The fecal microbiome of young pups is simple, dominated by only a few pioneering bacterial taxa. These taxa are present at low levels in the microbiota of multiple maternal body sites, precluding a clear identification of maternal source. The pup microbiota begins diversifying after fourteen days, coinciding with the beginning of coprophagy and the consumption of solid foods. Pup stool bacterial community composition and diversity are not significantly different from dams from day 21 onwards. Short-read shotgun sequencing-based metagenomic profiling of young pups enabled the assembly of metagenome-assembled genomes for strain-level analysis of these pioneer Ligilactobacillus, Streptococcus, and Proteus species.

CONCLUSIONS: Assembly of the murine microbiome occurs over the first weeks of postnatal life and is largely complete by day 21. This detailed view of bacterial community development across multiple commonly employed mouse strains informs experimental design, allowing researchers to better target interventions before, during, or after the maturation of the bacterial microbiota. The source of pioneer bacterial strains appears heterogeneous, as the most abundant taxa identified in young pup stool were found at low levels across multiple maternal body sites, suggesting diverse routes for seeding of the murine microbiome.}, } @article {pmid39867878, year = {2024}, author = {Lin, F}, title = {Tuberculous meningitis diagnosis and treatment: classic approaches and high-throughput pathways.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1543009}, pmid = {39867878}, issn = {1664-3224}, mesh = {*Tuberculosis, Meningeal/diagnosis ; Humans ; *Mycobacterium tuberculosis ; *High-Throughput Nucleotide Sequencing ; Biomarkers ; Proteomics/methods ; Metagenomics/methods ; Metabolomics/methods ; Antitubercular Agents/therapeutic use ; }, abstract = {Tuberculous meningitis (TBM), a severe form of non-purulent meningitis caused by Mycobacterium tuberculosis (Mtb), is the most critical extrapulmonary tuberculosis (TB) manifestation, with a 30-40% mortality rate despite available treatment. The absence of distinctive clinical symptoms and effective diagnostic tools complicates early detection. Recent advancements in nucleic acid detection, genomics, metabolomics, and proteomics have led to novel diagnostic approaches, improving sensitivity and specificity. This review focuses on nucleic acid-based methods, including Xpert Ultra, metagenomic next-generation sequencing (mNGS), and single-cell sequencing of whole brain Tissue, alongside the diagnostic potential of metabolomic and proteomic biomarkers. By evaluating the technical features, diagnostic accuracy, and clinical applicability, this review aims to inform the optimization of TBM diagnostic strategies and explores the integration and clinical translation of multi-omics technologies.}, } @article {pmid39867819, year = {2025}, author = {Zhang, Y and Wu, J and Lin, Q and Ou, J and Qi, X and Zheng, Y and Li, F and Weng, Y}, title = {Infection Tracing and Virus Genomic Analysis of Two Cases of Human Infection with Avian Influenza A(H5N6) - Fujian Province, China, April-May 2024.}, journal = {China CDC weekly}, volume = {7}, number = {3}, pages = {107-112}, pmid = {39867819}, issn = {2096-7071}, abstract = {Global human cases of zoonotic influenza A(H5N6) have increased significantly in recent years, primarily due to widespread circulation of clade 2.3.4.4b virus since 2020. Concurrent with this trend, sporadic human infections with clade 2.3.4.4h H5N6 avian influenza virus continue to occur. The high mortality rate associated with H5N6 virus infections has emerged as a critical public health concern.

WHAT IS ADDED BY THIS REPORT?: Through comprehensive field epidemiological investigations and laboratory analyses, we identified the infection sources for these cases and conclusively ruled out human-to-human transmission. Genetic analyses revealed that while the virus maintains its avian host tropism, it has acquired mutations that may enhance human receptor binding affinity, viral replication capacity, pathogenicity, and neuraminidase inhibitor resistance.

The ongoing viral mutations increase the potential for H5 subtype avian influenza viruses to overcome species barriers and cause human epidemics. Enhanced surveillance strategies incorporating advanced technologies, such as metagenomic sequencing, are essential for early risk detection and management. Special attention should be directed toward cancer patients and immunocompromised individuals, who demonstrate increased susceptibility to avian influenza virus infections and require targeted prevention and control measures.}, } @article {pmid39867343, year = {2024}, author = {Guimarães, LO and Ribeiro, GO and da Couto, R and Ramos, EDSF and Morais, VDS and Telles-de-Deus, J and Helfstein, VC and Dos Santos, JM and Deng, X and Delwart, E and Pandey, RP and de Camargo-Neves, VLF and da Costa, AC and Kirchgatter, K and Leal, É}, title = {Exploring mosquito virome dynamics within São Paulo Zoo: insights into mosquito-virus-environment interactions.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1496126}, pmid = {39867343}, issn = {2235-2988}, mesh = {Animals ; Brazil ; *Virome ; *Mosquito Vectors/virology ; *Metagenomics ; Animals, Zoo/virology ; Arboviruses/genetics/classification/isolation & purification ; Culicidae/virology ; Aedes/virology ; Anopheles/virology ; Culex/virology ; Ecosystem ; }, abstract = {BACKGROUND: Mosquito-borne diseases have a significant public health threat worldwide, with arboviruses accounting for a high proportion of infectious diseases and mortality annually. Brazil, in particular, has been suffering outbreaks of diseases transmitted by mosquito viruses, notably those of the Aedes genus, such as dengue, Zika, and chikungunya. Against this background, the São Paulo Zoo is an intriguing ecological niche to explore the virome of mosquitoes, potentially shedding light on the dynamics of arbovirus transmission within a confined setting.

METHODS: In this study, we conducted a comprehensive metagenomic analysis of mosquitoes collected from diverse habitats within the zoo, focusing on the Aedes, Anopheles, and Culex genera. From 1,039 contigs of viral origin, we identified 229 viral species infecting mosquitoes, with the orders Picornavirales, Nodamuvirales and Sobelivirales being the most prevalent and abundant. The difference in virome composition was primarily driven by mosquito host species rather than specific collection sites or trap height.

RESULTS: Despite environmental disparities, the virome remained remarkably uniform across different areas of the zoo, emphasizing the strong association between mosquito species and their viral communities. Furthermore, we identified a core virome shared among mosquito species, highlighting potential cross-species transmission events and underscoring the need for targeted surveillance and control measures.

CONCLUSION: These results contribute to our understanding of the interplay between mosquitoes, the environment, and viruses, providing valuable insights for disease intervention strategies in mosquito-borne diseases.}, } @article {pmid39867288, year = {2025}, author = {Zhang, H and Zhang, X and Zheng, Y and Gu, X and Fu, Z and Gai, W and Wang, H}, title = {Impact of Herpesvirus Detection via Metagenomic Next-Generation Sequencing in Patients with Lower Respiratory Tract Infections.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {377-389}, pmid = {39867288}, issn = {1178-6973}, abstract = {PURPOSE: This study aimed to investigate the impact of herpesvirus detection by metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) on lower respiratory tract infections (LRTIs) patients' lung microbiome composition and prognosis.

PATIENTS AND METHODS: We initially enrolled 234 hospitalized patients with LRTIs who underwent BALF mNGS between February 2022 and May 2023. The study analyzed the clinical manifestations and the pulmonary microbial composition between herpesvirus detection (HD) and non-herpesvirus detection (non-HD) group.

RESULTS: After exclusions, a total of 201 patients were included, out of which 73 patients had herpesvirus detections (HD). The most frequently detected herpesviruses were Human herpesvirus 7 (HHV-7) (19.4%), Epstein-Barr virus (EBV) (12.4%), and cytomegalovirus (CMV) (10.4%). The HD group had a higher proportion of male patients (78.08% vs 55.04%, P = 0.001) and a greater incidence of hemoptysis and multilobar infiltrates compared non-HD group. Additionally, the HD group tended to have longer hospital stays compared to non-HD group, especially in immunosuppressed patients. Furthermore, in immunocompetent patients, there were significant differences in α diversity and β diversity between the HD group and non-HD group, but such differences were not observed in immunosuppressed patients.

CONCLUSION: The presence of herpesvirus in patients with non-critical LRTI is associated with longer hospital stays and alterations in the lung's microbial composition. Additionally, the impacts of herpesvirus presence are influenced by the immune status of the patients.}, } @article {pmid39866837, year = {2025}, author = {Zhao, P and Jiang, Z and Li, X and Ainiwaer, M and Li, L and Wang, D and Fan, L and Chen, F and Liu, J}, title = {Airway stenosis: classification, pathogenesis, and clinical management.}, journal = {MedComm}, volume = {6}, number = {2}, pages = {e70076}, pmid = {39866837}, issn = {2688-2663}, abstract = {Airway stenosis (AS) is a fibroinflammatory disease characterized by abnormal activation of fibroblasts and excessive synthesis of extracellular matrix, which has puzzled many doctors despite its relatively low prevalence. Traditional treatment such as endoscopic surgery, open surgery, and adjuvant therapy have many disadvantages and are limited in the treatment of patients with recurrent AS. Therefore, it is urgent to reveal the pathogenesis of AS and accelerate its clinical transformation. Based on the discovered pathogenesis, including fibrosis, inflammation, epithelial-mesenchymal transition, metabolic reprogramming, microbiome, genetic susceptibility, and other mechanisms, researchers have developed a series of treatments, such as drug therapy, gene therapy, stem cell therapy, growth factor therapy, protein therapy, and photodynamic therapy. This review introduces the classification of AS, explores the existing pathogenesis and preclinical treatments developed based on the pathogenesis, and finally summarizes the current clinical management. In addition, the prospect of exploring the interaction between different types of cells and between microorganisms and cells to identify the intersection of multiple mechanisms based on single-cell RNA sequencing, 16S rRNA gene sequencing and shotgun metagenomic sequencing is worth looking forward to.}, } @article {pmid39866751, year = {2025}, author = {Ren, Z and Luo, W and Li, H and Ding, H and Zhang, Y}, title = {Decrypting the phylogeny and metabolism of microbial dark matter in green and red Antarctic snow.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf003}, pmid = {39866751}, issn = {2730-6151}, abstract = {Antarctic snow harbors diverse microorganisms, including pigmented algae and bacteria, which create colored snow patches and influence global climate and biogeochemical cycles. However, the genomic diversity and metabolic potential of colored snow remain poorly understood. We conducted a genome-resolved study of microbiomes in colored snow from 13 patches (7 green and 6 red) on the Fildes Peninsula, Antarctica. Using metagenome assembly and binning, we reconstructed 223 metagenome-assembled genomes (MAGs), with 91% representing previously unexplored microbes. Green snow (GS) and red snow (RS) showed distinct MAGs profile, with Polaromonas and Ferruginibacter as the most abundant genera, respectively. GS exhibited higher alpha diversity with more unique and enriched MAGs, while RS showed greater variability with higher beta diversity. All MAGs contained genes encoding auxiliary activities (AAs), carbohydrate esterases (CEs), glycoside hydrolases (GHs), and glycosyl transferases (GTs), indicating microbial degradation of complex carbon substrates. The most abundant enzymes included GT2 (cellulose synthase), GT4 (sucrose synthase), CE1 (acetyl xylan esterase), GT41 (peptide beta-N-acetylglucosaminyltransferase), and CE10 (arylesterase). GS had a higher abundance of GTs, whereas RS was enriched in GHs. Furthermore, 56% of MAGs contained genes for inorganic nitrogen cycling, with 18 gene families involved in assimilatory nitrate reduction, dissimilatory nitrate reduction, and denitrification. Potential coupling of nitrogen cycling and carbohydrate metabolism was observed at both genome and community levels, suggesting close links between these pathways, particularly through nitrate reduction during carbohydrate degradation. This study enhances our understanding of microbial metabolic functions in polar ecosystems and highlights their roles in maintaining Antarctic ecological stability.}, } @article {pmid39866677, year = {2024}, author = {Violette, MJ and Hyland, E and Burgener, L and Ghosh, A and Montoya, BM and Kleiner, M}, title = {Meta-omics reveals role of photosynthesis in microbially induced carbonate precipitation at a CO2-rich geyser.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae139}, pmid = {39866677}, issn = {2730-6151}, abstract = {Microbially induced carbonate precipitation (MICP) is a natural process with potential biotechnological applications to address both carbon sequestration and sustainable construction needs. However, our understanding of the microbial processes involved in MICP is limited to a few well-researched pathways such as ureolytic hydrolysis. To expand our knowledge of MICP, we conducted an omics-based study on sedimentary communities from travertine around the CO2-driven Crystal Geyser near Green River, Utah. Using metagenomics and metaproteomics, we identified the community members and potential metabolic pathways involved in MICP. We found variations in microbial community composition between the two sites we sampled, but Rhodobacterales were consistently the most abundant order, including both chemoheterotrophs and anoxygenic phototrophs. We also identified several highly abundant genera of Cyanobacteriales. The dominance of these community members across both sites and the abundant presence of photosynthesis-related proteins suggest that photosynthesis could play a role in MICP at Crystal Geyser. We also found abundant bacterial proteins involved in phosphorous starvation response at both sites suggesting that P-limitation shapes both composition and function of the microbial community driving MICP.}, } @article {pmid39866676, year = {2024}, author = {Prabhu, A and Tule, S and Chuvochina, M and Bodén, M and McIlroy, SJ and Zaugg, J and Rinke, C}, title = {Machine learning and metagenomics identifies uncharacterized taxa inferred to drive biogeochemical cycles in a subtropical hypereutrophic estuary.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae067}, pmid = {39866676}, issn = {2730-6151}, abstract = {Anthropogenic influences have drastically increased nutrient concentrations in many estuaries globally, and microbial communities have adapted to the resulting hypereutrophic ecosystems. However, our knowledge of the dominant microbial taxa and their potential functions in these ecosystems has remained sparse. Here, we study prokaryotic community dynamics in a temporal-spatial dataset, from a subtropical hypereutrophic estuary. Screening 54 water samples across brackish to marine sites revealed that nutrient concentrations and salinity best explained spatial community variations, whereas temperature and dissolved oxygen likely drive seasonal shifts. By combining short and long read sequencing data, we recovered 2,459 metagenome-assembled genomes, proposed new taxon names for previously uncharacterised lineages, and created an extensive, habitat specific genome reference database. Community profiling based on this genome reference database revealed a diverse prokaryotic community comprising 61 bacterial and 18 archaeal phyla, and resulted in an improved taxonomic resolution at lower ranks down to genus level. We found that the vast majority (61 out of 73) of abundant genera (>1% average) represented unnamed and novel lineages, and that all genera could be clearly separated into brackish and marine ecotypes with inferred habitat specific functions. Applying supervised machine learning and metabolic reconstruction, we identified several microbial indicator taxa responding directly or indirectly to elevated nitrate and total phosphorus concentrations. In conclusion, our analysis highlights the importance of improved taxonomic resolution, sheds light on the role of previously uncharacterised lineages in estuarine nutrient cycling, and identifies microbial indicators for nutrient levels crucial in estuary health assessments.}, } @article {pmid39866568, year = {2025}, author = {Pucci, N and Ujčič-Voortman, J and Verhoeff, AP and Mende, DR}, title = {Priority effects, nutrition and milk glycan-metabolic potential drive Bifidobacterium longum subspecies dynamics in the infant gut microbiome.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e18602}, pmid = {39866568}, issn = {2167-8359}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Milk, Human/microbiology/chemistry/metabolism ; Infant ; *Bifidobacterium/metabolism/genetics ; *Bifidobacterium longum/metabolism ; Female ; *Polysaccharides/metabolism ; Infant, Newborn ; Feces/microbiology ; Metagenome ; Breast Feeding ; Male ; }, abstract = {BACKGROUND: The initial colonization of the infant gut is a complex process that defines the foundation for a healthy microbiome development. Bifidobacterium longum is one of the first colonizers of newborns' gut, playing a crucial role in the healthy development of both the host and its microbiome. However, B. longum exhibits significant genomic diversity, with subspecies (e.g., Bifidobacterium longum subsp. infantis and subsp. longum) displaying distinct ecological and metabolic strategies including differential capabilities to break down human milk glycans (HMGs). To promote healthy infant microbiome development, a good understanding of the factors governing infant microbiome dynamics is required.

METHODOLOGY: We analyzed newly sequenced gut microbiome samples of mother-infant pairs from the Amsterdam Infant Microbiome Study (AIMS) and four publicly available datasets to identify important environmental and bifidobacterial features associated with the colonization success and succession outcomes of B. longum subspecies. Metagenome-assembled genomes (MAGs) were generated and assessed to identify characteristics of B. longum subspecies in relation to early-life gut colonization. We further implemented machine learning tools to identify significant features associated with B. longum subspecies abundance.

RESULTS: B. longum subsp. longum was the most abundant and prevalent gut Bifidobacterium at one month, being replaced by B. longum subsp. infantis at six months of age. By utilizing metagenome-assembled genomes (MAGs), we reveal significant differences between and within B. longum subspecies in their potential to break down HMGs. We further combined strain-tracking, meta-pangenomics and machine learning to understand these abundance dynamics and found an interplay of priority effects, milk-feeding type and HMG-utilization potential to govern them across the first six months of life. We find higher abundances of B. longum subsp. longum in the maternal gut microbiome, vertical transmission, breast milk and a broader range of HMG-utilizing genes to promote its abundance at one month of age. Eventually, we find B. longum subsp. longum to be replaced by B. longum subsp. infantis at six months of age due to a combination of nutritional intake, HMG-utilization potential and a diminishment of priority effects.

DISCUSSION: Our results establish a strain-level ecological framework explaining early-life abundance dynamics of B. longum subspecies. We highlight the role of priority effects, nutrition and significant variability in HMG-utilization potential in determining the predictable colonization and succession trajectories of B. longum subspecies, with potential implications for promoting infant health and well-being.}, } @article {pmid39866262, year = {2025}, author = {Liu, C and Wu, W and Wang, L and Li, J}, title = {Case report: co-infection of Scedosporium and Mycobacterium in lungs.}, journal = {AME case reports}, volume = {9}, number = {}, pages = {3}, pmid = {39866262}, issn = {2523-1995}, abstract = {BACKGROUND: There are hundreds of pathogens that cause lung infections. Compared to infections caused by a single pathogen, mixed infections account for a larger proportion of pulmonary infections and have a more severe clinical presentation, while treatment options differ between the two. We aimed to explore the advantages of metagenomic next-generation sequencing (mNGS) in the diagnosis and treatment of mixed infections.

CASE DESCRIPTION: To investigate the specific pathogens in a 79-year-old male pneumonia patient who had recurrent cough with poor empirical treatment, we collected bronchoalveolar lavage fluid (BALF) from the patient and performed mNGS technology, along with Sanger sequencing and polymerase chain reaction (PCR) was carried out to confirm the authenticity of the pathogens detected by mNGS. The findings showed that rare pathogen Scedosporium boydii (S. boydii, reads: 18) and Mycobacterium avium complex (MAC, reads: 19) were detected, and the patient was subsequently transferred to another hospital for the same mNGS with the same results as the first detection. Therefore, combined treatment with voriconazole, ethambutol, azithromycin, and levofloxacin were given to the S. boydii and MAC for 1 week, and then patient's condition improved and discharged.

CONCLUSIONS: mNGS, a non-targeted sequencing technology, could improve the efficiency of clinical diagnosis for mixed infection of rare or atypical pathogens, bring new ideas for clinical pathogen diagnosis, and improve patient prognosis.}, } @article {pmid39865210, year = {2025}, author = {Dubovitskiy, N and Derko, A and Loginova, A and Khozyainova, A and Denisov, E and Apanasevich, M and Kokhanenko, A and Druzyaka, A and Shestopalov, A and Sharshov, K}, title = {Viral metagenomics in wild ducks reveals the presence of seadornaviruses in Siberia.}, journal = {Archives of virology}, volume = {170}, number = {2}, pages = {41}, pmid = {39865210}, issn = {1432-8798}, support = {122012400086-2//State funded budget projects (Russia)/ ; 23-44-00026//Russian Scientific Foundation/ ; }, mesh = {Animals ; Siberia ; *Ducks/virology ; *Metagenomics ; *Phylogeny ; Genome, Viral/genetics ; Bird Diseases/virology ; Animals, Wild/virology ; }, abstract = {Seadornavirus is a genus of mosquito-borne viruses that includes Banna virus, which was first discovered in human patients with encephalitis and fever, as well as Kadipiro virus and Liao ning virus. In this study, we used metagenomics to investigate the diversity of viruses in wild ducks and detected both Banna virus and Kadipiro virus in wild birds in Siberia. These data suggest that seadornaviruses, which were previously only found in South East Asia, are also circulating in Northern Eurasia.}, } @article {pmid39865153, year = {2025}, author = {Wu, Z and Jiang, M and Jia, M and Sang, J and Wang, Q and Xu, Y and Qi, L and Yang, W and Feng, L}, title = {The difference of oropharyngeal microbiome during acute respiratory viral infections in infants and children.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {127}, pmid = {39865153}, issn = {2399-3642}, support = {2022-I2M-CoV19-006//Chinese Academy of Medical Sciences (CAMS)/ ; }, mesh = {Humans ; *Respiratory Tract Infections/microbiology/virology ; Infant ; *Oropharynx/microbiology/virology ; *Microbiota ; Child, Preschool ; Male ; Female ; Child ; Acute Disease ; Virus Diseases/virology/microbiology/epidemiology ; }, abstract = {Acute respiratory infections (ARI) with multiple types of viruses are common in infants and children. This study was conducted to assess the difference of oropharyngeal microbiome during acute respiratory viral infection using whole-genome shotgun metagenomic sequencing. The overall taxonomic alpha diversity did not differ by the types of infected virus. The beta diversity differed by disease severity, disease-related symptoms, and types of infected virus. Nine species had significantly higher abundance in outpatients than in inpatients, with five of them in the genus Achromobacter. Three microbial community types were identified. The prevalence of community type (CT) 1 was higher among patients with influenza virus, enterovirus, and human adenvirus; CT2 was higher among patients with human metapneumovirus; and CT3 was higher among patients with respiratory syncytial virus and human adenvirus infections. Our results suggest that the oropharyngeal microbiome is associated with ARI disease severity, disease-related symptoms, and the types of infected virus.}, } @article {pmid39865091, year = {2025}, author = {Qi, YL and Zhang, HT and Li, M and Li, WJ and Hua, ZS}, title = {Recovery of nearly 3,000 archaeal genomes from 152 terrestrial geothermal spring metagenomes.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {151}, pmid = {39865091}, issn = {2052-4463}, support = {32170014//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42207145//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92251302//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Hot Springs/microbiology ; *Genome, Archaeal ; *Archaea/genetics/classification ; *Metagenome ; China ; *Phylogeny ; }, abstract = {Terrestrial geothermal springs, reminiscent of early Earth conditions, host diverse and abundant populations of Archaea. In this study, we reconstructed 2,949 metagenome-assembled genomes (MAGs) from 152 metagenomes collected over six years from 48 geothermal springs in Tengchong, China. Among these MAGs, 1,431 (49%) were classified as high-quality, while 1,518 (51%) were considered as medium-quality. Phylogenomic analysis revealed that these MAGs spanned 12 phyla, 27 classes, 67 orders, 147 families, 265 genera, and 475 species. Notably, 575 (19%) MAGs represented new taxa at various taxonomic levels, and 2,075 (70%) lacked nomenclature and effective descriptions. The most abundant phyla of archaeal genomes were Thermoproteota, Thermoplasmatota, and Micrarchaeota. The DRTY, ZMQ, and ZZQ geothermal springs were predominated by Archaea, particularly by Thermoproteia and Thermoplasmata. These draft genomes provide new data for studying species diversity and function within terrestrial geothermal spring archaeal communities, thus contributing to the conservation and utilization of thermophilic and hyperthermophilic microbial resources.}, } @article {pmid39864798, year = {2025}, author = {Nehra, C and Harshini, V and Shukla, N and Chavda, P and Bhure, M and Savaliya, K and Patil, S and Shah, T and Pandit, R and Patil, NV and Patel, AK and Kachhawaha, S and Kumawat, RN and Joshi, M and Joshi, CG}, title = {Ruminal microbial responses to Moringa oleifera feed in lactating goats (Capra hircus): A metagenomic exploration.}, journal = {New biotechnology}, volume = {86}, number = {}, pages = {87-96}, doi = {10.1016/j.nbt.2025.01.006}, pmid = {39864798}, issn = {1876-4347}, abstract = {The purpose of the current study was to explore the effects of Moringa oleifera feed on the taxonomy and function of the rumen microbial community, and further to evaluate its impact on milk yield and body weight in lactating goats. Nineteen goats were divided into moringa leaf diet (ML; n = 10) and masoor straw (MS; n = 9) groups. For each group fortnight milk yield and body weight was recorded. Rumen solid and liquid fraction samples were processed for metagenomic shotgun sequencing and further analysed. The pairwise comparison between the two groups showed a significant increase (p-value- <0.01) in milk yield of the ML goats after the 4th fortnight interval onwards. The metagenomic analysis revealed Bacteroidetes and Firmicutes are the most abundant phyla, with increased Bacteroidetes in response to the moringa diet. The ML group exhibited a reduction in microbial diversity, with an increase in Prevetolla and Bacteroidales populations which are positively associated with carbohydrate, protein, and VFA metabolism, and an increased proportions of Treponema sp., Ruminococcus sp., Ruminobacter amylophilus, and Aeromonas, indicating improved cellulose and nitrogen metabolism. KEGG analysis revealed significant changes in microbial gene pool and metabolic pathways, particularly in carbohydrate metabolism, propanoate metabolism, and fatty acid synthesis genes. These microbial and functional shifts are correlated with improvements in milk yield, growth rates, and potentially reduced methane emissions.This study highlighted the potential benefits of feeding moringa in the animal production system. However, furthermore experimental evidence including genetic and environmental effects is needed for a comprehensive understanding of moringa feed's impact on goat health and productivity.}, } @article {pmid39864640, year = {2025}, author = {Wang, BC and Jeng, ML and Tsai, JF and Wu, LW}, title = {Genome skimming for improved phylogenetics of Taiwanese phasmids (Insecta: Phasmatodea).}, journal = {Molecular phylogenetics and evolution}, volume = {205}, number = {}, pages = {108292}, doi = {10.1016/j.ympev.2025.108292}, pmid = {39864640}, issn = {1095-9513}, abstract = {Taiwan, a relatively young continental island, harbors a high proportion of endemic phasmids, reflecting its unique evolutionary history. However, a comprehensive phylogenetic framework to clarify these phasmids is still lacking. In this study, we sequenced ten of eleven valid genera and two undescribed species of Taiwanese phasmids (total 16 species) using the genome-skimming approach. We also integrated these sequences with public databases to create two aligned datasets: one comprising 92 taxa (mitogenomes) and the other 606 taxa (seven nuclear and mitochondrial genes), enabling us to examine their phylogenetic relationships using longer sequences and more samples. Our analyses show that Taiwanese phasmids should be categorized into six families, with a revised number of genera to 13. Furthermore, four species require taxonomic treatments: namely Micadina honei (Günther, 1940) comb. nov., Micadina truncatum (Shiraki, 1935) comb. nov., Otraleus okunii (Shiraki, 1935) comb. nov., and Ramulus granulatus (Shiraki, 1935) syn. nov. now recognized as Ramulus artemis (Westwood, 1859). While some Taiwanese genera exhibit polyphyletic relationships, our findings highlight the importance of taxon sampling, particularly for type species in resolving these systematic issues. The genome-skimming approach has proven to be an excellent method for producing comparable sequence datasets, facilitating the investigation of highly diverse insects, even when samples are old, small, or have highly fragmented DNAs.}, } @article {pmid39864304, year = {2025}, author = {Labarga, D and Mairata, A and Puelles, M and Wallner, A and Aziz, A and Alícia, P}, title = {Rootstocks and drought stress impact the composition and functionality of grapevine rhizosphere bacterial microbiota.}, journal = {Microbiological research}, volume = {293}, number = {}, pages = {128073}, doi = {10.1016/j.micres.2025.128073}, pmid = {39864304}, issn = {1618-0623}, abstract = {The microbiota, a component of the plant holobiont, plays an active role in the response to biotic and abiotic stresses. Nowadays, with recurrent drought and global warming, a growing challenge in viticulture is being addressed by different practices, including the use of adapted rootstocks. However, the relationships between these practices, abiotic stress and the composition and functions of the rhizosphere microbiota remain to be deciphered. This study aimed to unravel the impact of five rootstocks, water management and the combination of both on the rhizosphere bacterial microbiota in grapevines using shotgun metagenomics approach. The results showed that drought impacted the diversity, composition and functionality of the rhizosphere bacterial community. The genera Mycolicibacterium, Mycobacterium and Rhodococcus, and the bacterial functions, including DNA damage repair, fatty acid synthesis, sugar and amino acid transport, oxidative stress reduction, toxin synthesis and detoxification of exogenous compounds were significantly enriched under drought conditions. Rootstocks also significantly affected the rhizosphere bacterial richness but its influence on diversity and functionality compared to water management was weaker. Some taxa and function could be linked to water managements applied. The interaction between rootstocks and water management further influenced the rhizosphere composition, especially under drought conditions, where distinct clustering was observed for specific rootstocks. The results highlight the importance of conducting multifactorial studies to better understand their impact on shaping functional rhizosphere bacterial communities. This study paves the way for future research on beneficial bacterial inoculation and genetic engineering of rootstock to cope with drought stress.}, } @article {pmid39864165, year = {2025}, author = {Wang, XP and Han, NN and Yang, JH and Fan, NS and Jin, RC}, title = {Metagenomic insight into the diffusion signal factor mediated social traits of anammox consortia after starvation.}, journal = {Journal of environmental management}, volume = {375}, number = {}, pages = {124270}, doi = {10.1016/j.jenvman.2025.124270}, pmid = {39864165}, issn = {1095-8630}, mesh = {*Oxidation-Reduction ; Quorum Sensing ; Ammonium Compounds/metabolism ; Anaerobiosis ; Metagenomics ; Nitrogen/metabolism ; Microbial Consortia ; Wastewater/microbiology ; Geobacter/metabolism ; Bacteria/metabolism ; }, abstract = {Biomass starvation is common in biological wastewater treatment. As a social trait of microbial community, how quorum sensing (QS) regulated bacterial trade-off through interactions after starvation remains unclear. This study deciphered the mechanism of anaerobic ammonium oxidation (anammox) consortia in response to starvation, including reducing extracellular electron transfer (EET), adenosine 5'-triphosphate (ATP) content and amino acid metabolism. Metagenomic analysis has shown that the addition of the diffusion signal factor (DSF) resulted in a high abundance of antioxidant genes, which contributed to achieving redox balance in anammox bacteria. There was an enrichment of Geobacter and Methanosarcina, which were QS-responsive direct interspecific electron transfer participants. Furthermore, DSF stimulated the nitrogen and carbon metabolism of Ca. Kuenenia_stuttgartiensis, promoting syntrophy of metabolic intermediates within microbial community. This study highlighted the effect of DSF on the microbial interaction patterns and deciphered the QS-based social traits of anammox consortia after starvation, facilitating the stable operation of the anammox process.}, } @article {pmid39862584, year = {2025}, author = {Zheng, Z and Ji, W and Wang, X and Wang, X and Dai, S and Zhang, Z and Zhang, Y and Wang, X and Cao, S and Chen, M and Xie, B and Feng, J and Wu, D}, title = {Household waste-specific ambient air shows greater inhalable antimicrobial resistance risks in densely populated communities.}, journal = {Waste management (New York, N.Y.)}, volume = {194}, number = {}, pages = {309-317}, doi = {10.1016/j.wasman.2025.01.030}, pmid = {39862584}, issn = {1879-2456}, abstract = {Household waste is a hotspot of antibiotic resistance, which can be readily emitted to the ambient airborne inhalable particulate matters (PM10) during the day-long storage in communities. Nevertheless, whether these waste-specific inhalable antibiotic resistance genes (ARGs) are associated with pathogenic bacteria or pose hazards to local residents have yet to be explored. By high-throughput metagenomic sequencing and culture-based antibiotic resistance validation, we analyzed 108 airborne PM10 and nearby environmental samples collected across different types of residential communities in Shanghai, the most populous city in China. Compared to the cold-dry period, the warm-humid season had significantly larger PM10-associated antibiotic resistomes in all types of residential communities (T-test, P < 0.001), most of airborne ARGs in which were estimatedly originated from disposed household waste (∼ 30 %). In addition, the airborne bacteria were assembled in a deterministic approach (iCAMP, P < 0.01), where the waste-specific bacteria taxa including Acinetobacter, Pseudomonas, Rhodococcus, and Kocuria had the predominant niches in the airborne microbial assemblages. Notably, these waste-sourced bacteria were also identified as the primary airborne hosts of ARGs encoding the aminoglycoside resistances. Among them, some antibiotic resistant human pathogens, such as Pseudomonas aeruginosa and Acinetobacter baumannii, not only exhibited higher ARG horizontal gene transfer (HGT) potential across the microbial assemblages, but also imposed direct infection risks on the local residents by 2 min inhalation exposure per day. When the daily exposure duration increased to 11 min, the infection-induced illness burden became unignorably high, especially in densely populated urban communities, being twofold greater than rural areas.}, } @article {pmid39862030, year = {2025}, author = {Xie, J and Li, G and Lin, F and Bai, Z and Yu, L and Zhang, D and Zhang, B and Ye, J and Yu, R}, title = {Acute Q Fever after Kidney Transplantation: A Case Report.}, journal = {British journal of hospital medicine (London, England : 2005)}, volume = {86}, number = {1}, pages = {1-10}, doi = {10.12968/hmed.2024.0604}, pmid = {39862030}, issn = {1750-8460}, mesh = {Humans ; *Kidney Transplantation/adverse effects ; *Q Fever/diagnosis ; Male ; Middle Aged ; Immunocompromised Host ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {Aims/Background Patients receiving kidney transplant experience immunosuppression, which increases the risk of bacterial, viral, fungal, and parasitic infections. Q fever is a potentially fatal infectious disease that affects immunocompromised renal transplant recipients and has implications in terms of severe consequences for the donor's kidney. Case Presentation A patient with acute Q fever infection following kidney transplantation was admitted to the Tsinghua Changgung Hospital in Beijing, China, in March 2021. Next-generation sequencing (NGS) was used to diagnose Q fever in the patient. Based on the patient's blood test, we detected Rickettsia, the causative agent of Q fever and a zoonotic disease that can manifest in acute or chronic forms in humans. Comprehensive data on clinical symptoms, blood tests, chest computed tomography (CT), NGS, Immunoglobulin G (IgG) antibody titer, and therapeutic efficacy associated with Q fever infection following renal transplantation in this patient were gathered. Conclusion This is the first reported case of acute Q fever occurring in a Chinese renal transplant recipient detected using metagenomic NGS. This case underscores the need to consider acute Q fever as a possible differential diagnosis in kidney transplant recipients with fever of unknown origin.}, } @article {pmid39861970, year = {2025}, author = {Saati-Santamaría, Z and Navarro-Gómez, P and Martínez-Mancebo, JA and Juárez-Mugarza, M and Flores, A and Canosa, I}, title = {Genetic and species rearrangements in microbial consortia impact biodegradation potential.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf014}, pmid = {39861970}, issn = {1751-7370}, abstract = {Genomic reorganisation between species and horizontal gene transfer have been considered the most important mechanism of biological adaptation under selective pressure. Still, the impact of mobile genes in microbial ecology is far from being completely understood. Here we present the collection and characterisation of microbial consortia enriched from environments contaminated with emerging pollutants, such as non-steroidal anti-inflammatory drugs. We have obtained and further enriched two ibuprofen-degrading microbial consortia from two unrelated wastewater treatment plants. We have also studied their ability to degrade the drug and the dynamics of the reorganisations of the genetic information responsible for its biodegradation among the species within the consortium. Our results show that genomic reorganisation within microorganisms and species rearrangements occur rapidly and efficiently during the selection process, which may be facilitated by plasmids and/or transposable elements located within the sequences. We show the evolution of at least two different plasmid backbones on samples from different locations, showing rearrangements of genomic information, including genes encoding activities for IBU degradation. As a result, we found variations in the expression pattern of the consortia after evolution under selective pressure, as an adaptation process to the new conditions. This work provides evidence for changes in the metagenomes of microbial communities that allow adaptation under a selective constraint -ibuprofen as a sole carbon source- and represents a step forward in knowledge that can inspire future biotechnological developments for drug bioremediation.}, } @article {pmid39861854, year = {2025}, author = {Hyman, P}, title = {Are You My Host? An Overview of Methods Used to Link Bacteriophages with Hosts.}, journal = {Viruses}, volume = {17}, number = {1}, pages = {}, pmid = {39861854}, issn = {1999-4915}, mesh = {*Bacteriophages/genetics/physiology ; *Host Specificity ; *Bacteria/virology/genetics ; *Genome, Viral ; Metagenomics/methods ; }, abstract = {Until recently, the only methods for finding out if a particular strain or species of bacteria could be a host for a particular bacteriophage was to see if the bacteriophage could infect that bacterium and kill it, releasing progeny phages. Establishing the host range of a bacteriophage thus meant infecting many different bacteria and seeing if the phage could kill each one. Detection of bacterial killing can be achieved on solid media (plaques, spots) or broth (culture clearing). More recently, additional methods to link phages and hosts have been developed. These include methods to show phage genome entry into host cells (e.g., PhageFISH); proximity of phage and host genomes (e.g., proximity ligation, polonies, viral tagging); and analysis of genomes and metagenomes (e.g., CRISPR spacer analysis, metagenomic co-occurrence). These methods have advantages and disadvantages. They also are not measuring the same interactions. Host range can be divided into multiple host ranges, each defined by how far the phage can progress in the infection cycle. For example, the ability to effect genome entry (penetrative host range) is different than the ability to produce progeny (productive host range). These different host ranges reflect bacterial defense mechanisms that block phage growth and development at various stages in the infection cycle. Here, I present a comparison of the various methods used to identify bacteriophage-host relationships with a focus on what type of host range is being measured or predicted.}, } @article {pmid39861802, year = {2024}, author = {Musaeva, T and Fadeev, A and Pisareva, M and Eder, V and Ksenafontov, A and Korzhanova, M and Tsvetkov, V and Perederiy, A and Kiseleva, I and Danilenko, D and Lioznov, D and Komissarov, A}, title = {Development of Primer Panels for Whole-Genome Amplification and Sequencing of Human Seasonal Coronaviruses: hCoV-OC43, hCoV-HKU1, hCoV-229E, and hCoV-NL63.}, journal = {Viruses}, volume = {17}, number = {1}, pages = {}, pmid = {39861802}, issn = {1999-4915}, support = {#TVKQ-2024-0003 "Complex approach to genetic characterization and early identifications of pathogens with epidemic and pandemic potential using metagenomic sequencing"//Ministry of Health of the Russian Federation/ ; }, mesh = {Humans ; *Whole Genome Sequencing/methods ; *Seasons ; *Genome, Viral ; *Coronavirus/genetics/classification/isolation & purification ; *Coronavirus Infections/virology/epidemiology ; *Phylogeny ; Russia/epidemiology ; Retrospective Studies ; Coronavirus OC43, Human/genetics/isolation & purification/classification ; Coronavirus 229E, Human/genetics/isolation & purification/classification ; Coronavirus NL63, Human/genetics/isolation & purification ; Nasopharynx/virology ; Respiratory Tract Infections/virology/epidemiology ; }, abstract = {Human seasonal coronaviruses (hCoVs) are a group of viruses that affect the upper respiratory tract. While seasonal patterns and the annual variability of predominant hCoV species are well-documented, their genetic and species diversity in St. Petersburg and across Russia remains largely unexplored. In this study, we developed a two-pool, long-amplicon (900-1100 bp) PCR primer panel for the whole-genome sequencing of four seasonal hCoV species. The panel was validated using nasopharyngeal swab samples collected within the Global Influenza Hospital Surveillance Network (GIHSN) project. Over a period of six epidemiological seasons from 2017 to 2023, we retrospectively analyzed 14,704 nasopharyngeal swabs collected from patients hospitalized in St. Petersburg clinics. Of these samples, 5010 (34.07%) tested positive for respiratory viruses, with 424 (2.88% of all samples) identified as seasonal human coronaviruses. The assessment of species diversity showed that predominant hCoV species alternate between seasons. Whole-genome sequences for 85 seasonal human coronaviruses (hCoVs) with >70% genome coverage were obtained, including 23 hCoV-OC43, 6 hCoV-HKU1, 39 hCoV-229E, and 17 hCoV-NL63. These represent the first near-complete genomes of seasonal hCoVs from the Russian Federation, addressing a significant gap in the genomic epidemiology of these viruses. A detailed phylogenetic analysis of the sequenced genomes was conducted, highlighting the emergence of hCoV-229E subclades 7b.1 and 7b.2, which carry numerous substitutions in the Spike protein. Additionally, we sequenced a historical hCoV-229E isolate collected in the USSR in 1979, the oldest sequenced 229E virus from Eurasia, and demonstrated that it belongs to Genotype 2. The newly developed PCR-based sequencing protocol for seasonal hCoVs is straightforward and well-suited for genomic surveillance, providing a valuable tool to enhance our understanding of the genetic diversity of human seasonal coronaviruses.}, } @article {pmid39861468, year = {2025}, author = {Fricker, AD and Sejane, K and Desai, M and Snyder, MW and Duran, L and Mackelprang, R and Bode, L and Ross, MG and Flores, GE}, title = {A Pilot Study Exploring the Relationship Between Milk Composition and Microbial Capacity in Breastfed Infants.}, journal = {Nutrients}, volume = {17}, number = {2}, pages = {}, pmid = {39861468}, issn = {2072-6643}, support = {R21 HD104028/HD/NICHD NIH HHS/United States ; SC1GM136546/GM/NIGMS NIH HHS/United States ; R01 HD099813/HD/NICHD NIH HHS/United States ; SC1 GM136546/GM/NIGMS NIH HHS/United States ; R01HD099813/HD/NICHD NIH HHS/United States ; R21HD104028/HD/NICHD NIH HHS/United States ; }, mesh = {Humans ; *Milk, Human/chemistry/microbiology ; Pilot Projects ; Female ; *Gastrointestinal Microbiome ; Infant ; *Breast Feeding ; *Oligosaccharides/analysis ; Adult ; *Feces/microbiology/chemistry ; Cross-Sectional Studies ; Male ; Body Mass Index ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation & purification ; Overweight/microbiology ; Infant, Newborn ; Obesity/microbiology ; }, abstract = {BACKGROUND: Maternal obesity may contribute to childhood obesity in a myriad of ways, including through alterations of the infant gut microbiome. For example, maternal obesity may contribute both directly by introducing a dysbiotic microbiome to the infant and indirectly through the altered composition of human milk that fuels the infant gut microbiome. In particular, indigestible human milk oligosaccharides (HMOs) are known to shape the composition of the infant gut microbiome. The goal of this study was to characterize the HMO profiles of normal-weight and overweight mothers and to quantitatively link HMO concentrations to the taxonomic composition and functional potential of the infant gut microbiome.

METHODS: Normal-weight (BMI = 18.5-24.9; n = 9) and overweight/obese (OW/OB; BMI > 25; n = 11) breastfeeding mothers and their infants were enrolled in this single-center, cross-sectional pilot study. Human milk from the mothers and rectal stool swabs from the infants were collected 7-9 weeks postpartum. The HMO composition, microbiome composition, and microbial functions were assessed using HPLC, 16S rRNA gene sequencing, and metagenomic sequencing, respectively.

RESULTS: Neither the HMO profiles nor the infant microbiome composition varied according to maternal BMI status. Taxonomically, the gut microbiota of infants were dominated by typical gut lineages including Bifidobacterium. Significant correlations between individual HMOs and bacterial genera were identified, including for Prevotella, a genus of the Bacteroidota phylum that was positively correlated with the concentrations of lacto-N-neotetraose (LNnT) and lacto-N-hexaose (LNH). Using metagenomic assembled genomes, we were also able to identify the broad HMO-degradative capacity across the Bifidobacterium and Prevotella genera.

CONCLUSIONS: These results suggest that the maternal BMI status does not impact the HMO profiles of human milk. However, select HMOs were correlated with specific bacterial taxa, suggesting that the milk composition influences both the taxonomic composition and the functional capacity of the infant gut microbiome.}, } @article {pmid39860994, year = {2025}, author = {Shringi, S and Shah, DH and Carney, K and Verma, A}, title = {Pathogen Detection and Resistome Analysis in Healthy Shelter Dogs Using Whole Metagenome Sequencing.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {1}, pages = {}, pmid = {39860994}, issn = {2076-0817}, support = {Grant#19KC001//an institutional research grant from Richard A. Gillespie College of Veterinary Medicine, Lincoln Memorial University/ ; }, mesh = {Animals ; Dogs/microbiology ; *Feces/microbiology ; *Metagenome ; Drug Resistance, Microbial/genetics ; Bacteria/genetics/drug effects/isolation & purification ; Virginia/epidemiology ; Kentucky/epidemiology ; Tennessee/epidemiology ; Metagenomics/methods ; }, abstract = {According to the Humane Society, 25 to 40 percent of pet dogs in the United States are adopted from animal shelters. Shelter dogs can harbor bacterial, viral, fungal, and protozoal pathogens, posing risks to canine and human health. These bacterial pathogens may also carry antibiotic resistance genes (ARGs), serving as a reservoir for antimicrobial resistance (AMR) transmission. This study aimed to utilize whole metagenome sequencing (WMS) to screen for microbial pathogens and assess the resistome in healthy shelter dogs. Fecal samples from 58 healthy shelter dogs across 10 shelters in Kentucky, Tennessee, and Virginia were analyzed using WMS. Genomic DNA was extracted, and bioinformatics analyses were performed to identify pathogens and ARGs. The WMS detected 53 potentially zoonotic or known pathogens including thirty-eight bacterial species, two protozoa, five yeast species, one nematode, four molds, and three viruses. A total of 4560 ARGs signatures representing 182 unique genes across 14 antibiotic classes were detected. Tetracycline resistance genes were most abundant (49%), while β-lactam resistance genes showed the highest diversity with 75 unique ARGs. ARGs were predominantly detected in commensal bacteria; however, nearly half (18/38, 47.4%) of known bacterial pathogens detected in this study carried ARGs for resistance to one or more antibiotic classes. This study provides evidence that healthy shelter dogs carry a diverse range of zoonotic and antibiotic-resistant pathogens, posing a transmission risk through fecal shedding. These findings highlight the value of WMS for pathogen detection and AMR surveillance, informing therapeutic and prophylactic strategies to mitigate the transmission of pathogens among shelter dog populations and the risk associated with zoonoses.}, } @article {pmid39860966, year = {2024}, author = {Laryushina, Y and Samoilova-Bedych, N and Turgunova, L and Marchenko, A and Turgunov, Y and Kozhakhmetov, S and Suieubayev, M and Mukhanbetzhanov, N and Kabdulina, N}, title = {Interrelationships of the Intestinal Microbiome, Trimethylamine N-Oxide and Lipopolysaccharide-Binding Protein with Crohn's Disease Activity.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {1}, pages = {}, pmid = {39860966}, issn = {2076-0817}, support = {AP14871959//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; }, mesh = {Humans ; *Methylamines/metabolism ; *Gastrointestinal Microbiome/physiology ; *Crohn Disease/microbiology/metabolism ; Female ; Male ; Adult ; *Acute-Phase Proteins/metabolism/analysis ; *Feces/microbiology/chemistry ; Middle Aged ; *Membrane Glycoproteins/metabolism ; Carrier Proteins/metabolism ; Young Adult ; Lipopolysaccharides/metabolism ; }, abstract = {UNLABELLED: Crohn's disease (CD) is a multifactorial inflammatory bowel disease whose pathogenetic mechanisms are a field of ongoing study. Changes in the intestinal microbiome in CD may influence metabolite production and reflect the disease's severity. We investigate the relationship between trimethylamine N-oxide (TMAO) and lipopolysaccharide-binding protein (LPS) levels and changes in the gut microbiome in patients with CD of various degrees of activity.

METHODS: In total, 29 CD patients and 15 healthy individuals were investigated for their levels of TMAO by HPLC-MS, and LPS protein by ELISA and metagenomic 16 s-sequencing of feces was performed.

RESULTS: We found significant differences in TMAO levels in patients in the remission/mild and moderate/severe groups compared to the control group (p = 0.02 and p = 0.014), changes in alpha diversity with the Shannon index (p = 0. 0151 and p = 0.0018) and in beta diversity (ANOSIM p = 0.009 and PERMANOVA p = 0.005) in both groups compared to controls. Strongly positive correlations in TMAO levels and mixed correlations of LPS with alpha diversity metrics were found, as well as significant correlations with microbiota species.

CONCLUSIONS: Changes in the level of metabolites may reflect specific disturbances in the composition of the intestinal microbiome at different degrees of severity of CD.}, } @article {pmid39860395, year = {2025}, author = {Ullah, N and Fusco, L and Ametrano, L and Bartalucci, C and Giacobbe, DR and Vena, A and Mikulska, M and Bassetti, M}, title = {Diagnostic Approach to Pneumonia in Immunocompromised Hosts.}, journal = {Journal of clinical medicine}, volume = {14}, number = {2}, pages = {}, pmid = {39860395}, issn = {2077-0383}, abstract = {In immunocompromised patients, pneumonia presents a diagnostic challenge due to diverse etiologies, nonspecific symptoms, overlapping radiological presentation, frequent co-infections, and the potential for rapid progression to severe disease. Thus, timely and accurate diagnosis of all pathogens is crucial. This narrative review explores the latest advancements in microbiological diagnostic techniques for pneumonia in immunocompromised patients. It covers major available microbiological tools for diagnosing both community-acquired and hospital-acquired pneumonia, encompassing a wide spectrum of pathogens including bacterial, viral, fungal, and parasitic. While traditional culture methods remain pivotal in identifying many pneumonia-causing etiologies, their limitations in sensitivity and time to results have led to the rise of non-invasive antigen tests and molecular diagnostics. These are increasingly employed alongside cultures and microscopy for more efficient diagnosis, mainly in viral and fungal infections. Lastly, we report the future of pneumonia diagnostics, exploring the potential of metagenomics and CRISPR/Cas13a for more precise and rapid pathogen detection in immunocompromised populations.}, } @article {pmid39859429, year = {2025}, author = {Vicente-Valor, J and Tesolato, S and Paz-Cabezas, M and Gómez-Garre, D and Ortega-Hernández, A and de la Serna, S and Domínguez-Serrano, I and Dziakova, J and Rivera, D and Jarabo, JR and Gómez-Martínez, AM and Hernando, F and Torres, A and Iniesta, P}, title = {Fecal Microbiota Strongly Correlates with Tissue Microbiota Composition in Colorectal Cancer but Not in Non-Small Cell Lung Cancer.}, journal = {International journal of molecular sciences}, volume = {26}, number = {2}, pages = {}, pmid = {39859429}, issn = {1422-0067}, support = {PI19/00073//Carlos III Health Institute (Ministerio de Economía y Competitividad), Spain and co-funded by the European Union through the European Regional Development Fund (ERDF) 'A way to make Europe'/ ; }, mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/microbiology ; *Feces/microbiology ; *Colorectal Neoplasms/microbiology ; *Lung Neoplasms/microbiology ; Female ; Male ; Middle Aged ; Aged ; RNA, Ribosomal, 16S/genetics ; Microbiota/genetics ; Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; Adult ; }, abstract = {Microbiota could be of interest in the diagnosis of colorectal and non-small cell lung cancer (CRC and NSCLC). However, how the microbial components of tissues and feces reflect each other remains unknown. In this work, our main objective is to discover the degree of correlation between the composition of the tissue microbiota and that of the feces of patients affected by CRC and NSCLC. Specifically, we investigated tumor and non-tumor tissues from 38 recruited patients with CRC and 19 with NSCLC. DNA from samples was submitted for 16S rDNA metagenomic sequencing, followed by data analysis through the QIIME2 pipeline and further statistical processing with STATA IC16. Tumor and non-tumor tissue selected genera were highly correlated in both CRC and NSCLC (100% and 81.25%). Following this, we established tissue-feces correlations, using selected genera from a LEfSe analysis previously published. In CRC, we found a strong correlation between the taxa detected in feces and those from colorectal tissues. However, our data do not demonstrate this correlation in NSCLC. In conclusion, our findings strongly reinforce the utility of fecal microbiota as a non-invasive biomarker for CRC diagnosis, while highlighting critical distinctions for NSCLC. Furthermore, our data demonstrate that the microbiota components of tumor and non-tumor tissues are similar, with only minor differences being detected.}, } @article {pmid39859368, year = {2025}, author = {Resman Rus, K and Bosilj, M and Triglav, T and Jereb, M and Zalaznik, M and Klešnik, M and Češljarac, D and Matičič, M and Avšič-Županc, T and Rus, T and Korva, M}, title = {Metagenomic Sequencing for Diagnosing Listeria-Induced Rhombencephalitis in Patient and Contaminated Cheese Samples: A Case Report.}, journal = {International journal of molecular sciences}, volume = {26}, number = {2}, pages = {}, pmid = {39859368}, issn = {1422-0067}, support = {P3-0083//The Slovenian Research and Innovation Agency/ ; J3-2515//The Slovenian Research and Innovation Agency/ ; }, mesh = {Humans ; *Cheese/microbiology ; Adult ; *Metagenomics/methods ; *Listeria monocytogenes/genetics/isolation & purification ; *Listeriosis/diagnosis/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; Hemolysin Proteins/genetics ; Heat-Shock Proteins/genetics ; Bacterial Toxins/genetics ; Encephalitis/diagnosis/microbiology ; Male ; Rhombencephalon/microbiology ; }, abstract = {Among the various causes of rhomboencephalitis, Listeria monocytogenes infection is the most common. However, conventional microbiological methods often yield negative results, making diagnosis challenging and leading to extensive, often inconclusive, diagnostics. Advanced molecular techniques like metagenomic next-generation sequencing (mNGS) offer a powerful and efficient approach to pathogen identification. We present a case of life-threatening rhomboencephalitis in a 32-year-old immunocompetent patient where extensive microbiological, immunological, and biochemical tests were inconclusive. Given the patient's consumption of unpasteurized homemade cheese, neurolisteriosis was suspected, and mNGS was employed on clinical samples (CSF, serum, urine) and the food source to identify the pathogen. mNGS detected L. monocytogenes in both patient samples and the cheese. Mapping reads were distributed across the genome, with 18.9% coverage in clinical samples and 11.8% in the cheese sample. Additionally, the Listeriolysin (hlyA) gene was detected with 22.3% coverage in clinical samples and 12.3% in the food source, confirming neurolisteriosis. The patient fully recovered following antibiotic treatment. This case underscores the importance of mNGS in diagnosing CNS infections when conventional methods yield negative results, and supports its inclusion in diagnostic protocols for suspected neurolisteriosis, particularly when traditional methods prove inadequate.}, } @article {pmid39858934, year = {2025}, author = {Wang, M and Valizadegan, N and Fields, CJ and Donovan, SM}, title = {Fecal Microbiome and Metabolomic Profiles of Mixed-Fed Infants Are More Similar to Formula-Fed than Breastfed Infants.}, journal = {Microorganisms}, volume = {13}, number = {1}, pages = {}, pmid = {39858934}, issn = {2076-2607}, support = {R01 DK107561/DK/NIDDK NIH HHS/United States ; R01 DK138032/DK/NIDDK NIH HHS/United States ; 1R01DK107561-05A1/NH/NIH HHS/United States ; 1R01DK138032-01A1/NH/NIH HHS/United States ; }, abstract = {Many infants consume both human milk and infant formula (mixed-fed); however, few studies have investigated how mixed feeding affects the gut microbiome composition and metabolic profiles compared to exclusive breastfeeding or formula feeding. Herein, how delivery mode and early nutrition affect the microbiome and metabolome of 6-week-old infants in the STRONG Kids2 cohort was investigated. Fecal samples were collected from exclusively breastfed (BF; n = 25), formula-fed (FF; n = 25) or mixed-fed (MF; n = 25) participants. Within each feeding group, infants were either delivered vaginally (VD; n = 13) or by Cesarean section (CS; n = 12). Feeding mode affects the fecal microbiome diversity, composition, and functional potential, as well as metabolomic profiles regardless of delivery mode. Alpha and beta diversity of MF differed from that of BF (p < 0.05) but were comparable to FF infants. Functional analyses have shown 117 potential metabolic pathways differed between BF and FF, 112 between BF and MF, and 8 between MF and FF infants (p < 0.05, q < 0.10). Fecal metabolomic profiles of MF and FF clustered together and separated from BF infants. In total, 543 metabolites differed between BF and FF, 517 between BF and MF, and 3 between MF and FF (p < 0.05, q < 0.10). Delivery mode affected overall microbial composition (p = 0.022) at the genus level and 24 potential functional pathways, with 16 pathways being higher in VD than CS infants (p < 0.05, q < 0.10). Metabolomic analysis identified 47 differential metabolites between CS and VD, with 39 being lower in CS than VD (p < 0.05, q < 0.10). In summary, fecal microbiota composition and function and metabolite profiles of 6-week-old MF infants are closer to FF than BF infants.}, } @article {pmid39858902, year = {2025}, author = {Bednarska, NG and Håberg, AK}, title = {Understanding Patterns of the Gut Microbiome May Contribute to the Early Detection and Prevention of Type 2 Diabetes Mellitus: A Systematic Review.}, journal = {Microorganisms}, volume = {13}, number = {1}, pages = {}, pmid = {39858902}, issn = {2076-2607}, abstract = {The rising burden of type 2 diabetes mellitus (T2DM) is a growing global public health problem, particularly prominent in developing countries. The early detection of T2DM and prediabetes is vital for reversing the outcome of disease, allowing early intervention. In the past decade, various microbiome-metabolome studies have attempted to address the question of whether there are any common microbial patterns that indicate either prediabetic or diabetic gut microbial signatures. Because current studies have a high methodological heterogeneity and risk of bias, we have selected studies that adhered to similar design and methodology. We performed a systematic review to assess if there were any common changes in microbiome belonging to diabetic, prediabetic and healthy individuals. The cross-sectional studies presented here collectively covered a population of 65,754 people, with 1800 in the 2TD group, 2770 in the prediabetic group and 61,184 in the control group. The overall microbial diversity scores were lower in the T2D and prediabetes cohorts in 86% of the analyzed studies. Re-programming of the microbiome is potentially one of the safest and long-lasting ways to eliminate diabetes in its early stages. The differences in the abundance of certain microbial species could serve as an early warning for a dysbiotic gut environment and could be easily modified before the onset of disease by changes in lifestyle, taking probiotics, introducing diet modifications or stimulating the vagal nerve. This review shows how metagenomic studies have and will continue to identify novel therapeutic targets (probiotics, prebiotics or targets for elimination from flora). This work clearly shows that gut microbiome intervention studies, if performed according to standard operating protocols using a predefined analytic framework (e.g., STORMS), could be combined with other similar studies, allowing broader conclusions from collating all global cohort studies efforts and eliminating the effect-size statistical insufficiency of a single study.}, } @article {pmid39858899, year = {2025}, author = {Fernández-Sánchez, V and Plascencia-Nieto, ES and Cureño-Díaz, MA and Durán-Manuel, EM and Rodríguez-Tovar, AV and Calzada-Mendoza, CC and Cruz-Cruz, C and Loyola-Cruz, MÁ and Álvarez-Sánchez, ME and Bravata-Alcántara, JC and Vásquez-Jiménez, E and Gutiérrez-Muñoz, VH and Blanco-Hernández, DMR and Nicolás-Sayago, L and Rojas-Bernabé, A and García-Hernández, O and Gómez-Zamora, E and Ruíz-Valdés, M and Castro-Escarpulli, G and Bello-López, JM}, title = {Massive Sequencing of V3-V4 Hypervariable Region in Pyogenic Liver Abscesses Reveals the Presence of Unusual Bacteria Not Detected by Classical Culture Methods.}, journal = {Microorganisms}, volume = {13}, number = {1}, pages = {}, pmid = {39858899}, issn = {2076-2607}, abstract = {Pyogenic liver abscesses (PLAs) are serious infections in which doctors often fail in identifying the causative agent due to microbiological limitations. These limitations in detecting uncommon pathogens complicate the treatment and recovery. Molecular techniques, like massive sequencing, enable the detection of uncommon pathogens and highlight the shortcomings of traditional cultures. The aim of this work was to characterise the bacterial composition of PLAs through massive sequencing of the V3-V4 hypervariable region of the 16S rRNA gene in cases where conventional culture methods were negative. Purulent material was collected from three patients with PLAs at Hospital Juárez de México. Classical and molecular microbiological cultures were performed in parallel. Metagenomic DNA was extracted and massively sequenced (16S rRNA gene) using the Illumina MiSeq platform. A bioinformatic analysis was performed to determine the diversity at six different taxa levels and the relative abundances. The culture methods were not sufficient to detect the causative agent of the PLAs. However, the massive sequencing revealed the causative agents of the monomicrobial and polymicrobial infectious foci, with Gardnerella vaginalis, Lactobacillus iners, and Prevotella timonensis as the dominant bacteria. The massive sequencing revealed the presence of unusual pathogens that traditional culture failed to detect. There is an immediate need for molecular or comprehensive microbiological culture techniques to search for unusual bacteria in the diagnosis of PLAs.}, } @article {pmid39858891, year = {2025}, author = {Malik, PK and Kolte, AP and Trivedi, S and Tamilmani, G and Mohapatra, A and Vaswani, S and Belevendran, J and Sahoo, A and Gopalakrishnan, A and Bhatta, R}, title = {Anti-Methanogenic Potential of Seaweeds and Impact on Feed Fermentation and Rumen Microbiome In Vitro.}, journal = {Microorganisms}, volume = {13}, number = {1}, pages = {}, pmid = {39858891}, issn = {2076-2607}, support = {CRP D31031//IAEA/ ; }, abstract = {A series of in vitro studies were conducted to explore the anti-methanogenic potential of five seaweeds collected from the Indian sea and to optimize the level(s) of incorporation of the most promising seaweed(s) into a straw and concentrate diet to achieve a significant reduction in methane (CH4) production without disturbing rumen fermentation characteristics. A chemical composition analysis revealed a notable ash content varying between 55 and 70% in seaweeds. The crude protein content was highly variable and ranged between 3.25 and 15.3% of dry matter. Seaweeds contained appreciable concentrations of tannins and saponins. Among the seaweeds, Spyridia filamentosa exhibited significantly higher CH4 production, whereas the percentage of CH4 in total gas was significantly lower in the cases of Kappaphycus alvarezii and Sargassum wightii. The ranking of seaweeds in terms of CH4 production (mL/g OM) is as follows: Sargassum wightii < Kappaphycus alvarezii < Acanthophora specifera < Padina gymnospora < Spyridia filamentosa. A remarkable decrease of 31-42% in CH4 production was recorded with the incremental inclusion of Kappaphycus alvarezii at levels of 3-5% of the dry matter in the diet. The addition of Sargassum wightii led to a significant decrease of 36-48% in CH4 emissions when incorporated at levels of 4-5% of dry matter, respectively. The findings of this study revealed a significant decrease in the numbers of total protozoa and Entodinomorphs, coupled with increasing abundances of sulfate-reducing microbes and minor methanogens. Metagenome data revealed that irrespective of the seaweed and treatment, the predominant microbial phyla included Bacteroidota, Bacillota, Pseudomonadota, Actinomycetota, Fibrobacterota, and Euryarchaeota. The prevalence of Methanobrevibacter was similar across treatments, constituting the majority (~79%) of the archaeal community. The results also demonstrated that the supplementation of Kappaphycus alvarezii and Sargassum wightii did not alter the feed fermentation pattern, and therefore, the reduction in CH4 production in the present study could not be attributed to it. Animal studies are warranted to validate the extent of reduction in CH4 production and the key processes involved by supplementation with Kappaphycus alvarezii and Sargassum wightii at the recommended levels.}, } @article {pmid39858847, year = {2025}, author = {Zeng, X and Wang, Q and Song, Q and Liang, Q and Sun, Y and Song, F}, title = {Effects of Different Nitrogen Fertilizer Application Rates on Soil Microbial Structure in Paddy Soil When Combined with Rice Straw Return.}, journal = {Microorganisms}, volume = {13}, number = {1}, pages = {}, pmid = {39858847}, issn = {2076-2607}, support = {CZKYF2023-1-B015//Heilongjiang Scientific Research Institutions/ ; }, abstract = {Metagenomic sequencing of the microbial soil community was used to assess the effect of various nitrogen fertilizer treatments in combination with constant rice straw return to the soil in the tiller layer of Northeast China's black paddy soil used for rice production. Here, we investigated changes in the composition, diversity, and structure of soil microbial communities in the soil treated with four amounts of nitrogen fertilizers (53, 93, 133, and 173 kg/ha) applied to the soil under a constant straw return of 7500 kg/ha, with a control not receiving N. The relationships between soil microbial community structure and soil physical and chemical properties were determined. The results showed that the available K content of the soil significantly (p < 0.05) increased in soil receiving the lowest N-fertilizer dose. When applied at high amounts, N-fertilizer changed the Chao1 and ACE indices of the soil microorganisms (p < 0.05), and the treatments resulted in significant differences in the β-diversity of the soil microorganisms. By NMDS analysis it was demonstrated that the treatment significantly affected the structure of the soil microbial communities. Redundancy analysis showed that the main physicochemical drivers behind these differences were total nitrogen, total potassium, ammonium nitrogen, total phosphorus, and available potassium. The soil microbial communities in the control treatment were negatively correlated with nitrate and ammonium nitrogen; the lowest N-fertilizer treatment produced positive correlations with total nitrogen, total potassium, and total phosphorus and negative correlations with ammonium nitrogen; the highest dose negatively correlated with total nitrogen, available potassium, available phosphorus, total phosphorus, and pH. This study showed that moderate N fertilizer application is an effective way to increase soil microbial diversity and improve soil quality. This experiment provides technical support for the application of the alternative fertilizer technology of straw return to the field and provides a theoretical basis for rational fertilization of paddy fields in a cold climate.}, } @article {pmid39858794, year = {2024}, author = {Zou, Y and Zou, Q and Yang, H and Han, C}, title = {Investigation of Intestinal Microbes of Five Zokor Species Based on 16S rRNA Sequences.}, journal = {Microorganisms}, volume = {13}, number = {1}, pages = {}, pmid = {39858794}, issn = {2076-2607}, support = {201929/WT_/Wellcome Trust/United Kingdom ; 2022ZD0117700//the National Science and Technology Major Project/ ; }, abstract = {Zokor is a group of subterranean rodents that are adapted to underground life and feed on plant roots. Here, we investigated the intestinal microbes of five zokor species (Eospalax cansus, Eospalax rothschildi, Eospalax smithi, Myospalax aspalax, and Myospalax psilurus) using 16S amplicon technology combined with bioinformatics. Microbial composition analysis showed similar intestinal microbes but different proportions among five zokor species, and their dominant bacteria corresponded to those of herbivores. To visualize the relationships among samples, PCoA and PERMANOVA tests showed that the intestinal microbes of zokors are largely clustered by host species, but less so by genetics and geographical location. To find microbes that differ among species, LefSe analysis identified Lactobacillus, Muribaculaceae, Lachnospiraceae_NK4A136_group, unclassified_f_Christensenellaceae, and Desulfovibrio as biomarkers for E. cansus, E. rothschildi, E. smithi, M. aspalax, and M. psilurus, respectively. PICRUSt metagenome predictions revealed enriched microbial genes for carbohydrate and amino acid metabolism in E. cansus and E. smithi, and for cofactor and vitamin metabolism as well as glycan biosynthesis and metabolism in E. rothschildi, M. aspalax, and M. psilurus. Our results demonstrated differences in the microbial composition and functions among five zokor species, potentially related to host genetics, and host ecology including dietary habits and habitat environment. These works would provide new insight into understanding how subterranean zokors adapt to their habitats by regulating intestinal microbes.}, } @article {pmid39858581, year = {2024}, author = {Koreeda, T and Honda, H and Onami, JI}, title = {Snowflake Data Warehouse for Large-Scale and Diverse Biological Data Management and Analysis.}, journal = {Genes}, volume = {16}, number = {1}, pages = {}, pmid = {39858581}, issn = {2073-4425}, mesh = {*Computational Biology/methods ; Humans ; Cloud Computing ; Data Management/methods ; High-Throughput Nucleotide Sequencing/methods ; Genomics/methods ; }, abstract = {With the increasing speed of genomic, transcriptomic, and metagenomic data generation driven by the advancement and widespread adoption of next-generation sequencing technologies, the management and analysis of large-scale, diverse data in the fields of life science and biotechnology have become critical challenges. In this paper, we thoroughly discuss the use of cloud data warehouses to address these challenges. Specifically, we propose a data management and analysis framework using Snowflake, a SaaS-based data platform. We further demonstrate its convenience and effectiveness through concrete examples, such as disease variant analysis and in silico drug discovery. By introducing Snowflake, researchers can efficiently manage and analyze a wide array of biological data, enabling the discovery of new biological insights through integrated analysis. Through these specific methodologies and application examples, we aim to accelerate research progress in the field of bioinformatics.}, } @article {pmid39858184, year = {2025}, author = {Zhou, YH and Liu, XP and Gu, XM and Lv, HX and Yang, Y and Cai, ZX and Di, B and Wang, CK and Gao, YY and Jin, L}, title = {Effects of Dietary Nano-Composite of Copper and Carbon on Antioxidant Capacity, Immunity, and Cecal Microbiota of Weaned Ira White Rabbits.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {2}, pages = {}, pmid = {39858184}, issn = {2076-2615}, support = {2023YFD1600500//National Key Research and Development Program of China/ ; 2023N0008//Agricultural Guiding (Key) Project of Fujian Provincial Science and Technology Department/ ; 2022L3085//Science and Technology Development Projects Funded by Chinese Central and Local Governments/ ; KFB23099A//Science and Technology Innovation Special Fund Project of Fujian Agriculture and Forestry University/ ; 2022J01587//Project of Natural Science Foundation of Fujian Province/ ; K83139297, 2019-2022//Fujian Specialist Funds of Chicken Industrial System in China/ ; }, abstract = {This experiment investigated the effects of dietary supplementation with nano-composites of copper and carbon (NCCC) on antioxidants, immune functions, and the cecum microbiota of weaned Ira white rabbits. A total of 240 weaned 35-day-old Ira white rabbits were randomly allocated to five dietary treatments (n = 6 per treatment, each replicate consisted of eight rabbits) that included the control group (CON) with a basal diet, the SAL group with 60 mg/kg salinomycin (SAL) in addition to the basal diet, and the NCCC I, II, III groups, which were supplemented with 50, 100, and 200 mg/kg NCCC, respectively, in addition to the basal diet. The test lasted for 28 d. The results showed that dietary NCCC supplementation increased the liver Cu/Zn-SOD content and up-regulated the gene expression of Cu/Zn-SOD (p < 0.05), while also reducing the content of MDA in the liver and enhancing the antioxidant capacity of Ira white rabbits. Moreover, the NCCC diet supplementation reduced the content of IL-6 and down-regulated the relative expression of IL-6 and IL-1β genes in the jejunum of Ira white rabbits (p < 0.05). In addition, the metagenomic analysis of 16 S rRNA showed significant differences in the cecal microbial structure of weaned Ira white rabbits in the NCCC III group compared with the CON, NCCC I, and NCCC II groups (p < 0.05). Firmicutes and Bacteroidetes were the dominant phyla of cecal microorganisms in weaned Ira rabbits in the NCCC diet groups. The dominant genera included unidentified Eubacteriaceae, unclassified Lachnospiraceae, Christensenellaceae, and Ruminococcus. Furthermore, the relative abundance of Ruminococcus in the NCCC I and II groups was lower than that in the CON group in the cecum of Ira white rabbits (p < 0.05). In summary, our results showed that diet supplementation with NCCC could enhance the antioxidant capacity in the liver, alleviate intestinal inflammation, and regulate the structure of intestinal flora, improving the health of Ira white rabbits.}, } @article {pmid39857726, year = {2025}, author = {Chou, MJ and Cheng, CH and Wang, HC and Tsai, MJ and Sheu, CC and Chang, WA}, title = {Investigating the Pulmonary Host Response of Acinetobacter baumannii Infection-Associated Pneumonia by Metagenomic Next-Generation Sequencing.}, journal = {Biomedicines}, volume = {13}, number = {1}, pages = {}, pmid = {39857726}, issn = {2227-9059}, support = {KMUH111-1M06//Kaohsiung Medical University Chung-Ho Memorial Hospital/ ; }, abstract = {Background: For investigating the host response in Acinetobacter baumannii associated pneumonia, we analyzed the host genetic sequences obtained from metagenomic next-generation sequencing (mNGS). Methods: The samples for mNGS were bronchoalveolar lavage fluid (BALF) collected from the lungs of patients infected with A. baumannii and from patients without bacterial infections. BALF samples from patients with pneumonia were collected from the lungs of patients infected with A. baumannii with New Delhi metallo-β-lactamase (NDM, before treatment), A. baumannii with NDM (post-treatment), A. baumannii without resistant genes, and those without bacterial infection. Partek was used for investigating enriched functions and pathways related to the pulmonary host response to pneumonia caused by A. baumannii with NDM infection and A. baumannii without antimicrobial-resistant genes. The STRING was employed for identifying protein interaction pathways related to the pulmonary host response to pneumonia caused by A. baumannii without antimicrobial-resistant genes. Results: In pulmonary host response to pneumonia caused by A. baumannii with NDM, five immune system-related pathways and five pathways related to signal transduction were identified. No significant differences were observed in the immune system and signal transduction pathways in the pulmonary host response to pneumonia caused by A. baumannii without antimicrobial-resistant genes. However, significant differences were noted in the phagosome, ferroptosis, and regulation of the actin cytoskeleton in cellular processes. Conclusions: mNGS provides information not only on pathogen gene expression but also on host gene expression. In this study, we found that pneumonia with A. baumannii carrying the NDM resistance gene triggers stronger immune responses in the lung, while pneumonia with A. baumannii lacking antimicrobial resistance genes is more linked to iron-related pathways.}, } @article {pmid39857615, year = {2024}, author = {Giampani, A and Simitsopoulou, M and Sdougka, M and Paschaloudis, C and Roilides, E and Iosifidis, E}, title = {The Combinational Effect of Enhanced Infection Control Measures and Targeted Clinical Metagenomics Surveillance on the Burden of Endemic Carbapenem and Other β-Lactam Resistance Among Severely Ill Pediatric Patients.}, journal = {Biomedicines}, volume = {13}, number = {1}, pages = {}, pmid = {39857615}, issn = {2227-9059}, support = {xx//Procter & Gamble and Gilead Sciences and by the Department of Biology of Aristotle University of Thessaloniki/ ; }, abstract = {Background: Antimicrobial resistance (AMR) is recognized as one of the most important global public health threats. There is an urgent need to reduce the spread of these multidrug-resistant bacteria (MDR-B), particularly in extremely vulnerable patients. The aim of this study was to investigate whether targeted gene amplification performed directly on clinical samples can be used simultaneously with a bundle of enhanced infection control measures in a Pediatric Intensive Care Unit (PICU) endemic to MDR-B. Methods: This study had three phases: (1) the baseline phase was performed prior to intervention when first screening and sample collection were performed; (2) the intervention phase was performed when various enhanced infection control measures (EICM) were applied; and (3) the maintenance phase occurred when EICMs were combined with the implementation of targeted molecular surveillance. The presence of four carbapenemase genes, blaKPC, blaOXA-48-like, blaVIM, and blaNDM, as well as the β-lactamase genes blaTEM and blaSHV, was evaluated by PCR after DNA isolation directly from stool samples. The results were compared to culture-based phenotypic analysis. Results and Conclusions: The implementation of EICM appeared to reduce the resistance burden in this sample endemic to an MDR-B clinical setting. The direct implementation of a targeted and customized rapid molecular detection assay to clinical samples seems to be an effective clinical tool for the evaluation of EICM measures.}, } @article {pmid39857379, year = {2025}, author = {Wu, H and Qin, B and Yang, G and Ji, P and Gao, Y and Zhang, L and Wang, B and Liu, G}, title = {The Protective Effects of Melatonin on Hainan Black Goats Under Heat Stress: Understanding Its Actions and Mechanisms.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {14}, number = {1}, pages = {}, pmid = {39857379}, issn = {2076-3921}, support = {32302749//National Natural Science Foundation of China/ ; ZDYF2021XDNY174//Hainan Province key research and development plan/ ; }, abstract = {As the global climate changes, high temperatures will cause heat stress, which significantly affects the productive efficiency of livestock. Currently, there is a lack of efficient methods to use in targeting this issue. In this study, we report that melatonin supplementation may represent an alternative method to reduce the negative impact of heat stress on livestock, particularly in Hainan black goats. Our results show that melatonin treatment increased the average daily gain of Hainan black goats that were exposed to constantly high temperatures for two months compared to controls. Our mechanistic exploration revealed that melatonin treatment not only reduced the oxidative stress and inflammatory reaction caused by heat stress but also improved goats' metabolic capacity, promoting their growth and development. More importantly, for the first time, we observed that melatonin treatment modified the abundance of the intestinal microflora, altering the metabolism of the goats, which further improved their tolerance to constant heat stress.}, } @article {pmid39857331, year = {2025}, author = {Liu, Y and Zhang, Y and Yao, H and Zheng, Z and Zhao, W and Lin, G}, title = {Analysis on Bacterial Community of Noctiluca scintillans Algal Blooms Near Pingtan Island, China.}, journal = {Biology}, volume = {14}, number = {1}, pages = {}, pmid = {39857331}, issn = {2079-7737}, support = {No. 2022L3010//Fujian Normal University/ ; }, abstract = {Noctiluca scintillans, known as a global red tide species, is a common red tide species found in Pingtan Island. To examine the bacterial community structure in different environments during the red tide period of N. scintillans on Pingtan Island, samples were collected from the Algal Bloom Area (ABA), Transition Area (TA), and Non-Algal Bloom Area (NBA) on 6 April 2022, and the environmental physicochemical factors and bacterial community were determined. The outbreak of N. scintillans red tide significantly impacted the water quality and bacterial community structure in the affected sea area. The water quality in the ABA has deteriorated markedly, with the contents of COD, NH4[+]-N, and PO4[3-] in the ABA being significantly higher than those in the TA and NBA, while the pH is significantly lower than that in the TA and NBA. The richness, diversity, and evenness of the bacterial community in the ABA are all lower than those of the TA and NBA. For instance, the Shannon index values of the three sampling points are 4.41, 5.41, and 6.37, respectively. At the phylum level, the dominant bacterial phyla in the ABA are Proteobacteria, Firmicutes, and Cyanobacteria; in the TA, they are Proteobacteria, Bacteroidetes, and Firmicutes; and in the NBA, they are Proteobacteria, Bacteroidetes, and Cyanobacteria. At the genus level, the dominant bacterial genera in the ABA are Vibrio, Carnobacterium, Candidatus_Megaira, Planktomarina, and Pseudoalteromonas; in the TA, they are Vibrio, Planktomarina, Lentibacter, Glaciecola, and Jannaschia; and in the NBA, they are Planktomarina, Amylibacter, NS5_marine_group, Aurantivirga, and marine_metagenome. In the ABA, the combined proportion of Vibrio and Carnobacterium exceeds 50%, with Vibrio_splendidus accounting for 93% of the total Vibrio population. These research results can provide a scientific basis for clarifying the environmental characteristics and bacterial composition during the large-scale N. scintillans red tide in Pingtan Island.}, } @article {pmid39857318, year = {2025}, author = {Kashchenko, G and Taldaev, A and Adonin, L and Smutin, D}, title = {Investigating Aerobic Hive Microflora: Role of Surface Microbiome of Apis Mellifera.}, journal = {Biology}, volume = {14}, number = {1}, pages = {}, pmid = {39857318}, issn = {2079-7737}, support = {No 075-15-2022-305//Ministry of Science and Higher Education of the Russian Federation within the framework of state support for the creation and development of World-Class Research Centers 'Digital Biodesign and Personalized Healthcare'./ ; }, abstract = {This study investigated the surface microbiome of the honeybee (Apis mellifera), focusing on the diversity and functional roles of its associated microbial communities. While the significance of the microbiome to insect health and behavior is increasingly recognized, research on invertebrate surface microbiota lags behind that of vertebrates. A combined metagenomic and cultivation-based approach was employed to characterize the bacterial communities inhabiting the honeybee exoskeleton. Our findings reveal a complex and diverse microbiota exhibiting significant spatial and environmental heterogeneity. The identification of antimicrobial compound producers, validated through both culture and metagenomic analyses, including potentially novel Actinobacteria species, underscores the potential impact of these microbial communities on honeybee health, behavior, and hive dynamics. This research contributes to a more profound ecological understanding of the honeybee microbiome, particularly in its winter configuration.}, } @article {pmid39857299, year = {2025}, author = {Ramos Lopez, D and Flores, FJ and Espindola, AS}, title = {MeStanG-Resource for High-Throughput Sequencing Standard Data Sets Generation for Bioinformatic Methods Evaluation and Validation.}, journal = {Biology}, volume = {14}, number = {1}, pages = {}, pmid = {39857299}, issn = {2079-7737}, support = {OKL03271//Oklahoma State University - Oklahoma Agricultural Experiment Station/ ; }, abstract = {Metagenomics analysis has enabled the measurement of the microbiome diversity in environmental samples without prior targeted enrichment. Functional and phylogenetic studies based on microbial diversity retrieved using HTS platforms have advanced from detecting known organisms and discovering unknown species to applications in disease diagnostics. Robust validation processes are essential for test reliability, requiring standard samples and databases deriving from real samples and in silico generated artificial controls. We propose a MeStanG as a resource for generating HTS Nanopore data sets to evaluate present and emerging bioinformatics pipelines. MeStanG allows samples to be designed with user-defined organism abundances expressed as number of reads, reference sequences, and predetermined or custom errors by sequencing profiles. The simulator pipeline was evaluated by analyzing its output mock metagenomic samples containing known read abundances using read mapping, genome assembly, and taxonomic classification on three scenarios: a bacterial community composed of nine different organisms, samples resembling pathogen-infected wheat plants, and a viral pathogen serial dilution sampling. The evaluation was able to report consistently the same organisms, and their read abundances as provided in the mock metagenomic sample design. Based on this performance and its novel capacity of generating exact number of reads, MeStanG can be used by scientists to develop mock metagenomic samples (artificial HTS data sets) to assess the diagnostic performance metrics of bioinformatic pipelines, allowing the user to choose predetermined or customized models for research and training.}, } @article {pmid39857256, year = {2025}, author = {Dai, W and Zhu, H and Chen, J and Chen, H and Dai, D and Wu, J}, title = {Metagenomic Insights into Pigeon Gut Microbiota Characteristics and Antibiotic-Resistant Genes.}, journal = {Biology}, volume = {14}, number = {1}, pages = {}, pmid = {39857256}, issn = {2079-7737}, support = {BK20210005//Natural Science Foundation of Jiangsu Province/ ; jit-b-202105//Research Foundation for Advanced Talents/ ; 202413573100Y//College Students' Innovation Training Program/ ; 21KJB310015//Natural Science Research of Jiangsu Higher Education Institutions of China/ ; }, abstract = {BACKGROUND: Antibiotics were extensively used in the pigeon breeding industry previously to promote growth and prevent disease, leading to the spread of antibiotic-resistant genes (ARGs) in gut microbes, which has become a major public health concern.

METHODS: A metagenomic analysis was performed to investigate the gut microbial communities and ARGs in young and older pigeons in Nanjing, Jiangsu Province, China.

RESULTS: There were obviously distinct gut microbiota and functional compositions between young and older pigeons. Both Pseudomonadota and Uroviricota were dominant in young and older pigeons. Although sharing 24 gut microbiota phyla between young and older pigeons, Bacillota and Pseudomonadota were the dominant microbial phyla in them, respectively. Besides the shared metabolic pathways and biosynthesis of secondary metabolites, biosynthesis of amino acids was the most abundant Kyoto Encyclopedia of Genes and Genomes (KEGG) function in young pigeons, while microbial metabolism in diverse environments was abundant in older pigeons. A total of 142 ARGs conferring multidrug resistance, tetracycline, and aminoglycoside resistance were identified; the most abundant gene in young pigeons was tetracycline-tetW, while in older pigeons, it was multidrug-acrB.

CONCLUSIONS: Our findings revealed significant differences in the gut microbial communities and ARGs between young and older pigeons. This study enhances our understanding of pigeon gut microbiota and antibiotic resistomes, contributing to knowledge-based sustainable pigeon meat production.}, } @article {pmid39856911, year = {2025}, author = {Li, S and Han, Y and Yan, M and Qiu, S and Lu, J}, title = {Machine Learning and Multi-Omics Integration to Reveal Biomarkers and Microbial Community Assembly Differences in Abnormal Stacking Fermentation of Sauce-Flavor Baijiu.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {2}, pages = {}, pmid = {39856911}, issn = {2304-8158}, support = {Guizhou Provincial Science and Technology Foundation (NATURAL SCIENCE) (Basic Research on Science and Technology Cooperation in Guizhou Province - ZK [2023] General 149)//Jun Lu/ ; Guizhou Provincial Science and Technology Foundation (NATURAL SCIENCE) (Basic Research on Science and Technology Cooperation in Guizhou Province - ZK [2023] General 150).//Jun Lu/ ; }, abstract = {Stacking fermentation is critical in sauce-flavor Baijiu production, but winter production often sees abnormal fermentations, like Waistline and Sub-Temp fermentation, affecting yield and quality. This study used three machine learning models (Logistic Regression, KNN, and Random Forest) combined with multi-omics (metagenomics and flavoromics) to develop a classification model for abnormal fermentation. SHAP analysis identified 13 Sub-Temp Fermentation and 9 Waistline microbial biomarkers, along with 9 Sub-Temp Fermentation and 12 Waistline flavor biomarkers. Komagataeibacter and Gluconacetobacter are key for normal fermentation, while Ligilactobacillus and Lactobacillus are critical in abnormal cases. Excessive acid and ester markers caused unbalanced aromas in abnormal fermentations. Additionally, ecological models reveal the bacterial community assembly in abnormal fermentations was influenced by stochastic factors, while the fungal community assembly was influenced by deterministic factors. RDA analysis shows that moisture significantly drove Sub-Temp fermentation. Differential gene analysis and KEGG pathway enrichment identify metabolic pathways for flavor markers. This study provides a theoretical basis for regulating stacking fermentation and ensuring Baijiu quality.}, } @article {pmid39856901, year = {2025}, author = {Bai, C and Fan, B and Hao, J and Yao, Y and Ran, S and Wang, H and Li, H and Wei, R}, title = {Changes in Microbial Community Diversity and the Formation Mechanism of Flavor Metabolites in Industrial-Scale Spontaneous Fermentation of Cabernet Sauvignon Wines.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {2}, pages = {}, pmid = {39856901}, issn = {2304-8158}, support = {2023BQ103//Science and Technology Innovation Fund of Shanxi Agricultural University/ ; LYNJ202110//Research and application of key technologies for sustainable development of wine industry/ ; 2023AB004-01//Xinjiang Corps financial science and technology plan project/ ; }, abstract = {The key flavor compound formation pathways resulting from indigenous microorganisms during the spontaneous fermentation of wine have not been thoroughly described. In this study, high-throughput metagenomic sequencing and untargeted metabolomics were utilized to investigate the evolution of microbial and metabolite profiles during spontaneous fermentation in industrial-scale wine production and to elucidate the formation mechanisms of key flavor compounds. Metabolome analysis showed that the total amount of esters, fatty acids, organic acids, aldehydes, terpenes, flavonoids, and non-flavonoids increased gradually during fermentation. Enrichment analysis indicated that metabolic pathways related to the synthesis, decomposition, transformation, and utilization of sugars, amino acids, and fatty acids were involved in the formation of key flavor compounds in wine. Metagenomic analysis revealed that Saccharomyces, Hanseniaspora, Zygosaccharomyces, Wickerhamiella, Lactobacillus, and Fructobacillus were the dominant taxa during spontaneous fermentation. They were significantly positively correlated with organic acids, fatty acids, esters, phenols, aldehydes, terpenes, and phenols. In conclusion, this research provides new insights into the metabolic pathways of key flavor compounds formed by indigenous microorganisms during wine fermentation.}, } @article {pmid39856742, year = {2025}, author = {Benitez, AJ and Tanes, C and Friedman, ES and Zackular, JP and Ford, E and Gerber, JS and DeRusso, PA and Kelly, A and Li, H and Elovitz, MA and Wu, GD and Zemel, B and Bittinger, K}, title = {Antibiotic exposure is associated with minimal gut microbiome perturbations in healthy term infants.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {21}, pmid = {39856742}, issn = {2049-2618}, support = {UL1 TR001878/TR/NCATS NIH HHS/United States ; UL1TR001878//NIH National Center for Research Resources Clinical and Translational Science Program/ ; KL2 TR001879/TR/NCATS NIH HHS/United States ; unrestricted donation//American Beverage Foundation for a Healthy America/ ; R01DK107565/DK/NIDDK NIH HHS/United States ; R35GM138369/GM/NIGMS NIH HHS/United States ; KL2TR001879/TR/NCATS NIH HHS/United States ; R01 DK107565/DK/NIDDK NIH HHS/United States ; R35 GM138369/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/adverse effects/pharmacology ; Infant ; *Feces/microbiology/chemistry ; Female ; *Bile Acids and Salts/metabolism ; Male ; Prospective Studies ; *Breast Feeding ; Longitudinal Studies ; Infant, Newborn ; Metagenomics ; Bacteria/classification/genetics/drug effects/isolation & purification ; Child, Preschool ; Black or African American ; Amoxicillin ; Bifidobacterium/drug effects/isolation & purification/genetics ; White ; }, abstract = {BACKGROUND: The evolving infant gut microbiome influences host immune development and later health outcomes. Early antibiotic exposure could impact microbiome development and contribute to poor outcomes. Here, we use a prospective longitudinal birth cohort of n = 323 healthy term African American children to determine the association between antibiotic exposure and the gut microbiome through shotgun metagenomics sequencing as well as bile acid profiles through liquid chromatography-mass spectrometry.

RESULTS: Stool samples were collected at ages 4, 12, and 24 months for antibiotic-exposed (n = 170) and unexposed (n = 153) participants. A short-term substudy (n = 39) collected stool samples at first exposure, and over 3 weeks following antibiotics initiation. Antibiotic exposure (predominantly amoxicillin) was associated with minimal microbiome differences, whereas all tested taxa were modified by breastfeeding. In the short-term substudy, we observed microbiome differences only in the first 2 weeks following antibiotics initiation, mainly a decrease in Bifidobacterium bifidum. The differences did not persist a month after antibiotic exposure. Four species were associated with infant age. Antibiotic exposure was not associated with an increase in antibiotic resistance gene abundance or with differences in microbiome-derived fecal bile acid composition.

CONCLUSIONS: Short-term and long-term gut microbiome perturbations by antibiotic exposure were detectable but substantially smaller than those associated with breastfeeding and infant age.}, } @article {pmid39856709, year = {2025}, author = {Li, D and Chen, W and Luo, W and Zhang, H and Liu, Y and Shu, D and Wei, G}, title = {Seed microbiomes promote Astragalus mongholicus seed germination through pathogen suppression and cellulose degradation.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {23}, pmid = {39856709}, issn = {2049-2618}, support = {42177106//National Natural Science Foundation of China/ ; 42177106//National Natural Science Foundation of China/ ; 42177106//National Natural Science Foundation of China/ ; 42177106//National Natural Science Foundation of China/ ; 42177106//National Natural Science Foundation of China/ ; 42177106//National Natural Science Foundation of China/ ; 42177106//National Natural Science Foundation of China/ ; }, mesh = {*Seeds/microbiology ; *Germination ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; *Cellulose/metabolism ; Astragalus Plant/microbiology ; Soil Microbiology ; Metagenome ; }, abstract = {BACKGROUND: Seed-associated microorganisms play crucial roles in maintaining plant health by providing nutrients and resistance to biotic and abiotic stresses. However, their functions in seed germination and disease resistance remain poorly understood. In this study, we investigated the microbial community assembly features and functional profiles of the spermosphere and endosphere microbiomes related to germinated and ungerminated seeds of Astragalus mongholicus by using amplicon and shotgun metagenome sequencing techniques. Additionally, we aimed to elucidate the relationship between beneficial microorganisms and seed germination through both in vitro and in vivo pot experiments.

RESULTS: Our findings revealed that germination significantly enhances the diversity of microbial communities associated with seeds. This increase in diversity is driven through environmental ecological niche differentiation, leading to the enrichment of potentially beneficial probiotic bacteria such as Pseudomonas and Pantoea. Conversely, Fusarium was consistently enriched in ungerminated seeds. The co-occurrence network patterns revealed that the microbial communities within germinated and ungerminated seeds presented distinct structures. Notably, germinated seeds exhibit more complex and interconnected networks, particularly for bacterial communities and their interactions with fungi. Metagenome analysis showed that germinated seed spermosphere soil had more functions related to pathogen inhibition and cellulose degradation. Through a combination of culture-dependent and germination experiments, we identified Fusarium solani as the pathogen. Consistent with the metagenome analysis, germination experiments further demonstrated that bacteria associated with pathogen inhibition and cellulose degradation could promote seed germination and vigor. Specifically, Paenibacillus sp. significantly enhanced A. mongholicus seed germination and plant growth.

CONCLUSIONS: Our study revealed the dynamics of seed-associated microorganisms during seed germination and confirmed their ecological role in promoting A. mongholicus seed germination by suppressing pathogens and degrading cellulose. This study offers a mechanistic understanding of how seed microorganisms facilitate successful seed germination, highlighting the potential for leveraging these microbial communities to increase plant health. Video Abstract.}, } @article {pmid39856417, year = {2025}, author = {Mamawal, DRD and Rivera, WL}, title = {Combined application of metagenomics and FEAST to trace sources of microbial eukaryotic contamination in the Pasig-Marikina-San Juan (PAMARISAN) river system in Metro Manila, Philippines.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {2}, pages = {196}, pmid = {39856417}, issn = {1573-2959}, support = {E-249//National Research Council of the Philippines/ ; E-249//National Research Council of the Philippines/ ; }, mesh = {*Rivers/microbiology/chemistry ; *Environmental Monitoring ; Philippines ; *Metagenomics ; Animals ; Eukaryota/genetics ; Feces/microbiology ; Water Microbiology ; }, abstract = {Microbial eukaryotes are vital to global microbial diversity, but there is limited information about their composition and sources in contaminated surface waters. This study examined the pathogens and potential sources of microbial eukaryotic communities in polluted sink environments using the 18S rDNA amplicon sequencing combined with the fast expectation-maximization for microbial source tracking (FEAST) program. Six sampling sites were selected along the Pasig-Marikina-San Juan (PAMARISAN) River System, representing different locations within the waterway and classified as sinks (n = 12), whereas animal fecal samples collected from various farms were classified as sources (n = 29). Taxonomic composition revealed Stramenopila, Alveolata, Rhizaria (SAR), Archaeplastida, and Excavata in the rivers, accounting for 85.1%, 13.2%, and 0.36% mean abundance of microbial sink communities, respectively. Clinically relevant human pathogens were also observed in sink environments. The correlation test demonstrated that dissolved oxygen, total suspended solids, pH, temperature, fecal coliform count, and phosphates were important environmental factors driving community variations. Moreover, FEAST results indicated that sewage (19.6%) was the primary source of microbial eukaryotes, followed by duck (0.644%) and cow (0.566%) feces. Spatio-seasonal variations showed higher contributions at downstream stations and during the wet season, highlighting the role of rainfall in enhancing microbial dispersal. Results from community-based microbial source tracking can be used to explore factors shaping microbial eukaryotes in freshwater environments, assess potential pathogen-related hazards, and inform river conservation and management strategies. Furthermore, this also serves as preliminary data for microbial eukaryotic source tracking in the Philippines, laying groundwork for future research.}, } @article {pmid39856391, year = {2025}, author = {Tisza, MJ and Lloyd, RE and Hoffman, K and Smith, DP and Rewers, M and Javornik Cregeen, SJ and Petrosino, JF}, title = {Longitudinal phage-bacteria dynamics in the early life gut microbiome.}, journal = {Nature microbiology}, volume = {10}, number = {2}, pages = {420-430}, pmid = {39856391}, issn = {2058-5276}, support = {U01 DK063821/DK/NIDDK NIH HHS/United States ; UC4 DK063863/DK/NIDDK NIH HHS/United States ; UL1 TR002535/TR/NCATS NIH HHS/United States ; U01 DK063790/DK/NIDDK NIH HHS/United States ; UL1 TR000064/TR/NCATS NIH HHS/United States ; HHSN267200700014C/LM/NLM NIH HHS/United States ; U01 DK063836/DK/NIDDK NIH HHS/United States ; U01 DK063829/DK/NIDDK NIH HHS/United States ; U01 DK063865/DK/NIDDK NIH HHS/United States ; UC4 DK095300/DK/NIDDK NIH HHS/United States ; U01 DK63865//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; UC4 DK063861/DK/NIDDK NIH HHS/United States ; UC4 DK063829/DK/NIDDK NIH HHS/United States ; UC4 DK063821/DK/NIDDK NIH HHS/United States ; U01 DK63821//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; UC4 DK117483/DK/NIDDK NIH HHS/United States ; UC4 DK063836/DK/NIDDK NIH HHS/United States ; UC4 DK112243/DK/NIDDK NIH HHS/United States ; U01 DK124166/DK/NIDDK NIH HHS/United States ; U01 DK063861/DK/NIDDK NIH HHS/United States ; U01 DK63829//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; U01 DK128847/DK/NIDDK NIH HHS/United States ; UC4 DK063865/DK/NIDDK NIH HHS/United States ; U01 DK063863/DK/NIDDK NIH HHS/United States ; UC4 DK106955/DK/NIDDK NIH HHS/United States ; UC4 DK100238/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Bacteriophages/genetics/physiology/classification ; Infant ; *Bacteria/virology/genetics/classification/isolation & purification ; Child, Preschool ; Longitudinal Studies ; Metagenome ; Diabetes Mellitus, Type 1/microbiology/virology ; Feces/microbiology ; Female ; Male ; Metagenomics ; Infant, Newborn ; }, abstract = {Microbial colonization of the human gut occurs soon after birth, proceeds through well-studied phases and is affected by lifestyle and other factors. Less is known about phage community dynamics during infant gut colonization due to small study sizes, an inability to leverage large databases and a lack of appropriate bioinformatics tools. Here we reanalysed whole microbial community shotgun sequencing data of 12,262 longitudinal samples from 887 children from four countries across four years of life as part of the The Environmental Determinants of Diabetes in the Young (TEDDY) study. We developed an extensive metagenome-assembled genome catalogue using the Marker-MAGu pipeline, which comprised 49,111 phage taxa from existing human microbiome datasets. This was used to identify phage marker genes and their integration into the MetaPhlAn 4 bacterial marker gene database enabled simultaneous assessment of phage and bacterial dynamics. We found that individual children are colonized by hundreds of different phages, which are more transitory than bacteria, accumulating a more diverse phage community over time. Type 1 diabetes correlated with a decreased rate of change in bacterial and viral communities in children aged one and two. The addition of phage data improved the ability of machine learning models to discriminate samples by country. Finally, although phage populations were specific to individuals, we observed trends of phage ecological succession that correlated well with putative host bacteria. This resource improves our understanding of phage-bacteria interactions in the developing early life microbiome.}, } @article {pmid39856104, year = {2025}, author = {Özcan, E and Yu, KB and Dinh, L and Lum, GR and Lau, K and Hsu, J and Arino, M and Paramo, J and Lopez-Romero, A and Hsiao, EY}, title = {Dietary fiber content in clinical ketogenic diets modifies the gut microbiome and seizure resistance in mice.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {987}, pmid = {39856104}, issn = {2041-1723}, support = {R01 NS115537/NS/NINDS NIH HHS/United States ; R01NS115537//U.S. Department of Health & Human Services | NIH | National Institute of Neurological Disorders and Stroke (NINDS)/ ; }, mesh = {*Diet, Ketogenic ; Animals ; *Gastrointestinal Microbiome ; *Dietary Fiber/administration & dosage ; *Seizures/diet therapy/metabolism ; Mice ; Male ; Humans ; Mice, Inbred C57BL ; Disease Models, Animal ; Infant Formula ; Female ; }, abstract = {The gut microbiome modulates the anti-seizure effects of the ketogenic diet, but how specific dietary formulations differentially modify the gut microbiome in ways that impact seizure outcome is poorly understood. We find that medical ketogenic infant formulas vary in macronutrient ratio, fat source, and fiber content and differentially promote resistance to 6-Hz seizures in mice. Dietary fiber, rather than fat ratio or source, drives substantial metagenomic shifts in a model human infant microbial community. Addition of fiber to a fiber-deficient ketogenic formula restores seizure resistance, and supplementing protective formulas with excess fiber potentiates seizure resistance. By screening 13 fiber sources and types, we identify metagenomic responses in the model community that correspond with increased seizure resistance. Supplementing with seizure-protective fibers enriches microbial genes related to queuosine biosynthesis and preQ0 biosynthesis and decreases genes related to sucrose degradation and TCA cycle, which are also seen in seizure-protected mice that are fed fiber-containing ketogenic formulas. This study reveals that different formulations of ketogenic diets, and dietary fiber content in particular, differentially impact seizure outcome in mice, likely by modifying the gut microbiome. Understanding interactions between diet, microbiome, and host susceptibility to seizures could inform novel microbiome-guided approaches to treat refractory epilepsy.}, } @article {pmid39856097, year = {2025}, author = {Pidgeon, R and Mitchell, S and Shamash, M and Suleiman, L and Dridi, L and Maurice, CF and Castagner, B}, title = {Diet-derived urolithin A is produced by a dehydroxylase encoded by human gut Enterocloster species.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {999}, pmid = {39856097}, issn = {2041-1723}, support = {PJT-437944//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Santé du Canada)/ ; }, mesh = {Humans ; *Coumarins/metabolism ; *Gastrointestinal Microbiome ; *Operon/genetics ; Feces/microbiology ; Diet ; Bacterial Proteins/metabolism/genetics ; Proteomics ; }, abstract = {Urolithin A (uroA) is a polyphenol derived from the multi-step metabolism of dietary ellagitannins by the human gut microbiota. Once absorbed, uroA can trigger mitophagy and aryl hydrocarbon receptor signaling pathways, altering host immune function, mitochondrial health, and intestinal barrier integrity. Most individuals harbor a microbiota capable of uroA production; however, the mechanisms underlying the dehydroxylation of its catechol-containing precursor (uroC) are unknown. Here, we use a combination of untargeted bacterial transcriptomics, proteomics, and comparative genomics to uncover an inducible uroC dehydroxylase (ucd) operon in Enterocloster species. We show that the ucd operon encodes a predicted molybdopterin-dependent enzyme complex that dehydroxylates urolithins at a specific position (9-OH). By interrogating publicly available metagenomics datasets, we observed that uroC-metabolizing Enterocloster species and ucd operon genes are prevalent in human feces. In ex vivo experiments with human fecal samples, only samples actively transcribing ucd could produce uroA, possibly explaining differences in urolithin metabolism between individuals. Collectively, this work identifies Enterocloster species and the ucd operon as important contributors to uroA production and establishes a multi-omics framework to further our mechanistic understanding of polyphenol metabolism by the human gut microbiota.}, } @article {pmid39856057, year = {2025}, author = {Hu, H and Huang, Y and Yang, F and Ma, L and Zhang, J and Deng, X and Ma, N and Wang, K and Tao, Y and Lin, Q and Li, Y and Bai, X and Pan, H}, title = {Metagenome-assembled microbial genomes (n = 3,448) of the oral microbiomes of Tibetan and Duroc pigs.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {141}, pmid = {39856057}, issn = {2052-4463}, mesh = {Animals ; *Metagenome ; Swine/microbiology ; *Mouth/microbiology ; *Microbiota ; Genome, Microbial ; Metagenomics ; Tibet ; }, abstract = {Compared with leaner breeds, local Chinese pig breeds have distinct intestinal microbial, as determined by metagenomic techniques, and the interactions between oral microorganisms and their hosts are also gradually being clarified. However, the high host genome content means that few metagenome-based oral microbiomes have been reported. Here, we combined dilution-based metagenomic sequencing and binning approaches to extract the microbial genomes from the oral microbiomes of Tibetan and Duroc pigs. The host contamination rates were reduced to 13.64%, a quarter of the normal metagenomic level (65.25% on average). Medium-high-quality metagenome-assembled genomes (MAGs; n = 3,448) spanning nine phyla were retrieved and 70.79% were novel species. Of the nonredundant MAGs, only 13.37% were shared, revealing the strong disparities between Tibetan and Duroc pigs. The oral microbial diversity of the Duroc pig was greater than that of the Tibetan pig. We present the first large-scale dilute-based metagenomic data on the pig oral microbiome, which should facilitate further investigation of the functions of oral microorganisms in pigs.}, } @article {pmid39855705, year = {2025}, author = {Hao, M and Hu, L and Han, M and Li, C and Chang, H and Luo, J and Jiang, H}, title = {[Mining and characterization of new enzymes based on Phi29 DNA polymerase].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {41}, number = {1}, pages = {427-436}, doi = {10.13345/j.cjb.240222}, pmid = {39855705}, issn = {1872-2075}, mesh = {*DNA-Directed DNA Polymerase/metabolism/genetics ; Bacillus Phages/enzymology/genetics ; Metagenome ; Bacteriophages/enzymology/genetics ; Viral Proteins/genetics/metabolism ; }, abstract = {In recent years, the bacteriophage Φ29 (Phi29) DNA polymerase has garnered increasing attention due to its high-fidelity amplification capacity at constant temperatures. To advance the industrial application of this type of isothermal polymerases, this study mined and characterized new enzymes from the microbial metagenome based on the known Phi29 DNA polymerase sequence. The results revealed that a new enzyme, Php29 DNA polymerase, was identified in the microbial metagenome with plants as the hosts. This enzyme exhibited higher strand displacement activity, with a 59.5% similarity to bacteriophage Φ29. Experimental validation demonstrated that the enzyme had 3'→5' exonuclease activity, and its amplification products can serve as substrates for further catalytic reactions. The discovery and validation of Php29 DNA polymerase gives insights into the future industrial application of isothermal polymerases.}, } @article {pmid39855427, year = {2025}, author = {Coffman, KA}, title = {The roles of viruses in tephritid pest multitrophic interactions and an outlook for biological control.}, journal = {Current opinion in insect science}, volume = {68}, number = {}, pages = {101333}, doi = {10.1016/j.cois.2025.101333}, pmid = {39855427}, issn = {2214-5753}, abstract = {Tephritid fruit fly pests remain a considerable problem for agricultural fruit production around the world. New control methods that do not rely on synthetic insecticides are increasingly desirable to diversify tephritid pest management programs. Biological control through the release of parasitoid wasps has historically provided effective suppression of fruit fly pests, although molecular factors that influence the success of fruit fly parasitoids are understudied. Microbes have been demonstrated to facilitate myriad interactions between insects and their environment and have been the subject of recent investigation within tephritids. Specifically, the diversity and function of viruses found within fruit flies and associated parasitoids is an emerging field of research that has the potential to deepen our understanding of previously hidden factors that facilitate sustainable pest control. Most work to date has focused on identifying resident viral communities within fruit flies using metagenomic and metatranscriptomic sequencing approaches. Additionally, a growing body of evidence has revealed a multitude of functional dynamics that viruses have with fruit fly hosts, including vertically transmitted commensal viruses and parasitoid-vectored pathogens. Heritable viruses transmitted by fruit fly parasitoids, in particular, have been shown to play prominent roles in fruit fly multitrophic interactions, in which viral infection can shape the survival rate and host range of infected parasitoids. Furthermore, at least one parasitoid virus represents a lethal pathogen to a wide range of fruit fly pest species. Parasitoid viruses could therefore present novel opportunities to leverage natural antagonistic interactions for fruit fly pest control innovations.}, } @article {pmid39855018, year = {2025}, author = {Yu, Y and Huang, W and Tang, S and Xiang, Y and Yuan, L and Zhu, X and Yin, H and Dang, Z and Niu, J}, title = {Metagenomic and enzymatic mechanisms underpinning efficient water treatment of 2-ethylhexyl diphenyl phosphate (EHDPP) by the microbial consortium 8-ZY.}, journal = {Water research}, volume = {275}, number = {}, pages = {123178}, doi = {10.1016/j.watres.2025.123178}, pmid = {39855018}, issn = {1879-2448}, abstract = {The ubiquitous presence, potential toxicity, and persistence of 2-ethylhexyl diphenyl phosphate (EHDPP) in the environment have raised significant concerns. In this study, we successfully isolate a novel microbial consortium, named 8-ZY, and we demonstrate its remarkable ability to degrade EHDPP using an extremely low concentration of the inoculate. A total of 11 degradation metabolites were identified, including hydrolysis, hydroxylated, methylated, glucuronide-conjugated, and previously unreported byproducts, enabling us to propose new transformation pathways. Further, we unveiled the active members of the microbial consortium 8-ZY during the degradation of EHDPP. We observed the presence of diverse active populations, which included Bradyrhizobium, Rhodopseudomonas, Sphingomonas, Hyphomicrobium, Chitinophaga, Aminobacter, and Ralstonia. A metagenomic analysis revealed the presence of genes that encode phosphatase, phosphodiesterase, cytochrome P450, and hydroxylase enzymes, thus indicating their crucial role in EHDPP degradation. Furthermore, we successfully isolated Burkholderia cepacia ZY1, Sphingopyxis terrae ZY2, and Amycolatopsis ZY3 from the 8-ZY consortium, confirming their significance in EHDPP degradation and metabolite formation. These findings underscored the diversity of strains and functional genes responsible for the transformation of EHDPP within the consortium 8-ZY, highlighting the essential role of synergistic interactions during EHDPP biodegradation processes. Molecular docking and dynamics simulation suggested that alkaline phosphatase, cytochrome P450, and hydroxylase stably bonded to EHDPP within their respective active pockets, targeting distinct sites on the EHDPP molecule. These findings provide a comprehensive understanding of the transformation mechanisms of OPEs and contribute valuable insights into their fate in the environment.}, } @article {pmid39854991, year = {2025}, author = {Pei, Y and Lei, A and Wang, M and Sun, M and Yang, S and Liu, X and Liu, L and Chen, H}, title = {Novel tetracycline-degrading enzymes from the gut microbiota of black soldier fly: Discovery, performance, degradation pathways, mechanisms, and application potential.}, journal = {Journal of hazardous materials}, volume = {488}, number = {}, pages = {137286}, doi = {10.1016/j.jhazmat.2025.137286}, pmid = {39854991}, issn = {1873-3336}, abstract = {The antibiotic tetracycline (TC) is an emerging pollutant frequently detected in various environments. Although enzymatic remediation is a promising strategy for mitigating TC contamination, the availability of effective TC-degrading enzymes remains limited, and their mechanisms and applications are not fully understood. This study developed a comprehensive TC-degrading enzyme library from the gut microbiome of the highly TC-resistant saprophagous insect, black soldier fly larvae (BSFL), using an integrated metagenomic and comparative metatranscriptomic approach, identifying 105 potential novel TC-degradation genes. Bioinformatics analysis of 10 selected genes underscored the novelty of the identified enzymes. Among these, Trg2 demonstrated strong binding affinity and significant degradation capacity for TC. Key functional amino acid residues, including Thr231, Ala64, Ala82, Gly68, Gly79, and Ser81, were identified as essential for the interaction between TC and Trg2. Six TC degradation pathways were proposed, involving the transformation of TC into 19 metabolites through de-grouping, ring opening, oxidation, reduction, and addition reactions, effectively reducing TC toxicity. Furthermore, Trg2 exhibited resilience under harsh conditions, maintaining the capacity to remove about 45 % of the total TC in mariculture wastewater across eight successive batches. This study advances the understanding of TC degradation mechanisms and highlights the potential application of novel enzymes for bioremediation purposes.}, } @article {pmid39854777, year = {2025}, author = {Mardalisa, and Wang, R and Sabar, MA and Matsuura, N and Hara-Yamamura, H and Honda, R}, title = {Different fates between extracellular and intracellular antimicrobial resistome in full-scale activated sludge and membrane bioreactor processes.}, journal = {Water research}, volume = {274}, number = {}, pages = {123155}, doi = {10.1016/j.watres.2025.123155}, pmid = {39854777}, issn = {1879-2448}, abstract = {Treated effluent of wastewater treatment plants (WWTPs) are major sources of extracellular antimicrobial resistance genes (eARGs) into aquatic environments. This study aimed to clarify the fate and origins of eARGs from influent to treated effluent at a full-scale WWTP. The compositions of eARG and intracellular ARG (iARG) were acquired via shotgun metagenomic sequencing in influent wastewater, activated sludge, and treated effluent of the target WWTP, where identical wastewater was treated by conventional activated sludge (CAS) and membrane bioreactor (MBR) processes. The proportion of eARGs to iARGs increased from influent to effluent in both processes, reaching almost half of the total ARG. Most eARGs in influent were associated with clinically important antimicrobials, whereas eARGs in sludge and effluent were dominated by aminoglycoside resistance genes of aadA and APH variants. Although the eARGs composition in influent wastewater mirrored that of iARGs, a substantial shift occurred in activated sludge and effluent, highlighting the presence of distinct dissemination and reduction mechanisms between eARGs and iARGs. Notably, the origin of eARGs in treated effluent was mainly iARGs in the effluent rather than the carryover of eARG from activated sludge, which were substantially reduced in MBR, compared to CAS. Consequently, these differences in selective mechanisms led to different fates between eARG and iARG during wastewater treatment.}, } @article {pmid39854281, year = {2025}, author = {Gurbich, TA and Beracochea, M and De Silva, NH and Finn, RD}, title = {mettannotator: a comprehensive and scalable Nextflow annotation pipeline for prokaryotic assemblies.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btaf037}, pmid = {39854281}, issn = {1367-4811}, abstract = {SUMMARY: In recent years there has been a surge in prokaryotic genome assemblies, coming from both isolated organisms and environmental samples. These assemblies often include novel species that are poorly represented in reference databases creating a need for a tool that can annotate both well-described and novel taxa, and can run at scale. Here, we present mettannotator-a comprehensive, scalable Nextflow pipeline for prokaryotic genome annotation that identifies coding and non-coding regions, predicts protein functions, including antimicrobial resistance, and delineates gene clusters. The pipeline summarises the results of these tools in a GFF (General Feature Format) file that can be easily utilised in downstream analysis or visualised using common genome browsers. Here, we show how it works on 200 genomes from 29 prokaryotic phyla, including isolate genomes and known and novel metagenome-assembled genomes, and present metrics on its performance in comparison to other tools.

The pipeline is written in Nextflow and Python and published under an open source Apache 2.0 licence. Instructions and source code can be accessed at https://github.com/EBI-Metagenomics/mettannotator. The pipeline is also available on WorkflowHub: https://workflowhub.eu/workflows/1069.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid39853798, year = {2025}, author = {Lutz, KC and Neugent, ML and Bedi, T and De Nisco, NJ and Li, Q}, title = {A Generalized Bayesian Stochastic Block Model for Microbiome Community Detection.}, journal = {Statistics in medicine}, volume = {44}, number = {3-4}, pages = {e10291}, pmid = {39853798}, issn = {1097-0258}, support = {1R01DK131267-01/NH/NIH HHS/United States ; AT-2030-20200401//Welch Foundation/ ; 1F32DK128975-01A1/NH/NIH HHS/United States ; 2210912//National Science Foundation/ ; R01 GM141519/GM/NIGMS NIH HHS/United States ; 1R01GM141519/NH/NIH HHS/United States ; 2113674//National Science Foundation/ ; R01 DK131267/DK/NIDDK NIH HHS/United States ; F32 DK128975/DK/NIDDK NIH HHS/United States ; }, mesh = {*Bayes Theorem ; Humans ; *Microbiota/genetics ; *Markov Chains ; Computer Simulation ; Female ; Monte Carlo Method ; Stochastic Processes ; Models, Statistical ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; }, abstract = {Advances in next-generation sequencing technology have enabled the high-throughput profiling of metagenomes and accelerated microbiome studies. Recently, there has been a rise in quantitative studies that aim to decipher the microbiome co-occurrence network and its underlying community structure based on metagenomic sequence data. Uncovering the complex microbiome community structure is essential to understanding the role of the microbiome in disease progression and susceptibility. Taxonomic abundance data generated from metagenomic sequencing technologies are high-dimensional and compositional, suffering from uneven sampling depth, over-dispersion, and zero-inflation. These characteristics often challenge the reliability of the current methods for microbiome community detection. To study the microbiome co-occurrence network and perform community detection, we propose a generalized Bayesian stochastic block model that is tailored for microbiome data analysis where the data are transformed using the recently developed modified centered-log ratio transformation. Our model also allows us to leverage taxonomic tree information using a Markov random field prior. The model parameters are jointly inferred by using Markov chain Monte Carlo sampling techniques. Our simulation study showed that the proposed approach performs better than competing methods even when taxonomic tree information is non-informative. We applied our approach to a real urinary microbiome dataset from postmenopausal women. To the best of our knowledge, this is the first time the urinary microbiome co-occurrence network structure in postmenopausal women has been studied. In summary, this statistical methodology provides a new tool for facilitating advanced microbiome studies.}, } @article {pmid39853685, year = {2025}, author = {Sun, Y and Gan, Z and Liu, S and Zhang, S and Zhong, W and Liu, J and Huang, X and He, W and Zhong, H and Cao, Q}, title = {Metagenomic and Transcriptomic Analysis Reveals Crosstalk Between Intratumor Mycobiome and Hosts in Early-Stage Nonsmoking Lung Adenocarcinoma Patients.}, journal = {Thoracic cancer}, volume = {16}, number = {2}, pages = {e15527}, pmid = {39853685}, issn = {1759-7714}, support = {220904094208//Fifth Affiliated Hospital of Sun Yat-sen University Qingdong Cao's talent-attracting fund/ ; 3320104100430//Exploration and Practice of a Tri-Party Personalized Oncology Strategy Based on Precision Medicine in Patient-Doctor-Research Collaboration/ ; }, mesh = {Humans ; *Lung Neoplasms/microbiology/genetics/pathology ; *Adenocarcinoma of Lung/microbiology/genetics/pathology ; *Mycobiome ; Female ; *Metagenomics/methods ; Male ; Middle Aged ; Gene Expression Profiling ; Aged ; Transcriptome ; Prognosis ; Tumor Microenvironment ; Case-Control Studies ; }, abstract = {BACKGROUND: The mycobiome in the tumor microenvironment of non-smokers with early-stage lung adenocarcinoma (ES-LUAD) has been minimally investigated.

METHODS: In this study, we conducted ultra-deep metagenomic and transcriptomic sequencing on 128 samples collected from 46 nonsmoking ES-LUAD patients and 41 healthy controls (HC), aiming to characterize the tumor-resident mycobiome and its interactions with the host.

RESULTS: The results revealed that ES-LUAD patients exhibited fungal dysbiosis characterized by reduced species diversity and significant imbalances in specific fungal abundances. Concurrently, microbial functional analysis revealed significant alterations associated with genes such as ribosomal proteins and histones. We observed correlations between Yarrowia lipolytica, Saccharomyces paradoxus, and tumor-infiltrating immune cells (TIICs), and identified a strong association (|rho| > 0.7) between S. paradoxus and 14 transcription factors. A signature of three prognostic genes (GRIA1, CDO1, FHL1) closely associated with S. paradoxus was identified and they suggest that the interaction between the mycobiome and the host may contribute to prolonged overall survival (OS). Finally, a predictive model based on six fungi demonstrated decent classification performance in distinguishing ES-LUAD cases from HCs (AUC = 0.724).

CONCLUSIONS: Our study demonstrates that the interactions between the mycobiome and transcriptome within tumors may help elucidate the pathogenic mechanisms of ES-LUAD. Fungi, as a potential predictive tool, can be used as an additional resource for accurately detecting and discriminating individuals with ES-LUAD.}, } @article {pmid39853270, year = {2025}, author = {Cardones, AR and Emiola, A and Hall, R and Sung, AD and Zhang, JY and Petty, AJ and Puza, C and Bohannon, LM and Bush, AT and Lew, MV and Fleming, E and Jin, YJ and Nichols, KR and Jain, V and Gregory, SG and Sullivan, KM and Chao, NJ and Oh, J}, title = {Cutaneous dysbiosis characterizes the post-allogeneic hematopoietic stem cell transplantation period.}, journal = {Blood advances}, volume = {}, number = {}, pages = {}, doi = {10.1182/bloodadvances.2021004792}, pmid = {39853270}, issn = {2473-9537}, abstract = {Gut dysbiosis is linked to mortality and the development of graft-versus-host disease (GVHD) after hematopoietic stem cell transplantation (HSCT), but the impact of cutaneous dysbiosis remains unexplored. We performed a pilot observational study and obtained retroauricular and forearm skin swabs from 12 adult patients prior to conditioning chemotherapy/radiation, and at 1-week, 1-month and 3-months after allogeneic HSCT, and performed shotgun metagenomic sequencing. The cutaneous microbiome among HSCT patients was enriched for gram-negative bacteria such as E coli and Pseudomonas, fungi, and viruses. Enrichment with bacteriophages and Polyomavirus sp, was observed among patients who died within 1-year, while we observed longitudinal stability of the cutaneous microbiome at the 3-month time point among those who survived beyond 1 year post-HSCT, although these may simply be a reflection of the overall medical status of the patients. There was no association with fungal abundance and any of the outcomes observed. The cutaneous microbiome may be a reservoir of pathobionts among allogeneic HSCT patients. Our findings suggest that cutaneous dysbiosis exists post-HSCT, but the ultimate implication of this to patient outcomes remains to be seen. Larger studies are required.}, } @article {pmid39853010, year = {2024}, author = {Alexiev, A and Stretch, E and Kasschau, KD and Wilson, LB and Truong, L and Tanguay, RL and Sharpton, TJ}, title = {Clearing the Air on Pollutant Disruptions of the Gut-Brain Axis: Developmental Exposure to Benzo[a]pyrene Disturbs Zebrafish Behavior and the Gut Microbiome in Adults and Subsequent Generations.}, journal = {Toxics}, volume = {13}, number = {1}, pages = {}, pmid = {39853010}, issn = {2305-6304}, support = {1R01ES030226/ES/NIEHS NIH HHS/United States ; T32ES007060/ES/NIEHS NIH HHS/United States ; P30 ES030287/ES/NIEHS NIH HHS/United States ; R01 ES030226/ES/NIEHS NIH HHS/United States ; T32 ES007060/ES/NIEHS NIH HHS/United States ; }, abstract = {Developmental exposure to benzo[a]pyrene (BaP), a ubiquitous environmental pollutant, has been linked to various toxic effects, including multigenerational behavioral impairment. While the specific mechanisms driving BaP neurotoxicity are not fully understood, recent work highlights two important determinants of developmental BaP neurotoxicity: (1) the aryl hydrocarbon receptor (AHR), which induces host metabolism of BaP, and (2) the gut microbiome, which may interact with BaP to affect its metabolism, or be perturbed by BaP to disrupt the gut-brain axis. We utilized the zebrafish model to explore the role of AHR, the gut microbiome, and their interaction, on BaP-induced neurotoxicity. We tested (1) how developmental BaP exposure and AHR2 perturbation in zebrafish link to adult behavior, (2) how these variables associate with the structure and function of the adult zebrafish gut metagenome, and (3) whether these associations are multigenerational. Our findings reveal a reticulated axis of association between BaP exposure, developmental AHR2 expression, the zebrafish gut metagenome, and behavior. Results indicate that AHR2 is a key modulator of how BaP elicits neurotoxicity and microbiome dysbiosis. Additionally, this axis of association manifests generationally. These findings demonstrate the importance of studying pollutant-microbiome interactions and elucidate the role of specific host genes in neurotoxicity and dysbiosis.}, } @article {pmid39852519, year = {2024}, author = {Zhang, W and Li, Y and Chu, Y and Liu, H and Jing, H and Xia, Q}, title = {Deep-Sea Ecosystems as an Unexpected Source of Antibiotic Resistance Genes.}, journal = {Marine drugs}, volume = {23}, number = {1}, pages = {}, pmid = {39852519}, issn = {1660-3397}, support = {KJRC2023C37//the innovational Found for the scientific and technological personnel of Hainan Province/ ; 183446KYSB20210002//the International Partnership Program of Chinese Academy of Sciences for Big Science/ ; 2022YFC2805400//the National Key R&D Program of China/ ; 2022YFC2805505//the National Key R&D Program of China/ ; }, mesh = {*Ecosystem ; *Drug Resistance, Microbial/genetics ; *Metagenomics/methods ; *Anti-Bacterial Agents/pharmacology ; Geologic Sediments/microbiology ; Seawater/microbiology ; Genes, Bacterial/genetics ; Bacteria/genetics/drug effects ; Drug Resistance, Bacterial/genetics ; }, abstract = {The deep-sea ecosystem, a less-contaminated reservoir of antibiotic resistance genes (ARGs), has evolved antibiotic resistance for microbes to survive and utilize scarce resources. Research on the diversity and distribution of these genes in deep-sea environments is limited. Our metagenomics study employed short-read-based (SRB) and assembled-contig-based (ACB) methods to identify ARGs in deep-sea waters and sediments and assess their potential pathogenicity. SRB prediction was found to be more effective for studying the abundance and diversity of these genes, while combining both methods better illustrated the relationship of ARGs with the hosts. Deep-sea waters (DSW) and trenches had the highest diversity of ARGs, including β-lactams, multidrug resistance genes, and rifamycins. Mobile genetic elements, such as IncQ and RP4 plasmids, were also identified. The ratio of nonsynonymous to synonymous substitutions (pN/pS) values of these genes suggest different evolutionary strategies in response to deep-sea conditions and possible human impacts. These resistome profiles provide valuable insights into their natural origins as well as the ecological and evolutionary implications of antibiotic resistance in deep-sea ecosystems. The exploration of the global distribution of ARGs in diverse deep-sea environments is a novel approach that will assist in understanding their potential reservoirs and evolutionary mechanisms. Therefore, employing a comprehensive approach to studying ARGs is particularly necessary. Unique microbial life in deep-sea ecosystems, especially in deep-sea cold seeps sediments (DSCSS), deep-sea waters (DSW), and trench waters (TW), could be a valuable source of new antibiotics and resistance discovery.}, } @article {pmid39852467, year = {2025}, author = {Akkad, A and Nanda, N}, title = {New Diagnostics for Fungal Infections in Transplant Infectious Disease: A Systematic Review.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {11}, number = {1}, pages = {}, pmid = {39852467}, issn = {2309-608X}, abstract = {Fungal infections are common in highly immunosuppressed, solid organ transplant recipients. They can be quite difficult to diagnose in a timely manner; thus, we present a review of current studies focusing on broad categories of molecular diagnostics, i.e., metagenomic sequencing, magnetic resonance, and gas chromatography mass spectrometry. We further discuss their syndrome-specific utilization in the diagnosis of fungemia and disseminated disease, pneumonia, and central nervous system infections. We assess the level of evidence of their utility as fungal diagnostics particularly in solid organ transplant recipients using the STARD criteria. In addition, we provide future research directions to substantiate and appropriately utilize these platforms in clinical practice. Directed polymerase chain reaction testing and targeted metagenomic sequencing are being used clinically and show the most promise, though only in conjunction with conventional methods at this time. The majority of these platforms contain limited data, and thus further larger studies are needed in order to properly implement their use.}, } @article {pmid39851614, year = {2025}, author = {Srila, W and Sripilai, K and Binlateh, T and Thammanichanon, P and Tiskratok, W and Noisa, P and Jitprasertwong, P}, title = {Relationship Between the Salivary Microbiome and Oral Malodor Metabolites in Older Thai Individuals with Periodontitis and the Cytotoxic Effects of Malodor Compounds on Human Oral Squamous Carcinoma (HSC-4) Cells.}, journal = {Dentistry journal}, volume = {13}, number = {1}, pages = {}, pmid = {39851614}, issn = {2304-6767}, support = {NRIIS number 4285350//National Science, Research, and Innovation Fund (NSRF)/ ; //Thailand Science Research and Innovation/ ; //Suranaree University of Technology/ ; }, abstract = {Background/Objectives: Halitosis is primarily caused by the activity of oral microorganisms. In this study, we employed metagenomic sequencing and metabolomic approaches to investigate the differences in salivary microbiota and metabolite profiles between individuals with halitosis and periodontitis and healthy controls. Additionally, we expanded the study to examine how oral malodorous compounds interact with human oral squamous carcinoma (HSC-4) cells. Methods: Saliva samples were collected and analyzed using Ultra-High Performance Liquid Chromatography-Mass Spectrometry (UHPLC-MS) to identify metabolites. We then assessed the correlations between the microbiota and metabolites. Furthermore, the impact of oral malodorous substances on HSC-4 cells was investigated by evaluating apoptosis, antioxidant activity, and inflammatory properties. Results: The microbiota and metabolite profiles showed significant differences between the halitosis with periodontitis group and the periodontally healthy group. The halitosis with periodontitis group exhibited significantly higher relative abundances of eight genera: Tannerella, Selenomonas, Bacteroides, Filifactor, Phocaeicola, Fretibacterium, Eubacterium saphenum, and Desulfobulbus. In contrast, the periodontally healthy group showed significantly higher relative abundances of Family XIII UCG-001, Haemophilus, and Streptobacillus. Two metabolites, 2,3-dihydro-1H-indole and 10,11-dihydro-12R-hydroxy-leukotriene E4, were significantly higher in individuals with halitosis and periodontitis. In the treatment of HSC-4 cells with metabolites, dimethyl sulfide (DMS) did not show significant effects while indole appeared to induce cell death in HSC-4 cells by triggering apoptotic pathways. Additionally, both indole and DMS affected the inflammatory and antioxidant properties of HSC-4 cells. Conclusions: This study provides insights into the mechanisms of halitosis by exploring the correlations between microbiota and metabolite profiles. Furthermore, oral metabolites were shown to impact the cellular response of HSC-4 cells.}, } @article {pmid39851362, year = {2025}, author = {Shabangu, KP and Chetty, M and Bakare, BF}, title = {Metagenomic Insights into Pollutants in Biorefinery and Dairy Wastewater: rDNA Dominance and Electricity Generation in Double Chamber Microbial Fuel Cells.}, journal = {Bioengineering (Basel, Switzerland)}, volume = {12}, number = {1}, pages = {}, pmid = {39851362}, issn = {2306-5354}, support = {1/CX/CSRD VA/United States ; 2//Durban University of Technology (DUT)/ ; 3//Cape Peninsula University of Technology (CPUT)/ ; }, abstract = {This study evaluates the potential of biorefinery and dairy wastewater as substrates for electricity generation in double chamber Microbial Fuel Cells (DCMFC), focusing on their microbial taxonomy and electrochemical viability. Taxonomic analysis using 16S/18S rDNA-targeted DGGE and high-throughput sequencing identified Proteobacteria as dominant in biorefinery biomass, followed by Firmicutes and Bacteriodota. In dairy biomass, Lactobacillus (77.36%) and Clostridium (15.70%) were most prevalent. Biorefinery wastewater exhibited the highest bioelectrochemical viability due to its superior electrical conductivity and salinity, achieving a voltage yield of 65 mV, compared to 75.2 mV from mixed substrates and 1.7 mV from dairy wastewater. Elevated phosphate levels in dairy wastewater inhibited bioelectrochemical processes. This study recommends Biorefinery wastewater as the most suitable purely organic substrate for efficient bioelectricity generation and scaling up of MFCs, emphasising the importance of substrate selection for optimal energy output for practical and commercial viability.}, } @article {pmid39851307, year = {2025}, author = {Tan, JJM and Keng, ZX and Chong, SH and Pan, GT and Singh, A and Supramaniam, C and Khoiroh, I}, title = {Efficient Degradation of Industrial Biowaste via In-Vessel Composting-Technical and Microbial Assessments.}, journal = {Bioengineering (Basel, Switzerland)}, volume = {12}, number = {1}, pages = {}, pmid = {39851307}, issn = {2306-5354}, support = {N/A//KPT Recycle Sdn. Bhd./ ; }, abstract = {In this study, a pilot-scale in-vessel composter was used to treat a mixture of industrial biowaste, with soybean curd residue and saw dust as the major substrates. The composter is capable of treating up to 350 tons/month of waste, producing up to 150 tons/month of high-quality compost within a retention time of 7-10 days. The final compost has an average nitrogen-phosphorus-potassium content of 6%, moisture content of 28%, pH of 6.1, organic matter of 68%, and carbon-nitrogen ratio of 19:1. It also has a good amount of humic acid and macronutrients. Composts from all stages of the composting process-pre-mix, directly after discharge, after one-month of curing, and right before packaging-were evaluated with metagenomic analysis to identify the microbes that may add value to the compost.}, } @article {pmid39850835, year = {2025}, author = {Zhang, Q and Zhen, M and Wang, X and Zhao, F and Dong, Y and Wang, X and Gao, S and Wang, J and Shi, W and Zhang, Y}, title = {Antibiotic exposure enriches streptococci carrying resistance genes in periodontitis plaque biofilms.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e18835}, pmid = {39850835}, issn = {2167-8359}, mesh = {Humans ; *Biofilms/drug effects/growth & development ; *Periodontitis/microbiology/drug therapy ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; *Streptococcus/drug effects/genetics ; Female ; Male ; Adult ; *Dental Plaque/microbiology ; *Amoxicillin/pharmacology/therapeutic use ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Drug Resistance, Bacterial/genetics ; Microbiota/drug effects/genetics ; Tetracycline/pharmacology/therapeutic use ; Metronidazole/pharmacology/therapeutic use ; Clindamycin/pharmacology/therapeutic use ; }, abstract = {BACKGROUND: Periodontitis is not always satisfactorily treated with conventional scaling and root planing, and adjunctive use of antibiotics is required in clinical practice. Therefore, it is important for clinicians to understand the diversity and the antibiotic resistance of subgingival microbiota when exposed to different antibiotics.

MATERIALS AND METHODS: In this study, subgingival plaques were collected from 10 periodontitis patients and 11 periodontally healthy volunteers, and their microbiota response to selective pressure of four antibiotics (amoxicillin, metronidazole, clindamycin, and tetracycline) were evaluated through 16S rRNA gene amplicon and metagenomic sequencing analysis. Additionally, sensitive and resistant strains were isolated and cultured in vitro for resistance evaluation.

RESULTS: Cultivation of subgingival microbiota revealed the oral microbiota from periodontitis patients were more resistant to antibiotics than that of healthy. Significant differences were also observed for the microbial community between with and without antibiotics (especially amoxicillin and tetracycline) treated in periodontitis group.

CONCLUSION: Overall, after the two antibiotics (amoxicillin and tetracycline) exposed, the oral subgingival microbiota in periodontitis patients exhibited different diversity and composition. Streptococcus may account for oral biofilm-specific antibiotic resistance in periodontitis. This provides information for personalized treatment of periodontitis.}, } @article {pmid39850616, year = {2025}, author = {Du, B and Shama, A and Zhang, Y and Chen, B and Bu, Y and Chen, PA and Lin, C and Liu, J and Zheng, J and Li, Z and Chen, Q and Sun, Y and Fu, X}, title = {Gut microbiota and plasma metabolites in pregnant mothers and infant atopic dermatitis: A multi-omics study.}, journal = {The World Allergy Organization journal}, volume = {18}, number = {1}, pages = {101017}, pmid = {39850616}, issn = {1939-4551}, abstract = {BACKGROUND: Many studies reported the influence of infants' gut microbiota on atopic dermatitis (AD) postnatally, yet the role of maternal gut microbiota and plasma metabolites in infants' AD remains largely unexplored.

METHODS: Sixty-three pregnant mother-infants were enrolled and followed after childbirth in Guangzhou, China. Demographic information, maternal stool and plasma samples, and records for infants' AD were collected. Maternal gut microbiota/metabolome and plasma metabolome were profiled using shotgun metagenomics and non-targeted metabolomics. Logistic regression and multi-omics analysis were used to explore characteristic maternal gut microbiota in the AD and health groups.

RESULTS: The α-diversity of maternal gut microbiota in health group was significantly higher than AD group (Shannon diversity P = 0.02, Simpson diversity P = 0.04). Short-chain fatty acids (SCFAs) producing microorganisms, including Faecalibacterium, Roseburia, Butyricicoccus, and Ruminococcus, as well as the abundance of phenylalanine, tyrosine, and tryptophan biosynthesis pathway, were enriched in health group (LDA>2 and P < 0.05). Virulent factors (VFs) involved in immune modulation were enriched in the health group, while VFs involving in adhesin were enriched in the AD group (P < 0.05). Metabolomic analysis showed that a polyunsaturated fatty acid/linoleic acid, 13S-hydroxyoctadecadienoic, were negatively associated with AD in both the gut and plasma samples (FDR<0.05). Several other linoleic acids and flavonoids were negatively associated with AD (FDR<0.05). Neural network analysis revealed that microorganisms enriched in health group may produce these protective fatty acids.

CONCLUSIONS: Our findings show that maternal gut microorganisms/metabolites and plasma metabolites during pregnancy impact subsequent pathogenesis of infants AD. This illuminates new strategies against early AD in offspring.}, } @article {pmid39850588, year = {2024}, author = {Ji, L and Zhao, R and Pei, Y and Sun, Y and Sun, X and Ji, L and Wang, X and Liu, Y and Shen, Q and Yang, S and Wang, Y and Zhang, W}, title = {Identification and characterization of multiple novel viruses in fecal samples of cormorants.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1528233}, pmid = {39850588}, issn = {2297-1769}, abstract = {INTRODUCTION: Cormorants, as protected wild animals by the State Forestry Administration of China, have a broad distribution across China. Previous studies have shown that they can be infected with multiple viruses in the Flaviviridae, Orthomyxoviridae, Paramyxoviridae, and Polyomaviridae families. There is limited knowledge about the other viruses that cormorants may carry and infect.

METHODS: In this study, we employed viral metagenomics to identify novel viruses in the fecal samples collected from cormorants in Xiamen City, Fujian Province, China.

RESULTS: Two novel viruses were identified, including one novel picornavirus named Cormhepa01 and one novel avain hepevirus named CormhepaE. The genome of Cormhepa01 is 7,463 bp in length, which encodes a 2,260 aa polyprotien. Similar to other known picornaviruses, the conserved NTPase, proteinase, and polymerase motifs are presented in the 2C, 3C, and 3D proteins separately. Based on the phylogenetic analysis and amino acid sequence alignment, the CormhepaE may be assigned to a new picornavirus genus. The partial genome of CormhepaE is 6,546 bp in length. Compared with other avian hepatitis E virus strains, CormhepaE has multiple variable sites, which are distributed in motifs of the methyltransferase, helicase, and RdRp domains, separately. Based on the phylogenetic analysis, CormhepaE, together with another strain MG737712 isolated from sparrow, formed a new species of the Avihepevirus genus in the Hepeviridae family.

CONCLUSION: We identified and characterized two novel cormorant viruses in this study. The findings of this study increase our understanding of the diversity of viruses in cormorants and provide practical viral genome information for the prevention and treatment of potential viral diseases affecting this species.}, } @article {pmid39850127, year = {2024}, author = {Fakhraldeen, SA and Madhusoodhanan, R and Habibi, N and Al-Haddad, S and Alagarsamy, S and Habeebullah, SFK and Al-Zakri, WM and Thuslim, F and Fernandes, L and Al-Yamani, F and Al-Said, T}, title = {Shotgun metagenomics reveals the interplay between microbiome diversity and environmental gradients in the first marine protected area in the northern Arabian Gulf.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1479542}, pmid = {39850127}, issn = {1664-302X}, abstract = {INTRODUCTION: The northwest Arabian Gulf encounters significant anthropogenic pressures, including nutrient enrichment from coastal development and effluent discharge.

METHODS: This study presents the first shotgun metagenomics-based characterization of microbial communities in Kuwaiti waters of the northwest Arabian Gulf, focusing on Kuwait's first Marine Protected Area (MPA) in Sulaibikhat Bay, a vital nursery ground for commercially important fish.

RESULTS: Analysis revealed significantly higher microbial diversity within the MPA compared to adjacent waters, with Rhodobacteraceae (27.8%) and Flavobacteriaceae (15.3%) being dominant. Elevated inorganic phosphorus, nitrogen, and salinity were key factors driving this diversity. Multivariate analysis highlighted phosphate as a critical component affecting the MPA microbial community structure, particularly for the families Microbacteriaceae, Flavobacteriaceae, and Rhodobacteraceae.

DISCUSSION: This study underscores the ecological importance of MPAs and highlights the impact of nutrient enrichment and other environmental stressors on microbial diversity, emphasizing the need to reduce nutrient influx to mitigate eutrophication and enhance marine ecosystem resilience in stressed environments.}, } @article {pmid39849759, year = {2025}, author = {Peng, Q and Huang, J and Li, S and Chen, Z and Zhu, Q and Yuan, H and Li, J and Massou, BB and Xie, G}, title = {Dynamics of microbial communities and metabolites during the fermentation of Ningxia goji berry wine: An integrated metagenomics and metabolomics approach.}, journal = {Food research international (Ottawa, Ont.)}, volume = {201}, number = {}, pages = {115609}, doi = {10.1016/j.foodres.2024.115609}, pmid = {39849759}, issn = {1873-7145}, mesh = {*Fermentation ; *Wine/analysis/microbiology ; *Metabolomics ; *Metagenomics ; *Microbiota ; Volatile Organic Compounds/analysis/metabolism ; Bacteria/metabolism/genetics/classification ; Fruit ; Taste ; Food Microbiology ; }, abstract = {Ningxia Goji Berry Wine (NGBW), a traditional Chinese fermented beverage, exhibits complex flavor quality changes during fermentation, the mechanisms of which remain insufficiently elucidated. This study aimed to elucidate the dynamic shifts in physicochemical properties, metabolites, and microbial communities throughout the controlled fermentation process of NGBW. Metabolomic analysis identified 8 key differential volatile metabolites (VOCs) and 406 differential non-volatile metabolites. The enrichment analysis of KEGG metabolic pathways revealed that, during the fermentation of NGBW, ten critical metabolic pathways-Purine metabolism, Glycine, Serine, and Threonine metabolism, Galactose metabolism, and the Citric Acid (TCA) Cycle-play essential roles. Amplicon sequencing indicated that 25 bacterial genera dominated the microbial ecosystem (relative abundance ≥ 0.1 %). Spearman correlation analysis revealed significant associations between 5 core microorganism and flavor compounds, and 25 core microbes with non-volatile metabolites, suggesting their pivotal roles in flavor formation. This study provides a theoretical basis for optimizing the fermentation process and enhancing the flavor quality of NGBW.}, } @article {pmid39849638, year = {2025}, author = {Peña-López, Y and Tareen, NG and Zhang, B and Raman, I and Arana, CA and Zhu, C and Liu, Y and Selvakumar, P and van Oers, NSC and Morris, S and Hooper, LV and Copley, LAB and Raj, P}, title = {Joint fluid multi-omics improves diagnostic confidence during evaluation of children with presumed septic arthritis.}, journal = {Pediatric rheumatology online journal}, volume = {23}, number = {1}, pages = {9}, pmid = {39849638}, issn = {1546-0096}, support = {Biomedical award 2020//Hartwell Foundation/ ; }, mesh = {Humans ; *Arthritis, Infectious/diagnosis/immunology ; Child ; Female ; Male ; Child, Preschool ; *Synovial Fluid/immunology/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Proteomics/methods ; Prospective Studies ; Metagenomics/methods ; Adolescent ; Arthritis, Juvenile/diagnosis/immunology ; Infant ; Osteomyelitis/diagnosis/immunology ; Diagnosis, Differential ; Knee Joint ; Multiomics ; }, abstract = {BACKGROUND: An accurate diagnosis of septic versus reactive or autoimmune arthritis remains clinically challenging. A multi-omics strategy comprising metagenomic and proteomic technologies were undertaken for children diagnosed with presumed septic arthritis to advance clinical diagnoses and care for affected individuals.

METHODS: Twelve children with suspected septic arthritis were prospectively enrolled to compare standard of care tests with a rapid multi-omics approach. The multi-omics combined bacterial 16S rRNA metagenomics, single cell transcriptomics, and proteomics on knee joint fluid specimens. The diagnostic value of the multi-omics was ascertained relative to standard of care culture and PCR-negative results.

RESULTS: Ten children with suspected primary septic arthritis and two with acute hematogenous osteomyelitis (AHO) diagnoses were assessed. Joint fluid bacterial cultures were positive for 6/12 (50%) patients, consistent with elevated inflammatory markers (IL-4, IL-6, IL-17A, TNF-a, etc.). Metagenomic bacterial sequencing results were 100% concordant with the culture results. Six patients were culture- and PCR-negative. Multiomics analyses of the 6 culture negative patients established that 2/6 culture-negative children had inflammatory arthritis with potential Juvenile idiopathic arthritis (JIA) and 1 had post-Streptococcal Reactive Arthritis. The children without any bacteremia had autoantibodies (IgGs) in the joint-fluid targeting several nuclear antigens (i.e., dsDNA, histones, Jo-1, scl-70, Ro/SS-A, SmDs, CENP-A along with non-nuclear antigens i.e. Albumin, Collagens, Myosin, Laminin, etc. Single cell transcriptomics confirmed an abundance of CD4[+] follicular helper T (Tfh), CD8 + T cells and B cells in the autoantibody positive subjects. The combination of 16S DNA sequencing (p = 0.006), cytokine assays (p = 0.009) and autoantibody profiling (p = 0.02) were significantly distinct between those children with and without infections. This improved the diagnostic confidence for 9 of 12 (75%) children, key for treatment decisions.

CONCLUSIONS: The multiomics approach rapidly identified children with bacterial or autoimmune inflammatory conditions, improving diagnostic and treatment strategies for those with presumptive septic arthritis.}, } @article {pmid39849445, year = {2025}, author = {Xie, H and Chen, Z and Wu, G and Wei, P and Gong, T and Chen, S and Xu, Z}, title = {Application of metagenomic next-generation sequencing (mNGS) to describe the microbial characteristics of diabetic foot ulcers at a tertiary medical center in South China.}, journal = {BMC endocrine disorders}, volume = {25}, number = {1}, pages = {18}, pmid = {39849445}, issn = {1472-6823}, support = {[2021]76//the High-level Hospital and Clinical Specialty Discipline Construction Programme for Fujian Medical Development, China/ ; 2023J01692//Fujian Provincial Natural Science Foundation of China/ ; 2022J01243//Fujian Provincial Natural Science Foundation of China/ ; 2020Y9094//the Joint Funds for the innovation of science and Technology，Fujian province, China/ ; 2023Y9213//the Joint Funds for the innovation of science and Technology，Fujian province, China/ ; 2021Y9068//the Joint Funds for the innovation of science and Technology，Fujian province, China/ ; 82002034//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Diabetic Foot/microbiology/diagnosis ; China/epidemiology ; *High-Throughput Nucleotide Sequencing/methods ; *Tertiary Care Centers ; Male ; Female ; *Metagenomics/methods ; Middle Aged ; Aged ; Microbiota/genetics ; Adult ; }, abstract = {BACKGROUND: Diabetic foot ulcers (DFUs) are characterized by dynamic wound microbiome, the timely and accurate identification of pathogens in the clinic is required to initiate precise and individualized treatment. Metagenomic next-generation sequencing (mNGS) has been a useful supplement to routine culture method for the etiological diagnosis of DFUs. In this study, we utilized a routine culture method and mNGS to analyze the same DFU wound samples and the results were compared.

METHODS: Forty samples from patients with DFUs at a tertiary medical center in South China were collected, the microorganisms were identified with mNGS and routine culture method simultaneously.

RESULTS: The results showed that the positive detection rate of microorganisms in DFUs with mNGS was much higher (95% vs. 60%). Thirteen strains of microorganisms were detected with routine culture method, and seventy-seven strains were detected with mNGS. Staphylococcus aureus was the most common microorganism detected with culture method, while Enterococcus faecalis was the most common microorganism detected with mNGS. The false negative rate of the culture method was 35%, that was, 14 samples with negative results with culture method were found to be positive with mNGS.

CONCLUSION: The mNGS method had a higher positive detection rate and identified a broader spectrum of microorganisms in DFUs, thus, mNGS provided a more comprehensive understanding of the microbiome of DFUs to facilitate the development of timely and optimal treatment.

TRIAL REGISTRATION: The study was conducted in accordance with the Declaration of Helsinki and approved by the Ethical Review Committee of the Fujian Medical University Union Hospital (approval number 2021KY054).}, } @article {pmid39849165, year = {2025}, author = {Sandhu, S and Kumar, S and Singh, P and Singh, BP and Jurel, SK and Lal, N and Mohit, and Sharma, V and Rai, N and Chand, P}, title = {Metagenomic profiling of plaque microbiota in Indian subjects: identified hidden ecological tapestry.}, journal = {Current genetics}, volume = {71}, number = {1}, pages = {3}, pmid = {39849165}, issn = {1432-0983}, mesh = {Humans ; *Dental Plaque/microbiology ; *Metagenomics/methods ; Male ; *Microbiota/genetics ; Female ; India/epidemiology ; Adult ; *Metagenome ; *RNA, Ribosomal, 16S/genetics ; Middle Aged ; Young Adult ; Adolescent ; Bacteria/genetics/classification/isolation & purification ; Streptococcus/genetics/isolation & purification/classification ; }, abstract = {Dental plaque biofilms are the primary etiologic factor for various chronic oral infectious diseases. In recent years, dental plaque shows enormous potential to know about an individual microbiota. Various microbiome studies of oral cavity from different geographical locations reveals abundance of microbial species. Although, the representation of Indian population in this respect is limited, which make us curious to undergo this study. This study investigates the dental plaque microbiota of North Indian individuals based on their age, gender, and dietary patterns; specifically, food preference and availability of water source using 16 S rRNA metagenomics analysis. The findings from this study revealed that Streptococcus levels are high across genders, age groups, and water source, highlighting its role as a predominant dental caries associated species like Streptococcus mutans, Streptococcus pyogenes, Streptococcus sobrinus and Streptococcus oralis in the studied population groups. Additionally, the abundance of Actinomyces is observed higher in young individuals and females whereas Fusobacterium and Leptotrichia were high in elderly individuals. Moreover, non-vegetarians have higher abundance of Streptococcus and Fusobacterium, whereas vegetarians show higher abundance of Prevotella and Leptotrichia. The study also highlights the influence of water type on bacterial composition of dental plaque in the studied population i.e., individuals consuming underground water has high abundance of Streptococcus, whereas individuals consuming RO water exhibit elevated Prevotella and Leptotrichia. Insights emerged from the analysis illuminates the complex dynamics of microbiota in dental plaque among North Indians. This study also highlight that this variation of microbiome is influenced by age, gender, and dietary habits (vegetarian or non-vegetarian lifestyle). These results will fill a significant knowledge gap regarding the Indian dental plaque microbiome but also offer a foundation to conduct metagenome studies and potential therapeutic implications for future personalized oral health interventions.}, } @article {pmid39849009, year = {2025}, author = {Calderón-Osorno, M and Rojas-Villalta, D and Lejzerowicz, F and Cortés, J and Arias-Andres, M and Rojas-Jimenez, K}, title = {The influence of depth on the global deep-sea plasmidome.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {2959}, pmid = {39849009}, issn = {2045-2322}, support = {SIA 0483-21//Universidad Nacional de Costa Rica/ ; C1455//Vicerrectoría de Investigacion de la Universidad Costa Rica/ ; C2650//Vicerrectoría de Investigacion de la Universidad Costa Rica/ ; C3509//Vicerrectoría de Investigacion de la Universidad Costa Rica/ ; }, mesh = {*Plasmids/genetics ; Metagenome ; Seawater/microbiology ; Ecosystem ; Oceans and Seas ; Gammaproteobacteria/genetics/classification ; Alphaproteobacteria/genetics ; }, abstract = {Plasmids play a crucial role in facilitating genetic exchange and enhancing the adaptability of microbial communities. Despite their importance, environmental plasmids remain understudied, particularly those in fragile and underexplored ecosystems such as the deep-sea. In this paper we implemented a bioinformatics pipeline to study the composition, diversity, and functional attributes of plasmid communities (plasmidome) in 81 deep-sea metagenomes from the Tara and Malaspina expeditions, sampled from the Pacific, Atlantic, and Indian Oceans at depths ranging from 270 to 4005 m. We observed an association between depth and plasmid traits, with the 270-1000 m range (mesopelagic samples) exhibiting the highest number of plasmids and the largest plasmid sizes. Plasmids of Alphaproteobacteria and Gammaproteobacteria were predominant across the oceans, particularly in this depth range, which also showed the highest species diversity and abundance of metabolic pathways, including aromatic compound degradation. Surprisingly, relatively few antibiotic resistance genes were found in the deep-sea ecosystem, with most being found in the mesopelagic layer. These included classes such as beta-lactamase, biocide resistance, and aminoglycosides. Our study also identified the MOBP and MOBQ relaxase families as prevalent across various taxonomic classes. This research underscores the importance of studying the plasmidome independently from the chromosomal context. Our limited understanding of the deep-sea's microbial ecology, especially its plasmidome, necessitates caution in human activities like mining. Such activities could have unforeseen impacts on this largely unexplored ecosystem.}, } @article {pmid39848523, year = {2025}, author = {Yu, MF and Chen, L and Liu, G and Liu, W and Yang, Y and Ma, L}, title = {Metagenomic deciphers the mobility and bacterial hosts of antibiotic resistance genes under antibiotics and heavy metals co-selection pressures in constructed wetlands.}, journal = {Environmental research}, volume = {269}, number = {}, pages = {120921}, doi = {10.1016/j.envres.2025.120921}, pmid = {39848523}, issn = {1096-0953}, abstract = {Both antibiotics and heavy metals exert significant selection pressures on antibiotic-resistance genes (ARGs). This study aimed to investigate the co-selection effects of doxycycline (DC) and cadmium (Cd) on ARGs in constructed wetlands (CWs). The results demonstrated that under antibiotic and heavy metal co-selection pressures, single high concentration DC/Cd or double high, relative abundances of metagenomics assembled genomes all reached 55.1%; meanwhile, the average ratio of ARG-containing contigs located on chromosomes was 61.8% (ranging from 50.4% to 70.6%) suggesting a more stable inheritance of ARGs. Antibiotic and heavy metal co-selection in single high concentration DC/Cd or double high groups stimulate the enrichment of ARG host bacteria, which exhibited complex multiple-resistant patterns accompanied by a host-specific pattern. Additionally, the potential transfer abilities of ARGs mediated by plasmids and integrative and conjugative elements (ICEs) were enhanced under single high-concentration DC/Cd or double high stresses. Together, antibiotic and heavy metal co-selection pressures increased occurrence frequencies of ARGs, MGEs, and their combinations and altered structural communities of ARG host bacteria, increasing the risk of the spread of ARGs. This study was helpful in understanding the dissemination of ARGs and simultaneously preventing the spread of heavy metal-resistant bacteria and ARGs under antibiotic and heavy metal co-selection in small- and micro-wetlands.}, } @article {pmid39848515, year = {2025}, author = {Zhang, M and Bai, L and Yao, Z and Li, W and Yang, W}, title = {Seasonal lake ice cover drives the restructuring of bacteria-archaea and bacteria-fungi interdomain ecological networks across diverse habitats.}, journal = {Environmental research}, volume = {269}, number = {}, pages = {120907}, doi = {10.1016/j.envres.2025.120907}, pmid = {39848515}, issn = {1096-0953}, abstract = {The coexistence of different microbial communities is fundamental to the sustainability of many ecosystems, yet our understanding of the relationships among microbial communities in plateau cold-region lakes affected by seasonal ice cover remains limited. This research involved investigating three lakes in the Inner Mongolia segment of the Yellow River basin during frozen and unfrozen periods in two habitats: water bodies and sediments. The research examined the composition and function of bacteria, archaea, and fungi across different times and habitats within the basin, their response to environmental variables in water and sediment, and inter-domain interactions between bacteria-archaea and bacteria-fungi were compared using interdomain ecological network (IDEN). The findings indicate significant variations in the structures of bacterial, archaeal, and fungal communities across different periods and habitats, with the pH of the water body being a crucial environmental variable affecting microbial community composition. In the frozen period, the functionality of microbial communities, especially in terms of energy metabolism, was significantly impacted, with water bodies experiencing more pronounced effects than sediments. Archaea and fungi significantly contribute to the stability of bacterial communities across various habitats, especially in ice-covered conditions, where stronger associations between bacterial communities, archaea, and fungi promote the microbial communities' adaptability to cold stress. Furthermore, our results indicate that the primary environmental variable influencing the structure of IDENs is the nutrient salt content in both water bodies and sediments. This study broadens our understanding of the responses and feedback mechanisms of inter-domain microbial interactions in lakes influenced by seasonal ice cover.}, } @article {pmid39848447, year = {2025}, author = {Zhang, L and Fan, R and Li, W and Li, G and Luo, W and Xu, Z}, title = {Unravelling biotic and abiotic mechanisms of mature compost to alleviate gaseous emissions in kitchen waste composting by metagenomic analysis.}, journal = {Bioresource technology}, volume = {419}, number = {}, pages = {132102}, doi = {10.1016/j.biortech.2025.132102}, pmid = {39848447}, issn = {1873-2976}, mesh = {*Composting/methods ; *Metagenomics/methods ; *Methane/metabolism ; Gases ; Soil Microbiology ; Ammonia/metabolism ; Soil/chemistry ; Refuse Disposal/methods ; Carbon Dioxide/metabolism ; Hydrogen-Ion Concentration ; Nitrous Oxide/metabolism ; }, abstract = {Mature compost can reduce gaseous emissions in composting, but its regulation mechanisms via biotic and abiotic functions are largely unknown. This study used fresh and inactivated mature compost as additives in kitchen waste composting to unveil the relevant mechanisms using metagenomic analysis. Results showed that mature compost reduce gaseous emission by improving physiochemical properties and inoculating functional microbes. The abiotic function of mature compost alleviated methane and nitrous oxide emission by 20 % via enhancing air diffusion and pH to limit the activity of mcr, mtr, norB/C, and narG/H hosts. Compared to inactivated mature compost, the microbes in fresh counterpart promoted organic mineralization to slightly enhance ammonia release by 9 %, but alleviated 13 % of carbon dioxide emission through microbial humification to impel carbon sequestration. Therefore, another specialistic strategy (e.g. Calcium magnesium phosphate addition to form struvite Crystallization) should be integrated with mature compost to synergistically reduce gaseous emissions.}, } @article {pmid39848182, year = {2025}, author = {Wang, X and Liu, TC and Wang, XW and Dang, CC and Tan, X and Lu, Y and Liu, BF and Xing, DF and Ren, NQ and Xie, GJ}, title = {Microbial manganese redox cycling drives co-removal of nitrate and ammonium.}, journal = {Journal of environmental management}, volume = {375}, number = {}, pages = {124095}, doi = {10.1016/j.jenvman.2025.124095}, pmid = {39848182}, issn = {1095-8630}, mesh = {*Manganese/metabolism ; *Oxidation-Reduction ; *Nitrates/metabolism ; *Ammonium Compounds/metabolism ; Nitrogen/metabolism ; Sewage/microbiology ; }, abstract = {Manganese (Mn), abundant in the Earth's crust, can act as an oxidant or a reductant for diverse nitrogen biotransformation processes. However, the functional microorganisms and their metabolic pathways, as well as interactions, remain largely elusive. Here, a microbial consortium was enriched from a mixture of freshwater sediments and activated sludge by feeding ammonium, nitrate and Mn(II), which established manganese-driven co-removal of nitrate and ammonium with removal rates of 5.83 and 2.30 mg N L[-1] d[-1], respectively. The batch tests and metagenomic analyses revealed a nitrate-dependent anaerobic manganese oxidation (NDMO) process mediated by Anaerolineales and Phycisphaerales and a manganese reduction coupled to anaerobic ammonium oxidation (Mnammox) process mediated by Chthonomonadales. Based on identified key genes involved in the nitrogen and manganese metabolic pathways, nitrate was likely reduced to nitrite and nitrogen gas in the NDMO process while ammonium was oxidized to nitrite in the Mnammox process, which in turn fuelled the Anammox process carried out by Candidatus Brocadia. This revealed the microbial interactions of NDMO, Mnammox, and Anammox processes responsible for manganese-driven co-removal of ammonium and nitrate. These findings provide a potential solution for biological nitrogen removal and expand our understanding of the nitrogen and manganese biogeochemical cycles.}, } @article {pmid39847964, year = {2025}, author = {Liang, Y and Wang, W}, title = {A Balamuthia amoebic encephalitis survivor in China, and literature review.}, journal = {Diagnostic microbiology and infectious disease}, volume = {111}, number = {3}, pages = {116698}, doi = {10.1016/j.diagmicrobio.2025.116698}, pmid = {39847964}, issn = {1879-0070}, abstract = {Balamuthia amoebic encephalitis (BAE) is a rare, fatal parasitic infection of the central nervous system, with a current mortality rate above 95%. The high fatality rate is largely attributed to atypical clinicopathological features, delayed diagnosis, and the absence of effective treatment methods, so quick recognition of this disease is vital. In this paper, we present a survivor of BAE, who was confirmed through histologic examination and metagenomic next-generation sequencing (mNGS) of brain lesions. This case, unlike most previous reports, was a successful survival case. It highlights the critical need for differential diagnosis in patients with central nervous system infectious diseases, particularly those with a history of skin lesions and patients presenting multifocal brain lesions. Moreover, mNGS could serve as a useful tool in rapid identification of causative rare pathogens. The application of decompressive craniectomy may offer treatment opportunities and improve the survival rate of BAE. The case description was followed by a review of the literatures, in order to improve clinicians' understanding of this disease.}, } @article {pmid39847933, year = {2025}, author = {Malla, MA and Nomalihle, M and Featherston, J and Kumar, A and Amoah, ID and Ismail, A and Bux, F and Kumari, S}, title = {Comprehensive profiling and risk assessment of antibiotic resistomes in surface water and plastisphere by integrated shotgun metagenomics.}, journal = {Journal of hazardous materials}, volume = {487}, number = {}, pages = {137180}, doi = {10.1016/j.jhazmat.2025.137180}, pmid = {39847933}, issn = {1873-3336}, abstract = {The ever-increasing microplastics (MPs) and antibiotic-resistance genes (ARGs) in aquatic ecosystems has become a serious global challenging issue. However, the impact of different pollution sources on microbiome and antibiotic resistome in surface water (SW) and plastisphere (PS) remains largely elusive. Here, shotgun metagenomics was used to analyze microbiome structure and antibiotic resistome in SW and PS under the influence of different pollution sources. Pseudomonas were the most abundant genus, followed by Flavobacterium, Acinetobacter, Acidovorax, and Limnohabitans. However, their relative abundance varied significantly both across the sampling sites and habitats i.e. SW and PS (p < 0.05). Additionally, various ARGs were detected in SW and PS, with PS (372) having significantly more potential ARGs than SW (293). The results further showed significant variations in the relative abundance of potential pathogenic bacteria across the sampling sites and habitats (p < 0.05). Further moreover, significant differences were observed in antibiotic resistome risk scores, ARGs and MGEs across different habitats. Over all, this study suggests that pollution source and water quality parameters had a significant impact on microbiome composition and antibiotic resistome in SW and PS.}, } @article {pmid39847904, year = {2025}, author = {Feng, C and Zhang, X and Gao, G and Ren, K and Li, Z and Xu, Z and Wei, D and Zhang, J}, title = {A new insight on simultaneous water purification and greenhouse gas reduction by constructing sulfur-siderite driven autotrophic denitrification pathways in constructed wetlands.}, journal = {Water research}, volume = {274}, number = {}, pages = {123130}, doi = {10.1016/j.watres.2025.123130}, pmid = {39847904}, issn = {1879-2448}, abstract = {Sulfur-siderite driven autotrophic denitrification (SSAD) has received increasing attention for nutrient removal in constructed wetlands (CWs). Nevertheless, its effectiveness in simultaneous water purification and greenhouse gases (GHGs) reduction remains obscure. In this study, three vertical flow constructed wetlands (VFCWs), filled with quartz sand (CCW), sulfur (S-CW), and sulfur-siderite mixed substrates (SS-CW), were constructed to investigate the underlying mechanisms of SSAD on water purification enhancement and GHGs reduction. Results indicated that SSAD optimized the carbon, nitrogen, phosphorus, and sulfur transformation processes and enhanced the electron transfer system activity (ETSA) in CWs. Meanwhile, it resulted in the highest total nitrogen (TN) removal efficiency (91.6 ± 2.2 %) and the lowest methane (CH4) and nitrous oxide (N2O) emissions from SS-CW. Compared with CCW, the reduction efficiencies of CH4 and N2O were 76.7 ± 6.7 % and 93.4 ± 2.2 %, respectively. This was mainly ascribed to constructing ammonia oxidation coupled with iron reduction (Feammox), SSAD and multi-electron driven anaerobic oxidation of methane (AOM) pathway in SS-CW which could achieve co-emission reduction of CH4 and N2O. Analysis of the functional genes and microbial community structure revealed that higher abundance of genes associated with GHGs mitigation, more denitrifying bacteria and methanotrophic bacteria were enriched in SS-CW. Further analysis of metagenomic results showed that both the electron transfer pathway and the GHGs mitigation pathway were significantly enhanced in SS-CW. The results of this study provide a new insight into using SSAD as a method to improve the nutrient removal efficiency of CWs while reducing GHGs.}, } @article {pmid39847397, year = {2024}, author = {Deng, Z and Lan, Z and Zhu, H and Ren, H and Jin, Z and Jiang, J and Lan, T and Zhou, J and Wang, J and Wan, P and Guo, Y and Xu, B and Zhu, H and Wen, Z}, title = {Metagenomic next-generation sequencing for the detection of bacterial translocation in the blood of patients following liver, biliary tract or pancreatic surgery.}, journal = {The British journal of surgery}, volume = {112}, number = {1}, pages = {}, pmid = {39847397}, issn = {1365-2168}, support = {82160128//National Natural Science Foundation of China/ ; ZA20220492//Self-Raised Project of Guangxi Health Committee/ ; }, } @article {pmid39847144, year = {2025}, author = {Niemelä, LRK and Pásztor, A and Frey, AD}, title = {Generation of ribosomal protein S1 mutants for improving of expression of difficult to translate mRNAs.}, journal = {Applied microbiology and biotechnology}, volume = {109}, number = {1}, pages = {20}, pmid = {39847144}, issn = {1432-0614}, support = {562/31/2014//Tekes/ ; }, mesh = {*Escherichia coli/genetics/metabolism ; *Ribosomal Proteins/genetics ; *RNA, Messenger/genetics ; *Mutation ; 5' Untranslated Regions/genetics ; Protein Biosynthesis ; Operon ; Escherichia coli Proteins/genetics/metabolism ; Gene Library ; }, abstract = {Metagenomes present a source for novel enzymes, but under 1% of environmental microbes are cultivatable. Because of its useful properties, Escherichia coli has been used as a host organism in functional genomic screens. However, due to differing expression machineries in the expression host compared to the source organism of the DNA sequences, screening outcomes can be biased. Here, we focused on one of the limiting processes-translation initiation. To that end, we created an operon-like screening system in E. coli to select mutants of the ribosomal protein S1 with more relaxed sequence requirements for 5'-untranslated regions of mRNAs. We created two mutation libraries of the ribosomal protein S1, one covering domains 3 and 4 (D3-D4) and the second covering domains 3 to 5 (D3-D5). Most mutants from library D3-D4 proofed to be specific for a particular UTR sequence and improved only expression from a single construct. Only mutant 3 from library D3-D4 led to increased expression of four different reporters improving fluorescence levels by up to 21%. Mutants isolated from D3-D5 library led up to 90% higher expression compared to the control, though the mutants with highest improvements exhibited a specialist phenotype. The most promising mutant, mutant 4, exhibited a generalist phenotype and showed increased expression in all six reporter strains compared to the control. This could indicate the potential for a more promiscuous translation initiation of metagenomic sequences in E. coli although at the price of smaller increases compared to specialist mutants. KEY POINTS: • An operon-like selection system allowed to isolate generalist and specialist S1 mutants. • S1 mutants improved translation of mRNAs with 5'-UTRs from metagenomic sequences. • Use of S1 mutants could increase coverage from metagenomic libraries in functional screens.}, } @article {pmid39846163, year = {2025}, author = {Jena, PK and Arditi, M and Noval Rivas, M}, title = {Gut Microbiota Alterations in Patients With Kawasaki Disease.}, journal = {Arteriosclerosis, thrombosis, and vascular biology}, volume = {}, number = {}, pages = {}, doi = {10.1161/ATVBAHA.124.321201}, pmid = {39846163}, issn = {1524-4636}, support = {R01 HL139766/HL/NHLBI NIH HHS/United States ; R01 HL159297/HL/NHLBI NIH HHS/United States ; R01 HL149972/HL/NHLBI NIH HHS/United States ; R01 AI157274/AI/NIAID NIH HHS/United States ; R01 HL170580/HL/NHLBI NIH HHS/United States ; }, abstract = {The intestinal microbiota influences many host biological processes, including metabolism, intestinal barrier functions, and immune responses in the gut and distant organs. Alterations in its composition have been associated with the development of inflammatory disorders and cardiovascular diseases, including Kawasaki disease (KD). KD is an acute pediatric vasculitis of unknown etiology and the leading cause of acquired heart disease in children in the United States. The presence of gastrointestinal symptoms in the acute phase of KD has been associated with an increased risk of treatment resistance and the development of coronary artery aneurysms. Studies report alterations in fecal bacterial communities of patients with KD, characterized by the blooming of pathogenic bacteria and decreased relative abundance of short-chain fatty acid-producing bacteria. However, causality and functionality cannot be established from these observational patient cohorts of KD. This highlights the need for more advanced and rigorous studies to establish causality and functionality in both experimental models of KD vasculitis and patient cohorts. Here, we review the evidence linking an altered gut microbiota composition to the development of KD, assess the potential mechanisms involved in this process, and discuss the potential therapeutic value of these observations.}, } @article {pmid39846015, year = {2025}, author = {Cousson, A and Pablo, AL and Cournac, L and Piton, G and Dezette, D and Robin, A and Taschen, E and Bernard, L}, title = {Ultra pure high molecular weight DNA from soil for Nanopore shotgun metagenomics and metabarcoding sequencing.}, journal = {MethodsX}, volume = {14}, number = {}, pages = {103134}, pmid = {39846015}, issn = {2215-0161}, abstract = {Soil microbes are among the most abundant and diverse organisms on Earth but remain poorly characterized. New technologies have made possible to sequence the DNA of uncultivated microorganisms in soil and other complex ecosystems. Genome assembly is crucial for understanding their functional potential. Nanopore sequencing technologies allow to sequence long DNA fragments, optimizing production of metagenome-assembled genomes compared to short-read technology. Extracting DNA with a very high purity and high molecular weight is key to get the most out of this long read technologies. Here we present two extraction protocols to get DNA with high purity. First protocol is optimized to reach DNA quality suiting Nanopore shotgun metagenomics. It uses a non-toxic centrifugation gradient to separate bacterial cells from soil to extract DNA directly on cells. The median length of the acquired DNA sequences (N50) was 3 to 7 times greater than previously published in the literature, achieving an N50 of ∼14 kb. The other, a modification of a commercially available MP Biomedical DNA extraction kit, yielded high-purity DNA for full-length 16S Oxford Nanopore metabarcoding, with an N50 of ∼8 kb. The MP-based protocol achieves higher yields of ultra-pure DNA compared to the Nycodenz protocol, at the expense of shorter fragment lengths.}, } @article {pmid39845824, year = {2024}, author = {Fang, J and Fang, H and Guo, P and Peng, Y and Chen, P}, title = {Strongyloides stercoralis combined with concurrent multiple pathogens infections in an immunosuppressed patient: a case report.}, journal = {Frontiers in medicine}, volume = {11}, number = {}, pages = {1519065}, pmid = {39845824}, issn = {2296-858X}, abstract = {BACKGROUND: Strongyloides stercoralis is an opportunistic pathogenic parasite. Most individuals with normal immune function may not exhibit significant symptoms, and the signs are atypical, which can easily lead to missed diagnoses and delayed treatment. People with underlying diseases and weakened immunity are prone to develop severe conditions after infection with Strongyloides stercoralis.

CASE PRESENTATION: We report an immunocompromised patient in whom the pathogen was initially not detectable using traditional parasitic detection techniques. However, Strongyloides stercoralis was identified in both the alveolar lavage fluid and blood through metagenomic next-generation sequencing. Subsequently, Strongyloides stercoralis was detected in the alveolar lavage fluid after multiple rounds of testing using traditional microscopic examination techniques. Based on the mNGS results and other examination findings, the patient was diagnosed with Strongyloides stercoralis in combination with concurrent multiple pathogens infections. After the combined drug therapy of Meropenem, Vancomycin, and Albendazole, the patient's condition was gradually brought under control.

CONCLUSION: This case demonstrates the advantage of integrating traditional detection methods with metagenomics next-generation sequencing technology in the etiological diagnosis of immunocompromised individuals. It is conducive to clarifying the etiological diagnosis of patients and thereby facilitating the timely initiation of corresponding treatments.}, } @article {pmid39845819, year = {2024}, author = {Feng, Q and Yuan, H and Ma, J and Guo, Z and Xia, X and Zhao, G}, title = {Invasive Klebsiella pneumoniae liver abscess syndrome complicated by carbapenem-resistant Acinetobacter baumannii infection: a case report.}, journal = {Frontiers in medicine}, volume = {11}, number = {}, pages = {1511734}, pmid = {39845819}, issn = {2296-858X}, abstract = {BACKGROUND: A liver abscess caused by hypervirulent Klebsiella pneumoniae can lead to multiple invasive extrahepatic infections, including lung abscesses, endophthalmitis, brain abscesses, and necrotizing fasciitis. This condition, known as Klebsiella pneumoniae liver abscess invasion syndrome, progresses rapidly and is associated with severe illness, high disability rates, and significant mortality. However, bloodstream infections with co-infection involving carbapenem-resistant Acinetobacter baumannii are exceedingly rare.

CASE PRESENTATION: The Emergency Medicine Department of the First People's Hospital of Kunshan successfully treated a male patient diagnosed with liver, lung, and prostate abscesses. The patient underwent puncture and drainage, with analysis of the drainage fluid, sputum culture, and metagenomic next-generation sequencing (m-NGS) revealing a co-infection with blood-borne Klebsiella pneumoniae and Acinetobacter baumannii. Guided by drug sensitivity test results, the patient received treatment with polymyxin and cefoperazone sodium-sulbactam sodium for infection control and liver protection. The treatment was successful, and the patient fully recovered and was discharged.

CONCLUSION: By reporting this rare case and highlighting the drug resistance of the bacteria, we propose a new diagnosis and treatment plan for managing Klebsiella pneumoniae combined with carbapenem-resistant Acinetobacter baumannii infection, along with a literature review.}, } @article {pmid39845816, year = {2024}, author = {Shao, S and Liu, J and Wu, Z and Wu, S}, title = {Chlamydophila psittaci pneumonia followed by lower gastrointestinal ischemic necrosis: a case report.}, journal = {Frontiers in medicine}, volume = {11}, number = {}, pages = {1394897}, pmid = {39845816}, issn = {2296-858X}, abstract = {BACKGROUND: Psittacosis, also known as parrot fever, is an uncommon infectious disease caused by Chlamydophila psittaci (C. psittaci). While C. psittaci infections are usually not life-threatening, the pathogenesis and associated complications are not yet fully understood.

CASE DESCRIPTION: A 54-year-old male was hospitalized due to a cough, accompanied by expectoration and dyspnea. After admission, the patient's breathing rapidly deteriorated, and despite the use of a ventilator, it was challenging to maintain respiratory function. While initiating extracorporeal membrane oxygenation (ECMO) and empirical anti-infection treatments, the alveolar lavage fluid was collected and examined by metagenomics next generation sequencing (mNGS). The mNGS result indicated C. psittaci. Subsequently, the anti-infection regimen was immediately adjusted. The respiratory function improved on the 13th day after admission, and ECMO was withdrawn. However, the patient developed abdominal distension and intestinal edema. After intravenous infusion therapy, intestinal ischemia and necrosis occurred and surgical resection was performed. The patient's condition improved after the operation and he was transferred to a local hospital for rehabilitation.

CONCLUSION: This case report demonstrates the development of intestinal ischemic necrosis following severe C. psittaci pneumonia. This unique association has not been reported previously and highlights the importance of potential gastrointestinal complications in severe C. psittaci pneumonia, which are often underestimated. Timely diagnoses and treatments of such infections and complications are necessary to achieve favorable clinical outcomes.}, } @article {pmid39845646, year = {2024}, author = {Hadrich, I and Turki, M and Chaari, I and Abdelmoula, B and Gargouri, R and Khemakhem, N and Elatoui, D and Abid, F and Kammoun, S and Rekik, M and Aloulou, S and Sehli, M and Mrad, AB and Neji, S and Feiguin, FM and Aloulou, J and Abdelmoula, NB and Sellami, H}, title = {Gut mycobiome and neuropsychiatric disorders: insights and therapeutic potential.}, journal = {Frontiers in cellular neuroscience}, volume = {18}, number = {}, pages = {1495224}, pmid = {39845646}, issn = {1662-5102}, abstract = {BACKGROUND: The human gut mycobiome, a minor but integral component of the gut microbiome, has emerged as a significant player in host homeostasis and disease development. While bacteria have traditionally been the focus of gut microbiome studies, recent evidence suggests that fungal communities (mycobiota) may also play a crucial role in modulating health, particularly in neuropsychiatric disorders.

OBJECTIVE: This review aims to provide a comprehensive overview of current knowledge on the relationship between the gut mycobiome and neuropsychiatric disorders, exploring the potential of targeting fungal communities as a novel therapeutic strategy.

METHODS: We summarized recent findings from metagenomic analyses that characterize the diversity and composition of gut mycobiota and discuss how these communities interact with the host and other microorganisms via the gut-brain axis. Key methodologies for studying mycobiota, such as high-throughout sequencing and bioinformatics approaches, were also reviewed to highlight advances in the field.

RESULTS: Emerging research links gut mycobiota dysbiosis to conditions such as schizophrenia, Alzheimer's disease, autism spectrum disorders, bipolar disorder, and depression. Studies indicate that specific fungal populations, such as Candida and Saccharomyces, may influence neuroinflammation, gut permeability and immune responses, thereby affecting mental health outcomes.

CONCLUSION: Understanding the gut mycobiome's role in neuropsychiatric disorders opens new avenues for therapeutic interventions, including antifungal treatments, probiotics, and dietary modifications. Future research should integrate multi-omics approaches to unravel the complex interkingdom interactions within the gut ecosystem, paving the way for personalized medicine in mental health care.}, } @article {pmid39845316, year = {2024}, author = {Yang, HS and Zhang, J and Feng, HX and Qi, F and Kong, FJ and Zhu, WJ and Liang, CY and Zhang, ZR}, title = {Characterizing microbial communities and their correlation with genetic mutations in early-stage lung adenocarcinoma: implications for disease progression and therapeutic targets.}, journal = {Frontiers in oncology}, volume = {14}, number = {}, pages = {1498524}, pmid = {39845316}, issn = {2234-943X}, abstract = {BACKGROUND: Lung adenocarcinoma (LUAD), the most prevalent form of lung cancer. The transition from adenocarcinoma in situ (AIS), and minimally invasive adenocarcinoma (MIA) to invasive adenocarcinoma (IAC) is not fully understood. Intratumoral microbiota may play a role in LUAD progression, but comprehensive stage-wise analysis is lacking.

METHODS: Tumor and bronchoalveolar lavage fluid (BALF) samples from patients with AIS/MIA or IAC were collected for next-generation sequencing to characterize microbial diversity and composition. DNA extraction involved lysing samples with nuclease and protease, followed by homogenization and elution. Sequencing libraries were prepared and sequenced on the Illumina platform. Whole exome sequencing was performed to identify somatic mutations and genetic variants. Bioinformatics analysis, including taxonomic annotation with Kraken2 and de novo assembly with MEGAHIT, was conducted to process metagenomic data. Correlation analysis was performed to link microbial species with mutated genes using custom R scripts.

RESULTS: Metagenomic analysis revealed a distinct microbial profile in IAC compared to AIS/MIA, with increased abundance of Bacteroidetes and Firmicutes in the IAC group. Bosea sp. and Microbacterium paludicola, were less abundant in IAC, suggesting a potential protective role in early-stage disease. Conversely, Mycolicibacterium species were more prevalent in IAC, indicating a possible contribution to disease progression. Genetic sequencing identified PTPRZ1 strongly correlating with microbial composition, suggesting a mechanistic link between microbiota and genetic alterations in LUAD.

CONCLUSION: This study characterizes microbial communities in various stages of LUAD, revealing links between microbiota and genetic mutations. The unique microbiota suggests its role in LUAD progression and as a therapeutic target.}, } @article {pmid39845046, year = {2024}, author = {Almuhaideb, E and Hasan, NA and Grim, C and Rashed, SM and Parveen, S}, title = {Comparative evaluation of specimen type and processing conditions for studying oyster microbiomes.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1504487}, pmid = {39845046}, issn = {1664-302X}, abstract = {Metagenomic sequencing is increasingly being employed to understand the assemblage and dynamics of the oyster microbiome. Specimen collection and processing steps can impact the resultant microbiome composition and introduce bias. To investigate this systematically, a total of 54 farmed oysters were collected from Chesapeake Bay between May and September 2019. Six different specimen types and processing methods were evaluated for microbial community composition using shotgun metagenomics, namely fresh oyster homogenate (FOH), oyster homogenate after simulated temperature abuse (AOH), Luria broth-enriched oyster homogenate (EOH), dissected stomach homogenate (DSH), hemolymph (HLM), and stomach-gut content (SGC). In general, DSH, EOH, and FOH yielded the highest DNA concentration, while EOH had the highest microbial reads, followed by DSH, HLM, and FOH. HLM produced the highest bacterial species alpha diversity, followed by AOH, EOH, and SGC. Although alpha diversities did not differ significantly, beta-diversity measurements showed significant dissimilarity among methods (p < 0.05) indicating that the specimen types and processing steps do play an important role in representing the composition of the bacterial community. Bacterial species that had the highest log mean abundance included Cyanobium sp. PCC 7001 in FOH, Vibrio vulnificus in AOH, EOH, and DSH, and lastly Synechococcus sp. CB0205 in the DSH, HML, and SGC samples. EOH displayed higher bacterial hits, distinct microbial composition, and higher values of bacterial, phages, and antimicrobial resistance gene reads. Therefore, if studying the overall oyster microbial community, prioritizing optimum specimen collection and processing methods that align with the overall goal of the study is recommended.}, } @article {pmid39844919, year = {2025}, author = {Naim, W and Manetsberger, J and Lavilla Lerma, L and Benomar, N and Caballero Gómez, N and Cuesta-Bertomeu, IS and Gata Díaz, JÁ and Abriouel, H}, title = {Impact of disinfection methods used in the slaughterhouse environment on microbiome diversity throughout the meat production chain.}, journal = {Current research in microbial sciences}, volume = {8}, number = {}, pages = {100336}, pmid = {39844919}, issn = {2666-5174}, abstract = {Slaughterhouse environments are prone to microbial contamination, influenced by factors like set-up, size and area as well as disinfection practices. Thus, effective control measures are crucial to prevent the spread of pathogens and their contaminant genes (antimicrobial resistance genes and virulence factors) throughout the food chain. In the present study, we assessed the microbial contamination in environmental surfaces of three slaughterhouses located in the Jaén province (Spain). We also evaluated the impact of different disinfection strategies on microbial loads and diversity by means of culture dependent and independent methods. The results revealed a statistically significant inter- and intra-specific differences in microbial loads including the most important pathogens such as pseudomonads, staphylococci, Escherichia coli, Salmonella sp. and Campylobacter jejuni. Disinfection strategies using routine disinfectant (used by the slaughterhouse), HLE disinfectant, UV, or combinations thereof showed varying effectiveness. The newly developed sustainable HLE disinfectant was most effective, while UV had the lowest disinfection strength, and routine disinfectants failed to eradicate all pathogens. Metagenomic analysis identified Pseudomonadota as the dominant phylum, followed by Actinomycetota and Bacteroidota. Results furthermore indicated shifts from sacrifice to cold rooms, with an increase in Gammaproteobacteria, particularly Moraxellaceae (represented by Psychrobacter cryohalolentis) over Acinetobacter sp. In conclusion, this study highlights the potential of HLE disinfectant (alone or in combination with the routine disinfectant) as a more effective disinfection measure on environmental surfaces, particularly for combating multi-drug resistant pathogens compared to other disinfection methods currently used.}, } @article {pmid39844843, year = {2024}, author = {Shi, T and Lin, Y and Zheng, X and Ruan, H and Zhang, R and Liu, Y and Xu, S and Wang, H}, title = {Metagenomic next-generation sequencing for the clinical identification of spinal infection-associated pathogens.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1437665}, pmid = {39844843}, issn = {2235-2988}, mesh = {Humans ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; Male ; Female ; Middle Aged ; Aged ; Adult ; Bacteria/genetics/isolation & purification/classification ; Young Adult ; Aged, 80 and over ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: This study aimed to evaluate the efficacy of metagenomic next-generation sequencing (mNGS) technology for identifying pathogens associated with spinal infection (SI).

METHODS: A retrospective analysis was conducted on clinical data from 193 patients with suspected SI between August 2020 and September 2024. Based on histopathological results, the patients were divided into the SI group (n=162) and the non-SI group (n=31). The diagnostic performance of mNGS technology was compared with that of laboratory examination, imaging examination, and microbial culture.

RESULTS: Among SI group, mNGS detected 135 pathogens in 77.78% (126/162) of the cases, including nine cases of multiple infections. One or more pathogens were detected using mNGS in 86 patients with SI and negative microbial cultures. Staphylococcus aureus (22.22%, n=30) and Mycobacterium tuberculosis (22.22%, n=30) were the major pathogens, while various rare pathogens such as anaerobes, Brucella, and Coxiella burnetii were also detected. For the 40 cases with positive results for both culture- and mNGS-based identification, high consistency (77.50%) was observed. Antibiotic use did not significantly affect the mNGS detection rate (P = 0.45). There was no significant difference in the positivity rate of mNGS between CT-guided needle biopsy (80.00%) and surgical sampling (77.17%) (P = 0.72). The sensitivity of mNGS (77.78%) was significantly higher than that of traditional microbial culture (27.16%), and the specificity was similar (90.32% vs. 96.77%). Although the sensitivities of erythrocyte sedimentation rate-based assay (91.36%), magnetic resonance imaging (88.27%), and C-reactive protein-based assay (87.65%) were better than those of mNGS, their specificities were generally low (20%-40%).

CONCLUSION: The pathogens responsible for SI are complex and diverse. As a novel diagnostic method, mNGS exhibits a high sensitivity and extensive pathogen coverage for SI diagnosis. When combined with imaging and laboratory indicators, mNGS can significantly improve the accuracy of SI diagnosis and provide strong support for clinical treatment.}, } @article {pmid39844841, year = {2024}, author = {Chen, X and Liang, Y and Yang, W and He, W and Xing, Z and Li, S and Cai, S and Fu, J and Peng, X and Chen, M and Wu, J}, title = {Application of metagenomic next-generation sequencing in the diagnosis of post-stroke infections: a case series study using multiple sample types.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1386377}, pmid = {39844841}, issn = {2235-2988}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Male ; Female ; Retrospective Studies ; Aged ; Middle Aged ; *Stroke ; Sensitivity and Specificity ; Bacteria/genetics/isolation & purification/classification ; Aged, 80 and over ; }, abstract = {BACKGROUND: Metagenomic high-throughput sequencing (mNGS) represents a powerful tool for detecting nucleic acids from various pathogens, such as bacteria, fungi, viruses and parasites, in clinical samples. Despite its extensively employed in the pathogen diagnosis for various infectious diseases, its application in diagnosing stroke-related infection, and its potential impact on clinical decision-making, anti-infection treatment, clinical intervention, and patient prognosis remain insufficiently explored. Additionally, while mNGS offers promising potential, it facts limitations related to sensitivity, specificity, cost, and standardization, which could influence its integration into routine clinical practice.

METHODS: We retrospectively analyzed 18 stroke patients admitted to the First Affiliated Hospital of Medical College of Shantou University from January to February 2023, comparing culture-based methods with mNGS detection, and assessing its significance in etiological diagnosis. Additionally, we evaluated the performance differences among various sequencing platforms.

RESULTS: Among the 18 stroke patients enrolled, pulmonary infections were identified in 7 cases, urinary tract infections in 1 case, central nervous system infections in 10 cases, and combined pulmonary and central nervous system infections in 2 cases, with 2 cases yielding negative results. mNGS detected pathogens in 13 cases, aligning with clinical diagnoses (75% concordance), whereas culture-based methods yielded positive results in only 6 cases (22% concordance). Importantly, for 9 of the 18 patients, adjustments to anti-infective treatment regimens based on mNGS results led to improved symptomatic relief and infection control. This suggests that mNGS can contribute to more timely and precise treatment modifications, particularly for infections with low pathogen loads, potentially enhancing clinical outcomes.

CONCLUSION: Our findings highlights the utility of mNGS in diagnosing stroke-associated infections by providing a more comprehensive etiological diagnosis compared to traditional method. While mNGS shows promise in enhancing diagnostic accuracy and guiding clinical treatment, it high cost and technical challenges need addressing before widespread clinical adoption. Future research should focus on optimizing mNGS protocols, integration it with convertional diagnostic tools, and evaluating its cost-effectiveness and clinical impact through larger, multicentric studies.}, } @article {pmid39844833, year = {2024}, author = {Wang, M and Jin, Y and Zhang, W and Ye, L and Shao, H}, title = {Identifying subgroup of severe community-acquired pneumonia based on clinical metagenomics, a multicenter retrospective cohort study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1516620}, pmid = {39844833}, issn = {2235-2988}, mesh = {Humans ; *Community-Acquired Infections/microbiology/mortality ; Male ; Retrospective Studies ; Female ; *Metagenomics/methods ; Middle Aged ; Aged ; *C-Reactive Protein/analysis ; Procalcitonin/blood ; Pneumonia/microbiology/mortality/drug therapy ; Biomarkers/blood ; Adrenal Cortex Hormones/therapeutic use ; Respiration, Artificial ; Intensive Care Units ; }, abstract = {OBJECTIVE: Severe community-acquired pneumonia (sCAP) is one of the major diseases within the ICU. We hypothesize that subtyping sCAP based on simple inflammatory markers, organ dysfunction, and clinical metagenomics results is feasible.

METHOD: In this study, we retrospectively enrolled immunocompetent sCAP patients requiring invasive mechanical ventilation, who underwent clinical metagenomics from 17 medical centers. We collected data on potentially pathogenic species reported by clinical metagenomics and clinical information for all patients. Latent class analysis (LCA) was applied to routine clinical parameters such as gender, age, white blood cell (WBC), lymphocytes, C-reactive protein (CRP), and Procalcitonin (PCT), identifying two optimally fitting models.

RESULTS: A total of 569 patients were enrolled. Compared to class B, class A was characterized by a younger age, higher CRP and PCT levels, and a higher incidence of coagulation dysfunction, liver failure, circulatory failure, and renal failure. However, the mortality rates were similar between the two groups. In class A, more cases of Streptococcus spp. and fewer cases of HSV-1 and Candida spp. were detected. Among the patients in the two phenotypes, 48.7% and 57.5% received corticosteroid treatment, respectively. In the class A, corticosteroid treatment was not associated with patient mortality (unadjusted hazard ratio (HR)=0.988; 95% confidence interval (CI), 0.634-1.541; p=0.959). In contrast, in the class B group, the use of corticosteroids was associated with a reduced mortality rate (adjusted HR=0.719; 95% CI, 0.525-0.986; p=0.04). Additional analysis showed that in class B, methylprednisolone was associated with reduced mortality (adjusted HR=0.61; 95% CI, 0.44-0.86; p=0.005), while dexamethasone was not associated with mortality (adjusted HR=1.4; 95% CI, 0.89-2.22; p=0.148). In addition, after dose conversion, the results showed that higher doses of corticosteroids in class B were associated with increased mortality (adjusted HR=1.01; 95% CI, 1.00-1.01; p=0.005).

CONCLUSION: We identified two classes based on clinical metagenomics and clinical features. Class B exhibited a better response to corticosteroid compared to class A. The rapid identification of these phenotypes could facilitate the screening of sCAP patients responsive to corticosteroid in future prospective clinical trials.}, } @article {pmid39844349, year = {2025}, author = {Fonseca de Souza, L and Oliveira, HG and Pellegrinetti, TA and Mendes, LW and Bonatelli, ML and Dumaresq, ASR and Sinatti, VVC and Pinheiro, JB and Azevedo, JL and Quecine, MC}, title = {Co-inoculation with Bacillus thuringiensis RZ2MS9 and rhizobia improves the soybean development and modulates soil functional diversity.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {2}, pages = {}, pmid = {39844349}, issn = {1574-6941}, support = {2021/12378-4//FAPESP/ ; 166644/2020-0//National Council for Scientific and Technological Development/ ; 69242/2018-8//H.G.O./ ; 22.1.08498.01.0//T.A.P./ ; }, mesh = {*Glycine max/microbiology/growth & development ; *Soil Microbiology ; *Bacillus thuringiensis/genetics/growth & development ; *Soil/chemistry ; Rhizobium/genetics ; Quorum Sensing ; Microbiota ; Phosphorus/metabolism ; Biodiversity ; }, abstract = {Despite the beneficial effects of plant growth-promoting rhizobacteria on agriculture, understanding the consequences of introducing foreign microbes into soil taxonomic and functional diversity is necessary. This study evaluated the effects co-inoculation of soybean with Bacillus thuringiensis (Bt) RZ2MS9 and commercial rhizobia on the natural microbial community structure and functional potential. Our results indicated that soybean development was positively influenced by co-inoculation, plants exhibited greater height and a higher number of pods, and no reductions in productivity estimates. Soil prokaryotic diversity and community structure remained unchanged by Bt RZMS9 inoculation or co-inoculation with rhizobia 147 days after sowing. However, functional diversity was influenced by sole Bt inoculation, potentially due to community quorum sensing disruption by N-acyl homoserine lactone hydrolases. The genes enriched by co-inoculation were mostly related to soil phosphorus cycling, with gcd showing the most pronounced increase. The nifA genes increased when rhizobia alone were inoculated, suggesting that this pathway could be affected by Bt RZ2MS9 inoculation. This study demonstrates the synergistic activity of rhizobia and Bt RZ2MS9 on soybean development, without significantly interfering with natural microbial community, presenting a promising approach for sustainable crop management.}, } @article {pmid39844180, year = {2025}, author = {Chen, J and Pan, Q and Lu, L and Huang, X and Wang, S and Liu, X and Lun, J and Xu, X and Su, H and Guo, F and Yang, L and You, L and Xiao, H and Luo, W and Liu, HF and Pan, Q}, title = {Atg5 deficiency in basophils improves metabolism in lupus mice by regulating gut microbiota dysbiosis.}, journal = {Cell communication and signaling : CCS}, volume = {23}, number = {1}, pages = {40}, pmid = {39844180}, issn = {1478-811X}, support = {No. 82070757, 82270770//National Natural Science Foundation of China/ ; No. 82070757, 82270770//National Natural Science Foundation of China/ ; 2022B1212030003//Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Noncommunicable Diseases/ ; 2022B1212030003//Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Noncommunicable Diseases/ ; 2022B1212030003//Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Noncommunicable Diseases/ ; 2021A05067//Science and Technology Planning Project of Zhanjiang City/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Lupus Erythematosus, Systemic/metabolism ; *Basophils/metabolism ; *Dysbiosis ; Mice ; *Autophagy-Related Protein 5/genetics/metabolism ; Mice, Inbred MRL lpr ; Mice, Knockout ; Female ; Autophagy ; Mice, Inbred C57BL ; }, abstract = {Autophagic activation in immune cells, gut microbiota dysbiosis, and metabolic abnormalities have been reported separately as characteristics of systemic lupus erythematosus (SLE). Elucidating the crosstalk among the immune system, commensal microbiota, and metabolites is crucial to understanding the pathogenesis of autoimmune diseases. Emerging evidence shows that basophil activation plays a critical role in the pathogenesis of SLE; however, the underlying mechanisms remain largely unknown. Here, we investigated the effects of autophagic inhibition on the pathogenesis of basophils in SLE using Autophagy-related gene 5 (Atg5) knockout (Atg5[-/-]) as an autophagic inhibitor. Specifically, we knocked out basophilic Atg5 in vivo to investigate its impact on lupus metabolism. Furthermore, Atg5[-/-] basophils were transferred to basophil-depleted MRL/MpJ-Fas[lpr] (MRL/lpr) mice to study their effect on disease metabolism. Metagenomic and targeted metabolomic sequencing results indicated considerable reduction in the levels of plasma autoantibodies and inflammatory cytokines in the Atg5[-/-] basophil transfer group compared with that in the control group. Transplanting Atg5[-/-] basophils improved the gut microbiota balance in MRL/lpr mice, increasing the abundance of beneficial bacteria, such as Ligilactobacillus murinus and Faecalitalea rodentium, and reducing that of potentially pathogenic bacteria such as Phocaeicola salanitronis. The transplantation of Atg5-deficient basophils improved lupus symptoms by modulating lipid and amino acid metabolism. This improvement was linked to changes in the gut microbiota, particularly an increase in Ligilactobacillus murinus and Faecalitalea rodentium populations. These microbial shifts are believed to promote the production of beneficial metabolites, such as γ-linolenic acid and oleoyl-1-palmitoyl-sn-glycero-3-phosphocholine, while reducing the levels of harmful metabolites such as arginine. These alterations in the metabolic profile contribute to the alleviation of lupus symptoms. Collectively, these findings reveal a novel role of basophil autophagy in SLE, highlighting its potential as a therapeutic target.}, } @article {pmid39843539, year = {2025}, author = {Laczkó, L and Nagy, NA and Nagy, Á and Maroda, Á and Sály, P}, title = {An updated reference genome of Barbatula barbatula (Linnaeus, 1758).}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {137}, pmid = {39843539}, issn = {2052-4463}, support = {OTKA PD142602//Nemzeti Kutatási, Fejlesztési és Innovációs Hivatal (NKFI Office)/ ; }, mesh = {Animals ; *Genome ; *Microsatellite Repeats ; Cypriniformes/genetics ; }, abstract = {The stone loach Barbatula barbatula is a benthic fish species widely distributed throughout Europe, primarily inhabiting stony upper sections of stream networks. This study presents an updated genome assembly of B. barbatula, contributing to the species' available genomic resources for downstream applications such as conservation genetics. The draft assembly was 550 Mbp in size, with an N50 of 11.21 Mbp. We used the species' available chromosome scaffolds to finish the genome. The final assembly had a BUSCO score of 96.7%. We identified 23270 protein-coding genes, and the proteome exhibited high completeness with BUSCO (93.1%) and OMArk (90.81%). Despite using multiple approaches to reduce duplicate contigs, we observed a relatively high duplicate ratio of 6.1% (BUSCO) and 8.52% (OMArk) in the annotations. We aimed to find microsatellite loci present in both the species' publicly available genome and the new assembly to aid marker development for downstream analyses. This dataset serves as a reference for genomic analysis and is useful for developing markers to study the species' biodiversity and support conservation efforts.}, } @article {pmid39843522, year = {2025}, author = {Bray, AS and Broberg, CA and Hudson, AW and Wu, W and Nagpal, RK and Islam, M and Valencia-Bacca, JD and Shahid, F and Hernandez, GE and Nutter, NA and Walker, KA and Bennett, EF and Young, TM and Barnes, AJ and Ornelles, DA and Miller, VL and Zafar, MA}, title = {Klebsiella pneumoniae employs a type VI secretion system to overcome microbiota-mediated colonization resistance.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {940}, pmid = {39843522}, issn = {2041-1723}, support = {AI166642//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R21 AI166642/AI/NIAID NIH HHS/United States ; T32 AI007151/AI/NIAID NIH HHS/United States ; T32 AI007401/AI/NIAID NIH HHS/United States ; AI178595//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01 AI173244/AI/NIAID NIH HHS/United States ; T32 GM127261/GM/NIGMS NIH HHS/United States ; R21 AI178595/AI/NIAID NIH HHS/United States ; AI173244//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R21 AI132925/AI/NIAID NIH HHS/United States ; }, mesh = {*Klebsiella pneumoniae/genetics/metabolism ; *Type VI Secretion Systems/genetics/metabolism ; Animals ; *Gastrointestinal Microbiome/genetics ; Mice ; *Klebsiella Infections/microbiology ; Gene Expression Regulation, Bacterial ; Gastrointestinal Tract/microbiology ; Bacterial Proteins/metabolism/genetics ; DNA Transposable Elements/genetics ; Female ; Mice, Inbred C57BL ; }, abstract = {Microbial species must compete for space and nutrients to persist in the gastrointestinal (GI) tract, and our understanding of the complex pathobiont-microbiota interactions is far from complete. Klebsiella pneumoniae, a problematic, often drug-resistant nosocomial pathogen, can colonize the GI tract asymptomatically, serving as an infection reservoir. To provide insight on how K. pneumoniae interacts with the resident gut microbiome, we conduct a transposon mutagenesis screen using a murine model of GI colonization with an intact microbiota. Among the genes identified were those encoding a type VI secretion system (T6SS), which mediates contact-dependent killing of gram-negative bacteria. From several approaches, we demonstrate that the T6SS is critical for K. pneumoniae gut colonization. Metagenomics and in vitro killing assays reveal that K. pneumoniae reduces Betaproteobacteria species in a T6SS-dependent manner, thus identifying specific species targeted by K. pneumoniae. We further show that T6SS gene expression is controlled by several transcriptional regulators and that expression only occurs in vitro under conditions that mimic the gut environment. By enabling K. pneumoniae to thrive in the gut, the T6SS indirectly contributes to the pathogenic potential of this organism. These observations advance our molecular understanding of how K. pneumoniae successfully colonizes the GI tract.}, } @article {pmid39843444, year = {2025}, author = {Bechtold, EK and Ellenbogen, JB and Villa, JA and de Melo Ferreira, DK and Oliverio, AM and Kostka, JE and Rich, VI and Varner, RK and Bansal, S and Ward, EJ and Bohrer, G and Borton, MA and Wrighton, KC and Wilkins, MJ}, title = {Metabolic interactions underpinning high methane fluxes across terrestrial freshwater wetlands.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {944}, pmid = {39843444}, issn = {2041-1723}, support = {DE-SC0007144//U.S. Department of Energy (DOE)/ ; DE-SC0023084//U.S. Department of Energy (DOE)/ ; DE-SC0021067//U.S. Department of Energy (DOE)/ ; DE-SC0022191//U.S. Department of Energy (DOE)/ ; P30 CA046934/CA/NCI NIH HHS/United States ; DESC0023297//U.S. Department of Energy (DOE)/ ; EAR-2029686//National Science Foundation (NSF)/ ; DE-SC0012088//U.S. Department of Energy (DOE)/ ; DE-SC000054//U.S. Department of Energy (DOE)/ ; DE-SC0023456//U.S. Department of Energy (DOE)/ ; DEB-1754756//National Science Foundation (NSF)/ ; PRFB-2109592//National Science Foundation (NSF)/ ; DESC000054//U.S. Department of Energy (DOE)/ ; DE-SC0021350//U.S. Department of Energy (DOE)/ ; }, mesh = {*Methane/metabolism ; *Wetlands ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Fresh Water/microbiology ; Metagenome ; Bacteria/metabolism/genetics/classification ; Climate Change ; }, abstract = {Current estimates of wetland contributions to the global methane budget carry high uncertainty, particularly in accurately predicting emissions from high methane-emitting wetlands. Microorganisms drive methane cycling, but little is known about their conservation across wetlands. To address this, we integrate 16S rRNA amplicon datasets, metagenomes, metatranscriptomes, and annual methane flux data across 9 wetlands, creating the Multi-Omics for Understanding Climate Change (MUCC) v2.0.0 database. This resource is used to link microbiome composition to function and methane emissions, focusing on methane-cycling microbes and the networks driving carbon decomposition. We identify eight methane-cycling genera shared across wetlands and show wetland-specific metabolic interactions in marshes, revealing low connections between methanogens and methanotrophs in high-emitting wetlands. Methanoregula emerged as a hub methanogen across networks and is a strong predictor of methane flux. In these wetlands it also displays the functional potential for methylotrophic methanogenesis, highlighting the importance of this pathway in these ecosystems. Collectively, our findings illuminate trends between microbial decomposition networks and methane flux while providing an extensive publicly available database to advance future wetland research.}, } @article {pmid39843376, year = {2025}, author = {Pichon, M and Burucoa, C and , }, title = {Diagnostic performance of the DISQVER metagenomic sequencing tool for the identification of pathogens in febrile neutropenic patients: the ADNEMIA trial.}, journal = {BMJ open}, volume = {15}, number = {1}, pages = {e087773}, pmid = {39843376}, issn = {2044-6055}, mesh = {Humans ; *Metagenomics/methods ; Prospective Studies ; High-Throughput Nucleotide Sequencing ; Chemotherapy-Induced Febrile Neutropenia/diagnosis ; Febrile Neutropenia/diagnosis/microbiology ; Multicenter Studies as Topic ; Proof of Concept Study ; Anti-Bacterial Agents/therapeutic use ; Hematologic Neoplasms/complications ; }, abstract = {INTRODUCTION: While intensive protocols in onco-haematology have improved survival rates for patients with haematological malignancies, they have also resulted in an increased incidence of infection associated with therapy-induced immunosuppression (including chemotherapy-induced febrile neutropenia; FN). The occurrence of FN, associated with high morbidity and mortality, necessitates broad-spectrum antibiotic therapy, occasioning delayed chemotherapy and resulting in a loss of opportunity for the patient. Considering that without an identified pathogen, a 10% mortality rate can ensue, documentation is essential to the optimisation of antibiotic therapy. However, blood culture (the reference test) is limited for several reasons: such as fastidious culture, antibiotic treatment prior to sampling or insufficient sample volume. Sequencing technologies have led to the development of diagnostic approaches based on the detection of circulating DNA in blood. This study will aim to assess the clinical utility of metagenomic next-generation sequencing (mNGS)-DISQVER technology in detecting pathogenic microorganisms from blood samples of patients undergoing high-risk FN treatment.

METHODS AND ANALYSIS: This nationwide, prospective, multicentre, interventional, proof-of-concept clinical trial will enrol 200 patients. Will include patients≥18 years old, treated for malignancy, at high risk of FN (Multinational Association for Supportive Care in Cancer score≤21) with an expected duration of neutropenia≥7 days. Patients who received antibiotic treatment within 24 hours prior to enrolment, have previously participated and/or have enhanced protection will be excluded. The primary outcome will be determined by considering the microorganisms responsible for this FN, weighted by the assessment of an adjudication committee. Secondary outcomes will evaluate patient management depending on the arm. The second secondary outcome will be determined by the duration of conventional assessment, frequency of microorganisms detected during routine care and percentage distribution of theoretical adjustments made to anti-infective treatment based on microorganisms diagnosed using the mNGS-DISQVER tool as compared with conventional practices. Identifying the pathogens responsible for high-risk FN from a blood sample, using an unbiased technique, can provide microbiological documentation and may even reveal unexpected microorganisms in these profoundly immunocompromised patients.

ETHICS AND DISSEMINATION: The protocol received approval from the Comité de Protection des Personnes Sud-Méditerranée II. All participants will provide informed consent before participation. The trial has been registered on ClinicalTrials.gov (identifier NCT06075888). The results of the main trial and each of the secondary endpoints will be submitted for publication in a peer-reviewed journal.

TRIAL REGISTRATION NUMBER: ClinicalTrials.gov NCT06075888.}, } @article {pmid39842557, year = {2025}, author = {Loman, BR}, title = {Communities, mysteries, and pathophysiologies - Are gut microbes key to a healthy mind?.}, journal = {Brain, behavior, and immunity}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.bbi.2025.01.012}, pmid = {39842557}, issn = {1090-2139}, } @article {pmid39842302, year = {2025}, author = {Li, H and Zhang, X and Zhaxi, Y and Pan, C and Zhang, Z and Pan, J and Shahzad, K and Sun, F and Zhen, Y and Jinmei, J and Zhao, W and Song, T}, title = {Integrative multi-omics analysis reveals liver-gut axis adaptation in high-altitude goats.}, journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics}, volume = {54}, number = {}, pages = {101422}, doi = {10.1016/j.cbd.2025.101422}, pmid = {39842302}, issn = {1878-0407}, abstract = {The liver-gut axis is an important regulatory axis for the host's metabolic functions. The study of liver gene expression, changes in metabolic products and the regulation of gut microbial communities in plateau animals under harsh environments can reveal the mechanisms by which Tibetan goats adapt to the plateau environment. This study employs transcriptome, metabolome and metagenomic analyses to reveal the differences in genes, metabolism, and gut microbiota between Jianzhou big-eared goats (JBG) and Xizang cashmere goats (TCG), which is of significant importance for improving survival models of high-altitude ruminants. The results showed that there were 553 DEGs in the liver of JBG and TCG. Hepatic metabolomic analysis revealed significant differences in metabolic activity between the JBG and TCG groups, with notable increases in glycerophospholipid and retinol metabolic pathways. The gut microbiota, including Andreesenia, Dielma, Oscillibacter, Agrobacterium, Hyella and Thermosinus, interact with liver metabolites and can regulate the high-altitude adaptability of goats. This study reveals that TCG enhance immune regulation and energy utilization efficiency by regulating liver gene expression, modulating metabolic pathways, and improving gut microbiota, thereby helping TCG maintain healthy survival capabilities in hypoxic and high-radiation environments.}, } @article {pmid39841201, year = {2025}, author = {Geng, P and Zhao, N and Zhou, Y and Harris, RS and Ge, Y}, title = {Faecalibacterium prausnitzii regulates carbohydrate metabolic functions of the gut microbiome in C57BL/6 mice.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2455503}, doi = {10.1080/19490976.2025.2455503}, pmid = {39841201}, issn = {1949-0984}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Mice, Inbred C57BL ; Mice ; *Carbohydrate Metabolism ; *Faecalibacterium prausnitzii/metabolism/genetics ; *Phylogeny ; *Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Probiotics/administration & dosage ; Male ; Metagenome ; }, abstract = {The probiotic impact of microbes on host metabolism and health depends on both host genetics and bacterial genomic variation. Faecalibacterium prausnitzii is the predominant human gut commensal emerging as a next-generation probiotic. Although this bacterium exhibits substantial intraspecies diversity, it is unclear whether genetically distinct F. prausnitzii strains might lead to functional differences in the gut microbiome. Here, we isolated and characterized a novel F. prausnitzii strain (UT1) that belongs to the most prevalent but underappreciated phylogenetic clade in the global human population. Genome analysis showed that this butyrate-producing isolate carries multiple putative mobile genetic elements, a clade-specific defense system, and a range of carbohydrate catabolic enzymes. Multiomic approaches were used to profile the impact of UT1 on the gut microbiome and associated metabolic activity of C57BL/6 mice at homeostasis. Both 16S rRNA and metagenomic sequencing demonstrated that oral administration of UT1 resulted in profound microbial compositional changes including a significant enrichment of Lactobacillus, Bifidobacterium, and Turicibacter. Functional profiling of the fecal metagenomes revealed a markedly higher abundance of carbohydrate-active enzymes (CAZymes) in UT1-gavaged mice. Accordingly, UT1-conditioned microbiota possessed the elevated capability of utilizing starch in vitro and exhibited a lower availability of microbiota-accessible carbohydrates in the gut. Further analysis uncovered a functional network wherein UT1 reduced the abundance of mucin-degrading CAZymes and microbes, which correlated with a concomitant reduction of fecal mucin glycans. Collectively, our results reveal a crucial role of UT1 in facilitating the carbohydrate metabolism of the gut microbiome and expand our understanding of the genetic and phenotypic diversity of F. prausnitzii.}, } @article {pmid39840975, year = {2025}, author = {Ge, B and McDonald, RC and Yang, Q and Domesle, KJ and Sarria, S and Li, X and Hsu, C-H and Jarvis, KG and Tadesse, DA}, title = {Exploring animal food microbiomes and resistomes via 16S rRNA gene amplicon sequencing and shotgun metagenomics.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0223024}, doi = {10.1128/aem.02230-24}, pmid = {39840975}, issn = {1098-5336}, abstract = {As a diverse and complex food matrix, the animal food microbiota and repertoire of antimicrobial resistance (AMR) genes remain to be better understood. In this study, 16S rRNA gene amplicon sequencing and shotgun metagenomics were applied to three types of animal food samples (cattle feed, dry dog food, and poultry feed). ZymoBIOMICS mock microbial community was used for workflow optimization including DNA extraction kits and bead-beating conditions. The four DNA extraction kits (AllPrep PowerViral DNA/RNA Kit, DNeasy Blood & Tissue Kit, DNeasy PowerSoil Kit, and ZymoBIOMICS DNA Miniprep Kit) were compared in animal food as well as the use of peptide nucleic acid blockers for 16S rRNA gene amplicon sequencing. Distinct microbial community profiles were generated, which varied by animal food type and DNA extraction kit. Employing peptide nucleic acid blockers prior to 16S rRNA gene amplicon sequencing was comparable with post-sequencing in silico filtering at removing chloroplast and mitochondrial sequences. There was a good agreement between 16S rRNA gene amplicon sequencing and shotgun metagenomics on community profiles in animal feed data sets; however, they differed in taxonomic resolution, with the latter superior at resolving at the species level. Although the overall prevalence of AMR genes was low, resistome analysis of animal feed data sets by shotgun metagenomics revealed 10 AMR gene/protein families, including beta-lactamases, erythromycin/lincomycin/pristinamycin/tylosin, fosfomycin, phenicol, and quinolone. Future expansion of microbiome and resistome profiling in animal food will help better understand the bacterial and AMR gene diversity in these commodities and help guide pathogen control and AMR prevention efforts.IMPORTANCEWith the growing interest and application of metagenomics in understanding the structure/composition and function of diverse microbial communities along the One Health continuum, this study represents one of the first attempts to employ these advanced sequencing technologies to characterize the microbiota and AMR genes in animal food. We unraveled the effects of DNA extraction kits on sample analysis by 16S rRNA gene amplicon sequencing and showed similar efficacies of two strategies at removing chloroplast and mitochondrial reads. The in-depth analysis using shotgun metagenomics shed light on the community compositions and the presence of an array of AMR genes in animal food. This exploration of microbiomes and resistomes in representative animal food samples by both sequencing approaches laid important groundwork for future metagenomic investigations to gain a better understanding of the baseline/core microbiomes and associated AMR functions in these diverse commodities and help guide pathogen control and AMR prevention efforts.}, } @article {pmid39840973, year = {2025}, author = {Wu, DG and Harris, CR and Kalis, KM and Bowen, M and Biddle, JF and Farag, IF}, title = {Comparative metagenomics of tropical reef fishes show conserved core gut functions across hosts and diets with diet-related functional gene enrichments.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0222924}, doi = {10.1128/aem.02229-24}, pmid = {39840973}, issn = {1098-5336}, abstract = {UNLABELLED: Fish gut microbial communities are important for the breakdown and energy harvesting of the host diet. Microbes within the fish gut are selected by environmental and evolutionary factors. To understand how fish gut microbial communities are shaped by diet, three tropical fish species (hawkfish, Paracirrhites arcatus; yellow tang, Zebrasoma flavescens; and triggerfish, Rhinecanthus aculeatus) were fed piscivorous (fish meal pellets), herbivorous (seaweed), and invertivorous (shrimp) diets, respectively. From fecal samples, a total of 43 metagenome assembled genomes (MAGs) were recovered from all fish diet treatments. Each host-diet treatment harbored distinct microbial communities based on taxonomy, with Proteobacteria, Bacteroidota, and Firmicutes being the most represented. Based on their metagenomes, MAGs from all three host-diet treatments demonstrated a baseline ability to degrade proteinaceous, fatty acid, and simple carbohydrate inputs and carry out central carbon metabolism, lactate and formate fermentation, acetogenesis, nitrate respiration, and B vitamin synthesis. The herbivorous yellow tang harbored more functionally diverse MAGs with some complex polysaccharide degradation specialists, while the piscivorous hawkfish's MAGs were more specialized for the degradation of proteins. The invertivorous triggerfish's gut MAGs lacked many carbohydrate-degrading capabilities, resulting in them being more specialized and functionally uniform. Across all treatments, several MAGs were able to participate in only individual steps of the degradation of complex polysaccharides, suggestive of microbial community networks that degrade complex inputs.

IMPORTANCE: The benefits of healthy microbiomes for vertebrate hosts include the breakdown of food into more readily usable forms and production of essential vitamins from their host's diet. Compositions of microbial communities in the guts of fish in response to diet have been studied, but there is a lack of a comprehensive understanding of the genome-based metabolic capabilities of specific microbes and how they support their hosts. Therefore, we assembled genomes of several gut microbes collected from the feces of three fish species that were being fed different diets to illustrate how individual microbes can carry out specific steps in the degradation and energy utilization of various food inputs and support their host. We found evidence that fish gut microbial communities share several core functions despite differences in microbial taxonomy. Herbivorous fish harbored a functionally diverse microbial community with plant matter degraders, while the piscivorous and invertivorous fish had microbiomes more specialized in protein degradation.}, } @article {pmid39840396, year = {2025}, author = {Qin, L and Liang, M and Song, J and Chen, P and Zhang, S and Zhou, Y and Li, H and Tang, J and Ma, Y and Yang, B and Xu, J and Zhang, J}, title = {Utilizing Targeted Next-Generation Sequencing for Rapid, Accurate, and Cost-Effective Pathogen Detection in Lower Respiratory Tract Infections.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {329-340}, pmid = {39840396}, issn = {1178-6973}, abstract = {OBJECTIVE: To evaluate the diagnostic performance and clinical impact of targeted next-generation sequencing (tNGS) in patients with suspected lower respiratory tract infections.

METHODS: Following propensity score matching, we compared the diagnostic performances of tNGS and metagenomic next-generation sequencing (mNGS). Furthermore, the diagnostic performance of tNGS was compared with that of culture, and its clinical impact was assessed.

RESULTS: After propensity score matching, the coincidence rate of tNGS was comparable to that of mNGS (82.9% vs 73.9%, P=0.079). The detection rates for bacterial, viral, fungal, and mixed infections were not significantly different (P>0.05). Bacterial-viral co-infection (16.7%) was the most common mixed infection detected by tNGS. tNGS showed a higher detection rate than culture (75.2% vs 19.0%, P<0.01). The positive detection rate by tNGS was not significantly different between immunocompromised and immunocompetent patients (88.6% vs 80.5%, P=0.202), but was significantly higher than that by culture (P<0.001). Moreover, 65 patients (44.5%) had their medications modified based on the tNGS results, and the majority exhibited notable improvement regardless of treatment adjustment.

CONCLUSION: tNGS performs comparably to mNGS and surpasses culture in detecting lower respiratory tract infections. Nevertheless, tNGS is faster and more cost-effective than mNGS, making it highly significant for guiding rational treatment.}, } @article {pmid39840283, year = {2024}, author = {Yan, B and Nam, Y and Li, L and Deek, RA and Li, H and Ma, S}, title = {Recent advances in deep learning and language models for studying the microbiome.}, journal = {Frontiers in genetics}, volume = {15}, number = {}, pages = {1494474}, pmid = {39840283}, issn = {1664-8021}, support = {R01 GM123056/GM/NIGMS NIH HHS/United States ; U24 OD035523/OD/NIH HHS/United States ; }, abstract = {Recent advancements in deep learning, particularly large language models (LLMs), made a significant impact on how researchers study microbiome and metagenomics data. Microbial protein and genomic sequences, like natural languages, form a language of life, enabling the adoption of LLMs to extract useful insights from complex microbial ecologies. In this paper, we review applications of deep learning and language models in analyzing microbiome and metagenomics data. We focus on problem formulations, necessary datasets, and the integration of language modeling techniques. We provide an extensive overview of protein/genomic language modeling and their contributions to microbiome studies. We also discuss applications such as novel viromics language modeling, biosynthetic gene cluster prediction, and knowledge integration for metagenomics studies.}, } @article {pmid39839678, year = {2025}, author = {Modha, S and Hughes, J and Orton, RJ and Lytras, S}, title = {Expanding the genomic diversity of human anelloviruses.}, journal = {Virus evolution}, volume = {11}, number = {1}, pages = {veaf002}, pmid = {39839678}, issn = {2057-1577}, abstract = {Anelloviruses are a group of small, circular, single-stranded DNA viruses that are found ubiquitously across mammalian hosts. Here, we explored a large number of publicly available human microbiome datasets and retrieved a total of 829 anellovirus genomes, substantially expanding the known diversity of these viruses. The majority of new genomes fall within the three major human anellovirus genera: Alphatorquevirus, Betatorquevirus, and Gammatorquevirus, while we also present new genomes of the under-sampled Hetorquevirus, Memtorquevirus, and Samektorquevirus genera. We performed recombination analysis and show evidence of extensive recombination across all human anelloviruses. Interestingly, more than 95% of the detected events are between members of the same genus and only 15 inter-genus recombination events were detected. The breakpoints of recombination cluster in hotspots at the ends and outside of the ORF1 gene, while a recombination coldspot was detected within the gene. Our analysis suggests that anellovirus evolution is governed by homologous recombination; however, events between distant viruses or ones producing chimaeric ORF1s likely lead to nonviable recombinants. The large number of genomes further allowed us to examine how essential genomic features vary across anelloviruses. These include functional domains in the ORF1 protein and the nucleotide motif of the replication loop region, required for the viruses' rolling-circle replication. A subset of the genomes assembled in both this and previous studies are completely lacking these essential elements, opening up the possibility that anellovirus intracellular populations contain nonstandard viral genomes. However, low-read depth of the metagenomically assembled contigs may partly explain the lack of some features. Overall, our study highlights key features of anellovirus genomics and evolution, a largely understudied group of viruses whose potential in virus-based therapeutics is recently being explored.}, } @article {pmid39839264, year = {2024}, author = {Wu, H and Cao, H and Gao, X and Shi, C and Wang, L and Gao, B}, title = {The role of metagenomic next-generation sequencing in diagnosing and managing post-kidney transplantation infections.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1473068}, pmid = {39839264}, issn = {2235-2988}, mesh = {*Kidney Transplantation/adverse effects ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Bacteria/genetics/isolation & purification/classification ; Postoperative Complications/diagnosis ; }, abstract = {Kidney transplantation (KT) is a life-saving treatment for patients with end-stage renal disease, but post-transplant infections remain one of the most significant challenges. These infections, caused by a variety of pathogens, can lead to prolonged hospitalization, graft dysfunction, and even mortality, particularly in immunocompromised patients. Traditional diagnostic methods often fail to identify the causative organisms in a timely manner, leading to delays in treatment and poorer patient outcomes. This review explores the application of metagenomic next-generation sequencing (mNGS) in the diagnosis of post-KT infections. mNGS allows for the rapid, comprehensive detection of a wide range of pathogens, including bacteria, viruses, fungi, and parasites, without the need for culture-based techniques. We discuss the advantages of mNGS in early and accurate pathogen identification, its role in improving patient management, and the potential challenges in its clinical implementation. Additionally, we consider the future prospects of mNGS in overcoming current diagnostic limitations and its potential for guiding targeted therapies, particularly in detecting antimicrobial resistance and emerging pathogens. This review emphasizes the promise of mNGS as an essential tool in improving the diagnosis and treatment of infections in KT recipients.}, } @article {pmid39839123, year = {2024}, author = {Monteiro, AFM and da Silva, FS and Cruz, ACR and da Silva, SP and Queiroz, ALN and Casseb, LMN and Martins, LC and Medeiros, DBA}, title = {Viral diversity in wild rodents in the regions of Canaã de Carajás and Curionopólis, State of Pará, Brazil.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1502462}, pmid = {39839123}, issn = {1664-302X}, abstract = {Wild rodents serve as crucial reservoirs for zoonotic viruses. Anthropogenic and environmental disruptions, particularly those induced by mining activities, can destabilize rodent populations and facilitate the emergence of viral agents. In the Canaã dos Carajás and Curionópolis regions of Brazil, significant environmental changes have occurred due to mining expansion, potentially creating conditions conducive to the emergence of rodent-associated viral diseases. This study aimed to investigate the viral diversity in wild rodents captured in Canaã dos Carajás and Curionópolis, Pará, between 2017 and 2019. A total of 102 rodent samples were taxonomically identified through karyotyping and screened for anti-Orthohantavirus antibodies using the ELISA method. Subsequently, nucleotide sequencing and bioinformatics analyses were conducted on 14 selected samples to characterize the virome. This selection was based on the most commonly associated rodent genera as reservoirs of Orthohantavirus and Mammarenavirus. Of the 102 samples tested via ELISA, 100 were negative, and two showed optical density at the cutoff point. Sequencing of the 14 samples generated approximately 520 million reads, with 409 million retained after quality control. These reads were categorized into 53 viral families, including both DNA and RNA viruses, with Retroviridae, Baculoviridae, and Microviridae being the most abundant. Viral contigs were identified, including one fragment related to Arenaviridae and three to Filoviridae. Metagenomic analysis revealed high viral diversity in the sampled rodents, with the presence of viral families of public health concern, such as Arenaviridae and Filoviridae. The findings suggest that increased human activities associated with mining may contribute to the emergence of these viruses, underscoring the need for ongoing surveillance to prevent potential outbreaks.}, } @article {pmid39839120, year = {2024}, author = {Yu, J and Yang, S and Zhang, X and Liu, X and Tang, X and Wang, L and Chen, J and Luo, H and Liu, C and Song, C}, title = {Corrigendum: Integrating metagenomics and culturomics to uncover the soil bacterial community in Asparagus cochinchinensis cultivation.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1545445}, doi = {10.3389/fmicb.2024.1545445}, pmid = {39839120}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2024.1467864.].}, } @article {pmid39839104, year = {2024}, author = {Mendoza, JE and Tineo, D and Chuquibala-Checan, B and Atalaya-Marin, N and Taboada-Mitma, VH and Tafur-Culqui, J and Tarrillo, E and Gómez-Fernández, D and Goñas, M and Reyes-Reyes, MA}, title = {Global perspectives on the biodegradation of LDPE in agricultural systems.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1510817}, pmid = {39839104}, issn = {1664-302X}, abstract = {The increasing use of plastics globally has generated serious environmental and human health problems, particularly in the agricultural sector where low-density polyethylene (LDPE) and other plastics are widely used. Due to its low recycling rate and slow degradation process, LDPE is a major source of pollution. This paper addresses the problem of plastic accumulation in agriculture, focusing on LDPE biodegradation strategies. The studies reviewed include recent data and the methodologies used include state-of-the-art technologies and others that have been used for decades, to monitor and measure the degree of biodegradation that each treatment applied can have, including SEM, GCMS, HPLC, and microscopy. The countries investigating these biodegradation methodologies are identified, and while some countries have been developing them for some years, others have only begun to address this problem in recent years. The use of microorganisms such as bacteria, fungi, algae, and insect larvae that influence its decomposition is highlighted. A workflow is proposed to carry out this type of research. Despite the advances, challenges remain, such as optimizing environmental conditions to accelerate the process and the need for further research that delves into microbial interactions in various environmental contexts.}, } @article {pmid39838963, year = {2024}, author = {Guan, J and Ji, Y and Peng, C and Zou, W and Tang, X and Shang, J and Sun, Y}, title = {GOPhage: protein function annotation for bacteriophages by integrating the genomic context.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {1}, pages = {}, pmid = {39838963}, issn = {1477-4054}, support = {11209823//City University of Hong Kong/ ; }, mesh = {*Bacteriophages/genetics ; *Genome, Viral ; *Molecular Sequence Annotation ; *Viral Proteins/genetics/metabolism ; Genomics/methods ; Computational Biology/methods ; Software ; }, abstract = {Bacteriophages are viruses that target bacteria, playing a crucial role in microbial ecology. Phage proteins are important in understanding phage biology, such as virus infection, replication, and evolution. Although a large number of new phages have been identified via metagenomic sequencing, many of them have limited protein function annotation. Accurate function annotation of phage proteins presents several challenges, including their inherent diversity and the scarcity of annotated ones. Existing tools have yet to fully leverage the unique properties of phages in annotating protein functions. In this work, we propose a new protein function annotation tool for phages by leveraging the modular genomic structure of phage genomes. By employing embeddings from the latest protein foundation models and Transformer to capture contextual information between proteins in phage genomes, GOPhage surpasses state-of-the-art methods in annotating diverged proteins and proteins with uncommon functions by 6.78% and 13.05% improvement, respectively. GOPhage can annotate proteins lacking homology search results, which is critical for characterizing the rapidly accumulating phage genomes. We demonstrate the utility of GOPhage by identifying 688 potential holins in phages, which exhibit high structural conservation with known holins. The results show the potential of GOPhage to extend our understanding of newly discovered phages.}, } @article {pmid39838455, year = {2025}, author = {Liao, H and Li, J and Wang, YZ and Li, H and An, XL and Wang, T and Chang, RY and Zhu, YG and Su, JQ}, title = {Evolutionary diversification and succession of soil huge phages in glacier foreland.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {18}, pmid = {39838455}, issn = {2049-2618}, support = {4237070301//National Natural Science Foundation of China/ ; 42161134002//National Natural Science Foundation of China/ ; STEP, 2021QZKK0103//Second Tibetan Plateau Scientific Expedition and Research Program/ ; }, mesh = {*Soil Microbiology ; *Ice Cover/virology ; *Bacteriophages/genetics/classification/isolation & purification ; *Phylogeny ; *Genome, Viral ; Metagenomics ; Tibet ; Evolution, Molecular ; Soil ; }, abstract = {BACKGROUND: Huge phages (genome size ≥ 200 kb) have been detected in diverse habitats worldwide, infecting a variety of prokaryotes. However, their evolution and adaptation strategy in soils remain poorly understood due to the scarcity of soil-derived genomes.

RESULTS: Here, we conduct a size-fractioned (< 0.22 μm) metagenomic analysis across a 130-year chronosequence of a glacier foreland in the Tibetan Plateau and discovered 412 novel viral operational taxonomic units (vOTUs) of huge phages. The phylogenomic and gene-shared network analysis gained insights into their unique evolutionary history compared with smaller phages. Their communities in glacier foreland revealed a distinct pattern between the early (≤ 41 years) and late stages (> 41 years) based on the macrodiveristy (interspecies diversity) analysis. A significant increase in the diversity of huge phages communities following glacier retreat were observed according to current database. The phages distributed across sites within late stage demonstrated a remarkable higher microdiversity (intraspecies diversity) compared to other geographic range such as the intra early stage, suggesting that glacial retreat is key drivers of the huge phage speciation. Alongside the shift in huge phage communities, we also noted an evolutionary and functional transition between the early and late stages. The identification of abundant CRISPR-Cas12 and type IV restriction-modification (RM) systems in huge phages indicates their complex mechanisms for adaptive immunity.

CONCLUSIONS: Overall, this study unravels the importance of climate change in shaping the composition, evolution, and function of soil huge phage communities, and such further understanding of soil huge phages is vital for broader inclusion in soil ecosystem models. Video Abstract.}, } @article {pmid39838431, year = {2025}, author = {Sun, Q and Li, BR and Li, DH and Wang, XY and Wang, QY and Jiang, ZM and Ning, SB and Sun, T}, title = {WKB ameliorates DSS-induced colitis through inhibiting enteric glial cells activation and altering the intestinal microbiota.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {93}, pmid = {39838431}, issn = {1479-5876}, support = {No. 22YXQN034//Air Force Medical Center Youth Talent Program Project/ ; No. 2020-4-5123//Capital's Funds for Health Improvement and Research/ ; }, mesh = {Animals ; *Dextran Sulfate ; *Gastrointestinal Microbiome ; *Colitis/pathology/microbiology/chemically induced/complications ; *Mice, Inbred C57BL ; Male ; *Neuroglia/metabolism/pathology ; Cytokines/metabolism ; Colon/pathology/microbiology ; Permeability ; Body Weight ; Inflammation/pathology ; Intestinal Mucosa/pathology/microbiology/metabolism ; Mice ; }, abstract = {BACKGROUND: Inflammatory bowel disease (IBD) is a chronic condition influenced by diet, which affects gut microbiota and immune functions. The rising prevalence of IBD, linked to Western diets in developing countries, highlights the need for dietary interventions. This study aimed to assess the impact of white kidney beans (WKB) on gut inflammation and microbiota changes, focusing on their effects on enteric glial cells (EGCs) and immune activity in colitis.

METHODS: Male C57BL/6 mice were divided into four groups: normal diet (ND), ND with 2.5% dextran sulfate sodium (DSS) for colitis induction, ND with 20% WKB, and WKB with 2.5% DSS. The dietary intervention lasted 17 weeks, with DSS given in the final week. Colonic inflammation was assessed by body weight, disease activity index, and histopathology. Epithelial barrier integrity was evaluated using immunofluorescence, transmission electron microscopy, and permeability assays. EGCs activity was analyzed via immunofluorescence and quantitative real-time PCR. Immune responses were measured using flow cytometry and cytokine profiling, while gut microbiota changes were examined through metagenomic sequencing.

RESULTS: WKB supplementation significantly alleviated DSS-induced colitis in mice, evidenced by reduced weight loss, disease activity, and improved colonic histology. This effect was linked to enhanced mucosal barrier integrity, seen through increased tight junction protein and Muc2 expression, accompanied by favorable ultrastructural changes. WKB modulated EGCs activity via TNF-like cytokine 1 A inhibition, resulting in reduced glial fibrillary acidic protein expression. Immunologically, it downregulated Th1 and Th17 pro-inflammatory cells, increased Treg cells, and altered cytokine profiles (reduced TNF-α, IFN-γ, IL-17; increased IL-10). Metagenomic analysis showed that WKB restored gut microbiota balance, particularly enhancing beneficial bacteria like Akkermansia. KEGG pathway analysis further indicated that WKB supplementation improved key metabolic pathways, notably those related to phenylalanine, tyrosine, and tryptophan biosynthesis, thereby countering DSS-induced metabolic disruptions.

CONCLUSIONS: WKB shows promise for treating IBD by enhancing mucosal barriers, inhibiting EGCs activity, balancing Th1/Th17/Treg cells, and restoring gut microbiota and metabolic homeostasis, thereby alleviating colitis symptoms.}, } @article {pmid39838419, year = {2025}, author = {Liu, X and Ding, H and Zhang, X and Ta, N and Zhao, J and Zhang, Q and Liu, H and Sun, M and Zhang, X}, title = {Dynamic changes in the gastrointestinal microbial communities of Gangba sheep and analysis of their functions in plant biomass degradation at high altitude.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {17}, pmid = {39838419}, issn = {2049-2618}, mesh = {Animals ; Sheep/microbiology ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Altitude ; *Biomass ; Metagenome ; Animal Feed/microbiology ; Archaea/genetics/classification ; Gastrointestinal Tract/microbiology ; Plants/microbiology ; }, abstract = {BACKGROUND: While Gangba sheep being well known for their unique flavour and nutritional value, harsh environmental factors negatively affect their growth and development, leading to poor productivity. The gastrointestinal tract microbiota plays an important role in host nutrient absorption and metabolism. The identification of dynamic changes in the gastrointestinal microbial communities and their functions is an important step towards improving animal production performance and health.

RESULTS: A comprehensive multi-omics survey of the microbial communities of the Gangba sheep gastrointestinal tract was performed under three distinct feeding strategies: natural grazing, semi-grazing with supplementation, and barn feeding. The dynamic changes, cross-kingdom partnerships and functional potential profiles were analysed and the results revealed that the feeding strategies had a greater impact on the microbial communities than the site of the gastrointestinal tract. The different microbial associations among the groups were revealed by co-occurrence networks based on the amplicon sequence variants (ASVs). Moreover, a Gangba sheep gastrointestinal microbial genomic catalogue was constructed for the first time, including 1146 metagenome-assembled genomes (MAGs) with completeness > 50% and contamination < 10%, among which, 504 bacterial and 15 archaeal MAGs were of high quality with completeness > 80% and contamination < 10%. About 40% of the high-quality MAGs displaying enzyme activity were related to the microbial species that contribute to plant biomass degradation. Most of these enzymes were expressed in rumen metatranscriptome datasets, especially in Prevotella spp. and Ruminococcus spp., suggesting that gastrointestinal microbial communities in ruminants play major roles in the digestion of plant biomass to provide nutrition and energy for the host.

CONCLUSIONS: These findings suggest that feeding strategies are the primary cause of changes in the gastrointestinal microbiome. Diversification of livestock feed might be an effective strategy to maintain the diversity and ecological multifunctionality of microbial communities in the gastrointestinal tract. Additionally, the catalogue of microbial genomes and the encoded biomass-degrading enzymes identified here provide insights into the potential microbial functions of the gastrointestinal tract of Gangba sheep at high altitudes. This paves the way for microbial interventions to improve the growth performance, productivity and product quality of ruminant livestock. Video Abstract.}, } @article {pmid39838369, year = {2025}, author = {Fan, J and Zeng, F and Zhong, H and Cai, J and Shen, W and Cheng, C and He, C and Liu, Y and Zhou, Y and Chen, S and Zhu, Y and Liu, T and Zheng, JS and Wang, L and Chen, YM and Ma, W and Zhou, D}, title = {Potential roles of cigarette smoking on gut microbiota profile among Chinese men.}, journal = {BMC medicine}, volume = {23}, number = {1}, pages = {25}, pmid = {39838369}, issn = {1741-7015}, mesh = {Humans ; Male ; *Gastrointestinal Microbiome ; *Cigarette Smoking/adverse effects ; Middle Aged ; Adult ; China ; RNA, Ribosomal, 16S/genetics ; Asian People ; Actinomyces ; Aged ; East Asian People ; }, abstract = {BACKGROUND: Cigarette smoking is posited as a potential factor in disrupting the balance of the human gut microbiota. However, existing studies with limited sample size have yielded inconclusive results.

METHODS: Here, we assessed the association between cigarette smoking and gut microbial profile among Chinese males from four independent studies (N total = 3308). Both 16S rRNA and shotgun metagenomic sequencing methods were employed, covering 206 genera and 237 species. Microbial diversity and abundance were compared among non-smokers, current smokers, and former smokers.

RESULTS: Actinomyces[g], Atopobium[g], Haemophilus[g], Turicibacter[g], and Lachnospira[g] were found to be associated with smoking status (current smokers vs. non-smokers). Metagenomic data provided a higher resolution at the species level, particularly for the Actinomyces[g] branch. Additionally, serum γ-glutamylcysteine (γ-Glu-Cys) was found to have a potential role in connecting smoking and Actinomyces[g]. Furthermore, we revealed putative mediation roles of the gut microbiome in the associations between smoking and common diseases including cholecystitis and type 2 diabetes.

CONCLUSIONS: We characterized the gut microbiota profile in male smokers and further revealed their potential involvement in mediating the impact of smoking on health outcomes. These findings advance our understanding of the intricate association between cigarette smoking and the gut microbiome.}, } @article {pmid39838275, year = {2025}, author = {Nabisubi, P and Kanyerezi, S and Kebirungi, G and Sserwadda, I and Nsubuga, M and Kisitu, G and Nahirya, PN and Mulindwa, B and Akabwai, GP and Nantongo, S and Kekitiinwa, A and Kigozi, E and Luutu, NM and Katabazi, FA and Kalema, L and Katabalwa, A and Jjingo, D and Mboowa, G}, title = {Beyond the fever: shotgun metagenomic sequencing of stool unveils pathogenic players in HIV-infected children with non-malarial febrile illness.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {96}, pmid = {39838275}, issn = {1471-2334}, support = {U2R TW010672/TW/FIC NIH HHS/United States ; TMA2020CDF-3159//European and Developing Countries Clinical Trials Partnership/ ; }, mesh = {Humans ; *Feces/microbiology/virology ; *Metagenomics ; Female ; *HIV Infections/complications/microbiology/virology ; Male ; Child, Preschool ; Child ; Fever/microbiology ; Uganda/epidemiology ; Infant ; Candida albicans/genetics/isolation & purification/classification/pathogenicity ; Giardia/genetics/isolation & purification/classification ; Bacteroides/genetics/isolation & purification/classification ; Gastrointestinal Microbiome/genetics ; }, abstract = {BACKGROUND: Non-malarial febrile illnesses (NMFI) pose significant challenges in HIV-infected children, often leading to severe complications and increased morbidity. While traditional diagnostic approaches focus on specific pathogens, shotgun metagenomic sequencing offers a comprehensive tool to explore the microbial landscape underlying NMFI in this vulnerable population ensuring effective management.

METHODS: In this study, we employed shotgun metagenomics to analyse stool samples from HIV-infected children at the Baylor Children's Clinic Uganda presenting with non-malarial febrile illness. Samples were collected and subjected to DNA extraction at the Molecular and Genomics Laboratory, Makerere University followed by shotgun metagenomics sequencing at the Chan Zuckerberg Biohub San Francisco. Bioinformatics analysis was conducted to identify and characterise the microbial composition and potential pathogenic taxa associated with NMFI using the CZID pipeline.

RESULTS: Our findings reveal a diverse array of microbial taxa in the stool samples of HIV-infected children with NMFI. Importantly, shotgun metagenomics revealed potentially pathogenic players including Trichomonas vaginalis, Candida albicans, Giardia, and Bacteroides in stool from this patient population. This sheds light on the complexities of microbial interactions that potentially underpin non-malarial febrile illness in this group. Taxonomic profiling identified recognised pathogens and comorbidities and revealed possible new correlations with NMFI, shedding light on the pathophysiology of fever in HIV-infected children.

CONCLUSION: Shotgun metagenomics is a valuable method for understanding the gut microbial landscape of NMFI in HIV-infected children, providing a comprehensive approach to pathogen identification and characterisation. By revealing potential pathogenic actors beyond the fever, this work demonstrates how metagenomic sequencing may improve our knowledge of infectious illnesses in vulnerable groups and inspire targeted therapies for better clinical care and outcomes.}, } @article {pmid39838107, year = {2025}, author = {Teso-Pérez, C and López-Gazcón, A and Peralta-Sánchez, JM and Martínez-Bueno, M and Valdivia, E and Fárez-Vidal, ME and Martín-Platero, AM}, title = {Bacteriocin-Producing Enterococci Modulate Cheese Microbial Diversity.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {175}, pmid = {39838107}, issn = {1432-184X}, support = {PEJ2018-003019-A//Plan Estatal de Garantía Juvenil (Fondo Social Europeo, Gobierno de España/ ; Group BIO 309//PAIDI Program/ ; A-BIO-083-UGR18//Programa Operativo FEDER Andalucía 2014-2020/ ; }, mesh = {*Cheese/microbiology ; *Bacteriocins/metabolism/biosynthesis ; *Enterococcus/metabolism/genetics ; *Microbiota ; Biodiversity ; Food Microbiology ; RNA, Ribosomal, 16S/genetics ; Milk/microbiology ; Animals ; }, abstract = {Cheese production involves various lactic acid bacteria (LAB) that break down lactose, milk proteins, and fats, producing key nutrients and influencing the cheese's flavor. They form communities that play a crucial role in determining the cheese's organoleptic properties. The composition of cheeses' microbial communities is shaped by physicochemical factors (e.g., temperature, pH, and salinity) and biological factors (i.e. microbial interactions). While starter cultures are introduced to control these communities, non-starter LAB represent a significant portion of the final microbial assemblage, but their interactions remain unclear. LAB often produce bacteriocins, antimicrobial peptides that antagonize other bacteria, but their role within LAB communities is not fully understood. This study aimed to assess the impact of bacteriocin production on LAB diversity in cheese, using Enterococcus as a model organism, a common bacteriocin producer. We analyzed enterocin production of enterococcal isolates by antimicrobial assays and microbial diversity differences in raw milk cheeses by two approaches: 16S RNA gene amplicon metagenomic sequencing for the whole microbial community and multi-locus sequence analysis (MLSA) for the enterococcal diversity. Our results revealed that LAB communities were dominated by lactococci, lactobacilli, and streptococci, with enterococci present in lower numbers. However, cheeses containing bacteriocin-producing enterococci exhibited higher microbial diversity. Interestingly, the highest diversity occurred at low levels of bacteriocin producers, but this effect was not observed within enterococcal populations. These findings suggest that bacteriocin production plays a key role in shaping LAB communities during cheese ripening, although further research is needed to understand its broader implications in other microbial ecosystems.}, } @article {pmid39837861, year = {2025}, author = {Kagaya, Y and Zhang, Z and Ibtehaz, N and Wang, X and Nakamura, T and Punuru, PD and Kihara, D}, title = {NuFold: end-to-end approach for RNA tertiary structure prediction with flexible nucleobase center representation.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {881}, pmid = {39837861}, issn = {2041-1723}, support = {DMS2151678//NSF | Directorate for Mathematical & Physical Sciences | Division of Mathematical Sciences (DMS)/ ; R01GM133840, R01GM123055//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R01 GM123055/GM/NIGMS NIH HHS/United States ; CMMI1825941//NSF | ENG/OAD | Division of Civil, Mechanical and Manufacturing Innovation (CMMI)/ ; IIS2211598//NSF | Directorate for Computer & Information Science & Engineering | Division of Information and Intelligent Systems (Information & Intelligent Systems)/ ; R01 GM133840/GM/NIGMS NIH HHS/United States ; MCB1925643//NSF | BIO | Division of Molecular and Cellular Biosciences (MCB)/ ; DBI2003635, DBI2146026//NSF | BIO | Division of Biological Infrastructure (DBI)/ ; }, mesh = {*Nucleic Acid Conformation ; *RNA/chemistry/genetics ; Deep Learning ; Computational Biology/methods ; Neural Networks, Computer ; Sequence Alignment/methods ; Software ; }, abstract = {RNA plays a crucial role not only in information transfer as messenger RNA during gene expression but also in various biological functions as non-coding RNAs. Understanding mechanical mechanisms of function needs tertiary structure information; however, experimental determination of three-dimensional RNA structures is costly and time-consuming, leading to a substantial gap between RNA sequence and structural data. To address this challenge, we developed NuFold, a novel computational approach that leverages state-of-the-art deep learning architecture to accurately predict RNA tertiary structures. NuFold is a deep neural network trained end-to-end for the output structure from the input sequence. NuFold incorporates a nucleobase center representation, which enables flexible conformation of ribose rings. Benchmark study showed that NuFold clearly outperformed energy-based methods and demonstrated comparable results with existing state-of-the-art deep-learning-based methods. NuFold exhibited a particular advantage in building correct local geometries of RNA. Analyses of individual components in the NuFold pipeline indicated that the performance improved by utilizing metagenome sequences for multiple sequence alignment and increasing the number of recycling. NuFold is also capable of predicting multimer complex structures of RNA by linking the input sequences.}, } @article {pmid39837860, year = {2025}, author = {Alser, M and Eudine, J and Mutlu, O}, title = {Taming large-scale genomic analyses via sparsified genomics.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {876}, pmid = {39837860}, issn = {2041-1723}, mesh = {*Genomics/methods ; Humans ; High-Throughput Nucleotide Sequencing/methods ; Algorithms ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Software ; Databases, Genetic ; }, abstract = {Searching for similar genomic sequences is an essential and fundamental step in biomedical research. State-of-the-art computational methods performing such comparisons fail to cope with the exponential growth of genomic sequencing data. We introduce the concept of sparsified genomics where we systematically exclude a large number of bases from genomic sequences and enable faster and memory-efficient processing of the sparsified, shorter genomic sequences, while providing comparable accuracy to processing non-sparsified sequences. Sparsified genomics provides benefits to many genomic analyses and has broad applicability. Sparsifying genomic sequences accelerates the state-of-the-art read mapper (minimap2) by 2.57-5.38x, 1.13-2.78x, and 3.52-6.28x using real Illumina, HiFi, and ONT reads, respectively, while providing comparable memory footprint, 2x smaller index size, and more correctly detected variations compared to minimap2. Sparsifying genomic sequences makes containment search through very large genomes and large databases 72.7-75.88x (1.62-1.9x when indexing is preprocessed) faster and 723.3x more storage-efficient than searching through non-sparsified genomic sequences (with CMash and KMC3). Sparsifying genomic sequences enables robust microbiome discovery by providing 54.15-61.88x (1.58-1.71x when indexing is preprocessed) faster and 720x more storage-efficient taxonomic profiling of metagenomic samples over the state-of-the-art tool (Metalign).}, } @article {pmid39837758, year = {2025}, author = {Mizuno, Y and Yoshimura, T and Sawada, K and Tsuge, K and Nagano, Y and Yoshizaki, Y and Goto, M and Kobayashi, G}, title = {Crucial role of early addition of Wickerhamiella versatilis in enhancing aroma formation during soy sauce fermentation.}, journal = {Journal of bioscience and bioengineering}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jbiosc.2024.12.010}, pmid = {39837758}, issn = {1347-4421}, abstract = {In modern Japanese soy sauce production, sealed outdoor fermentation tanks are used to ferment moromi with halotolerant starter cultures: the lactic acid bacterium Tetragenococcus halophilus and yeasts Wickerhamiella versatilis and Zygosaccharomyces rouxii. T. halophilus and W. versatilis are added in the early fermentation stage, while Z. rouxii is introduced about 1 month later to initiate alcoholic fermentation. Both W. versatilis and Z. rouxii contribute to the production of volatile organic compounds (VOC), with 4-ethylguaiacol (4-EG), uniquely produced by W. versatilis, being essential for the characteristic aroma of soy sauce. Prior metagenomic and metabolomic analyses indicated that 4-EG production occurs prior to Z. rouxii fermentation, though the increase in W. versatilis proportion follows it. Additional omics analysis of a production batch confirmed similar microbial and VOC dynamics, with no clear relationship between W. versatilis increase and 4-EG levels. To investigate this, a laboratory-scale experiment was conducted using filter-sterilized moromi supernatant as a medium, with staggered inoculations of the two yeasts. Viable cell density, 4-EG, and ethanol were measured as indicators of fermentation activity. Results showed that when W. versatilis was inoculated before Z. rouxii, 4-EG production commenced earlier, while W. versatilis cell density and ethanol production increased only after Z. rouxii fermentation began. Under these conditions, 4-EG and ethanol production were highest, suggesting that the presence rather than the increase of W. versatilis is crucial for 4-EG production. Consequently, the early addition of W. versatilis was considered an effective strategy to enhance 4-EG and VOC production in moromi.}, } @article {pmid39837331, year = {2025}, author = {Valdés-Mas, R and Leshem, A and Zheng, D and Cohen, Y and Kern, L and Zmora, N and He, Y and Katina, C and Eliyahu-Miller, S and Yosef-Hevroni, T and Richman, L and Raykhel, B and Allswang, S and Better, R and Shmueli, M and Saftien, A and Cullin, N and Slamovitz, F and Ciocan, D and Ouyang, KS and Mor, U and Dori-Bachash, M and Molina, S and Levin, Y and Atarashi, K and Jona, G and Puschhof, J and Harmelin, A and Stettner, N and Chen, M and Suez, J and Honda, K and Lieb, W and Bang, C and Kori, M and Maharshak, N and Merbl, Y and Shibolet, O and Halpern, Z and Shouval, DS and Shamir, R and Franke, A and Abdeen, SK and Shapiro, H and Savidor, A and Elinav, E}, title = {Metagenome-informed metaproteomics of the human gut microbiome, host, and dietary exposome uncovers signatures of health and inflammatory bowel disease.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2024.12.016}, pmid = {39837331}, issn = {1097-4172}, abstract = {Host-microbiome-dietary interactions play crucial roles in regulating human health, yet their direct functional assessment remains challenging. We adopted metagenome-informed metaproteomics (MIM), in mice and humans, to non-invasively explore species-level microbiome-host interactions during commensal and pathogen colonization, nutritional modification, and antibiotic-induced perturbation. Simultaneously, fecal MIM accurately characterized the nutritional exposure landscape in multiple clinical and dietary contexts. Implementation of MIM in murine auto-inflammation and in human inflammatory bowel disease (IBD) characterized a "compositional dysbiosis" and a concomitant species-specific "functional dysbiosis" driven by suppressed commensal responses to inflammatory host signals. Microbiome transfers unraveled early-onset kinetics of these host-commensal cross-responsive patterns, while predictive analyses identified candidate fecal host-microbiome IBD biomarker protein pairs outperforming S100A8/S100A9 (calprotectin). Importantly, a simultaneous fecal nutritional MIM assessment enabled the determination of IBD-related consumption patterns, dietary treatment compliance, and small intestinal digestive aberrations. Collectively, a parallelized dietary-bacterial-host MIM assessment functionally uncovers trans-kingdom interactomes shaping gastrointestinal ecology while offering personalized diagnostic and therapeutic insights into microbiome-associated disease.}, } @article {pmid39837034, year = {2025}, author = {Liu, W and Chen, Z and Li, T and Wen, X}, title = {Geographical distribution and risk of antibiotic resistance genes in sludge anaerobic digestion process across China.}, journal = {Journal of hazardous materials}, volume = {487}, number = {}, pages = {137290}, doi = {10.1016/j.jhazmat.2025.137290}, pmid = {39837034}, issn = {1873-3336}, abstract = {Anaerobic digestion (AD) is gaining increasing attention as the central reservoir of antibiotic resistance genes (ARGs), while the geographical distribution of ARGs in AD is neglected. Accordingly, a sampling scheme on full-scale AD plants across China was implemented, and the resistome therein was excavated. The abundance of ARGs in AD sludge ranged from 0.198 to 0.574 copies/cell. Some of the frequently reported and emergent ARGs were detected in our AD system. Both the abundance and composition of ARGs presented significant differences between the south and north regions of China, hinting the physical/economic factors may function in the formation of ARG profiles. The risk scores of AD samples were in middle of domestic and hospital wastewater. Risk scores were significantly higher in the north. Besides, the proportion of Rank I and Rank II ARGs was also higher in north, which explained the regional difference of ARG composition in a micro-perspective. This study provides a fundamental survey on the of ARG level and profile in AD process across China, reveals the biogeography of ARGs and inspires the control strategies of antibiotic resistance.}, } @article {pmid39836258, year = {2025}, author = {Mandal, M and Ghosh, B and Mandal, S}, title = {Comparison of the rhizospheric soil bacteriomes of Oryza sativa and Solanum melongena crop cultivars reveals key genes and pathways involved in biosynthesis of ectoine, lysine, and catechol meta-cleavage.}, journal = {Functional & integrative genomics}, volume = {25}, number = {1}, pages = {20}, pmid = {39836258}, issn = {1438-7948}, mesh = {*Oryza/genetics/metabolism/microbiology ; *Rhizosphere ; *Soil Microbiology ; *Lysine/biosynthesis/metabolism ; *Catechols/metabolism ; *Solanum melongena/genetics/microbiology/metabolism ; }, abstract = {Rice (Oryza sativa L.), Poaceae family, forms staple diet of half of world's population, and brinjal (Solanum melongena L.), an important solanaceous crop, are consumed worldwide. Rhizosphere research is gaining importance towards application of knowledge for improving productivity, sustainable agricultural practice, and rhizoremediation for nature restoration. While there are reports on rhizobacteriome of rice, studies comparing structural, functional and metabolomic traits of microbial communities in rhizospheres of rice and brinjal are not yet available. We demonstrated, in Oryza sativa (1144-Hybrid, Dhiren, Local Saran cultivars) and Solanum melongena (Jhiloria, Chandtara, Jotshna cultivars) rhizospheres from Malda, India, using integrated approach of 16 S ribosomal sequencing, shotgun metagenomics, and microbial metabolomics to decipher microbial diversity, association with soil physicochemical characteristics, key genes and pathways. Ectoine biosynthesis was significantly expressed in brinjal (Jhiloria), but not in rice rhizosphere. The dominant brinjal rhizobacteriome-specific bacteria comprised Thermus sp., Petrobacter succinatimandens, Thermoanaerobacter sp., and Diaphorobacter sp., that were involved in house-keeping functions including pentose phosphate pathway, biosynthesis of amino acids, lipopolysaccharide, and photosynthesis. The dominant bacteria unique to rice rhizobacteriome (Local Saran) consisted of Aeromonas sp., associated with catechol meta-cleavage, while Clostridium sp., Faecalibacterium prausnitzii, and Roseburia sp. were involved with lysine biosysnthesis in rice (1144-Hybrid). Our results imply novel information for improved breeding of brinjal specific cultivar with enhanced ectoine production associated with osmotic stress tolerance, rice specific cultivars with enhanced lysine production significant to human nutrition and catechol removal for the maintenance of environmental quality.}, } @article {pmid39836086, year = {2025}, author = {Xia, R and Yin, X and Balcazar, JL and Huang, D and Liao, J and Wang, D and Alvarez, PJJ and Yu, P}, title = {Bacterium-Phage Symbiosis Facilitates the Enrichment of Bacterial Pathogens and Antibiotic-Resistant Bacteria in the Plastisphere.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c08265}, pmid = {39836086}, issn = {1520-5851}, abstract = {The plastisphere, defined as the ecological niche for microbial colonization of plastic debris, has been recognized as a hotspot of pathogenic and antibiotic-resistant bacteria. However, the interactions between bacteria and phages facilitated by the plastisphere, as well as their impact on microbial risks to public health, remain unclear. Here, we analyzed public metagenomic data from 180 plastisphere and environmental samples, stemming from four different habitats and two plastic types (biodegradable and nonbiodegradable plastics) and obtained 611 nonredundant metagenome-assembled genomes (MAGs) and 4061 nonredundant phage contigs. The plastisphere phage community exhibited decreased diversity and virulent proportion compared to those found in environments. Indexes of phage-host interaction networks indicated significant associations of phages with pathogenic and antibiotic-resistant bacteria (ARB), particularly for biodegradable plastics. Known phage-encoded auxiliary metabolic genes (AMGs) were involved in nutrient metabolism, antibiotic production, quorum sensing, and biofilm formation in the plastisphere, which contributed to enhanced competition and survival of pathogens and ARB hosts. Phages also carried transcriptionally active virulence factor genes (VFGs) and antibiotic resistance genes (ARGs), and could mediate their horizontal transfer in microbial communities. Overall, these discoveries suggest that plastisphere phages form symbiotic relationships with their hosts, and that phages encoding AMGs and mediating horizontal gene transfer (HGT) could increase the source of pathogens and antibiotic resistance from the plastisphere.}, } @article {pmid39835966, year = {2025}, author = {Levine, BH and Hoffman, JM}, title = {Microbiome transplants may not improve health and longevity in Drosophila melanogaster.}, journal = {Biology open}, volume = {14}, number = {1}, pages = {}, pmid = {39835966}, issn = {2046-6390}, support = {R00 AG059920/AG/NIA NIH HHS/United States ; //Augusta University; University of South Carolina/ ; R00AG059920/NH/NIH HHS/United States ; }, mesh = {Animals ; *Drosophila melanogaster/microbiology/physiology ; *Longevity ; *Gastrointestinal Microbiome ; Female ; Male ; Microbiota ; }, abstract = {The gut microbiome, which is composed of bacteria, viruses, and fungi, and is involved in multiple essential physiological processes, changes measurably as a person ages, and can be associated with negative health outcomes. Microbiome transplants have been proposed as a method to improve gut function and reduce or reverse multiple disorders, including age-related diseases. Here, we take advantage of the laboratory model organism, Drosophila melanogaster, to test the effects of transplanting the microbiome of a young fly into middle-aged flies, across multiple genetic backgrounds and both sexes, to test whether age-related lifespan could be increased, and late-life physical health declines mitigated. Our results suggest that, overall, microbiome transplants do not improve longevity and may even be detrimental in flies, and the health effects of microbiome transplants were minor, but sex- and genotype-dependent. This discovery supports previous evidence that axenic flies, those with no gut microbiome, live healthier and longer lives than their non-axenic counterparts. The results of this study suggest that, at least for fruit flies, microbiome transplants may not be a viable intervention to improve health and longevity, though more research is still warranted.}, } @article {pmid39835383, year = {2025}, author = {Liu, J and Yang, B and Wu, Y and Yang, G and Zha, X and Jiang, W}, title = {Significance of Combining Bronchoalveolar Lavage Fluid With Targeted Next-Generation Sequencing in the Pathogen Detection-Based Diagnosis of Pulmonary Infections.}, journal = {The clinical respiratory journal}, volume = {19}, number = {1}, pages = {e70046}, pmid = {39835383}, issn = {1752-699X}, support = {8252//Tianjin Clinical Key Specialty Construction Project Funding (2024) - Respiratory Department/ ; }, mesh = {Humans ; *Bronchoalveolar Lavage Fluid/microbiology ; Male ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; Female ; Middle Aged ; Aged ; Adult ; Respiratory Tract Infections/diagnosis/microbiology ; Metagenomics/methods ; China/epidemiology ; }, abstract = {OBJECTIVE: In this study, we investigated the application value of bronchoalveolar lavage fluid (BALF) combined with targeted next-generation sequencing (tNGS) in the pathogen detection-based diagnosis of patients with lung infections.

METHOD: A retrospective analysis was conducted on patients who underwent tracheoscopy and conventional microbiological tests (CMTs) on BALF, coupled with metagenomic next-generation sequencing (mNGS) or tNGS. This investigation encompassed individuals with suspected lung infections at Tianjin First Central Hospital from March 2023 to July 2023. Diagnostic rates based on pathogens detected via tNGS were compared with CMTs within the tNGS group. Additionally, diagnostic rates obtained through tNGS were compared with mNGS between the two groups.

RESULTS: The data of a total of 169 patients (78 in the tNGS group and 91 in the mNGS group) were collected, and 145 patients (67 in the tNGS group and 78 in the mNGS group) were finally diagnosed with lung infections. The comprehensive positive pathogen detection-based diagnosis rate for tNGS was 86.6%, with a single-pathogen lung infection diagnosis rate of 85.7% and a mixed-pathogen pulmonary infection diagnosis rate of 88.0%. In contrast, the overall positive pathogen detection-based diagnosis rate for CMTs was 38.8%, comprising a single-pathogen pulmonary infection diagnosis rate of 28.6% and a mixed-pathogen pulmonary infection diagnosis rate of 20.0%. The difference in positive diagnosis rate was deemed statistically significant (p < 0.05). In the mNGS group, the overall pathogen detection-based diagnosis rate was 89.7%, with a single-pathogen pulmonary infection diagnosis rate of 84.9%, and a 100% diagnosis rate for mixed-pathogen pulmonary infections. There was no statistically significant difference in the positive diagnosis rate when compared with the tNGS group (p > 0.05).

CONCLUSION: In patients with pulmonary infections, the diagnosis rate based on BALF pathogen detection using tNGS exceeded that of CMTs, showing no statistically significant difference compared to mNGS.}, } @article {pmid39834891, year = {2025}, author = {Zhao, D and Zhang, L and Sun, Q and Cheng, J}, title = {A Case Report of Chlamydia psittaci Infective Endocarditis Complicated With Pneumonia.}, journal = {Case reports in infectious diseases}, volume = {2025}, number = {}, pages = {7536462}, pmid = {39834891}, issn = {2090-6625}, abstract = {Psittacosis is a zoonotic disease caused by Chlamydia psittaci and is commonly found in birds and poultry. Human infection is uncommon, and most cases are sporadic. Infection of extrapulmonary organs by Chlamydia psittaci is extremely rare. A rare case of infective endocarditis complicated by pneumonia caused by Chlamydia psittaci was reported, which was diagnosed using metagenomic next-generation sequencing (mNGS). The patient recovered after receiving appropriate anti-infective treatment. Discussion on the pathogenesis, diagnosis, and treatment of this disease based on recent literature reports aimed to improve the prognosis of similar patients and enhance the understanding of clinicians.}, } @article {pmid39834703, year = {2024}, author = {Deng, Y and Wu, W and Huang, X and Yang, X and Yu, Y and Zhang, Z and Hu, Z and Zhou, X and Zhou, K and Liu, Y and Zhang, L}, title = {Characterization of rhizosphere bacterial communities in oilseed rape cultivars with different susceptibility to Plasmodiophora brassicae infection.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1496770}, pmid = {39834703}, issn = {1664-462X}, abstract = {Rhizosphere microbiomes are constantly mobilized during plant-pathogen interactions, and this, in turn, affects their interactions. However, few studies have examined the activities of rhizosphere microbiomes in plants with different susceptibilities to soil-borne pathogens, especially those that cause clubroot disease. In this study, we compared the rhizosphere bacterial community in response to infection of Plasmodiophora brassicae among the four different clubroot susceptibility cultivars of oilseed rape (Brassica napus). Our results revealed obvious differences in the responses of rhizosphere bacterial community to the P. brassicae infection between the four cultivars of oilseed rape. Several bacterial genera that are associated with the nitrogen cycle, including Limnobacter, Thiobacillus, Anaeromyxobacter, Nitrosomonas, Tumebacillus, and Halomonas, showed significantly different changes between susceptible and resistant cultivars in the presence of P. brassicae infection. Moreover, increased connectedness and robustness were exhibited in the rhizosphere bacterial community co-occurrence network in clubroot-susceptible cultivars that were infected with P. brassicae, while only slight changes were observed in clubroot-resistant cultivars. Metagenomic analysis of microbial metabolism also indicated differences in the rhizosphere bacterial community between susceptible and resistant cultivars that were infected with P. brassicae. Functional analysis of the nitrogen cycle showed that genes related to nitrification (nxrB) were upregulated in susceptible cultivars, while genes related to assimilatory nitrate reduction (nasA, narB, and nirA) were upregulated in resistant cultivars that were infected with P. brassicae. These findings indicate that the synthesis and assimilation process of NO3 [-] content were promoted in susceptible and resistant cultivars, respectively. Our study revealed differences in the characteristics of rhizosphere bacterial communities in response to P. brassicae infection between clubroot-susceptible and clubroot-resistant cultivars as well as the potential impact of these differences on the plant-P. brassicae interaction.}, } @article {pmid39834589, year = {2025}, author = {D'aes, J and Fraiture, MA and Bogaerts, B and Van Laere, Y and De Keersmaecker, SCJ and Roosens, NHC and Vanneste, K}, title = {Metagenomics-based tracing of genetically modified microorganism contaminations in commercial fermentation products.}, journal = {Food chemistry. Molecular sciences}, volume = {10}, number = {}, pages = {100236}, pmid = {39834589}, issn = {2666-5662}, abstract = {Genetically modified microorganisms (GMM) are frequently employed for the production of microbial fermentation products such as food enzymes. Although presence of the GMM or its recombinant DNA in the final product is not authorized, contaminations occur frequently. Insight into the contamination source of a GMM is of crucial importance to allow the competent authorities to take appropriate action. The aim of this study was to explore the feasibility of a metagenomic shotgun sequencing approach to investigate microbial contamination in fermentation products, focusing on source tracing of GMM strains using innovative strain deconvolution and phylogenomic approaches. In most cases, analysis of 16 GMM-contaminated food enzyme products supported finding the same GM producer strains in different products, while often multiple GMM contaminations per product were detected. Presence of AMR genes in the samples was strongly associated with GMM contamination, emphasizing the potential public health risk. Additionally, a variety of other microbial contaminations were detected, identifying a group of samples with a conspicuously similar contamination profile, which suggested that these samples originated from the same production facility or batch. Together, these findings highlight the need for guidelines and quality control for traceability of these products to ensure the safety of consumers. This study demonstrates the added value of metagenomics to obtain insight in the microbial contamination profiles, as well as their underlying relationships, in commercial microbial fermentation products. The proposed approach may be applied to other types of microbial fermentation products and/or to other (genetically modified) producer strains.}, } @article {pmid39834026, year = {2025}, author = {Alleman, AB and Stolyar, S and Marx, CJ and Leducq, JB}, title = {Led astray by 16S rRNA: phylogenomics reaffirms the monophyly of Methylobacterium and lack of support for Methylorubrum as a genus.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf011}, pmid = {39834026}, issn = {1751-7370}, abstract = {Although the 16S (and 18S) rRNA gene has been an essential tool in classifying prokaryotes, using a single locus to revise bacteria taxonomy can introduce unwanted artifacts. There was a recent proposition to split the Methylobacterium genus, which contains diverse plant-associated strains and is important for agriculture and biotechnology, into two genera. Resting strongly on the phylogeny of 16S rRNA, 11 species of Methylobacterium were transferred to a newly proposed genus Methylorubrum. Numerous recent studies have independently questioned Methylorubrum as a valid genus, but the prior revision has left discrepancies amongst taxonomic databases. Here, we review phylogenomic and phenotypic evidence against Methylorubrum as a genus and call for its abandonment. Because Methylobacterium sensu lato forms a consistent and monophyletic genus, we argue for the restoration of the former and consensual Methylobacterium taxonomy. The large genomic, phenotypic, and ecological diversity within Methylobacterium however suggests complex evolutionary and adaptive processes and support the description of the most basal clade of Methylobacterium (group C) as a distinct genus in future work. Overall, this perspective demonstrates the danger of solely relying upon the 16S rRNA gene as a delimiter of genus level taxonomy and that further attempts must include more robust phenotypic and phylogenomic criteria.}, } @article {pmid39833973, year = {2025}, author = {Rampanelli, E and Romp, N and Troise, AD and Ananthasabesan, J and Wu, H and Gül, IS and De Pascale, S and Scaloni, A and Bäckhed, F and Fogliano, V and Nieuwdorp, M and Bui, TPN}, title = {Gut bacterium Intestinimonas butyriciproducens improves host metabolic health: evidence from cohort and animal intervention studies.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {15}, pmid = {39833973}, issn = {2049-2618}, mesh = {Animals ; *Gastrointestinal Microbiome ; Humans ; Mice ; Feces/microbiology ; Male ; Lysine/metabolism ; Female ; Fermentation ; Butyrates/metabolism ; Cohort Studies ; Clostridiales/metabolism/classification ; Fructose/metabolism ; Mice, Inbred C57BL ; Middle Aged ; Obesity/microbiology/metabolism ; Probiotics/administration & dosage/metabolism ; Disease Models, Animal ; }, abstract = {BACKGROUND: The human gut microbiome strongly influences host metabolism by fermenting dietary components into metabolites that signal to the host. Our previous work has shown that Intestinimonas butyriciproducens is a prevalent commensal bacterium with the unique ability to convert dietary fructoselysine to butyrate, a well-known signaling molecule with proven health benefits. Dietary fructoselysine is an abundant Amadori product formed in foods during thermal treatment and is part of foods rich in dietary advanced glycation end products which have been associated with cardiometabolic disease. It is therefore of interest to investigate the causal role of this bacterium and fructoselysine metabolism in metabolic disorders.

RESULTS: We assessed associations of I. butyriciproducens with metabolic risk biomarkers at both strain and functional levels using a human cohort characterized by fecal metagenomic analysis. We observed that the level of the bacterial strain as well as fructoselysine fermentation genes were negatively associated with BMI, triglycerides, HbA1c, and fasting insulin levels. We also investigated the fructoselysine degradation capacity within the Intestinimonas genus using a culture-dependent approach and found that I. butyriciproducens is a key player in the butyrogenic fructoselysine metabolism in the gut. To investigate the function of I. butyriciproducens in host metabolism, we used the diet-induced obesity mouse model to mimic the human metabolic syndrome. Oral supplementation with I. butyriciproducens counteracted body weight gain, hyperglycemia, and adiposity. In addition, within the inguinal white adipose tissue, bacterial administration reduced inflammation and promoted pathways involved in browning and insulin signaling. The observed effects may be partly attributable to the formation of the short-chain fatty acids butyrate from dietary fructoselysine, as butyrate plasma and cecal levels were significantly increased by the bacterial strain, thereby contributing to the systemic effects of the bacterial treatment.

CONCLUSIONS: I. butyriciproducens ameliorates host metabolism in the context of obesity and may therefore be a good candidate for new microbiota-therapeutic approaches to prevent or treat metabolic diseases. Video Abstract.}, } @article {pmid39833926, year = {2025}, author = {Li, Z and Zhao, C and Mao, Z and Zhang, F and Dong, L and Song, C and Chen, Y and Fu, X and Ao, Z and Xiong, Y and Hui, Q and Song, W and Penttinen, P and Zhang, S}, title = {Structure and metabolic function of spatiotemporal pit mud microbiome.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {10}, pmid = {39833926}, issn = {2524-6372}, support = {2022HX04//Youth Fund of Postdoctor/ ; 2021JDJQ0038//Youth Fund of Sichuan Province/ ; }, abstract = {BACKGROUND: Pit mud (PM) hosts diverse microbial communities, which serve as a medium to impart flavor and quality to Baijiu and exhibit long-term tolerance to ethanol and acids, resulting in a unique ecosystem. However, the ecology and metabolic functions of PM remain poorly understood, as many taxa in PM represent largely novel lineages. In this study, we used a combination of metagenomic analysis and chemical derivatization LC-MS analysis to provide a comprehensive overview of microbial community structure, metabolic function, phylogeny, horizontal gene transfer, and the relationship with carboxyl compounds in spatiotemporal PM samples.

RESULTS: Our findings revealed three distinct stages in the spatiotemporal changes of prokaryotic communities in PM: an initial phase dominated by Lactobacillus, a transitional phase, and a final state of equilibrium. Significant variations in α- and β-diversity were observed across different spatial and temporal PM samples. We identified 178 medium- and high-quality non-redundant metagenome-assembled genomes (MAGs), and constructed their phylogenetic tree, depicting their roles in the carbon, nitrogen, and sulfur cycles. The Wood-Ljungdahl pathway and reverse TCA cycle were identified as the main carbon fixation mechanisms, with both hydrogenotrophic and aceticlastic methanogens playing a major role in methane production, and methylotrophic pathway observed in older PM. Furthermore, we identified relationships between prokaryotes and 29 carboxyl metabolites, including medium- and long-chain fatty acids. Horizontal gene transfer (HGT) was widespread in PM, particularly among clostridia, Bacteroidota, Bacilli, and Euryarchaeota, and was shown to play critical roles in fermentation dynamics, carbon fixation, methane production, and nitrogen and sulfur metabolism.

CONCLUSION: Our study provides new insights into the evolution and function of spatiotemporal PM, as well as its interactions with carboxyl metabolites. Lactobacillus dominated in new PM, while methanogens and clostridia were predominant in older or deeper PM layers. The three distinct stages of prokaryotic community development in PM and HGT played critical roles in metabolic function of spatiotemporal PM. Furthermore, this study highlights the importance of α-diversity, β-diversity, methanogens, and Clostridium as useful indicators for assessing PM quality in the production of high-quality Baijiu.}, } @article {pmid39833778, year = {2025}, author = {Yang, X and Liu, Z and Liu, X and Li, Q and Huang, H and Wei, Y and Sun, T}, title = {Severe pneumonia due to concurrent Legionella pneumophila and Acinetobacter baumannii infections: a case report.}, journal = {BMC pulmonary medicine}, volume = {25}, number = {1}, pages = {29}, pmid = {39833778}, issn = {1471-2466}, support = {2024KY589//Zhejiang Province Medical and Health Science and Technology Plan Project/ ; 2022RKX26//Lishui Municipal Science and Technology Bureau Project/ ; }, mesh = {Humans ; Male ; Middle Aged ; *Acinetobacter baumannii/isolation & purification ; *Legionella pneumophila/isolation & purification ; *Anti-Bacterial Agents/therapeutic use ; *Legionnaires' Disease/diagnosis/drug therapy/complications/microbiology ; *Acinetobacter Infections/drug therapy/diagnosis ; *Tomography, X-Ray Computed ; Community-Acquired Infections/microbiology/drug therapy ; Pneumonia, Bacterial/microbiology/drug therapy/diagnosis/complications ; Coinfection ; Drug Resistance, Multiple, Bacterial ; }, abstract = {BACKGROUND: Legionella pneumophila is an uncommon pathogen causing community-acquired atypical pneumonia. Acinetobacter baumannii is a major pathogen responsible for hospital-acquired pneumonia, but it rarely causes serious infections in a community setting. Without prompt and appropriate treatments, infection from either of these two pathogens can cause a high mortality rate. Concurrent infection from both L. pneumophila and A. baumannii can cause serious outcomes, but it has rarely been reported previously.

CASE PRESENTATION: A 45-year-old male presented to our hospital with a productive cough and fever after staying in a local hotel. His chest computed tomography (CT) scan showed bilateral lower-lobe infiltration and left pleural effusion. Empirical antibiotics, including piperacillin-tazobactam, levofloxacin, meropenem, and doxycycline, were administered to him to treat community-acquired pneumonia. However, his condition deteriorated very rapidly, and he required endotracheal intubation and mechanical ventilation for respiratory support. Finally, metagenomic next-generation sequencing (mNGS) of his bronchoalveolar lavage fluid identified L. pneumophila and A. baumannii. The sputum culture demonstrated multidrug-resistant A. baumannii. He was diagnosed with pneumonia by concurrent infections from both L. pneumophila and A. baumannii. After careful consideration of the antibiotic susceptibility results and the antibacterial mechanism of each antibiotic, we switched the antibiotics to omadacycline and cefoperazone/sulbactam. His clinical symptoms gradually subsided. The repeat chest CT image showed no infiltration or pleural effusion.

CONCLUSIONS: Community-acquired pneumonia can be caused by concurrent infections of both L. pneumophila and A. baumannii. Close clinical monitoring, early pathogen detection and antibiotic susceptability tests, and appropriate antibiotic regimen adjustments should be applied to these patients who failed initial antibiotic treatments.}, } @article {pmid39833544, year = {2025}, author = {Yan, X and Liu, Y and Hu, T and Huang, Z and Li, C and Guo, L and Liu, Y and Li, N and Zhang, H and Sun, Y and Yi, L and Wu, J and Feng, J and Zhang, F and Jiang, T and Tu, C and He, B}, title = {A compendium of 8,176 bat RNA viral metagenomes reveals ecological drivers and circulation dynamics.}, journal = {Nature microbiology}, volume = {10}, number = {2}, pages = {554-568}, pmid = {39833544}, issn = {2058-5276}, support = {32192423//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32022083//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32192424//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32371562//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Chiroptera/virology ; Animals ; China ; *Metagenome ; *Virome/genetics ; *RNA Viruses/genetics/classification/isolation & purification ; Phylogeny ; RNA, Viral/genetics ; Humans ; Genetic Variation ; Genome, Viral/genetics ; Metagenomics/methods ; }, abstract = {Bats are natural hosts for many emerging viruses for which spillover to humans is a major risk, but the diversity and ecology of bat viruses is poorly understood. Here we generated 8,176 RNA viral metagenomes by metatranscriptomic sequencing of organ and swab samples from 4,143 bats representing 40 species across 52 locations in China. The resulting database, the BtCN-Virome, expands bat RNA virus diversity by over 3.4-fold. Some viruses in the BtCN-Virome are traced to mammals, birds, arthropods, mollusks and plants. Diet, infection dynamics and environmental parameters such as humidity and forest coverage shape virus distribution. Compared with those in the wild, bats dwelling in human settlements harboured more diverse viruses that also circulated in humans and domestic animals, including Nipah and Lloviu viruses not previously reported in China. The BtCN-Virome provides important insights into the genetic diversity, ecological drivers and circulation dynamics of bat viruses, highlighting the need for surveillance of bats near human settlements.}, } @article {pmid39833341, year = {2025}, author = {Zhang, C and Yu, Y and Yue, L and Chen, Y and Chen, Y and Liu, Y and Guo, C and Su, Q and Xiang, Z}, title = {Gut microbiota profiles of sympatric snub-nosed monkeys and macaques in Qinghai-Tibetan Plateau show influence of phylogeny over diet.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {95}, pmid = {39833341}, issn = {2399-3642}, support = {32171487//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31870509//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32400413//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Phylogeny ; *Diet ; Tibet ; RNA, Ribosomal, 16S/genetics ; Colobinae/microbiology ; Macaca mulatta ; Macaca/microbiology ; Bacteria/classification/genetics/isolation & purification ; }, abstract = {The unique environment of the Qinghai-Tibetan Plateau provides a great opportunity to study how primate intestinal microorganisms adapt to ecosystems. The 16S rRNA gene amplicon and metagenome analysis were conducted to investigate the correlation between gut microbiota in primates and other sympatric animal species living between 3600 and 4500 m asl. Results showed that within the same geographical environment, Macaca mulatta and Rhinopithecus bieti exhibited a gut microbiome composition similar to that of Tibetan people, influenced by genetic evolution of host, while significantly differing from other distantly related animals. The gut microbiota of plateau species has developed similar strategies to facilitate their hosts' adaptation to specific environments, including broadening its dietary niche and enhancing energy absorption. These findings will enhance our comprehension of the significance of primate gut microbiota in adapting to specific habitats.}, } @article {pmid39833183, year = {2025}, author = {Nunn, BL and Timmins-Schiffman, E and Mudge, MC and Plubell, DL and Chebli, G and Kubanek, J and Riffle, M and Noble, WS and Harvey, E and Nunn, TA and Rynearson, T and Huntemann, M and LaButti, K and Foster, B and Foster, B and Roux, S and Palaniappan, K and Mukherjee, S and Reddy, TBK and Daum, C and Copeland, A and Chen, IA and Ivanova, NN and Kyrpides, NC and Glavina Del Rio, T and Eloe-Fadrosh, EA}, title = {Author Correction: Microbial Metagenomes Across a Complete Phytoplankton Bloom Cycle: High-Resolution Sampling Every 4 Hours Over 22 Days.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {113}, doi = {10.1038/s41597-025-04445-7}, pmid = {39833183}, issn = {2052-4463}, } @article {pmid39832809, year = {2025}, author = {Miebach, J and Green, D and Strittmatter, M and Mallinger, C and Le Garrec, L and Zhang, QY and Foucault, P and Kunz, C and Gachon, CMM}, title = {Importance, structure, cultivability, and resilience of the bacterial microbiota during infection of laboratory-grown Haematococcus spp. by the blastocladialean pathogen Paraphysoderma sedebokerense: evidence for a domesticated microbiota and its potential for biocontrol.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {2}, pages = {}, pmid = {39832809}, issn = {1574-6941}, support = {BB/P027806/1//UK Research and Innovation/ ; H2020-BG1-2016//Horizon Europe/ ; //MNHN/ ; }, mesh = {*Microbiota ; *Chlorophyta/microbiology/growth & development ; *Bacteria/genetics/classification/growth & development/isolation & purification ; Ascomycota/genetics/growth & development/physiology ; Metagenomics ; Biological Control Agents ; }, abstract = {Industrial production of the unicellular green alga Haematococcus lacustris is compromised by outbreaks of the fungal pathogen Paraphysoderma sedebokerense (Blastocladiomycota). Here, using axenic algal and fungal cultures and antibiotic treatments, we show that the bacterial microbiota of H. lacustris is necessary for the infection by P. sedebokerense and that its modulation affects the outcome of the interaction. We combined metagenomics and laboratory cultivation to investigate the diversity of the bacterial microbiota associated to three Haematococcus species and monitor its change upon P. sedebokerense infection. We unveil three types of distinct, reduced bacterial communities, which likely correspond to keystone taxa in the natural Haematococcus spp. microbiota. Remarkably, the taxonomic composition and functionality of these communities remained stable during infection. The major bacterial taxa identified in this study have been cultivated by us or others, paving the way to developing synthetic communities to experimentally explore interactions within this tripartite system. We discuss our results in the light of emerging evidence concerning the structuring and domestication of plant and animal microbiota, thus providing novel experimental tools and a new conceptual framework necessary to enable the engineering of Haematococcus spp. microbiota toward the biocontrol of P. sedebokerense.}, } @article {pmid39831119, year = {2024}, author = {Lenka, J and González-Tortuero, E and Kuba, S and Ferry, N}, title = {Bacterial community profiling and identification of bacteria with lignin-degrading potential in different gut segments of African palm weevil larvae (Rhynchophorus phoenicis).}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1401965}, pmid = {39831119}, issn = {1664-302X}, abstract = {The microbiota within the guts of insects plays beneficial roles for their hosts, such as facilitating digestion and extracting energy from their diet. The African palm weevil (APW) lives within and feeds on the high lignin-containing trunk of palm trees; therefore, their guts could harbour a large community of lignin-degrading microbes. In this study, we aimed to explore the bacterial community within the gut of the APW larvae, specifically with respect to the potential for lignin degradation in various gut segments as a first step to determining the viability of mining bacterial lignin-degrading enzymes for the bioconversion of lignocellulosic biomass to biofuels and biomaterials. Bacterial metagenomic DNA was extracted from the foregut, midgut, and hindgut of larvae of the APW, and the V3-V4 hypervariable region of the 16S rRNA gene was sequenced using the Illumina MiSeq platform. The generated data were analysed and taxonomically classified to identify the different bacterial phylotypes within the gut community cumulatively and per gut segment. We then determined the presence, diversity, and abundance of bacteria associated with lignin degradation within each larval gut compartment as a basis for suggesting the gut segment(s) where lignin degradation occurs the most. All sequences were classified and belonged to the bacterial kingdom. Firmicutes (54.3%) and Proteobacteria (42.5%) were the most dominant phyla within the gut, followed distantly by Bacteroidota (1.7%) and Actinobacteriota (1.4%). Enterococcus, Levilactobacillus, Lactococcus, Shimwellia, Megasphaera, Klebsiella, Pectinatus, Salmonella, Lelliotia, and Enterobacter constituted the most abundant genera found across all gut segments. The foregut and midgut had many similar genera, whilst the hindgut appeared unique. Overall, 29.5% of total gut bacteria comprising 21 genera were lignin degraders found predominantly in the Firmicutes and Proteobacteria phyla (56.8 and 39.5%, respectively), then moderately in Actinobacteriota (2.5%) and Bacteroidota (1.1%). The most abundant ligninolytic genera were Levilactobacillus (46.4%), Klebsiella (22.9%), Enterobacter (10.7%), Lactiplantibacillus (5.9%), Citrobacter (2.2%), Corynebacterium (1.8%), Paucilactobacillus (1.8%), Serratia (1.5%), Bacteroides (1.1%), and Leucobacter (1.0%) found in different amounts in different gut compartments. The foregut had the most diverse and highest abundance of lignin-degrading phylotypes, and we present reasons that point to the foregut as the main location for the depolymerization of lignin in the APW larval gut.}, } @article {pmid39830903, year = {2025}, author = {Cambray, GA and Kalinski, JJ}, title = {Microbial Characterization of a Zambian Honey Vinegar.}, journal = {Food science & nutrition}, volume = {13}, number = {1}, pages = {e4549}, pmid = {39830903}, issn = {2048-7177}, abstract = {Forest Fruits Organic Honey Vinegar (FFOHV) is a spontaneously fermented (yeast) and acetified (Acetic Acid Bacteria-AAB) Miombo Woodland honey vinegar developed in Zambia. Live vinegars containing live microbial cultures are marketed for their probiotic health benefits. The correlation between a well-developed gut microbiome and human health is well studied and fermented products such as live vinegar containing AAB contribute to a healthy gut microbiome. This study details a metagenomic analysis of stable, bottled FFOHV (Zambia) alongside two commercially available live vinegar products: Bragg Organic Apple Cider Vinegar (BOACV) and Nature's Source Apple Cider Vinegar (NSACV). FFOHV contained representatives of five bacterial and nine fungal genera, compared to BOACV with two bacterial and five fungal, and NSACV containing no bacterial and six fungal genera. FFOHV and BOACV showed a dominance of Komagataeibacter bacterial species. The dominant yeast was Vanrija humicola present in all three vinegar samples. FFOHV contained greater diversity of genera, with the notable species Monascus purpureus-a microbe that produces several health-enhancing compounds. The analysis showed that FFOHV is a microbially diverse product containing several potentially health-enhancing microbes. Graphical Abstract Text: This study presents a metagenomic analysis of Forest Fruits Organic Honey Vinegar (FFOHV) from Zambia, compared with two commercial live cider vinegars: Bragg Organic Apple Cider Vinegar (BOACV) and Nature's Source Apple Cider Vinegar (NSACV). FFOHV exhibited a richer microbial diversity, containing five bacterial and nine fungal genera, including the health-promoting species Monascus purpureus. Both FFOHV and BOACV were dominated by Komagataeibacter species, with Vanrija humicola as the prevalent yeast across all samples. This confirmed FFOHV's unique potential probiotic benefits.}, } @article {pmid39830168, year = {2024}, author = {Zhao, Y and Zhao, M and Zhang, W}, title = {Identification of a novel papillomavirus in oral swabs from giant pandas (Ailuropoda melanoleuca).}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1457471}, pmid = {39830168}, issn = {2297-1769}, abstract = {To fully characterize papillomavirus diversity in giant pandas (Ailuropoda melanoleuca), we identified a novel papillomavirus (named AmPV5, GenBank accession number MZ357114) in oral swabs from giant pandas with the help of viral metagenomics technology in this study. The complete circular genome of AmPV5 is 7,935 bp in length, with a GC content of 39.1%. It encodes five early genes (E1, E2, E4, E6, and E7), two late genes (L1 and L2), and features conserved zinc-binding domains (CXXC- (X)28/29-CXXC) in E6 and E7 genes. E7 protein has an LxCxE domain (pRB binding) in its N-terminal region. The nucleotide sequence of AmPV5 L1 gene shares < 70% identity with other related sequences available in the GenBank database. Phylogenetic analysis indicated that AmPV5 fell within the Lambdapapillomavirus genus but formed a monophyletic branch away from other papillomaviruses found in Ailuropoda melanoleuca, Canis, Felis catus, Panthera uncia, Enhydra lutris, and Procyon lotor. According to the International Committee on Taxonomy of Viruses (ICTV) classification guidelines, AmPV5 is classified as a new species within the Lambdapapillomavirus genus. The discovery provides valuable insights into the viral diversity in giant pandas and highlights the need for continued surveillance of wildlife pathogens. Future studies should explore the potential role of AmPV5 in the health and disease ecology of this endangered species.}, } @article {pmid39830096, year = {2025}, author = {Fei, C and Booker, A and Klass, S and Vidyarathna, NK and Ahn, SH and Mohamed, AR and Arshad, M and Glibert, PM and Heil, CA and Martínez Martínez, J and Amin, SA}, title = {Friends and foes: symbiotic and algicidal bacterial influence on Karenia brevis blooms.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycae164}, pmid = {39830096}, issn = {2730-6151}, abstract = {Harmful Algal Blooms (HABs) of the toxigenic dinoflagellate Karenia brevis (KB) are pivotal in structuring the ecosystem of the Gulf of Mexico (GoM), decimating coastal ecology, local economies, and human health. Bacterial communities associated with toxigenic phytoplankton species play an important role in influencing toxin production in the laboratory, supplying essential factors to phytoplankton and even killing blooming species. However, our knowledge of the prevalence of these mechanisms during HAB events is limited, especially for KB blooms. Here, we introduced native microbial communities from the GoM, collected during two phases of a Karenia bloom, into KB laboratory cultures. Using bacterial isolation, physiological experiments, and shotgun metagenomic sequencing, we identified both putative enhancers and mitigators of KB blooms. Metagenome-assembled genomes from the Roseobacter clade showed strong correlations with KB populations during HABs, akin to symbionts. A bacterial isolate from this group of metagenome-assembled genomes, Mameliella alba, alleviated vitamin limitations of KB by providing it with vitamins B1, B7 and B12. Conversely, bacterial isolates belonging to Bacteroidetes and Gammaproteobacteria, Croceibacter atlanticus, and Pseudoalteromonas spongiae, respectively, exhibited strong algicidal properties against KB. We identified a serine protease homolog in P. spongiae that putatively drives the algicidal activity in this isolate. While the algicidal mechanism in C. atlanticus is unknown, we demonstrated the efficiency of C. atlanticus to mitigate KB growth in blooms from the GoM. Our results highlight the importance of specific bacteria in influencing the dynamics of HABs and suggest strategies for future HAB management.}, } @article {pmid39830095, year = {2025}, author = {Junca, H and Steube, A and Mrowietz, S and Stallhofer, J and Vital, M and Dos Anjos Borges, LG and Pieper, DH and Stallmach, A}, title = {Bacterial and viral assemblages in ulcerative colitis patients following fecal microbiota and fecal filtrate transfer.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycae167}, pmid = {39830095}, issn = {2730-6151}, abstract = {Fecal microbiota filtrate transfer is discussed as a safe alternative to fecal microbiota transfer (FMT) to treat ulcerative colitis. We investigated modulation of viral and bacterial composition during fecal microbiota filtrate transfer followed by FMT in six patients with active ulcerative colitis (where clinical activity improved in three patients after filtrate transfer) and combined 16S ribosomal RNA gene amplicon sequencing with a virome analysis pipeline including fast viral particle enrichment and metagenome mapping to detect frequencies of 45,033 reference bacteriophage genomes. We showed that after antibiotic treatment and during filtrate transfer, the bacterial community typically adopted a stable composition distinct to that before antibiotic treatment, with no change toward a donor community. FMT in contrast typically changed the bacterial community to a community with similarity to donor(s). There were no indications of an establishment of predominant donor viruses during filtrate transfer but a remodeling of the virome. In contrast, the establishment of donor viruses during FMT correlated with the predicted hosts established during such transfer. Our approach warrants further investigation in a randomized trial to evaluate larger therapeutic interventions in a comparable and efficient manner.}, } @article {pmid39829898, year = {2025}, author = {Ni, M and Fan, Y and Liu, Y and Li, Y and Qiao, W and Davey, LE and Zhang, XS and Ksiezarek, M and Mead, E and Touracheau, A and Jiang, W and Blaser, MJ and Valdivia, RH and Fang, G}, title = {Epigenetic phase variation in the gut microbiome enhances bacterial adaptation.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39829898}, issn = {2692-8205}, support = {R35 GM139655/GM/NIGMS NIH HHS/United States ; }, abstract = {The human gut microbiome within the gastrointestinal tract continuously adapts to variations in diet, medications, and host physiology. A central strategy for genetic adaptation is epigenetic phase variation (ePV) mediated by bacterial DNA methylation, which can regulate gene expression, enhance clonal heterogeneity, and enable a single bacterial strain to exhibit variable phenotypic states. Genome-wide and site-specific ePV have been well characterized in human pathogens' antigenic variation and virulence factor production. However, the role of ePV in facilitating adaptation within the human microbiome remains poorly understood. Here, we comprehensively cataloged genome-wide and site-specific ePV in human infant and adult gut microbiomes. First, using long-read metagenomic sequencing, we detected genome-wide ePV mediated by complex structural variations of DNA methyltransferases, highlighting the ones associated with antibiotics or fecal microbiota transplantation. Second, we analyzed an extensive collection of public short-read metagenomic sequencing datasets, uncovering a greater prevalence of genome-wide ePV in the human gut microbiome. Third, we quantitatively detected site-specific ePVs using single-molecule methylation analysis to identify dynamic variations associated with antibiotic treatment or probiotic engraftment. Finally, we performed an in-depth assessment of an Akkermansia muciniphila isolate from an infant, highlighting that ePV can regulate gene expression and enhance the bacterial adaptive capacity by employing a bet-hedging strategy to increase tolerance to differing antibiotics. Our findings indicate that epigenetic modifications are a common and broad strategy used by bacteria in the human gut to adapt to their environment.}, } @article {pmid39829854, year = {2025}, author = {Ghazi, AR and Thompson, KN and Bhosle, A and Mei, Z and Yan, Y and Wang, F and Wang, K and Franzosa, EA and Huttenhower, C}, title = {Quantifying Metagenomic Strain Associations from Microbiomes with Anpan.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39829854}, issn = {2692-8205}, support = {R24 DK110499/DK/NIDDK NIH HHS/United States ; }, abstract = {Genetic and genomic variation among microbial strains can dramatically influence their phenotypes and environmental impact, including on human health. However, inferential methods for quantifying these differences have been lacking. Strain-level metagenomic profiling data has several features that make traditional statistical methods challenging to use, including high dimensionality, extreme variation among samples, and complex phylogenetic relatedness. We present Anpan, a set of quantitative methods addressing three key challenges in microbiome strain epidemiology. First, adaptive filtering designed to interrogate microbial strain gene carriage is combined with linear models to identify strain-specific genetic elements associated with host health outcomes and other phenotypes. Second, phylogenetic generalized linear mixed models are used to characterize the association of sub-species lineages with such phenotypes. Finally, random effects models are used to identify pathways more likely to be retained or lost by outcome-associated strains. We validated our methods by simulation, showing that we achieve more accurate effect size estimation and a lower false positive rate compared to alternative methodologies. We then applied our methods to a dataset of 1,262 colorectal cancer patients, identifying functionally adaptive genes and strong phylogenetic effects associated with CRC status, sometimes complementing and sometimes extending known species-level microbiome CRC biomarkers. Anpan's methods have been implemented as a publicly available R library to support microbial community strain and genetic epidemiology in a variety of contexts, environments, and phenotypes.}, } @article {pmid39829744, year = {2025}, author = {Tang, G and Carr, AV and Perez, C and Sarmiento, KR and Levy, L and Lampe, JW and Diener, C and Gibbons, SM}, title = {Metagenomic estimation of absolute bacterial biomass in the mammalian gut through host-derived read normalization.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39829744}, issn = {2692-8205}, support = {P30 CA015704/CA/NCI NIH HHS/United States ; R01 DK133468/DK/NIDDK NIH HHS/United States ; }, abstract = {Absolute bacterial biomass estimation in the human gut is crucial for understanding microbiome dynamics and host-microbe interactions. Current methods for quantifying bacterial biomass in stool, such as flow cytometry, qPCR, or spike-ins (i.e., adding cells or DNA from an organism not normally found in a sample), can be labor-intensive, costly, and confounded by factors like water content, DNA extraction efficiency, PCR inhibitors, and other technical challenges that add bias and noise. We propose a simple, cost-effective approach that circumvents some of these technical challenges: directly estimating bacterial biomass from metagenomes using bacterial-to-host (B:H) read ratios. We compare B:H ratios to the standard methods outlined above, demonstrating that B:H ratios are useful proxies for bacterial biomass in stool and possibly in other host-associated substrates. We show how B:H ratios can be used to track antibiotic treatment response and recovery in both mice and humans, which showed 403-fold and 45-fold reductions in bacterial biomass during antibiotic treatment, respectively. Our results indicate that host and bacterial metagenomic DNA fractions in human stool fluctuate longitudinally around a stable mean in healthy individuals, and the average host read fraction varies across healthy individuals by < 8-9 fold. B:H ratios offer a convenient alternative to other absolute biomass quantification methods, without the need for additional measurements, experimental design considerations, or machine learning algorithms, enabling retrospective absolute biomass estimates from existing stool metagenomic data.}, } @article {pmid39828685, year = {2025}, author = {Chen, Y and Yi, ZT and Yu, HL and Wu, XY and Wang, JP and Nie, C and Li, H and Li, SH and Yan, QL and He, TW and Chen, MC and Yang, XY and Wen, JY and Lv, LJ}, title = {Does preeclampsia impact the gut microbiota of preterm offspring during early infancy?.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {84}, pmid = {39828685}, issn = {1479-5876}, support = {2019A1515110389//Basic and Applied Basic Research Foundation of Guangdong Province/ ; }, mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; *Pre-Eclampsia/microbiology ; Pregnancy ; Infant, Newborn ; *Infant, Premature ; Adult ; Feces/microbiology ; Biodiversity ; }, abstract = {Preeclampsia (PE) is a pregnancy complication characterized by high blood pressure and organ damage. This study investigates the differences in the gut microbiota between preterm neonates born to mothers with PE and those born to mothers without PE (PR), aiming to understand how maternal health conditions like PE influence neonatal gut microbiota. The early gut microbiota plays a crucial role in neonatal health, and disturbances in its development can have long-term consequences. Fecal samples were collected from preterm neonates of PE and PR mothers at 2 and 6 weeks postpartum and analyzed using shotgun metagenomic sequencing. We found that PE significantly affected the gut microbial composition of preterm neonates, particularly at 2 weeks postpartum. The gut microbial diversity in the PE_2 group was notably lower compared to the PR_2 group, with no significant difference observed between the PR_6 and PE_6 groups. At the phylum level, Firmicutes and Proteobacteria were predominant, with significant differences observed, particularly a lower abundance of Actinobacteria in the PE_2 group. At the genus level, Escherichia, Enterococcus, and Klebsiella were more prevalent in the PE_2 group, whereas Bifidobacterium and Cutibacterium dominated the PR_2 group. The gut virome analysis showed no significant differences among the groups. Functional analysis revealed distinct metabolic pathway activities across the groups, suggesting that early disturbances due to PE impact the establishment of healthy gut microbiota. These findings underscore the substantial influence of maternal health on the early development of the neonatal gut microbiota and highlight the potential long-term health consequences. Additionally, the differences in metabolic pathways further emphasize the impact of preeclampsia on gut microbiota functionality.}, } @article {pmid39828574, year = {2025}, author = {Ma, XY and A, XR and Ma, JD and Zhou, JW and Cheng, P and Tang, Y}, title = {[Differential analysis of intestinal flora in patients with hepatic blastomycosis based on second-generation sequencing].}, journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]}, volume = {59}, number = {1}, pages = {101-109}, doi = {10.3760/cma.j.cn112150-20240620-00487}, pmid = {39828574}, issn = {0253-9624}, support = {2022‑ZJ‑T01//Qinghai Province 2022 Innovation Platform Construction Special Project/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Case-Control Studies ; *Feces/microbiology ; High-Throughput Nucleotide Sequencing ; Echinococcosis, Hepatic/microbiology ; Metagenomics/methods ; }, abstract = {Exploring the variability of the intestinal flora of patients with hepatic blastocysticercosis and searching for members of the intestinal microflora that may play a role in the disease process by means of macro-genome sequencing technology. A case-control study was used to include fecal samples from patients with hepatic vesicular schistosomiasis admitted to Qinghai Provincial People's Hospital between October 2023 and January 2024 and individuals attending health checkups. The experimental group (AE group) consisted of 10 patients with liver vesicular schistosomiasis and the control group (NC group) consisted of 9 individuals attending health checkups. Macrogenomic sequencing was performed on these two groups of samples using the Illumina Novaseq 6000 sequencing platform, using fastp (v0.20.1) to remove junctions, and bbmap (v38.93-0) to remove the hosted sequences, followed by sequence splicing using MEGAHIT (v1.2.9), and then using prodigal (v2.6.3) to The spliced scaffold was subjected to ORF prediction and translated into amino acid sequences, followed by the construction of a non-redundant gene set using MMSeqs2 (v13.45111), and finally compared with the non-redundant gene set using salmon (v1.8.0). Species were annotated by the non-redundant database, species abundance was calculated in each sample, and the two sets were tested using Wilcoxon rank sum test. Finally, the differences in intestinal flora between the two groups were statistically analyzed using linear discriminant analysis, and the correlation between the differential intestinal flora and clinical indicators was analyzed using redundancy analysis (RDA). The results showed that the effective data volume of each sample was distributed from 10.41 to 12.46 G. The number of ORFs in the de-redundantly constructed gene catalogue (non-redundant gene set) was 4 951 408, and the annotation rate of the non-redundant genes was 97.97% when compared with the NR database. The ages of the study subjects in the two groups were (44.78±4.58) years in the NC group and (42.90±10.44) years in the AE group, and the difference was not statistically significant (t=0.530, P=0.476). The two groups were matched for body mass index (BMI) (t=2.368, P=0.142), gender (χ[2]=0.200, P=0.655), and dietary habits. There was no statistically significant difference in alpha diversity in the AE group (ACE index, t=0.942; chao1 index, t=0.947; shannon index, t=0.813, the simpson's index, t=0.613, P>0.05), while beta diversity analysis showed significant differences in the overall structure of the two communities (Stress=0.054 5). A total of 120 species were annotated at the phylum level, of which two differed. While 1 736 species were annotated at the genus level, 69 were different, and 309 were different at the species level. The AE group ranked the top 6 in terms of abundance of Anaplasma, Escherichiaceae, Clostridium, Alternaria, Ruminalia, and Treponema spp. at the genus level; whereas, Segatella, Prevotella, E. faecalis, Rossella, and beneficial rod-shaped bacteria were more abundant in the NC group. There were differences in the abundance and diversity of intestinal flora between the two groups, and the structure of community composition was significantly different. Statistical results by linear discriminant analysis (LDA) showed that LDA scores >2 in the NC group included beneficial bacillus spp. and E. faecalis spp. in young infants, etc. LDA scores >2 in the AE group at the mid-species level included Clostridium polterococcus, unknown microorganisms in the genus Clostridium intestinalis, Hathaway's Henkett's bacillus, and Clostridium oryzae in the genus Clostridium refractory to culture and small Clostridium spp. in the AE group. Clostridium intestinalis. The RDA results showed a negative correlation between beneficial rod genera and liver function indices, and a positive correlation between Clostridium intestinalis genera and liver function indices. In conclusion, patients with hepatic blastomycosis have altered intestinal flora abundance and diversity, with significant structural changes in community composition and differences in several genera, including Mycobacterium anisopliae and Clostridium intestinalis, and imbalances in the intestinal flora may affect hepatic function by influencing intestinal metabolites and may have an impact on the development of hepatic blastomycosis, a finding that warrants further in-depth study.}, } @article {pmid39828197, year = {2025}, author = {Lin, B and Zhang, Y and Hao, Y and Lu, M and Xiang, H and Ding, D and Niu, S and Li, K and Li, J and Huang, Z}, title = {Insights into nitrogen metabolism and humification process in aerobic composting facilitated by microbial inoculation.}, journal = {Environmental research}, volume = {269}, number = {}, pages = {120894}, doi = {10.1016/j.envres.2025.120894}, pmid = {39828197}, issn = {1096-0953}, abstract = {To enhance the retention of compost nutrients, specifically in nitrogen metabolism and humification, compound microbial agents were added during the aerobic composting of bagasse pith and buffalo manure. The introduction of the microbial agent successfully colonized the mixture, boosted the degradation capacity of organic matter, and facilitated the formation of nitrogenous substances and humic substances (HSs). The incorporation of a composite microbial inoculum led to a substantial rise in total Kjeldahl nitrogen (TKN) by 62.04%, nitrate nitrogen (NO- 3-N) by 291.65%, and amino acid (AA) by 78.77%. Furthermore, this intervention resulted in achieving a humic acid (HA) to fulvic acid (FA) ratio of 1.64. Metagenomic sequencing revealed enhanced synergistic interactions among microorganisms through inoculation, increasing the abundance of functional genes related to nitrification and nitrogen fixation compared to the uninoculated control. Spearman correlation analysis identified unclassified_c__Deltaproteobacteria, unclassified_f__Planctomycetaceae, Chryseosolibacter, unclassified_f__Hyphomicrobiaceae as the principal producers of HA. This research provides insights into the interactions between nitrogen metabolism and humification in composting, aiming to effectively retain compost nutrients and support the long-term sustainability of agriculture.}, } @article {pmid39828044, year = {2025}, author = {Carluccio, M and Sabatino, R and Borgomaneiro, G and Cesare, AD and Rizzo, L}, title = {Bacterial community dynamics in a biofilm-based process after electro-assisted Fenton pre-treatment of real olive mill wastewater.}, journal = {Bioresource technology}, volume = {419}, number = {}, pages = {132095}, doi = {10.1016/j.biortech.2025.132095}, pmid = {39828044}, issn = {1873-2976}, mesh = {*Biofilms ; *Olea ; *Wastewater/chemistry/microbiology ; *Bacteria ; Iron/pharmacology/chemistry ; Hydrogen Peroxide/pharmacology ; Bioreactors/microbiology ; Water Purification/methods ; Industrial Waste ; Biodegradation, Environmental ; }, abstract = {In this work, the effect of the electro-assisted Fenton (EAF) process on the bacterial community of a moving bed biofilm reactor (MBBR) for olive mill wastewater (OMW) co-treatment with urban wastewater (UWW) was investigated. According to metagenomic analysis, pre-treatment by EAF, while removing total phenols (TPHs) up to 84 % ± 3 % and improving biodegradability of OMW from 0.38 to 0.62, led to the emergence of bacterial genera in the MBBR (R2) that were not detected under conditions without pre-treatment (R1). Indeed, in that condition, Candidatus Competibacter replaced Amaricoccus as dominant denitrifying bacteria. In both cases, the bacterial community composition matched with high simultaneous nitrification-denitrification efficiency (up to 98 %). Finally, Chlorobium (2.5-4.1 %), sulphate-reducing bacteria and Geobacter (up to 1.6 ± 0.4 %), anaerobic bacteria that utilise iron oxides, were observed exclusively with EAF application, suggesting potential for the development of new integrated microbial electrochemical systems.}, } @article {pmid39827989, year = {2025}, author = {Cheng, CK and Ye, L and Wang, Y and Wang, YL and Xia, Y and Wong, SH and Chen, S and Huang, Y}, title = {Exercised gut microbiota improves vascular and metabolic abnormalities in sedentary diabetic mice through gut‒vascular connection.}, journal = {Journal of sport and health science}, volume = {}, number = {}, pages = {101026}, doi = {10.1016/j.jshs.2025.101026}, pmid = {39827989}, issn = {2213-2961}, abstract = {BACKGROUND: Exercise elicits cardiometabolic benefits, reducing the risks of cardiovascular diseases and type 2 diabetes. This study aimed to investigate the vascular and metabolic effects of gut microbiota from exercise-trained donors on sedentary mice with type 2 diabetes and the potential mechanism.

METHODS: Leptin receptor-deficient diabetic (db/db) and nondiabetic (db/m[+]) mice underwent running treadmill exercise for 8 wk, during which fecal microbiota transplantation (FMT) was parallelly performed from exercise-trained to sedentary diabetic (db/db) mice. Endothelial function, glucose homeostasis, physical performance, and vascular signaling of recipient mice were assessed. Vascular and intestinal stresses, including inflammation, oxidative stress, and endoplasmic reticulum (ER) stress, were investigated. RNA sequencing analysis on mouse aortic and intestinal tissues was performed. Gut microbiota profiles of recipient mice were evaluated by metagenomic sequencing.

RESULTS: Chronic exercise improved vascular and metabolic abnormalities in donor mice. Likewise, FMT from exercised donors retarded body weight gain and slightly improved grip strength and rotarod performance in recipient mice. Exercise-associated FMT enhanced endothelial function in different arteries, suppressed vascular and intestinal stresses, and improved glucose homeostasis in recipient mice, with noted microRNA-181b upregulation in aortas and intestines. Altered gut microbiota profiles and gut-derived factors (e.g., short-chain fatty acids and glucagon-like peptide-1) as well as improved intestinal integrity shall contribute to the cardiometabolic benefits, implying a gut‒vascular connection.

CONCLUSION: This proof-of-concept study indicates that exercised microbiota confers cardiometabolic benefits on sedentary db/db mice, extending the beneficial mechanism of exercise through gut‒vascular communication. The findings open up new therapeutic opportunities for cardiometabolic diseases and shed light on the development of exercise mimetics by targeting the gut microbiota.}, } @article {pmid39827799, year = {2025}, author = {Kuroda, K and Yamamoto, K and Isshiki, R and Tokizawa, R and Shiiba, C and Hino, S and Yamano, N and Usui, E and Miyakawa, T and Miura, T and Kamino, K and Tamaki, H and Nakayama, A and Narihiro, T}, title = {Metagenomic and metatranscriptomic analyses reveal uncharted microbial constituents responsible for polyhydroxybutyrate biodegradation in coastal waters.}, journal = {Journal of hazardous materials}, volume = {487}, number = {}, pages = {137202}, doi = {10.1016/j.jhazmat.2025.137202}, pmid = {39827799}, issn = {1873-3336}, abstract = {Polyhydroxybutyrate (PHB) has attracted attention as a representative polymer for biodegradable plastics produced by microorganisms. Since information regarding the fate of PHB released into the environment is limited, it is necessary to identify them based on metagenomic information. We estimated the PHB biodegradability in coastal water samples collected from 15 near shore sites around Japan using oxygen consumption as an indicator in laboratory-scale incubation experiments and conducted 16S rRNA gene-based microbial community profiling. The PHB-biodegradation-rate was significantly positively correlated with the diversity indices of the microbial community in seawater prior to incubation, indicating that seawater with higher diversity is more advantageous for biodegradation. We identified 41 operational taxonomic units exhibiting a significant positive correlation between their abundance and PHB-degradation-rates; these included several microorganisms with hitherto unreported PHB-degrading ability. Next, we analyzed gene expression patterns over incubation time using seawater samples employing metagenomic and metatranscriptomic approaches. Fifty-seven putative extracellular PHB/PHA depolymerase genes were found in 38 metagenomic bins and their expression changed with increasing biodegradation rates, indicating that PHB released into the marine environment is subject to degradation by phylogenetically diverse PHB-depolymerase-producing bacteria. These findings should contribute to expanding the knowledge on degradation of biodegradable plastics by complex marine microbial ecosystems.}, } @article {pmid39827796, year = {2025}, author = {He, LX and He, LY and Tang, YJ and Qiao, LK and Xu, MC and Zhou, ZY and Bai, H and Zhang, M and Ying, GG}, title = {Deciphering spread of quinolone resistance in mariculture ponds: Cross-species and cross-environment transmission of resistome.}, journal = {Journal of hazardous materials}, volume = {487}, number = {}, pages = {137198}, doi = {10.1016/j.jhazmat.2025.137198}, pmid = {39827796}, issn = {1873-3336}, abstract = {Mariculture is known to harbor antibiotic resistance genes (ARGs), which can be released into marine ecosystems via oceanic farming ponds, posing a public health concern. In this study, metagenomic sequencing was used to decipher the profiles of quinolone-resistant microbiomes and the mechanisms of quinolone resistance in sediment, seawater, and fish gill samples from five mariculture ponds. Residues of both veterinary-specific (enrofloxacin and sarafloxacin) and prohibited quinolones (ofloxacin, ciprofloxacin, pefloxacin, norfloxacin, and lomefloxacin) were detected. We identified a total of 285 subtypes of ARGs across all samples. Pathogens played a crucial role in the prevalence and distribution of these ARGs. Out of the annotated 629 bacterial species, 42 were identified as pathogenic, predominantly belonging to the Proteobacteria phylum. Notably, the Acinetobacter genus was prevalent in the gills and exhibited correlations with various ARGs. The presence of the plasmid-mediated quinolone resistance (PMQR) genes in various bacterial species and the identification of sulfonamide resistance genes across different samples indicated the potential for cross-species and cross-environment transmission of ARGs. Metagenomic binning revealed that Exiguobacterium harbored five ARGs (vanA, vanB, fexA, msr(G), mefF), while Shewanella carried six ARGs (blaOXA-436, adeF, qacl, ANT (2'')-Ia, dfrA1, rsmA). Mutations in gyrA and parC contributed to quinolone resistance in these multidrug-resistant Exiguobacterium and Shewanella. Our findings suggest a potential for ARG transmission across various bacterial species and environments in mariculture. This study emphasized the risk of resistance spread within the mariculture ecosystem.}, } @article {pmid39827519, year = {2025}, author = {Lin, W and Zhao, K and Wu, Q and Xu, F and Cui, L and Lin, H and Ye, C and Yu, X}, title = {Biofilms on pipelines shape the microbiome and antibiotic resistome in drinking water.}, journal = {Water research}, volume = {274}, number = {}, pages = {123136}, doi = {10.1016/j.watres.2025.123136}, pmid = {39827519}, issn = {1879-2448}, abstract = {Biofilms in the drinking water distribution system (DWDS) provide shelter for pathogens and antibiotic resistance genes (ARGs). However, how biofilms alter the microbiome and antibiotic resistome in tap water, as well as the precise quantitative evaluation of their health risks, remains unclear. Herein, biofilm reactors supplied with municipal drinking water were operated for 120 days. Metagenomic sequencing identified significant differences in microbial compositions among the biofilms, influent, and effluents. A total of 69-305 ARGs were detected in this DWDS, and ARG abundances increased in the biofilms (0.246-1.576 cpc) and effluents (0.309-0.503 cpc) compared to the influent (0.131 cpc). Metagenomic assembly pinpointed potential pathogenic ARG hosts such as Acinetobacter, Pseudomonas, and Escherichia. The co-occurrence of ARGs and mobile genetic elements indicated potential mobility, which was further supported by transformation assays demonstrating gene transfers at a frequency of 10[-6]. Furthermore, source tracking revealed that biofilms contributed high proportions (19 %-34 %) to the ARG profiles of effluents. The ARG risk scores increased from the influent (20.39) to the effluents (39.85-55.50), with highest level (55.50) in the cast iron effluent. Overall, this study provides novel insights into the impacts of biofilm growth on the microbiome and antibiotic resistome in tap water, along with their potential health risks in the DWDS.}, } @article {pmid39827261, year = {2025}, author = {Guccione, C and Patel, L and Tomofuji, Y and McDonald, D and Gonzalez, A and Sepich-Poore, GD and Sonehara, K and Zakeri, M and Chen, Y and Dilmore, AH and Damle, N and Baranzini, SE and Hightower, G and Nakatsuji, T and Gallo, RL and Langmead, B and Okada, Y and Curtius, K and Knight, R}, title = {Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {825}, pmid = {39827261}, issn = {2041-1723}, support = {R01 CA241728/CA/NCI NIH HHS/United States ; DP1 AT010885/AT/NCCIH NIH HHS/United States ; R01 CA270235/CA/NCI NIH HHS/United States ; AGA Research Scholar Award AGA2022-13-05//AGA Research Foundation/ ; NIH/NIGMS T32GM007198//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R21 HG013433/HG/NHGRI NIH HHS/United States ; T32 GM007198/GM/NIGMS NIH HHS/United States ; CDC award 75D301-22-C-14717//U.S. Department of Health & Human Services | Centers for Disease Control and Prevention (CDC)/ ; NIH Pioneer DP1AT010885//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; U19 AG063744/AG/NIA NIH HHS/United States ; NCI U24CA248454//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; P30 DK120515/DK/NIDDK NIH HHS/United States ; P30 CA023100/CA/NCI NIH HHS/United States ; U24 CA248454/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Metagenomics/methods ; *Genome, Human ; Female ; Male ; Feces/microbiology ; High-Throughput Nucleotide Sequencing/methods ; Microbiota/genetics ; Metagenome/genetics ; Computational Biology/methods ; Skin/microbiology ; }, abstract = {As next-generation sequencing technologies produce deeper genome coverages at lower costs, there is a critical need for reliable computational host DNA removal in metagenomic data. We find that insufficient host filtration using prior human genome references can introduce false sex biases and inadvertently permit flow-through of host-specific DNA during bioinformatic analyses, which could be exploited for individual identification. To address these issues, we introduce and benchmark three host filtration methods of varying throughput, with concomitant applications across low biomass samples such as skin and high microbial biomass datasets including fecal samples. We find that these methods are important for obtaining accurate results in low biomass samples (e.g., tissue, skin). Overall, we demonstrate that rigorous host filtration is a key component of privacy-minded analyses of patient microbiomes and provide computationally efficient pipelines for accomplishing this task on large-scale datasets.}, } @article {pmid39827180, year = {2025}, author = {Van Goethem, MW and Bezuidt, OKI and Pierneef, R and Vikram, S and Hopkins, DW and Aspray, T and Hall, G and Woodborne, S and Hogg, ID and Northen, TR and Kong, W and Daffonchio, D and Cowan, DA and Van de Peer, Y and Delgado-Baquerizo, M and Makhalanyane, TP}, title = {Novel adaptive immune systems in pristine Antarctic soils.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {2368}, pmid = {39827180}, issn = {2045-2322}, support = {118981//National Research Foundation/ ; 118981//National Research Foundation/ ; 118981//National Research Foundation/ ; 118981//National Research Foundation/ ; 118981//National Research Foundation/ ; 118981//National Research Foundation/ ; 110717//South African National Antarctic Programme/ ; 110717//South African National Antarctic Programme/ ; 110717//South African National Antarctic Programme/ ; 110717//South African National Antarctic Programme/ ; 110717//South African National Antarctic Programme/ ; 110717//South African National Antarctic Programme/ ; }, mesh = {Antarctic Regions ; *Soil Microbiology ; *Phylogeny ; *CRISPR-Cas Systems ; Microbiota/genetics ; Metagenomics/methods ; Adaptive Immunity/genetics ; Genome, Bacterial ; Bacteria/genetics ; Prophages/genetics ; Metagenome ; }, abstract = {Antarctic environments are dominated by microorganisms, which are vulnerable to viral infection. Although several studies have investigated the phylogenetic repertoire of bacteria and viruses in these poly-extreme environments with freezing temperatures, high ultra violet irradiation levels, low moisture availability and hyper-oligotrophy, the evolutionary mechanisms governing microbial immunity remain poorly understood. Using genome-resolved metagenomics, we test the hypothesis that Antarctic poly-extreme high-latitude microbiomes harbour diverse adaptive immune systems. Our analysis reveals the prevalence of prophages in bacterial genomes (Bacteroidota and Verrucomicrobiota), suggesting the significance of lysogenic infection strategies in Antarctic soils. Furthermore, we demonstrate the presence of diverse CRISPR-Cas arrays, including Class 1 arrays (Types I-B, I-C, and I-E), alongside systems exhibiting novel gene architecture among their effector cas genes. Notably, a Class 2 system featuring type V variants lacks CRISPR arrays, encodes Cas1 and Cas2 adaptation module genes. Phylogenetic analysis of Cas12 effector proteins hints at divergent evolutionary histories compared to classified type V effectors and indicates that TnpB is likely the ancestor of Cas12 nucleases. Our findings suggest substantial novelty in Antarctic cas sequences, likely driven by strong selective pressures. These results underscore the role of viral infection as a key evolutionary driver shaping polar microbiomes.}, } @article {pmid39827174, year = {2025}, author = {Peng, Q and Lin, L}, title = {Comparative metagenomics reveals the metabolic flexibility of coastal prokaryotic microbiomes contributing to lignin degradation.}, journal = {Biotechnology for biofuels and bioproducts}, volume = {18}, number = {1}, pages = {9}, pmid = {39827174}, issn = {2731-3654}, support = {2023YFC3403500//National Key Research and Development Program of China/ ; 32370115//National Natural Science Foundation of China/ ; }, abstract = {Coastal wetlands are rich in terrestrial organic carbon. Recent studies suggest that microbial consortia play a role in lignin degradation in coastal wetlands, where lignin turnover rates are likely underestimated. However, the metabolic potentials of these consortia remain elusive. This greatly hinders our understanding of the global carbon cycle and the "bottom-up" design of synthetic consortia to enhance lignin conversion. Here, we developed two groups of lignin degrading consortia, L6 and L18, through the 6- and 18-month in situ lignin enrichments in the coastal East China Sea, respectively. Lignin degradation by L18 was 3.6-fold higher than L6. Using read-based analysis, 16S rRNA amplicon and metagenomic sequencing suggested that these consortia possessed varied taxonomic compositions, yet similar functional traits. Further comparative metagenomic analysis, based on metagenomic assembly, revealed that L18 harbored abundant metagenome-assembled genomes (MAGs) that encoded diverse and unique lignin degradation gene clusters (LDGCs). Importantly, anaerobic MAGs were significantly enriched in L18, highlighting the role of anaerobic lignin degradation. Furthermore, the generalist taxa, which possess metabolic flexibility, increased during the extended enrichment period, indicating the advantage of generalists in adapting to heterogenous resources. This study advances our understanding of the metabolic strategies of coastal prokaryotic consortia and lays a foundation for the design of synthetic communities for sustainable lignocellulose biorefining.}, } @article {pmid39827146, year = {2025}, author = {Angel, NZ and Sullivan, MJ and Alsheikh-Hussain, A and Fang, L and MacDonald, S and Pribyl, A and Wills, B and Tyson, GW and Hugenholtz, P and Parks, DH and Griffin, P and Wood, DLA}, title = {Metagenomics: a new frontier for routine pathology testing of gastrointestinal pathogens.}, journal = {Gut pathogens}, volume = {17}, number = {1}, pages = {4}, pmid = {39827146}, issn = {1757-4749}, abstract = {BACKGROUND: Accurate and comprehensive identification of enteropathogens, causing infectious gastroenteritis, is essential for optimal patient treatment and effective isolation processes in health care systems. Traditional diagnostic techniques are well established and optimised in low-cost formats. However, thorough testing for a wider range of causal agents is time consuming and remains limited to a subset of pathogenic organisms. Metagenomic next-generation sequencing (mNGS) allows the identification of all pathogens in a sample in a single test, without a reliance on culture or introduction of target selection bias. This study aims to determine the ability to routinely apply mNGS testing, in comparison to traditional culture or polymerase chain reaction (PCR) based tests, for the identification of causal pathogens for gastrointestinal infections.

RESULTS: The performance of mNGS, PCR and microscopy, culture and sensitivity (MCS) assays was established using 2,619 prospectively collected faecal samples from patients with symptomology indicative of infectious gastroenteritiss. Commonly experienced pathogens including Aeromonas spp, Campylobacter spp, Salmonella spp and Giardia spp, in single and co-infected patients, were used to establish test outcomes. When testing for these organisms, using the combined result from either or both PCR and MCS testing as the comparator, the mNGS assay had clinically acceptable sensitivity (89.2-100%). Further, the mNGS assay detected 14 additional enteropathogens, that were either not detected or not tested, by initial PCR/MCS testing.

CONCLUSIONS: The advantage of mNGS compared to other syndromic testing systems is the broad range of detectable targets and the ability to interrogate samples without clinician informed or assay specific bias. With the development of newer sequencing assays, it is now feasible to test for a wide range of target organisms in a sample using a single mNGS test. Overall, the mNGS based approach enabled pathogen detection that was comparable to conventional diagnostics and was shown to have the potential to be extended for the detection of many pathogens and genes of clinical interest. In conclusion, the mNGS assay offers an easy, sample to answer workflow with rapid detection of enteropathogens and has the potential to improve diagnosis, therapy and infection control precautions.}, } @article {pmid39826761, year = {2025}, author = {Zhou, Z and Liu, S and Saleem, M and Liu, F and Hu, R and Su, H and Dong, D and Luo, Z and Wu, Y and Zhang, Y and He, Z and Wang, C}, title = {Unraveling phase-dependent variations of viral community, virus-host linkage, and functional potential during manure composting process.}, journal = {Bioresource technology}, volume = {419}, number = {}, pages = {132081}, doi = {10.1016/j.biortech.2025.132081}, pmid = {39826761}, issn = {1873-2976}, mesh = {*Composting/methods ; *Manure/virology ; Bacteria/genetics ; Metagenome ; Virome ; }, abstract = {The temporal dynamics of bacterial and fungal communities significantly impact the manure composting process, yet viral communities are often underexplored. Bulk metagenomes, viromes, metatranscriptomes, and metabolomes were integrated to investigate dynamics of double-stranded DNA (dsDNA) virus and virus-host interactions throughout a 63-day composting process. A total of 473 viral operational taxonomic units (vOTUs), predominantly Caudoviricetes, showed distinct phase-dependent differentiation. In phase I (initial-mesophilic), viruses targeted Gammaproteobacteria and Firmicutes, utilizing restriction-modification (RM) systems. In phase II (thermophilic-maturing), viruses infected Alphaproteobacteria, Chloroflexi, and Planctomycetes, employing CRISPR-Cas systems. Lysogenic and lytic viruses exerting differential effects on bacterial pathogens across phases. Additionally, six types of auxiliary metabolic genes (AMGs) related to galactose and cysteine metabolisms were identified. The homologous lineages of AMGs with bacterial genes, along with the significant temporal correlation observed between virus-host-metabolite interactions, underscore the critical yet often overlooked role of viral communities in modulating microbial metabolisms and pathogenesis within composting ecosystems.}, } @article {pmid39826760, year = {2025}, author = {Zhang, Z and Zhang, C and Yang, Y and Zhang, Z and Guo, K and Zhang, X and Qin, Z and Huang, J and Li, Y}, title = {Roles of nitrite in facilitating nitrogen and sulfur conversion in the hybrid bioreactor of Sulfate-reduced ammonium oxidation and anaerobic ammonium oxidation.}, journal = {Bioresource technology}, volume = {419}, number = {}, pages = {132085}, doi = {10.1016/j.biortech.2025.132085}, pmid = {39826760}, issn = {1873-2976}, mesh = {*Bioreactors ; *Sulfur/metabolism ; *Oxidation-Reduction ; *Nitrogen/metabolism ; *Sulfates/metabolism ; Anaerobiosis ; *Nitrites/metabolism ; *Ammonium Compounds/metabolism ; Sewage/microbiology ; }, abstract = {The hybrid bioreactor combining sulfate-reducing ammonium oxidation (Sulfammox) and Anammox offered potential for simultaneous nitrogen and sulfur removal, but the removal efficiency and microbial mechanism remain unclear. This study demonstrated that in the hybrid bioreactor, the ammonium utilization rate (AUR) of Sulfammox increased by 5.42 times. The promotion of NO2[-] on nitrogen and sulfur conversion in Sulfammox could be attributed to: 1) Increasing extracellular polymers substance (EPS) accelerated the stratification of granule sludge; 2) Increasing the relative abundance of Candidatus Brocadia by 29.55 times and Candidatus Anammoxoglobus by 3.17 times; 3) Upregulating the expression of nitrification (amo, hao and nxr) and sulfur metabolism (sat, aprAB dsr and sox) genes, associated with the pathways NH4[+]→NH2OH → NO2[-]→NO3[-] and SO4[2-]→S[2-]→SO4[2-]. Moreover, Candida Brocadia sapporoensis emerged as a potential specie of Sulfammox, mediating nitrification by hao and nxr, and sulfate reduction by sat and aprAB, thereby enabling electron transfer between nitrogen and sulfur.}, } @article {pmid39826606, year = {2025}, author = {Hidalgo, KJ and Cueva, LG and Giachini, AJ and Schneider, MR and Soriano, AU and Baessa, MP and Martins, LF and Oliveira, VM}, title = {Long-term microbial functional responses in soil contaminated with biofuel/fossil fuel blends triggered by different bioremediation treatments.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {368}, number = {}, pages = {125685}, doi = {10.1016/j.envpol.2025.125685}, pmid = {39826606}, issn = {1873-6424}, abstract = {The use of biofuel blends with fossil fuels is widespread globally, raising concerns over novel contamination types in environments impacted by these mixtures. This study investigates the microbial functional in soils contaminated by biofuel and fossil fuel blends and subjected to various bioremediation treatments. Using metagenomic analysis, it was compared hydrocarbon degradation functional profiles across areas polluted with ethanol/gasoline and biodiesel/diesel blends. Results indicate that long-term natural attenuation areas exhibited distinct functional profiles compared to actively bioremediated areas. However, same hydrocarbon degradation genes were enriched across all areas, highlighting functional redundancy despite taxonomic variation in hydrocarbon-degrading microbes. Finally, several of the keystone species found were hydrocarbon degraders, such as members of the families Clostridiaceae and Comamonadaceae, representing potential targets for biostimulation in future remediation efforts. This long-term, field-scale study uniquely focuses on the functional profiles of microbial communities, offering new insights into the bioremediation of complex biofuel/fossil fuel contaminants in situ.}, } @article {pmid39826254, year = {2025}, author = {Oliveira de Farias, B and Saggioro, EM and Montenegro, KS and Magaldi, M and Oliveira Santos, HS and Pimenta, RL and Bianco, K and Clementino, MM}, title = {Degradation of plasmid-mediated resistance genes in poultry slaughterhouse wastewater employing a UV/H2O2 process: A metagenomic approach.}, journal = {Chemosphere}, volume = {372}, number = {}, pages = {144109}, doi = {10.1016/j.chemosphere.2025.144109}, pmid = {39826254}, issn = {1879-1298}, mesh = {Animals ; *Plasmids/genetics ; *Wastewater/microbiology ; *Hydrogen Peroxide ; *Poultry ; *Abattoirs ; *Ultraviolet Rays ; *Escherichia coli/genetics/drug effects ; Metagenomics ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Waste Disposal, Fluid/methods ; }, abstract = {Poultry slaughterhouse effluents are important hotspots for the spread of both antibiotic-resistant bacteria (ARBs) and antibiotic resistance genes (ARGs), contributing to the antimicrobial resistance (AMR). This study reports a novel investigation to assess the effects of UV/H2O2 treatment on the removal of metaplasmidome-mediated ARGs from poultry slaughterhouse effluents. The effluent samples were subjected at 0.005-0.15 mol L[-1] of H2O2 and pH conditions (3, 5, 7 and 9). Bacterial community (rrs 16S rRNA), Escherichia coli (uidA) antimicrobial resistance (sul1 and int1) and metagenomic plasmid DNA removal were assessed. The UV/H2O2 treatment employing H2O2 = 0.01 mol L[-1] at pH 3 resulted in decreased of several markers (uidA, sul1 and int1). A metaplasmidome indicated the persistence of Burkholderiales order. The UV/H2O2 process reduced plasmid-associated ARGs by 92.5% and 90.4% at pH 3 and 7, respectively. Persistent genes were mainly composed of genes associated with efflux pumps and resistance to beta-lactams and fluoroquinolones. These findings contribute to mitigate the spread of AMR in the agricultural sector, especially through the implementation of more efficient treatments, and reducing the use of antibiotics in livestock farming.}, } @article {pmid39826029, year = {2025}, author = {Reuben, RC and Torres, C}, title = {Integrating the milk microbiome signatures in mastitis: milk-omics and functional implications.}, journal = {World journal of microbiology & biotechnology}, volume = {41}, number = {2}, pages = {41}, pmid = {39826029}, issn = {1573-0972}, mesh = {*Milk/microbiology ; Animals ; *Microbiota ; Female ; *Metagenomics/methods ; *Mastitis/microbiology ; Mastitis, Bovine/microbiology ; Proteomics ; Humans ; Cattle ; Bacteria/classification/genetics/isolation & purification ; Dysbiosis/microbiology ; }, abstract = {Mammalian milk contains a variety of complex bioactive and nutritional components and microorganisms. These microorganisms have diverse compositions and functional roles that impact host health and disease pathophysiology, especially mastitis. The advent and use of high throughput omics technologies, including metagenomics, metatranscriptomics, metaproteomics, metametabolomics, as well as culturomics in milk microbiome studies suggest strong relationships between host phenotype and milk microbiome signatures in mastitis. While single omics studies have undoubtedly contributed to our current understanding of milk microbiome and mastitis, they often provide limited information, targeting only a single biological viewpoint which is insufficient to provide system-wide information necessary for elucidating the biological footprints and molecular mechanisms driving mastitis and milk microbiome dysbiosis. Therefore, integrating a multi-omics approach in milk microbiome research could generate new knowledge, improve the current understanding of the functional and structural signatures of the milk ecosystem, and provide insights for sustainable mastitis control and microbiome management.}, } @article {pmid39825576, year = {2025}, author = {Fouché, J and Lebre, PH and Melville, HA and Cowan, DA}, title = {The Functional and Structural Succession of Mesic-Grassland Soil Microbiomes Beneath Decomposing Large Herbivore Carcasses.}, journal = {Environmental microbiology}, volume = {27}, number = {1}, pages = {e70022}, pmid = {39825576}, issn = {1462-2920}, mesh = {*Soil Microbiology ; Animals ; *Microbiota ; *Herbivory ; *Grassland ; *Bacteria/classification/genetics/metabolism ; *RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; Carbon/metabolism ; }, abstract = {Plant detritus is abundant in grasslands but decomposes slowly and is relatively nutrient-poor, whereas animal carcasses are labile and nutrient-rich. Recent studies have demonstrated that labile nutrients from carcasses can significantly alter the long-term soil microbial function at an ecosystem scale. However, there is a paucity of knowledge on the functional and structural response and temporal scale of soil microbiomes beneath large herbivore carcasses. This study compared microbiome functions and structures of soil beneath Connochaetes taurinus (hereafter 'wildebeest') carcasses at various postmortem intervals of decomposition to matched control samples over 18 months. Microbial functions were compared by their community-level physiological profiles determined by sole-carbon substrate utilisation and structures by metagenomic sequences using 16S rRNA gene markers. Overall metabolism and metabolic diversity remained increased and functionally dissimilar to control soils throughout the experimental period, with successive sole-carbon substrate utilisation observed. Conversely, diversity was initially reduced and structurally dissimilar from the control soil but recovered within the experimental period. The study contributes to the knowledge of carcass decomposition by investigating the long-term soil microbiome dynamics resulting from large herbivore carcasses decomposing in a mesic grassland. Microbial functional succession and ecologically relevant bacterial biomarkers of soil beneath the decomposing carcasses were identified for various postmortem intervals.}, } @article {pmid39824927, year = {2025}, author = {Prasad, BVV and Atmar, RL and Ramani, S and Palzkill, T and Song, Y and Crawford, SE and Estes, MK}, title = {Norovirus replication, host interactions and vaccine advances.}, journal = {Nature reviews. Microbiology}, volume = {}, number = {}, pages = {}, pmid = {39824927}, issn = {1740-1534}, support = {P01 AI057788/AI/NIAID NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; }, abstract = {Human noroviruses (HuNoVs) are the leading cause of acute gastroenteritis worldwide in all age groups and cause significant disease and economic burden globally. To date, no approved vaccines or antiviral therapies are available to treat or prevent HuNoV illness. Several candidate vaccines are in clinical trials, although potential barriers to successful development must be overcome. Recently, significant advances have been made in understanding HuNoV biology owing to breakthroughs in virus cultivation using human intestinal tissue-derived organoid (or enteroid) cultures, advances in structural biology technology combined with epitope mapping and increased metagenomic sequencing. New and unexpected strain-specific differences in pandemic versus non-pandemic virus structures, replication properties and virus-host interactions, including host factors required for susceptibility to infection and pathogenesis, are discussed.}, } @article {pmid39824780, year = {2025}, author = {Wu, X and Peng, J and Malik, AA and Peng, Z and Luo, Y and Fan, F and Lu, Y and Wei, G and Delgado-Baquerizo, M and Liesack, W and Jiao, S}, title = {A Global Relationship Between Genome Size and Encoded Carbon Metabolic Strategies of Soil Bacteria.}, journal = {Ecology letters}, volume = {28}, number = {1}, pages = {e70064}, doi = {10.1111/ele.70064}, pmid = {39824780}, issn = {1461-0248}, support = {42122050//National Science Foundation for Excellent Young Scholars of China/ ; 42277307 & 41977038//National Natural Science Foundation of China/ ; 2021YFD1900500//National Key Research and Development Program of China/ ; }, mesh = {*Soil Microbiology ; *Carbon/metabolism ; *Bacteria/metabolism/genetics ; *Genome, Bacterial ; *Genome Size ; Gene Transfer, Horizontal ; Microbiota ; Biomass ; }, abstract = {Microbial traits are critical for carbon sequestration and degradation in terrestrial ecosystems. Yet, our understanding of the relationship between carbon metabolic strategies and genomic traits like genome size remains limited. To address this knowledge gap, we conducted a global-scale meta-analysis of 2650 genomes, integrated whole-genome sequencing data, and performed a continental-scale metagenomic field study. We found that genome size was tightly associated with an increase in the ratio between genes encoding for polysaccharide decomposition and biomass synthesis that we defined as the carbon acquisition-to-biomass yield ratio (A/Y). We also show that horizontal gene transfer played a major evolutionary role in the expanded bacterial capacities in carbon acquisition. Our continental-scale field study further revealed a significantly negative relationship between the A/Y ratio and soil organic carbon stocks. Our work demonstrates a global relationship between genome size and the encoded carbon metabolic strategies of soil bacteria across terrestrial microbiomes.}, } @article {pmid39824489, year = {2025}, author = {Yu, Z and Somasundaram, S and Yan, M}, title = {Rumen protozoa and viruses: New insights into their diversity and potential roles through omics lenses-A review.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2024-25780}, pmid = {39824489}, issn = {1525-3198}, abstract = {The rumen microbiome is essential for breaking down indigestible plant material, supplying ruminants with most of their metabolizable energy and protein. While research has primarily focused on bacteria and archaea, protozoa and viruses (phages) have only gained attention in recent years. Protozoa contribute to feed digestion and fermentation, but as predators, they regulate microbial populations by lysing large quantities of microbial cells (the primary protein source for ruminants) and influence the amount of microbial protein reaching the small intestines, along with other mechanisms of interactions. While rumen viruses (or phages) are abundant and diverse, they remain the least understood component of the rumen ecosystem. They can profoundly affect the rumen microbiome by directly lysing their hosts and reprogramming host metabolism through multiple mechanisms, including gene transfer and alteration of central carbon metabolism. Recent advances in omics technologies have deepened our understanding of these viruses, revealing their complex roles in rumen function. This review integrates current knowledge and recent discoveries from omics studies, highlighting the transformative impact of omics-based approaches. It also identifies critical knowledge gaps and outlines future research directions, including selective inhibition of rumen protozoa, development of phages as potential intervention tools to manage specific undesirable rumen microbes, and the causal impacts of rumen viruses on microbial dynamics and animal productivity.}, } @article {pmid39824262, year = {2025}, author = {Özdemir, A and Sarzhanov, F and Doğruman-Al, F and Gündoğdu, A and Nalbantoğlu, U and Yozgat, A and Yıldız, BD and Büyüktuncer, Z}, title = {Exploring the complex interplay of Blastocystis, morbid obesity, and bariatric surgery on gut microbial dynamics.}, journal = {Microbial pathogenesis}, volume = {200}, number = {}, pages = {107306}, doi = {10.1016/j.micpath.2025.107306}, pmid = {39824262}, issn = {1096-1208}, abstract = {This study examines Blastocystis dynamics in 15 individuals undergoing sleeve gastrectomy. Molecular detection involved DNA extraction, RT-PCR, and sequencing, while 16S rRNA sequencing via Illumina MiSeq analyzed the intestinal microbiome. Statistical analysis through SPSS considered a significance level of p < 0.05. Postoperative colonization of Blastocystis was observed in previously negative individuals, revealing subtypes and shifts in microbial taxa. Blastocystis-positive participants post-bariatric surgery showed a significant increase in Lachnospira, alongside higher abundances of Bacteroides, Oscillospira, Barnesiellaceae, and Rikenellaceae, with reduced Lactobacillus levels compared to Blastocystis-negative individuals. Collective analysis highlighted higher Clostridiales and RF32 in Blastocystis-positive post-surgery individuals, coupled with decreased Enterobacteriaceae. The study challenges previous notions, suggesting a complex interplay between Blastocystis, morbid obesity, and bariatric surgery. Despite limitations, including small sample sizes and absent gut microbiome diversity comparisons, this pioneering research calls for further investigation into the intricate mechanisms and implications for metabolic health. This study is registered at clinicaltrials.gov (NCT05085769).}, } @article {pmid39824110, year = {2025}, author = {Gou, Y and Liu, Y and Hu, A and Mao, G and Dong, R and Li, S and Liu, P and Liu, Y and Ji, M}, title = {Dissemination of genes associated with antibiotic resistance and bacterial virulence during ecosystem succession in two Tibetan glacier forefields.}, journal = {The Science of the total environment}, volume = {963}, number = {}, pages = {178514}, doi = {10.1016/j.scitotenv.2025.178514}, pmid = {39824110}, issn = {1879-1026}, mesh = {*Ice Cover/microbiology ; Tibet ; *Ecosystem ; *Drug Resistance, Microbial/genetics ; Virulence/genetics ; Bacteria/genetics ; Virulence Factors/genetics ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; }, abstract = {The release of pathogens and DNA from the cryosphere (glacier, permafrost, and, sea ice) has become a new threat to society and environment. Due to enhanced glacier retreat, the size of glacier forefields has greatly expanded. Herein, we used a combination of metagenomic and metatranscriptomic methods and adopted a sequence-based approach to investigate the distribution and changing patterns of virulence factor genes (VFGs) and antibiotic resistance genes (ARGs) in two glacier forefields. The forefields are separated by approximately 400 km located in the center and north of the Tibetan Plateau, which are used to demonstrate the gene dissemination capacity across short (10 m) and long (730 m) spatial transects. The results revealed a diverse range of actively transcribed VFGs and ARGs. The relative abundance of ARG reduced with ecosystem succession, while that of VFG was similar, suggesting that the ARG is under a stronger environmental selection pressure. VFGs and ARGs were dominated by those associated with adherence and vancomycin resistance, respectively. Notably, toxin production related genes were identified but a low abundance, indicating a low risk to health in glacier forefields. The dissemination risks were low for both VFGs and ARGs, which was strongly constrained by dispersal limitation. Additionally, the limited dissemination was mainly through vertical transmission, instead of horizontal transfer. In conclusion, the sequence-based approach revealed a low risk to health in recently deglaciated areas, with the risk of VFGs and ARGs being disseminated into downstream ecosystems remaining low.}, } @article {pmid39824023, year = {2025}, author = {Guo, X and Yu, P and Guo, J and Zhao, HP and Lai, CY}, title = {Viral auxiliary roles in hydrolytic and biosynthetic metabolism regulate prokaryotic microbial interactions in anaerobic digestion.}, journal = {Water research}, volume = {274}, number = {}, pages = {123140}, doi = {10.1016/j.watres.2025.123140}, pmid = {39824023}, issn = {1879-2448}, abstract = {Anaerobic digestion (AD) viruses have gained recognition as significant regulators of microbial interactions within AD communities, yet their ecological roles remain largely unexplored. In this study, we investigated the ecological roles of AD viruses in regulating microbial interactions among syntrophic hosts. We recovered 3921 diverse viral sequences from four full-scale anaerobic digesters and confirmed their widespread presence across 127 global metagenomic sampling sites (with >95 % sequence similarity), underscoring the ubiquity of prokaryotic viruses in AD-related systems. Through the construction of virus-prokaryote interactions (66.8 % validated at the transcriptional level) and analysis of viral-host transcriptional abundances, we identified significant associations between AD viruses and key processes, including hydrolysis, acidogenesis, and methanogenesis. Notably, polyvalent viruses were found to interact with both hydrolytic and fermentative communities. We further characterized viral auxiliary metabolism, hydrolytic substrate spectra, and microbial auxotrophy, showing that viruses not only could enhance the breakdown of complex substrates (e.g., cellulose, chitin, peptidoglycan) but also potentially supported the biosynthesis of essential nutrients (e.g., cysteine, methionine, heme, and cobalamin). These activities were proposed to regulate resource fluxes through alternating lysogenic and lytic cycles. Phylogenetic analysis of viral gene and horizontal gene transfer (HGT) identification suggest that AD viruses employ promiscuous infection on syntrophic hosts, potentially as an adaptive evolutionary strategy in the AD ecosystem. This study provides new insights into the ecological roles of AD viruses, highlighting their potential impact on the stability and functionality of AD systems.}, } @article {pmid39823425, year = {2025}, author = {Wang, F and Wang, X and Duan, J and Yang, S and Wei, J and Yang, S and Zheng, Q}, title = {The impact of straw and its post-pyrolysis incorporation on functional microbes and mineralization of organic carbon in yellow paddy soil.}, journal = {PloS one}, volume = {20}, number = {1}, pages = {e0314984}, pmid = {39823425}, issn = {1932-6203}, mesh = {*Soil Microbiology ; *Carbon/metabolism ; *Soil/chemistry ; *Charcoal/chemistry ; *Fertilizers ; Pyrolysis ; Oryza/growth & development/metabolism ; Carbon Cycle ; China ; }, abstract = {The impact of straw and biochar on carbon mineralization and the function of carbon cycle genes in paddy soil is important for soil nutrient management and the transformation of carbon pools. This research is based on a five-year field experiment with four treatments: no fertilizer application (CK); chemical fertilizer only (NPK); straw combined with chemical fertilizer (NPKS); and biochar combined with chemical fertilizer (NPKB). By integrating indoor mineralization culture with metagenomic approaches, we analyzed the response of organic carbon mineralization and carbon cycle genes in typical paddy soil from Guizhou Province, China, to different fertilization treatments. The result shows that the various fertilization treatments significantly increased the levels of soil organic carbon, dissolved organic carbon, microbial biomass carbon, and readily oxidizable organic carbon. The NPKS treatment increased the rate of soil organic carbon mineralization, whereas the NPKB treatment decreased it. Overall, the NPK and NPKB treatments increased the relative abundance of carbon fixation genes. The NPKS treatment increased the relative abundance of carbon degradation genes. The NPKS treatment increased the abundance of Proteobacteria, whereas the NPKB treatment decreased the abundance of Actinobacteria. Biochar after straw pyrolysis can reduce carbon loss and enhance sequestration of soil carbon, whereas straw decreases soil organic carbon stability, accelerating the transformation of soil carbon pools. Future research should encompass long-term impact assessments to comprehensively understand the enduring effects of these fertilization treatments on soil carbon mineralization and the function of carbon cycle genes.}, } @article {pmid39823339, year = {2025}, author = {van der Loos, LM and Steinhagen, S and Stock, W and Weinberger, F and D'hondt, S and Willems, A and De Clerck, O}, title = {Low functional change despite high taxonomic turnover characterizes the Ulva microbiome across a 2000-km salinity gradient.}, journal = {Science advances}, volume = {11}, number = {3}, pages = {eadr6070}, pmid = {39823339}, issn = {2375-2548}, mesh = {*Ulva/genetics ; *Salinity ; *Microbiota ; Bacteria/genetics/classification/metabolism ; Metagenome ; Metagenomics/methods ; }, abstract = {The green seaweed Ulva relies on associated bacteria for morphogenesis and is an important model to study algal-bacterial interactions. Ulva-associated bacteria exhibit high turnover across environmental gradients, leading to the hypothesis that bacteria contribute to the acclimation potential of the host. However, the functional variation of these bacteria in relation to environmental changes remains unclear. We analyzed 91 Ulva samples across a 2000-kilometer Atlantic-Baltic Sea salinity gradient using metagenomic sequencing. Metabolic reconstruction of 639 metagenome-assembled genomes revealed widespread potential for carbon, nitrogen, sulfur, and vitamin metabolism. Although the R[2] value for salinity explained 70% of taxonomic variation, it accounted only for 17% of functional variation. The limited variation was attributed to typical high-salinity bacteria exhibiting enrichment in genes for thiamine, pyridoxal, and betaine biosynthesis, which likely contribute to stress mitigation and osmotic homeostasis in response to salinity variations. Our results emphasize the importance of functional profiling to understand the seaweed holobiont and its collective response to environmental change.}, } @article {pmid39823337, year = {2025}, author = {Wu, D and Seshadri, R and Kyrpides, NC and Ivanova, NN}, title = {A metagenomic perspective on the microbial prokaryotic genome census.}, journal = {Science advances}, volume = {11}, number = {3}, pages = {eadq2166}, pmid = {39823337}, issn = {2375-2548}, mesh = {*Metagenomics/methods ; *Phylogeny ; *Archaea/genetics/classification ; *Bacteria/genetics/classification ; *Metagenome ; Humans ; Genome, Archaeal ; Genome, Bacterial ; Genome, Microbial ; }, abstract = {Following 30 years of sequencing, we assessed the phylogenetic diversity (PD) of >1.5 million microbial genomes in public databases, including metagenome-assembled genomes (MAGs) of uncultivated microbes. As compared to the vast diversity uncovered by metagenomic sequences, cultivated taxa account for a modest portion of the overall diversity, 9.73% in bacteria and 6.55% in archaea, while MAGs contribute 48.54% and 57.05%, respectively. Therefore, a substantial fraction of bacterial (41.73%) and archaeal PD (36.39%) still lacks any genomic representation. This unrepresented diversity manifests primarily at lower taxonomic ranks, exemplified by 134,966 species identified in 18,087 metagenomic samples. Our study exposes diversity hotspots in freshwater, marine subsurface, sediment, soil, and other environments, whereas human samples yielded minimal novelty within the context of existing datasets. These results offer a roadmap for future genome recovery efforts, delineating uncaptured taxa in underexplored environments and underscoring the necessity for renewed isolation and sequencing.}, } @article {pmid39823335, year = {2025}, author = {Santoro, EP and Cárdenas, A and Villela, HDM and Vilela, CLS and Ghizelini, AM and Duarte, GAS and Perna, G and Saraiva, JP and Thomas, T and Voolstra, CR and Peixoto, RS}, title = {Inherent differential microbial assemblages and functions associated with corals exhibiting different thermal phenotypes.}, journal = {Science advances}, volume = {11}, number = {3}, pages = {eadq2583}, pmid = {39823335}, issn = {2375-2548}, mesh = {*Anthozoa/microbiology/metabolism/physiology ; Animals ; *Microbiota ; *Phenotype ; Symbiosis ; Metagenomics/methods ; Bacteria/metabolism/genetics ; }, abstract = {Certain coral individuals exhibit enhanced resistance to thermal bleaching, yet the specific microbial assemblages and their roles in these phenotypes remain unclear. We compared the microbial communities of thermal bleaching-resistant (TBR) and thermal bleaching-sensitive (TBS) corals using metabarcoding and metagenomics. Our multidomain approach revealed stable distinct microbial compositions between thermal phenotypes. Notably, TBR corals were inherently enriched with microbial eukaryotes, particularly Symbiodiniaceae, linked to photosynthesis, and the biosynthesis of antibiotic and antitumor compounds and glycosylphosphatidylinositol-anchor proteins, crucial for cell wall regulation and metabolite exchange. In contrast, TBS corals were dominated by bacterial metabolic genes related to nitrogen, amino acid, and lipid metabolism. The inherent microbiome differences between TBR and TBS corals, already observed before thermal stress, point to distinct holobiont phenotypes associated to thermal bleaching resistance, offering insights into mechanisms underlying coral response to climate-induced stress.}, } @article {pmid39823322, year = {2025}, author = {Gebert, JT and Scribano, FJ and Engevik, KA and Huleatt, EM and Eledge, MR and Dorn, LE and Philip, AA and Kawagishi, T and Greenberg, HB and Patton, JT and Hyser, JM}, title = {Viroporin activity is necessary for intercellular calcium signals that contribute to viral pathogenesis.}, journal = {Science advances}, volume = {11}, number = {3}, pages = {eadq8115}, pmid = {39823322}, issn = {2375-2548}, support = {F31 DK132942/DK/NIDDK NIH HHS/United States ; S10 OD028480/OD/NIH HHS/United States ; F30 DK131828/DK/NIDDK NIH HHS/United States ; F32 DK130288/DK/NIDDK NIH HHS/United States ; R01 DK115507/DK/NIDDK NIH HHS/United States ; T32 DK007664/DK/NIDDK NIH HHS/United States ; R01 AI158683/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Rotavirus/pathogenicity ; Mice ; *Viral Nonstructural Proteins/metabolism/genetics ; *Calcium Signaling ; *Rotavirus Infections/virology/metabolism ; Calcium/metabolism ; Humans ; Viroporin Proteins/metabolism/genetics ; Glycoproteins/metabolism/genetics ; Toxins, Biological/metabolism ; Immunity, Innate ; Host-Pathogen Interactions ; Disease Models, Animal ; Cell Line ; }, abstract = {Viruses engage in a variety of processes to subvert host defenses and create an environment amenable to replication. Here, using rotavirus as a prototype, we show that calcium conductance out of the endoplasmic reticulum by the virus encoded ion channel, NSP4, induces intercellular calcium waves that extend beyond the infected cell and contribute to pathogenesis. Viruses that lack the ability to induce this signaling show diminished viral shedding and attenuated disease in a mouse model of rotavirus diarrhea. This implicates nonstructural protein 4 (NSP4) as a virulence factor and provides mechanistic insight into its mode of action. Critically, this signaling induces a transcriptional signature characteristic of interferon-independent innate immune activation, which is not observed in response to a mutant NSP4 that does not conduct calcium. This implicates calcium dysregulation as a means of pathogen recognition, a theme broadly applicable to calcium-altering pathogens beyond rotavirus.}, } @article {pmid39822514, year = {2024}, author = {Tan, L and Chen, B and Xu, Y and Wen, Z and Feng, B and Chen, D and Wang, X and Cui, X and Hu, D}, title = {Clinical value of metagenomic sequencing in system evaluation of potential donors and donor-derived infection in kidney transplantation.}, journal = {American journal of translational research}, volume = {16}, number = {12}, pages = {7707-7715}, pmid = {39822514}, issn = {1943-8141}, abstract = {OBJECTIVE: To explore the application and the clinical value of metagenomic sequencing in system evaluation of potential kidney donors, along with donor-derived infection in kidney transplantation.

METHODS: A prospective study was conducted on 40 voluntary renal donors in Ningbo Urology and Kidney Disease hospital from January 2021 to August 2023. The results of donor pathogen fed back by metagenomic sequencing were analyzed to understand the clinical significance of metagenomic sequencing in donor evaluation.

RESULTS: (1) Detection rate of pathogens. The probability of pathogens detected by traditional laboratories and metagenomic sequencing was 72.50% and 90.00%, respectively. Compared with traditional laboratory tests, metagenomic sequencing detected significantly more pathogens (P < 0.05). The percentage of co-infection of multiple pathogens detected by traditional laboratory tests (31.03%) in donors was significantly lower than that detected by metagenomic sequencing (88.89%) (P < 0.001). Traditional laboratory tests detected bacteria in 20 donors and fungi in 9 donors, but its performance on detecting viruses and mycoplasmas was limited. Metagenomic sequencing detected bacteria in 30 donors, fungi in 12 donors, viruses in 9 donors, and mycoplasmas in 9 donors. The positive rates of bacteria, viruses and mycoplasmas detected by metagenomic sequencing were significantly higher than those detected by traditional laboratory tests (P < 0.05). (2) Predictive value. The sensitivity, specificity, positive predictive value, and negative predictive value of metagenomic sequencing were 97.30%, 100.00%, 100% and 75.00%, respectively, while those of traditional laboratory tests were 78.39%, 100.00%, 100.00% and 27.27%, respectively. (3) The diagnostic efficiency of metagenomic sequencing was superior to that of traditional laboratory tests. (4) Time needed for result feedback. From specimen collection to the result feedback given to the clinician, the time required for traditional laboratory tests was longer than that for metagenomic sequencing, with significant differences (P < 0.001). In addition, the required time for traditional laboratory tests in detecting bacterial positivity was longer than that for metagenomic sequencing, with a statistically significant difference (P < 0.001).

CONCLUSION: This study probes into the application of metagenomic sequencing in the evaluation of donor pathogens, especially in negative samples detected by traditional laboratory tests. Our findings suggest that metagenomic sequencing can improve the sensitivity and specificity of diagnosis, increase the detection rate of pathogens, and minimize the turnover time.}, } @article {pmid39822451, year = {2024}, author = {Hazan, S and Bao, G and Vidal, A and Sfera, A}, title = {Gut Microbiome Alterations Following Oral Serum-Derived Bovine Immunoglobulin Administration in the Management of Dysbiosis.}, journal = {Cureus}, volume = {16}, number = {12}, pages = {e75884}, pmid = {39822451}, issn = {2168-8184}, abstract = {INTRODUCTION: Inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) are chronic disorders of the gastrointestinal tract associated with gut microbiota dysbiosis and inflammation. Serum-derived bovine immunoglobulin (SBI) is used to manage IBS and IBD and has shown prebiotic-like effects in ex vivo models. Re-establishing a healthy gut microbiome with novel treatments like SBI could help treat the underlying causes of these diseases leading to higher and sustained patient response. The objective of this study was to assess whether supplementation with SBI would improve dysbiosis in IBD and IBS patients.

METHODS: This cross-sectional, single-site study had each participant serving as their own control. Stool samples from 18 patients with either IBS or IBD were analyzed before and after SBI administration. The relative abundance of bacterial diversity was assessed using metagenomic next-generation sequencing-based profiling.

RESULTS: Species diversity statistically significantly increased for measures of richness (Shannon index) (p < 0.0082) and evenness (Gini-Simpson index) (p < 0.0017). Phylum-level changes showed a 2.7-fold increase in Actinobacteria (p = 0.0181), 0.66-fold decrease in Bacteroidetes (p = 0.0401), and 0.38-fold decrease in Proteobacteria (p = 0.0071) after treatment with SBI. At the genus level, the relative abundances showed decreased Alistipes (p = 0.0121) and decreased Bacteroides (p = 0.0108) as well as increased Bifidobacterium (p = 0.0204), compared to pre-treatment levels. At the genus level, a 1.8-fold increase of Bifidobacterium breve (p = 0.0225) occurred upon treatment with SBI.

CONCLUSION: These findings confirm the prebiotic effects of SBI and suggest an additional mechanism of action in managing IBD and IBS symptoms. SBI re-establishes homeostasis in patients with IBD and IBS by decreasing Proteobacteria and increasing Bifidobacteria and species diversity. These insights highlight the promise of new therapeutic strategies for managing IBS and IBD by targeting dysbiosis and underscore the potential of personalized treatments based on a patient's gut microbiome profile.}, } @article {pmid39821458, year = {2025}, author = {Mathew, DE and Soni, A and Dhimmar, A and Gajjar, A and Parab, AS and Phakatkar, SS and Sahastrabudhe, H and Manohar, CS and Shinde, PB and Mantri, VA}, title = {Characterization, Bio-Prospection, and Comparative Metagenomics of Bacterial Communities Revealing the Predictive Functionalities in Wild and Cultured Samples of Industrially Important Red Seaweed Gracilaria dura.}, journal = {Current microbiology}, volume = {82}, number = {2}, pages = {85}, pmid = {39821458}, issn = {1432-0991}, support = {HCP 024//Council for Scientific and Industrial Research, India/ ; }, mesh = {*Gracilaria/microbiology ; *Metagenomics ; *Bacteria/genetics/classification/isolation & purification ; *Phylogeny ; Microbiota ; Seaweed/microbiology ; Metagenome ; Proteobacteria/genetics/isolation & purification/classification ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The present study explores the microbial community associated with the industrially important red seaweed Gracilaria dura to determine the diversity and biotechnological potential through culture and metagenomics approaches. In the first part of the investigation, we isolated and characterized 75 bacterial morphotypes, with varied colony characteristics and metabolic diversity from the wild seaweed. Phylogenetic analysis identified isolates in Proteobacteria, Firmicutes, and Actinobacteria, with Bacillus sp. being prevalent. B. licheniformis and Streptomyces sp. were notable in producing important enzymes like L-asparaginase, and polysaccharide lyases. Antimicrobial activity was significant in 21% of isolates, effective against seaweed pathogens such as Vibrio and Xanthomonas. Rhodococcus pyridinivorans showed strong pyridine degradation, suggesting bioremediation potential. Several isolates exhibited phosphate solubilization and nitrate indicating the roles of bacteria as algal growth promoters and biocontrol agents. Subsequent metagenome analysis of wild and cultured samples provides insights into bacterial communities associated with G. dura, revealing their distribution and functional roles. Proteobacteria (~ 95%) dominated the communities, further bacterial groups involved in algal growth, carpospore liberation, stress resistance, biogeochemical cycles, and biomedical applications were identified. A notable difference in bacteriomes was observed between the samples, with 25% remaining stable. The samples are cultured in the lab to generate seedlings for farming and serve as germplasm storage during the monsoon season. Microbiome surveys are crucial for understanding the association of pathogens and the overall health of the seedlings, supporting successful seaweed farming. Our findings provide valuable insights into G. dura-associated microbial communities and their role in algal growth, which has aquacultural implications.}, } @article {pmid39821111, year = {2025}, author = {Mohammed, MM and Sekar, P and Al Jamal, J and Abu Taha, L and Bachir, A and Al Kawas, S}, title = {Comparative analysis of salivary antimicrobial resistance genes in dental students: A PCR and questionnaire study.}, journal = {PloS one}, volume = {20}, number = {1}, pages = {e0315450}, pmid = {39821111}, issn = {1932-6203}, mesh = {Humans ; Male ; Female ; *Saliva/microbiology ; Adult ; *Students, Dental ; Surveys and Questionnaires ; Young Adult ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Bacteria/genetics ; DNA, Bacterial/genetics ; }, abstract = {INTRODUCTION: Antimicrobial resistance (AMR) is a major global healthcare challenge, with limited treatment options due to the decline in new antibiotics. The human oral cavity, home to diverse bacteria, is crucial for maintaining oral and systemic health. Recent studies suggest that saliva may serve as a reservoir for AMR genes. However, there is a lack of research on this topic in the UAE and most Middle Eastern countries. This study investigated the presence of AMR genes in saliva from forty 5th-year dental students and forty 1st-year dental students.

MATERIALS & METHODS: Demographic and health information was collected via a 28-question structured questionnaire. Real-Time PCR was used to detect a panel of preselected AMR genes in bacterial DNA from saliva samples.

RESULTS: Participants' ages ranged from 20 to 31 years, with 41 females and 39 males. The prevalence of AMR genes varied: blaCTX-M grp 1 (29%), blaCTX-M grp 9 (85%), blaCTX-M grp 8 (39%), blaOXA-48 (69%), blaKPC-1 (6%), blaVIM (49%), DHA (53%), ACC (25%), MOX (59%), armA (83%), and rmtB (63%). There were no significant differences in AMR gene prevalence between 5th-year and 1st-year students or between male and female students.

CONCLUSION: The study revealed a high occurrence of AMR genes in the oral microbiome. Comprehensive metagenomic analysis is recommended to further evaluate the prevalence and relative abundance of these genes in the UAE population. Establishing a database for these ARGs could aid in effective future monitoring.}, } @article {pmid39820425, year = {2025}, author = {Huang, H and Cheng, Z and Wang, Y and Qiao, G and Wang, X and Yue, Y and Gao, Q and Peng, S}, title = {Multi-omics dataset of individual variations in growth performance of large yellow croaker.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {90}, pmid = {39820425}, issn = {2052-4463}, mesh = {Animals ; *Perciformes/genetics/growth & development ; *Gastrointestinal Microbiome ; Metabolomics ; Transcriptome ; Metagenomics ; China ; Multiomics ; }, abstract = {Large yellow croaker (Larimichthys crocea) is a highly economically important marine fish species in China. However, substantial individual variations in growth performance have emerged as a limiting factor for the sustainable development of the large yellow croaker industry. Gut microbiota plays a crucial role in fish growth and development by regulating metabolic processes. To explore these dynamics, we employed metagenomics, transcriptomics, and untargeted metabolomics to comprehensively analyze the structure of the intestinal microbiome and its relationship with intestinal metabolism and host gene expression. We constructed association models for "gut microbiota-differentially expressed genes", "differentially expressed genes-metabolites," and "gut microbiota-metabolites." Sequencing data and LC-MS/MS raw data have been deposited in NCBI and MetaboLights databases for public access. Our findings offer critical insights into the molecular mechanisms underlying growth variations in L. crocea and provide valuable data for the selective breeding of improved strains.}, } @article {pmid39819730, year = {2025}, author = {Liu, X and Tang, Y and Chen, H and Liu, JX and Sun, HZ}, title = {Rumen DNA virome and its relationship with feed efficiency in dairy cows.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {14}, pmid = {39819730}, issn = {2049-2618}, support = {32322077//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Rumen/virology/microbiology ; Cattle ; *Virome ; *High-Throughput Nucleotide Sequencing ; *Animal Feed/virology ; Female ; DNA, Viral/genetics ; Metagenome ; Viruses/classification/genetics/isolation & purification ; }, abstract = {BACKGROUND: The rumen harbors a diverse virome that interacts with other microorganisms, playing pivotal roles in modulating metabolic processes within the rumen environment. However, the characterization of rumen viruses remains incomplete, and their association with production traits, such as feed efficiency (FE), has not been documented. In this study, rumen fluid from 30 Chinese Holstein dairy cows was analyzed using next-generation sequencing (NGS) and High-Fidelity (HiFi) sequencing to elucidate the rumen DNA virome profile and uncover potential viral mechanisms influencing FE.

RESULTS: Integrated NGS and HiFi sequencing enhanced the length, completeness, and resolution of viral operational taxonomic units (vOTUs) compared to NGS. A total of 6,922 vOTUs were identified, including 4,716 lytic and 1,961 temperate vOTUs. At the family level, lytic viruses were predominantly from Siphoviridae (30.35%) and Schitoviridae (23.93%), while temperate viruses were primarily Siphoviridae (67.21%). The study annotated 2,382 auxiliary metabolic genes (AMGs), comprising 1,752 lytic virus-associated AMGs across 51 functional categories and 589 temperate virus-associated AMGs across 29 categories. Additionally, 2,232 vOTU-host metagenome-assembled genome (hMAG) linkages were predicted, with Firmicutes_A (33.60%) and Bacteroidota (33.24%) being the most prevalent host phyla. Significant differences in viral populations were observed between high and low FE groups across multiple taxonomic levels (P < 0.05). Two pathways were proposed to explain how rumen viruses might modulate FE: (1) Lytic viruses could lyse beneficial host bacteria linked to favorable cattle phenotypes, such as vOTU1836 targeting Ruminococcaceae, resulting in diminished organic acid production and consequently lower FE; (2) AMG-mediated host metabolism modulation, exemplified by GT2 carried by vOTU0897, which may enhance Lachnospiraceae fermentation capacity, increasing organic acid production and thereby improving FE.

CONCLUSIONS: This study constructed a comprehensive rumen DNA virome profile for Holstein dairy cows, elucidating the structural and functional complexity of rumen viruses, the roles of AMGs, and vOTU-hMAG linkages. The integration of these data offers novel insights into the mechanisms by which rumen viruses may regulate nutrient utilization, potentially influencing FE in dairy cows. Video Abstract.}, } @article {pmid39819379, year = {2025}, author = {Terzin, M and Robbins, SJ and Bell, SC and Lê Cao, KA and Gruber, RK and Frade, PR and Webster, NS and Yeoh, YK and Bourne, DG and Laffy, PW}, title = {Gene content of seawater microbes is a strong predictor of water chemistry across the Great Barrier Reef.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {11}, pmid = {39819379}, issn = {2049-2618}, mesh = {*Seawater/microbiology ; *Coral Reefs ; *Bacteria/classification/genetics/isolation & purification ; *Metagenomics/methods ; *Microbiota/genetics ; Archaea/genetics/classification ; Salinity ; Seasons ; Synechococcus/genetics/classification ; }, abstract = {BACKGROUND: Seawater microbes (bacteria and archaea) play essential roles in coral reefs by facilitating nutrient cycling, energy transfer, and overall reef ecosystem functioning. However, environmental disturbances such as degraded water quality and marine heatwaves, can impact these vital functions as seawater microbial communities experience notable shifts in composition and function when exposed to stressors. This sensitivity highlights the potential of seawater microbes to be used as indicators of reef health. Microbial indicator analysis has centered around measuring the taxonomic composition of seawater microbial communities, but this can obscure heterogeneity of gene content between taxonomically similar microbes, and thus, microbial functional genes have been hypothesized to have more scope for predictive potential, though empirical validation for this hypothesis is still pending. Using a metagenomics study framework, we establish a functional baseline of seawater microbiomes across offshore Great Barrier Reef (GBR) sites to compare the diagnostic value between taxonomic and functional information in inferring continuous physico-chemical metrics in the surrounding reef.

RESULTS: Integrating gene-centric metagenomics analyses with 17 physico-chemical variables (temperature, salinity, and particulate and dissolved nutrients) across 48 reefs revealed that associations between microbial functions and environmental parameters were twice as stable compared to taxonomy-environment associations. Distinct seasonal variations in surface water chemistry were observed, with nutrient concentrations up to threefold higher during austral summer, explained by enhanced production of particulate organic matter (POM) by photoautotrophic picocyanobacteria, primarily Synechococcus. In contrast, nutrient levels were lower in winter, and POM production was also attributed to Prochlorococcus. Additionally, heterotrophic microbes (e.g., Rhodospirillaceae, Burkholderiaceae, Flavobacteriaceae, and Rhodobacteraceae) were enriched in reefs with elevated dissolved organic carbon (DOC) and phytoplankton-derived POM, encoding functional genes related to membrane transport, sugar utilization, and energy metabolism. These microbes likely contribute to the coral reef microbial loop by capturing and recycling nutrients derived from Synechococcus and Prochlorococcus, ultimately transferring nutrients from picocyanobacterial primary producers to higher trophic levels.

CONCLUSION: This study reveals that functional information in reef-associated seawater microbes more robustly associates with physico-chemical variables than taxonomic data, highlighting the importance of incorporating microbial function in reef monitoring initiatives. Our integrative approach to mine for stable seawater microbial biomarkers can be expanded to include additional continuous metrics of reef health (e.g., benthic cover of corals and macroalgae, fish counts/biomass) and may be applicable to other large-scale reef metagenomics datasets beyond the GBR. Video Abstract.}, } @article {pmid39818083, year = {2025}, author = {Pandey, B and Pandey, AK and Bhardwaj, L and Dubey, SK}, title = {Biodegradation of acetaminophen: Current knowledge and future directions with mechanistic insights from omics.}, journal = {Chemosphere}, volume = {372}, number = {}, pages = {144096}, doi = {10.1016/j.chemosphere.2025.144096}, pmid = {39818083}, issn = {1879-1298}, mesh = {*Acetaminophen/metabolism ; *Biodegradation, Environmental ; Humans ; Metabolomics ; Environmental Pollutants/metabolism ; Genomics ; Proteomics ; }, abstract = {Acetaminophen (APAP), one of the most frequently used antipyretic and analgesic medications, has recently grown into a persistent organic contaminant of emerging concern due to its over-the-counter and widespread use. The excessive accumulation of APAP and its derivatives in various environmental matrices is threatening human health and the ecosystem. The complexity of APAP and its intermediates augments the need for adequate innovative and sustainable strategies for the remediation of contaminated environments. Bioremediation serves as an efficient, eco-friendly, cost-effective, and sustainable approach to mitigate the toxic impacts of APAP. The present review provides comprehensive insights into the ecotoxicity of APAP, its complex biodegradation pathways, and the various factors influencing biodegradation. The omics approaches viz., genomics/metagenomics, transcriptomics/metatranscriptomics, proteomics, and metabolomics have emerged as powerful tools for understanding the diverse APAP-degraders, degradation-associated genes, enzymatic pathways, and metabolites. The outcomes revealed amidases, deaminases, oxygenases, and dioxygenases as the lead enzymes mediating degradation via 4-aminophenol, hydroquinone, hydroxyquinol, 3-hydroxy-cis, cis-muconate, etc. as the major intermediates. Overall, a holistic approach with the amalgamation of omics aspects would accelerate the bioaugmentation processes and play a significant role in formulating strategies for remediating and reducing the heavy loads of acetaminophen from the environmental matrices.}, } @article {pmid39817161, year = {2024}, author = {Aththanayaka, AMMTB and Dayananda, BSWMTB and Ranasinghe, HAK and Amarasinghe, LD}, title = {Evolution of dirofilariasis diagnostic techniques from traditional morphological analysis to molecular-based techniques: a comprehensive review.}, journal = {Frontiers in parasitology}, volume = {3}, number = {}, pages = {1427449}, pmid = {39817161}, issn = {2813-2424}, abstract = {Dirofilariasis, caused by the nematode Dirofilaria spp., poses significant challenges in diagnosis due to its diverse clinical manifestations and complex life cycle. This comprehensive literature review focuses on the evolution of diagnostic methodologies, spanning from traditional morphological analyses to modern emerging techniques in the context of dirofilariasis diagnosis. The review traces the historical progression of diagnostic modalities, encompassing traditional approaches such as microscopic examination, serological tests (including ELISA and IFA), radiographic imaging, ultrasonography, and necropsy, which laid the foundation for subsequent advancements. The integration of molecular diagnostics marks a significant turning point in dirofilariasis diagnosis with the adoption of polymerase chain reaction (PCR) assays and real-time PCR (qPCR) facilitating enhanced sensitivity and specificity. Furthermore, recent strides in next-generation sequencing (NGS) technologies, including whole-genome sequencing (WGS), targeted sequencing (TS), metagenomic sequencing (MS), and RNA sequencing (transcriptome sequencing), have revolutionized the landscape of dirofilariasis diagnostics. Emerging techniques such as loop-mediated isothermal amplification (LAMP), digital PCR (dPCR), and digital microfluidics are also explored for their potential to augment diagnostic accuracy. The review addresses challenges associated with standardizing molecular protocols, tackling false positives/negatives, and discusses the advantages and limitations of each technique. By providing a comprehensive overview of dirofilariasis diagnostic strategies, from traditional to cutting-edge methods, this review aims to enhance understanding of the disease's diagnostic landscape. The insights gained have implications for improved disease management and guide future research endeavors toward refining diagnostic protocols and advancing therapeutic interventions.}, } @article {pmid39816454, year = {2025}, author = {Samanta, A and Sarma, MS}, title = {"Post-Kasai Portoenterostomy Cholangitis: What Have We Learnt So Far?".}, journal = {Journal of clinical and experimental hepatology}, volume = {15}, number = {3}, pages = {102471}, pmid = {39816454}, issn = {0973-6883}, abstract = {Post-Kasai portoenterostomy (KPE) cholangitis is one of the most common complications that has a negative impact on liver function and native liver survival. Early diagnosis and judicious empiric antimicrobial management are, therefore, important to prevent further liver damage and decompensation. However, there is no consensus regarding the standard definition of post-KPE cholangitis, and established guidelines on evaluation and management are also lacking. Metagenomic next-generation sequencing, a new molecular diagnostic technique, has the potential for detecting broader spectrum of pathogens, especially in blood culture-negative patients. Antibiotic prophylaxis to prevent cholangitis has been widely used, but questions over the choice of antibiotics, route of administration, and optimal duration remain unsettled. The available evidence on the efficacy of antibiotic prophylaxis in preventing cholangitis has shown conflicting results. This review offers a summary of the current research on advances in diagnostic approaches, including molecular techniques, and therapeutic challenges in managing intractable cholangitis.}, } @article {pmid39816362, year = {2024}, author = {Gong, Z and Ye, G and Xu, S and He, X}, title = {The characteristics of intestinal flora of Tibetan sheep in different regions at high altitude were revealed based on metagenomic technique.}, journal = {Heliyon}, volume = {10}, number = {14}, pages = {e34380}, pmid = {39816362}, issn = {2405-8440}, abstract = {Tibetan sheep play a vital role in the livelihoods of herders and are an important part of the ecosystem of the Tibetan Plateau. In order to study the characteristics of the gut microorganisms of Tibetan sheep at high altitude, this study employed macrogenomic techniques to analyse the diversity and differences in the gut flora of Tibetan sheep in different regions of high altitude and high cold. The results demonstrated that at the phylum level, the dominant phylum in the ileo-cecum segment of Tibetan sheep in Qilian, Henan and Gonghe counties was identical, namely Euryarchaeota, Firmicutes and Ascomycota. At the level of the archaebacterial genus, the dominant bacteria of the ileocecal segment of Tibetan sheep in Qilian County, Henan County and Gonghe County were Methanobrevibacter. At the level of bacterial genus, the dominant bacteria of Tibetan sheep ileocecal in Qilian County and Henan County were Bacteroides, while in Gonghe County, the dominant bacteria were Bifidobacterium. At the level of fungal genus, there were notable differences in the abundance of Tibetan sheep ileocecal genus across different regions. However, the abundance of cecum genus exhibited a more consistent trend across regions. From the perspective of functional prediction, the metabolic pathways enriched in the intestinal segments of Tibetan sheep in different regions were found to be identical, with the relative abundance of each functional gene also being essentially uniform. This result will provide a foundation for further research on the mechanism of action of gut microbes in ruminants at high altitude and alpine regions.}, } @article {pmid39816186, year = {2025}, author = {Tian, J and Wang, C and Song, P and You, Z and Jia, X and Li, X and Pang, F}, title = {Predictive Application Value of Metagenomic Next-Generation Sequencing in the Resistance of Carbapenem-Resistant Enterobacteriaceae.}, journal = {The Canadian journal of infectious diseases & medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale}, volume = {2025}, number = {}, pages = {6619016}, pmid = {39816186}, issn = {1712-9532}, abstract = {Objective: Although metagenomic next-generation sequencing (mNGS) technology has achieved notable outcomes in pathogen detection, there remains a gap in the research regarding its application in predicting the antibiotic resistance of pathogenic bacteria. This study aims to analyze the clinical application value of mNGS in predicting the resistance of carbapenem-resistant Enterobacteriaceae (CRE), as well as the relevant influencing factors, thereby providing valuable insights for clinical antimicrobial therapy. Methods: Nonduplicate isolates of Enterobacterales bacteria collected from Liaocheng People's Hospital from April 2023 to June 2024 were selected, and CRE bacteria were screened. mNGS was used to detect resistance genes, and the results were compared with those of polymerase chain reaction (PCR) to evaluate the specificity and sensitivity of gene detection. Furthermore, the performance of mNGS in identifying pathogenic microorganisms and predicting antibiotic resistance was assessed by comparing the sequencing results with those of antimicrobial susceptibility testing (AST). Results: A total of 46 isolates were confirmed as CRE through traditional AST and were further identified using the Vitek MS and Vitek 2 systems. The results indicated 27 isolates of Klebsiella pneumoniae, 14 isolates of Escherichia coli, 2 isolates of Enterobacter hormaechei, 2 isolates of Enterobacter cloacae, and 1 isolate of Citrobacter freundii. These isolates were subjected to both mNGS and PCR for detection. The calculation of the area under the receiver operating characteristic (ROC) curve demonstrated the reliability of mNGS in detecting resistance genes. Conclusion: mNGS demonstrated high sensitivity in predicting the presence of carbapenemase resistance genes in CRE, showing potential in early indication of isolate resistance information, thereby facilitating timely guidance for clinical treatment strategies.}, } @article {pmid39816160, year = {2025}, author = {Kaur, A and Russell, I and Liu, R and Holland, A and Bhandari, R and Potnis, N}, title = {Navigating Host Immunity and Concurrent Ozone Stress: Strain-Resolved Metagenomics Reveals Maintenance of Intraspecific Diversity and Genetic Variation in Xanthomonas on Pepper.}, journal = {Evolutionary applications}, volume = {18}, number = {1}, pages = {e70069}, pmid = {39816160}, issn = {1752-4571}, abstract = {The evolving threat of new pathogen variants in the face of global environmental changes poses a risk to a sustainable crop production. Predicting and responding to how climate change affects plant-pathosystems is challenging, as environment affects host-pathogen interactions from molecular to the community level, and with eco-evolutionary feedbacks at play. To address this knowledge gap, we studied short-term within-host eco-evolutionary changes in the pathogen, Xanthomonas perforans, on resistant and susceptible pepper in the open-top chambers (OTCs) under elevated Ozone (O3) conditions in a single growing season. We observed increased disease severity with greater variance on the resistant cultivar under elevated O3, yet no apparent change on the susceptible cultivar. Despite the dominance of a single pathogen genotype on the susceptible cultivar, the resistant cultivar supported a heterogeneous pathogen population. Altered O3 levels led to a strain turnover, with a relatively greater gene flux on the resistant cultivar. Both standing genetic variation and de novo parallel mutations contributed toward evolutionary modifications during adaptation onto the resistant cultivar. The presence of elevated O3, however, led to a relatively higher genetic polymorphism, with random and transient mutations. Population heterogeneity along with genetic variation, and the promotion of interdependency are mechanisms by which pathogen responds to stressors. While parallel mutations may provide clues to predicting long-term pathogen evolution and adaptive potential. And, a high proportion of transient mutations suggest less predictable pathogen evolution under climatic alterations. This knowledge is relevant as we study the risk of pathogen emergence and the mechanisms and constraints underlying long-term pathogen adaptation under climatic shifts.}, } @article {pmid39814151, year = {2025}, author = {Qiao, X and Zhang, L and Yuan, T and Wu, Y and Geng, Y and Li, Y and Li, B and Zhang, L and Zhuang, WQ and Yu, K}, title = {Mixotrophic anammox bacteria outcompete dissimilatory nitrate reduction and denitrifying bacteria in propionate-containing wastewater.}, journal = {Bioresource technology}, volume = {419}, number = {}, pages = {132077}, doi = {10.1016/j.biortech.2025.132077}, pmid = {39814151}, issn = {1873-2976}, mesh = {*Wastewater/microbiology ; *Denitrification ; *Propionates/metabolism ; *Nitrates/metabolism ; *Oxidation-Reduction ; Bacteria/metabolism ; Nitrogen/metabolism ; Ammonia/metabolism ; Anaerobiosis ; Ammonium Compounds/metabolism ; }, abstract = {Organic carbon can influence nitrogen removal during the anaerobic ammonia oxidation (anammox) process. Propionate, a common organic compound in pretreated wastewater, its impacts on mixotrophic anammox bacteria and the underlying mechanisms have not been fully elucidated. This study investigated the core metabolism and shift in behavior patterns of mixotrophic Candidatus Brocadia sapporoensis (AMXB) under long-term propionate exposure. Genome-resolved metagenomic analysis revealed that AMXB could convert nitrate generated by anammox bacteria to ammonium via the DNRA pathway, leveraging propionate as an electron donor. This recycled ammonium was then used to sustain the anammox process, thereby enhancing nitrogen removal efficiency. Notably, AMXB grew more efficiently than DNRA and denitrifying bacteria due to its more energy-efficient propionate metabolic pathway. This finding suggests that AMXB, as a mixotrophic anammox bacterium, has a competitive advantage in nitrogen metabolism in low C/N wastewater, contributing to efficient nitrogen removal.}, } @article {pmid39814067, year = {2024}, author = {Ji, J and Jung, S}, title = {PredCMB: predicting changes in microbial metabolites based on the gene-metabolite network analysis of shotgun metagenome data.}, journal = {Bioinformatics (Oxford, England)}, volume = {41}, number = {1}, pages = {}, pmid = {39814067}, issn = {1367-4811}, support = {//National Research Foundation of Korea/ ; 2022R1A2C1007345//Korea government/ ; }, mesh = {*Metagenome ; *Metagenomics/methods ; Humans ; Metabolomics/methods ; Metabolic Networks and Pathways ; Microbiota/genetics ; Inflammatory Bowel Diseases/microbiology/metabolism/genetics ; Metabolome ; Stomach Neoplasms/metabolism/microbiology/genetics ; }, abstract = {MOTIVATION: Microbiota-derived metabolites significantly impact host biology, prompting extensive research on metabolic shifts linked to the microbiota. Recent studies have explored both direct metabolite analyses and computational tools for inferring metabolic functions from microbial shotgun metagenome data. However, no existing tool specifically focuses on predicting changes in individual metabolite levels, as opposed to metabolic pathway activities, based on shotgun metagenome data. Understanding these changes is crucial for directly estimating the metabolic potential associated with microbial genomic content.

RESULTS: We introduce Predicting Changes in Microbial metaBolites (PredCMB), a novel method designed to predict alterations in individual metabolites between conditions using shotgun metagenome data and enzymatic gene-metabolite networks. PredCMB evaluates differential enzymatic gene abundance between conditions and estimates its influence on metabolite changes. To validate this approach, we applied it to two publicly available datasets comprising paired shotgun metagenomics and metabolomics data from inflammatory bowel disease cohorts and the cohort of gastrectomy for gastric cancer. Benchmark evaluations revealed that PredCMB outperformed a previous method by demonstrating higher correlations between predicted metabolite changes and experimentally measured changes. Notably, it identified metabolite classes exhibiting major alterations between conditions. By enabling the prediction of metabolite changes directly from shotgun metagenome data, PredCMB provides deeper insights into microbial metabolic dynamics than existing methods focused on pathway activity evaluation. Its potential applications include refining target metabolite selection in microbial metabolomic studies and assessing the contributions of microbial metabolites to disease pathogenesis.

Freely available to non-commercial users at https://www.sysbiolab.org/predcmb.}, } @article {pmid39813953, year = {2025}, author = {Knight, ME and Farkas, K and Wade, M and Webster, G and Pass, DA and Perry, W and Kille, P and Singer, A and Jones, DL}, title = {Wastewater-based analysis of antimicrobial resistance at UK airports: Evaluating the potential opportunities and challenges.}, journal = {Environment international}, volume = {195}, number = {}, pages = {109260}, doi = {10.1016/j.envint.2025.109260}, pmid = {39813953}, issn = {1873-6750}, mesh = {*Wastewater/microbiology ; *Airports ; United Kingdom ; Drug Resistance, Bacterial/genetics ; Aircraft ; Environmental Monitoring ; Anti-Bacterial Agents/analysis ; Metagenomics ; }, abstract = {With 40 million annual passenger flights, airports are key hubs for microbial communities from diverse geographic origins to converge, mix, and distribute. Wastewater derived from airports and aircraft represent both a potential route for the global dispersion of antimicrobial resistant (AMR) organisms and an under-utilised resource for strengthening global AMR surveillance. This study investigates the abundance and diversity of antimicrobial resistance genes (ARGs) in wastewater samples collected from airport terminals (n = 132), aircraft (n = 25), and a connected wastewater treatment plant (n = 11) at three international airports in the UK (London Heathrow, Edinburgh and Bristol). A total of 76 ARGs were quantified using high throughput qPCR (HT-qPCR) while a subset of samples (n = 30) was further analysed by metagenomic sequencing. Our findings reveal that aircraft wastewater resistomes were compositionally distinct from those observed at airport terminals, despite their similar diversity. Notably, flights originating from Asia and Africa carried a higher number of unique ARGs compared to those from Europe and North America. However, clustering of the ARG profile displayed no overall association with geography. Edinburgh terminal and pumping station wastewater had compositionally comparable resistomes to that of the connected urban wastewater treatment plant, though further research is needed to determine the relative contributions of the local population and international travellers. This study provides the first comprehensive investigation of AMR in wastewater from both aircraft and terminals across multiple international airports. Our results highlight aircraft wastewater as a potential route for cross-border AMR transmission and a valuable tool for global AMR surveillance. However, the findings also underscore the limitations and need for standardised approaches for AMR monitoring in airport environments, to effectively mitigate the global spread of AMR and enhance public health surveillance strategies.}, } @article {pmid39813930, year = {2025}, author = {Urbelienė, N and Gasparavičiūtė, R and Vaitekūnas, J and Meškienė, R and Valantinaitė, U and Kruopis, P and Gudiukaitė, R and Meškys, R}, title = {A screening method for polyester films-degrading microorganisms and enzymes.}, journal = {Journal of hazardous materials}, volume = {487}, number = {}, pages = {137177}, doi = {10.1016/j.jhazmat.2025.137177}, pmid = {39813930}, issn = {1873-3336}, abstract = {Enzymatic degradation of plastic pollution offers a promising environmentally friendly waste management strategy, however, suitable biocatalysts must be screened and developed. Traditional screening methods using soluble or solubilised polymers do not necessarily identify enzymes that are effective against solid or crystalline polymers. This study presents a simple, time-saving and cost-effective method for identifying microorganisms and enzymes capable of degrading polymeric films. The method was tested on polycaprolactone (PCL), polyethylene terephthalate (PET), polylactate (PLA) and polyhydroxybutyrate/polyhydroxyvalerate (PHB/PHV) films. It involves two steps: first, screening for PCL diol (PCLD)-degrading microorganisms on agar plates, and second, testing these microorganisms on polyester films. Using this screening method, over 100 PCLD-degrading microorganisms and 27 E. coli clones carrying genomic or metagenomic DNA fragments have been isolated. In addition, recombinant cutinases from Streptomyces scabiei and Thermobifida fusca have been tested. Approximately 66 % of the microorganisms forming halos on PCLD agar plates hydrolysed PCL and 6 % - the biaxially oriented PET film. In addition, five PLA- and four PHB/PHV-degrading esterases have been identified. The proposed method is effective for detecting both wild-type and recombinant microorganisms, as well as recombinant enzymes from in vitro transcription-translation reactions. Screening for thermostable and thermophilic enzymes, including those resistant to organic solvents or environmental inhibitors, is also easily implemented.}, } @article {pmid39813926, year = {2025}, author = {Qu, C and Tang, J and Liu, J and Wang, W and Song, F and Cheng, S and Tang, X and Tang, CJ}, title = {Quorum sensing-enhanced electron transfer in anammox consortia: A mechanism for improved resistance to variable-valence heavy metals.}, journal = {Journal of hazardous materials}, volume = {487}, number = {}, pages = {137130}, doi = {10.1016/j.jhazmat.2025.137130}, pmid = {39813926}, issn = {1873-3336}, abstract = {Quorum sensing (QS) is recognized for enhancing bacterial resistance against heavy metals by regulating the production of extracellular substances that hinder metal penetration into the intracellular environment. However, it remains unclear whether QS contributes to resistance by regulating electron transfer, thereby transforming metals from more toxic to less toxic forms. This study investigated the regulatory mechanism of acyl-homoserine lactone (AHL)-mediated QS on electron transfer under As(III) and Cr(VI) stress. Metagenomic binning results revealed that Candidatus Brocadia sinica serves as a major contributor to AHL production for regulating heavy metal resistance, while other symbiotic bacteria offer complementary resistance pathways. In these bacteria, the AHL synthesis gene htdS plays a pivotal role in QS regulation of electron transfer and heavy metal resistance. Experimental findings demonstrated that AHL increased the electron transport system activity by 19.8 %, and upregulated electron transfer gene expression by 1.1- to 6.9-fold. The enhanced electron transfer facilitated a 28.7 % increase in the transformation of As(III) to less toxic As(V) and monomethylarsonic acid, ultimately achieving efficient nitrogen removal under As(III) stress. This study expands our understanding of how QS strengthens bacterial resistance to heavy metals, offering novel strategies for enhancing nitrogen removal of anammox in heavy metal-contaminated environments.}, } @article {pmid39813892, year = {2024}, author = {Su, R and Zhao, D and Zhang, X and Zhang, H and Cheng, J and Xu, L and Wu, QL and Zeng, J}, title = {Dissimilatory nitrate reduction pathways drive high nitrous oxide emissions and nitrogen retention under the flash drought in the largest freshwater lake in China.}, journal = {Water research}, volume = {274}, number = {}, pages = {123075}, doi = {10.1016/j.watres.2024.123075}, pmid = {39813892}, issn = {1879-2448}, abstract = {Flash drought (FD) events induced by climate change may disrupt the normal hydrological regimes of floodplain lakes and affect the plant-microbe mediated dissimilatory nitrate reduction (DNR), i.e., denitrification, anammox and dissimilatory nitrate reduction to ammonium (DNRA), thus having important consequences for nitrous oxide (N2O) emissions and nitrogen (N) retention. However, the responses of the DNR pathways in the floodplain lake to the record-breaking FD in 2022 in Yangtze River of China, as well as the underlying microbial mechanisms and feedbacks to climate change remain poorly understood. Here, we collected exposed sediments and Carex cinerascens-associated soils in the littoral wetlands of Poyang Lake during 2022 FD and the dry seasons prior to and after this event. The potential DNR rates and the synergistic metabolism of microbial guilds involved in DNR were investigated using [15]N isotope pairing technique, high-throughput and metagenomic sequencing. We found that the in situ N2O fluxes in the littoral wetlands were highest during the flash drought, especially in the exposed sediments. The potential DNRA rates were highest under flash drought conditions, and DNRA dominated the DNR for both exposed sediments (80.4 %) and Carex cinerascens-associated soils (57.5 %). Nutrients (i.e., N and P) and DNRA bacterial communities played a key role in producing the extremely high N2O fluxes from exposed sediments, which could be explained by the synergistic metabolism of DNRA bacteria and denitrifiers through the exchange of the key intermediates in DNR. Therefore, the climate change-induced flash drought promoted greater nitrous oxide emissions and N retention in the littoral wetlands of Poyang Lake, producing a greater flux of greenhouse gas emissions and elevating the risk of lake eutrophication. Hence, flash droughts reinforce a positive feedback between climate change and nitrous oxide emission from these aquatic ecosystems.}, } @article {pmid39813691, year = {2024}, author = {Sumboh, JG and Agyenkwa-Mawuli, K and Schwinger, E and Donkor, IO and Akorli, J and Dwomoh, D and Ashong, Y and Osabutey, D and Ababio, FO and Nusbaum, O and Humphries, D and Cappello, M and Koram, KA and Kwofie, SK and Wilson, MD}, title = {Investigating Environmental Determinants of Hookworm Transmission using GPS Tracking and Metagenomics Technologies.}, journal = {The American journal of tropical medicine and hygiene}, volume = {}, number = {}, pages = {}, doi = {10.4269/ajtmh.24-0384}, pmid = {39813691}, issn = {1476-1645}, abstract = {To identify potential sources of hookworm infections in a Ghanaian community of endemicity that could be targeted to interrupt transmission, we tracked the movements of infected and noninfected persons to their most frequented locations. Fifty-nine participants (29 hookworm positives and 30 negatives) wore GPS trackers for 10 consecutive days. Their movement data were captured in real time and overlaid on a community grid map. Soil samples were collected and divided into two parts: one for determining the physical and chemical properties and the other for culture of helminth larvae. Soil parameters were determined using standard methods, and the number of larvae recovered from Baermann cultures (expressed as larvae per gram of soil) was recorded. We found no significant difference in the larval counts between sites of infected and noninfected participants (P = 0.59). Sandy-loam soil, pH, and effective cation exchange capacity were associated with high larval recovery counts (P <0.001), whereas nitrogen and clay content were associated with low counts (P <0.001). Genomic DNA was extracted from helminth larvae, and species were identified using metagenomic analysis of DNA sequences. The dominant helminth species identified were Panagrolaimus superbus, Parastrongyloides trichosuri, Trichuris trichiura (human whipworm), and Ancylostoma caninum (dog hookworm). Despite Necator americanus being the predominant species in the community, no larvae of this species were identified. This study, however, demonstrates the feasibility of applying molecular tools for identifying environmental factors and places associated with exposure to human and zoonotic helminths, including areas that may be targeted to break transmission in communities where infection is endemic.}, } @article {pmid39813598, year = {2025}, author = {Ren, M and Xia, Y and Pan, H and Zhou, X and Yu, M and Ji, F}, title = {Duodenal-jejunal bypass ameliorates MASLD in rats by regulating gut microbiota and bile acid metabolism through FXR pathways.}, journal = {Hepatology communications}, volume = {9}, number = {2}, pages = {}, pmid = {39813598}, issn = {2471-254X}, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Receptors, Cytoplasmic and Nuclear/metabolism ; Rats ; *Bile Acids and Salts/metabolism ; *Duodenum/surgery/metabolism/microbiology ; Male ; *Fecal Microbiota Transplantation ; Jejunum/surgery/metabolism ; Rats, Sprague-Dawley ; Disease Models, Animal ; Fatty Liver/metabolism ; Anti-Bacterial Agents/pharmacology ; Diet, High-Fat ; Gastric Bypass ; Insulin Resistance ; }, abstract = {BACKGROUND: Although bariatric and metabolic surgical methods, including duodenal-jejunal bypass (DJB), were shown to improve metabolic dysfunction-associated steatotic liver disease (MASLD) in clinical trials and experimental rodent models, their underlying mechanisms remain unclear. The present study therefore evaluated the therapeutic effects and mechanisms of action of DJB in rats with MASLD.

METHODS: Rats with MASLD were randomly assigned to undergo DJB or sham surgery. Rats were orally administered a broad-spectrum antibiotic cocktail (Abx) or underwent fecal microbiota transplantation to assess the role of gut microbiota in DJB-induced improvement of MASLD. Gut microbiota were profiled by 16S rRNA gene sequencing and metagenomic sequencing, and bile acids (BAs) were analyzed by BA-targeted metabolomics.

RESULTS: DJB alleviated hepatic steatosis and insulin resistance in rats with diet-induced MASLD. Abx depletion of bacteria abrogated the ameliorating effects of DJB on MASLD. Fecal microbiota transplantation from rats that underwent DJB improved MASLD in high-fat diet-fed recipients by reshaping the gut microbiota, especially by significantly reducing the abundance of Clostridium. This, in turn, suppressed secondary BA biosynthesis and activated the hepatic BA receptor, farnesoid X receptor. Inhibition of farnesoid X receptor attenuated the ameliorative effects of post-DJB microbiota on MASLD.

CONCLUSIONS: DJB ameliorates MASLD by regulating gut microbiota and BA metabolism through hepatic farnesoid X receptor pathways.}, } @article {pmid39812972, year = {2025}, author = {de Oliveira, RVF and Garrido, LM and Padilla, G}, title = {Decontamination of DNA sequences from a Streptomyces genome for optimal genome mining.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, pmid = {39812972}, issn = {1678-4405}, support = {001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 2015/17177-6//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; }, abstract = {Despite meticulous precautions, contamination of genomic DNA samples is not uncommon, which can significantly compromise the analysis of microorganisms' whole-genome sequencing data, thus affecting all subsequent analyses. Thanks to advancements in software and bioinformatics techniques, it is now possible to address this issue and prevent the loss of the entire dataset obtained in a contaminated whole-genome sequencing, where the DNA of another bacterium is present. In this study, it was observed that the sequencing reads from Streptomyces sp. BRB040, generated using the HiSeq System platform (Illumina Inc., San Diego, USA), were contaminated with the DNA of Bacillus licheniformis. To eliminate the contamination in Streptomyces sp. BRB040, a combination of tools available on the Galaxy platform and other web-based resources were used (MeDuSa and Blast). The contaminated reads were treated as a metagenome to isolate the genome of the contaminating organism. They were assembled using the metaSPAdes, resulting in a large scaffold of 4.187 Mb, which was identified as Bacillus licheniformis. After the identification of the contaminating organism, its genome was used as a filter to remove sequencing reads that could align using then Bowtie 2 software for this step. Once the contaminated reads were removed a new assembly was performed using the Unicycler software, yielding 117 contigs with a total size of 7.9 Mb. The completeness of this genome was assessed through BUSCO, resulting in a completeness of 95.9%. We also used an alternative tool (BBduk) to eliminate contaminated reads and the resulting assembly by Unicycler generated 85 contigs with a total size of 8.3 Mb and completeness of 99.5%. These results were better than the assembly obtained via SPAdes, which generated less complete genomes (maximum of 97.8% completeness) compared to Unicycler and which was unable to perform an adequate assembly of the data obtained from decontamination by BBduk. When compared with the uncontaminated BRB040 genome, which has a total size of 8.2 Mb and completeness of 99.8%, this pipeline revealed that the assembly performed with the decontaminated reads via BBduk presented better results, with completeness 0.3% lower than the reference. The genome mining of both genomes using antiSMASH 7.0 revealed the number of 24 Biosynthetic Gene Clusters (BGCs) for BBduk data as well as in the control assembly of the BRB040. In silico decontamination process allows the genome mining of BGCs despite the loss of nucleotides. These findings show that contamination can be effectively removed from a genome using readily available online tools, while preserving a dataset suitable for extracting valuable insights into the secondary metabolism of the target organism. This approach is particularly beneficial in scenarios where resequencing samples is not immediately feasible.}, } @article {pmid39812647, year = {2025}, author = {Selami, N and Zitouni-Haouar, FE and Zerouki, C and Aibeche, C and Draou, N and Khelil, O and Choubane, S and Maatallah, M and Madani, I and Ouenzar, K and Zemmour, A and Kerkoud, M and Mnasri, B and Moumen, B and Vriet, C and Djabeur, A}, title = {Pseudomonas retamae sp. nov., a novel endophytic bacterium with plant growth-promoting potential, isolated from root nodules of Retama monosperma in Northwestern Algeria.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {75}, number = {1}, pages = {}, doi = {10.1099/ijsem.0.006646}, pmid = {39812647}, issn = {1466-5034}, mesh = {*Pseudomonas/genetics/isolation & purification/classification ; *RNA, Ribosomal, 16S/genetics ; *Phylogeny ; Algeria ; *DNA, Bacterial/genetics ; *Nucleic Acid Hybridization ; *Endophytes/genetics/isolation & purification/classification ; *Multilocus Sequence Typing ; *Sequence Analysis, DNA ; *Bacterial Typing Techniques ; *Root Nodules, Plant/microbiology ; *Base Composition ; Genome, Bacterial ; Fatty Acids ; }, abstract = {A thorough polyphasic taxonomic study, integrating genome-based taxonomic approaches, was carried out to characterize the RB5[T] strain isolated from root nodules of Retama monosperma growing on the coastal dunes of Bousfer Beach (Oran, Algeria). The 16S rRNA gene sequence analysis revealed that strain RB5[T] had the highest similarity to Pseudomonas granadensis LMG27940[T] (98.94%) and Pseudomonas gozinkensis IzPS32d[T] (98.73%). Phylogenetic studies, including both 16S rRNA gene sequence and multilocus sequence analysis using 16S rRNA, gyrB and rpoD housekeeping genes, positioned RB5[T] in a distinct branch alongside its closest relative, P. granadensis LMG27940[T]. Phylogenomic analysis using the Bac120 marker set and Type (Strain) Genome Server confirmed the unique position of RB5[T] and its close relationship with P. granadensis LMG27940[T]. Similarly, genomic comparisons using average nucleotide identity based on blast (ANIb) and digital DNA-DNA hybridization (dDDH) revealed values of 92.85 and 59.3%, respectively, when compared with its closest relative, P. granadensis LMG27940[T]. Both values fall below the established species delimitation thresholds of 95-96% for ANIb and 70% for dDDH, providing strong genomic evidence that strain RB5[T] represents a novel species. Further average nucleotide identity comparisons with unclassified Pseudomonas spp. (384 genomes) and metagenomic-derived genomes from the Genome Taxonomy Database (GTDB) showed values between 84.27 and 89.2%, indicating that strain RB5[T] belongs to a unique evolutionary line. The genome of RB5[T], with a size of 6 311 310 bp and a G+C content of 60%, harbours several key genes associated with plant growth-promoting traits, making it a promising candidate for sustainable agriculture. Phenotypically, RB5[T] strain is an aerobic, rod-shaped, Gram-negative, non-spore-forming bacterium that is motile with a single polar flagellum. It grows under a wide range of temperature (4-42 °C) and pH (5-10) conditions and tolerates up to 6% (w/v) NaCl. The main cellular fatty acid composition of RB5[T] includes C16:0, C17:0 cyclo and the summed features 3 consisting of C16:1 ω7c/C16:1 ω6c. Based on the phylogenetic, phenotypic, chemotaxonomic and genome comparison analyses, strain RB5[T] was identified as a novel species of the genus Pseudomonas, for which the name Pseudomonas retamae sp. nov. is proposed. The type strain is RB5[T] (=DSM 117471[T]=LMG 33633[T]=CIP 112482[T]).}, } @article {pmid39812555, year = {2025}, author = {Bell, PT and Baird, T and Goddard, J and Olagoke, OS and Burke, A and Subedi, S and Davey, TR and Anderson, J and Sarovich, DS and Price, EP}, title = {Evaluating the feasibility, sensitivity, and specificity of next-generation molecular methods for pleural infection diagnosis.}, journal = {Microbiology spectrum}, volume = {13}, number = {2}, pages = {e0196024}, pmid = {39812555}, issn = {2165-0497}, support = {2021-04-CRG//Wishlist (Wishlist Inc.)/ ; AQIRF0362018//State of Queensland | Advance Queensland (AdvanceQld)/ ; AQIRF095-2020-CV//State of Queensland | Advance Queensland (AdvanceQld)/ ; }, mesh = {Humans ; Prospective Studies ; Male ; Female ; *Bacteria/genetics/isolation & purification/classification ; Aged ; Middle Aged ; *Sensitivity and Specificity ; Molecular Diagnostic Techniques/methods ; Pleural Effusion/microbiology/diagnosis ; Bacterial Infections/diagnosis/microbiology ; Feasibility Studies ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Adult ; Pleural Diseases/diagnosis/microbiology ; Aged, 80 and over ; }, abstract = {Pleural infections are common and associated with substantial healthcare costs, morbidity, and mortality. Accurate diagnosis remains challenging due to low culture positivity rates, frequent polymicrobial involvement, and non-specific diagnostic biomarkers. Here, we undertook a prospective study examining the feasibility and performance of molecular methods for diagnosing suspected pleural infection. We prospectively characterized 26 consecutive clinically suspected pleural infections, and 10 consecutive patients with suspected non-infective pleural effusions, using shotgun metagenomics, bacterial metataxonomics, quantitative PCR, and conventional culture. Molecular methods exhibited excellent diagnostic performance, with each method identifying 54% (14 out of 26) positive cases among the pleural infection cohort, versus 38% (10 out of 26) with culture. Metagenomics and bacterial metataxonomics unveiled complex polymicrobial infections that were not captured by culture. Dominant microbes included streptococci (Streptococcus intermedius, Streptococcus pyogenes, and Streptococcus mitis), Prevotella spp. (Prevotella oris and Prevotella pleuritidis), staphylococci (S. aureus and S. saprophyticus), and Klebsiella pneumoniae. However, we encountered challenges that complicated pleural infection interpretation, including: (i) uncertainties regarding microbial pathogenicity and the impact of prior antibiotic therapy on diagnostic performance; (ii) lack of a clinical diagnostic gold-standard for molecular performance comparisons; (iii) potential microbial contamination during specimen collection or processing; and (iv) difficulties distinguishing background microbial noise from true microbial signal in low-biomass specimens. This pilot study demonstrates the potential utility and value of molecular methods in diagnosing pleural infection and highlights key concepts and challenges that should be addressed when designing larger prospective trials.IMPORTANCEConfident pleural infection diagnosis is often challenging due to low culture positivity rates, frequent polymicrobial involvement, and non-specific diagnostic biomarkers. Limitations of conventional diagnostic tests result in prolonged and inappropriately broad-spectrum antimicrobial use, encouraging antimicrobial resistance and leading to avoidable adverse effects. Here, we demonstrate the feasibility, utility, and challenges associated with the use of culture-independent molecular techniques for accurate pleural infection diagnosis in a real-world clinical setting. These data will help to inform the design of larger prospective clinical trials and identify potential obstacles to be overcome before next-generation sequencing technologies can be integrated into routine clinical practice.}, } @article {pmid39812347, year = {2025}, author = {Gustafson, KL and Rodriguez, TR and McAdams, ZL and Coghill, LM and Ericsson, AC and Franklin, CL}, title = {Failure of colonization following gut microbiota transfer exacerbates DSS-induced colitis.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2447815}, pmid = {39812347}, issn = {1949-0984}, support = {T32 GM008396/GM/NIGMS NIH HHS/United States ; T32 OD011126/OD/NIH HHS/United States ; U42 OD010918/OD/NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Colitis/microbiology/chemically induced/pathology ; *Dextran Sulfate ; Mice ; *Disease Models, Animal ; *Mice, Inbred C57BL ; *Fecal Microbiota Transplantation ; Bacteria/classification/isolation & purification/genetics/metabolism ; Female ; Specific Pathogen-Free Organisms ; Feces/microbiology ; Inflammatory Bowel Diseases/microbiology ; Male ; }, abstract = {To study the impact of differing specific pathogen-free gut microbiomes (GMs) on a murine model of inflammatory bowel disease, selected GMs were transferred using embryo transfer (ET), cross-fostering (CF), and co-housing (CH). Prior work showed that the GM transfer method and the microbial composition of donor and recipient GMs can influence microbial colonization and disease phenotypes in dextran sodium sulfate-induced colitis. When a low richness GM was transferred to a recipient with a high richness GM via CH, the donor GM failed to successfully colonize, and a more severe disease phenotype resulted when compared to ET or CF, where colonization was successful. By comparing CH and gastric gavage for fecal material transfer, we isolated the microbial component of this effect and determined that differences in disease severity and survival were associated with microbial factors rather than the transfer method itself. Mice receiving a low richness GM via CH and gastric gavage exhibited greater disease severity and higher expression of pro-inflammatory immune mediators compared to those receiving a high richness GM. This study provides valuable insights into the role of GM composition and colonization in disease modulation.}, } @article {pmid39810418, year = {2025}, author = {Yu, H and Liu, S and Zhang, D and Hu, R and Chen, P and Liu, H and Zhou, Q and Tan, W and Hu, N and He, Z and Ding, D and Yan, Q}, title = {Specific Enrichment of arsM-Carrying Microorganisms with Nitrogen Fixation and Dissimilatory Nitrate Reduction Function Enhances Arsenic Methylation in Plant Rhizosphere Soil.}, journal = {Environmental science & technology}, volume = {59}, number = {3}, pages = {1647-1660}, doi = {10.1021/acs.est.4c10242}, pmid = {39810418}, issn = {1520-5851}, mesh = {*Arsenic/metabolism ; *Rhizosphere ; *Nitrogen Fixation ; *Soil Microbiology ; *Nitrates/metabolism ; Methylation ; Soil Pollutants/metabolism ; Soil/chemistry ; }, abstract = {Plants can recruit microorganisms to enhance soil arsenic (As) removal and nitrogen (N) turnover, but how microbial As methylation in the rhizosphere is affected by N biotransformation is not well understood. Here, we used acetylene reduction assay, arsM gene amplicon, and metagenome sequencing to evaluate the influence of N biotransformation on As methylation in the rhizosphere of Vetiveria zizanioides, a potential As hyperaccumulator. V. zizanioides was grown in mining soils (MS) and artificial As-contaminated soils (AS) over two generations in a controlled pot experiment. Results showed that the content of dimethylarsinic acid in the rhizosphere was significantly positively correlated with the rate of N fixation and the activity of nitrite reductase. The As-methylating species (e.g., Flavisolibacter and Paraflavitalea) were significantly enriched in the root-associated compartments in the second generation of MS and AS. Notably, higher abundance of genes involved in N fixation (nifD, nifK) and dissimilatory nitrate reduction to ammonium (narG/H, nirB/D/K/S) was detected in the second generation of MS than in the first generation. The metabolic pathway analysis further demonstrated that N fixing-stimulative and DNRA-stimulative As-methylating species could provide ammonium to enhance the synthesis of S-adenosyl-l-methionine, serving as methyl donors for soil As methylation. This study highlights two important N conversion-stimulative As-methylating pathways and has important implications for enhancing phytoremediation in As-contaminated soils.}, } @article {pmid39810263, year = {2025}, author = {Nychas, E and Marfil-Sánchez, A and Chen, X and Mirhakkak, M and Li, H and Jia, W and Xu, A and Nielsen, HB and Nieuwdorp, M and Loomba, R and Ni, Y and Panagiotou, G}, title = {Discovery of robust and highly specific microbiome signatures of non-alcoholic fatty liver disease.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {10}, pmid = {39810263}, issn = {2049-2618}, mesh = {*Non-alcoholic Fatty Liver Disease/microbiology ; Humans ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; Middle Aged ; Bacteria/classification/genetics/isolation & purification ; Machine Learning ; Metagenomics/methods ; Adult ; Obesity/microbiology ; Metagenome ; }, abstract = {BACKGROUND: The pathogenesis of non-alcoholic fatty liver disease (NAFLD) with a global prevalence of 30% is multifactorial and the involvement of gut bacteria has been recently proposed. However, finding robust bacterial signatures of NAFLD has been a great challenge, mainly due to its co-occurrence with other metabolic diseases.

RESULTS: Here, we collected public metagenomic data and integrated the taxonomy profiles with in silico generated community metabolic outputs, and detailed clinical data, of 1206 Chinese subjects w/wo metabolic diseases, including NAFLD (obese and lean), obesity, T2D, hypertension, and atherosclerosis. We identified highly specific microbiome signatures through building accurate machine learning models (accuracy = 0.845-0.917) for NAFLD with high portability (generalizable) and low prediction rate (specific) when applied to other metabolic diseases, as well as through a community approach involving differential co-abundance ecological networks. Moreover, using these signatures coupled with further mediation analysis and metabolic dependency modeling, we propose synergistic defined microbial consortia associated with NAFLD phenotype in overweight and lean individuals, respectively.

CONCLUSION: Our study reveals robust and highly specific NAFLD signatures and offers a more realistic microbiome-therapeutics approach over individual species for this complex disease. Video Abstract.}, } @article {pmid39810145, year = {2025}, author = {Xiang, H and Zhang, L and Yang, L and Cai, M and Ma, Y and Zhang, Y}, title = {Asymptomatic lung abscess of aspergillus in a female without previous lung diseases or immunocompromise: a case report.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {66}, pmid = {39810145}, issn = {1471-2334}, support = {BRWEP2024W042180101//Beijing Research Ward Excellence Program/ ; }, mesh = {Humans ; Female ; Adult ; *Lung Abscess/microbiology/drug therapy/diagnosis ; *Aspergillus/isolation & purification/genetics ; *Pulmonary Aspergillosis/diagnosis/microbiology/drug therapy ; *Antifungal Agents/therapeutic use ; Tomography, X-Ray Computed ; Voriconazole/therapeutic use ; Lung/microbiology/diagnostic imaging/pathology ; }, abstract = {BACKGROUND: Chronic pulmonary abscess usually results from bacterial or mycobacterium infection, but rarely from aspergillosis. Chronic pulmonary aspergillosis is usually found in a person with structural lung disease or immunocompromise. Here, we report a case of chronic lung abscess of aspergillosis without immunocompromise, structural lung diseases or even clinical symptoms.

CASE PRESENTATION: A 43-year-old female was found a mass shadow with central liquid anechoic area in the apical posterior segment of the left upper lung lobe by chest computerized tomography for 1 month, but had no any systematic or respiratory complaints. The percutaneous abscess puncture was performed and 30 milliliters of yellow purulent fluid were aspirated from the liquid anechoic area. Then Aspergillus terreus was detected by both fluid culture and metagenomics next-generation sequencing. Interestingly, this patient had no history of tuberculosis or chronic pulmonary diseases. Other immunocompromised conditions were also denied through history inquest and laboratory tests. Ultimately, the catheterization and drainage of the lung abscess and 6 months of antifungal therapy with standard dose of voriconazole brought the woman a favorable outcome.

CONCLUSION: Aspergillus lung abscess can occasionally occur in a person without pre-existent lung cavity and immune suppression, which is prone to misdiagnosis because of the rarity and the symptom-free.}, } @article {pmid39809974, year = {2025}, author = {Jia, W and Chan, JC and Wong, TY and Fisher, EB}, title = {Diabetes in China: epidemiology, pathophysiology and multi-omics.}, journal = {Nature metabolism}, volume = {7}, number = {1}, pages = {16-34}, pmid = {39809974}, issn = {2522-5812}, mesh = {Humans ; China/epidemiology ; *Diabetes Mellitus/epidemiology ; Risk Factors ; Prevalence ; Metabolomics ; Multiomics ; }, abstract = {Although diabetes is now a global epidemic, China has the highest number of affected people, presenting profound public health and socioeconomic challenges. In China, rapid ecological and lifestyle shifts have dramatically altered diabetes epidemiology and risk factors. In this Review, we summarize the epidemiological trends and the impact of traditional and emerging risk factors on Chinese diabetes prevalence. We also explore recent genetic, metagenomic and metabolomic studies of diabetes in Chinese, highlighting their role in pathogenesis and clinical management. Although heterogeneity across these multidimensional areas poses major analytic challenges in classifying patterns or features, they have also provided an opportunity to increase the accuracy and specificity of diagnosis for personalized treatment and prevention. National strategies and ongoing research are essential for improving diabetes detection, prevention and control, and for personalizing care to alleviate societal impacts and maintain quality of life.}, } @article {pmid39809928, year = {2025}, author = {Lai, LM and Chen, QG and Liu, Y and Zhao, R and Cao, ML and Yuan, L}, title = {The value of metagenomic next-generation sequencing in the diagnosis of fever of unknown origin.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {1963}, pmid = {39809928}, issn = {2045-2322}, support = {20242BAB20430//the Natural Science Foundation of Jiangxi Province/ ; 2021B723//the Science and Technology Program of Jiangxi Traditional Chinese Medicine/ ; }, mesh = {Humans ; *Fever of Unknown Origin/diagnosis/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; Male ; *Metagenomics/methods ; Female ; Retrospective Studies ; Middle Aged ; Adult ; Aged ; Sensitivity and Specificity ; Young Adult ; Adolescent ; Metagenome ; Aged, 80 and over ; }, abstract = {Fever of unknown origin (FUO) caused by infection is a disease state characterized by complex pathogens and remains a diagnostic dilemma. Metagenomic next-generation sequencing (mNGS) technology is a promising diagnostic tool for identifying pathogenic microbes of FUO caused by infection. Little is known about the clinical impact of mNGS in the etiological diagnosis of FUO. This study focuses on the value of mNGS in the etiologic diagnosis of FUO by diagnostic performance, further clarifying the value of mNGS in clinical management. In a single-centre retrospective cohort study, 263 FUO patients who underwent both mNGS and culture at the First Affiliated Hospital of Nanchang University were enrolled from December 2020 to February 2023. The sensitivity and specificity of culture and mNGS were analyzed based on the final clinical diagnosis as the gold standard to assess the diagnostic value of mNGS in FUO cases. Among the 263 patients, 69.96%(184/263) cases were diagnosed as infectious diseases, of which lower respiratory tract infections were the most common, accounting for 53.26%(98/184). 30.04%(79/263) cases had a diagnosis of non-infectious disease. From these cases, mNGS identified 150 true-positive cases, 21 false-positive cases, 58 true-negative cases, and 34 false-negative cases. The sensitivity of mNGS in infection diagnosis was much higher than that of culture [81.52%(150/184) vs. 47.28%(87/184)], but the specificity was the opposite[73.42%(58/79) vs. 84.81%(67/79)]. mNGS had a receiver operating characteristic (ROC) curve of 0.775 for infectious disease, which was significantly higher than that of culture (0.661, P < 0.05). mNGS detection revealed that bacteria were the most commonly identified potential pathogens. The top causative pathogens identified were Acinetobacter baumannii. Of the 263 patients with FUO, clinical management of 48.67% (128/263) patients was positively affected by mNGS, and 51.33% (135/263) patients were not affected by mNGS(P = 0.1074). To sum up, infectious diseases are the principal cause of FUO. mNGS could significantly improve the detected pathogen spectrum of FUO caused by infection. However, the FUO disease spectrum is relatively broad, including a large number of non-infectious diseases. Therefore, Further investigation is warranted into the specific clinical scenarios for which mNGS may offer the greatest clinical diagnostic value.}, } @article {pmid39809768, year = {2025}, author = {Fahur Bottino, G and Bonham, KS and Patel, F and McCann, S and Zieff, M and Naspolini, N and Ho, D and Portlock, T and Joos, R and Midani, FS and Schüroff, P and Das, A and Shennon, I and Wilson, BC and O'Sullivan, JM and Britton, RA and Murray, DM and Kiely, ME and Taddei, CR and Beltrão-Braga, PCB and Campos, AC and Polanczyk, GV and Huttenhower, C and Donald, KA and Klepac-Ceraj, V}, title = {Early life microbial succession in the gut follows common patterns in humans across the globe.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {660}, pmid = {39809768}, issn = {2041-1723}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Infant ; *Feces/microbiology ; Female ; Metagenome ; Male ; Bifidobacterium/genetics/isolation & purification ; Infant, Newborn ; Faecalibacterium prausnitzii/genetics ; Child Development ; }, abstract = {Characterizing the dynamics of microbial community succession in the infant gut microbiome is crucial for understanding child health and development, but no normative model currently exists. Here, we estimate child age using gut microbial taxonomic relative abundances from metagenomes, with high temporal resolution (±3 months) for the first 1.5 years of life. Using 3154 samples from 1827 infants across 12 countries, we trained a random forest model, achieving a root mean square error of 2.56 months. We identified key taxonomic predictors of age, including declines in Bifidobacterium spp. and increases in Faecalibacterium prausnitzii and Lachnospiraceae. Microbial succession patterns are conserved across infants from diverse human populations, suggesting universal developmental trajectories. Functional analysis confirmed trends in key microbial genes involved in feeding transitions and dietary exposures. This model provides a normative benchmark of "microbiome age" for assessing early gut maturation that may be used alongside other measures of child development.}, } @article {pmid39809763, year = {2025}, author = {Armetta, J and Li, SS and Vaaben, TH and Vazquez-Uribe, R and Sommer, MOA}, title = {Metagenome-guided culturomics for the targeted enrichment of gut microbes.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {663}, pmid = {39809763}, issn = {2041-1723}, support = {NNF20CC0035580//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF17CO0028232//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20CC0035580//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF17CO0028232//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20CC0035580//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF17CO0028232//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20CC0035580//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF17CO0028232//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; grant agreement No. 813781//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; grant agreement No. 813781//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; no. ALTF 137-2018//European Molecular Biology Organization (EMBO)/ ; no. GNT1166180//Department of Health | National Health and Medical Research Council (NHMRC)/ ; }, mesh = {*Gastrointestinal Microbiome/genetics/drug effects ; Humans ; *Metagenome ; *Phylogeny ; Culture Media/chemistry ; Bacteria/genetics/metabolism/classification ; Feces/microbiology ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; Caffeine ; }, abstract = {The gut microbiome significantly impacts human health, yet cultivation challenges hinder its exploration. Here, we combine deep whole-metagenome sequencing with culturomics to selectively enrich for taxa and functional capabilities of interest. Using a modified commercial base medium, 50 growth modifications were evaluated, spanning antibiotics, physico-chemical conditions, and bioactive compounds. Whole-metagenome sequencing identified medium additives, like caffeine, that enhance taxa often associated with healthier subjects (e.g., Lachnospiraceae, Oscillospiraceae, Ruminococcaceae). We also explore the impact of modifications on the composition of cultured communities and establish a link between medium preference and microbial phylogeny. Leveraging these insights, we demonstrate that combinations of media modifications can further enhance the targeted enrichment of taxa and metabolic functions, such as Collinsella aerofaciens, or strains harboring biochemical pathways involved in dopamine metabolism. This streamlined, scalable approach unlocks the potential for selective enrichment, advancing microbiome research by understanding the impact of different cultivation parameters on gut microbes.}, } @article {pmid39809266, year = {2025}, author = {Wang, D and Jiang, Y and Jiang, J and Pan, Y and Yang, Y and Fang, X and Liang, L and Li, H and Dong, Z and Fan, S and Ma, D and Zhang, XS and Li, H and He, Y and Li, N}, title = {Gut microbial GABA imbalance emerges as a metabolic signature in mild autism spectrum disorder linked to overrepresented Escherichia.}, journal = {Cell reports. Medicine}, volume = {6}, number = {1}, pages = {101919}, doi = {10.1016/j.xcrm.2024.101919}, pmid = {39809266}, issn = {2666-3791}, mesh = {*Gastrointestinal Microbiome/genetics ; *Autism Spectrum Disorder/metabolism/microbiology/genetics ; *gamma-Aminobutyric Acid/metabolism ; Humans ; Animals ; Female ; Male ; Mice ; Child ; Child, Preschool ; Metabolomics/methods ; RNA, Ribosomal, 16S/genetics ; Escherichia/metabolism/genetics ; Feces/microbiology ; Glutamic Acid/metabolism ; Mice, Inbred C57BL ; Escherichia coli/genetics/metabolism ; Metabolome ; }, abstract = {Gut microbiota (GM) alterations have been implicated in autism spectrum disorder (ASD), yet the specific functional architecture remains elusive. Here, employing multi-omics approaches, we investigate stool samples from two distinct cohorts comprising 203 children with mild ASD or typical development. In our screening cohort, regression-based analysis for metabolomic profiling identifies an elevated γ-aminobutyric acid (GABA) to glutamate (Glu) ratio as a metabolic signature of ASD, independent of age and gender. In the validating cohort, we affirm the GABA/Glu ratio as an ASD diagnostic indicator after adjusting for geography, age, gender, and specific food-consuming frequency. Integrated analysis of metabolomics, 16S rRNA sequencing, and metagenomics reveals a correlation between overrepresented Escherichia and disrupted GABA metabolism. Furthermore, we observe social behavioral impairments in weaning mice transplanted with E. coli, suggesting a potential link to ASD symptomatology. Collectively, these findings provide insights into potential diagnostic and therapeutic strategies aimed at evaluating and restoring gut microbial neurotransmitter homeostasis.}, } @article {pmid39809157, year = {2024}, author = {Xu, H and Liu, Y and Niu, H and Cai, X and Zhan, F}, title = {Characteristics, symptoms, and outcomes of patients with Vibrio vulnificus infection in Hainan, China: A retrospective study.}, journal = {Medicine}, volume = {103}, number = {47}, pages = {e40706}, pmid = {39809157}, issn = {1536-5964}, mesh = {Humans ; Male ; *Vibrio Infections/epidemiology/diagnosis/therapy ; Female ; Retrospective Studies ; Middle Aged ; China/epidemiology ; Aged ; *Vibrio vulnificus/isolation & purification ; Adult ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {With global temperatures on the rise and an expanding seafood trade, infections by Vibrio vulnificus, particularly in warm coastal areas like Hainan, China, are increasingly prevalent. These bacteria are notorious for causing grave infections with a high fatality rate. This study aims to dissect the clinical features, laboratory findings, treatment modalities, and patient outcomes associated with V vulnificus infections in Hainan Province. The medical records and clinical data of intensive care unit patients from Hainan General Hospital were retrospectively analyzed. Conventional sequencing and metagenomic sequencing were used to identify V vulnificus. The study involved 10 patients (9 males and 1 female) with a median age of 60.5 years, predominantly fishermen, with infections mainly occurring between May and October. Of note, 2 cases were linked to plant-related injuries. The typical manifestations included fever, pain, swelling, hemorrhagic vesicles, septic shock, and multi-organ dysfunction. It was found that delayed hospital admissions were associated with elevated Sequential Organ Failure Assessment and Acute Physiology and Chronic Health Evaluation II scores and increased mortality. Laboratory results indicated a robust inflammatory response, and interventions comprised antibiotic therapy and surgical procedures. A mortality rate of 50% was recorded. Vigilance for V vulnificus infections is crucial in coastal locales. The study endorses immediate and assertive treatment strategies, including the use of targeted antibiotics and surgical interventions, to enhance patient survival rates. A call for heightened awareness, intensified surveillance, and expanded research is essential to combat this life-threatening condition.}, } @article {pmid39808116, year = {2024}, author = {Zárate, A and Díaz-González, L and Taboada, B}, title = {VirDetect-AI: a residual and convolutional neural network-based metagenomic tool for eukaryotic viral protein identification.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {1}, pages = {}, pmid = {39808116}, issn = {1477-4054}, mesh = {*Metagenomics/methods ; *Neural Networks, Computer ; *Viral Proteins/genetics ; Humans ; Viruses/genetics/classification ; Genome, Viral ; Animals ; Eukaryota/genetics ; Artificial Intelligence ; Metagenome ; Algorithms ; }, abstract = {This study addresses the challenging task of identifying viruses within metagenomic data, which encompasses a broad array of biological samples, including animal reservoirs, environmental sources, and the human body. Traditional methods for virus identification often face limitations due to the diversity and rapid evolution of viral genomes. In response, recent efforts have focused on leveraging artificial intelligence (AI) techniques to enhance accuracy and efficiency in virus detection. However, existing AI-based approaches are primarily binary classifiers, lacking specificity in identifying viral types and reliant on nucleotide sequences. To address these limitations, VirDetect-AI, a novel tool specifically designed for the identification of eukaryotic viruses within metagenomic datasets, is introduced. The VirDetect-AI model employs a combination of convolutional neural networks and residual neural networks to effectively extract hierarchical features and detailed patterns from complex amino acid genomic data. The results demonstrated that the model has outstanding results in all metrics, with a sensitivity of 0.97, a precision of 0.98, and an F1-score of 0.98. VirDetect-AI improves our comprehension of viral ecology and can accurately classify metagenomic sequences into 980 viral protein classes, hence enabling the identification of new viruses. These classes encompass an extensive array of viral genera and families, as well as protein functions and hosts.}, } @article {pmid39807898, year = {2025}, author = {Forry, SP and Servetas, SL and Dootz, JN and Hunter, ME and Kralj, JG and Filliben, JJ and Jackson, SA}, title = {A sensitivity analysis of methodological variables associated with microbiome measurements.}, journal = {Microbiology spectrum}, volume = {13}, number = {2}, pages = {e0069624}, pmid = {39807898}, issn = {2165-0497}, mesh = {*Metagenomics/methods ; *Feces/microbiology ; Humans ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification ; Sequence Analysis, DNA/methods ; Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; DNA, Bacterial/genetics ; }, abstract = {The experimental methods employed during metagenomic sequencing analyses of microbiome samples significantly impact the resulting data and typically vary substantially between laboratories. In this study, a full factorial experimental design was used to compare the effects of a select set of methodological choices (sample, operator, lot, extraction kit, variable region, and reference database) on the analysis of biologically diverse stool samples. For each parameter investigated, a main effect was calculated that allowed direct comparison both between methodological choices (bias effects) and between samples (real biological differences). Overall, methodological bias was found to be similar in magnitude to real biological differences while also exhibiting significant variations between individual taxa, even between closely related genera. The quantified method biases were then used to computationally improve the comparability of data sets collected under substantially different protocols. This investigation demonstrates a framework for quantitatively assessing methodological choices that could be routinely performed by individual laboratories to better understand their metagenomic sequencing workflows and to improve the scope of the datasets they produce.IMPORTANCEMethod-specific bias is a well-recognized challenge in metagenomic sequencing characterization of microbiome samples, but rigorous bias quantification is challenging. This report details a full factorial exploration of 48 experimental protocols by systematically varying microbiome sample, iterations of material production, laboratory personnel, DNA extraction kit, marker gene selection, and reference databases. Quantification of the biases associated with each parameter revealed similar magnitudes of variation arising from real biological differences and from varied analysis procedures. Furthermore, these measurement biases varied substantially with taxa, even between closely related genera. However, computational correction of method bias using a reference material was demonstrated that significantly harmonized metagenomic sequencing results collected using different analysis protocols.}, } @article {pmid39807869, year = {2025}, author = {Sáenz, JS and Rios-Galicia, B and Seifert, J}, title = {Antiviral defense systems in the rumen microbiome.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0152124}, doi = {10.1128/msystems.01521-24}, pmid = {39807869}, issn = {2379-5077}, abstract = {The continuous interaction between phages and their respective hosts has resulted in the evolution of multiple bacterial immune mechanisms. However, the diversity and prevalence of antiviral defense systems in complex communities are still unknown. We therefore investigated the diversity and abundance of viral defense systems in 3,038 high-quality bacterial and archaeal genomes from the rumen. In total, 14,241 defense systems and 31,948 antiviral-related genes were identified. Those genes represented 114 unique system types grouped into 49 families. We observed a high prevalence of defense systems in the genomes. However, the number of defense systems, defense system families, and system density varied widely from genome to genome. Additionally, the number of defense system per genome correlated positively with the number of defense system families and the genome size. Restriction modification, Abi, and cas system families were the most common, but many rare systems were present in only 1% of the genomes. Antiviral defense systems are prevalent and diverse in the rumen, but only a few are dominant, indicating that most systems are rarely present. However, the collection of systems throughout the rumen may represent a pool of mechanisms that can be shared by different members of the community and modulate the phage-host interaction.IMPORTANCEPhages may act antagonistically at the cell level but have a mutualistic interaction at the microbiome level. This interaction shapes the structure of microbial communities and is mainly driven by the defense mechanism. However, the diversity of such mechanism is larger than previously thought. Because of that, we described the abundance and diversity of the antiviral defense system of a collection of genomes, metagenome-assembled genomes (MAGs) and isolates, from the rumen. While defense mechanisms seem to be prevalent among bacteria and archaea, only a few were common. This suggests that most of these defense mechanisms are not present in many rumen microbes but could be shared among different members of the microbial community. This is consistent with the "pan-immune system" model, which appears to be common across different environments.}, } @article {pmid39807864, year = {2025}, author = {Nakatsu, G and Ko, D and Michaud, M and Franzosa, EA and Morgan, XC and Huttenhower, C and Garrett, WS}, title = {Virulence factor discovery identifies associations between the Fic gene family and Fap2[+] fusobacteria in colorectal cancer microbiomes.}, journal = {mBio}, volume = {16}, number = {2}, pages = {e0373224}, pmid = {39807864}, issn = {2150-7511}, support = {R01 CA154426/CA/NCI NIH HHS/United States ; //Cancer Research UK (CRUK)/ ; R01CA154426//HHS | NIH | National Cancer Institute (NCI)/ ; }, mesh = {Humans ; *Virulence Factors/genetics ; *Colorectal Neoplasms/microbiology/genetics/pathology ; Bacterial Proteins/genetics/metabolism ; Gastrointestinal Microbiome/genetics ; Fusobacterium/genetics/pathogenicity/metabolism ; Multigene Family ; Genome, Bacterial ; Lectins/genetics/metabolism ; Fusobacteria/genetics/metabolism/pathogenicity ; }, abstract = {Fusobacterium is a bacterium associated with colorectal cancer (CRC) tumorigenesis, progression, and metastasis. Fap2 is a fusobacteria-specific outer membrane galactose-binding lectin that mediates Fusobacterium adherence to and invasion of CRC tumors. Advances in omics analyses provide an opportunity to profile and identify microbial genomic features that correlate with the cancer-associated bacterial virulence factor Fap2. Here, we analyze genomes of Fusobacterium colon tumor isolates and find that a family of post-translational modification enzymes containing Fic domains is associated with Fap2 positivity in these strains. We demonstrate that Fic family genes expand with the presence of Fap2 in the fusobacterial pangenome. Through comparative genomic analysis, we find that Fap2[+] Fusobacteriota are highly enriched with Fic gene families compared to other cancer-associated and human gut microbiome bacterial taxa. Using a global data set of CRC shotgun metagenomes, we show that fusobacterial Fic and Fap2 genes frequently co-occur in the fecal microbiomes of individuals with late-stage CRC. We further characterize specific Fic gene families harbored by Fap2[+] Fusobacterium animalis genomes and detect recombination events and elements of horizontal gene transfer via synteny analysis of Fic gene loci. Exposure of a F. animalis strain to a colon adenocarcinoma cell line increases gene expression of fusobacterial Fic and virulence-associated adhesins. Finally, we demonstrate that Fic proteins are synthesized by F. animalis as Fic peptides are detectable in F. animalis monoculture supernatants. Taken together, our study uncovers Fic genes as potential virulence factors in Fap2[+] fusobacterial genomes.IMPORTANCEAccumulating data support that bacterial members of the intra-tumoral microbiota critically influence colorectal cancer progression. Yet, relatively little is known about non-adhesin fusobacterial virulence factors that may influence carcinogenesis. Our genomic analysis and expression assays in fusobacteria identify Fic domain-containing genes, well-studied virulence factors in pathogenic bacteria, as potential fusobacterial virulence features. The Fic family proteins that we find are encoded by fusobacteria and expressed by Fusobacterium animalis merit future investigation to assess their roles in colorectal cancer development and progression.}, } @article {pmid39807156, year = {2025}, author = {Song, H and Tithi, SS and Brown, C and Aylward, FO and Jensen, R and Zhang, L}, title = {Virseqimprover: an integrated pipeline for viral contig error correction, extension, and annotation.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e18515}, pmid = {39807156}, issn = {2167-8359}, mesh = {*Genome, Viral/genetics ; *Metagenomics/methods ; *Software ; Contig Mapping/methods ; Molecular Sequence Annotation/methods ; Computational Biology/methods ; }, abstract = {Despite the recent surge of viral metagenomic studies, it remains a significant challenge to recover complete virus genomes from metagenomic data. The majority of viral contigs generated from de novo assembly programs are highly fragmented, presenting significant challenges to downstream analysis and inference. To address this issue, we have developed Virseqimprover, a computational pipeline that can extend assembled contigs to complete or nearly complete genomes while maintaining extension quality. Virseqimprover first examines whether there is any chimeric sequence based on read coverage, breaks the sequence into segments if there is, then extends the longest segment with uniform depth of coverage, and repeats these procedures until the sequence cannot be extended. Finally, Virseqimprover annotates the gene content of the resulting sequence. Results show that Virseqimprover has good performances on correcting and extending viral contigs to their full lengths, hence can be a useful tool to improve the completeness and minimize the assembly errors of viral contigs. Both a web server and a conda package for Virseqimprover are provided to the research community free of charge.}, } @article {pmid39807079, year = {2025}, author = {Björnberg, A and Nestor, D and Peker, N and Sinha, B and Couto, N and Rossen, J and Sundqvist, M and Mölling, P}, title = {Critical Steps in Shotgun Metagenomics-Based Diagnosis of Bloodstream Infections Using Nanopore Sequencing.}, journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica}, volume = {133}, number = {1}, pages = {e13511}, pmid = {39807079}, issn = {1600-0463}, mesh = {Humans ; *Metagenomics/methods ; *Nanopore Sequencing/methods ; *DNA, Bacterial/genetics/blood ; Bacteremia/diagnosis/microbiology ; Reproducibility of Results ; }, abstract = {Shotgun metagenomics offers a broad detection of pathogens for rapid blood stream infection of pathogens but struggles with often low numbers of pathogens combined with high levels of human background DNA in clinical samples. This study aimed to develop a shotgun metagenomics protocol using blood spiked with various bacteria and to assess bacterial DNA extraction efficiency with human DNA depletion. The Blood Pathogen Kit (Molzym) was used to extract DNA from EDTA-whole blood (WB) and plasma samples, using contrived blood specimens spiked with bacteria for shotgun metagenomics diagnostics via Oxford Nanopore sequencing and PCR-based library preparation. Results showed that bacterial reads were higher in WB than plasma. Differences for Staphylococcus aureus and Streptococcus pneumoniae were more pronounced compared to Escherichia coli. Plasma samples exhibited better method reproducibility, with more consistent droplet digital PCR results for human DNA. The study found that extraction was more efficient for Gram-positive bacteria than Gram-negative, suggesting that the human DNA depletion exerts a negative effect on Gram-negative bacteria. Overall, shotgun metagenomics needs further optimisation to improve bacterial DNA recovery and enhance pathogen detection sensitivity. This study highlights some critical steps in the methodology of shotgun metagenomic-based diagnosis of blood stream infections using Nanopore sequencing.}, } @article {pmid39806507, year = {2025}, author = {Zhang, D and Cao, Y and Dai, B and Zhang, T and Jin, X and Lan, Q and Qian, C and He, Y and Jiang, Y}, title = {The virome composition of respiratory tract changes in school-aged children with Mycoplasma pneumoniae infection.}, journal = {Virology journal}, volume = {22}, number = {1}, pages = {10}, pmid = {39806507}, issn = {1743-422X}, support = {No. Q202342//Scientific Research Program of Wuxi Health Commission/ ; No. 32201990//National Natural Science Foundation of China/ ; No. BK20210461//Natural Science Foundation of Jiangsu Province of China/ ; No. SBQN22013//Hospital-level project of Northern Jiangsu People's Hospital/ ; }, mesh = {Humans ; Child ; *Virome ; Male ; Female ; *Mycoplasma pneumoniae/genetics/isolation & purification/classification ; *Pneumonia, Mycoplasma/epidemiology/microbiology/virology ; Viruses/classification/isolation & purification/genetics ; Metagenomics ; Bronchoalveolar Lavage Fluid/virology/microbiology ; Respiratory System/virology/microbiology ; COVID-19/virology/epidemiology ; Respiratory Tract Infections/virology/microbiology/epidemiology ; Adolescent ; }, abstract = {BACKGROUND: Mycoplasma pneumoniae (MP) is a common pathogen for respiratory infections in children. Previous studies have reported respiratory tract microbial disturbances associated with MP infection (MPI); however, since the COVID-19 pandemic, respiratory virome data in school-aged children with MPI remains insufficient. This study aims to explore the changes in the respiratory virome caused by MPI after the COVID-19 pandemic to enrich local epidemiological data.

METHODS: Clinical samples from 70 children with MPI (70 throat swab samples and 70 bronchoalveolar lavage fluid (BALF) samples) and 78 healthy controls (78 throat swab samples) were analyzed using viral metagenomics. Virus reads were calculated and normalized using MEGAN.6, followed by statistical analysis.

RESULTS: Principal Coordinate Analysis (PCoA) showed that viral community diversity is a significant difference between disease cohorts and healthy controls. After MPI, the number of virus species in the upper respiratory tract (URT) increased obviously, and the abundance of families Poxviridae, Retroviridae, and Iridoviridae, which infect vertebrates, rose evidently, particularly the species BeAn 58,085 virus (BAV). Meanwhile, phage alterations in the disease cohorts were predominantly characterized by increased Myoviridae and Ackermannviridae families and decreased Siphoviridae and Salasmaviridae families (p < 0.01). In addition, some new viruses, such as rhinovirus, respirovirus, dependoparvovirus, and a novel gemykibvirus, were also detected in the BALF of the disease cohort.

CONCLUSIONS: This cross-sectional research highlighted the respiratory virome characteristics of school-aged children with MPI after the COVID-19 outbreak and provided important epidemiological information. Further investigation into the impact of various microorganisms on diseases will aid in developing clinical treatment strategies.}, } @article {pmid39806455, year = {2025}, author = {Liu, Z and Yao, X and Chen, C and Zhao, Y and Dong, C and Sun, L and Zhao, J and Zhang, B and Yu, Z and Cheng, D and Zhu, L and Hu, B}, title = {Growth of microbes in competitive lifestyles promotes increased ARGs in soil microbiota: insights based on genetic traits.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {8}, pmid = {39806455}, issn = {2049-2618}, support = {22206166//National Natural Science Foundation of China/ ; 22193061//National Natural Science Foundation of China/ ; 22193061//National Natural Science Foundation of China/ ; 2020YFC1806903//National Key Research and Development Program of China/ ; 2023M733056//China Postdoctoral Science Foundation awards the fellowship/ ; ES202118//Open Project of State Key Laboratory of Urban Water Resource and Environment, Harbin Institute and Technology/ ; 2022HT0025//Zhejiang Province Ecological Environment Research and Results Promotion Project/ ; }, mesh = {*Soil Microbiology ; *Bacteria/genetics/classification/isolation & purification/drug effects ; *Anti-Bacterial Agents/pharmacology ; *Microbiota/genetics ; Metagenomics ; Genes, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Oxytetracycline/pharmacology ; Soil/chemistry ; Drug Resistance, Bacterial/genetics ; }, abstract = {BACKGROUND: The widespread selective pressure of antibiotics in the environment has led to the propagation of antibiotic resistance genes (ARGs). However, the mechanisms by which microbes balance population growth with the enrichment of ARGs remain poorly understood. To address this, we employed microcosm cultivation at different antibiotic (i.e., Oxytetracycline, OTC) stresses across the concentrations from the environmental to the clinical. Paired with shot-gun metagenomics analysis and quantification of bacterial growth, trait-based assessment of soil microbiota was applied to reveal the association between key ARG subtypes, representative bacterial taxa, and functional-gene features that drive the growth of ARGs.

RESULTS: Our results illuminate that resistome variation is closely associated with bacterial growth. A non-monotonic change in ARG abundance and richness was observed over a concentration gradient from none to 10 mg/l. Soil microbiota exposed to intermediate OTC concentrations (i.e., 0.1 and 0.5 mg/l) showed greater increases in the total abundance of ARGs. Community compositionally, the growth of representative taxa, i.e., Pseudomonadaceae was considered to boost the increase of ARGs. It has chromosomally carried kinds of multidrug resistance genes such as mexAB-oprM and mexCD-oprJ could mediate the intrinsic resistance to OTC. Streptomycetaceae has shown a better adaptive ability than other microbes at the clinical OTC concentrations. However, it contributed less to the ARGs growth as it represents a stress-tolerant lifestyle that grows slowly and carries fewer ARGs. In terms of community genetic features, the community aggregated traits analysis further indicates the enhancement in traits of resource acquisition and growth yield is driving the increase of ARGs abundance. Moreover, optimizations in energy production and conversion, alongside a streamlining of bypass metabolic pathways, further boost the growth of ARGs in sub-inhibitory antibiotic conditions.

CONCLUSION: The results of this study suggest that microbes with competitive lifestyles are selected under the stress of environmental sub-inhibitory concentrations of antibiotics and nutrient scarcity. They possess greater substrate utilization capacity and carry more ARGs, due to this they were faster growing and leading to a greater increase in the abundance of ARGs. This study has expanded the application of trait-based assessments in understanding the ecology of ARGs propagation. And the finding illustrated changes in soil resistome are accompanied by the lifestyle switching of the microbiome, which theoretically supports the ARGs control approach based on the principle of species competitive exclusion. Video Abstract.}, } @article {pmid39806416, year = {2025}, author = {Chen, L and Ye, Z and Li, J and Wang, L and Chen, Y and Yu, M and Han, J and Huang, J and Li, D and Lv, Y and Xiong, K and Tian, D and Liao, J and Seidler, U and Xiao, F}, title = {Gut bacteria Prevotellaceae related lithocholic acid metabolism promotes colonic inflammation.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {55}, pmid = {39806416}, issn = {1479-5876}, support = {81873556//National Natural Science Foundation of China/ ; 82170546//National Natural Science Foundation of China/ ; CCCF-QF-2022B67-3//China Crohn's & Colitis Foundation/ ; 2023B02//Tongji Hospital Fund/ ; }, mesh = {Animals ; *Lithocholic Acid/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Colitis/microbiology/pathology/chemically induced/metabolism ; Humans ; *Dextran Sulfate ; *Mice, Inbred C57BL ; Male ; Inflammation/pathology ; Feces/microbiology ; Female ; Colon/pathology/microbiology/metabolism ; Bile Acids and Salts/metabolism ; Inflammatory Bowel Diseases/microbiology/pathology/metabolism ; Mice ; Signal Transduction ; Middle Aged ; }, abstract = {BACKGROUND: The conversion of primary bile acids to secondary bile acids by the gut microbiota has been implicated in colonic inflammation. This study investigated the role of gut microbiota related bile acid metabolism in colonic inflammation in both patients with inflammatory bowel disease (IBD) and a murine model of dextran sulfate sodium (DSS)-induced colitis.

METHODS: Bile acids in fecal samples from patients with IBD and DSS-induced colitis mice, with and without antibiotic treatment, were analyzed using ultraperformance liquid chromatography-mass spectrometry (UPLC-MS). The composition of the microbiota in fecal samples from IBD patients and DSS-colitis mice was characterized via Illumina MiSeq sequencing of the bacterial 16S rRNA gene V3-V4 region. Metagenomic profiling further identified metabolism-related gene signatures in stool samples from DSS-colitis mice. Histological analysis, quantitative PCR (qPCR) and Western Blotting were conducted on colonic samples from DSS-induced colitis mice to assess colonic inflammation, mucosal barrier integrity, and associated signaling pathways. The multivariate analysis of bile acids was conducted using Soft Independent Modelling of Class Analogy (SIMCA, Umetrics, Sweden). The relation between the relative abundance of specific phyla/genera and bile acid concentration was assess through Spearman's correlation analyses. Finally, lithocholic acid (LCA), the key bile acid, was administered via gavage to evaluate its effect on colonic inflammation and mucosal barrier integrity.

RESULTS: In patients with IBD, the composition of colonic bile acids and gut microbiota was altered. Moreover, changes in the gut microbiota further modulate the composition of bile acids in the intestine. As the gut microbiota continues to shift, the bile acid profile undergoes additional alterations. The aforementioned alterations were also observed in mice with DSS-induced colitis. The study revealed a correlation between dysbiosis of the gut microbiota and modifications in the profile of colonic bile acids, notably LCA observed in both patients with IBD and mice with DSS-induced colitis. Through multivariate analysis, LCA was identified as the key bile acid that significantly affects colonic inflammation and the integrity of mucosal barrier. Subsequent experiments confirmed that LCA supplementation effectively mitigated the inhibitory effects of gut microbiota on colitis progression in mice, primarily through the activation of the sphingosine-1-phosphate receptor 2 (S1PR2)/NF-κB p65 signaling pathway. Analysis of the microbiome and metagenomic data revealed changes in the gut microbiota, notably an increased abundance of an unclassified genus within the family Prevotellaceae in DSS-induced colitis mice. Furthermore, a positive correlation was observed between the relative abundance of Prevotellaceae and bile acid biosynthesis pathways, as well as colonic LCA level.

CONCLUSIONS: These findings suggest that LCA and its positively correlated gut bacteria, Prevotellaceae, are closely associated with intestinal inflammation. Targeting colonic inflammation may involve inhibiting LCA and members of the Prevotellaceae family as potential therapeutic strategies.}, } @article {pmid39806046, year = {2025}, author = {Sun, L and Liu, X and Zhou, L and Wang, H and Lian, C and Zhong, Z and Wang, M and Chen, H and Li, C}, title = {Shallow-water mussels (Mytilus galloprovincialis) adapt to deep-sea environment through transcriptomic and metagenomic insights.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {46}, pmid = {39806046}, issn = {2399-3642}, support = {42276153, 42106134, 42106100, 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; *Mytilus/microbiology/genetics/immunology ; *Transcriptome ; *Microbiota ; Metagenomics ; Symbiosis/genetics ; Adaptation, Physiological/genetics ; Seawater/microbiology ; Metagenome ; }, abstract = {Recent studies have unveiled the deep sea as a rich biosphere, populated by species descended from shallow-water ancestors post-mass extinctions. Research on genomic evolution and microbial symbiosis has shed light on how these species thrive in extreme deep-sea conditions. However, early adaptation stages, particularly the roles of conserved genes and symbiotic microbes, remain inadequately understood. This study examined transcriptomic and microbiome changes in shallow-water mussels Mytilus galloprovincialis exposed to deep-sea conditions at the Site-F cold seep in the South China Sea. Results reveal complex gene expression adjustments in stress response, immune defense, homeostasis, and energy metabolism pathways during adaptation. After 10 days of deep-sea exposure, shallow-water mussels and their microbial communities closely resembled those of native deep-sea mussels, demonstrating host and microbiome convergence in response to adaptive shifts. Notably, methanotrophic bacteria, key symbionts in native deep-sea mussels, emerged as a dominant group in the exposed mussels. Host genes involved in immune recognition and endocytosis correlated significantly with the abundance of these bacteria. Overall, our analyses provide insights into adaptive transcriptional regulation and microbiome dynamics of mussels in deep-sea environments, highlighting the roles of conserved genes and microbial community shifts in adapting to extreme environments.}, } @article {pmid39805953, year = {2025}, author = {Daruka, L and Czikkely, MS and Szili, P and Farkas, Z and Balogh, D and Grézal, G and Maharramov, E and Vu, TH and Sipos, L and Juhász, S and Dunai, A and Daraba, A and Számel, M and Sári, T and Stirling, T and Vásárhelyi, BM and Ari, E and Christodoulou, C and Manczinger, M and Enyedi, MZ and Jaksa, G and Kovács, K and van Houte, S and Pursey, E and Pintér, L and Haracska, L and Kintses, B and Papp, B and Pál, C}, title = {ESKAPE pathogens rapidly develop resistance against antibiotics in development in vitro.}, journal = {Nature microbiology}, volume = {10}, number = {2}, pages = {313-331}, pmid = {39805953}, issn = {2058-5276}, mesh = {*Anti-Bacterial Agents/pharmacology ; Humans ; *Microbial Sensitivity Tests ; Pseudomonas aeruginosa/drug effects/genetics/growth & development ; Drug Resistance, Bacterial/genetics ; Mutation ; Escherichia coli/drug effects/genetics/growth & development ; Metagenomics ; Gastrointestinal Microbiome/drug effects ; Acinetobacter baumannii/drug effects/genetics/growth & development ; Klebsiella pneumoniae/drug effects/genetics/growth & development ; Drug Resistance, Multiple, Bacterial/genetics ; Gram-Negative Bacteria/drug effects/genetics ; }, abstract = {Despite ongoing antibiotic development, evolution of resistance may render candidate antibiotics ineffective. Here we studied in vitro emergence of resistance to 13 antibiotics introduced after 2017 or currently in development, compared with in-use antibiotics. Laboratory evolution showed that clinically relevant resistance arises within 60 days of antibiotic exposure in Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa, priority Gram-negative ESKAPE pathogens. Resistance mutations are already present in natural populations of pathogens, indicating that resistance in nature can emerge through selection of pre-existing bacterial variants. Functional metagenomics showed that mobile resistance genes to antibiotic candidates are prevalent in clinical bacterial isolates, soil and human gut microbiomes. Overall, antibiotic candidates show similar susceptibility to resistance development as antibiotics currently in use, and the corresponding resistance mechanisms overlap. However, certain combinations of antibiotics and bacterial strains were less prone to developing resistance, revealing potential narrow-spectrum antibacterial therapies that could remain effective. Finally, we develop criteria to guide efforts in developing effective antibiotic candidates.}, } @article {pmid39805403, year = {2025}, author = {Wolf, PG and Welsh, C and Binion, B and Dai, H and Oliveira, ML and Hamm, A and Goldberg, S and Buobu, PS and Schering, T and Vergis, S and Kessee, N and Gomez, SL and Yazici, C and Maienschein-Cline, M and Byrd, DA and Gaskins, HR and Ridlon, JM and Mutlu, E and Greening, C and Tussing-Humphreys, L}, title = {Secondary Bile Acid Derivatives Are Contributors to the Fecal Bile Acid Pool and Associated With Bile Acid-Modulating Nutrients.}, journal = {The Journal of nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tjnut.2024.12.035}, pmid = {39805403}, issn = {1541-6100}, abstract = {BACKGROUND: Accumulation of hydrophobic bile acids (BAs) is linked with cancer development. However, derivatives of deoxycholic acid (DCA) and lithocholic acid (LCA) produced via bacterial metabolism may mitigate the proinflammatory and cytotoxic effects of hydrophobic BAs. The impact of diet on secondary BA derivative production has not been determined.

OBJECTIVES: This study aimed to study the associations between BA-modulating nutrients and the composition of secondary BAs and their derivatives.

METHODS: Stool and blood were collected from 138 participants aged 45-75 y that self-identified as Black or non-Hispanic White. BAs were extracted from stool and serum and quantified using LC/ESI-MS/MS. Energy, macronutrients, micronutrients, and specific dietary nutrients were estimated from two 24-h diet recalls. The abundance of genes for microbial BA metabolism was assessed from stool metagenomes. Kendall τ correlation and regression-based modeling were performed to determine associations between BA categories, microbial genes, and select energy-adjusted dietary variables (alcohol, calcium, coffee, fiber, fat, and protein).

RESULTS: Participants had a mean age of 60 y and a mean BMI of 31 kg/m[2]. BA derivatives were present in all participant stools, with lagodeoxycholic acid being the most abundant derivative quantified. Analysis of stool microbial metagenomes revealed the presence of genes for secondary BA derivative production in all participants. Protein is positively associated with the accumulation of secondary BAs. monounsaturated fatty acids (MUFA)s were negatively associated with high abundant derivatives of DCA in regression models. Total fiber and coffee intake were positively correlated with increased conversion of BAs to derivatives. Race and smoking status were significant predictors of associations between dietary variables and BA derivatives.

CONCLUSION: Protein, MUFAs, total fiber and coffee are significantly associated with concentrations of secondary BAs and their derivatives. Future work should account for social and structural influences on dietary intake and its relationship with BA-elicited cancer risk.}, } @article {pmid39805250, year = {2024}, author = {Bortoluzzi, C and Ghanbari, M and Gonzáles, JC and Bohórquez, JO and Paredes, R and Mauri, Y and Lozano-Poveda, CA}, title = {Precision biotic as an effective replacement of hydrolyzed yeast and butyrate in antibiotic free diets of broiler chickens raised under field conditions.}, journal = {Poultry science}, volume = {104}, number = {2}, pages = {104664}, pmid = {39805250}, issn = {1525-3171}, abstract = {A total of 1,436,000 Ross 380 AP broiler chicks were included in the experiment, which was conducted in two cycles with 20 houses per cycle and 35,900 birds per house. The objective was to evaluate, under field conditions, the impact of a precision biotic (PB) on the growth performance and cecal microbiome of broiler chickens, in comparison to enzymatically hydrolyzed yeast (EHY) and butyrate (BT) in an antibiotic-free diet. Each cycle consisted of six (6) houses under PB supplementation, and 14 houses under the regular dietary program used by the integration. Body weight (BW), feed intake (FI), and feed conversion ratio (FCR) were assessed at processing age, ranging from 39 to 45 d. Birds had ad libitum access to water and feed. On day 29, cecal content from 7 birds per house (42 birds per treatment) were collected for microbiome analysis by applying shotgun metagenomics approach. The performance data were analyzed by ANCOVA, house was considered as the experimental unit for growth performance (n = 20; P < 0.05), and the bird for microbiome analysis (n = 84; P < 0.05). Both treatment groups performed below the strain target in terms of BW, but better in terms of FCR. There were no significant differences (P > 0.05) between both groups on the growth performance, indicating that PB effectively replaced EHY and BT without compromising growth. However, significant functional changes were observed in the microbiome of birds fed PB, with enrichment in the pathways related to carbon and nitrogen metabolism. These changes were associated with an increased carbon metabolism index (P = 0.05), which can lead to higher endogenous short-chain fatty acids (SCFAs) production. Overall, by potentially increasing SCFA production by the intestinal microbiome, PB supported the growth performance of chickens similar to that achieved with EHY and BT.}, } @article {pmid39805166, year = {2025}, author = {Memon, FU and Zhu, Y and Cui, Y and Feng, X and Ahmad, S and Zeng, P and Nabi, F and Hao, D and Huang, Z and Tettamanti, G and Tian, L}, title = {Gut microbial communities and transcriptional profiles of black soldier fly (Hermitia illucens) larvae fed on fermented sericulture waste.}, journal = {Waste management (New York, N.Y.)}, volume = {194}, number = {}, pages = {158-168}, doi = {10.1016/j.wasman.2025.01.011}, pmid = {39805166}, issn = {1879-2456}, abstract = {Sericulture waste poses significant challenges to industrial and environmental safety. Black soldier fly larvae (BSFL) offer a promising solution for organic waste management by converting it into insect protein. This study aimed to develop a microbial fermented method for utilizing sericulture waste to feed BSFL and explore the underlying mechanisms. Our results showed that all fermented sericulture waste groups had positive effects on body weight, survival rate, substrate consumption rate, and substrate conversion rate. Metagenomic analysis revealed a notable increase in the abundances of commensal genera, including Sedimentibacter, Clostridium, Enterococcus, Bacteroides, and Bacillus, in the gut of BSFL fed on sericulture waste fermented with the most effective combination of microbial strains (B. subtilis, B. licheniformis, and E. faecalis). In contrast, BSFL reared on unfermented sericulture waste exhibited higher abundances of potentially pathogenic and harmful genera, including Providencia, Klebsiella, Escherichia, Brucella, and Enterobacter. Clusters of orthologous genes (COG) analysis indicated that altered microbial communities in the fermented group mainly participated in metabolic pathways, defense mechanism, and signal transduction mechanism. Transcriptome analysis further revealed that the upregulated genes were functionally associated with key metabolic pathways and immune mechanisms in the fermented group. These findings underscore the pivotal role of selected microbial fermentation in utilizing sericulture waste as BSFL feed, providing a sustainable solution for organic waste management.}, } @article {pmid39805015, year = {2025}, author = {Chuckran, PF and Estera-Molina, K and Nicolas, AM and Sieradzki, ET and Dijkstra, P and Firestone, MK and Pett-Ridge, J and Blazewicz, SJ}, title = {Codon bias, nucleotide selection, and genome size predict in situ bacterial growth rate and transcription in rewetted soil.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {3}, pages = {e2413032122}, pmid = {39805015}, issn = {1091-6490}, support = {SCW1632//U.S. Department of Energy (DOE)/ ; DE-SC0020163//U.S. Department of Energy (DOE)/ ; DE-SC0016247//U.S. Department of Energy (DOE)/ ; SCW1589//U.S. Department of Energy (DOE)/ ; SCW1421//U.S. Department of Energy (DOE)/ ; }, mesh = {*Soil Microbiology ; *Bacteria/genetics/classification/growth & development ; *Codon Usage ; *Soil/chemistry ; *Genome Size ; Metagenome ; Codon/genetics ; Genome, Bacterial ; Transcription, Genetic ; Nucleotides/genetics ; }, abstract = {In soils, the first rain after a prolonged dry period represents a major pulse event impacting soil microbial community function, yet we lack a full understanding of the genomic traits associated with the microbial response to rewetting. Genomic traits such as codon usage bias and genome size have been linked to bacterial growth in soils-however, often through measurements in culture. Here, we used metagenome-assembled genomes (MAGs) with [18]O-water stable isotope probing and metatranscriptomics to track genomic traits associated with growth and transcription of soil microorganisms over one week following rewetting of a grassland soil. We found that codon bias in ribosomal protein genes was the strongest predictor of growth rate. We also found higher growth rates in bacteria with smaller genomes, suggesting that reduced genome size enables a faster response to pulses in soil bacteria. Faster transcriptional upregulation of ribosomal protein genes was associated with high codon bias and increased nucleotide skew. We found that several of these relationships existed within phyla, indicating that these associations between genomic traits and activity could be generalized characteristics of soil bacteria. Finally, we used publicly available metagenomes to assess the distribution of codon bias across a pH gradient and found that microbial communities in higher pH soils-which are often more water limited and pulse driven-have higher codon usage bias in their ribosomal protein genes. Together, these results provide evidence that genomic characteristics affect soil microbial activity during rewetting and pose a potential fitness advantage for soil bacteria where water and nutrient availability are episodic.}, } @article {pmid39804694, year = {2025}, author = {Puller, V and Plaza Oñate, F and Prifti, E and de Lahondès, R}, title = {Impact of simulation and reference catalogues on the evaluation of taxonomic profiling pipelines.}, journal = {Microbial genomics}, volume = {11}, number = {1}, pages = {}, pmid = {39804694}, issn = {2057-5858}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Computer Simulation ; Benchmarking ; Bacteria/classification/genetics ; Metagenomics/methods ; Microbiota/genetics ; }, abstract = {Microbiome profiling tools rely on reference catalogues, which significantly affect their performance. Comparing them is, however, challenging, mainly due to differences in their native catalogues. In this study, we present a novel standardized benchmarking framework that makes such comparisons more accurate. We decided not to customize databases but to translate results to a common reference to use the tools with their native environment. Specifically, we conducted two realistic simulations of gut microbiome samples, each based on a specific taxonomic profiler, and used two different taxonomic references to project their results, namely the Genome Taxonomy Database and the Unified Human Gastrointestinal Genome. To demonstrate the importance of using such a framework, we evaluated four established profilers as well as the impact of the simulations and that of the common taxonomic references on the perceived performance of these profilers. Finally, we provide guidelines to enhance future profiler comparisons for human microbiome ecosystems: (i) use or create realistic simulations tailored to your biological context (BC), (ii) identify a common feature space suited to your BC and independent of the catalogues used by the profilers and (iii) apply a comprehensive set of metrics covering accuracy (sensitivity/precision), overall representativity (richness/Shannon) and quantification (UniFrac and/or Aitchison distance).}, } @article {pmid39804671, year = {2025}, author = {Broderick, CM and Benucci, GMN and Bachega, LR and Miller, GD and Evans, SE and Hawkes, CV}, title = {Long-term climate establishes functional legacies by altering microbial traits.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {39804671}, issn = {1751-7370}, mesh = {*Soil Microbiology ; *Carbon Cycle ; *Metagenomics ; Soil/chemistry ; Droughts ; Climate ; Bacteria/genetics/classification/metabolism/isolation & purification ; Microbiota ; Climate Change ; Seasons ; Carbon/metabolism ; }, abstract = {Long-term climate history can influence rates of soil carbon cycling but the microbial traits underlying these legacy effects are not well understood. Legacies may result if historical climate differences alter the traits of soil microbial communities, particularly those associated with carbon cycling and stress tolerance. However, it is also possible that contemporary conditions can overcome the influence of historical climate, particularly under extreme conditions. Using shotgun metagenomics, we assessed the composition of soil microbial functional genes across a mean annual precipitation gradient that previously showed evidence of strong climate legacies in soil carbon flux and extracellular enzyme activity. Sampling coincided with recovery from a regional, multi-year severe drought, allowing us to document how the strength of climate legacies varied with contemporary conditions. We found increased investment in genes associated with resource cycling with historically higher precipitation across the gradient, particularly in traits related to resource transport and complex carbon degradation. This legacy effect was strongest in seasons with the lowest soil moisture, suggesting that contemporary conditions-particularly, resource stress under water limitation-influences the strength of legacy effects. In contrast, investment in stress tolerance did not vary with historical precipitation, likely due to frequent periodic drought throughout the gradient. Differences in the relative abundance of functional genes explained over half of variation in microbial functional capacity-potential enzyme activity-more so than historical precipitation or current moisture conditions. Together, these results suggest that long-term climate can alter the functional potential of soil microbial communities, leading to legacies in carbon cycling.}, } @article {pmid39804518, year = {2025}, author = {Claytor, JD and Lin, DL and Magnaye, KM and Guerrero, YS and Langelier, CR and Lynch, SV and El-Nachef, N}, title = {Effect of Fecal Microbiota Transplant on Antibiotic Resistance Genes Among Patients with Chronic Pouchitis.}, journal = {Digestive diseases and sciences}, volume = {}, number = {}, pages = {}, pmid = {39804518}, issn = {1573-2568}, abstract = {BACKGROUND: Pouchitis is common among patients with ulcerative colitis (UC) who have had colectomy with ileal pouch-anal anastomosis. Antibiotics are first-line therapy for pouch inflammation, increasing the potential for gut colonization with multi-drug resistant organisms (MDRO). Fecal microbial transplant (FMT) is being studied in the treatment of pouchitis and in the eradication of MDRO. Prior work using aerobic antibiotic culture disks suggests that some patients with chronic pouchitis may regain fluoroquinolone sensitivity after FMT. However, gut MDRO include anaerobic, fastidious organisms that are difficult to culture using traditional methods.

AIM: We aimed to assess whether FMT reduced the abundance of antibiotic resistance genes (ARG) or affected resistome diversity, evenness, or richness in patients with chronic pouchitis.

METHODS: We collected clinical characteristics regarding infections and antibiotic exposures for 18 patients who had previously been enrolled in an observational study investigating FMT as a treatment for pouchitis. Twenty-six pre- and post-FMT stool samples were analyzed using FLASH (Finding Low Abundance Sequences by Hybridization), a CRISPR/Cas9-based shotgun metagenomic sequence enrichment technique that detects acquired and chromosomal bacterial ARGs. Wilcoxon rank sum tests were used to assess differences in clinical characteristics, ARG counts, resistome diversity and ARG richness, pre- and post-FMT.

RESULTS: All 13 of the patients with sufficient stool samples for analysis had recently received antibiotics for pouchitis prior to a single endoscopic FMT. Fecal microbiomes of all patients had evidence of multi-drug resistance genes and ESBL resistance genes at baseline; 62% encoded fluoroquinolone resistance genes. A numerical decrease in overall ARG counts was noted post-FMT, but no statistically significant differences were noted (P = 0.19). Richness and diversity were not significantly altered. Three patients developed infections during the 5-year follow-up period, none of which were associated with MDRO.

CONCLUSION: Antibiotic resistance genes are prevalent among antibiotic-exposed patients with chronic pouchitis. FMT led to a numerical decrease, but no statistically significant change in ARG, nor were there significant changes in the diversity, richness, or evenness of ARGs. Further investigations to improve FMT engraftment and to optimize FMT delivery in patients with inflammatory pouch disorders are warranted.}, } @article {pmid39804408, year = {2025}, author = {Macdonald, JFH and Han, Y and Astafyeva, Y and Bergmann, L and Gurschke, M and Dirksen, P and Blümke, P and Schneider, YKH and Alawi, M and Lippemeier, S and Andersen, JH and Krohn, I}, title = {Exploring Tetraselmis chui microbiomes-functional metagenomics for novel catalases and superoxide dismutases.}, journal = {Applied microbiology and biotechnology}, volume = {109}, number = {1}, pages = {6}, pmid = {39804408}, issn = {1432-0614}, support = {AquaHealth FKZ 031B0945C//Bundesministerium für Bildung und Forschung/ ; SuReMetS FKZ 031B0944A//Bundesministerium für Bildung und Forschung/ ; }, mesh = {*Superoxide Dismutase/genetics/metabolism ; *Metagenomics ; *Antioxidants/metabolism ; *Catalase/metabolism/genetics ; *Microbiota ; Microalgae/genetics/enzymology ; Chlorophyta/genetics/enzymology ; Bacteria/genetics/enzymology/classification/isolation & purification ; }, abstract = {The focus on microalgae for applications in several fields, e.g. resources for biofuel, the food industry, cosmetics, nutraceuticals, biotechnology, and healthcare, has gained increasing attention over the last decades. In this study, we investigate the microbiome of the cultured microalga Tetraselmis chui (T. chui) to highlight their potential for health benefits. In this context, biomolecules like antioxidants play a crucial role in the well-being of living organisms as they metabolise harmful reactive oxygen species (ROS) to reduce oxidative stress. Impaired processing of ROS leads to damaged cells and increases the risk of cancer, inflammatory diseases, and diabetes, among others. Here, we identify, characterise, and test bacterial antioxidants derived from the T. chui microbiome metagenome dataset. We identified 258 genes coding for proteins with potential antioxidant activity. Of those, four novel enzymes are expressed and identified as two superoxide dismutases (SOD), TcJM_SOD2 and TcIK_SOD3, and two catalases (CAT), TcJM_CAT2 and TcIK_CAT3. Extensive analyses characterised all implemented enzymes as active even in concentrations down to 25 ng*ml[-1] for the SODs and 15 ng*ml[-1] for the CATs. Furthermore, sequence-based analyses assign TcJM_SOD2 and TcIK_SOD3 to iron superoxide dismutases (Fe SODs) and TcJM_CAT2 and TcIK_CAT3 to heme-containing catalases. These candidates are phylogenetically classified within the phylum Pseudomonadota. Regarding the biotechnological potential, a toxicity assay did not indicate any harmful effects. The introduced enzymes may benefit medical applications and expand the potential of microalgae microbiomes. KEY POINTS: • Omics-based discoveries of antioxidant enzymes from Tetraselmis chui microbiome • Two superoxide dismutases and two catalases are identified and tested for activity • Enzyme sensitivity highlights biotechnological potential of microalgae microbiomes.}, } @article {pmid39803536, year = {2025}, author = {Kettenburg, G and Ranaivoson, HC and Andrianianina, A and Andry, S and Henry, AR and Davis, RL and Laboune, F and Longtine, ER and Godbole, S and Horigan, S and Ruhs, EC and Raharinosy, V and Randriambolamanantsoa, TH and Lacoste, V and Heraud, JM and Dussart, P and Douek, DC and Brook, CE}, title = {Picornaviridae and Caliciviridae diversity in Madagascar fruit bats is driven by cross-continental genetic exchange.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.12.31.630946}, pmid = {39803536}, issn = {2692-8205}, abstract = {Bats are reservoir hosts for numerous well-known zoonotic viruses, but their broader virus-hosting capacities remain understudied. Picornavirales are an order of enteric viruses known to cause disease across a wide range of mammalian hosts, including Hepatitis A in humans and foot-and-mouth disease in ungulates. Host-switching and recombination drive the diversification of Picornavirales worldwide. Divergent Caliciviridae and Picornaviridae (families within the Picornavirales) have been described in bats across mainland Africa, but surveillance for these viruses has been rare in the Southwest Indian Ocean Islands. Bats live in close proximity to and are consumed widely as a food source by humans in Madagascar, providing opportunities for zoonotic transmission. Prior work in Madagascar has described numerous evolutionarily divergent bat viruses, some with zoonotic potential. Using metagenomic Next Generation Sequencing of urine and fecal samples obtained from three species of endemic Malagasy fruit bats (Eidolon dupreanum , Pteropus rufus , and Rousettus madagascariensis), we recovered 13 full-length and 37 partial-length genomic sequences within the order Picornavirales (36 Picornaviridae and 14 Caliciviridae sequences), which we identify and describe here. We find evidence that genetic exchange between mainland African bat and Madagascar bat Picornavirales likely shaped the diversification patterns of these novel sequences through recombination events between closely related Picornavirales ; thus far, high host fidelity appears to have limited these viruses from spilling over into other species.}, } @article {pmid39803511, year = {2024}, author = {Schulz, F and Yan, Y and Weiner, AKM and Ahsan, R and Katz, LA and Woyke, T}, title = {Protists as mediators of complex microbial and viral associations.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39803511}, issn = {2692-8205}, support = {R15 HG010409/HG/NHGRI NIH HHS/United States ; }, abstract = {Microbial eukaryotes (aka protists) are known for their important roles in nutrient cycling across different ecosystems. However, the composition and function of protist-associated microbiomes remains largely elusive. Here, we employ cultivation-independent single-cell isolation and genome-resolved metagenomics to provide detailed insights into underexplored microbiomes and viromes of over 100 currently uncultivable ciliates and amoebae isolated from diverse environments. Our findings reveal unique microbiome compositions and hint at an intricate network of complex interactions and associations with bacterial symbionts and viruses. We observed stark differences between ciliates and amoebae in terms of microbiome and virome compositions, highlighting the specificity of protist-microbe interactions. Over 115 of the recovered microbial genomes were affiliated with known endosymbionts of eukaryotes, including diverse members of the Holosporales, Rickettsiales, Legionellales, Chlamydiae, Dependentiae , and more than 250 were affiliated with possible host-associated bacteria of the phylum Patescibacteria. We also identified more than 80 giant viruses belonging to diverse viral lineages, of which some were actively expressing genes in single cell transcriptomes, suggesting a possible association with the sampled protists. We also revealed a wide range of other viruses that were predicted to infect eukaryotes or host-associated bacteria. Our results provide further evidence that protists serve as mediators of complex microbial and viral associations, playing a critical role in ecological networks. The frequent co-occurrence of giant viruses and diverse microbial symbionts in our samples suggests multipartite associations, particularly among amoebae. Our study provides a preliminary assessment of the microbial diversity associated with lesser-known protist lineages and paves the way for a deeper understanding of protist ecology and their roles in environmental and human health.}, } @article {pmid39803498, year = {2024}, author = {Arp, G and Jiang, A and Dufault-Thompson, K and Levy, S and Zhong, A and Wassan, JT and Grant, M and Li, Y and Hall, B and Jiang, X}, title = {Gut Bacteria Encode Reductases that Biotransform Steroid Hormones.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39803498}, issn = {2692-8205}, support = {R35 GM155208/GM/NIGMS NIH HHS/United States ; }, abstract = {The metabolism of steroids by the gut microbiome affects hormone homeostasis, impacting host development, mental health, and reproductive functions. In this study, we identify the Δ[4]-3-ketosteroid 5β-reductase, 3β-hydroxysteroid dehydrogenase/Δ[5-4] isomerase, and Δ[6]-3-ketosteroid reductase enzyme families encoded by common human gut bacteria. Through phylogenetic reconstruction and mutagenesis, We show that 5β-reductase and Δ[6]-3-ketosteroid reductase have evolved to specialize in converting diverse 3-keto steroid hormones into their 5β- and Δ[6]-reduced derivatives. We also find that the novel 3β-hydroxysteroid dehydrogenase/Δ[5-4] isomerase is fused with 5β-reductase in multiple species, streamlining the multi-step conversion of pregnenolone, a steroid hormone precursor, into epipregnanolone. Through metagenomic analysis, we reveal that these enzymes are prevalent in healthy populations, being enriched in females over males. These findings provide the molecular basis for studying microbial steroid metabolism in the gut, offering insights into its potential impact on hormonal health in hosts, especially in the context of women's health.}, } @article {pmid39802822, year = {2025}, author = {French, RK and Anderson, S and Cain, K and Digby, A and Greene, TC and Miskelly, CM and Muller, CG and Taylor, MW and Recovery Team, K and Geoghegan, JL and Holmes, EC}, title = {Diversity and cross-species transmission of viruses in a remote island ecosystem: implications for wildlife conservation.}, journal = {Virus evolution}, volume = {11}, number = {1}, pages = {veae113}, pmid = {39802822}, issn = {2057-1577}, abstract = {The ability of viruses to emerge in new species is influenced by aspects of host biology and ecology, with some taxa harbouring a high diversity and abundance of viruses. However, how these factors shape virus diversity at the ecosystem scale is often unclear. To better understand the pattern and determinants of viral diversity within an ecosystem, and to describe the novel avian viruses infecting an individual avian community, we performed a metagenomic snapshot of the virome from the entire avian community on remote Pukenui/Anchor Island in Aotearoa New Zealand. Through total RNA sequencing of 18 bird species, we identified 50 avian viruses from 9 viral families, of which 96% were novel. Of note, passerines (perching birds) exhibited high viral abundance and diversity, with viruses found across all nine viral families identified. We also identified numerous viruses infecting seabirds on the Island, including megriviruses, hepaciviruses, and hepatoviruses, while parrots exhibited an extremely low diversity of avian viruses. Within passerines, closely related astroviruses and hepatoviruses, and multiple identical hepe-like viruses, were shared among host species. Phylogenetic reconciliation analysis of these viral groups revealed a mixture of co-divergence and cross-species transmission, with virus host-jumping relatively frequent among passerines. In contrast, there was no evidence for recent cross-species virus transmission in parrots or seabirds. The novel pegiviruses and a flavivirus identified here also pose intriguing questions regarding their origins, pathogenicity, and potential impact on vertebrate hosts. Overall, these results highlight the importance of understudied remote island ecosystems as refugia for novel viruses, as well as the intricate interplay between host ecology and behaviour in shaping viral communities.}, } @article {pmid39802798, year = {2024}, author = {Blank, RB and Bu, K and Chen, W and Cunningham, I and Sokolove, J and Lahey, L and Heguy, A and Medina, R and Ubeda, C and Nayak, RR and Hu, J and Cantor, A and Lee, J and Clemente, JC and Scher, JU}, title = {Multi-omic Biomarkers Distinguish Rheumatoid Arthritis in Discordant Monozygotic Twins.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {39802798}, support = {UL1 TR001445/TR/NCATS NIH HHS/United States ; R03 AR072182/AR/NIAMS NIH HHS/United States ; UC2 AR081034/AR/NIAMS NIH HHS/United States ; T32 AR069515/AR/NIAMS NIH HHS/United States ; R01 AR074500/AR/NIAMS NIH HHS/United States ; }, abstract = {BACKGROUND: Although genetic factors have been identified in the pathogenesis of rheumatoid arthritis (RA), the concordance rate in monozygotic (MZ) twins is low, suggesting that other features contribute to disease development. Further, the relative contribution of such non-genetic elements in identical twins have not been characterized. Here, we aimed to measure differentiating host and microbial biomarkers of RA by studying MZ twins discordant for disease using a multi-omics approach.

METHODS: Eight pairs of MZ twins discordant for RA (n=16) were enrolled. Gut microbiome was assessed using shotgun metagenomic sequencing. Autoantibodies, cytokines, and other plasma proteins were measured in both plasma and feces. Levels of short and medium-chain fatty acids from serum and feces were quantified using gas chromatography mass spectrometry (GC-MS).

RESULTS: While overall microbiome diversity and composition did not significantly differ between twins, we observed a decrease in Blautia faecis in affected twins. Affected twins had higher concentrations of both fecal and plasma citrullinated and non-citrullinated autoantibodies, as well as significantly lower concentrations of fecal butyrate and propionate.

CONCLUSION: Multi-omics biomarkers differentiate MZ twins discordant for RA. Blautia faecis, which is associated with reduced inflammatory cytokine expression, was decreased in RA twins. Similarly, short-chain fatty acids, known to have immune modulatory effects, were decreased in affected twins, suggesting further bi-directional interactions between inflammation at the gut barrier and disease state. If confirmed in other cohorts, exhaustive multi-omics approaches may improve our understanding of RA pathogenesis and potentially contribute to novel diagnostics and co-adjuvant therapies.}, } @article {pmid39802519, year = {2025}, author = {Yan, C and Qiu, J and Pan, X and Huang, X and Pan, L and Wang, C and Mao, M}, title = {Mixed Pulmonary Infection, Asthma, and Nephrotic Syndrome in a Patient Diagnosed with Selective IgA Deficiency: A Case Report.}, journal = {Journal of inflammation research}, volume = {18}, number = {}, pages = {127-132}, pmid = {39802519}, issn = {1178-7031}, abstract = {Patients with selective IgA deficiency could have various clinical presentations ranging from asymptomatic to severe respiratory or gastrointestinal tract infection, as well as autoimmune disease and allergic reactions. Selective IgA deficiency is relatively common in Caucasians, but it is rare in the Asian population, meaning it could be easily missed in the clinic. In this study, we report a 26-year-old man with a history of asthma and nephrotic syndrome. He presented with symptoms of pulmonary infection, and his condition quickly deteriorated to respiratory failure that required endotracheal intubation and mechanical ventilation. Sputum smear; sputum, blood, and bronchoalveolar lavage fluid culture; and metagenomic sequencing examination identified multiple mixed pathogens, including Mycobacterium chelonae-abscessus, Pseudomonas aeruginosa, Candida parapsilosis, Acinetobacter baumannii, and Klebsiella cepacia. Finally, he was diagnosed with selective IgA deficiency after a laboratory test detected an extremely low serum IgA level (<0.06 g/L). The patient died of septic shock and multiorgan failure despite aggressive management with a combination of antibiotics and supportive care. We report this case to remind clinicians about this rare disease in the Asian population. Patients with multisystem illnesses that are related to immune dysregulation, such as asthma or nephrotic syndrome, should be tested for immune system disorder. Rare and mixed pathogens should be considered during antibiotic selection in patients with selective IgA deficiency.}, } @article {pmid39801738, year = {2024}, author = {Harmak, Z and Kone, AS and Ghouzlani, A and Ghazi, B and Badou, A}, title = {Beyond Tumor Borders: Intratumoral Microbiome Effects on Tumor Behavior and Therapeutic Responses.}, journal = {Immune network}, volume = {24}, number = {6}, pages = {e40}, pmid = {39801738}, issn = {1598-2629}, abstract = {The human body contains a diverse array of microorganisms, which exert a significant impact on various physiological processes, including immunity, and can significantly influence susceptibility to various diseases such as cancer. Recent advancements in metagenomic sequencing have uncovered the role of intratumoral microbiome, which covertly altered the development of cancer, the growth of tumors, and the response to existing treatments through multiple mechanisms. These mechanisms involve mainly DNA damage induction, oncogenic signaling pathway activation, and the host's immune response modulation. To explore novel therapeutic options and effectively target and regulate the intratumoral microbiome, a comprehensive understanding of these processes is indispensable. Here, we will explore various potential actions of the intratumoral microbiome concerning the initiation and progression of tumors. We will examine its impact on responses to chemotherapy, radiotherapy, and immunotherapy. Additionally, we will discuss the current state of knowledge regarding the use of genetically modified bacteria as a promising treatment option for cancer.}, } @article {pmid39801456, year = {2025}, author = {Torozan, DA and Laczny, CC and Roomp, K and Wilmes, P and Fleckenstein, J and Schneider, JG}, title = {Metagenomic Profiling of Oral Microbiome Dynamics During Chemoradiotherapy in Head and Neck Squamous Cell Carcinoma Patients.}, journal = {Cancer medicine}, volume = {14}, number = {1}, pages = {e70589}, pmid = {39801456}, issn = {2045-7634}, support = {863664//H2020 European Research Council/ ; }, mesh = {Humans ; Male ; *Chemoradiotherapy/adverse effects ; Female ; Middle Aged ; *Squamous Cell Carcinoma of Head and Neck/microbiology/therapy ; *Microbiota/radiation effects ; Aged ; *Metagenomics/methods ; *Head and Neck Neoplasms/microbiology/therapy ; *Saliva/microbiology ; Prospective Studies ; Mouth/microbiology ; Adult ; Case-Control Studies ; Metagenome ; }, abstract = {BACKGROUND: We explored the interaction between the oral microbiome and the development of radiation-induced mucositis in patients with head and neck squamous cell cancer (HNSCC) undergoing chemoradiotherapy (CRT). We prospectively studied the oral microbiome and compared it to healthy controls. Additionally, we compared patients with low-grade (LGM) vs. high-grade mucositis (HGM).

METHODS: Ten HNSCC patients scheduled for CRT were included. Saliva samples were characterized prior to, during, and nine months after CRT using metagenomic sequencing. We similarly characterized samples from seven healthy controls. We assessed alpha and beta diversity and examined abundances at different taxonomic levels between (sub)groups.

RESULTS: Patients exhibited significantly reduced alpha diversity compared to controls at all times (p ⟨ 0.05). Differential abundance of taxa between patients and controls was observed at baseline. In patients, the relative abundance of Staphylococcus aureus and Escherichia coli increased significantly during CRT. Capnocytophaga spp. was associated with the definitive CRT patients' subgroup. At baseline, two fungal families (Melampsoraceae and Herpotrichiellaceaea) were more abundant in patients who later developed HGM. No differentially abundant taxa were found between LGM vs. HGM during irradiation.

CONCLUSION: Our findings support the hypothesis that CRT, as well as HNSCC itself, influences the composition of the oral microbiome. Microbial markers found in patients who later developed HGM should be evaluated using independent cohorts to qualify their specific biomarker potential.}, } @article {pmid39800795, year = {2025}, author = {Pagac, MP and Davient, B and Plado, LA and Lam, HYI and Lee, SM and Ravikrishnan, A and Chua, WLE and Muralidharan, S and Sridharan, A and Irudayaswamy, AS and Srinivas, R and Wearne, S and Mohamed Naim, AN and Ho, EXP and Ng, HQA and Kwah, JS and Png, E and Bendt, AK and Wenk, MR and Torta, F and Nagarajan, N and Common, J and Chong, YS and Tham, EH and Shek, LP and Loo, EXL and Chambers, J and Yew, YW and Loh, M and Dawson, TL}, title = {Life stage impact on the human skin ecosystem: lipids and the microbial community.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {13}, pmid = {39800795}, issn = {2055-5008}, mesh = {Humans ; *Skin/microbiology ; Female ; Adult ; *Microbiota ; *Oxylipins/metabolism ; *Lipid Metabolism ; *Lipidomics/methods ; Child ; Malassezia ; Keratinocytes/microbiology/metabolism ; Middle Aged ; Male ; Metagenomics/methods ; Sebum/metabolism ; Interleukin-6/metabolism ; Interleukin-1beta/metabolism ; Aged ; Coculture Techniques ; Adolescent ; Bacteria/classification/metabolism/genetics/isolation & purification ; Young Adult ; Host Microbial Interactions ; Ecosystem ; }, abstract = {Sebaceous free fatty acids are metabolized by multiple skin microbes into bioactive lipid mediators termed oxylipins. This study investigated correlations between skin oxylipins and microbes on the superficial skin of pre-pubescent children (N = 36) and adults (N = 100), including pre- (N = 25) and post-menopausal females (N = 25). Lipidomics and metagenomics revealed that Malassezia restricta positively correlated with the oxylipin 9,10-DiHOME on adult skin and negatively correlated with its precursor, 9,10-EpOME, on pre-pubescent skin. Co-culturing Malassezia with keratinocytes demonstrated a link between 9,10-DiHOME and pro-inflammatory cytokines IL-1β and IL-6 production. We also observed strong correlations between other skin oxylipins and microbial taxa, highlighting life stage differences in sebum production and microbial community composition. Our findings imply a complex host-microbe communication system mediated by lipid metabolism occurring on human skin, warranting further research into its role in skin health and disease and paving the way towards novel therapeutic targets and treatments.}, } @article {pmid39800316, year = {2025}, author = {He, S and Xue, W and Wu, X and Liang, Z and Gao, J and Qin, W and Wei, H and Zhou, L and Yuan, H and Xie, L}, title = {The application value of targeted next-generation sequencing using bronchoalveolar lavage fluid samples in community-acquired pneumonia in children.}, journal = {Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy}, volume = {31}, number = {3}, pages = {102610}, doi = {10.1016/j.jiac.2025.102610}, pmid = {39800316}, issn = {1437-7780}, abstract = {BACKGROUND: The precise identification of pathogens responsible for community-acquired pneumonia (CAP) in children is essential for effective treatment. However, the performance of targeted next-generation sequencing (tNGS) in the detection of pathogens associated with CAP in children remains unclear.

METHODS: In this study, 216 children diagnosed with CAP were enrolled, and bronchoalveolar lavage fluid (BALF) samples underwent detection through tNGS, culture, and multiplex quantitative polymerase chain reaction (qPCR).

RESULTS: In 208 children, tNGS identified a total of 389 strains of microorganisms, including 111 Mycoplasma pneumoniae, 123 bacteria, 127 viruses, and 28 fungi. Among the cases, 89 presented as single-pathogen detection, while 119 exhibited multiple pathogens co-detection. The positive detection rates of bacteria and fungi through tNGS were significantly higher than those achieved through the traditional culture method, with rates of 56.9 % vs 8.3 % for bacteria and 13.0 % vs 4.2 % for fungi, respectively. The overall agreement between tNGS and multiplex qPCR ranged from 89.4 % to 99.1 %, with Kappa values ranging from 0.541 to 0.912 (P = 0.000).

CONCLUSIONS: The tNGS technique demonstrates rapid and effective capabilities in identifying a wide array of pathogens with a detection sensitivity that surpasses traditional culture methodologies while exhibiting a high degree of consistency with multiplex qPCR in detecting respiratory viruses. The tNGS detection method can serve as an important complement to traditional diagnostic approaches; however, caution must be exercised when interpreting tNGS findings due to its heightened sensitivity which may lead to identification of pathogens that are not necessarily responsible for causing disease.}, } @article {pmid39800299, year = {2025}, author = {Pang, S and Cai, X and Yang, L and Zhou, J and Li, X and Xia, S}, title = {Microbial synergy mechanism of hydrogen flux influence on hydrogen-based partial denitrification coupled with anammox in a membrane biofilm reactor.}, journal = {Environmental research}, volume = {268}, number = {}, pages = {120827}, doi = {10.1016/j.envres.2025.120827}, pmid = {39800299}, issn = {1096-0953}, abstract = {The hydrogen-based partial denitrification coupled with anammox (H2-PDA) biofilm system effectively achieves low-carbon and high-efficiency biological nitrogen removal. However, the effects and biological interaction mechanism of H2 flux with the H2-PDA system have not yet been understood. This study assessed the effects of H2 flux on interactions among anammox bacteria (AnAOB), denitrifying bacteria (DB), and sulfate-reducing bacteria (SRB) coexisting in a H2-PDA system. Results showed the simultaneous removal of 40 mg/L ammonium nitrogen (NH4[+]-N) and 50 mg/L nitrate nitrogen (NO3[-]-N) in the H2-PDA system at a flux of 0.13-0.14 e[-] eq/(m[2]·d) without additional organic carbon. Candidatus_Brocadia was involved in H2 oxidation and was negatively associated with the heterotrophic Thauera genus (DB). The expression of nirS and dsrA was increased to 5.6 × 10[5] copies/gSS and 2.1 × 10[5] copies/gSS, respectively, with excessive H2 flux (0.17 e[-] eq/(m[2]·d). This study provides technical guidance for understanding and applying the H2-PDA technology for low-carbon wastewater treatment.}, } @article {pmid39799988, year = {2025}, author = {Chen, L and Wu, Z and Niu, J and Wang, Y and Cai, M and Xi, J and Cui, Y and Cheng, L and Fan, X}, title = {Simultaneous nitrogen removal and phosphorus recovery in granular sludge-based partial denitrification/anammox-hydroxyapatite precipitation (PD/A-HAP) process under low C/N ratio and dissolved oxygen limitation.}, journal = {Bioresource technology}, volume = {419}, number = {}, pages = {132045}, doi = {10.1016/j.biortech.2025.132045}, pmid = {39799988}, issn = {1873-2976}, mesh = {*Phosphorus/metabolism ; *Nitrogen ; *Sewage/microbiology ; *Denitrification ; *Durapatite/chemistry ; *Oxygen/metabolism ; *Carbon ; Bioreactors ; Chemical Precipitation ; Water Purification/methods ; Oxidation-Reduction ; Anaerobiosis ; }, abstract = {This study integrates partial denitrification/Anammox (PD/A) with hydroxyapatite (HAP) crystallization in a single reactor, achieving simultaneous nitrogen and phosphorus removal along with phosphorus recovery. By adjusting pH, sludge concentration, low COD/TN ratio, and applying moderate dissolved oxygen stress, the system operated stably and promoted the synergistic growth of HAP and biomass. Results showed a nitrogen removal efficiency (NRE) of 94.13 % and a phosphorus removal efficiency (PRE) of 73.6 %. Metagenomic analysis revealed that under dissolved oxygen stress, The abundance of Candidatus Brocadia increased from 1 % to 26.1 %, significantly boosting anammox activity. indicating enhanced microbial activity. The upregulation of related genes (sdh, suc, hzs) further boosted AnAOB activity. HAP was identified as the main inorganic component of the granule. This process shows strong potential for nitrogen and phosphorus removal with resource recovery in wastewater treatment.}, } @article {pmid39799815, year = {2025}, author = {Zhao, S and Zhang, H and Zhu, Y and Xing, Z and Chen, W and Dong, B and Zheng, Z and Ji, C and Xue, Y and Liu, X}, title = {Residual heavy metals and antibiotic pollution in abandoned breeding areas along the northeast coast of Hainan Island, China.}, journal = {Marine pollution bulletin}, volume = {212}, number = {}, pages = {117518}, doi = {10.1016/j.marpolbul.2024.117518}, pmid = {39799815}, issn = {1879-3363}, abstract = {To assess the environmental status of an abandoned aquaculture and breeding area in the northeast coast of the Hainan Island, surface and well water, sediment and surface soils were sampled and analyzed for conventional physicochemical properties, heavy metals and antibiotics. Metagenome tests were also conducted to determine the composition and diversity of the microbial community in typical habitats. Affected by the discharge of wastewater from higher-place pond aquaculture, coastal freshwater rivers have undergone significant salinization, Cl[-] and Na[+] were as high as 4.51 × 10[3] and 1.42 × 10[3] mg/L. The 3 hand-pumped wells surveyed were also suffered from varying degrees of salinization and heavy metal pollution, especially the threat of arsenic pollution. Compared with the local background values, significantly higher valves of Cu, Zn, As and Cd were observed in the surface soil and sediment, and the average concentrations for Cu, Zn, As and Cd are 5.71, 17.6, 15.4 and 0.09 mg/kg respectively. For As，the Nemerow index ranges from 7 to 16 and the geoaccumulation index is between 2 and 4, indicating moderate to severe pollution levels in surface soil. 14 antibiotics were detected in the soil and sediment samples, and the highest total amount was 73 μg/kg, with tetracycline being the dominant antibiotic. Sediment and forest soil showed different microbial community and the genetic diversity index of sediment was lower than that of the forest soils. For typical vegetation soil, the genetic diversity followed the order as P. elliottii × P. caribaea > Eucalyptus > C. equisetifolia. Among the soil and sediment samples, the highest abundances of antibiotic resistance genes (ARGs) were associated with elfamycin, peptide, rifamycin, and the most common antibiotic resistance mechanisms were antibiotic target alteration (54.5 %), antibiotic efflux (27.6 %) and antibiotic target replacement (12.1 %). The metal resistance genes (MRGs) for Cu, Fe, and Zn resistance were the main MRGs in the samples. This study identified the potential ecological environment risk factors in the abandoned coastal breeding areas, and suggested continuous monitoring and assessment of the residual pollutant abatement processes in the future.}, } @article {pmid39799800, year = {2025}, author = {Floyd, B and Gaston, F and Saadoon, R and Shaikh, N and Bakir, M}, title = {Disseminated histoplasmosis in a 4-month-old infant presenting with prolonged fever and pancytopenia: A case report.}, journal = {Journal de mycologie medicale}, volume = {35}, number = {1}, pages = {101532}, doi = {10.1016/j.mycmed.2025.101532}, pmid = {39799800}, issn = {1773-0449}, abstract = {BACKGROUND: Histoplasmosis is the most prevalent endemic mycosis in the United States, typically affecting immunocompromised individuals. Diagnosis of histoplasmosis in immunocompetent patients is rare, particularly among young infants, with only a few cases reported.

CASE PRESENTATION: We present a 4-month-old female with a history of prematurity who initially presented with 11 days of fever. She visited her local emergency department, where she was diagnosed with Rhino/enterovirus bronchiolitis. Pancytopenia was noted at that time, attributed to viral bone marrow suppression. Persistent fever and pancytopenia led to her transfer to our hospital for further evaluation and treatment. On admission, she exhibited hepatosplenomegaly, pancytopenia, elevated procalcitonin, and lactate dehydrogenase levels. Additionally, T cell deficiency was observed. Initially, there was concern for hemophagocytic lymphohistiocytosis; however, bone marrow biopsy and aspirate confirmed T cell deficiency. As fever persisted on day 19, further investigations were conducted, including a positive beta-D-glucan assay. Subsequent urine and serum Histoplasma antigen tests were positive, with metagenomic sequencing confirming the diagnosis of histoplasmosis. Treatment comprised one week of amphotericin B followed by three months of oral itraconazole. Resolution of fever, pancytopenia, T cell deficiency, and hepatosplenomegaly occurred, and the patient has shown no signs of recurrence to date.

CONCLUSIONS: This case serves as a reminder to clinicians regarding the necessity of considering disseminated histoplasmosis in young infants who present with fever of unknown origin, pancytopenia, and hepatosplenomegaly, despite its rarity. Failure to do so can lead to fatal outcomes.}, } @article {pmid39799674, year = {2025}, author = {Li, Y and Qin, W and Xin, X and Tang, C and Huang, Y and He, X and Chen, L and Yu, G and Yu, F}, title = {Dynamic impact of polyethylene terephthalate nanoplastics on antibiotic resistance and microplastics degradation genes in the rhizosphere of Oryza sativa L.}, journal = {Journal of hazardous materials}, volume = {487}, number = {}, pages = {137173}, doi = {10.1016/j.jhazmat.2025.137173}, pmid = {39799674}, issn = {1873-3336}, abstract = {This study examined the effects of polyethylene terephthalate (PET) nanoplastics on the rhizosphere of Oryza sativa L., focusing on dynamic changes and interactions among microbial communities, antibiotic resistance genes (ARGs) and microplastic degradation genes (MDGs). PET exposure altered the structure and function of soil microbial, enabling specific microbial groups to thrive in polluted environments. High-dose PET treatments markedly increased the abundance and dissemination of ARGs, primarily via resistance mechanisms such as antibiotic efflux and target alteration. By providing additional carbon sources and surfaces for microbial attachment, PET stimulated the growth of microorganisms harboring MDGs, resulting in an increase in MDGs abundance. The elevated expression of MDGs facilitated the propagation of ARGs, with overlapping host microorganisms suggesting that certain microbial groups exhibit dual metabolic capabilities, enabling them to endure both antibiotic and microplastic pressures. Toxic byproducts of microplastic degradation, such as mono-ethylhexyl phthalate, further promoted ARGs dissemination by increasing horizontal gene transfer frequency. Structural equation modeling revealed that PET indirectly influenced ARGs and MDGs expression by altering soil C/N ratio, available phosphorus, and enzyme activities. Thus, nanoscale PET exacerbates ecological risks to soil microbial communities by driving co-propagation of ARGs and MDGs, highlighting the persistent threat of composite pollution to agroecosystems.}, } @article {pmid39799113, year = {2025}, author = {Tyagi, A and Choi, YY and Shan, L and Vinothkanna, A and Lee, ES and Chelliah, R and Barathikannan, K and Raman, ST and Park, SJ and Jia, AQ and Choi, GP and Oh, DH}, title = {Limosilactobacillus reuteri fermented brown rice alleviates anxiety improves cognition and modulates gut microbiota in stressed mice.}, journal = {NPJ science of food}, volume = {9}, number = {1}, pages = {5}, pmid = {39799113}, issn = {2396-8370}, support = {4299990913942//the fourth Brain Korea (BK) 21 Plus Project/ ; 4299990913942//the fourth Brain Korea (BK) 21 Plus Project/ ; }, abstract = {Chronic stress disrupts gut microbiota homeostasis, contributing to anxiety and depression. This study explored the effects of Limosilactobacillus reuteri fermented brown rice (FBR) on anxiety using an ICR mouse chronic mild stress (CMS) model. Anxiety was assessed through body weight, corticosterone levels, neurotransmitter profiles, and behavioral tests. A four-week FBR regimen reduced corticosterone, restored neurotransmitters like gamma-aminobutyric acid (GABA) and serotonin, and improved anxiety-related behaviors. Metagenomic (16S rRNA) and metabolomic analyses revealed enhanced amino acid metabolism, energy metabolism, and short-chain fatty acid (SCFA) production in FBR-treated mice. FBR-enriched beneficial gut bacteria, aligning the microbiota profile with that of non-stressed mice. FBR also modulated GABA receptor-related gene expression, promoting relaxation. Network pharmacology identified quercetin, GABA, glutamic acid, phenylalanine, and ferulic acid as bioactive compounds with neuroprotective potential. These findings highlight FBR's potential as a gut-brain axis-targeted therapeutic for anxiety and stress-related disorders.}, } @article {pmid39798925, year = {2025}, author = {Aleksandrova, RR and Nieuwenhuis, LM and Karmi, N and Zhang, S and Swarte, JC and Björk, JR and Gacesa, R and Blokzijl, H and Connelly, MA and Weersma, RK and Lisman, T and Festen, EAM and de Meijer, VE and , }, title = {Gut microbiome dysbiosis is not associated with portal vein thrombosis in patients with end-stage liver disease: a cross-sectional study.}, journal = {Journal of thrombosis and haemostasis : JTH}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jtha.2024.12.036}, pmid = {39798925}, issn = {1538-7836}, abstract = {BACKGROUND: Portal vein thrombosis (PVT) is a common complication in patients with end-stage liver disease (ESLD). The portal vein in patients with ESLD is proposedly an inflammatory vascular bed due to translocation of endotoxins and cytokines from the gut. We hypothesized that a proinflammatory gut microbiome and elevated trimethylamine N-oxide (TMAO), a driver of thrombosis, may contribute to PVT development.

OBJECTIVES: We investigated whether gut microbiome diversity, bacterial species, metabolic pathways, and TMAO levels are associated with PVT in patients with ESLD.

METHODS: Fecal samples, plasma samples, and data from patients with ESLD and healthy controls were collected through the TransplantLines Biobank and Cohort Study. PVT was defined as a thrombus in the portal vein within a year prior to or after fecal sample collection. Fecal samples were analyzed using Shotgun Metagenomic Sequencing, and TMAO levels were measured in plasma using a Vantera Clinical Analyzer.

RESULTS: One hundred two patients with ESLD, of which 23 with PVT, and 246 healthy controls were included. No significant difference in gut microbiome diversity was found between patients with PVT and without PVT (P = .18). Both ESLD groups had significantly lower alpha diversity than controls. Bacteroides fragilis and 3 Clostridiales species were increased in patients with PVT compared with without PVT. TMAO levels between the 3 groups were not significantly different.

CONCLUSION: We observed profound differences in gut microbiota between patients with ESLD and controls, but minimal differences between patients with ESLD with or without PVT. In our cohort, a gut-derived proinflammatory state was not associated with presence of PVT in patients with ESLD.}, } @article {pmid39798664, year = {2025}, author = {Wu, Y and Liu, X and Yin, M and Pei, Y and Cui, Y and Li, J and Zhu, Y and Guo, W and Li, D}, title = {Combining metagenomic sequencing and molecular docking to understand signaling molecule degradation characteristics of quorum quenching consortia.}, journal = {Environmental research}, volume = {268}, number = {}, pages = {120815}, doi = {10.1016/j.envres.2025.120815}, pmid = {39798664}, issn = {1096-0953}, abstract = {Quorum quenching consortia (QQC) enriched by special substrates for bioaugmentation is a promising QQ technology to reduce biofouling, sludge yield, and sludge bulking. However, the effect of substrate type on the performance of QQC is still a research gap. This study selected three different substrates, regular AHLs (N-octanoyl-l-homoserine lactone, C8), 3-oxo-AHLs (3-oxo-octanoyl)-l-homoserine lactone, 3-oxo-C8), and AHLs analogs (γ-caprolactone, GCL) to enrich three QQC (C8-QQC, 3OC8-QQC, GCL-QQC). Combining metagenomic sequencing, protein prediction, and molecular docking to fill the above gaps from the perspective of bacteria and enzymes. The performance of the three QQC decreased with the increasing complexity of the molecular structure of the substrates. This decline was attributed to more complex substrate enriched with more bacteria, lacking QQ genes in the QQC. All QQC degraded N-acetyl-l-homoserine lactones (AHLs) via acylase and lactonase. C8-QQC and 3OC8-QQC showed stronger degradation capabilities for N-(3-oxo-hexanoyl)-L-homoserine lactone (3OC6) compared to N-hexanoyl-L-homoserine lactone (C6), whereas GCL-QQC exhibited stronger degradation for C6. Molecular docking results showed that in 3OC8-QQC and C8-QQC, most enzymes exhibited stronger degradation capabilities for long-chain and 3OAHLs. However, in GCL-QQC, more QQ enzymes showed stronger degradation for C6 than for 3OC6, explaining the observed differences in AHL degradation. β-Oxidation metabolic pathways in bins revealed differences in their abilities to metabolize octanoic acid from C8 and 3-oxo-octanoic acid from 3OC8, which influenced their abundance in the respective QQC. The study findings offer insights into the relationship between substrates and QQC performance at the gene and protein levels.}, } @article {pmid39798656, year = {2025}, author = {Xing, F and Ma, X and Sun, B and Wang, T and Lian, F and Wang, L and Fu, Z}, title = {Enhancing anammox granular sludge for mainstream anammox process by adding iron-loaded diatomite: Performance and intrinsic mechanism.}, journal = {Environmental research}, volume = {268}, number = {}, pages = {120806}, doi = {10.1016/j.envres.2025.120806}, pmid = {39798656}, issn = {1096-0953}, abstract = {Iron-loaded diatomite (Fe-DE) was developed as the innovative material to enhance anammox granular sludge (AnGS) and mainstream anammox performance. By adding Fe-DE with the Fe:DE ratio of 1:20 and the dosage of 3 g/L, the start-up period of mainstream anammox process was shortened from 29 d to 17 d and its nitrogen removal rate was increased from 0.234 kg N/(m[3]·d) to 0.437 kg N/(m[3]·d). AnGS generated more hydrophobic functional groups and redox substances, forming the robust particle structure and improving the electron transfer of anammox reaction. In addition, the key genes PleC, PleD and TrpE/G, related to quorum sensing, increased from 502.69, 91.18 and 18.25 CPM to 532.84, 103.66 and 19.96 CPM. The key genes hzs and hdh related to anammox process also increased by 30.76% and 24.26%. As a result, formation of AnGS was promoted and the enrichment level of Candidatus Brocadia was improved. This study provides a novel insight into the development of innovative material for enhancing mainstream anammox process.}, } @article {pmid39798650, year = {2025}, author = {Zhang, X and Guo, W and Zhang, Z and Gao, P and Tang, P and Liu, T and Yao, X and Li, J}, title = {Insights into the mobility and bacterial hosts of antibiotic resistance genes under dinotefuran selection pressure in aerobic granular sludge based on metagenomic binning and functional modules.}, journal = {Environmental research}, volume = {268}, number = {}, pages = {120807}, doi = {10.1016/j.envres.2025.120807}, pmid = {39798650}, issn = {1096-0953}, abstract = {Dinotefuran (DIN) is toxic to non-target organisms and accelerates the evolution of antibiotic resistance, which poses a problem for the stable operation of the activated sludge process in wastewater treatment plants (WWTPs). However, the emergence and the transfer mechanism of antibiotic resistance genes (ARGs) in activated sludge systems under DIN stress remains unclear. Thus, in the study, the potential impact of DIN on ARGs and virulence factor genes (VFGs) in aerobic granular sludge (AGS) was investigated in depth using metagenomic binning and functional modules. It was found that DIN stress increased the total abundance of ARGs, mobile genetic elements (MGEs), and VFGs in the AGS system, with the highest abundance of fabG (4.6%), tnpA (55.6%) and LPS (39.0%), respectively. The proliferation of the enteric pathogens Salmonella enterica and Escherichia coli in the system indicates that DIN induces exposure of harmless bacteria to the infected environment. The genera Nitrospira (1169 ARG subtypes) and Dechloromonas (663 ARG subtypes) were identified as the potentially antibiotic-resistant bacteria carrying the most ARGs and MGEs in the metagenome-assembled genomes. Co-localization patterns of some ARGs, MGEs, and the SOS response-related gene lexA were observed on metagenome-assembled contigs under high levels of DIN exposure, suggesting DIN stimulated ROS production (101.8% increase over control), altered cell membrane permeability, and increased the potential for horizontal gene transfer (HGT). Furthermore, the DNA damage caused by DIN in AGS led to the activation of the antioxidant system and the SOS repair response, which in turn promoted the expression of the type IV secretion system and HGT through the flagellar channel. This study extends the previously unappreciated DIN understanding of the spread and associated risks of ARGs and VFGs in the AGS system of WWTPs. It elucidates how DIN facilitates HGT, offering a scientific basis for controlling emerging contaminant-induced resistance.}, } @article {pmid39798533, year = {2025}, author = {Mao, X and Yin, X and Yang, Y and Gao, F and Li, S and Shi, X and Deng, Y and Li, L and Leung, KMY and Zhang, T}, title = {Longitudinal metagenomic analysis on antibiotic resistome, mobilome, and microbiome of river ecosystems in a sub-tropical metropolitan city.}, journal = {Water research}, volume = {274}, number = {}, pages = {123102}, doi = {10.1016/j.watres.2025.123102}, pmid = {39798533}, issn = {1879-2448}, abstract = {Rivers play an important role as reservoirs and sinks for antibiotic resistance genes (ARGs). However, it remains underexplored for the resistome and associated mobilome in river ecosystems, and hosts of riverine ARGs particularly the pathogenic ones are rarely studied. This study for the first time conducted a longitudinal metagenomic analysis to unveil the resistome, mobilome, and microbiome in river water, by collecting samples from 16 rivers in Hong Kong over a three-year period and using both short-read and long-read sequencing. Results revealed that aminoglycoside, bacitracin, β-lactam, macrolide lincosamide-streptogramin, and sulfonamide were the predominant ARG types in the river water samples. Riverine ARGs exhibited high spatial variations in abundance and diversity. Environmental factors such as fecal coliform count, Escherichia coli count, 5-day biochemical oxygen demand (BOD5), dissolved oxygen (DO), and total organic carbon (TOC) had a significant correlation to the absolute concentrations of ARGs. Nanopore sequencing was used to reveal the physical genetic linkage of mobile genetic elements (MGEs) with ARGs in river water samples. The results showed that qacEdelta, transposase, integrase, and Tn916 had a high prevalence in ARG-carrying long reads. Host tracking using ARG-carrying reads identified 23 pathogenic bacteria species that harbored ARGs. Some ARGs were shared by different bacterial groups. This study presented a nuanced insight of resistome in river water by a longitudinal metagenomic analysis and deepened our understanding of common and divergent riverine antimicrobial resistant risk across the regional patterns.}, } @article {pmid39798461, year = {2025}, author = {Silvester, R and Perry, WB and Webster, G and Rushton, L and Baldwin, A and Pass, DA and Healey, N and Farkas, K and Craine, N and Cross, G and Kille, P and Weightman, AJ and Jones, DL}, title = {Metagenomics unveils the role of hospitals and wastewater treatment plants on the environmental burden of antibiotic resistance genes and opportunistic pathogens.}, journal = {The Science of the total environment}, volume = {961}, number = {}, pages = {178403}, doi = {10.1016/j.scitotenv.2025.178403}, pmid = {39798461}, issn = {1879-1026}, mesh = {*Wastewater/microbiology ; *Waste Disposal, Fluid ; *Metagenomics ; *Hospitals ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Bacteria/drug effects/genetics ; Drug Resistance, Bacterial/genetics ; Environmental Monitoring ; }, abstract = {Antimicrobial resistance (AMR) is a global health challenge, with hospitals and wastewater treatment plants (WWTPs) serving as significant pathways for the dissemination of antibiotic resistance genes (ARGs). This study investigates the potential of wastewater-based epidemiology (WBE) as an early warning system for assessing the burden of AMR at the population level. In this comprehensive year-long study, effluent was collected weekly from three large hospitals, and treated and untreated wastewater were collected monthly from three associated community WWTPs. Metagenomic analysis revealed a significantly higher relative abundance and diversity of ARGs in hospital wastewater than in WWTPs. Notably, ARGs conferring resistance to clinically significant antibiotics such as β-lactams, aminoglycosides, sulfonamides, and tetracyclines were more prevalent in hospital effluents. Conversely, resistance genes associated with rifampicin and MLS (macrolides-lincosamide-streptogramin) were more commonly detected in the WWTPs, particularly in the treated effluent. Network analysis identified the potential bacterial hosts, which are the key carriers of these ARGs. The study further highlighted the variability in ARG removal efficiencies across the WWTPs, with none achieving complete elimination of ARGs or a significant reduction in bacterial diversity. Additionally, ARG profiles remained relatively consistent in hospital and community wastewater throughout the study, indicating a persistent release of a baseload of ARGs and pathogenic bacteria into surface waters, potentially polluting aquatic environments and entering the food chain. The study underscores the need for routine WBE surveillance, enhanced wastewater treatment strategies, and hospital-level source control measures to mitigate AMR dissemination into the environment.}, } @article {pmid39798326, year = {2025}, author = {Tang, Q and Zhao, Y and Li, X and Zhang, J and Li, J and Zhao, C and Pang, Y and Li, W and Huang, Q and Xiong, J and Qian, K and Liu, Z and Guo, J}, title = {Glyphosate and spinetoram alter viral communities with different effects on antibiotic resistance genes in the bumblebee gut.}, journal = {Journal of environmental management}, volume = {374}, number = {}, pages = {124079}, doi = {10.1016/j.jenvman.2025.124079}, pmid = {39798326}, issn = {1095-8630}, mesh = {Animals ; *Glyphosate ; Bees/virology/drug effects ; *Drug Resistance, Microbial/genetics ; Glycine/analogs & derivatives/pharmacology/toxicity ; }, abstract = {Limited research investigating the impact of pesticides on antibiotic resistance genes (ARGs) and viral community in the gut of wild animals. In this study, we employed metagenomic to investigate the effects of glyphosate and spinetoram on the gut viral communities, ARGs, and their interactions in a key wild pollinator, bumblebees. The results showed that both 2.5 mg/L glyphosate and 2.5 mg/L spinetoram did not significantly alter the α-diversity of the ARGs (p > 0.05). However, spinetoram significantly enriched core ARG subtypes, such as Bado_rpoB_RIF, Bbif_ileS_MUP, and CRP, and total abundance of ARGs (p < 0.05). In contrast, glyphosate had no significant impact on ARG subtypes or total abundance (p > 0.05). The mantel test (R = 0.455, p = 0.020) and Procrustes analysis (M[2] = 0.095, p = 0.069) revealed a significant correlation between the bacterial community and ARGs. Although glyphosate and spinetoram had no significant effect on the relative abundance of mobile ARGs (p > 0.05), both significantly altered the alpha diversity (p < 0.05) and compositional structure (one-way PERMANOVA, p = 0.003) of the gut viral communities, with glyphosate increasing the abundance of lytic phages (p < 0.05). Notably, a phage and host relationship network constructed revealed no evidence of phage-mediated ARGs transduction, but five associations between lytic phages and antibiotic-resistant bacteria (ARB) were identified. Furthermore, glyphosate and spinetoram exposure significantly reduced the total relative abundance of these five lytic phages in the viral community (p < 0.001), indicating that phages primarily function in lysing ARBs. These findings suggest that glyphosate may inhibit the enrichment of ARGs by increasing the abundance of lytic phages, while spinetoram may promote the enrichment of total ARGs by affecting the bacterial community.}, } @article {pmid39798310, year = {2025}, author = {Zhou, HZ and Wang, BQ and Ma, YH and Sun, YY and Zhou, HL and Song, Z and Zhao, Y and Chen, W and Min, J and Li, JW and He, T}, title = {The combination of metagenomics and metabolomics reveals the effect of nitrogen fertilizer application driving the remobilization of immobilization remediation cadmium and rhizosphere microbial succession in rice.}, journal = {Journal of hazardous materials}, volume = {487}, number = {}, pages = {137117}, doi = {10.1016/j.jhazmat.2025.137117}, pmid = {39798310}, issn = {1873-3336}, abstract = {The remobilization of cadmium (Cd) in contaminated farmland soil due to nitrogen fertilizer addition has raised significant concerns regarding the effectiveness of immobilization remediation. This study investigated the effects of ammonia nitrogen (NH4[+]-N) and nitrogen (NO3[-]-N) application (100 kg/ha) on the remobilization of immobilization of remediation Cd (bound to clay palygorskite) during various growth stages of rice through field experiments. Our findings revealed that increased organic acid secretion (e.g., benzoic acid and malic acid) from rice roots, induced by NH4[+]-N, significantly enhanced the NH4NO3-extractable Cd content. Consequently, the concentration of Cd in brown rice varied from 39.84 to 43.25 μg/kg to 78.31-90.44 μg/kg. While NO3[-]-N exhibited a relatively weaker capacity for Cd remobilization (Cd content in brown rices: 50.17-65.23 μg/kg). Meanwhile, the organic acid secretion in roots inhibited the expression of most functional genes (e.g., nifK and napA), leading to shifts in microbial communities and functional metabolism (e.g., Cd[2+] exporting). According to the results of metagenome-assembled genome (MAG) composition, specific MAGs with fewer functional annotations were enriched under NH4[+]-N treatment, may further increased risk of Cd exposure in rice by stimulating amt expression. Interaction analysis of metabolic products and microbial communities indicated acids linked to branched-chain amino acid (BCAA) metabolism and urea cycle might serve as a potentially key process influencing microbial dynamics.}, } @article {pmid39798223, year = {2025}, author = {Larsson, SC and Ericson, U and Dekkers, KF and Arage, G and Rašo, LM and Sayols-Baixeras, S and Hammar, U and Baldanzi, G and Nguyen, D and Nielsen, HB and Holm, JB and Risérus, U and Michaëlsson, K and Sundström, J and Smith, JG and Engström, G and Ärnlöv, J and Orho-Melander, M and Fall, T and Ahmad, S}, title = {Meat intake in relation to composition and function of gut microbiota.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {45}, number = {}, pages = {124-133}, doi = {10.1016/j.clnu.2024.12.034}, pmid = {39798223}, issn = {1532-1983}, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Male ; Female ; Middle Aged ; Adult ; Diet/methods/statistics & numerical data ; Meat/microbiology ; Aged ; Red Meat/microbiology ; Metagenomics/methods ; Biomarkers/blood ; }, abstract = {OBJECTIVE: Meat intake is suggested to affect gut microbiome composition and the risk of chronic diseases. We aimed to identify meat-associated gut microbiome features and their association with host factors.

DESIGN: Gut microbiota species were profiled by deep shotgun metagenomics sequencing in 9669 individuals. Intake of white meat, unprocessed red meat, and processed red meat was assessed using a food frequency questionnaire. The associations of meat intake with alpha-diversity and relative abundance of gut microbiota species were tested using linear regression models with adjustment for dietary fiber intake, body mass index, and other potential confounders. Meat-associated species were further assessed for association with enrichment of microbial gene function, meat-associated plasma metabolites, and clinical biomarkers.

RESULTS: Higher intake of processed red meat was associated with reduced alpha microbial diversity. White meat, unprocessed, and processed red meat intakes were associated with 36, 14, and 322 microbiota species, respectively. Species associated with processed red meat were enriched for bacterial pathways like amino acid degradation, while those negatively linked were enriched for pathways like homoacetogenesis. Furthermore, species positively associated with processed red meat were to a large extent associated with reduced trimethylamine N-oxide and glutamine levels but increased creatine and carnitine metabolites, fasting insulin and glucose, C-reactive protein, apolipoprotein A1, and triglyceride levels and higher blood pressure.

CONCLUSION: This largest to date population-based study on meat and gut microbiota suggests that meat intake, particularly processed red meat, may modify the gut microbiota composition, functional capacity, and health-related biomarkers.}, } @article {pmid39797569, year = {2025}, author = {Rogers, AB and Kale, V and Baldi, G and Alberdi, A and Gilbert, MTP and Gupta, D and Limborg, MT and Li, S and Payne, T and Petersen, B and Rasmussen, JA and Richardson, L and Finn, RD}, title = {HoloFood Data Portal: holo-omic datasets for analysing host-microbiota interactions in animal production.}, journal = {Database : the journal of biological databases and curation}, volume = {2025}, number = {}, pages = {}, pmid = {39797569}, issn = {1758-0463}, mesh = {Animals ; *Chickens/microbiology ; Host Microbial Interactions/genetics ; Salmon/microbiology ; Microbiota ; Databases, Genetic ; Gastrointestinal Microbiome ; }, abstract = {The HoloFood project used a hologenomic approach to understand the impact of host-microbiota interactions on salmon and chicken production by analysing multiomic data, phenotypic characteristics, and associated metadata in response to novel feeds. The project's raw data, derived analyses, and metadata are deposited in public, open archives (BioSamples, European Nucleotide Archive, MetaboLights, and MGnify), so making use of these diverse data types may require access to multiple resources. This is especially complex where analysis pipelines produce derived outputs such as functional profiles or genome catalogues. The HoloFood Data Portal is a web resource that simplifies access to the project datasets. For example, users can conveniently access multiomic datasets derived from the same individual or retrieve host phenotypic data with a linked gut microbiome sample. Project-specific metagenome-assembled genome and viral catalogues are also provided, linking to broader datasets in MGnify. The portal stores only data necessary to provide these relationships, with possible linking to the underlying repositories. The portal showcases a model approach for how future multiomics datasets can be made available. Database URL: https://www.holofooddata.org.}, } @article {pmid39797470, year = {2025}, author = {Záhonová, K and Kaur, H and Furgason, CC and Smirnova, AV and Dunfield, PF and Dacks, JB}, title = {Comparative Analysis of Protist Communities in Oilsands Tailings Using Amplicon Sequencing and Metagenomics.}, journal = {Environmental microbiology}, volume = {27}, number = {1}, pages = {e70029}, pmid = {39797470}, issn = {1462-2920}, support = {e-INFRA CZ (90254)//the Ministry of Education, Youth and Sports of the Czech Republic/ ; CRDPJ 542973-19//Natural Sciences and Engineering Research Council of Canada/ ; RES0021028//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Alberta ; *Metagenomics/methods ; *Oil and Gas Fields ; *Eukaryota/genetics/classification ; RNA, Ribosomal, 18S/genetics ; Biodiversity ; Phylogeny ; }, abstract = {The Canadian province of Alberta contains substantial oilsands reservoirs, consisting of bitumen, clay and sand. Extracting oil involves separating bitumen from inorganic particles using hot water and chemical diluents, resulting in liquid tailings waste with ecotoxicologically significant compounds. Ongoing efforts aim to reclaim tailings-affected areas, with protist colonisation serving as one assessment method of reclamation progress. Oilsands-associated protist communities have mainly been evaluated using amplicon sequencing of the 18S rRNA V4 region; however, this barcode may overlook important protist groups. This study examined how community assessment methods between the V4 and V9 regions differ in representing protist diversity across four oilsands-associated environments. The V9 barcode identified more operational taxonomical units (OTUs) for Discoba, Metamonada and Amoebozoa compared with the V4. A comparative shotgun metagenomics approach revealed few eukaryotic contigs but did recover a complete Paramicrosporidia mitochondrial genome, only the second publicly available from microsporidians. Both V4 and V9 markers were informative for assessing community diversity in oilsands-associated environments and are most effective when combined for a comprehensive taxonomic estimate, particularly in anoxic environments.}, } @article {pmid39797441, year = {2025}, author = {McCorison, CB and Kim, T and Donato, JJ and LaPara, TM}, title = {Proximity-Ligation Metagenomic Sequence Analysis Reveals That the Antibiotic Resistome Makes Significant Transitions During Municipal Wastewater Treatment.}, journal = {Environmental microbiology}, volume = {27}, number = {1}, pages = {e70036}, pmid = {39797441}, issn = {1462-2920}, support = {//Minnesota Environment and Natural Resources Trust Fund/ ; }, mesh = {*Wastewater/microbiology ; *Metagenomics ; *Bioreactors/microbiology ; *Sewage/microbiology ; *Bacteria/genetics/drug effects/classification ; Metagenome ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Water Purification ; Waste Disposal, Fluid ; Drug Resistance, Microbial/genetics ; }, abstract = {Shotgun and proximity-ligation metagenomic sequencing were used to generate thousands of metagenome assembled genomes (MAGs) from the untreated wastewater, activated sludge bioreactors, and anaerobic digesters from two full-scale municipal wastewater treatment facilities. Analysis of the antibiotic resistance genes (ARGs) in the pool of contigs from the shotgun metagenomic sequences revealed significantly different relative abundances and types of ARGs in the untreated wastewaster compared to the activated sludge bioreactors or the anaerobic digesters (p < 0.05). In contrast, these results were statistically similar when comparing the ARGs in the pool of MAGs, suggesting that proximity-ligation metagenomic sequencing is particularly useful for pairing ARGs with their hosts but less adept at discerning quantitative differences in ARG types and relative abundances. For example, numerous MAGs of the genera Acinetobacter, Enterococcus, Klebsiella and Pseudomonas were identified in the untreated wastewater, many of which harboured plasmid-borne and/or chromosomal-borne ARGs; none of these MAGs, however, were detected in the activated sludge bioreactors or anaerobic digesters. In conclusion, this research demonstrates that the antibiotic resistome undergoes significant transitions in both the relative abundance and the host organisms during the municipal wastewater treatment process.}, } @article {pmid39796619, year = {2025}, author = {Johnson, AJ and Alvear, A and Knights, D and Chow, LS and Bantle, AE}, title = {A Randomized Pilot Study of Time-Restricted Eating Shows Minimal Microbiome Changes.}, journal = {Nutrients}, volume = {17}, number = {1}, pages = {}, pmid = {39796619}, issn = {2072-6643}, support = {KL2TR002492//National Institutes of Health, National Center of Advancing Translational Sciences/ ; UL1TR002494//National Institutes of Health, National Center for Advancing Translational Sciences/ ; K23DK115906/DK/NIDDK NIH HHS/United States ; 17SFR-2YR50LC//Healthy Foods, Healthy Lives Institute at the University of Minnesota/ ; }, mesh = {Humans ; Pilot Projects ; *Gastrointestinal Microbiome ; Male ; *Feces/microbiology ; Female ; Adult ; Obesity/microbiology ; Middle Aged ; Body Composition ; Fasting ; Time Factors ; }, abstract = {OBJECTIVE: TRE is an emerging approach in obesity treatment, yet there is limited data on how it influences gut microbiome composition in humans. Our objective was to characterize the gut microbiome of human participants before and after a TRE intervention. This is a secondary analysis of a previously published clinical trial examining the effects of time-restricted eating (TRE).

METHODS: In a previously published, 12-week randomized controlled trial, Chow et al. evaluated the effects of an 8-h TRE intervention on body composition in human participants. Chow et al. demonstrated significant reductions in weight, lean mass, and visceral fat in the TRE group compared to those following time-unrestricted eating (non-TRE). Stool samples were collected by a subset of those participants using home kits at both baseline and post-intervention for shotgun metagenomic sequencing for this secondary analysis. Microbiome community composition was compared before and after intervention as alpha and beta diversity.

RESULTS: Sixteen participants provided stool samples (eight in the TRE group and eight in the non-TRE group). Stool samples were collected from all participants at at least one time point, but both pre- and post-treatment samples were available from only five participants who completed both baseline and post-treatment collections. In alignment with the findings of Chow et al., the participants in the TRE group of the secondary analysis who collected microbiome sample(s) successfully reduced their eating window from an average of 15.3 ± 0.8 h at baseline to 9.3 ± 1.7 h during the intervention (mean ± SD, p < 0.001) and the non-TRE group's eating window remained unchanged. While the TRE group lost weight and visceral fat mass, no effect of the TRE intervention was observed on alpha diversity (Shannon index, Simpson index, and number of taxa, linear mixed models), beta diversity (Bray-Curtis, PERMANOVA), even after controlling for weight and visceral fat changes.

CONCLUSIONS: Our analysis did not detect any significant differences in gut microbiome composition or diversity indices between participants undergoing a TRE intervention and those in the control group. The study's findings are limited by a small sample size, short duration, and the collection of stool samples at only two time points. Future studies with larger sample sizes, longer durations, and more frequent sampling, and collection of detailed dietary data are needed to better understand the relationship between TRE and gut microbiome dynamics.}, } @article {pmid39796584, year = {2024}, author = {Firrman, J and Deyaert, S and Mahalak, KK and Liu, L and Baudot, A and Joossens, M and Poppe, J and Cameron, SJS and Van den Abbeele, P}, title = {The Bifidogenic Effect of 2'Fucosyllactose Is Driven by Age-Specific Bifidobacterium Species, Demonstrating Age as an Important Factor for Gut Microbiome Targeted Precision Medicine.}, journal = {Nutrients}, volume = {17}, number = {1}, pages = {}, pmid = {39796584}, issn = {2072-6643}, support = {8072-41000-102-00D//United States Department of Agriculture/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Trisaccharides/pharmacology ; *Bifidobacterium/drug effects ; Infant ; *Feces/microbiology ; Aged ; Adult ; Child, Preschool ; *Precision Medicine ; Middle Aged ; Child ; Female ; Male ; Age Factors ; Young Adult ; Adolescent ; Milk, Human/chemistry ; Oligosaccharides/pharmacology ; Lactose ; }, abstract = {BACKGROUND: The human gut microbiota develops in concordance with its host over a lifetime, resulting in age-related shifts in community structure and metabolic function. Little is known about whether these changes impact the community's response to microbiome-targeted therapeutics. Providing critical information on this subject, faecal microbiomes of subjects from six age groups, spanning from infancy to 70-year-old adults (n = six per age group) were harvested. The responses of these divergent communities to treatment with the human milk oligosaccharide 2'-fucosyllactose (2'FL), fructo-oligosaccharides (FOS), and lactose was investigated using the Ex vivo SIFR[®] technology that employs bioreactor fermentation and is validated to be predictive of clinical findings. Additionally, it was evaluated whether combining faecal microbiomes of a given age group into a single pooled microbiome produced similar results as the individual microbiomes.

RESULTS: First, marked age-dependent changes in community structure were identified. Bifidobacterium levels strongly declined as age increased, and Bifidobacterium species composition was age-dependent: B. longum, B. catenulatum/pseudocatenulatum, and B. adolescentis were most prevalent for breastfed infants, toddlers/children, and adults, respectively. Metabolomic analyses (LA-REIMS) demonstrated that these age-dependent differences particularly impacted treatment effects of 2'FL (more than FOS/lactose). Further analysis revealed that while 2'FL enhanced production of short-chain fatty acids (SCFAs) and exerted potent bifidogenic effects, regardless of age, the specific Bifidobacterium species enhanced by 2'FL, as well as subsequent cross-feeding interactions, were highly age-dependent. Furthermore, single-pooled microbiomes produced results that were indicative of the average treatment response for each age group. Nevertheless, pooled microbiomes had an artificially high diversity, thus overestimating treatment responses (especially for infants), did not recapitulate interindividual variation, and disallowed for the correlative analysis required to unravel mechanistic actions.

CONCLUSIONS: Age is an important factor in shaping the gut microbiome, with the dominant taxa and their metabolites changing over a lifetime. This divergence affects the response of the microbiota to therapeutics, demonstrated in this study using 2'FL. These results evidence the importance of screening across multiple age groups separately to provide granularity of how therapeutics impact the microbiome and, consequently, human health.}, } @article {pmid39796532, year = {2024}, author = {Paterson, S and Majchrzak, M and Gómez-Garre, D and Ortega-Hernández, A and Sánchez-González, S and de la Fuente, MÁ and Gómez-Cortés, P and Hernández-Ledesma, B}, title = {Role of Simulated Nannochloropsis gaditana Digests in Shaping Gut Microbiota and Short-Chain Fatty Acid Levels.}, journal = {Nutrients}, volume = {17}, number = {1}, pages = {}, pmid = {39796532}, issn = {2072-6643}, support = {PID2021-122989OB-I00//Ministerio de Ciencia, Innovación y Universidades/ ; PIPF-2022/BIO-24996//Comunidad Autónoma de Madrid/ ; }, mesh = {*Gastrointestinal Microbiome/physiology/drug effects ; Humans ; *Fatty Acids, Volatile/metabolism ; *Microalgae ; *Fermentation ; Stramenopiles/metabolism ; RNA, Ribosomal, 16S ; Bacteria/metabolism/classification/genetics ; Colon/microbiology/metabolism ; }, abstract = {The connection between gut microbiota and factors like diet is crucial for maintaining intestinal balance, which in turn impacts the host's overall health. Nannochloropsis gaditana microalgae is a sustainable source of bioactive compounds, mainly known for its used in aquaculture and extraction of bioactive lipids, with potential health benefits whose effects on human gut microbiota are still unknown. Therefore, the goal of this work was to assess the impact of N. gaditana on human gut microbiota composition and derived metabolites by combining the INFOGEST protocol and in vitro colonic fermentation process to evaluate potential effects on human gut microbiota conformation through 16S rRNA gene sequencing and its metabolic functionality. The results have demonstrated the ability of the digests from N. gaditana to significantly modify gut microbiota composition, promoting an increase in beneficial bacterial genera such as Akkermansia, Butyricicoccus, Eisenbergiella, Lachnoclostridium, and Marvinbryantia, in contrast to inulin, after 48 h of colonic fermentation. Additionally, the digests increased the levels of both major and minor short-chain fatty acids (SCFAs), particularly butyric and valeric acids, considered as intestinal biomarkers, and increased ammonium production. This research has demonstrated, for the first time, the potential of N. gaditana microalgae as a sustainable agent for influencing the composition and functionality of human gut microbiota.}, } @article {pmid39796518, year = {2024}, author = {Vega-Rojas, A and Haro, C and Molina-Abril, H and Guil-Luna, S and Santos-Marcos, JA and Gutierrez-Mariscal, FM and Garcia-Fernandez, H and Caballero-Villarraso, J and Rodriguez-Ariza, A and Lopez-Miranda, J and Perez-Martinez, P and Hervas, A and Camargo, A}, title = {Gut Microbiota Interacts with Dietary Habits in Screenings for Early Detection of Colorectal Cancer.}, journal = {Nutrients}, volume = {17}, number = {1}, pages = {}, pmid = {39796518}, issn = {2072-6643}, support = {PI-0055-2021//Consejería de Salud y Consumo/ ; PI-0156-2016//Consejería de Salud y Consumo/ ; AGL2015-67896-P//Ministerio de Ciencia, Innovación y Universidades/ ; n.a.//European Union/ ; CP14/00114//Instituto de Salud Carlos III/ ; PI19/00299//Instituto de Salud Carlos III/ ; DTS19/00007//Instituto de Salud Carlos III/ ; PI22/00925//Instituto de Salud Carlos III/ ; C1-0001-2022//Andalusian Health Service/ ; }, mesh = {Humans ; *Colorectal Neoplasms/microbiology/diagnosis ; *Gastrointestinal Microbiome ; *Early Detection of Cancer/methods ; Male ; Female ; Middle Aged ; *Feeding Behavior ; *Colonoscopy ; Aged ; Adenocarcinoma/microbiology ; Occult Blood ; Diet ; Colonic Polyps/microbiology/diagnosis ; Feces/microbiology ; }, abstract = {BACKGROUND/OBJECTIVES: Gut microbiota interacts with nutrients, which may be relevant to assigning a microbial signature to colorectal cancer (CRC). We aim to evaluate the potential of gut microbiota combined with dietary habits in the early detection of pathological findings related to CRC in the course of a screening program.

METHODOLOGY: The colonoscopy performed on 152 subjects positive for fecal occult blood test showed that 6 subjects had adenocarcinoma, 123 had polyps, and 23 subjects had no pathological findings. Gut microbiota was analyzed by 16S metagenomic. Caret package was used to build the classification models in R.

RESULTS: Random forest (RF) classifier models were used to test the potential of gut microbiota alone or combined with dietary habits as a biomarker to discern between individuals with CRC-related lesions (polyps or adenocarcinoma) versus individuals without pathological findings. RF classifier models yielded an area under the curve of 0.790 using gut microbiota data, 0.710 using dietary habits data, and 0.804 in the combined model including gut microbiota and dietary habits data. The abundance of Suterella, Oscillospirales, Proteobacteria, and Burkholderiales was highly discriminant between groups, together with the consumption of fruit and vegetables and the consumption of carbonated and/or sweetened beverages.

CONCLUSIONS: Our results suggest that the interaction between gut microbiota and dietary habits is relevant when a microbial signature is used as a marker in CRC. Moreover, gut microbiota signature and information about the dietary habits of the individuals seem to be important for improving screening programs for the early detection of CRC.}, } @article {pmid39796476, year = {2024}, author = {Andersen, CJ and Fernandez, ML}, title = {Emerging Biomarkers and Determinants of Lipoprotein Profiles to Predict CVD Risk: Implications for Precision Nutrition.}, journal = {Nutrients}, volume = {17}, number = {1}, pages = {}, pmid = {39796476}, issn = {2072-6643}, mesh = {Humans ; *Cardiovascular Diseases/blood/prevention & control ; *Biomarkers/blood ; *Lipoproteins/blood ; Precision Medicine/methods ; Risk Factors ; Heart Disease Risk Factors ; Nutritional Status ; Risk Assessment ; }, abstract = {Biomarkers constitute a valuable tool to diagnose both the incidence and the prevalence of chronic diseases and may help to inform the design and effectiveness of precision nutrition interventions. Cardiovascular disease (CVD) continues to be the foremost cause of death all over the world. While the reasons that lead to increased risk for CVD are multifactorial, dyslipidemias, plasma concentrations of specific lipoproteins, and dynamic measures of lipoprotein function are strong biomarkers to predict and document coronary heart disease incidence. The aim of this review is to provide a comprehensive evaluation of the biomarkers and emerging approaches that can be utilized to characterize lipoprotein profiles as predictive tools for assessing CVD risk, including the assessment of traditional clinical lipid panels, measures of lipoprotein efflux capacity and inflammatory and antioxidant activity, and omics-based characterization of lipoprotein composition and regulators of lipoprotein metabolism. In addition, we discuss demographic, genetic, metagenomic, and lifestyle determinants of lipoprotein profiles-such as age, sex, gene variants and single-nucleotide polymorphisms, gut microbiome profiles, dietary patterns, physical inactivity, obesity status, smoking and alcohol intake, and stress-which are likely to be essential factors to explain interindividual responses to precision nutrition recommendations to mitigate CVD risk.}, } @article {pmid39796430, year = {2025}, author = {Chen, Q and He, S and Li, M and Sui, Y and Kong, B and Wen, R}, title = {Metagenomic Reveals the Role of Autochthonous Debaryomyces hansenii in the Fermentation and Flavor Formation of Dry Sausage.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {1}, pages = {}, pmid = {39796430}, issn = {2304-8158}, support = {U22A20547//Baohua Kong/ ; 32172232//Qian Chen/ ; }, abstract = {The effect of Debaryomyces hansenii SH4, a typical aroma enhancer, on flavor formation of the dry fermented sausage was investigated using gas chromatography-mass spectrometry and metagenomic sequencing. The results showed that inoculation with D. hansenii SH4 promoted volatile compound formation from carbohydrate and amino acid metabolism and accelerated ester synthesis. The enzymes, genes, and microorganisms involved in the formation pathway of volatile compounds based on microbial metabolism were predicted and constructed into a metabolic pathway network. D. hansenii, Lactobacillus curvatus, Lactobacillus sakei, Lactobacillus plantarum, Leuconostoc fallax, Weissella minor, and Staphylococcus and Candida species were found to be the predominant functional microbes for flavor development in dry sausage. This study established a new insight into the metagenome-based bioinformatic effects of D. hansenii SH4 as a starter culture on the microbial synthesis of key volatile compounds in dry sausage.}, } @article {pmid39796346, year = {2024}, author = {Román-Camacho, JJ and Santos-Dueñas, IM and García-García, I and García-Martínez, T and Peinado, RA and Mauricio, JC}, title = {Correlating Microbial Dynamics with Key Metabolomic Profiles in Three Submerged Culture-Produced Vinegars.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {1}, pages = {}, pmid = {39796346}, issn = {2304-8158}, support = {PID2021-127766OB-I00//Ministerio de Ciencia, Innovación y Universidades/ ; }, abstract = {Although vinegar is a product obtained by a well-known bioprocess from a technical point of view, the complex microbiota responsible for its production and their involvement in the organoleptic profiles are not clear yet. In this work, three acetification profiles in submerged culture using both synthetic and raw materials from Andalusia (Spain) were characterized by metagenomic (16S rRNA amplicon sequencing) and metabolomic tools (stir-bar sorptive extraction with thermo-desorption coupled to gas chromatography-mass spectrometry (SBSE-TD-GC-MS) and high-performance liquid chromatography (HPLC)). A total of 29 phyla, 208 families, and many more genera were identified, comprising bacteria and archaea as well as 75 metabolites, including minor volatile compounds, amino acids, biogenic amines, and other nitrogenous compounds. It can be concluded that Komagataeibacter and Acetobacter were not only the predominant genera but also the ones that most influenced vinegar metabolite profiles by using different metabolic strategies for mutual collaboration, and together with other microbial groups, some of them were previously practically unknown in vinegar. These results can be of interest not only to deepen the basic knowledge about vinegar but also to the vinegar industry by elucidating microbial succession and the key associated metabolites.}, } @article {pmid39796296, year = {2024}, author = {Lee, JH and Son, H and Subramaniyam, S and Lim, HJ and Park, S and Choi, RY and Kim, IW and Seo, M and Kweon, HY and Kim, Y and Kim, SW and Choi, JS and Shin, Y}, title = {Impact of Edible Insect Polysaccharides on Mouse Gut Microbiota: A Study on White-Spotted Flower Chafer Larva (Protaetia brevitarsis seulensis) and Silkworm Pupa (Bombyx mori).}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {1}, pages = {}, pmid = {39796296}, issn = {2304-8158}, support = {PJ01673101//the Cooperative Research Program for Agriculture Science and Technology Development (Project no. PJ01673101)/ ; }, abstract = {The increasing global population and the environmental consequences of meat consumption have led to the exploration of alternative sources of protein. Edible insects have gained attention as a sustainable and nutritionally rich meat alternative. We investigated the effects of two commonly consumed insects, Protaetia brevitarsis seulensis larva and Bombyx mori pupa, on beneficial gut microbiota growth, using whole 16s metagenome sequencing to assess diet-associated changes. Seven-week-old female C57BL/6J mice were administered the edible insects, along with fracto-oligosaccharide (FOS) as a positive control and sham (phosphate buffer saline (PBS)) as a negative control, to assess the relative abundance of insect-diet-associated gut microbes. In total, 567 genera and 470 species were observed, and among these, 15 bacterial genera were differentially abundant in all three groups. These results show that among the two insects, Bombyx mori pupa polysaccharides have a greater ability to regulate beneficial probiotics and next-generation probiotics. In particular, Lactococcus garvieae, which has promising effects on the gastrointestinal tracts of humans and animals, was significantly enriched in both Protaetia brevitarsis seulensis larva and Bombyx mori pupa polysaccharides, similar to fracto-oligosaccharide. The results suggest that the consumption of these insects, particularly polysaccharides, can enhance the growth of beneficial gut microbes, potentially leading to improved overall health in healthy populations.}, } @article {pmid39796082, year = {2024}, author = {Kim, DG and Lee, CM and Lee, YS and Yoon, SH and Kim, SY}, title = {Isolation of a Novel Low-Temperature-Active and Organic-Solvent-Stable Mannanase from the Intestinal Metagenome of Hermetia illucens.}, journal = {International journal of molecular sciences}, volume = {26}, number = {1}, pages = {}, pmid = {39796082}, issn = {1422-0067}, support = {Project No. PJ008604//Rural Development Administration/ ; }, mesh = {*Mannans/metabolism ; Animals ; Phylogeny ; Metagenome ; Diptera/microbiology ; Mannosidases/metabolism/genetics/chemistry ; Gastrointestinal Microbiome ; Substrate Specificity ; Amino Acid Sequence ; Galactans/metabolism ; Enzyme Stability ; Cold Temperature ; Plant Gums/chemistry/metabolism ; Hydrogen-Ion Concentration ; Intestines/microbiology ; Solvents/chemistry ; Recombinant Proteins/metabolism/genetics/chemistry ; Galactose/analogs & derivatives ; }, abstract = {The black soldier fly, Hermetia illucens, is a voracious scavenger of various organic materials; therefore, it could be exploited as a biological system for processing daily food waste. In order to survey novel hydrolytic enzymes, we constructed a fosmid metagenome library using unculturable intestinal microorganisms from H. illucens. Through functional screening of the library on carboxymethyl cellulose plates, we identified a fosmid clone, the product of which displayed hydrolytic activity. Sequence analysis of the fosmid revealed a novel mannan-degrading gene, ManEM6, composed of 1185 base pairs encoding 394 amino acids, with a deduced 20-amino-acid N-terminal signal peptide sequence. The conceptual translation of ManEM6 exhibited the highest identity (78%) to endo-1,4-β-mannosidase from Dysgonomonas mossii. Phylogenetic and domain analyses indicated that ManEM6 encodes a novel mannanase with a glycoside hydrolase family 26 domain. The recombinant protein rManEM6 showed its highest activity at 40 °C and pH 7.0, and it remained stable in the range of pH 5-10.0. rManEM6 hydrolyzed substrates with β-1,4-glycosidic mannoses, showing maximum enzymatic activity toward locust bean gum galactomannan, while it did not hydrolyze p-nitrophenyl-β-pyranosides, demonstrating endo-form mannosidase activity. rManEM6 was highly stable under stringent conditions, including those of polar organic solvents, as well as reducing and denaturing reagents. Therefore, ManEM6 may be an attractive candidate for the degradation of mannan under high-organic-solvent and protein-denaturing processes in the food and feed industries.}, } @article {pmid39795878, year = {2024}, author = {Niecwietajewa, I and Banasiewicz, J and Zaremba-Wróblewski, G and Majewska, A}, title = {Exploring the Link Between Infections and Primary Osteoarthritis: A Next-Generation Metagenomic Sequencing Approach.}, journal = {International journal of molecular sciences}, volume = {26}, number = {1}, pages = {}, pmid = {39795878}, issn = {1422-0067}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Osteoarthritis, Knee/microbiology/genetics ; Female ; Male ; Aged ; Prospective Studies ; Pilot Projects ; Middle Aged ; Synovial Fluid/microbiology ; Synovial Membrane/microbiology ; Metagenome ; }, abstract = {This prospective pilot study examined the association between microorganisms and knee osteoarthritis by identifying pathogens in the synovial membrane, synovial fluid, and blood samples from two patients with primary bilateral knee osteoarthritis, using metagenomic next-generation sequencing (mNGS). Intraoperatively, during routine knee arthroplasty procedures, we collected the following 12 samples from each patient: two synovial membrane samples, two synovial fluid samples, and two venous blood samples. After DNA isolation and library construction, each sample was subjected to deep whole-genome sequencing using the DNBSEQT17 platform with the read length PE150 as the default. Metagenomic sequencing data were mapped to the NCBI NT database to determine species abundance. The predominant species in all samples tested were classified under the Enterobacterales order, the most abundant being Yersinia enterocolitica. The second and third most common microorganisms detected were Escherichia coli and autotrophic, Gram-negative bacteria Synechococcus sp., which is a bioaerosol component, indicating a risk of inhalation of the toxic metabolites of this latter microorganism. This article provides an initial exploration of mNGS use to study the etiopathogenetic mechanisms of knee osteoarthritis (OA). While our analysis identified bacterial DNA, particularly from Yersinia, further cross-sectional studies in larger populations with and without OA are needed to determine the role of these agents in OA pathogenesis.}, } @article {pmid39795003, year = {2024}, author = {Kaszab, E and Sós, E and Bali, K and Sós-Koroknai, V and Perge, E and Ursu, K and Marton, S and Hoitsy, M and Kemenesi, G and Bányai, K}, title = {Near-Complete Avipoxvirus Genome Assembled from Skin Lesions of Dead Eurasian Crane (Grus grus).}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {1}, pages = {}, pmid = {39795003}, issn = {2076-2615}, support = {RRF-2.3.1-21-2022-00001//National Research, Development and Innovation Office/ ; RRF-2.3.1-21-2022-00010//National Research, Development and Innovation Office/ ; }, abstract = {Avian pox is a globally spread viral disease affecting a wide spectrum of wild and domesticated bird species. The disease is caused by a diverse group of large DNA viruses, namely, avipoxviruses (genus Avipoxvirus, family Poxviridae). In this study, gross pathological examination and histopathological examination of skin lesions and several organs suggested acute poxvirus infection of a Eurasian crane (Grus grus, Linnaeus, 1758). Avipoxvirus infection was confirmed by testing wart-like lesions via gene-specific PCR assay and sequencing the obtained amplicon. Phylogenetic analysis of the gene encoding the DNA polymerase revealed that the crane poxvirus clustered in clade A, subclade A3. A large fragment of the poxvirus genome (306,477 bp in length) was assembled from the DNA of a skin specimen. Our study reaffirms previous findings that even complex virus genomes can be determined from a metagenomic assemblage generated directly from avian tissue samples without prior virus isolation, a promising approach for the epidemiologic surveillance of avipoxvirus infections in wild birds and domestic poultry.}, } @article {pmid39795000, year = {2024}, author = {Dai, Z and Xie, B and Xie, C and Xiang, J and Wang, X and Li, J and Zheng, R and Wang, Y}, title = {Comparative Metagenomic Analysis of the Gut Microbiota of Captive Pangolins: A Case Study of Two Species.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {1}, pages = {}, pmid = {39795000}, issn = {2076-2615}, support = {2021C02044//Key R&D Program Projects in Zhejiang Province/ ; }, abstract = {Pangolins, one of the most trafficked mammals, face significant health challenges in captivity, including digestive disorders and immune dysfunctions. These issues are closely linked to alterations in their gut microbiota, which play vital roles in the host metabolism, immunity, and overall health. This study investigated the differences in the gut microbiota composition and function between two pangolin species, Chinese pangolins (Manis pentadactyla) and Malayan pangolins (Manis javanica), under identical captive conditions to better understand their ecological adaptability and health implications. Using metagenomic sequencing, fecal samples from eight adult captive pangolins were analyzed, including four male Malayan pangolins and three male and one female Chinese pangolins. Comparative analyses of the alpha and beta diversities, microbial community structure, and functional profiles were performed. Both species harbored gut microbiota dominated by Firmicutes, Bacteroidetes, and Proteobacteria. However, the Chinese pangolins exhibited higher microbial diversity (Shannon index, p = 0.042; Simpson index, p = 0.037) and lower relative abundance of Proteobacteria compared with the Malayan pangolins. A functional analysis revealed significant differences in the metabolic pathways, where the Chinese pangolins demonstrated a higher potential for fiber degradation, whereas the Malayan pangolins exhibited elevated levels of antibiotic resistance genes and pathogenic taxa, such as Escherichia coli. These findings suggest that captivity duration and environmental stress likely contribute to the observed differences, with the Malayan pangolins experiencing greater dysbiosis due to longer captivity periods. This study provides valuable insights into the role of gut microbiota in pangolin health and offers a foundation for improving conservation strategies and captive care protocols.}, } @article {pmid39794871, year = {2025}, author = {Samodova, D and Stankevic, E and Søndergaard, MS and Hu, N and Ahluwalia, TS and Witte, DR and Belstrøm, D and Lubberding, AF and Jagtap, PD and Hansen, T and Deshmukh, AS}, title = {Salivary proteomics and metaproteomics identifies distinct molecular and taxonomic signatures of type-2 diabetes.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {5}, pmid = {39794871}, issn = {2049-2618}, support = {74550801//European Foundation for the Study of Diabetes/ ; NNF18CC0034900; NNF23SA0084103//Novo Nordisk Fonden/ ; NNF18CC0034900; NNF23SA0084103//Novo Nordisk Fonden/ ; }, mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/metabolism ; *Saliva/microbiology ; *Proteomics/methods ; Male ; Middle Aged ; Female ; *Microbiota ; Biomarkers/metabolism ; Bacterial Proteins/genetics ; Adult ; Bacteria/classification/metabolism/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Computational Biology/methods ; Salivary Proteins and Peptides/metabolism ; Case-Control Studies ; Aged ; }, abstract = {BACKGROUND: Saliva is a protein-rich body fluid for noninvasive discovery of biomolecules, containing both human and microbial components, associated with various chronic diseases. Type-2 diabetes (T2D) imposes a significant health and socio-economic burden. Prior research on T2D salivary microbiome utilized methods such as metagenomics, metatranscriptomics, 16S rRNA sequencing, and low-throughput proteomics.

RESULTS: We conducted ultrafast, in-depth MS-based proteomic and metaproteomic profiling of saliva from 15 newly diagnosed T2D individuals and 15 age-/BMI-matched healthy controls (HC). Using state-of-the-art proteomics, over 4500 human and bacterial proteins were identified in a single 21-min run. Bioinformatic analysis revealed host signatures of altered immune-, lipid-, and glucose-metabolism regulatory systems, increased oxidative stress, and possible precancerous changes in T2D saliva. Abundance of peptides for bacterial genera such as Neisseria and Corynebacterium were altered showing biomarker potential, offering insights into disease pathophysiology and microbial applications for T2D management.

CONCLUSIONS: This study presents a comprehensive mapping of salivary proteins and microbial communities, serving as a foundational resource for enhancing understanding of T2D pathophysiology. The identified biomarkers hold promise for advancing diagnostics and therapeutic approaches in T2D and its associated long-term complication Video Abstract.}, } @article {pmid39794645, year = {2025}, author = {Dirks, RAM and Sosef, NP and Zwartkruis-Nahuis, JTM and Thijssen, MMA and Jansen, CCC and Boxman, ILA}, title = {A Metagenomic Survey of Virological Hazards in Market-Ready Oysters.}, journal = {Food and environmental virology}, volume = {17}, number = {1}, pages = {16}, pmid = {39794645}, issn = {1867-0342}, mesh = {Animals ; *Metagenomics ; *Ostreidae/virology ; *Food Contamination/analysis ; *Shellfish/virology ; Norovirus/genetics/classification/isolation & purification ; Metagenome ; Netherlands ; Genome, Viral ; Viruses/genetics/classification/isolation & purification ; Food Safety ; }, abstract = {Viral contamination of bivalve molluscs, such as oysters, is a well-recognized food safety risk. The aim of this study was to assess virological hazards in market-ready oysters on the Dutch market. Non-targeted metagenome analysis was first performed on norovirus spiked-in samples showing linear and sensitive detection of norovirus GI.2 and GII.4 down to 14 and 5 genome copies per reaction, respectively. Subsequently, metagenomic measurements were performed to detect vertebrate viral genomes present in 24 undepurated B-area samples and 144 market-ready oyster samples taken in November up to and including February of the years 2015-2021. Genome sequences from fifteen viral species were identified in market-ready oysters which are associated with infections in humans and were detected above the genomic coverage threshold (5%) applied. Among these, the two genera from the Caliciviridae family, norovirus and sapovirus were detected at high prevalence (44 and 30%). Additionally, adeno-associated dependoparvovirus A and B as well as Aichi virus A and B (ribo)nucleic acids were detected (42, 33, 6, and 11%). Nucleic acids from virus species in oysters included potentially hazardous Picobirnavirus, Anellovirus, and multiple Circoviridae and Genomoviridae species. By integrating metagenome analysis into the monitoring process, researchers, food producers and regulatory bodies can gain valuable insights into the viral communities present in the food chain. This allows for the detection of potential pathogenic hazards at an early stage, providing an opportunity for tailored monitoring programs and targeted interventions to maintain the sanitary quality of the production area and safeguard public health.}, } @article {pmid39794618, year = {2025}, author = {Nguyen, HP and Le, BT and Nguyen, HN and Nguyen, TT and Duong, TH and Hoang, TC and Duy, NPT and Nguyen, MV and Duong, LN and Le, LQ and Pham, TT}, title = {Demonstration of adapted packed-bed bioreactor for accurate and rapid estimation of biochemical oxygen demand: insights into the influence of microbial community structure and functions.}, journal = {World journal of microbiology & biotechnology}, volume = {41}, number = {2}, pages = {31}, pmid = {39794618}, issn = {1573-0972}, support = {NCUD.02-2019.52//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; NCUD.02-2019.52//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; NCUD.02-2019.52//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; NCUD.02-2019.52//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; NCUD.02-2019.52//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; NCUD.02-2019.52//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; NCUD.02-2019.52//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; NCUD.02-2019.52//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; NCUD.02-2019.52//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; }, mesh = {*Bioreactors/microbiology ; *Wastewater/microbiology/chemistry ; *Biological Oxygen Demand Analysis ; *Microbial Consortia ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Metagenomics/methods ; Biodegradation, Environmental ; Cocos/microbiology ; Glucose/metabolism ; Azo Compounds/metabolism ; Metagenome ; }, abstract = {This study demonstrated a novel approach to accurately estimate 5-day biochemical oxygen demand (BOD5) in textile wastewater using a microbial consortium from food processing wastewater fixed on coconut fibers. Although glucose-glutamic acid (GGA) has been widely known as the most preferred substrates for microbial respiration, its calibration surprisingly resulted in an overestimation of BOD5 in textile wastewater due to its lower utilization rate compared to that of textile wastewater. After being adapted with a new nutrient environment composed of GGA and textile wastewater, the adapted packed-bed bioreactors (PBBRs) was capable of accurate estimation of BOD5 in textile wastewater using GGA standard solution. Metagenomic analysis revealed the dominance of the genera Enterobacter, Acinetobacter, Chryseobacterium, and Comamonas in the adapted microbial community, which are recognized for their significant potential in azo dye degradation. The imputed metagenome showed an enhanced showed an enhanced abundance of "Amino Acid Degradation" and "Carbohydrate Degradation" functions, confirming the improved ability of adapted community to utilization of GGA in the standard solution. These findings suggest that adaptation of exogenous microbial consortium to a nutrient environment composed of GGA and target wastewater may shift the community to that dominated by strains having both utilization ability of GGA and target compounds which, in turn, enhance the accuracy of the adapted PBBRs for estimation of BOD5 in target wastewater.}, } @article {pmid39794474, year = {2025}, author = {Yin, Q and da Silva, AC and Zorrilla, F and Almeida, AS and Patil, KR and Almeida, A}, title = {Ecological dynamics of Enterobacteriaceae in the human gut microbiome across global populations.}, journal = {Nature microbiology}, volume = {10}, number = {2}, pages = {541-553}, pmid = {39794474}, issn = {2058-5276}, support = {MR/W016184/1//RCUK | Medical Research Council (MRC)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Enterobacteriaceae/genetics/classification/isolation & purification ; Metagenome ; Enterobacteriaceae Infections/microbiology ; Feces/microbiology ; Machine Learning ; }, abstract = {Gut bacteria from the Enterobacteriaceae family are a major cause of opportunistic infections worldwide. Given their prevalence among healthy human gut microbiomes, interspecies interactions may play a role in modulating infection resistance. Here we uncover global ecological patterns linked to Enterobacteriaceae colonization and abundance by leveraging a large-scale dataset of 12,238 public human gut metagenomes spanning 45 countries. Machine learning analyses identified a robust gut microbiome signature associated with Enterobacteriaceae colonization status, consistent across health states and geographic locations. We classified 172 gut microbial species as co-colonizers and 135 as co-excluders, revealing a genus-wide signal of colonization resistance within Faecalibacterium and strain-specific co-colonization patterns of the underexplored Faecalimonas phoceensis. Co-exclusion is linked to functions involved in short-chain fatty acid production, iron metabolism and quorum sensing, while co-colonization is linked to greater functional diversity and metabolic resemblance to Enterobacteriaceae. Our work underscores the critical role of the intestinal environment in the colonization success of gut-associated opportunistic pathogens with implications for developing non-antibiotic therapeutic strategies.}, } @article {pmid39794073, year = {2025}, author = {Kitsios, GD and Morris, A}, title = {Blurred Lines on the Dysbiosis Spectrum: Pneumocystis Colonization vs Infection by Metagenomics.}, journal = {Chest}, volume = {167}, number = {1}, pages = {3-5}, doi = {10.1016/j.chest.2024.08.038}, pmid = {39794073}, issn = {1931-3543}, } @article {pmid39793869, year = {2025}, author = {Xu, W and Wu, L and Geng, M and Zhou, J and Bai, S and Nguyen, DV and Ma, R and Wu, D and Qian, J}, title = {Biochar@MIL-88A(Fe) accelerates direct interspecies electron transfer and hydrogen transfer in waste activated sludge anaerobic digestion: Exploring electron transfer and biomolecular mechanisms.}, journal = {Environmental research}, volume = {268}, number = {}, pages = {120810}, doi = {10.1016/j.envres.2025.120810}, pmid = {39793869}, issn = {1096-0953}, abstract = {Adding additives exogenously is an effective strategy to enhance methanogenic activity and improve AD stability. Corn straw-based biochar@MIL-88A(Fe) (BM) was synthesized herewith and used as an exogenous additive to boost methane (CH4) production. After adding BM at 250 mg/g WAS VS, the accumulative CH4 production and maximum CH4 yield increased by 1.2 and 1.9 times, respectively, with CH4 comprising 88% of the biogas. BM accelerated electron transfer through its unsaturated sites and surface functional groups, while also enhancing metabolic functions for facilitating enzymatic activities and converting organic substrates. The abundance of syntrophic bacteria and methanogen were higher after BM addition. BM-mediated DIET and IHT pathways effectively oxidized propionate and butyrate, promoting methane generation. Higher expression of key genes involved in methane production correlated with shifts in microbial structure and increased CH4 yield after BM dosage. The invention of BM may provide more solutions for addressing low energy recovery during AD.}, } @article {pmid39793775, year = {2025}, author = {Li, X and Ning, L and Zhao, H and Gu, C and Han, Y and Xu, W and Si, Y and Xu, Y and Wang, R and Ren, Q}, title = {Jiawei Ermiao Granules (JWEMGs) clear persistent HR-HPV infection though improving vaginal microecology.}, journal = {Journal of ethnopharmacology}, volume = {341}, number = {}, pages = {119342}, doi = {10.1016/j.jep.2025.119342}, pmid = {39793775}, issn = {1872-7573}, mesh = {Female ; Humans ; *Vagina/microbiology/drug effects/pathology ; *Papillomavirus Infections/drug therapy ; *Drugs, Chinese Herbal/pharmacology ; Adult ; Middle Aged ; Microbiota/drug effects ; Antiviral Agents/pharmacology ; Cytokines/metabolism ; Young Adult ; }, abstract = {Jiawei Ermiao Granules (JWEMGs), a traditional Chinese herbal formulation, has been widely used in China for the treatment of human papillomavirus (HPV) infections. However, the underlying mechanisms through which it exerts its antiviral effects remain poorly understood.

AIM OF THE STUDY: This study aimed to investigate the potential mechanisms by which JWEMGs modulate vaginal microecology and clear HPV infections, utilizing clinical trials, metagenomic sequencing, and in vitro models.

MATERIALS AND METHODS: Clinical indicators related to vaginal microecology, such as vaginal pH, cleanliness, Nugent score, Donders score, catalase, neuraminidase, and leukocyte esterase, were evaluated in 65 patients with high-risk HPV (HR-HPV) infection. The study examined the impact of two courses of oral JWEMGs on these clinical parameters. Additionally, metagenomic sequencing was performed on vaginal lavage samples from 33 patients to assess the alteration of the vaginal microbiome following JWEMGs treatment. Immunohistochemistry was used to detect ALPK1 expression in cervical exfoliated cells, and ELISA was employed to measure cytokine levels in vaginal lavage fluid. JWEMGs intervention was applied to HaCaT-HPV E6/E7 cells to evaluate its effects on restoring α-kinase 1 (ALPK1) expression and promoting the secretion of cytokines and chemokines.

RESULTS: Treatment with JWEMGs significantly improved several clinical indicators, including cleanliness, pH, Nugent score, Donders score, catalase, neuraminidase, and leukocyte esterase, in HR-HPV-infected patients. Furthermore, JWEMGs therapy led to an increased abundance of Lactobacillus species, especially Lactobacillus crispatus, and a marked reduction in Gardnerella species. JWEMGs treatment also significantly promoted ALPK1 expression in cervical exfoliated cells and augmented the secretion of key cytokines, including IL-6, IL-8, and TNF-α. In parallel, in vitro results showed that JWEMGs substantially enhanced IL-6, IL-8, TNF-α, CCL2, CCL5, and CCL7 secretion in HaCaT-HPV E6/E7 cells, which correlated with the activation of the ALPK1/NF-κB signaling pathway.

CONCLUSION: In conclusion, JWEMGs treatment effectively remodels the vaginal microbiota and bolsters mucosal immunity in the lower genital tract, thereby improving the vaginal microecology in HR-HPV-infected individuals. In vitro findings further demonstrated that JWEMGs promote cytokine and chemokine expression, activating the ALPK1/NF-κB pathway.}, } @article {pmid39793486, year = {2025}, author = {Eckermann, H and Lustermans, H and Parnanen, K and Lahti, L and de Weerth, C}, title = {Maternal pre- and postnatal stress and maternal and infant gut microbiota features.}, journal = {Psychoneuroendocrinology}, volume = {172}, number = {}, pages = {107273}, doi = {10.1016/j.psyneuen.2024.107273}, pmid = {39793486}, issn = {1873-3360}, abstract = {BACKGROUND: Maternal stress can have short and long term adverse (mental) health effects for the mother and her child. Previous evidence suggests that the gut microbiota may be a potential mediator and moderator for the effects of stress via various pathways. This study explored the maternal microbiota trajectory during pregnancy as well as the association between pre- and postnatal maternal stress and features of the maternal and infant gut microbiota during and after pregnancy. In line with previous research, we hypothesized that maternal stress would be positively related to maternal and infant microbiota volatility and that infants of highly stressed mothers would show a relative increase in Proteobacteria and a relative decrease in Bifidobacterium.

METHODS: We collected maternal stool samples at 18 and 32 weeks of pregnancy and 8 months postpartum. Infant stools samples were obtained at 2, 6 and 12 weeks and 8 months postpartum. All samples were analyzed using shotgun metagenome sequencing. We also collected several measures of maternal stress (self-reported depression, anxiety, and stress, and hair cortisol and cortisone), most at the same time points as the microbiota samples.

RESULTS: Our data indicated that the maternal microbiota does not undergo drastic changes from the second to the third trimester of pregnancy but that the postpartum microbiota differs significantly from the prenatal microbiota. Furthermore, we identified associations between several stress measures and maternal and infant gut microbiota features at different time points including positive and negative associations with alpha diversity, beta diversity and individual microbial phyla and species relative abundances. Also, the maternal stress composite score, the perceived stress score and the log-ratio of hair cortisol and cortisone were all positively associated with infant microbiota volatility.

CONCLUSION: Our study provides evidence that maternal prenatal and postnatal stress is related to both the maternal and the infant microbiota. Collectively, this and previous studies indicate that maternal stress does not uniformly associate with most gut microbial features. Instead, the associations are highly time point specific. Regarding infant microbiota volatility, we have consistently found a positive association between stress and infant microbiota volatility. This warrants future research investigating this link in more depth.}, } @article {pmid39793467, year = {2025}, author = {Cardacino, A and Turco, S and Balestra, GM}, title = {Seasonal dynamics of kiwifruit microbiome: A case study in a KVDS-affected orchard.}, journal = {Microbiological research}, volume = {292}, number = {}, pages = {128044}, doi = {10.1016/j.micres.2024.128044}, pmid = {39793467}, issn = {1618-0623}, mesh = {*Soil Microbiology ; *Plant Diseases/microbiology ; *Microbiota ; *Seasons ; *Actinidia/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Fungi/classification/genetics/isolation & purification ; *Plant Roots/microbiology ; Italy ; Metagenomics ; Temperature ; }, abstract = {Over the past decade, Italian kiwifruit orchards and overall production have faced a significant threat from Kiwifruit Vine Decline Syndrome (KVDS). Despite the insights gained from metagenomics studies into the microbial communities associated with the disease, unanswered questions still remain. In this study, the evolution of bacterial, fungal, and oomycetes communities in soil and root endosphere at three different time points during the vegetative season was investigated for the first time in a KVDS-affected orchard in the Lazio Region. The fungal and oomycetes genera previously associated with the syndrome, including Fusarium, Ilyonectria, Thelonectria, Phytophthora, Pythium and Globisporangium, were identified in both groups. In contrast, the characterization of bacterial communities revealed the first instance of the presence of the genus Ralstonia in soil and root samples. The microbiome composition shifts between KVDS-affected and asymptomatic plants were significant as evidenced by the results, particularly after a temperature increase. This temperature change coincided with the onset of severe disease symptoms and may indicate a key role in the progression of KVDS.}, } @article {pmid39793444, year = {2025}, author = {Verheijden, RJ and van Eijs, MJM and Paganelli, FL and Viveen, MC and Rogers, MRC and Top, J and May, AM and van de Wijgert, JHHM and Suijkerbuijk, KPM and , }, title = {Gut microbiome and immune checkpoint inhibitor toxicity.}, journal = {European journal of cancer (Oxford, England : 1990)}, volume = {216}, number = {}, pages = {115221}, doi = {10.1016/j.ejca.2025.115221}, pmid = {39793444}, issn = {1879-0852}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Immune Checkpoint Inhibitors/adverse effects ; Male ; Female ; Middle Aged ; Aged ; Prospective Studies ; *Neoplasms/drug therapy/microbiology ; Dysbiosis/chemically induced/microbiology ; Adult ; Feces/microbiology ; }, abstract = {BACKGROUND: Multiple studies have suggested that gut microbiome may influence immune checkpoint inhibitor (ICI) efficacy, but its association with immune-related adverse events (irAEs) is less well studied. In this prospective cohort study, we assessed whether gut microbiome composition at start, or changes during ICI, are associated with severe irAEs.

METHODS: Stool samples of cancer patients treated with anti-PD-1 ± anti-CTLA-4 were analyzed using 16S rRNA gene sequencing and metagenomic shotgun sequencing. Differences in alpha and beta diversity between patients with and without severe irAE were assessed, as well as differential relative abundance (RA) of taxa, MetaCyc pathways, and seven prespecified literature-based bacterial groups including pathobionts and Ruminococcaceae.

FINDINGS: We analyzed 497 samples of 195 patients before and soon after starting ICI, at severe irAE onset and after starting immunosuppression. Mean RA of the pathobionts group was significantly higher in patients who developed a severe irAE (8.2 %) compared to those who did not (4.8 %; odds ratio 1.40; 95 %CI 1.07-1.87) at baseline, and also early during ICI treatment and at severe irAE onset. A significantly stronger decrease in RA of Ruminococcaceae after starting ICI was observed in patients who developed a severe irAE compared to those who did not. RAs of Ruminococcaceae, the genus Ruminococcus, and the species R. bromii and R. callidus were significantly lower at severe irAE onset compared to other time points.

INTERPRETATION: Gut microbiome dysbiosis signaled by higher RA of pathobionts and decrease in RA of Ruminococcaceae may predispose to severe irAEs.}, } @article {pmid39793291, year = {2025}, author = {Jahanshahi, DA and Barzani, MRR and Bahram, M and Ariaeenejad, S and Kavousi, K}, title = {Metagenomic exploration and computational prediction of novel enzymes for polyethylene terephthalate degradation.}, journal = {Ecotoxicology and environmental safety}, volume = {289}, number = {}, pages = {117640}, doi = {10.1016/j.ecoenv.2024.117640}, pmid = {39793291}, issn = {1090-2414}, mesh = {*Polyethylene Terephthalates/chemistry ; *Biodegradation, Environmental ; *Metagenomics ; *Soil Microbiology ; *Soil Pollutants/analysis ; Machine Learning ; Enzymes/metabolism/genetics ; }, abstract = {As a global environmental challenge, plastic pollution raises serious ecological and health concerns owing to the excessive accumulation of plastic waste, which disrupts ecosystems, harms wildlife, and threatens human health. Polyethylene terephthalate (PET), one of the most commonly used plastics, has contributed significantly to this growing crisis. This study offers a solution for plastic pollution by identifying novel PET-degrading enzymes. Using a combined approach of computational analysis and metagenomic workflow, we identified a diverse array of genes and enzymes linked to plastic degradation. Our study identified 1305,282 unmapped genes, 36,000 CAZymes, and 317 plastizymes in the soil samples were heavily contaminated with plastic. We extended our approach by training machine learning models to discover candidate PET-degrading enzymes. To overcome the scarcity of known PET-degrading enzymes, we used a Generative Adversarial Network (GAN) model for dataset augmentation and a pretrained deep Evolutionary Scale Language Model (ESM) to generate sequence embeddings for classification. Finally, 21 novel PET-degrading enzymes were identified. These enzymes were further validated through active site analysis, amino acid composition analysis, and 3D structure comparison. Additionally, we isolated bacterial strains from contaminated soils and extracted plastizymes to demonstrate their potential for environmental remediation. This study highlights the importance of biotechnological solutions for plastic pollution, emphasizing scalable, cost-effective processes and the integration of computational and metagenomic methods.}, } @article {pmid39791120, year = {2024}, author = {Huang, H and Yang, Y and Wang, X and Wen, B and Yang, X and Zhong, W and Wang, Q and He, F and Li, J}, title = {Gut virome dysbiosis impairs antitumor immunity and reduces 5-fluorouracil treatment efficacy for colorectal cancer.}, journal = {Frontiers in oncology}, volume = {14}, number = {}, pages = {1501981}, pmid = {39791120}, issn = {2234-943X}, abstract = {INTRODUCTION: Despite the established influence of gut bacteria, the role of the gut virome in modulating colorectal cancer (CRC) patient chemotherapy response remains poorly understood. In this study, we investigated the impact of antiviral (AV) drug-induced gut virome dysbiosis on the efficacy of 5-FU in CRC treatment.

METHODS: Using a subcutaneous CRC mouse model, we assessed tumor growth and immune responses following AV treatment, fecal microbiota transplantation (FMT), and 5-FU administration.

RESULTS: AV therapy reduced the abundance of gut DNA and RNA viruses, leading to accelerated tumor growth, shortened survival, and diminished chemotherapy efficacy. FMT restored the gut virome, improving tumor suppression and extending the survival of 5-FU-treated mice. Metagenomic sequencing revealed significant changes in virome composition, AV treatment expanded Kahnovirus, Petivirales, and Enterogokushovirus, whereas FMT enriched Peduovirus STYP1, Mahlunavirus rarus, and Jouyvirus ev207. AV treatment reduced the number of dendritic cells and CD8+ T cells in peripheral blood and tumor tissues, impairing antitumor immunity, FMT reversed these deficiencies. To further investigate the underlying mechanisms, we examined the TLR3-IRF3-IFN-β pathway, essential for recognizing viral RNA and triggering immune responses. AV treatment downregulated this pathway, impairing immune cell recruitment and reducing chemotherapy efficacy, while activation of TLR3 with Poly(I:C) restored pathway function and enhanced the effectiveness of 5-FU.

DISCUSSION: These findings suggest the importance of maintaining gut virome integrity or activating TLR3 as adjunct strategies to enhance chemotherapy outcomes in CRC patients.}, } @article {pmid39790984, year = {2025}, author = {Paiva, P and Teixeira, LMC and Wei, R and Liu, W and Weber, G and Morth, JP and Westh, P and Petersen, AR and Johansen, MB and Sommerfeldt, A and Sandahl, A and Otzen, DE and Fernandes, PA and Ramos, MJ}, title = {Unveiling the enzymatic pathway of UMG-SP2 urethanase: insights into polyurethane degradation at the atomic level.}, journal = {Chemical science}, volume = {16}, number = {5}, pages = {2437-2452}, pmid = {39790984}, issn = {2041-6520}, abstract = {The recently discovered metagenomic urethanases UMG-SP1, UMG-SP2, and UMG-SP3 have emerged as promising tools to establish a bio-based recycling approach for polyurethane (PU) waste. These enzymes are capable of hydrolyzing urethane bonds in low molecular weight dicarbamates as well as in thermoplastic PU and the amide bond in polyamide employing a Ser-Ser cis -Lys triad for catalysis, similar to members of the amidase signature protein superfamily. Understanding the catalytic mechanism of these urethanases is crucial for enhancing their enzymatic activity and improving PU bio-recycling processes. In this study, we employed hybrid quantum mechanics/molecular mechanics methods to delve into the catalytic machinery of the UMG-SP2 urethanase in breaking down a model PU substrate. Our results indicate that the reaction proceeds in two stages: STAGE 1 - acylation, in which the enzyme becomes covalently bound to the PU substrate, releasing an alcohol-leaving group; STAGE 2 - deacylation, in which a catalytic water hydrolyzes the enzyme:ligand covalent adduct, releasing the product in the form of a highly unstable carbamic acid, expected to rapidly decompose into an amine and carbon dioxide. We found that STAGE 1 comprises the rate-limiting step of the overall reaction, consisting of the cleavage of the substrate's urethane bond by its ester moiety and the release of the alcohol-leaving group (overall Gibbs activation energy of 20.8 kcal mol[-1]). Lastly, we identified point mutations that are expected to enhance the enzyme's turnover for the hydrolysis of urethane bonds by stabilizing the macrodipole of the rate-limiting transition state. These findings expand our current knowledge of urethanases and homolog enzymes from the amidase signature superfamily, paving the way for future research on improving the enzymatic depolymerization of PU plastic materials.}, } @article {pmid39789504, year = {2025}, author = {Duan, J and Ding, J and Wei, Y and Zhang, Y and You, Z and Li, D and Chen, C}, title = {Metagenomic analysis identifying a polymicrobial pulmonary infection in a non-HIV immunocompromised patient: a case report.}, journal = {BMC pulmonary medicine}, volume = {25}, number = {1}, pages = {12}, pmid = {39789504}, issn = {1471-2466}, support = {2019WS113//the Medical Science and Technology Development Foundation of Department of Health of Shandong Province/ ; }, mesh = {Humans ; Male ; Middle Aged ; *Immunocompromised Host ; *Metagenomics ; *Coinfection/diagnosis ; *Bronchoalveolar Lavage Fluid/microbiology ; High-Throughput Nucleotide Sequencing ; Pneumocystis carinii/isolation & purification/genetics ; Nocardia/isolation & purification/genetics ; Tomography, X-Ray Computed ; Pneumonia, Pneumocystis/diagnosis/drug therapy/microbiology ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {BACKGROUND: Polymicrobial pulmonary infections, common in immunocompromised patients, often manifest more severe symptoms than monomicrobial infections. Clinical diagnosis delays may lead to mortality, emphasizing the importance of fast and accurate diagnosis for these patients. Metagenomic next-generation sequencing (mNGS), as an unbiased method capable of detecting all microbes, is a valuable tool to identify pathogens, particularly in cases where infections are difficult to diagnosis using conventional methods.

CASE PRESENTATION: A 50-year-old male patient was admitted due to cough, expectoration and dyspnea. CT scan revealed diffuse inflammatory and cavernous lung lesion, and blood examination suggested a polymicrobial infection. However, no etiology was found by routine examination. mNGS of bronchoalveolar lavage fluid(BALF)simultaneously detected the presence of Pneumocystis jirovecii (P.jirovecii), Aspergillus fumigates (A.fumigates), Nocardia farcinica (N.farcinica), Salmonella enterica subsp. enterica (S.enterica subsp. enterica), and cytomegalovirus (CMV). The patient was successfully treated with compound sulfamethoxazole (SMZ-TMP), cefoperazone/sulbactam (SCF), moxifloxacin (MXF), voriconazole (VCZ), and ganciclovir. The patient recovered after two weeks of anti-infection therapy and maintained good health at a six-month follow-up.

CONCLUSION: For immunocompromised patients with multiple infections and atypical symptoms, mNGS emerged as a reliable approach to pathogen detection and guiding antibiotic therapy.}, } @article {pmid39789442, year = {2025}, author = {Tu, Y and Deng, M and Zhang, X and Xiang, T and Wu, D}, title = {Dabie bandavirus and Mycoplasma pneumoniae co-infection: a case report.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {47}, pmid = {39789442}, issn = {1471-2334}, support = {82000601//National Natural Science Foundation of China/ ; 20224BAB206022, 20232A CB216004//Natural Science Foundation of Jiangxi Province/ ; }, mesh = {Humans ; Male ; *Coinfection/microbiology/virology ; Middle Aged ; *Mycoplasma pneumoniae/isolation & purification/genetics ; *Pneumonia, Mycoplasma/complications/drug therapy/diagnosis/microbiology ; Severe Fever with Thrombocytopenia Syndrome/diagnosis/virology ; Immunoglobulin M/blood ; }, abstract = {BACKGROUND: Severe fever with thrombocytopenia syndrome (SFTS) is an emerging infectious disease caused by Dabie bandavirus (DBV). We report a case of DBV and Mycoplasma pneumoniae (MP) co-infection.

CASE PRESENTATION: Here we reported a 57-year-old healthy male who was admitted with the presentations of fever, cough, hemoptysis, and hypotension. Laboratory investigations revealed thrombocytopenia, leukopenia, and organ dysfunction of liver and kidney. Seroconversion from Mycoplasma IgM antibody to IgG was recorded, and SFTS was confirmed through metagenomic next-generation sequencing. In addition, hemophagocytic lymphohistiocytosis was diagnosed in the context of DBV and MP coinfection. The patient exhibited a rapid recovery following treatment with omadacycline and essential symptomatic and supportive treatment.

CONCLUSIONS: We firstly reported a case with DBV and MP coinfection, which reminded us that the symptoms of DBV infection were bewildering and easy to miss diagnosis when it was co-infection with other etiologies.}, } @article {pmid39789436, year = {2025}, author = {Cao, T and Guo, Y and Lin, L and Wang, D and Liu, Z and Zou, X and Ke, Y and Lv, Z}, title = {Effect of folpet on hypoglycaemia, intestinal microbiota, and drug resistance genes in mice.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {11}, pmid = {39789436}, issn = {1471-2180}, support = {JCYJ20210324124014040//Shenzhen Science and Technology Program/ ; JCYJ20210324124201004//Shenzhen Science and Technology Program/ ; SZSM202011008//Sanming Project of Medicine in Shenzhen/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/genetics ; Mice ; *Hypoglycemia/genetics/chemically induced ; Blood Glucose/metabolism/drug effects ; Sulfonamides/pharmacology ; Bacteria/drug effects/genetics/classification/isolation & purification ; Male ; Metagenomics ; }, abstract = {BACKGROUND: Folpet is a nonspecific sulfonamide fungicide widely used to protect crops from mildew. However, the in vivo effects of folpet on glucose metabolism homeostasis, gut microbiota, and abundance of drug resistance genes remain unknown. The purpose of this study was to assess the effects of the pesticide, folpet, on glucose metabolism homeostasis, and folpet-induced changes in the intestinal microbiota and resistance genes in mice.

METHODS: Mice were orally administered folpet at 0, 1, 10, and 100 mg/kg body weight/day for 5 weeks. Blood sugar levels in mice were measured after 5 weeks of folpet administration. Metagenomic sequencing and drug resistance gene analyses were performed to explore changes in the abundance of gut microbiota members and drug resistance genes in mice after folpet administration. Correlation analysis was performed using metabolomics to explore the relationship between intestinal microbiota, drug resistance genes, and glucose metabolism.

RESULTS: Mice in the folpet group had significantly lower blood glucose levels than those in the control group. The abundance of Atopobium, Libanicoccus, Collinsella, and Parabacteroides in the intestinal microbiota of folpet-treated mice was significantly higher than that in the control group. However, the abundance of Mailhella, Bilophila, Roseburia, and Bacteroides were reduced in folpet-treated mice. Compared with the control group, the abundance of APH6-Ic and AAC6-Ie-APH2-Ia resistance genes in mice treated with folpet significantly increased. The abundance of tetQ, ermE, and BahA resistance genes was significantly reduced after folpet treatment.

CONCLUSIONS: Folpet is associated with changes in the abundance of gut microbiota in mice and may also affect the abundance of drug-resistance genes and the regulation of blood glucose levels.}, } @article {pmid39788986, year = {2025}, author = {Patova, A and Ribeiro, PA and Murillo, FJ and Riesgo, A and Taboada, S and Pomponi, SA and Rapp, HT and Kenchington, E and Xavier, JR}, title = {Population genomics and connectivity of Vazella pourtalesii sponge grounds of the northwest Atlantic with conservation implications of deep sea vulnerable marine ecosystems.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {1540}, pmid = {39788986}, issn = {2045-2322}, mesh = {*Metagenomics ; *Porifera/genetics/metabolism ; Atlantic Ocean ; *Ecosystem ; *Aquatic Organisms/genetics/metabolism ; *Conservation of Natural Resources ; Hunting/statistics & numerical data ; Animal Distribution ; Animals ; Polymorphism, Single Nucleotide/genetics ; Nova Scotia ; }, abstract = {Sponges are key ecosystem engineers that shape, structure and enhance the biodiversity of marine benthic communities globally. Sponge aggregations and reefs are recognized as vulnerable marine ecosystems (or VMEs) due to their susceptibility to damage from bottom-contact fishing gears. Ensuring their long-term sustainability, preservation, and ecosystem functions requires the implementation of sound scientific conservation tools. Here, the genetic diversity, structure, and connectivity of the deep-sea glass sponge, Vazella pourtalesii (Schmidt, 1870), was investigated using 1,102 neutral SNPs obtained in RADseq. This species is distributed across the northwest Atlantic from Florida, USA to Nova Scotia, Canada and we sequenced samples covering this full distribution and provided evidence of strong genetic structure with two distinct clusters: Florida together with the Carolina Shelves and the Scotian Shelf. We estimated moderate levels of diversity with low migration across large distances (> 1000 kms) and high connectivity at smaller scales (< 300 kms). Further, fishing pressure on genetic diversity was evaluated, within two Sponge Conservation Areas (SCAs) on the Scotian Shelf. Those areas have different disturbance histories, and cumulative fishing pressure. Slightly lower levels of genetic diversity were found inside the SCAs, and yet they encompassed a high proportion of the diversity observed within the Scotian Shelf. We provide baseline data for future monitoring of the SCAs, discussing our findings in the light of existing area-based management tools.}, } @article {pmid39788961, year = {2025}, author = {Banerjee, G and Papri, SR and Huang, H and Satapathy, SK and Banerjee, P}, title = {Deep sequencing-derived Metagenome Assembled Genomes from the gut microbiome of liver transplant patients.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {39}, pmid = {39788961}, issn = {2052-4463}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Liver Transplantation ; *Metagenome ; High-Throughput Nucleotide Sequencing ; Akkermansia ; Fatty Liver/microbiology ; }, abstract = {Recurrence of metabolic dysfunction-associated steatotic liver disease (MASLD) after liver transplantation (LT) is a continuing concern. The role of gut microbiome dysbiosis in MASLD initiation and progression has been well established. However, there is a lack of comprehensive gut microbiome shotgun sequence data for patients experiencing MASLD recurrence after LT. In this data descriptor, we describe a dataset of deep metagenomic sequences of a well-defined LT recipient population. Community-based analysis revealed a high abundance of Akkermansia muciniphila, consistently observed in most patient samples with a low (0-2) MASLD Activity Score (NAS). We constructed 357 metagenome-assembled genomes (MAGs), including 220 high-quality MAGs (>90% completion). The abundance of different species of Bacteroides MAGs dominated in patient samples with NAS > 5 ("definite MASH"). In contrast, the MAGs of A. muciniphila, Akkermansia sp., and Blutia sp. dominated in samples from patients without MASH (NAS = 0-2). In addition, the phylogenetic analysis of A. muciniphila and Akkermansia sp. MAGs identified two new phylogroups of Akkermansia that are distinct from the previously reported three phylogroups.}, } @article {pmid39788783, year = {2025}, author = {Franz, K and Markó, L and Mähler, A and Chakaroun, R and Heinitz, S and Schlögl, H and Sacher, J and Steckhan, N and Dechend, R and Adams, N and Andersen, M and Glintborg, D and Viehweger, M and Bahr, LS and Forslund-Startceva, SK}, title = {Sex hormone-dependent host-microbiome interactions and cardiovascular risk (XCVD): design of a longitudinal multi-omics cohort study.}, journal = {BMJ open}, volume = {15}, number = {1}, pages = {e087982}, pmid = {39788783}, issn = {2044-6055}, mesh = {Humans ; *Cardiovascular Diseases/microbiology/epidemiology ; Longitudinal Studies ; Male ; Female ; *Gonadal Steroid Hormones/metabolism/blood ; *Gastrointestinal Microbiome ; Host Microbial Interactions ; Transgender Persons ; Research Design ; Heart Disease Risk Factors ; Adult ; Sex Reassignment Procedures ; Multiomics ; }, abstract = {INTRODUCTION: Cardiovascular diseases (CVDs) present differently in women and men, influenced by host-microbiome interactions. The roles of sex hormones in CVD outcomes and gut microbiome in modifying these effects are poorly understood. The XCVD study examines gut microbiome mediation of sex hormone effects on CVD risk markers by observing transgender participants undergoing gender-affirming hormone therapy (GAHT), with findings expected to extrapolate to cisgender populations.

METHODS AND ANALYSES: This observational, longitudinal cohort study includes baseline, 1- and 2-year follow-ups with transgender participants beginning GAHT. It involves comprehensive phenotyping and microbiome genotyping, integrating computational analyses of high-dimensional data. Microbial diversity will be assessed using gut, skin, and oral samples via 16S rRNA and shotgun metagenomic sequencing of gut samples. Blood measurements will include sex hormones, CVD risk markers, cardiometabolic parameters, cytokines, and immune cell counts. Hair samples will be analysed for cortisol. Participants will complete online questionnaires on physical activity, mental health, stress, quality of life, fatigue, sleep, pain, and gender dysphoria, tracking medication use and diet to control for confounders. Statistical analyses will integrate phenomic, lifestyle, and multi-omic data to model health effects, testing gut microbiome mediation of CVD risk as the endocrine environment shifts between that typical for cisgender men to women and vice versa.

ETHICS AND DISSEMINATION: The study adheres to Good Clinical Practice and the Declaration of Helsinki. The protocol was approved by the Charité Ethical Committee (EA1/339/21). Signed informed consent will be obtained. Results will be published in peer-reviewed journals and conferences and shared as accessible summaries for participants, community groups, and the public, with participants able to view their data securely after public and patient involvement review for accessibility.

TRIAL REGISTRATION NUMBER: The XCVD study was registered on ClinicalTrials.gov (NCT05334888) as 'Sex-differential host-microbiome CVD risk - a longitudinal cohort approach (XCVD)" on 4 April 2022. Data set link can be found at https://classic.

CLINICALTRIALS: gov/ct2/show/NCT05334888.}, } @article {pmid39786931, year = {2025}, author = {Ni, B and Xiao, L and Lin, D and Zhang, TL and Zhang, Q and Liu, Y and Chen, Q and Zhu, D and Qian, H and Rillig, MC and Zhu, YG}, title = {Increasing pesticide diversity impairs soil microbial functions.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {2}, pages = {e2419917122}, pmid = {39786931}, issn = {1091-6490}, support = {41991332//MOST | National Natural Science Foundation of China (NSFC)/ ; 42307027//MOST | National Natural Science Foundation of China (NSFC)/ ; 42222701//MOST | National Natural Science Foundation of China (NSFC)/ ; 2022A-163-G//Ningbo Yongjiang Talent Project/ ; 2021-DST-004//Ningbo S&T project/ ; 2023321//Youth Innovation Promotion Association, Chinese Academy of Sciences/ ; }, mesh = {*Soil Microbiology ; *Pesticides ; *Bacteria/genetics/metabolism/classification/drug effects ; *Soil/chemistry ; *Fertilizers ; *Nitrogen/metabolism ; Phosphorus/metabolism ; Carbon/metabolism ; Sulfur/metabolism ; Agriculture/methods ; Metagenomics/methods ; Microbiota/drug effects ; }, abstract = {Pesticide application is essential for stabilizing agricultural production. However, the effects of increasing pesticide diversity on soil microbial functions remain unclear, particularly under varying nitrogen (N) fertilizer management practices. In this study, we investigated the stochasticity of soil microbes and multitrophic networks through amplicon sequencing, assessed soil community functions related to carbon (C), N, phosphorus (P), and sulfur (S) cycling, and characterized the dominant bacterial life history strategies via metagenomics along a gradient of increasing pesticide diversity under two N addition levels. Our findings show that higher pesticide diversity enriches the abundance of bacterial specialists and opportunists capable of degrading or resisting pesticides, reducing the proportion of bacterial generalists in the absence of N addition. These shifts can complicate multitrophic microbial networks. Under increased pesticide diversity, selective pressure may drive bacteria to streamline their average genome size to conserve energy while enhancing C, N, P, and S metabolic capacities, thus accelerating soil nutrient loss. In comparison, N addition was found to reduce bacterial niche differentiation at higher pesticide diversity, mitigating the impacts of network complexity and functional traits associated with pesticide diversity, ultimately alleviating soil nutrient loss. Our results reveal the contrasting impacts of pesticide diversity on microbial functions under different N input scenarios and emphasize that strategic N fertilizer management can mitigate the ecological effects of pesticide use in agricultural systems.}, } @article {pmid39781513, year = {2025}, author = {Wagatsuma, R and Nishikawa, Y and Hosokawa, M and Takeyama, H}, title = {vClean: assessing virus sequence contamination in viral genomes.}, journal = {NAR genomics and bioinformatics}, volume = {7}, number = {1}, pages = {lqae185}, pmid = {39781513}, issn = {2631-9268}, mesh = {*Genome, Viral/genetics ; *Metagenomics/methods ; Machine Learning ; Viruses/genetics/isolation & purification ; DNA Contamination ; Software ; Sequence Analysis, DNA/methods ; }, abstract = {Recent advancements in viral metagenomics and single-virus genomics have improved our ability to obtain the draft genomes of environmental viruses. However, these methods can introduce virus sequence contaminations into viral genomes when short, fragmented partial sequences are present in the assembled contigs. These contaminations can lead to incorrect analyses; however, practical detection tools are lacking. In this study, we introduce vClean, a novel automated tool that detects contaminations in viral genomes. By applying machine learning to the nucleotide sequence features and gene patterns of the input viral genome, vClean could identify contaminations. Specifically, for tailed double-stranded DNA phages, we attempted accurate predictions by defining single-copy-like genes and counting their duplications. We evaluated the performance of vClean using simulated datasets derived from complete reference genomes, achieving a binary accuracy of 0.932. When vClean was applied to 4693 genomes of medium or higher quality derived from public ocean metagenomic data, 1604 genomes (34.2%) were identified as contaminated. We also demonstrated that vClean can detect contamination in single-virus genome data obtained from river water. vClean provides a new benchmark for quality control of environmental viral genomes and has the potential to become an essential tool for environmental viral genome analysis.}, } @article {pmid39781512, year = {2025}, author = {Sato, N and Katayama, K and Miyaoka, D and Uematsu, M and Saito, A and Fujimoto, K and Uematsu, S and Imoto, S}, title = {stana: an R package for metagenotyping analysis and interactive application based on clinical data.}, journal = {NAR genomics and bioinformatics}, volume = {7}, number = {1}, pages = {lqae191}, pmid = {39781512}, issn = {2631-9268}, mesh = {Humans ; *Software ; *Gastrointestinal Microbiome/genetics ; Crohn Disease/genetics/microbiology ; Metagenomics/methods ; Parkinson Disease/genetics ; Kidney Failure, Chronic/genetics ; Metagenome/genetics ; }, abstract = {Metagenotyping of metagenomic data has recently attracted increasing attention as it resolves intraspecies diversity by identifying single nucleotide variants. Furthermore, gene copy number analysis within species provides a deeper understanding of metabolic functions in microbial communities. However, a platform for examining metagenotyping results based on relevant grouping data is lacking. Here, we have developed the R package, stana, for the processing and analysis of metagenotyping results. The package consists of modules for preprocessing, statistical analysis, functional analysis and visualization. An interactive analysis environment for exploring the metagenotyping results was also developed and publicly released with over 1000 publicly available metagenome samples related to human diseases. Three examples exploring the relationship between the metagenotypes of the gut microbiome and human diseases are presented-end-stage renal disease, Crohn's disease and Parkinson's disease. The results suggest that stana facilitated the confirmation of the original study's findings and the generation of a new hypothesis. The GitHub repository for the package is available at https://github.com/noriakis/stana.}, } @article {pmid39781508, year = {2024}, author = {Park, SS and Park, SH and Jeong, HT and Shin, MS and Kim, MK and Kim, BK and Yoon, HS and Kim, SH and Kim, TW}, title = {The effect of treadmill exercise on memory function and gut microbiota composition in old rats.}, journal = {Journal of exercise rehabilitation}, volume = {20}, number = {6}, pages = {205-212}, pmid = {39781508}, issn = {2288-176X}, abstract = {Aging is associated with declines in memory function and significant change in gut microbiota. In this study, we investigated how exercise affects age-related memory decline and inflammation, and gut microbiota diversity. Bl6 mice were divided into control, control and exercise, old, and old and exercise groups. Treadmill exercise was performed once a day, 5 days a week for 8 consecutive weeks. Short-term memory was assessed using step-through test and spatial learning memory was assessed using Morris water maze task. Enzyme-linked immunosorbent assay was performed for the proinflammatory cytokines, tumor necrosis factor (TNF)-α and interleukin (IL)-6, in the hippocampus. Western blot analysis was conducted for the neurotrophic factors, brain-derived neurotrophic factor (BDNF) and tyrosine kinase B (TrkB), in the hippocampus. In addition, fecal samples were collected for sequencing and metagenomic analysis. Old rats showed decline in short-term memory and spatial learning memory. Increment of TNF-α and IL-6 concentration with decrement of BDNF and TrkB expression were observed in the old rats. Decreased diversity of gut microbiota composition and decreased beneficial gut microbiota were found in the old rats. However, treadmill exercise improved short-term memory, decreased TNF-α and IL-6 concentration, and increased BDNF and TrkB expression in the old rats. Treadmill exercise also increased the diversity of gut microbiota composition and affected the increase of beneficial gut microbiota in the old rats. In conclusion, treadmill exercise reduced age-related inflammatory markers and effectively improved memory decline while enhancing the diversity and abundance of beneficial gut microbiota.}, } @article {pmid39780485, year = {2024}, author = {Wei, A and Zhan, H and Xiao, Z and Zhao, W and Jiang, X}, title = {A novel framework for phage-host prediction via logical probability theory and network sparsification.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {1}, pages = {}, pmid = {39780485}, issn = {1477-4054}, support = {62372205//National Natural Science Foundation of China/ ; ZDI145-56//National Language Commission Key Research Project/ ; KJ02502022-0450//Fundamental Research Funds for Central Universities/ ; 2022CFB289//Natural Science Foundation of Hubei Province of China/ ; CCNU24JC032//Self-determined Research Funds of CCNU from the Colleges' Basic Research and Operation of MOE/ ; }, mesh = {*Bacteriophages/genetics ; Probability Theory ; Algorithms ; Host-Pathogen Interactions ; Computational Biology/methods ; Bacteria/virology/genetics ; }, abstract = {Bacterial resistance has emerged as one of the greatest threats to human health, and phages have shown tremendous potential in addressing the issue of drug-resistant bacteria by lysing host. The identification of phage-host interactions (PHI) is crucial for addressing bacterial infections. Some existing computational methods for predicting PHI are suboptimal in terms of prediction efficiency due to the limited types of available information. Despite the emergence of some supporting information, the generalizability of models using this information is limited by the small scale of the databases. Additionally, most existing models overlook the sparsity of association data, which severely impacts their predictive performance as well. In this study, we propose a dual-view sparse network model (DSPHI) to predict PHI, which leverages logical probability theory and network sparsification. Specifically, we first constructed similarity networks using the sequences of phages and hosts respectively, and then sparsified these networks, enabling the model to focus more on key information during the learning process, thereby improving prediction efficiency. Next, we utilize logical probability theory to compute high-order logical information between phages (hosts), which is known as mutual information. Subsequently, we connect this information in node form to the sparse phage (host) similarity network, resulting in a phage (host) heterogeneous network that better integrates the two information views, thereby reducing the complexity of model computation and enhancing information aggregation capabilities. The hidden features of phages and hosts are explored through graph learning algorithms. Experimental results demonstrate that mutual information is effective information in predicting PHI, and the sparsification procedure of similarity networks significantly improves the model's predictive performance.}, } @article {pmid39780272, year = {2025}, author = {Albert, E and Kis, IE and Kiss, K and K-Jánosi, K and Révész, T and Biksi, I}, title = {Serotype distribution and antimicrobial susceptibility of Streptococcus suis isolates from porcine diagnostic samples in Hungary, 2020-2023.}, journal = {Porcine health management}, volume = {11}, number = {1}, pages = {3}, pmid = {39780272}, issn = {2055-5660}, abstract = {BACKGROUND: Streptococcus suis (S. suis) is a major swine pathogen and a significant zoonotic agent, causing substantial economic losses in the swine sector and having considerable public health importance. The control and management of S. suis-related conditions has become increasingly challenging due to the multitude of involved serotypes with varying antimicrobial resistance patterns. Here, we report the serological distribution and antimicrobial susceptibility of S. suis isolates isolated form clinical samples of Hungarian large-scale swine farms.

RESULTS: Between 2020 and 2023, altogether 296 S. suis isolates were obtained from diseased pigs of 64 Hungarian pig operations. Serotyping of the isolates was carried out by using molecular methods (cps-typing). The isolated strains belonged to 24 single cps-types. The most frequently detected cps-types during the four years of this passive survey were 9 (19.6%), 2 (19.3%), 1/2 (18.9%) and 7 (14.5%). The brain, spleen, endocardial valve thrombus and lung proved to be the most frequent site of S. suis strain isolation, and animals 29-75 days of age were affected in the highest proportion. Antimicrobial susceptibility testing of the isolates was performed by determining the minimal inhibitory concentration for 15 antimicrobial agents of veterinary and human importance using a commercial microdilution assay. More than 90% of the tested isolates proved to be susceptible to the examined beta-lactams, cephalosporins and florfenicol, as well as to rifampicin, trimethoprim/sulfamethoxazole and vancomycin. Phenotypic resistance profiles (resistotypes) of clindamycin-tetracyclin (3.8%), clindamycin-erythromycin-tetracyclin (8.4%) and clindamycin-erythromycin-tetracyclin-trimethoprim / sulfamethoxazole (3.8%) were most frequently detected. Vancomycin resistance was observed in the case of 1 S. suis strain.

CONCLUSIONS: The dominance of S. suis cps-types 9, 2, 1/2 and 7 in Hungary over the four years of this study aligns with previous reports from several countries worldwide. The presence of highly susceptible S. suis isolates suggests a prudent antibiotic usage and treatment practice in the surveyed Hungarian swine operations. In contrary, the presence of several resistotypes could indicate the problem of antibiotic resistance in the future.}, } @article {pmid39779932, year = {2025}, author = {Wei, Y and Zhu, Y and Yang, L and Chen, C and Yue, M and Mao, Z and Wang, Y and Li, Q and Li, Y and Lv, J and Xue, W}, title = {Effects of oil pollution on the growth and rhizosphere microbial community of Calamagrostis epigejos.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {1278}, pmid = {39779932}, issn = {2045-2322}, support = {22NYYF029//Xi'an Agricultural Technology R&D Projects/ ; S2024-JC-YB-2574//Natural Science Foundation of Science and Technology Department of Shaanxi Province/ ; 2020ZDLSF06-01//Natural Science Foundation of Science and Technology Department of Shaanxi Province/ ; 2021K-25//Strategic Reserve Talent Training Program of Shaanxi Academy of Sciences/ ; 2023JH-NJGG-0167//Xi'an Science Technology Bureau Fund/ ; KRDL K6-2207039//the Project of the First Investigation of Wild Plants Resources in Xi'an/ ; }, mesh = {*Soil Microbiology ; *Rhizosphere ; *Fungi/genetics ; *Bacteria/genetics/classification ; *Archaea/genetics/growth & development/metabolism ; Petroleum Pollution/adverse effects ; Petroleum ; Microbiota/drug effects ; Soil Pollutants ; }, abstract = {Bacteria, fungi, archaea, and viruses are reflective organisms that indicate soil health. Investigating the impact of crude oil pollution on the community structure and interactions among bacteria, fungi, archaea, and viruses in Calamagrostis epigejos soil can provide theoretical support for remediating crude oil pollution in Calamagrostis epigejos ecosystems. In this study, Calamagrostis epigejos was selected as the research subject and subjected to different levels of crude oil addition (0 kg/hm[2], 10 kg/hm[2], 40 kg/hm[2]). Metagenomic sequencing technology was employed to analyze the community structure and diversity of soil bacteria, fungi, archaea, and viruses. Additionally, molecular ecological network analysis was integrated to explore species interactions and ecosystem stability within these microbial communities. The functional profiles of soil microorganisms were elucidated based on data from the KEGG database. Results demonstrated a significant increase in petroleum hydrocarbon content, polyphenol oxidase activity, hydrogen peroxide enzyme activity, and acid phosphatase activity upon crude oil addition, while β-glucosidase content, fiber disaccharide hydrolase content, and tiller number decreased (P < 0.05). Proteobacteria and Actinobacteria were identified as dominant bacterial phyla; Ascomycota, Basidiomycota, and Mucoromycota were found to be dominant fungal phyla; Thaumarchaeota emerged as a dominant archaeal phylum; and Uroviricota represented a dominant viral phylum. The diversity of soil bacterial, fungal, archaeal, and viral communities increased with higher amounts of added crude oil. Ecological network analysis revealed a robust collaborative relationship among bacterial, fungal, archaeal, and viral community species in the control treatment (CK), while strong competitive relationships were observed among these species in the treatments with 10% (F10) and 40% (F40) crude oil concentrations. Structural equation modeling analysis indicated significant positive correlations between fungal community, viral community, enzyme activity, and plant growth; conversely, bacterial and archaeal communities showed significant negative correlations with plant growth (P < 0.05). Correlation analysis identified acid phosphatase as the primary environmental factor influencing soil microbial function. Acid phosphatase levels along with tiller number, aboveground biomass, and petroleum hydrocarbons significantly influenced the fungal community (P < 0.05), while underground biomass had a significant impact on the archaeal community (P < 0.05). Acid phosphatase levels along with cellulose-hydrolyzing enzymes, tiller number, and petroleum hydrocarbons exhibited significant effects on the viral community (P < 0.05). This study investigated variations in bacterial, fungal, archaeal, and viral communities under different crude oil concentrations as well as their driving factors, providing a theoretical foundation for evaluating Calamagrostis epigejos' potential to remediate crude oil pollution.}, } @article {pmid39779925, year = {2025}, author = {He, X and Hu, M and Xu, Y and Xia, F and Tan, Y and Wang, Y and Xiang, H and Wu, H and Ji, T and Xu, Q and Wang, L and Huang, Z and Sun, M and Wan, Y and Cui, P and Liang, S and Pan, Y and Xiao, S and He, Y and Song, R and Yan, J and Quan, X and Wei, Y and Hong, C and Liao, W and Li, F and El-Omar, E and Chen, J and Qi, X and Gao, J and Zhou, H}, title = {The gut-brain axis underlying hepatic encephalopathy in liver cirrhosis.}, journal = {Nature medicine}, volume = {}, number = {}, pages = {}, pmid = {39779925}, issn = {1546-170X}, support = {82372305//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Up to 50-70% of patients with liver cirrhosis develop hepatic encephalopathy (HE), which is closely related to gut microbiota dysbiosis, with an unclear mechanism. Here, by constructing gut-brain modules to assess bacterial neurotoxins from metagenomic datasets, we found that phenylalanine decarboxylase (PDC) genes, mainly from Ruminococcus gnavus, increased approximately tenfold in patients with cirrhosis and higher in patients with HE. Cirrhotic, not healthy, mice colonized with R. gnavus showed brain phenylethylamine (PEA) accumulation, along with memory impairment, symmetrical tremors and cortex-specific neuron loss, typically found in patients with HE. This accumulation of PEA was primarily driven by decreased monoamine oxidase-B activity in both the liver and serum due to cirrhosis. Targeting PDC or PEA reversed the neurological symptoms induced by R. gnavus. Furthermore, fecal microbiota transplantation from patients with HE to germ-free cirrhotic mice replicated these symptoms and further corroborated the efficacy of targeting PDC or PEA. Clinically, high baseline PEA levels were linked to a sevenfold increased risk of HE after intrahepatic portosystemic shunt procedures. Our findings expand the understanding of the gut-liver-brain axis and identify a promising therapeutic and predictive target for HE.}, } @article {pmid39779716, year = {2025}, author = {Gałęcka, I and Rychlik, A and Całka, J}, title = {Influence of selected dosages of plastic microparticles on the porcine fecal microbiome.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {1269}, pmid = {39779716}, issn = {2045-2322}, support = {2020/37/N/NZ7/01383//Narodowe Centrum Nauki/ ; The Regional Initiative of Excellence Program//Minister of Science Poland/ ; }, mesh = {Animals ; Swine ; *Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Microplastics/toxicity ; Female ; Plastics ; Bacteria/classification/genetics/isolation & purification ; }, abstract = {Studies conducted so far have shown that nano- and microplastic may disturb the intestinal microenvironment by interacting with the intestinal epithelium and the gut microbiota. Depending on the research model used, the effect on the microbiome is different-an increase or decrease in selected taxa resulting in the development of dysbiosis. Dysbiosis may be associated with intestinal inflammation, development of mental disorders or diabetes. The aim of the study was to analyze the intestinal microbiome in 15 gilts divided into 3 research groups (n = 5; control group, receiving micropartices at a dose 0.1 g/day (LD) and 1 g/day (HD)). Feaces were collected before and after 28 days of exposure to PET microplastics. The analysis of the intestinal microbiome was performed using next-generation sequencing. Alpha and beta diversity indices were compared, showing, that repetition affected only the abundance indices in the control and LD groups, but not in the HD group. The relationships between the number of reads at the phylum, genus and species level and the microplastic dose were calculated using statistical methods (r-Pearson correlation, generalized regression model, analysis of variance). The statistical analysis revealed, that populations of Family XIII AD3011 group, Coprococcus, V9D2013 group, UCG-010 and Sphaerochaeta increased with increasing MP-PET dose. The above-mentioned taxa are mainly responsible for the production of short-chain fatty acids (SCFA). It may be assumed, that SCFA are one of the mechanisms involved in the response to oral exposure to MP-PET.}, } @article {pmid39779308, year = {2025}, author = {Nguyen-Tiêt, A and Puente-Sánchez, F and Bertilsson, S and Aalto, SL}, title = {Identifying Bacteria Responsible for Non-Sulphate-Based Hydrogen Sulphide Production in Aquaculture.}, journal = {Environmental microbiology}, volume = {27}, number = {1}, pages = {e70024}, doi = {10.1111/1462-2920.70024}, pmid = {39779308}, issn = {1462-2920}, support = {1051-00044B//Danmarks Frie Forskningsfond/ ; }, mesh = {*Hydrogen Sulfide/metabolism ; *Aquaculture ; *Cysteine/metabolism ; *Bacteria/metabolism/genetics/classification ; *RNA, Ribosomal, 16S/genetics ; Bioreactors/microbiology ; Sulfates/metabolism ; Phylogeny ; Metagenome ; Metagenomics ; }, abstract = {The unintended microbiological production of hydrogen sulphide (H2S) poses a significant challenge in engineered systems, including sewage treatment plants, landfills and aquaculture systems. Although sulphur-rich amino acids and other substrates conducive to non-sulphate-based H2S production are frequently present, the capacity and potential of various microorganisms to perform sulphate-free H2S production remain unclear. In this study, we identify the identity, activity and genomic characteristics of bacteria that degrade cysteine to produce H2S in anaerobic enrichment bioreactors seeded with material from aquaculture systems. Our comparison with canonical sulphate-reducing bacteria reveals that both sulphur sources contribute to microbial H2S production, with cysteine facilitating a more rapid process compared to sulphate. 16S rRNA amplicon sequencing and metagenomic analysis identified four bacterial families-Dethiosulfatibacteraceae, Fusobacteriaceae, Vibrionaceae and Desulfovibrionaceae-as central to non-sulphate H2S production. Metagenome- and metatranscriptome-assembled genomes elucidated the primary cysteine degradation pathway mediated by cysteine desulphidase cyuA and indicated that some bacteria may also utilise cysteine as a carbon source in sulphate-based H2S production.}, } @article {pmid39779118, year = {2025}, author = {Wang, C and Bin, Z and Wang, L and Zhu, G and Tang, S and Chen, Y and Xiao, D and Guo, X}, title = {Metagenomic and metabolomic profiling analyses to unravel the formation mechanism of n-propanol during the first and second round of Jiangxiangxing Baijiu fermentation.}, journal = {Food research international (Ottawa, Ont.)}, volume = {200}, number = {}, pages = {115459}, doi = {10.1016/j.foodres.2024.115459}, pmid = {39779118}, issn = {1873-7145}, mesh = {*Fermentation ; *Metabolomics/methods ; *1-Propanol/metabolism ; *Metagenomics/methods ; Lactobacillus/metabolism/genetics ; Alcoholic Beverages/microbiology ; Pichia/metabolism/genetics ; Saccharomyces cerevisiae/metabolism/genetics ; Food Microbiology ; Microbiota ; }, abstract = {N-propanol is one of the higher alcohols, a moderate amount of n-propanol is beneficial for the harmony of the liquor body, whereas excessive or repeated intake will lead to discomfort and pose significant harm to human health. In actual production process of Jiangxiangxing Baijiu, the n-propanol content of the base baijiu in first round (FR) is far higher than that of second round (SR). Nevertheless, the formation mechanism and the key n-propanol producing microbials remain unclear and this limits the quality control of baijiu fermentation. Here, we combined metagenomics and metabolomics to verify the biosynthesis pathway of n-propanol and to identify characteristic microorganisms in FR and SR. The results showed that the preliminary period of pit fermentation was critical for the accumulation of n-propanol. FR was enriched in Lactobacillus plantarum, Lactobacillus ponits, Lactobacillus brevis and Lactobacillus panis, while it was harbored greater abundances of Pichia kudriazevii, Saccharomyces cerevisiae and Lactobacillus acetotolerans in SR. Function analysis combined with KEGG providing comprehensive evidence for the main synthetic pathways of n-propanol in Jiangxiangxing baijiu, and L. panis was key microbial. In addition, the experiments of inoculating L. panis and L. acetotolerans in situ indicated L. panis was mainly responsible for n-propanol production while L. acetotolerans not conducive to the production of n-propanol. Besides, the bioturbation effect on microbiota and flavor compounds were also analyzed. These results are useful for elucidating the mechanism of flavor formation in baijiu fermentation and promoting the further application of bioturbation technology in the traditional fermentation industry.}, } @article {pmid39778648, year = {2025}, author = {Bellanco, A and Requena, T and Martínez-Cuesta, MC}, title = {Polysorbate 80 and carboxymethylcellulose: A different impact on epithelial integrity when interacting with the microbiome.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {196}, number = {}, pages = {115236}, doi = {10.1016/j.fct.2025.115236}, pmid = {39778648}, issn = {1873-6351}, mesh = {*Polysorbates/pharmacology ; *Carboxymethylcellulose Sodium/chemistry ; *Gastrointestinal Microbiome/drug effects ; Humans ; Emulsifying Agents ; Bacteria/drug effects/classification/genetics/metabolism ; }, abstract = {The consumption of dietary emulsifiers, including polysorbate 80 (P80) and sodium carboxymethylcellulose (CMC), has raised safety concerns due to its interaction with the intestinal microbiome. This study demonstrated that increasing concentrations of P80 and CMC added to a dynamic four-stage gut microbiota model (BFBL gut simulator) altered the microbiome composition and impacted epithelial integrity in a dose-dependent manner. 16S rDNA amplicon-based metagenomics analysis revealed that these emulsifiers increased microbial groups with proinflammatory capacities while decreasing microbial taxa known to enhance barrier function. Increasing doses of P80 significantly decreased Bacteroides dorei and Akkermansia, taxa associated with anti-inflammatory potential, while increasing doses of CMC were linked to a higher abundance of Ruminococcus torques and Hungatella, which negatively impact barrier function. Both emulsifiers displayed a different impact on epithelial integrity when interacting with the microbiome. On one hand, supernatants from the BFBL simulator fed with P80 disrupted epithelial integrity to a lesser extent than the additive alone. On the other hand, both the microbiota and the supernatants from the BFBL simulator fed with CMC diminished the epithelial integrity, though the additive itself did not. These findings highlight the need to incorporate the gut microbiome in the risk assessment of these additives.}, } @article {pmid39778631, year = {2025}, author = {Harriman, D and Ng, A and Bronowski, M and Kazakov, H and Nguan, C and Dang, T and Sherwood, K and Miller, A and Lange, D}, title = {Characterizing the urobiome and associated metabolic profiles during acute rejection in renal transplant patients: A pilot study.}, journal = {Transplant immunology}, volume = {89}, number = {}, pages = {102170}, doi = {10.1016/j.trim.2024.102170}, pmid = {39778631}, issn = {1878-5492}, abstract = {Characteristic alterations in the urinary microbiome, or urobiome, are associated with renal transplant pathology. To date, there has been no direct study of the urobiome during acute allograft rejection. The goal of this study was to determine if unique urobiome alterations are present during acute rejection in renal transplant recipients. We performed shotgun metagenomic sequencing of 32 mid-stream urine samples obtained from 15 transplant recipients pre-transplant, 1- and 3-months post-transplant, and at time of rejection discovered with for-cause biopsy. Within individuals, there was a 40-60 % difference in urobiome composition from pre-to-post-transplant in both rejectors and non-rejectors. The taxa Ureaplasma was enriched in rejectors compared to non-rejectors. However, a greater number of microbial genes were enriched in non-rejectors compared to rejectors, except for genes associated with tetracycline resistance, the lysophosphatidic acid synthesis pathway, and tryptophanyl-tRNA synthetase. Together, our findings suggest that the urobiome is significantly altered post-transplant with certain taxa and/or microbial genes potentially associated with acute allograft rejection/inflammation.}, } @article {pmid39778056, year = {2025}, author = {Silva, JK and Hervé, V and Mies, US and Platt, K and Brune, A}, title = {A Novel Lineage of Endosymbiotic Actinomycetales: Genome Reduction and Acquisition of New Functions in Bifidobacteriaceae Associated With Termite Gut Flagellates.}, journal = {Environmental microbiology}, volume = {27}, number = {1}, pages = {e70010}, pmid = {39778056}, issn = {1462-2920}, support = {//Max-Planck-Gesellschaft/ ; }, mesh = {*Symbiosis ; Animals ; *Isoptera/microbiology ; *Genome, Bacterial ; *RNA, Ribosomal, 16S/genetics ; *Phylogeny ; *Actinomycetales/genetics/metabolism ; Gene Transfer, Horizontal ; Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology/parasitology ; Metagenome ; }, abstract = {Cellulolytic flagellates are essential for the symbiotic digestion of lignocellulose in the gut of lower termites. Most species are associated with host-specific consortia of bacterial symbionts from various phyla. 16S rRNA-based diversity studies and taxon-specific fluorescence in situ hybridization revealed a termite-specific clade of Actinomycetales that colonise the cytoplasm of Trichonympha spp. and other gut flagellates, representing the only known case of intracellular Actinomycetota in protists. Comparative analysis of eleven metagenome-assembled genomes from lower termites allowed us to describe them as new genera of Bifidobacteriaceae. Like the previously investigated Candidatus Ancillula trichonymphae, they ferment sugars via the bifidobacterium shunt but, unlike their free-living relatives, experienced significant genome erosion. Additionally, they acquired new functions by horizontal gene transfer from other gut bacteria, including the capacity to produce hydrogen. Members of the genus Ancillula (average genome size 1.56 ± 0.2 Mbp) retained most pathways for the synthesis of amino acids, including a threonine/serine exporter, providing concrete evidence for the basis of the mutualistic relationship with their host. By contrast, Opitulatrix species (1.23 ± 0.1 Mbp) lost most of their biosynthetic capacities, indicating that an originally mutualistic symbiosis is on the decline.}, } @article {pmid39777846, year = {2025}, author = {Liu, R and He, X and Ren, G and Li, DW and Zhao, M and Lehtovirta-Morley, L and Todd, JD and Zhang, XH and Liu, J}, title = {Niche Partitioning and Intraspecific Variation of Thaumarchaeota in Deep Ocean Sediments.}, journal = {Environmental microbiology}, volume = {27}, number = {1}, pages = {e70018}, doi = {10.1111/1462-2920.70018}, pmid = {39777846}, issn = {1462-2920}, support = {41976101//National Natural Science Foundation of China/ ; 92051115//National Natural Science Foundation of China/ ; 92251303//National Natural Science Foundation of China/ ; 202141009//Fundamental Research Funds for the Central Universities/ ; 202172002//Fundamental Research Funds for the Central Universities/ ; 2022QNLM030004-3//Laoshan Laboratory/ ; LSKJ202203206//Laoshan Laboratory/ ; ZR2022YQ38//Natural Science Foundation of Shandong Province/ ; ZR2024JQ006//Natural Science Foundation of Shandong Province/ ; }, mesh = {*Geologic Sediments/microbiology ; *Archaea/genetics/classification ; *Phylogeny ; Oceans and Seas ; Metagenome ; Ecosystem ; Seawater/microbiology ; Metagenomics ; Ammonia/metabolism ; Genome, Archaeal ; }, abstract = {Deep-sea sediments contain a large number of Thaumarchaeota that are phylogenetically distinct from their pelagic counterparts. However, their ecology and evolutionary adaptations are not well understood. Metagenomic analyses were conducted on samples from various depths of a 750-cm sediment core collected from the Mariana Trench Challenger Deep. The abundance of Thaumarchaeota and archaeal amoA generally decreased with depth, except for an unexpected peak midway through the core. The thaumarchaeotal metagenome-assembled genomes were classified into diverse phylogenetic clusters associated with amoA-NP-γ, amoA-NP-θ, and amoA-NP-δ of ammonia-oxidising Thaumarchaeota and non-ammonia-oxidising lineages. The most abundant group was within amoA-NP-γ, which is usually found in coastal and shallow habitats, indicating potential niche expansion from marine shallow to hadal environments. This benthic group showed within-species genomic variations compared to the previously identified Hadal water group, suggesting microdiversification of hadal Thaumarchaeota along with niche separation between benthic and pelagic environments. Evolutionary adaptations associated with the benthic-to-pelagic transition included reduced genome size, loss of motility/cell adhesion, altered energy metabolism, and different mechanisms for substrate acquisition and regulation (e.g., ammonium). These findings offer new insights into the evolution of hadal Thaumarchaeota and demonstrate, for the first time, intraspecies-level genomic variation in Thaumarchaeota related to the benthic-versus-pelagic niche partitioning in the deep ocean.}, } @article {pmid39777550, year = {2025}, author = {Byers, AK and Wakelin, SA and Condron, L and Black, A}, title = {Land Use Change Disrupts the Network Complexity and Stability of Soil Microbial Carbon Cycling Genes Across an Agricultural Mosaic Landscape.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {167}, pmid = {39777550}, issn = {1432-184X}, mesh = {*Soil Microbiology ; *Carbon Cycle ; New Zealand ; *Agriculture ; *Soil/chemistry ; *Microbiota ; *Bacteria/genetics/classification/metabolism ; Carbon/metabolism ; Gene Regulatory Networks ; Forests ; Ecosystem ; }, abstract = {To understand the effects of agricultural land use change and management on soil carbon (C) cycling, it is crucial to examine how these changes can influence microbial soil C cycling. Network analysis can offer insights into the structure, complexity, and stability of the soil microbiome in response to environmental disturbances, including land use change. Using SparCC-based co-occurrence networks, we studied how land use change impacts the connectivity, complexity, and stability of microbial C-cycling gene networks across an agricultural mosaic landscape in Canterbury, New Zealand. The most densely connected networks were found in land uses that were under the most intensive agricultural management, or under naturally regenerating vegetation. The microbial C-cycling gene networks from both land uses presented high network connectivity, low modularity, and a low proportion of negative gene interactions. In contrast, microbial C-cycling genes from native forests, which had the most stable and undisturbed plant cover, had the lowest network connectivity, highest modularity, and a greater proportion of negative gene interactions. Although the differences in total soil C content between land uses were small, the large effects of land use on the network structure of microbial C-cycling genes may have important implications for long-term microbial soil C cycling. Furthermore, this research highlights the value of using microbial network analysis to study the metabolic gene interactions shaping the functional structure of soil microbial communities in a manner not typically captured by more traditional forms of microbial diversity analysis.}, } @article {pmid39777544, year = {2025}, author = {Qiao, L and Zheng, X and Zhao, J and Wu, B and Hao, Y and Li, X and Helal, MMU and Zheng, J}, title = {Genetic dissection of flag leaf morphology traits and fine mapping of a novel QTL (Qflw.sxau-6BL) in bread wheat (Triticum aestivum L.).}, journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik}, volume = {138}, number = {1}, pages = {21}, pmid = {39777544}, issn = {1432-2242}, support = {202302140601001//Key Research and Development Project of Shanxi Province/ ; 202201140601025-2//Grant Science and Technology special project in Shanxi Province/ ; 202303021222043//Youth Project of Shanxi Province/ ; 2023CYJSTX02//Modern Agro-industry Technology Research System/ ; }, mesh = {*Triticum/genetics/anatomy & histology/growth & development ; *Quantitative Trait Loci ; *Chromosome Mapping/methods ; *Plant Leaves/anatomy & histology/genetics/growth & development ; *Phenotype ; Genetic Linkage ; Genetic Markers ; Haploidy ; Genotype ; }, abstract = {Total 60-QRC for FLM traits were detected by meta-genomics analysis, nine major and stable QTL identified by DH population and validated, and a novel QTL Qflw.sxau-6BL was fine mapped. The flag leaf is an "ideotypic" morphological trait providing photosynthetic assimilates in wheat. Although flag leaf morphology (FLM) traits had been extensively investigated through genetic mapping, there is a desire for FLM-related loci to be validated in multi-environments and fine mapping. In order to identify the stable genomic regions for FLM traits, we conducted a meta-genomic analysis based on reports from 2008 to 2024. Experimentally, a doubled haploid (DH) population was used to assess the genetic regions associated with FLM traits in nine environments. The meta-genomic analysis extracted 60 QTL-rich clusters (QRC), 45 of which were verified in marker-trait association (MTA) study. Nine major and stable QTL were found being associated with FLM traits across three-to-seven environments including BLUP, with phenotypic variance explained (PVE) ranging from 5.05 to 34.95%. The KASP markers of the nine QTL were validated (P < 0.005) in more than three environments using a panel of diverse wheat collections from Shanxi Province in China. Two co-located major and stable QTL viz. Qflw.sxau-6B.5 and Qfla.sxau-6B.4 were found novel and contributed to increase FLW by 12.09-19.21% and FLA by 5.45-13.28%. They also demonstrated high recombination rates in LD analysis based on the resequencing of 145 wheat landmark cultivars. The fine mapping of Qflw.sxau-6BL narrowed it down to a 1.27 Mb region as a result of the combined genotypic and phenotypic analysis for secondary mapping population. Comparing to NIL-ND3338, the NIL-LF5064 showed higher FLW by 20.45-27.37%, thousand-grain weight by 1.88-2.57% and grain length by 0.47-2.30% across all environments. The expression analysis of 11 tissues revealed seven highly expressed genes within the fine map region. This study provides a genetic basis for the FLM traits for further map-based cloning of FLW genes in wheat.}, } @article {pmid39777507, year = {2025}, author = {Shelton, AN and Yu, FB and Grossman, AR and Bhaya, D}, title = {Abundant and active community members respond to diel cycles in hot spring phototrophic mats.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {39777507}, issn = {1751-7370}, support = {2125965//NSF/ ; 1921429//BBSRC-NSF/BIO/ ; //Office of Science of the U.S. Department of Energy/ ; }, mesh = {*Hot Springs/microbiology ; Metagenome ; Photosynthesis ; Phototrophic Processes ; Bacteria/genetics/classification/isolation & purification/metabolism ; Metagenomics ; Microbiota ; Transcriptome ; }, abstract = {Photosynthetic microbial mats in hot springs can provide insights into the diel behaviors of communities in extreme environments. In this habitat, photosynthesis dominates during the day, leading to super-oxic conditions, with a rapid transition to fermentation and anoxia at night. Multiple samples were collected from two springs over several years to generate metagenomic and metatranscriptomic datasets. Metagenome-assembled genomes comprised 71 taxa (in 19 different phyla), of which 12 core taxa were present at high abundance in both springs. The eight most active taxa identified by metatranscriptomics were an oxygenic cyanobacterium (Synechococcus sp.), five anoxygenic phototrophs from three different phyla, and two understudied heterotrophs from phylum Armatimonadota. In all eight taxa, a significant fraction of genes exhibited a diel expression pattern, although peak timing varied considerably. The two abundant heterotrophs exhibit starkly different peak timing of expression, which we propose is shaped by their metabolic and genomic potential to use carbon sources that become differentially available during the diel cycle. Network analysis revealed pathway expression patterns that had not previously been linked to diel cycles, including ribosome biogenesis and chaperones. This provides a framework for analyzing metabolically coupled communities and the dominant role of the diel cycle.}, } @article {pmid39777151, year = {2024}, author = {Nhung, PTT and Le, HTT and Nguyen, QH and Huyen, DT and Quyen, DV and Song, LH and Van Thuan, T and Tran, TTT}, title = {Identifying fecal microbiota signatures of colorectal cancer in a Vietnamese cohort.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1388740}, pmid = {39777151}, issn = {1664-302X}, abstract = {BACKGROUND: Colorectal cancer (CRC) is among the top three causes of global cancer mortality. In Vietnam, CRC is the third leading cause of death in women and the fourth cause of cancer mortality in men. A large number of metagenomic studies have reported the relationship between altered composition and function of the gut microbiota with CRC, but this relationship in low- and middle-income countries including Vietnam (with an estimated population of 100.3 million people in 2023, ranking 16th largest country by population in the world) is not well-explored.

METHODS: We collected clinical data and fecal samples from 43 CRC patients and 44 healthy control subjects. The total community DNA of microorganisms was extracted from the fecal samples and analyzed for microbiota composition using Illumina MiSeq amplicon sequencing targeting the V3-V4 region of the 16S rRNA gene.

RESULTS: We identified a significant difference in the overall fecal microbiota composition between CRC patients and healthy controls, and we detected several CRC-associated microbial signatures in fecal samples of Vietnamese patients with CRC, which overlapped with signatures from other countries and meta-analyses. Although patients with (n = 8) and without (n = 35) type 2 diabetes (T2D) exhibited distinct gut microbiota composition compared to healthy controls, increased relative abundances of putatively pathogenic species including Parvimonas micra, Peptostreptococcus stomatis, and Prevotella intermedia were consistent biomarkers for CRC. In contrast, several health-associated species were significantly depleted in CRC patients such as Lactobacillus johnsonii and Bifidobacterium longum in CRC/non-T2D patients, Ruminococcus species, Bacteroides uniformis, and Phascolarctobacterium faecium in CRC/T2D patients, and Butyricicoccus pullicaecorum in both CRC groups combined.

CONCLUSION: Our findings confirm alterations in gut microbiota composition in CRC in a pilot Vietnamese cohort and highlight several gut microbial taxa that may have inhibitory or driver roles in CRC. This and future studies will enable the development of cancer diagnostics and treatment strategies for CRC in Vietnam, with a focus on targeting the microbiota.}, } @article {pmid39776843, year = {2024}, author = {Zhang, X and Wu, Z and Shao, S}, title = {Pulmonary mucormycosis in an immunocompetent young female: a case report and literature review.}, journal = {Frontiers in medicine}, volume = {11}, number = {}, pages = {1491489}, pmid = {39776843}, issn = {2296-858X}, abstract = {Mucormycosis is considered a rare but highly lethal fungal infection, often occurring in patients with poorly controlled diabetes or immunosuppression. Pulmonary mucormycosis progresses rapidly and is often associated with pulmonary infarction and hemoptysis. In this case report, we presented a young, immunocompetent female patient with newly diagnosed diabetes who was diagnosed early with Rhizopus delemar infection through metagenomic next-generation sequencing. Despite early diagnosis, the infection progressed rapidly, invading the tracheal cartilage and upper mediastinal soft tissue, ultimately leading to the patient's unfortunate demise.}, } @article {pmid39776838, year = {2024}, author = {Li, MJ and Zhou, SF and Zhang, Y and Zhang, Y and Fu, WB}, title = {Unveiling the dark side of Prevotella: a case of fatal pneumonia from a common probiotic.}, journal = {Frontiers in medicine}, volume = {11}, number = {}, pages = {1382134}, pmid = {39776838}, issn = {2296-858X}, abstract = {Prevotella is often considered a Bacteroides complex associated with a healthy plant-based diet that acts as a "probiotic" throughout the body's entire digestive tract from the mouth to the anus. Previous studies have not reported that this "probiotic" colonizing the human body could cause severe pneumonia. This case report describes a 56-year-old healthy female worker with gum pain followed by fever. Despite prompt medical attention given by the use of empirical antibiotics and tooth and oral cleaning, the disease rapidly progressed to retropharyngeal abscess and severe pneumonia. Although the surgeon performed pharynx and cervical incisions and drainage, the patient's symptoms were not significantly relieved. After repeated blood culture and sputum culture, no positive findings were found. Fortunately, Prevotella oris was found in the peripheral blood of the patient by metagenomic next-generation sequencing (mNGS). The disease was controlled quickly by changing the targeted antibiotics according to the guidelines for the detection of pathogenic bacteria. Three months after discharge, the patient's symptoms did not resolve, and reexamination with computerized tomography (CT) showed that the neck and chest were normal. This case is unique in that it shows that normally colonized Prevotella oris could also cause fatal pneumonia as an opportunistic pathogen. Our goal is to highlight that serious infections that rapidly develop from common symptoms in an era of widespread antibiotic use not only increase patient misunderstanding but also lead to over detection and testing of such symptoms by clinicians. Expanding the pathogenic characteristics of special pathogens through the literature and using accurate mNGS may be the technical tool for resolving this contradiction.}, } @article {pmid39776755, year = {2025}, author = {Niu, X and Qiu, S and Zheng, Y and Li, L and Tian, E and Liu, J and Gai, W and Zhang, Q and Jin, H}, title = {A Rare Q-Fever Infection Diagnosed Using Metagenomic Next-Generation Sequencing in Liver Transplantation Patient: A Case Report and Literature Review.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {25-30}, pmid = {39776755}, issn = {1178-6973}, abstract = {Q fever is a zoonotic disease caused by the Gram-negative bacterium Coxiella burnetii, typically transmitted through exposure to infected animal secretions. As the clinical signs of Q-fever are largely non-specific in humans, a definitive diagnosis can often be overlooked, particularly when physicians fail to consider C. burnetii on the list of differentials. This case report describes Q-fever in a male patient who had previously undergone orthotopic liver transplantation. The patient had a sudden onset of fever and received the anti-infective moxifloxacin which proved ineffective. Despite the comprehensive laboratory tests and CT imaging that were performed, the etiology remained undetermined. The patient's blood was subjected to metagenomic next-generation sequencing (mNGS), which identified C. burnetii, after which the patient was treated with doxycycline and recovered well. Eight literature articles on Q fever infection in solid organ transplant recipients were reviewed. To our knowledge, this is the first case of Q fever identified by mNGS in an organ transplantation patient. The case underscores the potential of mNGS has in aiding the rapid detection of rare pathogens in immunocompromised patients.}, } @article {pmid39776437, year = {2024}, author = {Tang, J and Wang, K and Xu, H and Han, J}, title = {Metagenomic next-generation sequencing of cerebrospinal fluid: a diagnostic approach for varicella zoster virus-related encephalitis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1509630}, pmid = {39776437}, issn = {2235-2988}, mesh = {Humans ; Male ; Female ; *High-Throughput Nucleotide Sequencing ; Middle Aged ; *Metagenomics/methods ; Aged ; Retrospective Studies ; Adult ; *Herpesvirus 3, Human/genetics/isolation & purification ; *Encephalitis, Varicella Zoster/diagnosis/cerebrospinal fluid ; China ; Cerebrospinal Fluid/virology ; }, abstract = {PURPOSE: Varicella zoster virus-related encephalitis (VZV-RE) is a rare and often misdiagnosed condition caused by an infection with the VZV. It leads to meningitis or encephalitis, with patients frequently experiencing poor prognosis. In this study, we used metagenomic next-generation sequencing (mNGS) to rapidly and accurately detect and identify the VZV pathogen directly from cerebrospinal fluid (CSF) samples, aiming to achieve a definitive diagnosis for encephalitis patients.

METHODS: In this retrospective study, we analyzed the clinical characteristics and laboratory evaluations of 28 patients at the Harrison International Peace Hospital in Hebei, China, between 2018 and 2024. These patients were diagnosed with neurological disorders using mNGS techniques applied to CSF.

RESULTS: In this cohort of 28 patients, 11 were females and 17 males, with a median age of 65 (IQR: 42.3-70). VZV-RE presented with a range of clinical manifestations, the most common being headaches (81.2%), fever>38°C (42.9%), and vomiting (42.9%). Less frequent symptoms include personality changes (10.7%), speech impairments (21.4%), cranial nerve involvement (21.4%), altered consciousness (17.9%) and convulsions (3.6%). Herpes zoster rash was observed in 35.7% of the cases. Neurological examination revealed nuchal rigidity in only 5 patients. CSF analysis indicated mild pressure and protein levels increase, with all patients having negative bacterial cultures. Abnormal electroencephalogram (EEG) findings were noted in 10.7% (N=3), and encephalorrhagia on Magnetic Resonance Imaging (MRI) was observed in 3.6%. VZV-RE was confirmed through mNGS analysis of CSF within three days of admission. All patients received empiric treatment with acyclovir or valacyclovir, with 21.4% receiving hormonotherapy, and 7.14% receiving immunoglobulin therapy. At the three-month follow-up, 10.7% of the patients had persistent neurologic sequelae, and the mortality rate was 3.6%.

CONCLUSIONS: Performing mNGS on CSF offers a rapidly and precisely diagnostic method for identifying causative pathogens in patients with VZV central nervous system (CNS) infections, especially when traditional CNS examination results are negative. Furthermore, the cases reported highlight the positive therapeutic effect of ganciclovir in treating VZV infections.}, } @article {pmid39775567, year = {2025}, author = {Kalaiselvi, P and Haripriya, RJ and Saravanan, VS and Davamani, V and Sebastian, SP and Parameswari, E and Poornima, R and Bharani, A and Maheswari, M}, title = {Formulation and evaluation of the effective microorganisms in sewage treatment.}, journal = {Environmental science and pollution research international}, volume = {32}, number = {5}, pages = {2298-2323}, pmid = {39775567}, issn = {1614-7499}, mesh = {*Sewage ; *Waste Disposal, Fluid/methods ; Bacteria ; Water Purification/methods ; Wastewater/chemistry/microbiology ; }, abstract = {Effective microorganisms pose a great potential in wastewater treatment. In the present study, effective microorganisms' formulations were developed using different organic substrates that support the growth of more beneficial microorganisms for sewage treatment. Based on the metagenomic analysis and biochemical profile information, the fish waste-based effective microorganisms' formulation was identified as the effective formulation. Metagenomic analysis showed that fish-based effective microorganisms' formulation had the Lactobacillus and Acetobacter groups of bacteria. The dominant groups were Lactobacillus pontis (64.85%), Acetobacter aceti (8.92%), and Lactobacillus reuteri (8.98%). The developed fish waste-based effective microorganisms' formulation was used to treat the sewage water with different concentrations. Effective microorganisms' formulation at 3% showed appreciable results. It recorded a significant reduction in BOD from 389.2 to 117.9 mg L[-1] and COD from 820.5 to 257.1 mg L[-1] in 96 h. It also significantly decreased the concentration of ammoniacal and nitrate nitrogen, phosphorus, sulphate, and coliforms. Besides, the effective microorganisms' formulation ensured the reduced level of odour from sewage water. Therefore, we can effectively use the effective microorganisms' formulation for sewage water treatment and recycling.}, } @article {pmid39775111, year = {2025}, author = {Lee, J and Xiang, K and Au, E and Sarabi, S and Acosta, N and Bhatnagar, S and Van Doorn, J and Bertazzon, S and Conly, JM and Rennert-May, E and Pitout, JDD and Lee, BE and Pang, X and O'Grady, C and Frankowski, K and Hubert, CRJ and Parkins, MD}, title = {Longitudinal monitoring of sewershed resistomes in socioeconomically diverse urban neighborhoods.}, journal = {Communications medicine}, volume = {5}, number = {1}, pages = {7}, pmid = {39775111}, issn = {2730-664X}, abstract = {BACKGROUND: Understanding factors associated with antimicrobial resistance (AMR) distribution across populations is a necessary step in planning mitigation measures. While associations between AMR and socioeconomic-status (SES), including employment and education have been increasingly recognized in low- and middle-income settings, connections are less clear in high-income countries where SES remains an important influence on other health outcomes.

METHODS: We explored the relationship between SES and AMR in Calgary, Canada using spatially-resolved wastewater-based surveillance of resistomes detected by metagenomics across eight socio-economically diverse urban neighborhoods. Resistomes were established by shotgun-sequencing of wastewater pellets, and qPCR of targeted-AMR genes. SES status was established using 2021 Canadian census data. Conducting this comparison during the height of COVID-related international travel restrictions (Dec. 2020-Oct. 2021) allowed the hypotheses linking SES and AMR to be assessed with limited confounding. These were compared with sewage metagenomes from 244 cities around the world, linked with Human Development Index (HDI).

RESULTS: Wastewater metagenomes from Calgary's socioeconomically diverse neighborhoods exhibit highly similar resistomes, with no quantitative differences (p > 0.05), low Bray-Curtis dissimilarity, and no significant correlations with SES. By comparison, dissimilarity is observed between globally-sourced resistomes (p < 0.05), underscoring the homogeneity of resistomes in Calgary's sub-populations. The analysis of globally-sourced resistomes alongside Calgary's resistome further reveals lower AMR burden in Calgary relative to other cities around the world. This is particularly pronounced for the most clinically-relevant AMR genes (e.g., beta-lactamases, macrolide-lincosamide-streptogramin).

CONCLUSIONS: This work showcases the effectiveness of inclusive and comprehensive wastewater-based surveillance for exploring the interplay between SES and AMR.}, } @article {pmid39774647, year = {2025}, author = {Yagita-Sakamaki, M and Ito, T and Sakaguchi, T and Shimma, S and Li, B and Okuzaki, D and Motooka, D and Nakamura, S and Hase, K and Fukusaki, E and Kikuchi, A and Nagasawa, T and Kumanogoh, A and Takeda, K and Kayama, H}, title = {Intestinal Foxl1+ cell-derived CXCL12 maintains epithelial homeostasis by modulating cellular metabolism.}, journal = {International immunology}, volume = {}, number = {}, pages = {}, doi = {10.1093/intimm/dxae068}, pmid = {39774647}, issn = {1460-2377}, abstract = {Several mesenchymal cell populations are known to regulate intestinal stem cell (ISC) self-renewal and differentiation. However, the influences of signaling mediators derived from mesenchymal cells other than ISC niche factors on epithelial homeostasis remain poorly understood. Here, we show that host and microbial metabolites, such as taurine and GABA, act on PDGFRαhigh Foxl1high sub-epithelial mesenchymal cells to regulate their transcription. In addition, we found that CXCL12 produced from Foxl1high sub-epithelial mesenchymal cells induces epithelial cell cycle arrest through modulation of the mevalonate-cholesterol synthesis pathway, which suppresses tumor progression in ApcMin/+ mice. We identified that Foxl1high sub-epithelial cells highly express CXCL12 among colonic mesenchymal cells. Foxl1-cre; Cxcl12f/f mice showed an increased number of Ki67+ colonic epithelial cells. CXCL12-induced Ca2+ mobilization facilitated phosphorylation of AMPK in intestinal epithelial cells, which inhibits the maturation of SREBPs that are responsible for mevalonate pathway activation. Furthermore, Cxcl12 deficiency in Foxl1-expressing cells promoted tumor development in the small and large intestines of ApcMin/+ mice. Collectively, these results demonstrate that CXCL12 secreted from Foxl1high mesenchymal cells manipulates intestinal epithelial cell metabolism, which links to the prevention of tumor progression in ApcMin/+ mice.}, } @article {pmid39774426, year = {2024}, author = {Segura, D and Sharma, D and Espin-Garcia, O}, title = {Comparing subsampling strategies for metagenomic analysis in microbial studies using amplicon sequence variants versus operational taxonomic units.}, journal = {PloS one}, volume = {19}, number = {12}, pages = {e0315720}, pmid = {39774426}, issn = {1932-6203}, mesh = {Humans ; *Metagenomics/methods ; *RNA, Ribosomal, 16S/genetics ; Gastrointestinal Microbiome/genetics ; Microbiota/genetics ; Infant ; Sequence Analysis, DNA/methods ; Bacteria/genetics/classification ; Metagenome/genetics ; }, abstract = {The microbiome is increasingly regarded as a key component of human health, and analysis of microbiome data can aid in the development of precision medicine. Due to the high cost of shotgun metagenomic sequencing (SM-seq), microbiome analyses can be done cost-effectively in two phases: Phase 1-sequencing of 16S ribosomal RNA, and Phase 2-SM-seq of an informative subsample. Existing research suggests strategies to select the subsample based on biological diversity and dissimilarity metrics calculated using operational taxonomic units (OTUs). However, the microbiome field has progressed towards amplicon sequencing variants (ASVs), as they provide more precise microbe identification and sample diversity information. The aim of this work is to compare the subsampling strategies for two-phase metagenomic studies when using ASVs instead of OTUs, and to propose data driven strategies for subsample selection through dimension reduction techniques. We used 199 samples of infant-gut microbiome data from the DIABIMMUNE project to generate ASVs and OTUs, then generated subsamples based on five existing biologically driven subsampling methods and two data driven methods. Linear discriminant analysis Effect Size (LEfSe) was used to assess differential representation of taxa between the subsamples and the overall sample. The use of ASVs showed a 50-93% agreement in the subsample selection with the use of OTUs for the subsampling methods evaluated, and showed a similar bacterial representation across all methods. Although sampling using ASVs and OTUs typically lead to similar results for each subsample, ASVs had more clades that differed in expression levels between allergic and non-allergic individuals across all sample sizes compared to OTUs, and led to more biomarkers discovered at Phase 2-SM-seq level.}, } @article {pmid39773989, year = {2025}, author = {Bbosa, N and Ssemwanga, D and Weiss, SL and Kalungi, S and Mawanda, A and Ssentudde, R and Ssekyeru, E and Ssekagiri, A and Kiiza, R and Rwankindo, C and Buule, J and Namagembe, HS and Nabirye, S and Nassolo, JP and Downing, R and Lutwama, J and Lutalo, T and Kyobe Bosa, H and Berg, MG and Rodgers, MA and Averhoff, F and Cloherty, GA and Kaleebu, P}, title = {Identification of Anthrax as the Cause of a Cluster of Unexplained Deaths, Uganda, 2023: The Role of Metagenomic Next-Generation Sequencing and Postmortem Specimens.}, journal = {The American journal of tropical medicine and hygiene}, volume = {}, number = {}, pages = {}, doi = {10.4269/ajtmh.24-0489}, pmid = {39773989}, issn = {1476-1645}, abstract = {Between April and November 2023, 27 unexplained human deaths that presented with swelling of the arms, skin sores with black centers, difficulty in breathing, obstructed swallowing, headaches, and other body aches were reported in Kyotera District, Uganda by the Public Health Emergency Operations Center. Subsequently, the death of cattle on farms and the consumption of carcass meat by some residents were also reported. Field response teams collected clinical/epidemiological data and autopsy samples to determine the cause of deaths. Metagenomic next-generation sequencing (mNGS) and target enrichment sequencing conducted on postmortem samples confirmed Bacillus anthracis, the etiological agent of anthrax disease, as the cause of the deaths. Applying mNGS to autopsy specimens is useful as a retrospective tool for identifying high-consequence pathogens during suspected outbreaks of unknown etiology.}, } @article {pmid39773899, year = {2025}, author = {Han, F and Ou, J and Huang, N}, title = {Invasive Eye Infection Caused by Trichoderma Harzianum.}, journal = {The American journal of tropical medicine and hygiene}, volume = {}, number = {}, pages = {}, doi = {10.4269/ajtmh.24-0037}, pmid = {39773899}, issn = {1476-1645}, abstract = {Trichoderma is a widely distributed thermophilic fungus that grows on moist soil, fallen leaves, and rotten wood. It plays an important role in agricultural production, food processing, and soil. However, some forms of Trichoderma can infect humans. Aggressive infections are more common in immunocompromised patients, with manifestations ranging from focal to disseminated infections. Here, we report a case of an invasive eye infection in China. The patient, a healthy 64-year-old man, was inadvertently struck by a puncture vine, injuring his eye and resulting in reduced visual acuity, lacrimation, and redness in the right eye. Upon admission, he was diagnosed with right eye perforation injury, right eye iris damage, right eye vitreous opacity, and right eye infection. After completion of the relevant auxiliary examinations, the diagnosis was confirmed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and metagenomic next-generation sequencing, and the patient responded to antifungal therapy.}, } @article {pmid39773654, year = {2025}, author = {Taylor, W and Bohm, K and Dyet, K and Weaver, L and Pattis, I}, title = {Comparative analysis of qPCR and metagenomics for detecting antimicrobial resistance in wastewater: a case study.}, journal = {BMC research notes}, volume = {18}, number = {1}, pages = {5}, pmid = {39773654}, issn = {1756-0500}, mesh = {*Wastewater/microbiology ; *Metagenomics/methods ; *RNA, Ribosomal, 16S/genetics ; *Real-Time Polymerase Chain Reaction/methods ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial/genetics ; Bacteria/genetics/drug effects/isolation & purification/classification ; Sewage/microbiology ; Drug Resistance, Microbial/genetics ; Humans ; }, abstract = {OBJECTIVE: The World Health Organization (WHO) has declared antimicrobial resistance (AMR) as one of the top threats to global public health. While AMR surveillance of human clinical isolates is well-established in many countries, the increasing threat of AMR has intensified efforts to detect antibiotic resistance genes (ARGs) accurately and sensitively in environmental samples, wastewater, animals, and food. Using five ARGs and the 16S rRNA gene, we compared quantitative PCR (qPCR) and metagenomic sequencing (MGS), two commonly used methods to uncover the wastewater resistome. We compared both methods by evaluating ARG detection through a municipal wastewater treatment chain.

RESULTS: Our results demonstrate that qPCR was more sensitive than MGS, particularly in diluted samples with low ARG concentrations such as oxidation pond water. However, MGS was potentially more specific and has less risk of off-target binding in concentrated samples such as raw sewage. MGS analysis revealed multiple subtypes of each gene which could not be distinguished by qPCR; these subtypes varied across different sample types. Our findings affect the conclusions that can be drawn when comparing different sample types, particularly in terms of inferring removal rates or origins of genes. We conclude that both methods appear suitable to profile the resistome of wastewater and other environmental samples, depending on the research question and type of sample.}, } @article {pmid39773117, year = {2025}, author = {Albert, E and Biksi, I and Laczkó, L and Miló, L and Cseri, K and Bőkényné Tóth, R and Papp, D and Halmay, D and Bódai, E and Bakos, Z}, title = {Streptococcus hillyeri isolated from septic pleuritis in a horse.}, journal = {Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc}, volume = {}, number = {}, pages = {10406387241306724}, pmid = {39773117}, issn = {1943-4936}, abstract = {Here we report the isolation of Streptococcus hillyeri from a thoracic sample from a horse. A 17-y-old Hungarian Sport Horse mare was referred to the equine clinic of the University of Veterinary Medicine Budapest, Hungary, with suspected pleuritis. Upon arrival, the horse was febrile and had tachycardia, severe inspiratory dyspnea, and tachypnea. Thoracic ultrasonography revealed severe bilateral pleural effusion, and a large area of lung consolidation. After sampling of both hemithoraces, 66 L of turbid exudate were drained. Based on these findings, a tentative diagnosis of septic pleuritis was made, and the horse was immediately started on a course of broad-spectrum antibiotics, a NSAID, an anticoagulant, and intravenous fluids. Despite intensive care, the clinical parameters deteriorated, and the horse was euthanized 6 d later. Cytology confirmed septic pleuritis, with short chains or groups of coccoid bacteria. Anaerobic culture yielded gram-positive cocci from both hemithoraces in almost pure culture, which we identified as S. hillyeri by 16S rDNA and whole-genome analysis. Additionally, we identified 4 previously unassigned Streptococcus sp. sequences as S. hillyeri. Of these, 3 were obtained from aborted equine fetuses and a fourth from a donkey mastitis case, supporting the pathogenic nature of S. hillyeri in these host species.}, } @article {pmid39772992, year = {2025}, author = {Zeng, Y and You, X and You, C}, title = {Rare Cause of Chest Wall Abscess: Salmonella Enterica Infection Based on Metagenomics Next-Generation Sequencing Diagnosis.}, journal = {Surgical infections}, volume = {}, number = {}, pages = {}, doi = {10.1089/sur.2024.316}, pmid = {39772992}, issn = {1557-8674}, } @article {pmid39772877, year = {2025}, author = {Ahmed, MA and Campbell, BJ}, title = {Genome-resolved adaptation strategies of Rhodobacterales to changing conditions in the Chesapeake and Delaware Bays.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0235724}, doi = {10.1128/aem.02357-24}, pmid = {39772877}, issn = {1098-5336}, abstract = {UNLABELLED: The abundant and metabolically versatile aquatic bacterial order, Rhodobacterales, influences marine biogeochemical cycles. We assessed Rhodobacterales metagenome-assembled genome (MAG) abundance, estimated growth rates, and potential and expressed functions in the Chesapeake and Delaware Bays, two important US estuaries. Phylogenomics of draft and draft/closed Rhodobacterales genomes from this study and others placed 46 nearly complete MAGs from these bays into 11 genera, many were not well characterized. Their abundances varied between the bays and were influenced by temperature, salinity, and silicate and phosphate concentrations. Rhodobacterales genera possessed unique and shared genes for transporters, photoheterotrophy, complex carbon degradation, nitrogen, and sulfur metabolism reflecting their seasonal differences in abundance and activity. Planktomarina genomospecies were more ubiquitous than the more niche specialists, HIMB11, CPC320, LFER01, and MED-G52. Their estimated growth rates were correlated to various factors including phosphate and silicate concentrations, cell density, and light. Metatranscriptomic analysis of four abundant genomospecies commonly revealed that aerobic anoxygenic photoheterotrophy-associated transcripts were highly abundant at night. These Rhodobacterales also differentially expressed genes for CO oxidation and nutrient transport and use between different environmental conditions. Phosphate concentrations and light penetration in the Chesapeake Bay likely contributed to higher estimated growth rates of HIMB11 and LFER01, respectively, in summer where they maintained higher ribosome concentrations and prevented physiological gene expression constraints by downregulating transporter genes compared to the Delaware Bay. Our study highlights the spatial and temporal shifts in estuarine Rhodobacterales within and between these bays reflected through their abundance, unique metabolisms, estimated growth rates, and activity changes.

IMPORTANCE: In the complex web of global biogeochemical nutrient cycling, the Rhodobacterales emerge as key players, exerting a profound influence through their abundance and dynamic activity. While previous studies have primarily investigated these organisms within marine ecosystems, this study delves into their roles within estuarine environments using a combination of metagenomic and metatranscriptomic analyses. We uncovered a range of Rhodobacterales genera, from generalists to specialists, each exhibiting distinct abundance patterns and gene expression profiles. This diversity equips them with the capacity to thrive amidst the varying environmental conditions encountered within dynamic estuarine habitats. Crucially, our findings illuminate the adaptable nature of estuarine Rhodobacterales, revealing their various energy production pathways and diverse resource management, especially during phytoplankton or algal blooms. Whether adopting a free-living or particle-attached existence, these organisms demonstrate remarkable flexibility in their metabolic strategies, underscoring their pivotal role in driving ecosystem dynamics within estuarine ecosystems.}, } @article {pmid39772868, year = {2025}, author = {Hart, LN and Zepernick, BN and Natwora, KE and Brown, KM and Obuya, JA and Lomeo, D and Barnard, MA and Okech, EO and , and Kiledal, EA and Den Uyl, PA and Olokotum, M and Wilhelm, SW and McKay, RM and Drouillard, KG and Sherman, DH and Sitoki, L and Achiya, J and Getabu, A and Otiso, KM and Bullerjahn, GS and Dick, GJ}, title = {Metagenomics reveals spatial variation in cyanobacterial composition, function, and biosynthetic potential in the Winam Gulf, Lake Victoria, Kenya.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0150724}, doi = {10.1128/aem.01507-24}, pmid = {39772868}, issn = {1098-5336}, support = {F31 ES036421/ES/NIEHS NIH HHS/United States ; }, abstract = {The Winam Gulf in the Kenyan region of Lake Victoria experiences prolific, year-round cyanobacterial harmful algal blooms (cyanoHABs) which pose threats to human, livestock, and ecosystem health. To our knowledge, there is limited molecular research on the gulf's cyanoHABs, and thus, the strategies employed for survival and proliferation by toxigenic cyanobacteria in this region remain largely unexplored. Here, we used metagenomics to analyze the Winam Gulf's cyanobacterial composition, function, and biosynthetic potential. Dolichospermum was the dominant bloom-forming cyanobacterium, co-occurring with Microcystis at most sites. Microcystis and Planktothrix were more abundant in shallow and turbid sites. Metagenome-assembled genomes (MAGs) of Dolichospermum harbored nitrogen fixation genes, suggesting diazotrophy as a potential mechanism supporting the proliferation of Dolichospermum in the nitrogen-limited gulf. Over 300 biosynthetic gene clusters (BGCs) putatively encoding the synthesis of toxins and other secondary metabolites were identified across the gulf, even at sites where there were no visible cyanoHAB events. Almost all BGCs identified had no known synthesis product, indicating a diverse and novel biosynthetic repertoire capable of synthesizing harmful or potentially therapeutic metabolites. Microcystis MAGs contained mcy genes encoding the synthesis of hepatotoxic microcystins which are a concern for drinking water safety. These findings illustrate the spatial variation of bloom-forming cyanobacteria in the Winam Gulf and their available strategies to dominate different ecological niches. This study underscores the need for further use of genomic techniques to elucidate the dynamics and mitigate the potentially harmful effects of cyanoHABs and their associated toxins on human, environmental, and economic health.IMPORTANCEThe Winam Gulf (Kenya) is a vital resource that experiences prolific cyanobacterial harmful algal blooms (cyanoHABs). Bloom-forming cyanobacteria produce cyanotoxins, threatening human and environmental health, recreation, and fishing. However, cyanotoxin production in the gulf has not been linked to a specific type of cyanobacteria. We used DNA sequencing of whole microbial communities to track the species of cyanobacteria present across the gulf and investigate the genes responsible for synthesis of known and novel toxins. Our results reveal Dolichospermum as the main bloom-forming cyanobacteria in the gulf, often co-occurring with high abundance of toxigenic Microcystis. Over 300 unique gene clusters were found, with most predicted to encode the synthesis of uncharacterized molecules. These results provide initial insights into the diverse biosynthetic potential encoded by cyanobacteria in the Winam Gulf and underscore the need to further elucidate and investigate the effects of known and novel molecules produced in cyanoHABs in this region.}, } @article {pmid39772804, year = {2025}, author = {Cottingham, H and Judd, LM and Wisniewski, JA and Wick, RR and Stanton, TD and Vezina, B and Macesic, N and Peleg, AY and Okeke, IN and Holt, KE and Hawkey, J}, title = {Targeted sequencing of Enterobacterales bacteria using CRISPR-Cas9 enrichment and Oxford Nanopore Technologies.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0141324}, doi = {10.1128/msystems.01413-24}, pmid = {39772804}, issn = {2379-5077}, abstract = {UNLABELLED: Sequencing DNA directly from patient samples enables faster pathogen characterization compared to traditional culture-based approaches, but often yields insufficient sequence data for effective downstream analysis. CRISPR-Cas9 enrichment is designed to improve the yield of low abundance sequences but has not been thoroughly explored with Oxford Nanopore Technologies (ONT) for use in clinical bacterial epidemiology. We designed CRISPR-Cas9 guide RNAs to enrich the human pathogen Klebsiella pneumoniae, by targeting multi-locus sequence type (MLST) and transfer RNA (tRNA) genes, as well as common antimicrobial resistance (AMR) genes and the resistance-associated integron gene intI1. We validated enrichment performance in 20 K. pneumoniae isolates, finding that guides generated successful enrichment across all conserved sites except for one AMR gene in two isolates. Enrichment of MLST genes led to a correct allele call in all seven loci for 8 out of 10 isolates that had depth of 30× or more in these regions. We then compared enriched and unenriched sequencing of three human fecal samples spiked with K. pneumoniae at varying abundance. Enriched sequencing generated 56× and 11.3× the number of AMR and MLST reads, respectively, compared to unenriched sequencing, and required approximately one-third of the computational storage space. Targeting the intI1 gene often led to detection of 10-20 proximal resistance genes due to the long reads produced by ONT sequencing. We demonstrated that CRISPR-Cas9 enrichment combined with ONT sequencing enabled improved genomic characterization outcomes over unenriched sequencing of patient samples. This method could be used to inform infection control strategies by identifying patients colonized with high-risk strains.

IMPORTANCE: Understanding bacteria in complex samples can be challenging due to their low abundance, which often results in insufficient data for analysis. To improve the detection of harmful bacteria, we implemented a technique aimed at increasing the amount of data from target pathogens when combined with modern DNA sequencing technologies. Our technique uses CRISPR-Cas9 to target specific gene sequences in the bacterial pathogen Klebsiella pneumoniae and improve recovery from human stool samples. We found our enrichment method to significantly outperform traditional methods, generating far more data originating from our target genes. Additionally, we developed new computational techniques to further enhance the analysis, providing a thorough method for characterizing pathogens from complex biological samples.}, } @article {pmid39772525, year = {2025}, author = {Yum, SJ and Yu, SY and Kim, SM and Jeong, HG}, title = {Antibiotic Resistance Genes and Microbiota in Brassica oleracea var. acephala Cultivated in South Korea: Potential for Resistance Transmission.}, journal = {Journal of agricultural and food chemistry}, volume = {73}, number = {3}, pages = {2156-2166}, pmid = {39772525}, issn = {1520-5118}, mesh = {*Brassica/microbiology ; Republic of Korea ; *Microbiota/drug effects ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Antimicrobial resistance (AMR) poses a critical global public health challenge. This study investigates the microbiome of Brassica oleracea var. acephala (kale) to evaluate the role of food production systems, particularly plant-derived foods, in AMR dissemination. Using 16S rRNA gene sequencing and metagenomic shotgun sequencing, we analyzed microbial diversity and antimicrobial resistance genes (ARGs) in kale samples. Results showed significant regional differences in microbiota composition and ARG distribution, with traditional fertilizer use linked to higher ARG prevalence in coliform bacteria compared to farms using other fertilization methods. Additionally, we confirmed ARG transfer potential by Klebsiella pneumoniae within coliform populations. Storage conditions notably affected microbial dynamics, with higher temperatures promoting K. pneumoniae growth in washed samples. These findings revealed the importance of AMR research in plant-derived foods and highlight the need for improved agricultural practices to mitigate the risks associated with high ARG abundance in coliform bacteria.}, } @article {pmid39772193, year = {2024}, author = {Buigues, J and Viñals, A and Martínez-Recio, R and Monrós, JS and Sanjuán, R and Cuevas, JM}, title = {Complete Genomes of DNA Viruses in Fecal Samples from Small Terrestrial Mammals in Spain.}, journal = {Viruses}, volume = {16}, number = {12}, pages = {}, pmid = {39772193}, issn = {1999-4915}, support = {CIAICO/2022/110//Conselleria de Educación, Universidades y Empleo (Generalitat Valenciana)/ ; PID2020-118602RB-I00//Ministerio de Ciencia e Innovación (MICINN)/ ; }, mesh = {Animals ; *Feces/virology ; *DNA Viruses/genetics/classification/isolation & purification ; *Genome, Viral ; Spain ; *Phylogeny ; *Mammals/virology ; }, abstract = {Viromics studies are allowing us to understand not only the enormous diversity of the virosphere, but also the potential threat posed by the emerging viruses. Regarding the latter, the main concern lies in monitoring the presence of RNA viruses, but the zoonotic potential of some DNA viruses, on which we have focused in the present study, should also be highlighted. For this purpose, we analyzed 160 fecal samples from 14 species of small terrestrial mammals, 9 of them belonging to the order Rodentia. This allowed us to identify a total of 25 complete or near-complete genomes belonging to the families Papillomaviridae, Polyomaviridae, Adenoviridae, Circoviridae, and Genomoviridae, 18 of which could be considered new species or types. Our results provide a significant increase in the number of complete genomes of DNA viruses of European origin with zoonotic potential in databases, which are at present under-represented compared to RNA viruses. In addition, the characterization of whole genomes is of relevance for the further study of the evolutionary forces governing virus adaptation, such as recombination, which may play an important role in cross-species transmission.}, } @article {pmid39772171, year = {2024}, author = {Silva, SLSD and Silva, SPD and Aragão, CF and Gorayeb, IS and Cruz, ACR and Dias, DD and Nascimento, BLSD and Chiang, JO and Casseb, LMN and Nunes Neto, JP and Martins, LC and Vasconcelos, PFDC}, title = {Investigation of RNA Viruses in Culicoides Latreille, 1809 (Diptera: Ceratopogonidae) in a Mining Complex in the Southeastern Region of the Brazilian Amazon.}, journal = {Viruses}, volume = {16}, number = {12}, pages = {}, pmid = {39772171}, issn = {1999-4915}, mesh = {Animals ; *Ceratopogonidae/virology ; Brazil ; *RNA Viruses/genetics/classification/isolation & purification ; *Phylogeny ; *Insect Vectors/virology ; Metagenomics ; Genome, Viral ; }, abstract = {The biting midges Culicoides Latreille, 1809 (Diptera: Ceratopogonidae) is highly relevant to epidemiology and public health, as it includes species that are potential vectors of human and animal arboviruses. The aim of this study was to investigate the presence of RNA viruses in species of the genus Culicoides collected in the Carajás mining complex in the state of Pará. The biting midges were collected in the municipalities of Canaã dos Carajás, Curionópolis and Marabá and morphologically identified. A total of 1139 specimens of seven Culicoides species were grouped into eight pools and subjected to metagenomic analysis. Eight new insect-specific viruses (ISVs) were characterized and assigned to the order Tolivirales, the families Chuviridae, Nodaviridae, Iflaviridae, Mesoniviridae, and Flaviviridae, and the taxon Negevirus. All viruses identified were assigned to clades, families and taxa never reported in Culicoides in Brazil. This study demonstrated that biting midges harbor a significant diversity of RNA viruses, many of which are still unknown, highlighting the importance of studies aiming at virome of these insects.}, } @article {pmid39771135, year = {2024}, author = {Li, Z and Yuan, D}, title = {Metagenomic Analysis Reveals the Effects of Microplastics on Antibiotic Resistance Genes in Sludge Anaerobic Digestion.}, journal = {Toxics}, volume = {12}, number = {12}, pages = {}, pmid = {39771135}, issn = {2305-6304}, support = {No. 52170097//the National Natural Science Foundation of China/ ; }, abstract = {Sewage sludge is recognized as both a source and a reservoir for antibiotic resistance genes (ARGs). Within an anaerobic digestion (AD) system, the presence of microplastics (MPs) has been observed to potentially facilitate the proliferation of these ARGs. Understanding the influence of MPs on microbial behavior and horizontal gene transfer (HGT) within the AD system is crucial for effectively managing the dissemination of ARGs in the environment. This study utilized metagenomic approaches to analyze the dynamics of various types of ARGs and potential microbial mechanisms under exposure to MPs during the AD process. The findings indicated that MPs in the AD process can enhance the proliferation of ARGs, with the extent of this enhancement increasing with the dosage of MPs: polyethylene (PE), polyethylene terephthalate (PET), and polylactic acid (PLA) MPs increased the abundance of ARGs in the anaerobic digestion system by up to 29.90%, 18.64%, and 14.15%, respectively. Additionally, the presence of MPs increased the relative abundance of mobile genetic elements (MGEs) during the AD process. Network correlation analysis further revealed that plasmids represent the predominant category of MGEs involved in the HGT of ARGs. Propionibacterium and Alicycliphilus were identified as the primary potential hosts for these ARGs. The results of gene function annotation indicated that exposure to MPs led to an increased the relative abundance of genes related to the production of reactive oxygen species (ROS), alterations in membrane permeability, ATP synthesis, and the secretion of extracellular polymeric substances (EPS). These genes play crucial roles in influencing the HGT of ARGs.}, } @article {pmid39771131, year = {2024}, author = {Wang, K and Shen, D and Guo, Z and Zhong, Q and Huang, K}, title = {Contamination Characteristics of Antibiotic Resistance Genes in Multi-Vector Environment in Typical Regional Fattening House.}, journal = {Toxics}, volume = {12}, number = {12}, pages = {}, pmid = {39771131}, issn = {2305-6304}, support = {2023YFD1800400//National Key Research and Development Program of China/ ; SJCX19-0129//postgraduate Research & Practice Innovation Program of Jiangsu Province/ ; }, abstract = {Antibiotic resistance genes (ARGs) are emerging as significant environmental contaminants, posing potential health risks worldwide. Intensive livestock farming, particularly swine production, is a primary contributor to the escalation of ARG pollution. In this study, we employed metagenomic sequencing and quantitative polymerase chain reaction to analyze the composition of microorganisms and ARGs across four vectors in a typical swine fattening facility: dung, soil, airborne particulate matter (PM), and fodder. Surprisingly, soil and PM harbored a higher abundance of microorganisms and ARGs than dung. At the same time, fodder was more likely to carry eukaryotes. Proteobacteria exhibited the highest propensity for carrying ARGs, with proportions 9-20 times greater than other microorganisms. Furthermore, a strong interrelation among various ARGs was observed, suggesting the potential for cooperative transmission mechanisms. These findings underscore the importance of recognizing soil and PM as significant reservoirs of ARGs in swine facilities alongside dung. Consequently, targeted measures should be implemented to mitigate their proliferation, mainly focusing on airborne PM, which can rapidly disseminate via air currents. Proteobacteria, given their remarkable carrying capacity for ARGs with the primary resistance mechanism of efflux, represent a promising avenue for developing novel control strategies against antibiotic resistance.}, } @article {pmid39770918, year = {2024}, author = {Masedunskas, A and de Ciutiis, I and Hein, LK and Ge, A and Kong, YX and Qi, M and Mainali, D and Rogerson-Wood, L and Kroeger, CM and Aguirre Candia, YA and Cagigas, ML and Wang, T and Hutchinson, D and Sabag, A and Passam, FH and Piccio, L and Sargeant, TJ and Fontana, L}, title = {Investigating the Impact of Glycogen-Depleting Exercise Combined with Prolonged Fasting on Autophagy and Cellular Health in Humans: A Randomised Controlled Crossover Trial.}, journal = {Nutrients}, volume = {16}, number = {24}, pages = {}, pmid = {39770918}, issn = {2072-6643}, support = {APP1177797//National Health and Medical Research Council/ ; }, mesh = {Humans ; *Autophagy ; *Fasting ; *Cross-Over Studies ; *Glycogen/metabolism ; *Exercise/physiology ; Adult ; Middle Aged ; Male ; Young Adult ; Female ; Aged ; Leukocytes, Mononuclear/metabolism ; Adolescent ; }, abstract = {IMPORTANCE: Although prolonged fasting has become increasingly popular, the favourable biological adaptations and possible adverse effects in humans have yet to be fully elucidated.

OBJECTIVE: To investigate the effects of a three-day water-only fasting, with or without exercise-induced glycogen depletion, on autophagy activation and the molecular pathways involved in cellular damage accumulation and repair in healthy humans.

DESIGN: A randomised, single-centre, two-period, two-sequence crossover trial. The primary outcome is autophagic activity, assessed as flux in peripheral blood mononuclear cells (PBMCs) measured in the context of whole blood. Secondary outcomes include changes in body composition, heart rate variability, endothelial function, and genomic, epigenomic, metabolomic, proteomic, and metagenomic adaptations to fasting in plasma, platelets, urine, stools, and PBMCs. Detailed profiling of circulating immune cell populations and their functional states will be assessed by flow cytometry.

SETTING: All clinical investigations will be undertaken at the Charles Perkins Centre Royal Prince Alfred Hospital clinic, University of Sydney, Australia.

PARTICIPANTS: Twenty-four individuals aged 18 to 70 years, with a BMI of 20-40 kg/m[2], free of major health conditions other than obesity.

DISCUSSION: While autophagic flux induction through fasting has garnered interest, there is a notable lack of human studies on this topic. This trial aims to provide the most detailed and integrated analysis of how three days of prolonged water-only fasting, combined with glycogen-depleting exercise, affects autophagy activation and other crucial metabolic and molecular pathways linked to cellular, metabolic, and immune health. Insights from this study may pave the way for safe and effective strategies to induce autophagy, offering potential preventive interventions for a range of chronic conditions.}, } @article {pmid39770890, year = {2024}, author = {Wells, RK and Torres, A and Mau, MK and Maunakea, AK}, title = {Racial-Ethnic Disparities of Obesity Require Community Context-Specific Biomedical Research for Native Hawaiians and Other Pacific Islanders.}, journal = {Nutrients}, volume = {16}, number = {24}, pages = {}, pmid = {39770890}, issn = {2072-6643}, support = {P20GM139753//NIH-NIGMS/ ; R01MD016593//NIH-NIMHD/ ; R56MD014630//NIH-NIMHD/ ; UG03HL169657//NIH-NHLBI/ ; }, mesh = {Humans ; *Biomedical Research ; Gastrointestinal Microbiome ; Hawaii/epidemiology ; Health Status Disparities ; *Native Hawaiian or Pacific Islander ; *Obesity/ethnology ; Pacific Island People ; }, abstract = {Compared to the general population of Hawai'i, Native Hawaiians and Other Pacific Islanders (NHPI) shoulder a disproportionately high risk for obesity-related cardiometabolic disorders, such as type 2 diabetes and cardiovascular disease. The gut microbiome is an area of rapid research interest for its role in regulating adjacent metabolic pathways, offering novel opportunities to better understand the etiology of these health disparities. Obesity and the gut microbiome are influenced by regional, racial-ethnic, and community-specific factors, limiting the generalizability of current literature for understudied populations. Additionally, anthropometric and directly measured obesity indices are variably predictive of adiposity and metabolic health risk in this diverse population. Thus, further NHPI-inclusive research is required to adequately characterize community-specific factors in the context of obesity-related disease etiology. Culturally responsible research ethics and scientific communication are crucial to conducting such research, especially among indigenous and understudied populations. In this review, we explore these limitations in current literature, emphasizing the urgent need for NHPI-inclusive research to assess community-specific factors accurately. Such accuracy in Indigenous health research may ensure that findings relevant to individual or public health recommendations and/or policies are meaningful to the communities such research aims to serve.}, } @article {pmid39770844, year = {2024}, author = {Yang, F and Liu, M and Wang, X and Hong, Y and Yao, Q and Chang, X and Shi, G and Chen, W and Tian, B and Hegazy, A}, title = {Differences in the Microbial Composition and Function of the Arundo donax Rhizosphere Under Different Cultivation Conditions.}, journal = {Microorganisms}, volume = {12}, number = {12}, pages = {}, pmid = {39770844}, issn = {2076-2607}, support = {2024ZC035//Henan Academy of Agricultural Sciences/ ; CARS-24-G-15//National Characteristic Vegetable Industry Technology System/ ; 2211111110100//Key R & D Projects in Henan Province/ ; 2024TD38, 2024TD43//Henan Academy of Agricultural Sciences Science and Technology Innovation Team/ ; 241100110200//Independent Innovation Project of Major Science and Technology Special Project of Henan Province/ ; }, abstract = {Rhizosphere microorganisms play an important role in the health and development of root systems. Investigating the microbial composition of the rhizosphere is central to understanding the inter-root microbial function of Arundo donax under various cultivation conditions. To complement the metagenomic study of the Arundo donax rhizosphere, here, an amplicon-based metagenomic survey of bacteria and fungi was selected as a practical approach to analyzing the abundance, diversity index, and community structure of rhizosphere bacteria and fungi, as well as to study the effects of different cultivation methods on rhizosphere microbial diversity. Next-generation sequencing and QIIME2 analysis were used. The results indicated that microbial community richness, diversity, and evenness of the hydroponic samples were lower than those of soil samples when examining the α diversity indices of bacteria and fungi using Chao1, ACE, and Shannon metrics. In particular, the relative abundances of Proteobacteria, Rhizobiales, and Incertae sedis in hydroponic materials were higher, while Basidiomycota, Ascomycota, and Actinobacteriota dominated the flora in soil materials when comparing the numbers of OTUs and the ACE community richness estimator. Furthermore, the rhizosphere of hydroponic A. donax contained a higher abundance of nitrogen-fixing bacteria and photosynthetic bacteria, which contribute to root formation. Additionally, there was a significant presence of Basidiomycota, Ascomycota, and Actinobacteriota in soil A. donax, which can form hyphae. This reveals that the microbial community composition of the A. donax rhizosphere is significantly different under various cultivation conditions, suggesting that employing two distinct culturing techniques for Arundo donax may alter the microbiome. Furthermore, it provides technical support for the synergistic interaction between Arundo donax and rhizosphere microorganisms so as to better use the relationship between Arundo donax and basic microorganisms to solve the problems of Arundo donax growth and ecological restoration.}, } @article {pmid39770834, year = {2024}, author = {Brunner-Mendoza, C and Calderón-Ezquerro, MDC and Guerrero-Guerra, C and Sanchez-Flores, A and Salinas-Peralta, I and Toriello, C}, title = {Diversity and Composition of the Airborne Fungal Community in Mexico City with a Metagenomic Approach.}, journal = {Microorganisms}, volume = {12}, number = {12}, pages = {}, pmid = {39770834}, issn = {2076-2607}, abstract = {Airborne fungi are widely distributed in the environment and originate from various sources like soil, plants, decaying organic matter, and even indoor environments. Exposure to airborne fungal spores can cause allergic reactions, asthma, and respiratory infections. Certain fungi can cause serious infections, particularly in individuals with weakened immune systems. An aerobiological study was conducted to detect airborne fungi using metagenomics in three areas of Mexico City, each representing different degrees of urbanization, during the dry and rainy seasons of 2017. Seasonality showed a significant role in the composition of airborne fungi. Ascomycota predominated in the three areas sampled during dry and rainy seasons, with the genera Cladosporium and Penicillium presenting the highest relative abundances across seasons. The Agaromycetes showed an increase during the rainy season. Regarding the areas, the north and center sites showed similar meteorological conditions and fungal community composition patterns. According to the Shannon and Simpson indices, the south area showed a greater species diversity during the dry season. These insights into the interactions between urbanization, seasonality, and airborne microbial communities could contribute to more effective urban management, reduced health risks, and the promotion of sustainable development.}, } @article {pmid39770808, year = {2024}, author = {Mas Martinez, I and Pushkareva, E and Keilholz, LA and Linne von Berg, KH and Karsten, U and Kammann, S and Becker, B}, title = {Role of Climate and Edaphic Factors on the Community Composition of Biocrusts Along an Elevation Gradient in the High Arctic.}, journal = {Microorganisms}, volume = {12}, number = {12}, pages = {}, pmid = {39770808}, issn = {2076-2607}, abstract = {Biological soil crusts are integral to Arctic ecosystems, playing a crucial role in primary production, nitrogen fixation and nutrient cycling, as well as maintaining soil stability. However, the composition and complex relationships between the diverse organisms within these biocrusts are not well studied. This study investigates how the microbial community composition within Arctic biocrusts is influenced by environmental factors along an altitudinal gradient (101 m to 314 m). Metagenomic analyses were used to provide insights into the community composition, revealing that temperature, pH, and nutrient availability significantly shaped the community. In contrast, altitude did not directly influence the microbial composition significantly. Eukaryotic communities were dominated by Chloroplastida and fungi, while Proteobacteria and Actinobacteria prevailed among prokaryotes. Cyanobacteria, particularly orders such as Pseudoanabaenales, Pleurocapsales, and Nostocales, emerged as the most abundant photoautotrophic organisms. Our findings highlight the impact of environmental gradients on microbial diversity and the functional dynamics of biocrusts, emphasizing their critical role in Arctic tundra ecosystems. Arctic biocrusts are intricate micro-ecosystems, whose structure is strongly shaped by local physicochemical parameters, likely affecting essential ecological functions.}, } @article {pmid39770795, year = {2024}, author = {Yuan, N and Wang, K and Liang, M and Zhou, J and Yu, R}, title = {Exploring the Influence of Biochar-Supported Nano-Iron Oxide on Phosphorus Speciation Transformation and Bacterial Community Structure in Aerobic Pig Manure Composting Processes.}, journal = {Microorganisms}, volume = {12}, number = {12}, pages = {}, pmid = {39770795}, issn = {2076-2607}, support = {XDA28080400//Rui Yu/ ; 20210101109JC//Rui Yu/ ; YDZJ202301ZYTS232//Rui Yu/ ; }, abstract = {Existing studies have demonstrated the positive effects of nano-sized iron oxide on compost maturity, yet the impact of nano-sized iron oxide on phosphorus speciation and bacterial communities during the composting process remains unclear. In this study, pig manure and straw were used as raw materials, with biochar-supported nano-sized iron oxide (BC-Fe3O4NPs) as an additive and calcium peroxide (CaO2) as a co-agent, to conduct an aerobic composting experiment with pig manure. Four treatments were tested: CK (control), F1 (1% BC-Fe3O4NPs), F2 (5% BC-Fe3O4NPs), and F3 (5% BC-Fe3O4NPs + 5% CaO2). Key findings include the following. (1) BC-Fe3O4NPs increased compost temperatures, with F3 reaching 61℃; F1 showed optimal maturity (C/N ratio: 12.90). (2) BC-Fe3O4NPs promoted stable phosphorus forms; Residual-P proportions were higher in F1, F2, and F3 (25.81%, 51.16%, 51.68%) than CK (19.32%). (3) Bacterial phyla Firmicutes, Actinobacteria, and Proteobacteria dominated. BC-Fe3O4NPs altered community composition, especially on day 7. Firmicutes dominated CK, F1, and F3; Proteobacteria dominated F2. At the genus level, day 7 showed Corynebacterium (CK), Clostridum (F1, F3), and Caldibacillus (F2) as predominant. (4) Pearson correlation analysis revealed shifted correlations between phosphorus forms and bacterial phyla after BC-Fe3O4NPs addition. Firmicutes positively correlated with NaOH-OP in F1 during the thermophilic phase, facilitating phosphate release and adsorption by BC-Fe3O4NPs. The significance of correlations diminished with increasing additive concentration; in F3, all phyla positively correlated with various phosphorus forms.}, } @article {pmid39770783, year = {2024}, author = {Xu, W and Zhang, D and Su, H and Xu, Y and Hu, X and Wen, G and Cao, Y}, title = {Impact of Biochar Addition on Biofloc Nitrifying Bacteria and Inorganic Nitrogen Dynamics in an Intensive Aquaculture System of Shrimp.}, journal = {Microorganisms}, volume = {12}, number = {12}, pages = {}, pmid = {39770783}, issn = {2076-2607}, abstract = {In this study, an eight-week culture trial of Penaeus vannamei juveniles was conducted in commercial intensive systems to compare the impacts of biochar and molasses addition on biofloc nitrifying bacteria and inorganic nitrogen dynamics under limited water exchange conditions. During the trial, the biofloc concentration (in terms of VSS and TSS), quantities of total bacteria (TB) and total Vibrio (TV), and ratio of TV/TB in the culture water were lower in the biochar group compared to the molasses group. Metagenomic sequencing analysis revealed that the bacterial community composition of bioflocs showed higher α-diversity and complexity in the biochar group compared to the molasses group. Moreover, the abundance of nitrifying bacterial genera and functional genes in bioflocs was higher in the biochar group compared to the molasses group. Inorganic nitrogen dynamics showed that NH4[+]-N and NO2[-]-N were better controlled in the biochar group compared to the molasses group, as reflected by lower peaks of NH4[+]-N and NO2[-]-N and higher NO3[-]-N concentrations. Excellent production performance of shrimp was achieved, which in turn proved the reliable effect of biochar addition on the mediation of inorganic nitrogen transformation through nitrifying bacteria. These results showed that biochar addition could promote biofloc nitrifying bacteria and nitrification to more effectively control harmful nitrogen for shrimp efficient production. This study provides a practical example for the biochar application in biofloc-based systems for intensive aquaculture.}, } @article {pmid39770772, year = {2024}, author = {Long, Y and Zhang, X and Peng, X and Yang, H and Ni, H and Zou, L and Long, Z}, title = {Metagenomic Analysis Revealing the Impact of Water Contents on the Composition of Soil Microbial Communities and the Distribution of Major Ecological Functional Genes in Poyang Lake Wetland Soil.}, journal = {Microorganisms}, volume = {12}, number = {12}, pages = {}, pmid = {39770772}, issn = {2076-2607}, support = {31960015//The National Natural Science Foundation of China/ ; 20192BAB204001//Natural Science Foundation of Jiangxi Province, China/ ; }, abstract = {Poyang Lake is the largest freshwater lake in China, which boasts unique hydrological conditions and rich biodiversity. In this study, metagenomics technology was used to sequence the microbial genome of soil samples S1 (sedimentary), S2 (semi-submerged), and S3 (arid) with different water content from the Poyang Lake wetland; the results indicate that the three samples have different physicochemical characteristics and their microbial community structure and functional gene distribution are also different, resulting in separate ecological functions. The abundance of typical ANME archaea Candidatus Menthanoperedens and the high abundance of mcrA in S1 mutually demonstrate prominent roles in the methane anaerobic oxidation pathway during the methane cycle. In S2, the advantageous bacterial genus Nitrospira with ammonia oxidation function is validated by a large number of nitrification functional genes (amoA, hao, nxrA), manifesting in that it plays a monumental role in nitrification in the nitrogen cycle. In S3, the dominant bacterial genus Nocardioides confirms a multitude of antibiotic resistance genes, indicating their crucial role in resistance and their emphatic research value for microbial resistance issues. The results above have preliminarily proved the role of soil microbial communities as indicators predicting wetland ecological functions, which will help to better develop plans for restoring ecological balance and addressing climate change.}, } @article {pmid39770762, year = {2024}, author = {Chin, YW and Hong, SP and Lim, SD and Yi, SH}, title = {Investigation of Microbial Community of Korean Soy Sauce (Ganjang) Using Shotgun Metagenomic Sequencing and Its Relationship with Sensory Characteristics.}, journal = {Microorganisms}, volume = {12}, number = {12}, pages = {}, pmid = {39770762}, issn = {2076-2607}, support = {P0020991//Ministry of Trade, Industry and Energy/ ; }, abstract = {The microbial community of a soy sauce is one of the most important factors in determining the sensory characteristics of that soy sauce. In this study, the microbial communities and sensory characteristics of twenty samples of Korean soy sauce (ganjang) were investigated using shotgun metagenome sequencing and descriptive sensory analysis, and their correlations were explored by partial least square (PLS) regression analysis. The metagenome analysis identified 1332 species of bacteria, yeasts, molds, and viruses across 278 genera, of which Tetragenococcus, Bacillus, and Enterococcus accounted for more than 80% of the total community. In the fungal community, Zygosaccharomyces rouxii, Candida versatilis, Rhodotorula taiwanensis, Debaryomyces hansenii, and Aspergillus oryzae were dominant, while the viral community consisted entirely of bacteriophages, with Bacillus phages SIOphi accounting for 93%. According to the results of the PLS analysis, desirable sensory characteristics, such as umami, sweet, and roasted soybean, as well as preference, were associated with Tetragenococcus, Lysinibacillus, Enterococcus, Staphylococcus, Lactobacillus, Pediococcus, and Weissella. The musty flavor, which is a typical property of traditional fermented foods, was related to Halomonas and Psychrobacte, while the bitter, acrid taste and sour smell were closely associated with Chromohalobacter. The results of this study provide comprehensive information on the microbial community of ganjang and may be used to select starter cultures for soy sauces.}, } @article {pmid39770761, year = {2024}, author = {de Campos, GM and de Mello Costa, TC and Silveira, RM and Valença, IN and Bezerra, RDS and Darrigo Junior, LG and Vieira, ACJ and Mesquita, CC and Laurindo, PDS and Cunha, RG and Kashima, S and Covas, DT and Simões, BP and Sampaio, SC and Elias, MC and Giovanetti, M and Slavov, SN}, title = {Viral Metagenomics in Patients Who Underwent Allogeneic Hematopoietic Stem Cell Transplantation (HSCT): A Brazilian Experience.}, journal = {Microorganisms}, volume = {12}, number = {12}, pages = {}, pmid = {39770761}, issn = {2076-2607}, support = {2017/23205-8; 2021/11944-6; 2023/12155-0; 2019/08528-0; 2019/07861-8//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; }, abstract = {Viral infections are one of the most important causes of morbidity and mortality among patients undergoing allogeneic hematopoietic stem cell transplantation (HSCT). Immunosuppression may lead to the reactivation of latent viruses or the acquisition of new infections, resulting in severe clinical outcomes. The early detection of viral reactivations is crucial for effective patient management and post-transplant care. In this study, we employed next-generation metagenomics to assess changes in viral abundance and detect clinically significant viruses in allogeneic HSCT patients. A total of 20 patients from the Transplant Unit of the University Hospital of the Faculty of Medicine of Ribeirão Preto, University of São Paulo were included, with plasma samples collected at three time points: D + 0 (pre-transplantation), D + 30 (30 days post-transplantation), and D + 100 (~100 days post-transplantation). A higher presence of clinically relevant viruses, such as the cytomegalovirus (CMV), the Epstein-Barr virus (EBV) and adenoviruses, were predominantly detected at D + 30. The diversity of commensal viruses, primarily anelloviruses, increased gradually, with the highest abundance and variability detected at D + 100. Viruses with clinical importance for HSCT, including CMV, adenovirus and EBV, were confirmed and characterized at the molecular level, showing generally high cycle threshold values. Our findings demonstrate a rise in anellovirus abundance following allogeneic HSCT, with the highest levels observed at D + 100. Notably, D + 30 was identified as a critical time point for the reactivation of clinically significant viruses. This study underscores the potential of metagenomics in the identification of clinically relevant viruses and highlights the importance of monitoring latent viruses in immunocompromised populations, including allogeneic HSCT patients.}, } @article {pmid39770743, year = {2024}, author = {Peng, X and Li, S and Dou, W and Li, M and Gontcharov, AA and Peng, Z and Qi, B and Wang, Q and Li, Y}, title = {Metagenomic Insight into the Associated Microbiome in Plasmodia of Myxomycetes.}, journal = {Microorganisms}, volume = {12}, number = {12}, pages = {}, pmid = {39770743}, issn = {2076-2607}, support = {31770011//National Natural Science Foundation of China/ ; }, abstract = {During the trophic period of myxomycetes, the plasmodia of myxomycetes can perform crawling feeding and phagocytosis of bacteria, fungi, and organic matter. Culture-based studies have suggested that plasmodia are associated with one or several species of bacteria; however, by amplicon sequencing, it was shown that up to 31-52 bacteria species could be detected in one myxomycete, suggesting that the bacterial diversity associated with myxomycetes was likely to be underestimated. To fill this gap and characterize myxomycetes' microbiota and functional traits, the diversity and functional characteristics of microbiota associated with the plasmodia of six myxomycetes species were investigated by metagenomic sequencing. The results indicate that the plasmodia harbored diverse microbial communities, including eukaryotes, viruses, archaea, and the dominant bacteria. The associated microbiomes represented more than 22.27% of the plasmodia genome, suggesting that these microbes may not merely be parasitic or present as food but rather may play functional roles within the plasmodium. The six myxomycetes contained similar bacteria, but the bacteria community compositions in each myxomycete were species-specific. Functional analysis revealed a highly conserved microbial functional profile across the six plasmodia, suggesting they may serve a specific function for the myxomycetes. While the host-specific selection may shape the microbial community compositions within plasmodia, functional redundancy ensures functional stability across different myxomycetes.}, } @article {pmid39770729, year = {2024}, author = {García, G and Soto, J and Netherland, M and Hasan, NA and Buchaca, E and Martínez, D and Carlin, M and de Jesus Cano, R}, title = {Evaluating the Effects of Sugar Shift[®] Symbiotic on Microbiome Composition and LPS Regulation: A Double-Blind, Placebo-Controlled Study.}, journal = {Microorganisms}, volume = {12}, number = {12}, pages = {}, pmid = {39770729}, issn = {2076-2607}, support = {No Grant Number//The BioCollective Foundation/ ; }, abstract = {(1) Background: This study evaluated the effects of BiotiQuest[®] Sugar Shift[®], a novel probiotic formulation, for its impact on gut microbiome composition and metabolic health in type 2 diabetes mellitus (T2D). T2D is characterized by chronic inflammation and gut microbiome imbalances, yet the therapeutic potential of targeted probiotics remains underexplored. (2) Methods: In a 12-week randomized, double-blind, placebo-controlled trial, 64 adults with T2D received either Sugar Shift or placebo capsules twice daily. Each dose provided 18 billion CFU of eight GRAS-certified bacterial strains and prebiotics. Clinical samples were analyzed for metabolic markers, and microbiome changes were assessed using 16S rRNA sequencing and metagenomics. (3) Results: Sugar Shift significantly reduced serum lipopolysaccharide (LPS) levels, improved insulin sensitivity (lower HOMA-IR scores), and increased short-chain fatty acid (SCFA)-producing genera, including Bifidobacterium, Faecalibacterium, Fusicatenibacter, and Roseburia. Pro-inflammatory taxa like Enterobacteriaceae decreased, with reduced LPS biosynthesis genes and increased SCFA production genes. The Lachnospiraceae:Enterobactericeae ratio emerged as a biomarker of reduced inflammation. (4) Conclusions: These findings demonstrate the potential of Sugar Shift to restore gut homeostasis, reduce inflammation, and improve metabolic health in T2D. Further studies are warranted to explore its long-term efficacy and broader application in metabolic disease management.}, } @article {pmid39770715, year = {2024}, author = {Johnson, BT and White, BJ and Amachawadi, RG and Kleinhenz, MD and Farney, JK and Shippy, TD and Larson, RL}, title = {Determining the Effect of Varied Proportions of Cohort Administered Tulathromycin at Arrival on Nasopharyngeal Microbiota and Performance Characteristics in Yearling Steers in the First 56 Days on Feed.}, journal = {Microorganisms}, volume = {12}, number = {12}, pages = {}, pmid = {39770715}, issn = {2076-2607}, abstract = {Metaphylaxis or treating the entire population of cattle at arrival with an antimicrobial has been studied extensively in the cattle industry; however, little information is available on the impacts of treating only a proportion of the population with antimicrobials at arrival. The study objective was to determine potential associations between the proportion of animals in a pen treated with antimicrobial therapy with pen performance and nasopharyngeal microbiome. Yearling steers (n = 160) were randomly allocated to study pens (n = 40) and pens were systematically randomized to one of two antimicrobial treatments (META: all four head received tulathromycin; MIXED: two of four head randomly selected to receive tulathromycin). The study was conducted in conjunction with an essential oil feeding trial. Deep nasal pharyngeal (DNP) swabs were collected from every steer at Days 0, 14, 28, and 56. All DNP swabs were individually cultured for Pasteurella multocida and Mannheimia haemolytica. Samples of DNA were extracted from DNP swabs, pooled by pen, and analyzed by metagenomic shotgun sequencing to compare nasopharyngeal microbiome composition and quantity of resistance genes between test groups. Neither antimicrobial nor essential oil treatment groups had any significant associations with performance or DNP microbiome. Sampling day was significantly associated with alpha and beta diversity at the species level. Shannon's diversity and Inverse Simpson diversity were significantly lower on Day 14 versus both Day 0 and Day 56. These data indicated a shift in microbial populations across study days; however, the microbiome diversity and relative abundance were not significantly different between antimicrobial treatment groups.}, } @article {pmid39770698, year = {2024}, author = {Kurakawa, T and Kani, K and Chudan, S and Nishikawa, M and Tabuchi, Y and Sakamoto, K and Nagai, Y and Ikushiro, S and Furusawa, Y}, title = {Rice Kefiran Ameliorates Obesity and Hepatic Steatosis Through the Change in Gut Microbiota.}, journal = {Microorganisms}, volume = {12}, number = {12}, pages = {}, pmid = {39770698}, issn = {2076-2607}, support = {20K05929//JSPS KAKENHI/ ; n/a//Takeda Science Foundation/ ; n/a//Tojuro Iijima Foundation for Food Science and Technology/ ; n/a//LOTTE Foundation/ ; }, abstract = {Obesity is a global epidemic and a significant risk factor for various diseases. Obesity and dysbiosis are associated, drawing attention to the mechanisms that regulate the gut microbiota. In this study, we focused on the postbiotic effects of rice kefiran (Kef), a functional product of Lactobacillus kefiranofaciens cultured in a rice-based medium, on obesity and its complications. Although Kef has the potential to improve obesity, the underlying mechanisms remain unknown. Therefore, we aimed to elucidate the mechanisms underlying changes in gut microbiota. The administration of Kef significantly suppressed diet-induced body weight gain, reduced liver fat accumulation, and modestly improved insulin resistance. Among the gut bacteria, Lachnospiraceae and Lachnoclostridium, which were positively correlated with obesity, decreased in mice administered Kef. In contrast, Bacteroides and Alistipes, both reported to ameliorate obesity, were increased. Consistent with the changes in the gut microbiota, Kef increased fecal acetate levels, which ameliorated obesity and hepatic steatosis. Predictive metagenomic analysis suggested that Kef administration increased the abundance of KEGG orthologs, associated with carbohydrate metabolism and improvements in insulin resistance. In conclusion, Kef improves diet-induced obesity, hepatic steatosis, and insulin resistance by regulating the gut microbiota's composition.}, } @article {pmid39770685, year = {2024}, author = {Han, Y and He, J and Li, M and Peng, Y and Jiang, H and Zhao, J and Li, Y and Deng, F}, title = {Unlocking the Potential of Metagenomics with the PacBio High-Fidelity Sequencing Technology.}, journal = {Microorganisms}, volume = {12}, number = {12}, pages = {}, pmid = {39770685}, issn = {2076-2607}, support = {SQ2023YFE0102739//National Key Research and Development Program of China/ ; 2022A1515110819//Youth project of Guangdong Foshan joint fund of the Guangdong Natural Science Foundation/ ; 32170430//National Natural Science Foundation of China/ ; }, abstract = {Traditional methods for studying microbial communities have been limited due to difficulties in culturing and sequencing all microbial species. Recent advances in third-generation sequencing technologies, particularly PacBio's high-fidelity (HiFi) sequencing, have significantly advanced metagenomics by providing accurate long-read sequences. This review explores the role of HiFi sequencing in overcoming the limitations of previous sequencing methods, including high error rates and fragmented assemblies. We discuss the benefits and applications of HiFi sequencing across various environments, such as the human gut and soil, which provides broader context for further exploration. Key studies are discussed to highlight HiFi sequencing's ability to recover complete and coherent microbial genomes from complex microbiomes, showcasing its superior accuracy and continuity compared to other sequencing technologies. Additionally, we explore the potential applications of HiFi sequencing in quantitative microbial analysis, as well as the detection of single nucleotide variations (SNVs) and structural variations (SVs). PacBio HiFi sequencing is establishing a new benchmark in metagenomics, with the potential to significantly enhance our understanding of microbial ecology and drive forward advancements in both environmental and clinical applications.}, } @article {pmid39770646, year = {2024}, author = {Qu, J and Lu, X and Liu, T and Qu, Y and Xing, Z and Wang, S and Jing, S and Zheng, L and Wang, L and Wang, X}, title = {Macrogenomic Analysis Reveals Soil Microbial Diversity in Different Regions of the Antarctic Peninsula.}, journal = {Microorganisms}, volume = {12}, number = {12}, pages = {}, pmid = {39770646}, issn = {2076-2607}, support = {Grant No. 2021CXGC011306//Research and Development Program of Shandong Province, China, (Major Science and Technology Innovation Project)/ ; MEEST-2021-05//the Key Funded with the MNR Key Laboratory of Eco-Environmental Science and Technology, China,/ ; Grant No. ZR2020MD002//Natural Science Foundation of Shandong Province/ ; Grant No. 20230304002YY//Research and Development Program of Jilin Province, China (Major Science and Technology Innovation Project)/ ; NO.KF2022006//Open Fund of Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education/ ; Grant SM15B01, SM19B70 and SM19B28//The Doctoral Science Research Foundation of Yantai University/ ; 2320004-SM20RC02//Yantai "double-hundred project"/ ; }, abstract = {(1) Background: The unique geographical and climatic conditions of the Antarctic Peninsula contribute to distinct regional ecosystems. Microorganisms are crucial for sustaining the local ecological equilibrium. However, the variability in soil microbial community diversity across different regions of the Antarctic Peninsula remains underexplored. (2) Methods: We utilized metagenome sequencing to investigate the composition and functionality of soil microbial communities in four locations: Devil Island, King George Island, Marambio Station, and Seymour Island. (3) Results: In the KGI region, we observed increased abundance of bacteria linked to plant growth promotion and the degradation of pollutants, including PAHs. Conversely, Marambio Station exhibited a significant reduction in bacterial abundance associated with iron and sulfur oxidation/reduction. Notably, we identified 94 antibiotic resistance genes (ARGs) across 15 classes of antibiotics in Antarctic soils, with those related to aminoglycosides, β-lactamase, ribosomal RNA methyltransferase, antibiotic efflux, gene regulatory resistance, and ABC transporters showing a marked influence from anthropogenic activities. (4) Conclusions: This study carries substantial implications for the sustainable use, advancement, and conservation of microbial resources in Antarctic soils.}, } @article {pmid39770612, year = {2024}, author = {Yang, B and Yang, J and Chen, R and Chai, J and Wei, X and Zhao, J and Zhao, Y and Deng, F and Li, Y}, title = {Metagenome-Assembled Genomes of Pig Fecal Samples in Nine European Countries: Insights into Antibiotic Resistance Genes and Viruses.}, journal = {Microorganisms}, volume = {12}, number = {12}, pages = {}, pmid = {39770612}, issn = {2076-2607}, support = {2023YFE0124400//the National Key Research and Development Program of China/ ; 2022A1515110819//Youth Project of Guangdong Foshan joint fund of the Guangdong Natural Science Foundation/ ; 2019B030301010//Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding/ ; }, abstract = {Gut microbiota plays a crucial role in the health and productivity of pigs. However, the spread of antibiotic resistance genes (ARGs) and viruses within the pig intestinal microbiota poses significant threats to animal and public health. This study utilized 181 pig samples from nine European countries and employed metagenomic assembly methods to investigate the dynamics and distribution of ARGs and viruses within the pig intestinal microbiota, aiming to observing their associations with potential bacterial hosts. We identified 4605 metagenome-assembled genomes (MAGs), corresponding to 19 bacterial phyla, 97 families, 309 genera, and a total of 449 species. Additionally, 44 MAGs were classified as archaea. Analysis of ARGs revealed 276 ARG types across 21 ARG classes, with Glycopeptide being the most abundant ARG class, followed by the class of Multidrug. Treponema D sp016293915 was identified as a primary potential bacterial host for Glycopeptide. Aligning nucleotide sequences with a viral database, we identified 1044 viruses. Among the viral genome families, Peduoviridae and Intestiviridae were the most prevalent, with CAG-914 sp000437895 being the most common potential host species for both. These findings highlight the importance of MAGs in enhancing our understanding of the gut microbiome, revealing microbial diversity, antibiotic resistance, and virus-bacteria interactions. The data analysis for the article was based on the public dataset PRJEB22062 in the European Nucleotide Archive.}, } @article {pmid39770607, year = {2024}, author = {Petrilli, R and Fabbretti, A and Pucci, K and Pagliaretta, G and Napolioni, V and Falconi, M}, title = {Development and Characterization of Ammonia Removal Moving Bed Biofilms for Landfill Leachate Treatment.}, journal = {Microorganisms}, volume = {12}, number = {12}, pages = {}, pmid = {39770607}, issn = {2076-2607}, support = {BVC000035, Convenzione Eco Elpidiense//Eco Elpidiense Company, Porto Sant' Elpidio (FM), Italy/ ; }, abstract = {Urbanization growth has intensified the challenge of managing and treating increasing amounts of municipal solid waste (MSW). Landfills are commonly utilized for MSW disposal because of their low construction and operation costs. However, this practice produces huge volumes of landfill leachate, a highly polluting liquid rich in ammoniacal nitrogen (NH3-N), organic compounds, and various heavy metals, making it difficult to treat in conventional municipal wastewater treatment plants (WWTPs). In recent years, research has shown that microbial biofilms, developed on carriers of different materials and called "moving bed biofilm reactors" (MBBRs), may offer promising solutions for bioremediation. This study explored the biofilm development and the nitrification process of moving bed biofilms (MBBs) obtained from high ammonia-selected microbial communities. Using crystal violet staining and confocal laser-scanning microscopy, we followed the biofilm formation stages correlating nitrogen removal to metagenomic analyses. Our results indicate that MBBs unveiled a 10-fold more enhanced nitrification rate than the dispersed microbial community present in the native sludge of the Porto Sant'Elpidio (Italy) WWTP. Four bacterial families, Chitinophagaceae, Comamonadaceae, Sphingomonadaceae, and Nitrosomonadaceae, accumulate in structured biofilms and significantly contribute to the high ammonium removal rate of 80% in 24 h as estimated in leachate-containing wastewaters.}, } @article {pmid39770592, year = {2024}, author = {Gonzalez-Escalona, N and Kwon, HJ and Chen, Y}, title = {Nanopore Sequencing Allows Recovery of High-Quality Completely Closed Genomes of All Cronobacter Species from Powdered Infant Formula Overnight Enrichments.}, journal = {Microorganisms}, volume = {12}, number = {12}, pages = {}, pmid = {39770592}, issn = {2076-2607}, support = {This research was funded by the Food and Drug Administration Foods Program Intramural Funds//United States Food and Drug Administration/ ; }, abstract = {Precision metagenomic approaches using Oxford Nanopore Technology (ONT) sequencing has been shown to allow recovery of complete genomes of foodborne bacteria from overnight enrichments of agricultural waters. This study tests the applicability of a similar approach for Cronobacter genome recovery from powdered infant formula (PIF) overnight enrichments, where Cronobacter typically dominates the overall microbiome (>90%). This study aimed to test whether using ONT sequencing of overnight PIF enrichments could recover a completely closed Cronobacter genome for further genomic characterization. Ten PIF samples, each inoculated with different Cronobacter strains, covering Cronobacter sakazakii, C. muytjensii, C. dublinensis, C. turicensis, and C. universalis, were processed according to the Bacteriological Analytical Manual (BAM) protocol. Real-time quantitative PCR (qPCR) was used for initial screening (detection and quantification) of the overnight enrichments and confirmed that the inoculated PIF samples after the overnight enrichment had high levels of Cronobacter (10[7] to 10[9] CFU/mL). DNA from overnight PIF enrichments was extracted from the enrichment broth and sequenced using ONT. Results showed that ONT sequencing could accurately identify, characterize, and close the genomes of Cronobacter strains from overnight PIF enrichments in 3 days, much faster than the nearly 2 weeks required by the current BAM method. Complete genome recovery and species differentiation were achieved. This suggests that combining qPCR with ONT sequencing provides a rapid, cost-effective alternative for detecting and characterizing Cronobacter in PIF, enabling timely corrective actions during outbreaks.}, } @article {pmid39770383, year = {2024}, author = {Romano, G and Ferrari, G and Pitrolo, AMG and Rovida, F and Piralla, A and Baldanti, F}, title = {Tracing the Origin, Spread, and Molecular Evolution of Dengue Type 1 Cases That Occurred in Northern Italy in 2023.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {12}, pages = {}, pmid = {39770383}, issn = {2076-0817}, support = {PE00000007//NextGenerationEU-MUR PNRR Extended Partnership initiative on Emerging Infectious Diseases/ ; SURVEID Project, program 2022//Center for Disease Prevention and Control (CCM) of the Italian Ministry of Health/ ; }, mesh = {*Dengue Virus/genetics/isolation & purification ; *Dengue/epidemiology/transmission/virology ; Humans ; Italy/epidemiology ; *Aedes/virology ; Animals ; *Phylogeny ; *Genotype ; *Mosquito Vectors/virology ; *Disease Outbreaks ; *Evolution, Molecular ; Male ; Female ; }, abstract = {The dengue virus (DENV) is a mosquito-borne flavivirus endemic to many tropical and subtropical regions. Over the past few decades, the global incidence of dengue has risen dramatically, with the virus now present in over 100 countries, putting nearly half of the world's population at risk. This increase is attributed to several factors, including urbanization, climate change, and global travel, which facilitate the spread of both the virus and its mosquito vectors. While dengue is primarily associated with tropical regions, outbreaks in temperate areas are becoming increasingly common due to the spread of Aedes albopictus, a competent vector for DENV that can adapt to cooler climates. This study investigates the molecular dynamics and geographic evolution of DENV type 1 (DENV-1) strains isolated from 13 patients during an autochthonous outbreak in Lombardy, Northern Italy, between August and September 2023. Additionally, Aedes albopictus mosquitoes were collected from a neighboring area to assess their potential role in the outbreak. A metagenomic approach was used to recover DENV-1 consensus sequences from clinical samples. Genotype classification and phylogenetic analyses were performed using Bayesian methods and a comprehensive dataset of DENV-1 sequences from other countries. The Italian autochthonous strains clustered with South American strains collected between 2020 and 2023, specifically those belonging to genotype V, subtype D. Bayesian analysis estimated a mean evolutionary substitution rate of 8.234 × 10[-4] substitutions per site per year (95% HPD interval: 7.1448 × 10[-4]-9.3343 × 10[-4]), with the time to the most recent common ancestor (tMRCA) dating back to 1972 (95% HPD interval: 1968-1976). These findings suggest the likely introduction of the virus into the region from endemic areas in South America, followed by local transmission. This study offers valuable insights into the dynamics of the DENV-1 outbreak in Lombardy, underscoring the importance of genomic surveillance in monitoring viral spread and evolution. The findings emphasize the critical need for enhanced molecular and entomological surveillance to detect and respond to emerging autochthonous DENV cases in temperate regions where competent vectors, such as Aedes albopictus, are present. Public health strategies should prioritize integrated vector management, real-time genomic monitoring, and awareness campaigns to mitigate the risk of future outbreaks. These measures are essential to address the growing threat posed by the geographic expansion of the dengue virus.}, } @article {pmid39769095, year = {2024}, author = {Mohan, B and Majeed, A and Thingujam, D and Burton, SS and Cowart, KE and Pajerowska-Mukhtar, KM and Mukhtar, MS}, title = {Amplicon Sequencing Analysis of Submerged Plant Microbiome Diversity and Screening for ACC Deaminase Production by Microbes.}, journal = {International journal of molecular sciences}, volume = {25}, number = {24}, pages = {}, pmid = {39769095}, issn = {1422-0067}, support = {IOS-2038872//National Science Foundation/ ; 2418230//National Science Foundation/ ; }, mesh = {*Carbon-Carbon Lyases/genetics/metabolism ; *Microbiota/genetics ; *Plants/microbiology ; Bacteria/genetics/classification/enzymology ; Metagenomics/methods ; Phylogeny ; Biodiversity ; }, abstract = {Submerged plants can thrive entirely underwater, playing a crucial role in maintaining water quality, supporting aquatic organisms, and enhancing sediment stability. However, they face multiple challenges, including reduced light availability, fluctuating water conditions, and limited nutrient access. Despite these stresses, submerged plants demonstrate remarkable resilience through physiological and biochemical adaptations. Additionally, their interactions with microbial communities are increasingly recognized as pivotal in mitigating these environmental stresses. Understanding the diversity of these microbial communities is crucial for comprehending the complex interactions between submerged plants and their environments. This research aims to identify and screen microbes from submerged plant samples capable of producing 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase and to explore microbial diversity through metagenomic analysis. Microbes were isolated and screened for ACC deaminase production, and metagenomic techniques, including co-occurrence network analysis, were used to examine microbial diversity and interactions within the communities. ACC deaminase-producing microbes can significantly enhance plant metabolism under stress conditions. The identification of the culturable bacteria revealed that most of these microbes belong to the genera Pseudomonas, Bacillus, and Acinetobacter. A total of 177 microbial strains were cultured, with molecular identification revealing 79 reductant, 86 non-reductant, and 12 uncultured strains. Among 162 samples screened for ACC deaminase activity, 50 tested positive. To further understand microbial dynamics, samples were collected from both natural sources and artificial pond reservoirs to assess the impact of the location on flood-associated microbiomes in submerged plants. Metagenomic analysis was conducted on both the epiphytic and endophytic samples. By exploring the overall composition and dynamics of microbial communities associated with submerged plants, this research seeks to deepen our understanding of plant-microbe interactions in aquatic environments. The microbial screening helped to identify the diverse microbes associated with ACC deaminase activity in submerged plants and amplicon sequencing analysis paved the way towards identifying the impact of the location in shaping the microbiome and the diversity associated with endophytic and epiphytic microbes. Co-occurrence network analysis further highlighted the intricate interactions within these microbial communities. Notably, ACC deaminase activity was observed in plant-associated microbes across different locations, with distinct variations between epiphytic and endophytic populations as identified through co-occurrence network analysis.}, } @article {pmid39768398, year = {2024}, author = {Al-Awthan, YS and Mir, R and Alatawi, FA and Alatawi, AS and Almutairi, FM and Khafaga, T and Shohdi, WM and Fakhry, AM and Alharbi, BM}, title = {Metagenome Analysis Identified Novel Microbial Diversity of Sandy Soils Surrounded by Natural Lakes and Artificial Water Points in King Salman Bin Abdulaziz Royal Natural Reserve, Saudi Arabia.}, journal = {Life (Basel, Switzerland)}, volume = {14}, number = {12}, pages = {}, pmid = {39768398}, issn = {2075-1729}, abstract = {BACKGROUND: Soil microbes play a vital role in the ecosystem as they are able to carry out a number of vital tasks. Additionally, metagenomic studies offer valuable insights into the composition and functional potential of soil microbial communities. Furthermore, analyzing the obtained data can improve agricultural restoration practices and aid in developing more effective environmental management strategies.

METHODOLOGY: In November 2023, sandy soil samples were collected from ten sites of different geographical areas surrounding natural lakes and artificial water points in the Tubaiq conservation area of King Salman Bin Abdulaziz Royal Natural Reserve (KSRNR), Saudi Arabia. In addition, genomic DNA was extracted from the collected soil samples, and 16S rRNA sequencing was conducted using high-throughput Illumina technology. Several computational analysis tools were used for gene prediction and taxonomic classification of the microbial groups.

RESULTS: In this study, sandy soil samples from the surroundings of natural and artificial water resources of two distinct natures were used. Based on 16S rRNA sequencing, a total of 24,563 OTUs were detected. The metagenomic information was then categorized into 446 orders, 1036 families, 4102 genera, 213 classes, and 181 phyla. Moreover, the phylum Pseudomonadota was the most dominant microbial community across all samples, representing an average relative abundance of 34%. In addition, Actinomycetes was the most abundant class (26%). The analysis of clustered proteins assigned to COG categories provides a detailed understanding of the functional capabilities and adaptation of microbial communities in soil samples. Amino acid metabolism and transport were the most abundant categories in the soil environment.

CONCLUSIONS: Metagenome analysis of sandy soils surrounding natural lakes and artificial water points in the Tubaiq conservation area of KSRNR (Saudi Arabia) has unveils rich microbial activity, highlighting the complex interactions and ecological roles of microbial communities in these environments.}, } @article {pmid39768341, year = {2024}, author = {Maffia, A and Scotti, R and Wood, T and Muscolo, A and Lepore, A and Acocella, E and Celano, G}, title = {Transforming Agricultural and Sulfur Waste into Fertilizer: Assessing the Short-Term Effects on Microbial Biodiversity via a Metagenomic Approach.}, journal = {Life (Basel, Switzerland)}, volume = {14}, number = {12}, pages = {}, pmid = {39768341}, issn = {2075-1729}, support = {FARB2023//University of Salerno and the doctoral research funds of the Mediterranean University of Reggio Calabria./ ; }, abstract = {Fungi and soil bacteria are vital for organic matter decomposition and biogeochemical cycles, but excessive synthetic fertilizer use contributes to soil degradation and loss of biodiversity. Despite this, about 97% of soil microorganisms are unculturable, making them difficult to study. Metagenomics offers a solution, enabling the direct extraction of DNA from soil to uncover microbial diversity and functions. This study utilized metagenomics to analyze the rhizosphere of two-year-old Tonda di Giffoni hazelnut saplings treated with synthetic NPK, composted olive pomace, and an innovative fertilizer derived from sulfur-based agro-industrial waste stabilized with bentonite clay. Using 16S rDNA for bacteria and ITS2 for fungi, Illumina sequencing provided insights into microbial responses to different fertilizer treatments. The results highlighted a significant increase in the abundance of beneficial microorganisms such as Thiobacillus, Pseudoxanthomonas, and Thermomyces, especially when organic materials were included. Additionally, microbial biodiversity improved with organic inputs, as shown by increased species richness (Chao1) and diversity (Bray-Curtis) greater than 20% compared with NPK and unfertilized soils (CTR). These findings emphasize the importance of organic fertilization in enhancing soil microbial health, offering a sustainable approach to improving soil quality and hazelnut productivity.}, } @article {pmid39766799, year = {2024}, author = {Xu, X and Gao, X and Gui, C and Wang, H and Liu, X and Wu, G}, title = {Metagenomic Insights into the Enhancement of Bioavailable Nitrogen in Continuous Cropping Soil Through the Application of Traditional Chinese Medicine Residue Following Fumigation.}, journal = {Genes}, volume = {15}, number = {12}, pages = {}, pmid = {39766799}, issn = {2073-4425}, support = {32060639//National Natural Science Foundation of China/ ; 32060640//National Natural Science Foundation of China/ ; 32260704//National Natural Science Foundation of China/ ; 202105AC160037//Reserve Talents Project for Yunnan Young and Middle-aged Academic and Technical Leaders c/ ; 202205AC160077//Reserve Talents Project for Yunnan Young and Middle-aged Academic and Technical Leadersc/ ; NA//Hunan Engineering Research Center for Green Prevention and Control of Soil-borne Diseases/ ; NA//Hunan Engineering Research Center for Research and Development of plant resources in Nanling area, Hunan Province/ ; }, mesh = {*Soil Microbiology ; *Fumigation/methods ; *Nitrogen/metabolism ; *Rhizosphere ; *Soil/chemistry ; *Fertilizers/analysis ; Metagenomics/methods ; Medicine, Chinese Traditional/methods ; Bacteria/genetics/drug effects/growth & development ; Microbiota/drug effects ; Metagenome ; Capsicum/growth & development/microbiology/drug effects/genetics ; }, abstract = {Background/Objectives: Chemical fumigation can effectively inhibit the occurrence of soil-borne diseases; however, this approach can negatively affect the structure of the soil microbial community. The combination of soil fumigant and organic fertilizer application thus represents a widely adopted strategy in agricultural practice. Traditional Chinese medicine residue (TCMR) is a high-quality organic fertilizer; however, the impact of post-fumigation TCMR application on keystone taxa and their functional traits remains uncertain. Methods: This study examined the effects of five fertilization treatments on the diversity, key species, and related functional genes of microbial communities in rhizosphere soil of continuous cropping pepper. Results: Chemical fumigation followed by TCMR application markedly enhanced soil nutrient content in the rhizosphere and significantly influenced microbial community composition as well as functional gene patterns associated with microbial nitrogen cycling. It was also strongly correlated with soil bioavailable nitrogen content. The abundance of keystone bacterial species (Pseudomonadota, Actinomycetota, and Bacillota) substantially increased following TCMR application, alongside a notable rise in Ascomycota abundance within the fungal community. This shift contributed to an increase in beneficial bacterial abundance while reducing that of harmful bacteria. Additionally, TCMR addition affected the abundance of denitrification and DNRA genes involved in nitrogen cycling; specifically, nirB and nirK were strongly associated with soil organic nitrogen content. Conclusions: The combined application of chemical fumigants and TCMR modified the composition of keystone microbial community species by influencing rhizosphere soil TN and other nutrients, and these alterations were linked to multiple nitrogen-cycling functional genes.}, } @article {pmid39766512, year = {2024}, author = {Ota, Y and Chen, F and Prah, I and Mahazu, S and Watanabe, K and Kinoshita, T and Gu, Y and Nukui, Y and Saito, R}, title = {Metatranscriptomic Analysis Reveals Actively Expressed Antimicrobial-Resistant Genes and Their Hosts in Hospital Wastewater.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {12}, pages = {}, pmid = {39766512}, issn = {2079-6382}, support = {23H03551//Japan Society for the Promotion of Science/ ; JP20wm0125007, JP20wm0225004, JP22wm0225022//Japan Agency for Medical Research and Development/ ; None//Morinomiyako Medical Research Foundation/ ; }, abstract = {Antimicrobial resistance is a major global concern and economic threat, necessitating a reliable monitoring approach to understand its frequency and spread via the environment. Hospital wastewater serves as a critical reservoir for antimicrobial-resistant organisms; however, its role in resistance gene distribution and dissemination remains poorly understood. This study integrates metagenomic and metatranscriptomic analyses, elucidating the dynamics of antimicrobial resistance in hospital wastewater. Integrated metagenomic and metatranscriptomic sequencing were used to identify actively expressed antimicrobial-resistant genes and antimicrobial-resistant bacteria, offering comprehensive insights into antimicrobial resistance dynamics in hospital wastewater. Liquid chromatography-tandem mass spectrometry analysis revealed the presence of ampicillin, sulbactam, levofloxacin, sulfamethoxazole, and trimethoprim in the sample, which could apply selective pressure on antimicrobial resistance gene expression. While multidrug resistance genes were the most prevalent sequences in both metagenome-assembled genomes and plasmids, plasmid-derived sequences showed a high mRNA/DNA ratio, emphasizing the presence of functionally expressed antimicrobial resistance genes on plasmids rather than on chromosomes. The metagenomic and metatranscriptomic analyses revealed Serratia nevei MAG14 with high mRNA levels of antimicrobial resistance genes; moreover, multidrug-resistant Serratia sp., genetically related to MAG14, was isolated from the wastewater, supporting the phenotypic characterization of crucial antimicrobial-resistant bacteria and validating the genome analysis results. The findings underscore key genes and bacteria as targets for antimicrobial resistance surveillance in hospital wastewater to protect public and environmental health.}, } @article {pmid39765529, year = {2024}, author = {Kou, X and Liu, Y and Xiang, F and Zhang, X and Khan, MZ and Wu, B and Wang, H and Gong, Y and Wang, C and Ma, Q and Li, Y}, title = {Insights into the Donkey Hindgut Microbiome Using Metagenome-Assembled Genomes.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {24}, pages = {}, pmid = {39765529}, issn = {2076-2615}, support = {32102564//National Natural Science Foundation of China/ ; }, abstract = {The gut microbiota plays an important role in the digestion, absorption, and metabolism of nutrients, as well as in the immunity, health, and behavior of donkeys. While reference genomes and gut microbial gene catalogs have been helpful in understanding the composition of the donkey, there is still a significant gap in sequencing and understanding the functional aspects of donkey gut microbial genomes. In this study, we analyzed metagenomic sequencing data from 26 donkeys' gut samples and successfully assembled 844 microbial metagenome-assembled genomes (MAGs). Surprisingly, 678 (80.33%) of these MAGs appear to belong to previously unidentified species. Our analysis further revealed a total of 292,980 predicted carbohydrate-active enzymes (CAZymes) and 257,893 polysaccharide utilization loci (PULs). Interestingly, these enzymes and loci displayed relatively low similarity matches in public databases. We found that the higher abundances of 36 MAGs in the cecum (such as Prevotella, Desulfovibrio, Alistipes, and Treponema_D) and 9 MAGs in the dorsal colon (such as Limimorpha, Saccharofermentans, and Lactobacillus) were associated with a diverse array of carbohydrate-degrading pathways. Network analysis identified Prevotella and Dysosmobacter as connectors, while Saccharofermentans and Akkermansia were shown as provincial hubs. This suggests their crucial roles in complex carbohydrate degradation and hindgut metabolism in donkeys. These findings underscore the complexity of hindgut metabolism in donkeys and expand our understanding of their gut microbiome. Overall, this study provides a comprehensive catalog of donkey gut microbial genes, revealing novel carbohydrate-degrading enzymes and offering new insights for future research on the donkey gut microbiome.}, } @article {pmid39765202, year = {2025}, author = {Zhang, D and Li, J and Zhang, G and Xu, Y}, title = {Decoding the trajectory of antibiotic resistance genes in saline and alkaline soils: Insights from different fertilization regimes.}, journal = {Environment international}, volume = {195}, number = {}, pages = {109247}, doi = {10.1016/j.envint.2024.109247}, pmid = {39765202}, issn = {1873-6750}, mesh = {*Soil/chemistry ; *Soil Microbiology ; *Fertilizers ; *Salinity ; *Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Hydrogen-Ion Concentration ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/drug effects ; }, abstract = {The soil salinity and alkalinity play an important role in the occurrence and proliferation of antibiotic resistance genes (ARGs). Yet, little is known the underlying mechanism by which soil salinity and alkalinity affect antibiotic resistance evolution. Here we investigated the ARGs variation in soil salinity and alkalinity environments created by different fertilization, and explored the biological mechanisms that salinity and alkalinity alter the evolutionary paradigm of antibiotic resistance. The results showed the soil treated by organic fertilizer exhibited a low salinity, neutral level (TSD 239.20 μS/cm, pH 7.17). The ARG abundance in the OF treatment was the highest, keeping an average of 67.83 TPM. Beside the effect of direct input of organic fertilizer at the beginning, it was important to note that, ARGs abundance during planting showed significant correlations with pH and electric conductivity. We observed that changes in microbial survival strategies under different salinity and alkalinity conditions further affected ARG hosts abundance. Indoor experiments demonstrated that there was a survival trade-off between the growth of resistant bacteria and the evolution of antibiotic resistance in salinity and alkalinity environments. Meta-genomic and Meta-transcriptomic analysis consistently demonstrated bacterial antibiotic resistance was primarily associated with pyruvate, energy and lipid metabolic pathways. The functional gene related to salinity and alkalinity, like cysH, cysK, plsB and plsC showed negative correlations with MDR. Prokaryotic transcription assays validated these relations. This study well explains the prevalence of soil ARGs after different fertilization regimes and will give a deeper understanding for the effect of soil salinity and alkalinity on antibiotic resistance evolution.}, } @article {pmid39765196, year = {2025}, author = {Caballero-Gómez, J and Ávalos, G and Matas-Méndez, P and Figueiredo, AM and Castro-Scholten, S and Jiménez-Martín, D and Köster, PC and Santín, M and Bailo, B and Cano-Terriza, D and Sarmento, P and Neves, N and Carrapato, C and González-Barrio, D and Mateo, M and García-Bocanegra, I and Dashti, A and Sánchez, S and Carmena, D}, title = {Dietary profiles of wild carnivores and Blastocystis occurrence: The case of the endangered Iberian lynx (Lynx pardinus) and systematic review.}, journal = {Research in veterinary science}, volume = {184}, number = {}, pages = {105518}, doi = {10.1016/j.rvsc.2024.105518}, pmid = {39765196}, issn = {1532-2661}, mesh = {Animals ; *Lynx/parasitology ; *Blastocystis/genetics/isolation & purification ; Portugal ; Spain ; *Feces/parasitology ; *Endangered Species ; *Animals, Wild/parasitology ; Diet/veterinary ; Blastocystis Infections/veterinary/epidemiology ; }, abstract = {Recent molecular and metagenomic studies have revealed that the obligate anaerobic protist Blastocystis is found more prevalently and with higher subtype diversities in herbivore species than in carnivore species. However, information on wild carnivore species is scarce. Here, we investigated the presence of Blastocystis by molecular methods in fecal DNA samples of free-ranging and captive Iberian lynxes from Spain (n = 243) and Portugal (n = 30). In addition, a systematic review was conducted to obtain information on the Blastocystis prevalence rates and subtype diversities reported in free-living and captive wild carnivores worldwide during the period 2000-2024. Blastocystis was not detected by PCR in any of the samples investigated. Analyses of the data gathered from our systematic review revealed that Blastocystis is uncommon either in free-living (2.1 %, 29/1377) or captive (8.5 %, 100/1175) wild carnivore species. Many of these findings seem to result from accidental acquisition via prey animals, scavenging, contaminated water/feed (free-ranging wild carnivores), or cross-species transmission among animals sharing enclosures (captive wild carnivores). Comparative metagenomic studies analyzing gut microbiota profiles of carnivores are needed to fully understand how microbial communities affect Blastocystis colonization.}, } @article {pmid39765072, year = {2025}, author = {Khan, M and Nizamani, MM and Asif, M and Kamran, A and He, G and Li, X and Yang, S and Xie, X}, title = {Comprehensive approaches to heavy metal bioremediation: Integrating microbial insights and genetic innovations.}, journal = {Journal of environmental management}, volume = {374}, number = {}, pages = {123969}, doi = {10.1016/j.jenvman.2024.123969}, pmid = {39765072}, issn = {1095-8630}, mesh = {*Biodegradation, Environmental ; *Metals, Heavy/metabolism ; Microbiota ; Ecosystem ; Humans ; }, abstract = {The increasing contamination of ecosystems with heavy metals (HMs) due to industrial activities raises significant jeopardies to environmental health and human well-being. Addressing this issue, recent advances in the field of bioremediation have highlighted the potential of plant-associated microbiomes and genetically engineered organisms (GEOs) to mitigate HMs pollution. This review explores recent advancements in bioremediation strategies for HMs detoxification, with particular attention to omics technologies such as metagenomics, metabolomics, and metaproteomics in deepening the understanding of microbial interactions and their potential for neutralizing HMs. Additionally, Emerging strategies and technologies in GEOs and microorganism-aided nanotechnology have proven to be effective bioremediation tools, particularly for alleviating HM contamination. Despite the promising strategies developed in laboratory settings, several challenges impede their practical application, including ecological risks, regulatory limitations, and public concerns regarding the practice of genetically modified organisms. A comprehensive approach that involves interdisciplinary research is essential to enhance the efficacy and safety of bioremediation technologies. This approach should be coupled with robust regulatory frameworks and active public engagement to ensure environmental integrity and societal acceptance. This review underscores the importance of developing sustainable bioremediation strategies that align with ecological conservation goals and public health priorities.}, } @article {pmid39764958, year = {2025}, author = {Lei, L and Yu, J and Liu, L and Gong, C and Gao, Y and Zhang, Z and Zhang, R and Zhuang, H and Shan, S}, title = {Unveiling soil-borne antibiotic resistome and their associated risks: A comparative study of antibiotic and non-antibiotic pharmaceutical factories.}, journal = {Journal of hazardous materials}, volume = {486}, number = {}, pages = {137127}, doi = {10.1016/j.jhazmat.2025.137127}, pmid = {39764958}, issn = {1873-3336}, abstract = {Antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) are extensively documented within antibiotic pharmaceutical factories. Notably, non-antibiotic pharmaceuticals also represent a significant portion of the pharmaceuticals market. However, the comparative analyses of soil-borne ARG profiles and associated risks in different categories of pharmaceutical factories remain limited. This study conducted metagenomic sequencing on soil samples collected from both antibiotic and non-antibiotic pharmaceutical factories, alongside isolated ARB from soil, wastewater, groundwater, and air. Our results indicated the significant discrepancies in soil-borne ARG profiles, comprising abundance, diversity, and composition, in different categories of pharmaceutical factories (P < 0.05), which mainly driven by antibiotic residues. Significantly, bacterial pathogens were the important soil-borne ARG hosts, potentially posing risks to human health. In addition, the full-length nucleotide sequences of sul1, tetA, and TEM-1 were similar among soil, wastewater, groundwater, and air, suggesting the cross-media ARG dissemination within pharmaceutical settings. Through macrophage and Galleria mellonella infection models, the isolated antibiotic-resistant Escherichia coli strains possessed relatively high virulence. Overall, the findings provide valuable insights into the discrepancies in soil-borne ARG profiles and associated risks across different types of pharmaceutical factories, offering critical data for the targeted prevention and control of soil-borne ARG contamination in pharmaceutical production settings.}, } @article {pmid39764445, year = {2024}, author = {Li, J and Tian, Y and Wang, Y and Jin, L}, title = {dna2bit: high performance genomic distance estimation software for microbial genome analysis.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1521181}, pmid = {39764445}, issn = {1664-302X}, abstract = {dna2bit is an ultra-fast software specifically engineered for microbial genome analysis, particularly adept at calculating genome distances within metagenome and single amplified genome datasets. Distinguished from existing software such as Mash and Dashing, dna2bit employs feature hashing technique and Hamming distance to achieve enhanced speed and memory utilization, without sacrifice in the accuracy of average nucleotide identity calculations. dna2bit has promising applications in various domains such as average nucleotide identity approximation, metagenomic sequence clustering, and homology querying. dna2bit significantly boosts computational efficiency in handling large datasets including single amplified genomes, thereby facilitating a better understanding of the population heterogeneity and comparative genomics of microorganisms. dna2bit is available at https://github.com/lijuzeng/dna2bit.}, } @article {pmid39764236, year = {2024}, author = {Liu, M and Xue, R and Jin, S and Gu, K and Zhao, J and Guan, S and Xie, X and Su, J and Wang, L}, title = {Metabolomic and metagenomic analyses elucidate the role of intercropping in mitigating continuous cropping challenges in tobacco.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1447225}, pmid = {39764236}, issn = {1664-462X}, abstract = {INTRODUCTION: Crop rotation of tobacco with other crops could effectively break the negative impact of continuous tobacco cropping, but the mechanisms of intercropping system effects on tobacco, especially on the rhizosphere, are not clear.

METHODS: In this study, we investigated the impact of intercropping system on the diversity and function of tobacco metabolites and microorganisms through metabolomic and metagenomic analyses of the tobacco rhizosphere microenvironment intercropped with maize and soybean.

RESULTS: The results showed that the contents of huperzine b, chlorobenzene, and P-chlorophenylalanine in tobacco rhizosphere soils differed significantly among soybean-tobacco and maize-tobacco intercropping system. Chlorobenzene and P-chlorophenylalanine had the highest relative abundance under the soybean-tobacco intercropping system, and huperzine b had the highest relative abundance in the maize-tobacco cropping system. At the phylum level, the three most dominant strains were the same across all treatments: Proteobacteria, Actinobacteria, and Acidobacteria, with only minor differences in their abundance, with the fourth most abundant strain in both the tobacco monoculture. KEGG enrichment analysis of the tobacco rhizosphere soil microbiome revealed that intercropping significantly increased the abundance of metabolites in the ABC transporters pathway and up-regulated the LivK, LivH, Livg, LivM, and LivF genes of the branched-chain amino acid pathway.

DISCUSSION: Collectively, our results indicate that the intercropping could enhance the activity of Livs to enhance the ABC transport pathway, and thus improve the transmembrane transport ability of tobacco roots, thus reducing the negative impact of continuous tobacco cropping. At the same time, the maize-tobacco intercropping could promote the production and transportation of phenolic acids, flavonoids, and other bioactive substances in the tobacco root system, which could enhance tobacco adaptation capacity to abiotic stress.}, } @article {pmid39764202, year = {2025}, author = {Munjita, SM and Kalonda, A and Mubemba, B and Vanaerschot, M and Tato, C and Mwakibete, L and Tembo, J and Chitanga, S and Changula, K and Kajihara, M and Muleya, W and Sawa, H and Takada, A and Bates, M and Munsaka, S and Simulundu, E}, title = {Evidence of multiple bacterial, viral, and parasitic infectious disease agents in Mastomys natalensis rodents in riverine areas in selected parts of Zambia.}, journal = {Infection ecology & epidemiology}, volume = {15}, number = {1}, pages = {2441537}, pmid = {39764202}, issn = {2000-8686}, abstract = {BACKGROUND: Infectious disease agents pose significant threats to humans, wildlife, and livestock, with rodents carrying a third of these agents, many linked to human diseases. However, the range of pathogens in rodents and the hotspots for disease remain poorly understood.

AIM: This study evaluated the prevalence of viral, bacterial, and parasitic pathogens in Mastomys natalensis rodents in riverine and non-riverine areas in selected districts in Zambia.

METHODS: The study applied metagenomic next generation sequencing (mNGS). Tissues analysed included semen, foetal tissues, and blood-rich organs (liver, spleen, kidneys, and lungs). A multivariate logistic regression model explored the relationship between pathogen presence and host or ecological factors.

RESULTS: A total of 182 rodents were captured, and 14 pathogens were detected in 10.4% of the samples (19/182). Detected organisms included zoonoses (Klebsiella michiganensis, Klebsiella pneumoniae, Salmonella enterica, and Bartonella elizabethae); Emerging zoonoses (Elizabethkingia miricola, Klebsiella variicola, Bartonella tribocorum, and Cardiovirus B); among others (Eimeria papillata etc). Riverine areas showed higher odds of pathogen presence (OR = 8.45; p < 0.001; 95% CI: 3.07-23.26).

CONCLUSION: These results suggest that M. natalensis harbours multiple infectious agents with zoonotic potential, and riverine regions may be key hotspots for rodent-borne pathogens in Zambia.}, } @article {pmid39763902, year = {2024}, author = {Chege, M and Ferretti, P and Webb, S and Macharia, RW and Obiero, G and Kamau, J and Alberts, SC and Tung, J and Akinyi, MY and Archie, EA}, title = {Eukaryotic composition across seasons and social groups in the gut microbiota of wild baboons.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39763902}, issn = {2692-8205}, support = {P2C HD065563/HD/NICHD NIH HHS/United States ; R35 GM128716/GM/NIGMS NIH HHS/United States ; R01 AG053330/AG/NIA NIH HHS/United States ; R01 AG071684/AG/NIA NIH HHS/United States ; R21 AG055777/AG/NIA NIH HHS/United States ; }, abstract = {BACKGROUND: Animals coexist with complex microbiota, including bacteria, viruses, and eukaryotes (e.g., fungi, protists, and helminths). While the composition of bacterial and viral components of animal microbiota are increasingly well understood, eukaryotic composition remains neglected. Here we characterized eukaryotic diversity in the microbiomes in wild baboons and tested the degree to which eukaryotic community composition was predicted by host social group membership, sex, age, and season of sample collection.

RESULTS: We analyzed a total of 75 fecal samples collected between 2012 and 2014 from 73 wild baboons in the Amboseli ecosystem in Kenya. DNA from these samples was subjected to shotgun metagenomic sequencing, revealing members of the kingdoms Protista, Chromista, and Fungi in 90.7%, 46.7%, and 20.3% of samples, respectively. Social group membership explained 11.2% of the global diversity in gut eukaryotic species composition, but we did not detect statistically significant effect of season, host age, and host sex. Across samples, the most prevalent protists were Entamoeba coli (74.66% of samples), Enteromonas hominis (53.33% of samples), and Blastocystis subtype 3 (38.66% of samples), while the most prevalent fungi included Pichia manshurica (14.66% of samples), and Ogataea naganishii (6.66% of samples).

CONCLUSIONS: Protista, Chromista, and Fungi are common members of the gut microbiome of wild baboons. More work on eukaryotic members of primate gut microbiota is essential for primate health monitoring and management strategies.}, } @article {pmid39763865, year = {2024}, author = {Gonzalez, FL and Ranaivoson, HC and Andrianiaina, A and Andry, S and Raharinosy, V and Randriambolamanantsoa, TH and Lacoste, V and Dussart, P and Héraud, JM and Brook, CE}, title = {Genomic characterization of novel bat kobuviruses in Madagascar: implications for viral evolution and zoonotic risk.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39763865}, issn = {2692-8205}, support = {DP2 AI171120/AI/NIAID NIH HHS/United States ; R01 AI129822/AI/NIAID NIH HHS/United States ; R25 GM066522/GM/NIGMS NIH HHS/United States ; }, abstract = {Kobuviruses (family Picornaviridae, genus Kobuvirus) are enteric viruses that infect a wide range of both human and animal hosts. Much of the evolutionary history of kobuviruses remains elusive, largely due to limited screening in wildlife. Bats have been implicated as major sources of virulent zoonoses, including coronaviruses, henipaviruses, and filoviruses, though much of the bat virome still remains uncharacterized. While most bat virus research has historically focused on immediately recognizable zoonotic clades (e.g. SARS-related coronaviruses), a handful of prior reports catalog kobuvirus infection in bats and posit the role of bats as potential progenitors of downstream kobuvirus evolution. As part of a multi-year study, we carried out metagenomic Next Generation Sequencing (mNGS) on fecal samples obtained from endemic, wild-caught Madagascar fruit bats to characterize potentially zoonotic viruses circulating within these populations. The wild bats of Madagascar represent diverse Asian and African phylogeographic histories, presenting a unique opportunity for viruses from disparate origins to mix, posing significant public health threats. Here, we report detection of kobuvirus RNA in Malagasy fruit bat (Eidolon dupreanum) feces and undertake phylogenetic characterization of one full genome kobuvirus sequence, which nests within the Aichivirus A clade - a kobuvirus clade known to infect a wide range of hosts including humans, rodents, canids, felids, birds, and bats. Given the propensity of kobuviruses for recombination and cross-species infection, further characterization of this clade is critical to accurate evaluation of future zoonotic threats.}, } @article {pmid39763701, year = {2025}, author = {Hereira-Pacheco, S and Arias-Del Razo, I and Miranda-Carrazco, A and Dendooven, L and Estrada-Torres, A and Navarro-Noya, YE}, title = {Metagenomic analysis of fungal assemblages at a regional scale in high-altitude temperate forest soils: alternative methods to determine diversity, composition and environmental drivers.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e18323}, pmid = {39763701}, issn = {2167-8359}, mesh = {*Soil Microbiology ; *Forests ; *Metagenomics/methods ; *Fungi/genetics/classification/isolation & purification ; *Altitude ; Mexico ; Mycobiome/genetics ; Biodiversity ; }, abstract = {BACKGROUND: Understanding the diversity and distribution of fungal communities at a regional scale is important since fungi play a crucial role in ecosystem functioning. Our study used environmental metagenomics to determine fungal communities in mountainous forest soils in the central highlands of Mexico.

METHODS: We used four different bioinformatic workflows to profile fungal assemblages, i.e., Geneious+UNITE, single- and paired-end microbial community profiling (MiCoP), and Kraken2.

RESULTS: The workflows yielded different results; one detected a higher abundance of ectomycorrhizal (EcM) and saprophytic fungi, while the other identified more saprophytic and pathogenic fungi. Environmental, vegetation, and geographical factors determined the spatial distribution of soil fungi at a regional scale. Potential hydrogen (pH), calcium (Ca), magnesium (Mg), and silt content were detected as common drivers of fungal communities across different datasets enriched towards a functional guild. Vegetation traits were found to be more influential in shaping symbiotrophic fungi composition than saprotrophic and pathogenic fungi. This highlights the importance of considering vegetation traits when studying fungal community diversity and distribution. Clustering patterns of sampling points near the volcanoes indicated shared environmental and vegetation characteristics. A weak but significant distance decay in taxonomic similarity revealed that dispersal limitation contributed to fungal community composition, although it was not the primary factor in this study. Overall, this study provides important insights into the challenges and opportunities of studying fungal communities at a regional scale using metagenomic data.}, } @article {pmid39763640, year = {2024}, author = {Gao, Y and Wu, J and Zeng, J and Huo, X and Lou, K}, title = {Beyond the desert sands: decoding the relationship between camels, gut microbiota, and antibiotic resistance through metagenomics.}, journal = {Science in One Health}, volume = {3}, number = {}, pages = {100071}, pmid = {39763640}, issn = {2949-7043}, abstract = {BACKGROUND: Camels, known as the enduring "ships of the desert," host a complex gut microbiota that plays a crucial role in their survival in extreme environments. However, amidst the fascinating discoveries about the camel gut microbiota, concerns about antibiotic resistance have emerged as a significant global challenge affecting both human and animal populations. Indeed, the continued use of antibiotics in veterinary medicine has led to the widespread emergence of antibiotic-resistant bacteria, which has worsened through gene transfer.

METHODS: This study offers a deeper examination of this pressing issue by harnessing the potent tools of metagenomics to explore the intricate interplay between the camel (Camelus ferus) gut microbiota and antibiotic resistance.

RESULTS: Samples from wild camels yielded varying amounts of raw and clean data, generating scaftigs and open reading frames. The camel fecal microbiome was dominated by bacteria (mainly Bacillota and Bacteriodota), followed by viruses, archaea, and eukaryota. The most abundant genera were the Bacteroides, Ruminococcus, and Clostridium. Functional annotation revealed enriched pathways in metabolism, genetic information processing, and cellular processes, with key pathways involving carbohydrate transport and metabolism, replication, and amino acid transport. CAZy database analysis showed high abundances of glycoside hydrolases and glycosyl transferases. Antibiotic resistance gene (ARG) analysis identified Bacillota and Bacteroidota as the main reservoirs, with vancomycin resistance genes being the most prevalent. This study identified three major resistance mechanisms: antibiotic target alteration, antibiotic target protection, and antibiotic efflux.

CONCLUSION: These findings contribute to a broader understanding of antibiotic resistance within animal microbiomes and provide a foundation for further investigations of strategies to manage and mitigate antibiotic resistance.}, } @article {pmid39763347, year = {2025}, author = {Higashino, A and Nakamura, K and Osada, N}, title = {Population Genomics of Japanese Macaques (Macaca fuscata): Insights Into Deep Population Divergence and Multiple Merging Histories.}, journal = {Genome biology and evolution}, volume = {17}, number = {1}, pages = {}, pmid = {39763347}, issn = {1759-6653}, support = {DRA016173//National Institute of Genetics/ ; }, mesh = {Animals ; *Macaca fuscata/genetics ; *Genetic Variation ; Japan ; Gene Flow ; Genetics, Population ; Metagenomics ; Whole Genome Sequencing ; }, abstract = {The influence of long-term climatic changes such as glacial cycles on the history of living organisms has been a subject of research for decades, but the detailed population dynamics during the environmental fluctuations and their effects on genetic diversity and genetic load are not well understood on a genome-wide scale. The Japanese macaque (Macaca fuscata) is a unique primate adapted to the cold environments of the Japanese archipelago. Despite the past intensive research for the Japanese macaque population genetics, the genetic background of Japanese macaques at the whole-genome level has been limited to a few individuals, and the comprehensive demographic history and genetic differentiation of Japanese macaques have been underexplored. We conducted whole-genome sequencing of 64 Japanese macaque individuals from 5 different regions, revealing significant genetic differentiation and functional variant diversity across populations. In particular, Japanese macaques have low genetic diversity and harbor many shared and population-specific gene loss, which might contribute to population-specific phenotypes. Our estimation of population demography using phased haplotypes suggested that, after the strong population bottleneck shared among all populations around 400 to 500 kya, the divergence among populations initiated around 150 to 200 kya, but there has been the time with strong gene flow between some populations after the split, indicating multiple population split and merge events probably due to habitat fragmentation and fusion during glacial cycles. These findings not only present a complex population history of Japanese macaques but also enhance their value as research models, particularly in neuroscience and behavioral studies. This comprehensive genomic analysis sheds light on the adaptation and evolution of Japanese macaques, contributing valuable insights to both evolutionary biology and biomedical research.}, } @article {pmid39763003, year = {2025}, author = {Feng, Y and Lu, X and Zhao, J and Li, H and Xu, J and Li, Z and Wang, M and Peng, Y and Tian, T and Yuan, G and Zhang, Y and Liu, J and Zhang, M and Zhu La, AT and Qu, G and Mu, Y and Guo, W and Wu, Y and Zhang, Y and Wang, D and Hu, Y and Kan, B}, title = {Regional antimicrobial resistance gene flow among the One Health sectors in China.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {3}, pmid = {39763003}, issn = {2049-2618}, support = {2022YFC2303900//National Key Research and Development Program of China/ ; 22193064//major projects of the National Natural Science Foundation of China/ ; }, mesh = {Humans ; China ; *Gene Transfer, Horizontal ; *One Health ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Anti-Bacterial Agents/pharmacology ; *Gene Flow ; Feces/microbiology ; Drug Resistance, Bacterial/genetics ; Food Microbiology ; Metagenomics/methods ; Genes, Bacterial/genetics ; }, abstract = {BACKGROUND: Antimicrobial resistance poses a significant threat to global health, with its spread intricately linked across human, animal, and environmental sectors. Revealing the antimicrobial resistance gene (ARG) flow among the One Health sectors is essential for better control of antimicrobial resistance.

RESULTS: In this study, we investigated regional ARG transmission among humans, food, and the environment in Dengfeng, Henan Province, China by combining large-scale metagenomic sequencing with culturing of resistant bacterial isolates in 592 samples. A total of 40 ARG types and 743 ARG subtypes were identified, with a predominance of multidrug resistance genes. Compared with microbes from human fecal samples, those from food and environmental samples showed a significantly higher load of ARGs. We revealed that dietary habits and occupational exposure significantly affect ARG abundance. Pseudomonadota, particularly Enterobacteriaceae, were identified as the main ARG carriers shaping the resistome. The resistome in food samples was found more affected by mobile genetic elements (MGEs), whereas in environmental samples, it was more associated with the microbial composition. We evidenced that horizontal gene transfer (HGT) mediated by plasmids and phages, together with strain transmission, particularly those associated with the Enterobacteriaceae members, drive regional ARG flow. Lifestyle, dietary habits, and occupational exposure are all correlated with ARG dissemination and flies and food are important potential sources of ARGs to humans. The widespread mobile carbapenemase gene, OXA-347, carried by non-Enterobacteriaceae bacteria in the human gut microbiota, requires particular attention. Finally, we showed that machine learning models based on microbiome profiles were effective in predicting the presence of carbapenem-resistant strains, suggesting a valuable approach for AMR surveillance.

CONCLUSIONS: Our study provides a full picture of regional ARG transmission among the One Health sectors in a county-level city in China, which facilitates a better understanding of the complex routes of ARG transmission and highlights new points of focus for AMR surveillance and control. Video Abstract.}, } @article {pmid39762979, year = {2025}, author = {Oh, S and Kim, J and Shin, CM and Lee, HJ and Lee, HS and Park, KU}, title = {Metagenomic characterization of oral microbiome signatures to predict upper gastrointestinal and pancreaticobiliary cancers: a case-control study.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {20}, pmid = {39762979}, issn = {1479-5876}, support = {16-2021-0007//Seoul National University Bundang Hospital/ ; }, mesh = {Humans ; Case-Control Studies ; *Metagenomics/methods ; *Pancreatic Neoplasms/microbiology/diagnosis ; Female ; Male ; Middle Aged ; *Microbiota/genetics ; Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; Aged ; Metagenome ; Saliva/microbiology ; Biliary Tract Neoplasms/microbiology/diagnosis ; Gastrointestinal Neoplasms/microbiology/diagnosis ; }, abstract = {BACKGROUND: This study investigated the oral microbiome signatures associated with upper gastrointestinal (GI) and pancreaticobiliary cancers.

METHODS: Saliva samples from cancer patients and age- and sex-matched healthy controls were analyzed using 16S rRNA-targeted sequencing, followed by comprehensive bioinformatics analysis.

RESULTS: Significant dissimilarities in microbial composition were observed between cancer patients and controls across esophageal cancer (EC), gastric cancer (GC), biliary tract cancer (BC), and pancreatic cancer (PC) groups (R[2] = 0.067, = 0.075, = 0.068, and = 0.044; p = 0.001, = 0.001, = 0.002, and = 0.004, respectively). Additionally, the oral microbiome composition significantly differed by the four cancer sites (p = 0.001 for EC vs. GC, EC vs. BC, EC vs. PC, GC vs. BC, and GC vs. PC; p = 0.013 for BC vs. PC). We built oral metagenomic classifiers to predict cancer and selected specific microbial taxa with diagnostic properties. For EC, the classifier differentiated cancer patients and controls with good accuracy (area under the curve [AUC] = 0.791) and included three genera: Akkermansia, Escherichia-Shigella, and Subdoligranulum. For GC, the classifier exhibited high discriminative power (AUC = 0.961); it included five genera (Escherichia-Shigella, Gemella, Holdemanella, Actinomyces, and Stomatobaculum) and three species (Eubacterium sp. oral clone EI074, Ruminococcus sp. Marseille-P328, and Leptotrichia wadei F0279). However, microbial taxa with diagnostic features for BC and PC were not identified.

CONCLUSIONS: These findings suggested that the oral microbiome composition may serve as an indicator of tumorigenesis in upper GI and pancreaticobiliary cancers. The development of oral metagenomic classifiers for EC and GC demonstrates the potential value of microbial biomarkers in cancer screening.}, } @article {pmid39762940, year = {2025}, author = {Lin, CY and Cross, TL and Swanson, KS}, title = {Comparison of mucosal microbiota populations across the gastrointestinal tract of healthy dogs.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {2}, pmid = {39762940}, issn = {2524-4671}, support = {ILLU-538-937//USDA National Institute of Food and Agriculture/ ; }, abstract = {The gastrointestinal (GI) microbiota plays a crucial role in host health and disease in dogs, but the knowledge regarding the mucosal associated microbiota along the GI tract is limited in dogs. Therefore, the objective of this study was to characterize the phylogeny and predicted functional capacity of microbiota residing on the gut mucosa across five GI regions of healthy young adult and geriatric dogs fed different diets. Twelve weanling (8 weeks old) and 12 senior (11.1 years old) beagles were randomly assigned to be fed an animal product-based diet or plant product-based diet for 12 months. At that time, mucosal samples from the stomach, duodenum, jejunum, ileum, and mid-colon were collected. DNA was extracted and the hypervariable region 4 (V4) of the 16S rRNA gene was amplified to assess microbiota using Illumina MiSeq sequencing. Data were analyzed using QIIME 1.9.1. and Statistical Analyses of Metagenomic Profiles software 2.1.3. Gene predictions were made using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States. Taxonomic assessment revealed a greater (p < 0.05) species richness in the mid-colon compared with other segments. Principal coordinates analysis of weighted UniFrac distances demonstrated distinct clusters of stomach, ileum, and mid-colon samples, indicating the presence of unique microbial communities in these regions. The predominant phyla in all five segments were Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria and Fusobacteria, but their relative abundances varied between segments. Proteobacteria had a decreasing relative abundance from the stomach to mid-colon (q < 0.05). The ileum had the highest while the stomach had the lowest relative abundance of Firmicutes (q < 0.05). The duodenum had a higher abundance of Bacteroidetes than the stomach and ileum (q < 0.05). The mid-colon had a higher Fusobacteria relative abundance than other regions (q < 0.05). The predicted functional capacities of the microbiota in the stomach differed from those in the other segments. Age and diet of dog did not significantly impact the taxonomy or predicted functional capacities of the mucosal microbiota. In conclusion, our findings demonstrate distinct characteristics of the mucosal microbiota across various segments of canine GI tract.}, } @article {pmid39762435, year = {2025}, author = {Fackelmann, G and Manghi, P and Carlino, N and Heidrich, V and Piccinno, G and Ricci, L and Piperni, E and Arrè, A and Bakker, E and Creedon, AC and Francis, L and Capdevila Pujol, J and Davies, R and Wolf, J and Bermingham, KM and Berry, SE and Spector, TD and Asnicar, F and Segata, N}, title = {Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals.}, journal = {Nature microbiology}, volume = {10}, number = {1}, pages = {41-52}, pmid = {39762435}, issn = {2058-5276}, support = {U01 CA230551/CA/NCI NIH HHS/United States ; microTOUCH-101045015)//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, mesh = {*Gastrointestinal Microbiome ; Humans ; *Diet ; *Diet, Vegetarian ; *Diet, Vegan ; *Bacteria/classification/genetics/isolation & purification ; Female ; Vegans ; Male ; Adult ; Metagenomics ; Feces/microbiology ; Middle Aged ; Diet, Western/adverse effects ; }, abstract = {As plant-based diets gain traction, interest in their impacts on the gut microbiome is growing. However, little is known about diet-pattern-specific metagenomic profiles across populations. Here we considered 21,561 individuals spanning 5 independent, multinational, human cohorts to map how differences in diet pattern (omnivore, vegetarian and vegan) are reflected in gut microbiomes. Microbial profiles distinguished these common diet patterns well (mean AUC = 0.85). Red meat was a strong driver of omnivore microbiomes, with corresponding signature microbes (for example, Ruminococcus torques, Bilophila wadsworthia and Alistipes putredinis) negatively correlated with host cardiometabolic health. Conversely, vegan signature microbes were correlated with favourable cardiometabolic markers and were enriched in omnivores consuming more plant-based foods. Diet-specific gut microbes partially overlapped with food microbiomes, especially with dairy microbes, for example, Streptococcus thermophilus, and typical soil microbes in vegans. The signatures of common western diet patterns can support future nutritional interventions and epidemiology.}, } @article {pmid39762302, year = {2025}, author = {Kim, MJ and Song, MH and Ji, YS and Park, JW and Shin, YK and Kim, SC and Kim, G and Cho, B and Park, H and Ku, JL and Jeong, SY}, title = {Cell free supernatants of Bifidobacterium adolescentis and Bifidobacterium longum suppress the tumor growth in colorectal cancer organoid model.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {935}, pmid = {39762302}, issn = {2045-2322}, support = {2021M3H9A1030151//National Research Foundation, South Korea/ ; }, mesh = {Humans ; *Colorectal Neoplasms/microbiology/pathology/metabolism ; *Bifidobacterium longum/metabolism ; *Organoids/microbiology/metabolism ; *Gastrointestinal Microbiome ; *Bifidobacterium adolescentis/metabolism ; Female ; Male ; Probiotics ; Middle Aged ; Aged ; Cell Proliferation ; Cell Line, Tumor ; }, abstract = {The probiotic gut microbiome and its metabolites are pivotal in regulating host metabolism, inflammation, and immunity. Host genetics, colonization at birth, the host lifestyle, and exposure to diseases and drugs determine microbial composition. Dysbiosis and disruption of homeostasis in the beneficial microbiome have been reported to be involved in the tumorigenesis and progression of colorectal cancer (CRC). However, the influence of bacteria-secreted metabolites on CRC growth is yet to be fully elucidated. In this study, we compared the microbial composition of CRC patients to healthy controls to identify distinct patterns of microbiota-derived metabolites in CRC patients. Metagenomic analysis demonstrated that beneficial bacteria strains; Blautia producta, Bifidobacterium adolescentis, and Bifidobacterium longum decreased, while Parabacteroides distasonis and Bacteroides ovatus were more prevalent in the CRC patient group. Treatment of cancer organoid lines with microbial culture supernatants from Blautia producta, Bifidobacterium adolescentis, and Bifidobacterium longum showed remarkable inhibition of cancer growth. This study demonstrates that the bacterial metabolites depleted in CRC patients may inhibit cancer growth and highlights the effects of microbiome-derived metabolites on CRC growth.}, } @article {pmid39762227, year = {2025}, author = {Ding, J and Liu, F and Zeng, J and Gu, H and Huang, J and Wu, B and Shu, L and Yan, Q and He, Z and Wang, C}, title = {Depth heterogeneity of lignin-degrading microbiome and organic carbon processing in mangrove sediments.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {5}, pmid = {39762227}, issn = {2055-5008}, mesh = {*Geologic Sediments/microbiology ; *Lignin/metabolism ; *Microbiota ; *Carbon/metabolism ; *Wetlands ; *Metagenomics/methods ; Bacteria/genetics/classification/metabolism/isolation & purification ; Biomass ; Metagenome ; Sequence Analysis, DNA ; }, abstract = {Mangrove ecosystems are globally recognized for their blue carbon (C) sequestration capacity. Lignocellulosic detritus constitutes the primary C input to mangrove sediments, but the microbial processes involved in its bioprocessing remain unclear. Using lignocellulosic analysis and metagenomic sequencing across five 100-cm sediment cores, we found a high proportion of lignin (95.0-97.7%) within sediments' lignocellulosic detritus, with a small fraction of lignin-degrading genes (1.24-1.98%) of lignin-degrading genes within the carbohydrate-active enzyme coding genes. Depth stratification was observed in genes and microbial communities involved in lignin depolymerization and mineralization of lignin monomer derivatives. Further microbe-centered analyses of biomass production rates and adaptive metabolism revealed diminished microbial C use efficiency potential and augmented "enzyme latch" with increasing sediment depths. These findings enhance our understanding of sedimentary organic C cycling and storage in coastal blue C ecosystems.}, } @article {pmid39762210, year = {2025}, author = {Mi, J and Jing, X and Ma, C and Shi, F and Cao, Z and Yang, X and Yang, Y and Kakade, A and Wang, W and Long, R}, title = {Publisher Correction: A metagenomic catalogue of the ruminant gut archaeome.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {408}, doi = {10.1038/s41467-024-55731-8}, pmid = {39762210}, issn = {2041-1723}, } @article {pmid39762171, year = {2025}, author = {Li, HX and An, R and Li, J and Xie, XL and Jin, H and Li, QR and Zhou, GX and Liu, AJ}, title = {[Pediatric cardiac allograft transplantation: a clinicopathological study of twelve recipient hearts].}, journal = {Zhonghua bing li xue za zhi = Chinese journal of pathology}, volume = {54}, number = {1}, pages = {46-51}, doi = {10.3760/cma.j.cn112151-20240610-00377}, pmid = {39762171}, issn = {0529-5807}, mesh = {Humans ; *Heart Transplantation ; *Cardiomyopathy, Dilated/pathology/surgery/genetics ; Child ; Adolescent ; Child, Preschool ; Myocarditis/pathology ; Allografts ; Myocardium/pathology ; Male ; Transplantation, Homologous ; Female ; Myocytes, Cardiac/pathology ; }, abstract = {Objective: To analyze the morphologic changes and the extent of severity in end-stage heart disease; and to explore the correlation with their clinical features. Methods: Twelve cases of recipients who underwent pediatric cardiac allograft transplantation were collected from May 2022 to November 2023 at the Seventh Medical Center of People's Liberation Army of China General Hospital. Gross pathologic examinations were performed and morphological changes were observed under a light microscope after HE, Masson's trichrome, and reticulin staining. Semi-quantitative analysis of morphologic changes was performed. One case received DMD genetic testing, one received mtDNA variation testing for mitochondriopathy, and 1 received metagenomics next-generation sequencing. Clinical data and related literature were reviewed for comprehensive analysis. Results: There were 12 recipient hearts including 11 dilated cardiomyopathy (DCM) and 1 fulminant myocarditis (FM). The median age of DCM was 12 years (range, 3 to 15 years). DCM showed cardiomyocyte hypertrophy, cardiomyocyte disarray, nuclear morphological changes, interstitial fibrosis and fatty infiltration. One DCM was confirmed as Becker muscular dystrophy by DMD genetic testing. No pathogenic mutations were found in 1 patient that received mtDNA variation testing. H. influenzae was detected in the case of FM. FM showed diffuse and full-thickness inflammatory cell infiltration by large numbers of lymphocytes and plasma cells, scattered eosinophils, and few neutrophils. Conclusions: Cardiac transplantation is an excellent treatment for end-stage heart disease. The morphological features of DCM include cardiomyocyte hypertrophy, nuclear morphological changes, interstitial fibrosis and fatty infiltration. The severity of the lesion is influenced by multiple factors. FM predominantly presents diffuse infiltration of lymphocytes and plasma cells.}, } @article {pmid39762111, year = {2025}, author = {Al-Shakhshir, S and Quraishi, MN and Mullish, B and Patel, A and Vince, A and Rowe, A and Homer, V and Jackson, N and Gyimah, D and Shabir, S and Manzoor, S and Cooney, R and Alrubaiy, L and Quince, C and van Schaik, W and Hares, M and Beggs, AD and Efstathiou, E and Rimmer, P and Weston, C and Iqbal, T and Trivedi, PJ}, title = {FAecal micRobiota transplantation in primary sclerosinG chOlangitis (FARGO): study protocol for a randomised, multicentre, phase IIa, placebo-controlled trial.}, journal = {BMJ open}, volume = {15}, number = {1}, pages = {e095392}, pmid = {39762111}, issn = {2044-6055}, mesh = {Adult ; Female ; Humans ; Male ; *Cholangitis, Sclerosing/therapy ; Clinical Trials, Phase II as Topic ; *Fecal Microbiota Transplantation/methods ; Gastrointestinal Microbiome ; Inflammatory Bowel Diseases/therapy/microbiology ; Multicenter Studies as Topic ; Randomized Controlled Trials as Topic ; Treatment Outcome ; }, abstract = {INTRODUCTION: Primary sclerosing cholangitis (PSC) is the classical hepatobiliary manifestation of inflammatory bowel disease (IBD). The strong association between gut and liver inflammation has driven several pathogenic hypotheses to which the intestinal microbiome is proposed to contribute. Pilot studies of faecal microbiota transplantation (FMT) in PSC and IBD are demonstrated to be safe and associated with increased gut bacterial diversity. However, the longevity of such changes and the impact on markers of disease activity and disease progression have not been studied. The aim of this clinical trial is to determine the effects of repeated FMT as a treatment for PSC-IBD.

METHODS AND ANALYSIS: FAecal micRobiota transplantation in primary sclerosinG chOlangitis (FARGO) is a phase IIa randomised placebo-controlled trial to assess the efficacy and safety of repeated colonic administration of FMT in patients with non-cirrhotic PSC-IBD. Fifty-eight patients will be recruited from six sites across England and randomised in a 1:1 ratio between active FMT or FMT placebo arms. FMT will be manufactured by the University of Birmingham Microbiome Treatment Centre, using stool collected from rigorously screened healthy donors. A total of 8 weekly treatments will be delivered; the first through colonoscopic administration (week 1) and the remaining seven via once-weekly enema (up to week 8). Participants will then be followed on a 12-weekly basis until week 48 from the first treatment visit. The primary efficacy outcome will be to determine the effect of FMT on serum alkaline phosphatase values over time (end of study at 48 weeks). Key secondary outcomes will be to evaluate the impact of FMT on other liver biochemical parameters, PSC risk scores, circulating and imaging markers of liver fibrosis, health-related quality of life measures, IBD activity and the incidence of PSC-related clinical events. Key translational objectives will be to identify mucosal metagenomic, metatranscriptomic, metabolomic and immunological pathways associated with the administration of FMT.

ETHICS AND DISSEMINATION: The protocol was approved by the South Central-Hampshire B Research Ethics Committee (REC 23/SC/0147). Participants will be required to provide written informed consent. The results of this trial will be disseminated through national and international presentations and peer-reviewed publications.

TRIAL REGISTRATION NUMBER: The trial was registered at ClinicalTrials.gov on 23 February 2024 (NCT06286709). Weblink: Study Details | FAecal Microbiota Transplantation in primaRy sclerosinG chOlangitis | ClinicalTrials.gov.}, } @article {pmid39762107, year = {2025}, author = {Weldegebreal, F and Ayana, DA and Wilfong, T and Dheresa, M and Yadeta, TA and Negesa, AS and Demmu, YM and Tesfa, T and Alemu, TN and Eticha, TG and Geremew, A and Roba, KT and Abdissa, A and Assefa, N and Negash, AA and Cools, P and Tura, AK}, title = {Relationship between vaginal and gut microbiome and pregnancy outcomes in eastern Ethiopia: a protocol for a longitudinal maternal-infant cohort study (the EthiOMICS study).}, journal = {BMJ open}, volume = {15}, number = {1}, pages = {e092461}, pmid = {39762107}, issn = {2044-6055}, mesh = {Humans ; Female ; Ethiopia ; Pregnancy ; *Gastrointestinal Microbiome/genetics ; *Vagina/microbiology ; Infant, Newborn ; Longitudinal Studies ; *Pregnancy Outcome ; Infant ; Feces/microbiology ; Research Design ; Milk, Human/microbiology ; Adult ; }, abstract = {INTRODUCTION: Although evidence exists on the impact of microbiota on pregnancy outcomes in many high-resource settings, there is a lack of research in many low-resource settings like Ethiopia. This study aims to fill this gap by studying the gut and vaginal microbiota changes throughout pregnancy and assess how these changes relate to pregnancy outcomes among a cohort of pregnant women in eastern Ethiopia.

METHODS AND ANALYSIS: Vaginal and stool samples will be collected using DNA/RNA Shield Collection kits three times starting at 12-22 weeks, 28-36 weeks and at birth (within 7 days). Postnatally, newborns' skin swabs (at birth) and rectal swabs will be obtained until 2 years of age. Moreover, breast milk samples at birth and 6 months and environmental samples (water, indoor air and soil) will be collected at enrolment, birth, 6, 12 and 24 months post partum. DNA will be extracted using Roche kits. Metagenomic sequencing will be performed to identify metataxonomic profiling and assess variations in microbial profiles, and α and β diversity of the microbiota. Information on socioeconomic, behavioural, household and biological factors will be collected at enrolment. The collected data will be coded, entered into EpiData 3.1 and analysed using Stata 17.

ETHICS AND DISSEMINATION: The Institutional Health Research Ethics Review Committee (Ref No. IHRERC/033/2022) of Haramaya University, Ethiopia has approved this study ethically. Written informed consent regarding the study and sample storage for biobanking will be obtained from all participants. Results will be published in international peer-reviewed journals, and summaries will be provided to the study funders. Clinical study data will be submitted to Data Compass (https://datacompass.lshtm.ac.uk/), and molecular profiles of the microbiome and whole-genome sequences will be submitted to the European Nucleotide Archive (https://www. ebi.ac.uk/ena). Requests for data should be directed to daberaf@gmail.com. The decision to share data will be made by the study steering committee under the College of Health and Medical Sciences, Haramaya University, Ethiopia.}, } @article {pmid39761759, year = {2025}, author = {Yan, M and Shang, L and Wang, Y and Wang, C and Cao, B}, title = {Metagenomic next-generation sequencing on treatment strategies and prognosis of patients with lower respiratory tract infections: A systematic review and meta-analysis.}, journal = {International journal of antimicrobial agents}, volume = {65}, number = {3}, pages = {107440}, doi = {10.1016/j.ijantimicag.2024.107440}, pmid = {39761759}, issn = {1872-7913}, abstract = {OBJECTIVES: Controversy exists regarding the benefits of metagenomic next-generation sequencing (mNGS) in lower respiratory tract infections (LRTIs). We assessed the impact of mNGS on the treatment and prognosis of LRTI patients through a systematic review and meta-analysis.

METHODS: A literature search was conducted in PubMed, Embase, and CENTRAL databases up to 19 February 2024. Studies investigating the clinical value of mNGS in patients with LRTIs were included. The Risk-of-Bias Tool for randomized controlled trials and the Newcastle-Ottawa scale for observational studies were used to assess risk of bias. Antibiotic change rates and prognostic outcomes were evaluated using random-effects analyses with 95% confidence intervals (CIs). This study is registered with PROSPERO, CRD42024509738.

RESULTS: Twelve studies were included in the meta-analysis. The use of mNGS was associated with a higher rate of antibiotic change (odds ratio, 2.47; 95% CI, 1.42-4.28; P < 0.01). Consistent findings were observed in adults, patients with severe LRTIs, and in those who underwent mNGS testing exclusively on bronchoalveolar lavage fluid. We also observed a reduction in in-hospital mortality (odds ratio, 0.49; 95% CI, 0.36-0.67; P < 0.01), though no significant impact on length of hospital stay was observed (mean difference, -1.79; 95% CI, -5.20 -1.63; P = 0.31).

CONCLUSIONS: This meta-analysis indicates that the application of mNGS may lead to changes in antibiotic prescriptions for patients with LRTIs, and might reduce the risk of mortality. However, large-scale randomized controlled clinical trials are urgently needed to validate the findings of this study.}, } @article {pmid39761739, year = {2025}, author = {Yavorov-Dayliev, D and Milagro, FI and Ayo, J and Oneca, M and Goyache, I and López-Yoldi, M and FitzGerald, JA and Crispie, F and Cotter, PD and Aranaz, P}, title = {Pediococcus acidilactici CECT 9879 (pA1c®) and heat inactivated pA1c® (pA1c® HI) ameliorate gestational diabetes mellitus in mice.}, journal = {Life sciences}, volume = {362}, number = {}, pages = {123359}, doi = {10.1016/j.lfs.2024.123359}, pmid = {39761739}, issn = {1879-0631}, mesh = {Animals ; Female ; Pregnancy ; Mice ; *Diabetes, Gestational/metabolism/microbiology ; *Mice, Inbred C57BL ; *Probiotics/therapeutic use/administration & dosage ; *Gastrointestinal Microbiome ; *Pediococcus acidilactici/metabolism ; Insulin Resistance ; Blood Glucose/metabolism ; Hot Temperature ; }, abstract = {AIMS: Gestational diabetes mellitus (GDM) is the most common complication of pregnancy and is known to be associated with an increased risk of postpartum metabolic disease. Based on the important role that the intestinal microbiota plays in blood glucose regulation and insulin sensitivity, supplementation of probiotic and postbiotic strains could improve glucose metabolism and tolerance in GDM.

MAIN METHODS: 56 4-week-old female C57BL/6J-mice were divided into 4 groups (n = 14 animals/group): control (CNT), high-fat/high-sucrose (HFS), pA1c® alive (pA1c®) and heat-inactivated pA1c® (pA1c®HI). Serum biochemical parameters were analyzed, gene expression analyses were conducted, and fecal microbiota composition was evaluated by shot-gun sequencing.

KEY FINDINGS: pA1c®- and pA1c® HI-supplemented groups presented reduced fasting blood glucose levels and reduced insulin resistance during gestation and exhibited lower visceral adiposity and increased muscle tissue, together with an improvement in intrahepatic TGs content and ALT levels. Liver gene expression analyses demonstrated that pA1c® and pA1c® HI activities were mediated by modulation of the insulin receptor, but also by an overexpression of beta-oxidation genes, and downregulation of fatty acid biosynthesis genes. Shot-gun metagenomics demonstrated that Pediococcus acidilactici was detected in the feces of all the pA1c® and pA1c® HI-group after the supplementation period (75 % of the microbial profile was Pediococcus acidilactici) in only nine weeks of supplementation, and modulated gut microbiota composition.

SIGNIFICANCE: These results may be considered as future perspectives for the development of preventive, even therapeutic options for GDM based on hyperglycemia reduction, blood glucose regulation, hepatic steatosis attenuation and insulin resistance alleviation.}, } @article {pmid39761715, year = {2025}, author = {Vasudeva, G and Sidhu, C and Vaid, K and Priyadarshini, P and Kumar, V and Krishnan, M and Singh, B and Pinnaka, AK}, title = {Bioremediation of catecholic pollutants with novel oxygen-insensitive catechol 2,3-dioxygenase and its potential in biomonitoring of catechol in wastewater.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {367}, number = {}, pages = {125613}, doi = {10.1016/j.envpol.2024.125613}, pmid = {39761715}, issn = {1873-6424}, mesh = {*Catechols/metabolism ; *Wastewater/chemistry ; *Catechol 2,3-Dioxygenase/metabolism/genetics ; *Biodegradation, Environmental ; *Water Pollutants, Chemical/metabolism/analysis ; Molecular Docking Simulation ; Environmental Monitoring/methods ; Oxygen/metabolism ; }, abstract = {The oxygenases are essential in the bioremediation of xenobiotic pollutants. To overcome cultivability constraints, this study aims to identify new potential extradiol dioxygenases using the functional metagenomics approach. RW1-4CC, a novel catechol 2,3-dioxygenase, was isolated using functional metagenomics approach, expressed in a heterologous system, and characterized thoroughly using state-of-the-art techniques. The serial truncation mutations of the C-terminal tail increase the catalytic efficiency of truncated proteins against the 2,3-dihydroxybiphenyl (2,3-DHB). RW1-4CC lose its 50% of activity at 60 °C, with its optimum temperature at 15 °C, whereas the truncated proteins were found to be more stable at extended temperature range, i.e., both RW1-4CC-A and RW1-4CC-B retained 50% of their activity at 75 °C, with their temperature optima at 55 °C and 65 °C, respectively. The molecular docking studies further confirmed the high binding affinity of truncated proteins for the 2,3-DHB than catechol. The molecular modeling analysis revealed the difference in iron-binding and substrate interacting environment of RW1-4CC and its truncated proteins. The efficiency of purified RW1-4CC to detect catechol was evaluated using a gold screen-printed electrode by cyclic voltammetry. RW1-4CC detected catechol in wastewater and artificial seawater up to the concentration of 100 μm, which makes it reliable for catechol detection.}, } @article {pmid39761633, year = {2025}, author = {Lake, BB and McAdams, ZL and Ericsson, AC and Reinero, C and Gull, T and Lyons, BM}, title = {Feline urethral obstruction alters the urinary microbiota and comparison to oral, preputial, and rectal microbiotas.}, journal = {American journal of veterinary research}, volume = {86}, number = {2}, pages = {}, doi = {10.2460/ajvr.24.07.0213}, pmid = {39761633}, issn = {1943-5681}, mesh = {Animals ; Cats ; *Cat Diseases/microbiology/urine ; *Microbiota ; Male ; *Urethral Obstruction/veterinary/microbiology ; *Rectum/microbiology ; *RNA, Ribosomal, 16S/genetics ; Female ; Prospective Studies ; Mouth/microbiology ; Case-Control Studies ; }, abstract = {OBJECTIVE: To document differences in the microbiota of healthy cats versus cats with urethral obstruction (UO); compare the urinary microbiota with the oral, preputial, and rectal microbiota; and demonstrate that 16S rRNA gene sequencing will reveal rich and diverse urinary microbiota.

METHODS: 15 client-owned cats with UO and 15 age-matched healthy cats were included from July 2020 through April 2021. Exclusion criteria were evidence of urinary tract infection, urolithiasis, antimicrobial administration, urinary catheterization in the past 30 days, or a comorbidity. This study was a prospective, observational study. Both groups had a baseline CBC, chemistry panel, urinalysis, urine culture, and focal bladder ultrasound. Swabs of the cystocentesis site, buccal mucosa, rectum, prepuce, and urinary samples were collected, and 16S rRNA gene sequencing was used to compare the groups and sites.

RESULTS: Differences in the microbiota richness and diversity were found in the urine of cats with UO (n = 15) compared to healthy cats (15), along with differences in the preputial and oral samples, supporting the presence of a urinary dysbiosis in cats with UO.

CONCLUSIONS: Our preliminary data demonstrates a dramatic change in the urinary microbiota of cats with UO along with changes in microbiota in other sites compared to healthy cats.

CLINICAL RELEVANCE: A urinary dysbiosis in cats with UO has been minimally supported in prior studies using 16S rRNA gene sequencing. Although these are preliminary results, documenting this dysbiosis in cats with UO provides a potential avenue for novel therapeutics.}, } @article {pmid39761113, year = {2025}, author = {Kardailsky, A and Durán-Vinet, B and Nester, G and Ayad, ME and Raes, EJ and Jeunen, GJ and Miller, AK and McVey, P and Corrigan, S and Fraser, M and Goncalves, P and Burnell, S and Bennett, A and Rauschert, S and Bayer, PE}, title = {Monitoring the Land and Sea: Enhancing Efficiency Through CRISPR-Cas Driven Depletion and Enrichment of Environmental DNA.}, journal = {The CRISPR journal}, volume = {}, number = {}, pages = {}, doi = {10.1089/crispr.2024.0050}, pmid = {39761113}, issn = {2573-1602}, abstract = {Characterizing biodiversity using environmental DNA (eDNA) represents a paradigm shift in our capacity for biomonitoring complex environments, both aquatic and terrestrial. However, eDNA biomonitoring is limited by biases toward certain species and the low taxonomic resolution of current metabarcoding approaches. Shotgun metagenomics of eDNA enables the collection of whole ecosystem data by sequencing all molecules present, allowing characterization and identification. Clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-associated proteins (Cas)-based methods have the potential to improve the efficiency of eDNA metagenomic sequencing of low-abundant target organisms and simplify data analysis by enrichment of target species or nontarget DNA depletion before sequencing. Implementation of CRISPR-Cas in eDNA has been limited due to a lack of interest and support in the past. This perspective synthesizes current approaches of CRISPR-Cas to study underrepresented taxa and advocate for further application and optimization of depletion and enrichment methods of eDNA using CRISPR-Cas, holding promise for eDNA biomonitoring.}, } @article {pmid39760260, year = {2025}, author = {You, H and Yang, B and Liu, H and Wu, W and Yu, F and Lin, N and Yang, W and Hu, B and Liu, Y and Zou, H and Hao, S and Xiao, Y and Xu, T and Jiang, Y}, title = {Unravelling distinct patterns of metagenomic surveillance and respiratory microbiota between two P1 genotypes of Mycoplasma pneumoniae.}, journal = {Emerging microbes & infections}, volume = {14}, number = {1}, pages = {2449087}, pmid = {39760260}, issn = {2222-1751}, mesh = {Humans ; *Mycoplasma pneumoniae/genetics/isolation & purification ; *Pneumonia, Mycoplasma/epidemiology/microbiology ; Retrospective Studies ; Child ; Female ; Male ; Child, Preschool ; *Microbiota ; Adolescent ; *Metagenomics ; *Genotype ; Middle Aged ; Adult ; COVID-19/epidemiology/microbiology ; Young Adult ; Infant ; Aged ; Bronchoalveolar Lavage Fluid/microbiology ; }, abstract = {To unravel distinct patterns of metagenomic surveillance and respiratory microbiota between Mycoplasma pneumoniae (M. pneumoniae) P1-1 and P1-2 and to explore the impact of the COVID-19 pandemic on epidemiological features, we conducted a multicentre retrospective study which spanned 90,886 pneumonia patients, among which 3164 cases M. pneumoniae were identified. Our findings revealed a concurrent outbreak of M. pneumoniae, with the positivity rate rising sharply to 9.62% from July 2023, compared to the 0.16% to 4.06% positivity rate observed during the 2020-2022 COVID-19 pandemic. P1-1 had a higher odds ratio of co-detecting opportunistic pathogens. However, no significant differences were observed in the co-detection odds ratio between children and other age groups in P1-2. This study is the first to demonstrate differences in relative abundance, diversity of respiratory microbiota and co-detection rate of opportunistic pathogen between M. pneumoniae P1-1 and P1-2. Through bronchoalveolar lavage (BAL) metagenomic and host transcriptomic analyses, we identified variations in co-detection rates of M. pneumoniae P1-1 genotype with opportunistic pathogens like S. pneumoniae, alterations in respiratory microbiota composition, lung inflammation, and disruption of ciliary function. Consistent with the results of host transcriptome, we found that P1-1 infections were associated with significantly higher rates of requiring respiratory support and mechanical ventilation compared to P1-2 infections (Fisher's exact test, p-value = 0.035/0.004). Our study provides preliminary evidence of clinical severity between M. pneumoniae strains, underscoring the need for ongoing research and development of targeted therapeutic strategies.}, } @article {pmid39760247, year = {2025}, author = {Lee, CE and Messer, LF and Wattiez, R and Matallana-Surget, S}, title = {Decoding Microbial Plastic Colonisation: Multi-Omic Insights Into the Fast-Evolving Dynamics of Early-Stage Biofilms.}, journal = {Proteomics}, volume = {}, number = {}, pages = {e202400208}, doi = {10.1002/pmic.202400208}, pmid = {39760247}, issn = {1615-9861}, support = {//Joint UKRI Natural Environment Research Council (NERC) and National Research Foundation (NRF) Singapore/ ; NE/V009621/1//UKRI NERC/NRF/ ; NRF-SEAP-2020-0001//UKRI NERC/NRF/ ; NE/S007342/1//NERC Scottish Universities Partnership for Environmental Research (SUPER) Doctoral Training Partnership (DTP)/ ; }, abstract = {Marine plastispheres represent dynamic microhabitats where microorganisms colonise plastic debris and interact. Metaproteomics has provided novel insights into the metabolic processes within these communities; however, the early metabolic interactions driving the plastisphere formation remain unclear. This study utilised metaproteomic and metagenomic approaches to explore early plastisphere formation on low-density polyethylene (LDPE) over 3 (D3) and 7 (D7) days, focusing on microbial diversity, activity and biofilm development. In total, 2948 proteins were analysed, revealing dominant proteomes from Pseudomonas and Marinomonas, with near-complete metagenome-assembled genomes (MAGs). Pseudomonas dominated at D3, whilst at D7, Marinomonas, along with Acinetobacter, Vibrio and other genera became more prevalent. Pseudomonas and Marinomonas showed high expression of reactive oxygen species (ROS) suppression proteins, associated with oxidative stress regulation, whilst granule formation, and alternative carbon utilisation enzymes, also indicated nutrient limitations. Interestingly, 13 alkanes and other xenobiotic degradation enzymes were expressed by five genera. The expression of toxins, several type VI secretion system (TVISS) proteins, and biofilm formation proteins by Pseudomonas indicated their competitive advantage against other taxa. Upregulated metabolic pathways relating to substrate transport also suggested enhanced nutrient cross-feeding within the more diverse biofilm community. These insights enhance our understanding of plastisphere ecology and its potential for biotechnological applications.}, } @article {pmid39760015, year = {2025}, author = {Utama, GL and Sahab, NRM and Nurmilah, S and Yarlina, VP and Subroto, E and Balia, RL}, title = {Unveiling microbial dynamics in terasi spontaneous fermentation: Insights into glutamate and GABA production.}, journal = {Current research in food science}, volume = {10}, number = {}, pages = {100950}, pmid = {39760015}, issn = {2665-9271}, abstract = {Terasi, a traditional Indonesian seafood product made from shrimp, undergoes fermentation facilitated by a consortium of microorganisms, including Lactic Acid Bacteria (LAB) and yeast, which contribute to its distinctive umami flavor. This study investigates the microbial dynamics and production of key metabolites, including γ-aminobutyric acid (GABA), during terasi fermentation. Total Plate Count (TPC) and High-Performance Liquid Chromatography (HPLC) were used to monitor changes in glutamate and GABA levels, with glutamate increasing from 105.18 mg/mL on day 3-139.19 mg/mL on day 14, and GABA rising from 90.49 mg/mL to 106.98 mg/mL over the same period. Metagenomic analysis using high-throughput sequencing of bacterial 16 S rRNA identified Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidota as dominant phyla. While LAB populations remained relatively stable, yeast became detectable from day 4. Notably, core bacterial genera such as Vibrio, Macrococcus, Staphylococcus, Exiguobacterium, Jeotgalicoccus, Prevotella, Salinicoccus, Bacillus, Pseudarthrobacter, and Vagococcus were highly abundant and played significant roles in GABA production, likely due to their glutamate decarboxylase activity. These findings reveal a clear correlation between microbial succession and metabolite production, offering valuable insights into the fermentation process of terasi. This study enhances the understanding of traditional food fermentation and presents opportunities to optimize beneficial compounds in terasi products.}, } @article {pmid39759837, year = {2024}, author = {Li, J and Dong, C and Xiang, S and Wei, H and Lai, Q and Wei, G and Gong, L and Huang, Z and Zhou, D and Wang, G and Shao, Z}, title = {Key bacteria decomposing animal and plant detritus in deep sea revealed via long-term in situ incubation in different oceanic areas.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae133}, pmid = {39759837}, issn = {2730-6151}, abstract = {Transport of organic matter (OM) occurs widely in the form of animal and plant detritus in global oceans, playing a crucial role in global carbon cycling. While wood- and whale-falls have been extensively studied, the in situ process of OM remineralization by microorganisms remains poorly understood particularly in pelagic regions on a global scale. Here, enrichment experiments with animal tissue or plant detritus were carried out in three deep seas for 4-12 months using the deep-sea in situ incubators. We then performed community composition analyses as well as metagenomic and metatranscriptomic analyses. The results revealed strikingly similar microbial assemblages responsible for decomposing animal and plant detritus. Genes encoding peptidases and glucoside hydrolases were highly abundant and actively transcribed in OM enrichments, which confirmed the roles of these enriched microbial assemblages in organic decomposition. Marinifilaceae, Desulfocapsaceae, Spirochaetaceae, and o-Peptostreptococcales were found to potentially contribute to nitrogen fixation. These core bacteria, acting as cosmopolitan anaerobes in decomposing fast-sinking particulate OM, may have been underestimated in terms of their role in deep-sea microbial-mediated biogeochemical cycles during conventional sampling and diversity survey.}, } @article {pmid39759836, year = {2024}, author = {Nesbø, CL and Kublanov, I and Yang, M and Sharan, AA and Meyer, T and Edwards, EA}, title = {High quality Bathyarchaeia MAGs from lignocellulose-impacted environments elucidate metabolism and evolutionary mechanisms.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae156}, pmid = {39759836}, issn = {2730-6151}, abstract = {The archaeal class Bathyarchaeia is widely and abundantly distributed in anoxic habitats. Metagenomic studies have suggested that they are mixotrophic, capable of CO2 fixation and heterotrophic growth, and involved in acetogenesis and lignin degradation. We analyzed 35 Bathyarchaeia metagenome-assembled genomes (MAGs), including the first complete circularized MAG (cMAG) of the Bathy-6 subgroup, from the metagenomes of three full-scale pulp and paper mill anaerobic digesters and three laboratory methanogenic enrichment cultures maintained on pre-treated poplar. Thirty-three MAGs belong to the Bathy-6, lineage while two are from the Bathy-8 lineage. In our previous analysis of the microbial community in the pulp mill digesters, Bathyarchaeia were abundant and positively correlated to hydrogenotrophic and methylotrophic methanogenesis. Several factors likely contribute to the success of the Bathy-6 lineage compared to Bathy-8 in the reactors. The Bathy-6 genomes are larger than those of Bathy-8 and have more genes involved in lignocellulose degradation, including carbohydrate-active enzymes not present in the Bathy-8. Bathy-6 also shares the Bathyarchaeal O-demethylase system recently identified in Bathy-8. All the Bathy-6 MAGs had numerous membrane-associated pyrroloquinoline quinone-domain proteins that we suggest are involved in lignin modification or degradation, together with Radical-S-adenosylmethionine (SAM) and Rieske domain proteins, and AA2, AA3, and AA6-family oxidoreductases. We also identified a complete B12 synthesis pathway and a complete nitrogenase gene locus. Finally, comparative genomic analyses revealed that Bathyarchaeia genomes are dynamic and have interacted with other organisms in their environments through gene transfer to expand their gene repertoire.}, } @article {pmid39759024, year = {2024}, author = {Sena, F and Ingervo, E and Khan, S and Prjibelski, A and Schmidt, S and Tomescu, A}, title = {Flowtigs: Safety in flow decompositions for assembly graphs.}, journal = {iScience}, volume = {27}, number = {12}, pages = {111208}, pmid = {39759024}, issn = {2589-0042}, abstract = {A decomposition of a network flow is a set of weighted walks whose superposition equals the flow. In this article, we give a simple and linear-time-verifiable complete characterization (flowtigs) of walks that are safe in such general flow decompositions, i.e., that are subwalks of any possible flow decomposition. We provide an O(mn)-time algorithm that identifies all maximal flowtigs and represents them inside a compact structure. On the practical side, we study flowtigs in the use-case of metagenomic assembly. By using the species abundances as flow values of the metagenomic assembly graph, we can model the possible assembly solutions as flow decompositions into weighted closed walks. On simulated data, compared to reporting unitigs or maximal safe walks based only on the graph structure, reporting flowtigs results in a notably more contiguous assembly. On real data, we frame flowtigs as a heuristic and provide an algorithm that is guided by this heuristic.}, } @article {pmid39759010, year = {2024}, author = {Klaes, S and Madan, S and Deobald, D and Cooper, M and Adrian, L}, title = {Revealing taxonomy, activity, and substrate assimilation in mixed bacterial communities by GroEL-proteotyping-based stable isotope probing.}, journal = {iScience}, volume = {27}, number = {12}, pages = {111249}, pmid = {39759010}, issn = {2589-0042}, abstract = {Protein-based stable isotope probing (protein-SIP) can link microbial taxa to substrate assimilation. Traditionally, protein-SIP requires a sample-specific metagenome-derived database for samples with unknown composition. Here, we describe GroEL-prototyping-based stable isotope probing (GroEL-SIP), that uses GroEL as a taxonomic marker protein to identify bacterial taxa (GroEL-proteotyping) coupled to SIP directly linking identified taxa to substrate consumption. GroEL-SIP's main advantages are that (1) it can be performed with a sample-independent database and (2) sample complexity can be reduced by enriching GroEL proteins, increasing sensitivity and reducing instrument time. We applied GroEL-SIP to pure cultures, synthetic bicultures, and a human gut model using [2]H-, [18]O-, and [13]C-labeled substrates. While [2]H and [18]O allowed assessing general activity, [13]C enabled differentiation of substrate source and utilized metabolic pathways. GroEL-SIP offers fast and straightforward protein-SIP analyses of highly abundant families in mixed bacterial communities, but further work is needed to improve sensitivity, resolution, and database coverage.}, } @article {pmid39758340, year = {2024}, author = {Shang, X and Fu, Y and Wang, Y and Yan, S}, title = {Ramulus Mori (Sangzhi) alkaloids ameliorate high-fat diet induced obesity in rats by modulating gut microbiota and bile acid metabolism.}, journal = {Frontiers in endocrinology}, volume = {15}, number = {}, pages = {1506430}, pmid = {39758340}, issn = {1664-2392}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Diet, High-Fat/adverse effects ; *Obesity/metabolism/drug therapy ; Rats ; Male ; *Bile Acids and Salts/metabolism ; *Rats, Sprague-Dawley ; *Alkaloids/pharmacology ; Lipid Metabolism/drug effects ; Liver/metabolism/drug effects ; Receptors, G-Protein-Coupled/metabolism ; }, abstract = {OBJECTIVE: The objective of this study is to investigate the ability of Ramulus Mori (Sangzhi) alkaloid tablets (SZ-A) to ameliorate obesity and lipid metabolism disorders in rats subjected to a high-fat diet (HFD) through metagenomics, untargeted lipidomics, targeted metabolism of bile acid (BA), and BA pathways, providing a novel perspective on the management of metabolic disorders.

METHODS: In this research, HFD-fed rats were concurrently administered SZ-A orally. We measured changes in body weight (BW), blood lipid profiles, and liver function to assess therapeutic effects. Liver lipid status was visualized through H&E and Oil Red O. Gut microbiota composition was elucidated using metagenomics. The LC-MS-targeted metabolomics approach was utilized to define the fecal BA profiles. Furthermore, the lipid metabolomics of adipose tissue samples was investigated using an LC-MS analysis platform. The expression levels of the BA receptor were determined by western blotting. Additionally, serum insulin (INS), glucagon-like peptide-1 (GLP-1), and inflammatory cytokines were quantified using an ELISA kit. The integrity of the colonic epithelial barrier was assessed using immunofluorescence.

RESULTS: SZ-A notably decreased BW and blood lipid levels in obese rats while also alleviating liver injury. Additionally, SZ-A reduced the serum levels of leptin (LEP), INS, and GLP-1, indicating its potential to modulate key metabolic hormones. Most notably, SZ-A substantially improved gut microbiota composition. Specifically, it reshaped the gut microbiota structure in HFD-fed rats by increasing the relative abundance of beneficial bacteria, such as Bacteroides, while decreasing the populations of potentially harmful bacteria, such as Dorea and Blautia. At the BA level, SZ-A decreased the levels of harmful BAs, including hyodeoxycholic acid (HDCA), deoxycholic acid (DCA), 12-keto lithocholic acid (12-KLCA), lithocholic acid (LCA), and muricholic acid (MDCA). Between the model group and SZ-A, 258 differentially abundant metabolites were detected, with 72 upregulated and 186 downregulated. Furthermore, these BAs are implicated in the activation of the FXR-FGF15 and TGR5-GLP-1 pathways in the intestine. This activation helps to alleviate HFD-fed intestinal inflammation and restore intestinal barrier damage by modulating inflammatory cytokines and bolstering the intestinal barrier's capabilities.

CONCLUSIONS: Our findings indicate that SZ-A effectively modulates BW, serum lipid profiles, and liver function in HFD-fed rats. Moreover, SZ-A exerts a positive influence on inflammatory cytokines, thereby mitigating inflammation and promoting the restoration of the intestinal barrier. Significantly, our research indicates that adjusting the gut microbiome and BA levels could serve as an effective approach for both preventing and treating obesity and related metabolic dyslipidemia.}, } @article {pmid39757511, year = {2025}, author = {Tanca, A and Masia, S and Giustacchini, P and Uzzau, S}, title = {Fecal Metaproteomics as a Tool to Monitor Functional Modifications Induced in the Gut Microbiota by Ketogenic Diet: A Case Study.}, journal = {Proteomics}, volume = {}, number = {}, pages = {e202400191}, doi = {10.1002/pmic.202400191}, pmid = {39757511}, issn = {1615-9861}, support = {//Italian MIUR/ ; }, abstract = {Metaproteomics is a valuable approach to characterize the biological functions involved in the gut microbiota (GM) response to dietary interventions. Ketogenic diets (KDs) are very effective in controlling seizure severity and frequency in drug-resistant epilepsy (DRE) and in the weight loss management in obese/overweight individuals. This case study provides proof of concept for the suitability of metaproteomics to monitor changes in taxonomic and functional GM features in an individual on a short-term very low-calorie ketogenic diet (VLCKD, 4 weeks), followed by a low-calorie diet (LCD). A marked increase in Akkermansia and Pseudomonadota was observed during VLCKD and reversed after the partial reintroduction of carbohydrates (LCD), in agreement with the results of previous metagenomic studies. In functional terms, the relative increase in Akkermansia was associated with an increased production of proteins involved in response to stress and biosynthesis of gamma-aminobutyric acid. In addition, VLCKD caused a relative increase in enzymes involved in the synthesis of the beta-ketoacid acetoacetate and of the ketogenic amino acid leucine. Our data support the potential of fecal metaproteomics to investigate the GM-dependent effect of KD as a therapeutic option in obese/overweight individuals and DRE patients.}, } @article {pmid39757089, year = {2025}, author = {Shen, N}, title = {[Issues in the diagnosis of pneumonia in elderly patients].}, journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases}, volume = {48}, number = {1}, pages = {4-7}, doi = {10.3760/cma.j.cn112147-20240912-00543}, pmid = {39757089}, issn = {1001-0939}, support = {2022YFC2303200//The National Key Research and Development Program of China/ ; }, mesh = {Humans ; Aged ; *Pneumonia/diagnosis ; Risk Factors ; Aged, 80 and over ; Comorbidity ; }, abstract = {In elderly patients, the onset of pneumonia is often subtle and typical respiratory symptoms are less common. Instead, non-specific presentations such as altered mental status and loss of appetite should be closely monitored. The sensitivity of chest X-rays and routine laboratory tests is often low, so a comprehensive assessment including risk factors is required. The presence of multiple comorbidities, including chronic respiratory disease, cardiovascular disease, and diabetes mellitus, is prevalent in this population and complicates early diagnosis. Polypharmacy further adds to the diagnostic and therapeutic challenges. Due to difficulties in specimen collection, high risks associated with invasive testing and atypical pathogen distributions, conventional microbiological detection methods often fail to meet clinical needs. Nucleic acid testing techniques, such as metagenome next-generation sequencing, offer a rapid and sensitive alternative for detecting a wide range of pathogens, including those not identified by conventional methods, as well as rare, multiple, or mixed infections. This approach also has the advantage of not being influenced by prior antibiotic use, making it a crucial role in diagnosing pneumonia in the elderly. However, it is imperative to select appropriate and high-quality specimen types and to interpret the results accurately, taking into account the clinical context and indications for testing. Timely and precise diagnosis is essential to improve the prognosis of pneumonia in elderly patients.}, } @article {pmid39756957, year = {2024}, author = {Kurashita, H and Hatamoto, M and Tomita, S and Yamaguchi, T and Narihiro, T and Kuroda, K}, title = {Comprehensive Insights into Potential Metabolic Functions of Myxococcota in Activated Sludge Systems.}, journal = {Microbes and environments}, volume = {39}, number = {4}, pages = {}, doi = {10.1264/jsme2.ME24068}, pmid = {39756957}, issn = {1347-4405}, mesh = {*Sewage/microbiology/parasitology ; *Myxococcales/genetics/metabolism/classification ; Metagenomics ; Phylogeny ; Metagenome ; Glycolysis ; Citric Acid Cycle/genetics ; }, abstract = {Myxobacteria, belonging to the phylum Myxococcota, are ubiquitous in soil, marine, and other environments. A recent metagenomic sequencing ana-lysis showed that Myxococcota are predominant in activated sludge systems; however, their metabolic traits remain unclear. In the present study, we exami-ned the potential biological functions of 46 metagenomic bins of Myxococcota reconstructed from activated sludge samples from four municipal sewage treatment plants. The results obtained showed that most Myxococcota bins had an almost complete set of genes associated with glycolysis and the TCA cycle. The Palsa-1104 and Polyangiales bins contained the glycoside hydrolase GH5 and peptidase M23, which are presumably involved in lysis of the cell wall and cellular cytoplasm, suggesting that some Myxococcota from activated sludge prey on other microorganisms. The cell contact-dependent predatory functions of Myxococcus xanthus are conserved in the family Myxococcaceae, but not in other families. Two bins belonging to Palsa-1104 had phototrophic gene clusters, indicating the potential for heterotrophic and autotrophic metabolism by these microbes. In assessments of the social behavior of Myxococcota in activated sludge, the FruA gene and C-signal gene, which are involved in the regulation of fruiting body formation, were lacking in Myxococcota bins, suggesting their inability to form fruiting bodies. In addition, multiple bins of Myxococcota had novel secondary metabolite biosynthesis gene clusters that may be used for the predation of other bacteria in activated sludge. Our metagenome-based ana-lyses provide novel insights into the microbial interactions associated with Myxococcota in activated sludge ecosystems.}, } @article {pmid39756663, year = {2025}, author = {Ovis-Sánchez, JO and Vital-Jácome, M and Buitrón, G and Cervantes-Avilés, P and Carrillo-Reyes, J}, title = {Antibiotic resistance reduction mechanisms during thermophilic anaerobic digestion of microalgae-bacteria aggregates.}, journal = {Bioresource technology}, volume = {419}, number = {}, pages = {132037}, doi = {10.1016/j.biortech.2025.132037}, pmid = {39756663}, issn = {1873-2976}, mesh = {*Microalgae/metabolism ; Anaerobiosis ; *Bacteria/metabolism/drug effects/genetics ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Temperature ; Bioreactors/microbiology ; Wastewater/microbiology ; Drug Resistance, Bacterial/drug effects ; }, abstract = {Microalgae-bacteria-based systems are an emerging and promising approach for wastewater treatment plants (WWTP), having nutrient and antibiotic resistance removal comparable to conventional technologies. Still, antibiotic-resistance genes and bacteria (ARG and ARB) can proliferate in microalga-bacteria aggregates (MABA), a concern to control. Different temperature regimes of MABA continuous anaerobic digestion (AD), thermophilic (55 °C), and mesophilic (35 °C) were evaluated in this study as a strategy to eliminate ARB and ARGs. Plate counting techniques and metagenomic-based analysis revealed that thermophilic temperature had a better performance, achieving ARB log reductions of 1.1 to 1.7 for various antibiotics and significantly reduced ARG abundance up to 19.5 ± 0.8 ppm. The microbiome selection, the mobilome restriction, and directed functionality to thermal stress resistance were the main mechanisms responsible for resistome reduction at thermophilic conditions. Thermophilic AD effectively manages antibiotic resistance in microalgae-bacteria aggregates, which has important implications for wastewater treatment and reduces environmental risks.}, } @article {pmid39756573, year = {2025}, author = {Shen, H and Li, Y and Pi, Q and Tian, J and Xu, X and Huang, Z and Huang, J and Pian, C and Mao, S}, title = {Unveiling novel antimicrobial peptides from the ruminant gastrointestinal microbiomes: A deep learning-driven approach yields an anti-MRSA candidate.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2025.01.005}, pmid = {39756573}, issn = {2090-1224}, abstract = {INTRODUCTION: Antimicrobial peptides (AMPs) present a promising avenue to combat the growing threat of antibiotic resistance. The ruminant gastrointestinal microbiome serves as a unique ecosystem that offers untapped potential for AMP discovery.

OBJECTIVES: The aims of this study are to develop an effective methodology for the identification of novel AMPs from ruminant gastrointestinal microbiomes, followed by evaluating their antimicrobial efficacy and elucidating the mechanisms underlying their activity.

METHODS: We developed a deep learning-based model to identify AMP candidates from a dataset comprising 120 metagenomes and 10,373 metagenome-assembled genomes derived from the ruminant gastrointestinal tract. Both in vivo and in vitro experiments were performed to examine and validate the antimicrobial activities of the AMP candidates that were selected through bioinformatic analysis and subsequently synthesized chemically. Additionally, molecular dynamics simulations were conducted to explore the action mechanism of the most potent AMP candidate.

RESULTS: The deep learning model identified 27,192 potential secretory AMP candidates. Following bioinformatic analysis, 39 candidates were synthesized and tested. Remarkably, all synthesized peptides demonstrated antimicrobial activity against Staphylococcus aureus, with 79.5% showing effectiveness against multiple pathogens. Notably, Peptide 4, which exhibited the highest antimicrobial activity against methicillin-resistant Staphylococcus aureus (MRSA), confirmed this effect in a mouse model with wound infection, exhibiting a low propensity for resistance development and minimal cytotoxicity and hemolysis towards mammalian cells. Molecular dynamics simulations provided insights into the mechanism of Peptide 4, primarily its ability to disrupt bacterial cell membranes, leading to cell death.

CONCLUSION: This study highlights the power of combining deep learning with microbiome research to uncover novel therapeutic candidates, paving the way for the development of next-generation antimicrobials like Peptide 4 to combat the growing threat of MRSA would infections. It also underscores the value of utilizing ruminant microbial resources.}, } @article {pmid39756329, year = {2025}, author = {Dai, J and Li, M and He, J and Duan, L and Zhu, X and Liu, L and Meng, M and Shao, X and Zhu, G}, title = {Gut microbiota changes are associated with abnormal metabolism activity in children and adolescents with obsessive-compulsive disorder.}, journal = {Journal of psychiatric research}, volume = {181}, number = {}, pages = {728-737}, doi = {10.1016/j.jpsychires.2024.12.041}, pmid = {39756329}, issn = {1879-1379}, mesh = {Humans ; *Obsessive-Compulsive Disorder/metabolism/microbiology ; Adolescent ; *Gastrointestinal Microbiome/physiology ; Male ; Child ; Female ; *Feces/microbiology ; *RNA, Ribosomal, 16S ; Metabolomics ; Metagenomics ; }, abstract = {Obsessive-compulsive disorder (OCD) is a chronic and disabling psychiatric disorder characterized by recurrent intrusive thoughts or repetitive behaviors. We sought to better understand the structure of gut microbiota in first visit registration, treatment-naive children and adolescents with OCD, and the relationship between gut microbiota and fecal metabolites. Thus we studied the gut microbial population using 16 S rRNA sequencing in 49 children (8-17 years of age) with OCD, 42 healthy controls (HCs). We found a significant decrease in α-diversity in the OCD group, and the OCD and HC groups had distinctive intestinal flora. To further investigate the potential interaction effects between OCD and functional pathways of the intestinal flora, the 19 OCD patients and 18 aged-matched HCs were selected to undergo metagenomics analysis. We showed that several functional pathways of gut microbiota in patients with OCD were disrupted, such as glucolipid metabolism, amino acid metabolism, steroid biosynthesis, and the second messenger system. Changes in the clinical characteristics of OCD patients were associated with specific bacteria. Metabolomics analysis was also performed on stool samples from 91 subjects. Intestinal microflora metabolite expression in OCD patients was disturbed, and the related metabolic pathway functions were abnormal. Abnormal metabolites of gut microbiota in OCD patients are mainly involved in folate biosynthesis, the prion disease pathway, and the amino acid metabolic network. This study detailed the intestinal microbiota of children and adolescents with OCD. Our study suggests possible modalities for early OCD intervention by targeting the specific bacteria associated with neurotransmitter metabolism.}, } @article {pmid39756287, year = {2025}, author = {Yu, Q and Shen, G and Zhao, F and Fan, Y and Xue, H and Bao, Y and Ren, H and Geng, J}, title = {Removal of mixed PhACs by combined UV/H2O2 and biologically activated carbon process: Toxicity assessment, transformation products and microbial community.}, journal = {Journal of environmental management}, volume = {373}, number = {}, pages = {123980}, doi = {10.1016/j.jenvman.2024.123980}, pmid = {39756287}, issn = {1095-8630}, mesh = {*Hydrogen Peroxide ; *Charcoal ; *Water Pollutants, Chemical/toxicity ; *Zebrafish ; Animals ; *Ultraviolet Rays ; Carbamazepine/toxicity ; }, abstract = {This study examined the removal and toxicity reduction of mixed pharmaceutically active compounds (PhACs), including carbamazepine, erythromycin, gemfibrozil, and diclofenac, in the UV/H2O2 tandem with biologically activated carbon (UV/H2O2-BAC) process and explored potential detoxification mechanisms. Results indicated that the combined process effectively removed the mixed PhACs, with the UV/H2O2 segment being the primary contributor. As distinct from concentration removal, the effluent toxicity significantly increased after UV/H2O2 treatment. Multi-parameter toxicity assessments indicated that UV/H2O2 treatment significantly inhibited the activity of luminescent bacteria, interfered with the developmental toxicity of zebrafish embryos, and affected the oxidative stress and metabolic levels of zebrafish larvae. After BAC treatment, the toxicity of the UV/H2O2 effluent significantly decreased, particularly at an empty bed contact time of 45 min. Suspect and non-target screening were used to elucidate further the potential causes of toxicity fluctuations along the treatment flow from the transformation products (TPs) perspective. A total of 58 unique TPs were identified in the tandem process, of which 49 were initially identified in UV/H2O2. Over 85% of TPs in UV/H2O2 exhibited potential toxicity, with nearly 60% predicted to exhibit higher toxicity than parent. After BAC treatment, above 90% of TPs were effectively reduced. Metagenomics indicated that 8 taxa, including Paracoccus, were potentially dominant functional bacteria involved in the degradation of target substances. This study provided valuable insights into the feasibility and effectiveness of the UV/H2O2-BAC process for removing PhACs from the perspective of toxicity reduction.}, } @article {pmid39756247, year = {2025}, author = {Kim, MJ and Kim, KE and Kim, HJ and Kim, YJ and Lee, TK and Kim, SM and Cha, HG and Jung, SW}, title = {Co-occurrence patterns between Chlorophyta and nucleocytoplasmic large DNA virus in coastal ecosystem, South Korea.}, journal = {Marine environmental research}, volume = {204}, number = {}, pages = {106944}, doi = {10.1016/j.marenvres.2025.106944}, pmid = {39756247}, issn = {1879-0291}, mesh = {Republic of Korea ; *Chlorophyta/virology ; *Ecosystem ; DNA Viruses/genetics ; Phytoplankton/virology ; Seawater/virology ; Environmental Monitoring ; Phycodnaviridae/genetics ; }, abstract = {Nucleocytoplasmic large DNA viruses (NCLDVs) are known to infect phytoplankton and play a significant role in regulating their population dynamics. In this study, we aimed to investigate the co-occurrence patterns between phytoplankton and NCLDVs in the southern coastal ecosystem of South Korea. We collected seawater every month from March 2018 to December 2020 and analyzed the samples using Cytochrome c Oxidase subunit I metabarcoding and metagenomic analyses. Chlorophyta (36.08%) was the most abundant eukaryotic taxon, with Bathycoccaceae (58.25%) and Mamiellaceae (41.51%) being the most dominant families within Chlorophyta. Bathycoccaceae was dominant in winter, whereas Mamiellaceae was dominant in summer. In the NCLDV community, Phycodnaviridae (75.12%) was found to be the major family. The co-occurrence pattern of Phycodnaviridae showed a high correlation with Bathycoccaceae and Mamiellaceae, which is explained by the "boom-and-bust" concept. In particular, we predicted co-occurrence patterns between Bathycoccus prasinos and Prasnovirus, with known infectious relationships, and confirmed co-occurrence patterns between B. prasinos and Coccolithovirus and Micromonas pusilla and Prymnesiovirus, with unknown infectious relationships. These co-occurrence patterns between Chlorophyta and Phycodnaviridae provide valuable insights into the control of pico-sized primary production and the microbial loop of the coastal ecosystem.}, } @article {pmid39756219, year = {2024}, author = {Mao, Y and Shisler, JL and Nguyen, TH}, title = {Enhanced detection for antibiotic resistance genes in wastewater samples using a CRISPR-enriched metagenomic method.}, journal = {Water research}, volume = {274}, number = {}, pages = {123056}, doi = {10.1016/j.watres.2024.123056}, pmid = {39756219}, issn = {1879-2448}, abstract = {The spread of antibiotic resistance genes (ARGs) in the environment is a global public health concern. To date, over 5000 genes have been identified to express resistance to antibiotics. ARGs are usually low in abundance for wastewater samples, making them difficult to detect. Metagenomic sequencing and quantitative polymerase chain reaction (qPCR), two conventional ARG detection methods, have low sensitivity and low throughput limitations, respectively. We developed a CRISPR-Cas9-modified next-generation sequencing (NGS) method to enrich the targeted ARGs during library preparation. The false negative and false positive of this method were determined based on a mixture of bacterial isolates with known whole-genome sequences. Low values of both false negative (2/1208) and false positive (1/1208) proved the method's reliability. We compared the results obtained by this CRISPR-NGS and the conventional NGS method for six untreated wastewater samples. As compared to the ARGs detected in the same samples using the regular NGS method, the CRISPR-NGS method found up to 1189 more ARGs and up to 61 more ARG families in low abundances, including the clinically important KPC beta-lactamase genes in the six wastewater samples collected from different sources. Compared to the regular NGS method, the CRISPR-NGS method lowered the detection limit of ARGs from the magnitude of 10[-4] to 10[-5] as quantified by qPCR relative abundance. The CRISPR-NGS method is promising for ARG detection in wastewater. A similar workflow can also be applied to detect other targets that are in low abundance but of high diversity.}, } @article {pmid39756076, year = {2025}, author = {Harima, H and Qiu, Y and Sasaki, M and Ndebe, J and Penjaninge, K and Simulundu, E and Kajihara, M and Ohnuma, A and Matsuno, K and Nao, N and Orba, Y and Takada, A and Ishihara, K and Hall, WW and Hang'ombe, BM and Sawa, H}, title = {First identification and whole genome characterization of rotavirus C in pigs in Zambia.}, journal = {Virology}, volume = {603}, number = {}, pages = {110385}, doi = {10.1016/j.virol.2024.110385}, pmid = {39756076}, issn = {1096-0341}, mesh = {Animals ; Zambia/epidemiology ; *Rotavirus Infections/veterinary/virology/epidemiology ; Swine ; *Genome, Viral ; *Rotavirus/genetics/classification/isolation & purification ; *Swine Diseases/virology/epidemiology ; *Phylogeny ; *Feces/virology ; *Genotype ; Whole Genome Sequencing ; Metagenomics ; RNA, Viral/genetics ; }, abstract = {Rotavirus C (RVC) causes acute gastroenteritis in neonatal piglets. Despite the clinical importance of RVC infection, the distribution and prevalence in pig populations in most African countries remains unknown. In this study, we identified RVC in Zambian pigs by metagenomic analysis. The full genome sequence of the RVC revealed two different VP4 sequences, implying that two different RVC strains (ZP18-77-c1 and ZP18-77-c2) were present in the same sample. Genetic analyses demonstrated that all segments of ZP18-77-c1 and ZP18-77-c2 showed high nucleotide sequence identities (87.7-94.5%) to known porcine RVC strains, and ZP18-77-c1 and ZP18-77-c2 strains were assigned to genotype constellations, G1-P[4]/P[14]-I13-R5-C5-M1-A7-N9-T10-E5-H1. We further screened RVC genomes among pig feces collected in Zambia (n = 147) by RT-qPCR, and 78 samples (53.1%) were positive. This study demonstrated the first full genome sequence of African RVC strains with a relatively high prevalence of RVC infection in the pig populations in Zambia.}, } @article {pmid39756070, year = {2024}, author = {Wei, A and Xiao, Z and Fu, L and Zhao, W and Jiang, X}, title = {Predicting phage-host interactions via feature augmentation and regional graph convolution.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {1}, pages = {}, doi = {10.1093/bib/bbae672}, pmid = {39756070}, issn = {1477-4054}, support = {62372205//National Natural Science Foundation of China/ ; ZDI145-56//National Language Commission Key Research Project/ ; KJ02502022-0450//Fundamental Research Funds for Central Universities/ ; 2022CFB289//Natural Science Foundation of Hubei Province of China/ ; CCNU24JC032//Colleges' Basic Research and Operation of MOE/ ; }, mesh = {*Bacteriophages ; *Deep Learning ; Algorithms ; Computational Biology/methods ; Host-Pathogen Interactions ; }, abstract = {Identifying phage-host interactions (PHIs) is a crucial step in developing phage therapy, which is the promising solution to addressing the issue of antibiotic resistance in superbugs. However, the lifestyle of phages, which strongly depends on their host for life activities, limits their cultivability, making the study of predicting PHIs time-consuming and labor-intensive for traditional wet lab experiments. Although many deep learning (DL) approaches have been applied to PHIs prediction, most DL methods are predominantly based on sequence information, failing to comprehensively model the intricate relationships within PHIs. Moreover, most existing approaches are limited for sub-optimal performance, due to the potential risk of overfitting induced by the highly data sparsity in the task of PHIs prediction. In this study, we propose a novel approach called MI-RGC, which introduces mutual information for feature augmentation and employs regional graph convolution to learn meaningful representations. Specifically, MI-RGC treats the presence status of phages in environmental samples as random variables, and derives the mutual information between these random variables as the dependency relationships among phages. Consequently, a mutual information-based heterogeneous network is construted as feature augmentation for sequence information of phages, which is utilized for building a sequence information-based heterogeneous network. By considering the different contributions of neighboring nodes at varying distances, a regional graph convolutional model is designed, in which the neighboring nodes are segmented into different regions and a regional-level attention mechanism is employed to derive node embeddings. Finally, the embeddings learned from these two networks are aggregated through an attention mechanism, on which the prediction of PHIs is condcuted accordingly. Experimental results on three benchmark datasets demonstrate that MI-RGC derives superior performance over other methods on the task of PHIs prediction.}, } @article {pmid39755199, year = {2025}, author = {Liu, L and Zhu, G and Hu, J and Chen, H and Zhai, Y}, title = {An unignorable human health risk posed by antibiotic resistome and microbiome in urban rivers: Insights from Beijing, China.}, journal = {Environmental research}, volume = {268}, number = {}, pages = {120752}, doi = {10.1016/j.envres.2025.120752}, pmid = {39755199}, issn = {1096-0953}, abstract = {Urban rivers are the main water bodies humans frequently come into contact with, so the risks posed are closely monitored. Antibiotic resistance genes (ARGs) residues in reclaimed water pose serious risks to human health. There are urgent needs to improve the understanding of distribution of and risks posed by ARGs in urban rivers. In this study, shotgun metagenomic approach was used to characterize ARGs, mobile genetic elements (MGEs), and virulence factors (VFs) in water and sediment from Xinfeng River in Beijing and to identify microbes, potential antibiotic resistant bacteria, and human pathogens (HPs). MGE, microbial community, VF, and ARG co-occurrences were used to assess the environmental risks posed by ARGs. The results indicated that quinolone was the most abundant ARG type and that tufA and fusA were the two dominant ARG subtypes. Wetland effluent increased ARG abundance in the river, and the effect was detected even 50 m downstream. ARG abundances and distribution in the river had difference in different seasons. The dominant bacteria in the river were Proteobacteria, Bacteroidetes, and Actinobacteria, and 59 HPs were detected. In total, 69 MGEs and 19 VFs were found. Co-occurrence networks indicated that potential antibiotic resistant bacteria, MGEs, VFs, and ARGs in the river significantly correlated, indicating the potential risks posed by ARGs. The results improve our understanding of ARG distribution and environmental risks in urban river water. More attention should be paid to controlling environmental risks posed by ARGs in urban river and reclaimed water.}, } @article {pmid39755076, year = {2025}, author = {Zahrebelnei, F and Lima, D and de Lara, LS and Gryczak, DW and Carmo, TASD and Urrea-Valencia, S and Galvão, CW and Etto, RM and Pessôa, CA and Wohnrath, K}, title = {A sensitive electrochemical DNA biosensor for detecting the genome of a plant growth-promoting bacteria.}, journal = {Talanta}, volume = {286}, number = {}, pages = {127484}, doi = {10.1016/j.talanta.2024.127484}, pmid = {39755076}, issn = {1873-3573}, abstract = {The challenge of increasing food production while maintaining environmental sustainability can be addressed by using biofertilizers such as Azospirillum, which can enhance plant growth and colonize more than 100 plant species. The success of this biotechnology depends on the amount of plant growth-promoting bacteria associated with the plant during crop development. However, monitoring bacterial population dynamics after inoculation requires time-consuming, laborious, and costly procedures. To address these issues, this study describes an effective electrochemical DNA biosensor to detect Azospirillum brasilense. The biosensor comprises a glassy carbon electrode modified with a nanocomposite based on carbon nanotubes and gold nanoparticles capped with 3-n-propylpyridinium chloride silsesquioxane, followed by the immobilization of a thiolated probe oligonucleotide that binds specifically to the A. brasilense genome (AZOgenome). The nanocomposite was characterized utilizing spectroscopic and morphological methods. Its presence on the biosensor's surface enhanced electrochemical responses due to its excellent electrocatalytic properties, as observed during electrochemical impedance spectroscopy and cyclic voltammetry experiments. The biosensor enabled the detection of AZOgenome after the hybridization event, which alters the electrochemical response of the electrode and was rapidly detected by square wave voltammetry. The detection range of the bacterial genome was 1.17 pmol L[-1] to 146.8 pmol L[-1], with LOD and LOQ of 0.261 and 0.322 pmol L[-1], respectively, and sensitivity of -15.560 μA/log [AZOgenome] (pmol L[-1]). The biosensor showed good selectivity and reproducibility, with a coefficient of variation of -5.69 %, in addition to satisfactory sensitivity and stability for up to seven weeks. These promising analytical features allowed the quantification of A. brasilense in low concentrations in soil metagenomic DNA samples.}, } @article {pmid39754807, year = {2025}, author = {Wang, Y and Zhang, Q and Li, H and Teng, Y and Wang, H}, title = {Metagenomic analysis reveals the effects of potassium ferrate and steel slag on fate of ARGs in anaerobic sludge digestion system.}, journal = {Journal of environmental management}, volume = {373}, number = {}, pages = {123981}, doi = {10.1016/j.jenvman.2024.123981}, pmid = {39754807}, issn = {1095-8630}, mesh = {*Sewage/microbiology ; Anaerobiosis ; *Metagenomics ; Potassium Compounds/pharmacology ; Drug Resistance, Microbial/genetics ; Steel ; Iron Compounds ; }, abstract = {Waste activated sludge (WAS) pose a potential risk for the spread of antibiotic resistance genes (ARGs). This study estimated the effect of sludge on antibiotic resistance genes (ARGs) in anaerobic sludge digestion process. Metagenomic analysis revealed anaerobic sludge with potassium ferrate (PF) and the modified PF loaded steel slag (MPF-SS) brought an increase of ARGs during digestion process. PF was found to effectively reduce most of the high-risk ARGs (i.e., acrB and mexW). Furthermore, network and correlation analysis among ARGs and genera verified that PF significantly increased the potential ARGs hosts. Mechanistic analysis revealed that PF induced oxidative stress behavior of anaerobic digestion microorganisms, and observably upregulated the relative genes about SOS response-related. These findings provide insights into the mechanism underlining PF for ARGs fate and its risk during anaerobic sludge digestion, which could offer practical guidance on the sustainable management of WAS.}, } @article {pmid39754646, year = {2025}, author = {Shaffer, M and North, D and Bibby, K}, title = {Evaluating Nanotrap Microbiome Particles as A Wastewater Viral Concentration Method.}, journal = {Food and environmental virology}, volume = {17}, number = {1}, pages = {10}, pmid = {39754646}, issn = {1867-0342}, support = {1748019//National Science Foundation/ ; }, mesh = {*Wastewater/virology/microbiology ; *Microbiota ; *Viruses/isolation & purification/classification/genetics ; Metagenomics/methods ; Bacteria/isolation & purification/classification/genetics/virology ; Tobamovirus/isolation & purification/genetics/classification ; }, abstract = {Wastewater-based surveillance has emerged as a powerful approach to monitoring infectious diseases within a community. Typically, wastewater samples are concentrated before viral analyses to improve sensitivity. Current concentration methods vary in time requirements, costs, and efficiency. Here, we evaluated the concentration efficiency and bias of a novel viral concentration approach, Nanotrap Microbiome Particles (NMP), in wastewater. NMP concentration efficiency was target-specific, with significantly lower concentrations of the bacterial indicator HF183 and viral indicator Carjivirus (formerly crAssphage) relative to direct extraction (1.2 × 10[5] vs. 3.4 × 10[5] GC/mL and 2.0 × 10[5] vs. 1.2 × 10[5] GC/mL, respectively), but significantly higher concentrations of the viral fecal indicator Pepper Mild Mottle Virus (PMMoV) relative to direct extraction (1.4 × 10[5] vs. 8.4 × 10[3] GC/mL). Targeted metagenomic sequencing showed that NMP resulted in significantly more unique species reads per sample than direct extractions (p < 0.001) by detecting species that went undetected by direct extractions. Key viral families identified with high abundances were Adenoviridae, Caliciviridae, Herpesviridae, Papillomaviridae, and Polyomaviridae. NMP showed differential ability for concentrating clinically relevant viral families, suggesting that the technology should be evaluated and optimized for specific viral targets before implementation.}, } @article {pmid39754220, year = {2025}, author = {Karwowska, Z and Aasmets, O and , and Kosciolek, T and Org, E}, title = {Effects of data transformation and model selection on feature importance in microbiome classification data.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {2}, pmid = {39754220}, issn = {2049-2618}, mesh = {Humans ; *Machine Learning ; *Gastrointestinal Microbiome/genetics ; *Algorithms ; *Metagenomics/methods ; Microbiota/genetics ; Bacteria/classification/genetics ; Biomarkers ; Metagenome ; }, abstract = {BACKGROUND: Accurate classification of host phenotypes from microbiome data is crucial for advancing microbiome-based therapies, with machine learning offering effective solutions. However, the complexity of the gut microbiome, data sparsity, compositionality, and population-specificity present significant challenges. Microbiome data transformations can alleviate some of the aforementioned challenges, but their usage in machine learning tasks has largely been unexplored.

RESULTS: Our analysis of over 8500 samples from 24 shotgun metagenomic datasets showed that it is possible to classify healthy and diseased individuals using microbiome data with minimal dependence on the choice of algorithm or transformation. Presence-absence transformations performed comparably to abundance-based transformations, and only a small subset of predictors is necessary for accurate classification. However, while different transformations resulted in comparable classification performance, the most important features varied significantly, which highlights the need to reevaluate machine learning-based biomarker detection.

CONCLUSIONS: Microbiome data transformations can significantly influence feature selection but have a limited effect on classification accuracy. Our findings suggest that while classification is robust across different transformations, the variation in feature selection necessitates caution when using machine learning for biomarker identification. This research provides valuable insights for applying machine learning to microbiome data and identifies important directions for future work.}, } @article {pmid39753925, year = {2025}, author = {Bora, SS and Ronghang, R and Das, P and Naorem, RS and Hazarika, DJ and Gogoi, R and Banu, S and Barooah, M}, title = {Endophytic Microbial Community Structure and Dynamics Influence Agarwood Formation in Aquilaria malaccensis Lam.}, journal = {Current microbiology}, volume = {82}, number = {2}, pages = {66}, pmid = {39753925}, issn = {1432-0991}, mesh = {*Thymelaeaceae/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Endophytes/genetics/classification/isolation & purification ; *Fungi/genetics/classification/isolation & purification ; Microbiota ; Metagenomics ; Wood/microbiology ; Metagenome ; }, abstract = {Aquilaria malaccensis Lam., an Agarwood-producing tree native to Southeast Asia, secretes oleoresin, a resin with diverse applications, in response to injuries. To explore the role of endosphere microbial communities during Agarwood development, we utilized a metagenomics approach across three stages: non-symptomatic (NC), symptomatic early (IN), and symptomatic mature (IN1). The NC metagenome was dominated by Bacillus (19.15%), Klebsiella (13.25%), and Pantoea (12.46%) among bacteria and Saccharomyces (15.92%) among fungi. Notably, bacterial chemotaxis pathway genes were more prevalent in NC (2.14%) compared to IN (0.92%) and IN1 (1.16%), suggesting microbial chemotactic behavior. In the IN stage, Klebsiella (27.05%) and Saccharomyces (34.81%) were the dominant genera. The IN1 metagenome featured Pantoea (8.92%) and Neurospora (8.24%) as leading bacterial and fungal genera, respectively. Functional genes associated with defense mechanisms, lipid transport, and secondary metabolite biosynthesis were increasingly represented in IN1, indicating an enhanced microbial response as infection progresses. Ecological indices, including a high Shannon-Wiener index (H' = 4.467) and Simpson's dominance (1 - D = 0.9697), alongside Pielou's evenness index (J = 0.7034), highlighted a dynamic and diverse microbial community at the mature infection stage, reflecting the complex interactions within the Aquilaria endosphere during Agarwood formation.}, } @article {pmid39753668, year = {2025}, author = {Rohwer, RR and Kirkpatrick, M and Garcia, SL and Kellom, M and McMahon, KD and Baker, BJ}, title = {Two decades of bacterial ecology and evolution in a freshwater lake.}, journal = {Nature microbiology}, volume = {10}, number = {1}, pages = {246-257}, pmid = {39753668}, issn = {2058-5276}, support = {DEB-0822700//National Science Foundation (NSF)/ ; DEB-1440297//National Science Foundation (NSF)/ ; MCB-9977903//National Science Foundation (NSF)/ ; DEB-1344254//National Science Foundation (NSF)/ ; WIS01789//U.S. Department of Agriculture (United States Department of Agriculture)/ ; WIS01516//U.S. Department of Agriculture (United States Department of Agriculture)/ ; R01-GM116853//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; DBI-2011002//National Science Foundation (NSF)/ ; DEB-1831730//National Science Foundation (NSF)/ ; R01 GM116853/GM/NIGMS NIH HHS/United States ; DEB-0702395//National Science Foundation (NSF)/ ; DEB-2025982//National Science Foundation (NSF)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DEB-9632853//National Science Foundation (NSF)/ ; DEB-0217533//National Science Foundation (NSF)/ ; }, mesh = {*Lakes/microbiology ; *Bacteria/genetics/classification/isolation & purification ; *Microbiota/genetics ; Metagenome ; Seasons ; Phylogeny ; Genome, Bacterial ; Evolution, Molecular ; Biological Evolution ; }, abstract = {Ecology and evolution are considered distinct processes that interact on contemporary time scales in microbiomes. Here, to observe these processes in a natural system, we collected a two-decade, 471-metagenome time series from Lake Mendota (Wisconsin, USA). We assembled 2,855 species-representative genomes and found that genomic change was common and frequent. By tracking strain composition via single nucleotide variants, we identified cyclical seasonal patterns in 80% and decadal shifts in 20% of species. In the dominant freshwater family Nanopelagicaceae, environmental extremes coincided with shifts in strain composition and positive selection of amino acid and nucleic acid metabolism genes. These genes identify organic nitrogen compounds as potential drivers of freshwater responses to global change. Seasonal and long-term strain dynamics could be regarded as ecological processes or, equivalently, as evolutionary change. Rather than as distinct interacting processes, we propose a conceptualization of ecology and evolution as a continuum to better describe change in microbial communities.}, } @article {pmid39753565, year = {2025}, author = {Chen, YC and Su, YY and Chu, TY and Wu, MF and Huang, CC and Lin, CC}, title = {PreLect: Prevalence leveraged consistent feature selection decodes microbial signatures across cohorts.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {3}, pmid = {39753565}, issn = {2055-5008}, support = {NSTC 112-2221-E-A49 -106 -MY3//Ministry of Science and Technology, Taiwan (Ministry of Science and Technology of Taiwan)/ ; NSTC 109-2221-E-010 -014 -MY3//Ministry of Science and Technology, Taiwan (Ministry of Science and Technology of Taiwan)/ ; NSTC 109-2221-E-010 -014 -MY3//Ministry of Science and Technology, Taiwan (Ministry of Science and Technology of Taiwan)/ ; NSTC 112-2221-E-A49 -106 -MY3//Ministry of Science and Technology, Taiwan (Ministry of Science and Technology of Taiwan)/ ; NSTC 109-2221-E-010 -014 -MY3//Ministry of Science and Technology, Taiwan (Ministry of Science and Technology of Taiwan)/ ; NSTC 109-2221-E-010 -014 -MY3//Ministry of Science and Technology, Taiwan (Ministry of Science and Technology of Taiwan)/ ; NSTC 109-2221-E-010 -014 -MY3//Ministry of Science and Technology, Taiwan (Ministry of Science and Technology of Taiwan)/ ; MOHW112-TDU-B-222-124013//Ministry of Health and Welfare (Ministry of Health and Welfare, Taiwan)/ ; MOHW111-TDU-B-221-114007//Ministry of Health and Welfare (Ministry of Health and Welfare, Taiwan)/ ; MOHW112-TDU-B-222-124013//Ministry of Health and Welfare (Ministry of Health and Welfare, Taiwan)/ ; MOHW111-TDU-B-221-114007//Ministry of Health and Welfare (Ministry of Health and Welfare, Taiwan)/ ; }, mesh = {Humans ; *Colorectal Neoplasms/microbiology ; Microbiota ; Bacteria/genetics/classification/isolation & purification ; Machine Learning ; Gastrointestinal Microbiome ; Cohort Studies ; Glycerophospholipids ; Computational Biology/methods ; Lipopolysaccharides ; Metagenomics/methods ; }, abstract = {The intricate nature of microbiota sequencing data-high dimensionality and sparsity-presents a challenge in identifying informative and reproducible microbial features for both research and clinical applications. Addressing this, we introduce PreLect, an innovative feature selection framework that harnesses microbes' prevalence to facilitate consistent selection in sparse microbiota data. Upon rigorous benchmarking against established feature selection methodologies across 42 microbiome datasets, PreLect demonstrated superior classification capabilities compared to statistical methods and outperformed machine learning-based methods by selecting features with greater prevalence and abundance. A significant strength of PreLect lies in its ability to reliably identify reproducible microbial features across varied cohorts. Applied to colorectal cancer, PreLect identifies key microbes and highlights crucial pathways, such as lipopolysaccharide and glycerophospholipid biosynthesis, in cancer progression. This case study exemplifies PreLect's utility in discerning clinically relevant microbial signatures. In summary, PreLect's accuracy and robustness make it a significant advancement in the analysis of complex microbiota data.}, } @article {pmid39753133, year = {2025}, author = {Hyde, VR and Zhou, C and Fernandez, JR and Chatterjee, K and Ramakrishna, P and Lin, A and Fisher, GW and Çeliker, OT and Caldwell, J and Bender, O and Sauer, PJ and Lugo-Martinez, J and Bar, DZ and D'Aiuto, L and Shemesh, OA}, title = {Anti-herpetic tau preserves neurons via the cGAS-STING-TBK1 pathway in Alzheimer's disease.}, journal = {Cell reports}, volume = {44}, number = {1}, pages = {115109}, doi = {10.1016/j.celrep.2024.115109}, pmid = {39753133}, issn = {2211-1247}, mesh = {Humans ; *Alzheimer Disease/metabolism/pathology/virology ; *Nucleotidyltransferases/metabolism ; *Membrane Proteins/metabolism ; *tau Proteins/metabolism ; *Protein Serine-Threonine Kinases/metabolism ; *Neurons/metabolism ; *Herpesvirus 1, Human ; *Signal Transduction ; Phosphorylation ; Interferon Regulatory Factor-3/metabolism ; NF-kappa B/metabolism ; Brain/metabolism/pathology ; }, abstract = {Alzheimer's disease (AD) diagnosis relies on the presence of extracellular β-amyloid (Aβ) and intracellular hyperphosphorylated tau (p-tau). Emerging evidence suggests a potential link between AD pathologies and infectious agents, with herpes simplex virus 1 (HSV-1) being a leading candidate. Our investigation, using metagenomics, mass spectrometry, western blotting, and decrowding expansion pathology, detects HSV-1-associated proteins in human brain samples. Expression of the herpesvirus protein ICP27 increases with AD severity and strongly colocalizes with p-tau but not with Aβ. Modeling in human brain organoids shows that HSV-1 infection elevates tau phosphorylation. Notably, p-tau reduces ICP27 expression and markedly decreases post-infection neuronal death from 64% to 7%. This modeling prompts investigation into the cGAS-STING-TBK1 pathway products, nuclear factor (NF)-κB and IRF-3, which colocalizes with ICP27 and p-tau in AD. Furthermore, experimental activation of STING enhances tau phosphorylation, while TBK1 inhibition prevents it. Together, these findings suggest that tau phosphorylation acts as an innate immune response in AD, driven by cGAS-STING.}, } @article {pmid39752831, year = {2024}, author = {Li, Z and Liu, B and Cao, B and Cun, S and Liu, R and Liu, X}, title = {The potential role of viruses in antibiotic resistance gene dissemination in activated sludge viromes.}, journal = {Journal of hazardous materials}, volume = {486}, number = {}, pages = {137046}, doi = {10.1016/j.jhazmat.2024.137046}, pmid = {39752831}, issn = {1873-3336}, abstract = {The dissemination of antibiotic resistance genes (ARGs) in activated sludge (AS) systems poses significant environmental and public health challenges. The role of viruses, primarily bacteriophages, in storing and spreading ARGs in AS systems remains largely unexplored. This study characterized the viral community, virus-associated ARGs (vir_ARGs), and mobile genetic elements (MGEs) of aerobic AS viromes from eight wastewater treatment plants (WWTPs) in eastern China. 78,604 viral operational taxonomic units (vOTUs) were identified, including 1685 temperate vOTUs (T-vOTUs). Five ARG types were detected in 37 vOTUs, indicating a low proportion of ARG-carrying viruses. The co-occurrence rate between vir_ARGs and MGEs was 37.83 %, and six ARG-carrying vOTUs contained multiple MGEs, indicating a transfer potential of vir_ARGs. Additionally, ARG and MGE profiles of AS metagenomes were analyzed to evaluate the transfer potential of phage activity on ARGs. The results showed that phage-associated MGEs showed a significant coupling with both the abundance and composition of ARGs, suggesting a potential role of phages in ARG propagation. These findings offer preliminary insights into understanding the viral resistome and its transfer potential in AS systems. Future research necessitates rigorous pure culture and molecular biology experiments to elucidate the precise mechanisms through which viruses contribute to the dissemination and persistence of ARGs.}, } @article {pmid39752554, year = {2025}, author = {Abdelrazek, S and Rodriguez Salamanca, L and Vinatzer, BA}, title = {Metagenomic Sequencing of Tomato Plants with Wilt Symptoms Allows for Strain-Level Pathogen Identification and Genome-Based Characterization.}, journal = {Phytopathology}, volume = {}, number = {}, pages = {}, doi = {10.1094/PHYTO-09-24-0279-R}, pmid = {39752554}, issn = {0031-949X}, abstract = {Diseases that affect the vascular system or the pith are of great economic impact since they can rapidly destroy the affected plants, leading to complete loss in production. Fast and precise identification is thus important to inform containment and management, but many identification methods are slow because they are culture-dependent and they do not reach strain resolution. Here we used culture-independent long-read metagenomic sequencing of DNA extracted directly from stems of two tomato samples that displayed wilt symptoms. We obtained enough sequencing reads to assemble high quality metagenome-assembled genomes (MAGs) of Ralstonia solanacearum from one sample and of Pseudomonas corrugata from the other. The genome sequences allowed us to identify both pathogens to strain level using the genomerxiv platform, perform phylogenetic analyses, predict virulence genes, and infer antibiotic and copper resistance. In the case of R. solanacearum, it was straightforward to exclude the pathogen from being the Select Agent Race 3 biovar 2. Using the Branchwater tool, it was also possible to determine the world-wide distribution of both pathogen strains based on public metagenomic sequences. The entire analysis could have been completed within two days starting with sample acquisition. Steps necessary towards establishing metagenomic sequencing as a more routine approach in plant diseases clinics are discussed.}, } @article {pmid39752256, year = {2025}, author = {Chen, X and Toth, CRA and Guo, S and Luo, F and Howe, J and Nesbo, CL and Edwards, EA}, title = {Visualization of Syntrophic Benzene-Fermenting Desulfobacterota ORM2 in a Methanogenic Enrichment Culture Using Fluorescence In Situ Hybridization.}, journal = {Environmental science & technology}, volume = {59}, number = {1}, pages = {591-602}, doi = {10.1021/acs.est.4c08254}, pmid = {39752256}, issn = {1520-5851}, mesh = {*In Situ Hybridization, Fluorescence ; *Benzene/metabolism ; Methane/metabolism ; Fermentation ; Biodegradation, Environmental ; Deltaproteobacteria/metabolism/genetics ; }, abstract = {Benzene degradation under anoxic conditions was first reported more than 25 years ago; however, the activation mechanism in the absence of oxygen remains elusive. Progress has been hindered by the difficulty in cultivating anaerobic benzene-degrading enrichment cultures. Our laboratory has sustained a methanogenic enrichment culture harboring Desulfobacterota ORM2, a benzene fermenter distinct from any known genus but related to other known or predicted benzene degraders. ORM2's slow doubling time (∼30 days) and extended lag phase after inoculation complicate its study. We developed a fluorescent in situ hybridization (FISH) probe for ORM2, revealing rod-shaped cells of variable length that tend to cluster with other organisms, particularly methanogens. Microscopy and genomic evidence suggest that ORM2 may produce extracellular polymeric substances, facilitating cell aggregation and possibly consuming energy that contributes to the lag phase. Interestingly, higher benzene concentrations (90-120 mg/L) appeared to reduce cell aggregation. This study visualized the cells of Desulfobacterota ORM2 within a methanogenic community, offering insights into spatial organization and potential strategies to enhance its growth rate.}, } @article {pmid39752189, year = {2025}, author = {Bloomfield, SJ and Hildebrand, F and Zomer, AL and Palau, R and Mather, AE}, title = {Ecological insights into the microbiology of food using metagenomics and its potential surveillance applications.}, journal = {Microbial genomics}, volume = {11}, number = {1}, pages = {}, doi = {10.1099/mgen.0.001337}, pmid = {39752189}, issn = {2057-5858}, mesh = {*Metagenomics/methods ; *Food Microbiology ; Metagenome ; Bacteria/genetics/classification/isolation & purification ; Salmonella/genetics/isolation & purification/classification ; Drug Resistance, Bacterial/genetics ; Escherichia coli/genetics/isolation & purification/classification ; }, abstract = {A diverse array of micro-organisms can be found on food, including those that are pathogenic or resistant to antimicrobial drugs. Metagenomics involves extracting and sequencing the DNA of all micro-organisms on a sample, and here, we used a combination of culture and culture-independent approaches to investigate the microbial ecology of food to assess the potential application of metagenomics for the microbial surveillance of food. We cultured common foodborne pathogens and other organisms including Escherichia coli, Klebsiella/Raoultella spp., Salmonella spp. and Vibrio spp. from five different food commodities and compared their genomes to the microbial communities obtained by metagenomic sequencing following host (food) DNA depletion. The microbial populations of retail food were found to be predominated by psychrotrophic bacteria, driven by the cool temperatures in which the food products are stored. Pathogens accounted for a small percentage of the food metagenome compared to the psychrotrophic bacteria, and cultured pathogens were inconsistently identified in the metagenome data. The microbial composition of food varied amongst different commodities, and metagenomics was able to classify the taxonomic origin of 59% of antimicrobial resistance genes (ARGs) found on food to the genus level, but it was unclear what percentage of ARGs were associated with mobile genetic elements and thus transferable to other bacteria. Metagenomics may be used to survey the ARG burden, composition and carriage on foods to which consumers are exposed. However, food metagenomics, even after depleting host DNA, inconsistently identifies pathogens without enrichment or further bait capture.}, } @article {pmid39749666, year = {2024}, author = {Defazio, G and Tangaro, MA and Pesole, G and Fosso, B}, title = {kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {1}, pages = {}, pmid = {39749666}, issn = {1477-4054}, support = {CN_00000013//National Centre on High-Performance Computing, Big Data and Quantum Computing/ ; PNC0000002//Complementary National Plan PNC-I.1/ ; CUP H93C22000560003//Life Science Hub Puglia/ ; }, mesh = {*Metagenome ; *Software ; *Metagenomics/methods ; *Algorithms ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; Microbiota/genetics ; }, abstract = {The advent of high-throughput sequencing (HTS) technologies unlocked the complexity of the microbial world through the development of metagenomics, which now provides an unprecedented and comprehensive overview of its taxonomic and functional contribution in a huge variety of macro- and micro-ecosystems. In particular, shotgun metagenomics allows the reconstruction of microbial genomes, through the assembly of reads into MAGs (metagenome-assembled genomes). In fact, MAGs represent an information-rich proxy for inferring the taxonomic composition and the functional contribution of microbiomes, even if the relevant analytical approaches are not trivial and still improvable. In this regard, tools like CAMITAX and GTDBtk have implemented complex approaches, relying on marker gene identification and sequence alignments, requiring a large processing time. With the aim of deploying an effective tool for fast and reliable MAG taxonomic classification, we present here kMetaShot, a taxonomy classifier based on k-mer/minimizer counting. We benchmarked kMetaShot against CAMITAX and GTDBtk by using both in silico and real mock communities and demonstrated how, while implementing a fast and concise algorithm, it outperforms the other tools in terms of classification accuracy. Additionally, kMetaShot is an easy-to-install and easy-to-use bioinformatic tool that is also suitable for researchers with few command-line skills. It is available and documented at https://github.com/gdefazio/kMetaShot.}, } @article {pmid39749435, year = {2025}, author = {Allen, BS and Kidd, M and Sue, PK and Filkins, LM}, title = {A Committee-Based Diagnostic Stewardship Model for Pathogen Metagenomic Sequencing in Children.}, journal = {The journal of applied laboratory medicine}, volume = {10}, number = {1}, pages = {59-65}, doi = {10.1093/jalm/jfae084}, pmid = {39749435}, issn = {2576-9456}, mesh = {Humans ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Child ; Child, Preschool ; Infant ; Male ; Female ; Retrospective Studies ; Adolescent ; Cell-Free Nucleic Acids/blood ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) for pathogen detection offers the potential for broad pathogen detection directly from clinical specimens. However, the yield and impact of testing is variable, financial cost is high, and questions surrounding its optimal use remain. Our pediatric institution used a clinical committee-based approach to discuss and approve or deny mNGS test requests. In this study, we evaluate the patient characteristics for which mNGS testing was considered, test yield, and clinical impact of mNGS results when employing this model of diagnostic stewardship.

METHODS: Patients for which plasma cell-free DNA mNGS testing was requested and assessed by the clinical committee between August 1, 2018, and April 30, 2021, were included. The committee discussion emails were used to evaluate reasons for making the test request and treatment plans. Patient characteristics and additional clinical information were gathered by chart review. For approved cases, the clinical impact of the mNGS results were retrospectively adjudicated by infectious disease and clinical microbiology experts.

RESULTS: Twelve requests for plasma cell-free DNA mNGS were evaluated and 9 were approved. mNGS results led to a positive clinical management change in 55% of approved requests. Negative clinical impact of mNGS testing did not occur during the study. The patients for which testing requests were denied had resolution of symptoms without further intervention.

CONCLUSIONS: This committee-based test request approval diagnostic stewardship model has the potential to support high-yield mNGS testing while using healthcare resources responsibly.}, } @article {pmid39749434, year = {2025}, author = {Graf, EH and Bryan, A and Bowers, M and Grys, TE}, title = {One Size Fits Small: The Narrow Utility for Plasma Metagenomics.}, journal = {The journal of applied laboratory medicine}, volume = {10}, number = {1}, pages = {171-183}, doi = {10.1093/jalm/jfae122}, pmid = {39749434}, issn = {2576-9456}, mesh = {Humans ; *Metagenomics/methods ; Communicable Diseases/diagnosis/microbiology/blood ; }, abstract = {Metagenomic sequencing of plasma has been advertised by Karius, Inc. as a way to diagnose a variety of infectious syndromes. Due to the lack of robust evidence of clinical utility, our laboratory began actively stewarding Karius testing. Microbiology Directors recommended cancelation of Karius orders when certain criteria were identified. We set out to review Karius test requests in a 52-month period of stewardship, during which we recommended cancellation on 21 of 57 orders (37%). Of Karius tests sent on samples with negative conventional testing, only 3 (7%) had positive results for Karius with plausible explanatory etiologies. Of these three cases, two were empirically covered for the positive finding without improvement and one case was never treated. Twelve (29%) had positive results that were noted by infectious diseases (ID) to reflect insignificant detections. Given the 4-fold higher detection of insignificant Karius results, we set out to systematically analyze the literature for the experience of insignificant detections at other centers. When we compared studies that included healthy controls or had clinical adjudication of positive Karius findings by ID physicians, we found a median of 17.5% of individual patients that had positive insignificant detections of potential pathogenic bacteria or fungi. The most frequently detected species were as likely to be clinically adjudicated to be insignificant as they were to be significant within the same studies. Overall, these findings highlight limited utility of Karius testing and a need for careful stewardship, not only to ensure it is sent on patients who may benefit, but also to ensure results of potential pathogens are interpreted cautiously.}, } @article {pmid39749183, year = {2024}, author = {Indio, V and Gonzales-Barron, U and Oliveri, C and Lucchi, A and Valero, A and Achemchem, F and Manfreda, G and Savini, F and Serraino, A and De Cesare, A}, title = {Comparative analysis of the microbiome composition of artisanal cheeses produced in the Mediterranean area.}, journal = {Italian journal of food safety}, volume = {13}, number = {4}, pages = {12818}, pmid = {39749183}, issn = {2239-7132}, abstract = {In the PRIMA project ArtiSaneFood, the microbiological parameters of several artisanal cheeses produced in the Mediterranean area have been quantified. In this pilot study, we selected four of these artisanal cheese products from Italy, Portugal, Spain, and Morocco to investigate and compare their microbiomes in terms of taxonomic composition, presence of reads of foodborne pathogens, as well as virulence and antimicrobial resistance genes. Lactococcus, Streptococcus and Lactobacillus were the most represented genera in the Portuguese and Spanish cheeses, Streptococcus in the Italian cheese, and Enterococcus, Klebsiella, Escherichia, and Citrobacter in the Moroccan products. The correlation analysis indicated a negative association between the abundance of some lactic acid bacteria (i.e., Lactococcus, Lactobacillus, Streptococcus, and Leuconostoc) and foodborne pathogenic genera, like Escherichia and Salmonella. The analysis of pathogen abundance, virulence factors, and antimicrobial resistance genes showed a strong clusterization based on the cheese type, confirming that the presence of potential human health risk determinants was higher in the artisanal products derived from unpasteurized milk that underwent spontaneous fermentation.}, } @article {pmid39749179, year = {2024}, author = {Troja, F and Indio, V and Savini, F and Seguino, A and Serraino, A and Fuschi, A and Remondini, D and De Cesare, A}, title = {Monitoring and preventing foodborne outbreaks: are we missing wastewater as a key data source?.}, journal = {Italian journal of food safety}, volume = {13}, number = {4}, pages = {12725}, pmid = {39749179}, issn = {2239-7132}, abstract = {In 2022, the number of foodborne outbreaks in Europe increased by 43.9%, highlighting the need to improve surveillance systems and design outbreak predictive tools. This review aims to assess the scientific literature describing wastewater surveillance to monitor foodborne pathogens in association with clinical data. In the selected studies, the relationship between peaks of pathogen concentration in wastewater and reported clinical cases is described. Moreover, details on analytical methods to detect and quantify pathogens as well as wastewater sampling procedures are discussed. Few papers show a statistically significant correlation between high concentrations of foodborne pathogens in wastewater and the occurrence of clinical cases. However, monitoring pathogen concentration in wastewater looks like a promising and cost-effective strategy to improve foodborne outbreak surveillance. Such a strategy can be articulated in three steps, where the first one is testing wastewater with an untargeted method, like shotgun metagenomic, to detect microorganisms belonging to different domains. The second consists of testing wastewater with a targeted method, such as quantitative polymerase chain reaction, to quantify those specific pathogens that in the metagenomic dataset display an increasing trend or exceed baseline concentration thresholds. The third involves the integrated wastewater and clinical data analysis and modeling to find meaningful epidemiological correlations and make predictions.}, } @article {pmid39748884, year = {2024}, author = {Zhou, H and Pei, Y and Xie, Q and Nie, W and Liu, X and Xia, H and Jiang, J}, title = {Diagnosis and insight into the unique lung microbiota of pediatric pulmonary tuberculosis patients by bronchoalveolar lavage using metagenomic next-generation sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1492881}, pmid = {39748884}, issn = {2235-2988}, mesh = {Humans ; *Tuberculosis, Pulmonary/diagnosis/microbiology ; Female ; *Bronchoalveolar Lavage Fluid/microbiology ; *High-Throughput Nucleotide Sequencing ; Male ; Child ; *Microbiota/genetics ; *Lung/microbiology ; Child, Preschool ; *Metagenomics/methods ; Sensitivity and Specificity ; Adolescent ; Mycobacterium tuberculosis/genetics/isolation & purification ; Infant ; Bronchoalveolar Lavage ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Although previous studies have reported the dysregulation of respiratory tract microbiota in infectious diseases, insufficient data exist regarding respiratory microbiota imbalances in the lower respiratory tracts of children with pulmonary tuberculosis (PTB). In this study, we assessed the value of mNGS in the pathogen diagnosis and microbiome analysis of PTB patients using bronchoalveolar lavage fluid (BALF) samples.

METHODS: A total of 64 participants, comprising 43 pediatric PTB and 21 pediatric pneumonia patients were recruited in the present study. BALF samples were collected from the above participants. Parallel comparisons between mNGS and conventional microbial test (CMT) pathogen detection were performed. Moreover, the diversity and structure of all 64 patients' lung BALF microbiomes were explored using the mNGS data.

RESULTS: Comparing to the final clinical diagnosis, mNGS in BALF samples produced a sensitivity of 46.51%, which was lower than that of TB-PCR (55.00%) and Xpert (55.00%). The diagnostic efficacy of PTB can be highly enhanced by mNGS combined with TB-PCR (AUC=0.8140, P<0.0001). There were no significant differences in the diversity either between patients with TB and pneumonia. Positive mNGS pathogen results in pediatric PTB patients significantly affect the β-diversity of the pulmonary microbiota. In addition, significant taxonomic differences were found in BALF specimens from patients with PTB and pneumonia, both of which have unique bacterial compositions.

CONCLUSIONS: mNGS is valuable in the etiological diagnosis of PTB, and can reveal pulmonary microecological characteristics. For pediatric PTB patients, the mNGS should be implemented early and complementary to CMTs.}, } @article {pmid39748068, year = {2025}, author = {Li, S and Ma, X and Mei, H and Chang, X and He, P and Sun, L and Xiao, H and Wang, S and Li, R}, title = {Association between gut microbiota and short-chain fatty acids in children with obesity.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {483}, pmid = {39748068}, issn = {2045-2322}, support = {2019ZYYD051//the Special Projects for the Central Government to Guide the Development of Local Science and Technology/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Child ; Male ; *Fatty Acids, Volatile/metabolism/blood ; Female ; Adolescent ; *Pediatric Obesity/microbiology/metabolism/blood ; Case-Control Studies ; Feces/microbiology ; Metabolome ; Metagenomics/methods ; Body Mass Index ; }, abstract = {The gut microbiome and its metabolites may be important role in regulating the pathogenesis of obesity. This study aimed to characterize the gut microbiome and short-chain fatty acid (SCFA) metabolome in obese children. This case-control study recruited children aged 7‒14 years and divided them into a normal group (NG) and an obese group (OG) based on their body mass index. Whole-genome shotgun metagenomic analysis was performed on fecal samples from the OG and NG groups to characterize the signatures and functional potential of the gut microbiota. Serum metabolite profiles were analyzed using high-performance liquid chromatography/mass spectrometry (LC/MS). The Statistical Package for the Social Sciences (SPSS, version 26) and R software were used for data analysis. A total of 99 children were recruited, with 49 in the OG and 50 in the NG. At the phylum level, Proteobacteria were significantly more abundant in children in the OG than those in the NG. At the genus level, Oscillibacter and Alistipes were significantly lower in children in the OG than those in the NG. Caproate levels significantly increased, whereas butyrate and isobutyrate levels decreased in children in the OG than those in the NG. Kyoto encyclopedia of genes and genomes (KEGG) functional analysis revealed 28 enriched KEGG pathways, of which/with the phosphotransferase system (PTS) and enhanced biofilm formation by Escherichia coli were particularly significant in the OG. Spearman's correlation analysis indicated that the genus Oscillibacter and species Clostridium_sp._CAG:302 connect serum metabolites and the gut microbiota in childhood obesity. Childhood obesity is correlated with the symbiotic status of the gut microbiota. The microbiota influences human metabolism via specific pathways, particularly butyrate, caproate, and the genus Oscillibacter, all closely associated with obesity.}, } @article {pmid39747695, year = {2025}, author = {Wang, X and Fang, Y and Liang, W and Cai, Y and Wong, CC and Wang, J and Wang, N and Lau, HC and Jiao, Y and Zhou, X and Ye, L and Mo, M and Yang, T and Fan, M and Song, L and Zhou, H and Zhao, Q and Chu, ES and Liang, M and Liu, W and Liu, X and Zhang, S and Shang, H and Wei, H and Li, X and Xu, L and Liao, B and Sung, JJY and Kuang, M and Yu, J}, title = {Gut-liver translocation of pathogen Klebsiella pneumoniae promotes hepatocellular carcinoma in mice.}, journal = {Nature microbiology}, volume = {10}, number = {1}, pages = {169-184}, pmid = {39747695}, issn = {2058-5276}, support = {82173191//National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)/ ; }, mesh = {Animals ; *Carcinoma, Hepatocellular/microbiology/pathology ; *Klebsiella pneumoniae/pathogenicity/genetics ; Mice ; *Liver Neoplasms/microbiology/pathology/metabolism ; Humans ; *Toll-Like Receptor 4/metabolism/genetics ; *Gastrointestinal Microbiome ; *Klebsiella Infections/microbiology ; *Bacterial Translocation ; *Liver/microbiology/pathology ; Fecal Microbiota Transplantation ; Disease Models, Animal ; Mice, Inbred C57BL ; Male ; Carcinogenesis ; Cell Proliferation ; Bacterial Proteins/metabolism/genetics ; }, abstract = {Hepatocellular carcinoma (HCC) is accompanied by an altered gut microbiota but whether the latter contributes to carcinogenesis is unclear. Here we show that faecal microbiota transplantation (FMT) using stool samples from patients with HCC spontaneously initiate liver inflammation, fibrosis and dysplasia in wild-type mice, and accelerate disease progression in a mouse model of HCC. We find that HCC-FMT results in gut barrier injury and translocation of live bacteria to the liver. Metagenomic analyses and bacterial culture of liver tissues reveal enrichment of the gut pathogen Klebsiella pneumoniae in patients with HCC and mice transplanted with the HCC microbiota. Moreover, K. pneumoniae monocolonization recapitulates the effect of HCC-FMT in promoting liver inflammation and hepatocarcinogenesis. Mechanistically, K. pneumoniae surface protein PBP1B interacts with and activates TLR4 on HCC cells, leading to increased cell proliferation and activation of oncogenic signalling. Targeting gut colonization using K. oxytoca or TLR4 inhibition represses K. pneumoniae-induced HCC progression. These findings indicate a role for an altered gut microbiota in hepatocarcinogenesis.}, } @article {pmid39747694, year = {2025}, author = {Hsu, TY and Nzabarushimana, E and Wong, D and Luo, C and Beiko, RG and Langille, M and Huttenhower, C and Nguyen, LH and Franzosa, EA}, title = {Profiling lateral gene transfer events in the human microbiome using WAAFLE.}, journal = {Nature microbiology}, volume = {10}, number = {1}, pages = {94-111}, pmid = {39747694}, issn = {2058-5276}, support = {K23DK125838//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; R24DK110499//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; Research Scholars Award//American Gastroenterological Association (AGA)/ ; Career Development Award//Crohn's and Colitis Foundation (Crohn's & Colitis Foundation)/ ; T32CA009001//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; U54DE023798//U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; }, mesh = {Humans ; *Gene Transfer, Horizontal ; *Microbiota/genetics ; *Metagenome ; *Phylogeny ; *Algorithms ; Bacteria/genetics/classification/isolation & purification ; Metagenomics/methods ; Genome, Bacterial ; Computational Biology/methods ; }, abstract = {Lateral gene transfer (LGT), also known as horizontal gene transfer, facilitates genomic diversification in microbial populations. While previous work has surveyed LGT in human-associated microbial isolate genomes, the landscape of LGT arising in personal microbiomes is not well understood, as there are no widely adopted methods to characterize LGT from complex communities. Here we developed, benchmarked and validated a computational algorithm (WAAFLE or Workflow to Annotate Assemblies and Find LGT Events) to profile LGT from assembled metagenomes. WAAFLE prioritizes specificity while maintaining high sensitivity for intergenus LGT. Applying WAAFLE to >2,000 human metagenomes from diverse body sites, we identified >100,000 high-confidence previously uncharacterized LGT (~2 per microbial genome-equivalent). These were enriched for mobile elements, as well as restriction-modification functions associated with the destruction of foreign DNA. LGT frequency was influenced by biogeography, phylogenetic similarity of involved pairs (for example, Fusobacterium periodonticum and F. nucleatum) and donor abundance. These forces manifest as networks in which hub taxa donate unequally with phylogenetic neighbours. Our findings suggest that human microbiome LGT may be more ubiquitous than previously described.}, } @article {pmid39747693, year = {2025}, author = {Michoud, G and Peter, H and Busi, SB and Bourquin, M and Kohler, TJ and Geers, A and Ezzat, L and , and Battin, TJ}, title = {Mapping the metagenomic diversity of the multi-kingdom glacier-fed stream microbiome.}, journal = {Nature microbiology}, volume = {10}, number = {1}, pages = {217-230}, pmid = {39747693}, issn = {2058-5276}, support = {Vanishing Glaciers Project//NOMIS Stiftung (NOMIS Foundation)/ ; }, mesh = {*Microbiota/genetics ; *Rivers/microbiology ; *Metagenome ; *Bacteria/genetics/classification/isolation & purification ; *Ice Cover/microbiology ; Biofilms/growth & development ; Metagenomics ; Fungi/genetics/classification ; Geologic Sediments/microbiology ; Ecosystem ; Viruses/genetics/classification ; Biodiversity ; Phylogeny ; }, abstract = {Glacier-fed streams (GFS) feature among Earth's most extreme aquatic ecosystems marked by pronounced oligotrophy and environmental fluctuations. Microorganisms mainly organize in biofilms within them, but how they cope with such conditions is unknown. Here, leveraging 156 metagenomes from the Vanishing Glaciers project obtained from sediment samples in GFS from 9 mountains ranges, we report thousands of metagenome-assembled genomes (MAGs) encompassing prokaryotes, algae, fungi and viruses, that shed light on biotic interactions within glacier-fed stream biofilms. A total of 2,855 bacterial MAGs were characterized by diverse strategies to exploit inorganic and organic energy sources, in part via functional redundancy and mixotrophy. We show that biofilms probably become more complex and switch from chemoautotrophy to heterotrophy as algal biomass increases in GFS owing to glacier shrinkage. Our MAG compendium sheds light on the success of microbial life in GFS and provides a resource for future research on a microbiome potentially impacted by climate change.}, } @article {pmid39747692, year = {2025}, author = {Olm, MR and Spencer, SP and Takeuchi, T and Silva, EL and Sonnenburg, JL}, title = {Metagenomic immunoglobulin sequencing reveals IgA coating of microbial strains in the healthy human gut.}, journal = {Nature microbiology}, volume = {10}, number = {1}, pages = {112-125}, pmid = {39747692}, issn = {2058-5276}, support = {T32DK007056//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; K08DK134856//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; K08 DK134856/DK/NIDDK NIH HHS/United States ; DP1AT009892//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; T32 DK007056/DK/NIDDK NIH HHS/United States ; F32DK128865//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; }, mesh = {Humans ; *Immunoglobulin A/immunology ; *Gastrointestinal Microbiome/genetics ; *Feces/microbiology ; *Metagenomics/methods ; *Bacteria/genetics/classification/immunology/metabolism ; Host Microbial Interactions/immunology ; Healthy Volunteers ; Intestinal Mucosa/microbiology/immunology/metabolism ; }, abstract = {IgA, the primary human antibody secreted from the gut mucosa, shapes the intestinal microbiota. Methodological limitations have hindered defining which microbial strains are targeted by IgA and the implications of binding. Here we develop a technique, metagenomic immunoglobulin sequencing (MIg-seq), that provides strain-level resolution of microbes coated by IgA and use it to determine IgA coating levels for 3,520 gut microbiome strains in healthy human faeces. We find that both health and disease-associated bacteria are targeted by IgA. Microbial genes are highly predictive of IgA binding levels; in particular, mucus degradation genes are correlated with high binding, and replication rates are significantly reduced for microbes bound by IgA. We demonstrate that IgA binding is more correlated with host immune status than traditional relative abundance measures of microbial community composition. This study introduces a powerful technique for assessing strain-level IgA binding in human stool, paving the way for deeper understanding of IgA-based host-microbe interactions.}, } @article {pmid39747535, year = {2025}, author = {Wongsamart, R and Somboonna, N and Cheibchalard, T and Klankeo, P and Ruampatana, J and Nuntapaitoon, M}, title = {Probiotic Bacillus licheniformis DSMZ 28710 improves sow milk microbiota and enhances piglet health outcomes.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {17}, pmid = {39747535}, issn = {2045-2322}, support = {764002-DT//Ratchadapisek Sompoch Endowment Fund 2021/ ; 764002-DT//Ratchadapisek Sompoch Endowment Fund 2021/ ; //the Second Century Fund (C2F)/ ; //the Second Century Fund (C2F)/ ; //the Second Century Fund (C2F)/ ; //the Second Century Fund (C2F)/ ; CU_FRB65_hea(68)_131_23_61//Thailand Research Fund, Thailand Science Research and Innovation Fund Chulalongkorn University/ ; FOOD_FF_68_013_3100_003//Thailand Research Fund, Thailand Science Research and Innovation Fund Chulalongkorn University/ ; }, mesh = {Animals ; *Probiotics/administration & dosage ; Swine ; *Milk/microbiology ; *Microbiota ; *Bacillus licheniformis ; RNA, Ribosomal, 16S/genetics ; Female ; Colostrum/microbiology ; Dietary Supplements ; Animal Feed ; }, abstract = {Maintaining a diverse and balanced sow milk microbiome is essential to piglet development. Thus, this study aimed to examine the effects of probiotic Bacillus licheniformis supplementation on the microbiome composition of sow colostrum and milk, and to review associated health findings in piglets. B. licheniformis DSMZ 28710 was supplemented at 10 g/day as feed additive before predicted farrowing until weaning by top dressing. Colostrum and milk samples were collected for metagenomic DNA extraction, 16s rRNA sequencing, and bioinformatics analyses for bacterial microbiota diversity. Results indicated that the supplementation increased the abundances of beneficial bacteria, such as Lactobacillus, Pediococcus, Bacteroides, and Bifidobacterium, while decreasing the abundances of pathogenic bacteria, such as Staphylococcus aureus, Enterobacteriaceae, and Campylobacter in the colostrum. The supplementation increased diversity while maintaining richness and evenness. Moreover, the rise in predicted microbial community metabolic function in membrane transport pathways provides crucial evidence showing that the supplementation is potentially beneficial to piglets, as these pathways are important for providing nutrients and immunity to offspring. This research highlights the importance of microbiome composition in sow milk and the potential of B. licheniformis supplementation as a means to improve piglet health and development.}, } @article {pmid39747287, year = {2025}, author = {Delgadillo, DR and Borelli, JL and Mayer, EA and Labus, JS and Cross, MP and Pressman, SD}, title = {Biological, environmental, and psychological stress and the human gut microbiome in healthy adults.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {362}, pmid = {39747287}, issn = {2045-2322}, mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; Adult ; *Stress, Psychological/microbiology ; Male ; *RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Phylogeny ; Middle Aged ; Metagenome ; }, abstract = {Emerging research suggests that the gut microbiome plays a crucial role in stress. We assess stress-microbiome associations in two samples of healthy adults across three stress domains (perceived stress, stressful life events, and biological stress /Respiratory Sinus Arrhythmia; RSA). Study 1 (n = 62; mean-age = 37.3 years; 68% female) and Study 2 (n = 74; mean-age = 41.6 years; female only) measured RSA during laboratory stressors and used 16S rRNA pyrosequencing to classify gut microbial composition from fecal samples. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States was used to predict functional pathways of metagenomes. Results showed differences in beta diversity between high and low stressful life events groups across both studies. Study 1 revealed differences in beta diversity between high and low RSA groups. In Study 1, the low perceived stress group was higher in alpha diversity than the high perceived stress group. Levels of Clostridium were negatively associated with RSA in Study 1 and levels Escherichia/Shigella were positively associated with perceived stress in Study 2. Associations between microbial functional pathways (L-lysine production and formaldehyde absorption) and RSA are discussed. Findings suggest that certain features of the gut microbiome are differentially associated with each stress domain.}, } @article {pmid39747236, year = {2025}, author = {Roberts Kingman, GA and Kipness, JL and Rothschild, LJ}, title = {Raiding nature's genetic toolbox for UV-C resistance by functional metagenomics.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {223}, pmid = {39747236}, issn = {2045-2322}, mesh = {*Metagenomics/methods ; *Ultraviolet Rays ; }, abstract = {As we assess the habitability of other worlds, we are limited by being able to only study terrestrial life adapted to terrestrial conditions. The environments found on Earth, though tremendously diverse, do not approach the multitude of potentially habitable environments beyond Earth, and so limited terrestrial adaptive capabilities tell us little about the fundamental biochemical boundaries of life. One approach to this problem is to use experimental laboratory evolution to adapt microbes to these novel environmental conditions. This approach can be dramatically improved through functional metagenomics, large-scale introduction of foreign genetic material to screen for phenotypes in a new host organism. This takes advantage of Earth's immense biological diversity with high-throughput screening for genetic tools that can facilitate adaptation. We address a key gap in functional metagenomics work by exploring the impact of the experimental parameters chosen for functional metagenomics libraries. Experimental design dictates both fragment size and copy number, and we show that both can have outsized effects on the resultant phenotypes in non-intuitive ways. These results highlight the potential of functional metagenomics for adapting life rapidly to challenging new environments, with important implications in both astrobiology and bioindustry, while also emphasizing the impacts of decisions in experimental design.}, } @article {pmid39746973, year = {2025}, author = {Inskeep, WP and Jay, ZJ and McKay, LJ and Dlakić, M}, title = {Respiratory processes of early-evolved hyperthermophiles in sulfidic and low-oxygen geothermal microbial communities.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {277}, pmid = {39746973}, issn = {2041-1723}, support = {1950770//National Science Foundation (NSF)/ ; }, mesh = {Hot Springs/microbiology ; *Pyrobaculum/classification/enzymology/genetics ; *Microbiota ; *Hot Temperature ; *Bacteria/classification/enzymology/genetics ; Anaerobiosis ; Electron Transport ; *Sulfur/metabolism ; *Arsenic/metabolism ; *Cytochrome b Group/metabolism ; *Oxidoreductases/metabolism ; Geothermal Energy ; Phylogeny ; Energy Metabolism ; }, abstract = {Thermophilic microbial communities growing in low-oxygen environments often contain early-evolved archaea and bacteria, which hold clues regarding mechanisms of cellular respiration relevant to early life. Here, we conducted replicate metagenomic, metatranscriptomic, microscopic, and geochemical analyses on two hyperthermophilic (82-84 °C) filamentous microbial communities (Conch and Octopus Springs, Yellowstone National Park, WY) to understand the role of oxygen, sulfur, and arsenic in energy conservation and community composition. We report that hyperthermophiles within the Aquificota (Thermocrinis), Pyropristinus (Caldipriscus), and Thermoproteota (Pyrobaculum) are abundant in both communities; however, higher oxygen results in a greater diversity of aerobic heterotrophs. Metatranscriptomics revealed major shifts in respiratory pathways of keystone chemolithotrophs due to differences in oxygen versus sulfide. Specifically, early-evolved hyperthermophiles express high levels of high-affinity cytochrome bd and CydAA' oxidases in suboxic sulfidic environments and low-affinity heme Cu oxidases under microaerobic conditions. These energy-conservation mechanisms using cytochrome oxidases in high-temperature, low-oxygen habitats likely played a crucial role in the early evolution of microbial life.}, } @article {pmid39746693, year = {2024}, author = {Wang, ZH and Li, LH and Xue, SL and Zhu, ZL and Xu, J and Lu, TY and Wang, Y and Qiu, HY and Han, Y and Chen, SN and Tang, XW and Jin, ZM and Li, CX and Sun, AN and Wu, DP}, title = {[Reactivation of cytomegalovirus and its influencing factors in patients with B-lymphocyte malignancy after CAR-T cell therapy].}, journal = {Zhonghua xue ye xue za zhi = Zhonghua xueyexue zazhi}, volume = {45}, number = {11}, pages = {1005-1009}, doi = {10.3760/cma.j.cn121090-20240703-00249}, pmid = {39746693}, issn = {0253-2727}, mesh = {Humans ; Retrospective Studies ; *Cytomegalovirus ; *Cytomegalovirus Infections/therapy ; *Immunotherapy, Adoptive/methods ; *Virus Activation ; Risk Factors ; B-Lymphocytes ; Male ; Female ; Antibodies, Monoclonal, Humanized ; }, abstract = {Objective: This study aimed to analyze cytomegalovirus (CMV) reactivation and its influencing factors in patients with B-lymphocyte malignancy who received chimeric antigen receptor T (CAR-T) cell therapy. Methods: This study retrospectively reviewed patients with B-lymphocyte malignancy who received CAR-T cell therapy in the First Affiliated Hospital of Soochow University from January 2021 to December 2023. The data of patients who underwent CMV-DNA detection and/or pathogen metagenomic sequencing twice or more within 100 days after CAR-T cell therapy were analyzed. The clinical characteristics of the CMV reactivation and non-activation groups were compared. The factors related to CMV reactivation were analyzed with the Chi-square test and nonparametric rank sum test, and the risk factors were examined with Logistic regression. Results: This study included 86 patients, among whom 18 (20.9%) had CMV reactivation, and the median time of reactivation was 20 (1-95) days. All of the 18 patients had CMV viremia, and no CMV disease was observed. Seven patients turned to the latent state after continuing acyclovir antiviral therapy, and 11 patients returned to the latent state after upgrading the antiviral therapy to first-line drugs, including ganciclovir and foscarnet sodium. Six or more courses of anti-tumor treatment before CAR-T cell therapy, allogeneic hematopoietic stem cell transplantation within 2 years before CAR-T cell therapy, non-remission before treatment, and the use of high-dose glucocorticoids and/or tocilizumab were related to CMV reactivation, among which allogeneic hematopoietic stem cell transplantation within 2 years pre-treatment and the use of high-dose glucocorticoids and/or tocilizumab treatment were independent risk factors for CMV reactivation. Conclusion: Patients with B-lymphocyte malignancy who received CAR-T cell therapy have the risk of CMV reactivation, especially for those who received allogeneic hematopoietic stem cell transplantation within 2 years pre-treatment and those who received high-dose glucocorticoids and/or tocilizumab treatment.}, } @article {pmid39746689, year = {2024}, author = {Feng, SZ and Xu, CH}, title = {[Improving the application of metagenomic next-generation sequencing for pathogen diagnosis in infections related to hematological diseases].}, journal = {Zhonghua xue ye xue za zhi = Zhonghua xueyexue zazhi}, volume = {45}, number = {11}, pages = {982-985}, doi = {10.3760/cma.j.cn121090-20241029-00423}, pmid = {39746689}, issn = {0253-2727}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Hematologic Diseases/diagnosis/complications ; *Metagenomics/methods ; Communicable Diseases/diagnosis ; }, abstract = {Patients with hematologic diseases are prone to infections, and infection-related mortality is high in this population. Accurate diagnosis of infectious pathogens is crucial; however, conventional microbiological testing often fails to meet clinical needs, presenting a significant challenge in clinical practice. Metagenomic next-generation sequencing (mNGS), with its high sensitivity, broad coverage, and short turnaround time, has been widely adopted in diagnosing infectious diseases. This article focuses on the application of mNGS technology in diagnosing infectious pathogens in patients with hematologic diseases. It analyzes the challenges encountered in clinical practice and explores future trends in the field. This work aims to provide clinicians with an in-depth understanding of the value and limitations of mNGS in diagnosing infections in hematologic patients, and to promote its rational application.}, } @article {pmid39745461, year = {2025}, author = {Filho, RM and Mengoni, C and Bruno, JS and Fregnani, ER and Segata, N and Camargo, AA and Heidrich, V}, title = {Metagenome-assembled genomes from irradiated human dental plaque.}, journal = {Microbiology resource announcements}, volume = {14}, number = {2}, pages = {e0091724}, pmid = {39745461}, issn = {2576-098X}, abstract = {We provide 309 quality-controlled bacterial metagenome-assembled genomes recovered from supragingival plaque metagenomes. Samples were collected from head and neck cancer patients following radiotherapy, so the recovered genomes can be useful to investigate the effects of oral cavity irradiation on oral microbiome members.}, } @article {pmid39745444, year = {2025}, author = {Jiang, X and Ma, W}, title = {Metagenome-assembled genome of Staphylococcus nepalensis from urban bats in China.}, journal = {Microbiology resource announcements}, volume = {14}, number = {2}, pages = {e0122224}, pmid = {39745444}, issn = {2576-098X}, abstract = {We conducted metagenomic sequencing on a stool sample collected from urban-dwelling Pipistrellus abramus and obtained a metagenome-assembled genome of Staphylococcus nepalensis. Phylogenetic analysis revealed that this strain is closely related to the one isolated from dogs, forming a distinct clade separate from the reference genome.}, } @article {pmid39745433, year = {2025}, author = {Grüterich, L and Woodhouse, JN and Mueller, P and Tiemann, A and Ruscheweyh, H-J and Sunagawa, S and Grossart, H-P and Streit, WR}, title = {Assessing environmental gradients in relation to dark CO2 fixation in estuarine wetland microbiomes.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {1}, pages = {e0217724}, pmid = {39745433}, issn = {1098-5336}, support = {407270017//Deutsche Forschungsgemeinschaft (DFG)/ ; 502681570//Deutsche Forschungsgemeinschaft (DFG)/ ; }, mesh = {*Wetlands ; *Carbon Dioxide/metabolism ; *Microbiota ; *Estuaries ; *Carbon Cycle ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Soil Microbiology ; }, abstract = {UNLABELLED: The rising atmospheric concentration of CO2 is a major concern to society due to its global warming potential. In soils, CO2-fixing microorganisms are preventing some of the CO2 from entering the atmosphere. Yet, the controls of dark CO2 fixation are rarely studied in situ. Here, we examined the gene and transcript abundance of key genes involved in microbial CO2 fixation along major environmental gradients within estuarine wetlands. A combined multi-omics approach incorporating metabarcoding, deep metagenomic, and metatranscriptomic analyses confirmed that wetland microbiota harbor four out of seven known CO2 fixation pathways, namely, the Calvin cycle, reverse tricarboxylic acid cycle, Wood-Ljungdahl pathway, and reverse glycine pathway. These pathways are transcribed at high frequencies along several environmental gradients, albeit at different levels depending on the environmental niche. Notably, the transcription of the key genes for the reverse tricarboxylic acid cycle was associated with high nitrate concentration, while the transcription of key genes for the Wood-Ljungdahl pathway was favored by reducing, O2-poor conditions. The transcript abundance of the Calvin cycle was favored by niches high in organic matter. Taxonomic assignment of transcripts implied that dark CO2 fixation was mainly linked to a few bacterial phyla, namely, Desulfobacterota, Methylomirabilota, Nitrospirota, Chloroflexota, and Pseudomonadota.

IMPORTANCE: The increasing concentration of atmospheric CO2 has been identified as the primary driver of climate change and poses a major threat to human society. This work explores the mostly overlooked potential of light-independent CO2 fixation by soil microbes (a.k.a. dark CO2 fixation) in climate change mitigation efforts. Applying a combination of molecular microbial tools, our research provides new insights into the ecological niches where CO2-fixing pathways are most active. By identifying how environmental factors, like oxygen, salinity and organic matter availability, influence these pathways in an estuarine wetland environment, potential strategies for enhancing natural carbon sinks can be developed. The importance of our research is in advancing the understanding of microbial CO2 fixation and its potential role in the global climate system.}, } @article {pmid39745426, year = {2025}, author = {Gulyaeva, A and Liu, L and Garmaeva, S and Kruk, M and Weersma, RK and Harmsen, HJM and Zhernakova, A}, title = {Identification and characterization of Faecalibacterium prophages rich in diversity-generating retroelements.}, journal = {Microbiology spectrum}, volume = {13}, number = {2}, pages = {e0106624}, pmid = {39745426}, issn = {2165-0497}, mesh = {*Prophages/genetics/isolation & purification ; *Retroelements ; Humans ; *Metagenomics ; Genome, Viral/genetics ; Gastrointestinal Microbiome ; Computational Biology/methods ; Host Specificity ; Bacteriophages/genetics/classification/isolation & purification/physiology ; Genome, Bacterial/genetics ; Phylogeny ; Genetic Variation ; }, abstract = {Metagenomics has revealed the incredible diversity of phages within the human gut. However, very few of these phages have been subjected to in-depth experimental characterization. One promising method of obtaining novel phages for experimental characterization is through induction of the prophages integrated into the genomes of cultured gut bacteria. Here, we developed a bioinformatic approach to prophage identification that builds on prophage genomic properties, existing prophage-detecting software, and publicly available virome sequencing data. We applied our approach to 22 strains of bacteria belonging to the genus Faecalibacterium, resulting in identification of 15 candidate prophages, and validated the approach by demonstrating the activity of five prophages from four of the strains. The genomes of three active phages were identical or similar to those of known phages, while the other two active phages were not represented in the Viral RefSeq database. Four of the active phages possessed a diversity-generating retroelement (DGR), and one retroelement had two variable regions. DGRs of two phages were active at the time of the induction experiments, as evidenced by nucleotide variation in sequencing reads. We also predicted that the host range of two active phages may include multiple bacterial species. Finally, we noted that four phages were less prevalent in the metagenomes of inflammatory bowel disease patients compared to a general population cohort, a difference mainly explained by differences in the abundance of the host bacteria. Our study highlights the utility of prophage identification and induction for unraveling phage molecular mechanisms and ecological interactions.IMPORTANCEWhile hundreds of thousands of phage genomes have been discovered in metagenomics studies, only a few of these phages have been characterized experimentally. Here, we explore phage characterization through bioinformatic identification of prophages in genomes of cultured bacteria, followed by prophage induction. Using this approach, we detect the activity of five prophages in four strains of commensal gut bacteria Faecalibacterium. We further note that four of the prophages possess diversity-generating retroelements implicated in rapid mutation of phage genome loci associated with phage-host and phage-environment interactions and analyze the intricate patterns of retroelement activity. Our study highlights the potential of prophage characterization for elucidating complex molecular mechanisms employed by the phages.}, } @article {pmid39745394, year = {2024}, author = {Geers, AU and Michoud, G and Busi, SB and Peter, H and Kohler, TJ and Ezzat, L and , and Battin, TJ}, title = {Deciphering the biosynthetic landscape of biofilms in glacier-fed streams.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0113724}, doi = {10.1128/msystems.01137-24}, pmid = {39745394}, issn = {2379-5077}, abstract = {UNLABELLED: Glacier-fed streams are permanently cold, ultra-oligotrophic, and physically unstable environments, yet microbial life thrives in benthic biofilm communities. Within biofilms, microorganisms rely on secondary metabolites for communication and competition. However, the diversity and genetic potential of secondary metabolites in glacier-fed stream biofilms remain poorly understood. In this study, we present the first large-scale exploration of biosynthetic gene clusters (BGCs) from benthic glacier-fed stream biofilms sampled by the Vanishing Glaciers project from the world's major mountain ranges. We found a remarkable diversity of BGCs, with more than 8,000 of them identified within 2,868 prokaryotic metagenome-assembled genomes, some of them potentially conferring ecological advantages, such as UV protection and quorum sensing. The BGCs were distinct from those sourced from other aquatic microbiomes, with over 40% of them being novel. The glacier-fed stream BGCs exhibited the highest similarity to BGCs from glacier microbiomes. BGC composition displayed geographic patterns and correlated with prokaryotic alpha diversity. We also found that BGC diversity was positively associated with benthic chlorophyll a and prokaryotic diversity, indicative of more biotic interactions in more extensive biofilms. Our study provides new insights into a hitherto poorly explored microbial ecosystem, which is now changing at a rapid pace as glaciers are shrinking due to climate change.

IMPORTANCE: Glacier-fed streams are characterized by low temperatures, high turbidity, and high flow. They host a unique microbiome within biofilms, which form the foundation of the food web and contribute significantly to biogeochemical cycles. Our investigation into secondary metabolites, which likely play an important role in these complex ecosystems, found a unique genetic potential distinct from other aquatic environments. We found the potential to synthesize several secondary metabolites, which may confer ecological advantages, such as UV protection and quorum sensing. This biosynthetic diversity was positively associated with the abundance and complexity of the microbial community, as well as concentrations of chlorophyll a. In the face of climate change, our study offers new insights into a vanishing ecosystem.}, } @article {pmid39744910, year = {2024}, author = {de Moura Barbosa Leite, D and de Paula, TS and Hajdu, E}, title = {The complete mitochondrial genome of the deep-sea methanotrophic sponges Hymedesmia methanophila and Iophon methanophila: leveraging 'waste' in metagenomic data.}, journal = {Journal of genetics}, volume = {103}, number = {}, pages = {}, pmid = {39744910}, issn = {0973-7731}, mesh = {*Genome, Mitochondrial ; Animals ; *Porifera/microbiology/genetics ; *Phylogeny ; *Metagenomics/methods ; Methane/metabolism ; Metagenome ; High-Throughput Nucleotide Sequencing ; DNA, Mitochondrial/genetics ; RNA, Transfer/genetics ; }, abstract = {A significant proportion of next-generation sequencing (NGS) data ends up not being used since they comprise information out-of-scope of the primary studies. This 'waste' of potential can be harnessed to explore organellar genomes, such as the mitochondrial DNA, and be used for evolutionary, conservation and biodiversity research. We present the complete mitochondrial genomes of the deep-sea methanotrophic sponges Hymedesmia methanophila and Iophon methanophila (Demospongiae, Poecilosclerida) retrieved from previously published whole metagenome sequencing data. The predicted mitogenome of H. methanophila (18,657 bp) and I. methanophila (18,718 bp) present the characteristic arrangement observed among Poecilosclerida sponges. These mtDNAs encode the usual set of 14 proteins, two ribosomal RNA, and 24 or 23 transfer RNA genes, respectively, with intergenic regions amounting ~5% of their total length. The overall similarity of these mitogenomes to those of phylogenetic relatives, both in organization and divergence, suggests that neither their extremophilic habitat in asphalt seeps within the deep sea nor their symbiotic association with methaneoxidizing bacteria imposed a major influence on the evolution of their mitochondrial genome. This research shows how metagenomic data can be leveraged to extract additional genetic knowledge from primary metagenome sources, and by exploiting previously unexplored sequencing data, valuable information can be unlocked to shed light on the evolutionary dynamics of diverse organisms inhabiting extreme environments.}, } @article {pmid39744404, year = {2024}, author = {Adjele, JJB and Devi, P and Kumari, P and Yadav, A and Tchuenchieu Kamgain, AD and Mouafo, HT and Medoua, GN and Essia, JJN and Chauhan, NS and Pandey, R}, title = {Exploring the influence of age and diet on gut microbiota development in children during the first 5 years: a study from Yaoundé, Cameroon.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1512111}, pmid = {39744404}, issn = {1664-302X}, abstract = {INTRODUCTION: The development of the human gut microbiota is shaped by factors like delivery mode, infant feeding practices, maternal diet, and environmental conditions. Diet plays a pivotal role in determining the diversity and composition of the gut microbiome, which in turn impacts immune development and overall health during this critical period. The early years, which are vital for microbial shaping, highlight a gap in understanding how the shift from milk-based diets to solid foods influences gut microbiota development in infants and young children, particularly in Yaoundé, Cameroon.

METHODS: This study involved an analysis of the gut microbiota composition in 70 children aged ≤5 years through 16S rDNA gene metagenomic sequencing of fecal metagenomic DNA. The participants were grouped into four age categories: 0-6 months, 7-12 months, 13-24 months, and 25-60 months.

RESULTS: We observed a reduction in microbial diversity in the younger age groups, which increased progressively with age. At the taxonomic level, our analysis identified Firmicutes as the predominant phylum, with its abundance rising in older age groups, suggesting a maturation of the microbiota characterized by distinct genera associations. In the 0-6 month age group, we noted an enrichment of Lactobacilli and Bifidobacteria, which may play a crucial role in modulating and supporting immune system development during infancy. After 6 months, we found a higher prevalence of Clostridium, Bacillus, Roseburia, and Faecalibacterium, which are associated with fiber fermentation and the production of short-chain fatty acids (SCFAs).

CONCLUSION: These findings underscore the influence of milk products and complementary diets on gut microbiota across various age groups, promoting increased diversity essential for healthy gut development. More such studies in the LMICs would augment and strengthen understanding towards functional microbiome.}, } @article {pmid39744158, year = {2024}, author = {Jiménez-Arroyo, C and Molinero, N and Sabater, C and Margolles, A and Terrón-Camero, LC and Andrés-León, E and Ramos, M and Del Val, M and Moreno-Arribas, MV}, title = {Gut microbiome and clinical and lifestyle host factors associated with recurrent positive RT-PCR for SARS-CoV-2.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1494193}, pmid = {39744158}, issn = {2235-2988}, mesh = {Humans ; *COVID-19/microbiology/virology/diagnosis ; *Gastrointestinal Microbiome/genetics ; *SARS-CoV-2/genetics/isolation & purification ; Male ; Female ; Middle Aged ; *Feces/microbiology/virology ; Adult ; Metagenomics/methods ; Life Style ; Aged ; }, abstract = {BACKGROUND: SARS-CoV-2 and COVID-19 are still active in the population. Some patients remained PCR-positive for more than 4 weeks, called "persistently PCR-positive". Recent evidence suggests a link between the gut microbiota and susceptibility to COVID-19, although no studies have explored persistent PCR conditions. We aimed to evaluate the relationship between persistent positive SARS-CoV-2 RT-PCR, the gut microbiome, and individual host determinants.

METHODS: A shotgun metagenomic analysis was conducted on fecal samples from 28 individuals affected by COVID-19. Patients were divided into two groups: those who had cleared the virus within 30 days (designated as the control group) (n = 15), and those who remained PCR-positive beyond 30 days (called the PCR+ group) (n = 13). We also investigated the correlation between prolonged viral clearance and several additional factors, including clinical parameters, immune responses, microbial metabolites, and dietary habits.

RESULTS: The composition and functionality of the microbiome varied based on the duration of positivity as determined by PCR. Compared to the control group, the persistent PCR+ group exhibited elevated pathogen levels and augmented diversity in functional gene families (p-value < 0.05). A multi-omics analysis integrating metagenomics, metabolites, and metadata also revealed the specific contribution of certain blood markers in this group, including basophils, IgM, IgG (both general and specific for SARS-CoV-2), and markers of liver damage. Unhealthy diet was identified as a significant factor influencing the duration of PCR positivity.

CONCLUSIONS: These findings indicate that the gut microbiome may play a role in delayed viral clearance and persistent positive RT-PCR results. Our study also contributes to the understanding of the role of host factors as mediators linking the gut microbiota and disease outcomes. Further large-scale studies must confirm these data; however, they suggest the relevance of monitoring microbiome changes in the early post-viral years to control SARS-CoV-2 and providing individual healthcare support.}, } @article {pmid39743584, year = {2025}, author = {Ezzat, L and Peter, H and Bourquin, M and Busi, SB and Michoud, G and Fodelianakis, S and Kohler, TJ and Lamy, T and Geers, A and Pramateftaki, P and Baier, F and Marasco, R and Daffonchio, D and Deluigi, N and Wilmes, P and Styllas, M and Schön, M and Tolosano, M and De Staercke, V and Battin, TJ}, title = {Diversity and biogeography of the bacterial microbiome in glacier-fed streams.}, journal = {Nature}, volume = {637}, number = {8046}, pages = {622-630}, pmid = {39743584}, issn = {1476-4687}, mesh = {*Ice Cover/microbiology ; *Rivers/microbiology ; *Microbiota/genetics ; *Biodiversity ; *Bacteria/classification/genetics/isolation & purification ; *Phylogeny ; *Phylogeography ; Metagenomics ; DNA Barcoding, Taxonomic ; Climate Change ; }, abstract = {The rapid melting of mountain glaciers and the vanishing of their streams is emblematic of climate change[1,2]. Glacier-fed streams (GFSs) are cold, oligotrophic and unstable ecosystems in which life is dominated by microbial biofilms[2,3]. However, current knowledge on the GFS microbiome is scarce[4,5], precluding an understanding of its response to glacier shrinkage. Here, by leveraging metabarcoding and metagenomics, we provide a comprehensive survey of bacteria in the benthic microbiome across 152 GFSs draining the Earth's major mountain ranges. We find that the GFS bacterial microbiome is taxonomically and functionally distinct from other cryospheric microbiomes. GFS bacteria are diverse, with more than half being specific to a given mountain range, some unique to single GFSs and a few cosmopolitan and abundant. We show how geographic isolation and environmental selection shape their biogeography, which is characterized by distinct compositional patterns between mountain ranges and hemispheres. Phylogenetic analyses furthermore uncovered microdiverse clades resulting from environmental selection, probably promoting functional resilience and contributing to GFS bacterial biodiversity and biogeography. Climate-induced glacier shrinkage puts this unique microbiome at risk. Our study provides a global reference for future climate-change microbiology studies on the vanishing GFS ecosystem.}, } @article {pmid39743281, year = {2024}, author = {Xia, J and Jiang, JH and Zhao, Y and Ma, X and Wu, DP and Chen, SN and Chen, F}, title = {[Clinical Characteristics of Pneumocystis Jiroveci Pneumonia after Allogeneic Hematopoietic Stem Cell Transplantation].}, journal = {Zhongguo shi yan xue ye xue za zhi}, volume = {32}, number = {6}, pages = {1882-1887}, doi = {10.19746/j.cnki.issn.1009-2137.2024.06.038}, pmid = {39743281}, issn = {1009-2137}, mesh = {Humans ; *Hematopoietic Stem Cell Transplantation/adverse effects ; *Pneumonia, Pneumocystis/diagnosis ; Male ; Adult ; Female ; Middle Aged ; Adolescent ; Retrospective Studies ; *Pneumocystis carinii/isolation & purification ; *Transplantation, Homologous ; Young Adult ; }, abstract = {OBJECTIVE: To summarize the clinical characteristics of patients with combined pneumocystis jiroveci pneumonia (PJP) after allogeneic hematopoietic stem cell transplantation (allo-HSCT).

METHODS: The clinical manifestations, laboratory tests, imaging findings, and treatment outcomes of 21 allo-HSCT patients with PJP diagnosed at the First Affiliated Hospital of Soochow University and Soochow Hopes Hematology Hospital from July 2018 to July 2023 were retrospective analyzed.

RESULTS: Among the 21 patients, the male -to-female ratio was 2.5∶1, and the median age was 36 years old with a range of 15-62 years. The median time to diagnosis of PJP after transplantation was 225 days. The clinical manifestations lack specificity, and the main clinical symptoms include respiratory symptoms (dyspnea, cough, sputum, etc.) and fever. Laboratory examination revealed peripheral blood lymphocyte counts decreased in 15 cases, CD4[+] T lymphocyte absolute values less than 200 cells/μl in 19 patients, C-reactive protein levels significantly increased in 20 patients, lactate dehydrogenase levels increased in 14 patients, and 1,3-β-D-glucan detection levels increased in 14 patients. Chest CT manifestations can be divided into three types: ground glass type, nodular type, and mixed type. Among them, the incidence of ground glass type was the highest (18/21), with 2 cases of nodular type and 1 case of mixed type. The sequence number of Pneumocystis jiroveci was detected through mNGS (15-57 570), and 11 patients had mixed infections. In terms of treatment, TMP-SMX, Caspofungin, and methylprednisolone were administered, and 17 patients achieved improvement in their condition. Four patients died, all of whom died from respiratory failure.

CONCLUSION: PJP is a critically ill condition after hematopoietic stem cell transplantation, and diagnosis is difficult. Early diagnosis can achieve better prognosis. The sensitivity of mNGS in diagnosing PJP is high, providing the possibility of early and accurate diagnosis for clinical practice, which is worthy of application and promotion.}, } @article {pmid39743194, year = {2025}, author = {Ye, G and Chen, G and Avellán-Llaguno, RD and Cao, Y and Huang, Q}, title = {Distinctive gut antibiotic resistome, potential health risks and underlying pathways upon cerebral ischemia-reperfusion injury.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {367}, number = {}, pages = {125614}, doi = {10.1016/j.envpol.2024.125614}, pmid = {39743194}, issn = {1873-6424}, mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Anti-Bacterial Agents/pharmacology ; *Reperfusion Injury ; Drug Resistance, Microbial/genetics ; Brain Ischemia ; Metagenomics ; Humans ; }, abstract = {Antibiotic resistance genes (ARGs) as emerging pollutants pose health risks to humans and the environment. Gut microbiota is an important reservoir for ARGs and hotspot for ARG acquisition and dissemination. Non-antibiotic factors (such as disease pathophysiology) affect ARG emergence and dissemination. Cerebral ischemia-reperfusion injury (I/R) commonly occurs in stroke patients. However, effects of I/R on ARG emergence and dissemination are unknown. Therefore, metagenomics was used to unveil selective collection of gut antibiotic resistome and its health risks, key ARG hosts and underlying pathways upon I/R. Changes in gut antibiotic resistome upon I/R were characterized by tetracycline ARG accumulation and decreases in aminoglycoside and glycopeptide ARGs. Besides, changes in gut antibiotic resistome were corrected with those in gut microbiota from phylum to species, serum lipid accumulation and glucose depletion upon I/R. Additionally, health risks of gut microbial multidrug ARGs (such as abem, adek and TolC), macA, aph(3')-I and carO, co-localized with mobile gene elements, were increased upon I/R. Moreover, phyla Firmicutes (especially order Eubacteriales, class Clostridia) and Bacteroidota were key ARG hosts in gut microbiota of I/R gerbils. Furthermore, suppression of vancomycin resistance, and lantibiotic biosynthesis and immunity, disturbances in peptidoglycan biosynthesis and hydrolysis, activation of antimicrobial peptide resistance, lipopolysaccharide biosynthesis, teichoic acid biosynthesis, arabinogalactan biosynthesis, aromatic compound degradation, oxidative phosphorylation, the tricarboxylic acid cycle and its anaplerotic pathways were observed in upon I/R. This study provides novel insights and intervention targets related to selective collection of gut antibiotic resistome and its potential health risks upon I/R.}, } @article {pmid39742975, year = {2025}, author = {Dougherty, PE and Pedersen, MS and Forero-Junco, LM and Carstens, AB and Raaijmakers, JM and Riber, L and Hansen, LH}, title = {Novel bacteriophages targeting wheat phyllosphere bacteria carry DNA modifications and single-strand breaks.}, journal = {Virus research}, volume = {352}, number = {}, pages = {199524}, pmid = {39742975}, issn = {1872-7492}, mesh = {*Triticum/microbiology/virology ; *Bacteriophages/genetics/classification/isolation & purification/physiology ; *Phylogeny ; *Genome, Viral ; DNA, Viral/genetics ; DNA Breaks, Single-Stranded ; Erwinia/virology/genetics ; Pseudomonas/virology/genetics ; Metagenome ; Microbiota ; Pseudomonas Phages/genetics/classification/isolation & purification ; Bacteria/virology/genetics/classification ; }, abstract = {The phyllosphere microbiome can positively or negatively impact plant health and growth, but we currently lack the tools to control microbiome composition. Contributing to a growing collection of bacteriophages (phages) targeting bacteria living in the wheat phyllosphere, we here isolate and sequence eight novel phages targeting common phyllosphere Erwinia and Pseudomonas strains, including two jumbo phages. We characterize genomic, phylogenetic, and morphological traits from these phages and argue for establishing four novel viral genera. We also search the genomes for anti-defense systems and investigate DNA modifications using Nanopore sequencing. In Pseudomonas phage Rembedalsseter we find evidence of 13 motif-associated single-stranded DNA breaks. A bioinformatics search revealed that 60 related Pseudomonas phages are enriched in the same motif, suggesting these single-stranded nicks may be widely distributed in this family of phages. Finally, we also search the Sequence Read Archive for similar phages in public metagenomes. We find close hits to the Erwinia jumbo-phage Kaldavass in a wide variety of plant, food, and wastewater metagenomes including a near-perfect hit from a Spanish spinach sample, illustrating how interconnected geographically distant phages can be.}, } @article {pmid39742897, year = {2025}, author = {Jumaylawee, HRH and Komijani, M and Shahrjerdi, S and Sargolzaei, J}, title = {The interplay of gut microbiota and heavy metals in multiple sclerosis patients.}, journal = {Microbial pathogenesis}, volume = {199}, number = {}, pages = {107269}, doi = {10.1016/j.micpath.2024.107269}, pmid = {39742897}, issn = {1096-1208}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Metals, Heavy/blood ; *Multiple Sclerosis/microbiology ; *Feces/microbiology/chemistry ; *RNA, Ribosomal, 16S/genetics ; Male ; Adult ; Female ; Arsenic/analysis ; Interleukin-10/blood/metabolism ; Middle Aged ; Bacteria/classification/isolation & purification/genetics ; Metagenomics ; Mass Spectrometry ; Young Adult ; Nickel ; }, abstract = {Multiple Sclerosis (MS) is a chronic inflammatory disease characterized by central nervous system (CNS). In this study, the concentration of heavy metals was measured in stool samples of MS patients by Inductively Coupled Plasma-Mass Spectroscopy (ICP-MS) method and compared with healthy people. Also, another goal of this study is to investigate the alteration of the gut microbiome of MS patients by metagenomics technique based on the 16S rRNA gene sequencing. The IL-10 ELISA assay showed no significant differences between the serum level of the IL-10 in the patients and the control group (p = 0.510). Heavy metal measurement by ICP-MS showed significantly higher levels of arsenic (As, Mean = 32.77 μg/kg), nickel (Ni, Mean = 7.154 μg/kg), manganese (Mn, Mean = 3723 μg/kg), and zinc (Zn, Mean = 5508 μg/kg) in the stool samples of the MS group compared to the control group, while concentrations of iron (Fe, Mean = 9585 μg/kg), lead (Pb, Mean = 18.54 μg/kg), titanium (Ti, Mean = 69.69 μg/kg), and tin (Sn, Mean = 13.92 μg/kg) were significantly lower. The result of gut microbiome analysis showed an increase in the abundance of the Verrumicrobiaceae, Lachnospiraceae and Ruminococcaceae families was considerably increased in MS patients compared to the control group (p < 0.05). This study reports that high levels of heavy metals such as Ars, Ni, Mn, and Zn, deficiency of Fe, Pb, Ti, and Sn, and alteration of the gut microbiome are involved in the pathogenesis of MS. The novelty of this study lies in its multi-faceted approach to understanding MS by integrating the measurement of heavy metals in stool samples with the analysis of gut microbiome alterations, thereby providing comprehensive insights into heavy metals, the gut microbiome, and potential therapeutic avenues. This study suggests several potential applications and practical implications based on its findings regarding heavy metals, gut microbiome alterations, and IL-10 levels in MS. First, the identification of elevated levels of specific heavy metals and deficiencies in others may lead to targeted screening and monitoring, informing preventive strategies for MS patients. Additionally, the observed gut microbiome changes could facilitate the development of microbiome-based therapies, such as probiotics or dietary interventions, aimed at restoring microbial balance. Finally, exploring the interplay between heavy metals, gut microbiome, and immune response may guide the creation of novel therapeutic interventions, ultimately enhancing treatment efficacy and providing new avenues for managing MS, thereby alleviating the burden of this chronic condition.}, } @article {pmid39742816, year = {2025}, author = {Li, L and Nielsen, J and Chen, Y}, title = {Personalized gut microbial community modeling by leveraging genome-scale metabolic models and metagenomics.}, journal = {Current opinion in biotechnology}, volume = {91}, number = {}, pages = {103248}, doi = {10.1016/j.copbio.2024.103248}, pmid = {39742816}, issn = {1879-0429}, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Precision Medicine/methods ; *Metagenomics/methods ; Models, Biological ; }, abstract = {The impact of the gut microbiome on human health is increasingly recognized as dysbiosis has been found to be associated with a spectrum of diseases. Here, we review the databases of genome-scale metabolic models (GEMs), which have paved the way for investigations into the metabolic capabilities of gut microbes and their interspecies dynamics. We further discuss the strategies for developing community-level GEMs, which are crucial for understanding the complex interactions within microbial communities and between the microbiome and its host. Such GEMs can guide the design of synthetic microbial communities for disease treatment. Finally, we explore advances in personalized gut microbiome modeling. These advancements broaden our mechanistic understanding and hold promise for applications in precision medicine and therapeutic interventions.}, } @article {pmid39742418, year = {2025}, author = {Hodges, AL and Walker, LR and Everding, T and Mote, BE and Vu, HLX and Ciobanu, DC}, title = {Metagenomic Detection and Genome Assembly of Novel PRRSV-2 Strain Using Oxford Nanopore Flongle Flow Cell.}, journal = {Journal of animal science}, volume = {}, number = {}, pages = {}, doi = {10.1093/jas/skae395}, pmid = {39742418}, issn = {1525-3163}, abstract = {Porcine reproductive and respiratory syndrome virus (PRRSV) is the causative agent of a syndrome characterized by reproductive failure and respiratory complications (PRRS). Early detection and classification of PRRSV strains are vital for appropriate management strategies to minimize loss following outbreaks. The most widely used classification method for PRRSV is based on open reading frame 5 (ORF5) sequences. However, the effectiveness of the ORF5-based classification system in accurately representing genetic variation is under scrutiny because ORF5 constitutes less than 5% of the 15kb-long genome. In this study, a single Oxford Nanopore Flongle flow cell was used to identify and assemble the genome of a strain sampled in May of 2022 from a Midwest research farm. Based on comparisons with available PRRSV genomes, the assembled genome was determined to be a novel PRRSV-2 strain belonging to the 1-4-4 L1C.5 ORF5-based lineage. Phylogenetic analyses of ORF5 and whole-genome sequences demonstrated differences in clustering between PRRSV strains, supporting the inability of ORF5 to capture genome-wide variation. For example, high levels of variation were observed within ORF1a, which encodes the hypervariable nsp2 protein. Comparison of the newly assembled genome with the genome of a highly characterized strain (VR2332 PRRSV-2) identified a 100 amino acid deletion within nsp2 characteristic of NADC34-like PRRSV. Oxford Nanopore Technologies' Flongle flow cell has been proven in this study to provide a rapid, cost-effective and accessible approach for whole-genome sequencing of PRRSV strains present within clinical samples necessary for strain-specific genome-wide characterization.}, } @article {pmid39742313, year = {2024}, author = {Kerek, A and Szabó, E and Szabó, Á and Papp, M and Bányai, K and Kardos, G and Kaszab, E and Bali, K and Jerzsele, Á}, title = {Corrigendum: Investigating antimicrobial resistance genes in probiotic products for companion animals.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1531511}, doi = {10.3389/fvets.2024.1531511}, pmid = {39742313}, issn = {2297-1769}, abstract = {[This corrects the article DOI: 10.3389/fvets.2024.1464351.].}, } @article {pmid39742307, year = {2024}, author = {Lian, ZH and Salam, N and Tan, S and Yuan, Y and Li, MM and Li, YX and Liu, ZT and Hu, CJ and Lv, AP and OuYang, YT and Lu, CY and Zhang, JY and Chen, Y and Chen, LB and Luo, ZH and Ma, B and Hua, ZS and Jiao, JY and Li, WJ and Liu, L}, title = {Metagenomic analysis sheds light on the mixotrophic lifestyle of bacterial phylum Zhuqueibacterota.}, journal = {iMeta}, volume = {3}, number = {6}, pages = {e249}, pmid = {39742307}, issn = {2770-596X}, abstract = {Zhuqueibacterota is a novel bacterial phylum proposed based on hot spring metagenomes and public metagenome-assembled genomes, classified within the Fibrobacterota-Chlorobiota-Bacteroidota superphylum. This globally distributed phylum consists of one class and five orders, with the majority of its members being facultative anaerobes. Notably, the order Zhuqueibacterales utilizes hydrogen as an electron donor for carbon fixation through the Calvin Benson Bassham cycle. Phylogenetic and metabolic analyses reveal the phylum's key role in the carbon cycle, with frequent horizontal gene transfer events influencing its evolutionary trajectory.}, } @article {pmid39742304, year = {2024}, author = {Li, J and Huang, F and Zhou, Y and Huang, T and Tong, X and Zhang, M and Chen, J and Zhang, Z and Du, H and Liu, Z and Zhou, M and Xiahou, Y and Ai, H and Chen, C and Huang, L}, title = {Comprehensive lung microbial gene and genome catalogs assist the mechanism survey of Mesomycoplasma hyopneumoniae strains causing pig lung lesions.}, journal = {iMeta}, volume = {3}, number = {6}, pages = {e258}, pmid = {39742304}, issn = {2770-596X}, abstract = {Understanding the community structure of the lower respiratory tract microbiome is crucial for elucidating its roles in respiratory tract diseases. However, there are few studies about this topic due to the difficulty in obtaining microbial samples from both healthy and disease individuals. Here, using 744 high-depth metagenomic sequencing data of lower respiratory tract microbial samples from 675 well-phenotyped pigs, we constructed a lung microbial gene catalog containing the largest scale of 10,031,593 nonredundant genes to date, 44.8% of which are novel. We obtained 356 metagenome-assembled genomes (MAGs) which were further clustered into 256 species-level genome bins with 41.8% being first reported in the current databases. Based on these data sets and through integrated analysis of the isolation of the related bacterial strains, in vitro infection, and RNA sequencing, we identified and confirmed that Mesomycoplasma hyopneumoniae (M. hyopneumoniae) MAG_47 and its adhesion-related virulence factors (VFs) were associated with lung lesions in pigs. Differential expression levels of adhesion- and immunomodulation-related VFs likely determined the heterogenicity of adhesion and pathogenicity among M. hyopneumoniae strains. M. hyopneumoniae adhesion activated several pathways, including nuclear factor kappa-light-chain-enhancer of activated B, mitogen-activated protein kinase, cell apoptosis, T helper 1 and T helper 2 cell differentiation, tumor necrosis factor signaling, interleukin-6/janus kinase 2/signal transducer and activator of transcription signaling, and response to reactive oxygen species, leading to cilium loss, epithelial cell‒cell barrier disruption, and lung tissue lesions. Finally, we observed the similar phylogenetic compositions of the lung microbiome between humans with Mycoplasma pneumoniae and pigs infected with M. hyopneumoniae. The results provided important insights into pig lower respiratory tract microbiome and its relationship with lung health.}, } @article {pmid39742297, year = {2024}, author = {Shen, X and Jin, H and Zhao, F and Kwok, LY and Zhao, Z and Sun, Z}, title = {Short-term probiotic supplementation affects the diversity, genetics, growth, and interactions of the native gut microbiome.}, journal = {iMeta}, volume = {3}, number = {6}, pages = {e253}, pmid = {39742297}, issn = {2770-596X}, abstract = {The precise mechanisms through which probiotics interact with and reshape the native gut microbiota, especially at the species and genetic levels, remain underexplored. This study employed a high-dose probiotic regimen of Bifidobacterium animalis subsp. lactis [200 billion colony forming units (CFU)/day] over 7 days among healthy participants. Weekly fecal samples were collected for metagenomic sequencing analysis. We found that probiotic intake can significantly enhance the diversity of the gut microbiome and impact single nucleotide variations, growth rates, and network interactions of the resident intestinal bacteria. These adaptive changes in the gut microbiota indicate the swift evolutionary responses of native bacteria to the ecological disturbance presented by probiotic supplementation. Notably, the microbial community appears to undergo rapid and multifaceted ecological adjustments, potentially preceding longer-term evolutionary changes. This knowledge lays the groundwork for further exploration into the mechanisms underlying probiotic-mediated modulation of the gut microbiome, highlighting the necessity of encompassing ecological and evolutionary perspectives in the design and optimization of probiotic applications.}, } @article {pmid39741954, year = {2024}, author = {Delanghe, L and De Boeck, I and Van Malderen, J and Gehrmann, T and Allonsius, CN and Bron, PA and Claes, I and Hagendorens, M and Leysen, J and Wittouck, S and Lebeer, S}, title = {The inner elbow skin microbiome contains Lactobacillus among its core taxa and varies with age, season and lifestyle.}, journal = {Microbiome research reports}, volume = {3}, number = {4}, pages = {43}, pmid = {39741954}, issn = {2771-5965}, abstract = {Background: The human skin microbiome plays an essential role in protecting against pathogens and other external substances. This open ecosystem is also influenced by personal and environmental factors, but the precise impact of these factors, such as lifestyle and season, is understudied. We focused here on the inner elbow, a skin site prone to inflammatory conditions like atopic dermatitis and psoriasis. Methods: We collected skin swabs from the inner elbow of 52 children and adults, with no signs of skin disorders, in the winter and summer seasons. Samples were analyzed using metagenomic shallow shotgun sequencing. In addition, metadata were collected using questionnaires on health, lifestyle, and environmental factors. Results: The core inner elbow community, taxa with a prevalence of 95% or higher, consisted of several well-known skin taxa, such as Staphylococcus hominis, Staphylococcus capitis, Staphylococcus epidermidis, and Cutibacterium acnes. In addition, Streptococcus and Lactobacillus species were also found to be highly prevalent members of the skin microbiota, especially in the age group up to 3 years old. Of all investigated factors, age appeared to be the major driver defining the skin microbiome composition and longitudinal stability over the seasons. Differential abundance analysis using three statistical tests also pointed out that specific skin species were significantly associated with sampling season, age, hygiene practices, vitamin D supplements, probiotics, and the number of household members. Conclusion: This study identifies novel factors influencing the inner elbow skin microbiome composition and paves the way for future comparative and intervention studies in skin disorders such as atopic dermatitis.}, } @article {pmid39741952, year = {2024}, author = {Shen, X and Leng, B and Zhang, S and Kwok, LY and Zhao, F and Zhao, J and Sun, Z and Zhang, J}, title = {Secondary analysis reveals gut microbiota differences in patients with Parkinson's disease and/or cognitive impairment.}, journal = {Microbiome research reports}, volume = {3}, number = {4}, pages = {42}, pmid = {39741952}, issn = {2771-5965}, abstract = {Background: Parkinson's disease (PD) is a neurodegenerative disorder, and the main clinical characteristics are bradykinesia and muscle stiffness. Cognitive impairment (CI) is a prevalent non-motor manifestation observed in individuals with PD. According to disease severity, it can be divided into PD with mild cognitive impairment (MCI) and PD dementia. CI in PD patients may precede motor symptoms, and the gut microbiota plays an important role in PD pathogenesis. Therefore, gut microbiota may be one of the diagnostic targets for PD-CI. Methods: This study compared the gut microbiota of 43 PD-CI patients [Montreal Cognitive Assessment (MoCA) score < 26] and 38 PD patients without CI (MoCA ≥ 26). Patients' neuropsychological conditions, depression scale, and brain structure scanned by magnetic resonance imaging (MRI) were also recorded. The fecal metagenomic datasets of patients with PD, PD-CI, and CI only were retrieved from public databases for reanalysis to explore the relationship between PD, CI, and gut microbiota. Results: We found that the cortical thickness and the volume of the hippocampus, gray matter, and thalamus were significantly reduced among patients with PD-CI compared to PD without CI (P < 0.05). Moreover, the gut microbiome in patients with PD-CI had fewer short-chain fatty acid (SCFA) producing bacteria and more pathogenic bacteria. There were also alterations in patterns of metabolic pathway-encoding genes. Additionally, PD affected gut microbiota more than CI. Conclusion: CI may aggravate the severity of PD, but it did not drastically alter subjects' gut microbiota. This study reveals the relationship between gut microbiota, PD, and CI.}, } @article {pmid39741946, year = {2024}, author = {Wosinska, L and Walsh, LH and Walsh, CJ and Cotter, PD and Guinane, CM and O'Sullivan, O}, title = {Cataloging metagenome-assembled genomes and microbial genes from the athlete gut microbiome.}, journal = {Microbiome research reports}, volume = {3}, number = {4}, pages = {41}, pmid = {39741946}, issn = {2771-5965}, abstract = {Aim: Exercise has been increasingly recognized as a potential influencer of the gut microbiome. Nevertheless, findings remain incongruous, particularly in relation to sport-specific patterns. Methods: In this study, we harness all publicly available data from athlete gut microbiome shotgun studies to explore how exercise may influence the gut microbiota through metagenomic assembly supplemented with short read-based taxonomic profiling. Through this analysis, we provide insights into exercise-associated taxa and genes, including the identification and annotation of putative novel species from the analysis of approximately 2,000 metagenome-assembled genomes (MAGs), classified as high-quality (HQ) MAGs and assembled as part of this investigation. Results: Our metagenomic analysis unveiled potential athlete-associated microbiome patterns at both the phylum and species levels, along with their associated microbial genes, across a diverse array of sports and individuals. Specifically, we identified 76 species linked to exercise, with a notable prevalence of the Firmicutes phylum. Furthermore, our analysis detected MAGs representing potential novel species across various phyla, including Bacteroidota, Candidatus Melainabacteria, Elusimicrobia, Firmicutes, Lentisphaerae, Proteobacteria, Tenericutes, and Verrucomicrobiota. Conclusion: In summary, this catalog of MAGs and their corresponding genes stands as the most extensive collection yet compiled from athletes. Our analysis has discerned patterns in genes associated with exercise. This underscores the value of employing shotgun metagenomics, specifically a MAG recovery strategy, for pinpointing sport-associated microbiome signatures. Furthermore, the identification of novel MAGs holds promise for developing probiotics and deepening our comprehension of the intricate interplay between fitness and the microbiome.}, } @article {pmid39741888, year = {2024}, author = {Li, T and Liu, S}, title = {A Lumbar Drug-Resistant Tuberculosis: A Case Report and Review of Literature.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {5867-5873}, pmid = {39741888}, issn = {1178-6973}, abstract = {INTRODUCTION: Tuberculosis is prevalent in high-burden countries. However, spinal multi-drug resistant tuberculosis (MDR-TB) in patients with normal immune function is a disease that is prone to misdiagnosis and even delayed diagnosis. Recently, we successfully treated one such patient.

CASE PRESENTATION: A 46-year-old male patients with lower back pain associated with recurrent fever 2 months before admission. The patient was misdiagnosed as a suppurative spinal infection and failed to respond to treatment for 2 months. The muscle strength of both lower limbs decreased progressively. We performed two operations to clear the lesion and decompress the spinal canal, during which we found a fish-like inflammatory tissue mimicking a suppurative infection. Finally, the patient was diagnosed with lumbar MDR-TB by culture, Xpert MTB/RIF and metagenomic next-generation sequencing (mNGS). The second-line anti-tuberculosis treatment (ATT) is cycloserine + para-aminosalicylic acid + ethambutol + levofloxacin + linezolid. Finally, the patient's symptoms were relieved and the muscle strength of both lower limbs recovered.

CONCLUSION: This case prompt MDR-TB of the spine is not a typical clinical symptoms and imaging examination is the lack of specificity, when for the diagnosis of patients with spinal bone destruction unclear or treatment is invalid, can diagnostic anti-tuberculosis treatment. For patients with spinal instability or spinal canal occupying, early surgical removal of lesions, tissue culture, Xpert MTB/RIF and mNGS to identify pathogens and drug resistance, timely diagnosis and treatment can maximize the prognosis of spinal MDR-TB.}, } @article {pmid39741524, year = {2024}, author = {Khatiebi, S and Kiprotich, K and Onyando, Z and Mwaura, J and Wekesa, C and Chi, CN and Mulambalah, C and Okoth, P}, title = {High-Throughput Shotgun Metagenomics of Microbial Footprints Uncovers a Cocktail of Noxious Antibiotic Resistance Genes in the Winam Gulf of Lake Victoria, Kenya.}, journal = {Journal of tropical medicine}, volume = {2024}, number = {}, pages = {7857069}, pmid = {39741524}, issn = {1687-9686}, abstract = {Background: A diverse range of pollutants, including heavy metals, agrochemicals, pharmaceutical residues, illicit drugs, personal care products, and other anthropogenic contaminants, pose a significant threat to aquatic ecosystems. The Winam Gulf of Lake Victoria, heavily impacted by surrounding human activities, faces potential contamination from these pollutants. However, studies exploring the presence of antibiotic resistance genes (ARGs) in the lake remain limited. In the current study, a shotgun metagenomics approach was employed to identify ARGs and related pathways. Genomic DNA was extracted from water and sediment samples and sequenced using the high-throughput Illumina NovaSeq platform. Additionally, phenotypic antibiotic resistance was assessed using the disk diffusion method with commonly used antibiotics. Results: The analysis of metagenomes sequences from the Gulf ecosystem and Comprehensive Antibiotic Resistance Database (CARD) revealed worrying levels of ARGs in the lake. The study reported nine ARGs from the 37 high-risk resistant gene families previously documented by the World Health Organization (WHO). Proteobacteria had the highest relative abundance of antibiotic resistance (53%), Bacteriodes (4%), Verrucomicrobia (2%), Planctomycetes Chloroflexi, Firmicutes (2%), and other unclassified bacteria (39%). Genes that target protection, replacement, change, and antibiotic-resistant efflux were listed in order of dominance. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed antibiotic resistance to beta-lactamase and vancomycin. Phenotypic resistance to vancomycin, tetracycline, sulfamethoxazole, erythromycin, trimethoprim, tetracycline, and penicillin was reported through the zone of inhibition. Conclusions: This study highlights that the Winam Gulf of Lake Victoria in Kenya harbors a diverse array of antibiotic-resistant genes, including those conferring multidrug resistance. These findings suggest that the Gulf could be serving as a reservoir for more antibiotic-resistant genes, posing potential risks to both human health and aquatic biodiversity. The insights gained from this research can guide policy development for managing antibiotic resistance in Kenya.}, } @article {pmid39741321, year = {2024}, author = {Shao, L and Cai, G and Fu, J and Zhang, W and Ye, Y and Ling, Z and Ye, S}, title = {Gut microbial 'TNFα-sphingolipids-steroid hormones' axis in children with autism spectrum disorder: an insight from meta-omics analysis.}, journal = {Journal of translational medicine}, volume = {22}, number = {1}, pages = {1165}, pmid = {39741321}, issn = {1479-5876}, support = {LY22C010001//Natural Science Foundation of Zhejiang Province/ ; 2022KY1451//Zhejiang Provincial Medical and Health Science and Technology Plan/ ; 2022KY971//Zhejiang Provincial Medical and Health Science and Technology Plan/ ; 31870839//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Autism Spectrum Disorder/microbiology/blood/metabolism ; *Gastrointestinal Microbiome ; *Tumor Necrosis Factor-alpha/metabolism/blood ; *Sphingolipids/blood/metabolism ; Child ; *Steroids/blood/metabolism ; Metabolomics ; Male ; Female ; Hormones/blood/metabolism ; Metagenomics ; Child, Preschool ; Dysbiosis/microbiology ; Feces/microbiology ; }, abstract = {BACKGROUND: Autism spectrum disorder (ASD) is a persistent neurodevelopmental disorder affecting brains of children. Mounting evidences support the associations between gut microbial dysbiosis and ASD, whereas detailed mechanisms are still obscure.

METHODS: Here we probed the potential roles of gut microbiome in ASD using fecal metagenomics and metabolomics.

RESULTS: Children with ASD were found to be associated with augmented serum cytokines milieu, especially TNFα. Metagenomic analysis generated 29 differential species and 18 dysregulated functional pathways such as Bifidobacterium bifidum, Segatella copri, and upregulated 'Sphingolipid metabolism' in children with ASD. Metabolomics revealed steroid hormone dysgenesis in children with ASD with lower abundances of metabolites such as estriol, estradiol and deoxycorticosterone. A three-way association analysis showed positive correlations between TNFα and microbial function potentials such as 'Bacterial toxins' and 'Lysosome', indicating the contribution of microbial dysbiosis to neuroinflammation. TNFα also correlated positively with 'Sphingolipid metabolism', which further showed negative correlations with metabolites estriol and deoxycorticosterone. Such results, in consistent with current findings, revealed the contribution of increased TNFα to upregulated sphingolipid metabolism, which further impaired steroid hormone biosynthesis.

CONCLUSION: Our study proposed the gut microbial 'TNFα-sphingolipids-steroid hormones' axis in children with ASD, which may provide new perspectives for developing gut microbiome-based treatments in the future.}, } @article {pmid39740553, year = {2024}, author = {Lin, YJ and Hsieh, PH and Mao, CC and Shih, YH and Chen, SH and Lin, CY}, title = {Interpretation of machine learning-based prediction models and functional metagenomic approach to identify critical genes in HBCD degradation.}, journal = {Journal of hazardous materials}, volume = {486}, number = {}, pages = {136976}, doi = {10.1016/j.jhazmat.2024.136976}, pmid = {39740553}, issn = {1873-3336}, abstract = {Hexabromocyclododecane (HBCD) poses significant environmental risks, and identifying HBCD-degrading microbes and their enzymatic mechanisms is challenging due to the complexity of microbial interactions and metabolic pathways. This study aimed to identify critical genes involved in HBCD biodegradation through two approaches: functional annotation of metagenomes and the interpretation of machine learning-based prediction models. Our functional analysis revealed a rich metabolic potential in Chiang Chun soil (CCS) metagenomes, particularly in carbohydrate metabolism. Among the machine learning algorithms tested, random forest models outperformed others, especially when trained on datasets reflecting the degradation patterns of species like Dehalococcoides mccartyi and Pseudomonas aeruginosa. These models highlighted enzymes such as EC 1.8.3.2 (thiol oxidase) and EC 4.1.1.43 (phenylpyruvate decarboxylase) as inhibitors of degradation, while EC 2.7.1.83 (pseudouridine kinase) was linked to enhanced degradation. This dual-methodology approach not only deepens our understanding of microbial functions in HBCD degradation but also provides an unbiased view of the microbial and enzymatic interactions involved, offering a more targeted and effective bioremediation strategy.}, } @article {pmid39740461, year = {2025}, author = {Rana, S and Pandey, H and Shridhar, V and Tiwary, P and Kukreti, S and Arunachalam, K and Singh, V}, title = {Structural and functional analysis of rhizospheric bacterial diversity in the Pranmati basin, Himalayan critical zone observatory.}, journal = {Journal of environmental management}, volume = {373}, number = {}, pages = {123872}, doi = {10.1016/j.jenvman.2024.123872}, pmid = {39740461}, issn = {1095-8630}, mesh = {*Soil Microbiology ; *Rhizosphere ; Bacteria ; Soil/chemistry ; Microbiota ; Ecosystem ; Biodiversity ; Forests ; }, abstract = {The study explores the structural and functional dynamics of rhizospheric bacterial diversity in the Pranmati basin, focusing on their ecological significance, diversity, and functional roles across dominant vegetation types; Rhododendron arboreum, Myrica esculenta, and Quercus leucotrichophora. The research provides critical insights into soil health and ecosystem functioning by analysing rhizospheric soil properties among the selected vegetations. The research findings reveal that Myrica esculenta exhibits the highest root colonization (95.8%) and moisture content (92.6%), while Quercus leucotrichophora shows the lowest (76.2% and 83.2%), respectively. The microbial community is predominantly composed of Proteobacteria, with 62-65% abundance across different vegetation types. Key genera such as Bacillus, Acinetobacter, and Paenibacillus are notably enriched, highlighting their significant role in phosphate solubilization and nutrient cycling. Venn diagram analysis identified 136 common bacterial species among vegetation types reflecting ecological significance in forest ecosystem. The functional metabolism, diversity indices, and core microbiome analysis underscore the distinct microbial profiles associated with different vegetation types, which are crucial for overall forest soil health. The importance of this research lies in its contribution to environmental management by providing a comprehensive understanding of how microbial communities interact with various vegetation types and influence soil health in the Pranmati basin. These insights are essential for developing targeted strategies to enhance soil fertility and manage forest ecosystems in terms of conservation and restoration efforts in sensitive ecological regions. This study is pioneer as it establishes a functional analysis of rhizospheric bacterial diversity in the Pranmati basin, offering a baseline data for future research on bacterial community structure and their functional role in Himalayan Critical Zone Observatory to the best of our knowledge.}, } @article {pmid39739308, year = {2024}, author = {Chaabane, F and Pillonel, T and Bertelli, C}, title = {MeSS and assembly_finder: a toolkit for in silico metagenomic sample generation.}, journal = {Bioinformatics (Oxford, England)}, volume = {41}, number = {1}, pages = {}, pmid = {39739308}, issn = {1367-4811}, mesh = {*Metagenomics/methods ; *Software ; Microbiota/genetics ; Computational Biology/methods ; Humans ; Computer Simulation ; Metagenome ; Sequence Analysis, DNA/methods ; }, abstract = {SUMMARY: The intrinsic complexity of the microbiota combined with technical variability render shotgun metagenomics challenging to analyze for routine clinical or research applications. In silico data generation offers a controlled environment allowing for example to benchmark bioinformatics tools, to optimize study design, statistical power, or to validate targeted applications. Here, we propose assembly_finder and the Metagenomic Sequence Simulator (MeSS), two easy-to-use Bioconda packages, as part of a benchmarking toolkit to download genomes and simulate shotgun metagenomics samples, respectively. Outperforming existing tools in speed while requiring less memory, MeSS reproducibly generates accurate complex communities based on a list of taxonomic ranks and their abundance.

All code is released under MIT License and is available on https://github.com/metagenlab/MeSS and https://github.com/metagenlab/assembly_finder.}, } @article {pmid39739208, year = {2024}, author = {Yu, J and Gao, Y and Bi, H and Zhang, Y and Tang, K and Guo, D and Xie, X}, title = {Preliminary exploration of metagenomic sequencing for pathogenic identification in infectious uveitis.}, journal = {Journal of ophthalmic inflammation and infection}, volume = {14}, number = {1}, pages = {70}, pmid = {39739208}, issn = {1869-5760}, abstract = {PURPOSE: To evaluate the advantages and clinical utility of metagenomic sequencing (MGS) in diagnosing infectious uveitis pathogens.

METHODS: A retrospective study was conducted on 20 infectious uveitis patients (20 eyes) who received treatments at the Affiliated Eye Hospital of Shandong University of Traditional Chinese Medicine from May 2020 to February 2021. Anterior aqueous humor of the patients was collected and analyzed using MGS. Then, pathogenic microorganisms that cause uveitis were identified through bioinformatic analyses based on the sequencing data of MGS. Finally, the pathogens identified by MGS were verified using both enzyme-linked immune sorbent assay (ELISA) and quantitative PCR (qPCR).

RESULTS: MGS was used to detect viral pathogens in four patients, bacterial pathogens in two patients, and viral and bacterial pathogens in one patient. Among these seven subjects, five were verified by either ELISA or qPCR.

CONCLUSIONS: MGS holds significant value and promising potential in diagnosing infectious uveitis pathogens. However, it cannot completely replace the traditional diagnostic techniques and still needs to be integrated with conventional methods to enhance the sensitivity and specificity of pathogen detection. As a pioneering technology, MGS will advance the field of pathogen diagnosis in infectious uveitis.}, } @article {pmid39738768, year = {2024}, author = {Deo, L and Osborne, JW and Benjamin, LK}, title = {Harnessing microbes for heavy metal remediation: mechanisms and prospects.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {1}, pages = {116}, pmid = {39738768}, issn = {1573-2959}, mesh = {*Metals, Heavy/metabolism ; *Biodegradation, Environmental ; *Soil Pollutants/metabolism ; Soil Microbiology ; Environmental Restoration and Remediation/methods ; Bacteria/metabolism ; }, abstract = {Contamination by heavy metals (HMs) poses a significant threat to the ecosystem and its associated micro and macroorganisms, leading to ill effects on humans which necessitate the requirement of effective remediation strategies. Microbial remediation leverages the natural metabolic abilities of microbes to overcome heavy metal pollution effectively. Some of the mechanisms that aids in the removal of heavy metals includes bioaccumulation, biosorption, and biomineralization. Metals such as Cd, Pb, As, Hg, and Cr are passively adsorbed by energy independent process onto the surface by exopolysaccharide sequestration or utilizing energy to transfer metals into the cell and interact with the biomolecules to be sequestered, or being converted into its various valencies, thereby reducing the toxicity. Application of hyperaccumulators has shown to be effective in the removal of HMs especially while augmented with microbes to the rhizosphere region. Omics studies which include metabolomics and metagenomics provide significant information about the microbial diversities and metabolic processes involved in heavy metal remediation, allowing the development of more reliable and sustainable bioremediation approaches. This review also summarizes the recent advancements in microbial remediation, including genetic engineering and nanotechnology that has revolutionized and offered an unprecedented control and precision in the removal of HMs. These innovations hold a promising stand for enhancing remediation efficiency, scalability, and cost-effectiveness.}, } @article {pmid39738315, year = {2024}, author = {Ecklu-Mensah, G and Miller, R and Maseng, MG and Hawes, V and Hinz, D and Kim, C and Gilbert, JA}, title = {Modulating the human gut microbiome and health markers through kombucha consumption: a controlled clinical study.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {31647}, pmid = {39738315}, issn = {2045-2322}, mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; *Biomarkers ; Diet, Western/adverse effects ; Feces/microbiology ; *Gastrointestinal Microbiome ; Probiotics/administration & dosage ; Kombucha Tea ; Cholesterol, HDL/blood ; Insulin Resistance ; Inflammation ; }, abstract = {Fermented foods are becoming more popular due to their purported links to metabolic health and the gut microbiome. However, direct clinical evidence for the health claims is lacking. Here, we describe an eight-week clinical trial that explored the effects of a four-week kombucha supplement in healthy individuals consuming a Western diet, randomized into the kombucha (n = 16) or control (n = 8) group. We collected longitudinal stool and blood samples to profile the human microbiome and inflammation markers. We did not observe significant changes in either biochemical parameters or levels of circulating markers of inflammation across the entire cohort. However, paired analysis between baseline and end of intervention time points within kombucha or control groups revealed increases in fasting insulin and in HOMA-IR in the kombucha group whereas reductions in HDL cholesterol were associated with the control group. Shotgun metagenomic analysis revealed the relative abundance of Weizmannia, a kombucha-enriched probiotic and several SCFA producing taxa to be overrepresented in consumers at the end of the intervention. Collectively, in our healthy cohort consuming a Western diet, a short-term kombucha intervention induced modest impacts on human gut microbiome composition and biochemical parameters, which may be attributed to relatively small number of participants and the extensive inter-participant variability.}, } @article {pmid39738309, year = {2024}, author = {Tawfiq, R and Niu, K and Hoehndorf, R and Kulmanov, M}, title = {DeepGOMeta for functional insights into microbial communities using deep learning-based protein function prediction.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {31813}, pmid = {39738309}, issn = {2045-2322}, support = {URF/1/4675-01-01, URF/1/4355-01- 01, URF/1/4697-01-01, URF/1/5041-01- 01, REI/1/5334-01-01, FCC/1/1976-46-01, and FCC/1/1976- 34-01//King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR)/ ; URF/1/4675-01-01, URF/1/4355-01- 01, URF/1/4697-01-01, URF/1/5041-01- 01, REI/1/5334-01-01, FCC/1/1976-46-01, and FCC/1/1976- 34-01//King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR)/ ; URF/1/4675-01-01, URF/1/4355-01- 01, URF/1/4697-01-01, URF/1/5041-01- 01, REI/1/5334-01-01, FCC/1/1976-46-01, and FCC/1/1976- 34-01//King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR)/ ; URF/1/4675-01-01, URF/1/4355-01- 01, URF/1/4697-01-01, URF/1/5041-01- 01, REI/1/5334-01-01, FCC/1/1976-46-01, and FCC/1/1976- 34-01//King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR)/ ; }, mesh = {*Deep Learning ; *Microbiota ; Gene Ontology ; Computational Biology/methods ; Proteins/metabolism ; Bacteria/metabolism/genetics ; Bacterial Proteins/metabolism/genetics ; Software ; }, abstract = {Analyzing microbial samples remains computationally challenging due to their diversity and complexity. The lack of robust de novo protein function prediction methods exacerbates the difficulty in deriving functional insights from these samples. Traditional prediction methods, dependent on homology and sequence similarity, often fail to predict functions for novel proteins and proteins without known homologs. Moreover, most of these methods have been trained on largely eukaryotic data, and have not been evaluated on or applied to microbial datasets. This research introduces DeepGOMeta, a deep learning model designed for protein function prediction as Gene Ontology (GO) terms, trained on a dataset relevant to microbes. The model is applied to diverse microbial datasets to demonstrate its use for gaining biological insights. Data and code are available at https://github.com/bio-ontology-research-group/deepgometa.}, } @article {pmid39738126, year = {2024}, author = {Zhang, S and Song, W and Marinos, G and Waschina, S and Zimmermann, J and Kaleta, C and Thomas, T}, title = {Genome-scale metabolic modelling reveals interactions and key roles of symbiont clades in a sponge holobiont.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {10858}, pmid = {39738126}, issn = {2041-1723}, mesh = {*Symbiosis ; *Porifera/microbiology/metabolism ; Animals ; *Microbiota/genetics ; *Metabolic Networks and Pathways/genetics ; Bacteria/metabolism/genetics/classification ; Phylogeny ; Genome ; Genome, Bacterial ; Models, Biological ; Metagenomics/methods ; }, abstract = {Sponges harbour complex microbiomes and as ancient metazoans and important ecosystem players are emerging as powerful models to understand the evolution and ecology of symbiotic interactions. Metagenomic studies have previously described the functional features of sponge symbionts, however, little is known about the metabolic interactions and processes that occur under different environmental conditions. To address this issue, we construct here constraint-based, genome-scale metabolic networks for the microbiome of the sponge Stylissa sp. Our models define the importance of sponge-derived nutrients for microbiome stability and discover how different organic inputs can result in net heterotrophy or autotrophy of the symbiont community. The analysis further reveals the key role that a newly discovered bacterial taxon has in cross-feeding activities and how it dynamically adjusts with nutrient inputs. Our study reveals insights into the functioning of a sponge microbiome and provides a framework to further explore and define metabolic interactions in holobionts.}, } @article {pmid39736848, year = {2024}, author = {Hellwig, P and Kautzner, D and Heyer, R and Dittrich, A and Wibberg, D and Busche, T and Winkler, A and Reichl, U and Benndorf, D}, title = {Tracing active members in microbial communities by BONCAT and click chemistry-based enrichment of newly synthesized proteins.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae153}, pmid = {39736848}, issn = {2730-6151}, abstract = {A comprehensive understanding of microbial community dynamics is fundamental to the advancement of environmental microbiology, human health, and biotechnology. Metaproteomics, defined as the analysis of all proteins present within a microbial community, provides insights into these complex systems. Microbial adaptation and activity depend to an important extent on newly synthesized proteins (nP), however, the distinction between nP and bulk proteins is challenging. The application of BONCAT with click chemistry has demonstrated efficacy in the enrichment of nP in pure cultures for proteomics. However, the transfer of this technique to microbial communities and metaproteomics has proven challenging and thus it has not not been used on microbial communities before. To address this, a new workflow with efficient and specific nP enrichment was developed using a laboratory-scale mixture of labelled Escherichia coli and unlabeled yeast. This workflow was then successfully applied to an anaerobic microbial community with initially low bioorthogonal non-canonical amino acid tagging efficiency. A substrate shift from glucose to ethanol selectively enriched nP with minimal background. The identification of bifunctional alcohol dehydrogenase and a syntrophic interaction between an ethanol-utilizing bacterium and two methanogens (hydrogenotrophic and acetoclastic) demonstrates the potential of metaproteomics targeting nP to trace microbial activity in complex microbial communities.}, } @article {pmid39735180, year = {2024}, author = {Jiang, C and Feng, J and Shan, B and Chen, Q and Yang, J and Wang, G and Peng, X and Li, X}, title = {Predicting microbe-disease associations via graph neural network and contrastive learning.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1483983}, pmid = {39735180}, issn = {1664-302X}, abstract = {In the contemporary field of life sciences, researchers have gradually recognized the critical role of microbes in maintaining human health. However, traditional biological experimental methods for validating the association between microbes and diseases are both time-consuming and costly. Therefore, developing effective computational methods to predict potential associations between microbes and diseases is an important and urgent task. In this study, we propose a novel computational framework, called GCATCMDA, for forecasting potential associations between microbes and diseases. Firstly, we construct Gaussian kernel similarity networks for microbes and diseases using known microbe-disease association data. Then, we design a feature encoder that combines graph convolutional network and graph attention mechanism to learn the node features of networks, and propose a feature dual-fusion module to effectively integrate node features from each layer's output. Next, we apply the feature encoder separately to the microbe similarity network, disease similarity network, and microbe-disease association network, and enhance the consistency of features for the same nodes across different association networks through contrastive learning. Finally, we pass the microbe and disease features into an inner product decoder to obtain the association scores between them. Experimental results demonstrate that the GCATCMDA model achieves superior predictive performance compared to previous methods. Furthermore, case studies confirm that GCATCMDA is an effective tool for predicting microbe-disease associations in real situations.}, } @article {pmid39735176, year = {2025}, author = {Bhatia, Z and Kumar, S and Seshadri, S}, title = {Fecal microbiota transplantation as a potential therapeutic approach to improve impaired glucose tolerance via gut microbiota modulation in rat model.}, journal = {Journal of diabetes and metabolic disorders}, volume = {24}, number = {1}, pages = {28}, pmid = {39735176}, issn = {2251-6581}, abstract = {OBJECTIVES: To investigate the impact of diet-induced gut microbiota alterations on type 2 diabetes and assess the therapeutic potential of Fecal Microbiota Transplantation (FMT) in restoring a balanced gut microenvironment.

METHODS: To induce type 2 diabetes, rats were fed a high-sugar high-fat diet (HSFD) for 90 days. After diabetes induction, animals were divided into an HSFD control group, a metformin group (100 mg/kg), and an FMT group (100 mg/kg), receiving treatment for an additional 90 days. Fasting blood glucose levels, glucose tolerance, serum markers (HbA1C, free fatty acids, lipopolysaccharides, pro-inflammatory and anti-inflammatory cytokines), and gut microbiota profiles via cecal metagenome sequencing were analyzed post-treatment.

RESULTS: FMT effectively restored gut microbiota composition to a profile similar to healthy controls, rebalancing the Firmicutes/Bacteroidetes ratio and increasing beneficial taxa, including Prevotella ruminicola, Akkermansia muciniphila, Roseburia, and Faecalibacterium prausnitzii. These microbial shifts corresponded with significant metabolic improvements: FMT reduced inflammatory markers (LPS and FFA), lowered HbA1c, and improved glucose tolerance. Enhanced gut barrier integrity observed in FMT-treated animals likely contributed to reduced endotoxemia and systemic inflammation, distinguishing FMT's metabolic effects from those of metformin. Notably, FMT addressed the dysbiosis associated with HSFD, promoting microbial resilience and mitigating the metabolic disruptions linked to type 2 diabetes.

CONCLUSION: These findings underscore the potential of FMT as a targeted therapeutic approach to modulate gut microbiota composition and mitigate metabolic dysregulation induced by high sugar high fat diet.}, } @article {pmid39734744, year = {2024}, author = {Li, M and Li, W and Wang, C and Ji, L and Han, K and Gong, J and Dong, S and Wang, H and Zhu, X and Du, B and Liu, K and Jiang, J and Wang, C}, title = {Growth-promoting effects of self-selected microbial community on wheat seedlings in saline-alkali soil environments.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {12}, number = {}, pages = {1464195}, pmid = {39734744}, issn = {2296-4185}, abstract = {Saline-alkali land is a type of soil environment that causes poor crop growth and low yields. Its management and utilization are, therefore of great significance for increasing arable land resources, ensuring food security, and enhancing agricultural production capacity. The application of plant growth-promoting rhizobacteria (PGPR) is an effective way to promote the establishment of symbiotic relationships between plants and the rhizosphere microenvironment, plant growth and development, and plant resistance to saline-alkali stress. In this study, multiple saline-alkali-resistant bacteria were screened from a saline-alkali land environment and some of them were found to have significantly promotive effects on the growth of wheat seedlings under saline-alkali stress. Using these PGPR, a compound microbial community was selectively obtained from the root-zone soil environment of wheat seedlings, and the metagenomic sequencing analysis of wheat root-zone soil microbiomes was performed. As a result, a compound microbial agent with a Kocuria dechangensis 5-33:Rossellomorea aquimaris S-3:Bacillus subtilis BJYX:Bacillus velezensis G51-1 ratio of 275:63:5:1 was obtained through the self-selection of wheat seedlings. The synthetic compound microbial agent significantly improved the growth of wheat seedlings in saline-alkali soil, as the physiological plant height, aboveground and underground fresh weights, and aboveground and underground dry weights of 21-day-old wheat seedlings were increased by 27.39% (p < 0.01), 147.33% (p < 0.01), 282.98% (p < 0.01), 194.86% (p < 0.01), and 218.60% (p < 0.01), respectively. The promoting effect of this compound microbial agent was also greater than that of each strain on the growth of wheat seedlings. This microbial agent could also regulate some enzyme activities of wheat seedlings and the saline-alkali soil, thereby, promoting the growth of these seedlings. In this study, we analyze an efficient microbial agent and the theoretical basis for promoting the growth of wheat seedlings under saline-alkali stress, thereby, suggesting an important solution for the management and utilization of saline-alkali land.}, } @article {pmid39733825, year = {2024}, author = {Xu, Y and Peng, M and Zhou, T and Yang, Y and Xu, P and Xie, T and Cao, X and Chen, B and Ouyang, J}, title = {Diagnostic performance of metagenomic next-generation sequencing among hematological malignancy patients with bloodstream infections after antimicrobial therapy.}, journal = {The Journal of infection}, volume = {90}, number = {2}, pages = {106395}, doi = {10.1016/j.jinf.2024.106395}, pmid = {39733825}, issn = {1532-2742}, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is an effective method for detecting pathogenic pathogens of bloodstream infection (BSI). However, there is no consensus on whether the use of antibiotics affects the diagnostic performance of mNGS. We conducted a prospective clinical study aiming to evaluate the effect of antimicrobial treatment on mNGS.

METHODS: Blood samples were collected for mNGS testing within 24 h of culture-confirmed with BSI, with re-examination conducted every 2-3 days.

RESULTS: A total of 38 patients with BSI were enrolled. The mNGS positive (mNGS-pos) rate declined sharply after the use of antibiotics, with only 17 (44.78%) patients remaining mNGS-pos while the rest were mNGS negative (mNGS-neg). The median duration of pathogen identification was significantly longer for mNGS compared to blood culture (BC) (4 days vs 1 days; P < 0.0001). A positivity duration of ≥ 3 days was an independent risk factor of septic shock (OR, 20.671; 95% CI, 1.958-218.190; P = 0.012). Patients with mNGS-pos and mNGS-neg differed by the median duration of fever (6 days vs 3 days; P = 0.038), rates of drug resistance (35.3% vs 4.8%; P = 0.017), rates of septic shock (47.1% vs 14.3%; P = 0.029), and 28-day mortality (29.4% vs 4.8%; P = 0.041).

CONCLUSIONS: The antimicrobial treatment will greatly reduce the positive rate of mNGS. The duration of mNGS is significantly longer than that of BC. The prolonged duration of mNGS suggests an increased risk of septic shock and could be identified as a high-risk factor of adverse infection outcome, requiring more aggressive anti-infective treatment measures.}, } @article {pmid39733577, year = {2025}, author = {Heisi, HD and Nkuna, R and Matambo, T}, title = {Rhizosphere microbial community structure and PICRUSt2 predicted metagenomes function in heavy metal contaminated sites: A case study of the Blesbokspruit wetland.}, journal = {The Science of the total environment}, volume = {959}, number = {}, pages = {178147}, doi = {10.1016/j.scitotenv.2024.178147}, pmid = {39733577}, issn = {1879-1026}, mesh = {*Wetlands ; *Metals, Heavy/analysis ; *Biodegradation, Environmental ; *Microbiota ; *Rhizosphere ; South Africa ; *Soil Microbiology ; Soil Pollutants/analysis ; Metagenome ; Bacteria/classification/genetics ; Eichhornia/microbiology ; Fungi ; Poaceae/microbiology ; Typhaceae ; }, abstract = {This study investigated the microbial diversity inhabiting the roots (rhizosphere) of macrophytes thriving along the Blesbokspruit wetland, South Africa's least conserved Ramsar site. The wetland suffers from decades of pollution from mining wastewater, agriculture, and sewage. The current study focused on three macrophytes: Phragmites australis (common reed), Typha capensis (bulrush), and Eichhornia crassipes (water hyacinth). The results revealed a greater abundance and diversity of microbes (Bacteria and Fungi) associated with the free-floating E. crassipes compared to P. australis and T. capensis. Furthermore, the correlation between microbial abundance and metals, showed a strong correlation between fungal communities and metals such as nickel (Ni) and arsenic (As), while bacterial communities correlated more with lead (Pb) and chromium (Cr). The functional analysis predicted by PICRUSt2 identified genes related to xenobiotic degradation, suggesting the potential of these microbes to break down pollutants. Moreover, specific bacterial groups - Proteobacteria, Verrucomicrobia, Cyanobacteria, and Bacteroidetes - were linked to this degradation pathway. These findings suggest a promising avenue for microbe-assisted phytoremediation, a technique that utilizes plants and their associated microbes to decontaminate polluted environments.}, } @article {pmid39732910, year = {2024}, author = {Yang, J and Wu, X and Zhang, Q and Lin, C and Yu, Y and Zhang, X and Liu, H and An, Y}, title = {Metagenomic next-generation sequencing and galactomannan testing for the diagnosis of invasive pulmonary aspergillosis.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {31389}, pmid = {39732910}, issn = {2045-2322}, support = {Zhengzhou University, 518-23240003/518-23240004//This study was supported by the Zhengzhou Collaborative Innovation Major Project/ ; Zhengzhou University, 518-23240003/518-23240004//This study was supported by the Zhengzhou Collaborative Innovation Major Project/ ; Zhengzhou University, 518-23240003/518-23240004//This study was supported by the Zhengzhou Collaborative Innovation Major Project/ ; }, mesh = {Humans ; *Mannans/analysis ; *Galactose/analogs & derivatives ; Male ; *High-Throughput Nucleotide Sequencing/methods ; Female ; Middle Aged ; *Invasive Pulmonary Aspergillosis/diagnosis ; Retrospective Studies ; *Metagenomics/methods ; Aged ; *Bronchoalveolar Lavage Fluid/microbiology/chemistry ; Adult ; ROC Curve ; Sensitivity and Specificity ; }, abstract = {To evaluate the diagnostic value of metagenomic next-generation sequencing (mNGS) and galactomannan (GM) testing in invasive pulmonary aspergillosis (IPA) and to compare mNGS with other diagnostic approaches (serum/bronchoalveolar lavage fluid (BALF)-GM and conventional microbiological tests (CMTs) including sputum smears and culture, BALF fungal culture, and bronchial brushing). In all, 237 patients were enrolled in this retrospective study, including 120 patients with IPA and 117 with non-IPA pulmonary infections treated at Henan Provincial People's Hospital between June 2021 and February 2024. The diagnostic performance of mNGS was compared to conventional diagnostic methods including serum GM, BALF-GM, sputum smear microscopy, sputum culture, bronchial brushings, and BALF culture. The proportion of patients with underlying diseases was significantly higher in the IPA group than in the non-IPA group (P < 0.05). Compared to conventional diagnostic methods for IPA, mNGS showed higher diagnostic efficacy, with a sensitivity of 92.5% and a specificity of 94.02%. The area under the receiver operating characteristic curve (AUC) for BALF-GM for diagnosing IPA was 0.8, with an optimal cutoff value of 0.546, sensitivity of 66.7%, and specificity of 82.1%. The combination of mNGS and BALF-GM testing further improved diagnostic performance (sensitivity of 96.67% and specificity of 78.63%). mNGS testing has excellent diagnostic efficacy for IPA, which is further enhanced by combining it with BALF-GM testing. This approach has considerable potential for the early diagnosis and targeted treatment of IPA.}, } @article {pmid39732868, year = {2024}, author = {Liu, Y and Wang, F and Zhou, Z and Liu, B and Wu, Z and Pan, X}, title = {Profiling and comprehensive analysis of microbiome and ARGs of nurses and nursing workers in China: a cross-sectional study.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {31301}, pmid = {39732868}, issn = {2045-2322}, support = {2018YFC2000500//National Key Research and Development Program of China/ ; }, mesh = {Humans ; Cross-Sectional Studies ; China/epidemiology ; *Nurses ; *Microbiota/genetics ; Female ; Adult ; Male ; Feces/microbiology ; Cross Infection/microbiology/epidemiology ; Gastrointestinal Microbiome ; Hand/microbiology ; Bacteria/genetics/isolation & purification/drug effects/classification ; Metagenomics/methods ; Hand Hygiene ; }, abstract = {Hospital-acquired infection (HAI) and antimicrobial resistance (AMR) represent major challenges in healthcare system. Despite numerous studies have assessed environmental and patient samples, very few studies have explored the microbiome and resistome profiles of medical staff including nursing workers. This cross-sectional study was performed in a tertiary hospital in China and involved 25 nurses (NSs), 25 nursing workers (NWs), and 55 non-medical control (NC). Stool samples from all participants and hand samples (i.e., the microbiome sample from hand skin, which were collected by swabbing both hands with a sponge-swab soaked with neutralized buffer and centrifuging the liquid buffer) from NSs and NWs were collected for metagenomic analysis. Metagenomic analysis revealed that medical staff exhibited lower abundances of beneficial species such as Blautia, and Bifidobacterium in the gut microbiome. However, an important potential pathogen, Staphylococcus haemolyticus, was enriched in the hands of NWs, suggesting a considerable prevalence of pathogenesis and multi-drug resistance. Accordantly, ARG analysis revealed worse hand hygiene among NWs than among NSs, characterized by a higher diversity of ARGs and a higher abundance of ARGs conferring multi-drug resistance including mdtF, acrB, AcrF and evgS. This study provides a comprehensive overview of the microbial and ARG profiles in the gut and hands of NSs and NWs. The higher abundance of potential pathogens and diverse multi-drug resistant ARGs in NWs hands indicates insufficient hand hygiene and a higher risk of HAI in this subgroup. This study is the first to highlight the critical need to improve hand hygiene among NWs, thus mitigating the risks of AMR and HAI.}, } @article {pmid39732792, year = {2024}, author = {Pan, J and Zhang, X and Shi, D and Tian, X and Xu, L and Lu, X and Dong, M and Yao, P and Pan, Z and Ling, Z and Wu, N and Yao, H}, title = {Short-chain fatty acids play a key role in antibody response to SARS-CoV-2 infection in people living with HIV.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {31211}, pmid = {39732792}, issn = {2045-2322}, support = {SYS202202//Shandong Provincial Laboratory Project/ ; 2022ZFJH003//Fundamental Research Funds for the Central Universities/ ; 2022R52029//Zhejiang Plan for the Special Support for Top-notch Talents/ ; }, mesh = {Humans ; *Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome/immunology ; *HIV Infections/immunology/virology/microbiology ; *COVID-19/immunology/blood/virology ; *SARS-CoV-2/immunology ; Male ; Female ; Middle Aged ; *Antibodies, Viral/blood/immunology ; Adult ; Antibody Formation/immunology ; }, abstract = {High SARS-CoV-2-specific antibody levels can protect against SARS-CoV-2 reinfection. The gut microbiome can affect a host's immune response. However, its role in the antibody response to SARS-CoV-2 in people living with HIV (PLWH) remains poorly understood. Here, we categorised PLWH and healthy individuals into high- and low-antibody-response groups. Shotgun metagenomic sequencing and targeted metabolomic assays were used to investigate the differences in the gut microbiome and metabolic functions between the high- and low-antibody-response groups. PLWH demonstrated a higher abundance of short-chain fatty acid (SCFA)-producing species, accompanied by high serum levels of several SCFAs, in the high-antibody-response group than in the low-antibody-response group. In contrast, healthy individuals demonstrated higher enrichment of pilus-bearing bacterial species, with flagella-expressing genes, in the high-antibody-response group than in the low-antibody-response group. Therefore, gut-microbiota-derived SCFAs play a key role in antibody responses in PLWH but not in healthy individuals. Our results afford a novel understanding of how the gut microbiome and its metabolites are associated with host immunity. Moreover, they may facilitate the exploration of modalities to prevent SARS-CoV-2 reinfection through various gut-microbiota-targeted interventions tailored to different populations.}, } @article {pmid39732609, year = {2025}, author = {Tegegne, HA and Savidge, TC}, title = {Leveraging human microbiomes for disease prediction and treatment.}, journal = {Trends in pharmacological sciences}, volume = {46}, number = {1}, pages = {32-44}, pmid = {39732609}, issn = {1873-3735}, support = {P01 AI152999/AI/NIAID NIH HHS/United States ; T32 AI141349/AI/NIAID NIH HHS/United States ; R01 NR013497/NR/NINR NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; R01 DK130517/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Humans ; Computational Biology ; Metagenomics ; *Microbiota ; Precision Medicine/methods ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The human microbiome consists of diverse microorganisms that inhabit various body sites. As these microbes are increasingly recognized as key determinants of health, there is significant interest in leveraging individual microbiome profiles for early disease detection, prevention, and drug efficacy prediction. However, the complexity of microbiome data, coupled with conflicting study outcomes, has hindered its integration into clinical practice. This challenge is partially due to demographic and technological biases that impede the development of reliable disease classifiers. Here, we examine recent advances in 16S rRNA and shotgun-metagenomics sequencing, along with bioinformatics tools designed to enhance microbiome data integration for precision diagnostics and personalized treatments. We also highlight progress in microbiome-based therapies and address the challenges of establishing causality to ensure robust diagnostics and effective treatments for complex diseases.}, } @article {pmid39732438, year = {2024}, author = {Alhasani, AT and Modasia, AA and Anodiyil, M and Corsetti, M and Aliyu, AI and Crooks, C and Marciani, L and Reid, J and Yakubov, GE and Avery, A and Harris, H and Warren, FJ and Spiller, RC}, title = {Mode of Action of Psyllium in Reducing Gas Production from Inulin and its Interaction with Colonic Microbiota: A 24-H, Randomized, Placebo-Controlled Trial in Healthy Human Volunteers.}, journal = {The Journal of nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tjnut.2024.12.017}, pmid = {39732438}, issn = {1541-6100}, abstract = {BACKGROUND: Recent studies show that the increase in breath hydrogen (BH2) and symptoms after ingestion of inulin are reduced by coadministering psyllium (PI).

OBJECTIVES: To determine if slowing delivery of inulin to the colon by administering it in divided doses would mimic the effect of PI. Primary endpoint was the BH2 area under the curve AUC0-24 h. Secondary endpoints included BH2 AUC0-6 h, 6-12 h, and 12-24 h. Exploratory endpoints included the correlation of BH2 AUC0-24 h with dietary fermentable oligo-, di-, monosaccharides, and polyols (FODMAPs) intake and in vitro fermentation results.

METHODS: A total of 17 healthy adults were randomly assigned to a single-blind, 3-arm, crossover trial. All consumed 20 g inulin (I) powder dissolved in 500 mL water and mixed with either 20 g maltodextrin (control) or 20 g PI consumed as a single dose or 20 g inulin given in divided doses (DDI), 62.5 mL every 45 min over 6 h. Twenty-four-hour BH2, dietary FODMAP intake, stool microbiota, and gas production in vitro were measured. Responders were defined as those whose AUC0-24 h BH2 was reduced by PI, whereas nonresponders showed no reduction.

RESULTS: Compared with control, PI did not reduce average BH2 AUC0-24 h, whereas DDI increased it, P < 0.0002. DDI and PI both significantly reduced BH2 AUC0-6 h compared with the control, P < 0.0001. However, subsequently, DDI significantly increased BH2 from 6 to 12 h (P < 0.0001) and overnight (12-24 h) (P < 0.0001), whereas PI did so only overnight (P = 0.0002). Nonresponders showed greater release of arabinose during in vitro fermentation and higher abundance of 2 species, Clostridium spp. AM22_11AC and Phocaeicola dorei, which also correlated with BH2 production on PI. Dietary FODMAP intake tended to correlate inversely with BH2 AUC0-24 h (r = -0.42, P = 0.09) and correlated with microbiome community composition.

CONCLUSIONS: DDI, like PI, reduces early BH2 production. PI acts by delaying transit to the colon but not reducing colonic fermentation over 24 h. Dietary FODMAP intake correlates with BH2 response to inulin and the microbiome. This trial was registered at www.

CLINICALTRIALS: gov as NCT05619341.}, } @article {pmid39732373, year = {2025}, author = {Yin, S and Wang, YX and Hou, C and Wang, J and Xu, J and Jiang, X and Chen, D and Mu, Y and Shen, J}, title = {Deciphering the key role of biofilm and mechanisms in high-strength nitrogen removal within the anammox coupled partial S[0]-driven autotrophic denitrification system.}, journal = {Bioresource technology}, volume = {419}, number = {}, pages = {132020}, doi = {10.1016/j.biortech.2024.132020}, pmid = {39732373}, issn = {1873-2976}, mesh = {*Biofilms ; *Denitrification/physiology ; *Nitrogen/metabolism ; *Autotrophic Processes ; Oxidation-Reduction ; Sulfur/metabolism ; Bioreactors ; Bacteria/metabolism ; Wastewater/microbiology ; Anaerobiosis/physiology ; Nitrates/metabolism ; }, abstract = {Anammox coupled partial S[0]-driven autotrophic denitrification (PS[0]AD) technology represents an innovative approach for removing nitrogen from wastewater. The research highlighted the crucial role of biofilm on sulfur particles in the nitrogen removal process. Further analysis revealed that sulfur-oxidizing bacteria (SOB) are primarily distributed in the inner layer of the biofilm, while anammox bacteria (AnAOB) are relatively evenly distributed in inner and outer layers, with Thiobacillus and Candidatus Brocadia being the dominant species, respectively. Except for anammox and PS[0]AD processes, [15]N isotope labeling tests determined that sulfur reshaped nitrogen metabolism pathways, providing solid evidence for the occurrence of sulfammox process. SOB and AnAOB collaborate in nitrogen and sulfur conversion, with SOB-drived PS[0]AD processes reducing nitrate to nitrite for AnAOB to remove ammonia. Conversely, the nitrate produced from anammox process can be reused by SOB. Metagenomic analyses verified that SOB drove the PS[0]AD process through encoding soxBYZ gene, while AnAOB might play an important role in simultaneously driving the anammox and sulfammox processes. These findings underscore the importance of biofilm and clarify the nitrogen-sulfur cycle mechanisms within the coupled system.}, } @article {pmid39732159, year = {2024}, author = {Yadav, V and Kilambi, R and Sharma, R and Mohapatra, N and Sasturkar, SV and Dawar, A and Rastogi, A and Saini, M and Sharma, D and Trehanpati, N and Kale, PR and Pamecha, V and Ramakrishna, G}, title = {Radiocarbon dating of gallstones for timeline of formation, dormancy analysis, and correlation with chemical/microbial composition: a pilot study on gallstone geobiology.}, journal = {Journal of gastrointestinal surgery : official journal of the Society for Surgery of the Alimentary Tract}, volume = {29}, number = {3}, pages = {101937}, doi = {10.1016/j.gassur.2024.101937}, pmid = {39732159}, issn = {1873-4626}, abstract = {BACKGROUND: India has a high incidence of gallstones, which can cause chronic inflammation and increase the risk of gallbladder cancer. Understanding the age and composition of gallstones can provide insights into their formation and growth. This study used radiocarbon dating ([14]C dating), Fourier transform infrared (FTIR) spectroscopy, and metagenome analysis to explore the natural history, deposition rate, and microbial/chemical composition of gallstones.

METHODS: In this pilot study, 3 cholesterol gallstones were chosen with different tissue histopathologies (normal, metaplasia, and dysplasia), and respective layers were analyzed for [14]C bomb-pulse dating and FTIR for age and chemical composition, respectively. The core of each gallstone was subjected to scanning electron microscopy and further to 16S rRNA sequencing for microbial analysis.

RESULTS: The [14]C data indicated that the largest stone with dysplastic epithelium formed over 6 years, whereas stones with metaplasia and normal pathology took 13 and 12 years to develop, respectively. Furthermore, the largest stone was dormant for 6 years before the individual experienced acute pain, whereas the other 2 stones laid dormant for 7 and 18 years. FTIR analysis revealed that all 3 gallstones were primarily composed of cholesterol. In addition, calcium oxalate, calcium carbonate, and calcium bilirubinate were present in stones with underlying dysplasia. The 16S rRNA analysis revealed an increased abundance of Corynebacterium sp. in stones associated with metaplasia and dysplasia. Moreover, pathogenic Klebsiella and Escherichia coli species were abundant in calcium oxalate-rich gallstones with underlying dysplasia.

CONCLUSION: Overall, the pilot study established the feasibility of [14]C bomb pulse for evaluating the timeline of gallstone formation. In addition, [14]C dating combined with FTIR/metagenome analysis helped in understanding the natural history of gallstone-associated disease.}, } @article {pmid39731892, year = {2024}, author = {Zhao, J and Huang, Y and Hu, S and Chen, Z and Chen, B and Qi, W and Wang, L and Liu, H}, title = {Impact of adaptation time on lincomycin removal in riverbank filtration: A long-term sand column study.}, journal = {Journal of hazardous materials}, volume = {486}, number = {}, pages = {136950}, doi = {10.1016/j.jhazmat.2024.136950}, pmid = {39731892}, issn = {1873-3336}, abstract = {Riverbank filtration (RBF) is an effective pretreatment technology for drinking water, removing organic micropollutants (OMPs) mainly through biodegradation. Despite documented improvements in OMP removal with extended adaptation time, the mechanisms remain poorly understood. This study assessed the removal of 128 OMPs over 82 d in a simulated RBF system, identified those with improved removal, and analyzed their properties. Additionally, microbial community shifts after 400 d of lincomycin exposure were studied to understand the underlying mechanisms. We found that the removal efficiencies of 24 OMPs, including lincomycin and fluconazole, improved by 3-77 % over 82 d while being positively correlated with the presence of tertiary amides and secondary sulfonamides. Lincomycin removal efficiency rose from 20 % to 95 % over 68 days and stayed high. We identified eight potential degradation products of lincomycin, occurring primarily via hydroxylation, N-demethylation, and amide hydrolysis. Additionally, lincomycin notably increased the abundances of specific antibiotic-resistant bacteria (e.g., Thiobacillus, 8.3-fold) and ammonia-oxidizing archaea (e.g., Nitrososphaera, 46.8-fold). The β-lactam resistance gene in Thiobacillus and the amoA gene in Nitrososphaera may enhance lincomycin's removal by promoting its hydrolysis and hydroxylation. Overall, this study provides insights into OMP biodegradation mechanisms and the impact of ng/L levels of lincomycin on microbial communities.}, } @article {pmid39731890, year = {2024}, author = {Zhang, Y and Zhu, D and Zhou, S and Gong, H and Dai, X}, title = {Antibiotic resistome during two-stage partial nitritation/anammox process for sludge anaerobic digestion reject water treatment.}, journal = {Journal of hazardous materials}, volume = {486}, number = {}, pages = {136967}, doi = {10.1016/j.jhazmat.2024.136967}, pmid = {39731890}, issn = {1873-3336}, abstract = {Anaerobic digestion (AD) reject water serves as a significant reservoir for antibiotic resistance genes (ARGs), underscoring the importance of understanding ARGs dynamics during treatment processes. Partial nitritation /anammox (PN/A) has become an increasingly adopted process, while comprehensive investigation on ARG behavior within this system, especially in full-scale, remains limited. This study explores the distribution of ARGs in a full-scale two-stage PN/A system, with an anaerobic/anoxic/oxic (AAO) system for comparison. The sludge in partial nitritation (PN) stage exhibited higher ARG abundance (0.82 copy/cell) compared to that in anammox stage (0.21-0.26 copy/cell). In anammox sludge samples, 95.8-99.1 % of the mobile genetic elements (MGEs) were identified as tnpA, while the PN stage showing greater diversity. Some ARGs co-occur in the same contigs, and some of these ARGs belong to different ARGs types, which is related to multi-antibiotic resistance, with the highest frequency observed in the PN stage. The abundance of contigs with ARG-MGE co-occurrence, suggesting the possibility of horizontal gene transfer (HGT), was most prevalent in the AAO system. Potential ARG hosts were identified by metagenomic binning, and some functional bacteria, like Nitrosomonas, were regarded as ARGs host. This study offers a comprehensive analysis of the complexities of ARGs distribution within full-scale two-stage PN/A systems treating AD reject water.}, } @article {pmid39731826, year = {2024}, author = {Zhou, G and Wang, YS and Wang, HJ and Sun, TL and Peng, RQ and Li, SJ and Peng, H and Wen, X and Zhu, XX and Zhu, YQ and Cui, ZB and Shi, QS and Xie, XB}, title = {Exploring the gut microbiota and metabolome of Lateolabrax japonicus: A multi-omics approach.}, journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics}, volume = {54}, number = {}, pages = {101408}, doi = {10.1016/j.cbd.2024.101408}, pmid = {39731826}, issn = {1878-0407}, abstract = {The intestinal microbiota plays a crucial role in the health and development of fish, engaging in intricate interactions with the host organism. As a significant species in aquaculture, Lateolabrax japonicus serves as an exemplary model for investigating these interactions and their subsequent effects on growth and health. This study utilized a multi-omics approach, incorporating metagenomic sequencing and non-targeted metabolomics, to delineate the gut microbiota and metabolome of L. japonicus throughout various developmental phases. Collected from a meticulously controlled aquaculture setting, the intestinal microbiota of L. japonicus underwent high-throughput sequencing to scrutinize microbial DNA and enumerate metabolites. The metagenomic analysis uncovered a heterogeneous gut microbiota in L. japonicus, predominantly composed of Proteobacteria and Firmicutes, with marked heterogeneity in microbial composition across developmental stages. A particularly noteworthy discovery was the prevalence of the genus Acinetobacter, which may significantly influence health and disease resistance. The metabolomic profiling discerned 4479 metabolites, each exhibiting pronounced stage-specific metabolic signatures, particularly within lipid, amino acid, and energy metabolism pathways. The correlation analysis between microbiota and metabolites highlighted the substantial impact of specific genera, such as Acinetobacter and Gaeumannomyces, on the metabolic milieu. This study provides a comprehensive overview of the dynamic shifts in the gut microbiota and metabolome of L. japonicus, highlighting stage-specific transitions that could be pivotal for refining aquaculture practices. The findings underscore the complex interdependence between microbiota composition and metabolic function, providing valuable insights into the modulation of fish health and growth.}, } @article {pmid39731654, year = {2024}, author = {Rahimlou, S and Hosseyni Moghadam, MS and Gazis, R and Karlsen-Ayala, E and Bahram, M and James, TY and Tedersoo, L}, title = {Unveiling root nodulation in Tribulus terrestris and Roystonea regia via metagenomics analysis.}, journal = {Molecular genetics and genomics : MGG}, volume = {300}, number = {1}, pages = {9}, pmid = {39731654}, issn = {1617-4623}, support = {1399PUT//Estonian Research Council/ ; 635PRG//Estonian Research Council/ ; }, mesh = {*Symbiosis/genetics ; *Metagenomics/methods ; *Phylogeny ; *Tribulus/genetics ; Plant Root Nodulation/genetics ; Nitrogen Fixation/genetics ; Root Nodules, Plant/microbiology/genetics ; Metagenome/genetics ; Plant Roots/microbiology/genetics ; Endophytes/genetics/isolation & purification ; Bacteria/genetics/classification/isolation & purification ; }, abstract = {Root nodule symbiosis is traditionally recognized in the Fabales, Fagales, Cucurbitales, and Rosales orders within the Rosid I clade of angiosperms. However, ambiguous root nodule formation has been reported in Zygophyllaceae and Roystonea regia (Arecaceae), although a detailed analysis has yet to be conducted. We aimed to perform morphological analyses of root structures in these plants and utilize metagenomic techniques to identify and characterize the bacterial populations within the nodule-like structures. We collected root samples of Tribulus terrestris (Zygophyllaceae) and Roystonea regia from West Asia and the Caribbean, respectively. We conducted detailed morphological analyses of nodule-like structures, isolated and genome-sequenced the endophytes, and employed metagenomic techniques to identify the bacterial populations within these formations. We observed nodule-like structures in both plant species. Symbiosomes, which are hallmark structures of nodulating plants, were not detected. Metagenome sequence data analysis revealed potential nodulating and nitrogen-fixing bacteria in the nodule-like structures of both species. Canonical nodulation and nitrogen-fixation genes were identified in microbes associated with the nodules. However, the phylogenomic analysis showed that the bacteria isolated from T. terrestris and R. regia are within Gammaproteobacteria and Bacilli, which are not typically known as nodulating bacteria. The observed structures differ significantly from traditional nodules found in legumes and actinorhizal plants, suggesting unique characteristics with hosting nitrogen-fixing bacteria. Although bacteria identified through in silico analysis or culture are well-known nitrogen-fixers, their specific role in root nodule formation remains to be investigated.}, } @article {pmid39731186, year = {2024}, author = {Shi, J and Liu, R and Qiu, J and Wei, C and Pan, D and Xiang, T and Cheng, N}, title = {Pulmonary infection caused by Tropheryma whipplei: a case report and review of the literature.}, journal = {Journal of medical case reports}, volume = {18}, number = {1}, pages = {613}, pmid = {39731186}, issn = {1752-1947}, support = {GJJ2200217//Science and Technology Research Project of the Education Department of Jiangxi Province/ ; }, mesh = {Humans ; Female ; Aged ; *Tropheryma/isolation & purification ; *Anti-Bacterial Agents/therapeutic use ; Whipple Disease/diagnosis/drug therapy/microbiology ; Tomography, X-Ray Computed ; Pneumonia, Bacterial/microbiology/diagnosis/drug therapy ; High-Throughput Nucleotide Sequencing ; Doxycycline/therapeutic use ; Bronchoalveolar Lavage Fluid/microbiology ; }, abstract = {BACKGROUND: Tropheryma whipplei pneumonia is an infrequent medical condition. The clinical symptoms associated with this disease are nonspecific, often resulting in misdiagnosis or missed diagnosis. Therefore, sharing and summarizing the experiences in the diagnosis and treatment of this disease can deepen global understanding and awareness of it.

CASE PRESENTATION: The patient is a 78-year-old married Han Chinese female who was admitted to the hospital after experiencing fever, dry cough, and fatigue for 4 days. A lung computed tomography scan revealed inflammatory exudation in the lower left lung, accompanied by pleural effusion. The bronchoalveolar lavage fluid was subjected to further analysis using metagenomic next-generation sequencing, which identified 41 genetic sequences associated with Tropheryma whipplei. Consequently, she was diagnosed with Tropheryma whipplei pneumonia. After initiating treatment with doxycycline and biapenem, the patient's symptoms showed significant improvement. Upon discharge, the patient continued treatment with a combination of doxycycline and hydroxychloroquine, which was discontinued after 4 days. At 12-month follow-up, the patient reported overall good health, with no symptoms of fever, cough, or any other discomfort.

CONCLUSION: Tropheryma whipplei pneumonia is a rare condition with nonspecific symptoms. The application of metagenomic next-generation sequencing technology in pulmonary infections helps to rapidly identify rare pathogens, providing a solid foundation for precise and effective antibacterial treatment for patients.}, } @article {pmid39731160, year = {2024}, author = {Virtanen, S and Saqib, S and Kanerva, T and Ventin-Holmberg, R and Nieminen, P and Holster, T and Kalliala, I and Salonen, A}, title = {Metagenome-validated combined amplicon sequencing and text mining-based annotations for simultaneous profiling of bacteria and fungi: vaginal microbiota and mycobiota in healthy women.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {273}, pmid = {39731160}, issn = {2049-2618}, mesh = {Humans ; *Vagina/microbiology ; Female ; *RNA, Ribosomal, 16S/genetics ; *Fungi/genetics/classification/isolation & purification ; *Bacteria/genetics/classification/isolation & purification ; *Microbiota/genetics ; *Metagenome ; *Data Mining ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Mycobiome ; Healthy Volunteers ; DNA, Bacterial/genetics ; }, abstract = {BACKGROUND: Amplicon sequencing of kingdom-specific tags such as 16S rRNA gene for bacteria and internal transcribed spacer (ITS) region for fungi are widely used for investigating microbial communities. So far most human studies have focused on bacteria while studies on host-associated fungi in health and disease have only recently started to accumulate. To enable cost-effective parallel analysis of bacterial and fungal communities in human and environmental samples, we developed a method where 16S rRNA gene and ITS1 amplicons were pooled together for a single Illumina MiSeq or HiSeq run and analysed after primer-based segregation. Taxonomic assignments were performed with Blast in combination with an iterative text-extraction-based filtration approach, which uses extensive literature records from public databases to select the most probable hits that were further validated by shotgun metagenomic sequencing.

RESULTS: Using 50 vaginal samples, we show that the combined run provides comparable results on bacterial composition and diversity to conventional 16S rRNA gene amplicon sequencing. The text-extraction-based taxonomic assignment-guided tool provided ecosystem-specific bacterial annotations that were confirmed by shotgun metagenomic sequencing (VIRGO, MetaPhlAn, Kraken2). Fungi were identified in 39/50 samples with ITS sequencing while in the metagenome data fungi largely remained undetected due to their low abundance and database issues. Co-abundance analysis of bacteria and fungi did not show strong between-kingdom correlations within the vaginal ecosystem of healthy women.

CONCLUSION: Combined amplicon sequencing for bacteria and fungi provides a simple and cost-effective method for simultaneous analysis of microbiota and mycobiota within the same samples. Conventional metagenomic sequencing does not provide sufficient fungal genome coverage for their reliable detection in vaginal samples. Text extraction-based annotation tool facilitates ecosystem-specific characterization and interpretation of microbial communities by coupling sequence homology to microbe metadata readily available through public databases. Video Abstract.}, } @article {pmid39731152, year = {2024}, author = {Liang, L and Kong, C and Li, J and Liu, G and Wei, J and Wang, G and Wang, Q and Yang, Y and Shi, D and Li, X and Ma, Y}, title = {Distinct microbes, metabolites, and the host genome define the multi-omics profiles in right-sided and left-sided colon cancer.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {274}, pmid = {39731152}, issn = {2049-2618}, support = {No. 22PJD013//Shanghai Pujiang Program/ ; Nos. 81920108026 and 82372594//National Natural Science Foundation of China/ ; No.23410710500//Shanghai Science and Technology Development Foundation/ ; }, mesh = {Humans ; *Colonic Neoplasms/microbiology/genetics/metabolism ; *Gastrointestinal Microbiome/genetics ; Male ; *RNA, Ribosomal, 16S/genetics ; Female ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Middle Aged ; Metabolomics ; Metabolome ; Feces/microbiology ; Aged ; Exome Sequencing ; Metagenomics/methods ; Multiomics ; }, abstract = {BACKGROUND: Studies have reported clinical heterogeneity between right-sided colon cancer (RCC) and left-sided colon cancer (LCC). However, none of these studies used multi-omics analysis combining genetic regulation, microbiota, and metabolites to explain the site-specific difference.

METHODS: Here, 494 participants from a 16S rRNA gene sequencing cohort (50 RCC, 114 LCC, and 100 healthy controls) and a multi-omics cohort (63 RCC, 79 LCC, and 88 healthy controls) were analyzed. 16S rRNA gene, metagenomic sequencing, and metabolomics analyses of fecal samples were evaluated to identify tumor location-related bacteria and metabolites. Whole-exome sequencing (WES) and transcriptome sequencing (RNA-seq) were conducted to obtain the mutation burden and genomic expression pattern.

RESULTS: We found unique profiles of the intestinal microbiome, metabolome, and host genome between RCC and LCC. The bacteria Flavonifractor plautii (Fp) and Fusobacterium nucleatum, the metabolites L-phenylalanine, and the host genes PHLDA1 and WBP1 were the key omics features of RCC; whereas the bacteria Bacteroides sp. A1C1 (B.A1C1) and Parvimonas micra, the metabolites L-citrulline and D-ornithine, and the host genes TCF25 and HLA-DRB5 were considered the dominant omics features in LCC. Multi-omics correlation analysis indicated that RCC-enriched Fp was related to the accumulation of the metabolite L-phenylalanine and the suppressed WBP1 signal in RCC patients. In addition, LCC-enriched B.A1C1 was associated with the accumulation of the metabolites D-ornithine and L-citrulline as well as activation of the genes TCF25, HLA-DRB5, and AC079354.1.

CONCLUSION: Our findings identify previously unknown links between intestinal microbiota alterations, metabolites, and host genomics in RCC vs. LCC, suggesting that it may be possible to treat colorectal cancer (CRC) by targeting the gut microbiota-host interaction. Video Abstract.}, } @article {pmid39731100, year = {2024}, author = {You, Y and Ni, YM and Shi, G}, title = {Diagnostic accuracy of metagenomic next-generation sequencing in pulmonary tuberculosis: a systematic review and meta-analysis.}, journal = {Systematic reviews}, volume = {13}, number = {1}, pages = {317}, pmid = {39731100}, issn = {2046-4053}, mesh = {Humans ; *Tuberculosis, Pulmonary/diagnosis/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Mycobacterium tuberculosis/genetics/isolation & purification ; *Bronchoalveolar Lavage Fluid/microbiology ; *Sputum/microbiology ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) has emerged as a promising tool in clinical practice due to its unbiased approach to pathogen detection. Its diagnostic performance in pulmonary tuberculosis (PTB), however, remains to be fully evaluated.

OBJECTIVE: This study aims to systematically review and Meta-analyze the diagnostic accuracy of mNGS in patients with PTB.

METHODS: We conducted a literature search in PubMed (MEDLINE), Web of Science, Cochrane, and EMBASE databases, including studies published up to 2024. Studies comparing the diagnostic accuracy of mNGS with other methods such as Xpert-MTB/RIF and Mycobacteria tuberculosis (MTB) culture using bronchoalveolar lavage fluid (BALF), sputum, and lung biopsy tissue were included. Preclinical studies, review articles, editorials, conference abstracts, and book chapters were excluded. Statistical analysis was performed using Rev-man5, R package metabias, and Stata software.

RESULTS: Thirteen studies met the inclusion criteria and were included in the meta-analysis. The pooled sensitivity and specificity of mNGS for PTB were 83% (95% CI: 69-91%) and 99% (95% CI: 92-100%), respectively. Subgroup analyses revealed that in BALF, mNGS demonstrated a pooled sensitivity of 73% (95% CI: 61-82%) and specificity of 98% (95% CI: 92-100%); in the sputum, the pooled sensitivity was 60% (95% CI: 38-87%) with a specificity of 99% (95% CI: 96-100%); and in the lung biopsy tissue, the pooled sensitivity was 71% (95% CI: 38-95%) and the specificity was 98% (95% CI: 93-100%). For Xpert-MTB/RIF, the pooled sensitivity and specificity were 72% (95% CI: 53-85%) and 100% (95%CI: 100-100%), respectively. Subgroup analyses demonstrated that in BALF, Xpert-MTB/RIF exhibited a pooled sensitivity of 69% (95% CI: 53-81%) and a specificity of 100% (95% CI: 77-100%). The pooled sensitivity and specificity of mycobacteria culture were 50% (95% CI: 36-64%) and 100% (95% CI: 83-100%), respectively. Subgroup analyses indicated that in BALF, the pooled sensitivity of mycobacteria culture was 44% (95% CI: 37-52%) with a specificity of 100% (95% CI: 8-100%); in the sputum, the pooled sensitivity was 42% (95% CI: 21-65%) and the specificity was 100% (95% CI: 100-100%). When combining mNGS with Xpert-MTB/RIF, the pooled sensitivity and specificity were 79% (95% CI: 40-97%) and 98% (95% CI: 95-100%), respectively.

CONCLUSION: mNGS demonstrates similar diagnostic accuracy to Xpert-MTB/RIF in PTB and outperforms mycobacteria culture in terms of sensitivity. Furthermore, mNGS exhibits good detection capabilities across various PTB clinical samples.

PROSPERO CRD42023427586.}, } @article {pmid39730362, year = {2024}, author = {Liu, W and Liu, Z and Fan, X and Li, D and Zhao, T and Niu, Y and Baima, Y and Wen, D and Li, B and Huang, X}, title = {Brassica rapa L. polysaccharide mitigates hypobaric hypoxia-induced oxidation and intestinal damage via microbiome modulation.}, journal = {NPJ science of food}, volume = {8}, number = {1}, pages = {112}, pmid = {39730362}, issn = {2396-8370}, support = {XZ202401ZY0033//Key Research and Development Program in Xizang Autonomous Region/ ; XZ202301ZY0018N//Key Research and Development Program in Xizang Autonomous Region/ ; 32060761//National Natural Science Foundation of China/ ; }, abstract = {The high-altitude, low-pressure, and hypoxia environment poses a significant threat to human health, particularly causing intestinal damage and disrupting gut microbiota. This study investigates the protective effects of Brassica rapa L. crude polysaccharides (BRP) on intestinal damage in mice exposed to hypobaric hypoxic conditions. Results showed that oxidative stress and inflammation levels were elevated in the hypoxia group, while BRP intervention significantly increased antioxidant enzyme activities (SOD, GSH-Px, T-AOC) and reduced inflammatory markers (IL-6, IL-1β, TNF-α). BRP also restored intestinal barrier function by enhancing claudin-1, occludin, and ZO-1 expression. Notably Chromatographic and metagenomic analyses revealed that BRP enriched butyrate levels, promoted beneficial bacteria like Akkermansia muciniphila and Leuconostoc lactis, and upregulated L-arginine biosynthesis II and L-methionine biosynthesis III pathways to enhance antioxidant activity. Fecal microbiota transfer experiments confirmed the role of gut microbiota in mediating BRP's protective effects, providing valuable insights into prebiotic-based therapeutic strategies for hypobaric hypoxia-induced intestinal damage.}, } @article {pmid39730187, year = {2025}, author = {Yan, M and Andersen, TO and Pope, PB and Yu, Z}, title = {Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases.}, journal = {Genome research}, volume = {}, number = {}, pages = {}, doi = {10.1101/gr.279825.124}, pmid = {39730187}, issn = {1549-5469}, abstract = {Metagenomics, particularly genome-resolved metagenomics, have significantly deepened our understanding of microbes, illuminating their taxonomic and functional diversity and roles in ecology, physiology, and evolution. However, eukaryotic populations within various microbiomes, including those in the mammalian gastrointestinal (GI) tract, remain relatively underexplored in metagenomic studies owing to the lack of comprehensive reference genome databases and robust bioinformatic tools. The GI tract of ruminants, particularly the rumen, contains a high eukaryotic biomass but a relatively low diversity of ciliates and fungi, which significantly impacts feed digestion, methane emissions, and rumen microbial ecology. In the present study, we developed GutEuk, a bioinformatics tool that improves upon the currently available Tiara and EukRep in accurately identifying eukaryotic sequences from metagenomes. GutEuk is optimized for high precision across different sequence lengths. It can also distinguish fungal and protozoal sequences, further elucidating their unique ecological, physiological, and nutritional impacts. GutEuk was shown to facilitate comprehensive analyses of protozoa and fungi within more than 1000 rumen metagenomes, revealing a greater genomic diversity among protozoa than previously documented. We further curated several ruminant eukaryotic protein databases, significantly enhancing our ability to distinguish the functional roles of ruminant fungi and protozoa from those of prokaryotes. Overall, the newly developed package GutEuk and its associated databases create new opportunities for the in-depth study of GI tract eukaryotes.}, } @article {pmid39730090, year = {2025}, author = {Nguyen, TV and Kim, NK and Lee, SH and Trinh, HP and Park, HD}, title = {Gene abundance and microbial syntrophy as key drivers of anaerobic digestion revealed through 16S rRNA gene and metagenomic analysis.}, journal = {Chemosphere}, volume = {370}, number = {}, pages = {144028}, doi = {10.1016/j.chemosphere.2024.144028}, pmid = {39730090}, issn = {1879-1298}, mesh = {Anaerobiosis ; *RNA, Ribosomal, 16S/genetics ; *Wastewater/microbiology ; *Metagenomics ; *Bacteria/metabolism/genetics/classification ; Butyrates/metabolism ; Acetates/metabolism ; Bioreactors/microbiology ; Waste Disposal, Fluid ; }, abstract = {Genes in microorganisms influence the biological processes in anaerobic digestion (AD). However, key genes involved in the four metabolic steps (hydrolysis, acidogenesis, acetogenesis, and methanogenesis) remain largely unexplored. This study investigated the abundance and distribution of key functional genes in full-scale anaerobic digesters processing food waste (FWDs) and municipal wastewater (MWDs) through 16S rRNA gene and shotgun metagenomic analysis. Our results revealed that FWDs exhibited a higher abundance of key genes in the metabolic steps, despite having significantly lower microbial diversity compared to MWDs. Pathways and genes associated with syntrophic oxidation of acetate (SAO) and butyrate (SBO) were more present in FWDs. SAO potentially used both the conventional reversed Wood-Ljungdahl pathway and its integration with the glycine cleavage system in FWDs, which complements pathways for acetate oxidation under ammonia stress conditions. Similarly, genes associated with SBO (atoB and croR) were notably more prevalent in FWDs compared to MWDs with an 8.4-fold and 108-fold increase, respectively, indicating the adaptation of SBO bacteria to convert butyrate into acetate. The higher abundance of key genes in FWDs was driven by microbes adapting to the feedstock compositions with higher levels of substrate content, volatile fatty acids, and ammonia. This study quantified the genes central to AD metabolism and uncovered the contributions of microbial diversity, gene abundance, syntrophy, and feedstock characteristics to the functionality of AD processes. These findings enhance understanding of the microbial ecology in AD and provide a foundation for developing innovative strategies to enhance biogas production and waste management.}, } @article {pmid39729886, year = {2025}, author = {Tang, H and Chen, Y and Tang, X and Wei, M and Hu, J and Zhang, X and Xiang, D and Yang, Q and Han, D}, title = {Yield of clinical metagenomics: insights from real-world practice for tissue infections.}, journal = {EBioMedicine}, volume = {111}, number = {}, pages = {105536}, pmid = {39729886}, issn = {2352-3964}, mesh = {Humans ; *Metagenomics/methods ; Male ; Female ; Middle Aged ; Adult ; *High-Throughput Nucleotide Sequencing ; Retrospective Studies ; Cross-Sectional Studies ; Aged ; China/epidemiology ; Metagenome ; Young Adult ; Adolescent ; Child ; }, abstract = {BACKGROUND: While metagenomic next-generation sequencing (mNGS) has been acknowledged as a valuable diagnostic tool for infections, its clinical validity and impact on patient management when using fresh tissue samples remains uncertain.

METHODS: We conducted a retrospective cross-sectional study involving patients who underwent tissue mNGS at a tertiary hospital in China from February 2021 to February 2024, aiming to assess its ability to detect plausible pathogens and its clinical validity and impact.

FINDINGS: A total of 520 mNGS results from 508 patients were analysed, detecting plausible pathogens in 302 (58.1%) tests, including 260 single-pathogen and 42 (13.9%) multi-pathogen results. Rare pathogens, such as Balamuthia mandrillaris, Bartonella henselae, and Sporothrix globosa, were identified. Of the multi-pathogen results, 22 were with predominance of anaerobes. mNGS showed higher positivity in cases with high initial suspicion of infection than those used for ruling out infection (PR 1.961, 95% CI: 1.604-2.394) and in patients living with HIV (PR 1.312, 95% CI: 1.047-1.643) or solid organ transplant recipients (PR 1.346, 95% CI: 1.103-1.643) compared to immunocompetent individuals. Sensitivity and specificity for diagnosing confirmed/probable infections were 85.0% (95% CI: 76.7%-93.3%) and 93.7% (95% CI: 86.8%-100.0%), respectively. mNGS influenced clinical management in 258 (49.6%) cases by identifying new infections and in 112 (21.5%) by excluding infections. It prompted initiation (20.2%), modification (23.1%), or discontinuation (6.3%) of antimicrobial therapy.

INTERPRETATION: mNGS demonstrates high diagnostic accuracy for tissue infections. Its impact on clinical management highlights the need to integrate it into current diagnostic practices.

FUNDING: National Natural Science Foundation of China (No. 82472371), "Leading Geese" Research and Development Plan of Zhejiang Province (No. 2024C03218), and Pudong New Area Joint Project (PW2021D-09).}, } @article {pmid39729871, year = {2025}, author = {Adyari, B and Zhang, L and Maravić, A and Chen, J and Li, L and Gad, M and Yu, CP and Hu, A}, title = {Urbanization enhances consumer protist-driven ARGs dissemination in riverine ecosystems.}, journal = {Environment international}, volume = {195}, number = {}, pages = {109238}, doi = {10.1016/j.envint.2024.109238}, pmid = {39729871}, issn = {1873-6750}, mesh = {*Urbanization ; *Rivers/microbiology/chemistry ; China ; *Ecosystem ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Eukaryota/genetics ; }, abstract = {Despite the emergence of antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARBs), how biological inter-trophic interactions, modulated by watershed urbanization, shape the resistome remains unexplored. We collected water samples from the highly urbanized (western: 65 % built land, sewage-affected) and lesser-urbanized (northern: 25 % built land, drinking water source) downstream tributaries of the Jiulong River in southeast China over dry and wet seasons. We utilized metagenomic and amplicon (16S and 18S rDNA) sequencing to investigate the relationships among microeukaryotic algae, consumer protists, bacterial communities, and the resistome. Metagenomic results showed that ARG-MGE-carrying contigs (mobile ARGs), rather than ARG-carrying contigs (non-mobile ARGs), exhibited more pronounced discrepancies between tributaries. A higher total abundance of ARGs and a greater number of co-shared ARGs between pathogen and non-pathogen bacteria were observed in the more urbanized western tributary. Structural equation modeling revealed that consumer protist-bacteria and algae-bacteria cohesions predominantly influenced the resistome in the western and northern tributaries, respectively. Additionally, consumer protists had more significant associations (511 out of 634) with bacteria carrying mobile ARGs in western tributary, while algae had more significant associations (73 out of 105) in northern tributary. These results highlight the distinct inter-trophic driving factors of the resistome modulated by watershed urbanization.}, } @article {pmid39729867, year = {2025}, author = {Gao, FZ and Jia, WL and Li, B and Zhang, M and He, LY and Bai, H and Liu, YS and Ying, GG}, title = {Contaminant-degrading bacteria are super carriers of antibiotic resistance genes in municipal landfills: A metagenomics-based study.}, journal = {Environment international}, volume = {195}, number = {}, pages = {109239}, doi = {10.1016/j.envint.2024.109239}, pmid = {39729867}, issn = {1873-6750}, mesh = {*Waste Disposal Facilities ; *Metagenomics ; China ; *Bacteria/genetics/drug effects ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Humans ; Genes, Bacterial ; Solid Waste ; Refuse Disposal ; }, abstract = {Municipal landfills are hotspot sources of antimicrobial resistance (AMR) and are also important habitats of contaminant-degrading bacteria. However, high diversity of antibiotic resistance genes (ARGs) in landfills hinders assessing AMR risks in the affected environment. More concerned, whether there is co-selection or enrichment of antibiotic-resistant bacteria and contaminant-degrading bacteria in these extremely polluted environments is far less understood. Here, we collected metagenomic datasets of 32 raw leachate and 45 solid waste samples in 22 municipal landfills of China. The antibiotic resistome, antibiotic-resistant bacteria and contaminant-degrading bacteria were explored, and were then compared with other environmental types. Results showed that the antibiotic resistome in landfills contained 1,403 ARG subtypes, with the total abundance over the levels in natural environments and reaching the levels in human feces and sewage. Therein, 49 subtypes were listed as top priority ARGs for future surveillance based on the criteria of enrichment in landfills, mobilizable and present in pathogens. By comparing to those in less contaminated river environments, we elucidated an enrichment of antibiotic-resistant bacteria with contaminant-degrading potentials in landfills. Bacteria in Pseudomonadaceae, Moraxellaceae, Xanthomonadaceae and Enterobacteriaceae deserved the most concerns since 72.2 % of ARG hosts were classified to them. Klebsiella pneumoniae, Acinetobacter nosocomialis and Escherichia coli were abundant multidrug-resistant pathogenic species in raw leachate (∼10.2 % of total microbiomes), but they rarely carried contaminant-degradation genes. Notably, several bacterial genera belonging to Pseudomonadaceae had the most antibiotic-resistant, pathogenic, and contaminant-degrading potentials than other bacteria. Overall, the findings highlight environmental selection for contaminant-degrading antibiotic-resistant pathogens, and provide significant insights into AMR risks in municipal landfills.}, } @article {pmid39729842, year = {2025}, author = {Wang, M and Zhao, J and Gu, Y and Wu, Y and Liu, Y and Tang, Z and Xu, Y and Mao, X and Zhang, J and Tian, W}, title = {Deciphering the mechanism of rhizosphere microecosystem in modulating rice cadmium accumulation via integrating metabolomics and metagenomics.}, journal = {The Science of the total environment}, volume = {959}, number = {}, pages = {178181}, doi = {10.1016/j.scitotenv.2024.178181}, pmid = {39729842}, issn = {1879-1026}, mesh = {*Cadmium/metabolism/analysis ; *Oryza/microbiology/metabolism ; *Rhizosphere ; *Soil Pollutants/metabolism/analysis ; Metabolomics ; Metagenomics ; Soil Microbiology ; Microbiota ; }, abstract = {Cadmium (Cd) accumulation in rice poses significant risks to human health. The Cd accumulation levels vary widely among cultivars and are strongly associated with the rhizosphere microecosystem. However, the underlying mechanisms remain poorly understood. Here, we conducted a field experiment in Cd-contaminated areas with 24 popular regional cultivars. These cultivars were categorized into high Cd accumulation (HA) and low Cd accumulation (LA) groups based on their grain Cd content. Rhizosphere soil physicochemical properties were monitored, and key metabolites, microbiomes, and their interaction contributing to Cd accumulation were analyzed using omics-sequencing technologies and bioinformatics analysis. Metabolomic analysis identified distinct rhizosphere metabolite profiles between the HA and LA groups, with key metabolites showing strong correlations with Cd accumulation. Key metabolites in the LA group were linked to reduced Cd uptake and enhanced antioxidant defense mechanisms, while those in the HA group were associated with increased Cd mobility and uptake. Metagenomic analysis of the rhizosphere soil showed that the LA group harbored a more diverse and interconnected microbial community, with tax such as Syntrophaceae, Anaerolineae, Thermoflexales, and Syntrophales, along with metabolite such as disopyramide, playing central roles in Cd immobilization and detoxification. Additionally, the enhanced carbon, nitrogen, and phosphorus cycling in the LA group suggests a more robust nutrient assimilation process that supports plant growth and reduces Cd uptake. This study highlights the critical role of the rhizosphere microecosystem in regulating Cd accumulation and underscores the potential of selecting rice cultivars with favorable rhizosphere traits as a strategy for reducing Cd uptake.}, } @article {pmid39729273, year = {2025}, author = {Randall, E and Keillor, B and Cooke, DEL}, title = {The Use of eDNA Metabarcoding to Detect and Identify Phytophthora in Water Samples.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2892}, number = {}, pages = {117-138}, pmid = {39729273}, issn = {1940-6029}, mesh = {*Phytophthora/genetics/isolation & purification ; *DNA Barcoding, Taxonomic/methods ; Water/chemistry ; Water Microbiology ; Metagenomics/methods ; }, abstract = {We describe a protocol to amplify DNA barcodes of known and unknown taxa of Phytophthora and related plant pathogenic oomycetes from a range of environments. The methods focus on sampling pathogen propagules from water using in situ sampling and filtration equipment and buffers that enable efficient storage and DNA extraction for later downstream processing.}, } @article {pmid39728955, year = {2024}, author = {Kalaignazhal, G and Sejian, V and Velayudhan, SM and Mishra, C and Rebez, EB and Chauhan, SS and DiGiacomo, K and Lacetera, N and Dunshea, FR}, title = {Applications of Next-Generation Sequencing Technologies and Statistical Tools in Identifying Pathways and Biomarkers for Heat Tolerance in Livestock.}, journal = {Veterinary sciences}, volume = {11}, number = {12}, pages = {}, pmid = {39728955}, issn = {2306-7381}, abstract = {The climate change-associated abnormal weather patterns negatively influences the productivity and performance of farm animals. Heat stress is the major detrimental factor hampering production, causing substantial economic loss to the livestock industry. Therefore, it is important to identify heat-tolerant breeds that can survive and produce optimally in any given environment. To achieve this goal, a clearer understanding of the genetic differences and the underlying molecular mechanisms associated with climate change impacts and heat tolerance are a prerequisite. Adopting next-generation biotechnological and statistical tools like whole transcriptome analysis, whole metagenome sequencing, bisulphite sequencing, genome-wide association studies (GWAS), and selection signatures provides an opportunity to achieve this goal. Through these techniques, it is possible to identify permanent genetic markers for heat tolerance, and by incorporating those markers in marker-assisted breeding selection, it is possible to achieve the target of breeding for heat tolerance in livestock. This review gives an overview of the recent advancements in assessing heat tolerance in livestock using such 'omics' approaches and statistical models. The salient findings from this research highlighted several candidate biomarkers that have the potential to be incorporated into future heat-tolerance studies. Such approaches could revolutionise livestock production in the changing climate scenario and support the food demands of the growing human population.}, } @article {pmid39728946, year = {2024}, author = {Kim, SH and Miguel, M and Naing, YP and Cho, YI and Lee, SS}, title = {Maternal Transmission of Rotavirus to Calves and Comparison of Colostrum and Fecal Microbiota in Holstein and Hanwoo Cattle.}, journal = {Veterinary sciences}, volume = {11}, number = {12}, pages = {}, pmid = {39728946}, issn = {2306-7381}, support = {NRF-2021R1C1C2014102//National Research Foundation of Korea (NRF) grant funded by the Korea government (Ministry of Science and ICT)/ ; }, abstract = {This study aimed to evaluate rotavirus transmission to calves and analyze microbial communities in cow milk and neonatal calf feces within dairy and beef cattle. A total of 20 cattle, Hanwoo (n = 10), and Holstein (n = 10) were allotted for the study, with each breed comprising five cows and five calves. Colostrum samples were obtained from the dam, while feces were obtained from both the dam and calf. Group A rotavirus was identified in the fecal samples through real-time reverse transcription PCR (RT-qPCR). Bacterial communities present in the colostrum and bovine feces were explored using 16S rRNA metagenomic sequencing. The RT-qPCR results showed that the Cq value of one calf and one cow in the Holstein group was < 35, confirming the presence of rotavirus, whereas the Cq value in the Hanwoo group was > 35, indicating a negative result. For the bacterial communities, significant differences (p < 0.05) were found between the colostrum and fecal samples from the dams and calves, but there were no significant differences between Hanwoo and Holstein cattle. Alpha diversity analysis showed that the Chao1 and Shannon indices revealed significant differences (p < 0.05) among the sample types (cow colostrum, cow feces, and calf feces). The bacterial communities in various sample types from both Hanwoo and Holstein cattle were dominated by the phyla Firmicutes, Proteobacteria, and Bacteroidetes. In addition, the genera shared between the cow colostrum and calf fecal microbiota were higher than those shared between cow and calf feces. Overall, the current study detected rotavirus in Holstein but not in Hanwoo cattle; however, no clear evidence showed the transmission of rotavirus from dam to calf. Moreover, significant variations in bacterial compositions were observed among calf feces, cow feces, and colostrum samples, suggesting the presence of unique microbial profiles.}, } @article {pmid39728937, year = {2024}, author = {Murgia, C and Cubeddu, T and Burrai, GP and Alberti, A and Bertolotti, L and Colitti, B and Prearo, M and Pastorino, P and Esposito, G and Mandrioli, L and Barbera, G and Sanna, MA and Polinas, M and Soto, E and Antuofermo, E}, title = {Systemic Granulomatosis in the Meagre Argyrosomus regius: Fishing for a Plausible Etiology.}, journal = {Veterinary sciences}, volume = {11}, number = {12}, pages = {}, pmid = {39728937}, issn = {2306-7381}, support = {DM 737/2021 risorse 2022 -2023//"Bando interno per la ricerca collaborativa tra Ateneo di Sassari e Ateneo di Cagliari-DM 737/2021 risorse 2022 -2023", Finanziato dall'Unione europea-NextGenerationEU./ ; }, abstract = {Meagre (Argyrosomus regius) is one of the fast-growing species considered for sustainable aquaculture development along the Mediterranean and Eastern Atlantic coasts. The emergence of Systemic Granulomatosis (SG), a disease marked by multiple granulomas in various tissues, poses a significant challenge in meagre aquaculture. In the current study, we investigate the association of Mycobacterium spp. and SG in offshore aquaculture facilities in Sardinia, Italy. A total of 34 adult seemingly healthy meagre were arbitrarily collected and analyzed, combining histological, microbiological, molecular, metagenomics, and in situ techniques to investigate the presence of pathogens. Ziehl-Neelsen (ZN), periodic acid-schiff (PAS), and Giemsa stains were performed for the detection of acid-fast bacteria, common parasites, and fungi within granulomas, respectively. Granulomas were detected in 91% (31/34) of fish. The affected organs were kidney (88%), liver (47%), heart (41%), intestine (17.6%), and brain (5%). Acid-fast staining, along with Mycobacterium spp. specific quantitative PCR (qPCR), in situ hybridization (ISH) assay, and microbiological analyses showed negative results for the detection of Mycobacterium spp. and other bacteria implicated in granuloma formation. However, PCR amplification and sequencing of the 65-kDa heat shock protein gene revealed the presence of M. chelonae in 13% of both formalin-fixed and frozen liver tissues. Bacterial isolation failed to detect nontuberculous mycobacteria (NTM) and other bacteria typically associated with granulomas. Consistently, the use of an M. chelonae-specific probe in ISH failed to identify this bacterial species in granulomas. Collectively, results do not support the role of M. chelonae in the development of granulomas and suggest rejecting the hypothesis of a potential link between NTM and SG.}, } @article {pmid39728500, year = {2024}, author = {Alarifi, SN and Alyamani, EJ and Alarawi, M and Alquait, AA and Alolayan, MA and Aldossary, AM and El-Rahman, RAA and Mir, R}, title = {Integrative Metagenomic Analyses Reveal Gut Microbiota-Derived Multiple Hits Connected to Development of Diabetes Mellitus.}, journal = {Metabolites}, volume = {14}, number = {12}, pages = {}, pmid = {39728500}, issn = {2218-1989}, abstract = {BACKGROUND/OBJECTIVES: Type 2 diabetes mellitus (T2DM) is a chronic metabolic disorder associated with gut dysbiosis. To investigate the association between gut microbiota and T2DM in a Saudi Arabian population.

METHODS: We conducted a comparative analysis of fecal microbiota from 35 individuals, including both T2DM patients and healthy controls. 16S rRNA gene sequencing was employed to characterize the microbial community structure.

RESULTS: Our findings revealed significant differences in microbial composition between the two groups. The T2DM group exhibited a higher abundance of Firmicutes and lower levels of Bacteroidetes compared to the healthy control group. At the genus level, T2DM patients showed a decrease in butyrate-producing bacteria such as Bacteroides and Akkermansia, while an increase in Ruminococcus and Prevotella was observed. Additionally, the T2DM group had a higher abundance of Faecalibacterium, Agathobacter, and Lachnospiraceae, along with a lower abundance of Bacteroides.

CONCLUSIONS: These results suggest that alterations in gut microbiota composition may contribute to the development of T2DM in the Saudi Arabian population. Further large-scale studies are needed to validate these findings and explore potential therapeutic interventions targeting the gut microbiome.}, } @article {pmid39728494, year = {2024}, author = {Cox, A and Nowshad, F and Callaway, E and Jayaraman, A}, title = {Integrated Metagenomic and Metabolomic Analysis of In Vitro Murine Gut Microbial Cultures upon Bisphenol S Exposure.}, journal = {Metabolites}, volume = {14}, number = {12}, pages = {}, pmid = {39728494}, issn = {2218-1989}, support = {R56 ES033052/ES/NIEHS NIH HHS/United States ; T32 ES026568/ES/NIEHS NIH HHS/United States ; 1R56ES033052-01A1/ES/NIEHS NIH HHS/United States ; }, abstract = {BACKGROUND: The gut microbiota are an important interface between the host and the environment, mediating the host's interactions with nutritive and non-nutritive substances. Dietary contaminants like Bisphenol A (BPA) may disrupt the microbial community, leaving the host susceptible to additional exposures and pathogens. BPA has long been a controversial and well-studied contaminant, so its structural analogues like Bisphenol S (BPS) are replacing it in consumer products, but have not been well studied.

METHODS: This study aimed to determine the impact of BPS on C57BL/6 murine gut microbiota using shotgun metagenomic sequencing and the metabolomic profiling of in vitro anaerobic cultures.

RESULTS: The results demonstrated that a supraphysiologic BPS dose did not overtly distort the metagenomic or metabolomic profiles of exposed cultures compared to controls. A distinct BPS-associated metabolite profile was not observed, but several metabolites, including saturated fatty acids, were enriched in the BPS-exposed cultures. In the absence of a BPS-associated enterotype, Lactobacillus species specifically were associated with BPS exposure in a discriminant model.

CONCLUSIONS: Our study provides evidence contrasting the effects of BPS in the gut microbiome to its predecessor, BPA, but also emphasizes the role of inter-animal variation in microbiome composition, indicating that further study is needed to characterize BPS in this context.}, } @article {pmid39728308, year = {2024}, author = {Li, M and Zhu, D and Diao, Q and Liu, X and Bi, X and Dong, J and Sun, J and Xi, Y and Zhang, K}, title = {Clinical Features, Microbiological Characteristics, and Drug Sensitivity Analysis of Rare Human Spinal Pythiosis Strain.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {10}, number = {12}, pages = {}, pmid = {39728308}, issn = {2309-608X}, abstract = {Pythiosis, a rare and formidable infectious disease caused by Pythium insidiosum, is characterized by profound uncertainties in achieving definitive diagnoses, suboptimal outcomes, and an exceptionally high mortality rate. Here, we present a rare case of human spinal pythiosis in southern China. With advanced metagenomic sequencing technology, Pythium insidiosum was pinpointed as the causative pathogen. We discovered that the inoculation of either tissue fragments or homogenate yielded more successful results and enabled a moderate extension of the culture duration to 5-10 days through an exhaustive comparison of diverse inoculation and culture conditions for general clinical specimens. A pronounced genetic affinity of the isolated strain towards the Pythium insidiosum strain MCC 13 was detected after a comprehensive whole-genome sequencing analysis. Antifungal agents exhibited negligible sensitivity towards Pythium insidiosum in an antimicrobial susceptibility test. Conversely, antibacterial agents such as oxazolidinones, tetracyclines, macrolides, and amphenicols demonstrated varying degrees of sensitivity, albeit with most of their minimum inhibitory concentrations (MICs) substantially surpassing the safe concentration ranges for effective clinical treatment. Notably, tigecycline stood out as a promising candidate, exhibiting favorable therapeutic effects at moderate concentrations, making it a potential drug of choice for the control of pythiosis. A combined susceptibility test suggested that combinations of tetracyclines with macrolides, oxazolidinones, and amphenicols exhibited synergistic antibacterial effects, with the combination of doxycycline and trimethoprim-sulfamethoxazole (TMP-SMX) in particular playing a pivotal role. To our surprise, the MICs of iron chelators, specifically deferiprone and deferoxamine, against the strain were exceedingly low, which led to the speculation that exogenous iron chelators may have competitively inhibited the iron-chelating enzymes of the strain. The research derived from this single, rare case has certain limitations, but considering that there are currently no reports of invasive infections of deep organs in humans caused by Pythium insidiosum, the above findings can offer novel insights into the treatment of invasive pythiosis. Combination therapy based on tetracyclines, especially tigecycline, the use of TMP-SMX, and the adjunctive use of iron chelators, represent promising approaches to tackle the clinical challenges in the treatment of invasive pythiosis. However, further studies, including similar cases of spinal pythiosis and in vivo trials, are still needed to validate them. In addition, while paying attention to the therapeutic potentials of the above plans, we should also closely monitor the risks and side effects that may arise from excessive MICs or the expanded use of related drugs during the treatment process.}, } @article {pmid39728114, year = {2024}, author = {Um, S and Jeong, H and Park, JE and Seo, J and Jung, SH and Bae, M and Lee, KT and Moon, K}, title = {Isolation and Characterization of Bioactive Compounds from Saccharomonospora sp. CMS18 and Their Antifungal Properties.}, journal = {Marine drugs}, volume = {22}, number = {12}, pages = {}, pmid = {39728114}, issn = {1660-3397}, mesh = {*Antifungal Agents/pharmacology/chemistry/isolation & purification ; *Candida albicans/drug effects ; *Cryptococcus neoformans/drug effects ; *Candida glabrata/drug effects ; Republic of Korea ; *Microbial Sensitivity Tests ; Indoles/pharmacology/chemistry/isolation & purification ; Saccharomycetales/drug effects ; Caspofungin/pharmacology ; Magnetic Resonance Spectroscopy ; }, abstract = {In this study, metagenomic analysis was employed to investigate the bacterial communities in the Muan tidal mudflat of the Republic of Korea. We used metagenomic analysis to identify the microbial community in tidal soil dominated by Proteobacteria. From this environment, the bacterial strain, Saccharomonospora sp. CMS18, was isolated and yielded two previously unknown compounds, penipaline D (3) and N-acetyl-dimethylallyltryptophan (4). The chemical structures of the isolated compounds along with 6-dimethylallyl-indole (1), 6-dimethylallyltryptophan (2), penipaline D (3), and N-acetyl-dimethylallyltryptophan (4) were structurally investigated using HR-ESI-MS and NMR spectroscopy. The isolated compound 6-dimethylallyl-indole (1) demonstrated broad-spectrum antifungal activity, with IC50 value of 0.04 mM against Candida glabrata and 0.35 mM against both Candida albicans and Cryptococcus neoformans. Additionally, it exhibited additive interaction with caspofungin against C. albicans.}, } @article {pmid39727489, year = {2024}, author = {Popchenko, MI and Karpov, DS and Gladysh, NS and Kovalev, MA and Volodin, VV and Krasnov, GS and Bogdanova, AS and Bolsheva, NL and Fedorova, MS and Kudryavtseva, AV}, title = {Composition, Seasonal Dynamics and Metabolic Potential of the Rhizosphere Microbiome Associated with Wild White Poplar.}, journal = {Biotech (Basel (Switzerland))}, volume = {13}, number = {4}, pages = {}, pmid = {39727489}, issn = {2673-6284}, support = {075-15-2019-1660//Ministry of Science and Higher Education of the Russian Federation/ ; 22-14-00404//Russian Science Foundation/ ; }, abstract = {The white poplar (Populus alba) is a dioecious woody plant with significant potential for the phytoremediation of soils. To realize this potential, it is necessary to utilize growth-promoting microorganisms. One potential source of such beneficial microorganisms is the rhizosphere community of wild-growing trees. However, the structure, dynamics, and metabolism of the rhizosphere community of wild-growing white poplar remain poorly understood. To ascertain seasonal dynamics, species diversity, and metabolic potential, we sequenced 16S rRNA genes in metagenomes derived from 165 soil samples collected in spring and autumn from the root surfaces of 102 trees situated in disparate geographical locations. The three most prevalent phyla across all samples are Proteobacteria, Actinobacteriota, and Acidobacteriota. At the order level, the most prevalent orders are Sphingomonadales and Rhizobiales. Accordingly, the families Sphingomonadaceae and Rhizobiaceae were identified as dominant. The rhizospheric microbiome exhibited substantial inter-seasonal variation. Six families, including Caulobacteraceae, Xanthomonadaceae, Chitinophagaceae, Chthoniobacteraceae, Sphingomonadaceae, and Rhizobiaceae, exhibited alterations (spring-to-autumn) across all geographical locations under study. Members of the Rhizobiaceae family, which includes nitrogen-fixing bacteria, can provide poplar with plant-available forms of nitrogen such as nitrate and ammonium. The rhizosphere microbiome may facilitate the conversion of inorganic sulfur into sulfur-containing amino acids, cysteine and methionine, that are bioavailable to plants. Furthermore, the rhizosphere microbiome is capable of synthesizing amino acids, organic acids (including Krebs cycle acids), and some lipids and sugars. Consequently, the rhizosphere community can stimulate poplar growth by providing it with readily available forms of nitrogen and sulfur, as well as building blocks for the synthesis of proteins, nucleic acids, and other macromolecules. Many of these pathways, including nitrogen fixation, were subjected to seasonal changes.}, } @article {pmid39727002, year = {2024}, author = {Wei, A and Xiao, Z and Fu, L and Zhao, W and Jiang, X}, title = {Predicting phage-host interactions via feature augmentation and regional graph convolution.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {1}, pages = {}, pmid = {39727002}, issn = {1477-4054}, support = {62372205//National Natural Science Foundation of China/ ; ZDI145-56//National Language Commission Key Research Project/ ; KJ02502022-0450//Fundamental Research Funds for Central Universities/ ; 2022CFB289//Natural Science Foundation of Hubei Province of China/ ; CCNU24JC032//Colleges' Basic Research and Operation of MOE/ ; }, mesh = {*Bacteriophages ; *Deep Learning ; Algorithms ; Computational Biology/methods ; Host-Pathogen Interactions ; }, abstract = {Identifying phage-host interactions (PHIs) is a crucial step in developing phage therapy, which is the promising solution to addressing the issue of antibiotic resistance in superbugs. However, the lifestyle of phages, which strongly depends on their host for life activities, limits their cultivability, making the study of predicting PHIs time-consuming and labor-intensive for traditional wet lab experiments. Although many deep learning (DL) approaches have been applied to PHIs prediction, most DL methods are predominantly based on sequence information, failing to comprehensively model the intricate relationships within PHIs. Moreover, most existing approaches are limited for sub-optimal performance, due to the potential risk of overfitting induced by the highly data sparsity in the task of PHIs prediction. In this study, we propose a novel approach called MI-RGC, which introduces mutual information for feature augmentation and employs regional graph convolution to learn meaningful representations. Specifically, MI-RGC treats the presence status of phages in environmental samples as random variables, and derives the mutual information between these random variables as the dependency relationships among phages. Consequently, a mutual information-based heterogeneous network is construted as feature augmentation for sequence information of phages, which is utilized for building a sequence information-based heterogeneous network. By considering the different contributions of neighboring nodes at varying distances, a regional graph convolutional model is designed, in which the neighboring nodes are segmented into different regions and a regional-level attention mechanism is employed to derive node embeddings. Finally, the embeddings learned from these two networks are aggregated through an attention mechanism, on which the prediction of PHIs is condcuted accordingly. Experimental results on three benchmark datasets demonstrate that MI-RGC derives superior performance over other methods on the task of PHIs prediction.}, } @article {pmid39726957, year = {2024}, author = {Zhang, C and La, Y and Ma, X and Zhandui, P and Wu, X and Guo, X and Yan, P and Dunzhu, L and Liang, C}, title = {The effects of different doses of compound enzyme preparations on the production performance, meat quality and rumen microorganisms of yak were studied by metagenomics and transcriptomics.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1491551}, pmid = {39726957}, issn = {1664-302X}, abstract = {Yak (Bos grunniens) is a large ruminant endemic to the Tibetan plateau. The addition of enzyme complexes to feed can significantly improve their growth performance. Therefore, studying the effects of ruminant compound enzyme preparations dosage on yak rumen microorganisms and production performance is crucial to promoting the development of the yak industry. This study aimed to determine the effects of feeding yaks with different doses of ruminant enzyme compounds on the performance, meat quality, and rumen microorganisms of yaks. Three kinds of experimental diets with doses of 0.5 g/kg (LE group), 1 g/kg (ME group), and 2 g/kg (HE group) were selected to determine the growth index, meat quality, serum biochemical indexes, rumen fluid pH and other indexes of the three experimental groups. Metagenomics studies were used to investigate the differences in rumen microbial composition and function among yak groups, and transcriptome sequencing of the longest dorsal muscle was performed to reveal the expression of differential genes among different groups. It was determined that the levels of dietary enzyme complexes significantly affected growth performance, rumen fluid pH, and serum biochemical indices. At the phylum level, the dominant phylum in all three treatment groups was Bacteroidota, Bacillota, Kiritimatiellota, and Pseudomonadota. At the genus level, Prevotella, Methanobrevibacter, Oscillibacter. Fibrobacter showed statistically significant differences in abundance (p < 0.05). CAZymes family analysis revealed significant differences in GHs, CTs, and CEs among the three groups. Genome-wide differential gene expression in the longest muscle of the yak back was analyzed by RNA-seq between the three experimental groups. Some DEGs were found to be enriched in the ECM, PI3K-Akt, PPAR, and protein digestion and absorption receptor pathways. Combined metagenomics and transcriptomics analyses revealed that some microorganisms were significantly associated with the genes COL11A1, POSTN, and PTHLH, which are involved in growth metabolism. In summary, this study investigated the effects and interrelationships of ruminant complex enzymes on yak performance, meat quality, and rumen environment. The results of this study provide a scientific basis for adding ruminant enzymes to yaks.}, } @article {pmid39725980, year = {2024}, author = {Xu, J and Ren, X and Huang, X and Jin, Y and Wang, M and Zhong, L and He, G and Wang, S and Wang, Q and Dai, M and Xiong, Y and Xu, Y and He, X and Pan, Y and Wang, H and Xia, Q and Shao, H and Huang, L and Cai, H}, title = {Epidemiological and clinical characteristics of ammonia-producing microorganisms in the lungs of patients with severe pneumonia: a multicentre cohort study.}, journal = {Journal of translational medicine}, volume = {22}, number = {1}, pages = {1148}, pmid = {39725980}, issn = {1479-5876}, support = {82202356//the National Natural Science Foundation of China/ ; LTGY24H190001//the Zhejiang Provincial Natural Science Fund/ ; }, mesh = {Humans ; Male ; Female ; Middle Aged ; Cohort Studies ; Aged ; *Lung/microbiology/pathology ; *Pneumonia/microbiology ; Ammonia/metabolism ; Intensive Care Units ; Bronchoalveolar Lavage Fluid/microbiology ; Risk Factors ; Ureaplasma/isolation & purification/genetics ; }, abstract = {BACKGROUND: Ureaplasma urealyticum, Ureaplasma parvum, and Mycoplasma hominis were widely known as ammonia-producing microorganisms and can cause hyperammonemia, leading to cerebral edema and altered consciousness, which represent serious complications in lung transplant recipients. However, there is limited knowledge on the epidemiology and outcomes of infections caused by U. urealyticum, U. parvum, and M. hominis in non-transplant patients with severe pneumonia in the ICU.

METHODS: Patients with severe pneumonia who underwent clinical metagenomics of bronchoalveolar lavage fluid (BALF) at the intensive care units (ICUs) of 17 medical centers from January 2019 to March 2023 were enrolled. All cases were divided into the positive group and the negative group based on whether U. urealyticum, U. parvum, or M. hominis was detected in lower respiratory tract. The clinical characteristics and outcomes were compared among the groups. The survival analysis after propensity score matching (PSM) was used to evaluate whether the mortality rate of U. urealyticum, U. parvum, and M. hominis positive patients were increased. Multivariate logistic regression was used to evaluate whether these microbials positivity were a risk factor for central nervous system dysfunction.

RESULTS: In a total number of 1737 patients, 55 patients (3.17%) in the positive group and 1682 patients (96.83%) in the negative group. Patients in the positive group were younger, had a greater proportion of male patients, and had a longer time from ICU admission to clinical metagenomics testing. In contrast, the negative group had a higher proportion of patients with cerebrovascular disease. After PSM, there was no statistically significant difference in 28-day mortality following ICU admission between the two groups (hazard ratio [HR], 0.842; 95% confidence interval [CI], 0.489-1.451; p = 0.536). Multivariate logistic regression analysis showed an association between the detection of U. urealyticum, U. parvum, or M. hominis and neurological dysfunction (odds ratio [OR], 1.84; 95% CI 1.04-3.24; p = 0.035).

CONCLUSION: The detection of U. urealyticum, U. parvum, or M. hominis in the lungs of patients is associated with neurological dysfunction.}, } @article {pmid39725359, year = {2025}, author = {Shi, X and Yasuda, S and Wang, Z and Hu, Y and Wu, G and Lens, P and Zhan, X}, title = {Microbial transitions and degradation pathways driven by butyrate concentration in mesophilic and thermophilic anaerobic digestion under low hydrogen partial pressure.}, journal = {Bioresource technology}, volume = {419}, number = {}, pages = {132012}, doi = {10.1016/j.biortech.2024.132012}, pmid = {39725359}, issn = {1873-2976}, mesh = {Anaerobiosis ; *Methane/metabolism ; *Butyrates/metabolism ; *Hydrogen/metabolism ; Temperature ; Bioreactors/microbiology ; Bacteria/metabolism ; Pressure ; }, abstract = {Butyrate accumulation significantly affects the efficiency and stability of anaerobic digestion, while its specific impact on methane yield and butyrate degradation remains unclear. This study investigated how butyrate concentrations (2.0, 5.0, 10.0, and 20.0 g COD/L) affected methane production and butyrate degradation at 37 °C and 55 °C. Methane yield decreased when butyrate concentrations exceeded 10.0 g COD/L. Methanogenesis transitioned from the acetoclastic to the hydrogenotrophic pathway with butyrate concentration increasing at 37 °C, but this transition wasn't observed at 55 °C. Butyrate was fully degraded at butyrate concentrations of 2.0-20.0 g COD/L. Iso-butyrate production was observed at 37 °C, while it only occurred with 20 g COD/L butyrate at 55 °C. Metagenomic analysis identified distinct microbes responsible for butyrate degradation at each temperature, and revealed a novel iso-butyrate metabolic pathway. These insights significantly advance the comprehension of microbial and enzymatic mechanisms driving butyrate degradation and methane production.}, } @article {pmid39725324, year = {2024}, author = {Kieffer, N and Böhm, ME and Berglund, F and Marathe, NP and Gillings, MR and Larsson, DGJ}, title = {Identification of novel FosX family determinants from diverse environmental samples.}, journal = {Journal of global antimicrobial resistance}, volume = {41}, number = {}, pages = {8-14}, doi = {10.1016/j.jgar.2024.12.018}, pmid = {39725324}, issn = {2213-7173}, abstract = {OBJECTIVES: This study aimed to identify novel fosfomycin resistance genes across diverse environmental samples, ranging in levels of anthropogenic pollution. We focused on fosfomycin resistance, and given its increasing clinical importance, explored the prevalence of these genes within different environmental contexts.

METHODS: Metagenomic DNA was extracted from wastewater and sediment samples collected from sites in India, Sweden, and Antarctica. Class 1 integron gene cassette libraries were prepared, and resistant clones were selected on fosfomycin-supplemented media. Long-read sequencing was performed followed by bioinformatics analysis to identify novel fosfomycin resistance genes. The genes were cloned and functionally characterized in E. coli, and the impact of phosphonoformate on the enzymes was assessed.

RESULTS: Four novel fosfomycin resistance genes were identified. Phylogenetic analysis placed these genes within the FosX family, a group of metalloenzymes that hydrolyse fosfomycin without thiol conjugation. The genes were subsequently renamed fosE2, fosI2, fosI3, and fosP. Functional assays confirmed that these genes conferred resistance to fosfomycin in E. coli, with MIC ranging from 32 μg/ml to 256 μg/ml. Unlike FosA/B enzymes, these FosX-like proteins were resistant to phosphonoformate inhibitory action. A fosI3 homolog was identified in Pseudomonas aeruginosa, highlighting potential clinical relevance.

CONCLUSIONS: This study expands the understanding of fosfomycin resistance by identifying new FosX family members across diverse environments. The lack of phosphonoformate inhibition underscores the clinical importance of these poorly studied enzymes, which warrant further investigation, particularly in pathogenic contexts.}, } @article {pmid39724798, year = {2025}, author = {Simon, SA and Aschmann, V and Behrendt, A and Hügler, M and Engl, LM and Pohlner, M and Rolfes, S and Brinkhoff, T and Engelen, B and Könneke, M and Rodriguez-R, LM and Bornemann, TLV and Nuy, JK and Rothe, L and Stach, TL and Beblo-Vranesevic, K and Leuko, S and Runzheimer, K and Möller, R and Conrady, M and Huth, M and Trabold, T and Herkendell, K and Probst, AJ}, title = {Earth's most needed uncultivated aquatic prokaryotes.}, journal = {Water research}, volume = {273}, number = {}, pages = {122928}, doi = {10.1016/j.watres.2024.122928}, pmid = {39724798}, issn = {1879-2448}, mesh = {*Bacteria/genetics ; *Archaea/genetics ; Ecosystem ; }, abstract = {Aquatic ecosystems house a significant fraction of Earth's biosphere, yet most prokaryotes inhabiting these environments remain uncultivated. While recently developed genome-resolved metagenomics and single-cell genomics techniques have underscored the immense genetic breadth and metabolic potential residing in uncultivated Bacteria and Archaea, cultivation of these microorganisms is required to study their physiology via genetic systems, confirm predicted biochemical pathways, exploit biotechnological potential, and accurately appraise nutrient turnover. Over the past two decades, the limitations of culture-independent investigations highlighted the importance of cultivation in bridging this vast knowledge gap. Here, we collected more than 80 highly sought-after uncultivated lineages of aquatic Bacteria and Archaea with global ecological impact. In addition to fulfilling critical roles in global carbon, nitrogen, and sulfur cycling, many of these organisms are thought to partake in key symbiotic relationships. This review highlights the vital contributions of uncultured microbes in aquatic ecosystems, from lakes and groundwater to the surfaces and depths of the oceans and will guide current and future initiatives tasked with cultivating our planet's most elusive, yet highly consequential aquatic microflora.}, } @article {pmid39724786, year = {2025}, author = {Ma, X and Zhang, J and Jiang, Q and Li, YX and Yang, G}, title = {Human microbiome-derived peptide affects the development of experimental autoimmune encephalomyelitis via molecular mimicry.}, journal = {EBioMedicine}, volume = {111}, number = {}, pages = {105516}, pmid = {39724786}, issn = {2352-3964}, mesh = {*Encephalomyelitis, Autoimmune, Experimental/immunology/etiology/microbiology/metabolism ; Animals ; Humans ; *Molecular Mimicry ; Mice ; *Myelin-Oligodendrocyte Glycoprotein/immunology ; *Gastrointestinal Microbiome ; Multiple Sclerosis/etiology/immunology/microbiology/metabolism ; Peptides/immunology/chemistry ; Disease Models, Animal ; Protein Binding ; CD4-Positive T-Lymphocytes/immunology/metabolism ; Receptors, Antigen, T-Cell/metabolism ; Microbiota ; Peptide Fragments/immunology/metabolism ; Histocompatibility Antigens Class II/metabolism/immunology ; Female ; Computational Biology/methods ; }, abstract = {BACKGROUND: Gut commensal microbiota has been identified as a potential environmental risk factor for multiple sclerosis (MS), and numerous studies have linked the commensal microorganism with the onset of MS. However, little is known about the mechanisms underlying the gut microbiome and host-immune system interaction.

METHODS: We employed bioinformatics methodologies to identify human microbial-derived peptides by analyzing their similarity to the MHC II-TCR binding patterns of self-antigens. Subsequently, we conducted a range of in vitro and in vivo assays to assess the encephalitogenic potential of these microbial-derived peptides.

FINDINGS: We analyzed 304,246 human microbiome genomes and 103 metagenomes collected from the MS cohort and identified 731 nonredundant analogs of myelin oligodendrocyte glycoprotein peptide 35-55 (MOG35-55). Of note, half of these analogs could bind to MHC II and interact with TCR through structural modeling of the interaction using fine-tuned AlphaFold. Among the 8 selected peptides, the peptide (P3) shows the ability to activate MOG35-55-specific CD4[+] T cells in vitro. Furthermore, P3 shows encephalitogenic capacity and has the potential to induce EAE in some animals. Notably, mice immunized with a combination of P3 and MOG35-55 develop severe EAE. Additionally, dendritic cells could process and present P3 to MOG35-55-specific CD4[+] T cells and activate these cells.

INTERPRETATION: Our data suggests the potential involvement of a MOG35-55-mimic peptide derived from the gut microbiota as a molecular trigger of EAE pathogenesis. Our findings offer direct evidence of how microbes can initiate the development of EAE, suggesting a potential explanation for the correlation between certain gut microorganisms and MS prevalence.

FUNDING: National Natural Science Foundation of China (82371350 to GY).}, } @article {pmid39724227, year = {2024}, author = {Shahid, U and Hooi, SL and Lim, SY and Mohd Aris, A and Khor, BC and Ayub, Q and Tan, HS}, title = {Metagenomic surveillance of microbial community and antibiotic resistant genes associated with Malaysian wastewater during the COVID-19 pandemic.}, journal = {Current genetics}, volume = {71}, number = {1}, pages = {1}, pmid = {39724227}, issn = {1432-0983}, mesh = {*Wastewater/microbiology ; *COVID-19/epidemiology ; Malaysia/epidemiology ; *Metagenomics/methods ; *SARS-CoV-2/genetics ; Humans ; Drug Resistance, Microbial/genetics ; Pandemics ; Microbiota/genetics ; Metagenome ; Bacteria/genetics/classification/drug effects ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; }, abstract = {Wastewater is a reservoir of pathogens and hotspots for disseminating antibiotic resistance genes across species. The metagenomic surveillance of wastewater provides insight into the native microbial community, antibiotic-resistance genes (ARGs) and mobile genetic elements. t. The COVID-19 pandemic has caused wider dissemination of ARGs and resistant bacteria in wastewater. Although immensely significant, no research has been performed on the Malaysian wastewater microbial community and ARGs or their correlation with COVID-19 infections. This study utilised a 16S metagenomics approach to characterise the microbial community in Malaysian wastewater during high and low-case phases of the pandemic. Bacteria belonging to Bacteriodales, Bacillales, Actinomycetales and opportunistic pathogens-Arcobacters, Flavobacteria, and Campylobacterales, Neisseriales, were enriched during higher COVID-19 pandemic (active cases). Additionally, copy number profiling of ARGs in water samples showed the prevalence of elements conferring resistance to antibiotics like sulphonamides, cephalosporins, and colistin. The high prevalence of intI1 and other ion-based transporters in samples highlights an extensive risk of horizontal gene transfer to previously susceptible species. Our study emphasises the importance of wastewater surveillance in understanding microbial community dynamics and ARG dissemination, particularly during public health crises like the COVID-19 pandemic.}, } @article {pmid39724159, year = {2024}, author = {Ulbrich, J and Jobe, NE and Jones, DS and Kieft, TL}, title = {Cave Pools in Carlsbad Caverns National Park Contain Diverse Bacteriophage Communities and Novel Viral Sequences.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {163}, pmid = {39724159}, issn = {1432-184X}, support = {NCKRI-NMT Internal Seed Grant Program//National Cave and Karst Research Institute/ ; }, mesh = {*Caves ; *Parks, Recreational ; *Bacteriophages/genetics/isolation & purification/classification ; *Bacteria/genetics/classification/isolation & purification/virology ; *RNA, Ribosomal, 16S/genetics ; California ; Metagenome ; Phylogeny ; Virome ; Biodiversity ; }, abstract = {Viruses are the most abundant biological entities on Earth, and they play a critical role in the environment and biosphere where they regulate microbial populations and contribute to nutrient cycling. Environmental viruses have been the most studied in the ocean, but viral investigations have now spread to other environments. Here, viral communities were characterized in four cave pools in Carlsbad Caverns National Park to test the hypotheses that (i) viral abundance is ten-fold higher than prokaryotic cell abundance in cavern pools, (ii) cavern pools contain novel viral sequences, and (iii) viral communities in pools from developed portions of the cave are distinct from those of pools in undeveloped parts of the same cave. The relationship between viral and microbial abundance was determined through direct epifluorescence microscopy counts. Viral metagenomes were constructed to examine viral diversity among pools, identify novel viruses, and characterize auxiliary metabolic genes (AMGs). Bacterial communities were characterized by 16S rRNA gene amplicon sequencing. Epifluorescence microscopy showed that the ratio of viral-like particles (VLPs) to microorganisms was approximately 22:1 across all sites. Viral communities from pools with higher tourist traffic were more similar to each other than to those from less visited pools, although surprisingly, viruses did not follow the same pattern as bacterial communities, which reflected pool geochemistry. Bacterial hosts predicted from viral sequences using iPHoP showed overlap with both rare and abundant genera and families in the 16S rRNA gene dataset. Gene-sharing network analysis revealed high viral diversity compared to a reference viral database as well as to other aquatic environments. AMG presence showed variation in metabolic potential among the four pools. Overall, Carlsbad Cavern harbors novel viruses with substantial diversity among pools within the same system, indicating that caves are likely an important repository for unexplored viromes.}, } @article {pmid39723822, year = {2025}, author = {Beauchemin, ET and Hunter, C and Maurice, CF}, title = {Dextran sodium sulfate-induced colitis alters the proportion and composition of replicating gut bacteria.}, journal = {mSphere}, volume = {10}, number = {1}, pages = {e0082524}, pmid = {39723822}, issn = {2379-5042}, support = {Frederick Banting and Charles Best Canada Graduate Scholarship-Master's//Canadian Government | Canadian Institutes of Health Research (CIHR)/ ; Ferrings Pharmaceuticals Fellowship//Faculty of Medicine, McGill University (McGill Faculty of Medicine)/ ; Doctoral Research grant//FRQ | Fonds de recherche du Québec - Nature et technologies (FRQNT)/ ; 950-230748 X-242502//Canada Research Chairs (Chaires de recherche du Canada)/ ; PJT-149098//Canadian Government | Canadian Institutes of Health Research (CIHR)/ ; Innovators award//Kenneth Rainin Foundation (KRF)/ ; Owens Catchpaugh IBD Graduate Research Award//McGill University Health Centre (MUHC)/ ; }, mesh = {*Dextran Sulfate/pharmacology ; *Colitis/chemically induced/microbiology ; *Gastrointestinal Microbiome/drug effects ; Biodiversity ; Male ; Female ; Animals ; Mice ; Feces/microbiology ; }, abstract = {The bacteria living in the human gut are essential for host health. Though the composition and metabolism of these bacteria are well described in both healthy hosts and those with intestinal disease, less is known about the metabolic activity of the gut bacteria prior to, and during, disease development-especially regarding gut bacterial replication. Here, we use a recently developed single-cell technique alongside existing metagenomics-based tools to identify, track, and quantify replicating gut bacteria both ex vivo and in situ in the dextran sodium sulfate (DSS) mouse model of colitis. We show that the proportion of replicating gut bacteria decreases when mice have the highest levels of inflammation and returns to baseline levels as mice begin recovering. In addition, we report significant alterations in the composition of the replicating gut bacterial community ex vivo during colitis development. On the taxa level, we observe significant changes in the abundance of taxa such as the mucus-degrading Akkermansia and the poorly described Erysipelatoclostridium genus. We further demonstrate that many taxa exhibit variable replication rates in situ during colitis, including Akkermansia muciniphila. Lastly, we show that colitis development is positively correlated with increases in the presence and abundance of bacteria in situ which are predicted to be fast replicators. This could suggest that taxa with the potential to replicate quickly may have an advantage during intestinal inflammation. These data support the need for additional research using activity-based approaches to further characterize the gut bacterial response to intestinal inflammation and its consequences for both the host and the gut microbial community.IMPORTANCEIt is well known that the bacteria living inside the gut are important for human health. Indeed, the type of bacteria that are present and their metabolism are different in healthy people versus those with intestinal disease. However, less is known about how these gut bacteria are replicating, especially as someone begins to develop intestinal disease. This is particularly important as it is thought that metabolically active gut bacteria may be more relevant to health. Here, we begin to address this gap using several complementary approaches to characterize the replicating gut bacteria in a mouse model of intestinal inflammation. We reveal which gut bacteria are replicating, and how quickly, as mice develop and recover from inflammation. This work can serve as a model for future research to identify how actively growing gut bacteria may be impacting health, or why these particular bacteria tend to thrive during intestinal inflammation.}, } @article {pmid39723812, year = {2025}, author = {Wang, H and Jin, H and Wang, J and Wang, X and Li, X and Yan, J and Yang, Y}, title = {Dehalogenimonas Strain W from Estuarine Sediments Dechlorinates 1,2-Dichloroethane under Elevated Salinity.}, journal = {Environmental science & technology}, volume = {59}, number = {1}, pages = {779-790}, doi = {10.1021/acs.est.4c08999}, pmid = {39723812}, issn = {1520-5851}, mesh = {*Salinity ; Geologic Sediments/microbiology ; Ethylene Dichlorides/metabolism ; }, abstract = {Organohalide-respiring bacteria (OHRB) have been found in various environments and play an indispensable role in the biogeochemical cycling and detoxification of halogenated organic compounds (HOCs). Currently, few ORHB have been reported to perform reductive dechlorination under high salinity conditions, indicating a knowledge gap on the diversity of OHRB and the survival strategy of OHRB in saline environments (e.g., estuarine, marine). This study reports the characterization of an enrichment culture dominated by a new Dehalogenimonas population strain W derived from estuarine sediments, which demonstrates the capability to dechlorinate 1,2-dichloroethane (1,2-DCA) to ethene under elevated salinity (≥5.1% NaCl, w/v). Metagenomic and proteomic analyses revealed that the distinctive high-salinity dechlorination of strain W is primarily attributed to a putative reductive dehalogenase (RDase) DdeA, which shares >91.4% amino acid identity with the dihaloeliminating RDase DcpA from other Dehalogenimonas strains. Additionally, ectoine biosynthesis enzymes (EctABC) contribute to the strain's salt tolerance. These findings underscore the potential of OHRB, particularly Dehalogenimonas, to detoxify HOCs in high-salinity environments, such as estuarine and marine ecosystems, by employing compatible solutes as an adaptive mechanism.}, } @article {pmid39723191, year = {2024}, author = {Kuang, Y and Tan, W and Hu, C and Dai, Z and Bai, L and Wang, J and Liao, H and Chen, H and He, R and Zhu, P and Liu, J and Xie, C and Ke, Z and Tang, KJ}, title = {Diagnosis value of targeted and metagenomic sequencing in respiratory tract infection.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1498512}, pmid = {39723191}, issn = {2235-2988}, mesh = {Humans ; *Respiratory Tract Infections/diagnosis/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Bronchoalveolar Lavage Fluid/microbiology ; *Sensitivity and Specificity ; Male ; Female ; Middle Aged ; Adult ; Aged ; Young Adult ; Bacteria/genetics/isolation & purification/classification ; Aged, 80 and over ; }, abstract = {BACKGROUND: Targeted next-generation sequencing (tNGS) has become a trending tool in the field of infection diagnosis, but concerns are also raising about its performance compared with metagenomic next-generation sequencing (mNGS). This study aims to explore the clinical feasibility of a tNGS panel for respiratory tract infection diagnosis and compare it with mNGS in the same cohort of inpatients.

METHODS: 180 bronchoalveolar lavage fluid samples were collected and sent to two centers for mNGS and tNGS blinded tests, respectively. The concordance between pathogen reports of both methods and the clinical significance among samples with/without known etiology was further evaluated.

RESULTS: Overall, both methods displayed high agreement on pathogen reports, as the average percent agreement reached 95.29%. But tNGS presented a slightly higher detection rate per species than mNGS (PWilcoxon=1.212e-05; standard mean difference = 0.2887091), as detection rates for 32 out of 48 species were higher than those of mNGS. Due to limitations of panel coverage, tNGS identified 28 fewer species than mNGS, among which only 3 were considered clinically relevant. In reference to composite reference standard, accuracy, sensitivity, and specificity combining both tNGS and mNGS reached 95.61%, 96.71%, and 95.68%, respectively, while positive prediction value (PPV) was low at 48.13%, which was caused by low agreement regarding opportunistic pathogens. tNGS and mNGS improved the etiology identification in 30.6% (55/180) and 33.9% (61/180) cases, respectively.

CONCLUSION: Collectively, tNGS presented a similar overall performance in pathogen identification compared to mNGS, but outperformed in some pathogens. This study also demonstrated that deployment of tNGS significantly improves etiology identification in routine practice and provides hints for clinical decisions. The low agreement between clinical diagnosis and NGS reports towards opportunistic pathogens implies that adjudication is essential for report interpretation. Finally, We proposed tNGS as a diagnosis option in clinical practice due to its cost-efficiency.}, } @article {pmid39723142, year = {2024}, author = {Ma, W and Yin, L and Hu, Y and Liu, X and Guo, Z and Zhong, B and Qiu, H and Li, J}, title = {Multi-omics analysis reveals interactions between host and microbes in Bama miniature pigs during weaning.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1482925}, pmid = {39723142}, issn = {1664-302X}, abstract = {INTRODUCTION: There are complex interactions between host and gut microbes during weaning, many of the mechanisms are not yet fully understood. Previous research mainly focuses on commercial pigs, whereas limited information has been known about the host and gut microbe interactions in miniature pigs.

METHODS: To address the issue in Bama miniature piglets that were weaned 30 days after birth, we collected samples on days 25 and 36 for metabolomics, transcriptomics, and microgenomics analysis.

RESULTS AND DISCUSSION: The average daily weight gain of piglets during weaning was only 58.1% and 40.6% of that during 0-25 days and 36-60 days. Metabolomic results identified 61 significantly different metabolites (SDMs), of which, the most significantly increased and decreased SDMs after weaning were ectoine and taurocholate, respectively, indicating the occurrence of inflammation. Metagenomic analysis identified 30 significantly different microbes before and after weaning. Bacteria related to decreasing intestinal inflammation, such as Megasphaera, Alistipes and Bifidobacterium, were enriched before weaning. While bacteria related to infection such as Chlamydia, Clostridium, Clostridioides, and Blautia were enriched after weaning. The carbohydrate enzymes CBM91, CBM13, GH51_1, and GH94 increase after weaning, which may contribute to the digestion of complex plant fibers. Furthermore, we found the composition of antibiotic resistance genes (ARGs) changed during weaning. Transcriptomic analysis identified 147 significantly differentially expressed genes (DEGs). The upregulated genes after weaning were enriched in immune response categories, whereas downregulated genes were enriched in protein degradation. Combining multi-omics data, we identified significant positive correlations between gene MZB1, genera Alistipes and metabolite stachydrine, which involve anti-inflammatory functions. The reduced abundance of bacteria Dialister after weaning had strong correlations with the decreased 2-AGPE metabolite and the downregulated expression of RHBDF1 gene. Altogether, the multi-omics study reflects dietary changes and gut inflammation during weaning, highlighting complex interactions between gut microbes, host genes and metabolites."}, } @article {pmid39722737, year = {2024}, author = {Zhou, P and Zhang, D and Fu, J and Zhu, D and Li, S}, title = {Evaluation of Different Sampling Methods Combined with Metagenomic Next-Generation Sequencing of Respiratory Specimens in Etiological Diagnosis of Patients with Severe Pneumonia.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {5729-5738}, pmid = {39722737}, issn = {1178-6973}, abstract = {OBJECTIVE: To evaluate the value of respiratory specimens collected via different sampling methods combined with metagenomic next-generation sequencing (mNGS) in the etiological diagnosis of severe pneumonia.

METHODS: A total of 117 patients with severe pneumonia between 2019 and 2024 were included in this study, with 60 patients undergoing endotracheal aspiration (ETA) and 57 undergoing bronchoalveolar lavage (BAL), respectively. Patient records were retrospectively reviewed. Both ETA and BAL samples were tested using mNGS and conventional microbiological tests (CMT) to compare the detection rates, microbial profiles and their effects on clinical outcomes.

RESULTS: The positive rates of mNGS for ETA and BAL samples were 96.7% and 80.7%, respectively, which were higher than CMT. A total of 39 pathogenic microorganisms were detected, of which Klebsiella pneumoniae, Candida albicans and herpes simplex virus-4 (HSV-4), and cytomegalovirus (CMV) were the most commonly detected as bacteria, fungi and viruses, respectively. The percentages of Pseudomonas aeruginosa (30.0% vs 12.3%, p = 0.019) and Stenotrophomonas maltophilia (25.0% vs 8.8%, p = 0.020) were significantly higher in the ETA group compared to the BALF group. The detection rate of three or more microorganisms was notably higher in the ETA group. No significant differences existed in antibiotics adjustment between the groups. The ETA group experienced a higher frequency of continuous renal replacement therapy (CRRT), mechanical ventilation and complications. There was no significant difference in the hospital length of stay, duration of mechanical ventilation and mortality between both groups.

CONCLUSION: Respiratory specimens collected by different sampling methods yield different microbial findings. ETA and BAL combined with mNGS play a role in guiding the pathogenetic diagnosis of patients with severe pneumonia. However, it is recommended that their sampling methods be determined by clinical symptoms and patient conditions.}, } @article {pmid39722736, year = {2024}, author = {Chen, J and Wang, J and Deng, Z and Li, Y and Liu, Y and Zhou, J}, title = {Clinical Features of 50 Cases of Chlamydia psittaci Pneumonia Identified Through Metagenomic Next-Generation Sequencing.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {5775-5784}, pmid = {39722736}, issn = {1178-6973}, abstract = {BACKGROUND: Our objective was to analyze the clinical and imaging features of Chlamydia psittaci pneumonia to enhance its diagnostic accuracy.

METHODS: We systematically reviewed the cases of Chlamydia psittaci diagnosed by next-generation sequencing at the Hunan University of Medicine General Hospital between March 2019 and June 2024, summarizing and analyzing their clinical characteristics and imaging features.

RESULTS: A total of 50 cases that met the inclusion criteria were ultimately included in the study analysis. The median age of the patients was 62.96±11.08 years. Notably, 46 patients (92%) had potential exposure to birds or poultry. Forty-six patients (92%) temperature ≥39.0 °C, 37 patients (74%) had cough, 34 patients (68%) had moist rale, and 39 patients (78%) had a relatively slow pulse. Laboratory tests indicated that over 70% of patients exhibited elevated infection markers, accompanied by abnormalities in liver and renal function, electrolyte levels, and cardiac enzymes. Meanwhile, the patient's white blood cell count was normal. Chest CT (Computed Tomography) frequently revealed flaky shadows (94%), thoracic effusions (68%), and thickened pleura (54%). Bronchoscopy revealed significant bronchial mucosal hyperemia, swelling (93.478%), and reduced secretion (56.522%). A total of 44 patients (88%) showed a gradual improvement over 12 days. Forty patients (80%) were treated with doxycycline. Fifty patients were classified into two groups according to whether severe pneumonia occurred after admission. WBC (white blood cell), N% (percentage of neutrophils), NLR (Neutrophil-to-lymphocyte ratio), PLR (platelet/lymphocyte ratio), SII (platelet*Neutrophil/lymphocyte ratio), and PCT (procalcitonin) are indicators that suggest severe cases.

CONCLUSION: The combination of the following indicators is expected to aid in diagnosis of Chlamydia psittaci pneumonia: opportunities to come into contact with birds or poultry, high fever, relatively slow pulse, and elevated infection indicators accompanied by organ injury. Treatment with doxycycline was effective and resulted in favorable prognosis.}, } @article {pmid39722590, year = {2025}, author = {Wu, WK and Lo, YL and Chiu, JY and Hsu, CL and Lo, IH and Panyod, S and Liao, YC and Chiu, THT and Yang, YT and Kuo, HC and Zou, HB and Chen, YH and Chuang, HL and Yen, JJY and Wang, JT and Chiu, HM and Hsu, CC and Kuo, CH and Sheen, LY and Kao, HL and Wu, MS}, title = {Gut microbes with the gbu genes determine TMAO production from L-carnitine intake and serve as a biomarker for precision nutrition.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2446374}, doi = {10.1080/19490976.2024.2446374}, pmid = {39722590}, issn = {1949-0984}, mesh = {*Methylamines/metabolism ; *Gastrointestinal Microbiome ; *Carnitine/metabolism ; Humans ; *Biomarkers/analysis ; Male ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Feces/microbiology ; Female ; Animals ; Adult ; Mice ; Multigene Family ; Middle Aged ; Metagenomics ; Precision Medicine ; }, abstract = {Gut microbial metabolism of L-carnitine, which leads to the production of detrimental trimethylamine N-oxide (TMAO), offers a plausible link between red meat consumption and cardiovascular risks. Several microbial genes, including cntA/B, the cai operon, and the recently identified gbu gene cluster, have been implicated in the conversion of dietary L-carnitine into TMA(O). However, the key microbial genes and associated gut microbes involved in this pathway have not been fully explored. Utilizing the oral carnitine challenge test (OCCT), which specifically measures TMAO production from L-carnitine intake and identifies TMAO producer phenotypes, we compared the abundance of microbial genes between low- and high-TMAO producers across three independent cohorts. Our findings consistently revealed that the gbu gene cluster, rather than cntA/B or the cai operon, was significantly enriched in high-TMAO producers. We further analyzed 292 paired multi-omic datasets from OCCT and shotgun metagenomic sequencing, which demonstrated a significant positive correlation between the abundance of fecal gbu genes and L-carnitine-induced TMAO production, with gbuB showing the strongest correlation. Interestingly, these fecal gbu genes were found to increase with L-carnitine supplementation and decrease with a plant-based diet. Notably, we verified a previously uncultured gbu-containing bacterium, JAGTTR01 sp018223385, as the major contributor to TMA formation in the human gut. We isolated these gbu-containing gut microbes and confirmed their role in TMA/TMAO production using anaerobic incubation and a gnotobiotic mouse model. Using an in-house collection of gbu-containing isolates, we developed a qPCR-based method to quantify fecal gbuB and validated its correlation with L-carnitine-mediated TMAO production as measured by OCCT. Overall, these findings suggest that gbu-containing gut microbes are crucial for TMAO increases following L-carnitine intake and may serve as biomarkers or targets for personalized nutrition.}, } @article {pmid39722539, year = {2025}, author = {Zepeda-Rivera, MA and Eisele, Y and Baryiames, A and Wu, H and Mengoni, C and Piccinno, G and McMahon, EF and LaCourse, KD and Jones, DS and Hauner, H and Minot, SS and Segata, N and Dewhirst, FE and Johnston, CD and Bullman, S}, title = {Fusobacterium sphaericum sp. nov., isolated from a human colon tumor adheres to colonic epithelial cells and induces IL-8 secretion.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2442522}, doi = {10.1080/19490976.2024.2442522}, pmid = {39722539}, issn = {1949-0984}, mesh = {Humans ; *Interleukin-8/metabolism/genetics ; *Colonic Neoplasms/microbiology/pathology ; *Fusobacterium/isolation & purification/genetics ; *Epithelial Cells/microbiology ; *Phylogeny ; Bacterial Adhesion ; Colon/microbiology/pathology ; Feces/microbiology ; Adenocarcinoma/microbiology/pathology ; Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Genome, Bacterial ; }, abstract = {Cancerous tissue is a largely unexplored microbial niche that provides a unique environment for the colonization and growth of specific bacterial communities, and with it, the opportunity to identify novel bacterial species. Here, we report distinct features of a novel Fusobacterium species, F. sphaericum sp. nov. (Fs), isolated from primary colon adenocarcinoma tissue. We acquire the complete closed genome and associated methylome of this organism and phylogenetically confirm its classification into the Fusobacterium genus, with F. perfoetens as its closest neighbor. Fs is phenotypically and genetically distinct, with morphological analysis revealing its coccoid shape, that while similar to F. perfoetens is rare for most Fusobacterium members. Fs displays a metabolic profile and antibiotic resistance repertoire consistent with other Fusobacterium species. In vitro, Fs has adherent and immunomodulatory capabilities, as it intimately associates with human colon cancer epithelial cells and promotes IL-8 secretion. An analysis of the prevalence and abundance of Fs in > 20,000 human metagenomic samples shows that it is a rarely detected member within human stool with variable relative abundance, found in both healthy controls and patients with colorectal cancer (CRC). Our study sheds light on a novel bacterial species isolated directly from the human CRC tumor niche and given its in vitro interaction with cancer epithelial cells suggests that its role in human health and disease warrants further investigation.}, } @article {pmid39722326, year = {2025}, author = {Liu, X and Chen, Y and Liu, Y and Hu, Y and Wang, K and Huang, L and Ke, X and Peng, L and Guo, Z}, title = {Protective effects and mechanisms of extracts of Gleditsia sinensis Lam. Thorn on DSS-induced colitis in mice.}, journal = {Journal of ethnopharmacology}, volume = {340}, number = {}, pages = {119244}, doi = {10.1016/j.jep.2024.119244}, pmid = {39722326}, issn = {1872-7573}, mesh = {Animals ; *Dextran Sulfate ; *Plant Extracts/pharmacology ; Mice ; Male ; *Gastrointestinal Microbiome/drug effects ; *Cytokines/metabolism ; *Mice, Inbred C57BL ; Colitis/chemically induced/drug therapy/pathology ; Disease Models, Animal ; Colon/drug effects/pathology/metabolism ; Anti-Inflammatory Agents/pharmacology ; Colitis, Ulcerative/chemically induced/drug therapy/pathology ; }, abstract = {Inflammatory Bowel Disease (IBD), encompassing Ulcerative Colitis (UC) and Crohn's Disease (CD), stems from a multifaceted interaction of hereditary, immunological, ecological, and microbial elements. Current treatments have limitations, necessitating new therapeutic approaches.

AIM OF THE STUDY: This study investigates the safeguarding impacts and fundamental processes of extracts of Gleditsia sinensis Lam. thorn (EGST) in a dextran sulfate sodium (DSS)-induced colitis model in mice.

MATERIALS AND METHODS: A total of 180g of dried EGST were prepared, and untargeted metabolomic profiling using high-resolution liquid chromatography electrospray ionization orbitrap mass spectrometry (HR-LC-ESI-Orbitrap-MS) identified 930 compounds. UC model mice were administered 3% DSS for 7 d, followed by EGST treatment. The analysis encompassed physiological and pathological evaluations, serum cytokine ELISA, gut microbiota (GM) metagenomic sequencing, GC-MS metabolomics, mRNA sequencing, and Western Blot.

RESULTS: EGST markedly mitigated colitis symptoms, evidenced by reduced weight loss, lower DAI scores, and less colon shortening. It also decreased levels of pro-inflammatory cytokines (TNF-α, IL-6, IL-1β) while boosting IL-10. Histological examination revealed diminished tissue damage, restoration of crypts, and reduced inflammation, with barrier integrity maintained via upregulation of occludin and ZO-1. Metagenomic sequencing demonstrated that EGST modulated the GM, enhancing the levels of Firmicutes and Bacteroidetes while reducing the levels of Proteobacteria and Verrucomicrobia. Metabolomic analysis indicated that EGST influenced critical pathways, including those involving D-amino acids, glutathione, cysteine, and methionine metabolism. Furthermore, mRNA sequencing identified 2625 differentially expressed genes (DEGs), comprising 1729 with increased and 896 with decreased expression, and highlighted EGST's impact on the PPARγ/AMPK/NF-κB pathway.

CONCLUSION: Overall, EGST mitigates DSS-induced colitis through modulation of GM, metabolic profiles, and gene expression, suggesting its promise as a naturally derived treatment for colitis.}, } @article {pmid39721532, year = {2025}, author = {Chauhan, A and Jain, A and Kolton, M and Pathak, A}, title = {Impacts of long-term irrigation of municipally-treated wastewater to the soil microbial and nutrient properties.}, journal = {The Science of the total environment}, volume = {959}, number = {}, pages = {178143}, doi = {10.1016/j.scitotenv.2024.178143}, pmid = {39721532}, issn = {1879-1026}, mesh = {*Wastewater ; *Soil Microbiology ; *Agricultural Irrigation/methods ; *Soil/chemistry ; *Waste Disposal, Fluid/methods ; Microbiota ; Nitrogen/analysis ; }, abstract = {Reusing treated wastewater (TWW) for crop irrigation has shown to provide environmental and economic benefits as well as drawbacks. This study was conducted using soils collected from a wastewater reuse facility in Tallahassee, FL, mainly to elucidate the long-term impact(s) of TWW irrigation on soil microbiome and nutrient status. Approximately 890 ha of land have been spray-irrigated with TWW since the 1980's to grow fodder crops. Soil cores were collected from six irrigated and six control sites at depths of 0-15, 15-30, and 30-60 cm during summer and winter, followed by nutrient analysis and assessment of bacterial, fungal, and denitrifier communities using SSU rRNA, ITS, nirK, nirS, and nosZ phylogenetic markers. TWW irrigation significantly increased soil pH, soluble salts, nitrate, phosphate, calcium, magnesium, and organic matter, alongside shifts in the prokaryotic and fungal community structures, particularly in summer. Beta-diversity analyses indicated that wastewater quality and season collectively explained 23 % of prokaryotic community similarity and 9.8 % of fungal community dissimilarity. Indicator species analysis, supported by random forest machine learning, identified 37 prokaryotic and 11 fungal bioindicators whose occurrences varied significantly with wastewater quality and season. Key nitrogen-cycling microbes included ammonia-oxidizing families of Nitrosomonadaceae, Nitrosopumilaceae, Nitrososphaeraceae, Nitrosotaleaceae, and comammox-performing Nitrospiraceae. The fungal community was predominated by Ascomycota (78.6 % ± 4.2 %). FUNGuild analysis showed dominant trophic levels of symbiotrophs, saprotrophs, and pathotrophs, averaging 42 % ± 7.1 %. Overall, this study points to the long-term impacts of TWW irrigation on the studied soil properties and microbial communities.}, } @article {pmid39720963, year = {2024}, author = {Guha, SK and Niyogi, S}, title = {Microbial Dynamics in COVID-19: Unraveling the Impact of Human Microbiome on Disease Susceptibility and Therapeutic Strategies.}, journal = {Current microbiology}, volume = {82}, number = {1}, pages = {59}, pmid = {39720963}, issn = {1432-0991}, mesh = {Humans ; *COVID-19/microbiology/virology ; *SARS-CoV-2 ; *Microbiota ; *Dysbiosis/microbiology ; Disease Susceptibility ; Probiotics/therapeutic use ; Gastrointestinal Microbiome ; }, abstract = {This review explores the bidirectional relationship between the human microbiome and SARS-CoV-2 infection, elucidating its implications for COVID-19 susceptibility, severity, and therapeutic strategies. Metagenomic analyses reveal notable alterations in microbiome composition associated with SARS-CoV-2 infection, impacting disease severity and clinical outcomes. Dysbiosis within the respiratory, gastrointestinal, oral, and skin microbiomes exacerbates COVID-19 pathology through immune dysregulation and inflammatory pathways. Understanding these microbial shifts is pivotal for devising targeted therapeutic interventions. Notably, co-infection of oral pathogens with SARS-CoV-2 worsens lung pathology, while gut microbiome dysbiosis influences viral susceptibility and severity. Potential therapeutic approaches targeting the microbiome include probiotics, antimicrobial agents, and immunomodulatory strategies. This review underscores the importance of elucidating host-microbiota interactions to advance precision medicine and public health initiatives in combating COVID-19 and other infectious diseases.}, } @article {pmid39720735, year = {2024}, author = {Meng, LN and Li, G}, title = {Two rare cases of severe community-acquired bloodstream infections: a clinical case report.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1364391}, pmid = {39720735}, issn = {1664-3224}, mesh = {Humans ; Anti-Bacterial Agents/therapeutic use ; Bacteremia/drug therapy/microbiology/diagnosis ; *Community-Acquired Infections/microbiology/diagnosis ; Klebsiella Infections/diagnosis/therapy/drug therapy ; Klebsiella pneumoniae ; Staphylococcal Infections/drug therapy/diagnosis/therapy ; Staphylococcus aureus ; }, abstract = {BACKGROUND: The escalating demographic shift towards an aging population and the widespread occurrence of immunological diseases have contributed to an elevation in the frequency of community-acquired infections. Notably, among these infections, community-acquired bloodstream infections (CABSI) stand out due to their significant lethality. Detailed medical history inquiries, assessment of underlying immune status, detection of the source of infection, and initial precise identification and treatment of the infectious agents can improve the prognosis of CABSI.

CASE DESCRIPTION: In this paper, two incidences of severe CABSI with insidious onset and rapid progression are described. Both patients had compromised basic immunity: one developed the infection following unhygienic dietary practices, and the other after repeated enemas leading to intestinal damage. Blood genomic sequencing revealed the presence of Klebsiella pneumoniae and Staphylococcus aureus in the respective cases, with the origin of the infection traced back to the gastrointestinal tract. Both patients experienced positive outcomes following targeted antibiotic therapy, fluid resuscitation, support for organ function, and surgical interventions. Nevertheless, one patient manifested dry gangrene in the extremities during the course of treatment, potentially associated with the administration of vasoconstrictor drugs, considering the compromised baseline vascular conditions.

CONCLUSION: Clinicians are advised to expeditiously uncover concealed medical histories and potential sources of infection in patients, thoroughly investigate the origin of the infection, and initiate early genomic testing to ascertain the specific nature of the infection. This proactive approach aims to facilitate precise treatment strategies and, consequently, enhance the overall prognosis.}, } @article {pmid39720732, year = {2024}, author = {Chen, X and Jiang, C and Song, W and Sun, T and Yan, J and Xu, W and You, K}, title = {Case report: Identification of a Chinese patient with RAG1 mutations initially presenting as autoimmune hemolytic anemia.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1498066}, pmid = {39720732}, issn = {1664-3224}, mesh = {Humans ; *Anemia, Hemolytic, Autoimmune/genetics/diagnosis ; Female ; Infant ; Mutation ; China ; East Asian People ; Homeodomain Proteins ; }, abstract = {Mutations in the recombination-activating gene 1, a pivotal component essential for V(D)J recombination and the formation of T- and B-cell receptors, can result in autoimmune hemolytic anemia, a rare hematological condition characterized by the autoantibody-mediated destruction of red blood cells. Herein, we report the case of a 1-year-and-4-month-old girl who presented with progressively aggravated anemia, fever, and cough. Autoimmune hemolytic anemia was confirmed by bone marrow aspiration and Coombs test. During treatment, the patient experienced two episodes of severe pneumonia and respiratory failure. Next-generation metagenomic sequencing of sputum samples confirmed the presence of cytomegalovirus and Pneumocystis jirovecii infections. Additionally, lymphocyte subset analysis revealed a T-B+ immunodeficiency. Whole exome and Sanger sequencing revealed a pathogenic recombinase-activating gene 1 mutation (c.2095C>T, p.Arg699Trp) and a likely pathogenic variant (c.2690G>A, p.Arg897Gln), resulting in a missense mutation in the amino acid sequence of the coding protein. Consequently, the patient was diagnosed with a recombination-activating gene 1 mutation and autoimmune hemolytic anemia as the initial presentation. This study reports a case of a recombination-activating gene 1 mutation in China and documents a combination of mutation sites and associated clinical phenotypes that were previously unreported. In this study, we outline the diverse clinical phenotypes observed in cases of recombination-activating gene 1 mutations presenting with autoimmune hemolytic anemia, aiming to facilitate timely diagnosis and appropriate treatment.}, } @article {pmid39720617, year = {2024}, author = {Chen, H and Qiu, M and Xu, H and Guo, P and Peng, Y}, title = {Application of Metagenomics Next-Generation Sequencing on Diagnosis of Disseminated Infection Caused by Rhizomucor pusillus in an Acute Lymphoblastic Leukemia Patient.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {5707-5713}, pmid = {39720617}, issn = {1178-6973}, abstract = {BACKGROUND: Rhizomucor pusillus is one of the major pathogens in mucormycosis. Infection due to R. pusillus is rare and has a high mortality rate, especially disseminated mucormycosis infections. Rapid and accurate pathogen identification is important for the development of targeted antifungal therapies.

CASE PRESENTATION: We presented a case of disseminated R. pusillus infection, identified through metagenomics next-generation sequencing (mNGS), in a 4-year-old patient with acute lymphoblastic leukemia. On days 22, 23, and 28, R. pusillus was detected in bronchoalveolar lavage fluid, blood, and hydrothorax, respectively, through mNGS. The patient developed lung, pleural, and blood disseminated lesions caused by R. pusillus infection. Subsequently, the patient was treated with antifungal therapy, including posaconazole, amphotericin B, and isacconazole, with supportive treatment. However, with the continuous deterioration of symptoms, the patient's family decided to give up treatment. The patient eventually died of multiple-organ failure on day 34.

CONCLUSION: mNGS facilitates prompt diagnosis of disseminated R. pusillus infections. The successful application of mNGS provided a new perspective for the clinician, underscoring the technique's potential for rapid diagnostic etiology. mNGS has the capability to identify pathogens at the species level, which is a significant asset in guiding clinical medication decisions.}, } @article {pmid39720616, year = {2024}, author = {Zhang, A and Wang, Z and Sheng, H and Yang, J}, title = {Systemic Scedosporium apiospermum Infection Affecting Multiple Sites After Near-Drowning: A Case Report.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {5739-5744}, pmid = {39720616}, issn = {1178-6973}, abstract = {Scedosporium apiospermum (S. apiospermum) can cause fungal infections in near-drowning victims, and an increasing number of cases have been reported. However, cases of bone and joint infections caused by S. apiospermum are rare. In this case, a 35-year-old otherwise healthy Chinese female presented with aspiration pneumonia and knee arthritis after accidentally falling into sewage and near-drowning and underwent macrogenomic second-generation sequencing of arthrocentesis fluid, which showed S. apiospermum. However, new lesions involving the hip joint and spine continued to develop under voriconazole monotherapy. The patient was treated with voriconazole combined with amphotericin B cholesterol sulfate lipid complex for 30 consecutive days. The patient's symptoms improved significantly. This case highlights the robust invasiveness of S. apiospermum and the extensive spread of infection, underscoring the importance of prompt diagnosis and treatment. A combined therapeutic approach may offer a safe and efficacious option for managing S. apiospermum infection.}, } @article {pmid39720533, year = {2024}, author = {Levallois, V and Andreace, F and Le Gal, B and Dufresne, Y and Peterlongo, P}, title = {The backpack quotient filter: A dynamic and space-efficient data structure for querying k-mers with abundance.}, journal = {iScience}, volume = {27}, number = {12}, pages = {111435}, pmid = {39720533}, issn = {2589-0042}, abstract = {Genomic data sequencing is crucial for understanding biological systems. As genomic databases like the European Nucleotide Archive expand exponentially, efficient data manipulation is essential. A key challenge is querying these databases to determine the presence or absence of specific sequences and their abundance within datasets. This paper presents the Backpack Quotient Filter (BQF), a data structure for indexing k-mers (substrings of length k), which offers greater space efficiency than the Counting Quotient Filter (CQF). The BQF maintains essential features such as abundance information and dynamicity, with an extremely low false positive rate of less than 10 - 5 % . Our method redefines abundance information handling and implements an independent strategy for space efficiency. The BQF uses four times less space than the CQF on complex datasets such as sea-water metagenomics sequences. Additionally, its space efficiency improves with larger datasets, addressing the need for scalable data solutions.}, } @article {pmid39719725, year = {2024}, author = {Deng, K and Shen, L and Xue, Z and Li, BY and Tang, J and Zhao, H and Xu, F and Miao, Z and Cai, X and Hu, W and Fu, Y and Jiang, Z and Liang, X and Xiao, C and Shuai, M and Gou, W and Yue, L and Xie, Y and Sun, TY and Guo, T and Chen, YM and Zheng, JS}, title = {Association of the EAT-Lancet diet, serial measures of serum proteome and gut microbiome, and cardiometabolic health: a prospective study of Chinese middle-aged and elderly adults.}, journal = {The American journal of clinical nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ajcnut.2024.10.011}, pmid = {39719725}, issn = {1938-3207}, abstract = {BACKGROUND: The EAT-Lancet diet was reported to be mutually beneficial for the human cardiometabolic system and planetary health. However, mechanistic evidence linking the EAT-Lancet diet and human cardiometabolic health is lacking.

OBJECTIVES: We aimed to investigate the role of blood proteins in the association between the EAT-Lancet diet and cardiometabolic health and explore the underlying gut microbiota-blood protein interplay.

METHODS: Our study was based on a prospective cohort including 3742 Chinese participants enrolled from 2008-2013 with serum proteome data repeatedly measured ≤3 times (Nproteome = 7514) and 1195 with gut metagenomic data measured ≤2 times over 9 y (Nmicrobiota = 1695). Least absolute shrinkage and selection operator and multivariable linear regression were used to explore the associations of the EAT-Lancet diet (assessed by semi-quantitative food frequency questionnaire) with serum proteins and gut microbes. Linear mixed-effect model and logistic regression were used to examine the associations of selected proteins with 11 cardiometabolic risk factors and 4 cardiometabolic diseases, respectively. Mediation analysis was used to identify potential mediation effects. Multiple comparisons were adjusted using the Benjamini-Hochberg method.

RESULTS: The mean (standard deviation) age of enrolled participants was 58.4 (6.1) y (31.6% men). The EAT-Lancet diet was prospectively associated with 4 core proteins, including α-2-macroglobulin (A2M) (pooled β: 0.12; 95% confidence interval [CI]: 0.05, 0.2), retinol-binding protein 4 (pooled β: -0.14; 95% CI: -0.24, -0.04), TBC1 domain family member 31 (pooled β: -0.11; 95% CI: -0.22, 0), and adenylate kinase 4 (pooled β: -0.19; 95% CI: -0.3, -0.08). The identified proteins were prospectively associated with cardiometabolic diseases (pooled odds ratio ranged from 0.8-1.18) and risk factors (pooled β ranged from -0.1 to 0.12), mediating the association between the EAT-Lancet diet and blood triglycerides. We then identified 5 gut microbial biomarkers of the EAT-Lancet diet, and discovered a potential gut microbiota-blood protein interplay (EAT-Lancet diet→Rothia mucilaginosa→A2M) underlying the EAT-Lancet diet-cardiometabolic health association.

CONCLUSIONS: Our study presents key molecular evidence to support the role of EAT-Lancet diet adherence in promoting cardiometabolic health.}, } @article {pmid39719706, year = {2025}, author = {Zhang, AN and Gaston, JM and Cárdenas, P and Zhao, S and Gu, X and Alm, EJ}, title = {CRISPR-Cas spacer acquisition is a rare event in human gut microbiome.}, journal = {Cell genomics}, volume = {5}, number = {1}, pages = {100725}, pmid = {39719706}, issn = {2666-979X}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *CRISPR-Cas Systems/genetics ; Gene Transfer, Horizontal/genetics ; Bacteriophages/genetics ; Bifidobacterium longum/genetics ; Metagenome/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Genome, Bacterial/genetics ; }, abstract = {Host-parasite relationships drive the evolution of both parties. In microbe-phage dynamics, CRISPR functions as an adaptive defense mechanism, updating immunity via spacer acquisition. Here, we investigated these interactions within the human gut microbiome, uncovering low frequencies of spacer acquisition at an average rate of one spacer every ∼2.9 point mutations using isolates' whole genomes and ∼2.7 years using metagenome time series. We identified a highly prevalent CRISPR array in Bifidobacterium longum spreading via horizontal gene transfer (HGT), with six spacers found in various genomic regions in 15 persons from the United States and Europe. These spacers, targeting two prominent Bifidobacterium phages, comprised 76% of spacer occurrence of all spacers targeting these phages in all B. longum populations. This result suggests that HGT of an entire CRISPR-Cas system introduced three times more spacers than local CRISPR-Cas acquisition in B. longum. Overall, our findings identified key ecological and evolutionary factors in prokaryote adaptive immunity.}, } @article {pmid39719433, year = {2024}, author = {Jia, M and Fan, Y and Ma, Q and Yang, D and Wang, Y and He, X and Zhao, B and Zhan, X and Qi, Z and Ren, Y and Dong, Z and Zhu, F and Wang, W and Gao, Y and Ma, X}, title = {Gut microbiota dysbiosis promotes cognitive impairment via bile acid metabolism in major depressive disorder.}, journal = {Translational psychiatry}, volume = {14}, number = {1}, pages = {503}, pmid = {39719433}, issn = {2158-3188}, support = {82230044//National Science Foundation of China | Key Programme/ ; 82171505//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Depressive Disorder, Major/metabolism/microbiology ; *Bile Acids and Salts/metabolism ; Male ; Female ; *Dysbiosis/metabolism/complications ; *Cognitive Dysfunction/metabolism/etiology/microbiology ; Adult ; Middle Aged ; Feces/microbiology ; Metabolomics ; Case-Control Studies ; Brain-Gut Axis ; }, abstract = {Evidence suggests that complex interactions among the gut microbiome, metabolic abnormalities, and brain have important etiological and therapeutic implications in major depressive disorder (MDD). However, the influence of microbiome-gut-brain cross-talk on cognitive impairment in MDD remains poorly characterized. We performed serum metabolomic profiling on 104 patients with MDD and 77 healthy controls (HCs), and also performed fecal metagenomic sequencing on a subset of these individuals, including 79 MDD patients and 60 HCs. The findings were validated in a separate cohort that included 40 patients with MDD and 40 HCs using serum-targeted metabolomics. Abnormal bile acid metabolism was observed in patients with MDD, which is related to cognitive dysfunction. The following gut microbiota corresponded to changes in bile acid metabolism and enzyme activities involved in the bile acid metabolic pathway, including Lachnospiraceae (Blautia_massiliensis, Anaerostipes_hadrus, Dorea_formicigenerans, and Fusicatenibacter_saccharivorans), Ruminococcaceae (Ruminococcus_bromii, Flavonifractor_plautii, and Ruthenibacterium_lactatiformans), and Escherichia_coli. Furthermore, a combinatorial marker classifier that robustly differentiated patients with MDD from HCs was identified. In conclusion, this study provides insights into the gut-brain interactions in the cognitive phenotype of MDD, indicating a potential therapeutic strategy for MDD-associated cognitive impairment by targeting the gut microbiota and bile acid metabolism.}, } @article {pmid39719199, year = {2025}, author = {Qi, Y and Fu, R and Yan, C and Liu, X and Liu, N}, title = {Enrichment of a heterotrophic nitrifying and aerobic denitrifying bacterial consortium: Microbial community succession and nitrogen removal characteristics and mechanisms.}, journal = {Bioresource technology}, volume = {419}, number = {}, pages = {132013}, doi = {10.1016/j.biortech.2024.132013}, pmid = {39719199}, issn = {1873-2976}, mesh = {*Denitrification ; *Nitrification ; *Nitrogen/metabolism ; Aerobiosis ; *Heterotrophic Processes ; *Microbial Consortia/physiology ; Bacteria/metabolism ; }, abstract = {This study cultivated a bacterial consortium (S60) from landfill leachate that exhibited effective heterotrophic nitrification and aerobic denitrification (HN-AD) properties. Under aerobic conditions, the removal of NH4[+]-N reached 100 % when the S60 consortium utilised NH4[+]-N either as the sole nitrogen source or in combination with NO2[-]-N and NO3[-]-N. Optimal HN-AD performance was achieved with sodium acetate as a carbon source and a pH of 7.0-8.0, dissolved oxygen concentration of 4.0-5.0 mg/L, and a C/N ratio of 10. Furthermore, the presence of functional genes (amoA, hao, napA, nirK, nirS, nosZ), hydroxylamine oxidase, nitrate reductase, and nitrite reductase was confirmed in the S60 consortium. Drawing from these findings, two HN-AD pathways were delineated: NH4[+]-N → NH2OH → NO2[-]-N → NO3[-]-N → NO2[-]-N → NO → N2O → N2 and NH4[+]-N → NH2OH → N2O → N2. Metagenomic binning analysis of the S60 consortium uncovered complete pathways for dissimilatory nitrate reduction and denitrification within Halomonas, Zobellella, Stutzerimonas, Marinobacter, and Pannonibacter. These findings offer new insights into the application of HN-AD bacteria and their collaborative nitrogen removal in environments with varying nitrogen sources.}, } @article {pmid39719115, year = {2024}, author = {Slavov, SN}, title = {Routine Detection of Viruses Through Metagenomics: Where Do We Stand?.}, journal = {The American journal of tropical medicine and hygiene}, volume = {}, number = {}, pages = {}, doi = {10.4269/ajtmh.24-0652}, pmid = {39719115}, issn = {1476-1645}, } @article {pmid39719110, year = {2024}, author = {Koné, A and Kané, F and Neal, A and Konate, I and Coulibaly, B and Dabitao, DK and Diarra, B and Sanogo, I and Sarro, YDS and Coulibaly, TA and Diallo, D and Samake, S and Dicko, I and Diallo, M and Diarra, A and Coulibaly, MD and Keita, D and Coulibaly, N and Koloma, I and Perou, M and Diarra, HB and Cisse, BE and Togo, ACG and Coulibaly, G and Traoré, FG and Sanogo, M and Diakité, M and Aboulhab, J and Akpa, E and Fouth-Tchos, K and Shaw-Saliba, K and Collins, J and Lu, XJ and Nischay, M and Wickiser, JK and Briese, T and Lipkin, WI and Chen, RY and Doumbia, S and Dao, S}, title = {Adding Virome Capture Metagenomic Sequencing to Conventional Laboratory Testing Increases Unknown Fever Etiology Determination in Bamako, Mali.}, journal = {The American journal of tropical medicine and hygiene}, volume = {}, number = {}, pages = {}, doi = {10.4269/ajtmh.24-0449}, pmid = {39719110}, issn = {1476-1645}, abstract = {Unexplained fever poses significant diagnostic challenges in resource-limited settings like Bamako, Mali, where overlapping endemic diseases include malaria, HIV/AIDS, yellow fever, typhoid, and others. This study aimed to elucidate the infectious etiologies of acute febrile illnesses in this context. Acute febrile patients of any age were enrolled after informed consent or assent. Baseline clinical and demographic data were collected, and samples were analyzed by using rapid diagnostic tests, reverse transcriptase polymerase chain reaction, ELISA, and virus-targeted metagenomic sequencing (virome capture sequencing platform for vertebrate viruses [VirCapSeq-VERT]). Among 108 enrolled subjects, most were male (51.9%) and under 15 years old (56.5%). Measles virus was identified in 39.8% of cases, primarily among children. Other findings included Plasmodium spp. (12%), Salmonella spp. (13%), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; 8.7%). The virome capture sequencing platform for vertebrate viruses was used for 101 subjects, corroborating many routine test results and identifying additional cases of measles virus (1), SARS-CoV-2 (5), and numerous other agents. Notably, nearly all subjects showed evidence of herpesviruses (90%) and anelloviruses (98%). Hemorrhagic fever viruses were not observed. With the inclusion of VirCapSeq-VERT, identifiable pathogens were found in 79.6% of cases, leaving 20.4% without a clear etiology. The identification of more than one concurrent pathogen was common (41.5%). Integrating metagenomic sequencing with routine laboratory diagnostic testing enhances the detection of pathogens in acute febrile illnesses, highlighting its potential value in identifying infectious etiologies in resource-limited settings.}, } @article {pmid39718972, year = {2025}, author = {Pittaluga, AM and Miccoli, FE and Guerrero, LD and Relling, AE}, title = {Effect of multispecies fungal extract supplementation on growth performance, nutrient digestibility, ruminal fermentation, and the rumen microbiome composition of beef cattle fed forage-based diets.}, journal = {Journal of animal science}, volume = {103}, number = {}, pages = {}, pmid = {39718972}, issn = {1525-3163}, support = {//Biopremix Technologies LLC/ ; OHO01461//USDA National Institute of Food and Agriculture/ ; }, mesh = {Animals ; Cattle/physiology/growth & development ; *Rumen/microbiology/metabolism ; *Animal Feed/analysis ; *Digestion/drug effects ; *Diet/veterinary ; *Fermentation ; *Dietary Supplements/analysis ; Male ; *Gastrointestinal Microbiome/drug effects ; *Animal Nutritional Physiological Phenomena ; Female ; Cross-Over Studies ; Fungi ; Random Allocation ; Nutrients/metabolism ; }, abstract = {Our objective was to evaluate the effect of a multispecies fungal extract (MFE) on growth performance, apparent total tract digestibility (ATTD), fermentation characteristics, and rumen microbiome composition of beef cattle fed forage-based diets. For experiment 1, ruminally cannulated Angus × SimAngus cows (n = 4; body weight [BW] = 569 ± 21 kg) were used in a randomized crossover design with two 21-d study periods and a 23-d washout period to evaluate the effect of dietary inclusion of an MFE on in situ digestion, ruminal fermentation, and the composition of the rumen microbiome. Treatments consisted of a forage-based diet with or without the inclusion of a MFE. Rumen samples were collected on days 5, 10, and 20. Experiment 2 evaluated different inclusion rates of the MFE in a randomized complete block design using Angus × SimAngus-crossbred steers (n = 80; BW = 370 ± 44 kg). Steers were blocked by BW and randomly assigned to one of four treatments (2 pens/treatment): diet with no MFE, 0.02%, 0.04%, and 0.08% of the MFE (dry matter [DM] basis). Steers were fed a forage-based diet for 122 d. Subsets of 10 steers/treatment were randomly selected for the determination of ATTD on d 20, 40, and 60. All data were analyzed using the MIXED procedure of SAS. In exp 1, adding the MFE to the diet tended to increase the ruminal disappearance rate of the DM on day 10 (P = 0.06). No interactions or treatment effects were observed for the short-chain fatty acid profile of the rumen fluid (P ≥ 0.13). Metagenomic analysis of the rumen microbiome showed an MFE × d interaction for the Fibrobacter genus (P = 0.01), which on day 20 was less abundant in the rumen of cows fed the MFE. In exp 2, steers supplemented with 0.04% of MFE had a lower average daily gain and were lighter at the end of the experiment (cubic, P ≤ 0.04) compared to steers supplemented with 0.02% MFE. Steers fed the diet with 0.02% of MFE had the greatest gain-to-feed ratio among the MFE-supplemented groups (cubic, P < 0.01). Dietary inclusion of the MFE increased neutral detergent fiber digestibility (linear, P = 0.05). Steers supplemented with 0.04% of MFE had the greatest acid detergent fiber digestibility among treatments (quadratic, P = 0.03). Collectively, results showed that ruminal disappearance rate and digestibility of forage-based diets increased due to MFE supplementation, but did not translate into growth performance improvements or beneficially alter rumen fermentation.}, } @article {pmid39718649, year = {2024}, author = {Sanusi, IO and Olutona, GO and Wawata, IG and Onohuean, H and Adepoju, AA}, title = {Geospatial monitoring and human health risk assessment of pharmaceutical residues in groundwater and surface water in Kampala and Mbarara Districts, Uganda.}, journal = {Environmental geochemistry and health}, volume = {47}, number = {2}, pages = {30}, pmid = {39718649}, issn = {1573-2983}, mesh = {Uganda ; *Groundwater/chemistry ; *Water Pollutants, Chemical/analysis ; Humans ; Risk Assessment ; *Environmental Monitoring ; Pharmaceutical Preparations/analysis ; Seasons ; Geographic Information Systems ; }, abstract = {This study investigated the occurrence, concentration and human health risks of five pharmaceutical residues-metronidazole, sulfamethoxazole, ciprofloxacin, carbamazepine, and caffeine-in groundwater and surface water samples from Kampala and Mbarara districts of Uganda. The present study also employed techniques of remote sensing and geographic information system (GIS); thereby, emphasizing the importance of thematic mapping, land use classification, and spatial buffering to evaluate pharmaceutical contaminants in an environmental setting. The risk quotient (RQ) approach was also employed to assess the risk of exposure to the pharmaceutical contaminants. Caffeine was found with the highest average concentration in groundwater (53.515 µg/L), whereas carbamazepine had the highest average concentration in surface water (48.635 µg/L) during the dry season. Ciprofloxacin consistently recorded the lowest average concentrations in both groundwater and surface water across all seasons. Overall, the data revealed high concentrations of pharmaceutical residues in surface water compared to groundwater during both seasons, except for caffeine which was not detected in surface water across the seasons. Notable seasonal changes were also observed in caffeine and metronidazole concentrations, indicating the role of human activities and environmental factors in influencing contamination patterns during specific seasons. The factor analysis revealed that consumption rate of pharmaceuticals and anthropogenic activities are the main factors responsible for the contamination of groundwater and surface water. Moreover, results revealed that the risk of adverse human health effects for carbamazepine and metronidazole during both seasons were high (RQ > 1), thereby highlighting the prioritization of frequent monitoring by the environmental protection agencies. Given that the combined risk of exposure for all the pharmaceuticals exceeded one, adopting stringent pharmaceutical disposal and control measures are essential for mitigating potential human health risks associated with their exposure. Further investigation into optimal and effective pharmaceutical remediation strategies for both groundwater and surface water are highly recommended.}, } @article {pmid39718602, year = {2024}, author = {Lotankar, M and Houttu, N and Mokkala, K and Laitinen, K}, title = {Diet-Gut Microbiota Relations: Critical Appraisal of Evidence From Studies Using Metagenomics.}, journal = {Nutrition reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/nutrit/nuae192}, pmid = {39718602}, issn = {1753-4887}, abstract = {Diet may influence the gut microbiota and subsequently affect the host's health. Recent developments in methods analyzing the composition and function of the gut microbiota allow a deeper understanding of diet-gut microbiota relationships. A state-of-the-art methodology, shotgun metagenomics sequencing, offers a higher taxonomic resolution of the gut microbiota at the bacterial species and strain levels, and more accurate information regarding the functional potential of gut microbiota. Here, the available evidence on the relationship between diet and gut microbiota was critically reviewed, focusing on results emerging from recent metagenomics sequencing studies applied in randomized controlled trials and observational studies. The PubMed and Embase databases were used to search publications between January 2011 and September 2023. Thus far, the number of studies is limited, and the study designs and methods utilized have been variable. Nevertheless, the cumulative evidence from interventions relates to dietary fiber as a modifier of bacterial species, such as Anaerostipes hadrus and Faecalibacterium prausnitzii. Furthermore, observational studies have detected associations between different dietary patterns and food groups with certain microbial species. Utilization of metagenomics sequencing is becoming more common and will undoubtedly provide further insights into diet-gut microbiota relationships at the species level as well as their functional pathways in the near future. For reproducible results and to draw reliable conclusions across various studies on diet-gut microbiota relationships, there is a need for harmonization of the study designs and standardized ways of reporting.}, } @article {pmid39718600, year = {2024}, author = {Koujalagi, T and Ruhal, R}, title = {Mitigating Health Risks Through Environmental Tracking of Pseudomonas aeruginosa.}, journal = {Current microbiology}, volume = {82}, number = {1}, pages = {57}, pmid = {39718600}, issn = {1432-0991}, mesh = {*Pseudomonas aeruginosa/genetics/drug effects/isolation & purification ; Humans ; *Pseudomonas Infections/microbiology/epidemiology ; Environmental Monitoring ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Environmental Microbiology ; }, abstract = {Pseudomonas aeruginosa is a prevalent nosocomial pathogen and a significant reservoir of antimicrobial resistance genes in residential and built environments. It is also widespread in various indoor and outdoor settings, including sewage, surface waters, soil, recreational waters (both treated and untreated), and industrial effluents. Surveillance efforts for P. aeruginosa are primarily focused on hospitals rather than built environments. However, evidence links multidrug-resistant P. aeruginosa of human origin with activity in built environments and hospital settings. Consequently, tracking this pathogen across all environments is crucial for understanding the mechanisms of reverse transmission from built environments to humans. This review explores public health hygiene by examining the prevalence of P. aeruginosa in various environments, its sequence types, the factors contributing to multidrug resistance, and the identification methods through global surveillance. Whole-genome sequencing with sequence typing and real-time quantitative PCR are widely used to identify and study antimicrobial-resistant strains worldwide. Additionally, advanced techniques such as functional metagenomics, next-generation sequencing, MALDI-TOF, and biosensors are being extensively employed to detect antimicrobial-resistant strains and mitigate the ongoing evolution of bacterial resistance to antibiotics. Our review strongly underscores the importance of environmental monitoring of P. aeruginosa in preventing human infections. Furthermore, strategic planning in built environments is essential for effective epidemiological surveillance of P. aeruginosa and the development of comprehensive risk assessment models.}, } @article {pmid39717932, year = {2025}, author = {Combrink, LL and Golcher-Benavides, J and Lewanski, AL and Rick, JA and Rosenthal, WC and Wagner, CE}, title = {Population Genomics of Adaptive Radiation.}, journal = {Molecular ecology}, volume = {34}, number = {2}, pages = {e17574}, doi = {10.1111/mec.17574}, pmid = {39717932}, issn = {1365-294X}, support = {1556963//NSF/ ; 2224892//NSF/ ; 2109825//NSF Postdoctoral Research Fellowship in Biology/ ; }, mesh = {*Gene Flow ; *Genetics, Population ; *Genetic Speciation ; *Phylogeny ; Hybridization, Genetic ; Genetic Variation ; Genomics ; Adaptation, Physiological/genetics ; Metagenomics ; Animals ; Adaptation, Biological/genetics ; }, abstract = {Adaptive radiations are rich laboratories for exploring, testing, and understanding key theories in evolution and ecology because they offer spectacular displays of speciation and ecological adaptation. Particular challenges to the study of adaptive radiation include high levels of species richness, rapid speciation, and gene flow between species. Over the last decade, high-throughput sequencing technologies and access to population genomic data have lessened these challenges by enabling the analysis of samples from many individual organisms at whole-genome scales. Here we review how population genomic data have facilitated our knowledge of adaptive radiation in five key areas: (1) phylogenetics, (2) hybridization, (3) timing and rates of diversification, (4) the genomic basis of trait evolution, and (5) the role of genome structure in divergence. We review current knowledge in each area, highlight outstanding questions, and focus on methods that facilitate detection of complex patterns in the divergence and demography of populations through time. It is clear that population genomic data are revolutionising the ability to reconstruct evolutionary history in rapidly diversifying clades. Additionally, studies are increasingly emphasising the central role of gene flow, re-use of standing genetic variation during adaptation, and structural genomic elements as facilitators of the speciation process in adaptive radiations. We highlight hybridization-and the hypothesized processes by which it shapes diversification-and questions seeking to bridge the divide between microevolutionary and macroevolutionary processes as rich areas for future study. Overall, access to population genomic data has facilitated an exciting era in adaptive radiation research, with implications for deeper understanding of fundamental evolutionary processes across the tree of life.}, } @article {pmid39717705, year = {2024}, author = {Ben Chéhida, S and Devi Bunwaree, H and Hoareau, M and Moubset, O and Julian, C and Blondin, L and Filloux, D and Lavergne, C and Roumagnac, P and Varsani, A and Martin, DP and Lett, JM and Lefeuvre, P}, title = {Increase of niche filling with increase of host richness for plant-infecting mastreviruses.}, journal = {Virus evolution}, volume = {10}, number = {1}, pages = {veae107}, pmid = {39717705}, issn = {2057-1577}, abstract = {Now that it has been realized that viruses are ubiquitous, questions have been raised on factors influencing their diversity and distribution. For phytoviruses, understanding the interplay between plant diversity and virus species richness and prevalence remains cardinal. As both the amplification and the dilution of viral species richness due to increasing host diversity have been theorized and observed, a deeper understanding of how plants and viruses interact in natural environments is needed to explore how host availability conditions viral diversity and distributions. From a unique dataset, this study explores interactions of Mastrevirus species (family Geminiviridae) with Poales order hosts across 10 sites from three contrasting ecosystems on La Réunion. Among 273 plant pools, representing 61 Poales species, 15 Mastrevirus species were characterized from 22 hosts. The analysis revealed a strong association of mastreviruses with hosts from agroecosystems, the rare presence of viruses in coastal grasslands, and the absence of mastreviruses in subalpine areas, areas dominated by native plants. This suggests that detected mastreviruses were introduced through anthropogenic activities, emphasizing the role of humans in shaping the global pathobiome. By reconstructing the realized host-virus infection network, besides revealing a pattern of increasing viral richness with increasing host richness, we observed increasing viral niche occupancies with increasing host species richness, implying that virus realized richness at any given site is conditioned on the global capacity of the plant populations to host diverse mastreviruses. Whether this tendency is driven by synergy between viruses or by an interplay between vector population and plant richness remains to be established.}, } @article {pmid39717545, year = {2024}, author = {Ma, J and Jiang, Y and He, Y and Zhou, H}, title = {The value of metagenomic next-generation sequencing with blood samples for the diagnosis of disseminated tuberculosis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1456119}, pmid = {39717545}, issn = {2235-2988}, mesh = {Humans ; Male ; *High-Throughput Nucleotide Sequencing/methods ; Female ; *Metagenomics/methods ; Middle Aged ; Adult ; *Tuberculosis/diagnosis/microbiology/blood ; *HIV Infections/diagnosis/complications/blood ; *Mycobacterium tuberculosis/genetics ; *Sensitivity and Specificity ; Aged ; CD4 Lymphocyte Count ; Young Adult ; }, abstract = {OBJECTIVE: The aim of this study was to assess the clinical value of metagenomic next-generation sequencing (mNGS) of blood samples for the identification of disseminated tuberculosis (DTB).

METHODS: A total of 48 individuals suspected of DTB were enrolled. All patients underwent mNGS of peripheral blood and conventional microbiological tests. Patient characteristics were collected from their medical records.

RESULTS: A total of 28 patients were diagnosed with DTB, whereas 20 patients were confirmed as non-DTB cases. In the DTB groups, 19 (67.9%) contained TB sequences, with specific reads of TB ranging from 1 to 219. The TB sequence was more detectable by mNGS in male patients, those with elevated PCT levels, those who are HIV positive, and those with a decreased CD4 T-cell count. The HIV-positive group shows higher TB mNGS reads (p = 0.012) and TB mNGS sensitivity (p = 0.05). The sensitivity of TB mNGS in blood samples was 80% for HIV-infected patients and 44.4% for non-HIV-infected individuals (p = 0.05). The non-HIV group had a higher prevalence of miliary tuberculosis (p = 0.018), and extrapulmonary tuberculosis was more prevalent in the HIV-positive group.

CONCLUSION: Our research has shown that the mNGS of blood samples has excellent sensitivity for the diagnosis of DTB. The TB sequence was more detectable by mNGS in patients with elevated PCT levels, those who are HIV positive, and those with a decreased CD4 T-cell count.}, } @article {pmid39717490, year = {2024}, author = {Shah, JR and Sohail, MR and Lasco, T and Goss, JA and Mohajer, MA and Khalil, S}, title = {Clinical utility of plasma microbial cell-free DNA sequencing in determining microbiologic etiology of infectious syndromes in solid organ transplant recipients.}, journal = {Therapeutic advances in infectious disease}, volume = {11}, number = {}, pages = {20499361241308643}, pmid = {39717490}, issn = {2049-9361}, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is increasingly being used for microbial detection in various infectious syndromes. However, data regarding the use of mNGS in solid organ transplant recipients (SOTR) are lacking.

OBJECTIVES: To describe and analyze real-world clinical impact of mNGS using plasma microbial cell-free DNA (mcfDNA) in SOTR.Design: Retrospectively reviewed all adult SOTR who underwent mNGS testing using plasma mcfDNA at Baylor St Luke's Medical Center from March 2017 to February 2023.

METHODS: Clinical impact (positive, neutral, and negative) was assessed using standardized objective criteria. Three Infectious Diseases physicians independently performed clinical adjudication to determine the correlation of mcfDNA results with clinical diagnosis. A descriptive analysis of the patient and clinical characteristics was performed.

RESULTS: A total of 113 mcfDNA tests in liver (42%), kidney (35%), lung (20%) and heart (13%) transplant recipients were performed in the study period. The most common clinical syndromes were pneumonia (36%), fever of unknown origin (16%), and intra-abdominal infections (15%). Most (80, 71%) of the mcfDNA test results were positive for microorganisms. Twenty-seven (24%) cases were classified as positive clinical impact, 82 (73%) were neutral and 4 (3%) were negative, respectively.

CONCLUSION: In SOTR, mcfDNA sequencing can add a positive clinical impact in a quarter of the cases and identify microorganisms beyond conventional microbiological testing across clinical syndromes. The negative clinical impact was rare. However, larger prospective studies are needed to define the optimal timing and utilization of mcfDNA in the sequence of diagnostic evaluation for syndrome-specific workup in SOTR.

SUMMARY: Metagenomic next-generation sequencing (mNGS) is a novel diagnostic tool that can identify difficult-to-detect microorganisms in SOTR. Our study demonstrates that the mNGS test resulted in a positive clinical impact in 1 out of 4 patients.}, } @article {pmid39717271, year = {2024}, author = {Wang, B and Tan, S and Wu, M and Feng, Y and Yan, W and Yun, Q and Ji, X and Lin, R and Zhao, Z}, title = {Effects of two Bacillus velezensis strains isolated from different sources on the growth of Capsicum annum.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1504660}, pmid = {39717271}, issn = {1664-302X}, abstract = {Microbial inoculants offer an environmentally friendly approach to enhance plant growth and control disease. In this study, two Bacillus velezensis strains, HKSSLJEBR3 (R3) and Ya-1 were isolated from pepper plant roots and tropical rainforest soil, respectively. Both strains exhibited strong antifungal activity against Fusarium oxysporum f. sp. capsici, with inhibition rates of 48.54 ± 0.66% for R3 and 49.35 ± 1.44% for Ya-1. In greenhouse trials, R3 significantly boosted pepper growth, with a 22.12% increase in plant height, 46.44% more leaves, and 56.29% greater fresh weight. These enhancements were likely due to the strong affinity between R3 and pepper plants. Both strains also improved soil quality, with R3 increasing available potassium (AK) by 5.13% and soil organic matter (SOM) by 4.03%, while Ya-1 showed more significant increases. Metagenomic analysis revealed that both strains altered the rhizosphere microbiome, with R3 promoting Pseudomonas and suppressing Fusarium. These results suggest that the R3 strain has strong potential for enhancing pepper growth, improving soil health, and reshaping the rhizosphere microbiome.}, } @article {pmid39717063, year = {2024}, author = {Peng, HB and Liu, Y and Hou, F and Zhao, S and Zhang, YZ and He, ZY and Liu, JY and Xiong, HF and Sun, LY}, title = {Clinical Application of Metagenomic Next-Generation Sequencing (mNGS) in Patients with Early Pulmonary Infection After Liver Transplantation.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {5685-5698}, pmid = {39717063}, issn = {1178-6973}, abstract = {PURPOSE: To examine the clinical utility of metagenomic next-generation sequencing (mNGS) in individuals with early pulmonary infection following liver transplantation.

PATIENTS AND METHODS: mNGS and traditional detection results were retrospectively collected from 99 patients with pulmonary infection within one week following liver transplantation. These patients were admitted to the Department of Critical Liver Diseases at Beijing Friendship Hospital from February 2022 to February 2024, along with their general clinical data.

RESULTS: mNGS exhibited a significantly higher detection rate than traditional methods (92.93% vs 54.55%, P < 0.05) and was more effective in identifying mixed infections (67.68% vs 14.81%, P < 0.05). mNGS identified 303 pathogens in 92 patients, with Enterococcus faecium, Pneumocystis jirovecii, and human herpesvirus types 5 and 7 being the most prevalent bacteria, fungi, and viruses. A total of 26 positive cases were identified through traditional culture methods (sputum and bronchoalveolar lavage fluid), with 18 cases consistent with mNGS detection results, representing 69.23% consistency. Among the three drug-resistant bacteria that showed positivity in mNGS and traditional culture, the presence of drug-resistance genes-mecA in Staphylococcus aureus; KPC-2, KPC-9, KPC-18, KPC-26, OXA27, OXA423 in Klebsiella pneumoniae; and OXA488 and NDM6 in Pseudomonas aeruginosa-reliably predicted drug-resistance phenotype. The treatment regimen for 76 of the 92 patients with positive mNGS relied on these results; 74 exhibited significant symptom improvement, yielding a 97.37% recovery rate. The overall prognosis was favorable.

CONCLUSION: mNGS offers rapid detection, a high positivity rate, insensitivity to antibiotics, and a superior ability to detect mixed infections in patients with early post-transplant pulmonary infections. Additionally, mNGS shows good consistency with traditional culture and can predict drug-resistant phenotypes to guide targeted antibiotic therapy for early-stage post-transplant pulmonary infection after liver transplantation. Patients whose antibiotic therapy is based on mNGS results have experienced decreased mortality rates and overall improved prognosis.}, } @article {pmid39716679, year = {2025}, author = {Bai, X and Wu, J and Zhang, B and Zhao, H and Tian, F and Wang, B}, title = {Metagenomics reveals functional profiles of soil nitrogen and phosphorus cycling under different amendments in saline-alkali soil.}, journal = {Environmental research}, volume = {267}, number = {}, pages = {120686}, doi = {10.1016/j.envres.2024.120686}, pmid = {39716679}, issn = {1096-0953}, mesh = {*Phosphorus/analysis ; *Soil Microbiology ; *Soil/chemistry ; *Nitrogen/metabolism ; *Metagenomics ; China ; Manure/microbiology ; Nitrogen Cycle ; Fertilizers/analysis ; Salinity ; Alkalies/chemistry ; Microbiota ; }, abstract = {High salinity, low fertility and poor structure in saline-alkali soils led to nutrient cycling slow and microbial activity loss. The application of amendments has proven effective in enhancing soil nutrients, which significantly affects soil nitrogen and phosphorus cycling process. However, the specific impact of different amendments on the microbial functional potential related to nutrient cycling in saline-alkali soils remains unclear. Hence, metagenomics sequencing was used to investigate soil microbial communities and nitrogen and phosphorus cycling genes in response to different amendments, and to examine the influence of soil physicochemical properties on functional genes in the Hetao irrigation district of China. The results showed that amendments application enriched the Proteobacteria abundance, while inhibiting oligotrophic groups such as Chloroflexi. Compared to the control (CK), the combined application of desulfurization gypsum and cattle manure (DC) notably increased nasA (assimilatory nitrate reduction) and nirB (dissimilatory nitrate reduction), as well as phoD and phoA genes (organic P mineralization). Furthermore, soil AK and AP were primary factors affecting microbial communities and N and P cycling genes. Overall, this study offers valuable insights into soil nitrogen and phosphorus cycling genes and their interactions in response to different amendments, where the application of amendments affects nitrogen and phosphorus cycling by altering soil nutrient availability.}, } @article {pmid39716651, year = {2025}, author = {Xu, K and Liu, P and Qin, X and Wang, X and Shi, L and Wang, P and Wu, X and Xiao, H and Zhao, H and Zhong, Y and Zhang, C}, title = {Bacteriophage diversity and novelty revealed by metaviromic analysis of the gut virome in the medicinal Blaps rynchopetera.}, journal = {Microbial pathogenesis}, volume = {199}, number = {}, pages = {107249}, doi = {10.1016/j.micpath.2024.107249}, pmid = {39716651}, issn = {1096-1208}, mesh = {*Bacteriophages/genetics/isolation & purification/classification ; Animals ; *Genome, Viral ; *Virome ; *Gastrointestinal Microbiome ; *Coleoptera/virology ; *High-Throughput Nucleotide Sequencing ; Phylogeny ; DNA Viruses/genetics ; DNA, Viral/genetics ; Metagenomics ; }, abstract = {The medicinal beetle Blaps rynchopetera is recognized for its antibacterial, anti-inflammatory, and immune-regulating properties. This study utilized metaviromics technology to systematically characterize the viral community within the gut of B. rynchopetera through high-throughput sequencing of gut contents, with a specific focus on the composition of its bacteriophage community. The sequencing generated 15,394 contigs exceeding 200 bp, which were assembled into 577 viral operational taxonomic units. Among these, dsDNA viruses constituted 52.33%, ssDNA viruses 11.09%, and Nucleo-Cytoplasmic Large DNA Viruses 11.78%, with 24.80% remaining unknown. Bacteriophages were the predominant viral community members, comprising 65.86% of the total, mainly distributed among five families: Peduoviridae, Schitoviridae, Drexlerviridae, Autographiviridae, and Casjensviridae, with 40.21% of the bacteriophages belonging to unclassified genera. Deep genomic assembly yielded 34 complete bacteriophage sequences, including nine sequences lacking significant similarity to existing viral genomes in BLAST analysis. The remaining sequences were classified as follows: four in Stephanstirmvirinae, three in Schitoviridae, three in Peduoviridae, one in Autographiviridae, one in Guernseyvirinae, one in Herelleviridae, one in Gordonclarkvirinae, one in Chaseviridae, and one in Salmondvirus, while nine bacteriophages remained unclassified. The results indicate that the gut bacteriophage community of B. rynchopetera is diverse and species-rich, exhibiting distinct characteristics compared to bacteriophage communities from honey bees and mosquitoes. These findings lay a foundation for further investigation into virus-microbiota interactions and virus-host relationships within the gut of B. rynchopetera.}, } @article {pmid39716502, year = {2025}, author = {Zheng, J and Li, YY and Lu, YS and Wang, D and Liu, C and Peng, HL and Shi, CH and Xie, KZ and Zhang, K and Sun, LL and Zhou, CM and Gu, WJ}, title = {Impact of different continuous fertilizations on the antibiotic resistome associated with a subtropical triple-cropping system over one decade.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {367}, number = {}, pages = {125564}, doi = {10.1016/j.envpol.2024.125564}, pmid = {39716502}, issn = {1873-6424}, mesh = {*Fertilizers/analysis ; *Soil Microbiology ; *Drug Resistance, Microbial/genetics ; *Agriculture/methods ; *Soil/chemistry ; Anti-Bacterial Agents/pharmacology ; Manure ; Animals ; Crops, Agricultural ; Zea mays/genetics ; }, abstract = {The prevalence of antibiotic resistance genes (ARGs) in agricultural soils has garnered significant attention. However, the long-term impacts of various nitroge (N)-substitution fertilization regimes on the distribution of soil ARGs and their dominant drivers in a subtropical triple-cropping system remain largely unexplored. This study employed a metagenomic approach to analyze soil ARGs, microbial communities, mobile genetic elements (MGEs), and viruses from a maize-maize-cabbage rotation field experiment with five different fertilization regimes. Soil samples were collected in 2012 and 2021. A total of 615 unique ARG subtypes were identified, with multidrug, bacitracin, and rifamycin resistance genes being the most abundant. Notably, ARG types. the continuous application of fresh chicken manure (CM) over 10 years significantly increased both the count of unique ARG subtypes and the total ARG abundance compared to other fertilization regimes, such as inorganic fertilizer and composted chicken manure. Specifically, the abundance of genes associated with antibiotic target replacement (e.g., sul1 and sul2) in the CM-treated soil rose by 8.83-fold from 2021 to 2012. Our random forest analysis revealed that the abundance of three MGEs (QacEdelta, plasmids, and IstB), two viral families (Myoviridae and Podoviridae), two bacterial phyla (Chloroflexi and Planctomycetes), and two environmental factors (pH and soil organic matter (SOM)) significantly influenced the distribution of ARGs. Furthermore, variance decomposition analysis underscored the critical roles of the three MGEs and the two viral families in the dissemination of ARGs, suggesting that horizontal gene transfer (HGT) may play a key role in ARG spread. These findings enhance our understanding of how different fertilization practices influence ARG dissemination in subtropical triple-cropping agroecosystems over the long term and provide valuable insights for optimizing fertilization management strategies.}, } @article {pmid39716130, year = {2024}, author = {Gao, X and Chen, L and Yang, S and Zhu, C and Wang, D}, title = {Donor-derived carbapenem-resistant Klebsiella Pneumoniae infections leading to retroperitoneal abscesses in kidney transplant recipients: a report of two cases.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {1459}, pmid = {39716130}, issn = {1471-2334}, support = {LQZD-QG//Key specialty of Joint Logistic Medicine of the Joint Logistic Support Force/ ; }, mesh = {Humans ; Male ; *Kidney Transplantation/adverse effects ; Middle Aged ; *Klebsiella Infections/microbiology/drug therapy ; *Klebsiella pneumoniae/isolation & purification/genetics ; *Anti-Bacterial Agents/therapeutic use ; Carbapenems/therapeutic use/pharmacology ; Tissue Donors ; Transplant Recipients ; Retroperitoneal Space/microbiology ; Abdominal Abscess/microbiology ; Drainage ; }, abstract = {BACKGROUND: Retroperitoneal abscesses caused by donor-derived Carbapenem-Resistant Klebsiella Pneumoniae (CRKP) infections are rare and often challenging to diagnose early due to a lack of specific symptoms.

CASE PRESENTATION: In case one, a 64-year-old male presented with unexplained fever and emaciation three months after undergoing a kidney transplant for end-stage renal disease. Metagenomic Next-Generation Sequencing identified CRKP in peripheral blood samples, and CT scans confirmed a retroperitoneal abscess. Considering the infectious status of the donor and other recipients, donor-derived infection (DDI) was suspected. Surgical incision and drainage were performed along with anti-infection treatment and immunosuppressive agents were adjusted. There was no recurrence of infection after a six-month follow-up. In case two, a 45-year-old male was readmitted due to light red pus discharge from the drainage tube fistula on day 32 after undergoing a kidney transplant for end-stage renal disease. A CT scan confirmed a retroperitoneal abscess between the kidney allograft and the spinal column. Based on the culture results of the purulent sample and perfusion fluid from the donor kidney, DDI was suspected, leading to prompt surgical incision and drainage, along with anti-infection treatment. After a five-month follow-up period, no infection recurrence was observed.

CONCLUSIONS: This study reported two cases of retroperitoneal abscesses caused by DDI following kidney transplantation, highlighting the importance of considering donor-derived CRKP infections in transplant recipients presenting with unexplained symptoms. Timely interventions are crucial for effective management and prevention of recurrence.}, } @article {pmid39716092, year = {2024}, author = {Chapman, JA and Wroot, E and Brown, T and Beck, LC and Embleton, ND and Berrington, JE and Stewart, CJ}, title = {Characterising the metabolic functionality of the preterm neonatal gut microbiome prior to the onset of necrotising enterocolitis: a pilot study.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {533}, pmid = {39716092}, issn = {1471-2180}, mesh = {Humans ; *Enterocolitis, Necrotizing/microbiology/metabolism ; *Gastrointestinal Microbiome ; Pilot Projects ; Infant, Newborn ; *Infant, Premature ; Female ; Male ; Bacteria/classification/metabolism/isolation & purification/genetics ; Feces/microbiology ; Case-Control Studies ; Metagenome ; }, abstract = {BACKGROUND: Necrotising enterocolitis (NEC) is a devastating bowel disease that primarily occurs in infants born prematurely and is associated with abnormal gut microbiome development. While gut microbiome compositions associated with NEC have been well studied, there is a lack of experimental work investigating microbiota functions and their associations with disease onset. The aim of this pilot study was to characterise the metabolic functionality of the preterm gut microbiome prior to the onset of NEC compared with healthy controls.

RESULTS: Eight NEC infants were selected of median gestation 26.5 weeks and median day of life (DOL) of NEC onset 20, with one sample used per infant, collected within one to eight days (median four) before NEC onset. Each NEC case was matched to a control infant based on gestation and sample DOL, the main driver of microbiome composition in this population, giving a total cohort of 16 infants for this study. Dietary exposures were well matched. The microbiota of NEC and control infants showed similar wide-ranging metabolic functionalities. All 94 carbon sources were utilised to varying extents but NEC and control samples clustered separately by supervised ordination based on carbon source utilisation profiles. For a subset of eight samples (four NEC, four control) for which pre-existing metagenome data was available, microbiome composition was found to correlate significantly with metabolic activity measured on Biolog plates (p = 0.035). Comparisons across all 16 samples showed the NEC microbiota to have greater utilisation of carbon sources that are the products of proteolytic fermentation, specifically amino acids. In pairwise comparisons, L-methionine was highly utilised in NEC samples, but poorly utilised in controls (p = 0.043). Carbon sources identified as discriminatory for NEC also showed a greater enrichment for established markers of inflammatory disease, such as inflammatory bowel disease, irritable bowel syndrome and diverticular disease.

CONCLUSIONS: Before NEC onset, the preterm gut microbiota showed greater metabolic utilisation of amino acids, potentially indicating a shift from predominantly saccharolytic to proteolytic fermentation. Products of amino acid breakdown could therefore act as biomarkers for NEC development. A larger study is warranted, ideally with infants from multiple sites.}, } @article {pmid39716085, year = {2024}, author = {Meyer-Rust, KA and Strickland, A and Lee, BY and Sevigny, JL and Bradt, G and Brown, BL}, title = {Diet of the blue crab (Callinectes sapidus) during range expansion in Great Bay Estuary, New Hampshire.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1238}, pmid = {39716085}, issn = {1471-2164}, support = {P20 GM103506/GM/NIGMS NIH HHS/United States ; TBD//College of Life Sciences and Agriculture, University of New Hampshire/ ; TBD//New Hampshire Sea Grant, University of New Hampshire/ ; TBD//School of Marine Science and Ocean Engineering, University of New Hampshire/ ; TBD//New Hampshire Agricultural Experiment Station/ ; }, mesh = {Animals ; *Brachyura/genetics ; *Estuaries ; *Diet ; New Hampshire ; Bays ; Metagenomics/methods ; Ecosystem ; }, abstract = {Great Bay Estuary (GBE), within the rapidly warming Gulf of Maine, has experienced significant ecological shifts this century due to naturalization of invasive species. The range expansion of the American blue crab (Callinectes sapidus) currently underway from the mid-Atlantic northward brings the possibility of similar ecological shifts. This study accounts recent trapping and diet analysis of C. sapidus in GBE. Diet is an important component of understanding how the blue crab range expansion may affect GBE ecosystem functions. Across all sites and trap types, 27 blue crabs were captured. Metagenomic analysis of shotgun sequencing techniques were used on the gut contents of blue crabs captured. Most specimens had > 50% Eukaryote sequences. Overall results of this gut content study confirm a mixed diet indicative of an opportunistic feeder. Using metagenomics to analyze the diet of blue crabs as they establish viable populations in GBE will be a useful tool for predicting how these range expanding organisms are interacting within this important estuarine ecosystem, which will promote sustainable development by informing end users who may be affected by these crabs to help them meet their needs in the present and future. This project falls within Global Goal SDG14: Life Below Water.}, } @article {pmid39716039, year = {2025}, author = {Du, Q and Liu, X and Zhang, R and Hu, G and Liu, Q and Wang, R and Ma, W and Hu, Y and Fan, Z and Li, J}, title = {Placental and Fetal Microbiota in Rhesus Macaque: A Case Study Using Metagenomic Sequencing.}, journal = {American journal of primatology}, volume = {87}, number = {1}, pages = {e23718}, doi = {10.1002/ajp.23718}, pmid = {39716039}, issn = {1098-2345}, support = {//This work was supported by the National Natural Science Foundation of China (32171607)/ ; }, mesh = {Animals ; *Macaca mulatta/microbiology ; Female ; Pregnancy ; *Fetus/microbiology ; *Placenta/microbiology ; *Microbiota ; *Metagenomics ; Umbilical Cord/microbiology ; Gastrointestinal Microbiome ; }, abstract = {Recent evidence challenging the notion of a sterile intrauterine environment has sparked research into the origins and effects of fetal microbiota on immunity development during gestation. Rhesus macaques (RMs) serve as valuable nonhuman primate models due to their similarities to humans in development, placental structure, and immune response. In this study, metagenomic analysis was applied to the placenta, umbilical cord, spleen, gastrointestinal tissues of an unborn RM fetus, and the maternal intestine, revealing the diversity and functionality of microbes in these tissues. Additionally, gut metagenomic data of adult Rhesus macaques from our previous study, along with data from a human fetus obtained from public databases, were included for comparison. We observed substantial microbial sharing between the mother and fetus, with the microbial composition of the placenta and umbilical cord more closely resembling that of the fetal organs than the maternal intestine. Notably, compared with other adult RMs, there was a clear convergence between maternal and fetal microbiota, alongside distinct differences between the microbiota of adults and the fetus, which underscores the unique microbial profiles in fetal environments. Furthermore, the fetal microbiota displayed a less developed carbohydrate metabolism capacity than adult RMs. It also shared antibiotic resistance genes with both maternal and adult RM microbiomes, indicating potential vertical transmission. Comparative analysis of the metagenomes between the RM fetus and a human fetus revealed significant differences in microbial composition and genes, yet also showed similarities in certain abundant microbiota. Collectively, our results contribute to a more comprehensive understanding of the intrauterine microbial environment in macaques.}, } @article {pmid39715919, year = {2024}, author = {Jiang, ZB and Zhang, H and Tian, JJ and Guo, HH and Zhou, LR and Ma, XL}, title = {The Microbial Diversity of Biological Moss Crust: Application in Saline-Alkali Soil Management.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {162}, pmid = {39715919}, issn = {1432-184X}, support = {82160672//the National Natural Science Foundation of China/ ; 2022AAC05041 and 2023AAC05048//Outstanding Youth Program of Ningxia Natural Science Foundation/ ; 2021BEB04019//the Key R&D Projects in Ningxia/ ; 2021AAC03210 and 2019AAC03113//the Ningxia Natural Science Foundation/ ; }, mesh = {*Soil/chemistry ; *Soil Microbiology ; *Bryophyta/microbiology ; China ; Biodiversity ; Alkalies/analysis ; Salinity ; Bacteria/classification/genetics/isolation & purification/metabolism ; Chlorophyll/analysis ; }, abstract = {Soil salinization poses a substantial threat to global food security, particularly under the influence of climate change, and is recognized as one of the most urgent challenges in land degradation. This study aims to elucidate the challenges associated with managing arid and semi-arid saline-alkali lands in China's Ningxia province and propose feasible solutions. To assess moss crust colonization, we measured changes in organic matter and chlorophyll levels. Additionally, we investigated the impact of an interlayer composed of Goji berry root bark using liquid chromatography-mass spectrometry analysis, biological enzyme activity analysis, and metagenomic sequencing. A total of 45 endophytes were isolated from the moss crust. The most significant colonization of moss crusts was observed when the Goji berry root bark was used as the interlayer, resulting in a significant increase in chlorophyll content. Several responses were identified as pivotal factors facilitating moss crust growth when the Goji berry root bark was used as the interlayer. In saline-alkali soil, the Goji berry root bark interlayer increased the activities of sucrase, urease, and alkaline phosphatase. Metagenomic data analysis revealed variations in the relative abundance of microorganisms at the phylum level, although these differences were not statistically significant. Evaluation of the impact of physical isolation and moss crust transplantation on the ecological restoration of saline-alkali soil using liquid chromatography-tandem mass spectrometry and metagenomic sequencing indicated that the Goji berry root bark as a physical isolation method promotes moss crust colonization in saline-alkali soil and increases soil organic matter and nutrient elements, offering valuable insights for the ecological management of saline-alkali land and serving as a reference for future research in this field.}, } @article {pmid39714548, year = {2024}, author = {Wang, W and Zhang, Z and Sun, M and Li, C and Yan, M and Wang, C}, title = {Mechanism of decolorization and degradation of direct brown D3G by a halo-thermophilic consortium.}, journal = {Extremophiles : life under extreme conditions}, volume = {29}, number = {1}, pages = {11}, pmid = {39714548}, issn = {1433-4909}, support = {22B610001//the Key Scientific Research Project in Colleges and Universities of Henan Province of China/ ; HDXJJG2023-058//the teaching reform project of Henan University/ ; }, mesh = {*Azo Compounds/metabolism/chemistry ; Microbial Consortia ; Biodegradation, Environmental ; Halomonas/metabolism ; Coloring Agents/metabolism/chemistry ; Laccase/metabolism ; Bacillus/metabolism ; }, abstract = {Azo dye wastewater has garnered significant attention from researchers because of its association with high-temperature, high-salt, and high-alkali conditions. In this study, consortium ZZ efficiently decolorized brown D3G under halophilic and thermophilic conditions. he results indicated that consortium ZZ, which was mainly dominated by Marinobacter, Bacillus, and Halomonas, was achieved decolorization rates ranging from 1 to 10% at temperatures between 40 °C and 50 °C, while maintaining a pH range of 7 to 10 for direct brown D3G degradation. Through the comprehensive utilization of UV-vis spectral analysis, Fourier transform infrared (FTIR), gas chromatography mass spectrometric (GC-MS) techniques, as well as metagenomic analysis, the decolorization and degradation pathway of direct brown by consortium ZZ was proposed. The azo dye reductase, lignin peroxidase, and laccase were also highly expressed in the decolorization process. Additionally, phytotoxicity tests using seeds of Cucumis sativus and Oryza sativa revealed that the intermediates generated showed no significant toxicity compared with distilled water. This investigation elucidated the pivotal contribution of consortium ZZ to azo dye degradation and provided novel theoretical insights along with practical guidance for azo dye treatment at halo-thermophilic conditions.}, } @article {pmid39714212, year = {2025}, author = {Fang, Y and Meng, L and Xia, J and Gotoh, Y and Hayashi, T and Nagasaki, K and Endo, H and Okazaki, Y and Ogata, H}, title = {Genome-resolved year-round dynamics reveal a broad range of giant virus microdiversity.}, journal = {mSystems}, volume = {10}, number = {1}, pages = {e0116824}, pmid = {39714212}, issn = {2379-5077}, support = {21H05057//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; Nos. 2018-31//Kyoto University | Institute for Chemical Research, Kyoto University (ICR)/ ; Nos. 2017-25//Kyoto University | Institute for Chemical Research, Kyoto University (ICR)/ ; 22H00384//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 22H00385//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 16H06279//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 16H06429//Ministry of Education, Culture, Sports, Science and Technology (MEXT)/ ; 16K21723//Ministry of Education, Culture, Sports, Science and Technology (MEXT)/ ; 16H06437//Ministry of Education, Culture, Sports, Science and Technology (MEXT)/ ; Nos. 2021-33//Kyoto University | Institute for Chemical Research, Kyoto University (ICR)/ ; Nos. 2019-33//Kyoto University | Institute for Chemical Research, Kyoto University (ICR)/ ; }, mesh = {*Genome, Viral ; *Seawater/virology ; *Giant Viruses/genetics ; Metagenome ; Metagenomics ; Phylogeny ; Genetic Variation/genetics ; Seasons ; Biodiversity ; }, abstract = {Giant viruses are crucial for marine ecosystem dynamics because they regulate microeukaryotic community structure, accelerate carbon and nutrient cycles, and drive the evolution of their hosts through co-evolutionary processes. Previously reported long-term observations revealed that these viruses display seasonal fluctuations in abundance. However, the underlying genetic mechanisms driving such dynamics of these viruses remain largely unknown. In this study, we investigated the dynamics of giant viruses using time-series metagenomes from eutrophic coastal seawater samples collected over 20 months. A newly developed computational pipeline generated 1,065 high-quality genomes covering six major giant virus lineages. These genomic data revealed year-round recovery of the viral community structure at the study site and distinct dynamics of viral populations that were classified as persistent (n = 9), seasonal (n = 389), sporadic (n = 318), or others. By profiling the intra-species nucleotide-resolved microdiversity through read mapping, we also identified year-round recovery dynamics at subpopulation level for viruses classified as persistent or seasonal. Our results further indicated that giant viruses with broader niche breadth tended to exhibit higher levels of microdiversity. We argue that greater microdiversity of viruses likely enhances adaptability and thus survival under the virus-host arms race during prolonged interactions with their hosts.IMPORTANCERecent genome-resolved metagenomic surveys have uncovered the vast genomic diversity of giant viruses, which play significant roles in aquatic ecosystems by acting as bloom terminators and influencing biogeochemical cycles. However, the relationship between the ecological dynamics of giant viruses and underlying genetic structures of viral populations remains unresolved. In this study, we performed deep metagenomic sequencing of seawater samples collected across a time-series from a coastal area in Japan. The results revealed a significant positive correlation between microdiversity and temporal persistence of giant virus populations, suggesting that population structure is a crucial factor for adaptation and survival in the interactions with their hosts.}, } @article {pmid39714211, year = {2025}, author = {Facimoto, CT and Clements, KD and White, WL and Handley, KM}, title = {Hindguts of Kyphosus sydneyanus harbor phylogenetically and genomically distinct Alistipes capable of degrading algal polysaccharides and diazotrophy.}, journal = {mSystems}, volume = {10}, number = {1}, pages = {e0100724}, pmid = {39714211}, issn = {2379-5077}, support = {UOAX1808-CR-2//the New Zealand Ministry of Business, Innovation and Employment Endeavour/ ; }, mesh = {Animals ; *Phylogeny ; *Polysaccharides/metabolism ; Bacteroidetes/genetics/metabolism ; Genome, Bacterial ; Symbiosis ; Metagenome ; Humans ; Fishes/microbiology ; }, abstract = {The genus Alistipes (Bacteroidota) is most often associated with human clinical samples and livestock. However, Alistipes are also prevalent in the hindgut of the marine herbivorous fish Kyphosus sydneyanus (Silver Drummer), and analysis of their carbohydrate-active enzyme (CAZyme) encoding gene repertoires suggests Alistipes degrade macroalgal biomass to support fish nutrition. To further explore host-associated traits unique to K. sydneyanus-derived Alistipes, we compared 445 high-quality genomes of Alistipes available in public databases (e.g., human and ruminant associated) with 99 metagenome-assembled genomes (MAGs) from the K. sydneyanus gut. Analyses showed that Alistipes from K. sydneyanus are phylogenetically distinct from other hosts and comprise 26 species based on genomic average nucleotide identity (ANI) analyses. Ruminant- and fish-derived Alistipes had significantly smaller genomes than human-derived strains, and lower GC contents, possibly reflecting a symbiotic relationship with their hosts. The fish-derived Alistipes were further delineated by their genetic capacity to fix nitrogen, biosynthesize cobalamin (vitamin B12), and utilize marine polysaccharides (e.g., alginate and carrageenan). The distribution of CAZymes encoded by Alistipes from K. sydneyanus was not phylogenetically conserved. Distinct CAZyme gene compositions were observed between closely related species. Conversely, CAZyme gene clusters (operons) targeting the same substrates were found across diverse species. Nonetheless, transcriptional data suggest that closely related Alistipes target specific groups of substrates within the fish hindgut. Results highlight host-specific adaptations among Alistipes in the fish hindgut that likely contribute to K. sydneyanus digesting their seaweed diet, and diverse and redundant carbohydrate-degrading capabilities across these Alistipes species.IMPORTANCEDespite numerous reports of the Alistipes genus in humans and ruminants, its diversity and function remain understudied, and there is no clear consensus on whether it positively or negatively impacts host health. Given the symbiotic role of gut communities in the Kyphosus sydneyanus hindgut, where Alistipes are prevalent, and the diversity of carbohydrate-active enzymes (CAZymes) encoded that likely contribute to the breakdown of important substrates in the host diet, it is likely that this genus provides essential services to the fish host. Therefore, considering its metabolism in various contexts and hosts is crucial for understanding the ecology of the genus. Our study highlights the distinct genetic traits of Alistipes based on host association, and the potential of fish-associated Alistipes to transform macroalgae biomass into nutraceuticals (alginate oligosaccharides, β-glucans, sulfated galactans, and sulfated fucans).}, } @article {pmid39714209, year = {2025}, author = {Payne, PE and Knobbe, LN and Chanton, P and Zaugg, J and Mortazavi, B and Mason, OU}, title = {Uncovering novel functions of the enigmatic, abundant, and active Anaerolineae in a salt marsh ecosystem.}, journal = {mSystems}, volume = {10}, number = {1}, pages = {e0116224}, pmid = {39714209}, issn = {2379-5077}, support = {2342607//National Science Foundation (NSF)/ ; 1643486//National Science Foundation (NSF)/ ; 1438092//National Science Foundation (NSF)/ ; 503678//Joint Genome Institute (JGI)/ ; }, mesh = {*Wetlands ; *Rhizosphere ; Metagenome ; Soil Microbiology ; Carbon Cycle ; Phylogeny ; Bacteria, Anaerobic/genetics/metabolism ; Ecosystem ; }, abstract = {Anaerolineae, particularly uncultured representatives, are one of the most abundant microbial groups in coastal salt marshes, dominating the belowground rhizosphere, where over half of plant biomass production occurs. However, this class generally remains poorly understood, particularly in a salt marsh context. Here, novel Anaerolineae metagenome-assembled genomes (MAGs) were generated from the salt marsh rhizosphere representing Anaerolineales, Promineifilales, JAAYZQ01, B4-G1, JAFGEY01, UCB3, and Caldilineales orders. Metagenome and metatranscriptome reads were mapped to annotated MAGs, revealing nearly all Anaerolineae encoded and transcribed genes required for oxidation of carbon compounds ranging from simple sugars to complex polysaccharides, fermentation, and carbon fixation. Furthermore, the majority of Anaerolineae expressed genes involved in anaerobic and aerobic respiration and secondary metabolite production. The data revealed that the belowground salt marsh Anaerolineae in the rhizosphere are important players in carbon cycling, including degradation of simple carbon compounds and more recalcitrant plant material, such as cellulose, using a diversity of electron acceptors and represent an unexplored reservoir of novel secondary metabolites.IMPORTANCEGiven that coastal salt marshes are recognized as biogeochemical hotspots, it is fundamentally important to understand the functional role of the microbiome in this ecosystem. In particular, Anaerolineae are abundant members of the salt marsh rhizosphere and have been identified as core microbes, suggesting they play an important functional role. Yet, little is known about the metabolic pathways encoded and expressed in this abundant salt marsh clade. Using an 'omics-based approach, we determined that Anaerolineae are capable of oxidizing a range of carbon compounds, including simple sugars to complex carbon compounds, while also encoding fermentation and carbon fixation. Surprisingly, Anaerolineae encoded and transcribed genes involved in aerobic respiration, which was unexpected given the reduced nature of the salt marsh rhizosphere. Finally, the majority of Anaerolineae appear to be involved in secondary metabolite production, suggesting that this group represents an unexplored reservoir of novel and important secondary metabolites.}, } @article {pmid39714193, year = {2025}, author = {Midot, F and Goh, KM and Liew, KJ and Lau, SYL and Espenberg, M and Mander, Ü and Melling, L}, title = {Temporal dynamics of soil microbial C and N cycles with GHG fluxes in the transition from tropical peatland forest to oil palm plantation.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {1}, pages = {e0198624}, pmid = {39714193}, issn = {1098-5336}, support = {P015 790102009//The Twelfth Malaysian Plan through Ministry of Education, Innovation, and Talent Development of Sarawak/ ; FRGS/1/2023/STG02/UTM/02/1,Q.J130000.3854.22H63//Ministry of Higher Education of Malaysia through the Fundamental Research Grant Scheme and UTM Fundamental Research Grant/ ; No 101079192 (MLTOM23003R)//European Union Horizon program/ ; No 101096403 (MLTOM23415R)//EC | European Research Council (ERC)/ ; PRG-2302//Estonian Research Council/ ; }, mesh = {*Soil Microbiology ; *Greenhouse Gases/analysis ; *Forests ; Malaysia ; *Microbiota ; Methane/metabolism/analysis ; Nitrogen Cycle ; Carbon Cycle ; Soil/chemistry ; Nitrous Oxide/analysis/metabolism ; Nitrogen/analysis/metabolism ; Carbon/analysis/metabolism ; Wetlands ; Bacteria/classification/genetics/metabolism/isolation & purification ; Arecaceae ; Agriculture ; }, abstract = {Tropical peatlands significantly influence local and global carbon and nitrogen cycles, yet they face growing pressure from anthropogenic activities. Land use changes, such as peatland forests conversion to oil palm plantations, affect the soil microbiome and greenhouse gas (GHG) emissions. However, the temporal dynamics of microbial community changes and their role as GHG indicators are not well understood. This study examines the dynamics of peat chemistry, soil microbial communities, and GHG emissions from 2016 to 2020 in a logged-over secondary peat swamp forest in Sarawak, Malaysia, which transitioned to an oil palm plantation. This study focuses on changes in genetic composition governing plant litter degradation, methane (CH4), and nitrous oxide (N2O) fluxes. Soil CO2 emission increased (doubling from approximately 200 mg C m[-2] h[-1]), while CH4 emissions decreased (from 200 µg C m[-2] h[-1] to slightly negative) following land use changes. The N2O emissions in the oil palm plantation reached approximately 1,510 µg N m[-2] h[-1], significantly higher than previous land uses. The CH4 fluxes were driven by groundwater table, humification levels, and C:N ratio, with Methanomicrobia populations dominating methanogenesis and Methylocystis as the main CH4 oxidizer. The N2O fluxes correlated with groundwater table, total nitrogen, and C:N ratio with dominant nirK-type denitrifiers (13-fold nir to nosZ) and a minor role by nitrification (a threefold increase in amoA) in the plantation. Proteobacteria and Acidobacteria encoding incomplete denitrification genes potentially impact N2O emissions. These findings highlighted complex interactions between microbial communities and environmental factors influencing GHG fluxes in altered tropical peatland ecosystems.IMPORTANCETropical peatlands are carbon-rich environments that release significant amounts of greenhouse gases when drained or disturbed. This study assesses the impact of land use change on a secondary tropical peat swamp forest site converted into an oil palm plantation. The transformation lowered groundwater levels and changed soil properties. Consequently, the oil palm plantation site released higher carbon dioxide and nitrous oxide compared to previous land uses. As microbial communities play crucial roles in carbon and nitrogen cycles, this study identified environmental factors associated with microbial diversity, including genes and specific microbial groups related to nitrous oxide and methane emissions. Understanding the factors driving microbial composition shifts and greenhouse gas emissions in tropical peatlands provides baseline information to potentially mitigate environmental consequences of land use change, leading to a broader impact on climate change mitigation efforts and proper land management practices.}, } @article {pmid39714168, year = {2025}, author = {Bhosle, A and Jackson, MI and Walsh, AM and Franzosa, EA and Badri, DV and Huttenhower, C}, title = {Response of the gut microbiome and metabolome to dietary fiber in healthy dogs.}, journal = {mSystems}, volume = {10}, number = {1}, pages = {e0045224}, pmid = {39714168}, issn = {2379-5077}, support = {A-2019-687-HL//Hill's Pet Nutrition (Hill's)/ ; }, mesh = {Animals ; *Dietary Fiber/metabolism ; Dogs/microbiology ; *Gastrointestinal Microbiome/physiology ; *Metabolome/physiology ; *Feces/microbiology ; Male ; Female ; }, abstract = {UNLABELLED: Dietary fiber confers multiple health benefits originating from the expansion of beneficial gut microbial activity. However, very few studies have established the metabolic consequences of interactions among specific fibers, microbiome composition, and function in either human or representative animal models. In a study design reflective of realistic population dietary variation, fecal metagenomic and metabolomic profiles were analyzed from healthy dogs fed 12 test foods containing different fiber sources and quantities (5-13% as-fed basis). Taxa and functions were identified whose abundances were associated either with overall fiber intake or with specific fiber compositions. Fourteen microbial species were significantly enriched in response to ≥1 specific fiber source; enrichment of fiber-derived metabolites was more pronounced in response to these fiber sources. Positively associated fecal metabolites, including short-chain fatty acids, acylglycerols, fiber bound sugars, and polyphenols, co-occurred with microbes enriched in specific food groups. Critically, the specific metabolite pools responsive to differential fiber intake were dependent on differences both in individual microbial community membership and in overall ecological configuration. This helps to explain, for the first time, differences in microbiome-diet associations observed in companion animal epidemiology. Thus, our study corroborates findings in human cohorts and reinforces the role of personalized microbiomes even in seemingly phenotypically homogeneous subjects.

IMPORTANCE: Consumption of dietary fiber changes the composition of the gut microbiome and, to a larger extent, the associated metabolites. Production of health-relevant metabolites such as short-chain fatty acids from fiber depends both on the consumption of a specific fiber and on the enrichment of beneficial metabolite-producing species in response to it. Even in a seemingly homogeneous population, the benefit received from fiber consumption is personalized and emphasizes specific fiber-microbe-host interactions. These observations are relevant for both population-wide and personalized nutrition applications.}, } @article {pmid39714161, year = {2025}, author = {Neumann, CJ and Mohammadzadeh, R and Woh, PY and Kobal, T and Pausan, M-R and Shinde, T and Haid, V and Mertelj, P and Weiss, E-C and Kolovetsiou-Kreiner, V and Mahnert, A and Kumpitsch, C and Jantscher-Krenn, E and Moissl-Eichinger, C}, title = {First-year dynamics of the anaerobic microbiome and archaeome in infants' oral and gastrointestinal systems.}, journal = {mSystems}, volume = {10}, number = {1}, pages = {e0107124}, pmid = {39714161}, issn = {2379-5077}, support = {10.55776/KLI784 and 10.55776/DOC31//Austrian Science Fund (FWF)/ ; }, mesh = {Humans ; Infant ; *Mouth/microbiology ; *Gastrointestinal Microbiome/physiology ; *Breast Feeding ; Female ; Male ; Archaea/classification ; Gastrointestinal Tract/microbiology ; Anaerobiosis/physiology ; Microbiota/physiology ; Longitudinal Studies ; }, abstract = {UNLABELLED: Recent research provides new insights into the early establishment of the infant gut microbiome, emphasizing the influence of breastfeeding on the development of gastrointestinal microbiomes. In our study, we longitudinally examined the taxonomic and functional dynamics of the oral and gastrointestinal tract (GIT) microbiomes of healthy infants (n = 30) in their first year, focusing on the often-over-looked aspects, the development of archaeal and anaerobic microbiomes. Breastfed (BF) infants exhibit a more defined transitional phase in their oral microbiome compared to non-breastfed (NBF) infants, marked by a decrease in Streptococcus and the emergence of anaerobic genera such as Granulicatella. This phase, characterized by increased alpha-diversity and significant changes in beta-diversity, occurs earlier in NBF infants (months 1-3) than in BF infants (months 4-6), suggesting that breastfeeding supports later, more defined microbiome maturation. We demonstrated the presence of archaea in the infant oral cavity and GIT microbiome from early infancy, with Methanobrevibacter being the predominant genus. Still, transient patterns show that no stable archaeome is formed. The GIT microbiome exhibited gradual development, with BF infants showing increased diversity and complexity between the third and eighth months, marked by anaerobic microbial networks. NBF infants showed complex microbial co-occurrence patterns from the start. These strong differences between BF and NBF infants' GIT microbiomes are less pronounced on functional levels than on taxonomic levels. Overall, the infant microbiome differentiates and stabilizes over the first year, with breastfeeding playing a crucial role in shaping anaerobic microbial networks and overall microbiome maturation.

IMPORTANCE: The first year of life is a crucial period for establishing a healthy human microbiome. Our study analyses the role of archaea and obligate anaerobes in the development of the human oral and gut microbiome, with a specific focus on the impact of breastfeeding in this process. Our findings demonstrated that the oral and gut microbiomes of breastfed infants undergo distinct phases of increased dynamics within the first year of life. In contrast, the microbiomes of non-breastfed infants are more mature from the first month, leading to a steadier development without distinct transitional phases in the first year. Additionally, we found that archaeal signatures are present in infants under 1 year of age, but they do not form a stable archaeome. In contrast to this, we could track specific bacterial strains transitioning from oral to gut or persisting in the gut over time.}, } @article {pmid39714117, year = {2024}, author = {Caille, C and Duhamel, S and Latifi, A and Rabouille, S}, title = {Adaptive Responses of Cyanobacteria to Phosphate Limitation: A Focus on Marine Diazotrophs.}, journal = {Environmental microbiology}, volume = {26}, number = {12}, pages = {e70023}, pmid = {39714117}, issn = {1462-2920}, support = {//LEFE-CYBER/ ; }, mesh = {*Adaptation, Physiological ; *Cyanobacteria/metabolism/genetics ; Nitrogen Fixation ; *Phosphates/metabolism ; Phosphorus/metabolism ; *Seawater/chemistry/microbiology ; }, abstract = {Phosphorus is an essential component of numerous macromolecules and is vital for life. Its availability significantly influences primary production, particularly in oligotrophic environments. Marine diazotrophic cyanobacteria, which play key roles in biogeochemical cycles through nitrogen fixation (N2 fixation), have adapted to thrive in phosphate (Pi)-poor areas. However, the molecular mechanisms that facilitate their adaptation to such conditions remain incompletely understood. Bacteria have evolved various strategies to cope with Pi limitation, including detecting Pi availability, utilising high-affinity Pi transporters, and hydrolyzing dissolved organic phosphorus (DOP) with various enzymes. This review synthesises current knowledge regarding how cyanobacteria adapt to Pi scarcity, with particular emphasis on subtropical marine free-living diazotrophs and their ability to utilise diverse DOP molecules. Omics approaches, such as (meta)genomics and (meta)transcriptomics, reveal the resilience of marine diazotrophs in the face of Pi scarcity and highlight the need for further research into their molecular adaptive strategies. Adaptation to Pi limitation is often intertwined with the broader response of cyanobacteria to multiple limitations and stresses. This underscores the importance of understanding Pi adaptation to assess the ecological resilience of these crucial microorganisms in dynamic environments, particularly in the context of global climate change.}, } @article {pmid39714075, year = {2025}, author = {Minty, M and Germain, A and Sun, J and Kaglan, G and Servant, F and Lelouvier, B and Misselis, E and Neagoe, RM and Rossella, M and Cardellini, M and Burcelin, R and Federici, M and Fernandez-Real, JM and Blasco-Baque, V}, title = {Identifying the location-dependent adipose tissue bacterial DNA signatures in obese patients that predict body weight loss.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2439105}, doi = {10.1080/19490976.2024.2439105}, pmid = {39714075}, issn = {1949-0984}, mesh = {Humans ; *Weight Loss ; *Obesity/microbiology/genetics/metabolism ; *DNA, Bacterial/genetics ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification/metabolism ; Female ; Male ; *Bariatric Surgery ; Adult ; Adipose Tissue/metabolism/microbiology ; Middle Aged ; Longitudinal Studies ; }, abstract = {Recent sets of evidence have described profiles of 16S rDNA sequences in host tissues, notably in fat pads that are significantly overrepresented and can serve as signatures of metabolic disease. However, these recent and original observations need to be further detailed and functionally defined. Here, using state-of-the-art targeted DNA sequencing and discriminant predictive approaches, we describe, from the longitudinal FLORINASH cohort of patients who underwent bariatric surgery, visceral, and subcutaneous fat pad-specific bacterial 16SrRNA signatures. The corresponding Porphyromonadaceae, Campylobacteraceae, Prevotellaceae, Actimomycetaceae, Veillonellaceae, Anaerivoracaceae, Fusobacteriaceae, and the Clostridium family XI 16SrRNA DNA segment profiles are signatures of the subcutaneous adipose depot while Pseudomonadaceae and Micrococcacecae, 16SrRNA DNA sequence profiles characterize the visceral adipose depot. In addition, we have further identified that a specific pre-bariatric surgery adipose tissue bacterial DNA signature predicts the efficacy of body weight loss in obese patients 5-10 years after the surgery. 16SrRNA signatures discriminate (ROC ~ 1) the patients who did not maintain bodyweight loss and those who did. Second, from the 16SrRNA sequences we infer potential pathways suggestive of catabolic biochemical activities that could be signatures of subcutaneous adipose depots that predict body weight loss.}, } @article {pmid39713824, year = {2024}, author = {Karesh, WB}, title = {Shifting from wildlife disease threats to wildlife health.}, journal = {Revue scientifique et technique (International Office of Epizootics)}, volume = {Special Edition}, number = {}, pages = {141-144}, doi = {10.20506/rst.SE.3568}, pmid = {39713824}, issn = {0253-1933}, mesh = {Animals ; *Animals, Wild ; Humans ; Zoonoses/prevention & control ; Conservation of Natural Resources ; Animal Diseases/prevention & control/epidemiology ; }, abstract = {The evolution of wildlife disease management and surveillance, as documented in the World Organisation for Animal Health's Scientific and Technical Review, reflects a deepening understanding of the links between wildlife health, ecosystem integrity and human well-being. Early work, beginning with the World Assembly of Delegates in 1954, primarily focused on diseases like rabies. This focus expanded over time to include broader concerns such as the impacts of climate change, habitat loss and increased human-wildlife interactions on wildlife health. By the late 20th century, the emphasis had shifted towards improved practices for wildlife disease control and the development of advanced diagnostic methods and vaccines. Articles in the Review highlight the growing complexity of wildlife diseases and the need for holistic management strategies. The adoption in recent years of cutting-edge technologies like CRISPR-Cas systems and metagenomics points to a future of more proactive and integrated approaches to wildlife disease management. There is still a need to address not just the consequences of wildlife diseases but also their anthropogenic drivers. The latest perspectives advocate for nature-based solutions, expanded partnerships and systems-level thinking to effectively tackle 21st-century challenges in wildlife and biodiversity conservation.}, } @article {pmid39713101, year = {2024}, author = {Zhou, Q and Yang, J and Feng, Y and Yang, Z and Wang, Y and Zhang, Z and Zhang, T and Liu, W and Xu, Y and Yang, Y and Huang, J}, title = {Analysis of the effects of Bacillus velezensis HJ-16 inoculation on tobacco leaves based on multi-omics methods.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {12}, number = {}, pages = {1493766}, pmid = {39713101}, issn = {2296-4185}, abstract = {In this study, a strain isolated from the surface of flue-cured tobacco leaves, identified as Bacillus velezensis HJ-16, was applied in the solid-state fermentation of tobacco leaves. This strain, known for producing thermally stable enzymes, including amylase, cellulase, and protease, significantly improved the sensory qualities of tobacco, enhancing aromatic intensity, density, and softness, while reducing irritation. Whole-genome sequencing and functional annotation revealed that B. velezensis HJ-16 possesses a single circular chromosome containing genes associated with enzyme production and metabolic activities, particularly in carbohydrate metabolism and amino acid metabolism. Untargeted metabolomics analysis identified significant changes in non-volatile metabolites induced by fermentation. These metabolites were enriched in pathways related to flavonoid biosynthesis, alkaloid biosynthesis, aromatic amino acid metabolism, lipid metabolism, and carbon metabolism. Metagenomic analysis showed that Bacillus became the dominant genus on the tobacco leaf surface following inoculation with B. velezensis HJ-16, altering the microbial community composition, reducing diversity and evenness, and enhancing microbial metabolic activity. These findings underscore the potential of B. velezensis HJ-16 as a biotechnological tool to improve tobacco leaf quality.}, } @article {pmid39712896, year = {2024}, author = {Son, SH and Kang, MG and Kang, A and Kang, Y and Kim, K and Kwak, MJ and Song, M and Kim, Y}, title = {Gut microbiome and metabolome library construction based on age group using short-read and long-read sequencing techniques in Korean traditional canine species Sapsaree.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1486566}, pmid = {39712896}, issn = {1664-302X}, abstract = {This study investigated age-related changes in the gut microbiota and metabolome of Sapsaree dogs through metagenomic and metabolomic analyses. Using Illumina (short-read) and Nanopore (long-read) sequencing technologies, we identified both common and unique bacterial genera in the dogs across different age groups. In metagenomic analysis, Firmicutes were predominant at the family level. At the genus level, Lactobacillus, Streptococcus, Romboutsia, and Clostridium XI were the most abundant, and the bacterial genera typically considered beneficial were less prevalent in senior dogs, whereas the genera associated with pathogenicity were more abundant. These findings suggest age-related shifts in gut microbiota composition. Metabolomic analysis showed distinct clustering of metabolites based on the age group, with changes in metabolite profiles correlating with metagenomic findings. Although Illumina and Nanopore methods provided distinctive results, the genera detected by both methods exhibited similar trends across all age groups in Sapsaree dogs. These findings highlight the relationship between ages, metabolite profiles and gut microbiota composition in dogs, suggesting the need for further research to explore this relation in greater depth.}, } @article {pmid39712641, year = {2024}, author = {Shalini, TS and Prathiviraj, R and Senthilraja, P}, title = {Metagenomic analysis and bioactive profiling of kombucha fermentation: antioxidant, antibacterial activities, and molecular docking insights into gastric cancer therapeutics.}, journal = {Toxicology research}, volume = {13}, number = {6}, pages = {tfae224}, pmid = {39712641}, issn = {2045-452X}, abstract = {Kombucha is fermented and produced with a biofilm called a symbiotic culture of bacteria and yeast, which is drunk all over the world for its beneficial effects on human health and energy levels. The metagenomic study of kombucha frequently detected microorganisms in proteobacteria, firmicutes, and actinobacteria. And also, yeast and fungi are Ascomycota and Basidiomycota is present in green leaf and sugarcane juice fermented kombucha. The kombucha extracts' biological activities were assessed using pH, total phenolic content, antioxidant, antibacterial, and anticancer activity. Fermentation may enhance biological activity and the generation of bioactive substances. These results showed the pH -3.1 ± 0.2 and TPC -0.721 μg/mL of gallic acid equivalent. The antioxidant radicals scavenging activity of kombucha was evaluated by DPPH, ABTS, H2O2 and TAC. The bioactive chemicals identified by FT-IR and HR-LC/MS analysis of Kombucha totaled 45 components. The identified compounds were further move on to perform molecular docking study against gastric cancer target proteins 4H9M, 2DQ7 and 1TVO are binding with Nequinate compounds showing best LibDock scores 105.12, 114.49, and 108.97. So, this study suggests that knowledge can potentially active bioactive compounds are present in kombucha and it's stimulated the mechanism of gastrointestinal transit. Additionally, the metagenomic analysis gives strength to understand the bacterial and fungal distribution and its molecular mechanism from Kombucha.}, } @article {pmid39712493, year = {2024}, author = {Liu, HH and Lin, TT and Zhang, QJ and Zhang, L and Fang, JY and Hu, L}, title = {Effect of Helicobacter pylori-related chronic gastritis on gastrointestinal microorganisms and brain neurotransmitters in mice.}, journal = {Frontiers in pharmacology}, volume = {15}, number = {}, pages = {1472437}, pmid = {39712493}, issn = {1663-9812}, abstract = {The effects of Helicobacter pylori (Hp)-related chronic gastritis on gastrointestinal microorganisms or brain neurotransmitters are not fully understood. Here, this study selected SPF C57BL/6 mice to set up a Hp-related chronic gastritis experiment group and a blank control group, and used omics to explore the specific effects of Hp-related chronic gastritis on gastrointestinal microorganisms and brain neurotransmitters in mice. The Tyramine (TyrA) content in the female experiment group's brain was considerably reduced compared to the female control group (p < 0.01), and TyrA was strongly correlated with 13 gastrointestinal microorganisms with significant differences, such as Acinetobacter_baumannii (p < 0.05). The His content in the male experiment group's brain was significantly higher than that in the male control group (p < 0.05), and His was strongly correlated with four gastrointestinal microorganisms with significant differences, such as Acinetobacter_baumannii (p < 0.05). The Levodopa (DOPA) content in the female control group's brain was significantly lower than that in the male control group (p < 0.05), and DOPA was strongly correlated with 19 gastrointestinal microorganisms with significant differences, such as Achromobacter_xylosoxidans (p < 0.05). The contents of L-Glutamine (Gln), L-Glutamine (GABA), Noradrenaline hydrochloride (NE), and Adrenaline hydrochloride (E) in the female experiment group's brain were significantly lower than those in the male experiment group (p < 0.05), and Gln, GABA, NE, and E were strongly correlated with 41, 28, 40, and 33 gastrointestinal microorganisms with significant differences (p < 0.05), respectively. These results indicate that Hp-related chronic gastritis could affect gastrointestinal microorganisms and brain neurotransmitters in mice with certain gender differences, and the changes in brain neurotransmitters might be related to the changes in gastrointestinal microorganisms.}, } @article {pmid39711694, year = {2024}, author = {Sehgal, N and Pajuelo, MJ and Gilman, RH and Pickering, AJ and Earl, AM and Worby, CJ and Nadimpalli, ML}, title = {Effects of commonly used antibiotics on children's developing gut microbiomes and resistomes in peri-urban Lima, Peru.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {39711694}, support = {KL2 TR002545/TR/NCATS NIH HHS/United States ; R01 AI108695/AI/NIAID NIH HHS/United States ; T32 ES012870/ES/NIEHS NIH HHS/United States ; U19 AI110818/AI/NIAID NIH HHS/United States ; }, abstract = {BACKGROUND: The effects of antibiotic use on children's gut microbiomes and resistomes are not well characterized in middle-income countries, where pediatric antibiotic consumption is exceptionally common. We characterized the effects of antibiotics commonly used by Peruvian children (i.e., amoxicillin, azithromycin, cefalexin, sulfa-trimethoprim) on gut diversity, genera, and antibiotic resistance gene (ARG) abundance from 3-16 months.

METHODS: This study included 54 children from a prospective cohort of enteric infections in peri-urban Lima, 2016-2019. Stool collected at 3, 6, 7, 9, 12, and 16 months underwent DNA extraction and short-read metagenomic sequencing. We profiled the taxonomy of stool metagenomes and assessed ARG abundance by aligning reads to the ResFinder database. We used daily surveillance data (40,662 observations) to tabulate the number of antibiotic courses consumed in the 30 days prior to stool sampling. Using linear mixed models, the association of recent antibiotic use with species richness, diversity, gut genera, and ARG abundance over time was examined.

RESULTS: Most children were vaginally delivered (73%), received breastmilk almost daily over the study period, and belonged to socioeconomically diverse households. Amoxicillin, azithromycin, cefalexin, and sulfa-trimethoprim did not impact gut diversity or genera abundance. Azithromycin use significantly impacted ARGs from the macrolide, aminoglycoside, and folate pathway antagonist classes. Amoxicillin use significantly increased total ARGs. Antibiotics' effects on ARGs appeared to be independent of gut microbiome changes.

CONCLUSION: Common antibiotics like amoxicillin and azithromycin may be key drivers of the gut resistome but not the microbiome during early childhood in this setting with frequent breastfeeding.}, } @article {pmid39711517, year = {2025}, author = {Long, L and Xu, XL and Duan, YF and Long, L and Chen, JY and Yin, YH and Zhu, YG and Huang, Q}, title = {Extracellular Vesicles Are Prevalent and Effective Carriers of Environmental Allergens in Indoor Dust.}, journal = {Environmental science & technology}, volume = {59}, number = {4}, pages = {1969-1983}, pmid = {39711517}, issn = {1520-5851}, mesh = {*Extracellular Vesicles ; *Allergens ; *Dust ; Humans ; Air Pollution, Indoor ; China ; }, abstract = {The global incidence of allergic diseases is rising and poses a substantial threat to human health. Allergenic proteins released by various allergenic species play a critical role in the pathogenesis of allergic diseases and have been widely detected in the environmental matrix. However, the release, presence and interaction of environmental allergens with human body remain to be elucidated. In this study, we reported the widespread of allergen-harboring extracellular vesicles (EVs) in indoor dust from 75 households across five provinces in China. Particle size and abundance of EVs were correlated with specific environmental factors. EVs showed long persistence and high resistance to environmental stress. Metagenomics and metaproteomics data revealed that most indoor allergenic species released allergens within the EVs into dust. A higher abundance of allergenic species and their derived EVs was observed in urban areas compared to rural areas. ELISA confirmed the allergenic activity of the EV-associated allergens. Allergens are common components and even markers of EVs, as evidenced by the data compilation of various allergenic species. The proportion of EV-associated allergens varied across species. EVs facilitated allergen entry into epithelial cells. Intranasally administered EVs can be rapidly transported to the lungs and gastrointestinal tract. EV-associated allergens exhibited higher allergenicity compared with non-EV allergens. Our findings elucidate a vesicle pathway through which environmental allergens are released, persist, and trigger allergic responses within EVs.}, } @article {pmid39711113, year = {2025}, author = {Olivares, C and Ruppé, E and Ferreira, S and Corbel, T and Andremont, A and de Gunzburg, J and Guedj, J and Burdet, C}, title = {A modelling framework to characterize the impact of antibiotics on the gut microbiota diversity.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2442523}, doi = {10.1080/19490976.2024.2442523}, pmid = {39711113}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/pharmacology/administration & dosage ; *Feces/microbiology ; *Bacteria/classification/genetics/drug effects/isolation & purification ; *RNA, Ribosomal, 16S/genetics ; Adult ; Ceftazidime/pharmacology/administration & dosage ; Male ; Moxifloxacin/pharmacology/administration & dosage ; Drug Combinations ; Ceftriaxone/pharmacology/administration & dosage ; Female ; Azabicyclo Compounds/pharmacology/administration & dosage ; Biodiversity ; Young Adult ; Healthy Volunteers ; Piperacillin, Tazobactam Drug Combination ; }, abstract = {Metagenomic sequencing deepened our knowledge about the role of the intestinal microbiota in human health, and several studies with various methodologies explored its dynamics during antibiotic treatments. We compared the impact of four widely used antibiotics on the gut bacterial diversity. We used plasma and fecal samples collected during and after treatment from healthy volunteers assigned to a 5-day treatment either by ceftriaxone (1 g every 24 h through IV route), ceftazidime/avibactam (2 g/500 mg every 8 h through IV route), piperacillin/tazobactam (1 g/500 mg every 8 h through IV route) or moxifloxacin (400 mg every 24 h through oral route). Antibiotic concentrations were measured in plasma and feces, and bacterial diversity was assessed by the Shannon index from 16S rRNA gene profiling. The relationship between the evolutions of antibiotic fecal exposure and bacterial diversity was modeled using non-linear mixed effects models. We compared the impact of antibiotics on gut microbiota diversity by simulation, using various reconstructed pharmacodynamic indices. Piperacillin/tazobactam was characterized by the highest impact in terms of intensity of perturbation (maximal [IQR] loss of diversity of 27.3% [1.9; 40.0]), while moxifloxacin had the longest duration of perturbation, with a time to return to 95% of baseline value after the last administration of 13.2 d [8.3; 19.1]. Overall, moxifloxacin exhibited the highest global impact, followed by piperacillin/tazobactam, ceftazidime/avibactam and ceftriaxone. Their AUC between day 0 and day 42 of the change of diversity indices from day 0 were, respectively, -13.2 Shannon unit.day [-20.4; -7.9], -10.9 Shannon unit.day [-20.4; -0.6] and -10.1 Shannon unit.day [-18.3; -4.6]. We conclude that antibiotics alter the intestinal diversity to varying degrees, both within and between antibiotics families. Such studies are needed to help antibiotic stewardship in using the antibiotics with the lowest impact on the intestinal microbiota.}, } @article {pmid39710721, year = {2024}, author = {Zhou, N and Chen, W and Xia, L and Li, M and Ye, H and Lv, C and Chen, Y and Cheng, Z and Park, TJ and Ho, PL and Gao, X and Guo, X and Zhao, H and Cao, H and Zhu, Y}, title = {Metagenomic insights into the resistome, mobilome, and virulome of dogs with diverse lifestyles.}, journal = {Animal microbiome}, volume = {6}, number = {1}, pages = {76}, pmid = {39710721}, issn = {2524-4671}, support = {No. 2020-01//Shanghai Jiao Tong University Integrated Innovation Fund/ ; No. 32170141//National Natural Science Foundation of China/ ; No. 20-365//China Medical Board/ ; No.19201901//Health and Medical Research Fund/ ; 2024YFE0199000//National Key Research and Development Program of China/ ; }, abstract = {BACKGROUND: Dogs-whether pets, rural, or stray-exhibit distinct living styles that influence their fecal microbiota and resistomes, yet these dynamics remain underexplored. This study aimed to analyze and compare the fecal microbiota and resistomes of three groups of dogs (37 pets, 20 rural, and 25 stray dogs) in Shanghai, China.

RESULTS: Metagenomic analysis revealed substantial differences in fecal microbial composition and metabolic activities among the dog groups. Pet dogs displayed the lowest microbial diversity. Using Shapley Additive Explanations (SHAP), an interpretable machine learning approach, Ligilactobacillus emerged as the most diverse genus, with significantly higher SHAP values in stray dogs, suggesting enhanced adaptability to more variable and less controlled environments. Across all samples, 587 antibiotic resistance genes (ARGs) were identified, conferring resistance to 14 antibiotic classes. A striking observation was the detection of mcr-1 in one pet dog, indicating a potential public health risk. The floR gene was identified as a key differentiator in resistance profiles, particularly in pet and rural dogs, likely due to antibiotic exposure in their environments.

CONCLUSION: This study provides the first comprehensive assessment of fecal microbiota and resistome variations among dogs with different lifestyles, revealing a less resilient microbiome and heightened antimicrobial resistance in pet dogs, which could have public health implications.}, } @article {pmid39710261, year = {2024}, author = {Guerreiro, JF and Pires, AJ and Nunes, M and Esteves, A and Chambel, L and Pascoal, P and Pereira, M and Fangueiro, D and Tavares, L and Dias, R and Bexiga, R and Oliveira, M}, title = {Biochar supplementation affects the microbiome of recycled manure solids for cow bedding: a metagenomic analysis.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2024-25616}, pmid = {39710261}, issn = {1525-3198}, abstract = {The widespread use of Recycled Manure Solids (RMS) as cow bedding material is not without risks, since cattle manure may act as a vehicle for pathogenic and antimicrobial resistant bacteria dissemination. Thus, our aim was to evaluate RMS-supplemented with a pine biochar produced in Portugal as a new cow bedding material, since the use of biochar has been shown to have the potential to mitigate the impact of relevant bacterial species when added to animal manure microbiota. Our experimental setup consisted on fresh RMS samples that were collected on a commercial dairy farm and placed in naturally-ventilated containers for a total of 4 groups: 1-non-supplemented RMS; 2-RMS supplemented with 2.5% (wt/wt) of biochar; 3-RMS supplemented with 5% (wt/wt) of biochar; and 4-RMS supplemented with 10% (wt/wt) of biochar. Sampling was performed at 4 different incubation times (0, 5, 15 and 30 d) and in 2 distinct seasons: April-May (humid season) and June-July (dry season). The resulting 32 samples were subjected to DNA extraction and their microbiome profile determined through complete 16S rDNA gene sequencing using Nanopore next-generation sequencing. We observed that biochar supplementation clearly altered the microbiome of RMS, which was reflected in changes in populations' diversity and their relative abundance of relevant pathogenic bacteria. In particular, we found that long-term storage (30 d) was more beneficial than short-term storage, an effect that was more evident for samples supplemented with 2.5% or 5% biochar. In both seasons, those concentrations of biochar led to a decrease in the levels of several mastitis-causing agents (Enterobacteriaceae, streptococci, enterococci and staphylococci). In addition, we also observed a reduction in the levels of Salmonella spp. and Gram-positive bacilli in the biochar-supplemented samples. Unexpectedly, however, those same conditions yielded an increase in the abundance of Brucella spp., a group which includes important infectious agents, highlighting the need for a deeper evaluation of the impact of biochar supplementation of RMS to ensure the future safe and sustainable use of this environmental-friendly resource in animal production.}, } @article {pmid39710013, year = {2025}, author = {He, B and Xu, S and Schooling, CM and Leung, GM and Ho, JWK and Au Yeung, SL}, title = {Gut microbiome and obesity in late adolescence: A case-control study in "Children of 1997" birth cohort.}, journal = {Annals of epidemiology}, volume = {101}, number = {}, pages = {58-66}, doi = {10.1016/j.annepidem.2024.12.009}, pmid = {39710013}, issn = {1873-2585}, mesh = {Humans ; *Gastrointestinal Microbiome ; Case-Control Studies ; Female ; Male ; Adolescent ; *Pediatric Obesity/microbiology/epidemiology ; *Feces/microbiology ; Diabetes Mellitus, Type 2/microbiology/epidemiology ; Birth Cohort ; Bacteroides/isolation & purification ; }, abstract = {PURPOSE: Although the gut microbiome is important in human health, its relation to adolescent obesity remains unclear. Here we assessed the associations of the gut microbiome with adolescent obesity in a case-control study.

METHODS: In the "Children of 1997" birth cohort, participants with and without obesity at ∼17.4 years were 1:1 matched on sex, physical activity, parental education and occupation (n = 312). Fecal gut microbiome composition and pathways were assessed via shotgun metagenomic sequencing. The association of microbiota species with obesity was evaluated using conditional logistic regression. We explored the association of the obesity-relevant species with adolescent metabolomics using multivariable linear regression, and causal relationships with type 2 diabetes using Mendelian randomization analysis.

RESULTS: Gut microbiota in the adolescents with obesity exhibited lower richness (p = 0.031) and evenness (p = 0.014) compared to controls. Beta diversity revealed differences in the microbiome composition in two groups (p = 0.034). Lower relative abundance of Clostridium spiroforme, Clostridium phoceensis and Bacteroides uniformis were associated with higher obesity risk (q<0.15). Lower Bacteroides uniformis was associated with higher branched-chain amino acid, potentially contributing to higher type 2 diabetes risk.

CONCLUSION: Adolescents with obesity had a distinct gut microbiota profile compared to the controls, possibly linked to metabolic pertubation and related diseases.}, } @article {pmid39709811, year = {2025}, author = {Chi, C and Zheng, Y and Shi, Y and Lyu, C and Jiang, X and Zhang, Y and Wang, C}, title = {Harmless treatment of cyanide tailings by functional bacteria: Degradation of cyanide and the secondary pollutant ammonia nitrogen.}, journal = {Journal of hazardous materials}, volume = {485}, number = {}, pages = {136939}, doi = {10.1016/j.jhazmat.2024.136939}, pmid = {39709811}, issn = {1873-3336}, mesh = {*Cyanides/metabolism ; *Ammonia/metabolism/chemistry ; *Bacteria/metabolism/genetics ; *Biodegradation, Environmental ; Nitrogen/metabolism/chemistry ; Nitrification ; Water Pollutants, Chemical/metabolism/toxicity ; Industrial Waste ; }, abstract = {The eco-friendly treatment of cyanide tailings (CT) using microorganisms is a cost-effective and promising technology. However, this process often generates the secondary pollutants, such as ammonia nitrogen (NH4[+]-N), which can adversely impacts the surrounding environment. The accumulation of NH4[+]-N is also toxic to cyanide-degrading microorganisms, presenting a significant challenge in achieving simultaneous cyanide degradation and NH4[+]-N mitigation. In this study, a group of functional bacteria CG305-1 with the ability to degrade cyanide and perform nitrification and denitrification was successfully enriched for the first time and used to treat CT by in situ microbial drenching technology. Results demonstrated that the total cyanide (CNT) concentration in the leaching solution decreased from 49.96 ± 1.51 mg/L to 0.19 ± 1.11 mg/L. NH4[+]-N was degraded to 0.25 ± 0.18 mg/L, and nitrate nitrogen (NO3[-]-N) was reduced to 0.41 ± 0.20 mg/L. Furthermore, CNT in the CT leachate was reduced to 0.94 ± 0.11 mg/L, meeting the storage standard for CT leachate (CNT < 5 mg/L). The potential synergistic microbial degradation mechanisms were elucidated through Scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), and Metagenomic sequencing. This study provides significant insights into green and sustainable methods for the harmless treatment of CT.}, } @article {pmid39709798, year = {2025}, author = {Wang, RX and Zhou, HB and Gao, JX and Bai, WF and Wang, J and Bai, YC and Jiang, SY and Chang, H and Shi, SL}, title = {Metagenomics and metabolomics to investigate the effect of Amygdalus mongolica oil on intestinal microbiota and serum metabolites in rats.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {136}, number = {}, pages = {156335}, doi = {10.1016/j.phymed.2024.156335}, pmid = {39709798}, issn = {1618-095X}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Male ; *Metabolomics ; *Rats, Sprague-Dawley ; Rats ; Metagenomics ; Plant Oils/pharmacology ; Fibrosis ; Kidney/drug effects ; Renal Insufficiency, Chronic/blood/drug therapy/microbiology ; }, abstract = {BACKGROUND: Renal fibrosis (RF) is an inevitable consequence of multiple manifestations of progressive chronic kidney diseases (CKDs). Mechanism of Amygdalus mongolica (Maxim.) in the treatment of RF needs further investigation.

PURPOSE: The study further investigated the potential mechanism of A. mongolica in the treatment of RF.

METHODS: A rat model of RF was induced by unilateral ureteral obstruction (UUO), followed by treatment with varying dosages of A. mongolica oil for 4 weeks. Body weight was measured weekly. We detected serum levels of interleukin (IL)-6, IL-1β, type Ⅲ procollagen (Col-Ⅲ), type IV collagen (Col-Ⅳ), laminin (LN), hyaluronidase (HA), and tissue levels of albumin (ALB), blood urea nitrogen (BUN), creatinine (Cre), superoxide dismutase (SOD), malondialdehyde (MDA), and hydroxyproline (HYP). Shotgun metagenomics analyzed the composition of the intestinal microbiota. High-performance liquid chromatography coupled with a quadrupole-exactive mass spectrometer (HPLC-Q-Exactive-MS) monitored changes in metabolite levels in serum and gut. Multiple reaction monitoring-mass spectrometry (MRM-MS) determined the levels of amino acids in serum.

RESULTS: A. mongolica oil significantly alleviated indicators related to RF (p < 0.05). A. mongolica oil reduced the ratio of Firmicutes to Bacteroidetes and restored the balance of intestinal microbiota in rats with RF. A. mongolica oil modulated levels of metabolites in gut content and serum. It regulated 11 metabolic pathways including arachidonic acid metabolism. Targeted metabolomics of amino acids showed that 17 amino acids were significantly changed by A. mongolica oil, including L-glycine, L-serine and L-glutamine.

CONCLUSION: A. mongolica oil regulates intestinal microbiota and metabolites, restoring amino acid metabolism to treat RF.}, } @article {pmid39709651, year = {2025}, author = {Cheng, E and Hung, SC and Lin, TY}, title = {Association of trimethylamine N-oxide and metabolites with kidney function decline in patients with chronic kidney disease.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {44}, number = {}, pages = {239-247}, doi = {10.1016/j.clnu.2024.12.001}, pmid = {39709651}, issn = {1532-1983}, mesh = {Humans ; *Methylamines/blood ; Female ; *Renal Insufficiency, Chronic/blood/physiopathology ; Male ; Aged ; *Gastrointestinal Microbiome/physiology ; *Glomerular Filtration Rate ; Prospective Studies ; *Carnitine/blood ; Middle Aged ; *Choline/blood ; Kidney/physiopathology ; Disease Progression ; Betaine/blood/analogs & derivatives ; }, abstract = {BACKGROUND: Trimethylamine N-oxide (TMAO) is a gut microbial metabolite derived from dietary l-carnitine and choline. High plasma TMAO levels are associated with cardiovascular disease and overall mortality, but little is known about the associations of TMAO and related metabolites with the risk of kidney function decline among patients with chronic kidney disease (CKD).

METHODS: We prospectively followed 152 nondialysis patients with CKD stages 3-5 and measured plasma TMAO and related metabolites (trimethylamine [TMA], choline, carnitine, and γ-butyrobetaine) via liquid chromatography‒mass spectrometry. An estimated glomerular filtration rate (eGFR) slope >3 ml/min/per 1.73 m[2] per year was defined as a rapid decline. We performed logistic regression to determine the probability of rapid or slow eGFR decline, with each metabolite as the main predictor. The gut microbiota was profiled via whole metagenomic sequencing.

RESULTS: The participants had a median age of 66 years, 41.4 % were women, 39.5 % had diabetes, and the median eGFR was 23 mL/min/1.73 m[2]. A rapid decrease in the eGFR occurred in 65 patients (42.8 %) over a median follow-up of 3.3 years. After adjustment for baseline eGFR, proteinuria, and clinical factors, plasma TMAO levels were independently associated with increased odds of rapid eGFR decline (odds ratio, 2.42; 95 % CI, 1.36-4.32), whereas plasma TMA, choline, carnitine, and γ-butyrobetaine levels were not. Patients who exhibited rapid eGFR decline had a distinct gut microbial composition characterized by increased α-diversity and an abundance of TMA-producing bacteria, including those of the genera Desulfovibrio and Collinsella tanakaei, as well as increased expression of the TMA-producing enzymes bbuA and cutC.

CONCLUSION: Our findings suggest the relevance of plasma TMAO in the progression of kidney disease among patients with CKD.}, } @article {pmid39709594, year = {2025}, author = {Smith, MZ and York, M and Townsend, KS and Martin, LM and Gull, T and Coghill, LM and Ericsson, AC and Johnson, PJ}, title = {Effects of orally administered clioquinol on the fecal microbiome of horses.}, journal = {Journal of veterinary internal medicine}, volume = {39}, number = {1}, pages = {e17276}, pmid = {39709594}, issn = {1939-1676}, mesh = {Animals ; Horses ; *Feces/microbiology ; *Clioquinol/pharmacology/administration & dosage ; Female ; Male ; Administration, Oral ; Prospective Studies ; Gastrointestinal Microbiome/drug effects ; RNA, Ribosomal, 16S/genetics ; Cohort Studies ; }, abstract = {BACKGROUND: Whereas restoration of fecal consistency after treatment with clioquinol for chronic diarrhea and free fecal water syndrome has been attributed to its antiprotozoal properties, actions of clioquinol on the colonic bacterial microbiota have not been investigated.

OBJECTIVES: Characterize the dynamics of fecal microbial diversity before, during, and after PO administration of clioquinol to healthy horses.

STUDY DESIGN: Experimental prospective cohort study using a single horse group.

METHODS: Eight healthy adult horses received PO clioquinol (10 g, daily) for 7 days. Feces were obtained daily for 7 days before, during, and after conclusion of treatment, and again 3 months later. Libraries of 16S rRNA V4 region amplicons generated from fecal DNA were sequenced using the Illumina sequencing platform. Bioinformatic analysis was undertaken with QIIME2 and statistical analyses included analysis of variance (ANOVA) and permutational multivariate ANOVA (PERMANOVA).

RESULTS: The richness and composition of the fecal microbiome was altered after administration of clioquinol, reaching a maximum effect by the fifth day of administration. Changes included a 90% decrease in richness, and compensatory expansion of facultative anaerobes including Streptococcaceae, Enterococcaceae, and Enterobacteriaceae. Multiple horses had Salmonella cultured from feces.

MAIN LIMITATIONS: Limitations including lack of control group and modest sample size are obviated by robust longitudinal study design and strong effect size associated with drug exposure.

CONCLUSIONS: Clioquinol has broad-spectrum antibacterial effects on the fecal microbiome of horses, but spares certain bacterial families including several pathogens and pathobionts. Clioquinol should be used with caution in horses, in an environment free of contamination with fecal pathogens.}, } @article {pmid39709451, year = {2024}, author = {Mushraf, S and Chawla, K and Fayaz, SMA and Mathew, AJ and Reddy, GPK and Kappettu Gadahad, MR and Shenoy, PA and Devi, V and Adiga, S and Nayak, V}, title = {Exploring the effects of probiotics on olanzapine-induced metabolic syndrome through the gut microbiota.}, journal = {Gut pathogens}, volume = {16}, number = {1}, pages = {77}, pmid = {39709451}, issn = {1757-4749}, abstract = {BACKGROUND: Maintaining gut microbial homeostasis is crucial for human health, as imbalances in the gut microbiota (GM) can lead to various diseases, including metabolic syndrome (MS), exacerbated by the use of antipsychotic medications such as olanzapine (OLZ). Understanding the role of the GM in OLZ-induced MS could lead to new therapeutic strategies. This study used metagenomic analysis to explore the impact of OLZ on the GM composition and examined how probiotics can mitigate its adverse effects in a rat model. Changes in weight, blood pressure, and lipid levels, which are key parameters defining MS, were assessed. Additionally, this study investigated serotonin, dopamine, and histopathological changes to explore their possible link with the microbiota-gut-brain axis (MGBA).

RESULTS: OLZ had an antagonistic effect on serotonin and dopamine receptors, and it was consistently found to alter the composition of the GM, with an increase in the relative abundance (RA) of the Firmicutes/Bacteroidetes phyla ratio and TM7 genera, indicating that the anticommonsal action of OLZ affects appetite and energy expenditure, contributing to obesity, dyslipidemia and increased blood pressure, which are core components of MS. Hepatic steatosis and intestinal damage in OLZ-treated rat tissues further indicate its role in MS. Conversely, the administration of probiotics, either alone or in combination with OLZ, was found to mitigate these OLZ-induced symptoms of MS by altering the GM composition. These alterations included increases in the abundances of the taxa Bacteroidetes, Actinobacteria, Prevotella, Blautia, Bacteroides, Bacteroidales, and Ruminococcaceae and a decrease in Firmicute abundance. These changes helped maintain gut barrier integrity and modulated neurotransmitter levels, suggesting that probiotics can counteract the adverse metabolic effects of OLZ by restoring the GM balance. Moreover, this study highlights the modulation of the MGBA by OLZ as a potential mechanism through which probiotics modulate serotonin and dopamine levels, influencing metabolic health.

CONCLUSION: These findings emphasise the significant impact of OLZ on the GM and its contribution to MS. These findings suggest that interventions targeting the GM, such as probiotics, could mitigate the metabolic side effects of OLZ. Future research should focus on developing integrative treatment approaches that consider the health of the gut microbiome in managing antipsychotic-induced adverse effects.}, } @article {pmid39709449, year = {2024}, author = {Dos Santos, SJ and Copeland, C and Macklaim, JM and Reid, G and Gloor, GB}, title = {Vaginal metatranscriptome meta-analysis reveals functional BV subgroups and novel colonisation strategies.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {271}, pmid = {39709449}, issn = {2049-2618}, support = {20170705//Weston Family Foundation/ ; }, mesh = {Humans ; Female ; *Vagina/microbiology ; *Vaginosis, Bacterial/microbiology ; *Microbiota/genetics ; *Transcriptome ; *Bacteria/genetics/classification/isolation & purification ; Biofilms/growth & development ; Metagenomics/methods ; }, abstract = {BACKGROUND: The application of '-omics' technologies to study bacterial vaginosis (BV) has uncovered vast differences in composition and scale between the vaginal microbiomes of healthy and BV patients. Compared to amplicon sequencing and shotgun metagenomic approaches focusing on a single or few species, investigating the transcriptome of the vaginal microbiome at a system-wide level can provide insight into the functions which are actively expressed and differential between states of health and disease.

RESULTS: We conducted a meta-analysis of vaginal metatranscriptomes from three studies, split into exploratory (n = 42) and validation (n = 297) datasets, accounting for the compositional nature of sequencing data and differences in scale between healthy and BV microbiomes. Conducting differential expression analyses on the exploratory dataset, we identified a multitude of strategies employed by microbes associated with states of health and BV to evade host cationic antimicrobial peptides (CAMPs); putative mechanisms used by BV-associated species to resist and counteract the low vaginal pH; and potential approaches to disrupt vaginal epithelial integrity so as to establish sites for adherence and biofilm formation. Moreover, we identified several distinct functional subgroups within the BV population, distinguished by genes involved in motility, chemotaxis, biofilm formation and co-factor biosynthesis. After defining molecular states of health and BV in the validation dataset using KEGG orthology terms rather than community state types, differential expression analysis confirmed earlier observations regarding CAMP resistance and compromising epithelial barrier integrity in healthy and BV microbiomes and also supported the existence of motile vs. non-motile subgroups in the BV population. These findings were independent of the enzyme classification system used (KEGG or EggNOG).

CONCLUSIONS: Our findings highlight a need to focus on functional rather than taxonomic differences when considering the role of microbiomes in disease and identify pathways for further research as potential BV treatment targets. Video Abstract.}, } @article {pmid39708838, year = {2024}, author = {Luo, Q and Zhang, S and Butt, H and Chen, Y and Jiang, H and An, L}, title = {PhyImpute and UniFracImpute: two imputation approaches incorporating phylogeny information for microbial count data.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {1}, pages = {}, pmid = {39708838}, issn = {1477-4054}, support = {R01ES027013//National Institute of Health/ ; ARZT-1361620-H22-149//United States Department of Agriculture/ ; }, mesh = {*Phylogeny ; Algorithms ; Humans ; Computational Biology/methods ; Microbiota/genetics ; }, abstract = {Sequencing-based microbial count data analysis is a challenging task due to the presence of numerous non-biological zeros, which can impede downstream analysis. To tackle this issue, we introduce two novel approaches, PhyImpute and UniFracImpute, which leverage similar microbial samples to identify and impute non-biological zeros in microbial count data. Our proposed methods utilize the probability of non-biological zeros and phylogenetic trees to estimate sample-to-sample similarity, thus addressing this challenge. To evaluate the performance of our proposed methods, we conduct experiments using both simulated and real microbial data. The results demonstrate that PhyImpute and UniFracImpute outperform existing methods in recovering the zeros and empowering downstream analyses such as differential abundance analysis, and disease status classification.}, } @article {pmid39708826, year = {2024}, author = {Hu, Y and Zhang, ZY and Wang, F and Zhuang, K and Xu, X and Liu, DS and Fan, HZ and Yang, L and Jiang, K and Zhang, DK and Xu, L and Tang, JH and Liu, XM and He, C and Shu, X and Xie, Y and Lau, JYW and Zhu, Y and Du, YQ and Graham, DY and Lu, NH}, title = {Effects of amoxicillin dosage on cure rate, gut microbiota, and antibiotic resistome in vonoprazan and amoxicillin dual therapy for Helicobacter pylori: a multicentre, open-label, non-inferiority randomised controlled trial.}, journal = {The Lancet. Microbe}, volume = {}, number = {}, pages = {100975}, doi = {10.1016/j.lanmic.2024.100975}, pmid = {39708826}, issn = {2666-5247}, abstract = {BACKGROUND: Vonoprazan and amoxicillin (VA) dual therapy as a mainstream Helicobacter pylori regimen has gained momentum worldwide, but the optimum dosages remain unclear. We aimed to compare the efficacy and safety of VA dual therapy with 2 g amoxicillin or 3 g amoxicillin, and to assess the short-term effects of therapy on the gut microbiota and antibiotic resistome.

METHODS: We conducted an open-label, non-inferiority randomised controlled trial at 12 centres in China. Individuals infected with H pylori, aged 18-70 years, and without previous eradication therapy were recruited. Participants were randomly assigned at a 1:1 ratio (block size of six) to receive vonoprazan (20 mg twice a day) with either low-dose amoxicillin (1 g twice a day; LVA therapy) or high-dose amoxicillin (1 g three times a day; HVA therapy) for 14 days. Gastric biopsies were collected before treatment for detection of antibiotic resistance. Stool samples were collected at baseline, week 2, and week 8-10 for shotgun metagenomic sequencing. The primary outcome was the eradication rate of H pylori, assessed by [13]C urea breath test, in both intention-to-treat and per-protocol analyses. Secondary outcomes were adverse events, adherence, antibiotic resistance, and alterations to the gut microbiota and antibiotic resistome. The margin used to establish non-inferiority was -0·10. The trial was registered with ClinicalTrials.gov, NCT05649709.

FINDINGS: Between Feb 13, 2023, and Jan 25, 2024, 504 patients (204 [40%] male and 300 [60%] female; mean age 43 years [SD 13]) were randomly assigned to LVA therapy or HVA therapy (n=252 in each group). No infections were resistant to amoxicillin. The H pylori eradication rate was 85·3% (215 of 252; 95% CI 80·4 to 89·2) in the LVA group and 86·5% (218 of 252; 81·7 to 90·2) in the HVA group in the intention-to-treat analysis (p=0·70) and 88·8% (213 of 240; 84·1 to 92·2) and 92·4% (218 of 236; 88·3 to 95·1), respectively, in the per-protocol analysis (p=0·18). The efficacy of LVA was non-inferior to HVA in the intention-to-treat analysis (risk difference -1·2%, 95% CI -7·3 to 4·9, p=0·0022) and the per-protocol analysis (-3·6%, -9·0 to 1·7, p=0·0085). 31 (12%) patients in the LVA group and 43 (17%) patients in the HVA group reported adverse events. Adherence to therapy was 97% in the LVA group and 96% in the HVA group. The diversity of gut microbiota decreased after treatment but was restored to baseline at week 8-10 in both groups. The abundance of beta-lactam-related resistance genes was increased at week 2 after treatment, and was restored to pretreatment level at week 8-10 for the LVA group but not the HVA group.

INTERPRETATION: LVA dual therapy was effective and non-inferior to HVA dual therapy as first-line treatment of H pylori infection and showed a non-lasting effect on the abundance of beta-lactam-related resistance genes. High amoxicillin dosage (eg, 3 g per day) is not required to achieve high cure rates with vonoprazan dual therapy.

FUNDING: National Natural Science Foundation of China, Project for Academic and Technical Leaders of Major Disciplines in Jiangxi Province, and Key Research and Development Program of Jiangxi Province.}, } @article {pmid39708657, year = {2025}, author = {Ren, Y and Sun, J and Mao, X}, title = {Protein degradation mechanisms during refrigerated storage of gazami crab (Portunus trituberculatus) at endogenous and microbial-derived enzyme levels.}, journal = {Food chemistry}, volume = {469}, number = {}, pages = {142449}, doi = {10.1016/j.foodchem.2024.142449}, pmid = {39708657}, issn = {1873-7072}, mesh = {*Brachyura/enzymology/metabolism ; Animals ; *Food Storage ; *Proteolysis ; *Refrigeration ; Bacteria/enzymology/metabolism/classification/genetics/isolation & purification ; Shellfish/analysis ; Peptide Hydrolases/metabolism/chemistry ; Arthropod Proteins/metabolism/chemistry/genetics ; }, abstract = {During storage, the proteins of gazami crab (Portunus trituberculatus) are prone to hydrolysis into amino acids and biogenic amines, in which enzymes play a critical role. However, studies exploring spoilage mechanisms from the perspective of enzymes are limited. This study identified 84 endogenous and 52 microbial-derived proteolytic enzymes and peptidases by proteomics and metagenomics. There are 7 endogenous amino acid deaminases, primarily degrade glutamate and aspartate. Additionally, 25 amino acid deaminases of microbial origin were identified, which mainly degrade serine. The formation of biogenic amines involved 14 enzymes, all of which were microbial in origin, primarily synthesizing putrescine from arginine. The main microbial contributors to these enzymes were Photobacterium, Vibrio, and Aliivibrio, accounting for 63.87 %, 15.51 %, and 8.69 % at the end of refrigeration, respectively. This study provides insights into the mechanisms of quality deterioration in gazami crab during refrigeration, from the perspectives of metabolic enzymes and microbial activity.}, } @article {pmid39708598, year = {2025}, author = {Sun, D and Shi, X and Shen, Y and Liu, Y and Luo, S and Jin, Y and Zhai, W and Liu, L and Deng, Z and Sun, C and Liu, D and Yang, X and Xie, Y and Krüger-Haker, H and Wu, C and Schwarz, S and Shen, J and Chen, Y and Ma, S and Wang, Y}, title = {Comparative efficacy of anaerobic digestion systems in removing antimicrobial resistance genes from swine wastewater.}, journal = {Journal of hazardous materials}, volume = {485}, number = {}, pages = {136868}, doi = {10.1016/j.jhazmat.2024.136868}, pmid = {39708598}, issn = {1873-3336}, mesh = {Animals ; *Wastewater/microbiology ; Swine ; Anaerobiosis ; *Anti-Bacterial Agents/pharmacology ; Bioreactors ; Waste Disposal, Fluid/methods ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; Bacteria/genetics/metabolism ; }, abstract = {Swine farm wastewater is a major reservoir of antimicrobial resistance genes (ARGs). Anaerobic digestion (AD), widely implemented in farms, has been extensively studied for ARG removal. However, a comparative study on ARG removal efficiency across the four principal AD systems - up-flow anaerobic sludge blanket (UASB), continuous stirred tank reactor (CSTR), buried biogas digester (BBD), and septic tank (SPT) - is lacking. Herein, we employed metagenomic sequencing, ultra-performance liquid chromatography-tandem mass spectrometry, as well as atomic absorption spectrometry/atomic fluorescence spectrophotometry, and revealed that UASB and CSTR achieved higher removal efficiencies for both ARGs (67% and 57%) and antibiotic residues (100% and 90%) compared to BBD and SPT. Acinetobacter, Escherichia, Pseudomonas and Streptococcus were the primary ARG hosts, comprising over 65% of the total abundance in influent samples. UASB and CSTR systems demonstrated superior removal efficiencies for both mobile genetic elements (MGEs) and antibiotic residues, both of which had essential impacts on ARG profiles. In addition, heavy metals might contribute to variation in ARGs through horizontal gene transfer. Collectively, the variation in microbial communities and better removal of both MGEs and antibiotic residues contribute to the remarkable ARG removal efficiency of UASB and CSTR, therefore, advocating for the widespread adoption of these two AD systems in swine farms.}, } @article {pmid39708450, year = {2024}, author = {Gao, B and Chen, L and Wu, L and Zhang, S and Zhao, S and Mo, Z and Chen, Z and Tu, P}, title = {Association between microplastics and the functionalities of human gut microbiome.}, journal = {Ecotoxicology and environmental safety}, volume = {290}, number = {}, pages = {117497}, doi = {10.1016/j.ecoenv.2024.117497}, pmid = {39708450}, issn = {1090-2414}, abstract = {As an integral part of humans, the gut microbiome plays a significant role in the physiological and pathological processes of the host, and dysbiosis of the gut microbiome is linked to various diseases. The impact of microplastics on the diversity and composition of human gut microbiome has been reported previously. However, effects of microplastics on the functionality of the gut microbiome in humans have not been well studied. In the present study, concentrations of microplastics in human blood were detected through pyrolysis-gas chromatography/mass spectrometry in 39 adults. Five types of microplastics were found in human blood, including polyvinyl chloride, polyethylene, polypropylene, polystyrene, and polyamide 66. Shotgun metagenomic sequencing was further employed to analyze the metagenomes of the human stool samples and fecal samples from mice exposed to microplastics. Associations were found between microplastics and microbial species, as well as microbial genes encoding invasion-related virulence factors, quorum sensing, autoinducer and transporter system, and microplastic biodegradation enzymes. The findings are of significance to improve the understanding of functional changes in the gut microbiome associated with microplastic exposure, as well as raising awareness regarding the health risks of microplastics in the human population.}, } @article {pmid39708135, year = {2024}, author = {Martiniuc, C and Taveira, I and Abreu, F and Cabral, AS and Paranhos, R and Seldin, L and Jurelevicius, D}, title = {Insights into the dynamics and evolution of Rummeliibacillus stabekisii prophages in extreme environments: from Antarctic soil to spacecraft floors.}, journal = {Extremophiles : life under extreme conditions}, volume = {29}, number = {1}, pages = {10}, pmid = {39708135}, issn = {1433-4909}, mesh = {Antarctic Regions ; *Extreme Environments ; *Prophages/genetics ; *Soil Microbiology ; Spacecraft ; Evolution, Molecular ; Lysogeny ; Bacillaceae/genetics/virology/isolation & purification ; }, abstract = {Since prophages can play a multifaceted role in bacterial evolution, this study aims to characterize the virome of Rummeliibacillus stabekisii, a bacterium isolated from different environments, including Antarctic soil and NASA spacecraft floors. From the analyses, it was found that the Antarctic strain, PP9, had the largest number of prophages, including intact ones, indicating potential benefits for survival in adverse conditions. In contrast, other strains harbored predominantly degenerate prophages, suggesting a dynamic process of gene gain and loss during evolution. Furthermore, strain PP9 exhibited polylysogeny, a strategy capable of increasing its competitive advantage by providing a broader spectrum of defensive mechanisms. In addition, evidence demonstrates that prophage regions in PP9 act as hotspots for recombination events, favoring the insertion of different phages and possible antimicrobial resistance genes. Finally, lytic cycle induction experiments revealed at least two intact prophages active in PP9. In this way, understanding the interaction between viruses and bacteria can provide valuable information about microbial evolution and adaptation in extreme environments, such as Antarctica.}, } @article {pmid39707929, year = {2024}, author = {Shahzaib, M and Muaz, M and Zubair, MH and Kayani, MUR}, title = {MiCK: a database of gut microbial genes linked with chemoresistance in cancer patients.}, journal = {Database : the journal of biological databases and curation}, volume = {2024}, number = {}, pages = {}, pmid = {39707929}, issn = {1758-0463}, mesh = {Humans ; *Neoplasms/genetics/drug therapy ; *Gastrointestinal Microbiome/genetics ; *Drug Resistance, Neoplasm/genetics ; *Databases, Genetic ; }, abstract = {Cancer remains a global health challenge, with significant morbidity and mortality rates. In 2020, cancer caused nearly 10 million deaths, making it the second leading cause of death worldwide. The emergence of chemoresistance has become a major hurdle in successfully treating cancer patients. Recently, human gut microbes have been recognized for their role in modulating drug efficacy through their metabolites, ultimately leading to chemoresistance. The currently available databases are limited to knowledge regarding the interactions between gut microbiome and drugs. However, a database containing the human gut microbial gene sequences, and their effect on the efficacy of chemotherapy for cancer patients has not yet been developed. To address this challenge, we present the Microbial Chemoresistance Knowledgebase (MiCK), a comprehensive database that catalogs microbial gene sequences associated with chemoresistance. MiCK contains 1.6 million sequences of 29 gene types linked to chemoresistance and drug metabolism, curated manually from recent literature and sequence databases. The database can support downstream analysis as it provides a user-friendly web interface for sequence search and download functionalities. MiCK aims to facilitate the understanding and mitigation of chemoresistance in cancers by serving as a valuable resource for researchers. Database URL: https://microbialchemreskb.com/.}, } @article {pmid39707568, year = {2024}, author = {Yang, X and Yuan, R and Yang, S and Dai, Z and Di, N and Yang, H and He, Z and Wei, M}, title = {A salt-tolerant growth-promoting phyllosphere microbial combination from mangrove plants and its mechanism for promoting salt tolerance in rice.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {270}, pmid = {39707568}, issn = {2049-2618}, mesh = {*Oryza/microbiology/growth & development ; *Salt Tolerance ; *Plant Leaves/microbiology ; Microbiota ; Rhizosphere ; Pantoea/genetics ; Soil Microbiology ; Bacillus/genetics/isolation & purification/physiology ; Bacteria/genetics/classification/isolation & purification ; Wetlands ; Rhizophoraceae/microbiology ; Quorum Sensing ; }, abstract = {BACKGROUND: Mangrove plants growing in the high salt environment of coastal intertidal zones colonize a variety of microorganisms in the phyllosphere, which have potential salt-tolerant and growth-promoting effects. However, the characteristics of microbial communities in the phyllosphere of mangrove species with and without salt glands and the differences between them remain unknown, and the exploration and the agricultural utilization of functional microbial resources from the leaves of mangrove plants are insufficient.

RESULTS: In this study, we examined six typical mangrove species to unravel the differences in the diversity and structure of phyllosphere microbial communities between mangrove species with or without salt glands. Our results showed that a combination of salt-tolerant growth-promoting strains of Pantoea stewartii A and Bacillus marisflavi Y25 (A + Y25) was constructed from the phyllosphere of mangrove plants, which demonstrated an ability to modulate osmotic substances in rice and regulate the expression of salt-resistance-associated genes. Further metagenomic analysis revealed that exogenous inoculation with A + Y25 increased the rice rhizosphere's specific microbial taxon Chloroflexi, thereby elevating microbial community quorum sensing and ultimately enhancing ionic balance and overall microbial community function to aid salt resistance in rice.

CONCLUSIONS: This study advances our understanding of the mutualistic and symbiotic relationships between mangrove species and their phyllosphere microbial communities. It offers a paradigm for exploring agricultural beneficial microbial resources from mangrove leaves and providing the potential for applying the salt-tolerant bacterial consortium to enhance crop adaptability in saline-alkaline land. Video Abstract.}, } @article {pmid39707567, year = {2024}, author = {Feng, X and Xing, P and Tao, Y and Wang, X and Wu, QL and Liu, Y and Luo, H}, title = {Functional traits and adaptation of lake microbiomes on the Tibetan Plateau.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {264}, pmid = {39707567}, issn = {2049-2618}, support = {2023A1515012162//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2022M712195//the China Postdoctoral Science Foundation/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; U2102216//the National Natural Science Foundation of China/ ; 92251304//the National Natural Science Foundation of China/ ; 92251304//the National Natural Science Foundation of China/ ; AoE/M-403/16//the Hong Kong Research Grants Council Area of Excellence Scheme/ ; }, mesh = {*Lakes/microbiology ; Tibet ; *Microbiota/genetics ; *Phylogeny ; *Bacteria/classification/genetics ; Metagenome ; Salinity ; Climate Change ; Ecosystem ; Adaptation, Physiological ; }, abstract = {BACKGROUND: Tibetan Plateau is credited as the "Third Pole" after the Arctic and the Antarctic, and lakes there represent a pristine habitat ideal for studying microbial processes under climate change.

RESULTS: Here, we collected 169 samples from 54 lakes including those from the central Tibetan region that was underrepresented previously, grouped them to freshwater, brackish, and saline lakes, and generated a genome atlas of the Tibetan Plateau Lake Microbiome. This genomic atlas comprises 8271 metagenome-assembled genomes featured by having significant phylogenetic and functional novelty. The microbiomes of freshwater lakes are enriched with genes involved in recalcitrant carbon degradation, carbon fixation, and energy transformation, whereas those of saline lakes possess more genes that encode osmolyte transport and synthesis and enable anaerobic metabolism. These distinct metabolic features match well with the geochemical properties including dissolved organic carbon, dissolved oxygen, and salinity that distinguish between these lakes. Population genomic analysis suggests that microbial populations in saline lakes are under stronger functional constraints than those in freshwater lakes. Although microbiomes in the Tibet lakes, particularly the saline lakes, may be subject to changing selective regimes due to ongoing warming, they may also benefit from the drainage reorganization and metapopulation reconnection.

CONCLUSIONS: Altogether, the Tibetan Plateau Lake Microbiome atlas serves as a valuable microbial genetic resource for biodiversity conservation and climate research. Video Abstract.}, } @article {pmid39707560, year = {2024}, author = {Wang, H and Sun, C and Li, Y and Chen, J and Zhao, XM and Chen, WH}, title = {Complementary insights into gut viral genomes: a comparative benchmark of short- and long-read metagenomes using diverse assemblers and binners.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {260}, pmid = {39707560}, issn = {2049-2618}, support = {T2225015//National Natural Science Foundation of China/ ; 32070660//National Natural Science Foundation of China/ ; 2020YFA0712403//National Key Research and Development Program of China/ ; 2019YFA0905600//National Key Research and Development Program of China/ ; 82161138017//NNSF-VR Sino-Swedish Joint Research Programme/ ; }, mesh = {*Genome, Viral/genetics ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Gastrointestinal Microbiome/genetics ; *Metagenome/genetics ; *Feces/virology ; Metagenomics/methods ; Virome/genetics ; Viruses/genetics/classification ; Benchmarking ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: Metagenome-assembled viral genomes have significantly advanced the discovery and characterization of the human gut virome. However, we lack a comparative assessment of assembly tools on the efficacy of viral genome identification, particularly across next-generation sequencing (NGS) and third-generation sequencing (TGS) data.

RESULTS: We evaluated the efficiency of NGS, TGS, and hybrid assemblers for viral genome discovery using 95 viral-like particle (VLP)-enriched fecal samples sequenced on both Illumina and PacBio platforms. MEGAHIT, metaFlye, and hybridSPAdes emerged as the optimal choices for NGS, TGS, and hybrid datasets, respectively. Notably, these assemblers recovered distinct viral genomes, demonstrating a remarkable degree of complementarity. By combining individual assembler results, we expanded the total number of nonredundant high-quality viral genomes by 4.83 ~ 21.7-fold compared to individual assemblers. Among them, viral genomes from NGS and TGS data have the least overlap, indicating the impact of data type on viral genome recovery. We also evaluated four binning methods, finding that CONCOCT incorporated more unrelated contigs into the same bins, while MetaBAT2, AVAMB, and vRhyme balanced inclusiveness and taxonomic consistency within bins.

CONCLUSIONS: Our findings highlight the challenges in metagenome-driven viral discovery, underscoring tool limitations. We advocate for combined use of multiple assemblers and sequencing technologies when feasible and highlight the urgent need for specialized tools tailored to gut virome assembly. This study contributes essential insights for advancing viral genome research in the context of gut metagenomics. Video Abstract.}, } @article {pmid39707557, year = {2024}, author = {Santamarina-García, G and Yap, M and Crispie, F and Amores, G and Lordan, C and Virto, M and Cotter, PD}, title = {Shotgun metagenomic sequencing reveals the influence of artisanal dairy environments on the microbiomes, quality, and safety of Idiazabal, a raw ewe milk PDO cheese.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {262}, pmid = {39707557}, issn = {2049-2618}, support = {IT1568-22//Eusko Jaurlaritza/ ; IT1568-22//Eusko Jaurlaritza/ ; IT1568-22//Eusko Jaurlaritza/ ; PIF19/31//Euskal Herriko Unibertsitatea/ ; }, mesh = {*Cheese/microbiology ; Animals ; *Milk/microbiology ; *Microbiota ; *Metagenomics ; Sheep/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Female ; Dairying ; Food Microbiology ; Metagenome ; }, abstract = {BACKGROUND: Numerous studies have highlighted the impact of bacterial communities on the quality and safety of raw ewe milk-derived cheeses. Despite reported differences in the microbiota among cheese types and even producers, to the best of our knowledge, no study has comprehensively assessed all potential microbial sources and their contributions to any raw ewe milk-derived cheese, which could suppose great potential for benefits from research in this area. Here, using the Protected Designation of Origin Idiazabal cheese as an example, the impact of the environment and practices of artisanal dairies (including herd feed, teat skin, dairy surfaces, and ingredients) on the microbiomes of the associated raw milk, whey, and derived cheeses was examined through shotgun metagenomic sequencing.

RESULTS: The results revealed diverse microbial ecosystems across sample types, comprising more than 1300 bacterial genera and 3400 species. SourceTracker analysis revealed commercial feed and teat skin as major contributors to the raw milk microbiota (45.6% and 33.5%, respectively), being a source of, for example, Lactococcus and Pantoea, along with rennet contributing to the composition of whey and cheese (17.4% and 41.0%, respectively), including taxa such as Streptococcus, Pseudomonas_E or Lactobacillus_H. Functional analysis linked microbial niches to cheese quality- and safety-related metabolic pathways, with brine and food contact surfaces being most relevant, related to genera like Brevibacterium, Methylobacterium, or Halomonas. With respect to the virulome (virulence-associated gene profile), in addition to whey and cheese, commercial feed and grass were the main reservoirs (related to, e.g., Brevibacillus_B or CAG-196). Similarly, grass, teat skin, or rennet were the main contributors of antimicrobial resistance genes (e.g., Bact-11 or Bacteriodes_B). In terms of cheese aroma and texture, apart from the microbiome of the cheese itself, brine, grass, and food contact surfaces were key reservoirs for hydrolase-encoding genes, originating from, for example, Lactococcus, Lactobacillus, Listeria or Chromohalobacter. Furthermore, over 300 metagenomic assembled genomes (MAGs) were generated, including 60 high-quality MAGs, yielding 28 novel putative species from several genera, e.g., Citricoccus, Corynebacterium, or Dietzia.

CONCLUSION: This study emphasizes the role of the artisanal dairy environments in determining cheese microbiota and, consequently, quality and safety. Video Abstract.}, } @article {pmid39707511, year = {2024}, author = {Ma, X and Hu, X and Liu, K and Wang, W and Jia, W and Gao, H and Lu, M and Liu, J and Chen, Y and Ma, Y and Li, Y and Nie, Y}, title = {Spatiotemporal differences induced changes in the structure and function of the gut microbiota in an endangered ungulate.}, journal = {Animal microbiome}, volume = {6}, number = {1}, pages = {74}, pmid = {39707511}, issn = {2524-4671}, support = {32225033, 32071496, 32100399//National Natural Science Foundation of China/ ; 32225033, 32071496, 32100399//National Natural Science Foundation of China/ ; 32225033, 32071496, 32100399//National Natural Science Foundation of China/ ; 32225033, 32071496, 32100399//National Natural Science Foundation of China/ ; 32225033, 32071496, 32100399//National Natural Science Foundation of China/ ; 32225033, 32071496, 32100399//National Natural Science Foundation of China/ ; 32225033, 32071496, 32100399//National Natural Science Foundation of China/ ; 32225033, 32071496, 32100399//National Natural Science Foundation of China/ ; 32225033, 32071496, 32100399//National Natural Science Foundation of China/ ; 32225033, 32071496, 32100399//National Natural Science Foundation of China/ ; 32225033, 32071496, 32100399//National Natural Science Foundation of China/ ; 32225033, 32071496, 32100399//National Natural Science Foundation of China/ ; No. 2022YFF1301500//Ministry of Science and Technology of China/ ; No. 2022YFF1301500//Ministry of Science and Technology of China/ ; No. 2022YFF1301500//Ministry of Science and Technology of China/ ; No. 2022YFF1301500//Ministry of Science and Technology of China/ ; No. 2022YFF1301500//Ministry of Science and Technology of China/ ; No. 2022YFF1301500//Ministry of Science and Technology of China/ ; No. 2022YFF1301500//Ministry of Science and Technology of China/ ; No. 2022YFF1301500//Ministry of Science and Technology of China/ ; No. 2022YFF1301500//Ministry of Science and Technology of China/ ; No. 2022YFF1301500//Ministry of Science and Technology of China/ ; No. 2022YFF1301500//Ministry of Science and Technology of China/ ; No. 2022YFF1301500//Ministry of Science and Technology of China/ ; }, abstract = {The composition and function of animal gut microbiota are shaped by various factors, among which diet is one of the major factors. Diet is affected by seasonal shifts and geographical differences, which in turn impact the host's nutritional levels. To adapt to these environmental changes, the gut microbiome often produces matching responses. Understanding the relationships among the environment, diet, host and the gut microbiome is helpful for exploring the environmental adaptation of wildlife. Here, we chose wild sika deer (Cervus nippon), which is composed natural allopatric populations, to explore how the environment shapes the gut microbiome and affects the relationship between microbiota composition and function and the mutual adaptation of the seasonal living environment to seasonal dietary changes. To this purpose we used DNA metabarcoding, 16S RNA gene amplification sequencing, metagenomic shotgun sequencing and nutritional analyses to comprehensively examine the relationships among the forage plant, nutrient status and host gut microbiome. Our analyses showed spatiotemporal differences in diet between the Tiebu and Hunchun regions, which ultimately led to varying intakes of protein, cellulose, and soluble sugar. The microbiome composition and function showed unique characteristics in each group, and significant differences were detected at the gene level for the protein absorption and metabolism pathway, the carbohydrate metabolic absorption pathway, and cellulase enzyme function, which are related to nutrition. We also found differences in the pathogenic bacteria and resistance mechanisms genes of the gut microbiota in different groups. Our results showed that the gut microbiome of allopatric populations adapts to changes in food composition and nutrition in different seasons and areas to help the host cope with spatiotemporal changes in the living environment. At the same time, varying levels of human activity can have potential health impacts on wild animals.}, } @article {pmid39707494, year = {2024}, author = {Li, C and Liu, K and Gu, C and Li, M and Zhou, P and Chen, L and Sun, S and Li, X and Wang, L and Ni, W and Li, M and Hu, S}, title = {Gastrointestinal jumbo phages possess independent synthesis and utilization systems of NAD.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {268}, pmid = {39707494}, issn = {2049-2618}, mesh = {*Bacteriophages/genetics/classification/isolation & purification ; Animals ; *Genome, Viral/genetics ; *NAD/metabolism ; *Phylogeny ; Humans ; Gastrointestinal Microbiome ; Swine ; Sheep ; Metagenomics ; Horses ; Cattle ; Bacteria/virology/genetics ; Deer/virology ; DNA Replication ; }, abstract = {BACKGROUND: Jumbo phages, phages with genomes > 200 kbp, contain some unique genes for successful reproduction in their bacterial hosts. Due to complex and massive genomes analogous to those of small-celled bacteria, how jumbo phages complete their life cycle remains largely undefined.

RESULTS: In this study, we assembled 668 high-quality jumbo phage genomes from over 15 terabytes (TB) of intestinal metagenomic data from 955 samples of 5 animal species (cow, sheep, pig, horse, and deer). Within them, we obtained a complete genome of 716 kbp in length, which is the largest phage genome so far reported in the gut environments. Interestingly, 174 out of the 668 jumbo phages were found to encode all genes required for the synthesis of NAD[+] by the salvage pathway or Preiss-Handler pathway, referred to as NAD-jumbo phage. Besides synthesis genes of NAD[+], these NAD-jumbo phages also encode at least 15 types of NAD[+]-consuming enzyme genes involved in DNA replication, DNA repair, and counterdefense, suggesting that these phages not only have the capacity to synthesize NAD[+] but also redirect NAD[+] metabolism towards phage propagation need in hosts. Phylogenetic analysis and environmental survey indicated NAD-jumbo phages are widely present in the Earth's ecosystems, including the human gut, lakes, salt ponds, mine tailings, and seawater.

CONCLUSION: In summary, this study expands our understanding of the diversity and survival strategies of phages, and an in-depth study of the NAD-jumbo phages is crucial for understanding their role in ecological regulation. Video Abstract.}, } @article {pmid39707478, year = {2024}, author = {He, Z and Hou, Y and Li, Y and Bei, Q and Li, X and Zhu, YG and Liesack, W and Rillig, MC and Peng, J}, title = {Increased methane production associated with community shifts towards Methanocella in paddy soils with the presence of nanoplastics.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {259}, pmid = {39707478}, issn = {2049-2618}, mesh = {*Methane/metabolism ; *Soil Microbiology ; *Soil/chemistry ; *Oryza/microbiology ; Microbiota ; Polyethylene ; Soil Pollutants ; Metagenomics ; Archaea/metabolism/genetics/classification ; Carbon/metabolism ; Plastics ; }, abstract = {BACKGROUND: Planetary plastic pollution poses a major threat to ecosystems and human health in the Anthropocene, yet its impact on biogeochemical cycling remains poorly understood. Waterlogged rice paddies are globally important sources of CH4. Given the widespread use of plastic mulching in soils, it is urgent to unravel whether low-density polyethylene (LDPE) will affect the methanogenic community in flooded paddy soils. Here, we employed a combination of process measurements, short-chain and long-chain fatty acid (SCFAs and LCFAs) profiling, Fourier-transform ion cyclotron resonance mass spectrometry, quantitative PCR, metagenomics, and mRNA profiling to investigate the impact of LDPE nanoplastics (NPs) on dissolved organic carbon (DOC) and CH4 production in both black and red paddy soils under anoxic incubation over a 160-day period.

RESULTS: Despite significant differences in microbiome composition between the two soil types, both exhibited similar results to NPs exposure. NPs induced a change in DOC content and CH4 production up to 1.8-fold and 10.1-fold, respectively. The proportion of labile dissolved organic matter decreased, while its recalcitrance increased. Genes associated with the degradation of complex carbohydrates and aromatic carbon were significantly enriched. The elevated CH4 production was significantly correlated to increases in both the PCR-quantified mcrA gene copy numbers and the metagenomic methanogen-to-bacteria abundance ratio. Notably, the latter was linked to an enrichment of the hydrogenotrophic methanogenesis pathway. Among 391 metagenome-assembled genomes (MAGs), the abundance of several Syntrophomonas and Methanocella MAGs increased concomitantly, suggesting that the NPs treatments stimulated the syntrophic oxidation of fatty acids. mRNA profiling further identified Methanosarcinaceae and Methanocellaceae to be the key players in the NPs-induced CH4 production.

CONCLUSIONS: The specific enrichment of Syntrophomonas and Methanocella indicates that LDPE NPs stimulate the syntrophic oxidation of LCFAs and SCFAs, with Methanocella acting as the hydrogenotrophic methanogen partner. Our findings enhance the understanding of how LDPE NPs affect the methanogenic community in waterlogged paddy soils. Given the importance of this ecosystem, our results are crucial for elucidating the mechanisms that govern carbon fluxes, which are highly relevant to global climate change.}, } @article {pmid39707381, year = {2024}, author = {Elton, L and Williams, A and Ali, S and Heaphy, J and Pang, V and Commins, L and O'Brien, C and Yetiş, Ö and Caine, E and Ward, I and Muzslay, M and Yui, S and Karia, K and Shore, E and Rofael, S and Mack, DJF and McHugh, TD and Wey, EQ}, title = {Tracing the transmission of carbapenem-resistant Enterobacterales at the patient: ward environmental nexus.}, journal = {Annals of clinical microbiology and antimicrobials}, volume = {23}, number = {1}, pages = {108}, pmid = {39707381}, issn = {1476-0711}, mesh = {Humans ; *Enterobacteriaceae Infections/microbiology/transmission ; *Carbapenem-Resistant Enterobacteriaceae/genetics/isolation & purification/drug effects ; *Wastewater/microbiology ; *beta-Lactamases/genetics ; *Whole Genome Sequencing ; Anti-Bacterial Agents/pharmacology ; Carbapenems/pharmacology ; Microbial Sensitivity Tests ; Cross Infection/microbiology/transmission ; Bacterial Proteins/genetics ; Enterobacter/genetics/drug effects/isolation & purification ; }, abstract = {INTRODUCTION: Colonisation and infection with Carbapenem-resistant Enterobacterales (CRE) in healthcare settings poses significant risks, especially for vulnerable patients. Genomic analysis can be used to trace transmission routes, supporting antimicrobial stewardship and informing infection control strategies. Here we used genomic analysis to track the movement and transmission of CREs within clinical and environmental samples.

METHODS: 25 isolates were cultured from clinical patient samples or swabs, that tested positive for OXA-48-like variants using the NG-Test® CARBA-5 test and whole genome sequenced (WGS) using Oxford Nanopore Technologies (ONT). 158 swabs and 52 wastewater samples were collected from the ward environment. 60 isolates (matching clinical isolate genera; Klebsiella, Enterobacter, Citrobacter and Escherichia) were isolated from the environmental samples using selective agar. Metagenomic sequencing was undertaken on 36 environmental wastewater and swab samples.

RESULTS: 21/25 (84%) clinical isolates had > 1 blaOXA gene and 19/25 (76%) harboured > 1 blaNDM gene. Enterobacterales were most commonly isolated from environmental wastewater samples 27/52 (51.9%), then stick swabs 5/43 (11.6%) and sponge swabs 5/115 (4.3%). 11/60 (18%) environmental isolates harboured > 1 blaOXA gene and 1.9% (1/60) harboured blaNDM-1. blaOXA genes were found in 2/36 (5.5%) metagenomic environmental samples.

CONCLUSIONS: Potential for putative patient-patient and patient-ward transmission was shown. Metagenomic sampling needs optimization to improve sensitivity.}, } @article {pmid39707302, year = {2024}, author = {Zhang, N and Zhang, X and Guo, Y and Zheng, Y and Gai, W and Yang, Z}, title = {Clinical and metagenomic predicted antimicrobial resistance in pediatric critically ill patients with infectious diseases in a single center of Zhejiang.}, journal = {Annals of clinical microbiology and antimicrobials}, volume = {23}, number = {1}, pages = {107}, pmid = {39707302}, issn = {1476-0711}, support = {2021YFC2701800, 2021YFC2701801//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Critical Illness ; Female ; Male ; Retrospective Studies ; Child, Preschool ; Child ; Infant ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; China ; *Intensive Care Units, Pediatric ; Drug Resistance, Bacterial/genetics ; Metagenomics ; Microbial Sensitivity Tests ; High-Throughput Nucleotide Sequencing ; Communicable Diseases/drug therapy/microbiology ; Adolescent ; Prognosis ; Bacteria/genetics/drug effects/classification/isolation & purification ; }, abstract = {BACKGROUND: Antimicrobial resistance (AMR) poses a significant threat to pediatric health; therefore, precise identification of pathogens as well as AMR is imperative. This study aimed at comprehending antibiotic resistance patterns among critically ill children with infectious diseases admitted to pediatric intensive care unit (PICU) and to clarify the impact of drug-resistant bacteria on the prognosis of children.

METHODS: This study retrospectively collected clinical data, identified pathogens and AMR from 113 children's who performed metagenomic next-generation sequencing for pathogen and antibiotic resistance genes identification, and compared the clinical characteristic difference and prognostic effects between children with and without AMR detected.

RESULTS: Based on the presence or absence of AMR test results, the 113 patients were divided into Antimicrobial resistance test positive group (AMRT+, n = 44) and Antimicrobial resistance test negative group (AMRT-, n = 69). Immunocompromised patients (50% vs. 28.99%, P = 0.0242) and patients with underlying diseases (70.45% vs. 40.58%, P = 0.0019) were more likely to develop resistance to antibiotics. Children in the AMRT + group showed significantly increased C-reaction protein, score of pediatric sequential organ failure assessment and pediatric risk of mortality of children and longer hospital stay and ICU stay in the AMRT + group compared to the AMRT+- group (P < 0.05). Detection rate of Gram-negative bacteria was significantly higher in the AMRT + group rather than Gram-positive bacteria (n = 45 vs. 31), in contrast to the AMRT- group (n = 10 vs. 36). Cephalosporins, β-lactams/β-Lactamase inhibitors, carbapenems and sulfonamides emerged as the most common types of drug resistance in children. Resistance rates to these antibiotics exhibited considerable variation across common pathogens, including Klebsiella pneumoniae, Pseudomonas aeruginosa and Acinetobacter baumannii.

CONCLUSIONS: The development of drug resistance in bacteria will significantly affect the prognosis of patients. The significant differences in drug resistance of common pathogenic bacteria indicate that identification of drug resistance is important for the rational use of antibiotics and patient prognosis.}, } @article {pmid39707301, year = {2024}, author = {Shan, X and Li, Z and Dong, L}, title = {A case of pneumonia caused by infection with Tropheryma whipplei complicated by cryptococcus during treatment with a Janus kinase inhibitor: a case report.}, journal = {BMC pulmonary medicine}, volume = {24}, number = {1}, pages = {625}, pmid = {39707301}, issn = {1471-2466}, mesh = {Humans ; Male ; Adult ; *Cryptococcosis/drug therapy/diagnosis/microbiology ; *Tropheryma/isolation & purification ; *Janus Kinase Inhibitors/therapeutic use/adverse effects ; *Whipple Disease/drug therapy/diagnosis/complications ; Tomography, X-Ray Computed ; Cryptococcus/isolation & purification ; Pyrimidines/therapeutic use ; Opportunistic Infections/microbiology/drug therapy/diagnosis ; Anti-Bacterial Agents/therapeutic use ; Bronchoalveolar Lavage Fluid/microbiology ; }, abstract = {This report describes the case of a 41-year-old male patient complaining of a hacking cough. The patient was treated with a Janus kinase (JAK) inhibitor for psoriasis. Blood tests revealed mild lymphopenia and high levels of serum cryptococcal antigen. Chest computed tomography revealed infection in the lower lobe of the left lung. Metagenomic next-generation sequencing of bronchoalveolar lavage fluid revealed Tropheryma whipplei. Tropheryma whipplei and Cryptococcus antimicrobial therapies were sequentially administered. During follow-up, the patient showed clinical and radiographic improvement. Tropheryma whipplei is an opportunistic Gram-positive rod-shaped bacterium belonging to the family Actinomycetes. Lung involvement is an unusual but classic manifestation of Whipple's disease. This is the first report of pneumonia caused by infection with Tropheryma whipplei complicated by Cryptococcus. To our knowledge, this is the first case report of Tropheryma whipplei infection following the use of JAK inhibitors. Clinicians should be aware of opportunistic infections that can occur during treatment with JAK inhibitors.}, } @article {pmid39707169, year = {2024}, author = {Carrasco-Villanueva, M and Wang, C and Wei, C}, title = {Identification of diversity-generating retroelements in host-associated and environmental genomes: prevalence, diversity, and roles.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1227}, pmid = {39707169}, issn = {1471-2164}, support = {2023YFF1001600//National Key Research and Development Program of China/ ; 32170643//National Natural Science Foundation of China/ ; 20ZR1428200, 22ZR1433600//Natural Science Foundation of Shanghai Municipality/ ; }, mesh = {*Retroelements ; *Phylogeny ; Humans ; *Genetic Variation ; Bacteria/genetics/classification ; Metagenome ; Archaea/genetics ; RNA-Directed DNA Polymerase/genetics ; }, abstract = {BACKGROUND: The diversity-generating retroelements (DGRs) are a family of genetic elements that can produce mutations in target genes often related to ligand-binding functions, which possess a C-type lectin (CLec) domain that tolerates massive variations. They were first identified in viruses, then in bacteria and archaea from human-associated and environmental genomes. This DGR mechanism represents a fast adaptation of organisms to ever- changing environments. However, their existence, phylogenetic and structural diversity, and functions in a wide range of environments are largely unknown.

RESULTS: Here we present a study of DGR systems based on metagenome-assembled genomes (MAGs) from host-associated, aquatic, terrestrial and engineered environments. In total, we identified 861 non-redundant DGR-RTs and ~ 5.7% are new. We found that microbes associated with human hosts harbor the highest number of DGRs and also exhibit a higher prevalence of DGRs. After normalizing with genome size and including more genome data, we found that DGRs occur more frequently in organisms with smaller genomes. Overall, we identified nine main clades in the phylogenetic tree of reverse transcriptases (RTs), some comprising specific phyla and cassette architectures. We identified 38 different cassette patterns and 6 of them were shown in at least 10 DGRs, showing differences in terms of the numbers, arrangements, and orientations of their components. Finally, most of the target genes were related to ligand-binding and signaling functions, but we discovered a few cases in which the VRs were situated in domains different from the CLec.

CONCLUSIONS: Our research sheds light on the widespread prevalence of DGRs within environments and taxa, and supports the DGR phylogenetic divergence in different organisms. These variations might also occur in their structures since some cassette architectures were common in specific underrepresented phyla. In addition, we suggest that VRs could be found in domains different to the CLec, which should be further explored for organisms in scarcely studied environments.}, } @article {pmid39706917, year = {2024}, author = {Chang, WS and Harvey, E and Mahar, JE and Firth, C and Shi, M and Simon-Loriere, E and Geoghegan, JL and Wille, M}, title = {Improving the reporting of metagenomic virome-scale data.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1687}, pmid = {39706917}, issn = {2399-3642}, mesh = {Animals ; Humans ; Genome, Viral ; Metagenome ; *Metagenomics/methods ; *Virome/genetics ; *Viruses/genetics/classification ; }, abstract = {Over the last decade metagenomic sequencing has facilitated an increasing number of virome-scale studies, leading to an exponential expansion in understanding of virus diversity. This is partially driven by the decreasing costs of metagenomic sequencing, improvements in computational tools for revealing novel viruses, and an increased understanding of the key role that viruses play in human and animal health. A central concern associated with this remarkable increase in the number of virome-scale studies is the lack of broadly accepted "gold standards" for reporting the data and results generated. This is of particular importance for animal virome studies as there are a multitude of nuanced approaches for both data presentation and analysis, all of which impact the resulting outcomes. As such, the results of published studies can be difficult to contextualise and may be of reduced utility due to reporting deficiencies. Herein, we aim to address these reporting issues by outlining recommendations for the presentation of virome data, encouraging a transparent communication of findings that can be interpreted in evolutionary and ecological contexts.}, } @article {pmid39706308, year = {2025}, author = {Wang, Z and Jiang, C and Nnorom, MA and Avignone-Rossa, C and Yang, K and Guo, B}, title = {Multi-faceted effects and mechanisms of granular activated carbon to enhance anaerobic ammonium oxidation (anammox) for nitrogen removal from wastewater.}, journal = {Bioresource technology}, volume = {418}, number = {}, pages = {132001}, doi = {10.1016/j.biortech.2024.132001}, pmid = {39706308}, issn = {1873-2976}, mesh = {*Nitrogen/metabolism ; *Oxidation-Reduction ; *Wastewater/chemistry ; Anaerobiosis ; *Bioreactors ; *Ammonium Compounds/metabolism ; Charcoal/chemistry ; Denitrification ; Sewage/microbiology ; Water Purification/methods ; Bacteria/metabolism ; }, abstract = {Nitrogen removal via anammox is efficient but challenged by their slow growth. Adding granular activated carbon (GAC) increased the total nitrogen removal rate to 66.99 g-N/m[3]/day, compared to 50.00 g-N/m[3]/day in non-GAC reactor. Both reactors dominated by Candidatus Brocadia (non-GAC: 36.25 %, GAC: 35.5 %) but GAC improved specific anammox activity. Functional metabolic profiling from metagenomic analysis unveiled that GAC enhanced pathways associated with electron shuttle production, potentially promoting intra/extracellular electron transfer. In nitrogen metabolism, GAC is indicated to facilitate anammox N2H4 synthesis process, and inhibit nitrification and full denitrification processes, functioned by Nitrosomonas and Castellaniella which are more abundant in the non-GAC reactor. GAC also enhanced dissimilatory nitrate reduction to ammonium and partial denitrification processes, providing anammox with NH4[+]/NO, which was conducted by Anaerolineae members (29.7 % in GAC-reactor and 7.8 % in non-GAC reactor sludge). This research illuminated the intricate microbial nitrogen cycling networks affected by GAC in anammox systems.}, } @article {pmid39706307, year = {2025}, author = {Zhang, B and Liu, J and Cai, C and Zhou, Y}, title = {Membrane photobioreactor for biogas capture and conversion - Enhanced microbial interaction in biofilm.}, journal = {Bioresource technology}, volume = {418}, number = {}, pages = {131999}, doi = {10.1016/j.biortech.2024.131999}, pmid = {39706307}, issn = {1873-2976}, mesh = {*Biofilms ; *Biofuels/microbiology ; *Photobioreactors/microbiology ; *Microalgae/metabolism ; *Membranes, Artificial ; *Methane/metabolism ; Microbial Interactions/physiology ; Carbon Dioxide/metabolism ; }, abstract = {The urgency to mitigate greenhouse gas emissions has driven interest in sustainable biogas utilization. This study investigates a 1 L enclosed membrane photobioreactor (MPBR) using a microalgae-methanotroph coculture for biogas capture. Operating with a hydraulic and solid retention time of 7 days and a biogas loading rate of 2.7 L /day, the introduction of gas membrane module increased CO2-C and CH4-C uptake rates by 12 % and 50 %, respectively. Biofilm formation on the membrane surface enhanced system performance, with imaging analyses revealing methanotroph predominantly located near the membrane surface and photosynthetic microorganisms distributed throughout. Metagenomic analysis showed shifts in key metabolic pathways, including increased abundance of soluble methane monooxygenase genes and enhanced vitamin B synthesis in the biofilm. These findings highlight the spatial organization and metabolic interactions in methanotroph-microalgae coculture system, providing insights into the role of membrane-induced biofilms in improving MPBR performance for sustainable biogas utilization.}, } @article {pmid39706000, year = {2025}, author = {Zhang, X and Huang, Z and Zhong, Z and Li, Q and Bian, F}, title = {Forest management impacts on soil phosphorus cycling: Insights from metagenomics in Moso bamboo plantations.}, journal = {Journal of environmental management}, volume = {373}, number = {}, pages = {123735}, doi = {10.1016/j.jenvman.2024.123735}, pmid = {39706000}, issn = {1095-8630}, mesh = {*Phosphorus/metabolism ; *Soil/chemistry ; *Forests ; *Metagenomics ; *Soil Microbiology ; Ecosystem ; }, abstract = {Bamboo forests are crucial ecosystems and provide essential ecological and economic services in both tropical and subtropical regions. Soil phosphorus (P), a vital nutrient for plant growth, is fundamental to the productivity and health of bamboo forests. However, the microbial mechanisms through which management practices affect soil P processes in bamboo forests remain poorly understood. This study employed metagenomics to examine alterations in microbial P cycling in Moso bamboo plantations under three distinct management conditions. The results revealed that intensive management (M2, annual fertilization, selective harvesting, and understory vegetation removal) significantly increased soil inorganic P (Pi) by 61.76% and 87.39% compared to extensive management (M1, selective bamboo trunk and shoot harvesting every two years) and non-management (M0), respectively, while decreasing soil organic P (Po) by 50.41% and 41.05%. Forest management significantly altered the bacterial communities: Firmicutes, WPS-2, and Acidobacteriales were represented in M2, Xanthobacteraceae in M1, and Chloroflexi AD3, Acidothermus, and Subgroup_2 in M0. M2 significantly increased the community-level habitat niche breadth and weakened the deterministic process of bacterial community assembly relative to M1 and M0 (p ≤ 0.05). Furthermore, functional metagenomics showed that the total abundance of genes related to Po mineralization, P transportation, and P regulation was significantly lower (p ≤ 0.05) in M2 than in M0 and M1. pstA, pstB, and pstC were more abundant in M2 (p ≤ 0.05), whereas phnN, phnI, phnG, phoA, phoD, phnC, phnD, and phnE were more abundant in M1 (p ≤ 0.05), and phnF was significantly abundant in M0 (p ≤ 0.05). A partial least squares path model indicated that soil bacterial community and P cycling genes had direct effects on Pi and Po, respectively. These findings enhance our understanding of the links between forest management practices and P cycling, providing insights for improving soil functionality and nutrient balance.}, } @article {pmid39705954, year = {2025}, author = {Basile, A and Riggio, FP and Tescari, M and Chebbi, A and Sodo, A and Bartoli, F and Imperi, F and Caneva, G and Visca, P}, title = {Metagenome-resolved functional traits of Rubrobacter species implicated in rosy discoloration of ancient frescoes in two Georgian Cathedrals.}, journal = {The Science of the total environment}, volume = {958}, number = {}, pages = {178135}, doi = {10.1016/j.scitotenv.2024.178135}, pmid = {39705954}, issn = {1879-1026}, mesh = {*Metagenome ; RNA, Ribosomal, 16S ; Biofilms ; Phylogeny ; Actinobacteria/genetics ; }, abstract = {Pink biofilm formation on stone monuments and mural paintings poses serious harm to cultural heritage preservation. Pink biofilms are globally widespread and recalcitrant to eradication, often causing recurrences after restoration. Yet, the ecological drivers of pink biofilm formation and the metabolic functions sustaining the growth of pigment-producing biodeteriogens remain unclear. In this study, a combined approach integrating physicochemical investigations, scanning electron microscopy, 16S rRNA sequence-based analysis of the prokaryotic community, metagenomic deep sequencing, and metabolic profiling, was applied to determine the etiology of rosy discoloration of ancient frescoes in the Gelati and the Martvili Cathedrals (Georgia). Martvili samples showed greater diversity than Gelati samples, though Actinomycetota predominated in both samples. Rubrobacter-related sequences were detected in all sampling sites, showing an overwhelming abundance in Gelati samples. Reconstruction of metagenome-assembled genomes (MAGs) and phylogenetic analyses highlighted significant intra-genus diversity for Rubrobacter-related sequences, most of which could not be assigned to any formally described Rubrobacter species. Metabolic profiling of the Gelati metagenomes suggests that carbon-fixing autotrophic bacteria and proteinaceous substances in the plaster could contribute to sustaining the chemoorganotrophic members of the community. Complete pathways for β-carotene and bacterioruberin synthesis were identified in Rubrobacter MAGs, consistent with the Raman spectroscopy-based detection of these pigments in fresco samples. Gene clusters for the synthesis of secondary metabolites endowed with antibiotic activity were predicted from the annotation of Rubrobacter MAGs, along with genes conferring resistance to several antimicrobials and biocides. In conclusion, genome-resolved metagenomics provided robust evidence of a causal relationship between contamination by Rubrobacter-related carotenoid-producing bacteria and the rosy discoloration of Georgian frescoes, with relevant implications for rational biodeteriogen-targeted restoration strategies.}, } @article {pmid39705480, year = {2024}, author = {Lu, S and Sun, L and Cao, L and Zhao, M and Guo, Y and Li, M and Duan, S and Zhai, Y and Zhang, X and Wang, Y and Gai, W and Cui, X}, title = {Analysis of lung microbiota in pediatric pneumonia patients using BALF metagenomic next-generation sequencing: A retrospective observational study.}, journal = {Medicine}, volume = {103}, number = {51}, pages = {e40860}, pmid = {39705480}, issn = {1536-5964}, support = {202139//Clinical Medical peronnel training programs/ ; }, mesh = {Child ; Child, Preschool ; Female ; Humans ; Infant ; Male ; *Bronchoalveolar Lavage Fluid/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; *Lung/microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; *Pneumonia/genetics/microbiology ; Pneumonia, Mycoplasma/microbiology/diagnosis ; Retrospective Studies ; Severity of Illness Index ; }, abstract = {The contribution of the lung microbiota to pneumonia in children of varying severity remains poorly understood. This study utilized metagenomic next-generation sequencing (mNGS) technology to elucidate the characteristics of lung microbiota and their association with disease severity. This retrospective study analyzed bronchoalveolar lavage fluid (BALF) mNGS data of 92 children diagnosed with pneumonia between January 2021 and July 2022. A comparative analysis of the lung microbiota was conducted between the severe pneumonia (SP) (n = 44) and non-severe pneumonia (NSP) (n = 48) groups. Compared to conventional microbiological tests (CMT), mNGS had a higher positivity rate in etiology detection (68% vs 100%). In the NSP group, the predominant type of infection was Mycoplasma pneumoniae single infection, whereas in the SP group, the main type involved a combination of M pneumoniae and bacterial infection. The top 3 identified microbial taxa in both the groups were M pneumoniae, Rothia mucilaginosa, and Schaalia odontolyticus. Although there were no significant differences in the α and β diversity of the lung microbiota between the SP and NSP groups, the abundance of M pneumoniae was higher in the SP group (P = .053). Spearman analysis indicated a highly significant positive correlation between the abundance of Prevotella melaninogenica and M pneumoniae (P < .001). Our analysis identified an association between M pneumoniae infections and disease severity. This study provides a foundation for a better understanding of the pathogenesis of pediatric pneumonia and the relationship between microorganisms.}, } @article {pmid39705298, year = {2024}, author = {Oliveira, V and Cleary, DFR and Polónia, ARM and Huang, YM and Rocha, U and Voogd, NJ and Gomes, NCM}, title = {Unravelling a Latent Pathobiome Across Coral Reef Biotopes.}, journal = {Environmental microbiology}, volume = {26}, number = {12}, pages = {e70008}, doi = {10.1111/1462-2920.70008}, pmid = {39705298}, issn = {1462-2920}, support = {VH-NG-1248 Micro "BigData"//Helmholtz Young Investigator Grant/ ; MNPH 104403//Marine National Parks Headquarter, Taiwan/ ; MOST 105-2621-B-346-002//Ministry of Science and Technology, Taiwan/ ; DOI: 10.54499/DL57/2016/CP1482/CT0109//Foundation for Science and Technology/ ; PTDC/BIA29/MIC/6473/2014 - POCI-01-0145-FEDER-01//Foundation for Science and Technology/ ; SFRH/BPD/117563/2016//Foundation for Science and Technology/ ; UIDP/50017/2020 + UIDB/50017/2020 + LA/P/0094/2020//Foundation for Science and Technology/ ; }, mesh = {*Coral Reefs ; Animals ; *Anthozoa/microbiology ; *Bacteria/genetics/classification ; *Microbiota ; Virulence Factors/genetics ; }, abstract = {Previous studies on disease in coral reef organisms have neglected the natural distribution of potential pathogens and the genetic factors that underlie disease incidence. This study explores the intricate associations between hosts, microbial communities, putative pathogens, antibiotic resistance genes (ARGs) and virulence factors (VFs) across diverse coral reef biotopes. We observed a substantial compositional overlap of putative bacterial pathogens, VFs and ARGs across biotopes, consistent with the 'everything is everywhere, but the environment selects' hypothesis. However, flatworms and soft corals deviated from this pattern, harbouring the least diverse microbial communities and the lowest diversity of putative pathogens and ARGs. Notably, our study revealed a significant congruence between the distribution of putative pathogens, ARGs and microbial assemblages across different biotopes, suggesting an association between pathogen and ARG occurrence. This study sheds light on the existence of this latent pathobiome, the disturbance of which may contribute to disease onset in coral reef organisms.}, } @article {pmid39705278, year = {2024}, author = {Kanyerezi, S and Guerfali, FZ and Anzaku, AA and Babaleye, OA and Calvert-Joshua, T and Nguinkal, JA and Amoo, OP and Atri, C and Khan, W and Saleh, I and Nisar, MI and Kasambula, AS and Morapedi, K and Mboowa, G}, title = {Wastewater metagenomics in Africa: Opportunities and challenges.}, journal = {PLOS global public health}, volume = {4}, number = {12}, pages = {e0004044}, pmid = {39705278}, issn = {2767-3375}, abstract = {The advent of metagenomics has dramatically expanded our understanding of microbial communities, particularly through the study of wastewater, which serves as a rich source of microbial data. In Africa, wastewater metagenomics presents unparalleled opportunities for public health monitoring, antimicrobial resistance (AMR) tracking, and the discovery of new microbial species and functions. Utilizing high-throughput sequencing (HTS) technologies, this method allows for direct analysis of nucleic acids from wastewater samples, providing a cost-effective and comprehensive approach for pathogen surveillance. The potential of wastewater metagenomics in Africa is vast. It can revolutionize public health monitoring by acting as an early warning system for infectious disease outbreaks, offering near real-time data to shape effective responses. This is especially critical in densely populated urban areas with poor sanitation, where the risk of disease spread is high. Moreover, this approach enables the detection of emerging pathogens and insights into environmental health. However, the implementation of wastewater metagenomics in Africa faces several challenges. These include variability in wastewater composition due to differing local customs, limited infrastructure for sequencing and data analysis, and a shortage of bioinformatics expertise. Socio-political and ethical issues also complicate data sharing and the equitable distribution of benefits. To overcome these challenges, there is a need to enhance capacity through collaborative training, infrastructural development, and international partnerships. Investing and sustaining local genomics and bioinformatics infrastructure and expertise is crucial. Moreover, establishing robust data governance frameworks and engaging communities are essential for leveraging metagenomics to advance scientific knowledge and deliver tangible health and economic benefits. With strategic planning and collaboration, Africa can harness the transformative potential of wastewater metagenomics to improve disease surveillance, combat AMR, and foster scientific innovation, contributing significantly to sustainable development and improved quality of life.}, } @article {pmid39704517, year = {2025}, author = {Agudelo-Romero, P and Caparros-Martin, JA and Sharma, A and Saladié, M and Sly, PD and Stick, SM and O'Gara, F and , }, title = {Virome assembly reveals draft genomes of native Pseudomonas phages isolated from a paediatric bronchoalveolar lavage sample.}, journal = {Microbiology resource announcements}, volume = {14}, number = {2}, pages = {e0103024}, pmid = {39704517}, issn = {2576-098X}, support = {STICK10K0//Cystic Fibrosis Foundation (CFF)/ ; EU-634486//European Commission (EC)/ ; SSPC-2/PharM5//Science Foundation Ireland (SFI)/ ; 13/TIDA/B2625//Science Foundation Ireland (SFI)/ ; 14/TIDA/2438//Science Foundation Ireland (SFI)/ ; 15/TIDA/2977//Science Foundation Ireland (SFI)/ ; CF-2017-0757-P//Enterprise Ireland Commercialisation Fund/ ; Google Cloud Education Program grant//Google for Education/ ; Theme Collaboration Award 2023//Telethon Kids Institute Theme Collaboration Award 2023/ ; STICK19K0//Cystic Fibrosis Foundation (CFF)/ ; NHMRC115648//DHAC | National Health and Medical Research Council (NHMRC)/ ; APP1183640//DHAC | National Health and Medical Research Council (NHMRC)/ ; OGARA1710//Cystic Fibrosis Foundation (CFF)/ ; HRB-ILP-POR-2019-004//Health Research Board (HRB)/ ; MRCG-2018-16//Irish Thoracic Society (ITS)/ ; MRCG-2014-6//Irish Thoracic Society (ITS)/ ; Glenn Brown Memorial Grant 2017//The Institute for Respiratory Health/ ; }, abstract = {We present lung virome data recovered through shotgun metagenomics in bronchoalveolar lavage fluid from an infant with cystic fibrosis, who tested positive for Stenotrophomonas maltophilia infection. Using a bioinformatic pipeline for virus characterization in shotgun metagenomic data, we identified five viral contigs representing Pseudomonas phages classified as Caudoviricetes.}, } @article {pmid39703701, year = {2024}, author = {Jia, X and Li, Q and Yang, X and Li, D and Jin, Z}, title = {Comparative analysis of the gut microbiota composition and diversity in Erinaceus amurensis from the Wandashan Mountain range area based on metagenomics.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1479352}, pmid = {39703701}, issn = {1664-302X}, abstract = {This study aimed to preliminarily explore the composition and diversity of intestinal bacteria in Erinaceus amurensis during breeding period, aiding in the field rescue and population conservation efforts of Erinaceus amurensis. This also provides foundational data for further research on the prevention and screening of Emerging Zoonotic Infectious Diseases and the experimental animalization of wild Erinaceus amurensis. Between April and July 2023, we collected 13 fresh fecal samples from Erinaceus amurensis at the Sishan Forest Farm in Jidong County, Heilongjiang Province, situated within the Wandashan Mountain range. Utilizing metagenomic sequencing technology, we conducted a comparative analysis of the gut microbiota composition and diversity in wild Erinaceus amurensis across different genders and between adult and fetal individuals within the same habitat. Our results revealed significant differences (P < 0.01) in the classification and diversity of gut microbiota between genders and between adult and fetal Erinaceus amurensis. Specifically, the dominant bacterial groups in the gut of Erinaceus amurensis were Pseudomonas, Proteobacteria, and Enterobacteriaceae. In male and female Erinaceus amurensis, the dominant bacterial groups were Pseudomonas, Bacteroides, and Firmicutes, with variations in bacterial abundance and diversity. While male and female Erinaceus amurensis exhibited similar microbial compositions, they displayed significant differences in specific bacterial classifications. The dominant bacterial group in fetal Erinaceus amurensis was Proteobacteria, which demonstrated lower diversity and abundance compared to the adult group. Furthermore, the types and abundance of pathogenic or opportunistic pathogens in the gut of fetal Erinaceus amurensis and male Erinaceus amurensis were higher than those in female Erinaceus amurensis. The analysis of experimental results indicates that Erinaceus amurensis in this region either have or are at risk of developing inflammation related to the intestinal and urinary tracts, as well as skin-related issues. Consequently, it is advised that forestry and wildlife conservation personnel in this area prioritize treatment against these specific pathogens when conducting rescue operations for Erinaceus amurensis in the wild.}, } @article {pmid39703432, year = {2024}, author = {Zhao, J and Pierre Both, J and Konstantinidis, KT}, title = {Approximate nearest neighbor graph provides fast and efficient embedding with applications for large-scale biological data.}, journal = {NAR genomics and bioinformatics}, volume = {6}, number = {4}, pages = {lqae172}, pmid = {39703432}, issn = {2631-9268}, abstract = {Dimension reduction (DR or embedding) algorithms such as t-SNE and UMAP have many applications in big data visualization but remain slow for large datasets. Here, we further improve the UMAP-like algorithms by (i) combining several aspects of t-SNE and UMAP to create a new DR algorithm; (ii) replacing its rate-limiting step, the K-nearest neighbor graph (K-NNG), with a Hierarchical Navigable Small World (HNSW) graph; and (iii) extending the functionality to DNA/RNA sequence data by combining HNSW with locality sensitive hashing algorithms (e.g. MinHash) for distance estimations among sequences. We also provide additional features including computation of local intrinsic dimension and hubness, which can reflect structures and properties of the underlying data that strongly affect the K-NNG accuracy, and thus the quality of the resulting embeddings. Our library, called annembed, is implemented, and fully parallelized in Rust and shows competitive accuracy compared to the popular UMAP-like algorithms. Additionally, we showcase the usefulness and scalability of our library with three real-world examples: visualizing a large-scale microbial genomic database, visualizing single-cell RNA sequencing data and metagenomic contig (or population) binning. Therefore, annembed can facilitate DR for several tasks for biological data analysis where distance computation is expensive or when there are millions to billions of data points to process.}, } @article {pmid39703404, year = {2024}, author = {Huang, K and Zhang, X and Xiong, N and Sun, L and Zhao, X and Zhou, K and Wu, J}, title = {First metagenomic sequencing for the analysis of microbial community populations of adults and pupae of Melophagus ovinus in Xinjiang, China.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1462772}, pmid = {39703404}, issn = {2297-1769}, abstract = {INTRODUCTION: Melophagus ovinus, a parasite on the body surface of sheep, directly attacks the host through biting and sucking blood and may also transmit pathogens in the process. There are currently only a few studies on the microbial composition of M. ovinus, while there are no such studies on pupae.

METHODS: In this study, samples AT-1 to AT-4 each contained four M. ovinus individuals, while sample AT-5 comprised four M. ovinus pupae, all used for metagenomic sequencing and analysis. Melophagus ovinus adults and pupae were collected from four regions in Xinjiang, China. DNA was extracted from the samples, amplified, and sequenced using the Illumina Novaseq 6000 System; finally, the sequencing data were analyzed using molecular biology software.

RESULTS AND DISCUSSION: From all samples, a total of 32 phyla, comprising 372 genera and 1,037 species, were detected. The highest microbial diversity was observed in Kuqa City (AT-2) and Qira County (AT-4). Pupae exhibited 40 unique microbial genera (AT-5) but did not have the highest microbial diversity. Proteobacteria was the dominant phylum in all samples. The dominant genera included Bartonella, Wolbachia, Pseudomonas, and Arsenophonus. This is the first study to report most of the bacteria (e.g., Pseudomonas versuta and Arsenophonus nasoniae), fungi (e.g., Saitoella complicata), viruses (e.g., Orf virus and Wolbachia phage WO), and protozoa (e.g., Trypanosoma theileri and Babesia bigemina) in M. ovinus. This study has enriched the microbial diversity data of M. ovinus, and the pathogens it carries may pose a threat to public health safety and the economy of related industries, necessitating further research to develop effective biological control strategies.}, } @article {pmid39702789, year = {2025}, author = {Kaur, S and Patel, BCK and Collen, A and Malhotra, R}, title = {The microbiome and the eye: a new era in ophthalmology.}, journal = {Eye (London, England)}, volume = {39}, number = {3}, pages = {436-448}, pmid = {39702789}, issn = {1476-5454}, mesh = {Humans ; *Microbiota/physiology ; *Eye Diseases/microbiology/therapy ; *Ophthalmology ; *Gastrointestinal Microbiome/physiology ; Eye/microbiology ; Fecal Microbiota Transplantation ; }, abstract = {The human microbiome has progressively been recognised for its role in various disease processes. In ophthalmology, complex interactions between the gut and distinct ocular microbiota within each structure and microenvironment of the eye has advanced our knowledge on the multi-directional relationships of these ecosystems. Increasingly, studies have shown that modulation of the microbiome can be achieved through faecal microbiota transplantation and synbiotics producing favourable outcomes for ophthalmic diseases. As ophthalmologists, we are obliged to educate our patients on measures to cultivate a healthy gut microbiome through a range of holistic measures. Further integrative studies combining microbial metagenomics, metatranscriptomics and metabolomics are necessary to fully characterise the human microbiome and enable targeted therapeutic interventions.}, } @article {pmid39702650, year = {2024}, author = {Vriend, EMC and Galenkamp, H and Herrema, H and Nieuwdorp, M and van den Born, BH and Verhaar, BJH}, title = {Machine learning analysis of sex and menopausal differences in the gut microbiome in the HELIUS study.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {152}, pmid = {39702650}, issn = {2055-5008}, support = {189235//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 09150182010020/ZONMW_/ZonMw/Netherlands ; 101141346/ERC_/European Research Council/International ; }, mesh = {*Gastrointestinal Microbiome ; Humans ; Female ; *Machine Learning ; Male ; Middle Aged ; *Menopause ; Aged ; Sex Factors ; Metagenomics/methods ; Adult ; Cohort Studies ; Bacteria/classification/genetics/isolation & purification ; Feces/microbiology ; }, abstract = {Sex differences in the gut microbiome have been examined previously, but results are inconsistent, often due to small sample sizes. We investigated sex and menopausal differences in the gut microbiome in a large multi-ethnic population cohort study, including 5166 participants. Using machine learning models, we revealed modest associations between sex and menopausal status, and gut microbiota composition (AUC 0.61-0.63). After adjustments for age, cardiovascular risk factors, and diet, a part of the associations of the highest-ranked gut microbes with sex were attenuated, but most associations remained significant. In contrast, most associations with menopausal status were driven by age and lost significance after adjustment. Using pathway analyses on metagenomic data, we identified sex differences in vitamin B6 synthesis and stachyose degradation pathways. Since some of sex differences in gut microbiome composition and function could not be explained by covariates, we recommend sex stratification in future microbiome studies.}, } @article {pmid39702405, year = {2024}, author = {Soufi, HH and Porch, R and Korchagina, MV and Abrams, JA and Schnider, JS and Carr, BD and Williams, MA and Louca, S}, title = {Taxonomic variability and functional stability across Oregon coastal subsurface microbiomes.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1663}, pmid = {39702405}, issn = {2399-3642}, mesh = {Oregon ; *Microbiota/genetics ; *Geologic Sediments/microbiology ; *RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; Phylogeny ; Metagenomics/methods ; Biodiversity ; }, abstract = {The factors shaping microbial communities in marine subsurface sediments remain poorly understood. Here, we analyzed the microbiome of subsurface sediments within a depth range of 1.6-1.9 m, at 10 locations along the Oregon coast. We used metagenomics to reconstruct the functional structure and 16S rRNA gene amplicon sequencing to estimate the taxonomic composition of microbial communities, accompanied by physicochemical measurements. Functional community structure, in terms of the proportions of various gene groups, was remarkably stable across samples, despite the latter covering a region spanning over 300 km. In contrast, taxonomic composition was highly variable, especially at the level of amplicon sequence variants (ASVs) and operational taxonomic units (OTUs). Mantel correlation tests between compositional dissimilarities and geographic distances revealed only a moderate influence of distance on composition. Regression models predicting taxonomic dissimilarities and considering up to 20 physicochemical variables as predictors, almost always failed to select a significant predictor, suggesting that variation in local conditions does not explain the high taxonomic variability. Permutation null models of community assembly revealed that taxa tend to strongly segregate, i.e., exclude each other. We conclude that biological interactions are important drivers of taxonomic variation in subsurface sediments, and that this variation can decouple from functional structure.}, } @article {pmid39702006, year = {2024}, author = {Demirkan, A and van Dongen, J and Finnicum, CT and Westra, HJ and Jankipersadsing, S and Willemsen, G and Ijzerman, RG and Boomsma, DI and Ehli, EA and Bonder, MJ and Fu, J and Franke, L and Wijmenga, C and de Geus, EJC and Kurilshikov, A and Zhernakova, A}, title = {Linking the gut microbiome to host DNA methylation by a discovery and replication epigenome-wide association study.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1224}, pmid = {39702006}, issn = {1471-2164}, mesh = {*DNA Methylation ; *Gastrointestinal Microbiome/genetics ; Humans ; *Epigenome ; *Genome-Wide Association Study ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; CpG Islands/genetics ; Middle Aged ; Adult ; Netherlands ; }, abstract = {Microbiome influences multiple human systems, but its effects on gene methylation is unknown. We investigated the relations between gene methylation in blood and the abundance of common gut bacteria profiled by 16s rRNA gene sequencing in two population-based Dutch cohorts: LifeLines-Deep (LLD, n = 616, discovery) and the Netherlands Twin Register (NTR, n = 296, replication). In LLD, we also explored microbial pathways using data generated by shotgun metagenomic sequencing (n = 683). Methylation in both cohorts was profiled in blood samples using the Illumina 450K array. Discovery and replication analysis identified two independent CpGs associated with the genus Eggerthella: cg16586104 (Pmeta-analysis = 3.21 × 10[-11]) and cg12234533 (Pmeta-analysis = 4.29 × 10[-10]). We also show that microbiome can mediate the effect of environmental factors on host gene methylation. In this first association study linking epigenome to microbiome, we found and replicated the associations of two CpGs to the abundance of genus Eggerthella and identified microbiome as a mediator of the exposome. These associations are observational and suggest further investigation in larger and longitudinal set-ups.}, } @article {pmid39701966, year = {2024}, author = {Oskolkov, N and Sandionigi, A and Götherström, A and Canini, F and Turchetti, B and Zucconi, L and Mimmo, T and Buzzini, P and Borruso, L}, title = {Unraveling the ancient fungal DNA from the Iceman gut.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1225}, pmid = {39701966}, issn = {1471-2164}, mesh = {*DNA, Ancient/analysis ; Humans ; *DNA, Fungal/genetics ; Metagenomics/methods ; Gastrointestinal Microbiome/genetics ; Gastrointestinal Tract/microbiology ; Mummies/microbiology ; Computational Biology/methods ; Fungi/genetics/classification ; }, abstract = {BACKGROUND: Fungal DNA is rarely reported in metagenomic studies of ancient samples. Although fungi are essential for their interactions with all kingdoms of life, limited information is available about ancient fungi. Here, we explore the possibility of the presence of ancient fungal species in the gut of Ötzi, the Iceman, a naturally mummified human found in the Tyrolean Alps (border between Italy and Austria).

METHODS: A robust bioinformatic pipeline has been developed to detect and authenticate fungal ancient DNA (aDNA) from muscle, stomach, small intestine, and large intestine samples.

RESULTS: We revealed the presence of ancient DNA associated with Pseudogymnoascus genus, with P. destructans and P. verrucosus as possible species, which were abundant in the stomach and small intestine and absent in the large intestine and muscle samples.

CONCLUSION: We suggest that Ötzi may have consumed these fungi accidentally, likely in association with other elements of his diet, and they persisted in his gut after his death due to their adaptability to harsh and cold environments. This suggests the potential co-occurrence of ancient humans with opportunistic fungal species and proposes and validates a conservative bioinformatic approach for detecting and authenticating fungal aDNA in historical metagenomic samples.}, } @article {pmid39701896, year = {2025}, author = {Haas, AL and Bradley, BT and Hanson, KE}, title = {Recent Developments in Culture-Independent Fungal Diagnostics.}, journal = {Infectious disease clinics of North America}, volume = {39}, number = {1}, pages = {41-56}, doi = {10.1016/j.idc.2024.11.004}, pmid = {39701896}, issn = {1557-9824}, mesh = {Humans ; *Mycoses/diagnosis/microbiology ; *Fungi/isolation & purification/genetics ; *Molecular Diagnostic Techniques/methods ; Nucleic Acid Amplification Techniques/methods ; Sensitivity and Specificity ; Antigens, Fungal/analysis ; Microbiological Techniques/methods ; }, abstract = {Culture-independent diagnostics for fungi potentially offer increased sensitivity and more rapid results relative to culture. Recent developments include new platforms for fungal cell wall antigen detection, commercially available targeted nucleic acid amplification tests, and the use of sequencing-based technologies for the detection and identification of a broad range of fungal pathogens. Although these tests are not without limitations, many more commercially available platforms now exist, and efforts to increase the standardization of laboratory-developed tests are ongoing. Additionally, implementation studies are beginning to delineate the optimal use cases for molecular diagnostics across a range of fungal diseases and at-risk populations.}, } @article {pmid39701829, year = {2025}, author = {McAlister, JS and Blum, MJ and Bromberg, Y and Fefferman, NH and He, Q and Lofgren, E and Miller, DL and Schreiner, C and Candan, KS and Szabo-Rogers, H and Reed, JM}, title = {An interdisciplinary perspective of the built-environment microbiome.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {1}, pages = {}, pmid = {39701829}, issn = {1574-6941}, support = {CCF 2200140//U.S. National Science Foundation/ ; }, mesh = {*Microbiota ; *Built Environment ; Humans ; Interdisciplinary Research ; }, abstract = {The built environment provides an excellent setting for interdisciplinary research on the dynamics of microbial communities. The system is simplified compared to many natural settings, and to some extent the entire environment can be manipulated, from architectural design to materials use, air flow, human traffic, and capacity to disrupt microbial communities through cleaning. Here, we provide an overview of the ecology of the microbiome in the built environment. We address niche space and refugia, population, and community (metagenomic) dynamics, spatial ecology within a building, including the major microbial transmission mechanisms, as well as evolution. We also address landscape ecology, connecting microbiomes between physically separated buildings. At each stage, we pay particular attention to the actual and potential interface between disciplines, such as ecology, epidemiology, materials science, and human social behavior. We end by identifying some opportunities for future interdisciplinary research on the microbiome of the built environment.}, } @article {pmid39701698, year = {2024}, author = {Bao, YY and Li, MX and Gao, XX and Wei, WJ and Huang, WJ and Lin, LZ and Wang, H and Zheng, NN and Li, HK}, title = {[Astragalus polysaccharides improve adipose tissue aging in naturally aged mice via indole-3-lactic acid].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {49}, number = {22}, pages = {5998-6007}, doi = {10.19540/j.cnki.cjcmm.20240508.401}, pmid = {39701698}, issn = {1001-5302}, mesh = {Animals ; Mice ; *Aging/drug effects ; *Adipose Tissue/drug effects/metabolism ; *Polysaccharides/pharmacology ; *Indoles/pharmacology ; Male ; *Astragalus Plant/chemistry ; 3T3-L1 Cells ; Humans ; Adipocytes/drug effects/metabolism/cytology ; Mice, Inbred C57BL ; Cellular Senescence/drug effects ; Drugs, Chinese Herbal/pharmacology/administration & dosage ; Gastrointestinal Microbiome/drug effects ; }, abstract = {Plant polysaccharides are effective components that widely present in traditional Chinese medicine(TCM), exhibiting rich biological activities. However, as most plant polysaccharides cannot be directly absorbed and utilized by the human digestive system, it is now believed that their mode of action mainly involves interaction with intestinal microbiota, leading to the production of functional small molecules. The efficacy of Astragalus polysaccharide(APS) is extensive, including weight loss, improvement of fatty liver, reduction of blood lipids, and enhancement of insulin sensitivity, which may also be related to the regulation of intestinal microbiota. Adipose tissue senescence is an important characteristic of the physiological aging process in the body, often occurring prior to the aging of other important organs. Its main features include the accumulation of senescent cells and exacerbation of inflammation within the tissue. Therefore, to explore the potential protective effects of APS on aging, the improvement of adipose tissue aging phenotype in naturally aging mice was observed using APS, and combined with metagenomic metabolomics, corresponding microbial metabolic functional molecules were identified. Furthermore, functional tests in cell aging models were conducted. The results showed that APS significantly improved the adipocyte aging characteristics of naturally aging mice: specifically reducing aging-induced adipocyte hypertrophy; decreasing the protein expression of aging markers cyclin-dependent kinase inhibitor p21(P21) and multiple tumor suppressor 1(P16); lowering the tissue inflammation reaction. Metagenomic metabolomic analysis of serum from mice in each group revealed that APS significantly increased the content of indole-3-lactic acid(ILA) in naturally aging mice. Further in vitro studies showed that ILA could improve the aging of 3T3-L1 mouse embryonic fibroblasts induced by bleomycin, reduce the protein expression of the aging marker P21, alleviate inflammation, and enhance the ability of preadipocytes to mature. Therefore, APS had the efficacy of protecting naturally aging mice, and its action may be related to the increase in the intestinal microbiota metabolite ILA. This study suggested that TCM may serve as an important entry point for explaining the mechanism of action of TCM by regulating intestinal microbiota and their functional metabolites.}, } @article {pmid39701526, year = {2024}, author = {Sinclair, KD}, title = {Developmental epigenetics: Understanding genetic and sexually dimorphic responses to parental diet and outcomes following assisted reproduction.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2024-25811}, pmid = {39701526}, issn = {1525-3198}, abstract = {The developmental integrity and wellbeing of offspring are influenced by events that occur in utero, particularly around the time of conception. While extraneous factors such as environmental temperature and exposure to environmental chemicals can each have a bearing on these events, the epigenetic mechanisms that direct cellular differentiation during early development in ruminants are best described for studies which have investigated the effects of parental nutrition or pregnancy outcomes following assisted reproduction. In this article the case is made that the genetic constitution of an individual directs epigenetic responses to environmental stimuli, and consideration in this regard is also given to the origins of sexual dimorphism and mechanisms of germline intergenerational inheritance. These aspects are considered in the context of epigenetic modifications that take place during the normal course of gametogenesis and embryogenesis, and again following either dietary or procedural interventions such as embryo culture. A recurring feature of such interventions, irrespective of species, is that one carbon metabolic pathways are invariably disrupted, and this affects the provision of methyl groups for chromatin and RNA methylation. Inter-specific variation in how these pathways operate, both within the liver and in germ cells, indicates that ruminants may be particularly sensitive in this regard. Recent advances in genomic technologies should enable rapid progress in these areas. Knowledge gained can be integrated into breed improvement programs and used to tailor management practices to specific breeds and strains (including sexes) within breeds. Ultimately, consideration should be given to integrating metagenomics into analyses of genetic-directed epigenetic programming of animal development.}, } @article {pmid39701375, year = {2025}, author = {Corbett, GA and Corcoran, S and Feehily, C and Soldati, B and Rafferty, A and MacIntyre, DA and Cotter, PD and McAuliffe, FM}, title = {Preterm-birth-prevention with Lactobacillus crispatus oral probiotics: Protocol for a double blinded randomised placebo-controlled trial (the PrePOP study).}, journal = {Contemporary clinical trials}, volume = {149}, number = {}, pages = {107776}, doi = {10.1016/j.cct.2024.107776}, pmid = {39701375}, issn = {1559-2030}, mesh = {Humans ; Female ; *Probiotics/administration & dosage/therapeutic use ; Double-Blind Method ; *Vagina/microbiology ; Pregnancy ; *Premature Birth/prevention & control/microbiology ; *Lactobacillus crispatus ; *Lactobacillus ; *Gastrointestinal Microbiome ; *Lacticaseibacillus rhamnosus ; Adult ; Administration, Oral ; Infant, Newborn ; }, abstract = {INTRODUCTION: Effective spontaneous preterm birth (sPTB) prevention is an urgent unmet clinical need. Vaginal depletion of Lactobacillus crispatus is linked to sPTB. This trial will investigate impact of an oral Lactobacillus spp. probiotic product containing an L. crispatus strain with other Lactobacilli spp., on the maternal vaginal and gut microbiome in pregnancies high-risk for sPTB.

METHODS: A double-blind, placebo-controlled, randomised trial will be performed at the National Maternity Hospital Dublin, Ireland. Inclusion criteria are women with history of sPTB or mid-trimester loss, cervical surgery (cone biopsy or two previous large-loop-excision-of-transformation-zone) or uterine anomaly. The intervention is oral supplementation for twelve weeks with probiotic or identical placebo. The probiotic will contains: ◦ 4 billion CFU Lactobacillus crispatus Lbv 88(2x10[9]CFU/Capsule) ◦ 4 billion CFU Lactobacillus rhamnosus Lbv 96(2x10[9]CFU/Capsule) ◦ 0.8 billion CFU Lactobacillus jensenii Lbv 116(0.4x10[9]CFU/Capsule) ◦ 1.2 billion CFU Lactobacillus gasseri Lbv 150(0.6x10[9]CFU/Capsule). Investigators and participants will be blinded to assignment.

RESULTS: The primary outcome is detectable L. crispatus in the vaginal microbiome after twelve weeks of treatment, measured using high-throughput DNA sequencing. A total of 126 women are required to detect a 25 % increase in detectable L. crispatus. Secondary outcomes include impact of intervention on the gut microbiome and metabolome, rate of sPTB and mid-trimester loss, neonatal outcomes and maternal morbidity.

CONCLUSIONS: This randomised trial will investigate ability of an oral probiotic containing L. crispatus to increase its abundance in the vaginal microbiome, both directly by horizontal transfer and indirectly via microbiome and metabolome of the gut.}, } @article {pmid39701354, year = {2025}, author = {Liu, J and Zhou, M and Zhou, L and Dang, R and Xiao, L and Tan, Y and Li, M and Yu, J and Zhang, P and Hernández, M and Lichtfouse, E}, title = {Methane production related to microbiota in dairy cattle feces.}, journal = {Environmental research}, volume = {267}, number = {}, pages = {120642}, doi = {10.1016/j.envres.2024.120642}, pmid = {39701354}, issn = {1096-0953}, mesh = {Animals ; *Methane/metabolism/biosynthesis ; Cattle ; *Feces/microbiology ; *Archaea/metabolism/genetics ; Bacteria/metabolism/genetics/classification ; Microbiota ; Dairying ; }, abstract = {Methane (CH4) emission from livestock feces, led by ruminants, shows a profound impact on global warming. Despite this, we have almost no information on the syntrophy of the intact microbiome metabolisms, from carbohydrates to the one-carbon units, covering multiple stages of ruminant development. In this study, syntrophic effects of polysaccharide degradation and acetate-producing bacteria, and methanogenic archaea were revealed through metagenome-assembled genomes from water saturated dairy cattle feces. Although CH4 is thought to be produced by archaea, more edges, nodes, and balanced interaction types revealed by network analysis provided a closed bacteria-archaea network. The CH4 production potential and pathways were further evaluated through dynamic, thermodynamic and [13]C stable isotope analysis. The powerful CH4 production potential benefited from the metabolic flux: classical polysaccharides, soluble sugar (glucose, galactose, lactose), acetate, and CH4 produced via typical acetoclastic methanogenesis. In comparison, a cooperative model dominated by hydrogenotrophic methanogenic archaea presented a weak ability to generate CH4. Our findings comprehensively link carbon and CH4 metabolism paradigm to specific microbial lineages which are shaped related to developmental stages of the dairy cattle, directing influencing global warming from livestock and waste treatment.}, } @article {pmid39700995, year = {2025}, author = {Xu, X and Hao, Y and Cai, Z and Cao, Y and Jia, W and Zhao, J and White, JC and Ma, C}, title = {Nanoscale‑boron nitride positively alters rhizosphere microbial communities and subsequent cucumber (Cucumis sativa) growth: A metagenomic analysis.}, journal = {The Science of the total environment}, volume = {958}, number = {}, pages = {178115}, doi = {10.1016/j.scitotenv.2024.178115}, pmid = {39700995}, issn = {1879-1026}, mesh = {*Rhizosphere ; *Soil Microbiology ; *Cucumis sativus/microbiology ; *Microbiota/drug effects ; Metagenomics ; Boron Compounds ; Plant Growth Regulators ; Soil/chemistry ; }, abstract = {Boron (B) deficiency affects over 132 crop species globally, making effective B supplement crucial for enhancing agricultural yield and health. This study explores an innovative application of nanoscale boron nitride (nano-BN) as a sustainable solution for addressing B deficiency in crops. Cucumber seedlings were treated with different contents of nano-BN under greenhouse conditions and both B and N ionic treatments were set as comparisons. Results show that soil application of 10 mg/kg nano-BN achieved a remarkable 15.8 % increase in fresh weight compared to the control. Notably, nano-BN exhibited superior efficiency in providing essential micronutrients without inducing toxicity as compared to traditional ionic B sources. Phytohormone correlation analysis reveals that nano-BN application significantly enhances levels of indole-3-acetic acid (IAA) and cytokinins while reducing abscisic acid (ABA), fostering optimal plant growth conditions. Furthermore, increases in dissolved organic matter (DOM) and dissolved organic carbon (DOC) levels in the rhizosphere improve nutrient availability and promote beneficial microbial activity in the soil as affected by nano-BN. Metagenomics techniques were used to investigate the impact of nano-BN on soil carbon and nitrogen cycling, alongside its effects on the soil microbiome. The upregulation of genes associated with fermentation pathways as affected by nano-BN suggests the enhanced carbon cycling. Additionally, nano-BN upregulated a number of functional genes involved in nitrogen-based processes, leading to a significant increase in microorganisms harboring nitrogen-fixing genes, including Phenylobacterium, Novosphingobium, and Reyranella. Overall, these findings provide valuable insight into the application of nano-BN in agriculture to sustainably increase crop productivity and enhance the efficiency of carbon and nitrogen cycling.}, } @article {pmid39700989, year = {2025}, author = {Liu, F and Zeng, J and Ding, J and Wang, C and He, Z and Liu, Z and Shu, L}, title = {Microbially-driven phosphorus cycling and its coupling mechanisms with nitrogen cycling in mangrove sediments.}, journal = {The Science of the total environment}, volume = {958}, number = {}, pages = {178118}, doi = {10.1016/j.scitotenv.2024.178118}, pmid = {39700989}, issn = {1879-1026}, mesh = {*Phosphorus/metabolism ; *Geologic Sediments/microbiology ; *Nitrogen/metabolism ; *Nitrogen Cycle ; Microbiota ; Wetlands ; Bacteria/metabolism ; }, abstract = {The phosphorus (P) cycle plays a crucial role in the biogeochemical cycling of mangrove sediments. However, the diversity of microbially-driven P-cycling and its coupling with nitrogen (N)-cycling remain poorly understood. In this study, we used metagenomic approaches to investigate microbial P-cycling and its potential interactions with N-cycling in mangrove sediments. Our results revealed that pH, total carbon, and total nitrogen were key environmental factors influencing the diversity of P-cycling microbial communities. Phosphorus metabolic pathways differed among mangrove sediment depths. In surface sediments (0-5 cm), microbial communities primarily acquired readily available inorganic phosphorus, whereas, in deeper sediments (>60 cm), they hydrolyzed more persistent triphosphates, reabsorbed nucleotides, and sourced free phosphate, reflecting a shift in phosphorus transport modes. We also identified glutamate metabolism as a potential pathway linking P-cycling with N-cycling, with these functions co-occurring in both contigs and genomes. Additionally, the diversity of microbial communities associated with the P-cycling increased with sediment depth, suggesting that microbially-driven P-cycling diversifies as depth increases. This study provides new insights into P-cycling and its potential coupling with N-cycling through glutamate metabolism, its coupling with N-cycling through glutamate metabolism.}, } @article {pmid39700951, year = {2025}, author = {Gu, H and Hu, X and Zhang, J and Li, Y and Yu, Z and Liu, J and Sui, Y and Jin, J and Liu, X and Wang, G}, title = {Biogeographic patterns of viral communities, ARG profiles and virus-ARG associations in adjacent paddy and upland soils across black soil region.}, journal = {Journal of hazardous materials}, volume = {485}, number = {}, pages = {136909}, doi = {10.1016/j.jhazmat.2024.136909}, pmid = {39700951}, issn = {1873-3336}, mesh = {*Soil Microbiology ; *Soil/chemistry ; Viruses/genetics ; Drug Resistance, Microbial/genetics ; Oryza/virology ; China ; Bacteria/genetics ; Agriculture ; }, abstract = {Biogeographic distribution of prokaryotic and eukaryotic communities has been extensively studied. Yet, our knowledge of viral biogeographic patterns, the corresponding driving factors and the virus-resistome associations is still limited. Here, using metagenomic analysis, we explored the viral communities and profiles of antibiotic resistance genes (ARGs) in 30 fields of paddy (rice soils, RS) and upland soils (corn soils, CS) at a regional scale across black soil region of Northeast China. Our finding revealed that viral communities displayed significant distance-decay relationships, and environmental variables largely dominated viral community patterns in agricultural soils. Compared to RS, viral community in CS harbored significantly higher viral α-diversity and distinct β-diversity, and exhibited a higher turnover along with environmental gradients and spatial distance. However, no clear latitudinal diversity gradient (LDG) pattern was observed in viral diversity over large-scale sampling for RS and CS, and heterogeneous distribution of soil viruses was well maintained over large-scale sampling. Soil pH was the important influential factor driving viral community, and the high soil nutrient levels negatively affected viral diversity. Uroviricota, Nucleocytoviricota and Artverviricota were the main viral phyla in agricultural soils, and virus-host linkages spanned 17 prokaryotic phyla, including Actinobacteriota and Proteobacteria. Besides, 2578 ARG subtypes were retrieved and conferred resistance to 27 types of antibiotics, in which multidrug was the predominant ARG type in Mollisols. Procrustes analysis showed the significant contribution of viral community to ARG profiles, which was more obvious in CS compared to RS. We identified 9.61 % and 11.4 % of soil viruses carried at least one ARG can infect multi-host in RS and CS. Furthermore, 43 and 77 complete viral metagenome-assembled genome (vMAG) were reconstructed in RS and CS, respectively. Notably, the lysogenic phages in RS contained 29.7 % of ARGs, a higher proportion than the 12.5 % found in CS. Overall, our study underscored the prevalent distribution of viral communities and ARG profiles at a large spatial scale, and the distinct ecological strategies of virus-ARG associations in adjacent paddy and upland soils.}, } @article {pmid39700725, year = {2025}, author = {Petersen, JF and Valk, LC and Verhoeven, MD and Nierychlo, MA and Singleton, CM and Dueholm, MKD and Nielsen, PH}, title = {Diversity and physiology of abundant Rhodoferax species in global wastewater treatment systems.}, journal = {Systematic and applied microbiology}, volume = {48}, number = {1}, pages = {126574}, doi = {10.1016/j.syapm.2024.126574}, pmid = {39700725}, issn = {1618-0984}, mesh = {*Wastewater/microbiology/chemistry ; *Phylogeny ; *RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; Metagenome ; Water Purification ; Sequence Analysis, DNA ; Denmark ; Biodiversity ; Oxidation-Reduction ; Genome, Bacterial/genetics ; }, abstract = {Wastewater treatment plants rely on complex microbial communities for bioconversion and removal of pollutants, but many process-critical species are still poorly investigated. One of these genera is Rhodoferax, an abundant core genus in wastewater treatment plants across the world. The genus has been associated with many metabolic traits such as iron reduction and oxidation and denitrification. We used 16S rRNA gene amplicon data to uncover the diversity and abundance of Rhodoferax species in Danish and global treatment plants. Publicly available metagenome-assembled genomes were analyzed based on phylogenomics to delineate species and assign taxonomies based on the SeqCode. The phylogenetic analysis of "Rhodoferax" revealed that species previously assigned to Rhodoferax in wastewater treatment plants should be considered as at least eight different genera, with five representing previously undescribed genera. Genome annotation showed potential for several key-bioconversions in wastewater treatment, such as nitrate reduction, carbohydrate degradation, and accumulations of various storage compounds. Iron oxidation and reduction capabilities were not predicted for abundant species. Species-resolved FISH-Raman was performed to gain an overview of the morphology and ecophysiology of selected taxa to clarify their potential role in global wastewater treatment systems. Our study provides a first insight into the functional and ecological characteristics of several novel genera abundant in global wastewater treatment plants, previously assigned to the Rhodoferax genus.}, } @article {pmid39700724, year = {2025}, author = {Mao, YL and Dong, XY and Tao, CQ and Wu, ZP and Shi, XW and Hou, J and Cui, HL}, title = {Natronorarus salvus gen. nov., sp. nov., Halalkalicoccus ordinarius sp. nov., and Halalkalicoccus salilacus sp. nov., halophilic archaea from a soda lake and two saline lakes, and proposal to classify the genera Halalkalicoccus and Natronorarus into Halalkalicoccaceae fam. nov. in the order Halobacteriales within the class Halobacteria.}, journal = {Systematic and applied microbiology}, volume = {48}, number = {1}, pages = {126577}, doi = {10.1016/j.syapm.2024.126577}, pmid = {39700724}, issn = {1618-0984}, mesh = {*Lakes/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Phylogeny ; China ; *DNA, Archaeal/genetics/chemistry ; *Sequence Analysis, DNA ; *Base Composition ; Sodium Chloride/metabolism ; Halobacteriales/classification/genetics/isolation & purification ; Nucleic Acid Hybridization ; Halobacteriaceae/classification/genetics/isolation & purification ; Metagenomics ; Salinity ; Hydrogen-Ion Concentration ; }, abstract = {Four novel halophilic archaeal strains CGA53[T], CG83[T], FCH27[T], and SEDH24 were isolated from a soda lake and two saline lakes in China, respectively. Strain CGA53[T] showed the highest 16S rRNA gene similarity (92.6%) to Salinilacihabitans rarus AD-4[T], and the other three strains were found to be related to Halalkalicoccus species with similarities of 97.6-98.3%. Metagenomic studies indicated that these four strains are low abundant inhabitants detected in these hypersaline environments, and only one MAG of Chagannuoer Soda Lake (CG) could be assigned to the genus Halalkalicoccus. Their growth occurred at 20-60 °C (optima, 42, 37, 37-42, and 35 °C), 0.9-5.1 M NaCl (optima, 3.9, 2.6, 3.5, and 3 M), and 0-1.0 M MgCl2 (optima, 0.5, 0.7, and 0.1) and pH 5.5-10.5 (optima, 9.0, 7.5, 7.0, and 7.0), respectively. Phylogenetic and phylogenomic analyses revealed that strains CG83[T], FCH27[T], and SEDH24 cluster with the current species of the genus Halalkalicoccus, and strain CGA53[T] forms an independent branch separated from this genus. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and average amino acid identity (AAI) values among strains CGA53[T], CG83[T], FCH27[T], SEDH24, and the type species of the current genera within the class Halobacteria were 67.4-81.6%, 16.5-28.6% and 49.7-74.1%, respectively, clearly lower than the cutoff values for species demarcation. Strain CGA53[T] may represent a novel species of a new genus according to the cutoff value for genus demarcation of 65% AAI. Diverse differential phenotypic characteristics, such as nutrition, biochemical activities, antibiotic sensitivity, and H2S formation, were found among these four strains and Halalkalicoccus species. Genome-based classification supported that strains CGA53[T], CG83[T], FCH27[T], SEDH24, and the current species of Halalkalicoccus represent a novel family of the order Halobacteriales within the class Halobacteria.}, } @article {pmid39700673, year = {2024}, author = {Zhang, Z and Zhou, L and Li, H and Li, L and Liu, H}, title = {Diagnostic performance of metagenomic next-generation sequencing based on alveolar lavage fluid in unexplained lung shadows.}, journal = {Diagnostic microbiology and infectious disease}, volume = {111}, number = {3}, pages = {116651}, doi = {10.1016/j.diagmicrobio.2024.116651}, pmid = {39700673}, issn = {1879-0070}, abstract = {BACKGROUND: Unexplained lung shadows are challenging in respiratory medicine, with both infectious and non-infectious etiologies. Lung biopsy is definitive but invasive, prompting a need for non-invasive alternatives. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) is emerging as a promising diagnostic tool.

METHODS: We retrospectively analyzed 105 patients with unexplained lung shadows, collecting general information, mNGS results from BALF, and clinical diagnosis. We evaluated mNGS's diagnostic performance by comparing with final diagnosis.

RESULTS: mNGS showed good diagnostic performance in differentiating infectious from non-infectious causes. The specificity and accuracy for bacteria and fungi exceeded 90%, while the sensitivity and precision for fungi were lower than for bacteria. Atypical pathogens were frequently identified, especially in mixed infections.

CONCLUSIONS: mNGS of BALF is efficient in diagnosing infectious and non-infectious causes of unexplained lung shadows. While effective for bacteria and fungi detection, the sensitivity and precision for fungi are lower.}, } @article {pmid39700412, year = {2024}, author = {Duan, HN and Hearne, G and Polikar, R and Rosen, GL}, title = {The Naïve Bayes classifier++ for metagenomic taxonomic classification-query evaluation.}, journal = {Bioinformatics (Oxford, England)}, volume = {41}, number = {1}, pages = {}, pmid = {39700412}, issn = {1367-4811}, support = {1936791//National Science Foundation/ ; }, mesh = {*Bayes Theorem ; *Metagenomics/methods ; *Software ; Algorithms ; Databases, Genetic ; }, abstract = {MOTIVATION: This study examines the query performance of the NBC++ (Incremental Naive Bayes Classifier) program for variations in canonicality, k-mer size, databases, and input sample data size. We demonstrate that both NBC++ and Kraken2 are influenced by database depth, with macro measures improving as depth increases. However, fully capturing the diversity of life, especially viruses, remains a challenge.

RESULTS: NBC++ can competitively profile the superkingdom content of metagenomic samples using a small training database. NBC++ spends less time training and can use a fraction of the memory than Kraken2 but at the cost of long querying time. Major NBC++ enhancements include accommodating canonical k-mer storage (leading to significant storage savings) and adaptable and optimized memory allocation that accelerates query analysis and enables the software to be run on nearly any system. Additionally, the output now includes log-likelihood values for each training genome, providing users with valuable confidence information.

Source code and Dockerfile are available at http://github.com/EESI/Naive_Bayes.}, } @article {pmid39699489, year = {2024}, author = {Souza, PJ and Fernandes, J and Coelho, TA and Cosentino, M and D'arc, M and Alves, PDG and Guterres, A and Vilar, EM and Lemos, ERS and Cordeiro-Estrela, P and Santos, AFA and Oliveira, RC}, title = {A newly bat-borne hantavirus detected in Seba's short-tailed bats (Carollia perspicillata) in the Brazilian Atlantic Rainforest.}, journal = {Memorias do Instituto Oswaldo Cruz}, volume = {119}, number = {}, pages = {e240132}, pmid = {39699489}, issn = {1678-8060}, mesh = {Animals ; *Chiroptera/virology ; Brazil/epidemiology ; *Orthohantavirus/genetics/classification/isolation & purification ; *Phylogeny ; *Rainforest ; RNA, Viral/genetics/analysis ; Reverse Transcriptase Polymerase Chain Reaction ; Hantavirus Infections/veterinary/epidemiology/virology ; }, abstract = {BACKGROUND: Bat-borne hantaviruses have been identified worldwide but little is known about neotropical bats in the megadiverse biomes of the American continent. Although serological evidence has hinted at hantavirus circulation in Brazil, the scarce number of genomic detection represents a gap to understand viral diversity, prevalence, and ecology of bat-borne hantaviruses.

OBJECTIVE: We aim to investigate and evaluate the presence and prevalence of bat-borne hantavirus in the Brazilian Atlantic Forest.

METHODS: Here in, 97 lung and kidney tissue samples from bats captured in the Brazilian Atlantic Rainforest were submitted to hantavirus-specific nested reverse transcription-polymerase chain reaction (RT-PCR) targeted the hantaviral L segment and metagenomic analysis.

FINDINGS: Hantavirus RNA was detected in five tissue fragments of 20 Seba's short-tailed bats (Carollia perspicillata). Phylogenetic analysis, based on partial L-segment sequence using maximum likelihood method, demonstrated that the identified virus formed a monophyletic clade and a highly divergent bat-borne lineage comprising other recent strains found in the genus Carollia from South America.

MAIN CONCLUSIONS: Our findings suggest the presence of a novel bat-borne hantavirus in Brazil, tentatively named Mamanguape virus (MGPV). Additional genomic data will help to extend our knowledge about the classification of MGPV within the Hantaviridae family and the evolution origins of new world bat-borne hantaviruses.}, } @article {pmid39699221, year = {2025}, author = {Lustermans, JJM and Sereika, M and Burdorf, LDW and Albertsen, M and Schramm, A and Marshall, IPG}, title = {Extracellular electron transfer genes expressed by candidate flocking bacteria in cable bacteria sediment.}, journal = {mSystems}, volume = {10}, number = {1}, pages = {e0125924}, pmid = {39699221}, issn = {2379-5077}, support = {DNRF136//Danmarks Grundforskningsfond (DNRF)/ ; S004523N//Flanders Research FWO/ ; TopBOF//University Antwerp TopBOF program/ ; Microflora Danica//Poul Due Jensens Fond (Poul Due Jensen Foundation)/ ; HORIZON-MSCA-2023-PF-01: 101152850//EC | Horizon Europe | Excellent Science | HORIZON EUROPE Marie Sklodowska-Curie Actions (MSCA)/ ; }, mesh = {*Geologic Sediments/microbiology ; Electron Transport ; *Bacteria/genetics/metabolism/isolation & purification ; *RNA, Ribosomal, 16S/genetics ; Metagenomics ; Sulfides/metabolism ; Oxidation-Reduction ; }, abstract = {UNLABELLED: Cable bacteria, filamentous sulfide oxidizers that live in sulfidic sediments, are at times associated with large flocks of swimming bacteria. It has been proposed that these flocks of bacteria transport electrons extracellularly to cable bacteria via an electron shuttle intermediate, but the identity and activity of these bacteria in freshwater sediment remain mostly uninvestigated. Here, we elucidate the electron exchange capabilities of the bacterial community by coupling metagenomics and metatranscriptomics to 16S rRNA amplicon-based correlations with cable bacteria over 155 days. We identified candidate flocking bacteria as bacteria containing genes for motility and extracellular electron transfer including synthesis genes for potential extracellular electron shuttles: phenazines and flavins. Based on these criteria, 22 MAGs were from candidate flockers, which constituted 21.4% of all 103 MAGs. Of the candidate flocking bacteria, 42.1% expressed extracellular electron transfer genes. The proposed flockers belonged to a large variety of metabolically versatile taxonomic groups: 18 genera spread across nine phyla. Our data suggest that cable bacteria in freshwater sediments engage in electric relationships with diverse exoelectrogenic microbes. This community, found in deeper anoxic sediment layers, is involved in sulfur, carbon, and metal (in particular Fe) cycling and indirectly utilizes oxygen here by extracellularly transferring electrons to cable bacteria.

IMPORTANCE: Cable bacteria are ubiquitous, filamentous bacteria that couple sulfide oxidation to the reduction of oxygen at up to centimeter distances in sediment. Cable bacterial impact extends beyond sulfide oxidation via interactions with other bacteria that flock around cable bacteria and use them as electron acceptor "shortcut" to oxygen. The exact nature of this interspecies electric interaction remained unknown. With metagenomics and metatranscriptomics, we determined what extracellular electron transport processes co-occur with cable bacteria, demonstrating the identity and metabolic capabilities of these potential flockers. In sediments, microbial activities are sharply divided into anaerobic and aerobic processes, with oxygen reaching only millimeters deep. Cable bacteria extend the influence of oxygen to several centimeters, revealing a new class of anaerobic microbial metabolism with cable bacteria as electron acceptors. This fundamentally changes our understanding of sediment microbial ecology with wide-reaching consequences for sulfur, metal (in particular Fe), and carbon cycling in freshwater and marine sediments.}, } @article {pmid39699218, year = {2025}, author = {Kalu, CM and Mudau, KL and Ntobeng, LR and Masindi, V and Tekere, M}, title = {Antibiotic resistance genes profile of selected drinking water treatment plants in South Africa as impacted by different treatment stages.}, journal = {Microbiology resource announcements}, volume = {14}, number = {2}, pages = {e0093424}, pmid = {39699218}, issn = {2576-098X}, support = {2022/2023-00801//Water Research Commission (WRC)/ ; }, abstract = {Water treatment plants treat raw water making it suitable for consumption. Treatment stages are linked to the quality status of the treatment. The classes of antibiotic resistance genes as impacted by treatment stages remain under explored. We report the classes of antibiotic resistance genes (ARGs) from shotgun metagenomes as influenced by treatment stages.}, } @article {pmid39699190, year = {2025}, author = {Prattico, C and Gonzalez, E and Dridi, L and Jazestani, S and Low, KE and Abbott, DW and Maurice, CF and Castagner, B}, title = {Identification of novel fructo-oligosaccharide bacterial consumers by pulse metatranscriptomics in a human stool sample.}, journal = {mSphere}, volume = {10}, number = {1}, pages = {e0066824}, pmid = {39699190}, issn = {2379-5042}, support = {DO-16//UofA | Canadian Glycomics Network (GlycoNet)/ ; PJT-437944//Canadian Government | Canadian Institutes of Health Research (CIHR)/ ; }, mesh = {Humans ; *Feces/microbiology ; *Gastrointestinal Microbiome ; *Oligosaccharides/metabolism ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Prebiotics ; Gene Expression Profiling ; Metagenomics/methods ; Fermentation ; RNA, Ribosomal, 16S/genetics ; Transcriptome ; Dietary Fiber/metabolism ; }, abstract = {UNLABELLED: Dietary fibers influence the composition of the human gut microbiota and directly contribute to its downstream effects on host health. As more research supports the use of glycans as prebiotics for therapeutic applications, the need to identify the gut bacteria that metabolize glycans of interest increases. Fructo-oligosaccharide (FOS) is a common diet-derived glycan that is fermented by the gut microbiota and has been used as a prebiotic. Despite being well studied, we do not yet have a complete picture of all FOS-consuming gut bacterial taxa. To identify new bacterial consumers, we used a short exposure of microbial communities in a stool sample to FOS or galactomannan as the sole carbon source to induce glycan metabolism genes. We then performed metatranscriptomics, paired with whole metagenomic sequencing, and 16S amplicon sequencing. The short incubation was sufficient to cause induction of genes involved in carbohydrate metabolism, like carbohydrate-active enzymes (CAZymes), including glycoside hydrolase family 32 genes, which hydrolyze fructan polysaccharides like FOS and inulin. Interestingly, FOS metabolism transcripts were notably overexpressed in Blautia species not previously reported to be fructan consumers. We therefore validated the ability of different Blautia species to ferment fructans by monitoring their growth and fermentation in defined media. This pulse metatranscriptomics approach is a useful method to find novel consumers of prebiotics and increase our understanding of prebiotic metabolism by CAZymes in the gut microbiota.

IMPORTANCE: Complex carbohydrates are key contributors to the composition of the human gut microbiota and play an essential role in the microbiota's effects on host health. Understanding which bacteria consume complex carbohydrates, or glycans, provides a mechanistic link between dietary prebiotics and their beneficial health effects, an essential step for their therapeutic application. Here, we used a pulse metatranscriptomics pipeline to identify bacterial consumers based on glycan metabolism induction in a human stool sample. We identified novel consumers of fructo-oligosaccharide among Blautia species, expanding our understanding of this well-known glycan. Our approach can be applied to identify consumers of understudied glycans and expand our prebiotic repertoire. It can also be used to study prebiotic glycans directly in stool samples in distinct patient populations to help delineate the prebiotic mechanism.}, } @article {pmid39699181, year = {2025}, author = {Olson, N and Lamar, F and Mucache, H and Fafetine, J and Saíde, J and Milisse, A and Brito, DRA and Jesser, KJ and Levy, K and Freeman, MC and Nadimpalli, ML}, title = {Farm-to-fork changes in poultry microbiomes and resistomes in Maputo City, Mozambique.}, journal = {mSystems}, volume = {10}, number = {1}, pages = {e0103724}, pmid = {39699181}, issn = {2379-5077}, support = {5T32ES012870//HHS | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; T32AI138952//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; T32 ES007032/ES/NIEHS NIH HHS/United States ; 5T32ES007032-37, 5T32ES012870-15//HHS | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; T32 AI138952/AI/NIAID NIH HHS/United States ; OPP 1189339//Bill and Melinda Gates Foundation (GF)/ ; T32 ES012870/ES/NIEHS NIH HHS/United States ; //Rollins School of Public Health Dean's Pilot and Innovation Award/ ; }, mesh = {Animals ; Mozambique/epidemiology ; *Chickens/microbiology ; *Feces/microbiology ; Microbiota/genetics ; Farms ; Drug Resistance, Bacterial/genetics ; Humans ; Poultry/microbiology ; Gastrointestinal Microbiome/genetics ; Bacteria/genetics/drug effects/isolation & purification/classification ; Metagenomics ; }, abstract = {UNLABELLED: Increasing demand for poultry has spurred poultry production in low- and middle-income countries like Mozambique. Poultry may be an important source of foodborne, antimicrobial-resistant bacteria to consumers in settings with limited water, sanitation, and hygiene infrastructure. The Chicken Exposures and Enteric Pathogens in Children Exposed through Environmental Pathways (ChEEP ChEEP) study was conducted in Maputo City, Mozambique from 2019 to 2021 to quantify enteric pathogen exposures along the supply chain for commercial and local (i.e., scavenger) chicken breeds. Here, we performed metagenomic sequencing of total DNA from banked ChEEP ChEEP samples to characterize fecal and carcass microbiomes and resistome diversity between chicken breeds and along the supply chain. Fecal samples (n = 26) were collected from commercial and local chickens at production sites and markets and carcass (n = 49) and rinse bucket samples (n = 26) from markets. We conducted taxonomic profiling and identified antimicrobial resistance genes (ARGs) from metagenomic sequence data, focusing especially on potential human pathogens and "high-risk" ARGs. We estimated alpha diversity for each sample and compared by site and breed. We estimated Bray-Curtis dissimilarity between samples and examined clustering. We found that commercial and local chickens harbored distinct fecal potential pathogens and resistomes at production and market sites. Many potentially pathogenic bacteria and ARGs present in chicken fecal samples are also present on carcasses sold to consumers. Finally, commercial chicken carcasses contain high-risk ARGs that are not necessarily introduced from chicken feces. These results indicate markets are an important site of exposure to potentially pathogenic bacteria and high-risk ARGs.

IMPORTANCE: While chicken eggs and meat are a critical protein source in low-income settings, antibiotics are routinely fed to chickens with consequences for selection of antimicrobial resistance. Evaluating how poultry gut bacterial communities, including potential human pathogens and high-risk antimicrobial resistance genes, differ from farm to market could help identify where to target interventions to minimize transmission risks to human populations. In this study in Maputo City, Mozambique, we found compositional differences between commercial and local chicken breeds at production and market sites. We also found that while all potentially pathogenic bacteria and many high-risk antimicrobial resistance genes persisted from production and market through processing, some resistance genes were detected on carcass samples only after processing, suggesting human or environmental contamination is occurring within markets. Overall, our findings indicate that open-air markets may represent a critical juncture for human exposures to pathogens and antimicrobial resistance genes from poultry and poultry products.}, } @article {pmid39698321, year = {2024}, author = {Lyu, J and Huang, J and Huang, J and Hu, H and Wang, Q and Ding, H and Li, H and Fang, X and Zhang, W}, title = {Rising challenges in periprosthetic joint infections: a focus on rare pathogens and their clinical implications.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1451398}, pmid = {39698321}, issn = {2235-2988}, mesh = {Humans ; *Prosthesis-Related Infections/microbiology ; Male ; Female ; Aged ; Retrospective Studies ; Middle Aged ; *Arthroplasty, Replacement, Knee/adverse effects ; *Anti-Bacterial Agents/therapeutic use ; *Arthroplasty, Replacement, Hip/adverse effects ; Risk Factors ; Treatment Outcome ; Bacteria/isolation & purification/classification/genetics ; Aged, 80 and over ; Coinfection/microbiology ; C-Reactive Protein/analysis ; }, abstract = {OBJECTIVES: The study aimed to evaluate differences in clinical characteristics and treatment outcomes of periprosthetic joint infection (PJI) attributed to rare versus common pathogens.

METHODS: Data on PJI patients who underwent hip or knee arthroplasty at our center from April 2013 to December 2022 were retrospectively collected. Among the 219 enrolled patients, we compared 32 cases of PJI caused by rare pathogens with 187 controls of PJI caused by common pathogens, analyzing demographic information, clinical characteristics, and treatment outcomes.

RESULTS: In demographic data, the Charlson comorbidity index and preoperative invasive procedures were identified as risk factors for rare pathogen PJI. Clinically, the rare pathogen cohort exhibited a significantly higher rate of sinus tract formation compared to those with common bacteria PJI. In terms of laboratory findings, the mean serum C-reactive protein (CRP) was significantly lower in the rare pathogen group. This cohort also had a significantly lower culture positivity rate and a higher rate of polymicrobial co-infections. The median hospital stay was statistically longer for rare pathogen PJI cases than for those with common bacteria PJI. Furthermore, the rare pathogen group required longer antibiotic treatments and had higher rates of antibiotic-related adverse events, although reinfection rates did not significantly differ.

CONCLUSION: PJI caused by rare pathogens exhibits distinct clinical presentations. With advances in diagnostic techniques such as metagenomic next-generation sequencing (mNGS), optimized culture methods, and an interdisciplinary approach facilitating early targeted treatment, rare pathogen PJIs may achieve outcomes comparable to those of typical cases.}, } @article {pmid39698295, year = {2024}, author = {Bovio-Winkler, P and Cabezas, A and Etchebehere, C}, title = {Unveiling the hidden diversity and functional role of Chloroflexota in full-scale wastewater treatment plants through genome-centric analyses.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae050}, pmid = {39698295}, issn = {2730-6151}, abstract = {The phylum Chloroflexota has been found to exhibit high abundance in the microbial communities from wastewater treatment plants (WWTPs) in both aerobic and anaerobic systems. However, its metabolic role has not been fully explored due to the lack of cultured isolates. To address this gap, we use publicly available metagenome datasets from both activated sludge (AS) and methanogenic (MET) full-scale wastewater treatment reactors to assembled genomes. Using this strategy, 264 dereplicated, medium- and high-quality metagenome-assembled genomes (MAGs) classified within Chloroflexota were obtained. Taxonomic classification revealed that AS and MET reactors harbored distinct Chloroflexota families. Nonetheless, the majority of the annotated MAGs (166 MAGs with >85% completeness and < 5% contamination) shared most of the metabolic potential features, including the ability to degrade simple sugars and complex polysaccharides, fatty acids and amino acids, as well as perform fermentation of different products. While Chloroflexota MAGs from MET reactors showed the potential for strict fermentation, MAGs from AS harbored the potential for facultatively aerobic metabolism. Metabolic reconstruction of Chloroflexota members from AS unveiled their versatile metabolism and suggested a primary role in hydrolysis, carbon removal and involvement in nitrogen cycling, thus establishing them as fundamental components of the ecosystem. Microbial reference genomes are essential resources for understanding the potential functional role of uncultured organisms in WWTPs. Our study provides a comprehensive genome catalog of Chloroflexota for future analyses aimed at elucidating their role in these ecosystems.}, } @article {pmid39697828, year = {2024}, author = {Guo, Y and Cao, Y and He, B and Dong, X and Bi, M and Wang, X and Gao, T and Liu, X and Wang, K and Wang, Y and Zhang, H and Sun, Y and Gao, W and Zhang, Y and Jia, Z}, title = {The First Case of Serogroup Y Neisseria meningitidis and An Expanded Investigation of Healthy Carriers - Shijiazhuang City, Hebei Province, China, 2023.}, journal = {China CDC weekly}, volume = {6}, number = {47}, pages = {1242-1247}, pmid = {39697828}, issn = {2096-7071}, abstract = {Neisseria meningitidis (Nm) is a bacterial pathogen that causes meningococcal disease. Serogroups A, B, C, W, X, and Y account for the vast majority of cases. However, invasive meningococcal disease (IMD) caused by NmY is rare in China and has been reported only in Tianjin, Guangdong, Shanghai, and Hunan provinces and cities.

WHAT IS ADDED BY THIS REPORT?: This article reports the first case of NmY:cc23 meningococcal disease in Hebei Province, confirmed by metagenomic sequencing. We also present the results of expanded surveillance in the healthy population associated with the case.

NmY has caused multiple case reports across China, especially in southern cities. The first report of a serogroup Y case in Hebei Province, and the carriage rate in the healthy population, reminds us to increase public health attention on Nm. The results of this study suggest that surveillance of the Nm carriage rate among healthy carriers and serogroup changes in Nm should be strengthened.}, } @article {pmid39697658, year = {2024}, author = {Yu, J and Yang, S and Zhang, X and Liu, X and Tang, X and Wang, L and Chen, J and Luo, H and Liu, C and Song, C}, title = {Integrating metagenomics and culturomics to uncover the soil bacterial community in Asparagus cochinchinensis cultivation.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1467864}, pmid = {39697658}, issn = {1664-302X}, abstract = {Asparagus cochinchinensis is a medicinal plant in China, which has gained attention owing its protective effect in human health. However, there are seldom studies to systematically reveal the rhizosphere bacterial community of A. cochinchinensis. In this study, we employed metagenomics and culturomics to analyze the bacterial community composition and diversity in continuous rhizosphere soil of A. cochinchinensis. Meanwhile, we assessed the effect of soil physicochemical properties on the bacterial community. Results showed that the most abundant TAXA is a taxon belonging to the family Streptomycetaceae, the genus Mycobacterium and the species Oligotropha carboxidovorans. The bacterial communities across various areas were similar. Significant differences of exchangeable magnesium and available phosphorus level were observed between three groups. Furthermore, bacterial community structure correlated closely with soil physicochemical properties. Additionally, a total of 103 strains were isolated and identified, representing 28 species. Based on this study, the rhizosphere bacterial community of A. cochinchinensis might influence its growth and development. The rhizosphere strains were isolated and their function request further investigation. This study firstly revealed the bacterial community in the A. cochinchinensis rhizosphere soil, providing valuable references for its quality improvement in practical cultivation process.}, } @article {pmid39697332, year = {2024}, author = {Guo, Y and Zhang, J and Chai, R and Yang, Y and Tian, K and Shi, G and Zhang, L}, title = {Cerebral schistosomiasis in a 3-year-old girl due to Schistosoma japonicum: a case report.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1502627}, pmid = {39697332}, issn = {1664-3224}, mesh = {Humans ; Female ; *Schistosoma japonicum ; Child, Preschool ; Animals ; *Schistosomiasis japonica/diagnosis/drug therapy/parasitology ; *Praziquantel/therapeutic use ; Magnetic Resonance Imaging ; Neuroschistosomiasis/diagnosis/drug therapy ; Brain/parasitology/diagnostic imaging/pathology ; Anthelmintics/therapeutic use ; Treatment Outcome ; }, abstract = {INTRODUCTION: Cerebral schistosomiasis is a rare but severe manifestation of Schistosoma japonicum infection, often leading to significant neurological impairment. This case report details the clinical presentation, diagnostic challenges, and treatment of a 3-year-old girl with cerebral schistosomiasis in Sichuan, China.

CASE DESCRIPTION: A 3-year-old girl from a rural area in Sichuan, China, presented with a 3-month history of unstable walking, left facial paralysis, drowsiness, and intermittent fever. Brain MRI revealed giant polycystic lesions in the right temporal, parietal, and occipital lobes, suggestive of an abscess with ependymitis. Despite no history of travel to endemic areas or known freshwater exposure, the patient was diagnosed with cerebral schistosomiasis due to Schistosoma japonicum based on histological examination and metagenomic next-generation sequencing (mNGS) of brain tissue obtained through surgery. The patient underwent surgical resection of the lesions and received two courses of praziquantel combined with corticosteroids and anticonvulsants. Despite residual left-sided hemiplegia, her cognitive function remained comparable to that of her peers, and no recurrence of the disease was observed over three years of follow-up.

CONCLUSION: This case underscores the diagnostic challenges of cerebral schistosomiasis, particularly in non-endemic areas or in the absence of a clear history of freshwater exposure. Early surgical intervention combined with praziquantel treatment can lead to favorable outcomes, even in severe cases with extensive brain involvement.}, } @article {pmid39697208, year = {2024}, author = {Zhou, Y and Zou, Y and Zhou, L and Wei, H and Zou, YW and Guo, XR and Ye, YQ and Li, N and Lu, Y}, title = {Acute respiratory distress syndrome caused by Chlamydia psittaci: a case report and literature review.}, journal = {Frontiers in medicine}, volume = {11}, number = {}, pages = {1418241}, pmid = {39697208}, issn = {2296-858X}, abstract = {BACKGROUND: Psittacosis is a zoonotic disease with a low incidence rate and a lack of specificity in clinical manifestations, making it prone to be missed, misdiagnosed, and even cause delayed treatment for patients. Metagenomic next-generation sequencing (mNGS) was successfully performed for the diagnosis of a young patient with psittacosis progressing to acute respiratory distress syndrome (ARDS), and precisely targeted antibiotic treatment was promptly administered. Additionally, a comprehensive review was conducted on 68 cases of psittacosis complicated with ARDS, with the goal of improving the clinical awareness of this disease.

CASE PRESENTATION: This study reports a 37-year-old young female who was infected with Chlamydia psittaci (C. psittaci) after contact with parrots and eventually developed ARDS. The patient initially developed fever and sore throat, followed by cough and expectoration. Despite receiving empirical anti-infection treatment, the condition continued to progress rapidly, and severe dyspnea developed within a short period of time. She was subsequently transferred to the intensive care unit (ICU) and underwent tracheal intubation and mechanical ventilation due to acute respiratory failure. After the DNA sequence of C. psittaci in bronchoalveolar lavage fluid (BALF) was detected through mNGS, the patient received targeted antibiotic treatment with doxycycline and moxifloxacin, and her clinical symptoms gradually improved.

CONCLUSION: Epidemiological investigations and the application of mNGS are crucial for the early identification and diagnosis of psittacosis. For suspected psittacosis patients, the application of mNGS technology could promote early identification of pathogens and targeted antimicrobial therapy, which might improve patient prognosis. In addition, young psittacosis patients without underlying disease should also be vigilant about the possibility of developing severe cases.}, } @article {pmid39696809, year = {2024}, author = {Dianat, M and Straaten, S and Maritato, A and Wibberg, D and Busche, T and Blank, LM and Ebert, BE}, title = {Exploration of In Situ Extraction for Enhanced Triterpenoid Production by Saccharomyces cerevisiae.}, journal = {Microbial biotechnology}, volume = {17}, number = {12}, pages = {e70061}, pmid = {39696809}, issn = {1751-7915}, support = {031B0356B//Bundesministerium für Bildung und Forschung/ ; }, mesh = {*Saccharomyces cerevisiae/metabolism/genetics ; *Triterpenes/metabolism ; *Fermentation ; Metabolic Engineering/methods ; Chemical Fractionation/methods ; }, abstract = {Plant-derived triterpenoids are in high demand due to their valuable applications in cosmetic, nutraceutical, and pharmaceutical industries. To meet this demand, microbial production of triterpenoids is being developed for large-scale production. However, a prominent limitation of microbial synthesis is the intracellular accumulation, requiring cell disruption during downstream processing. Destroying the whole-cell catalyst drives up production costs and limits productivity and product yield per cell. Here, in situ product extraction of triterpenoids into a second organic phase was researched to address this limitation. An organic solvent screening identified water-immiscible isopropyl myristate as a suitable in situ extractant, enabling extraction of up to 90% of total triterpenoids from engineered Saccharomyces cerevisiae. Combining isopropyl myristate and β-cyclodextrins improved extraction efficiency. In a first configuration, repeated batch fermentation with sequential product extraction and cell recycling resulted in 1.8 times higher production than a reference fermentation without in situ product extraction. In the second configuration, yeast cells were in contact with the second organic phase throughout a fed-batch fermentation to continuously extract triterpenoids. This resulted in 90% product extraction and an extended production phase. Further improvement of triterpenoid production was not achieved due to microbial host limitations uncovered through omics analyses.}, } @article {pmid39696719, year = {2024}, author = {Herbold, CW and Noell, SE and Lee, CK and Vickers, CJ and Stott, MB and Eisen, JA and McDonald, IR and Cary, SC}, title = {Nutritional niches of potentially endemic, facultatively anaerobic heterotrophs from an isolated Antarctic terrestrial hydrothermal refugium elucidated through metagenomics.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {104}, pmid = {39696719}, issn = {2524-6372}, support = {UOW0802//Marsden Fund/ ; UOW0802//Marsden Fund/ ; }, abstract = {BACKGROUND: Tramway Ridge, a geothermal Antarctic Specially Protected Area (elevation 3340 m) located near the summit of Mount Erebus, is home to a unique community composed of cosmopolitan surface-associated micro-organisms and abundant, poorly understood subsurface-associated microorganisms. Here, we use shotgun metagenomics to compare the functional capabilities of this community to those found elsewhere on Earth and to infer in situ diversity and metabolic capabilities of abundant subsurface taxa.

RESULTS: We found that the functional potential in this community is most similar to that found in terrestrial hydrothermal environments (hot springs, sediments) and that the two dominant organisms in the subsurface carry high rates of in situ diversity which was taken as evidence of potential endemicity. They were found to be facultative anaerobic heterotrophs that likely share a pool of nitrogenous organic compounds while specializing in different carbon compounds.

CONCLUSIONS: Metagenomic insights have provided a detailed understanding of the microbe-based ecosystem found in geothermally heated fumaroles at Tramway Ridge. This approach enabled us to compare Tramway Ridge with other microbial systems, identify potentially endemic taxa and elucidate the key metabolic pathways that may enable specific organisms to dominate the ecosystem.}, } @article {pmid39696556, year = {2024}, author = {Amano, Y and Sachdeva, R and Gittins, D and Anantharaman, K and Lei, S and Valentin-Alvarado, LE and Diamond, S and Beppu, H and Iwatsuki, T and Mochizuki, A and Miyakawa, K and Ishii, E and Murakami, H and Jaffe, AL and Castelle, C and Lavy, A and Suzuki, Y and Banfield, JF}, title = {Diverse microbiome functions, limited temporal variation and substantial genomic conservation within sedimentary and granite rock deep underground research laboratories.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {105}, pmid = {39696556}, issn = {2524-6372}, support = {JPJ007597//The Ministry of Economy, Trade and Industry of Japan/ ; 19K05342//the Japan Society for the Promotion of Science/ ; OCE2049478//National Science Foundation/ ; DE-AC02-05CH11231//the Watershed Function Scientific Focus Area funded by the U.S. Department of Energy/ ; 2230766//NSF "Four Networks for Geologic Hydrogen Storage"/ ; }, abstract = {BACKGROUND: Underground research laboratories (URLs) provide a window on the deep biosphere and enable investigation of potential microbial impacts on nuclear waste, CO2 and H2 stored in the subsurface. We carried out the first multi-year study of groundwater microbiomes sampled from defined intervals between 140 and 400 m below the surface of the Horonobe and Mizunami URLs, Japan.

RESULTS: We reconstructed draft genomes for > 90% of all organisms detected over a four year period. The Horonobe and Mizunami microbiomes are dissimilar, likely because the Mizunami URL is hosted in granitic rock and the Horonobe URL in sedimentary rock. Despite this, hydrogen metabolism, rubisco-based CO2 fixation, reduction of nitrogen compounds and sulfate reduction are well represented functions in microbiomes from both URLs, although methane metabolism is more prevalent at the organic- and CO2-rich Horonobe URL. High fluid flow zones and proximity to subsurface tunnels select for candidate phyla radiation bacteria in the Mizunami URL. We detected near-identical genotypes for approximately one third of all genomically defined organisms at multiple depths within the Horonobe URL. This cannot be explained by inactivity, as in situ growth was detected for some bacteria, albeit at slow rates. Given the current low hydraulic conductivity and groundwater compositional heterogeneity, ongoing inter-site strain dispersal seems unlikely. Alternatively, the Horonobe URL microbiome homogeneity may be explained by higher groundwater mobility during the last glacial period. Genotypically-defined species closely related to those detected in the URLs were identified in three other subsurface environments in the USA. Thus, dispersal rates between widely separated underground sites may be fast enough relative to mutation rates to have precluded substantial divergence in species composition. Species overlaps between subsurface locations on different continents constrain expectations regarding the scale of global subsurface biodiversity.

CONCLUSIONS: Our analyses reveal microbiome stability in the sedimentary rocks and surprising microbial community compositional and genotypic overlap over sites separated by hundreds of meters of rock, potentially explained by dispersal via slow groundwater flow or during a prior hydrological regime. Overall, microbiome and geochemical stability over the study period has important implications for underground storage applications.}, } @article {pmid39695983, year = {2024}, author = {Su, L and Guo, J and Shi, W and Tong, W and Li, X and Yang, B and Xiang, Z and Qin, C}, title = {Metagenomic analysis reveals the community composition of the microbiome in different segments of the digestive tract in donkeys and cows: implications for microbiome research.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {530}, pmid = {39695983}, issn = {1471-2180}, support = {2021YFF0702900//National Key Research and Development Program of China/ ; 2023-PT180-01//Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences/ ; 2021-I2M-1-039, 2021-I2M-1-034//CAMS initiative for Innovative Medicine of China/ ; }, mesh = {Animals ; *Equidae/microbiology ; Cattle/microbiology ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; *Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Gastrointestinal Tract/microbiology ; Sequence Analysis, DNA/methods ; Metagenome ; Bacteroidetes/genetics/isolation & purification/classification ; }, abstract = {INTRODUCTION: The intestinal microbiota plays a crucial role in health and disease. This study aimed to assess the composition and functional diversity of the intestinal microbiota in donkeys and cows by examining samples collected from different segments of the digestive tract using two distinct techniques: direct swab sampling and faecal sampling.

RESULTS: In this study, we investigated and compared the effects of multiple factors on the composition and function of the intestinal microbial community. Approximately 300 GB of metagenomic sequencing data from 91 samples obtained from various segments of the digestive tract were used, including swabs and faecal samples from monogastric animals (donkeys) and polygastric animals (cows). We assembled 4,004,115 contigs for cows and 2,938,653 contigs for donkeys, with a total of 9,060,744 genes. Our analysis revealed that, compared with faecal samples, swab samples presented a greater abundance of Bacteroidetes, whereas faecal samples presented a greater abundance of Firmicutes. Additionally, we observed significant variations in microbial composition among different digestive tract segments in both animals. Our study identified key bacterial species and pathways via different methods and provided evidence that multiple factors can influence the microbial composition. These findings provide new insights for the accurate characterization of the composition and function of the gut microbiota in microbiome research.

CONCLUSIONS: The results obtained by both sampling methods in the present study revealed that the composition and function of the intestinal microbiota in donkeys and cows exhibit species-specific and region-specific differences. These findings highlight the importance of using standardized sampling protocols to ensure accurate and consistent characterization of the intestinal microbiota in various animal species. The implications and underlying mechanisms of these associations provide multiple perspectives for future microbiome research.}, } @article {pmid39695885, year = {2024}, author = {Galic, I and Bez, C and Bertani, I and Venturi, V and Stankovic, N}, title = {Herbicide-treated soil as a reservoir of beneficial bacteria: microbiome analysis and PGP bioinoculants in maize.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {107}, pmid = {39695885}, issn = {2524-6372}, support = {451-03-47/2023-01/ 200042//Ministarstvo Prosvete, Nauke i Tehnološkog Razvoja/ ; 451-03-47/2023-01/ 200042//Ministarstvo Prosvete, Nauke i Tehnološkog Razvoja/ ; Research and Training Grant 1818//FEMS/ ; }, abstract = {BACKGROUND: Herbicides are integral to agricultural weed management but can adversely affect non-target organisms, soil health, and microbiome. We investigated the effects of herbicides on the total soil bacterial community composition using 16S rRNA gene amplicon community profiling. Further, we aimed to identify herbicide-tolerant bacteria with plant growth-promoting (PGP) capabilities as a mitigative strategy for these negative effects, thereby promoting sustainable agricultural practices.

RESULTS: A bacterial community analysis explored the effects of long-term S-metolachlor application on soil bacterial diversity, revealing that the herbicide's impact on microbial communities is less significant than the effects of temporal factors (summer vs. winter) or agricultural practices (continuous maize cultivation vs. maize-winter wheat rotation). Although S-metolachlor did not markedly alter the overall bacteriome structure in our environmental context, the application of enrichment techniques enabled the selection of genera such as Pseudomonas, Serratia, and Brucella, which were rare in metagenome analysis of soil samples. Strain isolation revealed a rich source of herbicide-tolerant PGP bacteria within the culturable microbiome fraction, termed the high herbicide concentration tolerant (HHCT) bacterial culture collection. Within the HHCT collection, we isolated 120 strains that demonstrated significant in vitro PGP and biocontrol potential, and soil quality improvement abilities. The most promising HHCT isolates were combined into three consortia, each exhibiting a comprehensive range of plant-beneficial traits. We evaluated the efficacy and persistence of these multi-strain consortia during 4-week in pot experiments on maize using both agronomic parameters and 16S rRNA gene community analysis assessing early-stage plant development, root colonization, and rhizosphere persistence. Notably, 7 out of 10 inoculated consortia partners successfully established themselves and persisted in the maize root microbiome without significantly altering host root biodiversity. Our results further evidenced that all three consortia positively impacted both seed germination and early-stage plant development, increasing shoot biomass by up to 47%.

CONCLUSIONS: Herbicide-treated soil bacterial community analysis revealed that integrative agricultural practices can suppress the effects of continuous S-metolachlor application on soil microbial diversity and stabilize microbiome fluctuations. The HHCT bacterial collection holds promise as a source of beneficial bacteria that promote plant fitness while maintaining herbicide tolerance.}, } @article {pmid39695840, year = {2024}, author = {Gomathinayagam, S and Kanagalingam, S and Chandrasekaran, S and Krishnan, T and Kodiveri Muthukaliannan, G}, title = {Millennial-scale microbiome analysis reveals ancient antimicrobial resistance conserved despite modern selection pressures.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {110}, pmid = {39695840}, issn = {2524-6372}, support = {AMR/Fellowship/20/2022-ECD-lI//Indian Council of Medical Research/ ; }, abstract = {BACKGROUND: Antimicrobial resistance presents a formidable challenge, yet its existence predates the introduction of antibiotics. Our study delves into the presence of antimicrobial resistance genes (ARGs) in ancient permafrost microbiomes, comparing them with contemporary soil and pristine environments. Majority of the samples are from regions around Beringia, encompassing parts of Russia and Alaska, with only one sample originating from the Tien Shan Mountain range in Kyrgyzstan.

RESULTS: From over 2.3 tera basepairs of raw metagenomic data, retrieved from samples ranging in age from approximately 7,000 years to 1.1 million years, we assembled about 1.3 billion metagenomic contigs and explored the prevalence of ARGs within them. Our findings reveal a diverse array of ARGs in ancient microbiomes, akin to contemporary counterparts. On average, we identified 2 ARGs per rRNA gene in ancient samples. Actinomycetota, Bacillota, and several thermophiles were prominent carriers of ARGs in Chukochi and Kamchatkan samples. Conversely, ancient permafrost from the Tien Shan Mountain range exhibited no Thermophiles or Actinomycetota carrying ARGs. Both ancient and contemporary microbiomes showcased numerous divergent ARGs, majority of which have identity between 40 and 60% to genes in antibiotic resistance gene databases. To study the selection pressure on ARGs, we performed dN/dS analysis specifically on antibiotic inactivation-type ARGs, which exhibited purifying selection compared to contemporary genes.

CONCLUSION: Antibiotic resistance has existed throughout microbial evolution and will likely persist, as microbes have the capacity to develop and retain resistance genes through evolutionary processes. The classes of antimicrobial resistance genes profiled and the function of antibiotic-inactivating enzymes from ancient permafrost microbiomes do not seem to be very different from the genes found in the antibiotic era. Additionally, we retrieved 359 putative complete viruses from ancient microbiomes and none of them harboured any ARGs.}, } @article {pmid39695397, year = {2024}, author = {Wang, Y and Xiang, Y and Lei, C and Zheng, X and Wu, W and Zhang, Z and Qu, X}, title = {Liver abscess and splenic infarction due to Yersinia pseudotuberculosis bloodstream infection: a case report.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {1415}, pmid = {39695397}, issn = {1471-2334}, mesh = {Humans ; Male ; Adult ; *Yersinia pseudotuberculosis/isolation & purification/genetics ; *Yersinia pseudotuberculosis Infections/diagnosis/microbiology/drug therapy ; *Splenic Infarction/microbiology ; *Liver Abscess/microbiology ; Multiple Organ Failure ; Anti-Bacterial Agents/therapeutic use ; Bacteremia/microbiology/diagnosis/drug therapy ; Tomography, X-Ray Computed ; }, abstract = {BACKGROUND: Yersinia pseudotuberculosis is an emerging zoonotic intestinal pathogen primarily transmitted through contaminated food and water. Infections caused by Yersinia pseudotuberculosis are typically self-limiting, often presenting as gastroenteritis or "pseudoappendicitis," which is characterized by fever and abdominal pain. Although bloodstream infections with Yersinia pseudotuberculosis are rare, they can lead to multiple distant sites of infection, including abscesses in the liver, spleen, and kidneys, as well as in the hip and knee joints, particularly in individuals with underlying immunodeficiency.

CASE PRESENTATION: We report the case of a 40-year-old male patient who was admitted to the intensive care unit (ICU) with intermittent fever lasting for five days, followed by exacerbation of abdominal pain and distension one day after ingesting contaminated food. Upon admission, the patient exhibited severe hypotension, which rapidly progressed to signs of liver and kidney failure, ultimately leading to multiple organ dysfunction syndrome (MODS). Notably, abdominal computed tomography (CT) revealed evidence of a liver abscess and splenic infarction. The treatment regimen included fluid resuscitation, broad-spectrum antibiotics, vasopressors, continuous renal replacement therapy (CRRT), and plasma exchange. Blood cultures along with metagenomic next-generation sequencing (mNGS) confirmed an infection caused by Yersinia pseudotuberculosis. After 17 days in the ICU, the patient was transferred to the infectious disease department for an additional 14 days of treatment before being discharged. Three months post-discharge, follow-up visits indicated that the patient was in good health.

CONCLUSIONS: To the best of our knowledge, this case represents a rare instance of multiple organ dysfunction syndrome (MODS), liver abscess, and splenic infarction resulting from Yersinia pseudotuberculosis infection. The identification of the pathogen was facilitated by blood culture and metagenomic next-generation sequencing (mNGS) of blood samples. The administration of broad-spectrum antibiotics, along with active support for organ function, ultimately contributed to the patient's recovery.

CLINICAL TRIAL NUMBER: No applicable.}, } @article {pmid39695297, year = {2024}, author = {Conteville, LC and Silva, JVD and Andrade, BGN and Coutinho, LL and Palhares, JCP and Regitano, LCA}, title = {Recovery of metagenome-assembled genomes from the rumen and fecal microbiomes of Bos indicus beef cattle.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1385}, pmid = {39695297}, issn = {2052-4463}, mesh = {Animals ; Cattle/microbiology ; *Feces/microbiology ; *Metagenome ; *Rumen/microbiology ; *Phylogeny ; Gastrointestinal Microbiome ; Brazil ; Male ; Archaea/genetics/classification ; Bacteria/genetics/classification ; Microbiota ; }, abstract = {Nelore is a Bos indicus beef breed that is well-adapted to tropical environments and constitutes most of the world's largest commercial cattle herd: the Brazilian bovine herd. Despite its significance, microbial genome recovery from ruminant microbiomes has largely excluded representatives from Brazilian Nelore cattle. To address this gap, this study presents a comprehensive dataset of microbial genomes recovered from the rumen and feces of 52 Brazilian Nelore bulls. A total of 1,526 non-redundant metagenome-assembled genomes (MAGs) were recovered from their gastrointestinal tract, with 497 ruminal and 486 fecal classified as high-quality. Phylogenetic analysis revealed that the bacterial MAGs fall into 12 phyla, with Firmicutes and Bacteroidota being the most predominant, while all archaeal MAGs belong to the genus Methanobrevibacter. The exploration of these microbial genomes will provide valuable insights into the metabolic potential and functional roles of individual microorganisms within host-microbiome interactions, contributing to a better understanding of the microbiome's roles in bovine performance.}, } @article {pmid39695240, year = {2024}, author = {Shen, Y and An, Z and Xia, S and Ding, Q and Chen, K and Miao, Y and Wang, T and Zhong, J and Li, J and Wang, X and Wang, H}, title = {A multi-omics database of buffaloes from Yangtze valley reveals diversity of water buffalo (Bubalus bubalis).}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1375}, pmid = {39695240}, issn = {2052-4463}, support = {ZR2023QC252//Natural Science Foundation of Shandong Province (Shandong Provincial Natural Science Foundation)/ ; CARS-36//Earmarked Fund for China Agriculture Research System/ ; }, mesh = {*Buffaloes/genetics ; Animals ; Male ; China ; Transcriptome ; Metabolome ; Metagenome ; Rumen ; Multiomics ; }, abstract = {Asian water buffalo (Bubalus bubalis) is the fundamental livestock resource for local rural populations and holds a promising prospect of their milk and meat. Xuyi mountain (XYM) and Haizi (HZ) buffaloes from Yangtze valley comprises of species diversity of Asian water buffaloes. Current multi-omics enables identification of causal genes and elucidation of genetic regulatory mechanisms underlying complex traits in buffaloes. Here, we conducted the integrated analysis of metabolome and metagenome of rumen fluid, transcriptome and metabolome of blood, and whole genome sequence data from XYM (n = 7) and HZ (n = 10) male buffaloes. Our results revealed the apparent diversity of multi-layer omics profiles between two buffalo species. The built-up multi-omics database supports the discoveries of diversity in Asian water buffalo and potentially serves valuable resources for studying causal regulatory variants and their mechanisms.}, } @article {pmid39695203, year = {2024}, author = {Jeon, J and Park, Y and Lee, DH and Kim, JH and Jin, YK and Hong, JK and Lee, YM}, title = {Microbial profiling of the East Siberian Sea sediments using 16S rRNA gene and metagenome sequencing.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1350}, pmid = {39695203}, issn = {2052-4463}, mesh = {*Geologic Sediments/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Metagenome ; *Archaea/genetics/classification ; *Bacteria/genetics/classification ; Arctic Regions ; Microbiota ; Oceans and Seas ; Siberia ; }, abstract = {The Arctic Ocean is experiencing significant global warming, leading to reduced sea-ice cover, submarine permafrost thawing, and increased river discharge. The East Siberian Sea (ESS) undergoes more significant terrestrial inflow from coastal erosion and river runoff than other Arctic seas. Despite extensive research on environmental changes, microbial communities and their functions in the ESS, which are closely related to environmental conditions, remain largely unexplored. Here, we investigated microbial communities in ESS surface sediments spanning latitudes from 73°N to 77°N using 16S rRNA amplicon sequencing, and reconstructed 211 metagenome-assembled genomes (MAGs) using shotgun metagenome sequencing. Taxonomic analysis identified 209 bacterial MAGs, with the predominant phyla Pseudomonadota (n = 82), Actinobacteriota (n = 38), Desulfobacterota (n = 23), along with 2 archaeal MAGs of Thermoproteota. Notably, 86% of the MAGs (n = 183) could not be classified into known species, indicating the potential presence of novel and unidentified microorganisms in the ESS. This dataset provides invaluable information on the microbial diversity and ecological functions in the rapidly changing ESS.}, } @article {pmid39694980, year = {2024}, author = {Wang, S and Liu, Y and Li, Y and Gao, Y and Zou, Z and Xu, N and Song, Q and Liu, F and Song, Y and Wang, X and Fan, Z}, title = {Rapid, multiplex and automated detection of bacteria and fungi in endophthalmitis via a microfluidic real-time pcr system.}, journal = {Journal of ophthalmic inflammation and infection}, volume = {14}, number = {1}, pages = {64}, pmid = {39694980}, issn = {1869-5760}, abstract = {BACKGROUND: Endophthalmitis is an ophthalmologic emergency requiring accurate and rapid diagnosis for treatment. Currently, the diagnosis commonly relies on culture and molecular biology, which falls short of clinical rapid diagnosis. The purpose of this study was to evaluate the feasibility of a self-build Microfluidic Real-time Polymerase Chain Reaction (RT-PCR) System for rapidly identifying potential pathogens of endophthalmitis.

METHODS: This study included 22 patients who presented to Shenzhen Eye Hospital and the Ophthalmology Department of the Affiliated Hospital of Guizhou Medical University in China between January 2023 and March 2024. The samples were cultured using conventional methods and underwent Microfluidic RT-PCR and metagenomic next-generation sequencing (mNGS).

RESULTS: The Microfluidic RT-PCR System identified pathogens in 11 of 22 cases (50.00%), compared with 40.91% for microbiology culture. 14 cases (63.64%) had concordant results, and 5 cases were positive for the microfluidic system only. The agreements between culture and microfluidic system, as well as culture and mNGS were 100.00% (6/6) and 50.00% (3/6), respectively. The average waiting time for the microfluidic system was about 30 min if excepting DNA extraction time, which was much shorter than 2.88 days for culture and 1.57 days for mNGS.

CONCLUSION: The microfluidic-based RT-PCR system was preliminarily proved to be a sensitive, easy-to-operate, and rapid in-hospital technology. It is expected to become a rapid diagnostic platform for endophthalmitis.}, } @article {pmid39694283, year = {2025}, author = {Parde, D and Behera, M and Dash, RR}, title = {Assessment of reactor configurations and key factors for enhanced anammox-based nitrogen removal.}, journal = {Chemosphere}, volume = {370}, number = {}, pages = {143972}, doi = {10.1016/j.chemosphere.2024.143972}, pmid = {39694283}, issn = {1879-1298}, mesh = {*Nitrogen/metabolism ; *Bioreactors/microbiology ; *Waste Disposal, Fluid/methods ; *Wastewater/chemistry/microbiology ; Bacteria/metabolism/genetics ; Anaerobiosis ; Sewage/microbiology ; Oxidation-Reduction ; Biofilms ; Ammonium Compounds/metabolism ; Water Pollutants, Chemical/metabolism ; Carbon/metabolism ; }, abstract = {Wastewater treatment processes are continually evolving to meet stringent environmental standards while optimizing energy consumption and operational costs. With significant advantages over more traditional approaches, the anammox process has become a hopeful substitute for nitrogen removal. The objective of this work was to evaluate upflow anaerobic sludge blanket reactor (UASBR), moving bed biofilm reactor (MBBR), and sequential batch reactor (SBR) among diverse reactor configurations, in culturing anammox bacteria and achieving nitrogen removal efficiencies. Synthetic wastewater containing NH4[+]-N concentration and NO2[-]-N concentration of 80 ± 5 mg/L was introduced to the reactors, and observations were made for up to 150 days. This study found that the MBBR demonstrated superior anammox activity, achieving a total nitrogen removal efficiency (TNRE) of 94 ± 3%, SBR exhibited a TNRE of approximately 85 ± 3%, while UASB displayed TNRE of 73 ± 3%. The effect of varying carbon-to-nitrogen (C/N) ratios on nitrogen removal efficiencies was investigated, revealing a decrease in TNRE as the C/N ratio increased from 3 to 8. This study demonstrated the enhancing and inhibitory effects of C/N ratio, NO2[-]-N, and Fe concentrations. It revealed that Fe concentrations between 1 and 5 mg/L increase specific anammox activity (SAA), while concentrations between 5 and 10 mg/L negatively impact it. Additionally, NO2[-]-N concentrations above 150 mg/L significantly reduce SAA. Furthermore, a 16S rRNA metagenomic analysis of MBBR sludge samples revealed the significant presence of Candidatus Brocadia bacteria, constituting 20.4% of the microbial community. This research highlights the potential of MBBR in fostering anammox reactions and achieving efficient nitrogen removal in wastewater treatment applications.}, } @article {pmid39694238, year = {2025}, author = {Vermeersch, AS and Ducatelle, R and Geldhof, P and Opsomer, G}, title = {Invited review: Udder cleft dermatitis in dairy cows.}, journal = {Journal of dairy science}, volume = {108}, number = {1}, pages = {59-72}, doi = {10.3168/jds.2024-25086}, pmid = {39694238}, issn = {1525-3198}, mesh = {Animals ; Cattle ; Female ; *Dermatitis/microbiology/pathology/veterinary ; Lactation ; *Mammary Glands, Animal/microbiology/pathology ; *Mastitis, Bovine/microbiology/pathology ; Risk Factors ; }, abstract = {Udder cleft dermatitis (UCD) is a common dermatological condition of the udder skin in dairy cows. It is generally considered to be a multifactorial disease, being described in a rather limited amount of literature. Its cow and within-herd prevalence widely ranges between studies depending on the study characteristics, environment and breed. Known risk factors include husbandry practices and environmental factors, such as freestall housing, the use of mattresses as cubicle bases, and footbathing. Cow-related elements, such as udder conformation, parity, and lactation parameters are well-known risk factors for developing UCD. Despite being associated with a high incidence of veterinary-treated clinical mastitis and culling due to udder disease, the SCC of the milk is not influenced by UCD. Severe UCD lesions are characterized by chronic and persistent, dysregulated inflammation accompanied by hampered skin healing and an impaired skin barrier. There is a decrease in microbial diversity followed by dysbiosis and a concomitant overgrowth of opportunistic bacteria negatively affecting beneficial commensal bacteria. Concurrently, a shift in virulence factors most likely contributes to the creation of an environment favorable to pathogens. Anecdotally, mange mites have been associated with UCD but current literature refutes this. The role of treponemes remains inconclusive. Multiomics analysis of both transcriptomic and metagenomic severe UCD datasets, revealed the negative interaction of the facultative pathogen Streptococcus pyogenes with microbiome-associated virulence factors and the patient's transcriptome. No efficient curative treatments nor prevention strategies have been identified so far, although alginogel products have been described to have a positive effect on the healing process of severe lesions. All in all, UCD is a painful skin disease for which an array of miscellaneous risk factors have been identified. For the first time we assimilate literature on prevalence and risk factors, and results from recent elementary studies that provide insights into the pathogenesis of this challenging disease.}, } @article {pmid39694116, year = {2025}, author = {Zhong, S and Yang, YN and Huo, JX and Sun, YQ and Zhao, H and Dong, XT and Feng, JY and Zhao, J and Wu, CM and Li, YG}, title = {Cyanidin-3-rutinoside from Mori Fructus ameliorates dyslipidemia via modulating gut microbiota and lipid metabolism pathway.}, journal = {The Journal of nutritional biochemistry}, volume = {137}, number = {}, pages = {109834}, doi = {10.1016/j.jnutbio.2024.109834}, pmid = {39694116}, issn = {1873-4847}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Lipid Metabolism/drug effects ; *Anthocyanins/pharmacology ; Male ; *Dyslipidemias/drug therapy/metabolism ; *Mice, Inbred C57BL ; Morus/chemistry ; Mice ; Diet, High-Fat/adverse effects ; Fruit/chemistry ; Liver/metabolism/drug effects ; }, abstract = {Dyslipidemia is responsible for pathologies of cardiovascular diseases and gut microbiota plays an essential role in lipid metabolism. Dietary supplementation is an important supplement to medicine in management of dyslipidemia. Mori Fructus is a popular Asia medical food with various pharmacological benefits including anti-hyperlipidemia. Cyanidin-3-rutinoside (C3R) is the main anthocyanin component in Mori Fructus, but the lipid-lowering effect and underlying mechanism of Mori Fructus-derived C3R remains unknown. In this study, we assessed the beneficial effect of Mori Fructus-derived C3R in HFD-induced hyperlipidemic mice and investigated its potential mechanism through 16S rRNA-based metagenomics and transcriptomics analysis. Our results showed that C3R from Mori Fructus significantly decreased serum lipid levels and attenuated hepatic damage induced by HFD. Analysis of the gut microbiota revealed that C3R altered the specific gut micorbiota but not changed its diversity. Among changed genera, Family_XIII_UCG-001 was significantly enriched by C3R, and it was positively associated with HDL-c, but negatively related with TC, TG, LDL-c, insulin and body weight. Transcriptomic analysis showed that C3R activates the lipid metabolism related pathways including MAPK signaling pathway, Rap1 signaling pathway, Ras signaling pathway and PI3K-Akt signaling pathway. Additionally, correlation analysis unraveled that C3R-enriched Family_XIII_UCG-001 was negatively associated with C3R-inhibited genes of Camk2a, Eef1a2, Gad1, Kif5a and Sv2b, which further positively related with TC, TG, LDL-c, insulin and body weight, but negatively associated with HDL-c. In sum, C3R may inhibit expression of immune-related genes by enriching the Family_XIII_UCG-001 genus, further ameliorating lipid metabolism disorders in HFD-challenged mice. This study provides an optional strategy for the daily management of dyslipidemia.}, } @article {pmid39694112, year = {2025}, author = {Li, D and Liang, W and Sun, X and Sun, W and Liu, G and Zeng, EY}, title = {Long-term stability of comammox Nitrospira under weakly acidic conditions and their acid-adaptive mechanisms revealed by genome-centric metatranscriptomics.}, journal = {Bioresource technology}, volume = {418}, number = {}, pages = {131986}, doi = {10.1016/j.biortech.2024.131986}, pmid = {39694112}, issn = {1873-2976}, mesh = {Hydrogen-Ion Concentration ; *Acids/metabolism ; Gene Expression Profiling ; Transcriptome/genetics ; Bacteria/metabolism/genetics ; Genome, Bacterial ; Adaptation, Physiological ; Oxidation-Reduction ; Ammonia/metabolism ; RNA, Ribosomal, 16S/genetics ; Nitrification ; Gene Expression Regulation, Bacterial ; }, abstract = {Despite their widespread presence in acidic environments, the stability and adaptative mechanisms of complete ammonia oxidization (comammox) bacteria remain poorly understood. In this three-year study, comammox Nitrospira consistently dominated both abundance and activity in an acidic nitrifying reactor (pH = 6.3-6.8), as revealed by metagenomic and cDNA-based 16S rRNA sequencing. Batch tests demonstrated their decent nitrification down to pH 4.7, while ceasing at pH 4.2. Genome-centric metatranscriptomics revealed that comammox Nitrospira upregulated a Rh-type ammonium transporter to enhance substrate uptake under acidic conditions. Active proton transport, mediated by NADH dehydrogenases and F-type ATPase, was identified as a primary strategy for maintaining pH homeostasis in comammox Nitrospira. Genes associated with carbon acquisition, chemotaxis, and DNA repair were upregulated at low pH, suggesting these processes play roles in acid adaptation. These findings enhance the understanding of ecological roles and adaptive mechanisms of comammox bacteria in acidic environments.}, } @article {pmid39694110, year = {2025}, author = {Nguyen, TV and Trinh, HP and Park, HD}, title = {Genome-based analysis reveals niche differentiation among Firmicutes in full-scale anaerobic digestion systems.}, journal = {Bioresource technology}, volume = {418}, number = {}, pages = {131993}, doi = {10.1016/j.biortech.2024.131993}, pmid = {39694110}, issn = {1873-2976}, mesh = {Anaerobiosis ; *Genome, Bacterial ; Firmicutes/genetics ; Phylogeny ; Metagenome ; Bioreactors/microbiology ; }, abstract = {Fermentative Firmicutes species are key players in anaerobic digestion; however, their niche differentiation based on carbohydrate utilization in full-scale systems remains unclear. In this study, we investigated niche differentiation among four major Firmicutes classes using a genome-centric approach, reconstructing 39 high-quality metagenome-assembled genomes. Limnochordia and Clostridia exhibited the broadest substrate versatility, utilizing 24% and 18% of the predicted substrates, respectively. Although common substrates were shared, each class demonstrated unique substrate preferences driven by distinct functional and metabolic differences. Limnochordia and Clostridia possess unique carbohydrate-active enzyme families, such as GH177 and CBM91, which enable xylan and arabinan degradation. Bacilli were abundant with the GH1 and GH3 families, which are critical for cellulose degradation. Overall, the Firmicutes classes showed low overlap in substrate use and functional profiles, confirming significant niche differentiation. Our results demonstrate that Firmicutes occupy distinct dietary niches supporting insights into bacterial coexistence in anaerobic digestion systems.}, } @article {pmid39694109, year = {2025}, author = {Dai, B and Zhou, J and Wang, Z and Yang, Y and Wang, Z and He, J and Xia, S and Rittmann, BE}, title = {Hydrazine promoted nitrite reduction in partial-denitrification by enhancing organic-substrate uptake and electron transport.}, journal = {Bioresource technology}, volume = {418}, number = {}, pages = {131991}, doi = {10.1016/j.biortech.2024.131991}, pmid = {39694109}, issn = {1873-2976}, mesh = {*Hydrazines/metabolism ; *Nitrites/metabolism ; Electron Transport ; *Oxidation-Reduction ; *Denitrification ; Bacteria/metabolism ; Bioreactors ; Wastewater/chemistry ; }, abstract = {Partial denitrification coupled with anammox is a promising approach for sustainable nitrogen removal from wastewater. However, this coupling can be influenced by hydrazine (N2H4) released by anammox bacteria. This study aimed to reveal how N2H4 regulates partial denitrification. Short-term batch experiments showed that 0.5 to 10 mg N/L of N2H4 promoted nitrite (NO2[-]) accumulation, likely by inhibiting the electron transfer from cyt c to nitrite reductase. However, long-term exposure to N2H4 (0.5 and 1 mg N/L) shifted the microbial community and increased NO2[-] reduction. This exposure enriched the genera OLB8, Thauera, and f_Rhodocyclaceae, and increased the abundance of genes involved in EPS formation, substrate transport and electron transport. The long-term outcome was more NO2[-] reduction to N2 and more substrate (COD) oxidation. While N2H4 benefits NO2[-] accumulation in short-term, the mechanism is not sustainable, highlighting the importance of minimizing N2H4 release for successful in such coupled nitrogen removal systems.}, } @article {pmid39693984, year = {2025}, author = {Wang, Y and Wu, SL and Wei, W and Wu, L and Huang, S and Dai, X and Ni, BJ}, title = {pH-dependent medium-chain fatty acid synthesis in waste activated sludge fermentation: Metabolic pathway regulation.}, journal = {Journal of environmental management}, volume = {373}, number = {}, pages = {123722}, doi = {10.1016/j.jenvman.2024.123722}, pmid = {39693984}, issn = {1095-8630}, mesh = {*Sewage/microbiology ; *Fermentation ; Hydrogen-Ion Concentration ; *Fatty Acids/metabolism ; Metabolic Networks and Pathways ; Bioreactors ; }, abstract = {Transforming waste activated sludge (WAS) into medium-chain fatty acids (MCFAs) via chain elongation (CE) technology is sustainable, yet pH effects on this process are poorly understood. In this study, semi-continuous flow experiments demonstrated that WAS degradation was highest under alkaline pH (10) but unsuitable for CE. Continuous output of MCFAs indicated that CE could be successfully performed under acidic pH (5) and neutral pH (7). Moreover, neutral pH optimized MCFAs production, achieving higher MCFAs yield (8.9 ± 1.2 g COD/L), MCFAs selectivity (51.2 ± 7.3%), and WAS degradation (25.4 ± 0.4%) than acidic pH. Further metagenomic and metatranscriptomic analysis revealed that the reverse β-oxidation cycle was the primary CE pathway. The absence of CE-related microorganisms and enzymes under alkaline pH hindered MCFAs synthesis, while under acidic pH, carboxylate accumulation may reduce cellular protection capabilities and affect energy metabolism, thereby inhibiting anaerobic fermentation. Conversely, neutral pH enhanced amino acid and butyrate metabolic pathways, facilitating WAS degradation and SCFAs production, providing precursor substrates for MCFAs production. Additionally, neutral pH promoted the enrichment and activity of CE-related microorganisms and enzymes, contributing to the accumulation of high-concentration MCFAs. Notably, Clostridium_kluyveri and Sporanaerobacter_acetigenes were key CE-functional bacteria at neutral pH.}, } @article {pmid39693975, year = {2025}, author = {Bharti, S and Raj, A and Saratale, GD and Romanholo Ferreira, LF and Lucena de Souza, R and Mulla, SI and Bharagava, RN}, title = {A critical review on the symbiotic effect of bacteria and microalgae on treatment of sewage with biofertilizer production.}, journal = {Journal of environmental management}, volume = {373}, number = {}, pages = {123704}, doi = {10.1016/j.jenvman.2024.123704}, pmid = {39693975}, issn = {1095-8630}, mesh = {*Sewage ; *Microalgae ; *Fertilizers/analysis ; *Bacteria/metabolism ; Biomass ; Waste Disposal, Fluid/methods ; Symbiosis ; }, abstract = {Wastes like sewage, kitchen and industrial are the major sources of environmental pollution and health hazards. Sewage contains 99.9% water and 0.1% solid waste including urinal waste and faecal matter alongwith large amounts of nitrate, nitrite, ammonium and phosphate ions. Sewage may also contain a variety of harmful contaminants like analgesics, antihypertensive drugs, antibiotics, dioxin, furans, polychlorinated biphenyls, chlorinated hydrocarbon pesticides, chlorine derivatives and plasticizers etc. making it more harmfull to environment and public health. Hence, sewage must be adequately treated by an effective process before its final discharge into the environment. Biological treatment of sewage is an emerging idea in recent years, which has diverse economic and environmental advantages. Sewage treatment by bacteria and microalgae has numerous advantages as it removes various excessive nutrients from waste with large biomass production and also prevents the utilization of toxic chemicals in conventional treatment process. Microalgae-bacterial biomass have potential to be used as biofertilizers, bio-stimulants and bio-seed primers in agricultural field as these contain various biologically active substances like polysaccharides, carotenoids, free fatty acids, phenols, and terpenoids. This review paper mainly discussing the sewage characteristics and different kinds of organic and inorganic pollutants it contained alongwith its harmfull impacts on environment and public health. It also deals the different conventional as well as emerging treatment technologies and different factors affecting the treatment efficiency. In addition, the utilization of developed microalgal and bacterial biomass as biofertilizer and its effects on crop plant alongwith future prospects has been also discussed in detail.}, } @article {pmid39693966, year = {2025}, author = {Li, T and Wang, P and Zhi, Z and Guo, T and Zhou, J and Zhang, H and Cao, C and Cai, Y and Li, Y and Zhang, J}, title = {Free-caged rearing modes regulate chicken intestinal metabolism by influencing gut microbial homeostasis.}, journal = {Poultry science}, volume = {104}, number = {1}, pages = {104381}, pmid = {39693966}, issn = {1525-3171}, mesh = {Animals ; *Chickens ; *Gastrointestinal Microbiome/physiology ; *Homeostasis ; *Animal Husbandry/methods ; Cecum/microbiology/metabolism ; Housing, Animal ; Bacteria/classification/metabolism/genetics ; Male ; }, abstract = {Free-caged rearing modes, which prioritize animal welfare, are believed to enhance the quality of animal products. The impact of rearing modes on meat quality may play a key role in the superior quality of local chicken breeds. This study analyzed the cecal contents of free-range and caged black-bone chickens at different ages using metagenomic and metabolomic sequencing. We identified 32 metabolites and 367 microbial species significantly affected by the rearing mode. Linear discriminant analysis Effect Size (LefSe) highlighted five key microorganisms, Gemmiger formicilis, Bacteria unclassified, Bacteroides sp. ET225, Massilistercora timonensis, and Bacteroidales unclassified, that showed distinct abundance patterns across all age points. Among them, Bacteroides sp. ET225 and Massilistercora timonensis were positively associated with certain phospholipids and plant-derived metabolites, while negatively correlated with others like demissidine and acylcarnitine. Functional analysis revealed that rearing modes impact gut metabolites involved in gut metabolism as well as broader processes such as signal transduction, protein digestion, and autophagy. This study offers new insights into how rearing modes influence gut microbiota and metabolites, shedding light on the study of rearing mode-mediated muscle development and fat deposition.}, } @article {pmid39693773, year = {2024}, author = {Shen, D and Li, C and Guo, Z}, title = {Dynamics of antibiotic resistance in poultry farms via multivector analysis.}, journal = {Poultry science}, volume = {104}, number = {2}, pages = {104673}, pmid = {39693773}, issn = {1525-3171}, abstract = {This study examines the distribution of microbial communities and antibiotic resistance genes (ARGs) across various vectors in poultry farm environments. The results show that airborne particulate matter (PM) and soil harbor the highest counts of microbial genes, exceeding those found in poultry visceral samples, which display lower microbial diversity and ARG levels. This highlights environmental vectors, particularly soil and PM, as major reservoirs for ARGs. Proteobacteria, predominantly present in feces and feed, are identified as key carriers of ARGs, with resistance mechanisms primarily involving efflux and target modification. Notably, Chlamydia spp. in visceral samples, despite lower overall abundance, show a high proportion of ARGs, raising concerns about ARG persistence in poultry microbiota. Furthermore, a significant correlation between different ARGs was detected, indicating the possibility of cooperative transmission processes. The findings underline the role of PM in ARG transmission due to its mobility and capacity to retain ARGs across distances. Additionally, therapeutic antibiotics in feed may contribute to ARG proliferation in animal microbiomes, suggesting a need for improved management practices to mitigate ARG spread in poultry farming environments.}, } @article {pmid39693717, year = {2025}, author = {Tan, Q and Zhu, Y and Zhao, Y and Zheng, L and Wang, X and Xing, Y and Wu, H and Tian, Q and Zhang, Y}, title = {Comparative analysis of niche adaptation strategies of AOA, AOB, and comammox along a gate-controlled river-estuary continuum.}, journal = {Water research}, volume = {273}, number = {}, pages = {122964}, doi = {10.1016/j.watres.2024.122964}, pmid = {39693717}, issn = {1879-2448}, mesh = {*Rivers ; *Archaea/genetics/metabolism ; *Ammonia/metabolism ; Estuaries ; Bacteria/metabolism/genetics ; Oxidation-Reduction ; Salinity ; China ; Geologic Sediments/microbiology ; }, abstract = {Ammonia oxidizers are key players in the biogeochemical nitrogen cycle. However, in critical ecological zones such as estuaries, especially those affected by widespread anthropogenic dam control, our understanding of their occurrence, ecological performance, and survival strategies remains elusive. Here, we sampled sediments along the Haihe River-Estuary continuum in China, controlled by the Haihe Tidal Gate, and employed a combination of biochemical and metagenomic approaches to investigate the abundance, activity, and composition of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and complete ammonia oxidizers (comammox). We also conducted an extensive comparison of the salinity adaptation mechanisms of different ammonia oxidizers. We found that AOB (57.55 ± 11.46 %) dominated the nitrification process upstream of the tidal gate, while comammox (68.22 ± 14.42 %) played the major role downstream. Redundancy analysis results showed that total nitrogen, ammonium, and salinity were the primary factors influencing the abundance, activity, and contribution of ammonia oxidizers. The abundance and activity of AOB were significantly positively correlated with ammonium. KEGG annotation results showed that AOA Nitrososphaera, AOB Nitrosomonas, and comammox Nitrospira had 7, 31, and 22 genes associated to salinity adaptation, respectively, and were capable of employing both the "salt-in" and "salt-out" strategies. Metagenome assembly results indicated that comammox outperformed AOA primarily in compatible solute accumulation; AOA can synthesize glutamate, whereas comammox Nitrospira can additionally synthesize glycine betaine, choline, and trehalose. The tidal gate caused sharp shifts in ammonium (from 4.10 ± 3.28 mg·kg[-1] to 0.45 ± 0.10 mg·kg[-1]) and salinity (from 1.64 ± 0.48 ppt to 3.26 ± 0.89 ppt), playing a dominant role in driving niche differentiation of ammonia oxidizers along the Haihe River-Estuary continuum. These findings provide profound insights into the nitrogen cycle in freshwater-saltwater transition zones, especially in today's world where estuaries are widely controlled by tidal gates.}, } @article {pmid39693444, year = {2024}, author = {Ruff, SE and de Angelis, IH and Mullis, M and Payet, JP and Magnabosco, C and Lloyd, KG and Sheik, CS and Steen, AD and Shipunova, A and Morozov, A and Reese, BK and Bradley, JA and Lemonnier, C and Schrenk, MO and Joye, SB and Huber, JA and Probst, AJ and Morrison, HG and Sogin, ML and Ladau, J and Colwell, F}, title = {A global comparison of surface and subsurface microbiomes reveals large-scale biodiversity gradients, and a marine-terrestrial divide.}, journal = {Science advances}, volume = {10}, number = {51}, pages = {eadq0645}, pmid = {39693444}, issn = {2375-2548}, mesh = {*Microbiota/genetics ; *Biodiversity ; *Archaea/genetics/classification ; *Phylogeny ; *Bacteria/genetics/classification ; Metagenome ; Seawater/microbiology ; Ecosystem ; }, abstract = {Subsurface environments are among Earth's largest habitats for microbial life. Yet, until recently, we lacked adequate data to accurately differentiate between globally distributed marine and terrestrial surface and subsurface microbiomes. Here, we analyzed 478 archaeal and 964 bacterial metabarcoding datasets and 147 metagenomes from diverse and widely distributed environments. Microbial diversity is similar in marine and terrestrial microbiomes at local to global scales. However, community composition greatly differs between sea and land, corroborating a phylogenetic divide that mirrors patterns in plant and animal diversity. In contrast, community composition overlaps between surface to subsurface environments supporting a diversity continuum rather than a discrete subsurface biosphere. Differences in microbial life thus seem greater between land and sea than between surface and subsurface. Diversity of terrestrial microbiomes decreases with depth, while marine subsurface diversity and phylogenetic distance to cultured isolates rivals or exceeds that of surface environments. We identify distinct microbial community compositions but similar microbial diversity for Earth's subsurface and surface environments.}, } @article {pmid39693383, year = {2024}, author = {Arrington, EC and Tarn, J and Kivenson, V and Nunn, BL and Liu, RM and Paul, BG and Valentine, DL}, title = {Hydrocarbon metabolism and petroleum seepage as ecological and evolutionary drivers for Cycloclasticus.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrae247}, pmid = {39693383}, issn = {1751-7370}, abstract = {Aqueous-soluble hydrocarbons dissolve into the ocean's interior and structure deep-sea microbial populations influenced by natural oil seeps and spills. n-Pentane is a seawater-soluble, volatile compound abundant in petroleum products and reservoirs and will partially partition to the deep-water column following release from the seafloor. In this study, we explore the ecology and niche partitioning of two free-living Cycloclasticus strains recovered from seawater incubations with n-pentane and distinguish them as an open ocean variant and a seep-proximal variant, each with distinct capabilities for hydrocarbon catabolism. Comparative metagenomic analysis indicates the variant more frequently observed further from natural seeps encodes more general pathways for hydrocarbon consumption, including short-chain alkanes, aromatics, and long-chain alkanes, and also possesses redox versatility in the form of respiratory nitrate reduction and thiosulfate oxidation; in contrast, the seep variant specializes in short-chain alkanes and relies strictly on oxygen as the terminal electron acceptor. Both variants observed in our work were dominant ecotypes of Cycloclasticus observed during the Deepwater Horizon disaster, a conclusion supported by 16S rRNA gene analysis and read-recruitment of sequences collected from the submerged oil plume during active flow. A comparative genomic analysis of Cycloclasticus across various ecosystems suggests distinct strategies for hydrocarbon transformations among each clade. Our findings suggest Cycloclasticus is a versatile and opportunistic consumer of hydrocarbons and may have a greater role in the cycling of sulfur and nitrogen, thus contributing broad ecological impact to various ecosystems globally.}, } @article {pmid39693209, year = {2025}, author = {Yamamoto, A and Kawashima, A and Uemura, T and Nakano, K and Matsushita, M and Ishizuya, Y and Jingushi, K and Hase, H and Katayama, K and Yamaguchi, R and Sassi, N and Motoyama, Y and Nojima, S and Mita, M and Kimura, T and Motooka, D and Horibe, Y and Okuda, Y and Oka, T and Yamamichi, G and Tomiyama, E and Koh, Y and Yamamoto, Y and Kato, T and Hatano, K and Uemura, M and Imoto, S and Wada, H and Morii, E and Tsujikawa, K and Nonomura, N}, title = {A novel mouse model of upper tract urothelial carcinoma highlights the impact of dietary intervention on gut microbiota and carcinogenesis prevention despite carcinogen exposure.}, journal = {International journal of cancer}, volume = {156}, number = {7}, pages = {1439-1456}, pmid = {39693209}, issn = {1097-0215}, support = {19K09709//Japan Society for the Promotion of Science/ ; 21K20968//Japan Society for the Promotion of Science/ ; 22H03213//Japan Society for the Promotion of Science/ ; 22K09523//Japan Society for the Promotion of Science/ ; 22K18398//Japan Society for the Promotion of Science/ ; JP22ym0126809i0002//Japan Agency for Medical Research and Development/ ; JP23ama121054//Japan Agency for Medical Research and Development/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; Female ; *Disease Models, Animal ; Humans ; *Carcinogens/toxicity ; Male ; *Butylhydroxybutylnitrosamine ; Carcinogenesis ; Mice, Inbred BALB C ; Urinary Bladder Neoplasms/prevention & control/chemically induced/etiology/pathology ; Urologic Neoplasms/prevention & control/diet therapy/etiology/chemically induced/pathology ; Urothelium/pathology/metabolism/microbiology ; }, abstract = {Animal models of N-butyl-N-(4-hydroxy butyl) nitrosamine (BBN)-induced urothelial carcinoma (UC), particularly bladder cancer (BC), have long been established. However, the rare incidence of BBN-induced upper urinary tract UC (UTUC), which originates from the same urothelium as BC, remains elusive. The scarcity of animal models of UTUC has made it challenging to study the biology of UTUC. To address this problem, we tried to establish a novel mouse model of UTUC by treating multiple mice strains and sexes with BBN. The molecular consistency between the UTUC mouse model and human UTUC was confirmed using multi-omics analyses, including whole-exome, whole-transcriptome, and spatial transcriptome sequencing. 16S ribosomal RNA metagenome sequencing, metabolome analysis, and dietary interventions were employed to assess changes in the gut microbiome, metabolome, and carcinogenesis of UTUC. Of all treated mice, only female BALB/c mice developed UTUC over BC. Multi-omics analyses confirmed that the UTUC model reflected the molecular characteristics and heterogeneity of human UTUC with poor prognosis. Furthermore, the model exhibited increased Tnf-related inflammatory gene expression in the upper urinary tract and a low relative abundance of Parabacteroides distasonis in the gut. Dietary intervention, mainly without alanine, led to P. distasonis upregulation and successfully prevented UTUC, as well as suppressed Tnf-related inflammatory gene expression in the upper urinary tract despite the exposure to BBN. This is the first report to demonstrate a higher incidence of UTUC than BC in a non-engineered mouse model using BBN. Overall, this model could serve as a useful tool for comprehensively investigating UTUC in future studies.}, } @article {pmid39692728, year = {2024}, author = {Fiorito, G and Tosti, V and Polidoro, S and Bertozzi, B and Veronese, N and Cava, E and Spelta, F and Piccio, L and Early, DS and Raftery, D and Vineis, P and Fontana, L}, title = {Multi-omic analysis of biological aging biomarkers in long-term calorie restriction and endurance exercise practitioners: A cross-sectional study.}, journal = {Aging cell}, volume = {}, number = {}, pages = {e14442}, doi = {10.1111/acel.14442}, pmid = {39692728}, issn = {1474-9726}, support = {//Australian Youth and Health Foundation/ ; APP1177797//Australian NHMRC Investigator Grant/ ; //Bakewell Foundation/ ; }, abstract = {Calorie restriction (CR) and physical exercise (EX) are well-established interventions known to extend health span and lifespan in animal models. However, their impact on human biological aging remains unclear. With recent advances in omics technologies and biological age (BioAge) metrics, it is now possible to assess the impact of these lifestyle interventions without the need for long-term follow-up. This study compared BioAge biomarkers in 41 middle-aged and older adult long-term CR practitioners, 41 age- and sex-matched endurance athletes (EX), and 35 sedentary controls consuming Western diets (WD), through PhenoAge: a composite score derived from nine blood-biomarkers. Additionally, a subset of participants (12 CR, 11 EX, and 12 WD) underwent multi-omic profiling, including DNA methylation and RNAseq of colon mucosa, blood metabolomics, and stool metagenomics. A group of six young WD subjects (yWD) served as a reference for BioAge calculation using Mahalanobis distance across six omic layers. The results demonstrated consistently lower BioAge biomarkers in both CR and EX groups compared to WD controls across all layers. CR participants exhibited lower BioAge in gut microbiome and blood-derived omics, while EX participants had lower BioAge in colon mucosa-derived epigenetic and transcriptomic markers, suggesting potential tissue-specific effects. Multi-omic pathway enrichment analyses suggested both shared and intervention-specific mechanisms, including oxidative stress and basal transcription as common pathways, with ether lipid metabolism uniquely enriched in CR. Despite limitations due to sample size, these findings contribute to the broader understanding of the potential anti-aging effects of CR and EX, offering promising directions for further research.}, } @article {pmid39692706, year = {2024}, author = {Girão, M and Rego, A and Fonseca, AC and Cao, W and Jia, Z and Urbatzka, R and Leão, PN and Carvalho, MF}, title = {Actinomycetota From Macroalgae as Rich Source for Natural Products Discovery Revealed Through Culture-Dependent and -Independent Approaches.}, journal = {Microbial biotechnology}, volume = {17}, number = {12}, pages = {e70058}, pmid = {39692706}, issn = {1751-7915}, support = {C644915664-00000026//PRR, The Portuguese Republic and the European Union/ ; UIDB/04423/2020//European Regional Development Fund/ ; CEECIND/02968/2017//Fundação para a Ciência e a Tecnologia/ ; FRH/BD/145646/2019//Fundação para a Ciência e a Tecnologia/ ; }, mesh = {*Seaweed/microbiology ; *Biological Products/metabolism/pharmacology ; *Actinobacteria/genetics/metabolism/classification/isolation & purification ; Animals ; Portugal ; Cell Survival/drug effects ; Bioprospecting ; Zebrafish/microbiology ; Anti-Infective Agents/metabolism/pharmacology ; Humans ; Metagenomics ; }, abstract = {Actinomycetota are unrivalled producers of bioactive natural products, with strains living in association with macroalgae representing a prolific-yet largely unexplored-source of specialised chemicals. In this work, we have investigated the bioactive potential of Actinomycetota from macroalgae through culture-dependent and -independent approaches. A bioprospecting pipeline was applied to a collection of 380 actinobacterial strains, recovered from two macroalgae species collected in the Portuguese northern shore-Codium tomentosum and Chondrus crispus-in order to explore their ability to produce antibacterial, antifungal, anticancer and lipid-reducing compounds. Around 43% of the crude extracts showed activity in at least one of the screenings performed: 111 presented antimicrobial activity at 1 mg/mL, 83 significantly decreased cancer cells viability at 15 μg/mL and 5 reduced lipid content in zebrafish > 60% at 15 ug/mL. Dereplication of active extracts unveiled the presence of compounds that could explain most of the recorded results, but also unknown molecules in the metabolome of several strains, highlighting the opportunity for discovery. The bioactive potential of the actinobacterial community from the same macroalgae specimens, which served as the source for the aforementioned Actinomycetota collection, was also explored through metagenomics analysis, allowing to obtain a broader picture of its functional diversity and novelty. A total of 133 biosynthetic gene clusters recovered from metagenomic contigs and metagenome assembled genomes (MAGs). These were grouped into 91 gene cluster families, 83 of which shared less than 30% of similarity to database entries. Our findings provided by culture-dependent and -independent approaches underscore the potential held by actinomycetes from macroalgae as reservoirs for novel bioactive natural products.}, } @article {pmid39692191, year = {2025}, author = {Zou, X and Yan, M and Wang, Y and Ni, Y and Zhao, J and Lu, B and Liu, B and Cao, B}, title = {Accurate Diagnosis of Lower Respiratory Infections Using Host Response and Respiratory Microbiome from a Single Metatranscriptome Test of Bronchoalveolar Lavage Fluid.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {12}, number = {6}, pages = {e2405087}, pmid = {39692191}, issn = {2198-3844}, support = {2022YFA1304300//National Key R&D Program of China grant/ ; ZRJY2023-GG24//China-Japan Friendship Hospital elite program grant/ ; }, mesh = {Humans ; *Bronchoalveolar Lavage Fluid/microbiology ; Female ; Male ; *Respiratory Tract Infections/microbiology/diagnosis ; *Microbiota/genetics ; Middle Aged ; Retrospective Studies ; Aged ; Adult ; Transcriptome/genetics ; Gene Expression Profiling/methods ; }, abstract = {Lower respiratory tract infections (LRTIs) diagnosis is challenging because noninfectious diseases mimic its clinical features. The altered host response and respiratory microbiome following LRTIs have the potential to differentiate LRTIs from noninfectious respiratory diseases (non-LRTIs). Patients suspected of having LRTIs are retrospectively enrolled and a clinical metatranscriptome test is performed on bronchoalveolar lavage fluid (BALF). Transcriptomic and metagenomic analysis profiled the host response and respiratory microbiome in patients with confirmed LRTI (n = 126) or non-LRTIs (n = 75). Patients with evidenced LRTIs exhibited enhanced pathways on chemokine and cytokine response, neutrophile recruitment and activation, along with specific gene modules linked to LRTIs status and key blood markers. Moreover, LRTIs patients exhibited reduced diversity and evenness in the lower respiratory microbiome, likely driven by an increased abundance of bacterial pathogens. Host marker genes are selected, and classifiers are developed to distinguish patients with LRTIs, non-LRTIs, and indeterminate status, achieving an area under the receiver operating characteristic curve of 0.80 to 0.86 and validated in a subsequently enrolled cohort. Incorporating respiratory microbiome features further enhanced the classifier's performance. In summary, a single metatranscriptome test of BALF proved detailed profiles of host response and respiratory microbiome, enabling accurate LRTIs diagnosis.}, } @article {pmid39692041, year = {2024}, author = {Yang, Z and Zhang, Z and Jiang, S and Li, A and Song, H and Zhang, J}, title = {Diet shapes and maintains the personalized native gut microbiomes in mice.}, journal = {Journal of the science of food and agriculture}, volume = {}, number = {}, pages = {}, doi = {10.1002/jsfa.14073}, pmid = {39692041}, issn = {1097-0010}, support = {//National Natural Science Foundation of China (No. 32222066 and No. 32160545)/ ; }, abstract = {BACKGROUND: The gut microbiome plays a critical role in human health and disease. Different dietary backgrounds play an important role in the uniqueness and diversity of the gut microbiota in different individuals, which promotes heterogeneity in disease phenotypes and treatment responses. Here, we explored how diet affects the composition and function of the native gut microbiome of model mice, based on the shotgun metagenomic and metabolomic, by analyzing the gut microbiome of C57B/6J mice in different dietary backgrounds.

RESULTS: The gut microbiomes of mice receiving different diets consistently exhibit distinct compositions across bacterial species, strains, fungi and phages. This implies that native microbial communities cannot 'homogenize' rapidly becaise of priority effects and unchanging diets. Notably, hotspot bacteria such as Limosilactobacillus reuteri, Parabacteroides distasonis and Akkermansia muciniphila were significantly different among the groups. These species harbor diverse adaptive mutations, reflecting genomic evolutionary diversity. The functional profiles of the gut microbiota also exhibit selective differences, involving the capacity for carbohydrate, branched-chain amino acid and fatty acid synthesis, as well as virulence factors, carbohydrate-active enzymes and antibiotic resistance. Furthermore, the differences in the gut microbiota also propagate to the host's serum, where structural and specific metabolite differences were observed. Metabolites that directly impact host health, such as d-glucosamine 6-phosphate and testolic acid, also show significant differences between the different dietary groups.

CONCLUSION: Our findings underscore the profound influence of different dietary the composition and functionality of the gut microbiome, offering valuable insights into optimizing health outcomes through personalized nutritional interventions. © 2024 Society of Chemical Industry.}, } @article {pmid39691696, year = {2024}, author = {Klvanova, E and Videnska, P and Barton, V and Bohm, J and Splichalova, P and Koksova, V and Urik, M and Lanickova, B and Prokes, R and Budinska, E and Klanova, J and Borilova Linhartova, P}, title = {Resistome in the indoor dust samples from workplaces and households: a pilot study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1484100}, pmid = {39691696}, issn = {2235-2988}, mesh = {*Dust/analysis ; Pilot Projects ; *Workplace ; Humans ; Air Pollution, Indoor ; Bacteria/genetics/isolation & purification/drug effects/classification ; Family Characteristics ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial/genetics ; Air Microbiology ; Metagenome ; High-Throughput Nucleotide Sequencing ; Drug Resistance, Bacterial/genetics ; Real-Time Polymerase Chain Reaction ; }, abstract = {The antibiotic resistance genes (ARGs) limit the susceptibility of bacteria to antimicrobials, representing a problem of high importance. Current research on the presence of ARGs in microorganisms focuses mainly on humans, livestock, hospitals, or wastewater. However, the spectrum of ARGs in the dust resistome in workplaces and households has gone relatively unexplored. This pilot study aimed to analyze resistome in indoor dust samples from participants' workplaces (a pediatric hospital, a maternity hospital, and a research center) and households and compare two different approaches to the ARGs analysis; high-throughput quantitative PCR (HT-qPCR) and whole metagenome shotgun sequencing (WMGS). In total, 143 ARGs were detected using HT-qPCR, with ARGs associated with the macrolides, lincosamides, and streptogramin B (MLSB) phenotype being the most abundant, followed by MDR (multi-drug resistance) genes, and genes conferring resistance to aminoglycosides. A higher overall relative quantity of ARGs was observed in indoor dust samples from workplaces than from households, with the pediatric hospital being associated with the highest relative quantity of ARGs. WMGS analysis revealed 36 ARGs, of which five were detected by both HT-qPCR and WMGS techniques. Accordingly, the efficacy of the WMGS approach to detect ARGs was lower than that of HT-qPCR. In summary, our pilot data revealed that indoor dust in buildings where people spend most of their time (workplaces, households) can be a significant source of antimicrobial-resistant microorganisms, which may potentially pose a health risk to both humans and animals.}, } @article {pmid39691688, year = {2024}, author = {Ericson, U and Hellstrand, S and Larsson, A and Miari, M and Sayols-Baixeras, S and Dekkers, KF and Bergström, G and Malinovschi, A and Engström, G and Ärnlöv, J and Fall, T and Orho-Melander, M}, title = {A Swedish dietary guideline index, gut microbial α-diversity and prevalence of metabolic syndrome - observations in the Swedish CArdioPulmonary bioImage Study (SCAPIS).}, journal = {Food & nutrition research}, volume = {68}, number = {}, pages = {}, pmid = {39691688}, issn = {1654-661X}, abstract = {BACKGROUND: Metabolic syndrome (MetS) is characterized by coexisting risk factors for type 2 diabetes and cardiovascular disease. Diet is of importance in their aetiology, and gut microbiota (GM) may constitute a link between diet and metabolic health. Understanding the interplay between diet and GM could contribute novel insights for future dietary guidelines, and aid in preventive actions to motivate adherence to dietary guidelines.

OBJECTIVE: We intended to create a Swedish dietary guideline index (SweDGI) measuring adherence to 12 Swedish dietary guidelines and examine whether SweDGI and its components are associated with GM α-diversity (Shannon index) and prevalent MetS, and if the association between the Shannon index and MetS differs depending on SweDGI.

DESIGN: SweDGI was based on food-frequency data assessed 2014-2018 in 10,396 diabetes-free participants from the Malmö and Uppsala-sites of the Swedish CArdioPulmonary bioImage Study (SCAPIS) (50-64 y, 53% women). We estimated the Shannon index from shotgun metagenomic sequencing-data to assess microbial richness and evenness. We used a general linear model to examine cross-sectional SweDGI-Shannon associations and logistic regression for associations with MetS.

RESULTS: Most guidelines were followed by less than half of the participants. Men showed poorer adherence. Higher SweDGI was linked to higher Shannon index (P-trend across five SweDGI-groups = 1.7 × 10[-12]). Most guidelines contributed to this observation. Higher SweDGI and Shannon index were associated with lower MetS-prevalence, where the lowest prevalence was observed among those with both high SweDGI and high Shannon index (odds ratio:0.43; 95% confidence interval:0.35, 0.52). Both the Shannon index and SweDGI were associated with MetS, independently of the level of the other factor (P-interaction = 0.82).

CONCLUSIONS: We created a new index to comprehensively reflect adherence to the Swedish dietary guidelines in sub-cohorts within the large multicentre SCAPIS study. Better adherence was associated with a richer and more even GM and lower prevalence of MetS. The inverse association between the Shannon index and MetS was consistent at different levels of adherence to dietary guidelines.}, } @article {pmid39691489, year = {2024}, author = {Maimaiti, Z and Liu, L}, title = {Exploring the Microbial Landscape of Bone and Joint Infections: An Analysis Using 16S rRNA Metagenome Sequencing.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {5557-5566}, pmid = {39691489}, issn = {1178-6973}, abstract = {BACKGROUND: Bone and joint infections (BJIs) are challenging to diagnose. This study evaluated the utility of 16S rRNA gene sequencing in diagnosing BJIs, comparing it with conventional bacterial culture to explore microbial diversity in orthopedic infections.

METHODS: Thirty patients with BJIs were enrolled from January 2019 to September 2020 at a single orthopedic center. Diagnoses were based on the Musculoskeletal Infection Society standards. DNA extraction, 16S rRNA sequencing, and microbial composition analysis were performed. Conventional bacterial culture results were compared with metagenomics detection, and associations with blood routine and biochemical test factors were analyzed.

RESULTS: The study enrolled 30 patients with BJIs. Traditional bacterial culture successfully identified pathogens in 60% (18/30) of cases, predominantly Staphylococcus aureus. In contrast, 16S rRNA metagenomics sequencing revealed distinct microorganisms in all cases, it unveiled a diverse microbial landscape. The correlation between bacterial culture and metagenomics detection showcased both concordance and discrepancies. Consistency of detection between the two methods showed that metagenomics detection detected the same genus or species in 14 (87.5%) of the 16 samples identified as species by bacterial culture. In nearly half of the patients with negative cultures, pathogenic microorganisms were detected, highlighting the capability of 16S rRNA sequencing to identify microorganisms, even in samples with negative or unidentified culture results. Moreover, no significant correlation was observed between bacterial culture, metagenomics detection and the factors of blood routine and biochemical test.

CONCLUSION: This study deepens our understanding of the microbial complexity in BJIs. While traditional culture methods are cost-effective and practical, 16S rRNA gene sequencing proves valuable for complementary microbial analysis, particularly when traditional methods fail or rapid identification is critical. This emerging diagnostic approach can enhance the accuracy and speed of pathogen identification, enabling more effective interventions in the management of BJIs.}, } @article {pmid39691431, year = {2024}, author = {Zhang, J and Tan, S and Lyu, B and Yu, M and Lan, Y and Tang, R and Fan, Z and Guo, P and Shi, L}, title = {Differences in Gut Microbial Composition and Characteristics Among Three Populations of the Bamboo Pitviper (Viridovipera stejnegeri).}, journal = {Ecology and evolution}, volume = {14}, number = {12}, pages = {e70742}, pmid = {39691431}, issn = {2045-7758}, abstract = {The gut microbiota contributes to host health by facilitating nutrient uptake, digestion, energy metabolism, intestinal development, vitamin synthesis, and immunomodulation, and plays an important role in the growth and reproduction of the animal itself. Considering the paucity of research on the gut microbiota of wild snakes, this study focused on bamboo pitviper (Viridovipera stejnegeri) populations from Anhui, Guizhou, and Hunan, with multiple fecal samples collected from each population (six, five, and three, respectively). Total microbial DNA was extracted from the fecal samples using metagenomic next-generation sequencing and differences in gut microbial composition, abundance, and carbohydrate-active enzymes (CAZymes) were analyzed and compared among the three populations. Results showed no significant variance in the α-diversity of the gut microbes across the three populations, while principal coordinate analysis revealed significant differences in gut microbe composition. The four most abundant phyla in the gut microbiota of V. stejnegeri were Pseudomonadota, Bacteroidota, Actinomycetota, and Bacillota, while the four most abundant genera were Salmonella, Citrobacter, Bacteroides, and Yokenella. Linear discriminant analysis effect size demonstrated notable differences in gut microbial abundance among the three populations. Marked differences in CAZyme abundance were also observed across the microbial communities. Future studies should incorporate diverse ecological factors to evaluate their influence on the composition and function of gut microbiota.}, } @article {pmid39691376, year = {2024}, author = {Zhang, S and Gao, H and Zhang, G and Fang, M and Kong, Y and Jiang, L and Liu, Q and Wang, P and Liu, Y and Li, Y}, title = {Metavirome analysis of domestic sheep in Shaanxi, Gansu, and Ningxia, China.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1508617}, pmid = {39691376}, issn = {2297-1769}, abstract = {Sheep play an important role in China's agricultural development, but they are also potential hosts for many viruses, some of which have been identified as zoonotic pathogens, which may pose a serious threat to social public health and animal husbandry. Therefore, clarifying the characteristics of viruses in sheep will provide an important basis for the study of pathogenic ecology and viral evolution of viruses carried by sheep. We collected nasal and anal swabs from 688 sheep in 22 counties in Shaanxi, Gansu, and Ningxia, China, between January 2022 and July 2023, and utilized next-generation sequencing technology and bioinformatics approaches to identify the viruses in the samples. A total of 38 virus families carried by sheep were identified, including 12 ssRNA (+) virus families, 2 dsRNA virus families, 8 ssDNA (+) virus families, and 18 dsDNA virus families. Among them, Astroviridae, Coronaviridae, Picornaviridae, and Tobaniviridae in RNA virus families and Herpesviridae, Adenoviridae, and Circoviridae in DNA virus families are all viruses that are frequently detected in most ruminants. Alpha and beta diversity results showed that there was no difference in the overall richness and diversity of RNA and DNA viruses among the three provinces (p > 0.05). The evolutionary analysis demonstrated a tight link between the viral members carried by sheep and other ruminant viruses, implying that these viruses may spread across different species of ruminants. This study established a library of RNA and DNA viruses carried by sheep in the Shaanxi-Gansu-Ningxia region, providing an overview of the viruses present in this population. The findings offer valuable data for further research on virus evolution and monitoring in sheep.}, } @article {pmid39691165, year = {2025}, author = {Bescos, R and du Toit, L and Redondo-Rio, A and Warburton, PJ and Nicholas, TL and Kiernan, M and Burton, RA and Belfield, L and Montagut, G and Benavente, A and Vevers, W and Gabaldón, T and Brookes, Z and Casas-Agustench, P}, title = {The comparative effect of propolis and chlorhexidine mouthwash on oral nitrite-producing bacteria and blood pressure regulation.}, journal = {Journal of oral microbiology}, volume = {17}, number = {1}, pages = {2439636}, pmid = {39691165}, issn = {2000-2297}, abstract = {BACKGROUND: Propolis mouthwash (PROP-M) has demonstrated antibacterial properties like those of chlorhexidine mouthwash (CHX-M). However, its impact on the abundance of oral nitrite-producing species (NPS) and nitrite-producing activity (NPA) remains unexplored.

METHODS: Forty-five healthy individuals were randomised into 2 groups to rinse their mouth twice a day for seven days with either CHX-M (n = 21) or PROP-M (n = 24). Metagenomic sequencing (16S rRNA) was performed on saliva samples collected before and after each treatment. Additionally, salivary biomarkers and blood pressure were measured.

RESULTS: CHX-M increased the relative abundance of NPS (p < 0.001) but significantly impaired the NPA (p < 0.001) compared to baseline and PROP-M. No significant differences in the relative abundance of NPS and NPA were observed in the PROP-M group. However, a significant increase of plasma nitrate (+7 µmol/L, p = 0.047) and a decrease in systolic BP (-2 mmHg, p = 0.022) was observed in this group compared to the baseline.

CONCLUSION: The results indicate that PROP-M had a smaller effect on the abundance of NPS and NPA compared to CHX-M. Additionally, PROP-M reduced blood pressure in healthy individuals, but this effect was not associated with changes in the oral microbiome.}, } @article {pmid39690531, year = {2024}, author = {, }, title = {[Expert consensus on the application and practice of targeted next-generation sequencing in infectious diseases].}, journal = {Zhonghua yi xue za zhi}, volume = {104}, number = {48}, pages = {4375-4383}, doi = {10.3760/cma.j.cn112137-20240927-02208}, pmid = {39690531}, issn = {0376-2491}, support = {82341107//National Natural Science Foundation of China/ ; 2022YFA1304300//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Communicable Diseases/diagnosis ; China ; Consensus ; Metagenomics/methods ; }, abstract = {Targeted next-generation sequencing (tNGS) technology focuses on detecting pathogenic microorganisms and drug-resistant genes in clinical samples by designing specific primers or capture probes, providing evidence for the diagnosis, treatment and surveillance of infectious diseases. However, the current clinical application scenarios of tNGS and metagenomic next-generation sequencing (mNGS) are not clearly defined, and the tNGS systems from different manufacturers vary significantly in quality and results. There is an urgent need for consensus and standards regarding the clinical indications, laboratory processes, quality control, performance validation and interpretation of reports for this technology. In order to standardize the application and practice of tNGS in infectious diseases, experts in the fields of microbiology, infectious disease, respiratory disease, epidemiology and other fields from the Society of Clinical Microbiology of China International Exchange and Promotion Association for Medical and Healthcare discussed the above problems, wrote the expert consensus on the application and practice of tNGS in infectious diseases. This consensus summarizes the research on tNGS in infectious diseases, and proposes recommendations that are in line with clinical practice in China, so as to standardize the application and practice of tNGS in infectious diseases. The main contents include: consensus formulation process, clinical indications, technical points, wet and dry experiments, report and interpretation, and report template.}, } @article {pmid39690119, year = {2024}, author = {Di Gloria, L and Baldi, S and Curini, L and Bertorello, S and Nannini, G and Cei, F and Niccolai, E and Ramazzotti, M and Amedei, A}, title = {Experimental tests challenge the evidence of a healthy human blood microbiome.}, journal = {The FEBS journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/febs.17362}, pmid = {39690119}, issn = {1742-4658}, support = {//Ministry of University and Research (MUR)/ ; //FONZIE project (CUP B55F21007810001)/ ; //National Recovery and Resilience Plan (NRRP)/ ; }, abstract = {The advent of next-generation sequencing (NGS) technologies has made it possible to investigate microbial communities in various environments, including different sites within the human body. Therefore, the previously established belief of the sterile nature of several body sites, including human blood, has now been challenged. However, metagenomics investigation of areas with an anticipated low microbial biomass may be susceptible to misinterpretation. Here, we critically evaluate the results of 16S targeted amplicon sequencing performed on total DNA collected from healthy donors' blood samples while incorporating specific negative controls aimed at addressing potential bias to supplement and strengthen the research in this area. We prepared negative controls by increasing the initial DNA quantity through sequences that can be recognized and subsequently discarded. We found that only three organisms were sporadically present among the samples, and this was mostly attributable to bacteria ubiquitously present in laboratory reagents. Despite not fully confirming or denying the existence of healthy blood microbiota, our results suggest that living bacteria, or at least their residual DNA sequences, are not a common feature of human blood in healthy people. Finally, our study poses relevant questions on the design of controls in this research area that must be considered in order to avoid misinterpreted results that appear to contaminate current high-throughput research.}, } @article {pmid39689562, year = {2025}, author = {Liu, W and Wang, W and Jing, C and Yin, Z and Cai, Y}, title = {Novel arsenate-respiring bacteria drive arsenic biogeochemical cycling in Tibetan geothermal springs revealed by DNA-SIP based metagenomics.}, journal = {Journal of hazardous materials}, volume = {485}, number = {}, pages = {136899}, doi = {10.1016/j.jhazmat.2024.136899}, pmid = {39689562}, issn = {1873-3336}, mesh = {*Hot Springs/microbiology ; *Arsenic/metabolism ; Tibet ; *Metagenomics ; *Arsenates/metabolism ; *Bacteria/genetics/metabolism/classification ; }, abstract = {Arsenic (As) is a toxic element posing health risks globally, with geothermal environment as one of the hotspots. Arsenic biotransformation is mainly mediated by microorganisms which often employ diverse metabolic strategies for survival. However, the microorganisms responsible for As cycling and their survival strategies in geothermal environment in Tibet, the Third Pole, remain unclear. To address this knowledge gap, we investigated As biotransformation in representative geothermal springs using DNA-stable isotope probing (DNA-SIP) combined with metagenomic sequencing. As(V) reduction to the more toxic As(III) was found to be prevalent. Pseudomonas and Thermincola were identified as the dominant As(V)-reducing bacteria (AsRB). Metagenome-assembled genomes (MAGs) affiliated with AsRB contained abundant genes encoding As(V)-respiratory reductase (arrA, 1044.34 transcripts per million (TPM)), nitrate reduction pathway (e.g., narG), and Wood-Ljungdahl pathway (e.g., acsA), indicating their role as dissimilatory As(V)-reducing prokaryotes (DARPs) with diverse metabolic strategies. Here, Thermincola's potential of As(V) reduction via arrA and carbon fixation via Wood-Ljungdahl pathway was observed for the first time, which was found to be widespread in various ecosystems. Our study unravels the key players driving As biogeochemical cycle in Tibetan geothermal springs and provides insights into the genetic mechanisms enabling their survival in extreme environments.}, } @article {pmid39689559, year = {2025}, author = {Zhang, W and Zong, Y and Zhang, J and Ai, J and He, H and Li, L and Peng, S and Zhou, H and Wang, D and Wang, Q}, title = {Mechanistic insights into the viral microorganism inactivation during lime stabilization for wastewater sludges.}, journal = {Journal of hazardous materials}, volume = {485}, number = {}, pages = {136884}, doi = {10.1016/j.jhazmat.2024.136884}, pmid = {39689559}, issn = {1873-3336}, mesh = {*Calcium Compounds/pharmacology/chemistry ; *Oxides/chemistry/pharmacology ; *Sewage/virology ; *Virus Inactivation/drug effects ; Wastewater ; Waste Disposal, Fluid/methods ; Viruses/drug effects ; }, abstract = {The pathogens inactivation in wastewater sludges is vitally important for safely managing solid wastes and protecting public and environmental health especially in the emergency. Reports have shown the effectiveness of lime to kill virus pathogens in sludges, but mechanism of virus inactivation and related human diseases is unclear. This study evaluated representative limes of CaO/CaO2 on actual viral microorganism inactivation by viral metagenomic sequencing technology. As results, the CaO2 treatment enhanced the sludge hydrolysis and enveloped viral pathogens suppression via EPS structure destruction by oxidative radical generations; while CaO suppressed most of none-enveloped plant related viral pathogens. Most of the viromes of plant virus including Virgaviridae and Nodaviridae were inactivated by CaO, but the human virus-Feirsviridae and plant virus-Solemoviridae were occurred after lime stabilization compared to untreated sludge, with abundances of 1 %-37 % and 21 %-32 % in CaO-treated (CaO-T) and CaO2-treated (CaO2-T) samples, respectively. In addition, metatranscriptome analysis revealed distinct gene expression patterns between the CaO-T and CaO2-T sludges, in which lipopolysaccharide biosynthesis (LPS) and aminoacyl-tRNA synthetases (ARSs) in CaO-T, the formation of ribosome in CaO2-T were crucial to RNA virus regrowth in sludge. These findings suggested neither of CaO and CaO2 could completely suppress pathogens in sludge, and the effect of representative limes of CaO and CaO2 on the viral pathogen diversity, abundance, and metabolic function of the core microbiome on virus suppression and regrowth were ignored. Therefore, combined processes were recommended to provide possible alternatives for sludge safe management in pandemic emergencies.}, } @article {pmid39689421, year = {2025}, author = {Tang, XF and Guo, XP and Kuang, L and Chen, XJ and Sidikjan, N and Xu, TT and Jiang, S and Liu, M and Hou, LJ and Yang, Y}, title = {Comammox Nitrospira are the dominant ammonia oxidizers in the Yangtze estuarine biofilms.}, journal = {Water research}, volume = {273}, number = {}, pages = {122969}, doi = {10.1016/j.watres.2024.122969}, pmid = {39689421}, issn = {1879-2448}, mesh = {*Biofilms ; *Ammonia/metabolism ; *Estuaries ; *Oxidation-Reduction ; *Bacteria/metabolism/genetics ; Archaea/genetics/metabolism ; China ; Nitrification ; }, abstract = {Biofilms are indispensable ecological habitats for microbes that have garnered global attention and play a potential role in influencing the biogeochemical cycling of nitrogen. However, the biogeochemical significance of biofilms and the mechanisms by which they regulate nitrogen cycling remain elusive. In this study, we utilized DNA-stable isotope probing (DNA-SIP) labelling techniques in conjunction with metagenomics to reveal a nitrifying ecological niche in biofilms taken from the Yangtze Estuary, with those from sediment and water samples for comparison. Quantitative analysis showed that the amoA gene abundance of comammox Nitrospira (2.3 × 10[3] copies ng[-1] DNA) was significantly higher than that of ammonia-oxidizing archaea (AOA-amoA, 62.4 copies ng[-1] DNA) and ammonia-oxidizing bacteria (AOB-amoA, 218.1 copies ng[-1] DNA) in biofilms, and the average abundance of comammox Nitrospira showed the following order: water > biofilm > sediment. Moreover, the NOB nxrB gene was more abundant than the amoA gene of ammonia oxidizers in all three media. DNA-SIP further revealed that the active comammox Nitrospira clade A mediates the nitrification process in biofilms with peak abundance at a buoyant density of 1.715 g mL[-1]. Active nitrifying bacteria exhibit metabolic diversity in both biofilms and sediments, and occupy unique nitrifying ecological niches. Additionally, the co-occurrence network showed that chlorophyll a, NO3[-] and salinity emerged as the predominant physicochemical factors affecting the nitrogen transformation genes in biofilms. Taken together, this study indicates that biofilms constitute an emerging nitrifying ecological niche in estuarine environments and deepens our understanding of the mechanisms by which biofilms function in marine biogeochemistry.}, } @article {pmid39689125, year = {2024}, author = {McGowan, J and Richards, TA and Hall, N and Swarbreck, D}, title = {Multiple independent genetic code reassignments of the UAG stop codon in phyllopharyngean ciliates.}, journal = {PLoS genetics}, volume = {20}, number = {12}, pages = {e1011512}, pmid = {39689125}, issn = {1553-7404}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Ciliophora/genetics ; *Genetic Code ; *Codon, Terminator/genetics ; *Phylogeny ; RNA, Transfer/genetics ; Evolution, Molecular ; }, abstract = {The translation of nucleotide sequences into amino acid sequences, governed by the genetic code, is one of the most conserved features of molecular biology. The standard genetic code, which uses 61 sense codons to encode one of the 20 standard amino acids and 3 stop codons (UAA, UAG, and UGA) to terminate translation, is used by most extant organisms. The protistan phylum Ciliophora (the 'ciliates') are the most prominent exception to this norm, exhibiting the grfeatest diversity of nuclear genetic code variants and evidence of repeated changes in the code. In this study, we report the discovery of multiple independent genetic code changes within the Phyllopharyngea class of ciliates. By mining publicly available ciliate genome datasets, we discovered that three ciliate species from the TARA Oceans eukaryotic metagenome dataset use the UAG codon to putatively encode leucine. We identified novel suppressor tRNA genes in two of these genomes which are predicted to decode the reassigned UAG codon to leucine. Phylogenomics analysis revealed that these three uncultivated taxa form a monophyletic lineage within the Phyllopharyngea class. Expanding our analysis by reassembling published phyllopharyngean genome datasets led to the discovery that the UAG codon had also been reassigned to putatively code for glutamine in Hartmannula sinica and Trochilia petrani. Phylogenomics analysis suggests that this occurred via two independent genetic code change events. These data demonstrate that the reassigned UAG codons have widespread usage as sense codons within the phyllopharyngean ciliates. Furthermore, we show that the function of UAA is firmly fixed as the preferred stop codon. These findings shed light on the evolvability of the genetic code in understudied microbial eukaryotes.}, } @article {pmid39688845, year = {2024}, author = {Oteo-García, G and Mutti, G and Caldon, M and Oosthuitzen, O and ManfrediniK, M and Capelli, C}, title = {Reconstructing micro-evolutionary dynamics shaping local variation in southern African populations using genomics, metagenomics and personal metadata.}, journal = {Journal of anthropological sciences = Rivista di antropologia : JASS}, volume = {102}, number = {}, pages = {123-143}, doi = {10.4436/JASS.10204}, pmid = {39688845}, issn = {2037-0644}, mesh = {Humans ; Namibia ; *Metagenomics ; *Saliva/microbiology/virology ; *Microbiota/genetics ; Male ; Female ; Adult ; Lesotho ; Genomics ; Genetic Variation ; Young Adult ; Middle Aged ; Adolescent ; Black People/genetics ; }, abstract = {Geography is a well-known factor shaping genetic variation in human populations. However, the potential role played by cultural variables remains much understudied. This study investigates the impact of socio-cultural variables on genomic similarity and the saliva microbiome, using data from populations in Lesotho and Namibia. Geographic distance within Lesotho increases genetic differentiation, while shared clan affiliation surprisingly increases it. In Namibia, ethnicity is the predominant factor influencing genetic affinity. Saliva metagenomic data shows a negative correlation between age and alpha diversity, with notable differences in host-interacting taxa and viral load. These findings highlight the role of geography in shaping genetic affinity even at small scales and the complex influences of cultural factors. The saliva microbiome appears primarily affected by unrecorded individual behaviors rather than geographic or cultural variables. At population-level these oral microbiomes reveal insights into some dietary habits, oral health, and also the communal viral load, which appears to have greater incidence in Lesotho possibly related to the long-term effects of the HIV epidemic in the country.}, } @article {pmid39688758, year = {2024}, author = {Řezanka, P and Řezanka, M and Kyselová, L and Řezanka, T}, title = {Characterization of Archaea membrane lipids in radioactive springs using shotgun lipidomics.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, pmid = {39688758}, issn = {1874-9356}, support = {MZE-RO1923//Ministerstvo Zemědělství/ ; RVO61388971//Mikrobiologický Ústav, Akademie Věd České Republiky/ ; }, abstract = {Lipids from microorganisms, and especially lipids from Archaea, are used as taxonomic markers. Unfortunately, knowledge is very limited due to the uncultivability of most Archaea, which greatly reduces the importance of the diversity of lipids and their ecological role. One possible solution is to use lipidomic analysis. Six radioactive sources were investigated, two of which are surface (Wettinquelle and Radonka) and four deep from the Svornost mine (Agricola, Behounek, C1, and Curie). A total of 15 core lipids and 82 intact polar lipids were identified from the membranes of microorganisms in six radioactive springs. Using shotgun lipidomics, typical Archaea lipids were identified in spring water, namely dialkyl glycerol tetraethers, archaeol, hydroxyarchaeol and dihydroxyarchaeol. Diverse groups of polar heads were formed in archaeal IPLs, whose polar heads are formed mainly by hexose, deoxyhexose, and phosphoglycerol. The analysis was performed using shotgun lipidomics and the structure of all molecular species was confirmed by tandem mass spectrometry. After acid hydrolysis, a mixture of polar compounds was obtained from the polar head. Further analysis by GC-MS confirmed that the carbohydrates were glucose and rhamnose. Analysis by HPLC-MS of diastereoisomers of 2-(polyhydroxyalkyl)-3-(O-tolylthiocarbamoyl)thiazolidine-4(R)-carboxylates revealed that both L-rhamnose and D-glucose are present in spring samples only in varying amounts. The glycoside composition depends on the type of spring, that is, Wettinquelle and Radonka springs are basically shallow groundwater, while the samples from the Svornost mine are deep groundwater and do not contain glycosides with rhamnose. This method enables quick screening for characteristic Archaea lipids, allowing decisions on whether to pursue further analyses, such as metagenomic analysis, to directly confirm the presence of Archaea.}, } @article {pmid39688617, year = {2024}, author = {Zhao, Y and Mao, R and Zhong, Y and Lu, J and Gong, B and Yi, W and Zeng, Z}, title = {Application of metagenomic next-generation sequencing in pathogen detection for patients with lower respiratory tract infections caused by multidrug-resistant organisms and analysis of related factors.}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {71}, number = {4}, pages = {273-279}, doi = {10.1556/030.2024.02463}, pmid = {39688617}, issn = {1588-2640}, mesh = {Humans ; *Respiratory Tract Infections/microbiology/diagnosis ; Male ; Female ; *High-Throughput Nucleotide Sequencing/methods ; Middle Aged ; Retrospective Studies ; *Metagenomics/methods ; *Drug Resistance, Multiple, Bacterial/genetics ; Aged ; *Bacteria/genetics/isolation & purification/drug effects/classification ; Adult ; Risk Factors ; Anti-Bacterial Agents/pharmacology ; }, abstract = {The incidence of lower respiratory tract infections (LRTIs) caused by multidrug-resistant organisms (MDRO) has been high in recent years. However, traditional etiological detection methods have not been able to meet the needs for clinical diagnosis and prognosis of LRTIs. The rapid development of metagenomic next-generation sequencing (mNGS) provides new insights for diagnosis and treatment of LRTIs. We conducted a retrospective study on 95 patients with lower respiratory tract infections caused by MDRO admitted to our respiratory department from January 2022 to December 2023. These patients underwent mNGS testing and conventional culture testing. Additionally, 150 patients without lower respiratory tract infections caused by MDRO during the same period were included as the non-MDRO group. General information was collected, and Logistic regression analysis was performed to identify risk factors for MDRO infections in patients with lower respiratory tract infections. Our results show that the time to pathogen detection by mNGS was 50.76 ± 1.730 h, that is significantly shorter than 55.53 ± 2.782 h required for conventional culture testing. The pathogen detection rate by mNGS was 89.47% (85/95), higher than the 67.37% (64/95) identified by conventional testing. In terms of pathogen genus distribution, mNGS detected a total of 279 pathogens, while conventional testing detected 121 pathogens. Logistic multivariate regression analysis identified that the use of more than two antibiotics, invasive procedures, invasive mechanical ventilation for ≥7 days, and stay in the respiratory intensive care unit (RICU) for ≥7 days were the main influencing factors for lower respiratory tract infections caused by MDRO (P < 0.05).}, } @article {pmid39687173, year = {2024}, author = {Yang, Q and Zhou, K and Shen, Y and Huang, R and Liu, L and Liao, S}, title = {A case report of successful treatment of pulmonary mucormycosis caused by Cunninghamella bertholletiae infection in a patient with T-lymphoblastic lymphoma.}, journal = {Heliyon}, volume = {10}, number = {23}, pages = {e36244}, pmid = {39687173}, issn = {2405-8440}, abstract = {Mucormycosis caused by Cunninghamella bertholletiae (C. bertholletiae) is a rare opportunistic infection in patients with hematological malignancies (HM), with high mortality rates. Herein, we first report a case of pulmonary mucormycosis (PM) with C. bertholletiae in a 25-year-old male recently diagnosed with T-lymphoblastic lymphoma (T-LBL). The diagnosis was established through chest computed tomography (CT), metagenomic next-generation sequencing (mNGS) of blood and bronchoalveolar lavage fluid (BALF), as well as histopathological examination. Hematoxylin and eosin (HE) staining of the surgical specimen revealed the presence of fungal hyphae. He was effectively treated with liposomal amphotericin B (L-AmB) and posaconazole enteric-coated tablets, followed by aggressive surgical debridement. In our case, the fungal infection was initially identified as C. bertholletiae using mNGS, which facilitated rapid and accurate diagnosis, enabling clinicians to initiate early intensive treatment. The case also emphasizes the importance of surgical debridement in addressing affected tissues and underscores the significance of a multidisciplinary approach in implementing this treatment strategy.}, } @article {pmid39686449, year = {2024}, author = {Luo, A and Li, C and Zhao, J and Wu, Y and Fu, R}, title = {Severe Epstein-Barr virus encephalitis with peripheral nerve damage: A case report.}, journal = {Medicine}, volume = {103}, number = {50}, pages = {e40804}, pmid = {39686449}, issn = {1536-5964}, mesh = {Humans ; Female ; Middle Aged ; *Epstein-Barr Virus Infections/complications/diagnosis ; *Encephalitis, Viral/diagnosis/virology ; Antiviral Agents/therapeutic use ; Herpesvirus 4, Human/genetics ; Peripheral Nervous System Diseases/virology/etiology/diagnosis ; Magnetic Resonance Imaging ; }, abstract = {RATIONALE: Epstein-Barr virus (EBV) is a B-lymphotropic double-stranded DNA virus. Most people infected with EBV are asymptomatic infection. Its clinical symptoms are rarely manifested as EBV encephalitis, and peripheral nerve damage is even rarer.

PATIENT CONCERNS: We report a case of a 49-year-old woman with a history of fever. The initial symptoms were numbness and weakness in the right hand, followed by slurred speech. Electromyography showed severe damage to the median nerve of the right wrist (involving sensory and motor fibers). Magnetic resonance imaging revealed multiple lesions in the bilateral cerebral hemispheres on T2 FLAIR images, and T1-enhanced images showed abnormal enhancement of the adjacent leptomeninges. Human herpesvirus 4 (EBV) has been detected in the cerebrospinal fluid using metagenomic next-generation sequencing (NGS). After antiviral treatment, the patient's symptoms continued to worsen.

DIAGNOSIS: Severe EBV encephalitis complicated with peripheral nerve damage.

INTERVENTIONS: Antiviral, hormone therapy.

OUTCOMES: At the patient's condition progressed, a new infarction occurred in the right frontal lobe lesion, with repeated high fever, rapid deterioration of multiple organ function, sudden respiratory failure, cardiac arrest, and death.

LESSONS: In patients with signs of encephalitis, cerebrospinal fluid NGS should be used as early as possible to confirm the diagnosis of EBV encephalitis. Timely and accurate treatment of central nervous system infections is expected to reduce the mortality rate and improve the quality of life of patients in later stages.}, } @article {pmid39684893, year = {2024}, author = {Parkar, N and Young, W and Olson, T and Hurst, C and Janssen, P and Spencer, NJ and McNabb, WC and Dalziel, JE}, title = {Peripherally Restricted Activation of Opioid Receptors Influences Anxiety-Related Behaviour and Alters Brain Gene Expression in a Sex-Specific Manner.}, journal = {International journal of molecular sciences}, volume = {25}, number = {23}, pages = {}, pmid = {39684893}, issn = {1422-0067}, support = {C10X1706//Ministry of Business, Innovation and Employment/ ; }, mesh = {Animals ; Male ; Female ; *Anxiety/metabolism ; Rats ; *Loperamide/pharmacology ; *Brain/metabolism/drug effects ; *Rats, Sprague-Dawley ; *Receptors, Opioid/metabolism/genetics ; Behavior, Animal/drug effects ; Gastrointestinal Microbiome/drug effects ; Hippocampus/metabolism/drug effects ; Enteric Nervous System/metabolism ; Gene Expression Regulation/drug effects ; Sex Factors ; Sex Characteristics ; }, abstract = {Although effects of stress-induced anxiety on the gastrointestinal tract and enteric nervous system (ENS) are well studied, how ENS dysfunction impacts behaviour is not well understood. We investigated whether ENS modulation alters anxiety-related behaviour in rats. We used loperamide, a potent μ-opioid receptor agonist that does not cross the blood-brain barrier, to manipulate ENS function and assess changes in behaviour, gut and brain gene expression, and microbiota profile. Sprague Dawley (male/female) rats were acutely dosed with loperamide (subcutaneous) or control solution, and their behavioural phenotype was examined using open field and elevated plus maze tests. Gene expression in the proximal colon, prefrontal cortex, hippocampus, and amygdala was assessed by RNA-seq and caecal microbiota composition determined by shotgun metagenome sequencing. In female rats, loperamide treatment decreased distance moved and frequency of supported rearing, indicating decreased exploratory behaviour and increased anxiety, which was associated with altered hippocampal gene expression. Loperamide altered proximal colon gene expression and microbiome composition in both male and female rats. Our results demonstrate the importance of the ENS for communication between gut and brain for normo-anxious states in female rats and implicate corticotropin-releasing hormone and gamma-aminobutyric acid gene signalling pathways in the hippocampus. This study also sheds light on sexually dimorphic communication between the gut and the brain. Microbiome and colonic gene expression changes likely reflect localised effects of loperamide related to gut dysmotility. These results suggest possible ENS pharmacological targets to alter gut to brain signalling for modulating mood.}, } @article {pmid39684853, year = {2024}, author = {Tynior, W and Kłósek, M and Salatino, S and Cuber, P and Hudy, D and Nałęcz, D and Chan, YT and Gustave, C and Strzelczyk, JK}, title = {Metagenomic Analysis of the Buccal Microbiome by Nanopore Sequencing Reveals Structural Differences in the Microbiome of a Patient with Molar Incisor Hypomineralization (MIH) Compared to a Healthy Child-Case Study.}, journal = {International journal of molecular sciences}, volume = {25}, number = {23}, pages = {}, pmid = {39684853}, issn = {1422-0067}, support = {PCN-1-111/N/2/O//Medical University of Silesia/ ; }, mesh = {Humans ; *Microbiota/genetics ; *Metagenomics/methods ; *Nanopore Sequencing/methods ; *Dental Enamel Hypoplasia/microbiology/genetics ; Child ; Mouth Mucosa/microbiology/pathology ; Male ; Female ; Bacteria/genetics/classification/isolation & purification ; Case-Control Studies ; Metagenome ; Incisor/microbiology ; Molar Hypomineralization ; }, abstract = {Molar incisor hypomineralization (MIH) is a qualitative developmental defect that affects the enamel tissue of permanent molars and can also occur in permanent incisors. Enamel affected by MIH has reduced hardness, increased porosity, and a higher organic content than unaffected enamel. These characteristics predispose the enamel to accumulation of bacteria and a higher prevalence of caries lesions. Through a groundbreaking metagenomic analysis of the buccal mucosal sample from a patient with MIH, we explored the intricacies of its microbiome compared to a healthy control using state-of-the-art nanopore long-read sequencing. Out of the 210 bacterial taxa identified in the MIH microbiome, we found Streptococcus and Haemophilus to be the most abundant genera. The bacteria with the highest read counts in the patient with MIH included Streptococcus mitis, Haemophilus parainfluenzae, Streptococcus pneumoniae, Rothia dentocariosa, and Gemella haemolysans. Our results revealed a striking contrast between healthy and MIH affected children, with a higher dominance and number of pathogenic species (S. pneumoniae, H. influenzae, and N. meningitidis) and reduced diversity in the MIH-affected patient. This distinct microbial profile not only sheds light on MIH-affected patients, but paves the way for future research, inspiring deeper understanding and larger scale studies.}, } @article {pmid39684830, year = {2024}, author = {Mansour, O and Fadeev, AV and Perederiy, AA and Danilenko, DM and Lioznov, DA and Komissarov, AB}, title = {Development of Primer Panels for Amplicon Sequencing of Human Parainfluenza Viruses Type 1 and 2.}, journal = {International journal of molecular sciences}, volume = {25}, number = {23}, pages = {}, pmid = {39684830}, issn = {1422-0067}, support = {TVKQ-2024-0003 "Complex approach to genetic characterization and early identifications of pathogens with epidemic and pandemic potential using metagenomic sequencing"//Ministry of Health of the Russian Federation/ ; }, mesh = {Humans ; *Parainfluenza Virus 1, Human/genetics/isolation & purification ; *Phylogeny ; *Genome, Viral ; *Parainfluenza Virus 2, Human/genetics/isolation & purification ; Russia ; DNA Primers/genetics ; RNA, Viral/genetics ; }, abstract = {Human parainfluenza viruses (hPIVs) are major contributors to respiratory tract infections in young children worldwide. Despite their global significance, genomic surveillance of hPIV1 and hPIV2 had not previously been conducted in Russia. This study aimed to develop a robust amplicon-based sequencing protocol for these viruses. The designed primer sets were tested on clinical samples containing hPIV RNA to evaluate their performance and efficiency. Sequencing results demonstrated high-quality genome data and efficient amplification across various Ct values. As a result, 41 hPIV1 and 13 hPIV2 near-complete genome sequences were successfully obtained from clinical specimens collected in Saint Petersburg (Russia). Phylogenetic analysis of the HN gene sequences showed that Russian hPIV1 strains clustered into clades II and III, while hPIV2 strains were distributed between clusters G1a and G3. The whole-genome-based trees confirmed the same distribution of the strains. These findings highlight the potential of our primer panels and contribute to a better understanding of the molecular characteristics and phylogenetic diversity of circulating hPIV strains. Notably, this study presents the first evolutionary analysis of hPIVs in Russia.}, } @article {pmid39684458, year = {2024}, author = {Salini, A and Zuliani, L and Gonnelli, PM and Orlando, M and Odoardo, A and Ragno, D and Aulitto, M and Zaccone, C and Fusco, S}, title = {Plastic-Degrading Microbial Consortia from a Wastewater Treatment Plant.}, journal = {International journal of molecular sciences}, volume = {25}, number = {23}, pages = {}, pmid = {39684458}, issn = {1422-0067}, support = {CUP B53D23015130001//MUR - Italian Ministry of University and Research in the framework of the Next Generation EU action/ ; }, mesh = {*Microbial Consortia ; *Wastewater/microbiology ; *Biodegradation, Environmental ; Sewage/microbiology ; Plastics/metabolism ; Bacteria/metabolism/classification/genetics/isolation & purification ; Microbiota ; }, abstract = {Plastic waste pollution has become a global crisis, with millions of tons of plastic expected to accumulate in landfills and in natural environments, posing a serious threat to wildlife and human health. As current recycling methods remain inefficient, there is an urgent need for innovative enzymatic solutions to break down plastics and enable a circular economy approach. In this study, we explore the plastic-degrading potential of microorganisms enriched from activated sludge (AS) sourced from a municipal wastewater treatment plant (WWTP)-a known microplastic-contaminated industrial niche. Five microbial consortia (i.e., microbiomes) were enriched under selective pressure using low-carbon conditions and high concentrations of polyester polymers, including post-consumer PET, post-consumer PLA, and virgin PLA. Enrichment was performed for 100 days at 37 °C and 50 °C, followed by microbiomes isolation and metagenomic analysis to identify plastic-active bacteria and their enzymes. The results revealed that PLA polymers, but not post-consumer PET, were effectively degraded by the microbiomes, as confirmed by nuclear magnetic resonance (NMR) and gel permeation chromatography (GPC), showing significant molecular weight reduction compared to the abiotic controls. Microbial community analysis highlighted a distinct enrichment profile driven by the polymer composition and the temperature. At 50 °C, the Bacillales order became the predominant population, whereas at 37 °C, a more diverse community within the Proteobacteria and Actinobacteria phyla were selected. Nonetheless, the enriched microbial communities at both temperatures included phyla with members known for polyester degradation. Moreover, at 50 °C, enrichment of putative PET/PLA hydrolases was also observed. These findings suggest that AS microorganisms are a reservoir of polyester-active enzymes, particularly PLA-depolymerases, and hold promise for advancing biotechnological strategies to mitigate plastic pollution through re- and up-cycling.}, } @article {pmid39684246, year = {2024}, author = {Domínguez-Pino, M and Mellado, S and Cuesta, CM and Grillo-Risco, R and García-García, F and Pascual, M}, title = {Metagenomics Reveals Sex-Based Differences in Murine Fecal Microbiota Profiles Induced by Chronic Alcohol Consumption.}, journal = {International journal of molecular sciences}, volume = {25}, number = {23}, pages = {}, pmid = {39684246}, issn = {1422-0067}, support = {2023-I024//the Spanish Ministry of Health-PNSD/ ; CIAICO/2021/203//GVA/ ; RD21/0009/0005//the Primary Addiction Care Research Network/ ; pro-ject IMPaCT-Data, exp. IMP/00019//FGG and RGR were supported by and partially funded by the Institute of Health Carlos III/ ; PID2023-146865OB-I00 and PID2021-124430OA-I00//MCIN/AEI/10.13039/501100011033/ FEDER/ ; }, mesh = {Animals ; Female ; Male ; *Feces/microbiology ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Toll-Like Receptor 4/genetics/metabolism ; *Metagenomics/methods ; *Mice, Knockout ; *RNA, Ribosomal, 16S/genetics ; *Ethanol/adverse effects ; Alcohol Drinking/adverse effects ; Mice, Inbred C57BL ; Sex Factors ; Dysbiosis/microbiology/chemically induced ; Sex Characteristics ; }, abstract = {Chronic ethanol exposure induces an inflammatory response within the intestinal tract, compromising mucosal and epithelial integrity and leading to dysbiosis of the gut microbiome. However, the specific roles of the gut microbiota in mediating ethanol-induced effects, as well as their interactions with the immune system, remain poorly characterized. This study aimed to evaluate sex-based differences in fecal microbiota profiles induced by chronic alcohol consumption and to assess whether TLR4 is involved in these effects. We analyzed the 16S rRNA gene sequencing of fecal samples from male and female wild-type (WT) and TLR4-knockout (TLR4-KO) mice with and without chronic ethanol exposure over a three-month period. Our findings provide evidence, for the first time, that male mice are more susceptible to the effects of ethanol on the fecal microbiota, since ethanol exposure induced greater alterations in the Gram-negative and -positive bacteria with immunogenic capacity in the WT male mice than in the female mice. We also demonstrate that the absence of immune receptor TLR4 leads to different microbiota in both sexes, showing anti-inflammatory and protective properties for intestinal barrier function and resulting in a phenotype more resistant to ethanol's effects. These findings may open new avenues for understanding the relationship between gut microbiota profiles and inflammation in the digestive system induced by chronic alcohol consumption.}, } @article {pmid39683635, year = {2024}, author = {Ouédraogo, LO and Deng, L and Ouattara, CA and Compaoré, A and Ouédraogo, M and Argaw, A and Lachat, C and Houpt, ER and Saidi, Q and Haerynck, F and Sonnenburg, J and Azad, MB and Tavernier, SJ and Bastos-Moreira, Y and Toe, LC and Dailey-Chwalibóg, T}, title = {Describing Biological Vulnerability in Small, Vulnerable Newborns in Urban Burkina Faso (DenBalo): Gut Microbiota, Immune System, and Breastmilk Assembly.}, journal = {Nutrients}, volume = {16}, number = {23}, pages = {}, pmid = {39683635}, issn = {2072-6643}, support = {INV-035474 & INV-036154/GATES/Bill & Melinda Gates Foundation/United States ; }, mesh = {Humans ; Burkina Faso ; Female ; Infant, Newborn ; *Gastrointestinal Microbiome ; *Milk, Human/immunology ; Prospective Studies ; *Vagina/microbiology/immunology ; *Immune System ; Pregnancy ; Breast Feeding ; Infant, Small for Gestational Age ; Adult ; }, abstract = {Background: Small vulnerable newborns (SVNs), including those born preterm, small for gestational age, or with low birth weight, are at higher risk of neonatal mortality and long-term health complications. Early exposure to maternal vaginal microbiota and breastfeeding plays a critical role in the development of the neonatal microbiota and immune system, especially in low-resource settings like Burkina Faso, where neonatal mortality rates remain high. Objectives: The DenBalo study aims to investigate the role of maternal and neonatal factors, such as vaginal and gut microbiota, immune development, and early nutrition, in shaping health outcomes in SVNs and healthy infants. Methods: This prospective cohort observational study will recruit 141 mother-infant pairs (70 SVNs and 71 healthy controls) from four health centers in Bobo-Dioulasso, Burkina Faso. The mother-infant pairs will be followed for six months with anthropometric measurements and biospecimen collections, including blood, breast milk, saliva, stool, vaginal swabs, and placental biopsies. Multi-omics approaches, encompassing metagenomics, metabolomics, proteomics, and immune profiling, will be used to assess vaginal and gut microbiota composition and functionality, immune cell maturation, and cytokine levels at critical developmental stages. Conclusions: This study will generate comprehensive data on how microbiota, metabolomic, and proteomic profiles, along with immune system development, differ between SVNs and healthy infants. These findings will guide targeted interventions to improve neonatal health outcomes and reduce mortality, particularly in vulnerable populations.}, } @article {pmid39682735, year = {2024}, author = {Hemmati, MA and Monemi, M and Asli, S and Mohammadi, S and Foroozanmehr, B and Haghmorad, D and Oksenych, V and Eslami, M}, title = {Using New Technologies to Analyze Gut Microbiota and Predict Cancer Risk.}, journal = {Cells}, volume = {13}, number = {23}, pages = {}, pmid = {39682735}, issn = {2073-4409}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Neoplasms/microbiology ; Machine Learning ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; }, abstract = {The gut microbiota significantly impacts human health, influencing metabolism, immunological responses, and disease prevention. Dysbiosis, or microbial imbalance, is linked to various diseases, including cancer. It is crucial to preserve a healthy microbiome since pathogenic bacteria, such as Escherichia coli and Fusobacterium nucleatum, can cause inflammation and cancer. These pathways can lead to the formation of tumors. Recent advancements in high-throughput sequencing, metagenomics, and machine learning have revolutionized our understanding of the role of gut microbiota in cancer risk prediction. Early detection is made easier by machine learning algorithms that improve the categorization of cancer kinds based on microbiological data. Additionally, the investigation of the microbiome has been transformed by next-generation sequencing (NGS), which has made it possible to fully profile both cultivable and non-cultivable bacteria and to understand their roles in connection with cancer. Among the uses of NGS are the detection of microbial fingerprints connected to treatment results and the investigation of metabolic pathways implicated in the development of cancer. The combination of NGS with machine learning opens up new possibilities for creating customized medicine by enabling the development of diagnostic tools and treatments that are specific to each patient's microbiome profile, even in the face of obstacles like data complexity. Multi-omics studies reveal microbial interactions, biomarkers for cancer detection, and gut microbiota's impact on cancer progression, underscoring the need for further research on microbiome-based cancer prevention and therapy.}, } @article {pmid39682313, year = {2024}, author = {Mazzei, M and Sorvillo, B and Sgorbini, M and Bindi, F and Perelli, A and Laus, F}, title = {The Role of Viral Pathogens in Horse Respiratory Diseases: A Cytological and Molecular Approach Using Next-Generation Sequencing.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {23}, pages = {}, pmid = {39682313}, issn = {2076-2615}, abstract = {(1) Background: Respiratory problems may be associated with pathogens among which viruses may play an important role in causing or promoting clinical signs. However, traditional diagnostic methods for equine infectious diseases, such as PCR, are limited to known pathogens and often miss rare or novel viruses. Metagenomic next-generation sequencing is a transformative method that allows the sequencing of all genomes present in a sample. Recent studies have used next-generation sequences to identify viral sequences in horses with unexplained respiratory symptoms, revealing potential links between viruses and respiratory problems. The aim of the study was to verify a relationship between respiratory diseases and the presence of viral agents through molecular analyses, applied to bronchoalveolar lavage fluid obtained from horses with history or presence of clinical signs of respiratory diseases. (2) Methods: A cohort of 14 horses was enrolled. All the subjects were submitted to a clinical assessment of the respiratory tract, thoracic ultrasound evaluation, respiratory tract endoscopy, and bronchoalveolar lavage. The latter one was used for cytological analysis, DNA and RNA extraction, and molecular biology analysis. (3) Results: No positive results were obtained in the molecular studies except for a sequence of 753 bp obtained by next-generation sequences, with complete homology to Equid gammaherpesvirus 2 strains. The samples were taken from a thoroughbred female horse aged 2 years old and referred for poor performance and sporadic cough at the beginning of the training session. (4) Conclusions: viral involvement may be not common in horses with respiratory diseases. We cannot exclude that the lack of virus detection may be due to the small sample size of the population included.}, } @article {pmid39681550, year = {2024}, author = {Baddouri, L and Hannig, M}, title = {Probiotics as an adjunctive therapy in periodontitis treatment-reality or illusion-a clinical perspective.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {148}, pmid = {39681550}, issn = {2055-5008}, mesh = {*Probiotics/therapeutic use/administration & dosage ; Humans ; *Periodontitis/therapy/microbiology ; Treatment Outcome ; }, abstract = {Periodontitis, a prevalent oral health issue, involves various microorganisms and clinical effects. This review examines probiotics as adjunctive therapy for periodontitis by analyzing forty clinical studies. Findings showed mixed results due to differences in study design, probiotic types, and clinical parameters; however, probiotics improved outcomes in severe cases. Caution is advised when interpreting these results, as longer follow-up periods reveal variability and potential regression in effects.}, } @article {pmid39681310, year = {2025}, author = {Tobar, Z and Lee, KY and Gaa, ME and Moore, BP and Li, X and Pitesky, ME}, title = {Evaluation of 16s Long Read Metabarcoding for Characterizing the Microbiome and Salmonella Contamination of Retail Poultry Meat.}, journal = {Journal of food protection}, volume = {88}, number = {2}, pages = {100434}, doi = {10.1016/j.jfp.2024.100434}, pmid = {39681310}, issn = {1944-9097}, mesh = {Animals ; *Salmonella/isolation & purification ; *Meat/microbiology ; *Food Contamination/analysis ; *Microbiota ; Poultry ; RNA, Ribosomal, 16S/genetics ; Food Microbiology ; Chickens/microbiology ; Humans ; }, abstract = {The traditional gold standard for detection of Salmonella in meat products is bacterial culture with enrichment. While this method is highly sensitive, it is slow and provides an incomplete assessment of isolate taxonomy in positive samples. This study presents a novel PCR-based detection assay which amplifies the 16s-ITS-23s region which is an approximately 2,500 base pair region of the larger ribosomal rrn operon. Intra-assay variation was assessed by splitting each biological sample into 3 technical replicates. Limits of detection (LOD) were assessed by utilizing a serial dilution of a pure culture of Salmonella enterica subsp. enterica serovar Heidelberg spiked into either sterile 1 × PBS or 1 × PBS rinsate of a Salmonella culture-negative chicken meat sample. Results indicate the 16s metabarcoding assay evaluated here could not be reliably used for the detection of Salmonella in adulterated retail meat samples as the LOD observed, 4.70 log colony forming units (CFU)/ml, is above the expected concentration of Salmonella in retail poultry meat samples which previous studies have shown range from under 1 to 2 log CFU/ml. However, due to greater taxonomic resolution afforded by using 16s long reads, the assay allowed alpha diversity assessment of the microbiome of raw poultry meat with the ability to assign taxonomy to the species and strain level for some amplicon sequence variants (ASV). This indicates this process may have value characterizing biodiversity and pathogen contamination of poultry samples in earlier steps of the poultry meat production process where bacterial contamination concentrations are likely to be higher.}, } @article {pmid39680298, year = {2025}, author = {Han, L and Lin, C and Lan, Y and Hua, Y and Wu, J and Fan, Z and Li, Y}, title = {Metagenomic Analysis of Gut Microbiome of Persistent Pulmonary Hypertension of the Newborn.}, journal = {Cardiovascular toxicology}, volume = {25}, number = {1}, pages = {135-147}, pmid = {39680298}, issn = {1559-0259}, support = {2021YFQ0061//Technology Project of Sichuan Province of China/ ; 82270249//National Natural Science Foundation of China/ ; }, mesh = {Humans ; Infant, Newborn ; *Gastrointestinal Microbiome ; *Metagenomics ; *Feces/microbiology ; Case-Control Studies ; Male ; *Bacteria/genetics/isolation & purification/classification/metabolism/growth & development ; Female ; Persistent Fetal Circulation Syndrome/microbiology/genetics ; Dysbiosis ; Host-Pathogen Interactions ; Intestines/microbiology ; }, abstract = {Persistent pulmonary hypertension of the newborn (PPHN) is one of the most common diseases in the neonatal intensive care unit which severely affects neonatal survival. Gut microbes play an increasingly important role in human health, but there are rarely reported how gut microbiota contribute to PPHN. In our study, the metagenomic sequencing of feces from 12 PPHN's neonates and 8 controls were performed to expose the relation between neonatal gut microbes and PPHN disease. Firstly, we found that the abundance of Actinobacteria, Proteobacteria, Bacteroidetes were significantly increased in PPHN compared with controls, but the Firmicutes components was reduced. And some pathogenic strains (like Vibrio metschnikovii) were significantly enriched in the PPHN compared with controls. Secondly, functional annotation of genes found that PPHN up-regulated transmembrane transport, but down-regulated ribosome and ATP binding. Lastly, microbial metabolic pathway enrichment analysis indicated that some metabolic pathway in PPHN were conflicting and contradictory, showed that an abnormally increased metabolism, disturbed protein synthesis and genomic instability in the PPHN neonate. Our results contribute to understanding the changes in the species and function of gut microbiota in PPHN, thus providing a theoretical basis for the explanation and treatment of PPHN.}, } @article {pmid39679737, year = {2024}, author = {Zhao, H and Wang, T}, title = {Debiased high-dimensional regression calibration for errors-in-variables log-contrast models.}, journal = {Biometrics}, volume = {80}, number = {4}, pages = {}, doi = {10.1093/biomtc/ujae153}, pmid = {39679737}, issn = {1541-0420}, mesh = {Humans ; Calibration ; *Models, Statistical ; Gastrointestinal Microbiome ; Computer Simulation ; Regression Analysis ; Bias ; Linear Models ; Biometry/methods ; Data Interpretation, Statistical ; Metagenomics/methods/statistics & numerical data ; }, abstract = {Motivated by the challenges in analyzing gut microbiome and metagenomic data, this work aims to tackle the issue of measurement errors in high-dimensional regression models that involve compositional covariates. This paper marks a pioneering effort in conducting statistical inference on high-dimensional compositional data affected by mismeasured or contaminated data. We introduce a calibration approach tailored for the linear log-contrast model. Under relatively lenient conditions regarding the sparsity level of the parameter, we have established the asymptotic normality of the estimator for inference. Numerical experiments and an application in microbiome study have demonstrated the efficacy of our high-dimensional calibration strategy in minimizing bias and achieving the expected coverage rates for confidence intervals. Moreover, the potential application of our proposed methodology extends well beyond compositional data, suggesting its adaptability for a wide range of research contexts.}, } @article {pmid39679708, year = {2025}, author = {Liu, Z and Jiang, C and Yin, Z and Ibrahim, IA and Zhang, T and Wen, J and Zhou, L and Jiang, G and Li, L and Yang, Z and Huang, Y and Yang, Z and Gu, Y and Meng, D and Yin, H}, title = {Ecological features of microbial community linked to stochastic and deterministic assembly processes in acid mine drainage.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {1}, pages = {e0102824}, pmid = {39679708}, issn = {1098-5336}, support = {2023YFE0114500//MOST | National Key Research and Development Program of China (NKPs)/ ; 92351303//MOST | National Natural Science Foundation of China (NSFC)/ ; BX20230437//Postdoctoral Fellowship Program of CPSF/ ; }, mesh = {*Microbiota ; *Mining ; *Bacteria/genetics/classification/isolation & purification/metabolism ; Phylogeny ; Stochastic Processes ; Metagenomics ; Acids/metabolism ; Metagenome ; }, abstract = {UNLABELLED: Ecological processes greatly shape microbial community assembly, but the driving factors remain unclear. Here, we compiled a metagenomic data set of microbial communities from global acid mine drainage (AMD) and explored the ecological features of microbial community linked to stochastic and deterministic processes from the perspective of species niche position, interaction patterns, gene functions, and viral infection. Our results showed that dispersal limitation (DL) (48.5%~93.5%) dominated the assembly of phylogenetic bin in AMD microbial community, followed by homogeneous selection (HoS) (3.1%~39.2%), heterogeneous selection (HeS) (1.4%~22.2%), and drift (DR) (0.2%~2.7%). The dominant process of dispersal limitation was significantly influenced by niche position in temperature (r = -0.518, P = 0.007) and dissolved oxygen (r = 0.471, P = 0.015). Network stability had a significantly negative correlation with the relative importance of dispersal limitation, while it had a positive correlation with selection processes, implying changes in network properties could be mediated by ecological processes. Furthermore, we found that ecological processes were mostly related to the gene functions of energy production and conversion (C), and amino acid transport and metabolism (E). Meanwhile, our results showed that the number of proviruses and viral genes involved in arsenic (As) resistance is negatively associated with the relative importance of ecological drift in phylogenetic bin assembly, implying viral infection might weaken ecological drift. Taken together, these results highlight that ecological processes are associated with ecological features at multiple levels, providing a novel insight into microbial community assembly in extremely acidic environments.

IMPORTANCE: Unraveling the forces driving community assemblage is a core issue in microbial ecology, but how ecological constraints impose stochasticity and determinism remains unknown. This study presents a comprehensive investigation to uncover the association of ecological processes with species niche position, interaction patterns, microbial metabolisms, and viral infections, which provides novel insights into community assembly in extreme environments.}, } @article {pmid39679619, year = {2024}, author = {Steinbach, E and Belda, E and Alili, R and Adriouch, S and Dauriat, CJG and Donatelli, G and Dumont, JL and Pacini, F and Tuszynski, T and Pelloux, V and Jacques, F and Creusot, L and Coles, E and Taillandier, P and Vazquez Gomez, M and Masi, D and Mateo, V and André, S and Kordahi, M and Rouault, C and Zucker, JD and Sokol, H and Genser, L and Chassaing, B and Le Roy, T and Clément, K}, title = {Comparative analysis of the duodenojejunal microbiome with the oral and fecal microbiomes reveals its stronger association with obesity and nutrition.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2405547}, pmid = {39679619}, issn = {1949-0984}, mesh = {Humans ; *Obesity/microbiology ; *Feces/microbiology ; Female ; Male ; Middle Aged ; *Gastrointestinal Microbiome ; Adult ; *Duodenum/microbiology ; *Bacteria/classification/isolation & purification/genetics/metabolism ; Jejunum/microbiology ; Mouth/microbiology ; Nutritional Status ; }, abstract = {The intestinal microbiota is increasingly recognized as a crucial player in the development and maintenance of various chronic conditions, including obesity and associated metabolic diseases. While most research focuses on the fecal microbiota due to its easier accessibility, the small intestine, as a major site for nutrient sensing and absorption, warrants further investigation to determine its microbiota composition and functions. Here, we conducted a clinical research project in 30 age- and sex-matched participants with (n = 15) and without (n = 15) obesity. Duodenojejunal fluid was obtained by aspiration during endoscopy. Phenotyping included clinical variables related to metabolic status, lifestyle, and psychosocial factors using validated questionnaires. We performed metagenomic analyses of the oral, duodenojejunal, and fecal microbiome, alongside metabolomic data from duodenojejunal fluid and feces, integrating these data with clinical and lifestyle information. Our results highlight significant associations between duodenojejunal microbiota composition and usual dietary intake, as well as clinical phenotypes, with larger effect sizes than the associations between these variables and fecal microbiota. Notably, we found that the duodenojejunal microbiota of patients with obesity exhibited higher diversity and showed distinct differences in the abundance of several duodenojejunal microbiota species compared with individuals without obesity. Our findings support the relevance of studying the role of the small intestinal microbiota in the pathogenesis of nutrition-related diseases.}, } @article {pmid39679617, year = {2024}, author = {McAdams, ZL and Gustafson, KL and Russell, AL and Self, R and Petry, AL and Lever, TE and Ericsson, AC}, title = {Supplier-origin gut microbiomes affect host body weight and select autism-related behaviors.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2385524}, pmid = {39679617}, issn = {1949-0984}, mesh = {*Gastrointestinal Microbiome ; Animals ; Mice ; Male ; *Autism Spectrum Disorder/microbiology ; *Body Weight ; Female ; *Behavior, Animal ; Disease Models, Animal ; Humans ; Brain-Gut Axis/physiology ; Bacteria/classification/isolation & purification/genetics ; Autistic Disorder/microbiology/psychology ; }, abstract = {Autism spectrum disorders (ASD) are complex human neurodiversities increasing in prevalence within the human population. In search of therapeutics to improve quality-of-life for ASD patients, the gut microbiome (GM) has become a promising target as a growing body of work supports roles for the complex community of microorganisms in influencing host behavior via the gut-brain-axis. However, whether naturally-occurring microbial diversity within the host GM affects these behaviors is often overlooked. Here, we applied a model of population-level differences in the GM to a classic ASD model - the BTBR T[+] Itpr3[tf]/J mouse - to assess how complex GMs affect host behavior. Leveraging the naturally occurring differences between supplier-origin GMs, our data demonstrate that differing, complex GMs selectively effect host ASD-related behavior - especially neonatal ultrasonic communication - and reveal a male-specific effect on behavior not typically observed in this strain. We then identified that the body weight of BTBR mice is influenced by the postnatal GM which was potentially mediated by microbiome-dependent effects on energy harvest in the gut. These data provide insight into how variability within the GM affects host behavior and growth, thereby emphasizing the need to incorporate microbial diversity within the host GM as an experimental factor in biomedical research.}, } @article {pmid39679616, year = {2024}, author = {Seki, D and Kirkegaard, R and Osvatic, J and Hausmann, B and Séneca, J and Pjevac, P and Berger, A and J Hall, L and Wisgrill, L and Berry, D}, title = {Gut microbiota genome features associated with brain injury in extremely premature infants.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2410479}, pmid = {39679616}, issn = {1949-0984}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; *Infant, Extremely Premature ; *Brain Injuries/microbiology/genetics ; *Feces/microbiology ; Female ; Male ; Bacteria/genetics/classification/isolation & purification/metabolism ; Genome, Bacterial ; Cohort Studies ; }, abstract = {Severe brain damage is common among premature infants, and the gut microbiota has been implicated in its pathology. Although the order of colonizing bacteria is well described, the mechanisms underlying aberrant assembly of the gut microbiota remain elusive. Here, we employed long-read nanopore sequencing to assess abundances of microbial species and their functional genomic potential in stool samples from a cohort of 30 extremely premature infants. We identify several key microbial traits significantly associated with severe brain damage, such as the genomic potential for nitrate respiration and iron scavenging. Members of the Enterobacteriaceae were prevalent across the cohort and displayed a versatile metabolic potential, including pathogenic and nonpathogenic traits. Predominance of Enterobacter hormaechei and Klebsiella pneumoniae were associated with an overall loss of genomic functional redundancy as well as poor neurophysiological outcome. These findings reveal microbial traits that may be involved in exacerbating brain injury in extremely premature infants and provide suitable targets for therapeutic interventions.}, } @article {pmid39679007, year = {2025}, author = {Wen, HQ and Chen, GL and Li, YS and Tian, T and Pan, Y and Yu, HQ}, title = {An inconvenient impact: Unveiling the overlooked differences in crystalline forms of iron (hydro)oxides on anaerobic digestion.}, journal = {Water research X}, volume = {26}, number = {}, pages = {100286}, pmid = {39679007}, issn = {2589-9147}, abstract = {Iron (hydro)oxides are commonly used to enhance anaerobic digestion due to their cost-effectiveness and versatility. However, the influence of crystalline structure on digestion performance is often overlooked despite their unique characteristics. In this study, we investigated how different crystalline forms of FeOOH affect substrate utilization, sludge activity, and the microbiomes in up-flow anaerobic sludge blanket (UASB) reactors. The crystalline structure of FeOOH impacted reactor performance, with γ-FeOOH, β-FeOOH, and α-FeOOH showing decreasing effectiveness, as reflected in chemical oxygen demand (COD) removal efficiencies of 99.0 %, 98.3 % and 97.1 %, respectively. FeOOH crystals influenced the secretion of extracellular polymeric substances (EPS) and sludge activity by releasing Fe ions at varying rates, leading to Fe accumulation in EPS in the order of β-FeOOH > γ-FeOOH > α-FeOOH. Additionally, γ-FeOOH supported the most stable microbial community structure, as indicated by the highest Alpha diversity index. This stability was associated with increased levels of Mesotoga and Syntrophus, along with the highest coenzyme F420 activity, which was approximately twice as high as in other groups. These findings underscore the crucial role of the crystalline structure of iron oxides in enhancing anaerobic digestion, emphasizing that biocompatibility should be a priority when optimizing digestion performance.}, } @article {pmid39678985, year = {2024}, author = {Sahoo, S and Behera, MR and Mishra, B and Kar, S and Sahoo, P and Sahoo, N and Biswal, S}, title = {Microbial Diversity and Resistome in Milk of Cows with Subclinical Mastitis in a Coastal District of Odisha, India.}, journal = {Indian journal of microbiology}, volume = {64}, number = {4}, pages = {1627-1636}, pmid = {39678985}, issn = {0046-8991}, abstract = {Mastitis is a globally prevalent bacterial disease of lactating cows. Prevention and control of this multi-etiological complex disease relies upon administration of antibiotics. This has led to the emergence of newer multi-drug resistant strains. In the current study, milk samples from subclinical mastitis cows and their healthy counterparts were subjected to Illumina-based whole genome metagenome sequencing to explore bacterial communities and antibiotic resistance genes associated with mastitis-affected and healthy udder. Bovine milk microbiome in subclinical mastitis-affected cows were dominated by pathogenic bacteria such as Acinetobacter baylyi, Acinetobacter pittii, Streptococcus agalactiae, Streptococcus suis, Streptococcus uberis, Aeromonas hydrophila, Aeromonas enteropelogenes, Lactococcus lactis, Corynebacterium resistens and Kocuria rhizophila. We observed higher bacterial abundance and diversity in milk of cows suffering from subclinical mastitis as compared to apparently healthy cows. Resistant genes against fluoroquinolones, peptides, β-lactams, tetracyclines and macrolides were detected in the subclinical group. In contrast, genes resistant to aminoglycosides, penams and β-lactams were found in healthy cow milk. The findings of the study expand our knowledge of bacterial diversity and associated resistant genes found in the milk of mastitis-affected and healthy cow milk.}, } @article {pmid39678952, year = {2024}, author = {Sinha, T and Talukdar, NC}, title = {Phylum Level Diversity of Plant Interior Bacteria in Seeds, Supernatant and Pellet Phases of Seed Suspension of Mustard Plant.}, journal = {Indian journal of microbiology}, volume = {64}, number = {4}, pages = {1587-1597}, pmid = {39678952}, issn = {0046-8991}, abstract = {Our previous study explored the bacterial endophytic diversity in a certain quantity of mustard seeds using culture dependent method by development of new isolation strategies. No bacterial colony was initially observed in supernatant obtained after centrifugation of mustard seed suspension. This was later overcome by usage of surfactant whereas pellet part showed presence of bacterial colonies on media. In our present study, presence of bacteria was examined in supernatant and whether the diversity was similar to that of pellet and seeds by culture independent approach. In addition, growth of bacterial colonies on media is explained using GC-MS. In this study, Proteobacteria was the dominant bacterial phyla followed by Firmicutes in pellet, supernatant and seed. This indicated that bacteria were present in supernatant but may not be viable when plated on media. This is either due to antimicrobial compounds or oil-imposed difficulty during their isolation which might have hindered their survival. GC-MS study revealed the presence of compounds with antimicrobial property as suggested by previous literature. Our research conducts fundamental investigations to address the primary objective of understanding the bacterial diversity in mustard seed, pellet, and supernatant. Further research using workflows of metagenomics and metabolomics approaches can enrich our understanding ofthe diversity of microorganisms in seeds.}, } @article {pmid39678942, year = {2024}, author = {Anjaria, P and Koringa, P and Bhavsar, P and Soni, M and Desai, M and Nayak, J and Chowdhury, S and Jangid, K and Brahmbhatt, MN}, title = {Metagenomic Analysis Reveals the Complex Microbial Landscape of Market Chicken Meat.}, journal = {Indian journal of microbiology}, volume = {64}, number = {4}, pages = {1846-1855}, pmid = {39678942}, issn = {0046-8991}, abstract = {UNLABELLED: The safety of meat from a microbiological standpoint is of paramount concern to public health, given the potential for bacterial contaminants to grow and persist during processing and storage. To address this issue, a culture-independent approach targeting the V3-V4 region of the 16S rRNA gene was utilized to investigate the inherent bacterial communities present in 10 chicken meat samples obtained from retail markets. Amplicons were sequenced using the Illumina MiSeq platform, and unique amplicon sequence variants (ASVs) were identified using the DADA2 pipeline. Results indicated the presence of 5 phyla, 7 classes, 16 orders, 33 families, 59 genera, and 273 unique ASVs. The dominant families were Flavobacteriaceae, Moraxellaceae, Enterobacteriaceae, Wohlfahrtiimonadaceae, Morganellaceae, and Pseudomonadaceae, comprising 27.03, 22.04, 15.67, 9.40, 7.92, and 5.02% of the identified families, respectively. Functional analysis using PICRUSt showed a diverse range of functional pathways. These findings have significant implications for policymaking regarding food safety and public health. Regular monitoring of bacterial communities in meat products is crucial to ensure their safety for consumption. This study demonstrates the utility of culture-independent approaches in characterizing microbial communities, which can provide valuable information for ensuring food safety and safeguarding public health.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-024-01249-y.}, } @article {pmid39678577, year = {2024}, author = {Cheng, W and Zhou, J and Li, C and Yao, J and Zhang, X and Mao, F and Gao, Z and Jiang, L and Xu, H}, title = {Severe pneumonia caused by Elizabethkingia anophelis combined with Acinetobacter baumannii infection: a case report.}, journal = {American journal of translational research}, volume = {16}, number = {11}, pages = {6821-6827}, pmid = {39678577}, issn = {1943-8141}, abstract = {Elizabethkingia anophelis is an obligate aerobic, Gram-negative bacillus belonging to the family of Weeksellacease. In recent years, there has been a gradual increase in E. anophelis related infections, especially in chronically hospitalized, immunocompromised populations that often develop severe pneumonia. Severe pneumonia is one of the common critical illnesses. Next-generation sequencing technologies developed based on PCR and gene chip technologies play an important role in the identification of pathogenic microorganisms and in molecular diagnosis. In this case, we report an elderly male patient diagnosed with severe pneumonia during the COVID-19 pandemic. The causative organisms were clearly identified as Elizabethkingia anophelis combined with Acinetobacter baumannii by next-generation sequencing. He was discharged from the hospital after being given cefoperazone sulbactam sodium and minocycline, as well as nebulized inhalation of chymotrypsin, salbutamol, and budesonide to assist ventilation. This article summarizes the diagnosis and treatment of this patient in order to share the experience of the subsequent treatments.}, } @article {pmid39678030, year = {2024}, author = {Szklenarik, G and Kiraly, P and Szegvari, G and Dora, D and Lohinai, Z}, title = {Predicting cancer-related mycobiome aspects in gastrointestinal cancers: a systematic review.}, journal = {Frontiers in medicine}, volume = {11}, number = {}, pages = {1488377}, pmid = {39678030}, issn = {2296-858X}, abstract = {BACKGROUND: Colonization of the human gut and tumor tissue by non-pathogenic fungi has emerged as a potential risk factor associated with cancer epidemics. Therefore, we aimed to conduct a systematic review to assess the role of fungal colonization in gastrointestinal (GI) tumors in increasing diagnostic efficiency.

METHODS: A PubMed citation search was conducted for publications up to and including March 2023, followed by full-text screening. Results were reported according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 guidelines. According to the Patient, Intervention, Comparison, Outcome (PICO) framework, patients diagnosed with early-and advanced-stage GI cancers, GI adenoma patients, and healthy subjects were included with metagenomic (MG) or internal transcribed spacer (ITS) sequencing on tumor tissue, adjacent normal tissue, stool, and blood samples.

RESULTS: Fourteen studies were eligible based on the inclusion criteria and methodological quality. Studies were conducted in stool (n = 8) or tissue (n = 7) as the most common specimens to be used for molecular analysis. In the collected data, ITS was used in n = 10 cases and metagenomic analyses in n = 3 cases. Observing the interindividual variability, we found that the Ascomycota/Basidiomycota (A/B) ratio from healthy to cancer state decreased in n = 2, increased in n = 1 cases, and did not change significantly in n = 2 studies. An increase in the relative abundance of Malassezia was identified in n = 4, of Candida in n = 5, of Saccharomyces in n = 2, and of Aspergillus in n = 2 cases. Intraindividual differences in the A/B ratio were identified in cancer and adjacent tissue (n = 4) and cancer vs. stool (n = 1) studies. Intraindividual variability of the A/B ratio showed an increase in n = 2 and no change in n = 3 studies for cancer tissue.

CONCLUSION: In conclusion, the advent of highly sensitive sequencing methods may aid in the identification and the differentiation of cancerous from healthy human fungal colonizations with potential future diagnostic applications. Further studies are needed to establish reliable biomarkers for GI cancer screening.}, } @article {pmid39677809, year = {2024}, author = {Nguyen, AT and Ratnasiri, K and Heitmann, GB and Tazin, S and Anderson, C and Hanif, S and Yeamin, A and Shoab, AK and Shanta, IS and Jahan, F and Hossain, S and Mahmud, ZH and Jubair, M and Rahman, M and Rahman, M and Ercumen, A and Benjamin-Chung, J}, title = {Pathogens and Antimicrobial Resistance Genes in Household Environments: A Study of Soil Floors and Cow Dung in Rural Bangladesh.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39677809}, issn = {2692-8205}, support = {F31 AI179107/AI/NIAID NIH HHS/United States ; R01 HD108196/HD/NICHD NIH HHS/United States ; }, abstract = {In low- and middle-income countries, living in homes with soil floors and animal cohabitation may expose children to fecal organisms, increasing risk of enteric and antimicrobial-resistant infections. Our objective was to understand whether cow cohabitation in homes with soil floors in rural Bangladesh contributed to the presence and diversity of potential pathogens and antimicrobial resistance genes (ARGs) in the home. In 10 randomly selected households in rural Sirajganj District, we sampled floor soil and cow dung, which is commonly used as sealant in soil floors. We extracted DNA and performed shotgun metagenomic sequencing to explore potential pathogens and ARGs in each sample type. We detected 6 potential pathogens in soil only, 49 pathogens in cow dung only, and 167 pathogens in both soil and cow dung. Pathogen species with relative abundances >5% in both soil floors and cow dung from the same households included E. coli (N=8 households), Salmonella enterica (N=6), Klebsiella pneumoniae (N=2), and Pseudomonas aeruginosa (N=1). Cow dung exhibited modestly higher pathogen genus richness compared to soil floors (Wilcoxon signed-rank test p=0.002). Using Bray-Curtis dissimilarity, pathogen species community composition differed between floors and cow dung (PERMANOVA p<0.001). All soil floors and cow dung samples contained ARGs against antibiotic classes including sulfonamides, rifamycin, aminoglycosides, lincosamides, and tetracycline. Paired floor and cow dung samples shared ARGs against rifamycin. Our findings support the development of interventions to reduce soil and animal feces exposure in rural, low-income settings.}, } @article {pmid39677801, year = {2024}, author = {Kindschuh, WF and Austin, GI and Meydan, Y and Park, H and Urban, JA and Watters, E and Pollak, S and Saade, GR and Chung, J and Mercer, BM and Grobman, WA and Haas, DM and Silver, RM and Serrano, M and Buck, GA and McNeil, R and Nandakumar, R and Reddy, U and Wapner, RJ and Kav, AB and Uhlemann, AC and Korem, T}, title = {Early prediction of preeclampsia using the first trimester vaginal microbiome.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39677801}, issn = {2692-8205}, support = {T15 LM007079/LM/NLM NIH HHS/United States ; U10 HD063036/HD/NICHD NIH HHS/United States ; UL1 TR001108/TR/NCATS NIH HHS/United States ; R01 CA245894/CA/NCI NIH HHS/United States ; U01 HL145358/HL/NHLBI NIH HHS/United States ; R01 HD114715/HD/NICHD NIH HHS/United States ; R01 HD106017/HD/NICHD NIH HHS/United States ; U10 HD063046/HD/NICHD NIH HHS/United States ; U10 HD063072/HD/NICHD NIH HHS/United States ; U10 HD063037/HD/NICHD NIH HHS/United States ; T32 GM007367/GM/NIGMS NIH HHS/United States ; U10 HD063048/HD/NICHD NIH HHS/United States ; F30 HD108886/HD/NICHD NIH HHS/United States ; U10 HD063047/HD/NICHD NIH HHS/United States ; U10 HD063041/HD/NICHD NIH HHS/United States ; P30 CA013696/CA/NCI NIH HHS/United States ; U10 HD063020/HD/NICHD NIH HHS/United States ; UL1 TR000153/TR/NCATS NIH HHS/United States ; U54 HD080784/HD/NICHD NIH HHS/United States ; U10 HD063053/HD/NICHD NIH HHS/United States ; }, abstract = {Preeclampsia is a severe obstetrical syndrome which contributes to 10-15% of all maternal deaths. Although the mechanisms underlying systemic damage in preeclampsia-such as impaired placentation, endothelial dysfunction, and immune dysregulation-are well studied, the initial triggers of the condition remain largely unknown. Furthermore, although the pathogenesis of preeclampsia begins early in pregnancy, there are no early diagnostics for this life-threatening syndrome, which is typically diagnosed much later, after systemic damage has already manifested. Here, we performed deep metagenomic sequencing and multiplex immunoassays of vaginal samples collected during the first trimester from 124 pregnant individuals, including 62 who developed preeclampsia with severe features. We identified multiple significant associations between vaginal immune factors, microbes, clinical factors, and the early pathogenesis of preeclampsia. These associations vary with BMI, and stratification revealed strong associations between preeclampsia and Bifidobacterium spp., Prevotella timonensis, and Sneathia vaginalis. Finally, we developed machine learning models that predict the development of preeclampsia using this first trimester data, collected ~5.7 months prior to clinical diagnosis, with an auROC of 0.78. We validated our models using data from an independent cohort (MOMS-PI), achieving an auROC of 0.80. Our findings highlight robust associations among the vaginal microbiome, local host immunity, and early pathogenic processes of preeclampsia, paving the way for early detection, prevention and intervention for this devastating condition.}, } @article {pmid39677745, year = {2024}, author = {Singh, NP and Khan, J and Patro, R}, title = {Alevin-fry-atac enables rapid and memory frugal mapping of single-cell ATAC-seq data using virtual colors for accurate genomic pseudoalignment.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39677745}, issn = {2692-8205}, support = {R01 HG009937/HG/NHGRI NIH HHS/United States ; }, abstract = {Ultrafast mapping of short reads to transcriptomic and metagenomic references via lightweight mapping techniques such as pseudoalignment has demonstrated success in substantially accelerating several types of analyses without much loss in accuracy compared to alignment-based approaches. The application of pseudoalignment to large reference sequences - like the genome - is, however, not trivial, due to the large size of the references or "targets" (i.e. chromosomes) and the presence of repetitive sequences within an individual reference sequence. This can lead to multiple matching locations for a k -mer within a single reference, which in turn can lead to false positive mappings and incorrect reference assignments for a read when the colors across the k -mer matches for a read are aggregated. Even when the read is determined to map to the appropriate reference, the increased occurrence of k -mer multi-matches within a reference can prevent the determination of the correct approximate position of the read, which is often critical in applications that map short reads to the genome.}, } @article {pmid39677482, year = {2024}, author = {Stachler, E and Gnirke, A and McMahon, K and Gomez, M and Stenson, L and Guevara-Reyes, C and Knoll, H and Hill, T and Hill, S and Messer, KS and Arizti-Sanz, J and Albeez, F and Curtis, E and Samani, P and Wewior, N and O'Connor, DH and Vuyk, W and Khoury, S and Schnizlein, MK and Rockey, NC and Broemmel, Z and Mina, M and Madoff, LC and Wohl, S and O'Connor, L and Brown, CM and Ozonoff, A and Park, DJ and MacInnis, BL and Sabeti, PC}, title = {Establishing methods to monitor H5N1 influenza virus in dairy cattle milk.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {39677482}, support = {U01 AI151812/AI/NIAID NIH HHS/United States ; U19 AI110818/AI/NIAID NIH HHS/United States ; }, abstract = {Highly Pathogenic Avian Influenza strain H5N1 has caused a multi-state outbreak among US dairy cattle, spreading across 15 states and infecting hundreds of herds since its onset. We rapidly developed and optimized PCR-based detection assays and sequencing protocols to support H5N1 molecular surveillance. Using 214 retail milk from 20 states for methods development, we found that H5N1 concentrations by digital PCR strongly correlated with qPCR cycle threshold (Ct) values, with dPCR exhibiting greater sensitivity. We also found that metagenomic sequencing after hybrid selection was best for higher concentration samples while amplicon sequencing performs best for lower concentrations. By establishing these methods, we were able to support the creation of a statewide surveillance program to test bulk milk samples monthly from all cattle dairy farms within Massachusetts, which remain negative to date. The methods, workflow, and recommendations described here provide a framework for others aiming to conduct H5N1 surveillance efforts.}, } @article {pmid39676850, year = {2024}, author = {Lu, Y and Gai, W and Li, M and Zheng, Y and Zhang, X and Zhou, Y and Zhou, J and Duan, J and Ruan, Y}, title = {Psittacosis Pneumonia Features, Distinguishing Characteristics, and Outcomes: A Retrospective Study.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {5523-5533}, pmid = {39676850}, issn = {1178-6973}, abstract = {PURPOSE: Psittacosis is an often-neglected cause of community acquired pneumonia (CAP). The limited diagnostic methods for psittacosis pneumonia invariably result in an unfavourable prognosis. Consequently, the early detection of psittacosis pneumonia is crucial. This study aimed to analyse the characteristics, clinical features and treatments of the patients to improve early diagnosis and outcomes.

PATIENTS AND METHODS: We retrospectively analyzed the clinical features and outcomes of 52 cases of psittacosis pneumonia diagnosed with next-generation sequencing (NGS) from January 2022 to August 2024 in a local tertiary hospital in China.

RESULTS: Of the 52 patients, 18 had a clear exposure to poultry or birds. The main clinical manifestations included fever (100%, 52/52), cough (75.0%, 39/52), fatigue (57.7%, 30/352), and dyspnea (36.5%, 19/52). Significant elevations in neutrophil counts (NEUT), C-reactive protein (CRP), alanine aminotransferase (ALT), aspartate aminotransferase (AST), D-dimer, lactate dehydrogenase (LDH), creatine kinase (CK), interleukin-6 (IL-6) and interferon-γ (IFN-γ), as well as reductions in lymphocyte (LY) and albumin (ALB) were observed. The main chest computed tomography (CT) features were consolidated. Eight patients diagnosed with severe CAP (SCAP) exhibited higher NEUT, CRP, procalcitonin (PCT), blood urea nitrogen (BUN), creatinine, D-Dimer and IL-6 levels, as well as lower oxygen index. The interval between the onset of symptoms and diagnosis was 6-34 days. C. psittaci infection was identified by metagenomic NGS (mNGS) or targeted NGS (tNGS) in all cases, and the average length of hospital stay for these patients was 9.4 days. Following the identification of the aetiology, all patients were promptly initiated on tetracycline- or fluoroquinolone-based therapy, with complete recovery observed in all cases.

CONCLUSION: Patients exposed to poultry should be alert to Chlamydia psittaci pneumonia. The application of NGS has improved the diagnostic accuracy of C. psittaci pneumonia, reduced unnecessary use of antibiotics, and shortened the course of disease. Patients who received tetracycline-based therapy showed a good prognosis.}, } @article {pmid39676846, year = {2024}, author = {Chen, YC and Chang, FY and Shang, ST and Wang, YC}, title = {Novel Use of Metagenomic Next-Generation Sequencing in Diagnosing Streptococcus intermedius Meningitis and Ventriculitis: A Case Report and Literature Review.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {5507-5512}, pmid = {39676846}, issn = {1178-6973}, abstract = {BACKGROUND: Streptococcus intermedius is a commensal microflora commonly found in various mucosal sites in the respiratory, gastrointestinal, and genitourinary tracts. It causes invasive suppurative infections including liver and brain abscesses along with thoracic empyema. However, it rarely causes meningitis without abscess formation.

CASE PRESENTATION: A 56-year-old immunocompetent man who presented with fever and headache. Bacterial meningitis was confirmed using cerebrospinal fluid analysis. Magnetic resonance imaging of the brain revealed leptomeningitis and ventriculitis. However, conventional methods, such as microbiological culture failed to identify the causative pathogens. Metagenomic next-generation sequencing of cerebrospinal fluid revealed the presence of S. intermedius. It allowed us the optimal treatment for him. The patient underwent antibiotic treatment with 6-week duration of ceftriaxone administration accompanied by surgical intervention, resulting in a favorable prognosis.

CONCLUSION: Herein, we report a rare case of meningitis and ventriculitis caused by S. intermedius using metagenomic next-generation sequencing. The patient recovered well after antibiotic treatment and surgery. We present this rare case and summarize previous studies to remind clinicians that timely identification of the pathogen and optimal treatment are crucial for management of S. intermedius-induced infections.}, } @article {pmid39676844, year = {2024}, author = {Shi, S and Gai, W and Huang, H and Zheng, Y and Zhang, X and Dai, Y and Wu, C}, title = {Adjunctive Diagnosis of Mycobacterium gordonae Pneumonia by Metagenomic Next-Generation Sequencing in an Immunocompetent Patient: A Case Report and Literature Review.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {5481-5489}, pmid = {39676844}, issn = {1178-6973}, abstract = {INTRODUCTION: Mycobacterium gordonae is a nonpathogenic pathogen commonly found in nature and is generally considered a contaminant in clinical practice. Although there have been few reported cases of infection, most of them are secondary to immunosuppression. This paper described a rare case of globular shadow in the chest of an immunocompetent male who was diagnosed with M. gordonae pulmonary disease. He went to the hospital with chest pains that had lasted for more than two weeks. The routine clinical pathogen detection failed to discover the cause of the infection. Although metagenomic next-generation sequencing (mNGS) of the lung tissue was negative, M. gordonae was detected in the background microorganism with only one read. Based on the pathological results, it was considered to be the causative pathogen. Two months of treatment with rifampicin, ethambutol, clarithromycin, and levofloxacin resulted in significant reduction and absorption of lung lesions. No abnormalities were detected in either lung one year later. The lack of positive culture and other conventional microbiological test results make this case is not a strictly confirmed case. This study also explored the clinical features and treatment options of 32 cases of M. gordonae pulmonary disease through a systematic review of the literature. Although there is no standard recommended treatment regimen for M. gordonae infection, but combination therapy with macrolides, rifampicin, and ethambutol has been proven effective.

CONCLUSION: This case highlights that when the clinical highly suspected of infection, mNGS can contribute to the early identification of non-tuberculous Mycobacterium (NTM) even with low reads, when clinical suspicion is high. Analyzing background microorganisms in sterile samples may help diagnose rare pathogens.}, } @article {pmid39676299, year = {2024}, author = {Raju, NP and Ansari, A and Patil, G and Sheeraz, MS and Kukade, S and Kumar, S and Kapley, A and Qureshi, A}, title = {Antibiotic Resistance Dissemination and Mapping in the Environment Through Surveillance of Wastewater.}, journal = {Journal of basic microbiology}, volume = {}, number = {}, pages = {e2400330}, doi = {10.1002/jobm.202400330}, pmid = {39676299}, issn = {1521-4028}, abstract = {Antibiotic resistance is one of the major health threat for humans, animals, and the environment, according to the World Health Organization (WHO) and the Global Antibiotic-Resistance Surveillance System (GLASS). In the last several years, wastewater/sewage has been identified as potential hotspots for the dissemination of antibiotic resistance and transfer of resistance genes. However, systematic approaches for mapping the antibiotic resistance situation in sewage are limited and underdeveloped. The present review has highlighted all possible perspectives by which the dynamics of ARBs/ARGs in the environment may be tracked, quantified and assessed spatio-temporally through surveillance of wastewater. Moreover, application of advanced methods like wastewater metagenomics for determining the community distribution of resistance at large has appeared to be promising. In addition, monitoring wastewater for antibiotic pollution at various levels, may serve as an early warning system and enable policymakers to take timely measures and build infrastructure to mitigate health crises. Thus, by understanding the alarming presence of antibiotic resistance in wastewater, effective action plans may be developed to address this global health challenge and its associated environmental risks.}, } @article {pmid39676101, year = {2024}, author = {Wang, C and Zhang, C and He, S and Wang, Q and Gao, H}, title = {The microbiome alterations of supragingival plaque among adolescents using clear aligners: a metagenomic sequencing analysis.}, journal = {Progress in orthodontics}, volume = {25}, number = {1}, pages = {48}, pmid = {39676101}, issn = {2196-1042}, support = {PY2023038//Science research cultivation program of stomatological hospital, Southern medical university/ ; PY2023043//Science research cultivation program of stomatological hospital, Southern medical university/ ; B2023274//Guangdong Medical Research Fund/ ; B2022013//Guangdong Medical Research Fund/ ; }, mesh = {Humans ; Adolescent ; *Dental Plaque/microbiology ; Male ; *Microbiota ; Female ; *Biofilms ; Child ; *Capnocytophaga ; Neisseria ; Metagenomics/methods ; Virulence Factors/genetics ; }, abstract = {BACKGROUND: White spot lesions (WSLs) may develop in adolescents undergoing clear aligner (CA) therapy with poor oral hygiene. The specific effects of CAs on the microbial composition and functional characteristics of supragingival plaques remain unclear. The present study investigated the shift in the supragingival microbial community induced by CAs in adolescents through metagenomic technology.

METHODS: Fifteen adolescents (12-15 years old) with Invisalign appliances were recruited. Supragingival plaque specimens were obtained twice, before treatment (T1) and three months after treatment (T2). All the bacterial plaque specimens were analyzed for microbial communities and functions using metagenomic analyses.

RESULTS: A total of 2,840,242,722 reads disclosed 180 phyla, 3,975 genera, and 16,497 microbiome species. During the first three months, the microbial community was relatively stable. The genus level revealed a higher relative abundance of Capnocytophaga, Neisseria, and Arachnia in the T2 period. Furthermore, the functional analysis suggested that the relative abundances of folate biosynthesis, biotin metabolism and biofilm formation-vibrio cholerae were increased in the T2 period compared to the T1 period. Finally, virulence factor analysis demonstrated that the relative abundance of genes associated with type IV pili (VF0082) and polar flagella (VF0473) was higher in the T2 period than in the T1 period.

CONCLUSION: In adolescents undergoing CA therapy with poor plaque control, caries progresses quickly within three months and noticeable WSLs develop on the tooth surface. Although the microbial community remained relatively steady and CA therapy did not cause significant changes in the overall functional gene composition in the first three months, virulence factors, including type IV pili and flagella, were more abundant and actively contributed to microorganism adhesion and biofilm formation.}, } @article {pmid39675582, year = {2025}, author = {Yan, J and Zhang, X and Guo, W and Wu, S and Chen, Y}, title = {Evidences of the electrogenic sulfur oxidation in constructed wetlands.}, journal = {Chemosphere}, volume = {370}, number = {}, pages = {143951}, doi = {10.1016/j.chemosphere.2024.143951}, pmid = {39675582}, issn = {1879-1298}, mesh = {*Wetlands ; *Oxidation-Reduction ; *Sulfur/metabolism ; *Sulfides/metabolism ; *Sulfates/metabolism ; Waste Disposal, Fluid/methods ; Bacteria/metabolism/genetics ; Iron ; }, abstract = {The sulfur redox cycling, mainly involving sulfide oxidation and sulfate reduction, remains a crucial factor that regulates the treatment performance of constructed wetlands (CWs). However, anoxic environments normally prevail in the CW systems, harboring vast reduced sulfur and sulfur minerals, where the occurrence and mechanism of anoxic sulfide oxidation remain unknown. In this study, CW microcosms filled with quartz sand (Qtz) and pyrite (Pyt) were established to investigate the anoxic sulfur oxidation under the bioelectrochemical manipulations. As a result, the δ[34]S-sulfate increased from 8.75 ± 0.29‰ in the influent to 51.74 ± 16.21‰ (Pyt) and 46.12 ± 25.95‰ (Qtz) at the anoxic zone under the open-circuit condition, and to 34.50 ± 6.99‰ (Pyt) and 42.53 ± 19.59‰ (Qtz) at that under the close-circuit conditions. This suggested the concurrent sulfate reduction and electrogenic sulfide oxidation in the systems. Based on a modified isotopic fractionation model, the electrogenic sulfide oxidation were further calculated (i.e., up to 87.58 and 265.13 mgS·m[-2]·d[-1] in Qtz and Pyt, respectively). Results of fluorescence in situ hybridization and metagenomic analyses demonstrated the occurrence of filamentous bacteria belonging to Desulfobulbaceae, with relative abundances of 0.32 ± 0.00% and 0.88 ± 0.25% in the anoxic zones of Qtz and Pyt, respectively. Pyrite was found to upregulate the functional genes encoding microbial transformation of elemental sulfur, sulfide, and thiosulfate. Interspecies network analyses revealed mutual relationships between the filamentous bacteria and microorganisms involved in sulfur, iron, and carbon transformations. Together, this study provided new insights to the electrogenic sulfide oxidation in CWs.}, } @article {pmid39675462, year = {2024}, author = {Wang, H and Liu, Q and Abouelfetouh, MM and Li, H and Zhu, H and Zhu, C and Kiani, FA and Ding, Y}, title = {The role of the hypothalamus-gut microbiota in the pathogenesis of periparturient fatty liver disease in dairy cows.}, journal = {Veterinary journal (London, England : 1997)}, volume = {309}, number = {}, pages = {106290}, doi = {10.1016/j.tvjl.2024.106290}, pmid = {39675462}, issn = {1532-2971}, abstract = {During the periparturient period, dairy cows experience negative energy balance due to reduced feed intake, leading to adipose tissue breakdown, liver damage, and fat accumulation. This study examined the gut-liver-brain axis to explore the link between fatty liver disease, changes in hypothalamic appetite-related neurons, and microbiome shifts in dairy cows. Thirty cows were monitored, with daily DMI recordings and blood sampling. Postpartum brain, liver, and ileal contents were collected from 10 selected cows, divided into two groups: H-DMI (slight DMI decrease) and L-DMI (severe DMI decrease). The L-DMI group of cows exhibited higher plasma NEFA, BHBA, ALT, and AST levels, along with severe hepatic steatosis and lipid accumulation. Transcriptome sequencing of the hypothalamic arcuate nucleus (ARC) revealed decreased expression of Hypocretin Neuropeptide Precursor (HCRT), orexin-A (OX-A), Orexin Receptor Type 1 (OX1R), and Cannabinoid Receptor 1 (CB1) in the L-DMI group, while Pro-opiomelanocortin (POMC) and Melanocortin 4 Receptor (MC4R) expression increased. Metagenomic analysis of ileal contents showed reduced abundance of Ruminococcus spp. in the L-DMI group, which may be associated with fatty liver disease (FL). Integrated omics analysis showed that increased MC4R expression was correlated with the elevated abundance of bacteria such as Akkermansia glycaniphila, and reduced abundance of species such as Methanobrevubacter thaueri and Ruminococcus spp. Decreased HCRT expression was also linked to Akkermansia glycaniphila. In conclusion, these changes may affect DMI through the OX-A/POMC pathway, with neurological and gut microbiome alterations potentially leading to appetite suppression, negative energy balance, and the development of fatty liver disease.}, } @article {pmid39675450, year = {2025}, author = {Ye, X and Niu, X and Li, L and Lv, M and Zhang, D and Chen, D and Line, Y and Yang, Z}, title = {Insights into the impact of 6PPD-Q and 6PPD on nitrogen metabolism and microbial community in the anammox system.}, journal = {Environmental research}, volume = {266}, number = {}, pages = {120485}, doi = {10.1016/j.envres.2024.120485}, pmid = {39675450}, issn = {1096-0953}, mesh = {*Nitrogen/metabolism ; Water Pollutants, Chemical/metabolism ; Microbiota/drug effects ; Bacteria/metabolism/genetics ; Waste Disposal, Fluid/methods ; Wastewater/microbiology ; Bioreactors/microbiology ; Oxidation-Reduction ; Anaerobiosis ; }, abstract = {N-(1,3-Dimethylbutyl)-N'-phenyl-p-phenylenediamine (6PPD) is an antioxidant commonly used in tire manufacturing, and its release into the environment has significantly increased due to rapid urbanization. When subjected to ozonation, 6PPD converts into the harmful pollutant 6PPD quinone (6PPDQ). These substances enter wastewater treatment plants (WWTPs) via stormwater runoff and pipelines, posing significant risks to the functional microorganisms. Anammox, a strictly controlled and sensitive microbial nitrogen removal process, is especially susceptible to the effects of the pollutants. This study investigates the comprehensive impact of 6PPD-Q and 6PPD on anammox communities based on characterization analysis and metagenomics. At environmental concentrations, 6PPD-Q at 200 ng/L-1000 ng/L led to the disintegration of anammox granules. Extended exposure to both 6PPD-Q and 6PPD significantly reduces the population of anammox bacteria (AnAOB). By utilizing organic matter from dead cells and incoming carbonate as a carbon source, the system evolved into a nitrogen metabolism network primarily focused on denitrification and dissimilatory nitrate reduction to ammonium (DNRA). This transformation was accompanied by a reshuffling of the microbial community and associated genes, resulting in an accumulation of NH4[+]-N. These findings underscore the toxicity of 6PPD-Q and 6PPD to anammox and stress the importance of incorporating 6PPD into regulatory and preventive strategies.}, } @article {pmid39675442, year = {2025}, author = {Tian, C and Yang, Q and Lv, H and Yue, F}, title = {Integrative analysis of gut microbiota and fecal metabolites in cynomolgus monkeys with spontaneous type 2 diabetes mellitus.}, journal = {Microbial pathogenesis}, volume = {199}, number = {}, pages = {107228}, doi = {10.1016/j.micpath.2024.107228}, pmid = {39675442}, issn = {1096-1208}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Feces/microbiology/chemistry ; *Macaca fascicularis ; *Diabetes Mellitus, Type 2/microbiology/metabolism ; *Fatty Acids, Volatile/metabolism/analysis ; *Metabolomics ; *Dysbiosis/microbiology ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Biomarkers ; Disease Models, Animal ; Metagenomics ; Male ; Metabolome ; }, abstract = {BACKGROUND: Accumulating evidence suggests that gut microbiota (GM) is clearly associated with the pathogenesis of type 2 diabetes mellitus (T2DM). However, the underlying mechanism of GM dysbiosis participates the onset of T2DM is not fully understood. The spontaneous T2DM cynomolgus monkeys are a powerful model for understanding the pathological mechanism of T2DM.

METHODS: Fecal samples were collected from 7 spontaneous T2DM cynomolgus monkeys and 7 healthy controls matched with similar age for multi-omics analysis, including shotgun metagenomic sequencing, untargeted metabolomics profiling, and targeted metabolomics focusing on short chain fatty acids (SCFAs). Lastly, the correlation network between differential gut microbial species and fecal metabolites was performed to explore the potential biomarkers of T2DM.

RESULTS: We found that 17 low-abundance species showed significant differences between the two groups. Analysis of gut microbial functions revealed that 16 KEGG pathways and 51 KEGG modules were significantly different in the two groups. Meanwhile, 276 fecal DEMs were identified, and these DEMs were enriched in the KEGG pathways, including Nucleotide metabolism, ABC transporters, Purine metabolism and so on. Lastly, Spearman correlation network analysis showed that the species of Anaerostipes_hadrus and Lachnoanaerobaculum_umeaense, and the metabolites including Glycerophospho-N-palmitoyl ethanolamine and 2-Hydroxycinnamic acid might serve as potential biomarkers of T2DM.

CONCLUSIONS: Our study provides novel insights into specific alterations in the GM composition, gene functions, and fecal metabolic profiles in spontaneous T2DM cynomolgus monkeys.}, } @article {pmid39675328, year = {2025}, author = {Wang, J and Cheng, Z and Su, Y and Wang, J and Chen, D and Chen, J and Wu, X and Chen, A and Gu, Z}, title = {Metagenomics and metatranscriptomics insights into microbial enhancement of H2S removal and CO2 assimilation.}, journal = {Journal of environmental management}, volume = {373}, number = {}, pages = {123714}, doi = {10.1016/j.jenvman.2024.123714}, pmid = {39675328}, issn = {1095-8630}, mesh = {*Carbon Dioxide/metabolism ; *Bioreactors ; *Hydrogen Sulfide/metabolism ; *Metagenomics ; Bacteria/metabolism/genetics ; }, abstract = {This study focuses on the coupled process of bio-enhanced absorption and biodesulfurization for the toxic gas H2S and the greenhouse gas CO2. The results show that on the basis of stabilized absorption of H2S and CO2 by alkaline solution (Stage I), the addition of air-lift bioreactor process solution in the absorption column enhanced their absorption (Stage II). Specifically, at constant inlet concentrations of H2S and CO2 of 3% (30,000 ppmv) and 30% (300,000 ppmv), respectively, the outlet gases were primarily H2S, CO2, and N2. And the outlet H2S and CO2 concentrations decreased from 10,038 ± 1166 ppmv and 49,897 ± 2545 ppmv in Stage I to 940 ± 163 ppmv and 21,000 ± 2165 ppmv in Stage II. S[0]-producing performance (348 ± 20-503 ± 23 mg S/L) and biomass concentration (467 ± 13-677 ± 55 mg/L) in the subsequent bioreactor also increased in response to the enhanced absorption of H2S and CO2. Biologically enhanced H2S and CO2 absorption differs from physicochemical factors in that it depends on several physiological parameters such as microbial community composition and gene expression levels. In this study, the sulfur autotrophic denitrifying bacteria Thioalkalivibrio and Arenimonas had high abundance and activity (abundance: 69.5% and 21.1%, expression: 82.4% and 13.9%), and they were the main contributors to the bio-enhanced absorption of H2S and CO2 in this system. In addition, the main factor for enhanced H2S absorption could be the high expression of sulfide:quinone oxidoreductase (SQR, encoding gene sqr) (45 ± 9 to 821 ± 102 transcripts per million). Enhanced CO2 absorption could have been achieved by the oxidation of more H2S generating more energy to increase the carboxylation activity of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco, encoding genes rbcLS). Enhanced H2S absorption enhances CO2 absorption and facilitates microbial growth, which in turn benefits the metabolism of H2S, creating a complementary biologically enhanced absorption. This study provides a novel strategy, demonstrating the potential of autotrophic sulfide-oxidizing microorganisms in the simultaneous removal of H2S and assimilation of CO2, and offers a deeper understanding of the underlying mechanisms.}, } @article {pmid39675160, year = {2024}, author = {Yuan, X and Zhang, Y and Pang, L and Zhang, X and Kang, Y and Hei, G and Li, X and Song, X}, title = {Insulin resistance links dysbiosis of gut microbiota with cognitive impairment in first-episode drug-naïve schizophrenia.}, journal = {Psychoneuroendocrinology}, volume = {172}, number = {}, pages = {107255}, doi = {10.1016/j.psyneuen.2024.107255}, pmid = {39675160}, issn = {1873-3360}, abstract = {This study aimed to explore the relationship among gut microbiota imbalance, the homeostasis model of assessment of insulin resistance (HOMA-IR) and cognitive impairments in patients with schizophrenia (SCZ). We conducted a case-control study involving 189 first-episode, drug-naïve SCZ patients and 115 healthy controls (HCs). Main methods adopted included metagenomics analysis, glucose metabolism assessment, and cognitive function evaluation using the MATRICS Consensus Cognitive Battery (MCCB). Fecal microbiota composition was analyzed via high-throughput sequencing of 16S ribosomal RNA. Patients with SCZ showed a higher likelihood of developing IR (23 %), compared to HCs (12 %). The IR group exhibited significantly higher levels of fasting blood glucose (FBG), fasting insulin (FINS), HOMA-IR, and homeostasis model assessment-β (HOMA-β), while showing lower insulin sensitivity index (ISI) levels (all p < 0.05). Patients with IR demonstrated lower scores in working memories (WM), verbal learning (HVLT) and reasoning and problem solving (RPS), compared to those without IR. Additionally, microbiota analysis revealed that IR patients had higher abundance of Negativicutes, Streptococcaceae, Enterobacteriaceae, Lachnoclostridium, Dialister, Klebsiella, and Enterobacter, and lower abundance of Flavonifractor and Rikenellaceae. Notably, Negativicutes, Streptococcaceae, Lachnoclostridium, Flavonifractor, and Rikenellaceae were shared between SCZ and IR conditions. Mediation analysis indicated that the relative abundance of Streptococcaceae have an indirect effect on WM through HOMA-IR (β=-0.148, SE=0.067, 95 %CI=-0.280 to -0.020). The study suggests that IR may play a mediating role in the relationship between gut microbiota dysbiosis and cognitive impairments in patients with SCZ, which could point to potential new avenues for therapeutic interventions.}, } @article {pmid39675116, year = {2025}, author = {Chai, Z and Tian, Z and Zheng, M and Wang, B and Li, Y and Cui, J and Ju, F and Niu, J and Guo, J}, title = {The functional dominance and metabolic diversity of comammox Nitrospira in recirculating aquaculture systems.}, journal = {Water research}, volume = {273}, number = {}, pages = {122949}, doi = {10.1016/j.watres.2024.122949}, pmid = {39675116}, issn = {1879-2448}, mesh = {*Aquaculture ; *Ammonia/metabolism ; *Bacteria/metabolism/genetics/classification ; *Archaea/metabolism/genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Oxidation-Reduction ; }, abstract = {As a newly discovered group of ammonia-oxidizing microorganisms, complete ammonia oxidizing (comammox) Nitrospira has been widely found in various oligotrophic ecosystems. However, their activity and ecological niche is still unclear in recirculating aquaculture systems (RAS). This study aimed to compare the abundance and activity of comammox Nitrospira, ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), and elucidate metabolic versatility of comammox Nitrospira in RAS. Quantitative PCR (qPCR) results showed that either comammox Nitrospira or AOB numerically predominated, while comammox Nitrospira and AOA shared similar low ammonia niches. Specifically, DNA-based stable isotope probing in conjunction with high-throughput 16S rRNA gene amplicon sequencing revealed that comammox Nitrospira accounted for 79.1 %, 97.5 %, 91.9 % and 97.6 % in the active ammonia-oxidizing community in four selected typical samples representing high abundance of comammox, AOA, and AOB, respectively. Phylogenetic analysis of heavy fraction DNA further identified novel comammox species from Nitrospira nitrificans cluster and clade A.2 acting as active species in different freshwater aquariums. Moreover, metagenome-assembled genome analysis revealed them as novel species with stress resistance and metabolic diversity compared with known comammox Nitrospira. This study underscores the dominant role of comammox Nitrospira as active ammonia-oxidizers in RAS and presents two novel comammox MAGs with metabolic flexibility, enriching our understanding of the nitrification process in oligotrophic artificial ecosystems.}, } @article {pmid39674354, year = {2025}, author = {Huang, L and Lv, Q and Ren, F and Wang, L and Song, Y and Wang, L and Xu, H and Zhang, G}, title = {Unlocking new electron transport routes: Insights into enhanced long-chain fatty acid conversion in valorization of lipid-rich waste.}, journal = {Bioresource technology}, volume = {418}, number = {}, pages = {131979}, doi = {10.1016/j.biortech.2024.131979}, pmid = {39674354}, issn = {1873-2976}, mesh = {*Fatty Acids, Volatile/metabolism ; *Fermentation ; Electron Transport ; Fatty Acids/metabolism ; Oxidation-Reduction ; Lipids/chemistry ; }, abstract = {In this study, the alkaline fermentation of combined lipid-rich waste (LRW) was explored to produce volatile fatty acids (VFAs). By introducing sulfate as an external electron acceptor, the long-chain fatty acid (LCFA) metabolic pathway was enhanced, achieving a VFA yield of 671.1 ± 21.9 mg COD/g VSS-an increase of 4.7 times compared to the control-under conditions of high lipid content (10 g/L). Significant conversion of LCFAs, such as oleic and linolenic acids, was achieved via the β-oxidation pathway, which also led to a synergistic enhancement of the fermentation of non-lipidic organic matter. Key functional genes from five LCFA metabolic modules were identified, revealing diverse electron transport routes, including non-syntrophic and syntrophic LCFA oxidation mediated by differentiated microbial function groups. Genome-centric metagenomics analysis further identified microbial functional groups responsible for the reconstructed pathways, offering new insights into optimizing LRW recycling and VFA production in anaerobic fermentation systems.}, } @article {pmid39674265, year = {2024}, author = {Ravishankar, S and Perez, V and Davidson, R and Roca-Rada, X and Lan, D and Souilmi, Y and Llamas, B}, title = {Filtering out the noise: metagenomic classifiers optimize ancient DNA mapping.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {1}, pages = {}, pmid = {39674265}, issn = {1477-4054}, support = {CE170100015//Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage/ ; GA204260//NHMRC SYNERGY/ ; //Australian Government Research Training Program Scholarship/ ; //Portuguese National Funds/ ; }, mesh = {*DNA, Ancient/analysis ; *Metagenomics/methods ; *Sequence Analysis, DNA/methods ; Humans ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; Workflow ; DNA Contamination ; }, abstract = {Contamination with exogenous DNA presents a significant challenge in ancient DNA (aDNA) studies of single organisms. Failure to address contamination from microbes, reagents, and present-day sources can impact the interpretation of results. Although field and laboratory protocols exist to limit contamination, there is still a need to accurately distinguish between endogenous and exogenous data computationally. Here, we propose a workflow to reduce exogenous contamination based on a metagenomic classifier. Unlike previous methods that relied exclusively on DNA sequencing reads mapping specificity to a single reference genome to remove contaminating reads, our approach uses Kraken2-based filtering before mapping to the reference genome. Using both simulated and empirical shotgun aDNA data, we show that this workflow presents a simple and efficient method that can be used in a wide range of computational environments-including personal machines. We propose strategies to build specific databases used to profile sequencing data that take into consideration available computational resources and prior knowledge about the target taxa and likely contaminants. Our workflow significantly reduces the overall computational resources required during the mapping process and reduces the total runtime by up to ~94%. The most significant impacts are observed in low endogenous samples. Importantly, contaminants that would map to the reference are filtered out using our strategy, reducing false positive alignments. We also show that our method results in a negligible loss of endogenous data with no measurable impact on downstream population genetics analyses.}, } @article {pmid39674156, year = {2025}, author = {Erkorkmaz, BA and Zeevi, D and Rudich, Y}, title = {Dust storm-driven dispersal of potential pathogens and antibiotic resistance genes in the Eastern Mediterranean.}, journal = {The Science of the total environment}, volume = {958}, number = {}, pages = {178021}, doi = {10.1016/j.scitotenv.2024.178021}, pmid = {39674156}, issn = {1879-1026}, mesh = {*Dust/analysis ; *Drug Resistance, Microbial/genetics ; *Air Microbiology ; Environmental Monitoring ; Iran ; Saudi Arabia ; Iraq ; Microbiota/drug effects ; Air Pollutants/analysis ; }, abstract = {The atmosphere hosts a microbiome that connects distant ecosystems yet remains relatively unexplored. In this study, we tested the hypothesis that dust storms enhance the spread of pathogenic microorganisms and whether these microorganisms carry antibiotic resistance and virulence-related genes in the Eastern Mediterranean. We collected air samples during a seasonal transition period, capturing data from 13 dusty days originating from Middle Eastern sources, including the Saharan Desert, Iraq, Iran, and Saudi Arabia, and 32 clear days, with temperatures ranging from 16.5 to 27.1 °C. Using metagenomic analysis, we identified several facultative pathogens like Klebsiella pneumoniae, Stenotrophomonas maltophilia, and Aspergillus fumigatus, which are linked to human respiratory diseases, and others like Zymoseptoria tritici, Fusarium poae, and Puccinia striiformis, which are harmful to wheat. The abundance of these pathogens increased during dust storms and with rising temperatures. Although we did not find strong evidence that these species harbored antibiotic resistance or virulence-related genes, which could be linked to their pathogenic potential, dust storms transported up to 125 times more total antibiotic resistance genes, as measured by RPKM abundance, compared to clear conditions. These levels during dust storms far exceeded those found in other ecosystems. While further research is needed to determine whether dust storms and temperature variations pose an immediate threat to public health and the environment, our findings underscore the importance of continuous monitoring of atmospheric microbiomes. This surveillance is crucial for assessing potential risks to human health and ecosystem stability, particularly in the face of accelerating global climate change.}, } @article {pmid39674142, year = {2025}, author = {Shi, W and Tian, Z and Luan, X and Wang, Y and Chi, Y and Zhang, H and Zhang, Y and Yang, M}, title = {Porous polyurethane biocarriers could enhance system nitrification resilience under high organic loading by retaining key functional bacteria.}, journal = {Water research}, volume = {272}, number = {}, pages = {122950}, doi = {10.1016/j.watres.2024.122950}, pmid = {39674142}, issn = {1879-2448}, mesh = {*Polyurethanes ; *Nitrification ; *Bioreactors ; *Bacteria/metabolism ; Waste Disposal, Fluid/methods ; Biofilms ; Wastewater ; Sewage/microbiology ; Porosity ; }, abstract = {Resilience to increasing organic loading rates (OLRs) is the key to maintaining stable performance in treating industrial wastewater. First, this study compared the stability, particularly the nitrification performance, of two lab-scale moving bed biofilm reactors (MBBRs) filled with porous polyurethane biocarriers with two conventional activated sludge reactors (ASRs) in the treatment of synthetic coking wastewater under OLRs increasing from 0.3 kg to 1.5 kg COD m[-3] day[-1]. In comparison with the ASRs, which could only achieve complete nitrification (99.31 % ± 0.43 %) at an OLR of 0.7 kg COD m[-3] day[-1], the MBBRs could achieve efficient NH4[+]-N removal (99.45 % ± 0.21 %) at an OLR as high as 1.3 kg COD m[-3] day[-1]. Even at an OLR of 1.5 kg COD m[-3] day[-1] where nitrification was inhibited, the porous polyurethane biocarriers in the MBBRs still maintained a highly diversified bacterial community (Shannon index, 4.34 ± 0.31) by retaining the slow-growing nitrifying bacteria and phenol-degrading bacteria, including Methyloversatilis and Acinetobacter, whose phenol degradation functions were confirmed by metagenome-assembled genome extraction and analysis, while the ASRs lost diversity (Shannon index, 1.41 ± 0.45) due to the sequential occurrence of filamentous and viscous sludge bulking. The advantage of the MBBR was further verified in a full-scale coking wastewater treatment system, where a reactor series filled with 4.35 % porous polyurethane biocarriers exhibited better NH4[+]-N removal of 99.57 % ± 0.34 % compared to 96.85 % ± 2.56 % for a conventional one under an OLR of 0.54 ± 0.12 kg COD m[-3] day[-1]. The results could contribute to the development of more effective and resilient treatment systems for industrial wastewater.}, } @article {pmid39673954, year = {2025}, author = {Manzi, HP and Qin, D and Yang, K and Li, H and Kiki, C and Nizeyimana, JC and Cui, L and Sun, Q}, title = {Unveiling bisphenol A-degrading bacteria in activated sludge through plating and [13]C isotope labeled single-cell Raman spectroscopy.}, journal = {Journal of hazardous materials}, volume = {485}, number = {}, pages = {136862}, doi = {10.1016/j.jhazmat.2024.136862}, pmid = {39673954}, issn = {1873-3336}, mesh = {*Benzhydryl Compounds/metabolism ; *Sewage/microbiology ; *Phenols/metabolism ; *Spectrum Analysis, Raman ; *Carbon Isotopes ; *Biodegradation, Environmental ; *Bacteria/metabolism/genetics ; Endocrine Disruptors/metabolism ; Single-Cell Analysis ; Isotope Labeling ; Water Pollutants, Chemical/metabolism ; Bisphenol A Compounds ; }, abstract = {Bacteria play a crucial role in biodegradation of recalcitrant endocrine-disrupting compounds (EDCs), such as bisphenol A (BPA). However, in-situ identification of BPA-degrading bacteria remains technically challenging. Herein, we employed a conventional plating isolation (PI) and a new single cell Raman spectroscopy coupled with stable isotope probing (Raman-SIP) approach to enrich and identify BPA-degrading bacteria from activated sludge (AS). AS-inhabitant bacteria were exposed to either [12]C-BPA or [13]C-BPA as sole carbon source over three consecutive generations. While PI relies on colony proliferation on agar media, Raman-SIP enables identification of in situ BPA-degrading bacteria in a culture-independent way. The results showed that BPA dissipation correlated with increased bacterial growth. The uptake of [13]C-BPA by single cells was verified by Raman spectra, suggesting occurrence of both metabolic and biosynthesis processes. This direct tracking of the fate of [13]C-BPA within cells highlights the advantages of Raman-SIP over PI technique. PI isolated four BPA-degrading bacterial strains belonging to Comamonas, Pseudomonas, and Herbaspirillum genera. Meanwhile, Raman-SIP identified labeled cells belonging to Comamonas and Pseudomonas genera. Metagenomics of labeled cells revealed the presence of fifteen genes associated with benzene ring cleavage. This study provides a novel Raman-SIP approach for detecting and characterizing BPA-assimilating bacteria at a single cell level.}, } @article {pmid39673943, year = {2025}, author = {Guo, H and Li, R and Su, Y and Xue, S and Li, N and Chen, F and Zhangsun, X and Zhang, H and Liu, X and Huang, T}, title = {Deciphering the antibiotic resistome in stratified source water reservoirs in China: Distribution, risk, and ecological drive.}, journal = {Journal of hazardous materials}, volume = {485}, number = {}, pages = {136734}, doi = {10.1016/j.jhazmat.2024.136734}, pmid = {39673943}, issn = {1873-3336}, mesh = {China ; *Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/drug effects ; Genes, Bacterial ; Water Microbiology ; Drug Resistance, Bacterial/genetics ; Water Supply ; Drug Resistance, Microbial/genetics ; }, abstract = {The proliferation and dissemination of antibiotic resistance genes (ARGs) in source water reservoirs may pose a threat to human health. This study investigated the antibiotic resistance in stratified reservoirs in China across different seasons and spatial locations. In total, 120 ARG subtypes belonging to 15 ARG types were detected with an abundance ranging from 171.06 to 793.71 × /Gb. Multidrug, tetracycline, aminoglycoside, and bacitracin resistance genes were dominant in the reservoirs. The abundance and transfer potential of ARGs were notably higher, especially during the stratified period, with markedly elevated levels in the bottom layer compared to the surface layer. Metagenomic assembly yielded 1357 ARG-carrying contigs, belonging to 83 resistant bacterial species, of which 13 were identified as human pathogen bacteria (HPB). HPB hosts (Sphingomonas sp., Burkholderiales sp., and Ralstonia sp., etc.) were super carriers of ARGs. Genes including ompR, bacA, golS, and ugd carried on HPB plasmids exhibited higher abundance in the water, warranting attention to the risk of resistance transmission. Environmental pressures have caused a shift in the assembly mechanism of ARGs, transitioning from a random process in surface water to a deterministic process in bottom water. The results of this study will deepen people's understanding of the ARG risk in stratified reservoirs.}, } @article {pmid39673746, year = {2024}, author = {Quraishi, MN and Cheesbrough, J and Rimmer, P and Mullish, BH and Sharma, N and Efstathiou, E and Acharjee, A and Gkoutus, G and Patel, A and Marchesi, JR and Camuzeaux, S and Chappell, K and Valdivia-Garcia, MA and Ferguson, J and Brookes, M and Walmsley, M and Rossiter, A and van Schaik, W and McInnes, RS and Cooney, R and Trauner, M and Beggs, A and Iqbal, T and Trivedi, PJ}, title = {Open label vancomycin in primary sclerosing cholangitis-inflammatory bowel disease: improved colonic disease activity and associations with changes in host-microbiome-metabolomic signatures.}, journal = {Journal of Crohn's & colitis}, volume = {}, number = {}, pages = {}, doi = {10.1093/ecco-jcc/jjae189}, pmid = {39673746}, issn = {1876-4479}, abstract = {BACKGROUND: We conducted a single-arm interventional study, to explore mucosal changes associated with clinical remission under oral vancomycin (OV) treatment, in primary sclerosing cholangitis associated inflammatory bowel disease (PSC-IBD); NCT05376228.

METHOD: Fifteen patients with PSC and active colitis (median faecal calprotectin 459µg/g; median total Mayo score 5) were treated with OV (125mg QID) for 4 weeks and followed-up for a further 4 weeks of treatment withdrawal (8 weeks, end-of-study). Colonic biopsies were obtained at baseline and week 4. Clinical assessments, and serum and stool samples (metagenomics, metatranscriptomics and metabolomics) were collected at weeks 0, 2, 4 and 8. The primary efficacy outcome measure was induction of clinical remission.

RESULTS: OV resulted in clinical remission in 12/15 patients and significant reductions in faecal calprotectin. OV was associated with reduced abundances of Lachnospiraceae, genera Blautia and Bacteroides; and enrichment of Enterobacteriaceae, and genera Veillonella, Akkermansia and Escherichia. OV treatment was associated with downregulation of multiple metatranscriptomic pathways (including short chain fatty acid [SCFA] metabolism and bile acid [BA] biotransformation), along with host genes and multiple pathways involved in inflammatory responses and antimicrobial defence; and an upregulation of genes associated with extracellular matrix repair. OV use resulted in loss of specific faecal SCFAs and secondary BAs, including lithocholic acid derivatives. Colitis activity relapsed following OV withdrawal, with host mucosal and microbial changes trending towards baseline.

CONCLUSION: Four weeks of OV induces remission in PSC-IBD activity, associated with a reduction in gut bacterial diversity and compositional changes relating to BA and SCFA homeostasis.}, } @article {pmid39673707, year = {2024}, author = {Huang, KD and Müller, M and Sivapornnukul, P and Bielecka, AA and Amend, L and Tawk, C and Lesker, TR and Hahn, A and Strowig, T}, title = {Dietary selective effects manifest in the human gut microbiota from species composition to strain genetic makeup.}, journal = {Cell reports}, volume = {43}, number = {12}, pages = {115067}, doi = {10.1016/j.celrep.2024.115067}, pmid = {39673707}, issn = {2211-1247}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Diet ; Adult ; Male ; Bacteria/genetics/classification ; Female ; Genetic Variation ; Middle Aged ; }, abstract = {Diet significantly influences the human gut microbiota, a key player in health. We analyzed shotgun metagenomic sequencing data from healthy individuals with long-term dietary patterns-vegan, flexitarian, or omnivore-and included detailed dietary surveys and blood biomarkers. Dietary patterns notably affected the bacterial community composition by altering the relative abundances of certain species but had a minimal impact on microbial functional repertoires. However, diet influenced microbial functionality at the strain level, with diet type linked to strain genetic variations. We also found molecular signatures of selective pressure in species enriched by specific diets. Notably, species enriched in omnivores exhibited stronger positive selection, such as multiple iron-regulating genes in the meat-favoring bacterium Odoribacter splanchnicus, an effect that was also validated in independent cohorts. Our findings offer insights into how diet shapes species and genetic diversity in the human gut microbiota.}, } @article {pmid39673340, year = {2024}, author = {Hosseini, SA and Julian, C and Galzi, S and Filloux, D and Roumagnac, P}, title = {First report of saffron-associated mastrevirus 1 from saffron in Iran.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-11-24-2462-PDN}, pmid = {39673340}, issn = {0191-2917}, abstract = {In spring 2022, 40 leaf samples of saffron plants harboring a wide variety of symptoms, including curling, yellowing, mosaic, dwarfing and leaf malformation were collected from three Khorasan provinces in Iran. These samples were processed using the virion-associated nucleic acid-based metagenomics approach (Moubset et al., 2022). Noteworthy, 147 contigs with a size >500 bp distributed among 35 samples with multiple symptomatic patterns (curling, yellowing, mosaic, dwarfing and leaf malformation) shared >90% nucleotide identity with saffron-associated mastrevirus 1 (SaM1) (Martínez-Fajardo et al., 2024). This virus has recently been detected from transcriptomic datasets from saffron (Crocus sativus L.) collected in India. SaM1 was proposed to belong to a new species of the Mastrevirus genus (Geminiviridae family) and was tentatively named Saffron-associated mastrevirus 1 (Martínez-Fajardo et al., 2024). In addition, contigs assigned to saffron potyviruses, including saffron latent virus, turnip mosaic virus and bean yellow mosaic virus were assembled from the 40 saffron samples pinpointing that no conclusion could be made on the causal virus of observed symptoms. Total DNAs of the 40 saffron samples were further extracted using the DNeasy Plant Mini Kit (Qiagen) and were tested for the presence of SaM1 using a primer pair amplifying a 327 bp long fragment located in the coat protein of SaM1 (CSAV_2F 5'-TTTAAGTCAGGGTCTGGAGATG-3'and CSAV_3R 5'-GGCATACTGTAACCTCGTCTTC). Amplification conditions were: an initial denaturation at 95°C for 10 min, 30 cycles at 95°C for 30 sec, 55°C for 30 sec, 72°C for 45 sec, and a final extension step at 72°C for 10 min. This PCR test confirmed that 28/40 samples tested positive for SaM1. Total DNAs from one sample (#69-32) testing positive for SaM1 was further amplified using Phi29 DNA polymerase (TempliPhi, GE Healthcare) by rolling circle amplification (RCA) as previously described (Shepherd et al., 2008). RCA products were used as a template for PCR amplification of the complete genome of SaM1 using abutting primers (CSAV_PST1F 5'-CTGCAGTTGCGGTAAGTCTATGTTGGCTG-3' and CSAV_PST1R 5'- CTGCAGAGACAACGATTCCCAAAATTACTTTGTTCC-3'). Amplification conditions were: an initial denaturation at 95°C for 10 min, 30 cycles at 95°C for 30 sec, 55°C for 1 min, 72°C for 2 min and 30 sec, and a final extension step at 72°C for 10 min. Amplification products of approximately 2.7 Kbp were gel purified, ligated to pGEM-T Easy (Promega) and sequenced by standard Sanger sequencing using a primer walking approach (Azenta, Germany). The arrangement of open reading frames within the 2,724 nt circular DNA of the CSAV_A9PstI clone (accession number PQ392009) is similar to those reported for mastreviruses, including the coat protein (CP), the movement protein (MP), the replication-associated protein (Rep) and the RepA protein. In addition, CSAV_A9PstI sequence shares 95.3% genome-wide identity with SaM1 consensus sequence assembled from transcriptomics data (Martínez-Fajardo et al., 2024). Overall, these results indicate that SaM1 is widely present in saffron in different regions of Northeast Iran. In addition, while all tested plant were infected by several viruses, the etiology of SaM1 remains to be determined precisely. To our knowledge, this is the first report of saffron-associated mastrevirus 1 from saffron in Iran.}, } @article {pmid39673321, year = {2024}, author = {Zhou, H and Xiao, L and Deng, Y and Wang, R and Li, Q and Ye, Y and Pei, X and Sun, L and Zhang, Y and Pan, F}, title = {Efficient degradation of tetracycline by Mn(III)-microbial complexes mediated by mnOx@ACF in sequencing batch reactors: performance, mechanism, and effect on microbial community structure.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {90}, number = {11}, pages = {3111-3122}, pmid = {39673321}, issn = {0273-1223}, support = {51908432//National Natural Science Foundation of China/ ; 2023AFB277//Natural Science Foundation of Hubei Province/ ; }, mesh = {*Bioreactors ; *Tetracycline/chemistry ; *Manganese Compounds/chemistry ; *Water Pollutants, Chemical/chemistry ; *Oxides/chemistry ; Manganese/chemistry ; Charcoal/chemistry ; Waste Disposal, Fluid/methods ; Bacteria/metabolism/genetics/drug effects ; }, abstract = {Engineered nanomaterials are widely used in water and wastewater treatment processes, and minimizing their adverse effects on biological treatment processes in wastewater treatment plants has become the primary focus. In this study, activated carbon fiber (ACF)-loaded manganese oxide nanomaterials (MnOx@ACF) were synthesized. A small-scale sequencing batch reactor (SBR) was constructed to simulate the synergistic degradation of pollutants by nanomaterials and microorganisms and the effects of nanomaterials on the structure of the microbial community in a wastewater treatment plant. The MnOx@ACF exhibited efficient removal of pollutants (98.7% in 30 cycles) and chemical oxygen demand (COD 96.4% in 30 cycles) through the formation of Mn-microbial complexes and enhanced cycling between Mn(III) and Mn(II) over 30 operating cycles. Metagenome analysis results showed that the microbial population composition and functional abundance increased when the SBR was exposed to different dosages of MnOx@ACF for a long time, among which 0.2 g/L MnOx@ACF exhibited the highest stimulation and influence on the functional abundance of microorganisms, which showed optimum ecological effects.}, } @article {pmid39673281, year = {2024}, author = {Wu, R and Su, Y and Liao, J and Shen, J and Ma, Y and Gao, W and Dong, Z and Dai, Y and Yao, K and Ge, J}, title = {Exome Sequencing Identified Susceptible Genes for High Residual Risks in Early-Onset Coronary Atherosclerotic Disease.}, journal = {Clinical cardiology}, volume = {47}, number = {12}, pages = {e70066}, pmid = {39673281}, issn = {1932-8737}, support = {//This study was supported by the National Key Research and Development Program of China (Grant No. 2016YFC1301200 and 2016YFC1301202) from the Ministry of Sciences and Technology of the People's Republic of China, Clinical Research Plan of Shanghai Hospital Development Center (No. SHDC2020CR1007A), and National Natural Science Foundation of China (82170460), and the National Science Foundation of Shanghai (Grant 21ZR1412700). Dr. Wu was funded by Outstanding Resident Clinical Postdoctoral Program of Zhongshan Hospital Affiliated to Fudan University (2023ZSQN32, 2024ZYYS-004)./ ; }, mesh = {Adult ; Aged ; Female ; Humans ; Male ; Middle Aged ; Age of Onset ; Coronary Angiography ; *Coronary Artery Disease/genetics ; *Exome Sequencing ; *Genetic Predisposition to Disease ; Phenotype ; Risk Assessment/methods ; Risk Factors ; }, abstract = {AIMS: Despite the tremendous improvement in therapeutic medication and intervention for coronary atherosclerotic disease (CAD), residual risks remain. Exome sequencing enables identification of rare variants and susceptibility genes for residual risks of early-onset coronary atherosclerotic disease (EOCAD) with well-controlled conventional risk factors.

METHODS: We performed whole-exome sequencing of subjects who had no conventional risk factors, defined as higher body mass index, smoking, hypertension and dyslipidemia, screened from 1950 patients with EOCAD (age ≤ 45 years, at least 50% stenosis of coronary artery by angiography), and selected control subjects from 1006 elder (age ≥ 65 years) with < 30% coronary stenosis. Gene-based association analysis and clinical phenotypic comparison were conducted.

RESULTS: Subjects without defined conventional risk factors accounted for 4.72% of young patients. Totally, 6 genes might be associated with residual risk of EOCAD, namely CABP1 (OR = 22.19, p = 0.02), HLA-E (OR = 22.19, p = 0.02), TOE1 (OR = 33.6, p = 0.002), HPSE2 (OR = 11.1, p = 0.04), CHST14 (OR = 22.19, p = 0.02) as well as KLHL8 (OR = 22.19, p = 0.02). Phenotypic analysis displayed the levels of low-density lipoprotein cholesterol in carriers of mutations from CABP1, HLA-E, TOE1, and HPSE2 were significantly elevated compared to noncarriers. Notably, extracellular matrix-associated CHST14 and fibrinogen-associated KLHL8 both displayed possible correlation with increased neutrophil proportion and decreased monocyte percentage (both p < 0.05), exerting potential effects on the residual inflammatory risks of EOCAD.

CONCLUSION: The study identified six genes related to dyslipidemia and inflammation pathways with potential association with residual risk of EOCAD, which will contribute to precision-based prevention in these patients.

TRIAL REGISTRATION: The GRAND study was registered at www.

CLINICALTRIALS: gov on July 14, 2015, and the registry number is NCT02496858.}, } @article {pmid39673188, year = {2025}, author = {Gomaa, F and Rogers, DR and Utter, DR and Powers, C and Huang, IT and Beaudoin, DJ and Zhang, Y and Cavanaugh, C and Edgcomb, VP and Bernhard, JM}, title = {Array of metabolic pathways in a kleptoplastidic foraminiferan protist supports chemoautotrophy in dark, euxinic seafloor sediments.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {39673188}, issn = {1751-7370}, support = {80NSSC21K0478/NASA/NASA/United States ; }, mesh = {*Foraminifera/metabolism/genetics ; *Geologic Sediments/microbiology ; *Metabolic Networks and Pathways/genetics ; *Chemoautotrophic Growth ; Anaerobiosis ; Metagenome ; Symbiosis ; Gene Expression Profiling ; Seawater/microbiology ; Transcriptome ; }, abstract = {Investigations of the metabolic capabilities of anaerobic protists advances our understanding of the evolution of eukaryotic life on Earth and for uncovering analogous extraterrestrial complex microbial life. Certain species of foraminiferan protists live in environments analogous to early Earth conditions when eukaryotes evolved, including sulfidic, anoxic and hypoxic sediment porewaters. Foraminifera are known to form symbioses as well as to harbor organelles from other eukaryotes (chloroplasts), possibly bolstering the host's independence from oxygen. The full extent of foraminiferal physiological capabilities is not fully understood. To date, evidence for foraminiferal anaerobiosis was gleaned from specimens first subjected to stresses associated with removal from in situ conditions. Here, we report comprehensive gene expression analysis of benthic foraminiferal populations preserved in situ on the euxinic (anoxic and sulfidic) bathyal seafloor, thus avoiding environmental alterations associated with sample recovery, including pressure reduction, sunlight exposure, warming, and oxygenation. Metatranscriptomics, metagenome-assembled genomes, and measurements of substrate uptake were used to study the kleptoplastidic foraminifer Nonionella stella inhabiting sulfur-oxidizing bacterial mats of the Santa Barbara Basin, off California. We show N. stella energy generation under dark euxinia is unusual because it orchestrates complex metabolic pathways for ATP production and carbon fixation through the Calvin cycle. These pathways include extended glycolysis, anaerobic fermentation, sulfide oxidation, and the presence of a membrane-bound inorganic pyrophosphatase, an enzyme that hydrolyzes inorganic pyrophosphate to actively pump protons across the mitochondrial membrane.}, } @article {pmid39672497, year = {2025}, author = {Zhou, L and Zhang, L and Dang, R and Han, G and Liu, J and Zhou, M and Xiao, L}, title = {Microbiota-induced asymmetry in coastal methane emission potential under experimental precipitation gradients.}, journal = {Environmental research}, volume = {266}, number = {}, pages = {120601}, doi = {10.1016/j.envres.2024.120601}, pmid = {39672497}, issn = {1096-0953}, mesh = {*Methane/metabolism ; *Microbiota ; China ; *Rain ; Wetlands ; Soil Microbiology ; Air Pollutants/analysis/toxicity ; }, abstract = {Climate models predict that the frequency and intensity of extreme precipitation events will increase globally. Despite carbon budget in coastal wetlands is known to be sensitive to precipitation variability, in where CH4 productions and potential mechanisms remain poorly understood. We investigated CH4 emission potential and its drivers after 7-year of field experiments with five precipitation gradients (-60%, -40%, ambient condition, +40%, +60%) in Yellow River Delta, China. The response of CH4 emission potential to precipitation gradients exhibited significant asymmetry, with the highest emission potential occurring under +40% precipitation. [13]C-isotope tracing experiment discovered the primary contribution of acetoclastic methanogenic pathway. +40% precipitation significantly improved the accumulation of aboveground biomass, soil organic carbon and total nitrogen. Microbial community abundance, but not composition, referring to metagenome-assembled genomes also actively responded to precipitation changes. For example, +40% precipitation increased the relative abundance of Methanosarcinia and Methanobacteria. Furthermore, CH4 emission potential was also promoted by higher microbial enzyme activity. Collectively, CH4 emission potential in response to 7-year experimental precipitations was regulated by microbiota-driven, showing obvious asymmetry.}, } @article {pmid39672231, year = {2024}, author = {Luo, HY and Fang, J and Zhang, WH and Chan, KC and Chan, YM and Dong, CX and Li, SL and Lyu, AP and Xu, J}, title = {Dissecting the anti-obesity components of ginseng: How ginseng polysaccharides and ginsenosides target gut microbiota to suppress high-fat diet-induced obesity.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2024.12.002}, pmid = {39672231}, issn = {2090-1224}, abstract = {INTRODUCTION: Ginseng demonstrates therapeutic potential in treating obesity, with both experimental and clinical studies suggesting its anti-obesity effects are mediated by gut microbiota. Nonetheless, the specific chemical components responsible for this effect remain largely unidentified.

OBJECTIVES: This study aims to investigate the anti-obesity effects and mechanisms of ginseng polysaccharides (GP) and ginsenosides (GS), the primary chemical components of ginseng, with a focus on their impact on gut microbiota.

METHODS: The impact of GP and GS on high-fat diet (HFD)-induced obesity was assessed using a mouse model. Molecular mechanisms were explored through a combination of chemical analysis, metagenomics, RT-qPCR, ELISA, and biochemical assays.

RESULTS: GP or GS administration effectively prevented adiposity in HFD-fed mice, and both effects were mediated by gut microbiota. Chemical analysis revealed diverse glycosyl groups in GP and GS. Metagenomics data suggested that GP-enriched species, e.g., Bacteroides stercorirosoris and Clostridiales bacterium encoded carbohydrate-active enzymes GH35, GH43 and PL9_1, while GS-enriched Sulfurospirillum halorespirans encoded GH16_5. These enzymes facilitated the utilization of glycosyl groups in GP and GS, selectively stimulating bacterial growth and reshaping the gut microbiota. Furthermore, bacterial species enriched by GP or GS encoded specific functional genes involved in short-chain fatty acid (SCFA) synthesis (K00625 and K00925 for GP; K18118, K00100, and K18122 for GS) and intestinal gluconeogenesis (IGN) (K01678, K00024, and K01596 for GP; K18118 and K00278 for GS). Consequently, the SCFA-GLP-1/PYY signaling and IGN were activated by both GP and GS to ameliorate obesity phenotypes.

CONCLUSION: GP and GS, containing diverse glycosyl groups, selectively stimulate specific gut bacteria, triggering mechanisms involved in SCFA-GLP-1/PYY signaling and IGN activation to reduce adiposity in HFD-fed mice. The study enhances understanding of the chemical components crucial for the gut microbiota-mediated anti-obesity effect of ginseng. The mechanistic understanding provides valuable insights for developing ginseng-based drugs or health products to combat obesity.}, } @article {pmid39672065, year = {2025}, author = {Ye, F and Deng, M and Sun, Z and Op den Camp, HJM and Wu, J and Wang, Y and Hong, Y}, title = {What causes the urban river to look darker? An underestimated source of sulfide production in methanogenic metabolism.}, journal = {Journal of hazardous materials}, volume = {485}, number = {}, pages = {136847}, doi = {10.1016/j.jhazmat.2024.136847}, pmid = {39672065}, issn = {1873-3336}, mesh = {*Rivers/microbiology/chemistry ; *Sulfides/metabolism ; *Geologic Sediments/microbiology ; *Methane/metabolism ; Cities ; Sulfur-Reducing Bacteria/metabolism/genetics ; }, abstract = {The blackening and increased smelling of waterbodies steadily affect urban aquatic ecology. Sulfide is recognized as the key substance responsible for the darkening of urban rivers. However, the pathway of sulfide production and the underling microbial mechanisms in urban rivers are not fully understood. This study executes a comprehensive approach to investigate mechanism of sulfide production within urban river sediments, integrating field survey, laboratory incubations, and metagenomic sequencing. The results reveal that both sulfide concentrations and sulfidogenic activities in darker river sediments are significantly higher than in lighter rivers. Both the sulfate-reducing bacteria (SRB) and methanogenic communities are closely related to the sulfide content in the sediments. The finding that inhibiting SRB enhanced the potential sulfide production rate suggests the importance of methanogen-derived processes as a sulfide source in sediments. Notably, the abundance of methylated thiol coenzyme M methyltransferase genes increased 53-fold upon after the continuous methionine amendment, confirming that methanogen-derived processes, rather than SRB-derived ones, dominated sulfide production when methylated sulfur compounds are abundant. Overall, this study highlights the potential significance of methanogenesis as a hitherto underestimated sulfide source in urban river sediments, providing valuable insights for optimizing strategies to prevent and mitigate the deterioration of urban aquatic ecosystems.}, } @article {pmid39671945, year = {2025}, author = {Justine, EE and Lee, HJ and Jung, KH and Lee, YS and Kim, YJ}, title = {Methane emission mitigation of Paenibacillus yonginensis DCY84[T] incorporated with silicate on paddy rice (Oryzae sativa L.) plantation revealed in soil microbiome profiling.}, journal = {The Science of the total environment}, volume = {958}, number = {}, pages = {177996}, doi = {10.1016/j.scitotenv.2024.177996}, pmid = {39671945}, issn = {1879-1026}, mesh = {*Oryza/microbiology ; *Soil Microbiology ; *Silicates ; *Methane/metabolism ; *Paenibacillus/physiology/metabolism ; *Microbiota ; Biodegradation, Environmental ; Agriculture/methods ; }, abstract = {Anthropogenic methane emissions from paddy cultivation contribute to greenhouse gas levels owing to the anaerobic conditions in flooded rice fields, which promotes the activity of methanogenic bacteria. This study explored bioremediation strategies to mitigate methane release through the application of plant growth-promoting rhizobacteria combined with silicate in rice cultivation. Rice seeds were coated with Paenibacillus yonginensis DCY84[T], with and without the addition of silicate, prior to sowing. Results revealed notable reduction in methane flux during the peak growth stage of rice in seeds treated with DCY84[T] (27.215 ± 1.975 mg m[-2] h[-1]), with a further reduction observed when silicate was also applied (23.592 ± 3.112 mg m[-2] h[-1]), compared to untreated seeds (37.305 ± 2.990 mg m[-2] h[-1]). Additionally, treatment with DCY84[T] (28.24 ± 0.55 g) resulted in an increase in rice yield (p < 0.05), as evidenced by a greater 1000-grain weight compared to both the control group (26.91 ± 0.09 g) and the application of silicate (27.37 ± 0.57 g). The beta diversity of the soil microbial community highlighted distinct differences between the treated and control groups, indicating DCY84[T] inoculation with or without silicate altered the soil microbial structure. Particularly, the treated groups showed dominance of the phylum Proteobacteria, especially the classes Alphaproteobacteria and Deltaproteobacteria. Furthermore, the addition of silicate to DCY84[T]-coated rice seeds resulted in a higher abundance of bacterial families, such as Anaerolinaceae, Clostridiceae, and Nitrospirae which compete with methanogens for organic substrates, thereby reducing their methane production. Notably, the DCY84[T]-silicate treatment group showed higher levels of methane metabolism biomarkers such as formate dehydrogenase within the soil microbiome, which correlated with the observed reduction in methane emissions. These findings suggest that coating rice seeds with DCY84[T] and silicate prior to sowing effectively mediates methane production and release during rice cultivation by promoting beneficial soil bacterial communities.}, } @article {pmid39671869, year = {2025}, author = {Feng, Y and Song, Y and Zhu, M and Li, M and Gong, C and Luo, S and Mei, W and Feng, H and Tan, W and Song, C}, title = {Microbes drive more carbon dioxide and nitrous oxide emissions from wetland under long-term nitrogen enrichment.}, journal = {Water research}, volume = {272}, number = {}, pages = {122942}, doi = {10.1016/j.watres.2024.122942}, pmid = {39671869}, issn = {1879-2448}, mesh = {*Wetlands ; *Nitrous Oxide ; *Carbon Dioxide ; *Nitrogen ; *Soil Microbiology ; Greenhouse Gases ; Methane/metabolism ; Soil/chemistry ; }, abstract = {Wetlands are frequently regarded as weak carbon dioxide (CO2) sinks, the largest natural sources of methane (CH4), and weak sources of nitrous oxide (N2O). Anthropogenic activities and climate change-induced nitrogen (N) enrichment may affect wetland carbon (C) and N cycling via soil microbes, consequently modifying the original greenhouse gas (GHG) emissions. However, the effects and mechanisms of the duration and rate of N inputs on wetland GHG emissions remain uncertain and controversial. Therefore, this study conducted an in situ field experiment to investigate the effects and driving mechanisms of long-term N enrichment on wetland GHG emissions throughout the 2023 growing season by using the static opaque chambers method. Soil microbial composition and function were also analyzed through metagenomic sequencing. The results showed that N enrichment significantly increased wetland CO2 emissions, which were associated with the abundance of microbial C-fixing functional genes and the soil C content. Although nitrogen enrichment tended to suppress CH4 emissions, the effect was not significant. High N enrichment created a powerful wetland N2O source driven by the abundance of microbial nitrification function genes and microbial species. Vegetation influenced wetland GHG emissions by altering soil carbon content. This study elucidates the response mechanism of wetland GHG emissions to long-term nitrogen enrichment, thereby furnishing a theoretical basis for wetland conservation and nitrogen management.}, } @article {pmid39671861, year = {2025}, author = {Buzzanca, D and Giordano, M and Chiarini, E and Ferrocino, I and Cocolin, L and Zeppa, G and Alessandria, V}, title = {Delving into Roccaverano PDO cheese: A comprehensive examination of microbial diversity and flavour profiles compared to non-PDO cheeses.}, journal = {International journal of food microbiology}, volume = {429}, number = {}, pages = {111014}, doi = {10.1016/j.ijfoodmicro.2024.111014}, pmid = {39671861}, issn = {1879-3460}, mesh = {*Cheese/microbiology ; *Volatile Organic Compounds/analysis ; *Taste ; Italy ; *Microbiota ; Humans ; Food Microbiology ; Flavoring Agents/analysis ; Bacteria/classification/isolation & purification/genetics ; Fungi/isolation & purification/classification/genetics ; Odorants/analysis ; Gas Chromatography-Mass Spectrometry ; }, abstract = {Roccaverano Protected Designation of Origin (PDO) is a fresh soft cheese produced in Roccaverano area (Italy). This study aimed to evaluate Roccaverano PDO microbiota, together with aromatic profile and sensory analysis to be compared with 15 non-PDO cheeses of the same type. Microbiota was evaluated through shotgun metagenomics sequencing, while GC-MS analysis was conducted to study volatile organic compounds (VOCs) presence and concentration. Sensory analyses were conducted through ONAF (Italian National Organization of Cheese Tasters) evaluation parameters followed by flash profile sensory analysis of selected cheeses. The results demonstrated Lactococcus lactis predominance in both non-PDO and PDO cheeses, while Streptococcus thermophilus was more abundant in non-PDO group. A higher abundance of Kluyveromyces lactis was observed in Roccaverano PDO, which exhibited greater fungal diversity compared to non-PDO cheeses. Metagenome-Assembled Genomes of 26 L. lactis and 19 Leuconostoc mesenteroides showed absence of significant differences in terms of average nucleotide identity and pangenomes partitions. The ONAF sensory evaluation demonstrated a higher average score of Roccaverano PDO group. Flash profile analysis demonstrated that lactic aroma/odour, acid, astringent, vegetal odour, exotic fruit and fermented aroma, hazelnut flavour and sweet were associated with high ONAF scores. The concentration of butanoic acid, 2-methyl-, ethyl ester and butanoic acid, 3-methyl- (sweat, acid, rancid related) were higher in PDO cheeses, while reads related to butanoate metabolism were less abundant compared to non-PDO samples. Several fungal species (included K. lactis) were associated with astringents, acid and chalky flavours. Roccaverano PDO demonstrates unique characteristics even maintaining a certain degree of variability between samples.}, } @article {pmid39671837, year = {2025}, author = {Li, S and Zhen, Y and Chen, Y and Mi, T}, title = {Geochemical and microbial controls on methane distribution in coastal sediments: A case study from the Bohai and South Yellow Seas, China.}, journal = {Marine pollution bulletin}, volume = {211}, number = {}, pages = {117448}, doi = {10.1016/j.marpolbul.2024.117448}, pmid = {39671837}, issn = {1879-3363}, mesh = {*Geologic Sediments/chemistry/microbiology ; *Methane/analysis ; China ; *Oceans and Seas ; Environmental Monitoring ; Microbiota ; Seasons ; }, abstract = {CH4 is among the most potent greenhouse gases. In this study, we investigated one of the important CH4 production hotspots, the continental margins. We examined the spatiotemporal distributions of CH4 in sediment cores from the Bohai and South Yellow Seas, China. Using real-time PCR and metagenomic sequencing, we analyzed the microbial communities related to CH4 production. Our results indicated that concentrations of CH4 generally increased with depth gradually, minimal seasonal variation observed between spring and summer. Notably, spatial heterogeneity, rather than temporal variation, was the predominant factor affecting CH4 distribution and methanogen community differences in sediments. Furthermore, the structure of microbial communities, in conjunction with environmental factors, significantly impacts potential CH4 production. These findings provide valuable insights into the mechanisms underlying methane production and its environmental controls in marine sediments.}, } @article {pmid39671103, year = {2024}, author = {Zhang, K and Mu, G and Wu, W and Wang, P and Shang, J and Li, C and Deng, Q and Fang, S and Wang, H and Zhang, S}, title = {An isolate of human blood-associated partitivirus naturally infects the phytopathogenic fungus Bipolaris maydis.}, journal = {Archives of virology}, volume = {170}, number = {1}, pages = {17}, pmid = {39671103}, issn = {1432-8798}, support = {No. 31972243//National Natural Science Foundation of China/ ; No. 2022JBXM03//the Science and Technology Project of Guizhou Tobacco Company/ ; }, mesh = {Humans ; *Phylogeny ; China ; *Bipolaris ; Genome, Viral ; Fungal Viruses/isolation & purification/classification/genetics ; RNA, Viral/genetics ; RNA Viruses/genetics/isolation & purification/classification ; RNA, Double-Stranded/genetics ; Double Stranded RNA Viruses/genetics/isolation & purification/classification ; }, abstract = {Human blood-associated partitivirus (HuBPV) was first identified through metagenomic analysis of serum samples from two Peruvians, but its natural host remains unknown. Here, we report the detection of an HuBPV strain (HuBPV-Bm) in the phytopathogenic fungus Bipolaris maydis strain HN11 in Hubei Province, China. The dsRNA1 and dsRNA2 of HuBPV-Bm show more than 97.6% and 98.8% nucleotide sequence identity, respectively, to those from the metagenomically discovered HuBPV strain (HuBPV-M). Notably, HuBPV-Bm contains a third dsRNA segment that was not reported for HuBPV-M. All mycelia derived from individual asexual spores of HN11 tested positive for HuBPV-Bm, as did nine out of 293 B. maydis strains collected across Hubei.}, } @article {pmid39670752, year = {2025}, author = {Peterson, D and Weidenmaier, C and Timberlake, S and Gura Sadovsky, R}, title = {Depletion of key gut bacteria predicts disrupted bile acid metabolism in inflammatory bowel disease.}, journal = {Microbiology spectrum}, volume = {13}, number = {2}, pages = {e0199924}, pmid = {39670752}, issn = {2165-0497}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Bile Acids and Salts/metabolism ; *Inflammatory Bowel Diseases/microbiology/metabolism ; *Feces/microbiology ; *Clostridium/genetics/metabolism/isolation & purification ; Animals ; Mice ; Bacteria/classification/genetics/metabolism/isolation & purification ; Operon ; Metagenomics ; Metagenome ; }, abstract = {The gut microbiome plays a key role in bile acid (BA) metabolism, where a diversity of metabolic products contribute to human health and disease. In particular, Inflammatory Bowel Disease (IBD) is characterized by a low concentration of secondary bile acids (SBAs), whose transformation from primary bile acids (PBAs) is an essential function performed solely by gut bacteria. BA-transformation activity mediated by the bile acid inducible (bai) operon has been functionally characterized in the genus Clostridium, and homologous bai gene sequences have been found in metagenome-assembled genomes (MAGs) belonging to other taxa in the human gut, but it is unclear which species of bai-carrying bacteria perform physiologically significant amounts of bile acid transformation in healthy and sick individuals. Here, we analyzed hundreds of stool samples with paired metagenomic and metabolomic data from IBD patients and controls and found that the abundance of the bai operon in metagenomic samples was highly predictive of that sample's high- or low-SBA metabolic state. We further found that bai genes from the Clostridium species best characterized as BA transformers were more prevalent in IBD patients than in non-IBD controls, while bai genes from uncharacterized taxa known only from MAGs were much more physiologically relevant in non-IBD samples. These un-isolated clades of BA-transforming bacteria merit further research; as beyond their prevalence in the human population, we found some cases in which they engrafted in IBD patients who had undergone fecal microbiota transplantation and experienced a clinical response.IMPORTANCEIn this paper, we identify specific bacteria that perform an important metabolic function in the human gut and demonstrate that in the guts of a large subset of patients with IBD, these bacteria are missing and the function is defective. This is a rare example where the correlation between the absence of specific bacteria and the dysfunction of metabolism is directly observed, not in mice nor in the lab, but in physiologic microbial communities in the human gut. Our results point to a path for studying how a small but important set of bacteria is affected by conditions in the IBD gut and perhaps to the development of interventions to mitigate the loss of these bacteria in IBD.}, } @article {pmid39670743, year = {2025}, author = {Wang, Y and Guo, C and He, J}, title = {Aquatic circoviruses: emerging pathogens in global aquaculture - from discovery to disease management.}, journal = {Journal of virology}, volume = {99}, number = {1}, pages = {e0173724}, pmid = {39670743}, issn = {1098-5514}, mesh = {Animals ; *Aquaculture ; *Fish Diseases/virology/epidemiology/transmission ; *Fishes/virology ; Host-Pathogen Interactions ; Communicable Diseases, Emerging/virology/epidemiology/veterinary/transmission ; Host Specificity ; Disease Management ; Genetic Variation ; }, abstract = {The expansion of global aquaculture has brought challenges from emerging pathogens, resulting in disease-related production losses across various regions. Among these pathogens, aquatic circoviruses-small, single-stranded DNA viruses initially detected in barbel (Barbus barbus)-have now been identified in multiple aquaculture species. These viruses have been associated with various clinical manifestations in economically important fish, crustacean, and mollusk species, including acute hemorrhage syndrome, which has shown mortality rates up to 95% in controlled laboratory infections of turbot. This review consolidates current knowledge on aquatic circoviruses, focusing on their genetic diversity, epidemiology, pathogenesis, and management strategies. The analysis encompasses observed host range patterns, documented instances of cross-species transmission, and evolutionary characteristics, such as host-specific clustering and recombination events. Research gaps are highlighted, particularly in understanding viral pathogenic mechanisms, host-pathogen interactions, and their ecological roles within aquatic ecosystems. We evaluate recent advances in diagnostic methods, including targeted vaccine design and RNA interference technology. The review outlines future research priorities, including elucidating cross-species transmission potential, developing effective treatments, and assessing the full economic impact of these viruses on aquaculture. By providing a comprehensive overview, this review aims to guide future research efforts and inform strategies to mitigate the impact of circoviruses on aquaculture sustainability.}, } @article {pmid39670058, year = {2024}, author = {Kantor, EJH and Robicheau, BM and Tolman, J and Archibald, JM and LaRoche, J}, title = {Metagenomics reveals the genetic diversity between sublineages of UCYN-A and their algal host plastids.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae150}, pmid = {39670058}, issn = {2730-6151}, abstract = {UCYN-A (or Cand. Atelocyanobacterium thalassa) has been recognized as a globally distributed, early stage, nitrogen-fixing organelle (the "nitroplast") of cyanobacterial origin present in the haptophyte alga Braarudosphaera bigelowii. Although the nitroplast was recognized as UCYN-A2, not all sublineages of UCYN-A have been confirmed as nitroplasts, and full genomes are still lacking for several known sublineages. We investigated the differences between UCYN-A sublineages by sequencing and assembly of metagenomic sequences acquired from cultured biomass from NW Atlantic seawater, which yielded near-complete Metagenome Assembled Genomes (MAGs) corresponding to UCYN-A1, -A4, and the plastid of the UCYN-A4-associated B. bigelowii. Weekly time-series data paired with the recurrence of specific microbes in cultures used for metagenomics gave further insight into the microbial community associated with the algal/UCYN-A complex. The UCYN-A1 MAG was found to have 99% average nucleotide identity (ANI) to the Pacific-derived reference genome despite its Atlantic Ocean origin. Comparison of the UCYN-A4 MAG (the initial genome sequenced from this sublineage) to other genomes showed that UCYN-A4 is sufficiently genetically distinct from both UCYN-A1 and UCYN-A2 (ANI of ~83% and ~85%, respectively) to be considered its own sublineage, but more similar to UCYN-A2 than -A1, supporting its possible classification as a nitroplast. The B. bigelowii plastid sequence was compared with published plastid sequences (sharing 78% ANI with Chrysochromulina parva) adding to our understanding of genomic variation across Haptophyta organelles and emphasizing the need for further full genomic sequencing of B. bigelowii genotypes and their organelles.}, } @article {pmid39670023, year = {2024}, author = {Zhang, D and Fan, J and Liu, X and Gao, X and Zhou, Q and Zhao, J and Xu, Y and Zhong, W and Oh, IJ and Chen, M and Wang, M}, title = {Lower respiratory tract microbiome is associated with checkpoint inhibitor pneumonitis in lung cancer patients.}, journal = {Translational lung cancer research}, volume = {13}, number = {11}, pages = {3189-3201}, pmid = {39670023}, issn = {2218-6751}, abstract = {BACKGROUND: The gut microbiome is associated with the occurrence and severity of immune-related adverse events (irAEs) in cancer patients undergoing immunotherapy. However, the relationship between the lower respiratory tract (LRT) microbiome and checkpoint inhibitor pneumonitis (CIP) in lung cancer patients who underwent immunotherapy is unclear. The aim of the present study was to investigate the associations between the LRT microbiome and CIP in lung cancer patients receiving immunotherapy.

METHODS: This retrospective study included lung cancer patients who received immunotherapy and had metagenomic next-generation sequencing (mNGS) results of LRT specimens [bronchoalveolar lavage fluid (BALF)]. Based on their final diagnosis, the patients were allocated to either the CIP group or the non-CIP group. We conducted an exploratory analysis of the LRT microbiome in the CIP and non-CIP patients, delineating the microbial composition, and comparing the differences between the two groups.

RESULTS: In total, 52 lung patients were included in the study, of whom 33 were allocated to the CIP group and 19 to the non-CIP group. The alpha- and beta-diversity analyses revealed no significant differences between the two groups. In the CIP group, the dominant phyla were Firmicutes (41.7%), Acinetobacter (18.2%), and Proteobacteria (16.3%). In the non-CIP group, the dominant phyla were Firmicutes (38.2%), Acinetobacter (18.4%), and Proteobacteria (17.8%). Notably, the relative abundance of the Proteobacteria phylum (P<0.001) and Firmicutes phylum (P=0.01) was significantly higher in the CIP group than the non-CIP group.

CONCLUSIONS: The elevated relative abundance of the Proteobacteria and Firmicutes phyla in the LRT samples is associated with CIP in lung cancer patients.}, } @article {pmid39764025, year = {2023}, author = {Bartlett, A and Blakeley-Ruiz, JA and Richie, T and Theriot, CM and Kleiner, M}, title = {Large Quantities of Bacterial DNA and Protein in Common Dietary Protein Source Used in Microbiome Studies.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39764025}, issn = {2692-8205}, support = {P30 DK034987/DK/NIDDK NIH HHS/United States ; R35 GM138362/GM/NIGMS NIH HHS/United States ; }, abstract = {Diet has been shown to greatly impact the intestinal microbiota. To understand the role of individual dietary components, defined diets with purified components are frequently used in diet-microbiota studies. Many of the frequently used defined diets use purified casein as the protein source. Previous work indicated that this casein contains microbial DNA potentially impacting results of microbiome studies. Other diet-based microbially derived molecules that may impact microbiome measurements, such as proteins detected by metaproteomics, have not been determined for casein. Additionally, other protein sources used in microbiome studies have not been characterized for their microbial content. We used metagenomics and metaproteomics to identify and quantify microbial DNA and protein in a casein-based defined diet to better understand potential impacts on metagenomic and metaproteomic microbiome studies. We further tested six additional defined diets with purified protein sources with an integrated metagenomic-metaproteomic approach and show that contaminating microbial protein is unique to casein within the tested set as microbial protein was not identified in diets with other protein sources. We also illustrate the contribution of diet-derived microbial protein in diet-microbiota studies by metaproteomic analysis of stool samples from germ-free mice (GF) and mice with a conventional microbiota (CV) following consumption of diets with casein and non-casein protein. This study highlights a potentially confounding factor in diet-microbiota studies that must be considered through evaluation of the diet itself within a given study.}, } @article {pmid39669776, year = {2024}, author = {Li, D and Li, M and Gao, H and Hu, K and Xie, R and Fan, J and Huang, M and Liao, C and Han, C and Guo, Z and Chen, X and Li, M}, title = {Integrative multiomics analysis reveals association of gut microbiota and its metabolites with susceptibility to keloids.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1475984}, pmid = {39669776}, issn = {1664-302X}, abstract = {Keloid scarring is a fibroproliferative disease of the skin, which can significantly impact one's quality of life through cosmetic concerns, physical discomfort (itchy; painful), restricted movement, and psychological distress. Owing to the poorly understood pathogenesis of keloids and their high recurrence rate, the efficacy of keloid treatment remains unsatisfactory, particularly in patients susceptible to multiple keloids. We conducted fecal metagenomic analyzes and both untargeted and targeted plasma metabolomics in patients with multiple keloids (MK, n = 56) and controls with normal scars (NS, n = 60); tissue-untargeted metabolomics (MK, n = 35; NS, n = 32), tissue-targeted metabolomics (MK, n = 41; NS, n = 36), and single-cell sequencing analyzes (GSE163973). Differences in the gut microbiota composition, plasma metabolites, and tissue metabolites were observed between the MK and NS groups; the core gut microbiota, Oxalobacter formigenes, Bacteroides plebeius, and Parabacteroides distasonis, were identified via the gut microbiome co-occurrence network. Single-cell data helped clarify the specific cells affected by plasma metabolites. An area under the curve analysis using a random forest model based on fecal metagenomics, plasma metabolomics, and tissue metabolomics revealed that gut bacteria, plasma, and tissue metabolites were effective in distinguishing between MK and NS groups. Decreased Bacteroides plebeius could lower uracil levels, altering systemic lipid metabolism, which may change the metabolic phenotype of secretory reticular fibroblasts in wounds, potentially leading to MK. These findings may open new avenues for understanding the multifactorial nature of keloid formation from the gut-skin axis and highlight the potential for novel therapeutic strategies targeting keloid lesions and the underlying systemic imbalances affected by the gut microbiome.}, } @article {pmid39669685, year = {2024}, author = {Oh, S and Gravel-Pucillo, K and Ramos, M and Schatz, MC and Davis, S and Carey, V and Morgan, M and Waldron, L}, title = {AnVILWorkflow: A runnable workflow package for Cloud-implemented bioinformatics analysis pipelines.}, journal = {F1000Research}, volume = {13}, number = {}, pages = {1257}, pmid = {39669685}, issn = {2046-1402}, support = {U24 HG010263/HG/NHGRI NIH HHS/United States ; }, mesh = {*Workflow ; *Computational Biology/methods ; *Cloud Computing ; *Software ; Genomics/methods ; Humans ; }, abstract = {Advancements in sequencing technologies and the development of new data collection methods produce large volumes of biological data. The Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) provides a cloud-based platform for democratizing access to large-scale genomics data and analysis tools. However, utilizing the full capabilities of AnVIL can be challenging for researchers without extensive bioinformatics expertise, especially for executing complex workflows. We present the AnVILWorkflow R package, which enables the convenient execution of bioinformatics workflows hosted on AnVIL directly from an R environment. AnVILWorkflow simplifies the setup of the cloud computing environment, input data formatting, workflow submission, and retrieval of results through intuitive functions. We demonstrate the utility of AnVILWorkflow for three use cases: bulk RNA-seq analysis with Salmon, metagenomics analysis with bioBakery, and digital pathology image processing with PathML. The key features of AnVILWorkflow include user-friendly browsing of available data and workflows, seamless integration of R and non-R tools within a reproducible analysis pipeline, and accessibility to scalable computing resources without direct management overhead. AnVILWorkflow lowers the barrier to utilizing AnVIL's resources, especially for exploratory analyses or bulk processing with established workflows. This empowers a broader community of researchers to leverage the latest genomics tools and datasets using familiar R syntax. This package is distributed through the Bioconductor project (https://bioconductor.org/packages/AnVILWorkflow), and the source code is available through GitHub (https://github.com/shbrief/AnVILWorkflow).}, } @article {pmid39669577, year = {2024}, author = {Gao, C and Wei, G and Zhang, C and Wang, C and Li, C and Li, R and Su, Z and Zheng, Z}, title = {Pneumocystis jirovecii pneumonia increases the 3-months mortality of anti-MDA5-antibody-positive dermatomyositis patients.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1504380}, pmid = {39669577}, issn = {1664-3224}, mesh = {Humans ; *Dermatomyositis/immunology/mortality ; *Pneumonia, Pneumocystis/immunology/mortality ; Male ; Female ; Middle Aged ; Retrospective Studies ; *Pneumocystis carinii/immunology ; *Interferon-Induced Helicase, IFIH1/immunology ; Aged ; Risk Factors ; Autoantibodies/immunology/blood ; Adult ; Bronchoalveolar Lavage Fluid/immunology/microbiology ; Prognosis ; Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use ; }, abstract = {BACKGROUND: Anti-melanoma differentiation-associated gene 5 antibody-positive dermatomyositis (anti-MDA5+DM) patients are associated with considerable mortality, and opportunistic infections including Pneumocystis jirovecii pneumonia (PJP)is the main cause. This study was to identify clinical characteristics, risk factors, and prognostic factors of PJP diagnosed by bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) in anti-MDA5+ DM patients.

METHODS: In this retrospective observational study, all patients admitted with suspected pneumonia were detected for mNGS in BALF. The demographics, comorbidities, laboratory parameters, and treatments of the patients were compared and analyzed in both groups to identify the potential risk factors for PJP and death via Logistic regression and Cox proportional hazards regression, respectively.

RESULTS: Overall, 92 patients were included in this study, 46(50.0%) were defined as PJP+ group, and the other 46 (50.0%) as PJP- group, and 31(67.4%) PJP occurred in the first 3 months. Increased neutrophil-lymphocyte ratio (NLR) and CRP were independent risk factors for PJP occurrence, while trimethoprim-sulfamethoxazole (TMP/SMZ) prophylaxis was an independent protective factor (all p<0.05). The three-months mortality rate was higher in the PJP+ group compared to PJP- group (43.5% vs 23.9%, p=0.047). Rapidly progressive interstitial lung disease (RPILD) was a main predictor of mortality in anti-MDA5+DM patients with PJP, whereas glucocorticoid use was a significant protective factor.

CONCLUSIONS: PJP has high prevalence and mortality in anti-MDA5+DM, while TMP/SMZ prophylaxis significantly reduces PJP risk. Mortality in PJP+ patients is primarily concentrated within the first 3 months, associated with RPILD. Early intervention with corticosteroids and prophylactic measures are crucial in reducing mortality.}, } @article {pmid39669269, year = {2024}, author = {Lee, KH and Kim, YO and Dho, SH and Yong, JJH and Oh, HS and Lee, JH and Yang, SJ and Cha, I and Chun, J and Lee, EH and Jeong, SJ and Woo, W and Choi, JP and Han, SH and Choi, GB and Huh, JR and Kim, LK and Song, YG}, title = {Altered gut microbiome in convalescent patients with coronavirus disease 2019.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1455295}, pmid = {39669269}, issn = {2235-2988}, mesh = {Humans ; *COVID-19/microbiology ; *Gastrointestinal Microbiome ; Male ; Female ; *Feces/microbiology/virology ; Middle Aged ; Prospective Studies ; *SARS-CoV-2/isolation & purification ; Longitudinal Studies ; *RNA, Ribosomal, 16S/genetics ; Adult ; Severity of Illness Index ; Convalescence ; Bacteria/classification/isolation & purification/genetics ; Aged ; }, abstract = {INTRODUCTION: Coronavirus disease 2019 (COVID-19) alters the gut microbiome. This study aimed to assess the association between the disease severity of COVID-19 and changes in stool microbes through a seven-month follow-up of stool collection.

METHODS: We conducted a multicentre, prospective longitudinal study of 58 COVID-19 patients and 116 uninfected controls. Differences in the gut microbiota were analysed using 16S ribosomal RNA sequencing. The first stool samples were collected at an early convalescent phase of COVID-19, and the second sample was collected at least seven months after COVID-19 infection.

RESULTS AND DISCUSSION: At the order level, Eubacteriales and Bifidobacteriales decreased, while Bacteroidales and Burkholderiales increased in the COVID-19 group compared to the controls. Alpha diversity also decreased in COVID-19 patients compared to controls, with imperfect recovery of the gut microbiome after seven months. The compositional change in the gut microbiome between the early and late convalescent phases was largest in the moderate and severe groups. The severity of COVID-19 was the most influential clinical variable for microbiome composition (Sum of Sqs = 0.686, P = 0.006), and its effect persisted even after partialling out other effects such as antibiotic use and age. Thus, our study indicates a possible interaction between respiratory viral infection and the composition of the gut microbiota community, warranting future mechanistic and prospective longitudinal studies. Additionally, we were able to detect microbiome changes in patients who were re-infected with SARS-CoV-2. Notably, the dominant bacteria in the re-infected group were Lachnospiraceae and Faecalimonas umbilicata, compared to the one-time infected group.}, } @article {pmid39667971, year = {2024}, author = {Ji, L and Chen, X and Chen, B and Jin, N and Yang, J}, title = {Diagnostic Value of Cerebrospinal Fluid Sequencing for Neurosyphilis with Cognitive Impairment.}, journal = {Biomedical and environmental sciences : BES}, volume = {37}, number = {11}, pages = {1334-1337}, doi = {10.3967/bes2024.167}, pmid = {39667971}, issn = {2214-0190}, mesh = {Humans ; Anti-Bacterial Agents/therapeutic use ; *Cognitive Dysfunction/diagnosis/etiology ; High-Throughput Nucleotide Sequencing ; *Neurosyphilis/diagnosis/cerebrospinal fluid/complications/drug therapy ; Treponema pallidum/genetics/isolation & purification ; }, abstract = {Neurosyphilis (NS) is an infectious disease caused by Treponema pallidum invading the central nervous system. It can manifest at any stage of syphilis, and is often misdiagnosed due to its atypical and progressive symptoms. The increasing incidence of NS underscores the necessity for early and accurate diagnosis. Here, we present a case where routine cerebrospinal fluid metagenomic next-generation sequencing (mNGS) was used to diagnose a patient with neurosyphilis. The patient exhibited cognitive impairment and was initially diagnosed with cerebral infarction due to syphilitic cerebral arteritis. Thus, the patient was treated with dual antiplatelet therapy (aspirin and clopidogrel) and statins to stabilize the plaques. Neurosyphilis was treated with penicillin sodium injections, resulting in significant improvement in the patient's mental state. This case is a rare instance of neurosyphilis associated with cerebral infarction. These findings suggest that mNGS is a valuable tool in diagnosing neurosyphilis, potentially improving diagnostic accuracy and patient outcomes.}, } @article {pmid39667481, year = {2025}, author = {Hu, S and Lu, P and Feng, Y and Chen, A and Han, G}, title = {Elucidating the role of the genus Pseudomonas involved in coumarin degradation.}, journal = {Environmental research}, volume = {266}, number = {}, pages = {120603}, doi = {10.1016/j.envres.2024.120603}, pmid = {39667481}, issn = {1096-0953}, mesh = {*Coumarins/metabolism ; *Pseudomonas/genetics/metabolism ; *Biodegradation, Environmental ; Soil Microbiology ; Soil Pollutants/metabolism ; }, abstract = {Coumarin, a synthetic chemical and phytotoxin, exhibits hepatotoxicity and carcinogenicity, posing threats to both human health and environmental safety. Microbial degradation effectively mitigates environmental contamination. In this study, a coumarin-degrading bacterial consortium designated as XDS-7 with Pseudomonas as the key degrader was obtained. However, there is a lack of comprehensive perspective on the key role of the genus Pseudomonas involved in coumarin degradation. We employed the consortium XDS-7 as a model system to investigate the critical role of the genus Pseudomonas involved in coumarin degradation. Metagenomic binning analysis indicated that bin 14 (Pseudomonas sp.) contains the full complement of genes required for coumarin degradation. A coumarin-degrading bacterium, Pseudomonas sp. strain X4, was isolated from consortium XDS-7 using a traditional enrichment method supplemented with chloramphenicol. Genomic analysis demonstrated that strain X4 carries a suite of genes to completely degrade coumarin. Bioinformatics analysis revealed that putative coumarin-degrading bacteria are widely distributed across diverse bacteria of the genus Pseudomonas. In addition, strain X4 completely removed 100 mg kg[-1] of coumarin from contaminated soil within 48 h and 100 mg L[-1] of coumarin from contaminated wastewater within 4 h. This study will greatly enhance our understanding and utilization of these valuable bioresources.}, } @article {pmid39667480, year = {2025}, author = {Zhu, Q and Du, Y and Zheng, Y and Hu, Z and Liu, Z and Hu, J and Hou, H}, title = {Quorum quenching inhibits the formation and electroactivity of electrogenic biofilm by weakening intracellular c-di-GMP and extracellular AHL-mediated signal communication.}, journal = {Environmental research}, volume = {266}, number = {}, pages = {120604}, doi = {10.1016/j.envres.2024.120604}, pmid = {39667480}, issn = {1096-0953}, mesh = {*Biofilms/growth & development ; *Quorum Sensing ; *Cyclic GMP/analogs & derivatives/metabolism ; Signal Transduction ; Acyl-Butyrolactones/metabolism ; Geobacter/physiology/metabolism ; }, abstract = {Electrogenic biofilm formation has been shown to be induced by intracellular c-di-GMP signaling and extracellular quorum sensing, but their interactions have been rarely explored. This study explored the effects of quorum quenching (induced by adding acylase) on electrogenic biofilm development and its underlying mechanisms. Quorum quenching impaired the electricity generation and electroactivity of electrogenic biofilms as indicated by dye decolorization rate. It significantly decreased the proportion of typical exoelectrogen Geobacter from 62.0% to 36.5% after 90 days of operation, and enriched some other functional genera (e.g., Dysgonomonas and Sphaerochaeta) to ensure normal physiological function. Moreover, metagenomic analysis revealed that the addition of acylase weakened the potential of chemical communication, as indicated by the decrease in the abundance of genes encoding the production of AHL and c-di-GMP, and the increase in the abundance of aiiA and pvdQ genes (encoding quorum quenching) and cdgC gene (responsible for c-di-GMP breakdown). Functional contribution analysis indicated that Geobacter was a major contributor to hdtS gene (encoding AHL synthesis). These findings demonstrated that quorum quenching adversely impaired not only quorum sensing but also intracellular c-di-GMP signaling, ultimately inhibiting the development of biofilm. This work lays the foundation for regulating electrogenic biofilm development and improving the performance of microbial electrochemical system using signal communication strategy.}, } @article {pmid39667337, year = {2025}, author = {Chen, YT and Reid, T and Weisener, C}, title = {Microbial community and functional shifts across agricultural and urban landscapes within a Lake Erie watershed.}, journal = {Journal of environmental management}, volume = {373}, number = {}, pages = {123683}, doi = {10.1016/j.jenvman.2024.123683}, pmid = {39667337}, issn = {1095-8630}, mesh = {*Lakes/microbiology ; *Agriculture ; *Nitrogen/metabolism/analysis ; *Microbiota ; Ontario ; Ecosystem ; }, abstract = {The role of sediment microbial communities in regulating the loss and retention of nutrients in aquatic ecosystems has been increasingly recognised. However, in the Great Lakes, where nutrient mitigation focuses on harmful algal blooms, there are limited studies examining the fundamental role of water/sediment microbes in nutrient biogeochemical cycling. Little is understood in this regard considering the increase in anthropogenic pressure on in-stream biological processes impacting nutrient flux to lakes. In this study, metagenomic and metatranscriptomic approaches were used to investigate the microbial community and gene regulation. The study focused on nitrogen (N) metabolism in a nutrient-polluted watershed of Lake Erie in southwestern Ontario, Canada. Nutrients and microbial analyses of water and sediments were collected in 2020 and 2021 from Sturgeon Creek headwaters to the nearshore of Lake Erie. Results showed no significant shifts in community structure with nutrient concentrations or land use. Metabolically, active genes involved in denitrification (consisting of 32-53% of N metabolic transcripts) showed the highest expression within agricultural and wetland dominant locations. Based on active gene expression patterns, the urbanised location coinciding with peak nitrate (NO3[-]) concentrations showed the greatest potential for nitrous oxide (N2O) emission and nitrogen loss along this transect. In contrast to denitrification, direct nitrification (5-21% of N metabolic transcripts) increased two-fold approaching downstream and nearshore lake locations. Across this river-lake corridor, expression of key functional genes associated with N transformation showed strong correlation with the change in concentrations of aqueous NO3[-] and nitrite (NO2[-]) and the ratio of NO2[-]/NO3[-]. Our findings demonstrated a clear link between sediment microbial metabolism and overlying water chemistry in this lotic system. We suggest that future studies assessing nutrient mitigation consider sediment biogeochemical processes and N-metabolising bacteria, and their fundamental role and cooperative relationship with nutrient and hydrological dynamics of overlying waters.}, } @article {pmid39667160, year = {2025}, author = {Zhang, M and Liu, L and Yang, X and Kang, Y and Qin, Q and Fu, Y and Zhu, L and Xu, Y}, title = {Virulence phenotype alteration impacts nosocomial pathogen persistence on inanimate surfaces in hospital settings.}, journal = {The Science of the total environment}, volume = {958}, number = {}, pages = {177877}, doi = {10.1016/j.scitotenv.2024.177877}, pmid = {39667160}, issn = {1879-1026}, mesh = {*Klebsiella pneumoniae/pathogenicity/genetics ; Virulence ; *Cross Infection/microbiology ; Humans ; China ; Phenotype ; Hospitals ; Mice ; Animals ; Polymorphism, Single Nucleotide ; }, abstract = {The hospital setting serves as a critical conduit for pathogen dissemination, particularly amid the escalating concern of nosocomial infections in China. Currently, most studies use metagenomics to investigate microbial communities in hospital settings, with less focus on the transmission strategies of individual bacteria. In our study, we identified two Klebsiella pneumoniae strains exhibiting different mucoid characteristics. The strain designated as KPE was obtained from a well sanitized ward, while the strain KPH was isolated from the sputum samples of patients within the identical ward. We characterized the KPE strain as not lethal to mice and showed a distinct hypomuciod phenotype, strikingly different from the virulent KPH isolate. Two strains harbored the single nucleotide polymorphism (SNP) mutations in the virulence-related gene rmpA and wcaJ promoter regions, resulting in the downregulation of mucoid regulatory gene rmpA and capsule synthesis genes. Consequently, this led to diminished production of capsular polysaccharides and weakened virulence in the KPE strain. Furthermore, the KPE strain exhibited an elevated capacity for acquiring antibiotic-resistant plasmids and greater material survival ability. These findings indicated that mucoid changes enable K. pneumoniae strains to survive better on inanimate surfaces, promoting their persistence ward environment and further transmission in patients.}, } @article {pmid39667043, year = {2025}, author = {He, W and Zhang, DF and Li, XJ and Wang, HC and Wang, LQ and Yuan, Y}, title = {Description of Albidovulum litorale sp. nov., Albidovulum marisflavi sp. nov., Albidovulum salinarum sp. nov., and Albidovulum sediminicola sp. nov., and proposal for reclassification of the genus Defluviimonas as a later heterotypic synonym of Albidovulum.}, journal = {Systematic and applied microbiology}, volume = {48}, number = {1}, pages = {126576}, doi = {10.1016/j.syapm.2024.126576}, pmid = {39667043}, issn = {1618-0984}, mesh = {*RNA, Ribosomal, 16S/genetics ; *Phylogeny ; China ; *Geologic Sediments/microbiology ; *DNA, Bacterial/genetics ; *Bacterial Typing Techniques ; *Sequence Analysis, DNA ; Fatty Acids/analysis/chemistry ; Base Composition ; Metagenomics ; Seawater/microbiology ; Nucleic Acid Hybridization ; Genome, Bacterial/genetics ; }, abstract = {Four Gram-stain-negative, aerobic, rod-shaped bacteria, designated WL0002[T], WL0024[T], WL0050[T], and WL0075[T], were isolated from sediment in the coastal areas of Nantong City, China. Metagenomic analysis revealed higher relative abundance of taxa closely related to the four strains in sediment (0.79-2.0 %) than in water (0.34-1.3 %) (Mann-Whitney U test: p < 0.001). Phylogenetic analysis based on 16S rRNA gene and the bac120 gene set both suggested that the four strains are closely related to the genus Defluviimonas. Additionally, Albidovulum inexpectatum DSM 12048[T] formed a distinct branch within Defluviimonas. The evolutionary distance (ED) and percentage of conserved proteins (POCP) analysis indicated that the four strains and the genus strains of Albidovulum and Defluviimonas should be recognized as a single genus. Genomic relatedness analysis among the four strains and type strains of the genera Albidovulum and Defluviimonas was below species delimitation thresholds, except for strains WL0024[T] and "D. salinarum" CAU 1641[T], which should belong to the same species. Based on phenotypic and genotypic characterization, the four strains should be recognized as novel species in Albidovulum, and it is reasonable to reclassify the genus Defluviimonas as a later heterotypic synonym of Albidovulum, consistent with the classification of the Genome Taxonomy Database (GTDB). Four names are proposed as follows: Albidovulum marisflavi sp. nov. (type strain WL0002[T] = MCCC 1K06013[T] = JCM 34653[T] = GDMCC 1.2437[T]), Albidovulum salinarum sp. nov. (WL0024[T] = MCCC 1K06062[T] = JCM 34656[T] = GDMCC 1.2438[T]), Albidovulum litorale sp. nov. (WL0050[T] = MCCC 1K07524[T] = JCM 35566[T] = GDMCC 1.3084[T]), and Albidovulum sediminicola sp. nov. (WL0075[T] = MCCC 1K06064[T] = JCM 34660[T] = GDMCC 1.2419[T]).}, } @article {pmid39665754, year = {2024}, author = {Srinivas, P and Peterson, SB and Gallagher, LA and Wang, Y and Mougous, JD}, title = {Beyond genomics in Patescibacteria: A trove of unexplored biology packed into ultrasmall bacteria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {51}, pages = {e2419369121}, pmid = {39665754}, issn = {1091-6490}, support = {na//Howard Hughes Medical Institute (HHMI)/ ; }, mesh = {*Genomics/methods ; Genome, Bacterial ; Phylogeny ; Metagenomics/methods ; }, abstract = {Patescibacteria, also known as the Candidate Phyla Radiation, are a diverse clade of largely uncultivated, small bacteria that comprise a significant proportion of all bacterial diversity. The few members that have been cultivated exhibit a fascinating life cycle in which they grow as obligate epibionts on the surface of host bacteria. In this Perspective, we make the case that the study of these unique, divergent, and poorly characterized organisms represents an exciting frontier in microbiology. This burgeoning field has already achieved several critical breakthroughs, including metagenomic sequence-based reconstructions of the metabolic and biosynthetic capabilities of diverse Patescibacteria and the development of generalizable strategies for their cultivation and genetic manipulation. We argue these that advances, among others, should pave the way toward a molecular understanding of the complex interactions that undoubtedly underpin the relationship between Patescibacteria and their hosts.}, } @article {pmid39665565, year = {2025}, author = {Gao, X and Liang, H and Hu, T and Zou, Y and Xiao, L}, title = {Cultivated genome references for protein database construction and high-resolution taxonomic annotation in metaproteomics.}, journal = {Microbiology spectrum}, volume = {13}, number = {2}, pages = {e0175524}, pmid = {39665565}, issn = {2165-0497}, support = {No. 32100009//MOST | National Natural Science Foundation of China (NSFC)/ ; No.XMHT20220104017//Shenzhen Municipal Science and Technology Innovation Council | Shenzhen Key Laboratory Fund ()/ ; }, mesh = {*Proteomics/methods ; *Metagenomics/methods ; *Databases, Protein ; *Gastrointestinal Microbiome/genetics ; Bacterial Proteins/genetics/metabolism ; Peptides/genetics/metabolism ; Molecular Sequence Annotation ; Genome, Bacterial/genetics ; Metagenome ; Bacteria/genetics/classification ; }, abstract = {Metaproteomics offers a profound understanding of the functional dynamics of the gut microbiome, which is crucial for personalized healthcare strategies. The selection of an appropriate database is a critical step for the identification of peptides and proteins, as well as for the provision of accurate taxonomic and functional annotations. The matched metagenomic-derived database is considered to be the best, but its limitations include the identification of low-abundance organisms and taxonomic resolution. Herein, we constructed a protein database (DBCGR2) based on Cultivated Genome Reference 2 (CGR2) and developed a complete peptide-centric analysis workflow for database searching and for the annotation of taxonomy and function. This workflow was subsequently appraised in comparison with metagenomics-derived databases for the analysis of metaproteomic data. Our findings suggested that the performance of DBCGR2 in identification was comparable with metagenomics-derived databases with improvement in identification rates of peptides from low-abundance species. The database searching results could be fully annotated using the pepTaxa taxonomic annotation approach developed in this study, and the taxonomic resolution was enhanced to strain level. Additionally, the results demonstrated that the sensitivity of functional annotation could be enhanced by employing DBCGR2. Overall, the DBCGR2 combined with pepTaxa can be considered an alternative for metaproteomic data analysis with superior analysis performances.IMPORTANCEMass spectrometry-based metaproteomics offers a profound understanding of the gut microbial taxonomy and functionality. The databases utilized in the analysis of metaproteomic data are crucial, as they determine the identification of proteins that can be recognized and linked to overall human health, in addition to the quality of taxonomic and functional annotation. Among the most effective approaches for constructing protein databases is the utilization of metagenomic sequencing to create matched databases. However, the database, derived from isolated genomes, has yet to undergo rigorous testing for their efficacy and accuracy in protein identification and taxonomic and functional annotation. Here, we constructed a protein database DBCGR2 derived from Cultivated Genome Reference 2 (CGR2) and a complete workflow for data analysis. We compared the performances of DBCGR2 and metagenomics-derived databases. Our results indicated that DBCGR2 can be regarded as an alternative to metagenomics-derived databases, which contribute to metaproteomic data analysis.}, } @article {pmid39665561, year = {2025}, author = {Unzueta-Martínez, A and Girguis, PR}, title = {Taxonomic diversity and functional potential of microbial communities in oyster calcifying fluid.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {1}, pages = {e0109424}, pmid = {39665561}, issn = {1098-5336}, support = {2109473//National Science Foundation (NSF)/ ; 9208//Gordon and Betty Moore Foundation (GBMF)/ ; }, mesh = {Animals ; *Microbiota ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Archaea/classification/genetics/metabolism ; Metagenomics ; Calcification, Physiologic ; Ostreidae/microbiology ; Biomineralization ; Viruses/classification/genetics ; Biodiversity ; }, abstract = {UNLABELLED: Creating and maintaining an appropriate chemical environment is essential for biomineralization, the process by which organisms precipitate minerals to form their shells or skeletons, yet the mechanisms involved in maintaining calcifying fluid chemistry are not fully defined. In particular, the role of microorganisms in facilitating or hindering animal biomineralization is poorly understood. Here, we investigated the taxonomic diversity and functional potential of microbial communities inhabiting oyster calcifying fluid. We used shotgun metagenomics to survey calcifying fluid microbial communities from three different oyster harvesting sites. There was a striking consistency in taxonomic composition across the three collection sites. We also observed archaea and viruses that had not been previously identified in oyster calcifying fluid. Furthermore, we identified microbial energy-conserving metabolisms that could influence the host's calcification, including genes involved in sulfate reduction and denitrification that are thought to play pivotal roles in inorganic carbon chemistry and calcification in microbial biofilms. These findings provide new insights into the taxonomy and functional capacity of oyster calcifying fluid microbiomes, highlighting their potential contributions to shell biomineralization, and contribute to a deeper understanding of the interplay between microbial ecology and biogeochemistry that could potentially bolster oyster calcification.

IMPORTANCE: Previous research has underscored the influence of microbial metabolisms in carbonate deposition throughout the geological record. Despite the ecological importance of microbes to animals and inorganic carbon transformations, there have been limited studies characterizing the potential role of microbiomes in calcification by animals such as bivalves. Here, we use metagenomics to investigate the taxonomic diversity and functional potential of microbial communities in calcifying fluids from oysters collected at three different locations. We show a diverse microbial community that includes bacteria, archaea, and viruses, and we discuss their functional potential to influence calcifying fluid chemistry via reactions like sulfate reduction and denitrification. We also report the presence of carbonic anhydrase and urease, both of which are critical in microbial biofilm calcification. Our findings have broader implications in understanding what regulates calcifying fluid chemistry and consequentially the resilience of calcifying organisms to 21st century acidifying oceans.}, } @article {pmid39665547, year = {2025}, author = {De Koch, MD and Krupovic, M and Fielding, R and Smith, K and Schiavone, K and Hall, KR and Reid, VS and Boyea, D and Smith, EL and Schmidlin, K and Fontenele, RS and Koonin, EV and Martin, DP and Kraberger, S and Varsani, A}, title = {Novel lineage of anelloviruses with large genomes identified in dolphins.}, journal = {Journal of virology}, volume = {99}, number = {1}, pages = {e0137024}, pmid = {39665547}, issn = {1098-5514}, mesh = {Animals ; *Genome, Viral ; *Phylogeny ; *Open Reading Frames ; *Dolphins/virology ; *Anelloviridae/genetics/classification ; Capsid Proteins/genetics ; Metagenomics ; }, abstract = {UNLABELLED: Anellovirus infections are ubiquitous in mammals but lack any clear disease association, suggesting a commensal virus-host relationship. Although anelloviruses have been identified in numerous mammalian hosts, their presence in members of the family Delphinidae has yet to be reported. Here, using a metagenomic approach, we characterize complete anellovirus genomes (n = 69) from four Delphinidae host species: short-finned pilot whale (Globicephala macrorhynchus, n = 19), killer whale (Orcinus orca, n = 9), false killer whale (Pseudorca crassidens, n = 6), and pantropical spotted dolphin (Steno attenuatus, n = 1). Sequence comparison of the open reading frame 1 (ORF1) encoding the capsid protein, the only conserved gene shared by all anelloviruses, shows that the Delphinidae anelloviruses form a novel genus-level clade that encompasses 22 unique species-level groupings. We provide evidence that different Delphinidae species can be co-infected by multiple anelloviruses belonging to distinct species groupings. Notably, the ORF1 protein of the Delphinidae anelloviruses is considerably larger than those encoded by all previously described anelloviruses from other hosts (spanning 14 vertebrate orders and including 27 families). Comprehensive analysis of the ORF1 sequences and predicted protein structures showed that the increased size of these proteins results from divergent elaborations within the capsid-distal P2 subdomain and elongation of the C-terminal domain of ORF1. Comparative structural and phylogenetic analyses suggest that acquisition of the P2 subdomain and its diversification occurred convergently in the anelloviruses associated with primate and Delphinidae hosts. Collectively, our results further the appreciation of diversity and evolution of the ubiquitous and enigmatic viruses in the family Anelloviridae.

IMPORTANCE: Anelloviruses are ubiquitous in mammals, but their infection has not yet been linked to any disease, suggesting a commensal virus-host relationship. Here, we describe the first anelloviruses associated with diverse species of dolphins. The dolphinid anelloviruses represent a new genus (tentatively named "Qoptorquevirus") and encode open reading frame 1 (ORF1) (capsid) proteins that are considerably larger than those encoded by previously described anelloviruses from other hosts. Comprehensive analysis of the ORF1 sequences and predicted protein structures revealed the underlying structural basis for such an extravagant ORF1 size and suggested that ORF1 size increased convergently in the anelloviruses associated with primate and Delphinidae hosts, respectively. Collectively, our results provide insights into the diversity and evolution of Anelloviridae. Further exploration of the anellovirus diversity, especially in the host species that have not yet been sampled, is expected to further clarify their evolutionary trajectory and explain the unusual virus-host commensal relationship.}, } @article {pmid39665540, year = {2024}, author = {Zulk, JJ and Patras, KA and Maresso, AW}, title = {The rise, fall, and resurgence of phage therapy for urinary tract infection.}, journal = {EcoSal Plus}, volume = {12}, number = {1}, pages = {eesp00292023}, pmid = {39665540}, issn = {2324-6200}, support = {1F31DK136201-01//National Institutes of Health NIDDK/ ; U19AI157981//National Institutes of Health NIAID/ ; U19 AI157981/AI/NIAID NIH HHS/United States ; F31 DK136201/DK/NIDDK NIH HHS/United States ; Chateaubriand Fellowship//Office for Science and Technology of the Embassy of France in the United States (OST)/ ; }, mesh = {*Phage Therapy ; *Urinary Tract Infections/therapy/microbiology ; Humans ; Animals ; *Uropathogenic Escherichia coli ; *Bacteriophages ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Escherichia coli Infections/therapy/microbiology ; Biofilms ; Drug Resistance, Bacterial ; }, abstract = {In the face of rising antimicrobial resistance, bacteriophage therapy, also known as phage therapy, is seeing a resurgence as a potential treatment for bacterial infections including urinary tract infection (UTI). Primarily caused by uropathogenic Escherichia coli, the 400 million UTI cases annually are major global healthcare burdens and a primary cause of antibiotic prescriptions in the outpatient setting. Phage therapy has several potential advantages over antibiotics including the ability to disrupt bacterial biofilms and synergize with antimicrobial treatments with minimal side effects or impacts on the microbiota. Phage therapy for UTI treatment has shown generally favorable results in recent animal models and human case reports. Ongoing clinical trials seek to understand the efficacy of phage therapy in individuals with asymptomatic bacteriuria and uncomplicated cystitis. A possible challenge for phage therapy is the development of phage resistance in bacteria during treatment. While resistance frequently develops in vitro and in vivo, resistance can come with negative consequences for the bacteria, leaving them susceptible to antibiotics and other environmental conditions and reducing their overall virulence. "Steering" bacteria toward phage resistance outcomes that leave them less fit or virulent is especially useful in the context of UTI where poorly adherent or slow-growing bacteria are likely to be flushed from the system. In this article, we describe the history of phage therapy in treating UTI and its current resurgence, the state of its clinical use, and an outlook on how well-designed phage therapy could be used to "steer" bacteria toward less virulent and antimicrobial-susceptible states.}, } @article {pmid39665430, year = {2024}, author = {Sitthicharoenchai, P and Zhang, J and Tian, L and Stasko, J and Hashish, A and Hsueh, CS and Sato, Y and Hause, B and El-Gazzar, M}, title = {High mortality associated with avian reoviral hepatitis in young quail (Colinus virginianus).}, journal = {Veterinary pathology}, volume = {}, number = {}, pages = {3009858241302842}, doi = {10.1177/03009858241302842}, pmid = {39665430}, issn = {1544-2217}, abstract = {High mortality in bobwhite quail chicks (Colinus virginianus) (35%-85%) was reported from a grower flock in Iowa during July and August of 2022. Two diagnostic submissions of dead, 3-day-old quail chicks were received. Postmortem examination revealed multifocal, pinpoint, pale tan foci in the liver of all birds. Histologic examination revealed moderate to severe, acute, multifocal, random necrotizing hepatitis with multinucleated cells and dystrophic mineralization. Metagenomic sequencing of liver detected orthoreovirus. A high level of avian reovirus (ARV) RNA was identified by real-time reverse transcriptase-PCR. ARV was successfully isolated from liver and lung on the Leghorn male hepatoma cell line. In addition, electron microscopy revealed orthoreovirus viral particles and virus factories in the formalin-fixed livers and viral-infected cell culture. This case highlights ARV as a potential cause of hepatitis in quail chicks and should be considered in the differential diagnosis.}, } @article {pmid39663251, year = {2024}, author = {Zhang, Q and Li, X and Wang, Z and Shen, S and Wang, J and Chen, J and Shi, X and Wang, S and Cao, J and Deng, Y and Meng, H and Ma, L}, title = {A pilot study of the relationship between salivary microbial characteristics and endocrine and immune function in patients with burning mouth syndrome.}, journal = {Clinical oral investigations}, volume = {29}, number = {1}, pages = {11}, pmid = {39663251}, issn = {1436-3771}, support = {A2024608//Medical Research Foundation of Guangdong Province/ ; 2023A1515011945//Guangdong Basic and Applied Basic Research Foundation/ ; 2023A1515011945//Guangdong Basic and Applied Basic Research Foundation/ ; 2023A1515011945//Guangdong Basic and Applied Basic Research Foundation/ ; }, mesh = {Humans ; *Saliva/microbiology ; *Burning Mouth Syndrome/microbiology ; Pilot Projects ; Female ; Male ; Adult ; *Enzyme-Linked Immunosorbent Assay ; Case-Control Studies ; Dysbiosis/microbiology ; Biomarkers/analysis ; Hydrocortisone/metabolism/analysis ; Sequence Analysis, DNA ; Salivary Proteins and Peptides/analysis ; }, abstract = {OBJECTIVES: To explore the potential role of oral bacteria in the pathogenesis of burning mouth syndrome (BMS).

MATERIALS AND METHODS: Fifteen patients with BMS and 15 healthy controls were enrolled in this study. The relative abundance and diversity of salivary bacterial strains were analyzed using metagenomic DNA sequencing. The functionality of non-redundant genes was obtained by comparing the mmseqs2 with the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. BMS relating salivary protein markers were detected using enzyme-linked immunosorbent assay (ELISA).

RESULTS: Partial least-squares discriminant analysis (PLS-DA) revealed that the salivary bacterial profiles of the BMS group (mean age: 38.9 ± 2.2 years) differed significantly from those of the control group (mean age: 34.1 ± 2.3 years) in terms of the abundance of dominant phyla, classes, orders, families, genera and species. Functional analysis revealed distinct endocrine and immune functions in the BMS group. The salivary cortisol and α-amylase levels were significantly higher, and salivary interleukn-6 levels were significantly lower in the BMS group than in the control group. Species contribution analysis of endocrine and immune functions revealed that Streptococcus mitis was an important contributor to endocrine and immune functions in the BMS group.

CONCLUSIONS: Salivary dysbiosis related to endocrine and immune functions may be a possible cause of BMS.

CLINICAL RELEVANCE: These findings could assist in the diagnosis and therapy of BMS.

CLINICAL TRIAL NUMBER: Not applicable.}, } @article {pmid39662846, year = {2025}, author = {Shen, Y and Zhao, G and Wan, D and Liu, M and Peng, T and Zhang, W and Wang, P and He, Q}, title = {Dual-layer elemental sulfur-packed denitrification reactor to control sulfate generation and sulfide discharge by two-point inlet and internal recirculation.}, journal = {Bioresource technology}, volume = {418}, number = {}, pages = {131965}, doi = {10.1016/j.biortech.2024.131965}, pmid = {39662846}, issn = {1873-2976}, mesh = {*Denitrification ; *Bioreactors ; *Sulfates/metabolism ; *Sulfur/metabolism ; *Sulfides/metabolism/chemistry ; *Nitrates/metabolism ; Water Purification/methods ; Bacteria/metabolism ; }, abstract = {In this study, an elemental sulfur (S[0]) autotrophic denitrification reactor (SADR) and a wood chunk and S[0] mixotrophic denitrification reactor (WSMDR) were constructed with dual-layers to effectively remove nitrate from water using two-inlets and internal recirculation. The denitrification rates were 66-114 and 70-104 g-N/(m[3]·d) for the SADR and WSMDR, respectively. Sulfate production was 5.5-5.9 and 3.2-4.5 mg SO4[2-]/mg reduced N in the SADR and WSMDR, respectively, being lower than theoretical value. In addition, there was no sulfide emission from either reactor. Chlorobium, Chlorobaculum, Ignavibacterium, Sulfuritalea, and Thiobacillus were involved in nitrate reduction in both reactors. Chlorobiaceae had the highest abundance and played an essential role in maintaining the integrity of the co-occurrence pattern. The abundance of functional genes positively correlated with the denitrification performance. This study demonstrates that the operation of two-inlets and internal recirculation can effectively reduce byproduct generation, thereby promoting the practical application of the SADR and WSMDR.}, } @article {pmid39662821, year = {2024}, author = {Groenewegen, B and van Lingen, E and Kovynev, A and van den Berg, AJ and Berssenbrugge, EKL and Sanders, IMJG and van Prehn, J and van Nood, E and Goorhuis, A and Kuijper, EJ and Smits, WK and Wiese, M and Keller, JJ and Ducarmon, QR and Terveer, EM and , }, title = {The presence of Clostridioides difficile in faeces before and after faecal microbiota transplantation and its relation with recurrent C. difficile infection and the gut microbiota in a Dutch cohort.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmi.2024.12.003}, pmid = {39662821}, issn = {1469-0691}, abstract = {OBJECTIVES: The objectives of this study are to investigate the presence of Clostridioides difficile in faeces of patients with recurrent C. difficile infection (rCDI) before and after faecal microbiota transplantation (FMT) and to identify risk factors for faecal C. difficile and C. difficile infection (CDI) recurrence.

METHODS: n = 83 faecal sample triads (pre-FMT [∼1 day], post-FMT [∼3 weeks], and a corresponding FMT donor sample), and n = 22 long-term (∼1-3 years) follow-up faecal samples were collected from FMT-treated patients. The presence of C. difficile in faeces was assessed by enrichment broth culture and PCR (tcdB gene) and associated with patient characteristics, FMT outcome, duration of pre-FMT vancomycin, FMT donor, post-FMT antibiotic use, and faecal microbiota composition (shotgun metagenomics).

RESULTS: The FMT cure rate for rCDI was 92.8% (77/83), with six early CDI recurrences (<2 months post-FMT). Toxigenic C. difficile was cultured in 27.7% (23/83) of all patients post-FMT, 23.4% (18/77) of patients cured 2 months post-FMT, and 13.6% (3/22) at long-term follow-up. Early CDI recurrence (n = 6) was associated with positive C. difficile culture post-FMT (21.7% [5/23] vs. 1.7% [1/60], p 0.01), post-FMT antibiotics (30.0% [3/10] vs. 4.6% [3/65], p 0.03), and a short course of pre-FMT vancomycin (median 6.0 days, IQR [5-12] vs. 18 days, IQR [10.8-29], p < 0.05). Additionally, positive C. difficile culture directly pre-FMT was associated with a short course of pre-FMT vancomycin (median 9 days IQR [5-18] vs. 17 days, IQR [10-29.2], p 0.04). Gut microbiota analyses did not reveal signatures associated with C. difficile culture result, despite statistically non-significant trends in relative abundances of the Enterobacteriaceae family, and Dorea, Roseburia, and Clostridiales species.

DISCUSSION: Although eradication of C. difficile is not required for clinical cure of rCDI by FMT, it is associated with reduced prevalence of early CDI recurrence, as are the full completion of pre-FMT vancomycin (at least 10 days) and avoiding post-FMT antibiotics.}, } @article {pmid39662756, year = {2024}, author = {Hodgkiss, R and Acharjee, A}, title = {Unravelling metabolite-microbiome interactions in inflammatory bowel disease through AI and interaction-based modelling.}, journal = {Biochimica et biophysica acta. Molecular basis of disease}, volume = {1871}, number = {3}, pages = {167618}, doi = {10.1016/j.bbadis.2024.167618}, pmid = {39662756}, issn = {1879-260X}, abstract = {Inflammatory Bowel Diseases (IBDs) are chronic inflammatory disorders of the gastrointestinal tract and colon affecting approximately 7 million individuals worldwide. The knowledge of specific pathology and aetiological mechanisms leading to IBD is limited, however a reduced immune system, antibiotic use and reserved diet may initiate symptoms. Dysbiosis of the gut microbiome, and consequently a varied composition of the metabolome, has been extensively linked to these risk factors and IBD. Metagenomic sequencing and liquid-chromatography mass spectrometry (LC-MS) of N = 220 fecal samples by Fransoza et al., provided abundance data on microbial genera and metabolites for use in this study. Identification of differentially abundant microbes and metabolites was performed using a Wilcoxon test, followed by feature selection of random forest (RF), gradient-boosting (XGBoost) and least absolute shrinkage operator (LASSO) models. The performance of these features was then validated using RF models on the Human Microbiome Project 2 (HMP2) dataset and a microbial community (MICOM) model was utilised to predict and interpret the interactions between key microbes and metabolites. The Flavronifractor genus and microbes of the families Lachnospiraceae and Oscillospiraceae were found differential by all models. Metabolic pathways commonly influenced by such microbes in IBD were CoA biosynthesis, bile acid metabolism and amino acid production and degradation. This study highlights distinct interactive microbiome and metabolome profiles within IBD and the highly potential pathways causing disease pathology. It therefore paves way for future investigation into new therapeutic targets and non-invasive diagnostic tools for IBD.}, } @article {pmid39662692, year = {2024}, author = {Costigan, CM and Warren, FJ and Duncan, AP and Hoad, CL and Lewis, N and Hill, T and Crooks, CJ and Morgan, PS and Ciacci, C and Iovino, P and Sanders, DS and Hildebrand, F and Gowland, PA and Spiller, RC and Marciani, L}, title = {One Year of Gluten-Free Diet Impacts Gut Function and Microbiome in Celiac Disease.}, journal = {Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cgh.2024.11.006}, pmid = {39662692}, issn = {1542-7714}, abstract = {BACKGROUND & AIMS: Currently, the main treatment for celiac disease (CD) is the gluten-free diet (GFD). This observational cohort study investigated the impact of CD and 1 year of GFD on gut function and microbiome.

METHODS: A total of 36 newly diagnosed patients and 36 healthy volunteers (HVs) were studied at baseline and at 12-month follow-up. Small bowel water content (SBWC), whole gut transit time (WGTT), and colon volumes were measured by magnetic resonance imaging. Stool sample DNA was subjected to shotgun metagenomic sequencing. Species-level abundances and gene functions, including CAZymes (carbohydrate active enzymes) were determined.

RESULTS: SBWC was significantly higher in people with CD (157 ± 15 mL) vs (HVs 100 ± 12 mL) (P = .003). WGTT was delayed in people with CD (68 ± 8 hours) vs HVs (41 ± 5 hours) (P = .002). The differences reduced after 12 months of GFD but not significantly. Well-being in the CD group significantly improved after GFD but did not recover to control values. CD fecal microbiota showed a high abundance of proteolytic gene functions, associated with Escherichia coli, Enterobacter, and Peptostreptococcus. GFD significantly reduced Bifidobacteria and increased Blautia wexlerae. Microbiome composition correlated positively with WGTT, colonic volume, and Akkermansia municphilia but negatively with B wexerelae. Following GFD, the reduction in WGTT and colonic volume was significantly associated with increased abundance of B wexlerae. There were also significant alterations in CAZyme profiles, specifically starch- and arabinoxylan-degrading families.

CONCLUSIONS: CD impacted gut function and microbiota. GFD ameliorated but did not reverse these effects, significantly reducing Bifidobacteria associated with reduced intake of resistant starch and arabinoxylan from wheat.

CLINICALTRIALS: gov, number: NCT02551289.}, } @article {pmid39662474, year = {2024}, author = {Mi, K and Xu, R and Liu, X}, title = {RFW captures species-level metagenomic functions by integrating genome annotation information.}, journal = {Cell reports methods}, volume = {4}, number = {12}, pages = {100932}, pmid = {39662474}, issn = {2667-2375}, mesh = {Humans ; *Metagenomics/methods ; *Molecular Sequence Annotation ; *Algorithms ; Metagenome/genetics ; Software ; Colorectal Neoplasms/genetics ; Autism Spectrum Disorder/genetics ; }, abstract = {Functional profiling of whole-metagenome shotgun sequencing (WMS) enables our understanding of microbe-host interactions. We demonstrate microbial functional information loss by current annotation methods at both the taxon and community levels, particularly at lower read depths. To address information loss, we develop a framework, RFW (reference-based functional profile inference on WMS), that utilizes information from genome functional annotations and taxonomic profiles to infer microbial function abundances from WMS. Furthermore, we provide an algorithm for absolute abundance change quantification between groups as part of the RFW framework. By applying RFW to several datasets related to autism spectrum disorder and colorectal cancer, we show that RFW augments downstream analyses, such as differential microbial function identification and association analysis between microbial function and host phenotype. RFW is open source and freely available at https://github.com/Xingyinliu-Lab/RFW.}, } @article {pmid39662407, year = {2025}, author = {Wang, Y and Yi, H and Li, G and Li, A and Wang, H and Ding, D}, title = {Influence of enriched nitrate reducing bacteria communities on bacterial community structure and groundwater condition during in situ bioremediation of nitrate in acidic uranium-contaminated groundwater.}, journal = {The Science of the total environment}, volume = {958}, number = {}, pages = {177896}, doi = {10.1016/j.scitotenv.2024.177896}, pmid = {39662407}, issn = {1879-1026}, mesh = {*Groundwater/microbiology/chemistry ; *Nitrates/metabolism ; *Biodegradation, Environmental ; *Uranium/metabolism ; *Bacteria/metabolism ; China ; *Water Pollutants, Radioactive/metabolism ; Microbiota ; Water Pollutants, Chemical/metabolism/analysis ; }, abstract = {In-situ leaching (ISL) is the predominant technology used in uranium mining currently, although it leads to significant environmental challenges. Nitrates, a key component in leaching agents, not only pose a threat to human health but also impede the bioreduction of U(VI) in uranium-contaminated water. In this study, the nitrate reducing bacterial (NRB) communities adapted to acidic uranium-contaminated groundwater from a site in Northwest China were gained by an enrichment micro-model. The effects of the NRB communities on the groundwater parameters and microbial diversity were evaluated using the groundwater-core column leaching system during the in-situ bioremediation of nitrate. The enrichment experiments revealed that NRB communities adapted to acidic uranium-contaminated groundwater were successfully enriched, of which Tumebacillus was the main functional bacterium. The column leaching experiment results showed that adding NRB communities successfully reduced nitrate levels from 100.91 mg/L to 0.7 mg/L in just 8 days, improved groundwater acidity and redox conditions. Additionally, the metagenomic analysis showed that introducing NRB communities increased biomass and indigenous NRB, but decreased microbial diversity. The KEGG enrichment analysis suggested that butanoate metabolism and valine, leucine and isoleucine degradation were promoted by adding enriched NRB communities. This research lays the groundwork for nitrate removal from contaminated groundwater in areas affected by ISL in uranium mines, setting the stage for future in situ bioremediation of U(VI).}, } @article {pmid39662353, year = {2025}, author = {Cao, L and Garcia, SL and Wurzbacher, C}, title = {Profiling trace organic chemical biotransformation genes, enzymes and associated bacteria in microbial model communities.}, journal = {Journal of hazardous materials}, volume = {485}, number = {}, pages = {136811}, doi = {10.1016/j.jhazmat.2024.136811}, pmid = {39662353}, issn = {1873-3336}, mesh = {*Biotransformation ; *Sulfamethoxazole/metabolism ; *Water Pollutants, Chemical/metabolism ; Bacteria/genetics/metabolism ; Caffeine/metabolism ; Carbamazepine/metabolism ; Gabapentin/metabolism ; Atenolol/metabolism ; Ibuprofen/metabolism ; gamma-Aminobutyric Acid/metabolism ; Trimethoprim/metabolism ; Cyclohexanecarboxylic Acids/metabolism ; Biodegradation, Environmental ; Amines/metabolism ; Organic Chemicals/metabolism ; Metagenome ; Wastewater ; }, abstract = {Microbial biotransformation of trace organic chemicals (TOrCs) is an essential process in wastewater treatment to eliminate environmental pollution. Understanding TOrC biotransformation mechanisms, especially at their original concentrations, is important to optimize treatment performance, whereas our current knowledge is limited. Here, we investigated the biotransformation of seven TOrCs by 24 model communities. The genome-centric analyses unraveled potential biotransformation drivers concerning functional genes, enzymes, and responsible bacteria. We obtained efficient model communities for completely removing ibuprofen, caffeine, and atenolol, with transformation efficiencies between 0 % and 45 % for sulfamethoxazole, carbamazepine, trimethoprim, and gabapentin. Biotransformation performance was not fully reflected by the presence of known biotransformation genes and enzymes in the metagenomes of the communities. Functional similar homologs to existing biotransformation genes and enzymes (e.g., long-chain-fatty-acid-CoA ligase encoded by fadD and fadD13 gene) could play critical roles in TOrC metabolism. Finally, we identified previously undescribed degrading strains, e.g., Rhodococcus qingshengii for caffeine, carbamazepine, sulfamethoxazole, and ibuprofen biotransformation, and potential transformation enzymes, e.g., SDR family oxidoreductase targeting sulfamethoxazole and putative hypothetical proteins for caffeine, atenolol and gabapentin biotransformation. This study provides fundamental insights into naturally assembled low-complexity degrader communities that can help to identify and tackle the current research gaps on biotransformation.}, } @article {pmid39662346, year = {2025}, author = {Yang, L and Sun, Y and Zhang, J and Zhu, L and Xu, Z and Liang, Y and Song, X and Chen, X}, title = {Multi-omics reveal an overlooked pathway for H2S production induced by bacterial biogenesis from composting.}, journal = {Journal of hazardous materials}, volume = {485}, number = {}, pages = {136827}, doi = {10.1016/j.jhazmat.2024.136827}, pmid = {39662346}, issn = {1873-3336}, mesh = {*Hydrogen Sulfide/metabolism ; *Bacteria/metabolism/genetics/drug effects ; *Glycine/analogs & derivatives/metabolism ; *Composting ; Alkynes/metabolism ; Soil Microbiology ; Cystathionine gamma-Lyase/metabolism ; Sulfates/metabolism ; Multiomics ; }, abstract = {Sulfate reduction has long been considered a leading cause of hydrogen sulfide (H2S) emissions from composting, causing serious air pollution and health threats. H2S biogenesis through cysteine cleavage is a known pathway for bacteria to resist oxidative stress. However, whether the biogenesis pathway exacerbates H2S emission during composting with dramatic temperature changes and oxidative stress is largely unknown. Here, we used DL-propargylglycine (PAG), an inhibitor of cysteine lyase (cystathionine γ-lyase), to explore the contribution of biogenesis pathway to H2S production during composting with different aeration rates. We found that PAG addition significantly inhibited H2S emission by 45.52 % and 19.74 % at high and low aeration rates, respectively. PAG addition reduced the diversity of core bacteria associated with H2S production. Metagenomic and metaproteomic analysis further revealed that PAG decreased the abundance of sulfate reduction genes, down-regulated the expression of cysteine lyases, and up-regulated the catalase expression. Therefore, both sulfate reduction and biosynthesis contributed to the H2S production, and PAG inhibited both pathways. Finally, microbial pure culture experiment further verified the effectiveness of PAG in reducing H2S emission of composting. This work reveals an overlooked pathway for H2S production during composting, which fills the research gap in the role of the biogenesis pathway in composting H2S emission. This provides breakthrough guidance for future environmental management and pollution control at source.}, } @article {pmid39660920, year = {2025}, author = {Zavarzina, DG and Maslov, AA and Merkel, AY and Kharitonova, NA and Klyukina, AA and Baranovskaya, EI and Baydariko, EA and Potapov, EG and Zayulina, KS and Bychkov, AY and Chernyh, NA and Bonch-Osmolovskaya, EA and Gavrilov, SN}, title = {Analogs of Precambrian microbial communities formed de novo in Caucasian mineral water aquifers.}, journal = {mBio}, volume = {16}, number = {1}, pages = {e0283124}, pmid = {39660920}, issn = {2150-7511}, mesh = {*Groundwater/microbiology/chemistry ; *Mineral Waters/microbiology ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Microbiota ; Archaea/genetics/classification/metabolism ; Phylogeny ; Metagenomics ; }, abstract = {The microbiome of deep continental aquifers is considered the most slowly evolving part of the biosphere. The Yessentukskoye Mineral Water Basin (YMWB), located in the pre-Caucasus region, contains three closely spaced but distinct aquifers, the Upper Cretaceous, the Lower Cretaceous, and the Upper Jurassic, which represent unique objects for subsurface biosphere research due to gas-hydrogeochemical and thermal anomalies of the area. We analyzed the geological and hydrogeochemical parameters of the three aquifers and a recharge area of the YMWB and investigated their microbial communities using metagenomic and cultivation-based approaches within a long-term survey. Correlation analysis of the obtained data revealed stable and highly stratified microbial communities inhabiting four distinct ecosystems. Their structure and the metabolic traits of their prokaryotic populations were similar to those presumed to have dominated the Earth's biosphere during several critical periods of its evolutionary history, that is, the Early Archean, the period of banded iron formations accumulation, and the Great Oxidation Event. Among the YMWB strata, the Upper Jurassic aquifer, supersaturated with CO2, influenced by magmatic activity, and highly enriched with thermophilic autotrophic hydrogenotrophic acetogens, turned out to be the first described modern ecosystem based on the primary production by a process predicted to support the Last Universal Common Ancestor (LUCA). The characterization of the YMWB microbial communities reveals a contemporary model environment of the early stages of Earth's development and thus contributes to the understanding of the evolutionary traits in microbial populations that may have played a critical role in the formation of the modern biosphere.IMPORTANCEContinental subsurface environments are estimated to harbor up to one-fifth of the planet's total biomass, representing the most stable and slowly evolving part of the biosphere. Among the deep subsurface inhabitants, the microbial communities of drinking mineral waters remain the least studied. Our interdisciplinary study of the Yessentukskoye Mineral Water Basin shows how hydrochemical and hydrodynamic factors shape different subsurface ecosystems, whose microbial populations influence the composition of mineral waters. A comprehensive analysis reveals the similarity of these ecosystems to those predicted for the early Earth. The deepest of the studied aquifers is the first described modern ecosystem with the most probable primary producer performing hydrogenotrophic acetogenesis. Thus, our results contribute to the understanding of the genesis of modern drinking water resources and expand the knowledge of the evolutionary traits that may have played a critical role in the formation of the Earth's biosphere.}, } @article {pmid39660898, year = {2025}, author = {Su, G and Huang, P and Liu, D and Xing, G and Guo, R and Li, S and Fan, S and Cheng, L and Yan, Q and Yang, W}, title = {Gut mycobiome alterations and network interactions with the bacteriome in patients with atherosclerotic cardiovascular disease.}, journal = {Microbiology spectrum}, volume = {13}, number = {1}, pages = {e0218224}, pmid = {39660898}, issn = {2165-0497}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Mycobiome ; Male ; Female ; *Bacteria/classification/genetics/isolation & purification ; Middle Aged ; *Fungi/classification/genetics/isolation & purification ; Aged ; *Atherosclerosis/microbiology ; Cardiovascular Diseases/microbiology ; Metagenomics ; Feces/microbiology ; }, abstract = {The connection between the gut mycobiome and atherosclerotic cardiovascular disease (ACVD) is largely uncharted. In our study, we compared the gut fungal communities of 214 ACVD patients with those of 171 healthy controls using shotgun metagenomic sequencing and examined their interactions with gut bacterial communities and network key taxa. The gut mycobiome composition in ACVD patients is significantly different, showing a rise in opportunistic pathogens like Candida albicans, Exophiala spinifera, and Malassezia restricta, with Exophiala and Malassezia showing the most significant changes (Wilcoxon rank-sum test, P < 0.001, fold change >10). Network analysis revealed a less interconnected and more uneven gut microbial network in ACVD patients. Network key taxa identified in the ACVD gut microbiome network include Malassezia globosa c182, Nakaseomyces glabratus c88, Malassezia arunalokei c192, and Penicillium sumatraense c22. Predictive models that integrated both bacterial and fungal taxa enhanced prediction accuracy, underscoring the critical role of gut fungi in ACVD. Our findings offer a thorough understanding of the link between the gut mycobiome and ACVD progression, which is vital for directing future therapeutic research.IMPORTANCEACVD is a leading cause of death and morbidity worldwide. While the role of the gut microbiome in ACVD development is recognized, the contribution of the gut mycobiome remains largely unexplored. Our study reveals significant alterations in the gut mycobiome of ACVD patients and identifies key fungal taxa associated with the disease. These findings underscore the importance of the gut mycobiome in the pathogenesis of ACVD and offer new avenues for developing preventive and therapeutic strategies targeting the gut fungal community. Our results provide valuable insights into the complex interplay between gut fungi and bacteria in ACVD, paving the way for novel therapeutic approaches.}, } @article {pmid39660707, year = {2024}, author = {Cai, Z and Zhang, X and Song, Y and Jiang, Y and Jiang, L and Li, T and Sun, X}, title = {Performance of metagenomic next-generation sequencing for microbiological diagnosis of infectious uveitis.}, journal = {Journal of medical microbiology}, volume = {73}, number = {12}, pages = {}, pmid = {39660707}, issn = {1473-5644}, mesh = {Humans ; *Uveitis/diagnosis/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Female ; Middle Aged ; Male ; Adult ; *Sensitivity and Specificity ; Aged ; Young Adult ; Bacteria/isolation & purification/genetics/classification ; Adolescent ; }, abstract = {Introduction. Diagnosis of uveitis is challenging due to the multitude of possible pathogenies. Identifying infectious and non-infectious uveitis is of great clinical significance. Recently, metagenomic next-generation sequencing (mNGS) was used to detect infectious and non-infectious uveitis, but its efficacy has not been widely evaluated.Hypothesis. Compared with routine diagnostic tests (RDTs), mNGS is more effective in identifying infectious and non-infectious uveitis.Aim. To describe the microbiological diagnostic performance of mNGS in detecting infectious and non-infectious uveitis.Methodology. Patients with suspected infectious uveitis of uncertain pathogenesis were tested by mNGS and RDTs. Infectious and non-infectious uveitis were grouped according to the final diagnosis based on comprehensive analysis of the test results and the effect of therapy. The test results were used to assess the performance of mNGS in actual clinical practice.Results. Fifty-eight cases were enrolled in this project, including 32 cases of infectious uveitis and 26 cases of non-infectious uveitis. The sensitivity of mNGS was 96.88%, which was much higher than that of RDTs. The detected pathogenic micro-organisms included bacteria, fungi, viruses, Toxoplasma gondii and Bartonella. Consequently, mNGS showed a high negative predictive value (NPV) of 94.74%, indicating that an mNGS negative should be a true negative result most of the time, but a low positive predictive value (PPV) of 79.49%.Conclusions. mNGS showed extremely high sensitivity but low specificity, which increased the detection rate of infectious uveitis pathogens but might result in false positives. The excellent NPV suggested that the identification of non-infectious uveitis is of considerable clinical importance.}, } @article {pmid39660354, year = {2024}, author = {Han, AR}, title = {Endometrial microbiome in reproductive failure: The possibility of metagenomic analysis.}, journal = {Clinical and experimental reproductive medicine}, volume = {}, number = {}, pages = {}, doi = {10.5653/cerm.2024.07171}, pmid = {39660354}, issn = {2233-8233}, abstract = {With the advent of metagenomics and 16S ribosomal RNA sequencing, growing attention has been dedicated to the endometrial microbiome. Research involving a relatively large cohort of healthy female participants has reported Lactobacillus dominance (LD) in the endometrial microbiome. Multiple studies have also shown that the loss of LD and/or increased microbial diversity within the endometrium are associated with reproductive failure. This phenomenon may stem from the loss of the immunomodulatory effects of Lactobacillus and the rise of proinflammatory responses triggered by pathogenic proliferation. Recent research has employed personalized antibiotic therapy followed by probiotic supplementation, tailored to the endometrial microbial composition of women with repeated implantation failure. The findings suggest that metagenomic analysis of the endometrial microbiome could be a valuable tool in addressing reproductive failure.}, } @article {pmid39660058, year = {2024}, author = {Boer, MD and Melkonian, C and Zafeiropoulos, H and Haas, AF and Garza, DR and Dutilh, BE}, title = {Improving genome-scale metabolic models of incomplete genomes with deep learning.}, journal = {iScience}, volume = {27}, number = {12}, pages = {111349}, pmid = {39660058}, issn = {2589-0042}, abstract = {Deciphering microbial metabolism is essential for understanding ecosystem functions. Genome-scale metabolic models (GSMMs) predict metabolic traits from genomic data, but constructing GSMMs for uncultured bacteria is challenging due to incomplete metagenome-assembled genomes, resulting in many gaps. We introduce the deep neural network guided imputation of reactomes (DNNGIOR), which uses AI to improve gap-filling by learning from the presence and absence of metabolic reactions across diverse bacterial genomes. Key factors for prediction accuracy are: (1) reaction frequency across all bacteria and (2) phylogenetic distance of the query to the training genomes. DNNGIOR predictions achieve an average F1 score of 0.85 for reactions present in over 30% of training genomes. DNNGIOR guided gap-filling was 14 times more accurate for draft reconstructions and 2-9 times for curated models than unweighted gap-filling.}, } @article {pmid39660047, year = {2024}, author = {Klapper, M and Stallforth, P}, title = {Accessing microbial natural products of the past.}, journal = {microLife}, volume = {5}, number = {}, pages = {uqae023}, pmid = {39660047}, issn = {2633-6693}, abstract = {Microbial natural products-low molecular weight compounds biosynthesized by microorganisms-form the foundation of important modern therapeutics, including antibiotics, immunomodulators, and anti-cancer agents. This perspective discusses and contrasts two emerging approaches for uncovering natural products of the past. On the one hand, ancestral sequence reconstruction allows recreating biosynthetic pathways that date back hundreds of millions of years. On the other hand, sequencing and de novo assembly of ancient DNA reveals the biosynthetic potential of ancient microbial communities up to 100 000 years. Together, these approaches unveil an otherwise hidden reservoir of functional and structural molecular diversity. They also offer new opportunities to study the biological function and evolution of these molecules within an archaeological context.}, } @article {pmid39660013, year = {2024}, author = {Abadikhah, M and Persson, F and Farewell, A and Wilén, BM and Modin, O}, title = {Viral diversity and host associations in microbial electrolysis cells.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae143}, pmid = {39660013}, issn = {2730-6151}, abstract = {In microbial electrolysis cells (MECs), microbial communities catalyze conversions between dissolved organic compounds, electrical energy, and energy carriers such as hydrogen and methane. Bacteria and archaea, which catalyze reactions on the anode and cathode of MECs, interact with phages; however, phage communities have previously not been examined in MECs. In this study, we used metagenomic sequencing to study prokaryotes and phages in nine MECs. A total of 852 prokaryotic draft genomes representing 278 species, and 1476 phage contigs representing 873 phage species were assembled. Among high quality prokaryotic genomes (>95% completion), 55% carried a prophage, and the three Desulfobacterota spp. that dominated the anode communities all carried prophages. Geobacter anodireducens, one of the bacteria dominating the anode communities, carried a CRISPR spacer showing evidence of a previous infection by a Peduoviridae phage present in the liquid of some MECs. Methanobacteriaceae spp. and an Acetobacterium sp., which dominated the cathodes, had several associations with Straboviridae spp. The results of this study show that phage communities in MECs are diverse and interact with functional microorganisms on both the anode and cathode.}, } @article {pmid39660009, year = {2024}, author = {Ruiz-Blas, F and Bartholomäus, A and Yang, S and Wagner, D and Henny, C and Russell, JM and Kallmeyer, J and Vuillemin, A}, title = {Metabolic features that select for Bathyarchaeia in modern ferruginous lacustrine subsurface sediments.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae112}, pmid = {39660009}, issn = {2730-6151}, abstract = {Ferruginous conditions prevailed through Earth's early oceans history, yet our understanding of biogeochemical cycles in anoxic iron-rich, sulfate-poor sediments remains elusive in terms of redox processes and organic matter remineralization. Using comprehensive geochemistry, cell counts, and metagenomic data, we investigated the taxonomic and functional distribution of the microbial subsurface biosphere in Lake Towuti, a stratified ferruginous analogue. Below the zone in which pore water becomes depleted in electron acceptors, cell densities exponentially decreased while microbial assemblages shifted from iron- and sulfate-reducing bacterial populations to fermentative anaerobes and methanogens, mostly selecting Bathyarchaeia below the sulfate reduction zone. Bathyarchaeia encode metabolic machinery to cycle and assimilate polysulfides via sulfhydrogenase, sulfide dehydrogenase, and heterodisulfide reductase, using dissimilatory sulfite reductase subunit E and rubredoxin as carriers. Their metagenome-assembled genomes showed that carbon fixation could proceed through the complete methyl-branch Wood-Ljungdahl pathway, conducting (homo)acetogenesis in the absence of methyl coenzyme M reductase. Further, their partial carbonyl-branch, assumed to act in tetrahydrofolate interconversions of C1 and C2 compounds, could support close interactions with methylotrophic methanogens in the fermentation zone. Thus, Bathyarchaeia appeared capable of coupling sulfur-redox reactions with fermentative processes, using electron bifurcation in a redox-conserving (homo)acetogenic Wood-Ljungdahl pathway, and revealing geochemical ferruginous conditions at the transition between the sulfate reduction and fermentation zone as their preferential niche.}, } @article {pmid39659683, year = {2024}, author = {Liang, H and Zhu, Z and Fan, Y and Hu, J and Wu, J and Mu, Z and Li, Y and Wei, Q and Yang, C and Tian, J and Li, S}, title = {Integrated microbiomic and metabolomic dynamics of Yi traditional fermented liquor.}, journal = {Food chemistry: X}, volume = {24}, number = {}, pages = {102016}, pmid = {39659683}, issn = {2590-1575}, abstract = {This study examines the microbial community composition, metabolite characteristics, and the relationship between the two during the fermentation process of Yi traditional fermented liquor. Yi traditional fermented foods have a profound historical and cultural background, with significant ethnic characteristics. As a case in point, Yi traditional fermented liquor is typically prepared using local plants or traditional Chinese herbs as fermentation substrates and undergoes a lengthy fermentation process, resulting in a fermented beverage that is reputed to have beneficial effects on human health. These foods are not only characterised by a distinctive flavor profile, but are also perceived to possess certain health benefits in the context of traditional ethnic medicine and wellness practices. The community composition of bacteria and fungi was analyzed using 16S rRNA and ITS1 sequencing technologies, which revealed that microbial diversity was higher in the early stages of fermentation but gradually decreased as fermentation progressed. A total of 130 major volatile flavor compounds and 26 key metabolites were identified at different stages of fermentation. These included acids, sugars, amino acids and flavonoids, which significantly influence the flavor and nutritional value of the fermented products. The study indicates a significant correlation between specific microbial populations (such as yeasts) and key metabolites (such as flavonoids and amino acids). These findings emphasise the significance of the interplay between microbial communities and metabolites in shaping the quality and efficacy of fermented products. They offer a scientific foundation for optimizing traditional fermented food production processes.}, } @article {pmid39659682, year = {2024}, author = {Mao, H and Xu, Y and Lu, F and Ma, C and Zhu, S and Li, G and Huang, S and Zhang, Y and Hou, Y}, title = {An integrative multi-omics approach reveals metabolic mechanism of flavonoids during anaerobic fermentation of de'ang pickled tea.}, journal = {Food chemistry: X}, volume = {24}, number = {}, pages = {102021}, pmid = {39659682}, issn = {2590-1575}, abstract = {Anaerobic fermentation (AF) is critical process for Yunnan De'ang pickled tea production. Therefore, widely targeted metabolomics and metagenomics were integrated to reveal the AF mechanism. Lactic acid bacteria (LAB) (e.g. Lactiplantibacillus plantarum, Lactobacillus vaccinostercus and Lactobacillus paracollinoides) and yeasts like Candida metapsilosis and Cyberlindnera fabianii dominated in the AF. Based on bacterial community succession and metabolites variation, the whole AF processes were divided into two phases, i.e., before and after four months. A total of 327 characteristic metabolites (VIP >1.0, P < 0.05, and FC > 1.50 or < 0.67) were selected from the AF. Besides amino acids increase, LAB and yeasts also promoted non-galloylated catechins, and several simple flavones/flavonols, flavanones/flavanonols and methoxy flavones/flavonols accumulations along with galloylated catechins, flavonol/flavone glycosides and anthocyanins decrease during the AF. This study would improve the understanding about AF mechanism of tea-leaves from the perspectives of flavonoids metabolism and microbial community succession.}, } @article {pmid39659556, year = {2024}, author = {Huang, Z and Wang, L and Tong, J and Zhao, Y and Ling, H and Zhou, Y and Tan, Y and Xiong, X and Qiu, Y and Bi, Y and Pan, Z and Yang, R}, title = {Alterations in Gut Microbiota Correlate With Hematological Injuries Induced by Radiation in Beagles.}, journal = {International journal of microbiology}, volume = {2024}, number = {}, pages = {3096783}, pmid = {39659556}, issn = {1687-918X}, abstract = {Dynamics of gut microbiota and their associations with the corresponding hematological injuries postradiation remain to be elucidated. Using single whole-body exposure to [60]Co-γ ray radiation at the sublethal dose of 2.5 Gy, we developed a beagle model of acute radiation syndrome (ARS) and then monitored the longitudinal changes of gut microbiome and hematology for 45 days. We found that the absolute counts of circulating lymphocytes, neutrophils, and platelets were sharply declined postradiation, accompanied by a largely shifted composition of gut microbiome that manifested as a significantly increased ratio of Firmicutes to Bacteroidetes. In irradiated beagles, alterations in hematological parameters reached a nadir on day 14, sustaining for 1 week, which were gradually returned to the normal levels thereafter. However, no structural recovery of gut microbiota was observed throughout the study. Fecal metagenomics revealed that irradiation increased the relative abundances of genus Streptococcus, species Lactobacillus animalis and Lactobacillus murinus, but decreased those of genera Prevotella and Bacteroides. Metagenomic functions prediction demonstrated that 26 altered KEGG pathways were significantly enriched on Day 14 and 35 postradiation. Furthermore, a total of 43 bacterial species were found to correlate well with hematological parameters by Spearman's analysis. Our results provide an insight into the longitudinal changes in intestinal microbiota at different clinical stages during ARS in canine. Several key microbes those tightly associated with the hematological alterations may serve as biomarkers to discriminate the different phases of host with ARS.}, } @article {pmid39659426, year = {2024}, author = {Abildinova, GZ and Benberin, VV and Vochshenkova, TA and Afshar, A and Mussin, NM and Kaliyev, AA and Zhussupova, Z and Tamadon, A}, title = {The gut-brain-metabolic axis: exploring the role of microbiota in insulin resistance and cognitive function.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1463958}, pmid = {39659426}, issn = {1664-302X}, abstract = {The gut-brain-metabolic axis has emerged as a critical area of research, highlighting the intricate connections between the gut microbiome, metabolic processes, and cognitive function. This review article delves into the complex interplay between these interconnected systems, exploring their role in the development of insulin resistance and cognitive decline. The article emphasizes the pivotal influence of the gut microbiota on central nervous system (CNS) function, demonstrating how microbial colonization can program the hypothalamic-pituitary-adrenal (HPA) axis for stress response in mice. It further elucidates the mechanisms by which gut microbial carbohydrate metabolism contributes to insulin resistance, a key factor in the pathogenesis of metabolic disorders and cognitive impairment. Notably, the review highlights the therapeutic potential of targeting the gut-brain-metabolic axis through various interventions, such as dietary modifications, probiotics, prebiotics, and fecal microbiota transplantation (FMT). These approaches have shown promising results in improving insulin sensitivity and cognitive function in both animal models and human studies. The article also emphasizes the need for further research to elucidate the specific microbial species and metabolites involved in modulating the gut-brain axis, as well as the long-term effects and safety of these therapeutic interventions. Advances in metagenomics, metabolomics, and bioinformatics are expected to provide deeper insights into the complex interactions within the gut microbiota and their impact on host health. Overall, this comprehensive review underscores the significance of the gut-brain-metabolic axis in the pathogenesis and treatment of metabolic and cognitive disorders, offering a promising avenue for the development of novel therapeutic strategies targeting this intricate system.}, } @article {pmid39659424, year = {2024}, author = {Kilonzo-Nthenge, A and Rafiqullah, I and Netherland, M and Nzomo, M and Mafiz, A and Nahashon, S and Hasan, NA}, title = {Comparative metagenomics of microbial communities and resistome in southern farming systems: implications for antimicrobial stewardship and public health.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1443292}, pmid = {39659424}, issn = {1664-302X}, abstract = {Agricultural practices significantly influence microbial diversity and the distribution of virulence and antimicrobial resistance (AMR) genes, with implications for ecosystem health and food safety. This study used metagenomic sequencing to analyze 60 samples (30 per state) including water, soil, and manure (10 each) from Alabama (a mix of cattle and poultry sources) and Tennessee (primarily from cattle). The results highlighted a rich microbial diversity, predominantly comprising Bacteria (67%) and Viruses (33%), with a total of over 1,950 microbial species identified. The dominant bacterial phyla were Proteobacteria, Cyanobacteria, Actinobacteria, Firmicutes, and Bacteroidetes, with the viral communities primarily represented by Phixviricota and Uroviricota. Distinct state-specific microbial profiles were evident, with Alabama demonstrating a higher prevalence of viral populations and unique bacterial phyla compared to Tennessee. The influence of environmental and agricultural practices was reflected in the microbial compositions: soil samples were notably rich in Actinobacteria, water samples were dominated by Proteobacteria and Cyanobacteria, and manure samples from Alabama showed a predominance of Actinobacteria. Further analyses, including diversity assessment and enterotype clustering, revealed complex microbial structures. Tennessee showed higher microbial diversity and phylogenetic complexity across most sample types compared to Alabama, with poultry-related samples displaying distinct diversity trends. Principal Coordinate Analysis (PCoA) highlighted notable state-specific variations, particularly in manure samples. Differential abundance analysis demonstrated elevated levels of Deinococcus and Ligilactobacillus in Alabama, indicating regional effects on microbial distributions. The virulome analysis revealed a significant presence of virulence genes in samples from Alabama. The community resistome was extensive, encompassing 109 AMR genes across 18 antibiotic classes, with manure samples displaying considerable diversity. Ecological analysis of the interactions between AMR gene subtypes and microbial taxa revealed a sophisticated network, often facilitated by bacteriophages. These findings underscore the critical role of agricultural practices in shaping microbial diversity and resistance patterns, highlighting the need for targeted AMR mitigation strategies in agricultural ecosystems to protect both public health and environmental integrity.}, } @article {pmid39658215, year = {2024}, author = {Kneis, D and Tskhay, F and de la Cruz Barron, M and Berendonk, TU}, title = {Bacteria of the order Burkholderiales are original environmental hosts of type II trimethoprim resistance genes (dfrB).}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39658215}, issn = {1751-7370}, support = {01KI1909A (EMBARK)//German Ministry of Education and Research, BMBF/ ; }, mesh = {*Trimethoprim Resistance/genetics ; *Burkholderiales/genetics/drug effects ; Metagenome ; Soil Microbiology ; Trimethoprim/pharmacology ; Anti-Bacterial Agents/pharmacology ; Fresh Water/microbiology ; Genes, Bacterial ; Whole Genome Sequencing ; Phylogeny ; Metagenomics ; }, abstract = {It is consensus that clinically relevant antibiotic resistance genes have their origin in environmental bacteria, including the large pool of primarily benign species. Yet, for the vast majority of acquired antibiotic resistance genes, the original environmental host(s) has not been identified to date. Closing this knowledge gap could improve our understanding of how antimicrobial resistance proliferates in the bacterial domain and shed light on the crucial step of initial resistance gene mobilization in particular. Here, we combine information from publicly available long- and short-read environmental metagenomes as well as whole-genome sequences to identify the original environmental hosts of dfrB, a family of genes conferring resistance to trimethoprim. Although this gene family stands in the shadow of the more widespread, structurally different dfrA, it has recently gained attention through the discovery of several new members. Based on the genetic context of dfrB observed in long-read metagenomes, we predicted bacteria of the order Burkholderiales to function as original environmental hosts of the predominant gene variants in both soil and freshwater. The predictions were independently confirmed by whole-genome datasets and statistical correlations between dfrB abundance and taxonomic composition of environmental bacterial communities. Our study suggests that Burkholderiales in general and the family Comamonadaceae in particular represent environmental origins of dfrB genes, some of which now contribute to the acquired resistome of facultative pathogens. We propose that our workflow centered on long-read environmental metagenomes allows for the identification of the original hosts of further clinically relevant antibiotic resistance genes.}, } @article {pmid39658189, year = {2024}, author = {Dufault-Thompson, K and Levy, S and Hall, B and Jiang, X}, title = {Bilirubin reductase shows host-specific associations in animal large intestines.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39658189}, issn = {1751-7370}, mesh = {Animals ; *Phylogeny ; *Gastrointestinal Microbiome ; *Intestine, Large/microbiology ; *Oxidoreductases Acting on CH-CH Group Donors/genetics/metabolism ; Bilirubin/metabolism ; Heme/metabolism ; Bacteria/genetics/classification/isolation & purification/enzymology ; Metagenomics ; }, abstract = {Animal gastrointestinal tracts contain diverse metabolites, including various host-derived compounds that gut-associated microbes interact with. Here, we explore the diversity and evolution of bilirubin reductase, a bacterial enzyme that metabolizes the host-derived tetrapyrrole bilirubin, performing a key role in the animal heme degradation pathway. Through an analysis of the bilirubin reductase phylogeny and predicted structures, we found that the enzyme family can be divided into three distinct clades with different structural features. Using these clade definitions, we analyzed metagenomic sequencing data from multiple animal species, finding that bilirubin reductase is significantly enriched in the large intestines of animals and that the clades exhibit differences in distribution among animals. Combined with phylogenetic signal analysis, we find that the bilirubin reductase clades exhibit significant associations with specific animals and animal physiological traits like gastrointestinal anatomy and diet. These patterns demonstrate that bilirubin reductase is specifically adapted to the anoxic lower gut environment of animals and that its evolutionary history is complex, involving adaptation to a diverse collection of animals harboring bilirubin-reducing microbes. The findings suggest that bilirubin reductase evolution has been shaped by the host environment, providing a new perspective on heme metabolism in animals and highlighting the importance of the microbiome in animal physiology and evolution.}, } @article {pmid39658173, year = {2025}, author = {Xue, B and You, Y and Du, M and Ibrahim, A and Suo, H and Zhang, F and Zheng, J}, title = {Metagenomic analysis of Lactobacillus plantarum DACN768 inoculation effects on volatile flavor compounds, microbial succession, and flavor metabolic network in suansun.}, journal = {Food research international (Ottawa, Ont.)}, volume = {199}, number = {}, pages = {115382}, doi = {10.1016/j.foodres.2024.115382}, pmid = {39658173}, issn = {1873-7145}, mesh = {*Lactobacillus plantarum/metabolism/genetics ; *Volatile Organic Compounds/metabolism/analysis ; *Fermentation ; Flavoring Agents/metabolism ; Metabolic Networks and Pathways ; Metagenomics ; Food Microbiology ; Taste ; Gas Chromatography-Mass Spectrometry ; }, abstract = {This study analyzed volatile flavor compounds and microbial communities in Lactobacillus plantarum-fermented suansun (LPS), emphasizing the underlying metabolic pathways. A comparison with naturally fermented suansun (NFS) identified 56 volatile flavor compounds in LPS, detected via GC-MS, with levels peaking at 14 days. Alcohols, aldehydes, and esters were the primary components in both NFS and LPS. However, LPS contained significantly more and diverse aldehydes, likely due to L. plantarum's ability to convert free amino acids into aldehydes through the Ehrlich pathway, while keeping phenol levels consistently low. The analysis focused on the ten most abundant bacterial genera in LPS, with Weissella being the most dominant, followed by Lactobacillus, Lactococcus, and Enterococcus. Lactobacillus plantarum exhibited higher metabolic activity and stronger strain interactions compared to NFS. Metagenomic data revealed enhanced carbohydrate and amino acid metabolism in LPS, identifying key pathways contributing to flavor development. Glycolysis and gluconeogenesis, essential for lactic acid bacteria, were active in both LPS and NFS. Pyruvate and propionic acid were major intermediates, while tyrosine was the primary amino acid metabolized in NFS, serving as a main source of aldehydes, alcohols, phenols, and esters. Pyruvate kinase and hexokinase were critical enzymes for the synthesis of alcohols and phenols, primarily mediated by Lactobacillus and Lactococcus. Tyrosine metabolism, specifically through the 4-hydroxyphenylpyruvate and 4-hydroxyphenylacetic acid pathways, was crucial for the formation of phenol and p-cresol. These results offer new insights into the biochemical mechanisms driving flavor formation in suansun.}, } @article {pmid39658159, year = {2025}, author = {Zhang, H and Huang, S and Zhao, Y and Tian, HS and Lin, M and Xie, Y and Yu, Z}, title = {Modification of microporous bionanocomposite films with visible light-activated photocatalytic antimicrobial TNT-CuO nanoparticles for active fruit packaging.}, journal = {Food research international (Ottawa, Ont.)}, volume = {199}, number = {}, pages = {115356}, doi = {10.1016/j.foodres.2024.115356}, pmid = {39658159}, issn = {1873-7145}, mesh = {*Food Packaging/methods ; *Copper/chemistry/pharmacology ; *Light ; *Nanocomposites/chemistry ; *Fruit/microbiology/chemistry ; *Staphylococcus aureus/drug effects/growth & development ; *Chitosan/chemistry ; Blueberry Plants/chemistry ; Escherichia coli O157/drug effects/growth & development ; Food Preservation/methods ; Polyvinyl Alcohol/chemistry ; Cellulose/chemistry ; Nanoparticles/chemistry ; Anti-Infective Agents/pharmacology/chemistry ; Reactive Oxygen Species/metabolism ; Food Microbiology ; Metal Nanoparticles/chemistry ; Catalysis ; }, abstract = {Active packaging technologies are evolving to enhance the preservation of fresh produce by fighting against microbial contamination and controlling internal packaging atmospheres. This study introduced an active fruit packaging called MT film, created by modifying a microporous polyvinyl alcohol/chitosan/cellulose nanocrystal bionanocomposite film with CuO-doped titania nanotubes. The MT film, with an average micropore size of 2.4 μm, displayed excellent mechanical properties and hydrophobicity due to its crosslinked structure. When exposed to visible light, the MT film could produce reactive oxygen species, effectively inhibiting the growth of Staphylococcus aureus and Escherichia coli O157:H7. Moreover, experiments on blueberry preservation demonstrated that the MT film could remove excess CO2 and maintain a higher O2 level. Under visible light, this film significantly reduced total viable count (4.6 ± 0.2 log CFU/g) and mold colony count (2.6 ± 0.1 log CFU/g), with Bacillus and Ascochyta being the primary inhibited genera. These findings highlight the potential of MT film in utilizing visible light to prevent microbial growth on blueberries and regulating the gas exchange of food packaging. MT film holds promise as an active packaging solution to improve the quality and shelf life of fresh produce while reducing food losses in the supply chain.}, } @article {pmid39657855, year = {2025}, author = {Gu, Z and He, L and Liu, T and Xing, M and Feng, L and Luo, G}, title = {Exploring strategies for kitchen waste treatment and remediation from the perspectives of microbial ecology and genomics.}, journal = {Chemosphere}, volume = {370}, number = {}, pages = {143925}, doi = {10.1016/j.chemosphere.2024.143925}, pmid = {39657855}, issn = {1879-1298}, mesh = {*Oligochaeta ; Animals ; *Sewage/microbiology ; Biodegradation, Environmental ; Metagenomics ; Genomics ; Composting ; Soil Microbiology ; Lignin/metabolism ; Refuse Disposal/methods ; Bacteria/metabolism/genetics ; Ecology ; }, abstract = {Nowadays, the rapid growth of population has led to a substantial increase in kitchen waste and wasted sludge. Kitchen waste is rich in organic matter, including lignocellulose. Synergistic treatment involving kitchen waste and wasted sludge can enhance treatment process. Vermicomposting can facilitate microbial activities on organic matter. Nevertheless, the underlying mechanisms remain unclear. In this study, metagenomics was used to analyze microbial functional genes in vermicomposting. Redundancy analysis found that TOC, TN and DTN adversely affect earthworm growth and reproduction. The relative abundance of Bacteroidetes and Firmicutes increased with earthworms, thereby potentially augmenting lignocellulose degradation. The predominant functional genes included amino acid, carbohydrate, and inorganic ion conversion and metabolism. Metagenomics analysis demonstrated that GH1, GH3, GH5, GH6, GH9, GH12, GH44, GH48 and GH74, GT41, GT4, GT2, and GT51 were dominant. Furthermore, there was higher abundance of carbohydrate-active enzymes in the vermicomposting, particularly during the later phases (30-45 days). Co-occurrence network revealed that Cellvibrio in the vermicomposting exhibited a relatively dense positive correlation with other microbial groups. The findings elucidated the mechanism of vermicomposting as a promising approach for managing kitchen waste and wasted sludge.}, } @article {pmid39657789, year = {2025}, author = {Zdouc, MM and Blin, K and Louwen, NLL and Navarro, J and Loureiro, C and Bader, CD and Bailey, CB and Barra, L and Booth, TJ and Bozhüyük, KAJ and Cediel-Becerra, JDD and Charlop-Powers, Z and Chevrette, MG and Chooi, YH and D'Agostino, PM and de Rond, T and Del Pup, E and Duncan, KR and Gu, W and Hanif, N and Helfrich, EJN and Jenner, M and Katsuyama, Y and Korenskaia, A and Krug, D and Libis, V and Lund, GA and Mantri, S and Morgan, KD and Owen, C and Phan, CS and Philmus, B and Reitz, ZL and Robinson, SL and Singh, KS and Teufel, R and Tong, Y and Tugizimana, F and Ulanova, D and Winter, JM and Aguilar, C and Akiyama, DY and Al-Salihi, SAA and Alanjary, M and Alberti, F and Aleti, G and Alharthi, SA and Rojo, MYA and Arishi, AA and Augustijn, HE and Avalon, NE and Avelar-Rivas, JA and Axt, KK and Barbieri, HB and Barbosa, JCJ and Barboza Segato, LG and Barrett, SE and Baunach, M and Beemelmanns, C and Beqaj, D and Berger, T and Bernaldo-Agüero, J and Bettenbühl, SM and Bielinski, VA and Biermann, F and Borges, RM and Borriss, R and Breitenbach, M and Bretscher, KM and Brigham, MW and Buedenbender, L and Bulcock, BW and Cano-Prieto, C and Capela, J and Carrion, VJ and Carter, RS and Castelo-Branco, R and Castro-Falcón, G and Chagas, FO and Charria-Girón, E and Chaudhri, AA and Chaudhry, V and Choi, H and Choi, Y and Choupannejad, R and Chromy, J and Donahey, MSC and Collemare, J and Connolly, JA and Creamer, KE and Crüsemann, M and Cruz, AA and Cumsille, A and Dallery, JF and Damas-Ramos, LC and Damiani, T and de Kruijff, M and Martín, BD and Sala, GD and Dillen, J and Doering, DT and Dommaraju, SR and Durusu, S and Egbert, S and Ellerhorst, M and Faussurier, B and Fetter, A and Feuermann, M and Fewer, DP and Foldi, J and Frediansyah, A and Garza, EA and Gavriilidou, A and Gentile, A and Gerke, J and Gerstmans, H and Gomez-Escribano, JP and González-Salazar, LA and Grayson, NE and Greco, C and Gomez, JEG and Guerra, S and Flores, SG and Gurevich, A and Gutiérrez-García, K and Hart, L and Haslinger, K and He, B and Hebra, T and Hemmann, JL and Hindra, H and Höing, L and Holland, DC and Holme, JE and Horch, T and Hrab, P and Hu, J and Huynh, TH and Hwang, JY and Iacovelli, R and Iftime, D and Iorio, M and Jayachandran, S and Jeong, E and Jing, J and Jung, JJ and Kakumu, Y and Kalkreuter, E and Kang, KB and Kang, S and Kim, W and Kim, GJ and Kim, H and Kim, HU and Klapper, M and Koetsier, RA and Kollten, C and Kovács, ÁT and Kriukova, Y and Kubach, N and Kunjapur, AM and Kushnareva, AK and Kust, A and Lamber, J and Larralde, M and Larsen, NJ and Launay, AP and Le, NT and Lebeer, S and Lee, BT and Lee, K and Lev, KL and Li, SM and Li, YX and Licona-Cassani, C and Lien, A and Liu, J and Lopez, JAV and Machushynets, NV and Macias, MI and Mahmud, T and Maleckis, M and Martinez-Martinez, AM and Mast, Y and Maximo, MF and McBride, CM and McLellan, RM and Bhatt, KM and Melkonian, C and Merrild, A and Metsä-Ketelä, M and Mitchell, DA and Müller, AV and Nguyen, GS and Nguyen, HT and Niedermeyer, THJ and O'Hare, JH and Ossowicki, A and Ostash, BO and Otani, H and Padva, L and Paliyal, S and Pan, X and Panghal, M and Parade, DS and Park, J and Parra, J and Rubio, MP and Pham, HT and Pidot, SJ and Piel, J and Pourmohsenin, B and Rakhmanov, M and Ramesh, S and Rasmussen, MH and Rego, A and Reher, R and Rice, AJ and Rigolet, A and Romero-Otero, A and Rosas-Becerra, LR and Rosiles, PY and Rutz, A and Ryu, B and Sahadeo, LA and Saldanha, M and Salvi, L and Sánchez-Carvajal, E and Santos-Medellin, C and Sbaraini, N and Schoellhorn, SM and Schumm, C and Sehnal, L and Selem, N and Shah, AD and Shishido, TK and Sieber, S and Silviani, V and Singh, G and Singh, H and Sokolova, N and Sonnenschein, EC and Sosio, M and Sowa, ST and Steffen, K and Stegmann, E and Streiff, AB and Strüder, A and Surup, F and Svenningsen, T and Sweeney, D and Szenei, J and Tagirdzhanov, A and Tan, B and Tarnowski, MJ and Terlouw, BR and Rey, T and Thome, NU and Torres Ortega, LR and Tørring, T and Trindade, M and Truman, AW and Tvilum, M and Udwary, DW and Ulbricht, C and Vader, L and van Wezel, GP and Walmsley, M and Warnasinghe, R and Weddeling, HG and Weir, ANM and Williams, K and Williams, SE and Witte, TE and Rocca, SMW and Yamada, K and Yang, D and Yang, D and Yu, J and Zhou, Z and Ziemert, N and Zimmer, L and Zimmermann, A and Zimmermann, C and van der Hooft, JJJ and Linington, RG and Weber, T and Medema, MH}, title = {MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration.}, journal = {Nucleic acids research}, volume = {53}, number = {D1}, pages = {D678-D690}, pmid = {39657789}, issn = {1362-4962}, support = {//Conahcyt Mexico International PhD Studentship/ ; 32170080//National Natural Science Foundation of China/ ; 547394769//German Research Foundation/ ; 101066127//European Union/ ; NNF19SA0059360//Novo Nordisk Foundation INTERACT/ ; //Swedish Pharmaceutical Society PostDoc/ ; F32AT011475/AT/NCCIH NIH HHS/United States ; //Werner Siemens Foundation/ ; 027/E5/PG.02.00.PL/2024//Ministry of Education/ ; ANR-17-EUR-0007//EUR Saclay Plant Sciences-SPS/ ; PROYEXCEL_00012//Spanish "Junta de Andalucía"/ ; 1347411//CONAHCYT/ ; IM230100154//Australian Research Council Industry Fellowship/ ; 1229222N//Research Foundation-Flanders (FWO)/ ; R01 GM146224/GM/NIGMS NIH HHS/United States ; //Swiss Federal Government/ ; OSF.23.1.044//NWO Open Science Project 'BiG-CODEC'/ ; //NWO Merian/ ; 024.004.014//MiCRop Consortium/ ; CZIF2022-007203//Chan Zuckerberg Initiative Foundation/ ; BB/T007222/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; DP230102668//Australian Research Council Discovery Project/ ; 57/0009//Ministry of Education and Science of Ukraine/ ; //Delta Stewardship Council Delta Science Program/ ; T32 GM136629/GM/NIGMS NIH HHS/United States ; //Basic Science Research Program/ ; R01-GM146224/GM/NIGMS NIH HHS/United States ; K12 GM068524/GM/NIGMS NIH HHS/United States ; AUFF-E-2022-9-42//AUFF/ ; 10062709//UK Innovation Funding Agency (UKRI)/ ; CBET-2032243//U.S. National Science Foundation/ ; //University of Illinois/ ; //HZI POF IV Cooperativity and Creativity Project Call/ ; //Horizon Europe Marie Skłodowska-Curie Actions Postdoctoral Fellowship/ ; NE/T010959/1//Signals in the Soil/ ; ANR-24-CE20-7299-01//Agence Nationale de la Recherche/ ; DNRF137//Danish National Research Foundation/ ; OCENW.GROOT.2019.063//NWO-XL/ ; BB/V005723/2//BBSRC/ ; 101087181//EU/ ; 101000392//Horizon 2020/ ; 101072485//European Union's Horizon/ ; 10.55776/P 34036//Austrian Science Fund/ ; EP/X03142X/1//United Kingdom Research and Innovation/ ; 23/01956-2//São Paulo Research Foundation/ ; //Department of Biotechnology/ ; 222676//USDA Evans-Allen Research/ ; //Saarland University/ ; 102022750//SINTEF/ ; //Hans Fischer Society/ ; 21K06336//KAKENHI/ ; CF22-1239//Carlsberg Foundation/ ; ANR-22-CE44-0011-01 UMISYN//Agence Nationale de la Recherche/ ; 495740318//German Research Foundation/ ; 802736//European Union Horizon 2020/ ; //Strathclyde University Global Research Scholarship/ ; NNF22OC0079021//Novo Nordisk Foundation Postdoctoral Fellowship/ ; 101055020-COMMUNITY//ERC Advanced/ ; 101099528//European Innovation Council/ ; GNT2021638//National Health and Medical Research Council/ ; 757173//Consejo Nacional de Ciencia y Tecnología/ ; NA22NOS4200050//NERRS/ ; 865738/ERC_/European Research Council/International ; DGE 2241144//NSF GRFP/ ; //National Research Fund of Ukraine/ ; RYC2020-029240-I//Ministerio de Ciencia, Innovación y Universidades/ ; MR/V022334/1//UKRI Future Leaders Fellowship/ ; 102029187//SEP AGREE/ ; NNF22OC0078997//Novo Nodisk Foundation/ ; F31 ES036421/ES/NIEHS NIH HHS/United States ; KICH1.LWV04.21.013//NWO/ ; DM60066//Italian Ministry of Research/ ; 101117891-MeDiSyn//ERC Starting/ ; //European Union's Horizon 2020 Research/ ; NRF 2018R1A5A2023127//Korea Government (MSIT)/ ; PS00349981//Fulbright/ ; NRF-2020R1A6A1A03044512//Korean Government (MSIT)/ ; 735867//Consejo Nacional de Ciencia y Tecnología/ ; 3141-00013A//Innovation Fund Denmark/ ; CFB 2.0//Novo Nordisk Foundation/ ; 21/07038-0//São Paulo Research Foundation/ ; 2021YFA0909500//National Key Research and Development Program of China/ ; 101072485//European Union's Horizon Europe/ ; OCENW.XL21.XL21.088//NWO-XL/ ; //University Grants Commission/ ; //Natural Science and Research Council of Canada/ ; TTU 09.826//German Center for Infection Research/ ; //European Regional Development Fund/ ; 101072485//Horizon Europe Marie Skłodowska-Curie/ ; DNRF137//Danish National Research Foundation CeMiSt/ ; BB/X010953/1//Growing Health Institute Strategic Programme/ ; BB/X01097X/1//BBSRC Institute Strategic Program/ ; 802736//European Union's Horizon 2020/ ; //Alexander von Humboldt-Stiftung/ ; //UK Government Department for Environment, Food & Rural Affairs (DEFRA) Global Centre on Biodiversity for the Climate/ ; //Shanghai Pilot Program for Basic Research - Shanghai Jiao Tong University/ ; 102024676-14//POS BIOINFO 2024/ ; MR/W011247/1//UKRI Future Leaders Fellowship/ ; DGE 21-46756//National Science Foundation Graduate Research Fellowship/ ; 101106349//Marie Sklodowska-Curie/ ; T32-GM136629//Chemical-Biology Interface Training/ ; //University of Sydney/ ; 101000794//SECRETed EU Project Horizon 2020/ ; 2022R1C1C2004118//National Research Foundation of Korea/ ; //Indonesia Endowment Fund for Education Agency (LPDP)/ ; 101130799//European Union's Horizon/ ; 852600//Innovation Program ERC St/ ; //National Agri-Food Biotechnology Institute/ ; //German Academic Scholarship Foundation/ ; 205320_219638/SNSF_/Swiss National Science Foundation/Switzerland ; EXC-2124/1-09.029_0//Cluster of Excellence: Controlling Microbes to Fight Infection/ ; F32 AT011475/AT/NCCIH NIH HHS/United States ; 398967434-TRR 261//Deutsche Forschungsgemeinschaft/ ; 212747/SNSF_/Swiss National Science Foundation/Switzerland ; K445/2022//Leibniz Association/ ; NRF-RS-2024-00352229//Ministry of Science and ICT/ ; //Natural Sciences and Engineering Research Council of Canada Discovery/ ; VI.Veni.202.130//NWO Talent/ ; 106/IV/KS/11/2023//National Research and Innovation Agency/ ; T32GM136583/NH/NIH HHS/United States ; DE-AC02-05CH11231//U.S. Department of Energy/ ; }, mesh = {*Multigene Family ; *Databases, Genetic ; Biosynthetic Pathways/genetics ; Molecular Sequence Annotation ; Biological Products/metabolism/chemistry ; Data Curation ; }, abstract = {Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.}, } @article {pmid39657562, year = {2025}, author = {Du, Z and Du, Y and Wang, J and Zhang, Y and Lu, H and Zhang, F and Peng, Y}, title = {Acidophilic partial nitrification rapid startup and robustness validation for municipal wastewater treatment: Operation performance and microorganism insights.}, journal = {Water research}, volume = {272}, number = {}, pages = {122922}, doi = {10.1016/j.watres.2024.122922}, pmid = {39657562}, issn = {1879-2448}, mesh = {*Nitrification ; *Wastewater ; *Bioreactors ; *Waste Disposal, Fluid/methods ; Bacteria/metabolism/genetics ; Sewage/microbiology ; Nitrites/metabolism ; }, abstract = {Acidophilic partial nitrification (a-PN) is a promising short-flow nitrogen conversion biotechnology, but achieving a rapid startup remains a significant challenge. This study explored strategies for starting up a-PN in real municipal wastewater treatment using sequencing batch reactors (SBRs). The influent alkalinity-to-NH4[+] molar ratio was maintained at 0.5-0.6 in the control reactor (SBRa), while other reactors were supplemented with sodium formate (150 mg COD/L, SBRb), hydroxylamine (5 mg/L, SBRc), and sludge alkaline fermentation liquid (NH4[+]-N=227.97±7.08 mg/L, COD=2463.98±125.17 mg/L, SBRd). Results indicated that the system using the composite strategy with sodium formate addition achieved a 93.7 % nitrite accumulation ratio (NAR) within just 4 days. Furthermore, stable a-PN performance was maintained in the systems without external substrate addition with pH ranging from 5.7 to 7.4. The established a-PN systems demonstrated robust performance, maintained a high NAR of 92.84 %-98.84 %, even under the intense impact of traditional nitrification biomass for 13 consecutive days. Although the relative abundances of Nitrosomonas and Nitrospira temporarily increased, traditional ammonia oxidizing bacteria and nitrite oxidizing bacteria were completely eliminated, falling to undetectable levels after long-term operation. Notably, amo and hao genes exhibited opposite trends: amo decreased significantly from 356 reads to 22-46 reads, while hao substantially increased by 186.6 %-613.1 %, from 626 reads to 1168-2838 reads. This suggests that hao may play a more crucial functional role in the a-PN process, and unidentified nitrifying communities may be driving acidophilic partial nitrification. Overall, our study advances the understanding of rapid startup strategies of a-PN and provides novel perspectives on the microbial structure and functional genes involved in a-PN system.}, } @article {pmid39657473, year = {2025}, author = {Hao, Y and Guo, T and Li, H and Liu, W and Chen, Z and Wang, X and Guo, J}, title = {Study on the mechanism of regulating micromolar Fe utilization and promoting denitrification by guanosine monophosphate (GMP) based multi-signal functional material Hematin@Fe/GMP.}, journal = {Journal of environmental management}, volume = {373}, number = {}, pages = {123610}, doi = {10.1016/j.jenvman.2024.123610}, pmid = {39657473}, issn = {1095-8630}, mesh = {*Iron/metabolism ; *Denitrification ; *Guanosine Monophosphate/metabolism ; Hemin/metabolism ; Oxidation-Reduction ; }, abstract = {A novel multi-signal functional material consisting of Hematin, Fe, and guanosine monophosphate (GMP) was successfully constructed (Hematin@Fe/GMP) to enhance denitrification efficiency based on the signal network regulation of electron transfer, micromolar Fe utilization, and microbial community. Hematin@Fe/GMP enhanced nitrate reduction rate by 2.33-fold with a 9.9 mg L[-1] h[-1] reduction rate. The mechanisms of accelerated denitrification were elaborated deeply from the electrochemical experiments, microbial metabolism activity, key enzyme activity, gene expression, and microbial community. Specifically, electrochemical experiments and X-ray photoelectron spectroscopy demonstrated that the released redox signal (Fe[2+]/Fe[3+]) promoted the increased redox substances (extracellular polymeric substances, cytochrome c, and riboflavin) to accelerate electron transfer efficiency. Metagenomic analysis suggested the released Fe utilization signal modulated siderophores genes (fhuB, fhuC, and fhuD) to promote the uptake and utilization of micromolar Fe, which was more conducive to synthesizing cytochrome c. Moreover, extracellular polymeric substances (EPS) stripping experiments demonstrated that the membrane-anchored cyt-c could shuttle in EPS and bind with Hematin@Fe/GMP to form an electrical conduit for accelerating denitrification efficiency. In inhibition experiments, Hematin@Fe/GMP could break down electron transfer barriers and restore/compensate for the electron transfer chain. Meanwhile, Hematin@Fe/GMP could restore the electrical signal disruption and synergize with the enriched signaling-capable microorganisms (Stutzerimonas and Thauera) to regulate quorum sensing. This research introduced multi-signal modulation of Hematin@Fe/GMP on denitrification and provided strategies for accelerating the biological transformation process and effectively utilizing micromolar Fe in practical applications.}, } @article {pmid39657260, year = {2024}, author = {Davis, JA and Chinthala, SP and Monty-Bromer, CN and Senko, JM}, title = {Electrochemical Detection of Carbon Steel Corrosion Induced by Fermentative Bacteria From Natural Gas Transmission Lines.}, journal = {Environmental microbiology reports}, volume = {16}, number = {6}, pages = {e70058}, pmid = {39657260}, issn = {1758-2229}, support = {693JK31850003CAAP//Pipeline and Hazardous Materials Safety Administration/ ; }, mesh = {Corrosion ; *Steel/chemistry ; *Fermentation ; *Carbon/metabolism ; *Natural Gas/microbiology ; Bacteria/genetics/metabolism/classification/isolation & purification/growth & development ; Hydrogen-Ion Concentration ; Electrochemical Techniques/instrumentation ; Metagenome ; }, abstract = {The metabolic potential and corrosive activities of a fermentative bacterial enrichment culture from a natural gas transmission line were characterised. Three metagenome-assembled genomes (MAGs) attributable to Cytobacillus, Lacrimispora and Staphylococcus spp. were obtained. These MAGs hosted genes involved in the fermentation of carbohydrates to organic acids, which was reflected in the acidification of the growth medium by the culture. To evaluate the corrosive activities of the culture, it was incubated in a split chamber-zero resistance ammetry (SC-ZRA) format. This involved deploying carbon steel coupons immersed in liquid medium in opposing chambers of an electrochemical cell. Measurement of current between the coupons indicated the extent and mechanism of corrosion. When the enrichment culture was added to one side of an SC-ZRA incubation with bicarbonate-buffered medium, pH change and corrosion were minimal. In bicarbonate-free medium, the culture acidified the medium, induced electron transfer from the uninoculated chamber to the inoculated chamber, and caused mass loss. These results indicate that fermenter-induced microbially influenced corrosion (MIC) is due to localised fluid acidification, inducing anodic reactions on the metal surface exposed to the microorganisms and mass loss of the non-exposed metal.}, } @article {pmid39656346, year = {2025}, author = {Wu, H and Wang, Y and Yang, X and Lu, T and Luo, Y}, title = {Case report: diagnosis of neurobrucellosis in a non-endemic area child using metagenomic next-generation sequencing.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {44}, number = {2}, pages = {443-447}, pmid = {39656346}, issn = {1435-4373}, mesh = {Humans ; *Brucellosis/diagnosis/drug therapy/microbiology ; *High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; *Anti-Bacterial Agents/therapeutic use ; Brucella melitensis/genetics/isolation & purification ; Male ; Child ; Female ; Cerebrospinal Fluid/microbiology ; }, abstract = {Brucellosis with neurological symptoms at onset is rare in children and is frequently misdiagnosed or overlooked due to nonspecific clinical presentations, particularly in non-endemic areas. We report a case of neurobrucellosis in a child from a non-pastoral area, diagnosed via metagenomic next-generation sequencing (mNGS). The patient presented with headache and altered consciousness, accompanied by fever, projectile vomiting, seizures, and urinary incontinence. Physical examination indicated possible nuchal rigidity. Cerebrospinal fluid (CSF) analysis showed colorless and clear fluid, with a white blood cell count of 259 × 10[6]/L, 4.6% polymorphonuclear cells, positive protein qualitative test, protein level of 0.78 g/L, and glucose level of 1.66 mmol/L. Initial diagnosis suggested central nervous system infection, and empirical treatment led to improvement in consciousness. However, after a few days of stable body temperature, the patient experienced recurrent fever. Ultimately, mNGS of CSF identified Brucella melitensis, confirming neurobrucellosis. Following treatment with ceftriaxone, doxycycline, and rifampin, the patient's clinical symptoms improved significantly, and follow-up CSF analysis showed normalization of cell counts. This case highlights the early diagnostic utility of mNGS in CSF for neurobrucellosis and its role in differential diagnosis.}, } @article {pmid39656004, year = {2025}, author = {Jensen, EEB and Otani, S and Liachko, I and Auch, B and Aarestrup, FM}, title = {Using genomics to explore the epidemiology of vancomycin resistance in a sewage system.}, journal = {Microbiology spectrum}, volume = {13}, number = {1}, pages = {e0148924}, pmid = {39656004}, issn = {2165-0497}, support = {NNF16OC0021856//Novo Nordisk Fonden (NNF)/ ; }, mesh = {*Sewage/microbiology ; *Vancomycin Resistance/genetics ; *Genomics ; Anti-Bacterial Agents/pharmacology ; Metagenomics ; Enterococcus faecium/genetics/drug effects/isolation & purification ; Plasmids/genetics ; Vancomycin/pharmacology ; Enterococcus faecalis/genetics/drug effects/isolation & purification ; Bacterial Proteins/genetics ; Genome, Bacterial ; }, abstract = {VanHAX-mediated glycopeptide resistance has been consistently high in one of the three main sewer systems in Copenhagen, Lynetten, for +20 years. To explore this for other glycopeptide resistance genes, and whether the colonization has resulted in establishment of multiple bacterial taxa, we mapped 505 shotgun metagenomic data sets from the inlet of three sewage treatment plants to 831 different glycopeptide resistance genes. Only vanHAX and vanHBX genes were differentially abundant in Lynetten. Analyses of eight contigs suggested limited variations in the flanking regions. Proximity ligation metagenomic analysis of 12 samples from Lynetten identified 441 and 5 paired reads mapping to vanHAX and vanHBX, respectively. The other end of these reads was mapped to generated metagenomic-assembled genomes and NCBI using BLAST. vanHBX could only be linked to the phylum level (Bacillota). Plasmid analysis of vanHBX Hi-C contigs showed that these were mainly located on plasmids reported found in enterococci species. Most vanHAX-linked reads could only be linked to phylum and class level, but some reads were assigned to Enterococcus faecium (7 reads), Enterococcus faecalis (4 reads), Paenibacillus apiarius (2 reads), and Paenibacillus thiaminolyticus (27 reads). Ten of the 20 Hi-C contigs-containing vanHAX were annotated as plasmid, all reported found in Enterococcus species. This study shows that while Hi-C technology is valuable for linking antimicrobial resistance genes to bacterial taxa, it suffers from challenges in reliably mapping the linked read to a genomic region with sufficient taxonomic information. Our results also suggest that over the +20 years of colonizing a sewer system, vanHAX has not become widespread across multiple taxa, remaining primarily in E. faecalis and E. faecium, with the exception of Paenibacillus.IMPORTANCELong-term colonization of microbial communities with antimicrobial-resistant bacteria is expected to result in sharing of the resistance genes between several different bacterial taxa of the communities. We investigated microbiomes from a sewer, which have been colonized with glycopeptide-resistant bacteria harboring the mobile vanHAX gene cluster for a minimum of 20 years, using metagenomics sequencing and Hi-C. We found that despite the long-term presence in the sewer, the vanHAX genes have seemingly not disseminated widely.}, } @article {pmid39655960, year = {2025}, author = {Tian, Q and Ye, H and Zhou, X and Wang, J and Zhang, L and Sun, W and Duan, C and Fan, M and Zhou, W and Bi, C and Ye, Q and Wong, A}, title = {Evaluating the health risk of probiotic supplements from the perspective of antimicrobial resistance.}, journal = {Microbiology spectrum}, volume = {13}, number = {1}, pages = {e0001924}, pmid = {39655960}, issn = {2165-0497}, support = {SpF2021002//Wenzhou-Kean University Student Partnering with Faculty (SpF) research program/ ; SpF2021029//Wenzhou-Kean University Student Partnering with Faculty (SpF) research program/ ; }, mesh = {*Probiotics/administration & dosage/pharmacology ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Dietary Supplements ; Drug Resistance, Bacterial/genetics ; Streptomycin/pharmacology ; Caco-2 Cells ; Escherichia coli/drug effects/genetics ; Enterococcus faecalis/drug effects/genetics ; Microbial Sensitivity Tests ; Staphylococcus aureus/drug effects/genetics ; Erythromycin/pharmacology ; }, abstract = {UNLABELLED: Antimicrobial resistance remains a public health threat. Probiotics harboring antimicrobial resistant genes (ARGs) have, in recent years, been considered a potential health risk. Studies conducted on probiotics from increasingly popular health supplements have raised the possibility of transmitting ARGs to commensals in the human gut, concomitantly establishing a reservoir of ARGs and risking acquisition by opportunistic pathogens. Building on our previous study that reported multiple antibiotic resistance in probiotics of health supplements, in this research, we have attempted to detect their ARGs that may account for resistant phenotypes. ARGs responsible for tetracycline, macrolide, aminoglycoside, and glycopeptide resistance were prevalent in probiotics. Through laboratory adaptive evolution studies, we also show that streptomycin-adapted probiotics gained resistance to erythromycin, tetracycline, and doxycycline more effectively than non-adapted ones. When co-incubated with Enterococcus faecalis, Escherichia coli, or Staphylococcus aureus on Caco-2 and/or HCT-116 cells, streptomycin resistance was transferred from the adapted probiotics to generate transconjugants at frequencies comparable to or higher than that of other studies conducted through filter mating. Consistently, ARGs conferring resistance to streptomycin (aadA) and erythromycin [erm(B)-1] were detected in E. coli and S. aureus transconjugants, respectively, after co-incubation with streptomycin-adapted probiotics on Caco-2 cells. aadA and erm(B)-1 were both detected in E. faecalis transconjugant after the same co-incubation on HCT-116 cells. Our data and future comparative genomics and metagenomics studies conducted on animal models and in healthy, immunocompromised, and/or antibiotic-treated human cohorts will contribute to a more comprehensive understanding of probiotic consumption, application, and safety.

IMPORTANCE: Probiotics are becoming increasingly popular, with promising applications in food and medicine, but the risk of transferring ARGs to disease-causing bacteria has raised concerns. Our study detected ARGs in probiotics of health supplements conferring resistance to tetracycline, macrolide, aminoglycoside, and glycopeptide drugs. Streptomycin-adapted probiotics also gained resistance to other antibiotics more effectively than non-adapted ones. Importantly, we showed that streptomycin resistance could be transferred to other bacteria after co-incubation with probiotics on human intestinal cells. ARGs responsible for erythromycin and streptomycin resistance, which were initially absent in the recipient bacteria, were also detected in the transconjugants. Our data build the foundation for future studies that will be conducted on animal models and in humans and leveraging advanced metagenomics approaches to clarify the long-term health risk of probiotic consumption.}, } @article {pmid39655221, year = {2024}, author = {Contreras-Peruyero, H and Nuñez, I and Vazquez-Rosas-Landa, M and Santana-Quinteros, D and Pashkov, A and Carranza-Barragán, ME and Perez-Estrada, R and Guerrero-Flores, S and Balanzario, E and Muñiz Sánchez, V and Nakamura, M and Ramírez-Ramírez, LL and Sélem-Mojica, N}, title = {CAMDA 2023: Finding patterns in urban microbiomes.}, journal = {Frontiers in genetics}, volume = {15}, number = {}, pages = {1449461}, pmid = {39655221}, issn = {1664-8021}, abstract = {The Critical Assessment of Massive Data Analysis (CAMDA) addresses the complexities of harnessing Big Data in life sciences by hosting annual competitions that inspire research groups to develop innovative solutions. In 2023, the Forensic Challenge focused on identifying the city of origin for 365 metagenomic samples collected from public transportation systems and identifying associations between bacterial distribution and other covariates. For microbiome classification, we incorporated both taxonomic and functional annotations as features. To identify the most informative Operational Taxonomic Units, we selected features by fitting negative binomial models. We then implemented supervised models conducting 5-fold cross-validation (CV) with a 4:1 training-to-validation ratio. After variable selection, which reduced the dataset to fewer than 300 OTUs, the Support Vector Classifier achieved the highest F1 score (0.96). When using functional features from MIFASER, the Neural Network model outperformed other models. When considering climatic and demographic variables of the cities, Dirichlet regression over Escherichia, Enterobacter, and Klebsiella bacteria abundances suggests that population increase is indeed associated with a rise in the mean of Escherichia while decreasing temperature is linked to higher proportions of Klebsiella. This study validates microbiome classification using taxonomic features and, to a lesser extent, functional features. It shows that demographic and climatic factors influence urban microbial distribution. A Docker container and a Conda environment are available at the repository: GitHub facilitating broader adoption and validation of these methods by the scientific community.}, } @article {pmid39654977, year = {2024}, author = {Wu, J and Wang, D and He, WJ and Li, JY and Mo, X and Li, YJ}, title = {Allergen-specific sublingual immunotherapy altered gut microbiota in patients with allergic rhinitis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1454333}, pmid = {39654977}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Sublingual Immunotherapy/methods ; *Rhinitis, Allergic/therapy/microbiology/immunology ; Male ; Female ; Adult ; *Feces/microbiology ; Allergens/immunology ; Young Adult ; Animals ; Middle Aged ; Antigens, Dermatophagoides/immunology ; Dermatophagoides farinae/immunology ; Treatment Outcome ; Adolescent ; Metagenomics/methods ; }, abstract = {INTRODUCTION: Allergen-specific immunotherapy (AIT) induces long-term immune tolerance to allergens and is effective for treating allergic rhinitis (AR). However, the impact of sublingual immunotherapy (SLIT) on gut microbiota from AR patients and its correlation with treatment efficacy remains unclear.

METHODS: In the present study, we enrolled 24 AR patients sensitized to Dermatophagoides farinae (Der-f) and 6 healthy donors (HD). All AR patients received SLIT treatment using standardized Der-f drops. Stool samples were collected from AR patients before treatment, and 1- and 3-months post-treatment, as well as from HD, for metagenomic sequencing analysis.

RESULTS: AR patients had significantly lower richness and diversity in gut microbiota compared to HD, with notable alterations in composition and function. Besides, three months post-SLIT treatment, significant changes in gut microbiota composition at the genus and species levels were observed in AR patients. Streptococcus parasanguinis_B and Streptococcus parasanguinis, which were significantly lower in AR patients compared to HD, increased notably after three months of treatment. LEfSe analysis identified these species as markers distinguishing HD from AR patients and AR patients pre- from post-SLIT treatment. Furthermore, changes in the relative abundance of S. parasanguinis_B were negatively correlated with changes in VAS scores but positively correlated with changes in RCAT scores, suggesting a positive correlation with effective SLIT treatment.

DISCUSSION: SLIT treatment significantly alters the gut microbiota of AR patients, with S. parasanguinis_B potentially linked to its effectiveness. This study offers insights into SLIT mechanisms and suggests that specific strains may serve as biomarkers for predicting SLIT efficacy and as modulators for improving SLIT efficacy.}, } @article {pmid39654975, year = {2024}, author = {Jarmukhanov, Z and Mukhanbetzhanov, N and Vinogradova, E and Kozhakhmetov, S and Kushugulova, A}, title = {Gut metagenomic features of frailty.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1486579}, pmid = {39654975}, issn = {2235-2988}, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Frailty/microbiology/metabolism ; Male ; Female ; Aged ; Middle Aged ; *Feces/microbiology ; *Metagenomics/methods ; Kazakhstan ; Adult ; Metagenome ; Bacteria/classification/genetics/isolation & purification/metabolism ; Aged, 80 and over ; Metabolic Networks and Pathways/genetics ; }, abstract = {This study investigates the relationship between frailty severity and gut microbiome characteristics in adults in Kazakhstan. We analyzed 158 participants across four frailty severity (mild to very severe) using metagenomic sequencing of stool samples. Frailty was significantly correlated with age, weight, and functional measures like walking speed and grip strength. Microbial diversity decreased significantly with increasing frailty. Beta diversity analysis revealed distinct clustering patterns based at phylum level. Taxonomically, we observed a significant inverse correlation between Firmicutes abundance and frailty. Classes like Clostridia and Erysipelotrichia decreased with frailty, while Bacteroidia and Actinobacteria increased. At the family level, Oscillospiraceae showed a positive correlation with frailty. Functionally, we identified significant correlations between frailty measures and specific metabolic pathways. The frailty index negatively correlated with pathways involved in cobalamin, arginine and molybdenum cofactor biosynthesis and positively correlated with folate biosynthesis. Physical performance measures strongly correlated with pathways related to nucleotide biosynthesis, and one-carbon metabolism. We propose these identified features may constitute a "frailty-associated metabolic signature" in the gut microbiome. This signature suggests multiple interconnected mechanisms through which the microbiome may influence frailty development, including modulation of inflammation, alterations in energy metabolism, and potential impacts on muscle function through microbial metabolites.}, } @article {pmid39654973, year = {2024}, author = {Ding, H and Huang, J and Lin, L and Chen, Y and Wang, Q and Li, W and Huang, Y and Fang, X and Zhang, W}, title = {Shedding light on negative cultures in osteoarticular infections: leveraging mNGS to unravel risk factors and microbial profiles.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1457639}, pmid = {39654973}, issn = {2235-2988}, mesh = {Humans ; Female ; Risk Factors ; Male ; *High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; Child, Preschool ; Anti-Bacterial Agents/therapeutic use ; Child ; Osteomyelitis/microbiology/diagnosis ; Middle Aged ; Bacteria/genetics/classification/isolation & purification ; Infant ; Adult ; Adolescent ; Aged ; }, abstract = {BACKGROUND: The objective of this study is to utilize metagenomic next-generation sequencing (mNGS) to analyze the risk factors causing negative microbial cultures, comprehensively delineate the microbial profiles neglected by traditional cultures, and optimize the pathogenetic diagnostic procedure accordingly.

RESEARCH DESIGN AND METHODS: We enrolled 341 patients diagnosed with OI at our center between 2016 and 2022, and gathered data including age, gender, clinical diagnosis, duration of antibiotic use prior to sampling, microbial culture results, and mNGS results for these patients. According to microbial detection results, risk factors for negative microbial culture and mNGS results were investigated through univariate and multivariate analyses, and the microbial profile in cases with negative microbial cultures was summarized in conjunction with mNGS results. Building upon this, we suggest strategies to enhance the positivity rate of microbial cultures based on clinical experience.

RESULTS: Invasive osteoarticular infection (IOI), multi-infections, rare pathogen infections, and prior antibiotic use are risk factors for negative microbial cultures. When the duration of prior antibiotic use is ≥3 days, mNGS demonstrates significantly higher pathogen detection efficiency than microbial culture. Moreover, the risk of negative microbial culture increases by 4.8 times with the exposure to each additional risk factor (OR=4.043, 95%CI [2.835, 5.765], P<0.001). Additionally, over one-third of culture-negative OI involve polymicrobial infections or rare pathogens.

CONCLUSIONS: Clinicians should tailor microbial culture strategies based on patient conditions. When needed, they can collaborate with mNGS or optimize microbial culture conditions based on mNGS results to enhance the efficiency of pathogen diagnosis.}, } @article {pmid39654219, year = {2024}, author = {Wang, R and Lv, M and Fu, L and Zhao, J and Ni, Y and Li, T and Chen, Z and Li, F}, title = {A rare case report of infective endocarditis caused by Enterococcus gallinarum following renal laser lithotripsy.}, journal = {Medicine}, volume = {103}, number = {49}, pages = {e40802}, pmid = {39654219}, issn = {1536-5964}, support = {To Wang, Ruoxin MD, Ph.D.//the Scientific Research Grant of Shanghai Jiao Tong University Affiliated Sixth People's Hospital Medical Group/ ; }, mesh = {Humans ; Male ; Middle Aged ; *Enterococcus/isolation & purification ; *Anti-Bacterial Agents/therapeutic use ; *Endocarditis, Bacterial/microbiology/diagnosis/drug therapy ; Gram-Positive Bacterial Infections/diagnosis/microbiology ; Lithotripsy/adverse effects ; Heart Valve Prosthesis Implantation/adverse effects ; Daptomycin/therapeutic use ; }, abstract = {RATIONALE: Enterococcus gallinarum is a part of the normal fecal microbiota in the general population and animals, and is rarely isolated in clinical specimens. Due to the increasing use of immunosuppressants, invasive treatments, and overuse of antibiotics, infections caused by enterococci are gradually increasing.

PATIENT CONCERNS: A 48-year-old man was admitted to our hospital due to a persistent fever for 1 month after renal laser lithotripsy.

DIAGNOSES: The cardiac ultrasound showed a mass on the mitral valve leaflet of the left atrium. The metagenomic next-generation sequencing test results of blood and vegetation were positive, reporting a large number of characteristic reads of E. gallinarum. The patient was diagnosed with infective endocarditis.

INTERVENTIONS: Mechanical mitral valve replacement was performed, and daptomycin was administered during the perioperative period.

OUTCOMES: After 4 weeks of antibiotic treatment, the patient's inflammatory indexes were normal, and no abnormalities such as fever were found. Blood culture and metagenomic next-generation sequencing test results were negative. The patient was then discharged from the hospital.

LESSONS: This case emphasizes the possibility of E. gallinarum developing severe invasive infections after kidney surgery. Clinical doctors should strengthen their understanding of this type of bacteria, understand their sensitive characteristics and treatment principles.}, } @article {pmid39653697, year = {2024}, author = {Palladino, G and Nanetti, E and Scicchitano, D and Cinti, N and Foresto, L and Cozzi, A and Gonzalez Vara Rodriguez, A and Interino, N and Fiori, J and Turroni, S and Candela, M and Rampelli, S}, title = {Zonation of the Vitis vinifera microbiome in Vino Nobile di Montepulciano PDO production area.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1626}, pmid = {39653697}, issn = {2399-3642}, support = {818290//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; }, mesh = {*Vitis/microbiology ; *Microbiota/genetics ; Italy ; *Wine/microbiology ; Soil Microbiology ; Bacteria/genetics/classification/metabolism/isolation & purification ; Fungi/genetics/classification/metabolism ; Rhizosphere ; }, abstract = {The microbial dimension of the terroir is crucial for wine quality, as microbiomes contribute to plant biofertilization, stress tolerance and pathogen suppression. While microbial terroir can act as a biological signature at large scale, data for local contexts is lacking, hindering the characterization of regional microbial diversity in vineyards. Here, we define the microbial terroir of vineyards across the 12 sub-areas (Additional Geographic Units -AGUs) of the "Consorzio del Vino Nobile di Montepulciano DOCG" PDO area (Italy), a world-renowned wine-producing region. Rhizospheres of Vitis vinifera cultivar Sangiovese and soil samples were collected throughout the 2022 viticultural season and analyzed through an integrated metabarcoding/shotgun metagenomic approach, targeting bacteria and fungi. Wine metabolomics was also perfomed, projecting compositional and functional variations of the microbial terroir at the AGUs level into a corresponding variation in the product metabolic profile. Our findings reveal a unique taxonomic configuration of the Vino Nobile di Montepulciano terroir compared to other vineyards, with microbiomes being "AGU-specific" in taxonomic abundances and plant growth-promoting functions, confirming the potential relevance of characterizing and preserving the microbial terroir to safeguard high-quality traditional wines.}, } @article {pmid39653684, year = {2024}, author = {Chen, Y and Yang, C and Deng, Z and Xiang, T and Tan, J and Xu, J and Sun, D and Luo, F}, title = {Alterations of gut virome with close interaction in the progression of estrogen deficiency-induced osteoporosis.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2437250}, pmid = {39653684}, issn = {1949-0984}, mesh = {*Gastrointestinal Microbiome ; Animals ; Female ; *Virome ; Mice ; *Osteoporosis/virology ; Humans ; *Estrogens/metabolism ; Ovariectomy ; Bacteria/classification/genetics/isolation & purification/metabolism ; Mice, Inbred C57BL ; Disease Models, Animal ; Disease Progression ; }, abstract = {Previous research has established a link between gut microbiota and osteoporosis (OP) advancement. However, there remains a limited understanding of the crucial contribution of the gut virome in the onset and progression of OP. We employed metagenomic shotgun sequencing and gut virome sequencing to process the ovariectomy (OVX)-induced OP murine model, which revealed significant disparities in bacteriome and virome compositions between subjects with OP and healthy controls. One hundred and seventy-four altered viral strains were identified to participate in the multifaceted regulation of bone loss, involving immune modulation, microbial metabolic activity, and intricate host-virus dynamics. Our findings suggested that the gut virome may influence bone metabolism, potentially altering the balance of bone-modulating compounds like short-chain fatty acids. This comprehensive analysis of the gut virome in OP highlighted the diagnostic potential of combined gut viral and bacterial biomarkers for OP.}, } @article {pmid39653637, year = {2025}, author = {Lepcha, A and Kumar, R and Dindhoria, K and Bhargava, B and Pati, AM and Kumar, R}, title = {Metagenomic insights into the functional potential of non-sanitary landfill microbiomes in the Indian Himalayan region, highlighting key plastic degrading genes.}, journal = {Journal of hazardous materials}, volume = {484}, number = {}, pages = {136642}, doi = {10.1016/j.jhazmat.2024.136642}, pmid = {39653637}, issn = {1873-3336}, mesh = {India ; *Waste Disposal Facilities ; *Microbiota/genetics ; *Plastics ; *Metagenomics ; Biodegradation, Environmental ; Bacteria/genetics/metabolism/classification ; Metals, Heavy ; Soil Microbiology ; Soil Pollutants/metabolism ; Refuse Disposal ; }, abstract = {Solid waste management in the Indian Himalayan Region (IHR) is a growing challenge, intensified by increasing population and tourism, which strain non-sanitary landfills. This study investigates microbial diversity and functional capabilities within these landfills using a high-throughput shotgun metagenomic approach. Physicochemical analysis revealed that the Manali and Mandi landfill sites were under heavy metal contamination and thermal stress. Taxonomic annotation identified a dominance of bacterial phyla, including Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes, with genera like Pseudomonas and Bacillus prevalent. Squeezemeta analysis generated 9,216,983 open reading frames (ORFs) across the sampling sites, highlighting diverse metabolic potentials for heavy metal resistance and degrading organic, xenobiotics and plastic wastes. Hierarchical clustering and principal component analysis (PCA) identified distinct gene clusters in Manali and Mandi landfill sites, reflecting differences in pollution profiles. Functional redundancy of landfill microbiome was observed with notable xenobiotic and plastic degradation pathways. This is the first comprehensive metagenomic assessment of non-sanitary landfills in the IHR, providing valuable insights into the microbial roles in degrading persistent pollutants, plastic waste, and other contaminants in these stressed environments.}, } @article {pmid39653411, year = {2024}, author = {Shi, Z and Li, M and Zhang, C and Li, H and Zhang, Y and Zhang, L and Li, X and Li, L and Wang, X and Fu, X and Sun, Z and Zhang, X and Tian, L and Zhang, M and Chen, WH and Li, Z}, title = {Butyrate-producing Faecalibacterium prausnitzii suppresses natural killer/T-cell lymphoma by dampening the JAK-STAT pathway.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2024-333530}, pmid = {39653411}, issn = {1468-3288}, abstract = {BACKGROUND: Natural killer/T-cell lymphoma (NKTCL) is a highly aggressive malignancy with a dismal prognosis, and gaps remain in understanding the determinants influencing disease outcomes.

OBJECTIVE: To characterise the gut microbiota feature and identify potential probiotics that could ameliorate the development of NKTCL.

DESIGN: This cross-sectional study employed shotgun metagenomic sequencing to profile the gut microbiota in two Chinese NKTCL cohorts, with validation conducted in an independent Korean cohort. Univariable and multivariable Cox proportional hazards analyses were applied to assess associations between identified marker species and patient outcomes. Tumour-suppressing effects were investigated using comprehensive in vivo and in vitro models. In addition, metabolomics, RNA sequencing, chromatin immunoprecipitation sequencing, Western blot analysis, immunohistochemistry and lentiviral-mediated gene knockdown system were used to elucidate the underlying mechanisms.

RESULTS: We first unveiled significant gut microbiota dysbiosis in NKTCL patients, prominently marked by a notable reduction in Faecalibacterium prausnitzii which correlated strongly with shorter survival among patients. Subsequently, we substantiated the antitumour properties of F. prausnitzii in NKTCL mouse models. Furthermore, F. prausnitzii culture supernatant demonstrated significant efficacy in inhibiting NKTCL cell growth. Metabolomics analysis revealed butyrate as a critical metabolite underlying these tumour-suppressing effects, validated in three human NKTCL cell lines and multiple tumour-bearing mouse models. Mechanistically, butyrate suppressed the activation of Janus kinase-signal transducer and activator of transcription pathway through enhancing histone acetylation, promoting the expression of suppressor of cytokine signalling 1.

CONCLUSION: These findings uncover a distinctive gut microbiota profile in NKTCL and provide a novel perspective on leveraging the therapeutic potential of F. prausnitzii to ameliorate this malignancy.}, } @article {pmid39652203, year = {2024}, author = {Thillapudi, J and Mendonce, KC and Palani, N and Bhowmik, S and Rajadesingu, S}, title = {Revealing the nutritious treasures: an extensive investigation of health benefits of cultured dairy foods.}, journal = {Archives of microbiology}, volume = {207}, number = {1}, pages = {12}, pmid = {39652203}, issn = {1432-072X}, mesh = {Animals ; Humans ; *Cultured Milk Products/microbiology ; Functional Food ; Lactobacillales/genetics/metabolism ; }, abstract = {Cultured milk products including yogurt, buttermilk, and lassi have made their way into South Asian cuisine for hundreds of years and are extraordinarily beneficial to human health. With a study background on lactic acid bacteria (LAB), these products are scientifically proved to aid in strengthening the immune system, for their anti-mutagenic effects, suitability for those who are lactose intolerant, and for protection against cancer, osteoporosis, and gut disorders. As of now, no scientific attention has been given to the microbial diversity of cultured milk products despite its prominent production and importance in the culture. New emerging approaches for studying the genetic composition and metabolic features of microbial communities, such as metagenomics and metabolomics, will open up important sources of knowledge and be a significant tool for informing conservation. These products are highly valued worldwide in the management of cardiometabolic diseases (CMDs), which encompass hypertension, type 2 diabetes, and obesity. The aim of this article will therefore advocate for the health benefits as well as cultural importance of cultured milk products. Indian fermented milk products, along with their historical development, cultural, and research aspects, thereby, highlighting the potential of this kind of product in promoting global health through functional food application, with a focus on recent advancements in their therapeutic potential and applications.}, } @article {pmid39651889, year = {2025}, author = {Wang, J and Schamp, CN and Hudson, LK and Chaggar, HK and Bryan, DW and Garman, KN and Radosevich, M and Denes, TG}, title = {Whole-genome sequencing and metagenomics reveal diversity and prevalence of Listeria spp. from soil in the Nantahala National Forest.}, journal = {Microbiology spectrum}, volume = {13}, number = {1}, pages = {e0171224}, pmid = {39651889}, issn = {2165-0497}, mesh = {*Soil Microbiology ; *Listeria/genetics/classification/isolation & purification ; *Metagenomics ; *Whole Genome Sequencing ; North Carolina ; *Forests ; *Genome, Bacterial ; *Phylogeny ; Humans ; Listeriosis/microbiology/epidemiology/transmission ; Listeria monocytogenes/genetics/classification/isolation & purification ; Metagenome ; Prevalence ; Soil/chemistry ; }, abstract = {UNLABELLED: Listeria spp. are widely distributed environmental bacteria associated with human foodborne illness. The ability to detect and characterize Listeria strains in the natural environment will contribute to improved understanding of transmission routes of contamination. The current standard for surveillance and outbreak source attribution is whole-genome sequencing (WGS) of Listeria monocytogenes clinical isolates. Recently, metagenomic sequencing has also been explored as a tool for the detection of Listeria spp. in environmental samples. This study evaluated soil samples from four locations across altitudes ranging from 1,500 to 4,500 ft in the Nantahala National Forest in North Carolina, USA. Forty-two Listeria isolates were cultured and sequenced, and 12 metagenomes of soil bacterial communities were generated. These isolates comprised 14 distinct strains from five species, including Listeria cossartiae subsp. cayugensis (n = 8; n represents the number of distinct strains), L. monocytogenes (n = 3), "Listeria swaminathanii" (Lsw) (n = 1), Listeria marthii (n = 1), and Listeria booriae (n = 1). Most strains (n = 13) were isolated from lower altitudes (1,500 or 2,500 ft), while the L. swaminathanii strain was isolated from both higher (4,500 ft) and lower (1,500 ft) altitudes. Metagenomic analysis of soil described a reduction in both bacterial community diversity and relative abundance of Listeria spp. as the altitude increased. Soil pH and cation exchange capacity were positively correlated (P < 0.05) with the abundance of Listeria spp. as detected by metagenomics. By integrating culture-independent metagenomics with culture-based WGS, this study advances current knowledge regarding distribution of Listeria spp. in the natural environment and suggests the potential for future use of culture-independent methods in tracking the transmission of foodborne pathogens.

IMPORTANCE: As a foodborne pathogen, Listeria continues to cause numerous illnesses in humans and animals. Studying the diversity and distribution of Listeria in soil is crucial for understanding potential sources of contamination and developing effective strategies to prevent foodborne outbreaks of listeriosis. Additionally, examining the ecological niches and survival mechanisms of Listeria in natural habitats provides insights into its persistence and adaptability, informing risk assessments and public health interventions. This research contributes to a broader understanding of microbial ecology and the factors influencing foodborne pathogen emergence, ultimately enhancing food safety and protecting public health. Moreover, using a metagenomic approach provides a detailed understanding of the soil microbial ecosystems, leading to more effective monitoring and control of foodborne pathogens. This study also highlights the potential for integrating metagenomics into routine surveillance systems for food safety in the near future.}, } @article {pmid39651865, year = {2025}, author = {Howland, KE and Mouradian, JJ and Uzarski, DR and Henson, MW and Uzarski, DG and Learman, DR}, title = {Nutrient amendments enrich microbial hydrocarbon degradation metagenomic potential in freshwater coastal wetland microcosm experiments.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {1}, pages = {e0197224}, pmid = {39651865}, issn = {1098-5336}, mesh = {*Wetlands ; *Biodegradation, Environmental ; *Fresh Water/microbiology ; *Hydrocarbons/metabolism ; Bacteria/genetics/metabolism/classification ; Metagenomics ; Petroleum/metabolism ; Geologic Sediments/microbiology ; Nutrients/metabolism ; Microbiota ; Metagenome ; Benzene Derivatives/metabolism ; Volatile Organic Compounds/metabolism ; Toluene/metabolism ; Benzene/metabolism ; Water Pollutants, Chemical/metabolism ; }, abstract = {UNLABELLED: Biostimulating native microbes with fertilizers has proven to be a highly effective strategy to speed up biodegradation rates in microbial communities. This study investigates the genetic potential of microbes to degrade light synthetic crude oil in a freshwater coastal wetland. Experimental sediment microcosms were exposed to a variety of conditions (biological control, a light synthetic crude oil amendment, and light synthetic crude oil with nutrient amendment) and incubated for 30 days before volatile organic compounds (BTEX) were quantified and DNA was sequenced for metagenomic analysis. The resulting DNA sequences were binned into metagenome-assembled genomes (MAGs). Analyses of MAGs uncovered a 13-fold significant increase in the abundance of rate-limiting hydrocarbon degrading monooxygenases and dioxygenases, identified only in MAGs from the light synthetic crude oil with nutrient amendments. Further, complete degradation pathways for BTEX compounds were found only in MAGs resulting from the light synthetic crude with nutrient amendment. Moreover, volatile organic compounds (BTEX, cyclohexane, and naphthalene) analyses of microcosm sediments in the presence of nutrients documented that benzene was degraded below detection limits, toluene (98%) and ethylbenzene (67%) were predominantly reduced within 30 days. Results indicate that the genetic potential to degrade BTEX compounds in this freshwater wetland can be linked to the functional potential for bioremediation. BTEX compounds are typically more recalcitrant and tougher to degrade than alkanes. This study demonstrated that stimulating a microbial community with nutrients to enhance its ability to biodegrade hydrocarbons, even in a relatively nutrient-rich habitat like a freshwater wetland, is an effective remediation tactic.

IMPORTANCE: The impact of oil spills in a freshwater aquatic environment can pose dire social, economic, and ecological effects on the region. An oil spill in the Laurentian Great Lakes region has the potential to affect the drinking water of more than 30 million people. The light synthetic crude oil used in this experimental microcosm study is transported through an underground pipeline crossing the waterway between two Laurentian Great Lakes. This study collected metagenomic data (experiments in triplicate) and assessed the quantity of BTEX compounds, which connected microbial degradation function to gene potential. The resulting data documented the bioremediation capabilities of native microbes in a freshwater coastal wetland. This study also provided evidence for this region that bioremediation can be a viable remediation strategy instead of invasive physical methods.}, } @article {pmid39650650, year = {2024}, author = {Xue, Y and Mo, J and Cheng, K and Xue, Y and Chen, D and Lin, F and Chen, H}, title = {Case report: Unveiling the silent threat in the ICU - a case of disseminated invasive aspergillosis in a patient with fulminant myocarditis.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1481335}, pmid = {39650650}, issn = {1664-3224}, mesh = {Humans ; Female ; Adult ; *Myocarditis/diagnosis/etiology/therapy ; *Intensive Care Units ; Antifungal Agents/therapeutic use ; Invasive Pulmonary Aspergillosis/diagnosis/etiology ; Extracorporeal Membrane Oxygenation ; Aspergillosis/diagnosis/drug therapy ; Immunocompromised Host ; Positron Emission Tomography Computed Tomography ; }, abstract = {Invasive aspergillosis (IA) significantly increases mortality in critically ill patients in the ICU and its occurrence is closely related to immunocompromise. Dissemination of IA is easily misdiagnosed and mistreated due to its ability to invade multiple systems throughout the body and lack of typical clinical manifestations. In this case, a 25-year-old previously healthy woman was hospitalized with fulminant myocarditis and treated with veno-arterial extracorporeal membrane pulmonary oxygenation (VA-ECMO) support and intravenous acyclovir, high-dose methylprednisolone, and immunoglobulin. 6 days later, she was successfully weaned from VA-ECMO and underwent cardiac rehabilitation. On day 10, she developed a fever (Tmax 38.3°C) and an irritating cough and began to experience reduced vision over the right eye with eye pain, redness, photophobia, and tearing 2 days later. Administration of levofloxacin eye drops and tobramycin/dexamethasone eye ointment was ineffective. The patient was positive for serum Aspergillus galactomannan antigen. Positron emission tomography/computed tomography (PET/CT) scan showed multiple hypermetabolic cavitary nodules in both lungs (SUVmax3.6) and thickening of the ocular ring wall with hypermetabolism in the right eye (SUVmax3.2). Ophthalmologic examination revealed that her best-corrected visual acuity in the right eye was reduced to light perception with an intraocular pressure of 21 mmHg, and B-scan ultrasonography showed vitreous opacity and retinal edema with mild detachment in the right eye. Metagenomic next-generation sequencing (mNGS) identified a large number of Aspergillus fumigatus sequences in bronchoalveolar lavage fluid, blood, and aqueous humor from the right eye, supporting the diagnosis of pulmonary and ocular involvement due to disseminated IA. Vitrectomy, anterior chamber irrigation, combined with intravenous and intravitreal injections of voriconazole and liposomal amphotericin B eventually cured the patient. This case highlights the importance of early identification and intervention regarding disseminated IA in immunocompromised critically ill patients, especially in the presence of multiple organ involvement.}, } @article {pmid39650139, year = {2024}, author = {Liu, Y and Ghaffari, MH and Ma, T and Tu, Y}, title = {Impact of database choice and confidence score on the performance of taxonomic classification using Kraken2.}, journal = {aBIOTECH}, volume = {5}, number = {4}, pages = {465-475}, pmid = {39650139}, issn = {2662-1738}, abstract = {UNLABELLED: Accurate taxonomic classification is essential to understanding microbial diversity and function through metagenomic sequencing. However, this task is complicated by the vast variety of microbial genomes and the computational limitations of bioinformatics tools. The aim of this study was to evaluate the impact of reference database selection and confidence score (CS) settings on the performance of Kraken2, a widely used k-mer-based metagenomic classifier. In this study, we generated simulated metagenomic datasets to systematically evaluate how the choice of reference databases, from the compact Minikraken v1 to the expansive nt- and GTDB r202, and different CS (from 0 to 1.0) affect the key performance metrics of Kraken2. These metrics include classification rate, precision, recall, F1 score, and accuracy of true versus calculated bacterial abundance estimation. Our results show that higher CS, which increases the rigor of taxonomic classification by requiring greater k-mer agreement, generally decreases the classification rate. This effect is particularly pronounced for smaller databases such as Minikraken and Standard-16, where no reads could be classified when the CS was above 0.4. In contrast, for larger databases such as Standard, nt and GTDB r202, precision and F1 scores improved significantly with increasing CS, highlighting their robustness to stringent conditions. Recovery rates were mostly stable, indicating consistent detection of species under different CS settings. Crucially, the results show that a comprehensive reference database combined with a moderate CS (0.2 or 0.4) significantly improves classification accuracy and sensitivity. This finding underscores the need for careful selection of database and CS parameters tailored to specific scientific questions and available computational resources to optimize the results of metagenomic analyses.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42994-024-00178-0.}, } @article {pmid39650020, year = {2024}, author = {Vermeersch, AS and Van Nieuwerburgh, F and Gansemans, Y and Ali, M and Ducatelle, R and Geldhof, P and Deforce, D and Callens, J and Opsomer, G}, title = {Multi-omics analysis elucidates the host-microbiome interplay in severe udder cleft dermatitis lesions in dairy cows.}, journal = {JDS communications}, volume = {5}, number = {6}, pages = {598-601}, pmid = {39650020}, issn = {2666-9102}, abstract = {Udder cleft dermatitis is a skin disease in dairy cattle that is characterized by painful, large open wounds between the udder halves or at the front udder attachment. Its impact on animal welfare and production warrants an in-depth investigation of its pathogenesis. The present study delves into the pathophysiology of severe udder cleft dermatitis, employing a multi-omics approach by integrating transcriptomic and metagenomic data obtained from samples of severe udder cleft dermatitis lesions and healthy udder skin of dairy cattle. All dominant features selected from the virulence factor, taxonomic, and transcriptomic datasets, except for the facultative pathogen Streptococcus pyogenes, form a network that could be associated with the healthy udder skin. The severe udder cleft dermatitis-associated Streptococcus pyogenes exhibited a negative correlation with these virulence factors and genes, but was not correlated with the other commensal bacteria in the analysis. Examining the different components interacting with each other could advance our understanding of the pathogenesis of severe udder cleft dermatitis.}, } @article {pmid39648978, year = {2025}, author = {Ribero, MN and Schiaffino, MR and Filloy, J}, title = {Grassland Afforestation Drives Biotic Homogenisation of Soil Microbial Communities at a Regional Scale.}, journal = {Molecular ecology}, volume = {34}, number = {2}, pages = {e17617}, doi = {10.1111/mec.17617}, pmid = {39648978}, issn = {1365-294X}, support = {2018//Secretaría de Ciencia y Técnica, Universidad de Buenos Aires/ ; //Neotropical Grassland Conservancy/ ; PICT 2017//Agencia Nacional de Promoción Científica y Tecnológica/ ; //Consejo Nacional de Investigaciones Científicas y Técnicas/ ; }, mesh = {*Soil Microbiology ; *Grassland ; *Biodiversity ; Argentina ; *Microbiota/genetics ; *Fungi/genetics/classification ; Bacteria/genetics/classification ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; }, abstract = {Grassland afforestation poses a threat to biodiversity beyond land-use conversion. Diversity patterns are shaped by temporal dynamics, particularly, time since afforestation can decline beta diversity and lead to biotic homogenisation. Our study examines the effect of grassland afforestation on soil prokaryotic and fungal beta diversity. We evaluate the contributions of colonisation and extinction processes to beta diversity, as well as the replacement of endemic species by ubiquitous ones. Along a 200 km climatic gradient in Argentina's Pampas region, we analysed grasslands and mature eucalypt plantations at different times since afforestation. Soil samples were collected at each site and analysed using 16S (V3-V4) and ITS2 amplicon sequencing to identify prokaryotic and fungal communities, respectively. The analyses revealed biotic homogenisation at the transition from grassland to newly planted stands, evidenced by a decrease in intratreatment beta diversity. Increasing time since afforestation did not exacerbate this decline. However, our findings indicate that there are different responses between prokaryotes and fungi. The homogenisation of prokaryotes in young stands is due to the low heterogeneity in colonising communities. On the other hand, the decline in fungal beta diversity is likely caused by other mechanisms beyond extinction or replacement. The study highlights the impacts of the afforestation process on the beta diversity of soil microbial communities of grasslands, affecting taxonomic groups in different ways. Although microbial diversity may be partially restored in time in eucalypt plantations, it is important to investigate its underlying mechanisms and the ecological implications for microbial diversity and its spatial distribution.}, } @article {pmid39647796, year = {2025}, author = {Zhu, Y and Zhao, S and Qi, S and Zhang, H and Zhang, X and Li, S and Wang, X and Gu, J and Zhang, T and Xi, H and Liu, X}, title = {Effects of energetic compounds on soil microbial communities and functional genes at a typical ammunition demolition site.}, journal = {Chemosphere}, volume = {370}, number = {}, pages = {143913}, doi = {10.1016/j.chemosphere.2024.143913}, pmid = {39647796}, issn = {1879-1298}, mesh = {*Soil Microbiology ; *Trinitrotoluene/toxicity ; *Soil Pollutants/toxicity ; *Triazines ; *Microbiota/drug effects ; *Azocines ; Explosive Agents/toxicity ; Soil/chemistry ; Proteobacteria/genetics/drug effects ; Metagenomics ; }, abstract = {High concentrations of energetic compounds such as 2,4,6-trinitrotoluene (TNT), hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) in military-contaminated sites pose a serious threat to human health and ecosystems. Better understanding about their effects on microbial diversity and functional genes in soil of ammunition demolition sites is required. In this study, the information of soil microbial community composition was obtained by metagenomic sequencing, and the impacts of energetic compounds on microbial community structure at the level of functional genes and enzymes based on Nr (Non-Redundant Protein Sequence Database), KEGG (Kyoto Encyclopedia of Genes and Genomes), CAZy (Carbohydrate-Active enZymes Database) and other databases were discussed. The results showed that soil microbial diversity and functional gene abundance decreased significantly with the increase of the concentrations of energetic compounds. Conversely, the relative abundance of Proteobacteria increased significantly, reaching over 80% in the heavily TNT-contaminated area near explosive-wastewater pool. Furthermore, functional gene analysis indicated that Proteobacteria had an advantage in degrading energetic compounds, and thus had the potential to improve the soil quality at ammunition demolition sites. This study provides a scientific basis for the future remediation and management of contaminated soils at ammunition demolition sites, as well as for the selection of efficient degraders of energetic compounds.}, } @article {pmid39647771, year = {2025}, author = {Chen, R and Xu, R and Huang, J and Zhu, X and Tang, Y and Zhang, Y}, title = {N-acyl-homoserine-lactones as a critical factor for biofilm formation during the initial adhesion stage in drinking water distribution systems.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {366}, number = {}, pages = {125489}, doi = {10.1016/j.envpol.2024.125489}, pmid = {39647771}, issn = {1873-6424}, mesh = {*Biofilms ; *Drinking Water/microbiology/chemistry ; *Quorum Sensing ; *Acyl-Butyrolactones/metabolism ; Water Supply ; Stainless Steel ; }, abstract = {The N-acyl-homoserine-lactone (AHLs)-mediated quorum sensing (QS) system is crucial for the coordination of microbial behaviors within communities. However, the levels of AHLs in biofilms in drinking water distribution systems (DWDSs) and their impact on biofilm formation remain poorly understood. Herein, we simulated DWDSs via biofilm reactors to explore the presence and influence of AHLs during the initial stages of biofilm formation on pipe walls. Glass, polypropylene random copolymer (PP-R) and stainless steel (SS) were used as the coupon materials and the three parallel experimental groups were set up and named accordingly. The glass material is considered to form biofilms only minimally and is therefore used as a negative control. By day 30, the concentration of AHLs in biofilm phase in both PP-R group and SS group reached 1200-1800 ng/L. The predominant AHLs were C6-HSL, C8-HSL, and C10-HSL, with a significant positive correlation between AHLs and biofilm biomass. Metagenomic analysis revealed that microbes exhibiting significant differences among the three groups all demonstrated notable correlations with AHLs. Subsequent analysis of QS genes revealed that the genes associated with AHLs biosynthesis and QS receptors were more abundant in the PP-R and SS groups with biofilm formation. Additionally, we analyzed the abundance of genes related to cell motility, transmembrane transport, tricarboxylic acid cycle, and genetic information synthesis. The co-occurrence network indicates that these processes exhibit a strong correlation with QS genes. This study demonstrates the pivotal role of AHLs in microbial communication during the initial stages of biofilm formation in DWDSs and indicates that the regulatory pathways and mechanisms of AHLs may vary under different environmental conditions.}, } @article {pmid39647535, year = {2024}, author = {Casañas-Martínez, M and Barbero-Herranz, R and Alegre-González, D and Mosquera-Lozano, JD and Campo, RD and , }, title = {Fecal Microbiota Transplantation in a Long-Standing Auto-Brewery Syndrome with Complex Symptomatology.}, journal = {Journal of hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jhep.2024.12.005}, pmid = {39647535}, issn = {1600-0641}, } @article {pmid39647426, year = {2025}, author = {Ge, H and Li, C and Huang, C and Zhao, L and Cong, B and Liu, S}, title = {Bacterial community composition and metabolic characteristics of three representative marine areas in northern China.}, journal = {Marine environmental research}, volume = {204}, number = {}, pages = {106892}, doi = {10.1016/j.marenvres.2024.106892}, pmid = {39647426}, issn = {1879-0291}, mesh = {China ; *Bacteria/metabolism/genetics/classification ; *Geologic Sediments/microbiology ; Microbiota ; Estuaries ; Ecosystem ; Seawater/microbiology ; Biodiversity ; }, abstract = {Bacteria are essential components of ecosystems, participating in nutrient cycling and biogeochemical processes, and playing a crucial role in maintaining the stability of marine ecosystems. However, the biogeographic distribution patterns of bacterial diversity and metabolic functions in the estuarine and coastal areas of northern China remain unclear. Here, we used metagenomic sequencing to investigate the bacterial community composition and metabolic functions in sediments from the adjacent waters of the Yellow River Estuary, the Yellow Sea Cold Water Mass, and the adjacent waters of the Yangtze River Estuary. Among the 9164 species that were found, the most dominant microbial communities are Pseudomonadota, Actinomycetota, Bacteroidota, and Bacillota, but there are significant differences in the species composition in these three typical habitats. Amino acid metabolism and carbohydrate metabolic pathways were highly enriched. Glycoside hydrolases (GHs) predominate in carbon metabolism across all samples. In nitrogen metabolic pathway, genes related to organic degradation and synthesis are more abundant in the Yellow River Estuary than the other two habitats. In sulfur metabolic pathway, genes involved in assimilatory sulfate reduction are significantly enriched. Assimilatory sulfate reduction might be crucial for sulfur metabolism in coastal regions, with a full assimilatory nitrate reduction pathway found in Desulfobacterota. This research offers insights into the compositional diversity, metabolic functions, and biogeographic distribution patterns of bacterial communities in sediments from typical marine areas of northern China.}, } @article {pmid39647412, year = {2024}, author = {He, T and Xie, J and Jin, L and Zhao, J and Zhang, X and Liu, H and Li, XD}, title = {Seasonal dynamics of the phage-bacterium linkage and associated antibiotic resistome in airborne PM2.5 of urban areas.}, journal = {Environment international}, volume = {194}, number = {}, pages = {109155}, doi = {10.1016/j.envint.2024.109155}, pmid = {39647412}, issn = {1873-6750}, mesh = {*Bacteriophages/genetics ; *Particulate Matter ; China ; *Bacteria/genetics/drug effects ; *Seasons ; Humans ; Air Microbiology ; Cities ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Air Pollutants/analysis ; Metagenomics ; Drug Resistance, Bacterial/genetics ; Microbiota ; }, abstract = {Inhalable microorganisms in airborne fine particulate matter (PM2.5), including bacteria and phages, are major carriers of antibiotic resistance genes (ARGs) with strong ecological linkages and potential health implications for urban populations. A full-spectrum study on ARG carriers and phage-bacterium linkages will shed light on the environmental processes of antibiotic resistance from airborne dissemination to the human lung microbiome. Our metagenomic study reveals the seasonal dynamics of phage communities in PM2.5, their impacts on clinically important ARGs, and potential implications for the human respiratory microbiome in selected cities of China. Gene-sharing network comparisons show that air harbours a distinct phage community connected to human- and water-associated viromes, with 57 % of the predicted hosts being potential bacterial pathogens. The ARGs of common antibiotics, e.g., peptide and tetracycline, dominate both the antibiotic resistome associated with bacteria and phages in PM2.5. Over 60 % of the predicted hosts of vARG-carrying phages are potential bacterial pathogens, and about 67 % of these hosts have not been discovered as direct carriers of the same ARGs. The profiles of ARG-carrying phages are distinct among urban sites, but show a significant enrichment in abundance, diversity, temperate lifestyle, and matches of CRISPR (short for 'clustered regularly interspaced short palindromic repeats') to identified bacterial genomes in winter and spring. Moreover, phages putatively carry 52 % of the total mobile genetic element (MGE)-ARG pairs with a unique 'flu season' pattern in urban areas. This study highlights the role that phages play in the airborne dissemination of ARGs and their delivery of ARGs to specific opportunistic pathogens in human lungs, independent of other pathways of horizontal gene transfer. Natural and anthropogenic stressors, particularly wind speed, UV index, and level of ozone, potentially explained over 80 % of the seasonal dynamics of phage-bacterial pathogen linkages on antibiotic resistance. Therefore, understanding the phage-host linkages in airborne PM2.5, the full-spectrum of antibiotic resistomes, and the potential human pathogens involved, will be of benefit to protect human health in urban areas.}, } @article {pmid39647330, year = {2025}, author = {Xu, H and Zhu, D and Zhong, M and Li, C and Wen, C and Zhu, S and Li, Q and Luo, X}, title = {Source-oriented risks of heavy metals and their effects on resistance genes in natural biofilms.}, journal = {Journal of hazardous materials}, volume = {484}, number = {}, pages = {136735}, doi = {10.1016/j.jhazmat.2024.136735}, pmid = {39647330}, issn = {1873-3336}, mesh = {*Biofilms/drug effects ; *Metals, Heavy/toxicity ; *Water Pollutants, Chemical/toxicity ; Rivers/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Bacteria/drug effects/genetics ; }, abstract = {Heavy metal (HM) introduction from various land-use patterns can be a major source of metal resistance genes (MRGs) entering river environments. This influx can trigger the occurrence of other resistomes, such as antibiotic resistance genes (ARGs), by improving co-resistant conjugative transfer. Biofilms, which form at water-solid interfaces, could serve as potential hotspots for HMs and resistance genes. However, the enrichment of HMs from various sources within biofilms and their effect on resistomes remain undocumented. This study aims to investigate the physicochemical properties of biofilm samples collected from the Heihui River, a tributary of the Lancang River, and to analyze the concentrations of nine HMs (As, Cd, Co, Cr, Cu, Ni, Pb, V, and Zn) within these biofilms. The 16S rRNA gene and metagenomic high-throughput sequencing techniques were integrated to uncover the association between HM accumulation levels in biofilms and ecological and health risks, considering the presence of two resistance genes. Natural sources (Co, Cr), industrial (As, Cu, V), agricultural (Cd, Ni), and transportation activities (Pb, Zn) markedly contributed to HM presence within biofilms, with industrial activities posing higher noncarcinogenic and carcinogenic risks than other sources. The network-correlation analyses revealed higher levels of ARG-MRG coexistence in biofilms, with the ecological and health risk index of HMs in biofilms closely associated with the abundance of both resistance genes. Furthermore, the biofilm As concentration markedly affected the abundance and expression of ARGs and MRGs, with elevated As levels within biofilms significantly and positively influencing all four functional categories of MRGs. Water pH also indirectly impacted these functional types by modulating the ionic form of HMs within the biofilm matrix. Our findings underscore the significance of integrating biofilms into environmental management practices and standards for assessing environmental quality.}, } @article {pmid39647263, year = {2025}, author = {Fu, Y and Gou, W and Zhong, H and Tian, Y and Zhao, H and Liang, X and Shuai, M and Zhuo, LB and Jiang, Z and Tang, J and Ordovas, JM and Chen, YM and Zheng, JS}, title = {Diet-gut microbiome interaction and its impact on host blood glucose homeostasis: a series of nutritional n-of-1 trials.}, journal = {EBioMedicine}, volume = {111}, number = {}, pages = {105483}, pmid = {39647263}, issn = {2352-3964}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Blood Glucose/metabolism ; *Homeostasis ; Female ; Male ; Adult ; Metagenomics/methods ; Diet ; Middle Aged ; Metagenome ; Dietary Carbohydrates/metabolism ; }, abstract = {BACKGROUND: The interplay between diet and gut microbiome substantially influences host metabolism, but uncertainties remain regarding their relationships tailored for each subject given the huge inter-individual variability. Here we aim to investigate diet-gut microbiome interaction at single-subject resolution and explore its effects on blood glucose homeostasis.

METHODS: We conducted a series of nutritional n-of-1 trials (NCT04125602), in which 30 participants were assigned high-carbohydrate (HC) and low-carbohydrate (LC) diets in a randomized sequence across 3 pair of cross-over periods lasting 72 days. We used shotgun metagenomic sequencing and continuous glucose monitoring systems to profile the gut microbiome and blood glucose, respectively. An independent cohort of 1219 participants with available metagenomics data are included as a validation cohort.

FINDINGS: We demonstrated that the gut microbiome exhibited both intra-individually dynamic and inter-individually personalized signatures during the interventions. At the single-subject resolution, we observed person-specific response patterns of gut microbiota to interventional diets. Furthermore, we discovered a personal gut microbial signature represented by a carb-sensitivity score, which was closely correlated with glycemic phenotypes during the HC intervention, but not LC intervention. We validate the role of this score in the validation cohort and find that it reflects host glycemic sensitivity to the personal gut microbiota profile when sensing the dietary carbohydrate inputs.

INTERPRETATION: Our finding suggests that the HC diet modulates gut microbiota in a person-specific manner and facilitates the connection between gut microbiota and glycemic sensitivity. This study represents a new paradigm for investigating the diet-microbiome interaction in the context of precision nutrition.

FUNDING: This work was supported by the National Key R&D Program of China, National Natural Science Foundation of China and Zhejiang Provincial Natural Science Foundation of China.}, } @article {pmid39644935, year = {2025}, author = {Chu, Z and Tang, X and Li, Y and Li, J and Xiong, W and Yin, Y and Pan, X}, title = {Simultaneous removal of organic matter and inorganic nitrogen in Baijiu wastewater by methanotrophic denitrification.}, journal = {Bioresource technology}, volume = {418}, number = {}, pages = {131956}, doi = {10.1016/j.biortech.2024.131956}, pmid = {39644935}, issn = {1873-2976}, mesh = {*Nitrogen/metabolism ; *Wastewater/chemistry ; *Denitrification ; *Methane/metabolism ; Bioreactors ; Organic Chemicals/metabolism ; Water Purification/methods ; Spectroscopy, Fourier Transform Infrared ; Biological Oxygen Demand Analysis ; Oxidation-Reduction ; }, abstract = {Methanotroph could facilitate nitrogen removal during methane oxidation, and promote conversion of organic compounds by producing methane monooxygenase. Co-metabolic effect and mechanism of aerobic methane oxidation on the removal of nitrogen and organic matter from Baijiu wastewater were investigated using an improved denitrifying biological filter. It was found that the average removal efficiency of chemical oxygen demand (COD), total nitrogen (TN) and chroma increased by 17 %, 22 % and 10 % in reactor B with methane compared to reactor A with air only. Three-dimensional fluorescence spectroscopy and Fourier transform infrared spectroscopy analysis revealed that methanotroph co-metabolism was accompanied by eliminating nitrogen and organic matter as well as forming alcohol compounds. Metagenomic analyses revealed that Methylocaldum, the dominant genera in Reactor B, exerted a pivotal role in removing nitrogen and organic matter removal by supplying energy and catalysis. Functional genes pmoABC-amoABC could facilitate nitrogen and organic matter removal.}, } @article {pmid39644909, year = {2024}, author = {Mäklin, T and Taira, A and Arredondo-Alonso, S and Shao, Y and Stratton, MR and Lawley, TD and Aaltonen, LA and Corander, J}, title = {Geographical variation in the incidence of colorectal cancer and urinary tract cancer is associated with population exposure to colibactin-producing Escherichia coli.}, journal = {The Lancet. Microbe}, volume = {}, number = {}, pages = {101015}, doi = {10.1016/j.lanmic.2024.101015}, pmid = {39644909}, issn = {2666-5247}, abstract = {Biomedical research has implicated the bacterial metabolite colibactin as a causal risk factor for several cancer types, in particular, colorectal cancer. Colibactin has been known to drive tumorigenesis by inducing double-strand breaks in the DNA of epithelial cells exposed to colibactin-producing bacteria. Some phylogroup B2 Escherichia coli secrete colibactin during interbacterial warfare, concomitantly exposing the host to an increasing risk of DNA damage. This Personal View reviews the current knowledge about the cancer-colibactin interface and summarises metagenomics-based and population-genomics-based surveys to show that the prevalence of dominant colibactin-producing lineages of E coli varies considerably across geographical regions. The prevalence is further strongly associated with the age-standardised incidences of colorectal cancer, bladder cancer, and prostate cancer, suggesting that the degree of colibactin exposure in a population might contribute to the geographical variation of these cancers. Our observations provide a strong impetus for further research and the development of novel interventions to reduce the risks for colibactin-related cancers.}, } @article {pmid39644836, year = {2025}, author = {Wang, L and Wang, X and Wu, H and Fan, S and Lu, Z}, title = {Integration of metagenomic analysis and metabolic modeling reveals microbial interactions in activated sludge systems in response to nanoplastics and plasticizers.}, journal = {Water research}, volume = {271}, number = {}, pages = {122863}, doi = {10.1016/j.watres.2024.122863}, pmid = {39644836}, issn = {1879-2448}, mesh = {*Sewage/microbiology ; *Plasticizers ; Metagenomics ; Diethylhexyl Phthalate/toxicity/metabolism ; Microbial Interactions ; Bacteria/metabolism/genetics/drug effects ; Water Pollutants, Chemical/toxicity ; }, abstract = {Nanoplastics and plasticizers are prevalent in activated sludge and pose a potential threat to microbial communities in wastewater treatment systems. However, studies on the effects of nanoplastics and plasticizers on the interaction mechanisms and metabolic functions of microbial communities in activated sludge systems are still scarce. In this study, the responses of microbial interactions and metabolic functions to PVC nanoplastics (PVCNPs) and bis(2-ethylhexyl) phthalate (DEHP) in activated sludge were investigated via a combination of amplicon sequencing, metagenome sequencing, and metabolic modeling. The results revealed that DEHP had a significant effect on the microbial community under short-term exposure. DEHP contamination may increase vitamin B12 producers to enhance species collaboration in communities. Furthermore, community metabolic modeling revealed that DEHP-degrading bacteria could promote positive interactions among community members. The increased metabolic exchange flux of siderophores and glutathione in microbial communities under PVCNPs and DEHP contamination implied that microbial communities may maintain iron homeostasis in response to PVCNPs and DEHP contamination through interspecies collaboration. However, more data are needed to further validate these results. This study provides vital insights into the response mechanisms of microbial interactions to nanoplastic and plasticizer contamination in activated sludge systems.}, } @article {pmid39644773, year = {2025}, author = {Hu, Y and Hu, X and Jiang, L and Luo, J and Huang, J and Sun, Y and Qiao, Y and Wu, H and Zhou, S and Li, H and Li, J and Zhou, L and Zheng, S}, title = {Microbiome and metabolomics reveal the effect of gut microbiota on liver regeneration of fatty liver disease.}, journal = {EBioMedicine}, volume = {111}, number = {}, pages = {105482}, pmid = {39644773}, issn = {2352-3964}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Liver Regeneration ; Mice ; *Metabolomics/methods ; *Fatty Liver/metabolism/etiology/microbiology ; Male ; Diet, High-Fat/adverse effects ; Disease Models, Animal ; Metabolome ; Hepatectomy ; Mice, Inbred C57BL ; Metagenomics/methods ; Liver/metabolism ; RNA, Ribosomal, 16S/genetics ; Akkermansia ; }, abstract = {BACKGROUND: Metabolic dysfunction-associated fatty liver disease (MAFLD) is associated with impaired regenerative capacity and poor postoperative prognosis following hepatectomy. Previous research has highlighted the importance of the gut-liver axis in the physiological and pathological processes of the liver. However, the contribution of gut bacteria to the regeneration of livers with MAFLD and its metabolic regulatory mechanisms remain elusive.

METHODS: Partial hepatectomy (PHx) was performed on C57Bl/6J mice fed with high-fat diet (HFD) for 12 weeks. Pathological examination, immunohistochemistry, and qRT-PCR analysis were performed to assess the severity of steatosis and proliferative potential. The gut microbiome was examined by 16S rRNA gene sequencing and shotgun metagenomics, whereas liver metabolomics was analysed via untargeted and targeted metabolomics using liquid chromatography-tandem mass spectrometry (LC-MS).

FINDINGS: HFD-induced hepatic steatosis in mice led to impaired liver regeneration following PHx. The gut microbiota and liver metabolites were altered along with the liver regeneration process. Longitudinal time-series analysis revealed dynamic alterations in these data, whereas correlation analysis screened out bacterial candidates that potentially influence liver regeneration in MAFLD by modulating metabolic pathways. Among these bacteria, the dominant bacterium Akkermansia was selected for subsequent investigation. MAFLD mice gavaged with Akkermansia muciniphila (A. muciniphila) exhibited reduced liver lipid accumulation and accelerated liver regeneration, possibly through the regulation of the tricarboxylic acid (TCA) cycle.

INTERPRETATION: These data demonstrated the interplay between the gut microbiome, liver metabolomics, and liver regeneration in mice with MAFLD. A. muciniphila has the potential to serve as a clinical intervention agent to accelerate postoperative recovery in MAFLD.

FUNDING: This work was supported by the Research Project of Jinan Microecological Biomedicine Shandong Laboratory [JNL-2022008B]; the Zhejiang Provincial Natural Science Foundation of China [LZ21H180001]; the Fundamental Research Funds for the Central Universities [No. 2022ZFJH003].}, } @article {pmid39644571, year = {2025}, author = {Zhou, X and Li, Q and Shi, Z and Lu, W and Shu, C and Zhu, J and Wu, Y}, title = {Assessing the prevalence of human enteric viruses in hospital wastewater to evaluate the effectiveness of wastewater treatment systems.}, journal = {Ecotoxicology and environmental safety}, volume = {289}, number = {}, pages = {117488}, doi = {10.1016/j.ecoenv.2024.117488}, pmid = {39644571}, issn = {1090-2414}, mesh = {*Wastewater/virology ; *Hospitals ; *Norovirus/isolation & purification/genetics ; Humans ; *Sewage/virology ; *Rotavirus/isolation & purification/genetics ; Real-Time Polymerase Chain Reaction ; Waste Disposal, Fluid ; High-Throughput Nucleotide Sequencing ; Enterovirus/isolation & purification/genetics ; Prevalence ; Water Purification/methods ; }, abstract = {In this experiment, we employed Real-time PCR(RT-PCR) and metagenomic Next-Generation Sequencing (mNGS) techniques to detect the presence of Norovirus, Rotavirus Group A, Adenovirus Group F, and Astrovirus in untreated sewage from three major hospitals. A comparison with clinical lab test outcomes revealed Norovirus as having the highest infection rate, followed by Adenovirus Group F and Rotavirus Group A. Despite not testing for Astrovirus in clinical labs, its sewage detection rate was surpassed only by Norovirus, suggesting a potentially high clinical infection rate. Further analysis of these viruses in treated sewage revealed that chlorination failed to eliminate the virus, maintaining viral concentrations in the treated sewage between 10^2 and 10^3 copies/ml. Even though nucleic acid testing methods fail to detect viral actions, the possible danger they present to public safety should not be ignored. During this experiment, viral nucleic acid was extracted directly from the samples without prior concentration. This method, unlike conventional virus detection post-concentration, bypasses concerns such as recovery efficiency, offering a clearer representation of virus concentrations in water samples and facilitating easier operation.}, } @article {pmid39644540, year = {2024}, author = {Xiong, W and Dong, L and Zhu, N and Zhou, D and Li, S and Lv, J and Xu, M and Zhang, Y and Li, S}, title = {The diagnostic value of metagenomic next-generation sequencing in suspected pulmonary tuberculosis patients with scarce sputum or negative sputum etiological test results.}, journal = {Diagnostic microbiology and infectious disease}, volume = {111}, number = {3}, pages = {116633}, doi = {10.1016/j.diagmicrobio.2024.116633}, pmid = {39644540}, issn = {1879-0070}, abstract = {OBJECTIVE: To compare the diagnostic value between mNGS and conventional tests in suspected pulmonary tuberculosis (PTB) patients with scarce sputum or with negative sputum etiological test results.

METHODS: We enrolled eligible patients admitted to our department from 2018 to 2021. Their bronchoalveolar lavage fluid (BALF) and lung biopsy tissue samples were sent for mNGS and conventional tests. The diagnostic value of mNGS was compared respectively with that of conventional tests.

RESULTS: 94 of 226 enrolled patients were diagnosed PTB. The diagnostic concordance rate of mNGS was significantly higher than that of acid-fast staining in all samples (p < 0.001), as well as that of culture in BALF samples (p = 0.011). mNGS in parallel with conventional tests had significantly higher AUC than mNGS alone (p = 0.013).

CONCLUSIONS: mNGS has higher diagnostic value than some conventional tests. mNGS in parallel with conventional tests is more reliable to accurately diagnose these suspected PTB patients.}, } @article {pmid39644431, year = {2024}, author = {Kara, K and Pi Rci, G and Yılmaz Öztaş, S and Demi R, S and Yılmaz, K}, title = {Effect of milk thistle (Silybum marianum L.) oil on pro-inflammatory cytokines, acute phase proteins, rumen metagenomic profile, rumen fluid variables and performance in calves.}, journal = {Veterinary research communications}, volume = {49}, number = {1}, pages = {48}, pmid = {39644431}, issn = {1573-7446}, support = {TSA-2023-12255//Bilimsel Araştırma Projeleri, Erciyes Üniversitesi/ ; }, mesh = {Animals ; Cattle ; *Rumen/microbiology ; Female ; Male ; *Cytokines/metabolism/genetics ; *Plant Oils/pharmacology/administration & dosage ; *Acute-Phase Proteins/metabolism ; *Silybum marianum/chemistry ; *Diet/veterinary ; Dietary Supplements/analysis ; Animal Feed/analysis ; }, abstract = {The aim of this study was to determine the effect of milk thistle (Silybum marianum L., SM) oil supplementation on proinflammatory cytokines, acute phase proteins, rumen metagenomic profile, rumen fluid variables and performance during the milk feeding period of Holstein calves. In the present study, 24 calves that consumed quality and sufficient amount of colostrum (≥50 mg/ml IgG) after birth were divided into three groups, with 8 animals in each group (4 males + 4 females). Individually fed calves were given added SM oil as 0 µL/day/calf (Control group, SM0), 100 µL/day/calf (SM100) and 200 µL/day/calf (SM200). The ration containing concentrated feed mix (90%) + wheat straw (10%) was offered to the calves. SM oil did not change the ammonia nitrogen and pH values of the rumen fluid of calf (P>0.05). The molarities of PA, IBA, IVA and BSCFA in the rumen fluid increased linearly with SM oil dose (P<0.05). The relative abundance of Firmicutes linearly increased and the relative abundance of Actinobacteriota decreased with the addition of SM oil (P<0.05). Relative abundances of Erysipelotrichaceae_UCG_002, Eubacterium_coprostanoligenes_group, Clostridia_UCG_014, Lachnospiraceae_Unknown_1, Lachnospiraceae_NK3A20_group, Shuttleworthia, Selenomonadaceae_Uncultured_1, Rikenellaceae_RC9_gut_group and Succinivibrionaceae_UCG_001 linearly increased with SM oil (P<0.05). Relative abundances of Methanobrevibacter, Acetitomaculum, Olsenella and Megasphaera in calf rumen fluid linearly decreased with SM oil (P<0.05). Concentrations of TNF-α, IFN-ɣ, and SAA of calf' serum at weaning stage linearly decreased with SM oil doses (P<0.05). Serum IgA concentration increased with 100 µL SM oil /day (P<0.05). As a result, the addition of SM oil to calves has the potential to reduce the immune suppression of calves during the milk feeding period and at weaning time, has a positive effect on the microbiome involved in starch and protein catabolism in the rumen fluid, and increases the fermentation end products (PA, IVA and BA). Milk thistle oil has an inhibitory effect on methanogenic archaea and can be used as an anti-methanogenic feed additive and will contribute to the effective use of feed energy.}, } @article {pmid39643877, year = {2024}, author = {Cui, Z and Wang, S and Niu, J and Ma, J and Yang, H}, title = {Bifidobacterium species serve as key gut microbiome regulators after intervention in gestational diabetes mellitus.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {520}, pmid = {39643877}, issn = {1471-2180}, support = {22cz020401-4811009//National High Level Hospital Clinical Research/ ; 81830044//National Natural Science Foundation of China/ ; 2021YFC2700700//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Diabetes, Gestational/microbiology/metabolism/blood ; Pregnancy ; *Gastrointestinal Microbiome/genetics ; Female ; *Bifidobacterium/genetics ; Adult ; *Feces/microbiology ; Fatty Acids, Volatile/metabolism ; Dysbiosis/microbiology ; Genome-Wide Association Study ; Metagenome ; }, abstract = {Gut microbiome dysbiosis is associated with gestational diabetes mellitus (GDM), and its modulation represents a promising approach for enhancing glycemic control. In this study, we aimed to discover specific alterations in the gut microbiome through lifestyle management. We performed metagenome sequencing on fecal samples and measured short-chain fatty acid (SCFA) in plasma samples from 27 well-controlled GDM pregnancies before and after glycemic control. At the same time, 38 normal glucose tolerance (NGT) samples served as controls. Additionally, we employed two-sample Mendelian Randomization (MR) to validate our findings against Genome-Wide Association Study (GWAS) database. Our dynamic analysis revealed Bifidobacterium genus increased in GDM patients after intervention. The MR analysis confirmed that the family of Bifidobacteriaceae (OR 0.929, 95% CI, 0.886-0.975; P = 0.003) was the only negatively associated family with GDM. Further analysis indicated the increased abundance of Bifidobacterium species were negatively correlated with glycemic traits (Spearman rho mean - 0.32 ± 0.34) but positively correlated with plasma SCFA levels (Spearman rho mean 0.24 ± 0.19). Functional analysis revealed that the quorum-sensing pathway had the strongest effect on the ability of Bifidobacterium to promote glucose homeostasis (Spearman rho = -0.34), suggesting its role in regulating intestinal microbiota. Finally, the multivariable MR analysis demonstrated that two pathways, COLANSYN PWY and PWY 7323, responsible for cell surface compound synthesis in gram-negative bacteria, mediated 14.83% (P = 0.017) and 16.64% (P = 0.049) of the protective effects of Bifidobacteriaceae against GDM, respectively. In summary, Bifidobacterium is an effective gut microbiota regulator for GDM-related glucose homeostasis.}, } @article {pmid39643526, year = {2025}, author = {Yen, TY and Hsu, C and Lee, NC and Wu, CS and Wang, H and Lee, KY and Lin, CR and Lu, CY and Tsai, ML and Liu, TY and Lin, C and Chen, CY and Chang, LY and Lai, F and Huang, LM}, title = {Signatures of lower respiratory tract microbiome in children with severe community-acquired pneumonia using shotgun metagenomic sequencing.}, journal = {Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi}, volume = {58}, number = {1}, pages = {86-93}, doi = {10.1016/j.jmii.2024.11.011}, pmid = {39643526}, issn = {1995-9133}, mesh = {Humans ; *Community-Acquired Infections/microbiology ; Male ; Prospective Studies ; Child, Preschool ; Female ; *Metagenomics/methods ; Child ; *Microbiota/genetics ; Infant ; *Pneumonia/microbiology ; *High-Throughput Nucleotide Sequencing ; *Metagenome/genetics ; Bacteria/classification/genetics/isolation & purification ; Severity of Illness Index ; Intensive Care Units ; Respiratory System/microbiology ; Adolescent ; }, abstract = {BACKGROUND: Severe community-acquired pneumonia was associated with high morbidity and mortality in children. However, species-level microbiome of lower airway was sparse, and we used shotgun metagenomic next-generation sequencing to explore microbial signatures.

METHODS: We conducted a prospective cohort study to recruit children under 18 who required admission to an intensive care unit for community-acquired pneumonia between December 2019 and February 2022. Lower respiratory specimens were collected on admission for shotgun metagenomic sequencing. The children were divided into two groups. Critical cases were patients with respiratory failure requiring endotracheal ventilator support, and severe cases did not require intubation. Signatures of lower respiratory tract microbiome were compared between groups using an exact k-mer matching metagenomic analysis pipeline (Kraken 2) and a metagenome-assembled genomes pipeline (MetaWRAP).

RESULTS: Totally 66 children were enrolled, and 27 children were critical cases, and the rest were severe cases. There were significant differences in microbial community structure between different severity groups, and microbial abundance was negatively correlated with disease severity. The results showed that Haemophilus influenzae was more prominent in children who were critical, accompanied with increased expression of intracellular transport, secretion, and vesicle transport genes. Rothia mucilaginosa, Dolosigranulum pigrum, and Prevotella melaninogenica tended to be present in less severe community-acquired pneumonia group.

CONCLUSION: This study demonstrated that significantly different microbial community was associated with severity of community-acquired pneumonia requiring intensive care admission. Species-level shotgun metagenomic sequencing facilitates the exploration of potentially pathogenic or protective microbes and shed the light of probiotic development in lower respiratory tract.}, } @article {pmid39643486, year = {2024}, author = {Reyes-Sosa, MB and Valle-Gough, R and Ponce-Caballero, MDC and Arena-Ortiz, ML}, title = {Bacterial richness assessment in water and sediments in the northern coast of the Yucatan Peninsula.}, journal = {Revista Argentina de microbiologia}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ram.2024.10.009}, pmid = {39643486}, issn = {0325-7541}, abstract = {Given the importance of the coastal environments and the multiple ecological services that they provide, it is important to explore and understand the interactions that occur within them. The microbiome is a key factor for the understanding of the dynamics of these fragile sites. A metagenomic study based on the profiling of the 16S ribosomal gene was carried out in order to assess the bacterial diversity present in the northern coastal zone of the Yucatan Peninsula. The results showed that water and sediment samples share some similarities regarding the bacterial genera found, only differing in the quantitative part. Through a PCO (principal coordinates) analysis clear differences between sediment and water samples could be observed. The highest relative diversity was found in wetland and lagoon sediment samples, respectively. It was observed that 3-8% of the total sequence reads belonged to opportunistic genera such as: Vibrio in the sea samples and Capnocytophaga in the other environments. Salinity and pH were the factors which contributed the most to the differences among the communities in the various environments in the coastal zone. There is an important similarity in the sediments across the different environments within the studied coastal zone. The data presented herein contribute to setting a baseline for research in the coastal region of the Yucatan Peninsula.}, } @article {pmid39643362, year = {2024}, author = {Shen, C and Yu, Y and Zhang, X and Zhang, H and Chu, M and Yuan, B and Guo, Y and Li, Y and Zhou, J and Mao, J and Xu, X}, title = {The dynamic of physicochemical properties, volatile compounds and microbial community during the fermentation of Chinese rice wine with diverse cereals.}, journal = {Food research international (Ottawa, Ont.)}, volume = {198}, number = {}, pages = {115319}, doi = {10.1016/j.foodres.2024.115319}, pmid = {39643362}, issn = {1873-7145}, mesh = {Amino Acids/analysis/metabolism ; Bacteria/classification/metabolism ; Edible Grain/chemistry/microbiology ; Esters/analysis/metabolism ; *Fermentation ; Gas Chromatography-Mass Spectrometry ; Microbiota ; *Odorants/analysis ; *Oryza/chemistry ; Taste ; *Volatile Organic Compounds/analysis ; *Wine/analysis/microbiology ; }, abstract = {This study investigates the impact of liquid state fermentation on the key flavor compounds and microbial community structure in Chinese rice wine brewed from five different raw materials: buckwheat, sorghum, japonica rice, glutinous rice, and black rice. Using HS-SPME-GC-MS and HPLC, the volatile compounds were analyzed across various grain liquefaction methods, detecting 82 volatiles, including esters, alcohols, aldehydes, and acids. The concentration of flavor compounds such as esters, amino acids, phenolic acids, and organic acids varied significantly depending on the raw material used. Based on odor activity values, 31 key compounds were identified, including 15 ethyl esters, like ethyl laurate, responsible for the unique and complex aroma of the rice wines. Bitter amino acids, making up over 50 % of the total amino acids, were predominant. Among the varieties, the buckwheat-fermented wine exhibited the highest ester content (27.39 mg/L), nearly double that of other samples, along with elevated amino acids (1.47 mg/mL) and phenolic acids (904.29 mg/L). Black rice ranked second in amino acid content (0.93 mg/mL), while glutinous rice had the highest organic acid content (239.76 mg/mL). Metagenomic sequencing on the fifth day of fermentation revealed significant differences in microbial community structure among the raw materials. Saccharomyces, Aspergillus, Thermomyces, Epicoccus, and Albertella were dominant fungi, while Weissella, Thermoactinomyces, Bacillus, and Saccharopolyspora were dominant bacteria. Sensory analysis showed that buckwheat-fermented rice wine was distinguished by its honey, floral, creamy, and umami attributes, while balancing alcohol, acidity, bitterness, and Qu aroma. The results demonstrate the significant influence of raw material selection and liquefaction method on both flavor profile and microbial diversity in Chinese rice wine.}, } @article {pmid39643360, year = {2024}, author = {Li, N and Xu, W and Meng, L and Zhao, Y and Zhao, X and Zheng, N and Zhang, Y and Wang, J}, title = {Metagenomics reveals differences in spore-forming bacterial diversity in raw milk in different regions and seasons in China.}, journal = {Food research international (Ottawa, Ont.)}, volume = {198}, number = {}, pages = {115317}, doi = {10.1016/j.foodres.2024.115317}, pmid = {39643360}, issn = {1873-7145}, mesh = {*Seasons ; Animals ; *Milk/microbiology ; China ; *Spores, Bacterial/genetics ; *Metagenomics ; Food Microbiology ; Bacteria/genetics/classification/isolation & purification ; Biodiversity ; }, abstract = {The spore-forming bacteria in the dairy industry are notable for their spores resilience and capacity to survive heating processes, allowing them to germinate and enter the vegetative stage, potentially leading to spoilage of the milk. Additionally, these spores can form biofilms, becoming a persistent source of contamination in processing environments. In this study, we collected a total of 165 raw milk from six different parts in China in spring, summer, autumn, and winter, respectively. Metagenomics sequencing method was used to explore and compare the differences in spore-forming bacterial composition and diversity in raw milk samples. Among these samples, four genera and 207 species of spore-forming bacteria were identified, with the genus Bacillus and the species Paenibacillus darwinianus dominant. Seasonal variations had a greater impact on the composition and abundance of spore-forming bacteria in raw milk than regional differences. Notable, raw milk samples collected during the spring and summer exhibited a higher number of unique spore-forming bacterial species compared to those collected in other seasons. Moreover, different regions and seasons have their own dominant bacteria. Metabolism of cofactors and vitamins, energy metabolism, carbohydrate metabolism, and amino acid metabolism were the main metabolic pathways. Hence, specific strategies need to be adopted to prevent and control spore-forming bacteria in raw milk in different regions and seasons.}, } @article {pmid39643345, year = {2024}, author = {Jian, C and Sun, M and Ma, T and Wang, W and Lv, B and Wang, J and Su, X and Li, S and Guo, Y}, title = {Revealing the formation mechanisms of key flavor components during the fermentation of bamboo shoots by combining flavoromics and metagenomics.}, journal = {Food research international (Ottawa, Ont.)}, volume = {198}, number = {}, pages = {115361}, doi = {10.1016/j.foodres.2024.115361}, pmid = {39643345}, issn = {1873-7145}, mesh = {*Fermentation ; *Metagenomics ; *Taste ; *Volatile Organic Compounds/analysis/metabolism ; *Odorants/analysis ; *Metabolomics ; Flavoring Agents/metabolism ; Plant Shoots ; Fermented Foods/microbiology ; Bacteria/genetics/classification/metabolism ; Food Microbiology ; Amino Acids/analysis/metabolism ; Microbiota ; }, abstract = {Microbial metabolism plays a critical role in the flavor development of Guangxi fermented bamboo shoots (GFBS). To clarify the role of microorganisms in flavor formation and predict the metabolic pathways of key characteristic flavor compounds, this study employed metabolomics, Odor Activity Value (OAV), and Taste Activity Value (TAV) calculations, integrated with Partial Least Squares Discriminant Analysis (PLS-DA), to investigate changes in GFBS flavors-represented by volatile flavor compounds, organic acids, and free amino acids-across a 30-day fermentation period. Metagenomic datasets were used to identify taxonomic and functional changes in the microbial community. As a result, 26 characteristic flavor compounds (OAV or TAV > 1) were identified in mature GFBS, and 23 differential flavor compounds were identified at different fermentation stages using PLS-DA (VIP > 1.2). The top 10 microbial genera associated with these characteristic flavor compounds were identified, including Acinetobacter, Enterobacter, Raoultella, Enterococcus, Klebsiella, Lactococcus, Leuconostoc, Weissella, Lactiplantibacillus and Limosilactobacillus. Based on these findings, a predictive metabolic network of key flavor compounds in GFBS was constructed, providing a comprehensive understanding of the diverse metabolic roles of microorganisms during fermentation. This work lays a theoretical foundation for the standardized production and quality control of GFBS flavor.}, } @article {pmid39643336, year = {2024}, author = {Li, T and Cao, W and Li, D and Wei, C and Yan, Y and Zeng, X}, title = {Metagenomic insights into quorum sensing-associated microbial profiling and its correlations with flavor compounds of Maotai-flavor liquor: A case study of stacking fermented grains.}, journal = {Food research international (Ottawa, Ont.)}, volume = {198}, number = {}, pages = {115324}, doi = {10.1016/j.foodres.2024.115324}, pmid = {39643336}, issn = {1873-7145}, mesh = {*Quorum Sensing ; *Fermentation ; *Flavoring Agents/metabolism ; *Metagenomics/methods ; Taste ; Food Microbiology ; Bacteria/genetics/metabolism/classification ; Fungi/genetics/metabolism ; Edible Grain/microbiology ; Alcoholic Beverages/microbiology ; Microbiota ; }, abstract = {Stacking fermentation is typical process of Maotai-flavor Baijiu and microbial composition determine content of flavors. To date, the knowledge on the driving force of microbial composition was as yet unknown. Since quorum sensing molecule (QSM) plays an important role in modifying microbial interactions. Therefore, the objectives of the present study were: (1) to describe the microbial profile associated with QSM in stacking grains using metagenomics; (2) to elucidate how QSM shapes microbial interactions and accordingly regulates flavor synthesis. Results indicated that bacterial QSM including AI-2, DSF, and AHL as well as fungal QSM aromatic alcohols and farnesol were prevalent in the stacking fermented grains. Thereinto, AI-2 might be an important driving force of microbial composition due to its highest abundance. AI-2 in Limosilactobacillus fermentum, Pediococcus pentosaceus, and Weissella cibaria perhaps modified microbial interactions together with fungal QSM in Schizosaccharomyces pombe and Pichia membranifaciens. The role of AI-2 was much higher than that of fungal QSM. Furthermore, QSM indirectly influenced the synthesis of important flavors such as ethyl lactate, phenylethanol, and ethyl phenylacetate through the dynamic of microbial composition. Together, this current study for the first time explored the effects of QSM on microbial composition and flavor synthesis in the Baijiu field.}, } @article {pmid39643156, year = {2024}, author = {Wang, Y and Zeng, T and Tang, D and Cui, H and Wan, Y and Tang, H}, title = {Integrated Multi-Omics Analyses Reveal Lipid Metabolic Signature in Osteoarthritis.}, journal = {Journal of molecular biology}, volume = {}, number = {}, pages = {168888}, doi = {10.1016/j.jmb.2024.168888}, pmid = {39643156}, issn = {1089-8638}, abstract = {Osteoarthritis (OA) is the most common degenerative joint disease and the second leading cause of disability worldwide. Single-omics analyses are far from elucidating the complex mechanisms of lipid metabolic dysfunction in OA. This study identified a shared lipid metabolic signature of OA by integrating metabolomics, single-cell and bulk RNA-seq, as well as metagenomics. Compared to the normal counterparts, cartilagesin OA patients exhibited significant depletion of homeostatic chondrocytes (HomCs) (P = 0.03) and showed lipid metabolic disorders in linoleic acid metabolism and glycerophospholipid metabolism which was consistent with our findings obtained from plasma metabolomics. Through high-dimensional weighted gene co-expression network analysis (hdWGCNA), weidentified PLA2G2A as a hub gene associated with lipid metabolic disorders in HomCs. And an OA-associated subtype of HomCs, namely HomC1 (marked by PLA2G2A, MT-CO1, MT-CO2, and MT-CO3) was identified, which also exhibited abnormal activation of lipid metabolic pathways. This suggests the involvement of HomC1 in OA progression through the shared lipid metabolism aberrancies, which were further validated via bulk RNA-Seq analysis. Metagenomic profiling identified specific gut microbial species significantly associated with the key lipid metabolism disorders, including Bacteroides uniformis (P < 0.001, R = -0.52), Klebsiella pneumonia (P = 0.003, R = 0.42), Intestinibacter_bartlettii (P = 0.009, R = 0.38), and Streptococcus anginosus (P = 0.009, R = 0.38). By integrating the multi-omics features, a random forest diagnostic model with outstanding performance was developed (AUC = 0.97). In summary, this study deciphered the crucial role of a integrated lipid metabolic signature in OA pathogenesis, and established a regulatory axis of gut microbiota-metabolites-cell-gene, providing new insights into the gut-joint axis and precision therapy for OA.}, } @article {pmid39643107, year = {2025}, author = {Khedpande, N and Barve, K}, title = {Role of gut dysbiosis in drug-resistant epilepsy: Pathogenesis and available therapeutic strategies.}, journal = {Brain research}, volume = {1850}, number = {}, pages = {149385}, doi = {10.1016/j.brainres.2024.149385}, pmid = {39643107}, issn = {1872-6240}, mesh = {Humans ; *Dysbiosis ; *Gastrointestinal Microbiome/physiology/drug effects ; *Drug Resistant Epilepsy/drug therapy ; *Brain-Gut Axis/physiology/drug effects ; Anticonvulsants/therapeutic use ; Animals ; Blood-Brain Barrier/metabolism ; }, abstract = {Over 70 million people worldwide suffer from epilepsy, a persistent brain disorder. Although there are more than 20 antiseizure drugs available for the symptomatic treatment of epilepsy, about one-third of patients with epilepsy experience seizures that show resistance to pharmacotherapy. Since patients with drug-resistant epilepsy are more prone to physical injuries, psychosocial dysfunction, early death, and deteriorated life quality, the development of safer and more effective treatments is a crucial clinical need. The gut-brain axis and microbiome research advances have provided new insights into the pathophysiology of epilepsy, the resistance to anti-seizure medicine, and potential treatment targets. Inflammation, disturbance of the blood-brain barrier, and altered neurotransmitters are key pathways linked to gut dysbiosis. The characterization of microbial species and functional pathways has advanced thanks to metagenomic sequencing and high-throughput analysis. In this review, we elaborate on the gut-mediated molecular pathways involved in drug-resistant epilepsy, the gut- modulatory therapeutic options, and their combination with antiseizure medications for drug-resistant epilepsy.}, } @article {pmid39642837, year = {2025}, author = {Li, Y and Liu, K and Qiu, H and Chen, F and Zhang, J and Zheng, Z}, title = {Dynamics of antibiotic resistance genes and bacterial community structure within substrate biofilms.}, journal = {Journal of environmental management}, volume = {373}, number = {}, pages = {123512}, doi = {10.1016/j.jenvman.2024.123512}, pmid = {39642837}, issn = {1095-8630}, mesh = {*Biofilms/drug effects ; Drug Resistance, Microbial/genetics ; Wastewater/microbiology ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/drug effects ; Genes, Bacterial ; Microbiota ; }, abstract = {Biofilms that develop on the surface of substrates are critical for treating wastewater. The accumulation of antibiotic resistance genes (ARGs) within these biofilms is particularly noteworthy. Despite their importance, studies that focus on biofilms attached to substrate surfaces remain scarce. This investigation explored the prevalence and succession of ARGs and microbial dynamics in biofilms on different substrates (ceramic, biomass filter, and steel slag) versus water biofilms over a year. Results showed distinct differences in ARG profiles between water and substrate biofilms. Multidrug ARGs constituted 39.14-46.73% of all ARGs in the substrate biofilms, with macrolide ARGs making up 11.98-14.52%. Seasonal variations influenced the diversity of the ARGs, notably increasing during the spring. The neutral community model suggested that the ARG assembly was dominantly driven by stochastic process. Proteobacteria, Actinobacteria and Campylobacter emerged as the predominant phyla within these biofilms. The microbial community distribution was predominantly influenced by ammonium nitrogen (NH4[+]-N) (R[2] = 0.4113), temperature and total nitrogen (TN). Notably, temperature exerted a critical impact on the microbial community distribution (P = 0.001), identifying it as the principal factor for spatial arrangement. Furthermore, the structural variations of ARGs were primarily driven by total organic carbon (TOC) (R[2] = 0.3988), temperature, oxidation-reduction potential (ORP) and NH4[+]-N. Our findings provided new insights into the optimization of substrate selection and ecological management to manage ARG enrichment, offering a promising strategy for aquatic ecological restoration and pollution control.}, } @article {pmid39642832, year = {2025}, author = {Fu, J and Chen, S and Tan, Y and Zou, K and Yu, X and Ji, L and Zhang, J and Xiao, X and Wang, W and Zhao, K and Zou, L}, title = {Inoculation of thermophilic bacteria from giant panda feces into cattle manure reduces gas emissions and decreases resistance gene prevalence in short-term composting.}, journal = {Journal of environmental management}, volume = {373}, number = {}, pages = {123601}, doi = {10.1016/j.jenvman.2024.123601}, pmid = {39642832}, issn = {1095-8630}, mesh = {*Manure/microbiology ; *Composting ; Animals ; Cattle ; *Feces/microbiology ; *Bacteria/genetics ; }, abstract = {Here, thermophilic bacteria (TB) with cellulose degradation functions were screened from composting panda feces and applied to cattle manure composting. TB (Aeribacillus pallidus G5 and Parageobacillus toebii G12) inoculation led to remarkable improvement of the compost temperature, prolonging of the thermophilic stage and shortening of the composting process, resulting in increased manure harmlessness (GI ≥ 70%), compost humification, and greenhouse gas emission reduction (14.19%-22.57%), compared with the control compost, within 15 days of composting. In particular, G5 inoculation reduced NH3 emissions by 41.97% relative to control composts over 15 days. G5 was capable of rapidly colonizing in the composts, and its inoculation immediately enriched the genera of Firmicutes, and simultaneously decreased the genera of Proteobacteria, contributing to the elimination of harmful microorganisms. Notably, this strain lacked antibiotic resistance genes, and the absolute abundances of resistance genes and mobile genetic genes (MGEs) decreased the most (by 80.84%). Metagenomic analysis revealed that enzymes capable of producing CO2, N2O, and NH3 were generally inhibited, while CO2 fixation and N2O and NH3 reduction enzymes were enriched in the G5 compost, since metagenome-assembled genomes of Proteobacteria harbored more key genes and enzymes in complete pathways for producing N2O, NH3, and CO2. Moreover, Proteobacteria, such as Pseudomonas and Halopseudomonas, were the main host of resistance genes and MGEs. Overall, the gas emission could be reduced, and more efficient control of resistance genes could be achieved by inhibited the abundance of Proteobacteria during composting. This study provides a safe and effective microbial agent (A. pallidus) for manure treatment.}, } @article {pmid39642737, year = {2025}, author = {Medriano, CA and Kim, S and Kim, LH and Bae, S}, title = {Chronic Exposure of Adult Zebrafish to Polyethylene and Polyester-based Microplastics: Metabolomic and Gut Microbiome Alterations Reflecting Dysbiosis and Resilience.}, journal = {Journal of hazardous materials}, volume = {484}, number = {}, pages = {136691}, doi = {10.1016/j.jhazmat.2024.136691}, pmid = {39642737}, issn = {1873-3336}, mesh = {Animals ; *Zebrafish ; *Gastrointestinal Microbiome/drug effects ; *Dysbiosis/chemically induced ; *Microplastics/toxicity ; *Water Pollutants, Chemical/toxicity ; *Metabolomics ; *Polyesters ; *Polyethylene/toxicity ; }, abstract = {The study explored the ecotoxicological effects of chronic exposure to microplastic (MP) on adult zebrafish, focusing on environmentally relevant concentrations of polyethylene (PE) beads and polyester (PES). High-throughput untargeted metabolomics via UPLC-QToF-MS and 16S metagenomics for gut microbiota analysis were used to assess ecotoxicity in zebrafish exposed to varying concentrations of PE and PES. The VIP (Variable Importance in Projection) scores indicated PE exposure primarily impacted phospholipids, ceramides, and nucleotide-related compounds, while PES exposure led to alterations in lipid-related compounds, chitin, and amino acid derivatives. From MSEA (Metabolite Set Enrichment Analysis) and Mummichog analyses, PE and PES significantly disrupted key metabolomic pathways associated with inflammation, immune responses, and apoptosis, including leukotriene and arachidonic acid metabolism and the formation of putative anti-inflammatory metabolites from EPA. PE caused physical disruption and inflammation of the epithelial barrier, whereas PES affected gut microbiota interactions, impairing digestion and metabolism. Although alpha diversity within the gut microbiome remained stable, beta diversity analysis revealed significant shifts in microbial composition and structure, suggesting a disruption of functional balance and an increased susceptibility to pathogens. Chronic PE and PES exposures induced shifts in the gut microbial community and interaction network with potential increases in pathogenic bacteria and alteration in commensal bacteria, demonstrating the microbiome's resilience and adaptability to stressors of MPs exposure. High-throughput metabolomics and 16S metagenomics revealed potential chronic diseases associated with inflammation, immune system disorders, metabolic dysfunction, and gut dysbiosis, highlighting the complex relationship between gut microbiome resilience and metabolic disruption under MP-induced stress, with significant ecological implications.}, } @article {pmid39642431, year = {2025}, author = {Bertini, F and Catania, V and Scirè Calabrisotto, L and Dara, M and Bisanti, L and La Corte, C and Staropoli, M and Piazzese, D and Parisi, MG and Parrinello, D and Cammarata, M}, title = {A multi-comprehensive approach to assess the responses of the Mediterranean mussel Mytilus galloprovincialis (Lamarck, 1919) to a simulation of a diesel-oil mixture spill.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {279}, number = {}, pages = {107188}, doi = {10.1016/j.aquatox.2024.107188}, pmid = {39642431}, issn = {1879-1514}, mesh = {Animals ; *Mytilus/drug effects ; *Water Pollutants, Chemical/toxicity ; *Petroleum Pollution/adverse effects ; *Hemolymph/drug effects ; Biomarkers/metabolism ; Hydrocarbons/toxicity ; Phagocytosis/drug effects ; Gasoline/toxicity ; Microbiota/drug effects ; }, abstract = {Oil spills are a major cause of pollution impacting marine ecosystems. In this work, the effects of short-term exposure to three different concentrations of a hydrocarbon mixture (HC), that simulated the action of such an event, were investigated on Mytilus galloprovincialis specimens. Physiological effects were measured using a battery of biomarkers consisting of cellular activity (phagocytosis), immune-related enzymes, chaperonins (HSP70 and HSC70), and histomorphological alterations. Different concentrations of HC led to a significant decrease in phagocytosis, especially following high concentrations. Immune-related enzymes evaluated in hemolymph and digestive gland extract showed up-regulation, suggesting the activation of antioxidant, detoxicant, and inflammatory responses. Morphological alterations of digestive gland tubules were observed after exposure to the HC. HSP70 and HSC70 activity was up regulated following the treatments, indicating their involvement in maintaining organism homeostasis. In addition, the diversity and composition of hemolymph and digestive gland microbiota exposed to HC were analyzed by automated ribosomal intergenic spacer analysis (ARISA) and a Next Generation Sequencing (NGS) approach to evaluate the connection with hydrocarbon contamination. Metagenomic analysis revealed significant differences in the hemolymph and digestive gland microbiota composition between mussels exposed and unexposed to HC. Exposure to increasing HC concentrations had a positive effect on microbial diversity with clear adaptative responses, and an increase in the relative abundance of several known degrading bacterial genera, including Alcanivorax, Roseovarius, Pseudomonas, Vibrio, Oleibacter. These results show the utility of a multi-comprehensive approach to evaluating functional adaptation in terms of immunological dysfunctions and microbiota alteration in the sentinel organism M. galloprovincialis.}, } @article {pmid39641861, year = {2024}, author = {Leung, HKM and Lo, EKK and Chen, C and Zhang, F and Felicianna, and Ismaiah, MJ and El-Nezami, H}, title = {Probiotic Mixture Attenuates Colorectal Tumorigenesis in Murine AOM/DSS Model by Suppressing STAT3, Inducing Apoptotic p53 and Modulating Gut Microbiota.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {39641861}, issn = {1867-1314}, abstract = {Colorectal cancer (CRC) is one of the most common cancers worldwide. The standard CRC chemo drug, 5-Fluorouracil (5-FU), has a poor response rate and chemoresistance, prompting the need for a more effective and affordable treatment. In this study, we aimed to evaluate whether Prohep, a novel probiotic mixture, would alleviate azoxymethane/dextran sodium sulfate (AOM/DSS)-induced colorectal tumorigenesis and enhance 5-FU efficacy and its mechanism. Our results suggested that Prohep showed stronger anti-tumorigenesis effects than 5-FU alone or when combined in the AOM/DSS model. Prohep significantly reduced the total tumor count, total tumor size, caecum weight, colonic crypt depth, colonic inflammation, and collagen fibrosis. Prohep downregulated pro-inflammatory TNF-α and proliferative p-STAT3 and upregulated apoptotic p53. Metagenomics analysis indicated that Prohep-enriched Helicobacter ganmani, Desulfovibrio porci, Helicobacter hepaticus, and Candidatus Borkfalkia ceftriaxoniphila were inversely correlated to the total tumor count. In addition, Prohep-enriched Prevotella sp. PTAC and Desulfovibrio porci were negatively correlated to AOM/DSS enriched bacteria, while forming a co-existing community with other beneficial bacteria. From KEGG analysis, Prohep downregulated CRC-related pathways and enhanced pathways related to metabolites suppressing CRC like menaquinone, tetrapyrrole, aminolevulinic acid, and tetrahydrofolate. From Metacyc analysis, Prohep downregulated CRC-related peptidoglycan, LPS, and uric acid biosynthesis, and conversion. Prohep elevated the biosynthesis of the beneficial L-lysine, lipoic acid, pyrimidine, and palmitate. Prohep also elevated metabolic pathways related to energy utilization of lactic acid-producing bacteria (LAB) and acetate producers. Similarly, fecal acetate concentration was upregulated by Prohep. To sum up, Prohep demonstrated exceptional anti-tumorigenesis effects in the AOM/DSS model, which revealed its potential to develop into a novel CRC therapeutic in the future.}, } @article {pmid39641605, year = {2025}, author = {Bao, Z and Chen, B and Yu, K and Wei, Y and Liang, X and Yao, H and Liao, X and Xie, W and Yin, K}, title = {Microbiome dynamics and functional profiles in deep-sea wood-fall micro-ecosystem: insights into drive pattern of community assembly, biogeochemical processes, and lignocellulose degradation.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {1}, pages = {e0216524}, pmid = {39641605}, issn = {1098-5336}, support = {42090041, 42030502//MOST | National Natural Science Foundation of China (NSFC)/ ; 42306165//MOST | National Natural Science Foundation of China (NSFC)/ ; No. 2023JJB150027//| Natural Science Foundation of Guangxi Zhuang Autonomous Region (Guangxi Natural Science Foundation)/ ; No. 311022005//Innovation Group Project of Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2021SP204, SML2023SP215, SML2023SP218, SML2023SP205//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; }, mesh = {*Lignin/metabolism ; *Wood/microbiology/metabolism ; *Microbiota ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Fungi/genetics/classification/metabolism ; *Seawater/microbiology ; China ; Ecosystem ; Geologic Sediments/microbiology ; }, abstract = {Wood-fall micro-ecosystems contribute to biogeochemical processes in the oligotrophic deep ocean. However, the community assembly processes and biogeochemical functions of microbiomes in wood fall remain unclear. This study investigated the diversity, community structure, assembly processes, and functional profiles of bacteria and fungi in a deep-sea wood fall from the South China Sea using physicochemical indices, amplicon sequencing, and metagenomics. The results showed that distinct wood-fall contact surfaces exhibit habitat heterogeneity. The bacterial community of all contact surfaces and the fungal community of seawater contact surface (SWCS) were affected by homogeneous selection. In SWCS and transition region (TR), bacterial communities were influenced by dispersal limitation, whereas fungal communities were affected by homogenizing dispersal. The Venn diagram visualization revealed that the shared fungal community between SWCS and TR was dominated by Aspergillaceae. Additionally, the bacterial community demonstrated a higher genetic potential for sulfur, nitrogen, and methane metabolism than fungi. The sediment contact surface enriched modules were associated with dissimilatory sulfate reduction and methanogenesis, whereas the modules related to nitrate reduction exhibited enrichment characteristics in TR. Moreover, fungi showed a stronger potential for lignocellulase production compared to bacteria, with Microascaceae and Nectriaceae identified as potential contributors to lignocellulose degradation. These results indicate that environmental filtering and organism exchange levels regulated the microbial community assembly of wood fall. The biogeochemical cycling of sulfur, nitrogen, and methane was mainly driven by the bacterial community. Nevertheless, the terrestrial fungi Microascaceae and Nectriaceae might degrade lignocellulose via the combined action of multiple lignocellulases.IMPORTANCEThe presence and activity of microbial communities may play a crucial role in the biogeochemical cycle of deep-sea wood-fall micro-ecosystems. Previous studies on wood falls have focused on the microbiome diversity, community composition, and environmental impact, while few have investigated wood-fall micro-ecosystems by distinguishing among distinct contact surfaces. Our study investigated the microbiome dynamics and functional profiles of bacteria and fungi among distinct wood-fall contact surfaces. We found that the microbiome community assembly was regulated by environmental filtering and organism exchange levels. Bacteria drive the biogeochemical cycling of sulfur, nitrogen, and methane in wood fall through diverse metabolic pathways, whereas fungi are crucial for lignocellulose degradation. Ultimately, this study provides new insights into the driving pattern of community assembly, biogeochemical processes, and lignocellulose degradation in the microbiomes of deep-sea wood-fall micro-ecosystems, enhancing our comprehension of the ecological impacts of organic falls on deep-sea oligotrophic environments.}, } @article {pmid39641169, year = {2025}, author = {Yang, J and Lei, OK and Bhute, S and Kris-Etherton, PM and Lichtenstein, AH and Matthan, NR and Petersen, KS and Sabaté, J and Reboussin, DM and Lovato, L and Vitolins, MZ and Rajaram, S and Jacobs, JP and Huang, J and Taw, M and Yang, S and Li, Z}, title = {Impact of daily avocado consumption on gut microbiota in adults with abdominal obesity: an ancillary study of HAT, a randomized controlled trial.}, journal = {Food & function}, volume = {16}, number = {1}, pages = {168-180}, doi = {10.1039/d4fo03806a}, pmid = {39641169}, issn = {2042-650X}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Persea ; Female ; Male ; Adult ; Middle Aged ; *Obesity, Abdominal/diet therapy/metabolism/microbiology ; Feces/microbiology ; Bacteria/classification/genetics/isolation & purification/metabolism ; Diet ; }, abstract = {Objectives: This study aimed to investigate short-term and long-term impact of avocado consumption without caloric restriction on the gut microbiota of free-living adults with abdominal obesity. Methods: The Habitual Diet and Avocado Trial (HAT) was a 26-week, multi-center, randomized, controlled trial involving 1008 individuals with abdominal obesity. Participants were randomly assigned to the Avocado Supplemented Diet Group (AVO), receiving one avocado per day, or the Habitual Diet group (HAB), maintaining their usual dietary habits. Fecal samples were collected at baseline, week 4 and week 26 from a subset of participants recruited at a University of California Los Angeles site (n = 230). Fecal microbiota was assessed with shotgun metagenomics sequencing. Alpha diversity was assessed using the Chao1 and Shannon indices; beta diversity was assessed using Bray-Curtis dissimilarity with significance determined by repeated measures permutational multivariat analysis of variance. Potential association of intervention at week 4 and 26 with alpha diversity, species and metabolic pathways was examined using linear mixed effect models. Results: Compared to the HAB group, the AVO group had higher alpha diversity by 4 weeks, which persisted through the 26-week study period. Exploratory analysis based on healthy eating index-2015 (HEI-2015) indicated that participants with a low HEI score at baseline (≤52.7), had an increase in alpha diversity in the AVO group vs. HAB group. The AVO group had a significant change in beta diversity at week 26 compared to the HAB group. At the species level, the AVO group had significantly increased Faecalibacterium prausnitzii and Bacterium AF16_15 at week 26 compared to the HAB group. Functional analysis showed no significant difference in metabolic pathways between the HAB and AVO groups. Conclusions: Our findings document a potentially favorable effect of avocados on gut microbiota diversity. The prebiotic potential of avocados is more pronounced in individuals with a low diet quality score. This trial is registered at clinicaltrials.gov as NCT03528031 (https://clinicaltrials.gov/study/NCT03528031).}, } @article {pmid39641037, year = {2024}, author = {Wang, F and Zhan, Q and Yu, A and Chen, H and Zhang, Y and Yang, Q and Qu, T}, title = {Mediastinitis caused by Mycoplasma hominis in immunocompetent patients: A case series report and literature review.}, journal = {Heliyon}, volume = {10}, number = {22}, pages = {e39763}, pmid = {39641037}, issn = {2405-8440}, abstract = {BACKGROUND: Mycoplasma hominis, a commensal organism, is potentially pathogenic; its role in postoperative infections might be underestimated in cardiac surgery.

RESULTS: We reported two cases of postoperative M. hominis mediastinitis in immunocompetent patients with a DeBakey grade I aortic dissecting aneurysm and reviewed 10 other cases previously described. Among the 10 reviewed cases and our two cases, 11 patients were men (median age, 59 years; median onset of clinical symptoms time, 14.5 d after surgery; and mean peak of temperature, 38.5 ± 0.8 °C). In our reports, two patients underwent sternotomy site reopening and debridement before diagnosis was confirmed. Diagnosis was confirmed by prolonged culture and by performing metagenomic next-generation sequencing directly using the clinical samples. M. hominis was difficult to cover with initial empirical antibiotic therapy; the patient in this study showed complete improvement with long-term antimicrobial therapy. The targeted treatment duration for surviving patients among the reviewed cases ranged from three weeks to 16 months.

CONCLUSIONS: The diagnosis of extragenital M. hominis infections is difficult. Therefore, the role of M. hominis as a cause of postoperative infections during cardiac surgery should be considered. Diagnosis requires molecular techniques to complement culture.}, } @article {pmid39640900, year = {2024}, author = {Pahirah, N and Narkwichean, A and Taweechotipatr, M and Wannaiampikul, S and Duang-Udom, C and Laosooksathit, W}, title = {Comparison of Gut Microbiomes Between Neonates Born by Cesarean Section and Vaginal Delivery: Prospective Observational Study.}, journal = {BioMed research international}, volume = {2024}, number = {}, pages = {8302361}, pmid = {39640900}, issn = {2314-6141}, mesh = {Humans ; *Cesarean Section ; *Gastrointestinal Microbiome ; Infant, Newborn ; Female ; Prospective Studies ; *Delivery, Obstetric ; Pregnancy ; *RNA, Ribosomal, 16S/genetics ; Male ; Feces/microbiology ; Thailand ; Bifidobacterium ; }, abstract = {Background: Balanced diversity and abundance of gut microbiome play important roles in human health, including neonatal health. Though not established, there is evidence that the delivery route could alter the diversity of neonatal gut microbiomes. Objective: The objective of the study was to investigate the differences in the gut microbiomes of neonates delivered via cesarean section compared to those born by vaginal delivery and to identify the predominant microbial taxa present in each group. Study Design: A prospective observational study of 281 healthy neonates born between February 2021 and April 2023 at Her Royal Highness Maha Chakri Sirindhorn Medical Center, Srinakharinwirot University, Thailand, was performed. The study population was divided into two groups: 139 neonates born via vaginal delivery and 141 neonates born via cesarean section. The microbiota composition of each neonate's fecal sample was identified by using 16S ribosomal ribonucleic acid metagenomic sequencing. Results: Neonates delivered vaginally exhibited a gut microbiome with higher abundance and diversity than those delivered by cesarean delivery. Bifidobacterium was the dominant genus in both groups. Bifidobacterium breve was the dominant species and was significantly higher in cesarean-delivered neonates compared to those delivered vaginally (24.0% and 9.2%, respectively) (p < 0.001). However, the taxonomy of only 89 (64.0%) and 44 (31.43%) fecal samples could be identified from the vaginal and cesarean delivery groups, respectively. Conclusion: Route of delivery is associated with neonatal gut microbiome abundance and diversity. Neonates delivered via vaginal delivery exhibited higher diversity but lower abundance of the dominant species in the gut microbiome. Trial Registration: Thai Clinical Trials Registry identifier: TCTR20221024003.}, } @article {pmid39639912, year = {2024}, author = {Balingit, AK and Grande, PG and Nicolasora, AD and Polotan, FG and Pantoni, RA and Abulencia, MF and Chu, MYJ and Rivera, N and Oblepias, MS and Garcia, J}, title = {Clinical presentation and molecular diagnosis of a possible Mpox virus and Varicella zoster virus co-infection in an adult immunocompetent Filipino: a case report.}, journal = {Frontiers in public health}, volume = {12}, number = {}, pages = {1387636}, pmid = {39639912}, issn = {2296-2565}, mesh = {Adult ; Female ; Humans ; Chickenpox/diagnosis ; *Coinfection/diagnosis ; *Herpesvirus 3, Human/isolation & purification/genetics ; Philippines ; Switzerland ; Travel ; Varicella Zoster Virus Infection/diagnosis/complications ; *Mpox, Monkeypox/complications/diagnosis ; }, abstract = {We report the first travel-related case of a possible Mpox-Varicella zoster virus (VZV) co-infection in the Philippines, a country that is endemic for Varicella but non-endemic for Mpox. A 29-year-old Filipino, female, with a travel history to Switzerland and with no prior history of VZV infection sought consultation due to rashes. She presented with multiple papular, pustular, and vesicular skin lesions, some with umbilication and with irregular borders, on the face, neck, trunk, inguinal area, upper extremities, and right leg. She also had bilateral submandibular and post-auricular lymphadenopathies. Tzanck smear exhibited viral cytopathic effects. She tested positive for Mpox infection (Clade II) and Varicella infection via quantitative real-time polymerase chain reaction (qPCR) tests but with a high CT value obtained from the Mpox PCR. Shotgun metagenomic sequencing (mNGS) successfully recovered sequences from the Varicella zoster virus which corroborated with the high viral load detected using qPCR. In contrast, shotgun mNGS was not able to generate a Mpox consensus sequence due to very few reads mapped to the Mpox virus reference sequence, which raised the question if there was the presence of a true Mpox-Varicella co-infection in our patient. Nevertheless, systemic and topical acyclovir was given to the patient. She was discharged and continued home isolation for 30 days from the rash onset. Strategies have been formed by the country's healthcare facilities to properly identify Mpox infection. However, Mpox co-infection with other viral diseases presented a challenge in the proper diagnosis of our patient. This prompted a high index of suspicion and the usage of suitable diagnostic tests. With proper clinical evaluation and utilization of appropriate diagnostic tests, we were able to diagnose the first Filipino patient with a possible Mpox and Varicella zoster virus co-infection.}, } @article {pmid39639673, year = {2024}, author = {Wynne, JW and English, CJ and Vannetti, SM and Rigby, M and Quezada-Rodriguez, PR and Knüsel, R and Huynh, C and Schmidt-Posthaus, H}, title = {18S rRNA Metagenomic Analysis of Nodular Gill Disease in Swiss Rainbow Trout (Oncorhynchus mykiss).}, journal = {Journal of fish diseases}, volume = {}, number = {}, pages = {e14061}, doi = {10.1111/jfd.14061}, pmid = {39639673}, issn = {1365-2761}, support = {//CSIRO Julius Career Award/ ; //European Association of Fish Pathologists Small Grant Scheme/ ; //Swiss Food Safety and Veterinary Office/ ; //the Swiss Food Safety and Veterinary Office/ ; }, abstract = {Nodular gill disease (NGD) is a serious proliferative gill condition that affects farmed salmonids, particularly in Europe. While the cause of NGD remains unknown (and maybe multifactorial), various amoebae are often isolated from the gills of affected fish and can in some cases be seen associated with lesions by histopathology. The present study aimed to quantify the abundance of different amoeba species directly from the gills of rainbow trout affected by NGD and healthy controls. An 18S rRNA amplicon metagenomic approach was employed to profile the diversity and abundance of micro-eukaryotes (including amoebae) while suppressing the amplification of host DNA using a salmonid-specific C3 spacer blocking primer. The 18S rRNA metagenomics approach identified a diversity of micro-eukaryotes on the gills of rainbow trout, including the phylum's Amoebozoa, Diatomea, Platyhelminthes and Ciliophora. Rainbow trout clinically affected by NGD had a significantly higher abundance of a specific sequence (zOTU2) classified as Vannella sp. compared to healthy controls. A quantitative PCR assay was then developed and validated which accurately quantified the abundance of this Vannella sp. sequence from a NGD outbreak in a Swiss rainbow trout farm. Additional PCR and Sanger sequencing analysis of the zOTU2 sequence demonstrated that this sequence is most likely derived from Vannella mustalahtiana. Our study highlights the potential role of Vannella mustalahtiana in NGD in Switzerland and further describes a specific and validated diagnostic PCR assay for accurate detection of this Vannella species.}, } @article {pmid39639495, year = {2024}, author = {Alanzi, AR}, title = {Exploring Microbial Dark Matter for the Discovery of Novel Natural Products: Characteristics, Abundance Challenges and Methods.}, journal = {Journal of microbiology and biotechnology}, volume = {35}, number = {}, pages = {e2407064}, pmid = {39639495}, issn = {1738-8872}, mesh = {*Biological Products/metabolism ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Phylogeny ; Microbiota ; }, abstract = {The objective of this review is to investigate microbial dark matter (MDM) with a focus on its potential for discovering novel natural products (NPs). This first part will examine the characteristics and abundance of these previously unexplored microbial communities, as well as the challenges faced in identifying and harnessing their unique biochemical properties and novel methods in this field. MDMs are thought to hold great potential for the discovery of novel NPs, which could have significant applications in medicine, agriculture, and industry. In recent years, there has been a growing interest in exploring MDM to unlock its potential. In fact, developments in genome-sequencing technologies and sophisticated phylogenetic procedures and metagenomic techniques have contributed to drastically make important changes in our sights on the diversity of microbial life, including the very outline of the tree of life. This has led to the development of novel technologies and methodologies for studying these elusive microorganisms, such as single-cell genomics, metagenomics, and culturomics. These approaches enable researchers to isolate and analyze individual microbial cells, as well as entire communities, providing insights into their genetic and metabolic potential. By delving into the MDM, scientists hope to uncover new compounds and biotechnological advancements that could have far-reaching impacts on various fields.}, } @article {pmid39639405, year = {2024}, author = {Nechalová, L and Bielik, V and Hric, I and Babicová, M and Baranovičová, E and Grendár, M and Koška, J and Penesová, A}, title = {Gut microbiota and metabolic responses to a 12-week caloric restriction combined with strength and HIIT training in patients with obesity: a randomized trial.}, journal = {BMC sports science, medicine & rehabilitation}, volume = {16}, number = {1}, pages = {239}, pmid = {39639405}, issn = {2052-1847}, support = {UK/213/2022//Grant mladých UK/ ; APVV-17-0099//Agentúra na Podporu Výskumu a Vývoja/ ; VEGA 1/0260/21//Vedecká Grantová Agentúra MŠVVaŠ SR a SAV/ ; VEGA 2/0129/20//Vedecká Grantová Agentúra MŠVVaŠ SR a SAV/ ; }, abstract = {BACKGROUND: Nowadays, obesity has become a major health issue. In addition to negatively affecting body composition and metabolic health, recent evidence shows unfavorable shifts in gut microbiota in individuals with obesity. However, the effects of weight loss on gut microbes and metabolites remain controversial. Therefore, the purpose of this study was to investigate the effects of a 12-week program on gut microbiota and metabolic health in patients with obesity.

METHODS: We conducted a controlled trial in 23 male and female patients with obesity. Twelve participants completed a 12-week program of caloric restriction combined with strength and HIIT training (INT, pre-BMI 37.33 ± 6.57 kg/m[2]), and eleven participants were designated as non-intervention controls (pre-BMI 38.65 ± 8.07 kg/m[2]). Metagenomic sequencing of the V3-V4 region of the 16S rDNA gene from fecal samples allowed for gut microbiota classification. Nuclear magnetic resonance spectroscopy characterized selected serum and fecal metabolite concentrations.

RESULTS: Within INT, we observed a significant improvement in body composition; a significant decrease in liver enzymes (AST, ALT, and GMT); a significant increase in the relative abundance of the commensal bacteria (e.g., Akkermansia muciniphila, Parabacteroides merdae, and Phocaeicola vulgatus); and a significant decrease in the relative abundance of SCFA-producing bacteria (e.g., the genera Butyrivibrio, Coprococcus, and Blautia). In addition, significant correlations were found between gut microbes, body composition, metabolic health biomarkers, and SCFAs. Notably, the Random Forest Machine Learning analysis identified predictors (Butyrivibrio fibrisolvens, Blautia caecimuris, Coprococcus comes, and waist circumference) with a moderate ability to discriminate between INT subjects pre- and post-intervention.

CONCLUSIONS: Our results indicate that a 12-week caloric restriction combined with strength and HIIT training positively influences body composition, metabolic health biomarkers, gut microbiota, and microbial metabolites, demonstrating significant correlations among these variables. We observed a significant increase in the relative abundance of bacteria linked to obesity, e.g., Akkermansia muciniphila. Additionally, our study contributes to the ongoing debate about the role of SCFAs in obesity, as we observed a significant decrease in SCFA producers after a 12-week program.

TRIAL REGISTRATION: The trial was registered on [05/12/2014] with ClinicalTrials.gov (No: NCT02325804).}, } @article {pmid39639355, year = {2024}, author = {Benga, L and Rehm, A and Gougoula, C and Westhoff, P and Wachtmeister, T and Benten, WPM and Engelhardt, E and Weber, APM and Köhrer, K and Sager, M and Janssen, S}, title = {The host genotype actively shapes its microbiome across generations in laboratory mice.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {256}, pmid = {39639355}, issn = {2049-2618}, mesh = {Animals ; Mice ; Female ; *Genotype ; *Mice, Inbred BALB C ; *Mice, Inbred C57BL ; *Microbiota ; Male ; Maternal Inheritance ; Embryo, Mammalian/microbiology ; Host Microbial Interactions ; Pregnancy ; }, abstract = {BACKGROUND: The microbiome greatly affects health and wellbeing. Evolutionarily, it is doubtful that a host would rely on chance alone to pass on microbial colonization to its offspring. However, the literature currently offers only limited evidence regarding two alternative hypotheses: active microbial shaping by host genetic factors or transmission of a microbial maternal legacy.

RESULTS: To further dissect the influence of host genetics and maternal inheritance, we collected two-cell stage embryos from two representative wild types, C57BL6/J and BALB/c, and transferred a mixture of both genotype embryos into hybrid recipient mice to be inoculated by an identical microbiome at birth.

CONCLUSIONS: Observing the offspring for six generations unequivocally emphasizes the impact of host genetic factors over maternal legacy in constant environments, akin to murine laboratory experiments. Interestingly, maternal legacy solely controlled the microbiome in the first offspring generation. However, current evidence supporting maternal legacy has not extended beyond this initial generation, resolving the aforementioned debate. Video Abstract.}, } @article {pmid39639243, year = {2024}, author = {Li, J and Pan, D and Guo, Y and Zhang, B and Lu, X and Deng, C and Xu, F and Lv, Z and Chen, Q and Zheng, Y and Nong, S and Su, L and Qin, R and Jiang, F and Gai, W and Qin, G}, title = {Clinical application value of simultaneous plasma and bronchoalveolar lavage fluid metagenomic next generation sequencing in patients with pneumonia-derived sepsis.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {1393}, pmid = {39639243}, issn = {1471-2334}, mesh = {Humans ; *Bronchoalveolar Lavage Fluid/microbiology ; Male ; Female ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing ; *Sepsis/diagnosis/microbiology/mortality ; Middle Aged ; Aged ; *Metagenomics/methods ; Pneumonia/microbiology/diagnosis ; Intensive Care Units ; Prognosis ; Bacteria/isolation & purification/genetics/classification ; }, abstract = {BACKGROUND: Despite the increasing use of metagenomic next-generation sequencing (mNGS) in sepsis, identifying clinically relevant pathogens remains challenging. This study was aimed to evaluate the clinical utility of simultaneous plasma and bronchoalveolar lavage fluid (BALF) detection using mNGS.

METHODS: This retrospective study enrolled 95 patients with pneumonia-derived sepsis (PDS) admitted to the intensive care unit (ICU) between October 2021 and January 2023. Patients were divided into two groups: mNGS group (n = 60) and the non-mNGS group (n = 35), based on whether simultaneous plasma and BALF mNGS were conducted. All patients underwent conventional microbiological tests (CMT), including bacterial/fungal culture of peripheral blood and BALF, as well as sputum culture, detection of 1, 3-beta-D- glucan in BALF and RT-PCR testing. The clinical data of the enrolled patients were collected, and the detection performance and prognosis of plasma mNGS, BALF mNGS and CMT were compared.

RESULTS: The mNGS group exhibited a lower mortality rate than the non-mNGS group (35.0% vs. 57.1%, P = 0.034). Simultaneous detection in dual-sample resulted in a higher proportion of microorganisms identified as definite causes of sepsis alert compared to detection in either plasma or BALF alone (55.6% vs. 20.8% vs. 18.8%, P<0.001). Acinetobacter baumannii, Stenotrophomonas maltophilia, Candida albicans, and human mastadenovirus B were the primary strains responsible for infections in PDS patients. Patients with lower white blood cells and neutrophil indices had a greater consistency in dual-sample mNGS. Patients in the mNGS group had more antibiotic adjustments compared to the non-mNGS group (85.71% vs. 33.33%, P<0.001). The percentage of neutrophils was a risk factor for mortality in PDS patients (P = 0.002).

CONCLUSION: Dual sample mNGS has the advantage of detecting and determining the pathogenicity of more pathogens and has the potential to improve the prognosis of patients with PDS.}, } @article {pmid39639163, year = {2025}, author = {Taglialegna, A}, title = {Metagenomics for drug discovery.}, journal = {Nature reviews. Microbiology}, volume = {23}, number = {2}, pages = {67}, pmid = {39639163}, issn = {1740-1534}, } @article {pmid39639104, year = {2025}, author = {Knuth, MM and Campos, CV and Smith, K and Hutchins, EK and Lewis, S and York, M and Coghill, LM and Franklin, C and MacFarlane, AJ and Ericsson, AC and Magnuson, T and Ideraabdullah, F}, title = {Timing of standard chow exposure determines the variability of mouse phenotypic outcomes and gut microbiota profile.}, journal = {Lab animal}, volume = {54}, number = {1}, pages = {24-36}, pmid = {39639104}, issn = {1548-4475}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Mice, Inbred C57BL ; Male ; Mice ; Female ; *Diet/veterinary ; Phenotype ; Time Factors ; Animal Feed/analysis ; }, abstract = {Standard chow diets influence reproducibility in animal model experiments because chows have different nutrient compositions, which can independently influence phenotypes. However, there is little evidence of the role of timing in the extent of variability caused by chow exposure. Here we measured the impact of different diets (5V5M, 5V0G, 2920X and 5058) and timing of exposure (adult exposure (AE), lifetime exposure (LE) and developmental exposure (DE)) on growth and development, metabolic health indicators and gut bacterial microbiota profiles across genetically identical C57BL/6J mice. Diet drove differences in macro- and micronutrient intake for all exposure models. AE had no effect on phenotypic outcomes. However, LE mice exhibited significant sex-dependent diet effects on growth, body weight and body composition. LE effects were mostly absent in the DE model, where mice were exposed to chow differences only from conception to weaning. Both AE and LE models exhibited similar diet-driven beta diversity profiles for the gut bacterial microbiota, with 5058 diet driving the most distinct profile. However, compared with AE, LE effects on beta diversity were sex dependent, and LE mice exhibited nine times more differentially abundant bacterial genera, the majority of which were inversely affected by 2920X and 5058 diets. Our findings demonstrate that LE to different chow diets has the greatest impact on the reproducibility of several experimental measures commonly used in preclinical mouse model studies. Importantly, weaning mice from different diets onto the same diet for maturation may be an effective way to reduce unwanted phenotypic variability among experimental models.}, } @article {pmid39638008, year = {2025}, author = {Liu, LY and Dang, CC and Tan, X and Liu, BF and Lu, Y and Zhao, ZC and Wang, X and Wang, XW and Xing, DF and Ren, NQ and Xie, GJ}, title = {Thermophilic anaerobic ethane oxidation coupled with selenate and selenite reduction.}, journal = {Bioresource technology}, volume = {418}, number = {}, pages = {131934}, doi = {10.1016/j.biortech.2024.131934}, pmid = {39638008}, issn = {1873-2976}, mesh = {*Oxidation-Reduction ; *Selenic Acid/metabolism ; *Ethane/metabolism ; Anaerobiosis ; *Selenious Acid/metabolism ; *Selenium Compounds/metabolism/chemistry ; Biodegradation, Environmental ; }, abstract = {Anaerobic microorganisms are critical in regulating ethane in geothermal environments, where selenate and selenite are common contaminants. Although coupling ethane oxidation with selenate reduction has been demonstrated as feasible, such processes remain poorly explored in geothermal environments. This study addressed this gap by successfully enriching thermophilic anaerobic cultures capable of coupling ethane oxidation with selenate/selenite reduction, achieving selenate and selenite removal rate of 2.7 mg Se/L/d and 2.1 mg Se/L/d, respectively. Metagenomic analysis revealed a novel genus 'Candidatus Ethanivorans selenatireducens', which accounted for 16.0 % and 32.6 % of microbial communities in selenate- and selenite-dependent systems, respectively. This microorganism encoded pathways for anaerobic ethane oxidation via fumarate addition and genes required for the sequential reduction of selenate to elemental selenium. These findings unveiled a novel microbial mechanism linking ethane oxidation and selenate reduction in geothermal systems, providing new insights into the biogeochemical interaction between carbon and selenium in thermophilic environments.}, } @article {pmid39637857, year = {2024}, author = {Vaher, K and Cabez, MB and Parga, PL and Binkowska, J and van Beveren, GJ and Odendaal, ML and Sullivan, G and Stoye, DQ and Corrigan, A and Quigley, AJ and Thrippleton, MJ and Bastin, ME and Bogaert, D and Boardman, JP}, title = {The neonatal gut microbiota: A role in the encephalopathy of prematurity.}, journal = {Cell reports. Medicine}, volume = {5}, number = {12}, pages = {101845}, pmid = {39637857}, issn = {2666-3791}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics/physiology ; Infant, Newborn ; Female ; Male ; *Infant, Premature ; Feces/microbiology ; Brain/pathology/microbiology ; Brain Diseases/microbiology/pathology ; Gestational Age ; Magnetic Resonance Imaging/methods ; Premature Birth/microbiology ; }, abstract = {Preterm birth correlates with brain dysmaturation and neurocognitive impairment. The gut microbiome associates with behavioral outcomes in typical development, but its relationship with neurodevelopment in preterm infants is unknown. We characterize fecal microbiome in a cohort of 147 neonates enriched for very preterm birth using 16S-based and shotgun metagenomic sequencing. Delivery mode strongly correlates with the preterm microbiome shortly after birth. Low birth gestational age, infant sex assigned at birth, and antibiotics associate with microbiome composition at neonatal intensive care unit discharge. We integrate these data with term-equivalent structural and diffusion brain MRI. Bacterial community composition associates with MRI features of encephalopathy of prematurity. Particularly, abundances of Escherichia coli and Klebsiella spp. correlate with microstructural parameters in deep and cortical gray matter. Metagenome functional capacity analyses suggest that these bacteria may interact with brain microstructure via tryptophan and propionate metabolism. This study indicates that the gut microbiome associates with brain development following preterm birth.}, } @article {pmid39637856, year = {2025}, author = {Caty, SN and Alvarez-Buylla, A and Vasek, C and Tapia, EE and Martin, NA and McLaughlin, T and Golde, CL and Weber, PK and Mayali, X and Coloma, LA and Morris, MM and O'Connell, LA}, title = {Alkaloids are associated with increased microbial diversity and metabolic function in poison frogs.}, journal = {Current biology : CB}, volume = {35}, number = {1}, pages = {187-197.e8}, doi = {10.1016/j.cub.2024.10.069}, pmid = {39637856}, issn = {1879-0445}, mesh = {Animals ; *Alkaloids/metabolism ; *Microbiota ; *Anura/microbiology/metabolism ; Skin/microbiology/metabolism ; Bacteria/metabolism/classification/genetics/isolation & purification ; Poison Frogs ; }, abstract = {Shifts in host-associated microbiomes can impact both host and microbes.[1][,][2][,][3][,][4][,][5][,][6] It is of interest to understand how perturbations, like the introduction of exogenous chemicals,[7][,][8][,][9][,][10][,][11][,][12][,][13] impact microbiomes. In poison frogs (family Dendrobatidae), the skin microbiome is exposed to alkaloids that the frogs sequester for defense.[14][,][15][,][16][,][17][,][18][,][19] These alkaloids are antimicrobial[20][,][21][,][22]; however, their effect on the frogs' skin microbiome is unknown. To test this, we characterized microbial communities from field-collected dendrobatid frogs. Then, we conducted a laboratory experiment to monitor the effect of the alkaloid decahydroquinoline (DHQ) on the microbiome of two frog species with contrasting alkaloid loads in nature. In both datasets, we found that alkaloid-exposed microbiomes were more phylogenetically diverse, with an increase in diversity among rare taxa. To better understand the isolate-specific response to alkaloids, we cultured microbial isolates from poison frog skin and found that many isolates exhibited enhanced growth or were not impacted by the addition of DHQ. To further explore the microbial response to alkaloids, we sequenced the metagenomes from high- and low-alkaloid frogs and observed a greater diversity of genes associated with nitrogen and carbon metabolism in high-alkaloid frogs. From these data, we hypothesized that some strains may metabolize the alkaloids. We used stable isotope tracing coupled to nanoSIMS (nanoscale secondary ion mass spectrometry), which supported the idea that some of these isolates are able to metabolize DHQ. Together, these data suggest that poison frog alkaloids open new niches for skin-associated microbes with specific adaptations, such as alkaloid metabolism, that enable survival in this environment.}, } @article {pmid39637791, year = {2025}, author = {Xue, W and Zhang, S and Younas, F and Ma, R and Yu, X and Li, J and Wu, X and Liu, W and Duan, H and Wang, K and Cui, X and Cao, X and Cui, Z}, title = {The combined effects of tetracycline and glyphosate on growth and rhizosphere bacteria community in hulless barley over the whole growth period.}, journal = {Journal of hazardous materials}, volume = {484}, number = {}, pages = {136706}, doi = {10.1016/j.jhazmat.2024.136706}, pmid = {39637791}, issn = {1873-3336}, mesh = {*Hordeum/drug effects/growth & development/microbiology ; *Glyphosate ; *Glycine/analogs & derivatives/toxicity ; *Rhizosphere ; *Tetracycline/toxicity ; *Soil Microbiology ; Soil Pollutants/toxicity ; Herbicides/toxicity ; Bacteria/drug effects/genetics/metabolism/growth & development ; Hydrogen Peroxide/metabolism ; Plant Roots/drug effects/growth & development/microbiology ; Anti-Bacterial Agents/toxicity ; }, abstract = {The toxic effects of tetracycline and glyphosate on hulless barley and its environment, as well as their interrelationship, remain poorly understood. The present study aimed to identify biomarkers reflective of tetracycline and glyphosate toxicity, examine root damage and rhizosphere bacterial communities throughout the growth cycle, and assess the final grain quality. Results indicated that the hydrogen peroxide (H2O2) content in the underground parts of barley could serve as a sensitive biomarker for detecting tetracycline and glyphosate toxicity in barley. In addition, a synergistic effect between 5 mg/kg tetracycline and 5 mg/kg glyphosate was observed at the tillering stage, which not only induced H2O2 accumulation across all growth stages but also ultimately reduced seed quality. During the tillering phase, Proteobacteria dominanted, while Actinobacteria showed greater relative abundance during the jointing stage.By the ripening stage, Acidobacteria predominantly colonized the associated soils. Importantly, the study further identified metagenome-assembled genomes containing cytochrome P450 fragments capable of metabolizing these compounds. This study provides novel insights into the transformation of co-contaminants and the adaptive responses of rhizobacteria to tetracycline and glyphosate exposure, offering valuable information for agricultural practices.}, } @article {pmid39637780, year = {2025}, author = {Huang, C and Cui, M and Li, T and Zheng, C and Qiu, M and Shan, M and Li, B and Zhang, L and Yu, Y and Fang, H}, title = {Migration of fungicides, antibiotics and resistome in the soil-lettuce system.}, journal = {Journal of hazardous materials}, volume = {484}, number = {}, pages = {136725}, doi = {10.1016/j.jhazmat.2024.136725}, pmid = {39637780}, issn = {1873-3336}, mesh = {*Fungicides, Industrial/pharmacology/toxicity ; *Soil Microbiology ; *Anti-Bacterial Agents/pharmacology ; *Lactuca/microbiology/drug effects ; Bacteria/drug effects/genetics ; Gene Transfer, Horizontal ; Soil Pollutants/toxicity ; Genes, Bacterial ; }, abstract = {The emergence and spread of antibiotic resistance genes (ARGs) have become a serious issue in global agricultural production. However, understanding how these ARGs spread across different spatial scales, especially when exposed to both pesticides and antibiotics, has remained a challenge. Here, metagenomic assembly and binning methodologies were used to determine the spread pathway of ARGs in the soil-lettuce system under individual and combined exposure of fungicides (carbendazim and pyraclostrobin) and antibiotics (chlortetracycline and ciprofloxacin). These agrochemicals not only facilitated the spread of ARGs from soil to lettuce but also significantly elevated the risk of developing multi-antibiotic resistance among bacteria, especially to some antibiotic types (i.e. sulfonamide, aminoglycoside, quinolone, and tetracycline). ARGs could be migrated through distinct pathways, including both vertical and horizontal gene transfer, with plasmids playing a crucial role in facilitating the horizontal gene transfer. These transfer pathways have enabled key pathogenic bacteria belonging to the genera Acinetobacter, Pseudomonas, and Pantoea to acquire resistance and remain recalcitrant, posing the potential risk to crop health and food safety. In summary, our findings highlighted that fungicide and antibiotic could drive upward migration of ARGs in the soil-lettuce system and reduced the quality safety of agricultural products.}, } @article {pmid39637691, year = {2025}, author = {Yan, J and Zhang, X and Shi, X and Wu, J and Zhou, Z and Tang, Y and Bao, Z and Luo, N and Zhang, D and Chen, J and Zhang, H}, title = {Metagenomic insights into the rapid recovery mechanisms of prokaryotic community and spread of antibiotic resistance genes after seawater disinfection.}, journal = {Water research}, volume = {271}, number = {}, pages = {122887}, doi = {10.1016/j.watres.2024.122887}, pmid = {39637691}, issn = {1879-2448}, mesh = {*Seawater/microbiology ; *Disinfection ; *Drug Resistance, Microbial/genetics ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/drug effects ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; Disinfectants/pharmacology ; Genes, Bacterial ; }, abstract = {Disinfectants, such as bleaching powder, are widely employed in marine aquaculture worldwide to control the bacterial pathogens and eliminate antibiotic resistance genes (ARGs). Nevertheless, the rapid recovery of prokaryotic community compositions (PCCs) after disinfection may significantly influence the overall efficacy of disinfection. Presently, little is known about the rapid recovery mechanisms of PCCs and its impact on the removal of ARGs in seawater. In this study, 16S rRNA gene sequencing and metagenomic analysis were used to address the above concerns through simulating the disinfection process in aquaculture. The results showed that recovery of PCCs began within 16 h. The underlying mechanisms of the rapid recovery of PCCs were the synergistic interactions between microbes and the residues of disinfection-resistant bacteria (DRB). Disinfection resistance genes (DRGs) related to efflux pump serve as the primary molecular foundation providing DRB to resist disinfection. Among the 78 annotated ARGs, only 10 ARGs exhibited a significant decrease (P < 0.05) after 72 h, implying the ineffective removal of ARGs by bleaching powder. Furthermore, bacterial co-resistance to disinfectants and antibiotics was observed. Genome analysis of two highly resistant DRB from Pseudomonadaceae revealed that both DRB carried 16 DRGs, aiding the recovery of PCCs and the spread of ARGs. These findings provide novel insights in the mechanisms of the rapid recovery of PCCs and bacterial co-resistance to disinfectants and antibiotics, which can be crucial for the management of pathogens and antibiotic resistance in seawater.}, } @article {pmid39637538, year = {2024}, author = {Gu, T and Ni, Z and Zhao, Q and Li, R and Qiu, R and Zhang, WX}, title = {Control of arsenic methylation in paddy soils by iron nanoparticles.}, journal = {The Science of the total environment}, volume = {957}, number = {}, pages = {177828}, doi = {10.1016/j.scitotenv.2024.177828}, pmid = {39637538}, issn = {1879-1026}, mesh = {*Soil Pollutants/analysis ; *Iron/chemistry ; Methylation ; *Arsenic/analysis ; *Oryza ; *Soil/chemistry ; *Metal Nanoparticles ; Soil Microbiology ; }, abstract = {Rice, as the most essential food grain, is frequently exposed to high concentrations of arsenic. Among the arsenic species, dimethylarsenate (DMAs(V)) is preferentially translocated from paddy soils to rice grains, posing serious threats to food safety and yield. Herein, we report an efficient strategy for DMAs(V) mitigation in paddy soils with nanoscale Zero-Valent Iron (nZVI). Species and concentrations of arsenic in paddy porewater were monitored during a 28-d soil-water incubation. Effects of nZVI dose towards microbial sulfate reduction and methane generation potential in paddy soils, which are crucial for arsenic methylation and demethylation, were analyzed via metagenomic sequencing. Results demonstrated that the maximal DMAs(V) concentration in paddy porewater decreased from 0.37 to 0.04 μM in arsenic-contaminated paddy soils with nZVI dose increasing from 0 to 5.0 g/kg. Accordingly, the maximal concentration of inorganic arsenite (iAs(III)), which is the precursor of DMAs(V), decreased from 1.39 to 0.23 μM. Furthermore, the application of nZVI reshaped the structure of microbial community in paddy soils. Specifically, the relative abundance of δ-proteobacteria involved in sulfate reduction, which is crucial for iAs(III) methylation, waned from 7.62 % to 3.17 %, while that of Methanomicrobia for DMAs(V) demethylation and methanogenesis proliferated from 7.03 % to 13.62 %, with nZVI dose increasing from 0 to 5.0 g/kg. Via simultaneous inhibition of DMAs(V) formation and acceleration of DMAs(V) transformation, nZVI efficiently controls the accumulation of DMAs(V) in paddy porewater. In conclusion, these findings prove the efficient performance for DMAs(V) mitigation with nZVI and uncover its underlying mechanisms.}, } @article {pmid39637512, year = {2025}, author = {Wilkie, I and Orellana, LH}, title = {Elusive marine Verrucomicrobiota: Seasonally abundant members of the novel genera Seribacter and Chordibacter specialize in degrading sulfated glycans.}, journal = {Systematic and applied microbiology}, volume = {48}, number = {1}, pages = {126562}, doi = {10.1016/j.syapm.2024.126562}, pmid = {39637512}, issn = {1618-0984}, mesh = {*Polysaccharides/metabolism ; *Phylogeny ; *Seawater/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Genome, Bacterial/genetics ; Verrucomicrobia/genetics/classification/metabolism ; North Sea ; Seasons ; DNA, Bacterial/genetics ; Sulfates/metabolism ; Sequence Analysis, DNA ; Metagenome ; }, abstract = {Members of the phylum Verrucomicrobiota play a significant role in various ecosystems, yet they are underrepresented in databases due to their comparatively lower abundance and isolation challenges. The use of cultivation-independent approaches has unveiled their hidden diversity and specialized metabolic capabilities, yet many of these populations remain uncharacterized. In this study, we focus on members of the family MB11C04 associated with North Sea spring blooms. Our analyses revealed recurrent MB11C04 populations with increased abundance in the late stages of spring blooms over ten-years. By examining their genomic content, we identified specialized genetic features for the degradation of complex polysaccharides, particularly sulfated and fucose-rich compounds, suggesting their role in utilizing organic matter during the collapse of the bloom. Furthermore, we describe two novel genera each with a novel species (Seribacter gen. Nov., Chordibacter gen. Nov.) in accordance with the SeqCode initiative based on high quality metagenome-assembled genomes. We also propose a new name for the family MB11C04, Seribacteraceae. Our findings shed light on the ecological significance and metabolic potential of Verrucomicrobiota populations in spring bloom events.}, } @article {pmid39637246, year = {2024}, author = {Mahmoud, OK and Petri, F and El Zein, S and Fida, M and Diehn, FE and Verdoorn, JT and Schuetz, AN and Murad, MH and Nassr, A and Berbari, EF}, title = {What Is the Accuracy of 16S PCR Followed by Sanger Sequencing or Next-generation Sequencing in Native Vertebral Osteomyelitis? A Systematic Review and Meta-analysis.}, journal = {Clinical orthopaedics and related research}, volume = {}, number = {}, pages = {}, doi = {10.1097/CORR.0000000000003314}, pmid = {39637246}, issn = {1528-1132}, abstract = {BACKGROUND: Identifying a microorganism in patients with native vertebral osteomyelitis presents diagnostic challenges. Microorganism identification through culture-based methods is constrained by prolonged processing times and sensitivity limitations. Despite the availability of molecular diagnostic techniques for identifying microorganisms in native vertebral osteomyelitis, there is considerable variability in reported sensitivity and specificity across studies, leading to uncertainty in their clinical utility.

QUESTIONS/PURPOSES: What are the sensitivity, specificity, and diagnostic odds ratios for 16S broad-range PCR followed by Sanger sequencing (16S) and metagenomic next-generation sequencing (NGS) for detecting bacteria in native vertebral osteomyelitis?

METHODS: On June 29, 2023, we searched Cochrane, Embase, Medline, and Scopus for results from January 1970 to June 2023. Included studies involved adult patients with suspected native vertebral osteomyelitis undergoing molecular diagnostics-16S bacterial broad-range PCR followed by Sanger sequencing and shotgun or targeted metagenomic NGS-for bacteria detection. Studies involving nonnative vertebral osteomyelitis and cases of brucellar, tubercular, or fungal etiology were excluded. The reference standard for the diagnosis of native vertebral osteomyelitis was a composite clinical- and investigator-defined native vertebral osteomyelitis diagnosis. Diagnostic performance was assessed using a bivariate random-effects model. Risk of bias and diagnostic applicability were evaluated using the revised Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool. After a manual screening of 3403 studies, 10 studies (5 on 16S, 5 on NGS) were included in the present analysis, from which 391 patients were included from a total of 958 patients overall. Quality assessment via QUADAS-2 criteria showed moderate risk of bias and good applicability.

RESULTS: 16S showed 78% (95% confidence interval [CI] 95% CI 31% to 96%) sensitivity and 94% (95% CI 73% to 99%) specificity, whereas NGS demonstrated 82% (95% CI 63% to 93%) sensitivity and 71% (95% CI 37% to 91%) specificity. In addition, the diagnostic ORs were 59 (95% CI 9 to 388) and 11 (95% CI 4 to 35) for 16S and NGS, respectively. Summary receiver operating characteristic curves showed high test performance for 16S (area under the curve for 16S 95% [95% CI 93% to 97%] and for NGS 89% [95% CI 86% to 92%]). Certainty in estimates was moderate because of sample size limitations.

CONCLUSION: This meta-analysis found moderate-to-high diagnostic performance of molecular methods on direct patient specimens for the diagnosis of native vertebral osteomyelitis. When used as a complementary test to microbiological analyses, a positive 16S result rules in the diagnosis of native vertebral osteomyelitis, while further studies are needed to understand the role of NGS in the diagnosis of native vertebral osteomyelitis. When available, these tests should be used in addition to conventional microbiology, especially in complex cases with extensively negative standard microbiological test results, to detect fastidious bacteria or to confirm the causative bacteria when their isolation and pathogenicity are unclear. A large sample size is needed in future research to understand the use of these techniques as standalone tests for diagnosis.

LEVEL OF EVIDENCE: Level III, diagnostic study.}, } @article {pmid39636804, year = {2024}, author = {Calderon, MS and Bustamante, DE and Perez, J and Fernandez-Güimac, SLJ and Mendoza, JE and Barboza, JI and Ayala, RY and Carrion, JV}, title = {Diversity and functional role of bacterial microbiota in spontaneous coffee fermentation in northern Peru using shotgun metagenomics.}, journal = {Journal of food science}, volume = {89}, number = {12}, pages = {9692-9710}, doi = {10.1111/1750-3841.17583}, pmid = {39636804}, issn = {1750-3841}, support = {//Consejo Nacional de Ciencia, Tecnología e Innovación Tecnológica/ ; N° 030-2018-FONDECYT-BM-IADT-MU//Peruvian CONCYTEC under the projects Metacafé/ ; N° PE501081184-2022-PROCIENCIA//Metacafé 2.0/ ; //Vicerrectorado de Investigación (VRIN) de la UNTRM/ ; }, mesh = {*Fermentation ; Peru ; *Coffee/microbiology ; *Metagenomics/methods ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota ; Taste ; Coffea/microbiology ; Food Microbiology/methods ; }, abstract = {Peru is the ninth-largest coffee producer and the largest organic coffee exporter worldwide. Specific modifications in the microbial consortia during fermentation control the flavor of coffee. It is still unclear how fermentation duration affects microbial communities. This study aimed to provide insights into the diversity and functional behavior of the bacterial microbiome during coffee fermentation in northern Peru using shotgun metagenomics. Accordingly, metagenomic DNA was extracted and sequenced from samples of the liquid fraction during the short fermentation process (SFP) in Amazonas (6 and 12 h) and long fermentation process (LFP) in Cajamarca (6, 12, 18, 24, and 36 h). Our findings indicate that common (e.g., Acetobacter, Lactobacillus, Leuconostoc, and Weissella) and unique (e.g., Acidiphilium and Methylobacterium) acid-tolerant bacteria from the SFP and LFP play crucial roles and have a positive impact on the sensory qualities of coffee. Specifically, the LFP from San Ignacio might be associated with the high sensory quality of coffee based on the release of catalytic, hydrolase, oxidoreductase, transferase, and transporter enzymes in the InterPro and KEGG profiles. Additionally, these bacterial microorganisms metabolize several compounds (e.g., isoleucine, betaine, galactose, tryptophan, arginine, and cobalamin) into volatile compounds, mainly in the LFP, enhancing the flavor and aroma of coffees. This characteristic suggests that the LFP has a stronger effect on coffee quality than does the SFP on the basis of bacterial diversity and functional prediction. These findings provide new perspectives on the potential biotechnological uses of autochthonous microorganisms to produce superior-quality coffee beans from northern Peru.}, } @article {pmid39635985, year = {2025}, author = {Mulders, MCF and Van Koetsveld, PM and Feelders, RA and Hofland, LJ and de Herder, WW and Kraaij, R and Hofland, J}, title = {Gut microbial and functional alterations lead to metagenomic signatures for midgut neuroendocrine tumor patients and for carcinoid syndrome.}, journal = {Endocrine-related cancer}, volume = {32}, number = {2}, pages = {}, doi = {10.1530/ERC-24-0145}, pmid = {39635985}, issn = {1479-6821}, mesh = {Aged ; Female ; Humans ; Male ; Middle Aged ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; *Intestinal Neoplasms/diagnosis/genetics/microbiology/pathology ; *Malignant Carcinoid Syndrome/diagnosis/genetics/microbiology/pathology ; Metagenome ; Metagenomics/methods ; *Neuroendocrine Tumors/diagnosis/genetics/microbiology/pathology ; Prospective Studies ; }, abstract = {Midgut neuroendocrine tumors (NET) derive from enterochromaffin cells, which have a close interrelationship with intestinal microbiota. Recently, we have utilized 16S rRNA sequencing to uncover that midgut NET patients have a depleted gut microbiome and a specific fecal microbial signature. This study aims to validate these findings and to further characterize the role of microbes and microbial metabolic pathways in midgut NET patients with and without carcinoid syndrome (CS). Fecal samples from 60 midgut NET patients and 20 household-matched controls were subjected to whole metagenome sequencing. The gut microbial community composition of midgut NET patients differed from that of controls, with 2 genera, 17 species and 9 microbial pathways showing differential abundance (P < 0.001). No differences in the microbial composition were observed between midgut NET patients with and without CS (P > 0.05). However, we did observe changes in inter-genus correlations of Bacteroides, Odoribacter, Parasutterella, Klebsiella, Ruminococcus and Proteobacteria when comparing these two patient groups. A signature of 16 microbial species (area under the receiver operating characteristics (AUROC) curve 0.892) or 18 microbial pathways (AUROC 0.909) accurately predicted the presence of a midgut NET. Furthermore, a microbial signature consisting of 14 functional microbial pathways distinguished CS patients from non-CS patients (AUROC 0.807). Thus, this study confirms that the gut microbiome of midgut NET patients is altered at the metagenomic level, which is not related to the presence of CS. A fecal microbial signature could constitute a novel biomarker for the diagnosis of midgut NET or CS.}, } @article {pmid39635041, year = {2024}, author = {Dora, D and Revisnyei, P and Mihucz, A and Kiraly, P and Szklenarik, G and Dulka, E and Galffy, G and Lohinai, Z}, title = {Metabolic pathways from the gut metatranscriptome are associated with COPD and respiratory function in lung cancer patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1381170}, pmid = {39635041}, issn = {2235-2988}, mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/metabolism/physiopathology ; *Gastrointestinal Microbiome/genetics ; *Metabolic Networks and Pathways/genetics ; *Lung Neoplasms/microbiology/genetics ; Male ; *Feces/microbiology ; Female ; Aged ; Middle Aged ; Carcinoma, Non-Small-Cell Lung/genetics/microbiology ; Transcriptome ; Metagenomics/methods ; Bacteria/genetics/classification/isolation & purification/metabolism ; Streptococcus/genetics/isolation & purification/metabolism ; }, abstract = {INTRODUCTION: Changes in the human gut microbiome have been linked to various chronic diseases, including chronic obstructive pulmonary disease (COPD). While substantial knowledge is available on the genomic features of fecal communities, little is known about the microbiome's transcriptional activity. Here, we analyzed the metatranscriptomic (MTR) abundance of MetaCyc pathways, SuperPathways, and protein domain families (PFAM) represented by the gut microbiome in a cohort of non-small cell lung cancer (NSCLC) patients with- or without COPD comorbidity.

METHODS: Fecal samples of 40 NSCLC patients with- or without COPD comorbidity were collected at the time of diagnosis. Data was preprocessed using the Metaphlan3/Humann3 pipeline and BioCyc[©] to identify metabolic SuperPathways. LEfSe analysis was conducted on Pathway- and PFAM abundance data to determine COPD- and non-COPD-related clusters.

RESULTS: Key genera Streptococcus, Escherichia, Gemella, and Lactobacillus were significantly more active transcriptionally compared to their metagenomic presence. LEfSe analysis identified 11 MetaCyc pathways that were significantly overrepresented in patients with- and without COPD comorbidity. According to Spearman's rank correlation, Smoking PY showed a significant negative correlation with Glycolysis IV, Purine Ribonucleoside Degradation and Glycogen Biosynthesis I, and a significant positive correlation with Superpathway of Ac-CoA Biosynthesis and Glyoxylate cycle, whereas forced expiratory volume in the first second (FEV1) showed a significant negative correlation with Glycolysis IV and a significant positive correlation with Glycogen Biosynthesis I. Furthermore, COPD patients showed a significantly increased MTR abundance in ~60% of SuperPathways, indicating a universally increased MTR activity in this condition. FEV1 showed a significant correlation with SuperPathways Carbohydrate degradation, Glycan biosynthesis, and Glycolysis. Taxonomic analysis suggested a more prominent MTR activity from multiple Streptococcus species, Enterococcus (E.) faecalis, E. faecium and Escherichia (E.) coli than expected from their metagenomic abundance. Multiple protein domain families (PFAMs) were identified as more associated with COPD, E. faecium, E.coli, and Streptococcus salivarius, contributing the most to these PFAMs.

CONCLUSION: Metatranscriptome analysis identified COPD-related subsets of lung cancer with potential therapeutic relevance.}, } @article {pmid39634420, year = {2024}, author = {Lu, R and Li, D and Guo, Y and Cui, Z and Wei, Z and Fan, G and Zhang, W and Wang, Y and Gu, Y and Han, M and Liu, S and Meng, L}, title = {Comparative metagenomics highlights the habitat-related diversity in taxonomic composition and metabolic potential of deep-sea sediment microbiota.}, journal = {Heliyon}, volume = {10}, number = {22}, pages = {e39055}, pmid = {39634420}, issn = {2405-8440}, abstract = {Sediment plays a pivotal role in deep-sea ecosystems by providing habitats for a diverse range of microorganisms and facilitates the cycling processes of carbon, sulfur and nitrogen. Beyond the normal seafloor (NS), distinctive geographical features such as cold seeps (CS) and hydrothermal vent (HV) are recognized as life oases harboring highly diverse microbial communities. A global atlas of microorganisms can reveal the notable association between geological processes and microbial colonization. However, a comprehensive understanding of the systematic comparison of microbial communities in sediments across various deep-sea regions worldwide and their contributions to Earth's elemental cycles remains limited. Analyzing metagenomic data from 163 deep-sea sediment samples across 73 locations worldwide revealed that microbial communities in CS sediments exhibited the highest richness and diversity, followed by HV sediments, with NS sediments showing the lowest diversity. The NS sediments were predominantly inhabited by Nitrosopumilaceae, a type of ammonia-oxidizing archaea (AOA). In contrast, CSs and HVs were dominated by ANME-1, a family of anaerobic methane-oxidizing archaea (ANME), and Desulfofervidaceae, a family of sulfate-reducing bacteria (SRB), respectively. Microbial networks were established for each ecosystem to analyze the relationships and interactions among different microorganisms. Additionally, we analyzed the metabolic patterns of microbial communities in different deep-sea sediments. Despite variations in carbon fixation pathways in ecosystems with different oxygen concentrations, carbon metabolism remains the predominant biogeochemical cycle in deep-sea sediments. Benthic ecosystems exhibit distinct microbial potentials for sulfate reduction, both assimilatory and dissimilatory sulfate reduction (ASR and DSR), in response to different environmental conditions. The presence of nitrogen-fixing microorganisms in CS sediments may influence the global nitrogen balance. In this study, the significant differences in the taxonomic composition and functional potential of microbial communities inhabiting various deep-sea environments were investigated. Our findings emphasize the importance of conducting comparative studies on ecosystems to reveal the complex interrelationships between marine sediments and global biogeochemical cycles.}, } @article {pmid39634324, year = {2024}, author = {Shao, L and Zhang, B and Song, Y and Lyu, Z and Zhang, W and Yang, W and Fu, J and Li, J and Shi, J}, title = {Mucosal Hub Bacteria as Potential Targets for Improving High-Fat Diet-Related Intestinal Barrier Injury.}, journal = {The Canadian journal of infectious diseases & medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale}, volume = {2024}, number = {}, pages = {3652740}, pmid = {39634324}, issn = {1712-9532}, abstract = {Background: Intestinal barrier injury contributes to multiple diseases such as obesity and diabetes, whereas no treatment options are available. Methods: Due to close interactions between mucosal microbiome and intestinal barrier, we evaluated the potential of mucosal bacteria in providing targets for high-fat diet (HFD)-related intestinal barrier injury. Whole-genome metagenomics was used to evaluate mucosal microbiome, while intestinal barrier injury was estimated using serum LPS, FITC-dextran intensity, and ZO-1 protein. Results: We found that HFD induced significant fat accumulation in epididymal tissue at weeks 4 and 12, while ALT, LDL, and TC increased at week 12. Intestinal barrier injury was confirmed by elevated serum LPS at both weeks, upregulated FITC-dextran intensity, and decreased ZO-1 protein at week 12. Fourteen species such as Phocaeicola vulgatus differed in HFD-fed mice. The co-occurrence network of mucosal microbiome shifted from scale-free graph in controls to nearly random graph in HFD-fed mice. Besides, 10 hub bacteria especially Bacteroides ovatus decreased drastically in both mucosal and fecal samples of HFD-fed mice, correlated with intestinal permeability, ALT, and KEGG pathways such as "Mitochondrial biogenesis" and "metabolism". Moreover, Bacteroides ovatus has been confirmed to improve intestinal barrier function in a recent study. Conclusion: Mucosal hub bacteria can provide potential targets for improving HFD-related intestinal barrier function.}, } @article {pmid39633808, year = {2024}, author = {Guo, Y and Feng, H and Du, L and Yu, Z}, title = {Patterns of antibiotic resistance genes and virulence factor genes in the gut microbiome of patients with osteoarthritis and rheumatoid arthritis.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1427313}, pmid = {39633808}, issn = {1664-302X}, abstract = {BACKGROUND: The gut microbiome compositions of osteoarthritis (OA) and rheumatoid arthritis (RA) patients have been revealed; however, the functional genomics, particularly antibiotic resistance genes (ARGs) and virulence factor genes (VFGs), have not yet been explored.

METHODS: We used gut metagenomic data to elucidate the distribution of ARGs and VFGs. Building on these differences in gut microbiome, we developed a diagnostic model using a random forest classifier based on ARG and VFG abundances.

RESULTS: Our results indicated that both OA and RA patients exhibit significantly higher alpha diversity in ARGs, as measured by observed genes, the Shannon index, and the Simpson index, compared to healthy controls. However, this increased diversity is not significantly different between OA and RA patients. In contrast, VFGs showed higher diversity in RA patients than in healthy individuals, which was not as pronounced in OA patients. An analysis of the top 20 ARGs and VFGs revealed a largely similar composition between the three groups, with notable exceptions of certain genes that were uniquely enriched in either OA or RA patients. This suggests unique microbial patterns associated with each condition. Our beta diversity analysis further demonstrated distinct distributions of ARG and VFG profiles across the three groups, with several genes significantly enriched in both OA and RA patients, indicating potential markers for these diseases. The model achieved high accuracy (74.7-83.6%) when distinguishing both OA and RA from healthy controls using ARG profiles and substantial accuracy using VFG profiles.

CONCLUSION: These results support the potential of ARGs and VFGs as reliable biomarkers for diagnosing OA and RA.}, } @article {pmid39633804, year = {2024}, author = {Sharma, N and Das, BK and Bhattacharjya, BK and Chaudhari, A and Behera, BK and Kumar, AP and Chakraborty, HJ}, title = {Metagenomic insights into microbial community, functional annotation, and antibiotic resistance genes in Himalayan Brahmaputra River sediment, India.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1426463}, pmid = {39633804}, issn = {1664-302X}, abstract = {INTRODUCTION: The Brahmaputra, a major transboundary river of the Himalayas flowing predominantly through Northeast India, particularly Assam, is increasingly endangered by contamination due to rapid urbanization and anthropogenic pressures. These environmental changes pose significant risks at the microbial level, affecting nutrient cycling and productivity, and thereby impacting river ecosystem health. The next-generation sequencing technology using a metagenomics approach has revolutionized our understanding of the microbiome and its critical role in various aquatic environments.

METHODS: The present study aimed to investigate the structure of the bacterial community and its functional potentials within the sediments of the Brahmaputra River, India, using high-throughput shotgun metagenomics. Additionally, this study sought to explore the presence of antimicrobial resistance genes in the river's sediment.

RESULTS AND DISCUSSION: Shotgun metagenomics revealed a diverse bacterial community comprising 31 phyla, 52 classes, 291 families, 1,016 genera, and 3,630 species. Dominant phyla included Pseudomonadota (62.47-83.48%), Actinobacteria (11.10-24.89%), Bacteroidetes (0.97-3.82%), Firmicutes (0.54-3.94%), Cyanobacteria (0.14-1.70%), and Planctomycetes (0.30-0.78%). Functional profiling highlighted significant involvement in energy metabolism, amino acid and central carbon metabolism, stress response, and degradation pathways, emphasizing the microbial community's role in ecosystem functioning and resilience. Notably, 50 types of antibiotic resistance genes (ARGs) were detected, with resistance profiles spanning multidrug, aminoglycoside, β-lactam, fluoroquinolone, rifampicin, sulfonamide, and tetracycline classes. Network analysis underscored the intricate relationships among ARG subtypes, suggesting potential mechanisms of resistance propagation. Furthermore, plasmid-related genes and 185 virulence factor genes (VFGs) were identified, indicating additional layers of microbial adaptation and potential pathogenicity within the river sediments. This comprehensive microbial and functional profiling of the Brahmaputra's sediment metagenome provides crucial insights into microbial diversity, resistance potential, and ecological functions, offering a foundation for informed management and mitigation strategies to preserve river health and mitigate pollution impacts.}, } @article {pmid39633723, year = {2024}, author = {Heinzinger, M and Weissenow, K and Sanchez, JG and Henkel, A and Mirdita, M and Steinegger, M and Rost, B}, title = {Bilingual language model for protein sequence and structure.}, journal = {NAR genomics and bioinformatics}, volume = {6}, number = {4}, pages = {lqae150}, pmid = {39633723}, issn = {2631-9268}, abstract = {Adapting language models to protein sequences spawned the development of powerful protein language models (pLMs). Concurrently, AlphaFold2 broke through in protein structure prediction. Now we can systematically and comprehensively explore the dual nature of proteins that act and exist as three-dimensional (3D) machines and evolve as linear strings of one-dimensional (1D) sequences. Here, we leverage pLMs to simultaneously model both modalities in a single model. We encode protein structures as token sequences using the 3Di-alphabet introduced by the 3D-alignment method Foldseek. For training, we built a non-redundant dataset from AlphaFoldDB and fine-tuned an existing pLM (ProtT5) to translate between 3Di and amino acid sequences. As a proof-of-concept for our novel approach, dubbed Protein 'structure-sequence' T5 (ProstT5), we showed improved performance for subsequent, structure-related prediction tasks, leading to three orders of magnitude speedup for deriving 3Di. This will be crucial for future applications trying to search metagenomic sequence databases at the sensitivity of structure comparisons. Our work showcased the potential of pLMs to tap into the information-rich protein structure revolution fueled by AlphaFold2. ProstT5 paves the way to develop new tools integrating the vast resource of 3D predictions and opens new research avenues in the post-AlphaFold2 era.}, } @article {pmid39632779, year = {2024}, author = {Eyal, N and Williams, B and Esvelt, KM and Bambauer, J}, title = {Metagenomic Sequencing for Early Detection of Future Engineered Pandemics: Foreshadowing the Privacy Challenge.}, journal = {Health security}, volume = {22}, number = {6}, pages = {466-475}, doi = {10.1089/hs.2023.0140}, pmid = {39632779}, issn = {2326-5108}, } @article {pmid39632378, year = {2024}, author = {Li, Y and Hu, W and Lin, B and Ma, T and Zhang, Z and Hu, W and Zhou, R and Kwok, LY and Sun, Z and Zhu, C and Zhang, H}, title = {Omic characterizing and targeting gut dysbiosis in children with autism spectrum disorder: symptom alleviation through combined probiotic and medium-carbohydrate diet intervention - a pilot study.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2434675}, pmid = {39632378}, issn = {1949-0984}, mesh = {Humans ; *Autism Spectrum Disorder/diet therapy/microbiology ; Pilot Projects ; *Probiotics/administration & dosage ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology/diet therapy/therapy ; Male ; Child ; Female ; *Feces/microbiology/chemistry ; Child, Preschool ; Bacteria/classification/isolation & purification/genetics/metabolism ; Dietary Carbohydrates/metabolism/administration & dosage ; Bifidobacterium animalis ; }, abstract = {Autism spectrum disorder (ASD) currently lacks effective diagnostic and therapeutic approaches. Disruptions in the gut ecosystem have been observed in individuals with ASD, suggesting that targeting gut microbiota through probiotic and dietary supplementation may serve as a potential treatment strategy. This two-phase study aimed to characterize the fecal metagenome of children with ASD and investigate the beneficial effects of a combined probiotic and medium-carbohydrate intervention in ASD. Fecal metagenomes of children with ASD were compared to those of typically developing children, revealing intestinal dysbiosis in ASD, characterized by reduced levels of Prevotella sp. Dialister invisus, and Bacteroides sp. along with increased predicted abundances of inosine, glutamate, xanthine, and methylxanthine. The gut bacteriome and phageome exhibited high cooperativity. In a 3-month pilot study, Bifidobacterium animalis subsp. lactis Probio-M8 (Probio-M8) was administered alongside a medium-carbohydrate diet to Chinese children with ASD. The primary endpoint was the Childhood Autism Rating Scale (CARS), while the secondary endpoint was the Gastrointestinal Symptom Rating Scale (GSRS). A total of 72 autistic children were initially recruited for the intervention study, but only 53 completed the intervention. Probio-M8, in combination with dietary intervention, significantly improved CARS and GSRS scores, increased fecal levels of Bifidobacterium animalis, Akkermansia muciniphila, Fusicatenibacter saccharivorans, and Sutterella sp. while also reducing Blautia obeum (Benjamini-Hochberg corrected p ≤ 0.05 for all cases). The intervention also modulated fecal metabolites associated with the metabolism of amino acids (lysine), neurotransmitters (glutamate, γ-aminobutyric acid), polyunsaturated fatty acids (arachidonate, myristic acid), and vitamin B3. In conclusion, Probio-M8 combined with medium-carbohydrate diet effectively improved ASD symptoms, with associated changes in the gut microbiome and metabolome, supporting its potential as an adjunctive therapy for ASD.}, } @article {pmid39632177, year = {2024}, author = {Li, D and Li, L and Wang, P and Zhang, W}, title = {The application value of metagenomic next-generation sequencing technology in the detection of pathogens in patients with pneumonia after initial treatment failure.}, journal = {Asian journal of surgery}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.asjsur.2024.11.113}, pmid = {39632177}, issn = {0219-3108}, } @article {pmid39631543, year = {2025}, author = {Qu, M and Zheng, Y and Cheng, Z and Shi, Y and Wang, W and Wu, X and Chen, J}, title = {Mechanism of chlorobenzene removal in biotrickling filter enhanced by non-thermal plasma: Insights from biodiversity and functional gene perspectives.}, journal = {Bioresource technology}, volume = {418}, number = {}, pages = {131931}, doi = {10.1016/j.biortech.2024.131931}, pmid = {39631543}, issn = {1873-2976}, mesh = {*Chlorobenzenes/metabolism ; *Plasma Gases/pharmacology ; *Biodegradation, Environmental ; Filtration/methods ; Bacteria/metabolism/genetics ; Volatile Organic Compounds/metabolism ; Biodiversity ; Carbon Dioxide/metabolism ; Bioreactors ; }, abstract = {Biotrickling filter (BTF) technology is inefficient in the treatment of Cl-containing volatile organic compounds (VOCs) such as chlorobenzene (CB). This study adopted non-thermal plasma (NTP) as a pretreatment and conducted in-depth analyses, especially in microorganisms, to investigate strengthening mechanism of a NTP to a BTF in the process. The introduction of NTP enhance efficiency of CB removal from 65 % to 90 %, and CO2 generation from 60 % to 85 %. It is found that the protein content of the extracellular polymeric substances increases from 212 × 10[-3] mg·g[-1] filler to 299 × 10[-3] mg·g[-1] filler, thus CB capturing and utilization enhanced. Metagenomic analysis showed that bacteria with CB-degrading properties were enriched in BTF, and CB was involved in cellular metabolism as a carbon source. The presence of active substances from NTP is found to stimulate the ability of BTF treatment. The findings of this study will provide theoretical support for the application of NTP-BTF technology.}, } @article {pmid39631542, year = {2025}, author = {Xiong, Z and Chen, X and Zou, Z and Peng, L and Zou, L and Liu, B and Li, Q}, title = {Improving efficiency of bacterial degradation of polyethylene microplastics using atmospheric and room temperature plasma mutagenesis.}, journal = {Bioresource technology}, volume = {418}, number = {}, pages = {131930}, doi = {10.1016/j.biortech.2024.131930}, pmid = {39631542}, issn = {1873-2976}, mesh = {*Mutagenesis ; *Polyethylene/chemistry/metabolism ; *Biodegradation, Environmental ; *Plasma Gases ; *Microplastics ; *Temperature ; Bacteria/metabolism/genetics ; Atmosphere ; }, abstract = {In this study, the bacterium XZ-A was genetically modified using atmospheric and room temperature plasma mutagenesis (ARTP) to increase the degradation efficiency of polyethylene microplastics (PE-MPs) by up to 53.65 %. After 50 d of biodegradation, the mutagenized bacterium XZ-60S caused significant changes in the morphology, structure, thermal stability, and molecular weight of PE-MPs. The number average molecular weights and weight average molecular weights of the PE-MPs were significantly reduced by approximately 15.21 % and 4.80 %, respectively. Comparative genomic and transcriptomic analyses showed that XZ-60S had a total of 106 single nucleotide polymorphic sites, and the expression of genes encoding laccases was significantly increased; this may explain the improved degradation of PE-MPs by XZ-60S. In this study, the degradation of PE-MPs by bacteria was improved through ARTP mutagenesis, which provides a reference for selecting and breeding bacteria that are highly efficient at degrading PE-MPs.}, } @article {pmid39630952, year = {2024}, author = {Gao, F and Shen, Y and Wu, H and Laue, HE and Lau, FK and Gillet, V and Lai, Y and Shrubsole, MJ and Prada, D and Zhang, W and Liu, Z and Bellenger, JP and Takser, L and Baccarelli, AA}, title = {Associations of Stool Metal Exposures with Childhood Gut Microbiome Multiomics Profiles in a Prospective Birth Cohort Study.}, journal = {Environmental science & technology}, volume = {58}, number = {50}, pages = {22053-22063}, doi = {10.1021/acs.est.4c09642}, pmid = {39630952}, issn = {1520-5851}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Feces/microbiology ; Child ; *Metals ; Prospective Studies ; Female ; Male ; Birth Cohort ; Environmental Exposure ; Multiomics ; }, abstract = {Metal exposures are closely related to childhood developmental health. However, their effects on the childhood gut microbiome, which also impacts health, are largely unexplored using microbiome multiomics including the metagenome and metatranscriptome. This study examined the associations of fecal profiles of metal/element exposures with gut microbiome species and active functional pathways in 8- to 12-year-old children (N = 116) participating in the GESTation and Environment (GESTE) cohort study. We analyzed 19 stool metal and element concentrations (B, Na, Mg, Al, K, Ca, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Mo, Cd, Ba, and Pb). Covariate-adjusted linear regression models identified several significant microbiome associations with continuous stool metal/element concentrations. For instance, Zn was positively associated with Turicibacter sanguinis (coef = 1.354, q-value = 0.039) and negatively associated with Eubacterium eligens (coef = -0.794, q-value = 0.044). Higher concentrations of Cd were associated with lower Eubacterium eligens (coef = -0.774, q-value = 0.045). Additionally, a total of 490 significant functional pathways such as biosynthesis and degradation/utilization/assimilation were identified, corresponding to different functions, including amino acid synthesis and carbohydrate degradation. Our results suggest links among metal exposures, pediatric gut microbiome multiomics, and potential health implications. Future work will further explore their relation to childhood health.}, } @article {pmid39630239, year = {2024}, author = {Boonyapakron, K and Keiser, B and Prabmark, K and Aiewviriyasakul, K and Arunrattanamook, N and Jaruwat, A and Chitnumsub, P and Li, JY and Wong, TS and Zhao, XQ and Liu, CG and Wei, DQ and Champreda, V}, title = {Hyperthermophilic xylanase and thermophilicity analysis by molecular dynamic simulation with quantum mechanics.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {526}, pmid = {39630239}, issn = {1432-0614}, support = {B16F640052//PMU-B/ ; Grant No. 32070662//National Science Foundation of China/ ; 61832019//National Science Foundation of China/ ; 32030063//National Science Foundation of China/ ; 2023YFE0199200//Key Technologies Research and Development Program of Anhui Province/ ; LTSRF1819\15\21//Royal Academy of Engineering/ ; }, mesh = {*Molecular Dynamics Simulation ; *Endo-1,4-beta Xylanases/chemistry/genetics/metabolism ; *Enzyme Stability ; *Xylans/metabolism/chemistry ; *Oligosaccharides/metabolism/chemistry ; *Glucuronates/metabolism/chemistry ; Substrate Specificity ; Hot Temperature ; Cellulose/metabolism ; Hydrogen Bonding ; Quantum Theory ; Disaccharides/metabolism/chemistry ; Metagenome ; }, abstract = {Thermophilic xylanases catalyzing the cleavage of β-1,4-glycosidic bonds in xylan have applications in food, feed, biorefinery, and pulp industries. In this study, a hyperthermophilic endo-xylanase was obtained by further enhancement of thermal tolerance of a thermophilic GH11 xylanase originated from metagenome of bagasse pile based on rational design. Introducing N13F and Q34L to the previously reported X11P enzyme shifted the optimal working temperature to 85 °C and led to 20.7-fold improvement in thermostability at 90 °C along with a marked increase in Tm to 93.3 °C. X11PNQ enzyme converted xylan to prebiotic xylooligosaccharides with high specificity on xylobiose to xylohexaose and high operational stability at 85 °C, resulting in 10.3-folds yield improvement compared to the parental enzyme. Molecular dynamic simulation and quantum mechanical analysis revealed improved H-bonding networks within GH11 xylanase principal domains and greater dynamic cross-correlations. A novel thermostabilization mechanism by π-amide interaction with slightly lower interaction energy than the native H-bond, but compensated by increased occurrence frequency was firstly demonstrated for thermophilic enzymes. The enzyme represents one of the most thermostable xylanases ever reported with biotechnological potential. KEY POINTS: • Hyperthemophilic xylanase X11PNQ was obtained by rational design engineering. • X11PNQ showed specificity to prebiotic xylooligosaccharides (XOS) at 85 °C with improved t1/2 at 90 °C. • Novel thermostabilization by π-amide interaction was demonstrated by MD/QM.}, } @article {pmid39629792, year = {2024}, author = {González-García, S and Hamdan-Partida, A and Pérez-Ramos, J and Aguirre-Garrido, JF and Bustos-Hamdan, A and Bustos-Martínez, J}, title = {Comparison of the bacterial microbiome in the pharynx and nasal cavity of persistent, intermittent carriers and non-carriers of Staphylococcus aureus.}, journal = {Journal of medical microbiology}, volume = {73}, number = {12}, pages = {}, pmid = {39629792}, issn = {1473-5644}, mesh = {Humans ; *Pharynx/microbiology ; *Staphylococcus aureus/isolation & purification/genetics ; *Carrier State/microbiology ; *Nasal Cavity/microbiology ; *Microbiota ; *Staphylococcal Infections/microbiology ; Male ; Female ; Adult ; Young Adult ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; }, abstract = {Introduction. Staphylococcus aureus is a bacterium that colonizes various human sites. The pharynx has been considered as a site of little clinical relevance and little studied. Recently, it has been reported that S. aureus can colonize more the pharynx than the nose. In addition, S. aureus can persist in these sites for prolonged periods of time.Hypothesis. The composition of the pharyngeal and nasal microbiome will differ between persistent, intermittent carriers and non-carriers of S. aureus.Aim. Determine whether the pharyngeal and nasal microbiome is different between carriers and non-carriers of S. aureus.Methodology. S. aureus carriers were monitored by means of pharyngeal and nasal exudates of apparently healthy adult university students for 3 months. Samples from individuals of the same carrier type were pooled, and DNA was extracted and the 16S rRNA was sequenced. The sequences were analysed in MOTHUR v.1.48.0 software, by analysing the percentages of relative abundance in the STAMP 2.1.3 program, in addition to the predictive analysis of metabolic pathways in PICRUSt2.Results. A greater colonization of S. aureus was found in the pharynx than in the nose. The microbiomes of S. aureus carriers and non-carriers do not show significant differences. The main microbiome difference found was between pharyngeal and nasal microbiomes. No significant differences were found in the abundance of the genus Staphylococcus in pharyngeal and nasal S. aureus carriers and non-carriers. The nasal microbiome was found to have more variation compared to the pharyngeal microbiome, which appears to be more stable between individuals and pools. Predictive analysis of metabolic pathways showed a greater presence of Staphylococcus-associated pathways in the nose than in the pharynx.Conclusion. S. aureus can colonize and persist in the pharynx in equal or greater proportion than in the nose. No statistically significant differences were found in the microbiome of the pharyngeal and nasal carriers and non-carriers of S. aureus, but the pharyngeal and nasal microbiomes are different independent of the type of S. aureus carrier or non-carrier. Therefore, the microbiome apparently does not influence the persistence of S. aureus.}, } @article {pmid39629232, year = {2024}, author = {Zhang, W and Xiao, L and Shan, X and Dai, B and Tang, C and Xian, J and Yu, Y}, title = {Case report: Detection of non-O1/non-O139 Vibrio cholerae in a patient with hepatic space-occupying lesions using metagenomic next-generation sequencing.}, journal = {Frontiers in medicine}, volume = {11}, number = {}, pages = {1483027}, pmid = {39629232}, issn = {2296-858X}, abstract = {INTRODUCTION/BACKGROUND: Vibrio cholerae is the causative agent of the human intestinal infectious disease cholera, which includes a variety of serogroups. However, there have been very few cases of hepatic space-occupying lesions associated with this infection. Currently, there are various methods for detecting this pathogen, including metagenomic sequencing, which enables quicker and more accurate identification. In this study, metagenomic sequencing is employed to accurately identify non-O1/O139 Vibrio cholerae infections by analyzing the genetic material present in clinical samples.

PRESENTATION OF CASE: A 75-year-old man presented with diarrhea and fever after consuming crabs. The initial treatment improved the diarrhea, but a liver abscess developed later. Magnetic resonance imaging (MRI) of the liver revealed a hepatic space-occupying lesion. Upon further investigation, a Gram-negative, rod-shaped bacterium was cultured from the patient's liver puncture fluid, and Vibrio cholerae was detected in the same fluid using metagenomic next-generation sequencing (mNGS). The pathogen was confirmed to be non-O1/non-O139 Vibrio cholerae (NOVC) using polymerase chain reaction (PCR). Following treatment with piperacillin/tazobactam sodium and moxifloxacin, the patient's body temperature returned to normal, the liver abscess improved significantly, and he was subsequently discharged from the hospital.

DISCUSSION: This case study describes an elderly male patient with a hepatic space-occupying lesion. Multiple cultures of specimens failed to identify the underlying cause; however, advanced techniques such as mNGS and PCR confirmed an NOVC infection. This indicates that mNGS can serve as a valuable tool in diagnosing cases of unexplained liver infections.

CONCLUSION: The use of mNGS is significant for detecting and clinically diagnosing infectious pathogens in patients with unexplained space-occupying lesions.}, } @article {pmid39629213, year = {2024}, author = {Ramos, S and Júnior, E and Alegria, O and Vieira, E and Patroca, S and Cecília, A and Moreira, F and Nunes, A}, title = {Metagenomics insights into bacterial diversity and antibiotic resistome of the sewage in the city of Belém, Pará, Brazil.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1466353}, pmid = {39629213}, issn = {1664-302X}, abstract = {INTRODUCTION: The advancement of antimicrobial resistance is a significant public health issue today. With the spread of resistant bacterial strains in water resources, especially in urban sewage, metagenomic studies enable the investigation of the microbial composition and resistance genes present in these locations. This study characterized the bacterial community and antibiotic resistance genes in a sewage system that receives effluents from various sources through metagenomics.

METHODS: One liter of surface water was collected at four points of a sewage channel, and after filtration, the total DNA was extracted and then sequenced on an NGS platform (Illumina® NextSeq). The sequenced data were trimmed, and the microbiome was predicted using the Kraken software, while the resistome was analyzed on the CARD webserver. All ecological and statistical analyses were performed using the. RStudio tool.

RESULTS AND DISCUSSION: The complete metagenome results showed a community with high diversity at the beginning and more restricted diversity at the end of the sampling, with a predominance of the phyla Bacteroidetes, Actinobacteria, Firmicutes, and Proteobacteria. Most species were considered pathogenic, with an emphasis on those belonging to the Enterobacteriaceae family. It was possible to identify bacterial groups of different threat levels to human health according to a report by the U.S. Centers for Disease Control and Prevention. The resistome analysis predominantly revealed genes that confer resistance to multiple drugs, followed by aminoglycosides and macrolides, with efflux pumps and drug inactivation being the most prevalent resistance mechanisms. This work was pioneering in characterizing resistance in a sanitary environment in the Amazon region and reinforces that sanitation measures for urban sewage are necessary to prevent the advancement of antibiotic resistance and the contamination of water resources, as evidenced by the process of eutrophication.}, } @article {pmid39629129, year = {2024}, author = {Zhao, Q and Lu, Y and Duan, J and Du, D and Pu, Q and Li, F}, title = {Gut microbiota depletion and FXR inhibition exacerbates zonal hepatotoxicity of sunitinib.}, journal = {Theranostics}, volume = {14}, number = {18}, pages = {7219-7240}, pmid = {39629129}, issn = {1838-7640}, mesh = {Animals ; *Sunitinib/toxicity ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Chemical and Drug Induced Liver Injury/pathology/etiology ; *Liver/drug effects/pathology ; *Mice, Knockout ; *Receptors, Cytoplasmic and Nuclear/metabolism ; Male ; Hepatocytes/drug effects ; Mice, Inbred C57BL ; Endothelial Cells/drug effects ; Apoptosis/drug effects ; Bacteroidetes/drug effects ; Autophagy/drug effects ; }, abstract = {Rationale: Sunitinib is a small-molecule tyrosine kinase inhibitor associated with the side-effect of liver injury. The impaired cell type in liver and the hepatotoxicity mechanisms is still unclear. Methods: Spatial metabolomics, transmission electron microscopy, immunofluorescence co-staining, and isolation of bile duct cells and liver sinusoidal endothelial cells (LSECs) were used to evaluate the zonated hepatotoxicity of sunitinib. Farnesoid X receptor (FXR) conditional knockout mice, metagenomics analysis, bacteria clearance, bacterial culture, Parabacteroides distasonis and 3-oxolithocholic acid supplementation were used to evaluate the hepatotoxicity mechanisms of sunitinib. Results: Phenotype analysis found that hepatic autophagy, apoptosis, and mitochondrial injury were observed in vivo or in vitro after sunitinib treatment. By using spatial metabolomics and isolation of bile duct cells and LSECs, the zonated drug toxicity was observed around the portal vein. Hepatocytes, bile duct cells, and LSECs were damaged after sunitinib treatment. FXR inhibition and gut microbiota depletion aggravated sunitinib-induced liver injury. For diurnal variation, sunitinib-induced liver injury was enhanced at night compared with that at day, and FXR and gut microbiota participated in circadian rhythmic hepatotoxicity induced by sunitinib. Conclusions: Our data suggested activation of FXR and Parabacteroides distasonis supplementation may be used to improve sunitinib-induced hepatotoxicity.}, } @article {pmid39628602, year = {2024}, author = {Xu, M and Guo, Y and Song, X and Li, L and Xu, Z and Zhao, J and Zhao, J and Lin, H and Dong, S and Lu, J and Ding, W and Liu, P and Tang, J}, title = {Analysis on microbial communities and characteristic flavor metabolic of PXDB-meju by partially substituting wheat flour with soybean flour and gluten flour.}, journal = {Current research in food science}, volume = {9}, number = {}, pages = {100904}, pmid = {39628602}, issn = {2665-9271}, abstract = {Pixian Douban (PXDB) is one of the most popular condiments in China due to its unique flavor. Wheat flour that contains abundant nutrients is an important raw material in producing flavors during PXDB fermentation. In this study, wheat flour was substituted with soybean flour and gluten flour that have higher proteins in portions of 10.4% and 4.2% (F1), 8.9% and 7.2% (F2), 9.6% and 5.8% (F3). The results indicated that the substitutions increased the amino acid nitrogen content and improved flavor quality compared with traditional group (CT). Especially, the key amino acids including spartate, glutamic, arginine and lysine, and the phenylacetaldehyde as one of the most important volatile compounds exhibited preferable higher contents in F2 group than those in CT group. Metagenomic analysis showed that the abundances of predominant bacteria, including Kosakonia_cowanii, unclassified_f__Enterobacteriaceae and unclassified_g__Enterobacter, were higher in the F2 compared to the CT. Lupinus_albus and Plutella_xylostella were the top two fungi in relative abundance, with higher growth rates in F2 than in CT. Furthermore, metabolism pathway analysis revealed higher relative abundance of enzymes producing key amino acids and phenethylaldehyde in the F2 compared to the CT. Meanwhile, these enzymes were exclusively annotated to the Kosakonia_cowanii, Bacillus_velezensis and Escherichia_coli in F2. This study provided a theoretical foundation for improving PXDB flavor quality in industry production.}, } @article {pmid39628590, year = {2024}, author = {Zhang, ZF and Li, M}, title = {The way to uncovering and utilizing marine microbial resources.}, journal = {Engineering microbiology}, volume = {4}, number = {4}, pages = {100175}, pmid = {39628590}, issn = {2667-3703}, abstract = {Recently, Chen et al. published their breakthrough results on a marine microbial genomic catalog and genetic potentials in bioprospecting in Nature, providing unprecedented opportunities for development and utilization of genetic resources of marine microorganisms. To highlight this article, we summarized and highlighted their breakthroughs seriatim.}, } @article {pmid39628383, year = {2024}, author = {Wang, H and Feng, L and Pei, Z and Zhao, J and Lu, S and Lu, W}, title = {Gut microbiota metabolism of branched-chain amino acids and their metabolites can improve the physiological function of aging mice.}, journal = {Aging cell}, volume = {}, number = {}, pages = {e14434}, doi = {10.1111/acel.14434}, pmid = {39628383}, issn = {1474-9726}, support = {2022YFF1100403//National Key Research and Development Program of China/ ; HB2023003//Top Talent Support Program for young and middle-aged people of Wuxi Health Committee/ ; }, abstract = {The metabolism of branched-chain amino acids by gut microbiota can improve overall health and may reverse aging. In this study, we investigated Parabacteroides merdae, a gut microbe that is known to catabolise branched-chain amino acids (BCAAs). Three metabolites of BCAAs isovalerate, 2-methylbutyrate, and isobutyrate were used to treat D-gal induced aging mice. The results showed that these treatments could delay aging in mice by providing health benefits in reducing oxidative stress and inflammation, improving muscle capacity, reversing brain acetylcholine levels, and regulating blood glucose. The mechanism was preliminarily explored by combining the gut microbiota metagenome and faecal serum metabolome. Parabacteroides merdae altered the species composition and structure of the gut microbiota in mice. Increasing the abundance of beneficial bacteria, such as Bifidobacterium pseudolongum. Three metabolites affects the gut microbiota and the body's pathways of protein and improves the overall health through a variety of signaling pathways. Overall, regulating the gut microbiota involved in branched-chain amino acid metabolism to bring health benefits may be a new way of reversing aging.}, } @article {pmid39628196, year = {2024}, author = {Li, ZX and Li, JH and Zhang, Q and Lu, JJ and Gao, CH and Jin, DS and Xu, MG}, title = {[Response and Assembly Process of Soil Microbial Communities Under Different Reclamation Measures].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {45}, number = {12}, pages = {7326-7336}, doi = {10.13227/j.hjkx.202312247}, pmid = {39628196}, issn = {0250-3301}, mesh = {*Soil Microbiology ; *Fungi/classification ; *Bacteria/classification/genetics/growth & development/isolation & purification ; Mining ; Nitrogen ; Soil/chemistry ; Phosphorus ; Environmental Restoration and Remediation/methods ; Microbiota ; Ecosystem ; }, abstract = {Reclamation is essential for restoring the ecological function of soil in mining areas. However, the microbiological mechanism of soil ecological function reconstruction under different reclamation measures still needs to be clarified. Clarifying the characteristics of soil bacterial and fungal communities, assembly mechanisms, and their relationship with physicochemical properties under different reclamation measures is crucial for reshaping the ecological stability of soil in mining areas. Metagenomic sequencing technology was combined with the null model and neutral model to analyze the differences in soil microbial diversity, community composition, network structure, and community assembly process between the reclaimed natural recovery area （LH） and the reclamation fertilization area （MM）. The results suggested that： ① Compared with that in the LH treatment, the MM treatment significantly increased the soil nutrient content, and the total nitrogen （TN）, total phosphorus （TP）, available phosphorus （AP）, and available potassium （AK） contents increased by 34.70%, 72.72%, 468.98%, and 45.74%, respectively （P<0.05）. ② The dominant bacterial and fungal communities did not change under the LH and MM treatments； however, the abundance of bacterial communities changed significantly. Compared with that in the LH treatment, the relative abundance of Acidobacteria increased significantly by 5.4% in the MM treatment, while the relative abundance of Candidatus Rokubacteria decreased significantly by 235.72% （P<0.05）. Under different reclamation measures, the indicator microorganisms of bacterial and fungal communities changed. ③ Compared with that in the LH treatment, the MM treatment increased the complexity of bacterial networks, decreased the complexity of fungal networks, and increased the number of soil bacterial nodes and links. The reclamation measures transformed the key bacterial groups from Proteobacteria to Candidatus Rokubacteria and Planctomycetes. The key group of fungi was Ascomycota. 4.） The deterministic process dominated the assembly of bacterial and fungal communities. Homogeneous selection contributed the most to the bacterial community assembly in the LH treatment, and heterogeneous selection contributed the most to the MM treatment. The fungal communities were all dominated by heterogeneous selection. These results provide new insights into the soil microbial community structure and ecological function restoration in coal mining subsidence reclamation areas.}, } @article {pmid39628107, year = {2024}, author = {Zou, Y and Zou, X and Lin, C and Han, C and Zou, Q}, title = {Inference of functional differentiation of intestinal microbes between two wild zokor species based on metagenomics.}, journal = {Pest management science}, volume = {}, number = {}, pages = {}, doi = {10.1002/ps.8587}, pmid = {39628107}, issn = {1526-4998}, support = {//National Promoted Program of scientific and technological achievements in Forestry and Grassland/ ; //the National Key Program of Research and Development/ ; }, abstract = {BACKGROUND: Currently, there are fewer studies on the intestinal microbes of wild zokors, and it is unclear how zokors adapt to special underground environments by regulating their intestinal microbes. Here, we explored the function of intestinal microbes of Eospalax cansus and Eospalax rothschildi based on metagenomics.

RESULTS: Both zokor species have similar intestinal microbial composition, but E. cansus has a higher proportion of bacteria involved in carbohydrate degradation. Functional analysis based on KEGG and CAZy databases indicated that the intestinal microbes of E. cansus harboured stronger carbohydrate degradation ability, mainly in starch and sucrose metabolism, and further in cellulose degradation. Furthermore, the cellulase activity was significantly higher in E. cansus than that in E. rothschildi. Eospalax cansus has a stronger microbial fermentation ability due to an increase in fibre-degrading bacteria like unclassified_f_Lachnospiraceae, Ruminococcus, and Clostridium. In addition, the dominant bacteria isolated from zokor were Bacillus, some of which could degrade both cellulose and hemicellulose.

CONCLUSION: Metagenomic analysis and bacterial isolation experiments indicate that E. cansus has a stronger microbial cellulose-degrading capacity, possibly as an adaptation to its limited food resources underground. © 2024 Society of Chemical Industry.}, } @article {pmid39628067, year = {2025}, author = {Fujimoto, S and Hatano, K and Banno, E and Motooka, D and De Velasco, MA and Kura, Y and Toyoda, S and Hashimoto, M and Adomi, S and Minami, T and Yoshimura, K and Oka, T and Hata, J and Matsushita, M and Takao, T and Takada, S and Tsujimura, A and Kojima, Y and Obara, W and Nakamura, S and Uemura, H and Nonomura, N and Fujita, K}, title = {Comparative analysis of gut microbiota in hormone-sensitive and castration-resistant prostate cancer in Japanese men.}, journal = {Cancer science}, volume = {116}, number = {2}, pages = {462-469}, pmid = {39628067}, issn = {1349-7006}, support = {//Yakult Bio-Science Foundation/ ; //The Japanese Foundation for Prostate Research (JFPR)/ ; //The Japanese Urological Association/ ; }, mesh = {Male ; *Gastrointestinal Microbiome/genetics ; Animals ; Humans ; *Prostatic Neoplasms, Castration-Resistant/microbiology/genetics/pathology ; Mice ; Aged ; Japan ; *RNA, Ribosomal, 16S/genetics ; Mice, Transgenic ; Middle Aged ; Mice, Knockout ; Disease Progression ; Lactobacillus/genetics/isolation & purification ; Aged, 80 and over ; Disease Models, Animal ; East Asian People ; }, abstract = {Gut microbiota plays a crucial role in the development and progression of prostate cancer, with previous studies indicating that certain bacterial taxa are more abundant in castration-resistant prostate cancer (CRPC) compared to hormone-sensitive prostate cancer (HSPC). Notably, the composition of gut microbiota can vary significantly by geographic region, and Japanese individuals have a distinct microbial profile. However, research exploring these differences within Japanese populations remains limited. This study investigated the gut microbiota differences between Japanese men with HSPC and CRPC and further validated these findings using a transgenic mouse model. Rectal swab samples were collected from 140 Japanese men diagnosed with HSPC (n = 84) or CRPC (n = 56) between September 2020 and July 2022. Gut microbiota composition was analyzed using 16S rRNA gene sequencing. Additionally, Pten-KO mice, which model the progression from HSPC to CRPC, underwent similar microbiota analysis. Results revealed significant differences in gut microbiota composition between HSPC and CRPC patients. Specifically, the CRPC group showed a higher abundance of Firmicutes, including Gemella and Lactobacillus, compared to the HSPC group. These differences were mirrored in the mouse model, where CRPC mice also showed an increase in these bacteria. This study identifies distinct microbial differences between HSPC and CRPC in Japanese men, suggesting that Gemella and Lactobacillus may be associated with the progression to castration resistance in prostate cancer. These findings suggest that gut microbiota differences may be associated with prostate cancer progression. Further research is needed to explore the potential of targeting the microbiota as a therapeutic strategy.}, } @article {pmid39627869, year = {2024}, author = {Richy, E and Thiago Dobbler, P and Tláskal, V and López-Mondéjar, R and Baldrian, P and Kyselková, M}, title = {Long-read sequencing sheds light on key bacteria contributing to deadwood decomposition processes.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {99}, pmid = {39627869}, issn = {2524-6372}, support = {CZ.02.01.01/00/22_008/0004635//Ministry of Education, Youth and Sports of the Czech Republic/ ; }, abstract = {BACKGROUND: Deadwood decomposition is an essential ecological process in forest ecosystems, playing a key role in nutrient cycling and carbon sequestration by enriching soils with organic matter. This process is driven by diverse microbial communities encompassing specialized functions in breaking down organic matter, but the specific roles of individual microorganisms in this process are still not fully understood.

RESULTS: Here, we characterized the deadwood microbiome in a natural mixed temperate forest in Central Europe using PacBio HiFi long-read sequencing and a genome-resolved transcriptomics approach in order to uncover key microbial contributors to wood decomposition. We obtained high quality assemblies, which allowed attribution of complex microbial functions such as nitrogen fixation to individual microbial taxa and enabled the recovery of metagenome-assembled genomes (MAGs) from both abundant and rare deadwood bacteria. We successfully assembled 69 MAGs (including 14 high-quality and 7 single-contig genomes) from 4 samples, representing most of the abundant bacterial phyla in deadwood. The MAGs exhibited a rich diversity of carbohydrate-active enzymes (CAZymes), with Myxococcota encoding the highest number of CAZymes and the full complement of enzymes required for cellulose decomposition. For the first time we observed active nitrogen fixation by Steroidobacteraceae, as well as hemicellulose degradation and chitin recycling by Patescibacteria. Furthermore, PacBio HiFi sequencing identified over 1000 biosynthetic gene clusters, highlighting a vast potential for secondary metabolite production in deadwood, particularly in Pseudomonadota and Myxococcota.

CONCLUSIONS: PacBio HiFi long-read sequencing offers comprehensive insights into deadwood decomposition processes by advancing the identification of functional features involving multiple genes. It represents a robust tool for unraveling novel microbial genomes in complex ecosystems and allows the identification of key microorganisms contributing to deadwood decomposition.}, } @article {pmid39627685, year = {2024}, author = {Bradford, LM and Carrillo, C and Wong, A}, title = {Managing false positives during detection of pathogen sequences in shotgun metagenomics datasets.}, journal = {BMC bioinformatics}, volume = {25}, number = {1}, pages = {372}, pmid = {39627685}, issn = {1471-2105}, support = {OAF-2020-101088//Ontario Ministry of Agriculture, Food, and Rural Affairs (OMAFRA)/ ; }, mesh = {*Metagenomics/methods ; *Salmonella/genetics ; *Software ; False Positive Reactions ; Sensitivity and Specificity ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; Food Microbiology/methods ; }, abstract = {BACKGROUND: Culture-independent diagnostic tests are gaining popularity as tools for detecting pathogens in food. Shotgun sequencing holds substantial promise for food testing as it provides abundant information on microbial communities, but the challenge is in analyzing large and complex sequencing datasets with a high degree of both sensitivity and specificity. Falsely classifying sequencing reads as originating from pathogens can lead to unnecessary food recalls or production shutdowns, while low sensitivity resulting in false negatives could lead to preventable illness.

RESULTS: We used simulated and published shotgun sequencing datasets containing Salmonella-derived reads to explore the appearance and mitigation of false positive results using the popular taxonomic annotation softwares Kraken2 and Metaphlan4. Using default parameters, Kraken2 is sensitive but prone to false positives, while Metaphlan4 is more specific but unable to detect Salmonella at low abundance. We then developed a bioinformatic pipeline for identifying and removing reads falsely identified as Salmonella by Kraken2 while retaining high sensitivity. Carefully considering software parameters and database choices is essential to avoiding false positive sample calls. With well-chosen parameters plus additional steps to confirm the taxonomic origin of reads, it is possible to detect pathogens with very high specificity and sensitivity.}, } @article {pmid39626922, year = {2024}, author = {Vasudevan, HN and Lazar, AA and Reyes, K and Rong, DA and Arevalo, S and Federman, S and Chan, JW and Chiu, CY and Miller, S and Yom, SS}, title = {Comparison of Plasma Metagenomic Next-generation Sequencing and PCR Methods for Epstein-Barr Virus Viral Load Monitoring in Nasopharyngeal Carcinoma.}, journal = {Anticancer research}, volume = {44}, number = {12}, pages = {5445-5453}, doi = {10.21873/anticanres.17370}, pmid = {39626922}, issn = {1791-7530}, mesh = {Humans ; *Herpesvirus 4, Human/genetics/isolation & purification ; *Viral Load ; *Nasopharyngeal Carcinoma/virology/blood/diagnosis ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Female ; *Metagenomics/methods ; Middle Aged ; *Epstein-Barr Virus Infections/virology/blood/diagnosis ; *Polymerase Chain Reaction/methods ; *Nasopharyngeal Neoplasms/virology/blood/diagnosis ; Adult ; Aged ; DNA, Viral/blood/genetics ; }, abstract = {BACKGROUND/AIM: Plasma Epstein-Barr virus (EBV) viral load measurement is prognostic in nasopharyngeal carcinoma (NPC) disease monitoring; however, a consensus measurement approach does not exist. This study characterized the clinical performance of metagenomic next-generation sequencing (mNGS), an unbiased sequencing-based assay distinct from polymerase chain reaction (PCR) or targeted sequencing approaches, in 73 peripheral blood specimens from 32 patients diagnosed with NPC.

PATIENTS AND METHODS: Samples were analyzed for plasma EBV viral load either by mNGS profiling or PCR-based assays (either LMP2 or BAMHI-W PCR) and compared to tumor presence by clinical assessment. Plasma mNGS-based EBV detection was quantified as reads per million (RPM).

RESULTS: Plasma mNGS displayed similar overall performance (100% sensitivity, 86% specificity, 92% accuracy) to BAMHI-W PCR (100% sensitivity, 86% specificity, 94% accuracy) and superior performance to the LMP2 PCR assay (36% sensitivity, 56% specificity, 45% accuracy). In a subset of 13 patients who underwent longitudinal analysis, plasma mNGS EBV RPM correlated with cancer recurrence (95%CI Pre-CRT=232.10±214; 95%CI Post-CRT=0.34±0.32; 95%CI difference=-231.70±214; *p=0.03, paired t-test), suggesting plasma mNGS exhibits potential for monitoring recurrence.

CONCLUSION: Plasma mNGS is a distinct method for EBV titer measurement in NPC patients and more broadly, is a promising method for non-invasive monitoring of disease status for infection-associated malignancies.}, } @article {pmid39626557, year = {2025}, author = {Peng, Q and Cheng, S and Huang, X and Pu, Y and Xie, G}, title = {Comprehensive multi-omics analysis of fermented Chinese artichoke: Insights from Flavoromics, metagenomics, and untargeted metabolomics.}, journal = {Food chemistry}, volume = {467}, number = {}, pages = {142278}, doi = {10.1016/j.foodchem.2024.142278}, pmid = {39626557}, issn = {1873-7072}, mesh = {*Bacteria/metabolism/genetics/classification/isolation & purification ; *Cynara scolymus/chemistry/metabolism ; *Fermentation ; Fermented Foods/analysis/microbiology ; *Flavoring Agents/metabolism/chemistry ; *Metabolomics ; *Metagenomics ; Microbiota ; Multiomics ; *Taste ; *Volatile Organic Compounds/metabolism/chemistry/analysis ; }, abstract = {Fermented Chinese Artichoke, a traditional Chinese fermented vegetable, has a distinctive flavor profile shaped by its fermentation process. This study applied flavoromics, metagenomics, and untargeted metabolomics to comprehensively analyze flavor compounds, microbial communities, and metabolic transformations during fermentation. We identified 43 volatile organic compounds (VOCs), with Terpineol, 1-Hexanol, and Linalool as the predominant components. Metagenomic analysis highlighted Lactiplantibacillus plantarum, Priestia megaterium, and Pediococcus pentosaceus as the dominant species, while Lactiplantibacillus, Pediococcus, and Bacillus were key in flavor development. Untargeted metabolomics further revealed increases in organic acids, amino acids, and umami compounds, contributing to flavor enhancement. These findings offer valuable insights into flavor formation mechanisms in Fermented Chinese Artichoke and provide guidance for improving its industrial fermentation quality.}, } @article {pmid39626551, year = {2025}, author = {Xu, C and Han, A and Tian, Y and Sun, S}, title = {Based on computer simulation and experimental verification: mining and characterizing novel antimicrobial peptides from soil microbiome.}, journal = {Food chemistry}, volume = {467}, number = {}, pages = {142275}, doi = {10.1016/j.foodchem.2024.142275}, pmid = {39626551}, issn = {1873-7072}, mesh = {*Soil Microbiology ; *Antimicrobial Peptides/chemistry/pharmacology ; Microbiota ; Anti-Bacterial Agents/pharmacology/chemistry ; Computer Simulation ; Microbial Sensitivity Tests ; Klebsiella pneumoniae/drug effects ; Staphylococcus aureus/drug effects/growth & development ; Molecular Docking Simulation ; Escherichia coli/drug effects/genetics ; Bacteria/drug effects/genetics ; Molecular Dynamics Simulation ; }, abstract = {Antimicrobial peptides (AMPs) show great promise for enhancing food safety and extending shelf life, but traditional screening methods are complex and costly. To address these issues, we developed a deep learning-based prediction pipeline to identify potential AMPs from soil metagenomic data, achieving high accuracy (92.71 %) and precision (91.29 %). Based on model scoring, surface charge, and Hemopred and ToxinPred screenings, we identified nine candidate peptides. Peptide P4 (GTAWRWHYRARS) showed the best binding affinity to MrkH in molecular docking studies and was validated through molecular dynamics simulations. The chemically synthesized P4 demonstrated significant antimicrobial activity against Klebsiella pneumoniae, Escherichia coli, and Staphylococcus aureus, indicating its potential as an effective alternative to traditional food antimicrobial agents. This study highlights the effectiveness of our integrated prediction pipeline for discovering new AMPs.}, } @article {pmid39626421, year = {2024}, author = {Wang, J and Wu, D and Wu, Q and Chen, J and Zhao, Y and Wang, H and Liu, F and Yuan, Q}, title = {Vertical profiles of community and activity of methanotrophs in large lake and reservoir of Southwest China.}, journal = {The Science of the total environment}, volume = {957}, number = {}, pages = {177782}, doi = {10.1016/j.scitotenv.2024.177782}, pmid = {39626421}, issn = {1879-1026}, mesh = {China ; *Lakes/microbiology/chemistry ; *Methane/metabolism/analysis ; *Geologic Sediments/microbiology/chemistry ; Methylococcaceae/genetics/metabolism ; Oxidation-Reduction ; RNA, Ribosomal, 16S ; Environmental Monitoring ; Microbiota ; }, abstract = {Microbial methane oxidation plays a significant role in regulating methane emissions from lakes and reservoirs. However, the differences in methane oxidation activity and methanotrophic community between lakes and reservoirs remain inadequately characterized. In this study, sediment and water samples were collected from the large shallow lake (Dianchi) and deep reservoirs (Dongfeng and Hongjiadu) located in karst area, Southwest China. The results indicated that the rates of aerobic oxidation of methane (AeOM) in lake sediment ranged from 7.1 to 27.7 μg g[-1] d[-1], which was higher than that in reservoirs sediment (1.92 to 11.56 μg g[-1] d[-1]). Similarly, the average AeOM in the water column of lake (104.7 μg L[-1] d[-1]) was much higher than that of reservoirs (46 μg L[-1] d[-1]). The content of sediment organic carbon and dissolved inorganic carbon were important factors that influenced the rates of AeOM in sediment and water column, respectively. 16S rRNA genes sequencing revealed a higher relative abundance of methanotrophs in lake sediments compared to reservoir sediments. The dominant methanotrophic taxa in lake was Methylococcaceae (type Ib), while Methylomonadaceae (type Ia) was predominant in reservoirs. Meanwhile, anaerobic methane-oxidizing microorganisms Candidatus Methylomirabilis and Candidatus Methanoperedens were also abundant in sediments of reservoirs. However, metatranscriptomic analysis revealed that the type I methanotrophs, especially Methylobacter, was most active in the sediment of both lake and reservoir. Water depth and conductivity could be the key controlling factors of the structures of methanotrophic communities in sediment and water column, respectively. Metagenome-assembled genomes suggested that type I methanotrophs exhibited greater motility, as evidenced by a higher number of flagellar assembly genes, while type II methanotrophs demonstrated advantages in metabolic processes such as carbon, phosphorus, and methane metabolism.}, } @article {pmid39626398, year = {2025}, author = {Song, A and Si, Z and Xu, D and Wei, B and Wang, E and Chong, F and Fan, F}, title = {Lanthanum and cerium added to soil influence microbial carbon and nitrogen cycling genes.}, journal = {Journal of environmental management}, volume = {373}, number = {}, pages = {123509}, doi = {10.1016/j.jenvman.2024.123509}, pmid = {39626398}, issn = {1095-8630}, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Carbon/metabolism ; *Cerium ; *Nitrogen/metabolism ; *Lanthanum ; *Nitrogen Cycle ; Microbiota ; }, abstract = {The soil microbiome plays an important role in carbon (C) and nitrogen (N) processing and storage and is influenced by rare earth elements (REEs), which can have both direct and indirect effects on plant metabolic processes. Using conventional physicochemical methods and metagenomic-based analyses, we investigated REEs effects on soil respiration, soil mineral N, soil microbial community structure and functional genes related to C and N metabolism. High doses of cerium (0.16 and 0.32 mmol kg[-1] soil) increased CO2 net production rate by 59 and 42%, and N2O net production rate by 255 and 609%, respectively, compared to no REEs. Similarly, high doses of lanthanum (0.16 and 0.32 mmol kg[-1] soil) increased CO2 net production rate by 47 and 39%, and N2O net production rate by 105 and 187%, respectively. Increased soil respiration from altered relative abundances of key soil microorganisms associated with soil N cycling and organic matter degradation and functional genes encoding enzymes involved in C and N metabolism, accelerated N mineralization. Elevated REEs levels substantially increased the relative abundances of functional genes related to cellulose, chitin, glucans, hemicellulose, lignin, and peptidoglycan degradation. REEs also influenced multiple functional genes associated with the N cycle. The abundance of genes responsible for organic N degradation and synthesis, such as asnB, gdh_K15371, glsA, and gs, increased with elevated cerium and lanthanum concentrations. Similarly, the abundances of denitrification genes, including narl, narJ, narZ, and nosZ, also rose with increasing amounts of cerium and lanthanum. However, the decrease in narB and nirB gene abundance with increasing REE concentrations was attributed to the reduction of nitrate to amino groups. Our findings highlight the influence of REEs on key soil microorganisms associated with soil N cycling and organic matter degradation and key functional genes in soil C and N metabolism, with implications for agriculture, environmental protection, and human health.}, } @article {pmid39626197, year = {2024}, author = {Jéglot, A and Sanchez-Cid, C and Sørensen, SR and Schnorr, KM and Plauborg, F and Vogel, TM and Elsgaard, L}, title = {Bacterial bioaugmentation of woodchip bioreactors to increase nitrate removal in cold agricultural drainage water.}, journal = {Environmental technology}, volume = {}, number = {}, pages = {1-12}, doi = {10.1080/09593330.2024.2432483}, pmid = {39626197}, issn = {1479-487X}, abstract = {Woodchip bioreactors (WBRs) are biological systems designed to prevent excess nitrate (NO3[-]) leaching from agricultural fields to aquatic ecosystems. Nitrate is removed by microbial denitrification, but the enzyme-mediated process slows down at cold temperatures (<10°C), where NO3[-] removal in WBRs can be less than 20%. We studied the use of bacterial bioaugmentation in replicated test-scale WBRs (∼0.1 m[3]) as an environmental technology to increase NO3[-] removal at cold temperatures. Nitrate removal rates increased following injection of a nitrate-reducing inoculum (Pseudomonas proteolytica and Klebsiella sp.), but the effect disappeared within a week and was reproduced in control WBRs by injection of sterile medium (phosphate buffer saline). Metagenome analyses showed a shift in the bacterial community composition after bioaugmentation in the planktonic phase of the woodchip reactors, but not in the solid phase (woodchip matrix). Only in the planktonic phase, Pseudomonas and Klebsiella increased their relative abundance as monitored by 16S rRNA gene sequences. In addition, an increased abundance of genes related to NO3[-] transformation after bacterial inoculation was observed in the metagenomic sequences. After one week, bacterial community composition became similar to its initial state, indicating resilience of the WBR microbial communities. We conclude that improved inoculation methods are needed to unlock the potential of bioaugmentation to increase NO3[-] removal at cold temperatures and make it a relevant technology for practical use at field-scale.}, } @article {pmid39625881, year = {2024}, author = {Sun, B and Guo, J and Jin, H and Jin, Z and Sun, Y and Mao, Y and Xie, F and He, Y and Sun, Z and Li, W and Ivanov, I and Tian, H}, title = {MetaCONNET: A metagenomic polishing tool for long-read assemblies.}, journal = {PloS one}, volume = {19}, number = {12}, pages = {e0313515}, pmid = {39625881}, issn = {1932-6203}, mesh = {*Metagenomics/methods ; *Metagenome ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Software ; Animals ; Deep Learning ; }, abstract = {Accurate and high coverage genome assemblies are the basis for downstream analysis of metagenomic studies. Long-read sequencing technology is an ideal tool to facilitate the assemblies of metagenome, except for the drawback of usually producing reads with high sequencing error rate. Many polishing tools were developed to correct the sequencing error, but most are designed on the ground of one or two species. Considering the complexity and uneven depth of metagenomic study, we present a novel deep-learning polishing tool named MetaCONNET for polishing metagenomic assemblies. We evaluate MetaCONNET against Medaka, CONNET and NextPolish in accuracy, coverage, contiguity and resource consumption. Our results demonstrate that MetaCONNET provides a valuable polishing tool and can be applied to many metagenomic studies.}, } @article {pmid39625614, year = {2024}, author = {Saeng-Kla, K and Mhuantong, W and Termsaithong, T and Pinyakong, O and Sonthiphand, P}, title = {Biodegradation of Di-2-Ethylhexyl Phthalate by Mangrove Sediment Microbiome Impacted by Chronic Plastic Waste.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {27}, number = {1}, pages = {19}, pmid = {39625614}, issn = {1436-2236}, support = {FF-072/2567//Mahidol University (Fundamental Fund: fiscal year 2024 by National Science Research and Innovation Fund (NSRF)/ ; }, mesh = {*Diethylhexyl Phthalate/metabolism ; *Geologic Sediments/microbiology ; *Biodegradation, Environmental ; *Microbiota ; Water Pollutants, Chemical/metabolism ; Plastics/metabolism ; Gordonia Bacterium/metabolism/genetics ; Plasticizers/metabolism ; Wetlands ; Bacteria/metabolism/classification/genetics/isolation & purification ; }, abstract = {Plastic pollution through the leaching of di(2-ethylhexyl) phthalate (DEHP), a widely used plasticizer, has led to the emergence of mangrove pollution. This study aimed to assess the DEHP removal efficiency of indigenous mangrove sediment microbiomes and identify key DEHP degraders using microcosm construction and metagenomic analysis. During the 35-day incubation period, the indigenous mangrove sediment microbiome, affected by chronic plastic pollution, demonstrated a 99% degradation efficiency of 200 mg/kg DEHP. Spearman's correlation analysis suggested that Myxococcales, Methyloligellaceae, Mycobacterium, and Micromonospora were potentially responsible for DEHP degradation. Based on PICRUSt2, the DEHP-degrading pathway in the sediment was predicted to be an anaerobic process involving catechol metabolism through catC, pcaD, pcaI, pcaF, and fadA. Efficient bacterial isolates from the mangrove sediment, identified as Gordonia sp. and Gordonia polyisoprenivorans, were able to degrade DEHP (65-97%) within 7 days and showed the ability to degrade other phthalate esters (PAEs).}, } @article {pmid39624724, year = {2024}, author = {Liu, Z and Yin, Q and Fang, Y and Zhang, X and Xia, W and Jiao, Z and Song, T and Wan, H and Guo, T}, title = {Effect of exogenous thermophilic biocontrol agent inoculum on the high temperature chicken manure composting.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1484047}, pmid = {39624724}, issn = {1664-302X}, abstract = {INTRODUCTION: Aerobic composting is an effective method for utilizing chicken manure. However, its low carbon to nitrogen (C/N) ratio leads to slow heating and short high-temperature phases, which reduce composting efficiency and product quality.

METHODS: To address this issue, splinted mushroom cultivation residues were added to adjust the C/N ratio, and exogenous thermophilic composting strains were introduced to increase composting temperature. This study analyzed the relationship between physicochemical metabolites and microbial community structure during high-temperature chicken manure composting.

RESULTS AND DISCUSSION: Based on metagenomic and physicochemical analyses, results showed that the exogenous microbial agents extended the thermophilic phase by three-times, reduced the heating phase duration by 75%, and increased nitrogen, phosphorus, potassium, and soluble organic carbon contents by 3.61, 21.63, 7.21, and 39.03%, respectively. Genes associated with amino acid metabolism were significantly enriched during the heating phase, while genes involved in the tricarboxylic acid cycle were more active in the thermophilic phase. During the thermophilic phase, bacterial diversity and richness decreased compared to the heating and cooling phases. Functional microbes such as Bacillus, Caldicoprobacter, and Virgibacillus showed a positive correlation with the key differential metabolites. While Actinomadura, Saccharomonospora, Paenibacillus, and Aneurinibacillus displayed an opposite correlation. Further experiments demonstrated that the increased temperature during the thermophilic phase triggered the upregulation of oleic acid metabolism and piperidine metabolism pathways in functional microorganisms, leading to the production of heat stabilizers and protective agents like oleic acid, gallic acid, and 2-piperidone. This phenomenon helped maintain microbial viability during the thermophilic phase and improved composting efficiency.}, } @article {pmid39624721, year = {2024}, author = {Liu, C and Dan, H and Yang, Y and Du, Y and Hao, Z and Chen, L and Zhu, K and Liu, B and Niu, L and Zhao, Y and Wang, Y and Shen, L and Gan, M and Zhu, L}, title = {Enhanced immunity: the gut microbiota changes in high-altitude Tibetan pigs compared to Yorkshire pigs.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1469253}, pmid = {39624721}, issn = {1664-302X}, abstract = {INTRODUCTION: Long-term domestication in high-altitude environments has led to unique changes in the gut microbiota of Tibetan Pigs. This study aims to investigate specific alterations in the intestinal flora of Tibetan Pigs compared to Yorkshire pigs.

METHODS: We employed 16S rRNA and metagenomic sequencing technologies for comprehensive analysis of the gut microbiota. The data collected allowed us to assess microbial community structures and functional capabilities.

RESULTS: Our analysis revealed that Tibetan Pigs raised under a "free-range + supplementary feeding" model exhibited increased abundance of microbial communities associated with short-chain fatty acid synthesis and the digestion of cellulose and hemicellulose. Notably, the characteristic bacterium Rhodococcus, commonly found in high-altitude environments, was enriched in the gut microbiota of Tibetan Pigs, facilitating the efficient utilization of natural compounds and degradation of toxic substances. Additionally, the increased abundance of probiotics in these pigs enhances their immunity, which may involve mechanisms such as disrupting the structure of pathogenic bacteria and detoxifying harmful metabolites.

DISCUSSION: These findings underscore the advantages of Tibetan Pigs over common commercial breeds, highlighting their unique gut microbiota adaptations. Furthermore, they open new avenues for screening potential probiotics and developing genetic breeding strategies for improved livestock varieties.

CONCLUSION: Understanding the distinct gut microbiota of Tibetan Pigs provides valuable insights into their health benefits and resilience, contributing to future research on breed improvement and microbiome applications in agriculture.}, } @article {pmid39624636, year = {2024}, author = {Huang, H and Liu, Y and Liu, Y and Lin, J and Guo, H and Xu, Q and Zhang, H and Li, Z and Zhu, H and Ding, M}, title = {Analysis and Perception of Chlamydia psittaci Pneumonia: Novel Insights of the Rare Disease in Infectiology.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {5261-5275}, pmid = {39624636}, issn = {1178-6973}, abstract = {OBJECTIVE: To investigate and analyze the clinical features, diagnosis and treatment, and prognosis of rare Chlamydia psittaci pneumonia, and to improve the understanding of this rare disease.

METHODS: A retrospective analysis and exploration was performed for 33 cases of patients with Chlamydia psittaci pneumonia in the First Affiliated Hospital of Gannan Medical University from January 2017 to March 2024, and the clinical features, diagnosis, treatment and key points for differential diagnosis were summarized and analyzed. Meanwhile, the latest literature from PubMed was retrieved to systematically discuss the research progress in Chlamydia psittaci pneumonia.

RESULTS: A total of 33 patients with Chlamydia psittaci pneumonia were included in this study, including 21 males (63.64%) and 12 females (36.36%), with a median age of 59 (32-79) years. There were 27 cases (81.82%) of patients accompanied with a history of poultry contact, 22 patients (66.67%) had underlying diseases. In our study, patients with Chlamydia psittaci pneumonia were mainly affected in Autumn (21.21%) and Winter (54.55%). All patients had undergone bronchoscopy and obtained bronchoalverolar lavage fluid (BALF) for metagenomic next-generation sequencing (mNGS) detection, and mNGS results showed that all patients (100%) were co-infected with multiple pathogens including Chlamydia psittaci. All patients were given antimicrobial therapy after diagnosis, and no treatment-related adverse reactions or adverse events were observed in our study, the average length of hospitalization was 11.09 days. Fortunately, no death was observed in our study, and patients were all discharged from hospital after recovery and in favourable physical and psychological conditions after discharge.

CONCLUSION: Chlamydia psittaci pneumonia lacks specific clinical features or manifestations and tends to develop into severe exacerbation. mNGS could help to achieve an accurate diagnosis. Early administration of antibiotics can improve the prognosis of patients to the greatest extent.}, } @article {pmid39624158, year = {2024}, author = {Jimenez-Lopez, O and Ray, T and Dean, C and Slizovskiy, I and Deere, J and Wolf, T and Moore, S and Primus, A and Høy-Petersen, J and Finstad, S and Mo, J and Sørum, H and Noyes, N}, title = {The gut microbiome and resistome of yellow perch (Perca flavescens) living in Minnesota lakes under varying anthropogenic pressure.}, journal = {One health (Amsterdam, Netherlands)}, volume = {19}, number = {}, pages = {100933}, pmid = {39624158}, issn = {2352-7714}, abstract = {Anthropogenic activities can significantly impact wildlife in natural water bodies, affecting not only the host's physiology but also its microbiome. This study aimed to analyze the gut microbiome and antimicrobial resistance gene profile (i.e., the resistome) of yellow perch living in lakes subjected to different levels of anthropogenic pressure: wastewater effluent-impacted lakes and undeveloped lakes. Total DNA and RNA from gut content samples were extracted and sequenced for analysis. Results indicate that the gut resistome and microbiome of yellow perch differ between lakes, perhaps due to varying anthropogenic pressure. The resistome was predominated by macrolide resistance genes, particularly the MLS23S group, making up 53 % of resistome sequences from effluent-impacted lakes and 73 % from undeveloped lakes. The colistin resistance gene group (mcr) was detected in numerous samples, including variants associated with Aeromonas and the family Enterobacteriaceae. The gut microbiome across all samples was dominated by the phyla Proteobacteria, Firmicutes, and Actinobacteria, with the opportunistic pathogens Plesiomonas shigelloides and Aeromonas veronii more abundant in effluent-impacted lakes. Metagenomic analysis of wild fish samples offers valuable insights into the effects of anthropogenic pressures on microbial communities, including antimicrobial resistance genes, in water bodies.}, } @article {pmid39624075, year = {2024}, author = {Chen, X and Zheng, H and Wang, T and Feng, Z and Wang, J and Liu, Y and Qin, W and Kong, F and Qin, X}, title = {Early Hints of Metagenome Next-Generation Sequencing and Copy Number Variations Analysis: An Occult Case of Leptomeningeal Metastasis With Rapid Cognitive Decline.}, journal = {Clinical case reports}, volume = {12}, number = {12}, pages = {e9676}, pmid = {39624075}, issn = {2050-0904}, abstract = {Early detection and treatment are critical for improving the prognosis of patients with leptomeningeal metastasis. However, heterogeneous clinical manifestations, non-specific imaging, and limited sensitivity of cerebrospinal fluid cytology posed challenges to identifying leptomeningeal metastasis in the early stage. Here we reported a case of lung adenocarcinoma complaining of rapid cognitive decline, whose magnetic resonance imaging showed interstitial brain edema. Under the circumstances of negative cerebrospinal fluid cytology, metagenome next-generation sequencing and copy number variations analysis were applied, which indicated leptomeningeal metastasis and was confirmed in the subsequent cytology.}, } @article {pmid39624039, year = {2024}, author = {Sha, J and Shao, J and Lu, S and Zhang, M and Gu, C and Deng, Y and Zhang, J and Feng, Y}, title = {A case report of severe pneumonia caused by Aeromonas dhakensis infection complicated with severe atrial septal defect.}, journal = {Frontiers in medicine}, volume = {11}, number = {}, pages = {1476864}, pmid = {39624039}, issn = {2296-858X}, abstract = {Aeromonas dhakensis is an increasingly recognized human pathogen in recent years and was first isolated and reported in a sample of childhood diarrhea in Bangladesh. More and more cases of Aeromonas dhakensis infection have been reported in recent years. Here we report a case of severe pneumonia caused by Aeromonas dhakensis with severe atrial septal defect. The patient, a 56-year-old male, was admitted to the hospital with severe hypoxemia and severe septic shock. Detection of the patient's bronchoalveolar lavage fluid (BALF) and peripheral blood by the metagenomic next generation sequencing (mNGS) indicated Aeromonas dhakensis infection.}, } @article {pmid39623774, year = {2025}, author = {Hu, Y and Wang, ML and Yang, RL and Shao, ZK and Du, YH and Kang, Y and Zhu, YX and Xue, XF}, title = {Symbiotic bacteria play crucial roles in a herbivorous mite host suitability.}, journal = {Pest management science}, volume = {81}, number = {3}, pages = {1657-1668}, doi = {10.1002/ps.8571}, pmid = {39623774}, issn = {1526-4998}, support = {//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Symbiosis ; *Herbivory ; *Solanum lycopersicum/microbiology ; *Mites/physiology/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; Solanum melongena/microbiology ; Capsicum/microbiology ; Bacterial Physiological Phenomena ; Microbiota ; }, abstract = {BACKGROUND: The tomato russet mite (TRM), Aculops lycopersici, is a strictly herbivorous and economically significant pest that infests Solanaceae plants, but its host suitability varies, showing high performance on tomatoes. Although symbiotic bacteria have been suggested to play crucial roles in the host adaptation of herbivores, their effects on TRM remain unclear.

RESULTS: In this study, using next generation high-throughput sequencing of the bacterial 16S rRNA data, we identified the bacterial diversity and community composition of TRM feeding on tomato, eggplant, and chili. Our results show no significant difference in the bacterial community composition of TRM across three host plants. However, the relative density of Escherichia coli (TRM_Escherichia) showed 9.36-fold higher on tomato than on eggplant and chili. These results align with the observed TRM performance among three host plants. When TRM_Escherichia was reduced using antibiotics, the treated TRM decreased the population density on tomato. However, when we transferred TRM from eggplant to tomato, the population density of TRM increased, coinciding with an increase of the TRM_Escherichia density. These results indicate that TRM_Escherichia may affect the host suitability of TRM. Our fluorescence in situ hybridization (FISH) results further showed that TRM_Escherichia is primarily distributed in the salivary glands. Metagenomic data results suggest that TRM_Escherichia functions in food digestion and energy metabolism.

CONCLUSION: We provided the first comprehensive analysis of TRM bacterial communities. Our findings demonstrate that the symbiotic bacterium TRM_Escherichia may play crucial roles in the suitability of TRM feeding on different Solanaceae hosts. © 2024 Society of Chemical Industry.}, } @article {pmid39623670, year = {2024}, author = {Babady, NE and Chiu, CY and Craney, A and Gaston, DC and Hicklen, RS and Hogan, CA and John, TM and Stewart, AG}, title = {Diagnosis and management of invasive fungal diseases by next-generation sequencing: are we there yet?.}, journal = {Expert review of molecular diagnostics}, volume = {}, number = {}, pages = {1-14}, doi = {10.1080/14737159.2024.2436396}, pmid = {39623670}, issn = {1744-8352}, abstract = {INTRODUCTION: Invasive fungal diseases (IFDs) are a serious threat to immunocompromised patients. Routine diagnostic methods have limited performance in identifying IFDs. Next-generation sequencing (NGS), including metagenomic NGS (mNGS) and whole-genome sequencing (WGS), recently emerged as diagnostic methods that could provide more accurate and timely diagnoses and management of IFDs.

AREAS COVERED: This article describes the emergence of NGS as a diagnostic tool to address the limitations of current tests. The literature regarding its application and clinical utility in the diagnosis of IFDs is reviewed. Practical considerations, challenges, and opportunities as they relate to the development and implementation of mNGS and WGS for fungal pathogens are discussed.

EXPERT OPINION: NGS emerged over a decade ago with the potential to solve many of the challenges in diagnosing infectious diseases, including IFDs. However, published literature has yielded conflicting data about its clinical utility. The increased clinical adoption of NGS is improving our understanding of how to interpret and use its results to guide actionable decisions. Still, several gaps remain. As the cost, effort, and expertise involved in performing NGS decrease and the reporting of its results becomes standardized, NGS is poised to fill current gaps in the diagnosis of IFDs.}, } @article {pmid39623529, year = {2024}, author = {Ma, J and Sun, S and Cheng, X and Meng, C and Zhao, H and Fu, W and Gao, Y and Ma, L and Yang, Z and Yao, H and Su, J}, title = {Unraveling the role of gut microbiome in predicting adverse events in neoadjuvant therapy for rectal cancer.}, journal = {Human vaccines & immunotherapeutics}, volume = {20}, number = {1}, pages = {2430087}, pmid = {39623529}, issn = {2164-554X}, mesh = {Adult ; Aged ; Female ; Humans ; Male ; Middle Aged ; Chemoradiotherapy/adverse effects/methods ; *Feces/microbiology ; *Gastrointestinal Microbiome ; Immunotherapy/methods/adverse effects ; Metabolome ; Metabolomics ; Metagenomics/methods ; *Neoadjuvant Therapy/adverse effects/methods ; *Rectal Neoplasms/therapy/microbiology ; }, abstract = {Some patients may develop adverse events during neoadjuvant chemoradiotherapy combined with immunotherapy, influencing response rates. The roles of intestinal microbiome and its metabolites in therapeutic adverse events remain unclear. We collected baseline fecal samples from 21 patients with adverse events (AE group) and 11 patients without adverse events (Non-AE group). Their microbiota and metabolome were characterized using metagenomic shotgun sequencing and untargeted metabolomics. At the species level, the gut microbiota in the Non-AE group exhibits significantly higher abundance of Clostridium sp. Alistipes sp. and lower abundance of Lachnoclostridium sp. Weissella cibaria, Weissella confusa, compared to the AE group (p < .05). A total of 58 discriminative metabolites were identified between groups. Beta-alanine metabolism was scattered. Boc-beta-cyano-L-alanine and CoQ9 were significantly increased in patients without adverse events, while linoleic acid increased in patients with adverse events. The increased Alistipes sp. in the Non-AE group was positively correlated with Boc-beta-cyano-L-alanine and negatively correlated with linoleic acid (p < .05). We constructed a combined microbiome-metabolite model to distinguish Non-AE and AE patients with an AUC of 0.963 via the random forest algorithm. Our findings provided a novel insight into the interplay of multispecies microbial cluster and metabolites of rectal patients with adverse events in neoadjuvant chemoradiotherapy combined with immunotherapy. These microbiota and metabolites deserve further investigations to reveal their roles in adverse events, providing clues for better treatment scenarios.Trial registration number: ClinicalTrials.gov identifier: NCT05368051.}, } @article {pmid39623429, year = {2024}, author = {Jiang, J and Wei, Y and Li, S and Mo, J and Li, X and Cao, M and Wang, H}, title = {Study on the application of microfluidic-based in vitro diagnostic technology in pathogenic detection of respiratory tract infections.}, journal = {Journal of translational medicine}, volume = {22}, number = {1}, pages = {1092}, pmid = {39623429}, issn = {1479-5876}, support = {2022PY026//Health Bureau of Zhejiang Province/ ; 2024KY44//Health Bureau of Zhejiang Province/ ; }, mesh = {Humans ; *Respiratory Tract Infections/microbiology/diagnosis ; *Microfluidics/methods ; Male ; Female ; Middle Aged ; *ROC Curve ; Adult ; Aged ; High-Throughput Nucleotide Sequencing ; Bronchoalveolar Lavage Fluid/microbiology ; Young Adult ; Adolescent ; }, abstract = {OBJECTIVE: To investigate the clinical application value of microfluidic-based in vitro diagnostic (IVD) technology in pathogenic detection of respiratory tract infections.

METHODS: A total of 300 clinical samples, including blood, bronchoalveolar lavage fluid, and pleural effusion, were collected from patients with respiratory tract infections. The samples were randomly divided into three groups: A, B, and C, with 100 cases in each group. Group A used traditional microbiological detection methods, Group B used metagenomic next-generation sequencing (mNGS) technology, and Group C used both microfluidic-based IVD technology and traditional microbiological detection methods to detect pathogenic microorganisms in the clinical samples. The positive detection rate, detection time, and detection cost were compared among the groups. The diagnostic performance of each group was compared using the Receiver Operating Characteristic (ROC) curve.

RESULTS: Traditional microbiological detection identified 38 positive samples (38%), including 45 pathogens; mNGS technology identified 95 positive samples (95%), including 210 pathogens; microfluidic-based IVD technology identified 96 positive samples (96%), including 158 pathogens. Microfluidic-based IVD technology had a significantly higher positive detection rate for pathogenic microorganisms compared to traditional culture techniques (96% vs 38%, χ2 = 122.0, P < 0.01), and it was also faster and cheaper than mNGS technology. ROC analysis showed that compared to traditional microbiological culture results, microfluidic-based IVD technology had significantly increased sensitivity and specificity, similar to mNGS technology.

CONCLUSION: In respiratory infectious diseases, microfluidic-based IVD technology had a higher detection rate for pathogenic microorganisms than traditional culture methods, and it had advantages in detection time and cost compared to mNGS technology. It could also detect critical drug-resistant genes of pathogens. Hence, microfluidic-based IVD technology can be a viable option for diagnosis and treatment of respiratory infectious diseases.}, } @article {pmid39622769, year = {2024}, author = {Ivan, FX and Tiew, PY and Jaggi, TK and Thng, KX and Pang, PH and Ong, TH and Abisheganaden, JA and Koh, MS and Chotirmall, SH}, title = {Sputum metagenomics reveals a multidrug resistant Pseudomonas-dominant severe asthma phenotype in an Asian population.}, journal = {Respirology (Carlton, Vic.)}, volume = {}, number = {}, pages = {}, doi = {10.1111/resp.14863}, pmid = {39622769}, issn = {1440-1843}, support = {AcRF Tier 1 Grant (RT1/22)//Singapore Ministry of Education/ ; MOH-000710//Singapore Ministry of Health's National Medical Research Council/ ; MOH-001275-00//Singapore Ministry of Health's National Medical Research Council/ ; MOH-001356//Singapore Ministry of Health's National Medical Research Council/ ; MOH-001636//Singapore Ministry of Health's National Medical Research Council/ ; }, abstract = {BACKGROUND AND OBJECTIVE: While the lung microbiome in severe asthma has been studied, work has employed targeted amplicon-based sequencing approaches without functional assessment with none focused on multi-ethnic Asian populations. Here we investigate the clinical relevance of microbial phenotypes of severe asthma in Asians using metagenomics.

METHODS: Prospective assessment of clinical, radiological, and immunological measures were performed in a multi-ethnic Asian severe asthma cohort (N = 70) recruited across two centres in Singapore. Sputum was subjected to shotgun metagenomic sequencing and patients followed up for a 2-year period. Metagenomic assessment of sputum microbiomes, resistomes and virulomes were related to clinical outcomes.

RESULTS: The lung microbiome in a multi-ethnic Asian cohort with severe asthma demonstrates an increased abundance of Pseudomonas species. Unsupervised clustering of sputum metagenomes identified two patient clusters: C1 (n = 52) characterized by upper airway commensals and C2 (n = 18) dominated by established respiratory pathogens including M. catarrhalis, S. aureus and most significantly P. aeruginosa. C2 patients demonstrated a significantly increased exacerbation frequency on 2-year follow up and an antimicrobial resistome characterized by multidrug resistance. Virulomes appear indistinguishable between severe asthmatics with or without co-existing bronchiectasis, and C2 patients exhibit increased gene expression related to biofilm formation, effector delivery systems and microbial motility. Independent comparison of the C2 cluster to a non-asthmatic bronchiectasis cohort demonstrates analogous airway microbial virulence patterns.

CONCLUSION: Sputum metagenomics demonstrates a multidrug-resistant Pseudomonas-dominant severe asthma phenotype in Asians, characterized by poor clinical outcome including increased exacerbations which is independent of co-existing bronchiectasis.}, } @article {pmid39622690, year = {2024}, author = {Kim, S and Suh, DH and Lee, S and Kim, HS and Cho, SH and Woo, YR}, title = {Associations Between Skin Microbiome and Metabolome in the Pathogenesis of Atopic Dermatitis Patients With Scalp Involvement.}, journal = {Allergy, asthma & immunology research}, volume = {16}, number = {6}, pages = {668-681}, pmid = {39622690}, issn = {2092-7355}, support = {2021R1I1A1A01052146/NRF/National Research Foundation of Korea/Korea ; }, abstract = {PURPOSE: Atopic dermatitis (AD) is a chronic inflammatory skin condition influenced by various factors, such as the skin microbiome and metabolome. However, specific contributions of these factors to scalp involvement in AD still need to be explored. In this study, we aimed to assess the associations between the skin microbiome and metabolome in AD patients with scalp dermatitis and healthy controls (HCs).

METHODS: A total of 20 AD patients with scalp involvement and 16 HCs were recruited, and their skin samples were collected for analysis. Bioinformatic analysis and 16S rRNA metagenomic sequencing were performed, with gas chromatography time-of-flight mass spectrometry (GC-TOF-MS) conducted for AD-associated skin metabolites. Spearman correlation analysis was used to identify the correlations between AD-associated skin bacteria and metabolites.

RESULTS: The results revealed significant differences in bacterial taxa and metabolites between the lesional and non-lesional scalp skin samples of AD patients (groups LS and NL, respectively) and those of HCs (group HC). Notably, group LS showed a significantly increased relative abundance of the genus Staphylococcus and a decreased abundance of Cutibacterium compared to group HC. The reduced abundance of Cutibacterium was also observed when comparing LS to NL. The GC-TOF-MS analysis identified 33 significantly decreased metabolites and 17 significantly increased metabolites in groups LS and NL compared with group HC. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that amino acid-related metabolism was significantly altered in the metabolic pathway between groups LS, NL, and HC. Furthermore, Spearman correlation analysis showed significant correlations of the altered bacteria genera and skin metabolites between the 3 groups.

CONCLUSIONS: The results of this research provide valuable insights into the associations the skin microbiome and metabolome between groups LS, NL, and HC. Identifying these specific contributions may offer new avenues for understanding the pathogenesis of scalp involvement in AD patients and potentially lead to improving management strategies.}, } @article {pmid39621710, year = {2024}, author = {Mangoma, N and Zhou, N and Ncube, T}, title = {Metagenome-assembled genomes provide insight into the microbial taxonomy and ecology of the Buhera soda pans, Zimbabwe.}, journal = {PloS one}, volume = {19}, number = {12}, pages = {e0299620}, pmid = {39621710}, issn = {1932-6203}, mesh = {Zimbabwe ; *Metagenome ; *Phylogeny ; Metagenomics/methods ; Bacteria/genetics/classification ; Genome, Bacterial ; Ecosystem ; Microbiota/genetics ; Extreme Environments ; }, abstract = {The use of metagenomics has substantially improved our understanding of the taxonomy, phylogeny and ecology of extreme environment microbiomes. Advances in bioinformatics now permit the reconstruction of almost intact microbial genomes, called metagenome-assembled genomes (MAGs), from metagenomic sequence data, allowing for more precise cell-level taxonomic, phylogenetic and functional profiling of uncultured extremophiles. Here, we report on the recovery and characterisation of metagenome-assembled genomes from the Buhera soda pans located in eastern Zimbabwe. This ecosystem has not been studied despite its unique geochemistry and potential as a habitat for unique microorganisms. Metagenomic DNA from the soda pan was sequenced using the DNA Nanoball Sequencing (DNBSEQR) technique. Sequence analysis, done on the Knowledgebase (KBase) platform, involved quality assessment, read assembly, contig binning, and MAG extraction. The MAGs were subjected to taxonomic placement, phylogenetic profiling and functional annotation in order to establish their possible ecological roles in the soda pan ecosystem. A total of 16 bacterial MAGs of medium to high quality were recovered, all distributed among five phyla dominated by Pseudomonadota and Bacillota. Of the ten MAGs that were taxonomically classified up to genus level, five of them belonged to the halophilic/ haloalkaliphilic genera Alkalibacterium, Vibrio, Thioalkalivibrio, Cecembia and Nitrincola, underscoring the importance of haloalkaliphiles in the Buhera soda pans. Functional profiling revealed the possession of diverse carbohydrate-metabolising pathways by the MAGs, with glycolysis and the pentose phosphate pathways appearing to be key pathways in this ecosystem. Several MAGs possessed pathways that implicated them in some key aspects of the nitrogen and sulphur cycle. Some MAGs harboured both sulphate reduction and respiratory pathways, suggesting a possible mechanism of ATP biosynthesis through sulphate respiration. This study demonstrates the feasibility of the recovery and taxonomic and functional annotation of high quality microbial genomes from extreme environments, making it possible to establish the ecological roles and biotechnological potential of uncultured microorganisms.}, } @article {pmid39621607, year = {2024}, author = {Deel, HL and Manter, DK and Moore, JM}, title = {Rethreading the needle: A novel molecular index of soil health (MISH) using microbial functional genes to predict soil health management.}, journal = {PloS one}, volume = {19}, number = {12}, pages = {e0314072}, pmid = {39621607}, issn = {1932-6203}, mesh = {*Soil Microbiology ; *Soil/chemistry ; *RNA, Ribosomal, 16S/genetics ; Metagenome ; Bacteria/genetics/classification/isolation & purification ; Microbiota/genetics ; Machine Learning ; Ecosystem ; Genes, Microbial ; }, abstract = {Soil health relies on the actions and interactions of an abundant and diverse biological community. Current soil health assessments rely heavily on a suite of soil biological, chemical, and physical indicators, often excluding molecular information. Soil health is critical for sustainable agricultural production, and a comprehensive understanding of how microbial communities provide ecosystem services can help guide management practices. To explore the role of microbial function in soil health, 536 soil samples were collected from 26 U.S. states, representing 52 different crops and grazing lands, and analyzed for various soil health indicators. The bacterial functional profile was characterized using 16S ribosomal RNA gene sequencing paired with PICRUSt2 to predict metagenome functions. Functional data were used as predictors in eXtreme Gradient Boosting (XGBoost), a powerful machine learning algorithm, and enzymes important to soil health indicators were compiled into a Molecular Index of Soil Health (MISH). The overall MISH score significantly correlated with non-molecular measures of soil health and management practice adoption. Additionally, several new enzymes were identified as potential targets to better understand microbial mediation of soil health. This low-cost, DNA-based approach to measuring soil health is robust and generalizable across climates.}, } @article {pmid39621289, year = {2024}, author = {Salam, LB and Apollos, EE and Obayori, OS and Michael, GI}, title = {Physicochemistry and comparative metagenomics of a tropical estuary persistently inundated with anthropogenic pollutants.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, pmid = {39621289}, issn = {1874-9356}, abstract = {The physicochemistry, metabolic properties, and microbial community structure of a tropical estuary persistently inundated with anthropogenic pollutants were elucidated using diverse analytical tools and a shotgun metagenomics approach. The physicochemistry of the Awoye estuary surface water (AEW) and sediment (AES) revealed higher values in the sediment for most of the parameters analyzed, while aside from copper and zinc, the concentrations of the detected heavy metals (Cd, Cr, Pb, Fe, As, Ni, Hg, Mn, Se) in the water and sediment were higher than the acceptable thresholds. Hydrocarbon content analysis revealed increasingly high concentrations of high molecular weight polycyclic aromatic hydrocarbons (HMW PAHs) in the sediment. Structurally, the predominant taxa in the AEW metagenome are Proteobacteria (50.35%), Alphaproteobacteria (43.31%), Brevundimonas (49.96%), and Leptolyngbya boryana (14.93%), while in the sediment (AES) metagenome, Proteobacteria (53.03%), Gammaproteobacteria (28.66%), Azospirillum (6.51%), and Acidihalobacter prosperus (7.56%) were preponderant. Statistical analysis of the two microbiomes (AEW, AES) revealed significant statistical differences (P < 0.05) at all the hierarchical levels. Functional characterization of the two metagenomes revealed extensive adaptations of the sediment microbiome to various environmental stressors as evident in the high numbers of putative genes involved in the degradation of diverse classes of aromatic hydrocarbons, efflux, detoxification, and transport of heavy metals, and metabolism of organic/inorganic nutrients. Findings from this study revealed that the estuary sediment is the sink for most of the anthropogenic pollutants and harbors the more adapted microbiome that could serve as a potential bioresource for the bioremediation of the perturbed estuary.}, } @article {pmid39621260, year = {2025}, author = {Gigante, CM and Weigand, MR and Li, Y}, title = {Orthopoxvirus Genome Sequencing, Assembly, and Analysis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2860}, number = {}, pages = {39-63}, pmid = {39621260}, issn = {1940-6029}, mesh = {*Orthopoxvirus/genetics ; *Genome, Viral ; *High-Throughput Nucleotide Sequencing/methods ; Humans ; Computational Biology/methods ; Metagenomics/methods ; Poxviridae Infections/virology ; Sequence Analysis, DNA/methods ; Molecular Sequence Annotation ; Whole Genome Sequencing/methods ; }, abstract = {Poxviruses have exceptionally large genomes compared to most other viruses, which represent unique challenges to sequencing and assembly due to complex features such as repeat elements and low complexity sequences. The 2022 global mpox outbreak led to an unprecedented level of poxvirus sequencing as public health and research institutions faced with large sample numbers and demand for fast turnaround, merged NGS protocols designed for small RNA viruses with poxvirus expertise. Traditional manual assembly, checking, and editing of genomes was not feasible. Here, we present a protocol for metagenomic sequencing and orthopoxvirus genome assembly directly from DNA extracted from a patient lesion swab with no viral enrichment or host depletion. This sequencing approach is cost effective when using high throughput sequencing instruments and allows for detection of genomic insertions, deletions, and large rearrangement with confidence. We describe usage of two publicly available bioinformatic pipelines for genome assembly, quality control, annotation, and submission to sequence repositories.}, } @article {pmid39621089, year = {2024}, author = {Singh, K and Gupta, JK and Chanchal, DK and Shinde, MG and Kumar, S and Jain, D and Almarhoon, ZM and Alshahrani, AM and Calina, D and Sharifi-Rad, J and Tripathi, A}, title = {Natural products as drug leads: exploring their potential in drug discovery and development.}, journal = {Naunyn-Schmiedeberg's archives of pharmacology}, volume = {}, number = {}, pages = {}, pmid = {39621089}, issn = {1432-1912}, abstract = {Natural products have been pivotal in drug discovery, offering a wealth of bioactive compounds that significantly contribute to therapeutic developments. Despite the rise of synthetic chemistry, natural products continue to play a crucial role due to their unique chemical structures and diverse biological activities. This study reviews and evaluates the potential of natural products in drug discovery and development, emphasizing the integration of traditional knowledge with modern drug discovery methodologies and addressing the associated challenges. A comprehensive literature search was conducted across PubMed/MedLine, Scopus, Web of Science, Google Scholar, and Cochrane Library, covering publications from 2000 to 2023. Inclusion criteria focused on studies related to natural products, bioactive compounds, medicinal plants, phytochemistry, and AI applications in drug discovery. Data were categorized into source, extraction methods, bioactivity assays, and technological advances. The current review underscores the historical and ongoing importance of natural products in drug discovery. Technological advancements in chromatographic and spectroscopic techniques have improved the isolation and structural elucidation of bioactive compounds. AI and machine learning have streamlined the identification and optimization of natural product leads. Challenges such as biodiversity sustainability and development complexities are discussed, alongside innovative approaches like biosynthetic engineering and metagenomics. Natural products remain a vital source of novel therapeutic agents, providing unique chemical diversity and specific biological activities. Integrating traditional knowledge with modern scientific methods is essential for maximizing the potential of natural products in drug discovery. Despite existing challenges, ongoing research and technological advancements are expected to enhance the efficiency and success of natural product-based drug development.}, } @article {pmid39620486, year = {2024}, author = {Luo, Y and Sheikh, TMM and Li, X and Yuan, Y and Yao, F and Wang, M and Guo, X and Wu, J and Shafiq, M and Xie, Q and Jiao, X}, title = {Exploring the dynamics of gut microbiota, antibiotic resistance, and chemotherapy impact in acute leukemia patients: A comprehensive metagenomic analysis.}, journal = {Virulence}, volume = {15}, number = {1}, pages = {2428843}, pmid = {39620486}, issn = {2150-5608}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Metagenomics ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Male ; Female ; Adult ; Middle Aged ; Feces/microbiology ; Bacteria/genetics/drug effects/classification/isolation & purification ; Leukemia/drug therapy/microbiology/complications ; Drug Resistance, Microbial/genetics ; Aged ; Young Adult ; Antineoplastic Agents/adverse effects ; }, abstract = {Leukemia poses significant challenges to its treatment, and understanding its complex pathogenesis is crucial. This study used metagenomic sequencing to investigate the interplay between chemotherapy, gut microbiota, and antibiotic resistance in patients with acute leukemia (AL). Pre- and post-chemotherapy stool samples from patients revealed alterations in microbial richness, taxa, and antibiotic resistance genes (ARGs). The analysis revealed a decreased alpha diversity, increased dispersion in post-chemotherapy samples, and changes in the abundance of specific bacteria. Key bacteria such as Enterococcus, Klebsiella, and Escherichia coli have been identified as prevalent ARG carriers. Correlation analysis between gut microbiota and blood indicators revealed potential links between microbial species and inflammatory biomarkers, including C-reactive protein (CRP) and adenosine deaminase (ADA). This study investigated the impact of antibiotic dosage on microbiota and ARGs, revealing networks connecting co-occurring ARGs with microbial species (179 nodes, 206 edges), and networks associated with ARGs and antibiotic dosages (50 nodes, 50 edges). Antibiotics such as cephamycin and sulfonamide led to multidrug-resistant Klebsiella colonization. Our analyses revealed distinct microbial profiles with Salmonella enterica elevated post-chemotherapy in NF patients and Akkermansia muciniphila elevated pre-chemotherapy. These microbial signatures could inform strategies to modulate the gut microbiome, potentially mitigating the risk of neutropenic fever in patients undergoing chemotherapy. Finally, a comprehensive analysis of KEGG modules shed light on disrupted metabolic pathways after chemotherapy, providing insights into potential targets for managing side effects. Overall, this study revealed intricate relationships between gut microbiota, chemotherapy, and antibiotic resistance, providing new insights into improving therapy and enhancing patient outcomes.}, } @article {pmid39620359, year = {2024}, author = {López-Agudelo, VA and Falk-Paulsen, M and Bharti, R and Rehman, A and Sommer, F and Wacker, EM and Ellinghaus, D and Luzius, A and Sievers, LK and Liebeke, M and Kaser, A and Rosenstiel, P}, title = {Defective Atg16l1 in intestinal epithelial cells links to altered fecal microbiota and metabolic shifts during pregnancy in mice.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2429267}, pmid = {39620359}, issn = {1949-0984}, mesh = {Animals ; Female ; Pregnancy ; *Gastrointestinal Microbiome ; Mice ; *Feces/microbiology ; *Autophagy-Related Proteins/genetics/metabolism ; Bacteria/classification/genetics/isolation & purification/metabolism ; RNA, Ribosomal, 16S/genetics ; Intestinal Mucosa/microbiology/metabolism ; Epithelial Cells/microbiology/metabolism ; Crohn Disease/microbiology/metabolism ; Mice, Inbred C57BL ; Metagenomics ; Chemokine CXCL1/genetics/metabolism ; }, abstract = {Throughout gestation, the female body undergoes a series of transformations, including profound alterations in intestinal microbial communities. Changes gradually increase toward the end of pregnancy and comprise reduced α-diversity of microbial communities and an increased propensity for energy harvest. Despite the importance of the intestinal microbiota for the pathophysiology of inflammatory bowel diseases, very little is known about the relationship between these microbiota shifts and pregnancy-associated complications of the disease. Here, we explored the longitudinal dynamics of gut microbiota composition and functional potential during pregnancy and after lactation in Atg16l1[∆IEC] mice carrying an intestinal epithelial deletion of the Crohn's disease risk gene Atg16l1. Using 16S rRNA amplicon and shotgun metagenomic sequencing, we demonstrated divergent temporal shifts in microbial composition between Atg16l1 wildtype and Atg16l1[∆IEC] pregnant mice in trimester 3, which was validated in an independent experiment. Observed differences included microbial genera implicated in IBD such as Lachnospiraceae, Roseburia, Ruminococcus, and Turicibacter. Changes partially recovered after lactation. Additionally, metagenomic and metabolomic analyses suggest an increased capacity for chitin degradation, resulting in higher levels of free N-acetyl-glucosamine products in feces, alongside reduced glucose and myo-inositol levels in serum around the time of delivery. On the host side, we found that the immunological response of Atg16l1[∆IEC] mice is characterized by higher colonic mRNA levels of TNFα and CXCL1 in trimester 3 and a lower weight of offspring at birth. Understanding pregnancy-dependent microbiome changes in the context of IBD may constitute the first step in the identification of fecal microbial biomarkers and microbiota-directed therapies that could help improve precision care for managing pregnancies in IBD patients.}, } @article {pmid39620249, year = {2024}, author = {Kim, LY and Schüssler-Fiorenza Rose, SM and Mengelkoch, S and Moriarity, DP and Gassen, J and Alley, JC and Roos, LG and Jiang, T and Alavi, A and Thota, DD and Zhang, X and Perelman, D and Kodish, T and Krupnick, JL and May, M and Bowman, K and Hua, J and Liao, YJ and Lieberman, AF and Butte, AJ and Lester, P and Thyne, SM and Hilton, JF and Snyder, MP and Slavich, GM}, title = {California Stress, Trauma, and Resilience Study (CalSTARS) protocol: A multiomics-based cross-sectional investigation and randomized controlled trial to elucidate the biology of ACEs and test a precision intervention for reducing stress and enhancing resilience.}, journal = {Stress (Amsterdam, Netherlands)}, volume = {27}, number = {1}, pages = {2401788}, doi = {10.1080/10253890.2024.2401788}, pmid = {39620249}, issn = {1607-8888}, mesh = {Humans ; Cross-Sectional Studies ; *Stress, Psychological ; *Resilience, Psychological ; *Adverse Childhood Experiences ; California ; Adult ; Female ; Male ; Precision Medicine/methods ; Multiomics ; }, abstract = {Adverse Childhood Experiences (ACEs) are very common and presently implicated in 9 out of 10 leading causes of death in the United States. Despite this fact, our mechanistic understanding of how ACEs impact health is limited. Moreover, interventions for reducing stress presently use a one-size-fits-all approach that involves no treatment tailoring or precision. To address these issues, we developed a combined cross-sectional study and randomized controlled trial, called the California Stress, Trauma, and Resilience Study (CalSTARS), to (a) characterize how ACEs influence multisystem biological functioning in adults with all levels of ACE burden and current perceived stress, using multiomics and other complementary approaches, and (b) test the efficacy of our new California Precision Intervention for Stress and Resilience (PRECISE) in adults with elevated perceived stress levels who have experienced the full range of ACEs. The primary trial outcome is perceived stress, and the secondary outcomes span a variety of psychological, emotional, biological, and behavioral variables, as assessed using self-report measures, wearable technologies, and extensive biospecimens (i.e. DNA, saliva, blood, urine, & stool) that will be subjected to genomic, transcriptomic, proteomic, metabolomic, lipidomic, immunomic, and metagenomic/microbiome analysis. In this protocol paper, we describe the scientific gaps motivating this study as well as the sample, study design, procedures, measures, and planned analyses. Ultimately, our goal is to leverage the power of cutting-edge tools from psychology, multiomics, precision medicine, and translational bioinformatics to identify social, molecular, and immunological processes that can be targeted to reduce stress-related disease risk and enhance biopsychosocial resilience in individuals and communities worldwide.}, } @article {pmid39620245, year = {2024}, author = {Fukuda, S and Akatsu, T and Fujii, A and Kawano, S and Minegishi, Y and Ota, N}, title = {Commensal Neisseria Inhibit Porphyromonas Gingivalis Invasion of Gingival Epithelial Cells.}, journal = {Oral health & preventive dentistry}, volume = {22}, number = {}, pages = {609-616}, doi = {10.3290/j.ohpd.b5866430}, pmid = {39620245}, issn = {1757-9996}, mesh = {*Porphyromonas gingivalis ; *Gingiva/microbiology ; Humans ; *Epithelial Cells/microbiology ; *Neisseria ; *Microscopy, Electron, Scanning ; Flow Cytometry ; }, abstract = {PURPOSE: Periodontal disease is caused by periodontal invasion by pathogens such as Porphyromonas gingivalis. Although recent metagenomic analyses have shown that oral commensal bacteria are abundant in the mouth of healthy individuals, few studies have experimentally verified the benefits and functions of oral commensal bacteria in periodontal diseases. In this study, we focused on Neisseria among the oral commensal bacteria and aimed to experimentally verify its effects on P. gingivalis invasion.

MATERIALS AND METHODS: We evaluated the inhibitory effect of Neisseria spp. on P. gingivalis invasion using a flow cytometry-based invasion assay and analysed bacterial interactions by visualisation using scanning electron microscopy. Furthermore, we constructed a new experimental pre-mixed culture system that reproduced the interaction environment to evaluate the relevance of this interaction in invasion inhibition.

RESULTS: Flow cytometry-based invasion assays showed that all Neisseria spp. inhibited P. gingivalis invasion, with Neisseria mucosa and Neisseria elongata being particularly effective. Interaction analysis using scanning electron microscopy showed that N. mucosa and N. elongata, which have strong inhibitory effects on P. gingivalis invasion, interacted with P. gingivalis at high frequencies.

CONCLUSION: Commensal Neisseria was found to exert a beneficial function by directly interacting with P. gingivalis and inhibiting its invasion of gingival epithelial cells. These results suggest that Neisseria, as a probiotic or synbiotic oral commensal, may represent an innovative approach to preventing periodontal disease.}, } @article {pmid39620111, year = {2024}, author = {Zhao, J and Wang, C and Hu, J and Ma, R and Yu, B and Zhao, W and Wang, H and Gu, Y and Zhang, J}, title = {Corrigendum: Integrated metagenomics and metabolomics analyses revealed biomarkers in β-casein A2A2-type cows.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1518338}, doi = {10.3389/fvets.2024.1518338}, pmid = {39620111}, issn = {2297-1769}, abstract = {[This corrects the article DOI: 10.3389/fvets.2024.1438717.].}, } @article {pmid39620093, year = {2024}, author = {Thompson, CC and Wasielesky, W and Landuci, F and Lima, MS and Bacha, L and Perazzolo, LM and Lourenço-Marques, C and Soares, F and Pousão-Ferreira, P and Hanson, L and Gomez-Gil, B and Thompson, M and Varasteh, T and Silva, TA and Swings, J and Zhang, XH and de Souza, W and Thompson, FL}, title = {Understanding the role of microbes in health and disease of farmed aquatic organisms.}, journal = {Marine life science & technology}, volume = {6}, number = {4}, pages = {579-609}, pmid = {39620093}, issn = {2662-1746}, abstract = {Aquaculture is critical to reduce protein deficiencies and supplement the world's demand for seafood. However, the culture environment predisposes farmed animals to infectious diseases. In particular, the high density of fish, crustacean, mollusk, sea cucumber or algal species allows for the rapid spread of infectious diseases resulting in devastating losses. Massive amounts of antibiotics have been used to sustain aquaculture production. This has led to the critical need to evaluate the impact of current control measures and optimize disease management schemes with an emphasis on global impact and sustainability. Furthermore, local and global changes have enhanced the pathogens' effects over aquaculture settings because increased temperature and pollution may trigger virulence genes and toxin production. Technological developments including biofloc technology, integrated multitrophic systems, recirculating aquaculture systems and probiotics have contributed to enhancing aquaculture sustainability and reducing the need for high loads of antibiotics and other chemicals. Furthermore, biotechnological tools (e.g., omics and cell biology) have shed light on cellular processes in the health and disease of reared organisms. Metagenomics is a reliable and relatively quick tool to identify microbial communities in aquaculture settings.}, } @article {pmid39619951, year = {2024}, author = {Wang, X and Hu, X and He, W and Yin, JY}, title = {Inulin does not affect trimethylamine N-oxide formation in mice with a high-fat diet combined with choline and L-carnitine.}, journal = {Food science & nutrition}, volume = {12}, number = {11}, pages = {8968-8977}, pmid = {39619951}, issn = {2048-7177}, abstract = {Emerging evidence suggests that gut bacteria-derived trimethylamine N-oxide (TMAO) elevates the risk of cardiovascular disease, and dietary fiber holds the potential to attenuate TMAO formation. However, the effectiveness of dietary fiber, such as inulin, in inhibiting TMAO formation remains controversial. Therefore, this study investigated the effect of inulin supplementation on TMAO formation in mice with high TMAO levels induced by a high-fat diet (HFD) combined with choline and L-carnitine. Results showed that HFD treatment significantly elevated blood TMAO concentrations and increased the abundances of TMAO formation-associated gut bacteria, as well as the abundances of functional genes responsible for TMA formation. While the supplementation of choline and L-carnitine greatly enhanced blood trimethylamine (TMA) and TMAO levels, inulin supplementation did not significantly affect TMAO levels and had limited impact on TMA-associated gut bacteria, except for Desulfitobacterium hafniense.}, } @article {pmid39619731, year = {2024}, author = {Wen, S and Zeng, JJ and Li, Y}, title = {Rickettsia felis Pulmonary Infection Detected via Metagenomic Next-Generation Sequencing in a Clonorchiasis Patient: A Case Report.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {5189-5194}, pmid = {39619731}, issn = {1178-6973}, abstract = {Rickettsia felis (R. felis) is a Gram-negative obligate intracellular bacterium with a global presence across various hosts, including mammals, humans, and ectoparasites. Herein, we present a case of R. felis infection in a previously healthy 43-year-old male with a history of Clonorchis sinensis and recent corticosteroid use. The identification of R. felis was accomplished through metagenomic next-generation sequencing (mNGS) of the patient's bronchoalveolar lavage fluid (BALF). This case represents the first documented pulmonary infection caused by R. felis in China, confirmed by mNGS analysis of bronchoalveolar lavage fluid (BALF) and reported from Shenzhen, China.}, } @article {pmid39619691, year = {2024}, author = {Xie, R and Danso, B and Sun, J and Al-Tohamy, R and Khalil, MA and Schagerl, M and Ali, SS}, title = {Metagenomics analysis of bacterial community structure from wood- and soil-feeding termites: metabolic pathways and functional structures toward the degradation of lignocellulose and recalcitrant compounds.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1424982}, pmid = {39619691}, issn = {1664-302X}, abstract = {Some essential information on gut bacterial profiles and their unique contributions to food digestion in wood-feeding termites (WFT) and soil-feeding termites (SFT) is still inadequate. The feeding type of termites is hypothesized to influence their gut bacterial composition and its functionality in degrading lignocellulose or other organic chemicals. This could potentially provide alternative approaches for the degradation of some recalcitrant environmental chemicals. Therefore, metagenomic analysis can be employed to examine the composition and functional profiles of gut bacterial symbionts in WFT and SFT. Based on the metagenomic analysis of the 16S rRNA gene sequences of gut bacterial symbionts in the WFT, Microcerotermes sp., and the SFT, Pericapritermes nitobei, the findings revealed a total of 26 major bacterial phyla, with 18 phyla commonly represented in both termites, albeit in varying abundances. Spirochaetes dominated the bacterial symbionts in Microcerotermes sp. at 55%, followed by Fibrobacters, while Firmicutes dominated the gut bacteria symbionts in P. nitobei at 95%, with Actinobacteria coming in second at 2%. Furthermore, the Shannon and phylogenetic tree diversity indices, as well as the observed operational taxonomic units and Chao 1 richness indices, were all found to be higher in the WFT than in the SFT deduced from the alpha diversity analysis. Based on the principal coordinate analysis, exhibited a significant distance dissimilarity between the gut bacterial symbionts. The results showed that the gut bacterial composition differed significantly between the WFT and SFT. Furthermore, Tax4Fun analysis evaluated bacterial functions, revealing the predominance of carbohydrate metabolism, followed by amino acid metabolism and energy metabolism in both Microcerotermes sp. and P. nitobei termites. The results implicated that bacterial symbionts inhabiting the guts of both termites were actively involved in the degradation of lignocellulose and other recalcitrant compounds.}, } @article {pmid39619690, year = {2024}, author = {Wu, X and Liu, X and Xu, W and Chen, W and Zhong, Z and Tan, H and Xiang, T}, title = {A nested case-control study on the association of gut virome in early pregnancy and gestational diabetes mellitus.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1461259}, pmid = {39619690}, issn = {1664-302X}, abstract = {BACKGROUND: Recent studies have increasingly shown the connection between gut microbiome and gestational diabetes mellitus (GDM). However, no studies have explored the relationship between the gut virome and GDM, and the underlying mechanism remains unknown.

METHODS: We performed a nested case-control study within a follow-up cohort, enrolling 51 patients with GDM and 51 healthy controls. Shotgun metagenomics sequencing was used to explore gut virome profiles during early pregnancy.

RESULTS: Diversity analysis revealed no difference in the overall gut virome composition between two groups, however, we found greater abundance of Escherichia phage SH2026Stx1 (Q = 0.23), Enterobacteria phage mEp043 c-1 (Q = 0.21), crAssphage cr50_1 (Q = 0.21), Enterobacteria phage phi80 (Q = 0.21), and Escherichia phage HK106 (Q = 0.23) in GDM patients. Cross-kingdom correlation analysis showed the negative correlation between the gut bacterium Eubacterium eligens and three bacteriophages (Escherichia phage SH2026Stx1, Enterobacteria phage mEp043 c-1, and Escherichia phage HK106) in GDM group (r < 0, P < 0.05). Based on gut microbial features and clinical indicators, we constructed a new prediction model using random forest method for GDM with good predictive performance (AUC of 0.893, 95% CI: 0.736 ∼ 0.990).

CONCLUSION: This study is the first to investigate the relationship between the gut virome and GDM as well as the cross-kingdom correlation between gut viruses and bacteria in GDM. Our findings could enhance strategies for preventing and treating GDM from the perspective of gut microbiome, offering valuable insights into its pathogenesis.}, } @article {pmid39619689, year = {2024}, author = {Wang, C and Wang, D and Li, C and Ge, Z and Hao, L and Albasher, G and Feng, F and Sun, Y and Lyu, Y and Zheng, S}, title = {Microbial communities during the composting process of Agaricus subrufescens and their effects on mushroom agronomic and nutritional qualities.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1471638}, pmid = {39619689}, issn = {1664-302X}, abstract = {INTRODUCTION: Tunnel composting technology for preparing Agaricus subrufescens cultivation media can achieve a higher biological efficiency (BE) and a lower contamination rate (CR). However, this technology lacks in-depth and systematic study.

METHODS: In the present study, the changes in the microbiome and microbial metabolic functions were surveyed using metagenomic analysis. The physicochemical parameters, agronomic properties and nutritional qualities were also evaluated.

RESULTS AND DISCUSSION: Results showed that the contents of cellulose, hemicellulose and lignin dropped to 10.18, 11.58, 27.53%, respectively at the end of composting. The tunnel composting technology led to significant increases in crude protein content (32.56%) and crude fiber content (13.68%). Variations of physicochemical characteristics led to different successions of microbial communities. Bacteria manifested significantly higher abundance than fungi. Firmicutes, Actinobacteriota, Chloroffexi and Deinococcota were the predominant bacterial phyla. Ascomycota and Basidiomycota were the dominant fungal phyla in the thermophilic phase. Pseudonocardia, Truepera, and Thermopolyspora were positively correlated with the yield of A. subrufescens. In addition to TN, most of the physicochemical properties were significantly correlated with fungal communities in the thermophilic phase. The metabolisms of carbohydrate, amino acid and energy were the primary enrichment pathways. These findings deepen the understanding of microbial communities composition during the composting of A. subrufescens substrates. Moreover, this study provides a basis for improving tunnel composting technology.}, } @article {pmid39619659, year = {2024}, author = {Zhao, Y and Zhang, W and Zhang, X}, title = {Application of metagenomic next-generation sequencing in the diagnosis of infectious diseases.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1458316}, pmid = {39619659}, issn = {2235-2988}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Communicable Diseases/diagnosis/microbiology ; Molecular Diagnostic Techniques/methods ; Bacteria/genetics/isolation & purification/classification ; Viruses/genetics/isolation & purification/classification ; }, abstract = {Metagenomic next-generation sequencing (mNGS) is a transformative approach in the diagnosis of infectious diseases, utilizing unbiased high-throughput sequencing to directly detect and characterize microbial genomes from clinical samples. This review comprehensively outlines the fundamental principles, sequencing workflow, and platforms utilized in mNGS technology. The methodological backbone involves shotgun sequencing of total nucleic acids extracted from diverse sample types, enabling simultaneous detection of bacteria, viruses, fungi, and parasites without prior knowledge of the infectious agent. Key advantages of mNGS include its capability to identify rare, novel, or unculturable pathogens, providing a more comprehensive view of microbial communities compared to traditional culture-based methods. Despite these strengths, challenges such as data analysis complexity, high cost, and the need for optimized sample preparation protocols remain significant hurdles. The application of mNGS across various systemic infections highlights its clinical utility. Case studies discussed in this review illustrate its efficacy in diagnosing respiratory tract infections, bloodstream infections, central nervous system infections, gastrointestinal infections, and others. By rapidly identifying pathogens and their genomic characteristics, mNGS facilitates timely and targeted therapeutic interventions, thereby improving patient outcomes and infection control measures. Looking ahead, the future of mNGS in infectious disease diagnostics appears promising. Advances in bioinformatics tools and sequencing technologies are anticipated to streamline data analysis, enhance sensitivity and specificity, and reduce turnaround times. Integration with clinical decision support systems promises to further optimize mNGS utilization in routine clinical practice. In conclusion, mNGS represents a paradigm shift in the field of infectious disease diagnostics, offering unparalleled insights into microbial diversity and pathogenesis. While challenges persist, ongoing technological advancements hold immense potential to consolidate mNGS as a pivotal tool in the armamentarium of modern medicine, empowering clinicians with precise, rapid, and comprehensive pathogen detection capabilities.}, } @article {pmid39619641, year = {2024}, author = {Xia, T and Huang, F and Yun, F and Liu, Y and Wang, T and Wang, S and Jin, S and Ma, X and Wang, W and He, J and Teng, K and Zhong, J}, title = {Lacticaseibacillus rhamnosus LRJ-1 alleviates constipation through promoting gut Bacteroides-derived γ-aminobutyric acid production.}, journal = {Current research in food science}, volume = {9}, number = {}, pages = {100924}, pmid = {39619641}, issn = {2665-9271}, abstract = {Multiple gastrointestinal disorders are associated with impaired gut microbiota. Probiotic Lacticaseibacillus rhamnosus can improve bowel disorder, however, the action mechanism is poorly understood. We integrated multi-omics data from the gut metagenome, metabolome, and colon transcriptome of constipated mice underlying L. rhamnosus LRJ-1 treatment to provide insights into host-microbial metabolic pathway. We found that oral administration of L. rhamnosus LRJ-1 alleviated constipation in mice accompanied by the increased abundances of fecal γ-aminobutyric acid (GABA) and intestinal commensal Bacteroides, and the activation of host GABAergic synapses. B. uniformis was the most enriched Bacteroides species in constipated mice treated with L. rhamnosus LRJ-1, and contributed to the increased abundance of GABA in the gut. Administration of either B. uniformis ATCC 8492 or GABA alleviated constipation and increased gastrointestinal motility in constipated mice. Knockout of the GABA biosynthetic gad gene in B. uniformis ATCC 8492 decreased GABA production and blocked its beneficial effects on constipation. These results confirm the therapeutic potential of L. rhamnosus LRJ-1 in alleviating constipation through promoting gut commensal Bacteroides-derived GABA production. Targeting the gut microbiome to regulate GABA production may open new insights for efficient constipation treatment.}, } @article {pmid39619416, year = {2024}, author = {Petrone, ME and Charon, J and Grigg, MJ and William, T and Rajahram, GS and Westaway, J and Piera, KA and Shi, M and Anstey, NM and Holmes, EC}, title = {A virus associated with the zoonotic pathogen Plasmodium knowlesi causing human malaria is a member of a diverse and unclassified viral taxon.}, journal = {Virus evolution}, volume = {10}, number = {1}, pages = {veae091}, pmid = {39619416}, issn = {2057-1577}, support = {R01 AI160457/AI/NIAID NIH HHS/United States ; }, abstract = {The Apicomplexa are a phylum of single-celled eukaryotes that can infect humans and include the mosquito-borne parasite Plasmodium, the cause of malaria. Viruses that infect non-Plasmodium spp. disease-causing protozoa affect the pathogen life cycle and disease outcomes. However, only one RNA virus (Matryoshka RNA virus 1) has been identified in Plasmodium, and none have been identified in zoonotic Plasmodium species. The rapid expansion of the known RNA virosphere via metagenomic sequencing suggests that this dearth is due to the divergent nature of RNA viruses that infect protozoa. We leveraged newly uncovered data sets to explore the virome of human-infecting Plasmodium species collected in Sabah, east (Borneo) Malaysia. From this, we identified a highly divergent RNA virus in two human-infecting P. knowlesi isolates that is related to the unclassified group 'ormycoviruses'. By characterizing 15 additional ormycoviruses identified in the transcriptomes of arthropods, we show that this group of viruses exhibits a complex ecology as noninfecting passengers at the arthropod-mammal interface. With the addition of viral diversity discovered using the artificial intelligence-based analysis of metagenomic data, we also demonstrate that the ormycoviruses are part of a diverse and unclassified viral taxon. This is the first observation of an RNA virus in a zoonotic Plasmodium species. By linking small-scale experimental data to advances in large-scale virus discovery, we characterize the diversity and confirm the putative genomic architecture of an unclassified viral taxon. This approach can be used to further explore the virome of disease-causing Apicomplexa and better understand how protozoa-infecting viruses may affect parasite fitness, pathobiology, and treatment outcomes.}, } @article {pmid39619205, year = {2024}, author = {Hewson, I and Brandt, M and Budd, K and Breitbart, M and DeRito, C and Gittens, S and Henson, MW and Hylkema, A and Sevier, M and Souza, M and Vilanova-Cuevas, B and Von Hoene, S}, title = {Viral metagenomic investigation of two Caribbean echinoderms, Diadema antillarum (Echinoidea) and Holothuria floridana (Holothuria).}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e18321}, pmid = {39619205}, issn = {2167-8359}, mesh = {Animals ; *Metagenomics ; Caribbean Region ; *Genome, Viral/genetics ; Echinodermata/virology ; Metagenome ; Holothuria/virology/genetics ; Coral Reefs ; Viruses/genetics/isolation & purification/classification ; Virome/genetics ; }, abstract = {BACKGROUND: Echinoderms play crucial roles in coral reef ecosystems, where they are significant detritivores and herbivores. The phylum is widely known for its boom and bust cycles, driven by food availability, predation pressure and mass mortalities. Hence, surveillance of potential pathogens and associates of grossly normal specimens is important to understanding their roles in ecology and mass mortality.

METHODS: We performed viral surveillance in two common coral reef echinoderms, Diadema antillarum and Holothuria floridana, using metagenomics. Urchin specimens were obtained during the 2022 Diadema antillarum scuticociliatosis mass mortality event from the Caribbean and grossly normal H. floridana specimens from a reef in Florida. Viral metagenomes were assembled and aligned against viral genomes and protein encoding regions. Metagenomic reads and previously sequenced transcriptomes were further investigated for putative viral elements by Kraken2.

RESULTS: D. antillarum was devoid of viruses typically seen in echinoderms, but H. floridana yielded viral taxa similar to those found in other sea cucumbers, including Pisoniviricetes (Picornaviruses), Ellioviricetes (Bunyaviruses), and Magsaviricetes (Nodaviruses). The lack of viruses detected in D. antillarum may be due to the large amount of host DNA in viral metagenomes, or because viruses are less abundant in D. antillarum tissues when compared to H. floridana tissues. Our results also suggest that RNA amplification approach may influence viral representation in viral metagenomes. While our survey was successful in describing viruses associated with both echinoderms, our results indicate that viruses are less pronounced in D. antillarum than in other echinoderms. These results are important in context of wider investigation on the association between viruses and D. antillarum mass mortalities, since the conventional method used in this study was unsuccessful.}, } @article {pmid39618850, year = {2024}, author = {Liu, H and Feng, S and Tang, M and Tian, R and Zhang, S}, title = {Gut Commensal Bacteroides thetaiotaomicron Promote Atherothrombosis via Regulating L-Tryptophan Metabolism.}, journal = {Reviews in cardiovascular medicine}, volume = {25}, number = {11}, pages = {395}, pmid = {39618850}, issn = {2153-8174}, abstract = {BACKGROUND: Coronary thrombosis events continue to be the leading cause of morbidity and mortality worldwide. Recently, emerging evidence has highlighted the role of gut microbiota in cardiovascular disease, but few studies have systematically investigated the gut microbiota variation associated with atherothrombosis.

METHODS: We conducted multi-omics analysis (metagenomics sequencing and serum metabolomics) on 146 subjects from Peking Union Medical College Hospital-Coronary Artery Disease (PUMCH-CAD) cohort. We analyzed the key strains and metabolic pathways related to coronary artery disease (CAD) development, explored the bacterial functional pathway which contributes to atherothrombosis at strain level in depth. Single strain colonization procedures on germ free mice demonstrated the promotion of platelet activation and thrombotic phenotypes of the disordered gut microbiota.

RESULTS: Gut microbiome and serum metabolome shifts were apparent in cases of CAD progression, Bacteroides spp. disturbed the development of CAD by participating in lipopolysaccharide (LPS), menaquinone and methanogenesis pathways. Particularly, coronary thrombosis is characterized by increased circulatory levels of L-tryptophan, which correlate with Bacteroides thetaiotaomicron that has enriched biosynthetic potential. In germ free mice we demonstrate that Bacteroides thetaiotaomicron colonization could induce thrombosis, aggravate platelet hyperreactivity and augment fecal levels of L-tryptophan.

CONCLUSIONS: The disordered gut microbiota of CAD contributed to the occurrence and development of atherothrombosis. The key members of the bacterial and metabolic features may become biomarkers for predicting the cardiovascular thrombosis event. Targeting the microbial pathway may have the potential to reduce the incidence of cardiovascular disorders.

CLINICAL TRIAL REGISTRATION: ChiCTR2000033897, https://www.chictr.org.cn/showproj.html?proj=55023.}, } @article {pmid39618230, year = {2024}, author = {Li, H and Mao, X and Wu, Z and Yu, W}, title = {Omadacycline in the Treatment of Chlamydia psittaci Pneumonia: A Retrospective Study on Efficacy and Safety.}, journal = {British journal of hospital medicine (London, England : 2005)}, volume = {85}, number = {11}, pages = {1-12}, doi = {10.12968/hmed.2024.0381}, pmid = {39618230}, issn = {1750-8460}, mesh = {Humans ; Retrospective Studies ; Male ; Female ; *Anti-Bacterial Agents/therapeutic use/adverse effects ; Middle Aged ; *Chlamydophila psittaci/isolation & purification ; *Tetracyclines/therapeutic use/adverse effects ; Adult ; *Psittacosis/drug therapy/diagnosis/microbiology ; Treatment Outcome ; Aged ; C-Reactive Protein/analysis ; }, abstract = {Aims/Background Chlamydia psittaci is an obligate intracellular bacterium that primarily infects birds, but can cause respiratory infections in humans. Clinical evidence supporting the use of omadacycline for the treatment of Chlamydia psittaci pneumonia remains limited; therefore, this study aimed to evaluate the potential of omadacycline in treating Chlamydia psittaci pneumonia by analyzing the patients' clinical outcomes and the drug safety profile. Methods We retrospectively reviewed the medical records of 15 patients with Chlamydia psittaci pneumonia treated at the First Affiliated Hospital, Zhejiang University School of Medicine between January and December 2023. Following diagnosis with the aid of metagenomic next-generation sequencing, the patients received omadacycline for treatment, and their clinical outcomes and laboratory marker profiles were monitored to assess the treatment efficacy and safety. Results Significant improvements were observed in clinical symptoms and laboratory markers, including C-reactive protein (p < 0.001), procalcitonin (p = 0.001), neutrophil percentage (p < 0.001), and the SpO2/FiO2 ratio (p < 0.001), after treatment with omadacycline. A 100% cure rate was reported within 28 days of treatment initiation, with gastrointestinal disturbances being the most common side effect. Conclusion Omadacycline shows promise in treating Chlamydia psittaci pneumonia and is well tolerated by the users. However, further controlled trials involving larger samples are required to confirm the efficacy and safety of the drug.}, } @article {pmid39616917, year = {2024}, author = {Nassereddine, ZN and Opara, SD and Coutinho, OA and Qyteti, F and Book, R and Heinicke, MP and Napieralski, J and Tiquia-Arashiro, SM}, title = {Critical perspectives on advancing antibiotic resistant gene (ARG) detection technologies in aquatic ecosystems.}, journal = {The Science of the total environment}, volume = {957}, number = {}, pages = {177775}, doi = {10.1016/j.scitotenv.2024.177775}, pmid = {39616917}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents/analysis ; Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; *Ecosystem ; *Environmental Monitoring/methods ; Metagenomics/methods ; *Water Microbiology ; }, abstract = {The spread of antibiotic resistance genes (ARGs) in aquatic ecosystems poses a serious risk to environmental and public health, making advanced detection and monitoring methods essential. This review provides a fresh perspective and a critical evaluation of recent advances in detecting and monitoring ARGs in aquatic environments. It highlights the latest innovations in molecular, bioinformatic, and environmental techniques. While traditional methods like culture-based assays and polymerase chain reaction (PCR) remain important, they are increasingly being supplemented by high-throughput sequencing technologies applied to metagenomics. These technologies offer comprehensive insights into the diversity and distribution of ARGs in aquatic environments. The integration of bioinformatic tools and databases has improved the accuracy and efficiency of ARG detection, enabling the analysis of complex datasets and tracking the evolution of ARGs in aquatic settings. Additionally, new environmental monitoring methods, including novel biosensors, geographic information systems (GIS) applications, and remote sensing technologies, have emerged as powerful tools for real-time ARG surveillance in water systems. This review critically examines the challenges of standardizing these methodologies and emphasizes the need for interdisciplinary approaches to enhance ARG monitoring across different aquatic ecosystems. By assessing the strengths and limitations of various methods, this review aims to guide future research and the development of more effective strategies for managing antibiotic resistance in aquatic environments.}, } @article {pmid39616811, year = {2025}, author = {Riveros, A and Asefaw, BK and Wang, Q and Maqbool, T and Tang, Y and Jiang, D}, title = {Selenium treatment via integrating flow electrode capacitive deionization (FCDI) and bio-electrochemical systems (BES).}, journal = {Water research}, volume = {271}, number = {}, pages = {122844}, doi = {10.1016/j.watres.2024.122844}, pmid = {39616811}, issn = {1879-2448}, mesh = {*Selenium/chemistry ; *Electrodes ; Bioreactors ; Electrochemical Techniques ; Water Pollutants, Chemical ; }, abstract = {Selenium pollution in aquatic environments poses a major global challenge, with a significant gap in effective treatment technologies. In this study, we explored a novel approach integrating flow-electrode capacitive deionization (FCDI) with bio-electrochemical systems (BES) for the removal and reduction of selenate and selenite ions in one compact reactor. Our integrated system was electricity-driven, eliminating chemical usage. Up to 76 % selenium removal from the waste streams was achieved, followed by up to 66 % and 54 % reduction of selenate and selenite to elemental selenium respectively. The addition of acetate, a carbon source, enhanced selenate reduction by 14 % but lowered selenite reduction by 21 %, suggesting the substrate-dependent and bio-electrochemical-driven nature of selenate and selenite reduction respectively. Metagenomic sequencing revealed that Geobacter sulfurreducens and Pseudomonas stutzeri two known Se-reducing species, likely contributed to both selenite and selenate reduction through up-regulating functional genes related to sulfide reductase, fumarate reductase, and multi-heme c-type cytochromes. Thauera spp. and Alishewanella spp., two species not previously associated with selenium reduction, were likely involved in selenite reduction via the up-regulation of genes related to sulfite reductase and selenium reductase.}, } @article {pmid39616810, year = {2025}, author = {Yen, JH and Yeh, JF and Chan, CY and Tung, HH and Chi, KH and Chen, HC and Chen, WR and Chou, CC and Hsiao, TC}, title = {Unveiling the role of aeration tanks in the emission and enrichment of airborne antibiotic resistance genes in a wastewater treatment plant.}, journal = {Water research}, volume = {271}, number = {}, pages = {122866}, doi = {10.1016/j.watres.2024.122866}, pmid = {39616810}, issn = {1879-2448}, mesh = {*Wastewater/microbiology ; Drug Resistance, Microbial/genetics ; Waste Disposal, Fluid ; Genes, Bacterial ; Taiwan ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; }, abstract = {The aeration tanks in wastewater treatment plants (WWTPs) are important sources of airborne antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) due to bubble bursts at the air-liquid interface. This study employed an integrated metagenomic workflow, encompassing reference-based, assembly-based, and binning-based modules, to investigate resistomes in a WWTP in northern Taiwan. The role of aeration tanks in emitting airborne ARGs and their associated risks was assessed. The findings revealed a strong similarity between the ARG profiles in aeration tank wastewater and surrounding PM2.5, indicating atmospheric transmission of ARGs. Notably, the ARG level in PM2.5 (0.83 ± 0.11 ARGs/cell) was 59.6 % higher than in wastewater (0.52 ± 0.01 ARGs/cell). The assembly-based analysis showed that foam-forming bacteria such as Mycobacterium and Gordonia dominated ARGs-carrying contigs in PM2.5, suggesting that higher atomization capabilities of ARB contribute to airborne ARG prevalence. Furthermore, a significant proportion of stress response genes and increasing efflux pump resistance (122.6 %) in PM2.5 imply that mechanical forces during aerosolization and harsh atmospheric conditions select for airborne ARB capable of overcoming stress induced by dramatic environmental changes. Overall, the study indicates that ARG risk is intensified in PM2.5 due to their abundance, mobility, and pathogenicity. In conclusion, aeration tanks not only emit airborne ARGs but also cause an unexpected enrichment effect and exposure risk during aeration, highlighting the critical water-to-air transmission route of ARGs in WWTPs.}, } @article {pmid39616689, year = {2024}, author = {Naruse, H and Watanabe, N and Ohta, A and Shimizu, Y and Fukushima, T and Watanabe, A and Nakao, T and Taji, Y and Matsumoto, Y and Nakamura, S and Igarashi, Y and Takaki, A and Mitarai, S and Mitsutake, K and Tanaka, R and Ebihara, Y}, title = {Catheter-related bloodstream infection by a newly proposed "Mycobacterium toneyamachuris" in a boy with B-cell precursor acute lymphoblastic leukemia.}, journal = {Diagnostic microbiology and infectious disease}, volume = {111}, number = {3}, pages = {116626}, doi = {10.1016/j.diagmicrobio.2024.116626}, pmid = {39616689}, issn = {1879-0070}, abstract = {This report describes a 6-year-old boy who developed non-tuberculosis mycobacteria (NTM) catheter-related bloodstream infection (CRBSI) during treatment for B-cell precursor acute lymphoblastic leukemia. A Hickman catheter was inserted before starting treatment. He developed a fever during chemotherapy, and blood culture was drawn from the catheter. Blurred Gram-positive bacilli were found in Gram stain, looked positive in Ziehl-Neelsen stain, and were identified by matrix-assisted laser desorption/ionization-time of flight mass spectrometry as Mycobacterium mucogenicum phocaicum group. The administration of clarithromycin and amikacin was started and the Hickman catheter was removed. We performed genomic sequencing to obtain accurate identification, demonstrating that this microorganism was identified as "M. toneyamachuris" calculated by the average nucleotide identity index. Finally, a clinical diagnosis of CRBSI caused by "M. toneyamachuris" was made. Our findings suggest that genomic sequencing is available for the accurate identification of NTM species.}, } @article {pmid39616474, year = {2024}, author = {He, WW and Wang, WJ and Huang, ZX and Li, YL and Xia, QY and Shi, Y and Yang, B and Sun, HM}, title = {Mycobacterium paragordonae pulmonary disease with rapidly growing solitary lesions: a case report and literature review.}, journal = {Journal of infection in developing countries}, volume = {18}, number = {10}, pages = {1625-1631}, doi = {10.3855/jidc.18664}, pmid = {39616474}, issn = {1972-2680}, mesh = {Humans ; Female ; Aged ; *Mycobacterium Infections, Nontuberculous/diagnosis/microbiology/drug therapy/pathology ; *Tomography, X-Ray Computed ; Lung/pathology/microbiology/diagnostic imaging ; Nontuberculous Mycobacteria/isolation & purification/genetics ; Lung Diseases/microbiology/pathology/diagnosis/drug therapy ; Anti-Bacterial Agents/therapeutic use ; High-Throughput Nucleotide Sequencing ; }, abstract = {INTRODUCTION: Mycobacterium paragordonae (MPG) is a novel and uncommon nontuberculous mycobacterium (NTM). We describe a case of MPG pulmonary disease (MPGPD) with a single, rapidly growing, pulmonary mass, which has rarely been reported.

CASE REPORT: A chest CT scan of a 66-year-old woman revealed a rapidly growing solitary mass-like lesion in the upper lobe of the right lung, which was not seen in the previous chest CT scan six months ago. H&E-stained section of the CT-guided percutaneous lung tissue biopsy specimen showed chronic inflammatory changes with epithelioid granulomas. Metagenomic next-generation sequencing (mNGS) of lung tissue biopsy specimen identified MPG with a sequence number of 1617 and a confidence level of 99%. Because the subsequent MPG droplet digital PCR (MPG-ddPCR) test of the lung tissue biopsy was positive, she was eventually diagnosed with MPGPD. She was administered a quadruple oral regimen comprising clarithromycin, levofloxacin, rifampicin, and ethambutol according to the ATS/IDSA protocol for Mycobacterium gordonae (MG) infection. The chest CT scans showed a significant reduction in the lesion one month after the treatment and almost complete resolution four months later.

CONCLUSIONS: MPGPD is a rare NTM infection. The imaging manifestations of MPGPD are diverse and may even show rapid development. mNGS of tissue biopsy can enable prompt diagnosis of MPG infection and is a good alternative to routine NTM microbial testing. The ATS/IDSA protocol for MG infection is an effective treatment for MPG infection.}, } @article {pmid39616387, year = {2024}, author = {Huang, G and Peng, X}, title = {Genus Bithynia: morphological classification to molecular identification.}, journal = {Parasites & vectors}, volume = {17}, number = {1}, pages = {496}, pmid = {39616387}, issn = {1756-3305}, support = {82060376//National Natural Science Foundation of China/ ; No.2024GXNSFAA010039//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; }, mesh = {Animals ; *Snails/parasitology ; Trematode Infections/parasitology/veterinary ; Phylogeny ; Humans ; }, abstract = {Snails of the genus Bithynia, whose primary habitat is slow-flowing ponds and ditches, serve as the first intermediate hosts of liver fluke. Currently, approximately 200 million individuals worldwide are at risk of liver fluke infection, yet questions still persist regarding the taxonomic identification of Bithynia genus, a crucial player in the transmission of this disease. Accurate taxonomic classification of the Bithynia genus could significantly enhance current understanding of the disease's transmission mechanisms. In this article we comprehensively review the extensive research conducted on Bithynia genus, spanning past inquiries up to the latest findings. The primary emphasis is placed on exploring the taxonomic identification of this genus within various technological settings. We then present a consolidated analysis of the morphological taxonomic identification methods, highlighting their strengths and limitations. We also introduce a novel perspective on the future direction of identification and classification efforts for the members of this genus, emphasizing the crucial role Bithynia plays in the epidemiological cycle of liver fluke transmission. We conclude by urging researchers to prioritize the significance of the members of this genus in the epidemiological cycle of liver fluke transmission and in control measures for disease dissemination, within the context of the vector organisms.}, } @article {pmid39616358, year = {2024}, author = {Dell'Olio, A and Scott, WT and Taroncher-Ferrer, S and San Onofre, N and Soriano, JM and Rubert, J}, title = {Tailored impact of dietary fibers on gut microbiota: a multi-omics comparison on the lean and obese microbial communities.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {250}, pmid = {39616358}, issn = {2049-2618}, support = {79441//'European Union's Horizon 2020 Research and Innovation programme' for the Marie Skłodowska-Curie/ ; RYC2018-024850-I//Spanish Ministry of Science and Innovation for the Ramón y Cajal fellowship/ ; }, mesh = {*Dietary Fiber/metabolism ; *Obesity/microbiology ; *Gastrointestinal Microbiome ; *Malus/microbiology ; Humans ; Bacteria/classification/genetics/metabolism/isolation & purification ; Metagenomics ; Pectins/metabolism ; Metabolomics ; Cellulose/metabolism ; Bioreactors/microbiology ; Multiomics ; }, abstract = {BACKGROUND: Previous studies have shown that microbial communities differ in obese and lean individuals, and dietary fiber can help reduce obesity-related conditions through diet-gut microbiota interactions. However, the mechanisms by which dietary fibers shape the gut microbiota still need to be elucidated. In this in vitro study, we examined how apple fibers affect lean and obese microbial communities on a global scale. We employed a high-throughput micro-matrix bioreactor system and a multi-omics approach to identify the key microorganisms and metabolites involved in this process.

RESULTS: Initially, metagenomics and metabolomics data indicated that obese and lean microbial communities had distinct starting microbial communities. We found that obese microbial community had different characteristics, including higher levels of Ruminococcus bromii and lower levels of Faecalibacterium prausnitzii, along with an increased Firmicutes:Bacteroides ratio. Afterward, we exposed obese and lean microbial communities to an apple as a representative complex food matrix, apple pectin as a soluble fiber, and cellulose as an insoluble fiber. Dietary fibers, particularly apple pectin, reduced Acidaminococcus intestini and boosted Megasphaera and Akkermansia in the obese microbial community. Additionally, these fibers altered the production of metabolites, increasing beneficial indole microbial metabolites. Our results underscored the ability of apple and apple pectin to shape the obese gut microbiota.

CONCLUSION: We found that the obese microbial community had higher branched-chain amino acid catabolism and hexanoic acid production, potentially impacting energy balance. Apple dietary fibers, especially pectin, influenced the obese microbial community, altering both species and metabolites. Notably, the apple pectin feeding condition affected species like Klebsiella pneumoniae and Bifidobacterium longum. By using genome-scale metabolic modeling, we discovered a mutualistic cross-feeding relationship between Megasphaera sp. MJR8396C and Bifidobacterium adolescentis. This in vitro study suggests that incorporating apple fibers into the diets of obese individuals can help modify the composition of gut bacteria and improve metabolic health. This personalized approach could help mitigate the effects of obesity. Video Abstract.}, } @article {pmid39616255, year = {2024}, author = {Hämmerle, M and Guellil, M and Trgovec-Greif, L and Cheronet, O and Sawyer, S and Ruiz-Gartzia, I and Lizano, E and Rymbekova, A and Gelabert, P and Bernardi, P and Han, S and Rattei, T and Schuenemann, VJ and Marques-Bonet, T and Guschanski, K and Calvignac-Spencer, S and Pinhasi, R and Kuhlwilm, M}, title = {Screening great ape museum specimens for DNA viruses.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {29806}, pmid = {39616255}, issn = {2045-2322}, support = {10.47379/VRG20001//Vienna Science and Technology Fund (Wiener Wissenschafts-, Forschungs- und Technologiefonds)/ ; 864203//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 2020-03398//Vetenskapsådet (Swedish Research Council)/ ; }, mesh = {Animals ; *Museums ; *Phylogeny ; *DNA Viruses/genetics/isolation & purification ; *Genome, Viral ; Hominidae/virology ; High-Throughput Nucleotide Sequencing/methods ; Pan troglodytes/virology ; DNA, Viral/genetics ; Hepatitis B virus/genetics/isolation & purification ; }, abstract = {Natural history museum collections harbour a record of wild species from the past centuries, providing a unique opportunity to study animals as well as their infectious agents. Thousands of great ape specimens are kept in these collections, and could become an important resource for studying the evolution of DNA viruses. Their genetic material is likely to be preserved in dry museum specimens, as reported previously for monkeypox virus genomes from historical orangutan specimens. Here, we screened 209 great ape museum specimens for 99 different DNA viruses, using hybridization capture coupled with short-read high-throughput sequencing. We determined the presence of multiple viruses within this dataset from historical specimens and obtained several near-complete viral genomes. In particular, we report high-coverage (> 18-fold) hepatitis B virus genomes from one gorilla and two chimpanzee individuals, which are phylogenetically placed within clades infecting the respective host species.}, } @article {pmid39616151, year = {2024}, author = {Wang, J and Zhong, H and Chen, Q and Ni, J}, title = {Adaption mechanism and ecological role of CPR bacteria in brackish-saline groundwater.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {141}, pmid = {39616151}, issn = {2055-5008}, support = {52070002, 51721006, 51925901//National Natural Science Foundation of China (National Science Foundation of China)/ ; 52209078//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2023T160020//China Postdoctoral Science Foundation/ ; }, mesh = {*Groundwater/microbiology ; *Bacteria/genetics/classification/isolation & purification ; *Phylogeny ; Salinity ; Biodiversity ; Metagenome ; Adaptation, Physiological ; Nitrogen/metabolism ; Carbon/metabolism ; Sulfur/metabolism ; Metagenomics/methods ; Bacterial Physiological Phenomena ; }, abstract = {Candidate phyla radiation (CPR) constitutes a substantial fraction of bacterial diversity, yet their survival strategies and biogeochemical roles in brackish-saline groundwater remain unknown. By reconstructing 399 CPR metagenome-assembled genomes (MAGs) and 2007 non-CPR MAGs, we found that CPR, affiliated with 44 previously proposed phyla and 8 putative novel phyla, played crucial roles in maintaining the microbial stability and complexity in groundwater. Metabolic reconstructions revealed that CPR participated in diverse processes, including carbon, nitrogen, and sulfur cycles. Adaption of CPR to high-salinity conditions could be attributed to abundant genes associated with heat shock proteins, osmoprotectants, and sulfur reduction, as well as their cooperation with Co-CPR (non-CPR bacteria co-occurred with CPR) for metabolic support and resource exchange. Our study enhanced the understanding of CPR biodiversity in high-salinity groundwater, highlighting the collaborative roles of self-adaptive CPR bacteria and their reciprocal partners in coping with salinity stress, maintaining ecological stability, and mediating biogeochemical cycling.}, } @article {pmid39615696, year = {2024}, author = {Li, Z and Zhang, Q and Lian, X and Yin, C and Lin, Y and Wang, Y and Han, Z and Shen, F and Xu, Y and Wang, H and Wang, T}, title = {Value of metagenomic next-generation sequencing in the diagnosis of native pyogenic spinal infections: a multicenter, retrospective observational study.}, journal = {The spine journal : official journal of the North American Spine Society}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.spinee.2024.11.004}, pmid = {39615696}, issn = {1878-1632}, abstract = {BACKGROUND CONTEXT: The etiological diagnosis of pyogenic spinal infection is crucial for its precise antibiotic treatment. Traditional methods of detection are often slow and ineffective. In recent times, metagenomic next-generation sequencing (mNGS) has revolutionized pathogen detection, offering a more effective approach to disease management.

PURPOSE: Comparing mNGS with microbial culture to comprehensively explore the diagnostic value of mNGS in pyogenic spinal infections.

DESIGN: A multicenter, retrospective observational study.

PATIENT SAMPLE: In a multicenter retrospective observational study, we analyzed the data from 301 patients admitted in four selected hospitals with pyogenic spinal infections from December 2019 to February 2024.

OUTCOME MEASURES: Identification of pathogenic bacteria in patients.

METHODS: Obtain blood and lesion tissue or pus samples from the enrolled patients for microbial culture, serological and hematological laboratory tests, pathological examination, and mNGS analysis, followed by a comparative analysis of the results.

RESULTS: In our cohort of 301 cases of clinically diagnosed pyogenic spinal infections, 242 yielded etiological evidence. The most common gram-positive bacterium was Staphylococcus aureus, and the most common gram-negative bacterium was Escherichia coli. mNGS showed a significantly higher rate of detection (77.9%) compared with microbial culture (27.2%) with a notable difference (X² = 140.17, P < 0.001). In culture-negative samples, mNGS could detect pathogens in 73.1% of cases, and in culture-positive samples, it could detect pathogens in 91.5% of cases with 94.7% genus-level concordance. mNGS provided faster results (24-48 h) compared with the culture method (2-7 days).

CONCLUSIONS: mNGS serves as a valuable supplement to the culture method and shows potential in identifying the causative pathogen in native pyogenic spinal infections.}, } @article {pmid39615665, year = {2024}, author = {Kurukulasooriya, MRP and Tillekeratne, LG and Wijayaratne, WMDGB and Bodinayake, CK and Dilshan, UHBY and De Silva, AD and Nicholson, BP and Østbye, T and Woods, CW and Nagahawatte, AS}, title = {Prevalence and molecular epidemiology of methicillin-resistant Staphylococcus aureus in livestock farmers, livestock, and livestock products in southern Sri Lanka: A one health approach.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {126}, number = {}, pages = {105693}, doi = {10.1016/j.meegid.2024.105693}, pmid = {39615665}, issn = {1567-7257}, mesh = {*Methicillin-Resistant Staphylococcus aureus/genetics/isolation & purification/classification ; Sri Lanka/epidemiology ; *Livestock/microbiology ; Animals ; *Staphylococcal Infections/epidemiology/microbiology/veterinary/transmission ; Humans ; *Farmers ; Prevalence ; *One Health ; *Molecular Epidemiology ; }, abstract = {Methicillin-resistant Staphylococcus aureus (MRSA) colonization can lead to subsequent severe infections. Unlike community and hospital-associated types, Livestock-associated MRSA (LA-MRSA) transmits to humans through direct contact with livestock and contaminated livestock products. This study aimed to investigate MRSA prevalence and molecular epidemiology in livestock farmers, livestock, and livestock products, including LA-MRSA presence and MRSA abundance in human and animal nasal microbiome, in southern Sri Lanka using a One Health approach. Nasal swabs from farmers and livestock on 50 farms (Nov 2020 - Dec 2021) and livestock products were collected. MRSA was isolated and confirmed using standard microbiological techniques. Staphylococcal chromosomal cassette mec typing, spa typing, and multilocus sequence typing were performed. Identified clones were compared with hospital isolates. Metagenomics analysis was performed on selected samples. MRSA prevalence was 24.0 % (12/50) in farms, 7.9 % (12/152) in farmers, 2.1 % (5/240) in livestock, and 1.9 % (3/157) in products. Of 372 S. aureus collected from clinical cultures, 59.4 % were MRSA. MRSA clones were identified in farm personnel (CC5/ST5/t002, CC1/ST1/t127, and ST45/CC45/t026), livestock (CC5/ST5/t002), and clinical cultures (CC5/ST5/t002 and CC5/ST6/t304), with ST45/CC45/t026 and CC5/ST6/t304 reported for the first time in Sri Lanka. LA-MRSA clones (ST389/ST9) were not detected. Animals had more diverse nasal microbiomes and lower MRSA abundance (<1.4 %) compared to humans (>82.3 %). MRSA colonization prevalence in southern Sri Lanka was relatively low. Two new clones and no LA-MRSA clones were identified. This study highlights the importance of continuing MRSA surveillance under the One Health framework to identify MRSA transmission between humans, animals, and the environment.}, } @article {pmid39615467, year = {2025}, author = {Khandeparker, L and Kale, D and Hede, N and Anil, AC}, title = {Application of functional metagenomics in the evaluation of microbial community dynamics in the Arabian Sea: Implications of environmental settings.}, journal = {Journal of environmental management}, volume = {373}, number = {}, pages = {123449}, doi = {10.1016/j.jenvman.2024.123449}, pmid = {39615467}, issn = {1095-8630}, mesh = {*Metagenomics ; Cyanobacteria/genetics/metabolism ; Microbiota ; Seawater/microbiology ; Chlorophyll A/metabolism ; Climate Change ; }, abstract = {Ocean microbial communities form the base of marine food webs, facilitating energy transfer and nutrient cycling, thereby supporting higher trophic levels. We investigated their composition and functional profiles across depths (surface waters 0, 29, and 63 m and bottom waters 100, 150, and 200 m) in the central-eastern Arabian Sea (CEAS) using next-generation sequencing. It was hypothesized that the composition and functional diversity of these communities would be influenced by depth and environmental parameters. Our research showed that microbial communities vary with depth and are shaped by environmental factors like irradiance, temperature, dissolved oxygen, suspended particulate matter, chlorophyll a, and ammonia concentrations. Cyanobacteria (Prochlorococcus sp) and Mamiellaceae, belonging to picoeukaryotes, exhibited distinct depth-specific distributions up to subsurface chlorophyll maxima (SCM) at 63 m. On the other hand, a community shift in the microbial communities comprising Firmicutes, Bacteroidetes, and Actinobacteria phyla was observed at the deeper water depths. The profiling of functional genes pointed out the expression of carbon fixation by photosynthetic organisms at the surface (0, 29, and 63 m), which shifted to prokaryotic carbon fixation in deeper waters (0, 150, and 200 m). Microcosm experiments (mixing of surface water with water from the SCM) carried out simulating disturbances such as climate change forced mixing (cyclones), revealed shifts in microbial structure and function. It was observed that within 48 h, the carbon fixation activity changed from photosynthetic organisms to prokaryotes and indicated an increase in stress-related biosynthetic pathways such as expression of quorum sensing, biosynthesis of antibiotics, lipopolysaccharides, and secondary metabolites. These findings have implications for predictive modelling of food web dynamics and fisheries management in the context of climate change.}, } @article {pmid39615200, year = {2025}, author = {Wang, J and Zhang, F and Wang, Z and Liang, H and Du, Z and Zhang, Y and Lu, H and Peng, Y}, title = {Metagenomic insights into nitrite accumulation in sulfur-based denitrification systems utilizing different electron donors: Functional microbial communities and metabolic mechanisms.}, journal = {Water research}, volume = {270}, number = {}, pages = {122805}, doi = {10.1016/j.watres.2024.122805}, pmid = {39615200}, issn = {1879-2448}, mesh = {*Denitrification ; *Nitrites/metabolism ; *Sulfur/metabolism ; Bacteria/metabolism/genetics ; Electrons ; Nitrates/metabolism ; Bioreactors/microbiology ; }, abstract = {Sulfur-based autotrophic denitrification (SADN) offers new pathway for nitrite supply. However, sequential transformation of nitrogen and sulfur forms, and the functional microorganisms driving nitrite accumulation in SADN with different reduced inorganic sulfur compounds (RISCs), remain unclear. Desirable nitrite accumulation was achieved using elemental sulfur (S[0]-group), sulfide (S[2-]-group) and thiosulfate (S2O3[2-]-group) as electron donors. Under equivalent electron supply conditions, S2O3[2-]-group exhibited a superior nitrate conversion rate (NCR) of 0.285 kg N/(m[3]·d) compared to S[2-]-group (0.103 kg N/(m[3]·d)). Lower NCR in S[2-]-group was attributed to sulfide strongly inhibiting energy metabolism process of TCA cycle, resulting in reduced reaction rates. Moreover, the NCR of S[0]-group (0.035 kg N/(m[3]·d)) was poor due to the chemical inertness of S[0]. Specific microbial communities were selectively enriched in phylum level, with Proteobacteria increasing to an astonished 96.27-98.49 %. Comprehensive analyses of functional genus, genes, and metabolic pathways revealed significant variability in the active functional genus, with even the same genus showed significant metabolic differences in response to different RISCs. In S[0]-group, Thiomonas (10.0 %) and Acidithiobacillus (5.1 %) were the primary contributor to nitrite accumulation. Thiobacillus was the most abundant sulfur-oxidizing bacteria in S[2-]-group (43.84 %) and S2O3[2-]-group (18.92 %). In S[2-]-group, it contributed to nitrite accumulation, while in S2O3[2-]-group, it acted as a complete denitrifier (NO3[-]-N→N2). Notably, heterotrophic denitrifying bacteria, Comamonas (12.52 %), were crucial for nitrite accumulation in S2O3[2-]-group, predominating NarG while lacking NirK/S. Overall, this work advances our understanding of SADN systems with different RISCs, offering insights for optimizing nitrogen and sulfur removal.}, } @article {pmid39615045, year = {2024}, author = {Valentino, V and De Filippis, F and Marotta, R and Pasolli, E and Ercolini, D}, title = {Genomic features and prevalence of Ruminococcus species in humans are associated with age, lifestyle, and disease.}, journal = {Cell reports}, volume = {43}, number = {12}, pages = {115018}, doi = {10.1016/j.celrep.2024.115018}, pmid = {39615045}, issn = {2211-1247}, mesh = {Humans ; *Ruminococcus/genetics ; *Life Style ; Genome, Bacterial ; Adult ; Gastrointestinal Microbiome/genetics ; Metagenome ; Phylogeny ; Genomics/methods ; Male ; Middle Aged ; Female ; Aged ; }, abstract = {The genus Ruminococcus is dominant in the human gut, but higher levels of some species, such as R. gnavus, R. torques, and R. bromii, have been linked to health or disease. In this study, we analyzed >9,000 Ruminococcus metagenome-assembled genomes (MAGs) reconstructed from >5,000 subjects and revealed significant links between the prevalence of some species/subspecies and geographic origin, age, lifestyle, and disease, with subspecies prevalent in specific subpopulations showing divergent metabolic potential. Furthermore, Ruminococcus species from Lachnospiraceae encoded for carbohydrate-active enzymes (CAZy) potentially involved in the metabolism of human N- and O-glycans, whereas those from Oscillospiraceae appear to be more adapted toward fiber metabolism. These new findings contribute to elucidating the potential functional role of Ruminococcus in specific lifestyles and diseases and to decipher the diversity and the adaptation of members of this genus to the human gut.}, } @article {pmid39614549, year = {2024}, author = {Wicaksono, WA and Akinyemi, OE and Wassermann, B and Bickel, S and Suwanto, A and Berg, G}, title = {Traditionally produced tempeh harbors more diverse bacteria with more putative health-promoting properties than industrially produced tempeh.}, journal = {Food research international (Ottawa, Ont.)}, volume = {196}, number = {}, pages = {115030}, doi = {10.1016/j.foodres.2024.115030}, pmid = {39614549}, issn = {1873-7145}, mesh = {*Bacteria/genetics/classification/metabolism ; *Food Microbiology ; Humans ; Soy Foods/microbiology ; Fermentation ; Rhizopus/genetics/metabolism ; Hygiene ; Indonesia ; Microbiota ; Fermented Foods/microbiology ; }, abstract = {In recent years, there has been a significant shift towards industrialization in food production, resulting in the implementation of higher hygiene standards globally. Our study focused on examining the impact of hygiene standards on tempeh, a popular Rhizopus-based fermented soybean product native to Indonesia, and now famous around the world. We observed that tempeh produced with standardized hygiene measures exhibited a microbiome with comparable bacterial abundances but a markedly different community structure and function than traditionally produced tempeh. In detail, we found a decreased bacterial abundance of lactobacilli and enterobacteria, bacterial diversity, different indicator taxa, and significantly changed community structure in industrial tempeh. A similar picture was found for functional analysis: the quantity of bacterial genes was similar but qualitative changes were found for genes associated with human health. The resistome of tempeh varied based on its microbiome composition. The higher number of antimicrobial resistance genes in tempeh produced without standardized hygiene measures mainly belong to multidrug efflux pumps known to occur in plant-based food. Our findings were confirmed by functional insights into genomes and metagenome-assembled genomes from the dominant bacteria, e.g. Leuconostoc, Limosilactobacillus, Lactobacillus, Enterococcus, Paenibacillus, Azotobacter and Enterobacter. They harboured an impressive spectrum of genes important for human health, e.g. for production of vitamin B1, B7, B12, and K, iron and zinc transport systems and short chain fatty acid production. In conclusion, industrially produced tempeh harbours a less diverse microbiome than the traditional one. Although this ensures production at large scales as well as biosafety, in the long-term it can lead to potential effects for human gut health.}, } @article {pmid39614478, year = {2024}, author = {Yu, H and Li, Z and Zheng, D and Chen, C and Ge, C and Tian, H}, title = {Exploring microbial dynamics and metabolic pathways shaping flavor profiles in Huangjiu through metagenomic analysis.}, journal = {Food research international (Ottawa, Ont.)}, volume = {196}, number = {}, pages = {115036}, doi = {10.1016/j.foodres.2024.115036}, pmid = {39614478}, issn = {1873-7145}, mesh = {*Taste ; *Metagenomics/methods ; *Fermentation ; *Wine/microbiology/analysis ; *Metabolic Networks and Pathways ; Microbiota/genetics ; Oryza/microbiology ; Flavoring Agents/metabolism ; Humans ; Food Microbiology ; Odorants/analysis ; Male ; }, abstract = {In the production of Huangjiu (Chinese rice wine), fermentation microbiota plays a crucial role in flavor formation. This study investigates the microbial dynamics and metabolic pathways that shape the flavor profiles of Huangjiu using different starters. Sensory evaluation and metabolite analysis of six starters revealed significant differences in ester, fruity, and sweet aromas. Saccharomyces, Aspergillus, and Rhizopus were identified as the dominant genera significantly impacting fermentation. Metagenomic species and functional gene annotations of Huangjiu starters elucidated the metabolic pathways for key flavor compounds synthesis pathways. Enzyme genes involved in these pathways were classified and annotated to microbial genera using the NR database, identifying 231 classes of relevant catalytic enzymes and 154 microbial genera. A metabolic relationship between flavor compound formation and different microbial genera was established using catalytic enzymes as a bridge. This study highlights the impact of starter composition on the final product and provides new insights for optimizing starters to enhance Huangjiu flavor quality.}, } @article {pmid39614477, year = {2024}, author = {Yang, L and Fan, W and Xu, Y}, title = {Effects of storage period and season on the microecological characteristics of Jiangxiangxing high-temperature Daqu.}, journal = {Food research international (Ottawa, Ont.)}, volume = {196}, number = {}, pages = {115034}, doi = {10.1016/j.foodres.2024.115034}, pmid = {39614477}, issn = {1873-7145}, mesh = {*Seasons ; *Hot Temperature ; *Food Storage/methods ; *Microbiota ; Fermentation ; Bacteria/metabolism/classification ; Food Microbiology ; Metabolomics ; Proteomics ; China ; Metagenomics ; Camellia sinensis/microbiology/metabolism ; Fungi/metabolism/classification ; }, abstract = {Metagenomics, non-targeted metabolomics, and metaproteomics were employed to analyze the microecological succession of high-temperature Daqu during storage, elucidate the adaptation mechanism of the microbial community of Daqu to storage environments, and clarify the microecological characteristics of Daqu during different seasons. During storage, the relative abundances of Bacillus, Oceanobacillus, Staphylococcus, and Aspergillus in Daqu had significantly increased, while those of Kroppenstedtia, Saccharopolyspora, Thermoascus, and Thermomyces had significantly decreased. During the first 3 months of storage, compound metabolism of Daqu was primarily dominated by generation of small molecular substances and then shifted to metabolism of amino sugars. During the storage process, homogeneous selection (15.57 %) and homogeneous diffusion (14.86 %) of the microbial communities of Daqu were much larger than during the fermentation process, while the variable selection assembly (29.43 %) was smaller than during the fermentation process. Among the 2509 proteins identified in the four-season Daqu, bacterial protein expression was 1.46-fold greater than that of fungi. Seasonal factors influenced the function of Daqu by alterations to Bacillus subtilis, Oceanobacillus iheyensis, and Aspergillus nidulans and other microbial functions. Carbon and benzoic acid metabolism of Daqu was relatively increased during the spring, while metabolism of alkaloids and tyrosine was upregulated during the summer, amino acid synthesis and starch metabolism were enriched during the autumn, and peptidoglycan synthesis was relatively greater during the winter. Adjusting the moisture content of Daqu during the storage period was shown to reduce microecological differentiation caused by seasonal temperature variations.}, } @article {pmid39614390, year = {2024}, author = {Lai, Y and Zhou, F and Wang, H and He, X and Zhang, Q and Zhou, Y}, title = {Application of bronchoalveolar lavage fluid cytomorphology in diagnosing Nocardia otitidiscaviarum: a case report.}, journal = {Journal of medical case reports}, volume = {18}, number = {1}, pages = {577}, pmid = {39614390}, issn = {1752-1947}, support = {220906053235359//2022 Ministry of Education Industry-University Cooperation Collaborative Education Project/ ; 2021WJCY090//Hangzhou Biomedicine and Health Industry Development Supporting Science and Technology Special Project (Phase III, 2021)/ ; 2021WJCY272//Hangzhou Biomedicine and Health Industry Development Supporting Science and Technology Special Project (Phase V, 2021)/ ; }, mesh = {Humans ; Male ; *Nocardia Infections/diagnosis/microbiology/drug therapy ; Aged ; *Bronchoalveolar Lavage Fluid/microbiology ; *Nocardia/isolation & purification ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {BACKGROUND: Nocardiosis is a rare infectious disease, which is frequently underdiagnosed because of the distinct bacterial shape of the causative agent and its developmental history. The morphological analysis of bronchoalveolar lavage fluid can facilitate the detection of pathogenic bacteria by observing cellular-bacterial interactions.

CASE PRESENTATION: An immunocompetent 67-year-old male patient of Asian ethnicity developed a cough without apparent cause 20 days earlier. We initially discovered mycobacteria that appeared to be Nocardia in the cytomorphological examination of bronchoalveolar lavage fluid, which was later determined to be Nocardia otitidiscaviarum through metagenomic next-generation sequencing and microbiological cultures. The patient was eventually diagnosed with Nocardia pneumonitis after other testing and clinical signs were considered. After anti-infective treatment, the patient improved and was discharged.

CONCLUSION: Several diagnostic approaches were used in this case, and the importance of cell morphology as an early screening method was emphasized for suspected Nocardia infection.}, } @article {pmid39614169, year = {2024}, author = {Tang, H and Du, S and Niu, Z and Zhang, D and Tang, Z and Chen, H and Chen, Z and Zhang, M and Xu, Y and Sun, Y and Fu, X and Norback, D and Shao, J and Zhao, Z}, title = {Nasal, dermal, oral and indoor dust microbe and their interrelationship in children with allergic rhinitis.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {505}, pmid = {39614169}, issn = {1471-2180}, mesh = {Humans ; *Dust/analysis ; Male ; Child ; Female ; *Rhinitis, Allergic/microbiology ; Case-Control Studies ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/isolation & purification/genetics ; *Skin/microbiology ; *Mouth/microbiology ; *Microbiota ; Nasal Cavity/microbiology ; Air Pollution, Indoor/analysis ; Child, Preschool ; Metagenomics/methods ; Nose/microbiology ; }, abstract = {BACKGROUND: Allergic rhinitis (AR) subjects might have their microenvironment changed due to pathogenesis and living environment. Whether the nasal microbe in AR children differs from healthy subjects and how it interplays with dermal, oral and indoor dust microbe needs to be elucidated.

METHODS: In this case-control study, we analyzed and compared the bacterial characterization and associations in nasal, dermal, oral swab samples and dust samples in 62 children with physician-diagnosed AR(cases) and 51 age- and gender-matched healthy ones with no history of allergic diseases(controls). Full-length 16S rRNA sequencing(swabs) and shotgun metagenomics(dust) were applied. Bacterial diversity, composition, abundance difference characteristics and fast expectation-maximization for microbial source tracking(FEAST) analysis were performed and compared between cases and controls.

RESULTS: The α-diversity of dust microorganisms in AR was lower than that in control group (P = 0.034), and the β-diversity indices of microorganisms in nasal cavity (P = 0.020), skin (P = 0.001) and dust (P = 0.004) were significantly different from those in control group. At species levels, a total of 10, 15, 12, and 15 bacterial species were differentially enriched in either cases or controls in nasal, dermal, oral, and dust samples, respectively(Linear Discriminant Analysis(LDA) score > 2, P < 0.05). Staphylococcus epidermidis was the single species simultaneously more abundant in nasal, dermal and dust samples in AR children. By FEAST analysis, 8.85% and 10.11% of S. epidermidis in AR dermal and dust samples came from nasal cavity. These proportions were significantly higher than those in controls (2.70% and 3.86%) (P < 0.05). The same significantly higher transfer proportions(P < 0.05) were observed for Staphylococcus aureus enriched in the nasal cavity in AR children. Classification models by random forest regression at species levels showed, bacterial species enriched in indoor dust, nasal and dermal samples had substantial power in distinguishing AR children from healthy ones, with the highest power in the dust samples (AUC = 0.88) followed by nasal(AUC = 0.81) and dermal ones(AUC = 0.80).

CONCLUSIONS: Our study presented the microbial enrichment characteristics in AR children both in the living environment(dust) and body sites exposed to environment through inhalation(nasal cavity), contact(skin) and ingestion(oral cavity) pathways, respectively. Nasal S.epidermidis and S.aureus had dominant influences on dust and other body sites in AR children.}, } @article {pmid39614167, year = {2024}, author = {Mangoma, N and Zhou, N and Ncube, T}, title = {Metagenomic insights into the microbial community of the Buhera soda pans, Zimbabwe.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {510}, pmid = {39614167}, issn = {1471-2180}, mesh = {Zimbabwe ; *Metagenomics ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Microbiota/genetics ; Salinity ; Phylogeny ; Hydrogen-Ion Concentration ; Archaea/genetics/classification/metabolism/isolation & purification ; Water Microbiology ; }, abstract = {BACKGROUND: Soda pans are unique, natural aquatic environments characterised by elevated salinity and alkalinity, creating a distinctive and often extreme geochemistry. The microbiomes of soda pans are unique, with extremophiles such as halophiles, alkaliphiles and haloalkaliphiles being important. Despite being dominated by mostly unculturable inhabitants, soda pans hold immense biotechnological potential. The application of modern "omics-based" techniques helps us better understand the ecology and true extend of the biotechnological potential of soda pan microbiomes. In this study, we used a shotgun metagenomic approach to determine the microbial diversity and functional profile of previously unexplored soda pans located in Buhera, Eastern Zimbabwe. A combination of titrimetry and inductively coupled plasma optical emission spectroscopy (ICP‒OES) was used to perform physico-chemical analysis of the soda pan water.

RESULTS: Physicochemical analysis revealed that the Buhera soda pans are highly alkaline, with a pH range of 8.74 to 11.03, moderately saline (2.94 - 7.55 g/L), and have high carbonate (3625 mg/L) and bicarbonate ion (1325 mg/L) alkalinity. High levels of sulphate, phosphate, chloride and fluoride ions were detected. Metagenomic analysis revealed that domain Bacteria dominated the soda pan microbial community, with Pseudomonadota and Bacillota being the dominant phyla. Vibrio was shown to be the predominant genus, followed by Clostridium, Candidatus Brevefilum, Acetoanaerobium, Thioalkalivibrio and Marinilactibacillus. Archaea were also detected, albeit at a low prevalence of 1%. Functional profiling revealed that the Buhera soda pan microbiome is functionally diverse, has hydrolytic-enzyme production potential and is capable of supporting a variety of geochemical cycles.

CONCLUSIONS: The results of this pioneering study showed that despite their extreme alkalinity and moderate salinity, the Buhera soda pans harbour a taxonomically and functionally diverse microbiome dominated by bacteria. Future work will aim towards establishing the full extent of the soda pan's biotechnological potential, with a particular emphasis on potential enzyme production.}, } @article {pmid39613370, year = {2024}, author = {Zepernick, BN and Hart, LN and Chase, EE and Natwora, KE and Obuya, JA and Olokotum, M and Houghton, KA and Kiledal, EA and , and Sheik, CS and Sherman, DH and Dick, GJ and Wilhelm, SW and Sitoki, L and Otiso, KM and McKay, RML and Bullerjahn, GS}, title = {Molecular investigation of harmful cyanobacteria reveals hidden risks and niche partitioning in Kenyan Lakes.}, journal = {Harmful algae}, volume = {140}, number = {}, pages = {102757}, pmid = {39613370}, issn = {1878-1470}, support = {F31 ES036421/ES/NIEHS NIH HHS/United States ; P01 ES028939/ES/NIEHS NIH HHS/United States ; }, mesh = {*Lakes/microbiology ; *Cyanobacteria/genetics ; Kenya ; *Harmful Algal Bloom ; }, abstract = {Despite the global expansion of cyanobacterial harmful algal blooms (cHABs), research is biased to temperate systems within the global north, such as the Laurentian Great Lakes. This lack of diversity represents a significant gap in the field and jeopardizes the health of those who reside along at-risk watersheds in the global south. The African Great Lake, Lake Victoria, is understudied despite serving as the second largest lake by surface area and demonstrating year-round cHABs. Here, we address this knowledge gap by performing a molecular survey of cHAB communities in three anthropogenically and ecologically important freshwater systems of Victoria's Kenyan watershed: Winam Gulf (Lake Victoria), Lake Simbi and Lake Naivasha. We identified a bloom of non-toxic Dolichospermum and toxic Microcystis in the Winam Gulf, with data suggesting sulfur limitation shapes competition dynamics between these two bloom-formers. Though we did not detect a bloom in Naivasha, it contained the largest diversity of cHAB genera amongst the three lakes. In turn, our results indicated methane metabolism may allow non-toxic picoplankton to outcompete cHAB genera, while suggesting Synechococcus spp. serves as a methane source and sink in this system. Lake Simbi exhibited a non-toxic Limnospira bloom at the time of sampling with very low abundances of cHAB genera present. Subsequently, these results were employed to design a cHAB screening and risk assessment framework for local stakeholders. Cumulatively, this work serves to increase cHAB research efforts on the international scale while serving as an impetus for cHAB monitoring on the local scale.}, } @article {pmid39612873, year = {2025}, author = {Chen, M and Liu, Y and Zhou, Y and Pei, Y and Qu, M and Lv, P and Zhang, J and Xu, X and Hu, Y and Wang, Y}, title = {Deciphering antibiotic resistance genes and plasmids in pathogenic bacteria from 166 hospital effluents in Shanghai, China.}, journal = {Journal of hazardous materials}, volume = {483}, number = {}, pages = {136641}, doi = {10.1016/j.jhazmat.2024.136641}, pmid = {39612873}, issn = {1873-3336}, mesh = {*Plasmids/genetics ; China ; *Hospitals ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Humans ; Bacteria/genetics/drug effects ; Genes, Bacterial ; Wastewater/microbiology ; }, abstract = {Although previous studies using phenotypic or metagenomic approaches have revealed the patterns of antibiotic resistance genes (ARGs) in hospital effluents in local regions, limited information is available regarding the antibiotic resistome and plasmidome in human pathogenic bacteria in hospital effluents of megacity in China. To address this knowledge gap, we analyzed effluent samples from 166 hospitals across 13 geographical districts in Shanghai, China, using both cultivation-based approaches and metagenomics. A total of 357 strains were isolated from these samples, with the predominant species being Escherichia coli (n = 61), Aeromonas hydrophila (n = 57), Klebsiella pneumoniae (n = 48), and Aeromonas caviae (n = 42). Those identified indicator bacteria were classified into biosafety level 1 (BSL-1, 60 %) and BSL-2 (40 %). We identified 1237 ARG subtypes across 22 types, predominantly including beta-lactam, tetracycline, multidrug, polymyxin, and aminoglycoside resistance genes, using culture-enriched phenotypic metagenomics. Mobile genetic elements such as plasmids, transposons (tnpA), integrons (intI1), and insertion sequences (IS91) were abundant. We recovered 135 plasmids classified into mobilizable (n = 94) and non-mobilizable (n = 41) types. Additionally, 80 metagenome-assembled genomes (MAGs) were reconstructed from the hospital effluents for the assessment of ARG transmission risks, including genes for last-line antibiotics such as blaNDM, blaKPC, blaimiH, and mcr. This study is the first to comprehensively characterize and assess the risk of antimicrobial resistance levels and plasmidome in the hospital effluents of China's megacity, providing city-wide surveillance data and evidence to inform public health interventions.}, } @article {pmid39612821, year = {2025}, author = {Rosenqvist, T and Hilding, J and Suarez, C and Paul, CJ}, title = {Microbial communities in slow sand filters for drinking water treatment adapt to organic matter altered by ozonation.}, journal = {Water research}, volume = {270}, number = {}, pages = {122843}, doi = {10.1016/j.watres.2024.122843}, pmid = {39612821}, issn = {1879-2448}, mesh = {*Ozone ; *Drinking Water/microbiology ; *Water Purification/methods ; *Filtration ; Sand ; Bacteria/genetics ; Microbiota ; }, abstract = {Changing natural organic matter quality from anthropogenic activity and stricter requirements for micropollutant removal challenges existing systems for drinking water production. Ozonation of water followed by biofiltration, such as passage through a slow sand filter (SSF), is a partial solution. Biofiltration relies on biofilms (microbial communities within extracellular matrices). However, the effects of ozonation on SSF microbial communities are unknown. In this study, genome-resolved and read-based metagenomics were used to compare the microbial communities of two full-scale SSFs employing conventional pre-treatment to a 20 m[2] SSF operated in parallel with ozonation as additional pre-treatment. The SSF microbial community receiving ozonated water was less diverse than those receiving non-ozonated water. Families Hyphomicrobiaceae, Acetobacteraceae, Sphingomonadaceae and Burkholderiaceae were more abundant when ozone was used, as were genes for metabolism of single-carbon organic compounds. Conversely, genes for metabolism of aromatic compounds and fatty acids were less abundant. Metagenome assembled genomes associated with the non-ozonated SSFs were enriched with several glycoside hydrolases, while those associated with the ozonated SSF were enriched with genes for 1-2 carbon compound metabolism. No indications of increased microbial risk (pathogens or antibiotic resistance genes) were detected as a consequence of ozonation. This study shows how microbial communities of SSFs adapt to changes in organic matter quality, highlighting the key role of biofilters for production of safe and sustainable drinking water in a changing climate.}, } @article {pmid39612230, year = {2024}, author = {Zhang, Z and Yu, S and Gu, J and Tan, F and Wan, S and Gao, H and Qin, Z}, title = {Biochemical Characterization of a β-1,3-Glucanase from Bacteroidetes sp. Having Transglycosylase Activity Suitable to Synthesize β-Glucooligosaccharides.}, journal = {Journal of agricultural and food chemistry}, volume = {72}, number = {49}, pages = {27294-27303}, doi = {10.1021/acs.jafc.4c08008}, pmid = {39612230}, issn = {1520-5118}, mesh = {*Oligosaccharides/chemistry/metabolism ; *Bacterial Proteins/genetics/chemistry/metabolism ; *Bacteroidetes/enzymology/genetics ; Glucan 1,3-beta-Glucosidase/metabolism/genetics/chemistry ; Hydrolysis ; Substrate Specificity ; Hydrogen-Ion Concentration ; Glycoside Hydrolases/chemistry/genetics/metabolism ; Kinetics ; Enzyme Stability ; Glucans/metabolism/chemistry ; }, abstract = {β-1,3-Glucanases have prospective applications in areas such as functional oligosaccharide preparation, plant protection, and breweries. In this study, a glycoside hydrolase (GH) family 17 β-1,3-glucanase (BbGlc17A) from Bacteroidetes bacterium from a microbial mat metagenome from the Great Salt Lake was identified. BbGlc17A catalyzed the hydrolytic conversion of laminarin into β-glucooligosaccharides with polymerization degrees of 3-8. The optimal catalytic conditions of BbGlc17A were pH 6.5 and 30 °C. In addition to its hydrolytic activity, BbGlc17A also exhibited transglycosidase activities, involving catalysis of the formation of new β-1,6-glycosidic bonds. BbGlc17A exhibits the classic (β/α)8 TIM-barrel structure and possesses an elongated catalytic groove, distinguishing it from other typical β-1,3-glucanases, which promote the forward direction of the transglycoside reaction. This effectively highlights the potential of the enzyme to convert β-1,3-glucan into mixed functional oligosaccharides. These results reveal the catalytic properties and the application potential of the GH family 17 β-1,3-glucanase and provide valuable information about the group of carbohydrate-active enzymes in biochemistry.}, } @article {pmid39612216, year = {2024}, author = {Wang, T and Luo, Y and Kong, X and Fang, L and Zhu, L and Yu, B and Zheng, P and Huang, Z and Mao, X and Jie, Y and Luo, J and Yan, H and He, J}, title = {Multiomics comparative analysis of feces AMRGs of Duroc pigs and Tibetan and the effect of fecal microbiota transplantation on AMRGs upon antibiotic exposure.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0198324}, doi = {10.1128/spectrum.01983-24}, pmid = {39612216}, issn = {2165-0497}, abstract = {UNLABELLED: Fecal matter is recognized as both a reservoir and a transmission source for various antimicrobial resistance genes (AMRGs). However, the transcriptional activity of AMRGs in swine feces is not well understood. In addition, the effect of fecal microbiota transplantation (FMT) on the excretion of AMRGs has rarely been reported. Our study explored the diversity, abundance, transcriptional activity, and bacterial hosts of AMRGs in Tibetan and Duroc pig feces using metagenomic and metatranscriptomic sequencing technologies. We discovered a significantly higher genomic abundance of AMRGs in the feces of Duroc pigs compared to Tibetan pigs (P < 0.001), although the transcript levels did not show a significant difference. The results showed that the core composition of AMRGs in pig feces varied considerably, with the most transcriptionally active AMRGs being oqxB, tetQ, Bla1, dfrA1, and amrB. Furthermore, the Firmicutes phylum is the main host of AMRGs. By transplanting fecal flora from Tibetan and Duroc pigs into the intestines of Duroc Landrace Yorkshire (DLY) piglets after acute antibiotic exposure, we found that only Tibetan pig fecal flora significantly reduced AMRGs in the feces of DLY piglets (P < 0.05). The effectiveness of Tibetan pig fecal microorganisms in removing AMRGs from DLY pig feces was mainly influenced by microbial communities, especially the Bacteroidota phylum. These findings offer valuable insights for the prevention and control of AMRG pollution.

IMPORTANCE: To the best of our knowledge, this study represents the first comprehensive analysis of antimicrobial resistance gene (AMRGs) expression in the fecal microbiota of Tibetan and Duroc pigs, employing an integrated metagenomic and metatranscriptomic approach. Our findings indicate a higher risk of AMRGs transmission in the feces of Duroc pigs compared to Tibetan pigs. Given the escalating antimicrobial resistance crisis, novel therapeutic interventions are imperative to mitigate gut colonization by pathogens and AMRGs. In this regard, we investigated the impact of fecal microbiota from Tibetan and Duroc pig sources on AMRGs excretion in Duroc Landrace Yorkshire (DLY) piglets' feces following acute antibiotic exposure. Remarkably, only fecal microbiota sourced from Tibetan pigs exhibited a reduction in AMRGs excretion in DLY piglets' feces. This underscores the significance of evaluating the presence of AMRGs within donor fecal microbiota for effective AMRGs decolonization strategies.}, } @article {pmid39611829, year = {2025}, author = {Hameed, A and McDonagh, F and Sengupta, P and Miliotis, G and Sivabalan, SKM and Szydlowski, L and Simpson, A and Singh, NK and Rekha, PD and Raman, K and Venkateswaran, K}, title = {Neobacillus driksii sp. nov. isolated from a Mars 2020 spacecraft assembly facility and genomic potential for lasso peptide production in Neobacillus.}, journal = {Microbiology spectrum}, volume = {13}, number = {1}, pages = {e0137624}, pmid = {39611829}, issn = {2165-0497}, support = {Mars Program Office//NASA | Jet Propulsion Laboratory (JPL)/ ; IBSE//Indian Institute of Technology Madras (IITM)/ ; WSAI//Indian Institute of Technology Madras (IITM)/ ; }, mesh = {*Phylogeny ; *RNA, Ribosomal, 16S/genetics ; *Spacecraft ; *Mars ; Genome, Bacterial ; Fatty Acids/metabolism/analysis ; DNA, Bacterial/genetics ; Genomics ; Base Composition ; Bacillales/genetics/classification/isolation & purification/metabolism ; Soil Microbiology ; Peptides/metabolism ; Whole Genome Sequencing ; }, abstract = {UNLABELLED: During microbial surveillance of the Mars 2020 spacecraft assembly facility, two novel bacterial strains, potentially capable of producing lasso peptides, were identified. Characterization using a polyphasic taxonomic approach, whole-genome sequencing and phylogenomic analyses revealed a close genetic relationship among two strains from Mars 2020 cleanroom floors (179-C4-2-HS, 179-J1A1-HS), one strain from the Agave plant (AT2.8), and another strain from wheat-associated soil (V4I25). All four strains exhibited high 16S rRNA gene sequence similarity (>99.2%) and low average nucleotide identity (ANI) with Neobacillus niacini NBRC 15566[T], delineating new phylogenetic branches within the genus. Detailed molecular analyses, including gyrB (90.2%), ANI (86.4%), average amino acid identity (87.8%) phylogenies, digital DNA-DNA hybridization (32.6%), and percentage of conserved proteins (77.7%) indicated significant divergence from N. niacini NBRC 15566[T]. Consequently, these strains have been designated Neobacillus driksii sp. nov., with the type strain 179-C4-2-HS[T] (DSM 115941[T] = NRRL B-65665[T]). N. driksii grew at 4°C to 45°C, pH range of 6.0 to 9.5, and 0.5% to 5% NaCl. The major cellular fatty acids are iso-C15:0 and anteiso-C15:0. The dominant polar lipids include diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and an unidentified aminolipid. Metagenomic analysis within NASA cleanrooms revealed that N. driksii is scarce (17 out of 236 samples). Genes encoding the biosynthesis pathway for lasso peptides were identified in all N. driksii strains and are not commonly found in other Neobacillus species, except in 7 out of 26 recognized species. This study highlights the unique metabolic capabilities of N. driksii, underscoring their potential in antimicrobial research and biotechnology.

IMPORTANCE: The microbial surveillance of the Mars 2020 assembly cleanroom led to the isolation of novel N. driksii with potential applications in cleanroom environments, such as hospitals, pharmaceuticals, semiconductors, and aeronautical industries. N. driksii genomes were found to possess genes responsible for producing lasso peptides, which are crucial for antimicrobial defense, communication, and enzyme inhibition. Isolation of N. driksii from cleanrooms, Agave plants, and dryland wheat soils, suggested niche-specific ecology and resilience under various environmentally challenging conditions. The discovery of potent antimicrobial agents from novel N. driksii underscores the importance of genome mining and the isolation of rare microorganisms. Bioactive gene clusters potentially producing nicotianamine-like siderophores were found in N. driksii genomes. These siderophores can be used for bioremediation to remove heavy metals from contaminated environments, promote plant growth by aiding iron uptake in agriculture, and treat iron overload conditions in medical applications.}, } @article {pmid39611823, year = {2025}, author = {Carroll, AC and Mortimer, L and Ghosh, H and Reuter, S and Grundmann, H and Brinda, K and Hanage, WP and Li, A and Paterson, A and Purssell, A and Rooney, A and Yee, NR and Coburn, B and Able-Thomas, S and Antonio, M and McGeer, A and MacFadden, DR}, title = {Rapid inference of antibiotic susceptibility phenotype of uropathogens using metagenomic sequencing with neighbor typing.}, journal = {Microbiology spectrum}, volume = {13}, number = {1}, pages = {e0136624}, pmid = {39611823}, issn = {2165-0497}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Urinary Tract Infections/microbiology/drug therapy ; *Metagenomics ; *Klebsiella/genetics/drug effects ; *Microbial Sensitivity Tests ; *Escherichia coli/genetics/drug effects ; Phenotype ; Multilocus Sequence Typing ; Drug Resistance, Bacterial/genetics ; Escherichia coli Infections/microbiology/drug therapy ; Klebsiella Infections/microbiology/drug therapy/urine ; Bacterial Typing Techniques/methods ; }, abstract = {UNLABELLED: Timely diagnostic tools are needed to improve antibiotic treatment. Pairing metagenomic sequencing with genomic neighbor typing algorithms may support rapid clinically actionable results. We created resistance-associated sequence elements (RASE) databases for Escherichia coli and Klebsiella spp. and used them to predict antibiotic susceptibility in directly sequenced (Oxford Nanopore) urine specimens from critically ill patients. RASE analysis was performed on pathogen-specific reads from metagenomic sequencing. We evaluated the ability to predict (i) multi-locus sequence type (MLST) and (ii) susceptibility profiles. We used neighbor typing to predict MLST and susceptibility phenotype of E. coli (64/80) and Klebsiella spp. (16/80) from urine samples. When optimized by lineage score, MLST predictions were concordant for 73% of samples. Similarly, a RASE-susceptible prediction for a given isolate was associated with a specificity and a positive likelihood ratio (LR+) for susceptibility of 0.65 (95% CI, 0.54-0.76) and 2.26 (95% CI, 1.75-2.92), respectively, with an increase in the probability of susceptibility of 10%. A RASE-non-susceptible prediction was associated with a sensitivity and a negative likelihood ratio (LR-) for susceptibility of 0.79 (95% CI, 0.74-0.84) and 0.32 (95% CI, 0.24-0.43) respectively, with a decrease in the probability of susceptibility of 20%. Numerous antibiotic classes could reasonably be reconsidered empiric therapy by shifting empiric probabilities of susceptibility across relevant treatment thresholds. Moreover, these predictions can be available within 6 h. Metagenomic sequencing of urine specimens with neighbor typing provides rapid and informative predictions of lineage and antibiotic susceptibility with the potential to impact clinical decision-making.

IMPORTANCE: Urinary tract infections (UTIs) are a common diagnosis in hospitals and are often treated empirically with broad-spectrum antibiotics. These broad-spectrum agents can select for resistance in these bacteria and co-colonizing organisms. The use of narrow-spectrum agents is desirable as an antibiotic stewardship measure; however, it is counterbalanced by the need for adequate therapy. Identification of causative organisms and their antibiotic susceptibility can help direct treatment; however, conventional testing requires days to produce actionable results. Methods to quickly and accurately predict susceptibility phenotypes for pathogens causing UTI could thus improve both patient outcomes and antibiotic stewardship. Here, expanding on previous work showing accurate prediction for certain Gram-positive pathogens, we demonstrate how the use of RASE from metagenomic sequencing can provide informative and rapid phenotype prediction results for common Gram-negative pathogens in UTI, highlighting the future potential of this method to be used in clinical settings to guide empiric antibiotic selection.}, } @article {pmid39611812, year = {2025}, author = {Shi, M and Zhao, B and Cai, W and Yuan, H and Liang, X and Li, Z and Liu, X and Jin, Y and Liu, X and Wei, C}, title = {Multi-omics mechanical analysis of gut microbiota, carboxylic acids, and cardiac gene expression interaction triggering diabetic cardiomyopathy.}, journal = {mSystems}, volume = {10}, number = {1}, pages = {e0145024}, pmid = {39611812}, issn = {2379-5077}, support = {82170268,82200482//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Diabetic Cardiomyopathies/genetics/microbiology/metabolism ; Mice ; Male ; Carboxylic Acids/metabolism ; Metabolomics ; Diabetes Mellitus, Type 2/microbiology/genetics/metabolism ; Metagenomics ; Receptors, Leptin/genetics/metabolism ; Myocardium/metabolism ; Mice, Inbred C57BL ; Diabetes Mellitus, Experimental/microbiology/genetics/metabolism ; Multiomics ; }, abstract = {UNLABELLED: It is well known that gut microbial imbalance is a potential factor for the occurrence and development of diabetes mellitus (DM) and its complications. Moreover, the heart and gut microbiota can regulate each other through the gut-metabolite-heart axis. In this study, metagenomics, metabolomics, and transcriptomics were chosen to sequence the changes in gut microbiota, serum metabolite levels, and differentially expressed genes (DEGs) in leptin receptor-deficient db/db mice and analyze the correlation between serum metabolites and gut microbiota or DEGs. According to the results, there were significant differences in the 1,029 cardiac genes and 353 serum metabolites in diabetic mice of the db/db group, including DEGs enriched in the PPAR signaling pathway and increased short-chain carboxylic acids (CAs), when compared with the normal db/m group. According to metagenomics, the gut microbiota of mice in the db/db group were disrupted, and particularly Lachnospiraceae bacteria and Oscillospiraceae bacteria significantly decreased. Also, according to the Pearson correlation analysis, a significant positive correlation was found between CAs and PPAR signaling pathway-related DEGs, and a negative correlation was found between CAs and the abundance of the above-mentioned species. To sum up, type 2 diabetes mellitus (T2DM) can upregulate the expression of partial cardiac genes through the levels of serum short-chain CAs affected by gut microbiota, thus playing a role in the occurrence and development of diabetic cardiomyopathy (DCM).

IMPORTANCE: Our research results clearly link the changes in heart genes of T2DM and normal mice with changes in serum metabolites and gut microbiota, indicating that some genes in biological processes are closely related to the reduction of protective microbiota in the gut microbiota. This study provides a theoretical basis for investigating the mechanism of DCM and may provide preliminary evidence for the future use of gut microbiota therapy for DCM.}, } @article {pmid39611384, year = {2025}, author = {Redding, LE and Daniel, SG and Smith, A and Keenan, O and Barnhart, D and Zackular, JP}, title = {Comparison of Anaerobic Culture Methods for Detecting Clostridioides difficile in Bovine Faeces.}, journal = {Veterinary medicine and science}, volume = {11}, number = {1}, pages = {e70085}, pmid = {39611384}, issn = {2053-1095}, support = {//Pennsylvania Department of Agriculture/ ; }, mesh = {Female ; Animals ; Cattle ; *Feces/microbiology ; Clostridioides difficile/genetics/isolation & purification ; *Bacteriological Techniques/methods/standards/veterinary ; Shotgun Sequencing ; *Clostridium Infections/diagnosis/microbiology/veterinary ; Sensitivity and Specificity ; Culture Techniques/methods/standards/veterinary ; *Cattle Diseases/diagnosis/microbiology ; }, abstract = {BACKGROUND: The study of the epidemiology of Clostridioides difficile in populations is greatly facilitated by the ability to isolate and further characterize individual organisms, which requires effective culture protocols. In cattle, where little is known about the epidemiology of C. difficile, no studies have assessed or compared the performance of different assays for detecting C. difficile.

OBJECTIVES: This study compared two culture protocols for detecting C. difficile in bovine faeces from 121 gestating cows and 70 of their neonatal calves, while situating results obtained with each protocol relative to those obtained with shotgun metagenomic sequencing.

METHODS: Protocol 1 involved direct plating enrichment onto taurocholine-cycloserine-cefoxitin-fructose agar (TCCFA), while Protocol 2 included an ethanol shock step before plating on CCFA/ChromID agar. For both protocols, one aliquot underwent broth enrichment prior to plating, while the other aliquot did not.

RESULTS: Clostridioides difficile was detected following broth enrichment in two of the same calf samples using both protocols, and an additional cow sample was found to be positive with Protocol 2, though the difference in detection rates was not statistically significant (p = 1.0).

CONCLUSIONS: The detection of C. difficile in a much high number of these samples by shotgun metagenomics, albeit at low levels of relative abundance, suggests that neither of these culture protocols is sensitive when levels of abundance are low.}, } @article {pmid39611142, year = {2024}, author = {Zhang, L and Zhang, H and Su, S and Jia, Y and Liang, C and Fang, Y and Hong, D and Li, T and Ma, F}, title = {Risk factor assessment and microbiome analysis in peritoneal dialysis-related peritonitis reveal etiological characteristics.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1443468}, pmid = {39611142}, issn = {1664-3224}, mesh = {Humans ; *Peritonitis/microbiology/etiology/diagnosis ; *Peritoneal Dialysis/adverse effects ; Male ; Female ; Middle Aged ; Risk Factors ; *Gastrointestinal Microbiome ; Aged ; Risk Assessment ; Adult ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Peritoneal dialysis-related peritonitis (PDRP) is one of the most common complications of peritoneal dialysis (PD). Understanding the risk factors and etiological characteristics is indispensable for infection prevention and improving the outcome and life quality.

METHODS: A total of 70 PD patients were separated into the PDRP group (n=25) and the control group (n=45). Variables, including gender, age, body mass index, primary diseases, and history of basic diseases, in the two groups were analyzed to assess the risk factors of PDRP. Metagenomic next-generation sequencing (mNGS) and microbial culture were compared in detecting pathogenic microorganisms. Gut microbiota analysis was performed in 35 PDRP patients based on mNGS data.

RESULTS: Dialysis time and times of dialysate change were the risk factors of PDRP, and times of dialysate change was the independent risk factor of PDRP (p = 0.046). mNGS produced higher sensitivity (65.79%) than microbial culture (36.84%) in identifying pathogenic microorganisms. Staphylococcus aureus and Klebsiella pneumoniae (four cases) were the most frequent pathogens causing PDRP, followed by Staphylococcus capitis (three cases). β diversity of the gut microbiota was significantly different between patients with fewer times of dialysate change (≤4) and more (>5), as well as between patients with gram-positive (G+) bacterial and gram-negative (G-) bacterial infection.

CONCLUSION: The dialysis time and times of dialysate changes not only are risk factors for peritonitis in PD patients but also stimulate significant changes in the gut microbiome structure in PDRP patients. These findings may provide a novel viewpoint for the management of patients with PDRP.}, } @article {pmid39611100, year = {2024}, author = {Ye, X and Lin, Y and Yang, J and Qi, B and Wei, X and Huang, Y and Wang, L}, title = {Deciphering the pathogen heterogeneity for precise diagnosis and personalized therapeutics of infections after kidney transplantation: insights from metagenomic next-generation sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1456407}, pmid = {39611100}, issn = {2235-2988}, mesh = {*Kidney Transplantation/adverse effects ; Humans ; *High-Throughput Nucleotide Sequencing ; *Precision Medicine/methods ; *Metagenomics/methods ; Male ; COVID-19/diagnosis/virology ; Female ; Middle Aged ; Adult ; SARS-CoV-2/genetics/isolation & purification ; Sensitivity and Specificity ; Cytomegalovirus/genetics/isolation & purification ; Pneumocystis carinii/genetics/isolation & purification ; Cytomegalovirus Infections/diagnosis/virology/drug therapy ; }, abstract = {INTRODUCTION: The aim of this study was to compare the detection performance of mNGS against that of conventional tests (CT) in patients suffering from infection after kidney transplantation.

METHODS: A total of 138 samples from 85 kidney transplant patients with acute or chronic infections were simultaneously analyzed using mNGS and CT from July 2021 to August 2023.

RESULTS: Compared with CT, mNGS demonstrated a higher sensitivity (95.96% vs. 27.27%) but lower specificity (48.72% vs. 84.62%) in pathogen detection. Moreover, mNGS exhibited significant advantages in detecting mixed and rare infections. The pathogens commonly identified in kidney transplant patients were severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), followed by Pneumocystis jirovecii and Cytomegalovirus (CMV). mNGS guided the precise clinical diagnosis in 89.13% of cases and assisted in altering therapeutics from empirical antibiotic approaches to personalized plans in 56.10% of cases, including treatment escalation (40.65%), initiation (11.38%), drug adjustment (3.25%), and de-escalation (0.81%).

DISCUSSION: Our study demonstrated the superior detection performance of mNGS and its significant clinical value. This reflected the great potential of mNGS as a complementary clinical detection technology for kidney transplant patients.}, } @article {pmid39611041, year = {2024}, author = {Liu, L and Lian, ZH and Lv, AP and Salam, N and Zhang, JC and Li, MM and Sun, WM and Tan, S and Luo, ZH and Gao, L and Yuan, Y and Ming, YZ and OuYang, YT and Li, YX and Liu, ZT and Hu, CJ and Chen, Y and Hua, ZS and Shu, WS and Hedlund, BP and Li, WJ and Jiao, JY}, title = {Insights into chemoautotrophic traits of a prevalent bacterial phylum CSP1-3, herein Sysuimicrobiota.}, journal = {National science review}, volume = {11}, number = {11}, pages = {nwae378}, pmid = {39611041}, issn = {2053-714X}, abstract = {Candidate bacterial phylum CSP1-3 has not been cultivated and is poorly understood. Here, we analyzed 112 CSP1-3 metagenome-assembled genomes and showed they are likely facultative anaerobes, with 3 of 5 families encoding autotrophy through the reductive glycine pathway (RGP), Wood-Ljungdahl pathway (WLP) or Calvin-Benson-Bassham (CBB), with hydrogen or sulfide as electron donors. Chemoautotrophic enrichments from hot spring sediments and fluorescence in situ hybridization revealed enrichment of six CSP1-3 genera, and both transcribed genes and DNA-stable isotope probing were consistent with proposed chemoautotrophic metabolisms. Ancestral state reconstructions showed that the ancestors of phylum CSP1-3 may have been acetogens that were autotrophic via the RGP, whereas the WLP and CBB were acquired by horizontal gene transfer. Our results reveal that CSP1-3 is a widely distributed phylum with the potential to contribute to the cycling of carbon, sulfur and nitrogen. The name Sysuimicrobiota phy. nov. is proposed.}, } @article {pmid39609930, year = {2024}, author = {Paquette, AJ and Bhatnagar, S and Vadlamani, A and Gillis, T and Khot, V and Novotnik, B and De la Hoz Siegler, H and Strous, M and Rattray, JE}, title = {Ecology and biogeochemistry of the microbial underworld in two sister soda lakes.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {98}, pmid = {39609930}, issn = {2524-6372}, abstract = {BACKGROUND: Approximately 3.7 billion years ago, microbial life may have emerged in phosphate-rich salty ponds. Surprisingly, analogs of these environments are present in alkaline lake systems, recognized as highly productive biological ecosystems. In this study, we investigate the microbial ecology of two Canadian soda lake sediment systems characterized by naturally high phosphate levels.

RESULTS: Using a comprehensive approach involving geochemistry, metagenomics, and amplicon sequencing, we discovered that groundwater infiltration into Lake Goodenough sediments supported stratified layers of microbial metabolisms fueled by decaying mats. Effective degradation of microbial mats resulted in unexpectedly low net productivity. Evaporation of water from Last Chance Lake and its sediments led to saturation of brines and a habitat dominated by inorganic precipitation reactions, with low productivity, low organic matter turnover and little biological uptake of phosphorus, leading to high phosphate concentrations. Highly alkaline brines were found to be dominated by potentially dormant spore-forming bacteria. These saturated brines also hosted potential symbioses between Halobacteria and Nanoarchaeaota, as well as Lokiarchaea and bacterial sulfate reducers. Metagenome-assembled genomes of Nanoarchaeaota lacked strategies for coping with salty brines and were minimal for Lokiarchaea.

CONCLUSIONS: Our research highlights that modern analogs for origin-of-life conditions might be better represented by soda lakes with low phosphate concentrations. Thus, highly alkaline brine environments could be too extreme to support origin of life scenarios. These findings shed light on the complex interplay of microbial life in extreme environments and contribute to our understanding of early Earth environments.}, } @article {pmid39609882, year = {2024}, author = {Cloarec, LA and Bacchetta, T and Bruto, M and Leboulanger, C and Grossi, V and Brochier-Armanet, C and Flandrois, JP and Zurmely, A and Bernard, C and Troussellier, M and Agogué, H and Ader, M and Oger-Desfeux, C and Oger, PM and Vigneron, A and Hugoni, M}, title = {Lineage-dependent partitioning of activities in chemoclines defines Woesearchaeota ecotypes in an extreme aquatic ecosystem.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {249}, pmid = {39609882}, issn = {2049-2618}, mesh = {*Archaea/classification/genetics/metabolism ; *Lakes/microbiology ; *Phylogeny ; *Ecotype ; Ecosystem ; Metagenomics ; Microbiota ; Genome, Archaeal ; Water Microbiology ; Biodiversity ; }, abstract = {BACKGROUND: DPANN archaea, including Woesearchaeota, encompass a large fraction of the archaeal diversity, yet their genomic diversity, lifestyle, and role in natural microbiomes remain elusive. With an archaeal assemblage naturally enriched in Woesearchaeota and steep vertical geochemical gradients, Lake Dziani Dzaha (Mayotte) provides an ideal model to decipher their in-situ activity and ecology.

RESULTS: Using genome-resolved metagenomics and phylogenomics, we identified highly diversified Woesearchaeota populations and defined novel halophilic clades. Depth distribution of these populations in the water column showed an unusual double peak of abundance, located at two distinct chemoclines that are hotspots of microbial diversity in the water column. Genome-centric metatranscriptomics confirmed this vertical distribution and revealed a fermentative activity, with acetate and lactate as end products, and active cell-to-cell processes, supporting strong interactions with other community members at chemoclines. Our results also revealed distinct Woesearchaeota ecotypes, with different transcriptional patterns, contrasted lifestyles, and ecological strategies, depending on environmental/host conditions.

CONCLUSIONS: This work provides novel insights into Woesearchaeota in situ activity and metabolism, revealing invariant, bimodal, and adaptative lifestyles among halophilic Woesearchaeota. This challenges our precepts of an invariable host-dependent metabolism for all the members of this taxa and revises our understanding of their contributions to ecosystem functioning and microbiome assemblage. Video Abstract.}, } @article {pmid39609754, year = {2024}, author = {Wang, X and Li, H and Ma, L and Ren, J and Mahsa, F and Amin, AM and Zhao, J and Zhang, M and He, P}, title = {Toxoplasmosis in a case with multiple serous effusions and severe aplastic anemia.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {1361}, pmid = {39609754}, issn = {1471-2334}, support = {2023-XKCRC-06//Project of Clinical Research Center of Xi'an Jiaotong University/ ; 2022YFC2502700//National Key R&D Program/ ; 2022YFC2502700//National Key R&D Program/ ; }, mesh = {Humans ; *Anemia, Aplastic/complications ; Female ; Adult ; *Toxoplasma/genetics/isolation & purification ; *Toxoplasmosis/complications/parasitology/diagnosis ; Immunocompromised Host ; Stem Cell Transplantation ; Tomography, X-Ray Computed ; High-Throughput Nucleotide Sequencing ; Pleural Effusion/parasitology ; }, abstract = {Toxoplasmosis, a parasitic disease, can cause fatal multi-organ failure in immunocompromised patients. The lack of specificity in the symptoms and the need to confirm a diagnosis of tachyzoites in fluids or tissues through microscopic examination leads to a delay in reaching a diagnosis. A 28-year-old woman with severe aplastic anemia received stem cell transplantation seven months ago, presented with fever. Computed Tomography scan and ultrasonography showed moderate pleural, pericardial, peritoneal, and pelvic effusions. Metagenomic next-generation sequencing of blood and alveolar lavage fluid was done, 11,082 and 17,154 sequence readings of Toxoplasma gondii were detected, accounting for 1.34% and 17.09% of genome coverage, respectively. Then, marrow aspirate smears showed Toxoplasma gondii tachyzoites and pseudocyst. This case report alerts clinicians about Toxoplasma gondii infection in stem cell transplantation patients with multiple serous effusions and fever. Clinical trial: Not applicable.}, } @article {pmid39609616, year = {2024}, author = {Kim, M and Parrish, RC and Tisza, MJ and Shah, VS and Tran, T and Ross, M and Cormier, J and Baig, A and Huang, CY and Brenner, L and Neuringer, I and Whiteson, K and Harris, JK and Willis, AD and Lai, PS}, title = {Host DNA depletion on frozen human respiratory samples enables successful metagenomic sequencing for microbiome studies.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1590}, pmid = {39609616}, issn = {2399-3642}, support = {R01 AI144119/AI/NIAID NIH HHS/United States ; R21 AI175965/AI/NIAID NIH HHS/United States ; R35 GM133420/GM/NIGMS NIH HHS/United States ; T32 HL116275/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; *Metagenomics/methods ; *Microbiota/genetics ; *Sputum/microbiology ; *Cystic Fibrosis/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; Freezing ; Adult ; Cryopreservation ; Female ; High-Throughput Nucleotide Sequencing/methods ; Bacteria/genetics/isolation & purification/classification ; Sequence Analysis, DNA/methods ; Male ; Respiratory System/microbiology ; }, abstract = {Most respiratory microbiome studies use amplicon sequencing due to high host DNA. Metagenomics sequencing offers finer taxonomic resolution, phage assessment, and functional characterization. We evaluated five host DNA depletion methods on frozen nasal swabs from healthy adults, sputum from people with cystic fibrosis (pwCF), and bronchoalveolar lavage (BAL) from critically ill patients. Median sequencing depth was 76.4 million reads per sample. Untreated nasal, sputum, and BAL had 94.1%, 99.2%, and 99.7% host reads, respectively. Host depletion effects varied by sample type, generally increasing microbial reads, species and functional richness; this was mediated by higher effective sequencing depth. Rarefaction curves showed species richness saturation at 0.5-2 million microbial reads. Most methods did not change Morisita-Horn dissimilarity for BAL and nasal samples although the proportion of gram-negative bacteria decreased for sputum from pwCF. Freezing did not affect the viability of Staphylococcus aureus but reduced the viability of Pseudomonas aeruginosa and Enterobacter spp.; this was mitigated by adding a cryoprotectant. QIAamp-based host depletion minimally impacted gram-negative viability even in non-cryoprotected frozen isolates. While some host depletion methods may shift microbial composition, metagenomics sequencing without host depletion severely underestimates microbial diversity of respiratory samples due to shallow effective sequencing depth and is not recommended.}, } @article {pmid39608999, year = {2024}, author = {Climacosa, FMM and Anlacan, VMM and Gordovez, FJA and Reyes, JCB and Tabios, IKB and Manalo, RVM and Cruz, JMC and Asis, JLB and Razal, RB and Abaca, MJM and Dacasin, AB and Espiritu, APN and Gapaz, NCLL and Lee Yu, MHL}, title = {Monitoring drug Efficacy through Multi-Omics Research initiative in Alzheimer's Disease (MEMORI-AD): A protocol for a multisite exploratory prospective cohort study on the drug response-related clinical, genetic, microbial and metabolomic signatures in Filipino patients with Alzheimer's disease.}, journal = {BMJ open}, volume = {14}, number = {11}, pages = {e078660}, pmid = {39608999}, issn = {2044-6055}, mesh = {Humans ; *Alzheimer Disease/drug therapy/genetics ; Philippines ; Prospective Studies ; Aged ; Cholinesterase Inhibitors/therapeutic use ; Rivastigmine/therapeutic use ; Donepezil/therapeutic use ; Cross-Sectional Studies ; Memantine/therapeutic use ; Male ; Female ; Metabolomics ; Gastrointestinal Microbiome/drug effects ; Multiomics ; }, abstract = {INTRODUCTION: Dementia is one of the leading causes of disability among older people aged 60 years and above, with majority eventually being diagnosed with Alzheimer's disease (AD). Pharmacological agents approved for dementia include acetylcholinesterase enzyme (AChE) inhibitors like rivastigmine, donepezil and galantamine and the N-methyl-D-aspartate (NMDA) receptor antagonist memantine, prescribed as monotherapy or in combination with each other, depending on the severity of disease. There is currently no available study demonstrating the clinical response to these drugs for AD in the Filipino population. Hence, this protocol aims to characterise the clinical, genetic, microbial and metabolic factors associated with drug responses to donepezil, rivastigmine and/or memantine for AD in a cohort of Filipinos with late-onset AD.

METHODS AND ANALYSIS: This protocol involves a multisite descriptive study that will use two study designs: (1) a descriptive, cross-sectional study to characterise the clinical profile of Filipino dementia patients with AD and (2) an exploratory prospective cohort study to investigate drug response-related genetic, gut microbiome and metabolome signatures of a subset of the recruited AD patients. At least 153 patients with mild or moderate AD aged 65 years old and above will be recruited regardless of their treatment status. A subset of these patients (n=60) who meet inclusion and exclusion criteria will be included further in the exploratory cohort study. These patients will be grouped according to their baseline medications and will be observed for treatment response in 6 months. The cognitive, functional and behavioural domains of patients and levels of functioning will be measured using different assessment tools. Drug responses of Filipino patients will then be investigated employing multi-omics technology to characterise genetic variations via whole exome sequencing, gut microbiome profile via shotgun metagenomic sequencing and metabolome profile via liquid chromatography with mass spectrometry.

ETHICS AND DISSEMINATION: The study has received ethical clearance from the Department of Health Single Joint Research Ethics Board (SJREB-2022-15). Results of psychometric scales will be made available to enrolled patients. The study results will be presented at national/international conferences and published in international peer-reviewed scientific journals, and summaries of the results will be provided to the study funders and institutional review boards of the three tertiary referral hospitals.

TRIAL REGISTRATION NUMBER: Philippine Health Research Registry ID PHRR230220-0054116; ClinicalTrials.gov ID NCT05801380.}, } @article {pmid39608612, year = {2024}, author = {Tinganelli, W and Puspitasari-Kokko, A and Sokol, O and Helm, A and Simoniello, P and Schuy, C and Lerchl, S and Eckert, D and Oppermann, J and Rehm, A and Janssen, S and Engel, D and Moeller, R and Romano, R and Horst, F and Boscolo, D and Fournier, C and Durante, M and Weber, U}, title = {FLASH Bragg-Peak Irradiation With a Therapeutic Carbon Ion Beam: First In Vivo Results.}, journal = {International journal of radiation oncology, biology, physics}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ijrobp.2024.11.089}, pmid = {39608612}, issn = {1879-355X}, abstract = {PURPOSE: In recent years, ultra-high dose rate (UHDR) irradiation has emerged as a promising innovative approach to cancer treatment. Characteristic feature of this regimen, commonly referred to as FLASH effect, demonstrated primarily for electrons, photons, or protons, is the improved normal tissue sparing, whereas the tumor control is similar to the one of the conventional dose-rate (CDR) treatments. The FLASH mechanism is, however, unknown. One major question is whether this effect is maintained when using densely ionizing (high-LET) heavy nuclei.

METHODS MATERIALS: Here, we report the effects of 20 Gy UHDR heavy ion irradiation in clinically relevant conditions, ie, at high-LET in the spread-out Bragg peak of a [12]C beam using an osteosarcoma mouse model.

RESULTS: We show that UHDR irradiation was less toxic in the normal tissue compared with CDR while maintaining tumor control. The immune activation was also comparable in UHDR and CDR groups. Both UHDR and CDR exposures steered the metagenome toward a balanced state.

CONCLUSIONS: These results suggest that the UHDR irradiations can improve the safety and effectiveness of heavy ion therapy, and provide a crucial benchmark for current mechanistic FLASH models. However, additional experiments are needed to validate these findings across other animal and tumor models.}, } @article {pmid39608199, year = {2025}, author = {Bhat, AH and Malik, IM and Tak, H and Ganai, BA and Bharti, P}, title = {Host, parasite, and microbiome interaction: Trichuris ovis and its effect on sheep gut microbiota.}, journal = {Veterinary parasitology}, volume = {333}, number = {}, pages = {110356}, doi = {10.1016/j.vetpar.2024.110356}, pmid = {39608199}, issn = {1873-2550}, mesh = {Animals ; Sheep ; *Sheep Diseases/parasitology/microbiology ; *Gastrointestinal Microbiome ; *Trichuris ; *Host-Parasite Interactions ; *Trichuriasis/veterinary/parasitology/microbiology ; RNA, Ribosomal, 16S/genetics ; Cecum/microbiology/parasitology ; Bacteria/classification/genetics/isolation & purification ; }, abstract = {Sheep that are infected with gastrointestinal helminths experience a significant impact on their health and productivity. Among the helminths, nematodes like Haemonchus contortus, Oesophagostomum spp., Bunostomum trigonocephalum, Nematodirus battus, Trichostrongylus spp. and Teladorsagia circumcincta are particularly pathogenic. Understanding the interactions among parasites, hosts, and their microbiomes is crucial in developing new approaches in the management of parasites. This study examines the bacterial profile of Trichuris ovis, a highly prevalent nematode among Kashmir Merino sheep, and the influence of nematode infection on the caecal microbiome of its host. Sheep were selected based on T. ovis infection status, and samples were collected from infected and non-infected caecum. The 16S rRNA metagenomic analysis revealed distinct microbial communities in T. ovis, infected caecum, and non-infected caecum. Proteobacteria dominated the T. ovis microbiome, while infected caecum was rich in Bacteroidota and Spirochaetota, and non-infected caecum had a higher proportion of Firmicutes and Verrucomicrobiota. At the genus level, T. ovis was predominantly associated with Escherichia/Shigella, while infected caecum had higher proportions of Bacteroides, Prevotella, and Treponema. Non-infected caecum was characterized by WCHB1-41, Prevotella, and Succiniclasticum like genera. Alpha and beta diversity indicated significant differences in microbiome among the groups, with higher diversity observed in infected caecum. The study found T. ovis infection significantly alters the caecal microbiome of sheep, introducing potentially pathogenic bacteria and reducing beneficial ones. These findings underscore the complex relationship between host, parasite, and microbiome, highlighting the need for comprehensive strategies to manage helminth infections and their broader ecological impacts.}, } @article {pmid39607975, year = {2024}, author = {Abbasi, AM and Nasir, S and Bajwa, AA and Akbar, H and Ali, MM and Rashid, MI}, title = {A comparative study of the microbiomes of the ticks Rhipicephalus microplus and Hyalomma anatolicum.}, journal = {Parasite (Paris, France)}, volume = {31}, number = {}, pages = {74}, pmid = {39607975}, issn = {1776-1042}, support = {HEC-GCF-273//Higher Education Commission, Pakistan/ ; }, mesh = {Animals ; *Rhipicephalus/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Ixodidae/microbiology ; *Microbiota ; Pakistan ; Phylogeny ; Symbiosis ; Female ; Gastrointestinal Microbiome ; Coxiella/genetics/isolation & purification/classification ; Bacteria/classification/genetics/isolation & purification ; }, abstract = {Hyalomma anatolicum and Rhipicephalus microplus are tick species that are important vectors of numerous pathogens affecting both humans and livestock. Endosymbionts, such as Coxiella-like endosymbionts (CLE), Francisella-like endosymbionts (FLE), and Candidatus Midichloria, play a crucial role in the physiology and vector competence of these ticks. In this study, we investigated the microbial composition of H. anatolicum and R. microplus from four geographically distinct regions of Pakistan to assess whether environmental differences influence their microbiomes. We analyzed the ticks' gut microbiome targeting the V3-V4 hypervariable region of 16S rRNA for Illumina 16S metagenome NGS sequencing and processed overall 144 ticks. Analysis of gut bacterial composition resulted in observation of 1200 R. microplus and 968 H. anatolicum unique amplicon sequencing variants (ASVs). Relative abundance, Alpha diversity (Shannon, Faith's phylogenetic distance) and beta diversity metrics (Bray-Curtis, Jaccard and UniFrac) were analyzed and revealed that H. anatolicum ticks have significantly unique and diverse microbial communities with Acinetobacter indicus and Francisella-like endosymbionts dominating as opposed to Candidatus Midichloria. Rhipicephalus microplus exhibited results consistent with the previous studies with no major changes in microbiome including Coxiella-like endosymbionts as the major contributor. These findings suggest that geographical and environmental factors play a significant role in shaping the tick microbiome, with potential consequences for disease transmission and tick survivability. Further research is needed to elucidate the functional roles of these microbial shifts and their impact on public health and livestock in affected regions.}, } @article {pmid39607585, year = {2024}, author = {Huang, A and Marais, A and Zhang, Z and Candresse, T}, title = {Complete genome sequence of a new poacevirus infecting wild oat (Avena fatua L.) in France.}, journal = {Archives of virology}, volume = {169}, number = {12}, pages = {256}, pmid = {39607585}, issn = {1432-8798}, support = {China Scholarship Council//China Scholarship Council/ ; China Scholarship Council//China Scholarship Council/ ; }, mesh = {*Avena/virology ; *Genome, Viral/genetics ; *Plant Diseases/virology ; *Phylogeny ; France ; *Potyviridae/genetics/isolation & purification/classification ; Whole Genome Sequencing ; High-Throughput Nucleotide Sequencing ; Viral Proteins/genetics ; RNA, Viral/genetics ; 3' Untranslated Regions/genetics ; }, abstract = {Using a high-throughput sequencing (HTS) approach, we report the discovery of a new poacevirus (family Potyviridae) in symptomatic wild oat (Avena fatua L.) plants collected near Bordeaux, France, in June 2023. A nearly complete genome sequence of 10,292 nucleotides (nt) was obtained. The genome encodes a large 3189-amino-acid (aa) polyprotein with all of the expected hallmarks of those of Potyviridae members. The 3' untranslated region (UTR) is 195 nt long, and the 5' UTR, whose sequence is likely missing a few terminal nucleotides despite repeated efforts at 5' RACE, is unusually long (531 nt), like that of triticum mosaic virus (TrMV). Pairwise sequence comparisons and phylogenetic analysis showed that the new virus is most closely related to TrMV and to Poaceae Liege poacevirus, a virus that was identified recently in Poaceae members in Belgium by metagenomics. The common name "wild oat poacevirus 1" (WOPV1) is proposed for this novel virus, which should be accommodated in a new species in the genus Poacevirus. Given that WOPV1 was identified in plants that were coinfected by several other viruses, no conclusions can be drawn at this stage about its potential pathogenicity.}, } @article {pmid39606997, year = {2024}, author = {Li, ZH and Zhang, Q and Wang, HF and Yu, TB and Wang, YL and Ma, JL and Yin, CQ and Shen, F and Xu, YD and Lian, XF and Wang, T}, title = {[Multicenter study on the detection of pathogens in primary infectious diseases of the spine using metagenomic next-generation sequencing technology].}, journal = {Zhonghua wai ke za zhi [Chinese journal of surgery]}, volume = {62}, number = {12}, pages = {1128-1135}, doi = {10.3760/cma.j.cn112139-20240715-00337}, pmid = {39606997}, issn = {0529-5815}, support = {21-1-4-rkjk-2-nsh//Qingdao City Science and Technology Benefiting the People Demonstration and Guidance Special Support Project/ ; 22-3-7-smjk-5-nsh//Qingdao City Science and Technology Benefiting the People Demonstration and Guidance Special Support Project/ ; 22-3-7-smjk-5-nsh, 21-1-4-rkjk-2-nsh//Qingdao City Science and Technology Benefiting the People Demonstration and Guidance Special Support Project/ ; }, mesh = {Humans ; Male ; Retrospective Studies ; Female ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; Aged ; Adult ; Child ; Adolescent ; Aged, 80 and over ; *Metagenomics/methods ; Young Adult ; China ; Spinal Diseases/microbiology/diagnosis ; Communicable Diseases/diagnosis/microbiology ; Spine/microbiology ; }, abstract = {Objective: To explore the role of metagenomic next-generation sequencing (mNGS) in the diagnosis of pathogens in primary infectious diseases of the spine (IDS) and to reveal its pathogen spectrum. Methods: This is a retrospective multi-center case series study. Clinical data of 380 patients with primary IDS who were treated at four medical centers in China from December 2019 to April 2024 were retrospectively analyzed. Among them, 82 cases were from the Department of Spine Surgery at the Affiliated Hospital of Qingdao University, 129 cases were from the Orthopedics Section Ⅱ (Bone Infection), Public Health Clinical Center Affiliated to Shandong University, 112 cases were from the Department of Spine Surgery, Fuzhou Second General Hospital, and 57 cases were from the Department of Orthopedic Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine. There were 238 males and 242 females, with an age of (61.4±13.1) years (range: 10 to 91 years). Specimens from the site of spinal infection were obtained for pathogen culture, pathological examination, and mNGS detection preoperatively or intraoperatively in all patients. The number, types, and positive rates of pathogens detected by the two methods were analyzed and compared using the Chi-square test. Results: Among the 380 patients, 320 had confirmed pathogenic bacteria, with the highest proportion being pyogenic bacterial infections, accounting for 76.9% (246/320). The most common pathogen was Staphylococcus aureus, accounting for 22.8% (73/320). Brucella accounted for 13.8% (44/320); Mycobacterium tuberculosis accounted for 6.3% (20/320). Fungal infections accounted for 3.4% (11/320), mainly Aspergillus and Candida. In addition, Mycoplasma was detected in 3 cases (0.9%) and Benacox body in 4 cases (1.2%). The pathogen spectrum constructed by mNGS covered 46 types of pathogens, higher than the 22 types detected by traditional methods. The positive rate of mNGS was 80.8% (308/381), significantly higher than the 27.9% (106/381) of traditional methods (χ[2]=182.53, P<0.01). Conclusions: mNGS improves the positive rate of pathogen diagnosis in IDS, detecting a broader spectrum of pathogens, and serves as a valuable complement to traditional diagnostic methods. Combining both methods in the diagnosis of IDS can maximize detection rates, providing robust evidence for precise anti-infective treatment.}, } @article {pmid39606118, year = {2024}, author = {Lin, L and Luo, L and Wu, M and Chen, J and Liao, Y and Zhang, H}, title = {Utilizing metagenomic next-generation sequencing and phylogenetic analysis to identify a rare pediatric case of Naegleria fowleri infection presenting with fulminant myocarditis.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1463822}, pmid = {39606118}, issn = {1664-302X}, abstract = {BACKGROUND: Naegleria fowleri (N. fowleri), a rare and typically lethal amoeba, most commonly causes primary amoebic meningoencephalitis (PAM). This case report describes an exceptionally rare presentation of fulminant myocarditis as the primary manifestation in a 6-year-old child, diverging from the typical neurological pathogenesis associated with N. fowleri infection. Beyond neurological afflictions, the child developed arrhythmias and cardiac failure, necessitating treatment with extracorporeal membrane oxygenation (ECMO).

METHODS: Diagnosis was confirmed via metagenomic next-generation sequencing (mNGS) of both blood and cerebrospinal fluid (CSF). This analysis not only substantiated the infection but also revealed a potential new genotype of N. fowleri, designated k39_3, suggesting broader genetic diversity than previously recognized.

RESULTS: Immediate treatment with Amphotericin B (Am B) and rifampin was initiated upon diagnosis. Despite aggressive management and supportive care, the patient failed to maintain hemodynamic stability, continued to show a decrease in cardiac output, and exhibited relentless progression of central nervous system failure, culminating in death within 72 h.

CONCLUSION: Our report documents a rare pediatric case of N. fowleri infection presenting with fulminant myocarditis, revealing an unexpected clinical manifestation and broadening the known spectrum of its effects. This emphasizes the need for enhanced surveillance and targeted research to understand the pathogenic mechanisms and improve treatment strategies.}, } @article {pmid39605913, year = {2024}, author = {Chen, J and Ng, S and Xu, P and Chen, S and Li, S and Chen, X and Xie, L and Ge, J}, title = {Herbal formula xuling-jiangu improves bone metabolic balance in rats with ovariectomy-induced osteoporosis via the gut-bone axis.}, journal = {Frontiers in pharmacology}, volume = {15}, number = {}, pages = {1505231}, pmid = {39605913}, issn = {1663-9812}, abstract = {INTRODUCTION: The XuLing JianGu recipe (XLJGR) is an empirical traditional Chinese medicine formula used for the treatment of osteoporosis. This study aims to explore the effects of XLJGR on the intestinal microbiota composition and endogenous metabolites in ovariectomized (OVX) rats.

METHODS: An OVX rat model was established to evaluate the intervention effects of XLJGR. The measured indicators included bone density, serum bone metabolism markers, and an analysis of the types and abundances of intestinal microbiota, along with changes in endogenous metabolites. Additionally, MC3T3-E1 cells were used to validate the differential metabolites.

RESULTS: XLJGR significantly reduced the abundance of Bacteroides, Butyricicoccus, and other bacterial strains in the gut. KEGG metabolic pathway enrichment analysis showed that XLJGR intervention led to notable changes in pathways such as peptidoglycan biosynthesis, carbapenem biosynthesis, and vancomycin resistance. Moreover, XLJGR significantly upregulated key intestinal microbiota metabolites, including gabapentin(GAB), camphoric acid(CAA), and nonanedioic acid(AZA), thereby promoting the proliferation and osteogenic differentiation of MC3T3-E1 cells.

DISCUSSION: This study highlights the potential biomedical applications of XLJGR in promoting bone health by positively affecting intestinal microbiota and metabolic characteristics. These findings suggest that XLJGR may serve as a viable alternative in the treatment of osteoporosis, warranting further exploration of its therapeutic mechanisms and clinical applications.}, } @article {pmid39605612, year = {2024}, author = {Cumbo, F and Truglia, S and Weitschek, E and Blankenberg, D}, title = {Feature selection with vector-symbolic architectures: a case study on microbial profiles of shotgun metagenomic samples of colorectal cancer.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39605612}, issn = {2692-8205}, support = {U24 CA231877/CA/NCI NIH HHS/United States ; U24 HG006620/HG/NHGRI NIH HHS/United States ; }, abstract = {The continuingly decreasing cost of next-generation sequencing has recently led to a significant increase in the number of microbiome-related studies, providing invaluable information for understanding host-microbiome interactions and their relation to diseases. A common approach in metagenomics consists of determining the composition of samples in terms of the amount and types of microbial species that populate them, with the goal to identify microbes whose profiles are able to differentiate samples under different conditions with advanced feature selection techniques. Here we propose a novel backward variable selection method based on the hyperdimensional computing paradigm, which takes inspiration from how the human brain works in the classification of concepts by encoding features into vectors in a high-dimensional space. We validated our method on public metagenomic samples collected from patients affected by colorectal cancer in a case/control scenario, by performing a comparative analysis with other state-of-the-art feature selection methods, obtaining promising results.}, } @article {pmid39605597, year = {2024}, author = {Popowitch, EB and Tran, TH and Escapa, IF and Bhatt, E and Sozat, AK and Ahmed, N and Deming, C and Roberts, AQ and , and Segre, JA and Kong, HH and Conlan, S and Lemon, KP and Kelly, MS}, title = {Description of two novel Corynebacterium species isolated from human nasal passages and skin.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39605597}, issn = {2692-8205}, support = {K23 AI135090/AI/NIAID NIH HHS/United States ; R35 GM141806/GM/NIGMS NIH HHS/United States ; }, abstract = {Strains of two novel Corynebacterium species were cultured from samples of human nostrils and skin collected in the United States and Botswana. These strains demonstrated growth on Columbia Colistin-Nalidixic Acid agar with 5% sheep blood and in liquid media (brain heart infusion and tryptic soy broth) supplemented with Tween 80, a source of the fatty acid oleic acid. Cells were Gram-positive, non-spore-forming, non-motile bacilli that showed catalase but not oxidase activity. Major fatty acids in both of these species were 18:1 ω9c (oleic acid), 16:0 (palmitic acid), and 18:0 (stearic acid). Analysis of the 16S ribosomal RNA gene sequences identified these strains as belonging to the genus Corynebacterium (family Corynebacteriaceae). Whole-genome sequencing revealed that these strains formed distinct branches on a phylogenomic tree, with C. tuberculostearicum being the closest relative but with average nucleotide identities of < 95% relative to all previously described species. These results indicate that these strains represent novel species of Corynebacterium, for which we propose the names Corynebacterium hallux sp. nov., with the type strain CTNIH22[T] (=ATCC TSD-435[T]=DSM 117774[T]), and Corynebacterium nasorum sp. nov., with the type strain KPL3804[T] (=ATCC TSD-439[T]=DSM 117767[T]). We also describe the characteristics of two strains isolated from human nasal passages that are members of the recently named species Corynebacterium yonathiae.}, } @article {pmid39605587, year = {2024}, author = {Andermann, TM and Zeng, K and Guirales-Medrano, S and Groth, A and Ramachandran, BC and Sun, S and Sorgen, AA and Hill, L and Bush, AT and Liu, H and Jones, C and Roach, J and Conlon, BP and Rao, G and Chao, NJ and Fodor, AA and Sung, AD}, title = {The impact of transplant location on the gut microbiome and resistome in patients undergoing hematopoietic stem cell transplantation at home versus in the hospital.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.11.19.624359}, pmid = {39605587}, issn = {2692-8205}, abstract = {OBJECTIVES: Home-based hematopoietic stem cell transplantation (HCT) is a novel approach that has the potential to improve outcomes, however, the impact of transplant location on the gut microbiome remains uncharacterized. We hypothesized that patients randomized to undergo home HCT would have higher gut taxonomic diversity and lower antimicrobial resistance (AMR) gene abundance compared to those undergoing standard hospital HCT.

METHODS: We identified 28 patients enrolled in Phase II randomized trials of home (n=16) v. hospital (n=12) HCT at Duke and performed shotgun metagenomic sequencing of stools to compare taxonomic and AMR gene composition between groups. We performed a secondary analysis of patients from each group transplanted at an outpatient infusion clinic with those who underwent standard inpatient HCT ("outpatient" v. "inpatient").

RESULTS: No significant differences in duration of hospitalization were found in those randomized to home v. hospital HCT. Taxonomic and AMR gene α- and β-diversity were comparable. In contrast, secondary analyses demonstrated that patients from both home and hospital groups transplanted at an outpatient infusion clinic spent significantly less time in the hospital and demonstrated higher taxonomic α-diversity and differential β-diversity compared to standard inpatient HCT, although AMR gene α-diversity did not differ, and comparisons were confounded by both differences in transplant type and use of antibiotics.

CONCLUSIONS: Randomization by transplant location did not impact the gut microbiota to the same extent as the duration of hospitalization, although secondary analyses were heavily confounded. Even when taxonomic differences were observed, AMR genes were similar between groups.}, } @article {pmid39605360, year = {2024}, author = {Dai, Y and Qian, Y and Qu, Y and Guan, W and Xie, J and Wang, D and Butler, C and Dashper, S and Carroll, I and Divaris, K and Liu, Y and Wu, D}, title = {Longitudinal Microbiome-based Interpretable Machine Learning for Identification of Time-Varying Biomarkers in Early Prediction of Disease Outcomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39605360}, issn = {2692-8205}, support = {R03 DE034507/DE/NIDCR NIH HHS/United States ; U01 DE025046/DE/NIDCR NIH HHS/United States ; }, abstract = {Information generated from longitudinally-sampled microbial data has the potential to illuminate important aspects of development and progression for many human conditions and diseases. Identifying microbial biomarkers and their time-varying effects can not only advance our understanding of pathogenetic mechanisms, but also facilitate early diagnosis and guide optimal timing of interventions. However, longitudinal predictive modeling of highly noisy and dynamic microbial data (e.g., metagenomics) poses analytical challenges. To overcome these challenges, we introduce a robust and interpretable machine-learning-based longitudinal microbiome analysis framework, LP-Micro, that encompasses: (i) longitudinal microbial feature screening via a polynomial group lasso, (ii) disease outcome prediction implemented via machine learning methods (e.g., XGBoost, deep neural networks), and (iii) interpretable association testing between time points, microbial features, and disease outcomes via permutation feature importance. We demonstrate in simulations that LP-Micro can not only identify incident disease-related microbiome taxa but also offers improved prediction accuracy compared to existing approaches. Applications of LP-Micro in two longitudinal microbiome studies with clinical outcomes of childhood dental disease and weight loss following bariatric surgery yield consistently high prediction accuracy. The identified critical early predictive time points are informative and aligned with clinical expectations.}, } @article {pmid39604824, year = {2024}, author = {Li, X and Zhang, Z and Bai, H and Liu, Z}, title = {Analysis of vaginal microbiota during postpartum and postmenopausal periods based on metagenomics.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {501}, pmid = {39604824}, issn = {1471-2180}, mesh = {Humans ; Female ; *Vagina/microbiology ; *Postmenopause ; *Postpartum Period ; *Microbiota/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; Adult ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Postmenopausal and the postpartum periods are essential physiological phases that result in low estrogen levels in women; however, they are important to female reproductive health. Traditional as well as new detection methods (such as 16 S RNA sequencing) have limitations in detecting the composition of vaginal microbiota. Therefore, in this study, we used metagenomic detection technology to study the composition of vaginal microbiota in postmenopausal and postpartum women. Six women were randomly selected from each group (healthy women of childbearing age, postmenopausal group, and postpartum) for vaginal microecology, composition, α-diversity, linear discriminant analysis effect size (LEfSe), and Comprehensive Antibiotic Resistance Database (CARD) analyses.

RESULTS: We discovered that Lactobacillus dominance disappeared in postpartum and postmenopausal group women and that diversity increased. However, the proportions of Atopobium vaginae, Escherichia coli, and Streptococcus agalactiae significantly increased. Diversity was the highest in the postpartum period, with a significant increase in the proportions of A. vaginae, Gardnerella vaginalis, Prevotella, and occasionally, Chlamydia trachomatis. Linear discriminant analysis effect size analysis revealed that Lactobacillus crispatus and L. iners enrichment in the postpartum and menopausal periods was much lower than that in the childbearing age group. CARD analysis revealed that ABC-F ATP-binding cassette ribosomal protection protein subfamily gene abundance was significantly lower in the menopausal than in the childbearing age group, whereas the gimA family macrolide glycosyltransferase gene abundance was significantly higher.

CONCLUSIONS: The dominance of vaginal Lactobacillus in postpartum and menopausal women disappeared, while their diversity increased. In addition, the reproductive tract of postpartum women was susceptible to invasion by pathogenic microorganisms, which deserves clinical attention. When menopausal women receive treatment for vaginal infections, the likelihood that certain bacterial communities develop antibiotic resistance through ribosomal protection mechanisms is lower than that of women in the childbearing age, while the possibility of developing resistance to macrolides through glycosylation may increase. This, however, requires further research.}, } @article {pmid39604809, year = {2025}, author = {Li, Q and Wu, D and Song, Y and Zhang, L and Wang, T and Chen, X and Zhang, M}, title = {In vivo mechanism of the interaction between trimethylamine lyase expression and glycolytic pathways.}, journal = {Food & function}, volume = {16}, number = {1}, pages = {87-101}, doi = {10.1039/d4fo03809f}, pmid = {39604809}, issn = {2042-650X}, mesh = {Animals ; *Glycolysis ; Mice ; *Gastrointestinal Microbiome ; Male ; Glycine/metabolism/pharmacology ; Mice, Inbred C57BL ; Lyases/metabolism/genetics ; Methylamines/metabolism ; Diet ; Bacteria/genetics/classification/metabolism ; RNA, Ribosomal, 16S/genetics ; Choline/metabolism ; }, abstract = {Recent studies confirmed that host-gut microbiota interactions modulate disease-linked metabolite TMA production via TMA lyase. However, microbial enzyme production mechanisms remain unclear. In the present study, we investigated the impact of dietary and intervention factors on gut microbiota, microbial gene expression, and the interplay between TMA lyase and glycolytic pathways in mice. Using 16S rRNA gene sequencing, metagenomics, and metabolomics, the gut microbiota composition and microbial functional gene expression profiles related to TMA lyase and glycolytic enzymes were determined. The results revealed that distinct diets and intervention factors altered gut microbiota, gene expression, and metabolites linked to glycine metabolism and glycolysis. Notably, an arabinoxylan-rich diet suppressed genes linked to choline, glycine, glycolysis, and TMA lyase, favoring glycine utilization via pyruvate pathways. Glycolytic inhibitors amplified these effects, mainly inhibiting pyruvate kinase. Our findings underscored the crosstalk between TMA lyase and glycolytic pathways, regulating glycine levels, and suggested avenues for targeted interventions and personalized diets to curb choline TMA lyase production.}, } @article {pmid39604726, year = {2025}, author = {Chen-Liaw, A and Aggarwala, V and Mogno, I and Haifer, C and Li, Z and Eggers, J and Helmus, D and Hart, A and Wehkamp, J and Lamousé-Smith, ESN and Kerby, RL and Rey, FE and Colombel, JF and Kamm, MA and Olle, B and Norman, JM and Menon, R and Watson, AR and Crossette, E and Terveer, EM and Keller, JJ and Borody, TJ and Grinspan, A and Paramsothy, S and Kaakoush, NO and Dubinsky, MC and Faith, JJ}, title = {Gut microbiota strain richness is species specific and affects engraftment.}, journal = {Nature}, volume = {637}, number = {8045}, pages = {422-429}, pmid = {39604726}, issn = {1476-4687}, support = {R01 DK112978/DK/NIDDK NIH HHS/United States ; R01 DK124133/DK/NIDDK NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome ; *Fecal Microbiota Transplantation ; Humans ; Animals ; *Species Specificity ; *Feces/microbiology ; Mice ; Metagenome ; Male ; Female ; Lakes/microbiology ; Bacteria/classification/genetics/isolation & purification ; Biodiversity ; Soil Microbiology ; }, abstract = {Despite the fundamental role of bacterial strain variation in gut microbiota function[1-6], the number of unique strains of a species that can stably colonize the human intestine is still unknown for almost all species. Here we determine the strain richness (SR) of common gut species using thousands of sequenced bacterial isolates with paired metagenomes. We show that SR varies across species, is transferable by faecal microbiota transplantation, and is uniquely low in the gut compared with soil and lake environments. Active therapeutic administration of supraphysiologic numbers of strains per species increases recipient SR, which then converges back to the population average after dosing is ceased. Stratifying engraftment outcomes by high or low SR shows that SR predicts microbial addition or replacement in faecal transplants. Together, these results indicate that properties of the gut ecosystem govern the number of strains of each species colonizing the gut and thereby influence strain addition and replacement in faecal microbiota transplantation and defined live biotherapeutic products.}, } @article {pmid39604579, year = {2024}, author = {Hao, Z and Lu, Y and Hao, Y and Luo, Y and Wu, K and Zhu, C and Shi, P and Zhu, F and Lin, Y and Zeng, X}, title = {Fungal mycobiome dysbiosis in choledocholithiasis concurrent with cholangitis.}, journal = {Journal of gastroenterology}, volume = {}, number = {}, pages = {}, pmid = {39604579}, issn = {1435-5922}, support = {PWZxq2022-06//Key Disciplines Group Construction Project of Shanghai Pudong New Area Health Commission/ ; 82270636//National Natural Science Foundation of China/ ; 82070616//National Natural Science Foundation of China/ ; 82100608//National Natural Science Foundation of China/ ; PW2022D08//Joint Tackling Project of Pudong Health Committee of Shanghai/ ; PW2021A-38//Health and Family Planning Research Project of Pudong Health Committee of Shanghai/ ; PWYgf2021-02//Medical Discipline Construction Project of Pudong Health Committee of Shanghai/ ; 2022XD028//Talent Plan of the Shanghai Municipal Health Commission for Academic Leader/ ; }, abstract = {BACKGROUND: The gut mycobiome might have an important influence on the pathogenesis of choledocholithiasis concurrent with cholangitis (CC). The aim of this study was to characterize the fungal mycobiome profiles, explore the correlation and equilibrium of gut interkingdom network among bacteria-fungi-metabolites triangle in CCs.

METHODS: In a retrospective case-control study, we recruited patients with CC (n = 25) and healthy controls (HCs) (n = 25) respectively to analyze the gut fungal dysbiosis. Metagenomic sequencing was employed to characterize the gut mycobiome profiles, and liquid chromatography/mass spectrometry (LC/MS) analysis was used to quantify the metabolites composition.

RESULTS: The Shannon index displayed a reduction in fungal α-diversity in CCs compared to HCs (p = 0.041), and the overall fungal composition differed significantly between two groups. The dominant 7 fungi species with the remarkable altered abundance were identified (LDA score > 3.0, p < 0.05), including CC-enriched Aspergillus_niger and CC-depleted fungi Saccharomyces_boulardii. In addition, the correlations between CC-related fungi and clinical variables in CCs were analyzed. Moreover, the increased abundance ratio of Basidiomycota-to-Ascomycota and a dense linkage of bacteria-fungi interkingdom network in CCs were demonstrated. Finally, we identified 30 markedly altered metabolites in CCs (VIP > 1.0 and p < 0.05), including low level of acetate and butyrate, and the deeper understanding on the complexity of bacteria-fungi-metabolites triangle involving bile inflammation was verified.

CONCLUSION: Our investigation demonstrated a distinct gut fungal dysbiosis in CCs and proposed that, beyond bacteria, the more attention should be paid to significantly potential influence of fungi and bacteria-fungi-metabolites triangle interkingdom interactions on pathogenesis of CC.}, } @article {pmid39604411, year = {2024}, author = {Purushothaman, S and Meola, M and Roloff, T and Rooney, AM and Egli, A}, title = {Evaluation of DNA extraction kits for long-read shotgun metagenomics using Oxford Nanopore sequencing for rapid taxonomic and antimicrobial resistance detection.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {29531}, pmid = {39604411}, issn = {2045-2322}, support = {310030_192512//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 310030_192512//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 310030_192512//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 310030_192512//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 310030_192512//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; }, mesh = {*Metagenomics/methods ; *Nanopore Sequencing/methods ; *Drug Resistance, Bacterial/genetics ; DNA, Bacterial/genetics/isolation & purification ; Humans ; Bacteria/genetics/isolation & purification/classification ; }, abstract = {During a bacterial infection or colonization, the detection of antimicrobial resistance (AMR) is critical, but slow due to culture-based approaches for clinical and screening samples. Culture-based phenotypic AMR detection and confirmation require up to 72 hours (h) or even weeks for slow-growing bacteria. Direct shotgun metagenomics by long-read sequencing using Oxford Nanopore Technologies (ONT) may reduce the time for bacterial species and AMR gene identification. However, screening swabs for metagenomics is complex due to the range of Gram-negative and -positive bacteria, diverse AMR genes, and host DNA present in the samples. Therefore, DNA extraction is a critical initial step. We aimed to compare the performance of different DNA extraction protocols for ONT applications to reliably identify species and AMR genes using a shotgun long-read metagenomic approach. We included three different sample types: ZymoBIOMICS Microbial Community Standard, an in-house mock community of ESKAPE pathogens including Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Escherichia coli (ESKAPE Mock), and anonymized clinical swab samples. We processed all sample types with four different DNA extraction kits utilizing different lysis (enzymatic vs. mechanical) and purification (spin-column vs. magnetic beads) methods. We used kits from Qiagen (QIAamp DNA Mini and QIAamp PowerFecal Pro DNA) and Promega (Maxwell RSC Cultured Cells and Maxwell RSC Buccal Swab DNA). After extraction, samples were subject to the Rapid Barcoding Kit (RBK004) for library preparation followed by sequencing on the GridION with R9.4.1 flow cells. The fast5 files were base called to fastq files using Guppy in High Accuracy (HAC) mode with the inbuilt MinKNOW software. Raw read quality was assessed using NanoPlot and human reads were removed using Minimap2 alignment against the Hg38 genome. Taxonomy identification was performed on the raw reads using Kraken2 and on assembled contigs using Minimap2. The AMR genes were identified using Minimap2 with alignment against the CARD database on both the raw reads and assembled contigs. We identified all bacterial species present in the Zymo Mock Community (8/8) and ESKAPE Mock (6/6) with Qiagen PowerFecal Pro DNA kit (chemical and mechanical lysis) at read and assembly levels. Enzymatic lysis retrieved fewer aligned bases for the Gram-positive species (Staphylococcus aureus and Enterococcus faecium) from the ESKAPE Mock on the assembly level compared to the mechanical lysis. We detected the AMR genes from Gram-negative and -positive species in the ESKAPE Mock with the QIAamp PowerFecal Pro DNA kit on reads level with a maximum median time of 1.9 h of sequencing. Long-read metagenomics with ONT may reduce the turnaround time in screening for AMR genes. Currently, the QIAamp PowerFecal Pro DNA kit (chemical and mechanical lysis) for DNA extraction along with the Rapid Barcoding Kit for the ONT sequencing captured the best taxonomy and AMR identification for our specific use case.}, } @article {pmid39604397, year = {2024}, author = {Carey-Ewend, K and Popkin-Hall, ZR and Simkin, A and Muller, M and Hennelly, C and He, W and Moser, KA and Gaither, C and Niaré, K and Aghakanian, F and Feleke, S and Brhane, BG and Phanzu, F and Kashamuka, MM and Aydemir, O and Sutherland, CJ and Ishengoma, DS and Ali, IM and Ngasala, B and Kalonji, A and Tshefu, A and Parr, JB and Bailey, JA and Juliano, JJ and Lin, JT}, title = {Population genomics of Plasmodium ovale species in sub-Saharan Africa.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {10297}, pmid = {39604397}, issn = {2041-1723}, support = {R01 TW010870/TW/FIC NIH HHS/United States ; R01AI65537//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01AI129812//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; K24 AI134990/AI/NIAID NIH HHS/United States ; R01 AI065537/AI/NIAID NIH HHS/United States ; R01AI132547//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01TW010870//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01 AI129812/AI/NIAID NIH HHS/United States ; T32 AI070114/AI/NIAID NIH HHS/United States ; R21 AI152260/AI/NIAID NIH HHS/United States ; R21 AI148579/AI/NIAID NIH HHS/United States ; K24AI134990//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01 AI137395/AI/NIAID NIH HHS/United States ; T32AI070114//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R21AI148579//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R21AI152260//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01 AI132547/AI/NIAID NIH HHS/United States ; }, mesh = {*Plasmodium ovale/genetics/classification/isolation & purification ; Africa South of the Sahara/epidemiology ; Humans ; *Malaria/epidemiology/parasitology ; *Genome, Protozoan/genetics ; Genetic Variation ; Whole Genome Sequencing ; Tetrahydrofolate Dehydrogenase/genetics ; Phylogeny ; Merozoite Surface Protein 1/genetics ; Metagenomics ; Genomics/methods ; }, abstract = {Plasmodium ovale curtisi (Poc) and Plasmodium ovale wallikeri (Pow) are relapsing malaria parasites endemic to Africa and Asia that were previously thought to represent a single species. Amid increasing detection of ovale malaria in sub-Saharan Africa, we present a population genomic study of both species across the continent. We conducted whole-genome sequencing of 25 isolates from Central and East Africa and analyzed them alongside 20 previously published African genomes. Isolates are predominantly monoclonal (43/45), with their genetic similarity aligning with geography. Pow shows lower average nucleotide diversity (1.8×10[-4]) across the genome compared to Poc (3.0×10[-4]) (p < 0.0001). Signatures of selective sweeps involving the dihydrofolate reductase gene have been found in both species, as are signs of balancing selection at the merozoite surface protein 1 gene. Differences in the nucleotide diversity of Poc and Pow may reflect unique demographic history, even as similar selective forces facilitate their resilience to malaria control interventions.}, } @article {pmid39604394, year = {2024}, author = {Akiyama, S and Nishijima, S and Kojima, Y and Kimura, M and Ohsugi, M and Ueki, K and Mizokami, M and Hattori, M and Tsuchiya, K and Uemura, N and Kawai, T and Bork, P and Nagata, N}, title = {Multi-biome analysis identifies distinct gut microbial signatures and their crosstalk in ulcerative colitis and Crohn's disease.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {10291}, pmid = {39604394}, issn = {2041-1723}, mesh = {Humans ; *Colitis, Ulcerative/microbiology/genetics/virology ; *Crohn Disease/microbiology ; *Gastrointestinal Microbiome/genetics ; *Feces/microbiology ; Male ; *Metagenomics/methods ; Female ; *Bacteriophages/genetics ; Adult ; Escherichia coli/genetics/metabolism ; Middle Aged ; Japan ; Fungi/genetics ; Bacteria/genetics/metabolism/classification ; Metagenome/genetics ; Saccharomyces cerevisiae/genetics ; Bifidobacterium/genetics ; Virome/genetics ; Enterococcus faecium/genetics/pathogenicity ; Fatty Acids, Volatile/metabolism ; Young Adult ; China ; Case-Control Studies ; }, abstract = {The integrative multi-kingdom interaction of the gut microbiome in ulcerative colitis (UC) and Crohn's disease (CD) remains underinvestigated. Here, we perform shotgun metagenomic sequencing of feces from patients with UC and CD, and healthy controls in the Japanese 4D cohort, profiling bacterial taxa, gene functions, and antibacterial genes, bacteriophages, and fungi. External metagenomic datasets from the US, Spain, the Netherlands, and China were analyzed to validate our multi-biome findings. We found that Enterococcus faecium and Bifidobacterium spp. were enriched in both diseases. Enriched Escherichia coli was characteristic of CD and was linked to numerous antibiotic resistance genes involved in efflux pumps and adherent-invasive Escherichia coli virulence factors. Virome changes correlated with shifts in the bacteriome, including increased abundances of phages encoding pathogenic genes. Saccharomyces paradoxus and Saccharomyces cerevisiae were enriched in UC and CD, respectively. Saccharomyces cerevisiae and Escherichia coli had negative associations with short-chain fatty acid (SCFA)-producing bacteria in CD. Multi-biome signatures and their interactions in UC and CD showed high similarities between Japan and other countries. Since bacteria, phages, and fungi formed multiple hubs of intra- or trans-kingdom networks with SCFA producers and pathobionts in UC and CD, an approach targeting the interaction network may hold therapeutic promise.}, } @article {pmid39603713, year = {2024}, author = {Helfrich, PG and Feldman, J and Andrade-Barahona, E and Robertson, I and Foster, J and Hofacker, R and Dahlquist Selking, G and Sheik, CS and Cox, A}, title = {Aqueous copper geochemistry shapes the sediment microbial resistome in a recovering stream.}, journal = {Environmental microbiology reports}, volume = {16}, number = {6}, pages = {e70045}, pmid = {39603713}, issn = {1758-2229}, support = {800015-10297//Montana Department of Justice, Natural Resource Damage Program (NRDP) through the Butte Natural Resource Damage Restoration Council (BNRC)/ ; //Montana Tech Faculty Seed and Faculty Development Initiatives/ ; //Montana Tech Earth Science and Engineering Fellowship/ ; //Montana Water Center, Faculty Seed Grant/ ; }, mesh = {*Copper/metabolism ; *Geologic Sediments/microbiology/chemistry ; *Rivers/microbiology/chemistry ; *Bacteria/genetics/drug effects/classification/metabolism/isolation & purification ; Metagenome ; Water Pollutants, Chemical/metabolism ; Metagenomics ; Arsenic/metabolism ; Microbiota/genetics/drug effects ; }, abstract = {Aqueous metals are pervasive contaminants associated with historical mining. We produced and examined 16 metagenomes from a contaminated creek to investigate how anthropogenic metal contamination shapes the functional profiles of microbial communities. We then incorporated the metagenomic profiles and concurrently collected geochemical context into a multivariate model to examine correlations between stream geochemistry and microbial functional potential. Integrating the metagenomes with full geochemical profiles emphasised that even low metalloid concentrations shaped microbial functionality, seasonal shifts in copper bioavailability and arsenic exposure correlated with genetic variation, and copper resistomes were spatiotemporally distinct. This study provides new insights into microbial metabolic potential and microbe-metal(loid) interactions.}, } @article {pmid39603479, year = {2025}, author = {Guo, Q and Chen, X and Gong, H and Yang, J and Li, S and Zhu, D and Wang, X and Li, K and Zhang, Y and Zhou, S and Chen, K and Dai, X}, title = {Effect of inoculated sludge concentration on start-up of anammox reactor: Nitrogen removal performance and metabolic pathways.}, journal = {Bioresource technology}, volume = {418}, number = {}, pages = {131883}, doi = {10.1016/j.biortech.2024.131883}, pmid = {39603479}, issn = {1873-2976}, mesh = {*Sewage/microbiology ; *Bioreactors/microbiology ; *Nitrogen/metabolism ; *Bacteria/metabolism/genetics ; Anaerobiosis ; Metabolic Networks and Pathways ; Oxidation-Reduction ; }, abstract = {The anammox process is efficient for nitrogen removal but faces challenges due to slow bacterial growth and limited inoculated sludge supply. This study examined the effects of different inoculated sludge concentrations (3.5, 7, and 14 g/L) on start-up and nitrogen metabolism in anammox reactors. Three identical reactors were operated under controlled conditions, with comprehensive analysis of nitrogen removal efficiency, sludge characteristics, and microbial community dynamics through metagenomic and transcriptomic approaches. Results demonstrated that higher inoculated sludge concentrations accelerated reactor start-up, with the 14 g/L reactor achieving stable operation in 13 days compared to 44 days for the 3.5 g/L reactor. However, the improvement in nitrogen removal rate showed a boundary effect, not proportional to the increase in sludge concentration. Notably, reactors with higher inoculated sludge concentrations exhibited lower sludge loads but higher sludge yield coefficients. Metagenomic analysis revealed Candidatus Kuenenia as the dominant anammox bacteria, with decreasing hydrazine dehydrogenase (hdh) gene expression levels observed at higher sludge concentrations, suggesting hydrazine synthesis as a potential rate-limiting step. This study provides novel insights into the optimal range of inoculated sludge concentration for anammox reactor start-up and elucidates the underlying metabolic mechanisms, offering valuable guidance for practical engineering applications.}, } @article {pmid39603473, year = {2025}, author = {Li, Y and Tao, C and Li, S and Chen, W and Fu, D and Jafvert, CT and Zhu, T}, title = {Feasibility study of machine learning to explore relationships between antimicrobial resistance and microbial community structure in global wastewater treatment plant sludges.}, journal = {Bioresource technology}, volume = {417}, number = {}, pages = {131878}, doi = {10.1016/j.biortech.2024.131878}, pmid = {39603473}, issn = {1873-2976}, mesh = {*Machine Learning ; *Sewage/microbiology ; *Wastewater/microbiology ; Water Purification/methods ; Feasibility Studies ; Bacteria/drug effects/genetics ; Drug Resistance, Microbial/genetics ; Microbiota/drug effects ; China ; Drug Resistance, Bacterial/genetics ; }, abstract = {Wastewater sludges (WSs) are major reservoirs and emission sources of antibiotic resistance genes (ARGs) in cities. Identifying antimicrobial resistance (AMR) host bacteria in WSs is crucial for understanding AMR formation and mitigating biological and ecological risks. Here 24 sludge data from wastewater treatment plants in Jiangsu Province, China, and 1559 sludge data from genetic databases were analyzed to explore the relationship between 7 AMRs and bacterial distribution. The results of the Procrustes and Spearman correlation analysis were unsatisfactory, with p-value exceeding the threshold of 0.05 and no strong correlation (r > 0.8). In contrast, explainable machine learning (EML) using SHapley Additive exPlanation (SHAP) revealed Pseudomonadota as a major contributor (39.3 %-74.2 %) to sludge AMR. Overall, the application of ML is promising in analyzing AMR-bacteria relationships. Given the different applicable occasions and advantages of various analysis methods, using ML as one of the correlation analysis tools is strongly recommended.}, } @article {pmid39603470, year = {2025}, author = {Shang, Z and Zhang, X and Cheng, X and Li, S and Liang, X and Tao, Y and Sun, Y and Yu, Q and Li, Y}, title = {Impact of bioaugmentation on psychrophilic anaerobic digestion of corn straw.}, journal = {Bioresource technology}, volume = {417}, number = {}, pages = {131886}, doi = {10.1016/j.biortech.2024.131886}, pmid = {39603470}, issn = {1873-2976}, mesh = {Anaerobiosis ; *Methane/metabolism ; *Zea mays/metabolism ; Bioreactors ; Propionates/metabolism ; Cold Temperature ; }, abstract = {In order to investigate the mechanisms by which bioaugmentation affects psychrophilic anaerobic digestion (AD), this study introduced a psychrophilic methanogenic culture into the sequencing batch of psychrophilic AD systems. The findings demonstrated that bioaugmentation boosted the abundance of Smithella (23.2 times), Syntrophobacter (9.9 times), and Methanothrix (1.4 times) in the psychrophilic AD systems, accelerating acetate and propionate degradation and improving methane production (26 %). Metagenomic analysis showed that bioaugmentation increased the relative abundance of genes related to propionate degradation and methane production, such as propionyl-CoA synthetase (45 %) and acetyl-CoA synthetase (11 %). At the cellular level, genes related to prevention of cell damage and promotion of membrane fluidity were upregulated. This study revealed the effect of bioaugmentation on microbial metabolic activities related to conversion of propionate to methane and cold tolerance in psychrophilic AD.}, } @article {pmid39602961, year = {2025}, author = {Cuevas-Ferrando, E and Sánchez, G and Pérez-Cataluña, A}, title = {Exploring plant virus diversity in wastewater and reclaimed water through metagenomic analysis.}, journal = {Water research}, volume = {270}, number = {}, pages = {122827}, doi = {10.1016/j.watres.2024.122827}, pmid = {39602961}, issn = {1879-2448}, mesh = {*Wastewater/virology ; *Plant Viruses/genetics/isolation & purification ; *Metagenomics ; Waste Disposal, Fluid ; Water Purification ; High-Throughput Nucleotide Sequencing ; }, abstract = {The use of reclaimed water for agricultural activities is being widely employed to address drought and water scarcity. Nevertheless, the disinfection processes do not consistently facilitate the complete removal of all eukaryotic viruses within these reclaimed waters. Consequently, it may pose a risk not only to humans but also to irrigated plants. We analyzed 48 influent and 48 effluent samples from 4 different wastewater treatment plants (WWTPs) by high-throughput sequencing (HTS) to characterize plant-associated virome over a one-year period. Our results showed high levels of plant viruses in both influent and effluent waters. The predominant family identified was Virgaviridae, recognized for its high environmental persistence. Notably, the identification of Tomato Brown Rugose Fruit virus (ToBRFV), classified as a harmful organism by the European Union and subject to strict containment measures to control its spread, highlights the importance of monitoring reclaimed water to mitigate the spread of such viruses into the environment. These findings underscore the need of analyzing reclaimed water from a One Health perspective, ensuring its safety for humans, animals, plants, and the environment alike.}, } @article {pmid39602306, year = {2024}, author = {Pasolli, E and Mauriello, IE and Avagliano, M and Cavaliere, S and De Filippis, F and Ercolini, D}, title = {Bifidobacteriaceae diversity in the human microbiome from a large-scale genome-wide analysis.}, journal = {Cell reports}, volume = {43}, number = {12}, pages = {115027}, doi = {10.1016/j.celrep.2024.115027}, pmid = {39602306}, issn = {2211-1247}, mesh = {Humans ; *Phylogeny ; *Microbiota/genetics ; Metagenome ; Genome, Bacterial ; Genome-Wide Association Study ; Probiotics ; }, abstract = {We performed a large-scale genome-wide analysis aiming to investigate the prevalence and strain-level diversity of Bifidobacteriaceae species in the human microbiome. We considered 9,528 publicly available human metagenomes and integrated them with 1,192 isolate genomes from different sources. The prevalence and abundance of Bifidobacteriaceae species in humans was linked to multiple host characteristics: they were reduced in older people and enriched in populations characterized by Westernized lifestyles with geography-specific patterns. Phylogenetic analysis highlighted 110 Bifidobacteriaceae species-level genome bins (SGBs), with 32 found in humans and 8 in food and probiotic sources. Functional annotation revealed a great diversity in carbohydrate-active enzyme families across these SGBs. We found potential subspecies for most of the SGBs prevalent in humans and identified patterns driven by age and geography. We provided evidence that strains used in probiotics were rarely identified in humans, with the only exception represented by Bifidobacterium animalis. We finally evaluated that the abundance of Bifidobacteriaceae species exhibited moderate and variable capabilities to predict health status in case-control studies.}, } @article {pmid39601988, year = {2024}, author = {Rekadwad, BN and Shouche, YS and Jangid, K}, title = {Oil spill pollution and diversity analyses of resistant bacteria isolated from soil across the Arabian Sea and Bay of Bengal coastlines.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {12}, pages = {1265}, pmid = {39601988}, issn = {1573-2959}, mesh = {*Bacteria/classification/isolation & purification/genetics ; *Petroleum Pollution ; *Environmental Monitoring ; India ; *Soil Microbiology ; Biodiversity ; Bays/microbiology ; Drug Resistance, Bacterial ; }, abstract = {Pelagic transport causes oil pollution via international tanker routes in the open ocean across southern Asia and the Indian Territory. Nutrient-rich runoff from residential, commercial, and industrial wastes, oil tanker mishaps, and sailing flags have all resulted in pollution. The natural flow of ocean water from east to west dragged pollutants into Indian Territory. We have investigated that the severe deposition of oil spills and biohazardous wastes is causing faunal mortality. Microbiome analyses helped us understand the sample's microbial load. 16S amplicon metagenome analysis, followed by enumeration and confirmation using molecular methods, indicates the presence of diverse microbial profiles. The presence of non-native hydrocarbon- and AMR-resistant bacterial taxa, such as Brevundimonas, Staphylococcus spp., Mycolicibacterium, Spingomonas spp., Bacillus spp., Chitinophaga spp., Priestia spp., Domibacillus spp., Rossellomorea spp., and Acinetobacter spp., confirms the impacts of oil and urban pollution. This indicates that the coastal soil of Goa and Andhra Pradesh has hydrocarbon- and antibiotic-resistant bacteria, which confirms that the present pollution status and that high-traffic recreational activities put biodiversity and humans at risk of getting illnesses linked to antibiotic resistance.}, } @article {pmid39601762, year = {2025}, author = {Fahy, JV and Jackson, ND and Sajuthi, SP and Pruesse, E and Moore, CM and Everman, JL and Rios, C and Tang, M and Gauthier, M and Wenzel, SE and Bleecker, ER and Castro, M and Comhair, SA and Erzurum, SC and Hastie, AT and Moore, W and Israel, E and Levy, BD and Denlinger, L and Jarjour, NN and Johansson, MW and Mauger, DT and Phillips, BR and Sumino, K and Woodruff, PG and Peters, MC and Seibold, MA}, title = {Type 1 Immune Responses Related to Viral Infection Influence Corticosteroid Response in Asthma.}, journal = {American journal of respiratory and critical care medicine}, volume = {211}, number = {2}, pages = {194-204}, pmid = {39601762}, issn = {1535-4970}, support = {P01 HL132821/HL/NHLBI NIH HHS/United States ; U19 AI077439/AI/NIAID NIH HHS/United States ; P01 HL107202/NH/NIH HHS/United States ; P01 HL132821/NH/NIH HHS/United States ; R01 HL080414/NH/NIH HHS/United States ; R01 HL135156/NH/NIH HHS/United States ; U01 HL146002/NH/NIH HHS/United States ; U10 HL109086/NH/NIH HHS/United States ; U10 HL109146/NH/NIH HHS/United States ; U10 HL109152/NH/NIH HHS/United States ; U10 HL109164/NH/NIH HHS/United States ; U10 HL109168/NH/NIH HHS/United States ; U10 HL109172/NH/NIH HHS/United States ; U10 HL109250/NH/NIH HHS/United States ; U10 HL109257/NH/NIH HHS/United States ; }, mesh = {Humans ; *Asthma/immunology/drug therapy ; Male ; Female ; Adult ; Middle Aged ; *Sputum/virology/immunology ; *Adrenal Cortex Hormones/therapeutic use ; *Virus Diseases/immunology ; }, abstract = {Rationale: Corticosteroid-responsive type 2 (T2) inflammation underlies the T2-high asthma endotype. However, we hypothesized that type 1 (T1) inflammation, possibly related to viral infection, may also influence corticosteroid response. Objectives: To determine the frequency and within-patient variability of T1-high, T2-high, and T1/T2-high asthma endotypes and whether virally influenced T1-high disease influences corticosteroid response in asthma. Methods: Patients in SARP-3 (Severe Asthma Research Program-3) had sputum collected at baseline, after intramuscular (triamcinolone acetonide) corticosteroid treatment, and at 1- and 3-year follow-ups. Sputum cell RNA was used for whole-transcriptome gene network and viral metagenomic analyses. We then profiled patients as highly expressing T1 and/or T2 gene networks and established the influence of these endotypes on corticosteroid responsiveness and the likelihood of viral transcript detection in the airways. Measurements and Main Results: We found that 22% and 35% of patients with asthma highly expressed T1 and T2 network genes, respectively, and that 8.5% highly expressed both networks. Asthma severity outcomes were worse in T2-high compared with T1-high asthma and most severe in the T1-high/T2-high subgroup. Corticosteroid treatment strongly suppressed T2 but poorly suppressed T1 gene expression, and corticosteroid-associated improvements in FEV1 occurred only in patients with T1-low/T2-high disease and not in patients with T1-high/T2-high disease. Viral metagenomic analyses uncovered that 24% of asthma sputum samples tested positive for a respiratory virus, and high viral carriage was associated with 14-fold increased risk of T1-high disease. Conclusions: Airway T1 immune responses are relatively common in asthma, are largely corticosteroid resistant, and are associated with subclinical viral infection.}, } @article {pmid39601584, year = {2025}, author = {Chigwada, AD and Ogola, HJO and Tekere, M}, title = {A catalog of metagenomes and metagenome-assembled genomes from culture-enrichment microcosms containing polyethylene as carbon source.}, journal = {Microbiology resource announcements}, volume = {14}, number = {1}, pages = {e0068924}, pmid = {39601584}, issn = {2576-098X}, support = {SRUG2204203946//National Research Foundation (NRF)/ ; }, abstract = {We present a data set detailing enrichment microbial consortia degrading polyethylene (PE) plastic. Derived from 180-day microcosm incubations using landfill soil, seawater, and cow dung, the data set includes three metagenomes and 23 metagenome-assembled genomes that capture microbial community interactions, structures, and functions relevant to PE biodegradation.}, } @article {pmid39601556, year = {2024}, author = {Yang, J and Wang, H and Lin, X and Liu, J and Feng, Y and Bai, Y and Liang, H and Hu, T and Wu, Z and Lai, J and Liu, J and Zou, Y and Wei, S and Yan, P}, title = {Gut microbiota dysbiosis induced by alcohol exposure in pubertal and adult mice.}, journal = {mSystems}, volume = {9}, number = {12}, pages = {e0136624}, pmid = {39601556}, issn = {2379-5077}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Dysbiosis/chemically induced/microbiology ; Mice ; *Ethanol ; Male ; Mice, Inbred C57BL ; Metagenome/drug effects ; Liver/metabolism/drug effects/pathology ; Sexual Maturation/drug effects ; }, abstract = {UNLABELLED: Alcohol intake causes many diseases including neuropsychiatric symptoms, nutritional deficiency, progressive pancreatitis, liver cirrhosis, and ischemic heart disease. The gut microbiota changes significantly after alcohol exposure. Alcohol consumption tends to increase in underage and young people, but the feature of the gut microbiota in puberty remains largely unexplored. In this study, we conducted alcohol-exposed pubertal and adult mice model to investigate the intestinal damage and gut microbiota change. Interestingly, the responses of pubertal mice and adult mice after alcohol exposure were different. We found that alcohol dehydrogenase decreased and aldehyde dehydrogenase increased in the liver of pubertal mice, thus reducing the accumulation of toxic acetaldehyde. Furthermore, alcohol exposure caused less intestinal injury in pubertal mice. Through the analysis of metagenome assembly genome, we obtained many unrecognized bacterial genomes. Limosillactobacillus reuteri (cluster_56) and Lactobacillus intestinalis (cluster_57) were assembled from the samples of pubertal mice, which were involved in the production of indole acetic acid and the transformation of bile acids in response to alcohol exposure. This study provided a new insight to investigate the gut microbiota change and explained the difference of the gut microbiota after alcohol exposure between pubertal mice and adult mice.

IMPORTANCE: This study elucidates the significant impact of alcohol exposure on the gut microbiota and metabolic pathways in mice, highlighting the differential responses between adolescent and adult stages. Alcohol exposure was found to damage the intestinal barrier, alter the microbial composition by decreasing beneficial bacteria like Lactobacillus, and increase harmful bacteria such as Alistipes. The study also discovered unique microbial changes and resilience in pubertal mice. Species-level metagenomic analysis revealed specific microbial taxa and metabolic functions affected by alcohol. Metagenome-assembled genomes (MAGs) found many species that could not be annotated by conventional methods including many members of Lachnospiraceae, greatly expanding our understanding of the gut microbiota composition. These findings underscore the need for further research on alcohol's effects on various organs and the implications of microbial metabolites on disease progression.}, } @article {pmid39601555, year = {2024}, author = {Gao, Y and Zhang, H and Zhu, D and Guo, L}, title = {Different artificial feeding strategies shape the diverse gut microbial communities and functions with the potential risk of pathogen transmission to captive Asian small-clawed otters (Aonyx cinereus).}, journal = {mSystems}, volume = {9}, number = {12}, pages = {e0095424}, pmid = {39601555}, issn = {2379-5077}, support = {561119219//Scientific research start-up foundation from Lanzhou University/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Otters/microbiology ; *Feces/microbiology ; *Animal Feed/analysis/microbiology ; Animals, Zoo/microbiology ; Diet/veterinary ; Bacteria/genetics/isolation & purification/classification ; Fatty Acids, Volatile/metabolism ; }, abstract = {UNLABELLED: Captive otters raised in zoos are fed different artificial diets, which may shape gut microbiota. The objective is to evaluate the impacts of two different artificial diets on microbial communities and function capabilities and short-chain fatty acid (SCFA) profiles in healthy otters' feces. A total of 16 Asian small-clawed otters in two groups (n = 8) were selected. Group A otters were fed raw loaches supplemented with commercial cat food (LSCF) diet, and group B otters were fed raw crucian diet. The communities and functional capabilities of microbiota in feces were assessed with metagenomic sequencing. Captive otters fed two kinds of diets possessed different gut microbial communities and functional capabilities. Various pathogenic bacteria, like Escherichia coli and Clostridium perfringens, were enriched in the samples from the two groups, respectively. Most of the differential pathways of nutrient metabolism were significantly enriched in group A, and the distributions of carbohydrate enzymes in the two groups significantly differed from each other. Multiple resistance genes markedly accumulated in fecal samples of the group A otters with LSCF diet. Higher concentrations of SCFAs were also observed in group A otters. Two feeding strategies were both likely to facilitate the colonization and expansion of various pathogenic bacteria and the accumulation of resistance genes in the intestines of captive otters, suggesting that risk of pathogen transmission existed in the current feeding process. Commercial cat food could supplement various nutrients and provide a substrate for the production of SCFAs, which might be beneficial for the otters' intestinal fermentation and metabolism.

IMPORTANCE: Captive otters fed with different diets possessed distinct gut microbial communities and functions, with the enrichment of several pathogens and multiple resistance genes in their gut microbiota. The current artificial feeding strategies had the possibility to accelerate the colonization and proliferation of various pathogenic bacteria in the intestines of otters and the spread of resistance genes, increasing the risk of diseases. In addition, supplementation with commercial cat food had benefits for otters' intestinal fermentation and the metabolism of gut microbiota.}, } @article {pmid39601293, year = {2024}, author = {Liu, L and Cao, S and Lin, W and Gao, Z and Yang, L and Zhu, L and Yang, B and Zhang, G and Zhu, R and Wu, D}, title = {miMatch: a microbial metabolic background matching tool for mitigating host confounding in metagenomics research.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2434029}, pmid = {39601293}, issn = {1949-0984}, mesh = {*Metagenomics/methods ; Humans ; Gastrointestinal Microbiome ; Software ; Case-Control Studies ; Bacteria/genetics/classification/metabolism/isolation & purification ; Metagenome ; Propensity Score ; }, abstract = {Metagenomic research faces a persistent challenge due to the low concordance across studies. While matching host confounders can mitigate the impact of individual differences, the influence of factors such as genetics, environment, and lifestyle habits on microbial profiles makes it exceptionally challenging to create fully matched cohorts. The microbial metabolic background, which modulates microbial composition, reflects a cumulative impact of host confounders, serving as an ideal baseline for microbial sample matching. In this study, we introduced miMatch, an innovative metagenomic sample-matching tool that uses microbial metabolic background as a comprehensive reference for host-related variables and employs propensity score matching to build case-control pairs, even in the absence of host confounders. In the simulated datasets, miMatch effectively eliminated individual metabolic background differences, thereby enhancing the accuracy of identifying differential microbial patterns and reducing false positives. Moreover, in real metagenomic data, miMatch improved result consistency and model generalizability across cohorts of the same disease. A user-friendly web server (https://www.biosino.org/iMAC/mimatch) has been established to promote the integration of multiple metagenomic cohorts, strengthening causal relationships in metagenomic research.}, } @article {pmid39600953, year = {2024}, author = {Ma, T and Chu, J}, title = {Chemical structure metagenomics of microbial natural products: surveying nonribosomal peptides and beyond.}, journal = {Beilstein journal of organic chemistry}, volume = {20}, number = {}, pages = {3050-3060}, pmid = {39600953}, issn = {1860-5397}, abstract = {Bioactivity-guided fractionation (BGF) has historically been a fruitful natural product discovery workflow. However, it is plagued by increasing rediscovery rates in recent years and new methods capable of exploring the natural product chemical space more broadly and more efficiently is in urgent need. Chemical structure metagenomics as one such method is the theme of this Perspective. It emphasizes a chemical-structure-centered viewpoint toward natural product research. Key to chemical structure metagenomics is the ability to predict the structure of a natural product based on its biosynthetic gene sequences, which facilitated the discovery of numerous new bioactive molecules and helped uncover oversampled/underexplored niches of decades of BGF based discovery. While microbial nonribosomal peptides have been the focus of chemical structure metagenomics efforts thus far, it is in principle applicable to other natural product families. The future outlook of this new approach will also be discussed.}, } @article {pmid39600931, year = {2024}, author = {Pu, JF and Zhou, YL and Deng, M and Wu, J}, title = {Case report: A case of blood culture-negative Bartonella quintana endocarditis: blood mNGS is an efficient method for early diagnosis.}, journal = {Frontiers in medicine}, volume = {11}, number = {}, pages = {1449637}, pmid = {39600931}, issn = {2296-858X}, abstract = {Bartonella quintana is one of the main causes of blood culture-negative endocarditis, and routine blood culture and serological methods are difficult to achieve early diagnosis. We report a case of blood culture-negative Bartonella quintana endocarditis from southwestern Chongqing. The patient was a 67-year-old male scavenger who presented with heart failure without fever as the main clinical manifestation upon admission. He stated having had contact with stray cats in the past 2 months. The combination of clinical symptoms, echocardiography, and blood mNGS testing confirmed the infection of Bartonella quintana.}, } @article {pmid39600877, year = {2024}, author = {Cui, H and Ren, B and Wang, L and Chen, J and Li, J and Hu, W and Yang, Y}, title = {Enhanced pathogenicity and synergistic effects of co-infection with bovine viral diarrhea virus 1 and HoBi-like virus in cattle and guinea pigs.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1464745}, pmid = {39600877}, issn = {2297-1769}, abstract = {INTRODUCTION: The Bovine Viral Diarrhea Virus 1 (BVDV1) and HoBi-like virus (BVDV3), both within the same genus, share genomic homology and exhibit low antigenic cross-reactivity despite presenting similar clinical manifestations. In 2021, a bovine respiratory disease complex (BRDC) outbreak on two cattle farms in the Inner Mongolia Autonomous Region of China resulted in ten fatalities.

METHODS: Metagenomic and metatranscriptomic analyses were used to identify viral agents, including a co-infection case. A genetic evolution analysis assessed the relationships with related strains. Experimental infections in guinea pigs and calves evaluated the pathogenicity of the viruses.

RESULTS: Phylogenetic analysis of the BVDV3 isolate IM2201 revealed close relatedness to Brazilian strains, with 97.06% nucleotide homology to the highly virulent strain SV478/07. Experimental co-infection in guinea pigs resulted in more severe clinical signs, including fever, cough, diarrhea, and significant pathological changes, and led to a higher mortality rate (40%) compared to no mortality from single-virus infections with BVDV1 or BVDV3. Similarly, co-infected cattle exhibited more severe clinical signs, including bloody diarrhea and rectal temperatures exceeding 40°C, along with persistent viremia and nasal viral shedding from 7 to 21 days post-infection. Blood analysis revealed significant reductions in white blood cell counts, particularly in co-infected cattle.

DISCUSSION: This study highlights the enhanced pathogenicity and synergistic effects of BVDV1 and BVDV3 co-infection, exacerbating disease severity.}, } @article {pmid39600859, year = {2024}, author = {Lin, HY and Tan, QH}, title = {Metagenomic next-generation sequencing may assist diagnosis of osteomyelitis caused by Mycobacterium houstonense: A case report.}, journal = {World journal of orthopedics}, volume = {15}, number = {11}, pages = {1095-1100}, pmid = {39600859}, issn = {2218-5836}, abstract = {BACKGROUND: Mycobacterium houstonense (M. houstonense) belongs to the nontuberculous mycobacterium group. Infection caused by M. houstonense is prone to recurrence.

CASE SUMMARY: We present a patient who was diagnosed with osteomyelitis caused by M. houstonense and treated with a combination of cefoxitin, and amikacin combined with linezolid.

CONCLUSION: The emergence of metagenomic next-generation sequencing (NGS) has brought new hope for the diagnosis and treatment of listeria meningitis. NGS can analyze a large number of nucleic acid sequences in a short time and quickly determine the pathogen species in the sample. Compared with traditional cerebrospinal fluid culture, NGS can greatly shorten the diagnosis time and provide strong support for the timely treatment of patients. Regarding treatment, NGS can also play an important role. Rapid and accurate diagnosis can enable patients to start targeted treatment as soon as possible and improve the treatment effect. At the same time, by monitoring the changes in pathogen resistance, the treatment plan can be adjusted in time to avoid treatment failure.}, } @article {pmid39600479, year = {2024}, author = {Xu, DZ and Tan, QH}, title = {Infection with Listeria monocytogenes meningoencephalitis: A case report.}, journal = {World journal of clinical cases}, volume = {12}, number = {33}, pages = {6629-6634}, pmid = {39600479}, issn = {2307-8960}, abstract = {BACKGROUND: Listeria meningitis is an infectious disease of the central nervous system caused by Listeria monocytogenes. This bacterium is widely present in the natural environment and can be transmitted through channels such as food and water. Patients usually show symptoms such as fever, headache, and neck stiffness. In severe cases, coma, convulsions, or even death may occur. Traditional diagnostic methods, such as cerebrospinal fluid (CSF) culture and serological tests, have certain limitations. Although CSF culture is the "gold standard" for diagnosis, it is time-consuming and has a relatively low positivity rate. Serological detection may also result in false positive or false negative results. The emergence of metagenomic sequencing (mNGS) technology has led to a significant breakthrough in diagnosing Listeria meningitis, allowing quick and accurate detection of various pathogens in samples.

CASE SUMMARY: Here, we present the case of a previously healthy 64-year-old woman diagnosed with Listeria meningitis using mNGS. She was successfully treated with intravenous ampicillin and meropenem, without any complications.

CONCLUSION: Listeria meningitis must be considered, especially in patients who fail to show improvement with first-line antibiotic treatments. mNGS significantly reduces the diagnosis time, supporting timely treatment of patients.}, } @article {pmid39600212, year = {2024}, author = {Zhao, H and Zhang, Z and Nair, S and Li, H and He, C and Shi, Q and Zheng, Q and Cai, R and Luo, G and Xie, S and Jiao, N and Zhang, Y}, title = {Overlooked Vital Role of Persistent Algae-Bacteria Interaction in Ocean Recalcitrant Carbon Sequestration and Its Response to Ocean Warming.}, journal = {Global change biology}, volume = {30}, number = {11}, pages = {e17570}, pmid = {39600212}, issn = {1365-2486}, support = {tsqn202408283//Taishan Scholar Project of Shandong Province/ ; tsqn202312270//Taishan Scholar Project of Shandong Province/ ; QNESL OP202306//Qingdao New Energy Shandong Laboratory Open Project/ ; 42276105//National Natural Science Foundation of China/ ; 42476115//National Natural Science Foundation of China/ ; U1906216//National Natural Science Foundation of China/ ; //Ocean Negative Carbon Emissions (ONCE) program/ ; 2020YFA0607603//National Key Research and Development Program of China/ ; 2020YFA0608304//National Key Research and Development Program of China/ ; 2023YFE0113102//National Key Research and Development Program of China/ ; 2023220//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; }, mesh = {*Carbon Sequestration ; *Synechococcus/metabolism/growth & development/physiology ; *Oceans and Seas ; *Seawater/microbiology/chemistry ; Carbon/metabolism ; Global Warming ; Bacteria/metabolism ; }, abstract = {Long-term carbon sequestration by the ocean's recalcitrant dissolved organic carbon (RDOC) pool regulates global climate. Algae and bacteria interactively underpin RDOC formation. However, on the long-term scales, the influence of their persistent interactions close to in situ state on ocean RDOC dynamics and accumulation remains unclear, limiting our understanding of the oceanic RDOC pool formation and future trends under global change. We show that a Synechococcus-bacteria interaction model system viable over 720 days gradually accumulated high DOC concentrations up to 84 mg L[-1]. Concurrently, the DOC inertness increased with the RDOC ratio reaching > 50%. The identified Synechococcus-bacteria-driven RDOC molecules shared similarity with over half of those from pelagic ocean DOC. Importantly, we provide direct genetic and metabolite evidence that alongside the continuous transformation of algal carbon by bacteria to generate RDOC, Synechococcus itself also directly synthesized and released RDOC molecules, representing a neglected RDOC source with ~0.2-1 Gt y[-1] in the ocean. However, we found that although ocean warming (+4°C) can promote algal and bacterial growth and DOC release, it destabilizes and reduces RDOC reservoirs, jeopardizing the ocean's carbon sequestration capacity. This study unveils the previously underestimated yet significant role of algae and long-term algae-bacteria interactions in ocean carbon sequestration and its vulnerability to ocean warming.}, } @article {pmid39599910, year = {2024}, author = {Queiroz-Ferreira, MS and Dos Reis, LNA and de Noronha Fonseca, ME and Melo, FFS and Reis, A and Boiteux, LS and Pereira-Carvalho, RC}, title = {Reexamination of the Sida Micrantha Mosaic Virus and Sida Mottle Virus Complexes: Classification Status, Diversity, Cognate DNA-B Components, and Host Spectrum.}, journal = {Viruses}, volume = {16}, number = {11}, pages = {}, pmid = {39599910}, issn = {1999-4915}, mesh = {*Begomovirus/genetics/classification/isolation & purification ; *Phylogeny ; *Plant Diseases/virology ; *Genome, Viral ; *DNA, Viral/genetics ; Brazil ; Host Specificity ; Genetic Variation ; Malvaceae/virology ; Metagenomics/methods ; }, abstract = {Sida mottle virus (SiMoV) and Sida micrantha mosaic virus (SiMMV) are major Brazilian begomoviruses (Geminiviridae). However, the range of DNA-A identity of isolates of these viruses (81-100%) is not in agreement with the current criteria for Begomovirus species demarcation (<91%). To clarify this putative classification problem, we performed a comprehensive set of molecular analyses with all 53 publicly available isolates (with complete DNA-A genomes) designated as either SiMoV or SiMMV (including novel isolates obtained herein from nationwide metagenomics-based studies). Two well-defined phylogenetic clusters were identified. The SiMMV complex (n = 47) comprises a wide range of strains (with a continuum variation of 88.8-100% identity) infecting members of five botanical families (Malvaceae, Solanaceae, Fabaceae, Oxalidaceae, and Passifloraceae). The SiMoV group now comprises eight isolates (90-100% identity) restricted to Malvaceae hosts, including one former reference SiMMV isolate (gb|NC_077711) and SP77 (gb|FN557522; erroneously named as "true SiMMV"). Iteron analyses of metagenomics-derived information allowed for the discovery of the missing DNA-B cognate of SiMoV (93.5% intergenic region identity), confirming its bipartite nature. Henceforth, the correct identification of SiMoV and SiMMV isolates will be a crucial element for effective classical and biotech resistance breeding of the viral host species.}, } @article {pmid39599892, year = {2024}, author = {Gajurel, K and Dhakal, R and Deresinski, S}, title = {Arbovirus in Solid Organ Transplants: A Narrative Review of the Literature.}, journal = {Viruses}, volume = {16}, number = {11}, pages = {}, pmid = {39599892}, issn = {1999-4915}, mesh = {Humans ; *Arbovirus Infections/epidemiology/virology ; *Arboviruses ; *Organ Transplantation/adverse effects ; }, abstract = {The incidence of arbovirus infections has increased in recent decades. Other than dengue, chikungunya, and West Nile viruses, the data on arbovirus in solid organ transplant (SOT) are limited to case reports, and infections in renal transplant recipients account for most of the reported cases. Dengue and West Nile infections seem to be more severe with higher mortality in SOT patients than in the general population. Acute kidney injury is more frequent in patients with dengue and chikungunya although persistent arthralgia with the latter is less frequent. There is no clear relationship between arboviral infection and acute cellular rejection. Pre-transplant screening of donors should be implemented during increased arboviral activity but, despite donor screening and negative donor nucleic acid amplification test (NAT), donor derived infection can occur. NAT may be transiently positive. IgM tests lack specificity, and neutralizing antibody assays are more specific but not readily available. Other tests, such as immunohistochemistry, antigen tests, PCR, metagenomic assays, and viral culture, can also be performed. There are a few vaccines available against some arboviruses, but live vaccines should be avoided. Treatment is largely supportive. More data on arboviral infection in SOT are needed to understand its epidemiology and clinical course.}, } @article {pmid39599783, year = {2024}, author = {Vila-Nistal, M and Logares, R and Gasol, JM and Martinez-Garcia, M}, title = {Time Series Data Provide Insights into the Evolution and Abundance of One of the Most Abundant Viruses in the Marine Virosphere: The Uncultured Pelagiphages vSAG 37-F6.}, journal = {Viruses}, volume = {16}, number = {11}, pages = {}, pmid = {39599783}, issn = {1999-4915}, support = {PID2021-125175OB-I00//Agencia Estatal de Investigación/ ; CTM2015-70340-R//Agencia Estatal de Investigación/ ; RTI2018-101025-B-I00//Agencia Estatal de Investigación/ ; }, mesh = {*Seawater/virology ; *Metagenomics/methods ; Genome, Viral ; Phylogeny ; Evolution, Molecular ; Aquatic Organisms/virology ; Virome/genetics ; }, abstract = {Viruses play a pivotal role in ecosystems by influencing biochemical cycles and impacting the structure and evolution of their host cells. The widespread pelagiphages infect Pelagibacter spp., the most abundant marine microbe on Earth, and thus play a significant role in carbon transformation through the viral shunt. Among these viruses, the uncultured lytic pelagiphage vSAG 37-F6, uncovered by single-virus genomics, is likely the most numerous virus in the ocean. While previous research has delved into the diversity and spatial distribution of vSAG 37-F6, there is still a gap in understanding its temporal dynamics, hindering our insight into its ecological impact. We explored the temporal dynamics of vSAG 37-F6, assessing periodic fluctuations in abundance and evolutionary patterns using long- and short-term data series. In the long-term series (7 years), metagenomics showed negative selection acting on all viral genes, with a highly conserved overall diversity over time composed of a pool of yearly emergent, highly similar novel strains that exhibited a seasonal abundance pattern with two peaks during winter and fall and a decrease in months with higher UV radiation. Most non-synonymous polymorphisms occurred in structural viral proteins located in regions with low conformational restrictions, suggesting that many of the viral genes of this population are highly purified over its evolution. At the fine-scale resolution (24 h time series), combining digital PCR and metagenomics, we identified two peaks of cellular infection for the targeted vSAG 37-F6 viral strain (up to approximately 10[3] copies/ng of prokaryotic DNA), one before sunrise and the second shortly after midday. Considering the high number of co-occurring strains of this microdiverse virus, the abundance values at the species or genus level could be orders of magnitudes higher. These findings represent a significant advancement in understanding the dynamics of the potentially most abundant oceanic virus, providing valuable insights into ecologically relevant marine viruses.}, } @article {pmid39599728, year = {2024}, author = {Bedrač, L and Deutsch, L and Terzić, S and Červek, M and Šelb, J and Ašič, U and Verstraeten, LMG and Kuščer, E and Cvetko, F}, title = {Towards Precision Sports Nutrition for Endurance Athletes: A Scoping Review of Application of Omics and Wearables Technologies.}, journal = {Nutrients}, volume = {16}, number = {22}, pages = {}, pmid = {39599728}, issn = {2072-6643}, mesh = {Humans ; *Physical Endurance ; *Athletes ; *Wearable Electronic Devices ; *Sports Nutritional Physiological Phenomena ; Metabolomics/methods ; Precision Medicine/methods ; Biomarkers/blood ; Proteomics/methods ; Athletic Performance/physiology ; Nutrigenomics/methods ; Sports Nutritional Sciences ; Nutritional Status ; }, abstract = {BACKGROUND: Endurance athletes require tailored nutrition strategies to optimize performance, recovery, and training adaptations. While traditional sports nutrition guidelines provide a foundational framework, individual variability in metabolic responses underscores the need for precision nutrition, informed by genetic, biological, and environmental factors. This scoping review evaluates the application of systems biology-driven sports nutrition for endurance athletes, focusing on 'omics' and wearable technologies.

METHODS: A scoping review of the literature was conducted in PubMed, Scopus, and Web of Science in accordance with the PRISMA-ScR checklist. Research questions, search strategies, and eligibility criteria were guided by the Population-Concept-Context framework with the following inclusion criteria: original research in English, involving endurance athletes, systems biology approaches, and nutritional interventions or continuous glucose monitoring (CGM).

RESULTS: Fifty-two studies were included, with distance runners as the most studied cohort. Eleven studies used metagenomics, eleven CGM, ten nutrigenetics, ten metabolomics, seven multi-omics, one proteomics, one epigenomics, and one lipidomics. Over half (n = 31; 60%) were randomized controlled trials (RCTs) with generally high methodological quality.

CONCLUSIONS: Most studies were proof-of-concept investigations aimed at assessing biomarkers; however, the evidence linking these biomarkers to performance, recovery, and long-term health outcomes in endurance athletes remains insufficient. Future research should focus on well-powered replicated crossover RCTs, multivariate N-of-1 clinical trials, 360-degree systems-wide approaches, and the validation of genetic impacts on nutritional interventions to refine dietary guidelines.}, } @article {pmid39599719, year = {2024}, author = {Senaprom, S and Namjud, N and Ondee, T and Bumrungpert, A and Pongpirul, K}, title = {Sugar Composition of Thai Desserts and Their Impact on the Gut Microbiome in Healthy Volunteers: A Randomized Controlled Trial.}, journal = {Nutrients}, volume = {16}, number = {22}, pages = {}, pmid = {39599719}, issn = {2072-6643}, support = {FOODF67300006//Thailand Science Research and Innovation Fund Chulalongkorn University/ ; //The 90th Anniversary of Chulalongkorn University, Ratchadaphisek Somphot Fund/ ; //The Second Century Fund (C2F) for PhD Scholarship, Chulalongkorn University/ ; }, mesh = {Adolescent ; Adult ; Female ; Humans ; Male ; Middle Aged ; Young Adult ; Bacteria/classification/genetics ; *Dietary Sugars ; *Feces/microbiology ; *Gastrointestinal Microbiome ; Healthy Volunteers ; RNA, Ribosomal, 16S/genetics ; Thailand ; }, abstract = {BACKGROUND: The relationship between consuming Thai desserts-predominantly composed of carbohydrates-and gut microbiome profiles remains unclear. This study aimed to evaluate the effects of consuming various Thai desserts with different GI values on the gut microbiomes of healthy volunteers.

METHODS: This open-label, parallel randomized clinical trial involved 30 healthy individuals aged 18 to 45 years. Participants were randomly assigned to one of three groups: Phetchaburi's Custard Cake (192 g, low-GI group, n = 10), Saraburi's Curry Puff (98 g, medium-GI group, n = 10), and Lampang's Crispy Rice Cracker (68 g, high-GI group, n = 10), each consumed alongside their standard breakfast. Fecal samples were collected at baseline and 24 h post-intervention for metagenomic analysis of gut microbiome profiles using 16S rRNA gene sequencing.

RESULTS: After 24 h, distinct trends in the relative abundance of various gut microbiota were observed among the dessert groups. In the high-GI dessert group, the abundance of Collinsella and Bifidobacterium decreased compared to the low- and medium-GI groups, while Roseburia and Ruminococcus showed slight increases. Correlation analysis revealed a significant negative relationship between sugar intake and Lactobacillus abundance in the medium- and high-GI groups, but not in the low-GI group. Additionally, a moderately negative association was observed between Akkermansia abundance and sugar intake in the high-GI group. These bacteria are implicated in energy metabolism and insulin regulation. LEfSe analysis identified Porphyromonadaceae and Porphyromonas as core microbiota in the low-GI group, whereas Klebsiella was enriched in the high-GI group, with no predominant bacteria identified in the medium-GI group.

CONCLUSIONS: The findings suggest that Thai desserts with varying GI levels can influence specific gut bacteria, though these effects may be temporary.}, } @article {pmid39598209, year = {2024}, author = {Al-Awthan, YS and Mir, R and Alharbi, BM and Alatawi, AS and Almutairi, FM and Khafaga, T and Shohdi, WM and Fakhry, AM and Alatawi, MM}, title = {Metagenomic Analysis of Sediment Bacterial Diversity and Composition in Natural Lakes and Artificial Waterpoints of Tabuk Region in King Salman Bin Abdulaziz Royal Natural Reserve, Saudi Arabia.}, journal = {Life (Basel, Switzerland)}, volume = {14}, number = {11}, pages = {}, pmid = {39598209}, issn = {2075-1729}, abstract = {The Tabuk region is located in the northern part of Saudi Arabia, and it has an area of 117,000 km[2] between longitudes 26° N and 29° N and latitudes 34° E and 38° E. King Salman Bin Abdulaziz Royal Natural Reserve (KSRNR) is the largest natural reserve in Saudi Arabia and covers about 130,700 km[2]. It represents a new tourist attraction area in the Tabuk region. Human activities around the lake may lead to changes in water quality, with subsequent changes in microenvironment components, including microbial diversity. The current study was designed to assess possible changes in bacterial communities of the water sediment at some natural lakes and artificial waterpoints of KSRNR. Water samples were collected from ten different locations within KSRNR: W1, W2, W3 (at the border of the royal reserve); W4, W5, W6, W7 (at the middle); and W8, W9, and W10 (artificial waterpoints). The total DNA of the samples was extracted and subjected to 16S rRNA sequencing and metagenomic analysis; also, the environmental parameters (temperature and humidity) were recorded for all locations. Metagenomic sequencing yielded a total of 24,696 operational taxonomic units (OTUs), which were subsequently annotated to 193 phyla, 215 classes, 445 orders, 947 families, and 3960 genera. At the phylum level, Pseudomonadota dominated the microbial communities across all samples. At the class level, Gammaproteobacteria, Clostridia, Alphaproteobacteria, Bacilli, and Betaproteobacteria were the most prevalent. The dominant families included Enterobacteriaceae, Pseudomonadaceae, Clostridiaceae, Comamonadaceae, and Moraxellaceae. At the genus level, Pseudomonas, Clostridium, Acinetobacter, Paenibacillus, and Acidovorax exhibited the highest relative abundances. The most abundant species were Hungatella xylanolytica, Pseudescherichia vulneris, Pseudorhizobium tarimense, Paenibacillus sp. Yn15, and Enterobacter sp. Sa187. The observed species richness revealed substantial heterogeneity across samples using species richness estimators, Chao1 and ACE, indicating particularly high diversity in samples W3, W5, and W6. Current study results help in recognizing the structure of bacterial communities at the Tubaiq area in relation to their surroundings for planning for environmental protection and future restoration of affected ecosystems. The findings highlight the dominance of various bacterial phyla, classes, families, and genera, with remarkable species richness in some areas. These results underscore the influence of human activities on microbial diversity, as well as the significance of monitoring and conserving the reserve's natural ecosystems.}, } @article {pmid39598083, year = {2024}, author = {Neiroukh, D and Hajdarpasic, A and Ayhan, C and Sultan, S and Soliman, O}, title = {Gut Microbial Taxonomy and Its Role as a Biomarker in Aortic Diseases: A Systematic Review and Future Perspectives.}, journal = {Journal of clinical medicine}, volume = {13}, number = {22}, pages = {}, pmid = {39598083}, issn = {2077-0383}, abstract = {Background/Objectives: Evidence of the association between the gut microbiome and cardiovascular diseases has accumulated. An imbalance or dysbiosis of this system has been shown to play a role in the pathogenesis of cardiovascular events, including aortic diseases. We aimed to elucidate the findings of the gut microbial taxonomy associated with aortic diseases and their subtypes. Furthermore, we sought to investigate whether gut microbiome dysbiosis can be used as a biomarker for aortic disease detection and to identify which species can be disease-specific. Methods: A systematic search was conducted using the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines for original research papers on gut microbiome composition in patients with aortic disease, using patients without aortic disease as the control (i.e., healthy controls). The databases PubMed, Scopus, Cochrane, and Web of Science were used by employing the medical subject headings (MeSH) terms "aortic diseases", "microbiome"," microbiota", and "taxa" before August 2024. We extracted the study characteristics, study population, and gut microbiome in aortic disease, including microbiota taxa diversity and abundance, regardless of taxa level. The National Institutes of Health (NIH) Quality Assessment Tool was used to assess study quality. Data were synthesized narratively to address the heterogeneity of the studies. Results: In this review, twelve studies that have identified gut microbial species and their potential impact on aortic disease pathogenesis were included. The studies showed the phyla dominance of Bacillota, Pseudomonadota, Actinomycetota, Bacteroidota, and Euryarchaeota in aortic disease patients. We also included the taxa sequencing methods and those used to extract the microorganisms. Aortic diseases were categorized into Takayasu's arteritis, giant cell arteritis, aortic aneurysm, and aortic dissection. Aortic disease patients had a higher rate of dysbiosis when compared to the healthy control groups, with significantly different microbiome composition. Conclusions: Patients with aortic disease exhibit a distinct difference between their gut microbiota composition and that of the healthy controls, which suggests a potential biomarker role of gut dysbiosis. Further exploration of the microbiome and its metagenome interface can help identify its role in aortic disease pathogenesis in depth, generating future therapeutic options. However, a unified methodology is required to identify potential microbial biomarkers in cardiovascular and cardiometabolic diseases.}, } @article {pmid39597756, year = {2024}, author = {Rosaldo-Benitez, V and Ayil-Chan, GA and Labrín-Sotomayor, N and Valdéz-Ojeda, R and Peña-Ramírez, YJ}, title = {Eukaryotic Microalgae Communities from Tropical Karstic Freshwater Lagoons in an Anthropic Disturbance Gradient Microscopic and Metagenomic Analysis.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, pmid = {39597756}, issn = {2076-2607}, support = {5103711808//El Colegio de la Frontera Sur/ ; }, abstract = {The Yucatan aquifer sustains the people living in the Mayan forest and its associated fauna. Human activities threaten water quality and the environmental services associated with it. To assess the eukaryotic microalgae community structure as a bioindicator of water quality, we employed a combined approach of microscopic and shotgun metagenomics to identify specific genera associated with shifts in physicochemical parameters in three permanent lagoons located in Campeche, Mexico. We could identify highly complex and diverse communities independent of human activity intensity, harboring an average of 362 genera at each lagoon. Of those, 85 were affected by alkalinity, carbonates, water hardness, and cyanuric acid levels. Some genera, like Nannochloropsis and Thraustotheca, showed significant negative correlations with lead concentration. The functional annotation of genes revealed these communities' highly diverse metabolic capabilities and the pending work for extensive genomic characterization of rare clades.}, } @article {pmid39597750, year = {2024}, author = {Zell, R and Groth, M and Selinka, L and Selinka, HC}, title = {Metagenomic Analyses of Water Samples of Two Urban Freshwaters in Berlin, Germany, Reveal New Highly Diverse Invertebrate Viruses.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, pmid = {39597750}, issn = {2076-2607}, abstract = {In an attempt to explore the RNA viromes of two German rivers, we searched the virus particle contents of one 50 L water sample each from the Teltow Canal and the Havel River for viruses assumed to infect invertebrates. More than 330 complete and partial virus genomes up to a length of 37 kb were identified, with noda-like and reo-like viruses being most abundant, followed by bunya-like and birna-like viruses. Viruses related to the Permutotetraviridae, Nidovirales, Flaviviridae, Rhabdoviridae and Chuviridae as well as the unclassified Jῑngmén virus and Negev virus groups were also present. The results indicate a broad extent of recombinant virus genomes, supporting the concept of the modularity of eukaryotic viruses. For example, novel combinations of genes encoding replicase and structural proteins with a jellyroll fold have been observed. Less than 35 viruses could be assigned to existing virus genera. These are (i) an avian deltacoronavirus which was represented by only one short contig, albeit with 98% similarity, (ii) a seadornavirus and a rotavirus, and (iii) some 30 nodaviruses. All remaining viruses are novel and too diverse for accommodation in existing genera. Many of the virus genomes exhibit ORFans encoding hypothetical proteins of up to 2000 amino acids without conserved protein domains.}, } @article {pmid39597729, year = {2024}, author = {Alexandrescu, L and Suceveanu, AP and Stanigut, AM and Tofolean, DE and Axelerad, AD and Iordache, IE and Herlo, A and Nelson Twakor, A and Nicoara, AD and Tocia, C and Dumitru, A and Dumitru, E and Condur, LM and Aftenie, CF and Tofolean, IT}, title = {Intestinal Insights: The Gut Microbiome's Role in Atherosclerotic Disease: A Narrative Review.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, pmid = {39597729}, issn = {2076-2607}, abstract = {Recent advances have highlighted the gut microbiota as a significant contributor to the development and progression of atherosclerosis, which is an inflammatory cardiovascular disease (CVD) characterized by plaque buildup within arterial walls. The gut microbiota, consisting of a diverse collection of microorganisms, impacts the host's metabolism, immune responses, and lipid processing, all of which contribute to atherosclerosis. This review explores the complex mechanisms through which gut dysbiosis promotes atherogenesis. We emphasize the potential of integrating microbiota modulation with traditional cardiovascular care, offering a holistic approach to managing atherosclerosis. Important pathways involve the translocation of inflammatory microbial components, modulation of lipid metabolism through metabolites such as trimethylamine-N-oxide (TMAO), and the production of short-chain fatty acids (SCFAs) that influence vascular health. Studies reveal distinct microbial profiles in atherosclerosis patients, with increased pathogenic bacteria (Megamonas, Veillonella, Streptococcus) and reduced anti-inflammatory genera (Bifidobacterium, Roseburia), highlighting the potential of these profiles as biomarkers and therapeutic targets. Probiotics are live microorganisms that have health benefits on the host. Prebiotics are non-digestible dietary fibers that stimulate the growth and activity of beneficial gut bacteria. Interventions targeting microbiota, such as probiotics, prebiotics, dietary modifications, and faecal microbiota transplantation (FMT), present effective approaches for restoring microbial equilibrium and justifying cardiovascular risk. Future research should focus on longitudinal, multi-omics studies to clarify causal links and refine therapeutic applications.}, } @article {pmid39597714, year = {2024}, author = {Yang, T and He, Y and Yang, M and Gao, Z and Zhou, J and Wang, Y}, title = {Community Structure and Biodiversity of Active Microbes in the Deep South China Sea.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, pmid = {39597714}, issn = {2076-2607}, support = {42376149//National Natural Science Foundation of China/ ; }, abstract = {The deep ocean harbors a group of highly diversified microbes, while our understanding of the active microbes that are real contributors to the nutrient cycle remains limited. In this study, we report eukaryotic and prokaryotic communities in ~590 m and 1130 m depths using 16S and 18S rRNA Illumina reads (miTags) extracted from 15 metagenomes (MG) and 14 metatranscriptomes (MT). The metagenomic 16S miTags revealed the dominance of Gammaproteobacteria, Alphaproteobacteria, and Nitrososphaeria, while the metatranscriptomic 16S miTags were highly occupied by Gammaproteobacteria, Acidimicrobiia, and SAR324. The consistency of the active taxa between the two depths suggests the homogeneity of the functional microbial groups across the two depths. The eukaryotic microbial communities revealed by the 18S miTags of the metagenomic data are dominated by Polycystinea; however, they were almost all absent in the 18S metatranscriptomic miTags. The active eukaryotes were represented by the Arthropoda class (at 590 m depth), Dinophyceae, and Ciliophora classes. Consistent eukaryotic communities were also exhibited by the 18S miTags of the metatranscriptomic data of the two depths. In terms of biodiversity, the ACE and Shannon indices of the 590 m depth calculated using the 18S metatranscriptomic miTags were much higher than those of the 1130 m depth, while a reverse trend was shown for the indices based on the metagenomic data. Our study reports the active microbiomes functioning in the nutrient utilization and carbon cycle in the deep-sea zone, casting light on the quantification of the ecological processes occurring in the deep ocean.}, } @article {pmid39597671, year = {2024}, author = {Skliros, D and Kostakou, M and Kokkari, C and Tsertou, MI and Pavloudi, C and Zafeiropoulos, H and Katharios, P and Flemetakis, E}, title = {Unveiling Emerging Opportunistic Fish Pathogens in Aquaculture: A Comprehensive Seasonal Study of Microbial Composition in Mediterranean Fish Hatcheries.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, pmid = {39597671}, issn = {2076-2607}, support = {5010932//Operational Program Fisheries and Maritime 2014-2020/ ; }, abstract = {The importance of microbial communities in fish hatcheries for fish health and welfare has been recognized, with several studies mapping these communities during healthy rearing conditions and disease outbreaks. In this study, we analyzed the bacteriome of the live feeds, such as microalgae, rotifers, and Artemia, used in fish hatcheries that produce Mediterranean species. Our goal was to provide baseline information about their structure, emphasizing in environmental putative fish pathogenic bacteria. We conducted 16S rRNA amplicon Novaseq sequencing for our analysis, and we inferred 46,745 taxonomically annotated ASVs. Results showed that incoming environmental water plays a significant role in the presence of important taxa that constitute presumptive pathogens. Bio-statistical analyses revealed a relatively stable bacteriome among seasonal samplings for every hatchery but a diverse bacteriome between sampling stations and a distinct core bacteriome for each hatchery. Analysis of putative opportunistic fish pathogenic genera revealed some co-occurrence correlation events and a high average relative abundance of Vibrio, Tenacibaculum, and Photobacterium genera in live feeds, reaching a grand mean average of up to 7.3% for the hatchery of the Hellenic Center of Marine Research (HCMR), 12% for Hatchery A, and 11.5% for Hatchery B. Mapping the bacteriome in live feeds is pivotal for understanding the marine environment and distinct aquaculture practices and can guide improvements in hatchery management, enhancing fish health and sustainability in the Mediterranean region.}, } @article {pmid39597660, year = {2024}, author = {Rakitin, AL and Kulichevskaya, IS and Beletsky, AV and Mardanov, AV and Dedysh, SN and Ravin, NV}, title = {Verrucomicrobia of the Family Chthoniobacteraceae Participate in Xylan Degradation in Boreal Peat Soils.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, pmid = {39597660}, issn = {2076-2607}, support = {075-15-2022-318//Ministry of Science and Higher Education of the Russian Federation/ ; }, abstract = {The phylum Verrucomicrobiota is one of the main groups of soil prokaryotes, which remains poorly represented by cultivated organisms. The major recognized role of Verrucomicrobiota in soils is the degradation of plant-derived organic matter. These bacteria are particularly abundant in peatlands, where xylan-type hemicelluloses represent one of the most actively decomposed peat constituents. The aim of this work was to characterize the microorganisms capable of hydrolyzing xylan under the anoxic conditions typical of peatland soils. The laboratory incubation of peat samples with xylan resulted in the pronounced enrichment of several phylotypes affiliated with the Verrucomicrobiota, Firmicutes, and Alphaproteobacteria. Sequencing of the metagenome of the enrichment culture allowed us to recover high-quality metagenome-assembled genomes (MAGs) assigned to the genera Caproiciproducens, Clostridium, Bacillus (Firmicutes), and Rhizomicrobium (Alphaproteobacteria), Cellulomonas (Actinobacteriota) and the uncultured genus-level lineage of the family Chthoniobacteraceae (Verrucomicrobiota). The latter bacterium, designated "Candidatus Chthoniomicrobium xylanophilum" SH-KS-3, dominated in the metagenome and its MAG was assembled as a complete closed chromosome. An analysis of the SH-KS-3 genome revealed potential endo-1,4-beta-xylanases, as well as xylan beta-1,4-xylosidases and other enzymes involved in xylan utilization. A genome analysis revealed the absence of aerobic respiration and predicted chemoheterotrophic metabolism with the capacity to utilize various carbohydrates, including cellulose, and to perform fermentation or nitrate reduction. An analysis of other MAGs suggested that Clostridium and Rhizomicrobium could play the role of primary xylan degraders while other community members probably took advantage of the availability of xylo-oligosaccharides and xylose or utilized low molecular weight organics.}, } @article {pmid39597632, year = {2024}, author = {Köhler, JM and Ehrhardt, L and Günther, PM and Cao, J}, title = {Soil Bacteria in Archaeology: What Could Rank Abundance Functions Tell Us About Ancient Human Impacts on Microbial Communities?.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, pmid = {39597632}, issn = {2076-2607}, support = {scholarship for L.E.//Thüringer Landesgraduiertenförderung/ ; }, abstract = {Metagenomic analysis of soil bacterial communities based on 16S rRNA reflects a typical community composition containing a low number of high-abundance types and a very high number of low-abundance types. Here, the formation of characteristic rank order functions of bacterial abundance is investigated by modelling the dynamics of soil bacterial communities, assuming a succession of different bacterial populations that grow rapidly and decay more slowly. We found that the characteristic shape of typical rank order functions is well reflected by simulations. In addition, our model allowed us to investigate strong disturbances in the soil, which could be expected in cases of strongly changing local environmental conditions in soil, e.g., after translocation and covering of soil material. Such events could lead to the formation of shoulders in the rank order functions. Abundance rank orders observed in cases of some archaeological soil samples do indeed show such a shoulder and could be well interpreted by simulated rank order functions. As a result, it can be concluded that the investigations herein support our hypothesis that abundance rank orders contain information about the temporal order of developing bacterial types in changing communities and thus store information about local environmental conditions in the past, including ancient humans' impact on soil. This information can be used for interpretation of archeological findings and for reconstruction of different former human activities, as well as knowledge on the translocation of soil material in the past.}, } @article {pmid39597631, year = {2024}, author = {Li, Q and Wu, Y and Qi, X and Liu, Z and Wang, C and Ma, X and Ma, Y}, title = {Prickly Ash Seeds Improve the Ruminal Epithelial Development and Growth Performance of Hu Sheep by Modulating the Rumen Microbiota and Metabolome.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, pmid = {39597631}, issn = {2076-2607}, support = {KJJC-LX-2023-05//Technology Integration Technology Project of Linxia Beef and Sheep Industry Development Re-search Institute/ ; 23JRRA1448//Science and Technology Plan Project of Gansu Province/ ; GAU-XKTD-2022-20//Discipline Team Project of Gansu Agricultural University/ ; }, abstract = {It is known that the addition of feed rich in bioactive components to animal diets will affect rumen fermentation parameters and flora structure. However, research on the regulatory effects of prickly ash seeds (PASs) during rumen development or on the rumen microbiome and its metabolites in sheep is limited. The current study was designed to explore the effects of PASs on sheep rumen development and growth performance using metagenomics and metabolomics. Eighteen 3-month-old Hu lambs were randomly allotted to three different dietary treatment groups: 0% (basal diet, CK), 3% (CK with 3% PAS, low-dose PAS, LPS), and 6% (CK with 6% PAS, high-dose PAS, HPS) PASs. The lambs were slaughtered to evaluate production performance. Our results showed that dietary PAS addition improved the average daily gain and reduced the F/G ratio of the experimental animals. Additionally, the height and width of the rumen papilla in the treatment groups were significantly higher than those in the CK group. The fermentation parameters showed that the levels of acetate and butyrate were significantly higher in the LPS group than in the CK and HPS groups. The propionate levels in the HPS group were significantly higher than those in the CK and LPS groups. Metagenomics analysis revealed that PAS dietary supplementation improved the abundance of Clostridiales and Bacteroidales and reduced the abundance of Prevotella, Butyrivibrio, and Methanococcus. Metabolomic analyses revealed that increased metabolite levels, such as those of serotonin, L-isoleucine, and L-valine, were closely related to growth-related metabolic pathways. The correlations analyzed showed that papilla height and muscular thickness were positively and negatively correlated with serotonin and L-valine, respectively. Average daily gain (ADG) was positively and negatively correlated with L-valine and several Prevotella, respectively. In addition, muscular thickness was positively correlated with Sodaliphilus pleomorphus, four Prevotella strains, Sarcina_sp_DSM_11001, and Methanobrevibacter_thaueri. Overall, PAS addition improved sheep growth performance by regulating beneficial microorganism and metabolite abundances, facilitating bacterial and viral invasion resistance.}, } @article {pmid39597627, year = {2024}, author = {Vilo, C and Fábrega, F and Campos, VL and Gómez-Silva, B}, title = {Microbial Biodiversity in Sediment from the Amuyo Ponds: Three Andean Hydrothermal Lagoons in Northern Chile.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, pmid = {39597627}, issn = {2076-2607}, support = {FB 0001//ANID, Chile/ ; }, abstract = {The Amuyo Ponds (APs) are a group of three brackish hydrothermal lagoons located at 3700 m above sea level in a pre-Andean setting in the Atacama Desert. Each pond shows a conspicuous green (GP), red (RP), or yellow (YP) coloration, and discharges water rich in arsenic and boron into the Caritaya River (Camarones Basin, northern Chile). Microorganisms are subjected to harsh environmental conditions in these ponds, and the microbial composition and diversity in the Amuyo Ponds' sediments are unknown. The microbial life colonizing AP sediments was explored by metagenomics analyses, showing a diverse microbial life dominated by members of the bacterial domain, with nearly 800 bacterial genome sequences, and sequences associated with Archaea, Eukarya, and viruses. The genus Pseudomonas was more abundant in GP and YP sediments, while the genera Pseudomonas, Aeromonas, and Shewanella were enriched in RP sediments. Archaeal composition was similar in all sediments, and enriched with methanogens sequences from the Archaeoglobi and Halobacteria classes. Abundant fungi sequences were detected in all sediments from the phyla Blastocladiomycota and Ascomycota. We also report putative functional capabilities related to virulence and defense genes, the biosynthesis of secondary metabolites, and tolerance to arsenic. Thirteen bacterial and fourteen viral metagenome-assembled genomes were reconstructed and informed here. This work expands our knowledge on the richness of the microorganisms in the APs and open further studies on the ecology and genomics of this striking Andean geosite.}, } @article {pmid39597611, year = {2024}, author = {Lin, Q and Yang, P and Zhang, Y and Zhang, W and Wu, H}, title = {Metagenomic Insights into Coal Slag Remediation Effects on Soil and Microbial Health in Qinghai's Muli Coal Mine.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, pmid = {39597611}, issn = {2076-2607}, support = {2021YFC3201604//Hongping Wu/ ; }, abstract = {Long-term coal mining in the Muli coal mine area of Qinghai Province has degraded soil quality and reduced microbial diversity, making it imperative to implement effective ecological restoration measures to restore soil quality and enhance ecosystem functions. This study evaluated soil samples under 11 ecological restoration treatments using metagenomic sequencing combined with soil quality analysis to explore the responses of the microbial community structure and function to identify effective restoration measures. This study demonstrated that ecological restoration significantly increased the soil microbial diversity and richness, with the MLII1 (soil samples treated with a chemical weathering agent, attapulgite, and a microbial agent) and MLIII1 (soil samples treated with sheep manure (2.4 kg/m[2]), granular organic fertilizer (1.2 kg/m[2]), and the microbial agent) treatment groups performing exceptionally well. Further analysis of the functional networks revealed that although the MLII2 (soil samples treated with the chemical weathering agent and attapulgite) treatment group did not exhibit the highest species diversity, it exhibited the highest functional network complexity. The results of hierarchical clustering analysis showed that the microbial community of the MLII2 treatment group was most similar to that of the natural meadows compared to the other treatment groups. From the perspective of overall ecological restoration, this study concluded that the MLII2 treatment group exhibited the most favorable ecological restoration outcomes. This finding emphasizes the importance of not only enhancing microbial diversity but also prioritizing the restoration of community functions, especially for the recovery of fragile high-altitude ecosystems.}, } @article {pmid39597610, year = {2024}, author = {Gáspár, Z and Nagavci, B and Szabó, BG and Lakatos, B}, title = {Gut Microbiome Alteration in HIV/AIDS and the Role of Antiretroviral Therapy-A Scoping Review.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, pmid = {39597610}, issn = {2076-2607}, abstract = {(1) Background: The gut microbiota plays a crucial role in chronic immune activation associated with human immunodeficiency virus (HIV) infection, acquired immune deficiency syndrome (AIDS) pathogenesis, non-AIDS-related comorbidities, and mortality among people living with HIV (PLWH). The effects of antiretroviral therapy on the microbiome remain underexplored. This study aims to map the evidence of the impact of integrase strand transfer inhibitors (INSTI) and non-nucleoside reverse transcriptase inhibitors (NNRTI) on the gut microbiota of PLWH. (2) Methods: A scoping review was conducted using PubMed, Web of Science, and Embase, with reports collected following PRISMA for Scoping Reviews (PRISMA-ScR). (3) Results: Evidence suggests that INSTI-based regimes generally promote the restoration of alpha diversity, bringing it closer to that of seronegative controls, while beta diversity remains largely unchanged. INSTI-based therapies are suggested to be associated with improvements in microbiota composition and a tendency toward reduced inflammatory markers. In contrast, NNRTI-based treatments demonstrate limited recovery of alpha diversity and are linked to an increase in proinflammatory bacteria. (4) Conclusions: Based on the review of the current literature, it is indicated that INSTI-based antiretroviral therapy (ART) therapy facilitates better recovery of the gut microbiome.}, } @article {pmid39597593, year = {2024}, author = {Le Doujet, T and Haugen, P}, title = {The Microbiota of the Outer Gut Mucus Layer of the Migrating Northeast Arctic Cod (Gadus morhua) as Determined by Shotgun DNA Sequencing.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, pmid = {39597593}, issn = {2076-2607}, support = {257146//ERA-MarineBiotech/ ; 000000//UiT The Arctic University of Norway/ ; }, abstract = {Animals form functional units with their microbial communities, termed metaorganisms. Despite extensive research on some model animals, microbial diversity in many species remains unexplored. Here, we describe the taxonomic profile of the microbes from the outer gut mucus layer from the Northeast Arctic cod using a shotgun DNA sequencing approach. We focused on the mucus to determine if its microbial composition differs from that of the fecal microbiota, which could reveal unique microbial interactions and functions. Metagenomes from six individuals were analyzed, revealing three different taxonomic profiles: Type I is dominated in numbers by Pseudomonadaceae (44%) and Xanthomonadaceae (13%), Type II by Vibrionaceae (65%), and Type III by Enterobacteriaceae (76%). This stands in sharp contrast to the bacterial diversity of the transient gut content (i.e., feces). Additionally, binning of assembled reads followed by phylogenomic analyses place a high-completeness bin of Type I within the Pseudomonas fluorescens group, Type II within the Photobacterium phosphoreum clade, and Type III within the Escherichia/Shigella group. In conclusion, we describe the adherent bacterial diversity in the Northeast Arctic cod's intestine using shotgun sequencing, revealing different taxonomic profiles compared to the more homogenous transient microbiota. This suggests that the intestine contains two separate and distinct microbial populations.}, } @article {pmid39597583, year = {2024}, author = {Wen, M and Liu, Y and Feng, C and Li, Z}, title = {Metagenomic Analysis Reveals the Effects of Different Land Use Types on Functional Soil Phosphorus Cycling: A Case Study of the Yellow River Alluvial Plain.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, pmid = {39597583}, issn = {2076-2607}, support = {2019QZKK0501//the Second Tibetan Plateau Scientific Expedition and Research (STEP) program/ ; }, abstract = {Phosphorus (P) is a crucial limiting nutrient in soil ecosystems, significantly influencing soil fertility and plant productivity. Soil microorganisms adapt to phosphorus deficiency and enhance soil phosphorus effectiveness through various mechanisms, which are notably influenced by land use practices. This study examined the impact of different land use types (long-term continuous maize farmland, abandoned evolving grassland, artificial tamarisk forests, artificial ash forests, and wetlands) on soil phosphorus-cycling functional genes within the Tanyang Forest Farm in a typical region of the Yellow River alluvial plain using macro genome sequencing technology. The gene cluster related to inorganic phosphorus solubilization and organic phosphorus mineralization exhibited the highest relative abundance across different land use types (2.24 × 10[-3]), followed by the gene cluster associated with phosphorus transport and uptake (1.42 × 10[-3]), with the lowest relative abundance observed for the P-starvation response regulation gene cluster (5.52 × 10[-4]). Significant differences were found in the physical and chemical properties of the soils and the relative abundance of phosphorus-cycling functional genes among various land use types. The lowest relative abundance of soil phosphorus-cycling functional genes was observed in forestland, with both forestland types showing significantly lower gene abundance compared to wetland, farmland, and grassland. Correlation analysis and redundancy analysis (RDA) revealed a significant relationship between soil physicochemical properties and soil phosphorus-cycling functional genes, with ammonium nitrogen, organic carbon, total nitrogen, and pH being the main environmental factors influencing the abundance of these genes, explaining 70% of the variation in their relative abundance. Our study reveals land use's impact on soil phosphorus-cycling genes, offering genetic insights into microbial responses to land use changes.}, } @article {pmid39597569, year = {2024}, author = {Miura, H and Tsukahara, T and Inoue, R}, title = {Whole-Genome Metagenomic Analysis of Functional Profiles in the Fecal Microbiome of Farmed Sows with Different Reproductive Performances.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, pmid = {39597569}, issn = {2076-2607}, support = {23K14070//JSPS KAKENHI/ ; }, abstract = {Recent studies suggested an association between the reproductive performance of sows and their gut microbiota. To understand how the gut microbiota affect the reproductive performances of sows, we conducted a whole-genome metagenomic analysis on the fecal microbial functional profiles of sows with high and low reproductive performances. We used 60 sows from six farms (10 sows/farm), including 30 sows from three farms with higher reproductive performances (the mean number of weaned piglets/sow/year) (group H) and 30 sows from three farms with lower performances (group L). Fecal microbial DNA was subjected to a whole-genome metagenomic analysis. Biomarker exploration analysis identified "carbohydrate transport and metabolism" as the most discriminative function enriched in group H. Further analysis of carbohydrate-active enzymes revealed that the fecal microbiome of group H had a greater capacity to degrade dietary fiber, specifically cellulose and pectin. Group H also exhibited higher fecal short-chain fatty acid (SCFA) concentrations than group L, with the abundances of cellulose- and pectin-degrading genes showing significant positive correlations with fecal SCFA concentrations. Taxonomic analysis indicated greater contributions of Prevotella, Treponema, Ruminococcus, and Fibrobacter to cellulose and pectin degradation in the fecal microbiome in group H. In conclusion, higher reproductive performances of sows were, at least in part, associated with a greater microbial capacity for degrading cellulose and pectin, resulting in a higher SCFA production in the hindgut.}, } @article {pmid39597568, year = {2024}, author = {Jung, Y and Kim, I and Jung, DR and Ha, JH and Lee, EK and Kim, JM and Kim, JY and Jang, JH and Bae, JT and Shin, JH and Cho, YS}, title = {Aging-Induced Changes in Cutibacterium acnes and Their Effects on Skin Elasticity and Wrinkle Formation.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, pmid = {39597568}, issn = {2076-2607}, support = {HP23C0061//Korea Health Industry Development Institute/Republic of Korea ; }, abstract = {Skin aging involves biomechanical changes like decreased elasticity, increased wrinkle formation, and altered barrier function. The skin microbiome significantly impacts this process. Here, we investigated the effects of decreased Cutibacterium acnes abundance and increase in other skin microorganisms on skin biomechanical properties in 60 healthy Koreans from Seoul, divided into younger (20-29 years) and older (60-75 years) groups. Metagenomic sequencing and skin assessments showed that the older group exhibited decreased C. acnes dominance and increased microbial diversity, correlating with reduced skin elasticity and increased wrinkles. In the younger age group, the enriched pathways included zeatin biosynthesis, distinct biotin metabolism pathways, and cofactor and vitamin metabolism in the younger age group, whereas pathways related to lipid metabolism, energy metabolism, and responses to environmental stressors, including UV damage and pollution, were enriched in the older group, according to functional analysis results. Network analysis indicated higher microbial connectivity in the younger group, suggesting a more stable community, whereas the older group's community displayed higher modularity, indicating more independent and specialized clusters. This study enhances our understanding of the impact of skin microbiome changes on skin aging, particularly the anti-aging effects of C. acnes. Future research should focus on the physiological mechanisms of skin microbiota on skin aging and explore therapeutic potentials to enhance skin health.}, } @article {pmid39597565, year = {2024}, author = {Liu, J and Zhou, L and Lan, Y and Fan, J}, title = {Breed Selection of Poplars Imposes Greater Selection Pressure on the Rhizosphere Bacterial Community.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, pmid = {39597565}, issn = {2076-2607}, support = {2021YFD2201205 and 2021YFD2201203//National Key Research and Development Program of China/ ; }, abstract = {Breed selection alters the coevolution of plant-microbiome associations that have developed over long periods of natural evolution. We investigated the effects of breed selection on the rhizosphere microbiomes and metabolites of hybrid parents (I101 and 84K) and their offspring (Q1-Q5) using metagenomics and untargeted metabolomics. Rhizosphere archaeal, bacterial and fungal community β-diversity significantly differed among hybrid parents and offspring, but only the dominant bacterial phyla and bacterial community α-diversity revealed significant differences. Approximately 5.49%, 14.90% and 7.86% of the archaeal, bacterial and fungal species significantly differed among the poplar hybrid parents and offspring. Rhizosphere microbial functional genes and metabolites were both clustered into the following three groups: I101 and 84K; Q2 and Q4; and Q1, Q3 and Q5. Compared with the hybrid parents, 15 phytochemical compounds were enriched in the hybrid offspring and explained 7.15%, 18.24% and 6.68% of the total variation in the archaeal, bacterial and fungal community compositions, respectively. Rhizosphere metabolites significantly affected the bacterial community, rather than the archaeal and fungal communities. Our observations suggested that poplar breed selection imposed greater selection pressure on the rhizosphere bacterial community, which was mainly driven by metabolites.}, } @article {pmid39596778, year = {2024}, author = {Ulloa, F and Penati, M and Naegel, C and Tejeda, C and Hernández-Agudelo, M and Steuer, P and Salgado, M}, title = {Efficacy of Copper Ion Treatment on Bacteria and Antibiotic Residues Contained in Bovine Waste Milk.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {11}, pages = {}, pmid = {39596778}, issn = {2079-6382}, support = {1240730//Fondecyt/ ; }, abstract = {Background/Objectives: Waste milk harbors many bacteria and antibiotic residues. Calves fed with untreated waste milk have a higher incidence of scours and an increased risk of developing antimicrobial-resistant bacteria. This study aimed to evaluate the efficacy of treatment with copper ions on bacteria and antibiotics contained in bovine waste milk. Methods: Waste milk samples were collected from a dairy farm for seven weeks and were subjected to treatment with copper ions. Total bacterial counts, coliforms, Streptococcus, and Staphylococcus were assessed before and after treatment. Additionally, metagenomic analysis was performed to determine microbial diversity. Results: Before treatment, the total bacterial count average was 4.0 × 10[6] CFU/mL, 1.7 × 10[4] CFU/mL for coliforms, 2.6 × 10[6] CFU/mL for Streptococcus, and 5.4 × 10[2] CFU/mL for Staphylococcus Copper treatment significantly reduced bacterial counts within 15 min. Total bacteria decreased from 4.0 × 10[6] CFU/mL to 1.1 × 10[2] CFU/mL after 30 min; meanwhile, other groups were not detected. The most abundant groups were Lactococcus (29.94%), Pseudomonas (28.89%), and Enterobacteriaceae (21.19%). Beta-lactams were detected in five-sevenths samples, and in one sample they were detected before and at 15 min of treatment but not after 30 min. Conclusions: The effect of treatment with copper ions on the different bacterial groups was significantly effective but showed limited effect on the detection of antibiotics.}, } @article {pmid39596708, year = {2024}, author = {Gyraitė, G and Kataržytė, M and Espinosa, RP and Kalvaitienė, G and Lastauskienė, E}, title = {Microbiome and Resistome Studies of the Lithuanian Baltic Sea Coast and the Curonian Lagoon Waters and Sediments.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {11}, pages = {}, pmid = {39596708}, issn = {2079-6382}, support = {S-PD-22-80//Lietuvos Mokslo Taryba/ ; }, abstract = {BACKGROUND: the widespread use of antibiotics in human and veterinary medicine has contributed to the global challenge of antimicrobial resistance, posing significant environmental and public health risks.

OBJECTIVES: this study aimed to examine the microbiome and resistome dynamics across a salinity gradient, analyzing water and sediment samples from the Baltic Sea coast and the Curonian Lagoon between 2017 and 2023.

METHODS: the composition of the water and sediment bacterial community was determined by Full-Length Amplicon Metagenomics Sequencing, while ARG detection and quantification were performed using the SmartChipTM Real-Time PCR system.

RESULTS: the observed differences in bacterial community composition between the Baltic Sea coast and the Curonian Lagoon were driven by variations in salinity and chlorophyll a (chl a) concentration. The genera associated with infectious potential were observed in higher abundances in sediment than in water samples. Over 300 genes encoding antibiotic resistance (ARGs), such as aminoglycosides, beta-lactams, and multidrug resistance genes, were identified. Of particular interest were those ARGs that have previously been detected in pathogens and those currently classified as a potential future threat. Furthermore, our findings reveal a higher abundance and a distinct profile of ARGs in sediment samples from the lagoon compared to water.

CONCLUSIONS: these results suggest that transitional waters such as lagoons may serve as reservoirs for ARGs, and might be influenced by anthropogenic pressures and natural processes such as salinity fluctuation and nutrient cycling.}, } @article {pmid39596705, year = {2024}, author = {Moraes, BDGC and Martins, RCR and Fonseca, JVDS and Franco, LAM and Pereira, GCO and Bartelli, TF and Cortes, MF and Scaccia, N and Santos, CF and Musqueira, PT and Otuyama, LJ and Pylro, VS and Mariano, L and Rocha, V and Witkin, SS and Sabino, E and Guimaraes, T and Costa, SF}, title = {Impact of Exogenous Lactiplantibacillus plantarum on the Gut Microbiome of Hematopoietic Stem Cell Transplantation Patients Colonized by Multidrug-Resistant Bacteria: An Observational Study.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {11}, pages = {}, pmid = {39596705}, issn = {2079-6382}, support = {FAPESP//001/ ; }, abstract = {Background:Lactiplantibacillus plantarum can inhibit the growth of multidrug-resistant organisms (MDROs) and modulate the gut microbiome. However, data on hematopoietic stem cell transplantation (HSCT) are scarce. Aim: In an observational study, we assessed the impact of L. plantarum on the modulation of the gut microbiome in HSCT patients colonized by MDROs. Methods: Participants were allocated to an intervention group (IG = 22) who received capsules of L. plantarum (5 × 10[9] CFU) twice per day until the onset of neutropenia or a control group (CG = 20). The V4 region of the 16S bacterial rRNA gene was sequenced in 87 stool samples from a subset of 33 patients (IG = 20 and CG = 13). The Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) program was used to predict metagenome functions. Results:L. plantarum demonstrated an average 86% (±11%) drug-target engagement at 43 (±29) days of consumption and was deemed safe, well-tolerated, and associated with an increase in the abundance of the Lactobacillales (p < 0.05). A significant increase in Lactococcus and a reduction in Turicibacter (p < 0.05) were identified on the second week of L. plantarum use. Although Enterococcus abundance had a greater rise in the CG (p = 0.07), there were no significant differences concerning the Gram-negative MDROs. No serious adverse effects were reported in the IG. We observed a greater, non-significant pyruvate fermentation to propanoate I (p = 0.193) relative abundance in the IG compared with the CG. L. plantarum use was safe and tolerable by HSCT patients. Conclusions: While L. plantarum is safe and may impact Enterococcus and Turicibacter abundance, it showed no impact on Gram-negative MDRO abundance in HSCT patients.}, } @article {pmid39596488, year = {2024}, author = {Ali, S and Akhtar, MS and Siraj, M and Zaman, W}, title = {Molecular Communication of Microbial Plant Biostimulants in the Rhizosphere Under Abiotic Stress Conditions.}, journal = {International journal of molecular sciences}, volume = {25}, number = {22}, pages = {}, pmid = {39596488}, issn = {1422-0067}, mesh = {*Rhizosphere ; *Stress, Physiological ; Plants/metabolism/microbiology ; Soil Microbiology ; Mycorrhizae/physiology/metabolism ; Plant Development ; Plant Growth Regulators/metabolism ; Bacteria/metabolism/genetics ; }, abstract = {Microbial plant biostimulants offer a promising, sustainable solution for enhancing plant growth and resilience, particularly under abiotic stress conditions such as drought, salinity, extreme temperatures, and heavy metal toxicity. These biostimulants, including plant growth-promoting rhizobacteria, mycorrhizal fungi, and nitrogen-fixing bacteria, enhance plant tolerance through mechanisms such as phytohormone production, nutrient solubilization, osmotic adjustment, and antioxidant enzyme activation. Advances in genomics, metagenomics, transcriptomics, and proteomics have significantly expanded our understanding of plant-microbe molecular communication in the rhizosphere, revealing mechanisms underlying these interactions that promote stress resilience. However, challenges such as inconsistent field performance, knowledge gaps in stress-related molecular signaling, and regulatory hurdles continue to limit broader biostimulant adoption. Despite these challenges, microbial biostimulants hold significant potential for advancing agricultural sustainability, particularly amid climate change-induced stresses. Future studies and innovation, including Clustered Regularly Interspaced Short Palindromic Repeats and other molecular editing tools, should optimize biostimulant formulations and their application for diverse agro-ecological systems. This review aims to underscore current advances, challenges, and future directions in the field, advocating for a multidisciplinary approach to fully harness the potential of biostimulants in modern agriculture.}, } @article {pmid39596343, year = {2024}, author = {Wang, Y and Wang, C and Hou, L and Yang, X and Li, C and Cui, S and Ma, C and Wang, L and Zhang, L and Liu, Y and Guo, H and Pan, J}, title = {Microbial Diversity and Biodegradation Mechanism of Microorganisms in the Dingtao M2 Tomb.}, journal = {International journal of molecular sciences}, volume = {25}, number = {22}, pages = {}, pmid = {39596343}, issn = {1422-0067}, support = {Fundamental Research Funds for the Central Universities//University of Science and Technology Beijing/ ; }, mesh = {*Biodegradation, Environmental ; *Lignin/metabolism ; Wood/microbiology/metabolism ; Cellulose/metabolism ; China ; Talaromyces/metabolism/genetics ; Fungi/metabolism/genetics ; Peroxidases/metabolism ; Metagenomics/methods ; }, abstract = {The Dingtao M2 tomb, the largest and best-preserved imperial "Huangchangticou" tomb in China, holds great significance for its conservation. Currently, varying degrees of microbial degradation are occurring on the surfaces of the M2 tomb. This study aimed to determine the microbial diversity of the M2 tomb and its surrounding environment during July 2021 and August 2022. High-throughput metagenomic sequencing revealed that the dominant fungus on the surface of the tomb chamber was Dacrymyces stillatus (DTT1) in July 2021, which changed to Talaromyces pinophilus (DTT2) in August 2022. Enzymatic activities for cellulose and lignin degradation suggested that DTT1 has high levels of manganese peroxidase, lignin peroxidase, laccase, and cellulase. The wood of the tomb contained higher levels of Fe[2+] and Ca[2+], and experiments with different concentration gradients of these ions in the culture medium revealed that DTT1 exhibited greater activity of cellulose and lignin degradation in environments with higher concentrations of Fe[2+] and Ca[2+]. DTT2 degraded both cellulose and lignin. Lastly, a laboratory plate inhibition experiment demonstrated that isothiazolinone fungicide had a significant fungicidal effect on these two dominant fungi. This study provides valuable data and a theoretical basis for the preservation of the M2 tomb and other wooden cultural relics.}, } @article {pmid39596262, year = {2024}, author = {Mang, Q and Gao, J and Li, Q and Sun, Y and Xu, G and Xu, P}, title = {Probiotics Enhance Coilia nasus Growth Performance and Nutritional Value by Regulating Glucolipid Metabolism via the Gut-Liver Axis.}, journal = {International journal of molecular sciences}, volume = {25}, number = {22}, pages = {}, pmid = {39596262}, issn = {1422-0067}, support = {32302976//National Natural Science Foundation of China/ ; BK20230179//Natural Science Foundation of Jiangsu Province/ ; 2022YFD2400904//National Key Research and development Program of China/ ; JSGS[2021]134//Jiangsu Province seed industry revitalization "revealing-list" project/ ; }, mesh = {*Probiotics/pharmacology ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Liver/metabolism ; Nutritive Value ; Lipid Metabolism ; Fishes/metabolism/growth & development ; Animal Feed ; Glycolipids/metabolism ; }, abstract = {Large-scale intensive feeding triggered reduced growth performance and nutritional value. Exogenous probiotics can promote the growth performance and nutritional value of fish through improving the intestinal microbiota. However, detailed research on the correlation between the intestinal microbiota, growth performance, and nutritional value remains to be elucidated. Therefore, we performed metagenomic and metabolomic analysis to investigate the effects of probiotic addition to basal diet (1.0 × 10[8] CFU/g) (PF) and water (1.0 × 10[8] CFU/g) (PW) on the growth performance, muscle nutritional value, intestinal microbiota and their metabolites, and glucolipid metabolism in Coilia nasus. The results showed that FBW, BL, and SGR were enhanced in PF and PW groups. The concentrations of EAAs, TAAs, SFAs, MUFAs, and PUFAs were increased in PF and PW groups. Metagenomic and metabolic analyses revealed that bacterial community structure and metabolism were changed in the PF and PW groups. Moreover, adding probiotics to diet and water increased SCFAs and bile acids in the intestine. The gene expression associated with lipolysis and oxidation (hsl, pparα, cpt1, and acadm) and glycolysis (gck and pfk) was upregulated, while the gene expression associated with lipid synthesis (srebp1, acc, dgat, and elovl6) and gluconeogenesis (g6pca1, g6pca2, and pck) was downregulated in the liver. Correlation analysis displayed that hepatic glucolipid metabolism was regulated through the microbiota-gut-liver axis. Mantel test analysis showed that growth performance and muscle nutritional value were improved by the gut-liver axis. Our findings offered novel insights into the mechanisms that underlie the enhancement of growth performance and nutritional value in C. nasus and other fish by adding probiotics.}, } @article {pmid39595367, year = {2024}, author = {Pellegrini, F and Lanave, G and Caringella, F and Diakoudi, G and Salvaggiulo, A and Cavalli, A and Papaleo, A and Di Martino, B and Camero, M and Bányai, K and Matthijnssens, J and Martella, V}, title = {Identification of Recombinant Aichivirus D in Cattle, Italy.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {22}, pages = {}, pmid = {39595367}, issn = {2076-2615}, support = {. PE00000007, INF-ACT//Ministero dell'Università e della ricerca Piano Nazionale di Ripresa e Resilienza MUR PNRR Ex-tended Partnership initiative on Emerging Infectious Diseases/ ; National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, RRF-2.3.1-21-2022-00001//National Research, Development and Innovation Office, Hungary/ ; RRF-2.3.1-21-2022-00010 (National Laboratory of Virology)//National Research, Development and Innovation Office, Hungary/ ; }, abstract = {Kobuviruses (KoVs) are a group of small, non-enveloped RNA viruses classified in the genus Kobuvirus within the Picornaviridae family, comprising Aichivirus species A to F. KoVs have been identified in humans and several mammals, including domestic ungulates. This study investigated the presence of KoVs in a collection of bovine stool samples (n = 38) obtained from animals with enteritis or without clinical signs. By RT-PCR screening, KoV RNA was detected in 10/38 animals (26.3%). Six of the ten positive animals had enteric signs. On sequence analysis of the amplicons, eight strains were related to species Aichivirus B, commonly identified in cattle. In contrast, two strains (ITA/2019/572-1 and ITA/2020/bovine/30-2), displayed the highest nt identity (up to 97.1%) to cattle, yak, and goat Aichivirus D strains. On whole genome analysis, strains ITA/2019/572-1 and ITA/2020/30-2 showed 88.9% nt identity to each other and 87.8-90.3% nt to the bovine kobuvirus strain CHN/2021/ON730709 identified in China. Interestingly these three Aichivirus D strains showed a recombinant makeup, clustering with D1 genotype in the capsid region and with D2 genotype in the non-structural genes. These findings suggest that Aichivirus D KoVs are common components of livestock virome. Understanding the genetic diversity of KoVs in animals will be useful to improve the diagnostics and gather epidemiological data.}, } @article {pmid39595278, year = {2024}, author = {Zeng, Y and Mou, H and He, Y and Zhang, D and Pan, X and Zhou, L and Shen, Y and E, G}, title = {Effects of Key Rumen Bacteria and Microbial Metabolites on Fatty Acid Deposition in Goat Muscle.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {22}, pages = {}, pmid = {39595278}, issn = {2076-2615}, support = {32272834；32360813//National Natural Science Foundation of China/ ; SWU-XDJH202301//Fundamental Research Funds for the Central Universities/ ; }, abstract = {In this study, the fatty acid composition in the muscles of Hechuan white goats was correlated with the metabolome and metagenome of their rumen contents, and potential effects of the metabolites and microorganisms in the rumen on host muscle fatty acid deposition were analyzed. The results of the correlation analysis between the rumen content's metabolome and muscle fatty acid content showed that vitamin-B-related metabolites were significantly correlated with fatty acid content (p < 0.05). Most of these metabolites were positively correlated with stearic acid and negatively correlated with palmitic acid. In accordance with the level of fatty acid content, significant differences were found in the microbial species and abundance among groups at the species level. An abundance of Bacteroides, Ruminococcaceae P7, Eubacterium ruminant, and Prevotella in the rumen was significantly correlated with fatty acid content. These results provide data support for the development of targeted feeding management strategies to improve the quality of goat meat.}, } @article {pmid39595275, year = {2024}, author = {Thomson, P and Garrido, D and Santibáñez, R and Lara, F}, title = {Preliminary Functional Analysis of the Gut Microbiome in Colic Horses.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {22}, pages = {}, pmid = {39595275}, issn = {2076-2615}, support = {11231174//ANID. FONDECYT Iniciación/ ; }, abstract = {The gut microbiome plays a critical role in maintaining horse health, influencing digestion, immunity, and overall well-being. However, in certain conditions like colic, there is evidence of significant alterations in the microbial community. To analyze the composition of the fecal microbiome and the enriched predicted metabolic functions of horses with colic compared to a control group, 14 horses with colic and 14 control horses were recruited. From a stool sample, DNA extraction was carried out for subsequent 16S rRNA metagenomic analysis. The composition of the microbiome was analyzed from the sequences of each sample using the QIIME version 1.8.0 and DADA2 version 1.22 programs. PICRUSt2 was used to predict metabolic functions. Statistical analyses were performed with the Mann-Whitney U test from the Python scipy v1 package. The gut microbiomes of both groups were dominated by Firmicuteota, Bacteroidota, and Pseudomonadota phyla. Colic in horses was associated with reduced diversity, reduced abundance of Fibrobacter, and an increase in Streptococcus. The abundance of Firmicuteota was negatively correlated with Pseudomonadota and Actinobacteriota. The equine colic microbiome was predicted to be enriched in aerobic respiration pathways and fatty acid and amino acid degradation. These observations indicate discrete but important differences in the gut microbiome of colic horses.}, } @article {pmid39595245, year = {2024}, author = {Yu, M and Li, Z and Cui, Y and Rong, T and Tian, Z and Deng, D and Liu, Z and Zhang, R and Ma, X}, title = {An Integrated Profiling of Liver Metabolome and Transcriptome of Pigs Fed Diets with Different Starch Sources.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {22}, pages = {}, pmid = {39595245}, issn = {2076-2615}, support = {32372928//National Natural Science Foundation of China/ ; 2024A1515030187//Guangdong Basic and Applied Basic Research Foundation/ ; }, abstract = {Diets containing higher-amylose-content starches were proved to have some beneficial effects on monogastric animals, such as promoting the proliferation of intestinal probiotics. However, current research on the effects of diets with different starch sources on animals at the extraintestinal level is still very limited. We hypothesized that diets with different starch sources may affect lipid-related gene expression and metabolism in the liver of pigs. This study aimed to use adult pig models to evaluate the effects of diets with different starch sources (tapioca starch, TS; pea starch, PS) on the liver gene expressions and metabolism. In total, 48 growing pigs were randomly assigned to the TS and PS diets with 8 replicate pens/group and 3 pigs per pen. On day 44 of the experiment, liver samples were collected for metabolome and transcriptome analysis. Metabolome data suggested that different starch sources affected (p < 0.05) the metabolic patterns of liver. Compared with the TS diet, the PS diet increased (p < 0.05) some unsaturated fatty acids and several amino acids or peptide levels in the liver of pigs. Moreover, transcriptome data indicated the PS diets elevated (p < 0.05) fatty acid β-oxidation-related gene expression in the liver of pigs, and reduced (p < 0.05) unsaturated fatty acid metabolism-related gene expression. The results of quantitative real-time PCR confirmed that the PS diet upregulated (p < 0.05) the expression of acyl-CoA dehydrogenase very long chain (ACADVL), carnitine palmitoyl transferase (CPT) 1A, and malonyl-CoA decarboxylase (MLYCD), and downregulated (p < 0.05) the expression level of cytochrome P450 2U1 (CYP2U1) and aldehyde dehydrogenase 1B1 (ALDH1B1) in the liver. In addition, the results of a Mantel test indicated the muscle fatty acids were significantly closely correlated (p < 0.05) with liver gene expressions and metabolites. In summary, these findings suggest that diets containing higher amylose starches improved the lipid degradation and the unsaturated fatty acid levels in pig livers, and thus can generate some potential beneficial effects (such as anti-inflammatory and antioxidant) on pig health.}, } @article {pmid39595229, year = {2024}, author = {Gao, G and Jiao, Y and Kwok, LY and Zhong, Z}, title = {Gut Microbiome-Host Genetics Co-Evolution Shapes Adiposity by Modulating Energy and Lipid Metabolism in Selectively Bred Broiler Chickens.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {22}, pages = {}, pmid = {39595229}, issn = {2076-2615}, support = {SPKJ202208//the Science and Technology Programs of College of Food Science and Engineering, Inner Mongolia Agricultural University/ ; 2022110//Research support funds for high-level talents in public institutions at the autonomous region level in Inner Mongolia in 2022/ ; }, abstract = {Optimizing fat deposition is crucial for improving chicken production and meat quality. This study investigated the interactive roles of host genetics and gut microbiome in regulating abdominal fat deposition in selectively bred broiler chicken lines. We compared the gut microbiome composition and host whole-genome profiles between fat-line and lean-line broiler chickens that had been selectively bred for divergent abdominal fat levels over 15 generations. Despite identical dietary and environmental conditions, the two chicken lines exhibited significant differences in their gut microbiota. Lean-line broiler chickens exhibited an increased abundance of intestinal Lactobacillus and a decreased presence of potentially pathogenic species, such as Campylobacter coli, Corynebacterium casei, and Enterococcus faecalis. These microbial alterations were accompanied by shifts in the functional metagenome, with enrichment in pathways involved in energy metabolism and nutrient utilization in the lean-line chickens. Notably, the selective breeding process also led to genomic variations in the lean broilers, with single nucleotide polymorphisms predominantly observed in genes related to energy and lipid metabolism. Our findings suggest that the host-microbiome interactions play a key role in the divergent abdominal fat deposition phenotypes observed in these selectively bred chicken lines. The co-evolution of the gut microbiome and host genetics highlights the importance of considering both factors to optimize poultry production efficiency and meat quality. This study offers new insights into the intricate gut-genome interactions in chicken fat metabolism, paving the way for more effective breeding and microbiome-based strategies to manage adiposity in poultry.}, } @article {pmid39593380, year = {2024}, author = {Cardinali, F and Rampanti, G and Paderni, G and Milanović, V and Ferrocino, I and Reale, A and Boscaino, F and Raicevic, N and Ilincic, M and Osimani, A and Aquilanti, L and Martinovic, A and Garofalo, C}, title = {A comprehensive study on the autochthonous microbiota, volatilome, physico-chemical, and morpho-textural features of Montenegrin Njeguški cheese.}, journal = {Food research international (Ottawa, Ont.)}, volume = {197}, number = {Pt 1}, pages = {115169}, doi = {10.1016/j.foodres.2024.115169}, pmid = {39593380}, issn = {1873-7145}, mesh = {*Cheese/microbiology/analysis ; *Food Microbiology ; *Microbiota ; *Volatile Organic Compounds/analysis ; *Biogenic Amines/analysis ; Montenegro ; Bacteria/classification ; Odorants/analysis ; }, abstract = {The present study aims to deepen the knowledge of the microbiota, gross composition, physico-chemical and morpho-textural features, biogenic amines content and volatilome of Njeguški cheese, one of the most popular indigenous cheeses produced in Montenegro. Cheese samples were collected in duplicate from three different batches produced by three Montenegrin artisan producers. For the first time, the microbiota of Njeguški cheese was investigated using both culture-dependent techniques and metagenomic analysis. Coagulase positive staphylococci viable counts were below the detection limit of the analysis (<1 log cfu g[-1]). Salmonella spp., Listeria monocytogenes and staphylococcal enterotoxins were absent. However, relatively high viable counts of Enterobacteriaceae, Escherichia coli, Pseudomonadaceae and eumycetes were detected. Metataxonomic analysis revealed a core microbiome composed of Lactococcus lactis, Streptococcus thermophilus, Debaryomyces hansenii, and Kluyveromyces marxianus. Furthermore, the detection of opportunistic pathogenic yeasts such as Magnusiomyces capitatus and Wickerhamiella pararugosa, along with the variable content of biogenic amines, suggests the need for increased attention to hygienic conditions during Njeguški cheese production. Significant variability was observed in humidity (ranging from 38.37 to 45.58 %), salt content (ranging from 0.70 to 1.78 %), proteins content (ranging from 21.42 to 25.08 %), ash content (ranging from 2.97 to 4.05 %), hardness, springiness, and color among samples from different producers. Gas chromatography-mass spectrometry analysis showed a well-defined and complex volatilome profile of the Njeguški cheese, with alcohols (ethanol, isoamyl alcohol, phenetyl alcol), esters and acetates (ethyl acetate, ethyl butanoate, isoamyl acetate), ketones (acetoin, 2-butanone), and acids (acetic, butanoic, hexanoic acids) being the main chemical groups involved in aroma formation. This research will provide new insights into the still poorly explored identity of Njeguški cheese, thus serving as a first baseline for future studies aimed at protecting its tradition.}, } @article {pmid39593354, year = {2024}, author = {Peng, Q and Zheng, H and Zhou, H and Chen, J and Xu, Y and Wang, Z and Xie, G}, title = {Elucidating core microbiota in yellow wine (Huangjiu) through flavor-oriented synthesis and construction of microbial communities.}, journal = {Food research international (Ottawa, Ont.)}, volume = {197}, number = {Pt 1}, pages = {115139}, doi = {10.1016/j.foodres.2024.115139}, pmid = {39593354}, issn = {1873-7145}, mesh = {*Volatile Organic Compounds/analysis ; *Fermentation ; *Microbiota ; *Wine/analysis/microbiology ; *Taste ; Humans ; Gas Chromatography-Mass Spectrometry ; Solid Phase Microextraction ; Pentanols/metabolism/analysis ; Odorants/analysis ; Flavoring Agents/analysis ; China ; Male ; Saccharomyces cerevisiae/metabolism ; Food Microbiology ; Female ; Phenylethyl Alcohol/metabolism/analysis ; Adult ; Butanols ; }, abstract = {Huangjiu, a traditional Chinese alcoholic beverage with a history spanning thousands of years, holds significant cultural and economic value in China. Despite its importance, the complexity of Huangjiu fermentation and the intricate interactions within its microbial community remain underexplored. This study addresses this gap by identifying the core volatile organic compounds (VOCs) and key microorganisms that define the flavor profile of Huangjiu. We employed HS-SPME-GC-MS along with aroma reconstitution and omission experiments to identify core VOCs, including Isobutanol, Isoamyl alcohol, β-Phenylethanol, and others. Metagenomic sequencing combined with QPCR was used to analyze microbial communities, revealing the temporal and spatial dynamics during fermentation. A synthetic microbial community model was constructed using the core microbes identified: Saccharomyces cerevisiae, Lactobacillus brevis, Saccharopolyspora rectivirgula, Bacillus subtilis, Leuconostoc citreum, Lactobacillus plantarum, Lactobacillus curvatus, Lactobacillus casei, and Aspergillus oryzae. This model successfully replicated Huangjiu's core VOCs and sensory characteristics, increased alcohol content, and reduced acidity. Our study contributes valuable insights into the microbial influences on Huangjiu quality, paving the way for its enhanced production and providing a foundation for future research in fermented beverages.}, } @article {pmid39593339, year = {2024}, author = {Scarano, L and Peruzy, MF and Fallico, V and Blaiotta, G and Aponte, M and Anastasio, A and Murru, N}, title = {Provolone del Monaco PDO cheese: Lactic microflora, biogenic amines and volatilome characterization.}, journal = {Food research international (Ottawa, Ont.)}, volume = {197}, number = {Pt 1}, pages = {115257}, doi = {10.1016/j.foodres.2024.115257}, pmid = {39593339}, issn = {1873-7145}, mesh = {*Cheese/analysis/microbiology ; *Biogenic Amines/analysis ; *Lactobacillales/classification/genetics/isolation & purification ; *Volatile Organic Compounds/analysis ; Metagenome/genetics ; RNA, Ribosomal, 16S ; Microbiota/genetics ; Bacterial Load ; *Food Microbiology ; }, abstract = {One commercial production run of Provolone del Monaco - a long-ripened pasta filata cheese - was followed up to the end of ripening for a total of 20 samples. 371 LAB isolates were subject to genetic characterization followed by 16S rRNA gene sequencing. The dominant species were Lacticaseibacillus casei/paracasei (19.4 %), Streptococcus macedonicus (19.1 %) and Enterococcus faecalis (13.2 %). Strains were screened for features of technological interest or safety relevance. Tyramine-producing cultures were quite common, above all within enterococci. By MALDI TOF Mass Spectrometry, one Lactococcus lactis and one Enterococcus faecium strain proved to be bacteriocin producers. Four further cheese wheels from the same production run at 623 days of ripening were evaluated for volatile organic compounds, biogenic amines, and bacterial community by metagenomic sequencing. Three individual wheel samples shared a rather similar microbiome with Lactobacillus delbrueckii and Streptococcus thermophilus as the most represented species, while the fourth wheel appeared wholly different being dominated by Lentilactobacillus buchneri and St. infantarius. Additionally, this sample had the greatest content of biogenic amines and a different VOCs composition. Given the variance seen among cheese wheels processed and ripened under the same conditions, the search for adjunct cultures in the production of this cheese seems to be of utmost importance.}, } @article {pmid39593310, year = {2024}, author = {Li, X and Du, C and Zhao, Y and Li, J and Hu, Y and Dong, W and Peng, N and Zhao, S}, title = {Differences in microbial communities among different types of zaopei and their effects on quality and flavor of baijiu.}, journal = {Food research international (Ottawa, Ont.)}, volume = {197}, number = {Pt 1}, pages = {115224}, doi = {10.1016/j.foodres.2024.115224}, pmid = {39593310}, issn = {1873-7145}, mesh = {*Fermentation ; *Microbiota ; *Food Microbiology ; *Taste ; Ethanol/metabolism ; Fermented Foods/microbiology ; Lactobacillales/genetics/metabolism/classification ; Lactic Acid/metabolism/analysis ; Fungi/classification/genetics ; Acetic Acid/metabolism/analysis ; Oryza/microbiology ; Bacteria/classification/genetics/metabolism ; Flavoring Agents/analysis ; }, abstract = {Three types of zaopei (fermented grain) of xiaoqu light-flavor baijiu (XQZP), daqu light-flavor baijiu (DQZP), and strong-flavor baijiu (SFZP) at the end of fermentation and their dominant lactic acid bacteria were systematically compared and analyzed in this study. The results showed that these three types of zaopei differed significantly in acidity, reducing sugar content, and ethanol content, and that the main factors influencing their microbial community were acidity and lactic acid. The diversity and contents of flavor substances were significantly higher in SFZP than in DQZP and XQZP. Additionally, there was a strong correlation between dominant lactic acid bacteria and flavor substances in all three zaopei, but the correlation between fungi and flavor substances was higher than that between bacteria and flavor substances. Differential gene analysis revealed that the microbial activities followed the order of SFZP > DQZP > XQZP. The KEGG enrichment analysis indicated that the differential genes from different zaopei were enriched in different metabolic pathways. Furthermore, various microorganisms in 3 types of zaopei contained different functional genes, of which fungi mainly contained genes responsible for the synthesis of ethanol and acetic acid, while lactic acid bacteria mainly contained genes responsible for the synthesis of lactic acid. In XQZP, L. helveticus was dominant lactic acid bacteria prominent in acetic acid tolerance and lactic acid production; in DQZP, L. acetotolerans was remarkable in its tolerance to lactic acid, acetic acid, ethanol and lactic acid production; and in SFZP, A. jinshanensis was superior in acetic acid tolerance and production. Taken together, this study reveals the mechanism underlying flavor differences among three types of baijiu and provides valuable references for the development and utilization of baijiu microbial resources.}, } @article {pmid39592704, year = {2024}, author = {Hai, C and Hao, Z and Bu, L and Lei, J and Liu, X and Zhao, Y and Bai, C and Su, G and Yang, L and Li, G}, title = {Increased rumen Prevotella enhances BCAA synthesis, leading to synergistically increased skeletal muscle in myostatin-knockout cattle.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1575}, pmid = {39592704}, issn = {2399-3642}, support = {32360837, 32341052//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; Cattle ; *Myostatin/genetics/metabolism ; *Amino Acids, Branched-Chain/metabolism/biosynthesis ; *Prevotella/genetics/metabolism ; *Muscle, Skeletal/metabolism ; *Rumen/microbiology/metabolism ; Gene Knockout Techniques ; Gastrointestinal Microbiome/genetics ; }, abstract = {Myostatin (MSTN) is a negative regulator of muscle growth, and its relationship with the gut microbiota is not well understood. In this study, we observed increase muscle area and branched-chain amino acids (BCAAs), an energy source of muscle, in myostatin knockout (MSTN-KO) cattle. To explore the link between increased BCAAs and rumen microbiota, we performed metagenomic sequencing, metabolome analysis of rumen fluid, and muscle transcriptomics. MSTN-KO cattle showed a significant increase in the phylum Bacteroidota (formerly Bacteroidetes), particularly the genus Prevotella (P = 3.12e-04). Within this genus, Prevotella_sp._CAG:732, Prevotella_sp._MSX73, and Prevotella_sp._MA2016 showed significant upregulation of genes related to BCAA synthesis. Functional enrichment analysis indicated enrichment of BCAA synthesis-related pathways in both rumen metagenomes and metabolomes. Additionally, muscle transcriptomics indicated enrichment in muscle fiber and amino acid metabolism, with upregulation of solute carrier family genes, enhancing BCAA transport. These findings suggest that elevated rumen Prevotella in MSTN-KO cattle, combined with MSTN deletion, synergistically improves muscle growth through enhanced BCAA synthesis and transport.}, } @article {pmid39592438, year = {2024}, author = {Zhang, S and Wen, H and Chen, Y and Ning, J and Hu, D and Dong, Y and Yao, C and Yuan, B and Yang, S}, title = {Crosstalk between gut microbiota and tumor: tumors could cause gut dysbiosis and metabolic imbalance.}, journal = {Molecular oncology}, volume = {}, number = {}, pages = {}, doi = {10.1002/1878-0261.13763}, pmid = {39592438}, issn = {1878-0261}, support = {82303747//National Natural Science Foundation of China/ ; 2020GXLH-Y-010//Key Research and Development Projects of Shaanxi Province/ ; 2022JM-509//Natural Science Basic Research Program of Shaanxi Province/ ; }, abstract = {Gut microbiota has a proven link with the development and treatment of cancer. However, the causality between gut microbiota and cancer development is still unknown and deserves exploration. In this study, we aimed to explore the alterations in gut microbiota in murine tumor models and the crosstalk between the tumor and the gut microbiota. The subcutaneous and intravenous murine tumor models using both the colorectal cancer cell line MC38 and lung cancer cell line LLC were constructed. Then fecal samples before and after tumor inoculation were collected for whole metagenomics sequencing. Both subcutaneous and metastatic tumors markedly elevated the α-diversity of the gut microbiota. Relative abundance of Ligilactobacillus and Lactobacillus was reduced after subcutaneously inoculating tumor cells, whereas Bacteroides and Duncaniella were reduced in metastatic tumors, regardless of tumor type. At the species level, Lachnospiraceae bacterium was enriched after both subcutaneous and intravenous tumors inoculation, whereas levels of Muribaculaceae bacterium Isolate-110 (HZI), Ligilactobacillus murinus and Bacteroides acidifaciens reduced. Metabolic function analysis showed that the reductive pentose phosphate cycle, urea cycle, ketone body biosynthesis, ectoine biosynthesis, C4-dicarboxylic acid cycle, isoleucine biosynthesis, inosine 5'-monophosphate (IMP), and uridine 5'-monophosphate (UMP) biosynthesis were elevated after tumor inoculation, whereas the cofactor and vitamin biosynthesis were deficient. Principal coordinates analysis (PCoA) showed that subcutaneous and metastatic tumors partially shared the same effect patterns on gut microbiota. Furthermore, fecal microbiota transplantation revealed that this altered microbiota could influence tumor growth. Taken together, this study demonstrated that both colorectal cancer (MC38) and non-colorectal cancer (LLC) can cause gut dysbiosis and metabolic imbalance, regardless of tumor type and process of tumor inoculation, and this dysbiosis influenced the tumor growth. This research gives novel insights into the crosstalk between tumors and the gut microbiota.}, } @article {pmid39591974, year = {2024}, author = {Peng, Y and Zhu, J and Wang, S and Liu, Y and Liu, X and DeLeon, O and Zhu, W and Xu, Z and Zhang, X and Zhao, S and Liang, S and Li, H and Ho, B and Ching, JY and Cheung, CP and Leung, TF and Tam, WH and Leung, TY and Chang, EB and Chan, FKL and Zhang, L and Ng, SC and Tun, HM}, title = {A metagenome-assembled genome inventory for children reveals early-life gut bacteriome and virome dynamics.}, journal = {Cell host & microbe}, volume = {32}, number = {12}, pages = {2212-2230.e8}, doi = {10.1016/j.chom.2024.10.017}, pmid = {39591974}, issn = {1934-6069}, mesh = {*Gastrointestinal Microbiome/genetics ; Infant ; Humans ; *Virome/genetics ; *Metagenome/genetics ; Child, Preschool ; Infant, Newborn ; Child ; Bacteriophages/genetics/isolation & purification ; Bacteria/genetics/virology/classification ; Genome, Viral/genetics ; Feces/microbiology/virology ; Metagenomics/methods ; Female ; Bifidobacterium/genetics/isolation & purification/classification ; Phylogeny ; Male ; Genome, Bacterial ; }, abstract = {Existing microbiota databases are biased toward adult samples, hampering accurate profiling of the infant gut microbiome. Here, we generated a metagenome-assembled genome inventory for children (MAGIC) from a large collection of bulk and viral-like particle-enriched metagenomes from 0 to 7 years of age, encompassing 3,299 prokaryotic and 139,624 viral species-level genomes, 8.5% and 63.9% of which are unique to MAGIC. MAGIC improves early-life microbiome profiling, with the greatest improvement in read mapping observed in Africans. We then identified 54 candidate keystone species, including several Bifidobacterium spp. and four phages, forming guilds that fluctuated in abundance with time. Their abundances were reduced in preterm infants and were associated with childhood allergies. By analyzing the B. longum pangenome, we found evidence of phage-mediated evolution and quorum sensing-related ecological adaptation. Together, the MAGIC database recovers genomes that enable characterization of the dynamics of early-life microbiomes, identification of candidate keystone species, and strain-level study of target species.}, } @article {pmid39591767, year = {2025}, author = {Geng, Q and Wang, Z and Shi, T and Wen, C and Xu, J and Jiao, Y and Diao, W and Gu, J and Wang, Z and Zhao, L and Deng, T and Xiao, C}, title = {Cannabidiol regulates L-carnitine and butyric acid metabolism by modulating the gut microbiota to ameliorate collagen-induced arthritis.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {136}, number = {}, pages = {156270}, doi = {10.1016/j.phymed.2024.156270}, pmid = {39591767}, issn = {1618-095X}, mesh = {Animals ; *Cannabidiol/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Arthritis, Experimental/drug therapy/metabolism ; *Carnitine/pharmacology ; *Butyric Acid/pharmacology ; Rats ; *Dysbiosis/drug therapy ; Male ; *Arthritis, Rheumatoid/drug therapy ; }, abstract = {BACKGROUND: Rheumatoid arthritis (RA) is one of the most common autoimmune diseases, affecting multiple systems in the body. Cannabidiol (CBD) is one of the most medically valuable active ingredients in cannabis. At present, CBD has been shown to alleviate the progression of RA; however, owing to its multiple targets, the mechanism of CBD is not clear.

METHODS: On the basis of the gut microbiota, we explored the mechanism by which CBD inhibits RA progression. Metagenomic and nontargeted metabolomic analyses were used to determine the changes in the intestinal ecology and plasma metabolites of collagen-induced arthritis (CIA) rats after CBD treatment.

RESULTS: CBD reversed gut dysbiosis in CIA rats, notably altering the abundances of Allobaculum_unclassified, Allobaculum_fili, and Prevotella_unclassified. In addition, metabolomic analysis confirmed that CBD increased the contents of butyric acid and L-carnitine. Allobaculum could produce butyric acid and Prevotella could accelerate the metabolism of L-carnitine. In addition, in vitro experiments demonstrated that L-carnitine participated in the regulation of neutrophils, macrophages and RA-fibroblast-like synoviocytes (RA-FLSs), which was consistent with the synovial changes in CIA rats caused by CBD.

CONCLUSION: In summary, CBD increased the plasma contents of butyric acid and L-carnitine by altering the abundances of gut microbiota, thereby inhibiting inflammation in neutrophils, macrophages and RA-FLSs. Our study is the first to explain the mechanism by which CBD alleviates progression in CIA rats from the perspective of gut microbes and metabolites, providing new views into CBD mechanisms, which warrants clinical attention.}, } @article {pmid39591453, year = {2024}, author = {Wang, L and Liu, Y and Ni, H and Zuo, W and Shi, H and Liao, W and Liu, H and Chen, J and Bai, Y and Yue, H and Huang, A and Friedman, J and Si, T and Liu, Y and Chen, M and Dai, L}, title = {Systematic characterization of plant-associated bacteria that can degrade indole-3-acetic acid.}, journal = {PLoS biology}, volume = {22}, number = {11}, pages = {e3002921}, pmid = {39591453}, issn = {1545-7885}, mesh = {*Indoleacetic Acids/metabolism ; *Oryza/microbiology/metabolism ; *Arabidopsis/microbiology/metabolism ; *Plant Roots/microbiology/metabolism ; *Bacteria/metabolism/genetics ; Plant Growth Regulators/metabolism ; Rhizosphere ; Soil Microbiology ; Phylogeny ; Operon/genetics ; Microbiota/physiology ; Seedlings/microbiology/metabolism ; }, abstract = {Plant-associated microbiota affect pant growth and development by regulating plant hormones homeostasis. Indole-3-acetic acid (IAA), a well-known plant hormone, can be produced by various plant-associated bacteria. However, the prevalence of bacteria with the capacity to degrade IAA in the rhizosphere has not been systematically studied. In this study, we analyzed the IAA degradation capabilities of bacterial isolates from the roots of Arabidopsis and rice. Using genomics analysis and in vitro assays, we found that 21 out of 183 taxonomically diverse bacterial isolates possess the ability to degrade IAA. Through comparative genomics and transcriptomic assays, we identified iac-like or iad-like operon in the genomes of these IAA degraders. Additionally, the putative regulator of the operon was found to be highly conserved among these strains through protein structure similarity analysis. Some of the IAA degraders could utilize IAA as their carbon and energy source. In planta, most of the IAA degrading strains mitigated Arabidopsis and rice seedling root growth inhibition (RGI) triggered by exogenous IAA. Moreover, RGI caused by complex synthetic bacterial community can be alleviated by introducing IAA degraders. Importantly, we observed increased colonization preference of IAA degraders from soil to root according to the frequency of the biomarker genes in metagenome-assembled genomes (MAGs) collected from different habitats, suggesting that there is a close association between IAA degraders and IAA producers. In summary, our findings further the understanding of the functional diversity and potential biological roles of plant-associated bacteria in host plant root morphogenesis.}, } @article {pmid39590379, year = {2024}, author = {Fernández, M and Barahona, S and Gutierrez, F and Alcaíno, J and Cifuentes, V and Baeza, M}, title = {Bacterial Diversity, Metabolic Profiling, and Application Potential of Antarctic Soil Metagenomes.}, journal = {Current issues in molecular biology}, volume = {46}, number = {11}, pages = {13165-13178}, pmid = {39590379}, issn = {1467-3045}, support = {RG_02-18//Instituto Antartico Chileno/ ; ENL03/22//Vicerrectoria de Investigacion y Desarrollo, Universidad de Chile./ ; }, abstract = {Antarctica has attracted increasing interest in understanding its microbial communities, metabolic potential, and as a source of microbial hydrolytic enzymes with industrial applications, for which advances in next-generation sequencing technologies have greatly facilitated the study of unculturable microorganisms. In this work, soils from seven sub-Antarctic islands and Union Glacier were studied using a whole-genome shotgun metagenomic approach. The main findings were that the microbial community at all sites was predominantly composed of the bacterial phyla Actinobacteria and Cyanobacteria, and the families Streptomycetaceae and Pseudonocardiaceae. Regarding the xenobiotic biodegradation and metabolism pathway, genes associated with benzoate, chloroalkane, chloroalkene, and styrene degradation were predominant. In addition, putative genes encoding industrial enzymes with predicted structural properties associated with improved activity at low temperatures were found, with catalases and malto-oligosyltrehalose trehalohydrolase being the most abundant. Overall, our results show similarities between soils from different Antarctic sites with respect to more abundant bacteria and metabolic pathways, especially at higher classification levels, regardless of their geographic location. Furthermore, our results strengthen the potential of Antarctic soils as a source of industrially relevant enzymes.}, } @article {pmid39589812, year = {2025}, author = {Mercado-Evans, V and Branthoover, H and Chew, C and Serchejian, C and Saltzman, AB and Mejia, ME and Zulk, JJ and Cornax, I and Nizet, V and Patras, KA}, title = {Tamm-Horsfall protein augments neutrophil NETosis during urinary tract infection.}, journal = {JCI insight}, volume = {10}, number = {1}, pages = {}, pmid = {39589812}, issn = {2379-3708}, support = {F31 AI167538/AI/NIAID NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; T32 AI055449/AI/NIAID NIH HHS/United States ; S10 RR024574/RR/NCRR NIH HHS/United States ; F31 DK136201/DK/NIDDK NIH HHS/United States ; S10 OD026804/OD/NIH HHS/United States ; R01 DK128053/DK/NIDDK NIH HHS/United States ; F31 AI167547/AI/NIAID NIH HHS/United States ; }, mesh = {*Uromodulin/urine/metabolism ; *Urinary Tract Infections/immunology/metabolism/pathology ; Animals ; *Neutrophils/immunology/metabolism ; Mice ; Humans ; *Extracellular Traps/immunology/metabolism ; Female ; Disease Models, Animal ; Mice, Knockout ; Mice, Inbred C57BL ; }, abstract = {Urinary neutrophils are a hallmark of urinary tract infection (UTI), yet the mechanisms governing their activation, function, and efficacy in controlling infection remain incompletely understood. Tamm-Horsfall glycoprotein (THP), the most abundant protein in urine, uses terminal sialic acids to bind an inhibitory receptor and dampen neutrophil inflammatory responses. We hypothesized that neutrophil modulation is an integral part of THP-mediated host protection. In a UTI model, THP-deficient mice showed elevated urinary tract bacterial burdens, increased neutrophil recruitment, and more severe tissue histopathological changes compared with WT mice. Furthermore, THP-deficient mice displayed impaired urinary NETosis during UTI. To investigate the effect of THP on NETosis, we coupled in vitro fluorescence-based NET assays, proteomic analyses, and standard and imaging flow cytometry with peripheral human neutrophils. We found that THP increases proteins involved in respiratory chain, neutrophil granules, and chromatin remodeling pathways; enhances NETosis in an ROS-dependent manner; and drives NET-associated morphologic features including nuclear decondensation. These effects were observed only in the presence of a NETosis stimulus and could not be solely replicated with equivalent levels of sialic acid alone. We conclude that THP is a critical regulator of NETosis in the urinary tract, playing a key role in host defense against UTI.}, } @article {pmid39589660, year = {2024}, author = {Xue, X and Zhao, Z and Zhao, LB and Gao, YH and Xu, WH and Cai, WM and Chen, SH and Li, TJ and Nie, TY and Rui, D and Ma, Y and Qian, XS and Lin, JL and Liu, L}, title = {Gut microbiota changes in healthy individuals, obstructive sleep apnea patients, and patients treated using continuous positive airway pressure: a whole-genome metagenomic analysis.}, journal = {Sleep & breathing = Schlaf & Atmung}, volume = {29}, number = {1}, pages = {11}, pmid = {39589660}, issn = {1522-1709}, support = {22BJZ52//Military Health Care Project/ ; 23BJZ27//Military Health Care Project/ ; SYDW_KY[2021]04//Military experimental animal special research project/ ; }, mesh = {Humans ; *Continuous Positive Airway Pressure ; *Sleep Apnea, Obstructive/therapy/microbiology ; *Gastrointestinal Microbiome/physiology/genetics ; Male ; Middle Aged ; Female ; Adult ; *Metagenomics ; Polysomnography ; }, abstract = {PURPOSE: This study investigated variations in gut microbiota among severe obstructive sleep apnea (OSA) patients and changes in gut microbiota after continuous positive airway pressure (CPAP) treatment.

METHOD: From November 2020 to August 2021, laboratory-based polysomnography (PSG) was used to measure sleep parameters in healthy controls, severe OSA patients, and severe OSA patients treated with CPAP for three months. A fully automated biochemical analyzer was used to evaluate routine blood tests and biochemical indicators. Whole-genome metagenomic analysis was used to determine the microbial composition of gut samples from all participants. The relationships between gut microbiota and hypertension were examined using correlation analysis.

RESULT: The relative abundances of Bacteroides, Firmicutes, and Parabacteroides were significantly lower at the species level. Enterobacterales and Turicibacter were significantly higher in participants with severe OSA than healthy controls. Negative correlations were identified between Bacteroides coprocola and systolic blood pressure (SBP) (r =  - 0.710, P = 0.003) and diastolic blood pressure (DBP) (r =  - 0.615, P = 0.015). Conversely, a positive correlation was found between Escherichia coli and SBP (r = 0.568, P = 0.027).

CONCLUSION: The metabolic pathways and gut microbiota differed significantly between the control group and individuals with severe OSA. Additionally, CPAP therapy substantially changed the metabolic pathways and gut microbial composition among patients diagnosed with severe OSA. Correlation analysis further revealed a strong association between Escherichia coli, Bacteroides coprocola, and blood pressure levels.}, } @article {pmid39589588, year = {2024}, author = {Wanna, W and Aucharean, C and Jaeram, N}, title = {Analysis of Gut Microbiota Associated with WSSV Resistance in Litopenaeus vannamei.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {27}, number = {1}, pages = {10}, pmid = {39589588}, issn = {1436-2236}, support = {SCI6601054S//The National Science, Research and Innovation Fund (NSRF) and Prince of Songkla University/ ; SCI6601054S//The National Science, Research and Innovation Fund (NSRF) and Prince of Songkla University/ ; PSU_PHD2565-004//The Graduate School, Prince of Songkla University/ ; }, mesh = {Animals ; *Penaeidae/microbiology/virology ; *White spot syndrome virus 1/genetics ; *Gastrointestinal Microbiome/genetics ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; Disease Resistance/genetics ; Metagenome ; }, abstract = {Microorganisms in the digestive tract regulate the metabolism of host cells as well as stimulate the immune system of the host. If the microbiota is in good balance, it will promote the good health of the host. In this study, using 16S rRNA sequencing, we analyzed the microbiota of three groups of shrimp: a group of normal shrimp (control group), shrimp that were killed by infection with the white spot syndrome virus (WSSV) (susceptible group), and shrimp that survived WSSV infection (resistant group). The results showed that although the alpha diversity of the microbiota was barely affected by the WSSV, the bacterial communities in the three groups had different prevalences. The resistant group harbored significantly more bacteria than both the other groups. Remarkably, the resistant group had the greatest prevalence of the phylum Bacterioidetes, the families Rhodobacteraceae and Flavobacteriaceae, and the genus Nautella, suggesting their potential as biomarkers for shrimp resistance to WSSV infection. In addition, analysis of functional diversity in bacterial communities showed that the abundance of bacterial metagenomes in two groups infected with WSSV was mostly linked to metabolism and cellular processes. The susceptible WSSV group exhibited a significant reduction in amino acid metabolism. This result suggested that metabolism was the principal factor affecting the alteration in the microbiota after WSSV infection. This overview of the gut microbiota of shrimp infected with the WSSV offers crucial insights for aquaculture management and simplifies the use of control strategies in the future.}, } @article {pmid39589125, year = {2024}, author = {Zhang, Z and Tong, M and Ding, W and Liu, S and Jong, M-C and Radwan, AA and Cai, Z and Zhou, J}, title = {Changes in the diversity and functionality of viruses that can bleach healthy coral.}, journal = {mSphere}, volume = {9}, number = {12}, pages = {e0081624}, pmid = {39589125}, issn = {2379-5042}, mesh = {*Anthozoa/virology/microbiology ; Animals ; *Microbiota/genetics ; *Viruses/genetics/classification ; *Metagenomics ; Bacteria/genetics/classification/virology/isolation & purification ; Symbiosis ; Bacteriophages/genetics/physiology/classification/isolation & purification ; }, abstract = {UNLABELLED: Coral microbiomes play a crucial role in maintaining the health and functionality of holobionts. Disruption in the equilibrium of holobionts, including bacteria, fungi, and archaea, can result in the bleaching of coral. However, little is known about the viruses that can infect holobionts in coral, especially bacteriophages. Here, we employed a combination of amplicon and metagenomic analyses on Acropora muricata and Galaxea astreata to investigate the diversity and functionality of viruses in healthy and bleached corals. Analysis showed that the alpha diversity of holobionts (bacteria, eukaryotes, zooxanthellae, and lysogenic and lytic viruses) was higher in bleached corals than that in healthy corals. Meanwhile, bleached corals exhibited a relatively higher abundance of specific viral classes, including Revtraviricetes, Arfiviricetes, Faserviricetes, Caudoviricetes, Herviviricetes, and Tectiliviricetes; moreover, we found that the expression levels of functional genes involved in carbon and sulfur metabolism were enriched. An increase in Vibrio abundance has been reported as a notable factor in coral bleaching; our analysis also revealed an increased abundance of Vibrio in bleached coral. Finally, bleached corals contained a higher abundance of Vibrio phages and encoded more virulence factor genes to increase the competitiveness of Vibrio after coral bleaching. In conclusion, we attempted to understand the causes of coral bleaching from the perspective of phage-bacteria-coral tripartite interaction.

IMPORTANCE: Viruses, especially bacteriophages, outnumber other microorganisms by approximately 10-fold and represent the most abundant members of coral holobionts. Corals represent a model system for the study of symbiosis, the influence of viruses on organisms inhabiting healthy coral reef, the role of rapid horizontal gene transfer, and the expression of auxiliary metabolic genes. However, the least studied component of coral holobiont are viruses. Therefore, there is a critical need to investigate the viral community of viruses, and their functionality, in healthy and bleached coral. Here, we compared the composition and functionality of viruses in healthy and bleached corals and found that viruses may participate in the induction of coral bleaching by enhancing the expression of virulence genes and other auxiliary metabolic functions.}, } @article {pmid39588334, year = {2024}, author = {Zhang, J and Wu, L and Zhang, Z and Li, D and Han, R and Ye, L and Zhang, Y and Hong, J and Gu, W}, title = {Gut microbiota and metabolic profiles in adults with unclassified diabetes: a cross-sectional study.}, journal = {Frontiers in endocrinology}, volume = {15}, number = {}, pages = {1440984}, pmid = {39588334}, issn = {1664-2392}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Female ; Male ; Adult ; Case-Control Studies ; Cross-Sectional Studies ; *Diabetes Mellitus, Type 2/microbiology/metabolism/blood ; *Metabolome ; Diabetes Mellitus, Type 1/microbiology/metabolism/blood ; Biomarkers/blood ; Young Adult ; }, abstract = {AIMS: Our study, employing a multi-omics approach, aimed to delineate the distinct gut microbiota and metabolic characteristics in individuals under 30 with unclassified diabetes, thus shedding light on the underlying pathophysiological mechanisms.

METHODS: This age- and sex-matched case-control study involved 18 patients with unclassified diabetes, 18 patients with classic type 1 diabetes, 13 patients with type 2 diabetes, and 18 healthy individuals. Metagenomics facilitated the profiling of the gut microbiota, while untargeted liquid chromatography-mass spectrometry was used to quantify the serum lipids and metabolites.

RESULTS: Our findings revealed a unique gut microbiota composition in unclassified diabetes patients, marked by a depletion of Butyrivibrio proteoclasticus and Clostridium and an increase in Ruminococcus torques and Lachnospiraceae bacterium 8_1_57FAA. Comparative analysis identified the combined marker panel of five bacterial species, seven serum biomarkers, and three clinical parameters could differentiate patients with UDM from HCs with an AUC of 0.94 (95% CI 0.85-1). Notably, the gut microbiota structure of patients with unclassified diabetes resembled that of type 2 diabetes patients, especially regarding disrupted lipid and branched-chain amino acid metabolism.

CONCLUSIONS: Despite sharing certain metabolic features with type 2 diabetes, unclassified diabetes presents unique features. The distinct microbiota and metabolites in unclassified diabetes patients suggest a significant role in modulating glucose, lipid, and amino acid metabolism, potentially influencing disease progression. Further longitudinal studies are essential to explore therapeutic strategies targeting the gut microbiota and metabolites to modify the disease trajectory.}, } @article {pmid39588199, year = {2024}, author = {Cabrita, ARJ and Barroso, C and Fontes-Sousa, AP and Correia, A and Teixeira, L and Maia, MRG and Vilanova, M and Yergaliyev, T and Camarinha-Silva, A and Fonseca, AJM}, title = {Assessing functional properties of diet protein hydrolysate and oil from fish waste on canine immune parameters, cardiac biomarkers, and fecal microbiota.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1449141}, pmid = {39588199}, issn = {2297-1769}, abstract = {Locally produced fish hydrolysate and oil from the agrifood sector comprises a sustainable solution both to the problem of fish waste disposal and to the petfood sector with potential benefits for the animal's health. This study evaluated the effects of the dietary replacement of mainly imported shrimp hydrolysate (5%) and salmon oil (3%; control diet) with locally produced fish hydrolysate (5%) and oil (3.2%) obtained from fish waste (experimental diet) on systemic inflammation markers, adipokines levels, cardiac function and fecal microbiota of adult dogs. Samples and measurements were taken from a feeding trial conducted according to a crossover design with two diets (control and experimental diets), six adult Beagle dogs per diet and two periods of 6 weeks each. The experimental diet, with higher docosahexaenoic (DHA) and eicosapentaenoic (EPA) acids contents, decreased plasmatic triglycerides and the activity of angiotensin converting enzyme, also tending to decrease total cholesterol. No effects of diet were observed on serum levels of the pro-inflammatory cytokines interleukin (IL)-1β, IL-8, and IL-12/IL-23 p40, and of the serum levels of the anti-inflammatory adipokine adiponectin. Blood pressure, heart rate and echocardiographic measurements were similar between diets with the only exception of left atrial to aorta diameter ratio that was higher in dogs fed the experimental diet, but without clinical relevance. Diet did not significantly affect fecal immunoglobulin A concentration. Regarding fecal microbiome, Megasphaera was the most abundant genus, followed by Bifidobacterium, Fusobacterium, and Prevotella, being the relative abundances of Fusobacterium and Ileibacterium genera positively affected by the experimental diet. Overall, results from the performed short term trial suggest that shrimp hydrolysate and salmon oil can be replaced by protein hydrolysate and oil from fish by-products without affecting systemic inflammatory markers, cardiac structure and function, but potentially benefiting bacterial genera associated with healthy microbiome. Considering the high DHA and EPA contents and the antioxidant properties of fish oil and hydrolysate, it would be worthwhile in the future to assess their long-term effects on inflammatory markers and their role in spontaneous canine cardiac diseases and to perform metabolomic and metagenomics analysis to elucidate the relevance of microbiota changes in the gut.}, } @article {pmid39587811, year = {2024}, author = {Xu, N and Chen, B and Wang, Y and Lei, C and Zhang, Z and Ye, Y and Jin, M and Zhang, Q and Lu, T and Dong, H and Shou, J and Penuelas, J and Zhu, YG and Qian, H}, title = {Integrating Anthropogenic-Pesticide Interactions Into a Soil Health-Microbial Index for Sustainable Agriculture at Global Scale.}, journal = {Global change biology}, volume = {30}, number = {11}, pages = {e17596}, doi = {10.1111/gcb.17596}, pmid = {39587811}, issn = {1365-2486}, support = {22376187//National Natural Science Foundation of China/ ; 21777144//National Natural Science Foundation of China/ ; 21976161//National Natural Science Foundation of China/ ; LZ23B070001//Zhejiang Provincial Natural Science Foundation of China/ ; 2021YFA0909500//National Key Research and Development Program of China/ ; MMLKF23-03//Open Funding Project of the State Key Laboratory of Microbial Metabolism/ ; TED2021-132627 B-I00//MCIN, AEI/10.13039/501100011033 European Union Next Generation EU/PRTR/ ; PID2022-140808NB-I00//Spanish Government grants/ ; }, mesh = {*Soil Microbiology ; *Agriculture/methods ; *Pesticides/analysis ; Microbiota ; Sustainable Development ; Soil/chemistry ; Metagenome ; Soil Pollutants/analysis ; Machine Learning ; }, abstract = {Soil microbiota in intensive agriculture are threatened by pesticides, economic activities, and land-use changes. However, the interactions among these anthropogenic factors remain underexplored. By analyzing 2356 soil metagenomes from around the world, we developed a comprehensive soil health-microbial index that integrates microbial diversity, nutrient cycling potential, metabolic potential, primary productivity, and health risks to assess how the soil microbiota respond to anthropogenic factors. Our results indicated that the health-microbial index was the lowest with severe pesticide contamination. Pesticides, in combination with other anthropogenic and climatic factors, exacerbate the decline in this index. Machine learning predictions suggest that the health-microbial index in approximately 26% of global farmland could decline between 2015 and 2040, even under sustainable development scenarios. Even with strategies to reduce pesticide usage, we cannot completely halt the decline in the health-microbial index. Our findings highlight that sustaining soil microbial health on a global scale requires addressing not only pesticide management but also broader anthropogenic impacts.}, } @article {pmid39587696, year = {2024}, author = {Cuevas-Martínez, R and González-Chávez, SA and Bermúdez, M and Salas-Leiva, JS and Vázquez-Olvera, G and Hinojos-Gallardo, LC and Chaparro-Barrera, E and Pacheco-Silva, C and Romero-Sánchez, C and Villegas-Mercado, CE and Pacheco-Tena, C}, title = {Intermittent fasting reduces inflammation and joint damage in a murine model of rheumatoid arthritis: insights from transcriptomic and metagenomic analyses.}, journal = {BMC rheumatology}, volume = {8}, number = {1}, pages = {64}, pmid = {39587696}, issn = {2520-1026}, abstract = {BACKGROUND: Intermittent fasting (IF) has shown benefits in various pathological conditions. Although its anti-inflammatory potential has been recognized, its effects on the mechanism underlying rheumatoid arthritis (RA) remain insufficiently characterized. This study aimed to investigate the effects of IF in a murine model of RA.

METHODS: Collagen-induced arthritis (CIA) was developed in sixteen male DBA/1 mice, randomly assigned to two groups, with one undergoing IF every other day for four weeks. The effects of IF on joint inflammation and remodeling were evaluated clinically, histologically, and through tomography. Transcriptomic changes were characterized using expression microarrays, validated by RT-qPCR, and confirmed by immunohistochemistry. Additionally, modifications in gut microbiota were assessed through 16 S sequencing.

RESULTS: Mice subjected to IF significantly reduced the incidence and severity of clinical arthritis. Histological and radiographic assessments confirmed a decrease in inflammation and joint damage. Transcriptomic analysis revealed that IF led to the upregulation of 364 genes and the downregulation of 543 genes, with notable reductions in inflammatory signaling pathways associated with RA-related genes, including Cd72, Cd79a, Ifna, Il33, and Bglap 2. Notably, IL33 emerged as a pivotal mediator in the inflammatory processes mitigated by fasting. Key regulators associated with IF effects, such as CEBPA, FOXO1, HIF1A, PPARG, and PPARA, were identified, indicating a complex interplay between metabolic and inflammatory pathways. Furthermore, differential expression of microRNAs and lncRNAs, including miR-15b, miR-103-2, miR-302a, miR-6985, and miR- 5624, was observed. Metagenomic analysis indicated that IF enhanced the abundance and diversity of the gut microbiome, explicitly promoting anti-inflammatory bacterial populations, notably within the genus Ruminococcaceae.

CONCLUSION: Our findings suggest that IF exerts significant anti-inflammatory and immunoregulatory effects in the context of CIA. Given its non-risky nature, further investigation into the potential benefits of IF in patients with RA is warranted.

CLINICAL TRIAL NUMBER: Not applicable.}, } @article {pmid39587555, year = {2024}, author = {Halford, C and Le Viet, T and Edge, K and Russell, P and Moore, N and Trim, F and Moragues-Solanas, L and Lukaszewski, R and Weller, SA and Gilmour, M}, title = {Development of a clinical metagenomics workflow for the diagnosis of wound infections.}, journal = {BMC medical genomics}, volume = {17}, number = {1}, pages = {276}, pmid = {39587555}, issn = {1755-8794}, support = {BB/CCG1860/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/X011011/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/R015937/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; *Metagenomics/methods ; *Wound Infection/microbiology/diagnosis ; *Workflow ; Bacteria/genetics/isolation & purification/classification ; }, abstract = {BACKGROUND: Wound infections are a common complication of injuries negatively impacting the patient's recovery, causing tissue damage, delaying wound healing, and possibly leading to the spread of the infection beyond the wound site. The current gold-standard diagnostic methods based on microbiological testing are not optimal for use in austere medical treatment facilities due to the need for large equipment and the turnaround time. Clinical metagenomics (CMg) has the potential to provide an alternative to current diagnostic tests enabling rapid, untargeted identification of the causative pathogen and the provision of additional clinically relevant information using equipment with a reduced logistical and operative burden.

METHODS: This study presents the development and demonstration of a CMg workflow for wound swab samples. This workflow was applied to samples prospectively collected from patients with a suspected wound infection and the results were compared to routine microbiology and real-time quantitative polymerase chain reaction (qPCR).

RESULTS: Wound swab samples were prepared for nanopore-based DNA sequencing in approximately 4 h and achieved sensitivity and specificity values of 83.82% and 66.64% respectively, when compared to routine microbiology testing and species-specific qPCR. CMg also enabled the provision of additional information including the identification of fungal species, anaerobic bacteria, antimicrobial resistance (AMR) genes and microbial species diversity.

CONCLUSIONS: This study demonstrates that CMg has the potential to provide an alternative diagnostic method for wound infections suitable for use in austere medical treatment facilities. Future optimisation should focus on increased method automation and an improved understanding of the interpretation of CMg outputs, including robust reporting thresholds to confirm the presence of pathogen species and AMR gene identifications.}, } @article {pmid39587335, year = {2024}, author = {Liu, Y and Du, S and Sun, L and Li, Y and Liu, M and Sun, P and Bai, B and Ge, G and Jia, Y and Wang, Z}, title = {Volatile metabolomics and metagenomics reveal the effects of lactic acid bacteria on alfalfa silage quality, microbial communities, and volatile organic compounds.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1565}, pmid = {39587335}, issn = {2399-3642}, mesh = {*Volatile Organic Compounds/metabolism/analysis ; *Silage/microbiology/analysis ; *Metabolomics/methods ; *Microbiota ; *Metagenomics/methods ; *Medicago sativa/microbiology/metabolism ; Lactobacillales/metabolism/genetics ; Lactobacillus plantarum/metabolism/genetics ; }, abstract = {Lactic acid bacteria metabolism affects the composition of volatile organic compounds (VOCs) in alfalfa silage, which results in differences of odor and quality. The aim of this study was to reveal the effects of commercial Lactobacillus plantarum (CL), screened Lactobacillus plantarum (LP), and screened Pediococcus pentosaceus (PP) on quality, microbial community, and VOCs of alfalfa silage based on volatile metabolomics and metagenomics. The results showed that the LP and PP groups had higher sensory and quality grades, and the dominant bacteria were Lactiplantibacillus plantarum and Pediococcus pentosaceus. The main VOCs in alfalfa silage were terpenoids (25.29%), esters (17.08%), and heterocyclic compounds (14.43%), and esters such as methyl benzoate, ethyl benzoate, and ethyl salicylate were significantly increased in the LP and PP groups (P < 0.05). Correlation analysis showed that terpenoids, esters, and alcohols with aromatic odors were positively correlated with Lactiplantibacillus plantarum and Pediococcus pentosaceus. Microbial functions in carbohydrate and amino acid metabolism, biosynthesis of secondary metabolites, and degradation of aromatic compounds were significantly enriched. In conclusion, the addition of lactic acid bacteria can increase the aromatic substances in silage and further improve silage odor and quality.}, } @article {pmid39587088, year = {2024}, author = {Honorato, L and Paião, HGO and da Costa, AC and Tozetto-Mendoza, TR and Mendes-Correa, MC and Witkin, SS}, title = {Viruses in the female lower reproductive tract: a systematic descriptive review of metagenomic investigations.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {137}, pmid = {39587088}, issn = {2055-5008}, mesh = {Female ; Humans ; *Metagenomics/methods ; *Viruses/genetics/classification ; *Virome ; Microbiota ; Genitalia, Female/virology/microbiology ; Metagenome ; }, abstract = {The lower female reproductive tract (FRT) hosts a complex microbial environment, including eukaryotic and prokaryotic viruses (the virome), whose roles in health and disease are not fully understood. This review consolidates findings on FRT virome composition, revealing the presence of various viral families and noting significant gaps in knowledge. Understanding interactions between the virome, microbiome, and immune system will provide novel insights for preventing and managing lower genital tract disorders.}, } @article {pmid39586993, year = {2024}, author = {Zhao, Y and Bhatnagar, S}, title = {Epigenetic Modulations by Microbiome in Breast Cancer.}, journal = {Advances in experimental medicine and biology}, volume = {1465}, number = {}, pages = {55-69}, doi = {10.1007/978-3-031-66686-5_4}, pmid = {39586993}, issn = {0065-2598}, mesh = {Humans ; *Breast Neoplasms/genetics/microbiology ; *Epigenesis, Genetic ; Female ; *Tumor Microenvironment/genetics ; *Gene Expression Regulation, Neoplastic ; Microbiota/genetics ; Animals ; DNA Methylation ; Gastrointestinal Microbiome/genetics ; }, abstract = {Recent studies have identified a critical role of the diverse and dynamic microbiome in modulating various aspects of host physiology and intrinsic processes. However, the altered microbiome has also become a hallmark of cancer, which could influence the tumor microenvironment. Aberrations in epigenetic regulation of tumor suppressors, apoptotic genes, and oncogenes can accentuate breast cancer onset and progression. Interestingly, recent studies have established that the microbiota modulates the epigenetic mechanisms at global and gene-specific levels. While the mechanistic basis is unclear, the cross-talk between the microbiome and epigenetics influences breast cancer trajectory. Here, we review different epigenetic mechanisms of mammalian gene expression and summarize the host-associated microbiota distributed across the human body and their influence on cancer and other disease-related genes. Understanding this complex relationship between epigenetics and the microbiome holds promise for new insights into effective therapeutic strategies for breast cancer patients.}, } @article {pmid39586148, year = {2025}, author = {Jiang, X and Guo, H and Sun, J and Guan, Y and Xie, Z}, title = {Diagnostic value of metagenomic next-generation sequencing for bronchoalveolar lavage diagnostics in patients with lower respiratory tract infections.}, journal = {Diagnostic microbiology and infectious disease}, volume = {111}, number = {2}, pages = {116620}, doi = {10.1016/j.diagmicrobio.2024.116620}, pmid = {39586148}, issn = {1879-0070}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Female ; Retrospective Studies ; *Bronchoalveolar Lavage Fluid/microbiology/virology ; Middle Aged ; *Metagenomics/methods ; Adult ; *Respiratory Tract Infections/diagnosis/microbiology/virology ; Aged ; *Sensitivity and Specificity ; Young Adult ; Adolescent ; Child ; Child, Preschool ; Predictive Value of Tests ; Infant ; Bacterial Infections/diagnosis/microbiology ; Aged, 80 and over ; }, abstract = {BACKGROUND: Current diagnostic methods of lower respiratory tract infections (LRTIs) often lack specificity, underscoring the necessity for advanced technologies such as metagenomic next-generation sequencing (mNGS).

METHODS: This retrospective study compared bronchoalveolar lavage fluid (BALF) analysis using mNGS and conventional microbiological tests (CMT) to evaluate their effectiveness in pathogen identification and alignment with clinical diagnoses.

RESULTS: In this study involving 369 patients suspected of LTRIs, mNGS identified pathogens in 342 cases (92.7%), showing superior diagnostic performance compared to CMT (58.8%). The positive agreement and negative agreement rates of mNGS were 92.7% and 96.3%, respectively, both significantly higher than those of CMT (both p<0.001). The sensitivity, specificity, positive predictive value, and negative predictive value of mNGS were significantly higher than those of CMT, with values of 99.7% vs. 57.1%, 68.4% vs. 26.3%, 96.5% vs. 87.1%, and 96.3% vs. 6.3%, respectively (all p<0.001). Pathogen detection rates among the patients showed that 89.7% had evidence of LRTIs, with bacterial infections (20.1%), mycoplasma (13.6%), mycobacterium (4.3%), fungal (4.1%), viral (3.3%), and mixed infections (44.4%) being the most common. Furthermore, the study also differentiated the distribution of pathogens between adults and pediatric patients, and assessed the impact of pathogen types on severe outcomes using multivariate logistic regression, revealing that viral and fungal infections were more likely associated with severe symptoms, whereas mycoplasma infections typically presented with milder symptoms.

CONCLUSIONS: BALF mNGS proves effective for rapid, comprehensive pathogen detection in LRTIs, warranting its early use for enhanced diagnosis and management, especially across different age groups.}, } @article {pmid39585984, year = {2024}, author = {Padhi, C and Field, CM and Forneris, CC and Olszewski, D and Fraley, AE and Sandu, I and Scott, TA and Farnung, J and Ruscheweyh, HJ and Narayan Panda, A and Oxenius, A and Greber, UF and Bode, JW and Sunagawa, S and Raina, V and Suar, M and Piel, J}, title = {Metagenomic study of lake microbial mats reveals protease-inhibiting antiviral peptides from a core microbiome member.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {49}, pages = {e2409026121}, pmid = {39585984}, issn = {1091-6490}, support = {1-001369-000//Promedica Stiftung/ ; 205320_185077//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; 205320_219638//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; 310030_212802//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; n/a//Peter und Traudl Engelhorn Stiftung (Peter and Traudl Engelhorn Foundation)/ ; 897571//EC | Horizon Europe | Excellent Science | HORIZON EUROPE Marie Sklodowska-Curie Actions (MSCA)/ ; }, mesh = {*Lakes/microbiology ; *Antiviral Agents/pharmacology/chemistry ; *Microbiota ; *Metagenomics/methods ; Protease Inhibitors/pharmacology/metabolism ; Peptides/metabolism/chemistry ; Multigene Family ; Metagenome ; India ; Bacteria/drug effects/genetics/metabolism ; }, abstract = {In contrast to the large body of work on bioactive natural products from individually cultivated bacteria, the chemistry of environmental microbial communities remains largely elusive. Here, we present a comprehensive bioinformatic and functional study on a complex and interaction-rich ecosystem, algal-bacterial (microbial) mats of Lake Chilika in India, Asia's largest brackish water body. We report the bacterial compositional dynamics over the mat life cycle, >1,300 reconstructed environmental genomes harboring >2,200 biosynthetic gene clusters (BGCs), the successful cultivation of a widespread core microbiome member belonging to the genus Rheinheimera, heterologous reconstitution of two silent Rheinheimera biosynthetic pathways, and new compounds with potent protease inhibitory and antiviral activities. The identified substances, posttranslationally modified peptides from the graspetide and spliceotide families, were targeted among the large BGC diversity by applying a strategy focusing on recurring multi-BGC loci identified in diverse samples, suggesting their presence in successful colonizers. In addition to providing broad insights into the biosynthetic potential of a poorly studied community from sampling to bioactive substances, the study highlights the potential of ribosomally synthesized and posttranslationally modified peptides as a large, underexplored resource for antiviral drug discovery.}, } @article {pmid39585972, year = {2024}, author = {Jaffe, AL and Harrison, K and Wang, RZ and Taylor-Kearney, LJ and Jain, N and Prywes, N and Shih, PM and Young, J and Rocap, G and Dekas, AE}, title = {Cyanobacteria from marine oxygen-deficient zones encode both form I and form II Rubiscos.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {49}, pages = {e2418345121}, pmid = {39585972}, issn = {1091-6490}, support = {n/a//Stanford Science Fellows/ ; OCE-PRF//NSF (NSF)/ ; OCE-2143035//NSF (NSF)/ ; OCE-2022911//NSF (NSF)/ ; 561645//Simons Foundation (SF)/ ; }, mesh = {*Oxygen/metabolism ; *Ribulose-Bisphosphate Carboxylase/metabolism/genetics ; Seawater/microbiology ; Cyanobacteria/metabolism/genetics ; Carbon Cycle ; Photosynthesis ; Prochlorococcus/metabolism/genetics ; Phylogeny ; Bacterial Proteins/metabolism/genetics ; Carbon Dioxide/metabolism ; Pacific Ocean ; }, abstract = {Cyanobacteria are highly abundant in the marine photic zone and primary drivers of the conversion of inorganic carbon into biomass. To date, all studied cyanobacterial lineages encode carbon fixation machinery relying upon form I Rubiscos within a CO2-concentrating carboxysome. Here, we report that the uncultivated anoxic marine zone (AMZ) IB lineage of Prochlorococcus from pelagic oxygen-deficient zones (ODZs) harbors both form I and form II Rubiscos, the latter of which are typically noncarboxysomal and possess biochemical properties tuned toward low-oxygen environments. We demonstrate that these cyanobacterial form II enzymes are functional in vitro and were likely acquired from proteobacteria. Metagenomic analysis reveals that AMZ IB are essentially restricted to ODZs in the Eastern Pacific, suggesting that form II acquisition may confer an advantage under low-O2 conditions. AMZ IB populations express both forms of Rubisco in situ, with the highest form II expression at depths where oxygen and light are low, possibly as a mechanism to increase the efficiency of photoautotrophy under energy limitation. Our findings expand the diversity of carbon fixation configurations in the microbial world and may have implications for carbon sequestration in natural and engineered systems.}, } @article {pmid39585730, year = {2024}, author = {Khleborodova, A and Gamboa-Tuz, SD and Ramos, M and Segata, N and Waldron, L and Oh, S}, title = {lefser: implementation of metagenomic biomarker discovery tool, LEfSe, in R.}, journal = {Bioinformatics (Oxford, England)}, volume = {40}, number = {12}, pages = {}, pmid = {39585730}, issn = {1367-4811}, support = {R01 CA230551/CA/NCI NIH HHS/United States ; R01CA230551//National Cancer Institute of the National Institutes of Health/ ; }, mesh = {*Metagenomics/methods ; *Software ; Animals ; *Algorithms ; Mice ; Humans ; *Biomarkers ; }, abstract = {SUMMARY: LEfSe is a widely used Python package and Galaxy module for metagenomic biomarker discovery and visualization, utilizing the Kruskal-Wallis test, Wilcoxon Rank-Sum test, and Linear Discriminant Analysis. R/Bioconductor provides a large collection of tools for metagenomic data analysis but has lacked an implementation of this widely used algorithm, hindering benchmarking against other tools and incorporation into R workflows. We present the lefser package to provide comparable functionality within the R/Bioconductor ecosystem of statistical analysis tools, with improvements to the original algorithm for performance, accuracy, and reproducibility. We benchmark the performance of lefser against the original algorithm using human and mouse metagenomic datasets.

Our software, lefser, is distributed through the Bioconductor project (https://www.bioconductor.org/packages/release/bioc/html/lefser.html), and all the source code is available in the GitHub repository https://github.com/waldronlab/lefser.}, } @article {pmid39584840, year = {2024}, author = {Bernardin, JR and Young, EB and Gray, SM and Bittleston, LS}, title = {Bacterial community function increases leaf growth in a pitcher plant experimental system.}, journal = {mSystems}, volume = {9}, number = {12}, pages = {e0129824}, pmid = {39584840}, issn = {2379-5077}, mesh = {*Plant Leaves/microbiology/growth & development ; *Sarraceniaceae/microbiology ; *Microbiota/physiology ; *Bacteria/genetics ; Metagenomics ; }, abstract = {UNLABELLED: Across diverse ecosystems, bacteria and their hosts engage in complex relationships having negative, neutral, or positive interactions. However, the specific effects of leaf-associated bacterial community functions on plant growth are poorly understood. Although microbes can promote plant growth through various biochemical mechanisms, investigating the community's functional contributions to plant growth remains to be explored. To address this gap, we characterized the relationships between bacterial community function and host plant growth in the purple pitcher plant (Sarracenia purpurea). The main aim of our research was to investigate how different bacterial community functions affect the growth and nutrient content in the plant. Previous research has suggested that microbial communities aid in prey decomposition and subsequent nutrient acquisition in carnivorous plants, including S. purpurea. However, the specific functional roles of bacterial communities in plant growth and nutrient uptake are not well known. In this study, sterile, freshly opened pitchers were inoculated with three functionally distinct, pre-assembled bacterial communities. Bacterial community composition and function were measured over 8 weeks using physiological assays, metagenomics, and metatranscriptomics. Distinct community functions affected plant traits; a bacterial community enriched in decomposition was associated with larger leaves with almost double the biomass of control pitchers. Physiological differences in bacterial communities were supported by metatranscriptomics; for example, the bacterial community with the highest chitinase activity had greater expression of transcripts associated with chitinase enzymes. The relationship between bacterial community function and plant growth observed here indicates potential mechanisms, such as chitinase activity, for host-associated bacterial functions to support pitcher plant growth.

IMPORTANCE: This study addresses a gap in understanding the relationships between bacterial community function and plant growth. We inoculated sterile, freshly opened pitcher plant leaves with three functionally distinct bacterial communities to uncover potential mechanisms through which bacterial functions support plant health and growth. Our findings demonstrate that distinct community functions significantly influence plant traits, with some bacterial communities supporting more plant growth than in control pitchers. These results highlight the ecological roles of microbial communities in plants and thus ecosystems and suggest that nutrient cycling is an important pathway through which microbes support host plant health. This research provides valuable insights into plant-microbe interactions and the effects of diverse microbial community functions.}, } @article {pmid39584815, year = {2024}, author = {Holman, DB and Gzyl, KE and Kommadath, A}, title = {Florfenicol administration in piglets co-selects for multiple antimicrobial resistance genes.}, journal = {mSystems}, volume = {9}, number = {12}, pages = {e0125024}, pmid = {39584815}, issn = {2379-5077}, mesh = {Animals ; *Thiamphenicol/analogs & derivatives/pharmacology/administration & dosage ; Swine/microbiology ; *Anti-Bacterial Agents/pharmacology/administration & dosage ; *Feces/microbiology ; Drug Resistance, Multiple, Bacterial/genetics/drug effects ; Drug Resistance, Bacterial/genetics/drug effects ; }, abstract = {Antimicrobial use in food-producing animals such as pigs is a significant issue due to its association with antimicrobial resistance. Florfenicol is a broad-spectrum phenicol antibiotic used in swine for various indications; however, its effect on the swine microbiome and resistome is largely unknown. This study investigated these effects in piglets treated intramuscularly with florfenicol at 1 and 7 days of age. Fecal samples were collected from treated (n = 30) and untreated (n = 30) pigs at nine different time points up until 140 days of age, and the fecal metagenomes were sequenced. The fecal microbiomes of the two groups of piglets were most dissimilar in the immediate period following florfenicol administration. These differences were driven in part by an increase in the relative abundance of Clostridium scindens, Enterococcus faecalis, and Escherichia spp. in the florfenicol-treated piglets and Fusobacterium spp., Pauljensenia hyovaginalis, and Ruminococcus gnavus in the control piglets. In addition to selecting for florfenicol resistance genes (floR, fexA, and fexB), florfenicol also selected for genes conferring resistance to the aminoglycosides, beta-lactams, or sulfonamides up until weaning at 21 days of age. Florfenicol-resistant Escherichia coli isolated from these piglets were found to carry a plasmid with floR, along with tet(A), aph(6)-Id, aph(3″)-Ib, sul2, and blaTEM-1/blaCMY-2. A plasmid carrying fexB and poxtA (phenicols and oxazolidinones) was identified in florfenicol-resistant Enterococcus avium, Enterococcus faecium, and E. faecalis isolates from the treated piglets. This study highlights the potential for co-selection and perturbation of the fecal microbial community in pre-weaned piglets administered florfenicol.IMPORTANCEAntimicrobial use remains a serious challenge in food-animal production due to its linkage with antimicrobial resistance. Antimicrobial resistance can reduce the efficacy of veterinary treatment and can potentially be transferred to humans through the food chain or direct contact with animals and their environment. In this study, early-life florfenicol treatment in piglets altered the composition of the fecal microbiome and selected for many unrelated antimicrobial resistance genes up until weaning at 21 days of age. Part of this co-selection process appeared to involve an Escherichia coli plasmid carrying a florfenicol resistance gene along with genes conferring resistance to at least four other antimicrobial classes. In addition, florfenicol selected for certain genes that provide resistance to multiple antimicrobial classes, including the oxazolidinones. These results highlight that florfenicol can co-select for multiple antimicrobial resistance genes, and their presence on mobile genetic elements suggests the potential for transfer to other bacteria.}, } @article {pmid39583548, year = {2024}, author = {Romero-Yahuitl, V and Zarco-González, KE and Toriz-Nava, AL and Hernández, M and Velázquez-Fernández, JB and Navarro-Noya, YE and Luna-Guido, M and Dendooven, L}, title = {The archaeal and bacterial community structure in composted cow manures is defined by the original populations: a shotgun metagenomic approach.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1425548}, pmid = {39583548}, issn = {1664-302X}, abstract = {INTRODUCTION: Organic wastes are composted to increase their plant nutritional value, but little is known about how this might alter the bacterial and archaeal community structure and their genes.

METHODS: Cow manure was collected from three local small-scale farmers and composted under controlled conditions, while the bacterial and archaeal communities were determined using shotgun metagenomics at the onset and after 74 days of composting.

RESULTS: The bacterial, archaeal, methanogen, methanotrophs, methylotroph, and nitrifying community structures and their genes were affected by composting for 74 days, but the original composition of these communities determined the changes. Most of these archaeal and bacterial groups showed considerable variation after composting and between the cow manures. However, the differences in the relative abundance of their genes were much smaller compared to those of the archaeal or bacterial groups.

DISCUSSION: It was found that composting of different cow manures did not result in similar bacterial or archaeal communities, and the changes that were found after 74 days were defined by the original populations. However, more research is necessary to determine if other composting conditions will give the same results.}, } @article {pmid39583543, year = {2024}, author = {Li, Q and Lian, Y and Zhang, K and Chen, J and Chen, L and Wu, J and Zhang, Y and Chen, M and Zhang, W and Lu, M and Ma, J and Bai, A}, title = {Virome of red imported fire ants by metagenomic analysis in Guangdong, southern China.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1479934}, pmid = {39583543}, issn = {1664-302X}, abstract = {The red imported fire ant (RIFA) has made China its habitat for approximately 25 years, but few reports have described the species and amount of virus circulating in it. Researchers are currently exploring viruses associated with RIFAs as potential biological control agents against invasive ants. The present meta-transcriptome analysis revealed the virome of red imported fire ants in Guangdong, southern China, which included 17 viruses, including Solenopsis invicta virus 4-GD (SINV-4) and Guangdong Polycipiviridae ant virus 1 (GPAV1) in the Polycipiviridae family; Solenopsis invicta virus 1-GD (SINV-1), and Guangdong Dicistroviridae ant virus 2-3 (GDAV2-3) in the Dicistroviridae family; Guangdong Iflaviridae ant virus 4-9 (GIAV4-9) in the Iflaviridae family; Guangdong Parvoviridae ant virus 10 (GPAV10) in the Parvoviridae family; and Guangdong ant virus 11-15 (GAV11-15). A total of 15 novel viruses and 2 known viruses were identified in this study. These findings reveal the virome of red imported fire ants in Guangdong Province and present a different result from that of a similar study reported in the United States, providing more choices for potential classical biological control agents against red imported fire ants in China.}, } @article {pmid39583430, year = {2024}, author = {Minoretti, P and Fontana, JM and Yilmaz, Y}, title = {Pilots, Astronauts, and the Aerospace Microbiota: A Narrative Review of Occupational Impact.}, journal = {Cureus}, volume = {16}, number = {10}, pages = {e72268}, pmid = {39583430}, issn = {2168-8184}, abstract = {The human microbiota plays a crucial role in maintaining health and preventing disease; however, the effects of occupational exposure on the microbiota of aircrew and astronauts are not fully understood. This narrative review aims to synthesize the current knowledge on microbiota alterations in aerospace medicine, assess the potential of probiotics as a countermeasure, and identify key gaps that warrant further research. The references were identified through searching PubMed for English articles published between 2010 and 2024, using keywords related to microbiota, probiotics, aviation, spaceflight, pilots, and astronauts. Additionally, the bibliographies of relevant papers were reviewed. Studies in aerospace medicine were selected based on their focus on the occupational impact on microbiota and the use of probiotics in this context. For aircrew, initial studies indicate a decrease in beneficial gut bacteria, suggesting that probiotics could enhance gastrointestinal health, immunity, and overall well-being. However, unsupervised use of probiotics carries potential risks. Conversely, spaceflight induces significant changes in the gut, skin, oral, and nasal microbiota of astronauts, characterized by altered diversity and abundance of specific microbial taxa. These changes include a relative decrease in the abundance of beneficial gut bacteria, an increase in opportunistic pathogens, and evidence of microbial transfer between astronauts and spacecraft surfaces. While simulated space studies suggest the potential for probiotics to mitigate dysbiosis, direct testing done during actual spaceflight is lacking. The observed microbiota changes during spaceflight are associated with various health implications, including alterations in metabolic pathways and interactions between the microbial metabolic capabilities and the host's metabolism. In conclusion, this review highlights the profound impact of spaceflight on astronaut microbiota and the promising role of probiotics as an intervention in both space and aviation medicine. However, significant research gaps remain. These include elucidating the functional implications of microbial shifts, developing personalized countermeasures, and validating the efficacy of probiotics during spaceflight. Future studies should leverage advanced tools such as metagenomic analysis and longitudinal tracking of astronaut health to inform targeted interventions that support the well-being of aerospace personnel. Integrating data across different sites of the body and missions, facilitated by resources like the Space Omics and Medical Atlas (SOMA), can help identify consistent microbial changes induced by the unique occupational conditions of spaceflight and aviation. This integrated approach will be crucial for developing effective microbiota-based countermeasures to mitigate the occupational health risks associated with space and aviation.}, } @article {pmid39583157, year = {2024}, author = {Guo, RM and Li, XX and Zhou, YH and Liu, YJ and Li, J and Fu, GW and Zhao, H and Zhang, X and Zhao, YC}, title = {Early mNGS testing for diagnose and prognostic prediction of early onset pneumonia among in-hospital cardiac arrest patients undergoing extracorporeal cardiopulmonary resuscitation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1382273}, pmid = {39583157}, issn = {2235-2988}, mesh = {Humans ; Male ; Female ; Middle Aged ; *Extracorporeal Membrane Oxygenation ; Prognosis ; Retrospective Studies ; *Cardiopulmonary Resuscitation ; *Heart Arrest/therapy ; *High-Throughput Nucleotide Sequencing ; Metagenomics/methods ; Aged ; Pneumonia/diagnosis ; Bronchoalveolar Lavage Fluid/microbiology ; Adult ; }, abstract = {OBJECTIVES: Metagenomic next-generation sequencing (mNGS) is emerging as a novel diagnostic technology for various infectious diseases; however, limited studies have investigated its application in etiological diagnosis of early onset pneumonia (EOP) among patients undergoing extracorporeal cardiopulmonary resuscitation (ECPR) following in-hospital cardiac arrest (IHCA), The clinical significance of early mNGS in predicting short-term prognosis of IHCA patients after ECPR remains unclear.

METHODS: This retrospective study included 76 patients with IHCA who underwent ECPR at the First Affiliated Hospital of Zhengzhou University from January 2018 to December 2022. Baseline characteristics and etiological data of all patients during their hospitalization were collected and statistically analyzed. The primary outcome of this study was the diagnosis of EOP, while the secondary outcomes included successful extracorporeal membrane oxygenation (ECMO) weaning and survival at discharge. Additionally, the characteristics of bronchoalveolar lavage fluid (BALF) flora in these patients were compared by analyzing both mNGS results and culture results.

RESULTS: Multivariate logistic regression were employed to analyze the predictors of ECMO weaning failure, mortality at discharge, and the incidence of EOP. Ultimately, patients with lower SOFA scores on admission [OR (95%CI): 1.447 (1.107-1.890), p=0.007] and those who underwent early mNGS testing within 48 hours after ECPR [OR (95%CI): 0.273 (0.086-0.865), p=0.027] demonstrated a higher probability of successful weaning from ECMO. Patients with higher SOFA scores on admission [OR (95%CI): 2.404 (1.422-4.064), p=0.001], and elevated lactate levels [OR (95%CI): 1.176 (1.017-1.361), p=0.029] exhibited an increased likelihood of mortality at discharge. Furthermore, early mNGS detection [OR (95%CI): 0.186 (0.035-0.979), p=0.047], and lower CRP levels (48h-7d after ECMO) [OR (95%CI):1.011 (1.003-1.019), p=0.006] were associated with a reduced incidence of EOP. In addition, the pathogens detected by mNGS within 48 hours after ECPR were mainly oral colonizing bacteria and viruses, and viruses were in the majority, while all BALF cultures were negative. In contrast, between 48 hours and 7 days after ECPR, BALF cultures were positive in all EOP patients.

CONCLUSIONS: Early mNGS testing to identify microbial flora facilitates timely adjustment of antibiotic regimens, thereby reducing the incidence of EOP and improving short-term prognosis in patients undergoing ECPR following IHCA.}, } @article {pmid39582659, year = {2024}, author = {Chen, X and Yan, F and Qu, D and Wan, T and Xi, L and Hu, CY}, title = {Aroma characterization of Sichuan and Cantonese sausages using electronic nose, gas chromatography-mass spectrometry, gas chromatography-olfactometry, odor activity values and metagenomic.}, journal = {Food chemistry: X}, volume = {24}, number = {}, pages = {101924}, pmid = {39582659}, issn = {2590-1575}, abstract = {The interest of Chinese consumers in meat-free sausages has increased considerably due to their health benefits, but the aroma quality is far from reaching the traditional fermented meat sausages. This study evaluated the aroma characterization of Sichuan and Cantonese sausages using electronic nose (E-nose), gas chromatography-mass spectrometry (GC-MS), gas chromatography-olfactometry (GC-O), odor activity values (OAVs) and metagenomic. Ninety-eight volatile compounds were identified. Among them, 23 odorants were perceived, and their intensity differed in the two groups of sausages. There was a significant difference in the volatile compound profile between Sichuan and Cantonese cooked sausages. E-nose sensors could differentiate them through specific responses to these volatile compounds. Furthermore, there was a significant difference in microbial communities between Sichuan and Cantonese sausages. For aroma quality improvement of meat-free sausages, studies should focus on controlling the formation of aroma compounds by aroma precursors and using different microorganisms to produce diverse meat aromas. Our results provide a reference for the implementation of these strategies.}, } @article {pmid39582622, year = {2024}, author = {Nie, M and Yue, G and Wang, L and Zhang, Y}, title = {Short-term organic fertilizer substitution increases sorghum yield by improving soil physicochemical characteristics and regulating microbial community structure.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1492797}, pmid = {39582622}, issn = {1664-462X}, abstract = {INTRODUCTION: Chemical fertilizer reduction combined with organic fertilizer (organic fertilizer substitution) has a positive impact on crop productivity and sustainable development. However, the effects of short-term organic fertilizer substitution on microbial community structure and functions of sorghum rhizosphere soil and on sorghum yield remain unclear. Herein, this study investigated the short-term effects of organic fertilizer substitution on sorghum soil physicochemical properties, microbial community structure and enzyme activities using Metagenomic sequencing technology.

METHODS: The fertilization treatment included no fertilization (CK), pure chemical fertilizer N (CF), substitution of 25% chemical fertilizer N with organic N (NF25), substitution of 50% chemical fertilizer N with organic N (NF50), substitution of 75% chemical fertilizer N with organic N (NF75), and pure organic fertilizer N (NF100); soil samples were collected and analyzed in the flowering period of sorghum.

RESULTS AND DISCUSSION: The results showed that the suitable organic fertilizer substitution rate of sorghum field was 50%, and its yield was the highest among all treatments (9789.9 kg/hm[2]). Compared with the CF treatment, a medium ratio (50%) of organic fertilizer substitution significantly reduced soil alkalization (by 3.05%), improved soil nutrients, enhanced soil enzyme activities, and increased sorghum yield (P < 0.05). After organic fertilizer substitution treatment, higher protein, fat, and total starch levels accumulated in sorghum grains, and the tannin content of grains decreased. The effect of organic fertilizer substitution on bacterial diversity was greater than that on fungal diversity. Among the dominant bacterial phyla, the medium ratio of organic substitution treatment significantly increased the relative abundances of Proteobacteria (by 3.57%) and Actinomycetes (by 14.94%), and decreased the relative abundances of Acidobacteria (by 5.18%) and Planctomycetes (by 7.76%) compared with no fertilization, while the dominant fungal phyla did not respond significantly to the addition of organic fertilizer. Organic fertilizer substitution also improved soil microbial metabolic pathways, biosynthesis of secondary metabolites, and carbon metabolism. The biomarkers enriched in inorganic fertilizer treatment and organic fertilizer substitution treatments had similar relevant environmental elements but reversed correlation trends. Moreover, soil Alkali-hydrolyzable nitrogen and L-leucine aminopeptidase were important environmental factors influencing the structure of bacterial and fungal communities in sorghum soils, respectively. Soil nutrient levels and microbial communities together explained the variation in annual sorghum yield. The results of this study provide evidence that short-term organic fertilizer substitution increases sorghum yield by improving soil properties and regulating microbial community structure.}, } @article {pmid39582241, year = {2024}, author = {Zhang, M and Zhang, L and Suo, B and Wei, Y and Xu, Y and Jiang, M and Dong, J and Li, X and Song, Z and Liu, D}, title = {Distribution Characteristics and Impacting Factors of Drug CYP Enzymes and Transporters in the Gastrointestinal Tract of Chinese Healthy Subjects.}, journal = {Clinical pharmacology and therapeutics}, volume = {}, number = {}, pages = {}, doi = {10.1002/cpt.3497}, pmid = {39582241}, issn = {1532-6535}, abstract = {The abundance of drug metabolic enzymes (DMEs) and transporters (DTs) in the human gastrointestinal tract significantly affects xenobiotic exposure in the circulating system, the basis of these compounds acting on humans. However, accurately predicting individual exposure in healthy subjects remains challenging due to limited data on protein levels throughout the gastrointestinal tract within the same individuals and inadequate assessment of factors influencing these levels. Therefore, we conducted a clinical study to obtain biopsy samples from 8 different gastrointestinal segments in 24 healthy Chinese volunteers. Concurrently, blood and fecal samples were collected for genotypic analysis and fecal microbiota metagenomic sequencing. Using an optimized LC-MS/MS method, we quantified the absolute protein abundance of CYP2C9, CYP2C19, CYP2D6, CYP3A4, P-gp, and BCRP from the stomach to the colon. Our results revealed significant regional differences in protein expression: CYP3A4 was the most abundant in the small intestine, whereas CYP2C9 was predominantly found in the colon. CYP2D6 was primarily located in the ileum, while other DMEs/DTs showed higher concentrations in the jejunum. Meanwhile, the enzyme abundance in the small intestine and colon and the relative ratio of transporters in different regions to the jejunum were accurately calculated, providing valuable data for refining the physiological parameters in the virtual gastrointestinal tract of Chinese healthy population in PBBMs. Additionally, BMI, IBW, sex, age, genotype, and fecal microbiota were identified as critical factors influencing the protein levels of these DMEs/DTs throughout the gastrointestinal tract, with notable regional differences. Consequently, this study provides a unique foundation for understanding xenobiotic absorption in humans.}, } @article {pmid39582065, year = {2024}, author = {Velsko, IM and Fagernäs, Z and Tromp, M and Bedford, S and Buckley, HR and Clark, G and Dudgeon, J and Flexner, J and Galipaud, JC and Kinaston, R and Lewis, CM and Matisoo-Smith, E and Nägele, K and Ozga, AT and Posth, C and Rohrlach, AB and Shing, R and Simanjuntak, T and Spriggs, M and Tamarii, A and Valentin, F and Willie, E and Warinner, C}, title = {Exploring the potential of dental calculus to shed light on past human migrations in Oceania.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {10191}, pmid = {39582065}, issn = {2041-1723}, support = {EXC 2051, 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SRC 8038-06//National Geographic Society/ ; }, mesh = {Humans ; *Human Migration/history ; *Dental Calculus/microbiology/history ; Oceania ; *Microbiota/genetics ; Archaeology ; Phylogeny ; Pacific Islands ; Asia, Southeastern ; Metagenomics/methods ; DNA, Ancient/analysis ; History, Ancient ; Bacteria/genetics/classification/isolation & purification ; }, abstract = {The Pacific islands and Island Southeast Asia have experienced multiple waves of human migrations, providing a case study for exploring the potential of ancient microbiomes to study human migration. We perform a metagenomic study of archaeological dental calculus from 102 individuals, originating from 10 Pacific islands and 1 island in Island Southeast Asia spanning ~3000 years. Oral microbiome DNA preservation in calculus is far higher than that of human DNA in archaeological bone, and comparable to that of calculus from temperate regions. Oral microbial community composition is minimally driven by time period and geography in Pacific and Island Southeast Asia calculus, but is found to be distinctive compared to calculus from Europe, Africa, and Asia. Phylogenies of individual bacterial species in Pacific and Island Southeast Asia calculus reflect geography. Archaeological dental calculus shows good preservation in tropical regions and the potential to yield information about past human migrations, complementing studies of the human genome.}, } @article {pmid39581874, year = {2024}, author = {Li, Y and Pan, G and Wang, S and Li, Z and Yang, R and Jiang, Y and Chen, Y and Li, SC and Shen, B}, title = {Comprehensive human respiratory genome catalogue underlies the high resolution and precision of the respiratory microbiome.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {1}, pages = {}, pmid = {39581874}, issn = {1477-4054}, mesh = {Humans ; *Microbiota/genetics ; Genome, Human ; Metagenome ; Respiratory System/microbiology ; Bacteria/genetics/classification ; }, abstract = {The human respiratory microbiome plays a crucial role in respiratory health, but there is no comprehensive respiratory genome catalogue (RGC) for studying the microbiome. In this study, we collected whole-metagenome shotgun sequencing data from 4067 samples and sequenced long reads of 124 samples, yielding 9.08 and 0.42 Tbp of short- and long-read data, respectively. By submitting these data with a novel assembly algorithm, we obtained a comprehensive human RGC. This high-quality RGC contains 190,443 contigs over 1 kbps and an N50 length exceeding 13 kbps; it comprises 159 high-quality and 393 medium-quality genomes, including 117 previously uncharacterized respiratory bacteria. Moreover, the RGC contains 209 respiratory-specific species not captured by the unified human gastrointestinal genome. Using the RGC, we revisited a study on a pediatric pneumonia dataset and identified 17 pneumonia-specific respiratory pathogens, reversing an inaccurate etiological conclusion due to the previous incomplete reference. Furthermore, we applied the RGC to the data of 62 participants with a clinical diagnosis of infection. Compared to the Nucleotide database, the RGC yielded greater specificity (0 versus 0.444, respectively) and sensitivity (0.852 versus 0.881, respectively), suggesting that the RGC provides superior sensitivity and specificity for the clinical diagnosis of respiratory diseases.}, } @article {pmid39581825, year = {2024}, author = {Isali, I and Almassi, N and Nizam, A and Campbell, R and Weight, C and Gupta, S and Pooja, G and Fulmes, A and Mishra, K and Abbosh, P and Bukavina, L}, title = {State of the Art: The Microbiome in Bladder Cancer.}, journal = {Urologic oncology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.urolonc.2024.11.008}, pmid = {39581825}, issn = {1873-2496}, abstract = {This review assesses the current understanding of the relationship between the human microbiome and BCa. Recognizing how the microbiome affects the tumor microenvironment provides valuable insights into cancer biology, potentially uncovering interactions that could be leveraged to develop innovative therapeutic approaches. By clarifying these intricate microbial-tumor dynamics, novel targets for microbiome-based interventions can be identified, ultimately improving treatment effectiveness and patient outcomes. Current literature lacks comprehensive insights into the effects of BCa treatment on the microbiome and the prevalence of immunotherapy-related toxicities. Further research into the microbiome's role in BCa development could bridge the gap between fundamental research and therapeutic applications. Implementing microbiome surveillance, metagenomic sequencing, and metabolomics in clinical trials could deepen our understanding of BCa and its treatment. This review explores the existing understanding of the urine, tissue, and gut microbiomes and their connections to BCa. Enhanced knowledge of these relationships can pave the way for future research to identify reliable disease predictors, prognostic markers, and novel therapeutic targets.}, } @article {pmid39581538, year = {2024}, author = {Olie, SE and Staal, SL and van de Beek, D and Brouwer, MC}, title = {Diagnosing infectious encephalitis: a narrative review.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmi.2024.11.026}, pmid = {39581538}, issn = {1469-0691}, abstract = {BACKGROUND: Diagnosing infectious encephalitis can be challenging as it can be caused by a wide range of pathogens, with viruses being the most common cause. In a substantial number of patients, no pathogen is identified despite a clinical diagnosis of infectious encephalitis. Recent advancements in diagnostic testing have introduced new methods to address this diagnostic challenge and improve pathogen detection.

OBJECTIVES: The objective of this study is to provide a comprehensive clinical approach for diagnosing infectious encephalitis and explore novel diagnostic methods.

SOURCES: We searched PubMed to identify relevant literature on diagnosing encephalitis in English up to 1 September 2024, as well as included articles known by the authors.

CONTENT: Clinical characteristics may suggest a specific cause of infectious encephalitis, but are insufficient to guide treatment decisions. Therefore, cerebrospinal fluid (CSF) examination remains the cornerstone of the diagnostic process, with CSF leucocyte count being the most reliable predictor for central nervous system infections. CSF features can be normal, however, in a proportion of patients presenting with infectious encephalitis. A definite diagnosis of infectious encephalitis is established by microbiological or histopathological tests in ∼50% of patients. Additional investigations, including neuroimaging or electroencephalography, can provide evidence for encephalitis or help to identify alternate conditions, although their role is primarily supportive. Emerging diagnostic techniques, including next-generation sequencing metagenomics and unbiased serology (Phage ImmunoPrecipitation Sequencing), have the potential to increase the proportion of patients with a confirmed diagnosis. However, these techniques are not yet practical because of their complex analysis, long turnaround times and high costs.

IMPLICATIONS: Microbiological confirmation is paramount in the diagnosis of infectious encephalitis, but it is currently established in about half of cases. Although novel techniques show promise to increase the proportion of cause-specific diagnoses, they are not yet suitable for routine use. This highlights the ongoing need for advancements in diagnostic methods.}, } @article {pmid39581260, year = {2024}, author = {Lee, YH and Park, HJ and Jeong, SJ and Auh, QS and Jung, J and Lee, GJ and Shin, S and Hong, JY}, title = {Oral microbiome profiles of gingivitis and periodontitis by next-generation sequencing among a group of hospital patients in Korea: A cross-sectional study.}, journal = {Journal of oral biosciences}, volume = {}, number = {}, pages = {100591}, doi = {10.1016/j.job.2024.100591}, pmid = {39581260}, issn = {1880-3865}, abstract = {OBJECTIVES: The oral microbiome plays an important role in the development and progression of periodontal disease. The purpose of this study was to compare microbial profiles of oral cavities in good health, with gingivitis, and in a state of periodontitis, and to identify novel pathogens involved in periodontal diseases.

METHODS: One hundred and two participants, including 33 healthy controls, 41 patients with gingivitis, and 28 patients with periodontitis, were included in this cross-sectional study. Salivary oral microbiomes were investigated using 16S rRNA metagenomic sequencing, and the microbial profiles of each group were compared using age- and sex-adjusted general linear models.

RESULTS: The abundance of amplicon sequence variants and Chao1 diversity were significantly elevated in the gingivitis and periodontitis groups relative to healthy controls (p = 0.046). Based on linear discriminant analysis (LDA) scores (>2), Tenericutes, Mollicutes, Mycoplasmatales, Mycoplasmataceae, Mycoplasma, Bacteroidaceae, and Phocaeicola were significantly enriched in the gingivitis group, and Synergistetes, Synergistia, Synergistales, Synergistaceae, Fretibacterium, Sinanaerobacter, and Filifactor were enriched in the periodontitis group. The relative abundances of Fretibacterium fastidiosum, Sinanaerobacter chloroacetimidivorans, and Filifactor alocis (q = 0.008, all bacteria) were highest in the periodontitis group and lowest in the control group. The relative abundance of Treponema denticola was significantly elevated in the periodontitis group compared to the other two groups (q = 0.024).

CONCLUSIONS: Oral microbiomes differed between groups. T. denticola, F. fastidiosum, S. chloroacetimidivorans and F. alocis were significantly more abundant in the periodontitis group than in the control group. Additionally, the abundance of T. denticola and F. fastidiosum in the periodontitis group was significantly different from that in the gingivitis group.}, } @article {pmid39580945, year = {2025}, author = {Su, Y and Feng, L and Duan, X and Peng, H and Zhao, Y and Chen, Y}, title = {Deciphering the function of Fe3O4 in alleviating propionate inhibition during high-solids anaerobic digestion: Insights of physiological response and energy conservation.}, journal = {Water research}, volume = {270}, number = {}, pages = {122811}, doi = {10.1016/j.watres.2024.122811}, pmid = {39580945}, issn = {1879-2448}, mesh = {*Propionates/metabolism/pharmacology ; Anaerobiosis ; *Methane/metabolism ; Ferric Compounds/pharmacology ; Bioreactors ; Energy Metabolism/drug effects ; }, abstract = {Fe3O4 is a recognized addictive to enhance low solid anaerobic digestion (AD), while for high solid AD challenged by acidity inhibition, its feasibility and mechanism remain unclear. In this study, the positive effect of Fe3O4 on high-solids AD of food waste by regulating microbial physiology and energy conservation to enhance mutualistic propionate methanation was documented. The methane yield was increased by 36.7 % with Fe3O4, which because Fe3O4 alleviated propionate stress on methane generation, along with improved propionate degradation and methanogenic metabolism. Fe3O4 facilitated the production of extracellular polymeric substances and the formation of tightly bio-aggregates, fostering an enriched microbial population (e.g., Smithella and Methanosaeta) to resist propionate stress. Also, Fe3O4 up-regulated the genes in stress defense system, cytomembrane biosynthesis/function, metal irons transporter, cell division and enzyme synthesis, verifying its superiority on cellular physiology. In addition, energy-conservation strategies related to intracellular and extracellular electron transfer were enhanced by Fe3O4. Specifically, the enzyme expressions involved in reversed electron transfer and electron bifurcation coupled with direct interspecies electron transfer (DIET) were upregulated by at least 2.2 times with Fe3O4, providing sufficient energy to drive thermodynamic adverse methanogenesis from propionate-stressed condition. Consequently, the reinforced enzyme expression in the dismutation and DIET pathway make it to be the predominant drivers for enhanced methanogenic propionate metabolism. This study fills the knowledge gaps of Fe3O4-induced microbial physiological and energetic strategies to resist environmental stress, and has remarkable practical implicated for restoring inhibited bioactivities.}, } @article {pmid39580871, year = {2025}, author = {Kumar, S and Bhatia, Z and Seshadri, S}, title = {Formulated chitosan microspheres remodelled the altered gut microbiota and liver miRNA in diet-induced Type-2 diabetic rats.}, journal = {Carbohydrate research}, volume = {547}, number = {}, pages = {109301}, doi = {10.1016/j.carres.2024.109301}, pmid = {39580871}, issn = {1873-426X}, mesh = {*Chitosan/pharmacology/chemistry ; Animals ; *Gastrointestinal Microbiome/drug effects ; *MicroRNAs/metabolism ; *Microspheres ; Rats ; Male ; *Diabetes Mellitus, Type 2/drug therapy/metabolism ; *Diabetes Mellitus, Experimental/drug therapy/chemically induced/metabolism ; *Liver/drug effects/pathology/metabolism ; Hypoglycemic Agents/pharmacology/chemistry ; Metformin/pharmacology ; Diet, High-Fat/adverse effects ; }, abstract = {Chitosan was formulated into a microsphere and comprehensively characterized and evaluated for its anti-inflammatory potential and anti-diabetic properties against the high sugar fat diet-induced diabetic animals. The diabetic model was induced through feeding with a high-sugar fat diet. Metformin, a standard antidiabetic drug, and CMS (chitosan microspheres) were administered orally for 90 days as reversal strategies. Upon completion of the study, the following parameters, such as serum biochemistry, cytokine analysis, tissue histology, liver miRNA sequencing, and Shotgun metagenomics studies from stool samples, were performed. SEM images of the microsphere indicated a smooth morphology, while FTIR and DSC respectively, confirmed the presence of functional groups of chitosan and the thermal stability of the formulation. Following HSFD induction, all the parameters analyzed were altered compared to the control group. In both reversal groups, serum biochemical parameters were restored, which was at par with the control. A significant increase in the anti-inflammatory cytokine IL-10, and a remarkable reduction in TNF-α and MCP-1 inflammatory cytokines were observed in both reversal groups. Tissue histology indicated improvements in low-grade inflammation, induced in the diabetic group. miR-203 was upregulated in the CMS-treated group, while miR-103 was downregulated. The study further delved into the impact on gut microbiota and KEGG. Major phyla i.e., Bacteroidetes, Cyanobacteria, Firmicutes, Proteobacteria, and Verrucomicrobia showed restoration, while upregulation of DNA polymerase zeta in T2D showed reversal after the treatment. The formulation showed reversal at par with metformin and also confirms its anti-diabetic and anti-inflammatory activities of CMS, with microfloral and miR regulatory functions.}, } @article {pmid39580566, year = {2024}, author = {Gomes, WDS and Partelli, FL and Veloso, TGR and da Silva, MCS and Moreli, AP and Moreira, TR and Pereira, LL}, title = {Effects of Coffea canephora genotypes on the microbial community of soil and fruit.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {29035}, pmid = {39580566}, issn = {2045-2322}, support = {23186000886201801//Sul Serrana of Espírito Santo Free Admission Credit Cooperative- SICOOB/ ; 23186000886201801//Sul Serrana of Espírito Santo Free Admission Credit Cooperative- SICOOB/ ; 23186000886201801//Sul Serrana of Espírito Santo Free Admission Credit Cooperative- SICOOB/ ; }, mesh = {*Coffea/microbiology/genetics ; *Soil Microbiology ; *Fruit/microbiology ; *Genotype ; *Microbiota/genetics ; *Rhizosphere ; Bacteria/genetics/classification/isolation & purification ; Fungi/genetics/classification/isolation & purification ; Brazil ; Soil ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In recent years, the role of microbial communities in agricultural systems has received increasing attention, particularly concerning their impact on plant health and productivity. However, the influence of host plant genetic factors on the microbial composition of coffee plants remains largely unexplored. This study provides the first comprehensive investigation into how genotype affects the microbial communities present in the rhizosphere and fruits of Coffea canephora. Conducted on a commercial coffee farm in Brazil, we analyzed six genotypes of C. canephora var. Conilon. Soil and fruit samples were collected from which microbial DNA was extracted and sequenced, targeting the V3-V4 region of the 16 S rDNA and the ITS1 region for fungi. A total of 12,239,769 reads were generated from the 16 S rDNA and ITS1 regions. The PCoA revealed distinct patterns of beta diversity, with genotype 153 exhibiting significant isolation in soil bacterial communities. The dominant bacterial orders included Rhizobiales and Rhodobacterales, while the fungal community comprised diverse taxa from Saccharomycetales and Hypocreales. LEfSe analysis identified key metagenomic biomarkers, highlighting genotype Baiano 4 for its richness in fruit-associated taxa, whereas genotype 153 exhibited lower diversity in both soil and fruit samples. This work enhances our understanding of the microbiomes associated with different coffee genotypes, providing evidence of how host genetic variation influences microbial community composition. Our findings indicate that specific microbial taxa are enriched in the fruits and soil of various genotypes. Future research should focus on identifying these microorganisms and elucidating their specific functions within the rhizosphere and coffee fruits.}, } @article {pmid39580523, year = {2024}, author = {Li, J and Zhai, X and Chen, C and Zhang, R and Huang, X and Liu, Y}, title = {The intrahepatic bacterial metataxonomic signature of patients with hepatocellular carcinoma.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {29077}, pmid = {39580523}, issn = {2045-2322}, support = {32300081//the National Natural Science Foundation of China/ ; 23QA1406600//Shanghai Science and Technology Committee/ ; }, mesh = {Humans ; *Carcinoma, Hepatocellular/microbiology/pathology/metabolism ; *Liver Neoplasms/microbiology/pathology/metabolism ; Male ; Female ; Middle Aged ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; Aged ; Liver/microbiology/pathology/metabolism ; Microbiota ; Liver Cirrhosis/microbiology/pathology ; Adult ; }, abstract = {Dysbiosis of the gut-liver axis increases the risk of bacterial and metabolite influx into the liver, which may contribute to the development of hepatocellular carcinoma (HCC). In this study, we compared the microbiomes in HCC tumors and adjacent tissues. We examined the HCC tumors and adjacent tissues from 19 patients diagnosed with HCC. We find that the liver tissues from HCC patients with capsule invasion presented higher alpha diversity at the genus level than those without. The bacterial compositions in liver tissues of HCC patients at stage II differed from those at stage I and Advanced, respectively. Metagenomic profiling revealed that order Actinomycetales was enriched in the HCC patients at advanced stages. Order Lactobacillales, family Veillonellaceae, genera Rhodobacter and Megasphaera are enriched in tumors of HCC patients, whereas genus Pseudochrobactrum is enriched in the adjacent tissues from HCC patients. An increased abundance of class Actinobacteria and order Actinomycetales is observed in the HCC patients with cirrhosis. In contrast, phylum Firmicutes, classes Clostridia and Betaproteobacteria, and order Clostridiales are enriched in those without cirrhosis. The presence of various types of bacterial 16S rRNAs in HCC tumors and adjacent tissues indicates the presence of various bacterial communities therein. Our study provides information about differentially abundant intrahepatic bacteria in patients with HCC. The differences found may support possible diagnostic and personalized therapeutic implications for HCC.}, } @article {pmid39579702, year = {2025}, author = {Hou, J and Li, Y and Liu, M and Qu, Z and Du, Z and An, Y and Yang, F and Yao, Y}, title = {Significant effects of bioavailable heavy metals on antibiotic resistome in paddy soils as revealed by metagenomic analysis.}, journal = {Journal of hazardous materials}, volume = {482}, number = {}, pages = {136587}, doi = {10.1016/j.jhazmat.2024.136587}, pmid = {39579702}, issn = {1873-3336}, mesh = {*Soil Microbiology ; *Metals, Heavy/toxicity ; *Soil Pollutants/toxicity ; *Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Metagenomics ; Bacteria/drug effects/genetics ; Oryza/microbiology ; Anti-Bacterial Agents/pharmacology ; Metagenome/drug effects ; Drug Resistance, Bacterial/genetics ; Soil/chemistry ; }, abstract = {Heavy metals (HMs) act as a long-term selective pressure for the emergence and maintenance of antibiotic resistance genes (ARGs) in agricultural soils. However, the effects of HMs on ARG distributions in paddy soils and the underlying mechanisms remain unclear. In this study, 74 soil samples were collected from the paddy fields to explore the impact of HMs on ARG profiles. A total of 468 ARGs were detected in HM-contaminated soils. Variation partitioning analysis (VPA) and redundancy analysis (RDA) demonstrated that the bioavailable HMs contributed more significantly to ARG composition compared to the total HM content (8.59 % vs. 3.97 %). Structural equation models (SEMs) showed that bioavailable HMs affected ARGs mainly by negatively altering the microbial diversity. Furthermore, the co-occurrence analysis of ARGs and metal resistant genes (MRGs) was further performed at the metagenome-assembled genomes (MAGs) level. Consequently, 1145 MAGs that assigned to 29 bacterial phyla were found to concurrently harbor ARGs and MRGs, with the bacterial phyla Pseudomonadota being predominant ARG-MRG-carrying microbes for most coexistence types of ARGs and MRGs, i.e., multidrug-As, polymyxin-Cd, Quinolone-Cd, Beta-lactam-Pb, and multidrug-Zn. Our findings highlight that the extensive coexistence of ARG-MRG in microbial genomes is an important reason for the ARG pollution in HM-contaminated paddy soils.}, } @article {pmid39579692, year = {2025}, author = {Hu, R and Chen, X and Han, Y and Li, W and Zhang, S and Liu, Z and Wang, J and Lu, X and Luo, G and Zhang, S and Zhen, G}, title = {KOH-modified biochar enhances nitrogen metabolism of the chloroquine phosphate-disturbed anammox: Physical binding, EPS modulation and versatile metabolic hierarchy.}, journal = {Journal of hazardous materials}, volume = {482}, number = {}, pages = {136467}, doi = {10.1016/j.jhazmat.2024.136467}, pmid = {39579692}, issn = {1873-3336}, mesh = {*Charcoal/chemistry ; *Nitrogen/metabolism/chemistry ; *Potassium Compounds/chemistry/metabolism ; *Chloroquine/metabolism ; *Hydroxides/chemistry/metabolism ; Anaerobiosis ; Oxidation-Reduction ; Bacteria/metabolism ; Water Pollutants, Chemical/metabolism/chemistry ; Extracellular Polymeric Substance Matrix/metabolism/chemistry ; }, abstract = {Chloroquine phosphate (CQ) poses strong biotoxicity on anammox process, and thus detoxifying is essential for the stable operation of anammox in treating CQ-bearing wastewater. Biochar has been proven to simultaneously detoxify pollutant and modulate nitrogen cycle in anammox by its shelter effect and electron exchange capacity (EEC) ability. To further improve the ability of biochar to promote the nitrogen metabolism of anammox, a KOH modification strategy was used to tailor a high-EEC biochar in this work. KOH modified biochar can bind CQ for detoxification driven by hydrogen bond, π-π interaction, and electrostatic interaction. Meanwhile, the EEC of modified biochar increased by 70 % than that of pristine biochar, thus improving nitrogen removal efficiency by 55.6 % and 9.5 % than CQ and BC group, respectively. Besides, the microorganism regulated by modified biochar produced more α-helix configuration, improving EPS barrier ability to CQ and sludge granulation. Lastly, metagenomic analysis revealed that modified biochar can stimulate the Wood-Ljungdahl pathway, increased the relative abundance of CODH from 0.74 % in CQ to 1.00 % in modified BC group. It favored the proliferation of autotrophic microorganisms, especially increased the relative abundance of anammox bacteria by 86.8 % than CQ group. This work will shed the light on integrating high-EEC biochar into anammox to cope with the micropollutants stress.}, } @article {pmid39579348, year = {2024}, author = {Ramos-Barbero, MD and Aldeguer-Riquelme, B and Viver, T and Villamor, J and Carrillo-Bautista, M and López-Pascual, C and Konstantinidis, KT and Martínez-García, M and Santos, F and Rossello-Mora, R and Antón, J}, title = {Experimental evolution at ecological scales allows linking of viral genotypes to specific host strains.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39579348}, issn = {1751-7370}, support = {PID2021-126114NB-C41//Spanish Ministry of Science and Innovation projects METACIRCLE/ ; CIPROM/2021/006//European Regional Development Fund/ ; }, mesh = {*Genotype ; Metagenomics ; Genome, Viral ; Ponds/virology/microbiology ; Metagenome ; }, abstract = {Viruses shape microbial community structure and activity through the control of population diversity and cell abundances. Identifying and monitoring the dynamics of specific virus-host pairs in nature is hampered by the limitations of culture-independent approaches such as metagenomics, which do not always provide strain-level resolution, and culture-based analyses, which eliminate the ecological background and in-situ interactions. Here, we have explored the interaction of a specific "autochthonous" host strain and its viruses within a natural community. Bacterium Salinibacter ruber strain M8 was spiked into its environment of isolation, a crystallizer pond from a coastal saltern, and the viral and cellular communities were monitored for one month using culture, metagenomics, and microscopy. Metagenome sequencing indicated that the M8 abundance decreased sharply after being added to the pond, likely due to forces other than viral predation. However, the presence of M8 selected for two species of a new viral genus, Phoenicisalinivirus, for which 120 strains were isolated. During this experiment, an assemblage of closely related viral genomic variants was replaced by a single population with the ability to infect M8, a scenario which was compatible with the selection of a genomic variant from the rare biosphere. Further analysis implicated a viral genomic region putatively coding for a tail fiber protein to be responsible for M8 specificity. Our results indicate that low abundance viral genotypes provide a viral seed bank that allows for a highly specialized virus-host response within a complex ecological background.}, } @article {pmid39579086, year = {2024}, author = {Peng, C and Shang, J and Guan, J and Wang, D and Sun, Y}, title = {ViraLM: empowering virus discovery through the genome foundation model.}, journal = {Bioinformatics (Oxford, England)}, volume = {40}, number = {12}, pages = {}, pmid = {39579086}, issn = {1367-4811}, support = {11209823//Hong Kong Research Grants Council/ ; //Hong Kong Innovation and Technology Fund/ ; }, mesh = {*Viruses/genetics ; *Metagenomics/methods ; *Genome, Viral ; *Software ; Machine Learning ; Algorithms ; }, abstract = {MOTIVATION: Viruses, with their ubiquitous presence and high diversity, play pivotal roles in ecological systems and public health. Accurate identification of viruses in various ecosystems is essential for comprehending their variety and assessing their ecological influence. Metagenomic sequencing has become a major strategy to survey the viruses in various ecosystems. However, accurate and comprehensive virus detection in metagenomic data remains difficult. Limited reference sequences prevent alignment-based methods from identifying novel viruses. Machine learning-based tools are more promising in novel virus detection but often miss short viral contigs, which are abundant in typical metagenomic data. The inconsistency in virus search results produced by available tools further highlights the urgent need for a more robust tool for virus identification.

RESULTS: In this work, we develop ViraLM for identifying novel viral contigs in metagenomic data. By using the latest genome foundation model as the backbone and training on a rigorously constructed dataset, the model is able to distinguish viruses from other organisms based on the learned genomic characteristics. We thoroughly tested ViraLM on multiple datasets and the experimental results show that ViraLM outperforms available tools in different scenarios. In particular, ViraLM improves the F1-score on short contigs by 22%.

The source code of ViraLM is available via: https://github.com/ChengPENG-wolf/ViraLM.}, } @article {pmid39578925, year = {2024}, author = {Geers, AU and Buijs, Y and Schostag, MD and Elberling, B and Bentzon-Tilia, M}, title = {Exploring the biosynthesis potential of permafrost microbiomes.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {96}, pmid = {39578925}, issn = {2524-6372}, support = {DNRF 100//Danmarks Grundforskningsfond/ ; DNRF 137//Danmarks Grundforskningsfond/ ; DFF - 8048-00035B//Danmarks Frie Forskningsfond/ ; NNF21OC0070749//Novo Nordisk Fonden/ ; }, abstract = {BACKGROUND: Permafrost microbiomes are of paramount importance for the biogeochemistry of high latitude soils and while endemic biosynthetic domain sequences involved in secondary metabolism have been found in polar surface soils, the biosynthetic potential of permafrost microbiomes remains unexplored. Moreover, the nature of these ecosystems facilitates the unique opportunity to study the distribution and diversity of biosynthetic genes in relic DNA from ancient microbiomes. To explore the biosynthesis potential in permafrost, we used adenylation (AD) domain sequencing to evaluate non-ribosomal peptide (NRP) production in permafrost cores housing microbiomes separated at kilometer and kiloyear scales.

RESULTS: Permafrost microbiomes represented NRP repertoires significantly different from that of temperate soil microbiomes, but as for temperate soils, the estimated domain richness and diversity was strongly correlated to the bacterial taxonomic diversity across locations. Furthermore, we found significant differences in both community composition and AD domain composition across geographical and temporal distances. Overall, the vast majority of biosynthetic domains showed below 90% amino acid similarity to characterized BGCs, confirming the high degree of novelty of NRPs inherent to permafrost microbiomes. Using available metagenomic sequences, we further identified a high biosynthetic diversity beyond NRPs throughout arctic surface soils down to deep and ancient (megayear old) permafrost microbiomes.

CONCLUSION: We have shown that arctic permafrost microbiomes harbor a unique biosynthetic repertoire rich in hitherto undescribed NRPs. This diversity is driven by geographic separation across kilometer scales and by the bacterial taxonomic diversity between microbiomes confined in separate permafrost layers. Hence the permafrost biome represents a unique resource for studying secondary metabolism, and potentially for the discovery of novel drug leads.}, } @article {pmid39578870, year = {2024}, author = {Wang, Y and Chen, X and Huws, SA and Xu, G and Li, J and Ren, J and Xu, J and Guan, LL and Yao, J and Wu, S}, title = {Ileal microbial microbiome and its secondary bile acids modulate susceptibility to nonalcoholic steatohepatitis in dairy goats.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {247}, pmid = {39578870}, issn = {2049-2618}, mesh = {Animals ; *Non-alcoholic Fatty Liver Disease/microbiology ; *Goats ; *Bile Acids and Salts/metabolism ; *Gastrointestinal Microbiome ; *Ileum/microbiology ; *Liver/metabolism ; Mice ; Bacteria/classification/isolation & purification/genetics ; Disease Susceptibility ; Goat Diseases/microbiology ; Disease Models, Animal ; Female ; }, abstract = {BACKGROUND: Liver damage from nonalcoholic steatohepatitis (NASH) presents a significant challenge to the health and productivity of ruminants. However, the regulatory mechanisms behind variations in NASH susceptibility remain unclear. The gut‒liver axis, particularly the enterohepatic circulation of bile acids (BAs), plays a crucial role in regulating the liver diseases. Since the ileum is the primary site for BAs reabsorption and return to the liver, we analysed the ileal metagenome and metabolome, liver and serum metabolome, and liver single-nuclei transcriptome of NASH-resistant and susceptible goats together with a mice validation model to explore how ileal microbial BAs metabolism affects liver metabolism and immunity, uncovering the key mechanisms behind varied NASH pathogenesis in dairy goats.

RESULTS: In NASH goats, increased total cholesterol (TC), triglyceride (TG), and primary BAs and decreased secondary BAs in the liver and serum promoted hepatic fat accumulation. Increased ileal Escherichia coli, Erysipelotrichaceae bacterium and Streptococcus pneumoniae as well as proinflammatory compounds damaged ileal histological morphology, and increased ileal permeability contributes to liver inflammation. In NASH-tolerance (NASH-T) goats, increased ursodeoxycholic acid (UDCA), isodeoxycholic acid (isoDCA) and isolithocholic acid (isoLCA) in the liver, serum and ileal contents were attributed to ileal secondary BAs-producing bacteria (Clostridium, Bifidobacterium and Lactobacillus) and key microbial genes encoding enzymes. Meanwhile, decreased T-helper 17 (TH17) cells and increased regulatory T (Treg) cells proportion were identified in both liver and ileum of NASH-T goats. To further validate whether these key BAs affected the progression of NASH by regulating the proliferation of TH17 and Treg cells, the oral administration of bacterial UDCA, isoDCA and isoLCA to a high-fat diet-induced NASH mouse model confirmed the amelioration of NASH through the TH17 cell differentiation/IL-17 signalling/PPAR signalling pathway by these bacterial secondary BAs.

CONCLUSION: This study revealed the roles of ileal microbiome and its secondary BAs in resilience and susceptibility to NASH by affecting the hepatic Treg and TH17 cells proportion in dairy goats. Bacterial UDCA, isoDCA and isoLCA were demonstrated to alleviate NASH and could be novel postbiotics to modulate and improve the liver health in ruminants. Video Abstract.}, } @article {pmid39578769, year = {2024}, author = {Deng, H and Shi, Y and Xie, M and Zang, X and Zang, X and Ma, X and Han, W and He, J and Rao, Y and Ding, M and Ma, W and Wu, J and Pan, L and Xue, X}, title = {Diagnosis and treatment experience of Chlamydia psittaci pneumonia: A multicenter retrospective study in China.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {1333}, pmid = {39578769}, issn = {1471-2334}, support = {2021YFC2302100//National Key R&D Program of China/ ; 2021YFC2302100//National Key R&D Program of China/ ; 2023DTRXXY//Beijing Shijtan Hospital's "14th Five-Year Plan" Talent Cultivation Project/ ; 2023DTRXXY//Beijing Shijtan Hospital's "14th Five-Year Plan" Talent Cultivation Project/ ; }, mesh = {Humans ; Retrospective Studies ; Male ; China/epidemiology ; Female ; *Chlamydophila psittaci/isolation & purification ; Middle Aged ; *Psittacosis/diagnosis/drug therapy/microbiology ; Adult ; *Anti-Bacterial Agents/therapeutic use ; Aged ; C-Reactive Protein/analysis ; Chlamydial Pneumonia/diagnosis/drug therapy/microbiology ; }, abstract = {BACKGROUND: In recent years, clinical cases of Chlamydia psittaci pneumonia have gradually increased. Chlamydia psittaci pneumonia can quickly progress to severe pneumonia, leading to respiratory failure. Chlamydia psittaci cannot be detected by commonly used detection methods, leading to difficulties in clinical diagnosis and treatment, which may eventually develop into severe Chlamydia psittaci pneumonia. Therefore, we should improve our diagnostic and treatment capabilities for this disease.

METHODS: This article retrospectively studied 61 cases of pneumonia from 12 different provinces in China, and classified them into severe pneumonia and non-severe pneumonia. Divided into two groups, with 23 cases of severe pneumonia and 38 cases of non-severe pneumonia. We compared the two groups in terms of imaging, laboratory testing, treatment, prognosis, etc., hoping to provide better explanations and help clinical physicians better diagnose the disease.

RESULTS: There is no difference in age, gender, contact history, smoking history, or basic disease between severe and non-severe Chlamydia psittaci pneumonia. The most prominent symptom is fever, with a median body temperature of 39.7 ℃, and other symptoms similar to common respiratory infections. White blood cells and neutrophils may not show significant elevation, but C-reactive protein (CRP) and procalcitonin (PCT) will both show significant elevation, often accompanied by a decrease in arterial oxygen pressure. Some patients may experience liver and kidney dysfunction, but there is no statistically significant difference between the two groups. Doxycycline remains the preferred drug for severe Chlamydia psittaci pneumonia. The imaging mainly shows consolidation and bronchial inflation sign, and may also present with pleural effusion.

CONCLUSIONS: The imaging of Chlamydia psittaci pneumonia usually shows consolidation with bronchial inflation sign, which can also be manifested as ground glass changes or solid masses. Atypical images are prone to misdiagnosis in the early stages. There are some differences in laboratory examination and imaging between severe pneumonia and non-severe pneumonia, which can help identify severe patients in the early stage. Metagenomic next-generation sequencing (mNGS) played an important role in the diagnosis of all cases in this article. Timely treatment has a good prognosis for the disease, and imaging lesions can be completely absorbed.}, } @article {pmid39578630, year = {2024}, author = {Barber, DG and Child, HT and Joslin, GR and Wierzbicki, L and Tennant, RK}, title = {Statistical design approach enables optimised mechanical lysis for enhanced long-read soil metagenomics.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {28934}, pmid = {39578630}, issn = {2045-2322}, support = {CW648947-PT34767//Shell Research Ltd/ ; CW648947-PT34767//Shell Research Ltd/ ; CW648947-PT34767//Shell Research Ltd/ ; CW648947-PT34767//Shell Research Ltd/ ; CW648947-PT34767//Shell Research Ltd/ ; }, mesh = {*Metagenomics/methods ; *Soil Microbiology ; Soil/chemistry ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; }, abstract = {Metagenomic analysis has enabled insights into soil community structure and dynamics. Long-read sequencing for metagenomics can enhance microbial ecology by improving taxonomic classification, genome assembly, and functional annotation. However, protocols for purifying high-molecular weight DNA from soil are not yet optimised. We used a statistical design of experiments approach to enhance mechanical lysis of soil samples, increasing the length of purified DNA fragments. Low energy input into mechanical lysis improved DNA integrity, resulting in longer sequenced reads. Our optimized settings of 4 m s[-1] for 10 s increased fragment length by 70% compared to the manufacturer's recommendations. Longer reads from low intensity lysis produced longer contiguous sequences after assembly, potentially improving a range of down-stream analyses. Importantly, there was minimal bias exhibited in the microbial community composition due to lysis efficiency variations. We therefore propose a framework for improving the fragment lengths of DNA purified from diverse soil types, improving soil science research with long-read sequencing.}, } @article {pmid39578464, year = {2024}, author = {Nunn, BL and Timmins-Schiffman, E and Mudge, MC and Plubell, DL and Chebli, G and Kubanek, J and Riffle, M and Noble, WS and Harvey, E and Nunn, TA and Rynearson, T and Huntemann, M and LaButti, K and Foster, B and Foster, B and Roux, S and Palaniappan, K and Mukherjee, S and Reddy, TBK and Daum, C and Copeland, A and Chen, IA and Ivanova, NN and Kyrpides, NC and Glavina Del Rio, T and Eloe-Fadrosh, EA}, title = {Microbial Metagenomes Across a Complete Phytoplankton Bloom Cycle: High-Resolution Sampling Every 4 Hours Over 22 Days.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1270}, pmid = {39578464}, issn = {2052-4463}, support = {R21ES034337-01//U.S. Department of Health & Human Services | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; F31 ES032733/ES/NIEHS NIH HHS/United States ; 2041497//NSF | BIO | Division of Integrative Organismal Systems (IOS)/ ; IOS 2041497//NSF | BIO | Division of Integrative Organismal Systems (IOS)/ ; R21 ES034337/ES/NIEHS NIH HHS/United States ; }, mesh = {*Phytoplankton/genetics/growth & development ; *Metagenome ; *Bacteria/genetics/growth & development/classification ; *Archaea/genetics ; Eutrophication ; Microbiota ; Viruses/genetics/growth & development ; }, abstract = {In May and June of 2021, marine microbial samples were collected for DNA sequencing in East Sound, WA, USA every 4 hours for 22 days. This high temporal resolution sampling effort captured the last 3 days of a Rhizosolenia sp. bloom, the initiation and complete bloom cycle of Chaetoceros socialis (8 days), and the following bacterial bloom (2 days). Metagenomes were completed on the time series, and the dataset includes 128 size-fractionated microbial samples (0.22-1.2 µm), providing gene abundances for the dominant members of bacteria, archaea, and viruses. This dataset also has time-matched nutrient analyses, flow cytometry data, and physical parameters of the environment at a single point of sampling within a coastal ecosystem that experiences regular bloom events, facilitating a range of modeling efforts that can be leveraged to understand microbial community structure and their influences on the growth, maintenance, and senescence of phytoplankton blooms.}, } @article {pmid39577783, year = {2025}, author = {Calisto, R and Godinho, O and Devos, DP and Lage, OM}, title = {"Genome-based in silico assessment of biosynthetic gene clusters in Planctomycetota: Evidences of its wide divergent nature".}, journal = {Genomics}, volume = {117}, number = {1}, pages = {110965}, doi = {10.1016/j.ygeno.2024.110965}, pmid = {39577783}, issn = {1089-8646}, mesh = {*Multigene Family ; Genome, Bacterial ; Bacteria/genetics/metabolism ; Metagenome ; Computer Simulation ; }, abstract = {The biotechnological potential of Planctomycetota only recently started to be unveiled. 129 reference genomes and 5194 available genomes (4988 metagenome-assembled genomes (MAGs)) were analysed regarding the presence of Biosynthetic Gene Clusters (BGCs). By antiSMASH, 987 BGCs in the reference genomes and 22,841 BGCs in all the available genomes were detected. The classes Ca Uabimicrobiia, Ca Brocadiia and Planctomycetia had the higher number of BGC per genome, while Phycisphaerae had the lowest number. The most prevalent BGCs found in Planctomycetota reference genomes were terpenes, NRPS, type III PKS, type I PKS. As much as 88 % of the predicted regions had no similarity with known clusters in MIBiG database. This study strengthens the uniqueness of Planctomycetota for the isolation of new compounds and provide an overview of BGCs taxonomic distribution and of the type of predicted product. This outline allows the acceleration and focus of the research on drug discovery in Planctomycetota.}, } @article {pmid39577779, year = {2025}, author = {Wang, Y and Wei, W and Yang, D and Wu, L and Chen, X and Dai, X and Ni, BJ}, title = {Unraveling temperature effects on caproate and caprylate production from waste activated sludge.}, journal = {Bioresource technology}, volume = {417}, number = {}, pages = {131844}, doi = {10.1016/j.biortech.2024.131844}, pmid = {39577779}, issn = {1873-2976}, mesh = {*Sewage/microbiology ; *Temperature ; *Fatty Acids/metabolism ; Caproates/metabolism ; Hydrolysis ; }, abstract = {This study explored the impact of different temperatures on the continuous production of medium-chain fatty acids (MCFAs) from waste activated sludge (WAS). Experimental results showed that there was almost no MCFAs accumulation at 55 °C. Both 25 °C and 37 °C were suitable for MCFAs production, with 25 °C favoring high-value caprylate production. The metagenomic and metatranscriptomic analysis highlighted reverse β-oxidization as the main chain elongation (CE) cycle. The lack of CE-related microorganisms and enzymes at 55 °C hindered MCFAs production, in contrast to the heightened activity observed at 25 °C and 37 °C, with peak activity at 25 °C leading to increased longer-chain MCFAs synthesis. 37 °C promoted hydrolysis and acidification, resulting in a accumulation of higher short-chain fatty acids, but further elongation to MCFAs would be hindered by product toxicity. This research concludes that 25 °C is the most effective temperature for the production of WAS-derived MCFAs, offering significant economic advantages.}, } @article {pmid39577778, year = {2025}, author = {Chen, Y and Huang, M and Fu, Y and Gao, T and Gan, Z and Meng, F}, title = {Construction of polylactic acid plastisphere microbiota for enhancing nitrate reduction in denitrification biofilters.}, journal = {Bioresource technology}, volume = {417}, number = {}, pages = {131853}, doi = {10.1016/j.biortech.2024.131853}, pmid = {39577778}, issn = {1873-2976}, mesh = {*Denitrification ; *Polyesters/metabolism/chemistry ; *Nitrates/metabolism ; *Biofilms ; *Microbiota ; Bioreactors/microbiology ; Filtration/methods ; Water Purification/methods ; Biodegradation, Environmental ; }, abstract = {Developing methods for reusing biodegradable plastics, like polylactic acid (PLA) straws, is highly needed. Here, PLAs were applied to substitute traditional commercial ceramic media (CCM) in denitrification biofilters. During long-term operation, replacing CCM with PLA significantly enhanced nitrate removal efficiency from 32.68-54.39 % to 41.64-66.26 %. Ammonia nitrogen effluent maintained below 0.5 mg/L in all reactors. PLA plastisphere shaped unique microbial communities, i.e., denitrifying bacteria Bacillus, Pseudomonas and Acidovorax preferred to inhabit or degrade PLA. Compared to CCM biofilms, PLA diminished the importance of stochastic process in biofilm assembly of PLA plastisphere. Metagenomic sequencing suggested that PLA biofilms possessed greater metabolic capabilities of denitrification and glycolysis compared to CCM. Additionally, Bacillus strain P01 isolated from PLA plastisphere demonstrated strong PLA depolymerization. Overall, this study revealed that PLA serves as carbon source and biofilm carrier, offering a promising approach to integrating plastic reuse with wastewater treatment.}, } @article {pmid39577726, year = {2025}, author = {Wang, L and Wu, Y and Zhao, ZB and Jia, T and Liu, W}, title = {Applying cross-scale regulations to Sedum plumbizincicola for strengthening the bioremediation of the agricultural soil that contaminated by electronic waste dismantling and revealing the underlying mechanisms by multi-omics.}, journal = {Environmental research}, volume = {264}, number = {Pt 2}, pages = {120406}, doi = {10.1016/j.envres.2024.120406}, pmid = {39577726}, issn = {1096-0953}, mesh = {*Biodegradation, Environmental ; *Sedum/metabolism ; *Soil Pollutants/analysis ; *Electronic Waste ; Soil Microbiology ; Agriculture/methods ; Soil/chemistry ; Multiomics ; }, abstract = {Electronic waste dismantling has induced the surrounding agricultural soils suffered from combined contamination of heavy metals and organic pollutants. Lower efficiency and complex mechanisms of bioremediation remain to be resolved. Here, we adopted regulations to Sedum plumbizincicola cross aboveground and belowground scales to strengthen the bioremediation efficiency. Results showed that the S. plumbizincicola intercropping with the Astragalus sinicusL. that inoculated with Rhizobium had the highest performance in reductions of Cd, PBDEs and PCBs from soils by 0.11 mg/kg, 67.93 μg/kg and 38.91 μg/kg, respectively. Rhizosphere soil metabolomics analysis demonstrated that reductions in Cd and PBDEs significantly associated with 2-Methylhippuric acid and L-Saccharopine, which were involved in phenylalanine metabolism, biosynthesis of amino acids and lysine. Metagenomics analysis revealed that these functional pathways were mediated by Frankia, Mycobacterium, Blastococcus, etc. microbial taxa, which were also significantly altered by regulations. Moreover, regulation regimes significantly affected transcription genes of S. plumbizincicola. Functional annotation revealed that cross-scale regulations significantly improved bioremediation efficiency through microorganisms and metabolites in the rhizosphere and transcription genes of S. plumbizincicola, which were illustrated to promote plant growth and tolerance to environmental stress. Our integration of multi-omics provides comprehensive and deep insights into molecular mechanisms in the cross-scale regulations of S. plumbizincicola, which would favor remediation techniques advances for the soil contaminated by electronic waste dismantling.}, } @article {pmid39577583, year = {2024}, author = {Yu, K and He, B and Xiong, J and Kan, P and Sheng, H and Zhi, S and Zhu, DZ and Yao, Z}, title = {Deciphering basic and key traits of bio-pollutants in a long-term reclaimed water headwater urban stream.}, journal = {The Science of the total environment}, volume = {957}, number = {}, pages = {177696}, doi = {10.1016/j.scitotenv.2024.177696}, pmid = {39577583}, issn = {1879-1026}, mesh = {*Environmental Monitoring ; *Rivers/microbiology/chemistry ; Water Pollutants, Chemical/analysis ; Waste Disposal, Fluid/methods ; Acinetobacter baumannii/genetics ; China ; Drug Resistance, Microbial/genetics ; }, abstract = {Reclaimed water has been recognized as a stable water resource for ecological replenishment in riverine environment. However, information about the bio-pollutants spatial and temporal distributions and the associated risk in this environment remains insufficient. Herein, the bio-pollutant profile in a long-term reclaimed water headwater urban stream, including antibiotic resistance genes (ARGs), mobile genetic elements and pathogens, were revealed by metagenomics. Notably, the temporal variation in bio-pollutant levels exceeded spatial fluctuations, possibly due to the varied rainfall intensity. Specially, multidrug resistance genes and Acinetobacter baumannii (A. baumannii) were the dominant ARGs and pathogens, respectively, exhibiting higher abundance in the dry season, especially in the downstream of the receiving point, where the bio-risk also peaked. A. baumannii and Ralstonia solanacearum were found to be the main plasmids contributors inducing the horizontal gene transfer process in this stream. Overall, A. baumannii contributed over 50 % bio-risk values in most samples, indicating that it was the "overlord" in this headwater urban stream. This study revealed characteristics of bio-pollutants in a typical long-term reclaimed water headwater urban stream, highlighting the superiority of A. baumannii in bio-pollutants, which should be a key consideration in the bio-pollutants surveillance for reclaimed waters.}, } @article {pmid39577582, year = {2024}, author = {Mukherjee, S and Bhattacharya, R and Sarkar, O and Islam, S and Biswas, SR and Chattopadhyay, A}, title = {Gut microbiota perturbation and subsequent oxidative stress in gut and kidney tissues of zebrafish after individual and combined exposure to inorganic arsenic and fluoride.}, journal = {The Science of the total environment}, volume = {957}, number = {}, pages = {177519}, doi = {10.1016/j.scitotenv.2024.177519}, pmid = {39577582}, issn = {1879-1026}, mesh = {Animals ; *Zebrafish ; *Gastrointestinal Microbiome/drug effects ; *Oxidative Stress/drug effects ; *Arsenic/toxicity ; *Kidney/drug effects ; *Fluorides/toxicity ; *Water Pollutants, Chemical/toxicity ; }, abstract = {Chronic exposure to inorganic arsenic (iAs) and fluoride (F) affect gut health and potentially damage organs. The present study investigates the interplay between gut bacteria and oxidative stress (measured by MDA level, GSH level, catalase activity, Nrf2 translocation and expression) in zebrafish exposed to F (NaF 15 ppm) and As (As2O3 50 ppb) alone or in combination. Combined exposure to As and F reduced gut bacterial alteration and imposed less oxidative stress compared to F- exposure alone. V3-V4 metagenomic sequencing revealed Pseudomonas, Aeromonas and Plesiomonas genera dominated in As or F treated groups while As+F treated group was enriched in beneficial Lactococcus and Streptococcus genera. Functional KEGG analysis demonstrated treatment-specific changes in bacterial metabolism, host organismal systems, human diseases, as well as cellular processes of microbial community were significantly affected. When Aeromonas sp. isolated from F-treated fish gut, tagged with GFP-vector and fed (~3.2 × 10[6] CFU/mL) to untreated fish, induced oxidative stress in gut and kidney. Gut bacteria were found to both increase and mitigate iAs or F-toxicity, whereas As+F treatment promoted a protective response. Correlation analysis between gut microbial community at genus level and oxidative stress parameters of gut and kidney, showed Aeromonas and Plesiomonas genera are strongly correlated with oxidative stress (r = 0.5-0.9, p˂0.05). This study identifies microbiome biomarkers of iAs and F toxicity on gut-kidney axis.}, } @article {pmid39577388, year = {2025}, author = {Huang, P and Chen, Y and Yu, S and Zhou, Y}, title = {Propionic acid enhances H2 production in purple phototrophic bacteria: Insights into carbon and reducing equivalent allocation.}, journal = {Water research}, volume = {269}, number = {}, pages = {122799}, doi = {10.1016/j.watres.2024.122799}, pmid = {39577388}, issn = {1879-2448}, mesh = {*Propionates/metabolism ; *Hydrogen/metabolism ; *Fermentation ; Carbon/metabolism ; Fatty Acids, Volatile/metabolism ; Rhodopseudomonas/metabolism ; Polyhydroxyalkanoates/biosynthesis ; }, abstract = {Biohydrogen is gaining popularity as a clean and cost-effective energy source. Among the various production methods, photo fermentation (PF) with purple phototrophic bacteria (PPB) has shown great opportunity due to its high hydrogen yield. In practice, this yield is influenced by several factors, with the carbon source, particularly simple organic acid, being a key element that has attracted considerable research interest. Short-chain volatile fatty acids (VFAs), such as acetate, propionate, and butyrate, are widely found in waste streams and dark fermentation (DF) effluent. However, most studies on these VFAs focus mainly on performance evaluation, with few exploring the underlying mechanisms, which limits their applicability in real-world scenarios. To uncover the metabolic mechanisms, this study uses metagenomics to clarify the processes of reducing power production and distribution during substrate assimilation. Meanwhile, this study presents the impact of short-chain VFAs on biohydrogen, polyhydroxyalkanoates (PHA) and glycogen production by PPB. The results show that: (1) over long-term cultivation at similar COD consumption rates of 0.06 g COD/d, PPB possessed the highest hydrogen yield when fed with propionate (0.620 L H2·g COD[-1]) compared with butyrate (0.434) and acetate (0.361); (2) with propionate as the substrate, PPB accumulated less PHA (7 % of dry biomass) but more glycogen content (11 %), compared to butyrate (15 % PHA and 8 % glycogen) and acetate (21 % PHA and 5 % glycogen); (3) metagenomic analysis revealed that propionate resulted in the highest amounts of reducing equivalents, followed by butyrate and acetate; hydrogen production was the most efficient pathway for utilizing the reducing power with propionate, as the CO2 fixation and PHA or glycogen synthesis were ineffective for electron dissipation. This study offers insights into metabolic mechanism that could guide waste stream selection and pretreatment processes to provide favorable VFAs for the PF process, thereby enhancing PPB biohydrogen production performance in practical applications.}, } @article {pmid39577368, year = {2025}, author = {Yang, L and Yao, B and Zhang, S and Yang, Y and Wang, G and Pan, H and Zeng, X and Qiao, S}, title = {Division mechanism of labor in Diqing Tibetan Pigs gut microbiota for dietary fiber efficiently utilization.}, journal = {Microbiological research}, volume = {290}, number = {}, pages = {127977}, doi = {10.1016/j.micres.2024.127977}, pmid = {39577368}, issn = {1618-0623}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Dietary Fiber/metabolism ; Swine ; *Animal Feed ; *Feces/microbiology ; Tibet ; Bacteria/classification/genetics/metabolism/isolation & purification ; Metagenomics ; Xylose/metabolism ; Glycoside Hydrolases/metabolism ; Lactobacillus/metabolism/genetics ; }, abstract = {The Diqing Tibetan (TP) pig is an roughage tolerance breed that inhabits an area with the highest altitude distribution in the world and can be maintained on a diet containing 90 % forage material in confined production systems. Our results showed that TP pigs had a strong capability for high-efficiency utilization of arabinose and xylose. Metagenomic analysis revealed that the secretion of carbohydrate esterases was mainly undertaken by fecal strains of Microbacterium, Alistipes, Acinetobacter, and Faecalibacterium, while Microbacterium, Prevotella, Turicibacter, Lactobacillus, Clostridium, and Streptococcus were responsible for most of the secretion of glycoside hydrolases. Then, a brand new species, which was named Microbacterium sp. Qiao 01 was captured and appeared to have the highest fiber utilization ability in vitro, degrading 36.54 % of the neutral detergent fiber in corn stover. Our results provide strong evidence that efficient utilization of dietary fiber by TP pigs is due to the emergence of highly specialized microbial strategies in the gut. Microorganisms showed preferences and a clear division of labor in the degradation process of dietary fiber. This study has great practical significance for improving the utilization efficiency of livestock feed and alleviating the tension of food insecurity.}, } @article {pmid39577267, year = {2025}, author = {Ngo, C and Morrell, JM and Tummaruk, P}, title = {Boar semen microbiome: Insights and potential implications.}, journal = {Animal reproduction science}, volume = {272}, number = {}, pages = {107647}, doi = {10.1016/j.anireprosci.2024.107647}, pmid = {39577267}, issn = {1873-2232}, mesh = {Animals ; *Semen/microbiology ; Swine/microbiology/physiology ; Male ; *Microbiota ; Semen Analysis/veterinary ; Bacteria/classification/isolation & purification/genetics ; }, abstract = {The pioneers of next-generation sequencing technology and bioinformatic analyses initiated a new era in microbiology research by offering profound insights into bacterial microbiome communities. In the pig farming sector, while considerable attention has been devoted to the gut microbiome and the microbiome of the female reproductive tract, research on the microbiome of boar semen remains limited. Nonetheless, published studies have provided valuable insights, serving as important references and sparking ideas for further investigations into the seminal microbiome. Factors such as breed, seasons, feed additives, hygiene management, and antibiotic use are believed to exert a notable influence on the diversity and richness of bacterial genera in the boar seminal microbiome, potentially affecting semen quality. Moreover, current shifts towards sustainability in the swine industry, coupled with global guidelines concerning the prudent use of antibiotics in stored boar semen for artificial insemination, underscore the need for insights into factors influencing seminal bacteria. The objective of this review is to elucidate the current understanding of boar bacterial contents using conventional culture methods, as well as the boar seminal microbiome through metagenomics and bioinformatics. It also aims to review specific microbiome communities, such as those in the reproductive tract and gut, and their connections to semen quality. In addition, strategic enhancements for processing boar semen doses through alternative methods to improve seminal quality are proposed.}, } @article {pmid39577117, year = {2024}, author = {Mommert-Tripon, M and Parraud, D and Grosbois, C and Gaymard, A and Cheynet, V and Lina, B and Oriol, G and Laurent, F and Dupré, C and Semanas, Q and Bal, A and Generenaz, L and Pons, S and Brengel-Pesce, K and Guichard, A and Mouton, W and Morfin, F and Fleurie, A and Trouillet-Assant, S}, title = {Advancing respiratory virus diagnostics: integrating the nasal IFN-I score for improved viral detection.}, journal = {EBioMedicine}, volume = {110}, number = {}, pages = {105450}, pmid = {39577117}, issn = {2352-3964}, mesh = {Humans ; Male ; Female ; Middle Aged ; Adult ; Aged ; *Respiratory Tract Infections/diagnosis/virology ; *Interferon Type I ; SARS-CoV-2/isolation & purification/genetics/immunology ; COVID-19/diagnosis/virology ; Young Adult ; Adolescent ; Virus Diseases/diagnosis/virology ; Aged, 80 and over ; Child, Preschool ; Nasopharynx/virology ; Child ; Influenza, Human/diagnosis/virology ; }, abstract = {BACKGROUND: This study aimed to demonstrate the utility of the nasal Type I interferon (IFN-I) response as a marker for respiratory viral infections (RVIs) and its potential to enhance diagnosis when combined with first-line PCR tests for Influenza A/B, RSV, and SARS-CoV-2.

METHODS: Nasopharyngeal swabs (NPS) from patients at Hospices Civils de Lyon (November 2022-April 2024) suspected of viral infections (n = 788) and from healthy controls (n = 53) were analysed. The IFN-I score was measured using the FILMARRAY® IFN-I pouch prototype, which detects four interferon-stimulated genes. The study evaluated the performance of the IFN-I score in detecting samples positive for viruses by first-line PCR and assessed its benefit in diagnosing RVIs in samples initially classified as negative by PCR.

FINDINGS: Out of 788 NPS included, 504 (64%) were positive with the first-line PCR tests, and IFN-I score was significantly higher in those samples (median [IQR]: 13.00 [2.76-45.40]) compared to ones collected from healthy controls (1.09 [0.67-1.30]; p < 0.0001), with an area under the curve (AUC; 95% CI) of 0.92 (0.90-0.92). Moreover, out of the 284 NPS negative with first-line PCR tests, suspicion of viral infection according to IFN-I score was found in 63% of cases (178/284). Second-line test (BioFire® Respiratory Panel 2.1 plus) and viral metagenomic confirmed the presence of viruses 94% of cases.

INTERPRETATION: The study highlights the potential of integrating nasal IFN-I score into clinical workflows to improve RVI diagnosis and enhance preparedness for emerging viruses.

FUNDING: Public grant overseen by the French National Research Agency (ANR21-RHUS-08/ANR-23-CHIN-0001).}, } @article {pmid39577061, year = {2024}, author = {Mahanty, S and Pillay, K and Hardouin, EA and Andreou, D and Cvitanović, M and Darbha, GK and Mandal, S and Chaudhuri, P and Majumder, S}, title = {Whispers in the mangroves: Unveiling the silent impact of potential toxic metals (PTMs) on Indian Sundarbans fungi.}, journal = {Marine pollution bulletin}, volume = {209}, number = {Pt B}, pages = {117233}, doi = {10.1016/j.marpolbul.2024.117233}, pmid = {39577061}, issn = {1879-3363}, mesh = {*Wetlands ; *Environmental Monitoring ; *Metals, Heavy/analysis/toxicity ; India ; *Water Pollutants, Chemical/analysis/toxicity ; *Fungi ; Geologic Sediments/chemistry ; Biodiversity ; }, abstract = {This study investigates sediment samples from the Indian Sundarbans' mangrove habitat, where most samples were alkaline and hypersaline, except for one acidic sample. Elemental analysis revealed poor sediment quality, with elevated Enrichment Factors (2.20-9.7), Geo-accumulation indices (-2.19-1.19), Contamination Factors (0.61-3.18), and Pollution Load Indices (1.04-1.32). Toxic metal ions, including Pb, Cu, Ni, Cd, Zn, and Cr, were identified as key contributors to compromised sediment quality. These metals inhibit crucial sediment enzymes, such as CMC-cellulase, β-glucosidase, aryl sulfatase, urease, and phosphatases, essential for nutrient cycling and organic matter decomposition. A negative correlation was found between heavy metals and biodiversity, as indicated by the Shannon index, and a similar trend was observed with fungal load. The study highlights the adverse effects of persistent trace metals on the fungal community, potentially disrupting the mangrove ecosystem and suggests using manglicolous fungi as biological indicators of environmental health.}, } @article {pmid39576476, year = {2024}, author = {Zabolotneva, AA and Laskina, TA and Kharchev, DN and Shestopalov, AV}, title = {Effects of a Short-Term High-Fat Diet on Microbiota Biodiversity of the Small and Large Intestines of C57BL/6SPF Mice.}, journal = {Bulletin of experimental biology and medicine}, volume = {178}, number = {1}, pages = {17-23}, pmid = {39576476}, issn = {1573-8221}, mesh = {Animals ; *Diet, High-Fat/adverse effects ; Mice ; *Mice, Inbred C57BL ; *Gastrointestinal Microbiome/genetics ; Male ; *Intestine, Small/microbiology/metabolism ; *Intestine, Large/microbiology ; Lipid Metabolism ; Biodiversity ; Blood Glucose/metabolism ; }, abstract = {Long-term high-fat diet (HFD) promotes the formation of excess body weight and disorders of lipid metabolism and causes persistent dysbiotic changes in the intestinal microbial community. Changes in eating behavior, endocrine and immune functions of the host are associated with changes in the structure and functional activity of microbial communities. Short-term HFD may also influence the composition and function of the intestinal microbiota, but data on this issue are limited, and most papers are focused on the study of the large intestinal microbiota. The present study examined the effect of short-term HFD (4 weeks) on the structure of microbial communities in the small and large intestines of 24 mice. High-throughput metagenomic sequencing was performed on 48 samples of small and large intestine contents. It was revealed that short-term HFD in mice contributed to impaired glucose tolerance and increased the diversity of microbiota in the colon, but not of the small intestine, and also led to changes in the representation of certain microbial taxa (in particular Tenericutes and Verrucomicrobia). Furthermore, short-term HFD increased blood glucose levels compared to control mice (fed a normal diet), but did not affect lipid metabolism. The results will help to assess the contribution of environmental factors to the structure of microbial communities of the small and large intestines and may also be useful for correcting dysbiotic conditions, including when prescribing therapeutic diets (for example, a ketogenic diet).}, } @article {pmid39576436, year = {2024}, author = {Zhou, Z and Zheng, X and Hua, Y and Guo, M and Sun, X and Huang, Y and Dong, L and Yu, S}, title = {Enhancing nitrogen removal in combined sewage overflows by using bio-fluidized bed with ceramic waste powder carriers: effects and mechanisms.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {57}, pages = {65252-65263}, pmid = {39576436}, issn = {1614-7499}, support = {41861124004//National Natural Science Foundation of China/ ; }, mesh = {*Sewage ; *Ceramics ; *Nitrogen ; *Waste Disposal, Fluid/methods ; China ; Denitrification ; Powders ; Bioreactors ; }, abstract = {Micron-size ceramic waste powder (< 75 μm and 75-150 μm) was used as the carrier in a high-concentration powder carrier bio-fluidized bed (HPB) to treat simulated overflow sewage (CSOs). The sludge extracellular polymers (EPS), electron transfer capacity of EPS, nitrogen removal pathways, and microbiological characteristics were analyzed to gain insights into the nitrogen removal pathways and mechanisms. The results showed that only the effluent from the HPB (< 75 μm) could meet the stringent pollutant discharge standards in China of 50 mg/L for CODCr and 15 mg/L for total nitrogen from beginning to end. Meanwhile, the electrochemical performance tests indicated that the electron accepting and donating capacities of the sludge EPS in the HPB (< 75 μm) were 42.75% and 32.73% higher than those in the conventional activated sludge, meaning that ceramic powder carriers can increase the extracellular electron transfer capacity of the sludge and accelerate the denitrification process. Also, metagenomics analysis results showed that the relative abundances of the denitrification-related Nor genes were 28-39% higher in the HPB (< 75 μm) and HPB (75-150 μm) than in the conventional activated sludge (CAS). These results show that ceramic waste powders have the potential to be used as carriers in HPB systems to treat CSOs.}, } @article {pmid39576133, year = {2025}, author = {Kim, H and Ahn, J and Kim, J and Kang, H-S}, title = {Metagenomic insights and biosynthetic potential of Candidatus Entotheonella symbiont associated with Halichondria marine sponges.}, journal = {Microbiology spectrum}, volume = {13}, number = {1}, pages = {e0235524}, pmid = {39576133}, issn = {2165-0497}, support = {2022R1C1C2011203//National Research Foundation of Korea (NRF)/ ; 2022R1A2C4001258,2022R1A4A3022401//National Research Foundation of Korea (NRF)/ ; }, mesh = {Animals ; *Symbiosis ; *Porifera/microbiology ; *Metagenomics ; Genome, Bacterial ; Phylogeny ; Republic of Korea ; Multigene Family ; Biological Products/metabolism ; Metagenome ; Biosynthetic Pathways/genetics ; }, abstract = {Korea, being surrounded by the sea, provides a rich habitat for marine sponges, which have been a prolific source of bioactive natural products. Although a diverse array of structurally novel natural products has been isolated from Korean marine sponges, their biosynthetic origins remain largely unknown. To explore the biosynthetic potential of Korean marine sponges, we conducted metagenomic analyses of sponges inhabiting the East Sea of Korea. This analysis revealed a symbiotic association of Candidatus Entotheonella bacteria with Halichondria sponges. Here, we report a new chemically rich Entotheonella variant, which we named Ca. Entotheonella halido. Remarkably, this symbiont makes up 69% of the microbial community in the sponge Halichondira dokdoensis. Genome-resolved metagenomics enabled us to obtain a high-quality Ca. E. halido genome, which represents the largest (12 Mb) and highest quality among previously reported Entotheonella genomes. We also identified the biosynthetic gene cluster (BGC) of the known sponge-derived Halicylindramides from the Ca. E. halido genome, enabling us to determine their biosynthetic origin. This new symbiotic association expands the host diversity and biosynthetic potential of metabolically talented bacterial genus Ca. Entotheonella symbionts.IMPORTANCEOur study reports the discovery of a new bacterial symbiont Ca. Entotheonella halido associated with the Korean marine sponge Halichondria dokdoensis. Using genome-resolved metagenomics, we recovered a high-quality Ca. E. halido MAG (Metagenome-Assembled Genome), which represents the largest and most complete Ca. Entotheonella MAG reported to date. Pangenome and BGC network analyses revealed a remarkably high BGC diversity within the Ca. Entotheonella pangenome, with almost no overlapping BGCs between different MAGs. The cryptic and genetically unique BGCs present in the Ca. Entotheonella pangenome represents a promising source of new bioactive natural products.}, } @article {pmid39574841, year = {2024}, author = {Chen, AS and Kim, H and Nzabarushimana, E and Shen, J and Williams, K and Gurung, J and McGoldrick, J and Burke, KE and Nguyen, LH and Staller, K and Chung, DC and Xavier, RJ and Khalili, H}, title = {Composition and Function of the Gut Microbiome in Microscopic Colitis.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.10.28.24316293}, pmid = {39574841}, abstract = {BACKGROUND: Microscopic colitis (MC) is a common cause of chronic diarrhea, predominantly among older adults. Emerging evidence suggests that perturbations of gut microbiome and metabolome may play an important role in MC pathogenesis.

OBJECTIVE: To comprehensively characterize alterations of the gut microbial and metabolic composition in MC.

DESIGN: We established a longitudinal cohort of adult patients with MC and two control groups of individuals - chronic diarrhea controls and age- and sex-matched controls without diarrhea. Using stool samples, gut microbiome was analyzed by whole-genome shotgun metagenomic sequencing, and gut metabolome was profiled by ultra-high performance liquid chromatography-mass spectrometry. Per-feature enrichment analyses of microbial species, metabolic pathways, and metabolites were done using multivariable linear models both cross-sectionally comparing MC to controls and longitudinally according to disease activity. Lastly, we performed multi-omics association analyses to assess the relationship between microbiome and metabolome data.

RESULTS: We included 683 participants, 131 with active MC (66 with both active and remission samples), 159 with chronic diarrhea, and 393 age- and sex-matched controls without diarrhea. The stool microbiome in active MC was characterized by a lower alpha diversity as compared to controls and the remission phase of MC. Compared to controls, we identified eight enriched species in MC, most of which were pro-inflammatory oral-typical species, such as Veillonella dispar and Haemophilus parainfluenzae . In contrast, 11 species, including anti-inflammatory microbes such as Blautia glucerasea and Bacteroides stercoris, were depleted in MC. Similarly, pro-inflammatory metabolites, including lactosylceramides, ceramides, lysophospholipids, and lysoplasmalogens were enriched in active MC as compared to controls or MC cases in remission. Multi-omics association analyses revealed strong and concordant links between microbes, their metabolic pathways, and metabolomic profiles, supporting the tight interplay between disturbances in stool microbiome and metabolome in MC.

CONCLUSION: We observed a significant shift in stool microbial and metabolomic composition in MC. Our findings could be used in the future for development of non-invasive biomarkers for diagnosing and monitoring MC and developing novel therapeutics.

Microbiome dysbiosis has been proposed to contribute to microscopic colitis (MC) pathogenesis.However, previous studies have been limited by small sample sizes, reliance on 16S rRNA sequencing technique, potential confounding by stool consistency, and lack of functional analyses of microbiome and longitudinal data. Moreover, the metabolomic composition of MC remain largely unknown.

WHAT THIS STUDY ADDS: In this largest longitudinal MC cohort with two control groups - chronic diarrhea controls and controls without diarrhea, gut microbiome of MC is characterized by a lower alpha diversity, enriched pro-inflammatory oral-typical species and depleted anti-inflammatory beneficial species.Gut metabolome of MC shows significant enrichment of pro-inflammatory metabolites, including lactosylceramides, ceramides, lysophospholipids, and lysoplasmalogens. Multi-omics analyses demonstrate strong and concordant relationships between microbes, metabolic pathways, and metabolomic profiles.

Our findings could facilitate development of non-invasive biomarkers and novel therapeutics for MC.}, } @article {pmid39574671, year = {2024}, author = {Ndjite, GM and Jiang, A and Ravel, C and Grant, M and Jiang, X and Hall, B}, title = {Gut Microbial Utilization of the Alternative Sweetener, D-Allulose, via AlsE.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39574671}, issn = {2692-8205}, support = {R35 GM155208/GM/NIGMS NIH HHS/United States ; }, abstract = {D-allulose, a rare sugar with emerging potential as a low-calorie sweetener, has garnered attention as an alternative to other commercially available alternative sweeteners, such as sugar alcohols, which often cause severe gastrointestinal discomfort. D-allulose-6-phosphate 3-epimerase (AlsE) is a prokaryotic enzyme that converts D-allulose-6-phosphate into D-fructose-6-phopshate, enabling its use as a carbon source. However, the taxonomic breadth of AlsE across gut bacteria remains poorly understood, hindering insights into the utilization of D-allulose by microbial communities. In this study, we provide experimental evidence showing that Clostridium innocuum is capable of D-allulose metabolism via a homologous AlsE. A bioinformatics search of 85,202 bacterial genomes identified 116 bacterial species with AlsE homologs, suggesting a limited distribution of AlsE in bacteria. Additionally, Escherichia coli contains a copy of alsE, but it does not grow on D-allulose as a sole carbon source unless alsE is heterologously expressed. A metagenomic analysis revealed that 15.8% of 3,079 adult healthy human metagenomic samples that we analyzed contained alsE, suggesting a limited prevalence of the enzyme in the gut microbiome. These results suggest that the gut microbiome has limited capacity to metabolize D-allulose via alsE, supporting its use as an alternative sweetener with minimal impact on microbial composition and gastrointestinal symptoms. This finding also enables personalized nutrition, allowing diabetic individuals to assess their gut microbiota for alsE, and manage glycemic response while reducing gastrointestinal distress.}, } @article {pmid39574606, year = {2024}, author = {Rodrigues, PB and de Rezende Rodovalho, V and Sencio, V and Benech, N and Creskey, M and Silva Angulo, F and Delval, L and Robil, C and Gosset, P and Machelart, A and Haas, J and Descat, A and Goosens, JF and Beury, D and Maurier, F and Hot, D and Wolowczuk, I and Sokol, H and Zhang, X and Ramirez Vinolo, MA and Trottein, F}, title = {Integrative metagenomics and metabolomics reveal age-associated gut microbiota and metabolite alterations in experimental COVID-19.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.11.05.622058}, pmid = {39574606}, issn = {2692-8205}, abstract = {Aging is a key contributor of morbidity and mortality during acute viral pneumonia. The potential role of age-associated dysbiosis on disease outcomes is still elusive. In the current study, we used high-resolution shotgun metagenomics and targeted metabolomics to characterize SARS-CoV-2-associated changes in the gut microbiota from young (2-month-old) and aged (22-month-old) hamsters, a valuable model of COVID-19. We show that age-related dysfunctions in the gut microbiota are linked to disease severity and long-term sequelae in older hamsters. Our data also reveal age-specific changes in the composition and metabolic activity of the gut microbiota during both the acute phase (day 7 post-infection, D7) and the recovery phase (D22) of infection. Aged hamsters exhibited the most notable shifts in gut microbiota composition and plasma metabolic profiles. Through an integrative analysis of metagenomics, metabolomics, and clinical data, we identified significant associations between bacterial taxa, metabolites and disease markers in the aged group. On D7 (high viral load and lung epithelial damage) and D22 (body weight loss and fibrosis), numerous amino acids, amino acid-related molecules, and indole derivatives were found to correlate with disease markers. In particular, a persistent decrease in phenylalanine, tryptophan, glutamic acid, and indoleacetic acid in aged animals positively correlated with poor recovery of body weight and/or lung fibrosis by D22. In younger hamsters, several bacterial taxa (Eubacterium , Oscillospiraceae , Lawsonibacter) and plasma metabolites (carnosine and cis-aconitic acid) were associated with mild disease outcomes. These findings support the need for age-specific microbiome-targeting strategies to more effectively manage acute viral pneumonia and long-term disease outcomes.}, } @article {pmid39574598, year = {2024}, author = {Nguyen, UT and Salamzade, R and Sandstrom, S and Swaney, MH and Townsend, L and Wu, SY and Cheong, JZA and Sardina, JA and Ludwikoski, I and Rybolt, M and Wan, H and Carlson, C and Zarnowski, R and Andes, D and Currie, C and Kalan, L}, title = {Large-scale investigation for antimicrobial activity reveals novel defensive species across the healthy skin microbiome.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39574598}, issn = {2692-8205}, support = {R35 GM137828/GM/NIGMS NIH HHS/United States ; T32 GM135066/GM/NIGMS NIH HHS/United States ; U19 AI142720/AI/NIAID NIH HHS/United States ; }, abstract = {The human skin microbiome constitutes a dynamic barrier that can impede pathogen invasion by producing antimicrobial natural products. Gene clusters encoding for production of secondary metabolites, biosynthetic gene clusters (BGCs), that are enriched in the human skin microbiome relative to other ecological settings, position this niche as a promising source for new natural product mining. Here, we introduce a new human microbiome isolate collection, the EPithelial Isolate Collection (EPIC). It includes a large phylogenetically diverse set of human skin-derived bacterial strains from eight body sites. This skin collection, consisting of 980 strains is larger and more diverse than existing resources, includes hundreds of rare and low-abundance strains, and hundreds of unique BGCs. Using a large-scale co-culture screen to assess 8,756 pairwise interactions between skin-associated bacteria and potential pathogens, we reveal broad antifungal activity by skin microbiome members. Integrating 287 whole isolate genomes and 268 metagenomes from sampling sites demonstrates that while the distribution of BGC types is stable across body sites, specific gene cluster families (GCFs), each predicted to encode for a distinct secondary metabolite, can substantially vary. Sites that are dry or rarely moist harbor the greatest potential for discovery of novel bioactive metabolites. Among our discoveries are four novel bacterial species, three of which exert significant and broad-spectrum antifungal activity. This comprehensive isolate collection advances our understanding of the skin microbiomes biosynthetic capabilities and pathogen-fighting mechanisms, opening new avenues towards antimicrobial drug discovery and microbiome engineering.}, } @article {pmid39574575, year = {2024}, author = {Nickols, WA and McIver, LJ and Walsh, A and Zhang, Y and Nearing, JT and Asnicar, F and Punčochář, M and Segata, N and Nguyen, LH and Hartmann, EM and Franzosa, EA and Huttenhower, C and Thompson, KN}, title = {Evaluating metagenomic analyses for undercharacterized environments: what's needed to light up the microbial dark matter?.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39574575}, issn = {2692-8205}, support = {R24 DK110499/DK/NIDDK NIH HHS/United States ; U19 AI110820/AI/NIAID NIH HHS/United States ; }, abstract = {Non-human-associated microbial communities play important biological roles, but they remain less understood than human-associated communities. Here, we assess the impact of key environmental sample properties on a variety of state-of-the-art metagenomic analysis methods. In simulated datasets, all methods performed similarly at high taxonomic ranks, but newer marker-based methods incorporating metagenomic assembled genomes outperformed others at lower taxonomic levels. In real environmental data, taxonomic profiles assigned to the same sample by different methods showed little agreement at lower taxonomic levels, but the methods agreed better on community diversity estimates and estimates of the relationships between environmental parameters and microbial profiles.}, } @article {pmid39574437, year = {2024}, author = {Li, Y and Wang, B and Wang, Y and He, W and Wu, X and Zhang, X and Teng, X and Liu, L and Yang, H}, title = {Effect of stand age on rhizosphere microbial community assembly of dominant shrubs during sandy desert vegetation restoration.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1473503}, pmid = {39574437}, issn = {1664-462X}, abstract = {The rhizosphere microbial community helps govern biogeochemical cycling and facilitates complex plant-soil feedback. Understanding the evolutionary dynamics of microbial community structure and functional genes during vegetation succession is crucial for quantifying and understanding ecosystem processes and functions in restored sandy deserts. In this study, the rhizosphere microbial community structure of 11-66-year-old dominant shrubs in a desert revegetation area was examined using shotgun metagenomic sequencing. The interactions between the microbial community structure, functional gene abundances, soil properties, and plant characteristics of different stand ages were comprehensively investigated. The abundance of unique species first increased before subsequently decreasing with stand age, with shared species accounting for only 47.33%-59.42% of the total operational taxonomic units (OTUs). Copiotrophs such as Actinobacteria and Proteobacteria were found to dominate the rhizosphere soil microbial community, with their relative abundance accounting for 75.28%-81.41% of the total OTUs. There was a gradual shift in dominant microbial functional genes being involved in cellular processes towards those involved in environmental information processing and metabolism as stand age increased. Additionally, temporal partitioning was observed in both the microbial co-occurrence network complexity and topological parameters within the rhizosphere soil. Redundancy analysis revealed that dissolved organic carbon was the primary determinant influencing shifts in microbial community structure. Understanding the evolution of microbial community structure and function contributes to identifying potential mechanisms associating the soil microbiome with dominant sand-fixing shrubs as well as understanding the rhizosphere microbiome assembly process. These results shed light on the role of the rhizosphere microbiome in biogeochemical cycling and other ecosystem functions following revegetation of temperate sandy deserts.}, } @article {pmid39574252, year = {2024}, author = {Crombez, L and Descamps, A and Hirmz, H and Lambert, M and Calewaert, J and Siluk, D and Markuszewski, M and Biesemans, M and Petrella, G and Cicero, D and Cesaroni, S and Stokowy, T and Gerber, GK and Tataru, C and Naumovski, P and Elewaut, D and Van De Looverbosch, C and Calders, P and Van Den Noortgate, N and De Spiegeleer, B and Wynendaele, E and De Spiegeleer, A}, title = {The Saliva and Muscle Study (SaMu): Rationale and Protocol for Associations between Salivary Microbiome and Accelerated Muscle Ageing.}, journal = {The Journal of frailty & aging}, volume = {13}, number = {4}, pages = {331-340}, doi = {10.14283/jfa.2024.75}, pmid = {39574252}, issn = {2260-1341}, mesh = {Humans ; *Saliva/microbiology ; *Sarcopenia/microbiology ; Aged ; Cross-Sectional Studies ; Male ; Female ; Muscle Strength/physiology ; Aging/physiology ; Microbiota/physiology ; Muscle, Skeletal/microbiology ; Aged, 80 and over ; }, abstract = {BACKGROUND: The gut microbiome is recognized as a pivotal factor in the pathophysiology of sarcopenia-a condition marked by the accelerated loss of muscle strength, mass and function with ageing. Despite this well-known gut-muscle axis, the potential links between other microbial ecosystems and sarcopenia remain largely unexplored. The oral microbiome has been linked to various age-related health conditions such as rheumatoid arthritis and colorectal cancer. However, its potential association with sarcopenia is unknown. The Saliva and Muscle (SaMu) study seeks to address this knowledge gap.

METHODS: The SaMu study comprises three sequential phases. In phase 1, a cross-sectional analysis will be conducted on a cohort of 200 individuals aged 70 years or older to examine the relationship between salivary microbiome and sarcopenia status. Participants will be recruited in the three main places of living: general community, assisted living facilities and nursing homes. The salivary microbiome composition will be evaluated utilizing shotgun metagenomics sequencing, while sarcopenia status will be determined through muscle mass (determined by whole-body bioelectrical impedance analysis and calf circumference), muscle strength (grip strength and the 5-times-sit-to-stand test) and physical performance (usual walking speed). In addition to investigating the microbiome composition, the study aims to elucidate microbiome functions by exploring potential omic associations with sarcopenia. To achieve this, salivary proteomics, metabolomics and quorum sensing peptidomics will be performed. Covariates that will be measured include clinical variables (sociodemographic factors, health status, health-related behaviours, oral health and quality of life) as well as blood variables (immune profiling, hormones, kidney and liver function, electrolytes and haematocrit). In phase 2, an in-depth mechanistic analysis will be performed on an envisaged subcohort of 50 participants. This analysis will explore pathways in muscle tissue using histology, genomics and transcriptomics, focusing on (maximal) 25 healthy older adults and (maximal) 25 with severe sarcopenia. Phase 3 involves a two-year clinical follow-up of the initial participants from the cross-sectional analysis, along with a resampling of blood and saliva. Additionally, secondary outcomes like falls, hospitalization and mortality will be examined.

DISCUSSION: Using a salivary multi-omics approach, SaMu primarily aims to clarify the associations between the oral microbiome and sarcopenia. SaMu is expected to contribute to the discovery of predictive biomarkers of sarcopenia as well as to the identification of potential novel targets to prevent/tackle sarcopenia. This study-protocol is submitted for registration at the ISRCTN registry.}, } @article {pmid39574009, year = {2024}, author = {Kim, S and Thapa, I and Ali, H}, title = {A novel computational approach for the mining of signature pathways using species co-occurrence networks in gut microbiomes.}, journal = {BMC microbiology}, volume = {24}, number = {Suppl 1}, pages = {490}, pmid = {39574009}, issn = {1471-2180}, mesh = {*Gastrointestinal Microbiome/genetics ; *Inflammatory Bowel Diseases/microbiology ; Humans ; *Computational Biology/methods ; *Metagenome ; Bacteria/genetics/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; Data Mining ; }, abstract = {BACKGROUND: Advances in metagenome sequencing data continue to enable new methods for analyzing biological systems. When handling microbial profile data, metagenome sequencing has proven to be far more comprehensive than traditional methods such as 16s rRNA data, which rely on partial sequences. Microbial community profiling can be used to obtain key biological insights that pave the way for more accurate understanding of complex systems that are critical for advancing biomedical research and healthcare. However, such attempts have mostly used partial or incomplete data to accurately capture those associations.

METHODS: This study introduces a novel computational approach for the identification of co-occurring microbial communities using the abundance and functional roles of species-level microbiome data. The proposed approach is then used to identify signature pathways associated with inflammatory bowel disease (IBD). Furthermore, we developed a computational pipeline to identify microbial species co-occurrences from metagenome data at various granularity levels.

RESULTS: When comparing the IBD group to a control group, we show that certain co-occurring communities of species are enriched for potential pathways. We also show that the identified co-occurring microbial species operate as a community to facilitate pathway enrichment.

CONCLUSIONS: The obtained findings suggest that the proposed network model, along with the computational pipeline, provide a valuable analytical tool to analyze complex biological systems and extract pathway signatures that can be used to diagnose certain health conditions.}, } @article {pmid39574001, year = {2024}, author = {Wu, J and Li, M and Zhou, C and Rong, J and Zhang, F and Wen, Y and Qu, J and Wu, R and Miao, Y and Niu, J}, title = {Changes in amino acid concentrations and the gut microbiota composition are implicated in the mucosal healing of ulcerative colitis and can be used as noninvasive diagnostic biomarkers.}, journal = {Clinical proteomics}, volume = {21}, number = {1}, pages = {62}, pmid = {39574001}, issn = {1542-6416}, support = {82160107//National Natural Science Foundation of China/ ; 82170550//National Natural Science Foundation of China/ ; 81960108//National Natural Science Foundation of China/ ; 2023533Q03//535 Talent Project of the First Affiliated Hospital of Kunming Medical University/ ; 2023535D06//535 Talent Project of the First Affiliated Hospital of Kunming Medical University/ ; 202201AT070273//Basic Research Projects of Yunnan Province/ ; H-2019050//Yunnan Health Training Project of High-Level Talents/ ; }, abstract = {BACKGROUND: Mucosal healing is the therapeutic target for ulcerative colitis (UC). While amino acids (AAs) and the gut microbiota are known to be involved in the pathogenesis of UC, their specific roles in mucosal healing have not been fully defined.

OBJECTIVES: To longitudinally assess the changes in AA concentrations and the gut microbiota composition in the context of mucosal healing in UC patients, with the aim of identifying new biomarkers with predictive value for mucosal healing in UC patients and providing a new theoretical basis for dietary therapy.

METHODS: A total of 15 UC patients with infliximab-induced mucosal healing were enrolled. Serum and fecal AA concentrations before and after mucosal healing were determined via targeted metabolomics. A receiver operating characteristic (ROC) curve was plotted to evaluate the value of different AAs in predicting mucosal healing in UC patients. The changes in the composition of the fecal gut microbiota were analyzed via metagenomics, and bioinformatics was used to analyze the functional genes and metabolic pathways associated with different bacterial species. Spearman correlation analyses of fecal AAs with significantly different concentrations and the differentially abundant bacterial species before and after mucosal healing were performed.

RESULTS: 1. The fecal concentrations of alanine, aspartic acid, glutamic acid, glutamine, glycine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine and valine were significantly decreased after mucosal healing. The serum concentrations of alanine, cysteine and valine significantly increased, whereas that of aspartic acid significantly decreased. Glutamic acid, leucine, lysine, methionine and threonine could accurately predict mucosal healing in UC patients, and the area under the curve (AUC) was > 0.9. After combining the 5 amino acids, the AUC reached 0.96. 2. There were significant differences in the gut microbiota composition before and after mucosal healing in UC, characterized by an increase in the abundance of beneficial microbiota (Faecalibacterium prausnitzii and Bacteroides fragilis) and a decrease in the abundance of harmful microbiota (Enterococcus faecalis). LEfSe analysis identified 57 species that could predict mucosal healing, and the AUC was 0.7846. 3. Amino acid metabolic pathways were enriched in samples after mucosal healing, was associated with the abundance of multiple species, such as Faecalibacterium prausnitzi, Bacteroides fragilis, Bacteroides vulgatus and Alistipes putredinis. 4. The fecal concentrations of several AAs were negatively correlated with the abundance of a variety of beneficial strains, such as Bacteroides fragilis, uncultured Clostridium sp., Firmicutes bacterium CAG:103, Adlercreutzia equolifaciens, Coprococcus comes and positively correlated with the abundance of several harmful strains, such as Citrobacter freundii, Enterococcus faecalis, Klebsiella aerogenes, Salmonella enterica.

CONCLUSION: Altered concentrations of amino acids and their associations with the gut microbiota are implicated in the mucosal healing of UC patients and can serve as noninvasive diagnostic biomarkers.}, } @article {pmid39573993, year = {2024}, author = {Li, M and Li, Y and Li, X}, title = {The carpal tunnel syndrome caused by Arthrinium phaeospermum infection: first case report and literature review.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {1328}, pmid = {39573993}, issn = {1471-2334}, support = {No.2022020506)//Ningbo Top Medical and Health Research Program/ ; No.2022020506)//Ningbo Top Medical and Health Research Program/ ; No. 2022Z146//Ningbo Key Research and Development Program/ ; No. 2022Z146//Ningbo Key Research and Development Program/ ; }, mesh = {Humans ; Male ; *Carpal Tunnel Syndrome/surgery ; Debridement ; Flavobacteriaceae/isolation & purification/genetics ; Flavobacteriaceae Infections/microbiology/drug therapy/diagnosis ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: The carpal tunnel syndrome (CTS) caused by atypical infection is a therapeutic and diagnostic challenge. Atypical clinical presentations often lead to misdiagnosis and incorrect therapy.

CASE PRESENTATION: This article reports a case of deep infection leading to CTS manifestations. A male patient was admitted for numbness and pain of the left hand. Left carpal tunnel release, median nerve decompression with synovial resection were performed. Inflamed synovium and effusion were submitted for bacterial culture and metagenomic next-generation sequencing (mNGS). The etiologic agent was identified as Arthrinium phaeospermum and the patient recovered after surgical debridement and 10 months of therapy.

CONCLUSIONS: Diagnosis of mycotic infection of the hand is challenging as the presentation is similar to other conditions. mNGS is presented as a valuable diagnostic adjunct for uncovering unusual infectious agents.}, } @article {pmid39572861, year = {2024}, author = {Ding, Y and Ma, RA and Zhang, R and Zhang, H and Zhang, J and Li, S and Zhang, SY}, title = {Increased antibiotic resistance gene abundance linked to intensive bacterial competition in the phyllosphere across an elevational gradient.}, journal = {Environmental microbiology reports}, volume = {16}, number = {6}, pages = {e70042}, pmid = {39572861}, issn = {1758-2229}, support = {52270198//National Natural Science Foundation of China/ ; }, mesh = {*Bacteria/genetics/classification/isolation & purification ; *Phylogeny ; *Microbiota/genetics ; Biodiversity ; Metagenomics ; Genes, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Ecosystem ; Altitude ; Drug Resistance, Bacterial/genetics ; }, abstract = {Antibiotic resistance genes (ARGs) are ancient and widespread in natural habitats, providing survival advantages for microbiomes under challenging conditions. In mountain ecosystems, phyllosphere bacterial communities face multiple stress conditions, and the elevational gradients of mountains represent crucial environmental gradients for studying biodiversity distribution patterns. However, the distribution patterns of ARGs in the phyllosphere along elevational gradients, and their correlation with bacterial community structures, remain poorly understood. Here, we applied metagenomic analyses to investigate the abundance and diversity of ARGs in 88 phyllosphere samples collected from Mount Tianmu, a national natural reserve. Our results showed that the abundance of ARGs in the phyllosphere increased along elevational gradients and was dominated by multidrug resistance and efflux pumps. The composition of bacterial communities, rather than plant traits or abiotic factors, significantly affected ARG abundance. Moreover, increased ARG abundance was correlated with greater phylogenetic overdispersion and a greater proportion of negative associations in the bacterial co-occurrence networks, suggesting that bacterial competition primarily shapes phyllosphere resistomes. These findings constitute a major advance in the biodiversity of phyllosphere resistomes along elevations, emphasizing the significant impact of bacterial community structure and assembly on ARG distribution, and are essential for understanding the emergence of ARGs.}, } @article {pmid39572788, year = {2024}, author = {Pereira, FC and Ge, X and Kristensen, JM and Kirkegaard, RH and Maritsch, K and Szamosvári, D and Imminger, S and Seki, D and Shazzad, JB and Zhu, Y and Decorte, M and Hausmann, B and Berry, D and Wasmund, K and Schintlmeister, A and Böttcher, T and Cheng, JX and Wagner, M}, title = {The Parkinson's disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration.}, journal = {Nature microbiology}, volume = {9}, number = {12}, pages = {3165-3183}, pmid = {39572788}, issn = {2058-5276}, support = {R01AI141439//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01EB032391//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01 AI141439/AI/NIAID NIH HHS/United States ; R01 EB032391/EB/NIBIB NIH HHS/United States ; Z383-B//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; ZK-57//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; S10 OD024993/OD/NIH HHS/United States ; 10.55776; COE 7//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; 10.55776 COE 7//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; R35GM136223//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R35 GM136223/GM/NIGMS NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Iron/metabolism ; *Parkinson Disease/microbiology/metabolism/drug therapy ; *Feces/microbiology ; *Catechols/pharmacology/metabolism ; *Nitriles/pharmacology ; Homeostasis/drug effects ; Bacteria/genetics/drug effects/metabolism/classification/isolation & purification ; Metagenomics ; Antiparkinson Agents/pharmacology ; }, abstract = {Many human-targeted drugs alter the gut microbiome, leading to implications for host health. However, the mechanisms underlying these effects are not well known. Here we combined quantitative microbiome profiling, long-read metagenomics, stable isotope probing and single-cell chemical imaging to investigate the impact of two widely prescribed drugs on the gut microbiome. Physiologically relevant concentrations of entacapone, a treatment for Parkinson's disease, or loxapine succinate, used to treat schizophrenia, were incubated ex vivo with human faecal samples. Both drugs significantly impact microbial activity, more so than microbial abundance. Mechanistically, entacapone can complex and deplete available iron resulting in gut microbiome composition and function changes. Microbial growth can be rescued by replenishing levels of microbiota-accessible iron. Further, entacapone-induced iron starvation selected for iron-scavenging gut microbiome members encoding antimicrobial resistance and virulence genes. These findings reveal the impact of two under-investigated drugs on whole microbiomes and identify metal sequestration as a mechanism of drug-induced microbiome disturbance.}, } @article {pmid39572621, year = {2024}, author = {Rabenhorst, SHB and Ferrasi, AC and Barboza, MMO and Melo, VMM}, title = {Microbial composition of gastric lesions: differences based on Helicobacter pylori virulence profile.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {28890}, pmid = {39572621}, issn = {2045-2322}, support = {07939716/2020//Fundação Cearense de Apoio ao Desenvolvimento Científico e Tecnológico/ ; }, mesh = {Humans ; *Helicobacter pylori/pathogenicity/genetics ; *Helicobacter Infections/microbiology/pathology ; *Stomach Neoplasms/microbiology/pathology ; *Gastritis/microbiology/pathology ; Virulence ; *Gastric Mucosa/microbiology/pathology ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Aged ; Metaplasia/microbiology ; Adult ; Gastrointestinal Microbiome ; }, abstract = {Helicobacter pylori infection is a major risk factor for gastric adenocarcinomas. In the case of the intestinal subtype, chronic gastritis and intestinal metaplasia are well-known sequential steps in carcinogenesis. H. pylori has high genetic diversity that can modulate virulence and pathogenicity in the human host as a cag Pathogenicity Island (cagPAI). However, bacterial gene combinations do not always explain the clinical presentation of the disease, indicating that other factors associated with H. pylori may play a role in the development of gastric disease. In this context, we characterized the microbial composition of patients with chronic gastritis (inactive and active), intestinal metaplasia, and gastric cancer as well as their potential association with H. pylori. To this end, 16 S rRNA metagenomic analysis was performed on gastric mucosa samples from patients with different types of lesions and normal gastric tissues. Our main finding was that H. pylori virulence status can contribute to significant differences in the constitution of the gastric microbiota between the sequential steps of the carcinogenesis cascade. Differential microbiota was observed in inactive and active gastritis dependent of the H. pylori presence and status (p = 0.000575). Pseudomonades, the most abundant order in the gastritis, was associated the presence of non-virulent H. pylori in the active gastritis. Notably, there are indicator genera according to H. pylori status that are poorly associated with diseases and provide additional evidence that the microbiota, in addition to H. pylori, is relevant to gastric carcinogenesis.}, } @article {pmid39572618, year = {2024}, author = {Xiang, C and Wu, X and Li, T and Tang, X and Zhang, Y and Zeng, F and Xiang, H and Chen, T and Kuang, Z and Liu, F and Yang, T and Chen, X and Chen, J and Wu, Y and Huang, X and Wang, Y and Pan, C and Wang, Y}, title = {Effect of metagenomic next-generation sequencing on clinical outcomes in adults with severe pneumonia post-cardiac surgery: a single-center retrospective study.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {28907}, pmid = {39572618}, issn = {2045-2322}, support = {Grant no.2021YFS0380//Sichuan Science and Technology Department/ ; }, mesh = {Humans ; Male ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; Female ; Middle Aged ; *Cardiac Surgical Procedures/adverse effects ; *Metagenomics/methods ; Aged ; *Pneumonia/microbiology/diagnosis ; Bronchoalveolar Lavage Fluid/microbiology ; Postoperative Complications/microbiology/diagnosis ; Adult ; Intensive Care Units ; }, abstract = {Reports on the application of metagenomic next-generation sequencing (mNGS) in adult patients with severe pneumonia after cardiac surgery remain limited. This study aimed to evaluate the clinical outcomes of mNGS analysis of bronchoalveolar lavage fluid (BALF) in such patients.A retrospective cohort study was conducted on adult patients with severe pneumonia after cardiac surgery. Samples were collected from patients in the surgical intensive care unit (SICU) of Sichuan Provincial People's Hospital between January 2019 and March 2024. Upon diagnosis of severe pneumonia, bronchoalveolar lavage fluid was obtained via bronchoscopy within 24 h. The mNGS group was composed of patients tested using mNGS and conventional microbiological tests. BALF was detected only by the conventional microbiological test (CMT) method in the CMT group, which involved examining bacterial and fungal smears and cultures at least. We reviewed a total of 4,064 cardiac surgeries, and based on the inclusion criteria, a total of 113 adult patients with severe pneumonia after cardiac surgery were included in this study. The overall positive rate detected by mNGS was significantly higher than that of the culture method (98% vs. 58%, P<0.0001). After receipt of the microbiological results, the mNGS group exhibited a higher incidence of antibiotic adjustments in comparison to the CMT group (P = 0.0021). After adjusting the treatment plan based on microbial testing results, the mNGS group showed an improvement in ventilator-free days within 28 days (P = 0.0475), with a shorter duration of invasive ventilation compared to the CMT group (P = 0.0208). The detection of mNGS can significantly improve the Acute Physiology and Chronic Health Evaluation-II (APACHE II) score (P = 0.0161) and Sequential Organ Failure Assessment (SOFA) score (P = 0.0076) on the 7th day after admission to the SICU. In this study, the mNGS group showed signs of having a positive impact on the length of stay in ICU (median: 9 days, IQR: 7-10 days vs. median: 10 days, IQR: 8-13.75 days, P = 0.0538), length of stay in Hospital (median: 20 days, IQR: 17-28 days vs. median: 25 days, IQR: 18-29 days, P = 0.1558), mortality in 28 days (19% vs. 20%, P = 0.8794), in-hospital mortality (19% vs. 22%, P = 0.7123); however, statistical analysis did not confirm these differences to be significant. mNGS could serve as a valuable complement to conventional diagnostic approaches in adult patients with severe pneumonia after cardiac surgery, potentially improving diagnostic accuracy and leading to more precise and timely interventions, with significant potential to inform clinical decision-making and enhance patient outcomes.}, } @article {pmid39572587, year = {2024}, author = {Yang, S and Zheng, J and Mao, H and Vinitchaikul, P and Wu, D and Chai, J}, title = {Multiomics of yaks reveals significant contribution of microbiome into host metabolism.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {133}, pmid = {39572587}, issn = {2055-5008}, mesh = {Animals ; Cattle ; *Rumen/microbiology ; *Metagenomics/methods ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Gastrointestinal Microbiome ; Metabolomics/methods ; Methane/metabolism ; Animal Feed ; Metabolome ; Microbiota ; Multiomics ; }, abstract = {An intensive feeding system might improve the production cycle of yaks. However, how intensive feeding system contributes to yak growth is unclear. Here, multi-omics, including rumen metagenomics, rumen and plasma metabolomics, were performed to classify the regulatory mechanisms of intensive feeding system on yaks. Increased growth performance were observed. Rumen metagenomics revealed that Clostridium, Methanobrevibacter, Piromyces and Anaeromyces increased in the intensively fed yaks, contributing to amino acid and carbohydrate metabolism. The grazing yaks had more cellulolytic microbes. These microbiomes were correlated with the pathways of "Alanine aspartate and glutamate metabolism" and "Pyruvate metabolism". Intensive feeding increased methane degradation functions, while grazing yaks had higher methyl metabolites associated with methane production. These rumen microbiomes and their metabolites resulted in changes in plasma metabolome, finally influencing yaks' growth. Thus, an intensive feeding system altered the rumen microbiome and metabolism as well as host metabolism, resulting in improvements of yak growth.}, } @article {pmid39571816, year = {2024}, author = {Arros, P and Palma, D and Gálvez-Silva, M and Gaete, A and Gonzalez, H and Carrasco, G and Coche, J and Perez, I and Castro-Nallar, E and Galbán, C and Varas, MA and Campos, M and Acuña, J and Jorquera, M and Chávez, FP and Cambiazo, V and Marcoleta, AE}, title = {Life on the edge: Microbial diversity, resistome, and virulome in soils from the union glacier cold desert.}, journal = {The Science of the total environment}, volume = {957}, number = {}, pages = {177594}, doi = {10.1016/j.scitotenv.2024.177594}, pmid = {39571816}, issn = {1879-1026}, mesh = {*Soil Microbiology ; Antarctic Regions ; *Ice Cover/microbiology ; *Desert Climate ; *Bacteria/genetics ; *Microbiota ; Soil/chemistry ; Biodiversity ; }, abstract = {The high-latitude regions of Antarctica remain among the most remote, extreme, and least explored areas on Earth. Still, microbial life has been reported in these environments, with limited information on their genetic properties and functional capabilities. Although diverse autochthonous multidrug-resistant bacteria were found in Antarctic Peninsula soils, posing whether these soils could act as a source of resistance determinants that could emerge among pathogens, we still lack information regarding the resistome of areas closer to the South Pole. Moreover, no previous studies have evaluated the pathogenic potential of microbes inhabiting Antarctic soils. In this work, we combined metagenomic and culture-dependent approaches to investigate the microbial diversity, resistome, virulome, and mobile genetic elements (MGEs) in soils from Union Glacier, a cold desert in West Antarctica. Despite the extreme conditions, several bacterial phyla were found, predominating Actinomycetota and Pseudomonadota, with limited archaeal and fungal taxa. Contrastive with Ecology Glacier soils from King George Island, the Union Glacier soil bacterial community is significantly less diverse, mainly attributed to scarce moisture. We recovered >80 species-level representative genomes (SRGs) of predominant bacteria and an ammonia-oxidating nitrogen- and carbon-fixing archaeon from a novel species of Nitrosocosmicus. Several resistance and virulence genes were found in Union Glacier soils, similar to those in other Antarctic cold desert areas but significantly distinct from those observed in maritime Antarctica and other non-cryosphere biomes. Furthermore, we characterized bacterial isolates resistant to up to 24 clinical antibiotics, mainly Pseudomonas, Arthrobacter, Plantibacter, and Flavobacterium. Moreover, some isolates produced putative virulence factors, including siderophores, pyocyanins, and exoenzymes with hemolytic, lecithinase, protease, and DNAse activity. This evidence uncovers a largely unexplored resistome and virulome hosted by deep Antarctica's soil microbial communities and the presence of bacteria with pathogenic potential, highlighting the relevance of One Health approaches for environmental surveillance in this continent.}, } @article {pmid39571716, year = {2025}, author = {González-Parra, JA and Barrera-Conde, M and Kossatz, E and Veza, E and de la Torre, R and Busquets-Garcia, A and Robledo, P and Pizarro, N}, title = {Microbiota and social behavior alterations in a mouse model of down syndrome: Modulation by a synbiotic treatment.}, journal = {Progress in neuro-psychopharmacology & biological psychiatry}, volume = {136}, number = {}, pages = {111200}, doi = {10.1016/j.pnpbp.2024.111200}, pmid = {39571716}, issn = {1878-4216}, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; *Down Syndrome/genetics ; Mice ; *Synbiotics ; *Disease Models, Animal ; *Social Behavior ; Mice, Inbred C57BL ; Behavior, Animal/physiology ; Sex Characteristics ; }, abstract = {Sex differences in the composition and functionality of gut microbiota are an emerging field of interest in neurodevelopmental disorders, as they may help in understanding the phenotypic disparities between males and females. This study aimed to characterize sex-related specific alterations in gut microbiota composition in a mouse model of Down syndrome (Ts65Dn mice, TS mice) through the sequencing of the PCR-amplified 16S ribosomal DNA fraction. Moreover, it intended to examine whether the modulation of gut microbiota by the administration of a synbiotic (SYN) treatment would be beneficial for the behavioral alterations observed in male and female TS mice. Our results show that male, but not female, TS mice exhibit alterations in beta diversity compared to their wild-type (WT) littermates. Sex-dependent differences are also observed in the relative abundance of the classes Bacilli and Clostridia. Administering the SYN effectively counteracts hypersociability in females, and normalizes the overall abundance of Bacilli, specifically by increasing Lactobacillaceae. On the contrary, it rescues emotional recognition deficits in male TS mice and increases the relative abundance of the families Lactobacillaceae, Streptococcaceae and Atopobiaceae. In addition, a metagenome KEGG analysis of differentially enriched pathways shows relevant changes in the cofactor biosynthesis and the amino acid synthesis categories. Finally, following SYN treatment, both male and female TS mice exhibit a robust increase in propionic acid levels compared to WT littermates. These findings suggest sex-specific mechanisms that could link gut microbiota composition with behavior in TS mice, and underscore the potential of targeted gut microbiota interventions to modulate social abnormalities in neurodevelopmental disorders.}, } @article {pmid39571670, year = {2024}, author = {Kané, F and Collins, J and Koné, A and Keita, NY and Cisse, I and Koné, KM and Diallo, D and Konate, I and Dabitao, DK and Diarra, B and Sanogo, I and Coulibaly, TA and Diallo, M and Keita, D and Tangara, CO and Diakité, M and Dao, S and Fouth-Tchos, K and Aboulhab, J and Neal, A and Shaw-Saliba, K and Lu, XJ and Briese, T and Lipkin, WI and Guindo, I and Chen, RY and Wickiser, JK and Doumbia, S}, title = {Surveillance and agnostic capture sequencing of samples from individuals with rash-associated illness in Mali indicates regional transmission of measles virus from West and Central Africa.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {126}, number = {}, pages = {105691}, doi = {10.1016/j.meegid.2024.105691}, pmid = {39571670}, issn = {1567-7257}, mesh = {Humans ; *Measles/epidemiology/transmission/virology ; Mali/epidemiology ; *Measles virus/genetics/isolation & purification ; *Exanthema/virology ; *Phylogeny ; Child, Preschool ; Genome, Viral ; Infant ; Male ; Child ; Disease Outbreaks ; Female ; Genotype ; Adolescent ; }, abstract = {Measles is vaccine-preventable extremely contagious disease caused by the measles virus. High vaccination coverage is needed to prevent outbreaks of disease. Although molecular surveillance of measles is critical to characterize outbreaks and track viral evolution, few whole-genome sequences of measles virus from West Africa are available despite continual outbreaks in the region. Using VirCapSeq-VERT, an enhanced and comprehensive metagenomic sequencing technique that allows for simultaneous identification of all vertebrate viruses, 23 wild-type near-complete genomes of measles virus from across Mali were obtained from samples collected between January 2012 to October 2022. Other febrile rash illnesses were also identified by VirCapSeq-VERT, demonstrating the advantage of using broad detection agnostic methods when the clinical diagnosis is unclear. Whereas one measles virus sequence was consistent with measles vaccine-associated rash illness (VARI), the remaining 38 were classified within the B3.1 genotype. Broad surveillance throughout Mali reveals regional measles virus transmission across West and Central Africa into Mali, while local clinical testing in Bamako shows stable sequence conservation within genotype B3.1 evolving from Nigerian sequences. The genomic information generated in this study is critical in addressing the lack of whole genome sequences available in West Africa and these findings show the importance of phylogenetically tracking measles outbreaks given recent increases in measles cases globally.}, } @article {pmid39571342, year = {2024}, author = {Calvani, R and Giampaoli, O and Marini, F and Del Chierico, F and De Rosa, M and Conta, G and Sciubba, F and Tosato, M and Picca, A and Ciciarello, F and Galluzzo, V and Gervasoni, J and Di Mario, C and Santoro, L and Tolusso, B and Spagnoli, M and Tomassini, A and Aureli, W and Toto, F and Pane, S and Putignani, L and Miccheli, A and Marzetti, E and Landi, F and , }, title = {Beetroot juice intake positively influenced gut microbiota and inflammation but failed to improve functional outcomes in adults with long COVID: A pilot randomized controlled trial.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {43}, number = {12}, pages = {344-358}, doi = {10.1016/j.clnu.2024.11.023}, pmid = {39571342}, issn = {1532-1983}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; *Beta vulgaris/chemistry ; *Fruit and Vegetable Juices ; Pilot Projects ; Adult ; Double-Blind Method ; Middle Aged ; *COVID-19 ; *Inflammation ; Dietary Supplements ; Nitrates ; SARS-CoV-2 ; Young Adult ; }, abstract = {BACKGROUND & AIMS: Long-term effects of coronavirus disease 2019 (long COVID) develop in a substantial number of people following an acute COVID-19 episode. Red beetroot juice may have positive effects on multiple pathways involved in long COVID. The aim of this pilot study was to explore the impact of beetroot juice supplementation on physical function, gut microbiota, and systemic inflammation in adults with long COVID.

METHODS: A single-center, double-blind, placebo-controlled randomized trial was conducted to test the effects of 14 days of beetroot juice supplementation, rich in nitrates and betalains, on functional and biological outcomes in adults aged between 20 and 60 years with long COVID. Participants were randomized 1:1 to receive either daily oral supplementation with 200 mL beetroot juice (∼600 mg nitrate) or placebo (∼60 mg nitrate) for 14 days. The primary endpoint was the change from baseline to day 14 in a fatigue resistance test. Secondary outcomes included the distance walked on the 6-min walk test, handgrip strength, and flow-mediated dilation. Secondary endpoints also included changes from baseline in circulating inflammatory mediators and metagenomic and fecal water metabolomic profiles. Partial least squares discriminant analysis (PLS-DA) models were built to evaluate the differences in biological variables associated with the interventions.

RESULTS: Thirty-one participants were randomized in the study. Twenty-five of them (median (interquartile range) age 40 (10), 14 [56 %] women), received either beetroot juice (15) or placebo (10) and completed the study. At 14 days, fatigue resistance significantly improved from baseline (mean difference [standard error]: +21.8 [3.7] s; p < 0.001) with no significant differences between intervention groups. A significant increase from baseline in the distance walked on the 6-min walk test was observed (mean difference [standard error]: +30.0 [9.4] m; p = 0.03), which was not different between groups. Flow-mediated dilation did not differ between participants who received beetroot juice and those on placebo. PLS-DA models allowed correct classification of participants with 92.2 ± 4.4 % accuracy. Those who ingested red beetroot juice had a greater abundance of bacteria with well-known beneficial effects, including Akkermansia, Oscillospira, Prevotella, Roseburia, Ruminococcaceae, and Turicibacter, compared with placebo. Participants allocated to beetroot juice supplementation were also characterized by significantly higher levels of fecal nicotinate, trimethylamine, and markers of beetroot juice intake (e.g., 5,6-dihydroxyindole). Finally, higher levels of interferon gamma and macrophage inflammatory protein-1β were found in participants who consumed beetroot juice.

CONCLUSION: Beetroot juice supplementation for two weeks did not to induce significant improvements in functional outcomes in adults with long COVID compared with placebo. Beneficial effects were observed in both gut microbiota composition (i.e., increase in probiotic species) and inflammatory mediators.

TRIAL REGISTRATION: Trial was registered under ClinicalTrials.gov. Identifier no. NCT06535165.}, } @article {pmid39571299, year = {2024}, author = {Talavera Andújar, B and Pereira, SL and Busi, SB and Usnich, T and Borsche, M and Ertan, S and Bauer, P and Rolfs, A and Hezzaz, S and Ghelfi, J and Brüggemann, N and Antony, P and Wilmes, P and Klein, C and Grünewald, A and Schymanski, EL}, title = {Exploring environmental modifiers of LRRK2-associated Parkinson's disease penetrance: An exposomics and metagenomics pilot study on household dust.}, journal = {Environment international}, volume = {194}, number = {}, pages = {109151}, doi = {10.1016/j.envint.2024.109151}, pmid = {39571299}, issn = {1873-6750}, mesh = {Humans ; *Parkinson Disease/genetics ; *Dust/analysis ; *Leucine-Rich Repeat Serine-Threonine Protein Kinase-2/genetics ; Pilot Projects ; *Metagenomics ; Male ; Female ; Middle Aged ; Aged ; *Environmental Exposure ; Penetrance ; Metabolomics ; }, abstract = {Pathogenic variants in the Leucine-rich repeat kinase 2 (LRRK2) gene are a primary monogenic cause of Parkinson's disease (PD). However, the likelihood of developing PD with inherited LRRK2 pathogenic variants differs (a phenomenon known as "reduced penetrance"), with factors including age and geographic region, highlighting a potential role for lifestyle and environmental factors in disease onset. To investigate this, household dust samples from four different groups of individuals were analyzed using metabolomics/exposomics and metagenomics approaches: PD+/LRRK2+ (PD patients with pathogenic LRRK2 variants; n = 11), PD-/LRRK2+ (individuals with pathogenic LRRK2 variants but without PD diagnosis; n = 8), iPD (PD of unknown cause; n = 11), and a matched, healthy control group (n = 11). The dust was complemented with metabolomics and lipidomics of matched serum samples, where available. A total of 1,003 chemicals and 163 metagenomic operational taxonomic units (mOTUs) were identified in the dust samples, of which ninety chemicals and ten mOTUs were statistically significant (ANOVA p-value < 0.05). Reduced levels of 2-benzothiazolesulfonic acid (BThSO3) were found in the PD-/LRRK2+ group compared to the PD+/LRRK2+ . Among the significant chemicals tentatively identified in dust, two are hazardous chemical replacements: Bisphenol S (BPS), and perfluorobutane sulfonic acid (PFBuS). Furthermore, various lipids were found altered in serum including different lysophosphatidylethanolamines (LPEs), and lysophosphatidylcholines (LPCs), some with higher levels in the PD+/LRRK2+ group compared to the control group. A cellular study on isogenic neurons generated from a PD+/LRRK2+ patient demonstrated that BPS negatively impacts mitochondrial function, which is implicated in PD pathogenesis. This pilot study demonstrates how non-target metabolomics/exposomics analysis of indoor dust samples complemented with metagenomics can prioritize relevant chemicals that may be potential modifiers of LRRK2 penetrance.}, } @article {pmid39571000, year = {2024}, author = {Zapién-Campos, R and Bansept, F and Traulsen, A}, title = {Stochastic models allow improved inference of microbiome interactions from time series data.}, journal = {PLoS biology}, volume = {22}, number = {11}, pages = {e3002913}, pmid = {39571000}, issn = {1545-7885}, mesh = {*Stochastic Processes ; *Microbiota ; Models, Biological ; Metagenome ; Humans ; Microbial Interactions/physiology ; Algorithms ; }, abstract = {How can we figure out how the different microbes interact within microbiomes? To combine theoretical models and experimental data, we often fit a deterministic model for the mean dynamics of a system to averaged data. However, in the averaging procedure a lot of information from the data is lost-and a deterministic model may be a poor representation of a stochastic reality. Here, we develop an inference method for microbiomes based on the idea that both the experiment and the model are stochastic. Starting from a stochastic model, we derive dynamical equations not only for the average, but also for higher statistical moments of the microbial abundances. We use these equations to infer distributions of the interaction parameters that best describe the biological experimental data-improving identifiability and precision. The inferred distributions allow us to make predictions but also to distinguish between fairly certain parameters and those for which the available experimental data does not give sufficient information. Compared to related approaches, we derive expressions that also work for the relative abundance of microbes, enabling us to use conventional metagenome data, and account for cases where not a single host, but only replicate hosts, can be tracked over time.}, } @article {pmid39570026, year = {2024}, author = {Waterworth, SC and Solomons, GM and Kalinski, J-CJ and Madonsela, LS and Parker-Nance, S and Dorrington, RA}, title = {The unique and enigmatic spirochete symbiont of latrunculid sponges.}, journal = {mSphere}, volume = {9}, number = {12}, pages = {e0084524}, pmid = {39570026}, issn = {2379-5042}, support = {87583//National Research Foundation (NRF)/ ; 110612//National Research Foundation (NRF)/ ; 96185//South African Medical Research Council (SAMRC)/ ; 101038//National Research Foundation (NRF)/ ; }, mesh = {*Symbiosis ; Animals ; *Porifera/microbiology ; *Phylogeny ; Metagenome ; Spirochaetales/genetics/classification/physiology ; }, abstract = {Bacterial symbionts are critical members of many marine sponge holobionts. Some sponge-associated bacterial lineages, such as Poribacteria, sponge-associated unclassified lineage (SAUL), and Tethybacterales, appear to have broad-host ranges and associate with a diversity of sponge species, while others are more species-specific, having adapted to the niche environment of their host. Host-associated spirochete symbionts that are numerically dominant have been documented in several invertebrates including termites, starfish, and corals. However, dominant spirochete populations are rare in marine sponges, having thus far been observed only in Clathrina clathrus and various species within the Latrunculiidae family, where they are co-dominant alongside Tethybacterales symbionts. This study aimed to characterize these spirochetes and their potential role in the host sponge. Analysis of metagenome-assembled genomes from eight latrunculid sponges revealed that these unusual spirochetes are relatively recent symbionts and are phylogenetically distinct from other sponge-associated spirochetes. Functional comparative analysis suggests that the host sponge may have selected for these spirochetes due to their ability to produce terpenoids and/or possible structural contributions.IMPORTANCESouth African latrunculid sponges are host to co-dominant Tethybacterales and Spirochete symbionts. While the Tethybacterales are broad-host range symbionts, the spirochetes have not been reported as abundant in any other marine sponge except Clathrina clathrus. However, spirochetes are regularly the most dominant populations in marine corals and terrestrial invertebrates where they are predicted to serve as beneficial symbionts. Here, we interrogated eight metagenome-assembled genomes of the latrunculid-associated spirochetes and found that these symbionts are phylogenetically distinct from all invertebrate-associated spirochetes. The symbiosis between the spirochetes and their sponge host appears to have been established relatively recently.}, } @article {pmid39570022, year = {2024}, author = {Wang, W and Wang, H and Zou, X and Liu, Y and Zheng, K and Chen, X and Wang, X and Sun, S and Yang, Y and Wang, M and Shao, H and Liang, Y}, title = {A novel virus potentially evolved from the N4-like viruses represents a unique viral family: Poorviridae.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {12}, pages = {e0155924}, pmid = {39570022}, issn = {1098-5336}, mesh = {*Genome, Viral ; *Phylogeny ; China ; *Pseudoalteromonas/virology/genetics/isolation & purification ; Seawater/virology ; DNA Viruses/genetics/classification/isolation & purification ; Evolution, Molecular ; Capsid Proteins/genetics ; }, abstract = {UNLABELLED: Pseudoalteromonas are widely distributed in marine extreme habitats and exhibit diverse extracellular protease activity, which is essential for marine biogeochemical cycles. However, our understanding of viruses that infect Pseudoalteromonas remains limited. This study isolated a virus infecting Pseudoalteromonas nigrifaciens from Xiaogang in Qingdao, China. vB_PunP_Y3 comprises a linear, double-strand DNA genome with a length of 48,854 bp, encoding 52 putative open reading frames. Transmission electron microscopy demonstrates the short-tailed morphology of vB_PunP_Y3. Phylogenetic and genome-content-based analysis indicate that vB_PunP_Y3 represents a novel virus family named as Poorviridae, along with three high-quality uncultivated viral genomes. Biogeographical analyses show that Poorviridae is distributed across five viral ecological zones, and is predominantly detected in the Antarctic, Arctic, and bathypelagic zones. Comparative genomics analyses identified three of the seven hallmark proteins of N4-like viruses (DNA polymerase, major capsid protein, and virion-encapsulated RNA polymerase) from vB_PunP_Y3, combing with the protein tertiary structures of the major capsid protein, suggesting that vB_PunP_Y3 might evolve from the N4-like viruses.

IMPORTANCE: vB_PunP_Y3 is a unique strain containing three of the seven hallmark proteins of N4-like viruses, but is grouped into a novel family-level viral cluster with three uncultured viruses from metagenomics, named Poorviridae. This study enhanced the understanding about the genetic diversity, evolution, and distribution of Pseudoalteromonas viruses and provided insights into the novel evolution mechanism of marine viruses.}, } @article {pmid39569373, year = {2024}, author = {Talukdar, D and Sarkar, M and Ahrodia, T and Kumar, S and De, D and Nath, S and Jana, P and Verma, J and Mehta, O and Kothidar, A and Yodhaanjali, JR and Sharma, K and Bakshi, S and Singh, U and Kshetrapal, P and Wadhwa, N and Thiruvengadam, R and , and Nair, GB and Bhatnagar, S and Mukherjee, S and Das, B}, title = {Previse preterm birth in early pregnancy through vaginal microbiome signatures using metagenomics and dipstick assays.}, journal = {iScience}, volume = {27}, number = {11}, pages = {111238}, pmid = {39569373}, issn = {2589-0042}, abstract = {Annually, in India, 13% of all newborns are preterm, accounting for 23.4% of preterm birth (PTB) globally. The composition and diversity of the vaginal microbiome have a notable degree of ethnic inequality. For understanding differences in vaginal microbiome composition and functions between adverse and normal pregnancy, we have collected, processed and sequenced 600 high vaginal swab (HVS) samples across the three trimesters of pregnancy from 140 women who delivered at term and 60 women who delivered PTB, adopting a targeted metagenomics approach. The microbial signatures in HVS samples showed Lactobacillus genera to be highly abundant in term birth (TB), while in early pregnancy the abundances of Gardnerella, Atopobium, and Sneathia were found to be high in PTB. We further extended our analysis, identified specific microbial genomic signatures, and developed a dipstick assay for rapid identification of PTB-associated microbiota in HVS samples in low-resource settings.}, } @article {pmid39568836, year = {2024}, author = {Xie, X and Xi, X and Zhao, D and Zhao, Y and Yi, T and Chen, D and Liu, R and Qi, L and Pan, Z and Wang, H and Zhang, H and Ding, R and Du, H}, title = {Advancing pathogen and tumor copy number variation detection through simultaneous metagenomic next-generation sequencing: A comprehensive review.}, journal = {Heliyon}, volume = {10}, number = {21}, pages = {e38826}, pmid = {39568836}, issn = {2405-8440}, abstract = {In clinical practice, timely and accurate diagnosis can effectively reduce unnecessary treatment, avoid high medical costs, and prevent adverse prognoses. However, some patients with malignant tumors and those with infection often exhibit similar symptoms, which are difficult to distinguish, posing challenges in accurate clinical diagnosis. Metagenomic next-generation sequencing (mNGS) technology has been widely applied to confirm the source of infection. Recent studies have shown that for pathogen detection, mNGS technology can be used to perform chromosomal copy number variations (CNVs) analysis in two different analytical pipelines using the same wet test. mNGS technology has further demonstrated its utility in not only the determination of pathogenic microorganisms but also of CNVs, thereby facilitating early differential diagnosis for malignant tumors. In this review, we aim to analyze the diagnostic performance of mNGS technology in the simultaneous detection of pathogenic microorganisms and CNVs in current clinical practice and discuss the advantages and limitations of mNGS-CNV dual-omics detection technology. Our review highlights the need for more large-scale prospective research data on current mNGS-CNV dual-omics detection technology to provide more evidence-based results for researchers and clinicians and to promote the greater role of this technology in future clinical practice.}, } @article {pmid39568747, year = {2024}, author = {Liang, X and Liu, X and Huang, Z and Qiu, F and Jiang, Y and Li, C and Deng, Z and Wu, J}, title = {Case report: Metagenomic next-generation sequencing for the diagnosis of rare Nocardia aobensis infection in a patient with immune thrombocytopenia.}, journal = {Frontiers in medicine}, volume = {11}, number = {}, pages = {1425655}, pmid = {39568747}, issn = {2296-858X}, abstract = {BACKGROUND: Nocardiosis poses a diagnostic challenge due to its rarity in clinical practice, non-specific clinical symptoms and imaging features, and the limitations of traditional detection methods. Nocardia aobensis (N. aobensis) is rarely detected in clinical samples. Metagenomic next-generation sequencing (mNGS) offers significant advantages over traditional methods for rapid and accurate diagnosis of infectious diseases, especially for rare pathogens.

CASE PRESENTATION: A 52-year-old woman with a history of immune thrombocytopenia for over 2 years was hospitalized for recurrent fever and cough lasting for 10 days. Her initial diagnosis on admission was community-acquired pneumonia, based on chest computed tomography findings of lung inflammation lesion. Empirical treatment with moxifloxacin and trimethoprim-sulfamethoxazole (TMP-SMZ) was initiated. However, her condition failed to improve significantly even after 1 week of treatment. Bronchoalveolar lavage fluid (BALF) subjected to mNGS revealed the presence of N. aobensis, resulting in a diagnosis of pulmonary nocardiosis caused by N. aobensis. This diagnosis was also supported by Sanger sequencing of the BALF. After adjusting the antibiotic regimen to include TMP-SMZ in combination with imipenem, the patient's condition significantly improved. She was finally discharged with instructions to continue oral treatment with TMP-SMZ and linezolid for 6 months. The patient's first follow-up 1 month after discharge showed good treatment outcomes but with obvious side effects of the drugs. Consequently, the antibiotic regimen was changed to doxycycline, and the patient continued to improve.

CONCLUSION: We report the first detailed case of pulmonary nocardiosis caused by N. aobensis diagnosed by mNGS. mNGS could be an effective method that facilitates early diagnosis and timely decision-making for the treatment of nocardiosis, especially in cases that involve rare pathogens.}, } @article {pmid39568069, year = {2024}, author = {Bano, S and Wu, Q and Yu, S and Wang, X and Zhang, X}, title = {Soil properties drive nitrous oxide accumulation patterns by shaping denitrifying bacteriomes.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {94}, pmid = {39568069}, issn = {2524-6372}, support = {31971526//National Natural Science Foundation of China/ ; 2017YFD0200102//National Key Research and Development Program of China/ ; }, abstract = {In agroecosystems, nitrous oxide (N2O) emissions are influenced by both microbiome composition and soil properties, yet the relative importance of these factors in determining differential N2O emissions remains unclear. This study investigates the impacts of these factors on N2O emissions using two primary agricultural soils from northern China: fluvo-aquic soil (FS) from the North China Plain and black soil (BS) from Northeast China, which exhibit significant differences in physicochemical properties. In non-sterilized controls (NSC), we observed distinct denitrifying bacterial phenotypes between FS and BS, with BS exhibiting significantly higher N2O emissions. Cross-inoculation experiments were conducted by introducing extracted microbiomes into sterile recipient soils of both types to disentangle the relative contributions of soil properties and microbiomes on N2O emission potential. The results showed recipient-soil-dependent gas kinetics, with significantly higher N2O/(N2O + N2) ratios in BS compared to FS, regardless of the inoculum type. Metagenomic analysis further revealed significant shifts in denitrification genes and microbial diversity of the inoculated bacteriomes influenced by the recipient soil. The higher ratios of nirS/nosZ in FS and nirK/nosZ in BS indicated that the recipient soil dictates the formation of different denitrifying guilds. Specifically, the BS environment fosters nirK-based denitrifiers like Rhodanobacter, contributing to higher N2O accumulation, while FS supports a diverse array of denitrifiers, including Pseudomonas and Stutzerimonas, associated with complete denitrification and lower N2O emissions. This study underscores the critical role of soil properties in shaping microbial community dynamics and greenhouse gas emissions. These findings highlight the importance of considering soil physicochemical properties in managing agricultural practices to mitigate N2O emissions.}, } @article {pmid39568064, year = {2024}, author = {Sauma-Sánchez, T and Alcorta, J and Tamayo-Leiva, J and Díez, B and Bezuidenhout, H and Cowan, DA and Ramond, JB}, title = {Functional redundancy buffers the effect of poly-extreme environmental conditions on southern African dryland soil microbial communities.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {12}, pages = {}, pmid = {39568064}, issn = {1574-6941}, support = {FBIS160422162807//National Research Foundation/ ; 1210912//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; }, mesh = {*Soil Microbiology ; *Bacteria/genetics/classification ; *Archaea/genetics/classification ; *Microbiota ; *Salinity ; *Fungi/genetics/classification ; Climate Change ; Desert Climate ; Soil/chemistry ; Extreme Environments ; Africa, Southern ; Biodiversity ; }, abstract = {Drylands' poly-extreme conditions limit edaphic microbial diversity and functionality. Furthermore, climate change exacerbates soil desiccation and salinity in most drylands. To better understand the potential effects of these changes on dryland microbial communities, we evaluated their taxonomic and functional diversities in two Southern African dryland soils with contrasting aridity and salinity. Fungal community structure was significantly influenced by aridity and salinity, while Bacteria and Archaea only by salinity. Deterministic homogeneous selection was significantly more important for bacterial and archaeal communities' assembly in hyperarid and saline soils when compared to those from arid soils. This suggests that niche partitioning drives bacterial and archaeal communities' assembly under the most extreme conditions. Conversely, stochastic dispersal limitations drove the assembly of fungal communities. Hyperarid and saline soil communities exhibited similar potential functional capacities, demonstrating a disconnect between microbial structure and function. Structure variations could be functionally compensated by different taxa with similar functions, as implied by the high levels of functional redundancy. Consequently, while environmental selective pressures shape the dryland microbial community assembly and structures, they do not influence their potential functionality. This suggests that they are functionally stable and that they could be functional even under harsher conditions, such as those expected with climate change.}, } @article {pmid39567690, year = {2025}, author = {Borton, MA and McGivern, BB and Willi, KR and Woodcroft, BJ and Mosier, AC and Singleton, DM and Bambakidis, T and Pelly, A and Daly, RA and Liu, F and Freiburger, A and Edirisinghe, JN and Faria, JP and Danczak, R and Leleiwi, I and Goldman, AE and Wilkins, MJ and Hall, EK and Pennacchio, C and Roux, S and Eloe-Fadrosh, EA and Good, SP and Sullivan, MB and Wood-Charlson, EM and Miller, CS and Ross, MRV and Henry, CS and Crump, BC and Stegen, JC and Wrighton, KC}, title = {A functional microbiome catalogue crowdsourced from North American rivers.}, journal = {Nature}, volume = {637}, number = {8044}, pages = {103-112}, pmid = {39567690}, issn = {1476-4687}, support = {P30 CA046934/CA/NCI NIH HHS/United States ; }, mesh = {*Crowdsourcing ; *Microbiota/genetics ; *Rivers/microbiology ; United States ; Water Microbiology ; Transcriptome ; Carbon Cycle ; Metagenome ; Databases, Factual ; }, abstract = {Predicting elemental cycles and maintaining water quality under increasing anthropogenic influence requires knowledge of the spatial drivers of river microbiomes. However, understanding of the core microbial processes governing river biogeochemistry is hindered by a lack of genome-resolved functional insights and sampling across multiple rivers. Here we used a community science effort to accelerate the sampling, sequencing and genome-resolved analyses of river microbiomes to create the Genome Resolved Open Watersheds database (GROWdb). GROWdb profiles the identity, distribution, function and expression of microbial genomes across river surface waters covering 90% of United States watersheds. Specifically, GROWdb encompasses microbial lineages from 27 phyla, including novel members from 10 families and 128 genera, and defines the core river microbiome at the genome level. GROWdb analyses coupled to extensive geospatial information reveals local and regional drivers of microbial community structuring, while also presenting foundational hypotheses about ecosystem function. Building on the previously conceived River Continuum Concept[1], we layer on microbial functional trait expression, which suggests that the structure and function of river microbiomes is predictable. We make GROWdb available through various collaborative cyberinfrastructures[2,3], so that it can be widely accessed across disciplines for watershed predictive modelling and microbiome-based management practices.}, } @article {pmid39567665, year = {2024}, author = {Zhang, T and Hasegawa, Y and Waldor, MK}, title = {Enteric bacterial infection stimulates remodelling of bile metabolites to promote intestinal homeostasis.}, journal = {Nature microbiology}, volume = {9}, number = {12}, pages = {3376-3390}, pmid = {39567665}, issn = {2058-5276}, support = {P30 DK034854/DK/NIDDK NIH HHS/United States ; R01 AI042347/AI/NIAID NIH HHS/United States ; MKW//Howard Hughes Medical Institute (HHMI)/ ; }, mesh = {Animals ; Mice ; *Homeostasis ; *Citrobacter rodentium ; *Enterobacteriaceae Infections/microbiology/metabolism ; *Metabolome ; *Gastrointestinal Microbiome ; *Bile/metabolism ; Liver/metabolism/microbiology ; Listeria monocytogenes/genetics ; Mice, Inbred C57BL ; Intestines/microbiology ; Metabolomics ; Listeriosis/microbiology/metabolism ; Bile Acids and Salts/metabolism ; Specific Pathogen-Free Organisms ; }, abstract = {The liver makes bile, an aqueous solution critical for fat absorption, which is secreted into the duodenum. Despite extensive studies on bile salts, other components of bile are less well characterized. Here we used global metabolomic analysis on bile from specific-pathogen-free, germ-free, Citrobacter rodentium-infected or Listeria monocytogenes-infected mice and identified a metabolome of 812 metabolites that were altered by both microbiota and enteric infection. Hepatic transcriptomics identified enteric-infection-triggered pathways that probably underlie bile remodelling. Enteric infection increased levels of four dicarboxylates in bile, including itaconate. Analysis of Acod1[-/-] mice indicated that increased itaconate also increased tuft cell abundance, altered microbiota composition and function as detected by metagenomic analysis, and modulated host defence, leading to reduced Vibrio cholerae colonization. Our data suggest that enteric-infection-associated signals are relayed between the intestine and liver and induce transcriptional programmes that shape the bile metabolome, modifying the immunomodulatory and host defence functions of bile.}, } @article {pmid39567534, year = {2024}, author = {Wang, Z and Li, Z and Zhang, Y and Liao, J and Guan, K and Zhai, J and Meng, P and Tang, X and Dong, T and Song, Y}, title = {Root hair developmental regulators orchestrate drought triggered microbiome changes and the interaction with beneficial Rhizobiaceae.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {10068}, pmid = {39567534}, issn = {2041-1723}, mesh = {*Plant Roots/microbiology/metabolism ; *Droughts ; *Microbiota/physiology ; *Stress, Physiological ; Rhizobium/physiology/genetics ; Arabidopsis/microbiology/genetics/metabolism ; Metagenome ; Transcriptome ; Symbiosis ; }, abstract = {Drought is one of the most serious abiotic stresses, and emerging evidence suggest plant microbiome affects plant drought tolerance. However, there is a lack of genetic evidence regarding whether and how plants orchestrate the dynamic assembly of the microbiome upon drought. By utilizing mutants with enhanced or decreased root hair densities, we find that root hair regulators also affect drought induced root microbiome changes. Rhizobiaceae is a key biomarker taxa affected by root hair related mutants. We isolated and sequenced 1479 root associated microbes, and confirmed that several Rhizobium strains presented stress-alleviating activities. Metagenome, root transcriptome and root metabolome studies further reveal the multi-omic changes upon drought stress. We knocked out an ornithine cyclodeaminase (ocd) gene in Rhizobium sp. 4F10, which significantly dampens its stress alleviating ability. Our genetic and integrated multi-omics studies confirm the involvement of host genetic effects in reshaping a stress-alleviating root microbiome during drought, and provide mechanistic insights into Rhizobiaceae mediated abiotic stress protection.}, } @article {pmid39566691, year = {2025}, author = {An, X and Chen, S and Fu, J and Yang, C and Xiao, Y and Zhou, Z}, title = {Metabolic coupling of aerobic methane oxidation and short-cut nitrification and denitrification for anaerobic effluent treatment in photo-sequencing batch biofilm reactor.}, journal = {Bioresource technology}, volume = {417}, number = {}, pages = {131845}, doi = {10.1016/j.biortech.2024.131845}, pmid = {39566691}, issn = {1873-2976}, mesh = {*Methane/metabolism ; *Biofilms ; *Nitrification ; *Bioreactors ; *Oxidation-Reduction ; Anaerobiosis ; *Denitrification ; Aerobiosis ; Biofuels ; Ammonia/metabolism ; }, abstract = {This study explored the use of algae to supply oxygen in situ as an alternative to mechanical aeration for anaerobic effluent treatment in a photo-sequencing batch biofilm reactor (PSBBR). By establishing alternating aerobic (dissolved oxygen (DO) > 2 mg /L)/anoxic conditions (<0.5 mg-DO/L) through a 6-h off/6-h on biogas sparging cycle and continuous illumination (1500-3000 lux), the PSBBR achieved a significant ammonia removal rate of 15-25 mg N L[-1]d[-1]. This system demonstrated robust partial nitrification and nitrite reduction activities, coupled with aerobic methane oxidation. Metagenomic analysis revealed the enrichment of key microbial groups, including Leptolyngbyaceae, Methylocystis, Nitrosomonas and Hyphomicrobium. The key functional genes of methane (mmo, mdh, gfa, frm and fdh) and nitrogen (amo, hao, narGHI, and napAB) metabolisms were identified, while notably lacking nitrite oxidation genes. In conclusion, this study provides a promising post-treatment approach for anaerobic effluent through integrating biogas utilization with efficient nitrogen removal.}, } @article {pmid39566612, year = {2024}, author = {Callejas, IA and Kong, Y and Osborn, K and Hung, WC and Cira, M and Cason, T and Sloane, A and Shenkiryk, A and Masikip, A and Singh, A and Jones, A and Steele, JA and Jay, JA}, title = {The influence of urbanization and water reclamation plants on fecal indicator bacteria and antibiotic resistance in the Los Angeles River watershed: A case study with complementary monitoring methods.}, journal = {The Science of the total environment}, volume = {957}, number = {}, pages = {177577}, doi = {10.1016/j.scitotenv.2024.177577}, pmid = {39566612}, issn = {1879-1026}, mesh = {*Environmental Monitoring/methods ; *Rivers/microbiology ; *Urbanization ; *Feces/microbiology ; Los Angeles ; Drug Resistance, Microbial/genetics ; Water Microbiology ; Drug Resistance, Bacterial/genetics ; Bacteria/genetics ; Escherichia coli/genetics/drug effects ; }, abstract = {Urban land use and water reclamation plants (WRPs) can impact fecal indicator bacteria (FIB) and antimicrobial resistance (AMR) in coastal watersheds. However, there is a lack of studies exploring these effects on the US West Coast. Additionally, there is limited research using a complementary approach across culture-, qPCR-, and metagenomics-based techniques for characterizing environmental AMR. In this study, sixteen locations were sampled in the Los Angeles River, encompassing both upstream and downstream of three WRPs discharging into the river. Culture-dependent methods quantified Enterococcus, total coliforms, E. coli, and extended spectrum beta-lactamase-producing E. coli as a low-cost screening tool for AMR, while qPCR measured selected antibiotic resistance genes (ARGs): sul1, ermF, tetW, blaSHV, along with intI1 and 16S rRNA genes. Bacteroides HF183 and crAssphage markers were quantified via ddPCR. All samples underwent shotgun sequencing to investigate gene abundance and mobility and an overall risk score for AMR. Results reveal downstream sites contain ARGs at least two orders of magnitude greater than upstream locations. Developed areas had the highest ARG sequence abundances and the most ARG classes as indicated by metagenomic analysis. WRP effluent exhibited elevated ARGs and co-location of ARGs, mobile genetic elements, and pathogens. A culture-based assessment of AR in E. coli and Pseudomonas aeruginosa revealed increased resistance ratios for most antibiotics from upstream to downstream a WRP discharge point. This study highlights the impacts of land use and WRPs on ARGs and FIB, offering a multi-pronged analysis of AMR.}, } @article {pmid39566543, year = {2025}, author = {Uemura, T and Kawashima, A and Jingushi, K and Motooka, D and Saito, T and Sassi, N and Horibe, Y and Yamamoto, A and Liu, Y and Tani, M and Yoshimura, A and Oka, T and Okuda, Y and Yamamichi, G and Ishizuya, Y and Yamamoto, Y and Kato, T and Hatano, K and Tsujikawa, K and Wada, H and Nonomura, N}, title = {Bacterial information in serum extracellular vesicles reflects the inflammation of adherent perinephric fat.}, journal = {Cancer science}, volume = {116}, number = {2}, pages = {338-349}, pmid = {39566543}, issn = {1349-7006}, support = {JP2120988 and JP22K09469//Japan Society for the Promotion of Science/ ; }, mesh = {Humans ; *Extracellular Vesicles/metabolism ; Male ; Female ; *Carcinoma, Renal Cell/microbiology/pathology/blood ; *Kidney Neoplasms/pathology/blood/microbiology ; *RNA, Ribosomal, 16S/genetics ; Middle Aged ; *Inflammation/blood/microbiology/pathology ; *Adipose Tissue/microbiology/pathology ; *DNA, Bacterial/genetics ; Aged ; Metagenomics/methods ; Adult ; }, abstract = {Adipose tissue and bacterial flora are involved in metabolism in the human body. However, the relationship between the two remains unclear. Recently, the presence of circulating bacterial DNAs has been reported. We previously reported the utility of bacterial DNA in serum extracellular vesicles (EVs) for diagnosing patients with renal cell carcinoma (RCC). In this study, we aimed to assess whether there is a correlation between bacterial DNA in serum EVs and inflammation in adipose tissue. We undertook 16S rRNA metagenomic analysis of bacterial DNA in serum EVs from 77 patients with RCC (the derivation cohort). We discovered that DNAs from Enterobacteriaceae, Polaromonas, and Coxiellaceae were highly expressed in patients with low Mayo adhesive probability (MAP) scores. A lower MAP score reflects a reduced risk of dense adipose tissue and adhesions. Additionally, we combined these bacterial DNAs to create the EPC (Enterobacteriaceae, Polaromonas, Coxiellaceae) index that predicts a MAP score of 0. Subsequently, we undertook 16S rRNA metagenomic analysis of bacterial DNA in serum EVs from 32 patients with RCC (the validation cohort). The EPC index could distinguish patients with low MAP scores from those with high MAP scores in the derivation (area under the curve [AUC], 0.76; sensitivity, 56%; specificity, 85%) and validation (AUC, 0.81; sensitivity, 100%; specificity, 62%) cohorts. These results suggest that bacterial DNA in serum EVs could reflect the inflammation of adherent perinephric fat around the kidney.}, } @article {pmid39566459, year = {2025}, author = {Xian, Y and Cao, L and Lu, Y and Li, Q and Su, C and He, Y and Zhou, G and Chen, S and Gao, S}, title = {Metagenomics and metaproteomics reveal the effects of sludge types and inoculation modes on N,N-dimethylformamide degradation pathways and the microbial community involved.}, journal = {Journal of hazardous materials}, volume = {481}, number = {}, pages = {136548}, doi = {10.1016/j.jhazmat.2024.136548}, pmid = {39566459}, issn = {1873-3336}, mesh = {*Sewage/microbiology ; *Dimethylformamide/metabolism ; *Metagenomics ; *Biodegradation, Environmental ; *Proteomics ; Microbiota ; Anaerobiosis ; Bacteria/metabolism/genetics/classification ; Aerobiosis ; Methylamines/metabolism ; }, abstract = {This study demonstrated the effects of the sludge type and inoculation method on the N,N-dimethylformamide degradation pathway and associated microbial communities. The sludge type is critical for DMF metabolism, with acclimatized aerobic sludge having a significant advantage in terms of DMF metabolism performance, whereas acclimatized anaerobic sludge has a reduced DMF metabolism capacity. Metagenomic revealed increased abundances of Methanosarcina, Pelomona and Xanthobacter in the adapted anaerobic sludge, suggesting that anaerobic sludge can utilize the methyl products produced by DMF metabolism for growth. Adapted aerobic sludge had high Mycobacterium abundance, significantly boosting DMF hydrolysis. In addition, a large number of dmfA2 genes were found in aerobic sludge, more so in acclimatized sludge, indicating stronger DMF metabolism. Conversely, acclimatized anaerobic sludge showed lower abundance of dmd-tmd and mauA/B, qhpA genes, implying long-term DMF toxicity reduced anaerobic microbial activity. Metaproteomic analysis showed that Methanosarcina and Methanomethylovorans enzymes in anaerobic sludge metabolized dimethylamine and methylamine to methane, aiding DMF degradation. In the aerobic sludge, aminohydrolase proteins, which hydrolyze DMF, were significantly upregulated. These findings provide insights into DMF wastewater treatment.}, } @article {pmid39566458, year = {2025}, author = {Zhang, L and Jiang, L and Yan, W and Tao, H and Yao, C and An, L and Sun, Y and Hu, T and Sun, W and Qian, X and Gu, J}, title = {Exogenous additives reshape the microbiome and promote the reduction of resistome in co-composting of pig manure and mushroom residue.}, journal = {Journal of hazardous materials}, volume = {481}, number = {}, pages = {136544}, doi = {10.1016/j.jhazmat.2024.136544}, pmid = {39566458}, issn = {1873-3336}, mesh = {Animals ; *Composting ; *Manure/microbiology ; *Microbiota/drug effects ; Swine ; *Agaricales/genetics/drug effects ; Drug Resistance, Microbial/genetics ; Bacteria/genetics/drug effects ; Soil Microbiology ; Genes, Bacterial ; }, abstract = {Comprehensive understanding of the microbiome and resistome evolution in compost is crucial for guaranteeing the safety of organic fertilizers. Current studies using different composting systems and sequencing technologies have yielded varying conclusions on the efficacy of exogenous additives (EAs) in reducing antibiotic resistance genes (ARGs) in compost. This study employed metagenomics to investigate the impact of various EAs on microbial communities, ARGs, their coexistence with mobile genetic elements (MGEs), and ARG hosts in co-composting. Our results demonstrated that EAs significantly reshaped the microbial communities and facilitated a notable reduction in total ARG abundance and diversity, primarily by decreasing core ARGs. Cooperative rather than antagonistic relationships among bacteria. The RA changes in total ARGs are mainly caused by a decrease in the prevalence of core ARGs. Furthermore, EAs showed significant efficacy in reducing clinical ARGs, including cfxA, tetX1, cfxA6, vanA, and aac (6')-Ib', with diatomite (5 %) and zeolite (5 %) being the most effective. The effect of EAs on ARGs and microbial community assembly were stochastic processes. Composting stage and EAs jointly reduced the association between ARGs and MGEs in the composting system. The reduction of ARGs attributed to a decreased abundance of potential pathogenic ARG-associated hosts and diminished associations with MGEs. In conclusion, EAs present a straightforward and effective approach for promoting ARGs reduction in compost, offering crucial insights for assessing the environmental risks associated with the release of agricultural ARGs.}, } @article {pmid39566443, year = {2024}, author = {Zhang, L and Wang, B and Li, K and Su, Y and Wu, D and Zhan, M and Xie, B}, title = {The dynamics and assembly patterns of airborne pathogen communities in the municipal food waste treatment system and its risk implications.}, journal = {Environment international}, volume = {194}, number = {}, pages = {109143}, doi = {10.1016/j.envint.2024.109143}, pmid = {39566443}, issn = {1873-6750}, mesh = {*Air Microbiology ; *Bacteria/isolation & purification/genetics/classification ; *Particulate Matter/analysis ; Refuse Disposal ; Solid Waste ; Environmental Monitoring ; Seasons ; Air Pollutants/analysis ; Food Loss and Waste ; }, abstract = {While municipal solid waste (MSW) provides an ideal habitat for pathogen propagation, the dynamics and assembly of airborne pathogen communities in these environments remain largely unknown. Here, we combined amplicon and metagenomics with spatiotemporal sampling to study inhalable particulate matter-carried potential pathogenic bacteria at full-scale food waste treatment plants (FWTPs), alongside comparisons to urban air in the area. The results showed that pathogenic bacteria constituted a notable portion (64.5 % ± 20.6 %, n = 75) of the total bacterial communities in FWTPs-impacted air, with species and relative abundance 2-4 times higher than that of urban air, and contributed over 50 % of pathogens to the outdoor air. Airborne pathogen community structures were highly shaped by sampling sites (i.e. treatment units), but conserved across seasons (summer vs. winter) and particle sizes (PM2.5vs. PM10). Notably, Acinetobacter johnsonii-dominated pathogens (i.e. biofilm-related species) presented high levels of aerosolization and consistently occupied the upper-representative niches in all neutral models, highlighting their persistent exposure risk. Furthermore, pathogen community assembly was strongly driven by stochastic processes (58.8 %-96.8 %), while environmental variables explained only limited variations (3.4 %-28.7 %). In particular, the relative importance of stochastic processes clearly increased along an outdoor-to-indoor gradient (84.9 %-96.5 % vs. 71.3 %-76 %), which might be related to indoor anthropogenic activities that weaken microbial network stability and environmental filtering effects. This work enhances our knowledge of the dynamic behaviors and risk of airborne pathogen communities in MSW disposal and underscores the role of FWTPs in disseminating airborne pathogens.}, } @article {pmid39566206, year = {2024}, author = {Lv, N and Gong, P and Sun, H and Sun, X and Liu, Z and Xie, X and Xue, Y and Song, Y and Wu, K and Wang, T and Wu, Z and Zhang, L}, title = {Agricultural ecosystems rather than fertilization strategies drives structure and composition of the ureolytic microbial functional guilds.}, journal = {Journal of environmental management}, volume = {372}, number = {}, pages = {123148}, doi = {10.1016/j.jenvman.2024.123148}, pmid = {39566206}, issn = {1095-8630}, mesh = {*Agriculture ; *Fertilizers/analysis ; *Soil Microbiology ; *Ecosystem ; *Soil/chemistry ; Bacteria/metabolism/genetics ; Nitrogen/metabolism ; Urea/metabolism ; Urease/metabolism ; Fungi ; Archaea ; }, abstract = {Ureolytic microorganisms are significant in the transformation of soil nitrogen as they secrete urease to hydrolyze urea. This study aimed to investigate the effects of different fertilization regimes on ureolytic microbial functional guilds (bacteria, fungi, and archaea) in various agricultural ecosystems. Soil samples were collected from a long-term agricultural field experiment involving paddy and dryland soils. The experiment consisted of four fertilization treatments: nitrogen fertilizer (N), nitrogen fertilizer combined with composite urease/nitrification inhibitor (NI), nitrogen fertilizer combined with straw (NS), and nitrogen fertilizer combined with manure (NO). A metagenomic sequencing technique was used to assess the composition of ureolytic microbial functional guilds using the target ureC gene, along with the evaluation of soil physicochemical properties, the abundance of ureC genes from different microbial guilds, and the urease activity. The results showed that the NI treatment significantly increased the abundance of ureC genes from different microbial guilds in the two agricultural ecosystems compared with other fertilization treatments. In dryland soil, the abundance of ureC genes was positively correlated with urease activity. The ureolytic bacterial functional guild exhibits greater dominance at all taxonomic levels compared to the ureolytic fungal and archaeal functional guilds. The alpha diversity of ureolytic microbial functional guilds was greater in dryland soil than in paddy soil. Principal coordinate analysis showed that the structure of the ureolytic microbial functional guilds could be separated into two groups based on agricultural ecosystems. Phosphorus is a key environmental factor affecting the ureolytic microbial functional guilds in two agricultural ecosystems, and the structure of the ureolytic bacteria functional guild is more susceptible to pH. The results suggest that the structure of ureolytic microbial functional guilds is primarily determined by agricultural ecosystems rather than by fertilization treatments. Additionally, fertilization treatments across different agricultural ecosystems significantly impacted the community composition of ureolytic bacteria, fungi, and archaea microorganism.}, } @article {pmid39565134, year = {2024}, author = {Boshevska, G and Emmerich, P and von Possel, R and Jancheska, E and Buzharova, T and Kochinski, D and Tóth, GE and Cadar, D and Osmani, D}, title = {Genomic characterization of Orthonairovirus haemorrhagiae (Crimean-Congo hemorrhagic fever virus) outbreak in North Macedonia.}, journal = {Microbiology resource announcements}, volume = {13}, number = {12}, pages = {e0074924}, pmid = {39565134}, issn = {2576-098X}, abstract = {Crimean-Congo hemorrhagic fever virus (CCHFV) is a significant tick-borne virus causing severe hemorrhagic disease with high fatality rate. This report presents the genomic characterization of CCHFV strain from North Macedonia's first outbreak in over 50 years, emphasizing the importance of genomic surveillance in tracking virus evolution and spread patterns in this region.}, } @article {pmid39565113, year = {2024}, author = {Nowak, VV and Hou, P and Owen, JG}, title = {Microbial communities associated with marine sponges from diverse geographic locations harbor biosynthetic novelty.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {12}, pages = {e0072624}, pmid = {39565113}, issn = {1098-5336}, support = {Doctoral Scholarship//Victoria University of Wellington (WGTN)/ ; Contract 16/172//Manatu Hauora | Health Research Council of New Zealand (HRC)/ ; RDF-VUW1601//Royal Society Te Apārangi (Royal Society of New Zealand)/ ; RTVU1908 and UOAX2010//Ministry for Business Innovation and Employment (MBIE)/ ; }, mesh = {*Porifera/microbiology ; Animals ; New Zealand ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Metagenome ; *Microbiota ; Mediterranean Sea ; Multigene Family ; Metagenomics ; Phylogeny ; }, abstract = {Marine sponges are a prolific source of biologically active small molecules, many of which originate from sponge-associated bacteria. Identifying the producing bacteria is a key step in developing sustainable routes for the production of these metabolites. To facilitate the required computational analyses, we developed MetaSing, a reproducible singularity-based pipeline for assembly, identification of high-quality metagenome-assembled genomes (MAGs), and analysis of biosynthetic gene clusters (BGCs) from metagenomic short-read data. We applied this pipeline to metagenomic sequencing data from 16 marine sponges collected from New Zealand, Tonga, and the Mediterranean Sea. This analysis yielded 643 MAGs representing 510 species. Of the 2,670 BGCs identified across all samples, 70.8% were linked to a MAG. Comparison of BGCs to those identified from previously sequenced bacteria revealed high biosynthetic novelty in variety of underexplored phyla, including Poribacteria, Acidobacteriota, and Dadabacteria. Alongside the observation that each sample contains unique biosynthetic potential, this holds great promise for natural product discovery and for furthering the understanding of different sponge holobionts.IMPORTANCEDiscovery of new chemical compounds such as natural products is a crucial endeavor to combat the increasing resistance to antibiotics and other drugs. This manuscript demonstrates that microbial communities associated with marine sponges investigated in this work encode the potential to produce novel chemistry. Lesser studied bacterial taxa that are often difficult to cultivate are particularly rich in potential.}, } @article {pmid39565095, year = {2024}, author = {Bulka, O and Mahadevan, R and Edwards, EA}, title = {Pangenomic insights into Dehalobacter evolution and acquisition of functional genes for bioremediation.}, journal = {Microbial genomics}, volume = {10}, number = {11}, pages = {}, pmid = {39565095}, issn = {2057-5858}, mesh = {*Biodegradation, Environmental ; *Phylogeny ; *Genome, Bacterial ; Evolution, Molecular ; Bacterial Proteins/genetics/metabolism ; Genomics ; Gene Transfer, Horizontal ; Metagenome ; }, abstract = {Dehalobacter is a genus of organohalide-respiring bacteria that is recognized for its fastidious growth using reductive dehalogenases (RDases). In the SC05 culture, however, a Dehalobacter population also mineralizes dichloromethane (DCM) produced by chloroform dechlorination using the mec cassette, just downstream of its active RDase. A closed genome of this DCM-mineralizing lineage has previously evaded assembly. Here, we present the genomes of two novel Dehalobacter strains, each of which was assembled from the metagenome of a distinct subculture from SC05. A pangenomic analysis of the Dehalobacter genus, including RDase synteny and phylogenomics, reveals at least five species of Dehalobacter based on average nucleotide identity, RDase and core gene synteny, as well as differential functional genes. An integration hotspot is also pinpointed in the Dehalobacter genome, in which many recombinase islands have accumulated. This nested recombinase island encodes the active RDase and mec cassette in both SC05 Dehalobacter genomes, indicating the transfer of key functional genes between species of Dehalobacter. Horizontal gene transfer between these two novel Dehalobacter strains has implications for the evolutionary history within the SC05 subcultures and of the Dehalobacter genus as a whole, especially regarding adaptation to anthropogenic chemicals.}, } @article {pmid39564541, year = {2024}, author = {Sujith, P and Singh, JR and Jayalakshmi, S and Kandaswamy, K and Shaik, MR and Hussain, SA and Kari, ZA and Guru, A}, title = {Metagenomics approaches in the discovery and development of new bioactive compound of 8-demethoxy-10-deoxysteffimycin from mangrove sediments.}, journal = {3 Biotech}, volume = {14}, number = {12}, pages = {303}, pmid = {39564541}, issn = {2190-572X}, abstract = {A metagenomic library consisting of 15,000 clones was constructed from the mangrove sediment. An antimicrobially active clone from the metagenomic library PS49 was identified by function- based screening. This paper presents the results of the biochemical characterization and metagenomic library screening of the marine-derived antibiotic, 8-demethoxy-10-deoxysteffimycin. Plasmid libraries were constructed, and clones were produced using a metagenomic approach. Out of 15,000 clones, 81 clones were screened for antimicrobial activity, and five potential clones were selected. The activity of one clone was characterized and named as PS49. The bioactive compounds from the selected clone were checked for antimicrobial, antioxidant, and anticancer activities. The clone PS49 was tested against various pathogens including bacteria and fungi and it showed inhibitory effects against all the tested pathogens. The antimicrobially active fractions were then crystallized and subjected to spectroscopic analysis such as FTIR, NMR and LC-MS analysis. The substance from clone PS49 has finally been recognized, and the compound from clone PS49 has been identified as 8-demethoxy-10-deoxysteffimycin. The substances isolated from the PS49 clone exhibited strong anticancer activity against skin cancer-cell lines SK-MEL2. The compounds showed a reduction in cell viability with an increase in the compound concentration. The compounds obtained from clone PS49 showed an IC50 value of 85 µg/ml.}, } @article {pmid39564489, year = {2024}, author = {Liu, X and Zang, Y and Fan, S and Miao, X and Fu, M and Ma, X and Li, M and Zhang, X and Wang, Z and Xiao, J}, title = {Changes in the structure of the microbial community within the phycospheric microenvironment and potential biogeochemical effects induced in the demise stage of green tides caused by Ulva prolifera.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1507660}, pmid = {39564489}, issn = {1664-302X}, abstract = {Green tides caused by Ulva prolifera occur annually in the Yellow Sea of China, and the massive amount of biomass decomposing during the demise stage of this green tide has deleterious ecological effects. Although microorganisms are considered key factors influencing algal bloom demise, an understanding of the microbial-algae interactions within the phycospheric microenvironment during this process is still lacking. Here, we focused on the variations in phycospheric microbial communities during the late stage of the green tide in three typically affected areas of the Yellow Sea via metagenomic sequencing analysis. In total, 16.9 million reads obtained from 18 metagenome samples were incorporated into the assembled contigs (13.4 Gbp). The phycosphere microbial community composition and diversity changed visibly during the demise of U. prolifera. The abundances of algae-lysing bacteria, Flavobacteriaceae at the family level and Alteromonas, Maribacter, and Vibrio at the genus level increased significantly in the phycosphere. In addition, the levels of glycoside hydrolases (GHs) and polysaccharide lyases (PLs) enzymes, which decompose U. prolifera polysaccharides in the phycosphere, were greater. Therefore, the degradation of algal polysaccharides can increase the efficiency of carbon metabolism pathways in the phycospheric microenvironment. Most of the genes detected in the phycosphere, especially norC, nrfA, and nasA, were associated with nitrogen metabolism pathways and showed dynamics related to the demise of the large amount of organic matter released by a green tide. Therefore, the demise of green tide algae may affect the potential carbon and nitrogen cycles of the phycospheric microenvironment by driving changes in the structure and diversity of microbial communities. Our research provides a novel perspective to better understand the ecological impact of U. prolifera during the green tide demise stage.}, } @article {pmid39564488, year = {2024}, author = {Redondo-Río, Á and Mundy, CJ and Tamames, J and Pedrós-Alió, C}, title = {Specialized Bacteroidetes dominate the Arctic Ocean during marine spring blooms.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1481702}, pmid = {39564488}, issn = {1664-302X}, abstract = {A metagenomic time series from Arctic seawater was obtained from Dease Strait, to analyse the changes in bacterioplankton caused by the summer phytoplankton bloom. Bacterial clades specialized in the metabolism of polysaccharides, such as Bacteroidetes, became dominant along the bloom. These specialized taxa quickly displaced the microbial clades that dominate nutrient-poor waters during early spring, such as Archaea, Alpha-and Gammaproteobacteria. At the functional level, phyla Bacteroidetes, Planctomycetes, and Verrucomicrobia showed higher contents of polysaccharide-degradation functions. The Bacteroidetes community shifted toward species with higher polysaccharide-degrading capabilities, targeting algal polysaccharides in summer. Regarding transporters, Bacteroidetes dominated SusC-TonB transporters and had an exclusive family of glycoside-binding proteins (SusD). These proteins were used to identify polysaccharide-utilization loci that clustered transporters and polysaccharide-active enzymes, showing a higher level of specialization toward polysaccharide use. Altogether, these genomic features point to the genetic adaptations that promote the dominance of Bacteroidetes during phytoplankton blooms.}, } @article {pmid39563733, year = {2024}, author = {Iwata, J and Nakai, K}, title = {Editorial: Emerging talents in computational genomics.}, journal = {Frontiers in genetics}, volume = {15}, number = {}, pages = {1512594}, doi = {10.3389/fgene.2024.1512594}, pmid = {39563733}, issn = {1664-8021}, } @article {pmid39563700, year = {2024}, author = {Quezada-Romegialli, C and Quiroga-Carmona, M and D'Elía, G and Harrod, C and Storz, JF}, title = {Diet of Andean Leaf-Eared Mice (Phyllotis) Living at Extreme Elevations on Atacama Volcanoes: Insights From Metagenomics, DNA Metabarcoding, and Stable Isotopes.}, journal = {Ecology and evolution}, volume = {14}, number = {11}, pages = {e70591}, pmid = {39563700}, issn = {2045-7758}, support = {R01 HL159061/HL/NHLBI NIH HHS/United States ; }, abstract = {On the flanks of > 6000 m Andean volcanoes that tower over the Atacama Desert, leaf-eared mice (Phyllotis vaccarum) live at extreme elevations that surpass known vegetation limits. The diet of these mice in these barren, hyperarid environments has been the subject of much speculation. According to the arthropod fallout hypothesis, sustenance is provided by windblown insects that accumulate in snowdrifts ("aolian deposits"). Mice may also feed on saxicolous lichen or forms of cryptic vegetation that have yet to be discovered at such high elevations. We tested hypotheses about the diet of mice living at extreme elevations on Atacama volcanoes by combining metagenomic and DNA metabarcoding analyses of gut contents with stable isotope analyses of mouse tissues. Genomic analyses of contents of the gastrointestinal tract of a live-captured mouse from the summit of Volcán Llullaillaco (6739 m) revealed an opportunistic but purely herbivorous diet, including lichens. Although we found no evidence of animal DNA in gut contents of the summit mouse, stable isotope data indicate that mice from elevations at or near vegetation limits (~5100 m) include a larger fraction of animal prey in their diet than mice from lower elevations. Some plant species detected in the gut contents of the summit mouse are known to exist at lower elevations at the base of the volcano and in the surrounding Altiplano, suggesting that they may occur at higher elevations beneath the snowpack or in other cryptic microhabitats.}, } @article {pmid39563628, year = {2024}, author = {Goldberg, TL and Perez, AU and Campbell, LJ}, title = {Isopods infesting Atlantic bonefish (Albula vulpes) host novel viruses, including reoviruses related to global pathogens, and opportunistically feed on humans.}, journal = {Parasitology}, volume = {}, number = {}, pages = {1-11}, doi = {10.1017/S003118202400146X}, pmid = {39563628}, issn = {1469-8161}, support = {//Bonefish and Tarpon Trust/ ; }, abstract = {Isopods infest fish worldwide, but their role as disease vectors remains poorly understood. Here, we describe infestation of Atlantic bonefish (Albula vulpes) in Belize with isopods in two of three locations studied, with infestation rates of 15 and 44%. Isopods fed aggressively, and infested fish showed missing scales and scars. Gross morphologic and molecular phylogenetic analyses revealed the isopods to cluster within the family Aegidae and to be most closely related to members of the genus Rocinela, which are globally distributed micro-predators of fish. Metagenomic analysis of 10 isopods identified 11 viruses, including two novel reoviruses (Reovirales) in the families Sedoreoviridae and Spinareoviridae. The novel sedoreovirus clustered phylogenetically within an invertebrate-specific clade of viruses related to the genus Orbivirus, which contains arboviruses of global concern for mammal health. The novel spinareovirus clustered within the fish-infecting genus Aquareovirus, which contains viruses of global concern for fish health. Metagenomic analyses revealed no evidence of infection of bonefish with the novel aquareovirus, suggesting that viremia in bonefish is absent, low, or transient, or that isopods may have acquired the virus from other fish. During field collections, isopods aggressively bit humans, and blood meal analysis confirmed that isopods had fed on bonefish, other fish, and humans. Vector-borne transmission may be an underappreciated mechanism for aquareovirus transmission and for virus host switching between fish and other species, which has been inferred across viral families from studies of deep virus evolution.}, } @article {pmid39563409, year = {2024}, author = {Li, M and Chen, K and Chen, Y and Zhang, L and Cui, Y and Xiao, F and Liu, Z and Zhang, W and Jiang, J and Zhou, Q and Yan, J and Sun, Y and Guan, F}, title = {Integrative analysis of gut microbiome and host transcriptome reveal novel molecular signatures in Hashimoto's thyroiditis.}, journal = {Journal of translational medicine}, volume = {22}, number = {1}, pages = {1045}, pmid = {39563409}, issn = {1479-5876}, support = {82071952//Natural Science Foundation of China/ ; 82171873//Natural Science Foundation of China/ ; 82370806//Natural Science Foundation of China/ ; 82030058//Natural Science Foundation of China/ ; }, mesh = {Humans ; *Hashimoto Disease/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; *Transcriptome/genetics ; Female ; Male ; Adult ; Case-Control Studies ; MicroRNAs/genetics/metabolism ; Middle Aged ; ROC Curve ; RNA, Messenger/genetics/metabolism ; Gene Expression Profiling ; }, abstract = {BACKGROUND: Hashimoto's thyroiditis (HT) is an autoimmune disorder with unclear molecular mechanisms. While current diagnosis is well-established, understanding of the gut-thyroid axis in HT remains limited. This study aimed to uncover novel molecular signatures in HT by integrating gut metagenome and host transcriptome data (miRNA/mRNA), potentially elucidating disease pathogenesis and identifying new therapeutic targets.

METHODS: We recruited 31 early HT patients and 30 healthy controls in a two-stage study (discovery and validation). Blood and fecal samples underwent RNA and metagenomic sequencing, respectively. Integrative analysis included differential expression, weighted correlation network, correlation and random forest analyses. Regression models and ROC curve analysis were used to evaluate the significance of identified molecular signatures in HT.

RESULTS: Integrative analysis revealed subtle changes in gut microbiota diversity and composition in early HT, increased abundance of Bacillota_A and Spirochaetota at the phylum level, and significant differences in 24 genera and 67 species. Ecological network analysis indicated an imbalance in the gut microbiota with reduced inhibitory interactions against pathogenic genera in HT. Functional analysis showed changes in infection- and immune-related pathways. Three characteristic species (Salaquimonas_sp002400845, Clostridium_AI_sp002297865, and Enterocloster_citroniae) were identified as most relevant to HT. Analysis of miRNA and mRNA expression profiles uncovered pathways related to immune response, inflammation, infection, metabolism, proliferation, and thyroid cancer in HT. Based on correlations with HT and interactions between them, six characteristic RNAs (hsa-miR-548aq-3p, hsa-miR-374a-5p, GADD45A, IRS2, SMAD6, WWTR1) were identified. Furthermore, our study uncovered significant gut microbiota-host transcriptome interactions in HT, revealing enrichment in metabolic, immune, and cancer-related pathways, particularly with strong associations among those 9 key molecular signatures. The validation stage confirmed improved HT classification accuracy by combining these signatures (AUC = 0.95, ACC = 0.85), suggesting their potential significance in understanding HT pathogenesis.

CONCLUSION: Our study reveals novel molecular signatures linking gut microbiome and host transcriptome in HT, providing new insights into the disease pathogenesis. These findings not only enhance our understanding of the gut-thyroid axis but also suggest potential new directions for therapeutic interventions in HT.}, } @article {pmid39563023, year = {2025}, author = {Park, HA and Sung, J and Chang, Y and Ryu, S and Yoon, KJ and Kim, HL and Kim, HN}, title = {Metagenomic Analysis Identifies Sex-Related Gut Microbial Functions and Bacterial Taxa Associated With Skeletal Muscle Mass.}, journal = {Journal of cachexia, sarcopenia and muscle}, volume = {16}, number = {1}, pages = {e13636}, pmid = {39563023}, issn = {2190-6009}, support = {2023R1A2C2006416//National Research Foundation of Korea/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; *Muscle, Skeletal/microbiology ; *Metagenomics/methods ; Middle Aged ; Feces/microbiology ; Adult ; Bacteria/classification/genetics ; Metagenome ; }, abstract = {BACKGROUND: This study aimed to explore the association between gut microbiota functional profiles and skeletal muscle mass, focusing on sex-specific differences in a population under 65 years of age.

METHODS: Stool samples from participants were analysed using metagenomic shotgun sequencing. Skeletal muscle mass and skeletal muscle mass index (SMI) were quantified (SMI [%] = total appendage muscle mass [kg]/body weight [kg] × 100) using bioelectrical impedance analysis. Participants were categorized into SMI quartiles, and associations between gut microbiota, functional profiling and SMI were assessed by sex, adjusting for age, BMI and physical activity.

RESULTS: The cohort included 1027 participants (651 men, 376 women). In men, Escherichia coli (log2 fold change 3.08, q = 0.001), Ruminococcus_B gnavus (log2 fold change 2.89, q = 0.014) and Enterocloster sp001517625 (log2 fold change 2.47, q = 0.026) were more abundant in the lowest SMI compared to the highest SMI group. In contrast, Bifidobacterium bifidum (log2 fold change 3.13, q = 0.025) showed higher levels in the second lowest SMI group in women. Microbial pathways associated with amino acid synthesis (MET-SAM-PWY: log2 fold change 0.42; METSYN-PWY: log2 fold change 0.44; SER-GLYSYN-PWY: log2 fold change 0.20; PWY-5347: log2 fold change 0.41; P4-PWY: log2 fold change 0.53), N-acetylneuraminate degradation (log2 fold change 0.43), isoprene biosynthesis (log2 fold change 0.20) and purine nucleotide degradation and salvage (PWY-6353: log2 fold change 0.42; PWY-6608: log2 fold change 0.38; PWY66-409: log2 fold change 0.52; SALVADEHYPOX-PWY: log2 fold change 0.43) were enriched in the lowest SMI in men (q < 0.10). In women, the second lowest SMI group showed enrichment in energy-related pathways, including lactic acid fermentation (ANAEROFRUCAT-PWY: log2 fold change 0.19), pentose phosphate pathway (PENTOSE-P-PWY: log2 fold change 0.30) and carbohydrate degradation (PWY-5484: log2 fold change 0.31; GLYCOLYSIS: log2 fold change 0.29; PWY-6901: log2 fold change 0.27) (q < 0.05).

CONCLUSIONS: This study highlights sex-specific differences in gut microbiota and functional pathways associated with SMI. These findings suggest that gut microbiota may play a role in muscle health and point toward microbiota-targeted strategies for maintaining muscle mass.}, } @article {pmid39562866, year = {2024}, author = {Camacho-Mateu, J and Lampo, A and Ares, S and Cuesta, JA}, title = {Nonequilibrium microbial dynamics unveil a new macroecological pattern beyond Taylor's law.}, journal = {Physical review. E}, volume = {110}, number = {4-1}, pages = {044402}, doi = {10.1103/PhysRevE.110.044402}, pmid = {39562866}, issn = {2470-0053}, mesh = {*Models, Biological ; Microbiota ; }, abstract = {We introduce a comprehensive analytical benchmark, relying on Fokker-Planck formalism, to study microbial dynamics in the presence of both biotic and abiotic forces. In equilibrium, we observe a balance between the two kinds of forces, leading to no correlations between species abundances. This implies that real microbiomes, where correlations have been observed, operate out of equilibrium. Therefore, we analyze nonequilibrium dynamics, presenting an ansatz for an approximate solution that embodies the complex interplay of forces in the system. This solution is consistent with Taylor's law as a coarse-grained approximation of the relation between species abundance and variance, but implies subtler effects, predicting unobserved structure beyond Taylor's law. Motivated by this theoretical prediction, we refine the analysis of existing metagenomic data, unveiling a novel universal macroecological pattern. Finally, we speculate on the physical origin of Taylor's law: building upon an analogy with Brownian motion theory, we propose that Taylor's law emerges as a fluctuation-growth relation resulting from equipartition of environmental resources among microbial species.}, } @article {pmid39562308, year = {2024}, author = {Yang, Y and Xu, P and He, W and Tao, F}, title = {Metagenomic analysis reveals houseflies as indicators for monitoring environmental antibiotic resistance genes.}, journal = {Environmental microbiology reports}, volume = {16}, number = {6}, pages = {e70032}, pmid = {39562308}, issn = {1758-2229}, support = {32170105//National Natural Science Foundation of China/ ; MMLKF20-03//State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University/ ; }, mesh = {*Houseflies/microbiology/genetics ; *Metagenomics ; Animals ; *Anti-Bacterial Agents/pharmacology ; *Environmental Monitoring ; Genes, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Microbiota/genetics ; Bacteria/genetics/classification/drug effects/isolation & purification ; Drug Resistance, Bacterial/genetics ; }, abstract = {Given the threat to public health posed by antibiotic resistance transmission, environmental monitoring is essential for tracking antibiotic resistance genes (ARGs). Houseflies, being ubiquitous organisms capable of carrying and disseminating ARGs, serve as suitable indicators for environmental monitoring. In this study, we employ metagenomic approaches to investigate housefly body surface samples from five typical sites associated with human activities. The investigation reveals microbiome diversity among the samples, along with variations in the occurrence and mobility potential of ARGs. Metagenomic analysis indicates that the composition of ARGs on housefly body surfaces is influenced by environmental ARGs, which may be enriched on the housefly body surface. The resistance genes related to multidrug, β-lactam, bacitracin, and tetracycline were the predominant ARGs detected, with multidrug-related ARGs consistently exhibiting dominance. Furthermore, the abundance of ARGs in the different housefly body surface samples was found to correlate with the population density and mobility of the sampling site. Natural environments exhibited the lowest ARG abundance, while areas with higher population density and limited population mobility displayed higher ARG abundance. This study emphasizes the effectiveness of houseflies as monitors for environmental ARGs and underscores their potential for assessing and controlling antibiotic resistance risks in urban environments.}, } @article {pmid39561853, year = {2025}, author = {Oto, J and Herranz, R and Verger, P and Roca, M and Plana, E and Miralles, M and Martínez-Sarmiento, M and Vera-Donoso, CD and Medina, P}, title = {Validation of urine p-cresol glucuronide as renal cell carcinoma non-invasive biomarker.}, journal = {Journal of proteomics}, volume = {311}, number = {}, pages = {105357}, doi = {10.1016/j.jprot.2024.105357}, pmid = {39561853}, issn = {1876-7737}, mesh = {Humans ; *Carcinoma, Renal Cell/urine/diagnosis ; Female ; Male ; Middle Aged ; *Cresols/urine ; *Biomarkers, Tumor/urine ; *Kidney Neoplasms/urine ; Aged ; Glucuronides/urine ; Adult ; }, abstract = {Renal cell carcinoma (RCC) stands among the most lethal urological malignancies. Most RCCs are incidentally diagnosed as initial symptoms are unspecific. Novel, minimally-invasive diagnostic and prognostic methods for RCC are needed, ideally in urine. Using UPLC-Q-ToF MS untargeted metabolomic analysis in urine, we previously revealed p-cresol glucuronide as potential RCC diagnostic marker. Additionally, urine samples one-year post-nephrectomy revealed isobutyryl-l-carnitine and L-proline betaine as potential RCC prognostic markers. Our present aim was to validate these differences in an independent cohort of RCC patients and healthy controls to strengthen their value as non-invasive biomarkers. In an independent cohort of 69 RCC patients and 52 controls we validated an increase in p-cresol glucuronide in urine from patients at diagnosis compared to controls (P = 0.0043). It remained increased one-year post-nephrectomy (P = 0.0288). The value of p-cresol glucuronide for RCC diagnosis was assessed with ROC curves analysis (AUC = 0.66, 95 % Confidence Interval 0.56-0.76). The role of isobutyryl-l-carnitine and L-proline betaine as prognostic markers could not be validated and will require a larger cohort. Our findings confirm the value of p-cresol glucuronide in urine as diagnostic marker for RCC in an independent cohort. This non-invasive method holds promise for enhancing patient care by reducing the need for potentially risky diagnostic procedures. Further metaproteomics-oriented approaches towards the tyrosine oxidation pathway and microbiota metagenomics studies may promote a holistic management of RCC. SIGNIFICANCE: Current imaging techniques available to diagnose and monitor renal cell carcinoma (RCC) are harmful for the patient given the high-radiation dose, and unspecific in low-grade tumors. Thus, novel non-invasive biomarkers with diagnostic and prognostic capabilities are of utmost importance. Herein, we have validated urine p-cresol glucuronide as diagnostic marker for RCC. This novel non-invasive biomarker could improve accurate assessments of tumor behavior, while enhancing patient outcomes by reducing discomfort and detrimental side effects.}, } @article {pmid39561782, year = {2024}, author = {Lee, D and Ahn, K and Yun, K and Oh, Y and Park, YS and Kim, YS and Gim, JA and Mun, S and Mun, JW and Han, K and Ahn, YJ}, title = {Aerobic bacterial group as an early-stage biomarker from faecal samples of patients with colorectal cancer without distant metastasis.}, journal = {Beneficial microbes}, volume = {16}, number = {2}, pages = {201-219}, doi = {10.1163/18762891-bja00051}, pmid = {39561782}, issn = {1876-2891}, mesh = {Humans ; *Colorectal Neoplasms/pathology/microbiology/diagnosis ; *Feces/microbiology ; *RNA, Ribosomal, 16S/genetics ; Male ; *Gastrointestinal Microbiome/genetics ; Female ; Middle Aged ; *Biomarkers, Tumor/genetics ; Aged ; Early Detection of Cancer/methods ; Adult ; Metagenomics ; }, abstract = {The current approaches for detecting most colorectal polyps and early neoplasms lack sufficient sensitivity and specificity, potentially hindering treatment and ultimately reducing survival rates. Here, we performed a metagenomic analysis to identify microbiome markers in stool samples from patients with early-stage colorectal cancer (CRC). We compared the composition of gut microbiota between patients with CRC and healthy individuals, specifically focusing on patients with early-stage CRC, defined as those without core mutations (KRAS, BRAF) for CRC diagnosis, stable microsatellite instability, and distant metastasis. The aim of our study is to identify potential biomarkers from gut microbiota at different cancer stages in colorectal cancer (CRC) patients through 16S rRNA amplicon sequencing, thereby proposing a novel non-invasive method for the early diagnosis of CRC. Specific microbes were detected from groups divided based on the TNM criteria, with one group classified by tumour size only (named the T group) and another group with lymph node metastasis (named the TN group). Aerobic bacteria, such as Delftia, Stenotrophomonas, Sphingobacterium, Rhodococcus, Devosia, Ensifer, and Psychrobacter were predominantly detected in patients with CRC without lymph node metastasis. The diagnostic prediction was evaluated using the CatBoost algorithm; these microbes presented high diagnostic accuracy with a receiver operating characteristics-area under curve of 0.8, which was validated using qPCR. In conclusion, this study identified specific aerobic microbial groups as non-invasive biomarkers for early diagnosis in patients with CRC without genetic or environmental factors.}, } @article {pmid39561704, year = {2024}, author = {Wittmers, F and Comstock, J and Poirier, C and Needham, DM and Schulz, F and Malmstrom, R and Carlson, CA and Worden, AZ}, title = {Non-photosynthetic lineages sibling to Cyanobacteria associate with eukaryotes in the open ocean.}, journal = {Current biology : CB}, volume = {34}, number = {22}, pages = {R1133-R1134}, doi = {10.1016/j.cub.2024.09.009}, pmid = {39561704}, issn = {1879-0445}, mesh = {*Phylogeny ; *Eukaryota/genetics/classification ; Oceans and Seas ; Cyanobacteria/genetics/classification ; Bacteria/genetics/classification ; Seawater/microbiology ; Metagenome ; }, abstract = {Margulisbacteria are elusive uncultivated bacteria that have illuminated evolutionary transitions in the progenitor of Cyanobacteria, the latter being a critically important phylum that underpins oxygenic photosynthesis[1][,][2]. The non-photosynthetic Margulisbacteria were discovered in a sulfidic spring[3] and later in other habitats[4][5][6]. Currently, this candidate phylum partitions into the Riflemargulisbacteria, primarily from sediments and groundwater, the Termititenax from insect gut microbiomes, and the Marinamargulisbacteria, from marine samples[4][5][6]. We found that Marinamargulisbacteria amplicons were unusually distributed in size-fractionated samples from the sunlit photic and dark twilight zones of the ocean. Further, sequencing of wild marine protists rendered genomic information for distinct marinamargulisbacterial clades co-associated with uncultivated, non-photosynthetic Stramenopila and Opisthokonta protists. Phylogenomic analyses combining these data and available metagenome-assembled genomes (MAGs) and single-amplified genomes (SAGs) from sorted bacteria revealed new Marinamargulisbacteria lineages. The lineages delineate by their environment, forming clades comprising freshwater, marine pelagic, or sediment/hypoxic taxa. The remarkable diversity of Margulisbacteria indicates success in colonizing various habitats, potentially in a conserved strategy involving eukaryotic cells.}, } @article {pmid39561549, year = {2025}, author = {Liang, L and Pan, W and Mu, M and Zhang, L and Yang, X and Zhang, R and Du, L and Guo, X}, title = {Effect of microplastics concentration and size on pollutants removal and antibiotic resistance genes (ARGs) generation in constructed wetlands: A metagenomics insight.}, journal = {Journal of hazardous materials}, volume = {481}, number = {}, pages = {136555}, doi = {10.1016/j.jhazmat.2024.136555}, pmid = {39561549}, issn = {1873-3336}, mesh = {*Wetlands ; *Microplastics/toxicity ; *Water Pollutants, Chemical/toxicity ; *Metagenomics ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents ; Wastewater ; Genes, Bacterial ; Oxytetracycline ; Particle Size ; Polystyrenes/chemistry ; Nitrogen ; Phosphorus ; }, abstract = {The accrual of microplastics (MPs) and antibiotics poses synergistic threats to the environment. This study systemically examined the effect of environmental-level (μg/L) MPs (90-110 µm) and nanoplastics (NPs, 700 nm) on constructed wetlands (CWs) treating oxytetracycline-contaminated wastewater via metagenomics analysis. Polystyrene (PS) MPs notably hindered the removal of nitrogen, phosphorus, and oxytetracycline, particularly at high level (1000 μg/L), with removal rates of 73.34 %, 59.59 %, and 99.34 %, respectively. Among them, the removal of NH4[+]-N decreased the most in comparison to CK, at 15.26 %. Antibiotic resistance genes (ARGs) copies/16S rRNA ranged from 0.26 to 0.42 in CWs, exceeding that found in rivers by a factor of 1.5 to 2.5 times. The relative abundance of multidrug resistance genes (mdtB, acrB, mexF, mdtC, and mexT) and tetracycline resistance genes (txtA, tetG, and tetP) exhibited a pronounced increase under MPs exposure, ranging from 0.06 to 0.14 and 0.01 to 0.08 copies/16S rRNA, respectively. Redundancy and network analyses emphasized robust associations among contaminant reduction, ARG abundance, and microbial community. Partial least squares path modeling indicated MPs exerted a more profound influence on pollutant removal (coefficient = 0.8194), microbial community (coefficient = 0.3358) and ARGs dissemination (coefficient = 0.6566) compared to NPs. MPs concentrations significantly affects pollutants removal and ARGs proliferation, and MPs with larger sizes amplified ARG dissemination. This research highlights the influence of MPs on CW-mediated wastewater treatment and ARGs accumulation, offering valuable insights for developing ecological wastewater treatment strategies tailored to multi-pollutant scenarios. These insights are fundamental in developing sustainable solutions to the adverse impacts of MPs on ecosystems.}, } @article {pmid39561546, year = {2025}, author = {Ma, H and Khusnutdinova, AN and Lemak, S and Chernikova, TN and Golyshina, OV and Almendral, D and Ferrer, M and Golyshin, PN and Yakunin, AF}, title = {Polyesterase activity is widespread in the family IV carboxylesterases from bacteria.}, journal = {Journal of hazardous materials}, volume = {481}, number = {}, pages = {136540}, doi = {10.1016/j.jhazmat.2024.136540}, pmid = {39561546}, issn = {1873-3336}, mesh = {*Carboxylesterase/metabolism/genetics/chemistry ; *Polyesters/metabolism/chemistry ; Bacterial Proteins/metabolism/genetics/chemistry ; Bacteria/enzymology ; Carboxylic Ester Hydrolases/metabolism/genetics/chemistry ; Enzyme Stability ; Substrate Specificity ; }, abstract = {Enzyme-based depolymerization of plastics, including polyesters, has emerged as a promising approach for plastic waste recycling and reducing environmental plastic pollution. Currently, most of the known polyester-degrading enzymes are represented by a few natural and engineered PETases from the carboxylesterase family V. To identify novel groups of polyesterases, we selected 25 proteins from the carboxylesterase family IV, which share 22 % to 80 % sequence identity to the metagenomic thermophilic polyesterase IS12. All purified proteins were found to be active against chromogenic para-nitrophenyl esters with a preference for short acyl chains. Screening for polyesterase activity using emulsified polyesters demonstrated the presence of hydrolytic activity against bis(benzoyloxyethyl) terephthalate (3PET), polycaprolactone (PCL), and polylactic acid (PLA) in all tested proteins. Biochemical characterization of four selected polyesterases revealed high thermostability in CBA10055, whereas the mesophilic GEN0105 exhibited higher polyesterase activity. Two ancestral variants of GEN0105 showed higher thermostability and activity against PCL and PLA, but reduced activity with amorphous PET. Furthermore, six established PETases were found to be highly active against PCL and PLA. Thus, our results indicate that polyesterase activity is widespread in the family IV carboxylesterases, and that most polyesterases are promiscuous being able to degrade different polyesters.}, } @article {pmid39561190, year = {2024}, author = {Ward, CM and Onetto, CA and Borneman, AR}, title = {Adaptation During the Shift from Entomopathogen to Endosymbiont Is Accompanied by Gene Loss and Intensified Selection.}, journal = {Genome biology and evolution}, volume = {16}, number = {12}, pages = {}, pmid = {39561190}, issn = {1759-6653}, support = {//Australian Wine Research Institute/ ; //Australian Government/ ; //Wine Innovation Cluster/ ; }, mesh = {*Symbiosis/genetics ; Animals ; *Selection, Genetic ; *Hypocreales/genetics ; Genome, Fungal ; Adaptation, Physiological/genetics ; Phylogeny ; Evolution, Molecular ; Coleoptera/microbiology/genetics ; Insecta/microbiology/genetics ; }, abstract = {Fungi have been found to be associated with many insect species, with some species transitioning to reside within insects as symbionts. However, the evolutionary pressures and genomic consequences associated with this transition are not well understood. Pathogenic fungi of the genus Ophiocordyceps have undergone multiple, independent transitions from pathogen to endosymbiont lifestyles, where they reside within the fatty tissues of infected soft-scale insects transgenerationally without killing their hosts. To gain an understanding of the genomic adaptations underlying this life history shift, long-read sequencing was utilized to assemble the genomes of both the soft-scale insect Parthenolecanium corni and its Ophiocordyceps endosymbiont from a single insect. Assembly and metagenomic-based binning produced a highly contiguous genome for Pa. corni and a chromosome-level assembly for the Ophiocordyceps endosymbiont. The endosymbiont genome was characterized by 524 gene loss events compared to free-living pathogenic Ophiocordyceps relatives, with predicted roles in hyphal growth, cell wall integrity, metabolism, gene regulation, and toxin production. Contrasting patterns of selection were observed between the nuclear and mitochondrial genomes specific to the endosymbiont lineage. Intensified selection was most frequently observed across orthologs in the nuclear genome, whereas selection on most mitochondrial genes was found to be relaxed. Scans for positive selection were enriched within the fatty acid metabolism pathway with endosymbiont specific selection within three adjacent enzymes catalyzing the conversion of acetoacetate to acetyl-coenzyme A, suggesting that the endosymbiont lineage is under selective pressure to effectively exploit the lipid rich environment of the insect fat bodies in which it is found.}, } @article {pmid39560390, year = {2025}, author = {Lin, H and Wu, L and Zhang, L and Ta, QK and Liu, P and Song, J and Yang, X}, title = {Metagenome-based diversity and functional analysis of culturable microbes in sugarcane.}, journal = {Microbiology spectrum}, volume = {13}, number = {1}, pages = {e0198224}, pmid = {39560390}, issn = {2165-0497}, mesh = {*Saccharum/microbiology ; *Soil Microbiology ; *Rhizosphere ; *Bacteria/classification/genetics/isolation & purification ; *Metagenome ; *Microbiota/genetics ; *Metagenomics/methods ; Biodiversity ; Burkholderia/genetics/classification/isolation & purification ; Phylogeny ; }, abstract = {UNLABELLED: Sugarcane is a key crop for sugar and energy production, and understanding the diversity of its associated microbes is crucial for optimizing its growth and health. However, there is a lack of thorough investigation and use of microbial resources in sugarcane. This study conducted a comprehensive analysis of culturable microbes and their functional features in different tissues and rhizosphere soil of four diverse sugarcane species using metagenomics techniques. The results revealed significant microbial diversity in sugarcane's tissues and rhizosphere soil, including several important biomarker bacterial taxa identified, which are reported to engage in several processes that support plant growth, such as nitrogen fixation, phosphate solubilization, and the production of plant hormones. The Linear discriminant analysis Effect Size (LEfSe) studies identified unique microbial communities in different parts of the same sugarcane species, particularly Burkholderia, which exhibited significant variations across the sugarcane species. Microbial analysis of carbohydrate-active enzymes (CAZymes) indicated that genes related to sucrose metabolism were mostly present in specific bacterial taxa, including Burkholderia, Pseudomonas, Paraburkholderia, and Chryseobacterium. This study improves understanding of the diversities and functions of endophytes and rhizosphere soil microbes in sugarcane. Moreover, the approaches and findings of this study provide valuable insights for microbiome research and the use of comparable technologies in other agricultural fields.

IMPORTANCE: This work utilized metagenomics techniques for conducting a comprehensive examination of culturable microbes and their functional characteristics in various tissues and rhizosphere soil of four distinct sugarcane species. This study enhances comprehension of the diversity and functions of endophytes and rhizosphere soil microbes in sugarcane. Furthermore, the methodologies and discoveries of this work offer new perspectives for microbiome investigation and the use of similar technologies in other agricultural fields.}, } @article {pmid39559703, year = {2024}, author = {Chen, Y and Ma, T}, title = {Hematologic cancers and infections: how to detect infections in advance and determine the type?.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1476543}, pmid = {39559703}, issn = {2235-2988}, mesh = {Humans ; *Hematologic Neoplasms/complications ; *Biomarkers/blood ; *Mycoses/diagnosis/microbiology ; Bacterial Infections/diagnosis/microbiology ; High-Throughput Nucleotide Sequencing ; Cytokines/blood/metabolism ; Procalcitonin/blood ; }, abstract = {Infection is one of the leading causes of death in patients with hematologic cancers. Hematologic cancer patients with compromised immune systems are already susceptible to infections, which come on even more rapidly and are difficult to control after they develop neutrophil deficiencies from high-dose chemotherapy. After patients have developed an infection, the determination of the type of infection becomes a priority for clinicians. In this review, we summarize the biomarkers currently used for the prediction of infections in patients with hematologic cancers; procalcitonin, CD64, cytokines, and CD14 et al. can be used to determine bacterial infections, and (1-3)-β-D-glucan and galactomannan et al. can be used as a determination of fungal infections. We have also focused on the use of metagenomic next-generation sequencing in infections in patients with hematologic cancers, which has excellent clinical value in infection prediction and can detect microorganisms that cannot be detected by conventional testing methods such as blood cultures. Of course, we also focused on infection biomarkers that are not yet used in blood cancer patients but could be used as a future research direction, e.g., human neutrophil lipocalin, serum amyloid A, and heparin-binding protein et al. Finally, clinicians need to combine multiple infection biomarkers, the patient's clinical condition, local susceptibility to the type of infection, and many other factors to make a determination of the type of infection.}, } @article {pmid39559340, year = {2024}, author = {Wang, H and Ni, Z and Chang, Y}, title = {Prompt Diagnosis and Treatment of Japanese Spotted Fever with an Atypical Triad of Clinical Symptoms: A Case Report.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {5073-5077}, pmid = {39559340}, issn = {1178-6973}, abstract = {Japanese spotted fever (JSF) is a neglected and potentially fatal infectious disease. Delays in diagnosis and treatment of JSF are important causes of poor prognosis. We report a case of JSF in a 75-year-old farmer who, following autumn field work in Sichuan, China, presented with an atypical triad of clinical symptoms: high fever, petechial rash, and notably no eschar. Without appropriate diagnosis and treatment, she developed septic shock and acute respiratory distress syndrome. The diagnosis of JSF was confirmed by the identification of Rickettsia japonica by metagenomic next-generation sequencing (mNGS) of the blood. After one week of treatment with doxycycline, the patient's clinical symptoms subsided without any complaints of discomfort.}, } @article {pmid39559335, year = {2024}, author = {de Paula, TS and Leite, DMB and Lobo-Hajdu, G and Vacelet, J and Thompson, F and Hajdu, E}, title = {The complete mitochondrial DNA of the carnivorous sponge Lycopodina hypogea is putatively complemented by microDNAs.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e18255}, pmid = {39559335}, issn = {2167-8359}, mesh = {Animals ; *Porifera/genetics ; *DNA, Mitochondrial/genetics ; *Genome, Mitochondrial/genetics ; Gene Order ; Phylogeny ; RNA, Transfer/genetics ; }, abstract = {Carnivorous sponges (Porifera, Demospongiae, Cladorhizidae), contrary to the usual filter-feeding mechanism of sponges, are specialized in catching larger prey through adhesive surfaces or hook-like spicules. The mitochondrial DNA of sponges overall present several divergences from other metazoans, and while presenting unique features among major transitions, such as in calcarean and glass sponges, poriferan mitogenomes are relatively stable within their groups. Here, we report and discuss the mitogenome of Lycopodina hypogea (Vacelet & Boury-Esnault, 1996), which greatly vary from its subordinal counterparts in both structure and gene order. This mitogenome is seemingly multipartite into three chromosomes, two of them as microDNAs. The main chromosome, chrM1, is unusually large, 31,099 bp in length, has a unique gene order within Poecilosclerida, and presents two rRNA, 13 protein and 19 tRNA coding genes. Intergenic regions comprise approximately 40% of chrM1, bearing several terminal direct and inverted repeats (TDRr and TIRs) but holding no vestiges of former mitochondrial sequences, pseudogenes, or transposable elements. The nd4l and trnI(gau) genes are likely located in microDNAs thus comprising putative mitochondrial chromosomes chrM2, 291 bp, and chrM3, 140 bp, respectively. It is unclear which processes are responsible for the remarkable features of the of L. hypogea mitogenome, including a generalized gene rearrangement, long IGRs, and putative extrachromosomal genes in microDNAs.}, } @article {pmid39558935, year = {2024}, author = {Balestrini, VP and Pinto, OHB and Simmons, BA and Gladden, JM and Krüger, RH and Quirino, BF}, title = {Analysis of novel bacterial metagenome-assembled genomes from lignin-degrading microbial consortia.}, journal = {Current research in microbial sciences}, volume = {7}, number = {}, pages = {100302}, pmid = {39558935}, issn = {2666-5174}, abstract = {Despite recent progress, bacterial degradation of lignin is not completely understood. To address the mechanisms that bacteria from unknown taxonomic groups use to perform lignin-monomer degradation, functional analysis of bacterial metagenome-assembled genomes from soil-derived consortia enriched for microorganisms capable of degrading lignin was performed. A total of 232 metagenome-assembled genomes were recovered. After applying quality criteria of at least 70 % genome completeness and contamination less than or equal to 10 %, 39 genomes were obtained. From these, a total of 14 genomes from bacteria of unknown classification at lower taxonomic levels (i.e., only classified to the order level or higher) were chosen for further functional analysis. A global analysis of the potential ecological functions of these bacteria was performed, followed by a detailed analysis of monolignol degradation pathways. The phylum with the highest number of genomes was Proteobacteria. The genomes presented functions consistent with soil-derived bacteria, like denitrification, with different metabolic capacities related to the sulfur, chlorine, arsenic and carbon cycles, in addition to the degradation of plant cell wall components like cellulose, hemicellulose, and lignin. The Sphingomonadales_OP 08 genome showed the greatest potential to degrade cellulose and hemicellulose, although it does not appear to be able to degrade lignin. The Actinobacteria_BY 70 genome presented the highest number of enzymes and pathways related to the degradation of monolignols; furthermore, it showed the greatest potential for aromatic ring breakage by different fission pathways. The genomes of the two Actinobacteria showed the caffeic acid pathway, an important phenolic compound presenting several biological properties, such as antimicrobial and antioxidant. To our knowledge, this is the first time this pathway has been reported in this class of bacteria.}, } @article {pmid39558756, year = {2025}, author = {Paris, JR and King, RA and Ferrer Obiol, J and Shaw, S and Lange, A and Bourret, V and Hamilton, PB and Rowe, D and Laing, LV and Farbos, A and Moore, K and Urbina, MA and van Aerle, R and Catchen, JM and Wilson, RW and Bury, NR and Santos, EM and Stevens, JR}, title = {The Genomic Signature and Transcriptional Response of Metal Tolerance in Brown Trout Inhabiting Metal-Polluted Rivers.}, journal = {Molecular ecology}, volume = {34}, number = {1}, pages = {e17591}, pmid = {39558756}, issn = {1365-294X}, support = {BB/K003240/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; //University of Exeter/ ; WT097835MF/WT_/Wellcome Trust/United Kingdom ; Charityno.1135007,Companyno.06545646//Westcountry Rivers Trust, UK/ ; WT101650MA/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; //Environment Agency, UK/ ; }, mesh = {*Genome ; *Transcription, Genetic/drug effects ; *Adaptation, Physiological/drug effects/genetics ; *Rivers ; *Water Pollutants, Chemical/toxicity ; *Salmon/genetics/physiology ; Gene Expression Profiling ; Gene Expression Regulation/drug effects ; *Metals/toxicity ; United Kingdom ; Genetic Loci ; Gene Library ; Metagenomics ; Organ Specificity/drug effects ; Gene Ontology ; Animals ; }, abstract = {Industrial pollution is a major driver of ecosystem degradation, but it can also act as a driver of contemporary evolution. As a result of intense mining activity during the Industrial Revolution, several rivers across the southwest of England are polluted with high concentrations of metals. Despite the documented negative impacts of ongoing metal pollution, brown trout (Salmo trutta L.) survive and thrive in many of these metal-impacted rivers. We used population genomics, transcriptomics, and metal burdens to investigate the genomic and transcriptomic signatures of potential metal tolerance. RADseq analysis of six populations (originating from three metal-impacted and three control rivers) revealed strong genetic substructuring between impacted and control populations. We identified selection signatures at 122 loci, including genes related to metal homeostasis and oxidative stress. Trout sampled from metal-impacted rivers exhibited significantly higher tissue concentrations of cadmium, copper, nickel and zinc, which remained elevated after 11 days in metal-free water. After depuration, we used RNAseq to quantify gene expression differences between metal-impacted and control trout, identifying 2042 differentially expressed genes (DEGs) in the gill, and 311 DEGs in the liver. Transcriptomic signatures in the gill were enriched for genes involved in ion transport processes, metal homeostasis, oxidative stress, hypoxia, and response to xenobiotics. Our findings reveal shared genomic and transcriptomic pathways involved in detoxification, oxidative stress responses and ion regulation. Overall, our results demonstrate the diverse effects of metal pollution in shaping both neutral and adaptive genetic variation, whilst also highlighting the potential role of constitutive gene expression in promoting metal tolerance.}, } @article {pmid39558431, year = {2024}, author = {Bennett, AE and Kelsey, S and Saup, C and Wilkins, M and Malacrinò, A}, title = {Selenium alters the gene content but not the taxonomic composition of the soil microbiome.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {92}, pmid = {39558431}, issn = {2524-6372}, support = {NA//Ohio State University Center for Applied Plant Sciences/ ; }, abstract = {BACKGROUND: Microbiomes, essential to ecosystem processes, face strong selective forces that can drive rapid evolutionary adaptation. However, our understanding of evolutionary processes within natural systems remains limited. We investigated evolution in response to naturally occurring selenium in soils of different geological parental materials on the Western Slope of Colorado. Our study focused on examining changes in gene frequencies within microbial communities in response to selenium exposure.

RESULTS: Despite expectations of taxonomic composition shifts and increased gene content changes at high-selenium sites, we found no significant alterations in microbial diversity or community composition. Surprisingly, we observed a significant increase in differentially abundant genes within high-selenium sites.

CONCLUSIONS: These findings are suggestive that selection within microbiomes primarily drives the accumulation of genes among existing microbial taxa, rather than microbial species turnover, in response to strong stressors like selenium. Our study highlights an unusual system that allows us to examine evolution in response to the same stressor annually in a non-model system, contributing to understanding microbiome evolution beyond model systems.}, } @article {pmid39558258, year = {2024}, author = {Wu, HH and Zhao, PP and Wang, XM and Ren, YY and Fang, SY}, title = {Hearing loss as the first symptom of pneumonia caused by Chlamydia psittaci: a case report and literature review.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {1314}, pmid = {39558258}, issn = {1471-2334}, mesh = {Humans ; Male ; Aged ; *Chlamydophila psittaci/isolation & purification/genetics ; *Psittacosis/microbiology/drug therapy/diagnosis/complications ; *Anti-Bacterial Agents/therapeutic use ; Tomography, X-Ray Computed ; Hearing Loss, Sensorineural/microbiology/drug therapy ; Doxycycline/therapeutic use ; Bronchoalveolar Lavage Fluid/microbiology ; Moxifloxacin/therapeutic use ; High-Throughput Nucleotide Sequencing ; Pneumonia, Bacterial/microbiology/drug therapy/diagnosis/complications ; }, abstract = {BACKGROUND: The typical clinical symptoms of psittacosis pneumonia include fever, dry cough, and chills. Sudden sensorineural hearing loss is a relatively uncommon condition in pneumonia caused by Chlamydia psittaci. In this study, we reported a rare case of Chlamydia psittaci pneumonia presented as hearing loss.

CASE PRESENTATION: A 65-year-old man presented to our hospital with sudden hearing loss, cough with sputum, and fever for the last three days. Chest computed tomography revealed inflammation of the left lung and poor response to broad-spectrum antibiotics. The metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid identified the sequence of Chlamydia psittaci. Subsequently, antibiotic treatment was adjusted to doxycycline hydrochloride and moxifloxacin, resulting in significant improvement in both hearing loss and lung infection.

CONCLUSIONS: Sudden sensorineural hearing loss as an extrapulmonary feature of Chlamydia psittaci pneumonia is extremely rare. Although the exact mechanism remains unclear, this case report described a patient with sudden bilateral sensorineural hearing loss as a presenting feature of Chlamydia psittaci pneumonia, illustrating the importance of the extrapulmonary features of atypical pneumonia. The mNGS test could provide early diagnosis. Many patients had a good prognosis with prompt and effective treatment.}, } @article {pmid39558256, year = {2024}, author = {Liu, Y and Fang, M and Yuan, C and Yang, Y and Yu, L and Li, Y and Hu, L and Li, J}, title = {Combining interferon-γ release assays and metagenomic next-generation sequencing for diagnosis of pulmonary tuberculosis: a retrospective study.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {1316}, pmid = {39558256}, issn = {1471-2334}, support = {2208085MH264//Natural Science Foundation in Anhui Province/ ; 2021xkj138//Project Supported by Anhui Medical University/ ; 202304295107020043//Anhui Province clinical medical research transformation special project/ ; 2024AH040114//University research project in Anhui Province/ ; 2023AH010083//Anhui university scientific research project/ ; MTP2022A015//China Primary Health Care Foundation/ ; }, mesh = {Humans ; Retrospective Studies ; Male ; Female ; *Interferon-gamma Release Tests/methods ; *Tuberculosis, Pulmonary/diagnosis/microbiology/blood ; Middle Aged ; Adult ; *High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Interferon-gamma/blood ; Sensitivity and Specificity ; Aged ; ROC Curve ; Mycobacterium tuberculosis/genetics ; }, abstract = {BACKGROUND: Rapid diagnosis of pulmonary tuberculosis (PTB) is urgently needed. We aimed to improve diagnosis rates by combining tuberculosis-interferon (IFN)-γ release assays (TB-IGRA) with metagenomic next-generation sequencing (mNGS) for PTB diagnosis.

METHODS: A retrospective study of 29 PTB and 32 non-TB patients from our hospital was conducted between October 2022 and June 2023. Samples were processed for TB-IGRA and mNGS tests according to the manufacturer's protocol.

RESULTS: The levels of IFN-γ release in PTB patients were significantly higher than those in non-TB patients (604.15 ± 112.18 pg/mL, and 1.04 ± 0.38 pg/mL, respectively; p < 0.0001). Regarding presenting symptoms or signs, cough and thoracalgia were less common in PTB patients than in non-TB patients (p = 0.001 and p = 0.024, respectively). Total protein and albumin levels in the sera of PTB patients were significantly elevated compared to non-TB patients (p = 0.039 and p = 0.004, respectively). The area under the ROC curve (AUC) for TB-IGRA in PTB diagnosis was 0.939. With an optimal IFN-γ cut-off value of 14.3 pg/mL (Youden's index 0.831), sensitivity was 86.2% and specificity was 96.9%. ROC curve analysis for mNGS and TB-IGRA combined with mNGS showed AUCs of 0.879 and 1, respectively. The AUC of TB-IGRA combined with mNGS was higher than that of TB-IGRA and mNGS alone.

CONCLUSIONS: TB-IGRA combined with mNGS may be an effective method for diagnosing tuberculosis, and can be used in the clinical diagnosis of PTB.}, } @article {pmid39558184, year = {2025}, author = {Sayers, EW and Cavanaugh, M and Frisse, L and Pruitt, KD and Schneider, VA and Underwood, BA and Yankie, L and Karsch-Mizrachi, I}, title = {GenBank 2025 update.}, journal = {Nucleic acids research}, volume = {53}, number = {D1}, pages = {D56-D61}, pmid = {39558184}, issn = {1362-4962}, support = {/NH/NIH HHS/United States ; /NH/NIH HHS/United States ; }, mesh = {*Databases, Nucleic Acid ; Humans ; Software ; Internet ; Genomics ; Metagenome ; Animals ; }, abstract = {GenBank® (https://www.ncbi.nlm.nih.gov/genbank/) is a comprehensive, public data repository that contains 34 trillion base pairs from over 4.7 billion nucleotide sequences for 581 000 formally described species. Daily data exchange with the European Nucleotide Archive and the DNA Data Bank of Japan ensures worldwide coverage. We summarize the content of the database in 2025 and recent updates such as accelerated processing of influenza sequences and the ability to upload feature tables to Submission Portal for messenger RNA sequences. We provide an overview of the web, application programming and command-line interfaces that allow users to access GenBank data. We also discuss the importance of creating BioProject and BioSample records during submissions, particularly for viruses and metagenomes. Finally, we summarize educational materials and recent community outreach efforts.}, } @article {pmid39558081, year = {2024}, author = {Yang, M and Zhao, Y and Li, L and Qi, Y and Gao, P and Guo, J and Liu, J and Chen, Z and Zhao, J and Yu, L}, title = {Functional dynamics analysis of endophytic microbial communities during Amorphophallus muelleri seed maturation.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {28432}, pmid = {39558081}, issn = {2045-2322}, support = {YJL24014//Talent Introduction Program of Kunming University/ ; 202201AT070113//Yunnan Provincial Science and Technology Dep artment/ ; 202101AO070075//Yunnan Provincial Science and Technology Dep artment/ ; 202401AU070020//Yunnan Provincial Science and Technology Dep artment/ ; 202201AU070043//Yunnan Provincial Science and Technology Dep artment/ ; 202101BA070001-174//Yunnan Provincial Science and Technology Dep artment/ ; 202301AU070136//Yunnan Provincial Science and Technology Dep artment/ ; 2022J0644//Yunnan Education Department Research Project/ ; 2023J0827//Yunnan Education Department Research Project/ ; YNWR-QNBJ-2018-324//Yunnan Province Youth Talent Support Program/ ; }, mesh = {*Seeds/microbiology/growth & development ; *Endophytes/genetics ; *Microbiota/genetics ; *Amorphophallus/microbiology ; Metagenomics/methods ; Bacteria/genetics/classification ; Ascomycota/genetics ; Fungi/genetics/classification ; }, abstract = {Konjac seeds of Amorphophallus muelleri are produced through a unique form of apomixis in triploid parthenogenesis, and typically require a longer maturation period (approximately 8 months). To date, the relevant functions of endophytic microbial taxa during A. muelleri seed development and maturation remain largely unexplored. In this study, we analyzed the functional adaptability and temporal dynamics of endophytic microbial communities during three stages of A. muelleri seed maturation. Through metagenomic sequencing, we determined that the functions of the endophytic microbiome in A. muelleri seeds were driven by the seed maturation status, and the functions of the microbial communities in the seed coats and seeds differed significantly. The species annotation results show that Proteobacteria, Actinobacteria, Ascomycota, and Basidiomycota were the dominant bacterial and fungal communities in A. muelleri seeds at different maturation stages. The KEGG and COG functional gene annotation results revealed that the seed samples during the three maturation stages had higher KO functional diversity than the seed coat samples, and the COG functional diversity of the green and red seed samples was also significantly higher than that of the seed coat samples. At different maturation stages, microbial functional genes involved in energy production and conversion as well as carbon fixation were enriched in the A. muelleri seed coats, while microbial functional genes involved in signal transduction mechanisms, amino acid transport and metabolism, carbohydrate metabolism, and lipid metabolism were more highly expressed in the seeds. Moreover, in the middle to late stages of seed maturation, the microbial functional genes involved in the biosynthesis of resistant compounds such as phenols, flavonoids, and alkaloids were significantly enriched to enhance the resistance and environmental adaptation of A. muelleri seeds. The results verified that the functions of the endophytic microbial communities change dynamically during A. muelleri seed maturation to adapt to the current needs of the host plant, which has significant implications for the exploration and utilization of functional microbial resources in A. muelleri seeds.}, } @article {pmid39557257, year = {2024}, author = {Dong, J and Wang, L and Bai, Y and Huang, X and Chen, C and Liu, Y}, title = {Study on the physicochemical properties and immune regulatory mechanism of polysaccharide fraction from Aronia Melanocarpa fruit.}, journal = {International journal of biological macromolecules}, volume = {283}, number = {Pt 2}, pages = {137696}, doi = {10.1016/j.ijbiomac.2024.137696}, pmid = {39557257}, issn = {1879-0003}, mesh = {*Photinia/chemistry ; *Polysaccharides/pharmacology/chemistry ; Animals ; Mice ; *Fruit/chemistry ; *Gastrointestinal Microbiome/drug effects ; Chemical Phenomena ; Molecular Weight ; }, abstract = {Aronia Melanocarpa (Michx.) Elliott fruit has been extensively used in the food and medicinal fields. This study aimed to analyze the physicochemical properties of a polysaccharide fraction (AMP2) isolated from this fruit for the first time and investigated its immune regulatory mechanism. The physicochemical properties of AMP2 were determined using high-performance gel permeation chromatography, PMP derivatization-high performance liquid chromatography, Ultraviolet spectroscopy, and infrared spectroscopy. The metagenomic technology was applied to investigate the regulatory effects and mechanisms of AMP2 on the gut microbiota of immunosuppressed mice. The results showed that molecular weight of AMP2 was 83,444 Da, which was mainly composed of D-arabinose, D-xylose, D-mannose, D-rhamnose and D-glucose, and both β-type and α-type glycosidic bonds contained in its structure. AMP2 changed the composition of gut microbiota by increasing the number of beneficial and probiotic bacteria, thereby regulated the intestinal mucosal immune system of host. AMP2 improved intestinal immune system response and antimicrobial capacity through positive regulation of the NOD-like receptor signaling pathway and neutrophil extracellular trap formation. The results demonstrate the potential of AMP2 in immune regulation, providing a new perspective for its subsequent development and contributing to the development and application of related health foods.}, } @article {pmid39557245, year = {2024}, author = {Qin, X and Huang, W and Li, Q}, title = {Lignocellulose biodegradation to humic substances in cow manure-straw composting: Characterization of dissolved organic matter and microbial community succession.}, journal = {International journal of biological macromolecules}, volume = {283}, number = {Pt 3}, pages = {137758}, doi = {10.1016/j.ijbiomac.2024.137758}, pmid = {39557245}, issn = {1879-0003}, mesh = {*Humic Substances/analysis ; *Lignin/chemistry/metabolism ; *Manure/microbiology/analysis ; Cattle ; Animals ; *Composting/methods ; *Biodegradation, Environmental ; Microbiota ; }, abstract = {Composting, a sustainable practice, facilitates the biodegradation of organic waste, notably lignocellulosic biomass, into value-added humic substances. Despite its potential, the application of electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS) to characterize dissolved organic matter (DOM) for assessing the changes in maturity during cow manure-straw composting is underexplored. Furthermore, the link between these changes, microbial community succession, and the biochemical pathways of humus formation is seldom investigated. This study leveraged ESI FT-ICR MS and metagenomic analysis to elucidate the molecular changes in DOM, identified key microbes in humus formation, and traced the humus formation pathway during composting. The results highlighted the crucial role of microorganisms such as Thermobifida, Luteimonas, Ascomycota, and Chloroflexi in accelerating the breakdown and transformation of plant biopolymers. Large molecular nitrogen compounds from cow manure-straw were converted into unsaturated, aromatic oxygen compounds, which resemble humic substances in their chemical properties. The ESI FT-ICR MS data revealed that humus formation occurred through a series of reactions, including protein deamination, lignin delignification, and decarbonylation. This research offered new light on strategies to enhance the stabilization and humification of cow manure-straw composting, contributing to more effective composting processes.}, } @article {pmid39557129, year = {2025}, author = {Drane, K and Huerlimann, R and Jones, R and Whelan, A and Sheehan, M and Ariel, E and Kinobe, R}, title = {Concordance in molecular methods for detection of antimicrobial resistance: A cross sectional study of the influent to a wastewater plant.}, journal = {Journal of microbiological methods}, volume = {228}, number = {}, pages = {107069}, doi = {10.1016/j.mimet.2024.107069}, pmid = {39557129}, issn = {1872-8359}, mesh = {*Wastewater/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/drug effects/classification/isolation & purification ; Australia ; Metagenomics/methods ; Anti-Bacterial Agents/pharmacology ; Microbiota/genetics/drug effects ; Genes, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; }, abstract = {Methods that are used to characterise microbiomes and antimicrobial resistance genes (ARGs) in wastewater are not standardised. We used shotgun metagenomic sequencing (SM-Seq), RNA sequencing (RNA-seq) and targeted qPCR to compare microbial and ARG diversity in the influent to a municipal wastewater treatment plant in Australia. ARGs were annotated with CARD-RGI and MEGARes databases, and bacterial diversity was characterised by 16S rRNA gene sequencing and SM-Seq, with species annotation in SILVA/GreenGenes databases or Kraken2 and the NCBI nucleotide database respectively. CARD and MEGARes identified evenly distributed ARG profiles but MEGARes detected a richer array of ARGs (richness = 475 vs 320). Qualitatively, ARGs encoding for aminoglycoside, macrolide-lincosamide-streptogramin and multidrug resistance were the most abundant in all examined databases. RNA-seq detected only 32 % of ARGs identified by SM-Seq, but there was concordance in the qualitative identification of aminoglycoside, macrolide-lincosamide, phenicol, sulfonamide and multidrug resistance by SM-Seq and RNA-seq. qPCR confirmed the detection of some ARGs, including OXA, VEB and EREB, that were identified by SM-Seq and RNA-seq in the influent. For bacteria, SM-Seq or 16S rRNA gene sequencing were equally effective in population profiling at phyla or class level. However, SM-Seq identified a significantly higher species richness (richness = 15,000 vs 3750). These results demonstrate that SM-Seq with gene annotation in CARD and MEGARes are equally sufficient for surveillance of antimicrobial resistance in wastewater. For more precise ARG identification and quantification however, MEGARes presented a better resolution. The functionality of detected ARGs was not confirmed, but general agreement on the putative phenotypic resistance profile by antimicrobial class was observed between RNA-Seq and SM-Seq.}, } @article {pmid39557097, year = {2025}, author = {Zheng, X and Li, Y and Xu, J and Zhang, Q and Zhang, Y}, title = {Characterization of three novel dimethyl disulfide degrading bacteria and their potential degradation pathways.}, journal = {Bioresource technology}, volume = {417}, number = {}, pages = {131833}, doi = {10.1016/j.biortech.2024.131833}, pmid = {39557097}, issn = {1873-2976}, mesh = {*Disulfides/metabolism ; *Biodegradation, Environmental ; *Bacteria/metabolism/genetics ; Hydrogen Sulfide/metabolism ; Odorants ; Phylogeny ; Acinetobacter/metabolism/genetics ; Sulfides ; }, abstract = {Dimethyl disulfide (DMDS) is an odor compound characterized by the lowest olfactory threshold and high toxicity. It is indispensable to explore the bacteria with high resistance and degradation efficiency to DMDS. Acinetobacter lwoffii, Pseudomonas mendocina, and Myroides odoratus were isolated from kitchen waste. After 6 days of individual treatment, the removal rates were 34.22 %, 40.95 %, and 41.94 % respectively. The DMDS metabolic pathways based on metagenomic assays were discovered to be incomplete due to the insufficient annotation of some key genes in the current database. Following 3 days of treatment with bacterial consortia at ratios of 5:1 for A. lwoffii C2/ M. odoratus C7 and 1:1:1 for the three strains achieved 100 % DMDS removal. Additionally, the consortia reduced hydrogen sulfide (H2S) and dimethyl sulfide (DMS).This discovery broadens the spectrum of bacteria exhibiting high tolerance and efficient degradation of DMDS, with significant implications for DMDS removal and odor treatment.}, } @article {pmid39557096, year = {2025}, author = {Tan, Z and Chen, W and Wei, X and Qiu, Z and Zhuang, W and Zhang, B and Xie, J and Lin, Y and Ren, Y and Preis, S and Wei, C and Zhu, S}, title = {Virus-bacterium interaction involved in element cycles in biological treatment of coking wastewater.}, journal = {Bioresource technology}, volume = {416}, number = {}, pages = {131839}, doi = {10.1016/j.biortech.2024.131839}, pmid = {39557096}, issn = {1873-2976}, mesh = {*Wastewater/virology/microbiology ; *Coke ; *Bacteria/metabolism/genetics ; Viruses/metabolism ; Nitrogen ; Phosphorus ; Water Purification/methods ; Carbon/metabolism ; Metagenomics ; }, abstract = {Although prokaryotic microbes in coking wastewater (CWW) treatment have been comprehensively studied, the ecological functions of viruses remain unclear. A full-scale CWW biological treatment AOHO combination was studied for the virus-bacterium interactions involved in element cycles by metaviromics, metagenomics and physicochemical characteristics. Results showed the unique viromic profile with Cirlivirales and Petitvirales as the dominant viruses infecting functional bacteria hosts. The auxiliary metabolic genes (AMGs) focused on element cycles, including metabolisms of carbon (fadA), nitrogen (glnA), sulfur (mddA and cysK) and phosphorus (phoH). Other AMGs were involved in toxic tolerance of hosts, improving their cell membrane and wall robustness, antioxidant, DNA repair and cobalamin biosynthesis. Vice versa, the bloomed host provided fitness advantages for viruses. Dissolved oxygen was found to be the key factor shaping the distributions of viral community and AMGs. Summarizing, the study exposed the mutual virus-bacterium interaction in the AOHO combination providing stable treatment efficiency.}, } @article {pmid39556491, year = {2025}, author = {Shete, O and Ghosh, TS}, title = {Normal Gut Microbiomes in Diverse Populations: Clinical Implications.}, journal = {Annual review of medicine}, volume = {76}, number = {1}, pages = {95-114}, doi = {10.1146/annurev-med-051223-031809}, pmid = {39556491}, issn = {1545-326X}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; }, abstract = {The human microbiome is a sensor and modulator of physiology and homeostasis. Remarkable tractability underpins the promise of therapeutic manipulation of the microbiome. However, the definition of a normal or healthy microbiome has been elusive. This is in part due to the underrepresentation of minority groups and major global regions in microbiome studies to date. We review studies of the microbiome in different populations and highlight a commonality among health-associated microbiome signatures along with major drivers of variation. We also provide an overview of microbiome-associated therapeutic interventions for some widespread, widely studied diseases. We discuss sources of bias and the challenges associated with defining population-specific microbiome reference bases. We propose a roadmap for defining normal microbiome references that can be used for population-customized microbiome therapeutics and diagnostics.}, } @article {pmid39555414, year = {2024}, author = {Wang, J and Liu, H and Kou, X and Zhang, Y and Wang, Y and Chen, C and Xiang, Z and Wang, X and Su, C and Liu, Y}, title = {Toxic effects of DEHP and MEHP on gut-liver axis in rats via intestinal flora and metabolomics.}, journal = {iScience}, volume = {27}, number = {11}, pages = {111135}, pmid = {39555414}, issn = {2589-0042}, abstract = {Di (2-ethylhexyl) phthalate (DEHP) is an environmental endocrine disruptor and commonly used as a plasticizer. Exposure to DEHP and its active metabolite mono-2-ethylhexyl phthalate (MEHP) can lead to adverse health consequences; however, the toxic mechanism is remains unclear. In this research, male and female rats were exposed to DEHP and MEHP by oral gavage for 60 consecutive days. Pathological analysis revealed that DEHP and MEHP exposure could affect liver, heart, kidney, and testis tissues, as well as alter biochemical indicators. Metagenomics (16S rRNA gene sequencing) analysis indicated that DEHP and MEHP could reduce the diversity and alter the composition of the gut microbiota. Toxic exposure also affected the levels of short chain fatty acids (SCFAs), with noticeable variations between genders. Metabolomic analysis revealed that DEHP and MEHP could influence bile acids, amino acids, hormones, and lipids. These results demonstrate that exposure to DEHP and MEHP can induce toxicity in rats via the gut-liver axis.}, } @article {pmid39555017, year = {2024}, author = {Wang, S and Su, LY and Chen, J and Tian, Y and Zhou, H}, title = {Integrated multi-omics profiling highlights the diet-gut-brain axis in low-calorie diets promoted novelty-seeking behavior.}, journal = {Current research in food science}, volume = {9}, number = {}, pages = {100897}, pmid = {39555017}, issn = {2665-9271}, abstract = {The foods that we eat are closely linked to the development and function of neurophysiology, affecting mood, cognition, and mental health. Yet, it is not known whether and how dietary patterns affect brain function and mood. Here, we explored the impact of various diets on the behavior of mice. Low-calorie (LC) diet-fed mice exhibited increased novel exploratory behaviors, including novelty to new foods, objects, and environments. The host transcriptome sequencing showed an increase of Areg in the cerebral cortex of mice fed with LC, and IMPC showed that Areg knock-out mice exhibited significantly decreased exploration of novel environments. According to the metagenomic sequencing results, a significant increase in the levels of s_Schaedlerella and s_1XD8-76 was observed after LC feeding. Integrated analysis of microbiota metabolites and host transcriptomics suggested that 68 differential metabolites in LC-fed mice were associated with upregulation of Areg expression. This study demonstrates the powerful impact of LC feeding on the restoration of gut microbiota and the improvement of novelty-seeking behavior. In addition, this study supports the idea that microbiota-associated metabolites can modulate host gene transcription, which provides a link between dietary patterns and their impact on the emotional and cognitive centers of the brain.}, } @article {pmid39554614, year = {2024}, author = {Liu, R and Qiao, X and Shi, Y and Peterson, CB and Bush, WS and Cominelli, F and Wang, M and Zhang, L}, title = {Constructing phylogenetic trees for microbiome data analysis: A mini-review.}, journal = {Computational and structural biotechnology journal}, volume = {23}, number = {}, pages = {3859-3868}, pmid = {39554614}, issn = {2001-0370}, abstract = {As next-generation sequencing technologies advance rapidly and the cost of metagenomic sequencing continues to decrease, researchers now face an unprecedented volume of microbiome data. This surge has stimulated the development of scalable microbiome data analysis methods and necessitated the incorporation of phylogenetic information into microbiome analysis for improved accuracy. Tools for constructing phylogenetic trees from 16S rRNA sequencing data are well-established, as the highly conserved regions of the 16S gene are limited, simplifying the identification of marker genes. In contrast, metagenomic and whole genome shotgun (WGS) sequencing involve sequencing from random fragments of the entire gene, making identification of consistent marker genes challenging owing to the vast diversity of genomic regions, resulting in a scarcity of robust tools for constructing phylogenetic trees. Although bacterial sequence tree construction tools exist for upstream bioinformatics, many downstream researchers-those integrating these trees into statistical models or machine learning-are either unaware of these tools or find them difficult to use due to the steep learning curve of processing raw sequences. This is compounded by the fact that public datasets often lack phylogenetic trees, providing only abundance tables and taxonomic classifications. To address this, we present a comprehensive review of phylogenetic tree construction techniques for microbiome data (16S rRNA or whole-genome shotgun sequencing). We outline the strengths and limitations of current methods, offering expert insights and step-by-step guidance to make these tools more accessible and widely applicable in quantitative microbiome data analysis.}, } @article {pmid39553288, year = {2024}, author = {Chowdhury, S and Kullberg, RFJ and Haak, BW and Duran, C and Earny, VA and Eshwara, VK and Lawley, TD and Wiersinga, WJ and Mukhopadhyay, C}, title = {Gut Microbiome in Human Melioidosis: Composition and Resistome Dynamics from Diagnosis to Discovery.}, journal = {Open forum infectious diseases}, volume = {11}, number = {11}, pages = {ofae654}, pmid = {39553288}, issn = {2328-8957}, abstract = {BACKGROUND: Melioidosis, attributable to the soil-dwelling bacterium Burkholderia pseudomallei, stands as a paramount global health challenge, necessitating extended courses of antibiotics. While murine studies identified the gut microbiota as a modulator of bacterial dissemination during melioidosis, the human intestinal microbiota during melioidosis remains uncharacterized. Here, we characterized gut microbiota composition and antimicrobial resistance (AMR) genes at diagnosis, during treatment, and postdischarge for melioidosis. We hypothesized that the gut microbiota of melioidosis patients would be extensively distorted.

METHODS: In this prospective observational cohort, stool samples of patients with culture-confirmed melioidosis admitted to a tertiary care hospital in India were collected at diagnosis, 14 days after diagnosis, or discharge (whichever occurred first) and at 6 months postinfection. Family members or neighbors served as community controls. The gut microbiota and resistome were profiled by shotgun metagenomic sequencing.

RESULTS: We longitudinally analyzed the gut microbiota of 70 fecal samples from 28 patients and 16 community controls. At diagnosis, the gut microbiota of patients differed from that of controls, characterized by high abundances of potentially pathogenic bacteria, a loss of butyrate-producing bacteria, and higher levels of AMR genes. Microbiota composition and resistome remained different from community controls at 6 months, driven by total antibiotic exposure. During hospitalization, gut microbiota profiles were associated with secondary Klebsiella pneumoniae infections.

CONCLUSIONS: This first study on gut microbiota composition and resistome in human melioidosis showed extensive disruptions during hospitalization, with limited signs of restoration 6 months postinfection. Given the adverse outcomes linked with microbiome perturbations, limiting microbiota disruptions or using microbiota-restorative therapies (eg, butyrate-producing probiotics) may be beneficial.}, } @article {pmid39552867, year = {2024}, author = {Ma, R and Liu, Z and Zhang, L and Chen, C and Yuan, B and Luo, Y and Marcos, PJ and Tattevin, P and Zhang, W}, title = {Epidemiological characteristics of severe community-acquired pneumonia in children admitted to two tertiary hospitals in Shihezi, Xinjiang Region, China in 2023: a cross-sectional analysis.}, journal = {Journal of thoracic disease}, volume = {16}, number = {10}, pages = {6969-6982}, pmid = {39552867}, issn = {2072-1439}, abstract = {BACKGROUND: Severe community-acquired pneumonia (SCAP) in children is associated with high morbidity and mortality, and the data of epidemiological characteristics of SCAP in Shihezi area were inadequate. The main pathogens responsible for SCAP may vary dramatically according to the geographical area. We identified two tertiary hospitals with better medical level and the largest number of hospitalized children in Shihezi as sentinel hospitals. The primary purpose of the study is to cross-sectionally summarize the epidemiological characteristics of SCAP in children admitted to hospitals in Shihezi, Xinjiang, China in 2023.

METHODS: SCAP was defined as involving the respiratory and other systems, accompanied by significant systemic toxic symptoms. We prospectively included all patients <15 years old who diagnosed with SCAP according to the SCAP diagnostic criteria. We enrolled all patients <15 years who were diagnosed with SCAP during the study period (January to December 2023), a total of 309 cases were included from two sentinel hospitals in Shihezi, Xinjiang, from January to December 2023. Basic information and clinical data were collected on a standardized questionnaire, and respiratory samples were obtained for the detection of 27 respiratory pathogens using a panel, targeted next-generation sequencing (t-NGS), and metagenomic next-generation sequencing (mNGS).

RESULTS: We enrolled 309 patients aged 1-14 years: 157 males (50.8%) and 152 females (49.2%). There were 45 infants (1 month to 1 year, 14.6%), 33 toddlers (>1-3 years, 10.7%), 121 preschool children (>3-7 years, 39.2%), and 110 school-age children (>7-14 years, 35.6%). Overall, the number of SCAP cases in spring was 39 (12.6%), in summer was 44 (14.2%), in autumn was 137 (44.3%), and in winter was 89 (28.8%). A total of 572 pathogens were detected in this study, primarily Mycoplasma pneumoniae (MP) (n=120, 21.0%), respiratory syncytial virus (RSV) (n=82 strains, 14.3%), and Streptococcus pneumoniae (SP) (n=67, 11.7%). MP was prevalent mainly during the cold season of autumn, with its detection starting from July and reaching a peak detection rate in November. By studying the interaction among 22 common respiratory pathogens, we found a strong negative correlation between MP and SP, yet the highest number of co-infected cases involved MP and SP. Seventy-six (63.3% of all MP) SCAP were identified as macrolide-resistant (all with mutations at the A2063G site). MP SCAP was associated with prolonged illness duration and fever spikes. We observed incidence of pediatric SCAP showed an inverse trend with PM2.5 level changes.

CONCLUSIONS: The most common pathogens responsible for SCAP in the Shihezi region in 2023 were MP, RSV, and SP. MP was the primary cause of SCAP in children, and increased risk of co-infections, and high prevalence of macrolides resistance-all related to mutations at the A2063G site. Early identification of SCAP pathogen epidemiological characteristics can reduce severe case occurrence.}, } @article {pmid39552541, year = {2024}, author = {Singh, CK and Sodhi, KK}, title = {Targeting bioinformatics tools to study the dissemination and spread of antibiotic resistant genes in the environment and clinical settings.}, journal = {Critical reviews in microbiology}, volume = {}, number = {}, pages = {1-19}, doi = {10.1080/1040841X.2024.2429603}, pmid = {39552541}, issn = {1549-7828}, abstract = {Antibiotic resistance has expanded as a result of the careless use of antibiotics in the medical field, the food industry, agriculture, and other industries. By means of genetic recombination between commensal and pathogenic bacteria, the microbes obtain antibiotic resistance genes (ARGs). In bacteria, horizontal gene transfer (HGT) is the main mechanism for acquiring ARGs. With the development of high-throughput sequencing, ARG sequence analysis is now feasible and widely available. Preventing the spread of AMR in the environment requires the implementation of ARGs mapping. The metagenomic technique, in particular, has helped in identifying antibiotic resistance within microbial communities. Due to the exponential growth of experimental and clinical data, significant investments in computer capacity, and advancements in algorithmic techniques, the application of machine learning (ML) algorithms to the problem of AMR has attracted increasing attention over the past five years. The review article sheds a light on the application of bioinformatics for the antibiotic resistance monitoring. The most advanced tool currently being employed to catalog the resistome of various habitats are metagenomics and metatranscriptomics. The future lies in the hands of artificial intelligence (AI) and machine learning (ML) methods, to predict and optimize the interaction of antibiotic-resistant compounds with target proteins.}, } @article {pmid39552505, year = {2024}, author = {Hiraoka, S and Ijichi, M and Takeshima, H and Kumagai, Y and Yang, CC and Makabe-Kobayashi, Y and Fukuda, H and Yoshizawa, S and Iwasaki, W and Kogure, K and Shiozaki, T}, title = {Probe Capture Enrichment Sequencing of amoA Genes Improves the Detection of Diverse Ammonia-Oxidising Archaeal and Bacterial Populations.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e14042}, doi = {10.1111/1755-0998.14042}, pmid = {39552505}, issn = {1755-0998}, support = {JP19H04263//Japan Society for the Promotion of Science/ ; JP20K15444//Japan Society for the Promotion of Science/ ; JP21H03592//Japan Society for the Promotion of Science/ ; JP22H03716//Japan Society for the Promotion of Science/ ; JP22H04925//Japan Society for the Promotion of Science/ ; JP23H05411//Japan Society for the Promotion of Science/ ; JPMJCR11A3//Japan Science and Technology Agency/ ; JPMJCR19S2//Japan Science and Technology Agency/ ; JPMXD1521474594//Ministry of Education, Culture, Sports, Science and Technology/ ; }, abstract = {The ammonia monooxygenase subunit A (amoA) gene has been used to investigate the phylogenetic diversity, spatial distribution and activity of ammonia-oxidising archaeal (AOA) and bacterial (AOB), which contribute significantly to the nitrogen cycle in various ecosystems. Amplicon sequencing of amoA is a widely used method; however, it produces inaccurate results owing to the lack of a 'universal' primer set. Moreover, currently available primer sets suffer from amplification biases, which can lead to severe misinterpretation. Although shotgun metagenomic and metatranscriptomic analyses are alternative approaches without amplification bias, the low abundance of target genes in heterogeneous environmental DNA restricts a comprehensive analysis to a realisable sequencing depth. In this study, we developed a probe set and bioinformatics workflow for amoA enrichment sequencing using a hybridisation capture technique. Using metagenomic mock community samples, our approach effectively enriched amoA genes with low compositional changes, outperforming amplification and meta-omics sequencing analyses. Following the analysis of metatranscriptomic marine samples, we predicted 80 operational taxonomic units (OTUs) assigned to either AOA or AOB, of which 30 OTUs were unidentified using simple metatranscriptomic or amoA gene amplicon sequencing. Mapped read ratios to all the detected OTUs were significantly higher for the capture samples (50.4 ± 27.2%) than for non-capture samples (0.05 ± 0.02%), demonstrating the high enrichment efficiency of the method. The analysis also revealed the spatial diversity of AOA ecotypes with high sensitivity and phylogenetic resolution, which are difficult to examine using conventional approaches.}, } @article {pmid39551951, year = {2024}, author = {Yao, L and Devotta, H and Li, J and Lunjani, N and Sadlier, C and Lavelle, A and Albrich, WC and Walter, J and O'Toole, PW and O'Mahony, L}, title = {Dysrupted microbial tryptophan metabolism associates with SARS-CoV-2 acute inflammatory responses and long COVID.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2429754}, pmid = {39551951}, issn = {1949-0984}, mesh = {Humans ; *Tryptophan/metabolism/blood ; *COVID-19/immunology/microbiology ; *Gastrointestinal Microbiome ; Male ; Female ; *SARS-CoV-2/immunology ; *Cytokines/blood/metabolism ; Middle Aged ; Aged ; *Feces/microbiology/virology ; Post-Acute COVID-19 Syndrome ; Indoles/metabolism ; Indoleacetic Acids/metabolism/blood ; Inflammation ; Adult ; Dysbiosis/microbiology ; }, abstract = {Protection against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and risk of long COVID has been associated with the depletion or over-abundance of specific taxa within the gut microbiome. However, the microbial mechanisms mediating these effects are not yet known. We hypothesized that altered microbial production of tryptophan and its downstream derivatives might contribute to inappropriate immune responses to viral infection. In patients hospitalized with COVID-19 (n = 172), serum levels of tryptophan and indole-3-propionate (IPA) negatively correlated with serum levels of many proinflammatory mediators (including C-reactive protein and Serum amyloid A), while C-glycosyltryptophan (C-Trp), indole-3-lactic acid (ILA) and indole-3-acetic acid (IAA) levels were positively correlated with levels of acute phase proteins, proinflammatory cytokines, alarmins and chemokines. A similar pattern was observed in long COVID patients (n = 20) where tryptophan and IPA were negatively associated with a large number of serum cytokines, while C-Trp and IAA were positively associated with circulating cytokine levels. Metagenomic analysis of the fecal microbiota showed the relative abundance of genes encoding the microbial enzymes required for tryptophan production (e.g. anthranilate synthase) and microbial tryptophan metabolism was significantly lower in patients hospitalized with COVID-19 (n = 380) compared to healthy controls (n = 270). Microbial tryptophan metabolites reduced innate cell proinflammatory responses to cytosolic DNA sensor Stimulator of interferon genes (STING), toll-like receptor (TLR)-3 and TLR-4 stimulation in vitro, while IL-10 secretion was enhanced. Microbial tryptophan metabolites also modified ex vivo human lymphocyte responses by limiting the production of TH1 and TH17 associated cytokines, while enhancing secretion of IL-22. These data suggest that lower levels of tryptophan production and tryptophan metabolism by gut microbes may increase the risk of severe and chronic outcomes to SARS-CoV-2 infection due to impaired innate and adaptive responses to infection. Screening patients for lower-level microbiome capacity for tryptophan metabolism may help identify at-risk individuals.}, } @article {pmid39551884, year = {2024}, author = {Mamo, Z and Abera, S and Tafesse, M}, title = {Taxonomic and functional profiling of microbial community in municipal solid waste dumpsite.}, journal = {World journal of microbiology & biotechnology}, volume = {40}, number = {12}, pages = {384}, pmid = {39551884}, issn = {1573-0972}, support = {EN-1/17-1/18//Addis Ababa Science and Technology University/ ; }, mesh = {*Solid Waste ; *Bacteria/classification/genetics/metabolism ; *Waste Disposal Facilities ; *Microbiota ; *Metagenomics ; Phylogeny ; Refuse Disposal ; Biodegradation, Environmental ; Drug Resistance, Microbial/genetics ; Soil Microbiology ; }, abstract = {Understanding the microbial ecology of landfills is crucial for improving waste management strategies and utilizing the potential of these microbial communities for biotechnological applications. This study aimed to conduct a comprehensive taxonomic and functional profiling of the microbial community present in the Addis Ababa municipal solid waste dumpsite using a shotgun metagenomics sequencing approach. The taxonomic analysis of the sample revealed the significant presence of bacteria, with the Actinomycetota (56%), Pseudomonadota (23%), Bacillota (3%), and Chloroflexota (3%) phyla being particularly abundant. The most abundant KEGG categories were carbohydrates metabolism, membrane transport, signal transduction, and amino acid metabolism. The biodegradation and metabolism of xenobiotics, as well as terpenoids and polyketides, were also prevalent. Moreover, the Comprehensive Antibiotic Resistance Database (CARD) identified 52 antibiotic resistance gene (ARG) subtypes belonging to 14 different drug classes, with the highest abundances observed for glycopeptide, phosphonic acid, and multidrug resistance genes. Actinomycetota was the dominant phylum harboring ARGs, followed by Pseudomonadota and Chloroflexota. This study offers valuable insights into the taxonomic and functional diversity of the microbial community in the Addis Ababa municipal solid waste dumpsite. It sheds light on the widespread presence of metabolically versatile microbes, antibiotic resistance genes, mobile genetic elements, and pathogenic bacteria. This understanding can contribute to the creation of efficient waste management strategies and the investigation of possible biotechnological uses for these microbial communities.}, } @article {pmid39551377, year = {2025}, author = {Siew, SW and Khairi, MHF and Hamid, NA and Asras, MFF and Ahmad, HF}, title = {Shallow shotgun sequencing of healthcare waste reveals plastic-eating bacteria with broad-spectrum antibiotic resistance genes.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {364}, number = {Pt 1}, pages = {125330}, doi = {10.1016/j.envpol.2024.125330}, pmid = {39551377}, issn = {1873-6424}, mesh = {*Plastics ; *Bacteria/genetics/drug effects ; Medical Waste ; RNA, Ribosomal, 16S/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; }, abstract = {The burgeoning crises of antimicrobial resistance and plastic pollution are converging in healthcare settings, presenting a complex challenge to global health. This study investigates the microbial populations in healthcare waste to understand the extent of antimicrobial resistance and the potential for plastic degradation by bacteria. Our metagenomic analysis, using both amplicon and shallow shotgun sequencing, provided a comprehensive view of the taxonomic diversity and functional capacity of the microbial consortia. The viable bacteria in healthcare waste samples were analyzed employing full-length 16S rRNA sequencing, revealing a diverse bacterial community dominated by Firmicutes and Proteobacteria phyla. Notably, Proteus mirabilis VFC3/3 and Pseudomonas sp. VFA2/3 were detected, while Stenotrophomonas maltophilia VFV3/2 surfaced as the predominant species, holding implications for the spread of hospital-acquired infections and antimicrobial resistance. Antibiotic susceptibility testing identified multidrug-resistant strains conferring antimicrobial genes, including the broad-spectrum antibiotic carbapenem, underscoring the critical need for improved waste management and infection control measures. Remarkably, we found genes linked to the breakdown of plastic that encoded for enzymes of the esterase, depolymerase, and oxidoreductase classes. This suggests that specific bacteria found in medical waste may be able to reduce the amount of plastic pollution that comes from biological and medical waste. The information is helpful in formulating strategies to counter the combined problems of environmental pollution and antibiotic resistance. This study emphasises the importance of monitoring microbial communities in hospital waste in order to influence waste management procedures and public health policy. The findings highlight the need for a multidisciplinary approach to mitigate the risks associated with antimicrobial resistance and plastic waste, especially in hospital settings where they intersect most acutely.}, } @article {pmid39551356, year = {2025}, author = {Lalli, MK and Salo, TE and Hakola, L and Knip, M and Virtanen, SM and Vatanen, T}, title = {Associations between dietary fibers and gut microbiome composition in the EDIA longitudinal infant cohort.}, journal = {The American journal of clinical nutrition}, volume = {121}, number = {1}, pages = {83-99}, pmid = {39551356}, issn = {1938-3207}, mesh = {Humans ; *Dietary Fiber/administration & dosage ; *Gastrointestinal Microbiome ; Infant ; Longitudinal Studies ; Female ; Male ; Cross-Sectional Studies ; Infant Nutritional Physiological Phenomena ; Cohort Studies ; Milk, Human/chemistry ; Bacteria/classification/genetics ; Diet ; Feces/microbiology ; }, abstract = {BACKGROUND: The infant gut microbiome undergoes rapid changes in the first year of life, supporting normal development and long-term health. Although diet shapes this process, the role of fibers in complementary foods on gut microbiome maturation is poorly understood.

OBJECTIVES: We explored how the transition from human milk to fibers in complementary foods shapes the taxonomic and functional maturation of the gut microbiome within the first year of life.

METHODS: We assessed the longitudinal and cross-sectional development of infant gut microbiomes (N = 68 infants) and metabolomes (N = 33 infants) using linear mixed models to uncover their associations to dietary fibers and their food sources. Fiber intakes were assessed with 3-d food records (months 3, 6, 9, and 12) relying on CODEX-compliant fiber fraction values, and questionnaires tracked the overall complementary food introduction. Bacterial species were identified and quantified via MetaPhlAn2 from metagenomic data, and metabolomic profiles were obtained using 4 LC-MS methods.

RESULTS: We identified 176 complementary food fiber-bacterial species associations. First plant-based fibers associated with microbiota compositions similar to breastfeeding, and further associated with aromatic amino acid-derived metabolites, including 5-hydroxyindoleacetic acid (total dietary fiber - complementary foods (g) - β = 3.50, CI: 2.48, 4.52, P = 6.53 × 10[-5]). Distinct fibers from different food categories showed unique associations with specific bacterial taxa. Key species, such as Faecalibacterium prausnitznii, associated with oat fibers (g/MJ, β = 2.18, confidence interval: 1.36, 2.84, P = 6.12 × 10[-6]), reflective of maturing microbial communities. Fiber intake during weaning associated with shifts in metabolite profiles, including immunomodulatory metabolites, with fiber effects observed in a source- and timing-dependent manner, implicated in gradual microbiome diversification.

CONCLUSIONS: Introducing complementary dietary fibers during the weaning period supports gut microbiome diversification and stabilization. Even minor dietary variations shows significant associations with microbial taxa and functions from the onset of weaning, highlighting the importance of infant dietary recommendations that support the gut microbiome maturation during early life. This trial was registered at clinicaltrials.gov as registration number NCT01735123.}, } @article {pmid39551294, year = {2024}, author = {Zhang, G and Du, J and Zhang, C and Zhao, Z and Chen, Y and Liu, M and Chen, J and Fan, G and Ma, L and Li, S and Liu, K}, title = {Identification of a PET hydrolytic enzyme from the human gut microbiome unveils potential plastic biodegradation in human digestive tract.}, journal = {International journal of biological macromolecules}, volume = {283}, number = {Pt 3}, pages = {137732}, doi = {10.1016/j.ijbiomac.2024.137732}, pmid = {39551294}, issn = {1879-0003}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Polyethylene Terephthalates/metabolism/chemistry ; *Biodegradation, Environmental ; Hydrolysis ; Gastrointestinal Tract/microbiology/metabolism ; Metagenome ; Hydrolases/metabolism/genetics ; Plastics/chemistry ; Nanoparticles/chemistry ; }, abstract = {Widespread use of polyethylene terephthalate (PET) plastics and their recycling challenges have led to substantial accumulation of PET wastes in global environments, with inevitable consequences for their entry into the food chains. Recent studies have increasingly documented the ingestion of microplastics by humans through food and beverages. However, the fate of these microplastics within the gastrointestinal tract, particularly the role of the human gut microbiota, remains inadequately understood. To address this knowledge gap, we employed a bioinformatics workflow integrated with functional verification to investigate the PET digestion/degradation capabilities of intestinal microorganisms. This approach identified a novel PET hydrolase-HGMP01 from the human gut metagenome, which exhibits the capacity to hydrolyze PET nanoparticles. Moreover, comprehensive exploration for HGMP01 homologues in the human gut metagenome and metatranscriptome unveil their distribution in diverse intestinal microorganisms. This study provides biochemical evidence for an unforeseen role of human gut microbiome in plastic digestion, thus holding substantial implications for human health.}, } @article {pmid39551110, year = {2025}, author = {Adenaike, AS and Akpan, U and Oyedun, IO and Adewole, FA and Agbaje, M and Olusanya, OM and Arowosegbe, MO and Ikeobi, CON}, title = {Gut microbial composition differs among FUNAAB Alpha broiler chicken genotypes raised in a tropical environment.}, journal = {Microbial pathogenesis}, volume = {198}, number = {}, pages = {107126}, doi = {10.1016/j.micpath.2024.107126}, pmid = {39551110}, issn = {1096-1208}, mesh = {Animals ; *Chickens/microbiology ; *Gastrointestinal Microbiome/genetics ; *RNA, Ribosomal, 16S/genetics ; *Genotype ; *Tropical Climate ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; Feathers/microbiology ; Bacteroidetes/genetics/isolation & purification/classification ; Phylogeny ; Firmicutes/genetics/isolation & purification/classification ; Actinobacteria/genetics/classification/isolation & purification ; Biodiversity ; DNA, Bacterial/genetics ; Gastrointestinal Tract/microbiology ; }, abstract = {The gut microbiota of FUNAAB Alpha chickens plays a crucial role in determining their overall health and performance. Understanding the various types and diversity of microbiota in the gut of different genotypes of chickens is crucial for enhancing their well-being, productivity, and disease resistance. This study employed 16S rRNA and metagenomics analysis to examine the gut bacteria of three genotypes of FUNAAB Alpha broiler chickens, namely Naked neck, Frizzle, and Normal feather. There were three phyla observed in the three genotypes: Bacteroidetes, Actinobacteria, and Firmicutes. Through the utilisation of 16S rRNA sequencing, we successfully identified and categorised the various microbiota present within the gastrointestinal tract. Our study revealed notable variations in the composition and quantity of microbiota across the three genotypes, suggesting that each genotype possesses a distinct collection of gut bacteria. A wide range of microbiological diversity was observed within the community. Interestingly, the Normal feather chicken exhibited a greater number of operational taxonomic units (OTUs) compared to the Naked neck and Frizzle feather chicken. This study presents significant findings regarding the ceacal microbiota of FUNAAB Alpha chickens, emphasising the variations observed among different genotypes. It is crucial to study composition-modification techniques to enhance host health and performance, as well as to control zoonotic pathogens that can contaminate poultry products and threaten consumers' health.}, } @article {pmid39550955, year = {2024}, author = {Liu, S and Cao, J and Yu, J and Jian, M and Zou, L}, title = {Microplastics exacerbate the ecological risk of antibiotic resistance genes in wetland ecosystem.}, journal = {Journal of environmental management}, volume = {372}, number = {}, pages = {123359}, doi = {10.1016/j.jenvman.2024.123359}, pmid = {39550955}, issn = {1095-8630}, mesh = {*Wetlands ; *Drug Resistance, Microbial/genetics ; *Microplastics/toxicity ; China ; Ecosystem ; Lakes/microbiology ; }, abstract = {Wetlands are vital components of the global ecosystem, significantly influencing the retention and dissemination of microplastics (MPs) and antibiotic resistance genes (ARGs). However, the effects of different types of MPs on the environmental dynamics of ARGs within these ecosystems remain poorly understood. This study focused on the distribution and composition of ARGs associated with two primary types of MPs-polyethylene and polypropylene-within the Poyang Lake wetland, the largest freshwater lake in China, utilizing metagenomic analysis. The findings demonstrated that the bacterial communities and ARG profiles in the plastisphere were markedly distinct from those in the surrounding water. Specifically, thirteen opportunistic pathogens and forty subtypes of ARGs, primarily related to multidrug, bacitracin, and β-lactam resistance, were identified in the plastisphere. Notably, polyethylene exhibited four times more specific ARG subtypes than polypropylene. Procrustes analysis combined with network analysis indicated a lack of strong correlation between ARG abundance and bacterial populations, suggesting potential horizontal transfer of ARGs within the microbiota of the plastisphere. Additionally, three novel and functional β-lactamase genes were identified within this environment. This investigation highlights the role of MPs as reservoirs for ARGs, facilitating their exchange and posing risks to both ecological integrity and human health, thereby underscoring the need for increased attention in future research efforts.}, } @article {pmid39550949, year = {2024}, author = {Wu, ZL and Shi, WJ and Zhang, L and Xia, ZY and Gou, M and Sun, ZY and Tang, YQ}, title = {Investigating the robustness of microbial communities in municipal sludge anaerobic digestion under organic loading rate disturbance.}, journal = {Journal of environmental management}, volume = {372}, number = {}, pages = {123326}, doi = {10.1016/j.jenvman.2024.123326}, pmid = {39550949}, issn = {1095-8630}, mesh = {*Sewage/microbiology ; Anaerobiosis ; *Bioreactors/microbiology ; Waste Disposal, Fluid/methods ; Bacteria/metabolism/genetics/classification ; Microbiota ; }, abstract = {Anaerobic digestion (AD) frequently encounters disturbances due to variations in organic loading rates (OLRs), which can result in the failure of the sludge treatment process. However, there is a lack of comprehensive studies on the robustness of AD systems against OLR disturbances and the underlying mechanisms. In this study, the responses of reactor performance and active microbial communities in mesophilic AD were investigated and compared under conditions of OLR shock and OLR fluctuation. Statistical analysis confirmed that all reactors recovered from both types of OLR disturbance, indicating both functional and structural robustness of the mesophilic community. Based on metagenomics and metatranscriptomics analyses, it was observed that high diversity within the microbial community led to functional redundancy, which appears to be a key mechanism contributing to the robustness against OLR disturbances. Additionally, for the first time, the potential metabolic diversity of aerobic autotrophy bacteria in AD reactors was identified, including their roles in the utilization of glucose and acetate. Furthermore, the analysis of topological properties within the microbial interaction network was conducted, and the robustness of the community network was verified through the application of random node deletion attacks. The findings from this study provide valuable information for the effective regulation of microbial communities and the design of practical AD systems.}, } @article {pmid39550746, year = {2024}, author = {Karaca, C and Takcı, HAM}, title = {Role of gut microbiome in developing necrotizing enterocolitis.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, pmid = {39550746}, issn = {1874-9356}, support = {21-13192//Kilis 7 Aralık University of Research Project Committee/ ; }, abstract = {Necrotizing enterocolitis (NEC) is one of the most devastating intestinal diseases observed in preterm in the first days of life. Researchers have recently focused on potential predictive biomarkers for early and concomitant diagnoses. Thus, we inquired about the linkage of intestinal dysbiosis, one of the most important factors in NEC development to the gut microbiota. In this study, the systematic differences in the bacterial composition between neonates affected by NEC and healthy newborns were highlighted by metagenomic analysis. The next-generation sequencing of the V3-V4 variable region of the 16S rRNA gene and gene-specific qPCR analyzed the untargeted gut microbiota. Total bacteria, total and fecal coliform loads in stool samples with NEC were higher than control. OTU-level relative abundances of NEC infant was characterized by Firmicutes and Bacteroidetes at phylum levels. At the genus level, NEC stool was identified by the lack of Klebsiella and the presence of Roseburia, Blautia, and Parasutterella. Finally, Clostridium fessum was the predominant species of Clostridium genus in disease and healthy specimens at the species level, whereas Clostridium jeddahitimonense was at NEC diagnosis. Despite a strong relationship between pathophysiology and characterization of gut microbiota at a clinical diagnosis of NEC, our results emphasize the broad difficulty in identifying potential biomarkers.}, } @article {pmid39550535, year = {2024}, author = {Yadav, A and Subramanian, S}, title = {HiFiBGC: an ensemble approach for improved biosynthetic gene cluster detection in PacBio HiFi-read metagenomes.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1096}, pmid = {39550535}, issn = {1471-2164}, support = {Department of Biotechnology//Department of Biotechnology, Ministry of Science and Technology, India/ ; OLP0175//CSIR - Institute of Microbial Technology/ ; }, mesh = {*Multigene Family ; *Metagenome ; Metagenomics/methods ; Workflow ; High-Throughput Nucleotide Sequencing/methods ; Software ; Computational Biology/methods ; }, abstract = {BACKGROUND: Microbes produce diverse bioactive natural products with applications in fields such as medicine and agriculture. In their genomes, these natural products are encoded by physically clustered genes known as biosynthetic gene clusters (BGCs). Genome and metagenome sequencing advances have enabled high-throughput identification of BGCs as a promising avenue for natural product discovery. BGC mining from (meta)genomes using in silico tools has allowed access to a vast diversity of potentially novel natural products. However, a fundamental limitation has been the ability to assemble complete BGCs, especially from complex metagenomes. With their fragmented assemblies, short-read technologies struggle to recover complete BGCs, such as the long and repetitive nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS). Recent advances in long-read sequencing, such as the High Fidelity (HiFi) technology from PacBio, have reduced this limitation and can help retrieve both accurate and complete BGCs from metagenomes, warranting improvement in the existing BGC identification approach for better utilization of HiFi data.

RESULTS: Here, we present HiFiBGC, a command-line-based workflow to identify BGCs in PacBio HiFi metagenomes. HiFiBGC leverages an ensemble of assemblies from three HiFi-tailored metagenome assemblers and the reads not represented in these assemblies. Based on our analyses of four HiFi metagenomic datasets from four different environments, we show that HiFiBGC identifies, on average, 78% more BGCs than the top-performing single-assembler-based method. This increase is due to HiFiBGC's ensemble assembly approach, which improves recovery by 25%, as well as from the inclusion of mostly fragmented BGCs identified in the unmapped reads.

CONCLUSIONS: HiFiBGC is a computational workflow for identifying BGCs in long-read HiFi metagenomes, implemented majorly using Python programming language and workflow manager Snakemake. HiFiBGC is available on GitHub at https://github.com/ay-amityadav/HiFiBGC under the MIT license. The code related to the figures and analyses presented in the manuscript is available at https://github.com/ay-amityadav/HiFiBGC_analyses .}, } @article {pmid39550371, year = {2024}, author = {Yang, JX and Peng, Y and Yu, QY and Yang, JJ and Zhang, YH and Zhang, HY and Adams, CA and Willing, CE and Wang, C and Li, QS and Han, XG and Gao, C}, title = {Gene horizontal transfers and functional diversity negatively correlated with bacterial taxonomic diversity along a nitrogen gradient.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {128}, pmid = {39550371}, issn = {2055-5008}, mesh = {*Soil Microbiology ; Soil/chemistry ; *Nitrogen/metabolism/pharmacology ; *Biodiversity ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/metabolism ; Metagenome ; *Gene Transfer, Horizontal/drug effects ; }, abstract = {Horizontal gene transfer (HGT) mediated diversification is a critical force driving evolutionary and ecological processes. However, how HGT might relate to anthropogenic activity such as nitrogen addition, and its subsequent effect on functional diversity and cooccurrence networks remain unknown. Here we approach this knowledge gap by blending bacterial 16S rRNA gene amplicon and shotgun metagenomes from a platform of cessation of nitrogen additions and continuous nitrogen additions. We found that bacterial HGT events, functional genes, and virus diversities increased whereas bacterial taxonomic diversity decreased by nitrogen additions, resulting in a counterintuitive strong negative association between bacterial taxonomic and functional diversities. Nitrogen additions, especially the ceased one, complexified the cooccurrence network by increasing the contribution of vitamin B12 auxotrophic Acidobacteria, indicating cross-feeding. These findings advance our perceptions of the causes and consequences of the diversification process in community ecology.}, } @article {pmid39550223, year = {2024}, author = {Bosilj, M and Suljič, A and Zakotnik, S and Slunečko, J and Kogoj, R and Korva, M}, title = {MetaAll: integrative bioinformatics workflow for analysing clinical metagenomic data.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {6}, pages = {}, pmid = {39550223}, issn = {1477-4054}, support = {J3-50101//Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana and Slovenian Research and Innovation Agency/ ; }, mesh = {Humans ; *Metagenomics/methods ; *Computational Biology/methods ; *Workflow ; COVID-19/virology/diagnosis ; SARS-CoV-2/genetics ; Metagenome ; Software ; }, abstract = {Over the past decade, there have been many improvements in the field of metagenomics, including sequencing technologies, advances in bioinformatics and the development of reference databases, but a one-size-fits-all sequencing and bioinformatics pipeline does not yet seem achievable. In this study, we address the bioinformatics part of the analysis by combining three methods into a three-step workflow that increases the sensitivity and specificity of clinical metagenomics and improves pathogen detection. The individual tools are combined into a user-friendly workflow suitable for analysing short paired-end (PE) and long reads from metagenomics datasets-MetaAll. To demonstrate the applicability of the developed workflow, four complicated clinical cases with different disease presentations and multiple samples collected from different biological sites as well as the CAMI Clinical pathogen detection challenge dataset were used. MetaAll was able to identify putative pathogens in all but one case. In this case, however, traditional microbiological diagnostics were also unsuccessful. In addition, co-infection with Haemophilus influenzae and Human rhinovirus C54 was detected in case 1 and co-infection with SARS-Cov-2 and Influenza A virus (FluA) subtype H3N2 was detected in case 3. In case 2, in which conventional diagnostics could not find a pathogen, mNGS pointed to Klebsiella pneumoniae as the suspected pathogen. Finally, this study demonstrated the importance of combining read classification, contig validation and targeted reference mapping for more reliable detection of infectious agents in clinical metagenome samples.}, } @article {pmid39549663, year = {2024}, author = {Méndez, A and Maisto, F and Pavlović, J and Rusková, M and Pangallo, D and Sanmartín, P}, title = {Microbiome shifts elicited by ornamental lighting of granite facades identified by MinION sequencing.}, journal = {Journal of photochemistry and photobiology. B, Biology}, volume = {261}, number = {}, pages = {113065}, doi = {10.1016/j.jphotobiol.2024.113065}, pmid = {39549663}, issn = {1873-2682}, mesh = {*Microbiota ; *Silicon Dioxide/chemistry ; *Bacteria/genetics/radiation effects/isolation & purification/classification ; *Fungi/genetics ; Lighting ; Nanopore Sequencing ; Pilot Projects ; Archaea/genetics/radiation effects ; }, abstract = {Night-time outdoor illumination in combination with natural sunlight can influence the visible phototrophic colonizers (mainly algae) growing on stone facades; however, the effects on the microbiome (invisible to the naked eye) are not clear. The presence of stone-dwelling microbes, such as bacteria, diatoms, fungi, viruses and archaea, drives further biological colonization, which may exacerbate the biodeterioration of substrates. Considering the microbiome is therefore important for conservation of the built heritage. The impact of the following types of lighting on the relative abundance and diversity of the microbiome on granite ashlars was evaluated in a year-long outdoor pilot study: no lighting; lighting with a metal halide lamp (a traditional lighting system currently used to illuminate monuments); and lighting with a novel LED lamp (an environmentally sound prototype lamp with a biostatic effect, halting biological colonization by phototrophs, currently under trial). Culturable fractions of microbiome and whole-genome sequencing by metabarcoding with Oxford Nanopore Sequencing (MinION) was conducted for bacteria and fungi in order to complement both community characterization strategies. In addition, the possible biodeteriorative profiles of the isolated strains, relative to calcium carbonate precipitation/solubilisation and iron oxidation/reduction, were investigated by plate assays. Alpha and beta diversity indexes were also determined, along with the abundance of biocide and antibiotic resistance genes. Culture-dependent microbiological analysis failed to properly show changes in community composition, for which metagenomic approaches like MinION are better suited. Thus, MinION analysis identified shifts in the granite microbiome elicited by ornamental lighting. The novel LED lamp with the biostatic effect on phototrophs caused an increase in the diversity of bacteria and fungi. In this case, the microbiome was more similar to that in the unlit samples. In the samples illuminated by the metal halide lamp, dominance of bacteria was favoured and the presence of fungi was negligible.}, } @article {pmid39549623, year = {2025}, author = {White, CA and Antell, EH and Schwartz, SL and Lawrence, JE and Keren, R and Zhou, L and Yu, K and Zhuang, WQ and Alvarez-Cohen, L}, title = {Life history strategies determine response to SRT driven crash in anammox bioreactors.}, journal = {Water research}, volume = {268}, number = {Pt B}, pages = {122727}, doi = {10.1016/j.watres.2024.122727}, pmid = {39549623}, issn = {1879-2448}, mesh = {*Bioreactors/microbiology ; Anaerobiosis ; *RNA, Ribosomal, 16S/genetics ; Oxidation-Reduction ; Ammonium Compounds/metabolism ; Waste Disposal, Fluid/methods ; Bacteria/metabolism/genetics ; }, abstract = {Anaerobic ammonium oxidation (anammox) is a biological process often applied in wastewater treatment plants for nitrogen removal from highly concentrated side-stream effluents from anaerobic digesters. However, they are vulnerable to process instability prompted by operational shocks and microbial community imbalances, resulting in lengthy recovery times. These issues are further compounded by a lack of understanding of how sustained press disturbances influence the microbial ecology of the system. Here we investigate the response and recovery of an anammox membrane bioreactor to a solids retention time (SRT)-induced reactor crash using 16S rRNA gene and shotgun metagenomic sequencing. We observed a strong selection of bacterial groups based on reproduction strategies, with the Orders Rhodospirillales and Sphingobacteriales increasing from 1.0 % and 11.9 % prior to the crash to 31.9 % and 18.1 % during the crash respectively. The Orders Brocadiales and Anaerolineales decreased from 17.3 % and 28.3 % to 7.3 % and 1.4 % over the same time period, respectively. Metagenomic and metatranscriptomic analyses revealed differential crash responses in metabolically distinct groups of bacteria, with increased expression of genes for extracellular carbohydrate active enzymes, peptidases and membrane transporters. Following the crash, the reactor recovered to its prior state of nitrogen removal performance and pathway analysis demonstrated increased expression of genes related to exopolysaccharide biosynthesis and quorum sensing during the reactor recovery period. This study highlights the effects of reactor perturbations on microbial community dynamics in anammox bioreactors and provides insight into potential recovery mechanisms from severe disturbance.}, } @article {pmid39549575, year = {2025}, author = {Ma, R and Peng, L and Tang, R and Jiang, T and Chang, J and Li, G and Wang, J and Yang, Y and Yuan, J}, title = {Bioaerosol emission characteristics and potential risks during composting: Focus on pathogens and antimicrobial resistance.}, journal = {Journal of hazardous materials}, volume = {481}, number = {}, pages = {136466}, doi = {10.1016/j.jhazmat.2024.136466}, pmid = {39549575}, issn = {1873-3336}, mesh = {*Composting ; *Aerosols ; *Air Microbiology ; Bacteria/drug effects/genetics ; Fungi/drug effects/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Particulate Matter/toxicity ; Humans ; Drug Resistance, Bacterial/genetics ; Air Pollutants/toxicity/analysis ; }, abstract = {In this study, we analyzed bioaerosol emission characteristics and potential risks of antimicrobial resistance (AMR) during composting using the impaction culture method and metagenomic sequencing. The results showed that the highly saturated water vapor in the emission gas mitigated particulate matter emission during the thermophilic period. About the bioaerosols, the airborne aerobic bacterial emissions were suppressed as composting enters the mature period, and the airborne fungi are usually present as single-cell or small-cell aggregates (< 3.3 µm). In addition, the microbial community structure in bioaerosols was stable and independent of composting time. Most importantly, the PM2.5 in bioaerosols contained large amounts of antibiotic resistance genes (ARGs), potential pathogens, and multidrug resistant pathogens, which were diverse and present in high concentrations. Among them, ARGs concentrations encoding 21 antibiotics ranged from - 4.50 to 0.70 ppm/m[3] (Log10 ARGs). Among the 89 potential human pathogens detected, Escherichia coli, Salmonella enterica, Klebsiella pneumoniae, and Staphylococcus aureus were the only culturable potentially multidrug resistant pathogens carrying multiple ARGs encoding resistance at high concentrations (- 0.57 to 1.15 ppm/m[3] (Log10 ARGs)), and were more likely to persist and multiply in oligotrophic environments. Our findings indicate that composting technology can transfer AMR from solid compost to gas phase and increase the risk of AMR transmission.}, } @article {pmid39549023, year = {2024}, author = {Xiang, J and Chai, N and Li, L and Hao, X and Linghu, E}, title = {Alterations of Gut Microbiome in Patients with Colorectal Advanced Adenoma by Metagenomic Analyses.}, journal = {The Turkish journal of gastroenterology : the official journal of Turkish Society of Gastroenterology}, volume = {35}, number = {11}, pages = {859-868}, pmid = {39549023}, issn = {2148-5607}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Colorectal Neoplasms/microbiology/pathology ; Female ; Male ; *Adenoma/microbiology/pathology ; Middle Aged ; *Dysbiosis/microbiology ; *Feces/microbiology ; *Metagenomics/methods ; Case-Control Studies ; Aged ; Tryptophan/metabolism ; }, abstract = {BACKGROUND/AIMS: Colorectal cancer (CRC) is one of the deadliest cancers worldwide, mostly arising from adenomatous polyps. Mounting evidence has demonstrated that changes in the gut microbiome play key roles in CRC progression, while quite few studies focused on the altered microbiota architecture of advanced adenoma (AA), a crucial precancerous stage of CRC. Thus, we aimed to investigate the microbial profiles of AA patients.

MATERIALS AND METHODS: Fecal samples were collected from 26 AA patients and 26 age- and sex-matched normal controls (NC), and analyzed by shotgun metagenomic sequencing.

RESULTS: Gut microbial dysbiosis was observed in AA patients with lower alpha diversity. Advanced adenoma was characterized by an increased Bacillota/Bacteroidota ratio and higher Pseudomonadota levels compared to normal individuals. Linear discriminant analysis effect size (LEfSe) analysis was performed and identified 14 microbiota with significantly different abundance levels between AA and NC groups. Functional analysis revealed that tryptophan metabolism was upregulated in AA. Correspondingly, the expressions of gut microbes implicated in tryptophan metabolism also changed, including Akkermansia muciniphila, Bacteroides ovatus, Clostridium sporogenes, and Limosilactobacillus reuteri. The microbial network suggested that AA exhibited decreased correlation complexity, with Escherichia coli and Enterobacteriaceae unclassified harboring the strongest connectivity. A diagnostic model consisting of 3 microbial species was established based on random forest, yielding an area under the curve (AUC) of 0.799.

CONCLUSION: Our study profiled the alterations of the gut microbiome in AA patients, which may enrich the knowledge of microbial signatures along with colorectal tumorigenesis and provide promising biomarkers for AA diagnosis.}, } @article {pmid39548565, year = {2024}, author = {Grønbæk, IMB and Mollerup, S and Halkjær, SI and Paulsen, SJ and Pinholt, M and Westh, H and Petersen, AM}, title = {Faecal sample storage without ethanol for up to 24 h followed by freezing performs better than storage with ethanol for shotgun metagenomic microbiome analysis in patients with inflammatory and non-inflammatory intestinal diseases and healthy controls.}, journal = {BMC research notes}, volume = {17}, number = {1}, pages = {340}, pmid = {39548565}, issn = {1756-0500}, mesh = {Humans ; *Feces/microbiology ; *Ethanol ; *Gastrointestinal Microbiome/genetics ; *Specimen Handling/methods ; *Freezing ; Male ; Adult ; *Inflammatory Bowel Diseases/microbiology ; Female ; Metagenomics/methods ; Middle Aged ; Metagenome ; Case-Control Studies ; }, abstract = {OBJECTIVE: The influence of different faecal collection methods on metagenomic analyses remains under discussion, and there is no general agreement on which collection method is preferable for gut microbiome research. We compared faecal samples collected in tubes without preservatives with those containing 10 mL of 96% ethanol for gut microbiome research when the timeframe from defecation to freezing at - 80 °C was up to 24 h. We aimed to compare the collection methods on faeces from participants with inflammatory and non-inflammatory gastrointestinal disorders and healthy controls to investigate the most suitable method when considering data yield, human fraction of sequencing reads, and ease of use. We also examined the faecal sample homogeneity.

RESULTS: Faeces collected in tubes without preservatives resulted in more sequencing reads compared to faeces collected in tubes with 96% ethanol and were also easier to handle. The human fraction of total reads in faeces collected in ethanol from participants with inflammatory bowel disease was higher than all other samples. DNA extraction and sequencing from two different locations in the same faecal sample gave similar results and showed sample homogeneity.}, } @article {pmid39548381, year = {2024}, author = {Ke, Y and Jiang, Y and Yuan, Y and Chen, Y and Huang, J and Huang, C}, title = {Eosinophilic gastrointestinal diseases with overall gastrointestinal tract causing liver abscess in an older patient: a case report and literature review.}, journal = {BMC geriatrics}, volume = {24}, number = {1}, pages = {945}, pmid = {39548381}, issn = {1471-2318}, mesh = {Humans ; Aged ; Male ; *Eosinophilia/complications/diagnosis ; *Liver Abscess/complications/diagnosis ; *Klebsiella pneumoniae/isolation & purification ; *Enteritis/complications/diagnosis/microbiology ; *Klebsiella Infections/complications/diagnosis ; Gastritis/diagnosis/complications/microbiology ; Gastrointestinal Diseases/diagnosis/complications ; }, abstract = {BACKGROUND: Eosinophilic gastrointestinal diseases are the rare gastrointestinal disorders. To our knowledge, there have been no reports of eosinophilic gastrointestinal diseases with overall gastrointestinal tract involvement causing liver abscess in an older patient.

CASE PRESENTATION: We report a 68-year-old man with eosinophilic gastrointestinal disease with overall gastrointestinal tract involvement. He was admitted with suspected acute gastroenteritis, and histological examination showed eosinophilic infiltration accompanied by liver abscess. The collected pus was tested for Metagenomics Next-Generation Sequencing and confirmed the presence of Klebsiella pneumoniae.

CONCLUSIONS: We conducted a literature review on the complications of eosinophilic gastrointestinal diseases and discussed how eosinophilic gastrointestinal diseases lead to liver abscess caused by Klebsiella pneumoniae.}, } @article {pmid39547567, year = {2025}, author = {Chen, G and Wang, R and Ying, L and Eheneden, I and Ren, H and Sun, M}, title = {Sulfamethoxazole removal in nitrifying membrane aerated biofilms: Physiological responses and antibiotic resistance genes.}, journal = {Environmental research}, volume = {264}, number = {Pt 2}, pages = {120365}, doi = {10.1016/j.envres.2024.120365}, pmid = {39547567}, issn = {1096-0953}, mesh = {*Biofilms/drug effects ; *Sulfamethoxazole ; *Bioreactors/microbiology ; *Nitrification/drug effects ; Drug Resistance, Microbial/genetics ; Water Pollutants, Chemical ; Waste Disposal, Fluid/methods ; Anti-Bacterial Agents/pharmacology ; Membranes, Artificial ; Wastewater/microbiology ; }, abstract = {Efficient removal of ammonia nitrogen and sulfamethoxazole (SMX) from wastewater has become increasingly critical due to their detrimental effects on aquatic ecosystems and public health. This study aimed to investigate the nitrogen transformation and SMX removal in a membrane aerated biofilm reactor (MABR) under different SMX concentrations (0-200 μg L[-1]) with a nitrifying membrane bioreactor (MBR) as a control. Results suggested that SMX removal in MABR was better than that of MBR with SMX addition (50-200 μg L[-1]). Membrane aerated biofilms tended to secrete more extracellular polymeric substances (EPS) and generate less antioxidant enzymes in response to SMX stress when compared with nitrifying sludge in MBR. Metagenomic analysis indicated that distinct succession of microbial community was observed in both systems after SMX addition, and the relative abundance of nitrifying bacteria (Nitrosomonas, Nitrospira, and Nitrobacter) evidently decreased under SMX concentration of 200 μg L[-1]. The proliferation of predominant antibiotic resistance gene (ARG) sul2 was suppressed more obviously in MABR than that in MBR. Thus, this study provided extensive insights into the advantages of nitrifying MABR in simultaneous removal of ammonium and antibiotics with less risk of associated ARGs spread.}, } @article {pmid39547561, year = {2025}, author = {Xia, C and Cheng, W and Ren, M and Zhu, Y}, title = {Chromium(VI) and nitrate removal from groundwater using biochar-assisted zero valent iron autotrophic bioreduction: Enhancing electron transfer efficiency and reducing EPS accumulation.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {364}, number = {Pt 1}, pages = {125313}, doi = {10.1016/j.envpol.2024.125313}, pmid = {39547561}, issn = {1873-6424}, mesh = {*Groundwater/chemistry ; *Charcoal/chemistry ; *Chromium/metabolism ; *Extracellular Polymeric Substance Matrix/metabolism ; *Nitrates/metabolism ; *Water Pollutants, Chemical/metabolism ; *Iron/metabolism ; *Autotrophic Processes ; Denitrification ; Electron Transport ; Biodegradation, Environmental ; }, abstract = {Current strategies primarily utilize heterotrophic or mixotrophic bioreduction for the simultaneous removal of Cr(VI) and NO3[-] from groundwater. However, given the oligotrophic nature of groundwater, autotrophic bioreduction could be more appropriate, though it remains notably underdeveloped. Here, an autotrophic bioreduction technology utilizing biochar (BC)-assisted zero valent iron (ZVI) is proposed. The pyrolysis temperature of BC was optimized to enhance electron transfer efficiency and reduce extracellular polymeric substances (EPS) accumulation. BC500, with the superior electron transfer capabilities, was the most effective. After an 11-week period, the ZVI + BC500 biotic column still achieved 100% removal efficiency for Cr(VI) and 93.37 ± 0.33% for NO3[-], with initial concentrations of 26 mg/L and 50 mg/L, respectively. Its performance significantly surpasses that of ZVI alone, effectively reducing the interference of Cr(VI) on denitrification. The presence of quinone and phenolic compounds in BC500, serving as electron-accepting and electron-donating groups, improves the efficiency of electron transfer between ZVI and microbes. Metagenomic analysis showed an increase in the growth of autotrophic bacteria such as Hydrogenophaga spp. and Rhodanobacter denitrificans, and heterotrophic bacteria including Arenimonas daejeonensis and Chryseobacterium shandongense. The promotion facilitates the expression of genes associated with Cr(VI) reduction (chrR, nemA) and denitrification (narG, nirS). BC500 also enhanced EPS production, which facilitates the adsorption and reduction of Cr(VI), mitigating its inhibitory effects on denitrification. Notably, in the ZVI + BC500 biotic column, the accumulated EPS primarily consists of loosely bound EPS rather than tightly bound EPS, potentially reducing the risk of pore clogging during in-situ groundwater treatment.}, } @article {pmid39547283, year = {2025}, author = {Zelasko, S and Swaney, MH and Sandstrom, S and Lee, KE and Dixon, J and Riley, C and Watson, L and Godfrey, JJ and Ledrowski, N and Rey, F and Safdar, N and Seroogy, CM and Gern, JE and Kalan, L and Currie, C}, title = {Early-life upper airway microbiota are associated with decreased lower respiratory tract infections.}, journal = {The Journal of allergy and clinical immunology}, volume = {155}, number = {2}, pages = {436-450}, doi = {10.1016/j.jaci.2024.11.008}, pmid = {39547283}, issn = {1097-6825}, support = {U19 AI104317/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Microbiota ; *Respiratory Tract Infections/microbiology ; Male ; Infant ; Female ; Child, Preschool ; Mouth/microbiology ; Nose/microbiology ; }, abstract = {BACKGROUND: Microbial interactions mediating colonization resistance play key roles within the human microbiome, shaping susceptibility to infection from birth. The role of the nasal and oral microbiome in the context of early life respiratory infections and subsequent allergic disease risk remains understudied.

OBJECTIVES: Our aim was to gain insight into microbiome-mediated defenses and respiratory pathogen colonization dynamics within the upper respiratory tract during infancy.

METHODS: We performed shotgun metagenomic sequencing of nasal (n = 229) and oral (n = 210) microbiomes from our Wisconsin Infant Study Cohort at age 24 months and examined the influence of participant demographics and exposure history on microbiome composition. Detection of viral and bacterial respiratory pathogens by RT-PCR and culture-based studies with antibiotic susceptibility testing, respectively, to assess pathogen carriage was performed. Functional bioassays were used to evaluate pathogen inhibition by respiratory tract commensals.

RESULTS: Participants with early-life lower respiratory tract infection were more likely to be formula fed, attend day care, and experience wheezing. Composition of the nasal, but not oral, microbiome associated with prior lower respiratory tract infection, namely lower alpha diversity, depletion of Prevotella, and enrichment of Moraxella catarrhalis including drug-resistant strains. Prevotella originating from healthy microbiomes had higher biosynthetic gene cluster abundance and exhibited contact-independent inhibition of M catarrhalis.

CONCLUSIONS: These results suggest interbacterial competition affects nasal pathogen colonization. This work advances understanding of protective host-microbe interactions occurring in airway microbiomes that alter infection susceptibility in early life.}, } @article {pmid39547006, year = {2024}, author = {Nakanishi, H and Takada, A and Yoneyama, K and Kodama, S and Sakai, K and Saito, K}, title = {The utility of drowning site inference through metagenomic diatom analysis.}, journal = {Legal medicine (Tokyo, Japan)}, volume = {71}, number = {}, pages = {102548}, doi = {10.1016/j.legalmed.2024.102548}, pmid = {39547006}, issn = {1873-4162}, mesh = {*Diatoms/isolation & purification/classification/genetics ; *Drowning/diagnosis ; *Metagenomics/methods ; *Seawater ; Humans ; Fresh Water ; Principal Component Analysis ; Forensic Medicine/methods ; }, abstract = {The diatom test is one of the methods used to diagnose drowning in forensic autopsies. Metagenomic diatom analysis may reveal where a drowning occurred. We evaluated whether metagenomic diatom analysis could be used to infer waters, watersheds, and geographic locations using 166 water samples from 64 locations (freshwater: 55; seawater: 9). Principal component analysis (PCA) in all samples revealed no specific clusters for waters or watersheds. In one river, the three samples at the same site generally tended to be in close clusters, but there were some cases where the three sites were far from each other. The precise geographic location could thus not be reliably identified. However, PCA of data from dams, lakes, and retention basins revealed sites with independent clusters, suggesting unique diatom compositions. Diatoms of seawater were not detected in freshwater. The high number of Actinoptychus, Chaetoceros, and Skeletonema detected in seawater samples suggested that they are useful for seawater identification. This method required only 2 mL of water; it suggests that this method can be applied to actual samples. In summary, it was difficult to infer the geographic location and waters or watersheds, but the freshwater/seawater distinction could be easily made, and depending on the application, it may be useful in forensic science practice.}, } @article {pmid39546167, year = {2024}, author = {Rajeev, M and Cho, JC}, title = {Rhodobacteraceae are Prevalent and Ecologically Crucial Bacterial Members in Marine Biofloc Aquaculture.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {62}, number = {11}, pages = {985-997}, pmid = {39546167}, issn = {1976-3794}, mesh = {*Aquaculture ; *RNA, Ribosomal, 16S/genetics ; *Rhodobacteraceae/genetics/classification/isolation & purification/metabolism ; Animals ; Republic of Korea ; China ; Metagenomics ; Vietnam ; Phylogeny ; Microbiota ; Metagenome ; Seawater/microbiology ; }, abstract = {Bioflocs are microbial aggregates primarily composed of heterotrophic bacteria that play essential ecological roles in maintaining animal health, gut microbiota, and water quality in biofloc aquaculture systems. Despite the global adoption of biofloc aquaculture for shrimp and fish cultivation, our understanding of biofloc microbiota-particularly the dominant bacterial members and their ecological functions-remains limited. In this study, we employed integrated metataxonomic and metagenomic approaches to demonstrate that the family Rhodobacteraceae of Alphaproteobacteria consistently dominates the biofloc microbiota and plays essential ecological roles. We first analyzed a comprehensive metataxonomic dataset consisting of 200 16S rRNA gene amplicons collected across three Asian countries: South Korea, China, and Vietnam. Taxonomic investigation identified Rhodobacteraceae as the dominant and consistent bacterial members across the datasets. The predominance of this taxon was further validated through metagenomics approaches, including read taxonomy and read recruitment analyses. To explore the ecological roles of Rhodobacteraceae, we applied genome-centric metagenomics, reconstructing 45 metagenome-assembled genomes. Functional annotation of these genomes revealed that dominant Rhodobacteraceae genera, such as Marivita, Ruegeria, Dinoroseobacter, and Aliiroseovarius, are involved in vital ecological processes, including complex carbohydrate degradation, aerobic denitrification, assimilatory nitrate reduction, ammonium assimilation, and sulfur oxidation. Overall, our study reveals that the common practice of carbohydrate addition in biofloc aquaculture systems fosters the growth of specific heterotrophic bacterial communities, particularly Rhodobacteraceae. These bacteria contribute to maintaining water quality by removing toxic nitrogen and sulfur compounds and enhance animal health by colonizing gut microbiota and exerting probiotic effects.}, } @article {pmid39546027, year = {2024}, author = {Khamespanah, E and Asad, S and Vanak, Z and Mehrshad, M}, title = {Niche-Aware Metagenomic Screening for Enzyme Methioninase Illuminates Its Contribution to Metabolic Syntrophy.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {141}, pmid = {39546027}, issn = {1432-184X}, mesh = {*Carbon-Sulfur Lyases/genetics/metabolism ; *Metagenomics ; *Phylogeny ; *Bacteria/genetics/classification/enzymology/isolation & purification/metabolism ; Archaea/genetics/enzymology/classification ; Groundwater/microbiology ; Metagenome ; Seawater/microbiology ; }, abstract = {The single-step methioninase-mediated degradation of methionine (as a sulfur containing amino acid) is a reaction at the interface of carbon, nitrogen, sulfur, and methane metabolism in microbes. This enzyme also has therapeutic application due to its role in starving auxotrophic cancer cells. Applying our refined in silico screening pipeline on 33,469 publicly available genome assemblies and 1878 metagenome assembled genomes/single-cell amplified genomes from brackish waters of the Caspian Sea and the Fennoscandian Shield deep groundwater resulted in recovering 1845 methioninases. The majority of recovered methioninases belong to representatives of phyla Proteobacteria (50%), Firmicutes (29%), and Firmicutes_A (13%). Prevalence of methioninase among anaerobic microbes and in the anoxic deep groundwater together with the relevance of its products for energy conservation in anaerobic metabolism highlights such environments as desirable targets for screening novel methioninases and resolving its contribution to microbial metabolism and interactions. Among archaea, majority of detected methioninases are from representatives of Methanosarcina that are able to use methanethiol, the sulfur containing product from methionine degradation, as a precursor for methanogenesis. Branching just outside these archaeal methioninases in the phylogenetic tree, we recovered three methioninases belonging to representatives of Patescibacteria reconstructed from deep groundwater metagenomes. We hypothesize that methioninase in Patescibacteria could contribute to their syntrophic interactions where their methanogenic partners/hosts benefit from the produced 2-oxobutyrate and methanethiol. Our results underscore the significance of accounting for specific ecological niche in screening for enzyme variates with desired characteristics. Finally, complementing of our findings with experimental validation of methioninase activity confirms the potential of our in silico screening in clarifying the peculiar ecological role of methioninase in anoxic environments.}, } @article {pmid39545936, year = {2024}, author = {Mechikoff, MA and Collins, JP and Golder, P and Ingersoll, CM and McGarry, RE and Lu, XJ and Gokden, A and Cuff, A and Webber, BJ and Wallace, AB and Steel, JJ and Wickiser, JK and Balboni, AL}, title = {Application of Pan-Viral Metagenomic Sequencing on United States Air Force Academy Wastewater to Uncover Potential Causes of Acute Gastroenteritis.}, journal = {Military medicine}, volume = {}, number = {}, pages = {}, doi = {10.1093/milmed/usae518}, pmid = {39545936}, issn = {1930-613X}, support = {//Air Force Office of Scientific Research/ ; //Defense Health Agency/ ; //Skoll Foundation/ ; //Air Force Office of Scientific Research/ ; //Defense Health Agency/ ; //Skoll Foundation/ ; }, abstract = {INTRODUCTION: Wastewater surveillance is an important technique to monitor public health and is being studied extensively for pandemic prevention, force health protection and readiness, and as a potential early warning system for chem-bio defense. Wastewater surveillance has traditionally relied on techniques such as quantitative PCR or targeted sequencing, both of which are microbe- or disease-specific tools. Newer pan-viral metagenomics strategies may provide higher specificity for pathogens of interest, resulting in a lower false negative rate and reduced sequencing of undesired background nucleic acids. One such system, VirCapSeq-VERT, has been developed to target all vertebrate virus pathogens; until recently, its application has been limited to clinical samples. The objective of this study was to use VirCapSeq-VERT to interrogate wastewater samples from the U.S. Air Force Academy (USAFA), Colorado Springs, Colorado, to determine its utility in assessing complex samples and its potential application in public health surveillance.

MATERIALS AND METHODS: Biweekly samples were analyzed from February 2022 through May 2023. Samples were collected from the wastewater treatment facility at USAFA before treatment and stored at -20 °C until total nucleic acid (tNA: DNA and RNA) extraction. tNA was then subject to the probe-based capture system, VirCapSeq, and run through a collection of public bioinformatics pipelines to identify captured viral pathogens and perform phylogenetic analysis. It was determined by the USAFA IRB that the study was non-human subject research and was deemed exempt.

RESULTS: In total, 68 families of viruses were identified, comprising thousands of individual strains. This study focused on viruses responsible for gastrointestinal dysfunction as a test of the use of the VirCapSeq-VERT to identify human pathogenic viruses within a complex and highly enriched biological sample. Four enteric viruses dominated the wastewater samples, with Adenoviridae most prevalent before the cadet winter recess (December 17, 2022-January 4, 2023) and Astroviridae most abundant thereafter.

CONCLUSION: Although gastroenteritis outbreaks at USAFA are commonly attributed to norovirus because of clinical presentation and the acute nature of the illness-often diagnosed and treated without confirmatory stool testing-this virus was not found in high prevalence in these wastewater samples. Among adenoviruses, F serotype 41 predominated, suggesting a role in gastrointestinal infections among the cadet population. Phylogenetic investigation of adenovirus and norovirus exposed common variants with seasonal distributions. These findings may prompt correlational studies to assess the clinical predictive capability of VirCapSeq-VERT and to determine the utility of wastewater monitoring as an outbreak early warning system.}, } @article {pmid39545782, year = {2024}, author = {Zepernick, BN and Hart, LN and Natwora, KE and Brown, KM and Obuya, JA and Olokotum, M and Okech, EO and Keating, NG and Lomeo, D and Tebbs, EJ and , and Sheik, CS and Sherman, DH and Dick, GJ and Wilhelm, SW and Drouillard, KG and Lawrence, T and Getabu, A and Owuor, B and Shitandi, A and Omondi, R and Njiru, J and Sitoki, L and Otiso, KM and McKay, RML and Bullerjahn, GS}, title = {Metagenomic sequencing of cyanobacterial-dominated Lake Victoria-an African Great Lake.}, journal = {Microbiology resource announcements}, volume = {13}, number = {12}, pages = {e0079824}, pmid = {39545782}, issn = {2576-098X}, support = {F31 ES036421/ES/NIEHS NIH HHS/United States ; }, abstract = {We report 40 metagenomic libraries collected from the Winam Gulf of Lake Victoria during May-July of 2022-2023 and an additional eight opportunistic libraries from adjacent Lakes Simbi, Naivasha, and regional river systems. The sampling period captured cyanobacterial bloom events - shedding insight onto community composition and genomic potential.}, } @article {pmid39545734, year = {2025}, author = {Xu, T and Ni, Y and Li, H and Wu, S and Yan, S and Chen, L and Yu, Y and Wang, Y}, title = {Discovery and characterization of complete genomes of 38 head-tailed proviruses in four predominant phyla of archaea.}, journal = {Microbiology spectrum}, volume = {13}, number = {1}, pages = {e0049224}, pmid = {39545734}, issn = {2165-0497}, support = {32370151//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {*Archaea/genetics/virology/classification ; *Archaeal Viruses/genetics/classification ; *Phylogeny ; *Genome, Archaeal ; *Proviruses/genetics ; Genome, Viral/genetics ; CRISPR-Cas Systems ; }, abstract = {Archaea play a significant role in natural ecosystems and the human body. Archaeal viruses exert a considerable influence on the structure and composition of archaeal communities and their associated ecological environments. The present study revealed the complete genomes of 38 archaeal head-tailed proviruses through comprehensive data mining. The hosts of these proviruses were identified as belonging to the following four dominant phyla: Halobacteriota, Thermoplasmatota, Thermoproteota, and Nanoarchaeota. In addition to the 14 proviruses of halophilic archaea related to the Graaviviridae family, the remaining proviruses exhibited limited genetic similarities to known (pro)viruses, suggesting the existence of 14 potential novel families. Of the 38 archaeal proviruses, 30 have the potential to lyse host cells. Eleven proviruses contain genes linked to antiviral defense mechanisms, including those involved in restriction modification (RM), clustered regularly interspaced short palindromic repeat (CRISPR)-associated (CRISPR-Cas) nucleases, defense island system associated with restriction-modification (DISARM), and DNA degradation (Dnd). Moreover, auxiliary metabolic genes were identified in the proviruses of Bathyarchaeia and Halobacteriota archaea, including those involved in carbohydrate and amino acid metabolism. Our findings indicate the diversity of archaeal viruses, their interactions with archaeal hosts, and their roles in the adaptation of the host.IMPORTANCEThe field of archaeal virology has seen a rapid expansion through the use of metagenomics, yet the diversity of these viruses remains largely uncharted. In this study, the complete genomes of 38 novel archaeal proviruses were identified for the following four dominant phyla: Halobacteriota, Thermoplasmatota, Thermoproteota, and Nanoarchaeota. Two families and six genera of Archaea were the first to be identified as hosts for viruses. The proviruses were found to contain diverse genes that were involved in distinct adaptation strategies of viruses to hosts. Our findings contribute to the expansion of the lineages of archaeal viruses and highlight their intricate interactions and essential roles in enabling host survival and adaptation to diverse environmental conditions.}, } @article {pmid39545729, year = {2024}, author = {Beaudry, MS and Bhuiyan, MIU and Glenn, TC}, title = {Enriching the future of public health microbiology with hybridization bait capture.}, journal = {Clinical microbiology reviews}, volume = {37}, number = {4}, pages = {e0006822}, pmid = {39545729}, issn = {1098-6618}, support = {R01 AI148667/AI/NIAID NIH HHS/United States ; 75D30118C02889, 75D30120R67837//HHS | Centers for Disease Control and Prevention (CDC)/ ; 1R01AI148667-01A1//HHS | National Institutes of Health (NIH)/ ; }, mesh = {Humans ; Bacteria/genetics/classification/isolation & purification ; Fungi/classification/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; *Microbiological Techniques/methods/trends ; Nucleic Acid Hybridization/methods ; *Public Health ; }, abstract = {SUMMARYPublic health microbiology focuses on microorganisms and infectious agents that impact human health. For years, this field has relied on culture or molecular methods to investigate complex samples of public health importance. However, with the increase in accuracy and decrease in sequencing cost over the last decade, there has been a transition to the use of next-generation sequencing in public health microbiology. Nevertheless, many available sequencing methods (e.g., shotgun metagenomics and amplicon sequencing) do not work well in complex sample types, require deep sequencing, or have inherent biases associated with them. Hybridization bait capture, also known as target enrichment, brings in solutions for such limitations. It is an increasingly popular technique to simultaneously characterize many thousands of genetic elements while reducing the amount of sequencing needed (thereby reducing the sequencing costs). Here, we summarize the concept of hybridization bait capture for public health, reviewing a total of 35 bait sets designed in six key topic areas for public health microbiology [i.e., antimicrobial resistance (AMR), bacteria, fungi, parasites, vectors, and viruses], and compare hybridization bait capture to previously relied upon methods. Furthermore, we provide an in-depth comparison of the three most popular bait sets designed for AMR by evaluating each of them against three major AMR databases: Comprehensive Antibiotic Resistance Database, Microbial Ecology Group Antimicrobial Resistance Database, and Pathogenicity Island Database. Thus, this article provides a review of hybridization bait capture for public health microbiologists.}, } @article {pmid39545702, year = {2024}, author = {Zhang, M and Ma, L and Luo, J and Ren, T and Liu, S and Pan, L and Bao, Y and Li, F and Dai, Y and Pi, Z and Yue, H and Zheng, F}, title = {Low-Medium Polarity Ginsenosides from Wild Ginseng Improves Immunity by Activating the AhR/MAPK Pathway through Tryptophan Metabolism Driven by Gut Microbiota.}, journal = {Journal of agricultural and food chemistry}, volume = {72}, number = {47}, pages = {26142-26154}, doi = {10.1021/acs.jafc.4c06019}, pmid = {39545702}, issn = {1520-5118}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Panax/chemistry ; Mice ; *Tryptophan/metabolism ; *Ginsenosides/pharmacology/administration & dosage ; *Plant Extracts/pharmacology/administration & dosage ; *Receptors, Aryl Hydrocarbon/metabolism/genetics ; Male ; Bacteria/classification/genetics/metabolism/isolation & purification/drug effects ; Humans ; Immunity/drug effects ; MAP Kinase Signaling System/drug effects ; Spleen/drug effects/metabolism/immunology ; Intestinal Mucosa/metabolism/immunology/drug effects ; Mice, Inbred BALB C ; }, abstract = {The gut microbiota contribute significantly to the immune system. Low-medium polarity ginsenosides from wild ginseng (LWG) have potential immunomodulatory effects. However, how the LWG regulates gut microbiota to enhance immunity remains unclear. To explore the interaction between gut microbes and metabolites mediating LWG's immunomodulatory effects, this study examined LWG's impact on splenocytes and CTX-induced immunosuppressed mice. Metabolomic and metagenomic analyses were conducted in vivo to explore the mechanism by which LWG regulates gut microbiota to enhance immunity. In vitro data suggest that LWG at 4 μg/mL enhances the splenocyte activity. Furthermore, LWG effectively reduces symptoms in immunocompromised mice, including weight loss and intestinal mucosal damage. LWG alleviated gut microbiota disturbance, restored tryptophan metabolites (IA, IAA, and IPA), and significantly increased JNK, ERK, and p38MAPK protein levels, which were downstream of AhR. Our study demonstrated that LWG improves the immunity by reshaping gut microbiota, restoring intestinal mucosa, and boosting the gut microbiota-related metabolism of tryptophan to activate the AhR/MAPK pathway. This research offers new insights into the mechanism by which LWG regulates immune function.}, } @article {pmid39545400, year = {2025}, author = {Stern, DB and Raborn, RT and Lovett, SP and Boise, NR and Carrasquilla, L and Enke, S and Radune, D and Woodruff, DL and Wahl, KL and Rosovitz, MJ}, title = {Novel Toxin Biosynthetic Gene Cluster in Harmful Algal Bloom-Causing Heteroscytonema crispum: Insights into the Origins of Paralytic Shellfish Toxins.}, journal = {Genome biology and evolution}, volume = {17}, number = {1}, pages = {}, pmid = {39545400}, issn = {1759-6653}, support = {//Battelle National Biodefense Institute/ ; /DHS/DHS/United States ; //Science and Technology Directorate/ ; //National Biodefense Analysis and Countermeasures Center/ ; //Federally Funded Research and Development Center/ ; }, mesh = {*Harmful Algal Bloom ; *Multigene Family ; *Cyanobacteria/genetics/metabolism ; *Saxitoxin/genetics/biosynthesis ; *Phylogeny ; Marine Toxins/genetics/biosynthesis ; Dinoflagellida/genetics/metabolism ; Genome, Bacterial ; Gene Transfer, Horizontal ; }, abstract = {Caused by both eukaryotic dinoflagellates and prokaryotic cyanobacteria, harmful algal blooms are events of severe ecological, economic, and public health consequence, and their incidence has become more common of late. Despite coordinated research efforts to identify and characterize the genomes of harmful algal bloom-causing organisms, the genomic basis and evolutionary origins of paralytic shellfish toxins produced by harmful algal blooms remain at best incomplete. The paralytic shellfish toxin saxitoxin has an especially complex genomic architecture and enigmatic phylogenetic distribution, spanning dinoflagellates and multiple cyanobacterial genera. Using filtration and extraction techniques to target the desired cyanobacteria from nonaxenic culture, coupled with a combination of short- and long-read sequencing, we generated a reference-quality hybrid genome assembly for Heteroscytonema crispum UTEX LB 1556, a freshwater, paralytic shellfish toxin-producing cyanobacterium thought to have the largest known genome in its phylum. We report a complete, novel biosynthetic gene cluster for the paralytic shellfish toxin saxitoxin. Leveraging this biosynthetic gene cluster, we find support for the hypothesis that paralytic shellfish toxin production has appeared in divergent Cyanobacteria lineages through widespread and repeated horizontal gene transfer. This work demonstrates the utility of long-read sequencing and metagenomic assembly toward advancing our understanding of paralytic shellfish toxin biosynthetic gene cluster diversity and suggests a mechanism for the origin of paralytic shellfish toxin biosynthetic genes.}, } @article {pmid39544963, year = {2024}, author = {Wong, HL and Bulzu, PA and Ghai, R and Chiriac, MC and Salcher, MM}, title = {Ubiquitous genome streamlined Acidobacteriota in freshwater environments.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae124}, pmid = {39544963}, issn = {2730-6151}, abstract = {Acidobacteriota are abundant in soil, peatlands, and sediments, but their ecology in freshwater environments remains understudied. UBA12189, an Acidobacteriota genus, is an uncultivated, genome-streamlined lineage with a small genome size found in aquatic environments where detailed genomic analyses are lacking. Here, we analyzed 66 MAGs of UBA12189 (including one complete genome) from freshwater lakes and rivers in Europe, North America, and Asia. UBA12189 has small genome sizes (<1.4 Mbp), low GC content, and a highly diverse pangenome. In freshwater lakes, this bacterial lineage is abundant from the surface waters (epilimnion) down to a 300-m depth (hypolimnion). UBA12189 appears to be free-living from CARD-FISH analysis. When compared to other genome-streamlined bacteria such as Nanopelagicales and Methylopumilus, genome reduction has caused UBA12189 to have a more limited metabolic repertoire in carbon, sulfur, and nitrogen metabolisms, limited numbers of membrane transporters, as well as a higher degree of auxotrophy for various amino acids, vitamins, and reduced sulfur. Despite having reduced genomes, UBA12189 encodes proteorhodopsin, complete biosynthesis pathways for heme and vitamin K2, cbb3-type cytochrome c oxidases, and heme-requiring enzymes. These genes may give a selective advantage during the genome streamlining process. We propose the new genus Acidiparvus, with two new species named "A. lacustris" and "A. fluvialis". Acidiparvus is the first described genome-streamlined lineage under the phylum Acidobacteriota, which is a free-living, slow-growing scavenger in freshwater environments.}, } @article {pmid39544492, year = {2024}, author = {Xiao, S and Zhou, W and Caldwell, R and Decker, S and Oh, J and Milstone, AM}, title = {Association of Neonatal and Maternal Nasal Microbiome Among Neonates in the Intensive Care Unit.}, journal = {Open forum infectious diseases}, volume = {11}, number = {11}, pages = {ofae644}, pmid = {39544492}, issn = {2328-8957}, abstract = {The neonatal nasal microbiota may help protect neonates in the neonatal intensive care unit from pathogen colonization and infection. This preliminary study characterized the biodiversity of nasal microbiota comparing neonates in the neonatal intensive care unit and their mothers, highlighting the potential of strain sharing between mother-neonate pairs.}, } @article {pmid39544283, year = {2024}, author = {Li, S and Fan, S and Ma, Y and Xia, C and Yan, Q}, title = {Influence of gender, age, and body mass index on the gut microbiota of individuals from South China.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1419884}, pmid = {39544283}, issn = {2235-2988}, mesh = {Humans ; *Body Mass Index ; China ; Female ; Male ; Adult ; Middle Aged ; *Gastrointestinal Microbiome/genetics ; Age Factors ; *Feces/microbiology ; Sex Factors ; Young Adult ; Aged ; Bacteria/classification/genetics/isolation & purification ; Phylogeny ; }, abstract = {BACKGROUND: The symbiotic gut microbiota is pivotal for human health, with its composition linked to various diseases and metabolic disorders. Despite its significance, there remains a gap in systematically evaluating how host phenotypes, such as gender, age, and body mass index (BMI), influence gut microbiota.

We conducted an analysis of the gut microbiota of 185 Chinese adults based on whole-metagenome shotgun sequencing of fecal samples. Our investigation focused on assessing the effects of gender, age, and BMI on gut microbiota across three levels: diversity, gene/phylogenetic composition, and functional composition. Our findings suggest that these phenotypes have a minor impact on shaping the gut microbiome compared to enterotypes, they do not correlate significantly within- or between-sample diversity. We identified a substantial number of phenotype-associated genes and metagenomic linkage groups (MLGs), indicating variations in gut microflora composition. Specifically, we observed a decline in beneficial Firmicutes microbes, such as Eubacterium, Roseburia, Faecalibacterium and Ruminococcus spp., in both older individuals and those with higher BMI, while potentially harmful microbes like Erysipelotrichaceae, Subdoligranulum and Streptococcus spp. increased with age. Additionally, Blautia and Dorea spp. were found to increase with BMI, aligning with prior research. Surprisingly, individuals who were older or overweight exhibited a lack of Bacteroidetes, a dominant phylum in the human gut microbiota that includes opportunistic pathogens, while certain species of the well-known probiotics Bifidobacterium were enriched in these groups, suggesting a complex interplay of these bacteria warranting further investigation. Regarding gender, several gender-associated MLGs from Bacteroides, Parabacteroides, Clostridium and Akkermansia were enriched in females. Functional analysis revealed a multitude of phenotype-associated KEGG orthologs (KOs).

CONCLUSIONS/SIGNIFICANCE: Our study underscores the influence of gender, age, and BMI on gut metagenomes, affecting both phylogenetic and functional composition. However, further investigation is needed to elucidate the precise roles of these bacteria, including both pathogens and probiotics.}, } @article {pmid39544279, year = {2024}, author = {Hong, R and Lin, S and Zhang, S and Yi, Y and Li, L and Yang, H and Du, Z and Cao, X and Wu, W and Ren, R and Yao, X and Xie, B}, title = {Pathogen spectrum and microbiome in lower respiratory tract of patients with different pulmonary diseases based on metagenomic next-generation sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1320831}, pmid = {39544279}, issn = {2235-2988}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing ; *Microbiota/genetics ; *Metagenomics/methods ; Middle Aged ; Female ; Male ; Lung Diseases/microbiology ; Aged ; Lung/microbiology ; Bacteria/genetics/classification/isolation & purification ; Adult ; Respiratory System/microbiology ; Metagenome/genetics ; }, abstract = {INTRODUCTION: The homeostasis of the microbiome in lower respiratory tract is crucial in sustaining normal physiological functions of the lung. Different pulmonary diseases display varying degrees of microbiome imbalance; however, the specific variability and clinical significance of their microbiomes remain largely unexplored.

METHODS: In this study, we delineated the pathogen spectrum and commensal microorganisms in the lower respiratory tract of various pulmonary diseases using metagenomic sequencing. We analyzed the disparities and commonalities of the microbial features and examined their correlation with disease characteristics.

RESULTS: We observed distinct pathogen profiles and a diversity in lower airway microbiome in patients diagnosed with cancer, interstitial lung disease, bronchiectasis, common pneumonia, Nontuberculous mycobacteria (NTM) pneumonia, and severe pneumonia.

DISCUSSION: This study illustrates the utility of Metagenomic Next-generation Sequencing (mNGS) in identifying pathogens and analyzing the lower respiratory microbiome, which is important for understanding the microbiological aspect of pulmonary diseases and essential for their early and precise diagnosis.}, } @article {pmid39544117, year = {2024}, author = {Roslund, MI and Galitskaya, P and Saarenpää, M and Sinkkonen, A}, title = {Cultivar-dependent differences in plant bud microbiome and functional gene pathways in woody plants commonly used in urban green space.}, journal = {Letters in applied microbiology}, volume = {77}, number = {12}, pages = {}, doi = {10.1093/lambio/ovae110}, pmid = {39544117}, issn = {1472-765X}, support = {346 136//Strategic Research Council/ ; }, mesh = {*Microbiota ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; Metagenome ; Archaea/genetics/classification ; Plants/microbiology ; Humans ; Phylogeny ; Metagenomics ; }, abstract = {Plant richness and microbiota have been associated with plant health; hardly any studies have investigated how plant taxa differs in microbiota in the context of human health. We investigated the microbial differences in buds of 83 woody plant taxa used in urban green spaces in hemiboreal climate, using 16S rRNA and whole metagenome shotgun sequencing. Bud microbial community was the richest in Cotoneaster Nanshan and C. integerrimus, and Malus domestica cultivars "Sandra" and "Lobo" and poorest in Ribes glandulosum. Metagenomic shotgun sequencing of two M. domestica and four Ribes varieties confirmed differences in taxa in bud microbiota and indicated higher siderophore synthesis in Malus. Microbial richness, including bacteria, archaea, and viruses, and functional richness of gene pathways was higher in Malus compared to Ribes. The 10 most abundant amplicon sequence units, often referred as species, belonged to the phylum Proteobacteria. The differences between plant taxa were evident in classes Alpha- and Gammaproteobacteria, known for potential human health benefits. Since environmental microbiota contributes to human microbiota and immunoregulation, horticultural cultivars hosting rich microbiota may have human health benefits. Further studies are needed to confirm the effectiveness of microbially-oriented plant selection in optimizing human microbiota and planetary health.}, } @article {pmid39543873, year = {2024}, author = {Saraswat, I and Goel, A}, title = {Therapeutic Modulation of the Microbiome in Oncology: Current Trends and Future Directions.}, journal = {Current pharmaceutical biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.2174/0113892010353600241109132441}, pmid = {39543873}, issn = {1873-4316}, abstract = {Cancer is a predominant cause of mortality worldwide, necessitating the development of innovative therapeutic techniques. The human microbiome, particularly the gut microbiota, has become a significant element in cancer research owing to its essential role in sustaining health and influencing disease progression. This review examines the microbiome's makeup and essential functions, including immunological modulation and metabolic regulation, which may be evaluated using sophisticated methodologies such as metagenomics and 16S rRNA sequencing. The microbiome influences cancer development by promoting inflammation, modulating the immune system, and producing carcinogenic compounds. Dysbiosis, or microbial imbalance, can undermine the epithelial barrier and facilitate cancer. The microbiome influences chemotherapy and radiation results by modifying drug metabolism, either enhancing or reducing therapeutic efficacy and contributing to side effects and toxicity. Comprehending these intricate relationships emphasises the microbiome's significance in oncology and accentuates the possibility for microbiome-targeted therapeutics. Contemporary therapeutic approaches encompass the utilisation of probiotics and dietary components to regulate the microbiome, enhance treatment efficacy, and minimise unwanted effects. Advancements in research indicate that personalised microbiome-based interventions, have the potential to transform cancer therapy, by providing more effective and customised treatment alternatives. This study aims to provide a comprehensive analysis of the microbiome's influence on the onset and treatment of cancer, while emphasising current trends and future possibilities for therapeutic intervention.}, } @article {pmid39543781, year = {2024}, author = {Samuthpongtorn, C and Chan, AA and Ma, W and Wang, F and Nguyen, LH and Wang, DD and Okereke, OI and Huttenhower, C and Chan, AT and Mehta, RS}, title = {F. prausnitzii potentially modulates the association between citrus intake and depression.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {237}, pmid = {39543781}, issn = {2049-2618}, support = {U01 CA176726 to WW/CA/NCI NIH HHS/United States ; U01 CA176726/CA/NCI NIH HHS/United States ; R01MH091448/NH/NIH HHS/United States ; U01 CA176726 to WW/NH/NIH HHS/United States ; R01 NR019992/NR/NINR NIH HHS/United States ; R01 AG077489/AG/NIA NIH HHS/United States ; R00 DK119412/DK/NIDDK NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome ; Humans ; Female ; *Depression/microbiology ; Male ; *Citrus ; *Feces/microbiology ; Middle Aged ; *Faecalibacterium prausnitzii/genetics ; Diet ; Adult ; Metagenomics ; Longitudinal Studies ; S-Adenosylmethionine/metabolism ; Monoamine Oxidase/genetics/metabolism ; Prospective Studies ; }, abstract = {BACKGROUND: The gut microbiome modulates the effects of diet on host health, but it remains unclear which specific foods and microbial features interact to influence risk of depression. To understand this interplay, we leveraged decades of dietary and depression data from a longitudinal cohort of women (n = 32,427), along with fecal metagenomics and plasma metabolomics from a substudy (n = 207) nested in this cohort, as well as an independent validation cohort of men (n = 307).

RESULTS: We report that citrus intake and its components are prospectively associated with a lower risk of depression and altered abundance of 15 gut microbial species, including enriched Faecalibacterium prausnitzii. In turn, we found a lower abundance of F. prausnitzii and its metabolic pathway, S-adenosyl-L-methionine (SAM) cycle I in participants with depression. To explore causality, we found that lower SAM production by F. prausnitzii may decrease intestinal monoamine oxidase A gene expression implicated in serotonin and dopamine synthesis.

CONCLUSIONS: These data underscore the role of diet in the prevention of depression and offer a plausible explanation for how the intestinal microbiome modulates the influence of citrus on mental health. Video Abstract.}, } @article {pmid39543780, year = {2024}, author = {Zhao, XD and Gao, ZY and Peng, J and Konstantinidis, KT and Zhang, SY}, title = {Various microbial taxa couple arsenic transformation to nitrogen and carbon cycling in paddy soils.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {238}, pmid = {39543780}, issn = {2049-2618}, mesh = {*Soil Microbiology ; *Arsenic/metabolism ; *Bacteria/metabolism/classification/genetics ; *Oryza/metabolism ; *Nitrogen/metabolism ; *Oxidation-Reduction ; *Archaea/metabolism/genetics/classification ; *Soil/chemistry ; Carbon/metabolism ; Carbon Cycle ; Microbiota ; Arsenites/metabolism ; Arsenates/metabolism ; }, abstract = {BACKGROUND: Arsenic (As) metabolism pathways and their coupling to nitrogen (N) and carbon (C) cycling contribute to elemental biogeochemical cycling. However, how whole-microbial communities respond to As stress and which taxa are the predominant As-transforming bacteria or archaea in situ remains unclear. Hence, by constructing and applying ROCker profiles to precisely detect and quantify As oxidation (aioA, arxA) and reduction (arrA, arsC1, arsC2) genes in short-read metagenomic and metatranscriptomic datasets, we investigated the dominant microbial communities involved in arsenite (As(III)) oxidation and arsenate (As(V)) reduction and revealed their potential pathways for coupling As with N and C in situ in rice paddies.

RESULTS: Five ROCker models were constructed to quantify the abundance and transcriptional activity of short-read sequences encoding As oxidation (aioA and arxA) and reduction (arrA, arsC1, arsC2) genes in paddy soils. Our results revealed that the sub-communities carrying the aioA and arsC2 genes were predominantly responsible for As(III) oxidation and As(V) reduction, respectively. Moreover, a newly identified As(III) oxidation gene, arxA, was detected in genomes assigned to various phyla and showed significantly increased transcriptional activity with increasing soil pH, indicating its important role in As(III) oxidation in alkaline soils. The significant correlation of the transcriptional activities of aioA with the narG and nirK denitrification genes, of arxA with the napA and nirS denitrification genes and of arrA/arsC2 with the pmoA and mcrA genes implied the coupling of As(III) oxidation with denitrification and As(V) reduction with methane oxidation. Various microbial taxa including Burkholderiales, Desulfatiglandales, and Hyphomicrobiales (formerly Rhizobiales) are involved in the coupling of As with N and C metabolism processes. Moreover, these correlated As and N/C genes often co-occur in the same genome and exhibit greater transcriptional activity in paddy soils with As contamination than in those without contamination.

CONCLUSIONS: Our results revealed the comprehensive detection and typing of short-read sequences associated with As oxidation and reduction genes via custom-built ROCker models, and shed light on the various microbial taxa involved in the coupling of As and N and C metabolism in situ in paddy soils. The contribution of the arxA sub-communities to the coupling of As(III) oxidation with nitrate reduction and the arsC sub-communities to the coupling of As(V) reduction with methane oxidation expands our knowledge of the interrelationships among As, N, and C cycling in paddy soils. Video Abstract.}, } @article {pmid39543707, year = {2024}, author = {Wang, T and Ruan, Y and Xu, Q and Shen, Q and Ling, N and Vandenkoornhuyse, P}, title = {Effect of plant-derived microbial soil legacy in a grafting system-a turn for the better.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {234}, pmid = {39543707}, issn = {2049-2618}, mesh = {*Soil Microbiology ; *Microbiota ; *Bacteria/classification/genetics/metabolism ; Soil/chemistry ; Metagenome ; }, abstract = {BACKGROUND: Plant-soil feedback arises from microbial legacies left by plants in the soil. Grafting is a common technique used to prevent yield declines in monocultures. Yet, our understanding of how grafting alters the composition of soil microbiota and how these changes affect subsequent crop performance remains limited. Our experiment involved monoculturing ungrafted and grafted watermelons to obtain conditioned soils, followed by growing the watermelons on the conditioned soils to investigate plant-soil feedback effects.

RESULTS: Ungrafted plants grew better in soil previously conditioned by a different plant (heterospecific soil) while grafted plants grew better in soil conditioned by the same plant (conspecific soil). We demonstrated experimentally that these differences in growth were linked to changes in microorganisms. Using a supervised machine learning algorithm, we showed that differences in the relative abundance of certain genera, such as Rhizobium, Chryseobacterium, Fusarium, and Aspergillus, significantly influenced the conspecific plant-soil feedback. Metabolomic analyses revealed that ungrafted plants in heterospecific soil enriched arginine biosynthesis, whereas grafted plants in conspecific soil increased sphingolipid metabolism. Elsewhere, the metagenome-assembled genomes (MAGs) of ungrafted plants identified in heterospecific soil include Chryseobacterium and Lysobacter, microorganisms having been prominently identified in earlier research as contributors to plant growth. Metabolic reconstruction revealed the putative ability of Chryseobacterium to convert D-glucono-1,5-lactone to gluconic acid, pointing to distinct disease-suppressive mechanisms and hence distinct microbial functional legacies between grafted and ungrafted plants.

CONCLUSIONS: Our findings show a deep impact of the soil microbial reservoir on plant growth and suggest the necessity to protect and improve this microbial community in agricultural soils. The work also suggests possibilities of optimizing microbiota-mediated benefits through grafting herein, a way that "engineered" soil microbial communities for better plant growth. Video Abstract.}, } @article {pmid39543347, year = {2025}, author = {Neo, O and Singh, N and Cazares, A}, title = {A river of resistant genes uncovered by metagenomics.}, journal = {Nature reviews. Microbiology}, volume = {23}, number = {1}, pages = {8}, pmid = {39543347}, issn = {1740-1534}, } @article {pmid39543265, year = {2024}, author = {Stevens, BR and Roesch, LFW}, title = {Interplay of human ABCC11 transporter gene variants with axillary skin microbiome functional genomics.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {28037}, pmid = {39543265}, issn = {2045-2322}, mesh = {Humans ; *Microbiota/genetics ; *Polymorphism, Single Nucleotide ; *Skin/microbiology/metabolism ; Female ; *ATP-Binding Cassette Transporters/genetics/metabolism ; Male ; Haplotypes ; Genomics/methods ; Axilla/microbiology ; Adult ; Pedigree ; }, abstract = {The human armpit microbiome is metabolically entangled with skin cell physiology. This "meta-organism" symbiotic mutualism results in sweat either with or without odor (osmidrosis), depending on host ABCC11 gene haplotypes. Apocrine metabolism produces odorless S-glutathione conjugate that is transferred by ABCC11 transporters into secretory vesicles, deglutamylated to S-Cys-Gly-3M3SH thiol, and exuded to skin surface. An anthropogenic clade of skin bacteria then takes up the thiol and bioconverts it to malodorous 3-methyl-3-sulfanylhexan-1-ol (3M3SH). We hypothesized a familial meta-organism association of human ABCC11 gene non-synonymous SNP rs17822931 interplaying with skin microbiome 3M3SH biosynthesis. Subjects were genotyped for ABCC11 SNPs, and their haplotypes were correlated with axilla microbiome DNA sequencing profiles and predicted metagenome functions. A multigeneration family pedigree revealed a Mendelian autosomal recessive pattern: the C allele of ABCC11 correlated with bacterial Cys-S-conjugate β-lyase (PatB) gene known for Staphylococcus hominis biosynthesis of 3M3SH from human precursor; PatB was rescinded in hosts with homozygous TT alleles encoding ABCC11 loss-of-function mutation. We posit that a C allele encoding functional ABCC11 is key to delivering host conjugate precursors that shape heritable skin niche conditions favorable to harboring Staphylococcus having genomics of odor thiol production. This provides existential insights into human evolution and global regional population ancestries.}, } @article {pmid39543167, year = {2024}, author = {Sumithra, TG and Sharma, SRK and Suresh, G and Suja, G and Prasad, V and Gop, AP and Patil, PK and Gopalakrishnan, A}, title = {Gut microbes of a high-value marine fish, Snubnose Pompano (Trachinotus blochii) are resilient to therapeutic dosing of oxytetracycline.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {27949}, pmid = {39543167}, issn = {2045-2322}, support = {Grant No. CIBA/AINP-FH/2015-16//Indian Council of Agricultural Research/ ; BT/AAQ/3/SP28267/2018//Department of Biotechnology, Ministry of Science and Technology, India/ ; }, mesh = {*Oxytetracycline/pharmacology ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/pharmacology ; Fishes/microbiology ; Aquaculture/methods ; Dysbiosis/microbiology ; Metagenomics/methods ; Bacteria/drug effects/genetics/classification ; }, abstract = {Trachinotus blochii is a high-value tropical mariculture species. The present study evaluated the gut microbial impact of therapeutic exposure (80 mg/day/kg biomass for 10 days) to oxytetracycline, the most common aquaculture antibiotic in T. blochii. The cultivable counts, α-diversity measures of taxonomic and functional metagenomics, microbial dysbiosis (MD) index, and microbial taxon abundances showed the resilience of gut microbiota at 16-26 days of treatment. A significant reduction in bacterial abundance, diversity measures, Firmicutes and Actinobacteria and an increase in γ-Proteobacteria was recorded on the 6th and 11th day of treatment. The increased metagenomic stress signatures, decreased beneficial bacterial abundances, decreased abundance of microbial pathways on energy metabolism, and MD index indicated short-term transient stress during the initial days of therapeutic withdrawal, warranting health management measures. Therapeutic exposure reduced the abundance of fish pathogens, including Vibrio spp., kanamycin and ampicillin-resistant bacteria. Strikingly, oxytetracycline treatment did not increase tetracycline-resistant bacterial counts and the predicted abundance of tetracycline resistance encoding genes in the gut, illustrating that therapeutic application would not pose a risk in the context of antimicrobial resistance in short term. Altogether, the present study provides a foundation for oxytetracycline treatment to develop suitable risk minimization tactics in sustainable aquaculture.}, } @article {pmid39543100, year = {2024}, author = {Krinos, AI and Mars Brisbin, M and Hu, SK and Cohen, NR and Rynearson, TA and Follows, MJ and Schulz, F and Alexander, H}, title = {Missing microbial eukaryotes and misleading meta-omic conclusions.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {9873}, pmid = {39543100}, issn = {2041-1723}, support = {DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-SC0020347//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; }, mesh = {*Eukaryota/genetics/classification ; Phylogeny ; Databases, Genetic ; Cluster Analysis ; Metagenomics/methods ; }, abstract = {Meta-omics is commonly used for large-scale analyses of microbial eukaryotes, including species or taxonomic group distribution mapping, gene catalog construction, and inference on the functional roles and activities of microbial eukaryotes in situ. Here, we explore the potential pitfalls of common approaches to taxonomic annotation of protistan meta-omic datasets. We re-analyze three environmental datasets at three levels of taxonomic hierarchy in order to illustrate the crucial importance of database completeness and curation in enabling accurate environmental interpretation. We show that taxonomic membership of sequence clusters estimates community composition more accurately than returning exact sequence labels, and overlap between clusters can address database shortcomings. Clustering approaches can be applied to diverse environments while continuing to exploit the wealth of annotation data collated in databases, and selecting and evaluating these databases is a critical part of correctly annotating protistan taxonomy in environmental datasets. We argue that ongoing curation of genetic resources is crucial in accurately annotating protists in in situ meta-omic datasets. Moreover, we propose that precise taxonomic annotation of meta-omic data is a clustering problem rather than a feasible alignment problem.}, } @article {pmid39542977, year = {2024}, author = {da Rosa, MT and da Luz Wallau, G and Loreto, ELS}, title = {A novel picorna-like virus in the flatworm Stenostomum leucops (Catenulida).}, journal = {Archives of virology}, volume = {169}, number = {12}, pages = {244}, pmid = {39542977}, issn = {1432-8798}, mesh = {Animals ; *Phylogeny ; *Genome, Viral ; *Open Reading Frames ; *Picornaviridae/genetics/classification/isolation & purification ; RNA, Viral/genetics ; }, abstract = {We present the genome sequence and organization and evidence of persistence of a new picorna-like virus infecting the flatworm Stenostomum leucops. The complete genome sequence belongs to a virus with a positive single-stranded RNA genome with two open reading frames (ORFs) flanked by untranslated regions and a polyadenylated C-terminus. The ORFs encode proteins with conserved motifs typical of members of the order Picornavirales. Phylogenetic analysis confirmed membership in this viral order, and it was found to be closely related to viruses found in Biomphalaria (Mollusca) in France and a virus detected in a metagenomic analysis of water sources from the USA, suggesting widespread distribution. RT-PCR analysis revealed that this virus can be detected in a laboratory-grown worm isolate for at least five years, suggesting persistent infection. However, no apparent deleterious effects were observed in the worms in culture, suggesting a possible commensal relationship between the virus and the worms.}, } @article {pmid39542877, year = {2025}, author = {Vasudevan, G and Ramachandran, K and Tangavel, C and Nayagam, SM and Gopalakrishnan, C and Muthurajan, R and Sri Vijay Anand, KS and Rajasekaran, S}, title = {"Elucidating the immunomodulatory role of endocannabinoids in intervertebral disc degeneration".}, journal = {European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society}, volume = {34}, number = {1}, pages = {308-315}, pmid = {39542877}, issn = {1432-0932}, mesh = {Humans ; *Endocannabinoids/metabolism ; *Intervertebral Disc Degeneration/immunology/metabolism ; Adult ; Male ; Female ; Middle Aged ; }, abstract = {PURPOSE: The endocannabinoid system (ECS) has been well-established to play a crucial role in the regulation of several physiological processes as well as many inflammatory disease conditions. However, its role in intervertebral disc degeneration has been least explored. We aim to investigate the immunomodulatory role of endocannabinoids in regulating IVD health.

METHODS: The study population included 20 healthy volunteers (controls) and 40 patients with disc degeneration (disease group) (20 Modic and 20 Non Modic). 16S metagenome sequencing of the V3-V4 region was performed for the DNA extracted from NP tissue samples of both control and disease groups. Sequencing was carried out using the Novaseq 6000 platform using 250 bp paired-end chemistry. A global metabolic profile was obtained using the uHPLC system coupled with Q Exactive Plus Hybrid Quadrupole-Orbitrap mass spectrometer.

RESULTS: Our study revealed a higher prevalence of gram-negative bacteria, particularly opportunistic pathogens like Pseudomonas, in diseased discs (71-81%) compared to healthy controls (54%). Further investigation using metabolomics identified significant changes in the lipid profiles of diseased discs. We found that the signalling molecules of the ECS, 2-arachidonylglycerol (2-AG) and N-arachidonoylethanolamine (AEA), were significantly lower in diseased discs compared to controls (Log2FC -2.62 for 2-AG and  -3.15 for AEA). Conversely, pro-inflammatory metabolites like LTA4, HPETE, HETE, and Prostaglandin G2 were elevated in diseased discs, with a Log2 fold increase greater than 2.5.

CONCLUSION: The study reveals that the endocannabinoid metabolites (2-AG and AEA) of the ECS could be a significant molecule influencing susceptibility to infection and inflammation within the intervertebral discs, which could be a potential target for improving disc health.

LEVEL OF EVIDENCE: Diagnostic: individual cross-sectional studies with consistently applied reference standard and blinding.}, } @article {pmid39542187, year = {2025}, author = {Gurumayum, N and Devi, MB and Khound, P and Bhattacharya, A and Sarma, H and Khan, MR and Devi, R}, title = {Bioactive fraction of Musa balbisiana seed mitigates D-galactose-induced brain aging via SIRT1/PGC-1α/FoxO3a activation and intestinal barrier dysfunction by modulating gut microbiota and core metabolites.}, journal = {Free radical biology & medicine}, volume = {226}, number = {}, pages = {43-55}, doi = {10.1016/j.freeradbiomed.2024.11.016}, pmid = {39542187}, issn = {1873-4596}, mesh = {Animals ; *Galactose/adverse effects/toxicity ; *Gastrointestinal Microbiome/drug effects ; Rats ; *Seeds/chemistry ; *Sirtuin 1/metabolism/genetics ; *Plant Extracts/pharmacology ; *Aging/drug effects ; *Oxidative Stress/drug effects ; *Brain/metabolism/drug effects/pathology ; *Forkhead Box Protein O3/metabolism/genetics ; *Musa/chemistry ; *Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/metabolism/genetics ; Male ; Rats, Sprague-Dawley ; Glycation End Products, Advanced/metabolism ; Antioxidants/pharmacology/metabolism ; }, abstract = {Aging is an inevitable biological process, and emerging research has highlighted the potential of dietary and pharmacological interventions to decelerate the trajectory of age-related diseases and prolong the health span. This study evaluates the protective effects of Musa balbisiana seed on healthy aging using D-galactose-induced accelerated aging rats. The results suggested that the bioactive ethyl acetate fraction of Musa balbisiana seed extract (BF) exhibited protective effects against aging-induced oxidative stress by reducing oxidative DNA damage, advanced glycation end-product formation, and malondialdehyde levels while restoring antioxidant and glyoxalase enzyme activities. BF also ameliorated neurodegeneration by decreasing acetylcholinesterase enzyme activity and amyloid beta plaque formation. Histopathological analysis demonstrated the protective effects of BF against brain aging, liver disruption, renal damage, and intestinal barrier dysfunction. BF further restored intestinal permeability by upregulating the tight junctions (zonula occludens 1 and 2, claudin 1,2,3 and 4, and occludin) and mucin (mucin 2 and mucin 5ac) gene expression while downregulating the expression of inflammatory cytokines (IL-1β, IL-6, and TNF-α). BF significantly induced the phosphorylation of FoxO3a proteins and upregulated the gene expression of SIRT1, PGC-1α, and TFAM in the hippocampus. Next-generation sequencing (NGS) of 16s rRNA amplicons of fecal metagenomics DNA and metabolites profiling showed that BF intervention restructured the gut microbiota and altered core metabolites related to cholesterol metabolism. Overall, our findings demonstrated the multifaceted protective effects of Musa balbisiana seed against D-galactose-induced aging.}, } @article {pmid39542062, year = {2025}, author = {Wimalaweera, I and Zuo, F and Tang, Q and Sui, Q and Jinadasa, S and Weragoda, S and Ritigala, T and Weerasooriya, R and Wang, Y and Zhong, H and Makehelwala, M and Wei, Y}, title = {Synchronised removal of nitrogen and sulphate from rubber industrial wastewater by coupling of Sulfammox and sulphide-driven autotrophic denitrification in anaerobic membrane bioreactor.}, journal = {Bioresource technology}, volume = {416}, number = {}, pages = {131785}, doi = {10.1016/j.biortech.2024.131785}, pmid = {39542062}, issn = {1873-2976}, mesh = {*Bioreactors ; *Denitrification ; *Nitrogen/metabolism ; *Wastewater/chemistry ; *Sulfates/metabolism ; *Sulfides/metabolism ; *Rubber/metabolism ; *Industrial Waste ; Anaerobiosis ; Autotrophic Processes ; Waste Disposal, Fluid/methods ; Ammonium Compounds/metabolism ; Membranes, Artificial ; Oxidation-Reduction ; Biological Oxygen Demand Analysis ; }, abstract = {Global rubber industry, growing 4-6 % annually with 13.76 million Mt of rubber produced in 2019, significantly impacts the economy. This study explores coupling sulfate-dependent ammonium oxidation (Sulfammox) and sulfide-driven autotrophic denitrification (SDAD) within an anaerobic membrane bioreactor (AnMBR) to treat high-strength natural rubber wastewater. Over 225 days, the AnMBR system achieved maximal chemical oxygen demand (COD), total nitrogen (TN), ammonium nitrogen (NH4[+]-N), and sulfate sulfur (SO4[2-]-S) removal efficiencies of 58 %, 31 %, 13 %, and 45 %, respectively. TN is predominantly removed through Sulfammox (accounting for 49 % of NH4[+]-N removal), SDAD, and conventional denitrification pathways. Sulfate removal is achieved via Sulfammox (responsible for 43 % of SO4[2-]-S removal), and Dissimilatory sulfate-reducing (DSR) processes (contributing 57 % of SO4[2-]-S removal). Microbial analysis identified Desulfovibrio and Sulfurospirillum as key microbes, while metagenomic analysis highlighted crucial sulfur and nitrogen cycling pathways. The findings support Sulfammox and SDAD as promising eco-friendly strategies for treating ammonia- and sulfate-rich industrial wastewater.}, } @article {pmid39542060, year = {2025}, author = {Fu, J and Guo, T and Li, H and Liu, W and Chen, Z and Wang, X and Guo, J}, title = {Amorphous Cu/Fe nanoparticles with tandem intracellular and extracellular electron capacity for enhancing denitrification performance and recovery of co-contaminant suppressed denitrification.}, journal = {Bioresource technology}, volume = {416}, number = {}, pages = {131812}, doi = {10.1016/j.biortech.2024.131812}, pmid = {39542060}, issn = {1873-2976}, mesh = {*Denitrification ; *Iron/metabolism/chemistry ; *Copper/chemistry ; *Metal Nanoparticles/chemistry ; Electrons ; Bacteria/metabolism ; Nitrates/metabolism ; Water Pollutants, Chemical/metabolism ; Electron Transport ; }, abstract = {In this study, a functionally stable insoluble Cu/Fe nanoparticles (Cu/Fe NPs) were synthesized and applied denitrification with different contaminants. The results showed that 50 mg/L Cu/Fe NPs increased NO3[-]-N reduction rate up to 14.3 mg/(L·h) about 3 folds compared with the control system (4.7 mg/(L·h)), and Cu/Fe NPs exhibited excellent restorative effects on NO3[-]-N reduction under the stress of Cd[2+], Nitrovin and Methyl Orange. Meanwhile, electrochemical analyses, enzyme activities, and related genes abundance together showed that pilus, cytochrome c and flavin mononucleotide were electron carriers to tandem extracellular and intracellular, increasing electron flux acting on NO3[-]-N in the respiratory chain. Metagenomic sequencing showed that microbial metabolic activity, electroactive bacteria (EAB) abundance with bi-directional electron transfer and Cu/Fe-compatible bacterial abundance were increased. Furthermore, denitrification performance was maintained by establishing C-EAB-Cu/Fe NPs cycling network. This study provided insights and applications for expanding the use of insoluble mediators in denitrification systems.}, } @article {pmid39541983, year = {2024}, author = {Urtecho, G and Moody, T and Huang, Y and Sheth, RU and Richardson, M and Descamps, HC and Kaufman, A and Lekan, O and Zhang, Z and Velez-Cortes, F and Qu, Y and Cohen, L and Ricaurte, D and Gibson, TE and Gerber, GK and Thaiss, CA and Wang, HH}, title = {Spatiotemporal dynamics during niche remodeling by super-colonizing microbiota in the mammalian gut.}, journal = {Cell systems}, volume = {15}, number = {11}, pages = {1002-1017.e4}, doi = {10.1016/j.cels.2024.10.007}, pmid = {39541983}, issn = {2405-4720}, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Mice ; *Fecal Microbiota Transplantation/methods ; Mice, Inbred C57BL ; Gastrointestinal Tract/microbiology ; Dysbiosis/microbiology ; Mammals/microbiology ; Feces/microbiology ; }, abstract = {While fecal microbiota transplantation (FMT) has been shown to be effective in reversing gut dysbiosis, we lack an understanding of the fundamental processes underlying microbial engraftment in the mammalian gut. Here, we explored a murine gut colonization model leveraging natural inter-individual variations in gut microbiomes to elucidate the spatiotemporal dynamics of FMT. We identified a natural "super-donor" consortium that robustly engrafts into diverse recipients and resists reciprocal colonization. Temporal profiling of the gut microbiome showed an ordered succession of rapid engraftment by early colonizers within 72 h, followed by a slower emergence of late colonizers over 15-30 days. Moreover, engraftment was localized to distinct compartments of the gastrointestinal tract in a species-specific manner. Spatial metagenomic characterization suggested engraftment was mediated by simultaneous transfer of spatially co-localizing species from the super-donor consortia. These results offer a mechanism of super-donor colonization by which nutritional niches are expanded in a spatiotemporally dependent manner. A record of this paper's transparent peer review process is included in the supplemental information.}, } @article {pmid39541968, year = {2025}, author = {Nishijima, S and Stankevic, E and Aasmets, O and Schmidt, TSB and Nagata, N and Keller, MI and Ferretti, P and Juel, HB and Fullam, A and Robbani, SM and Schudoma, C and Hansen, JK and Holm, LA and Israelsen, M and Schierwagen, R and Torp, N and Telzerow, A and Hercog, R and Kandels, S and Hazenbrink, DHM and Arumugam, M and Bendtsen, F and Brøns, C and Fonvig, CE and Holm, JC and Nielsen, T and Pedersen, JS and Thiele, MS and Trebicka, J and Org, E and Krag, A and Hansen, T and Kuhn, M and Bork, P and , }, title = {Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations.}, journal = {Cell}, volume = {188}, number = {1}, pages = {222-236.e15}, doi = {10.1016/j.cell.2024.10.022}, pmid = {39541968}, issn = {1097-4172}, mesh = {*Gastrointestinal Microbiome ; *Feces/microbiology ; Humans ; Machine Learning ; Female ; Bacteria/classification/genetics/isolation & purification ; Male ; Metagenomics/methods ; Adult ; }, abstract = {The microbiota in individual habitats differ in both relative composition and absolute abundance. While sequencing approaches determine the relative abundances of taxa and genes, they do not provide information on their absolute abundances. Here, we developed a machine-learning approach to predict fecal microbial loads (microbial cells per gram) solely from relative abundance data. Applying our prediction model to a large-scale metagenomic dataset (n = 34,539), we demonstrated that microbial load is the major determinant of gut microbiome variation and is associated with numerous host factors, including age, diet, and medication. We further found that for several diseases, changes in microbial load, rather than the disease condition itself, more strongly explained alterations in patients' gut microbiome. Adjusting for this effect substantially reduced the statistical significance of the majority of disease-associated species. Our analysis reveals that the fecal microbial load is a major confounder in microbiome studies, highlighting its importance for understanding microbiome variation in health and disease.}, } @article {pmid39541850, year = {2025}, author = {Wang, Y and Li, H and Ding, K and Zhao, X and Liu, M and Xu, L and Gu, L and Li, J and Li, L and He, Q and Liang, J}, title = {Improved anaerobic digestion of food waste under ammonia stress by side-stream hydrogen domestication.}, journal = {Water research}, volume = {268}, number = {Pt B}, pages = {122770}, doi = {10.1016/j.watres.2024.122770}, pmid = {39541850}, issn = {1879-2448}, mesh = {Anaerobiosis ; *Ammonia/metabolism ; *Hydrogen/metabolism ; Methane/metabolism ; Sewage/microbiology ; Archaea/genetics/metabolism ; Bioreactors ; Food ; Food Loss and Waste ; }, abstract = {High ammonia concentration inhibits archaea's activity, causing the accumulation of H2 and acetate, which suppresses methane production in anaerobic digestion (AD). The study aimed to enhance microbial hydrogen metabolism through a side-stream hydrogen domestication (SHD) strategy, which involves applying hydrogen stimulation to a portion of the sludge separately. SHD maintained a stable methane yield of 407.5 mL/g VS at a high total ammonia nitrogen (TAN) concentration of 3.1 g/L. In contrast, the control group gradually decreased and stopped methane production at a TAN concentration of 2.3 g/L. Further analysis using enzyme activity assays, flow cytometry, and metagenomics explored the mechanisms underlying ammonia tolerance of SHD-treated group. SHD reshaped the microbial community, enriching homoacetogens and Methanosaeta-dominated methanogenic archaea. Key metabolic pathways including homoacetogenesis, butyrate degradation, propionate degradation, and methane production were enhanced. The activity of related enzymes also increased. Gene abundance in energy-generating pathways, such as glycolysis, was enhanced, ensuring adequate ATP production. Additionally, the high gene abundance of ion transport systems contributed to regulating proton imbalance and supplementing intracellular K[+]. This study provides important insights and practical guidance for developing novel techniques in the field of anaerobic digestion.}, } @article {pmid39541849, year = {2025}, author = {Guo, H and Li, R and Xue, S and Zhangsun, X and Huang, D and Li, Y and Li, N and Su, Y and Zhang, H and Huang, T}, title = {Considerable declines in odor in a drinking water reservoir: Variations of odorous community, precursor enzymes abundance, distribution, and environmental dominant factors.}, journal = {Water research}, volume = {268}, number = {Pt B}, pages = {122767}, doi = {10.1016/j.watres.2024.122767}, pmid = {39541849}, issn = {1879-2448}, mesh = {*Odorants ; *Drinking Water/microbiology ; Camphanes ; Water Supply ; Water Pollutants, Chemical ; Water Purification ; Nitrogen ; }, abstract = {The presence of 2-methylisoborneol (2-MIB) is acknowledged as a prevalent source of odor-related challenges in drinking water reservoirs. Among the three in situ experiments conducted in drinking water reservoir, the water-lifting aerator with bio-filling system exhibited the most pronounced overall effects. It achieved a remarkable 98.70 % removal of 2-MIB and a 99.30 % reduction in the abundance of the mic gene. Metagenomic sequencing identified key genes including methyl transferase gene (mtf), 2-MIB cyclase gene (mic), cyclic nucleotide-binding protein gene (cnb), underscoring the potential role of Actinobacteria, Cyanobacteria, and Proteobacteria communities in contributing to odor occurrences in the reservoir. Furthermore, the abundance of odorous precursor enzymes in the MVA pathway and MEP/DOXP pathway were inhibited in the systems with bio-filling. Total nitrogen (TN) and nitrate (NO3[-]-N) were identified as pivotal factors influencing the presence of 2-MIB odor-producing microorganisms. Effective management of odor-producing species in reservoir water was closely related to the efficient removal of pollutants. These findings will provide valuable insights for the development of odor removal techniques in reservoirs and offer researchers deeper understanding into the mechanisms underlying odor processes.}, } @article {pmid39541817, year = {2024}, author = {Czatzkowska, M and Wolak, I and Harnisz, M and Korzeniewska, E}, title = {Microbial diversity and biosafety judgment of digestates derived from different biogas plants for agricultural applications.}, journal = {Journal of environmental management}, volume = {371}, number = {}, pages = {123329}, doi = {10.1016/j.jenvman.2024.123329}, pmid = {39541817}, issn = {1095-8630}, mesh = {*Biofuels ; *Agriculture ; *Soil Microbiology ; Microbiota ; Biodegradation, Environmental ; Anaerobiosis ; Soil/chemistry ; Bacteria/classification ; }, abstract = {The composition of microbial communities is the key to effective anaerobic digestion (AD). The microbiome driving the AD process has been extensively researched, whereas the influence of specific substrates on the microbiome of digestate remains insufficiently investigated. Digestate has considerable potential for use in soil fertilization and bioremediation, therefore its biological safety should be monitored. Moreover, the knowledge about the composition of microbial communities and their interconnections in digestate should be extended, due to the impact on soil microbiota and its functionality. The aim of this study was a comprehensive assessment of the (1) sanitary quality, (2) core microbiome, and (3) microbial interactions in digestates collected from three full-scale agricultural biogas plants, with particular emphasis on their applicability from the perspective of the resident microbiota. Analyzed samples of digestate were derived from various substrates used for AD, including plant- and animal-based materials, and industrial waste. The study demonstrated that the phyla Bacillota, Bacteroidota, and Cloacimonadota were the most dominant in digestates regardless of the composition of the processed substrates, however, member composition at the genus level differed significantly between samples. In addition, we observed that microbial genera belonging to the less prevalent phyla play an integral role in the forming of microbial community interactions. Dominant microbial taxa with broad metabolic capabilities, potentially improving soil quality and functionality, have been identified. Moreover, we confirmed, that digestate samples were free of analyzed pathogenic bacteria and parasites. The study results indicate that digestate may have an immense fertilizing and bioremediation potential that has not been fully availed of to date.}, } @article {pmid39541434, year = {2024}, author = {Shi, L and Zhang, D and Yang, Q and Yang, J and Zhu, H}, title = {Distinction of clinical features and microbiological methods between Chlamydia psittaci and Legionella pneumophila pneumonia confirmed by metagenomic next-generation sequencing.}, journal = {Annals of medicine}, volume = {56}, number = {1}, pages = {2428433}, pmid = {39541434}, issn = {1365-2060}, mesh = {Humans ; Male ; *Chlamydophila psittaci/isolation & purification/genetics ; Female ; Retrospective Studies ; Middle Aged ; *Legionella pneumophila/isolation & purification/genetics ; *Psittacosis/diagnosis/microbiology/drug therapy ; Aged ; *Legionnaires' Disease/diagnosis/microbiology/drug therapy ; *Community-Acquired Infections/microbiology/diagnosis ; *High-Throughput Nucleotide Sequencing ; Metagenomics/methods ; Diagnosis, Differential ; Adult ; Prognosis ; }, abstract = {OBJECTIVES: Detection and diagnosis of Chlamydia psittaci (C. psittaci) pneumonia is often overlooked due to conventional methods limitations and similarity to other atypical community acquired pneumonia (CAP). Using mNGS, we aimed to distinguish psittacosis from legionellosis for early C. psittaci pneumonia diagnosis and better prognosis.

METHODS: Thirty-seven patients diagnosed with atypical CAP were enrolled in this retrospective study, including 14 C. psittaci pneumonia and 23 Legionella pneumophila (L. pneumophila) pneumonia. We collected and compared baseline, lab results, radiology imaging, conventional microbiological methods and more importantly, mNGS results of clinical samples, as well as the treatments and prognosis between psittacosis and legionellosis.

RESULTS: Patients with C. psittaci and L. pneumophila had similar symptoms and were presented with high levels of inflammatory markers. However, patients with C. psittaci pneumonia were more likely to have exposure to birds or parrots [11 (78.6%) vs. 2 (8.7%), p < 0.001], had higher proportions of fever and chill (p = 0.015 and 0.035), higher levels of hemoglobin and albumin (p = 0.002 and 0.018) compared with those with L. pneumophila. Of 14 C. psittaci patients, only one had positive IgM antibody, with no positive cultures. Early identification of pathogens by mNGS method contributed to timely antibiotics' adjustment and better outcomes then, yet with similar hospital mortality between two groups [7.1% (1/14) vs. 34.8% (8/23), p = 0.112].

CONCLUSION: Early mNGS detection of atypical pathogens in multiple samples improves on traditional methods, promptly adjust empirical antimicrobial treatment to pathogen-targeted antibiotics, further improve prognosis.}, } @article {pmid39541261, year = {2024}, author = {Golob, J and Rao, K and Berinstein, JA and Singh, P and Chey, WD and Owyang, C and Kamada, N and Higgins, PDR and Young, V and Bishu, S and Lee, AA}, title = {Why Symptoms Linger in Quiescent Crohn's Disease: Investigating the Impact of Sulfidogenic Microbes and Sulfur Metabolic Pathways.}, journal = {Inflammatory bowel diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/ibd/izae238}, pmid = {39541261}, issn = {1536-4844}, support = {K23 DK124567/DK/NIDDK NIH HHS/United States ; R03 DK139095/DK/NIDDK NIH HHS/United States ; /CCF/CCF/United States ; DK124567/NH/NIH HHS/United States ; }, abstract = {INTRODUCTION: Even in the absence of inflammation, persistent symptoms in patients with Crohn's disease (CD) are prevalent and worsen quality of life. We previously demonstrated enrichment in sulfidogenic microbes in quiescent Crohn's disease patients with (qCD + S) vs without persistent GI symptoms (qCD-S). Thus, we hypothesized that sulfur metabolic pathways would be enriched in stool while differentially abundant microbes would be associated with important sulfur metabolic pathways in qCD + S.

METHODS: We performed a multicenter observational study nested within SPARC IBD. Quiescent inflammation was defined by fecal calprotectin level < 150 mcg/g. Persistent symptoms were defined by CD-PRO2. Active CD (aCD) and non-IBD diarrhea-predominant irritable bowel syndrome (IBS-D) were included as controls.

RESULTS: Thirty-nine patients with qCD + S, 274 qCD-S, 21 aCD, and 40 IBS-D underwent paired shotgun metagenomic sequencing and untargeted metabolomic profiling. The fecal metabolome in qCD + S was significantly different relative to qCD-S and IBS-D but not aCD. Patients with qCD + S were enriched in sulfur-containing amino acid pathways, including cysteine and methionine, as well as serine, glycine, and threonine. Glutathione and nicotinate/nicotinamide pathways were also enriched in qCD + S relative to qCD-S, suggestive of mitochondrial dysfunction, a downstream target of H2S signaling. Multi-omic integration demonstrated that enriched microbes in qCD + S were associated with important sulfur metabolic pathways. Bacterial sulfur metabolic genes, including CTH, isfD, sarD, and asrC, were dysregulated in qCD + S. Finally, sulfur metabolites with and without sulfidogenic microbes showed good accuracy in predicting the presence of qCD + S.

DISCUSSION: Microbial-derived sulfur pathways and downstream mitochondrial function are perturbed in qCD + S, which implicate H2S signaling in the pathogenesis of this condition. Future studies will determine whether targeting H2S pathways results in improved quality of life in qCD + S.}, } @article {pmid39540836, year = {2024}, author = {Charles, P and Kumar, S and Girish Kumar, CP and Parameswaran, S and Viswanathan, P and Nachiappa Ganesh, R}, title = {Association of gut microbiota with allograft injury in kidney transplant recipients: a comparative profiling through 16S metagenomics and quantitative PCR.}, journal = {Journal of medical microbiology}, volume = {73}, number = {11}, pages = {}, doi = {10.1099/jmm.0.001934}, pmid = {39540836}, issn = {1473-5644}, mesh = {Humans ; *Kidney Transplantation/adverse effects ; *Gastrointestinal Microbiome ; Male ; *RNA, Ribosomal, 16S/genetics ; Female ; Middle Aged ; *Metagenomics/methods ; Adult ; Prospective Studies ; Longitudinal Studies ; *Graft Rejection/microbiology ; Real-Time Polymerase Chain Reaction/methods ; Bacteria/classification/genetics/isolation & purification ; Feces/microbiology ; Allografts/microbiology ; Transplant Recipients ; }, abstract = {Introduction. The existence of a mutual relationship between gut microbiota and immune homeostasis highlights its importance in the context of kidney transplantation.Gap statement. The translational utility of gut microbiota as a biomarker for allograft injury has not been assessed before.Aim. In this study, we aimed to characterize the gut microbial diversity in kidney transplant recipients and investigate the alterations in the gut microbial composition in association with allograft injury such as histopathological graft rejection and calcineurin inhibitor toxicity. In addition, we compared the gut microbial quantitation using 16S metagenomics and quantitative PCR (qPCR) to assess its translational utility.Methodology. In this prospective longitudinal cohort study, we enrolled 38 kidney transplant recipients and collected serial faecal specimens (n=114), once before the induction therapy, and twice after transplant, during the first and third month. We characterized the gut microbial composition through 16S rRNA sequencing and qPCR from the DNA isolates of the samples. The recipients were clinically followed up for a median of 600 days post-transplant. Histopathological evidence of allograft rejection and calcineurin inhibitor toxicity were used for the correlational analysis with gut microbial diversity.Results. Significant differences in the gut microbial diversity were observed between the pre- and post-transplant samples. Pre-transplant gut microbiota revealed a higher relative abundance of phylum Bacteroidetes in the allograft rejection group, and a higher relative abundance of phylum Firmicutes was observed in the histopathological features of calcineurin inhibitor toxicity (hCNI toxicity) group. We found a high concordance between 16S metagenomics and qPCR outputs for assessing the gut microbial diversity. Furthermore, the receiver operating characteristic curve analysis has also proven that the pre-transplant levels of gut microbial dysbiosis, as a potential predictive biomarker for allograft injury.Conclusion. Our pilot study found a strong statistical association of gut microbial dysbiosis with kidney allograft injury, highlighting the potential of gut microbiota as a predictive biomarker and that qPCR serves as a more reliable and economic tool for assessing dysbiosis paving the way for its translational utility.}, } @article {pmid39540753, year = {2024}, author = {Zhang, T and Liu, Y and Guo, X and Zhang, X and Zheng, X and Zhang, M and Bao, Y}, title = {VISTA: A Tool for Fast Taxonomic Assignment of Viral Genome Sequences.}, journal = {Genomics, proteomics & bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1093/gpbjnl/qzae082}, pmid = {39540753}, issn = {2210-3244}, abstract = {The rapid expansion of the number of viral genome sequences in public databases necessitates a scalable, universal, and automated preliminary taxonomic framework for comprehensive virus studies. Here, we introduce VISTA (Virus Sequence-based Taxonomy Assignment), a computational tool that employs a novel pairwise sequence comparison system and an automatic demarcation threshold identification framework for virus taxonomy. Leveraging physio-chemical property sequences, k-mer profiles, and machine learning techniques, VISTA constructs a robust distance-based framework for taxonomic assignment. Functionally similar to PASC (Pairwise Sequence Comparison), a widely used virus assignment tool based on pairwise sequence comparison, VISTA demonstrates superior performance by providing significantly improved separation for taxonomic groups, more objective taxonomic demarcation thresholds, greatly enhanced speed, and a wider application scope. We successfully applied VISTA to 38 virus families, as well as to the class Caudoviricetes. This demonstrates VISTA's scalability, robustness, and ability to automatically and accurately assign taxonomy to both prokaryotic and eukaryotic viruses. Furthermore, the application of VISTA to 679 unclassified prokaryotic virus genomes recovered from metagenomic data identified 46 novel virus families. VISTA is available as both a command line tool and a user-friendly web portal at https://ngdc.cncb.ac.cn/vista.}, } @article {pmid39540749, year = {2024}, author = {Pavia, MJ and Garber, AI and Avalle, S and Macedo-Tafur, F and Tello-Espinoza, R and Cadillo-Quiroz, H}, title = {Functional insights of novel Bathyarchaeia reveal metabolic versatility in their role in peatlands of the Peruvian Amazon.}, journal = {Microbiology spectrum}, volume = {12}, number = {12}, pages = {e0038724}, pmid = {39540749}, issn = {2165-0497}, abstract = {UNLABELLED: The decomposition of soil organic carbon within tropical peatlands is influenced by the functional composition of the microbial community. In this study, building upon our previous work, we recovered a total of 28 metagenome-assembled genomes (MAGs) classified as Bathyarchaeia from the tropical peatlands of the Pastaza-Marañón Foreland Basin (PMFB) in the Amazon. Using phylogenomic analyses, we identified nine genus-level clades to have representatives from the PMFB, with four forming a putative novel family ("Candidatus Paludivitaceae") endemic to peatlands. We focus on the Ca. Paludivitaceae MAGs due to the novelty of this group and the limited understanding of their role within tropical peatlands. Functional analysis of these MAGs reveals that this putative family comprises facultative anaerobes, possessing the genetic potential for oxygen, sulfide, or nitrogen oxidation. This metabolic versatility can be coupled to the fermentation of acetoin, propanol, or proline. The other clades outside Ca. Paludivitaceae are putatively capable of acetogenesis and de novo amino acid biosynthesis and encode a high amount of Fe[3+] transporters. Crucially, the Ca. Paludivitaceae are predicted to be carboxydotrophic, capable of utilizing CO for energy generation or biomass production. Through this metabolism, they could detoxify the environment from CO, a byproduct of methanogenesis, or produce methanogenic substrates like CO2 and H2. Overall, our results show the complex metabolism and various lineages of Bathyarchaeia within tropical peatlands pointing to the need to further evaluate their role in these ecosystems.

IMPORTANCE: With the expansion of the Candidatus Paludivitaceae family by the assembly of 28 new metagenome assembled genomes, this study provides novel insights into their metabolic diversity and ecological significance in peatland ecosystems. From a comprehensive phylogenic and functional analysis, we have elucidated their putative unique facultative anaerobic capabilities and CO detoxification potential. This research highlights their crucial role in carbon cycling and greenhouse gas regulation. These findings are essential for resolving the microbial processes affecting peat soil stability, offering new perspectives on the ecological roles of previously underexplored and underrepresented archaeal populations.}, } @article {pmid39540745, year = {2024}, author = {Huang, Y and Schomer, R and Reyes, MJR and Costa, K and Parales, RE and Whitaker, R and Dawson, SC}, title = {Metagenome-assembled genomes of freshwater Hyphomicrobium sp. G-191 and Methylophilus sp. enriched from Cedar Swamp, Woods Hole, MA.}, journal = {Microbiology resource announcements}, volume = {13}, number = {12}, pages = {e0060824}, pmid = {39540745}, issn = {2576-098X}, support = {22055876//National Science Foundation (NSF)/ ; //Gordon and Betty Moore Foundation (GBMF)/ ; //Simons Foundation (SF)/ ; //U.S. Department of Energy (DOE)/ ; }, abstract = {Hyphomicrobium are facultative denitrifying anaerobes capable of using one-carbon compounds as a sole carbon source. Hyphomicrobium sp. G-191 was enriched from Cedar Swamp, Woods Hole, Massachusetts, using a selective medium for methanol-utilizing bacteria. We present two draft metagenome-assembled genomes (MAGs) of a Hyphomicrobium and a Methylophilus species.}, } @article {pmid39540551, year = {2024}, author = {Vepštaitė-Monstavičė, I and Lukša, J and Strazdaitė-Žielienė, Ž and Serva, S and Servienė, E}, title = {Distinct microbial communities associated with health-relevant wild berries.}, journal = {Environmental microbiology reports}, volume = {16}, number = {6}, pages = {e70048}, pmid = {39540551}, issn = {1758-2229}, support = {S-PD-22-85//Lithuanian Research Council (LMTLT)/ ; }, mesh = {*Fruit/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Fungi/classification/genetics/isolation & purification ; *Microbiota ; Vaccinium vitis-idaea/chemistry/microbiology/genetics ; High-Throughput Nucleotide Sequencing ; Rosa/microbiology ; Phylogeny ; }, abstract = {Lingonberries (Vaccinium vitis-idaea L.), rowanberries (Sorbus aucuparia L.) and rosehips (Rosa canina L.) positively affect human health due to their healing properties, determined by a high content of bioactive compounds. The consumption of unprocessed wild berries is relevant and encouraged, making their in-depth microbiological characterization essential for food safety. This study presents the first high-throughput sequencing analysis of bacterial and fungal communities distributed on the surface of lingonberries, rowanberries and rosehips. Significant plant-defined differences in the taxonomic composition of prokaryotic and eukaryotic microbiota were observed. The bacterial community on rosehips was shown to be prevalent by Enterobacteriaceae, lingonberries by Methylobacteriaceae and rowanberries by Sphingomonadaceae representatives. Among the fungal microbiota, Dothioraceae dominated on rosehips and Exobasidiaceae on lingonberries; meanwhile, rowanberries were inhabited by a similar level of a broad spectrum of fungal families. Cultivable yeast profiling revealed that lingonberries were distinguished by the lowest amount and most distinct yeast populations. Potentially pathogenic to humans or plants, as well as beneficial and relevant biocontrol microorganisms, were identified on tested berries. The combination of metagenomics and a cultivation-based approach highlighted the wild berries-associated microbial communities and contributed to uncovering their potential in plant health, food and human safety.}, } @article {pmid39540428, year = {2025}, author = {Paysan-Lafosse, T and Andreeva, A and Blum, M and Chuguransky, SR and Grego, T and Pinto, BL and Salazar, GA and Bileschi, ML and Llinares-López, F and Meng-Papaxanthos, L and Colwell, LJ and Grishin, NV and Schaeffer, RD and Clementel, D and Tosatto, SCE and Sonnhammer, E and Wood, V and Bateman, A}, title = {The Pfam protein families database: embracing AI/ML.}, journal = {Nucleic acids research}, volume = {53}, number = {D1}, pages = {D523-D534}, pmid = {39540428}, issn = {1362-4962}, support = {221320/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; 823886//European Union's H2020 Marie Skłodowska-Curie Actions/ ; //European Molecular Biology Laboratory/ ; 2224128//National Science Foundation/ ; BB/X012492/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; //European Union-NextGenerationEU/ ; IR0000010//ElixirxNextGenIT/ ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Databases, Protein ; *Proteins/chemistry/classification/genetics ; Molecular Sequence Annotation ; Protein Domains ; Sequence Analysis, Protein ; Artificial Intelligence ; Deep Learning ; Software ; }, abstract = {The Pfam protein families database is a comprehensive collection of protein domains and families used for genome annotation and protein structure and function analysis (https://www.ebi.ac.uk/interpro/). This update describes major developments in Pfam since 2020, including decommissioning the Pfam website and integration with InterPro, harmonization with the ECOD structural classification, and expanded curation of metagenomic, microprotein and repeat-containing families. We highlight how AlphaFold structure predictions are being leveraged to refine domain boundaries and identify new domains. New families discovered through large-scale sequence similarity analysis of AlphaFold models are described. We also detail the development of Pfam-N, which uses deep learning to expand family coverage, achieving an 8.8% increase in UniProtKB coverage compared to standard Pfam. We discuss plans for more frequent Pfam releases integrated with InterPro and the potential for artificial intelligence to further assist curation. Despite recent advances, many protein families remain to be classified, and Pfam continues working toward comprehensive coverage of the protein universe.}, } @article {pmid39539714, year = {2024}, author = {Hauptmann, AL and Johansen, J and Stæger, FF and Nielsen, DS and Mulvad, G and Hanghøj, K and Rasmussen, S and Hansen, T and Albrechtsen, A}, title = {Gut heavy metal and antibiotic resistome of humans living in the high Arctic.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1493803}, pmid = {39539714}, issn = {1664-302X}, abstract = {Contaminants, such as heavy metals (HMs), accumulate in the Arctic environment and the food web. The diet of the Indigenous Peoples of North Greenland includes locally sourced foods that are central to their nutritional, cultural, and societal health but these foods also contain high concentrations of heavy metals. While bacteria play an essential role in the metabolism of xenobiotics, there are limited studies on the impact of heavy metals on the human gut microbiome, and it is so far unknown if and how Arctic environmental contaminants impact the gut microbes of humans living in and off the Arctic environment. Using a multiomics approach including amplicon, metagenome, and metatranscriptome sequencing, we identified and assembled a near-complete (NC) genome of a mercury-resistant bacterial strain from the human gut microbiome, which expressed genes known to reduce mercury toxicity. At the overall ecological level studied through α- and β-diversity, there was no significant effect of heavy metals on the gut microbiota. Through the assembly of a high number of NC metagenome-assembled genomes (MAGs) of human gut microbes, we observed an almost complete overlap between heavy metal-resistant strains and antibiotic-resistant strains in which resistance genes were all located on the same genetic elements.}, } @article {pmid39538984, year = {2024}, author = {Zhang, Y and Song, Z and Schilling, JS}, title = {Evaluation of DNA Extraction Methods for Microbial Community Profiling in Deadwood Decomposition.}, journal = {MicrobiologyOpen}, volume = {13}, number = {6}, pages = {e70007}, pmid = {39538984}, issn = {2045-8827}, support = {//Funding for the study was provided by a Jr. Faculty grant to J.S.S. from the Andrew W. Mellon Foundation (New York, NY)./ ; }, mesh = {*Wood/microbiology ; *Fungi/genetics/classification/isolation & purification ; *Bacteria/genetics/classification/isolation & purification ; *Betula/microbiology ; *DNA, Fungal/genetics ; *Microbiota/genetics ; Pinus/microbiology ; DNA, Bacterial/genetics ; Metagenomics/methods ; Sequence Analysis, DNA/methods ; }, abstract = {As technologies advance alongside metabarcoding and metagenomic resources, particularly for larger fungal genomes, DNA extraction methods must be optimized to meet higher thresholds, especially from complex environmental substrates. This study focused on extracting fungal genomic compounds from woody substrates, a challenge due to the embedment of endophytic and saprotrophic fungi within wood cells, the physical recalcitrance of wood, the adsorption of nucleic acids to wood polymers, and the release of downstream inhibitors. Hypothesizing that cetyltrimethylammonium bromide would be the best option, we compared prominent methods by extracting and sequencing microbial DNA from sound and decayed birch (Betula papyrifera) and pine (Pinus resinosa). DNA quantities varied significantly depending on extraction methods and decay stage. The quality of DNA, in terms of purity and integrity, significantly impacted whether the samples could be amplified and sequenced. However, amplicon sequencing of bacterial and fungal communities revealed no significant extraction bias. This, along with the sequencing effectiveness and cost/time efficiency, indicates that Qiagen is the gold standard for woody substrates. This study increases confidence in published amplicon data sets regardless of the extraction methods, provides a cost-benefit table for making protocol decisions, and offers guidance on fungal DNA extractions from complex organic substrates (sound and decayed wood) that would best suit future metagenomic efforts.}, } @article {pmid39538360, year = {2024}, author = {Malik, M and Chiers, K and Chantziaras, I and Maes, D}, title = {Porcine ear necrosis in nursery piglets is preceded by oral manipulations of the ear.}, journal = {Porcine health management}, volume = {10}, number = {1}, pages = {51}, pmid = {39538360}, issn = {2055-5660}, abstract = {BACKGROUND: Porcine ear necrosis (PEN) is characterized by dry crusts on the ear tip. The crusts often progress to moist and bloody lesions and may lead to partial loss of the ear tissue. The cause and pathophysiology of PEN are unknown. Skin infections, systemic infections, or ear biting have been suggested as a cause of PEN, but no proper evidence has been shown. The behavioural factor has not yet been investigated, therefore this study evaluated the importance of oral manipulations in the occurrence of PEN in nursery pigs. Three farms affected by PEN were visited weekly, and the prevalence and severity were recorded. Video recordings of the animals were performed, and the behaviour was evaluated. The presence of pathogens in the lesions and histological alterations were also analysed.

RESULTS: The highest percentage of pigs with PEN lesions in the farms ranged between 58 and 93%, with most lesions being of mild to moderate severity. The first ear lesions occurred about 1-2 weeks after an increase in the number of ear manipulations in the pens. The frequency of the ear manipulations clearly changed over time, and the number of oral ear manipulation behaviour significantly differed (P < 0.05) between pigs in pens with high and low PEN prevalence. Increased ear manipulation behaviour was significantly related to a subsequent increase in PEN lesions (OR = 4.3; P < 0.001). Metagenomic investigation of lesion scrapings revealed a variety of pathogens mostly with low abundance, where microscopic alterations were found mainly in the epidermis.

CONCLUSIONS: Oral manipulation of the ear pinnae by pen mates was followed by the development of PEN lesions one to two weeks later. This suggests that the behaviour played an important role in the PEN lesions formation in the nursery pigs of the three farms. Bacteria found in PEN lesions most probably were secondary to initial external skin damage, but their relevance needs to be investigated further.}, } @article {pmid39538341, year = {2024}, author = {Pearce, CS and Bukovsky, D and Douchant, K and Katoch, A and Greenlaw, J and Gale, DJ and Nashed, JY and Brien, D and Kuhlmeier, VA and Sabbagh, MA and Blohm, G and De Felice, FG and Pare, M and Cook, DJ and Scott, SH and Munoz, DP and Sjaarda, CP and Tusche, A and Sheth, PM and Winterborn, A and Boehnke, S and Gallivan, JP}, title = {Changes in social environment impact primate gut microbiota composition.}, journal = {Animal microbiome}, volume = {6}, number = {1}, pages = {66}, pmid = {39538341}, issn = {2524-4671}, support = {NFREF-2021-00936//New Frontiers in Research Fund/ ; }, abstract = {BACKGROUND: The gut microbiota (GM) has proven to be essential for both physical health and mental wellbeing, yet the forces that ultimately shape its composition remain opaque. One critical force known to affect the GM is the social environment. Prior work in humans and free-ranging non-human primates has shown that cohabitation and frequent social interaction can lead to changes in GM composition. However, it is difficult to assess the direction of causation in these studies, and interpretations are complicated by the influence of uncontrolled but correlated factors, such as shared diet.

RESULTS: We performed a 15-month longitudinal investigation wherein we disentangled the impacts of diet and social living conditions on GM composition in a captive cohort of 13 male cynomolgus macaques. The animals were in single housing for the first 3 months of the study initially with a variable diet. After baseline data collection they were placed on a controlled diet for the remainder of the study. Following this diet shift the animals were moved to paired housing for 6 months, enabling enhanced social interaction, and then subsequently returned to single housing at the end of our study. This structured sequencing of diet and housing changes allowed us to assess their distinct impacts on GM composition. We found that the early dietary adjustments led to GM changes in both alpha and beta diversity, whereas changes in social living conditions only altered beta diversity. With respect to the latter, we found that two particular bacterial families - Lactobacillaceae and Clostridiaceae - demonstrated significant shifts in abundance during the transition from single housing to paired housing, which was distinct from the shifts we observed based on a change in diet. Conversely, we found that other bacteria previously associated with sociality were not altered based on changes in social living conditions but rather only by changes in diet.

CONCLUSIONS: Together, these findings decouple the influences that diet and social living have on GM composition and reconcile previous observations in the human and animal literatures. Moreover, the results indicate biological alterations of the gut that may, in part, mediate the relationship between sociality and wellbeing.}, } @article {pmid39538316, year = {2024}, author = {Krasnikov, N and Gulyukin, A and Aliper, T and Yuzhakov, A}, title = {Complete genome characterization by nanopore sequencing of rotaviruses A, B, and C circulating on large-scale pig farms in Russia.}, journal = {Virology journal}, volume = {21}, number = {1}, pages = {289}, pmid = {39538316}, issn = {1743-422X}, support = {FGUG-2022-0018//Federal State Budget Scientific Institution "Federal Scientific Center VIEV", Moscow, Russia./ ; FGUG-2022-0018//Federal State Budget Scientific Institution "Federal Scientific Center VIEV", Moscow, Russia./ ; FGUG-2022-0018//Federal State Budget Scientific Institution "Federal Scientific Center VIEV", Moscow, Russia./ ; FGUG-2022-0018//Federal State Budget Scientific Institution "Federal Scientific Center VIEV", Moscow, Russia./ ; }, mesh = {Animals ; Swine ; *Rotavirus/genetics/classification/isolation & purification ; *Phylogeny ; *Genome, Viral ; *Nanopore Sequencing ; *Genotype ; *Swine Diseases/virology/epidemiology ; *Rotavirus Infections/virology/veterinary/epidemiology ; Russia/epidemiology ; Farms ; Whole Genome Sequencing ; Feces/virology ; RNA, Viral/genetics ; Metagenomics ; }, abstract = {BACKGROUND: Rotaviruses are the major etiological agents of gastroenteritis and diarrheal outbreaks in plenty of mammalian species. The genus Rotavirus is highly diverse and currently comprises nine genetically distinct species, and four of them (A, B, C, and H) are common for humans and pigs. There is a strong necessity to comprehend phylogenetic relationships among rotaviruses from different host species to assess interspecies transmission, specifically between humans and livestock. To reveal the genetic origin of rotaviruses from Russian pig farms, nanopore-based metagenomic sequencing was performed on the PCR-positive specimens.

METHODS: Samples were selected among the cases submitted to routine diagnostic or monitoring studies to the Laboratory of Biochemistry and Molecular Biology of "Federal Scientific Center VIEV" (Moscow, Russia). The selected positive samples were genotyped using nanopore sequencing method.

RESULTS: Five porcine RVA isolates were completely sequenced, and genotype analysis revealed various porcine G/P genogroups: G2, G3, G4, G5, G11 and P[6], P[7], P[13], P[23], P[27] with a typical backbone constellation I5-R1-C1-M1-A8-N1-T1/7-E1-H1. The RVB isolate was detected in combination with RVA in a rectal swab from a diseased pig in Krasnoyarsk Krai. It was characterized by the following genogroups: G15-P[X]-I11-R4-C4-M4-A8-N10-T4-E4-H7. The first complete porcine RVC genome from Russia was obtained with genomic constellation G6-P[5]-I14-R1-C1-M1-A7-N9-T6-E1-H1, and the phylogenetic analysis revealed putative novel genotype group for the VP6 gene-I14. Additionally, the first porcine kobuvirus isolate from Russia was phylogenetically characterized.

CONCLUSIONS: The applied nanopore sequencing method successfully genotyped the RV isolates and additionally revealed co-circulated species. The study demonstrates high genetic variability of Russian RVA isolates in VP4/VP7 genes and phylogenetically describes local RVB and RVC. Complete characterization of genomic segments is a crucial methodology in tracing the rotavirus's evolution and evaluating interspecies transmissions.}, } @article {pmid39538074, year = {2024}, author = {Pradhan, SS and Mahanty, A and Senapati, A and Mohapatra, PK and Adak, T}, title = {Influence of combined application of tetracycline and streptomycin on microbial diversity and function in rice soil.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {55}, pages = {64358-64373}, pmid = {39538074}, issn = {1614-7499}, mesh = {*Oryza ; *Soil Microbiology ; *Streptomycin/pharmacology ; *Soil/chemistry ; *Tetracycline ; Soil Pollutants ; Anti-Bacterial Agents/pharmacology ; }, abstract = {A microcosm experiment was performed to quantify the residues of antibiotics [tetracycline (TC), streptomycin (STR), and streptocycline (STC; a mixture of TC and STR)] in rice soil and to assess their impact on microbial community structure and function using Illumina-MiSeq metagenomic analysis. Antibiotics were applied at half the recommended dose (0.5RD), recommended dose (RD), and double the recommended dose (2RD). At RD, TC was degraded in soil within 9 days of its application, whereas it took 21 days for STR and STC to degrade below limit of quantification (LOQ) level. The residue data were fitted in decay models, and half-lives (DT50) were 46.5-53.3 h and 177.6-198 h for TC and STR, respectively. Soil enzyme activities (dehydrogenase, β-glucosidase, fluorescein diacetate hydrolase, acid phosphatase, alkaline phosphatase) were negatively affected in the antibiotic-treated soil. Targeted metagenomic analysis showed that the major bacterial phyla such as Chloroflexi, Actinobacteria, Planctomycetes, Crenarchaeota, and Gemmatimonadetes were suppressed by antibiotic treatments as compared to control. Shannon, Simpson, ACE, and Chao1 diversity indices showed that bacterial diversity decreased with the application of antibiotics, and decrease in bacterial diversity was more prominent in case of STC as compared to TC and STR. Overall, the combination of antibiotics negatively affected the soil microbial community structure and function in comparison to their individual application.}, } @article {pmid39537963, year = {2024}, author = {Sitthideatphaiboon, P and Somlaw, N and Zungsontiporn, N and Ouwongprayoon, P and Sukswai, N and Korphaisarn, K and Poungvarin, N and Aporntewan, C and Hirankarn, N and Vinayanuwattikun, C and Chanida, V}, title = {Dietary pattern and the corresponding gut microbiome in response to immunotherapy in Thai patients with advanced non-small cell lung cancer (NSCLC).}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {27791}, pmid = {39537963}, issn = {2045-2322}, support = {N35A660426//National Research Council of Thailand/ ; RA-MF-04/67//Rachadapisek Sompote Matching fund, Chulalongkorn University/ ; }, mesh = {Adult ; Aged ; Female ; Humans ; Male ; Middle Aged ; *Carcinoma, Non-Small-Cell Lung/drug therapy/microbiology/pathology ; *Diet ; Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; Immune Checkpoint Inhibitors/therapeutic use ; *Immunotherapy/methods ; *Lung Neoplasms/microbiology/drug therapy/pathology ; Progression-Free Survival ; Prospective Studies ; Southeast Asian People ; Thailand ; }, abstract = {Gut microbiota is considered a key player modulating the response to immune checkpoint inhibitors (ICI) in cancer. The effects of dietary pattern on this interaction is not well-studied. A prospective multicenter cohort of 95 patients with advanced non-small cell lung cancer (NSCLC) undergoing ICI therapy were enrolled. Stool shotgun metagenomic sequencing was performed. Three-day dietary patterns before ICI were assessed. Patients were categorized as hyperprogressive disease (HPD) if they exhibited a time to treatment failure of less than 2 months. All others were categorized as non-hyperprogressive disease (non-HPD). The correlation between dietary patterns, gut microbiome, and response to ICI therapy was analyzed. In the multivariate analysis, a high abundance of Firmicutes unclassified and the Ruminococcaceae family correlated with a significantly diminished progression-free survival (PFS) with an HR of 2.40 [P = 0.006] and 4.30 [P = 0.005], respectively. More specifically, within the subset of NSCLC patients treated solely with ICI therapy, a high abundance of Intestinimonas and the Enterobacteriaceae family were associated with substantially reduced PFS with an HR of 2.61 [P = 0.02] and HR 3.34 [P = 0.005], respectively. In our comprehensive dietary pattern analysis, the HPD group showed increased consumption of cholesterol, sodium, and fats beyond recommended levels compared to the non-HPD group. This group also displayed a tendency towards higher food pattern scores characterized by a high intake of fat and dairy products. Our study revealed a distinct association between the gut microbiome composition and treatment outcomes. The overall composition of diet might be related to ICI therapeutic outcomes.}, } @article {pmid39537661, year = {2024}, author = {Li, Z and Chen, J and Li, Y and Li, L and Zhan, Y and Yang, J and Wu, H and Li, S and Mo, X and Wang, X and Mi, Y and Zhou, X and Li, Y and Wang, J and Li, Y and Sun, R and Cai, W and Ye, F}, title = {Impact of SARS-CoV-2 infection on respiratory and gut microbiome stability: a metagenomic investigation in long-term-hospitalized COVID-19 patients.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {126}, pmid = {39537661}, issn = {2055-5008}, mesh = {Humans ; *COVID-19/microbiology/virology ; *Gastrointestinal Microbiome/genetics ; *SARS-CoV-2/genetics ; Male ; Middle Aged ; Female ; Aged ; *Metagenomics/methods ; Feces/microbiology/virology ; High-Throughput Nucleotide Sequencing ; Adult ; Hospitalization ; Bacteria/classification/genetics/isolation & purification ; Sputum/microbiology/virology ; Respiratory System/microbiology/virology ; Metagenome ; }, abstract = {During the coronavirus disease 2019 (COVID-19) pandemic, the exploration of microecology has been essential for elucidating the intricacies of infection mechanisms and the recovery of afflicted individuals. To decipher the interplay of microorganisms between the intestinal and respiratory tracts, we collected sputum and throat swabs and feces from COVID-19 patients and explored the mutual migration among intestinal and respiratory microorganisms. Using next-generation sequencing (NGS) technology, we investigated intestinal and respiratory microorganism intermigration in two patients with severe COVID-19 during their hospitalization. Notably, we observed an expedited recovery of microecological equilibrium in one patient harboring Mycobacterium avium. Comparative analyses between 32 healthy controls and 110 COVID-19 patients with different disease severities revealed alterations in predominant microorganisms inhabiting the respiratory and intestinal tracts of COVID-19 patients. Among the alterations, intestinal Bacteroides vulgatus (BV) was identified as a noteworthy microorganism that exhibited marked enrichment in patients with severe COVID-19. BV, when highly abundant, may inhibit the transitional growth of Escherichia coli/Enterococcus, indirectly prevent the overgrowth of salivary streptococci, and maintain lung/intestinal microecology stability. In summary, this study elucidates the bidirectional microbial intermigration between the intestinal and respiratory tracts in COVID-19 patients. These findings are expected to provide new ideas for the treatment and management of COVID-19, underscoring the essential role of microecology in infectious diseases. Nevertheless, a systematic study of the roles of BV in recovery from infection is required to gain a deeper understanding of the mechanisms of microbial migration.}, } @article {pmid39537082, year = {2024}, author = {Chettri, D and Verma, AK and Chirania, M and Verma, AK}, title = {Metagenomic approaches in bioremediation of environmental pollutants.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {363}, number = {Pt 2}, pages = {125297}, doi = {10.1016/j.envpol.2024.125297}, pmid = {39537082}, issn = {1873-6424}, mesh = {*Biodegradation, Environmental ; *Metagenomics/methods ; *Environmental Pollutants/metabolism ; Artificial Intelligence ; Microbiota ; }, abstract = {Metagenomics has emerged as a pivotal tool in bioremediation, providing a deeper understanding of the structure and function of the microbial communities involved in pollutant degradation. By circumventing the limitations of traditional culture-based methods, metagenomics enables comprehensive analysis of microbial ecosystems and facilitates the identification of new genes and metabolic pathways that are critical for bioremediation. Advanced sequencing technologies combined with computational and bioinformatics approaches have greatly enhanced our ability to detect sources of pollution and monitor dynamic changes in microbial communities during the bioremediation process. These tools enable the precise identification of key microbial players and their functional roles, and provide a deeper understanding of complex biodegradation networks. The integration of artificial intelligence (AI) with machine learning algorithms has accelerated the process of discovery of novel genes associated with bioremediation and has optimized metabolic pathway prediction. Novel strategies, including sequencing techniques and AI-assisted analysis, have the potential to revolutionize bioremediation by enabling the development of highly efficient, targeted, and sustainable remediation strategies for various contaminated environments. However, the complexity of microbial interactions, data interpretation, and high cost of these advanced technologies remain challenging. Future research should focus on improving computational tools, reducing costs, and integrating multidisciplinary approaches to overcome these limitations.}, } @article {pmid39537028, year = {2025}, author = {Liu, L and Nguyen, SM and Wang, L and Shi, J and Long, J and Cai, Q and Shrubsole, MJ and Shu, XO and Zheng, W and Yu, D}, title = {Associations of alcohol intake with gut microbiome: a prospective study in a predominantly low-income Black/African American population.}, journal = {The American journal of clinical nutrition}, volume = {121}, number = {1}, pages = {134-140}, pmid = {39537028}, issn = {1938-3207}, support = {P30 CA068485/CA/NCI NIH HHS/United States ; R01 CA275864/CA/NCI NIH HHS/United States ; R01 DK126721/DK/NIDDK NIH HHS/United States ; U01 CA202979/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; *Alcohol Drinking ; *Black or African American ; Feces/microbiology ; *Gastrointestinal Microbiome ; Poverty ; Prospective Studies ; }, abstract = {BACKGROUND: Alcohol intake can alter gut microbiome, which may subsequently affect human health. However, limited population-based, prospective studies have investigated associations of habitual and recent alcohol intake with the gut microbiome, particularly among Black/African American individuals.

OBJECTIVE: We examined the association of alcohol intake with gut microbiome in a predominantly low-income Black/African American population.

METHODS: We investigated the dose- and type-specific associations of habitual and recent alcohol intake with the gut microbiome among 538 Black/African American adults (150 males and 388 females). Habitual and recent alcohol intakes were assessed at cohort baseline (2002-2009) and stool collection (2018-2021), respectively. Gut microbiome was profiled using shotgun metagenomic sequencing. Generalized linear models were employed to evaluate the associations between alcohol intakes and gut microbiome composition, with adjustments for sociodemographic characteristics, other lifestyle factors, and comorbidities. False discovery rate (FDR) <0.1 was considered statistically significant.

RESULTS: The mean age at enrollment was 53.2 ± 7.7 y, with a mean interval of 13.8 y (range: 9.0-18.1 y) between baseline and stool sample collection. Recent alcohol intake was not significantly associated with microbial taxa abundance. However, habitual alcohol intake, both total amount and types of alcoholic beverages, showed significant associations with several microbial taxa abundance, primarily in males, including species within classes Clostridia, Bacilli, and Mahellia within Firmicutes. Specifically, total alcohol, beer, and red wine intakes were all inversely associated with genus MGYG-HGUT-02719 within class Clostridia (β = -2.26 to -0.09 per 1 drink/d increase). Red wine consumption was also inversely associated with the abundance of genera CAG-110, Oscillibacter, and Gemmiger within class Clostridia (β = -3.88 to -2.69), whereas positively associated with genus Absiella (β = 1.81) within class Bacilli. Most of these associations remained significant after additionally adjusting for BMI and baseline comorbidities.

CONCLUSIONS: We identified gut microbial taxa associated with habitual alcohol intake among Black/African American males, although the magnitudes of these associations were generally small. Further research is needed to determine if these bacteria modify alcohol-disease relationships.}, } @article {pmid39536991, year = {2025}, author = {Li, Z and Gao, W and Yuan, H and Pan, X and Yuan, R and Wang, W and Guan, L and Hu, L and Chen, Y and Cheng, Z and He, R and Zhang, L and Yang, B and Zhu, Q and Liang, M and Seki, E and Lin, R and Chu, H and Yang, L}, title = {Suppression of intestinal Ticam1 ameliorated MASH via Akkermansia muciniphila QAA37749.1 mediated betaine transformation.}, journal = {Biochimica et biophysica acta. Molecular basis of disease}, volume = {1871}, number = {1}, pages = {167571}, doi = {10.1016/j.bbadis.2024.167571}, pmid = {39536991}, issn = {1879-260X}, mesh = {Animals ; Mice ; *Akkermansia ; *Gastrointestinal Microbiome ; *Mice, Knockout ; Intestinal Mucosa/metabolism/microbiology/immunology/pathology ; Diet, High-Fat/adverse effects ; Male ; Fatty Liver/metabolism/pathology ; Mice, Inbred C57BL ; }, abstract = {BACKGROUND & AIMS: Gut inflammation caused by diets could damage the intestinal barrier, which increases the liver exposition to pathogenic substances. Toll-IL-1 receptor (TIR) domain-containing adaptor molecule-1 (Ticam1) is a key molecule in the Toll-like receptors (TLRs) pathway, which is important for the immune defense against pathogens such as bacteria or viruses. In this study, mouse intestinal epithelial cell (IEC) Ticam1 was knocked out to suppress the intestinal inflammation response in metabolic dysfunction-associated steatohepatitis (MASH) to investigate its influence on the development of MASH.

METHODS: The IEC-specific Ticam1 knockout (Ticam1[ΔIEC]) mice and the control (Ticam1[fl/fl]) mice were fed with high-fat high-fructose diet (HFD) for 22 weeks to evaluate the gut alteration and the MASH-associated disorders. The intestinal secreted immunoglobulin A (sIgA) and IgA-secreting immune cells were detected. Shotgun metagenomic sequencing was used to find the gut microbiome shift in different groups. Liquid chromatography mass spectrometry was also performed to evaluate the change of serum metabolites caused by the gut microbiome alteration.

RESULTS: The gut inflammation and gut barrier dysfunction were both alleviated in HFD-fed Ticam1[ΔIEC] mice, which had improved MASH disorders compared with Ticam1[fl/fl]. Additionally, HFD-fed Ticam1[ΔIEC] mice had increased sIgA and intestinal IgA-secreting immune cells. It showed a significantly higher content of Akkermansia muciniphila. We proved that Akkermansia muciniphila encoded a protein named QAA37749.1 that could promote the conversion of choline to betaine, through which the development of MASH was inhibited in HFD-Ticam1[ΔIEC] mice.

CONCLUSION: Deletion of IEC Ticam1 alleviated MASH disorder and gut dysfunction in mice. It enhanced the level of intestinal sIgA and the growth of Akkermansia muciniphila, which supported the betaine transformation by QAA37749.1. Suppressing IEC Ticam1 might be a promising strategy for MASH disorder.}, } @article {pmid39536943, year = {2024}, author = {Fadell, F and Saliba, R and El-Solh, AA}, title = {Bacteriology of Aspiration Pneumonia: The Lung Microbiome and the Changing Microbial Etiology.}, journal = {Seminars in respiratory and critical care medicine}, volume = {45}, number = {6}, pages = {626-633}, doi = {10.1055/s-0044-1792111}, pmid = {39536943}, issn = {1098-9048}, mesh = {Humans ; *Pneumonia, Aspiration/microbiology ; *Microbiota ; Lung/microbiology ; Dysbiosis/microbiology ; }, abstract = {Aspiration pneumonia refers to the process of alveolar inflammation induced by the inhalation of oropharyngeal secretions into the lower respiratory tract. Predisposing factors comprise swallowing dysfunction, impaired cough reflex, and degenerative neurological diseases. Accumulating evidence projects a fading contribution of anaerobic bacteria in aspiration pneumonia at the expense of Gram-negative bacilli, with Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa, becoming the predominant organisms recovered from respiratory specimens. Aspiration of oropharyngeal secretions colonized with respiratory pathogens induces a profound disequilibrium of the lung microbiota resulting in a state of dysbiosis. Understanding this complex temporal variability between microbiome-host associations was only made possible with the introduction of metagenomic sequencing. In this narrative review, we summarize existing knowledge and elaborate on the evolving microbiology of aspiration pneumonia including the link between oral microbiome and pulmonary aspiration. We also highlight the progress and challenges in instituting microbiome-targeted strategies for preventing and treating the sequelae of aspiration pneumonia.}, } @article {pmid39536756, year = {2024}, author = {Poulsen, CE and Vinding, R and Rasmussen, MA and Shah, S and Trivedi, U and Rodriguez, CL and Widdowson, ML and Jiang, J and Poulsen, CS and Eliasen, A and Chawes, B and Bønnelykke, K and Hansen, CHF and Sørensen, SJ and Thorsen, J and Stokholm, J}, title = {No association between the early-life gut microbiota and childhood body mass index and body composition.}, journal = {Med (New York, N.Y.)}, volume = {}, number = {}, pages = {100538}, doi = {10.1016/j.medj.2024.10.015}, pmid = {39536756}, issn = {2666-6340}, abstract = {BACKGROUND: The gut microbiota has been implicated in adult obesity, but the causality is still unclear. It has been hypothesized that an obesity-prone gut microbiota can be established in infancy, but only few studies have examined the early-life gut microbiota in relation to obesity in childhood, and no consistent associations have been reported. Here, we examine the association between the early-life gut microbiota and body mass index (BMI) development and body composition throughout childhood.

METHODS: Gut microbiota from stool were collected from 700 children in the Copenhagen Prospective Studies on Asthma in Childhood2010 (COPSAC2010) cohort at ages of 1 week, 1month, 1 year, 4 years, and 6 years and analyzed by 16S rRNA gene sequencing. Outcomes included BMI World Health Organization (WHO) Z scores (zBMI), overweight (zBMI > 1.04) and obesity (zBMI > 1.64) (0-10 years), and adiposity rebound and body composition from dual-energy X-ray absorptiometry at 6 years.

FINDINGS: The early-life gut microbiota diversity, overall composition, and individual taxon abundances in unsupervised and supervised models were not consistently associated with either current or later BMI Z scores, overweight, obesity, adiposity rebound, or body composition in childhood.

CONCLUSIONS: In a deeply characterized longitudinal birth cohort, we did not observe any consistent associations between the early-life gut microbiota and BMI or risk of obesity in later childhood. While this does not conclusively rule out a relationship, it suggests that if such associations exist, they may be more complex and potentially influenced by factors emerging later in life, including lifestyle changes.

FUNDING: COPSAC is funded by private and public research funds (all listed on www.copsac.com).}, } @article {pmid39536492, year = {2025}, author = {Chu, J and Ye, Y and Wu, YH}, title = {A glimpse of microbial potential in metal metabolism in the Clarion-Clipperton Fracture Zone in the eastern Pacific Ocean based on metagenomic analysis.}, journal = {Marine genomics}, volume = {79}, number = {}, pages = {101159}, doi = {10.1016/j.margen.2024.101159}, pmid = {39536492}, issn = {1876-7478}, mesh = {Pacific Ocean ; *Metagenome ; *Bacteria/genetics/metabolism/classification ; *Archaea/genetics/metabolism ; *Metagenomics ; Metals/metabolism ; Geologic Sediments/microbiology ; Microbiota ; }, abstract = {The polymetallic nodules distributed in the abyssal ocean floor are full of economic value, rich in manganese, iron, copper and rare-earth elements. Little is currently known about the diversity and the metabolic potential of microorganisms inhabiting the Clarion-Clipperton Fracture Zone (CCFZ) in eastern Pacific Ocean. In this study, the surface sediments (0-8 cm), which were divided into eight parts at 1 cm intervals were collected from the CCFZ. The microbial diversity and the metabolic potential of metal were examined by metagenomic sequencing and binning. The metal redox genes and metal transporter genes also showed a certain trend at different depths, the highest in the surface layer, about the same at 0-6 cm, and greater changes after >6 cm. 58 high- and medium metagenome-assembled genomes (MAGs) were recovered and assigned to 14 bacterial phyla and 1 archaeal phylum after dereplication. Alphaproteobacteria mainly carried out the oxidation of Fe/Mn and the reduction of Hg, Gammaproteobacteria mainly for the oxidation of Mn/Cu and the reduction of Cr/Hg and Methylomirabilota mainly for the oxidation of Mn and the reduction of As/Cr/Hg. Among the five Thermoproteota MAGs identified, only one had genes annotated for Mn oxidation, suggesting a limited but potentially significant role in this process at the bottom layer. By identifying the microbial diversity and the metabolic potential of metal in different depth, our study strengthens the understanding of metal metabolism in CCFZ and provides the foundation for further analyses of metal metabolism in such ecosystems.}, } @article {pmid39534702, year = {2024}, author = {Huang, J and Weng, H and Ye, L and Jiang, M and Chen, L and Li, Y and Li, H}, title = {Bronchoalveolar lavage fluid and lung biopsy tissue metagenomic next-generation sequencing in the diagnosis of pulmonary cryptococcosis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1446814}, pmid = {39534702}, issn = {2235-2988}, mesh = {Humans ; *Bronchoalveolar Lavage Fluid/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Female ; Retrospective Studies ; Middle Aged ; *Cryptococcosis/diagnosis/microbiology ; Biopsy ; *Metagenomics/methods ; *Sensitivity and Specificity ; *Lung/microbiology/pathology ; *Lung Diseases, Fungal/diagnosis/microbiology ; Aged ; Adult ; Cryptococcus neoformans/genetics/isolation & purification ; Antigens, Fungal ; Cryptococcus/genetics/isolation & purification ; ROC Curve ; }, abstract = {OBJECTIVE: To evaluate the diagnostic value of metagenomic next-generation sequencing (mNGS) in pulmonary cryptococcosis (PC) using bronchoalveolar lavage fluid (BALF) and lung biopsy tissue specimens.

METHODS: In this retrospective study, 321 patients diagnosed with lower respiratory tract diseases who underwent mNGS using BALF and LBT samples, between January 2021 and December 2023 were included. Individuals were classified into PC and non-PC groups according to the diagnostic criteria for PC, and conventional fungal cultures were performed. A serum/BALF cryptococcal antigen (CrAg) test was performed in some patients with PC. The diagnostic efficiencies of three methods for PC (mNGS, conventional culture, and CrAg) were compared. Additionally, two mNGS methods were used in this study: original mNGS (OmNGS, testing time from January 2021 to December 2022) and modified mNGS (MmNGS, testing time from January to December 2023). The diagnostic efficiency of the two mNGS methods on PC was simultaneously compared.

RESULTS: Among the 321 patients, 23 (7.2%) had PC and 298 (92.8%) did not. Compared with the composite reference standard for PC diagnosis, the sensitivity, specificity, and accuracy of mNGS for PC were 78.3% (95% confidence interval [CI], 55.8%-91.7%), 98.7% (95% CI, 96.4%-99.6%), and 97.2% (95% CI, 94.7%-98.7%), respectively. The sensitivity of mNGS was similar to that of CrAg (80.0%, 12/15) (P > 0.05). The diagnostic sensitivity of both mNGS and CrAg was higher than that of conventional culture (35.0%, 7/20) (P = 0.006, P = 0.016), and the combined detection of mNGS and CrAg further improved the diagnostic sensitivity of PC (93.3%, 14/15). The area under the receiver operating characteristic curve of mNGS was superior to that of conventional culture (0.885 vs. 0.675). In addition, the diagnostic sensitivity of PC was higher than that of OmNGS (P = 0.046).

CONCLUSION: The sensitivity of mNGS is better than that of conventional culture. The combination of mNGS and CrAg improves the testing sensitivity of Cryptococcus. MmNGS could further improve the detection of Cryptococcus. Conventional PC detection methods are indispensable and mNGS can be used as a rapid and accurate auxiliary diagnostic method for PC.}, } @article {pmid39533168, year = {2024}, author = {Zhang, Z and Wang, K and Zou, C and Zhao, T and Wu, W and Wang, C and Hua, Y}, title = {Comparison of microbial diversity and carbohydrate-active enzymes in the hindgut of two wood-feeding termites, Globitermes sulphureus (Blattaria: Termitidae) and Coptotermes formosanus (Blattaria: Rhinotermitidae).}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {470}, pmid = {39533168}, issn = {1471-2180}, support = {2024A1515012617//Guangdong Natural Science Foundation-General Program/ ; }, mesh = {Animals ; *Isoptera/microbiology ; *Gastrointestinal Microbiome ; *RNA, Ribosomal, 16S/genetics ; *Wood/microbiology ; *Bacteria/classification/genetics/enzymology/isolation & purification ; Phylogeny ; Glycoside Hydrolases/genetics/metabolism ; Lignin/metabolism ; Biodiversity ; }, abstract = {BACKGROUND: Wood-feeding termites have been employed as sources of novel and highly efficient lignocellulolytic enzymes due to their ability to degrade lignocellulose efficiently. As a higher wood-feeding termite, Globitermes sulphureus (Blattaria: Termitidae) plays a crucial role as a decomposer in regions such as Vietnam, Singapore, Myanmar, and Yunnan, China. However, the diversity of its gut microbiome and carbohydrate-active enzymes (CAZymes) remains unexplored. Here, we analyzed the diversity of hindgut microbial communities and CAZymes in a higher wood-feeding termite, G. sulphureus, and a lower wood-feeding termite, Coptotermes formosanus (Blattaria: Rhinotermitidae).

RESULTS: 16S rRNA sequencing revealed that Spirochaetota, Firmicutes, and Fibrobacterota were the dominant microbiota in the hindgut of the two termite species. At the phylum level, the relative abundances of Proteobacteria and Bacteroidota were significantly greater in the hindgut of C. formosanus than in G. sulphureus. At the genus level, the relative abundances of Candidatus_Azobacteroides and Escherichia-Shigella were significantly lower in the hindgut of G. sulphureus than in C. formosanus. Metagenomic analysis revealed that glycoside hydrolases (GHs) with cellulases and hemicellulases functions were not significantly different between G. sulphureus and C. formosanus. Interestingly, the cellulases in G. sulphureus were mainly GH5_2, GH5_4, GH6, GH9, and GH45, while the hemicellulases were mainly GH11, GH8, GH10, GH11, GH26, and GH53. In C. formosanus, the cellulases were mainly GH6 and GH9, and the hemicellulases were mainly GH5_7, GH5_21, GH10, GH12, and GH53. In addition, β-glucosidase, exo-β-1,4-glucanase, and endo-β-1,4-glucanase activities did not differ significantly between the two termite species, while xylanase activity was higher in G. sulphureus than in C. formosanus. The bacteria encoding GHs in G. sulphureus were mainly Firmicutes, Fibrobacterota, and Proteobacteria, whereas Bacteroidota and Spirochaetota were the main bacteria encoding GHs in C. formosanus.

CONCLUSIONS: Our findings characterized the microbial composition and differences in the hindgut microbiota of G. sulphureus and C. formosanus. Compared to C. formosanus, G. sulphureus is enriched in genes encoding for hemicellulase and debranching enzymes. It also highlights the rich diversity of GHs in the hindgut microbiota of G. sulphureus, including the GH5 subfamily, GH6, and GH48, with the GH6 and GH48 not previously reported in other higher termites. These results strengthen the understanding of the diversity of termite gut microbiota and CAZymes.}, } @article {pmid39529970, year = {2024}, author = {Han, S and Liu, J and Feng, Z and Mao, Y and Gao, H and Xie, Z and Qian, S and Xu, L}, title = {Fulminant myocarditis associated with human rhinovirus A66 infection: a case report.}, journal = {Frontiers in pediatrics}, volume = {12}, number = {}, pages = {1480724}, pmid = {39529970}, issn = {2296-2360}, abstract = {BACKGROUND: Human rhinoviruses (HRVs) are among the most common pathogens of upper respiratory infections, and they are responsible for the common cold. An increasing number of studies have shown that HRV is associated with more severe illness. However, HRV-associated fulminant myocarditis has rarely been reported.

PATIENT PRESENTATION: A previously healthy 8-year-old boy developed fever, fatigue, and vomiting for 3 days, with a subsequent exacerbation accompanied by confusion lasting for 9 h. The day before admission, the patient presented with oliguria, confusion, and hypotension, and he was suspected of having myocarditis. The patient was transferred to our hospital for further diagnosis and treatment. On admission, rough and moist rales were detected, and the heart sounds were muffled, accompanied by an irregular heart rhythm and a gallop. An electrocardiogram (EKG) revealed a wide QRS complex, ST-segment depression, premature ventricular contractions, and complete right bundle branch block. Laboratory tests revealed that brain natriuretic peptide (BNP), N-terminal pro BNP (NT-pro BNP), and cardiac biomarkers, such as troponin I, creatinine kinase (CK), and creatinine kinase-MB (CK-MB) were elevated. Additionally, echocardiography revealed an ejection fraction of approximately 28%. The child developed severe cardiac dysfunction and tissue hypoperfusion, and the cardiogenic shock could not be corrected despite active drug therapy. He had indications for ECMO implantation. A rarely reported rhinovirus, namely, A66, was detected in his bronchoalveolar lavage fluid and oropharyngeal swabs via metagenomic next-generation sequencing and a PCR assay. Bacterial culture of all the samples yielded negative results.

CONCLUSIONS: This case presents a patient with severe human rhinovirus A66 infection, which is likely responsible for fulminant myocarditis. This report facilitates prompt diagnosis and treatment of fulminant myocarditis. Clinicians should consider rhinovirus as a possible pathogen of fulminant myocarditis, especially when patients present with symptoms or signs of heart involvement.}, } @article {pmid39529632, year = {2024}, author = {Liu, X and Gan, Z and Lin, Z and Lin, X and Yuan, J and Rong, L and Chen, J and Liu, J and Li, Y and Hu, C}, title = {Exploring the value of hybrid capture-based next-generation sequencing technology in the suspected diagnosis of bloodstream infections.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e18471}, pmid = {39529632}, issn = {2167-8359}, mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Sepsis/blood/diagnosis/genetics/microbiology ; Humans ; Male ; Female ; Adult ; Middle Aged ; Aged ; Blood Culture ; Leukocytes/microbiology ; Fungi/isolation & purification ; Bacteria/isolation & purification ; }, abstract = {BACKGROUND: Determining the source of infection is significant for the treatment of bloodstream infections (BSI). The gold standard of blood infection detection, blood cultures, have low positive rates to meet clinical needs. In this study, we investigated the ability of hybrid capture-based next generation sequencing technology to detect pathogens in peripheral blood samples collected from patients with suspected BSI. Blood cultures and capture sequencing assays were also analyzed against the final clinical diagnoses.

METHODS: In this study, peripheral blood samples were collected from patients with fever, chills, and suspected BSI at Jinshazhou Hospital of Guangzhou University of Chinese Medicine from March 2023 to January 2024. All samples were tested by three different technologies: plasma capture sequencing technology, white blood cell capture sequencing technology, and blood culture. Relevant clinical diagnostic information was also collected. The performances of the blood cultures were then compared to those of both plasma capture sequencing technology and white blood cell capture sequencing technology.

RESULTS: A total of 98 patients were included in this study. The positive rates of probe capture next generation sequencing (NGS technology) in plasma and white blood cells were 81.63% and 65.31%, respectively, which were both significantly higher than that of the blood culture, which was 21.43% (p < 0.001). Taking blood culture as the standard control, the sensitivity and specificity of plasma capture sequencing were 85.71% and 71.43%, respectively, while the sensitivity and specificity of white blood cell sequencing were 76.19% and 81.82%, respectively. Upon final clinical diagnosis, the clinical agreement rates of the blood cultures, plasma capture sequencing, and white blood cell capture sequencing were 39.80%, 83.67%, and 73.47%, respectively.

CONCLUSION: Our study demonstrates the high accuracy of probe capture sequencing technology compared to blood cultures in the identification of pathogenic microorganisms in BSI upon final clinical diagnosis. Among the different sample types, white blood cell samples had a lower clinical compliance rate compared to plasma samples, possibly due to the higher host rate in cell samples, which impairs the sensitivity of pathogen detection.}, } @article {pmid39529146, year = {2024}, author = {Zhang, C and Liu, H and Jiang, X and Zhang, Z and Hou, X and Wang, Y and Wang, D and Li, Z and Cao, Y and Wu, S and Huws, SA and Yao, J}, title = {An integrated microbiome- and metabolome-genome-wide association study reveals the role of heritable ruminal microbial carbohydrate metabolism in lactation performance in Holstein dairy cows.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {232}, pmid = {39529146}, issn = {2049-2618}, mesh = {Animals ; Cattle ; *Rumen/microbiology/metabolism ; *Lactation ; Female ; *Genome-Wide Association Study ; *Polymorphism, Single Nucleotide ; *Carbohydrate Metabolism/genetics ; *Fatty Acids, Volatile/metabolism ; *Metabolome ; Gastrointestinal Microbiome/genetics ; Milk/microbiology/metabolism ; Microbiota/genetics ; Bacteria/classification/genetics/metabolism ; }, abstract = {BACKGROUND: Despite the growing number of studies investigating the connection between host genetics and the rumen microbiota, there remains a dearth of systematic research exploring the composition, function, and metabolic traits of highly heritable rumen microbiota influenced by host genetics. Furthermore, the impact of these highly heritable subsets on lactation performance in cows remains unknown. To address this gap, we collected and analyzed whole-genome resequencing data, rumen metagenomes, rumen metabolomes and short-chain fatty acids (SCFAs) content, and lactation performance phenotypes from a cohort of 304 dairy cows.

RESULTS: The results indicated that the proportions of highly heritable subsets (h[2] ≥ 0.2) of the rumen microbial composition (55%), function (39% KEGG and 28% CAZy), and metabolites (18%) decreased sequentially. Moreover, the highly heritable microbes can increase energy-corrected milk (ECM) production by reducing the rumen acetate/propionate ratio, according to the structural equation model (SEM) analysis (CFI = 0.898). Furthermore, the highly heritable enzymes involved in the SCFA synthesis metabolic pathway can promote the synthesis of propionate and inhibit the acetate synthesis. Next, the same significant SNP variants were used to integrate information from genome-wide association studies (GWASs), microbiome-GWASs, metabolome-GWASs, and microbiome-wide association studies (mWASs). The identified single nucleotide polymorphisms (SNPs) of rs43470227 and rs43472732 on SLC30A9 (Zn[2+] transport) (P < 0.05/nSNPs) can affect the abundance of rumen microbes such as Prevotella_sp., Prevotella_sp._E15-22, Prevotella_sp._E13-27, which have the oligosaccharide-degradation enzymes genes, including the GH10, GH13, GH43, GH95, and GH115 families. The identified SNPs of chr25:11,177 on 5s_rRNA (small ribosomal RNA) (P < 0.05/nSNPs) were linked to ECM, the abundance alteration of Pseudobutyrivibrio_sp. (a genus that was also showed to be linked to the ECM production via the mWASs analysis), GH24 (lysozyme), and 9,10,13-TriHOME (linoleic acid metabolism). Moreover, ECM, and the abundances of Pseudobutyrivibrio sp., GH24, and 9,10,13-TRIHOME were significantly greater in the GG genotype than in the AG genotype at chr25:11,177 (P < 0.05). By further the SEM analysis, GH24 was positively correlated with Pseudobutyrivibrio sp., which was positively correlated with 9,10,13-triHOME and subsequently positively correlated with ECM (CFI = 0.942).

CONCLUSION: Our comprehensive study revealed the distinct heritability patterns of rumen microbial composition, function, and metabolism. Additionally, we shed light on the influence of host SNP variants on the rumen microbes with carbohydrate metabolism and their subsequent effects on lactation performance. Collectively, these findings offer compelling evidence for the host-microbe interactions, wherein cows actively modulate their rumen microbiota through SNP variants to regulate their own lactation performance. Video Abstract.}, } @article {pmid39526141, year = {2024}, author = {Zhao, M and Li, Y and Chen, H and Chen, Y and Zheng, L and Wu, Y and Wang, K and Pan, Z and Yu, T and Wang, T}, title = {Metagenomic study of the microbiome and key geochemical potentials associated with architectural heritage sites: a case study of the Song Dynasty city wall in Shou County, China.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1453430}, pmid = {39526141}, issn = {1664-302X}, abstract = {Historical cultural heritage sites are valuable for all of mankind, as they reflect the material and spiritual wealth of by nations, countries, or specific groups during the development of human civilization. The types and functions of microorganisms that form biofilms on the surfaces of architectural heritage sites influence measures to preserve and protect these sites. These microorganisms contribute to the biocorrosion of architectural heritage structures through the cycling of chemical elements. The ancient city wall of Shou County is a famous architectural and cultural heritage site from China's Song Dynasty, and the protection and study of this site have substantial historical and cultural significance. In this study, we used metagenomics to study the microbial diversity and taxonomic composition of the Song Dynasty city wall in Shou County, a tangible example of Chinese cultural heritage. The study covered three main topics: (1) examining the distribution of bacteria in the biofilm on the surfaces of the Song Dynasty city wall in Shou County; (2) predicting the influence of bacteria involved in the C, N, and S cycles on the corrosion of the city wall via functional gene analysis; and (3) discussing cultural heritage site protection measures for biocorrosion-related bacteria to investigate the impact of biocorrosion on the Song Dynasty city wall in Shou County, a tangible example of Chinese cultural heritage. The study revealed that (1) the biofilm bacteria mainly belonged to Proteobacteria, Actinobacteria, Cyanobacteria, Bacteroidetes, and Firmicutes, which accounted for more than 70% of the total bacteria in the biofilms. The proportion of fungi in the microbial community of the well-preserved city wall was greater than that in the damaged city wall. The proportion of archaea was low-less than 1%. (2) According to the Shannon diversity index, the well-preserved portion of the ancient city wall had the highest diversity of bacteria, fungi, and archaea, and bacterial diversity on the good city wall was greater than that on the corroded city wall. (3) Bray-Curtis distances revealed that the genomes of the two good city walls were similar and that the genomes of the corroded city wall portions were similar. Researchers also detected human intestine-related bacteria in four locations on the city walls, with the proportion of these bacteria in the microbial community being greater on good city walls than on bad city walls. (4) KEGG functional analysis revealed that the energy metabolism and inorganic ion transport activities of the bacterial community on the corroded city wall were greater than those of the good city wall. (5) In the carbon cycle, the absence of active glycolysis, the ED pathway, and the TCA cycle played significant roles in the collapse of the east city wall. (6) The nitrogen cycling processes involved ammonia oxidation and nitrite reduction to nitrate. (7) In the sulfur cycle, researchers discovered a crucial differential functional gene, SoxY, which facilitates the conversion of thiosulfate to sulfate. This study suggests that, in the future, biological approaches can be used to help cultural heritage site protectors achieve targeted and precise protection of cultural relics through the use of microbial growth inhibition technology. The results of this study serve as a guide for the protection of cultural heritage sites in other parts of China and provide a useful supplement to research on the protection of world cultural heritage or architectural heritage sites.}, } @article {pmid39526134, year = {2024}, author = {Dop, C and Auvin, S and Mondot, S and Lepage, P and Ilhan, ZE}, title = {Longitudinal exposure to antiseizure medications shape gut-derived microbiome, resistome, and metabolome landscape.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae123}, pmid = {39526134}, issn = {2730-6151}, abstract = {The influence of chronically administered host-targeted drugs on the gut microbiome remains less understood compared to antibiotics. We investigated repetitive exposure effects of three common antiseizure medications [carbamazepine (CBZ), valproic acid, and levetiracetam] on the gut microbial composition, resistome, and metabolome using microcosms constructed from feces of young children. Microcosms were established by cultivating feces for 24 h (C0). These microcosms were daily transferred into fresh media for seven cycles (C1-C7) with antiseizure medications or carrier molecules, followed by four cycles without any drugs (C8-C11). The microbial dynamics and resistome of microcosms at C0, C1, C7, and C11 were assessed with 16S ribosomal ribonucleic acid gene sequencing or shotgun metagenome sequencing and real-time quantitative polymerase chain reaction analysis of the antimicrobial resistance genes, respectively. Metabolites of CBZ-treated and control microcosms at C0, C1, and C7 were evaluated using non-targeted metabolomics. Our findings revealed that the serial transfer approach longitudinally altered the microcosm composition. Among the medications, CBZ had the most substantial impact on the structure and metabolism of the feces-derived microcosms. The microbiome composition partially recovered during the drug-free period. Specifically, Bacteroides and Flavonifractor were depleted and Escherichia and Clostridium were enriched. Additionally, repetitive CBZ exposure increased the abundance and expression of genes related to various antibiotic resistance mechanisms, more specifically, efflux pumps and antibiotic target alteration. CBZ-induced changes in the microbiome were mirrored in the metabolome, with reductions in the citric acid cycle metabolites, glutamine, and spermidine, alongside increased levels of vitamin B6. Our study suggests that repetitive CBZ exposure may negatively impact gut microbial homeostasis and metabolism.}, } @article {pmid39525869, year = {2024}, author = {Xiong, Y and Xiang, D and Zhou, X and Huang, Y and Routy, JP and Zhu, B}, title = {Application of metagenomic next-generation sequencing with brain tissue biopsy for diagnosing intracranial lesions in people with HIV.}, journal = {Precision clinical medicine}, volume = {7}, number = {4}, pages = {pbae029}, pmid = {39525869}, issn = {2516-1571}, } @article {pmid39524766, year = {2024}, author = {Yagoubi, A and Giannakis, S and Chamekh, A and Kharbech, O and Chouari, R}, title = {Influence of decades-long irrigation with secondary treated wastewater on soil microbial diversity, resistome dynamics, and antibiotrophy development.}, journal = {Heliyon}, volume = {10}, number = {21}, pages = {e39666}, pmid = {39524766}, issn = {2405-8440}, abstract = {In arid and semi-arid regions, the use of treated wastewater (TWW) for irrigation is gaining ground to alleviate pressure on natural water sources. Despite said treatment, the existing methods fail to eliminate potentially dangerous contaminants. As such, this study assessed the impact of long-term TWW irrigation (5 and 25 years) on soil physicochemical properties and bacterial resistance to heavy metals (Pb, Cu, Cd) and antibiotics (tetracycline and amoxicillin). The results revealed heightened salinity and conductivity and reduced pH in irrigated soils. TWW induces harmful effects by reducing microbial density and size, leading to the disappearance of sensitive populations. Conversely, resilient populations, which mainly utilize antibiotics as a carbon source, have adapted. Metagenomic 16S amplicon sequencing analysis demonstrated a shift, notably reducing Actinobacteria, Bacteroidetes, and Firmicutes while increasing Acidobacteriota and Patescibacteria in treated soils. Operational Taxonomic Units affiliated with either Halomonadacea, or Saccharimonadacea and Vicinamibacteracea, were defined as indicators of the absence or presence of TWW contamination, respectively. We conclude that TWW irrigation significantly increases bacterial resistance to heavy metals, whereas the impact of antibiotics is nuanced, with antibiotrophy leveraging lower concentrations in treated soils.}, } @article {pmid39524709, year = {2024}, author = {Pan, X and Song, Y and Liang, Y and Feng, G and Wang, Z}, title = {Roseburia intestinalis: A possible target for vascular calcification.}, journal = {Heliyon}, volume = {10}, number = {21}, pages = {e39865}, pmid = {39524709}, issn = {2405-8440}, abstract = {With the advancement of metagenomics and metabolomics techniques, the crucial role of the gut microbiome in intestinal, cardiovascular, and metabolic disorders has been extensively explored. Vascular calcification (VC) is common in atherosclerosis, hypertension, diabetes mellitus, and chronic kidney disease. Moreover, it is a significant cause of cardiovascular diseases and mortality. Roseburia intestinalis, as a promising candidate for the next generation of probiotics, plays a substantial role in inhibiting the systemic inflammatory response and holds great potential in the treatment of intestinal diseases, cardiovascular diseases, and metabolic disorders. Its primary metabolite, butyrate, acts on specific receptors (GPR43, GPR41, GPR109a). It enters cells via transporters (MCT1, SMCT1), affecting gene expression through HDACs, PPARγ and Nrf2, promoting energy metabolism and changing the concentration of other metabolites (including AGEs, LPS, BHB) in the circulation to affect the body's life activities. In this paper, we focus on the possible mechanism of the primary metabolite butyrate of Roseburia intestinalis in inhibiting VC, which may become a potential therapeutic target for the treatment of VC and the ways to enhance its effect.}, } @article {pmid39524564, year = {2024}, author = {Ma, L and Li, R and Luan, H and Tang, J and Wang, L and Guo, T and Huang, S}, title = {Impacts of long-term different fertilization regimes on microbial utilization of straw-derived carbon in greenhouse vegetable soils: insights from its ecophysiological roles and temperature responses.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1486817}, pmid = {39524564}, issn = {1664-462X}, abstract = {As the largest organic carbon input in the agroecosystems, crop residues can increase soil carbon sequestration and crop production in greenhouse vegetable fields (GVFs). However, the soil microbiological mechanisms driving straw decomposition in GVFs under different incubation temperatures and fertilization treatments are not clear. Thus, soil samples were collected from a long-term field experiment included chemical fertilizer application alone (CF), 2/4 fertilizer N+2/4 organic fertilizer N (CM), 2/4 fertilizer N+1/4 organic fertilizer N+1/4 straw N (CMS), 2/4 fertilizer N+2/4 straw N (CS), and incubated with [13]C-labeled straw at different temperatures (15, 25, and 35°C) for 60 days. Organic-amended treatments (CM, CMS, and CS), especially CMS treatment, increased soil bacterial Alpha diversity before and after straw addition. Straw decomposition process was dominated by soil Proteobacteria, Actinobacteria, and Firmicutes for each treatments. The effect of incubation temperature on soil microbial community composition was higher than that of fertilization treatments. Soil Alphaproteobacteria and Actinomycetia were the most predominant class involved in straw decomposition. Gammaproteobacteria (Pseudomonas, Steroidobacter, Acidibacter, and Arenimonas) were the unique and predominant class involved in straw decomposition at medium and high temperatures as well as in the straw-amended treatments. Organic-amended treatments, especially straw-amended treatments, increased the relative abundance of glycosyl transferases (GT) and auxiliary activities (AA). Alphaproteobacteria, Actinomycetia, and Gammaproteobacteria had higher relative contribution to carbohydrase genes. In summary, the long-term organic-amended treatments altered the structure of soil microbial communities and increased soil bacterial diversity, with the CMS having a greater potential to enhance resistance to external environmental changes. Soil Alphaproteobacteria and Actinomycetia were responsible for the dominance of straw decomposition, and Gammaproteobacteria may be responsible for the acceleration of straw decomposition. Fertilization treatments promote straw decomposition by increasing the abundance of indicator bacterial groups involved in straw decomposition, which is important for isolating key microbial species involved in straw decomposition under global warming.}, } @article {pmid39524440, year = {2024}, author = {Ozaka, S and Sonoda, A and Kudo, Y and Ito, K and Kamiyama, N and Sachi, N and Chalalai, T and Kagoshima, Y and Soga, Y and Ekronarongchai, S and Ariki, S and Mizukami, K and Ishizawa, S and Nishiyama, M and Murakami, K and Takeda, K and Kobayashi, T}, title = {Daikenchuto, a Japanese herbal medicine, ameliorates experimental colitis in a murine model by inducing secretory leukocyte protease inhibitor and modulating the gut microbiota.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1457562}, pmid = {39524440}, issn = {1664-3224}, mesh = {Animals ; Humans ; Male ; Mice ; Anti-Inflammatory Agents/pharmacology ; *Colitis/chemically induced/drug therapy/microbiology ; Colon/drug effects/immunology/microbiology ; Cytokines/metabolism ; Dextran Sulfate ; Disease Models, Animal ; *Gastrointestinal Microbiome/drug effects ; Intestinal Mucosa/drug effects/immunology/microbiology ; Mice, Inbred C57BL ; Mice, Knockout ; *Panax/chemistry ; *Plant Extracts/pharmacology ; *Secretory Leukocyte Peptidase Inhibitor/metabolism/genetics ; *Zanthoxylum/chemistry ; *Zingiberaceae/chemistry ; }, abstract = {BACKGROUND: Inflammatory bowel disease (IBD) is a refractory inflammatory disorder of the intestine, which is probably triggered by dysfunction of the intestinal epithelial barrier. Secretory leukocyte protease inhibitor (SLPI) secreted by colon epithelial cells protects against intestinal inflammation by exerting anti-protease and anti-microbial activities. Daikenchuto (DKT) is one of the most commonly prescribed Japanese traditional herbal medicines for various digestive diseases. Although several animal studies have revealed that DKT exerts anti-inflammatory effects, its detailed molecular mechanism is unclear. This study aimed to clarify the anti-inflammatory mechanism of DKT using a murine colitis model, and to evaluate its potential as a therapeutic agent for IBD.

METHODS: Experimental colitis was induced in wild-type (WT) mice and SLPI-deficient (KO) mice by dextran sulfate sodium (DSS) after oral administration of DKT. The resultant clinical symptoms, histological changes, and pro-inflammatory cytokine levels in the colon were assessed. Expression of SLPI in the colon was detected by Western blotting and immunohistochemistry. Composition of the gut microbiota was analyzed by 16S rRNA metagenome sequencing and intestinal metabolites were measured by gas chromatography-mass spectrometry analysis. Intestinal epithelial barrier function was assessed by oral administration of FITC-dextran and immunostaining of tight junction proteins (TJPs).

RESULTS: Oral administration of DKT increased the number of butyrate-producing bacteria, such as Parabacteroides, Allobaculum, and Akkermansia, enhanced the levels of short-chain fatty acids, including butyrate, in the colon, induced SLPI expression, and ameliorated DSS-induced colitis in WT mice. We found that mouse colon carcinoma cell line treatment with either DKT or butyrate significantly enhanced the expression of SLPI. Moreover, supplementation of DKT protected the intestinal epithelial barrier with augmented expression of TJPs in WT mice, but not in KO mice. Finally, the composition of the gut microbiota was changed by DKT in WT mice, but not in KO mice, suggesting that DKT alters the colonic bacterial community in an SLPI-dependent manner.

CONCLUSION: These results indicate that DKT exerts anti-inflammatory effects on the intestinal epithelial barrier by SLPI induction, due, at least in part, to increased butyrate-producing bacteria and enhanced butyrate levels in the colon. These results provide insight into the mechanism of the therapeutic effects of DKT on IBD.}, } @article {pmid39521252, year = {2024}, author = {Hernández, LHA and da Paz, TYB and da Silva, SP and de Barros, BCV and Coelho, TFSB and Cruz, ACR}, title = {First description of a mobatvirus (Hantaviridae) in the Amazon region.}, journal = {Virus research}, volume = {350}, number = {}, pages = {199494}, pmid = {39521252}, issn = {1872-7492}, mesh = {Brazil ; *Chiroptera/virology ; Animals ; *Phylogeny ; *Genome, Viral ; *Orthohantavirus/genetics/classification/isolation & purification ; Metagenomics ; Hantavirus Infections/virology/veterinary ; RNA, Viral/genetics ; }, abstract = {From 1988-2023, Pará accounted for the highest proportion of deforestation among all states in the Brazilian Amazon. Specifically, 57.20 % of the territory in the Santa Bárbara municipality was deforested as of 2023. Since 2017, the Hantaviridae family has included viruses identified in nonrodent vertebrates, such as mobatviruses (from moles and bats). In the current metagenomic analysis of a pool of multiple organs of a Carollia brevicauda bat, we obtained sequences for three segments of the previously described Buritiense virus (BURV); to date, only the L segment had been sequenced for this mobatvirus. This study provides the first description of BURV in the Amazon region and provides information on the S and M segments of the virus. These findings corroborate the presence of BURV in Brazil in an area far from the site of the first detection and in another bat species.}, } @article {pmid39535623, year = {2025}, author = {Wang, L and Chen, Y and Wang, Q and Pan, J and Bao, R and Jin, W and Yao, Y and Fang, T and Li, N and Luan, S and Yin, X and Qin, L and Zhou, C and Zhu, P and Fu, A and Pang, B and Ji, Y and Hu, B and Miao, Q}, title = {Comparison of molecular testing methods for diagnosing non-tuberculous mycobacterial infections.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {44}, number = {1}, pages = {109-116}, pmid = {39535623}, issn = {1435-4373}, support = {ZSLCYJ202309//Special Program for Clinical Research of Zhongshan Hospital Affiliated to Fudan University/ ; }, mesh = {Humans ; *Mycobacterium Infections, Nontuberculous/diagnosis/microbiology ; *Nontuberculous Mycobacteria/genetics/isolation & purification/classification ; *High-Throughput Nucleotide Sequencing/methods ; *Molecular Diagnostic Techniques/methods ; *Sensitivity and Specificity ; Middle Aged ; Male ; Female ; Aged ; Multiplex Polymerase Chain Reaction/methods ; Adult ; Metagenomics/methods ; }, abstract = {PURPOSES: Rapid and accurate identification of non-tuberculous mycobacteria (NTM) is crucial yet challenging, promoting the development of novel molecular techniques such as amplification-based targeted high-throughput sequencing and metagenomic unbiased high-throughput sequencing. We aimed to evaluate the diagnostic value of these molecular techniques for NTM infection.

METHODS: A total of 115 clinical specimens from patients with confirmed NTM infection were subjected to multiplex polymerase chain reaction detection techniques (multi-PCR), metagenomic Next-Generation Sequencing (mNGS), targeted Next-Generation Sequencing (tNGS), and targeted Nanopore sequencing (tNanopore). Positivity rates and species identification were compared among these techniques.

RESULTS: The sensitivity of mNGS, tNGS, and multi-PCR in NTM-infection diagnosis was 44.3%, 42.6%, and 36.5%, respectively, while the sensitivity of the three methods in combination increased to 54.8%. The pathogen identification results of mNGS, tNGS and multi-PCR were matched in 80.6% (25/31) samples at the species level, among which 14 samples (45.2%) was completely matched at the subspecies level. The results of tNanopore, tNGS and mNGS at the species level were completely matched in 73.3% (22/30) samples.

CONCLUSIONS: These molecular assays demonstrated comparable performance in precisely identifying NTM species in clinical specimens, showing their promising potential as efficient and alternative tools for the rapid diagnosis of NTM disease.}, } @article {pmid39535126, year = {2024}, author = {Gao, P and Rinott, E and Dong, D and Mei, Z and Wang, F and Liu, Y and Kamer, O and Yaskolka Meir, A and Tuohy, KM and Blüher, M and Stumvoll, M and Stampfer, MJ and Shai, I and Wang, DD}, title = {Gut microbial metabolism of bile acids modifies the effect of Mediterranean diet interventions on cardiometabolic risk in a randomized controlled trial.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2426610}, pmid = {39535126}, issn = {1949-0984}, support = {K99 DK119412/DK/NIDDK NIH HHS/United States ; R01 NR019992/NR/NINR NIH HHS/United States ; P30 DK046200/DK/NIDDK NIH HHS/United States ; R01 AG077489/AG/NIA NIH HHS/United States ; RF1 AG083764/AG/NIA NIH HHS/United States ; R00 DK119412/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Diet, Mediterranean ; *Bile Acids and Salts/metabolism ; Male ; Female ; *Feces/microbiology/chemistry ; Middle Aged ; Adult ; Cardiometabolic Risk Factors ; Body Mass Index ; Bacteria/classification/metabolism/isolation & purification/genetics ; Lipids/blood ; Cardiovascular Diseases/prevention & control/metabolism ; Adiposity ; }, abstract = {Bile acids (BAs) undergo extensive microbial metabolism in the gut and exert hormone-like functions on physiological processes underlying metabolic risk. However, the extent to which gut BA profiles predict cardiometabolic risk and explain individual responses to dietary interventions in humans is still unclear. In the DIRECT-PLUS Trial, we conducted a multi-omics analysis of 284 participants randomized into three groups: healthy dietary guidelines and two Mediterranean diet (MedDiet) groups. We longitudinally measured 44 fecal BAs using liquid chromatography-mass spectrometry, the gut microbiome through shotgun metagenomic sequencing, and body adiposity and serum lipids at baseline, 6, and 18 months. Fecal levels of 14 BAs, such as lithocholic acid and ursodeoxycholic acid, were prospectively associated with body mass index (BMI) and serum lipid profiles (false discovery rate [q]<0.05). Baseline fecal BA levels significantly modified the beneficial effects of the MedDiet; for example, BMI reduction induced by MedDiet interventions was more pronounced in individuals with lower 12-dehydrocholic acid levels (q-interaction <0.001). We confirmed that the gut microbiome is a major modifier of the secondary BA pool in humans. Furthermore, the association of fecal BAs with body adiposity and serum lipids varied significantly in individuals with different abundances of gut microbes carrying BA metabolism enzymes, e.g. several Ruminococcus spp. In summary, our study identifies novel predictive biomarkers for cardiometabolic risk and offers new mechanistic insights to guide personalized dietary interventions.}, } @article {pmid39535043, year = {2025}, author = {Tegenfeldt, F and Kuznetsov, D and Manni, M and Berkeley, M and Zdobnov, EM and Kriventseva, EV}, title = {OrthoDB and BUSCO update: annotation of orthologs with wider sampling of genomes.}, journal = {Nucleic acids research}, volume = {53}, number = {D1}, pages = {D516-D522}, pmid = {39535043}, issn = {1362-4962}, support = {//University of Geneva/ ; //Swiss Institute of Bioinformatics/ ; }, mesh = {*Molecular Sequence Annotation/methods ; *Software ; *Databases, Genetic ; *Genomics/methods ; Animals ; Genome/genetics ; Eukaryota/genetics ; Humans ; Evolution, Molecular ; }, abstract = {OrthoDB (https://www.orthodb.org) offers evolutionary and functional annotations of orthologous genes in the widest sampling of eukaryotes, prokaryotes, and viruses, extending experimental gene function knowledge to newly sequenced genomes. We collect gene annotations, delineate hierarchical gene orthology and annotate the orthologous groups (OGs) with functional and evolutionary traits. OrthoDB is the leading resource for species diversity, striving to sample the most diverse and well-researched organisms with the highest quality genomic data. This update expands to include 5827 eukaryotic genomes. We have also added coding DNA sequences (CDSs) and gene loci coordinates. OrthoDB can be browsed, downloaded, or accessed using REST API, SPARQL/RDF and now also via API packages for Python and R Bioconductor. OrthoLoger (https://orthologer.ezlab.org), the tool used for inferring orthologs in OrthoDB, is now available as a Conda package and through BioContainers. ODB-mapper, a component of OrthoLoger, streamlines annotation of genes from newly sequenced genomes with OrthoDB evolutionary and functional descriptors. The benchmarking sets of universal single-copy orthologs (BUSCO), derived from OrthoDB, had correspondingly a major update. The BUSCO tool (https://busco.ezlab.org) has become a standard in genomics, uniquely capable of assessing both eukaryotic and prokaryotic species. It is applicable to gene sets, transcriptomes, genome assemblies and metagenomic bins.}, } @article {pmid39533545, year = {2024}, author = {Chen, J and Sun, Y and Luo, J and Wu, Y and Wang, K and Zhang, W and Fang, H}, title = {V-V ECMO for severe Chlamydia psittaci pneumonia presenting with sudden cardiac arrest: A case report and literature review.}, journal = {Medicine}, volume = {103}, number = {45}, pages = {e39808}, pmid = {39533545}, issn = {1536-5964}, mesh = {Humans ; Male ; Aged ; *Extracorporeal Membrane Oxygenation/methods ; *Chlamydophila psittaci/isolation & purification ; Psittacosis/diagnosis/complications/microbiology ; Heart Arrest/therapy/microbiology/etiology ; }, abstract = {RATIONALE: Psittacosis, also known as parrot fever, is an infectious disease caused by Chlamydia psittaci, which can lead to C psittaci pneumonia. Clinical manifestations are highly nonspecific, which can vary from asymptomatic infection to severe pneumonia and even death.

PATIENT CONCERNS: In this case presentation, we reported one 65-year-old male case of C psittaci pneumonia who was admitted to our hospital on December 2, 2022 due to the chief complaints of poor appetite and fatigue for 3 days as the clinical manifestations. He denied contact with birds but admitted riding horses 1 week ago.

DIAGNOSES: Chlamydia psittaci pneumonia of patient was confirmed through metagenomic sequencing of bronchoalveolar lavage fluid under bronchoscopy.

INTERVENTION: Patient was treated with V-V ECMO, invasive mechanical ventilation and CRRT.

OUTCOMES: On December 12, the patient was successfully weaned off V-V ECMO and discharged on December 20, 2022. During postoperative follow-up, CT scan in a local hospital revealed the infiltrative lesions of the lung were absent.

LESSONS: This case prompts that metagenomic next-generation sequencing is a feasible diagnostic tool for psittacosis, which can rapidly worsen and even cause sudden cardiac arrest. V-V ECMO might be a viable emergency therapeutic option.}, } @article {pmid39533199, year = {2024}, author = {Sane, S and Tene, SD and Diouara, AAM and Coundoul, S and Mbengue, M and Dieye, Y}, title = {Bacterial community in fresh fruits and vegetables sold in streets and open-air markets of Dakar, Senegal.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {471}, pmid = {39533199}, issn = {1471-2180}, mesh = {*Vegetables/microbiology ; Senegal ; *Fruit/microbiology ; *Bacteria/classification/isolation & purification/genetics ; *Food Microbiology ; Salmonella/isolation & purification/genetics/classification ; Escherichia coli/isolation & purification/genetics/classification ; Humans ; Vibrio/isolation & purification/genetics/classification ; Metagenomics ; Food Contamination/analysis ; }, abstract = {In the context of food transition, the agrifood sector has experienced increasingly strong demand for horticultural products. Fresh fruits and vegetables are mainly vehicles of microorganisms, including pathogens that cause human infections. Food safety and compliance with health standards in the fruits and vegetable value chain are significant concerns and multiple challenges, given the prevalence of foodborne pathologies in Southern countries, particularly in Senegal. This study aimed to describe the bacterial community and assess the microbiological quality of a range of fruits and vegetables sold on street stalls and open-air markets in Dakar, the capital city of Senegal. Samples purchased in seven sites were analyzed to isolate Escherichia coli (E. coli), Salmonella spp. and Vibrio spp. Some primary samples with a positive microbiological culture were subjected to DNA extraction and subsequent metagenomic analysis. A total of 240 fresh fruit and vegetable samples were collected, including lettuce (n = 40), tomatoes (n = 40), mango slices (n = 40), onion slices (n = 40), mint leaves (n = 40), strawberries and grapes (each n = 20). Of these samples, 50.83% (122/240) and 60.41% (145/240) were contaminated with E. coli and Vibrio spp., respectively, while Salmonella was not isolated in any product. E. coli and Vibrio spp. contamination levels, 1.3 10[3] to 6 10[6] Colonies Forming Units per gram of sample (CFU/g) and 4.55 10[2] to 8.73 10[6] CFU/g, respectively, were significantly above the thresholds acceptable for human consumption. The most contaminated samples were lettuce, with a prevalence of 98% (39/40) for E. coli and Vibrio spp. followed by mint leaves with 100% (40/40) and 93% (37/40) of the samples containing E. coli and Vibrio spp. respectively. Out of 46 samples sequenced, the metagenomic analysis revealed high contamination rates for E. coli, Vibrio spp. and Salmonella spp., with 100%, 67.39% and 93.47% of prevalence, respectively. On the other hand, the alpha diversity analysis shows high bacterial diversity in lettuce and mint leaf samples, while the beta diversity analysis highlighted the presence of two major clusters. Our results stress the need for a surveillance system that extends this investigation to a national scale while increasing the number of sampling sites and products analyzed.}, } @article {pmid39533109, year = {2024}, author = {Benoit, P and Brazer, N and de Lorenzi-Tognon, M and Kelly, E and Servellita, V and Oseguera, M and Nguyen, J and Tang, J and Omura, C and Streithorst, J and Hillberg, M and Ingebrigtsen, D and Zorn, K and Wilson, MR and Blicharz, T and Wong, AP and O'Donovan, B and Murray, B and Miller, S and Chiu, CY}, title = {Seven-year performance of a clinical metagenomic next-generation sequencing test for diagnosis of central nervous system infections.}, journal = {Nature medicine}, volume = {30}, number = {12}, pages = {3522-3533}, pmid = {39533109}, issn = {1546-170X}, support = {75D30121C12641//U.S. Department of Health & Human Services | Centers for Disease Control and Prevention (CDC)/ ; 75D30122C15360//U.S. Department of Health & Human Services | Centers for Disease Control and Prevention (CDC)/ ; }, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Central Nervous System Infections/diagnosis/cerebrospinal fluid/virology/microbiology ; *Metagenomics/methods ; Middle Aged ; Female ; Adult ; Male ; Aged ; Sensitivity and Specificity ; Child ; Adolescent ; Young Adult ; Infant ; Child, Preschool ; Aged, 80 and over ; Metagenome/genetics ; }, abstract = {Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) is an agnostic method for broad-based diagnosis of central nervous system (CNS) infections. Here we analyzed the 7-year performance of clinical CSF mNGS testing of 4,828 samples from June 2016 to April 2023 performed by the University of California, San Francisco (UCSF) clinical microbiology laboratory. Overall, mNGS testing detected 797 organisms from 697 (14.4%) of 4,828 samples, consisting of 363 (45.5%) DNA viruses, 211 (26.4%) RNA viruses, 132 (16.6%) bacteria, 68 (8.5%) fungi and 23 (2.9%) parasites. We also extracted clinical and laboratory metadata from a subset of the samples (n = 1,164) from 1,053 UCSF patients. Among the 220 infectious diagnoses in this subset, 48 (21.8%) were identified by mNGS alone. The sensitivity, specificity and accuracy of mNGS testing for CNS infections were 63.1%, 99.6% and 92.9%, respectively. mNGS testing exhibited higher sensitivity (63.1%) than indirect serologic testing (28.8%) and direct detection testing from both CSF (45.9%) and non-CSF (15.0%) samples (P < 0.001 for all three comparisons). When only considering diagnoses made by CSF direct detection testing, the sensitivity of mNGS testing increased to 86%. These results justify the routine use of diagnostic mNGS testing for hospitalized patients with suspected CNS infection.}, } @article {pmid39532872, year = {2024}, author = {Wang, YF and Liu, YJ and Fu, YM and Xu, JY and Zhang, TL and Cui, HL and Qiao, M and Rillig, MC and Zhu, YG and Zhu, D}, title = {Microplastic diversity increases the abundance of antibiotic resistance genes in soil.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {9788}, pmid = {39532872}, issn = {2041-1723}, mesh = {*Soil Microbiology ; *Microplastics ; *Drug Resistance, Microbial/genetics ; Soil/chemistry ; Soil Pollutants ; Metagenomics ; Genes, Bacterial ; Virulence Factors/genetics ; Bacteria/genetics/drug effects/classification ; Interspersed Repetitive Sequences/genetics ; Genetic Variation ; Metagenome/genetics ; Anti-Bacterial Agents/pharmacology ; }, abstract = {The impact of microplastics on antibiotic resistance has attracted widespread attention. However, previous studies primarily focused on the effects of individual microplastics. In reality, diverse microplastic types accumulate in soil, and it remains less well studied whether microplastic diversity (i.e., variations in color, shape or polymer type) can be an important driver of increased antibiotic resistance gene (ARG) abundance. Here, we employed microcosm studies to investigate the effects of microplastic diversity on soil ARG dynamics through metagenomic analysis. Additionally, we evaluated the associated potential health risks by profiling virulence factor genes (VFGs) and mobile genetic elements (MGEs). Our findings reveal that as microplastic diversity increases, there is a corresponding rise in the abundance of soil ARGs, VFGs and MGEs. We further identified microbial adaptive strategies involving genes (changed genetic diversity), community (increased specific microbes), and functions (enriched metabolic pathways) that correlate with increased ARG abundance and may thus contribute to ARG dissemination. Additional global change factors, including fungicide application and plant diversity reduction, also contributed to elevated ARG abundance. Our findings suggest that, in addition to considering contamination levels, it is crucial to monitor microplastic diversity in ecosystems due to their potential role in driving the dissemination of antibiotic resistance through multiple pathways.}, } @article {pmid39532844, year = {2024}, author = {Tan, JK and Servellita, V and Stryke, D and Kelly, E and Streithorst, J and Sumimoto, N and Foresythe, A and Huh, HJ and Nguyen, J and Oseguera, M and Brazer, N and Tang, J and Ingebrigtsen, D and Fung, B and Reyes, H and Hillberg, M and Chen, A and Guevara, H and Yagi, S and Morales, C and Wadford, DA and Mourani, PM and Langelier, CR and de Lorenzi-Tognon, M and Benoit, P and Chiu, CY}, title = {Laboratory validation of a clinical metagenomic next-generation sequencing assay for respiratory virus detection and discovery.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {9016}, pmid = {39532844}, issn = {2041-1723}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Respiratory Tract Infections/virology/diagnosis ; *Viruses/genetics/isolation & purification/classification ; Female ; Adult ; Middle Aged ; Male ; Sensitivity and Specificity ; Bronchoalveolar Lavage Fluid/virology ; Aged ; Child ; Adolescent ; Young Adult ; Viral Load/methods ; Child, Preschool ; }, abstract = {Tools for rapid identification of novel and/or emerging viruses are urgently needed for clinical diagnosis of unexplained infections and pandemic preparedness. Here we developed and clinically validated a largely automated metagenomic next-generation sequencing (mNGS) assay for agnostic detection of respiratory viral pathogens from upper respiratory swab and bronchoalveolar lavage samples in <24 h. The mNGS assay achieved mean limits of detection of 543 copies/mL, viral load quantification with 100% linearity, and 93.6% sensitivity, 93.8% specificity, and 93.7% accuracy compared to gold-standard clinical multiplex RT-PCR testing. Performance increased to 97.9% overall predictive agreement after discrepancy testing and clinical adjudication, which was superior to that of RT-PCR (95.0% agreement). To enable discovery of novel, sequence-divergent human viruses with pandemic potential, de novo assembly and translated nucleotide algorithms were incorporated into the automated SURPI+ computational pipeline used by the mNGS assay for pathogen detection. Using in silico analysis, we showed that after removal of all human viral sequences from the reference database, 70 (100%) of 70 representative human viral pathogens could still be identified based on homology to related animal or plant viruses. Our assay, which was granted breakthrough device designation from the US Food and Drug Administration (FDA) in August of 2023, demonstrates the feasibility of routine mNGS testing in clinical and public health laboratories, thus facilitating a robust and rapid response to the next viral pandemic.}, } @article {pmid39531866, year = {2025}, author = {Wang, Y and Deng, C and Wang, X}, title = {Characterization of a novel salt- and solvent-tolerant esterase Dhs82 from soil metagenome capable of hydrolyzing estrogenic phthalate esters.}, journal = {Biophysical chemistry}, volume = {316}, number = {}, pages = {107348}, doi = {10.1016/j.bpc.2024.107348}, pmid = {39531866}, issn = {1873-4200}, mesh = {*Phthalic Acids/metabolism/chemistry ; *Esterases/metabolism/chemistry/genetics ; *Esters/chemistry/metabolism ; *Solvents/chemistry ; *Metagenome ; Hydrolysis ; Soil Microbiology ; Molecular Docking Simulation ; }, abstract = {Esterases that can function under extreme conditions are important for industrial processing and environmental remediation. Here, we report the identification of a salt- and solvent-tolerant esterase, Dhs82, from a soil metagenomic library. Dhs82 prefers short-chain p-nitrophenyl (p-NP) esters and exhibits enzymatic activity up to 1460 ± 61 U/mg towards p-NP butyrate. Meanwhile, Dhs82 can catalyze the hydrolysis of dialkyl phthalate esters, especially the widely-used diethyl phthalate (DEP), dipropyl phthalate (DPP) and di-n-butyl phthalate (DBP). Importantly, as an acidic protein with negative charges dominating its surface, Dhs82 is highly active and extraordinarily stable at high salinity. This property is quite rare among previously reported esterases/hydrolases capable of degrading phthalate esters (PAEs). In addition, Dhs82 activity can be significantly enhanced in the presence of solvents over a concentration range of 10-30 % (v/v). Notably, Dhs82 also showed high stability towards these solvents and solvent concentrations as high as 50-60 % (v/v) are required to inactivate Dhs82. Furthermore, molecular docking revealed the key residues, including the catalytic triad (Ser156, His281, and Asp251) and the surrounding Gly84 and Gly85, involved in the interaction of Dhs82 with DBP, depicting how Dhs82 degrades PAEs as a family IV esterase. Together, these diverse properties make Dhs82 a valuable candidate for both basic research and biotechnological applications.}, } @article {pmid39531444, year = {2024}, author = {Ghosh, S and Ghosh, AJ and Islam, R and Sarkar, S and Saha, T}, title = {Lactobacillus plantarum KAD protects against high-fat diet-induced hepatic complications in Swiss albino mice: Role of inflammation and gut integrity.}, journal = {PloS one}, volume = {19}, number = {11}, pages = {e0313548}, pmid = {39531444}, issn = {1932-6203}, mesh = {Animals ; *Lactobacillus plantarum ; Mice ; *Diet, High-Fat/adverse effects ; *Probiotics/pharmacology/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; *Liver/pathology/metabolism/drug effects ; *Inflammation ; Male ; Oxidative Stress/drug effects ; }, abstract = {Hepatic complications are the major health issues associated with dietary intake of calorie saturated food e.g. high-fat diet (HFD). Recent studies have revealed the beneficial effects of probiotics in HFD fed mice with hepatic complications. Some probiotic Lactic acid bacteria (LAB) e.g. Lactobacillus plantarum have drawn our attention in managing hepatic complications. Here, we aim to elucidate the protective effects of L. plantarum KAD strain, isolated from ethnic fermented food 'Kinema' in HFD-fed mice as, a preventive approach. Eighteen Swiss albino mice were equally divided into 3 groups: Normal Diet (ND), negative control (HFD), and HFD-fed with oral L. plantarum KAD supplementation (LP). All the experimental groups were subjected to specific diet according to grouping for eight weeks. After completion of the regime, subjects were anesthetized and sacrificed. Organs, blood, and fecal samples were collected and stored appropriately. Physical indices, including body weight gain, organ co-efficients were calculated along with assessment of glycemic, lipidomic, hepatic, oxidative stress, inflammatory, and histological parameters. Gut microbiota analysis was performed using 16s V3-V4 fecal metagenomic profiling, and sequencing were done using Illumina Miseq system. Oral administration of L. plantarum KAD is found to significantly (p<0.05) restore metabolic health by normalizing glycemic, lipidomic, hepatic parameters, oxidative stress and inflammatory parameters. Moreover, LP group (7.08±0.52 mg/g) showed significantly (p<0.001) decreased hepatic triglyceride level compared to HFD group (20.07±1.32 mg/g). L. plantarum KAD improved the adipocytic, and colonic histomorphology with significantly better scoring pattern. LP group (1.83±0.41) showed a significantly (p<0.001) reduced hepatic score compared to negative control group (5.00±0.63), showing reduced hepatosteatosis, and immune infiltration. The strain modulated gut health by altering its microbial composition positively towards normalization. In conclusion, the results of the experiment suggest that prophylactic L. plantarum KAD administration has beneficial effects on the onset of HFD induced hepatic complications in mice. Further studies are needed, on this strain for its clinical use as dietary supplement.}, } @article {pmid39530915, year = {2024}, author = {Ergunay, K and Boldbaatar, B and Bourke, BP and Caicedo-Quiroga, L and Tucker, CL and Letizia, AG and Cleary, NG and Lilak, AG and Nyamdavaa, G and Tumenjargal, S and von Fricken, ME and Linton, YM}, title = {Metagenomic Nanopore Sequencing of Tickborne Pathogens, Mongolia.}, journal = {Emerging infectious diseases}, volume = {30}, number = {14}, pages = {105-110}, pmid = {39530915}, issn = {1080-6059}, mesh = {Animals ; Mongolia/epidemiology ; *Nanopore Sequencing/methods ; *Metagenomics/methods ; *Ticks/virology/microbiology ; *Tick-Borne Diseases/virology/epidemiology/microbiology ; Phylogeny ; Humans ; Borrelia/genetics/isolation & purification/classification ; Hemorrhagic Fever Virus, Crimean-Congo/genetics/isolation & purification/classification ; Anaplasma/genetics/isolation & purification ; Babesia microti/genetics/isolation & purification ; Nairovirus/genetics/isolation & purification/classification ; Metagenome ; Rickettsia/genetics/isolation & purification/classification ; }, abstract = {We performed nanopore-based metagenomic screening on 885 ticks collected from 6 locations in Mongolia and divided the results into 68 samples: 23 individual samples and 45 pools of 2-12 tick samples each. We detected bacterial and parasitic pathogens Anaplasma ovis, Babesia microti, Coxiella burnetii, Borrelia miyamotoi, Francisella tularensis subsp. holarctica and novicida, Spiroplasma ixodetis, Theileria equi, and Rickettsia spp., including R. raoultii, R. slovaca, and R. canadensis. We identified the viral pathogens Crimean-Congo hemorrhagic fever virus (2.9%), recently described Alongshan virus (ALSV) (2.9%), and Beiji nairovirus (5.8%). We assembled ALSV genomes, and maximum-likelihood analyses revealed clustering with viruses reported in humans and ticks from China. For ALSV, we identified surface glycoprotein markers associated with isolates from Asia viruses hosted by Ixodes persulcatus ticks. We also detected 20 virus species of unknown public health impact, including a near-complete Yanggou tick virus genome. Our findings demonstrate that nanopore sequencing can aid in detecting endemic and emerging tickborne pathogens.}, } @article {pmid39530358, year = {2024}, author = {Arandia-Gorostidi, N and Jaffe, AL and Parada, AE and Kapili, BJ and Casciotti, KL and Salcedo, RSR and Baumas, CMJ and Dekas, AE}, title = {Urea assimilation and oxidation support activity of phylogenetically diverse microbial communities of the dark ocean.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39530358}, issn = {1751-7370}, support = {507798//Simons Foundation Early Career Investigator Award AED/ ; 2143035//National Science Foundation CAREER Award to AED/ ; 1634297//NSF/ ; ECCS-2026822//National Science Foundation/ ; CEX2019-000928-S//Severo Ochoa Centre of Excellence/ ; 2020-BP-00179//Beatriu de Pinós Program/ ; //Stanford Science Fellows Program/ ; //National Science Foundation Postdoctoral Research Fellowship in Ocean Sciences/ ; }, mesh = {*Urea/metabolism ; *Oxidation-Reduction ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Pacific Ocean ; *Microbiota ; *Seawater/microbiology ; *Nitrification ; *Archaea/metabolism/genetics/classification ; *Metagenomics ; Phylogeny ; Metagenome ; Nitrogen/metabolism ; Ammonia/metabolism ; Urease/metabolism/genetics ; Ammonium Compounds/metabolism ; }, abstract = {Urea is hypothesized to be an important source of nitrogen and chemical energy to microorganisms in the deep sea; however, direct evidence for urea use below the epipelagic ocean is lacking. Here, we explore urea utilization from 50 to 4000 meters depth in the northeastern Pacific Ocean using metagenomics, nitrification rates, and single-cell stable-isotope-uptake measurements with nanoscale secondary ion mass spectrometry. We find that on average 25% of deep-sea cells assimilated urea-derived N (60% of detectably active cells), and that cell-specific nitrogen-incorporation rates from urea were higher than that from ammonium. Both urea concentrations and assimilation rates relative to ammonium generally increased below the euphotic zone. We detected ammonia- and urea-based nitrification at all depths at one of two sites analyzed, demonstrating their potential to support chemoautotrophy in the mesopelagic and bathypelagic regions. Using newly generated metagenomes we find that the ureC gene, encoding the catalytic subunit of urease, is found within 39% of deep-sea cells in this region, including the Nitrososphaeria (syn., Thaumarchaeota; likely for nitrification) as well as members of thirteen other phyla such as Proteobacteria, Verrucomicrobia, Plantomycetota, Nitrospinota, and Chloroflexota (likely for assimilation). Analysis of public metagenomes estimated ureC within 10-46% of deep-sea cells around the world, with higher prevalence below the photic zone, suggesting urea is widely available to the deep-sea microbiome globally. Our results demonstrate that urea is a nitrogen source to abundant and diverse microorganisms in the dark ocean, as well as a significant contributor to deep-sea nitrification and therefore fuel for chemoautotrophy.}, } @article {pmid39530242, year = {2025}, author = {Liu, F and Cai, B and Lian, S and Chang, X and Chen, D and Pu, Z and Bao, L and Wang, J and Lv, J and Zheng, H and Bao, Z and Zhang, L and Wang, S and Li, Y}, title = {MolluscDB 2.0: a comprehensive functional and evolutionary genomics database for over 1400 molluscan species.}, journal = {Nucleic acids research}, volume = {53}, number = {D1}, pages = {D1075-D1086}, pmid = {39530242}, issn = {1362-4962}, support = {2022YFD2400301//National Key R&D Program of China/ ; 32222085//National Natural Science Foundation of China/ ; 842341005//Fundamental Research Funds for the Central Universities/ ; 32130107//National Natural Science Foundation of China/ ; LSKJ202202804//Science & Technology Innovation Project of Laoshan Laboratory/ ; 2021ZLGX03//Key Research and Development Program of Shandong Province/ ; GML20220018//Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; //Taishan Scholar Project of Shandong Province/ ; }, mesh = {Animals ; *Mollusca/genetics/classification ; *Genomics/methods ; *Databases, Genetic ; Transcriptome ; Evolution, Molecular ; Genome/genetics ; Proteome/genetics ; Software ; Molecular Sequence Annotation ; }, abstract = {Mollusca represents the second-largest animal phylum but remains less explored genomically. The increase in high-quality genomes and diverse functional genomic data holds great promise for advancing our understanding of molluscan biology and evolution. To address the opportunities and challenges facing the molluscan research community in managing vast multi-omics resources, we developed MolluscDB 2.0 (http://mgbase.qnlm.ac), which integrates extensive functional genomic data and offers user-friendly tools for multilevel integrative and comparative analyses. MolluscDB 2.0 covers 1450 species across all eight molluscan classes and compiles ∼4200 datasets, making it the most comprehensive multi-omics resource for molluscs to date. MolluscDB 2.0 expands the layers of multi-omics data, including genomes, bulk transcriptomes, single-cell transcriptomes, proteomes, epigenomes and metagenomes. MolluscDB 2.0 also more than doubles the number of functional modules and analytical tools, updating 14 original modules and introducing 20 new, specialized modules. Overall, MolluscDB 2.0 provides highly valuable, open-access multi-omics platform for the molluscan research community, expediting scientific discoveries and deepening our understanding of molluscan biology and evolution.}, } @article {pmid39529629, year = {2024}, author = {Smith, GJ and van Alen, TA and van Kessel, MAHJ and Lücker, S}, title = {Simple, reference-independent assessment to empirically guide correction and polishing of hybrid microbial community metagenomic assembly.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e18132}, pmid = {39529629}, issn = {2167-8359}, mesh = {*Metagenomics/methods ; *Microbiota/genetics ; Metagenome/genetics ; High-Throughput Nucleotide Sequencing/methods ; Bioreactors/microbiology ; Sequence Analysis, DNA/methods ; Software ; }, abstract = {Hybrid metagenomic assembly of microbial communities, leveraging both long- and short-read sequencing technologies, is becoming an increasingly accessible approach, yet its widespread application faces several challenges. High-quality references may not be available for assembly accuracy comparisons common for benchmarking, and certain aspects of hybrid assembly may benefit from dataset-dependent, empiric guidance rather than the application of a uniform approach. In this study, several simple, reference-free characteristics-particularly coding gene content and read recruitment profiles-were hypothesized to be reliable indicators of assembly quality improvement during iterative error-fixing processes. These characteristics were compared to reference-dependent genome- and gene-centric analyses common for microbial community metagenomic studies. Two laboratory-scale bioreactors were sequenced with short- and long-read platforms, and assembled with commonly used software packages. Following long read assembly, long read correction and short read polishing were iterated up to ten times to resolve errors. These iterative processes were shown to have a substantial effect on gene- and genome-centric community compositions. Simple, reference-free assembly characteristics, specifically changes in gene fragmentation and short read recruitment, were robustly correlated with advanced analyses common in published comparative studies, and therefore are suitable proxies for hybrid metagenome assembly quality to simplify the identification of the optimal number of correction and polishing iterations. As hybrid metagenomic sequencing approaches will likely remain relevant due to the low added cost of short-read sequencing for differential coverage binning or the ability to access lower abundance community members, it is imperative that users are equipped to estimate assembly quality prior to downstream analyses.}, } @article {pmid39529240, year = {2024}, author = {Liu, S and Zhang, Z and Wang, X and Ma, Y and Ruan, H and Wu, X and Li, B and Mou, X and Chen, T and Lu, Z and Zhao, W}, title = {Biosynthetic potential of the gut microbiome in longevous populations.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2426623}, pmid = {39529240}, issn = {1949-0984}, mesh = {*Gastrointestinal Microbiome ; Humans ; *Feces/microbiology ; Aged ; *Metagenomics ; Multigene Family ; Aged, 80 and over ; Terpenes/metabolism ; Longevity ; Akkermansia/metabolism ; Adult ; Male ; Female ; Middle Aged ; Cohort Studies ; Biological Products/metabolism ; Metagenome ; Young Adult ; }, abstract = {Gut microbiome plays a pivotal role in combating diseases and facilitating healthy aging, and natural products derived from biosynthetic gene clusters (BGCs) of the human microbiome exhibit significant biological activities. However, the natural products of the gut microbiome in long-lived populations remain poorly understood. Here, we integrated six cohorts of long-lived populations, encompassing a total of 1029 fecal metagenomic samples, and employed the metagenomic single sample assembled BGCs (MSSA-BGCs) analysis pipeline to investigate the natural products and their associated species. Our findings reveal that the BGC composition of the extremely long-lived group differed significantly from that of younger elderly and young individuals across five cohorts. Terpene and Type I PKS BGCs were enriched in the extremely long-lived, whereas cyclic-lactone-autoinducer BGCs were more prevalent in the young. Association analysis indicated that terpene BGCs were strongly associated with the abundance of Akkermansia muciniphila, which was also more abundant in the long-lived elderly across at least three cohorts. We assembled 18 A. muciniphila draft genomes using metagenomic data from the extremely long-lived group across six cohorts and discovered that they all harbor two classes of terpene BGCs, which aligns with the 97 complete genomes of A. muciniphila strains retrieved from the NCBI database. The core domains of these two BGC classes are squalene/phytoene synthases involved in the biosynthesis of tri- and tetraterpenes. Furthermore, the abundance of fecal A. muciniphila was significantly associated with eight types of triterpenoids. Targeted terpenoid metabolomic analysis revealed that two triterpenoids, Holstinone C and colubrinic acid, were enriched in the A. muciniphila culture solution compared to the medium, thereby confirming the production of triterpenoids by A. muciniphila. The natural products derived from the gut of long-lived populations provide intriguing indications of their potential beneficial roles in regulating health.}, } @article {pmid39529113, year = {2024}, author = {Guo, M and He, S and Song, W and Mai, J and Yuan, X and Huang, Y and Xi, H and Sun, G and Chen, Y and Du, B and Liu, X}, title = {The Lachnospiraceae-butyric acid axis and its role in glucocorticoid-associated osteonecrosis.}, journal = {Journal of translational medicine}, volume = {22}, number = {1}, pages = {1015}, pmid = {39529113}, issn = {1479-5876}, support = {82074471//National Natural Science Foundation of China/ ; 81804117//National Natural Science Foundation of China/ ; MS202220//Jiangsu Administration of Traditional Chinese Medicine/ ; JSDW202252//Jiangsu Provincial Medical Key Discipline(Laboratory)Cultivation Unit/ ; }, mesh = {Humans ; *Glucocorticoids/adverse effects ; *Osteonecrosis/chemically induced/pathology ; *Gastrointestinal Microbiome/drug effects ; *Butyric Acid ; Male ; Female ; Middle Aged ; Inflammation ; }, abstract = {Glucocorticoids (GCs) are key inducers of osteonecrosis, yet not all patients treated with GCs develop glucocorticoid-associated osteonecrosis (GAON). The factors mediating this relationship are unclear. Studies have shown that gut microbiota and their metabolites influence bone metabolism, but their role in GAON is unclear. This study aimed to explore the connection between GAON and gut microbiota. Through bidirectional Mendelian randomization analysis, we identified 14 gut microbial taxa, including Lachnospiraceae (IVW, P = 0.011), associated with GAON. RNA-seq analysis revealed that GAON differentially expressed genes (DEGs) were enriched for intestinal inflammatory response mechanisms. We then compared patients who developed GAON (17 cases), those who did not (GAnON, 15 cases), and those untreated with GCs (Blank, 15 cases) for gut microbiota composition, short-chain fatty acids (SCFAs), and serum inflammatory factors. Our findings indicated a decrease in Lachnospiraceae abundance (GAON 17.13%, GAnON 12.51%, Blank 24.52%) in GC-treated patients. Serum inflammatory factors (IL-17 A, IL-33, and TNF-α) associated with GAON (59.603 ± 12.147, 89.337 ± 20.714, 42.584 ± 9.185) showed significant differences between Blank (1.446 ± 0.683, 11.534 ± 4.705, 4.682 ± 1.48) and GAnON (25.353 ± 8.181, 32.527 ± 7.352, 12.49 ± 3.217) groups, with a negative correlation between these factors and Lachnospiraceae levels. Butyric acid levels in SCFAs varied among groups (P<0.01) and correlated with Lachnospiraceae and inflammatory factors. Controlled experiments in GAON rats demonstrated butyric acid's osteoprotective role in GAON development (P<0.01). In conclusion, our study suggests that reduced Lachnospiraceae and butyric acid levels, along with increased inflammation due to GCs use, contribute to GAON. Butyric acid may mediate the effects of Lachnospiraceae and inflammation. Butyrate supplementation could potentially reduce GAON incidence, offering a novel approach for its clinical management.}, } @article {pmid39528484, year = {2024}, author = {Manghi, P and Filosi, M and Zolfo, M and Casten, LG and Garcia-Valiente, A and Mattevi, S and Heidrich, V and Golzato, D and Perini, S and Thomas, AM and Montalbano, S and Cancellieri, S and Waldron, L and Hall, JB and Xu, S and Volfovsky, N and Green Snyder, L and Feliciano, P and Asnicar, F and Valles-Colomer, M and Michaelson, JJ and Segata, N and Domenici, E}, title = {Large-scale metagenomic analysis of oral microbiomes reveals markers for autism spectrum disorders.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {9743}, pmid = {39528484}, issn = {2041-1723}, support = {MASTER-818368//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; ONCOBIOME-825410//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 1U01CA230551//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; }, mesh = {Humans ; *Autism Spectrum Disorder/microbiology ; Male ; Child ; Female ; *Mouth/microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; *Saliva/microbiology ; Cross-Sectional Studies ; *Biomarkers ; Siblings ; Metagenome ; Child, Preschool ; Adolescent ; }, abstract = {The link between the oral microbiome and neurodevelopmental disorders remains a compelling hypothesis, still requiring confirmation in large-scale datasets. Leveraging over 7000 whole-genome sequenced salivary samples from 2025 US families with children diagnosed with autism spectrum disorders (ASD), our cross-sectional study shows that the oral microbiome composition can discriminate ASD subjects from neurotypical siblings (NTs, AUC = 0.66), with 108 differentiating species (q < 0.005). The relative abundance of these species is highly correlated with cognitive impairment as measured by Full-Scale Intelligence Quotient (IQ). ASD children with IQ < 70 also exhibit lower microbiome strain sharing with parents (p < 10[-6]) with respect to NTs. A two-pronged functional enrichment analysis suggests the contribution of enzymes from the serotonin, GABA, and dopamine degradation pathways to the distinct microbial community compositions observed between ASD and NT samples. Although measures of restrictive eating diet and proxies of oral hygiene show relatively minor effects on the microbiome composition, the observed associations with ASD and IQ may still represent unaccounted-for underlying differences in lifestyle among groups. While causal relationships could not be established, our study provides substantial support to the investigation of oral microbiome biomarkers in ASD.}, } @article {pmid39528483, year = {2024}, author = {Sánchez, O and Stefanni, S and Bhadury, P}, title = {The deep sea biodiversity and conservation collection.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {27559}, pmid = {39528483}, issn = {2045-2322}, abstract = {The deep sea, defined as ocean depths below 200 m, encompasses vast and largely unexplored habitats, such as abyssal plains, hydrothermal vents, cold seeps, and ocean trenches. This environment supports a remarkable diversity of life forms adapted to extreme conditions, including high pressure, low temperatures, and complete darkness. The Deep Sea Biodiversity and Conservation Collection highlights the importance of these ecosystems and the unique adaptations of the organisms inhabiting these extreme environments, ranging from invertebrates like corals and sponges to diverse microbial communities. The Collection includes studies on coral distribution and ecosystem services, trophic dynamics at cold-water coral reefs, and microbial diversity using metabarcoding and metagenomics. Notable findings include insights into hydrothermal vent communities, the role of chemosynthesis in sustaining deep-sea life, and the adaptation of deep-sea invertebrates to varying depths. These studies underscore the critical need for conservation strategies for these fragile and understudied oceanic ecosystems to ensure their sustainability.}, } @article {pmid39528173, year = {2024}, author = {Caseiro, C and McGregor, NGS and Alves, VD and Carvalho, AL and Romão, MJ and Davies, GJ and Fontes, CMGA and Bule, P}, title = {Family GH157 enzyme exhibits broad linkage tolerance and a dual endo/exo-β-glucanase activity on β-glucans.}, journal = {International journal of biological macromolecules}, volume = {282}, number = {Pt 6}, pages = {137402}, doi = {10.1016/j.ijbiomac.2024.137402}, pmid = {39528173}, issn = {1879-0003}, mesh = {*beta-Glucans/metabolism/chemistry ; Substrate Specificity ; Hydrolysis ; Glycoside Hydrolases/chemistry/metabolism ; Hydrogen-Ion Concentration ; Kinetics ; Models, Molecular ; Catalytic Domain ; Temperature ; Crystallography, X-Ray ; Amino Acid Sequence ; }, abstract = {The structural and chemical diversity of β-glucans is reflected on the variety of essential biological roles tackled by these polysaccharides. This natural heterogeneity requires an elaborate assortment of enzymatic mechanisms to assemble, degrade or modify, as well as to extract their full biotechnological potential. Recent metagenomic efforts have provided an unprecedented growth in potential new biocatalysts, most of which remain unconfirmed or uncharacterized. Here we report the first biochemical and structural characterization of two bacterial β-glucanases from the recently created glycoside hydrolase family 157 (LaGH157 and BcGH157) and investigate their molecular basis for substrate hydrolysis. Structural analysis by X-ray crystallography revealed that GH157 enzymes belong to clan GH-A, possessing a (β/α)8-barrel fold catalytic domain, two β-sandwich accessory domains and two conserved catalytic glutamates residues, with relative positions compatible with a retaining mechanism of hydrolysis. Specificity screening and enzyme kinetics suggest that the enzymes prefer mixed-linkage glucans over β-1,3-glucans. Activity screening showed that both enzymes exhibit pH optimum at 6.5 and temperature optimum for LaGH157 and BcGH157 at 25 °C and 48 °C, respectively. Product analysis with HPAEC-PAD and LC-MS revealed that both enzymes are endo-1,3(4)-β-glucanases, capable of cleaving β-1,3 and β-1,4-linked glucoses, when preceded by a β-1,3 linkage. Moreover, BcGH157 needs a minimum of 4 subsites occupied for hydrolysis to occur, while LaGH157 only requires 3 subsites. Additionally, LaGH157 possesses exohydrolytic activity on β-1,3 and branching β-1,6 linkages. This unusual bifunctional endo-1,3(4)/exo-1,3-1,6 activity constitutes an expansion on our understanding of β-glucan deconstruction, with the potential to inspire future applications.}, } @article {pmid39528106, year = {2024}, author = {Nyawo, G and Naidoo, CC and Wu, BG and Kwok, B and Clemente, JC and Li, Y and Minnies, S and Reeve, B and Moodley, S and John, TJ and Karamchand, S and Singh, S and Pecararo, A and Doubell, A and Kyriakakis, C and Warren, R and Segal, LN and Theron, G}, title = {Bad company? The pericardium microbiome in people investigated for tuberculous pericarditis in an HIV-prevalent setting.}, journal = {Microbes and infection}, volume = {}, number = {}, pages = {105434}, doi = {10.1016/j.micinf.2024.105434}, pmid = {39528106}, issn = {1769-714X}, abstract = {BACKGROUND: The site-of-disease microbiome and predicted metagenome were evaluated in a cross-sectional study involving people with presumptive tuberculous pericarditis. We also explored the interaction between C-reactive protein (CRP) and the microbiome.

METHODS: People with effusions requiring diagnostic pericardiocentesis (n=139) provided pericardial fluid for sequencing and blood for CRP measurement.

RESULTS: Pericardial fluid microbiota differed in β-diversity among people with definite (dTB, n=91), probable (pTB, n=25), and non- (nTB, n=23) tuberculous pericarditis. dTBs were Mycobacterium-, Lacticigenium-, and Kocuria-enriched vs. nTBs. HIV-positive dTBs were Mycobacterium-, Bifidobacterium-, Methylobacterium-, and Leptothrix-enriched vs. HIV-negative dTBs. HIV-positive dTBs on ART were Mycobacterium- and Bifidobacterium-depleted vs. those not on ART. dTBs exhibited enrichment in short-chain fatty acid (SCFA) and mycobacterial metabolism pathways vs. nTBs. Additional non-pericardial involvement (pulmonary infiltrates) was associated with Mycobacterium-enrichment and Streptococcus-depletion. Mycobacterium reads were in 34 % (31/91) of dTBs, 8 % (2/25) of pTBs and 17 % (4/23) nTBs. People with CRP above (vs. below) the median value had different β-diversity (Pseudomonas-depleted). No correlation was found between enriched taxa in dTBs and CRP.

CONCLUSIONS: Pericardial fluid microbial composition varies by tuberculosis status, HIV (and ART) status and dTBs are enriched in SCFA-associated taxa. The clinical significance, including mycobacterial reads in nTBs and pTBs, requires evaluation.}, } @article {pmid39528052, year = {2025}, author = {Jiang, Q and Zhu, X and Sun, L and Xie, C and Wang, X and Ma, L and Yan, X}, title = {Akkermansia muciniphila Promotes SIgA Production and Alters the Reactivity Toward Commensal Bacteria in Early-Weaned Piglets.}, journal = {The Journal of nutrition}, volume = {155}, number = {1}, pages = {52-65}, doi = {10.1016/j.tjnut.2024.11.002}, pmid = {39528052}, issn = {1541-6100}, mesh = {Animals ; Swine ; *Immunoglobulin A, Secretory/metabolism ; *Weaning ; *Akkermansia ; *Gastrointestinal Microbiome ; *Feces/microbiology ; Male ; Mice ; Mice, Inbred C57BL ; Verrucomicrobia ; Bacteria/classification ; Intestines/microbiology/immunology ; }, abstract = {BACKGROUND: Secretory IgA (SIgA) is the first line of defense in protecting the intestinal epithelium against pathogenic bacteria, regulating gut microbiota composition, and maintaining intestinal homeostasis. Early weaning strategies may disrupt SIgA levels in piglet intestines, causing a decline in immune response and early weaning stress. However, the specific microbial mechanisms modulating SIgA in early-weaned piglets are not well understood.

OBJECTIVES: We hypothesized that Akkermansia muciniphila increases intestinal SIgA production in the early-weaned piglets.

METHODS: Fecal SIgA levels, SIgA-coated bacteria abundance, and fecal metagenomes were compared between 6 Huanjiang miniature (HM) and 6 Duroc×Landrace×Yorkshire (DLY) early-weaned piglets to identify bacterial species involved in SIgA modulation. Four bacterial species were investigated using 5 groups (Control, A. muciniphila, L. amylovorus, L. crispatus, and L. acidophilus) of male specific pathogen-free C57BL/6J mice, weaned 3 wk postbirth (n = 8/group). Subsequently, 10-d-old Landrace×Yorkshire (LY) piglets were randomly assigned to 3 groups (Control, 10[9]A. muciniphila, and 10[8]A. muciniphila) (n = 10/group) to evaluate the effect of orally administered A. muciniphila on intestinal SIgA production and microbial composition.

RESULTS: HM early-weaned piglets showed significantly higher SIgA levels [7.59 μg/mg, 95% confidence interval (CI): 3.2, 12, P = 0.002] and SIgA-coated bacteria abundance (8.64%, 95% CI: 3.2, 14, P = 0.014) than DLY piglets. In the mouse model, the administration of A. muciniphila significantly increased SIgA levels (3.50 μg/mg, 95% CI: 0.59, 6.4, P = 0.018), SIgA-coated bacteria abundance (9.06%, 95% CI: 4, 14, P = 0.018), and IgA[+] plasma cell counts (6.1%, 95% CI: 4.3, 8, P = 0.005). In the pig experiments, the oral administration of A. muciniphila to LY piglets significantly enhanced intestinal SIgA concentrations (4.22 μg/mg, 95% CI: 0.37, 8.5, P = 0.034) and altered the SIgA-coated bacterial landscape.

CONCLUSIONS: Early intervention with A. muciniphila in nursing piglets can increases intestinal SIgA production and alter the reactivity toward commensal bacteria upon early weaning.}, } @article {pmid39528031, year = {2025}, author = {Zhang, N and Zhu, D and Yao, Z and Zhu, DZ}, title = {Virus-prokaryote interactions assist pollutant removal in constructed wetlands.}, journal = {Bioresource technology}, volume = {416}, number = {}, pages = {131791}, doi = {10.1016/j.biortech.2024.131791}, pmid = {39528031}, issn = {1873-2976}, mesh = {*Wetlands ; *Bacteria/metabolism/genetics ; Nitrogen ; Viruses/metabolism/isolation & purification ; Water Pollutants, Chemical/metabolism ; Biodegradation, Environmental ; Denitrification ; }, abstract = {As a vital part of microbial communities, viruses in constructed wetlands (CWs) remain poorly explored, yet they could significantly affect pollutant removal. Here, two pilot-scale CWs were built to investigate the viral community under different hydraulic loading rates (HLRs) using in-depth metagenomic analysis. Gene-sharing networks suggested that the CWs were pools of unexplored viruses. A higher abundance of prokaryotic functional genes related to sulfur cycling and denitrification was observed in the higher HLR condition, which was associated with greater removal of total nitrogen and nitrate nitrogen compared to the lower HLR condition. Viruses also affect nitrogen pollutant removal by potentially infecting functional prokaryotes, such as denitrification bacteria and ammonia-oxidizing bacteria, and by providing auxiliary metabolic genes involved in sulfur and nitrogen cycling. These findings reveal the significance of viruses in pollutant removal in CWs and enhance the understanding of the relationship between engineering design parameters and performance from microbial perspectives.}, } @article {pmid39527864, year = {2025}, author = {de Castro Lins, P and Hamann, PRV and Lima, JCB and Gonçalves Barbosa, JAR and da Silva Correia, JL and de Andrade, IA and Knupp Dos Santos, DF and Quirino, BF and Krüger, RH}, title = {Biochemical characterization and structure prediction of the Cerrado soil CRB2(1) metagenomic dioxygenase.}, journal = {Enzyme and microbial technology}, volume = {182}, number = {}, pages = {110544}, doi = {10.1016/j.enzmictec.2024.110544}, pmid = {39527864}, issn = {1879-0909}, mesh = {*Dioxygenases/metabolism/genetics/chemistry ; *Soil Microbiology ; Substrate Specificity ; Kinetics ; Models, Molecular ; Metagenomics ; Amino Acid Sequence ; Bacterial Proteins/genetics/metabolism/chemistry ; Catalytic Domain ; Hydrogen-Ion Concentration ; Protein Conformation ; }, abstract = {Dioxygenases are enzymes involved in the conversion of polyconic aromatic hydroxycarbons (PAHs), attracting significant biotechnological interest for the conversion of recalcitrant organic compounds. Furthermore, few studies show that dioxygenases can take on the function of resistance genes in clones. This enzymatic versatility opens up new opportunities for elucidating the mechanisms of microbial resistance, as well as its biotechnological application. In this work, a Cerrado soil dioxygenase named CRB2(1) was biochemically characterized. The enzyme was shown to have optimal activity at pH 7; a temperature of 30 °C; and using iron ions as a cofactor for substrate cleavage. The kinetic catalytic parameters of CRB2(1) were Vmax = 0.02281 µM/min and KM = 97.6. Its predicted three-dimensional structure obtained using the Modeller software v9.22 based on the crystal structure of gentisate 1,2-dioxygenase from Silicibacter pomeroyi (GDOsp) (PDB ID 3BU7, resolution 2.80 Å, residues 17-374) revealed substrate binding to the cupin domain, where the active site is located. The analyzed substrates interact directly with the iron ion, coordinated by three histidine residues. Changing the iron ion charge modifies the binding between the active site and the substrates. Currently, there is a demand for enzymes that have biotechnological activities of interest. Metagenomics allows analyzing the biotechnological potential of several organisms at the same time, based on sequence and functional activity analyses.}, } @article {pmid39527509, year = {2024}, author = {Illidge, S and Kort, R and Hertzberger, R and , }, title = {'From women for women': A citizen science approach engaging women in the isolation and application of the vaginal health-associated bacterium Lactobacillus crispatus.}, journal = {PloS one}, volume = {19}, number = {11}, pages = {e0308526}, pmid = {39527509}, issn = {1932-6203}, mesh = {Humans ; Female ; *Vagina/microbiology ; *Probiotics ; *Lactobacillus crispatus/isolation & purification/genetics ; Adult ; *Vaginosis, Bacterial/microbiology/diagnosis ; *Microbiota ; Middle Aged ; Young Adult ; }, abstract = {A vaginal microbiome rich in Lactobacillus crispatus is associated with good reproductive and sexual health outcomes. Dysbiosis, indicated by the loss of Lactobacillus crispatus, is a risk factor for urogenital infections, such as the clinical diagnosis of bacterial vaginosis (BV) or urinary tract infections. While many scientists have explored probiotics using a conventional pharmaceutical approach, concerns about accessibility and affordability prompt an investigation into a preventive approach using this naturally occurring bacterium. Our study aimed to explore a potential woman-friendly vaginal probiotic product using the naturally occurring bacterium, Lactobacillus crispatus. Citizen scientists actively participated in a two-day practicum and successfully performed the procedures using self-collected vaginal swabs. The practicum received positive responses from participants who demonstrated notable engagement and enthusiasm. With expert guidance, participants without a laboratory background were able to execute assigned tasks successfully. From the Dutch crispatus Citizen Science Collective of 48 women, 22 succeeded in isolating their own Lactobacillus crispatus strains using a Loop-Mediated Isothermal Amplification (LAMP) protocol for identification. Additionally, 48 metagenomes and 54 whole genomes from 22 individuals were sequenced for comparative analysis. This project effectively engaged a community of women in the isolation of Lactobacillus crispatus strains from their vaginal microbiota, followed by in vitro characterization experiments and a hackathon for the development of a probiotic product. Our citizen science approach opens up collaboration possibilities and new avenues for exploration of vaginal health, facilitating community involvement and the development of targeted interventions to enhance women's well-being.}, } @article {pmid39526896, year = {2024}, author = {Wei, F and Jiang, H and Zhu, C and Zhong, L and Lin, Z and Wu, Y and Song, L}, title = {The co-fermentation of whole-grain black barley and quinoa improves murine cognitive impairment induced by a high-fat diet via altering gut microbial ecology and suppressing neuroinflammation.}, journal = {Food & function}, volume = {15}, number = {23}, pages = {11667-11685}, doi = {10.1039/d4fo02704c}, pmid = {39526896}, issn = {2042-650X}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Diet, High-Fat/adverse effects ; *Cognitive Dysfunction ; *Mice, Inbred C57BL ; *Chenopodium quinoa/chemistry ; Male ; *Hordeum/chemistry ; *Fermentation ; Neuroinflammatory Diseases/metabolism ; Lactobacillus ; Hippocampus/metabolism ; Brain-Gut Axis ; Bacteria/classification/genetics/isolation & purification ; }, abstract = {A high-fat diet (HFD) is associated with various adverse health outcomes, including cognitive impairment and an elevated risk of neurodegenerative conditions. This relationship is partially attributed to the influence of an HFD on the gut microbiota. The objective of this research was to evaluate the neuroprotective benefits of co-fermented black barley and quinoa with Lactobacillus (FG) against cognitive impairments triggered by an HFD and to investigate the microbiota-gut-brain axis mechanisms involved. C57BL/6J mice were randomized into four groups: the normal control group (NC, n = 10), the high-fat diet group (HFD, n = 10), the high-fat diet group supplemented with FG (HFG, 10 mL per kg BW, n = 10), and the high-fat diet group supplemented with Lactobacillus (HFL, 10 mL per kg BW, n = 10). Our results showed that the FG intervention enhanced the behavioral and locomotor skills of the mice, elevated the levels of dopamine (DA) and norepinephrine (NPI) in brain tissues, and alleviated synaptic ultrastructural damage in the hippocampus. Furthermore, FG intervention was observed to exert a protective effect on both the blood-brain barrier and the colonic barrier, as evidenced by an increase in the mRNA levels of Zona occludens-1 (ZO-1), Claudin-4, and Occludin in the hippocampus and colon. These beneficial effects may be attributed to FG's regulation of gut microbiota dysbiosis, which involves the restoration of intestinal flora diversity, reduction of the Firmicutes/Bacteroidetes (F/B) ratio, and a decrease in the levels of pro-inflammatory bacteria such as s_Escherichia coli E and g_Escherichia; moreover, there was an increase in the abundances of anti-inflammatory bacteria, such as s_Bacteroides thetaiotaomicron and s_Parabacteroides goldsteinii. Metagenomic analysis revealed that the FG treatment downregulated the lipopolysaccharide (LPS) pathway and upregulated neurotransmitter biosynthetic pathways. These probiotic effects of FG resulted in reduced production and "leakage" of LPS and decreased mRNA expression of Toll-like receptor 4 (Tlr4), cluster of differentiation 14 (CD14), and myeloid differentiation factor 88 (Myd88) in hippocampal and colon tissues. Consequently, a reduction was observed in the levels of inflammatory cytokines in the serum, hippocampus, and colon, along with suppression of the immunoreactivity of microglia and astrocytes. Our results suggest that FG may serve as an intervention strategy for preventing cognitive impairments caused by an HFD.}, } @article {pmid39526867, year = {2024}, author = {Guo, Z and Cao, J and Xu, R and Zhang, H and He, L and Gao, H and Zhu, L and Jia, M and Yang, Z and Xiong, W}, title = {Novel Photoelectron-Assisted Microbial Reduction of Arsenate Driven by Photosensitive Dissolved Organic Matter in Mine Stream Sediments.}, journal = {Environmental science & technology}, volume = {58}, number = {50}, pages = {22170-22182}, doi = {10.1021/acs.est.4c09647}, pmid = {39526867}, issn = {1520-5851}, mesh = {*Geologic Sediments/microbiology/chemistry ; Arsenates/metabolism ; Rivers/chemistry ; Mining ; }, abstract = {The microbial reduction of arsenate (As(V)) significantly contributes to arsenic migration in mine stream sediment, primarily driven by heterotrophic microorganisms using dissolved organic matter (DOM) as a carbon source. This study reveals a novel reduction pathway in sediments that photosensitive DOM generates photoelectrons to stimulate diverse nonphototrophic microorganisms to reduce As(V). This microbial photoelectrophic As(V) reduction (PEAsR) was investigated using microcosm incubation, which showed the transfer of photoelectrons from DOM to indigenous sediment microorganisms, thereby leading to a 50% higher microbial reduction rate of As(V). The abundance of two marker genes for As(V) reduction, arrA and arsC, increased substantially, confirming the microbial nature of PEAsR rather than a photoelectrochemical process. Photoelectron ion is unlikely to stimulate photolithoautotrophic growth. Instead, diverse nonphototrophic genera, e.g., Cupriavidus, Sphingopyxis, Mycobacterium, and Bradyrhizobium, spanning 13 orders became enriched by 10-50 folds. Metagenomic binning revealed their genetic potential to mediate the photoelectron-assisted reduction of As(V). These microorganisms contain essential genes involved in respiratory As(V) reduction, detoxification As(V) reduction, dimethyl sulfoxide reductase family, c-type cytochromes, and multiple heavy-metal resistance but lack a complete photosynthesis system. The novel microbial PEAsR pathway offers new insights into the interaction between photoelectron utilization and nonphototrophic As(V)-reducing microorganisms, which may have profound implications for arsenic pollution transportation in mine stream sediment.}, } @article {pmid39526797, year = {2024}, author = {Boutouchent, N and Vu, TNA and Landraud, L and Kennedy, SP}, title = {Metagenome-assembled genomes of 72 Escherichia coli strains from vaginal samples collected from pregnant women.}, journal = {Microbiology resource announcements}, volume = {13}, number = {12}, pages = {e0083124}, pmid = {39526797}, issn = {2576-098X}, abstract = {We report 72 metagenome-assembled genomes (MAGs) of Escherichia coli recovered from the vaginal microbiomes of pregnant women. The MAGs have an estimated median genome size of 5.1 Mb (IQR 4.9-5.3). The average number of unique genes identified per genome was 3,330 genes (IQR 3,356-3,501), with a mean of 1,708 per genome being annotated.}, } @article {pmid39526401, year = {2025}, author = {Jiang, Y and Wang, Y and Che, L and Yang, S and Zhang, X and Lin, Y and Shi, Y and Zou, N and Wang, S and Zhang, Y and Zhao, Z and Li, SC}, title = {GutMetaNet: an integrated database for exploring horizontal gene transfer and functional redundancy in the human gut microbiome.}, journal = {Nucleic acids research}, volume = {53}, number = {D1}, pages = {D772-D782}, pmid = {39526401}, issn = {1362-4962}, support = {20220814183301001//Shenzhen Science and Technology Program/ ; }, mesh = {*Gene Transfer, Horizontal ; Humans ; *Gastrointestinal Microbiome/genetics ; *Databases, Genetic ; Metagenome/genetics ; Metagenomics/methods ; Bacteria/genetics/classification ; }, abstract = {Metagenomic studies have revealed the critical roles of complex microbial interactions, including horizontal gene transfer (HGT) and functional redundancy (FR), in shaping the gut microbiome's functional capacity and resilience. However, the lack of comprehensive data integration and systematic analysis approaches has limited the in-depth exploration of HGT and FR dynamics across large-scale gut microbiome datasets. To address this gap, we present GutMetaNet (https://gutmetanet.deepomics.org/), a first-of-its-kind database integrating extensive human gut microbiome data with comprehensive HGT and FR analyses. GutMetaNet contains 21 567 human gut metagenome samples with whole-genome shotgun sequencing data related to various health conditions. Through systematic analysis, we have characterized the taxonomic profiles and FR profiles, and identified 14 636 HGT events using a shared reference genome database across the collected samples. These HGT events have been curated into 8049 clusters, which are annotated with categorized mobile genetic elements, including transposons, prophages, integrative mobilizable elements, genomic islands, integrative conjugative elements and group II introns. Additionally, GutMetaNet incorporates automated analyses and visualizations for the HGT events and FR, serving as an efficient platform for in-depth exploration of the interactions among gut microbiome taxa and their implications for human health.}, } @article {pmid39526369, year = {2025}, author = {Dmitrijeva, M and Ruscheweyh, HJ and Feer, L and Li, K and Miravet-Verde, S and Sintsova, A and Mende, DR and Zeller, G and Sunagawa, S}, title = {The mOTUs online database provides web-accessible genomic context to taxonomic profiling of microbial communities.}, journal = {Nucleic acids research}, volume = {53}, number = {D1}, pages = {D797-D805}, pmid = {39526369}, issn = {1362-4962}, support = {//ETH Zurich/ ; 51NF40_180575//NCCR/ ; //European Molecular Biology Laboratory/ ; 031A537B//Federal Ministry of Education and Research/ ; LT0050/2023-L//Human Frontier Science Program/ ; 205321_184955/SNSF_/Swiss National Science Foundation/Switzerland ; 101118531/ERC_/European Research Council/International ; /SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {*Internet ; *Databases, Genetic ; *Metagenome ; *Microbiota/genetics ; Genomics/methods ; Bacteria/genetics/classification ; Metagenomics/methods ; Phylogeny ; Software ; Genome, Bacterial ; }, abstract = {Determining the taxonomic composition (taxonomic profiling) is a fundamental task in studying environmental and host-associated microbial communities. However, genome-resolved microbial diversity on Earth remains undersampled, and accessing the genomic context of taxa detected during taxonomic profiling remains a challenging task. Here, we present the mOTUs online database (mOTUs-db), which is consistent with and interfaces with the mOTUs taxonomic profiling tool. It comprises 2.83 million metagenome-assembled genomes (MAGs) and 919 090 single-cell and isolate genomes from 124 295 species-level taxonomic units. In addition to being one of the largest prokaryotic genome resources to date, all MAGs in the mOTUs-db were reconstructed de novo in 117 902 individual samples by abundance correlation of scaffolds across multiple samples for improved quality metrics. The database complements the Genome Taxonomy Database, with over 50% of its species-level taxonomic groups being unique. It also offers interactive querying, enabling users to explore and download genomes at various taxonomic levels. The mOTUs-db is accessible at https://motus-db.org.}, } @article {pmid39526142, year = {2024}, author = {Chen, W and Liang, F and Zhang, Y and Zhang, Y and Lv, J and Jin, X and Ran, Y and Li, S and Sun, W}, title = {Metagenome-based characterization of the gut bacteriome, mycobiome, and virome in patients with chronic hepatitis B-related liver fibrosis.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1449090}, pmid = {39526142}, issn = {1664-302X}, abstract = {INTRODUCTION: The gut microbiota is believed to be directly involved in the etiology and development of chronic liver diseases. However, the holistic characterization of the gut bacteriome, mycobiome, and virome in patients with chronic hepatitis B-related liver fibrosis (CHB-LF) remains unclear.

METHODS: In this study, we analyzed the multi-kingdom gut microbiome (i.e., bacteriome, mycobiome, and virome) of 25 CHB-LF patients and 28 healthy individuals through whole-metagenome shotgun sequencing of their stool samples.

RESULTS: We found that the gut bacteriome, mycobiome, and virome of CHB-LF patients were fundamentally altered, characterized by a panel of 110 differentially abundant bacterial species, 16 differential fungal species, and 90 differential viruses. The representative CHB-LF-enriched bacteria included members of Blautia_A (e.g., B. wexlerae, B. massiliensis, and B. obeum), Dorea (e.g., D. longicatena and D. formicigenerans), Streptococcus, Erysipelatoclostridium, while some species of Bacteroides (e.g., B. finegoldii and B. thetaiotaomicron), Faecalibacterium (mainly F. prausnitzii), and Bacteroides_A (e.g., B. plebeius_A and B. coprophilus) were depleted in patients. Fungi such as Malassezia spp. (e.g., M. japonica and M. sympodialis), Candida spp. (e.g., C. parapsilosis), and Mucor circinelloides were more abundant in CHB-LF patients, while Mucor irregularis, Phialophora verrucosa, Hortaea werneckii, and Aspergillus fumigatus were decreases. The CHB-LF-enriched viruses contained 18 Siphoviridae, 12 Myoviridae, and 1 Podoviridae viruses, while the control-enriched viruses included 16 Siphoviridae, 9 Myoviridae, 2 Quimbyviridae, and 1 Podoviridae_crAss-like members. Moreover, we revealed that the CHB-LF-associated gut multi-kingdom signatures were tightly interconnected, suggesting that they may act together on the disease. Finally, we showed that the microbial signatures were effective in discriminating the patients from healthy controls, suggesting the potential of gut microbiota in the prediction of CHB-LF and related diseases.

DISCUSSION: In conclusion, our findings delineated the fecal bacteriome, mycobiome, and virome landscapes of the CHB-LF microbiota and provided biomarkers that will aid in future mechanistic and clinical intervention studies.}, } @article {pmid39526137, year = {2024}, author = {Clagnan, E and Costanzo, M and Visca, A and Di Gregorio, L and Tabacchioni, S and Colantoni, E and Sevi, F and Sbarra, F and Bindo, A and Nolfi, L and Magarelli, RA and Trupo, M and Ambrico, A and Bevivino, A}, title = {Culturomics- and metagenomics-based insights into the soil microbiome preservation and application for sustainable agriculture.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1473666}, pmid = {39526137}, issn = {1664-302X}, abstract = {Soil health is crucial for global food production in the context of an ever-growing global population. Microbiomes, a combination of microorganisms and their activities, play a pivotal role by biodegrading contaminants, maintaining soil structure, controlling nutrients' cycles, and regulating the plant responses to biotic and abiotic stresses. Microbiome-based solutions along the soil-plant continuum, and their scaling up from laboratory experiments to field applications, hold promise for enhancing agricultural sustainability by harnessing the power of microbial consortia. Synthetic microbial communities, i.e., selected microbial consortia, are designed to perform specific functions. In contrast, natural communities leverage indigenous microbial populations that are adapted to local soil conditions, promoting ecosystem resilience, and reducing reliance on external inputs. The identification of microbial indicators requires a holistic approach. It is fundamental for current understanding the soil health status and for providing a comprehensive assessment of sustainable land management practices and conservation efforts. Recent advancements in molecular technologies, such as high-throughput sequencing, revealed the incredible diversity of soil microbiomes. On one hand, metagenomic sequencing allows the characterization of the entire genetic composition of soil microbiomes, and the examination of their functional potential and ecological roles; on the other hand, culturomics-based approaches and metabolic fingerprinting offer complementary information by providing snapshots of microbial diversity and metabolic activities both in and ex-situ. Long-term storage and cryopreservation of mixed culture and whole microbiome are crucial to maintain the originality of the sample in microbiome biobanking and for the development and application of microbiome-based innovation. This review aims to elucidate the available approaches to characterize diversity, function, and resilience of soil microbial communities and to develop microbiome-based solutions that can pave the way for harnessing nature's untapped resources to cultivate crops in healthy soils, to enhance plant resilience to abiotic and biotic stresses, and to shape thriving ecosystems unlocking the potential of soil microbiomes is key to sustainable agriculture. Improving management practices by incorporating beneficial microbial consortia, and promoting resilience to climate change by facilitating adaptive strategies with respect to environmental conditions are the global challenges of the future to address the issues of climate change, land degradation and food security.}, } @article {pmid39525687, year = {2024}, author = {Yan, S and Liu, C and Luo, X and Wu, C and Zheng, Y and Zhuo, G and Zhen, G}, title = {Potential Application of Room Temperature Synthesized MIL-100(Fe) in Enhancing Methane Production in Microbial Electrolysis Cells-Anaerobic Digestion Treating Protein-Rich Wastewater.}, journal = {Chemical engineering journal (Lausanne, Switzerland : 1996)}, volume = {500}, number = {}, pages = {}, pmid = {39525687}, issn = {1385-8947}, support = {R21 AA021380/AA/NIAAA NIH HHS/United States ; }, abstract = {Microbial electrolysis cell-anaerobic digestion (MEC-AD) is an emerging technology for methane production. However, low substrate degradation efficiency remains a challenge when processing protein substrates. This study developed a MIL-100(Fe) carbon cloth anode to enhance methane production and substrate degradation in MEC-AD. The effects of MIL-100(Fe) prepared under hydrothermal (H-MIL-100(Fe)) and room temperature conditions (R-MIL-100(Fe)) were compared. Results indicated that H-MIL-100(Fe) and R-MIL-100(Fe) increased cumulative methane production by 16.01% and 14.99%, respectively compared to normal cloth, each influencing methane production through distinct mechanisms. Electrochemical characterization showed that H-MIL-100(Fe) enhanced the electrochemical performance more significantly due to the enrichment of Geotalea, with the oxidation current improved by 7.39-fold (R-MIL-100(Fe) increased it by only 2.95-fold) to promote growth of Methanobacterium. Metagenomic analysis revealed that R-MIL-100(Fe) tended to metabolize amino acids into methane rather than support cellular life activities, indicating its practicality under limited substrate concentration. In summary, R-MIL-100(Fe) shows greater potential for application due to its mild synthesis conditions and advantages in treating complex substrates.}, } @article {pmid39525658, year = {2024}, author = {Tran, DM and Nguyen, TH and Nguyen, AD}, title = {Shotgun metagenomics sequencing data of root microbial community of Huanglongbing-infected Citrus nobilis.}, journal = {Data in brief}, volume = {57}, number = {}, pages = {111061}, pmid = {39525658}, issn = {2352-3409}, abstract = {Huanglongbing (HLB) is the most serious citrus disease in Vietnam. For the first time, this paper reported root microbial data of HLB-infected Citrus nobilis grown in Dak Lak Province, Vietnam, for further work toward controlling this disease. Roots of HLB-infected C. nobilis were collected, and the genomic DNA was isolated. The Illumina platform was used to sequence the shotgun metagenomic library, and bioinformatic tools were used to analyze sequenced data. We found that 4 kingdoms, 27 phyla, 57 classes, 124 orders, 246 families, 722 genera, and 1758 species of the root microbiome were identified from the sample. Actinomycetota was the predominant phylum (47.37 %), and biosynthesis was the primary function (57.38 %) of the microbiome.}, } @article {pmid39525231, year = {2024}, author = {Xiang, H and Cai, M}, title = {Infections Combined With Myelin Oligodendrocyte Glycoprotein Antibody-Associated Disease: A Case Report and Systematic Review of the Literature.}, journal = {Cureus}, volume = {16}, number = {10}, pages = {e71229}, pmid = {39525231}, issn = {2168-8184}, abstract = {Myelinating oligodendrocyte glycoprotein antibody-associated disease (MOGAD) is an immune-mediated inflammatory demyelinating disease of the central nervous system. Its specific etiology and pathogenesis remain unclear. In recent years, there have been increasing reports of MOGAD occurring after infections. Even cases of concurrent infection and MOGAD have been documented. We report a clinical case of a 14-year-old male patient admitted to the hospital with a fever and loss of consciousness. He underwent thorough medical examinations. The results of second-generation sequencing of the metagenome of the cerebrospinal fluid revealed that he was infected with Haemophilus parainfluenzae, and serum testing showed positive MOG antibodies. He was discharged after improving with intravenous immunoglobulin and other treatments.}, } @article {pmid39524979, year = {2024}, author = {Zhang, Z and Tian, L}, title = {An Investigation into Diagnostic Strategies for Central Nervous System Infections Through the Integration of Metagenomic Next-Generation Sequencing and Conventional Diagnostic Methods.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {4865-4873}, pmid = {39524979}, issn = {1178-6973}, abstract = {PURPOSE: The optimal strategy for detecting central nervous system infections (CNSI) in cerebrospinal fluid (CSF) samples remains unclear.

METHODS: In a one-year, multicenter retrospective study, we examined the efficacy of metagenomic next-generation sequencing (mNGS) in comparison to conventional pathogen diagnostic techniques for CSF in diagnosing CNSI. We calculated the sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and Youden index for each diagnostic approach. Additionally, receiver operating characteristic (ROC) curves were constructed, and the area under the curve (AUC) was determined to assess the diagnostic performance of each method.

RESULTS: The study included 68 patients, comprising both adults and children, who were suspected of having CNSI. Through the application of comprehensive clinical interpretation (CCI), the sensitivity and specificity of mNGS were found to be 67.6% (95% confidence interval [CI]: 50.85-80.87%) and 45.8% (95% CI: 27.89-64.92%), respectively. In comparison, traditional pathogenic diagnostic methods indicated that the culture method demonstrated a sensitivity of 10.6% (95% CI: 4.63-22.6%) and a specificity of 100% (95% CI: 84.54-100%). Furthermore, the sensitivity and specificity of the peripheral blood nucleated cell count were determined to be 34.0% (95% confidence interval: 22.17-48.33%) and 57.1% (95% confidence interval: 36.54-75.53%), respectively. CSF nucleated cell count demonstrated a sensitivity of 66.0% (95% confidence interval [CI]: 51.67-77.83%) and a specificity of 61.9% (95% CI: 40.87-79.25%). In comparison, the CSF protein content exhibited a sensitivity of 63.8% (95% CI: 49.54-76.03%) and a specificity of 57.1% (95% CI: 36.54-75.53%). When combining mNGS with traditional methodologies, the overall sensitivity increased to 91.3% (95% CI: 79.67-96.56%), although the specificity was reduced to 18.2% (95% CI: 7.31-38.51%). The area under the ROC curve for culture, peripheral blood nucleated cell count, mNGS, CSF nucleated cell count, and CSF protein content were 0.8088, 0.6038, 0.6103, 0.5588, and 0.5588, respectively. The variation in CSF nucleated cell count did not significantly affect the diagnostic efficacy of mNGS.

CONCLUSION: Currently, both mNGS and traditional diagnostic methods encounter substantial challenges in diagnosing CNSI.}, } @article {pmid39523762, year = {2025}, author = {El Mouzan, M and Al Quorain, A and Assiri, A and Almasoud, A and Alsaleem, B and Aladsani, A and Al Sarkhy, A}, title = {Gut fungal profile in new onset treatment-naïve ulcerative colitis in Saudi children.}, journal = {Saudi journal of gastroenterology : official journal of the Saudi Gastroenterology Association}, volume = {31}, number = {1}, pages = {28-33}, pmid = {39523762}, issn = {1998-4049}, mesh = {Humans ; *Colitis, Ulcerative/microbiology/epidemiology ; Child ; Male ; Saudi Arabia/epidemiology ; Adolescent ; Female ; *Feces/microbiology ; Child, Preschool ; Gastrointestinal Microbiome ; Infant ; Young Adult ; Candida/isolation & purification/genetics ; Case-Control Studies ; DNA, Fungal/genetics/analysis ; Saccharomyces cerevisiae/genetics/isolation & purification ; Dysbiosis/microbiology/epidemiology ; }, abstract = {BACKGROUND: Although the role of fungi in gut inflammation in IBD has been suggested, data are still limited in ulcerative colitis (UC). Our aim was to describe the gut fungal profile in a pediatric UC in Saudi Arabia.

METHODS: Fecal samples from children with UC and control samples provided by healthy school children were collected. The fungal DNA was analyzed using Shotgun metagenomic procedures. Shannon alpha diversity, beta diversity, differential abundance, random forest classification algorithm, and area under the curve were analyzed.

RESULTS: There were 20 children with UC and 20 healthy school children. The median age and range were 13 (0.5-21) and 13 (7-16) years for children with UC and controls, respectively. Male subjects were 40% and 35% for UC and controls, respectively. At diagnosis, the UC extent was E4 (38%); E3 (25%); E2 (37%) and 35% had a PUCAI ≥65. The reduction of alpha diversity and the significant dissimilarity in children with UC were similar to those of most published studies. However, a significant difference was found at all taxa levels with a remarkable enhancement of Candida genus and Saccharomyces cerevisiae in children with UC. Three species were identified as fungal signatures and an area under the curve of 98.4% (95.1-100% CI), indicating an association with UC that has not been reported thus far.

CONCLUSION: We report significant fungal dysbiosis in children with UC consistent with published literature. However, the report of potential fungal signature and a strong association with UC deserves further studies with a bigger sample size from other populations.}, } @article {pmid39523638, year = {2024}, author = {Munjita, SM and Mubemba, B and Tembo, J and Bates, M and Munsaka, S}, title = {Rhipicephalus simus ticks: new hosts for phleboviruses.}, journal = {Parasitology}, volume = {151}, number = {9}, pages = {962-970}, pmid = {39523638}, issn = {1469-8161}, support = {RIA2016E-1609//European and Developing Countries Clinical Trials Partnership/ ; }, mesh = {*Rhipicephalus/microbiology/virology ; *Phlebovirus/classification/genetics ; Metagenome/genetics ; Genome, Viral/genetics ; Zambia ; Phylogeny ; Biodiversity ; Animals ; Disease Vectors ; }, abstract = {Ticks are widespread arthropods that transmit microorganisms of veterinary and medical significance to vertebrates, including humans. Rhipicephalus simus, an ixodid tick frequently infesting and feeding on humans, may play a crucial role in transmitting infectious agents across species. Despite the known association of many Rhipicephalus ticks with phleboviruses, information on R. simus is lacking. During a study in a riverine area in Lusaka Zambia, ten R. simus ticks were incidentally collected from the grass and bushes and subjected to metagenomic next generation sequencing (mNGS) in 2 pools of 5. Analysis detected a diverse microbial profile, including bacteria 82% (32/39), fungi 15.4% (6/39), and viruses 2.6% (1/39). Notably, viral sequence LSK-ZM-102022 exhibited similarity to tick phleboviruses, sharing 74.92% nucleotide identity in the RdRp gene and 72% in the NP gene with tick-borne phlebovirus (TBPV) from Greece and Romania, respectively. Its RNA-dependent RNA polymerase (RdRp) encoding region carried conserved RdRp and endonuclease domains characteristic of phenuiviridae viruses. Phylogenetic analysis positioned LSK-ZM-102022 in a distinct but lone lineage within tick phleboviruses basal to known species like brown dog tick phlebovirus and phlebovirus Antigone. Pair-wise genetic distance analysis revealed similar findings. This study emphasizes the urgency of further research on the ecology, transmission dynamics, and pathogenic potential of LSK-ZM-102022 and related TBPVs, crucial for local and global preparedness against emerging tick-borne diseases.}, } @article {pmid39523457, year = {2024}, author = {Chen, Y and Liu, S and Tan, S and Zheng, Y and Chen, Y and Yang, C and Lin, S and Mi, Y and Li, W}, title = {KRAS mutations promote the intratumoral colonization of enterotoxigenic bacteroides fragilis in colorectal cancer through the regulation of the miRNA3655/SURF6/IRF7/IFNβ axis.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2423043}, pmid = {39523457}, issn = {1949-0984}, mesh = {*Colorectal Neoplasms/microbiology/genetics/metabolism/pathology ; Humans ; *Bacteroides fragilis/genetics/metabolism ; *Proto-Oncogene Proteins p21(ras)/genetics/metabolism ; *MicroRNAs/genetics/metabolism ; *Mutation ; Animals ; Mice ; *Interferon-beta/metabolism/genetics ; *Interferon Regulatory Factor-7/metabolism/genetics ; Cell Line, Tumor ; Gastrointestinal Microbiome ; Mice, Nude ; Gene Expression Regulation, Neoplastic ; Female ; }, abstract = {KRAS mutations are associated with poor prognosis in colorectal cancer (CRC). Although the association between the gut microbiota and CRC has been extensively documented, it is unclear whether KRAS mutations can regulate the gut microbiota. Metagenomics has identified changes in the diversity of the gut microbiota in CRC due to KRAS mutations. Specifically, KRAS mutations positively correlate with the abundance of the bacteroides. Understanding how to regulate the classic carcinogenic bacterium within the bacteroides, such as enterotoxigenic bacteroides fragilis (ETBF), to enhance treatment efficacy of tumors is a key focus of research. Mechanistically, we found that the reduction of miR3655 is indispensable for KRAS mutation-promoted proliferation of CRC and the abundance of ETBF. miR3655 targets SURF6 to inhibit its transcription. Further transcriptomic sequencing revealed that SURF6 promotes intratumoral colonization of ETBF in CRC by inhibiting the nuclear translocation and transcription levels of the IRF7, affecting the activation of the IFNβ promoter. Regulating miR3655 and SURF6 can promote IFNβ secretion in CRC, directly killing ETBF. These data indicate that KRAS mutations affect the intratumoral colonization of ETBF in CRC through the miR3655/SURF6/IRF7/IFNβ axis. This provides new potential strategies for treating CRC associated with KRAS mutations or high levels of ETBF.}, } @article {pmid39523344, year = {2024}, author = {You, X and Yan, J and Herzog, J and Nobakhti, S and Campbell, R and Hoke, A and Hammamieh, R and Sartor, RB and Shefelbine, S and Kacena, MA and Chakraborty, N and Charles, JF}, title = {Bone loss with aging is independent of gut microbiome in mice.}, journal = {Bone research}, volume = {12}, number = {1}, pages = {65}, pmid = {39523344}, issn = {2095-4700}, support = {R01-AG046257//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; R01 AG046257/AG/NIA NIH HHS/United States ; P30-AR070253//U.S. Department of Health & Human Services | NIH | National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS)/ ; 997397//Crohn's and Colitis Foundation (Crohn's & Colitis Foundation)/ ; P40-OD010995//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; P30-DK034987//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Aging/physiology ; Male ; Mice ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Bone Resorption/microbiology ; Germ-Free Life ; }, abstract = {Emerging evidence suggests a significant role of gut microbiome in bone health. Aging is well recognized as a crucial factor influencing the gut microbiome. In this study, we investigated whether age-dependent microbial change contributes to age-related bone loss in CB6F1 mice. The bone phenotype of 24-month-old germ-free (GF) mice was indistinguishable compared to their littermates colonized by fecal transplant at 1-month-old. Moreover, bone loss from 3 to 24-month-old was comparable between GF and specific pathogen-free (SPF) mice. Thus, GF mice were not protected from age-related bone loss. 16S rRNA gene sequencing of fecal samples from 3-month and 24-month-old SPF males indicated an age-dependent microbial shift with an alteration in energy and nutrient metabolism potential. An integrative analysis of 16S predicted metagenome function and LC-MS fecal metabolome revealed an enrichment of protein and amino acid biosynthesis pathways in aged mice. Microbial S-adenosyl methionine metabolism was increased in the aged mice, which has previously been associated with the host aging process. Collectively, aging caused microbial taxonomic and functional alteration in mice. To demonstrate the functional importance of young and old microbiome to bone, we colonized GF mice with fecal microbiome from 3-month or 24-month-old SPF donor mice for 1 and 8 months. The effect of microbial colonization on bone phenotypes was independent of the microbiome donors' age. In conclusion, our study indicates age-related bone loss occurs independent of gut microbiome.}, } @article {pmid39523335, year = {2024}, author = {Ortiz-Severín, J and Hodar, C and Stuardo, C and Aguado-Norese, C and Maza, F and González, M and Cambiazo, V}, title = {Impact of salmon farming in the antibiotic resistance and structure of marine bacterial communities from surface seawater of a northern Patagonian area of Chile.}, journal = {Biological research}, volume = {57}, number = {1}, pages = {84}, pmid = {39523335}, issn = {0717-6287}, support = {Fondecyt-1211893//Agencia Nacional de Investigación y Desarrollo/ ; Millennium Science Initiative Program - ICN2021_044//Agencia Nacional de Investigación y Desarrollo/ ; Subvención a la Instalación en la Academia SA77210039//Agencia Nacional de Investigación y Desarrollo/ ; }, mesh = {Chile ; Animals ; *Seawater/microbiology ; *Aquaculture ; *Salmon/microbiology ; *Bacteria/drug effects/classification ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; }, abstract = {BACKGROUND: Aquaculture and salmon farming can cause environmental problems due to the pollution of the surrounding waters with nutrients, solid wastes and chemicals, such as antibiotics, which are used for disease control in the aquaculture facilities. Increasing antibiotic resistance in human-impacted environments, such as coastal waters with aquaculture activity, is linked to the widespread use of antibiotics, even at sub-lethal concentrations. In Chile, the world's second largest producer of salmon, aquaculture is considered the primary source of antibiotics residues in the coastal waters of northern Patagonia. Here, we evaluated whether the structure and diversity of marine bacterial community, the richness of antibiotic resistance bacteria and the frequency of antibiotic resistance genes increase in communities from the surface seawater of an area with salmon farming activities, in comparison with communities from an area without major anthropogenic disturbance.

RESULTS: The taxonomic structure of bacterial community was significantly different between areas with and without aquaculture production. Growth of the culturable fraction under controlled laboratory conditions showed that, in comparison with the undisturbed area, the bacterial community from salmon farms displayed a higher frequency of colonies resistant to the antibiotics used by the salmon industry. A higher adaptation to antibiotics was revealed by a greater proportion of multi-resistant bacteria isolated from the surface seawater of the salmon farming area. Furthermore, metagenomics data revealed a significant higher abundance of antibiotic resistant genes conferring resistance to 11 antibiotic families in the community from salmon farms, indicating that the proportion of bacteria carrying the resistance determinants was overall higher in salmon farms than in the undisturbed site.

CONCLUSIONS: Our results revealed an association between bacterial communities and antibiotic resistance from surface seawater of a coastal area of Chile. Although the total bacterial community may appear comparable between sites, the cultivation technique allowed to expose a higher prevalence of antibiotic resistant bacteria in the salmon farming area. Moreover, we demonstrated that metagenomics (culture-independent) and phenotypic (culture-dependent) methods are complementary to evaluate the bacterial communities' risk for antibiotic resistance, and that a human-influenced environment (such as salmon farms) can potentiate bacteria to adapt to environmental stresses, such as antibiotics.}, } @article {pmid39522897, year = {2024}, author = {Zhang, H and Yang, X and Chen, J and Jiang, Q and Yao, S and Chen, L and Xiang, X}, title = {Investigation of the mechanism by which Tegillarca granosa polysaccharide regulates non-alcoholic fatty liver disease in mice by modulating Lactobacillus Johnsonii.}, journal = {International journal of biological macromolecules}, volume = {282}, number = {Pt 6}, pages = {137259}, doi = {10.1016/j.ijbiomac.2024.137259}, pmid = {39522897}, issn = {1879-0003}, mesh = {Animals ; *Non-alcoholic Fatty Liver Disease/metabolism/drug therapy ; *Polysaccharides/pharmacology/chemistry ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Diet, High-Fat/adverse effects ; *Lactobacillus johnsonii/metabolism ; *Lipid Metabolism/drug effects ; Male ; Disease Models, Animal ; Liver/drug effects/metabolism ; RNA, Ribosomal, 16S/genetics ; Mice, Inbred C57BL ; }, abstract = {Non-alcoholic fatty liver disease (NAFLD), a prevalent chronic liver disease, is marked by excessive lipid deposition in the liver without alcohol abuse. Scapharca subcrenatum, a major Chinese farmed bivalve, yields S. subcrenatum polysaccharide (TGP), an active substance with known biological activity. Previous studies revealed TGP's significant regulatory effect on a high-fat diet (HFD)-induced NAFLD in mice. However, the precise mechanisms, particularly involving gut microbiota, remain unclear. In the current study, an antibiotic-treated mouse model was established to determine the mechanistic role of the gut microbiota in the observed anti-obesity effects of TGP. In addition, 16S rRNA genomic and metagenome-derived taxonomic analyses were performed to assess the gut microbial populations. The results showed that TGP selectively enhanced the number of the eosinophilic bacterium Lactobacillus johnsonii, which was reduced in HFD mice. Of note, the oral administration of L. johnsonii formulations to HFD mice alleviated NAFLD, and this was related to regulating lipid metabolism and the accumulation of lipids in the liver. Therefore, the current study uncovered a potential pathway for developing NAFLD treatment strategies based on the interaction between TGP and the gut microbiota.}, } @article {pmid39522830, year = {2025}, author = {Matamoros, BR and Serna, C and Wedel, E and Montero, N and Kirpekar, F and Gonzalez-Zorn, B}, title = {NpmC - a novel A1408 16S rRNA methyltransferase in the gut of humans and animals.}, journal = {International journal of antimicrobial agents}, volume = {65}, number = {1}, pages = {107382}, doi = {10.1016/j.ijantimicag.2024.107382}, pmid = {39522830}, issn = {1872-7913}, mesh = {*Methyltransferases/genetics/metabolism ; *RNA, Ribosomal, 16S/genetics ; *Aminoglycosides/pharmacology/metabolism ; Humans ; Animals ; *Escherichia coli/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; Sisomicin/analogs & derivatives/pharmacology ; Gastrointestinal Microbiome ; Escherichia coli Proteins/genetics/metabolism ; Methylation ; Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests ; }, abstract = {NpmA and NpmB are 16S rRNA methyltransferases that act on residue A1408 and confer high-level resistance to almost all aminoglycosides; however, these methyltransferases are rarely reported. A novel gene, npmC, was identified after analysisng all world-wide available metagenomic projects in a One Health context. This gene has a high level of similarity (91.5%) with npmA and up to 92.7% similarity at amino acidic level. The protein encoded by this gene presents the conserved motifs required for A1408 methylation. npmC was synthesized and its expression in Escherichia coli resulted in a high level of resistance to 4,5-disubstituted 2-deoxystreptamine (2-DOS) and 4-monosubstituted 2-DOS aminoglycosides, as well as moderate resistance to 4,6-disusbstituted 2-DOS aminoglycosides, including the last resort aminoglycoside, plazomicin. Methylation at residue A1408 was confirmed by mass spectrometry assays. Analysis of the npmC gene background revealed that its genetic context was associated with different insertion sequences that could mobilise the gene. Similarities in the genetic context between npmC and npmA indicate that they share a common ancestor. The immediate genetic context of this methyltransferase indicates a high relationship to the Eubacteriales order. This finding reveals the dark matter of the microbiome as a potential source of novel resistance genes, expands the list of the true pan-aminoglycoside 16S rRNA methyltransferases, which threaten the usefulness and development of next-generation aminoglycosides.}, } @article {pmid39522777, year = {2025}, author = {Martin, G and Rissanen, AJ and Garcia, SL and Peura, S}, title = {Dark carbon fixation is a common process in the water column of stratified boreal lakes.}, journal = {The Science of the total environment}, volume = {958}, number = {}, pages = {177433}, doi = {10.1016/j.scitotenv.2024.177433}, pmid = {39522777}, issn = {1879-1026}, mesh = {*Lakes/chemistry/microbiology ; *Carbon Cycle ; Sweden ; Photosynthesis ; Environmental Monitoring ; Bacteria/metabolism ; }, abstract = {CO2 fixation (i.e. primary production) is a key function of all ecosystems, providing the carbon and energy that fuel the entire food web. It also plays an important role in mitigating climate change as CO2 is the most important greenhouse gas. While photosynthesis is regarded as the most important carbon fixation pathway, prokaryotes able to fix carbon in the absence of light (chemolithoautotrophs) can also be a significant source of energy in a light-limited ecosystem. Boreal lakes, notoriously colored and stratified with respect to oxygen and nutrients, present ideal conditions for this so-called dark carbon fixation by the chemolithoautotrophs. However, the prevalence of dark carbon fixation in boreal lakes remains unknown. Here, we measured dark carbon fixation in Swedish lakes from the boreal and boreo-nemoral zones, during summer stratification. We detected dark carbon fixation in 16 out of the 17 lakes studied, and concluded that dark fixation is a widespread phenomenon in boreal lakes. Moreover, the average dark primary production ranged from 18.5 % in the epilimnion to 81.4 % in the hypolimnion of all tested lakes. Our data further suggests that chemolithoautotrophic activity is mostly driven by iron-oxidizing bacteria. The chemolithoautotrophic guild is diverse and seems to be composed of both ubiquitous bacteria, like Gallionellaceae or Chromatiaceae, and endemic taxa, such as Ferrovaceae, which appears to be favored by a low pH. These results are particularly exciting as they suggest that dark carbon fixation could partly compensate for the low photosynthetic capacity in lakes with dark-colored water.}, } @article {pmid39522205, year = {2024}, author = {Wang, Z and Cao, H and Jin, J and Thorley, E and Cava, J and Sun, Y and Zhang, L and Wang, N and Yang, Z}, title = {Diel asynchrony in the expanded characteristics of toxic cyanobacterial blooms revealed by integrated metabolomics and metagenomics.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {136403}, doi = {10.1016/j.jhazmat.2024.136403}, pmid = {39522205}, issn = {1873-3336}, mesh = {*Metabolomics ; *Cyanobacteria/genetics/metabolism ; *Metagenomics ; *Lakes/microbiology ; China ; Biomass ; Microbiota ; Phytoplankton/genetics/metabolism ; }, abstract = {We establish a field metabolomics protocol in Lake Taihu (China) and determined two critical parameters: the minimum amount of biomass for metabolomics and the daytime when metabolomes are stable. The minimum biomass is 475-950 µg dry weight (DW) or 204-408 ng DNA for F (phytoplankton) samples, and 940-1760 µg DW or 193-514 ng DNA for W (whole-water) samples. In a diel cycle, temporal taxonomical composition, metabolic state, and response to physiochemical factors progressed asynchronously between the F and W microbiomes. F peak growth (metabolic steady state) occurred 12-17 pm while W around 12 pm in metabolite identity, concentration, and molecular weight. 482 (∼50 %) metabolites highly correlated between the F and W microbiomes. Integrated analysis revealed different systematic changes between F and W sample, in taxon-associated metabolites, reactions, and biological functions: e.g., carbon metabolism and bioenergetics in F and amino acid metabolism and central metabolism in W samples. Metagenomics discovered important interspecific and intraspecific diversity using single-nucleotide polymorphism, and interactions between cyanobacteria and epibiotic bacteria. Diel intraspecific diversity shift inferred Microcystis aeruginosa and Anabaena sp. have different temperature optima experimentally verified. This integrated multi-omics protocol expands water microbiome analyses from conventional structure and function to diversity dynamics and interspecific metabolism and ecophysiology.}, } @article {pmid39522045, year = {2024}, author = {Cabezas, MP and Fonseca, NA and Muñoz-Mérida, A}, title = {MIMt: a curated 16S rRNA reference database with less redundancy and higher accuracy at species-level identification.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {88}, pmid = {39522045}, issn = {2524-6372}, support = {UIDB/04050/2020//FCT/ ; NORTE-01-0246-FEDER-000063//NORTE2020/ ; NORTE-01-0246-FEDER-000063//NORTE2020/ ; }, abstract = {MOTIVATION: Accurate determination and quantification of the taxonomic composition of microbial communities, especially at the species level, is one of the major issues in metagenomics. This is primarily due to the limitations of commonly used 16S rRNA reference databases, which either contain a lot of redundancy or a high percentage of sequences with missing taxonomic information. This may lead to erroneous identifications and, thus, to inaccurate conclusions regarding the ecological role and importance of those microorganisms in the ecosystem.

RESULTS: The current study presents MIMt, a new 16S rRNA database for archaea and bacteria's identification, encompassing 47 001 sequences, all precisely identified at species level. In addition, a MIMt2.0 version was created with only curated sequences from RefSeq Targeted loci with 32 086 sequences. MIMt aims to be updated twice a year to include all newly sequenced species. We evaluated MIMt against Greengenes, RDP, GTDB and SILVA in terms of sequence distribution and taxonomic assignments accuracy. Our results showed that MIMt contains less redundancy, and despite being 20 to 500 times smaller than existing databases, outperforms them in completeness and taxonomic accuracy, enabling more precise assignments at lower taxonomic ranks and thus, significantly improving species-level identification.}, } @article {pmid39522019, year = {2024}, author = {Wang, W and Chen, H and Wang, H and Fang, L and Wang, H and Ding, Y and Lu, Y and Wu, Q}, title = {Interpretation knowledge extraction for genetic testing via question-answer model.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1062}, pmid = {39522019}, issn = {1471-2164}, support = {62266012//National Natural Science Foundation of China/ ; 62272172//National Natural Science Foundation of China/ ; 2023A04J1051//Guangzhou Basic Research Program-Basic and Applied Basic Research Project/ ; 2023B003//Guangdong Institute of Scientific and Technical Information Strategic Studies Project/ ; }, mesh = {*Genetic Testing/methods ; Humans ; *Knowledge Bases ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Computational Biology/methods ; }, abstract = {BACKGROUND: Sequencing-based genetic testing is widely used in biomedical research, including pathogenic microorganism detection with metagenomic next-generation sequencing (mNGS). The application of sequencing results to clinical diagnosis and treatment relies on various interpretation knowledge bases. Currently, the existing knowledge bases are primarily built through manual knowledge extraction. This method requires professionals to read extensive literature and extract relevant knowledge from it, which is time-consuming and costly. Furthermore, manual extraction unavoidably introduces subjective biases. In this study, we aimed to automatically extract knowledge for interpreting mNGS results.

METHOD: We propose a novel approach to automatically extract pathogenic microorganism knowledge based on the question-answer (QA) model. First, we construct a MicrobeDB dataset since there is no available pathogenic microorganism QA dataset for training the model. The created dataset contains 3,161 samples from 618 published papers covering 224 pathogenic microorganisms. Then, we fine-tune the selected baseline model based on MicrobeDB. Finally, we utilize ChatGPT to enhance the diversity of training data, and employ data expansion to increase training data volume.

RESULTS: Our method achieves an Exact Match (EM) and F1 score of 88.39% and 93.18%, respectively, on the MicrobeDB test set. We also conduct ablation studies on the proposed data augmentation method. In addition, we perform comparative experiments with the ChatPDF tool based on the ChatGPT API to demonstrate the effectiveness of the proposed method.

CONCLUSIONS: Our method is effective and valuable for extracting pathogenic microorganism knowledge.}, } @article {pmid39521944, year = {2024}, author = {Rumi, MA and Oh, M and Davis, BC and Brown, CL and Juvekar, A and Vikesland, PJ and Pruden, A and Zhang, L}, title = {MetaCompare 2.0: differential ranking of ecological and human health resistome risks.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {12}, pages = {}, doi = {10.1093/femsec/fiae155}, pmid = {39521944}, issn = {1574-6941}, support = {#2004751//National Science Foundation/ ; 4813//Water Research Foundation/ ; }, mesh = {Humans ; *Metagenome ; Metagenomics/methods ; Wastewater/microbiology ; Bacteria/genetics/drug effects/classification ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; Risk Assessment ; Soil Microbiology ; }, abstract = {While numerous environmental factors contribute to the spread of antibiotic resistance genes (ARGs), quantifying their relative contributions remains a fundamental challenge. Similarly, it is important to differentiate acute human health risks from environmental exposure, versus broader ecological risk of ARG evolution and spread across microbial taxa. Recent studies have proposed various methods for achieving such aims. Here, we introduce MetaCompare 2.0, which improves upon original MetaCompare pipeline by differentiating indicators of human health resistome risk (potential for human pathogens of acute resistance concern to acquire ARGs) from ecological resistome risk (overall mobility of ARGs and potential for pathogen acquisition). The updated pipeline's sensitivity was demonstrated by analyzing diverse publicly-available metagenomes from wastewater, surface water, soil, sediment, human gut, and synthetic microbial communities. MetaCompare 2.0 provided distinct rankings of the metagenomes according to both human health resistome risk and ecological resistome risk, with both scores trending higher when influenced by anthropogenic impact or other stress. We evaluated the robustness of the pipeline to sequence assembly methods, sequencing depth, contig count, and metagenomic library coverage bias. The risk scores were remarkably consistent despite variations in these technological aspects. We packaged the improved pipeline into a publicly-available web service (http://metacompare.cs.vt.edu/) that provides an easy-to-use interface for computing resistome risk scores and visualizing results.}, } @article {pmid39521674, year = {2024}, author = {Stensvold, CR}, title = {Metabarcoding in gut protozoology.}, journal = {Trends in parasitology}, volume = {40}, number = {12}, pages = {1173-1182}, doi = {10.1016/j.pt.2024.10.015}, pmid = {39521674}, issn = {1471-5007}, mesh = {Animals ; *DNA Barcoding, Taxonomic ; High-Throughput Nucleotide Sequencing ; Humans ; Gastrointestinal Tract/parasitology ; Parasitology/methods/trends ; }, abstract = {Next-generation sequencing (NGS) methods include whole-genome sequencing, metagenomic analysis, and amplicon-based NGS, all of which are gaining territory in parasitology. A modality of particular interest within the field of gut protozoology is exhaustive metabarcoding of ribosomal genes in a complex matrix such as faeces, by which method, amplicon-based NGS enables the detection and differentiation of both eukaryotic and prokaryotic organisms, circumventing Sanger sequencing-based limitations and representing a one-fits-most approach. Apart from being a tool to break the code of intracellular genetic variation and tell mixed species infections apart, metabarcoding can produce data that can serve to augment our understanding of the interplay between the organisms within the gut.}, } @article {pmid39521543, year = {2024}, author = {Gleeson, M and Ridge, P and Sulaiman, I}, title = {Lung Microbiome: How to Appreciate and Apply It to Clinical Practice.}, journal = {Chest}, volume = {166}, number = {5}, pages = {925-927}, doi = {10.1016/j.chest.2024.06.3777}, pmid = {39521543}, issn = {1931-3543}, } @article {pmid39521075, year = {2024}, author = {Oliveira, OA and Estrada, CSD and Vidal, LO and Junior, LCC and Abril, G and Rezende, CE and Thompson, CC and Thompson, FL and Tschoeke, DA and Garcia, GD}, title = {Insights into the water microbiome dynamics of a large tropical estuary transition.}, journal = {The Science of the total environment}, volume = {957}, number = {}, pages = {177411}, doi = {10.1016/j.scitotenv.2024.177411}, pmid = {39521075}, issn = {1879-1026}, mesh = {*Estuaries ; *Microbiota ; Tropical Climate ; Environmental Monitoring ; Bacteria/classification/genetics ; Seasons ; Water Microbiology ; Brazil ; Biodiversity ; Methane/metabolism ; }, abstract = {Tropical estuarine systems play several ecological roles, such as acting as a nursery for biodiversity and cycling nutrients and greenhouse gases. However, the phylogenetic and metabolic diversity of estuarine microbiomes is not completely known. Furthermore, it is unclear how seasonal patterns may affect microbial diversity in these systems. The aim of the present study was to determine the metagenomic diversity and its major drivers in a large tropical estuarine system dominated by a mangrove forest in the South Atlantic around the Paraiba do Sul River. In total, 12.16 million shotgun sequences were generated (dry season: n = 8; wet season: n = 5), and water-quality parameters were evaluated for all locations. Metagenomic sequences were distributed between two patterns: (1) the dry season, in which the families Rhodobactereaceae and Flavobactereaceae increased, and (2) the wet season, in which Moraxellaceae, Pseudomonadaceae, Pseudoalteromonadaceae were more abundant. The dry season was characterized by higher salinity, nitrogen fixation, nitrification, and photosynthetic potential. In contrast, the wet season had higher carbon dioxide (CO2) and methane (CH4) production and a higher abundance of methanogenic, methylotrophic, and chemoorganotrophic bacteria in samples with low salinity. These findings suggest a possible relationship with the production of greenhouse gases during the wet period.}, } @article {pmid39520912, year = {2024}, author = {Zhao, L and Weng, W and Ni, M and Shen, H and Zhang, S and Chen, Y and Jia, R and Fan, L and Mao, Y and Qin, L and Liu, S and Wang, Y}, title = {Rubidium salt can effectively relieve the symptoms of DSS-induced ulcerative colitis.}, journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie}, volume = {181}, number = {}, pages = {117574}, doi = {10.1016/j.biopha.2024.117574}, pmid = {39520912}, issn = {1950-6007}, mesh = {*Colitis, Ulcerative/drug therapy/microbiology ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Dextran Sulfate ; Male ; Mice ; Mice, Inbred C57BL ; Salts ; Colon/drug effects/pathology/metabolism/microbiology ; Disease Models, Animal ; }, abstract = {Inflammatory bowel disease (IBD) is a chronic condition that afflicts individuals repeatedly and cannot be cured at present, which has seriously affected the quality of life of patients. Minerals Containing Rubidium (MCR) from Guangxi Yuechengling, which Professor Zhao Lichun purified, were explored. Against this backdrop, the present study investigates the efficacy of rubidium salt in ulcerative colitis. Rubidium salt reduced levels of inflammatory markers and improved intestinal barrier function through the Elisa kit, immunohistochemistry, and qPCR. Next, we detected the level of short-chain fatty acid and found that the content of propanoic acid, butyric acid, and n-butyric acid increased after treatment with rubidium salt. We used fecal metagenomics to explore the underlying reasons further and found that rubidium salt significantly adjusted the structure of intestinal flora, increased the abundance of beneficial bacteria such as lactobacillus and bifidobacterium, and inhibited the abundance of harmful bacteria such as Enterobacteriaceae and Escherichia coli. We also learned that rubidium salt directly weakened pathogenic bacteria's infection and survival ability by reducing the expression of virulence factors such as fimH, invA, and hilA and virulence genes such as acrA and ompR. Overall, rubidium salt can reduce harmful bacteria and increase beneficial bacteria. The increased beneficial bacteria help enhance the gut barrier and regulate inflammatory factors by raising the levels of short-chain fatty acids. A strengthened gut barrier further stabilizes microbial homeostasis, ultimately alleviating ulcerative colitis.}, } @article {pmid39520707, year = {2024}, author = {Lu, T and Ericsson, AC and Dietz, ZK and Cato, AK and Coghill, LM and Picking, WD and Picking, WL}, title = {Impact of an intranasal L-DBF vaccine on the gut microbiota in young and elderly mice.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2426619}, pmid = {39520707}, issn = {1949-0984}, support = {R01 AI138970/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Administration, Intranasal ; Mice ; *Feces/microbiology ; Female ; Shigella Vaccines/immunology/administration & dosage/genetics ; Lung/microbiology/immunology ; Shigella/immunology/genetics ; RNA, Ribosomal, 16S/genetics ; Age Factors ; Mice, Inbred BALB C ; Vaccination ; }, abstract = {Shigella spp. cause bacillary dysentery (shigellosis) with high morbidity and mortality in low- and middle-income countries. Infection occurs through the fecal-oral route and can be devastating for vulnerable populations, including infants and the elderly. These bacteria invade host cells using a type III secretion system (T3SS). No licensed vaccine yet exists for shigellosis, but we have generated a recombinant fusion protein, L-DBF, combining the T3SS needle tip protein (IpaD), translocator protein (IpaB), and the LTA1 subunit of enterotoxigenic E. coli labile toxin, which offers broad protection in a mouse model of lethal pulmonary infection. The L-DBF vaccine protects high-risk groups, including young and elderly mice. Here, we investigated how the gut microbiota of young and elderly mice responds to intranasal L-DBF vaccination formulated in an oil-in-water emulsion (ME). Samples from lungs, small intestines, and feces were collected on day 14 after 2 or 3 doses of L-DBF in ME. 16S rRNA gene sequencing revealed age-dependent changes in gut microbiota post-vaccination. The vaccine-induced changes were more prominent in the elderly mice and were most significant in the intestinal tract, indicating that vaccination by the intranasal route can have a tremendous impact on the gut environment. These findings provide insight into the communication between the intranasal mucosal surface following subunit vaccination and the microbiota at a distant mucosal site, thereby highlighting the impact of vaccination and the host's microbiome.}, } @article {pmid39520638, year = {2024}, author = {Abhadionmhen, AO and Asogwa, CN and Ezema, ME and Nzeh, RC and Ezeora, NJ and Abhadiomhen, SE and Echezona, SC and Udanor, CN}, title = {Machine Learning Approaches for Microorganism Identification, Virulence Assessment, and Antimicrobial Susceptibility Evaluation Using DNA Sequencing Methods: A Systematic Review.}, journal = {Molecular biotechnology}, volume = {}, number = {}, pages = {}, pmid = {39520638}, issn = {1559-0305}, abstract = {Microbial infections pose a substantial global health challenge, particularly impacting immunocompromised individuals and exacerbating the issue of antimicrobial resistance (AMR). High virulence of pathogens can lead to severe infections and prolonged antimicrobial treatment, increasing the risk of developing resistant strains. Integrating machine-learning (ML) with DNA sequencing technologies offers potential solutions by enhancing microbial identification, virulence assessment, and antimicrobial susceptibility evaluation. This review explores recent advancements in these integrated approaches, addressing current limitations and identifying gaps in the literature. A comprehensive literature search was conducted across databases including PubMed, Scopus, Web of Science, and IEEE Xplore, covering publications from January 2014 to June 2024. Using a detailed Boolean search string, relevant studies focusing on ML applications in microorganism identification, antimicrobial susceptibility testing, and microbial virulence were included. The screening process involved a two-stage review of titles, abstracts, and full texts, with data extraction and critical appraisal performed using the QIAO tool. Data were analyzed through narrative synthesis to identify common themes and innovations. Out of 1,650 initially identified records, 19 studies met the inclusion criteria. These studies primarily focused on AMR, with additional research on microbial virulence and identification. Machine learning algorithms such as Random Forest, Support Vector Machines, and Convolutional Neural Networks, combined with DNA sequencing techniques like Whole Genome Sequencing and Metagenomic Sequencing, demonstrated significant advancements in predictive accuracy and efficiency. High-quality studies achieved impressive performance metrics, including F1-scores up to 0.88 and AUC scores up to 0.96. The integration of ML and DNA sequencing technologies has significantly enhanced microbial analysis, improving the identification of pathogens, assessment of virulence, and evaluation of antimicrobial susceptibility. Despite advancements, challenges such as data quality, high costs, and model interpretability persist. This review highlights the need for continued innovation and provides recommendations for future research to address these limitations and improve disease management and public health strategies. The systematic review is registered with PROSPERO (CRD42024571347).}, } @article {pmid39520618, year = {2025}, author = {Men, Z and Chen, Z and Gu, X and Wang, Y and Zhang, X and Fang, F and Shen, M and Huang, S and Wu, S and Zhou, L and Bai, Z}, title = {Clinical relevance of lung microbiota composition in critically ill children with acute lower respiratory tract infections: insights from a retrospective analysis of metagenomic sequencing.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {44}, number = {1}, pages = {83-98}, pmid = {39520618}, issn = {1435-4373}, support = {H2023106//Medical Research Project of Jiangsu Provincial Commission of Health/ ; SKY2022178//Science and Technology Development Project of Suzhou/ ; SKJY2021108//Science and Technology Development Project of Suzhou/ ; BK20211077//Natural Science Foundation of Jiangsu Province/ ; BE2023714//Science and Technology Support Program of Jiangsu Province/ ; GSWS2019015//Gusu Health Talent Program/ ; ML13100423//Suzhou Medical College Clinician Scientist Program/ ; }, mesh = {Humans ; Retrospective Studies ; Male ; Female ; Child, Preschool ; *Metagenomics/methods ; Child ; *Lung/microbiology ; Infant ; *Microbiota/genetics ; *Respiratory Tract Infections/microbiology ; *Critical Illness ; *Bronchoalveolar Lavage Fluid/microbiology ; High-Throughput Nucleotide Sequencing ; Bacteria/classification/genetics/isolation & purification ; Prognosis ; Metagenome ; Severity of Illness Index ; Clinical Relevance ; }, abstract = {PURPOSE: Acute lower respiratory tract infections (ALRIs) is a leading cause of child mortality worldwide. Metagenomic next-generation sequencing (mNGS) identifies ALRIs pathogens and explores the lung microbiota's role in disease severity and clinical outcomes. This study examines the association between lung microbiota and ALRIs outcomes in children, exploring its potential as a prognostic biomarker.

METHODS: We retrospectively analyzed mNGS data from the bronchoalveolar lavage fluid (BALF) of 83 pediatric ALRIs patients from 2019 to 2023. Microbial diversity and relative abundances of specific taxa were compared between survivor and non-survivor groups, as well as between varying severity levels. LEfSe was employed to identify key biomarkers related to survival and disease severity.

RESULTS: Among the 83 patients, 68 survived and 15 died. Patients were also divided into a low severity group (n = 38) and a moderate-to-very-high severity group (n = 45) according to mPIRO score at admission. Significant differences in beta diversity were observed between the survival groups and across different severity levels. Prevotella, Haemophilus and Veillonella exhibited higher abundances in both the survivor and low severity groups, suggesting their potential as predictors of better outcomes. Conversely, Enterococcus and Acinetobacter baumannii were more prevalent in the non-survivor and moderate-to-very-high severity groups. Additionally, Streptococcus pneumoniae and Streptococcus mitis showed increased abundances in survivors. LEfSe further revealed that these microorganisms may predict outcomes and severity in ALRIs.

CONCLUSION: Our findings underscore the complex relationship between lung microbiota and ALRIs, with specific microbial profiles associated with disease severity and clinical outcomes. This underscores the need for further research to explore and validate its prognostic predictive capacity.

CLINICAL TRIAL NUMBER: Not applicable.}, } @article {pmid39520498, year = {2024}, author = {Ramfelt, O and Freel, KC and Tucker, SJ and Nigro, OD and Rappé, MS}, title = {Isolate-anchored comparisons reveal evolutionary and functional differentiation across SAR86 marine bacteria.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39520498}, issn = {1751-7370}, support = {P20 GM103466/GM/NIGMS NIH HHS/United States ; OCE-2149128//National Science Foundation/ ; OAR-2118222//Data Science Graduate Fellowship/ ; }, mesh = {*Phylogeny ; *Genome, Bacterial ; *Seawater/microbiology ; Gammaproteobacteria/genetics/classification/metabolism/isolation & purification ; Aquatic Organisms/genetics/classification ; }, abstract = {SAR86 is one of the most abundant groups of bacteria in the global surface ocean. However, since its discovery over 30 years ago, it has remained recalcitrant to isolation and many details regarding this group are still unknown. Here, we report the cellular characteristics from the first SAR86 isolate brought into culture, Magnimaribacter mokuoloeensis strain HIMB1674, and use its closed genome in concert with over 700 environmental genomes to assess the phylogenomic and functional characteristics of this order-level lineage of marine Gammaproteobacteria. The SAR86 order Magnimaribacterales invests significant genomic resources into the capacity for $\beta$-oxidation, which is present in most genomes with high gene copy numbers. This cyclical set of reactions appears to be fed by components of cell membranes that include lipids such as phosphatidylcholine, phosphatidylethanolamine, glycolipids, and sulfolipids. In addition to the widespread capacity to degrade the side chain of steroidal compounds via $\beta$-oxidation, several SAR86 sublineages also appear able to fully degrade the steroid polycyclic ring structure as well as other aromatic, polycyclic, and heterocyclic molecules. Read recruitment from publicly available metagenomes reveals that the Magnimaribacterales compose up to 6% of the global surface ocean microbial community. Only a subset of genera drives these high relative abundances, with some more globally dominant and others restricted to specific oceanic regions. This study provides an unprecedented foundation through which to understand this highly abundant yet poorly understood lineage of marine bacteria and charts a path to bring more representatives of this order into laboratory culture.}, } @article {pmid39520096, year = {2024}, author = {Logel, M and Tope, P and El-Zein, M and Gonzalez, E and Franco, EL}, title = {A Narrative Review of the Putative Etiologic Role and Diagnostic Utility of the Cervicovaginal Microbiome in Human Papillomavirus-Associated Cervical Carcinogenesis.}, journal = {Journal of medical virology}, volume = {96}, number = {11}, pages = {e70027}, pmid = {39520096}, issn = {1096-9071}, support = {//This work was supported by the Canadian Institutes of Health Research (grant FDN-143347 to E.L.F.) and Fonds de Recherche du Québec - Santé./ ; }, mesh = {Humans ; Female ; *Microbiota ; *Uterine Cervical Neoplasms/virology/diagnosis/microbiology ; *Papillomavirus Infections/diagnosis/virology/microbiology ; *Vagina/microbiology/virology ; *Cervix Uteri/microbiology/virology ; *Papillomaviridae/genetics/isolation & purification/classification ; Metagenomics/methods ; Carcinogenesis ; RNA, Ribosomal, 16S/genetics ; Bacteria/isolation & purification/genetics/classification ; Human Papillomavirus Viruses ; }, abstract = {The cervicovaginal microbiome (CVM) may contribute to human papillomavirus (HPV)-associated cervical carcinogenesis. We summarized the literature on the CVM in cervical carcinogenesis by searching Medline, Web of Science, and Embase for articles that sequenced the CVM using metagenomics. Additionally, we identified studies assessing the diagnostic role of the CVM in cervical carcinogenesis by searching PubMed. We performed an environmental scan of Google and Google Scholar to review common CVM characterization techniques. Twenty-eight records presented or summarized associations between the CVM and HPV acquisition, prevalence, persistence, clearance, and cervical lesions or cancer, while three studies identified bacterial taxa detecting high-risk HPV prevalence or cervical lesions. The area under the curve ranged from 0.802 to 0.952. 16S ribosomal RNA gene sequencing and whole metagenome sequencing have sufficient resolution to study the CVM bacteriome. Bacterial communities may have important implications in cervical cancer; however, there is a need for methodological standardization for CVM characterization.}, } @article {pmid39519924, year = {2024}, author = {Lohmaneeratana, K and Gutiérrez, G and Thamchaipenet, A and Wellinger, RE}, title = {Phytoplasma DNA Enrichment from Sugarcane White Leaves for Shotgun Sequencing Improvement.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {21}, pages = {}, pmid = {39519924}, issn = {2223-7747}, support = {2020/00001326//Universidad de Sevilla/ ; P20-RT-01220//Junta de Andalucía/European Union Regional Funds/ ; FF(KU)5.64//Kasetsart University Research and Development Institute/ ; //Bioinformatics Academic Association of Thailand (BAT)/ ; NRCT5-RRI63002-P02//Research and Researcher Fund for Industry, National Research Council of Thailand/ ; }, abstract = {Sugarcane white leaf (SCWL) disease, caused by Candidatus Phytoplasma sacchari, poses a significant threat to sugarcane cultivation. An obligate parasite, phytoplasma is difficult to culture in laboratory conditions, making the isolation of its DNA from the massive amount of plant host DNA extremely challenging. Yet, the appropriate amount and quality of plant microbiome-derived DNA are key for high-quality DNA sequencing data. Here, a simple, cost-effective, alternative method for DNA isolation was applied using a guanidine-HCl-hydroxylated silica (GuHCl-Silica)-based method and microbiome DNA enrichment based on size-selective low-molecular-weight (LMW) DNA by PEG/NaCl precipitation. qPCR analysis revealed a significant enrichment of phytoplasma DNA in the LMW fraction. Additionally, the NEBNext Microbiome DNA enrichment kit was utilized to further enrich microbial DNA, demonstrating a remarkable increase in the relative abundance of phytoplasma DNA to host DNA. Shotgun sequencing of the isolated DNA gave high-quality data on the metagenome assembly genome (MAG) of Ca. Phytoplasma sacchari SCWL with completeness at 95.85 and 215× coverage. The results indicate that this combined approach of PEG/NaCl size selection and microbiome enrichment is effective for obtaining high-quality genomic data from phytoplasma, surpassing previous methods in efficiency and resource utilization. This low-cost method not only enhances the recovery of microbiome DNA from plant hosts but also provides a robust framework for studying plant pathogens in complex plant models.}, } @article {pmid39519025, year = {2024}, author = {Zhang, T and Zhao, C and Li, N and He, Q and Gao, G and Sun, Z}, title = {Longitudinal and Multi-Kingdom Gut Microbiome Alterations in a Mouse Model of Alzheimer's Disease.}, journal = {International journal of molecular sciences}, volume = {25}, number = {21}, pages = {}, pmid = {39519025}, issn = {1422-0067}, support = {32325040//National Natural Science Foundation of China/ ; U22A20540//National Natural Science Foundation of China/ ; 2022YFD2100700//National Key R&D Program of China/ ; 2022YFSJ0017//Inner Mongolia Science & Technology Planning Project/ ; 2022110//Research support funds for high-level talents in public institutions at the autonomous region level in Inner Mongolia/ ; }, mesh = {Animals ; *Alzheimer Disease/microbiology/virology ; *Gastrointestinal Microbiome/genetics ; Mice ; *Disease Models, Animal ; Dysbiosis/microbiology ; Feces/microbiology ; Bacteria/classification/genetics ; Archaea/genetics ; Metagenomics/methods ; Fungi/genetics/classification ; Metagenome ; Longitudinal Studies ; }, abstract = {Gut microbial dysbiosis, especially bacteriome, has been implicated in Alzheimer's disease (AD). However, nonbacterial members of the gut microbiome in AD, such as the mycobiome, archaeome, and virome, are unexplored. Here, we perform higher-resolution shotgun metagenomic sequencing on fecal samples collected longitudinally from a mouse model of AD to investigate longitudinal and multi-kingdom gut microbiome profiling. Shotgun metagenomic sequencing of fecal samples from AD mice and healthy mice returns 41,222 bacterial, 414 fungal, 1836 archaeal, and 1916 viral species across all time points. The ecological network pattern of the gut microbiome in AD mice is characterized by more complex bacterial-bacterial interactions and fungal-fungal interactions, as well as simpler archaeal-archaeal interactions and viral-viral interactions. The development of AD is accompanied by multi-kingdom shifts in the gut microbiome composition, as evidenced by the identification of 1177 differential bacterial, 84 differential fungal, 59 differential archaeal, and 10 differential viral species between healthy and AD mice across all time points. In addition, the functional potential of the gut microbiome is partially altered in the development of AD. Collectively, our findings uncover longitudinal and multi-kingdom gut microbiome alterations in AD and provide a motivation for considering microbiome-based therapeutics during the prevention and treatment of AD.}, } @article {pmid39518901, year = {2024}, author = {Nahon, SMR and Trindade, FC and Yoshiura, CA and Martins, GC and Costa, IRCD and Costa, PHO and Herrera, H and Balestrin, D and Godinho, TO and Marchiori, BM and Valadares, RBDS}, title = {Impact of Agroforestry Practices on Soil Microbial Diversity and Nutrient Cycling in Atlantic Rainforest Cocoa Systems.}, journal = {International journal of molecular sciences}, volume = {25}, number = {21}, pages = {}, pmid = {39518901}, issn = {1422-0067}, support = {//VALE Research Institute/ ; }, mesh = {*Soil Microbiology ; *Cacao/microbiology/metabolism/genetics ; *Rainforest ; Soil/chemistry ; Agriculture/methods ; Nitrogen/metabolism ; Nitrogen Cycle ; Biodiversity ; Forestry/methods ; Microbiota ; Metagenomics/methods ; Ecosystem ; }, abstract = {Microorganisms are critical indicators of soil quality due to their essential role in maintaining ecosystem services. However, anthropogenic activities can disrupt the vital metabolic functions of these microorganisms. Considering that soil biology is often underestimated and traditional assessment methods do not capture its complexity, molecular methods can be used to assess soil health more effectively. This study aimed to identify the changes in soil microbial diversity and activity under different cocoa agroforestry systems, specially focusing on taxa and functions associated to carbon and nitrogen cycling. Soils from three different cocoa agroforestry systems, including a newly established agroforestry with green fertilization (GF), rubber (Hevea brasiliensis)-cocoa intercropping (RC), and cocoa plantations under Cabruca (cultivated under the shave of native forest) (CAB) were analyzed and compared using metagenomic and metaproteomic approaches. Samples from surrounding native forest and pasture were used in the comparison, representing natural and anthropomorphic ecosystems. Metagenomic analysis revealed a significant increase in Proteobacteria and Basidiomycota and the genes associated with dissimilatory nitrate reduction in the RC and CAB areas. The green fertilization area showed increased nitrogen cycling activity, demonstrating the success of the practice. In addition, metaproteomic analyses detected enzymes such as dehydrogenases in RC and native forest soils, indicating higher metabolic activity in these soils. These findings underscore the importance of soil management strategies to enhance soil productivity, diversity, and overall soil health. Molecular tools are useful to demonstrate how changes in agricultural practices directly influence the microbial community, affecting soil health.}, } @article {pmid39516921, year = {2024}, author = {Cheng, L and Tao, J and Lu, P and Liang, T and Li, X and Chang, D and Su, H and He, W and Qu, Z and Li, H and Mu, W and Zhang, W and Liu, N and Zhang, J and Cao, P and Jin, J}, title = {Manipulation in root-associated microbiome via carbon nanosol for plant growth improvements.}, journal = {Journal of nanobiotechnology}, volume = {22}, number = {1}, pages = {685}, pmid = {39516921}, issn = {1477-3155}, mesh = {*Microbiota/drug effects ; *Plant Roots/microbiology ; *Carbon/metabolism/chemistry ; *Soil Microbiology ; *Bacteria/metabolism ; *Rhizosphere ; *Plant Development/drug effects ; *Fungi ; Nicotiana/microbiology ; Soil/chemistry ; Nanostructures/chemistry ; Biomass ; }, abstract = {BACKGROUND: Modulating the microbiome with nanomaterials has been proposed to improve plant growth, and reduce reliance on external inputs. Carbon Nanosol (CNS) was attracted for its potential to improve plant productivity. However, the mechanism between CNS and rhizosphere microorganisms remained largely elusive.

RESULTS: Here, we tried to systematically explore the effects of CNS (600 and 1200 mg/L by concentration) on tobacco growth, soil physical properties, and root-associated microbiome. The influence of CNS on soil physicochemical properties and plant growth was significant and dose-dependent, leading to a 28.82% increase in biomass accumulation by 600 mg/L CNS. Comparison between the CNS-treated and control plants revealed significant differences in microbiome composition, including 1148 distinct ASVs (923 bacteria and 225 fungi), microbiome interactions, and metabolic function of root-associated microbiomes. Fungal and bacterial communities had different response patterns for CNS treatment, with phased and dose-dependent effects, with the most significant changes in microbial community structure observed at 1200 mg/L after 10 days of treatment. Microbial networks of CNS-treated plants had more nodes and edges, higher connectivity, and more hub microorganisms than those of control plants. Compared with control, CNS significantly elevated abundances of various bacterial biomarkers (such as Sphingomonas and Burkholderia) and fungi biomarkers (including Penicillium, Myceliophthora, and Talaromyces), which were potential plant-beneficial organisms. Functional prediction based on metagenomic data demonstrated pathways related to nutrient cycling being greatly enriched under CNS treatment. Furthermore, 391 culturable bacteria and 44 culturable fungi were isolated from soil and root samples. Among them, six bacteria and two fungi strains enriched upon CNS treatment were validated to have plant growth promotion effect, and two fungi (Cladosporium spp. and Talaromyces spp.) played their roles by mediating volatile organic compounds (VOCs). To some extent, the driving and shaping of the microbiome by CNS contributed to its impact on plant growth and development.

CONCLUSION: Our results revealed the key role of root-associated microbiota in mediating the interaction between CNS and plants, thus providing valuable insights and strategies for harnessing CNS to enhance plant growth.}, } @article {pmid39516585, year = {2024}, author = {Karlsson, ME and Forsberg, G and Rosberg, AK and Thaning, C and Alsanius, B}, title = {Impact of thermal seed treatment on spermosphere microbiome, metabolome and viability of winter wheat.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {27197}, pmid = {39516585}, issn = {2045-2322}, mesh = {*Triticum/microbiology/metabolism ; *Seeds/microbiology/metabolism ; *Microbiota ; *Metabolome ; Seedlings/microbiology/metabolism/growth & development ; Fusarium ; Hot Temperature ; }, abstract = {Thermal seed treatment can be used as an alternative method to prevent infection by seed-borne diseases, but exposure duration and temperature during thermal treatment are important to maintain high seed viability and emergence whilst decreasing infection rate. A method for predicting suitable treatment parameters to maintain viability and eliminate seed-borne pathogens is therefore needed. Seeds of winter wheat were subjected to thermal treatment at four levels of intensity and pre-treatments with or without imbibition. Treatment impact was measured by metabolome analysis using LC-MS and GC-MS, analysis of spermosphere bacterial and fungal metagenomes using Illumina MiSeq, and detection of presence of Fusarium spp. and Microdochium spp. using ddPCR. The results showed that moderate treatment intensity reduced signs of infection and increased seedling emergence. In imbibed samples, myo-inositol concentration and myo-inositol: glucose ratio were positively correlated with treatment intensity, whereas concentrations of glucose and citric acid were negatively correlated. No correlations were found for non-imbibed samples. Imbibition had a large significant impact on microbial community composition of the wheat spermosphere. Imbibition of wheat seeds prior to thermal treatment altered wheat spermosphere microbiota. The concentration of myo-inositol, potentially in combination with glucose, could be a candidate predictor for suitable thermal treatment intensity of wheat seeds.}, } @article {pmid39516195, year = {2024}, author = {Speth, DR and Zeller, LM and Graf, JS and Overholt, WA and Küsel, K and Milucka, J}, title = {Genetic potential for aerobic respiration and denitrification in globally distributed respiratory endosymbionts.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {9682}, pmid = {39516195}, issn = {2041-1723}, mesh = {*Symbiosis ; *Phylogeny ; *Denitrification ; Metagenome ; Aerobiosis ; Ciliophora/genetics/metabolism ; Groundwater/microbiology ; Gammaproteobacteria/genetics/metabolism ; Germany ; Electron Transport Complex IV/genetics/metabolism ; California ; Genome, Bacterial ; }, abstract = {The endosymbiont Candidatus Azoamicus ciliaticola was proposed to generate ATP for its eukaryotic host, an anaerobic ciliate of the Plagiopylea class, fulfilling a function analogous to mitochondria in other eukaryotic cells. The discovery of this respiratory endosymbiosis has major implications for both evolutionary history and ecology of microbial eukaryotes. However, with only a single species described, knowledge of its environmental distribution and diversity is limited. Here we report four complete, circular metagenome assembled genomes (cMAGs) representing respiratory endosymbionts inhabiting groundwater in California, Ohio, and Germany. These cMAGs form two lineages comprising a monophyletic clade within the uncharacterized gammaproteobacterial order UBA6186, enabling evolutionary analysis of their key protein complexes. Strikingly, all four cMAGs encode a cytochrome cbb3 oxidase, which indicates that these endosymbionts have the capacity for aerobic respiration. Accordingly, we detect these respiratory endosymbionts in diverse habitats worldwide, thus further expanding the ecological scope of this respiratory symbiosis.}, } @article {pmid39515835, year = {2024}, author = {Rooney, CM and Jeffery, IB and Mankia, K and Wilcox, MH and Emery, P}, title = {Dynamics of the gut microbiome in individuals at risk of rheumatoid arthritis: a cross-sectional and longitudinal observational study.}, journal = {Annals of the rheumatic diseases}, volume = {}, number = {}, pages = {}, doi = {10.1136/ard-2024-226362}, pmid = {39515835}, issn = {1468-2060}, abstract = {OBJECTIVES: This work aimed to resolve the conflicting reports on Prevotellaceae abundance in the development of rheumatoid arthritis (RA) and to observe structural, functional and temporal changes in the gut microbiome in RA progressors versus non-progressors.

METHODS: Individuals at risk of RA were defined by the presence of anticyclic citrullinated protein (anti-CCP) antibodies and new musculoskeletal symptoms without clinical synovitis. Baseline sampling included 124 participants (30 progressed to RA), with longitudinal sampling of 19 participants (5 progressed to RA) over 15 months at five timepoints. Gut microbiome taxonomic alterations were investigated using 16S rRNA amplicon sequencing and confirmed with shotgun metagenomic DNA sequencing on 49 samples.

RESULTS: At baseline, CCP+ at risk progressors showed significant differences in Prevotellaceae abundance compared with non-progressors, contingent on intrinsic RA risk factors and time to progression. Longitudinal sampling revealed gut microbiome instability in progressors 10 months before RA onset, a phenomenon absent in non-progressors. This may indicate a late microbial shift before RA onset, with Prevotellaceae contributing but not dominating these changes. Structural changes in the gut microbiome during arthritis development were associated with increased amino acid metabolism.

CONCLUSION: These data suggest conflicting reports on Prevotellaceae overabundance are likely due to sampling within a heterogeneous population along a dynamic disease spectrum, with certain Prevotellaceae strains/clades possibly contributing to the establishment and/or progression of RA. Gut microbiome changes in RA may appear at the transition to clinical arthritis as a late manifestation, and it remains unclear whether they represent a primary or secondary phenomenon.}, } @article {pmid39515437, year = {2025}, author = {Krushna Bhujbal, S and Preeti, and Joshi, A and Ghosh, P and Kumar Vijay, V}, title = {Investigating role of corn stover biochar supplementation on continuous pilot scale anaerobic digestion: Performance and microbial community dynamics.}, journal = {Bioresource technology}, volume = {416}, number = {}, pages = {131767}, doi = {10.1016/j.biortech.2024.131767}, pmid = {39515437}, issn = {1873-2976}, mesh = {*Zea mays/chemistry ; *Charcoal/pharmacology/chemistry ; Anaerobiosis ; *Methane/metabolism ; *Biofuels ; Pilot Projects ; Archaea/metabolism/genetics ; Bioreactors/microbiology ; }, abstract = {Biochar supplementation could facilitate microbial colonization and increase biogas and methane yield in anaerobic digestion (AD). This study investigated the impact of corn stover biochar (CSB) augmentation on the continuous pilot scale AD of rice straw. The CSB supplementation exhibited the daily average specific biogas and methane yield of 368.6 L/kg volatile solids (VS) and 230 L/kg VS, which were 35% and 37% higher than the control. Principle component analysis indicated that the VS reduction positively correlated with the daily average specific biogas and methane yield. Metagenomic analysis revealed that the CSB supplementation facilitated microbial colonization with the enrichment of unclassified genera from families Planococcaceae, Clostridiaceae, and Ruminococcaceae, and genus Clostridium and methanogenic archaea (Methanosarcina and Methanobacterium). The co-occurrence network revealed a notable shift in microbial interactions following the supplementation of CSB as an additive in AD. These results offer insights for enhancing the performance of the AD using CSB.}, } @article {pmid39515382, year = {2024}, author = {Shan, E and Zhang, X and Yu, Z and Hou, C and Pang, L and Guo, S and Liu, Y and Dong, Z and Zhao, J and Wang, Q and Yuan, X}, title = {Seawater warming rather than acidification profoundly affects coastal geochemical cycling mediated by marine microbiome.}, journal = {The Science of the total environment}, volume = {957}, number = {}, pages = {177365}, doi = {10.1016/j.scitotenv.2024.177365}, pmid = {39515382}, issn = {1879-1026}, mesh = {*Seawater/microbiology/chemistry ; *Microbiota ; *Climate Change ; Hydrogen-Ion Concentration ; Global Warming ; Denitrification ; Bacteria ; }, abstract = {The most concerning consequences of climate change include ocean acidification and warming, which can affect microbial communities and thus the biogeochemical cycling they mediate. Therefore, it is urgent to study the impact of ocean acidification and warming on microbial communities. In the current study, metagenomics was utilized to reveal how the structure and function of marine microorganisms respond to ocean warming and acidification. In terms of community structure, Non-metric Multidimensional Scaling analysis visualized the similarity or difference between the control and the warming or acidification treatments, but the inter-group differences were not significant. In terms of gene functionality, warming treatments showed greater effects on microbial communities than acidification. After treatment with warming, the relative abundance of genes associated with denitrification increased, suggesting that ocean nitrogen loss can increase with increased temperature. Conversely, acidification treatments apparently inhibited denitrification. Warming treatment also greatly affected sulfur-related microorganisms, increasing the relative abundance of certain sulfate-reducing prokaryote, and enriched microbial carbon-fixation pathways. These results provide information on the response strategies of coastal microorganisms in the changing marine environments.}, } @article {pmid39515333, year = {2024}, author = {Li, X and Zhang, J and Ma, D and Fan, X and Zheng, X and Liu, YX}, title = {Exploring protein natural diversity in environmental microbiomes with DeepMetagenome.}, journal = {Cell reports methods}, volume = {4}, number = {11}, pages = {100896}, pmid = {39515333}, issn = {2667-2375}, mesh = {*Microbiota/genetics ; Metagenome/genetics ; Deep Learning ; Metallothionein/genetics/metabolism ; Humans ; Software ; }, abstract = {Protein natural diversity offers a vast sequence space for protein engineering, and deep learning enables its detection from metagenomes/proteomes without prior assumptions. DeepMetagenome, a Python-based method, explores protein diversity through modules for training and analyzing sequence datasets. The deep learning model includes Embedding, Conv1D, LSTM, and Dense layers, with sequence feature analysis for data cleaning. Applied to metallothioneins from a database of over 146 million coding features, DeepMetagenome identified over 500 high-confidence metallothionein sequences, outperforming DIAMOND and CNN-based models. It showed stable performance compared to a Transformer-based model over 25 epochs. Among 23 synthesized sequences, 20 exhibited metal resistance. The tool also successfully explored the diversity of three additional protein families and is freely available on GitHub with detailed instructions.}, } @article {pmid39515321, year = {2024}, author = {Lin, Y and Xie, M and Lau, HC and Zeng, R and Zhang, R and Wang, L and Li, Q and Wang, Y and Chen, D and Jiang, L and Damsky, W and Yu, J}, title = {Effects of gut microbiota on immune checkpoint inhibitors in multi-cancer and as microbial biomarkers for predicting therapeutic response.}, journal = {Med (New York, N.Y.)}, volume = {}, number = {}, pages = {100530}, doi = {10.1016/j.medj.2024.10.007}, pmid = {39515321}, issn = {2666-6340}, abstract = {BACKGROUND: Gut bacteria are related to immune checkpoint inhibitors (ICIs). However, there is inconsistency in ICI-associated species, while the role of non-bacterial microbes in immunotherapy remains elusive. Here, we evaluated the association of trans-kingdom microbes with ICIs by multi-cohort multi-cancer analyses.

METHODS: We retrieved fecal metagenomes from 1,359 ICI recipients with four different cancers (metastatic melanoma [MM], non-small cell lung carcinoma [NSCLC], renal cell cancer [RCC], and hepatocellular carcinoma) from 12 published datasets. Microbiota composition was analyzed using the Wilcoxon rank test. The performance of microbial biomarkers in predicting ICI response was assessed by random forest. Key responder-associated microbes were functionally examined in vitro and in mice.

FINDINGS: Trans-kingdom gut microbiota (bacteria, eukaryotes, viruses, and archaea) was significantly different between ICI responders and non-responders in multi-cancer. Bacteria (Faecalibacterium prausnitzii, Coprococcus comes) and eukaryotes (Nemania serpens, Hyphopichia pseudoburtonii) were consistently enriched in responders of ≥2 cancer types or from ≥3 cohorts, contrasting with the depleted bacterium Hungatella hathewayi. Responder-associated species in each cancer were revealed, such as F. prausnitzii in MM and 6 species in NSCLC. These signature species influenced ICI efficacy by modulating CD8[+] T cell activity in vitro and in mice. Moreover, bacterial and eukaryotic biomarkers showed great performance in predicting ICI response in patients from discovery and two validation cohorts (MM: area under the receiver operating characteristic curve [AUROC] = 72.27%-80.19%; NSCLC: AUROC = 72.70%-87.98%; RCC: AUROC = 83.33%-89.58%).

CONCLUSIONS: This study identified trans-kingdom microbial signatures associated with ICI in multi-cancer and specific cancer types. Trans-kingdom microbial biomarkers are potential predictors of ICI response in patients with cancer.

FUNDING: Funding information is shown in the acknowledgments.}, } @article {pmid39515242, year = {2025}, author = {Wang, Y and Chen, S and Chen, Y and Xu, J and Zhou, J and He, Q and Lin, Z and Xu, KQ and Fan, G}, title = {Structure-activity relationship between crystal plane and pyrite-driven autotrophic denitrification efficacy: Electron transfer and metagenome-based microbial mechanism.}, journal = {Water research}, volume = {268}, number = {Pt B}, pages = {122756}, doi = {10.1016/j.watres.2024.122756}, pmid = {39515242}, issn = {1879-2448}, mesh = {*Denitrification ; Structure-Activity Relationship ; *Sulfides/chemistry/metabolism ; Nitrates/metabolism ; Water Purification ; *Electron Transport/genetics ; *Metagenome/genetics ; Bacteria/enzymology/genetics ; *Iron/chemistry/metabolism ; Electrochemistry ; Oxidation-Reduction ; *Microbiota ; }, abstract = {Pyrite-driven autotrophic denitrification (PAD) has been recognized as a promising treatment technology for nitrate removal. Although the occurrence of PAD has been found in recent years, there is a knowledge gap about effects of crystal plane of pyrite on the performance and mechanism of PAD system. Here, this study investigated the effects of crystal planes ({100}, {111} and {210} ) of single-crystal pyrite on denitrification performance, electron transfer, and microbial mechanism in PAD system. The removal efficiency of nitrate in B-{210} reached 100%, which was 1.67-fold and 2.86-fold higher than that of B-{100} and B-{111}, respectively. X-ray photoelectron spectroscopy and electrochemical results indicated that Fe-S bonds of pyrite with {210} crystal plane were more susceptible to breakage by Fe[3+] oxidation assault, and leaching microbially available Fe[2+] and sulfur intermediates to drive autotrophic denitrification. Metagenomic results suggested that community of functional pyrite-driven denitrifiers varied in response to crystal plane, and abundances of N-S transformation and EET-related microbes and genes in B-{210} notably up-regulated compared to B-{100} and B-{111} . In addition, this work proposed a dual-mode for electron transfer pathway during pyrite oxidation and nitrogen transformation in PAD system. In B-{210}, Fe(II)- and sulfur-driven denitrifiers obtained electron after pyrite oxidation-dissolution, and the enrichment of pyrite-oxidizing bacteria in B-{210} could enhance the electron transfer from pyrite through electron shuttles. This work highlighted that stronger surface reactivity and electron shuttle effect in B-{210} enhanced electron transfer, leading to favorable PAD performance in B-{210} . Overall, this study provides novel insights into the structure-activity relationship between the crystal plane structure of pyrite and denitrification activity in PAD system.}, } @article {pmid39515198, year = {2024}, author = {De Jaeghere, EA and Hamerlinck, H and Tuyaerts, S and Lippens, L and Van Nuffel, AMT and Baiden-Amissah, R and Vuylsteke, P and Henry, S and Trinh, XB and van Dam, PA and Aspeslagh, S and De Caluwé, A and Naert, E and Lambrechts, D and Hendrix, A and De Wever, O and Van de Vijver, KK and Amant, F and Vandecasteele, K and Verhasselt, B and Denys, HG}, title = {Associations of the gut microbiome with outcomes in cervical and endometrial cancer patients treated with pembrolizumab: Insights from the phase II PRIMMO trial.}, journal = {Gynecologic oncology}, volume = {191}, number = {}, pages = {275-286}, doi = {10.1016/j.ygyno.2024.10.020}, pmid = {39515198}, issn = {1095-6859}, mesh = {Humans ; Female ; *Antibodies, Monoclonal, Humanized/adverse effects/therapeutic use/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; Middle Aged ; *Uterine Cervical Neoplasms/drug therapy/microbiology/pathology ; *Endometrial Neoplasms/drug therapy/microbiology/pathology ; *Antineoplastic Agents, Immunological/adverse effects/therapeutic use ; Aged ; Adult ; Feces/microbiology ; }, abstract = {BACKGROUND: The phase II PRIMMO trial investigated a pembrolizumab-based regimen in patients with recurrent and/or metastatic cervical (CC) or endometrial (EC) carcinoma who had at least one prior line of systemic therapy. Here, exploratory studies of the gut microbiome (GM) are presented.

METHODS: The microbial composition of 77 longitudinal fecal samples obtained from 35 patients (CC, n = 15; EC, n = 20) was characterized using 16S rRNA gene sequencing. Analyses included assessment of alpha (Shannon index) and beta diversity (weighted UniFrac), unbiased hierarchical clustering, and linear discriminant analysis effect size. Correlative studies with demographics, disease characteristics, safety, efficacy, and immune monitoring data were performed.

RESULTS: Significant enrichment in multiple bacterial taxa was associated with the occurrence or resistance to severe treatment-related adverse events (overall or gastrointestinal toxicity specifically). Consistent differences in GM taxonomic composition before pembrolizumab initiation were observed between patients with favorable efficacy (e.g., enriched with Blautia genus) and those with poor efficacy (e.g., enriched with Enterobacteriaceae family and its higher-level taxa up to the phylum level, as well as Clostridium genus and its Clostridiaceae family). Two naturally occurring GM clusters with distinct bacterial compositions were identified. These clusters showed a more than four-fold differential risk for death (hazard ratio, 4.4 [95 % confidence interval, 1.9 to 10.3], P < 0.001) and were associated with interesting (but non-significant) trends in peripheral immune monitoring data.

CONCLUSION: Although exploratory, this study offers initial insights into the intricate interplay between the GM and clinical outcomes in patients with CC and EC treated with a pembrolizumab-based regimen.

TRIAL REGISTRATION: ClinicalTrials.gov (identifier NCT03192059) and EudraCT Registry (number 2016-001569-97).}, } @article {pmid39514951, year = {2025}, author = {Chen, J and Bi, Q and Mu, X and Wu, W and Liu, Q and Guo, Q and Xin, Q and Zhao, Z}, title = {Coxiella burnetii caused lumbar infection: A case report and literature review.}, journal = {Diagnostic microbiology and infectious disease}, volume = {111}, number = {1}, pages = {116594}, doi = {10.1016/j.diagmicrobio.2024.116594}, pmid = {39514951}, issn = {1879-0070}, mesh = {Male ; Humans ; Aged ; *Coxiella burnetii/isolation & purification/genetics ; *Q Fever/diagnosis/microbiology/drug therapy ; *Anti-Bacterial Agents/therapeutic use ; Animals ; Low Back Pain/etiology/microbiology ; Lumbar Vertebrae/microbiology ; Doxycycline/therapeutic use ; High-Throughput Nucleotide Sequencing ; Sheep ; Metagenomics ; Rifampin/therapeutic use ; }, abstract = {Coxiella burnetii (C. burnetii)is a significant microbe linked to the zoonotic disease Q fever, known for its atypical clinical manifestations and sporadic cases. It can cause lumbar infections. In this report, we present a 66-year-old male sheep farmer who experienced low back pain for five months, with worsening numbness in both lower limbs over two months. Several standard diagnostic tests were negative. Metagenomic next-generation sequencing (mNGS) was performed on lumbar spine tissue obtained via biopsy, identifying C. burnetii infection. After surgical excision of the lesion, the patient received a combination of levofloxacin, doxycycline, rifampicin, and supportive medications. Postoperatively, the patient's condition stabilized, showing a significant reduction in low back pain. This case highlights mNGS as a valuable tool for diagnosing rare infections, especially in patients with a history of animal exposure. It underscores the importance of considering zoonotic infections and the need for combined antibiotic and surgical management in suspected cases.}, } @article {pmid39513860, year = {2024}, author = {Stupak, A and Kwiatek, M and Gęca, T and Kwaśniewska, A and Mlak, R and Nawrot, R and Goździcka-Józefiak, A and Kwaśniewski, W}, title = {A Virome and Proteomic Analysis of Placental Microbiota in Pregnancies with and without Fetal Growth Restriction.}, journal = {Cells}, volume = {13}, number = {21}, pages = {}, pmid = {39513860}, issn = {2073-4409}, support = {DS 128//Medical University of Lublin/ ; }, mesh = {Humans ; Female ; *Fetal Growth Retardation/virology/metabolism/microbiology ; Pregnancy ; *Proteomics/methods ; *Placenta/virology/metabolism/microbiology ; *Virome ; Adult ; Microbiota ; Proteome/metabolism ; Viral Proteins/metabolism ; Case-Control Studies ; }, abstract = {INTRODUCTION: Metagenomic research has allowed the identification of numerous viruses present in the human body. Viruses may significantly increase the likelihood of developing intrauterine fetal growth restriction (FGR). The goal of this study was to examine and compare the virome of normal and FGR placentas using proteomic techniques.

METHODS: The study group of 18 women with late FGR was compared with 18 control patients with physiological pregnancy and eutrophic fetus. Proteins from the collected afterbirth placentas were isolated and examined using liquid chromatography linked to a mass spectrometer.

RESULTS: In this study, a group of 107 viral proteins were detected compared to 346 in the controls. In total, 41 proteins were common in both groups. In total, 64 proteins occurred only in the study group and indicated the presence of bacterial phages: E. coli, Bacillus, Mediterranenean, Edwardsiella, Propionibacterium, Salmonella, Paenibaciilus and amoebae Mimiviridae, Acanthamoeba polyphaga, Mimivivirus, Pandoravirdae, Miroviridae, Pepper plant virus golden mosaic virus, pol proteins of HIV-1 virus, and proteins of Pandoravirdae, Microviridae, and heat shock proteins of the virus Faustoviridae. Out of 297 proteins found only in the control group, only 2 viral proteins occurred statistically significantly more frequently: 1/hypothetical protein [uncultured Mediterranean phage uvMED] and VP4 [Gokushovirus WZ-2015a].

DISCUSSION: The detection of certain viral proteins exclusively in the control group suggests that they may play a protective role. Likewise, the proteins identified only in the study group could indicate a potentially pathogenic function. A virome study may be used to identify an early infection, evaluate its progress, and possible association with fetal growth restriction. Utilizing this technology, an individualized patient therapy is forthcoming, e.g., vaccines.}, } @article {pmid39513726, year = {2024}, author = {Zou, L and Zhang, Z and Chen, J and Guo, R and Tong, X and Ju, Y and Lu, H and Yang, H and Wang, J and Zong, Y and Xu, X and Jin, X and Xiao, L and Jia, H and Zhang, T and Liu, X}, title = {Unraveling the impact of host genetics and factors on the urinary microbiome in a young population.}, journal = {mBio}, volume = {15}, number = {12}, pages = {e0277324}, pmid = {39513726}, issn = {2150-7511}, mesh = {Humans ; Female ; *Microbiota/genetics ; Male ; Adult ; *Bacteria/genetics/classification/isolation & purification ; Young Adult ; Metagenomics ; China ; Host Microbial Interactions/genetics ; Urinary Tract/microbiology ; Whole Genome Sequencing ; Urine/microbiology ; Cohort Studies ; Adolescent ; }, abstract = {UNLABELLED: The significance of the urinary microbiome in maintaining health and contributing to disease development is increasingly recognized. However, a comprehensive understanding of this microbiome and its influencing factors remains elusive. Utilizing whole metagenomic and whole-genome sequencing, along with detailed metadata, we characterized the urinary microbiome and its influencing factors in a cohort of 1,579 Chinese individuals. Our findings unveil the distinctiveness of the urinary microbiome from other four body sites, delineating five unique urotypes dominated by Gardnerella vaginalis, Sphingobium fluviale, Lactobacillus iners, Variovorax sp. PDC80, and Acinetobacter junii, respectively. We identified 108 host factors significantly influencing the urinary microbiome, collectively explaining 12.92% of the variance in microbial composition. Notably, gender-related factors, including sex hormones, emerged as key determinants in defining urotype groups, microbial composition and pathways, with the urinary microbiome exhibiting strong predictive ability for gender (area under the curve [AUC] = 0.843). Furthermore, we discovered 43 genome-wide significant associations between host genetic loci and specific urinary bacteria, Acinetobacter in particular, linked to eight host loci (P < 5 × 10[-8]). These associations were also modulated by gender and sex hormone levels. In summary, our study provides novel insights into the impact of host genetics and other factors on the urinary microbiome, shedding light on its implications for host health and disease.

IMPORTANCE: The urinary microbiome, essential to human health, reveals its unique qualities in our study of 1,579 Chinese individuals. We identified distinctive microbial profiles, or "urotypes," and uncovered strong gender-related influences, particularly from sex hormones, on these microbial communities. Our research highlights significant genetic associations affecting specific urinary bacteria, indicating a deep interaction between our genetics and our microbiome. These insights not only enhance our understanding of the urinary microbiome's role in health and disease but also open new pathways for personalized medical strategies, making our findings crucial for future diagnostic and therapeutic innovations. This work underscores the intricate relationship between our body's biological processes and the microorganisms within, providing valuable knowledge for both scientific and medical communities.}, } @article {pmid39513695, year = {2024}, author = {Yan, G and Liu, Z and Teng, T and Dong, W and Lan, T and Fan, J and Tang, K and Qin, S and Nie, W}, title = {Metagenomic next-generation sequencing of osteoarticular tissue for the diagnosis of suspected osteoarticular tuberculosis.}, journal = {Microbiology spectrum}, volume = {12}, number = {12}, pages = {e0359823}, pmid = {39513695}, issn = {2165-0497}, abstract = {UNLABELLED: The objective of the study is to determine the accuracy of metagenomic next-generation sequencing (mNGS) in diagnosing osteoarticular tuberculosis (TB) infection and to compare it with mycobacteria growth indicator tube (MGIT) and Xpert assays. We retrospectively analyzed 162 patients admitted with suspected osteoarticular TB. Osteoarticular tissue (66.67%) and abscess specimens (33.33%) from patients were tested for MGIT, GeneXpert/RIF, and mNGS. mNGS assay detected 76 cases (46.9%) with bacterial, 63 cases (38.9%) with mycobacterial, 22 cases (13.6%) with fungal, and 1 case (0.6%) with actinomycetal organisms. These 162 pathogens were classified into 21 species. The most frequent species detected was Mycobacterium tuberculosis complex (29.0%), followed by Staphylococcus aureus (20.4%), Mycobacterium abscessus (5.6%), and Candida albicans (5.6%). Taking the "gold standard" TB diagnosis as the standard, the positive predictive values of mNGS, Xpert, and MGIT culture were both 100.00%. The negative predictive values of mNGS, Xpert, and MGIT culture and assays were 94.26%, 98.29%, and 88.46%, respectively. The sensitivity of mNGS detection (85.11%) was similar to that of Xpert (95.74%) and higher than that of MGIT culture (68.08%). The specificities of mNGS detection, Xpert, and MGIT culture were both 100.00%. The area under the curve value of the mNGS assay was 0.895 (95% CI: 0.830, 0.960), which was greater than that of the MGIT culture-based assay of 0.840 (95% CI: 0.757, 0.924), which was similar to 0.979 (95% CI: 0.945, 1.000) for Xpert assay. The pathogen detection rate of mNGS in diagnosing suspected osteoarticular TB exceeded that of conventional methods.

IMPORTANCE: In the detection of unknown infectious disease pathogens, the overall efficacy of traditional detection methods, such as culture, is low, and traditional PCR testing is also limited to the gene sequences of known pathogenic microorganisms. Metagenomic next-generation sequencing (mNGS) performs DNA sequencing by studying the entire microbial community genome in a given sample, without the need for isolation and culture. Previous studies have shown that mNGS performs better on pulmonary and extrapulmonary samples when compared with Xpert, traditional pathogenetic tests, and even parallel diagnostics. However, it should be emphasized that only a few studies have explored the performance of mNGS in detecting Mycobacterium tuberculosis in clinical samples associated with bone and joint infections. We conducted this retrospective study to provide additional data to support the use of mNGS in the clinical setting to identify pathogens within abscesses or tissue samples associated with bone and joint infections.}, } @article {pmid39512934, year = {2024}, author = {Dong, TS and Shera, S and Peters, K and Gee, GC and Beltrán-Sánchez, H and Wang, MC and Kilpatrick, LA and Zhang, X and Labus, JS and Vaughan, A and Church, A}, title = {Experiences of discrimination are associated with microbiome and transcriptome alterations in the gut.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1457028}, pmid = {39512934}, issn = {1664-302X}, support = {T32 DK007180/DK/NIDDK NIH HHS/United States ; R01 MD015904/MD/NIMHD NIH HHS/United States ; P30 DK041301/DK/NIDDK NIH HHS/United States ; K23 DK106528/DK/NIDDK NIH HHS/United States ; UL1 TR001881/TR/NCATS NIH HHS/United States ; R03 DK121025/DK/NIDDK NIH HHS/United States ; }, abstract = {BACKGROUND: Discrimination is a recognized psychosocial stressor that has been linked to various negative health outcomes. This study explored the impact of discrimination on gut health, specifically focusing on microbiome changes, predicted metagenomic differences, transcriptomic profiles, and the potential for using a multi-omic approach to predict discrimination to identify discrimination status for an individual. Methods: We conducted a comprehensive investigation involving male and premenopausal female participants, using the Everyday Discrimination Scale to classify them into either high or low discrimination. Multiple questionnaires were administered to evaluate participants' physiological, psychological, and perceived stressors. Two diet questionnaires were also administered. Stool samples were collected for microbiome analysis and RNA sequencing. Microbial composition changes were analyzed using the Shannon index and Chao1 richness estimator for alpha diversity and the Aitchison distance metric for beta diversity. Differential abundance was evaluated using MaAsLin2, followed by metatranscriptomics sequencing and annotation. A multi-omic approach utilizing random forest was used to assess the predictability of discrimination.

RESULTS: The study results showed that high discrimination was linked to higher gut microbiome species richness (Chao1, p = 0.02) and significant beta diversity differences (p = 0.04). Prevotella and Ruminococcaceae were both less abundant in the high discrimination group. High discrimination participants also reported higher levels of depression, anxiety, perceived stress, early life adversity, visceral sensitivity, and neuroticism than those in the low discrimination group. Gene expression analysis revealed distinctive patterns, with significant changes in genes associated with environmental sensing (two-component system) and metabolic pathways. In a plot comparing gene transcription to DNA content, certain genes showed higher expression levels in participants who experienced both high and low levels of discrimination. Our random forest classifier demonstrated the capability to accurately differentiate individuals with high and low discrimination in our training cohort (AUC = 0.91).

CONCLUSION: These findings illuminate the substantial impact of discrimination on gut health, encompassing microbiome composition, gene expression, and functional pathways. These findings suggest that discrimination is associated with internal biological changes that can be associated with negative health outcomes, opening research to examine novel pathways that can be used to mitigate the negative health effects of discrimination.}, } @article {pmid39512826, year = {2024}, author = {Yu, J and Zheng, Y and Liu, C and Xie, Z and Liu, Q and Yang, S and Tian, Q and Song, C and Chen, S}, title = {Multi-omics reveals the alleviating effect of berberine on ulcerative colitis through modulating the gut microbiome and bile acid metabolism in the gut-liver axis.}, journal = {Frontiers in pharmacology}, volume = {15}, number = {}, pages = {1494210}, pmid = {39512826}, issn = {1663-9812}, abstract = {The dysfunction of gut microbiome and bile acid metabolism might cause the incidence and relapse of ulcerative colitis (UC). Thus, natural products have been considered effective for UC through the regulation of gut microbiome and bile acid. In this study, we evaluated the regulatory effect of berberine on gut microbiome and bile acid metabolism in UC. Results showed that the relative abundances of beneficial bacteria showed a decreasing trend in the UC model, and the taurine conjugated bile acids increased from the liver tissue to the colon tissue. Berberine inhibited the colonization of harmful bacteria and promoted the primary bile acid metabolism. Moreover, we used multi-omics technology (metagenomics, metabolomics, and transcriptomics technology) to reveal that berberine restored the intestinal barrier function through bile acid/S1PR2/RhoA/ROCK pathway. The result of transmission electron microscopy directly showed that the damaged intestinal mucosal barrier was repaired through the berberine treatment. This study revealed the treatment influence on UC through multi-omics technology in vitro and in vivo models, which provides references for explaining the mechanism of berberine on UC.}, } @article {pmid39512798, year = {2024}, author = {Verma, D and Satyanarayana, T and Dias, PJ}, title = {Editorial: Microbial comparative genomics and pangenomics: new tools, approaches and insights into gene and genome evolution.}, journal = {Frontiers in genetics}, volume = {15}, number = {}, pages = {1490645}, pmid = {39512798}, issn = {1664-8021}, } @article {pmid39512622, year = {2024}, author = {Ylaya, EM and Grande, PG and Dancel, LL and Nicolasora, AD and Polotan, FG and Pantoni, RA and Melo, E and Ortia, SP and Manalo, JI and Abulencia, MF and Chu, MYJ and Dizon, TJ and Bucoy-Sy, MC and Adasa, G and Gianan-Gascon, A and Roman, AD}, title = {Case report: A comprehensive report on the first confirmed Mpox case in the Philippines during the 2022 Mpox global outbreak: from clinical presentation to shotgun metagenomic sequencing analysis.}, journal = {Frontiers in medicine}, volume = {11}, number = {}, pages = {1387407}, pmid = {39512622}, issn = {2296-858X}, abstract = {We report a case of a 31-year-old Filipino male with travel history to several European countries in July 2022. He developed five non-tender, well-defined, umbilicated pustules with erythematous borders on the upper lip, left gluteal area, bilateral knees, and left ankle. Skin punch biopsy findings were suggestive of a viral infection. Mpox infection from Clade II (previously known as the West African clade) was confirmed by detecting and amplifying the G2R_G, G2R_WA and C3L gene targets using qPCR. Shotgun metagenomic sequencing subsequently identified a Mpox genome sequence belonging to B.1.3 lineage of Clade IIb, associated with the current multi-country outbreak. Serologic varicella IgM test was positive but varicella PCR of the skin lesion and metagenomic sequencing did not indicate the presence of the varicella virus. The patient was discharged and continued isolation at home until all scabs had completely fallen off. The presence of pustules among patients with risk factors such as possible close physical contact with infected individuals in areas with reported cases of Mpox should raise suspicion for such an infection. Establishment and optimization of qPCR protocol were necessary to confirm Mpox infection. Metagenomic sequencing successfully characterized the etiologic agent of the first laboratory-confirmed Mpox case in the Philippines belonging to Clade IIb which is mainly responsible for the 2022 Mpox global outbreak.}, } @article {pmid39512611, year = {2024}, author = {Yuan, D and Ding, X and Chen, J and Zhao, Y and Wang, X and Zhu, J}, title = {Case report: A rare case of meningoencephalitis caused by Mycobacterium gordonae.}, journal = {Frontiers in medicine}, volume = {11}, number = {}, pages = {1416272}, pmid = {39512611}, issn = {2296-858X}, abstract = {Meningoencephalitis, an infectious disease affecting the nervous system, is primarily caused by a variety of pathogens. Non-tuberculous mycobacteria (NTM) have emerged as the leading causative agent of infections worldwide, but central nervous system infections resulting from NTM are infrequent in individuals with functioning immune systems. This case report highlights the diagnosis and treatment of a 26-year-old female patient who developed headaches 2 months post double eyelid surgery and was subsequently diagnosed with NTM meningoencephalitis through metagenomic next-generation sequencing (mNGS) analysis of cerebrospinal fluid. The patient underwent a comprehensive diagnostic and therapeutic protocol, resulting in a positive clinical outcome.}, } @article {pmid39511958, year = {2024}, author = {Dambietz, CA and Kintzinger, T and Schuler, F and Albers, A and Suntrup-Krueger, S and Fingerle, V and Meyer Zu Hörste, G and Thomas, C}, title = {Nanopore sequencing identifies Borrelia miyamotoi as an unexpected cause of meningitis after B cell depletion.}, journal = {Neuropathology and applied neurobiology}, volume = {50}, number = {6}, pages = {e13017}, pmid = {39511958}, issn = {1365-2990}, } @article {pmid39511594, year = {2024}, author = {Gui, L and Zuo, X and Feng, J and Wang, M and Chen, Z and Sun, Y and Qi, J and Chen, Z and Pathak, JL and Zhang, Y and Cui, C and Zhang, P and Guo, X and Lv, Q and Zhang, X and Zhang, Y and Gu, J and Lin, Z}, title = {Outgrowth of Escherichia is susceptible to aggravation of systemic lupus erythematosus.}, journal = {Arthritis research & therapy}, volume = {26}, number = {1}, pages = {191}, pmid = {39511594}, issn = {1478-6362}, support = {2024A1515010590//Natural Science Foundation of Guangdong Province, China/ ; JCYJ20220530154601004//Shenzhen Science and Technology Innovation Bureau/ ; 2020B1111170008//Guangdong Clinical Research Center of Immune disease/ ; SW201901//Ten & Five Project of the Third Affiliated Hospital of Sun Yat-Sen University/ ; A2675//Distinguished Young Scholar Candidates Program for The Third Affiliated Hospital of Sun Yat-Sen University/ ; }, mesh = {*Lupus Erythematosus, Systemic/microbiology/immunology/metabolism ; *Gastrointestinal Microbiome/physiology/immunology ; Animals ; Humans ; Female ; Mice ; *Mice, Inbred MRL lpr ; Adult ; *Feces/microbiology ; Male ; Dysbiosis/immunology/microbiology ; Middle Aged ; Escherichia coli/genetics/immunology ; Metagenomics/methods ; }, abstract = {BACKGROUND: Systemic lupus erythematosus (SLE) is linked to host gut dysbiosis. Here we performed faecal gut microbiome sequencing to investigate SLE-pathogenic gut microbes and their potential mechanisms.

METHODS: There were 134 healthy controls (HCs) and 114 SLE cases for 16 S ribosomal RNA (rRNA) sequencing and 97 HCs and 124 SLE cases for shotgun metagenomics. Faecal microbial changes and associations with clinical phenotypes were evaluated, and SLE-associated microbial genera were identified in amplicon analysis. Next, metagenomic sequencing was applied for accurate identification of microbial species and discovery of their metabolic pathways and immunogenic peptides both relevant to SLE. Finally, contribution of specific taxa to disease development was confirmed by oral gavage into lupus-prone MRL/lpr mice.

RESULTS: SLE patients had gut microbiota richness reduction and composition alteration, particularly lupus nephritis and active patients. Proteobacteria/Bacteroidetes (P/B) ratio was remarkably up-regulated, and Escherichia was identified as the dominantly expanded genus in SLE, followed by metagenomics accurately located Escherichia coli and Escherichia unclassified species. Significant associations primarily appeared among Escherichia coli, metabolic pathways of purine nucleotide salvage or peptidoglycan maturation and SLE disease activity index (SLEDAI), and between multiple epitopes from Escherichia coli and disease activity or renal involvement phenotype. Finally, gavage with faecal Escherichia revealed that it upregulated lupus-associated serum traits and aggravated glomerular lesions in MRL/lpr mice.

CONCLUSION: We characterize a novel SLE exacerbating Escherichia outgrowth and suggest its contribution to SLE procession may be partially associated with metabolite changes and cross-reactivity of gut microbiota-associated epitopes and host autoantigens. The findings could provide a deeper insight into gut Escherichia in the procession of SLE.}, } @article {pmid39510376, year = {2025}, author = {Huang, Y and You, Y and Wang, W and Chen, YH and Zhang, H and Li, QP and Liu, L and Tong, K and Sun, N and Hao, JR and Gao, C}, title = {Adenosine regulates depressive behavior in mice with chronic social defeat stress through gut microbiota.}, journal = {Neuropharmacology}, volume = {262}, number = {}, pages = {110209}, doi = {10.1016/j.neuropharm.2024.110209}, pmid = {39510376}, issn = {1873-7064}, mesh = {Animals ; *Gastrointestinal Microbiome/physiology/drug effects ; *Adenosine/metabolism ; Male ; Mice ; *Stress, Psychological/metabolism ; *Fecal Microbiota Transplantation ; *Social Defeat ; *Depression/therapy/metabolism ; Dysbiosis ; Humans ; Mice, Inbred C57BL ; Depressive Disorder, Major/metabolism/therapy ; Probiotics/administration & dosage/pharmacology ; Female ; }, abstract = {Major depressive disorder (MDD) is recognized as the most prevalent affective disorder worldwide. Metagenomic studies increasingly support a critical role for dysbiosis of gut microbiota in the development of depression. Previous studies have demonstrated that adenosine alleviates gut dysbiosis, suggesting that elevating adenosine levels could be a novel intervention for MDD; however, the mechanisms underlying this effect remain unclear. This study utilized 16S rRNA gene sequencing, fecal microbiota transplantation (FMT) and ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) to test the hypothesis that increased adenosine alleviates depressive behaviors in male mice subjected to chronic social defeat stress (CSDS) through alterations to gut microbiota. The data showed that depression-susceptible (SUS) mice exhibited gut dysbiosis, and FMT from SUS mice increased depression-like behaviors in healthy recipients. In SUS mice, adenosine supplementation ameliorated both depression-like behaviors and abnormalities in gut microbiota, and co-administration of probiotics and adenosine not only mitigated depression-like behaviors but also enhanced gut barrier integrity. By including 83 depressed adolescents and 67 healthy controls, this study found that the level of short-chain fatty acids (SCFAs) in the depression group was reduced, this finding parallels reductions seen in SUS mice and in recipient mice after FMT from SUS donors. Conversely, supplementation with either adenosine or probiotics led increased SCFAs concentrations in the serum of SUS mice. These findings suggest that adenosine may alleviate depression-like behaviors in CSDS mice by modulating the gut microbiota. This effect is likely associated with increased serum SCFAs, metabolites produced by the gut microbiota, following adenosine supplementation. This article is part of the Special Issue on "Personality Disorders".}, } @article {pmid39510362, year = {2024}, author = {Deng, YP and Yao, C and Fu, YT and Zhuo, Y and Zou, JL and Pan, HY and Peng, YY and Liu, GH}, title = {Analyses of the gut microbial composition of domestic pig louse Haematopinus suis.}, journal = {Microbial pathogenesis}, volume = {197}, number = {}, pages = {107106}, doi = {10.1016/j.micpath.2024.107106}, pmid = {39510362}, issn = {1096-1208}, mesh = {Animals ; Swine ; *Gastrointestinal Microbiome/genetics ; *Bacteria/classification/genetics/isolation & purification ; Symbiosis ; Phylogeny ; Swine Diseases/microbiology/parasitology ; Metagenomics ; Computational Biology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Haematopinus suis is an obligatory ectoparasite of the domestic pig, serving as a vector of several swine pathogens and posing great threats to the pig industry. The gut microbiome of lice is thought of an important mediator of their healthy physiology. However, there is a great paucity of lice-associated microbial communities' structure and function. The current study aimed to profile the gut microbiome and to understand the microbial functions of swine lice by metagenomic sequencing and bioinformatics analyses. In total, 102,358 (77.2 %) nonredundant genes were cataloged, by contrast, only a small proportion of genes were assigned to microbial taxa and functional assemblages. Bacteria of known or potential public health significance such as Anaplasma phagocytophilum, Chlamydia trachomatis, Waddlia chondrophila, Bacillus cereus, and Leptotrichia goodfellowii were observed in all samples. The integrated microbial profile further illustrated the evolutionary relevance of endosymbionts and detailed the functional composition, and findings suggested H. suis may acquire adenosylcobalamin by feeding due to an adenosylcobalamin synthesis defect and a lack of complete synthases of endosymbionts. Sucking lice contained fewer functional genes compared with ticks and fleas probably because of the obligate host specificity of parasitic lice. In addition, the genes from the intestines contained encompassed most of the microbial functional genes in sucking lice. A wide range of unknown taxonomic and functional assemblages were discovered, which improves our understanding related to microbial features and physiological activities of sucking lice. In general, this study increases the characterization of the microbiota of lice and offers clues for preventing and controlling lice infestation in swine production in the future.}, } @article {pmid39510356, year = {2025}, author = {Zhang, H and Wei, C and Chen, A and Ke, X and Li, Z and Qin, Z and Tian, Y and Wu, H and Qiu, G and Zhu, S}, title = {re-aerobic treatment and dissolved oxygen regulation in full-scale aerobic-hydrolysis and denitrification-aerobic process for achieving simultaneous detoxification and nitrification of coking wastewater.}, journal = {Bioresource technology}, volume = {416}, number = {}, pages = {131754}, doi = {10.1016/j.biortech.2024.131754}, pmid = {39510356}, issn = {1873-2976}, mesh = {*Nitrification ; *Wastewater/chemistry ; *Oxygen/metabolism ; *Denitrification ; Aerobiosis ; *Coke ; Nitrogen/metabolism ; Bioreactors ; Water Purification/methods ; Biodegradation, Environmental ; Waste Disposal, Fluid/methods ; Water Pollutants, Chemical/metabolism ; }, abstract = {The biological treatment of coking wastewater is a challenge. The application of prepositioned aerobic process has rarely been systematically reported, among which the detoxification and nitrification performance of the prepositioned aerobic unit (O1) is worthy of investigation. Results indicate that O1 achieves stable simultaneous detoxification and nitrification by regulating the dissolved oxygen, effectively maintaining ammonification, nitrosation, and complete nitrification phases. Microbial community structure, metabolic pathways and functional genes showed different preferences at different phases. High dissolved oxygen concentrations (2.20-3.00 mg/L) benefited the enrichment of carbon and nitrogen related major metabolic pathways and functional genes. BOD5/CODCr ratio, dissolved oxygen and toxic pollutants together shaped microbial community structure and nitrogen transformation processes. Based on the principle of DO regulation, it could assemble a biotransformation compartment for nitrogen removal from complex wastewaters through a pollutant detoxification mechanism of rapid microbial proliferation，and provides a promising approach for toxic industrial wastewater.}, } @article {pmid39510300, year = {2024}, author = {Zhou, S and Huang, Z and Song, J and Duan, Y and Guo, G and Wang, W and Ou, X and Gao, Y and Su, Y}, title = {Metagenomic analysis of the dichotomous role of uranium in regulating intracellular and extracellular antibiotic resistance genes in activated sludge.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {363}, number = {Pt 2}, pages = {125258}, doi = {10.1016/j.envpol.2024.125258}, pmid = {39510300}, issn = {1873-6424}, mesh = {*Uranium ; *Sewage/microbiology ; *Drug Resistance, Microbial/genetics ; *Metagenomics ; Genes, Bacterial ; Bacteria/genetics/drug effects ; Wastewater/microbiology ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Waste Disposal, Fluid/methods ; }, abstract = {Antibiotic resistance genes (ARGs) in activated sludge include intracellular ARGs (iARGs) and extracellular ARGs (eARGs), both of which are recognized as emerging pollutants. While the activated sludge process has been commonly considered for treating wastewater contaminated with radionuclide, the effects and mechanisms of radioactive heavy metals on the fate of iARGs and eARGs (i/e-ARGs) in activated sludge are largely elusive. Here, the distribution, mobility, and hosts of i/e-ARGs in activated sludge during environmental concentrations (50 μg/L and 5000 μg/L) of radioactive uranium (U) stress were explored via metagenomics. The results revealed that the total relative abundance of iARGs and eARGs decreased by 11.62% and 10.41%, respectively, after 90 days of 50 μg/L of U treatment. In contrast, both i/e-multi- and tetracycline ARGs remarkably increased after being exposed to 5000 μg/L of U. Additionally, exposure to 5000 μg/L of U triggered notable decrease in i/e-insertion sequences and plasmids abundance, but significantly enriched i/e-integrons (p < 0.05). Partial least squares pathway modelling indicated that the prevalence of iARGs and eARGs in activated sludge was primarily driven by bacterial hosts and functional genes, respectively. Our findings revealed the dichotomous variation landscape and mechanisms of i/e-ARGs dynamics in activated sludge during U exposure, offering valuable insights for controlling ARGs risk during radioactive wastewater treatment.}, } @article {pmid39510298, year = {2024}, author = {Song, J and Huang, Z and Gao, Y and Wang, W and Guo, G and Duan, Y and Zhou, S and Tang, Z}, title = {Metagenomic insight into the enrichment of antibiotic resistance genes in activated sludge upon exposure to nanoplastics.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {363}, number = {Pt 2}, pages = {125260}, doi = {10.1016/j.envpol.2024.125260}, pmid = {39510298}, issn = {1873-6424}, mesh = {*Sewage/microbiology ; *Drug Resistance, Microbial/genetics ; Metagenomics ; Bacteria/genetics/drug effects ; Gene Transfer, Horizontal ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; Water Pollutants, Chemical/toxicity ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Activated sludge is an important reservoir for the co-occurring emerging contaminants including nanoplastics (NPs) and antibiotic resistance genes (ARGs). However, the impacts and potential mechanisms of NPs on the fate of ARGs in activated sludge are not fully understood. Herein, we used metagenomic approach to investigate the responses of ARGs, host bacteria, mobile genetic elements (MGEs), and functional genes to polystyrene (PS) NPs at environmentally relevant (0.5 mg/L) and high stress concentrations (50 mg/L) in activated sludge. The results showed that 0.5 and 50 mg/L PS NPs increased the relative abundance of ARGs in the activated sludge by 58.68% and 46.52%, respectively (p < 0.05). Host tracking analysis elucidated that the hosts of ARGs were significantly enriched by PS NPs (p < 0.05), with Proteobacteria being the predominant host bacteria. Additionally, the occurrence of new ARGs hosts and the enrichment of MGEs and functional genes (i.e., genes related to SOS response, cell membrane permeability, and secretion system, etc.) indicated that PS NPs promoted horizontal gene transfer (HGT) of ARGs. Finally, path modeling analysis revealed that the proliferation of ARGs caused by PS NPs was primarily attributed to the enhancement of HGT and the enrichment of host bacteria. Our findings contribute to a comprehensive understanding of the spread risk of ARGs in activated sludge under NPs pollution.}, } @article {pmid39509737, year = {2024}, author = {Jang, JH and Kim, DB and Choi, Y and Amir, R and Cheong, DE and Chung, HJ and Ahn, SH and Kim, GJ and Lee, DW and Lee, OR and Kim, ES}, title = {Real-time monitoring of stromal NADPH levels in Arabidopsis using a metagenome-derived NADPH-binding fluorescent protein.}, journal = {Plant physiology and biochemistry : PPB}, volume = {217}, number = {}, pages = {109260}, doi = {10.1016/j.plaphy.2024.109260}, pmid = {39509737}, issn = {1873-2690}, mesh = {*Arabidopsis/metabolism/genetics ; *NADP/metabolism ; Luminescent Proteins/metabolism/genetics ; Photosynthesis ; Plants, Genetically Modified/metabolism ; Thylakoids/metabolism ; Plant Leaves/metabolism ; Chloroplasts/metabolism ; Nicotiana/metabolism/genetics ; }, abstract = {The light irradiation to the plant chloroplasts drives NADPH and ATP synthesis in the stroma via the electron transport chains within the thylakoid membranes. Conventional methods for assessing photosynthetic light reactions are often invasive or require specific conditions. While detection markers do not significantly affect plant growth itself, developing a method for the real-time and non-invasive detection of NADPH is a highly impactful and important research area in plant physiology and biochemistry. This study introduces a genetically encoded NADPH-binding blue fluorescent protein (mBFP) targeted to the chloroplast stroma or thylakoid membrane in Arabidopsis thaliana and Nicotiana benthamiana. Using two-photon microscopy, we monitored real-time stromal NADPH levels in transgenic leaves of Arabidopsis in response to light exposure. A mutant mBFP construct targeted to the thylakoid membrane allowed us to detect the stromal NADPH levels in real time under different light conditions. This in planta biosensor provides a non-invasive tool for studying photosynthetic responses to light more quantitatively and holds potential for optimizing light conditions in controlled-environment agriculture, such as indoor vertical farms, to improve crop productivity.}, } @article {pmid39509454, year = {2024}, author = {Tagirdzhanova, G and Saary, P and Cameron, ES and Allen, CCG and Garber, AI and Escandón, DD and Cook, AT and Goyette, S and Nogerius, VT and Passo, A and Mayrhofer, H and Holien, H and Tønsberg, T and Stein, LY and Finn, RD and Spribille, T}, title = {Microbial occurrence and symbiont detection in a global sample of lichen metagenomes.}, journal = {PLoS biology}, volume = {22}, number = {11}, pages = {e3002862}, pmid = {39509454}, issn = {1545-7885}, mesh = {*Lichens/genetics/microbiology/physiology ; *Symbiosis/genetics ; *Metagenome/genetics ; *Phylogeny ; *Bacteria/genetics/classification/isolation & purification ; Fungi/genetics/classification/isolation & purification/physiology ; Metagenomics/methods ; }, abstract = {In lichen research, metagenomes are increasingly being used for evaluating symbiont composition and metabolic potential, but the overall content and limitations of these metagenomes have not been assessed. We reassembled over 400 publicly available metagenomes, generated metagenome-assembled genomes (MAGs), constructed phylogenomic trees, and mapped MAG occurrence and frequency across the data set. Ninety-seven percent of the 1,000 recovered MAGs were bacterial or the fungal symbiont that provides most cellular mass. Our mapping of recovered MAGs provides the most detailed survey to date of bacteria in lichens and shows that 4 family-level lineages from 2 phyla accounted for as many bacterial occurrences in lichens as all other 71 families from 16 phyla combined. Annotation of highly complete bacterial, fungal, and algal MAGs reveals functional profiles that suggest interdigitated vitamin prototrophies and auxotrophies, with most lichen fungi auxotrophic for biotin, most bacteria auxotrophic for thiamine and the few annotated algae with partial or complete pathways for both, suggesting a novel dimension of microbial cross-feeding in lichen symbioses. Contrary to longstanding hypotheses, we found no annotations consistent with nitrogen fixation in bacteria other than known cyanobacterial symbionts. Core lichen symbionts such as algae were recovered as MAGs in only a fraction of the lichen symbioses in which they are known to occur. However, the presence of these and other microbes could be detected at high frequency using small subunit rRNA analysis, including in many lichens in which they are not otherwise recognized to occur. The rate of MAG recovery correlates with sequencing depth, but is almost certainly influenced by biological attributes of organisms that affect the likelihood of DNA extraction, sequencing and successful assembly, including cellular abundance, ploidy and strain co-occurrence. Our results suggest that, though metagenomes are a powerful tool for surveying microbial occurrence, they are of limited use in assessing absence, and their interpretation should be guided by an awareness of the interacting effects of microbial community complexity and sequencing depth.}, } @article {pmid39509330, year = {2024}, author = {Wang, M and Fontaine, S and Jiang, H and Li, G}, title = {ADAPT: Analysis of Microbiome Differential Abundance by Pooling Tobit Models.}, journal = {Bioinformatics (Oxford, England)}, volume = {40}, number = {11}, pages = {}, doi = {10.1093/bioinformatics/btae661}, pmid = {39509330}, issn = {1367-4811}, support = {R03DE031296/DE/NIDCR NIH HHS/United States ; }, mesh = {*Microbiota ; Humans ; *Metagenomics/methods ; *RNA, Ribosomal, 16S/genetics ; *Saliva/microbiology ; Software ; Infant ; Dental Caries/microbiology ; }, abstract = {MOTIVATION: Microbiome differential abundance analysis (DAA) remains a challenging problem despite multiple methods proposed in the literature. The excessive zeros and compositionality of metagenomics data are two main challenges for DAA.

RESULTS: We propose a novel method called "Analysis of Microbiome Differential Abundance by Pooling Tobit Models" (ADAPT) to overcome these two challenges. ADAPT interprets zero counts as left-censored observations to avoid unfounded assumptions and complex models. ADAPT also encompasses a theoretically justified way of selecting non-differentially abundant microbiome taxa as a reference to reveal differentially abundant taxa while avoiding false discoveries. We generate synthetic data using independent simulation frameworks to show that ADAPT has more consistent false discovery rate control and higher statistical power than competitors. We use ADAPT to analyze 16S rRNA sequencing of saliva samples and shotgun metagenomics sequencing of plaque samples collected from infants in the COHRA2 study. The results provide novel insights into the association between the oral microbiome and early childhood dental caries.

The R package ADAPT can be installed from Bioconductor at https://bioconductor.org/packages/release/bioc/html/ADAPT.html or from Github at https://github.com/mkbwang/ADAPT. The source codes for simulation studies and real data analysis are available at https://github.com/mkbwang/ADAPT_example.}, } @article {pmid39509322, year = {2024}, author = {Rödelsperger, C and Röseler, W and Athanasouli, M and Wighard, S and Herrmann, M and Sommer, RJ}, title = {Genome Assembly of the Nematode Rhabditoides Inermis From a Complex Microbial Community.}, journal = {Genome biology and evolution}, volume = {16}, number = {11}, pages = {}, pmid = {39509322}, issn = {1759-6653}, support = {//Max Planck Society/ ; }, mesh = {Animals ; *Phylogeny ; *Genome, Helminth ; Rhabditoidea/genetics/microbiology ; Microbiota ; }, abstract = {Free-living nematodes such as Caenorhabditis elegans and Pristionchus pacificus are powerful model systems for linking specific traits to their underlying genetic basis. To trace the evolutionary history of specific traits or genes, a robust phylogenomic framework is indispensable. In the context of the nematode family Diplogastridae to which P. pacificus belongs, the identity of a sister group has long been debated. In this work, we generated a pseudochromosome level genome assembly of the nematode Rhabditoides inermis, which has previously been proposed as the sister taxon. The genome was assembled from a complex microbial community that is stably associated with R. inermis isolates and that consists of multiple bacteria and a fungus, which we identified as a strain of Vanrija albida. The R. inermis genome spans 173.5Mb that are largely assembled into five pseudochromosomes. This chromosomal configuration likely arose from two recent fusions of different Nigon elements. Phylogenomic analysis did not support a sister group relationship between R. inermis and diplogastrids, but rather supports a sister group relationship between the monophyletic Diplogastridae and a group of genera of Rhabditidae including C. elegans and R. inermis. Thus, our work addresses for the first time the long lasting question about the sister group to diplogastrids at the phylogenomic level and provides with the genomes of R. inermis and the associated fungus V. albida valuable resources for future genomic comparisons.}, } @article {pmid39508593, year = {2024}, author = {Tran, TH and F Escapa, I and Roberts, AQ and Gao, W and Obawemimo, AC and Segre, JA and Kong, HH and Conlan, S and Kelly, MS and Lemon, KP}, title = {Metabolic capabilities are highly conserved among human nasal-associated Corynebacterium species in pangenomic analyses.}, journal = {mSystems}, volume = {9}, number = {12}, pages = {e0113224}, pmid = {39508593}, issn = {2379-5077}, support = {//HHS | NIH | National Human Genome Research Institute (NHGRI)/ ; //HHS | NIH | National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS)/ ; R35 GM141806/GM/NIGMS NIH HHS/United States ; K23 AI135090/AI/NIAID NIH HHS/United States ; R01 GM117174/GM/NIGMS NIH HHS/United States ; FPILOT45//Forsyth Institute/ ; R35 GM141806, R01 GM117174//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; }, mesh = {*Corynebacterium/genetics/metabolism ; Humans ; *Genome, Bacterial ; *Phylogeny ; Microbiota/genetics ; Genomics ; United States ; Nose/microbiology ; Botswana ; }, abstract = {UNLABELLED: Corynebacterium species are globally ubiquitous in human nasal microbiota across the lifespan. Moreover, nasal microbiota profiles typified by higher relative abundances of Corynebacterium are often positively associated with health. Among the most common human nasal Corynebacterium species are C. propinquum, C. pseudodiphtheriticum, C. accolens, and C. tuberculostearicum. To gain insight into the functions of these four species, we identified genomic, phylogenomic, and pangenomic properties and estimated the metabolic capabilities of 87 distinct human nasal Corynebacterium strain genomes: 31 from Botswana and 56 from the United States. C. pseudodiphtheriticum had geographically distinct clades consistent with localized strain circulation, whereas some strains from the other species had wide geographic distribution spanning Africa and North America. All species had similar genomic and pangenomic structures. Gene clusters assigned to all COG metabolic categories were overrepresented in the persistent versus accessory genome of each species indicating limited strain-level variability in metabolic capacity. Based on prevalence data, at least two Corynebacterium species likely coexist in the nasal microbiota of 82% of adults. So, it was surprising that core metabolic capabilities were highly conserved among the four species indicating limited species-level metabolic variation. Strikingly, strains in the U.S. clade of C. pseudodiphtheriticum lacked genes for assimilatory sulfate reduction present in most of the strains in the Botswana clade and in the other studied species, indicating a recent, geographically related loss of assimilatory sulfate reduction. Overall, the minimal species and strain variability in metabolic capacity implies coexisting strains might have limited ability to occupy distinct metabolic niches.

IMPORTANCE: Pangenomic analysis with estimation of functional capabilities facilitates our understanding of the full biologic diversity of bacterial species. We performed systematic genomic, phylogenomic, and pangenomic analyses with qualitative estimation of the metabolic capabilities of four common human nasal Corynebacterium species, along with focused experimental validations, generating a foundational resource. The prevalence of each species in human nasal microbiota is consistent with the common coexistence of at least two species. We identified a notably high level of metabolic conservation within and among species indicating limited options for species to occupy distinct metabolic niches, highlighting the importance of investigating interactions among nasal Corynebacterium species. Comparing strains from two continents, C. pseudodiphtheriticum had restricted geographic strain distribution characterized by an evolutionarily recent loss of assimilatory sulfate reduction in U.S. strains. Our findings contribute to understanding the functions of Corynebacterium within human nasal microbiota and to evaluating their potential for future use as biotherapeutics.}, } @article {pmid39508585, year = {2024}, author = {Androsiuk, L and Maane, S and Tal, S}, title = {CRISPR spacers acquired from plasmids primarily target backbone genes, making them valuable for predicting potential hosts and host range.}, journal = {Microbiology spectrum}, volume = {12}, number = {12}, pages = {e0010424}, pmid = {39508585}, issn = {2165-0497}, abstract = {In recent years, there has been a surge in metagenomic studies focused on identifying plasmids in environmental samples. Although these studies have unearthed numerous novel plasmids, enriching our understanding of their environmental roles, a significant gap remains: the scarcity of information regarding the bacterial hosts of these newly discovered plasmids. Furthermore, even when plasmids are identified within bacterial isolates, the reported host is typically limited to the original isolate, with no insights into alternative hosts or the plasmid's potential host range. Given that plasmids depend on hosts for their existence, investigating plasmids without the knowledge of potential hosts offers only a partial perspective. This study introduces a method for identifying potential hosts and host ranges for plasmids through alignment with CRISPR spacers. To validate the method, we compared the PLSDB plasmids database with the CRISPR spacers database, yielding host predictions for 46% of the plasmids. When compared with reported hosts, our predictions achieved 84% concordance at the family level and 99% concordance at the phylum level. Moreover, the method frequently identified multiple potential hosts for a plasmid, thereby enabling predictions of alternative hosts and the host range. Notably, we found that CRISPR spacers predominantly target plasmid backbone genes while sparing functional genes, such as those linked to antibiotic resistance, aligning with our hypothesis that CRISPR spacers are acquired from plasmid-specific regions rather than insertion elements from diverse sources. Finally, we illustrate the network of connections among different bacterial taxa through plasmids, revealing potential pathways for horizontal gene transfer.IMPORTANCEPlasmids are notorious for their role in distributing antibiotic resistance genes, but they may also carry and distribute other environmentally important genes. Since plasmids are not free-living entities and rely on host bacteria for survival and propagation, predicting their hosts is essential. This study presents a method for predicting potential hosts for plasmids and offers insights into the potential paths for spreading functional genes between different bacteria. Understanding plasmid-host relationships is crucial for comprehending the ecological and clinical impact of plasmids and implications for various biological processes.}, } @article {pmid39507946, year = {2024}, author = {Zhang, C and Li, Z and Chen, X and Wang, M and Yang, E and Xu, H and Wang, S}, title = {Risk factors for identifying pneumocystis pneumonia in pediatric patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1398152}, pmid = {39507946}, issn = {2235-2988}, mesh = {Humans ; *Pneumonia, Pneumocystis/diagnosis ; Risk Factors ; Male ; Female ; Retrospective Studies ; Child, Preschool ; Infant ; Child ; ROC Curve ; Coinfection/microbiology/diagnosis ; China/epidemiology ; Adolescent ; Cytomegalovirus Infections/complications/diagnosis ; Logistic Models ; Streptococcus pneumoniae/isolation & purification/genetics ; Dyspnea/etiology ; }, abstract = {OBJECTIVES: This study aimed to identify the risk factors and construct the diagnostic model associated with pneumocystis pneumonia (PCP) in pediatric patients.

METHODS: This retrospective observational study analyzed 34 cases of PCP and 51 cases of other types of pneumonia treated at Children's Hospital Affiliated to Shandong University between January 2021 and August 2023. Multivariate binary logistic regression was used to identify the risk factors associated with PCP. Receiver operating characteristic curves and calibration plots were constructed to evaluate the diagnostic model.

RESULTS: Twenty clinical variables significantly differed between the PCP and non-PCP groups. Multivariate binary logistic regression analysis revealed that dyspnea, body temperature>36.5°C, and age<1.46 years old were risk factors for PCP. The area under the curve of the diagnostic model was 0.958, the P-value of Hosmer-Lemeshow calibration test was 0.346, the R[2] of the calibration plot for the actual and predicted probability of PCP was 0.9555 (P<0.001), and the mean Brier score was 0.069. In addition, metagenomic next-generation sequencing revealed 79.41% (27/34) and 52.93% (28/53) mixed infections in the PCP and non-PCP groups, respectively. There was significantly more co-infection with cytomegalovirus and Streptococcus pneumoniae in the PCP group than that in the non-PCP group (p<0.05).

CONCLUSIONS: Dyspnea, body temperature>36.5°C, and age<1.46 years old were found to be independent risk factors for PCP in pediatric patients. The probability of co-infection with cytomegalovirus and S. pneumoniae in the PCP group was significantly higher than that in the non-PCP group.}, } @article {pmid39507669, year = {2024}, author = {Buytaers, FE and Berger, N and Van der Heyden, J and Roosens, NHC and De Keersmaecker, SCJ}, title = {The potential of including the microbiome as biomarker in population-based health studies: methods and benefits.}, journal = {Frontiers in public health}, volume = {12}, number = {}, pages = {1467121}, pmid = {39507669}, issn = {2296-2565}, mesh = {Humans ; *Biomarkers/analysis ; *Microbiota ; Population Health ; Health Status ; Public Health ; }, abstract = {The key role of our microbiome in influencing our health status, and its relationship with our environment and lifestyle or health behaviors, have been shown in the last decades. Therefore, the human microbiome has the potential to act as a biomarker or indicator of health or exposure to health risks in the general population, if information on the microbiome can be collected in population-based health surveys or cohorts. It could then be associated with epidemiological participant data such as demographic, clinical or exposure profiles. However, to our knowledge, microbiome sampling has not yet been included as biological evidence of health or exposure to health risks in large population-based studies representative of the general population. In this mini-review, we first highlight some practical considerations for microbiome sampling and analysis that need to be considered in the context of a population study. We then present some examples of topics where the microbiome could be included as biological evidence in population-based health studies for the benefit of public health, and how this could be developed in the future. In doing so, we aim to highlight the benefits of having microbiome data available at the level of the general population, combined with epidemiological data from health surveys, and hence how microbiological data could be used in the future to assess human health. We also stress the challenges that remain to be overcome to allow the use of this microbiome data in order to improve proactive public health policies.}, } @article {pmid39507397, year = {2024}, author = {Wang, H and Wang, H and Crowther, TW and Isobe, K and Reich, PB and Tateno, R and Shi, W}, title = {Metagenomic insights into inhibition of soil microbial carbon metabolism by phosphorus limitation during vegetation succession.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae128}, pmid = {39507397}, issn = {2730-6151}, abstract = {There is growing awareness of the need for regenerative practices in the fight against biodiversity loss and climate change. Yet, we lack a mechanistic understanding of how microbial community composition and functioning are likely to change alongside transition from high-density tillage to large-scale vegetation restoration. Here, we investigated the functional dynamics of microbial communities following a complete vegetation successional chronosequence in a subtropical zone, Southwestern China, using shotgun metagenomics approaches. The contents of total soil phosphorus (P), available P, litter P, and microbial biomass P decreased significantly during vegetation succession, indicating that P is the most critical limiting nutrient. The abundance of genes related to P-uptake and transport, inorganic P-solubilization, organic P-mineralization, and P-starvation response regulation significantly increased with successional time, indicating an increased microbial "mining" for P under P limitation. Multi-analysis demonstrated microbial P limitation strongly inhibits carbon (C) catabolism potential, resulting in a significant decrease in carbohydrate-active enzyme family gene abundances. Nevertheless, over successional time, microorganisms increased investment in genes involved in degradation-resistant compounds (lignin and its aromatic compounds) to acquire P resources in the litter. Our study provides functional gene-level insights into how P limitation during vegetation succession in subtropical regions inhibits soil microbial C metabolic processes, thereby advancing our understanding of belowground C cycling and microbial metabolic feedback during forest restoration.}, } @article {pmid39507337, year = {2024}, author = {Rizzo, C and Dastager, SG and Ay, H}, title = {Editorial: Microbial biodiversity and bioprospecting in polar ecosystems in the genomics era.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1504105}, pmid = {39507337}, issn = {1664-302X}, } @article {pmid39506649, year = {2024}, author = {Devic, M and Dennu, L and Lozano, JC and Mariac, C and Vergé, V and Schatt, P and Bouget, FY and Sabot, F}, title = {An INDEL genomic approach to explore population diversity of phytoplankton.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1045}, pmid = {39506649}, issn = {1471-2164}, mesh = {*Phytoplankton/genetics/classification ; *INDEL Mutation ; Genetic Variation ; Genomics/methods ; Genotype ; Phylogeny ; }, abstract = {BACKGROUND: Although metabarcoding and metagenomic approaches have generated large datasets on worldwide phytoplankton species diversity, the intraspecific genetic diversity underlying the genetic adaptation of marine phytoplankton to specific environmental niches remains largely unexplored. This is mainly due to the lack of biological resources and tools for monitoring the dynamics of this diversity in space and time.

RESULTS: To gain insight into population diversity, a novel method based on INDEL markers was developed on Bathycoccus prasinos (Mamiellophyceae), an abundant and cosmopolitan species with strong seasonal patterns. Long read sequencing was first used to characterize structural variants among the genomes of six B. prasinos strains sampled from geographically distinct regions in the world ocean. Markers derived from identified insertions/deletions were validated by PCR then used to genotype 55 B. prasinos strains isolated during the winter bloom 2018-2019 in the bay of Banyuls-sur-Mer (Mediterranean Sea, France). This led to their classification into eight multi-loci genotypes and the sequencing of strains representative of local diversity, further improving the available genetic diversity of B. prasinos. Finally, selected markers were directly tracked on environmental DNA sampled during 3 successive blooms from 2018 to 2021, showcasing a fast and cost-effective approach to follow local population dynamics.

CONCLUSIONS: This method, which involves (i) pre-identifying the genetic diversity of B. prasinos in environmental samples by PCR, (ii) isolating cells from selected environmental samples and (iii) identifying genotypes representative of B. prasinos diversity for sequencing, can be used to comprehensively describe the diversity and population dynamics not only in B. prasinos but also potentially in other generalist phytoplankton species.}, } @article {pmid39508239, year = {2024}, author = {Dames, NR and Rocke, E and Pitcher, G and Rybicki, E and Pfaff, M and Moloney, CL}, title = {Ecological roles of nano-picoplankton in stratified waters of an embayment in the southern Benguela.}, journal = {FEMS microbiology letters}, volume = {371}, number = {}, pages = {}, pmid = {39508239}, issn = {1574-6968}, support = {116142//National Research Foundation/ ; }, mesh = {South Africa ; *Archaea/classification/metabolism/isolation & purification/genetics ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Plankton/classification ; Microbiota ; Seawater/microbiology/chemistry ; Bays/microbiology ; Ecosystem ; Eukaryota/classification/physiology ; }, abstract = {Nano-picoplankton are the dominant primary producers during the postupwelling period in St Helena Bay, South Africa. Their dynamics on short timescales are not well-understood and neither are the community composition, structure, and potential functionality of the surrounding microbiome. Samples were collected over five consecutive days in March 2018 from three depths (1, 25, and 50 m) at a single sampling station in St Helena Bay. There was clear depth-differentiation between the surface and depth in both diversity and function throughout the sampling period for the archaea, bacteria, and eukaryotes. Daily difference in eukaryote diversity, was more pronounced at 1 and 25 m with increased abundances of Syndiniales and Bacillariophyta. Surface waters were dominated by photosynthetic and photoheterotrophic microorganisms, while samples at depth were linked to nitrogen cycling processes, with high abundances of nitrifiers and denitrifiers. Strong depth gradients found in the nutrient transporters for ammonia were good indicators of measured uptake rates. This study showed that nano-picoplankton dynamics were driven by light availability, nutrient concentrations, carbon biomass, and oxygenation. The nano-picoplankton help sustain ecosystem functioning in St Helena Bay through their ecological roles, which emphasizes the need to monitor this size fraction of the plankton.}, } @article {pmid39506101, year = {2024}, author = {Beránková, T and Arora, J and Romero Arias, J and Buček, A and Tokuda, G and Šobotník, J and Hellemans, S and Bourguignon, T}, title = {Termites and subsocial roaches inherited many bacterial-borne carbohydrate-active enzymes (CAZymes) from their common ancestor.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1449}, pmid = {39506101}, issn = {2399-3642}, mesh = {*Isoptera/microbiology/enzymology ; Animals ; *Bacteria/enzymology/genetics ; *Phylogeny ; Gastrointestinal Microbiome ; Cockroaches/microbiology/enzymology ; Metagenome ; Evolution, Molecular ; Bacterial Proteins/metabolism/genetics ; Carbohydrate Metabolism ; }, abstract = {Termites digest wood using Carbohydrate-Active Enzymes (CAZymes) produced by gut bacteria with whom they have cospeciated at geological timescales. Whether CAZymes were encoded in the genomes of their ancestor's gut bacteria and transmitted to modern termites or acquired more recently from bacteria not associated with termites is unclear. We used gut metagenomes from 195 termites and one Cryptocercus, the sister group of termites, to investigate the evolution of termite gut bacterial CAZymes. We found 420 termite-specific clusters in 81 bacterial CAZyme gene trees, including 404 clusters showing strong cophylogenetic patterns with termites. Of the 420 clusters, 131 included at least one bacterial CAZyme sequence associated with Cryptocercus or Mastotermes, the sister group of all other termites. Our results suggest many bacterial CAZymes have been encoded in the genomes of termite gut bacteria since termite origin, indicating termites rely upon many bacterial CAZymes endemic to their guts to digest wood.}, } @article {pmid39505993, year = {2024}, author = {Gulyás, G and Kakuk, B and Dörmő, Á and Járay, T and Prazsák, I and Csabai, Z and Henkrich, MM and Boldogkői, Z and Tombácz, D}, title = {Cross-comparison of gut metagenomic profiling strategies.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1445}, pmid = {39505993}, issn = {2399-3642}, support = {LP2020-8/2020//Magyar Tudományos Akadémia (Hungarian Academy of Sciences)/ ; FK 142676//Nemzeti Kutatási, Fejlesztési és Innovációs Hivatal (NKFI Office)/ ; }, mesh = {*Metagenomics/methods ; Animals ; *Gastrointestinal Microbiome/genetics ; Dogs ; *Feces/microbiology ; Computational Biology/methods ; Software ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; Gene Library ; }, abstract = {The rapid advancements in sequencing technologies and bioinformatics have enabled metagenomic research of complex microbial systems, but reliable results depend on consistent laboratory and bioinformatics approaches. Current efforts to identify best practices often focus on optimizing specific steps, making it challenging to understand the influence of each stage on microbial population analysis and compare data across studies. This study evaluated DNA extraction, library construction methodologies, sequencing platforms, and computational approaches using a dog stool sample, two synthetic microbial community mixtures, and various sequencing data sources. Our work, the most comprehensive evaluation of metagenomic methods to date. We developed a software tool, termed minitax, which provides consistent results across the range of platforms and methodologies. Our findings showed that the Zymo Research Quick-DNA HMW MagBead Kit, Illumina DNA Prep library preparation method, and the minitax bioinformatics tool were the most effective for high-quality microbial diversity analysis. However, the effectiveness of pipelines or method combinations is sample-specific, making it difficult to identify a universally optimal approach. Therefore, employing multiple approaches is crucial for obtaining reliable outcomes in microbial systems.}, } @article {pmid39505912, year = {2024}, author = {Mi, J and Jing, X and Ma, C and Shi, F and Cao, Z and Yang, X and Yang, Y and Kakade, A and Wang, W and Long, R}, title = {A metagenomic catalogue of the ruminant gut archaeome.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {9609}, pmid = {39505912}, issn = {2041-1723}, mesh = {Animals ; *Ruminants/microbiology ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Archaea/genetics/classification ; *Genome, Archaeal ; *Metagenome ; Methane/metabolism ; Phylogeny ; Gastrointestinal Tract/microbiology ; }, abstract = {While the ruminant gut archaeome regulates the gut microbiota and hydrogen balance, it is also a major producer of the greenhouse gas methane. However, ruminant gut archaeome diversity within the gastrointestinal tract (GIT) of ruminant animals worldwide remains largely underexplored. Here, we construct a catalogue of 998 unique archaeal genomes recovered from the GITs of ruminants, utilizing 2270 metagenomic samples across 10 different ruminant species. Most of the archaeal genomes (669/998 = 67.03%) belong to Methanobacteriaceae and Methanomethylophilaceae (198/998 = 19.84%). We recover 47/279 previously undescribed archaeal genomes at the strain level with completeness of >80% and contamination of <5%. We also investigate the archaeal gut biogeography across various ruminants and demonstrate that archaeal compositional similarities vary significantly by breed and gut location. The catalogue contains 42,691 protein clusters, and the clustering and methanogenic pathway analysis reveal strain- and host-specific dependencies among ruminant animals. We also find that archaea potentially carry antibiotic and metal resistance genes, mobile genetic elements, virulence factors, quorum sensors, and complex archaeal viromes. Overall, this catalogue is a substantial repository for ruminant archaeal recourses, providing potential for advancing our understanding of archaeal ecology and discovering strategies to regulate methane production in ruminants.}, } @article {pmid39505908, year = {2024}, author = {Xu, B and Song, P and Jiang, F and Cai, Z and Gu, H and Gao, H and Li, B and Liang, C and Qin, W and Zhang, J and Yan, J and Liu, D and Sun, G and Zhang, T}, title = {Large-scale metagenomic assembly provide new insights into the genetic evolution of gut microbiomes in plateau ungulates.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {120}, pmid = {39505908}, issn = {2055-5008}, support = {U20A2012//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2023M743743//China Postdoctoral Science Foundation/ ; }, mesh = {*Gastrointestinal Microbiome ; Animals ; *Metagenomics/methods ; *Evolution, Molecular ; China ; *Metagenome ; Bacteria/genetics/classification/isolation & purification ; Phylogeny ; Fatty Acids, Volatile/metabolism ; Genome, Bacterial ; }, abstract = {Trillions of microbes colonize the ungulate gastrointestinal tract, playing a pivotal role in enhancing host nutrient utilization by breaking down cellulose and hemicellulose present in plants. Here, through large-scale metagenomic assembly, we established a catalog of 131,416 metagenome-assembled genomes (MAGs) and 11,175 high-quality species-level genome bins (SGBs) from 17 species of ungulates in China. Our study revealed the convergent evolution of high relative abundances of carbohydrate-active enzymes (CAZymes) in the gut microbiomes of plateau-dwelling ungulates. Notably, two significant factors contribute to this phenotype: structural variations in their gut microbiome genomes, which contain more CAZymes, and the presence of novel gut microbiota species, particularly those in the genus Cryptobacteroides, which are undergoing independent rapid evolution and speciation and have higher gene densities of CAZymes. Furthermore, these enrichment CAZymes in the gut microbiomes are highly enrichment in known metabolic pathways for short-chain fatty acid (SCFA) production. Our findings not only provide a valuable genomic resource for understanding the gut microbiomes of ungulates but also offer fresh insights into the interaction between gut microbiomes and their hosts, as well as the co-adaptation of hosts and their gut microbiomes to their environments.}, } @article {pmid39505900, year = {2024}, author = {Bontemps, Z and Abrouk, D and Venier, S and Vergne, P and Michalet, S and Comte, G and Moënne-Loccoz, Y and Hugoni, M}, title = {Microbial diversity and secondary metabolism potential in relation to dark alterations in Paleolithic Lascaux Cave.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {121}, pmid = {39505900}, issn = {2055-5008}, mesh = {*Caves/microbiology ; *Secondary Metabolism ; *Metagenomics/methods ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Microbiota ; Biodiversity ; Metagenome ; Melanins/metabolism ; }, abstract = {Tourism in Paleolithic caves can cause an imbalance in cave microbiota and lead to cave wall alterations, such as dark zones. However, the mechanisms driving dark zone formation remain unclear. Using shotgun metagenomics in Lascaux Cave's Apse and Passage across two years, we tested metabarcoding-derived functional hypotheses regarding microbial diversity and metabolic potential in dark zones vs unmarked surfaces nearby. Taxonomic and functional metagenomic profiles were consistent across years but divergent between cave locations. Aromatic compound degradation genes were prevalent inside and outside dark zones, as expected from past biocide usage. Dark zones exhibited enhanced pigment biosynthesis potential (melanin and carotenoids) and melanin was evidenced chemically, while unmarked surfaces showed genes for antimicrobials production, suggesting that antibiosis might restrict the development of pigmented microorganisms and dark zone extension. Thus, this work revealed key functional microbial traits associated with dark zone formation, which helps understand cave alteration processes under severe anthropization.}, } @article {pmid39505140, year = {2024}, author = {Jiang, X and Zhang, Z and Wu, X and Li, C and Sun, X and Wu, F and Yang, A and Yang, C}, title = {Heterologous biosynthesis of betanin triggers metabolic reprogramming in tobacco.}, journal = {Metabolic engineering}, volume = {86}, number = {}, pages = {308-325}, doi = {10.1016/j.ymben.2024.11.002}, pmid = {39505140}, issn = {1096-7184}, mesh = {*Nicotiana/genetics/metabolism ; *Betacyanins/metabolism ; *Plants, Genetically Modified/metabolism/genetics ; Metabolic Engineering ; Nitrogen/metabolism ; Plant Leaves/metabolism/genetics ; Metabolic Reprogramming ; }, abstract = {Engineering of a specialized metabolic pathway in plants is a promising approach to produce high-value bioactive compounds to address the challenges of climate change and population growth. Understanding the interaction between the heterologous pathway and the native metabolic network of the host plant is crucial for optimizing the engineered system and maximizing the yield of the target compound. In this study, we performed transcriptomic, metabolomic and metagenomic analysis of tobacco (Nicotiana tabacum) plants engineered to produce betanin, an alkaloid pigment that is found in Caryophyllaceae plants. Our data reveals that, in a dose-dependent manor, the biosynthesis of betanin promotes carbohydrate metabolism and represses nitrogen metabolism in the leaf, but enhances nitrogen assimilation and metabolism in the root. By supplying nitrate or ammonium, the accumulation of betanin increased by 1.5-3.8-fold in leaves and roots of the transgenic plants, confirming the pivotal role of nitrogen in betanin production. In addition, the rhizosphere microbial community is reshaped to reduce denitrification and increase respiration and oxidation, assistant to suppress nitrogen loss. Our analysis not only provides a framework for evaluating the pleiotropic effects of an engineered metabolic pathway on the host plant, but also facilitates the development of novel strategies to balance the heterologous process and the native metabolic network for the high-yield and nutrient-efficient production of bioactive compounds in plants.}, } @article {pmid39505046, year = {2024}, author = {Liu, Y and Wang, Y and Shi, W and Wu, N and Liu, W and Francis, F and Wang, X}, title = {Enterobacter-infecting phages in nitrogen-deficient paddy soil impact nitrogen-fixation capacity and rice growth by shaping the soil microbiome.}, journal = {The Science of the total environment}, volume = {956}, number = {}, pages = {177382}, doi = {10.1016/j.scitotenv.2024.177382}, pmid = {39505046}, issn = {1879-1026}, mesh = {*Oryza/virology/microbiology ; *Soil Microbiology ; *Enterobacter/virology/physiology ; *Microbiota/physiology ; *Bacteriophages/physiology ; *Soil/chemistry ; *Nitrogen Fixation ; *Nitrogen ; Phylogeny ; }, abstract = {Bacteriophages ("phage") play important roles in nutrient cycling and ecology in environments by regulating soil microbial community structure. Here, metagenomic sequencing showed that a low relative abundance of nitrogen-fixing bacteria but high abundance of Enterobacter-infecting phages in paddy soil where rice plants showed nitrogen deficiency. From soil in the same field, we also isolated and identified a novel virulent phage (named here as Apdecimavirus NJ2) that infects several species of Enterobacter and characterized its impact on nitrogen fixation in the soil and in plants. It has the morphology of the Autographiviridae family, with a dsDNA genome of 39,605 bp, 47 predicted open reading frames and 52.64 % GC content. Based on genomic characteristics, comparative genomics and phylogenetic analysis, Apdecimavirus NJ2 should be a novel species in the genus Apdecimavirus, subfamily Studiervirinae. After natural or sterilized field soil was potted and inoculated with the phage, soil nitrogen-fixation capacity and rice growth were impaired, the abundance of Enterobacter decreased, along with the bacterial community composition and biodiversity changed compared with that of the unadded control paddy soil. Our work provides strong evidence that phages can affect the soil nitrogen cycle by changing the bacterial community. Controlling phages in the soil could be a useful strategy for improving soil nitrogen fixation.}, } @article {pmid39504700, year = {2025}, author = {Zheng, B and Zhou, L and Wang, J and Dong, P and Zhao, T and Deng, Y and Song, L and Shi, J and Wu, Z}, title = {The shifts in microbial interactions and gene expression caused by temperature and nutrient loading influence Raphidiopsis raciborskii blooms.}, journal = {Water research}, volume = {268}, number = {Pt B}, pages = {122725}, doi = {10.1016/j.watres.2024.122725}, pmid = {39504700}, issn = {1879-2448}, mesh = {*Temperature ; *Eutrophication ; *Cyanobacteria/genetics ; *Microbial Interactions ; Phosphorus ; Gene Expression ; Climate Change ; Nutrients ; }, abstract = {Climate change and the trophic status of water bodies are important factors in global occurrence of cyanobacterial blooms. The aim of this study was to explore the cyanobacteria‒bacterial interactions that occur during Raphidiopsis raciborskii (R. raciborskii) blooms by conducting microcosm simulation experiments at different temperatures (20 °C and 30 °C) and with different phosphorus concentrations (0.01 mg/L and 1 mg/L) using an ecological model of microbial behavior and by analyzing microbial self-regulatory strategies using weighted gene coexpression network analysis (WGCNA). Three-way ANOVA revealed significant effects of temperature and phosphorus on the growth of R. raciborskii (P < 0.001). The results of a metagenomics-based analysis of bacterioplankton revealed that the synergistic effects of both climate and trophic changes increased the ability of R. raciborskii to compete with other cyanobacteria for dominance in the cyanobacterial community. The antagonistic effects of climate and nutrient changes favored the occurrence of R. raciborskii blooms, especially in eutrophic waters at approximately 20 °C. The species diversity and richness indices differed between the eutrophication treatment group at 20 °C and the other treatment groups. The symbiotic bacterioplankton network revealed the complexity and stability of the symbiotic bacterioplankton network during blooms and identified the roles of key species in the network. The study also revealed a complex pattern of interactions between cyanobacteria and non-cyanobacteria dominated by altruism, as well as the effects of different behavioral patterns on R. raciborskii bloom occurrence. Furthermore, this study revealed self-regulatory strategies that are used by microbes in response to the dual pressures of temperature and nutrient loading. These results provide important insights into the adaptation of microbial communities in freshwater ecosystems to environmental change and provide useful theoretical support for aquatic environmental management and ecological restoration efforts.}, } @article {pmid39504699, year = {2025}, author = {Li, ZT and Zhao, HP}, title = {Sulfate-driven microbial collaboration for synergistic remediation of chloroethene-heavy metal pollution.}, journal = {Water research}, volume = {268}, number = {Pt B}, pages = {122738}, doi = {10.1016/j.watres.2024.122738}, pmid = {39504699}, issn = {1879-2448}, mesh = {*Metals, Heavy/metabolism ; *Biodegradation, Environmental ; *Sulfates/metabolism ; Bacteria/metabolism ; Water Pollutants, Chemical/metabolism ; }, abstract = {The treatment of heavy metal(loid) (HM) composite pollution has long posed a challenge for the bioremediation of organohalide-contaminated sites. Given the prevalent cohabitation of sulfate-reducing bacteria (SRB) with organohalide-respiring bacteria (OHRB), we proposed a sulfate-amendment strategy to achieve synergistic remediation of trichloroethene and diverse HMs [50μM of As(III), Ni(II), Cu(II), Pb(II)]. Correspondingly, 50-75 μM sulfate was introduced to HM inhibitory batches to investigate the enhancement effect of sulfate amendment on bio-dechlorination. Dechlorination kinetics and MATLAB modeling indicated that sulfate amendment comprehensively improved the reductive dechlorination performance in the presence of As(III), Ni(II), Pb(II) and mixed HMs, while no enhancement was observed under Cu(II) exposure. Additionally, sulfate introduction effectively accelerated the detoxification of Ni(II), Pb(II), Cu(II), and As(III), achieving removal efficiencies of 76.87 %, 64.01 %, 86.37 %, and 95.50 % within the first three days, respectively. Meanwhile, propionate dynamics and acetogenesis indicated enhanced carbon source and e-donor supply. 16S rRNA gene sequencing and metagenomic analysis results demonstrated that HM sequestration was accomplished jointly by SRB and HM-resistant bacteria via extracellular precipitation (metal sulfide) and intracellular sequestration, while their contribution depended on the specific coexisting HM species present. This study highlights the critical role of sulfate in the concurrent bioremediation of HM-organohalide composite contamination and provides insights for developing a cost-effective in-situ bioremediation strategy.}, } @article {pmid39504669, year = {2024}, author = {Jiang, K and Yang, X and Gao, Q and Ni, J and Feng, J and Wu, D and Zou, X and Hu, L and Liu, X and Song, Z and Wang, Z}, title = {Exogenous signaling molecules N-acyl-homoserine lactones promotes the reconstruction of sludge particles after impact with highly concentrated urea-formaldehyde resin microplastics.}, journal = {Journal of environmental management}, volume = {371}, number = {}, pages = {123179}, doi = {10.1016/j.jenvman.2024.123179}, pmid = {39504669}, issn = {1095-8630}, mesh = {*Sewage ; *Formaldehyde/chemistry ; *Acyl-Butyrolactones/metabolism ; *Microplastics ; *Urea/chemistry/metabolism ; Waste Disposal, Fluid/methods ; }, abstract = {In this study, exogenous N-acyl-homoserine lactones (AHLs) was added to resist the stress by high concentration (0.5 g/L) of urea formaldehyde resin microplastics (UF-MPs) on anaerobic granular sludge (AnGS), aiming to provide a viable strategy for AnGS to withstand elevated levels of UF-MPs toxicity elucidate the intricate regulatory mechanism of AHL-mediated AnGS-QS regulation. The results showed that the three different signaling molecules (C4-HSL, C6-HSL, and C8-HSL) improved the performance of AnGS under high concentration (0.5 g/L) urea-formaldehyde resin stress, and increased sludge COD removal (4.48%, 4.76%, and 3.35%, respectively) and methanogenic activity (8.38%, 1.92%, and 18.76%, respectively). The addition of C4-HSL has the best effect on sludge particle size and strength, which is attributed to the fact that C4-HSL can significantly increase the content of polysaccharides and proteins in tightly bound extracellular polymeric substances (TB-EPS) (27.1% and 27.1%, respectively). C8-HSL most obviously promotes energy metabolism and EPS biosynthesis gene expression. Metagenomic analysis showed that trace AHLs could promote the abundance of enzymes and functional genes related to the main pathway of methane metabolism, increase the relative abundance of Methanothrix of acetophilic methanogens from 27.79% in the control group to 27.85% (C4-HSL), 28.90% (64-HSL), and 30.03% (C8-HSL), thereby improving community stability.}, } @article {pmid39504117, year = {2024}, author = {Qin, X and Cheng, J and Qiu, Y and Guan, N and Gupta, TB and Wu, S and Jiang, Y and Yang, X and Man, C}, title = {Characterization of psychrotrophic and thermoduric bacteria in raw milk using a multi-omics approach.}, journal = {Microbial genomics}, volume = {10}, number = {11}, pages = {}, pmid = {39504117}, issn = {2057-5858}, mesh = {*Milk/microbiology ; Animals ; *Bacteria/classification/genetics/isolation & purification ; *Metagenomics/methods ; Proteomics ; Lactococcus/genetics/isolation & purification/classification ; China ; Chryseobacterium/genetics/isolation & purification/classification ; Psychrobacter/genetics/isolation & purification/classification ; Bacillus/genetics/isolation & purification/classification ; Acinetobacter/genetics/isolation & purification/classification ; Pseudomonas/genetics/isolation & purification/classification ; Escherichia/genetics/isolation & purification/classification ; Bacterial Proteins/genetics/metabolism ; Peptide Hydrolases/metabolism/genetics ; Multiomics ; }, abstract = {Psychrotrophic and thermoduric bacteria are the main reasons for the spoilage of dairy products. This study aims to address the composition and function of psychrotrophic and thermoduric bacteria in eight groups of raw milk samples obtained from Heilongjiang Province and Inner Mongolia (China). Microbial enumeration showed an average total bacterial count of 4.63 log c.f.u. ml[-1] and psychrotrophic bacterial counts of 4.82 log c.f.u. ml[-1]. The mean counts of mesophilic and thermophilic thermoduric bacteria were 3.68 log and 1.81 log c.f.u. ml[-1], respectively. Isolated psychrotrophic bacteria (26 genera and 50 species) and mesophilic thermoduric bacteria (20 genera and 32 species) showed high microbial diversity. Through metagenomic and proteomic analyses, significant disparities in the concentration and community structure of psychrotrophic and thermoduric bacteria were observed among different locations. A large number of peptidases were annotated by metagenomics, which may result in milk spoilage. They mainly come from some typical psychrotrophic and thermoduric bacteria, such as Chryseobacterium, Epilithonimonas, Pseudomonas, Psychrobacter, Acinetobacter, Lactococcus, Escherichia and Bacillus. However, the main proteins detected in fresh raw milk were associated with bacterial growth, reproduction and adaptation to cold environments. This investigation provides valuable insights into the microbial communities and protein profiles of raw milk, shedding light on the microbial factors contributing to milk deterioration.}, } @article {pmid39503509, year = {2024}, author = {Xiao, W and Weissman, JL and Johnson, PLF}, title = {Ecological drivers of CRISPR immune systems.}, journal = {mSystems}, volume = {9}, number = {12}, pages = {e0056824}, pmid = {39503509}, issn = {2379-5077}, support = {R21 GM147759/GM/NIGMS NIH HHS/United States ; R21GM147759//HHS | National Institutes of Health (NIH)/ ; }, mesh = {*CRISPR-Cas Systems/genetics ; Humans ; *RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/immunology ; Metagenomics ; }, abstract = {UNLABELLED: CRISPR-Cas is the only known adaptive immune system of prokaryotes. It is a powerful defense system against mobile genetic elements such as bacteriophages. While CRISPR-Cas systems can be found throughout the prokaryotic tree of life, they are distributed unevenly across taxa and environments. Since adaptive immunity is more useful in environments where pathogens persist or reoccur, the density and/or diversity of the host/pathogen community may drive the uneven distribution of CRISPR systems. We directly tested hypotheses connecting CRISPR incidence with prokaryotic density/diversity by analyzing 16S rRNA and metagenomic data from publicly available environmental sequencing projects. In terms of density, we found that CRISPR systems are significantly favored in lower abundance (less dense) taxa and disfavored in higher abundance taxa, at least in marine environments. When we extended this work to compare taxonomic diversity between samples, we found CRISPR system incidence strongly correlated with diversity in human oral environments. Together, these observations confirm that, at least in certain types of environments, the prokaryotic ecological context indeed plays a key role in selecting for CRISPR immunity.

IMPORTANCE: Microbes must constantly defend themselves against viral pathogens, and a large proportion of prokaryotes do so using the highly effective CRISPR-Cas adaptive immune system. However, many prokaryotes do not. We investigated the ecological factors behind this uneven distribution of CRISPR-Cas immune systems in natural microbial populations. We found strong patterns linking CRISPR-Cas systems to prokaryotic density within ocean environments and to prokaryotic diversity within human oral environments. Our study validates previous within-lab experimental results that suggested these factors might be important and confirms that local environment and ecological context interact to select for CRISPR immunity.}, } @article {pmid39503480, year = {2024}, author = {Li, M and Thieringer, PH and Bayer, B and Kellom, M and Santoro, AE}, title = {Genome sequence of Nitrosopumilus adriaticus CCS1 assembled from an ammonia-oxidizing enrichment culture.}, journal = {Microbiology resource announcements}, volume = {13}, number = {12}, pages = {e0069224}, pmid = {39503480}, issn = {2576-098X}, support = {J 4426/FWF_/Austrian Science Fund FWF/Austria ; 345889//Simons Foundation (SF)/ ; LI-SIAME-00001560//Simons Foundation (SF)/ ; MMI5541//Gordon and Betty Moore Foundation (GBMF)/ ; J4426-B//Austrian Science Fund (FWF)/ ; }, abstract = {We report the metagenome-assembled genome of an ammonia-oxidizing archaeon that is closely related to Nitrosopumilus adriaticus NF5 but shows distinct genomic features compared to strain NF5.}, } @article {pmid39503478, year = {2024}, author = {Sun, H and Liu, X and Wang, T and Liu, S and Zhang, R and Guo, X and Yu, Z and Zhao, Y and Shen, P and Zhang, Y}, title = {Rhizosphere microbiomes are closely linked to seagrass species: a comparative study of three coastal seagrasses.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {12}, pages = {e0175424}, pmid = {39503478}, issn = {1098-5336}, support = {U2106208//NSFC-Shandong Joint Fund/ ; 41976147//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {*Rhizosphere ; *Microbiota ; *Zosteraceae/microbiology ; China ; Bacteria/classification/genetics/isolation & purification/metabolism ; Soil Microbiology ; Alismatales/microbiology ; Metagenome ; }, abstract = {UNLABELLED: Seagrass meadows are important marine ecosystems in coastal areas, offering ecological and economic services to the mankind. However, these ecosystems are facing declines due to climate changes and human activities. Rhizosphere-associated microbiomes play critical roles in the survival and adaptation of seagrasses. While prior studies have explored the general microbial communities and their roles in seagrass meadows, there is a gap in understanding the specific rhizosphere microbiomes of different seagrass species and their interdependent relationships. Our study analyzed the microbial community composition and their metabolism in the rhizosphere of Ruppia sinensis (RS), Zostera japonica (ZJ), and Zostera marina (ZM) obtained from the coastal area of Shandong, China, using high throughput and metagenome sequencing. We found that Rhodobacteraceae, Desulfocapsaceae, and Sulfurovaceae were enriched in RS, ZJ, and ZM samples, respectively, compared with the other two seagrass species, and the bacterial connections were decreased from RS to ZM and ZJ samples. The abundances of nirKS and norBC, mediating denitrification, were higher in RS samples with 2.38% ± 0.59% and 2.14% ± 0.24%, respectively. RS samples also showed a higher level of genes in assimilatory sulfate reduction but lower levels in dissimilatory sulfate reduction and oxidation, with a greater ability to convert sulfide into L-cysteine and acetate. Metagenome-assembled genomes from metagenome of RS rhizosphere had a higher diversity and were assigned to eight phyla. Our study could provide a typical project to analyze the bacterial community structures and metabolic functions in the rhizosphere microbiomes of different seagrasses.

IMPORTANCE: Seagrasses are indispensable in marine ecosystems, offering numerous critical services, with their health significantly influenced by associated rhizosphere microbiomes. Although studies have investigated the microbial communities and their ecological roles in seagrass meadows, the correlations between rhizosphere microbiome and seagrass species from a particular geographic region are limited. Some studies concentrated on the bacterial composition within the rhizosphere of various seagrasses, but the functional aspects of these microbiomes remain unexplored. Our research delves into this void, revealing that Ruppia sinensis, Zostera japonica, and Zostera marina host diverse bacterial community in the composition, connections, functions, and metabolism, such as nitrogen and sulfur metabolism. Our study revealed that seagrass species play an important role in shaping the rhizosphere microbiomes in an equivalent environment, emphasizing the importance of seagrass species in shaping the rhizosphere microbial communities.}, } @article {pmid39503159, year = {2025}, author = {Wasserman, MG and Greenberg, J and Hall, B and Staffa, SJ and Sawicki, GS and Priebe, GP}, title = {Plasma Microbial Cell-Free DNA Metagenomic Next-Generation Sequencing in People With Cystic Fibrosis.}, journal = {Pediatric pulmonology}, volume = {60}, number = {1}, pages = {e27380}, doi = {10.1002/ppul.27380}, pmid = {39503159}, issn = {1099-0496}, support = {//This study was supported in part by the Institutional Centers for Clinical and Translational Research at Boston Children's Hospital. The Karius testing costs were covered by Karius, Inc./ ; }, } @article {pmid39503092, year = {2025}, author = {Wu, Y and You, Y and Wu, L and Du, M and Ibrahim, A and Suo, H and Zhang, F and Zheng, J}, title = {Integrated metagenomics and metatranscriptomics analyses reveal the impacts of different Lactiplantibacillus plantarum strains on microbial communities and metabolic profiles in pickled bamboo shoots.}, journal = {Food chemistry}, volume = {464}, number = {Pt 2}, pages = {141772}, doi = {10.1016/j.foodchem.2024.141772}, pmid = {39503092}, issn = {1873-7072}, mesh = {*Fermentation ; *Metagenomics ; *Lactobacillus plantarum/metabolism/genetics ; *Microbiota ; Plant Shoots/metabolism/chemistry/microbiology ; Metabolome ; Sasa/microbiology/metabolism ; }, abstract = {Effects of two different Lactobacillus plantarum fermentation processes on microbial communities and metabolic functions were evaluated using metagenomics and metatranscriptomics. Dominant species in Lactobacillus plantarum DACN4208 (LPIF8) and DACN4120 (LPIF10) were Lactobacillus pentosus and Lactobacillus plantarum, with Lactiplantibacillus comprised 75.31 % of the microbial community in LPIF10. Metatranscriptomic revealed that LPIF8 had more genes associated with carbohydrate-binding modules and auxiliary activities, totaling 7500 and 4000 genes, respectively. Metabolic reconstruction further showed that LPIF8 had the most genes involved in pyruvate and lactose metabolism, with 633 and 389 genes, respectively. In contrast, LPIF10 fewer genes related to the biosynthesis and metabolism of phenylalanine, tyrosine, and tryptophan. These results indicate that LPIF8 could efficiently improve fermentation efficiency and increase metabolic activity, while LPIF10 exhibited a more moderate and controlled metabolic process. These provide valuable insights into how different starter cultures influence the structure and metabolic functions of microbial communities in pickled bamboo shoots.}, } @article {pmid39502950, year = {2024}, author = {Kerek, A and Szabó, E and Szabó, Á and Papp, M and Bányai, K and Kardos, G and Kaszab, E and Bali, K and Jerzsele, Á}, title = {Investigating antimicrobial resistance genes in probiotic products for companion animals.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1464351}, pmid = {39502950}, issn = {2297-1769}, abstract = {INTRODUCTION: One of the greatest challenges of our time is antimicrobial resistance, which could become the leading cause of death globally within a few decades. In the context of One Health, it is in the common interest to mitigate the global spread of antimicrobial resistance by seeking alternative solutions, alongside appropriate drug selection and responsible use. Probiotics offer a potential avenue to reduce antibiotic usage; however, there is a scarcity of research that examines commercial products in terms of carrying antimicrobial resistance genes (ARGs) involved in resistance development through microbial vectors.

METHODS: Our study investigated 10 commercially available probiotic products for cats and dogs. Initially, we conducted phenotypic testing through determination of minimum inhibitory concentration (MIC) for antibiotics important in animal and public health. Subsequently, we performed next-generation sequencing (NGS) of the products to elucidate the genetic background behind the decrease in phenotypic sensitivity.

RESULTS: In total, 19 types of ARGs were identified, with 57.9% being found on plasmids, and in two cases, carriage as mobile genetic elements were found. One of the genes identified was the APH(3')-Ia gene, capable of inactivating aminoglycoside antibiotics through phosphotransferase enzyme production regulation, while the other was the tetS gene, capable of conferring reduced sensitivity to tetracycline antibiotics through target protection.

DISCUSSION: Our findings underscore the importance of approaching antimicrobial resistance investigations from a broader perspective. We suggest that further studies in this area are justified and raise questions regarding the need to extend legally required studies on probiotic products from their use in economic livestock to their use in companion animals.}, } @article {pmid39502785, year = {2024}, author = {Guccione, C and Patel, L and Tomofuji, Y and McDonald, D and Gonzalez, A and Sepich-Poore, GD and Sonehara, K and Zakeri, M and Chen, Y and Dilmore, AH and Damle, N and Baranzini, SE and Nakatsuji, T and Gallo, RL and Langmead, B and Okada, Y and Curtius, K and Knight, R}, title = {Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {39502785}, issn = {2693-5015}, support = {R01 CA241728/CA/NCI NIH HHS/United States ; DP1 AT010885/AT/NCCIH NIH HHS/United States ; R01 CA270235/CA/NCI NIH HHS/United States ; R21 HG013433/HG/NHGRI NIH HHS/United States ; T32 GM007198/GM/NIGMS NIH HHS/United States ; U19 AG063744/AG/NIA NIH HHS/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; P30 CA023100/CA/NCI NIH HHS/United States ; U24 CA248454/CA/NCI NIH HHS/United States ; }, abstract = {As next-generation sequencing technologies produce deeper genome coverages at lower costs, there is a critical need for reliable computational host DNA removal in metagenomic data. We find that insufficient host filtration using prior human genome references can introduce false sex biases and inadvertently permit flow-through of host-specific DNA during bioinformatic analyses, which could be exploited for individual identification. To address these issues, we introduce and benchmark three host filtration methods of varying throughput, with concomitant applications across low biomass samples such as skin and high microbial biomass datasets including fecal samples. We find that these methods are important for obtaining accurate results in low biomass samples (e.g., tissue, skin). Overall, we demonstrate that rigorous host filtration is a key component of privacy-minded analyses of patient microbiomes and provide computationally efficient pipelines for accomplishing this task on large-scale datasets.}, } @article {pmid39502242, year = {2024}, author = {Das, R and Tamang, B and Najar, IN and Bam, M and Rai, PK}, title = {Probiotic yeast characterization and fungal amplicon metagenomics analysis of fermented bamboo shoot products from Arunachal Pradesh, northeast India.}, journal = {Heliyon}, volume = {10}, number = {20}, pages = {e39500}, pmid = {39502242}, issn = {2405-8440}, abstract = {This study investigates the diverse fungal community and their probiotic functions present in ethnic fermented bamboo shoots of Arunachal Pradesh. Among 95 yeast isolates, 13 demonstrated notable probiotic attributes. These included growth at pH 3, bile tolerance, autoaggregation, co-aggregation, hydrophobicity, lysozyme tolerance and antimicrobial activity. Confirmation of some of the probiotic properties through specific primers enabled the detection of genes associated with acid and bile tolerance, antimicrobial activity, and adhesion. Probiotic yeasts were finally identified based on D1 and D2 sequences of large ribosomal subunit as Meyerozyma guilliermondii (BEP1, KGM1_3, NHR3), Meyerozyma caribbica (GEP7), Candida orthopsilopsis (ES1_2, EB1_2, EEGM2_4, GEP2, NEK9), Candida parasilopsis (HD1_1), Pichia kudriavzevii (NHR12), Pichia fermentans (BEP2), and Saccharomyces cerevisiae (NEP2). Fungal amplicon sequencing highlighted the predominance of Ascomycetes, particularly Pestalotiopsis and Penicillium genera. In this study we have perfomed a culture dependent isolation and probiotic study of yeasts and culture independent analysis of the fungal community present during the fermentation of bamboo shoots of Arunachal Pradesh which provides information about the beneficial properties of bamboo shoots as the reservoir of probiotic microorganisms.}, } @article {pmid39502191, year = {2024}, author = {Pilliol, V and Mahmoud Abdelwadoud, B and Aïcha, H and Lucille, T and Gérard, A and Hervé, T and Michel, D and Ghiles, G and Elodie, T}, title = {Methanobrevibacter oralis: a comprehensive review.}, journal = {Journal of oral microbiology}, volume = {16}, number = {1}, pages = {2415734}, pmid = {39502191}, issn = {2000-2297}, abstract = {Methanobrevibacter oralis (M. oralis) has predominated human oral microbiota methanogenic archaea as far back as the Palaeolithic era in Neanderthal populations and gained dominance from the 18[th] century onwards. M. oralis was initially isolated from dental plaque samples collected from two apparently healthy individuals allowing its first characterization. The culture of M. oralis is fastidious and has been the subject of several studies to improve its laboratory growth. Various PCR methods are used to identify M. oralis, targeting either the 16S rRNA gene or the mcrA gene. However, only one RTQ-PCR system, based on a chaperonin gene, offers specificity, and allows for microbial load quantification. Next-generation sequencing contributed five draft genomes, each approximately 2.08 Mb (±0.052 Mb) with a 27.82 (±0.104) average GC%, and two ancient metagenomic assembled genomes. M. oralis was then detected in various oral cavity sites in healthy individuals and those diagnosed with oral pathologies, notably periodontal diseases, and endodontic infections. Transmission pathways, possibly involving maternal milk and breastfeeding, remain to be clarified. M. oralis was further detected in brain abscesses and respiratory tract samples, bringing its clinical significance into question. This review summarizes the current knowledge about M. oralis, emphasizing its prevalence, associations with dysbiosis and pathologies in oral and extra-oral situations, and symbiotic relationships, with the aim of paving the way for further investigations.}, } @article {pmid39502187, year = {2024}, author = {Lu, S and Xie, G and Yuan, M and Zhou, Y and Wang, J and Jiang, J and Zhang, W and He, X and Chen, B}, title = {Metagenomic next-generation sequencing in diagnosing perinephric abscess infection caused by Trichomonas vaginalis.}, journal = {Precision clinical medicine}, volume = {7}, number = {4}, pages = {pbae027}, pmid = {39502187}, issn = {2516-1571}, } @article {pmid39501383, year = {2024}, author = {Jia, H and Liu, Y and Liu, T}, title = {Duration of onset, body temperature and C-reactive protein can be used to predict the results of pus culture in children with acute osteomyelitis of long bones.}, journal = {Italian journal of pediatrics}, volume = {50}, number = {1}, pages = {231}, pmid = {39501383}, issn = {1824-7288}, mesh = {Humans ; *Osteomyelitis/diagnosis/microbiology/blood ; Male ; Female ; *C-Reactive Protein/metabolism/analysis ; Child ; Child, Preschool ; *Body Temperature ; Acute Disease ; Retrospective Studies ; Infant ; Predictive Value of Tests ; Time Factors ; ROC Curve ; High-Throughput Nucleotide Sequencing ; Polymerase Chain Reaction ; }, abstract = {BACKGROUND: With the application of PCR testing and Metagenomic Next-Generation Sequencing(mNGS), the detection rate of causative organisms in paediatric bone and joint infections has been greatly improved. The aim of our study is to identify some indicators that could be used to distinguish the culture results to optimize the use of PCR and mNGS.

METHODS: In this study, a total of 117 cases of acute osteomyelitis of long bones in children who underwent pus culture were included. Patients were grouped as culture-negative (n:21) and culture-positive (n:96) groups according to the results of pus culture. Age, sex, duration of onset, maximum body temperature at onset, inflammatory indicators and D-dimer after admission were systematically collected for all patients and were compared for both groups. ROC curve (ROC) was used to evaluate the diagnostic efficiency of culture-negative. Logistic regression analysis was conducted to determine independent risk factors for culture-negative.

RESULTS: There was no significant difference in age, sex and erythrocyte sedimentation rate between culture-negative group and culture-positive group (P > 0.05). The duration of onset was longer, and the temperature, white blood cells, neutrophils count, C-reactive protein and D-dimer were less elevated in culture-negative acute osteomyelitis (P < 0.05). Duration of onset, maximum body temperature at onset, white blood cell count, neutrophil count, C-reactive protein, and D-dimer have certain diagnostic efficacy in judging the efficacy of negative culture. Logistic regression analysis indicated that the duration of onset more than 6.5 days, the maximum body temperature at onset lower than 38.35℃ and C-reactive protein lower than 78.40 mg/L were independent risk factors for negative culture (P < 0.05).

CONCLUSIONS: Our study revealed that duration of onset more than 6.5 days, maximum body temperature at onset lower than 38.35℃ and C-reactive protein lower than 78.40 mg/L were independent risk factors for predicting negative culture. In children with this type of acute osteomyelitis, we recommend that the pus be tested by PCR or mNGS as a priority.}, } @article {pmid39501184, year = {2024}, author = {Deng, J and Chen, X and Bu, Y and Zhang, J and Han, J}, title = {Exploring the appropriate situation of performing CSF mNGS in patients with proposed intracranial infections.}, journal = {BMC neurology}, volume = {24}, number = {1}, pages = {429}, pmid = {39501184}, issn = {1471-2377}, support = {2019014078Z//Hengshui Science and Technology Bureau/ ; }, mesh = {Humans ; Male ; Female ; Adult ; Middle Aged ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Aged ; Young Adult ; Adolescent ; }, abstract = {BACKGROUND: Identifying the responsible pathogen is crucial for precision medicine in intracranial infections, and Cerebrospinal Fluid (CSF) Metagenomic Next-Generation Sequencing (mNGS) is a reliable method for this detection. However, the indiscriminate utilization of this approach may impose a financial burden on both patients and society. The study aims to investigate the optimal conditions for applying CSF mNGS in patients with suspected intracranial infections, offering valuable references for precision medicine of intracranial infections.

METHODS: A total of 175 hospitalized patients presenting with suspected intracranial infections were selected for retrospective analysis. Base on the detection of responsible pathogens using CSF mNGS, the patients were categorized into two groups, responsible pathogens in Group A were detected but not in Group B. The types of responsible pathogens in group A and the final diagnosis of patients in group B were analyzed. Demographic data, clinical presentation, CSF analysis, imaging results, and electroencephalography (EEG) findings were analyzed for both groups. Finally, a scoring system was established to promptly assess the appropriateness of CSF mNGS for patients with suspected intracranial infections. Each independent predictor was assigned a score of 1, and the patients were subsequently scored. We advocate sending patients' CSF for mNGS when the cumulative score is ≥ 2.

RESULTS: In Group A, the predominant responsible pathogen was the varicella-zoster virus (VZV), while Group B exhibited the highest proportion of final diagnoses related to epilepsy. The logistic regression model indicates that headache [OR = 2.982, 95% CI (1.204-7.383), p = 0.018], increased cerebrospinal fluid white cell count [OR = 4.022, 95% CI (1.331-12.156), p = 0.014], and decreased cerebrospinal fluid glucose levels [OR = 9.006, 95% CI (2.778-29.194), P < 0.001] are independent predictive factors for intracranial infection pathogens detected by CSF mNGS. Under this scoring system, the sensitivity for detecting the responsible pathogen was 57.5%, and the specificity was 87.4%.

CONCLUSION: The likelihood of detecting the responsible pathogen through CSF mNGS in patients with suspected intracranial infections can be evaluated using the scoring system. Furthermore, it is crucial to consider the possibility of another condition, such as epilepsy, when the responsible pathogen is not detected using cerebrospinal fluid mNGS.}, } @article {pmid39500921, year = {2024}, author = {Stewart, RD and Oluwalana-Sanusi, AE and Munzeiwa, WA and Magoswana, L and Chaukura, N}, title = {Profiling the bacterial microbiome diversity and assessing the potential to detect antimicrobial resistance bacteria in wastewater in Kimberley, South Africa.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {26867}, pmid = {39500921}, issn = {2045-2322}, mesh = {*Wastewater/microbiology ; South Africa ; *Microbiota/genetics ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/classification/isolation & purification/drug effects ; RNA, Ribosomal, 16S/genetics ; Anti-Bacterial Agents/pharmacology ; Phylogeny ; }, abstract = {Wastewater treatment plants (WWTPs) are hotspots for pathogens, and can facilitate horizontal gene transfer, potentially releasing harmful genetic material and antimicrobial resistance genes into the environment. Little information exists on the composition and behavior of microbes in WWTPs, especially in developing countries. This study used environmental DNA (eDNA) techniques to examine the microbiome load of wastewater from WWTPs. The DNA was isolated from wastewater samples collected from the treatment trains of three WWTPs in Kimberley, South Africa, and the microbial diversity and composition was compared through 16 S rRNA gene sequencing. The microbes detected were of the Kingdom Bacteria, and of these, 48.27% were successfully identified to genus level. The majority of reads from the combined bacterial data fall within the class Gammaproteobacteria, which is known to adversely impact ecological and human health. Arcobacteraceae constituted 19% of the bacterial reads, which is expected as this family is widespread in aquatic environments. Interestingly, the most abundant bacterial group was Bacteroides, which contain a variety of antibiotic-resistant members. Overall, various antibiotic-resistant taxa were detected in the wastewater, indicating a concerning level of antibiotic resistance within the bacterial community. Therefore, eDNA analysis can be a valuable tool in monitoring and assessing the bacterial microbiome in wastewater, thus providing important information for the optimization and improvement of wastewater treatment systems and mitigate public health risks.}, } @article {pmid39500545, year = {2024}, author = {Hu, X and Bi, J and Yu, Q and Li, H}, title = {Metagenomics reveals the divergence of gut microbiome composition and function in two common pika species (Ochotona curzoniae and Ochotona daurica) in China.}, journal = {FEMS microbiology letters}, volume = {371}, number = {}, pages = {}, doi = {10.1093/femsle/fnae092}, pmid = {39500545}, issn = {1574-6968}, support = {42007026//National Natural Science Foundation of China/ ; }, mesh = {*Gastrointestinal Microbiome/genetics ; *Metagenomics ; China ; Animals ; *Lagomorpha/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Archaea/classification/genetics/isolation & purification ; Viruses/genetics/classification/isolation & purification ; }, abstract = {Gut microbiome plays crucial roles in animal adaptation and evolution. However, research on adaptation and evolution of small wild high-altitude mammals from the perspective of gut microbiome is still limited. In this study, we compared differences in intestinal microbiota composition and function in Plateau pikas (Ochotona curzoniae) and Daurian pikas (O. daurica) using metagenomic sequencing. Our results showed that microbial community structure had distinct differences in different pika species. Prevotella, Methanosarcina, Rhizophagus, and Podoviridae were abundant bacteria, archaea, eukaryotes, and viruses in Plateau pikas, respectively. However, Prevotella, Methanosarcina, Ustilago, and Retroviridae were dominated in Daurian pikas. Functional pathways related to carbohydrate metabolism that refer to the utilization of pectin, hemicellulose, and debranching enzymes were abundant in Plateau pikas, while the function for degradation of chitin, lignin, and cellulose was more concentrated in Daurian pikas. Pika gut had abundant multidrug resistance genes, followed by glycopeptide and beta-lactamase resistance genes, as well as high-risk antibiotic resistance genes, such as mepA, tetM, and bacA. Escherichia coli and Klebsiella pneumoniae may be potential hosts of mepA. This research provided new insights for adaptation and evolution of wild animals from perspective of gut microbiome and broadened our understanding of high-risk antibiotic resistance genes and potential pathogens of wild animals.}, } @article {pmid39500537, year = {2024}, author = {Slizovskiy, IB and Bonin, N and Bravo, JE and Ferm, PM and Singer, J and Boucher, C and Noyes, NR}, title = {Factors impacting target-enriched long-read sequencing of resistomes and mobilomes.}, journal = {Genome research}, volume = {34}, number = {11}, pages = {2048-2060}, pmid = {39500537}, issn = {1549-5469}, support = {R01 AI141810/AI/NIAID NIH HHS/United States ; R01 AI173928/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Animals ; *Metagenomics/methods ; Cattle ; Feces/microbiology ; Drug Resistance, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/methods ; Gastrointestinal Microbiome/genetics ; Interspersed Repetitive Sequences ; Sequence Analysis, DNA/methods ; Metagenome ; Bacteria/genetics/drug effects/classification ; Soil Microbiology ; }, abstract = {We investigated the efficiency of target-enriched long-read sequencing (TELSeq) for detecting antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) within complex matrices. We aimed to overcome limitations associated with traditional antimicrobial resistance (AMR) detection methods, including short-read shotgun metagenomics, which can lack sensitivity, specificity, and the ability to provide detailed genomic context. By combining biotinylated probe-based enrichment with long-read sequencing, we facilitated the amplification and sequencing of ARGs, eliminating the need for bioinformatic reconstruction. Our experimental design included replicates of human fecal microbiota transplant material, bovine feces, pristine prairie soil, and a mock human gut microbial community, allowing us to examine variables including genomic DNA input and probe set composition. Our findings demonstrated that TELSeq markedly improves the detection rates of ARGs and MGEs compared to traditional sequencing methods, underlining its potential for accurate AMR monitoring. A key insight from our research is the importance of incorporating mobilome profiles to better predict the transferability of ARGs within microbial communities, prompting a recommendation for the use of combined ARG-MGE probe sets for future studies. We also reveal limitations for ARG detection from low-input workflows, and describe the next steps for ongoing protocol refinement to minimize technical variability and expand utility in clinical and public health settings. This effort is part of our broader commitment to advancing methodologies that address the global challenge of AMR.}, } @article {pmid39500412, year = {2024}, author = {Regar, RK and Kamthan, M and Gaur, VK and Singh, SP and Mishra, S and Dwivedi, S and Mishra, A and Manickam, N and Nautiyal, CS}, title = {Microbiome divergence across four major Indian riverine water ecosystems impacted by anthropogenic contamination: A comparative metagenomic analysis.}, journal = {Chemosphere}, volume = {368}, number = {}, pages = {143672}, doi = {10.1016/j.chemosphere.2024.143672}, pmid = {39500412}, issn = {1879-1298}, mesh = {*Rivers/microbiology/chemistry ; *Microbiota/drug effects ; India ; *Metagenomics ; *Water Pollutants, Chemical/analysis ; Bacteria/genetics/classification/isolation & purification ; Environmental Monitoring/methods ; Biodiversity ; Ecosystem ; Metals, Heavy/analysis ; Water Microbiology ; Bacteriophages ; }, abstract = {Rivers are critical ecosystems that support biodiversity and local livelihoods. This study aimed to evaluate the effects of metal contamination and anthropogenic activities on microbial and phage community dynamics within major Indian river ecosystems, focusing on the Ganga, Narmada, Cauvery, and Gomti rivers -using metagenomic techniques, Biolog, and ICP-MS analysis. Significant variations in microbial communities were observed both within each river and across the four systems, influenced by ecological factors like geography and hydrology, as well as anthropogenic pressures. Downstream sites consistently exhibited higher microbial diversity, with prevalence of Acidobacteria, Actinobacteria, Verrucomicrobia, Firmicutes, and Nitrospirae dominating, while Proteobacteria and Bacteroides declined. The Ganga River showed a higher abundance of bacteriophages compared to other rivers, which gradually reduced with the increment of anthropogenic impact. Functional gene analysis revealed correlations between carbon utilization and metal resistance in contaminated sites. ICP-MS analysis indicates elevated chromium and lead levels in downstream sites of all rivers compared to upstream sites. Interestingly, pristine upstream sites in the Ganga had higher trace element levels than those in Narmada and Cauvery, likely due to its Himalayan origin. Both the Ganga and Cauvery rivers contained numerous metal resistance genes. The Alaknanda was identified as the primary source of microbial communities, bacteriophages, trace elements, and heavy metals in the Ganga. These findings offer new insights into anthropogenic influences on river microbial dynamics and highlight the need for targeted monitoring and management strategies to preserve river health.}, } @article {pmid39500192, year = {2024}, author = {Liu, W and Li, C and Li, B and Zhu, L and Ming, D and Jiang, L}, title = {Structure-guided discovery and rational design of a new poly(ethylene terephthalate) hydrolase from AlphaFold protein structure database.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {136389}, doi = {10.1016/j.jhazmat.2024.136389}, pmid = {39500192}, issn = {1873-3336}, mesh = {*Polyethylene Terephthalates/chemistry/metabolism ; *Hydrolases/chemistry/metabolism/genetics ; *Protein Engineering ; *Databases, Protein ; Protein Conformation ; Hydrolysis ; Bacterial Proteins/chemistry/metabolism/genetics ; Biodegradation, Environmental ; }, abstract = {Enzymatic degradation offers a promising eco-friendly solution to plastic pollution, especially for polyethylene terephthalate (PET). Current efforts have focused on screening PET-degrading enzymes from microbial and metagenomic sources and obtaining superior candidates with a limited set of templates. More efficient PET hydrolases are required for PET-waste biorefinery. Here, using a structure-guided bioinformatic workflow, we identified a novel PET hydrolase, LSPET4, from Micromonospora sp. HM5-17, by screening the AlphaFold protein structure database. LSPET4 features a unique carbohydrate-binding module (CBM) and a distinctive linear substrate binding conformation. The intrinsic CBM in LSPET4 exhibited superior binding ability on PET surfaces and enhanced PET hydrolysis performance compared to the previously reported most effective CBM3. Through rational protein engineering focused on stabilizing and modifying the linear substrate binding conformation, we developed LSPET4[M6] (D130P, N127F, Y96F, Q209E, A238K, D241S), a variant that achieved a 38.79-fold improvement in activity compared to the wild type, and was comparable to the reported most effective PET hydrolase derived from IsPETase, FAST-PETase at 45 ℃. This variant also demonstrated effectiveness in degrading various commercial PET materials, including PET food sealing films, PET strawberry boxes, and PET tomato boxes used in the food industry. This study not only provides a new template for protein engineering endeavors to create efficient biocatalysts for PET recycling but also offers an effective enzyme discovery approach to uncover enzymes of interest from the AlphaFold protein structure database.}, } @article {pmid39500133, year = {2025}, author = {Adalsteinsson, BT and Guðmundsson, H and Jasilionis, A and Schiøtt, M and Mikkelsen, MD and Guðmundsdóttir, EE and Sivakumar, P and Malmgren, A and Kaushik, T and Apelqvist, E and Vangsgaard, S and Leblay, R and Friðjónsson, Ó and Meyer, AS and Karlsson, EN and Hreggviðsson, GÓ}, title = {Targeted metagenomics - Enrichment for enzymes active on sulfated polysaccharides from seaweeds.}, journal = {Enzyme and microbial technology}, volume = {182}, number = {}, pages = {110528}, doi = {10.1016/j.enzmictec.2024.110528}, pmid = {39500133}, issn = {1879-0909}, mesh = {*Seaweed/metabolism ; *Polysaccharides/metabolism/chemistry ; *Metagenomics ; *Glycoside Hydrolases/metabolism/genetics/chemistry ; *Polysaccharide-Lyases/genetics/metabolism/chemistry/isolation & purification ; Substrate Specificity ; Sulfates/metabolism ; Phylogeny ; }, abstract = {Seaweeds (macroalgae) are an attractive resource for diverse microbial- and enzymatic production processes. They are abundant, underutilized, cheap, and rich in carbohydrates, and therefore have the potential to be used as a source of mono- or oligosaccharides, and as substrates for industrial fermentation processes. Many seaweed polysaccharides, including the sulfated polysaccharides ulvan and fucoidan, are however complex and heterogenous in structure, and there are currently few enzymes available to modify them, and understanding of their enzymatic depolymerization remains limited. The present study aimed to identify and characterize robust fucoidanases and ulvan lyases. Metagenomes were obtained from microbial enrichments from an intertidal hot-spring, genes identified that expressed putative fucoidanases and ulvan lyases, and following gene cloning and expression, the respective enzymes were screened for enzymatic activity. Consistent with their origin, the identified protein sequences were considerably divergent from previously characterized enzymes, with a 44 % average maximal sequence identity. In total, the study resulted in the characterization of 10 new fucoidanases (GH107 and GH168 families) and 8 new ulvan lyases (PL24, PL25 and PL40 families). Notably, the new fucoidanases appeared to have functional specificity towards fucoidan containing α-1,3 linked L-fucosyl and several functioned at high temperature. The study contributes a metagenomics-based approach to identify new seaweed polysaccharide degrading enzymes and an increased understanding of the diversity of such enzymes, which may have implications for the realization of biotechnology based valorization of seaweed biomass.}, } @article {pmid39499979, year = {2024}, author = {Zheng, X and Xu, M and Zhang, Z and Yang, L and Liu, X and Zhen, Y and Ye, Z and Wen, J and Liu, P}, title = {Microbial signatures in chronic thromboembolic pulmonary hypertension thrombi: Insights from metagenomic profiling of fresh and organized thrombi.}, journal = {Thrombosis research}, volume = {244}, number = {}, pages = {109204}, doi = {10.1016/j.thromres.2024.109204}, pmid = {39499979}, issn = {1879-2472}, mesh = {Humans ; Female ; Male ; Middle Aged ; *Hypertension, Pulmonary/microbiology ; *Metagenomics/methods ; *Pulmonary Embolism/microbiology ; Thrombosis/microbiology ; Aged ; Chronic Disease ; Adult ; Microbiota ; }, abstract = {OBJECTIVE: Many studies have reported microbial signatures in thrombi at major vascular sites, such as the coronary artery and the middle cerebral artery, which are critical for maintaining proper blood flow and oxygenation. Chronic thromboembolic pulmonary hypertension (CTEPH) is a condition involving non-resolving thrombosis that has not been fully studied. This study explored the microbial taxonomy and functional profiles of both fresh and organized thrombi associated with CTEPH to investigate the role of microbiota in thrombus non-resolving.

METHODS: In this study, 12 CTEPH fresh thrombi and 12 organized thrombi were collected from 14 patients with CTEPH. Metagenomic sequencing was employed to explore the genomic information of all microorganisms in the thrombus samples.

RESULTS: Our data demonstrated a diverse range of microorganisms in CTEPH thrombi, whether fresh or organized. Notably, a considerable proportion (54.7 %) of sequencing data could not be classified into the relative microbial taxa, highlighting the complexity and novelty of the thrombus ecosystem. Although there were no significant differences in microbial community structure between the two groups, the abundance of dominant microbial species varied. Leuconostoc sp. DORA 2, Staphylococcus aureus, and Aliidongia dinghuensis were common dominant species in CTEPH thrombus. Organized thrombus significantly increased the relative abundance of Staphylococcus aureus, which was confirmed to effectively distinguish between organized and fresh thrombi by LeFSe analysis and random forest analysis. Functional annotation using both the KEGG and eggNOG databases revealed that organized thrombi exhibit stronger metabolic functions, particularly in amino acid metabolism.

CONCLUSIONS: Our findings suggest that microbial composition and function may play an important role in thrombus organization. Targeting inflammation to prevent thrombosis presents promising opportunities for further research in this area.}, } @article {pmid39499858, year = {2024}, author = {Takamiya, H and Kouduka, M and Kato, S and Suga, H and Oura, M and Yokoyama, T and Suzuki, M and Mori, M and Kanai, A and Suzuki, Y}, title = {Genome-resolved metaproteogenomic and nanosolid characterization of an inactive vent chimney densely colonized by enigmatic DPANN archaea.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39499858}, issn = {1751-7370}, mesh = {*Hydrothermal Vents/microbiology ; *Archaea/genetics/metabolism/classification/isolation & purification ; *Genome, Archaeal ; Phylogeny ; Metagenomics ; Proteomics ; Ecosystem ; }, abstract = {Recent successes in the cultivation of DPANN archaea with their hosts have demonstrated an episymbiotic lifestyle, whereas the lifestyle of DPANN archaea in natural habitats is largely unknown. A free-living lifestyle is speculated in oxygen-deprived fluids circulated through rock media, where apparent hosts of DPANN archaea are lacking. Alternatively, DPANN archaea may be detached from their hosts and/or rock surfaces. To understand the ecology of rock-hosted DPANN archaea, rocks rather than fluids should be directly characterized. Here, we investigated a deep-sea hydrothermal vent chimney without fluid venting where our previous study revealed the high proportion of Pacearchaeota, one of the widespread and enigmatic lineages of DPANN archaea. Using spectroscopic methods with submicron soft X-ray and infrared beams, the microbial habitat was specified to be silica-filled pores in the inner chimney wall comprising chalcopyrite. Metagenomic analysis of the inner wall revealed the lack of biosynthetic genes for nucleotides, amino acids, cofactors, and lipids in the Pacearchaeota genomes. Genome-resolved metaproteomic analysis clarified the co-occurrence of a novel thermophilic lineage actively fixing carbon and nitrogen and thermophilic archaea in the inner chimney wall. We infer that the shift in metabolically active microbial populations from the thermophiles to the mesophilic DPANN archaea occurs after the termination of fluid venting. The infilling of mineral pores by hydrothermal silica deposition might be a preferred environmental factor for the colonization of free-living Pacearchaeota with ultrasmall cells depending on metabolites synthesized by the co-occurring thermophiles during fluid venting.}, } @article {pmid39499580, year = {2024}, author = {Zhang, X and Zhang, XX and Ma, L}, title = {New Horizons in Micro/Nanoplastic-Induced Oxidative Stress: Overlooked Free Radical Contributions and Microbial Metabolic Dysregulations in Anaerobic Digestion.}, journal = {Environmental science & technology}, volume = {58}, number = {48}, pages = {21251-21264}, doi = {10.1021/acs.est.4c08865}, pmid = {39499580}, issn = {1520-5851}, mesh = {*Oxidative Stress ; Anaerobiosis ; Free Radicals/metabolism ; *Reactive Oxygen Species/metabolism ; }, abstract = {Excessive production of reactive oxygen species (ROS) induced by micro/nanoplastics (MPs/NPs) is highly toxic to microbes. However, the mechanisms underlying ROS generation and metabolic regulation within anaerobic guilds remain poorly understood. In this study, we investigated the effects of environmentally relevant levels of polypropylene (PP)-MPs/NPs on oxidative stress and microbial ecology during anaerobic digestion (AD). Electron paramagnetic resonance spectroscopy revealed that PP-MPs/NPs elevated the concentrations of environmentally persistent free radicals (EPFRs) and derived hydroxyl radicals ([•]OH). EPFRs were identified as the primary contributors to [•]OH generation, as evidenced by a high Spearman correlation coefficient (r = 0.884, p < 0.001) and free radical-quenching studies. The formation of [•]OH enhanced ROS production by 86.2-100.9%, resulting in decreased cellular viability and methane production (by 37.5-50.5%) at 100 mg/g TS PP-MPs/NPs. Genome-centric metagenomic and metatranscriptomic analyses suggested that PP-MPs/NPs induced the reassembly of community structures, re-evolution of functional traits, and remodeling of interspecies interactions. Specifically, PP-MPs/NPs induced a shift in methanogen consortia from hydrogenotrophic Methanofollis sp. to acetoclastic and hydrogenotrophic Methanothrix soehngenii, primarily because of the latter's diverse ingestion patterns, electron bifurcation complexes, and ROS-scavenging abilities. Downregulation of genes associated with antioxidative defense systems (i.e., sodN, katA, and osmC) and ROS-driven redox signal transduction pathways (c-di-AMP and phosphorylation signaling pathways) provided insights into the mechanisms underlying ROS-induced microbial metabolic dysregulation. Our findings enhance the understanding of microbial ecological and metabolic traits under MPs/NPs stressors, facilitating the control of MPs/NPs toxicity and the stabilization of AD processes.}, } @article {pmid39499072, year = {2024}, author = {Agashe, R and George, J and Pathak, A and Fasakin, O and Seaman, J and Chauhan, A}, title = {Shotgun metagenomics analysis indicates Bradyrhizobium spp. as the predominant genera for heavy metal resistance and bioremediation in a long-term heavy metal-contaminated ecosystem.}, journal = {Microbiology resource announcements}, volume = {13}, number = {12}, pages = {e0024524}, pmid = {39499072}, issn = {2576-098X}, support = {1901371//National Science Foundation (NSF)/ ; 2200615//National Science Foundation (NSF)/ ; 0000602538//U.S. Department of Energy (DOE)/ ; DE-FE0032198//U.S. Department of Energy (DOE)/ ; W911NF2210145//U.S. Department of Defense (DOD)/ ; }, abstract = {Ten soil cores were collected from the long-term heavy metal-contaminated Savannah River Site (SRS) and studied using shotgun metagenomics. In-line with our previous reports, Bradyrhizobium spp. dominated the SRS soils, and thus we recommend that SRS bioremediation studies target the Bradyrhizobium genus.}, } @article {pmid39498981, year = {2024}, author = {Mukhanbetzhanov, N and Jarmukhanov, Z and Kozhakhmetov, S and Kushugulova, A}, title = {Metagenomic analysis reveals higher Coriobacteriia abundance in mare's milk consumers.}, journal = {Microbiology resource announcements}, volume = {13}, number = {12}, pages = {e0086224}, pmid = {39498981}, issn = {2576-098X}, abstract = {Our study reveals increased gut Coriobacteriia among mare's milk consumers; metagenomic analysis showed a higher prevalence of genera belonging to class Coriobacteriia in consumers vs non-consumers. This suggests interactions between traditional dairy practices and gut microbiome composition, indicating potential for microbiota modulation through dietary interventions.}, } @article {pmid39498576, year = {2024}, author = {Meramveliotakis, E and Ortego, J and Anastasiou, I and Vogler, AP and Papadopoulou, A}, title = {Habitat Association Predicts Population Connectivity and Persistence in Flightless Beetles: A Population Genomics Approach Within a Dynamic Archipelago.}, journal = {Molecular ecology}, volume = {33}, number = {23}, pages = {e17577}, pmid = {39498576}, issn = {1365-294X}, support = {EXCELLENCE/0421/0419//Research and Innovation Foundation/ ; }, mesh = {Animals ; *Coleoptera/genetics ; *Ecosystem ; *Genetics, Population ; *Gene Flow ; *Polymorphism, Single Nucleotide/genetics ; *Population Dynamics ; Islands ; Metagenomics ; Biological Evolution ; }, abstract = {Habitat association has been proposed to affect evolutionary dynamics through its control on dispersal propensity, which is considered a key trait for lineage survival in habitats of low durational stability. The Habitat Constraint hypothesis predicts different micro- and macroevolutionary patterns for stable versus dynamic habitat specialists, but the empirical evidence remains controversial and in insects mostly derives from winged lineages. We here use genome-wide SNP data to assess the effect of habitat association on the population dynamics of two closely related flightless lineages of the genus Eutagenia (Coleoptera: Tenebrionidae), which are co-distributed across the Cyclades islands in the Eastern Mediterranean but are associated with habitat types of different presumed stability: the psammophilous lineage is associated with dynamic sandy coastal habitats, while the geophilous lineage is associated with comparatively stable compact soil habitats. Our comparative population genomic and demographic analyses support higher inter-island gene flow in the psammophilous lineage, presumably due to the physical properties of dynamic sand-dune habitats that promote passive dispersal. We also find consistent bottlenecks in the psammophilous demes, suggesting that lineage evolution in the dynamic habitat is punctuated by local extinction and recolonisation events. The inferred demographic processes are surprisingly uniform among psammophilous demes, but vary considerably among geophilous demes depending on historical island connectivity, indicating more stringent constraints on the dynamic habitat lineage. This study extends the Habitat Constraint hypothesis by demonstrating that selection on dispersal traits is not the only mechanism that can drive consistent differences in evolutionary dynamics between stable versus dynamic habitat specialists.}, } @article {pmid39498478, year = {2025}, author = {Mukherjee, S and Stamatis, D and Li, CT and Ovchinnikova, G and Kandimalla, M and Handke, V and Reddy, A and Ivanova, N and Woyke, T and Eloe-Fardosh, EA and Chen, IA and Kyrpides, NC and Reddy, TBK}, title = {Genomes OnLine Database (GOLD) v.10: new features and updates.}, journal = {Nucleic acids research}, volume = {53}, number = {D1}, pages = {D989-D997}, pmid = {39498478}, issn = {1362-4962}, support = {DE-AC02-05CH11231//U.S. Department of Energy Office of Science/ ; }, mesh = {*Metadata ; *Genomics/methods ; *Databases, Genetic ; Internet ; Software ; Humans ; User-Computer Interface ; Genome/genetics ; Animals ; }, abstract = {The Genomes OnLine Database (GOLD; https://gold.jgi.doe.gov/) at the Department of Energy Joint Genome Institute is a comprehensive online metadata repository designed to catalog and manage information related to (meta)genomic sequence projects. GOLD provides a centralized platform where researchers can access a wide array of metadata from its four organization levels namely Study, Organism/Biosample, Sequencing Project and Analysis Project. GOLD continues to serve as a valuable resource and has seen significant growth and expansion since its inception in 1997. With its expanded role as a collaborative platform, it not only actively imports data from other primary repositories like National Center for Biotechnology Information but also supports contributions from researchers worldwide. This collaborative approach has enriched the database with diverse datasets, creating a more integrated resource to enhance scientific insights. As genomic research becomes increasingly integral to various scientific disciplines, more researchers and institutions are turning to GOLD for their metadata needs. To meet this growing demand, GOLD has expanded by adding diverse metadata fields, intuitive features, advanced search capabilities and enhanced data visualization tools, making it easier for users to find and interpret relevant information. This manuscript provides an update and highlights the new features introduced over the last 2 years.}, } @article {pmid39498413, year = {2024}, author = {Liang, H and Duan, X and Li, T and Hu, L and Guo, J}, title = {Disseminated Combined Talaromyces marneffei and Enterococcus faecium Bloodstream Infection Presenting as Gastrointestinal Perforation in a Patient with CARD9 Gene Mutation.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {4783-4790}, pmid = {39498413}, issn = {1178-6973}, abstract = {This study presents a case of Talaromyces marneffei combined with Enterococcus faecium bloodstream infection with gastrointestinal symptoms as the sole initial clinical manifestation.The patient is a resident of Shanghai and has no recent travel history to areas with a high risk of T. marneffei infection. He was admitted to the emergency room due to severe upper abdominal pain. Laboratory tests indicated elevated levels of white blood cells, rapid C-reactive protein, and procalcitonin, while the human immunodeficiency virus (HIV) test returned negative. An abdominal CT examination revealed gas and fluid accumulation in the abdominal cavity, raising suspicion for gastrointestinal perforation and peritonitis. Initially, he received symptomatic treatment for gastrointestinal perforation and abdominal infection, but his response to the treatment was poor.Through metagenomic next-generation sequencing (mNGS) and multiple blood cultures, a mixed infection of T. marneffei and E. faecium was identified in the patient's blood. Combination treatment with vancomycin and amphotericin B was initiated to manage the symptoms. However, we discovered genome-wide exon CARD9 mutations in the patient, complicating the treatment process. Ultimately, the delayed diagnosis of T. marneffei resulted in the patient's severe deterioration, rendering the anti-infective treatment ineffective, and leading to the patient's death.This report underscores the challenges associated with diagnosing T. marneffei infections in non-AIDS patients and in non-endemic regions. The diagnosis of disseminated infections poses significant difficulties, particularly when mixed infections are present, complicating clinical treatment. This highlights the critical importance of standardized blood cultures for the early diagnosis of T. marneffei. Additionally, we must prioritize timely whole-genome testing to identify potential immune gene mutations.}, } @article {pmid39498263, year = {2024}, author = {Barbitoff, YA and Khmelkova, DN and Pomerantseva, EA and Slepchenkov, AV and Zubashenko, NA and Mironova, IV and Kaimonov, VS and Polev, DE and Tsay, VV and Glotov, AS and Aseev, MV and Shcherbak, SG and Glotov, OS and Isaev, AA and Predeus, AV}, title = {Expanding the Russian allele frequency reference via cross-laboratory data integration: insights from 7452 exome samples.}, journal = {National science review}, volume = {11}, number = {10}, pages = {nwae326}, pmid = {39498263}, issn = {2053-714X}, abstract = {Population allele frequency is crucially important for accurate interpretation of known and novel variants in medical genetics. Recently, several large allele frequency databases, such as the Genome Aggregation Database (gnomAD), have been created to serve as a global reference for such studies. However, frequencies of many rare alleles vary dramatically between populations, and population-specific allele frequency is often more informative than the global one. Many countries and regions, including Russia, remain poorly studied from the genetic perspective. Here, we report the first successful attempt to integrate genetic information between major medical genetic laboratories in Russia. We construct RUSeq, an open, large-scale reference set of genetic variants by analyzing 7452 exome samples collected in two major Russian cities-Moscow and St. Petersburg. An ∼10-fold increase in sample size compared to previous studies allowed us to characterize extensive genetic diversity within the admixed Russian population with contributions from several major ancestral groups. We highlight 51 known pathogenic variants that are overrepresented in Russia compared to other European countries. We also identify several dozen high-impact variants that are present in healthy donors despite being annotated as pathogenic in ClinVar and falling within genes associated with autosomal dominant disorders. The constructed database of genetic variant frequencies in Russia has been made available to the medical genetics community through a variant browser available at http://ruseq.ru.}, } @article {pmid39498151, year = {2024}, author = {Dias, YJM and Dezordi, FZ and Wallau, GDL}, title = {EEfinder, a general purpose tool for identification of bacterial and viral endogenized elements in eukaryotic genomes.}, journal = {Computational and structural biotechnology journal}, volume = {23}, number = {}, pages = {3662-3668}, pmid = {39498151}, issn = {2001-0370}, abstract = {Horizontal gene transfer is a phenomenon of genetic material transmission between species with no parental relationship. It has been characterized among several major branches of life, including among prokaryotes, viruses and eukaryotes. The characterization of endogenous elements derived from viruses or bacteria provides a snapshot of past host-pathogen interactions and coevolution as well as reference information to remove false positive results from metagenomic studies. Currently there is a lack of general purpose standardized tools for endogenous elements screening which limits reproducibility and hinder comparative analysis between studies. Here we describe EEfinder, a new general purpose tool for identification and classification of endogenous elements derived from viruses or bacteria found in eukaryotic genomes. The tool was developed to include six common steps performed in this type of analysis: data cleaning, similarity search through sequence alignment, filtering candidate elements, taxonomy assignment, merging of truncated elements and flanks extraction. We evaluated the sensitivity of EEfinder to identify endogenous elements through comparative analysis using data from the literature and showed that EEfinder automatically detected 97 % of the EVEs compared to published results obtained by manual curation and detected an almost exact full integration of a Wolbachia genome described using wet-lab experiments. Therefore, EEfinder can effectively and systematically identify endogenous elements with bacterial/viral origin integrated in eukaryotic genomes. EEfinder is publicly available on https://github.com/WallauBioinfo/EEfinder.}, } @article {pmid39498086, year = {2024}, author = {Maghembe, RS and Magulye, MAK and Makaranga, A and Nsubuga, G and Sekyanzi, S and Moto, EA and Mwesigwa, S and Katagirya, E}, title = {Metagenome mining divulges virulent and multidrug resistant Pseudomonas aeruginosa ST242 and Klebsiella michiganensis ST∗1b23 coinfecting an 8-month-old meningitis infant under ICU in Kampala, Uganda, East Africa.}, journal = {Heliyon}, volume = {10}, number = {20}, pages = {e39455}, pmid = {39498086}, issn = {2405-8440}, abstract = {Pediatric meningitis is a global health problem, with insufficiently known pathogens and antibiotic resistance (AMR) especially in low-resource settings. Here, we sought to uncover the virulence and AMR of pathogens associated with infant meningitis, treated with ceftriaxone, in Kampala, Uganda. In a bid to isolate Klebsiella oxytoca, we coincidentally recovered a co-culture and challenged it with antibiotic susceptibility testing (AST) on a panel of 14 antibiotics. We then combined metagenome binning with antiSMASH/PRISM genome mining to unveil the pathogens, their virulence and molecular targets in relation to meningitis. From AST, the co-culture exhibited resistance to multiple aminoglycosides, fluroquinolones, and β-lactams, including ceftriaxone, the inherently used drug. From metagenome annotation, the first bin was identified as Pseudomonas aeruginosa ST242 and the second as Klebsiella michiganensis ST∗1b23. Among others, P. aeruginosa ST242 virulence factors include type 3 and type 6 secretion systems, biofilm, and nonribosomal peptides (NRPs) of the pyoverdine synthase operon, targeting claudin-5, a component of the tight junctions of the blood-brain barrier (BBB). The P. aeruginosa ST242 genome portrays intrinsic resistance to beta-lactamases (blaOXA-50 and blaPAO), aminoglycosides [aph(3')-IIb)], fluoroquinolones (crpP), tetracycline (tmexD2) and fosfomycin (fosA), among others. From K. michiganensis ST∗1b23 genome mining we elucidated a yersiniabactin-related metabolite, targeting the ligand-binding domain of the human polymeric immunoglobulin receptor (pIgR) and other components of the BBB. The K. michiganensis ST∗1b23 chromosome encodes the genes blaOXY-1 and OqxA/B, conferring resistance to β-lactams, fluoroquinolones, and trimethoprim respectively. Notably, we found one frameshift and nine substitution mutations conferring carbapenem and cephalosporin resistance mechanisms. Overall, our findings strongly suggest coinfection and a mechanistic crosstalk between P. aeruginosa ST242 and K. michiganensis ST∗1b23 in the pathogenesis of meningitis in this case. Importantly, ceftriaxone could be an inappropriate treatment choice for these pathogens. Hence, serious surveillance and experimental studies will improve the management of pediatric meningitis.}, } @article {pmid39497924, year = {2024}, author = {Li, L and Shao, J and Tong, C and Gao, W and Pan, P and Qi, C and Gao, C and Zhang, Y and Zhu, Y and Chen, C}, title = {Non-tuberculous mycobacteria enhance the tryptophan-kynurenine pathway to induce immunosuppression and facilitate pulmonary colonization.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1455605}, pmid = {39497924}, issn = {2235-2988}, mesh = {Humans ; *Tryptophan/metabolism ; *Kynurenine/metabolism ; *Nontuberculous Mycobacteria ; *Mycobacterium Infections, Nontuberculous/microbiology ; *Lung/microbiology/immunology ; Bronchoalveolar Lavage Fluid/microbiology ; Microbiota ; Metabolic Networks and Pathways ; Pseudomonas aeruginosa/genetics/metabolism ; Indoleamine-Pyrrole 2,3,-Dioxygenase/metabolism ; Metabolomics ; Immune Tolerance ; Metagenomics ; }, abstract = {The increasing prevalence of non-tuberculous mycobacterium (NTM) infections alongside tuberculosis (TB) underscores a pressing public health challenge. Yet, the mechanisms governing their infection within the lung remain poorly understood. Here, we integrate metagenomic sequencing, metabolomic sequencing, machine learning classifiers, SparCC, and MetOrigin methods to profile bronchoalveolar lavage fluid (BALF) samples from NTM/TB patients. Our aim is to unravel the intricate interplay between lung microbial communities and NTM/Mycobacterium tuberculosis infections. Our investigation reveals a discernible reduction in the compositional diversity of the lung microbiota and a diminished degree of mutual interaction concomitant with NTM/TB infections. Notably, NTM patients exhibit a distinct microbial community characterized by marked specialization and notable enrichment of Pseudomonas aeruginosa and Staphylococcus aureus, driving pronounced niche specialization for NTM infection. Simultaneously, these microbial shifts significantly disrupt tryptophan metabolism in NTM infection, leading to an elevation of kynurenine. Mycobacterium intracellulare, Mycobacterium paraintracellulare, Mycobacterium abscessus, and Pseudomonas aeruginosa have been implicated in the metabolic pathways associated with the conversion of indole to tryptophan via tryptophan synthase within NTM patients. Additionally, indoleamine-2,3-dioxygenase converts tryptophan into kynurenine, fostering an immunosuppressive milieu during NTM infection. This strategic modulation supports microbial persistence, enabling evasion from immune surveillance and perpetuating a protracted state of NTM infection. The elucidation of these nuanced microbial and metabolic dynamics provides a profound understanding of the intricate processes underlying NTM and TB infections, offering potential avenues for therapeutic intervention and management.}, } @article {pmid39497628, year = {2024}, author = {Steffen, KJ and Sorgen, AA and Fodor, AA and Carroll, IM and Crosby, RD and Mitchell, JE and Bond, DS and Heinberg, LJ}, title = {Early changes in the gut microbiota are associated with weight outcomes over 2 years following metabolic and bariatric surgery.}, journal = {Obesity (Silver Spring, Md.)}, volume = {32}, number = {11}, pages = {1985-1997}, doi = {10.1002/oby.24168}, pmid = {39497628}, issn = {1930-739X}, support = {1R01DK112585/DK/NIDDK NIH HHS/United States ; 3R01DK112585-01S1/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Bariatric Surgery/methods ; Female ; Male ; Middle Aged ; Adult ; *Weight Loss ; Longitudinal Studies ; Body Mass Index ; Treatment Outcome ; Obesity/surgery/microbiology ; Body-Weight Trajectory ; }, abstract = {OBJECTIVE: Metabolic and bariatric surgery (MBS) is associated with substantial, but variable, weight outcomes. The gut microbiome may be a factor in determining weight trajectory, but examination has been limited by a lack of longitudinal studies with robust microbiome sequencing. This study aimed to describe changes in the microbiome and associations with weight outcomes more than 2 years post surgery.

METHODS: Data were collected at two Midwestern U.S.

CENTERS: Adults undergoing primary MBS were assessed before and 1, 6, 12, 18, and 24 months after surgery. BMI and metagenomic sequencing occurred at each assessment. A linear growth mixture model determined class structure for weight trajectory.

RESULTS: A linear growth mixture model of participants (N = 124) revealed a two-class structure; one class had greater sustained weight loss relative to the other. Greater genus-level taxonomic changes in the microbiome composition at each time point were associated with being in the more favorable weight trajectory class, after controlling for surgery type. Higher Proteobacteria relative abundance at 1 month was predictive of percentage weight change at 6, 12, 18, and 24 months (p < 0.05 for all).

CONCLUSIONS: Greater genus-level taxonomic changes in the gut microbiota are associated with improved weight trajectory. Early changes in the gut microbiota may be an important indicator of MBS outcomes and durability.}, } @article {pmid39497067, year = {2024}, author = {Moeller, AH and Dillard, BA and Goldman, SL and Real, MVF and Sprockett, DD}, title = {Removal of sequencing adapter contamination improves microbial genome databases.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1033}, pmid = {39497067}, issn = {1471-2164}, support = {R01 DK139214/DK/NIDDK NIH HHS/United States ; R35 GM138284/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Databases, Genetic ; DNA Contamination ; Genome, Microbial ; Humans ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Cattle ; Mice ; Swine ; }, abstract = {Advances in assembling microbial genomes have led to growth of reference genome databases, which have been transformative for applied and basic microbiome research. Here we show that published microbial genome databases from humans, mice, cows, pigs, fish, honeybees, and marine environments contain significant sequencing-adapter contamination that systematically reduces assembly accuracy and contiguousness. By removing the adapter-contaminated ends of contiguous sequences and reassembling MGnify reference genomes, we improve the quality of assemblies in these databases.}, } @article {pmid39497050, year = {2024}, author = {Chen, Z and Xiang, K and Wang, K and Liu, B}, title = {Streptococcus salivarius pneumonia-associated pneumomediastinum: a case report and literature review.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {1238}, pmid = {39497050}, issn = {1471-2334}, mesh = {Humans ; Male ; *Mediastinal Emphysema/diagnostic imaging/microbiology ; Adult ; *Streptococcal Infections/microbiology/complications/drug therapy/diagnosis ; *Tomography, X-Ray Computed ; *Streptococcus salivarius/isolation & purification ; *Anti-Bacterial Agents/therapeutic use ; Pneumonia, Bacterial/microbiology/complications/drug therapy/diagnosis/diagnostic imaging ; Bronchoalveolar Lavage Fluid/microbiology ; }, abstract = {BACKGROUND: Streptococcus salivarius is an opportunistic pathogen, and there have been no reported cases of Streptococcus salivarius pneumonia to date. Pneumomediastinum is usually secondary to tracheal or esophageal injury and is very rare as a complication of pneumonia. We report a case of Streptococcus salivarius pneumonia complicated by pneumomediastinum, aiming to enhance clinicians' awareness of rare pathogens and uncommon complications in pneumonia.

CASE PRESENTATION: The patient, a 36-year-old male, presented with a persistent cough and sputum production for one week, accompanied by a sore throat that had developed just one day prior. Chest computed tomography (CT) disclosed pneumomediastinum alongside obstructive atelectasis in the left lower lobe. Streptococcus salivarius infection was conclusively identified through bronchoalveolar lavage metagenomic next-generation sequencing (mNGS), as well as smear and culture analyses. The patient was administered intravenous amoxicillin-clavulanate potassium for a duration of seven days as part of the anti-infection regimen. Given the stability of the patient's respiratory and circulatory systems, a tube drainage procedure was deemed unnecessary. Post-treatment, the patient's clinical symptoms notably improved. A subsequent chest CT scan revealed the re-expansion of the left lower lung and near-complete resolution of pneumomediastinum.

CONCLUSION: There are numerous pathogens that can cause pneumonia. While focusing on common pathogens, it is important not to overlook rare ones. When considering infections from rare pathogens, it is recommended to promptly perform a bronchoscopy and submit bronchoalveolar lavage fluid for mNGS to improve pathogen detection rates. During the diagnosis and treatment of pneumonia, it is crucial to be vigilant for rare complications. When a patient presents with symptoms such as dyspnea or subcutaneous emphysema, it is advisable to immediately perform a chest CT scan to rule out pneumomediastinum.}, } @article {pmid39496708, year = {2024}, author = {Payet, SD and Underwood, J and Berry, O and Saunders, T and Travers, MJ and Wakefield, CB and Miller, K and Newman, SJ}, title = {Population genomics informs the management of harvested snappers across north-western Australia.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {26598}, pmid = {39496708}, issn = {2045-2322}, mesh = {Animals ; *Polymorphism, Single Nucleotide ; Western Australia ; *Genetics, Population ; Fisheries ; Fishes/genetics ; Genetic Variation ; Metagenomics/methods ; Perciformes/genetics ; Australia ; }, abstract = {Failure to consider population structure when managing harvested fishes increases the risk of stock depletion, yet empirical estimates of population structure are often lacking for important fishery species. In this study, we characterise genetic variation in single nucleotide polymorphisms (SNPs) to assess population structure for three harvested species of tropical snappers across the broad (up to 300 km wide) and extensive (~ 4000 km) continental shelf of north-western Australia. Comparisons across ~ 300 individuals per species, showed remarkably similar patterns of genetic structure among Lutjanus sebae (red emperor), L. malabaricus (saddletail snapper) and Pristipomoides multidens (goldband snapper) despite subtle differences in biological and ecological traits. Low levels of genetic subdivision were reflected in an isolation by distance relationship where genetic connectivity increased with geographic proximity. This indicates extensive but not unlimited dispersal across the north-western Australian shelf. Our findings provide evidence of connectivity between current management areas, violating the assumption of multiple independent stocks. Spatial stock assessment models may be more suitable for the management of these species however demographic connectivity rates cannot be accurately estimated from the conventional population genetic approaches applied in this study. We recommend that managers aim to maintain adequate spawning biomass across current management areas, and assess stocks at finer scales, where practical.}, } @article {pmid39496275, year = {2024}, author = {Lazar, A and Phillips, RP and Kivlin, S and Bending, GD and Mushinski, RM}, title = {Understanding the ecological versatility of Tetracladium species in temperate forest soils.}, journal = {Environmental microbiology}, volume = {26}, number = {11}, pages = {e70001}, doi = {10.1111/1462-2920.70001}, pmid = {39496275}, issn = {1462-2920}, support = {DESC0016188//U.S. Department of Energy Office of Biological and Environmental Research, Terrestrial Ecosystem Science Program/ ; NE/S007350/1//UK Research and Innovation Natural Environment Research Council/ ; }, mesh = {*Soil Microbiology ; *Forests ; *Soil/chemistry ; Biodiversity ; Mycorrhizae/classification/genetics ; }, abstract = {Although Tetracladium species have traditionally been studied as aquatic saprotrophs, the growing number of metagenomic and metabarcoding reports detecting them in soil environments raises important questions about their ecological adaptability and versatility. We investigated the factors associated with the relative abundance, diversity and ecological dynamics of Tetracladium in temperate forest soils. Through amplicon sequencing of soil samples collected from 54 stands in six forest sites across the eastern United States, we identified 29 distinct Amplicon Sequence Variants (ASVs) representing Tetracladium, with large differences in relative abundance and small changes in ASV community composition among sites. Tetracladium richness was positively related to soil pH, soil temperature, total sulphur and silt content, and negatively related to plant litter quality, such as the lignin-to-nitrogen ratio and the lignocellulose index. Co-occurrence network analysis indicated negative relationships between Tetracladium and other abundant fungal groups, including ectomycorrhizal and arbuscular mycorrhizal fungi. Collectively, our findings highlight the ecological significance of Tetracladium in temperate forest soils and emphasize the importance of site-specific factors and microbial interactions in shaping their distribution patterns and ecological dynamics.}, } @article {pmid39495619, year = {2024}, author = {Malik, AA and Martiny, JBH and Ribeiro, A and Sheridan, PO and Weihe, C and Brodie, EL and Allison, SD}, title = {Bacterial population-level trade-offs between drought tolerance and resource acquisition traits impact decomposition.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39495619}, issn = {1751-7370}, support = {S10 OD010786/OD/NIH HHS/United States ; DE-SC0020382//US Department of Energy Genomic Science Program, BER, Office of Science projects/ ; 1S10OD010786-01//DNA Technologies and Expression Analysis Cores at the UC Davis Genome Center/ ; DE-AC02-05CH11231//Lawrence Berkeley National Laboratory/ ; }, mesh = {*Droughts ; *Soil Microbiology ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Ecosystem ; Plant Leaves/microbiology ; Metagenome ; Stress, Physiological ; Soil/chemistry ; Drought Resistance ; }, abstract = {Microbes drive fundamental ecosystem processes, such as decomposition. Environmental stressors are known to affect microbes, their fitness, and the ecosystem functions that they perform; yet, understanding the causal mechanisms behind this influence has been difficult. We used leaf litter on soil surface as a model in situ system to assess changes in bacterial genomic traits and decomposition rates for 18 months with drought as a stressor. We hypothesized that genome-scale trade-offs due to investment in stress tolerance traits under drought reduce the capacity for bacterial populations to carry out decomposition, and that these population-level trade-offs scale up to impact emergent community traits, thereby reducing decomposition rates. We observed drought tolerance mechanisms that were heightened in bacterial populations under drought, identified as higher gene copy numbers in metagenome-assembled genomes. A subset of populations under drought had reduced carbohydrate-active enzyme genes that suggested-as a trade-off-a decline in decomposition capabilities. These trade-offs were driven by community succession and taxonomic shifts as distinct patterns appeared in populations. We show that trait-trade-offs in bacterial populations under drought could scale up to reduce overall decomposition capabilities and litter decay rates. Using a trait-based approach to assess the population ecology of soil bacteria, we demonstrate genome-level trade-offs in response to drought with consequences for decomposition rates.}, } @article {pmid39495170, year = {2024}, author = {Bradford, LM and Yao, L and Anastasiadis, C and Cooper, AL and Blais, B and Deckert, A and Reid-Smith, R and Lau, C and Diarra, MS and Carrillo, C and Wong, A}, title = {Limit of detection of Salmonella ser. Enteritidis using culture-based versus culture-independent diagnostic approaches.}, journal = {Microbiology spectrum}, volume = {12}, number = {12}, pages = {e0102724}, pmid = {39495170}, issn = {2165-0497}, abstract = {UNLABELLED: To prevent the spread of foodborne illnesses, the presence of pathogens in the food chain is monitored by government agencies and food producers. The culture-based methods currently employed are sensitive but time- and labor-intensive, leading to increasing interest in exploring culture-independent diagnostic tests (CIDTs) for pathogen detection. However, few studies quantify the relative sensitivity and reliability of these CIDTs compared to current approaches. To address this issue, we conducted a comparison of the limit of detection (LOD50) for Salmonella between a culture-based method and three CIDTs: qPCR (targeting invA and stn), metabarcode (16S) sequencing, and shotgun metagenomic sequencing. Samples of chicken feed and chicken caecal contents were spiked with S. serovar Enteritidis and subjected to culture- and DNA-based detection methods. To explore the impact of non-selective enrichment on LOD50, all samples underwent both immediate DNA extraction and overnight enrichment prior to gDNA extraction. In addition to this spike-in experiment, feed and caecal samples acquired from the field were tested with culturing, qPCR, and metabarcoding. In general, LOD50 was comparable between qPCR and shotgun sequencing methods. Overnight microbiological enrichment resulted in an improvement in LOD50 with up to a three-log decrease. However, Salmonella reads were detected in some unspiked feed samples, suggesting false-positive detection of Salmonella. In addition, the LOD50 in feeds was three logs lower than in caecal contents, underscoring the impact of background microbiota on Salmonella detection using all methods.

IMPORTANCE: The appeal of culture-independent diagnostic tests (CIDTs) is increased speed with lowered cost, as well as the potential to detect multiple pathogen species in a single analysis and to monitor other areas of concern such as antimicrobial resistance genes or virulence factors. This study provides quantitative data on the sensitivity of CIDTs relative to current approaches, which is essential for determining the feasibility of implementing these methods in pathogen surveillance programs.}, } @article {pmid39494896, year = {2024}, author = {Hu, H and Zhang, Z and Chen, B and Zhang, Q and Xu, N and Paerl, HW and Wang, T and Hong, W and Penuelas, J and Qian, H}, title = {Potential health risk assessment of cyanobacteria across global lakes.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {11}, pages = {e0193624}, pmid = {39494896}, issn = {1098-5336}, support = {2023SZD0058//the Key Scientific and Technological Program of Hangzhou/ ; 21976161, 21777144, 22376187//MOST | National Natural Science Foundation of China (NSFC)/ ; CIVP20A6621//Fundación Ramón Areces (FRA)/ ; 1P01ES028939-01//Foundation for the National Institutes of Health (FNIH)/ ; 2023M743100//China Postdoctoral Science Foundation (China Postdoctoral Foundation Project)/ ; TED2021-132627B-I00//the Spanish Government/ ; P01 ES028939/ES/NIEHS NIH HHS/United States ; 42307158//MOST | National Natural Science Foundation of China (NSFC)/ ; 1831096, 1803697, 2108917//National Science Foundation (NSF)/ ; LZ23B070001//MOST | NSFC | NSFC-Zhejiang Joint Fund | | Natural Science Foundation of Zhejiang Province (ZJNSF)/ ; SGR2021-1333//the Catalan Government/ ; ZJ2023058//Zhejiang Provincial Postdoctoral Science Foundation/ ; }, mesh = {*Lakes/microbiology ; *Cyanobacteria/genetics/metabolism ; Risk Assessment ; Environmental Monitoring ; Humans ; Eutrophication ; Microcystins/biosynthesis ; }, abstract = {UNLABELLED: Cyanobacterial blooms pose environmental and health risks due to their production of toxic secondary metabolites. While current methods for assessing these risks have focused primarily on bloom frequency and intensity, the lack of comprehensive and comparable data on cyanotoxins makes it challenging to rigorously evaluate these health risks. In this study, we examined 750 metagenomic data sets collected from 103 lakes worldwide. Our analysis unveiled the diverse distributions of cyanobacterial communities and the genes responsible for cyanotoxin production across the globe. Our approach involved the integration of cyanobacterial biomass, the biosynthetic potential of cyanotoxin, and the potential effects of these toxins to establish potential cyanobacterial health risks. Our findings revealed that nearly half of the lakes assessed posed medium to high health risks associated with cyanobacteria. The regions of greatest concern were East Asia and South Asia, particularly in developing countries experiencing rapid industrialization and urbanization. Using machine learning techniques, we mapped potential cyanobacterial health risks in lakes worldwide. The model results revealed a positive correlation between potential cyanobacterial health risks and factors such as temperature, N2O emissions, and the human influence index. These findings underscore the influence of these variables on the proliferation of cyanobacterial blooms and associated risks. By introducing a novel quantitative method for monitoring potential cyanobacterial health risks on a global scale, our study contributes to the assessment and management of one of the most pressing threats to both aquatic ecosystems and human health.

IMPORTANCE: Our research introduces a novel and comprehensive approach to potential cyanobacterial health risk assessment, offering insights into risk from a toxicity perspective. The distinct geographical variations in cyanobacterial communities coupled with the intricate interplay of environmental factors underscore the complexity of managing cyanobacterial blooms at a global scale. Our systematic and targeted cyanobacterial surveillance enables a worldwide assessment of cyanobacteria-based potential health risks, providing an early warning system.}, } @article {pmid39494864, year = {2024}, author = {Luu, LDW and Rafique, R and Payne, M and Octavia, S and Robson, J and Sintchenko, V and Lan, R}, title = {Deciphering Bordetella pertussis epidemiology through culture-independent multiplex amplicon and metagenomic sequencing.}, journal = {Journal of clinical microbiology}, volume = {62}, number = {12}, pages = {e0117824}, pmid = {39494864}, issn = {1098-660X}, mesh = {*Bordetella pertussis/genetics/classification/isolation & purification ; Humans ; *Whooping Cough/epidemiology/diagnosis/microbiology ; Australia/epidemiology ; *Metagenomics/methods ; *Multiplex Polymerase Chain Reaction/methods ; Genotype ; DNA, Bacterial/genetics ; Child ; Child, Preschool ; Sensitivity and Specificity ; }, abstract = {UNLABELLED: Whooping cough (pertussis) has re-emerged despite high vaccine coverage in Australia and many other countries worldwide, partly attributable to genetic adaptation of the causative organism, Bordetella pertussis, to vaccines. Therefore, genomic surveillance has become essential to monitor circulating strains for these genetic changes. However, increasing uptake of PCR for the diagnosis of pertussis has affected the availability of cultured isolates for typing. In this study, we evaluated the use of targeted multiplex PCR (mPCR) amplicon sequencing and shotgun metagenomic sequencing for culture-independent typing of B. pertussis directly from respiratory swabs. We developed a nine-target mPCR amplicon assay that could accurately type major lineages [ptxP3/non-ptxpP3, fim3A/B, fhaB3/non-fhaB3, and epidemic lineages (ELs) 1-5] circulating in Australia. Validation using DNA from isolates and 178 residual specimens collected in 2010-2012 (n = 87) and 2019 (n = 91) showed that mPCR amplicon sequencing was highly sensitive with a limit of detection of 4.6 copies [IS481 cycle threshold (Ct) 27.3]. Shotgun metagenomic sequencing was successful in genotyping B. pertussis in 84% of clinical specimens with PCR Ct < 24 and was concordant with mPCR typing results. The results revealed an expansion of EL4 strains from 2010 to 2012 to 2019 in Australia and identified unrecognized co-circulating cases of Bordetella holmesii. This study provides valuable insight into the circulating lineages in Australia prior to the COVID-19 pandemic during which border closure and other interventions reduced pertussis cases to an all-time low, and paves the way for the genomic surveillance of B. pertussis in the era of culture-independent PCR-based diagnosis.

IMPORTANCE: In this paper, we evaluated the use of targeted multiplex PCR (mPCR) amplicon sequencing and shotgun metagenomic sequencing for culture-independent typing of Bordetella pertussis directly in respiratory swabs. We first developed a novel targeted mPCR amplicon sequencing assay that can type major circulating lineages and validated its accuracy and sensitivity on 178 DNA extracts from clinical swabs. We also demonstrate the feasibility of using deep metagenomic sequencing for determining strain lineage and markers of virulence, vaccine adaptation, macrolide resistance, and co-infections. Our culture-independent typing methods applied to clinical specimens revealed the expansion of a major global epidemic lineage in Australia (termed EL4) just prior to the COVID-19 pandemic. It also detected cases of previously hidden co-infections from another Bordetella species called Bordetella holmesii. These findings offer valuable insight into the circulating pertussis lineages in Australia prior to the COVID-19 pandemic during which border closure and other interventions reduced pertussis cases to an all-time low. It also provides comparative data for future surveillance as pertussis resurgence after the COVID-19 pandemic has been reported this year in Australia and many other countries. Overall, our paper demonstrates the utility, sensitivity, and specificity of mPCR amplicon and metagenomic sequencing-based culture-independent typing of B. pertussis, which not only paves the way for culture-independent genomic surveillance of B. pertussis but also for other pathogens in the era of PCR-based diagnosis.}, } @article {pmid39494554, year = {2024}, author = {Snaith, AE and Moran, RA and Hall, RJ and Casey, A and Ratcliffe, L and van Schaik, W and Whitehouse, T and McNally, A}, title = {Longitudinal genomic surveillance of a UK intensive care unit shows a lack of patient colonisation by multi-drug-resistant Gram-negative bacterial pathogens.}, journal = {Microbial genomics}, volume = {10}, number = {11}, pages = {}, pmid = {39494554}, issn = {2057-5858}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; *Intensive Care Units ; *Drug Resistance, Multiple, Bacterial/genetics ; United Kingdom/epidemiology ; *COVID-19/epidemiology ; *Escherichia coli/genetics/drug effects/isolation & purification ; Whole Genome Sequencing/methods ; SARS-CoV-2/genetics ; Cross Infection/epidemiology/microbiology ; Genome, Bacterial ; Anti-Bacterial Agents/pharmacology ; Gram-Negative Bacteria/genetics/drug effects/isolation & purification/classification ; Genomics ; }, abstract = {Vulnerable patients in an intensive care unit (ICU) setting are at high risk of infection from bacteria including gut-colonising Escherichia coli and Klebsiella species. Complex ICU procedures often depend on successful antimicrobial treatment, underscoring the importance of understanding the extent of patient colonisation by multi-drug-resistant organisms (MDROs) in large UK ICUs. Previous work on ICUs globally uncovered high rates of colonisation by transmission of MDROs, but the situation in UK ICUs is less understood. Here, we investigated the diversity and antibiotic resistance gene (ARG) carriage of bacteria present in one of the largest UK ICUs at the Queen Elizabeth Hospital Birmingham (QEHB), focusing primarily on E. coli as both a widespread commensal and a globally disseminated multi-drug-resistant pathogen. Samples were taken during highly restrictive coronavirus disease 2019 (COVID-19) control measures from May to December 2021. Whole-genome and metagenomic sequencing were used to detect and report strain-level colonisation of patients, focusing on E. coli sequence types (STs), their colonisation dynamics and antimicrobial resistance gene carriage. We found a lack of multi-drug resistance (MDR) in the QEHB. Only one carbapenemase-producing organism was isolated, a Citrobacter carrying bla KPC-2. There was no evidence supporting the spread of this strain, and there was little evidence overall of nosocomial acquisition or circulation of colonising E. coli. Whilst 22 different E. coli STs were identified, only 1 strain of the pandemic ST131 lineage was isolated. This ST131 strain was non-MDR and was found to be a clade A strain, associated with low levels of antibiotic resistance. Overall, the QEHB ICU had very low levels of pandemic or MDR strains, a result that may be influenced in part by the strict COVID-19 control measures in place at the time. Employing some of these infection prevention and control measures where reasonable in all ICUs might therefore assist in maintaining low levels of nosocomial MDR.}, } @article {pmid39494496, year = {2024}, author = {Su, Q and Li, YC and Zhuang, DH and Liu, XY and Gao, H and Li, D and Chen, Y and Ge, MX and Han, YM and Gao, ZL and Yin, FQ and Zhao, L and Zhang, YX and Yang, LQ and Zhao, Q and Luo, YJ and Zhang, Z and Kong, QP}, title = {Rewiring of Uric Acid Metabolism in the Intestine Promotes High-Altitude Hypoxia Adaptation in Humans.}, journal = {Molecular biology and evolution}, volume = {41}, number = {11}, pages = {}, pmid = {39494496}, issn = {1537-1719}, mesh = {Humans ; *Uric Acid/metabolism ; Male ; Adult ; *Acclimatization ; *Altitude ; *Gastrointestinal Microbiome ; Hypoxia/metabolism ; Altitude Sickness/metabolism ; Intestines/metabolism ; Feces ; Adaptation, Physiological ; Longitudinal Studies ; China ; }, abstract = {Adaptation to high-altitude hypoxia is characterized by systemic and organ-specific metabolic changes. This study investigates whether intestinal metabolic rewiring is a contributing factor to hypoxia adaptation. We conducted a longitudinal analysis over 108 days, with seven time points, examining fecal metabolomic data from a cohort of 46 healthy male adults traveling from Chongqing (a.s.l. 243 m) to Lhasa (a.s.l. 3,658 m) and back. Our findings reveal that short-term hypoxia exposure significantly alters intestinal metabolic pathways, particularly those involving purines, pyrimidines, and amino acids. A notable observation was the significantly reduced level of intestinal uric acid, the end product of purine metabolism, during acclimatization (also called acclimation) and additional two long-term exposed cohorts (Han Chinese and Tibetans) residing in Shigatse, Xizang (a.s.l. 4,700 m), suggesting that low intestinal uric acid levels facilitate adaptation to high-altitude hypoxia. Integrative analyses with gut metagenomic data showed consistent trends in intestinal uric acid levels and the abundance of key uric acid-degrading bacteria, predominantly from the Lachnospiraceae family. The sustained high abundance of these bacteria in the long-term resident cohorts underscores their essential role in maintaining low intestinal uric acid levels. Collectively, these findings suggest that the rewiring of intestinal uric acid metabolism, potentially orchestrated by gut bacteria, is crucial for enhancing human resilience and adaptability in extreme environments.}, } @article {pmid39494289, year = {2024}, author = {Rueangmongkolrat, N and Uthaipaisanwong, P and Kusonmano, K and Pruksangkul, S and Sonthiphand, P}, title = {The role of microbiomes in cooperative detoxification mechanisms of arsenate reduction and arsenic methylation in surface agricultural soil.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e18383}, pmid = {39494289}, issn = {2167-8359}, mesh = {*Soil Microbiology ; *Microbiota ; *Arsenates/metabolism ; *Arsenic/metabolism ; *Soil Pollutants/metabolism ; Methylation ; *Agriculture/methods ; Soil/chemistry ; Bacteria/metabolism/genetics/classification/isolation & purification ; Metagenomics ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Microbial arsenic (As) transformations play a vital role in both driving the global arsenic biogeochemical cycle and determining the mobility and toxicity of arsenic in soils. Due to the complexity of soils, variations in soil characteristics, and the presence and condition of overlying vegetation, soil microbiomes and their functional pathways vary from site to site. Consequently, key arsenic-transforming mechanisms in soil are not well characterized. This study utilized a combination of high-throughput amplicon sequencing and shotgun metagenomics to identify arsenic-transforming pathways in surface agricultural soils. The temporal and successional variations of the soil microbiome and arsenic-transforming bacteria in agricultural soils were examined during tropical monsoonal dry and wet seasons, with a six-month interval. Soil microbiomes of both dry and wet seasons were relatively consistent, particularly the relative abundance of Chloroflexi, Gemmatimonadota, and Bacteroidota. Common bacterial taxa present at high abundance, and potentially capable of arsenic transformations, were Bacillus, Streptomyces, and Microvirga. The resulting shotgun metagenome indicated that among the four key arsenic-functional genes, the arsC gene exhibited the highest relative abundance, followed by the arsM, aioA, and arrA genes, in declining sequence. Gene sequencing data based on 16S rRNA predicted only the arsC and aioA genes. Overall, this study proposed that a cooperative mechanism involving detoxification through arsenate reduction and arsenic methylation was a key arsenic transformation in surface agricultural soils with low arsenic concentration (7.60 to 10.28 mg/kg). This study significantly advances our knowledge of arsenic-transforming mechanisms interconnected with microbial communities in agricultural soil, enhancing pollution control measures, mitigating risks, and promoting sustainable soil management practices.}, } @article {pmid39494225, year = {2024}, author = {Jin, S and Xie, H and Wang, R}, title = {Otitis Media Progressing to Community-Acquired Meningitis in Diabetic Patients: A Case Report of K2-ST375 hypervirulent Klebsiella pneumoniae and Literature Review.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {4707-4716}, pmid = {39494225}, issn = {1178-6973}, abstract = {Community-acquired Klebsiella pneumoniae meningitis (CA-KPM) can rapidly progress to invasive infection in healthy individuals. We present the case of a 54-year-old man with a history of acute suppurative otitis media and uncontrolled type 2 diabetes mellitus (T2DM), who had been treated with oral antibiotics intermittently and irregularly for one month. His symptoms did not improve and continued to worsen, leading to fever and coma. Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) identified Klebsiella pneumoniae (KP) after 24 hours in the intensive care unit (ICU). Subsequent CSF culture confirmed a hypervirulent KP (hvKp) strain with capsular genotype K2 and sequence type (ST) 375. Fortunately, the patient made a full recovery with targeted antimicrobial therapy and was discharged. Despite the delayed diagnosis, the outcome was favorable. This case highlights the importance of clinicians, particularly otolaryngologists, maintaining a high index of suspicion for CA-KPM in patients with both otitis media and T2DM, emphasizing the need for timely multidisciplinary consultation.}, } @article {pmid39493671, year = {2024}, author = {Kleikamp, HBC and van der Zwaan, R and van Valderen, R and van Ede, JM and Pronk, M and Schaasberg, P and Allaart, MT and van Loosdrecht, MCM and Pabst, M}, title = {NovoLign: metaproteomics by sequence alignment.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae121}, pmid = {39493671}, issn = {2730-6151}, abstract = {Tremendous advances in mass spectrometric and bioinformatic approaches have expanded proteomics into the field of microbial ecology. The commonly used spectral annotation method for metaproteomics data relies on database searching, which requires sample-specific databases obtained from whole metagenome sequencing experiments. However, creating these databases is complex, time-consuming, and prone to errors, potentially biasing experimental outcomes and conclusions. This asks for alternative approaches that can provide rapid and orthogonal insights into metaproteomics data. Here, we present NovoLign, a de novo metaproteomics pipeline that performs sequence alignment of de novo sequences from complete metaproteomics experiments. The pipeline enables rapid taxonomic profiling of complex communities and evaluates the taxonomic coverage of metaproteomics outcomes obtained from database searches. Furthermore, the NovoLign pipeline supports the creation of reference sequence databases for database searching to ensure comprehensive coverage. We assessed the NovoLign pipeline for taxonomic coverage and false positive annotations using a wide range of in silico and experimental data, including pure reference strains, laboratory enrichment cultures, synthetic communities, and environmental microbial communities. In summary, we present NovoLign, a de novo metaproteomics pipeline that employs large-scale sequence alignment to enable rapid taxonomic profiling, evaluation of database searching outcomes, and the creation of reference sequence databases. The NovoLign pipeline is publicly available via: https://github.com/hbckleikamp/NovoLign.}, } @article {pmid39492525, year = {2023}, author = {Chen, Y and Yue, Y and Wang, J and Li, H and Wang, Z and Zheng, Z}, title = {Microbial community dynamics and assembly mechanisms across different stages of cyanobacterial bloom in a large freshwater lake.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {168207}, doi = {10.1016/j.scitotenv.2023.168207}, pmid = {39492525}, issn = {1879-1026}, abstract = {Cyanobacterial bloom caused by eutrophication in lakes has become one of the significant environmental problems worldwide. However, a notable research gap persists in understanding the environmental adaptation and community assembly of microbial dynamics in response to different blooming stages. Therefore, metagenomic sequencing was employed in this study to investigate alterations in the microbial community composition in water and sediment during different stages of cyanobacterial blooms in Lake Taihu. The results indicated significant spatiotemporal variations in physicochemical parameters across the early, medium, and late stages of a complete cyanobacteria bloom cycle. Diversity analysis further revealed that the temporal differences in the microbial community were substantially greater than spatial variations. Notably, during the medium-blooming stages in water, Microcystis emerged as the predominant detected cyanobacteria genus. Interestingly, the content of superoxide dismutase (SOD), malondialdehyde (MDA), and catalase (CAT) in sediment exceeded those in water by over 10 times, indicating that sediment-dwelling Cyanobacteria might constitute a crucial source of water blooms. Moreover, dissolved oxygen, pH, and water temperature were identified as the most influential environmental variables shaping the microbial community in the water. Stochasticity emerged as a prominent factor governing microbial community assembly across different bloom periods. Meanwhile, co-occurrence patterns suggested fewer interactions and instability between species in medium-blooming stages. Notably, the potential keystone phyla occupied crucial ecological niches. This research carries significant theoretical implications for managing cyanobacterial blooms in freshwater ecosystems.}, } @article {pmid39492355, year = {2023}, author = {Wu, X and Yu, Z and Yuan, S and Tawfik, A and Meng, F}, title = {An ecological explanation for carbon source-associated denitrification performance in wastewater treatment plants.}, journal = {Water research}, volume = {247}, number = {}, pages = {120762}, doi = {10.1016/j.watres.2023.120762}, pmid = {39492355}, issn = {1879-2448}, abstract = {The underlying mechanism associated with the roles of dosed carbon source in denitrification performance remains largely unknown. In this study, three denitrifying consortia (DNC) were constructed via evolutionary top-down enrichment method with well-defined conditions and specific carbon sources (acetate, glucose and their mixture). The reactor operation shows that nearly complete nitrate removal was achieved; however, the glucose feeding resulted in much higher concentrations of biomass and non-settable flocs. The 16S rRNA sequencing suggests that the bacterial diversity of the acetate-fed DNC was significantly higher than those of acetate/glucose-fed and glucose-fed DNCs. The dentrifying population in the acetate-fed DNC was dominated by Propionivibrio (16.1 %) and Thauera (3.4 %); whereas those of acetate/glucose- and glucose-fed DNCs were dominated by Pleomorphomonas (21.5 % and 26.3 %, respectively). Interestingly, the supernatant of acetate-fed DNC contained a high abundance of genera Thauera (averaged at 85.1 %), indicating the free-living nature of Thauera. Both PICURSt2 analysis of 16S rRNA sequencing and metagenomic analysis indicate that the acetate-fed DNC contained higher abundances of denitrifying genes; the acetate/glucose-fed and glucose-fed DNCs, in comparison, enriched genes related to glucose transportation and metabolism. Additionally, the acetate-fed DNC had better network stability than other two groups. This study adds important knowledge regarding the ecological traits of DNC, providing important clues for rational addition of carbon sources in wastewater treatment plants.}, } @article {pmid39492104, year = {2023}, author = {Qiu, M and Wu, Z and Song, J and Zheng, C and Zhan, X and Shan, M and Cui, M and Chen, L and Zhang, L and Yu, Y and Fang, H}, title = {Chlorothalonil drives the antibiotic resistome in earthworm guts.}, journal = {Journal of hazardous materials}, volume = {463}, number = {}, pages = {132831}, doi = {10.1016/j.jhazmat.2023.132831}, pmid = {39492104}, issn = {1873-3336}, abstract = {Earthworms are recognized as carriers of pollutants; however, how fungicide residues affect microbiota and antibiotic resistance genes (ARGs) in earthworm guts has remained unclear. In this work, changes in the earthworm gut microbiome and resistome were investigated after chlorothalonil (CTL) application. Earthworm activity accelerated the dissipation of CTL in soil, while metagenomic analysis revealed that CTL altered the ARG profile, leading to an increased abundance of ARGs in earthworm guts, particularly with respect to ARG subtypes CRP and OXA-427. CTL also reduced bacterial diversity and elevated the relative abundance of the phylum Proteobacteria, including a potential ARG host, Aeromonas, which is a known pathogen. Various bacterial genera from the Actinobacteria and Proteobacteria phyla were identified as broad-spectrum hosts for ARGs in earthworm guts. CTL could increase the abundance of multidrug efflux pump genes and enhance the abundance of mobile genetic elements, especially plasmids. Various co-occurrence patterns between plasmids and ARGs were also found after CTL treatments. It is concluded that CTL may act as a selective stress for ARGs and lead to an increase in their abundance by facilitating the proliferation of potential ARG hosts and enhancing plasmid-mediated horizontal transfer frequency of ARGs in earthworm guts.}, } @article {pmid39491376, year = {2023}, author = {Chowdhury, RR and Dhar, J and Robinson, SM and Lahiri, A and Basak, K and Paul, S and Banerjee, R}, title = {MACI: A machine learning-based approach to identify drug classes of antibiotic resistance genes from metagenomic data.}, journal = {Computers in biology and medicine}, volume = {167}, number = {}, pages = {107629}, doi = {10.1016/j.compbiomed.2023.107629}, pmid = {39491376}, issn = {1879-0534}, abstract = {Novel methodologies are now essential for identification of antibiotic resistant pathogens in order to resist them. Here, we are presenting a model, MACI (Machine learning-based Antibiotic resistance gene-specific drug Class Identification) that can take metagenomic fragments as input and predict the drug class of antibiotic resistant genes. In our study, we trained a model using the Comprehensive Antibiotic Resistance Database, containing 5138 representative sequences across 134 drug classes. Among these classes, 23 dominated, contributing 85% of the sequence data. The model achieved an average precision of 0.8389 ± 0.0747 and recall of 0.8197 ± 0.0782 for these 23 drug classes. Additionally, it exhibited higher performance (precision and recall: 0.8817 ± 0.0540 and 0.8620 ± 0.0493) for predicting multidrug resistant classes compared to single drug resistant categories (0.7923 ± 0.0669 and 0.7737 ± 0.0794). The model also showed promising results when tested on an independent data. We then analysed these 23 drug classes to identify class-specific overlapping nucleotide patterns. Five significant drug classes, viz. "Carbapenem; cephalosporin; penam", "cephalosporin", "cephamycin", "cephalosporin; monobactam; penam; penem", and "fluoroquinolone" were identified, and their patterns aligned with the functional domains of antibiotic resistance genes. These class-specific patterns play a pivotal role in rapidly identifying drug classes with antibiotic resistance genes. Further analysis revealed that bacterial species containing these five drug classes are associated with well-known multidrug resistance properties.}, } @article {pmid39491194, year = {2023}, author = {Larsen, S and Coleine, C and Albanese, D and Stegen, JC and Selbmann, L and Donati, C}, title = {Geology and elevation shape bacterial assembly in Antarctic endolithic communities.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {168050}, doi = {10.1016/j.scitotenv.2023.168050}, pmid = {39491194}, issn = {1879-1026}, abstract = {Ice free areas of continental Antarctica are among the coldest and driest environments on Earth, and yet, they support surprisingly diverse and highly adapted microbial communities. Endolithic growth is one of the key adaptations to such extreme environments and often represents the dominant life-form. Despite growing scientific interest, little is known of the mechanisms that influence the assembly of endolithic microbiomes across these harsh environments. Here, we used metagenomics to examine the diversity and assembly of endolithic bacterial communities across Antarctica within different rock types and over a large elevation range. While granite supported richer and more heterogeneous communities than sandstone, elevation had no apparent effect on taxonomic richness, regardless of rock type. Conversely, elevation was clearly associated with turnover in community composition, with the deterministic process of variable selection driving microbial assembly along the elevation gradient. The turnover associated with elevation was modulated by geology, whereby for a given elevation difference, turnover was consistently larger between communities inhabiting different rock types. Overall, selection imposed by elevation and geology appeared stronger than turnover related to other spatially-structured environmental drivers. Our findings indicate that at the cold-arid limit of life on Earth, geology and elevation are key determinants of endolithic bacterial heterogeneity. This also suggests that warming temperatures may threaten the persistence of such extreme-adapted organisms.}, } @article {pmid39490992, year = {2024}, author = {Cansdale, A and Chong, JPJ}, title = {MAGqual: a stand-alone pipeline to assess the quality of metagenome-assembled genomes.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {226}, pmid = {39490992}, issn = {2049-2618}, mesh = {*Metagenomics/methods ; *Metagenome ; Software ; Microbiota/genetics ; High-Throughput Nucleotide Sequencing/methods ; Bacteria/genetics/classification ; Humans ; }, abstract = {BACKGROUND: Metagenomics, the whole genome sequencing of microbial communities, has provided insight into complex ecosystems. It has facilitated the discovery of novel microorganisms, explained community interactions and found applications in various fields. Advances in high-throughput and third-generation sequencing technologies have further fuelled its popularity. Nevertheless, managing the vast data produced and addressing variable dataset quality remain ongoing challenges. Another challenge arises from the number of assembly and binning strategies used across studies. Comparing datasets and analysis tools is complex as it requires the quantitative assessment of metagenome quality. The inherent limitations of metagenomic sequencing, which often involves sequencing complex communities, mean community members are challenging to interrogate with traditional culturing methods leading to many lacking reference sequences. MIMAG standards aim to provide a method to assess metagenome quality for comparison but have not been widely adopted.

RESULTS: To address the need for simple and quick metagenome quality assignation, here we introduce the pipeline MAGqual (Metagenome-Assembled Genome qualifier) and demonstrate its effectiveness at determining metagenomic dataset quality in the context of the MIMAG standards.

CONCLUSIONS: The MAGqual pipeline offers an accessible way to evaluate metagenome quality and generate metadata on a large scale. MAGqual is built in Snakemake to ensure readability and scalability, and its open-source nature promotes accessibility, community development, and ease of updates. MAGqual is built in Snakemake, R, and Python and is available under the MIT license on GitHub at https://github.com/ac1513/MAGqual . Video Abstract.}, } @article {pmid39490844, year = {2024}, author = {Zhang, L and Xu, W and Jiang, J and Li, R and Gu, J and Liang, W}, title = {Metagenomic insights on promoting the removal of resistome in aerobic composting pig manure by lightly burned modified magnesite.}, journal = {The Science of the total environment}, volume = {957}, number = {}, pages = {177101}, doi = {10.1016/j.scitotenv.2024.177101}, pmid = {39490844}, issn = {1879-1026}, mesh = {*Manure/microbiology ; *Composting ; Animals ; Swine ; Drug Resistance, Microbial/genetics ; Metagenomics ; Metagenome ; Soil Microbiology ; Genes, Bacterial ; }, abstract = {The antibiotic resistance genes (ARGs) have become a serious issue facing public health. In this study, light-burned magnesite with a high specific surface area at 650 °C (MS650) was used for aerobic composting, evaluating its effect on the resistome during pig manure composting. Different concentrations of MS650 reduced the abundance of the resistome, including seven high-risk ARGs, class two metal and biocide resistance genes (MBRGs), and human pathogenic bacteria (HPBs). The addition of 2.5 % MS650 (L1) in the composting had the best reduction effect on ARGs, MBRGs and HPBs. ARG and microbial community assembly are deterministic processes. Proteobacteria and Actinobacteria was the main factor associated with the decrease in ARGs, followed by virulence factor genes (VFGs, 44.2 %). The reduction in MBRGs by MS650 mainly suppressed HGT by reducing the Isfinder abundance. To summarize, MS650 is an effective method to improve emission reduction of ARGs and MBRGs. This study provided a theoretical basis for improving the engineering application potential of MS650.}, } @article {pmid39490825, year = {2024}, author = {Liang, W and Yan, D and Zhang, M and Wang, J and Ni, D and Yun, S and Wei, X and Zhang, L and Fu, H}, title = {Unraveling methanogenesis processes and pathways for Quaternary shallow biogenic gas in aquifer systems through geochemical, genomic and transcriptomic analyses.}, journal = {The Science of the total environment}, volume = {955}, number = {}, pages = {177189}, doi = {10.1016/j.scitotenv.2024.177189}, pmid = {39490825}, issn = {1879-1026}, mesh = {*Methane/metabolism ; *Groundwater/chemistry/microbiology ; China ; Transcriptome ; Microbiota ; Gene Expression Profiling ; Genomics ; Environmental Monitoring ; }, abstract = {Shallow biogenic gas is crucial in global warming and carbon cycling. Considering the knowledge gap in the understanding of methanogenesis and metabolic mechanisms within shallow groundwater systems, we investigated Quaternary shallow biogenic gas resources from the Hetao Basin in North China, which were previously underexplored. We systematically analyzed the genesis of gas and formation water, microbial communities, methanogenic processes, and pathways using geochemistry, genomics, and transcriptomics. Our findings indicated that active freshwater environments are conducive to microbial activity and the generation of primary microbial gases. A diverse range of microbes with functions, such as hydrolysis (e.g., Caulobacter), acidogenesis, and hydrogen production (e.g., Sediminibacterium), synergistically contributed to the methanogenic process. Methanogens predominantly comprised hydrogenotrophic methanogens (e.g., Methanobacteriales), although H2-dependent methylotrophic methanogens (e.g., Methanofastidiosa) were also prevalent. The metabolic processes of the different methanogenic pathways were revealed based on functional gene analysis and mapping results. Furthermore, the composition of the community structure, functional predictions, metagenomics, and metatranscriptomics underscored the contribution of the hydrogenotrophic pathway, which ranged from 52.22 % to 79.23 %. The aceticlastic pathway exhibited high gene abundance and was primarily associated with methylotrophs and other potential pathways. The H2-dependent methylotrophic methanogenesis pathway was constrained by low metabolic activity. By revealing the methane production mechanism of biogenic gas in shallow aquifer systems, this study provides a new perspective and profound comprehension of its ecological and environmental implications worldwide.}, } @article {pmid39490771, year = {2024}, author = {Li, T and Coker, OO and Sun, Y and Li, S and Liu, C and Lin, Y and Wong, SH and Miao, Y and Sung, JJY and Yu, J}, title = {Multi-Cohort Analysis Reveals Altered Archaea in Colorectal Cancer Fecal Samples Across Populations.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2024.10.023}, pmid = {39490771}, issn = {1528-0012}, abstract = {BACKGROUND & AIMS: Archaea are important components of the host microbiome, but their roles in colorectal cancer (CRC) remain largely unclear. We aimed to elucidate the contribution of gut archaea to CRC across multiple populations.

METHODS: This study incorporated fecal metagenomic data from 10 independent cohorts across 7 countries and an additional in-house cohort, totaling 2101 metagenomes (748 CRC, 471 adenoma, and 882 healthy controls [HCs]). Taxonomic profiling was performed using Kraken2 against the Genome Taxonomy Database. Alterations of archaeal communities and their interactions with bacteria, as well as methanogenic functions were analyzed. A Random Forest model was used to identify multicohort diagnostic microbial biomarkers in CRC.

RESULTS: The overall archaeal alpha diversity shifted from HCs, patients with adenoma, to patients with CRC with the Methanobacteriota phylum enriched while the order Methanomassiliicoccales depleted. At the species level, Methanobrevibacter_A smithii and Methanobrevibacter_A sp002496065 were enriched, whereas 8 species, including Methanosphaera stadtmanae and Methanomassiliicoccus_A intestinalis, were depleted in patients with CRC across multiple cohorts. Among them, M stadtmanae, Methanobrevibacter_A sp900314695, and Methanocorpusculum sp001940805 exhibited a progressive decrease in the HC-adenoma-CRC sequence. CRC-depleted methanogenic archaea exhibited enhanced co-occurring interactions with butyrate-producing bacteria. Consistently, methanogenesis-related genes and pathways were enriched in patients with CRC. A model incorporating archaeal and bacterial biomarkers outperformed single-kingdom models in discriminating patients with CRC from healthy individuals with the area under the curve ranging from 0.744 to 0.931 in leave-one-cohort-out analysis.

CONCLUSIONS: This multicohort analysis uncovered significant alterations in gut archaea and their interactions with bacteria in healthy individuals, patients with adenoma, and patients with CRC. Archaeal biomarkers, combined with bacterial features, have potential as noninvasive diagnostic biomarkers for CRC.}, } @article {pmid39490764, year = {2024}, author = {Witkabel, P and Abendroth, C}, title = {A systematic literature review of microbial anammox consortia in UASB/ EGSB-reactors.}, journal = {Chemosphere}, volume = {367}, number = {}, pages = {143630}, doi = {10.1016/j.chemosphere.2024.143630}, pmid = {39490764}, issn = {1879-1298}, mesh = {*Bioreactors/microbiology ; *Bacteria/metabolism/genetics/classification ; *Oxidation-Reduction ; *Waste Disposal, Fluid/methods ; *Wastewater/microbiology ; *Archaea/metabolism/genetics ; Ammonium Compounds/metabolism ; Microbial Consortia ; Anaerobiosis ; Ammonia/metabolism ; }, abstract = {Anaerobic ammonium oxidation (anammox) poses an emerging research field as it can outstand previous processes of biological wastewater treatment in terms of efficiency and costs. Anammox bacteria have the ability to metabolise NH4[+] and NO2[-] to produce N2 under anaerobic conditions. Despite numerous studies, there is a lack of research on the co-occurrence and interrelationship of the predominant microbes that inhabit anammox-related processes. This systematic literature review follows the PSALSAR approach to assess metagenomic data on anammox bacteria and functional microbes in upstream reactors. Essential information on the physiology, metabolic pathways and inhibitory effects of anammox bacteria are reviewed and functional bacteria such as ammonia-oxidising bacteria (AOB), nitrite-oxidising bacteria (NOB), ammonia-oxidising Archaea (AOA) and denitrifying bacteria are identified. Candidatus Kuenenia and Candidatus Brocadia were the most frequently sequenced genera in the observed literature. Pseudomonadota, Chloroflexota and Bacteroidota were prevalent regardless of crucial operational parameters and configurations that affect the microbial community. Interrelationship analysis revealed a positive association between the versatility of a phylum's metabolism and its presence in the observed wastewater treatment literature. Several groups, such as Calditrichota, Myxococcota and Deinococcota are highly underrepresented, a finding that should be investigated in more detail. No evidence was found to suggest that high anammox ratios are correlated with high nitrogen removal efficiencies, as some studies found high efficiency despite low anammox abundance (<1%).}, } @article {pmid39490442, year = {2024}, author = {Gregoris, K and Pope, WH}, title = {Extraction of high-quality metagenomic DNA from the lichens Flavoparmelia caperata and Peltigera membranacea.}, journal = {Journal of microbiological methods}, volume = {227}, number = {}, pages = {107065}, doi = {10.1016/j.mimet.2024.107065}, pmid = {39490442}, issn = {1872-8359}, mesh = {*Lichens ; *Metagenomics/methods ; DNA, Fungal/genetics/isolation & purification ; Polymerase Chain Reaction/methods ; Microbiota/genetics ; Metagenome ; Ascomycota/genetics/classification/isolation & purification/chemistry ; }, abstract = {Lichens are composite organisms found throughout temperate terrestrial forests, with species-specific associations with industrial air pollution. Metagenomic analysis of lichen samples requires robust nucleic acid extraction methodology, a process that is challenging due to the protective cortex layers, high polysaccharide content, and the vast diversity of the internal microbiome. Our method includes physical lysis through garnet bead beating, chemical lysis using a sodium dodecyl sulfate buffer, phenol:chloroform:isoamyl alcohol extraction, and ethanol precipitation. The method was tested on three different lichen samples from two distinct species and yielded metagenomic DNA suitable for sequencing and PCR amplification. This procedure addresses the issues associated with DNA extraction from lichen using common laboratory equipment and reagents without the utilization of liquid nitrogen. This paper presents a cost-effective and accessible DNA extraction method for obtaining high-quality genetic material from dried and preserved lichen specimens.}, } @article {pmid39490096, year = {2025}, author = {Ji, J and Zhao, Y and Wu, G and Hu, F and Yang, H and Bai, Z and Jin, B and Yang, X}, title = {Responses of endogenous partial denitrification process to acetate and propionate as carbon sources: Nitrite accumulation performance, microbial community dynamic changes, and metagenomic insights.}, journal = {Water research}, volume = {268}, number = {Pt A}, pages = {122680}, doi = {10.1016/j.watres.2024.122680}, pmid = {39490096}, issn = {1879-2448}, mesh = {*Denitrification ; *Nitrites/metabolism ; *Propionates/metabolism ; *Carbon/metabolism ; *Acetates/metabolism ; Bioreactors ; Microbiota ; Nitrates/metabolism ; }, abstract = {Endogenous partial denitrification (EPD) offered a promising pathway for supplying nitrite to anammox, and it also enabled energy-efficient and cost-effective nitrogen removal. However, information about the impact of different carbon sources on the EPD system was limited, and the metabolic mechanisms remained unclear. This study operated the EPD system for 180 days with various acetate and propionate ratios over eight phases. The nitrate-to-nitrite transformation ratio (NTR) decreased from 81.7 % to 0.4 % as the acetate/propionate (Ac/Pr) ratio shifted from 3:0 to 0:3, but the NTR returned to 86.1 % after propionate was replaced with acetate. Typical cycles indicated that PHB (126.8 and 133.9 mg COD/g VSS, respectively) was mainly stored, facilitating a higher NTR (87.8 % and 67.7 %, respectively) on days 58 and 180 in the presence of acetate. In contrast, on day 158 in the presence of propionate, PHV (84.8 mg COD/g VSS) was predominantly stored, resulting in negligible nitrite accumulation (0.2 mg N/L). Metagenomic analysis revealed that the microbial community structure did not significantly change, and the (narGHI+napAB)/nirKS ratio consistently exceeded 7:2, despite variations in the carbon source. Compared with acetate, propionate as carbon source reduced the abundance of genes encoding NADH-producing enzymes (e.g., mdh), likely owing to a shift in PHAs synthesis and degradation pathways. Consequently, limited NADH affected electron distribution and transfer rates, thereby decreasing the nitrate reduction rate and causing nitrite produced by narGHI and napAB to be immediately reduced by nirKS. This study provided new insights and guidance for EPD systems to manage the conditions of carbon deficiency or complex carbon sources.}, } @article {pmid39489934, year = {2024}, author = {Guo, XP and Chen, XJ and Sidikjan, N and Sha, RR}, title = {Silver nanoparticles regulate antibiotic resistance genes by shifting bacterial community and generating anti-silver genes in estuarine biofilms.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {276}, number = {}, pages = {107131}, doi = {10.1016/j.aquatox.2024.107131}, pmid = {39489934}, issn = {1879-1514}, mesh = {*Biofilms/drug effects ; *Silver/toxicity ; *Metal Nanoparticles/toxicity ; *Estuaries ; *Drug Resistance, Microbial/genetics ; *Bacteria/drug effects/genetics ; Water Pollutants, Chemical/toxicity ; Genes, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology/toxicity ; }, abstract = {Biofilms are thought to be sinks for antibiotic resistance genes (ARGs) and nanoparticles (NPs), however, studies on the interactions between NPs and ARGs in biofilms are limited. This study focused on the occurrence and regulatory mechanisms of ARGs during the formation of biofilms with continuous treatment of zero-valent silver nanoparticles (Ag[0]-NPs) and Ag ions at an environmental concentration of 10 µg/L in the Yangtze Estuary. The biofilms could enrich large amounts of Ag, with the highest concentration of 97.60 mg/kg and 111.08 mg/kg in the Ag[0]-NPs and Ag ions group at 28 days. Compared to the blank at 28 days, the abundance of ARGs was reduced 2.2 times in the Ag[0]-NPs group, whereas it increased 1.3 times in the Ag ion group. Ag[0]-NPs and Ag ions induced the production of silver resistance genes (SRGs) or selected bacteria with SRGs in biofilms. Based on machine learning, the bacterial community, SRGs, and Ag concentration were the top three dominant regulators of ARGs, with 27.74 %, 25.57 %, and 17.93 % contributions, respectively. Structural equation modeling revealed that Ag could indirectly regulate ARGs by regulating the bacterial community in the Ag[0]-NPs group. Metagenomic sequencing further showed that most of the decreased ARGs were hosted by Betaproteobacteria in the Ag[0]-NPs groups. According to the KEGG pathway database, the possible molecular mechanism of Ag[0]-NPs/Ag ions regulating ARGs may be through the two-component system (arlS/silS-arlR) and beta-lactam resistance system (mexI-mexV-oprM/oprZ/smeF). Overall, this study provides new insights into the effects of Ag[0]-NPs at environmental concentrations on the ecological environment, especially regarding the mechanism of regulating ARGs in estuarine biofilms.}, } @article {pmid39487157, year = {2024}, author = {Wardi, M and Lemkhente, Z and Alla, AA and Slimani, N and Abali, M and Idaghdour, Y and Belmouden, A}, title = {Resistome analysis of wastewater treatment plants in Agadir city, Morocco, using a metagenomics approach.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {26328}, pmid = {39487157}, issn = {2045-2322}, mesh = {*Wastewater/microbiology ; Morocco ; *Metagenomics/methods ; Anti-Bacterial Agents/pharmacology ; Water Purification/methods ; Bacteria/genetics/drug effects ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; }, abstract = {Water scarcity has evolved into a pressing global issue, significantly impacting numerous regions worldwide. The use of treated wastewater stands out as a promising solution to this problem. However, the proliferation of various contaminants, primarily Antimicrobial Resistance Genes (ARGs), poses a significant challenge to its safe and sustainable use. In this study, we assessed the composition and abundance of 373 ARGs, corresponding to 31 different classes of antibiotics, in six wastewater treatment plants (WWTP) in Agadir city of Morocco. Influent and effluent samples were collected during the months of February and July in 2020, in addition to samples from the Atlantic Ocean. In total, 223 ARGs were uncovered, highlighting in particular resistance to aminoglycoside, macrolide lincosamide, beta-lactamase, chloramphenicol, sulfonamide, tetracycline, and other antibiotics. The mechanisms of action of these ARGs were mainly antibiotic inactivation, antibiotic target alteration, efflux pump and cellular protection. Mobile genetic elements (MGEs) were detected at high levels their co-occurrence with ARGs highlights their involvement in the acquisition and transmission of ARGs in microbial communities through horizontal gene transfer. While many wastewater treatment methods effectively reduce a large proportion of gene material and pathogens, a substantial fraction of ARGs and other contaminants persist in treated wastewater. This persistence poses potential risks to both human health and the environment, warranting the need of more effective treatment strategies.}, } @article {pmid39487149, year = {2024}, author = {Sato, T and Abe, K and Koseki, J and Seto, M and Yokoyama, J and Akashi, T and Terada, M and Kadowaki, K and Yoshida, S and Yamashiki, YA and Shimamura, T}, title = {Survivability and life support in sealed mini-ecosystems with simulated planetary soils.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {26322}, pmid = {39487149}, issn = {2045-2322}, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Ecosystem ; Ecological Systems, Closed ; Microbiota ; Life Support Systems ; Space Flight ; Extraterrestrial Environment ; Groundwater/microbiology ; Plants/microbiology/metabolism ; Cyanobacteria/growth & development/metabolism/physiology ; Animals ; }, abstract = {Establishing a sustainable life-support system for space exploration is a formidable challenge due to the vast distances, high costs, and environmental differences from Earth. Building upon the lessons from the Biosphere 2 experiment, we introduce the novel "Ecosphere" and "Biosealed" systems, self-sustaining ecosystems within customizable, enclosed containers. These systems incorporate terrestrial ecosystems and groundwater layers, offering a potential model for transplanting Earth-like biomes to extraterrestrial environments. Over 4 years, we conducted rigorous experiments and analyses to understand the dynamics of these enclosed ecosystems. We successfully mitigated moisture deficiency, a major obstacle to plant growth, by incorporating groundwater layers. Additionally, we quantified microbial communities proliferating in specific soils, including simulated lunar and Ryugu asteroid regolith, enhance plant cultivation in space environments. Metagenomic analysis of these simulated space soils revealed diverse microbial populations and their crucial role in plant growth and ecosystem stability. Notably, we identified symbiotic relationships between plants and Cyanobacteria, enhancing oxygen production, and demonstrated the potential of LED lighting as an alternative light source for plant cultivation in sun-limited space missions. We also confirmed the survival of fruit flies within these systems, relying on plant-produced oxygen and photosynthetic bacteria. Our research provides a comprehensive framework for developing future space life-support systems. The novelty of our work lies in the unique design of our enclosed ecosystems, incorporating groundwater layers and simulated extraterrestrial soils, and the detailed analysis of microbial communities within these systems. These findings offer valuable insights into the challenges and potential solutions for establishing sustainable human habitats in space, including the importance of microbial management and potential health concerns related to microbial exposure.}, } @article {pmid39485071, year = {2024}, author = {Hasegawa-Takano, M and Hosaka, T and Kojima, K and Nishimura, Y and Kurihara, M and Nakajima, Y and Ishizuka-Katsura, Y and Kimura-Someya, T and Shirouzu, M and Sudo, Y and Yoshizawa, S}, title = {Cyanorhodopsin-II represents a yellow-absorbing proton-pumping rhodopsin clade within cyanobacteria.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39485071}, issn = {1751-7370}, support = {JPMJAX21BK//JST, PRESTO/ ; JPMXD1521474594//MEXT Advancement of Technologies for Utilizing Big Data of Marine Life/ ; JP23ama121013//AMED/ ; 22H00557//MEXT/JSPS KAKENHI/ ; }, mesh = {*Cyanobacteria/genetics/metabolism/classification ; *Phylogeny ; *Rhodopsins, Microbial/genetics/metabolism/chemistry ; Proton Pumps/metabolism/genetics ; Bacterial Proteins/genetics/metabolism/chemistry ; Light ; Metagenomics ; }, abstract = {Microbial rhodopsins are prevalent in many cyanobacterial groups as a light-energy-harvesting system in addition to the photosynthetic system. It has been suggested that this dual system allows efficient capture of sunlight energy using complementary ranges of absorption wavelengths. However, the diversity of cyanobacterial rhodopsins, particularly in accumulated metagenomic data, remains underexplored. Here, we used a metagenomic mining approach, which led to the identification of a novel rhodopsin clade unique to cyanobacteria, cyanorhodopsin-II (CyR-II). CyR-IIs function as light-driven outward H+ pumps. CyR-IIs, together with previously identified cyanorhodopsins (CyRs) and cyanobacterial halorhodopsins (CyHRs), constitute cyanobacterial ion-pumping rhodopsins (CyipRs), a phylogenetically distinct family of rhodopsins. The CyR-II clade is further divided into two subclades, YCyR-II and GCyR-II, based on their specific absorption wavelength. YCyR-II absorbed yellow light (λmax = 570 nm), whereas GCyR-II absorbed green light (λmax = 550 nm). X-ray crystallography and mutational analysis revealed that the difference in absorption wavelengths is attributable to slight changes in the side chain structure near the retinal chromophore. The evolutionary trajectory of cyanobacterial rhodopsins suggests that the function and light-absorbing range of these rhodopsins have been adapted to a wide range of habitats with variable light and environmental conditions. Collectively, these findings shed light on the importance of rhodopsins in the evolution and environmental adaptation of cyanobacteria.}, } @article {pmid39484685, year = {2024}, author = {Fernandez-Garcia, MD and Garcia-Ibañez, N and Camacho, J and Gutierrez, A and Sánchez García, L and Calvo, C and Moreno-Docón, A and Menasalvas, AI and Medina, A and Perez-Ruiz, M and Nieto Toboso, MC and Muñoz-Almagro, C and Launes, C and Berengua, C and Cabrerizo, M and , and , }, title = {Enhanced echovirus 11 genomic surveillance in neonatal infections in Spain following a European alert reveals new recombinant forms linked to severe cases, 2019 to 2023.}, journal = {Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin}, volume = {29}, number = {44}, pages = {}, pmid = {39484685}, issn = {1560-7917}, mesh = {Humans ; Infant, Newborn ; Spain/epidemiology ; *Enterovirus B, Human/genetics/isolation & purification ; Male ; Female ; Infant ; *Genotype ; *Echovirus Infections/epidemiology/virology/diagnosis ; Child ; Child, Preschool ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Adult ; Genome, Viral/genetics ; Genomics ; }, abstract = {BackgroundIn 2023, a European alert was issued regarding an increase in severe enterovirus (EV) neonatal infections associated with echovirus 11 (E11) new lineage 1.AimTo analyse E11-positive cases between 2019 and 2023 to investigate whether the new lineage 1 circulated in Spain causing severe neonatal infections.MethodsEV-positive samples from hospitalised cases are sent for typing to the National Reference Enterovirus Laboratory. Available samples from 2022-23 were subjected to metagenomic next-generation sequencing.ResultsOf 1,288 samples genotyped, 103 were E11-positive (98 patients: 6 adults, 33 neonates, 89 children under 6 years; male to female ratio 1.9). E11 detection rate was similar before and after detection of the new lineage 1 in Spain in June 2022 (9.7% in 2019 vs 10.6% in 2023). The proportion of E11-infected ICU-admitted neonates in 2019-2022 (2/7) vs 2022-2023 (5/12) did not significantly differ (p = 0.65). In severe neonatal infections, 4/7 E11 strains were not linked to the new lineage 1. The three novel E11 recombinant genomes were associated with severe (n = 2) and non-severe (n = 1) cases from 2022-2023 and clustered outside the new lineage 1. Coinfecting pathogenic viruses were present in four of 10 E11-positive samples.ConclusionThe emergence of the new lineage 1 is not linked with an increase in incidence or severity of neonatal E11 infections in Spain. The detection of two novel E11 recombinants associated with severe disease warrants enhancing genomic and clinical surveillance.}, } @article {pmid39484515, year = {2024}, author = {Ottinger, S and Larson, AB and Mercado-Evans, V and Branthoover, H and Zulk, JJ and Serchejian, C and Mejia, ME and Hameed, ZA and Walde, R and Fleck, RC and Shea, AE and Patras, KA}, title = {Distinct maternofetal immune signatures delineate preterm birth onset following urinary tract infection.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39484515}, issn = {2692-8205}, support = {P30 CA125123/CA/NCI NIH HHS/United States ; S10 RR024574/RR/NCRR NIH HHS/United States ; F31 DK136201/DK/NIDDK NIH HHS/United States ; R01 DK128053/DK/NIDDK NIH HHS/United States ; F31 AI167547/AI/NIAID NIH HHS/United States ; F31 HD111236/HD/NICHD NIH HHS/United States ; F31 AI167538/AI/NIAID NIH HHS/United States ; }, abstract = {Preterm birth is the leading cause of infant mortality resulting in over one million neonatal deaths annually. Maternal urinary tract infection (UTI) during pregnancy increases risk for preterm birth; however, biological processes mediating UTI-associated preterm birth are not well-described. We established a murine maternal UTI model in which challenge with uropathogenic E. coli resulted in preterm birth in about half of dams. Dams experiencing preterm birth displayed excessive bladder inflammation and altered uteroplacental T cell polarization compared to non-laboring infected dams, with no differences in bacterial burdens. Additional factors associated with preterm birth included higher proportions of male fetuses and lower maternal serum IL-10. Furthermore, exogenous maternal IL-10 treatment absolved UTI-associated preterm birth but contributed to fetal growth restriction in this model. Using urine samples from a cohort of human pregnancies with or without UTI, we correlated urinary cytokines with birth outcomes and urine culture status. These analyses yielded a non-invasive, highly predictive three-model system for evaluating preterm birth risk implicating cytokines IL-10, IL-15, IL-1β, and IL-1RA. Our unique bimodal murine model coupled with patient samples provides a platform to investigate immunological and microbial factors governing UTI-associated preterm birth, revealing novel therapeutic opportunities to predict or prevent preterm birth.}, } @article {pmid39484483, year = {2024}, author = {Neugent, ML and Hulyalkar, NV and Ghosh, D and Zimmern, PE and Shulaev, V and De Nisco, NJ}, title = {Urinary biochemical ecology reveals microbiome-metabolite interactions and metabolic markers of recurrent urinary tract infection.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.10.22.619727}, pmid = {39484483}, issn = {2692-8205}, abstract = {Recurrent urinary tract infections (rUTIs) are a major clinical challenge in postmenopausal women and their increasing prevalence underscores the need to define interactions between the host and the urinary microbiome that may underlie rUTI susceptibility. A body of work has identified the taxonomic profile of the female urinary microbiome associate with aging, menopause, and urinay disease. However, how this microbial community engages with the host niche, including the local biochemical environment of the urogenital tract, in health and disease is yet to be fully defined. This study directly assesses differences in the biochemical environment of the urine, or biochemical ecology, associated with recurrent urinary tract infection (UTI) and defines a microbe-metabolite association network of the female urinary microbiome. By integrating metagenomic and metabolomic data collected from a controlled cohort of women with rUTI, we find that distinct metabolites, such as methionine sulfoxide (Met-SO) and trimethylamine oxide (TMAO), are associated with differences in urinary microbiome diversity. We observe associations between microbial and biochemical beta diversity and unique metabolic networks of uropathogenic Escherichia coli and uroprotective Lactobacillus species, highlighting potential metabolite-driven ecological shifts that may influence UTI susceptibility. We identify a urinary lipid signature of active rUTI that can accurately distinguish (AUC = 0.987) cases controls. Finally, using time-to-relapse data we identify deoxycholic acid (DCA) as a new prognostic indicator for rUTI recurrence. Together these findings suggest that systemic metabolic processes may influence susceptibility, opening new avenues for therapeutic intervention and the development of more accurate diagnostic and prognostic to improve patient outcomes.}, } @article {pmid39484258, year = {2024}, author = {Hillege, LE and Trepka, KR and Ziemons, J and Aarnoutse, R and Guthrie, BGH and de Vos-Geelen, J and Valkenburg-van Iersel, L and van Hellemond, IEG and Baars, A and Vestjens, JHMJ and Penders, J and Deutschbauer, A and Atreya, CE and Kidder, WA and Turnbaugh, PJ and Smidt, ML}, title = {Metagenomic analysis during capecitabine therapy reveals microbial chemoprotective mechanisms and predicts drug toxicity in colorectal cancer patients.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {39484258}, support = {R01 CA255116/CA/NCI NIH HHS/United States ; R01 DK114034/DK/NIDDK NIH HHS/United States ; R01 HL122593/HL/NHLBI NIH HHS/United States ; }, abstract = {PURPOSE: Unpredictable chemotherapy side effects are a major barrier to successful treatment. Cell culture and mouse experiments indicate that the gut microbiota is influenced by and influences anti-cancer drugs. However, metagenomic data from patients paired to careful side effect monitoring remains limited. Herein, we focus on the oral fluoropyrimidine capecitabine (CAP). We investigate CAP-microbiome interactions through metagenomic sequencing of longitudinal stool sampling from a cohort of advanced colorectal cancer (CRC) patients.

METHODS: We established a prospective cohort study including 56 patients with advanced CRC treated with CAP monotherapy across 4 centers in the Netherlands. Stool samples and clinical questionnaires were collected at baseline, during cycle 3, and post-treatment. Metagenomic sequencing to assess microbial community structure and gene abundance was paired with transposon mutagenesis, targeted gene deletion, and media supplementation experiments. An independent US cohort was used for model validation.

RESULTS: CAP treatment significantly altered gut microbial composition and pathway abundance, enriching for menaquinol (vitamin K2) biosynthesis genes. Transposon library screens, targeted gene deletions, and media supplementation confirmed that menaquinol biosynthesis protects Escherichia coli from drug toxicity. Microbial menaquinol biosynthesis genes were associated with decreased peripheral sensory neuropathy. Machine learning models trained in this cohort predicted hand-foot syndrome and dose reductions in an independent cohort.

CONCLUSION: These results suggest treatment-associated increases in microbial vitamin biosynthesis serve a chemoprotective role for bacterial and host cells, with implications for toxicities outside the gastrointestinal tract. We provide a proof-of-concept for the use of microbiome profiling and machine learning to predict drug toxicities across independent cohorts. These observations provide a foundation for future human intervention studies, more in-depth mechanistic dissection in preclinical models, and extension to other cancer treatments.}, } @article {pmid39483755, year = {2024}, author = {Pita, S and Myers, PN and Johansen, J and Russel, J and Nielsen, MC and Eklund, AC and Nielsen, HB}, title = {CHAMP delivers accurate taxonomic profiles of the prokaryotes, eukaryotes, and bacteriophages in the human microbiome.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1425489}, pmid = {39483755}, issn = {1664-302X}, abstract = {INTRODUCTION: Accurate taxonomic profiling of the human microbiome composition is crucial for linking microbial species to health outcomes. Therefore, we created the Clinical Microbiomics Human Microbiome Profiler (CHAMP), a comprehensive tool designed for the profiling of prokaryotes, eukaryotes, and viruses across all body sites.

METHODS: CHAMP uses a reference database derived from 30,382 human microbiome samples, covering 6,567 prokaryotic and 244 eukaryotic species, as well as 64,003 viruses. We benchmarked CHAMP against established profiling tools (MetaPhlAn 4, Bracken 2, mOTUs 3, and Phanta) using a diverse set of in silico metagenomes and DNA mock communities.

RESULTS: CHAMP demonstrated unparalleled species recall, F1 score, and significantly reduced false positives compared to all other tools benchmarked. The false positive relative abundance (FPRA) for CHAMP was, on average, 50-fold lower than the second-best performing profiler. CHAMP also proved to be more robust than other tools at low sequencing depths, highlighting its application for low biomass samples.

DISCUSSION: Taken together, this establishes CHAMP as a best-in-class human microbiome profiler of prokaryotes, eukaryotes, and viruses in diverse and complex communities across low and high biomass samples. CHAMP profiling is offered as a service by Clinical Microbiomics A/S and is available for a fee at https://cosmosidhub.com.}, } @article {pmid39483461, year = {2024}, author = {Chen, G and Ren, Q and Zhong, Z and Li, Q and Huang, Z and Zhang, C and Yuan, H and Feng, Z and Chen, B and Wang, N and Feng, Y}, title = {Exploring the gut microbiome's role in colorectal cancer: diagnostic and prognostic implications.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1431747}, pmid = {39483461}, issn = {1664-3224}, mesh = {*Colorectal Neoplasms/microbiology/diagnosis/immunology/etiology ; Humans ; *Gastrointestinal Microbiome/immunology ; Prognosis ; Animals ; Biomarkers, Tumor ; Early Detection of Cancer ; Metagenomics/methods ; }, abstract = {The intricate interplay between the gut microbiome and colorectal cancer (CRC) presents novel avenues for early diagnosis and prognosis, crucial for improving patient outcomes. This comprehensive review synthesizes current findings on the gut microbiome's contribution to CRC pathogenesis, highlighting its potential as a biomarker for non-invasive CRC screening strategies. We explore the mechanisms through which the microbiome influences CRC, including its roles in inflammation, metabolism, and immune response modulation. Furthermore, we assess the viability of microbial signatures as predictive tools for CRC prognosis, offering insights into personalized treatment approaches. Our analysis underscores the necessity for advanced metagenomic studies to elucidate the complex microbiome-CRC nexus, aiming to refine diagnostic accuracy and prognostic assessment in clinical settings. This review propels forward the understanding of the microbiome's diagnostic and prognostic capabilities, paving the way for microbiome-based interventions in CRC management.}, } @article {pmid39482600, year = {2024}, author = {Yang, Q and Chen, X and Kou, G and Ji, X}, title = {A rare case of prostatic malakoplakia with multidrug-resistant Escherichia coli: a case report.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {1226}, pmid = {39482600}, issn = {1471-2334}, mesh = {Humans ; Anti-Bacterial Agents/therapeutic use/pharmacology ; *Drug Resistance, Multiple, Bacterial ; *Escherichia coli/genetics/drug effects/isolation & purification ; *Escherichia coli Infections/microbiology/drug therapy ; High-Throughput Nucleotide Sequencing ; *Malacoplakia/drug therapy/microbiology ; Prostate/pathology/microbiology ; Prostatic Diseases/microbiology/drug therapy ; Sepsis/microbiology/drug therapy ; }, abstract = {Prostatic malakoplakia is an uncommon chronic inflammatory disorder, tumor-like but non-cancerous, the diagnosis of which pivots crucially on the identification of characteristic Michaelis-Gutmann bodies within the pathological tissue. We hereby present an inaugural case report of prostatic malakoplakia concurrent with sepsis caused by multidrug-resistant Escherichia coli, verified through blood culture and metagenomic next-generation sequencing (mNGS). The pathogenesis might be associated with infections by Escherichia coli, immune system irregularities, or lysosomal dysfunction. Although the patient had no chronic underlying diseases, he presented early with sepsis and multi-organ dysfunction. This case emphasizes the imperative to further investigate the association between malakoplakia and Escherichia coli, the necessity for prompt diagnosis, and the supportive role of mNGS, and the treatment strategy focuses on rapid control of infection and systemic inflammatory response.}, } @article {pmid39482450, year = {2024}, author = {Gao, L and Rao, MPN and Liu, YH and Wang, PD and Lian, ZH and Abdugheni, R and Jiang, HC and Jiao, JY and Shurigin, V and Fang, BZ and Li, WJ}, title = {SALINITY-Induced Changes in Diversity, Stability, and Functional Profiles of Microbial Communities in Different Saline Lakes in Arid Areas.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {135}, pmid = {39482450}, issn = {1432-184X}, support = {2021FY100900//National Science and Technology Fundamental Resources Investigation Program of China/ ; 2022D01A154//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022B0202110001//Key-Area Research and Development Programof Guangdong Province/ ; }, mesh = {*Lakes/microbiology/chemistry ; *Salinity ; *Archaea/genetics/classification/isolation & purification ; *Bacteria/genetics/classification/isolation & purification ; *Microbiota ; *RNA, Ribosomal, 16S/genetics ; *Biodiversity ; Geologic Sediments/microbiology ; Phylogeny ; Desert Climate ; Ecosystem ; }, abstract = {Saline lakes, characterized by high salinity and limited nutrient availability, provide an ideal environment for studying extreme halophiles and their biogeochemical processes. The present study examined prokaryotic microbial communities and their ecological functions in lentic sediments (with the salinity gradient and time series) using 16S rRNA amplicon sequencing and a metagenomic approach. Our findings revealed a negative correlation between microbial diversity and salinity. The notable predominance of Archaea in high-salinity lakes signified a considerable alteration in the composition of the microbial community. The results indicate that elevated salinity promotes homogeneous selection pressures, causing substantial alterations in microbial diversity and community structure, and simultaneously hindering interactions among microorganisms. This results in a notable decrease in the complexity of microbial ecological networks, ultimately influencing the overall ecological functional responses of microbial communities such as carbon fixation, sulfur, and nitrogen metabolism. Overall, our findings reveal salinity drives a notable predominance of Archaea, selects for species adapted to extreme conditions, and decreases microbial community complexity within saline lake ecosystems.}, } @article {pmid39480531, year = {2024}, author = {Dobrzyński, J and Naziębło, A}, title = {Paenibacillus as a Biocontrol Agent for Fungal Phytopathogens: Is P. polymyxa the Only One Worth Attention?.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {134}, pmid = {39480531}, issn = {1432-184X}, mesh = {*Plant Diseases/microbiology/prevention & control ; *Paenibacillus/physiology/metabolism ; *Paenibacillus polymyxa/physiology ; Biological Control Agents ; Fusarium/physiology ; Colletotrichum/physiology/growth & development ; Pest Control, Biological ; Rhizoctonia/physiology/growth & development ; Botrytis/growth & development/physiology ; Fungi/physiology ; }, abstract = {Control of fungal phytopathogens is a significant challenge in modern agriculture. The widespread use of chemical fungicides to control these pathogens often leads to environmental and food contamination. An eco-friendly alternative that can help reduce reliance on these chemicals is plant growth-promoting bacteria (PGPB), particularly those of the genus Paenibacillus, which appear to be highly effective. The review aims to summarize the existing knowledge on the potential of Paenibacillus spp. as fungal biocontrol agents, identify knowledge gaps, and answer whether other species of the genus Paenibacillus, in addition to Paenibacillus polymyxa, can also be effective biocontrol agents. Paenibacillus spp. can combat plant phytopathogens through various mechanisms, including the production of lipopeptides (such as fusaricidin, paenimyxin, and pelgipeptin), the induction of systemic resistance (ISR), hydrolytic enzymes (chitinase, cellulase, and glucanase), and volatile organic compounds. These properties enable Paenibacillus strains to suppress the growth of fungi such as Fusarium oxysporum, F. solani, Rhizoctonia solani, Botrytis cinerea, or Colletotrichum gloeosporioides. Notably, several strains of Paenibacillus, including P. polymyxa, P. illinoisensis KJA-424, P. lentimorbus B-30488, and P. elgii JCK1400, have demonstrated efficacy in controlling fungal diseases in plants. Importantly, many formulations with Paenibacillus strains have already been patented, and some are commercially available, but most of them contain only P. polymyxa. Nevertheless, considering the data presented in this review, we believe that other strains from the Paenibacillus genus (besides P. polymyxa) will also be commercialized and used in plant protection in the future. Importantly, there is still limited information regarding their impact on the native microbiota, particularly from the metataxonomic and metagenomic perspectives. Expanding knowledge in this area could enhance the effectiveness of biocontrol agents containing Paenibacillus spp., ensuring safe and sustainable use of biological fungicides.}, } @article {pmid39488700, year = {2024}, author = {Jiang, L and Han, L and Zhong, Y and Zhang, M and Li, J and Rao, G and Xiang, S}, title = {High utility of bronchoalveolar lavage fluid metagenomic next-generation sequencing approach for etiological diagnosis of pneumonia.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {1232}, pmid = {39488700}, issn = {1471-2334}, support = {2023GXNSFBA026096//Youth Science Foundation Project of Guangxi/ ; Z- A20220085//Guangxi Health and Wellness Commission Self-funded Project/ ; 2021AC04001//Guangxi Science and Technology Base and Talent Special Project/ ; 2021AC04001//Guangxi Science and Technology Base and Talent Special Project/ ; 2020032//the Science and Technology Project Foundation of Nanning/ ; }, mesh = {Humans ; *Bronchoalveolar Lavage Fluid/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Female ; Middle Aged ; *Metagenomics/methods ; Prospective Studies ; Aged ; China ; Adult ; Bacteria/isolation & purification/genetics/classification ; Pneumonia/diagnosis/microbiology ; Pneumonia, Bacterial/diagnosis/microbiology ; }, abstract = {BACKGROUND: For patients with pneumonia, the rapid detection of pathogens is still a major global problem in clinical practice because traditional diagnostic techniques for infection are time-consuming and insensitive. Metagenomic next-generation sequencing (mNGS) is a novel technique that has the potential to improve pathogen diagnosis. This study aimed to investigate the microbiological diagnostic ability of mNGS compared with conventional culture and to determine the optimal time to test patients for pneumonia.

METHODS: A prospective study using data from June 2020 to June 2021 was performed at a tertiary teaching hospital in China. We included 56 patients from all adult patients with a clinical diagnosis of pneumonia. Blood and bronchoalveolar lavage fluid (BALF) samples were taken for simultaneous mNGS and conventional culture testing.

RESULTS: All 56 patients underwent both conventional culture and mNGS. Of these patients, 37 were diagnosed with severe pneumonia and 17 were diagnosed with non-severe pneumonia. The top three pathogenic bacteria detected by mNGS were Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa. Enterococcus faecium was detected more frequently in the non-severe pneumonia group (4 vs. 0, p < 0.05). The findings revealed that the detection rate of mNGS (84%) was superior to that of conventional culture methods (48%). Notably, the percentage of mNGS-positive BALF samples (46/56, 82.14%) was significantly greater than that of blood samples (27/56, 48.21%). The etiological comparison demonstrated that mNGS-positive samples, which received clinical approval, tended to be associated with a more normalized temperature, lower PCO2 levels, and a higher SOFA score than mNGS-negative samples (p = 0.022, p = 0.0.028, and p = 0.038, respectively).

CONCLUSIONS: In this study, we discovered that the etiology of lung infections frequently involves multiple pathogens. The use of mNGS in BALF is instrumental for detecting nonviral pathogens associated with lung infections. Although the rate of positive blood NGS results is significantly influenced by various clinical factors, for patients suspected of having viral, Legionella, or tsutsugamushi infections, plasma mNGS could serve as a complementary diagnostic tool.}, } @article {pmid39488697, year = {2024}, author = {Yao, QH and Zhi, HL and Xia, XJ and Liu, ZH}, title = {Primary cutaneous infections with non-tuberculous mycobacteria: a report of 6 cases.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {1231}, pmid = {39488697}, issn = {1471-2334}, support = {202004A17//Hangzhou Science and Technology Bureau/ ; }, mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; Anti-Bacterial Agents/therapeutic use ; *Mycobacterium Infections, Nontuberculous/microbiology/drug therapy/diagnosis/pathology ; Mycobacterium marinum/isolation & purification/genetics ; *Nontuberculous Mycobacteria/isolation & purification/genetics/classification ; Retrospective Studies ; Skin/microbiology/pathology ; Skin Diseases, Bacterial/microbiology/drug therapy/diagnosis/pathology ; }, abstract = {BACKGROUND: The incidence of non-tuberculous mycobacterium infection has shown a gradual increasing trend in recent years, among which cutaneous manifestations as an important aspect. This study aimed to describe the clinical features and microbiological findings in 6 cases of primary cutaneous nontuberculous mycobacterium infection.

METHODS: In this retrospective study from June 2021 to June 2022, the clinical data and microbiological results of six cases diagnosed with primary cutaneous non-tuberculous mycobacterium infection in department of dermatology, Hangzhou Third People's Hospital were analyzed.

RESULTS: All six cases were primary cutaneous non-tuberculous mycobacterium infections, four of which had a history of trauma or exposure, and two had an underlying disease that could lead to compromised immunity. All patients presented with erythema nodular skin lesions, four on the upper or lower extremities, one on the face, and one on the right hip. The histopathological findings of five patients who underwent biopsy were granulomatous inflammatory changes with mixed infiltration. Laboratory cultures using tissue or tissue fluid were all successful, including four Mycobacterium marinum, one Mycobacterium abscessus, and one Mycobacterium avium. Metagenomics next-generation sequencing detected results consistent with culture colonies in only two cases. With the exception of case 4, all patients responded well to oral medication, with a course of treatment ranging from 4 months to 1 year, and the prognosis was good.

CONCLUSIONS: The clinical features of primary cutaneous non-tuberculous mycobacterium infection are often lacking in specificity, and the identification of related strains is difficult for a variety of reasons. Although the results of metagenomics next-generation sequencing are useful for pathogen spectrum identification, its diagnostic value should be carefully reevaluated under certain circumstances. Patients with suspected triggers who do not respond well to conventional treatments should be suspected as atypical infection and potential immunosuppression. If diagnosed and treated promptly, the prognosis of primary cutaneous non-tuberculous mycobacterium infection is generally good.}, } @article {pmid39488676, year = {2024}, author = {Qi, M and Du, Y and Guan, J and Ma, J and Li, W and Chen, Z and Duan, W}, title = {The clinical management and efficacy of metagenomic next-generation sequencing in patients with pyogenic spinal infection: a single-center cohort study.}, journal = {Journal of orthopaedic surgery and research}, volume = {19}, number = {1}, pages = {716}, pmid = {39488676}, issn = {1749-799X}, support = {No: L212039//Beijing Natural Science Foundation Grant/ ; No: 2022-PUMCH-D-004//National High Level Hospital Clinical Research Funding/ ; No: XMLX202138//Beijing Hospitals Authority Clinical Medicine Development of special funding support/ ; No. QML20210801//The "Young Talents" Program, supported by Beijing Municipal Hospital Administration/ ; No. Z221100007422019//Research and application of clinical characteristic diagnosis and treatment Program/ ; No.2023YFC2509700//National Key R&D Program of China, "Research on Prevention and Control of Common Diseases"，Supported by Ministry of Science & Technology of PRC/ ; }, mesh = {Humans ; Male ; Middle Aged ; Female ; Aged ; Adult ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Cohort Studies ; Treatment Outcome ; Epidural Abscess/microbiology ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {OBJECTIVE: This study aims to evaluate the clinical management and effectiveness of metagenomic next-generation sequencing (mNGS) in patients with pyogenic spinal infections.

METHODS: We conducted a retrospective review of 17 patients diagnosed with pyogenic spinal infections and treated at our institution between October 2022 and February 2024. The cohort included 8 males and 9 females, with a mean age of 63.59 ± 10.18 years (range: 41-71 years). The infections comprised 9 epidural abscesses, 6 intervertebral space infections, and 2 deep abscesses. All patients underwent open surgical procedures and mNGS-based bacterial identification using intraoperative pus or tissue specimens, in addition to conventional blood bacterial cultures. Clinical outcomes were assessed using CRP, PCT, WBC inflammatory markers, and VAS scores postoperatively.

RESULTS: All 17 patients with pyogenic spinal infections underwent open surgery and mNGS bacterial detection at our institution. Among the 17 patients, mNGS yielded positive results in 14 cases (82.4%), significantly higher than the 5.9% positivity rate of conventional bacterial cultures (p < 0.001). The mNGS test time was notably shorter than conventional cultures (1.0 vs. 5.88 days, p < 0.001). Postoperative antibiotic therapy was adjusted based on mNGS findings. There were significant reductions in postoperative VAS, WBC, PCT, and CRP values compared to preoperative levels (p < 0.01).

CONCLUSION: Metagenomic next-generation sequencing is effective in managing pyogenic spinal infections by facilitating rapid and sensitive detection of pathogens. This technique improves the timeliness and accuracy of diagnosis, highlighting its potential for broader clinical use.}, } @article {pmid39488668, year = {2024}, author = {Geat, N and Singh, D and Saha, P and Jatoth, R and Babu, PL and Devi, GSR and Lakhran, L and Singh, D}, title = {Deciphering Phyllomicrobiome of Cauliflower Leaf: Revelation by Metagenomic and Microbiological Analysis of Tolerant and Susceptible Genotypes Against Black Rot Disease.}, journal = {Current microbiology}, volume = {81}, number = {12}, pages = {439}, pmid = {39488668}, issn = {1432-0991}, mesh = {*Plant Diseases/microbiology ; *Plant Leaves/microbiology ; *Microbiota/genetics ; *Genotype ; *Brassica/microbiology ; *Metagenomics ; *Bacteria/genetics/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Xanthomonas campestris/genetics ; Phylogeny ; High-Throughput Nucleotide Sequencing ; }, abstract = {Understanding the phyllomicrobiome dynamics in cauliflower plants holds significant promise for enhancing crop resilience against black rot disease, caused by Xanthomonas campestris pv. campestris. In this study, the culturable microbiome and metagenomic profile of tolerant (BR-161) and susceptible (Pusa Sharad) cauliflower genotypes were investigated to elucidate microbial interactions associated with disease tolerance. Isolation of phyllospheric bacteria from asymptomatic and black rot disease symptomatic leaves of tolerant and susceptible cultivars yielded 46 diverse bacterial isolates. Molecular identification via 16S rRNA sequencing revealed differences in the diversity of microbial taxa between genotypes and health conditions. Metagenomic profiling using next-generation sequencing elucidated distinct microbial communities, with higher diversity observed in black rot disease symptomatic leaf of BR-161. Alpha and beta diversity indices highlighted differences in microbial community structure and composition between genotypes and health conditions. Taxonomic analysis revealed a core microbiome consisting of genera such as Xanthomonas, Psychrobacillus, Lactobacillus, and Pseudomonas across all the samples. Validation through microbiological methods confirmed the presence of these key genera. The findings provide novel insights into the phyllomicrobiome of black rot-tolerant and susceptible genotypes of cauliflower. Harnessing beneficial microbial communities identified in this study offers promising avenues for developing sustainable strategies to manage black rot disease and enhance cauliflower crop health and productivity.}, } @article {pmid39488617, year = {2024}, author = {Li, X and Cheng, R and Zhang, C and Shao, Z}, title = {Genomic diversity of phages infecting the globally widespread genus Sulfurimonas.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1428}, pmid = {39488617}, issn = {2399-3642}, support = {42376125//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2023J011383;2024J09050//Natural Science Foundation of Fujian Province (Fujian Provincial Natural Science Foundation)/ ; DY-XZ-04;DY135-B2-01//China Ocean Mineral Resources Research and Development Association (China Ocean Mineral Resources R&D Association)/ ; }, mesh = {*Bacteriophages/genetics/classification/physiology ; *Genome, Viral ; *Genetic Variation ; Phylogeny ; Metagenome ; Genomics/methods ; }, abstract = {The widespread bacterial genus Sulfurimonas is metabolically versatile and occupies a key ecological niche in different habitats, but its interaction with bacteriophages remains unexplored. Here we systematically investigated the genetic diversity, taxonomy and interaction patterns of Sulfurimonas-associated phages based on sequenced microbial genomes and metagenomes. High-confidence phage contigs related to Sulfurimonas were retrieved from various ecosystems, clustered into 61 viral operational taxonomic units across three viral realms, including Duplodnaviria, Monodnaviria and Varidnaviria. Head-tail phages of Caudoviricetes were assigned to 19 genus-level viral clusters, the majority of which were distantly related to known viruses. Notably, diverse double jelly-roll viruses and inoviruses were also linked to Sulfurimonas, representing two commonly overlooked phage groups. Historical and current phage infections were revealed, implying viral impact on the evolution of host adaptive immunity. Additionally, phages carrying auxiliary metabolic genes might benefit hosts by compensating or augmenting sulfur metabolism. This study highlights the diversity and novelty of Sulfurimonas-associated phages with divergent tailless lineages, providing basis for further investigation of phage-host interactions within this genus.}, } @article {pmid39488451, year = {2025}, author = {Xiao, C and Ide, K and Matsunaga, H and Kogawa, M and Wagatsuma, R and Takeyama, H}, title = {Metagenomic profiling of antibiotic resistance genes and their associations with the bacterial community along the Kanda River, an urban river in Japan.}, journal = {Journal of bioscience and bioengineering}, volume = {139}, number = {2}, pages = {147-155}, doi = {10.1016/j.jbiosc.2024.09.006}, pmid = {39488451}, issn = {1347-4421}, mesh = {*Rivers/microbiology ; Japan ; *Metagenomics ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/drug effects/isolation & purification ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; Water Microbiology ; Drug Resistance, Microbial/genetics ; Seasons ; Metagenome ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Antibiotic resistance genes (ARGs) present in urban rivers have the potential to disseminate antibiotic-resistant bacteria into other environments, posing significant threats to both ecological and public health. Although metagenomic analyses have been widely employed to detect ARGs in rivers, our understanding of their dynamics across different seasons in diverse watersheds remains limited. In this study, we performed a comprehensive genomic analysis of the Kanda River in Japan at 11 sites from upstream to estuary throughout the year to assess the spread of ARGs and their associations with bacterial communities. Analysis of 110 water samples using the 16S rRNA gene revealed variations in bacterial composition corresponding to seasonal changes in environmental parameters along the river. Shotgun metagenomics-based profiling of ARGs in 44 water samples indicated higher ARG abundance downstream, particularly during the summer. Weighted gene co-expression network analysis (WGCNA) linking bacterial lineages and ARGs revealed that 12 ARG subtypes co-occurred with 128 amplicon sequence variants (ASVs). WGCNA suggested potential hosts for ErmB, ErmF, ErmG, tetQ, tet (W/N/W), aadA2, and adeF, including gut-associated bacteria (e.g., Prevotella, Bacteroides, Arcobacter) and indigenous aquatic microbes (e.g., Limnohabitans and C39). In addition, Pseudarcobacter (a later synonym of Arcobater) was identified as a host for adeF, which was also confirmed by single cell genomics. This study shows that ARG distribution in urban rivers is affected by seasonal and geographical factors and demonstrates the importance of monitoring rivers using multiple types of genome sequencing, including 16S rRNA gene sequencing, metagenomics, and single cell genomics.}, } @article {pmid39488061, year = {2025}, author = {Zhao, Y and Zhang, J and Zheng, Y and Shi, J and Hu, Z and Xie, H and Guo, Z and Liang, S and Wu, H}, title = {Overlooked dissemination risks of antimicrobial resistance through green tide proliferation.}, journal = {Water research}, volume = {268}, number = {Pt B}, pages = {122714}, doi = {10.1016/j.watres.2024.122714}, pmid = {39488061}, issn = {1879-2448}, mesh = {*Seawater/microbiology ; Drug Resistance, Microbial/genetics ; Eutrophication ; Bacteria/drug effects/genetics ; Drug Resistance, Bacterial/genetics ; Ulva ; Gene Transfer, Horizontal ; }, abstract = {Green tides, particularly those induced by Enteromorpha, pose significant environmental challenges, exacerbated by climate change, coastal eutrophication, and other anthropogenic impacts. More concerningly, these blooms may influence the spread of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) within ecosystems. However, the manner in which Enteromorpha blooms affect the distribution and spread of antimicrobial resistance (AMR) remains uncertain. This study investigated ARG profiles, dynamic composition, and associated health risks within the Enteromorpha phycosphere and surrounding seawater in typical bays (Jiaozhou, Aoshan, and Lingshan) in the South Yellow Sea. The Enteromorpha phycosphere exhibited significantly higher ARG abundance (p < 0.05) but lower diversity compared to the surrounding seawater. Source-tracking and metagenomic analyses revealed that the phycosphere was the main contributor to the resistome of surrounding seawater. Moreover, resistant pathogens, especially ESKAPE pathogens, with horizontal gene transfer (HGT) potential, were more abundant in the phycosphere than in the surrounding seawater. The phycosphere released high-risk ARGs to the surrounding seawater during Enteromorpha blooms, posing serious health and ecological AMR risks in marine environments. This study highlights the significant role of Enteromorpha blooms in ARG spread and associated risks, urging a reassessment of AMR burden from a public health perspective.}, } @article {pmid39487991, year = {2024}, author = {Berckx, F and Van Nguyen, T and Hilker, R and Wibberg, D and Battenberg, K and Kalinowski, J and Berry, A and Pawlowski, K}, title = {Host dependent specialized metabolism of nitrogen export in actinorhizal nodules induced by Frankia cluster-2.}, journal = {Journal of experimental botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/jxb/erae446}, pmid = {39487991}, issn = {1460-2431}, abstract = {Frankia cluster-2 strains are diazotrophs that engage in root nodule symbiosis with actinorhizal plants of the Cucurbitales and the Rosales. Previous studies have shown that an assimilated nitrogen source, presumably arginine, is exported to the host in nodules of Datisca glomerata (Cucurbitales), while a different metabolite is exported in the nodules of Ceanothus thyrsiflorus (Rosales). To investigate if an assimilated nitrogen form is commonly exported to the host by cluster-2 strains, and which metabolite would be exported in Ceanothus, we analysed gene expression levels, metabolite profiles, and enzyme activities in nodules. We conclude that the export of assimilated nitrogen in symbiosis seems to be a common feature for Frankia cluster-2 strains, but which source is host-dependent. The export of assimilated ammonium to the host suggests that 2-oxoglutarate is drawn from the TCA cycle at a high rate. This specialised metabolism obviates the need for the reductive branch of the TCA cycle. We found several genes encoding enzymes of the central carbon and nitrogen metabolism were lacking in Frankia cluster-2 genomes: the glyoxylate shunt and succinate semialdehyde dehydrogenase. This led to a linearization of the TCA cycle, and we hypothesize this could explain the low saprotrophic potential of Frankia cluster-2.}, } @article {pmid39487448, year = {2024}, author = {Kosch, TA and Torres-Sánchez, M and Liedtke, HC and Summers, K and Yun, MH and Crawford, AJ and Maddock, ST and Ahammed, MS and Araújo, VLN and Bertola, LV and Bucciarelli, GM and Carné, A and Carneiro, CM and Chan, KO and Chen, Y and Crottini, A and da Silva, JM and Denton, RD and Dittrich, C and Espregueira Themudo, G and Farquharson, KA and Forsdick, NJ and Gilbert, E and Che, J and Katzenback, BA and Kotharambath, R and Levis, NA and Márquez, R and Mazepa, G and Mulder, KP and Müller, H and O'Connell, MJ and Orozco-terWengel, P and Palomar, G and Petzold, A and Pfennig, DW and Pfennig, KS and Reichert, MS and Robert, J and Scherz, MD and Siu-Ting, K and Snead, AA and Stöck, M and Stuckert, AMM and Stynoski, JL and Tarvin, RD and Wollenberg Valero, KC and , }, title = {The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1025}, pmid = {39487448}, issn = {1471-2164}, mesh = {Animals ; *Amphibians/genetics ; *Genomics/methods ; Conservation of Natural Resources/methods ; Genome ; }, abstract = {Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomic resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomic resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, anti-predator strategies, and resilience and adaptive responses. They also serve as essential models for studying broad genomic traits, such as evolutionary genome expansions and contractions, as they exhibit the widest range of genome sizes among all animal taxa and possess multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The emergence of long-read sequencing technologies, combined with advanced molecular and computational techniques that improve scaffolding and reduce computational workloads, is now making it possible to address some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC, https://mvs.unimelb.edu.au/amphibian-genomics-consortium) in early 2023. This burgeoning community already has more than 282 members from 41 countries. The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and call on the research and conservation communities to unite as part of the AGC to enable amphibian genomics research to "leap" to the next level.}, } @article {pmid39487079, year = {2025}, author = {Williams, AD and Leung, VW and Tang, JW and Hidekazu, N and Suzuki, N and Clarke, AC and Pearce, DA and Lam, TT}, title = {Ancient environmental microbiomes and the cryosphere.}, journal = {Trends in microbiology}, volume = {33}, number = {2}, pages = {233-249}, doi = {10.1016/j.tim.2024.09.010}, pmid = {39487079}, issn = {1878-4380}, mesh = {*Microbiota ; *Metagenomics ; *Environmental Microbiology ; Permafrost/microbiology ; Ice ; Bacteria/genetics/classification/isolation & purification ; Computational Biology/methods ; }, abstract = {In this review, we delineate the unique set of characteristics associated with cryosphere environments (namely, ice and permafrost) which present both challenges and opportunities for studying ancient environmental microbiomes (AEMs). In a field currently reliant on several assumptions, we discuss the theoretical and empirical feasibility of recovering microbial nucleic acids (NAs) from ice and permafrost with varying degrees of antiquity. We also summarize contamination control best practices and highlight considerations for the latest approaches, including shotgun metagenomics, and downstream bioinformatic authentication approaches. We review the adoption of existing software and provide an overview of more recently published programs, with reference to their suitability for AEM studies. Finally, we summarize outstanding challenges and likely future directions for AEM research.}, } @article {pmid39486651, year = {2025}, author = {Tang, X and Yao, Q and Jiang, X and Wang, C and Liu, Y and Li, C and Chen, Y and Liu, W and Chen, F and Wang, Y}, title = {Response of ammonium transformation in bioanodes to potential regulation: Performance, electromicrobiome and implications.}, journal = {Bioresource technology}, volume = {415}, number = {}, pages = {131731}, doi = {10.1016/j.biortech.2024.131731}, pmid = {39486651}, issn = {1873-2976}, mesh = {*Electrodes ; *Ammonium Compounds/metabolism ; *Nitrites/metabolism ; Biofilms ; Oxidation-Reduction ; Bioelectric Energy Sources/microbiology ; Bacteria/metabolism/genetics ; Nitrates/metabolism ; Denitrification ; Quaternary Ammonium Compounds/metabolism ; }, abstract = {Understanding how potential regulation affects ammonium transformation in bioanodes is crucial for promoting their application. This study explored the performance, electrochemical properties, electromicrobiome of bioanodes across potentials from 0.0 V to 0.4 V vs. standard hydrogen electrode (SHE). Higher anode potentials enhanced the performance of electroactive biofilms and ammonium removal but suppressed nitrite oxidation while favoring dissimilatory nitrate reduction (DNRA), leading to increased nitrite accumulation. A reduction in nitrite-oxidizing bacteria (NOB) and an increase in DNRA-related genes resulted in an optimal nitrite-to-ammonium ratio of 1.32 for the Anammox process. Higher anodic potentials (0.3 and 0.4 V) were less effective for TN removal than lower potentials (0, 0.1, and 0.2 V), likely due to increased NOB and denitrification genes at lower potentials enhancing nitrite oxidation and denitrification. These findings indicate that regulating anodic potential effectively directs ammonium transformation in bioanodes, optimizing its conversion to N2 or nitrite.}, } @article {pmid39486340, year = {2024}, author = {Zhang, H and Cheng, S and Yan, W and Zhang, Q and Jiang, B and Xing, Y and Zhang, B}, title = {Interplay between vanadium distribution and microbial community in soil-plant system.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {136303}, doi = {10.1016/j.jhazmat.2024.136303}, pmid = {39486340}, issn = {1873-3336}, mesh = {*Vanadium/metabolism ; *Soil Microbiology ; *Soil Pollutants/metabolism ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Microbiota ; Bacteria/metabolism/genetics/classification ; Biodegradation, Environmental ; Plant Roots/microbiology/metabolism ; }, abstract = {Soil-plant system play an essential role in distribution and transformation of vanadium (V). V shapes the diversity of soil communities, while soil microorganisms mediate V transformation. Plants also absorb V from surrounding soil. However, the study of microbial response to V stress in different soil-plant compartments is limited, and the metabolic functions driving V transformation across these systems remain elusive. The study investigates the distribution of V in soil-plant systems nearby a V smelter. 16S rRNA sequencing and metagenomics are utilized to reveal the microbial adaptation and V transformation in bulk soil, rhizosphere, and endosphere. Bothriochloa ischaemum (L.) Keng. (BK) exhibits higher phytoextraction potential (TF = 0.74 ± 0.26). Environmental variables, including pH, V, OM, and AP, show significant (p < 0.05) influence in soil community composition, with homogeneous selection governing the assembly processes in bulk soil and rhizosphere, while stochastic process dominates endospheric assembly. Metagenomic investigation revealed a coordinated metabolic pathway between functional taxa in soil and plants, which lead to root uptake and translocation. V stress is mitigated through Nocardioide, Microvirga, and Solirubrobacter, putatively harboring V(V) reduction genes n arG and mtrC in soil. In rhizosphere, citrate synthase gltA and alkaline phosphatase phoD exhibit functional potential to facilitate formation of V-complexation to increase V mobility. In endoshere, endophytic Enterobacter further detoxifies V(V), and likely promotes V translocation through siderophore biosynthesis gene, iucA. These findings enhance our understanding on interplay between V and microbial community in soil-plant systems, which is instrumental in developing mitigation plan for V contaminated sites.}, } @article {pmid39485561, year = {2024}, author = {Achudhan, AB and Saleena, LM}, title = {Comparative genomic analysis and characterization of novel high-quality draft genomes from the coal metagenome.}, journal = {World journal of microbiology & biotechnology}, volume = {40}, number = {12}, pages = {370}, pmid = {39485561}, issn = {1573-0972}, mesh = {*Coal/microbiology ; *Metagenome ; *Phylogeny ; *Bacteria/genetics/classification ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; Genomics/methods ; Metagenomics/methods ; Microbiota/genetics ; DNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Coal, a sedimentary rock harbours a complex microbial community that plays a significant role in its formation and characteristics. However, coal metagenome sequencing and studies were less, limiting our understanding of this complex ecosystem. This study aimed to reconstruct high-quality metagenome-assembled genomes (MAGs) from the coal sample collected in the Neyveli mine to explore the unrevealed diversity of the coal microbiome. Using Illumina sequencing, we obtained high-quality raw reads in FASTQ format. Subsequently, de novo assembly and binning with metaWRAP software facilitated the reconstruction of coal MAGs. Quality assessment using CheckM identified 10 High-Quality MAGs (HQ MAGs), 7 medium-quality MAGs (MQ MAGs), and 6 low-quality MAGs (LQ MAGs). Further analysis using GTDB-Tk revealed four HQ MAGs as known species like Dermacoccus abyssi, Sphingomonas aquatilis, Acinetobacter baumannii, and Burkholderia cenocepacia. The remaining six HQ MAGs were classified as Comamonas, Arthrobacter, Noviherbaspirillum, Acidovorax, Oxalicibacterium, and Bordetella and designated as novel genomes by the validation of digital DNA-DNA hybridization (dDDH). Phylogenetic analysis and further pangenome analysis across the phylogenetic groups revealed a similar pattern with a high proportion of cloud genes. We further analysed the functional potential of these MAGs and closely related genomes using COG. The comparative functional genomics revealed that novel genomes are highly versatile, potentially reflecting adaptations to the coal environment. BlastKOALA was used to conduct a detailed analysis of the metabolic pathways associated with the MAGs. This study highlights the comparative genomic analysis of novel coal genomes with their closely related genomes to understand the evolutionary relationships and functional properties.}, } @article {pmid39485064, year = {2024}, author = {Feng, L and Guo, Z and Yao, W and Mu, G and Zhu, X}, title = {Metagenomics and Untargeted Metabolomics Analysis Revealed the Probiotic and Postbiotic Derived from Lactiplantibacillus plantarum DPUL F232 Alleviate Whey Protein-Induced Food Allergy by Reshaping Gut Microbiota and Regulating Key Metabolites.}, journal = {Journal of agricultural and food chemistry}, volume = {72}, number = {45}, pages = {25436-25448}, doi = {10.1021/acs.jafc.4c08203}, pmid = {39485064}, issn = {1520-5118}, mesh = {Animals ; *Probiotics/pharmacology/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; Rats ; *Metabolomics ; *Whey Proteins/metabolism ; *Metagenomics ; *Rats, Sprague-Dawley ; Male ; Humans ; Immunoglobulin E/immunology/blood ; Food Hypersensitivity/immunology ; Lactobacillus plantarum ; Female ; }, abstract = {Postbiotics have emerged as a promising alternative to probiotics. However, it remains unclear whether postbiotics can exert regulatory effects on intestinal flora and metabolism as probiotics. Thus, we investigated the effects of probiotic and postbiotic in rats with whey protein-induced food allergy, which demonstrated that postbiotic intervention effectively alleviated allergy symptoms, reduced serum immunoglobulin E (IgE) and mast cell protease-1 (mMCP-1) levels, and regulated the type helper 1 cell/2 cell (Th1/Th2) balance in both serum and spleen. Metagenomic analysis revealed that postbiotics induced more significant changes in intestinal flora. Untargeted metabolomics analysis showed that both probiotics and postbiotics significantly up-regulated various differential metabolites, which were negatively correlated with immune indices, including malvidin-3-glucoside, 3,4-dihydroxymandelic acid, nicotinamide, triterpenoids, pirbuterol, and 4-hydroxybenzoic acid. This study confirms that postbiotics can alleviate food allergies and regulate intestinal flora and metabolites, which provides a valuable reference for the use of postbiotics in mitigating allergic diseases through gut microbiota and metabolite modulation.}, } @article {pmid39482414, year = {2024}, author = {Virachabadoss, VRA and Appavoo, MS and Paramasivam, KS and Karthikeyan, SV and Govindan, D}, title = {The addition of humic acid into soil contaminated with microplastics enhanced the growth of black gram (Vigna mungo L. Hepper) and modified the rhizosphere microbial community.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {54}, pages = {63343-63359}, pmid = {39482414}, issn = {1614-7499}, mesh = {*Humic Substances ; *Rhizosphere ; *Soil Pollutants ; *Soil Microbiology ; *Vigna/drug effects/growth & development ; *Microplastics ; *Soil/chemistry ; Microbiota/drug effects ; }, abstract = {Microplastics have polluted agricultural soils, posing a substantial risk to crop productivity. Moreover, the presence of microplastic pollution has caused a disturbance in the composition of the microbial community in the soil surrounding plant roots, therefore impacting the growth of beneficial bacteria. A study was conducted to examine if humic acid (HA) can counteract the harmful effects of microplastics (MPs) on the growth of black gram crops and the composition of the rhizosphere soil microbial community, to reduce the negative impacts of microplastics on these microorganisms and crops. The research was carried out using mud pots and the plastic utilized for the experiment consisted of 60% high-density polyethylene (HDPE) and 40% polypropylene (PP). The soil was enriched with lignite-based potassium humate, which had a pH range of 8.0-9.5 and with 65% humic acid. The experiment consisted of six treatments: T1, which served as the control without HA and MP; T2, which involved the use of HA at a concentration of 0.15% w/w; T3, which involved the use of MP at a concentration of 0.2% w/w; T4, which involved the use of MP at a concentration of 0.4% w/w; T5, which involved the combination of HA at a concentration of 0.15% w/w and MP at a concentration of 0.2% w/w; and T6, which involved the combination of HA at a concentration of 0.15% w/w and MP at a concentration of 0.4% w/w. The plant growth characteristics, including germination percentage, nodule number, and chlorophyll content, were measured. In addition, the DNA obtained from the rhizosphere soil was analyzed using metagenomics techniques to investigate the organization of the microbial population. Seedlings in soil polluted with MP exhibited delayed germination compared to seedlings in uncontaminated soil. Following 60 days of growth, the soil samples treated with T5 (0.2% MP and 0.15% HA w/w) had the highest population of bacteria and rhizobium, with counts 5.58 ± 0.02 and 4.90 ± 0.02 CFU g[-1] soil. The plants cultivated in T5 had the most elevated chlorophyll-a concentration (1.340 ± 0.06 mg g[-1]), and chlorophyll-b concentration (0.62 ± 0.02 mg g[-1]) while those cultivated in T3 displayed the lowest concentration of chlorophyll-a (0.59 ± 0.02 mg g[-1]) and chlorophyll-b (0.21 ± 0.04 mg g[-1]). Within the phylum, Proteobacteria had the highest prevalence in all treatments. However, when the soil was polluted with MPs, its relative abundance was reduced by 8.4% compared to the control treatment (T1). Conversely, treatment T5 had a 3.76% rise in relative abundance when compared to treatment T3. The predominant taxa found in soil polluted with MP were Sphingomonas and Bacillus, accounting for 19.3% of the total. Sphingomonas was the predominant genus (21.2%) in soil polluted with MP and supplemented with humic acid. Humic acid can be used as a soil amendment to mitigate the negative effects of MPs and enhance their positive advantages. Research has demonstrated that incorporating humic acid into soil is a viable method for maintaining the long-term integrity of soil's physical, chemical, and biological characteristics.}, } @article {pmid39482031, year = {2024}, author = {Hoffmann, A and Hoffmann, J and Ruegamer, T and Jung, N and Wong, RMY and Alt, V and Eysel, P and Jantsch, J}, title = {New diagnostic techniques for diagnosing facture-related infections.}, journal = {Injury}, volume = {55 Suppl 6}, number = {}, pages = {111898}, doi = {10.1016/j.injury.2024.111898}, pmid = {39482031}, issn = {1879-0267}, mesh = {Humans ; *Prosthesis-Related Infections/diagnosis/microbiology ; Fractures, Bone ; Algorithms ; Metagenomics/methods ; }, abstract = {The diagnosis of fracture-related infections (FRI) is challenging and requires interdisciplinary efforts. Many diagnostic approaches are based on the algorithms established for prosthetic joint infections (PJI). Data specific to FRI are limited. Microbiological diagnostics include tissue culture, sonication, and molecular methods. Novel metagenomic analyses are increasingly being used in clinical diagnostic practice. In addition to bacterial detection, the study of host tissue factors has the potential to transform the diagnostics of FRI by facilitating the assesment of clinical significance in clinical samples. The integration of host tissue analysis into microbiology reports has great potential to improve the diagnosis of FRI. This mini-review describes the potential improvement of diagnostic techniques by integrating new approaches into the diagnostic algorithm of fracture-related infections.}, } @article {pmid39482008, year = {2024}, author = {Ding, C and Chen, R and Guo, P and Yang, J and He, M}, title = {A case of Fitz-Hugh-Curtis syndrome diagnosed by noninvasive metagenomic next-generation sequencing.}, journal = {Taiwanese journal of obstetrics & gynecology}, volume = {63}, number = {6}, pages = {935-940}, doi = {10.1016/j.tjog.2024.04.020}, pmid = {39482008}, issn = {1875-6263}, mesh = {Humans ; Female ; *Pelvic Inflammatory Disease/microbiology/diagnosis ; *Chlamydia Infections/diagnosis/microbiology ; Young Adult ; *Chlamydia trachomatis/isolation & purification/genetics ; *High-Throughput Nucleotide Sequencing/methods ; *Peritonitis/diagnosis/microbiology/drug therapy ; *Metagenomics/methods ; Hepatitis/diagnosis/microbiology ; Ascitic Fluid/microbiology ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {OBJECTIVE: Fitz-Hugh-Curtis Syndrome (FHCS) is an inflammation of the liver capsule as a complication of pelvic inflammatory disease (PID) in sexually active women, mostly associated with Chlamydia trachomatis (C. trachomatis) and Neisseria gonorrhoeae. Classically presenting as sharp right upper quadrant pain, usually accompanied salpingitis and ascites. With nonspecific clinical presentation and poor specificity, definitive diagnosis needs tissue biopsy and culture by laparoscopy.

CASE REPORT: We report the case of a 22-year-old female with a 2-month history of abdominal pain and distention. Symptomatic relief when supportive treatments were given, with the ultrasound and PET-CT suggested advanced bilateral ovarian cancer. After metagenomic next-generation sequencing (mNGS) detected C. trachomatis in ascitic fluid. Following anti-infective medication, clinical improvement was satisfactory and the patient was discharged.

CONCLUSION: FHCS with distention was rare and challenging to diagnose. The mNGS would be a potent, non-invasive pathogen detection method with significant sensitivity and specificity.}, } @article {pmid39481932, year = {2025}, author = {Zhu, S and Mao, H and Sun, S and Yang, X and Zhao, W and Sheng, L and Chen, Z}, title = {Arbuscular mycorrhizal fungi promote functional gene regulation of phosphorus cycling in rhizosphere microorganisms of Iris tectorum under Cr stress.}, journal = {Journal of environmental sciences (China)}, volume = {151}, number = {}, pages = {187-199}, doi = {10.1016/j.jes.2024.02.029}, pmid = {39481932}, issn = {1001-0742}, mesh = {*Mycorrhizae/physiology ; *Phosphorus/metabolism ; *Rhizosphere ; *Soil Microbiology ; *Chromium/metabolism ; *Soil Pollutants/metabolism ; Iris Plant/metabolism ; Symbiosis ; }, abstract = {The mutualistic symbiotic system formed by clumping arbuscular mycorrhizal fungi (AMF) and plants can remediate heavy metal-contaminated soils. However, the specific mechanisms underlying the interaction between AMF and inter-root microbial communities, particularly their impact on organic phosphorus (P) cycling, remain unclear. This study investigated the gene regulation processes involved in inter-root soil phosphorus cycling in wetland plants, specifically Iris tectorum, following inoculation with AMF under varying concentrations of chromium (Cr) stress. Through macro-genome sequencing, we analyzed the composition and structure of the inter-root soil microbial community associated with Iris tectorum under greenhouse pot conditions. The results demonstrated significant changes in the diversity and composition of the inter-root soil microbial community following AMF inoculation, with Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria, and Bacteroidetes being the dominant taxa. Under Cr stress, species and gene co-occurrence network analysis revealed that AMF promoted the transformation process of organic phosphorus mineralization and facilitated inorganic phosphorus uptake. Additionally, network analysis of functional genes indicated strong aggregation of (pstS, pstA, pstC, TC.PIT, phoR, pp-gppA) genes, which collectively enhanced phosphorus uptake by plants. These findings shed light on the inter-root soil phosphorus cycling process during the co-remediation of Cr-contaminated soil by AMF-Iris tectorum symbiosis, providing valuable theoretical support for the application of AMF-wetland plant symbiosis systems to remediate heavy metal-contaminated soil.}, } @article {pmid39481794, year = {2024}, author = {Li, X and Li, Y and Wang, Y and Liu, Y and Riaz, L and Wang, Q and Zeng, X and Qin, Z and Irfan, M and Yang, Q}, title = {Methodology comparison of environmental sediment fungal community analysis.}, journal = {Environmental research}, volume = {263}, number = {Pt 3}, pages = {120260}, doi = {10.1016/j.envres.2024.120260}, pmid = {39481794}, issn = {1096-0953}, mesh = {*Geologic Sediments/microbiology ; *Fungi/genetics/isolation & purification/classification ; *RNA, Ribosomal, 18S/genetics ; *High-Throughput Nucleotide Sequencing ; DNA, Fungal/analysis ; DNA, Ribosomal Spacer/genetics ; Mycobiome ; Rivers/microbiology ; }, abstract = {Fungi play important roles in ecosystems. Analyzing fungal communities in environments has long been a challenge due to the large difference in compositions retrieved using different methods or sequencing regions, obscuring the true abundance and species information. Our study aimed to compare and determine more accurate approach for evaluating fungal populations in river sediment. To achieve this, different primer sets in the internal transcribed spacer (ITS) (ITS5/ITS1R, ITS1F/ITS2), 18S rRNA gene (0817F/1196R) for High-throughput sequencing (HTS), metagenomic shotgun sequencing (MS) directly from environmental samples, and HTS using ITS primers for the fungal samples collected from plate cultivation were used to characterize the fungal communities. We calculated diversity index and used FungalTraits to analyze methods preferences for fungal species. The study revealed that when analyzing the fungal species directly from environmental samples, amplification and sequencing of ITS region demonstrated more accuracy than MS and 18S rRNA gene sequencing methods, but displayed significant primer preference. Over 30 % fungal species from HTS after plate cultivation were not present in HTS from the environmental samples. NMDS analysis demonstrated significant disparities in species diversity among different methods, suggesting potential complementarity between them. Over 85% species identified by HTS using ITS primers belonged to filamentous fungi, while the MS mostly identified yeast (62%). Therefore, to get more accurate fungal community information in sediment, multiple methods were recommended by using cultivation, molecular biological methods dependent on PCR techniques like ITS1F/ITS2 primer for HTS and PCR independent method such as metagenomic shotgun sequencing techniques.}, } @article {pmid39481332, year = {2025}, author = {Yao, M and Ren, A and Yang, X and Chen, L and Wang, X and van der Meer, W and van Loosdrecht, MCM and Liu, G and Pabst, M}, title = {Unveiling the influence of heating temperature on biofilm formation in shower hoses through multi-omics.}, journal = {Water research}, volume = {268}, number = {Pt B}, pages = {122704}, doi = {10.1016/j.watres.2024.122704}, pmid = {39481332}, issn = {1879-2448}, mesh = {*Biofilms ; Proteomics ; Heating ; Metagenomics ; Hot Temperature ; Metagenome ; Multiomics ; }, abstract = {Shower systems provide unique environments that are conducive to biofilm formation and the proliferation of pathogens. The water heating temperature is a delicate decision that can impact microbial growth, balancing safety and energy consumption. This study investigated the impact of different heating temperatures (39 °C, 45 °C, 51 °C and 58 °C) on the shower hose biofilm (exposed to a final water temperature of 39 °C) using controlled full-scale shower setups. Whole metagenome sequencing and metaproteomics were employed to unveil the microbial composition and protein expression profiles. Overall, the genes and enzymes associated with disinfectant resistance and biofilm formation appeared largely unaffected. However, metagenomic analysis revealed a sharp decline in the number of total (86,371 to 34,550) and unique genes (32,279 to 137) with the increase in hot water temperature, indicating a significant reduction of overall microbial complexity. None of the unique proteins were detected in the proteomics experiments, suggesting smaller variation among biofilms on the proteome level compared to genomic data. Furthermore, out of 43 pathogens detected by metagenomics, only 5 could actually be detected by metaproteomics. Most interestingly, our study indicates that 45 °C heating temperature may represent an optimal balance. It minimizes active biomass (ATP) and reduces the presence of pathogens while saving heating energy. Our study offered new insights into the impact of heating temperature on shower hose biofilm formation and proposed optimal parameters that ensure biosafety while conserving energy.}, } @article {pmid39481331, year = {2025}, author = {Huang, DQ and Yang, JH and Han, NN and Yang, JH and Jiang, Y and Li, ZY and Jin, RC and Fan, NS}, title = {Microbial coadaptation drives the dynamic stability of microecology in mainstream and sidestream anammox systems under exposure of progesterone.}, journal = {Water research}, volume = {268}, number = {Pt B}, pages = {122694}, doi = {10.1016/j.watres.2024.122694}, pmid = {39481331}, issn = {1879-2448}, mesh = {*Progesterone/metabolism ; *Bioreactors ; Waste Disposal, Fluid/methods ; Wastewater/chemistry ; Bacteria/metabolism ; Nitrogen/metabolism ; Biodegradation, Environmental ; }, abstract = {Microbial cooperation determines the efficacy of wastewater biological treatment, and the adaptability of microorganisms to environmental stresses varies. Recently, extensive use of hormones results in their inevitable discharge into aquatic environment. Therefore, mainstream and sidestream anammox reactors were constructed in this study to evaluate their removal performance of progesterone and nitrogen simultaneously, the adaptability of anammox consortia to progesterone stress and the corresponding regulation mechanism. Both anammox processes had the resilience to progesterone stress, with the average nitrogen removal efficiency exceeding 90 %. At the same time, progesterone removal efficiency also exceeded 70 %. In contrast, microbial community in the mainstream reactors was more susceptible to progesterone interference. The adaptation of anammox consortia mainly depended on microbial cooperation and molecular regulation. Initially, bacteria secreted more extracellular polymeric substances to detain progesterone. Biodegradation also contributed to mitigating the side effect of progesterone, which was demonstrated by the proliferation of potential degrading bacteria such as Bacillus salacetis, Bacillus wiedmannii and Rhodococcus erythropolis. In addition, the enhancement of microbial interaction intensity drove their cooperation to enhance adaptability and maintain stable performance. Combined with metagenomic and metatranscriptomic analyses, such microbial adaptability was enhanced through molecular regulations, including the energy redistribution for amino acid synthesis and alteration of key metabolic pathways. Related functional gene expressions and microbial interactions were, in turn, regulated by quorum sensing. This work verifies the feasibility of anammox process in hormone-containing wastewater treatment and provides a holistic understanding of molecular mechanism of microbial interaction and coadaptation to stress.}, } @article {pmid39479767, year = {2024}, author = {Agosti, P and Kouraki, A and Dionisi, T and Addolorato, G and D'Innocenzo, L and Sorrentino, S and De Maio, F and De Candia, E and Blanco-Miguez, A and Bazzani, D and Bonadiman, A and Tonidandel, G and Bolzan, M and Gianniello, F and Passamonti, SM and Abbattista, M and Valdes, AM and Bucciarelli, P and Peyvandi, F and Menni, C}, title = {Gut Microbiome Diversity and Composition Correlates With Time in the Therapeutic Range in Patients on Warfarin Treatment: A Pilot Study.}, journal = {Arteriosclerosis, thrombosis, and vascular biology}, volume = {44}, number = {12}, pages = {2659-2661}, pmid = {39479767}, issn = {1524-4636}, support = {212904/WT_/Wellcome Trust/United Kingdom ; MR/M016560/1/MRC_/Medical Research Council/United Kingdom ; MR/W026813/1/MRC_/Medical Research Council/United Kingdom ; MR/Y010175/1/MRC_/Medical Research Council/United Kingdom ; }, } @article {pmid39479400, year = {2024}, author = {Chen, Y and Chen, C and Chen, W and Gai, W and Zheng, Y and Guo, Y and Wang, Z and Chen, Y and Cai, Z}, title = {Clinical Application of Metagenomic Next-Generation Sequencing in Sepsis Patients with Early Antibiotic Treatment.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {4695-4706}, pmid = {39479400}, issn = {1178-6973}, abstract = {PURPOSE: This study aimed to evaluate the clinical utility of metagenomic next-generation sequencing (mNGS) in sepsis patients who received early empirical antibiotic treatment.

PATIENTS AND METHODS: A retrospective analysis was conducted on clinical data from sepsis patients diagnosed in the Emergency Intensive Care Unit (EICU) between April 2019 and May 2023. All patients underwent standard conventional microbiological testing. Patients were categorized into either the mNGS group or the control group based on whether they underwent mNGS tests. Baseline variables were matched using propensity scores.

RESULTS: Out of 461 sepsis patients screened, 130 were included after propensity matching, with 65 patients in each group. Despite prior antibiotic treatment, 57 cases (87.69%) in the mNGS group had positive mNGS results, exceeding the culture detection rate (52.31%). Besides, a higher proportion of patients in the mNGS group experienced antibiotic adjustments compared to the control group (72.31% vs 53.85%). Mortality rates were also compared based on the duration of antibiotic exposure before mNGS sampling. Patients exposed to antibiotics for less than 24 hours had a lower mortality rate compared to those exposed for over 8 days (22.22% vs 42.86%). COX multivariate analysis identified mNGS testing, underlying diseases, lymphocyte percentage, infection site (respiratory and bloodstream) as independent risk factors for mortality in sepsis patients.

CONCLUSION: With increased antibiotic exposure time, the positive rate of culture testing significantly decreased (44.44% vs 59.52% vs 35.71%, P = 0.031), whereas the positive rate of mNGS remained stable (77.78% vs 88.10% vs 92.86%, P = 0.557). mNGS demonstrated less susceptibility to antibiotic exposure. Early mNGS detection positively impacted the prognosis of sepsis patients.}, } @article {pmid39478825, year = {2024}, author = {Wang, X and Gu, D and Zhang, L and Wu, Y and Zhang, R and Li, K and Ren, H}, title = {mNGS-identified cellulitis due to quinolone-resistant Edwardsiella tarda: a case report.}, journal = {Frontiers in medicine}, volume = {11}, number = {}, pages = {1413561}, pmid = {39478825}, issn = {2296-858X}, abstract = {Edwardsiella tarda is frequently isolated from aquatic animals and environments. While human infections caused by E. tarda are rare, some extraintestinal infections can be severe. This case report describes a patient with cellulitis of the right upper extremity of unknown origin. Metagenomic next-generation sequencing (mNGS) indicated that the patient was infected with E. tarda. Antimicrobial susceptibility testing revealed that the isolate was resistant to quinolones and trimethoprim/sulfamethoxazole. The isolate, positive for four virulence genes (fimA, gadB, mukF, and sodB), was confirmed to be virulent using the Galleria mellonella larvae model. Following early pus drainage and a 9-day course of imipenem, the patient ultimately recovered. This case report aimed to illustrate the presentation, diagnosis, and management of uncommon cellulitis caused by drug-resistant, virulent E. tarda.}, } @article {pmid39478626, year = {2024}, author = {Favero, F and Re, A and Dason, MS and Gravina, T and Gagliardi, M and Mellai, M and Corazzari, M and Corà, D}, title = {Characterization of gut microbiota dynamics in an Alzheimer's disease mouse model through clade-specific marker-based analysis of shotgun metagenomic data.}, journal = {Biology direct}, volume = {19}, number = {1}, pages = {100}, pmid = {39478626}, issn = {1745-6150}, mesh = {Animals ; *Alzheimer Disease/microbiology/genetics ; *Gastrointestinal Microbiome ; Mice ; *Metagenomics/methods ; *Disease Models, Animal ; Mice, Transgenic ; Feces/microbiology ; Metagenome ; }, abstract = {Alzheimer's disease (AD) is a complex neurodegenerative disorder significantly impairing cognitive faculties, memory, and physical abilities. To characterize the modulation of the gut microbiota in an in vivo AD model, we performed shotgun metagenomics sequencing on 3xTgAD mice at key time points (i.e., 2, 6, and 12 months) of AD progression. Fecal samples from both 3xTgAD and wild-type mice were collected, DNA extracted, and sequenced. Quantitative taxon abundance assessment using MetaPhlAn 4 ensured precise microbial community representation. The analysis focused on species-level genome bins (SGBs) including both known and unknown SGBs (kSGBs and uSGBs, respectively) and also comprised higher taxonomic categories such as family-level genome bins (FGBs), class-level genome bins (CGBs), and order-level genome bins (OGBs). Our bioinformatic results pinpointed the presence of extensive gut microbial diversity in AD mice and showed that the largest proportion of AD- and aging-associated microbiome changes in 3xTgAD mice concern SGBs that belong to the Bacteroidota and Firmicutes phyla, along with a large set of uncharacterized SGBs. Our findings emphasize the need for further advanced bioinformatic studies for accurate classification and functional analysis of these elusive microbial species in relation to their potential bridging role in the gut-brain axis and AD pathogenesis.}, } @article {pmid39478600, year = {2024}, author = {Chen, YJ and Altshuler, I and Freyria, NJ and Lirette, A and Góngora, E and Greer, CW and Whyte, LG}, title = {Arctic's hidden hydrocarbon degradation microbes: investigating the effects of hydrocarbon contamination, biostimulation, and a surface washing agent on microbial communities and hydrocarbon biodegradation pathways in high-Arctic beaches.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {81}, pmid = {39478600}, issn = {2524-6372}, abstract = {BACKGROUND: Canadian Arctic summer sea ice has dramatically declined due to global warming, resulting in the rapid opening of the Northwest Passage (NWP), slated to be a major shipping route connecting the Atlantic and Pacific Oceans by 2040. This development elevates the risk of oil spills in Arctic regions, prompting growing concerns over the remediation and minimizing the impact on affected shorelines.

RESULTS: This research aims to assess the viability of nutrient and a surface washing agent addition as potential bioremediation methods for Arctic beaches. To achieve this goal, we conducted two semi-automated mesocosm experiments simulating hydrocarbon contamination in high-Arctic beach tidal sediments: a 32-day experiment at 8 °C and a 92-day experiment at 4 °C. We analyzed the effects of hydrocarbon contamination, biostimulation, and a surface washing agent on the microbial community and its functional capacity using 16S rRNA gene sequencing and metagenomics. Hydrocarbon removal rates were determined through total petroleum hydrocarbon analysis. Biostimulation is commonly considered the most effective strategy for enhancing the bioremediation process in response to oil contamination. However, our findings suggest that nutrient addition has limited effectiveness in facilitating the biodegradation process in Arctic beaches, despite its initial promotion of aliphatic hydrocarbons within a constrained timeframe. Alternatively, our study highlights the promise of a surface washing agent as a potential bioremediation approach. By implementing advanced -omics approaches, we unveiled highly proficient, unconventional hydrocarbon-degrading microorganisms such as Halioglobus and Acidimicrobiales genera.

CONCLUSIONS: Given the receding Arctic sea ice and the rising traffic in the NWP, heightened awareness and preparedness for potential oil spills are imperative. While continuously exploring optimal remediation strategies through the integration of microbial and chemical studies, a paramount consideration involves limiting traffic in the NWP and Arctic regions to prevent beach oil contamination, as cleanup in these remote areas proves exceedingly challenging and costly.}, } @article {pmid39478562, year = {2024}, author = {Lai, X and Liu, S and Miao, J and Shen, R and Wang, Z and Zhang, Z and Gong, H and Li, M and Pan, Y and Wang, Q}, title = {Eubacterium siraeum suppresses fat deposition via decreasing the tyrosine-mediated PI3K/AKT signaling pathway in high-fat diet-induced obesity.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {223}, pmid = {39478562}, issn = {2049-2618}, mesh = {Animals ; Male ; Mice ; Diet, High-Fat/adverse effects ; *Eubacterium/metabolism ; *Gastrointestinal Microbiome ; *Obesity/microbiology/metabolism ; Phosphatidylinositol 3-Kinases/metabolism ; Proto-Oncogene Proteins c-akt/metabolism ; *Signal Transduction ; Swine ; }, abstract = {BACKGROUND: Obesity in humans can lead to chronic diseases such as diabetes and cardiovascular disease. Similarly, subcutaneous fat (SCF) in pigs affects feed utilization, and excessive SCF can reduce the feed efficiency of pigs. Therefore, identifying factors that suppress fat deposition is particularly important. Numerous studies have implicated the gut microbiome in pigs' fat deposition, but research into its suppression remains scarce. The Lulai black pig (LL) is a hybrid breed derived from the Laiwu pig (LW) and the Yorkshire pig, with lower levels of SCF compared to the LW. In this study, we focused on these breeds to identify microbiota that regulate fat deposition. The key questions were: Which microbial populations reduce fat in LL pigs compared to LW pigs, and what is the underlying regulatory mechanism?

RESULTS: In this study, we identified four different microbial strains, Eubacterium siraeum, Treponema bryantii, Clostridium sp. CAG:413, and Jeotgalibaca dankookensis, prevalent in both LW and LL pigs. Blood metabolome analysis revealed 49 differential metabolites, including tanshinone IIA and royal jelly acid, known for their anti-adipogenic properties. E. siraeum was strongly correlated with these metabolites, and its genes and metabolites were enriched in pathways linked to fatty acid degradation, glycerophospholipid, and glycerolipid metabolism. In vivo mouse experiments confirmed that E. siraeum metabolites curb weight gain, reduce SCF adipocyte size, increase the number of brown adipocytes, and regulate leptin, IL-6, and insulin secretion. Finally, we found that one important pathway through which E. siraeum inhibits fat deposition is by suppressing the phosphorylation of key proteins in the PI3K/AKT signaling pathway through the reduction of tyrosine.

CONCLUSIONS: We compared LW and LL pigs using fecal metagenomics, metabolomics, and blood metabolomics, identifying E. siraeum as a strain linked to fat deposition. Oral administration experiments in mice demonstrated that E. siraeum effectively inhibits fat accumulation, primarily through the suppression of the PI3K/AKT signaling pathway, a critical regulator of lipid metabolism. These findings provide a valuable theoretical basis for improving pork quality and offer insights relevant to the study of human obesity and related chronic metabolic diseases. Video Abstract.}, } @article {pmid39478083, year = {2024}, author = {Mehlferber, EC and Arnault, G and Joshi, B and Partida-Martinez, LP and Patras, KA and Simonin, M and Koskella, B}, title = {A cross-systems primer for synthetic microbial communities.}, journal = {Nature microbiology}, volume = {9}, number = {11}, pages = {2765-2773}, pmid = {39478083}, issn = {2058-5276}, support = {U19 AI157981/AI/NIAID NIH HHS/United States ; DBI-2209151//National Science Foundation (NSF)/ ; 1838299//NSF | BIO | Division of Integrative Organismal Systems (IOS)/ ; }, mesh = {*Microbiota ; Synthetic Biology/methods ; Microbial Consortia ; Humans ; Microbial Interactions ; }, abstract = {The design and use of synthetic communities, or SynComs, is one of the most promising strategies for disentangling the complex interactions within microbial communities, and between these communities and their hosts. Compared to natural communities, these simplified consortia provide the opportunity to study ecological interactions at tractable scales, as well as facilitating reproducibility and fostering interdisciplinary science. However, the effective implementation of the SynCom approach requires several important considerations regarding the development and application of these model systems. There are also emerging ethical considerations when both designing and deploying SynComs in clinical, agricultural or environmental settings. Here we outline current best practices in developing, implementing and evaluating SynComs across different systems, including a focus on important ethical considerations for SynCom research.}, } @article {pmid39477828, year = {2024}, author = {Žilka, M and Hrabovský, M and Dušička, J and Zahradníková, E and Gahurová, D and Ščevková, J}, title = {Comparative analysis of airborne fungal spore distribution in urban and rural environments of Slovakia.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {54}, pages = {63145-63160}, pmid = {39477828}, issn = {1614-7499}, support = {1/0180/22//Vedecká Grantová Agentúra MŠVVaŠ SR a SAV/ ; }, mesh = {Slovakia ; *Spores, Fungal ; *Air Microbiology ; *Environmental Monitoring ; Cities ; Seasons ; Fungi ; Air Pollutants/analysis ; }, abstract = {Monitoring airborne fungal spores is crucial for public health and plant production since they belong to important aeroallergens and phytopathogens. Due to different land use, their concentration can differ significantly between urban and rural areas. We monitored their spectrum and quantity on two geographically close sites with a different degree of urbanisation: Bratislava City and Kaplna Village in Slovakia, located 38 km apart. We recorded the spectrum of airborne fungal spores over a year and confirmed the microscopic results by amplicon-based metagenomic analysis. The main spore season of the most frequent genera lasted over a week longer in Kaplna, but its intensity was approximately two-fold higher in Bratislava. This can be possibly connected to the microclimatic conditions of the urban area (especially wind speed and heat island effect) and the lesser use of fungicides. Cladosporium was the dominant genus on both sites, influencing the intensity most significantly. Through statistical analysis of the influence of meteorological parameters on airborne fungal spore levels, we identified a significant relationship with temperature, while the impact of other parameters varied depending on the spore type and release mechanism. Our results show the differences in airborne fungal spore levels between urban and rural areas and highlight the necessity for more monitoring stations in various environments.}, } @article {pmid39477611, year = {2024}, author = {Hua, Q and Chi, X and Wang, Y and Xu, B}, title = {Biological damage of monocrotaline on the brain and intestinal tissues of Apis mellifera.}, journal = {Pesticide biochemistry and physiology}, volume = {205}, number = {}, pages = {106158}, doi = {10.1016/j.pestbp.2024.106158}, pmid = {39477611}, issn = {1095-9939}, mesh = {Animals ; Bees/drug effects ; *Brain/drug effects/metabolism ; *Monocrotaline/toxicity ; *Intestines/drug effects ; Oxidative Stress/drug effects ; Apoptosis/drug effects ; Gastrointestinal Microbiome/drug effects ; Antioxidants/metabolism ; }, abstract = {Monocrotaline (MCT) is a toxic alkaloid present in plants, posing a threat to animals in terrestrial ecosystems. However, little is known about its potential impacts on pollinating insects. Here, we report the effects of of MCT on the brains and intestines of foraging honeybees (Apis mellifera). MCT exposure resulted in a reduction in head weight and swelling of the abdomen in honeybees. Additionally, MCT exposure caused morphological damage to the brain, characterized by decreased antioxidant capacity and increased apoptosis, along with intestinal tissue damage that was accompanied by increased antioxidant capacity and apoptosis. Moreover, MCT altered the core gut microbial community structure in honeybees and increased the expression of antimicrobial peptide (AMP) genes in the midgut. These findings indicate that exposure to MCT activates the immune response in the honeybee gut, while the brain does not exhibit an immune response but instead experiences oxidative stress. This study provides a resource for future research exploring interactions between MCT and other insects, and can help deepen our understanding of MCT's potential impacts in ecosystems.}, } @article {pmid39477107, year = {2024}, author = {Liu, L and Han, X and Hu, J and Chen, H and Zhai, Y}, title = {Jointly considering multi-medium and full-cycle to better reveal distribution and removal of antibiotic resistance genes in long-term constructed wetland.}, journal = {The Science of the total environment}, volume = {955}, number = {}, pages = {177276}, doi = {10.1016/j.scitotenv.2024.177276}, pmid = {39477107}, issn = {1879-1026}, mesh = {*Wetlands ; *Drug Resistance, Microbial/genetics ; Beijing ; Genes, Bacterial ; Anti-Bacterial Agents/analysis ; Waste Disposal, Fluid/methods ; Environmental Monitoring ; }, abstract = {Constructed wetlands (CWs) have been proven to effectively remove antibiotic resistance genes (ARGs) at different experimental scales; however, there is still a lack of researches on the removal and monitoring of ARGs during the actual operation of full-scale CWs. To fill this gap, this study selected the Annan constructed wetland in Beijing as a case study and utilized quantitative sequencing, metagenomic analysis, and other technical methods to determine characteristics of ARGs in CWs during different operating periods. Furthermore, we analysed the overall removal characteristics of ARGs in the CW during different operating periods and differences of ARG distribution in three media. The dominant ARGs in the CW were quinolone, β-lactam and tetracycline, with subtypes of tufA and fusA. ARG distributions are significantly influenced by anthropic activities and seasonal changes. Three periods of the CW had good removal effects on special ARGs, but there were differences in the removal characteristics of different types and subtypes of ARGs. The CW had removal effects on four types of ARGs (such as multidrugs), 16 types of fusidic acid, and nine types of ARGs (such as bleomycin) during the dormancy, start-up, and operation periods, respectively. Among ARG subtypes, the CW had removal effects on 37, 53, and 51 subtypes during the dormancy, start-up, and operation periods, respectively. The subtypes that were removed mainly included those containing tetracycline, efflux pump, and β-lactam, mcr-1, and mcr-5 (colistin ARGs). For individual parts of CWs, the removal effects on the total abundance of ARGs were as follows: forebay > surface flow wetland > subsurface flow wetland. These findings provide insights for optimizing the purification efficiency of CWs for ARGs.}, } @article {pmid39477048, year = {2024}, author = {Vinayagam, S and Sekar, K and Rajendran, D and Meenakshisundaram, K and Panigrahi, A and Arumugam, DK and Bhowmick, IP and Sattu, K}, title = {The genetic composition of Anopheles mosquitoes and the diverse population of gut-microbiota within the Anopheles subpictus and Anopheles vagus mosquitoes in Tamil Nadu, India.}, journal = {Acta tropica}, volume = {260}, number = {}, pages = {107439}, doi = {10.1016/j.actatropica.2024.107439}, pmid = {39477048}, issn = {1873-6254}, mesh = {Animals ; *Anopheles/microbiology/genetics ; India ; *Phylogeny ; *Gastrointestinal Microbiome ; Mosquito Vectors/microbiology/genetics ; Bacteria/classification/genetics/isolation & purification ; Sequence Analysis, DNA ; Female ; DNA, Ribosomal Spacer/genetics ; }, abstract = {In recent days, in tropical and subtropical regions, secondary vectors of Anopheles mosquitoes are becoming more important in transmitting diseases to humans as primary vectors. Various molecular techniques have separated closely related Anopheles subpictus and Anopheles vagus mosquitoes based on their diversity with other mosquito species. Despite their widespread distribution, the An. subpictus and An. vagus mosquitoes, which carry Plasmodium in their salivary glands, were not considered primary malaria vectors in India. An. vagus mosquitoes are zoophilic and physically similar to An. subpictus. We intend to identify An. subpictus and An. vagus mosquito's sister species based on their Interspaced Transcribed Region-2 (ITS2). We isolated the midgut gDNA from each mosquito and used ITS2-PCR and Sanger sequencing to characterize the mosquito species. BioEdit software aligned the sequences, and MEGA7 built a phylogenetic tree from them. According to this study, the information gathered from these mosquito samples fits the An. subpictus species A form and the An. vagus Indian form. Furthermore, gut microbiome plays an important role in providing nutrients, immunity, and food processing, whereas mosquitoes' midgut microbiota changes their hosts and spreads illnesses. So, we used the Illumina sequencer to look at the gut microbiome diversity of An. subpictus and An. vagus mosquitoes using 16S rRNA-based metagenomic sequencing. Both mosquito species had an abundant phylum of Pseudomonadota (Proteobacteria), Bacillota, Bacteroidota, and Actinomycetota in their gut microbiomes. Notably, both mosquito species had the genus Serratia in their gut. In the subpictus midgut, the genus of Haematosprillum bacteria was dominant, whereas in the vagus mosquito, the genus of Salmonella was dominant. Notably, current research has observed the Sodalis spp. Bacterial genus for the first time.}, } @article {pmid39477000, year = {2024}, author = {Zhang, Y and Cai, Z and Wu, Z and Liang, H and Li, D and Fan, S and Gao, S and Chen, S and Lu, Y and Su, C}, title = {Effects of flotation reagents with aniline aerofloat and ammonium dibutyl dithiophosphate on a constructed rapid infiltration system: Performance and microbial metabolic pathways.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {363}, number = {Pt 2}, pages = {125218}, doi = {10.1016/j.envpol.2024.125218}, pmid = {39477000}, issn = {1873-6424}, mesh = {*Waste Disposal, Fluid/methods ; *Aniline Compounds ; *Wastewater/chemistry ; *Phosphorus ; Metabolic Networks and Pathways ; Water Pollutants, Chemical/metabolism ; Biological Oxygen Demand Analysis ; Adsorption ; }, abstract = {Aniline aerofloat (AAF) and ammonium dibutyl dithiophosphate (ADD) are the key flotation reagents in mineral processing. This study investigated the performance of the constructed rapid infiltration systems with coke and red mud as adsorbents for treatment AAF and ADD wastewater. Meanwhile, the effects of AAF and ADD on the microbial metabolic pathways of the systems were unraveled. Results showed that the AAF concentration in influent was 25 mg/L, which promoted chemical oxygen demand (COD) and total phosphorus (TP) removal of the A column (coke) and B column (red mud). While the COD and TP removal of the C column (coke) and D column (red mud) were inhibited with ADD concentration increasing to 50 mg/L and 100 mg/L. The AAF reduced the binding energy of coke C-O bond by 0.9 eV, and down-regulated the C-C bond ratio by 40.72%. The dominant phyla in the columns were Pseudomonadota and Actinomycetota. The pore structure of coke was more conducive to the growth of the Pseudomonadota, while the metal composition of red mud was more conducive to the redox reaction of microorganisms. The presence of phosphofructokinase (2.7.1.11)-related genes was up-regulated in column C compared to other columns. The ADD was beneficial to the expression of norC and nosZ functional genes during nitrogen metabolism process. In contrast, phosphorus metabolism genes were more expressed in the red mud column for treatment AAF wastewater. This study reveals the potential of coke and red mud for the treatment of flotation reagents wastewater, while providing a theoretical basis for the optimal selection of filler types in the constructed rapid infiltration systems.}, } @article {pmid39476698, year = {2024}, author = {Shu, Q and Gao, H and Li, RJ and Chen, HY and Na, GS}, title = {The source and dissemination of ARGs in pristine environments: Elucidating the role of migratory birds in the Arctic.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {136272}, doi = {10.1016/j.jhazmat.2024.136272}, pmid = {39476698}, issn = {1873-3336}, mesh = {Animals ; Arctic Regions ; *Feces/microbiology ; *Animal Migration ; *Birds/genetics ; Soil Microbiology ; Genes, Bacterial ; Deer/genetics ; Geologic Sediments/microbiology ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents ; Bacteria/genetics/classification ; Environmental Monitoring ; }, abstract = {Antibiotic resistance genes (ARGs) are a class of emerging contaminants that significantly threaten public health. In this work, the profiles of ARGs and microbial communities in the soil, sediment, migratory bird, and local deer fecal samples collected from the Arctic were characterized using a metagenomic approach. The results retrieved the baseline profiles of ARGs and identified the role of migratory birds in disseminating ARGs in the Arctic. A total of 26 ARG types and 718 subtypes were determined, and 131 core ARGs were identified. All the samples were dominated by multidrug resistance genes, and some genes resistant to antibiotics commonly used in anthropogenic were also detected. Characterization of ARGs in bird fecal samples was significantly distinct from other media, with higher abundance, richness, and unique ARGs detected. Proteobacteria was the most predominant phylum in soil and fecal samples, while Thaumarchaeota was prevalent in sediment samples. Firmicutes harbored the majority of ARGs in all samples. The results of FEAST indicated that migratory birds were crucial allochthonous ARG sources in the Arctic. These significant findings shed light on the global spread of ARGs and should facilitate efforts to map baseline levels of ARGs before the era of antibiotics.}, } @article {pmid39476326, year = {2024}, author = {Khan, FZA and Ahmed, S and Powell, AM}, title = {Vaginal Microbiome and the Risk of Preterm Birth in Women Living With HIV: A Scoping Review.}, journal = {American journal of reproductive immunology (New York, N.Y. : 1989)}, volume = {92}, number = {5}, pages = {e70011}, doi = {10.1111/aji.70011}, pmid = {39476326}, issn = {1600-0897}, support = {K23AI155296//National Institute of Allergy and Infectious Diseases/ ; }, mesh = {Humans ; Female ; *Vagina/microbiology ; *HIV Infections/immunology/complications/microbiology ; *Premature Birth/microbiology ; *Microbiota ; Pregnancy ; Pregnancy Complications, Infectious/microbiology/immunology ; }, abstract = {There are sparse data on the role of the vaginal microbiome (VMB) in pregnancy among pregnant women living with HIV (PWLWH) and its association with spontaneous preterm birth (sPTB). We conducted a scoping review to assess associations between vaginal microbiota and sPTB among PWLWH. Three studies were included, representing a total of 180 PWLWH out of 652 total pregnancies. All studies used modern DNA sequencing methods (16S rRNA amplification, metagenomics, or metatranscriptomics). PWLWH had higher VMB richness and diversity compared to HIV-uninfected pregnant women and higher sPTB rates in two of three studies. A higher proportion of sPTB among PWLWH was observed in those with Lactobacillus-deficient, anaerobe-dominant vaginal microbiota. In two of three studies, higher concentrations of vaginal inflammation markers were associated with increased VMB richness and diversity. HIV status was independently associated with sPTB. It is unclear if increased vaginal microbial diversity among PWLWH or increased vaginal inflammation contributes more to PTB, but HIV does appear to alter the VMB in pregnant individuals and may also affect PTB rates in microbiome-independent pathways. Given the limited number of studies, heterogeneity in sample size, sample collection methods, and inconsistent results it is difficult to causally link HIV, VMB, inflammatory cytokines, and sPTB.}, } @article {pmid39475924, year = {2024}, author = {Liu, S and Ren, J and Li, J and Yu, D and Xu, H and He, F and Li, N and Zou, L and Cao, Z and Wen, J}, title = {Characterizing the gut microbiome of diarrheal mink under farmed conditions: A metagenomic analysis.}, journal = {PloS one}, volume = {19}, number = {10}, pages = {e0312821}, pmid = {39475924}, issn = {1932-6203}, mesh = {Animals ; *Mink/microbiology ; *Gastrointestinal Microbiome/genetics ; *Diarrhea/microbiology/veterinary ; *Metagenomics/methods ; Metagenome ; Bacteria/genetics/classification/isolation & purification ; Bacteroidetes/genetics/isolation & purification ; Farms ; Feces/microbiology ; }, abstract = {This study aimed to comprehensively characterize the gut microbiota in diarrheal mink. We conducted Shotgun metagenomic sequencing on samples from five groups of diarrheal mink and five groups of healthy mink. The microbiota α-diversity and Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology did not show significant differences between the groups. However, significant differences were observed in microbiota β-diversity and the function of carbohydrate-active enzymes (CAZymes) between diarrheal and healthy mink. Specifically, The relative abundance of Firmicutes was lower, whereas that of Bacteroidetes was higher in diarrheal mink. Fusobacteria were enriched as invasive bacteria in the gut of diarrheal mink compared with healthy mink. In addition, Escherichia albertii was identified as a new bacterium in diarrheal mink. Regarding functions, nicotinate and nicotinamide metabolism and glycoside hydrolases 2 (GH2) family were the enhanced KEGG orthology and CAZymes in diarrheal mink. Furthermore, the diversity and number of antibiotic-resistant genes were significantly higher in the diarrheal mink group than in the healthy group. These findings enhance our understanding of the gut microbiota of adult mink and may lead to new approaches to the diagnosis and treatment of mink diarrhea.}, } @article {pmid39475341, year = {2024}, author = {Sánchez-Terrón, G and Martínez, R and Freire, MJ and Molina-Infante, J and Estévez, M}, title = {Gastrointestinal fate of proteins from commercial plant-based meat analogs: Silent passage through the stomach, oxidative stress in intestine, and gut dysbiosis in Wistar rats.}, journal = {Journal of food science}, volume = {89}, number = {12}, pages = {10294-10316}, pmid = {39475341}, issn = {1750-3841}, support = {//Ministerio de Ciencia e Innovación/ ; //Junta de Extremadura/ ; //Junta de Andalucía/ ; }, mesh = {Animals ; *Rats, Wistar ; Rats ; *Oxidative Stress ; *Gastrointestinal Microbiome/physiology ; Male ; *Dysbiosis ; Gastrointestinal Tract/metabolism/microbiology ; Dietary Proteins/metabolism ; Stomach/microbiology ; Digestion ; Meat Substitutes ; }, abstract = {Plant-based meat analogs (PBMAs) are common ultra-processed foods (UPFs) included in the vegan/vegetarian diets as presumed healthy alternatives to meat and meat products. However, such health claims need to be supported by scientific evidence. To gain further insight into this topic, two commercial UPFs typically sold as meat analogs, namely, seitan (S) and tofu (T), were included in a cereal-based chow and provided to Wistar rats for 10 weeks. A group of animals had, simultaneously, an isocaloric and isoprotein experimental diet formulated with cooked beef (B). In all cases, experimental chows (∼4 kcal/g feed) had their basal protein concentration increased from 14% to 30% using proteins from S, T, or B. Upon slaughter, in vivo protein digestibility was assessed, and the entire gastrointestinal tract (digests and tissues) was analyzed for markers of oxidative stress and untargeted metabolomics. Metagenomics was also applied to assess the variation of microbiota composition as affected by dietary protein. Diets based on PBMAs showed lower protein digestibility than those containing meat and promoted an intense luminal glycoxidative stress and an inflammatory intestinal response. The fermentation of undigested oxidized proteins from T in the colon of Wistar rats likely led to formation of mutagenic metabolites such as p-cresol. The presence of these compounds in the animal models raises concerns about the potential effects of full replacement of meat by certain PBMAs in the diet. Therefore, future research might target on translational human studies to shed light on these findings.}, } @article {pmid39475308, year = {2024}, author = {Schrago, CG and Mello, B}, title = {Challenges in Assembling the Dated Tree of Life.}, journal = {Genome biology and evolution}, volume = {16}, number = {10}, pages = {}, pmid = {39475308}, issn = {1759-6653}, mesh = {*Phylogeny ; Evolution, Molecular ; Gene Transfer, Horizontal ; }, abstract = {The assembly of a comprehensive and dated Tree of Life (ToL) remains one of the most formidable challenges in evolutionary biology. The complexity of life's history, involving both vertical and horizontal transmission of genetic information, defies its representation by a simple bifurcating phylogeny. With the advent of genome and metagenome sequencing, vast amounts of data have become available. However, employing this information for phylogeny and divergence time inference has introduced significant theoretical and computational hurdles. This perspective addresses some key methodological challenges in assembling the dated ToL, namely, the identification and classification of homologous genes, accounting for gene tree-species tree mismatch due to population-level processes along with duplication, loss, and horizontal gene transfer, and the accurate dating of evolutionary events. Ultimately, the success of this endeavor requires new approaches that integrate knowledge databases with optimized phylogenetic algorithms capable of managing complex evolutionary models.}, } @article {pmid39475249, year = {2024}, author = {Liang, Y and Huang, Z and Fan, S and Li, C and Huang, L and Huang, C and Hutchins, AP and Fang, C and Zhang, X}, title = {Highlight signatures of vaginal microbiota and metabolome contributed to the occurrence and recurrence of vulvovaginal candidiasis.}, journal = {Microbiology spectrum}, volume = {12}, number = {12}, pages = {e0152124}, pmid = {39475249}, issn = {2165-0497}, abstract = {UNLABELLED: Vulvovaginal candidiasis (VVC) is a common vaginal infectious disease caused by Candida. The high recurrence rate of VVC is a great clinical challenge, with recurrent VVC (RVVC) defined as four or more episodes within a year. In this study, we recruited 31 RVVC patients, 28 VVC patients, and 29 healthy women. Vaginal samples were collected for metagenomic and metabolic analysis. RVVC and VVC groups presented similar clinical symptoms, with only a significantly increased incidence of swelling in the VVC group. Vaginal microbiota in VVC/RVVC exhibited a decreased abundance of Lactobacillus and increased bacterial vaginosis-associated bacteria, such as Gardnerella, Prevotella, and Atopobium. Notably, Lactobacillus iners was higher in RVVC, suggesting not all Lactobacillus species are protective. Healthy women showed lower overall microbiota diversity, emphasizing single-species dominance for stability. Glycogen metabolism pathways were enriched in RVVC/VVC, and were correlated with Atopobium vaginae, Prevotella bivia, and Lactobacillus jensenii. Peptidoglycan synthesis pathways, associated with P. bivia, were enriched, with the substrate L-glutamate elevated in RVVC, possibly promoted by L. iners. These findings shed light on potential therapeutic targets for recurrent VVC, contributing to the understanding of the intricate interplay between the metabolism of vaginal microbiome and disease.

IMPORTANCE: This study enhances our knowledge of the vaginal microbiota dynamics and the role of associated metabolites in individuals with vulvovaginal candidiasis (VVC) and recurrent vulvovaginal candidiasis through shotgun sequencing and multi-omics analysis. The relationship between metabolites and vaginal microbiota and disease state was revealed. The accumulation of L-glutamate generated in glycogen metabolism, which is governed by Lactobacillus iners or bacterial vaginosis-associated bacteria, may contribute to the incidence and recurrence of VVC. Such insights have the potential to impact the treatment and prevention strategies for these common yet distressing conditions, potentially leading to targeted therapies and improved patient outcomes.}, } @article {pmid39475247, year = {2024}, author = {Xu, Z and Yeoh, YK and Tun, HM and Fei, N and Zhang, J and Morrison, M and Kamm, MA and Yu, J and Chan, FKL and Ng, SC}, title = {Variation in the metagenomic analysis of fecal microbiome composition calls for a standardized operating approach.}, journal = {Microbiology spectrum}, volume = {12}, number = {12}, pages = {e0151624}, pmid = {39475247}, issn = {2165-0497}, abstract = {The reproducibility in microbiome studies is limited due to the lack of one gold-standard operating procedure. The aim of this study was to examine the impact of protocol variations on microbiome composition using metagenomic data sets from a single center. We assessed the variation in a data set consisted of 2,722 subjects, including 9 subcohorts harboring healthy subjects and patients with various disorders, such as inflammatory bowel disease, colorectal cancer, and type 2 diabetes. Two different DNA extraction kits, with or without lyticase, and two sample storage methods were compared. Our results indicated that DNA extraction had the largest impact on gut microbiota diversity among all host factors and sample operating procedures. Healthy subjects matched by age, body mass index, and sample operating methods exhibited reduced, yet significant differences (PERMANOVA, P < 0.05) in gut microbiota composition across studies. The variations contributed by DNA extraction were primarily driven by different recovery efficiency of gram-positive bacteria, e.g., phyla Firmicutes and Actinobacteria. This was further confirmed by a parallel comparison of fecal samples from five healthy subjects and a standard mock community. In addition, the DNA extraction method influenced DNA biomass, quality, and the detection of specific lineage-associated diseases. Sample operating approach and batch effects should be considered for cohorts with large sample size or longitudinal cohorts to ensure that source data were appropriately generated and analyzed. Comparison between samples processed with inconsistent methods should be dealt with caution. This study will promote the establishment of a sample operating standard to enhance our understanding of microbiome and translating in clinical practice.IMPORTANCEThe reproducibility of human gut microbiome studies has been suboptimal across cohorts and study design choices. One possible reason for the disagreement is the introduction of systemic biases due to differences in methodologies. In our study, we utilized microbial metagenomic data sets from 2,722 fecal samples generated from a single research center to examine the extent to which sample storage and DNA extraction influence the quantification of microbial composition and compared this variable with other sources of technical and biological variation. Our research highlights the impact of DNA extraction methods when analyzing microbiome data and suggests that the microbiome profile may be influenced by differences in the extraction efficiency of bacterial species. With metagenomics sequencing being increasingly used in clinical biology, our findings provide insight into the challenges using metagenomics sequencing in clinical diagnostics, where the detection of certain species and its abundance relative to a "healthy reference" is key.}, } @article {pmid39474927, year = {2024}, author = {Milesi, VP}, title = {Redox Gradient Shapes the Chemical Composition of Peatland Microbial Communities.}, journal = {Geobiology}, volume = {22}, number = {6}, pages = {e70001}, doi = {10.1111/gbi.70001}, pmid = {39474927}, issn = {1472-4669}, support = {//Agence Nationale de la Recherche/ ; }, mesh = {*Oxidation-Reduction ; *Soil Microbiology ; *Soil/chemistry ; *Microbiota ; Bacteria/classification/genetics/metabolism ; Carbon/metabolism/analysis ; }, abstract = {The response of soil carbon to climate change and anthropogenic forcing depends on the relationship between the physicochemical variables of the environment and microbial communities. In anoxic soils that store large amounts of organic carbon, it can be hypothesized that the low amount of catabolic energy available leads microbial organisms to minimize the energy costs of biosynthesis, which may shape the composition of microbial communities. To test this hypothesis, thermodynamic modeling was used to assess the link between redox gradients in the ombrotrophic peatland of the Marcell Experimental Forest (Minnesota, USA) and the chemical and taxonomic composition of microbial communities. The average amino acid composition of community-level proteins, called hereafter model proteins, was calculated from shotgun metagenomic sequencing. The carbon oxidation state of model proteins decreases linearly from -0.14 at 10 cm depth to -0.17 at 150 cm depth. Calculating equilibrium activities of model proteins for a wide range of chemical conditions allows identification of the redox potential of maximum chemical activity. Consistent with redox measurements across peat soils, this model Eh decreases logarithmically from an average value of 300 mV at 10 cm depth, close to the stability domain of goethite relative to Fe[2+], to an average value of -200 mV at 150 cm, within the stability domain of CH4 relative to CO2. The correlation identified between the taxonomic abundance and the carbon oxidation state of model proteins enables predicting the evolution of taxonomic abundance as a function of model Eh. The model taxonomic abundance is consistent with the measured gene and taxonomic abundance, which evolves from aerobic bacteria at the surface including Acidobacteria, Proteobacteria, and Verrumicrobia, to anaerobes at depth dominated by Crenarchaeota. These results indicate that the thermodynamic forcing imposed by redox gradient across peat soils shapes both the chemical and taxonomic composition of microbial communities. By providing a mechanistic understanding of the relationship between microbial community and environmental conditions, this work sheds new light on the mechanisms that govern soil microbial life and opens up prospects for predicting geochemical and microbial evolution in changing environments.}, } @article {pmid39474102, year = {2024}, author = {Barbieri, G and Gigliucci, F and Brambilla, G and Morabito, S}, title = {Cross-Cutting Approach for the Characterization of Microbial Emerging Hazards in Agriculture Settings from Circular Economy-Driven Wastewater Streams.}, journal = {Environment & health (Washington, D.C.)}, volume = {2}, number = {2}, pages = {68-75}, pmid = {39474102}, issn = {2833-8278}, abstract = {The recycling of biowaste from municipal wastewater treatment plants (WWTPs) in agriculture represents a circular economy-driven source of water and nutrients to support food system sustainability. However, biowaste may represent the source of emerging hazards of anthropogenic and animal origin that can transfer from agricultural soils to related food production, posing a risk to consumers' health, as in the case of outbreaks due to the consumption of ready-to-eat leafy vegetables contaminated with pathogenic E. coli. From this perspective, we propose a combined strategy based on both classical methods and culture-independent metagenomics approaches to identify microbial hazards relevant to foodborne diseases in WWTP-related biowastes. The virulence genes targeted by real-time PCR, performed before and after the enrichment of the raw samples, may represent a proxy for the viability of pathogens, the presence of which is then confirmed via classical microbiological methods. Bioinformatics analysis of shotgun metagenomic sequences could assess the presence of genes associated with resistance to specific antimicrobials followed by phenotypic confirmation via cultivation of the raw samples in the presence of the predicted molecules. Bacterial 16S rDNA analysis supports biowaste traceability based on their taxonomic composition. This strategy would support a "One Health" Action based on a cross-cutting assessment of emerging food-borne risks along the food chain.}, } @article {pmid39474048, year = {2023}, author = {Wu, J and Zhang, S and Chen, Y and Zhao, J and Prosun, T and O'Brien, JW and Mueller, JF and Tscharke, BJ and Coin, LJM and Luby, SP and Hai, FI and Buchanan, T and Jiang, G}, title = {Associations between Wastewater Microbiome and Population Smoking Rate Identified Using Wastewater-Based Epidemiology.}, journal = {Environment & health (Washington, D.C.)}, volume = {1}, number = {6}, pages = {394-404}, pmid = {39474048}, issn = {2833-8278}, abstract = {Tobacco use is known to cause health damage, partly by changing the mouth, respiratory tract, and gut-related microbiomes. This study aims to identify the associations between the human microbiome detected in domestic wastewater and the population smoking rate. Metagenomic sequencing and a biomarker discovery algorithm were employed to identify microorganisms as potential microbial biomarkers of smoking through wastewater-based epidemiology. Wastewater samples were collected from selected catchments with low and high smoking rates, i.e., 11.2 ± 1.5% and 17.0 ± 1.6%, respectively. Using the linear discriminant analysis effect size (LEfSe) method, Neisseria, Desulfovibrio, Megamonas, Blautia, Fusicatenibacter, Granulicatella and Enterococcus were suggested as potential biomarker microorganisms. A higher abundance of pathogens, including Neisseria, Eikenella and Haemophilus, was associated with the high smoking rate, likely because of their colonization in smoking-disturbed human guts. The identified potential microbial biomarkers reflect the change of the human gut microbiome due to the long-term smoking behavior. The metagenomic analysis also indicates that smoking upregulates microbial gene expression of genetic information processing, environmental information processing, and cell wall peptidoglycan cleavage, while it downregulates amino acid, lipid, and galactose metabolisms. The findings demonstrate the potential of microbial biomarkers for the surveillance of smoking through a wastewater-based epidemiology approach.}, } @article {pmid39473909, year = {2024}, author = {Zhao, M and Yang, C and Zhu, L and Guo, X and Ma, H and Luo, Y and Wang, Q and Chen, J}, title = {Multiomics Analysis Reveals Significant Disparities in the Oral Microbiota and Metabolites Between Pregnant Women with and without Periodontitis.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {4665-4683}, pmid = {39473909}, issn = {1178-6973}, abstract = {INTRODUCTION: Our study investigated the disparities and correlations between oral microbiota and metabolites in pregnant patients with and without periodontitis.

METHODS: Subgingival plaque samples from all subjects were collected for shotgun metagenomic sequencing and broad-target metabolomics analysis.

RESULTS: Forty pathogens, including Porphyromonas gingivalis, Fusobacterium nucleatum, Eubacterium saphenum, Gemella morbillorum, Tannerella forsythia, Streptococcus anginosus group, Selenomonas sputigena etc, were significantly enriched in pregnant patients with periodontitis (PPP). Conversely, symbiotic species such as Morococcus cerebrosus, Streptococcus vestibularis, S. salivarius, S. mitis, and S. pneumoniae were significantly more abundant in healthy controls (HCs). A total of 87 predicted functional modules (PFMs) exhibited significant differences between the two groups; eight PFMs showed high enrichment in PPP with involvement of PPP-enriched species within these pathways. The remaining 79 PFMs encompassing ribonucleotide biosynthesis, carbohydrate, and amino acid metabolism were highly abundant in HCs. For oral microbial metabolome, a total of 105 metabolites related to 150 KEGG pathways displayed significant differences between the two groups. Pathways such as pyruvate metabolism, folate biosynthesis, vascular smooth muscle contraction, and AMPK/mTOR signaling pathway along with their associated metabolites were found to be enriched in PPP, while carbohydrate metabolism predominated among HCs. Spearman's rank correlation analysis revealed significant positive associations between species enriched in PPP and metabolites enriched in PPP, but significant negative associations between species enriched in PPP and metabolites enriched in HCs.

DISCUSSION: Our findings provide potential biomarkers for distinguishing periodontitis during pregnancy while offering valuable insights into mechanisms exploration and clinical intervention.}, } @article {pmid39473523, year = {2024}, author = {Dharnidharka, VR and Wylie, KM and Wylie, TN and Ruzinova, MB and Goss, CW and Storch, GA and Mehta-Shah, N and Byers, D and Walther, L and Jaza, L and Gu, H and Agarwal, M and Green, M and Moore, E and Swerdlow, SH and Silveira, F and Marks, LJ and Gratzinger, D and Bagg, A and Law, SC and Gandhi, M}, title = {The Post-transplant Lymphoproliferative Disorders-Metagenomic Shotgun Microbial Sequencing (PTLD-MSMS) Study Methods and Protocol.}, journal = {Transplantation direct}, volume = {10}, number = {11}, pages = {e1723}, pmid = {39473523}, issn = {2373-8731}, support = {R01 AI142135/AI/NIAID NIH HHS/United States ; }, abstract = {Post-transplant lymphoproliferative disorders (PTLDs) remain a feared complication of transplantation, with significant morbidity and mortality. The oncogenic Epstein-Barr virus (EBV) is a key pathogenic driver in 50%-80% of cases. Numerous prognostic indices, comprising multiple clinical, epidemiological and tumor characteristics, including EBV tumor positivity, do not consistently associate with worse patient survival, suggesting a potential role for EBV genome variants in determining outcome. However, the precision medicine tools for determining if a viral genome variant is pathogenic are very limited compared with human genome variants. Further, targeted studies have not implicated a specific viral etiological agent in EBV-negative PTLD. Using novel cutting-edge technologies, we are extracting viral nucleic acids from formalin-fixed, paraffin-embedded archived, or frozen PTLD tissues or plasma, to test for all vertebrate viruses simultaneously in an unbiased fashion, using metagenomic shotgun sequencing (MSS). We are collecting such samples from multiple transplant centers to address the following specific aims and close the following knowledge gaps: (1) Validate our novel observation that PTLD tissue positivity by MSS for anellovirus (and confirmed by PCR) serves as a biomarker for higher transplant recipient mortality after the diagnosis of PTLD; (2) determine the role of other oncogenic viruses in EBV-negative PTLD by unbiased MSS of multiple viral groupings, confirmed by other techniques; and (3) develop the necessary computational, algorithmic and software analytic tools required to determine association of EBV genome variants with worse presentations or outcomes in PTLD. Study completion will contribute to better patient care and may provide avenues for novel therapies.}, } @article {pmid39473051, year = {2024}, author = {Wang, Y and Chen, J and Ni, Y and Liu, Y and Gao, X and Tse, MA and Panagiotou, G and Xu, A}, title = {Exercise-changed gut mycobiome as a potential contributor to metabolic benefits in diabetes prevention: an integrative multi-omics study.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2416928}, pmid = {39473051}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; *Exercise ; Middle Aged ; *Mycobiome ; *Fungi/classification/genetics/isolation & purification ; *Feces/microbiology ; Proteomics ; Prediabetic State/microbiology/metabolism ; Metabolomics ; Bacteria/classification/isolation & purification/genetics/metabolism ; Adult ; Diabetes Mellitus, Type 2/microbiology/prevention & control ; Metagenomics ; Multiomics ; }, abstract = {BACKGROUND: The importance of gut microbes in mediating the benefits of lifestyle intervention is increasingly recognized. However, compared to the bacterial microbiome, the role of intestinal fungi in exercise remains elusive. With our established randomized controlled trial of exercise intervention in Chinese males with prediabetes (n = 39, ClinicalTrials.gov:NCT03240978), we investigated the dynamics of human gut mycobiome and further interrogated their associations with exercise-elicited outcomes using multi-omics approaches.

METHODS: Clinical variations and biological samples were collected before and after training. Fecal fungal composition was analyzed using the internal transcribed spacer 2 (ITS2) sequencing and integrated with paired shotgun metagenomics, untargeted metabolomics, and Olink proteomics.

RESULTS: Twelve weeks of exercise training profoundly promoted fungal ecological diversity and intrakingdom connection. We further identified exercise-responsive genera with potential metabolic benefits, including Verticillium, Sarocladium, and Ceratocystis. Using multi-omics approaches, we elucidated comprehensive associations between changes in gut mycobiome and exercise-shaped metabolic phenotypes, bacterial microbiome, and circulating metabolomics and proteomics profiles. Furthermore, a machine-learning algorithm built using baseline microbial signatures and clinical characteristics predicted exercise responsiveness in improvements of insulin sensitivity, with an area under the receiver operating characteristic (AUROC) of 0.91 (95% CI: 0.85-0.97) in the discovery cohort and of 0.79 (95% CI: 0.74-0.86) in the independent validation cohort (n = 30).

CONCLUSIONS: Our findings suggest that intense exercise training significantly remodels the human fungal microbiome composition. Changes in gut fungal composition are associated with the metabolic benefits of exercise, indicating gut mycobiome is a possible molecular transducer of exercise. Moreover, baseline gut fungal signatures predict exercise responsiveness for diabetes prevention, highlighting that targeting the gut mycobiome emerges as a prospective strategy in tailoring personalized training for diabetes prevention.}, } @article {pmid39472959, year = {2024}, author = {Martin-Cuadrado, AB and Rubio-Portillo, E and Rosselló, F and Antón, J}, title = {The coral Oculina patagonica holobiont and its response to confinement, temperature, and Vibrio infections.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {222}, pmid = {39472959}, issn = {2049-2618}, mesh = {*Anthozoa/microbiology ; Animals ; *Coral Reefs ; *Microbiota ; *Vibrio/genetics/classification/physiology/isolation & purification ; Symbiosis ; Temperature ; Bacteria/classification/genetics/isolation & purification ; Metagenomics ; Rhodobacteraceae/genetics/classification/isolation & purification/physiology ; Fungi/classification/genetics/isolation & purification ; Vibrionaceae/genetics/classification/isolation & purification ; Vibrio Infections/microbiology ; Climate Change ; }, abstract = {BACKGROUND: Extensive research on the diversity and functional roles of the microorganisms associated with reef-building corals has been promoted as a consequence of the rapid global decline of coral reefs attributed to climate change. Several studies have highlighted the importance of coral-associated algae (Symbiodinium) and bacteria and their potential roles in promoting coral host fitness and survival. However, the complex coral holobiont extends beyond these components to encompass other entities such as protists, fungi, and viruses. While each constituent has been individually investigated in corals, a comprehensive understanding of their collective roles is imperative for a holistic comprehension of coral health and resilience.

RESULTS: The metagenomic analysis of the microbiome of the coral Oculina patagonica has revealed that fungi of the genera Aspergillus, Fusarium, and Rhizofagus together with the prokaryotic genera Streptomyces, Pseudomonas, and Bacillus were abundant members of the coral holobiont. This study also assessed changes in microeukaryotic, prokaryotic, and viral communities under three stress conditions: aquaria confinement, heat stress, and Vibrio infections. In general, stress conditions led to an increase in Rhodobacteraceae, Flavobacteraceae, and Vibrionaceae families, accompanied by a decrease in Streptomycetaceae. Concurrently, there was a significant decline in both the abundance and richness of microeukaryotic species and a reduction in genes associated with antimicrobial compound production by the coral itself, as well as by Symbiodinium and fungi.

CONCLUSION: Our findings suggest that the interplay between microeukaryotic and prokaryotic components of the coral holobiont may be disrupted by stress conditions, such as confinement, increase of seawater temperature, or Vibrio infection, leading to a dysbiosis in the global microbial community that may increase coral susceptibility to diseases. Further, microeukaryotic community seems to exert influence on the prokaryotic community dynamics, possibly through predation or the production of secondary metabolites with anti-bacterial activity. Video Abstract.}, } @article {pmid39472637, year = {2024}, author = {Zhu, W and Chen, J and Sun, H and Lu, K and Liu, Y and Liu, L and Niu, G}, title = {Identification of a newly discovered virus from Culex and Armigeres mosquitoes in China.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {25935}, pmid = {39472637}, issn = {2045-2322}, support = {2022KJ263//Development Program for Youth Innovation Team in Colleges and Universities of Shandong Province/ ; 82104053//National Natural Science Foundation of China/ ; 2020GX014//Science and Technology Development Program in Weifang/ ; }, mesh = {Animals ; China ; *Phylogeny ; *Culex/virology ; *Genome, Viral ; Culicidae/virology ; Metagenomics/methods ; }, abstract = {Mosquito associated virus have always been a significant threat to global health. Metagenomics offers a straightforward and quantitative means to acquire the information of novel virus and has greatly enriched the content of mosquito associated virus databases. During an entomological surveillance for arthropod-borne viruses in China, we identified a previously unrecognized virus from mosquitoes, temporarily named Huajieling virus. In this study, a total of 3,960 mosquitoes were collected and then divided into 91 pools, according to location and species. QRT-PCR and nested PCR were performed to confirm the presence of Huajieling virus. Its genomic features and phylogenetic relationships were further analyzed. Our results showed that Huajieling virus was detected in 7 of the 91 mosquito pools and that the minimum infection rate (MIR) was 0.18% (7/3,960). One complete genome sequence and 2 viral partial sequences were obtained from the Huajieling virus-positive pools. Pairwise distances analysis indicated that these amplified sequences shared high nucleotide identity. Phylogenetic analysis demonstrated that Huajieling virus is most closely related to Wufeng shrew picorna-like virus 43, which belonging to Picornavirales. Further analyses indicated that Huajieling virus is a new member of unclassified Picornavirales, and is intermediate between the family Caliciviridae and Secoviridae in taxonomic status.}, } @article {pmid39472628, year = {2024}, author = {Yuan, L and Zhu, XY and Lai, LM and Chen, Q and Liu, Y and Zhao, R}, title = {Author Correction: Clinical application and evaluation of metagenomic next-generation sequencing in pathogen detection for suspected central nervous system infections.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {25984}, doi = {10.1038/s41598-024-76648-8}, pmid = {39472628}, issn = {2045-2322}, } @article {pmid39472593, year = {2024}, author = {Schmitz, D and Zwagemaker, F and Nooij, S and Janssens, TKS and Cremer, J and Verhagen, R and Vennema, H and Kroneman, A and Koopmans, MPG and Laros, JFJ and de Graaf, M}, title = {Accessible viral metagenomics for public health and clinical domains with Jovian.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {26018}, pmid = {39472593}, issn = {2045-2322}, support = {643476//European Union's Horizon H2020 grants COMPARE/ ; 874735//European Union's Horizon H2020 grants VEO/ ; }, mesh = {*Metagenomics/methods ; Humans ; *Public Health ; Software ; High-Throughput Nucleotide Sequencing/methods ; Viruses/genetics/classification/isolation & purification ; Computational Biology/methods ; }, abstract = {The integration of next-generation sequencing into clinical diagnostics and surveillance initiatives is impeded by the lack of data analysis pipelines that align with privacy legislation and laboratory certification protocols. To address these challenges, we developed Jovian, an open-source, virus-focused, metagenomic analysis workflow for Illumina data. Jovian generates scaffolds enriched with pertinent annotations, including taxonomic classification, combined with metrics needed for quality assessment (coverage depth, average GC content, localization of open reading frames, minority single nucleotide polymorphisms), and incorporates host and disease metadata. Interactive web-based reports with an audit trail are generated. Jovian was employed on four systems, hosted by three institutes, utilizing grid-computers, a high-performance compute singular server, and a Windows10 laptop. All systems yielded identical results with matching MD5sums. Comparison with a commercial online reference tool using viral gastroenteritis samples confirmed the identification of the same pathogens. Jovian provides comparable results to a commercially available online reference tool and generates identical results at different institutes with different IT architectures, proving it is portable and reproducible. Jovian addresses bottlenecks in the deployment of metagenomics within public health and clinical laboratories and has the potential to enhance the breadth of surveillance and testing programs, thereby fostering more effective public health interventions.}, } @article {pmid39472002, year = {2024}, author = {Yang, B and Zhang, C and Guan, C and Feng, X and Yan, D and Zhang, Z and Qin, Y and Xiong, S and Zhang, W and Cai, X and Hu, L}, title = {Analysis of the composition and function of rhizosphere microbial communities in plants with tobacco bacterial wilt disease and healthy plants.}, journal = {Microbiology spectrum}, volume = {12}, number = {12}, pages = {e0055924}, pmid = {39472002}, issn = {2165-0497}, abstract = {To explore the factors influencing the occurrence of bacterial wilt, the differences in the physicochemical properties, microbial community composition and function between rhizosphere soil of tobacco plants with bacterial wilt and healthy plants in the tobacco planting area of Fuzhou City, Jiangxi Province were analyzed and compared. The results showed that the rhizosphere soil of diseased tobacco exhibited significantly reduced levels of exchangeable potassium, water-soluble potassium, nitrate nitrogen, total nitrogen and pH, in comparison to the rhizosphere soil of healthy plants. Conversely, the available phosphorus content of the rhizosphere soil of diseased tobacco was significantly increased. The amount of Ralstonia solanacearum in soil was negatively correlated with pH, nitrate nitrogen and total nitrogen, and positively correlated with exchangeable potassium and water-soluble potassium. A total of 43 genera were significantly different between the two groups of rhizosphere soil, of which 24 genera were enriched in the rhizosphere of healthy plants, including Ideonella, Rhizophagus, Rhizobacter, Altererythrobacter and Ignavibacterium associated with plant disease resistance, Thermodesulfovibrio, Syntrophorhabdus, Syntrophus, Chlorobium, Hydrogenophaga and Limnohabitans associated with soil sulfur metabolism, as well as Ignavibacterium, Ideonella, Derxia and Azohydromonas associated with soil nitrogen cycling. Kyoto Encyclopedia of Genes and Genomes functional analysis of the unigenes obtained by metagenomic sequencing also showed that the differential unigenes were significantly enriched in the sulfur metabolism pathway. In addition, the rhizosphere soil of diseased tobacco plants exhibited a higher abundance of antibiotic-producing actinomycetes and an increased load of antibiotic resistance genes compared to that of healthy plants. In general, lower pH value, less content of nitrate nitrogen and total nitrogen, and more content of exchangeable potassium and water-soluble potassium could contribute to onset of bacterial wilt. Twenty-four genera, including Ideonella and Rhizophagus, may construct a healthy microecological network in the rhizosphere of tobacco plants. All these factors may interact with each other to control the development of bacterial wilt. This complicated interaction network needs to be explored further.IMPORTANCEPrevious studies have mainly focused on the differences in microbial species composition between healthy and diseased soils, but the differences in microbial community functions between two types of soil have not been well characterized. In this study, soil samples in diseased and healthy plant rhizospheres were collected for physicochemical property testing and metagenomic sequencing. We focused on analyzing the differences in physicochemical properties and microbial community functions between these soils, as well as the correlation between these factors and pathogen content. The results of this study provide a theoretical basis for further understanding the occurrence of tobacco bacterial wilt in the field.}, } @article {pmid39471749, year = {2024}, author = {Liu, X and Lu, B and Tang, H and Jia, X and Zhou, Q and Zeng, Y and Gao, X and Chen, M and Xu, Y and Wang, M and Tan, B and Li, J}, title = {Gut microbiome metabolites, molecular mimicry, and species-level variation drive long-term efficacy and adverse event outcomes in lung cancer survivors.}, journal = {EBioMedicine}, volume = {109}, number = {}, pages = {105427}, pmid = {39471749}, issn = {2352-3964}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Lung Neoplasms/drug therapy/immunology/pathology ; Male ; Female ; Middle Aged ; Aged ; Cancer Survivors ; Metabolome ; Metagenome ; Metagenomics/methods ; Immune Checkpoint Inhibitors/therapeutic use/adverse effects ; Treatment Outcome ; }, abstract = {BACKGROUND: The influence of the gut microbiota on long-term immune checkpoint inhibitor (ICI) efficacy and immune-related adverse events (irAEs) is poorly understood, as are the underlying mechanisms.

METHODS: We performed gut metagenome and metabolome sequencing of gut microbiotas from patients with lung cancer initially treated with anti-PD-1/PD-L1 therapy and explored the underlying mechanisms mediating long-term (median follow-up 1167 days) ICI responses and immune-related adverse events (irAEs). Results were validated in external, publicly-available datasets (Routy, Lee, and McCulloch cohorts).

FINDINGS: The ICI benefit group was enriched for propionate (P = 0.01) and butyrate/isobutyrate (P = 0.12) compared with the resistance group, which was validated in the McCulloch cohort (propionate P < 0.001, butyrate/isobutyrate P = 0.002). The acetyl-CoA pathway (P = 0.02) in beneficial species mainly mediated butyrate production. Microbiota sequences from irAE patients aligned with antigenic epitopes found in autoimmune diseases. Microbiotas of responsive patients contained more lung cancer-related antigens (P = 0.07), which was validated in the Routy cohort (P = 0.02). Escherichia coli and SGB15342 of Faecalibacterium prausnitzii showed strain-level variations corresponding to clinical phenotypes. Metabolome validation reviewed more abundant acetic acid (P = 0.03), propionic acid (P = 0.09), and butyric acid (P = 0.02) in the benefit group than the resistance group, and patients with higher acetic, propionic, and butyric acid levels had a longer progression-free survival and lower risk of tumor progression after adjusting for histopathological subtype and stage (P < 0.05).

INTERPRETATION: Long-term ICI survivors have coevolved a compact microbial community with high butyrate production, and molecular mimicry of autoimmune and tumor antigens by microbiota contribute to outcomes. These results not only characterize the gut microbiotas of patients who benefit long term from ICIs but pave the way for "smart" fecal microbiota transplantation. Registered in the Chinese Clinical Trial Registry (ChiCTR2000032088).

FUNDING: This work was supported by Beijing Natural Science Foundation (7232110), National High Level Hospital Clinical Research Funding (2022-PUMCH-A-072, 2023-PUMCH-C-054), CAMS Innovation Fund for Medical Sciences (CIFMS) (2022-I2M-C&T-B-010).}, } @article {pmid39471530, year = {2025}, author = {Qi, H and Lv, J and Liao, J and Jin, J and Ren, Y and Tao, Y and Wang, D and Alvarez, PJJ and Yu, P}, title = {Metagenomic insights into microalgae-bacterium-virus interactions and viral functions in phycosphere facing environmental fluctuations.}, journal = {Water research}, volume = {268}, number = {Pt A}, pages = {122676}, doi = {10.1016/j.watres.2024.122676}, pmid = {39471530}, issn = {1879-2448}, mesh = {*Microalgae/virology ; Bacteria/genetics ; Metagenomics ; Phylogeny ; Symbiosis ; Gene Transfer, Horizontal ; Viruses/genetics ; }, abstract = {Despite the ecological and biotechnological significance of microalgae-bacterium symbionts, the response of host-virus interactions to external environmental fluctuations and the role of viruses in phycosphere remain largely unexplored. Herein, we employed algal-bacterial granular sludge (ABGS) with varying light intensity and organic carbon loading to investigate the mechanisms of microalgae-bacterium-virus symbionts in response to environmental fluctuations. Metagenomics revealed that enhanced light intensity decreased the diversity of microalgae, so did the diversity of symbiotic bacteria and viruses. As carbon sources decreased, bacteria prompted horizontal gene transfer in phycosphere by 12.76 %-157.40 %, increased the proportion of oligotrophs as keystone species (0.00 % vs 14.29 %) as well as viruses using oligotrophs as hosts (18.52 % vs 25.00 %). Furthermore, virus-carried auxiliary metabolic genes (AMGs) and biosynthetic gene clusters (BGCs) encoding vitamin B12 synthesis (e.g., cobS), antioxidation (e.g., queC), and microbial aggregation (e.g., cysE). Additionally, phylogenetic and similarity analysis further revealed the evolutionary origin and potential horizontal transfer of the AMGs and BGCs, which could potentially enhance the adaptability of bacteria and eukaryotic microalgae. Overall, our research demonstrates that environmental fluctuations have cascading effects on the microalgae-bacteria-virus interactions, and emphasizes the important role of viruses in maintaining the stability of the phycosphere symbiotic community.}, } @article {pmid39471221, year = {2024}, author = {Buigues, J and Viñals, A and Martínez-Recio, R and Monrós, JS and Cuevas, JM and Sanjuán, R}, title = {Phylogenetic evidence supporting the nonenveloped nature of hepadnavirus ancestors.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {45}, pages = {e2415631121}, pmid = {39471221}, issn = {1091-6490}, support = {CIAICO/2022/110//Generalitat Valenciana (GVA)/ ; 101019724-EVADER//EC | ERC | HORIZON EUROPE European Research Council (ERC)/ ; PID2020-118602RB-I00//Ministerio de Ciencia e Innovación (MCIN)/ ; }, mesh = {*Phylogeny ; Animals ; *Hepadnaviridae/genetics/classification ; Chiroptera/virology ; Evolution, Molecular ; Feces/virology ; Genome, Viral ; }, abstract = {Reverse-transcribing animal DNA viruses include the hepadnaviruses, a well-characterized family of small enveloped viruses that infect vertebrates but also a sister group of nonenveloped viruses more recently discovered in fish and termed the nackednaviruses. Here, we describe the complete sequence of a virus found in the feces of an insectivorous bat, which encodes a core protein and a reverse transcriptase but no envelope protein. A database search identified a viral sequence from a permafrost sample as its closest relative. The two viruses form a cluster that occupies a basal phylogenetic position relative to hepadnaviruses and nackednaviruses, with an estimated divergence time of 500 My. These findings may lead to the definition of a "proto-nackednavirus" family and support the hypothesis that the ancestors of hepadnaviruses were nonenveloped.}, } @article {pmid39470730, year = {2025}, author = {Bağcı, C and Nuhamunada, M and Goyat, H and Ladanyi, C and Sehnal, L and Blin, K and Kautsar, SA and Tagirdzhanov, A and Gurevich, A and Mantri, S and von Mering, C and Udwary, D and Medema, MH and Weber, T and Ziemert, N}, title = {BGC Atlas: a web resource for exploring the global chemical diversity encoded in bacterial genomes.}, journal = {Nucleic acids research}, volume = {53}, number = {D1}, pages = {D618-D624}, pmid = {39470730}, issn = {1362-4962}, support = {161L0284C//Federal Ministry of Research and Education (BMBF)/ ; TTU09.716//German Centre for Infection Research (DZIF)/ ; NNF20CC0035580//Novo Nordisk Foundation/ ; //Saarland University/ ; //National Agri-Food Biotechnology Institute/ ; 101064285//Horizon Europe-Research and Innovation Framework Programme/ ; //Office of Science/ ; DE-AC02-05CH11231//Department of Energy/ ; }, mesh = {*Genome, Bacterial/genetics ; *Internet ; *Multigene Family ; Databases, Genetic ; Bacteria/genetics/metabolism/classification ; Metagenomics/methods ; Metagenome/genetics ; Biosynthetic Pathways/genetics ; Secondary Metabolism/genetics ; Software ; }, abstract = {Secondary metabolites are compounds not essential for an organism's development, but provide significant ecological and physiological benefits. These compounds have applications in medicine, biotechnology and agriculture. Their production is encoded in biosynthetic gene clusters (BGCs), groups of genes collectively directing their biosynthesis. The advent of metagenomics has allowed researchers to study BGCs directly from environmental samples, identifying numerous previously unknown BGCs encoding unprecedented chemistry. Here, we present the BGC Atlas (https://bgc-atlas.cs.uni-tuebingen.de), a web resource that facilitates the exploration and analysis of BGC diversity in metagenomes. The BGC Atlas identifies and clusters BGCs from publicly available datasets, offering a centralized database and a web interface for metadata-aware exploration of BGCs and gene cluster families (GCFs). We analyzed over 35 000 datasets from MGnify, identifying nearly 1.8 million BGCs, which were clustered into GCFs. The analysis showed that ribosomally synthesized and post-translationally modified peptides are the most abundant compound class, with most GCFs exhibiting high environmental specificity. We believe that our tool will enable researchers to easily explore and analyze the BGC diversity in environmental samples, significantly enhancing our understanding of bacterial secondary metabolites, and promote the identification of ecological and evolutionary factors shaping the biosynthetic potential of microbial communities.}, } @article {pmid39470619, year = {2024}, author = {Liu, X and Luo, Y and Chen, X and Wu, M and Xu, X and Tian, J and Gao, Y and Zhu, J and Wang, Z and Zhou, Y and Zhang, Y and Wang, X and Li, W and Lu, Q and Yao, X}, title = {Fecal microbiota transplantation against moderate-to-severe atopic dermatitis: A randomized, double-blind controlled explorer trial.}, journal = {Allergy}, volume = {}, number = {}, pages = {}, doi = {10.1111/all.16372}, pmid = {39470619}, issn = {1398-9995}, support = {//Nanjing Incubation Program for National Clinical Research Center/ ; //National Key Research and Development Program of China/ ; //CAMS Innovation Fund for Medical Sciences/ ; //Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences/ ; //National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) is a novel treatment for inflammatory diseases. Herein, we assess its safety, efficacy, and immunological impact in patients with moderate-to-severe atopic dermatitis (AD).

METHODS: In this randomized, double-blind, placebo-controlled clinical trial, we performed the efficacy and safety assessment of FMT for moderate-to-severe adult patients with AD. All patients received FMT or placebo once a week for 3 weeks, in addition to their standard background treatments. Patients underwent disease severity assessments at weeks 0, 1, 2, 4, 8, 12, and 16, and blood and fecal samples were collected for immunologic analysis and metagenomic shotgun sequencing, respectively. Safety was monitored throughout the trial.

RESULTS: Improvements in eczema area and severity index (EASI) scores and percentage of patients achieving EASI 50 (50% reduction in EASI score) were greater in patients treated with FMT than in placebo-treated patients. No serious adverse reactions occurred during the trial. FMT treatment decreased the Th2 and Th17 cell proportions among the peripheral blood mononuclear cells, and the levels of TNF-α, and total IgE in serum. By contrast, the expression levels of IL-12p70 and perforin on NK cells were increased. Moreover, FMT altered the abundance of species and functional pathways of the gut microbiota in the patients, especially the abundance of Megamonas funiformis and the pathway for 1,4-dihydroxy-6-naphthoate biosynthesis II.

CONCLUSION: FMT was a safe and effective therapy in moderate-to-severe adult patients with AD; the treatment changed the gut microbiota compositions and functions.}, } @article {pmid39470190, year = {2024}, author = {Toyomane, K and Kimura, Y and Fukagawa, T and Yamagishi, T and Watanabe, K and Akutsu, T and Asahi, A and Kubota, S and Sekiguchi, K}, title = {Metagenomic sequencing of CRISPRs as a new marker to aid in personal identification with low-biomass samples.}, journal = {mSystems}, volume = {9}, number = {11}, pages = {e0103824}, pmid = {39470190}, issn = {2379-5077}, support = {20K18991,24K20264//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; }, mesh = {Humans ; *Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; *Metagenomics/methods ; *Skin/microbiology ; Microbiota/genetics ; Sequence Analysis, DNA/methods ; Metagenome/genetics ; Genetic Markers/genetics ; }, abstract = {The high specificity of the human skin microbiome is expected to provide a new marker for personal identification. Metagenomic sequencing of clustered regularly interspaced short palindromic repeats (CRISPRs), which we call metaCRISPR typing, was shown to achieve personal identification accurately. However, the intra-individual variability observed in previous studies, which may be due to poor DNA yields from skin samples, has resulted in non-reproducible results. Furthermore, whether metaCRISPR typing can assist in the forensic human DNA analysis of low-biomass samples, from which the information obtained is insufficient, is unknown. In the present study, we sequenced serially diluted control streptococcal CRISPRs cloned into plasmids to determine the minimum copy number required to obtain reproducible results from metaCRISPR typing. We found that at least 10[2] copies of CRISPRs are necessary to obtain reproducible results. We then analyzed the skin swab samples using both metaCRISPR typing and human DNA typing. When the DNA extracted from the skin swabs was diluted, no information was obtained from six out of eight samples by human DNA typing. On the other hand, beta diversity indices of spacer sequences compared with reference samples were below 0.8 for three out of six samples, for which no information was obtained from human DNA analysis, indicating that the spacers observed in these samples were similar to those in the references. These results indicate that metaCRISPR typing may contribute to the identification of individuals from whom the samples were obtained, even in cases where human DNA yields are insufficient to perform human DNA analysis.IMPORTANCEPrevious studies have developed new personal identification methods utilizing personal differences in the skin microbiome. However, intra-individual diversity of skin microbiome may preclude the application of microbiome-based personal identification. Moreover, no study has compared microbiome-based personal identification and practical human DNA analysis. Here, we revealed that the results of metaCRISPR typing, a previously developed microbiome-based personal identification method, are stable if the copy number of the marker gene is sufficient. We then analyzed the skin swab samples using both metaCRISPR typing and human DNA analysis. Our results indicate that metaCRISPR typing may provide additional information for personal identification using low-biomass samples that cannot be used for conventional human DNA analysis.}, } @article {pmid39469852, year = {2024}, author = {Wu, J and Zhong, Y and Deng, Y and Yang, S and Wang, H and Yang, Q and Li, D and Song, J and Zhang, H and Peng, P}, title = {Sustainable Abiotic-Biotic Dechlorination of Perchloroethene with Sulfidated Nanoscale Zero-Valent Iron as Electron Donor Source.}, journal = {Environmental science & technology}, volume = {58}, number = {47}, pages = {20931-20941}, doi = {10.1021/acs.est.3c10948}, pmid = {39469852}, issn = {1520-5851}, mesh = {*Iron/chemistry ; *Electrons ; Tetrachloroethylene/chemistry/metabolism ; RNA, Ribosomal, 16S ; Bacteria/metabolism ; Groundwater/chemistry ; Halogenation ; }, abstract = {Combining organohalide-respiring bacteria with nanoscale zero-valent iron (nZVI) represents a promising approach for remediating chloroethene-contaminated aquifers. However, limited information is available regarding their synergistic dechlorinating ability for chloroethenes when nZVI is sulfidated (S-nZVI) under the organic electron donor-limited conditions typically found in deep aquifers. Herein, we developed a combined system utilizing a mixed culture containing Dehalococcoides (Dhc) and S-nZVI particles, which achieved sustainable dechlorination with repeated rounds of spiking with 110 μM perchloroethene (PCE). The relative abundance of Dhc considerably increased from 5.2 to 91.5% after five rounds of spiking with PCE, as evidenced by 16S rRNA gene amplicon sequencing. S-nZVI corrosion generated hydrogen as an electron donor for Dhc and other volatile fatty acid (VFA)-producing bacteria. Electron balance analysis indicated that 68.1% of electrons from Fe[0] consumed in S-nZVI were involved in dechlorination, and 6.2, 1.1, and 3.2% were stored in formate, acetate, and other VFAs, respectively. The produced acetate possibly served as a carbon source for Dhc. Metagenomic analysis revealed that Desulfovibrio, Syntrophomonas, Clostridium, and Mesotoga were likely involved in VFA production. These findings provide valuable insights into the synergistic mechanisms of biotic and abiotic dechlorination, with important implications for sustainable remediation of electron donor-limited aquifers contaminated by chloroethenes.}, } @article {pmid39469454, year = {2024}, author = {Wang, J and Li, M and Zhu, J and Cheng, L and Kong, P}, title = {Mycobacterium tuberculosis combine with EBV infection in severe adult meningoencephalitis: a rare case reports and literature review.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1361119}, pmid = {39469454}, issn = {2235-2988}, mesh = {Humans ; Male ; Middle Aged ; *Meningoencephalitis/diagnosis/microbiology/virology/drug therapy ; *Mycobacterium tuberculosis/isolation & purification ; *Epstein-Barr Virus Infections/complications/diagnosis ; *Magnetic Resonance Imaging ; *Tuberculosis, Meningeal/diagnosis/drug therapy/complications ; *Coinfection/microbiology ; Herpesvirus 4, Human/genetics/isolation & purification ; Brain/pathology/diagnostic imaging ; Antitubercular Agents/therapeutic use ; Antiviral Agents/therapeutic use ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Treatment Outcome ; }, abstract = {BACKGROUND: Tuberculous meningitis (TBM) with adults Epstein-Barr (EB) virus encephalitis is a very rare infectious disease, with a high mortality and disability. Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) is highly diagnostic. We report on a case of severe meningoencephalitis caused by co-infection with mycobacterium tuberculosis and EB virus. Brain MRI indicated a parenchyma lesion in the brain. mNGS of CSF indicated Mycobacterium tuberculosis and EB virus amplification, positive serum EB virus IgG antibodies, and improved symptoms after anti-tuberculosis and antiviral treatment. A re-examination of the brain MRI revealed that the significantly absorption of the lesions.

CASE REPORT: A 49-year-old male patient presented with a chief complaint of headache and fever with consciousness disturbance. The brain magnetic resonance imaging showed a lesions in the right parenchymal brain with uneven enhancement, accompanied by significantly increased intracranial pressure, elevated CSF cell count and protein levels, as well as notably decreased glucose and chloride levels. mNGS of CSF showed the coexistence of Mycobacterium tuberculosis and EBV. The patient was diagnosed as TBM with EBV encephalitis. The patient's symptoms gradually improved with the active administration of anti-tuberculosis combined with antiviral agents, the use of hormones to reduce inflammatory reaction, dehydration to lower intracranial pressure, and intrathecal injection. Subsequent follow-up brain magnetic resonance imaging indicated significant absorption of the lesions, along with a marked decrease in CSF count and protein levels, as well as obvious increase in glucose and chloride levels.

CONCLUSION: TBM associated with adult EBV encephalitis is extremely rare. The disease's early stages are severe and have a high fatality rate. A prompt and accurate diagnosis is particularly important. NGS of CSF is of great value for early diagnosis.}, } @article {pmid39469094, year = {2024}, author = {Wang, W and Wang, Y and Xin, X and Yin, Y and Zhao, C and Jin, Y}, title = {Metagenomic Next-Generation Sequencing Direct Diagnosis of Mixed Bacterial Meningitis in a Child: A Case Report.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {4643-4648}, pmid = {39469094}, issn = {1178-6973}, abstract = {BACKGROUND: Bacterial meningitis is a major cause of mortality and morbidity in children worldwide. Meanwhile, mixed bacterial meningitis is a rare entity. However, it is difficult to identify anaerobic pathogens using traditional culture methods. Disorders such as neurosurgical interventions are considered risk factors for the development of such cerebral infection. Early diagnosis and appropriate therapy may contribute to patient survival.

CASE PRESENTATION: We report the use of metagenomic next-generation sequencing (mNGS) to facilitate the diagnosis and treatment of polymicrobial meningitis in a 35-month-old male child with a history of detethering procedure for tethered cord syndrome (TCS). The mNGS tests identified six bacterial species from CSF specimens, including four ones of anaerobic bacteria. The subsequent examination of magnetic resonance imaging (MRI) revealed abnormal imaging findings of the lumbosacral area. The patient eventually recovered from severe infections due to long-term antibiotic treatment and radical surgery.

CONCLUSION: This case demonstrates the advantages of mNGS for the rapid and accurate diagnosis of mixed bacterial meningitis, highlighting its application of identifying uncommon pathogens in severe infections. For patients who suffered from exacerbated brain infection with history of detethering surgery, anaerobic cultivation is needed and empiric antibiotic therapy should consider mixed infection in these situations.}, } @article {pmid39468837, year = {2024}, author = {Wan, Y and Wong, OWH and Tun, HM and Su, Q and Xu, Z and Tang, W and Ma, SL and Chan, S and Chan, FKL and Ng, SC}, title = {Fecal microbial marker panel for aiding diagnosis of autism spectrum disorders.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2418984}, pmid = {39468837}, issn = {1949-0984}, mesh = {Humans ; *Feces/microbiology ; *Autism Spectrum Disorder/diagnosis/microbiology ; Female ; *Gastrointestinal Microbiome ; Male ; Child ; Child, Preschool ; *Biomarkers/analysis ; *Bacteria/isolation & purification/classification/genetics ; Metagenome ; Machine Learning ; }, abstract = {Accumulating evidence suggests that gut microbiota alterations influence brain function and could serve as diagnostic biomarkers and therapeutic targets. The potential of using fecal microbiota signatures to aid autism spectrum disorder (ASD) detection is still not fully explored. Here, we assessed the potential of different levels of microbial markers (taxonomy and genome) in distinguishing children with ASD from age and gender-matched typically developing peers (n = 598, ASD vs TD = 273 vs 325). A combined microbial taxa and metagenome-assembled genome (MAG) markers showed a better performance than either microbial taxa or microbial MAGs alone for detecting ASD. A machine-learning model comprising 5 bacterial taxa and 44 microbial MAG markers (2 viral MAGs and 42 bacterial MAGs) achieved an area under the receiving operator curve (AUROC) of 0.886 in the discovery cohort and 0.734 in an independent validation cohort. Furthermore, the identified biomarkers and predicted ASD risk score also significantly correlated with the core symptoms measured by the Social Responsiveness Scale-2 (SRS-2). The microbiome panel showed a superior classification performance in younger children (≤6 years old) with an AUROC of 0.845 than older children (>6 years). The model was broadly applicable to subjects across genders, with or without gastrointestinal tract symptoms (constipation and diarrhea) and with or without psychiatric comorbidities (attention deficit and hyperactivity disorder and anxiety). This study highlights the potential clinical validity of fecal microbiome to aid in ASD diagnosis and will facilitate studies to understand the association of disturbance of human gut microbiota and ASD symptom severity.}, } @article {pmid39468772, year = {2025}, author = {Chero-Sandoval, L and Higuera-Gómez, A and Martínez-Urbistondo, M and Castejón, R and Mellor-Pita, S and Moreno-Torres, V and de Luis, D and Cuevas-Sierra, A and Martínez, JA}, title = {Comparative assessment of phenotypic markers in patients with chronic inflammation: Differences on Bifidobacterium concerning liver status.}, journal = {European journal of clinical investigation}, volume = {55}, number = {2}, pages = {e14339}, pmid = {39468772}, issn = {1365-2362}, support = {CD22/00011//Instituto de Salud Carlos III/ ; Y2020/6600//Consejería de Educación, Juventud y Deporte, Comunidad de Madrid/ ; }, mesh = {Humans ; Female ; *Gastrointestinal Microbiome/genetics ; Male ; Adult ; Middle Aged ; *Bifidobacterium ; *Biomarkers/metabolism ; *Inflammation ; *Lupus Erythematosus, Systemic/microbiology/immunology ; Phenotype ; Feces/microbiology ; Liver ; Fatty Liver/microbiology ; }, abstract = {BACKGROUND: The relationship between systemic lupus erythematosus (SLE) and low-grade metabolic inflammation (MI) with the microbiota is crucial for understanding the pathogenesis of these diseases and developing effective therapeutic interventions. In this context, it has been observed that the gut microbiota plays a key role in the immune regulation and inflammation contributing to the exacerbation through inflammatory mediators. This research aimed to describe similarities/differences in anthropometric, biochemical, inflammatory, and hepatic markers as well as to examine the putative role of gut microbiota concerning two inflammatory conditions: SLE and MI.

METHODS: Data were obtained from a cohort comprising adults with SLE and MI. Faecal samples were determined by 16S technique. Statistical analyses compared anthropometric and clinical variables, and LEfSe and MetagenomeSeq were used for metagenomic data. An interaction analysis was fitted to investigate associations of microbiota with fatty liver index (FLI) depending on the inflammatory condition.

RESULTS: Participants with low-grade MI showed worse values in anthropometry and biochemicals compared with patients with SLE. The liver profile of patients with MI was unhealthier, while no relevant differences were found in most of the inflammatory markers between groups. LEfSe analysis revealed an overrepresentation of Bifidobacteriaceae family in SLE group. An interactive association between gut Bifidobacterium abundance and type of disease was identified for FLI values, suggesting an effect modification of the gut microbiota concerning liver markers depending on the inflammatory condition.

CONCLUSION: This study found phenotypical and microbial similarities and disparities between these two inflammatory conditions, evidenced in clinical and hepatic markers, and showed the interactive interplay between gut Bifidobacterium and liver health (measured by FLI) that occur in a different manner depending on the type of inflammatory disease. These results underscore the importance of personalized approaches and individual microbiota in the screening of different inflammatory situations, considering unique hepatic and microbiota profiles.}, } @article {pmid39468734, year = {2024}, author = {Papo, M and Cappy, P and Degachi, A and Woerther, PL and Saal, C and Charlotte, F and Brocheriou, I and Lhote, R and Trefond, L and Hié, M and Haroche, J and Pha, M and Cohen-Aubart, F and Mathian, A and Rodriguez, C and Amoura, Z}, title = {Lymphadenopathy in systemic lupus erythematosus: no microbial trigger found by shotgun metagenomics in a retrospective study on 38 patients.}, journal = {Rheumatology (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/rheumatology/keae578}, pmid = {39468734}, issn = {1462-0332}, abstract = {OBJECTIVES: Lymphadenopathy is a classical manifestation of systemic lupus erythematosus (SLE) flare, occurring in approximately half of patients during the course of the disease. Lymphadenopathy in SLE is frequently associated with fever. Microbial infection may play a role in SLE onset and flares. Objectives of this study were to describe lymphadenopathy in the course of SLE and identify potential infectious triggers using microbial metagenomic analysis.

METHODS: We performed a retrospective monocentric study of 38 patients with SLE who had lymph node biopsy at baseline or during follow-up. Shotgun metagenomics were performed in patient's lymph node biopsy to look for microbial RNA and/or DNA.

RESULTS: Lymph node pathological analyses revealed follicular and/or paracortical hyperplasia 73.7% of patients and histiocytic necrotizing lymphadenitis 23.7%. At the time of biopsy, SLE patients exhibited fever in 29%, splenomegaly in 10%, cutaneous manifestations in 47%, polyarthritis in 32%, seritis in 13% and lupus nephritis in 18%. Half of patients (50%) had increased CRP level, 35% had low C3, 65% had hypergammaglobulinemia. Microbial metagenomic analysis of lymph node biopsy did not reveal the presence of microbial DNA in 92% of patients, the presence of CMV in very small quantities in 2 patients, and the presence of HHV-7 in low quantities in a single patient.

CONCLUSION: Despite suggestion that certain microorganisms may play a role in the pathogenesis and flares of SLE, our microbial metagenomic analysis study did not highlight possible infectious triggering factors. Further and better-designed studies are needed to confirm these results.}, } @article {pmid39468445, year = {2024}, author = {Chen, Q and Chen, Z and Tan, Y and Wu, S and Zou, S and Liu, J and Song, S and Du, Q and Wang, M and Liang, K}, title = {Blood microbiota in HIV-infected and HIV-uninfected patients with suspected sepsis detected by metagenomic next-generation sequencing.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {1210}, pmid = {39468445}, issn = {1471-2334}, support = {PTXM2020008//Medical Science and Technology Innovation Platform Support Project of Zhongnan Hospital, Wuhan University/ ; cxpy2017043//Science and Technology Innovation Cultivation Fund of Zhongnan Hospital, Wuhan University/ ; TFJC2018004//Medical Science Advancement Program (Basic Medical Sciences) of Wuhan University/ ; 2020-PT320-004//Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences/ ; }, mesh = {Humans ; *HIV Infections/complications/microbiology ; Male ; Female ; Middle Aged ; *Sepsis/microbiology/blood ; *High-Throughput Nucleotide Sequencing ; Retrospective Studies ; Adult ; *Metagenomics/methods ; *Microbiota ; China ; Bacteria/classification/genetics/isolation & purification ; Aged ; }, abstract = {BACKGROUND: Information on the comparison of blood microbiota between human immunodeficiency virus (HIV)-infected and HIV-uninfected patients with suspected sepsis by metagenomic next-generation sequencing (mNGS) is limited.

METHODS: Retrospectively analysis was conducted in HIV-infected and HIV-uninfected patients with suspected sepsis at Changsha First Hospital (China) from March 2019 to August 2022. Patients who underwent blood mNGS testing were enrolled. The blood microbiota detected by mNGS were analyzed.

RESULTS: A total of 233 patients with suspected sepsis who performed blood mNGS were recruited in this study, including 79 HIV-infected and 154 HIV-uninfected patients. Compared with HIV-uninfected patients, the proportions of mycobacterium (p = 0.001), fungus (p < 0.001) and viruses (p < 0.001) were significantly higher, while the proportion of bacteria (p = 0.001) was significantly lower in HIV-infected patients. The higher positive rates of non-tuberculous mycobacteriosis (NTM, p = 0.022), Pneumocystis jirovecii (P. jirovecii) (p = 0.014), Talaromyces marneffei (T. marneffei) (p < 0.001) and cytomegalovirus (CMV) (p < 0.001) were observed in HIV-infected patients, compared with HIV-uninfected patients. In addition, compared with HIV-uninfected patients, the constituent ratio of T. marneffei (p < 0.001) in the fungus spectrum were significantly higher, while the constituent ratios of Candida (p < 0.001) and Aspergillus (p = 0.001) were significantly lower in HIV-infected patients.

CONCLUSIONS: Significant differences in the blood microbiota profiles exist between HIV-infected and HIV-uninfected patients with suspected sepsis.}, } @article {pmid39468253, year = {2024}, author = {Luna, N and Páez-Triana, L and Ramírez, AL and Muñoz, M and Goméz, M and Medina, JE and Urbano, P and Barragán, K and Ariza, C and Martínez, D and Hernández, C and Patiño, LH and Ramirez, JD}, title = {Microbial community dynamics in blood, faeces and oral secretions of neotropical bats in Casanare, Colombia.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {25808}, pmid = {39468253}, issn = {2045-2322}, support = {Internal funds//Universidad del Rosario/ ; }, mesh = {Animals ; *Chiroptera/microbiology/virology ; *Feces/microbiology/virology ; Colombia/epidemiology ; Microbiota/genetics ; Bacteria/genetics/classification/isolation & purification ; High-Throughput Nucleotide Sequencing ; Fungi/genetics/isolation & purification/classification ; Metagenomics/methods ; Mouth/microbiology/virology ; RNA, Ribosomal, 16S/genetics ; Viruses/genetics/isolation & purification/classification ; Saliva/microbiology/virology ; }, abstract = {Bats are known reservoirs for a wide range of pathogenic microorganisms, including viruses, bacteria, fungi, helminths, and protozoa, which can be transmitted and infect other zoonotic organisms. Various studies have utilised next-generation sequencing (NGS) to describe the pathogens associated with bats. Although most have characterised microbial communities in specific body fluids, few have analysed the composition and diversity of these microbial communities across different body fluids at the individual level. In this study, we employed two next-generation sequencing techniques: amplicon-based sequencing of the V4 hypervariable region of the 16S- and 18S-rRNA genes and viral metagenomics, to describe the prokaryotic, eukaryotic, and viral communities present in blood, faeces, and oral swab samples collected from two genera of bats (Carollia and Phyllostomus) in the department of Casanare, eastern Colombia. A total of 60 samples corresponding to the three bodily fluids were processed and analysed. The results indicated that the microbial communities across the body fluids were mainly composed of bacteria, fungi, protozoa, and various DNA and RNA viruses, showing a variability of microbial genera and species. The abundances, diversity metrics, and correlations of these microorganisms displayed patterns associated with bat genus and body fluids, suggesting that the ecological characteristics of these microbial communities may be influenced by the ecological and physiological traits of the bats. Additionally, we found similar community compositions of bacteria, some fungal genera, and viruses in the three body fluids, indicating a possible circulation of these microbes within the same bat. This could be due to microbial movement from the gut microbiota to other physiological systems or transmission via blood-feeding vectors. Furthermore, our results revealed the presence of various microbes of public health concern, including Bartonella spp., Mannheimia haemolytica, Rhodotorula spp., Piroplasmida spp., Toxoplasma gondii, Alphacoronavirus spp., and Bat circovirus. The abundance of these pathogenic microbial species across the three bodily fluids suggests potential transmission routes from bats to other organisms, which may contribute to the emergence of zoonotic disease outbreaks. These findings highlight the variability of microorganisms present within the same bat and the different pathogen-host interactions that may regulate the presence and transmission of these zoonotic microbes. Further research is required to elucidate the genomic features, ecological interactions, and biological activities of these microbial communities in bats.}, } @article {pmid39468234, year = {2024}, author = {Słowakiewicz, M and Borkowski, A and Perri, E and Działak, P and Tagliasacchi, E and Gradziński, M and Kele, S and Reuning, L and Kibblewhite, T and Whitaker, F and Reid, RP and Tucker, ME}, title = {Biofilms in modern CaCO3-supersaturated freshwater environments reveal viral proxies.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {25889}, pmid = {39468234}, issn = {2045-2322}, support = {2019/35/B/ST10/02190//Narodowe Centrum Nauki/ ; PLG/2023/016421//Akademia Górniczo-Hutnicza im. Stanislawa Staszica/ ; PLG/2023/016421//Akademia Górniczo-Hutnicza im. Stanislawa Staszica/ ; }, mesh = {*Biofilms/growth & development ; *Fresh Water/microbiology/virology ; *Calcium Carbonate/metabolism/chemistry ; Geologic Sediments/microbiology/virology ; Viruses/genetics/metabolism ; Principal Component Analysis ; Metagenomics/methods ; }, abstract = {Biofilms are mucilaginous-organic layers produced by microbial activity including viruses. Growing biofilms form microbial mats which enhance sediment stability by binding particles with extracellular polymeric substances and promoting growth through nutrient cycling and organic matter accumulation. They preferentially develop at the sediment-water interface of both marine and non-marine environments, and upon the growing surfaces of modern tufa and travertine. In this context, however, little is known about the factors, environmental or anthropogenic, which affect viral communities in freshwater spring settings. To explore this issue, geochemical and metagenomic data were subjected to multidimensional analyses (Principal Component Analysis, Classical Multidimensional Scaling, Partial Least Squares analysis and cluster analysis based on beta-diversity), and these show that viral composition is specific and dependent on environment. Indeed, waters precipitating tufa and travertine do vary in their geochemistry with their viruses showing distinct variability between sites. These differences between virus groups allow the formulation of a viral proxy, based on the Caudoviricetes/Megaviricetes ratio established on the most abundant groups of viruses. This ratio may be potentially used in analysing ancient DNA preserved in carbonate formations as an additional source of information on the microbiological community during sedimentation.}, } @article {pmid39467883, year = {2024}, author = {Saini, N and Aamir, M and Khan, ZA and Singh, VK and Sah, P and Mona, S}, title = {Deciphering Toxic Pollutants Breakdown Potential in Microbial Community of Chumathang Hot Spring, Ladakh, India via Shotgun Metagenome Sequencing.}, journal = {Current microbiology}, volume = {81}, number = {12}, pages = {430}, pmid = {39467883}, issn = {1432-0991}, mesh = {*Hot Springs/microbiology ; India ; *Biodegradation, Environmental ; *Metagenome ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Metagenomics ; Microbiota/genetics ; Phylogeny ; Persistent Organic Pollutants/metabolism ; Xenobiotics/metabolism ; High-Throughput Nucleotide Sequencing ; }, abstract = {Persistent Organic Pollutants (POPs) have been in focus of research due to their massive contamination of environment and bio-accumulation. Bioremediation and high-throughput research have gained momentum to curb the harmful effects of POPs. The present research has explored the microbial diversity of Chumathang Hot Spring, Ladakh, India, through Illumina metagenomic HiSeq 4000 sequencing platform and their potential to degrade persistent pollutants, especially xenobiotics. Taxonomic characterization based on raw metagenomic data illuminated the abundance of members of Pseudomonadota and Actinomyceota. The re-construction of the microbial genomes from assembled contigs and scaffolds using de novo assembler metaSPAdes and their further annotation through contig alignment with available reference genomes elucidated the landscape of the hot spring's microbes. The predominantly occupied key genera reported were Pannonibacter and Novosphingobium. Comparative genomic analysis established evolutionary relationships and functional diversities among hot spring microbial communities. The function annotation through MG-RAST has revealed their metabolic versatility of degrading a wide array of xenobiotic compounds, including caprolactam, dioxin, chlorobenzene, benzoate, and. Further, the hydroxylating dioxygenase (Saro_3901) was identified as a pivotal component in the aromatic degradation pathways, showcasing extensive metabolic interconnectivity. Interestingly, protein interaction network analysis identified hub genes like Saro_1233 (protocatechuate 4,5-dioxygenase alpha subunit), while Saro_3057 (amidase) was noted for its critical role in network communication and control. The resilience of thermal ecosystems, evidenced by robust enzymatic activity and degradation capability among organisms with < 95% genetic similarity, underscores their potential for industrial and bioremediation exploration, emphasizing the importance of preserving and studying biodiverse habitats.}, } @article {pmid39467681, year = {2024}, author = {Wang, HM and Zhang, MM and Lin, Y and Liu, Y and Xue, GH and Shi, L and Yuan, J and Li, XH}, title = {[Characteristics of intestinal microbiota in the acute phase of Kawasaki disease in infants and children].}, journal = {Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics}, volume = {26}, number = {10}, pages = {1101-1107}, pmid = {39467681}, issn = {1008-8830}, mesh = {Case-Control Studies ; Humans ; Infant ; Child, Preschool ; *Mucocutaneous Lymph Node Syndrome/microbiology ; *Gastrointestinal Microbiome ; Metagenomics ; Listeria monocytogenes ; Enterococcus hirae ; }, abstract = {OBJECTIVES: To study the composition, abundance, and functional profiles of the intestinal microbiota in infants and young children with Kawasaki disease (KD) during the acute phase, and to explore the potential role of intestinal microbiota in the pathogenesis of KD.

METHODS: Six children aged 0-3 years with acute KD admitted to the Department of Cardiology, Children's Hospital Affiliated to Capital Institute of Pediatrics from July to October 2021 were prospectively included as the KD group. Six age- and sex-matched healthy children who underwent physical examinations at the hospital during the same period were selected as the healthy control group. Metagenomics sequencing was used to detect and compare the differences in the microflora structure and functional profiles of fecal samples between the two groups.

RESULTS: There were significant differences in the structural composition and diversity of intestinal microbiota between the two groups (P<0.05). Compared with the healthy control group, the abundance of Listeria_monocytogenes (family Listeriaceae and genus Listeria), Bifidobacterium_rousetti, Enterococcus_avium, and Enterococcus_hirae was significantly higher in the intestinal microbiota in the KD group (|LDA|>2.0, P<0.05). The steroid degradation and apoptosis pathways were significantly upregulated in the KD group compared with the healthy control group, while the Bacterial_secretion_system, Sulfur_metabolism, Butanoate_metabolism, Benzoate_degradation, β-alanine metabolism, and α-linolenic acid pathways were significantly downregulated (|LDA|>2, P<0.05).

CONCLUSIONS: There are significant differences in the structure and diversity of intestinal microbiota between children aged 0-3 years with acute KD and healthy children, suggesting that disturbances in intestinal microbiota occur during the acute phase of KD. In particular, Listeria_monocytogenes, Enterococcus_avium, and Enterococcus_hirae may be involved in the pathogenesis of KD through steroid degradation and apoptosis pathways.}, } @article {pmid39465842, year = {2024}, author = {Li, C and Wang, F and Li, W and Sun, G and Yang, D and Yang, T and Yang, G and Liang, B and Huang, Y and Tang, W and Li, F and Ye, Y and Qian, C and Wu, H and Meng, Z}, title = {The diagnostic value of metagenomic next-generation sequencing in critically ill patients with sepsis: A retrospective cohort study.}, journal = {Medicine}, volume = {103}, number = {41}, pages = {e39987}, pmid = {39465842}, issn = {1536-5964}, support = {202001AY070001-204//joint project of Yunnan Science and Technology Department-Kunming Medical University Applied Basic Research/ ; Z-2016-23-2001-12//China International Medical Foundation Cardiovascular Multidisciplinary Integrated Thinking Research Fund/ ; }, mesh = {Humans ; *Sepsis/diagnosis/microbiology ; Male ; Retrospective Studies ; Female ; Middle Aged ; *Critical Illness ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Aged ; China ; Intensive Care Units ; Adult ; }, abstract = {Metagenomic next-generation sequencing (mNGS) is a new high-throughput sequencing method that may have great importance in early diagnosis and clinical management of sepsis. This study aimed to detect the difference between mNGS and comprehensive routine microbiological test (CMT), and to explore the diagnostic efficacy of mNGS in septic patients. This study retrospectively analyzed 150 sepsis patients who were admitted to the intensive care units of 4 hospitals in Southwest China from October 1, 2018, to October 1, 2021, and underwent both blood mNGS and CMT. The demographic and clinical characteristics of the patients were recorded, and the distribution of pathogens was analyzed. Additionally, the diagnostic performance and concordance between mNGS and CMT were compared to evaluate the etiological diagnostic value of mNGS in sepsis patients. In this study of 150 sepsis patients, bacterial infections were identified in 126 (84.0%), viral in 15 (10.0%), and fungal in 9 (6.0%). Among the sample types, sputum was most common, representing 62% of the total cases. Bronchoalveolar lavage fluid constituted 58.7%, blood 56.0%, with other specimens including pleural fluid at 29.3%, pus at 19.3%, swabs at 9.3%, cerebrospinal fluid at 8.7%, tissue at 6.0%, and bone marrow at 5.3%. mNGS demonstrated a diagnostic accuracy of 56.0% for sepsis, with a sensitivity of 84.4%, specificity of 26.0%, a positive predictive value of 54.6%, a negative predictive value of 61.3%. Metagenomic testing enables the rapid and early identification of infectious pathogens in sepsis patients, especially fungi and viruses. The study found that mNGS has high sensitivity in diagnosing sepsis patients, particularly for fungal and viral infections. mNGS technology is beneficial for critically ill sepsis patients.}, } @article {pmid39465298, year = {2024}, author = {Xiao, X and Singh, A and Giometto, A and Brito, IL}, title = {Segatella clades adopt distinct roles within a single individual's gut.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {114}, pmid = {39465298}, issn = {2055-5008}, support = {DP2 HL141007/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Fatty Acids, Volatile/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Genetic Variation ; Anti-Bacterial Agents/pharmacology ; Host Microbial Interactions ; Metagenomics/methods ; Drug Resistance, Bacterial ; Epithelial Cells/microbiology ; }, abstract = {Segatella is a prevalent genus within individuals' gut microbiomes worldwide, especially in non-Western populations. Although metagenomic assembly and genome isolation have shed light on its genetic diversity, the lack of available isolates from this genus has resulted in a limited understanding of how members' genetic diversity translates into phenotypic diversity. Within the confines of a single gut microbiome, we have isolated 63 strains from diverse lineages of Segatella. We performed comparative analyses that exposed differences in cellular morphologies, preferences in polysaccharide utilization, yield of short-chain fatty acids, and antibiotic resistance across isolates. We further show that exposure to Segatella isolates either evokes strong or muted transcriptional responses in human intestinal epithelial cells. Our study exposes large phenotypic differences within related Segatella isolates, extending this to host-microbe interactions.}, } @article {pmid39465163, year = {2024}, author = {Premsuriya, J and Leerach, N and Laosena, P and Hinthong, W}, title = {The effects of livestock grazing on physicochemical properties and bacterial communities of perlite-rich soil.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e18433}, pmid = {39465163}, issn = {2167-8359}, mesh = {*Soil Microbiology ; Animals ; Thailand ; *Soil/chemistry ; *Livestock/microbiology ; *Aluminum Oxide ; *Silicon Dioxide ; Mining ; Bacteria/genetics/classification/isolation & purification ; Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; }, abstract = {Livestock grazing has been proposed as a cost-effective way to reclaim post-mining lands. It can enhance soil fertility and biodiversity, but its impacts on soil quality and microbial communities vary across soil types. Moreover, waste from grazing raises concerns about pathogens that could pose risks to animal and human health. This study investigated the effects of grazing on post-mining perlite-rich soil in central Thailand. A comparative analysis of soil physicochemical properties and bacterial diversity was conducted between grazed and ungrazed sites. Bacterial diversity was assessed using 16S amplicon sequencing. The perlite-rich soil was found to be sandy, acidic, and to have low nutritional content. Grazing significantly improved the soil texture and nutrient content, suggesting its potential as a cost-effective reclamation strategy. The 16S metagenomic sequencing analysis revealed that microbial communities were impacted by livestock grazing. Specifically, shifts in the dominant bacterial phyla were identified, with increases in Firmicutes and Chloroflexi and a decrease in Actinobacteria. Concerns about increased levels of pathogenic Enterobacteriaceae due to grazing were not substantiated in perlite-rich soil. These bacteria were consistently found at low levels in all soil samples, regardless of livestock grazing. This study also identified a diverse population of Streptomycetaceae, including previously uncharacterized strains/species. This finding could be valuable given that this bacterial family is known for producing antibiotics and other secondary metabolites. However, grazing adversely impacted the abundance and diversity of Streptomycetaceae in this specific soil type. In line with previous research, this study demonstrated that the response of soil microbial communities to grazing varies significantly depending on the soil type, with unique responses appearing to be associated with perlite-rich soil. This emphasizes the importance of soil-specific research in understanding how grazing affects microbial communities. Future research should focus on optimizing grazing practices for perlite-rich soil and characterizing the Streptomycetaceae community for potential antibiotic and secondary metabolite discovery. The obtained findings should ultimately contribute to sustainable post-mining reclamation through livestock grazing and the preservation of valuable microbial resources.}, } @article {pmid39464836, year = {2024}, author = {Yao, Y and Zhao, H and Lu, H and Liu, X and Liu, H and Fu, Z and Li, C and Zhou, F and Hou, W and Shi, S}, title = {Crescentic Glomerulonephritis and Portal Hypertension with Chronic Q Fever: A Case Report and Comprehensive Literature Review.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {4599-4605}, pmid = {39464836}, issn = {1178-6973}, abstract = {Q fever, an infectious zoonotic disease caused by Coxiella burnetii, remains prevalent in China. Systemic infections can result in renal or hepatic complications; however, it is rare for both the kidneys and liver to be simultaneously affected. We present a case of a patient who exhibited fever, rapid deterioration in renal function, thrombocytopenia, and severe ascites. Renal biopsy revealed crescentic glomerulonephritis, while liver biopsy demonstrated non-cirrhotic portal hypertension. Metagenomic next-generation sequencing (mNGS) identified the presence of Coxiella burnetii in both venous blood and liver tissue samples. Notably, the patient's renal insufficiency and ascites showed a positive response to treatment for chronic Q fever. These findings provide valuable insights into the limited understanding of kidney and liver diseases associated with Q fever. Advanced diagnostic technologies, including mNGS and positron emission tomography/computed tomography (PET/CT), have been employed to identify Coxiella burnetii infection.}, } @article {pmid39464396, year = {2024}, author = {Ostos, I and Flórez-Pardo, LM and Camargo, C}, title = {A metagenomic approach to demystify the anaerobic digestion black box and achieve higher biogas yield: a review.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1437098}, pmid = {39464396}, issn = {1664-302X}, abstract = {The increasing reliance on fossil fuels and the growing accumulation of organic waste necessitates the exploration of sustainable energy alternatives. Anaerobic digestion (AD) presents one such solution by utilizing secondary biomass to produce biogas while reducing greenhouse gas emissions. Given the crucial role of microbial activity in anaerobic digestion, a deeper understanding of the microbial community is essential for optimizing biogas production. While metagenomics has emerged as a valuable tool for unravelling microbial composition and providing insights into the functional potential in biodigestion, it falls short of interpreting the functional and metabolic interactions, limiting a comprehensive understanding of individual roles in the community. This emphasizes the significance of expanding the scope of metagenomics through innovative tools that highlight the often-overlooked, yet crucial, role of microbiota in biomass digestion. These tools can more accurately elucidate microbial ecological fitness, shared metabolic pathways, and interspecies interactions. By addressing current limitations and integrating metagenomics with other omics approaches, more accurate predictive techniques can be developed, facilitating informed decision-making to optimize AD processes and enhance biogas yields, thereby contributing to a more sustainable future.}, } @article {pmid39464267, year = {2024}, author = {Wang, L and Wen, D and Qu, Y and Wang, Q and Liu, Y}, title = {Case report: A case of cutaneous anthrax guided by metagenomic next-generation sequencing technology.}, journal = {Frontiers in medicine}, volume = {11}, number = {}, pages = {1440130}, pmid = {39464267}, issn = {2296-858X}, abstract = {Anthrax is an acute zoonotic infectious disease caused by Bacillus anthracis. It is categorized as a Class B (reported within 24 h of onset, including pulmonary anthrax, which is managed as a Class A infectious disease and reported within 2 h of onset) infectious disease in China. Human anthrax infection primarily occurs through direct or indirect contact with infected animals. This study reports a case of cutaneous anthrax where typical anthrax colonies were observed in conventional microbial cultures, and large Gram-positive rods with squared ends were visible under the microscope. The results from metagenomic next-generation sequencing (mNGS) suggested the presence of Bacillus anthracis. This research explores the value of combining traditional microbiology with mNGS technology for the early diagnosis and therapy of infectious diseases.}, } @article {pmid39464202, year = {2024}, author = {Thomy, J and Schvarcz, CR and McBeain, KA and Edwards, KF and Steward, GF}, title = {Eukaryotic viruses encode the ribosomal protein eL40.}, journal = {Npj viruses}, volume = {2}, number = {1}, pages = {51}, pmid = {39464202}, issn = {2948-1767}, abstract = {Viruses in the phylum Nucleocytoviricota are large, complex and have an exceptionally diverse metabolic repertoire. Some encode hundreds of products involved in the translation of mRNA into protein, but none was known to encode any of the proteins in ribosomes, the central engines of translation. With the discovery of the eL40 gene in FloV-SA2, we report the first example of a eukaryotic virus encoding a ribosomal protein and show that this gene is also present and expressed in other uncultivated marine giant viruses. FloV-SA2 also encodes a "group II" viral rhodopsin, a viral light-activated protein of unknown function previously only reported in metagenomes. FloV-SA2 is thus a valuable model system for investigating new mechanisms by which viruses manipulate eukaryotic cell metabolism.}, } @article {pmid39462143, year = {2024}, author = {Boutouchent, N and Vu, TNA and Landraud, L and Kennedy, SP}, title = {Urogenital colonization and pathogenicity of E. Coli in the vaginal microbiota during pregnancy.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {25523}, pmid = {39462143}, issn = {2045-2322}, support = {Bourse Année Recherche (BAR) 2023-24//University Hospital of Rouen Normandy/ ; DOS0053477 SUB & DOS0053473 AR//Programme d'Investissements d'avenir and BPIfrance/ ; DOS0053477 SUB & DOS0053473 AR//Programme d'Investissements d'avenir and BPIfrance/ ; DOS0053477 SUB & DOS0053473 AR//Programme d'Investissements d'avenir and BPIfrance/ ; }, mesh = {Female ; Humans ; *Vagina/microbiology ; Pregnancy ; *Escherichia coli/genetics/pathogenicity ; *Microbiota ; *Escherichia coli Infections/microbiology ; Adult ; Bacteriuria/microbiology ; Pregnancy Complications, Infectious/microbiology ; Lactobacillus/genetics/isolation & purification ; }, abstract = {This study explores the role of the vaginal microbiota (VM) in the pathophysiology of asymptomatic bacteriuria (ASB) in a cohort of 1,553 pregnant women. Worldwide, E. coli remains the most common etiological agent of bacteriuria during pregnancy and also a major causative agent of newborn infections. A healthy VM is typically characterized by low diversity and is dominated by lactic acid-producing species, notably those from the Lactobacillus genus. Our results point to decreases in Lactobacillus spp associated with an increase of gut-microbiota-associated species from the Enterobacterales order. Escherichia coli exhibited the most pronounced increase in abundance within the VM during bacteriuria and was notably associated with ASB. Molecular typing and antimicrobial resistance characterization of 72 metagenome assembled E. coli genomes (MAGs) from these pregnant women revealed a genomic signature of extraintestinal pathogenic E. coli ("ExPEC") strains, which are involved in various extraintestinal infections such as urinary tract infections, newborn infections and bacteremia. Microbial diversity within the vaginal samples from which an E. coli MAG was obtained showed a substantial variation, primarily marked by a decrease in abundance of Lactobacillus species. Overall, our study shows how disruption in key bacterial group within the VM can disrupt its stability, potentially leading to the colonization by opportunistic pathogens.}, } @article {pmid39462132, year = {2024}, author = {Siallagan, ZL and Fadli, M and de Fretes, CE and Opier, RDA and Susanto, RD and Wei, Z and Suhardi, VSH and Nugrahapraja, H and Radjasa, OK and Dwivany, FM}, title = {Metagenomic analysis of deep-sea bacterial communities in the Makassar and Lombok Straits.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {25472}, pmid = {39462132}, issn = {2045-2322}, support = {#80NSSC18K0777//Physical Oceanography Program of the U.S. National Aeronautics and Space Administration (NASA) and through the University of Maryland/ ; }, mesh = {*Bacteria/genetics/classification ; *Metagenomics/methods ; *Seawater/microbiology ; *RNA, Ribosomal, 16S/genetics ; Phylogeny ; Biodiversity ; High-Throughput Nucleotide Sequencing ; Indonesia ; Metagenome ; Microbiota/genetics ; }, abstract = {The extreme conditions of the deep-sea environment, including limited light, low oxygen levels, high pressure, and nutrient scarcity, create a natural habitat for deep-sea bacteria. These remarkable microorganisms have developed unique strategies to survive and adapt to their surroundings. However, research on the diversity of deep-sea bacteria, both culture-dependent and culture-independent, in Indonesian waters remains insufficient. This study focused on exploring the biodiversity of deep-sea bacteria, specifically in the Makassar and Lombok Strait, the main Indonesian throughflow pathway characterized by relatively fertile water, which serves as an important deep-sea region. High-throughput DNA sequencing of full-length 16S rRNA was employed to construct a genomic database. The results of the bioinformatic analysis revealed that two stations, 48 and 50 (Makassar Strait), exhibited a more similar community structure of deep-sea bacteria than did station 33 (Lombok Strait). Among the predominant phyla found at a depth of 1000 m, the top ten were Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Planctomycetes, Acidobacteria, Nitrospinae, Verrucomicrobia, Candidatus Melainabacteria, and Cyanobacteria. Furthermore, the genera Colwellia, Moritella, Candidatus Pelagibacter, Alteromonas, and Psychrobacter consistently appeared at all three stations, albeit with varying relative abundance values. These bacterial genera share common characteristics, such as psychrophilic, halophilic, and piezophilic tendencies, and are commonly found in deep-sea ecosystem. The environmental conditions at a depth of 1000 m were relatively stable, with an average pressure 10 MPa, temperature 4.68 °C, salinity 34.58 PSU, pH 8.06, chlorophyll-a 0.29 µg/L, nitrate 3.19 µmol/L, phosphate 6.32 µmol/L and dissolved oxygen (DO) 2.90 mg/L. The bacterial community structures at the three sampling stations located at the same depth (1000 m) exhibited similarities, as indicated by the closely aligned similarity index values.}, } @article {pmid39461941, year = {2024}, author = {Xia, J and Yuan, Z and Jiang, F}, title = {Global metagenomic survey identifies sewage-derived hgcAB[+] microorganisms as key contributors to riverine methylmercury production.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {9262}, pmid = {39461941}, issn = {2041-1723}, support = {52425001//China National Funds for Distinguished Young Scientists/ ; U23A2049//National Natural Science Foundation of China (National Science Foundation of China)/ ; 51978289//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Methylmercury Compounds/analysis/metabolism ; *Sewage/microbiology ; *Rivers/microbiology/chemistry ; *Water Pollutants, Chemical/analysis/metabolism ; *Metagenomics ; China ; Environmental Monitoring ; Bacteria/genetics/classification/metabolism/isolation & purification ; Mercury/metabolism/analysis ; Metagenome ; }, abstract = {Methylmercury (MeHg) in aquatic systems poses a serious public health risk through bioaccumulation in the aquatic food web. In recent years, MeHg has been observed to increase to concerning levels globally in rivers near cities; however, the causes of this increase are not well understood. Here, we demonstrate the significant role of sewage contamination by analyzing over 1,300 publicly available metagenomes in urban rivers worldwide, and conducting experiments with water samples across China. We find that sewage contamination significantly increases the abundance of mercury (Hg)-methylating microorganisms in urban rivers globally. This increase is primarily attributed to the high abundance of active Hg-methylating microorganisms in sewage, which migrate to rivers via direct discharge or combined sewer overflows (CSOs), becoming key contributors to elevated riverine MeHg levels. Our findings underscore the importance of effectively eliminating Hg-methylating microorganisms from sewage to mitigate the public health risks associated with MeHg in urban rivers.}, } @article {pmid39461939, year = {2024}, author = {Gardiner, LJ and Marshall, M and Reusch, K and Dearden, C and Birmingham, M and Carrieri, AP and Pyzer-Knapp, EO and Krishna, R and Neal, AL}, title = {DGCNN approach links metagenome-derived taxon and functional information providing insight into global soil organic carbon.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {113}, pmid = {39461939}, issn = {2055-5008}, support = {BBS/E/RH/230003B//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/X010953/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, mesh = {*Soil Microbiology ; *Carbon/metabolism ; *Soil/chemistry ; *Metagenomics/methods ; *Metagenome ; Machine Learning ; Microbiota ; Carbon Cycle ; Bacteria/genetics/classification/isolation & purification/metabolism ; Neural Networks, Computer ; }, abstract = {Metagenomics can provide insight into the microbial taxa present in a sample and, through gene identification, the functional potential of the community. However, taxonomic and functional information are typically considered separately in downstream analyses. We develop interpretable machine learning (ML) approaches for modelling metagenomic data, combining the biological representation of species with their associated genetically encoded functions within models. We apply our methods to investigate soil organic carbon (SOC) stocks. First, we combine a diverse global set of soil microbiome samples with environmental data, improving the predictive performance of classic ML and providing new insights into the role of soil microbiomes in global carbon cycling. Our network analysis of predictive taxa identified by classical ML models provides context for their ecological significance, extending the focus beyond just the most predictive taxa to 'hidden' features within the model that might be considered less predictive using standard methods for explainability. We next develop unique graph representations for individual microbiomes, linking microbial taxa to their associated functions directly, enabling predictions of SOC via deep graph convolutional neural networks (DGCNNs). Interpretation of the DGCNNs distinguished between the importance of functions of key individual species, providing genome sequence differences, e.g., gene loss/acquisition, that associate with SOC. These approaches identify several members of the Verrucomicrobiaceae family and a range of genetically encoded functions, e.g., related to carbohydrate metabolism, as important for SOC stocks and effective global SOC predictors. These relatively understudied but widespread organisms could play an important role in SOC dynamics globally.}, } @article {pmid39461701, year = {2024}, author = {Jin, W and Yu, J and Wang, H and Jin, C and Zhao, Y and Wang, Y and Guo, L}, title = {Intra/extracellular electron transfer and metagenomic analysis elucidated the roles of magnetic iron powder (Fe3O4) on mixotrophic denitrification system.}, journal = {Environmental research}, volume = {263}, number = {Pt 3}, pages = {120237}, doi = {10.1016/j.envres.2024.120237}, pmid = {39461701}, issn = {1096-0953}, mesh = {*Denitrification ; Electron Transport ; Sewage/microbiology ; Metagenomics/methods ; Bacteria/metabolism/genetics ; Iron/metabolism ; Waste Disposal, Fluid/methods ; Ferric Compounds/metabolism/chemistry ; Oxidation-Reduction ; }, abstract = {Elemental iron provides a viable strategy to improve the denitrification efficiency by expediting electron transport. However, the roles of magnetic iron powder (Fe3O4) on mixotrophic denitrification remains unknown. In this study, the intra/extracellular electron transfer (IET/EET) and microbial metabolism mechanisms were explored in a Fe3O4-mediated sulfide-autotrophic and heterotrophic denitrification system. The results showed that Fe3O4 promoted the formation of dense clump structure with filamentous cross-linking in activated sludge. Fe3O4 could increase the coenzyme Q activity in IET and the content of free riboflavin and cytochrome c in EET. Metagenomic analysis indicated that denitrification, sulfide oxidation and sulfate reduction were the main pathways of nitrogen and sulfur metabolism, and the enriched denitrifying bacteria (Halomonas and Hypobacterium) and sulfur-oxidizing bacteria (Marinicella) could stably support nitrate removal. This study expands our understanding of the IET/EET during Fe3O4-mediated mixotrophic denitrification process, providing a novel insight for nitrogen removal from marine recirculating aquaculture wastewater.}, } @article {pmid39461614, year = {2024}, author = {Tian, X and Qin, X and Jia, X and Lyu, Q and Li, S and Jiang, L and Chen, L and Yan, Z and Huang, J}, title = {Lignocellulose degradation and temperature adaptation mechanisms during composting of mushroom residue and wood chips at low temperature with inoculation of psychrotolerant microbial agent.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {363}, number = {Pt 2}, pages = {125156}, doi = {10.1016/j.envpol.2024.125156}, pmid = {39461614}, issn = {1873-6424}, mesh = {*Lignin/metabolism ; *Composting ; *Wood ; *Cold Temperature ; Agaricales/physiology ; Biodegradation, Environmental ; Adaptation, Physiological ; Soil Microbiology ; Bacteria/metabolism/genetics ; }, abstract = {Low ambient temperature become the limiting factor of composting in cold regions, thus hindering the recycle of agricultural and forestry wastes. In this study, the composting of mushroom residue and wood chips (MRWC) under low temperature was successfully implemented with inoculation of psychrotolerant cellulolytic microbial agent. Composting entered thermophilic stage on third day and the peak temperature reached to 66.25 °C. After 84 days of composting, the degradation rate of cellulose and hemicellulose was 40.85% and 100%, respectively and the compost product was completely mature and met the requirements of organic fertilizer. Metagenomic and transcriptome sequencing were applied to reveal the microbial composition and their substrates conversion functions and adaptation mechanisms through low to high temperatures. Streptomyces, Mesorhizobium, Devosia, Aspergillus and Mucor were dominant genera in the microbial community that were rich in genes of lignocellulose degradation. Various genes related to low temperature adaptation (fatty acid, trehalose, mannitol, betaine metabolism and cold shock mechanism) and high temperature tolerance (heat shock and antioxidant) were detected during MRWC composting. These results indicated that microbes during composting constituted a high-efficiency lignocellulosic ultilization system in cold conditions. Besides, the microbes of microbial agent, especially Streptomyces and Aspergillus, possessed numerous genes involving in lignocellulose degradation and temperature adaptation and quite different temperature response patterns were found to perform in bacteria and fungi. The transcription levels of most these genes in Aspergillus exhibited significant differences under different substrates and temperature conditions, suggesting that the inoculum was crucial to the composting process and beneficial to maintain the temperature of piles. This study demonstrated that the application of psychrotolerant microbes was a promising strategy to increase the efficiency of composting in cold regions and these results could also provided the guidance for optimizing microbial agent.}, } @article {pmid39461337, year = {2024}, author = {Häcker, D and Siebert, K and Smith, BJ and Köhler, N and Riva, A and Mahapatra, A and Heimes, H and Nie, J and Metwaly, A and Hölz, H and Manz, Q and De Zen, F and Heetmeyer, J and Socas, K and Le Thi, G and Meng, C and Kleigrewe, K and Pauling, JK and Neuhaus, K and List, M and Pollard, KS and Schwerd, T and Haller, D}, title = {Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease.}, journal = {Cell host & microbe}, volume = {32}, number = {11}, pages = {2019-2034.e8}, doi = {10.1016/j.chom.2024.10.001}, pmid = {39461337}, issn = {1934-6069}, mesh = {*Crohn Disease/microbiology/therapy ; Animals ; Humans ; *Gastrointestinal Microbiome ; *Enteral Nutrition ; Mice ; *Feces/microbiology ; Child ; Female ; Male ; Germ-Free Life ; Adolescent ; Prospective Studies ; Interleukin-10/metabolism/genetics ; Metagenomics ; Fatty Acids/metabolism ; Disease Models, Animal ; Remission Induction ; Mice, Inbred C57BL ; Clostridiales ; Bacteria/classification/genetics ; }, abstract = {Exclusive enteral nutrition (EEN) is a first-line therapy for pediatric Crohn's disease (CD), but protective mechanisms remain unknown. We established a prospective pediatric cohort to characterize the function of fecal microbiota and metabolite changes of treatment-naive CD patients in response to EEN (German Clinical Trials DRKS00013306). Integrated multi-omics analysis identified network clusters from individually variable microbiome profiles, with Lachnospiraceae and medium-chain fatty acids as protective features. Bioorthogonal non-canonical amino acid tagging selectively identified bacterial species in response to medium-chain fatty acids. Metagenomic analysis identified high strain-level dynamics in response to EEN. Functional changes in diet-exposed fecal microbiota were further validated using gut chemostat cultures and microbiota transfer into germ-free Il10-deficient mice. Dietary model conditions induced individual patient-specific strain signatures to prevent or cause inflammatory bowel disease (IBD)-like inflammation in gnotobiotic mice. Hence, we provide evidence that EEN therapy operates through explicit functional changes of temporally and individually variable microbiome profiles.}, } @article {pmid39461216, year = {2025}, author = {Wirth, R and Shetty, P and Bagi, Z and Kovács, KL and Maróti, G}, title = {Feedstock-dependent antibiotic resistance gene patterns and expression profiles in industrial scale biogas plants revealed by meta-omics technology.}, journal = {Water research}, volume = {268}, number = {Pt A}, pages = {122650}, doi = {10.1016/j.watres.2024.122650}, pmid = {39461216}, issn = {1879-2448}, mesh = {*Biofuels ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Metagenome ; Wastewater/microbiology ; Sewage/microbiology ; Bioreactors ; Bacteria/genetics ; }, abstract = {This study investigated antimicrobial resistance in the anaerobic digesters of two industrial-scale biogas plants processing agricultural biomass and municipal wastewater sludge. A combination of deep sequencing and genome-centric workflow was implemented for metagenomic and metatranscriptomics data analysis to comprehensively examine potential antimicrobial resistance in microbial communities. Anaerobic microbes were found to harbour numerous antibiotic resistance genes (ARGs), with 58.85% of the metagenome-assembled genomes (MAGs) harbouring antibiotic resistance. A moderately positive correlation was observed between the abundance and expression of ARGs. ARGs were located primarily on bacterial chromosomes. A higher expression of resistance genes was observed on plasmids than on chromosomes. Risk index assessment suggests that most ARGs identified posed a significant risk to human health. However, potentially pathogenic bacteria showed lower ARG expression than non-pathogenic ones, indicating that anaerobic treatment is effective against pathogenic microbes. Resistomes at the gene category level were associated with various antibiotic resistance categories, including multidrug resistance, beta-lactams, glycopeptides, peptides, and macrolide-lincosamide-streptogramin (MLS). Differential expression analysis revealed specific genes associated with potential pathogenicity, emphasizing the importance of active gene expression in assessing the risks associated with ARGs.}, } @article {pmid39460615, year = {2024}, author = {Wen, J and Zhang, H and Chu, D and Chen, X and Feng, J and Wang, Y and Liu, G and Zhang, Y and Li, Y and Ning, K}, title = {Deep learning revealed the distribution and evolution patterns for invertible promoters across bacterial lineages.}, journal = {Nucleic acids research}, volume = {52}, number = {21}, pages = {12817-12830}, pmid = {39460615}, issn = {1362-4962}, support = {32071465//National Natural Science Foundation of China/ ; 2023YFA1800900//National Key Research and Development Program of China/ ; }, mesh = {*Promoter Regions, Genetic ; *Deep Learning ; *Bacteria/genetics/classification ; *Genome, Bacterial ; *Phylogeny ; *Evolution, Molecular ; Gene Expression Regulation, Bacterial ; Metagenome/genetics ; Biofilms ; }, abstract = {Invertible promoters (invertons) are crucial regulatory elements in bacteria, facilitating gene expression changes under stress. Despite their importance, their prevalence and the range of regulated gene functions are largely unknown. We introduced DeepInverton, a deep learning model that identifies invertons across a broad phylogenetic spectrum without using sequencing reads. By analyzing 68 733 bacterial genomes and 9382 metagenomes, we have uncovered over 200 000 nonredundant invertons and have also highlighted their abundance in pathogens. Additionally, we identified a post-Cambrian Explosion increase of invertons, paralleling species diversification. Furthermore, we revealed that invertons regulate diverse functions, including antimicrobial resistance and biofilm formation, underscoring their role in environmental adaptation. Notably, the majority of inverton identifications by DeepInverton have been confirmed by the in vitro experiments. The comprehensive inverton profiles have deepened our understanding of invertons at pan-genome and pan-metagenome scales, enabling a broad spectrum of applications in microbial ecology and synthetic biology.}, } @article {pmid39460431, year = {2024}, author = {Lin, B and Melnikov, V and Guo, S and Cao, Z and Ye, Z and Ye, Z and Ji, C and Chen, J and Wang, J and Zhang, H and Jiang, Y and Shi, C and Chen, Z and Zhang, Q and Ma, Z and Qiao, N and Chen, L and Wang, M and Wang, Y and Zhang, Z and Ye, H and Li, Y and Zhang, Y and Gao, R and Yu, Y}, title = {Concomitant gut dysbiosis and defective gut barrier serve as the bridges between hypercortisolism and chronic systemic inflammation in Cushing's disease.}, journal = {European journal of endocrinology}, volume = {191}, number = {5}, pages = {509-522}, doi = {10.1093/ejendo/lvae139}, pmid = {39460431}, issn = {1479-683X}, support = {82202906, 81972221, 81970716, 82170841, 82200921, 82370656, U21A20389, 82073640//National Natural Science Foundation of China/ ; SHDC12018X04//Shanghai Hospital Development Center/ ; 2023-I2M-C&T-B-125//CAMS Innovation Fund for Medical Sciences/ ; //National Project for Promoting the Diagnosis and Treatment of Major Diseases/ ; //MDT/ ; }, mesh = {Humans ; *Dysbiosis/metabolism ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Adult ; Middle Aged ; Caco-2 Cells ; *Inflammation/metabolism ; Feces/microbiology/chemistry ; Intestinal Mucosa/metabolism/microbiology ; Pituitary ACTH Hypersecretion/metabolism ; Cushing Syndrome/metabolism/microbiology ; Carrier Proteins/metabolism ; }, abstract = {OBJECTIVE: The aim of this study was to investigate the gut microbial signatures and related pathophysiological implications in patients with Cushing's disease (CD).

DESIGN AND METHODS: Twenty-seven patients with CD and 45 healthy controls were enrolled. Based on obtained metagenomics data, we performed correlation, network study, and genome interaction group (GIG) analysis. Fecal metabolomics and serum enzyme linked immunosorbent assay (ELISA) analysis were conducted in dichotomized CD patients. Caco-2 cells were incubated with gradient concentrations of cortisol for subsequent transepithelial electrical resistance (TEER) measurement, FITC-dextran transwell permeability assay, qPCR, and western blot analysis.

RESULTS: Gut microbial composition in patients with CD was notably different from that in healthy controls. Network analysis revealed that Eubacterium siraeum might serve as the core specie in the gut microbial system of CD patients. Subsequent GIG analysis identified the positive correlations between GIG9 and UFC. Further serum ELISA and fecal metabolomics uncovered that CD patients with elevated UFC levels were characterized with increased lipopolysaccharide binding protein (LBP). Moreover, remarkable positive association was found between LBP level and relative abundance of E. siraeum. TEER and FITC-dextran transwell assays demonstrated that hypercortisolism induced increased gut permeability. Further qPCR and western blot analysis suggested that dysregulated AhR/Claudin 2 axis might be involved in the development of hypercortisolism-induced defective gut barrier function.

CONCLUSIONS: Disease activity associated dysbiosis and defective gut barrier might jointly facilitate the development of systemic inflammation in patients with CD.}, } @article {pmid39459947, year = {2024}, author = {Vansia, R and Smadi, M and Phelan, J and Wang, A and Bilodeau, GJ and Pernal, SF and Guarna, MM and Rott, M and Griffiths, JS}, title = {Viral Diversity in Mixed Tree Fruit Production Systems Determined through Bee-Mediated Pollen Collection.}, journal = {Viruses}, volume = {16}, number = {10}, pages = {}, pmid = {39459947}, issn = {1999-4915}, support = {J-002323//Agriculture and Agri-Food Canada/ ; N-000212//Canadian Food Inspection Agency/ ; GRDI-SID-P-1903//Canadian Food Inspection Agency/ ; }, mesh = {*Pollen/virology ; Bees/virology ; Animals ; *Fruit/virology ; *Plant Diseases/virology ; *Plant Viruses/genetics/isolation & purification/classification ; *Pollination ; Virome/genetics ; Prunus/virology ; Metagenomics ; Trees/virology ; Malus/virology ; Ilarvirus/genetics/isolation & purification/classification ; Phylogeny ; Nepovirus/genetics/isolation & purification/classification/physiology ; }, abstract = {Commercially cultivated Prunus species are commonly grown in adjacent or mixed orchards and can be infected with unique or commonly shared viruses. Apple (Malus domestica), another member of the Rosacea and distantly related to Prunus, can share the same growing regions and common pathogens. Pollen can be a major route for virus transmission, and analysis of the pollen virome in tree fruit orchards can provide insights into these virus pathogen complexes from mixed production sites. Commercial honey bee (Apis mellifera) pollination is essential for improved fruit sets and yields in tree fruit production systems. To better understand the pollen-associated virome in tree fruits, metagenomics-based detection of plant viruses was employed on bee and pollen samples collected at four time points during the peak bloom period of apricot, cherry, peach, and apple trees at one orchard site. Twenty-one unique viruses were detected in samples collected during tree fruit blooms, including prune dwarf virus (PDV) and prunus necrotic ringspot virus (PNRSV) (Genus Ilarvirus, family Bromoviridae), Secoviridae family members tomato ringspot virus (genus Nepovirus), tobacco ringspot virus (genus Nepovirus), prunus virus F (genus Fabavirus), and Betaflexiviridae family member cherry virus A (CVA; genus Capillovirus). Viruses were also identified in composite leaf and flower samples to compare the pollen virome with the virome associated with vegetative tissues. At all four time points, a greater diversity of viruses was detected in the bee and pollen samples. Finally, the nucleotide sequence diversity of the coat protein regions of CVA, PDV, and PNRSV was profiled from this site, demonstrating a wide range of sequence diversity in pollen samples from this site. These results demonstrate the benefits of area-wide monitoring through bee pollination activities and provide new insights into the diversity of viruses in tree fruit pollination ecosystems.}, } @article {pmid39459879, year = {2024}, author = {da Costa, AC and Tozetto-Mendoza, TR and Foro Ramos, EDS and Bortoletto, P and Ferreira, NE and Honorato, L and Garcia Barbosa, EM and Paião, HGO and de Souza, AF and Linhares, IM and Spandorfer, SD and Leal, E and Mendes-Correa, MC and Witkin, SS}, title = {First Detection and Characterization of Smacovirus in the Human Vagina in Two Sequential Samples over a Twelve-Day Interval.}, journal = {Viruses}, volume = {16}, number = {10}, pages = {}, pmid = {39459879}, issn = {1999-4915}, mesh = {Humans ; Female ; *Vagina/virology ; *Phylogeny ; *Genome, Viral ; Adult ; Metagenomics/methods ; DNA, Viral/genetics ; DNA Viruses/genetics/isolation & purification/classification ; New York City ; Young Adult ; Middle Aged ; }, abstract = {BACKGROUND: Smacovirus is a CRESS-DNA virus identified almost exclusively in transient fecal samples from various vertebrate species.

OBJECTIVE: We evaluated human vaginal samples for the presence and maintenance of Smacovirus.

METHODS: Viral metagenomics analysis was performed on vaginal samples collected from 28 apparently healthy women in New York City, USA. Twenty-one of the women provided duplicate samples over a 12-21-day interval.

RESULTS: Phylogenetic analysis identified two samples from the same individual, collected over a twelve-day interval, that were positive for the complete Smacovirus genome. All detected sequence contigs belonged to a single variant of CRESS-DNA.

CONCLUSIONS: The continuous presence of Smacovirus in the human vagina over a twelve-day period was identified.}, } @article {pmid39459599, year = {2024}, author = {Ozer, H and Ozdemir, N and Ates, A and Koklu, R and Ozturk Erdem, S and Ozdemir, S}, title = {Circular Utilization of Coffee Grounds as a Bio-Nutrient through Microbial Transformation for Leafy Vegetables.}, journal = {Life (Basel, Switzerland)}, volume = {14}, number = {10}, pages = {}, pmid = {39459599}, issn = {2075-1729}, abstract = {This study explores the production of bio-nutrients from bioactive compound-rich spent coffee grounds (SCG) and biochar (BC) through composting after inoculation with a biological agent and its impact on the growth performance of garden cress and spinach. The SCG was composted with six doses of BC (0, 5, 10, 15, 20, and 25%). The compost with 10% BC exhibited the best maturity, humification, and phytotoxicity index values of dissolved organic carbon (DOC), humification index (E4/E6), and germination index (GI). A metagenome analysis showed that compost starter enhanced the bacterial community's relative abundance, richness, and diversity in SCG and BC treatments. This improvement included increased Patescibacteria, which can break down noxious phenolic compounds found in SCG and BC. The BC enriched the compost with phosphorus and potassium while preserving the nitrogen. In plant growth experiments, the total chlorophyll content in compost-treated garden cress and spinach was 2.47 and 4.88 mg g[-1], respectively, which was significantly greater (p ≤ 0.05) than in unfertilized plants and similar to the plants treated with traditional fertilizer. Overall, the results show that the compost of SCG + BC was well-suited for promoting the growth of garden cress and spinach, providing adequate nutrients as a fertilizer for these leafy vegetables.}, } @article {pmid39458495, year = {2024}, author = {Ohkusa, T and Kato, K and Sekizuka, T and Sugiyama, T and Sato, N and Kuroda, M}, title = {Comparison of the Gut Microbiota of Patients Who Improve with Antibiotic Combination Therapy for Ulcerative Colitis and Those Who Do Not: Investigation by Fecal Metagenomic Analyses.}, journal = {Nutrients}, volume = {16}, number = {20}, pages = {}, pmid = {39458495}, issn = {2072-6643}, mesh = {Humans ; *Colitis, Ulcerative/microbiology/drug therapy ; *Gastrointestinal Microbiome/drug effects ; *Feces/microbiology ; *Anti-Bacterial Agents/administration & dosage/pharmacology ; Male ; Female ; Adult ; Middle Aged ; *Metronidazole/administration & dosage ; *Drug Therapy, Combination ; Metagenomics/methods ; Amoxicillin/administration & dosage/pharmacology ; Tetracycline/pharmacology/administration & dosage ; Dysbiosis/microbiology ; Young Adult ; Treatment Outcome ; }, abstract = {Background/Objectives: The cause of ulcerative colitis (UC) may be related to commensal bacteria in genetically susceptible patients. We previously demonstrated that triple antibiotic combination therapy induces remission in patients with active UC in randomized controlled trials (RCTs). Now, we investigate changes in the gut microbiota of patients who responded to the antibiotic combination therapy. Methods: Thirty-one patients with UC given ATM/AFM (amoxicillin, metronidazole, and tetracycline or fosfomycin) therapy for two weeks were enrolled in this study. The clinical conditions of these UC patients were evaluated by the partial Mayo score. The gut microbiota was compared via the metagenomic shot gun analysis of fecal samples. Results: Of the 31 patients, 16 and 8 experienced complete and partial remission, respectively, over three months in response to ATM/AFM therapy, whereas ATM/AFM showed no efficacy in 7 patients. The dysbiosis before treatment in the active stage could be associated with increased populations of Bacteroides, Parabacteroides, Rickenella, Clostridium, Flavonifractor, Pelagibacter, Bordetella, Massilia, and Piscrickettsia species. Metagenomic analysis revealed dramatic changes in the gut microbiota at an early stage, that is, just two weeks after starting ATM/AFM therapy. After treatment in the responder group, the populations of bifidobacterium and lactobacilli species were significantly increased, while the population of bacteroides decreased. Conclusions: These results suggest that metagenomic analysis demonstrated a marked change in the gut microbiota after antibiotic combination treatment. In the triple antibiotic combination therapy, remission was associated with an increase in bifidobacterium and lactobacilli species.}, } @article {pmid39458465, year = {2024}, author = {Filardo, S and Di Pietro, M and Mastromarino, P and Porpora, MG and Sessa, R}, title = {A Multi-Strain Oral Probiotic Improves the Balance of the Vaginal Microbiota in Women with Asymptomatic Bacterial Vaginosis: Preliminary Evidence.}, journal = {Nutrients}, volume = {16}, number = {20}, pages = {}, pmid = {39458465}, issn = {2072-6643}, mesh = {Humans ; Female ; *Probiotics/administration & dosage ; *Vaginosis, Bacterial/microbiology/drug therapy/therapy ; *Vagina/microbiology ; Adult ; Prospective Studies ; Pilot Projects ; *Microbiota/drug effects ; Administration, Oral ; Young Adult ; Lactobacillus ; }, abstract = {BACKGROUND/OBJECTIVES: the vaginal microbiota is known to confer protection in the genital ecosystem, due to the predominance of different Lactobacillus species, playing a crucial role in women's health; alterations in the composition of the microbial communities in the vagina can be associated with the development of bacterial vaginosis (BV). Current therapy for BV involves oral or intravaginal administration of metronidazole or clindamycin, albeit the high recurrence rates suggest a need for alternative therapeutic tools, such as probiotics. Herein, the diversity and composition of vaginal microbiota in women with asymptomatic BV was investigated before and after the oral administration of a multi-strain probiotic formulation.

METHODS: a prospective observational pilot study with pre-post design was carried out from 1 June 2022, to 31 December 2022, on reproductive-age women with asymptomatic BV, as diagnosed via Nugent score, and matched healthy controls. The probiotic was administered to all study participants as acid-resistant oral capsules (twice daily), and a vaginal swab was collected at baseline and after 2 months of treatment, for the metagenomic analysis of 16s rDNA.

RESULTS: the diversity and richness of the vaginal microbiota in women with BV were significantly reduced after 2 months of supplementation with the oral probiotic, as evidenced by measures of α-diversity. Interestingly, some bacterial genera typically associated with dysbiosis, such as Megasphaera spp., were significantly decreased; whereas, at the same time, Lactobacillus spp. Doubled.

CONCLUSIONS: our preliminary results suggest that the multi-strain oral probiotic is a beneficial treatment specifically targeting the dysbiotic vaginal microenvironment.}, } @article {pmid39458402, year = {2024}, author = {Chen, X and Mo, L and Zhang, L and Huang, L and Gao, Z and Peng, J and Yu, Z and Zhang, X}, title = {Taxonomic Diversity, Predicted Metabolic Pathway, and Interaction Pattern of Bacterial Community in Sea Urchin Anthocidaris crassispina.}, journal = {Microorganisms}, volume = {12}, number = {10}, pages = {}, pmid = {39458402}, issn = {2076-2607}, support = {2023A1515011859//Guangdong Natural Science Foundation of China/ ; }, abstract = {Bacterial assemblages associated with sea urchin are critical to their physiology and ecology within marine ecosystems. In this study, we characterized the bacterial communities in wild sea urchin Anthocidaris crassispina captured in Daya Bay, South China Sea. A total of 363 amplicon sequence variants belonging to nine phyla and 141 genera were classified from intestine, body surface, and surrounding seawater samples. Proteobacteria, Firmicutes, and Bacteroidetes were the dominant bacteria phyla found in this study. A network analysis of bacterial interspecies interactions revealed varying complexity, stability, connectivity, and relationship patterns across the samples, with the most intricate network observed in the surrounding seawater. Metagenomic predictions highlighted the distinct bacterial metabolic pathways, with significant differences between intestine and seawater samples. Notably, pathways associated with polysaccharide degradation, including chitin derivatives, starch, and CoM biosynthesis, were markedly abundant, underscoring the gut microbiota's key role in digesting algae. In addition, other metabolic pathways in intestine samples were linked to immune response regulation of sea urchins. Overall, this study provides a comprehensive overview of the bacterial community structure and potential functional roles in A. crassispina.}, } @article {pmid39458395, year = {2024}, author = {Wang, L and Wang, Q and Zhou, Y}, title = {Oral Microbial Translocation Genes in Gastrointestinal Cancers: Insights from Metagenomic Analysis.}, journal = {Microorganisms}, volume = {12}, number = {10}, pages = {}, pmid = {39458395}, issn = {2076-2607}, abstract = {Along with affecting oral health, oral microbial communities may also be endogenously translocated to the gut, thereby mediating the development of a range of malignancies in that habitat. While species-level studies have proven the capability of oral pathogens to migrate to the intestine, genetic evidence supporting this mechanism remains insufficient. In this study, we identified over 55,000 oral translocation genes (OTGs) associated with colorectal cancer (CRC) and inflammatory bowel disease (IBD). These genes are primarily involved in signal transduction and cell wall biosynthesis and show consistency in their functions between IBD and CRC. Furthermore, we found that Leclercia adecarboxylata, a newly discovered opportunistic pathogen, has a significantly high abundance in the gut microbiota of colorectal cancer patients. OTGs of this pathogen were enriched in 15 metabolic pathways, including those associated with amino acid and cofactor metabolism. These findings, for the first time, provide evidence at the genetic level of the transfer of oral pathogens to the intestine and offer new insights into the understanding of the roles of oral pathogens in the development of gastrointestinal cancers.}, } @article {pmid39458354, year = {2024}, author = {Mateo, D and Carrión, N and Cabrera, C and Heredia, L and Marquès, M and Forcadell-Ferreres, E and Pino, M and Zaragoza, J and Moral, A and Cavallé, L and González-de-Echávarri, JM and Vicens, P and Domingo, JL and Torrente, M}, title = {Gut Microbiota Alterations in Alzheimer's Disease: Relation with Cognitive Impairment and Mediterranean Lifestyle.}, journal = {Microorganisms}, volume = {12}, number = {10}, pages = {}, pmid = {39458354}, issn = {2076-2607}, support = {PID2019-103888RB-I00//Ministerio de Ciencia e Innovación and Agencia Estatal de Investigación/ ; FI_B00314//Agència de Gestió d'Ajuts Universitaris i de Recerca/ ; }, abstract = {Recently, an association between dysbiosis of the gut microbiota (GMB) and the development of several diseases, such as Alzheimer's disease (AD), has been proposed. Dysbiosis involves changes in microbial diversity influenced by environmental factors, like diet or lifestyle. In this study, we investigated the role of GMB parameters in Spanish AD patients, assessing the impact of adherence to the Mediterranean lifestyle (ML), as well as to characterize these parameters in relation to neuropsychological, neuropsychiatric, emotional, and functionality parameters. A case-control study was conducted to investigate the association between the composition of the GMB and cognitive, emotional, neuropsychiatric, and functionality status in Spanish AD patients, along with a shotgun metagenomics approach. Richness and alpha-diversity were significantly lower in the AD group compared to the controls. PERMANOVA and ANOSIM tests of Bray-Curtis dissimilarity, Aitchison distance, and Jaccard similarity did not showed significant differences in beta-diversity between the two groups. Moreover, associations between various phyla of the AD group and orientation performance, food consumption, and activities of daily living were identified. Dysbiosis observed in Spanish AD patients is characterized by reductions in richness and alpha-diversity, alongside alterations in GMB composition, which may be linked to adherence to the ML and cognitive and functionality symptoms.}, } @article {pmid39458342, year = {2024}, author = {Tang, B and Wang, Y and Dong, Y and Cui, Q and Zeng, Z and He, S and Zhao, W and Lancuo, Z and Li, S and Wang, W}, title = {The Catalog of Microbial Genes and Metagenome-Assembled Genomes from the Gut Microbiomes of Five Typical Crow Species on the Qinghai-Tibetan Plateau.}, journal = {Microorganisms}, volume = {12}, number = {10}, pages = {}, pmid = {39458342}, issn = {2076-2607}, support = {2022-HZ-812//the program of science and technology international coop-654 eration project of Qinghai province/ ; }, abstract = {While considerable progress has been made in understanding the complex relationships between gut microbiomes and their hosts, especially in mammals and humans, the functions of these microbial communities in avian species remain largely unexplored. This gap in knowledge is particularly notable, given the critical roles gut microbiomes are known to play in facilitating crucial physiological functions, such as digestion, nutrient absorption, and immune system development. Corvidae birds are omnivorous and widely distributed across various habitats, exhibiting strong adaptability and often displaying the traits of accompanying humans. However, to date, information on species composition, sequenced genomes, and functional characteristics of crow gut microbes is lacking. Herein, we constructed the first relatively comprehensive crows gut microbial gene catalog (2.74 million genes) and 195 high-quality and medium-quality metagenome-assembled genomes using 53 metagenomic samples from five typical crow species (Pyrrhocorax pyrrhocorax, Corvus dauuricus, Corvus frugilegus, Corvus macrorhynchos, and Corvus corax) on the Qinghai-Tibetan Plateau. The species composition of gut microbiota at the phylum and genus levels was revealed for these five crow species. Simultaneously, numerous types of prevalent pathogenic bacteria were identified, indicating the potential of these crows to transmit diseases within the local community. At the functional level, we annotated a total of 356 KEGG functional pathways, six CAZyme categories, and 3607 virulence factor genes in the gut microbiomes of the crows. The gut microbiota of five distinct crow species underwent a comparative analysis, which uncovered significant differences in their composition, diversity, and functional structures. Over 36% of MAGs showed no overlap with existing databases, suggesting they might represent new species. Consequently, these findings enriched the dataset of microbial genomes associated with crows' digestive systems. Overall, this study offers crucial baseline information regarding the gut microbial gene catalog and genomes in crows, potentially aiding microbiome-based research, as well as an evaluation of the health risks to humans from the bacterial pathogens transmitted by wild birds.}, } @article {pmid39458305, year = {2024}, author = {Chakraborty, N and Hoke, A and Campbell, R and Holmes-Hampton, G and Kumar, VP and Moyler, C and Gautam, A and Hammamieh, R and Ghosh, SP}, title = {Ionizing Radiation Dose Differentially Affects the Host-Microbe Relationship over Time.}, journal = {Microorganisms}, volume = {12}, number = {10}, pages = {}, pmid = {39458305}, issn = {2076-2607}, support = {DM178020 and RAB23338//JPC-7 project and the AFRRI Intramural funding/ ; }, abstract = {Microorganisms that colonize in or on a host play significant roles in regulating the host's immunological fitness and bioenergy production, thus controlling the host's stress responses. Radiation elicits a pro-inflammatory and bioenergy-expensive state, which could influence the gut microbial compositions and, therefore, the host-microbe bidirectional relationship. To test this hypothesis, young adult mice were exposed to total body irradiation (TBI) at doses of 9.5 Gy and 11 Gy, respectively. The irradiated mice were euthanized on days 1, 3, and 9 post TBI, and their descending colon contents (DCCs) were collected. The 16S ribosomal RNAs from the DCCs were screened to find the differentially enriched bacterial taxa due to TBI. Subsequently, these data were analyzed to identify the metagenome-specific biofunctions. The bacterial community of the DCCs showed increased levels of diversity as time progressed following TBI. The abundance profile was the most divergent at day 9 post 11 Gy TBI. For instance, an anti-inflammatory and energy-harvesting bacterium, namely, Firmicutes, became highly abundant and co-expressed in the DCC with pro-inflammatory Deferribacteres at day 9 post 11 Gy TBI. A systems evaluation found a diverging trend in the regulation profiles of the functional networks that were linked to the bacteria and metabolites of the DCCs, respectively. Additionally, the network clusters associated with lipid metabolism and bioenergy synthesis were found to be activated in the DCC bacteria but inhibited in the metabolite space at day 9 post 11 Gy. Taking these results together, the present analysis indicated a disrupted mouse-bacteria symbiotic relationship as time progressed after lethal irradiation. This information can help develop precise interventions to ameliorate the symptoms triggered by TBI.}, } @article {pmid39457862, year = {2024}, author = {Liu, Y and Wang, Y and Wen, Y and Ma, L and Riqing, D and Jiang, M}, title = {Dietary Conversion from All-Concentrate to All-Roughage Alters Rumen Bacterial Community Composition and Function in Yak, Cattle-Yak, Tibetan Yellow Cattle and Yellow Cattle.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {20}, pages = {}, pmid = {39457862}, issn = {2076-2615}, support = {2023YFQ0076//Sichuan Science and Technology Program/ ; XM2023007//Southwest Minzu University Double World Class Project/ ; NQKJ-2023-07//Nagqu City science and technology Bureau key research and development project/ ; }, abstract = {The experiment was to compare the effects of switching all-concentrate to all-roughage diets on rumen microflora and functional metabolism of yak, cattle-yak, Tibetan yellow cattle and yellow cattle living in different altitudes. A total of 24 yaks, cattle-yaks, Tibetan yellow cattle and yellow cattle with a similar weight and good body condition aged 3.5 years were selected and divided into four groups according to species. They were fed a concentrate diet with 40% soybean meal and 60% corn meal for the first month (C group) and a roughage diet with dry corn stalks (100%) for the second month (R group); the formal experimental period was 60 d. These results showed that the conversion had a significant effect on the rumen microflora structure of the four herds, and the biggest difference between concentrate and roughage diets was yak and cattle-yak, followed by Tibetan yellow cattle and yellow cattle. At the phylum level, Bacteroidetes and Firmicutes still predominate in all groups. Compared with the C groups, the relative abundance of Lentisphaerae and Kiritimatiellaeota increased in all R groups, and Lentisphaerae was significantly increased in yak and cattle-yak (p < 0.05). At the genus and species levels, Prevotella had the highest abundance, and the relative abundances of Prevotella, Ruminococcus, Sarcina and Ruminobacter in R groups were lower, while the abundances of other differential genera, including Methanobrevibacter, Fibrobacter, Treponema, Eubacterium, Butyrivibrio, Succinivibrio and Succinimonas, were all higher. Roughage diets increased the number of unique genes and functional genes encoding different CAZymes in rumen microorganisms in all four herds. In the functional contribution analysis, with the exception of ABC transporters and methane metabolism, Prevotella was the main contributor to almost all of these functions. In methane metabolism, Methanobrevibacter had the highest relative abundance, followed by Prevotella, Clostridia and Bacteroidales in all groups. Compared with Tibetan yellow cattle and yellow cattle, yaks and cattle-yaks have better adaptability to roughage, and its utilization rate can be fully improved to reduce methane emission. The study indicates that when four herds are converted to high roughage at the later stage of feeding, the growth and reproduction of rumen microorganisms are affected, and the abundance and diversity of rumen microorganisms are increased to varying degrees. The transformation of concentrate to roughage diet can change the metabolic pathways of rumen microorganisms in yaks and finally affect the fermentation mode of rumen. The above results provide a theoretical basis for the research and development of fattening feeds for yaks, cattle-yaks, Tibetan yellow cattle and yellow cattle and the intensive feeding of livestock on the plateau.}, } @article {pmid39457554, year = {2024}, author = {Yang, X and Zhang, Y and Gao, C and Pan, Y and Du, S and Xiao, S and Zhou, Z}, title = {The Effect of Drugs on the Intestinal Microbiota in Crohn's Disease.}, journal = {Biomedicines}, volume = {12}, number = {10}, pages = {}, pmid = {39457554}, issn = {2227-9059}, support = {2023YFS0289//Sichuan Science and Technology Program/ ; }, abstract = {OBJECTIVE: We took advantage of a single-center cross-sectional study to investigate the effect of different drugs on intestinal microbiota and function in Crohn's disease.

METHODS: We studied the difference in fecal microbiota of Crohn's disease patients treated with mesalazine, azathioprine, and infliximab, as well as untreated patients, by metagenome and screened for differential microbiota. Further, we investigated functional differences in intestinal microbiota among the four groups.

RESULTS: Through metagenomic sequencing, we found that there was no difference between the four groups in ACE and Chao1 indices, but IFX and mesalazine improved species diversity and homogeneity compared to the untreated group, as evidenced by statistically significant differences in the Shannon index, Simpson index, and pielou_evenness. In addition, beta diversity suggested a difference between groups, but the difference was not significant. Non-parametric tests revealed differences between the four groups at the phylum level, class level, and genus level. Further analysis by LEfSe analysis revealed that the level of short-chain fatty acid-producing microbiota was increased in the treated groups, while there was no difference between the treated groups when compared to each other. Finally, the KEGG database and EggNOG database revealed that there were functional differences in intestinal microbiota among the four groups, including microbial metabolism pathway, cysteine and methionine metabolism pathway, cytoskeleton, etc. Conclusions: Mesalazine, azathioprine, and infliximab can all affect the intestinal microbiota and function in patients with Crohn's disease, and the drugs may alleviate intestinal inflammation in patients with Crohn's disease by modulating the intestinal microbiota.}, } @article {pmid39457500, year = {2024}, author = {Rembe, JD and Garabet, W and Lackmann, JW and Alizadehrahrouei, S and Augustin, M and Dissemond, J and Ibing, W and Köhrer, K and Pfeffer, K and Rommerskirchen, A and Scharf, SA and Wienemann, T and Wachtmeister, T and Schelzig, H and Stuermer, EK}, title = {Assessment and Monitoring of the Wound Micro-Environment in Chronic Wounds Using Standardized Wound Swabbing for Individualized Diagnostics and Targeted Interventions.}, journal = {Biomedicines}, volume = {12}, number = {10}, pages = {}, pmid = {39457500}, issn = {2227-9059}, support = {2021-28//Heinrich Heine University Düsseldorf/ ; 2020-21//Witten/Herdecke University/ ; //Jürgen Manchot Stiftung/ ; }, abstract = {Background/Objectives: Patient-specific diagnostic and therapeutic approaches are important in the care of people with chronic wounds. The heterogeneity of underlying disease profiles and the diversity of the wound micro-environment make generalized approaches difficult. While high-throughput molecular diagnostic methods are increasingly widespread and available, the analysis of objective biomolecular disease patterns has not found its way into everyday wound management. The aim of this study is to evaluate the use of wound swab samples for the analysis of biomarkers and disease patterns in people with chronic wounds. Methods: A sample cohort from the multicenter "Wound-BIOME" project was analyzed. The project aims to comprehensively investigate the local micro-environment of chronic wounds of various entities, healing tendencies and regeneration stages at the biomolecular level. A sample collection and handling protocol suitable for everyday use was tested and evaluated regarding feasibility for multiplex immunoassay, proteomics, small RNA sequencing (miRNA) and metagenome analyses (microbiomics). Results: It could be shown that standard wound swabs are well-suited for the analysis of the complex wound micro-environment using various high-throughput methods. Despite the sample heterogeneity, the quality was adequate to analyze biomolecular patterns. Conclusions: Initial analyses of protein signatures, microbial wound communities and miRNA patterns show promising results for future individualized diagnostics and targeted interventions.}, } @article {pmid39457438, year = {2024}, author = {Wei, Q and Song, Z and Chen, Y and Yang, H and Chen, Y and Liu, Z and Yu, Y and Tu, Q and Du, J and Li, H}, title = {Metagenomic Sequencing Elucidated the Microbial Diversity of Rearing Water Environments for Sichuan Taimen (Hucho bleekeri).}, journal = {Genes}, volume = {15}, number = {10}, pages = {}, pmid = {39457438}, issn = {2073-4425}, support = {(YSCX2035-011)//the Project of Original Innovation 2035/ ; (2022ZZCX093)//Sichuan Province financial independent innovation special project/ ; (SCCXTD-2024-15)//Sichuan Fresh Water Fish Innovation Team/ ; (cjb2024wzbh-011)//Ministry of Agriculture and Rural Affairs of the Yangtze River Basin Fisheries Administration Office-Artificial Breeding and Habitat Restoration of Sichuan taimen/ ; }, mesh = {Animals ; China ; *Metagenomics/methods ; Microbiota/genetics ; Water Microbiology ; Bacteria/genetics/classification ; Metagenome ; Biodiversity ; Fishes/microbiology/genetics ; Aquaculture/methods ; }, abstract = {BACKGROUND: Sichuan taimen (Hucho bleekeri) is a fish species endemic to China's upper Yangtze River drainage and has significant value as an aquatic resource. It was listed as a first-class state-protected wild animal by the Chinese government due to its very limited distribution and wild population at present.

METHODS: To elucidate the diversity of microorganisms in rearing water environments for H. bleekeri, metagenomic sequencing was applied to water samples from the Maerkang and Jiguanshan fish farms, where H. bleekeri were reared.

RESULTS: The results revealed that Pseudomonadota was the dominant phylum in the microbial communities of the water samples. Among the shared bacterial groups, Cyanobacteriota, Actinomycetota, Planctomycetota, Nitrospirota, and Verrucomicrobiota were significantly enriched in the water environment of Jiguanshan (p < 0.01), while Bacteroidota was more enriched in that of Maerkang (p < 0.01). Additionally, the Shannon diversity and Simpson index of the microbial community in the water environment of Maerkang were lower than in that of Jiguanshan.

CONCLUSIONS: The present study demonstrated the similarities and differences in the microbial compositions of rearing water environments for H. bleekeri, which are expected to benefit the artificial breeding of H. bleekeri in the future.}, } @article {pmid39457400, year = {2024}, author = {Arciuch-Rutkowska, M and Nowosad, J and Łuczyński, MK and Hussain, SM and Kucharczyk, D}, title = {Next-Generation Sequencing to Determine Changes in the Intestinal Microbiome of Juvenile Sturgeon Hybrid (Acipenser gueldenstaedtii♀ × Acipenser baerii♂) Resulting from Sodium Butyrate, Β-Glucan and Vitamin Supplementation.}, journal = {Genes}, volume = {15}, number = {10}, pages = {}, pmid = {39457400}, issn = {2073-4425}, support = {DWD/4/80/2020//Polish Ministry of Education and Science/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/genetics ; *beta-Glucans/pharmacology/administration & dosage ; *Butyric Acid/metabolism/pharmacology ; *Fishes/genetics/microbiology ; *High-Throughput Nucleotide Sequencing ; *Dietary Supplements ; *Vitamins/pharmacology/administration & dosage ; Animal Feed/analysis ; Male ; Female ; Hydrocortisone ; Muramidase/genetics ; }, abstract = {BACKGROUND/OBJECTIVES: The effect of sodium butyrate (NaB), β-glucan (βG) and vitamins in the diet on gut microbiome, cortisol level, lysozyme activity and growth parameters of juvenile hybrid sturgeon (Acipenser gueldenstaedtii♀ × Acipenser baerii♂) was determined.

METHODS: Sturgeon hybrids (n = 144) were divided into three groups with enriched feeding (mg/kg of feed): FQV1 (50 NaB; 20 βG; const. vitamins), FQV2 (150 NaB; 20 βG; const. vitamins), FQV3 (50 NaB; 60 βG; const. vitamins) and control (not supplemented), each group in triplicate, 12 fish in each repetition. Rearing was carried out for 30 days in controlled conditions. Gut microbiome was characterized using Next Generation Sequencing (NGS) of DNA samples isolated from intestinal content. Cortisol level was determined using the ELISA test. Lysozyme activity was measured by turbidimetric test.

RESULTS: Based on data obtained from NGS, it was determined that the FQV1 group is characterized by the highest values of diversity indices (Shannon, Simpson and Chao-1) and the largest number of ASVs (Amplicon Sequence Variants). The highest abundance of probiotic bacteria (Lactobacillus, Lactococcus) was determined in the FQV1 group. The highest cortisol concentration was determined in the control (33.26 ng/mL), while the lowest was in FQV3 (27.75 ng/mL). The highest lysozyme activity was observed in FQV1 (154.64 U/mL), and the lowest in FQV2 (104.39 U/mL) and control (121.37 U/mL) (p < 0.05). FQV2 was characterized by significantly more favorable values of breeding indicators (p < 0.05).

CONCLUSIONS: The obtained results prove that an appropriate composition of NaB, βG and vitamins can be used in the commercial breeding of juvenile hybrid sturgeons.}, } @article {pmid39457387, year = {2024}, author = {Naumova, OY and Dobrynin, PV and Khafizova, GV and Grigorenko, EL}, title = {The Association of the Oral Microbiota with Cognitive Functioning in Adolescence.}, journal = {Genes}, volume = {15}, number = {10}, pages = {}, pmid = {39457387}, issn = {2073-4425}, support = {P20HD091005//the Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; }, mesh = {Humans ; Male ; Adolescent ; *Cognition ; *Mouth/microbiology ; Child ; *Microbiota ; Saliva/microbiology ; Metagenomics/methods ; Bacteria/genetics/classification ; }, abstract = {Background: A growing body of research supports the role of the microbial communities residing in the digestive system in the host's cognitive functioning. Most of these studies have been focused on the gut microbiome and its association with clinical phenotypes in middle-aged and older adults. There is an insufficiency of population-based research exploring the association of normative cognitive functioning with the microbiome particularly with the oral microbiota. Methods: In this study, using metagenomics and metabolomics, we characterized the salivary microbiome diversity in a sample of 51 males of Hispanic and African American origin aged 12-18 years and explored the associations between the microbiome and the youths' cognitive performance captured with the Kaufman Assessment Battery for Children II (KABC-II). Results: Several bacterial species of the oral microbiota and related metabolic pathways were associated with cognitive function. In particular, we found negative associations between indicators of general intelligence and the relative abundance of Bacteroidetes and Lachnospiraceae and positive associations with Bifidobacteriaceae and Prevotella histicola sp. Among metabolic pathways, the super pathways related to bacterial cell division and GABA metabolism were linked to cognitive function. Conclusions: The results of our work are consistent with the literature reporting on the association between microbiota and cognitive function and support further population work to elucidate the potential for a healthy oral microbiome to improve cognitive health.}, } @article {pmid39456970, year = {2024}, author = {Yang, C and Wusigale, and You, L and Li, X and Kwok, LY and Chen, Y}, title = {Inflammation, Gut Microbiota, and Metabolomic Shifts in Colorectal Cancer: Insights from Human and Mouse Models.}, journal = {International journal of molecular sciences}, volume = {25}, number = {20}, pages = {}, pmid = {39456970}, issn = {1422-0067}, support = {2022YFHH0060//Inner Mongolia Autonomous Region Key R&D Plan Project/ ; NMGIRT2220//Inner Mongolia Autonomous Region Higher Education Institutions Innovation Team Development Plan/ ; }, mesh = {Animals ; *Colorectal Neoplasms/metabolism/microbiology/pathology ; *Gastrointestinal Microbiome ; Humans ; Mice ; *Inflammation/metabolism/microbiology ; *Disease Models, Animal ; Male ; Female ; Metabolomics/methods ; Metabolome ; Middle Aged ; Dextran Sulfate ; Dysbiosis/microbiology/metabolism ; Aged ; Feces/microbiology ; }, abstract = {Colorectal cancer (CRC) arises from aberrant mutations in colorectal cells, frequently linked to chronic inflammation. This study integrated human gut metagenome analysis with an azoxymethane and dextran sulfate sodium-induced CRC mouse model to investigate the dynamics of inflammation, gut microbiota, and metabolomic profiles throughout tumorigenesis. The analysis of stool metagenome data from 30 healthy individuals and 40 CRC patients disclosed a significant escalation in both gut microbiota diversity and abundance in CRC patients compared to healthy individuals (p < 0.05). Marked structural disparities were identified between the gut microbiota of healthy individuals and those with CRC (p < 0.05), characterized by elevated levels of clostridia and diminished bifidobacteria in CRC patients (p < 0.05). In the mouse model, CRC mice exhibited distinct gut microbiota structures and metabolite signatures at early and advanced tumor stages, with subtle variations noted during the intermediate phase. Additionally, inflammatory marker levels increased progressively during tumor development in CRC mice, in contrast to their stable levels in healthy counterparts. These findings suggest that persistent inflammation might precipitate gut dysbiosis and altered microbial metabolism. Collectively, this study provides insights into the interplay between inflammation, gut microbiota, and metabolite changes during CRC progression, offering potential biomarkers for diagnosis. While further validation with larger cohorts is warranted, the data obtained support the development of CRC prevention and diagnosis strategies.}, } @article {pmid39456772, year = {2024}, author = {Vilà-Quintana, L and Fort, E and Pardo, L and Albiol-Quer, MT and Ortiz, MR and Capdevila, M and Feliu, A and Bahí, A and Llirós, M and García-Velasco, A and Morell Ginestà, M and Laquente, B and Pozas, D and Moreno, V and Garcia-Gil, LJ and Duell, EJ and Pimenoff, VN and Carreras-Torres, R and Aldeguer, X}, title = {Metagenomic Study Reveals Phage-Bacterial Interactome Dynamics in Gut and Oral Microbiota in Pancreatic Diseases.}, journal = {International journal of molecular sciences}, volume = {25}, number = {20}, pages = {}, pmid = {39456772}, issn = {1422-0067}, support = {201912-31//Fundació la Marató de TV3/ ; 9986//European Molecular Biology Organization/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Metagenomics/methods ; *Bacteriophages/genetics ; *Feces/microbiology ; Pancreatic Neoplasms/microbiology/metabolism ; Male ; Mouth/microbiology ; Saliva/microbiology/metabolism ; Female ; Middle Aged ; Carcinoma, Pancreatic Ductal/microbiology/metabolism/virology ; Bacteria/genetics/classification/metabolism/isolation & purification ; Metagenome ; Pancreatitis, Chronic/microbiology/metabolism/virology ; Pancreatic Diseases/microbiology/metabolism/virology ; Aged ; Microbiota/genetics ; Adult ; }, abstract = {Individuals with pancreatic-related health conditions usually show lower diversity and different composition of bacterial and viral species between the gut and oral microbiomes compared to healthy individuals. We performed a thorough microbiome analysis, using deep shotgun sequencing of stool and saliva samples obtained from patients with chronic pancreatitis (CP), pancreatic ductal adenocarcinoma (PDAC), and healthy controls (HCs).We observed similar microbiota composition at the species level in both the gut and oral samples in PDAC patients compared to HCs, among which the most distinctive finding was that the abundance of oral-originated Fusobacterium nucleatum species did not differ between the oral and the gut samples. Moreover, comparing PDAC patients with HCs, Klebsiella oxytoca was significantly more abundant in the stool samples of PDAC patients, while Streptococcus spp. showed higher abundance in both the oral and stool samples of PDAC patients. Finally, the most important finding was the distinctive gut phage-bacterial interactome pattern among PDAC patients. CrAssphages, particularly Blohavirus, showed mutual exclusion with K. oxytoca species, while Burzaovirus showed co-occurrence with Enterobacteriaceae spp., which have been shown to be capable of inducing DNA damage in human pancreatic cells ex vivo. The interactome findings warrant further mechanistic studies, as our findings may provide new insights into developing microbiota-based diagnostic and therapeutic methods for pancreatic diseases.}, } @article {pmid39456764, year = {2024}, author = {Wang, X and Wang, Y and Yang, H and Liu, F and Cai, Y and Xiao, J and Fu, Q and Wan, P}, title = {Integrative Omics Strategies for Understanding and Combating Brown Planthopper Virulence in Rice Production: A Review.}, journal = {International journal of molecular sciences}, volume = {25}, number = {20}, pages = {}, pmid = {39456764}, issn = {1422-0067}, support = {CPSIBRF-CNRRI-202406//Fundamental Research Funds for Central Public Welfare Research Institute/ ; 2021YFD1401100//National Key Research and Development Program of China/ ; LY22C140008//Zhejiang Provincial Natural Science Foundation of China/ ; CARS-01//China Agriculture Research System/ ; CAAS-ASTIP-2021-CNRRI//Rice Pest Management Research Group of the Agri-cultural Science and Technology Innovation Program of China Academy of Agricultural Science/ ; }, mesh = {*Oryza/parasitology/genetics/microbiology ; *Hemiptera/genetics/pathogenicity ; Animals ; Genomics/methods ; Plant Diseases/parasitology/genetics/microbiology ; Virulence/genetics ; Proteomics/methods ; Metabolomics/methods ; Transcriptome ; Multiomics ; }, abstract = {The brown planthopper (Nilaparvata lugens, BPH) is a serious insect pest responsible for causing immense economic losses to rice growers around the globe. The development of high-throughput sequencing technologies has significantly improved the research on this pest, and its genome structure, gene expression profiles, and host-plant interactions are being unveiled. The integration of genomic sequencing, transcriptomics, proteomics, and metabolomics has greatly increased our understanding of the biological characteristics of planthoppers, which will benefit the identification of resistant rice varieties and strategies for their control. Strategies like more optimal genome assembly and single-cell RNA-seq help to update our knowledge of gene control structure and cell type-specific usage, shedding light on how planthoppers adjust as well. However, to date, a comprehensive genome-wide investigation of the genetic interactions and population dynamics of BPHs has yet to be exhaustively performed using these next-generation omics technologies. This review summarizes the recent advances and new perspectives regarding the use of omics data for the BPH, with specific emphasis on the integration of both fields to help develop more sustainable pest management strategies. These findings, in combination with those of post-transcriptional and translational modifications involving non-coding RNAs as well as epigenetic variations, further detail intricate host-brown planthopper interaction dynamics, especially regarding resistant rice varieties. Finally, the symbiogenesis of the symbiotic microbial community in a planthopper can be characterized through metagenomic approaches, and its importance in enhancing virulence traits would offer novel opportunities for plant protection by manipulating host-microbe interactions. The concerted diverse omics approaches collectively identified the holistic and complex mechanisms of virulence variation in BPHs, which enables efficient deployment into rice resistance breeding as well as sustainable pest management.}, } @article {pmid39456745, year = {2024}, author = {Chen, Y and Chen, Z and Li, X and Malik, K and Li, C}, title = {Metagenomic Analysis: Alterations of Soil Microbial Community and Function due to the Disturbance of Collecting Cordyceps sinensis.}, journal = {International journal of molecular sciences}, volume = {25}, number = {20}, pages = {}, pmid = {39456745}, issn = {1422-0067}, support = {2021-SF-A4//Major Science and Technology Project of Qinghai Province/ ; LHZX-2022-01//Chinese Academy of Sciences-People's Government of Qinghai Province on Sanjiangyuan National Park/ ; 〔2021〕794//Gansu Province Grassland Monitoring and Evaluation Technology Support Project of Gansu Province Forestry and Grassland Administration/ ; }, mesh = {*Soil Microbiology ; *Cordyceps/genetics/metabolism/growth & development ; *Metagenomics/methods ; *Microbiota/genetics ; Archaea/genetics/metabolism/classification ; Bacteria/genetics/classification/metabolism ; Metagenome ; Soil/chemistry ; }, abstract = {Soil microorganisms are critical to the occurrence of Cordyceps sinensis (Chinese Cordyceps), a medicinal fungi used in Traditional Chinese Medicine. The over-collection of Chinese Cordyceps has caused vegetation degradation and impacted the sustainable occurrence of Cordyceps. The effects of Chinese Cordyceps collection on soil microorganisms have not been reported. Metagenomic analysis was performed on the soil of collecting and non-collecting areas of production and non-production areas, respectively. C. sinensis collection showed no alteration in alpha-diversity but significantly affected beta-diversity and the community composition of soil microorganisms. In Cordyceps production, Thaumarchaeota and Crenarchaeota were identified as the dominant archaeal phyla. DNA repair, flagellar assembly, propionate metabolism, and sulfur metabolism were affected in archaea, reducing the tolerance of archaea in extreme habitats. Proteobacteria, Actinobacteria, Acidobacteria, Verrucomicrobia, and Nitrospirae were identified as the dominant bacterial phyla. The collection of Chinese Cordyceps enhanced the bacterial biosynthesis of secondary metabolites and suppressed ribosome and carbon metabolism pathways in bacteria. A more complex microbial community relationship network in the Chinese Cordyceps production area was found. The changes in the microbial community structure were closely related to C, N, P and enzyme activities. This study clarified soil microbial community composition and function in the Cordyceps production area and established that collection clearly affects the microbial community function by altering microbial community structure. Therefore, it would be important to balance the relationship between cordyceps production and microbiology.}, } @article {pmid39456741, year = {2024}, author = {He, H and Fang, C and Liu, L and Li, M and Liu, W}, title = {Environmental Driving of Adaptation Mechanism on Rumen Microorganisms of Sheep Based on Metagenomics and Metabolomics Data Analysis.}, journal = {International journal of molecular sciences}, volume = {25}, number = {20}, pages = {}, pmid = {39456741}, issn = {1422-0067}, support = {No. 2021YFD1600702//the National Key Research and Development Program of China/ ; }, mesh = {Animals ; *Rumen/microbiology/metabolism ; Sheep/microbiology ; *Metabolomics/methods ; *Metagenomics/methods ; *Gastrointestinal Microbiome ; Adaptation, Physiological ; Metabolome ; Metagenome ; Altitude ; }, abstract = {Natural or artificial selection causes animals to adapt to their environment. The adaptive changes generated by the rumen population and metabolism form the basis of ruminant evolution. In particular, the adaptive drive for environmental adaptation reflects the high-quality traits of sheep that have migrated from other places or have been distant from their origins for a long time. The Hu sheep is the most representative sheep breed in the humid and low-altitude environments (Tai Lake region) in East Asia and has been widely introduced into the arid and high-altitude environments (Tibetan Plateau and Hotan region), resulting in environmental adaptive changes in the Hu sheep. In this study, a joint analysis of the rumen microbial metagenome and metabolome was conducted on Hu sheep from different regions (area of origin and area of introduction) with the objective of investigating the quality traits of Hu sheep and identifying microorganisms that influence the adaptive drive of ruminants. The results demonstrated that the growth performance of Hu sheep was altered due to changes in rumen tissue and metabolism following their introduction to the arid area at relatively high altitude. Metagenomic and metabolomic analyses (five ramsper area) revealed that 3580 different microorganisms and 732 different metabolites were identified in the rumen fluid of arid sheep. Among these, the representative upregulated metabolites were 4,6-isocanedione, methanesulfonic acid and N2-succinyl-L-arginine, while the dominant microorganism was Prevotella ruminicola. The downregulated metabolites were identified as campesterol, teprenone and dihydroclavaminic acid, while the disadvantaged microorganisms were Dialister_succinatiphilus, Prevotella_sp._AGR2160, Prevotella_multisaccharivorax and Selenomonas_bovis. The results of the Pearson analysis indicated that the rumen microbiota and metabolite content of sheep were significantly altered and highly correlated following their relocation from a humid lowland to an arid upland. In particular, the observed changes in rumen microorganisms led to an acceleration of body metabolism, rendering sheep highly adaptable to environmental stress. Prevotella_ruminicola was identified as playing an important role in this process. These findings provide insights into the environmental adaptation mechanisms of sheep.}, } @article {pmid39456706, year = {2024}, author = {Adnane, M and Chapwanya, A}, title = {Microbial Gatekeepers of Fertility in the Female Reproductive Microbiome of Cattle.}, journal = {International journal of molecular sciences}, volume = {25}, number = {20}, pages = {}, pmid = {39456706}, issn = {1422-0067}, mesh = {Animals ; Cattle ; Female ; *Fertility ; *Microbiota ; Reproduction ; Dysbiosis/microbiology ; Genitalia, Female/microbiology ; }, abstract = {This review paper delves into the intricate relationship between the genital microbiome and fertility outcomes in livestock, with a specific focus on cattle. Drawing upon insights derived from culture-independent metagenomics studies, the paper meticulously examines the composition and dynamics of the genital microbiome. Through advanced techniques such as high-throughput sequencing, the review illuminates the temporal shifts in microbial communities and their profound implications for reproductive health. The analysis underscores the association between dysbiosis-an imbalance in microbial communities-and the development of reproductive diseases, shedding light on the pivotal role of microbial gatekeepers in livestock fertility. Furthermore, the paper emphasizes the need for continued exploration of uncharted dimensions of the female reproductive microbiome to unlock new insights into its impact on fertility. By elucidating the complex interplay between microbial communities and reproductive health, this review underscores the importance of innovative strategies aimed at enhancing fertility and mitigating reproductive diseases in livestock populations.}, } @article {pmid39456701, year = {2024}, author = {Yan, K and Sun, X and Fan, C and Wang, X and Yu, H}, title = {Unveiling the Role of Gut Microbiota and Metabolites in Autoimmune Thyroid Diseases: Emerging Perspectives.}, journal = {International journal of molecular sciences}, volume = {25}, number = {20}, pages = {}, pmid = {39456701}, issn = {1422-0067}, support = {82160154, 81670844//National Natural Science Foundation Project of China/ ; QKH-PTRC-GCC[2023]041//The Hundred-level Innovative Talent Foundation of Guizhou Province/ ; 18-ZY-001//The Program for Excellent Young Talents of Zunyi Medical University/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Animals ; Graves Disease/microbiology/metabolism/immunology ; Autoimmune Diseases/microbiology/metabolism ; Thyroid Hormones/metabolism ; Hashimoto Disease/microbiology/metabolism/immunology ; Thyroid Gland/metabolism/microbiology ; Fatty Acids, Volatile/metabolism ; }, abstract = {Autoimmune thyroid diseases (AITDs) are among the most prevalent organ-specific autoimmune disorders, with thyroid hormones playing a pivotal role in the gastrointestinal system's structure and function. Emerging evidence suggests a link between AITDs and the gut microbiome, which is a diverse community of organisms that are essential for digestion, absorption, intestinal homeostasis, and immune defense. Recent studies using 16S rRNA and metagenomic sequencing of fecal samples from AITD patients have revealed a significant correlation between a gut microbiota imbalance and the severity of AITDs. Progress in animal models of autoimmune diseases has shown that intervention in the gut microbiota can significantly alter the disease severity. The gut microbiota influences T cell subgroup differentiation and modulates the pathological immune response to AITDs through mechanisms involving short-chain fatty acids (SCFAs), lipopolysaccharides (LPSs), and mucosal immunity. Conversely, thyroid hormones also influence gut function and microbiota composition. Thus, there is a bidirectional relationship between the thyroid and the gut ecosystem. This review explores the pathogenic mechanisms of the gut microbiota and its metabolites in AITDs, characterizes the gut microbiota in Graves' disease (GD) and Hashimoto's thyroiditis (HT), and examines the interactions between the gut microbiota, thyroid hormones, T cell differentiation, and trace elements. The review aims to enhance understanding of the gut microbiota-thyroid axis and proposes novel approaches to mitigate AITD severity through gut microbiota modulation.}, } @article {pmid39456506, year = {2024}, author = {Qamar, H and He, R and Li, Y and Song, M and Deng, D and Cui, Y and Yu, M and Ma, X}, title = {Metabolome and Metagenome Integration Unveiled Synthesis Pathways of Novel Antioxidant Peptides in Fermented Lignocellulosic Biomass of Palm Kernel Meal.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {13}, number = {10}, pages = {}, pmid = {39456506}, issn = {2076-3921}, support = {2022SZ04//This work was supported by Science and Technology Program of Guangdong Province (2023B0202010020), the Modern Agricultural Industrial Park Project of Qingcheng District, Qingyuan City, Guangdong Province, State Key Laboratory of Swine and Poultry Breeding/ ; }, abstract = {Approximately one-third of the entire world's food resources are deemed to be wasted. Palm kernel meal (PKM), a product that is extensively generated by the palm oil industry, exhibits a unique nutrient-rich composition. However, its recycling is seldom prioritized due to numerous factors. To evaluate the impact of enzymatic pretreatment and Lactobacillus plantarum and Lactobacillus reuteri fermentation upon the antioxidant activity of PKM, we implemented integrated metagenomics and metabolomics approaches. The substantially enhanced (p < 0.05) property of free radicals scavenging, as well as total flavonoids and polyphenols, demonstrated that the biotreated PKM exhibited superior antioxidant capacity. Non-targeted metabolomics disclosed that the Lactobacillus fermentation resulted in substantial (p < 0.05) biosynthesis of 25 unique antioxidant biopeptides, along with the increased (p < 0.05) enrichment ratio of the isoflavonoids and secondary metabolites biosynthesis pathways. The 16sRNA sequencing and correlation analysis revealed that Limosilactobacillus reuteri, Pediococcus acidilactici, Lacticaseibacillus paracasei, Pediococcus pentosaceus, Lactiplantibacillus plantarum, Limosilactobacillus fermentum, and polysaccharide lyases had significantly dominated (p < 0.05) proportions in PMEL, and these bacterial species were strongly (p < 0.05) positively interrelated with antioxidants peptides. Fermented PKM improves nutritional value by enhancing beneficial probiotics, enzymes, and antioxidants and minimizing anti-nutritional factors, rendering it an invaluable feed ingredient and gut health promoter for animals, multifunctional food elements, or as an ingredient in sustainable plant-based diets for human utilization, and functioning as a culture substrate in the food sector.}, } @article {pmid39456444, year = {2024}, author = {Liu, Y and Huang, X and Li, C and Deng, P and Zhang, X and Hu, Y and Dai, Q}, title = {Effects of Ferulic Acid on Lipopolysaccharide-Induced Oxidative Stress and Gut Microbiota Imbalance in Linwu Ducks.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {13}, number = {10}, pages = {}, pmid = {39456444}, issn = {2076-3921}, support = {CARS-42-21//China Agriculture Research System/ ; 2023NK2043//Hunan Innovative Provincial Construction Special Program/ ; kq2402134//Natural Science Foundation of Changsha City, China/ ; }, abstract = {Oxidative stress is a major factor that limits the development of the poultry industry. Ferulic acid (FA) has an antioxidant effect in birds, but the mechanism is not fully understood. In this study, we stimulated oxidative stress in 28-day-old female Linwu ducks by lipopolysaccharide (LPS) and fed them a diet supplemented with FA for 28 days. Results showed that FA alleviated LPS-induced growth performance regression, oxidative stress, and microbiota imbalance in ducks. An integrated metagenomics and metabolomics analysis revealed that s_Blautia_obeum, s_Faecalibacterium_prausnitzii, s_gemmiger_formicilis, and s_Ruminococcaceae_bacterium could be the biomarkers in the antioxidant effect of FA, which interacted with dihydro-3-coumaric acid, L-phenylalanine, and 13(S)-HODE, and regulated the phenylalanine metabolism and PPAR signaling pathway. This study revealed the mechanism of the antioxidant effect of FA, which provided evidence of applying FA as a new antioxidant in commercial duck production.}, } @article {pmid39456104, year = {2024}, author = {Ortiz-Chura, A and Popova, M and Morgavi, DP}, title = {Ruminant microbiome data are skewed and unFAIR, undermining their usefulness for sustainable production improvement.}, journal = {Animal microbiome}, volume = {6}, number = {1}, pages = {61}, pmid = {39456104}, issn = {2524-4671}, support = {101000213-HoloRuminant//European Union's Horizon 2020 research and innovation programme/ ; 101000213-HoloRuminant//European Union's Horizon 2020 research and innovation programme/ ; 101000213-HoloRuminant//European Union's Horizon 2020 research and innovation programme/ ; }, abstract = {The ruminant microbiome plays a key role in the health, feed utilization and environmental impact of ruminant production systems. Microbiome research provides insights to reduce the environmental footprint and improve meat and milk production from ruminants. However, the microbiome composition depends on the ruminant species, habitat and diet, highlighting the importance of having a good representation of ruminant microbiomes in their local environment to translate research findings into beneficial approaches. This information is currently lacking. In this study, we examined the metadata of farmed ruminant microbiome studies to determine global representativeness and summarized information by ruminant species, geographic location, body site, and host information. We accessed data from the International Nucleotide Sequence Database Collaboration via the National Center for Biotechnology Information database. We retrieved 47,628 sample metadata, with cattle accounting for more than two-thirds of the samples. In contrast, goats, which have a similar global population to cattle, were underrepresented with less than 4% of the total samples. Most samples originated in Western Europe, North America, Australasia and China but countries with large ruminant populations in South America, Africa, Asia, and Eastern Europe were underrepresented. Microbiomes from the gastrointestinal tract were the most frequently studied, comprising about 87% of all samples. Additionally, the number of samples from other body sites such as the respiratory tract, milk, skin, reproductive tract, and fetal tissue, has markedly increased over the past decade. More than 40% of the samples lacked basic information and many were retrieved from generic taxonomic classifications where the ruminant species was manually recovered. The lack of basic information such as age, breed or sex can limit the reusability of the data for further analysis and follow-up studies. This requires correct taxonomic assignment of the ruminant host and basic metadata information using accepted ontologies adapted to host-associated microbiomes. Repositories should require this information as a condition of acceptance. The results of this survey highlight the need to encourage studies of the ruminant microbiome from underrepresented ruminant species and countries worldwide. This shortfall in information poses a challenge for the development of microbiome-based strategies to meet sustainability requirements, particularly in areas with expanding livestock production systems.}, } @article {pmid39456096, year = {2024}, author = {De Bernardini, N and Zampieri, G and Campanaro, S and Zimmermann, J and Waschina, S and Treu, L}, title = {pan-Draft: automated reconstruction of species-representative metabolic models from multiple genomes.}, journal = {Genome biology}, volume = {25}, number = {1}, pages = {280}, pmid = {39456096}, issn = {1474-760X}, mesh = {*Metagenome ; Genome, Bacterial ; Metabolic Networks and Pathways ; Genomics/methods ; }, abstract = {The accurate reconstruction of genome-scale metabolic models (GEMs) for unculturable species poses challenges due to the incomplete and fragmented genetic information typical of metagenome-assembled genomes (MAGs). While existing tools leverage sequence homology from single genomes, this study introduces pan-Draft, a pan-reactome-based approach exploiting recurrent genetic evidence to determine the solid core structure of species-level GEMs. By comparing MAGs clustered at the species-level, pan-Draft addresses the issues due to the incompleteness and contamination of individual genomes, providing high-quality draft models and an accessory reactions catalog supporting the gapfilling step. This approach will improve our comprehension of metabolic functions of uncultured species.}, } @article {pmid39456072, year = {2024}, author = {Zhang, Q and Sun, X and Pan, JB and Kong, G}, title = {Feasibility of mNGS in joint replacement patients exhibiting elevated ESR and CRP levels without an underlying diagnosis.}, journal = {European journal of medical research}, volume = {29}, number = {1}, pages = {515}, pmid = {39456072}, issn = {2047-783X}, mesh = {Humans ; *Blood Sedimentation ; Female ; Male ; *C-Reactive Protein/metabolism/analysis ; Aged ; Middle Aged ; *Arthroplasty, Replacement, Hip/methods/adverse effects ; *Prosthesis-Related Infections/diagnosis ; *Arthroplasty, Replacement, Knee/adverse effects/methods ; Feasibility Studies ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Aged, 80 and over ; Anti-Bacterial Agents/therapeutic use/administration & dosage ; }, abstract = {OBJECTIVE: The aim of this study is to investigate the viability of performing initial artificial joint replacement surgery in patients presenting with unexplained elevations in erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP) levels.

METHODS: A cohort of 22 patients, comprising 11 cases each for knee and hip joint replacements, who underwent initial artificial joint replacement surgery between November 2020 and January 2022, was recruited. All patients exhibited elevated levels of ESR and CRP prior to surgery, the etiology of which remained undetermined. Intraoperatively, joint effusion and periarticular tissues were preserved for subsequent bacterial culture and metagenomic next-generation sequencing (mNGS). Postoperatively, a combination of intravenous and local antibiotics was administered for anti-infective management. In cases where bacterial culture and/or mNGS yielded positive results, patients were diagnosed with periprosthetic joint infections (PJI) and underwent one-stage revision; conversely, negative findings led to the discontinuation of intravenous and local antibiotics therapy.

RESULTS: Among the cohort of 22 patients, bacterial cultures yielded negative results, while mNGS identified bacterial infection in 14 patients (63.63%), viral infection in 1 patient (4.55%), and yielded negative results in 7 patients (31.82%). All surgical incisions achieved per primam. Subsequent follow-up assessments conducted for more than 1 year postoperatively revealed absence of PJI among the patients, all of whom exhibited satisfactory progress in their rehabilitation exercises. Notably, the Knee Society Score (KSS) for knee joint patients significantly improved from a preoperative mean of 48.7 ± 3.3 points to 84.3 ± 2.2 points postoperatively, whereas the Harris Hip Score for hip joint patients increased significantly from preoperative mean of 50.6 ± 3.6 points to 87.1 ± 1.6 points (P < 0.01).

CONCLUSION: In cases where patients present with unexplained elevations in ESR and CRP levels, primary artificial joint replacement can be undertaken following a one-stage revision approach for PJI.}, } @article {pmid39455918, year = {2024}, author = {Yu, Z and Qian, Y and Lv, L and Hu, W}, title = {A case of severe psittacosis pneumonia complicated by splenic infarction.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {1203}, pmid = {39455918}, issn = {1471-2334}, mesh = {Humans ; Anti-Bacterial Agents/therapeutic use ; *Chlamydophila psittaci/isolation & purification ; *Psittacosis/complications/microbiology ; *Splenic Infarction/diagnostic imaging ; }, abstract = {CLINICAL DATA: Chlamydia psittaci pneumonia is a community-acquired pneumonia caused by Chlamydia psittaci. While severe cases may lead to critical conditions such as respiratory failure, splenic infarction is relatively uncommon. A severe patient with Chlamydia psittaci pneumonia admitted to our hospital experienced a splenic infarction during treatment. Fortunately, the patient's situation was improved after careful treatment. Now, the patient has been discharged. Further exploration of the mechanism of concurrent splenic infarction is required.

BACKGROUD: Psittacosis pneumonia, a zoonotic infectious disease transmitted from birds to humans, is caused by Chlamydia psittaci and represents a type of chlamydial pneumonia [1]. Insome instances, the disease may progress to severe pneumonia and respiratory failure, necessitating intensive support measures, including mechanical ventilation. The advent of technologies such as Metagenomic Next-Generation Sequencing (mNGS) for the etiological diagnosis of infectious diseases [2] has improved the diagnostic and treatment success rates for Psittacosis. Instances of severe chlamydial pneumonia with complications such as splenic infarction are uncommon. A patient with severe Psittacosis pneumonia complicated by splenic infarction was admitted to the Emergency Intensive Care Unit (EICU) of Haining People's Hospital and subsequently improved following effective anti-infective and anticoagulant therapy. This report is provided herein.}, } @article {pmid39455152, year = {2024}, author = {Liu, Q and Chen, X and Li, YC and He, YH and Li, J}, title = {[Functional Genes and Metabolic Pathways of Nitrogen Metabolism Microorganisms in Lake Sediments：A Case Study of Hongfeng Lake, Guizhou Province].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {45}, number = {10}, pages = {6086-6095}, doi = {10.13227/j.hjkx.202310134}, pmid = {39455152}, issn = {0250-3301}, mesh = {*Lakes/microbiology ; *Geologic Sediments/microbiology ; China ; *Nitrogen/metabolism ; *Bacteria/metabolism/classification/genetics ; *Archaea/genetics/metabolism/classification ; Metabolic Networks and Pathways ; Denitrification ; Nitrification ; Thiobacillus/metabolism/genetics ; Nitrogen Cycle ; Nitrogen Fixation ; }, abstract = {The nitrogen cycle is of great importance for material circulation and energy flow in lake ecosystems. It is driven by microorganisms in lake sediments and can contribute to balancing lake ecosystems. In this study, physical and chemical properties of the sediments sampled from Hongfeng Lake in Guizhou Province were assayed and analyzed using metagenomics to reveal relevant microorganisms, functional genes, metabolic pathways, and their relationships throughout nitrogen metabolism. The results showed that bacteria were dominant, and the top three relative abundant genera were Thiobacillus （16.64%）, Rubrivivax（9.43%）, and Nitrospira （7.09%）. Only six pathways, including nitrogen fixation, nitrification, denitrification, assimilatory nitrate reduction, dissimilatory nitrate reduction, and complete nitrification, were detected in total, of which denitrification and dissimilatory nitrate reduction were the primary processes, but anaerobic ammonia oxidation was not detected. Bacteria and archaea participated in these six pathways, while eukaryotes only functioned in dissimilatory nitrate reduction, denitrification, and complete nitrification. Ammonia nitrogen, nitrate nitrogen, and total phosphorus, as main environmental factors affecting the distribution of functional genes for nitrogen metabolism, differentiated with each other in their respective real-world conditions. A positive correlation （95.04%） was observed between the functional genes and microorganisms, and narG, narZ, and nxrA possessed the highest abundance and the highest host genes. On this basis, these findings are expected to further elucidate the nitrogen cycle of typical karst lakes in Guizhou Province.}, } @article {pmid39454389, year = {2024}, author = {Zhao, Z and Wu, F and Sun, J and Jiang, L and Zhang, Y and Wang, J and Shao, Z and Sun, Y and Duan, Z and Zhang, Y and Bai, T and Liu, Y and Qian, X and Gu, J and Wang, X}, title = {Metagenomic insights into the mechanism of sophorolipid in facilitating co-anaerobic digestion of mushroom residues and cattle manure: Functional microorganisms and metabolic pathway analysis.}, journal = {Journal of environmental management}, volume = {370}, number = {}, pages = {123048}, doi = {10.1016/j.jenvman.2024.123048}, pmid = {39454389}, issn = {1095-8630}, mesh = {*Manure ; Animals ; Cattle ; Anaerobiosis ; Methane/metabolism ; Metabolic Networks and Pathways ; Surface-Active Agents/metabolism ; Metagenomics ; Oleic Acids/metabolism ; }, abstract = {The present study aimed to enhance the co-anaerobic digestion system of mushroom residues and cattle manure by incorporating biosurfactant sophorolipid. Results demonstrated that the addition of 75 mg/L sophorolipid increased cumulative methane production by 33.68%, acetate content by 9-10 times, and the abundance of Methanosarcina by 69.22%. The electroactive microorganisms (Bacteroides, Petrimonas, etc.) were enriched, while the up-regulation of functional genes associated with carbohydrate metabolism and methane metabolism was observed. The metagenomic analysis revealed the significant involvement of inter-microbial communication and extracellular electron transfer in anaerobic digestion. Petrimonas was identified as the predominant host involved in cellular processes and environmental information processing. The supplementation of sophorolipid significantly enhanced its abundance during the late anaerobic digestion period (by 12.30%-64.84%). The results emphasize the crucial function of sophorolipid as biosurfactant in enhancing the efficiency of anaerobic digestion.}, } @article {pmid39454359, year = {2024}, author = {Yeap, CSY and Nguyen, NHA and Busche, T and Wibberg, D and Riha, J and Kruse, O and Cernik, M and Blifernez-Klassen, O and Sevcu, A}, title = {Transcriptomic analysis and cellular responses to nanoscale zero-valent iron in green microalga Raphidocelis subcapitata.}, journal = {Ecotoxicology and environmental safety}, volume = {286}, number = {}, pages = {117194}, doi = {10.1016/j.ecoenv.2024.117194}, pmid = {39454359}, issn = {1090-2414}, mesh = {*Iron/toxicity/chemistry ; *Water Pollutants, Chemical/toxicity ; *Transcriptome/drug effects ; *Microalgae/drug effects ; Gene Expression Profiling ; Chlorophyceae/drug effects/genetics ; }, abstract = {Nanoscale zero valent iron (nZVI) is used to remediate aquifers polluted by organochlorines or heavy metals and was also suggested to eliminate harmful algal blooms. nZVI can therefore affect microorganisms in the vicinity of the application area, including microalgae. However, studies on early transcriptomic effects of microalgae after exposure to nZVI are rare. Here, we described the early physiological and transcriptomic response of the freshwater ecological indicator green microalga, Raphidocelis subcapitata ATCC 22662, to 100 mg/L of reactive nZVI and non-reactive nano-magnetite (nFe3O4). The combined effect of shading and the release of total iron from nZVI posed a short-term inhibition effect leading to 15 % of deformed cells and cytosol leakage, while cells viability increased after 24 h. nZVI triggered a more pronounced transcriptomic response with (7380 differentially expressed genes [DEGs]) compared to nFe3O4 (4601 DEGs) after 1 h. nZVI, but not nFe3O4 increased the expression of genes function in DNA repair and replication, while deactivated carbohydrate-energy metabolisms, mitochondria signaling, and transmembrane ion transport. This study highlights an early fate assessment of algal cells under nZVI and nFe3O4 exposure using next-generation risk assessment methods and will serve as valuable information for safe and sustainable application of nZVI in water remediation.}, } @article {pmid39454358, year = {2024}, author = {Wen, R and Yang, M and Xu, Q and Xu, W and Zhou, Q and Ma, B and Lin, X and Lei, C and Wang, H}, title = {Assessing the pig microbial health impacts of smallholder farming.}, journal = {Ecotoxicology and environmental safety}, volume = {286}, number = {}, pages = {117204}, doi = {10.1016/j.ecoenv.2024.117204}, pmid = {39454358}, issn = {1090-2414}, mesh = {Animals ; Swine ; *Feces/microbiology ; Animal Husbandry ; China ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; Humans ; Bacteria/genetics/drug effects ; Escherichia coli/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; }, abstract = {The livestock industry has long been a hotspot environment for antibiotic resistance genes, with smallholder farming still holding a significant position in pig farming. However, the microbial antibiotic resistance and pathogen risks in pigs under the smallholder farming model remain unclear. We systematically analyzed the antibiotic resistance and microbial composition of pig feces from smallholder and large-scale farming models in Sichuan. The results indicated a lower abundance of antibiotic resistance genes (ARGs) and similar microbial composition in smallholder farming compared to large-scale farming. Beneficial bacteria were more abundant in small-scale farming, whereas large-scale farming exhibited more ARGs, virulence genes, and human pathogenic bacteria (HPBs), including ESBL Escherichia coli strains closely related to human strains, indicating higher zoonotic risk. The findings suggest that smallholder farming presents a relatively better microbial composition and resistance profile, highlighting its advantages over large-scale farming in terms of pig and human health. It is noteworthy that a considerable proportion of HPBs carrying ARGs still exist in the feces from smallholder farming, and given the openness of fecal handling, there remains a high risk of transmitting ARGs and pathogens to humans.}, } @article {pmid39454330, year = {2024}, author = {Yang, T and Wang, X and Ng, HY and Huang, S and Bi, X and Zheng, X and Zhou, X}, title = {Antibiotic resistance and resistome risks of inhalable bioaerosols at aeration tank of a full-scale wastewater treatment plant.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {136253}, doi = {10.1016/j.jhazmat.2024.136253}, pmid = {39454330}, issn = {1873-3336}, mesh = {*Wastewater/microbiology ; *Aerosols ; *Air Microbiology ; Particulate Matter/toxicity/analysis ; Bacteria/drug effects/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Waste Disposal, Fluid ; Air Pollutants/toxicity/analysis ; Drug Resistance, Bacterial/genetics ; }, abstract = {Antibiotic resistome could be aerosolized under wastewater aeration processes, however, their seasonal variation, mobility, hosts, aerosolization behavior, and risk, are largely unknown. Herein, the antibiotic resistant pollution associated with fine particulate matter (PM2.5) from the actual aeration tank (AerT), was analyzed using metagenomic assembly. The antibiotic resistance of AerT-PM2.5 was characterized by significant seasonality. Antibiotic resistance genes (ARGs) in AerT-PM2.5, exhibited higher enrichment and mobility and were harbored more by pathogens than those in upwind-PM2.5, regardless of sampling season. Mobile ARGs were mainly flanked by transposase. Totally, 18 pathogenic antibiotic-resistant bacteria (PARB) carried more than one ARG, including 9 PARB with multiple ARG types. Although wastewater exerted a dominant source contribution for the airborne ARGs (47.31-55.56 %) and PARB (46.18-64.32 %), aeration endowed differential aerosolization capacity for various ARGs and PARB from wastewater. Airborne antibiotic resistome was mainly determined by bacterial community and indirectly influenced by meteorological conditions (i.e., relative humidity). Higher PM2.5-borne resistome risk was observed in AerT than upwind, and the most serious resistome risk of AerT-PM2.5 was found in winter. This study emphasizes the importance of wastewater aeration processes in emission of airborne antibiotic resistome and offers referenced information for mitigating air pollution in wastewater treatment plants.}, } @article {pmid39453910, year = {2024}, author = {Mondal, N and Dutta, S and Chatterjee, S and Sarkar, J and Mondal, M and Roy, C and Chakraborty, R and Ghosh, W}, title = {Aquificae overcomes competition by archaeal thermophiles, and crowding by bacterial mesophiles, to dominate the boiling vent-water of a Trans-Himalayan sulfur-borax spring.}, journal = {PloS one}, volume = {19}, number = {10}, pages = {e0310595}, pmid = {39453910}, issn = {1932-6203}, mesh = {*Hot Springs/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/metabolism ; *Sulfur/metabolism ; Archaea/genetics/metabolism ; Phylogeny ; Microbiota/genetics ; Boron/metabolism ; Water Microbiology ; }, abstract = {Trans-Himalayan hot spring waters rich in boron, chlorine, sodium and sulfur (but poor in calcium and silicon) are known based on PCR-amplified 16S rRNA gene sequence data to harbor high diversities of infiltrating bacterial mesophiles. Yet, little is known about the community structure and functions, primary productivity, mutual interactions, and thermal adaptations of the microorganisms present in the steaming waters discharged by these geochemically peculiar spring systems. We revealed these aspects of a bacteria-dominated microbiome (microbial cell density ~8.5 × 104 mL-1; live:dead cell ratio 1.7) thriving in the boiling (85°C) fluid vented by a sulfur-borax spring called Lotus Pond, situated at 4436 m above the mean sea-level, in the Puga valley of eastern Ladakh, on the Changthang plateau. Assembly, annotation, and population-binning of >15-GB metagenomic sequence illuminated the numeral predominance of Aquificae. While members of this phylum accounted for 80% of all 16S rRNA-encoding reads within the metagenomic dataset, 14% of such reads were attributed to Proteobacteria. Post assembly, only 25% of all protein-coding genes identified were attributable to Aquificae, whereas 41% was ascribed to Proteobacteria. Annotation of metagenomic reads encoding 16S rRNAs, and/or PCR-amplified 16S rRNA genes, identified 163 bacterial genera, out of which 66 had been detected in past investigations of Lotus Pond's vent-water via 16S amplicon sequencing. Among these 66, Fervidobacterium, Halomonas, Hydrogenobacter, Paracoccus, Sulfurihydrogenibium, Tepidimonas, Thermus and Thiofaba (or their close phylogenomic relatives) were presently detected as metagenome-assembled genomes (MAGs). Remarkably, the Hydrogenobacter related MAG alone accounted for ~56% of the entire metagenome, even though only 15 out of the 66 genera consistently present in Lotus Pond's vent-water have strains growing in the laboratory at >45°C, reflecting the continued existence of the mesophiles in the ecosystem. Furthermore, the metagenome was replete with genes crucial for thermal adaptation in the context of Lotus Pond's geochemistry and topography. In terms of sequence similarity, a majority of those genes were attributable to phylogenetic relatives of mesophilic bacteria, while functionally they rendered functions such as encoding heat shock proteins, molecular chaperones, and chaperonin complexes; proteins controlling/modulating/inhibiting DNA gyrase; universal stress proteins; methionine sulfoxide reductases; fatty acid desaturases; different toxin-antitoxin systems; enzymes protecting against oxidative damage; proteins conferring flagellar structure/function, chemotaxis, cell adhesion/aggregation, biofilm formation, and quorum sensing. The Lotus Pond Aquificae not only dominated the microbiome numerically but also acted potentially as the main primary producers of the ecosystem, with chemolithotrophic sulfur oxidation (Sox) being the fundamental bioenergetic mechanism, and reductive tricarboxylic acid (rTCA) cycle the predominant carbon fixation pathway. The Lotus Pond metagenome contained several genes directly or indirectly related to virulence functions, biosynthesis of secondary metabolites including antibiotics, antibiotic resistance, and multi-drug efflux pumping. A large proportion of these genes being attributable to Aquificae, and Proteobacteria (very few were ascribed to Archaea), it could be worth exploring in the future whether antibiosis helped the Aquificae overcome niche overlap with other thermophiles (especially those belonging to Archaea), besides exacerbating the bioenergetic costs of thermal endurance for the mesophilic intruders of the ecosystem.}, } @article {pmid39452816, year = {2024}, author = {Al-Balushi, MA and Kyaw, HH and Myint, MTZ and Al-Abri, M and Dobretsov, S}, title = {Chemical Cleaning Techniques for Fouled RO Membranes: Enhancing Fouling Removal and Assessing Microbial Composition.}, journal = {Membranes}, volume = {14}, number = {10}, pages = {}, pmid = {39452816}, issn = {2077-0375}, support = {RC/SR-DVC-CEMB/22/01//Ministry of Higher Education/ ; }, abstract = {Membrane fouling, a major challenge in desalination, is addressed in this study by investigating three different chemical cleaning protocols (A, B, and C) targeting fouled reverse osmosis (RO) membranes and microbial community composition. Cleaning protocols A and B involve different chemical treatments selected based on preliminary tests and literature review, while protocol C follows the manufacturer's standard recommendation. Membrane morphology, foulant composition, and microbial community variability in fouled, virgin, and cleaned membranes are studied. Effective biofilm removal is observed across all protocols using scanning electron microscopy (SEM), while spectroscopic techniques highlight interactions between foulants and membranes. Importantly, a critical gap in understanding how cleaning strategies influence microbial communities on membranes is addressed. Shifts in dominant bacterial phyla (Proteobacteria, Firmicutes, and Actinobacteria) after cleaning are identified through 16S rRNA amplicon sequencing. Cleaning A showed the best results in reducing microbial counts and restoring composition similar to virgin membranes. Additionally, chemical treatment increased dominance of resistant genera such as Staphylococcus, Bacillus, Citrobacter, and Burkholderia. This study emphasizes the necessity for tailored fouling cleaning strategies for RO membranes, with Cleaning A is a promising solution, paving the way for enhanced water purification technologies.}, } @article {pmid39452613, year = {2024}, author = {Birth, N and Leppich, N and Schirmacher, J and Andreae, N and Steinkamp, R and Blanke, M and Meinicke, P}, title = {CoCoPyE: feature engineering for learning and prediction of genome quality indices.}, journal = {GigaScience}, volume = {13}, number = {}, pages = {}, pmid = {39452613}, issn = {2047-217X}, support = {ME 3138/8-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Software ; *Metagenome ; *Machine Learning ; Genomics/methods ; Metagenomics/methods ; Computational Biology/methods ; }, abstract = {BACKGROUND: The exploration of the microbial world has been greatly advanced by the reconstruction of genomes from metagenomic sequence data. However, the rapidly increasing number of metagenome-assembled genomes has also resulted in a wide variation in data quality. It is therefore essential to quantify the achieved completeness and possible contamination of a reconstructed genome before it is used in subsequent analyses. The classical approach for the estimation of quality indices solely relies on a relatively small number of universal single-copy genes. Recent tools try to extend the genomic coverage of estimates for an increased accuracy.

RESULTS: We developed CoCoPyE, a fast tool based on a novel 2-stage feature extraction and transformation scheme. First, it identifies genomic markers and then refines the marker-based estimates with a machine learning approach. In our simulation studies, CoCoPyE showed a more accurate prediction of quality indices than the existing tools. While the CoCoPyE web server offers an easy way to try out the tool, the freely available Python implementation enables integration into existing genome reconstruction pipelines.

CONCLUSIONS: CoCoPyE provides a new approach to assess the quality of genome data. It complements and improves existing tools and may help researchers to better distinguish between low-quality draft and high-quality genome assemblies in metagenome sequencing projects.}, } @article {pmid39452263, year = {2024}, author = {Monger, XC and Saucier, L and Gilbert, AA and Gosselin, S and Pouliot, É and Fournaise, S and Vincent, AT}, title = {Resilience of Loin Meat Microbiota and of Resistance Genes to a Chlortetracycline Treatment in Weaned Piglets.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {10}, pages = {}, pmid = {39452263}, issn = {2079-6382}, support = {ASC-14//Canadian Food Innovation Network/ ; }, abstract = {OBJECTIVES: This project studied the impact of a chlortetracycline treatment in weaning piglets on the taxonomy and antibiotic resistance gene (ARG) content of the microbiomes on carcasses and loins.

METHODS: Two groups of piglets from two farrowing barns with either an average or a lower sanitary health status were used. Each group was divided in half: a control group and a treatment group receiving feed supplemented with 660 g of chlortetracycline per tonne for 21 days. The piglets then went through fattening and were sent to the abattoir when they reached the targeted slaughter weight.

RESULTS: The microbiomes of the pig carcasses and loins were sampled, and DNA was extracted and sequenced with a whole-genome approach. The microbiomes of the carcasses differed depending on the farrowing barn source in both taxonomical composition and ARG content; however, the microbiomes on the loins were similar, regardless of the farrowing barn source and the treatment group.

CONCLUSIONS: While there were differences in the carcass microbiomes between treatments after processing by the abattoir, the loin microbiomes were consistent and unaffected by treatment with chlortetracycline or the sanitary status of the farrowing barn.}, } @article {pmid39452160, year = {2024}, author = {Nguyen, TQ and Dao, TK and Nguyen, HD and Phung, TBT and Pham, TTN and Nguyen, TVH and Trinh, TH and Le, HC and Le, TTH and Do, TH}, title = {Application of PCR-Based Techniques for the Identification of Genetic Fingerprint Diversity of Dominant Bacteria in Fecal Samples of Children with Diarrhea in Vietnam.}, journal = {Infectious disease reports}, volume = {16}, number = {5}, pages = {932-951}, pmid = {39452160}, issn = {2036-7430}, abstract = {In Vietnam, diarrhea, especially persistent diarrhea, is one of the most common diseases in children, while a significant proportion of cases are negative with pathogens; thus, there is an urgent need to understand gut bacterial dysbiosis. In this study, bacteria in the fecal samples of five healthy and ten diarrheal children were separated from other residues, then adopted to extract their metagenomic DNA for evaluating their diversity based on V3 and V6-V8 regions and the 16S rRNA gene by PCR-RFLP and PCR-DGGE. As a result, bacterial metagenomic DNAs with high quality, quantity and diversity were successfully extracted using a GeneJET kit and a chemical protocol. A sequence analysis of 73 representative DNA fragments from gels indicated a remarkable bacterial dysbiosis in all groups of diarrhea. Viral diarrhea was characterized by extremely reduced bacterial diversity with the blossom of Bifidobacterium and Streptococcus. Streptococcus was also the most abundant in persistent diarrhea. Beneficial bacteria that may play a role in the self- rebalance in intestinal bacterial communities, such as Bifidobacterium, Lactobacillus, and Enterococcus, were seen in all diarrheal groups, while Bacteroides and Akkermansia muciniphila were seen in the healthy group but absent in the diarrheal groups. This study provides additional evidence for a relationship between intestinal bacterial dysbiosis and diarrhea in children, emphasizing an increase in Streptococcus.}, } @article {pmid39452065, year = {2024}, author = {Fu, L and Shi, J and Huang, B}, title = {Binning Metagenomic Contigs Using Contig Embedding and Decomposed Tetranucleotide Frequency.}, journal = {Biology}, volume = {13}, number = {10}, pages = {}, pmid = {39452065}, issn = {2079-7737}, support = {61962005//National Natural Science Foundation of China/ ; GXDINBC202406//Open Project Program of Guangxi Key Laboratory of Digital Infra-structure/ ; }, abstract = {Metagenomic binning is a crucial step in metagenomic research. It can aggregate the genome sequences belonging to the same microbial species into independent bins. Most existing methods ignore the semantic information of contigs and lack effective processing of tetranucleotide frequency, resulting in insufficient and complex feature information extracted for binning and poor binning results. To address the above problems, we propose CedtBin, a metagenomic binning method based on contig embedding and decomposed tetranucleotide frequency. First, the improved BERT model is used to learn the contigs to obtain their embedding representation. Secondly, the tetranucleotide frequencies are decomposed using a non-negative matrix factorization (NMF) algorithm. After that, the two features are spliced and input into the clustering algorithm for binning. Considering the sensitivity of the DBSCAN clustering algorithm to input parameters, in order to solve the drawbacks of manual parameter input, we also propose an Annoy-DBSCAN algorithm that can adaptively determine the parameters of the DBSCAN algorithm. This algorithm uses Approximate Nearest Neighbors Oh Yeah (Annoy) and combines it with a grid search strategy to find the optimal parameters of the DBSCAN algorithm. On simulated and real datasets, CedtBin achieves better binning results than mainstream methods and can reconstruct more genomes, indicating that the proposed method is effective.}, } @article {pmid39450991, year = {2024}, author = {Du, S and Tong, X and Leung, MHY and Betts, RJ and Woo, AC and Bastien, P and Misra, N and Aguilar, L and Clavaud, C and Lee, PKH}, title = {Chronic exposure to polycyclic aromatic hydrocarbons alters skin virome composition and virus-host interactions.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39450991}, issn = {1751-7370}, support = {7020049//L'Oréal Research & Innovation, Pudong, China, and the City University of Hong Kong/ ; //L'Oréal Research & Innovation, Pudong, China/ ; 7020049//City University of Hong Kong/ ; }, mesh = {*Skin/virology/microbiology ; Female ; Humans ; *Virome ; *Polycyclic Aromatic Hydrocarbons/metabolism ; *Microbiota/drug effects ; *Bacteria/genetics/classification/isolation & purification/drug effects ; Viruses/classification/drug effects/genetics/isolation & purification ; China ; Adult ; Metagenome ; Host Microbial Interactions ; Air Pollutants ; }, abstract = {Exposure to polycyclic aromatic hydrocarbons (PAHs) in polluted air influences the composition of the skin microbiome, which in turn is associated with altered skin phenotypes. However, the interactions between PAH exposure and viromes are unclear. This study aims to elucidate how PAH exposure affects the composition and function of skin viruses, their role in shaping the metabolism of bacterial hosts, and the subsequent effects on skin phenotype. We analyzed metagenomes from cheek skin swabs collected from 124 Chinese women in our previous study and found that the viruses associated with the two microbiome cutotypes had distinct diversities, compositions, functions, and lifestyles following PAH exposure. Moreover, exposure to high concentrations of PAHs substantially increased interactions between viruses and certain biodegrading bacteria. Under high-PAH exposure, the viruses were enriched in xenobiotic degradation functions, and there was evidence suggesting that the insertion of bacteriophage-encoded auxiliary metabolic genes into hosts aids biodegradation. Under low-PAH exposure conditions, the interactions followed the "Piggyback-the-Winner" model, with Cutibacterium acnes being "winners," whereas under high-PAH exposure, they followed the "Piggyback-the-Persistent" model, with biodegradation bacteria being "persistent." These findings highlight the impact of air pollutants on skin bacteria and viruses, their interactions, and their modulation of skin health. Understanding these intricate relationships could provide insights for developing targeted strategies to maintain skin health in polluted environments, emphasizing the importance of mitigating pollutant exposure and harnessing the potential of viruses to help counteract the adverse effects.}, } @article {pmid39450961, year = {2024}, author = {Sansonetti, PJ and Doré, J}, title = {[The human microbiome proofed by the Anthropocene: from correlation to causality and intervention].}, journal = {Medecine sciences : M/S}, volume = {40}, number = {10}, pages = {757-765}, doi = {10.1051/medsci/2024121}, pmid = {39450961}, issn = {1958-5381}, mesh = {Humans ; *Microbiota/physiology ; Animals ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/microbiology ; Biodiversity ; Causality ; Climate Change ; }, abstract = {The deleterious effects of human activities on biodiversity in the vegetal and animal world, and on climate changes are now well-established facts. However, little is yet known on the impact of human activities on microbial diversity on the planet and more specifically on the human microbiota Large implementation of metagenomics allows exaustive microbial cataloguing with broad spatio-temporal resolution of human microbiota. A reduction in bacterial richness and diversity in the human microbiota, particularly in the intestinal tract, is now established and particularly obvious in the most industrialized regions of the planet. Massive, uncontrolled use of antibiotics, drastic changes in traditional food habits and some elements of the "global exposome" that remain to identify are usually considered as stressors accounting for this situation of "missing microbes". As a consequence, a dysbiotic situation develops, a "dysbiosis" being characterized by the erosion of the central core of shared bacterial species across individuals and the development of opportunistic "pathobionts" in response to a weaker barrier capacity of these impoverished microbiota. The current challenge is to establish a causality link between the extension of these dysbiotic situations and the steady emergence of epidemic, non-communicable diseases such as asthma, allergy, obesity, diabetes, autoimmune diseases and some cancers. Experimental animal models combined with controlled, prospective clinical interventions are in demand to consolidate causality links, with the understanding that in the deciphering of the mechanisms of alteration of the human-microbiome symbiosis resides a novel exciting chapter of medicine: "microbial medicine".}, } @article {pmid39449113, year = {2024}, author = {Harima, H and Qiu, Y and Sasaki, M and Ndebe, J and Penjaninge, K and Simulundu, E and Kajihara, M and Ohnuma, A and Matsuno, K and Nao, N and Orba, Y and Takada, A and Ishihara, K and Hall, WW and Hang'ombe, BM and Sawa, H}, title = {A first report of rotavirus B from Zambian pigs leading to the discovery of a novel VP4 genotype P[9].}, journal = {Virology journal}, volume = {21}, number = {1}, pages = {263}, pmid = {39449113}, issn = {1743-422X}, support = {JP23jm0110019//AMED and the Japan International Cooperation Agency (JICA) within the framework of the Science and Technology Research Partnership for Sustainable Development (SATREPS)/ ; JP243fa627005//Japan Agency for Medical Research and Development/ ; JP23wm0125008//Japan Program for Infectious Diseases Research and Infrastructure from AMED/ ; }, mesh = {Animals ; Swine ; Zambia/epidemiology ; *Rotavirus/genetics/classification/isolation & purification ; *Rotavirus Infections/virology/veterinary/epidemiology ; *Feces/virology ; *Swine Diseases/virology/epidemiology ; *Phylogeny ; *Genotype ; *Capsid Proteins/genetics ; *Genome, Viral/genetics ; Diarrhea/virology/veterinary/epidemiology ; Sequence Analysis, DNA ; RNA, Viral/genetics ; Metagenomics ; Prevalence ; }, abstract = {BACKGROUND: Rotavirus B (RVB) causes diarrhea in humans and pigs. Although various RVB strains were identified in humans and various animals globally, little is known about the epidemiology RVB infection in Africa. In this study, we attempted to examine the prevalence of RVB infection in pig populations in Zambia.

METHODS: Metagenomic analyses were conducted on pig feces collected in Zambia to detect double stranded RNA viruses, including RVB. To clarify the prevalence of RVB infection in pig populations in Zambia, 147 fecal samples were screened for the RVB detection by RT-qPCR. Full genome sequence of a detected RVB was determined by Sanger sequencing and genetically analyzed.

RESULTS: The metagenomic analyses revealed that RVB sequence reads and contigs of RVB were detected from one fecal sample collected from pigs in Zambia. RT-qPCR screening detected RVB genomes in 36.7% (54/147) of fecal samples. Among 54 positive samples, 13 were positive in non-diarrheal samples (n = 48, 27.1%) and 41 in diarrheal samples (n = 99, 41.4%). Genetic analyses demonstrated that all the segments of ZP18-18, except for VP4, had high nucleotide sequence identities (80.6-92.6%) with all other known RVB strains detected in pigs. In contrast, the VP4 sequence of ZP18-18 was highly divergent from other RVB strains (< 64.6% identities) and formed a distinct lineage in the phylogenetic tree. Notably, the VP8 subunit of the VP4 showed remarkably low amino acid identities (33.3%) to those of known RVB strains, indicating that the VP8 subunit of ZP18-18 was unique among RVB strains. According to the whole genome classification for RVB, ZP18-18 was assigned to a genotype constellation, G18-P[9]-I12-R4-C4-M4-A8-N10-T5-E4-H7 with the newly established VP4 genotype P[9].

CONCLUSIONS: This current study updates the geographical distribution and the genetic diversity of RVB. Given the lack of information regarding RVB in Africa, further RVB surveillance is required to assess the potential risk to humans and animals.}, } @article {pmid39449105, year = {2024}, author = {Rahlff, J and Westmeijer, G and Weissenbach, J and Antson, A and Holmfeldt, K}, title = {Surface microlayer-mediated virome dissemination in the Central Arctic.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {218}, pmid = {39449105}, issn = {2049-2618}, support = {2023-03310_VR//Vetenskapsrådet/ ; CTS20:128//Carl Tryggers Foundation/ ; 2022-04340//Vetenskapsrådet/ ; 224665/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; RA3432/1-1, project number: 446702140//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Arctic Regions ; *Virome ; Viruses/classification/genetics/isolation & purification ; Greenland ; Genome, Viral/genetics ; Water Microbiology ; Metagenomics/methods ; Ecosystem ; Microbiota ; }, abstract = {BACKGROUND: Aquatic viruses act as key players in shaping microbial communities. In polar environments, they face significant challenges such as limited host availability and harsh conditions. However, due to the restricted accessibility of these ecosystems, our understanding of viral diversity, abundance, adaptations, and host interactions remains limited.

RESULTS: To fill this knowledge gap, we studied viruses from atmosphere-close aquatic ecosystems in the Central Arctic and Northern Greenland. Aquatic samples for virus-host analysis were collected from ~60 cm depth and the submillimeter surface microlayer (SML) during the Synoptic Arctic Survey 2021 on icebreaker Oden in the Arctic summer. Water was sampled from a melt pond and open water before undergoing size-fractioned filtration, followed by genome-resolved metagenomic and cultivation investigations. The prokaryotic diversity in the melt pond was considerably lower compared to that of open water. The melt pond was dominated by a Flavobacterium sp. and Aquiluna sp., the latter having a relatively small genome size of 1.2 Mb and the metabolic potential to generate ATP using the phosphate acetyltransferase-acetate kinase pathway. Viral diversity on the host fraction (0.2-5 µm) of the melt pond was strikingly limited compared to that of open water. From the 1154 viral operational taxonomic units (vOTUs), of which two-thirds were predicted bacteriophages, 17.2% encoded for auxiliary metabolic genes (AMGs) with metabolic functions. Some AMGs like glycerol-3-phosphate cytidylyltransferase and ice-binding like proteins might serve to provide cryoprotection for the host. Prophages were often associated with SML genomes, and two active prophages of new viral genera from the Arctic SML strain Leeuwenhoekiella aequorea Arc30 were induced. We found evidence that vOTU abundance in the SML compared to that of ~60 cm depth was more positively correlated with the distribution of a vOTU across five different Arctic stations.

CONCLUSIONS: The results indicate that viruses employ elaborate strategies to endure in extreme, host-limited environments. Moreover, our observations suggest that the immediate air-sea interface serves as a platform for viral distribution in the Central Arctic. Video Abstract.}, } @article {pmid39448846, year = {2024}, author = {Wu, Z and Liu, S and Ni, J}, title = {Metagenomic characterization of viruses and mobile genetic elements associated with the DPANN archaeal superphylum.}, journal = {Nature microbiology}, volume = {9}, number = {12}, pages = {3362-3375}, pmid = {39448846}, issn = {2058-5276}, support = {U2240205//National Natural Science Foundation of China (National Science Foundation of China)/ ; 51721006//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92047303//National Natural Science Foundation of China (National Science Foundation of China)/ ; 423B2703//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Archaea/genetics/virology ; *Metagenomics ; *Interspersed Repetitive Sequences ; *Archaeal Viruses/genetics/classification ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Phylogeny ; Metagenome ; Genome, Viral/genetics ; Genome, Archaeal ; Virome/genetics ; Symbiosis ; }, abstract = {The archaeal superphylum DPANN (an acronym formed from the initials of the first five phyla discovered: Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanohaloarchaeota and Nanoarchaeota) is a group of ultrasmall symbionts able to survive in extreme ecosystems. The diversity and dynamics between DPANN archaea and their virome remain largely unknown. Here we use a metagenomic clustered regularly interspaced short palindromic repeats (CRISPR) screening approach to identify 97 globally distributed, non-redundant viruses and unclassified mobile genetic elements predicted to infect hosts across 8 DPANN phyla, including 7 viral groups not previously characterized. Genomic analysis suggests a diversity of viral morphologies including head-tailed, tailless icosahedral and spindle-shaped viruses with the potential to establish lytic, chronic or lysogenic infections. We also find evidence of a virally encoded Cas12f1 protein (probably originating from uncultured DPANN archaea) and a mini-CRISPR array, which could play a role in modulating host metabolism. Many metagenomes have virus-to-host ratios >10, indicating that DPANN viruses play an important role in controlling host populations. Overall, our study illuminates the underexplored diversity, functional repertoires and host interactions of the DPANN virome.}, } @article {pmid39448159, year = {2025}, author = {Diaz, M and Aird, H and Le Viet, T and Gutiérrez, AV and Larke-Mejia, N and Omelchenko, O and Moragues-Solanas, L and Fritscher, J and Som, N and McLauchlin, J and Hildebrand, F and Jørgensen, F and Gilmour, M}, title = {Microbial composition and dynamics in environmental samples from a ready-to-eat food production facility with a long-term colonization of Listeria monocytogenes.}, journal = {Food microbiology}, volume = {125}, number = {}, pages = {104649}, doi = {10.1016/j.fm.2024.104649}, pmid = {39448159}, issn = {1095-9998}, mesh = {*Listeria monocytogenes/genetics/isolation & purification/growth & development/classification ; *Fast Foods/microbiology ; Food Microbiology ; Microbiota ; Bacteria/genetics/classification/isolation & purification/growth & development ; Environmental Microbiology ; Metagenomics ; Pseudomonas fluorescens/genetics/isolation & purification/growth & development/classification ; Food Contamination/analysis ; }, abstract = {Listeria monocytogenes is a foodborne pathogen of significant concern for the food industry due to its remarkable ability to persist through safety control efforts, posing a subsequent health threat to consumers. Understanding the microbial communities coexisting with L. monocytogenes in food processing environments provides insights into its persistence mechanisms. We investigated the microbial communities on non-food contact surfaces in a facility producing ready-to-eat foods, known to harbour a ST121 L. monocytogenes strain over multiple years. A 10-week sampling period was coordinated with the company and public health authorities. Metagenomic analysis revealed a stable microbial composition dominated by Pseudomonas fluorescens. While highly related populations were present in high-care production zones, distinctive taxa characteristic of specific areas were observed (e.g., Sphingomonas aerolata). Although Listeria spp. were not detected in metagenomes, they were detected in cultured samples, suggesting low relative abundance in factory settings. The findings suggest that a stable resident microbiota, with distinct adaptations to different areas within the factory, was selected for by their collective ability to survive control efforts in this environment. Listeria spp. was a member of this microbial community, albeit at low abundance, and may likewise benefit from the mutualism of the overall microbial community.}, } @article {pmid39448157, year = {2025}, author = {Hou, S and Liang, Z and Wu, Q and Cai, Q and Weng, Q and Guo, W and Ni, L and Lv, X}, title = {Metagenomics reveals the differences in flavor quality of rice wines with Hongqu and Maiqu as the fermentation starters.}, journal = {Food microbiology}, volume = {125}, number = {}, pages = {104647}, doi = {10.1016/j.fm.2024.104647}, pmid = {39448157}, issn = {1095-9998}, mesh = {*Wine/analysis/microbiology ; *Fermentation ; *Oryza/microbiology/chemistry ; *Flavoring Agents/metabolism/chemistry/analysis ; *Taste ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Metagenomics ; *Volatile Organic Compounds/analysis/metabolism ; Biogenic Amines/analysis/metabolism ; Microbiota ; Fungi/classification/genetics/metabolism/isolation & purification ; }, abstract = {Chinese rice wine (CRW) is an alcoholic beverage made mainly from rice or grain through saccharification and fermentation with Jiuqu (starter). Jiuqu makes an important contribution to the formation of the flavor characteristics of rice wine. Hongqu and Maiqu are two kinds of Jiuqu commonly used in CRW brewing. This study compared the microbial community, biogenic amines (BAs), and volatile flavor components (VFCs) of two types of rice wine brewed with Hongqu and Maiqu as fermentation agents. The results showed that the amino acid content of rice wine fermented with Maiqu (MQW) was significantly lower than that of rice wine fermented with Hongqu (HQW). On the contrary, the majority of BAs in MQW were significantly higher than those in HQW, except for putrescine. Multivariate statistical analysis indicated that most of the VFCs detected were enriched in HQW, while ethyl 3-phenylpropanoate and citronellol were enriched in MQW. The results of metagenomic analysis showed that Weissiella, Enterobacter, Leuconostoc, Kosakonia, Saccharomyces, Aspergilus and Monascus were identified as the predominant microbial genera in HQW brewing process, while Saccharopolyspora, Lactococcus, Enterobacter, Leuconostoc, Kosakonia, Pediococcus, Pantoea, Saccharomyces, Aspergillus, Lichtheimia and Nakaseomyces were the predominant microbial genera in MQW brewing. In addition, some VFCs and BAs were strongly correlated with dominant microbial genera in HQW and MQW brewing. Bioinformatics analysis showed that the abundance of genes involved in BAs synthesis in MQW brewing was much higher than that in HQW brewing, while the abundances of genes related to metabolic pathway of characteristic VFCs in HQW brewing were obviously higher than those in MQW, which explained the differences in flavor quality between HQW and MQW from the perspective of microbial genes. Collectively, these findings provide scientific evidence for elucidating the contribution of different microbial genera to the formation of flavor quality of CRW, and is helpful for screening beneficial microbes to enhance flavor quality and drinking comfort of CRW.}, } @article {pmid39448156, year = {2025}, author = {Ren, D and Liu, S and Qin, H and Huang, M and Bai, X and Han, X and Zhang, S and Mao, J}, title = {Metagenomics-based insights into the microbial community dynamics and flavor development potentiality of artificial and natural pit mud.}, journal = {Food microbiology}, volume = {125}, number = {}, pages = {104646}, doi = {10.1016/j.fm.2024.104646}, pmid = {39448156}, issn = {1095-9998}, mesh = {*Metagenomics ; *Bacteria/genetics/classification/metabolism/isolation & purification/growth & development ; *Flavoring Agents/metabolism ; *Microbiota ; Fermentation ; Metagenome ; Taste ; Fermented Foods/microbiology ; Brassica/microbiology ; Food Microbiology ; }, abstract = {Strong-flavor Baijiu (SFB) production has relied on pit mud (PM) as a starter culture. The maturation time of natural PM (NPM) is about 30 years, so artificial PM (APM) with a shorter maturation time has attracted widespread attention. This study reveals the microbial and functional dissimilarities of APM and NPM, and helps to elucidate the different metabolic roles of microbes during substrate degradation and flavor formation. Significant differences in the microbial community were observed between APM and NPM, manifesting as variations in the abundance of core microorganisms. Total of 187 high-quality metagenome-assembled genomes (MAGs) were obtained based on the metagenomic binning technology, mainly including Firmicutes (n = 106), Bacteroidota (n = 15) and Chloroflexota (n = 14). Furthermore, the relative concentration of flavor compounds in 4-year APM was similar to those in 30-year NPM, but different from those in 100-year NPMs. Methanosarcina, Methanobacterium, Methanoculleus, Anaerolineae bacterium and Aminobacterium were the key bacteria responsible for the flavor differences. From a functional perspective, amino acid and carbohydrate metabolism were key functions of PM microbial, and showed differences between APM and NPM. Finally, substrate degradation and flavor generation pathways were found to exist in multiple microorganisms. Combine the relative abundance of microorganisms with the absolute abundance of enzymes, Clostridium, Lactobacillus, Petrimonas, Methanoculleus, Prevotella, Methanobacterium, Methanosarcina, Methanothrix, Proteiniphilum, Bellilinea, Anaerolinea, Anaeromassilibacillus, Syntrophomonas and Brevefilum were identified as the key microorganisms in APM and NPM.}, } @article {pmid39447963, year = {2024}, author = {Lee, S and Arefaine, B and Begum, N and Stamouli, M and Witherden, E and Mohamad, M and Harzandi, A and Zamalloa, A and Cai, H and Williams, R and Curtis, MA and Edwards, LA and Chokshi, S and Mardinoglu, A and Proctor, G and Moyes, DL and McPhail, MJ and Shawcross, DL and Uhlen, M and Shoaie, S and Patel, VC}, title = {Oral-gut microbiome interactions in advanced cirrhosis: characterisation of pathogenic enterotypes and salivatypes, virulence factors and antimicrobial resistance.}, journal = {Journal of hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jhep.2024.09.046}, pmid = {39447963}, issn = {1600-0641}, abstract = {BACKGROUND & AIMS: Cirrhosis complications are often triggered by bacterial infections with multidrug-resistant organisms. Alterations in the gut and oral microbiome in decompensated cirrhosis (DC) influence clinical outcomes. We interrogated: (i) gut and oral microbiome community structures, (ii) virulence factors (VFs) and antimicrobial resistance genes (ARGs) and (iii) oral-gut microbial overlap in patients with differing cirrhosis severity.

METHODS: Fifteen healthy controls (HCs), as well as 26 patients with stable cirrhosis (SC), 46 with DC, 14 with acute-on-chronic liver failure (ACLF) and 14 with severe infection without cirrhosis participated. Metagenomic sequencing was undertaken on paired saliva and faecal samples. 'Salivatypes' and 'enterotypes' based on genera clustering were assessed against cirrhosis severity and clinical parameters. VFs and ARGs were evaluated in oral and gut niches, and distinct resistotypes identified.

RESULTS: Salivatypes and enterotypes revealed a greater proportion of pathobionts with concomitant reduction in autochthonous genera with increasing cirrhosis severity and hyperammonaemia. Increasing overlap between oral and gut microbiome communities was observed in DC and ACLF vs. SC and HCs, independent of antimicrobial, beta-blocker and gastric acid-suppressing therapies. Two distinct gut microbiome clusters harboured genes encoding for the PTS (phosphoenolpyruvate:sugar phosphotransferase system) and other VFs in DC and ACLF. Substantial ARGs (oral: 1,218 and gut: 672) were detected (575 common to both sites). The cirrhosis resistome was distinct, with three oral and four gut resistotypes identified, respectively.

DISCUSSION: The degree of oral-gut microbial community overlap, frequency of VFs and ARGs all increase significantly with cirrhosis severity, with progressive dominance of pathobionts and loss of commensals. Despite similar antimicrobial exposure, patients with DC and ACLF have reduced microbial richness compared to patients with severe infection without cirrhosis, supporting the additive pathobiological effect of cirrhosis.

IMPACT AND IMPLICATIONS: This research underscores the crucial role of microbiome alterations in the progression of cirrhosis in an era of escalating multidrug resistant infections, highlighting the association and potential impact of increased oral-gut microbial overlap, virulence factors, and antimicrobial resistance genes on clinical outcomes. These findings are particularly significant for patients with decompensated cirrhosis and acute-on-chronic liver failure, as they reveal the intricate relationship between microbiome alterations and cirrhosis complications. This is relevant in the context of multidrug-resistant organisms and reduced oral-gut microbial diversity that exacerbate cirrhosis severity, drive hepatic decompensation and complicate treatment. For practical applications, these insights could guide the development of targeted microbiome-based therapeutics and personalised antimicrobial regimens for patients with cirrhosis to mitigate infectious complications and improve clinical outcomes.}, } @article {pmid39447919, year = {2025}, author = {Ji, J and Hu, F and Qin, J and Zhao, Y and Dong, Y and Yang, H and Bai, Z and Wu, G and Wang, Q and Jin, B}, title = {Comparation on the responses and resilience of single-Anammox system and synergistic partial-denitrification/anammox system to long-term nutrient starvation: Performance and metagenomic insights.}, journal = {Bioresource technology}, volume = {415}, number = {}, pages = {131694}, doi = {10.1016/j.biortech.2024.131694}, pmid = {39447919}, issn = {1873-2976}, mesh = {*Nitrogen ; *Denitrification ; Sewage/microbiology ; Bioreactors ; Anaerobiosis ; Metagenomics/methods ; Bacteria/metabolism ; Nutrients/metabolism ; Quorum Sensing ; Biomass ; Oxidation-Reduction ; Metagenome ; }, abstract = {Starvation disturbance was a common problem in biological sewage treatment processes. However, understanding about the responses and resilience of different active anammox biomass in autotrophic and heterotrophic systems to long-term nutrient starvation remains limited. This study compared responses and potential recovery mechanisms of autotrophic single-Anammox and heterotrophic synergistic partial-denitrification/anammox (PD/anammox) systems to prolonged starvation (31-40 days). After starvation, total inorganic nitrogen (TIN) removal efficiency of single-Anammox and synergistic PD/anammox systems decreased to 62.16 % and 78.52 %, respectively, of their original level. After the nutrient resupply, the performance of both systems gradually recovered to a similar-to-pre-starvation level at the rate of 1.26 %/day and 1.89 %/day, respectively. Compared with single-Anammox system, complex synergistic relationship of microorganisms and effective quorum sensing (QS) regulation strategies might mitigate the negative influences were caused by starvation and ensure the performance quickly return of synergistic PD/anammox system. This study would contribute to promote the application of Anammox technology.}, } @article {pmid39446649, year = {2024}, author = {Breselge, S and Bellassi, P and Barcenilla, C and Álvarez-Ordóñez, A and Morelli, L and Cotter, PD}, title = {Bifidobacterium fermentum sp. nov. and Bifidobacterium aquikefiricola sp. nov., isolated from water kefir.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {74}, number = {10}, pages = {}, pmid = {39446649}, issn = {1466-5034}, mesh = {*RNA, Ribosomal, 16S/genetics ; *Phylogeny ; *Bifidobacterium/genetics/isolation & purification/classification ; *DNA, Bacterial/genetics ; *Bacterial Typing Techniques ; *Sequence Analysis, DNA ; *Base Composition ; *Nucleic Acid Hybridization ; *Genome, Bacterial ; *Kefir/microbiology ; Fatty Acids/analysis ; }, abstract = {Four strains, representing two novel Bifidobacterium species, were isolated from water kefir, a fermented beverage. 16S rRNA gene analysis suggested that the novel species share high identities (98.82-98.89%) with Bifidobacterium aquikefiri LMG 28769[T]. Complete genomes were assembled with a short- and long-read hybrid sequencing approach. In agreement with the 16S rRNA gene analysis, phylogenetics with 117 marker genes places the novel species closest to B. aquikefiri LMG 28769[T] as well. The isolates have average nucleotide identity (ANI) scores ranging from 81.46 to 84.84% and digital DNA-DNA hybridization (dDDH) scores from 23.9 to 38.5% with the closest related species, as well as ANI scores between the proposed new species of 80.50%, indicating that the isolates represent two novel species. Matrix-assisted laser desorption/ionization-time of flight chemotaxonomic analysis supported the gene-based taxonomic placement. We propose the names Bifidobacterium fermentum sp. nov. and Bifidobacterium aquikefiricola sp. nov. for these novel species within the Bifidobacterium genus. The proposed type strain B. fermentum WK012_4_13[T] (= LMG 33104[T] = DSM 116073[T]; GenBank accession number GCF_041080835.1) has a genome size of 2.43 Mbp, with a G+C content of 56.00 mol%. The proposed type strain for B. aquikefiricola WK041_4_12[T] (= LMG 33105[T] = DSM 116074[T]; GenBank accession number GCF_041080795.1) has a genome size of 2.36 Mbp and a G+C content of 53.94 mol%. B. fermentum cells are Gram-positive staining, non-motile, non-spore-forming, fructose-6-phosphate phosphoketolase (F6PPK)-positive, catalase- and oxidase-negative and bacillary club shaped. B. aquikefiricola cells are Gram-positive staining, non-motile, non-spore-forming, F6PPK-positive, catalase- and oxidase-negative and square rod shaped.}, } @article {pmid39446191, year = {2024}, author = {Shi, K and Liu, Q and Ji, Q and He, Q and Zhao, XM}, title = {MicroHDF: predicting host phenotypes with metagenomic data using a deep forest-based framework.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {6}, pages = {}, pmid = {39446191}, issn = {1477-4054}, support = {62162019//National Natural Science Foundation of China/ ; 2018SHZDZX01//Shanghai Municipal Science and Technology Major Project/ ; //Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence/ ; //ZJLab/ ; //Guangxi Key Laboratory Fund of Embedded Technology and Intelligent System/ ; ZY22096025//Special Funds for Guiding Local Scientific and Technological Development by the Central Government/ ; YCSW2024357//Guilin University of Technology, Innovation Project of Guangxi Graduate Education/ ; }, mesh = {Humans ; *Phenotype ; *Deep Learning ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; *Inflammatory Bowel Diseases/microbiology/genetics ; Autism Spectrum Disorder/genetics/microbiology ; Liver Cirrhosis/genetics/microbiology ; Computational Biology/methods ; Machine Learning ; Metagenome ; ROC Curve ; }, abstract = {The gut microbiota plays a vital role in human health, and significant effort has been made to predict human phenotypes, especially diseases, with the microbiota as a promising indicator or predictor with machine learning (ML) methods. However, the accuracy is impacted by a lot of factors when predicting host phenotypes with the metagenomic data, e.g. small sample size, class imbalance, high-dimensional features, etc. To address these challenges, we propose MicroHDF, an interpretable deep learning framework to predict host phenotypes, where a cascade layers of deep forest units is designed for handling sample class imbalance and high dimensional features. The experimental results show that the performance of MicroHDF is competitive with that of existing state-of-the-art methods on 13 publicly available datasets of six different diseases. In particular, it performs best with the area under the receiver operating characteristic curve of 0.9182 ± 0.0098 and 0.9469 ± 0.0076 for inflammatory bowel disease (IBD) and liver cirrhosis, respectively. Our MicroHDF also shows better performance and robustness in cross-study validation. Furthermore, MicroHDF is applied to two high-risk diseases, IBD and autism spectrum disorder, as case studies to identify potential biomarkers. In conclusion, our method provides an effective and reliable prediction of the host phenotype and discovers informative features with biological insights.}, } @article {pmid39445812, year = {2024}, author = {Soueidan, A and Idiri, K and Becchina, C and Esparbès, P and Legrand, A and Le Bastard, Q and Montassier, E}, title = {Pooled analysis of oral microbiome profiles defines robust signatures associated with periodontitis.}, journal = {mSystems}, volume = {9}, number = {11}, pages = {e0093024}, pmid = {39445812}, issn = {2379-5077}, support = {RC 21_0250//Centre Hospitalier Universitaire de Nantes (CHU de Nantes)/ ; }, mesh = {Humans ; *Periodontitis/microbiology ; *Microbiota/genetics ; *Dysbiosis/microbiology ; Female ; *RNA, Ribosomal, 16S/genetics ; Adult ; Male ; Mouth/microbiology ; Middle Aged ; Metagenomics/methods ; Bacteria/genetics/classification/isolation & purification ; }, abstract = {UNLABELLED: Oral microbial dysbiosis has been associated with periodontitis in studies using 16S rRNA gene sequencing analysis. However, this technology is not sufficient to consistently separate the bacterial species to species level, and reproducible oral microbiome signatures are scarce. Obtaining these signatures would significantly enhance our understanding of the underlying pathophysiological processes of this condition and foster the development of improved therapeutic strategies, potentially personalized to individual patients. Here, we sequenced newly collected samples from 24 patients with periodontitis, and we collected available oral microbiome data from 24 samples in patients with periodontitis and from 214 samples in healthy individuals (n = 262). Data were harmonized, and we performed a pooled analysis of individual patient data. By metagenomic sequencing of the plaque microbiome, we found microbial signatures for periodontitis and defined a periodontitis-related complex, composed by the most discriminative bacteria. A simple two-factor decision tree, based on Tannerella forsythia and Fretibacterium fastidiosum, was associated with periodontitis with high accuracy (area under the curve: 0.94). Altogether, we defined robust oral microbiome signatures relevant to the pathophysiology of periodontitis that can help define promising targets for microbiome therapeutic modulation when caring for patients with periodontitis.

IMPORTANCE: Oral microbial dysbiosis has been associated with periodontitis in studies using 16S rRNA gene sequencing analysis. However, this technology is not sufficient to consistently separate the bacterial species to species level, and reproducible oral microbiome signatures are scarce. Here, using ultra-deep metagenomic sequencing and machine learning tools, we defined a simple two-factor decision tree, based on Tannerella forsythia and Fretibacterium fastidiosum, that was highly associated with periodontitis. Altogether, we defined robust oral microbiome signatures relevant to the pathophysiology of periodontitis that can help define promising targets for microbiome therapeutic modulation when caring for patients with periodontitis.}, } @article {pmid39444936, year = {2024}, author = {Zhang, J and He, Y and Chen, C and Hu, W and He, J and Ying, Y and Zhu, F}, title = {Bacterial Analysis of the Whole Blood in Chinese Healthy Donors Using 16S rDNA-Targeted Metagenomic Sequencing.}, journal = {The Canadian journal of infectious diseases & medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale}, volume = {2024}, number = {}, pages = {6635560}, pmid = {39444936}, issn = {1712-9532}, abstract = {Background: The presence of bacteria in the blood of healthy individuals remains controversial. This study explored the comprehensive bacterial profiles and specific biomarkers in different components of healthy Chinese blood donors. Methods: A total of 5230 whole blood (WB) specimens were collected. Among them, 5200 random samples were pooled into 26 mixed samples for bacterial profile analysis. The remaining 30 random samples were divided into 4 groups based on components: WB, plasma, red blood cells (RBCs), and buffy coat (BC). Subsequently, the amplicons of the bacterial 16S rDNA V3-V4 fragments were sequenced to measure the diversity and composition of the bacteria using next-generation sequencing. Results: The bacterial DNAs in the blood primarily originated from the Proteobacteria phylum. A total of 301 species of bacterial DNA were found in blood specimens, with 46 species being present among all groups. A significantly higher abundance of bacterial DNA was found in the plasma and RBCs compared to those in BC and WB. However, the plasma and RBC groups showed significantly higher species diversity and richness compared to the BC and WB groups. In addition, the WB group had a significantly different community structure and composition compared to the plasma and RBC groups but was similar to the BC group. Conclusion: The presence of bacterial DNA fragments was confirmed in blood from healthy Chinese donors. The bacterial DNA fragments enriched in plasma showed the highest diversity, followed by RBC, WB, and BC. These results provide a foundation for further research on the microbiome in the blood of healthy individuals.}, } @article {pmid39444743, year = {2024}, author = {Sun, Y and Wang, Y and Ji, L and Pei, Y and Sun, X and Ji, L and Shen, Q and Wang, X and Liu, Y and Yang, S and Zhang, W}, title = {Identification of multiple novel viruses in bar-headed goose feces from Tibet of China.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1485631}, pmid = {39444743}, issn = {2297-1769}, abstract = {INTRODUCTION: The bar-headed goose is a typical high-altitude bird that primarily inhabits alpine lakes and wetlands in Central Asia, with a remarkable ability to adapt to high elevations. Previous studies have shown that they can be infected with parasites such as Cryptosporidium spp. At present, there were few reports on its infection with the virus.

METHODS: In this study, we utilized viral metagenomics to conduct a detailed analysis of the viral components in the fecal samples of bar-headed geese (Anser indicus) from the Tibet region of China.

RESULTS: Multiple novel viruses were identified including four novel astroviruses, four novel caliciviruses, ten novel circoviruses, and nineteen novel parvoviruses. Among them, four astroviruses shared the highest amino acid sequence identities of 63.45-99.47% with different avastrovirus strains. Four caliciviruses and ten circoviruses were identified as unclassified caliciviruses and unclassified circoviruses, separately. Nineteen parvoviruses clustering into four groups maybe four different novel species of the genus Chaphamaparvovirus.

CONCLUSION: These newly discovered viruses have potential implications for the health of avian species, particularly bar-headed geese. This study not only helps us understand the health status of bar-headed geese, but also offers crucial genomic information for future disease prevention and treatment strategies.}, } @article {pmid39444680, year = {2024}, author = {Khara, A and Chakraborty, A and Modlinger, R and Synek, J and Roy, A}, title = {Comparative metagenomic study unveils new insights on bacterial communities in two pine-feeding Ips beetles (Coleoptera: Curculionidae: Scolytinae).}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1400894}, pmid = {39444680}, issn = {1664-302X}, abstract = {BACKGROUND: Climate change has recently boosted the severity and frequency of pine bark beetle attacks. The bacterial community associated with these beetles acts as "hidden players," enhancing their ability to infest and thrive on defense-rich pine trees. There is limited understanding of the environmental acquisition of these hidden players and their life stage-specific association with different pine-feeding bark beetles. There is inadequate knowledge on novel bacterial introduction to pine trees after the beetle infestation. Hence, we conducted the first comparative bacterial metabarcoding study revealing the bacterial communities in the pine trees before and after beetle feeding and in different life stages of two dominant pine-feeding bark beetles, namely Ips sexdentatus and Ips acuminatus. We also evaluated the bacterial association between wild and lab-bred beetles to measure the deviation due to inhabiting a controlled environment.

RESULTS: Significant differences in bacterial amplicon sequence variance (ASVs) abundance existed among different life stages within and between the pine beetles. However, Pseudomonas, Serratia, Pseudoxanthomonas, Taibaiella, and Acinetobacter served as core bacteria. Interestingly, I. sexdentatus larvae correspond to significantly higher bacterial diversity and community richness and evenness compared to other developmental stages, while I. acuminatus adults displayed higher bacterial richness with no significant variation in the diversity and evenness between the life stages. Both wild and lab-bred I. sexdentatus beetles showed a prevalence of the bacterial family Pseudomonadaceae. In addition, wild I. sexdentatus showed dominance of Yersiniaceae, whereas Erwiniaceae was abundant in lab-bred beetles. Alternatively, Acidobacteriaceae, Corynebacteriaceae, and Microbacteriaceae were highly abundant bacterial families in lab-bred, whereas Chitinophagaceae and Microbacteriaceae were highly abundant in wild I. accuminatus. We validated the relative abundances of selected bacterial taxa estimated by metagenomic sequencing with quantitative PCR.

CONCLUSION: Our study sheds new insights into bacterial associations in pine beetles under the influence of various drivers such as environment, host, and life stages. We documented that lab-breeding considerably influences beetle bacterial community assembly. Furthermore, beetle feeding alters bacteriome at the microhabitat level. Nevertheless, our study revisited pine-feeding bark beetle symbiosis under the influence of different drivers and revealed intriguing insight into bacterial community assembly, facilitating future functional studies.}, } @article {pmid39444361, year = {2024}, author = {Bravo, JE and Slizovskiy, I and Bonin, N and Oliva, M and Noyes, N and Boucher, C}, title = {The TELCoMB Protocol for High-Sensitivity Detection of ARG-MGE Colocalizations in Complex Microbial Communities.}, journal = {Current protocols}, volume = {4}, number = {10}, pages = {e70031}, pmid = {39444361}, issn = {2691-1299}, support = {R01 AI141810/AI/NIAID NIH HHS/United States ; R01 AI173928/AI/NIAID NIH HHS/United States ; 1R01AI173928-01A1//National Institute of Allergy and Infectious Diseases/ ; 5R01AI141810-04//National Institute of Allergy and Infectious Diseases/ ; }, mesh = {*Microbiota/genetics ; Metagenomics/methods ; Interspersed Repetitive Sequences/genetics ; Drug Resistance, Bacterial/genetics ; Bacteria/genetics/drug effects/isolation & purification/classification ; Genes, Bacterial/genetics ; }, abstract = {Understanding the genetic basis of antimicrobial resistance is crucial for developing effective mitigation strategies. One necessary step is to identify the antimicrobial resistance genes (ARGs) within a microbial population, referred to as the resistome, as well as the mobile genetic elements (MGEs) harboring ARGs. Although shotgun metagenomics has been successful in detecting ARGs and MGEs within a microbiome, it is limited by low sensitivity. Enrichment using cRNA biotinylated probes has been applied to address this limitation, enhancing the detection of rare ARGs and MGEs, especially when combined with long-read sequencing. Here, we present the TELCoMB protocol, a Snakemake workflow that elucidates resistome and mobilome composition and diversity and uncovers ARG-MGE colocalizations. The protocol supports both short- and long-read sequencing and does not require enrichment, making it versatile for various genomic data types. TELCoMB generates publication-ready figures and CSV files for comprehensive analysis, improving our understanding of antimicrobial resistance mechanisms and spread. © 2024 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Installing TELCOMB Locally Alternate Protocol: Installing TELCOMB on a SLURM Cluster Basic Protocol 2: Data Preprocessing Basic Protocol 3: Calculation of Resistome Distribution and Composition Basic Protocol 4: Identification of ARG-MGE Colocalizations.}, } @article {pmid39443951, year = {2024}, author = {Guo, W and Zhou, M and Li, F and Neves, ALA and Ma, T and Bi, S and Wang, W and Long, R and Guan, LL}, title = {Seasonal stability of the rumen microbiome contributes to the adaptation patterns to extreme environmental conditions in grazing yak and cattle.}, journal = {BMC biology}, volume = {22}, number = {1}, pages = {240}, pmid = {39443951}, issn = {1741-7007}, support = {31672453//National Natural Science Foundation of China/ ; 32402705//National Natural Science Foundation of China/ ; 2018F095R//Ministry of Alberta Agriculture and Forestry/ ; }, mesh = {Animals ; Cattle ; *Rumen/microbiology ; *Seasons ; *Gastrointestinal Microbiome/physiology ; Microbiota ; Adaptation, Physiological ; Bacteria/genetics/classification ; }, abstract = {BACKGROUND: The rumen microbiome plays an essential role in maintaining ruminants' growth and performance even under extreme environmental conditions, however, which factors influence rumen microbiome stability when ruminants are reared in such habitats throughout the year is unclear. Hence, the rumen microbiome of yak (less domesticated) and cattle (domesticated) reared on the Qinghai-Tibetan Plateau through the year were assessed to evaluate temporal changes in their composition, function, and stability.

RESULTS: Rumen fermentation characteristics and pH significantly shifted across seasons in both cattle and yak, but the patterns differed between the two ruminant species. Ruminal enzyme activity varied with season, and production of xylanase and cellulase was greater in yak compared to cattle in both fall and winter. The rumen bacterial community varied with season in both yak and cattle, with higher alpha diversity and similarity (beta diversity) in yak than cattle. The diversity indices of eukaryotic community did not change with season in both ruminant species, but higher similarity was observed in yak. In addition, the similarity of rumen microbiome functional community was higher in yak than cattle across seasons. Moreover, yak rumen microbiome encoded more genes (GH2 and GH3) related to cellulose and hemicellulose degradation compared to cattle, and a new enzyme family (GH160) gene involved in oligosaccharides was uniquely detected in yak rumen. The season affected microbiome attenuation and buffering values (stability), with higher buffering value in yak rumen microbiome than cattle. Positive correlations between antimicrobial resistance gene (dfrF) and CAZyme family (GH113) and microbiome stability were identified in yak, but such relationship was negatively correlated in cattle.

CONCLUSIONS: The findings of the potential of cellulose degradation, the relationship between rumen microbial stability and the abundance of functional genes varied differently across seasons and between yak and cattle provide insight into the mechanisms that may underpin their divergent adaptation patterns to the harsh climate of the Qinghai-Tibetan Plateau. These results lay a solid foundation for developing strategies to maintain and improve rumen microbiome stability and dig out the potential candidates for manufacturing lignocellulolytic enzymes in the yak rumen to enhance ruminants' performance under extreme environmental conditions.}, } @article {pmid39443733, year = {2024}, author = {Hudobenko, J and Di Gesù, CM and Mooz, PR and Petrosino, J and Putluri, N and Ganesh, BP and Rebeles, K and Blixt, FW and Venna, VR and McCullough, LD}, title = {Maternal dysbiosis produces long-lasting behavioral changes in offspring.}, journal = {Molecular psychiatry}, volume = {}, number = {}, pages = {}, pmid = {39443733}, issn = {1476-5578}, support = {RF1AG058463//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; R35NS132265//U.S. Department of Health & Human Services | NIH | National Institute of Neurological Disorders and Stroke (NINDS)/ ; MERIT Award//American Heart Association (American Heart Association, Inc.)/ ; }, abstract = {Advanced maternal age (AMA) is defined as a pregnancy in a woman older than 35 years of age. AMA increases the risk for both maternal and neonatal complications, including miscarriage and stillbirth. AMA has also been linked to neurodevelopmental and neuropsychiatric disorders in the offspring. Recent studies have found that age-associated compositional shifts in the gut microbiota contribute to altered microbial metabolism and enhanced inflammation in the host. We investigated the specific contribution of the maternal microbiome on pregnancy outcomes and offspring behavior by recolonizing young female mice with aged female microbiome prior to pregnancy. We discovered that pre-pregnancy colonization of young dams with microbiome from aged female donors significantly increased fetal loss. There were significant differences in the composition of the gut microbiome in pups born from dams recolonized with aged female biome that persisted through middle age. Offspring born from dams colonized with aged microbiome also had significant changes in levels of neurotransmitters and metabolites in the blood and the brain. Adult offspring from dams colonized with an aged microbiome displayed persistent depressive- and anxiety-like phenotypes. Collectively, these results demonstrate that age-related changes in the composition of the maternal gut microbiome contribute to chronic alterations in the behavior and physiology of offspring. This work highlights the potential of microbiome-targeted approaches, even prior to birth, may reduce the risk of neuropsychiatric disorders.}, } @article {pmid39443634, year = {2024}, author = {Stagaman, K and Kmiecik, MJ and Wetzel, M and Aslibekyan, S and Sonmez, TF and Fontanillas, P and , and Tung, J and Holmes, MV and Walk, ST and Houser, MC and Norcliffe-Kaufmann, L}, title = {Oral and gut microbiome profiles in people with early idiopathic Parkinson's disease.}, journal = {Communications medicine}, volume = {4}, number = {1}, pages = {209}, pmid = {39443634}, issn = {2730-664X}, abstract = {BACKGROUND: Early detection of Parkinson's disease (PD), a neurodegenerative disease with central and peripheral nerve involvement, ensures timely treatment access. Microbes influence nervous system health and are altered in PD.

METHODS: We examined gut and mouth microbiomes from recently diagnosed patients in a geographically diverse, matched case-control, shotgun metagenomics study.

RESULTS: Here, we show greater alpha-diversity in 445 PD patients versus 221 controls. The microbial signature of PD includes overabundance of 16 OTUs, including Streptococcus mutans and Bifidobacterium dentium, and depletion of 28 OTUs. Machine learning models indicate that subspecies level oral microbiome abundances best distinguish PD with reasonably high accuracy (area under the curve: 0.758). Microbial networks are disrupted in cases, with reduced connectivity between short-chain fatty acid-producing bacteria the the gut. Importantly, microbiome diversity metrics are associated with non-motor autonomic symptom severity.

CONCLUSIONS: Our results provide evidence that predictive oral PD microbiome signatures could possibly be used as biomarkers for the early detection of PD, particularly when there is peripheral nervous system involvement.}, } @article {pmid39443495, year = {2024}, author = {Wright, JR and Chen See, JR and Ly, TT and Tokarev, V and Pellegrino, J and Peachey, L and Anderson, SLC and Walls, CY and Hosler, M and Shope, AJ and Gulati, S and Toler, KO and Lamendella, R}, title = {Application of a metatranscriptomics technology, CSI-Dx, for the detection of pathogens associated with prosthetic joint infections.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {25100}, pmid = {39443495}, issn = {2045-2322}, mesh = {Humans ; *Prosthesis-Related Infections/diagnosis/microbiology ; *Synovial Fluid/microbiology ; Female ; Male ; Aged ; Middle Aged ; Bacteria/genetics/isolation & purification ; Gene Expression Profiling/methods ; Metagenomics/methods ; Transcriptome ; Sensitivity and Specificity ; Microbiota/genetics ; }, abstract = {Preoperative identification of causal organism(s) is crucial for effective prosthetic joint infection treatment. Herein, we explore the clinical application of a novel metatranscriptomic (MT) workflow, CSI-Dx, to detect pathogens associated with prosthetic joint infection. MT provides insight into transcriptionally active microbes, overcoming limitations of culture-based and available molecular methods. This study included 340 human synovial fluid specimens subjected to CSI-Dx and traditional culture-based methods. Exploratory analyses were conducted to determine sensitivity and specificity of CSI-Dx for detecting clinically-relevant taxa. Our findings provide insights into the active microbial community composition of synovial fluid from arthroplasty patients and demonstrate the potential clinical utility of CSI-Dx for aiding prosthetic joint infection diagnosis. This approach offers potential for improved sensitivity and acceptable specificity compared to synovial fluid culture, enabling detection of culturable and non-culturable microorganisms. Furthermore, CSI-Dx provides valuable information on antimicrobial resistance gene expression. While further optimization is needed, integrating metatranscriptomic technologies like CSI-Dx into routine clinical practice can revolutionize prosthetic joint infection diagnosis by offering a comprehensive and active snapshot of associated pathogens.}, } @article {pmid39443316, year = {2024}, author = {Zheng, HY and Wu, HX and Du, ZQ}, title = {Gut metagenome-derived image augmentation and deep learning improve prediction accuracy of metabolic disease classification.}, journal = {Yi chuan = Hereditas}, volume = {46}, number = {10}, pages = {886-896}, doi = {10.16288/j.yczz.24-086}, pmid = {39443316}, issn = {0253-9772}, mesh = {Humans ; *Deep Learning ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; *Support Vector Machine ; *Metabolic Diseases/genetics/microbiology ; Neural Networks, Computer ; Bayes Theorem ; }, abstract = {In recent years, statistics and machine learning methods have been widely used to analyze the relationship between human gut microbial metagenome and metabolic diseases, which is of great significance for the functional annotation and development of microbial communities. In this study, we proposed a new and scalable framework for image enhancement and deep learning of gut metagenome, which could be used in the classification of human metabolic diseases. Each data sample in three representative human gut metagenome datasets was transformed into image and enhanced, and put into the machine learning models of logistic regression (LR), support vector machine (SVM), Bayesian network (BN) and random forest (RF), and the deep learning models of multilayer perceptron (MLP) and convolutional neural network (CNN). The accuracy performance of the overall evaluation model for disease prediction was verified by accuracy (A), accuracy (P), recall (R), F1 score (F1), area under ROC curve (AUC) and 10 fold cross-validation. The results showed that the overall performance of MLP model was better than that of CNN, LR, SVM, BN, RF and PopPhy-CNN, and the performance of MLP and CNN models was further improved after data enhancement (random rotation and adding salt-and-pepper noise). The accuracy of MLP model in disease prediction was further improved by 4%-11%, F1 by 1%-6% and AUC by 5%-10%. The above results showed that human gut metagenome image enhancement and deep learning could accurately extract microbial characteristics and effectively predict the host disease phenotype. The source code and datasets used in this study can be publicly accessed in https://github.com/HuaXWu/GM_ML_Classification.git.}, } @article {pmid39443297, year = {2024}, author = {Xu, Y and Teng, Y and Dai, S and Liao, J and Wang, X and Hu, W and Guo, Z and Pan, X and Dong, X and Luo, Y}, title = {Atmospheric Trace Gas Oxidizers Contribute to Soil Carbon Fixation Driven by Key Soil Conditions in Terrestrial Ecosystems.}, journal = {Environmental science & technology}, volume = {58}, number = {49}, pages = {21617-21628}, doi = {10.1021/acs.est.4c06516}, pmid = {39443297}, issn = {1520-5851}, mesh = {*Soil/chemistry ; *Carbon Cycle ; *Ecosystem ; *Soil Microbiology ; Oxidation-Reduction ; Carbon ; Carbon Monoxide/analysis ; }, abstract = {Microbial oxidizers of trace gases such as hydrogen (H2) and carbon monoxide (CO) are widely distributed in soil microbial communities and play a vital role in modulating biogeochemical cycles. However, the contribution of trace gas oxidizers to soil carbon fixation and the driving environmental factors remain unclear, especially on large scales. Here, we utilized biogeochemical and genome-resolved metagenomic profiling, assisted by machine learning analysis, to estimate the contributions of trace gas oxidizers to soil carbon fixation and to predict the key environmental factors driving this process in soils from five distinct ecosystems. The results showed that phylogenetically and physiologically diverse H2 and CO oxidizers and chemosynthetic carbon-fixing microbes are present in the soil in different terrestrial ecosystems. The large-scale variations in soil carbon fixation were highly positively correlated with both the abundance and the activity of H2 and CO oxidizers (p < 0.05-0.001). Furthermore, soil pH and moisture-induced shifts in the abundance of H2 and CO oxidizers partially explained the variation in soil carbon fixation (55%). The contributions of trace gas oxidizers to soil carbon fixation in the different terrestrial ecosystems were estimated to range from 1.1% to 35.0%. The estimated rate of trace gas carbon fixation varied from 0.04 to 1.56 mg kg[-1] d[-1]. These findings reveal that atmospheric trace gas oxidizers may contribute to soil carbon fixation driven by key soil environmental factors, highlighting the non-negligible contribution of these microbes to terrestrial carbon cycling.}, } @article {pmid39442608, year = {2024}, author = {Li, Z and Lin, L and Xie, X and Ming, L and Li, S and Liu, L and Yuan, K and Lin, L and Hu, L and Luan, T and Chen, B}, title = {Metagenomic analysis manifesting intrinsic relatedness between antibiotic resistance genes and sulfate- and iron-reducing microbes in sediment cores of the Pearl River Estuary.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {363}, number = {Pt 1}, pages = {125176}, doi = {10.1016/j.envpol.2024.125176}, pmid = {39442608}, issn = {1873-6424}, mesh = {*Geologic Sediments/microbiology ; *Rivers/microbiology/chemistry ; *Iron ; *Drug Resistance, Microbial/genetics ; *Estuaries ; *Metagenomics ; Sulfates ; China ; Bacteria/genetics ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Antibiotic resistance is an increasingly concerned hotspot of human health. Microbial determinants that may affect the profiles of antibiotic resistance genes (ARGs) in the environments need be explored. Here, sediment cores in the Pearl River Estuary (PRE) were analyzed using metagenomic approaches. ARGs were vertically stratified in the PRE sediment cores in terms of both diversity and absolute levels. Multidrug resistance genes could account for approximately 65.0% of the total ARGs, followed by sulfonamides (19.1%), aminoglycosides (5.9%), beta-lactams (4.5%), etc. ARGs related to aminoglycosides, lincosamides, macrolides, sulfonamides and tetracyclines were preferentially enriched in the surface layers of sediment cores. Sulfate-reducing microbes (SRMs) (e.g., Desulfocapsa and Desulfobulbus) and iron-reducing microbes (IRMs) (e.g., Pseudomonas and Sulfurospirillum) were consistently popular and dominant in the PRE sediment cores. The total levels of both SRMs and IRMs were significantly correlated with those of ARGs in the PRE sediment cores (p < 0.01). Network analysis showed that SRM and IRM genera (i.e., Pseudomonas, Shewanella, and Desulfovibrio) had the high co-occurrence with multiple ARG subtypes in the PRE sediment cores such as rsmA, mexK, and mexF. This study highlighted that anaerobic microbes could play significant roles in shaping vertical ARG distribution in the sediments of aquatic environments.}, } @article {pmid39441997, year = {2024}, author = {Bolaños, LM and Michelsen, M and Temperton, B}, title = {Metagenomic time series reveals a Western English Channel viral community dominated by members with strong seasonal signals.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39441997}, issn = {1751-7370}, support = {NE/R010935/1//UK Natural Environment Research Council/ ; NE/R015953/1//National Capability Long-term Single Centre Science Programme, Climate Linked Atlantic Sector Science/ ; }, mesh = {*Seasons ; *Metagenomics ; *Seawater/virology/microbiology ; *Metagenome ; Viruses/genetics/classification/isolation & purification ; Virome/genetics ; }, abstract = {Marine viruses are key players of ocean biogeochemistry, profoundly influencing microbial community ecology and evolution. Despite their importance, few studies have explored continuous inter-seasonal viral metagenomic time series in marine environments. Viral dynamics are complex, influenced by multiple factors such as host population dynamics and environmental conditions. To disentangle the complexity of viral communities, we developed an unsupervised machine learning framework to classify viral contigs into "chronotypes" based on temporal abundance patterns. Analysing an inter-seasonal monthly time series of surface viral metagenomes from the Western English Channel, we identified chronotypes and compared their functional and evolutionary profiles. Results revealed a consistent annual cycle with steep compositional changes from winter to summer and steadier transitions from summer to winter. Seasonal chronotypes were enriched in potential auxiliary metabolic genes of the ferrochelatases and 2OG-Fe(II) oxygenase orthologous groups compared to non-seasonal types. Chronotypes clustered into four groups based on their correlation profiles with environmental parameters, primarily driven by temperature and nutrients. Viral contigs exhibited a rapid turnover of polymorphisms, akin to Red Queen dynamics. However, within seasonal chronotypes, some sequences exhibited annual polymorphism recurrence, suggesting that a fraction of the seasonal viral populations evolve more slowly. Classification into chronotypes revealed viral genomic signatures linked to temporal patterns, likely reflecting metabolic adaptations to environmental fluctuations and host dynamics. This novel framework enables the identification of long-term trends in viral composition, environmental influences on genomic structure, and potential viral interactions.}, } @article {pmid39441990, year = {2024}, author = {Uppal, S and Waterworth, SC and Nick, A and Vogel, H and Flórez, LV and Kaltenpoth, M and Kwan, JC}, title = {Repeated horizontal acquisition of lagriamide-producing symbionts in Lagriinae beetles.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39441990}, issn = {1751-7370}, support = {ERC CoG 819585//European Research Council through an ERC Consolidator/ ; 1845890//National Science Foundation/ ; }, mesh = {Animals ; *Symbiosis ; *Coleoptera/microbiology ; *Burkholderia/genetics/metabolism/classification/physiology ; Phylogeny ; Metagenomics ; Genome, Bacterial ; Gene Transfer, Horizontal ; }, abstract = {Microbial symbionts associate with multicellular organisms on a continuum from facultative associations to mutual codependency. In the oldest intracellular symbioses there is exclusive vertical symbiont transmission, and co-diversification of symbiotic partners over millions of years. Such symbionts often undergo genome reduction due to low effective population sizes, frequent population bottlenecks, and reduced purifying selection. Here, we describe multiple independent acquisition events of closely related defensive symbionts followed by genome erosion in a group of Lagriinae beetles. Previous work in Lagria villosa revealed the dominant genome-eroded symbiont of the genus Burkholderia produces the antifungal compound lagriamide, protecting the beetle's eggs and larvae from antagonistic fungi. Here, we use metagenomics to assemble 11 additional genomes of lagriamide-producing symbionts from 7 different host species within Lagriinae from 5 countries, to unravel the evolutionary history of this symbiotic relationship. In each host, we detected one dominant genome-eroded Burkholderia symbiont encoding the lagriamide biosynthetic gene cluster. However, we did not find evidence for host-symbiont co-diversification or for monophyly of the lagriamide-producing symbionts. Instead, our analyses support a single ancestral acquisition of the gene cluster followed by at least four independent symbiont acquisitions and subsequent genome erosion in each lineage. By contrast, a clade of plant-associated relatives retained large genomes but secondarily lost the lagriamide gene cluster. Our results, therefore, reveal a dynamic evolutionary history with multiple independent symbiont acquisitions characterized by a high degree of specificity and highlight the importance of the specialized metabolite lagriamide for the establishment and maintenance of this defensive symbiosis.}, } @article {pmid39441989, year = {2024}, author = {Bustos-Caparros, E and Viver, T and Gago, JF and Rodriguez-R, LM and Hatt, JK and Venter, SN and Fuchs, BM and Amann, R and Bosch, R and Konstantinidis, KT and Rossello-Mora, R}, title = {Ecological success of extreme halophiles subjected to recurrent osmotic disturbances is primarily driven by congeneric species replacement.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39441989}, issn = {1751-7370}, support = {PGC2018-096956-B-C41//Spanish Ministry of Science, Innovation and Universities/ ; //European Regional Development Funds/ ; PRE2019-088016//Spanish Government Ministry for Science and Innovation/ ; FEMS-GO-2020-254//Federation of European Microbiological Societies/ ; //DiSC of University of Innsbruck/ ; }, mesh = {*Osmotic Pressure ; Halobacteriaceae/genetics ; Biodiversity ; Salinity ; }, abstract = {To understand how extreme halophiles respond to recurrent disturbances, we challenged the communities thriving in salt-saturated (~36% salts) ~230 L brine mesocosms to repeated dilutions down to 13% (D13 mesocosm) or 20% (D20 mesocosm) salts each time mesocosms reached salt saturation due to evaporation (for 10 and 17 cycles, respectively) over 813 days. Depending on the magnitude of dilution, the most prevalent species, Haloquadratum walsbyi and Salinibacter ruber, either increased in dominance by replacing less competitive populations (for D20, moderate stress conditions), or severely decreased in abundance and were eventually replaced by other congeneric species better adapted to the higher osmotic stress (for D13, strong stress conditions). Congeneric species replacement was commonly observed within additional abundant genera in response to changes in environmental or biological conditions (e.g. phage predation) within the same system and under a controlled perturbation of a relevant environmental parameter. Therefore, a genus is an ecologically important level of diversity organization, not just a taxonomic rank, that persists in the environment based on congeneric species replacement due to relatively high functional overlap (gene sharing), with important consequences for the success of the lineage, and similar to the success of a species via strain-replacement. Further, our results showed that successful species were typically accompanied by the emergence of their own viral cohorts, whose intra-cohort diversity appeared to strongly covary with, and likely drive, the intra-host diversity. Collectively, our results show that brine communities are ecologically resilient and continuously adapting to changing environments by transitioning to alternative stable states.}, } @article {pmid39441337, year = {2024}, author = {Shi, J and Lei, Y and Li, Z and Jia, L and He, P and Cheng, Q and Zhang, Z and Lei, Z}, title = {Alteration of Cecal Microbiota by Antimicrobial Peptides Enhances the Rational and Efficient Utilization of Nutrients in Holstein Bulls.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {39441337}, issn = {1867-1314}, support = {GSA-XMLZ-2021-01//Gansu beef cattle quality fattening project/ ; GSSLCSX-2020-1//the local funding/ ; }, abstract = {We previously observed that supplementation with antimicrobial peptides facilitated the average daily weight gain, net meat, and carcass weights of Holstein bulls. To expand our knowledge of the possible impact of antimicrobial peptides on cecum microbiota, further investigations were conducted. In this study, 18 castrated Holstein bulls with insignificant weight differences and 10 months of age were split randomly into two groups. The control group (CK) was fed a basic diet, whereas the antimicrobial peptide group (AP) was supplemented with 8 g of antimicrobial peptides for 270 days. After slaughter, metagenomic and metabolomic sequencing analyses were performed on the cecum contents. The results showed significantly higher levels of amylase, cellulase, protease, and lipase in the CK than in the AP group (P ≤ 0.05). The levels of β-glucosidase and xylanase (P ≤ 0.05), and acetic and propionic acids (P ≤ 0.01), were considerably elevated in the AP than in the CK group. The metagenome showed variations between the two groups only at the bacterial level, and 3258 bacteria with differences were annotated. A total of 138 differential abundant genes (P < 0.05) were identified in the CAZyme map, with 65 genes more abundant in the cecum of the AP group and 48 genes more abundant in the cecum of the CK group. Metabolomic analysis identified 68 differentially expressed metabolites. Conjoint analysis of microorganisms and metabolites revealed that Lactobacillus had the greatest impact on metabolites in the AP group and Brumimicrobium in the CK group. The advantageous strains of the AP group Firmicutes bacterium CAG:110 exhibited a strong symbiotic relationship with urodeoxycholic acid and hyodeoxycholic acid. This study identified the classification characteristics, functions, metabolites, and interactions of cecal microbiota with metabolites that contribute to host growth performance. Antimicrobial peptides affect the cecal microorganisms, making the use of nutrients more efficient. The utilization of hemicellulose in the cecum of ruminants may contribute more than cellulose to their production performance.}, } @article {pmid39441336, year = {2025}, author = {Liu, X and Zhou, S and Yan, R and Xia, C and Xue, R and Wan, Z and Li, R and de Hoog, S and Ahmed, SA and Wang, Q and Song, Y}, title = {Evaluation of metagenomic next-generation sequencing (mNGS) combined with quantitative PCR: cutting-edge methods for rapid diagnosis of non-invasive fungal rhinosinusitis.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {44}, number = {1}, pages = {17-26}, pmid = {39441336}, issn = {1435-4373}, support = {[2023YFC2508200]//National Key Research and Development Program of Ministry of Science and Technology of the People's Republic of China/ ; }, mesh = {Humans ; Male ; *Sinusitis/microbiology/diagnosis ; Female ; *High-Throughput Nucleotide Sequencing/methods ; *Rhinitis/microbiology/diagnosis ; Middle Aged ; Adult ; *Metagenomics/methods ; *Real-Time Polymerase Chain Reaction/methods ; Aged ; Sensitivity and Specificity ; Young Adult ; Fungi/isolation & purification/genetics/classification ; Mycoses/diagnosis/microbiology ; Adolescent ; Aspergillus/genetics/isolation & purification ; Rhinosinusitis ; }, abstract = {PURPOSE: Fungal rhinosinusitis is a significant and growing health concern in arid regions, with an increasing incidence over recent decades. Without timely and appropriate management, it can lead to severe complications, including potential intracranial spread. This study aims to establish efficient and rapid diagnostics for non-invasive fungal rhinosinusitis (FRS), addressing the challenge of its difficult-to-culture diagnosis.

METHODS: Twenty-eight patients suspected of FRS were studied using endoscopic sinus surgery to obtain tissue samples for histopathology, direct microscopy, fungal culture, quantitative PCR (qPCR) and metagenomic next-generation sequencing (mNGS) detection. A patented qPCR targeting prevalent Aspergillus species was evaluated.

RESULTS: The patient cohort had a male-to-female ratio of 9:14, with disease duration up to 50 years. Histopathologically, 23 out of 28 cases were positive. Fungal culture exhibited a sensitivity of 21.74%, with one false positive. qPCR and mNGS showed 100% sensitivity and specificity, with a 100% consistency rate for identification at the species level (23/23), and potential detection of cases with co-infections. The most common pathogen was A. flavus, followed by A. fumigatus and A. niger. Two cases involved mixed infections of A. fumigatus and A. flavus.

CONCLUSION: qPCR and mNGS proved effective in rapidly identifying fungi from fresh sinus tissue that are challenging to culture, surpassing conventional methods. However, further evaluation and optimization with a larger cohort of patients are necessary. Histopathology is still recommended to confirm the clinical significance of the detected fungal species.}, } @article {pmid39440981, year = {2024}, author = {Collis, RM and Biggs, PJ and Burgess, SA and Midwinter, AC and Liu, J and Brightwell, G and Cookson, AL}, title = {Assessing antimicrobial resistance in pasture-based dairy farms: a 15-month surveillance study in New Zealand.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {11}, pages = {e0139024}, pmid = {39440981}, issn = {1098-5336}, support = {PRJ0126322//AgResearch Strategic Science Investment Fund/ ; //New Zealand Food Safety Science and Research Centre (NZFSSRC)/ ; }, mesh = {New Zealand ; *Dairying ; Animals ; *Feces/microbiology ; *Farms ; Cattle ; Bacteria/genetics/drug effects/classification/isolation & purification ; Anti-Bacterial Agents/pharmacology ; Soil Microbiology ; Drug Resistance, Bacterial/genetics ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Genes, Bacterial ; }, abstract = {Antimicrobial resistance is a global public and animal health concern. Antimicrobial resistance genes (ARGs) have been detected in dairy farm environments globally; however, few longitudinal studies have utilized shotgun metagenomics for ARG surveillance in pasture-based systems. This 15-month study aimed to undertake a baseline survey using shotgun metagenomics to assess the relative abundance and diversity of ARGs in two pasture-based dairy farm environments in New Zealand with different management practices. There was no statistically significant difference in overall ARG relative abundance between the two dairy farms (P = 0.321) during the study period. Compared with overseas data, the relative abundance of ARG copies per 16S rRNA gene in feces (0.08-0.17), effluent (0.03-0.37), soil (0.20-0.63), and bulk tank milk (0.0-0.12) samples was low. Models comparing the presence or absence of resistance classes found in >10% of all feces, effluent, and soil samples demonstrated no statistically significant associations (P > 0.05) with "season," and only multi-metal (P = 0.020) and tetracycline (P = 0.0003) resistance were significant at the "farm" level. Effluent samples harbored the most diverse ARGs, some with a recognized public health risk, whereas soil samples had the highest ARG relative abundance but without recognized health risks. This highlights the importance of considering the genomic context and risk of ARGs in metagenomic data sets. This study suggests that antimicrobial resistance on pasture-based dairy farms is low and provides essential baseline ARG surveillance data for such farming systems.IMPORTANCEAntimicrobial resistance is a global threat to human and animal health. Despite the detection of antimicrobial resistance genes (ARGs) in dairy farm environments globally, longitudinal surveillance in pasture-based systems remains limited. This study assessed the relative abundance and diversity of ARGs in two New Zealand dairy farms with different management practices and provided important baseline ARG surveillance data on pasture-based dairy farms. The overall ARG relative abundance on these two farms was low, which provides further evidence for consumers of the safety of New Zealand's export products. Effluent samples harbored the most diverse range of ARGs, some of which were classified with a recognized risk to public health, whereas soil samples had the highest ARG relative abundance; however, the soil ARGs were not classified with a recognized public health risk. This emphasizes the need to consider genomic context and risk as well as ARG relative abundance in resistome studies.}, } @article {pmid39440963, year = {2024}, author = {Wang, Y and Sun, Y and Huang, K and Gao, Y and Lin, Y and Yuan, B and Wang, X and Xu, G and Nussio, LG and Yang, F and Ni, K}, title = {Multi-omics analysis reveals the core microbiome and biomarker for nutrition degradation in alfalfa silage fermentation.}, journal = {mSystems}, volume = {9}, number = {11}, pages = {e0068224}, pmid = {39440963}, issn = {2379-5077}, support = {32171686//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {*Medicago sativa/microbiology/metabolism ; *Silage/microbiology ; *Fermentation ; *Microbiota/genetics ; Animals ; Biomarkers/metabolism ; Bacteria/genetics/metabolism/classification/isolation & purification ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; Cattle ; Multiomics ; }, abstract = {UNLABELLED: Alfalfa (Medicago sativa L.) is one of the most extensively cultivated forage crops globally, and its nutritional quality critically influences the productivity of dairy cows. Silage fermentation is recognized as a crucial technique for the preservation of fresh forage, ensuring the retention of its vital nutrients. However, the detailed microbial components and their functions in silage fermentation are not fully understood. This study integrated large-scale microbial culturing with high-throughput sequencing to thoroughly examine the microbial community structure in alfalfa silage and explored the potential pathways of nutritional degradation via metagenomic analysis. The findings revealed an enriched microbial diversity in silage, indicated by the identification of amplicon sequence variants. Significantly, the large-scale culturing approach recovered a considerable number of unique microbes undetectable by high-throughput sequencing. Predominant genera, such as Lactiplantibacillus, Leuconostoc, Lentilactobacillus, Weissella, and Liquorilactobacillus, were identified based on their abundance and prevalence. Additionally, genes associated with Enterobacteriaceae were discovered, which might be involved in pathways leading to the production of ammonia-N and butyric acid. Overall, this study offers a comprehensive insight into the microbial ecology of silage fermentation and provides valuable information for leveraging microbial consortia to enhance fermentation quality.

IMPORTANCE: Silage fermentation is a microbial-driven anaerobic process that efficiently converts various substrates into nutrients readily absorbable and metabolizable by ruminant animals. This study, integrating culturomics and metagenomics, has successfully identified core microorganisms involved in silage fermentation, including those at low abundance. This discovery is crucial for the targeted cultivation of specific microorganisms to optimize fermentation processes. Furthermore, our research has uncovered signature microorganisms that play pivotal roles in nutrient metabolism, significantly advancing our understanding of the intricate relationships between microbial communities and nutrient degradation during silage fermentation.}, } @article {pmid39440203, year = {2024}, author = {Wang, X and Guo, T and Zhang, Q and Zhao, N and Hu, L and Liu, H and Xu, S}, title = {Seasonal variations in composition and function of gut microbiota in grazing yaks: Implications for adaptation to dietary shift on the Qinghai-Tibet plateau.}, journal = {Ecology and evolution}, volume = {14}, number = {10}, pages = {e70337}, pmid = {39440203}, issn = {2045-7758}, abstract = {Gut microbiome of animals is affected by external environmental factors and can assist them in adapting to changing environments effectively. Consequently, elucidating the gut microbes of animals under different environmental conditions can provide a comprehensive understanding of the mechanisms of their adaptations to environmental change, with a particular focus on animals in extreme environments. In this study, we compared the structural and functional differences of the gut microbiome of grazing yaks between the summer and winter seasons through metagenomic sequencing and bioinformatics analysis. The results indicated that the composition and function of microbes changed significantly. The study demonstrated an increase in the relative abundance of Actinobacteria and a higher ratio of Firmicutes to Bacteroidetes (F/B) in winter, this process facilitated the adaptation of yaks to the consumption of low-nutrient forages in the winter. Furthermore, the network structure exhibited greater complexity in the winter. Forage nutrition exhibited a significant seasonal variation, with a notable impact on the gut microbiota. The metagenomic analysis revealed an increase in the abundance of enzymes related to amino acid metabolism, axillary activity, and mucin degradation in the winter. In conclusion, this study demonstrated that the gut microbiome of grazing yaks exhibits several adaptive characteristics that facilitate better nutrient accessibility and acid the host in acclimating to the harsh winter conditions. Furthermore, our study offers novel insights into the mechanisms of highland animal adaptation to external environments from the perspective of the gut microbiome.}, } @article {pmid39440036, year = {2024}, author = {Wang, S and Yang, S and Ma, J and Zhang, C and Li, Z and Wang, M and Yu, W and Liu, G}, title = {The first child with mixed invasive pulmonary Mucor and Aspergillus infection: a case report and literature review.}, journal = {Frontiers in medicine}, volume = {11}, number = {}, pages = {1387278}, pmid = {39440036}, issn = {2296-858X}, abstract = {PURPOSE: Coinfections or consecutive infections of Mucor and Aspergillus are exceedingly uncommon in children, we report the case to offer the valuable experience for colleagues facing similar situations.

CASE REPORT: This report documents the first recorded case of successful treatment for pulmonary mixed infection in a diabetic girl. Initially, the patient underwent treatment based on voriconazole, but the infection continued to deteriorate. Subsequently, bronchoalveolar lavage fluid culture and metagenomic next-generation sequencing (mNGS) were conducted, leading to a clear diagnosis of simultaneous infection by Aspergillus fumigatus and Rhizopus microsporus. Susceptibility testing revealed fungal resistance to voriconazole. Therefore, a combined treatment regimen of AmB liposomes and isavuconazole effectively eradicated the fungal infection.

CONCLUSION: This case underscores the importance of early and precise identification of fungal pathogens, determination of effective antifungal medications, and timely implementation of well-planned therapeutic strategies. Furthermore, we comprehensively reviewed 10 cases of pulmonary mixed infections involving Mucor and Aspergillus, summarizing their characteristics and identifying commonalities.}, } @article {pmid39440005, year = {2024}, author = {Tarradas-Alemany, M and Martínez-Puchol, S and Mejías-Molina, C and Itarte, M and Rusiñol, M and Bofill-Mas, S and Abril, JF}, title = {CAPTVRED: an automated pipeline for viral tracking and discovery from capture-based metagenomics samples.}, journal = {Bioinformatics advances}, volume = {4}, number = {1}, pages = {vbae150}, pmid = {39440005}, issn = {2635-0041}, abstract = {SUMMARY: Target Enrichment Sequencing or Capture-based metagenomics has emerged as an approach of interest for viral metagenomics in complex samples. However, these datasets are usually analyzed with standard downstream Bioinformatics analyses. CAPTVRED (Capture-based metagenomics Analysis Pipeline for tracking ViRal species from Environmental Datasets), has been designed to assess the virome present in complex samples, specially focused on those obtained by Target Enrichment Sequencing approach. This work aims to provide a user-friendly tool that complements this sequencing approach for the total or partial virome description, especially from environmental matrices. It includes a setup module which allows preparation and adjustment of the pipeline to any capture panel directed to a set of species of interest. The tool also aims to reduce time and computational cost, as well as to provide comprehensive, reproducible, and accessible results while being easy to costume, set up, and install.

Source code and test datasets are freely available at github repository: https://github.com/CompGenLabUB/CAPTVRED.git.}, } @article {pmid39438987, year = {2024}, author = {Rosenstein, R and Torres Salazar, BO and Sauer, C and Heilbronner, S and Krismer, B and Peschel, A}, title = {The Staphylococcus aureus-antagonizing human nasal commensal Staphylococcus lugdunensis depends on siderophore piracy.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {213}, pmid = {39438987}, issn = {2049-2618}, support = {GRK1708//Deutsche Forschungsgemeinschaft/ ; Cluster of Excellence EXC2124//Deutsche Forschungsgemeinschaft/ ; GRK1708//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Humans ; *Staphylococcus lugdunensis/metabolism/isolation & purification ; *Staphylococcus aureus/genetics ; *Nose/microbiology ; *Siderophores/metabolism ; *Staphylococcal Infections/microbiology ; Microbiota ; Adult ; Male ; Female ; Healthy Volunteers ; Symbiosis ; Carrier State/microbiology ; Middle Aged ; }, abstract = {BACKGROUND: Bacterial pathogens such as Staphylococcus aureus colonize body surfaces of part of the human population, which represents a critical risk factor for skin disorders and invasive infections. However, such pathogens do not belong to the human core microbiomes. Beneficial commensal bacteria can often prevent the invasion and persistence of such pathogens by using molecular strategies that are only superficially understood. We recently reported that the commensal bacterium Staphylococcus lugdunensis produces the novel antibiotic lugdunin, which eradicates S. aureus from the nasal microbiomes of hospitalized patients. However, it has remained unclear if S. lugdunensis may affect S. aureus carriage in the general population and which external factors might promote S. lugdunensis carriage to enhance its S. aureus-eliminating capacity.

RESULTS: We could cultivate S. lugdunensis from the noses of 6.3% of healthy human volunteers. In addition, S. lugdunensis DNA could be identified in metagenomes of many culture-negative nasal samples indicating that cultivation success depends on a specific bacterial threshold density. Healthy S. lugdunensis carriers had a 5.2-fold lower propensity to be colonized by S. aureus indicating that lugdunin can eliminate S. aureus also in healthy humans. S. lugdunensis-positive microbiomes were dominated by either Staphylococcus epidermidis, Corynebacterium species, or Dolosigranulum pigrum. These and further bacterial commensals, whose abundance was positively associated with S. lugdunensis, promoted S. lugdunensis growth in co-culture. Such mutualistic interactions depended on the production of iron-scavenging siderophores by supportive commensals and on the capacity of S. lugdunensis to import siderophores. Video Abstract CONCLUSIONS: These findings underscore the importance of microbiome homeostasis for eliminating pathogen colonization. Elucidating mechanisms that drive microbiome interactions will become crucial for microbiome-precision editing approaches.}, } @article {pmid39438902, year = {2024}, author = {Díaz-García, C and Moreno, E and Talavera-Rodríguez, A and Martín-Fernández, L and González-Bodí, S and Martín-Pedraza, L and Pérez-Molina, JA and Dronda, F and Gosalbes, MJ and Luna, L and Vivancos, MJ and Huerta-Cepas, J and Moreno, S and Serrano-Villar, S}, title = {Fecal microbiota transplantation alters the proteomic landscape of inflammation in HIV: identifying bacterial drivers.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {214}, pmid = {39438902}, issn = {2049-2618}, mesh = {Humans ; *Fecal Microbiota Transplantation ; *HIV Infections/therapy ; *Gastrointestinal Microbiome ; *Inflammation ; Male ; Middle Aged ; Female ; *Proteomics/methods ; Adult ; *Feces/microbiology ; Pilot Projects ; Double-Blind Method ; Bacteria/classification/isolation & purification/metabolism ; }, abstract = {BACKGROUND: Despite effective antiretroviral therapy, people with HIV (PWH) experience persistent systemic inflammation and increased morbidity and mortality. Modulating the gut microbiome through fecal microbiota transplantation (FMT) represents a novel therapeutic strategy. We aimed to evaluate proteomic changes in inflammatory pathways following repeated, low-dose FMT versus placebo.

METHODS: This double-masked, placebo-controlled pilot study assessed the proteomic impacts of weekly FMT versus placebo treatment over 8 weeks on systemic inflammation in 29 PWH receiving stable antiretroviral therapy (ART). Three stool donors with high Faecalibacterium and butyrate profiles were selected, and their individual stools were used for FMT capsule preparation. Proteomic changes in 345 inflammatory proteins in plasma were quantified using the proximity extension assay, with samples collected at baseline and at weeks 1, 8, and 24. Concurrently, we characterized shifts in the gut microbiota composition and annotated functions through shotgun metagenomics. We fitted generalized additive models to evaluate the dynamics of protein expression. We selected the most relevant proteins to explore their correlations with microbiome composition and functionality over time using linear mixed models.

RESULTS: FMT significantly reduced the plasma levels of 45 inflammatory proteins, including established mortality predictors such as IL6 and TNF-α. We found notable reductions persisting up to 16 weeks after the final FMT procedure, including in the expression of proteins such as CCL20 and CD22. We identified changes in 46 proteins, including decreases in FT3LG, IL6, IL10RB, IL12B, and IL17A, which correlated with multiple bacterial species. We found that specific bacterial species within the Ruminococcaceae, Succinivibrionaceae, Prevotellaceae families, and the Clostridium genus, in addition to their associated genes and functions, were significantly correlated with changes in inflammatory markers.

CONCLUSIONS: Targeting the gut microbiome through FMT effectively decreased inflammatory proteins in PWH, with sustained effects. These findings suggest the potential of the microbiome as a therapeutic target to mitigate inflammation-related complications in this population, encouraging further research and development of microbiome-based interventions. Video Abstract.}, } @article {pmid39438713, year = {2024}, author = {Gibbons, JA and Worthington, LM and Chiu, EG and Kates, HR and Carter, RR and Nelson, R and Zhang, M and Garrett, TJ and Ho, TTB}, title = {Severe anemia in preterm infants associated with increased bacterial virulence potential and metabolic disequilibrium.}, journal = {Pediatric research}, volume = {}, number = {}, pages = {}, pmid = {39438713}, issn = {1530-0447}, support = {K23 HL150300/HL/NHLBI NIH HHS/United States ; R21 HD112776/HD/NICHD NIH HHS/United States ; }, abstract = {BACKGROUND: Anemia in preterm infants is associated with gut dysbiosis and necrotizing enterocolitis. Our study aimed to identify the bacterial functions and metabolites that can explain the underlying mechanisms of anemia associated disease conditions.

METHODS: We conducted a case control study in preterm infants with cases having a hematocrit ≤ 25%. The control infants were matched by birth gestational age and weight. Fecal samples were collected before, at the onset, and after the onset of anemia in cases and with matched postnatal age in controls for metagenomics and metabolomics analyzes.

RESULTS: 18 anemic and 20 control infants with fecal samples collected at 17 days, 5 weeks, and 7 weeks postnatal age were included. Virulence factor potential, decrease in beta diversity evolution, and larger changes in metabolome were associated with severe anemia. Metabolite abundances of N-acetylneuraminate and butyrobetaine were associated with virulence factor potential. Anemic group had decreased prostaglandin and lactic acid levels.

CONCLUSION: Fecal omics data showed that severe anemia is associated with a pro-inflammatory gut microbiota with more virulent and less commensal anaerobic bacterial activities. Future studies can examine the link between anemia-associated dysbiosis and clinical outcomes and predict an infant-specific hematocrit threshold that negatively affects clinical outcomes.

IMPACT: Severe anemia in preterm infants contributes to a pro-inflammatory gut with greater bacterial virulence and less commensal bacterial activities. The multiomics approach using non-invasive fecal biospecimens identified functional and metabolic changes in the gut microbiota and these mechanistic changes are plausible explanations for anemia-associated disease conditions in preterm infants. Our findings identified biological changes of the gut environment in severely anemic preterm infants that can offer guidance for clinical management.}, } @article {pmid39438539, year = {2024}, author = {Guo, J and Li, Z and Liu, X and Jin, Y and Sun, Y and Yuan, Z and Zhang, W and Wang, J and Zhang, M}, title = {Response of the gut microbiota to changes in the nutritional status of red deer during winter.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {24961}, pmid = {39438539}, issn = {2045-2322}, support = {2572023AW20//National Key Fundamental Research Funds for the Central Universities, China/ ; 2572020BE02//National Key Fundamental Research Funds for the Central Universities, China/ ; QLKH [2023] 11//the Guizhou Forestry Administration Scientific Research Project/ ; 2023GZJB005//the Reward and Subsidy Fund Project of Guizhou Education University, Ministry of Science and Technology of the People's Republic of China and National Natural Science Foundation of China/ ; 32071512//the National Natural Science Foundation of China, NSFC/ ; 2023YFF1305000//National Key Research and Development Program of China: Migration and diffusion mechanism of wild animals and population control technology/ ; ZKKF2022179//the Opening Research Projects for the Think Tanks of Heilongjiang Provincial Universities/ ; }, mesh = {Animals ; *Deer/microbiology ; *Gastrointestinal Microbiome ; *Seasons ; *Nutritional Status ; Feces/microbiology ; Nitrogen/metabolism/analysis ; Creatinine ; }, abstract = {Unravelling abrupt alterations in the gut microbiota of wild species associated with nutritional stress is imperative but challenging for wildlife conservation. This study assessed the nutritional status of wild red deer during winter on the basis of changes in faecal nitrogen (FN) and urea nitrogen/creatinine (UN: C) levels and identified gut microbes associated with nutritional status via nutritional control experiments and metagenomic sequencing. The FN of wild red deer in winter 2022 was significantly lower than that in winter 2021 (p < 0.05, winter 2021: 1.37 ± 0.16% and winter 2022: 1.26 ± 0.22%), and the UN: C ratio increased (winter 2021: 2.19 ± 1.65 and winter 2022: 3.05 ± 3.50). Similar trends were found in late winter, which indicated greater nutritional pressure in winter (2022) and late winter. Compared with winter 2021, abundances of Ructibacterium and Butyrivibrio significantly increased, and Acetatifactor and Cuneatibacter significantly decreased during winter 2022 (p < 0.05). Compared with early winter, the cell growth and death pathways increased and lipid metabolism and its subpathway of secondary bile acid synthesis (ko00121) significantly decreased during late winter (p < 0.05), which was similar to the changes in malnourished experimental red deer. Abrupt alterations in the gut microbiota should receive increased attention when monitoring the nutritional health of wild ungulates. This study provides new insights and critical implications for the conservation of wild ungulate populations.}, } @article {pmid39438328, year = {2024}, author = {Varghese, P and Kumar, K and Sarkar, P and Karmakar, S and Shukla, SP and Kumar, S and Bharti, VS and Paul, T and Kantal, D}, title = {Impact of Triclosan on Bacterial Biodiversity and Sediment Enzymes - A Microcosm Study.}, journal = {Bulletin of environmental contamination and toxicology}, volume = {113}, number = {5}, pages = {59}, pmid = {39438328}, issn = {1432-0800}, support = {DST/TMD-EWO-WTI/2K19/EWFH/2019/214//Department of Science and Technology, Govt. of India/ ; }, mesh = {*Triclosan/toxicity ; *Geologic Sediments/microbiology/chemistry ; *Biodiversity ; *Water Pollutants, Chemical/analysis/toxicity ; *Bacteria/drug effects ; }, abstract = {Triclosan (TCS), a widely used antimicrobial biocide, has raised serious concern among the scientific community in recent years owing to its ubiquitous presence around the globe and toxicity to aquatic organisms. The current study investigated the alterations in bacterial diversity, nutrients, and sediment enzyme activity in TCS-exposed sediment. TCS concentrations of 3 mg/L (T1) and 6 mg/L (T2) were applied in a microcosm setup for 28 days to sediment collected from Versova Creek, Mumbai. Among sediment enzymes, dehydrogenase activity exhibited the greatest degree of variability in 3 mg/L exposed sediment. Nitrite, total nitrogen and urease exhibited higher concentrations in 6 mg/L TCS exposed sediment. The concentration of ammonia was observed to be decreasing in treatments exposed to 6 mg/L TCS. Total heterotrophic bacteria exhibited an increase in count in T1 and a decrease in T2. Metagenomics data showed a higher relative abundance of bacteria in T1 compared to T2 on the 28th day of sampling. Proteobacteria was found to be the most abundant phylum in all samples, and their relative abundance was reduced by 0.14% in T1 and 5.48% in T2. The results confirm the alterations in the composition of sediment bacterial communities and their enzymatic activities due to TCS exposure.}, } @article {pmid39438078, year = {2024}, author = {Wei, G and Wu, N and Zhao, K and Yang, S and Wang, L and Liu, Y}, title = {DeepCheck: multitask learning aids in assessing microbial genome quality.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {6}, pages = {}, pmid = {39438078}, issn = {1477-4054}, support = {2023YFD2200104//National Key Research and Development Program of China/ ; 32270664//National Natural Science Foundation of China/ ; }, mesh = {*Metagenome ; *Metagenomics/methods ; *Deep Learning ; Genome, Microbial ; Machine Learning ; Software ; }, abstract = {Metagenomic analyses facilitate the exploration of the microbial world, advancing our understanding of microbial roles in ecological and biological processes. A pivotal aspect of metagenomic analysis involves assessing the quality of metagenome-assembled genomes (MAGs), crucial for accurate biological insights. Current machine learning-based methods often treat completeness and contamination prediction as separate tasks, overlooking their inherent relationship and limiting models' generalization. In this study, we present DeepCheck, a multitasking deep learning framework for simultaneous prediction of MAG completeness and contamination. DeepCheck consistently outperforms existing tools in accuracy across various experimental settings and demonstrates comparable speed while maintaining high predictive accuracy even for new lineages. Additionally, we employ interpretable machine learning techniques to identify specific genes and pathways that drive the model's predictions, enabling independent investigation and assessment of these biological elements for deeper insights.}, } @article {pmid39437661, year = {2024}, author = {Sreenivasan, CC and Naveed, A and Uprety, T and Soni, S and Jacob, O and Adam, E and Wang, D and Li, F}, title = {Epidemiological investigation of equine rotavirus B outbreaks in horses in central Kentucky.}, journal = {Veterinary microbiology}, volume = {298}, number = {}, pages = {110278}, doi = {10.1016/j.vetmic.2024.110278}, pmid = {39437661}, issn = {1873-2542}, mesh = {Animals ; Horses ; Kentucky/epidemiology ; *Disease Outbreaks/veterinary ; *Rotavirus Infections/veterinary/epidemiology/virology ; *Horse Diseases/virology/epidemiology ; *Rotavirus/genetics/isolation & purification/classification ; *Phylogeny ; *Feces/virology ; Female ; Seroepidemiologic Studies ; Diarrhea/veterinary/virology/epidemiology ; Genome, Viral ; }, abstract = {Using metagenomic sequencing we identified equine rotavirus group B (ERVB) of ruminant origin in foal diarrhea outbreaks in the 2021 foaling season. To further investigate ERVB occurrence and determine its environmental stability, we collected mare and foal fecal samples from different farms in Central Kentucky during the 2022 foaling season. The RT-qPCR-based analyses showed that ERVB genome was detected in 16.67 % (42/252) of surveyed mare samples and 26.56 % (34/128) of foal samples. Furthermore, 94.12 % (16/17) of collected soil samples and 100 % (13/13) of water samples obtained from the ERVB-positive farm premises also tested weakly positive. In addition, ERVB genome fragments were detected in 58.33 % (7/12) of indoor samples collected from the equipment/barn/hospital wards during the outbreak period. Finally, the seroprevalence study showed 87 % (113/130) of surveyed horse serum samples were positive for ERVB antibodies. Despite unsuccessful attempts in ERVB cultivation, phylogenetic analyses showed that fecal ERVB strains representing 2022 and 2023 foal diarrhea outbreaks, like 2021 strains, were more closely related to ruminant rotavirus B than other viruses. Further sequence analyses revealed that none of the three viral capsid proteins, the primary targets of virus-neutralizing antibodies, exhibited notable mutations among ERVB strains circulated over the past three years. Our data demonstrated that ERVB was widespread in horses on affected farms with extreme stability in the farm environment. These findings continue to support the need for future surveillance of ERVB in horses and the surrounding environment, and the development of effective countermeasures to protect horses against this new viral disease.}, } @article {pmid39436938, year = {2024}, author = {Rocha, U and Kasmanas, JC and Toscan, R and Sanches, DS and Magnusdottir, S and Saraiva, JP}, title = {Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in prokaryotic metagenome-assembled genome recovery.}, journal = {PLoS computational biology}, volume = {20}, number = {10}, pages = {e1012530}, pmid = {39436938}, issn = {1553-7358}, mesh = {*Metagenome/genetics ; *Microbiota/genetics ; *Computer Simulation ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Bacteria/genetics/classification ; Genome, Bacterial/genetics ; }, abstract = {We hypothesize that sample species abundance, sequencing depth, and taxonomic relatedness influence the recovery of metagenome-assembled genomes (MAGs). To test this hypothesis, we assessed MAG recovery in three in silico microbial communities composed of 42 species with the same richness but different sample species abundance, sequencing depth, and taxonomic distribution profiles using three different pipelines for MAG recovery. The pipeline developed by Parks and colleagues (8K) generated the highest number of MAGs and the lowest number of true positives per community profile. The pipeline by Karst and colleagues (DT) showed the most accurate results (~ 92%), outperforming the 8K and Multi-Metagenome pipeline (MM) developed by Albertsen and collaborators. Sequencing depth influenced the accurate recovery of genomes when using the 8K and MM, even with contrasting patterns: the MM pipeline recovered more MAGs found in the original communities when employing sequencing depths up to 60 million reads, while the 8K recovered more true positives in communities sequenced above 60 million reads. DT showed the best species recovery from the same genus, even though close-related species have a low recovery rate in all pipelines. Our results highlight that more bins do not translate to the actual community composition and that sequencing depth plays a role in MAG recovery and increased community resolution. Even low MAG recovery error rates can significantly impact biological inferences. Our data indicates that the scientific community should curate their findings from MAG recovery, especially when asserting novel species or metabolic traits.}, } @article {pmid39436609, year = {2025}, author = {Singer, F and Kuhring, M and Renard, BY and Muth, T}, title = {Moving Toward Metaproteogenomics: A Computational Perspective on Analyzing Microbial Samples via Proteogenomics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2859}, number = {}, pages = {297-318}, pmid = {39436609}, issn = {1940-6029}, mesh = {*Proteogenomics/methods ; *Microbiota/genetics ; Computational Biology/methods ; Proteomics/methods ; Software ; Databases, Protein ; Metagenomics/methods ; Algorithms ; Metagenome ; Humans ; High-Throughput Nucleotide Sequencing/methods ; Mass Spectrometry/methods ; Proteome/genetics ; }, abstract = {Microbial sample analysis has received growing attention within the last decade, driven by important findings in microbiome research and promising applications in the biotechnological field. Modern mass spectrometry-based methodology has been established in this context, providing sufficient sensitivity, resolution, dynamic range, and throughput to analyze the so-called metaproteome of complex microbial mixtures from clinical or environmental samples. While proteomic analyses were previously restricted to common model organisms, next-generation sequencing technologies nowadays allow for the rapid and cost-efficient characterization of whole metagenomes of microbial consortia and specific genomes from non-model organisms to which microbes contribute by significant amounts. This proteogenomic approach, meaning the combined application of genomic and proteomic methods, enables researchers to create a protein database that presents a tailored blueprint of the microbial sample under investigation. This contribution provides an overview of the computational challenges and opportunities in proteogenomics and metaproteomics as of January 2018. For practical application, we first showcase an integrative proteogenomic method that circumvents existing reference databases by creating sample-specific transcripts. The underlying algorithm uses a graph network approach that combines RNA-Seq and peptide information. As a second example, we provide a tutorial for a simulation tool that estimates the computational limits of detecting microbial non-model organisms. This method evaluates the potential influence of error-tolerant searches and proteogenomic approaches on databases of interest. Finally, we discuss recommendations for developing future strategies that may help overcome present limitations by combining the strengths of genome- and proteome-based methods and moving toward an integrated metaproteogenomics approach.}, } @article {pmid39436239, year = {2024}, author = {Cheng, M and Zhou, H and Zhang, H and Zhang, X and Zhang, S and Bai, H and Zha, Y and Luo, D and Chen, D and Chen, S and Ning, K and Liu, W}, title = {Hidden Links Between Skin Microbiome and Skin Imaging Phenome.}, journal = {Genomics, proteomics & bioinformatics}, volume = {22}, number = {4}, pages = {}, doi = {10.1093/gpbjnl/qzae040}, pmid = {39436239}, issn = {2210-3244}, support = {32071465//National Natural Science Foundation of China/ ; 2018YFC0910502//National Key R&D Program of China/ ; }, mesh = {Humans ; *Skin/microbiology/metabolism/diagnostic imaging ; *Microbiota/genetics ; Male ; Female ; *Phenotype ; *Skin Aging ; Adult ; Middle Aged ; Metagenome ; }, abstract = {Despite the skin microbiome has been linked to skin health and diseases, its role in modulating human skin appearance remains understudied. Using a total of 1244 face imaging phenomes and 246 cheek metagenomes, we first established three skin age indices by machine learning, including skin phenotype age (SPA), skin microbiota age (SMA), and skin integration age (SIA) as surrogates of phenotypic aging, microbial aging, and their combination, respectively. Moreover, we found that besides aging and gender as intrinsic factors, skin microbiome might also play a role in shaping skin imaging phenotypes (SIPs). Skin taxonomic and functional α diversity was positively linked to melanin, pore, pigment, and ultraviolet spot levels, but negatively linked to sebum, lightening, and porphyrin levels. Furthermore, certain species were correlated with specific SIPs, such as sebum and lightening levels negatively correlated with Corynebacterium matruchotii, Staphylococcus capitis, and Streptococcus sanguinis. Notably, we demonstrated skin microbial potential in predicting SIPs, among which the lightening level presented the least error of 1.8%. Lastly, we provided a reservoir of potential mechanisms through which skin microbiome adjusted the SIPs, including the modulation of pore, wrinkle, and sebum levels by cobalamin and heme synthesis pathways, predominantly driven by Cutibacterium acnes. This pioneering study unveils the paradigm for the hidden links between skin microbiome and skin imaging phenome, providing novel insights into how skin microbiome shapes skin appearance and its healthy aging.}, } @article {pmid39436062, year = {2024}, author = {Aguirre, EG and Schwartzman, JA}, title = {Metagenome-assembled genomes of Macrocystis-associated bacteria.}, journal = {Microbiology resource announcements}, volume = {13}, number = {11}, pages = {e0071524}, pmid = {39436062}, issn = {2576-098X}, support = {//University of Southern California (SC)/ ; }, abstract = {Microbes are important for the development of kelp, but little is understood about the functions encoded by these microbes. Here, we assembled 1,794 metagenome-associated genomes (MAGs) from bacteria that colonize gametophytes of the giant kelp Macrocystis pyrifera. MAGs were grouped into 149 dereplicated strains. Functional annotation is also presented.}, } @article {pmid39435818, year = {2024}, author = {He, L and Yan, YT and Yuan, CY and Lin, QS and Yu, DT}, title = {Characteristics of soil viral communities in Cunninghamia lanceolata plantations with different stand ages.}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {35}, number = {9}, pages = {2543-2551}, doi = {10.13287/j.1001-9332.202409.007}, pmid = {39435818}, issn = {1001-9332}, mesh = {*Soil Microbiology ; *Cunninghamia/growth & development/virology ; Soil/chemistry ; Viruses/classification/isolation & purification/genetics ; China ; Virome ; Phosphorus/analysis ; }, abstract = {We investigated the dynamics of soil viral community in Cunninghamia lanceolata plantations with different stand ages (8, 21, 27, and 40 years old) in a subtropical region. The viral metagenomics and bioinformatics analysis were used to analyze the compositional and functional differences of soil viral communities across different stand ages, and to explore the environmental driving factors. The results showed that tailed phages dominated soil viral community in subtropical C. lanceolata plantations, with the highest proportion of Siphoviridae (19.6%-39.5%). There was significant difference in soil viral community structure among different stand ages, with the main driving factors being electrical conductance and available phosphorus. The metabolic functional genes encoded by viruses exhibited higher relative abundance. The α-diversity of soil viral function in mature C. lanceolata plantations was higher than other stands. There were significant differences in soil viral functional structure among different stand ages, which were mainly driven by ammonium nitrogen. During the development of C. lanceolata plantations, auxiliary metabolic genes encoded by virus related to nitrogen and phosphorus may regulate the metabolism of host microorganisms, thereby potentially impacting biogeochemical cycling of these elements.}, } @article {pmid39435753, year = {2024}, author = {Deng, A and Wang, J and Li, L and Shi, R and Li, X and Wen, T}, title = {Synoptic Variation Drives Genetic Diversity and Transmission Mode of Airborne DNA Viruses in Urban Space.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {11}, number = {46}, pages = {e2404512}, pmid = {39435753}, issn = {2198-3844}, support = {XDA17010503//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; CASPMI202202//Open Project Program of CAS Key Laboratory of Pathogenic Microbiology and Immunology/ ; 2024AC010//Central Government Special Fund for Building World-Class Universities (Disciplines) and Guiding Special Development/ ; 2024RC017//Starting Grants Program for Young Talents at China Agricultural University/ ; }, mesh = {*Air Microbiology ; *Genetic Variation/genetics ; *DNA Viruses/genetics ; Metagenomics/methods ; Cities ; Genome, Viral/genetics ; }, abstract = {Airborne viruses are ubiquitous and play critical roles in maintaining ecosystem balance, however, they remain unexplored. Here, it is aimed to demonstrate that highly diverse airborne viromes carry out specific metabolic functions and use different transmission modes under different air quality conditions. A total of 263.5-Gb data are collected from 13 air samples for viral metagenomic analysis. After assembly and curation, a total of 12 484 viral contigs (1.5-184.2 kb) are assigned to 221 genus-level clades belonging to 47 families, 19 orders, and 15 classes. The composition of viral communities is influenced by weather conditions, with the main biomarker being Caudoviricetes. The most dominant viruses in these air samples belong to the dsDNA Caudoviricetes (54.0%) and ssDNA Repensiviricetes (31.2%) classes. Twelve novel candidate viruses are identified at the order/family/genus levels by alignment of complete genomes and core genes. Notably, Caudoviricetes are highly prevalent in cloudy and smoggy air, whereas Repensiviricetes are highly dominant in sunny and rainy air. Diverse auxiliary metabolic genes of airborne viruses are mainly involved in deoxynucleotide synthesis, implying their unique roles in atmosphere ecosystem. These findings deepen the understanding of the meteorological impacts on viral composition, transmission mode, and ecological roles in the air that we breathe.}, } @article {pmid39435348, year = {2024}, author = {Li, Y and Shen, Y and Yang, H and Li, M and Jiang, L and Ma, W and Zhou, F and Su, T}, title = {Q Fever-Related Glomerulonephritis Unveiled by Metagenomic Next-Generation Sequencing.}, journal = {Kidney international reports}, volume = {9}, number = {10}, pages = {3062-3066}, pmid = {39435348}, issn = {2468-0249}, } @article {pmid39435150, year = {2024}, author = {Fu, Q and Ma, K and Zhao, J and Li, J and Wang, X and Zhao, M and Fu, X and Huang, D and Chen, H}, title = {Metagenomics unravel distinct taxonomic and functional diversities between terrestrial and aquatic biomes.}, journal = {iScience}, volume = {27}, number = {10}, pages = {111047}, pmid = {39435150}, issn = {2589-0042}, abstract = {Microbes in terrestrial and aquatic ecosystems play crucial roles in driving ecosystem functions, but currently, there is a lack of comparison regarding their taxonomic and functional diversities. Here, we conducted a global analysis to investigate the disparities in microbial taxonomy and microbial-mediated biogeochemical cycles between terrestrial and aquatic ecosystems. Results showed a higher relative abundance of bacteria, especially Actinobacteria and Acidobacteria, in soil than water metagenomes, leading to a greater proportion of genes related to membrane transport, regulatory, and cellular signaling. Moreover, there was a higher abundance of genes associated with carbohydrate, sulfur, and potassium metabolisms in the soil, while those involved in nitrogen and iron metabolisms were more prevalent in the water. Thus, both soil and water microbiomes exhibited unique taxonomic and functional properties associated with biogeochemical processes, providing valuable insights into predicting and understanding the adaptation of microbes in different ecosystems in the face of climate change.}, } @article {pmid39434927, year = {2024}, author = {Gong, Y and Wang, T}, title = {Toxoplasmosis-Associated Hemophagocytic Lymphohistiocytosis in a Liver Transplant Recipient.}, journal = {Cureus}, volume = {16}, number = {10}, pages = {e71843}, pmid = {39434927}, issn = {2168-8184}, abstract = {Toxoplasmosis is a rare parasitic infectious disease in solid organ transplant recipients. The disease is characterized by difficulties in diagnosis and high mortality. However, there have been no reported cases of hemophagocytic lymphohistiocytosis (HLH) caused by toxoplasmosis in liver transplant patients. Here, we present the case of an adult female liver transplant recipient who experienced a fatal outcome and developed secondary HLH following confirmation of toxoplasmosis through metagenomic next-generation sequencing. The patient exhibited symptoms, including high fever, skin rash, unconsciousness, and multiorgan failure. The condition met six out of eight criteria for HLH according to the HLH-2004 diagnostic criteria. Additionally, the H-score for this patient was 287 points, confirming the diagnosis of HLH. This represents the first reported case of toxoplasmosis-associated secondary HLH in an adult liver transplant recipient in China.}, } @article {pmid39434799, year = {2024}, author = {Ghabban, H and Albalawi, DA and Al-Otaibi, AS and Alshehri, D and Alenzi, AM and Alatawy, M and Alatawi, HA and Alnagar, DK and Bahieldin, A}, title = {Investigating the bacterial community of gray mangroves (Avicennia marina) in coastal areas of Tabuk region.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e18282}, pmid = {39434799}, issn = {2167-8359}, mesh = {*Soil Microbiology ; *Avicennia/microbiology ; Saudi Arabia ; *Bacteria/genetics/classification/isolation & purification ; *Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Wetlands ; }, abstract = {Mangrove vegetation, a threatened and unique inter-tidal ecosystem, harbours a complex and largely unexplored bacterial community crucial for nutrient cycling and the degradation of toxic pollutants in coastal areas. Despite its importance, the bacterial community composition of the gray mangrove (Avicennia marina) in the Red Sea coastal regions remains under-studied. This study aims to elucidate the structural and functional diversity of the microbiome in the bulk and rhizospheric soils associated with A. marina in the coastal areas of Ras Alshabaan-Umluj (Umluj) and Almunibrah-Al-Wajh (Al-Wajh) within the Tabuk region of Saudi Arabia. Amplicon sequencing targeting the 16S rRNA was performed using the metagenomic DNAs from the bulk and rhizospheric soil samples from Umluj and Al-Wajh. A total of 6,876 OTUs were recovered from all samples, of which 1,857 OTUs were common to all locations while the total number of OTUs unique to Al-wajh was higher (3,011 OTUs) than the total number of OTUs observed (1,324 OTUs) at Umluj site. Based on diversity indices, overall bacterial diversity was comparatively higher in rhizospheric soil samples of both sites. Comparing the diversity indices for the rhizosphere samples from the two sites revealed that the diversity was much higher in the rhizosphere samples from Al-Wajh as compared to those from Umluj. The most dominant genera in rhizosphere sample of Al-Wajh were Geminicoccus and Thermodesulfovibrio while the same habitat of the Umluj site was dominated by Propionibacterium, Corynebacterium and Staphylococcus. Bacterial functional potential prediction analyses showed that bacteria from two locations have almost similar patterns of functional genes including amino acids and carbohydrates metabolisms, sulfate reduction and C-1 compound metabolism and xenobiotics biodegradation. However, the rhizosphere samples of both sites harbour more genes involved in the utilization and assimilation of C-1 compounds. Our results reveal that bacterial communities inhabiting the rhizosphere of A. marina differed significantly from those in the bulk soil, suggesting a possible role of A. marina roots in shaping these bacterial communities. Additionally, not only vegetation but also geographical location appears to influence the overall bacterial composition at the two sites.}, } @article {pmid39434791, year = {2024}, author = {Zambrano-Alvarado, JI and Uyaguari-Diaz, MI}, title = {Insights into water insecurity in Indigenous communities in Canada: assessing microbial risks and innovative solutions, a multifaceted review.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e18277}, pmid = {39434791}, issn = {2167-8359}, mesh = {Humans ; Canada/epidemiology ; *Drinking Water/microbiology ; *Water Microbiology ; Water Insecurity ; Water Supply ; Water Purification/methods ; Water Quality ; Indigenous Canadians ; }, abstract = {Canada is considered a freshwater-rich country, despite this, several Indigenous reserves struggle with household water insecurity. In fact, some of these communities have lacked access to safe water for almost 30 years. Water quality in Canadian Indigenous reserves is influenced by several factors including source water quality, drinking water treatments applied, water distribution systems, and water storage tanks when piped water is unavailable. The objective of this multifaceted review is to spot the challenges and consequences of inadequate drinking water systems (DWS) and the available technical and microbiological alternatives to address water sanitation coverage in Indigenous reserves of Canada, North America (also known as Turtle Island). A comprehensive literature review was conducted using national web portals from both federal and provincial governments, as well as academic databases to identify the following topics: The status of water insecurity in Indigenous communities across Canada; Microbiological, chemical, and natural causes contributing to water insecurity; Limitations of applying urban-style drinking water systems in Indigenous reserves in Canada and the management of DWS for Indigenous communities in other high-income countries; and the importance of determining the microbiome inhabiting drinking water systems along with the cutting-edge technology available for its analysis. A total of 169 scientific articles matched the inclusion criteria. The major themes discussed include: The status of water insecurity and water advisories in Canada; the risks of pathogenic microorganisms (i.e., Escherichia coli and total coliforms) and other chemicals (i.e., disinfection by-products) found in water storage tanks; the most common technologies available for water treatment including coagulation, high- and low-pressure membrane filtration procedures, ozone, ion exchange, and biological ion exchange and their limitations when applying them in remote Indigenous communities. Furthermore, we reviewed the benefits and drawbacks that high throughput tools such as metagenomics (the study of genomes of microbial communities), culturomics (a high-efficiency culture approach), and microfluidics devices (microminiaturized instruments) and what they could represent for water monitoring in Indigenous reserves. This multifaceted review demonstrates that water insecurity in Canada is a reflection of the institutional structures of marginalization that persist in the country and other parts of Turtle Island. DWS on Indigenous reserves are in urgent need of upgrades. Source water protection, and drinking water monitoring plus a comprehensive design of culturally adapted, and sustainable water services are required. Collaborative efforts between First Nations authorities and federal, provincial, and territorial governments are imperative to ensure equitable access to safe drinking water in Indigenous reserves.}, } @article {pmid39434565, year = {2025}, author = {Blattner, LA and Lapellegerie, P and Courtney-Mustaphi, C and Heiri, O}, title = {Sediment Core DNA-Metabarcoding and Chitinous Remain Identification: Integrating Complementary Methods to Characterise Chironomidae Biodiversity in Lake Sediment Archives.}, journal = {Molecular ecology resources}, volume = {25}, number = {1}, pages = {e14035}, pmid = {39434565}, issn = {1755-0998}, mesh = {Animals ; *Chironomidae/genetics/classification ; *Lakes ; *DNA Barcoding, Taxonomic/methods ; *Geologic Sediments/chemistry ; *Biodiversity ; Switzerland ; Larva/genetics/classification ; DNA/genetics/chemistry ; Chitin ; Metagenomics/methods ; }, abstract = {Chironomidae, so-called non-biting midges, are considered key bioindicators of aquatic ecosystem variability. Data derived from morphologically identifying their chitinous remains in sediments document chironomid larvae assemblages, which are studied to reconstruct ecosystem changes over time. Recent developments in sedimentary DNA (sedDNA) research have demonstrated that molecular techniques are suitable for determining past and present occurrences of organisms. Nevertheless, sedDNA records documenting alterations in chironomid assemblages remain largely unexplored. To close this gap, we examined the applicability of sedDNA metabarcoding to identify Chironomidae assemblages in lake sediments by sampling and processing three 21-35 cm long sediment cores from Lake Sempach in Switzerland. With a focus on developing analytical approaches, we compared an invertebrate-universal (FWH) and a newly designed Chironomidae-specific metabarcoding primer set (CH) to assess their performance in detecting Chironomidae DNA. We isolated and identified chitinous larval remains and compared the morphotype assemblages with the data derived from sedDNA metabarcoding. Results showed a good overall agreement of the morphotype assemblage-specific clustering among the chitinous remains and the metabarcoding datasets. Both methods indicated higher chironomid assemblage similarity between the two littoral cores in contrast to the deep lake core. Moreover, we observed a pronounced primer bias effect resulting in more Chironomidae detections with the CH primer combination compared to the FWH combination. Overall, we conclude that sedDNA metabarcoding can supplement traditional remain identifications and potentially provide independent reconstructions of past chironomid assemblage changes. Furthermore, it has the potential of more efficient workflows, better sample standardisation and species-level resolution datasets.}, } @article {pmid39434181, year = {2024}, author = {Chen, CZ and Li, P and Liu, L and Sun, YJ and Ju, WM and Li, ZH}, title = {Seasonal variations of microbial communities and viral diversity in fishery-enhanced marine ranching sediments: insights into metabolic potentials and ecological interactions.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {209}, pmid = {39434181}, issn = {2049-2618}, support = {42277269//National Natural Science Foundation of China/ ; 42277269//National Natural Science Foundation of China/ ; 42277269//National Natural Science Foundation of China/ ; 42277269//National Natural Science Foundation of China/ ; KLMR-2022-03//Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, China/ ; KLMR-2022-03//Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, China/ ; KLMR-2022-03//Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, China/ ; KLMR-2022-03//Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, China/ ; }, mesh = {*Geologic Sediments/microbiology/virology ; *Seasons ; *Microbiota ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Viruses/classification/genetics/isolation & purification ; *Fisheries ; *Biodiversity ; Ecosystem ; Metagenome ; Sulfur/metabolism ; Metagenomics ; Carbon/metabolism ; Nitrogen/metabolism ; }, abstract = {BACKGROUND: The ecosystems of marine ranching have enhanced marine biodiversity and ecological balance and have promoted the natural recovery and enhancement of fishery resources. The microbial communities of these ecosystems, including bacteria, fungi, protists, and viruses, are the drivers of biogeochemical cycles. Although seasonal changes in microbial communities are critical for ecosystem functioning, the current understanding of microbial-driven metabolic properties and their viral communities in marine sediments remains limited. Here, we employed amplicon (16S and 18S) and metagenomic approaches aiming to reveal the seasonal patterns of microbial communities, bacterial-eukaryotic interactions, whole metabolic potential, and their coupling mechanisms with carbon (C), nitrogen (N), and sulfur (S) cycling in marine ranching sediments. Additionally, the characterization and diversity of viral communities in different seasons were explored in marine ranching sediments.

RESULTS: The current study demonstrated that seasonal variations dramatically affected the diversity of microbial communities in marine ranching sediments and the bacterial-eukaryotic interkingdom co-occurrence networks. Metabolic reconstruction of the 113 medium to high-quality metagenome-assembled genomes (MAGs) was conducted, and a total of 8 MAGs involved in key metabolic genes and pathways (methane oxidation - denitrification - S oxidation), suggesting a possible coupling effect between the C, N, and S cycles. In total, 338 viral operational taxonomic units (vOTUs) were identified, all possessing specific ecological characteristics in different seasons and primarily belonging to Caudoviricetes, revealing their widespread distribution and variety in marine sediment ecosystems. In addition, predicted virus-host linkages showed that high host specificity was observed, with few viruses associated with specific hosts.

CONCLUSIONS: This finding deepens our knowledge of element cycling and viral diversity in fisheries enrichment ecosystems, providing insights into microbial-virus interactions in marine sediments and their effects on biogeochemical cycling. These findings have potential applications in marine ranching management and ecological conservation. Video Abstract.}, } @article {pmid39434178, year = {2024}, author = {van Gogh, M and Louwers, JM and Celli, A and Gräve, S and Viveen, MC and Bosch, S and de Boer, NKH and Verheijden, RJ and Suijkerbuijk, KPM and Brand, EC and Top, J and Oldenburg, B and de Zoete, MR}, title = {Next-generation IgA-SEQ allows for high-throughput, anaerobic, and metagenomic assessment of IgA-coated bacteria.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {211}, pmid = {39434178}, issn = {2049-2618}, mesh = {Humans ; *Feces/microbiology ; *Gastrointestinal Microbiome ; *Metagenomics/methods ; *Immunoglobulin A/immunology ; *Bacteria/genetics/classification/immunology ; High-Throughput Nucleotide Sequencing/methods ; Inflammatory Bowel Diseases/microbiology/immunology ; }, abstract = {BACKGROUND: The intestinal microbiota plays a significant role in maintaining systemic and intestinal homeostasis, but can also influence diseases such as inflammatory bowel disease (IBD) and cancer. Certain bacterial species within the intestinal tract can chronically activate the immune system, leading to low-grade intestinal inflammation. As a result, plasma cells produce high levels of secretory antigen-specific immunoglobulin A (IgA), which coats the immunostimulatory bacteria. This IgA immune response against intestinal bacteria may be associated with the maintenance of homeostasis and health, as well as disease. Unraveling this dichotomy and identifying the immunostimulatory bacteria is crucial for understanding the relationship between the intestinal microbiota and the immune system, and their role in health and disease. IgA-SEQ technology has successfully identified immunostimulatory, IgA-coated bacteria from fecal material. However, the original technology is time-consuming and has limited downstream applications. In this study, we aimed to develop a next-generation, high-throughput, magnet-based sorting approach (ng-IgA-SEQ) to overcome the limitations of the original IgA-SEQ protocol.

RESULTS: We show, in various settings of complexity ranging from simple bacterial mixtures to human fecal samples, that our magnetic 96-well plate-based ng-IgA-SEQ protocol is highly efficient at sorting and identifying IgA-coated bacteria in a high-throughput and time efficient manner. Furthermore, we performed a comparative analysis between different IgA-SEQ protocols, highlighting that the original FACS-based IgA-SEQ approach overlooks certain nuances of IgA-coated bacteria, due to the low yield of sorted bacteria. Additionally, magnetic-based ng-IgA-SEQ allows for novel downstream applications. Firstly, as a proof-of-concept, we performed metagenomic shotgun sequencing on 10 human fecal samples to identify IgA-coated bacterial strains and associated pathways and CAZymes. Secondly, we successfully isolated and cultured IgA-coated bacteria by performing the isolation protocol under anaerobic conditions.

CONCLUSIONS: Our magnetic 96-well plate-based high-throughput next-generation IgA-SEQ technology efficiently identifies a great number of IgA-coated bacteria from fecal samples. This paves the way for analyzing large cohorts as well as novel downstream applications, including shotgun metagenomic sequencing, culturomics, and various functional assays. These downstream applications are essential to unravel the role of immunostimulatory bacteria in health and disease. Video Abstract.}, } @article {pmid39433961, year = {2024}, author = {Li, J and Shen, N and He, W and Pan, Y and Wu, J and Zhao, R and Mo, X and Li, Y}, title = {Gut microbiome impact on childhood allergic rhinitis and house dust mite IgE responses.}, journal = {Pediatric research}, volume = {}, number = {}, pages = {}, pmid = {39433961}, issn = {1530-0447}, abstract = {BACKGROUND: The correlation between the gut microbiota and airway inflammation in childhood allergic rhinitis (AR), particularly concerning allergen exposure, remains insufficiently explored. This study aimed to link gut microbiota changes with house dust mite (HDM)-specific IgE responses in pediatric AR.

METHODS: Using metagenomic shotgun sequencing, we compared the fecal microbiota of 60 children with HDM-AR to 48 healthy controls (HC), analyzing the link to IgE reactions. We examined the effects of oral Escherichia (E.) fergusonii treatment in mice sensitized with ovalbumin and HDM on allergic symptoms, mucosal cell infiltration, Th1/Th2/Tregs balance in the spleen, serum cytokine levels, and E. fergusonii presence in feces.

RESULTS: Children with HDM-AR have a less diverse gut microbiome and lower levels of E. fergusonii compared to controls, with a negative correlation between E. fergusonii abundance and HDM-specific IgE levels. In mice sensitized with OVA and HDM, oral administration of E. fergusonii improved allergic symptoms, reduced nasal eosinophils/mast cells infiltration and adjusted Th cell populations towards a non-allergic profile in splenic lymphocytes with exception of IFN-γ change in serum.

CONCLUSION: These findings underline the potential of targeting gut microbiota, particularly E. fergusonii, in managing childhood HDM-AR, suggesting a promising approach for future interventions.

IMPACT: The composition and distribution of gut microbiota in children with HDM-AR are significant changed. The abundance of Escherichia genus is decreased in HDM-AR children. HDM-specific IgE levels are strongly negatively associated with E. fergusonii abundance. Oral administration of E. fergusonii effectively suppresses allergic responses in murine model. These findings offer novel insights into the diagnosis and treatment of HDM-AR, which suggested that E. fergusonii holds promise as a potential therapeutic avenue for managing HDM-AR.}, } @article {pmid39433727, year = {2024}, author = {Lemaire, ON and Wegener, G and Wagner, T}, title = {Ethane-oxidising archaea couple CO2 generation to F420 reduction.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {9065}, pmid = {39433727}, issn = {2041-1723}, support = {WA 4053/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; WE 5492/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; WA 4053/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {*Oxidation-Reduction ; *Carbon Dioxide/metabolism ; *Ethane/metabolism/chemistry ; Archaea/metabolism/genetics ; Aldehyde Oxidoreductases/metabolism/genetics/chemistry ; Multienzyme Complexes/metabolism/genetics/chemistry ; Crystallography, X-Ray ; Archaeal Proteins/metabolism/genetics/chemistry ; Anaerobiosis ; Ferredoxins/metabolism ; Riboflavin/analogs & derivatives ; }, abstract = {The anaerobic oxidation of alkanes is a microbial process that mitigates the flux of hydrocarbon seeps into the oceans. In marine archaea, the process depends on sulphate-reducing bacterial partners to exhaust electrons, and it is generally assumed that the archaeal CO2-forming enzymes (CO dehydrogenase and formylmethanofuran dehydrogenase) are coupled to ferredoxin reduction. Here, we study the molecular basis of the CO2-generating steps of anaerobic ethane oxidation by characterising native enzymes of the thermophile Candidatus Ethanoperedens thermophilum obtained from microbial enrichment. We perform biochemical assays and solve crystal structures of the CO dehydrogenase and formylmethanofuran dehydrogenase complexes, showing that both enzymes deliver electrons to the F420 cofactor. Both multi-metalloenzyme harbour electronic bridges connecting CO and formylmethanofuran oxidation centres to a bound flavin-dependent F420 reductase. Accordingly, both systems exhibit robust coupled F420-reductase activities, which are not detected in the cell extract of related methanogens and anaerobic methane oxidisers. Based on the crystal structures, enzymatic activities, and metagenome mining, we propose a model in which the catabolic oxidising steps would wire electron delivery to F420 in this organism. Via this specific adaptation, the indirect electron transfer from reduced F420 to the sulphate-reducing partner would fuel energy conservation and represent the driving force of ethanotrophy.}, } @article {pmid39433639, year = {2025}, author = {Davidson, IM and Nikbakht, E and Haupt, LM and Ashton, KJ and Dunn, PJ}, title = {Methodological approaches in 16S sequencing of female reproductive tract in fertility patients: a review.}, journal = {Journal of assisted reproduction and genetics}, volume = {42}, number = {1}, pages = {15-37}, pmid = {39433639}, issn = {1573-7330}, mesh = {Female ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Genitalia, Female/microbiology ; Reproductive Techniques, Assisted ; Metagenomics/methods ; Computational Biology/methods ; Fertility/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: The female genital tract microbiome has become a particular area of interest in improving assisted reproductive technology (ART) outcomes with the emergence of next-generation sequencing (NGS) technology. However, NGS assessment of microbiomes currently lacks uniformity and poses significant challenges for accurate and precise bacterial population representation.

OBJECTIVE: As multiple NGS platforms and assays have been developed in recent years for microbiome investigation-including the advent of long-read sequencing technologies-this work aimed to identify current trends and practices undertaken in female genital tract microbiome investigations.

RESULTS: Areas like sample collection and transport, DNA extraction, 16S amplification vs. metagenomics, NGS library preparation, and bioinformatic analysis demonstrated a detrimental lack of uniformity. The lack of uniformity present is a significant limitation characterised by gap discrepancies in generation and interpretation of results. Minimal consistency was observed in primer design, DNA extraction techniques, sample transport, and bioinformatic analyses.

CONCLUSION: With third-generation sequencing technology highlighted as a promising tool in microbiota-based research via full-length 16S rRNA sequencing, there is a desperate need for future studies to investigate and optimise methodological approaches of the genital tract microbiome to ensure better uniformity of methods and results interpretation to improve clinical impact.}, } @article {pmid39432998, year = {2024}, author = {Ma, ZS and Li, L}, title = {Identifications of the potential in-silico biomarkers in lung cancer tissue microbiomes.}, journal = {Computers in biology and medicine}, volume = {183}, number = {}, pages = {109231}, doi = {10.1016/j.compbiomed.2024.109231}, pmid = {39432998}, issn = {1879-0534}, mesh = {Humans ; *Lung Neoplasms/microbiology/metabolism ; *Microbiota ; *Biomarkers, Tumor/genetics/metabolism ; Metagenome ; Computer Simulation ; }, abstract = {It is postulated that the tumor tissue microbiome is one of the enabling characteristics that can either promote or suppress the ability of tumors to acquire certain hallmarks of cancer. This underscores its critical importance in carcinogenesis, cancer progression, and therapy responses. However, characterizing the tumor microbiomes is extremely challenging because of their low biomass and severe difficulties in controlling laboratory-borne contaminants, which is further aggravated by lack of comprehensively effective computational approaches to identify unique or enriched microbial species associated with cancers. Here we take advantage of a recent computational framework by Ma (2024), termed metagenome comparison (MC) framework (MCF), which can detect treatment-specific, unique or enriched OMUs (operational metagenomic unit), or US/ES (unique/enriched species) when adapted for this study. We apply the MCF to reanalyze four lung cancer tissue microbiome datasets, which include samples from Lung Adenocarcinoma (LUAD), Lung Squamous Cell Carcinoma (LUSC), and their adjacent normal tissue (NT) controls. Our analysis is structured around three distinct schemes: Scheme I-separately detecting the US/ES for each of the four lung cancer microbiome datasets; Scheme II-consolidation of the four datasets followed by detection of US/ES in the combined datasets; Scheme III-construction of the union and intersection sets of US/ES derived from the results of the preceding two schemes. The generated lists of US/ES, including enriched microbial phyla, likely hold significant biomedical value for developing diagnostic and prognostic biomarkers for lung cancer risk assessment, improving the efficacy of immunotherapy, and designing novel microbiome-based therapies in lung cancer research.}, } @article {pmid39432940, year = {2024}, author = {Aseem, A and Sagar, P and Reddy, NS and Veleri, S}, title = {The antimicrobial resistance profile in poultry of Central and Southern India is evolving with distinct features.}, journal = {Comparative immunology, microbiology and infectious diseases}, volume = {114}, number = {}, pages = {102255}, doi = {10.1016/j.cimid.2024.102255}, pmid = {39432940}, issn = {1878-1667}, mesh = {Animals ; India/epidemiology ; *Chickens/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Feces/microbiology ; *Drug Resistance, Bacterial/genetics ; *Poultry/microbiology ; Poultry Diseases/microbiology/epidemiology ; Whole Genome Sequencing ; Microbial Sensitivity Tests ; Bacteria/drug effects/genetics/classification/isolation & purification ; Metagenomics ; }, abstract = {Antimicrobial resistance (AMR) is fast emerging and is depleting antibiotics repertoire. Poultry is a major source for AMR because focus to enhance its production by modern practices widely uses antibiotics. India and China are major producers of meat and have hotspots of AMR. The Central and Southern India were predicted as emerging hotspots for AMR in poultry but no data available to substantiate it. To this end, we collected chicken feces from poultry farms in these regions and isolated genomic DNA. Further, shotgun whole genome sequencing was performed for metagenomics analysis. For the first time, we report the AMR gene profiles in poultry from Kerala and Telangana. The samples exhibited a higher prevalence of gram-negative and anaerobic species. The high priority pathogens in India were detected, like E.coli, Clostridium perfringens, Klebsiella pneumonia Staphylococcus aureus, Enterococcous faecalis, Pseudomonas aeruginosa, Bacteriodes fragiles. Conspicuously, the Southern India had the highest abundance of AMR genes than the Central India. E.coli was significantly more prevalent in the southernmost zone of India than in other sites. Our data had many common AMR profile features of the European Union (EU) poultry farms but lacked mcr-1, which was a lately emerged AMR gene in E.coli. Our data revealed the extent of AMR gene evolved in the Central and Southern India. It is comparable to the EU data but severity is lesser than in the EU.}, } @article {pmid39432783, year = {2024}, author = {Oguro-Igashira, E and Murakami, M and Mori, R and Kuwahara, R and Kihara, T and Kohara, M and Fujiwara, M and Motooka, D and Okuzaki, D and Arase, M and Toyota, H and Peng, S and Ogino, T and Kitabatake, Y and Morii, E and Hirota, S and Ikeuchi, H and Umemoto, E and Kumanogoh, A and Takeda, K}, title = {The pyruvate-GPR31 axis promotes transepithelial dendrite formation in human intestinal dendritic cells.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {44}, pages = {e2318767121}, pmid = {39432783}, issn = {1091-6490}, support = {JP21H050430//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP21K07895//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP21gm1010004//Japan Agency for Medical Research and Development (AMED)/ ; JPMJSP213//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; J178501002//BD Biosciences (Becton Dickenson Biosciences)/ ; }, mesh = {Humans ; *Receptors, G-Protein-Coupled/metabolism ; *Dendritic Cells/metabolism ; *Pyruvic Acid/metabolism ; Intestinal Mucosa/metabolism/cytology ; Dendrites/metabolism ; Gastrointestinal Microbiome ; Signal Transduction ; Induced Pluripotent Stem Cells/metabolism/cytology ; Organoids/metabolism ; Intestines/cytology ; }, abstract = {The intestinal lumen is rich in gut microbial metabolites that serve as signaling molecules for gut immune cells. G-protein-coupled receptors (GPCRs) sense metabolites and can act as key mediators that translate gut luminal signals into host immune responses. However, the impacts of gut microbe-GPCR interactions on human physiology have not been fully elucidated. Here, we show that GPR31, which is activated by the gut bacterial metabolite pyruvate, is specifically expressed on type 1 conventional dendritic cells (cDC1s) in the lamina propria of the human intestine. Using human induced pluripotent stem cell-derived cDC1s and a monolayer human gut organoid coculture system, we show that cDC1s extend their dendrites toward pyruvate on the luminal side, forming transepithelial dendrites (TED). Accordingly, GPR31 activation via pyruvate enhances the fundamental function of cDC1 by allowing efficient uptake of gut luminal antigens, such as dietary compounds and bacterial particles through TED formation. Our results highlight the role of GPCRs in tuning the human gut immune system according to local metabolic cues.}, } @article {pmid39432658, year = {2024}, author = {Liu, B and Dai, W and Wei, J and Sun, S and Chen, W and Deng, Y}, title = {Knowledge framework and emerging trends of invasive pulmonary fungal infection: A bibliometric analysis (2003-2023).}, journal = {Medicine}, volume = {103}, number = {42}, pages = {e40068}, pmid = {39432658}, issn = {1536-5964}, mesh = {Humans ; *Bibliometrics ; Invasive Fungal Infections/epidemiology ; Lung Diseases, Fungal/epidemiology/microbiology ; COVID-19/epidemiology ; }, abstract = {The rising number of immunocompromised people has increased concerns about fungal infections as a severe public health issue. Invasive pulmonary fungal infections (IPFIs) are prevalent and often fatal, particularly for those with weakened immune systems. Understanding IPFIs is crucial. The work aims to offer a concise overview of the field's characteristics, main research areas, development paths, and trends. This study searched the Web of Science Core Collection on June 5, 2024, collecting relevant academic works from 2003 to 2023. Analysis was conducted using CiteSpace, VOSviewer, Bibliometrix Package in R, Microsoft Excel 2019, and Scimago Graphica. The study indicated that the USA, the University of Manchester, and Denning DW led in productivity and impact, while the Journal of Fungi topped the list in terms of publication volume and citations. High-frequency terms include "fungal infection," "invasive," "diagnosis," and "epidemiology." Keyword and trend analysis identified "influenza," "COVID-19," "invasive pulmonary aspergillosis," and "metagenomic next-generation sequencing" as emerging research areas. Over the last 2 decades, research on IPFI has surged, with topics becoming more profound. These insights offer key guidance on current trends, gaps, and the trajectory of IPFI studies.}, } @article {pmid39432094, year = {2024}, author = {Shafana Farveen, M and Narayanan, R}, title = {Omic-driven strategies to unveil microbiome potential for biodegradation of plastics: a review.}, journal = {Archives of microbiology}, volume = {206}, number = {11}, pages = {441}, pmid = {39432094}, issn = {1432-072X}, mesh = {*Biodegradation, Environmental ; *Plastics/metabolism ; *Microbiota ; Bacteria/metabolism/genetics/classification ; Proteomics ; Genomics ; Microbial Consortia ; }, abstract = {Plastic waste accumulation has lately been identified as the leading and pervasive environmental concern, harming all living beings, natural habitats, and the global market. Given this issue, developing ecologically friendly solutions, such as biodegradation instead of standard disposal, is critical. To effectively address and develop better strategies, it is critical to understand the inter-relationship between microorganisms and plastic, the role of genes and enzymes involved in this process. However, the complex nature of microbial communities and the diverse mechanisms involved in plastic biodegradation have hindered the development of efficient plastic waste degradation strategies. Omics-driven approaches, encompassing genomics, transcriptomics and proteomics have revolutionized our understanding of microbial ecology and biotechnology. Therefore, this review explores the application of omics technologies in plastic degradation studies and discusses the key findings, challenges, and future prospects of omics-based approaches in identifying novel plastic-degrading microorganisms, enzymes, and metabolic pathways. The integration of omics technologies with advanced molecular technologies such as the recombinant DNA technology and synthetic biology would guide in the optimization of microbial consortia and engineering the microbial systems for enhanced plastic biodegradation under various environmental conditions.}, } @article {pmid39432083, year = {2024}, author = {Xu, X and Liu, X and Liu, L and Chen, J and Guan, J and Luo, D}, title = {Metagenomic and transcriptomic profiling of the hypoglycemic and hypotriglyceridemic actions of Tremella fuciformis-derived polysaccharides in high-fat-diet- and streptozotocin-treated mice.}, journal = {Food & function}, volume = {15}, number = {22}, pages = {11096-11114}, doi = {10.1039/d4fo01870b}, pmid = {39432083}, issn = {2042-650X}, mesh = {Animals ; Mice ; *Diet, High-Fat/adverse effects ; *Hypoglycemic Agents/pharmacology ; Male ; *Basidiomycota/chemistry ; *Gastrointestinal Microbiome/drug effects ; *Diabetes Mellitus, Experimental/drug therapy ; *Polysaccharides/pharmacology ; Gene Expression Profiling ; Streptozocin ; Blood Glucose/metabolism ; Metagenomics ; Transcriptome ; }, abstract = {Mushroom polysaccharides have great anti-diabetes potential. The fruiting body of Tremella fuciformis is rich in polysaccharides. However, few studies have been performed to date on T. fuciformis-derived polysaccharides (TPs) in terms of anti-diabetes potential. Our previous studies showed that novel TPs with medium molecular weights exhibited the highest anti-skin aging activities among the tested samples in D-galactose-treated mice. In the present study, the effects of these novel TPs, named TP, on high-fat-diet- and streptozotocin-treated mice were assessed, and their potential biological mechanisms were explored by metagenomic and transcriptomic analyses. Oral administration of TP markedly reduced blood glucose and TG levels, alleviated emaciation, improved anti-oxidant capacity, and protected the functions of β-cells at a dose of 100 mg kg[-1] in diabetic mice. Meanwhile, the taxonomic compositions and functional properties of fecal microbiota were altered considerably by TP, as evidenced by partial restoration of the imbalanced gut microbiota and the higher abundances of Bacteroides, Phocaeicola, Bifidobacterium, and Alistipes compared to the model mice, corresponding to the upregulation of four enriched KEGG pathways of microbial communities such as the digestive system, cardiovascular disease, parasitic infectious disease, and cell growth and death. Further transcriptomic analysis of liver tissues identified 35 enriched KEGG pathways associated with metabolism and cellular signaling processes in response to TP. These results demonstrated the biological mechanisms underlying the hypoglycemic and hypotriglyceridemic activities of TP. The findings expanded our understanding of the anti-diabetic mechanisms for mushroom polysaccharides and provided new clues for future studies.}, } @article {pmid39431871, year = {2024}, author = {Tuladhar, ET and Chalise, BS and Khadka, B and Tamang, M and Neupane, J and Poudel, S and Droit, L and Mihindukulasuriya, KA and Elong Ngono, A and Basaula, YN and Shresta, S and Wang, D and Manandhar, KD}, title = {Human immunodeficiency virus-1 genome from patient with fever, Nepal.}, journal = {Microbiology resource announcements}, volume = {13}, number = {11}, pages = {e0076824}, pmid = {39431871}, issn = {2576-098X}, support = {U01 AI151810/AI/NIAID NIH HHS/United States ; 1U01AI151810//HHS | National Institutes of Health (NIH)/ ; }, abstract = {A patient with fever presented to the referral infectious disease hospital in Kathmandu, Nepal. Metagenomic sequencing of the patient's serum recovered a near-complete genome of human immunodeficiency virus-1 (HIV-1), distinct from previous HIV-1 genomes from Nepal in GenBank. It shared 92.48% nucleotide identity with an HIV-1 subtype C isolate from India.}, } @article {pmid39431789, year = {2024}, author = {Bickerstaff, JRM and Walsh, T and Court, L and Pandey, G and Ireland, K and Cousins, D and Caron, V and Wallenius, T and Slipinski, A and Rane, R and Escalona, HE}, title = {Chromosome Structural Rearrangements in Invasive Haplodiploid Ambrosia Beetles Revealed by the Genomes of Euwallacea fornicatus (Eichhoff) and Euwallacea similis (Ferrari) (Coleoptera, Curculionidae, Scolytinae).}, journal = {Genome biology and evolution}, volume = {16}, number = {11}, pages = {}, pmid = {39431789}, issn = {1759-6653}, support = {//ResearchPlus CSIRO Early Research Career Fellowship/ ; //Zimmerman Trust/ ; //ANIC-NRCA-CSIRO/ ; }, mesh = {Animals ; *Weevils/microbiology/genetics ; *Genome, Insect ; *Introduced Species ; Haploidy ; Chromosomes, Insect ; Coleoptera/microbiology/genetics ; }, abstract = {Bark and ambrosia beetles are among the most ecologically and economically damaging introduced plant pests worldwide. Life history traits including polyphagy, haplodiploidy, inbreeding polygyny, and symbiosis with fungi contribute to their dispersal and impact. Species vary in their interactions with host trees, with many attacking stressed or recently dead trees, such as the globally distributed Euwallacea similis (Ferrari). Other species, like the Polyphagous Shot Hole Borer Euwallacea fornicatus (Eichhoff), can attack over 680 host plants and is causing considerable economic damage in several countries. Despite their notoriety, publicly accessible genomic resources for Euwallacea Hopkins species are scarce, hampering our understanding of their invasive capabilities as well as modern control measures, surveillance, and management. Using a combination of long and short read sequencing platforms, we assembled and annotated high quality (BUSCO > 98% complete) pseudo-chromosome-level genomes for these species. Comparative macrosynteny analysis identified an increased number of pseudo-chromosome scaffolds in the haplodiploid inbreeding species of Euwallacea compared to diploid outbred species, due to fission events. This suggests that life history traits can impact chromosome structure. Further, the genome of E. fornicatus had a higher relative proportion of repetitive elements, up to 17% more, than E. similis. Metagenomic assembly pipelines identified microbiota associated with both species including Fusarium fungal symbionts and a novel Wolbachia strain. These novel genomes of haplodiploid inbreeding species will contribute to the understanding of how life history traits are related to their evolution and to the management of these invasive pests.}, } @article {pmid39431768, year = {2024}, author = {Tutagata, J and Pocquet, N and Trouche, B and Reveillaud, J}, title = {Dissection of Mosquito Ovaries, Midgut, and Salivary Glands for Microbiome Analyses at the Organ Level.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {212}, pages = {}, doi = {10.3791/67128}, pmid = {39431768}, issn = {1940-087X}, mesh = {Animals ; Female ; *Salivary Glands/microbiology ; *Microbiota/physiology ; *Ovary/microbiology ; Dissection/methods ; Culicidae/microbiology ; }, abstract = {The global burden of mosquito-transmitted diseases, including malaria, dengue, West Nile, Zika, Usutu, and yellow fever, continues to increase, posing a significant public health threat. With the rise of insecticide resistance and the absence of effective vaccines, new strategies are emerging that focus on the mosquito's microbiota. Nevertheless, the majority of symbionts remain resistant to cultivation. Characterizing the diversity and function of bacterial genomes in mosquito specimens, therefore, relies on metagenomics and subsequent assembly and binning strategies. The obtention and analysis of Metagenome-Assembled Genomes (MAGs) from separated organs can notably provide key information about the specific role of mosquito-associated microbes in the ovaries (the reproductive organs), the midgut (key for food digestion and immunity), or the salivary glands (essential for the transmission of vector-borne diseases as pathogens must colonize them to enter the saliva and reach the bloodstream during a blood meal). These newly reconstructed genomes can then pave the way for the development of novel vector biocontrol strategies. To this aim, it is required to isolate mosquito organs while avoiding cross-contamination between them or with microorganisms present in other mosquito organs. Here, we describe an optimized and contamination-free dissection protocol for studying mosquito microbiome at the organ level.}, } @article {pmid39431465, year = {2024}, author = {Hagan, J}, title = {Mapping the spread of antibiotic resistance genes in the coastal microbiome.}, journal = {BioTechniques}, volume = {76}, number = {9}, pages = {411-414}, doi = {10.1080/07366205.2024.2416379}, pmid = {39431465}, issn = {1940-9818}, mesh = {*Microbiota/genetics/drug effects ; *Metagenomics/methods ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Bacteria/genetics/drug effects ; Seawater/microbiology ; Genes, Bacterial/genetics ; Metagenome/genetics ; }, abstract = {StandfirstCoastal environments are becoming increasingly exposed to antibiotics through anthropogenic inputs. But how could emerging metagenomic techniques be used to map the spread of antibiotic resistance genes in the coastal microbiome?[Formula: see text].}, } @article {pmid39431456, year = {2025}, author = {Batty, CA and Pearson, VK and Olsson-Francis, K and Morgan, G}, title = {Volatile organic compounds (VOCs) in terrestrial extreme environments: implications for life detection beyond Earth.}, journal = {Natural product reports}, volume = {42}, number = {1}, pages = {93-112}, doi = {10.1039/d4np00037d}, pmid = {39431456}, issn = {1460-4752}, mesh = {*Volatile Organic Compounds/analysis/metabolism/chemistry ; *Extreme Environments ; Metabolomics/methods ; Earth, Planet ; Exobiology/methods ; Metagenomics/methods ; }, abstract = {Covering: 1961 to 2024Discovering and identifying unique natural products/biosignatures (signatures that can be used as evidence for past or present life) that are abundant, and complex enough that they indicate robust evidence of life is a multifaceted process. One distinct category of biosignatures being explored is organic compounds. A subdivision of these compounds not yet readily investigated are volatile organic compound (VOCs). When assessing these VOCs as a group (volatilome) a fingerprint of all VOCs within an environment allows the complex patterns in metabolic data to be unravelled. As a technique already successfully applied to many biological and ecological fields, this paper explores how analysis of volatilomes in terrestrial extreme environments could be used to enhance processes (such as metabolomics and metagenomics) already utilised in life detection beyond Earth. By overcoming some of the complexities of collecting VOCs in remote field sites, a variety of lab based analytical equipment and techniques can then be utilised. Researching volatilomics in astrobiology requires time to characterise the patterns of VOCs. They must then be differentiated from abiotic (non-living) signals within extreme environments similar to those found on other planetary bodies (analogue sites) or in lab-based simulated environments or microcosms. Such an effort is critical for understanding data returned from past or upcoming missions, but it requires a step change in approach which explores the volatilome as a vital additional tool to current 'Omics techniques.}, } @article {pmid39431411, year = {2024}, author = {Sobala, ŁF}, title = {LukProt: A Database of Eukaryotic Predicted Proteins Designed for Investigations of Animal Origins.}, journal = {Genome biology and evolution}, volume = {16}, number = {11}, pages = {}, pmid = {39431411}, issn = {1759-6653}, support = {2020/36/C/NZ8/00081//National Science Centre of Poland/ ; }, mesh = {Animals ; *Eukaryota/genetics ; *Databases, Protein ; Biological Evolution ; Evolution, Molecular ; Proteins/genetics ; }, abstract = {The origins and early evolution of animals are subjects with many outstanding questions. One problem faced by researchers trying to answer them is the absence of a comprehensive database with sequences from nonbilaterians. Publicly available data are plentiful but scattered and often not associated with proper metadata. A new database presented in this paper, LukProt, is an attempt at solving this issue. The database contains protein sequences obtained mostly from genomic, transcriptomic, and metagenomic studies and is an extension of EukProt (Richter DJ, Berney C, Strassert JFH, Poh Y-P, Herman EK, Muñoz-Gómez SA, Wideman JG, Burki F, de Vargas C. EukProt: a database of genome-scale predicted proteins across the diversity of eukaryotes. Peer Community J. 2022:2:e56. https://doi.org/10.24072/pcjournal.173). LukProt adopts the EukProt naming conventions and includes data from 216 additional animals. The database is associated with a taxonomic grouping (taxogroup) scheme suitable for studying early animal evolution. Minor updates to the database will contain species additions or metadata corrections, whereas major updates will synchronize LukProt to each new version of EukProt, and releases are permanently stored on Zenodo (https://doi.org/10.5281/zenodo.7089120). A BLAST server to search the database is available at: https://lukprot.hirszfeld.pl/. Users are invited to participate in maintaining and correcting LukProt. As it can be searched without downloading locally, the database aims to be a convenient resource not only for evolutionary biologists, but for the broader scientific community as well.}, } @article {pmid39431214, year = {2024}, author = {Zhu, X and Chen, J and Wu, S and Zeng, J and Sun, Y and Wu, X}, title = {Empyema Caused by Mixed Infection with Streptococcus intermedius and Streptococcus constellatus in a Patient with Previous Surgery for Oral Carcinoma: A Case Report.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {4447-4454}, pmid = {39431214}, issn = {1178-6973}, abstract = {BACKGROUND: The incidence of community-acquired empyema caused by the Streptococcus anginosus group (SAG) has been on the rise in the 2020s. To the best of our knowledge, while empyema caused individually by either strain has been reported, there are no reports on empyema caused by concurrent infection with these two strains. Here, we report for the first time empyema caused by concurrent infection with Streptococcus intermedius and Streptococcus constellatus (both SAG species) in a postoperative patient who had been treated for floor of the mouth carcinoma.

CASE PRESENTATION: A 61-year-old male patient who had undergone surgical treatment for floor of the mouth carcinoma 2 year earlier suddenly presented with left-sided chest pain. Chest computed tomography (CT) revealed encapsulated pleural effusion on the left side, which was diagnosed as empyema. Metagenomic next-generation sequencing(mNGS) of the pleural fluid sample indicated mixed infection caused by Streptococcus intermedius and Streptococcus constellatus. The patient's condition improved about 5 weeks after treatment with thoracic fluid drainage and cephalosporin antibiotics.

CONCLUSION: This case highlights the possibility of concurrent infection with two SAG strains in patients with empyema. Currently, it is unclear whether there is a definitive relationship between a surgical history of carcinoma of the floor of the mouth and empyema caused by infection with SAG strains. This case could, perhaps, serve as a reference for future related research on the topic.}, } @article {pmid39431056, year = {2024}, author = {Han, L and Hu, C and Du, Z and Yu, H and Du, Y and Li, L and Li, F and Wang, Y and Gao, X and Sun, X and Zhang, Z and Qin, Y}, title = {Association of glycerolipid metabolism with gut microbiota disturbances in a hamster model of high-fat diet-induced hyperlipidemia.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1439744}, pmid = {39431056}, issn = {2235-2988}, mesh = {Animals ; *Hyperlipidemias/metabolism/microbiology ; *Gastrointestinal Microbiome ; *Diet, High-Fat/adverse effects ; Cricetinae ; *Disease Models, Animal ; *Liver/metabolism ; Male ; *Lipid Metabolism ; *Feces/microbiology ; Metabolomics ; Bacteria/classification/isolation & purification/metabolism/genetics ; Metagenomics ; Lipids/blood ; }, abstract = {BACKGROUND: High-fat diet (HFD)-induced hyperlipidemia, which is associated with gut microbiota disturbances, remains a major public health challenge. Glycerolipid metabolism is responsible for lipid synthesis and is thus involved in the development of hyperlipidemia. However, possible association between the HFD-modulated gut microbiome and the glycerolipid metabolism pathway remains unclear.

METHODS: Hamsters were fed a HFD for 4 weeks to establish a hyperlipidemia model. Fecal, plasma and liver samples collected from hamsters fed a HFD or a normal chow diet (NCD) were used for integrative metagenomic and untargeted metabolomic analyses to explore changes in the composition and functions of the gut microbiota, and relevant metabolites. Spearman rank correlation analysis was used to explore correlations between gut microbes and circulating glycerolipid metabolites, gut microbes and lipids, and circulating glycerolipid metabolites and lipids.

RESULTS: The gut microbial composition of HFD hamsters showed significant alterations at the phylum, genus, and species levels that were skewed toward metabolic disorders compared with that of NCD hamsters. Functional characterization by KEGG analysis identified enrichment of the glycerolipid metabolism pathway in the gut microbiome of HFD hamsters. Plasma and liver metabolomics further indicated the upregulation and enrichment of glycerolipid metabolites in HFD hamsters. The Faecalibaculum, Allobaculum, and Eubacterium genera were positively correlated with plasma glycerolipid metabolites and lipid indices.

CONCLUSION: The findings of this study suggest an association between glycerolipid metabolism and the HFD-modulated gut microbiome that is involved in the development of hyperlipidemia.}, } @article {pmid39430957, year = {2024}, author = {Yao, QH and Xia, XJ and Zhi, HL and Liu, ZH}, title = {Extensive erythematous plaques of fungal origin in an overseas student: Cutaneous manifestation of coccidioidomycosis.}, journal = {Medical mycology case reports}, volume = {46}, number = {}, pages = {100674}, pmid = {39430957}, issn = {2211-7539}, abstract = {We present a case of Coccidioides posadasii infection which was contracted during study abroad. This coccidioidomycosis showed atypical manifestations and was diagnosed by a combination of tissue biopsy, metagenomic next-generation sequencing, internal transcribed spacer sequencing and culture. Initial treatment with fluconazole was not effective. Antifungal therapy was switched to voriconazole based on drug sensitivity results with good result. This case demonstrates the clinical significance of combining multiple diagnostic methods.}, } @article {pmid39430728, year = {2025}, author = {Zhang, Y and Xue, B and Mao, Y and Chen, X and Yan, W and Wang, Y and Wang, Y and Liu, L and Yu, J and Zhang, X and Chao, S and Topp, E and Zheng, W and Zhang, T}, title = {High-throughput single-cell sequencing of activated sludge microbiome.}, journal = {Environmental science and ecotechnology}, volume = {23}, number = {}, pages = {100493}, pmid = {39430728}, issn = {2666-4984}, abstract = {Wastewater treatment plants (WWTPs) represent one of biotechnology's largest and most critical applications, playing a pivotal role in environmental protection and public health. In WWTPs, activated sludge (AS) plays a major role in removing contaminants and pathogens from wastewater. While metagenomics has advanced our understanding of microbial communities, it still faces challenges in revealing the genomic heterogeneity of cells, uncovering the microbial dark matter, and establishing precise links between genetic elements and their host cells as a bulk method. These issues could be largely resolved by single-cell sequencing, which can offer unprecedented resolution to show the unique genetic information. Here we show the high-throughput single-cell sequencing to the AS microbiome. The single-amplified genomes (SAGs) of 15,110 individual cells were clustered into 2,454 SAG bins. We find that 27.5% of the genomes in the AS microbial community represent potential novel species, highlighting the presence of microbial dark matter. Furthermore, we identified 1,137 antibiotic resistance genes (ARGs), 10,450 plasmid fragments, and 1,343 phage contigs, with shared plasmid and phage groups broadly distributed among hosts, indicating a high frequency of horizontal gene transfer (HGT) within the AS microbiome. Complementary analysis using 1,529 metagenome-assembled genomes from the AS samples allowed for the taxonomic classification of 98 SAG bins, which were previously unclassified. Our study establishes the feasibility of single-cell sequencing in characterizing the AS microbiome, providing novel insights into its ecological dynamics, and deepening our understanding of HGT processes, particularly those involving ARGs. Additionally, this valuable tool could monitor the distribution, spread, and pathogenic hosts of ARGs both within AS environments and between AS and other environments, which will ultimately contribute to developing a health risk evaluation system for diverse environments within a One Health framework.}, } @article {pmid39430384, year = {2024}, author = {Takahashi, Y and Niwa, H and Ebisuda, Y and Mukai, K and Yoshida, T and Raidal, S and Padalino, B and Ohmura, H}, title = {Increased freedom of head movement mitigates stress and bacterial load in the airways of horses during transport.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1477653}, pmid = {39430384}, issn = {2297-1769}, abstract = {INTRODUCTION: Protection of horse welfare during transport is crucial. The aim of this study was to determine the effect of head and neck restraint on behavior and airway bacteria.

METHODS: In a randomized crossover study, six healthy Thoroughbreds were transported by road for 22 h in an individual bay with tight head restraint (50 cm short-rope) or loose head restraint (95 cm long-rope). Behavioral parameters relating to head position, eating, and stress were monitored during transportation. Tracheal wash samples were obtained 6 days before and immediately after transport for bacterial culture and metagenomic analysis.

RESULTS AND DISCUSSION: Compared to before transport, bacterial load (CFU/mL) after transport was significantly increased in the short-rope group (p = 0.04), whereas no changes were observed in the long-rope group. Transport significantly reduced Simpson index at phylum, class, order, and family levels in both groups (p < 0.001) of tracheal microbiota. In both groups, this reduction was associated with increases in the dominant members of relative abundance at phylum (Firmicutes: +24% in long-rope and +14% in short-rope), class (Bacilli: +20% in long-rope and +22% in short-rope) and family (Streptococcaceae: +22% in long-rope and +23% in short-rope) levels. Licking behavior during transportation with short-rope restraint was more frequent than in horses with long-rope restraint. These results suggest loose head restraint during transportation is likely to ameliorate stress and mitigate the associated increased bacterial load in the lower airways associated with transport. Further, head position during transportation is likely a more important determinant of airway hygiene and distress than duration of travel.}, } @article {pmid39429886, year = {2024}, author = {Peng, X and Feng, K and Yang, X and He, Q and Zhao, B and Li, T and Wang, S and Deng, Y}, title = {iNAP 2.0: Harnessing metabolic complementarity in microbial network analysis.}, journal = {iMeta}, volume = {3}, number = {5}, pages = {e235}, pmid = {39429886}, issn = {2770-596X}, abstract = {With the widespread adoption of metagenomic sequencing, new perspectives have emerged for studying microbial ecological networks, yielding metabolic evidence of interspecies interactions that traditional co-occurrence networks cannot infer. This protocol introduces the integrated Network Analysis Pipeline 2.0 (iNAP 2.0), which features an innovative metabolic complementarity network for microbial studies from metagenomics sequencing data. iNAP 2.0 sets up a four-module process for metabolic interaction analysis, namely: (I) Prepare genome-scale metabolic models; (II) Infer pairwise interactions of genome-scale metabolic models; (III) Construct metabolic interaction networks; and (IV) Analyze metabolic interaction networks. Starting from metagenome-assembled or complete genomes, iNAP 2.0 offers a variety of methods to quantify the potential and trends of metabolic complementarity between models, including the PhyloMint pipeline based on phylogenetic distance-adjusted metabolic complementarity, the SMETANA (species metabolic interaction analysis) approach based on cross-feeding substrate exchange prediction, and metabolic distance calculation based on parsimonious flux balance analysis (pFBA). Notably, iNAP 2.0 integrates the random matrix theory (RMT) approach to find the suitable threshold for metabolic interaction network construction. Finally, the metabolic interaction networks can proceed to analysis using topological feature analysis such as hub node determination. In addition, a key feature of iNAP 2.0 is the identification of potentially transferable metabolites between species, presented as intermediate nodes that connect microbial nodes in the metabolic complementarity network. To illustrate these new features, we use a set of metagenome-assembled genomes as an example to comprehensively document the usage of the tools. iNAP 2.0 is available at https://inap.denglab.org.cn for all users to register and use for free.}, } @article {pmid39429879, year = {2024}, author = {Lu, YX and Yang, JB and Li, CY and Tian, YH and Chang, RR and Kong, DS and Yang, SL and Wang, YF and Zhang, YB and Zhu, XS and Pan, WH and Kong, SY}, title = {Efficient and easy-to-use capturing three-dimensional metagenome interactions with GutHi-C.}, journal = {iMeta}, volume = {3}, number = {5}, pages = {e227}, pmid = {39429879}, issn = {2770-596X}, abstract = {Hi-C can obtain three-dimensional chromatin structure information and is widely used for genome assembly. We constructed the GutHi-C technology. As shown in the graphical abstract, it is a highly efficient and quick-to-operate method and can be widely used for human, livestock, and poultry gut microorganisms. It provides a reference for the Hi-C methodology of the microbial metagenome. DPBS, Dulbecco's phosphate-buffered saline; Hi-C, high-through chromatin conformation capture; LB, Luria-Bertani; NGS, next-generation sequencing; PCR, polymerase chain reaction; QC, quality control.}, } @article {pmid39429745, year = {2024}, author = {Fazal, BZ and Yahya, NA and Ling, CMWV and Wei, YC and Leow, TC and Halim, MA and Balakrishnan, KN and Budiman, C and Amin, Z}, title = {16S rRNA metagenomics data on the bacterial communities in Poring Hot Spring, Sabah, Malaysia.}, journal = {Data in brief}, volume = {57}, number = {}, pages = {110935}, pmid = {39429745}, issn = {2352-3409}, abstract = {Hot springs are known to harbor potentially unique microorganisms due to the extreme temperatures in which they thrive and their biotechnologically important enzymes that are active at high temperature, which are beneficial for various industries. Sabah, Malaysia, houses several hot springs, yet knowledge of their microbiological diversity remains limited. Here, the raw sequence data of bacterial communities in a hot spring through metagenomic analysis are revealed. The data were obtained by collecting water and sediment samples from Poring Hot Spring (PHS) in Ranau, Sabah, and their bacterial diversity was analyzed using 16S rRNA amplicon sequencing targeting the V3-V4 regions. The analysis identified bacterial diversity in both water and sediment samples, with 35 phyla, 76 families, and 90 genera in water, and 38 phyla, 114 families, and 128 genera in sediment. Proteobacteria dominated the water samples (87 %), while Cyanobacteria were most abundant in sediment samples (51 %). The most abundant genera in water were Tepidimonas, Hydrogenophilus and Methylothermus, whereas Geitlerinema, Calothrix and Nitrospira dominated the sediment. Sediment samples exhibited higher bacterial richness and diversity compared to water samples, as indicated by α-diversity analysis. Sequences and sample data are deposited in the NCBI Sequence Read Archive under Bioproject ID PRJNA982554 (Accession number: SRX20671661 to SRX20671666) at https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA982554&o=acc_s%3Aa).}, } @article {pmid39429648, year = {2024}, author = {Li, Z and Xu, B and Liu, J}, title = {Acute fibrinous and organizing pneumonia associated with Candida: A case report.}, journal = {Respiratory medicine case reports}, volume = {52}, number = {}, pages = {102120}, pmid = {39429648}, issn = {2213-0071}, abstract = {BACKGROUND: Acute fibrinous and organizing pneumonia (AFOP) is a rare form of pneumonia, is characterized by the deposition of fibrin in alveoli, the formation of fibrin spheres, and deposition of fibrin in alveolar junctions and bronchioles adjacent to or adjacent to the alveoli, forming institutional loose connective tissue.The clinical characteristics of AFOP lack specificity. We report a special case of AFOP that may be associated with Candida, so as to improve our understanding and diagnosis of AFOP.

RESULT: In this patient who was early misdiagnosed with community-acquired pneumonia (CAP), the empirical anti-infective treatment was ineffective, and various infectious and non-infectious factors were excluded. Flexible bronchoscopy was subsequently performed, and metagenomics Next Generation Sequencing (mNGS) of Bronchoalveolar lavage fluid (BALF) showed Candida albicans, and further ultrasound interventional percutaneous and lung puncture biopsy was performed to diagnose AFOP according to pathology, while mNGS of lung pathological tissue also suggested Candid. The patient recovered well on corticosteroids.

CONCLUSION: The clinical manifestation, laboratory examination and imaging examination of AFOP has no specificity, lung biopsy and pathological examination should be carried out to make a clear diagnosis by comprehensively considering the clinical manifestations, auxiliary examination, pathology and other aspects of the patients. After definite diagnosis, it is still necessary to rule out various diseases and environmental exposure and further classify them as idiopathic or secondary, so as to choose monotherapy or combination therapy.}, } @article {pmid39428758, year = {2024}, author = {Minot, SS and Mayer-Blackwell, K and Fiore-Gartland, A and Johnson, A and Self, S and Bhatti, P and Yao, L and Liu, L and Sun, X and Jinfa, Y and Kublin, J}, title = {Species- and subspecies-level characterization of health-associated bacterial consortia that colonize the human gut during infancy.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2414975}, pmid = {39428758}, issn = {1949-0984}, support = {R01 AI127100/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Infant ; *Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Male ; Female ; Metagenomics ; Microbial Consortia ; Metagenome ; Infant, Newborn ; Cohort Studies ; Cystic Fibrosis/microbiology ; }, abstract = {BACKGROUND: The human gut microbiome develops rapidly during infancy, a key window of development coinciding with the maturation of the adaptive immune system. However, little is known about the microbiome growth dynamics over the first few months of life and whether there are any generalizable patterns across human populations. We performed metagenomic sequencing on stool samples (n = 94) from a cohort of infants (n = 15) at monthly intervals in the first 6 months of life, augmenting our dataset with seven published studies for a total of 4,441 metagenomes from 1,162 infants.

RESULTS: Strain-level de novo analysis was used to identify 592 of the most abundant organisms in the infant gut microbiome. Previously unrecognized consortia were identified which exhibited highly correlated abundances across samples and were composed of diverse species spanning multiple genera. Analysis of a published cohort of infants with cystic fibrosis identified one such novel consortium of diverse Enterobacterales which was positively correlated with weight gain. While all studies showed an increased community stability during the first year of life, microbial dynamics varied widely in the first few months of life, both by study and by individual.

CONCLUSION: By augmenting published metagenomic datasets with data from a newly established cohort, we were able to identify novel groups of organisms that are correlated with measures of robust human development. We hypothesize that the presence of these groups may impact human health in aggregate in ways that individual species may not in isolation.}, } @article {pmid39428055, year = {2024}, author = {Hazra, D and Chawla, K and S M, F and Sintchenko, V and Magazine, R and Martinez, E and Pandey, A}, title = {The impact of anti-tuberculosis treatment on respiratory tract microbiome in pulmonary tuberculosis.}, journal = {Microbes and infection}, volume = {}, number = {}, pages = {105432}, doi = {10.1016/j.micinf.2024.105432}, pmid = {39428055}, issn = {1769-714X}, abstract = {The growing evidence has underscored the significance of interactions between the host and microbiota in respiratory health, presenting a novel perspective on disease management. Yet, comprehension of the respiratory microbiome shifts before and after anti-tuberculosis treatment is limited. This study compares respiratory microbiome profiles in untreated tuberculosis (UTB) and completed TB treatment (CTB) cases with healthy controls, using 16S rRNA sequencing on sputum samples. Significant reduction in sputum microbial alpha diversity was observed in both TB groups when compared to healthy controls (P < 0.05). Beta diversity analysis showed distinct clustering (P < 0.05). Linear discriminant analysis revealed an abundance of potentially pathogenic bacterial genera like Haemophilus, Pseudomonas, and Mycobacterium in the UTB group, while Streptococcus, Rothia, and Neisseria dominated in CTB samples. Healthy sputum microbiomes were enriched with Prevotella, Fusobacterium, Porphyromonadaceae_unclassified,andPeptostreptococcus. Moreover, predicted bacterial functional pathways showed significant differences among the three groups, mainly related to nutrient metabolism. These findings indicated significant microbial dysbiosis in sputum samples recovered from patients with pulmonary TB with an elevated presence of potentially pathogenic bacteria, depletion of beneficial genera, and downregulation of several essential metabolic pathways. Further exploration of respiratory microbiome-based diagnostic biomarkers and their role in targeted treatment strategies in tuberculosis is warranted.}, } @article {pmid39427901, year = {2024}, author = {Shruti, VC and Kutralam-Muniasamy, G and Pérez-Guevara, F}, title = {Viruses in the era of microplastics and plastispheres: Analytical methods, advances and future directions.}, journal = {The Science of the total environment}, volume = {955}, number = {}, pages = {177010}, doi = {10.1016/j.scitotenv.2024.177010}, pmid = {39427901}, issn = {1879-1026}, mesh = {*Microplastics/analysis ; *Viruses ; *Environmental Monitoring/methods ; Water Pollutants, Chemical/analysis ; Plastics/analysis ; }, abstract = {Research on microplastics and plastispheres now incorporates the study of viruses to evaluate their effects on the environment and human health. Sharing these new discoveries with the scientific community is crucial to fostering further research and collaborations. However, the current research and methodologies used are fragmented. To address this issue, this paper reviews the literature and the use of methodology developments in each study, identifying four emerging research areas: (1) viral interactions with microplastics; (2) viral population, diversity, and function in plastispheres; (3) the effects of viruses and plastic particles in host-associated environments; and (4) the impacts of viruses within plastispheres. To that end, the article is structured to streamline navigation and help readers easily access existing approaches, recent advancements, key findings, challenges, and opportunities in these areas. Our synthesis reveals that research methods include biochemical assays, omics techniques, spectroscopic analysis, and molecular and bioinformatic tools. Various mechanisms enable viruses to attach to microplastics and plastispheres, leading to widespread distribution and contributing to toxic effects and gene transfer. While the growing evidence is intriguing, there is still much to uncover about their ecological interactions, functions, and impacts.}, } @article {pmid39427542, year = {2024}, author = {Kuai, Y and Yao, Z and Pang, T and Wang, L and Gong, X and Cheng, Y and Liu, X and Fu, Q and Wang, S}, title = {Chronic dietary deoxynivalenol exposure interferes the intestinal microbial community structure and antibiotic resistome in laying hens.}, journal = {Ecotoxicology and environmental safety}, volume = {286}, number = {}, pages = {117213}, doi = {10.1016/j.ecoenv.2024.117213}, pmid = {39427542}, issn = {1090-2414}, mesh = {Animals ; *Trichothecenes/toxicity ; *Chickens/microbiology ; *Gastrointestinal Microbiome/drug effects ; Female ; *Animal Feed/analysis ; Drug Resistance, Microbial/genetics ; Intestines/drug effects/microbiology ; Diet/veterinary ; Dietary Exposure ; }, abstract = {Antibiotic resistance genes (ARGs) are critical emerging pollutants that have attracted considerable attention. Deoxynivalenol (DON) is one of the most prevalent mycotoxins in cereal crops worldwide, arising severe health hazards to both humans and animals. Even if numerous researches argue in favor of a notorious influence of DON on the gut, the effects of dietary DON exposure on the ARG profile in poultry intestine remain obscure. In this study, two separate feeding experiments using Jing Tint 6 laying hens exposed to 4.5 or 9.0 mg/kg DON were performed to explore the impact of dietary DON exposure on the microbial community structure and the profiles of ARGs in the intestine via 16S rDNA sequencing and metagenomics sequencing, respectively. In addition, growth performance and intestinal barrier function were also determined to assess the feasibility of using DON-contaminated feedstuffs inappropriate for pigs' consumption in laying hens. Chronic ingestion of DON at 9.0 mg/kg did not alter zootechnical parameters. However, histomorphological impairments were observed in liver and jejunum. Additionally, metagenomic sequencing revealed that dietary DON exposure at 9.0 mg/kg level dramatically changed the gut microbial structure and shifted the ARG profile. The abundance of tetracycline ARG subtype in the layer cecum was decreased, whereas the abundance of vancomycin ARG subtype was increased upon DON exposure. Co-occurrence network analysis identified that Prevotella was the major ARG host in the intestine of laying hens. In summary, our findings demonstrated that DON-contaminated feedstuffs inappropriate for pigs' consumption should be prudently used in hen production, and shed new light on the interactions between mycotoxins and ARGs in the poultry intestine.}, } @article {pmid39427349, year = {2025}, author = {Zhou, L and Zhang, X and Zhang, X and Wu, P and Wang, A}, title = {Insights into the carbon and nitrogen metabolism pathways in mixed-autotrophy/heterotrophy anammox consortia in response to temperature reduction.}, journal = {Water research}, volume = {268}, number = {Pt A}, pages = {122642}, doi = {10.1016/j.watres.2024.122642}, pmid = {39427349}, issn = {1879-2448}, mesh = {*Nitrogen/metabolism ; *Carbon/metabolism ; *Temperature ; *Autotrophic Processes ; Denitrification ; Heterotrophic Processes ; Microbial Consortia ; Oxidation-Reduction ; }, abstract = {While the multi-coupled anammox system boasts a substantial research foundation, the specific characteristics of its synergistic metabolic response to decreased temperatures, particularly within the range of 13-15 °C, remained elusive. In this study, we delve into the intricate carbon and nitrogen metabolism pathways of mixed-autotrophy/heterotrophy anammox consortia under conditions of temperature reduction. Our macrogenomic analyses reveal a compelling phenomenon: the stimulation of functional genes responsible for complete denitrification, suggesting an enhancement of this process during temperature reduction. This adaptation likely contributes to maintaining system performance amidst environmental challenges. Further metabolic functional recombination analyses highlight a dramatic shift in microbial community composition, with denitrifying MAGs (metagenome-assembled genomes) experiencing a substantial increase in abundance (up to 200 times) compared to autotrophic MAGs. This proliferation underscores the strong stimulatory effect of temperature reduction on denitrifying species. Notably, autotrophic MAGs play a pivotal role in supporting the glycolytic processes of denitrifying MAGs, underscoring the intricate interdependencies within the consortia. Moreover, metabolic variations in amino acid composition among core MAGs emerge as a crucial adaptation mechanism. These differences facilitate the preservation of enzyme activity and enhance the consortia's resilience to low temperatures. Together, these findings offer a comprehensive understanding of the microbial synergistic metabolism within mixed-autotrophy/heterotrophy anammox consortia under temperature reduction, shedding light on their metabolic flexibility and resilience in dynamic environments.}, } @article {pmid39427267, year = {2025}, author = {Singh, AB and Paul, T and Shukla, SP and Kumar, S and Kumar, S and Kumar, G and Kumar, K}, title = {Gut microbiome as biomarker for triclosan toxicity in Labeo rohita: bioconcentration, immunotoxicity and metagenomic profiling.}, journal = {Ecotoxicology (London, England)}, volume = {34}, number = {1}, pages = {102-111}, pmid = {39427267}, issn = {1573-3017}, support = {DST/TMD-EWO-WTI/2K19/EWFH/2019/214//Department of Science and Technology, Ministry of Science and Technology, India/ ; }, mesh = {Animals ; *Triclosan/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Water Pollutants, Chemical/toxicity ; *Cyprinidae ; *Biomarkers ; Metagenomics ; }, abstract = {Triclosan (TCS) is a lipophilic, broad spectrum antimicrobial agent commonly used in personal care products with a projected continuous escalation in aquatic environments in the post COVID 19 era. There is rich documentation in the literature on the alteration of physiological responses in fish due to TCS exposure; however, studies on gut associated bacteria of fish are still scarce. This is the first attempt to determine changes in bacterial community structure due to exposure of TCS on Labeo rohita, a commercially essential freshwater species, using 16S V3-V4 region ribosomal RNA (rRNA) next-generation sequencing (NGS). Chronic exposure of TCS at environmentally realistic concentrations viz. 1/5th (T1: 0.129 mg/L) and 1/10th (T2: 0.065 mg/L) of LC50 for 28 days resulted in the dose dependent bioconcentration of TCS in the fish gut. Prolonged exposure to TCS leads to disruption of gut bacteria evidenced by down regulation of the host immune system. Additionally, high-throughput sequencing analysis showed alternation in the abundance and diversity of microbial communities in the gut, signifying Proteobacteria and Verrucomicrobia as dominant phyla. Significant changes were also observed in the relative abundance of Chloroflexi and Gammatimonadetes phyla in TCS exposed groups. The study revealed that gut microbiome can be used as a biomarker in assessing the degree of TCS toxicity in commercially important fish species.}, } @article {pmid39426981, year = {2024}, author = {Lu, C and Liu, D and Wu, Q and Zeng, J and Xiong, Y and Luo, T}, title = {EphA2 blockage ALW-II-41-27 alleviates atherosclerosis by remodeling gut microbiota to regulate bile acid metabolism.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {108}, pmid = {39426981}, issn = {2055-5008}, support = {2023NSFSC1631//Department of Science and Technology of Sichuan Province (Sichuan Provincial Department of Science and Technology)/ ; 2023YFS0116//Department of Science and Technology of Sichuan Province (Sichuan Provincial Department of Science and Technology)/ ; 2022YFS0604//Department of Science and Technology of Sichuan Province (Sichuan Provincial Department of Science and Technology)/ ; Q22066//Education Department of Sichuan Province/ ; }, mesh = {Animals ; *Atherosclerosis/metabolism/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Bile Acids and Salts/metabolism ; Mice ; *Receptor, EphA2/metabolism ; *Diet, High-Fat/adverse effects ; Male ; Humans ; Disease Models, Animal ; Plaque, Atherosclerotic/etiology ; Mice, Inbred C57BL ; Bacteria/classification/isolation & purification/genetics/metabolism ; Dysbiosis ; }, abstract = {Coronary artery disease (CAD), a critical condition resulting from systemic inflammation, metabolic dysfunction, and gut microbiota dysbiosis, poses a global public health challenge. ALW-II-41-27, a specific inhibitor of the EphA2 receptor, has shown anti-inflammatory prosperities. However, the impact of ALW-II-41-27 on atherosclerosis has not been elucidated. This study aimed to examine the roles of pharmacologically inhibiting EphA2 and the underlying mechanism in ameliorating atherosclerosis. ALW-II-41-27 was administered to apoE[-/-] mice fed a high-fat diet via intraperitoneal injection. We first discovered that ALW-II-41-27 led to a significant reduction in atherosclerotic plaques, evidenced by reduced lipid and macrophage accumulation, alongside an increase in collagen and smooth muscle cell content. ALW-II-41-27 also significantly lowered plasma and hepatic cholesterol levels, as well as the colonic inflammation. Furthermore, gut microbiota was analyzed by metagenomics and plasma metabolites by untargeted metabolomics. ALW-II-41-27-treated mice enriched Enterococcus, Akkermansia, Eggerthella and Lactobaccilus, accompanied by enhanced secondary bile acids production. To explore the causal link between ALW-II-41-27-associated gut microbiota and atherosclerosis, fecal microbiota transplantation was employed. Mice that received ALW-II-41-27-treated mouse feces exhibited the attenuated atherosclerotic plaque. In clinical, lower plasma DCA and HDCA levels were determined in CAD patients using quantitative metabolomics and exhibited a negative correlation with higher monocytes EphA2 expression. Our findings underscore the potential of ALW-II-41-27 as a novel therapeutic agent for atherosclerosis, highlighting its capacity to modulate gut microbiota composition and bile acid metabolism, thereby offering a promising avenue for CAD.}, } @article {pmid39426960, year = {2024}, author = {Zheng, M and Wen, L and He, C and Chen, X and Si, L and Li, H and Liang, Y and Zheng, W and Guo, F}, title = {Sequencing-guided re-estimation and promotion of cultivability for environmental bacteria.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {9051}, pmid = {39426960}, issn = {2041-1723}, support = {No. 31670492//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 32270006//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 2021J01027//Natural Science Foundation of Fujian Province (Fujian Provincial Natural Science Foundation)/ ; }, mesh = {*RNA, Ribosomal, 16S/genetics ; *Sewage/microbiology ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Soil Microbiology ; Phylogeny ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; }, abstract = {The low cultivability of environmental bacteria has been widely acknowledged, but most previous estimates focused on the proportion of cultivable cells rather than cultivable taxa. Here, we estimate the proportions of cultivable cells and cultivable taxa for two sample types (soil and activated sludge) using cell counting, 16S rRNA gene amplicon sequencing, metagenomics, and cultivation on agar plates under various conditions. We find that the proportion of cultivable taxa exceeds that of cultivable cells at the sample level. A large proportion of cultivable taxa are taxonomically novel but tend to be present at very low abundance on agar plates, forming microcolonies, and some of them cease to grow during subculture. Compared with uncultivable taxa (under the conditions used in our study), cultivatable taxa tend to display higher metabolic activity as inferred by measuring rRNA copies per cell. Finally, we use the generated taxonomic and genomic information as a guide to isolate a strain representing a yet-uncultured class within the Bacteroidota and to enhance the cultivable diversity of Burkholderiales from activated sludge.}, } @article {pmid39426578, year = {2025}, author = {Tao, Y and Zeng, Y and Zeng, R and Gou, X and Zhou, X and Zhang, J and Nhamdriel, T and Fan, G}, title = {The total alkaloids of Berberidis Cortex alleviate type 2 diabetes mellitus by regulating gut microbiota, inflammation and liver gluconeogenesis.}, journal = {Journal of ethnopharmacology}, volume = {337}, number = {Pt 3}, pages = {118957}, doi = {10.1016/j.jep.2024.118957}, pmid = {39426578}, issn = {1872-7573}, mesh = {Animals ; *Diabetes Mellitus, Type 2/drug therapy/metabolism ; *Alkaloids/pharmacology ; Male ; *Gastrointestinal Microbiome/drug effects ; *Liver/drug effects/metabolism ; *Diabetes Mellitus, Experimental/drug therapy ; Rats ; *Rats, Sprague-Dawley ; *Hypoglycemic Agents/pharmacology ; *Gluconeogenesis/drug effects ; Inflammation/drug therapy ; Diet, High-Fat/adverse effects ; Plant Extracts/pharmacology ; Blood Glucose/drug effects ; }, abstract = {Type 2 diabetes mellitus (T2DM) has become a public health problem worldwide. There is growing interest in finding drugs to treat T2DM from herbal medicine. Berberidis Cortex is a traditional Tibetan herb commonly used in the treatment of T2DM, and alkaloids are its main active components. However, the anti-diabetic mechanisms of the total alkaloids of Berberidis Cortex (TBC) remain unclear.

AIM OF THE STUDY: The aim of this study was to evaluate the anti-T2DM efficacy of TBC and reveal the mechanisms behind its effects.

MATERIALS AND METHODS: UPLC-Q-Exactive Orbitrap MS technology was employed to qualitatively identify alkaloid components in TBC. T2DM rat models were induced by high-fat diet combined with streptozotocin, and then treated with different doses of TBC (43.5, 87, 174 mg/kg/d) for 40 days. Biochemical parameters, such as fasting blood glucose (FBG), oral glucose tolerance test (OGTT), glycated serum protein (GSP), homeostatic model assessment of insulin resistance (HOMA-IR), total cholesterol (TC), triglycerides (TG), and low-density lipoprotein cholesterol (LDL-C), alongside H&E and PAS staining were used to evaluate the anti-diabetic activity of TBC. More importantly, metagenomics, transcriptomics, targeted metabolomics, and Western blot analysis were integrated to reveal the underlying mechanisms of TBC for T2DM treatment.

RESULTS: TBC significantly reduced the levels of FBG, OGTT, GSP, HOMA-IR, TC, TG, and LDL-C, and improved the histopathological alterations of pancreatic and liver tissues in T2D rats. It also reduced serum levels of lipopolysaccharide (LPS) and several pro-inflammatory cytokines (IL-6, IL-1β and TNF-α). Gut microbiome analysis by metagenomics proved that TBC could improve gut microbiota dysbiosis, including an increase in some beneficial bacteria (e.g., Bifidobacterium pseudolongum and Lactobacillus acidophilus) and a decrease in some harmful bacteria (e.g., Marvinbryantia and Parabacteroides). Western blot analysis found that TBC significantly up-regulated the expression of three intestinal barrier related tight junction proteins (ZO-1, occludin, and claudin-1), and effectively suppressed several key proteins in the TLR4/MyD88/NF-κB inflammatory cascade, including TLR4, MyD88 and p-NF-κB p65. Moreover, hepatic transcriptomics analysis further revealed the regulatory role of TBC on gluconeogenesis related genes, such as Pgc, and Creb1. Targeted metabolomics and Western blot analysis showed that TBC improved BAs dysregulation in T2DM rats, specifically increasing TCDCA and CA levels, thereby activating several proteins in the FXR/FGF15 signaling axis (i.e., FXR, FGF15 and FGFR4), and then decreased the expression of p-CREB1 and PGC-1α to inhibit liver gluconeogenesis.

CONCLUSIONS: TBC can significantly improve hyperglycemia, insulin resistance, hyperlipidemia, and inflammation in T2DM rats. The mechanism is related to the regulation of multiple links, including improving gut microbiota dysbiosis, protecting the intestinal barrier by up-regulating the expression of three tight junction proteins, reducing inflammation by inhibiting the LPS/TLR4/MyD88/NF-κB pathway, and inhibiting liver gluconeogenesis by regulating BAs/FXR/FGF15 and CREB1/PGC-1α signaling pathways.}, } @article {pmid39426464, year = {2024}, author = {Tang, Y and Liu, X and Zhu, S and Jia, M and Liu, JX and Sun, HZ}, title = {New insights into the enteric methane production based on the archaeal genome atlas of ruminant gastrointestinal tract.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2024.09.016}, pmid = {39426464}, issn = {2090-1224}, abstract = {INTRODUCTION: As one of the important components of ruminant gastrointestinal tract (GIT) microbiome, archaea are involved in many biological processes, especially methanogenesis. In spite of being a well-recognised member of the mammalian gut microbiome, it remains poorly characterized, partly due to the lack of a unified reference genome catalog.

OBJECTIVES: This study aimed to construct a unified genome atlas that captures the wider diversity in archaea and is thus more appropriate for functional and taxonomic exploration of ruminant GIT archaea.

METHODS: We collected archaeal genomes from public sources and new data of this study. We performed phylogenetic and functional genomics analysis, prophage identification based on the genomes. Using collected genomes as a reference, we conducted metagenomic and metatranscriptomic analysis on rumen fluid samples from 18 dairy cows, and investigated the correlation between rumen archaeal communities and methane (CH4) production profiles.

RESULTS: We constructed the ruminant GIT archaeal genomes (RGAG) by compiling 405 strain-level (160 species) non-redundant archaeal genomes from more than 10 ruminant species. Investigating the functional heterogeneity and methanogenic structure within RGAG revealed that it possessed 1,124 (99.5%) unknown microbial biosynthetic gene clusters. A survey of RGAG-borne prophages identified 63 prophages with 122 host-beneficial genes and 18 auxiliary metabolic genes. The pipeline for both metagenomics and metatranscriptomics generated in the study revealed the roles of archaeal genomes under-assessed in general multi-omics analysis. The highly expressed genus Methanosphaera was negatively correlated with CH4 production at the RNA level.

CONCLUSION: A unified genome atlas of ruminant GIT archaea is constructed in the study. Our analyses revealed the advantages of metatranscriptomics over metagenomics in studying rumen archaeal communities and further demonstrated that the multifaceted functions of ruminant archaea remain undiscovered. Differences in rumen archaeal community structure among cattle with different CH4 production profiles may reflect the balance between rumen hydrogen production and methanogenesis. Our work provides a new resource for interrogating archaeal functions in the ruminant GIT and potential targets for future CH4 reduction.}, } @article {pmid39426111, year = {2024}, author = {Shang, KM and Elsheikha, HM and Ma, H and Wei, YJ and Zhao, JX and Qin, Y and Li, JM and Zhao, ZY and Zhang, XX}, title = {Metagenomic profiling of cecal microbiota and antibiotic resistome in rodents.}, journal = {Ecotoxicology and environmental safety}, volume = {286}, number = {}, pages = {117186}, doi = {10.1016/j.ecoenv.2024.117186}, pmid = {39426111}, issn = {1090-2414}, mesh = {Animals ; *Cecum/microbiology ; *Gastrointestinal Microbiome/drug effects/genetics ; *Rodentia/microbiology ; *Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/drug effects/classification ; Drug Resistance, Microbial/genetics ; Metagenomics ; Rats ; Drug Resistance, Bacterial/genetics ; High-Throughput Nucleotide Sequencing ; Metagenome ; }, abstract = {The rodent gut microbiota is a known reservoir of antimicrobial resistance, yet the distribution of antibiotic resistance genes (ARGs) within rodent cecal microbial communities and the specific bacterial species harboring these ARGs remain largely underexplored. This study employed high-throughput sequencing of 122 samples from five distinct rodent species to comprehensively profile the diversity and distribution of ARGs and to identify the bacterial hosts of these genes. A gene catalog of the rodent cecal microbiome was constructed, comprising 22,757,369 non-redundant genes. Analysis of the microbial composition and diversity revealed that Bacillota and Bacteroidota were the dominant bacterial phyla across different rodent species, with significant variations in species composition among the rodents. In total, 3703 putative antimicrobial resistance protein-coding genes were identified, corresponding to 392 unique ARG types classified into 32 resistance classes. The most enriched ARGs in the rodent cecal microbiome were associated with multidrug resistance, followed by glycopeptide and elfamycin antibiotics. Procrustes analysis demonstrated a correlation between the structure of the microbial community and the resistome. Metagenomic assembly-based host tracking indicated that most ARG-carrying contigs originated from the bacterial family Oscillospiraceae. Additionally, 130 ARGs showed significant correlations with mobile genetic elements. These findings provide new insights into the cecal microbiota and the prevalence of ARGs across five rodent species. Future research on a wider range of wild rodent species carrying ARGs will further elucidate the mechanisms underlying the transmission of antimicrobial resistance.}, } @article {pmid39425237, year = {2024}, author = {Zelasko, S and Swaney, MH and Sandstrom, S and Davenport, TC and Seroogy, CM and Gern, JE and Kalan, LR and Currie, CR}, title = {Upper respiratory microbial communities of healthy populations are shaped by niche and age.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {206}, pmid = {39425237}, issn = {2049-2618}, support = {U19AI142720/NH/NIH HHS/United States ; U19AI104317/NH/NIH HHS/United States ; F30AI169759/NH/NIH HHS/United States ; U19 AI142720/AI/NIAID NIH HHS/United States ; T32AI055397/NH/NIH HHS/United States ; U19 AI104317/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Microbiota ; *Mouth/microbiology ; Adult ; Infant ; Female ; *Bacteria/classification/genetics/isolation & purification ; Male ; Age Factors ; Child, Preschool ; Healthy Volunteers ; Metagenomics/methods ; Respiratory System/microbiology ; Metagenome ; }, abstract = {BACKGROUND: Alterations in upper respiratory microbiomes have been implicated in shaping host health trajectories, including by limiting mucosal pathogen colonization. However, limited comparative studies of respiratory microbiome development and functioning across age groups have been performed. Herein, we perform shotgun metagenomic sequencing paired with pathogen inhibition assays to elucidate differences in nasal and oral microbiome composition and intermicrobial interactions across healthy 24-month-old infant (n = 229) and adult (n = 100) populations.

RESULTS: We find that beta diversity of nasal and oral microbiomes varies with age, with nasal microbiomes showing greater population-level variation compared to oral microbiomes. Infant microbiome alpha diversity was significantly lower across nasal samples and higher in oral samples, relative to adults. Accordingly, we demonstrate significant differences in genus- and species-level composition of microbiomes between sites and age groups. Antimicrobial resistome patterns likewise varied across body sites, with oral microbiomes showing higher resistance gene abundance compared to nasal microbiomes. Biosynthetic gene clusters encoding specialized metabolite production were found in higher abundance across infant oral microbiomes, relative to adults. Investigation of pathogen inhibition revealed greater inhibition of gram-negative and gram-positive bacteria by oral commensals, while nasal isolates had higher antifungal activity.

CONCLUSIONS: In summary, we identify significant differences in the microbial communities inhabiting nasal and oral cavities of healthy infants relative to adults. These findings inform our understanding of the interactions impacting respiratory microbiome composition and functions related to colonization resistance, with important implications for host health across the lifespan. Video Abstract.}, } @article {pmid39425038, year = {2024}, author = {Woldeyohannis, NN and Desta, AF}, title = {Metagenome-based microbial community analysis of urine-derived fertilizer.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {418}, pmid = {39425038}, issn = {1471-2180}, mesh = {Humans ; *Fertilizers/analysis ; *Urine/microbiology ; *Bacteria/genetics/classification/isolation & purification ; *Struvite ; *Metagenome ; Microbiota/genetics ; Metagenomics/methods ; DNA, Bacterial/genetics ; Phylogeny ; }, abstract = {Phosphorus is essential for food production and its supply is limited. Urine is an excellent source of phosphorus and one way to produce fertilizer is through conversion of urine to struvite (MgNH3PO4.6H2O). The present study aimed to understand the bacterial portion of the microbial community composition and dynamics of plasmid-mediated antimicrobial resistant genes during the optimized process of struvite production from composite human urine. Samples for DNA extraction was collected from fresh urine, stored urine and struvite during the process of struvite production. Shotgun metagenomic analysis was employed to understand the bacterial community. The most dominant phyla in the fresh and stored urine samples were Pseudomonadata, which comprised of 60% and 43% respectively, followed by Bacillota, comprised of 25% and 39% respectively. The struvite sample was dominated by the phylum Bacilliota (61%), Pseudomonadota (18%) and bacteroidota (12%). Members of the above phyla persisted in dominating each sample accordingly. Member of the family Morganellaceae was dominant in the fresh sample while the stored urine and struvite samples were dominated by the family Clostridiaceae. A decrease of members of the class Gammaproteobacteria was observed from the fresh to the struvite sample though not statistically significant. The genus Pseudomonas remained to be the most dominant member of Gammaproteobacteria in the fresh and stored urine sample with OTU count of 12,116 and 6,155 with a marked decrease by half in the stored sample. On the other hand, members of the genera Clostridium, Enterococcus, Bacteroides in the stored samples and Clostridium, Alkaliphilus and Pseudomonas in the struvite samples were dominant. 96% of the identified genera were shared in all the samples and the antimicrobial resistance genes (ARGs) identified in the fresh urine were shared by the struvite but not by the stored urine (e.g. sul, cat, aph and aac members). The presence of high abundance of ARGs in struvite needs attention in the persistence and transmissibility of the ARGs before application for agriculture.}, } @article {pmid39424897, year = {2024}, author = {Jia, X and Wang, W and Wu, M and Pang, L and Yang, C and Ling, Y and Yi, Z and Zhang, X}, title = {Empirical assessment of the enrichment-based metagenomic methods in identifying diverse respiratory pathogens.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {24493}, pmid = {39424897}, issn = {2045-2322}, support = {81801991//the National Natural Science Foundation of China/ ; GW VI-11.1-09//three-Year Initiative Plan for Strengthening Public Health System Construction in Shanghai/ ; GWVI-2.2//three-Year Initiative Plan for Strengthening Public Health System Construction in Shanghai/ ; GWVI-11.1-15//three-Year Initiative Plan for Strengthening Public Health System Construction in Shanghai/ ; 20Y11911300//the 2020 Shanghai Science and Technology Innovation Action Plan Medical Innovation Research Special Project/ ; SHDC12022121//the Shanghai Hospital Development Center Foundation/ ; 2017ZX10103009-001//the National Science and Technology Major Project of China/ ; 2018ZX10305409-001-005//the National Science and Technology Major Project of China/ ; }, mesh = {*Metagenomics/methods ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Respiratory Tract Infections/microbiology/virology/diagnosis ; Bacteria/genetics/isolation & purification/classification ; Metagenome ; Viruses/genetics/isolation & purification/classification ; }, abstract = {Probe-based nucleic acid enrichment represents an effective route to enhance the detection capacity of next-generation sequencing (NGS) in a set of clinically diverse and relevant microbial species. In this study, we assessed the effect of the enrichment-based sequencing on identifying respiratory infections using tiling RNA probes targeting 76 respiratory pathogens and sequenced using both Illumina and Oxford Nanopore platforms. Forty respiratory swab samples pre-tested for a panel of respiratory pathogens by qPCR were used to benchmark the sequencing data. We observed a general improvement in sensitivity after enrichment. The overall detection rate increased from 73 to 85% after probe capture detected by Illumina. Moreover, enrichment with probe sets boosted the frequency of unique pathogen reads by 34.6 and 37.8-fold for Illumina DNA and cDNA sequencing, respectively. This also resulted in significant improvements on genome coverage especially in viruses. Despite these advantages, we found that library pooling may cause reads mis-assignment, probably due to crosstalk issues arise from post-capture PCR and from pooled sequencing, thus increasing the risk of bleed-through signal. Taken together, an overall improvement in the breadth and depth of pathogen coverage is achieved using enrichment-based sequencing method. For future applications, automated library processing and pooling-free sequencing could enhance the precision and timeliness of probe enrichment-based clinical metagenomics.}, } @article {pmid39424349, year = {2024}, author = {Zhang, Y and Wang, Z and Wang, F and Zhou, H and Zhang, L and Xie, B}, title = {Anaerobic Degradation of Aromatic and Aliphatic Biodegradable Plastics: Potential Mechanisms and Pathways.}, journal = {Environmental science & technology}, volume = {58}, number = {43}, pages = {19462-19474}, doi = {10.1021/acs.est.4c07554}, pmid = {39424349}, issn = {1520-5851}, mesh = {Anaerobiosis ; *Biodegradation, Environmental ; *Biodegradable Plastics/metabolism ; Plastics/metabolism ; }, abstract = {Biodegradable plastics (BDPs) have been widely used as substitutes for traditional plastics, and their environmental fate is a subject of intense research interest. Compared with the aerobic degradation of BDPs, their biodegradability under anaerobic conditions in environmental engineering systems remains poorly understood. This study aimed to investigate the degradability of BDPs composed of poly(butylene adipate-co-terephthalate) (PBAT), poly(lactide acid) (PLA), and their blends, and explore the mechanism underlying their microbial degradation under conditions of anaerobic digestion (AD). The BDPs readily depolymerized under thermophilic conditions but were hydrolyzed at a slow rate under conditions of mesophilic AD. After 45 days of thermophilic AD, a decrease in the molecular weight and significant increase in the production of methane and carbon dioxide production were observed. Network and metagenomics analyses identified AD as reservoirs of plastic-degrading bacteria that produce multiple plastic-degrading enzymes. PETase was identified as the most abundant plastic-degrading enzyme. A potential pathway for the anaerobic biodegradation of BDPs was proposed herein. The polymers of high molecular weight were subjected to abiotic hydrolysis to form oligomers and monomers, enabling subsequent microbial hydrolysis and acetogenesis. Ultimately, complete degradation was achieved predominantly via the pathway involved in the conversion of acetic acid to methane. These findings provide novel insight into the mechanism underlying the anaerobic degradation of BDPs and the microbial resources crucial for the efficient degradation of BDPs.}, } @article {pmid39424030, year = {2024}, author = {Wan, P and Liu, Y and Li, B and Yu, X and Jiang, L and Lv, W}, title = {Yeast-enhanced activated sludge for improved nitrogen removal in wastewater treatment: Focus on dissolved organic nitrogen degradation.}, journal = {Environmental research}, volume = {263}, number = {Pt 2}, pages = {120181}, doi = {10.1016/j.envres.2024.120181}, pmid = {39424030}, issn = {1096-0953}, mesh = {*Nitrogen/metabolism ; *Sewage/microbiology/chemistry ; *Bioreactors/microbiology ; *Waste Disposal, Fluid/methods ; *Water Pollutants, Chemical/metabolism ; Wastewater/chemistry/microbiology ; Candida tropicalis/metabolism ; Biodegradation, Environmental ; }, abstract = {Dissolved organic nitrogen (DON) in effluent of wastewater treatment plants (WWTP), particularly hydrophilic DON, is usually more effective than dissolved inorganic nitrogen (DIN) in stimulating phytoplankton growth and increases the risk of eutrophication in receiving waterbodies. Proteins, amino acids, and nucleic acids, which are the main sources of DON in the effluent, are produced during the hydrolysis of extracellular polymeric substances (EPS) in activated sludge. Herein, a yeast strain Candida tropicalis O2, which was highly efficient in degrading DON in EPS was screened. Within 48-h batch experiments, the DON removal rates of the extracted hydrophilic and hydrophobic EPS reached 68.26% and 59.27%, respectively. During the continuous 35-day operation of sequencing batch bioreactor (SBR) fed with synthetic wastewater, the yeast-enhanced activated sludge (AS-Y) reactor demonstrated a marked improvement in removing various pollutants compared to the traditional activated sludge (AS) reactor. Specifically, DON removal increased by 1.53 mg/L (24.75%), hydrophilic DON by 1.24 mg/L (27.13%), hydrophobic DON by 0.28 mg/L (12.08%), and COD removal by 4.04 mg/L (6.48%). Although the DIN removal decreased by 0.38 mg/L (3.86%), it did not attenuate the overall TN removal from the system, and an additional TN reduction of 1.15 mg/L (7.13%) was achieved. Metagenomic analysis showed that adding strain O2 slightly inhibited the DIN metabolism, and the relative abundances of napB, nirK/S, norB/C, and nosZ involved in denitrification somewhat decreased. Kyoto Encyclopedia of Genes and Genomes and Carbohydrate-Active Enzymes annotations revealed that adding strain O2 promoted amino acid and carbohydrate metabolism. The increased relative abundance of Candida indicated that strain O2 was able to colonize the sludge in AS-Y reactor, which was conducive to synergistic interactions with other microorganisms. This study provided a novel method for in situ improving nitrogen removal in WWTP and reducing the eutrophication risk of the effluent to receiving waterbodies.}, } @article {pmid39423892, year = {2024}, author = {Ouyang, W and Huang, Y and Li, C and Huang, W and Yuan, S and Liu, H}, title = {Control of dissolved H2 concentration enhances electron generation, transport and TCE reduction by indigenous microbial community.}, journal = {The Science of the total environment}, volume = {955}, number = {}, pages = {177014}, doi = {10.1016/j.scitotenv.2024.177014}, pmid = {39423892}, issn = {1879-1026}, mesh = {*Trichloroethylene/metabolism ; *Biodegradation, Environmental ; *Water Pollutants, Chemical/metabolism/analysis ; Hydrogen/metabolism ; Microbiota ; Electron Transport ; Bacteria/metabolism ; Oxidation-Reduction ; Electrons ; Groundwater/chemistry/microbiology ; }, abstract = {Electrokinetic enhanced bioremediation (EK-Bio) is practical for trichloroethene (TCE) dechlorination because the cathode can produce a wide range of dissolved H2 (DH) concentrations of 1.3-0 mg/L from the electrode to the aquifer. In this study, TCE dechlorination was investigated under different DH concentrations. The mechanisms were discussed by analyzing the microbial community structure and abundance of organohalide-respiring bacteria (OHRB) using 16S rRNA, and the gene abundances of key enzymes in the TCE electron transport chain using metagenomic analysis. The results showed that the moderate DH concentration of 0.19-0.53 mg/L exhibited the most pronounced TCE dechlorination, even better than the higher DH concentrations, due to the optimal redox environment, the enrichments of OHRB, reductive dehalogenase (rdhA) genes and key enzyme genes in the electron generation and transport chain. More electrons were obtained from H2 metabolism by Dehalobacter by promoting the formation of [NiFe] hydrogenase (HupS/L/C) or from glycolysis by versatile OHRB by stimulating the formation of formate and enriching formate dehydrogenase (FDH) under moderate DH conditions. In addition, the enhanced amino acid metabolism improved the vitamin K cycle for electron transport and enriched the reductive dechlorinating enzyme (RDase) genes. This study identifies the optimal DH concentration that facilitates bioremediation efficiency, provides insights into microbial community shifts and key enzymatic pathways in EK-Bio remediation.}, } @article {pmid39423786, year = {2025}, author = {Ren, H and Wang, R and Ying, L and Iyobosa, E and Chen, G and Zang, D and Tong, M and Li, E and Nerenberg, R}, title = {Removal of sulfamethoxazole in an algal-bacterial membrane aerated biofilm reactor: Microbial responses and antibiotic resistance genes.}, journal = {Water research}, volume = {268}, number = {Pt A}, pages = {122595}, doi = {10.1016/j.watres.2024.122595}, pmid = {39423786}, issn = {1879-2448}, mesh = {*Biofilms/drug effects ; *Bioreactors ; *Sulfamethoxazole/pharmacology ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/metabolism/drug effects ; Waste Disposal, Fluid ; Wastewater/microbiology ; }, abstract = {Antibiotics are frequently detected in wastewater, but often are poorly removed in conventional wastewater treatment processes. Combining microalgal and nitrifying bacterial processes may provide synergistic removal of antibiotics and ammonium. In this research, we studied the removal of the antibiotic sulfamethoxazole (SMX) in two different reactors: a conventional nitrifying bacterial membrane aerated biofilm reactor (bMABR) and algal-bacterial membrane aerated biofilm reactor (abMABR) systems. We investigated the synergistic removal of antibiotics and ammonium, antioxidant activity, microbial communities, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and their potential hosts. Our findings show that the abMABR maintained a high sulfamethoxazole (SMX) removal efficiency, with a minimum of 44.6 % and a maximum of 75.8 %, despite SMX inhibition, it maintained a consistent 25.0 % ammonium removal efficiency compared to the bMABR. Through a production of extracellular polymeric substances (EPS) with increased proteins/polysaccharides (PN/PS), the abMABR possibly allowed the microalgae-bacteria consortium to protect the bacteria from SMX inactivation. The activity of antioxidant enzymes caused by SMX was reduced by 62.1-98.5 % in the abMABR compared to the bMABR. Metagenomic analysis revealed that the relative abundance of Methylophilus, Pseudoxanthomonas, and Acidovorax in the abMABR exhibited a significant positive correlation with SMX exposure and reduced nitrate concentrations and SMX removal. Sulfonamide ARGs (sul1 and sul2) appeared to be primarily responsible for defense against SMX stress, and Hyphomicrobium and Nitrosomonas were the key carriers of ARGs. This study demonstrated that the abMABR system has great potential for removing SMX and reducing the environmental risks of ARGs.}, } @article {pmid39423213, year = {2024}, author = {Ma, J and Yang, X and He, J}, title = {Comprehensive gut microbiota composition and microbial interactions among the three age groups.}, journal = {PloS one}, volume = {19}, number = {10}, pages = {e0305583}, pmid = {39423213}, issn = {1932-6203}, mesh = {Humans ; *Gastrointestinal Microbiome ; Aged ; Aged, 80 and over ; Adult ; Middle Aged ; Male ; Aging ; Young Adult ; Microbial Interactions ; Female ; Bacteria/genetics/classification ; Age Factors ; Archaea/genetics ; }, abstract = {There is a growing interest in studying the microbiota associated with aging by integrating multiple longevity researches while minimizing the influence of confounding factors. Here, we reprocessed metagenomic sequencing data from four different aging research studies and evaluated potential confounding factors in order to minimize the batch effect. Subsequently, we detected the diversity and abundance of the gut microbiome in three different age cohorts. Out of 1053 different bacteria species, only four showed substantial depletion across different age groups: Ligilactobacillus ruminis, Turicibacter sp. H121, Blautia massiliensis, and Anaerostipes hadrus. Archaea accumulated more in young individuals compared to elderly and centenarians. Candida albicans was more prevalent in centenarians, but Nakaseomyces glabratus (also known as Candida glabrata) was more common in elderly adults. Shuimuvirus IME207 showed a significant increase in centenarians compared to both control groups. In addition, we utilized a Fisher's exact test to investigate topological properties of differentially abundant microbiota in the co-occurrence network of each age group. Microbial signatures specific to different age stages were identified based on the condition: the reads showing differential abundance were higher compared to the other age groups. Lastly, we selected Methanosarcina sp. Kolksee for the Y group, Prevotella copri for the E group and Shuimuvirus IME207 for the C group as representatives of age-related characteristics to study how their interactions change during the aging process. Our results provide crucial insights into the gut microbiome's ecological dynamics in relation to the aging process.}, } @article {pmid39422492, year = {2024}, author = {Lu, F and Huang, T and Chen, R and Yin, H}, title = {Multi-omics analysis reveals the interplay between pulmonary microbiome and host in immunocompromised patients with sepsis-induced acute lung injury.}, journal = {Microbiology spectrum}, volume = {12}, number = {12}, pages = {e0142424}, pmid = {39422492}, issn = {2165-0497}, abstract = {UNLABELLED: The mechanisms behind the high inflammatory state and immunocompromise in severe sepsis remain unclear. While microbiota's role in immune regulation is known, the impact of pulmonary microbiota on sepsis progression is not fully understood. This study aims to investigate pulmonary microbial characteristics in septic patients and their relationship with host immune-related genes and clinical features. Fifty-four sepsis patients were divided into the immunocompromised host (ICH) group (n = 18) and the control group (n = 36). Bronchoalveolar lavage fluid (BALF) was analyzed using metagenomic next-generation sequencing (mNGS) to assess the pulmonary microbiome, and transcriptomic sequencing evaluated host gene expression. The pulmonary microbiota network in the ICH group showed notable alterations. Symbiotic bacteria like Streptococcus salivarius and Streptococcus oralis were key taxa in the control group. In contrast, opportunistic pathogens such as Campylobacter concisus and Prevotella melaninogenica, typically linked to infections in various body sites, dominated in the ICH group. Transcriptomic analysis revealed differential genes between the two groups. The downregulated differential genes in the ICH group were primarily enriched in pathways related to T-cell activation and the Type I interferon signaling pathway, both crucial for the immune system. Further correlation analysis identified significant associations between certain microbes and host genes, as well as clinical indicators, particularly with species like Campylobacter concisus, Streptococcus salivarius, Streptococcus oralis, and several species of Veillonella. These findings suggest that alterations in the pulmonary microbiome, especially the presence of opportunistic pathogens, may contribute to immune dysregulation in immunocompromised septic patients, warranting further research to explore causal relationships.

IMPORTANCE: Recent research has substantiated the significant role of microbiota in immune regulation, which could influence high inflammatory state and immunocompromise in patients with severe sepsis, as well as provide new opportunities for acute lung injury induced by sepsis diagnosis and treatment. Our study identified some potential critical microbes (Campylobacter concisus and several species of Veillonella), which were correlated with immune-related genes and might be the novel target to regulate immunotherapy in sepsis.}, } @article {pmid39422474, year = {2024}, author = {Zhu, Q and Huang, S and Gonzalez, A and McGrath, I and McDonald, D and Haiminen, N and Armstrong, G and Vázquez-Baeza, Y and Yu, J and Kuczynski, J and Sepich-Poore, GD and Swafford, AD and Das, P and Shaffer, JP and Lejzerowicz, F and Belda-Ferre, P and Havulinna, AS and Méric, G and Niiranen, T and Lahti, L and Salomaa, V and Kim, H-C and Jain, M and Inouye, M and Gilbert, JA and Knight, R}, title = {Correction for Zhu et al., "Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy".}, journal = {mSystems}, volume = {9}, number = {11}, pages = {e0128924}, doi = {10.1128/msystems.01289-24}, pmid = {39422474}, issn = {2379-5077}, } @article {pmid39422129, year = {2024}, author = {Kanti Nath, B and Gupta, SD and Talukder, S and Tonu, NS and Raidal, SR and Forwood, JK and Sarker, S}, title = {Metagenomic Detection of Multiple Viruses in Monk Parakeet (Myiopsitta monachus) in Australia.}, journal = {Veterinary medicine and science}, volume = {10}, number = {6}, pages = {e70083}, pmid = {39422129}, issn = {2053-1095}, mesh = {Animals ; *Feces/virology/microbiology ; *Parakeets/virology ; Bird Diseases/virology/epidemiology/microbiology ; Australia ; Adenoviridae/isolation & purification/classification/genetics ; Parvoviridae/isolation & purification/genetics/classification ; Phylogeny ; Circovirus/genetics/isolation & purification/classification ; High-Throughput Nucleotide Sequencing/veterinary ; Victoria ; Circoviridae/isolation & purification/genetics/classification ; Virome ; Metagenomics ; }, abstract = {BACKGROUND: Birds are known to harbour many pathogens, including circovirus, herpesviruses, adenoviruses and Chlamydia psittaci. Some of these pose zoonotic risks, while others, such as beak and feather disease virus (BFDV), have a significant impact on the conservation of endangered bird species.

OBJECTIVES: This study was aimed to determine the faecal virome of a group of apparently healthy Monk parakeet using high-throughput sequencing.

METHODS: Fresh faecal samples were collected from four Monk parakeets at a pet shop in Melbourne, Australia. Virus enrichment and nucleic acid extraction were performed on the faecal samples, followed by high-throughput sequencing at the Australian Genome Research Facility (AGRF).

RESULTS: Utilising an established pipeline for high-throughput sequencing data analysis, this study revealed the presence of three viruses of the families Circoviridae, Parvoviridae and Adenoviridae. Subsequent sequence comparison and phylogenetic analyses further confirmed that the detected viruses belong to the genera Chaphamaparvovirus (unassigned species), Circovirus (species Circovirus parrot) and Siadenovirus (species Siadenovirus viridis).

CONCLUSION: Despite non-pathogenicity, the existence of multiple viruses within a bird species underscores the risk of these viruses spreading into the pet trade. Detection and a better understanding of avian viruses are crucial for the establishment of appropriate management and biosecurity measures in the domestic and international bird trade, which ultimately supports the conservation of vulnerable bird species.}, } @article {pmid39421628, year = {2024}, author = {Shaykhutdinov, IH and Iliasov, PV and Limareva, LV and Sustretov, AS and Kokorev, DA and Sokolov, AV}, title = {Biomineralization of Human Genomic DNA into ZIF-8, a Zeolite-Like Metal-Organic Framework.}, journal = {Sovremennye tekhnologii v meditsine}, volume = {16}, number = {1}, pages = {5-13}, pmid = {39421628}, issn = {2309-995X}, mesh = {Humans ; *Metal-Organic Frameworks/chemistry ; *DNA ; *Zeolites/chemistry ; Biomineralization ; Genome, Human ; Imidazoles/chemistry ; }, abstract = {UNLABELLED: The aim of the study was to assess the capabilities of human genomic DNA biomineralization into ZIF-8 metal-organic framework (MOF) preserving DNA sequence integrity after the encapsulation cycle and composite dissolving. The study is an initial stage of the project aimed at developing an abiotic vector to be used when working with native nucleic acids of an arbitrary size based on DNA@ZIF-8 composite.

MATERIALS AND METHODS: We studied human genomic DNA isolated from lymphocytes of peripheral blood of healthy volunteers using Proba-NK kit (DNA-Technology LLC, Russia). Genomic DNA purity and concentration was estimated spectrophotometrically at 260/280 nm using Tecan Infinity 200 Pro plate reader (Tecan Instruments, Austria). ZIF-8 was synthesized in the physiological conditions (37°C) by mixing zinc salt and 2-methylimidazole aqueous solutions at different molar ratios. Human genomic DNA was encapsulated into ZIF-8 in similar conditions. The obtained MOF and DNA@ZIF-8 composite were studied using X-ray powder diffraction at the Phaser D2 XRPD device (Bruker, USA), and the specific surface area was estimated using Autosorb iQ porosimetry analyzer (Quantachrome, USA). The encapsulated DNA was quantified by dissolving DNA@ZIF-8 composite in the citrate buffer. DNA integrity was assessed by real-time allele-specific PCR (AS-PCR) using the kits for single nucleotide polymorphisms (Lytech, Russia) at the Quantstudio 6 Pro PCR machine (Thermo Scientific, USA). In case of using the kits with electrophoretic detection, the amplification was performed on the thermal cycler T100 (Thermo Scientific, USA).

RESULTS: The polymer ZIF-8 and DNA@ZIF-8 composite were obtained at different molar ratios of zinc ions and 2-methylimidazole. We characterized their structure and specific surface area. Genomic DNA biomineralization efficacy was found to be about 7-8%. PCR indicated the integrity of non-selectively chosen loci within the biomineralized DNA.

CONCLUSION: The study confirmed the possibility of human genomic DNA encapsulation into ZIF-8 metal-organic framework. After the biomineralization, DNA was found to preserve feasibility to be used in studies to investigate genetic constructs.}, } @article {pmid39421601, year = {2024}, author = {Dopson, M and Rezaei Somee, M and González-Rosales, C and Lui, LM and Turner, S and Buck, M and Nilsson, E and Westmeijer, G and Ashoor, K and Nielsen, TN and Mehrshad, M and Bertilsson, S}, title = {Novel candidate taxa contribute to key metabolic processes in Fennoscandian Shield deep groundwaters.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae113}, pmid = {39421601}, issn = {2730-6151}, abstract = {The continental deep biosphere contains a vast reservoir of microorganisms, although a large proportion of its diversity remains both uncultured and undescribed. In this study, the metabolic potential (metagenomes) and activity (metatranscriptomes) of the microbial communities in Fennoscandian Shield deep subsurface groundwaters were characterized with a focus on novel taxa. DNA sequencing generated 1270 de-replicated metagenome-assembled genomes and single-amplified genomes, containing 7 novel classes, 34 orders, and 72 families. The majority of novel taxa were affiliated with Patescibacteria, whereas among novel archaea taxa, Thermoproteota and Nanoarchaeota representatives dominated. Metatranscriptomes revealed that 30 of the 112 novel taxa at the class, order, and family levels were active in at least one investigated groundwater sample, implying that novel taxa represent a partially active but hitherto uncharacterized deep biosphere component. The novel taxa genomes coded for carbon fixation predominantly via the Wood-Ljungdahl pathway, nitrogen fixation, sulfur plus hydrogen oxidation, and fermentative pathways, including acetogenesis. These metabolic processes contributed significantly to the total community's capacity, with up to 9.9% of fermentation, 6.4% of the Wood-Ljungdahl pathway, 6.8% of sulfur plus 8.6% of hydrogen oxidation, and energy conservation via nitrate (4.4%) and sulfate (6.0%) reduction. Key novel taxa included the UBA9089 phylum, with representatives having a prominent role in carbon fixation, nitrate and sulfate reduction, and organic and inorganic electron donor oxidation. These data provided insights into deep biosphere microbial diversity and their contribution to nutrient and energy cycling in this ecosystem.}, } @article {pmid39421252, year = {2024}, author = {Klaassens, ES and Baak, ML and Mekkes, NJ and Bongoni, R and Schaubeck, M}, title = {Effect of protein modification in synbiotic infant formula on probiotic metabolic activity and bacterial composition in an infant gut-model.}, journal = {Microbiome research reports}, volume = {3}, number = {3}, pages = {38}, pmid = {39421252}, issn = {2771-5965}, abstract = {Aim: Microbial colonization of the neonatal gut is pivotal in priming the infant's immune system. Human milk (HM) is the best nutrition for infants and supports the development of the microbiota due to prebiotic compounds and probiotic microorganisms. When exclusive breastfeeding is not possible, infant formula (IF) with probiotics is a strategy to support the infant's microbiome development. However, knowledge about the effects of the infant gut microbiota and different compounds in IF on individual probiotic strains is limited, as strain-level detection in a complex ecosystem is challenging. The aim of the present study was to show the effects of IF with different protein forms on the metabolic activity of two probiotic strains isolated from HM in a complex ecosystem. Methods: By using an ex-vivo infant gut model containing infant donor-microbiota, the effects of IF with either intact or extensively hydrolyzed protein on the metabolic activity of the donor microbiota, as well as two probiotic strains [Limosilactobacillus fermentum (L. fermentum) CECT 5716 (Lf) and Bifidobacterium breve (B. breve) DSM 32583 (Bb)], were analyzed. A new bioinformatic pipeline combined with a specific infant microbiome database was used to explore shotgun metagenome datasets (1200 Megabases) for taxonomic identification and strain-level tracking. Results: Both protein forms (i.e., intact or extensively hydrolyzed protein) in IF supported infant gut microbial metabolic activity equally, as evidenced by similar levels of short-chain fatty acids (SCFAs). Interestingly, gut microbial metabolic activity was found to be differently activated in a strain-dependent manner. Taxonomic profiling of the microbiome at the strain level enabled monitoring of the prevalence and abundance of both probiotic strains, even in a complex ecosystem. Conclusion: Food matrix and host microbiota interactions should be considered when evaluating strain-specific probiotic effects in the future.}, } @article {pmid39421249, year = {2024}, author = {Mueller, KD and Panzetta, ME and Davey, L and McCann, JR and Rawls, JF and Flores, GE and Valdivia, RH}, title = {Pangenomic analysis identifies correlations between Akkermansia species and subspecies and human health outcomes.}, journal = {Microbiome research reports}, volume = {3}, number = {3}, pages = {33}, pmid = {39421249}, issn = {2771-5965}, abstract = {Aim: Akkermansia are common members of the human gastrointestinal microbiota. The prevalence of these mucophilic bacteria, especially Akkermansia muciniphila (A. muciniphila), correlates with immunological and metabolic health. The genus Akkermansia in humans includes species with significantly larger genomes than A. muciniphila, leading us to postulate that this added genetic content may influence how they impact human metabolic and immunological health. Methods: We conducted a pangenomic analysis of 234 Akkermansia complete or near-complete genomes. We also used high-resolution species and subspecies assignments to reanalyze publicly available metagenomic datasets to determine if there are relationships between Akkermansia species and A. muciniphila clades with various disease outcomes. Results: Analysis of genome-wide average nucleotide identity, 16S rRNA gene identity, conservation of core Akkermansia genes, and analysis of the fatty acid composition of representative isolates support the partitioning of the genus Akkermansia into several species. In addition, A. muciniphila sensu stricto, the most prevalent Akkermansia species in humans, should be subdivided into two subspecies. For a pediatric cohort, we observed species-specific correlations between Akkermansia abundance with baseline obesity or after various interventions. For inflammatory bowel disease cohorts, we identified a decreased abundance of Akkermansia in patients with ulcerative colitis or Crohn's disease, which was species and subspecies-dependent. In patients undergoing immune checkpoint inhibitor therapies for non-small cell lung carcinoma, we observed a significant association between one A. muciniphila subspecies and survival outcomes. Conclusion: Our findings suggest that the prevalence of specific Akkermansia species and/or subspecies can be crucial in evaluating their association with human health, particularly in different disease contexts, and is an important consideration for their use as probiotics.}, } @article {pmid39420944, year = {2024}, author = {Chen, X and Zou, T and Ding, G and Jiang, S}, title = {Findings and methodologies in oral phageome research: a systematic review.}, journal = {Journal of oral microbiology}, volume = {16}, number = {1}, pages = {2417099}, pmid = {39420944}, issn = {2000-2297}, abstract = {BACKGROUND: The oral microbiome serves as both an indicator and a mediator of oral health. Evidence indicates that bacteriophages (phages) are widely present in the oral microbiome and exhibit diverse classifications and interactions with human cells and other microbes. These phages constitute the oral phageome, which potentially exerts significant yet unexplored effects on the interplay between oral and general health.

METHODS: Three databases (PubMed/MEDLINE, Embase and Scopus) were searched for metagenomic analyses that investigated the oral phageome. Eligible studies were synthesized based on their methodological approaches and findings.

RESULTS: A total of 14 articles were included in this systematic review. Among the 14 articles included, there were six studies that discussed disease-related alterations, along with a discursive examination of additional variables such as sampling niches, external interventions and methodologies. The phages that infect Streptococcus Actinomyces Haemophilus, and Veillonella have been discovered to be associated with chronic periodontitis, caries, and pancreatic ductal carcinoma.

CONCLUSIONS: This systematic review focuses on findings and methodologies in oral phageome studies, which were conducted using highly heterogeneous methodologies that explored the oral phageome in multiple directions while placing constraints on quantitative statistics. Combining different kinds of sample types, utilizing the characteristics of different methods, involving both DNA and RNA phages, and differentiating lysogenic and lytic phages should be the distinction of further studies.}, } @article {pmid39420836, year = {2024}, author = {Qu, W and Xu, Y and Yang, J and Shi, H and Wang, J and Yu, X and Chen, J and Wang, B and Zhuoga, D and Luo, M and Liu, R}, title = {Berberine alters the gut microbiota metabolism and impairs spermatogenesis.}, journal = {Acta biochimica et biophysica Sinica}, volume = {}, number = {}, pages = {}, doi = {10.3724/abbs.2024174}, pmid = {39420836}, issn = {1745-7270}, abstract = {Berberine (BBR) is used to treat diarrhea clinically. However, its reproductive toxicity is unclear. This study aims to investigate the impact of BBR on the male reproductive system. Intragastric BBR administration for 14 consecutive days results in a significant decrease in the serum testosterone concentration, epididymal sperm concentration, mating rate and fecundity of male mice. Testicular treatment with testosterone propionate (TP) partially reverses the damage caused by BBR to the male reproductive system. Mechanistically, the decrease in Muribaculaceae abundance in the gut microbiota of mice is the principal cause of the BBR-induced decrease in the sperm concentration. Both fecal microbiota transplantation (FMT) and polyethylene glycol (PEG) treatment demonstrate that Muribaculaceae is necessary for spermatogenesis. The intragastric administration of Muribaculaceae intestinale to BBR-treated mice restores the sperm concentration and testosterone levels. Metabolomic analysis reveals that BBR affects arginine and proline metabolism, of which ornithine level is downregulated. Combined analysis via 16S rRNA metagenomics sequencing and metabolomics shows that Muribaculaceae regulates ornithine level. The transcriptomic results of the testes indicate that the expressions of genes related to the low-density lipoprotein receptor (LDLR)-mediated testosterone synthesis pathway decrease after BBR administration. The transcriptional activity of the Ldlr gene in TM3 cells is increased with increased ornithine supplementation in the culture media, leading to increased testosterone synthesis. Overall, this study reveals an association between a BBR-induced decrease in Muribaculaceae abundance and defective spermatogenesis, providing a prospective therapeutic approach for addressing infertility-related decreases in serum testosterone triggered by changes in the gut microbiota composition.}, } @article {pmid39420635, year = {2025}, author = {Li, C and Sun, L and Jia, Z and Tang, Y and Liu, X and Zhang, J and Müller, C}, title = {Microbial Inoculants Drive Changes in Soil and Plant Microbiomes and Improve Plant Functions in Abandoned Mine Restoration.}, journal = {Plant, cell & environment}, volume = {48}, number = {2}, pages = {1162-1178}, doi = {10.1111/pce.15215}, pmid = {39420635}, issn = {1365-3040}, support = {//Jinchi Zhang acknowledges the funding support from Jiangsu Science and Technology Plan Project (BE2022420); the Innovation and Promotion of Forestry Science and Technology Program of Jiangsu Province (LYKJ[2021]30); the Scientific Research Project of Baishanzu National Park (2021ZDLY01); and the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD). Chong Li is grateful for the partial financial support from the Postgraduate Research and Practice Innovation Program of Jiangsu Province (KYCX21_0915), and the China Scholarship Council (202108320300)./ ; }, mesh = {*Soil Microbiology ; *Microbiota ; *Mining ; *Plant Roots/microbiology/physiology ; Plants/microbiology/metabolism ; Soil/chemistry ; Bacteria/metabolism ; Fungi/physiology ; Environmental Restoration and Remediation/methods ; }, abstract = {The application of microbial inoculants holds promise for the sustainable restoration of abandoned mine sites by affecting soil nutrients and microbial communities. However, the responses of plant microbial communities to microbial inoculants in mine restoration remain largely unknown. To bridge this knowledge gap, we conducted a 4-year field experiment at an abandoned carbonate mine site to assess the impacts of microbial inoculants on the soil-plant microbiome. Our findings revealed that microbial inoculants significantly changed roots, fine root bacterial and fungal communities. Further, no significant correlations were observed between the soil-plant nutrient content (Z-score) and microbial alpha diversity. However, a significantly positive correlation was found between the relative abundance of the keystone ecological cluster (Module #1) and soil-plant nutrient content. The application of microbial inoculants also increased complexity, albeit decreased stability of plant microbiome networks, alongside a reduction in stochastic assembly. Conversely, they decreased the complexity but increased the stability of soil microbiome networks, accompanied by an increase in stochastic assembly. Notably, the number of specifically enriched microbiome functional traits of roots and root nodules under the microbial inoculant treatments surpassed that of the control. In summary, our findings underscored the potential of microbial inoculants to enhance soil-plant functionality at abandoned mine restoration sites.}, } @article {pmid39420033, year = {2024}, author = {Majzoub, ME and Paramsothy, S and Haifer, C and Parthasarathy, R and Borody, TJ and Leong, RW and Kamm, MA and Kaakoush, NO}, title = {The phageome of patients with ulcerative colitis treated with donor fecal microbiota reveals markers associated with disease remission.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {8979}, pmid = {39420033}, issn = {2041-1723}, support = {988415//Crohn's and Colitis Foundation (Crohn's & Colitis Foundation)/ ; APP2011047//Department of Health | National Health and Medical Research Council (NHMRC)/ ; Investigator grant//Department of Health | National Health and Medical Research Council (NHMRC)/ ; Scientia fellowship//University of New South Wales (UNSW Australia)/ ; }, mesh = {Humans ; *Colitis, Ulcerative/therapy/microbiology/virology ; *Fecal Microbiota Transplantation ; *Bacteriophages/genetics/isolation & purification/physiology ; *Gastrointestinal Microbiome/genetics ; *Feces/microbiology/virology ; Double-Blind Method ; Male ; Female ; Metagenomics/methods ; Adult ; Dysbiosis/microbiology/therapy ; Middle Aged ; Virome/genetics ; Remission Induction ; Anti-Bacterial Agents/therapeutic use ; Biomarkers ; }, abstract = {Bacteriophages are influential within the human gut microbiota, yet they remain understudied relative to bacteria. This is a limitation of studies on fecal microbiota transplantation (FMT) where bacteriophages likely influence outcome. Here, using metagenomics, we profile phage populations - the phageome - in individuals recruited into two double-blind randomized trials of FMT in ulcerative colitis. We leverage the trial designs to observe that phage populations behave similarly to bacterial populations, showing temporal stability in health, dysbiosis in active disease, modulation by antibiotic treatment and by FMT. We identify a donor bacteriophage putatively associated with disease remission, which on genomic analysis was found integrated in a bacterium classified to Oscillospiraceae, previously isolated from a centenarian and predicted to produce vitamin B complex except B12. Our study provides an in-depth assessment of phage populations during different states and suggests that bacteriophage tracking has utility in identifying determinants of disease activity and resolution.}, } @article {pmid39419961, year = {2024}, author = {Becsei, Á and Fuschi, A and Otani, S and Kant, R and Weinstein, I and Alba, P and Stéger, J and Visontai, D and Brinch, C and de Graaf, M and Schapendonk, CME and Battisti, A and De Cesare, A and Oliveri, C and Troja, F and Sironen, T and Vapalahti, O and Pasquali, F and Bányai, K and Makó, M and Pollner, P and Merlotti, A and Koopmans, M and Csabai, I and Remondini, D and Aarestrup, FM and Munk, P}, title = {Author Correction: Time-series sewage metagenomics distinguishes seasonal, human-derived and environmental microbial communities potentially allowing source-attributed surveillance.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {8953}, doi = {10.1038/s41467-024-53282-6}, pmid = {39419961}, issn = {2041-1723}, } @article {pmid39419776, year = {2024}, author = {Ma, M and Ardalan, A and Van Dyk, A and Charles, TC and Horsman, GP}, title = {Discovery of a glyphosate oxidase in nature.}, journal = {FEMS microbiology letters}, volume = {371}, number = {}, pages = {}, pmid = {39419776}, issn = {1574-6968}, support = {STPGP-506399-2017//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {*Glyphosate ; *Glycine/analogs & derivatives/metabolism ; *Herbicides/metabolism ; *Amino Acid Oxidoreductases/genetics/metabolism/chemistry ; *Soil Microbiology ; Metagenomics ; Oxidation-Reduction ; }, abstract = {Glyphosate is the most used herbicide on Earth. After a half-century of use we know only two biodegradative pathways, each of which appears to degrade glyphosate incidentally. One pathway begins with oxidation of glyphosate catalysed by glycine oxidase (GO). To date, no naturally occurring GO enzymes preferentially oxidize glyphosate but nonetheless are sufficiently active to initiate its degradation. However, GO enzymes that preferentially oxidize glyphosate over glycine-i.e. glyphosate oxidases (GOXs)-may have evolved in environments facing prolonged glyphosate exposure. To test this hypothesis, we screened a metagenomic library from glyphosate-exposed agricultural soil and identified a GOX from clone 11AW19 (GO19) that prefers glyphosate over glycine by four orders of magnitude. This is the first GO isolated from a natural source exhibiting a glyphosate preference. Not only have we discovered the first GOX in nature, but we have also demonstrated the utility of functional metagenomics to find a GOX with greater catalytic efficiency and specificity than those engineered using directed evolution.}, } @article {pmid39419193, year = {2024}, author = {Chen, H and Zeng, M and Batool, SS and Zhao, Y and Yu, Z and Zhou, J and Liu, K and Huang, J}, title = {Metagenomic analysis reveals effects of gut microbiome in response to neoadjuvant chemoradiotherapy in advanced rectal cancer.}, journal = {Genomics}, volume = {116}, number = {6}, pages = {110951}, doi = {10.1016/j.ygeno.2024.110951}, pmid = {39419193}, issn = {1089-8646}, mesh = {Humans ; *Rectal Neoplasms/therapy/microbiology/genetics/metabolism ; *Gastrointestinal Microbiome ; *Neoadjuvant Therapy ; Chemoradiotherapy ; Female ; Male ; Middle Aged ; Metagenomics ; Aged ; Metagenome ; Feces/microbiology ; Bacteria/genetics/classification/metabolism ; }, abstract = {Neoadjuvant chemoradiotherapy can enhance survival rate of patients with advanced rectal cancer, but its effectiveness varies considerably. Previous studies have indicated that gut microbes may serve as biomarkers for predicting treatment efficacy. However, the specific roles of the gut microbiome in patients who have good response to nCRT remains unclear. In this study, shotgun metagenomic sequencing technology was used to analyze the fecal microbiome of patients with varying responses to nCRT. Our findings revealed that beneficial intestinal bacteria and genes from different metabolic pathways (carbohydrate metabolism, amino acid metabolism, and sulfur metabolism) were significantly enriched in patients with good response. Additionally, causal relationship in which microbial-derived GDP-D-rhamnose and butyrate could influence the response to nCRT was clarified. Our results offered new insights into the different response to nCRT, and provided valuable reference points for improving the effectiveness of nCRT in patients with advanced colorectal cancer.}, } @article {pmid39418906, year = {2024}, author = {Zhao, W and Ma, H and Gao, Z and Li, D and Lin, Y and Wu, C and Wei, L}, title = {Uncovering the toxic effects and adaptive mechanisms of aminated polystyrene nanoplastics on microbes in sludge anaerobic digestion system: Insight from extracellular to intracellular.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {136163}, doi = {10.1016/j.jhazmat.2024.136163}, pmid = {39418906}, issn = {1873-3336}, mesh = {*Polystyrenes/toxicity/chemistry ; *Sewage/microbiology ; Anaerobiosis ; Methane/metabolism/chemistry ; Molecular Docking Simulation ; Bacteria/drug effects/metabolism/genetics ; Microplastics/toxicity/chemistry ; Oxidative Stress/drug effects ; Nanoparticles/toxicity/chemistry ; Reactive Oxygen Species/metabolism ; Hydrolysis ; }, abstract = {The impacts of polystyrene nanoplastics (PS NPs) with amino functional groups on sludge anaerobic digestion process and the underlying microbial feedbacks remains unclear. Herein, PS NPs coated with and without amino functional groups were employed to explore their impacts on the sludge digestion performance. Experimental results showed that aminated PS NPs (PS-NH2) deteriorated the methane yield and hydrolysis rate. The Derjaguin-Landau-Verwey-Overbeek theory analysis suggested that the PS-NH2 decreased the interaction energy barrier, making it easier to contact with sludge and disrupting the structure of extracellular polymeric substances. Metagenomic analysis showed that the abundance of functional microbes (e.g., Longilinea, Leptolinea, and Methanosarcina) decreased, accompanied with lower network complexity and fewer keystone taxa. Molecular docking revealed that PS-NH2 occupy the antioxidant enzyme active binding sites through hydrogen bonding and hydrophobic interactions, impairing degradation of reactive oxygen species. The severe intracellular oxidative stress up-regulated genes associated with quorum sensing (e.g., luxI and luxR) and protein biosynthesis (e.g., algA, trpG and trpE), and further inducing compact tryptophan-like proteins as a defense against NPs. These findings provide new understanding of the toxic effects from PS-NH2 in biological systems and offer valuable insights into the regulation strategies aimed at alleviating NPs inhibition.}, } @article {pmid39418853, year = {2024}, author = {Aydin, F and Tarhane, S and Karakaya, E and Abay, S and Kayman, T and Güran, Ö and Bozkurt, E and Üzüm, N and Avci, A and Olgun, K and Jablonski, D and Güran, C and Burçin Saticioğlu, İ}, title = {Helicobacter cappadocius sp. nov., from lizards: The first psychrotrophic Helicobacter species.}, journal = {Systematic and applied microbiology}, volume = {47}, number = {6}, pages = {126557}, doi = {10.1016/j.syapm.2024.126557}, pmid = {39418853}, issn = {1618-0984}, mesh = {Animals ; *Helicobacter/genetics/classification/isolation & purification ; *RNA, Ribosomal, 16S/genetics ; *Phylogeny ; *DNA, Bacterial/genetics ; *Lizards/microbiology ; *Genome, Bacterial/genetics ; *Sequence Analysis, DNA ; *Base Composition ; *Bacterial Typing Techniques ; Helicobacter Infections/microbiology/veterinary ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Cloaca/microbiology ; }, abstract = {It was aimed to determine the prevalence of Helicobacter in some reptilian and amphibian species in Türkiye and to describe the bacteria. For this purpose, 73 cloacal swab samples were used as material. The description of the isolates was performed by detailed phenotypic tests, whole genome analyses, and MALDI-TOF MS. As a result of the phenotypic analysis, two helical, curved Gram-negative, motile isolates were recovered. It was determined through the analysis of 16S rRNA gene sequences that two isolates belonged to the genus Helicobacter. These isolates were found to be in a distinct group from other Helicobacter species. However, the 16S rRNA sequence did not match any identified species, with the closest match being Helicobacter mustelae strain R85-13-6[T], which had an identity level of 96.2 %. Additionally, it was found that strains faydin-H75[T] and faydin-H76 had a 99.3 % identity level for their 16S rRNA genes. After conducting dDDH and ANI analyses, it was found that strains faydin-H75[T] and their close neighbors H.anseris ATCC BAA-1299[T] shared 13.5 % and 68.8 % similarity, respectively. The genome size of the strains was 1.7 Mb while G + C contents were 33.5 %. Metagenomic analyses using IMNGS and Protologger tools revealed the presence of faydin-H75[T] in various lizard species with high similarity, confirming its broad distribution and host specificity. The results indicated that these two strains represent a novel species, for which we propose the name Helicobacter cappadocius with faydin-H75[T] (=NCTC014972 = LMG 33382 = DSM117062) as the respective type strain. The current novel species is the first Helicobacter species to exhibit a psychrotrophic feature.}, } @article {pmid39418785, year = {2024}, author = {Chen, J and Su, Z and Li, F and Cao, F and Xiong, F and Jiang, B and Xing, Y and Wen, D}, title = {The variation of resistome, mobilome and pathogen in domestic and industrial wastewater treatment systems.}, journal = {Environment international}, volume = {193}, number = {}, pages = {109051}, doi = {10.1016/j.envint.2024.109051}, pmid = {39418785}, issn = {1873-6750}, mesh = {*Wastewater/microbiology ; *Bacteria/genetics/drug effects ; Humans ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Waste Disposal, Fluid ; Metagenomics ; Genes, Bacterial ; Water Purification/methods ; Drug Resistance, Bacterial/genetics ; Interspersed Repetitive Sequences ; }, abstract = {Wastewater treatment plants (WWTPs), including both domestic and industrial facilities, are key contributors to antibiotic resistance genes (ARGs) and human pathogens in the environment. However, the characteristics and dissemination mechanisms of ARGs in domestic (SD) and industrial (SI) wastewater treatment systems remain unclear, leading to uncertainties in risk assessment. Based on metagenomic analysis, we observed significant differences in the compositions of resistome (ARGs and metal resistance genes, MRGs), mobilome (mobile genetic elements, MGEs), and bacterial community between SD and SI. SI exhibited lower diversity of ARGs but higher abundance of MRGs compared to SD. The removal efficiency of resistome was lower in the SI than that in the SD. MGEs emerged as the primary driver of ARG dissemination in the WWTPs, followed by the bacterial community. Environmental conditions (physicochemical parameters, heavy metals, and antibiotics) indirectly influenced the variation of resistome. Significantly, environmental conditions and MGEs highly influenced the composition of resistome in the SI, while bacterial community more associated with resistome in the SD. Additionally, we identified 36 human bacterial pathogens as potential hosts of ARGs, MRGs, and MGEs in wastewater samples. This study provides new insights on the dissemination mechanisms and risk assessment of antimicrobial resistance in the different types of WWTPs.}, } @article {pmid39418776, year = {2024}, author = {Xie, Q and Sun, J and Sun, M and Wang, Q and Wang, M}, title = {Perturbed microbial ecology in neuromyelitis optica spectrum disorder: Evidence from the gut microbiome and fecal metabolome.}, journal = {Multiple sclerosis and related disorders}, volume = {92}, number = {}, pages = {105936}, doi = {10.1016/j.msard.2024.105936}, pmid = {39418776}, issn = {2211-0356}, mesh = {*Neuromyelitis Optica/microbiology/immunology ; Humans ; *Gastrointestinal Microbiome/physiology ; *Feces/microbiology ; Animals ; Female ; Adult ; *Fecal Microbiota Transplantation ; Mice ; Male ; Metabolome/physiology ; Middle Aged ; }, abstract = {BACKGROUND: Neuromyelitis optica spectrum disorder (NMOSD) is a central nervous system inflammatory demyelinating immune-mediated ailment, which is influenced by genetic, epigenetic, and environmental elements. The escalating incidence of NMOSD in recent years implies alterations in environmental risk factors. Recent research has established a correlation between gut microbiomes and the development of NMOSD.

METHODS: Metagenomic shotgun sequencing and gas chromatography-mass spectrometry (GC-MS) were employed to assess alterations of the structure and function in the fecal microbiome, as well as levels of short-chain fatty acids (SCFAs) in fecal and blood samples, among individuals with neuromyelitis optica spectrum disorder (NMOSD) during the acute phase (n = 25), the remission phase (n = 11), and a group of healthy controls (HCs) (n = 24). We further explored the correlation between gut microbiota and the pathogenesis of NMOSD through fecal microbiota transplantation (FMT). The gut microbiome from human donors diagnosed with NMOSD or HCs was transplanted into germ-free mice, followed by an analysis of the alterations in the structure and functionality of the transplanted mice's gut microbiome. Additionally, the impact of microbiome transfer on the immunity and spinal cord of germ-free mice was assessed through various techniques, including ELISA, flow cytometry, western blot, histopathology, and transcriptome sequencing.

RESULTS: (1) At the taxonomic levels of genus and species, there were significant differences in the α-diversity of the microbiome between HCs and NMOSD patients in the acute phase, with NMOSD patients having higher species diversity. (2) In the acute phase, the gut microbiota of NMOSD patients was characterized by Ruminococcaceae_unclassified, Campylobacter, Parabacteroides, Lactobacillus, Akkermansia, Streptococcus oralis, Clostridium leptum, Clostridium asparagiforme, Firmicutes bacterium CAG 238, and Lactobacillus fermentum. (3) The relative abundances of Coprobacter, Turicimonas, Gemmiger, Enterobacter, Roseburia sp.CAG 471, Veillonella tobetsuensis, Proteobacteria bacterium CAG 139, Ruminococcus bicirculans, Lactococcus lactis, Flavonifractor plautii, and Streptococcus cristatus were notably lower in patients experiencing remission compared to NMOSD patients in the acute phase, On the other hand, the relative abundances of Flavonifractor (P = 0.049) and Clostridium aldenense (P = 0.049) were significantly higher. Following medication, the gut microbiome distribution in NMOSD patients during remission closely resembled that of healthy controls (HCs). (4) Compared with HCs, acetate levels in the feces of patients with NMOSD in the acute phase were significantly lower. (5) In addition, we transplanted feces from NMOSD patients into germ-free mice and revealed a significant increase in the levels of IL-6, IL-17A, and IL-23 in the blood of mice belonging to the NMOSD fecal transplantation (NFMT) group. Additionally, the IL-10 level exhibited a significant reduction. Moreover, the proportion of Th17 cells displayed a significant increase, while the proportion of Treg cells exhibited a significant decrease in the spleens of NFMT mice.

CONCLUSION: Patients in the acute phase of neuromyelitis optica spectrum disorder (NMOSD) exhibited imbalances in their gut microbiota and a deficiency in short-chain fatty acids (SCFAs). Following drug treatment, the composition of intestinal microbes in NMOSD patients during the remission phase closely resembled that of the healthy control population. The FMT experiment provided evidence of the significant association between intestinal flora and the pathogenesis of NMOSD. Consequently, investigating gut microbiota and identifying novel microbial markers hold promise for the diagnosis and treatment of NMOSD patients.}, } @article {pmid39418385, year = {2024}, author = {Lien, YW and Amendola, D and Lee, KS and Bartlau, N and Xu, J and Furusawa, G and Polz, MF and Stocker, R and Weiss, GL and Pilhofer, M}, title = {Mechanism of bacterial predation via ixotrophy.}, journal = {Science (New York, N.Y.)}, volume = {386}, number = {6719}, pages = {eadp0614}, doi = {10.1126/science.adp0614}, pmid = {39418385}, issn = {1095-9203}, mesh = {*Bacterial Adhesion ; *Bacteroidetes/physiology/ultrastructure ; Cryoelectron Microscopy ; Single-Cell Analysis ; *Type VI Secretion Systems/metabolism/ultrastructure ; *Vibrio/physiology/ultrastructure ; *Flagella/ultrastructure ; }, abstract = {Ixotrophy is a contact-dependent predatory strategy of filamentous bacteria in aquatic environments for which the molecular mechanism remains unknown. We show that predator-prey contact can be established by gliding motility or extracellular assemblages we call "grappling hooks." Cryo-electron microscopy identified the grappling hooks as heptamers of a type IX secretion system substrate. After close predator-prey contact is established, cryo-electron tomography and functional assays showed that puncturing by a type VI secretion system mediated killing. Single-cell analyses with stable isotope-labeled prey revealed that prey components are taken up by the attacker. Depending on nutrient availability, insertion sequence elements toggle the activity of ixotrophy. A marine metagenomic time series shows coupled dynamics of ixotrophic bacteria and prey. We found that the mechanism of ixotrophy involves multiple cellular machineries, is conserved, and may shape microbial populations in the environment.}, } @article {pmid39418300, year = {2024}, author = {Zhang, Y and Mao, M and Zhang, R and Liao, YT and Wu, VCH}, title = {DeepPL: A deep-learning-based tool for the prediction of bacteriophage lifecycle.}, journal = {PLoS computational biology}, volume = {20}, number = {10}, pages = {e1012525}, pmid = {39418300}, issn = {1553-7358}, mesh = {*Deep Learning ; *Bacteriophages/genetics/physiology ; *Computational Biology/methods ; Genome, Viral/genetics ; Natural Language Processing ; Neural Networks, Computer ; Algorithms ; Bacteria/virology/genetics ; }, abstract = {Bacteriophages (phages) are viruses that infect bacteria and can be classified into two different lifecycles. Virulent phages (or lytic phages) have a lytic cycle that can lyse the bacteria host after their infection. Temperate phages (or lysogenic phages) can integrate their phage genomes into bacterial chromosomes and replicate with bacterial hosts via the lysogenic cycle. Identifying phage lifecycles is a crucial step in developing suitable applications for phages. Compared to the complicated traditional biological experiments, several tools have been designed for predicting phage lifecycle using different algorithms, such as random forest (RF), linear support-vector classifier (SVC), and convolutional neural network (CNN). In this study, we developed a natural language processing (NLP)-based tool-DeepPL-for predicting phage lifecycles via nucleotide sequences. The test results showed that our DeepPL had an accuracy of 94.65% with a sensitivity of 92.24% and a specificity of 95.91%. Moreover, DeepPL had 100% accuracy in lifecycle prediction on the phages we isolated and biologically verified previously in the lab. Additionally, a mock phage community metagenomic dataset was used to test the potential usage of DeepPL in viral metagenomic research. DeepPL displayed a 100% accuracy for individual phage complete genomes and high accuracies ranging from 71.14% to 100% on phage contigs produced by various next-generation sequencing technologies. Overall, our study indicates that DeepPL has a reliable performance on phage lifecycle prediction using the most fundamental nucleotide sequences and can be applied to future phage and metagenomic research.}, } @article {pmid39418241, year = {2024}, author = {Song, C and Liu, F and Mei, Y and Cai, W and Cheng, K and Guo, D and Liu, Y and Shi, H and Duan, DD and Liu, Z}, title = {Integrated metagenomic and metabonomic mechanisms for the therapeutic effects of Duhuo Jisheng decoction on intervertebral disc degeneration.}, journal = {PloS one}, volume = {19}, number = {10}, pages = {e0310014}, pmid = {39418241}, issn = {1932-6203}, mesh = {Animals ; *Intervertebral Disc Degeneration/drug therapy/metabolism/microbiology ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; *Metabolomics/methods ; Rats ; *Gastrointestinal Microbiome/drug effects ; Male ; *Rats, Sprague-Dawley ; *Metagenomics/methods ; Metabolome/drug effects ; Feces/microbiology ; Disease Models, Animal ; }, abstract = {Intervertebral disc degeneration (IVDD) is a prevalent orthopedic condition with lower back pain as the predominant clinical presentation that challenges clinical treatment with few therapeutic options. Duhuo Jisheng Decoction (DHJSD) has been proven effective in the therapy of IVDD, but the precise underlying mechanisms remain not fully elucidated. The current study was designed to test our hypothesis that DHJSD may systematically correct the phenotypic disruption of the gut microbiota and changes in the serum metabolome linked to IVDD. Analysis of the active ingredients of DHJSD by ultra high performance liquid chromatography. An integrated metagenomic and metabonomic approach was used to analyze feces and blood samples from normal and IVDD rats. Compared to the control group, fiber ring pinning on the caudal 3 to caudal 5 segments of the rats caused IVDD and significantly altered the compositions of the intestinal microbiota and serum metabolites. Integrated analysis revealed commonly-altered metabolic pathways shared by both intestinal microbiota and serum metabolome of the IVDD rats. DHJSD inhibited the degenerative process and restored the compositions of the perturbed gut microbiota, particularly the relative abundance of commensal microbes of the Prevotellaceae family. DHJSD also corrected the altered metabolic pathways involved in the metabolism of glycine, serine, threonine, valine, the citric acid cycle, and biosynthesis of leucine and isoleucine. DHJSD inhibited the disc degeneration process by an integrated metagenomic and metabonomic mechanism to restore the microbiome profile and normalize the metabonomic pathways.}, } @article {pmid39417646, year = {2024}, author = {Wang, Q and Geng, L and Gao, Z and Sun, Y and Li, X and Sun, S and Luo, Y}, title = {Microalgae Enhances the Adaptability of Epiphytic Bacteria to Sulfamethoxazole Stress and Proliferation of Antibiotic Resistance Genes Mediated by Integron.}, journal = {Environmental science & technology}, volume = {58}, number = {43}, pages = {19397-19407}, doi = {10.1021/acs.est.4c04925}, pmid = {39417646}, issn = {1520-5851}, mesh = {*Microalgae/drug effects ; *Sulfamethoxazole/pharmacology ; *Drug Resistance, Microbial/genetics ; *Bacteria/drug effects/genetics/metabolism ; Integrons ; Anti-Bacterial Agents/pharmacology ; }, abstract = {The transmission of ARGs in the microalgae-associated epiphytic bacteria remains unclear under antibiotic exposure, apart from altering the microbial community structure. In this study, Chlorella vulgaris cocultured with bacteria screened from surface water was examined to explore the spread of ARGs in the presence of sulfamethoxazole (SMX). The extracellular polymers released by Chlorella vulgaris could reduce antibiotic-induced collateral damage to bacteria, thus increasing the diversity of the microalgae-associated epiphytic bacteria. The abundances of sul1 and intI1 in the phycosphere at 1 mg/L SMX dose increased by 290 and 28 times, respectively. Metagenomic sequencing further confirmed that SMX bioaccumulation stimulated the horizontal transfer of sul1 mediated by intI1 in the microalgae-associated epiphytic bacteria, while reactive oxygen species (ROS)-mediated oxidative stress induced the SOS response and thus enhanced the transformation of sul1 in the J group. This is the first study to verify that microalgae protect bacteria from antibiotic damage and hinder the spread of ARGs mediated by SOS response, while the transfer of ARGs mediated by integron is promoted due to the bioaccumulation of SMX in the phycosphere. The results contribute to present comprehensive understanding of the risk of ARG proliferation by the presence of emerging contaminants residues in river.}, } @article {pmid39417540, year = {2024}, author = {Ginatt, AA and Berihu, M and Castel, E and Medina, S and Carmi, G and Faigenboim-Doron, A and Sharon, I and Tal, O and Droby, S and Somera, T and Mazzola, M and Eizenberg, H and Freilich, S}, title = {A metabolic modeling-based framework for predicting trophic dependencies in native rhizobiomes of crop plants.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, pmid = {39417540}, issn = {2050-084X}, support = {US-5390-21//United States-Israel Binational Agricultural Research and Development Fund/ ; }, mesh = {*Rhizosphere ; *Malus/microbiology/metabolism ; *Microbiota ; Plant Roots/microbiology/metabolism ; Soil Microbiology ; Bacteria/metabolism/genetics/classification ; Crops, Agricultural/microbiology ; Metabolomics/methods ; Models, Biological ; }, abstract = {The exchange of metabolites (i.e., metabolic interactions) between bacteria in the rhizosphere determines various plant-associated functions. Systematically understanding the metabolic interactions in the rhizosphere, as well as in other types of microbial communities, would open the door to the optimization of specific predefined functions of interest, and therefore to the harnessing of the functionality of various types of microbiomes. However, mechanistic knowledge regarding the gathering and interpretation of these interactions is limited. Here, we present a framework utilizing genomics and constraint-based modeling approaches, aiming to interpret the hierarchical trophic interactions in the soil environment. 243 genome scale metabolic models of bacteria associated with a specific disease-suppressive vs disease-conducive apple rhizospheres were drafted based on genome-resolved metagenomes, comprising an in silico native microbial community. Iteratively simulating microbial community members' growth in a metabolomics-based apple root-like environment produced novel data on potential trophic successions, used to form a network of communal trophic dependencies. Network-based analyses have characterized interactions associated with beneficial vs non-beneficial microbiome functioning, pinpointing specific compounds and microbial species as potential disease supporting and suppressing agents. This framework provides a means for capturing trophic interactions and formulating a range of testable hypotheses regarding the metabolic capabilities of microbial communities within their natural environment. Essentially, it can be applied to different environments and biological landscapes, elucidating the conditions for the targeted manipulation of various microbiomes, and the execution of countless predefined functions.}, } @article {pmid39417505, year = {2025}, author = {Kanehisa, M and Furumichi, M and Sato, Y and Matsuura, Y and Ishiguro-Watanabe, M}, title = {KEGG: biological systems database as a model of the real world.}, journal = {Nucleic acids research}, volume = {53}, number = {D1}, pages = {D672-D677}, pmid = {39417505}, issn = {1362-4962}, support = {JPMJND2203//NBDC Database Integration Coordination Program/ ; //Japan Science and Technology Agency/ ; }, mesh = {*Databases, Genetic ; Software ; Humans ; }, abstract = {KEGG (https://www.kegg.jp/) is a database resource for representation and analysis of biological systems. Pathway maps are the primary dataset in KEGG representing systemic functions of the cell and the organism in terms of molecular interaction and reaction networks. The KEGG Orthology (KO) system is a mechanism for linking genes and proteins to pathway maps and other molecular networks. Each KO is a generic gene identifier and each pathway map is created as a network of KO nodes. This architecture enables KEGG pathway mapping to uncover systemic features from KO assigned genomes and metagenomes. Additional roles of KOs include characterization of conserved genes and conserved units of genes in organism groups, which can be done by taxonomy mapping. A new tool has been developed for identifying conserved gene orders in chromosomes, in which gene orders are treated as sequences of KOs. Furthermore, a new dataset called VOG (virus ortholog group) is computationally generated from virus proteins and expanded to proteins of cellular organisms, allowing gene orders to be compared as VOG sequences as well. Together with these datasets and analysis tools, new types of pathway maps are being developed to present a global view of biological processes involving multiple organism groups.}, } @article {pmid39417302, year = {2024}, author = {Li, J and Fang, W and Li, C and Cui, M and Qian, L and Jiang, Z and Jiang, Y and Shi, L and Xie, X and Guo, H and Li, P and Dong, Y and Xiu, W and Wang, Y and Wang, Y}, title = {Dissimilatory Iodate-Reducing Microorganisms Contribute to the Enrichment of Iodine in Groundwater.}, journal = {Environmental science & technology}, volume = {58}, number = {43}, pages = {19255-19265}, doi = {10.1021/acs.est.4c04455}, pmid = {39417302}, issn = {1520-5851}, mesh = {*Groundwater/microbiology ; *Iodates/metabolism ; *Iodine/metabolism ; China ; }, abstract = {Iodate reduction by dissimilatory iodate-reducing microorganisms (DIRMs) plays a crucial role in the biogeochemical cycling of iodine on Earth. However, the occurrence and distribution of DIRMs in iodine-rich groundwater remain unclear. In this study, we isolated the dissimilatory iodate-reducing bacteriumAzonexus hydrophilusstrain NCP973 from a geogenic high-iodine groundwater of China for the first time. The analysis of genome, transcriptome, and heterologous expression revealed that strain NCP973 uses the dissimilatory iodate-reducing enzyme IdrABP1P2 to reduce dissolved or in situ sediment-bound iodate to iodide. The location of IdrABP1P2 in the conjugative plasmid of strain NCP973 implies that IdrABP1P2 could be spread by horizontal gene transfer and allow the recipient microorganisms to participate in the enrichment of iodide in aquifers. Based on the global iodine-rich groundwater metagenomes and genomes, the identification of idrA showed that phylogenetically diverse DIRMs are widely distributed not only in geogenic high-iodine groundwater of China but also in radionuclide-contaminated groundwater of USA as well as in subsurface cavern waters in Germany and Italy. Moreover, the abundance of idrA was found to be higher in groundwater with a relatively high iodine content. Collectively, these results suggest that terrestrial iodine-affected groundwater systems are another important habitat for DIRMs in addition to marine environments, and their activity in aquifers triggers the mobilization and enrichment of iodine in groundwater worldwide.}, } @article {pmid39417122, year = {2024}, author = {Atugonza, C and Muwonge, A and Najjuka, CF and Kateete, DP and Katagirya, E and Mwesigwa, S and Asiimwe, B}, title = {Early changes in the gut microbiome among HIV-infected Individuals in Uganda initiating daily TMP/SMX.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {39417122}, support = {D43 TW010319/TW/FIC NIH HHS/United States ; }, abstract = {Daily cotrimoxazole (TMP/SXT) prophylaxis is part of the HIV treatment package for all new HIV-infected individuals in Uganda. Although this treatment has shown reduced morbidity and mortality in HIV, it remains controversial due to its contribution to developing antibiotic-resistant bacteria. Moreover, the effects of daily use of a broad-spectrum antibiotic on the gut microbiome remain unknown. To study the early effects, we analysed shotgun metagenome sequence data from stool samples of five newly HIV-infected individuals initiating TMP/SXT prophylaxis longitudinally for the first 30 days of treatment. Using shotgun metagenomics sequencing, we generated both taxonomic and functional profiles from each patient and compared gut microbial changes Pre- TMP/SXT and post-TMP/SXT on Day 5, Day 14, and Day 30. Daily TMP/SXT prophylaxis resulted in a shift characterised by an enrichment of Prevetollea and Ruminococcus genera members and the depletion of Lactococcus and Bacteroides genera members. Furthermore, these microbial shifts were associated with changes in the functional profile revealed by a differential abundance of pathways of amino acid metabolism, carbohydrate metabolism, and nucleotide biosynthesis linked to members of the Bacteroidaceae and Enterobacteriaceae families. TMP/SXT daily prophylaxis in HIV-infected individuals is associated with dramatic changes in microbial composition and functional profiles; however, other factors such as Age, Gender, HIV clinical stage, and ART regiment are at play. Further investigation is needed to examine the implication of these shifts on clinical management and outcomes among HIV patients.}, } @article {pmid39417080, year = {2024}, author = {You, R and Yu, Y and Shen, M and Zhang, Y and Hong, J and Kang, Y}, title = {Applications of different forms of nitrogen fertilizers affect soil bacterial community but not core ARGs profile.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1447782}, pmid = {39417080}, issn = {1664-302X}, abstract = {The objective of this study was to investigate the impact of various chemical nitrogen fertilizers on the profile of antibiotic resistance genes (ARGs) in soil. A microcosm experiment was conducted with four treatments, including CK (control with no nitrogen), AN (ammonium nitrogen), NN (nitrate nitrogen), and ON (urea nitrogen), and the abundance of ARGs was assessed over a 30-day period using a metagenomic sequencing approach. The levels of core ARGs varied between 0.16 and 0.22 copies per cell across different treatments over time. The abundance of core ARGs in the ON treatment closely resembled that of the CK treatment, suggesting that environmentally friendly nitrogen fertilizers, particularly those in controlled release formulations, may be preferable. The core ARG abundance in the AN and NN treatments exhibited noticeable fluctuations over time. Overall, chemical nitrogen fertilizers had minimal effects on the core ARG profile as determined by principal component analysis and clustering analyses. Conversely, distinct and significant changes in bacterial communities were observed with the use of different nitrogen fertilizers. However, the influence of nitrogen fertilizers on the core ARGs is limited due to the unaffected potential bacterial hosts. Nitrogen-cycling-related genes (NCRGs), such as those involved in nitrogen-fixing (nifK, nifD, nifH) and denitrification (narG, napA, nirK, norB, nosZ) processes, exhibit a positive correlation with ARGs (rosA, mexF, bacA, vanS), indicating a potential risk of ARG proliferation during intense denitrification activities. This study indicates that the application of chemical nitrogen has a minimal effect on the abundance of ARGs in soil, thereby alleviating concerns regarding the potential accumulation of ARGs due to the use of chemical nitrogen fertilizers.}, } @article {pmid39416816, year = {2024}, author = {Shamim, U and Yadav, A and Maurya, R and Devi, P and Kumari, P and Kanika, and Khare, K and Tarai, B and Pandey, R}, title = {Functional metagenomics highlights varied infection states with dynamics of pathogens and antibiotic resistance in lower respiratory tract infections.}, journal = {Heliyon}, volume = {10}, number = {19}, pages = {e38380}, pmid = {39416816}, issn = {2405-8440}, abstract = {BACKGROUND: Antimicrobial resistance (AMR) amongst pathogenic bacterial species poses significant challenges in treating infections of the lower respiratory tract (LRT), leading to higher hospitalization and mortality rates.

METHODS: Bronchoalveolar lavage fluid (BALF) from 84 clinically adjudicated LRTI patients were subjected to respiratory pathogen ID/AMR (RPIP) enrichment and sequencing followed by Explify and CZID seq data analysis to identify potential LRTI pathogens and associated AMR genes. Patients were categorized as LRTI-WP (with pneumonia) and LRTI-WoP (without pneumonia).

FINDINGS: mNGS achieved 100 % pathogen detection compared to 73 % through clinician-used BioFire panel. Predominant pathogens included Acinetobacter baumannii, Klebsiella pneumoniae along with detection of Aspergillus versicolor and Herpes simplex virus. Double and polymicrobial infections were captured, involving non-respiratory pathogens like Rothia mucilaginosa, Escherichia coli, and Moraxella osloensis. AMR detection highlighted macrolide (MPH; ERM) and Sulfonamide (SUL) rich resistome in 60 % of patients followed by extended spectrum beta lactamase (OXA) and tetracycline (TET). LRTI-WP showed high abundance of A. baumannii, majorly associated with MPH whereas K. pneumoniae with beta-lactams was comparable in both groups. Differences in clinical severity may stem from non-respiratory pathogens, newly recognized via mNGS. CZID seq pipeline validated and revealed additional microbes and AMR genes in the cohort.

INTERPRETATION: The prevalence of common pathogens like A. baumannii and K. pneumoniae along with the non-respiratory pathogens identified by RPIP-Explify and CZID seq provided an understanding to evaluate the LRTI. mNGS is crucial for precise pathogen and antibiotic resistance detection, vital for combating antibiotic resistance.}, } @article {pmid39416140, year = {2024}, author = {Majernik, SN and Beaver, L and Bradley, PH}, title = {Small amounts of misassembly can have disproportionate effects on pangenome-based metagenomic analyses.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39416140}, issn = {2692-8205}, support = {R35 GM151155/GM/NIGMS NIH HHS/United States ; }, abstract = {UNLABELLED: Individual genes from microbiomes can drive host-level phenotypes. To help identify such candidate genes, several recent tools estimate microbial gene copy numbers directly from metagenomes. These tools rely on alignments to pangenomes, which in turn are derived from the set of all individual genomes from one species. While large-scale metagenomic assembly efforts have made pangenome estimates more complete, mixed communities can also introduce contamination into assemblies, and it is unknown how robust pangenome-based metagenomic analyses are to these errors. To gain insight into this problem, we re-analyzed a case-control study of the gut microbiome in cirrhosis, focusing on commensal Clostridia previously implicated in this disease. We tested for differentially prevalent genes in the Lachnospiraceae, then investigated which were likely to be contaminants using sequence similarity searches. Out of 86 differentially prevalent genes, we found that 33 (38%) were probably contaminants originating in taxa such as Veillonella and Haemophilus, unrelated genera that were independently correlated with disease status. Our results demonstrate that even small amounts of contamination in metagenome assemblies, below typical quality thresholds, can threaten to overwhelm gene-level metagenomic analyses. However, we also show that such contaminants can be accurately identified using a method based on gene-to-species correlation. After removing these contaminants, we observe that several flagellar motility gene clusters in the Lachnospira eligens pangenome are associated with cirrhosis status. We have integrated our analyses into an analysis and visualization pipeline, PanSweep, that can automatically identify cases where pangenome contamination may bias the results of gene-resolved analyses.

IMPORTANCE: Metagenome-assembled genomes, or MAGs, can be constructed without pure cultures of microbes. Large scale efforts to build MAGs have yielded more complete pangenomes (i.e., sets of all genes found in one species). Pangenomes allow us to measure strain variation in gene content, which can strongly affect phenotype. However, because MAGs come from mixed communities, they can contaminate pangenomes with unrelated DNA, and how much this impacts downstream analyses has not been studied. Using a metagenomic study of gut microbes in cirrhosis as our test case, we investigate how contamination affects analyses of microbial gene content. Surprisingly, even small, typical amounts of MAG contamination (<5%) result in disproportionately high levels of false positive associations (38%). Fortunately, we show that most contaminants can be automatically flagged, and provide a simple method for doing so. Furthermore, applying this method reveals a new association between cirrhosis and gut microbial motility.}, } @article {pmid39416120, year = {2024}, author = {Richardson, M and Zhao, S and Sheth, RU and Lin, L and Qu, Y and Lee, J and Moody, T and Ricaurte, D and Huang, Y and Velez-Cortes, F and Urtecho, G and Wang, HH}, title = {SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39416120}, issn = {2692-8205}, support = {P30 DK132710/DK/NIDDK NIH HHS/United States ; R21 AI146817/AI/NIAID NIH HHS/United States ; R01 DK118044/DK/NIDDK NIH HHS/United States ; R01 AI132403/AI/NIAID NIH HHS/United States ; R01 EB031935/EB/NIBIB NIH HHS/United States ; }, abstract = {The local arrangement of microbes can profoundly impact community assembly, function, and stability. To date, little is known about the spatial organization of the human gut microbiome. Here, we describe a high-throughput and streamlined method, dubbed SAMPL-seq, that samples microbial composition of micron-scale sub-communities with split-and-pool barcoding to capture spatial colocalization in a complex consortium. SAMPL-seq analysis of the gut microbiome of healthy humans identified bacterial taxa pairs that consistently co-occurred both over time and across multiple individuals. These colocalized microbes organize into spatially distinct groups or "spatial hubs" dominated by Bacteroideceae, Ruminococceae, and Lachnospiraceae families. From a dietary perturbation using inulin, we observed reversible spatial rearrangement of the gut microbiome, where specific taxa form new local partnerships. Spatial metagenomics using SAMPL-seq can unlock new insights to improve the study of microbial communities.}, } @article {pmid39416080, year = {2024}, author = {Wang, Q and Wang, BY and Williams, S and Xie, H}, title = {Diversity and characteristics of the oral microbiome influenced by race and ethnicity.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39416080}, issn = {2692-8205}, support = {OT2 OD032581/OD/NIH HHS/United States ; R16 GM149359/GM/NIGMS NIH HHS/United States ; U54 MD007586/MD/NIMHD NIH HHS/United States ; UG3 HG013248/HG/NHGRI NIH HHS/United States ; }, abstract = {Periodontitis disproportionately affects racial/ethnic populations. Besides social determinants contributing to disparities in periodontal health, variations of oral microbial communities may also be a key factor influencing oral immune responses. To characterize the oral microbiome from different racial/ethnic populations, we collected 161 dental plaque samples from African Americans (AAs), Caucasian Americans (CAs), and Hispanic Americans (HAs) with clinical gingival health or biofilm-induced gingivitis on an intact periodontium. Using metagenomic sequencing, we found significant difference in diversity and abundance of microbial taxa in the dental plaque samples from AA, CA, and HA groups and unique microbial species that can only be detected in a particular racial/ethnic group. Moreover, we revealed racial/ethnic associated variations in functional potential of the oral microbiome, showing that diversity and abundance of antibiotic resistant genes were greater in the oral microbiome of the AAs than those in CAs or HAs, and that the AAs exhibited higher levels of genes involving in modification of glycoconjugates, oligo- and polysaccharides. These findings indicate more complex and higher virulence potential oral microbiome in AA and HA populations, which likely contributes to higher prevalence of periodontitis in AAs and HAs.}, } @article {pmid39416003, year = {2024}, author = {Jacoby, C and Scorza, K and Ecker, L and McMillin, M and Ramaswamy, R and Sundararajan, A and Sidebottom, AM and Lin, H and Dufault-Thompson, K and Hall, B and Jiang, X and Light, SH}, title = {Gut Bacteria Metabolize Natural and Synthetic Steroid Hormones via the Reductive OsrABC Pathway.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39416003}, issn = {2692-8205}, support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; R35 GM146969/GM/NIGMS NIH HHS/United States ; }, abstract = {Steroid hormone metabolism by the gut microbiome has multiple implications for mammalian physiology, but the underlying mechanisms and broader significance of this activity remains largely unknown. Here, we isolate a novel human gut bacterium, Clostridium steroidoreducens [T] strain HCS.1, that reduces cortisol, progesterone, testosterone, and related steroid hormones to 3β,5β-tetrahydrosteroid products. Through transcriptomics and heterologous enzyme profiling, we identify and biochemically characterize the C. steroidoreducens OsrABC reductive steroid hormone pathway. OsrA is a 3-oxo-Δ[1]-steroid hormone reductase that selectively targets the Δ[1]-bond present in synthetic steroid hormones, including the anti-inflammatory corticosteroids prednisolone and dexamethasone. OsrB is a promiscuous 3-oxo-Δ[4]-steroid hormone reductase that converts steroid hormones to 5β-dihydrosteroid intermediates. OsrC is a 3-oxo-5β-steroid hormone oxidoreductase that reduces 5β-intermediates to 3β,5β-tetrahydro products. We find that osrA and osrB homologs predict steroid hormone reductase activity in diverse gut bacteria and are enriched in Crohn's disease fecal metagenomes. These studies thus identify the basis of reductive steroid hormone metabolism in the gut and establish a link between inflammatory disease and microbial enzymes that deplete anti-inflammatory corticosteroids.}, } @article {pmid39415203, year = {2024}, author = {Tong, X and Luo, D and Leung, MHY and Lee, JYY and Shen, Z and Jiang, W and Mason, CE and Lee, PKH}, title = {Diverse and specialized metabolic capabilities of microbes in oligotrophic built environments.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {198}, pmid = {39415203}, issn = {2049-2618}, support = {BK20230230//Jiangsu Science and Technology Programme/ ; 11214721//Hong Kong Research Grants Council, General Research Fund/ ; R1016-20F//Hong Kong Research Grants Council, Research Impact Fund/ ; }, mesh = {Humans ; Hong Kong ; *Microbiota ; *Built Environment ; *Metagenome ; *Phylogeny ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Skin/microbiology ; Micrococcus luteus/genetics/metabolism ; Genome, Bacterial ; }, abstract = {BACKGROUND: Built environments (BEs) are typically considered to be oligotrophic and harsh environments for microbial communities under normal, non-damp conditions. However, the metabolic functions of microbial inhabitants in BEs remain poorly understood. This study aimed to shed light on the functional capabilities of microbes in BEs by analyzing 860 representative metagenome-assembled genomes (rMAGs) reconstructed from 738 samples collected from BEs across the city of Hong Kong and from the skin surfaces of human occupants. The study specifically focused on the metabolic functions of rMAGs that are either phylogenetically novel or prevalent in BEs.

RESULTS: The diversity and composition of BE microbiomes were primarily shaped by the sample type, with Micrococcus luteus and Cutibacterium acnes being prevalent. The metabolic functions of rMAGs varied significantly based on taxonomy, even at the strain level. A novel strain affiliated with the Candidatus class Xenobia in the Candidatus phylum Eremiobacterota and two novel strains affiliated with the superphylum Patescibacteria exhibited unique functions compared with their close relatives, potentially aiding their survival in BEs and on human skins. The novel strains in the class Xenobia possessed genes for transporting nitrate and nitrite as nitrogen sources and nitrosative stress mitigation induced by nitric oxide during denitrification. The two novel Patescibacteria strains both possessed a broad array of genes for amino acid and trace element transport, while one of them carried genes for carotenoid and ubiquinone biosynthesis. The globally prevalent M. luteus in BEs displayed a large and open pangenome, with high infraspecific genomic diversity contributed by 11 conspecific strains recovered from BEs in a single geographic region. The versatile metabolic functions encoded in the large accessory genomes of M. luteus may contribute to its global ubiquity and specialization in BEs.

CONCLUSIONS: This study illustrates that the microbial inhabitants of BEs possess metabolic potentials that enable them to tolerate and counter different biotic and abiotic conditions. Additionally, these microbes can efficiently utilize various limited residual resources from occupant activities, potentially enhancing their survival and persistence within BEs. A better understanding of the metabolic functions of BE microbes will ultimately facilitate the development of strategies to create a healthy indoor microbiome. Video Abstract.}, } @article {pmid39414630, year = {2024}, author = {Córdoba-Agudelo, M and Arboleda-Rivera, JC and Borrego-Muñoz, DA and Ramírez-Cuartas, CA and Pérez-Jaramillo, JE}, title = {Key Chemical Soil Parameters for the Assembly of Rhizosphere Bacteria Associated with Avocado Cv Hass Grafted on Landrace Rootstocks.}, journal = {Current microbiology}, volume = {81}, number = {12}, pages = {412}, pmid = {39414630}, issn = {1432-0991}, mesh = {*Persea/microbiology ; *Rhizosphere ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Soil/chemistry ; *Microbiota ; *RNA, Ribosomal, 16S/genetics ; *Plant Roots/microbiology ; Colombia ; Phylogeny ; }, abstract = {Avocado cultivation holds significant economic importance in many countries, ranking Colombia as the fifth largest global producer. Particularly, the Hass cultivar plays a pivotal role in Colombia's avocado industry, especially in the Department of Antioquia, the primary export region. This cultivar is grown under diverse soil and climate conditions and exhibits considerable genetic polymorphism due to the hybridization of varieties of agronomic significance, leading to a diverse array of landrace rootstocks. However, the role of soil conditions and rootstock genotype in structuring rhizosphere bacterial communities is still lacking. In addressing this knowledge gap, we investigated the influence of two soil conditions on the structure of rhizosphere bacterial communities associated with two landrace genotypes of Persea americana cv. Hass, utilizing 16S rRNA sequencing. Notably, no significant differences related to genotypes were observed. This study reports that the rhizosphere bacterial microbiome remains consistent across avocado landrace rootstocks, while variations in key parameters such as phosphorus, pH, Mg, and Ca drive distinct rhizosphere effects. Our results reveal that despite the soils having similar management, increases in these crucial parameters can lead to bacterial communities with lower alpha diversity and a more complex co-occurrence network. In addition, we found substantial variations in beta diversity, bacterial composition, and metagenome predictions between the two farms, underscoring the role of soil variables in shaping the bacterial microbiome. These findings provide valuable insights into the factors influencing the bacterial communities that may play a role in the health and productivity of crops with agro-industrial potential, such as Hass avocado.}, } @article {pmid39414169, year = {2024}, author = {Zhang, B and Zhang, N and Sui, H and Xue, R and Qiao, S}, title = {Unique ecology of biofilms and flocs: Bacterial composition, assembly, interaction, and nitrogen metabolism within deteriorated bioreactor inoculated with mature partial nitrification-anammox sludge.}, journal = {Bioresource technology}, volume = {414}, number = {}, pages = {131643}, doi = {10.1016/j.biortech.2024.131643}, pmid = {39414169}, issn = {1873-2976}, mesh = {*Biofilms ; *Bioreactors/microbiology ; *Nitrification ; *Sewage/microbiology ; *Nitrogen/metabolism ; *Bacteria/metabolism ; RNA, Ribosomal, 16S/genetics ; }, abstract = {This work unraveled discrepant ecological patterns between biofilms and flocs in a deteriorated bioreactor inoculated with mature partial nitrification-anammox (PN/A) sludge. Based on 16S rRNA analysis, a comprehensive evaluation of neutral and null models, along with niche width, delineated that the bacterial community assembly in biofilms and flocs was dominantly driven by the stochastic process, and dispersal limitation critically shaped the community assembly. Co-occurrence network analysis revealed that environmental stress caused decentralized and fragmented bacterial colonies, and anammox bacteria were mainly peripheral in biofilms network and less involved in interspecific interactions. Simultaneous PN/A and partial denitrification-anammox (PD/A) processes were identified, whereas PN and PD process primarily occurred in the biofilms and flocs, respectively, as evidenced by metagenomics. Collectively, these outcomes are expected to deepen the basic understanding of complex microbial community and nitrogen metabolism under environmental disturbance, thereby better characterizing and serving the artificial ecosystems.}, } @article {pmid39414063, year = {2024}, author = {Yu, Y and Li, Y and Sun, B and Cui, J and Liu, H and Sun, Y and Xu, Q and Boisse, N and Voelker, F and Matioszek, D and Favero, C and Kieffer, J and Li, Y and Lu, J and Li, H and Bao, M}, title = {Characterization and degradation mechanism of a newly isolated hydrolyzed polyacrylamide-degrading bacterium Alcaligenes faecalis EPDB-5 from the oilfield sludge.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {363}, number = {Pt 1}, pages = {125124}, doi = {10.1016/j.envpol.2024.125124}, pmid = {39414063}, issn = {1873-6424}, mesh = {*Biodegradation, Environmental ; *Alcaligenes faecalis/metabolism/genetics ; *Sewage/microbiology ; *Acrylic Resins/chemistry ; Oil and Gas Fields/microbiology ; Biofilms ; Waste Disposal, Fluid/methods ; Hydrolysis ; Water Pollutants, Chemical/metabolism ; Nitrogen/metabolism ; }, abstract = {Hydrolyzed polyacrylamide (HPAM) is posing serious threats to ecosystems. However, biodegradation is an effective method to remove HPAM owing to its low cost and environmental friendliness. In this study, Alcaligenes faecalis EPDB-5 was isolated as a highly efficient HPAM degrading strain from sludge contaminated with polymerized produced water from Daqing oilfield. Under the optimal conditions, the strain EPDB-5 demonstrated an impressive HPAM degradation rate of 86.05%, the total nitrogen (TN) removal of 71.96% and chemical oxygen demand (COD) removal of 67.98%. Meanwhile, it can maintain a stable degradation rate higher than 75% under different pH and temperature conditions. 27 genes that play a key role in HPAM degradation were annotated by metagenomics sequencing. The key genes were involved in multiple KEGG pathways, including biofilm formation, biosynthesis secondary metabolites, and metabolic pathways. SEM, GPC, and FTIR analyses revealed that the structure of HPAM after biodegradation showed pores, a significant decrease in molecular weight, -NH2 detachment, and carbon chain breakage. Particularly, we propose a possible mechanism of biofilm formation - HPAM degradation - biofilm disappearance and reorganization. Moreover, the degradation rate of strain EPDB-5 on real wastewater containing HPAM was 29.97% in only three days. This work expands our knowledge boundary about the HPAM degradation mechanism at the functional gene level, and supports the potential of strain EPDB-5 as a novel auxiliary microbial resource for the practical application of HPAM.}, } @article {pmid39413681, year = {2025}, author = {Wu, X and Qin, L and Song, M and Zhang, C and Guo, J and Yang, Z and Gao, Z and Qiu, M}, title = {Metagenomics combined with untargeted metabolomics to study the mechanism of miRNA-150-5p on SiO2 -induced acute lung injury.}, journal = {Journal of pharmaceutical and biomedical analysis}, volume = {252}, number = {}, pages = {116515}, doi = {10.1016/j.jpba.2024.116515}, pmid = {39413681}, issn = {1873-264X}, mesh = {Animals ; *Acute Lung Injury/chemically induced/metabolism ; Mice ; *Metabolomics/methods ; *Metagenomics/methods ; *MicroRNAs ; *Silicon Dioxide ; *Gastrointestinal Microbiome/drug effects ; Male ; Disease Models, Animal ; }, abstract = {Acute lung injury is a significant global health issue, and its treatment is becoming a hot topic of the researchers. To investigate the feasibility of miRNA-150-5p tail vein injection in the treatment of SiO2-induced acute lung injury through the regulation of gut microbiota and serum metabolites based on multiomics technology. Twenty-four mice were randomly divided into the control, SiO2 and miRNA-150-5p intervention groups. The SiO2 and miRNA-150-5p intervention groups received a single intranasal dose of 100 µL 4 % SiO2 suspension. Meanwhile, the miRNA-150-5p intervention group was administered with two tail vein injections of miRNA-150-5p (15 nmol each per mouse) on the day of successful modelling and on the third day post modelling. Metagenomics and metabolomics techniques were used to measure gut microbiota and serum metabolites, respectively. Tail vein injection of miRNA-150-5p improved SiO2-induced acute lung injury and reduced the secretion of inflammatory factors interleukin (IL)-6, tumour necrosis factor-α and IL-1β. These conditions altered the structure of gut microbiota, which resulted in the notable modulation of eight species at the species level. In addition, tail vein injection of miRNA-150-5p considerably reduced the levels of substances, such as phosphatidylethanolamine, phosphatidylcholine and phosphatidylinositol, in the glycerophospholipid metabolism and glycosylphosphatidylinositol-anchor biosynthesis pathways. Tail vein injection of miRNA-150-5p can alleviate acute lung injury. Combined metagenomics and untargeted metabolomics revealed the miRNA-150-5p-mitigated SiO2-induced acute lung injury that occurred through the regulation of gut microbiota and serum metabolites.}, } @article {pmid39413245, year = {2024}, author = {Wang, L and Yin, Z and Yan, W and Hao, J and Tian, F and Shi, J}, title = {Nitrate-dependent antimony oxidase in an uncultured Symbiobacteriaceae member.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39413245}, issn = {1751-7370}, support = {2023YFC3710004//National Key Research and Development Program of China/ ; 22276206//National Natural Science Foundation of China/ ; }, mesh = {*Antimony/metabolism ; *Nitrates/metabolism ; *Oxidation-Reduction ; *Oxidoreductases/metabolism/genetics ; *RNA, Ribosomal, 16S/genetics ; Phylogeny ; Metagenomics ; Rhodopseudomonas/enzymology/genetics/metabolism ; Microbiota ; }, abstract = {Autotrophic antimony (Sb) oxidation coupled to nitrate reduction plays an important role in the transformation and detoxification of Sb. However, the specific oxidase involved in this process has yet to be identified. Herein, we enriched the microbiota capable of nitrate-dependent Sb(III) oxidation and identified a new Sb(III) oxidase in an uncultured member of Symbiobacteriaceae. Incubation experiments demonstrated that nitrate-dependent Sb(III) oxidation occurred in the microcosm supplemented with Sb(III) and nitrate. Both the 16S rRNA gene and metagenomic analyses indicated that a species within Symbiobacteriaceae played a crucial role in this process. Furthermore, carbon-13 isotope labeling with carbon dioxide-fixing Rhodopseudomonas palustris in combination with nanoscale secondary ion mass spectrometry revealed that a newly characterized oxidase from the dimethylsulfoxide reductase family, designated as NaoABC, was responsible for autotrophic Sb(III) oxidation coupled with nitrate reduction. The NaoABC complex functions in conjunction with the nitrate reductase NarGHI, forming a redox loop that transfers electrons from Sb(III) to nitrate, thereby generating the energy necessary for autotrophic growth. This research offers new insights into the understanding of how microbes link Sb and nitrogen biogeochemical cycles in the environment.}, } @article {pmid39413127, year = {2024}, author = {Balinandi, S and Mulei, S and Whitmer, S and Nyakarahuka, L and Cossaboom, CM and Shedroff, E and Morales-Betoulle, M and Krapiunaya, I and Tumusiime, A and Kyondo, J and Baluku, J and Namanya, D and Torach, CR and Mutesi, J and Kiconco, J and Pimundu, G and Muyigi, T and Rowland, J and Nsawotebba, A and Ssewanyana, I and Muwanguzi, D and Kadobera, D and Harris, JR and Ario, AR and Atek, K and Kyobe, HB and Nabadda, S and Kaleebu, P and Mwebesa, HG and Montgomery, JM and Shoemaker, TR and Lutwama, JJ and Klena, JD}, title = {Crimean-Congo hemorrhagic fever cases diagnosed during an outbreak of Sudan virus disease in Uganda, 2022-23.}, journal = {PLoS neglected tropical diseases}, volume = {18}, number = {10}, pages = {e0012595}, pmid = {39413127}, issn = {1935-2735}, mesh = {Humans ; Uganda/epidemiology ; *Hemorrhagic Fever, Crimean/epidemiology/diagnosis/virology ; *Disease Outbreaks ; Male ; *Hemorrhagic Fever Virus, Crimean-Congo/genetics/isolation & purification/classification ; Female ; Adult ; Middle Aged ; Adolescent ; Young Adult ; Child ; Child, Preschool ; Phylogeny ; }, abstract = {BACKGROUND: In September 2022, Uganda experienced an outbreak of Sudan virus disease (SVD), mainly in central Uganda. As a result of enhanced surveillance activities for Ebola disease, samples from several patients with suspected viral hemorrhagic fever (VHF) were sent to the VHF Program at Uganda Virus Research Institute (UVRI), Entebbe, Uganda, and identified with infections caused by other viral etiologies. Herein, we report the epidemiologic and laboratory findings of Crimean-Congo hemorrhagic fever (CCHF) cases that were detected during the SVD outbreak response.

METHODOLOGY: Whole blood samples from VHF suspected cases were tested for Sudan virus (SUDV) by real-time reverse transcription-polymerase chain reaction (RT-PCR); and if negative, were tested for CCHF virus (CCHFV) by RT-PCR. CCHFV genomic sequences generated by metagenomic next generation sequencing were analyzed to ascertain strain relationships.

PRINCIPAL FINDINGS: Between September 2022 and January 2023, a total of 2,626 samples were submitted for VHF testing at UVRI. Overall, 13 CCHF cases (including 7 deaths; case fatality rate of 53.8%), aged 4 to 60 years, were identified from 10 districts, including several districts affected by the SVD outbreak. Four cases were identified within the Ebola Treatment Unit (ETU) at Mubende Hospital. Most CCHF cases were males engaged in livestock farming or had exposure to wildlife (n = 8; 61.5%). Among confirmed cases, the most common clinical symptoms were hemorrhage (n = 12; 92.3%), fever (n = 11; 84.6%), anorexia (n = 10; 76.9%), fatigue (n = 9; 69.2%), abdominal pain (n = 9; 69.2%) and vomiting (n = 9; 69.2%). Sequencing analysis showed that the majority of identified CCHFV strains belonged to the Africa II clade previously identified in Uganda. Two samples, however, were identified with greater similarity to a CCHFV strain that was last reported in Uganda in 1958, suggesting possible reemergence.

CONCLUSIONS/SIGNIFICANCE: Identifying CCHFV from individuals initially suspected to be infected with SUDV emphasizes the need for comprehensive VHF testing during filovirus outbreak responses in VHF endemic countries. Without expanded testing, CCHFV-infected patients would have posed a risk to health care workers and others while receiving treatment after a negative filovirus diagnosis, thereby complicating response dynamics. Additionally, CCHFV-infected cases could acquire an Ebola infection while in the ETU, and upon release because of a negative Ebola virus result, have the potential to spread these infections in the community.}, } @article {pmid39411387, year = {2024}, author = {Zhao, J and Wang, C and Hu, J and Ma, R and Yu, B and Zhao, W and Wang, H and Gu, Y and Zhang, J}, title = {Integrated metagenomics and metabolomics analyses revealed biomarkers in β-casein A2A2-type cows.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1438717}, pmid = {39411387}, issn = {2297-1769}, abstract = {In Holstein cows, β-casein, one of the most critical proteins in milk, exists in two main genotypes, A1 and A2. Herein, 45 Holstein cows [categorized into three groups based on β-casein A1A1, A1A2, and A2A2 genotypes (N = 15)] with the same feeding management and litter size were enrolled to explore differences in rumen microflora and metabolites across various β-casein genotypes. Rumen fluids were collected for metagenomics and metabolomics analyses. Metabolomics and weighted gene co-expression network analysis (WGCNA) revealed that arachidonic acid (AA), adrenic acid (AdA), glycocholic acid (GCA), and taurocholic acid (TCA) were significantly and positively correlated with milk fat % in dairy cows (p < 0.05). Furthermore, macro-genomics and Spearman's correlation analysis revealed significant positive correlations (p < 0.05) between the characteristic flora (g_Acetobacter, g_Pseudoxanthomonas, g_Streptococcus, and g_Pediococcus) and the five characteristic metabolites in the rumen of A2A2 dairy cows. Moreover, functional enrichment analysis revealed more genes enriched to the TRP channel's inflammatory mediator-regulated pathway and the mTOR signaling pathway in A2A2 genotyped cows. Additionally, the regulatory effects of AA on bovine mammary epithelial cells (BMECs) were examined using CCK-8, EdU, and qRT-PCR assays, revealing that AA promoted triglyceride (TG) synthesis and upregulated the milk fat marker genes including SREBF1, ACSS2, AGPAT6, and FASN. Overall, we identified characteristic microorganisms and metabolites in A2A2 Holstein cows and established that AA could be a biomarker for higher milk fat %.}, } @article {pmid39411197, year = {2024}, author = {Baumann, KBL and Mazzoli, A and Salazar, G and Ruscheweyh, HJ and Müller, B and Niederdorfer, R and Sunagawa, S and Lever, MA and Lehmann, MF and Bürgmann, H}, title = {Metagenomic and -transcriptomic analyses of microbial nitrogen transformation potential, and gene expression in Swiss lake sediments.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae110}, pmid = {39411197}, issn = {2730-6151}, abstract = {The global nitrogen (N) cycle has been strongly altered by anthropogenic activities, including increased input of bioavailable N into aquatic ecosystems. Freshwater sediments are hotspots with regards to the turnover and elimination of fixed N, yet the environmental controls on the microbial pathways involved in benthic N removal are not fully understood. Here, we analyze the abundance and expression of microbial genes involved in N transformations using metagenomics and -transcriptomics across sediments of 12 Swiss lakes that differ in sedimentation rates and trophic regimes. Our results indicate that microbial N loss in these sediments is primarily driven by nitrification coupled to denitrification. N-transformation gene compositions indicated three groups of lakes: agriculture-influenced lakes characterized by rapid depletion of oxidants in the sediment porewater, pristine-alpine lakes with relatively deep sedimentary penetration of oxygen and nitrate, and large, deep lakes with intermediate porewater hydrochemical properties. Sedimentary organic matter (OM) characteristics showed the strongest correlations with the community structure of microbial N-cycling communities. Most transformation pathways were expressed, but expression deviated from gene abundance and did not correlate with benthic geochemistry. Cryptic N-cycling may maintain transcriptional activity even when substrate levels are below detection. Sediments of large, deep lakes generally showed lower in-situ N gene expression than agriculture-influenced lakes, and half of the pristine-alpine lakes. This implies that prolonged OM mineralization in the water column can lead to the suppression of benthic N gene expression.}, } @article {pmid39410870, year = {2024}, author = {Matsubara, K and Li, J and Enomoto, Y and Takahashi, T and Ma, M and Ninomiya, R and Kazami, D and Miura, K and Hirayama, K}, title = {Beneficial Role of Heat-Treated Lactobacillus sakei HS-1 on Growth Performance, Nutritional Status and Gut Microbiota in Weaned Piglets.}, journal = {Journal of animal physiology and animal nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1111/jpn.14056}, pmid = {39410870}, issn = {1439-0396}, support = {//The authors received no specific funding for this work./ ; }, abstract = {In the swine industry, there is a strong need to replace an antibiotic growth promoter (AGP) used as feed additives in weaned piglets to enhance nutrient utilization in their diets and improve growth performance. Lactobacillus sakei HS-1 strain is a microbial preparation isolated from pickles. The study aim is to investigate the effectiveness of heat-treated L. sakei HS-1 strain (HT-LS) as a growth promoter in weaned piglets compared to colistin (CS), a widely used AGP. Eighteen crossbred weaned piglets (Landrace × Yorkshire × Duroc) of 21 days (average body weight [BW]: 7.06 ± 0.59 kg) were divided into three groups: fed the control diet (CT group), fed a diet supplemented with 30 ppm colistin sulphate (CS group), fed a diet supplemented with HT-LS at a concentration of 2.0 × 10[5] cells/g (LS group) until 49 days. The results indicated that LS group exhibited significantly higher average daily gain (p < 0.05) and higher BW (p < 0.1) compared with CT group, even higher than CS group. CS group showed higher growth performance compared to CT group but the differences were not statistically significant. In addition, LS group had higher (p < 0.05) or tended to higher (p < 0.1) concentrations of several plasma amino acids than the other two groups at 35 and 49 days. Faecal acetate concentration was higher (p < 0.1) in LS group than in CT group at 35 days. Blood immunoglobulin G concentration in LS group was significantly lower (p < 0.05) than in CT group at 35 and 49 days, and blood immunoglobulin A tended to be lower (p < 0.1) at 35 days than in CT group. LS group showed an increased abundance of g_Prevotella 7, g_Streptococcus and g_Lactobacillus (linear discriminant analysis [LDA] score ≥ 2.0). Predictive metagenomic analysis revealed an enrichment of the mixed acid fermentation pathway (LDA score ≥ 2.0). Furthermore, several gut microbes exhibited correlations with plasma amino acids (p < 0.01) and short-chain fatty acids in faeces (p < 0.01). These findings demonstrate that HT-LS improves the growth performance of weaned piglets by enhancing the efficient utilization of nutrients through gut microbiota modification.}, } @article {pmid39410242, year = {2024}, author = {Wang, B and Wu, W and Wang, Z and Chen, Z and Wang, X}, title = {Soil-Mulching Treatment Enhances the Content of Stilbene in Grape Berries: A Transcriptomic and Metabolomic Analysis.}, journal = {Foods (Basel, Switzerland)}, volume = {13}, number = {19}, pages = {}, pmid = {39410242}, issn = {2304-8158}, support = {[CX(21)2027]//Jiangsu Agricultural Science and Technology Innovation Fund/ ; }, abstract = {Soil mulching is a useful agronomic practice that promotes early fruit maturation and affects fruit quality. However, the regulatory mechanism of fruit metabolites under soil-mulching treatments remains unknown. In this study, variations in the gene sets and metabolites of grape berries after mulching (rice straw + felt + plastic film) using transcriptome and metagenomic sequencing were investigated. The results of the cluster analysis and orthogonal projection to latent structures discriminant analysis of the metabolites showed a difference between the mulching and control groups, as did the principal component analysis results for the transcriptome. In total, 36 differentially expressed metabolites were identified, of which 10 (resveratrol, ampelopsin F, piceid, 3,4'-dihydroxy-5-methoxystilbene, ε-viniferin, trans resveratrol, epsilon-viniferin, 3'-hydroxypterostilbene, 1-methyl-resveratrol, and pterostil-bene) were stilbenes. Their content increased after mulching, indicating that stilbene synthase activity increased after mulching. The weighted gene co-expression network analysis revealed that the turquoise and blue modules were positively and negatively related to stilbene compounds. The network analysis identified two seed genes (VIT_09s0054g00610, VIT_13s0156g00260) and two transcription factors (VIT_13s0156g00260, VIT_02s0025g04590). Overall, soil mulching promoted the accumulation of stilbene compounds in grapes, and the results provided key genetic information for further studies.}, } @article {pmid39410228, year = {2024}, author = {Kim, S and Kang, JY and Nguyen, QA and Lee, JS}, title = {Effects of Prebiotic Dietary Fibers on the Stimulation of the Mucin Secretion in Host Cells by In Vitro Gut Microbiome Consortia.}, journal = {Foods (Basel, Switzerland)}, volume = {13}, number = {19}, pages = {}, pmid = {39410228}, issn = {2304-8158}, support = {NRF-2021R1A2C1005811//National Research Foundation of Korea/ ; NRF-2023K2A9A1A01098813, FY2023//National Research Foundation of Korea/ ; KRIBB Research Initiative Program grant (KGM5482423)//Korea Research Institute of Bioscience and Biotechnology/ ; }, abstract = {The gastrointestinal microbiota are important for human health. Dietary intake may modulate the composition and metabolic function of the gut microbiome. We examined how the breakdown of prebiotic dietary fibers by the gut microbiome affects mucin secretion by intestinal epithelial cells. Metagenomic analyses of in vitro gut microbiome consortia revealed taxonomic profiles and genetic diversity of carbohydrate-active enzymes that digest polysaccharides. Two independent consortia exhibited different abilities to produce acetic acid, propionic acid, and butyric acid via the fermentation of polysaccharides derived from dietary fibers of grains and mushrooms. Although acetic acid generally had the highest concentration, the ratios of butyric acid and propionic acid to acetic acid varied depending on the polysaccharide source. These short-chain fatty acids affected morphological differentiation and mucin secretion in HT-29 human intestinal epithelial cells. These results suggest that prebiotic dietary fibers can be digested and metabolized by the gut microbiome to short-chain fatty acids, which can affect gut epithelial cells both directly and indirectly via the modulation of the gut microbiota and their enzymes.}, } @article {pmid39410210, year = {2024}, author = {Liang, J and Yuan, H and Fei, Y and Wang, H and Qu, C and Bai, W and Liu, G}, title = {Effects of Saccharomyces cerevisiae and Cyberlindnera fabianii Inoculation on Rice-Flavor Baijiu Fermentation.}, journal = {Foods (Basel, Switzerland)}, volume = {13}, number = {19}, pages = {}, pmid = {39410210}, issn = {2304-8158}, support = {2021ZDJS005//the Research Capacity Enhancement Project of Key Disciplines in Guangdong Province/ ; 2023KJ101//Guangdong Provincial Agricultural Science and Technology Innovation and Extension Project in 2023/ ; 2021B1212040013//Guangdong Provincial Key Laboratory of Lingnan Specialty Food Science and Technology/ ; }, abstract = {Rice-flavor baijiu is a distilled Chinese spirit prepared from Xiaoqu culture. However, its dull taste may be a market limitation. In order to enhance the flavor profile of rice-flavor baijiu, two ester-producing yeast strains (Saccharomyces cerevisiae and Cyberlindnera fabianii) were inoculated for fermentation. At the end of the fermentation, the total alcohol and ester contents had also increased by 43.3% and 29.8%, respectively, and the number of ester species had increased by eight. Additionally, eleven flavor substances had significant contributions in the inoculated fermentation process, including several different esters and alcohols. A macrogenomic analysis revealed that the majority of the gene abundances associated with the alcohol, acid, and ester pathways were elevated by the third day of inoculated fermentation, and greater abundances of Saccharomyces cerevisiae, Cyberlindnera fabianii, Lichtheimia ramosa, Rhizopus delemar, and Rhizopus oryzaefive, annotated with these genes, were observed from either the pre-fermentation stage or post-fermentation stage. The results demonstrate that two added strains are associated with an increase in the content of the flavor substances. These findings may prove beneficial in enhancing the quality of rice-flavor baijiu through using inoculated fermentation with ester-producing yeast.}, } @article {pmid39410149, year = {2024}, author = {Liang, Z and Chen, S and Wang, H and Wu, Q and Guo, W and Ni, L and Lv, X}, title = {Metagenomic and Metabolomic Profiling Reveals the Differences of Flavor Quality between Hongqu Rice Wines Fermented with Gutian Qu and Wuyi Qu.}, journal = {Foods (Basel, Switzerland)}, volume = {13}, number = {19}, pages = {}, pmid = {39410149}, issn = {2304-8158}, support = {No. 32472296; No. 32472295; No. 32072204//National Natural Science Foundation of China/ ; }, abstract = {Jiuqu (starter) makes an important contribution to the formation of the flavor characteristics of Hongqu rice wine (HQW). Gutian Qu (GTQ) and Wuyi Qu (WYQ) are two kinds of Jiuqu commonly used in HQW brewing, but the comparison of the two kinds of HQW is still insufficient at present. The objective of this study was to compare the dynamic changes of amino acids (AAs), higher alcohols (HAs), bioamines (BAs), volatile flavor compounds (VFCs), and microbial communities in HQW fermentation, with GTQ and WYQ as starter. This study used an automatic amino acid analyzer, GC, HPLC, and GC-MS to detect AAs, HAs, Bas, and VFCs during fermentation; metagenomic sequencing technology was used to elucidate the microbial community and its functional characteristics. The results showed that the contents of AAs and HAs in HQW brewed with WYQ (WYW) were significantly higher than those in HQW brewed with GTQ (GTW). On the contrary, the majority of BAs in GTW were significantly higher than those in WYW. The composition of VFCs in WYW and GTW were obviously different, as most of the VFCs were notably enriched in WYW, while ethyl caproate, isoamyl acetate, ethyl heptanoate, ethyl nonanoate, 1-decanol, citronellol, phenethyl acetate, and hexanoic acid were more abundant in GTW. Burkholderia gladioli, Pantoea dispersa, Weissella cibaria, Monascus purpureus, and Saccharomyces cerevisiae were the predominant microbial populations in GTW brewing at the species level, while Sphingomonas sp., Kosakonia cowanii, Enterobacter asburiae, Leuconostoc lactis, Aspergillus niger, and Saccharomyces cerevisiae were the dominant microbial species in WYW brewing. The abundance of functional genes involved in BAs biosynthesis were much higher in GTW brewing, while the abundance of functional genes related to the metabolism of characteristic VFCs were much higher in WYW brewing. Collectively, these findings provided evidence for elucidating the effects of Jiuqu and microbial communities on HQW flavor quality, and laid a solid foundation for the improvement of HQW flavor quality.}, } @article {pmid39409842, year = {2024}, author = {Xie, M and Fei, D and Guang, Y and Xue, F and Xu, J and Zhou, Y}, title = {Role of Metabolomics and Metagenomics in the Replacement of the High-Concentrate Diet with a High-Fiber Diet for Growing Yushan Pigs.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {19}, pages = {}, pmid = {39409842}, issn = {2076-2615}, support = {2021BDH80013//the Science and Technology Cooperation Program of Jiangxi/ ; 20192ACB60004//the Jiangxi Key Research and Development Program/ ; 2024SSY04211//the safe quality of agricultural products key laboratory of Jiangxi Province/ ; }, abstract = {The objective of this study was to investigate the regulatory effects of a high-fiber content feed on the productive performance, meat quality, and fat acid composition. A total of 18 120-day-old Yushan pigs with similar initial body weight were randomly allotted into high-concentrate diet (high energy, HE) and high-fiber diet (low energy, LE) treatments for the determination of regulatory effects on productive performance, meat quality, and fatty acid content. Further, blood metabolomic, gut microbiota, and liver energy-related gene expression measurements were used to investigate the underlying mechanisms. Results showed that the LE treatment significantly increased ADFI while decreasing carcass weight, fat percentage, and IMF. Metabolomic results showed that the high-fiber treatment significantly down-regulated metabolites that participated in lipid metabolism such as cyclic ADP-ribose and hippuric acid, while up-regulated metabolites were mainly enriched in nitrogen metabolism such as DL-arginine and propionylcarnitine (p < 0.05). Microbial results showed relative abundances of Lactobacillus and Bifidobacterium are significantly proliferated in the high-fiber feeding treatments (p < 0.05). Transcriptomic results showed that genes mainly enriched into the lipid metabolism are significantly up-regulated under the high-fiber dietary treatment (p < 0.05). Conclusion: higher dietary fiber significantly reduced dietary energy provision, effectively decreased the backfat and abdominal fat content of Yushan pigs through proliferating intestinal fiber-degradable bacteria, and up-regulating the hepatic lipolysis-related gene expression.}, } @article {pmid39409167, year = {2024}, author = {Evseev, P and Gutnik, D and Evpak, A and Kasimova, A and Miroshnikov, K}, title = {Origin, Evolution and Diversity of φ29-like Phages-Review and Bioinformatic Analysis.}, journal = {International journal of molecular sciences}, volume = {25}, number = {19}, pages = {}, pmid = {39409167}, issn = {1422-0067}, mesh = {*Bacteriophages/genetics/classification ; *Computational Biology/methods ; *Genome, Viral ; Evolution, Molecular ; Phylogeny ; Archaea/virology/genetics ; Capsid Proteins/genetics ; }, abstract = {Phage φ29 and related bacteriophages are currently the smallest known tailed viruses infecting various representatives of both Gram-positive and Gram-negative bacteria. They are characterised by genomic content features and distinctive properties that are unique among known tailed phages; their characteristics include protein primer-driven replication and a packaging process characteristic of this group. Searches conducted using public genomic databases revealed in excess of 2000 entries, including bacteriophages, phage plasmids and sequences identified as being archaeal that share the characteristic features of phage φ29. An analysis of predicted proteins, however, indicated that the metagenomic sequences attributed as archaeal appear to be misclassified and belong to bacteriophages. An analysis of the translated polypeptides of major capsid proteins (MCPs) of φ29-related phages indicated the dissimilarity of MCP sequences to those of almost all other known Caudoviricetes groups and a possible distant relationship to MCPs of T7-like (Autographiviridae) phages. Sequence searches conducted using HMM revealed the relatedness between the main structural proteins of φ29-like phages and an unusual lactococcal phage, KSY1 (Chopinvirus KSY1), whose genome contains two genes of RNA polymerase that are similar to the RNA polymerases of phages of the Autographiviridae and Schitoviridae (N4-like) families. An analysis of the tail tube proteins of φ29-like phages indicated their dissimilarity of the lower collar protein to tail proteins of all other viral groups, but revealed its possible distant relatedness with proteins of toxin translocation complexes. The combination of the unique features and distinctive origin of φ29-related phages suggests the categorisation of this vast group in a new order or as a new taxon of a higher rank.}, } @article {pmid39409144, year = {2024}, author = {Donchev, D and Stoikov, I and Diukendjieva, A and Ivanov, IN}, title = {Assessment of Skimmed Milk Flocculation for Bacterial Enrichment from Water Samples, and Benchmarking of DNA Extraction and 16S rRNA Databases for Metagenomics.}, journal = {International journal of molecular sciences}, volume = {25}, number = {19}, pages = {}, pmid = {39409144}, issn = {1422-0067}, support = {BG05M2OP001-1.002-0001-C04//European Regional Development Fund through the Operational Program Science and Education for Smart Growth 2014-2020/ ; not applicable//Biocampus Sofia Association/ ; }, mesh = {*RNA, Ribosomal, 16S/genetics ; *Milk/microbiology ; *Metagenomics/methods ; Animals ; *DNA, Bacterial/genetics/isolation & purification ; *Bacteria/genetics/classification/isolation & purification ; Flocculation ; Microbiota/genetics ; Water Microbiology ; }, abstract = {Water samples for bacterial microbiome studies undergo biomass concentration, DNA extraction, and taxonomic identification steps. Through benchmarking, we studied the applicability of skimmed milk flocculation (SMF) for bacterial enrichment, an adapted in-house DNA extraction protocol, and six 16S rRNA databases (16S-DBs). Surface water samples from two rivers were treated with SMF and vacuum filtration (VF) and subjected to amplicon or shotgun metagenomics. A microbial community standard underwent five DNA extraction protocols, taxonomical identification with six different 16S-DBs, and evaluation by the Measurement Integrity Quotient (MIQ) score. In SMF samples, the skimmed milk was metabolized by members of lactic acid bacteria or genera such as Polaromonas, Macrococcus, and Agitococcus, resulting in increased relative abundance (p < 0.5) up to 5.0 log fold change compared to VF, rendering SMF inapplicable for bacterial microbiome studies. The best-performing DNA extraction protocols were FastSpin Soil, the in-house method, and EurX. All 16S-DBs yielded comparable MIQ scores within each DNA extraction kit, ranging from 61-66 (ZymoBIOMICs) up to 80-82 (FastSpin). DNA extraction kits exert more bias toward the composition than 16S-DBs. This benchmarking study provided valuable information to inform future water metagenomic study designs.}, } @article {pmid39409119, year = {2024}, author = {Xiang, J and Zhang, N and Li, J and Zhu, Y and Cao, T and Wang, Y}, title = {Unveiling the Hidden Responses: Metagenomic Insights into Dwarf Bamboo (Fargesia denudata) Rhizosphere under Drought and Nitrogen Challenges.}, journal = {International journal of molecular sciences}, volume = {25}, number = {19}, pages = {}, pmid = {39409119}, issn = {1422-0067}, support = {2019QZKK0303//the Second Tibetan Plateau Scientific Expedition and Research Program (STEP)/ ; 31470621//National Natural Science Foundation of China/ ; }, mesh = {*Rhizosphere ; *Nitrogen/metabolism ; *Droughts ; *Metagenomics/methods ; Soil Microbiology ; Metagenome ; Stress, Physiological/genetics ; Poaceae/genetics/microbiology ; Plant Roots/microbiology/genetics ; Soil/chemistry ; }, abstract = {Dwarf bamboo (Fargesia denudata) is a crucial food source for the giant pandas. With its shallow root system and rapid growth, dwarf bamboo is highly sensitive to drought stress and nitrogen deposition, both major concerns of global climate change affecting plant growth and rhizosphere environments. However, few reports address the response mechanisms of the dwarf bamboo rhizosphere environment to these two factors. Therefore, this study investigated the effects of drought stress and nitrogen deposition on the physicochemical properties and microbial community composition of the arrow bamboo rhizosphere soil, using metagenomic sequencing to analyze functional genes involved in carbon and nitrogen cycles. Both drought stress and nitrogen deposition significantly altered the soil nutrient content, but their combination had no significant impact on these indicators. Nitrogen deposition increased the relative abundance of the microbial functional gene nrfA, while decreasing the abundances of nirK, nosZ, norB, and nifH. Drought stress inhibited the functional genes of key microbial enzymes involved in starch and sucrose metabolism, but promoted those involved in galactose metabolism, inositol phosphate metabolism, and hemicellulose degradation. NO3[-]-N showed the highest correlation with N-cycling functional genes (p < 0.01). Total C and total N had the greatest impact on the relative abundance of key enzyme functional genes involved in carbon degradation. This research provides theoretical and technical references for the sustainable management and conservation of dwarf bamboo forests in giant panda habitats under global climate change.}, } @article {pmid39408280, year = {2024}, author = {Nguyen, SM and Tran, TDC and Tran, TM and Wang, C and Wu, J and Cai, Q and Ye, F and Shu, XO}, title = {Influence of Peanut Consumption on the Gut Microbiome: A Randomized Clinical Trial.}, journal = {Nutrients}, volume = {16}, number = {19}, pages = {}, pmid = {39408280}, issn = {2072-6643}, support = {N/A//The Peanut Institute/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Arachis ; Male ; Female ; *Feces/microbiology ; Adult ; Bacteria/classification/genetics ; Vietnam ; Diet ; Middle Aged ; }, abstract = {Background: Peanut consumption could impact cardiometabolic health through gut microbiota, a hypothesis that remains to be investigated. A randomized clinical trial in Vietnam evaluated whether peanut consumption alters gut microbiome communities. Methods: One hundred individuals were included and randomly assigned to the peanut intervention and control groups. A total of 51 participants were provided with and asked to consume 50 g of peanuts daily, while 49 controls maintained their usual dietary intake for 16 weeks. Stool samples were collected before and on the last day of the trial. After excluding 22 non-compliant participants and those who received antibiotic treatment, 35 participants from the intervention and 43 from the control were included in the analysis. Gut microbiota composition was measured by shotgun metagenomic sequencing. Associations of changes in gut microbial diversity with peanut intervention were evaluated via linear regression analysis. Linear mixed-effects models were used to analyze associations of composition, sub-community structure, and microbial metabolic pathways with peanut intervention. We also performed beta regression analysis to examine the impact of peanut intervention on the overall and individual stability of microbial taxa and metabolic pathways. All associations with false discovery rate (FDR)-corrected p-values of <0.1 were considered statistically significant. Results: No significant changes were found in α- and β-diversities and overall gut microbial stability after peanut intervention. However, the peanut intervention led to lower enrichment of five phyla, five classes, two orders, twenty-four metabolic pathways, and six species-level sub-communities, with a dominant representation of Bifidobacterium pseudocatenulatum, Escherichia coli D, Holdemanella biformis, Ruminococcus D bicirculans, Roseburia inulinivorans, and MGYG-HGUT-00200 (p < 0.05 and FDR < 0.1). The peanut intervention led to the short-term stability of several species, such as Faecalibacterium prausnitzii F and H, and a metabolic pathway involved in nitrate reduction V (p < 0.05; FDR < 0.1), known for their potential roles in human health, especially cardiovascular health. Conclusions: In summary, a 16-week peanut intervention led to significant changes in gut microbial composition, species-level sub-communities, and the short-term stability of several bacteria, but not overall gut microbial diversity and stability. Further research with a larger sample size and a longer intervention period is needed to confirm these findings and investigate the direct impact of gut-microbiome-mediated health effects of peanut consumption. Trial registration: The International Traditional Medicine Clinical Trial Registry (ITMCTR). Registration number: ITMCTR2024000050. Retrospectively Registered 24 April 2024.}, } @article {pmid39407862, year = {2024}, author = {Alavi, SMA and Petri, F and Mahmoud, OK and Igwilo-Alaneme, R and El Zein, S and Nassr, AN and Gori, A and Berbari, EF}, title = {Culture-Negative Native Vertebral Osteomyelitis: A Narrative Review of an Underdescribed Condition.}, journal = {Journal of clinical medicine}, volume = {13}, number = {19}, pages = {}, pmid = {39407862}, issn = {2077-0383}, abstract = {The incidence of culture-negative NVO (CN-NVO) cases is increasing, presenting significant diagnostic and therapeutic challenges due to the inability to isolate causative organisms with conventional microbiological methods. Factors influencing the diagnosis of CN-NVO include prior antimicrobial therapy, low pathogen burden, fastidious or intracellular organisms, technical issues, and non-infectious mimickers. Diagnosis often relies on imaging modalities like magnetic resonance imaging (MRI) and computed tomography (CT)-guided biopsy, though these methods can sometimes fail to yield positive microbiological results. Advanced diagnostic tools, such as polymerase chain reaction (PCR), metagenomic next-generation sequencing (mNGS), and cell-free DNA analysis, may be necessary to identify the pathogen. The causative pathogen cannot be isolated in some patients, among which an empirical antimicrobial therapy should be initiated. This narrative review discusses the management, monitoring, surgical indications, and outcomes for patients with CN-NVO.}, } @article {pmid39407853, year = {2024}, author = {Laryushina, Y and Samoilova-Bedych, N and Turgunova, L and Kozhakhmetov, S and Alina, A and Suieubayev, M and Mukhanbetzhanov, N}, title = {Alterations of the Gut Microbiome and TMAO Levels in Patients with Ulcerative Colitis.}, journal = {Journal of clinical medicine}, volume = {13}, number = {19}, pages = {}, pmid = {39407853}, issn = {2077-0383}, support = {AP14871959//Science Committee of the Ministry of Education and Science of the Republic of Kazakhstan/ ; }, abstract = {Background: Ulcerative colitis (UC) is an idiopathic and heterogeneous large intestine disease, characterized by chronic mucosa and submucosa inflammation. Alteration of the intestinal microbiome in UC may be responsible for modifications in metabolite production. Aim: To investigate the microbiota status and trimethylamine-N-oxide (TMAO) metabolite levels in patients with UC according to clinical and endoscopic activity. Methods: As part of a grant project AP14871959 from September 2022 to October 2023, 31 patients with UC and 15 healthy volunteers over 18 years at the Clinic of NCJSC "KMU" were assessed for blood TMAO level and metagenomic sequencing of fecal microbiome. Results: A significant depletion of the main representatives of Bacteroides, Parabacteroides, Prevotella; and an increase in the relative abundance of the genera Actinomyces, Klebsiella, Limosilactobacillus, Streptococcus, Escherichia-Shigella were detected in patients with UC. The number of p_Actinobacteria (g_Collinsella) and p_Eubacterium (g_Xylanophilum) representatives with genes encoding TMA-trimethylamine conversion is significantly reduced in UC patients. TMAO levels were significantly lower in UC patients than in healthy individuals (0.233 µmol/L, p = 0.004). TMAO decreased with disease severity and significantly differed between patients with different activities (p = 0.034). Conclusions: The composition of the intestinal microbiome changes and the level of TMAO decreases in patients with UC at different activities.}, } @article {pmid39407346, year = {2024}, author = {Barcenilla, C and Cobo-Díaz, JF and Puente, A and Valentino, V and De Filippis, F and Ercolini, D and Carlino, N and Pinto, F and Segata, N and Prieto, M and López, M and Alvarez-Ordóñez, A}, title = {In-depth characterization of food and environmental microbiomes across different meat processing plants.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {199}, pmid = {39407346}, issn = {2049-2618}, support = {BOCYL-D-07072020-6//Junta de Castilla y León and the European Social Fund/ ; PRE2021-098910//Ministerio de Ciencia e Innovación, Spain/ ; }, mesh = {*Microbiota ; *Food Microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Meat Products/microbiology ; *Food Handling ; Environmental Microbiology ; Meat/microbiology ; RNA, Ribosomal, 16S/genetics ; Animals ; Phylogeny ; }, abstract = {BACKGROUND: Processing environments can be an important source of pathogenic and spoilage microorganisms that cross contaminate meat and meat products. The aim of this study was to characterize the microbiome of raw materials, processing environments and end products from 19 facilities producing different meat products.

RESULTS: The taxonomic profiles of the microbial communities evolved along processing, from raw materials to end products, suggesting that food contact (FC) surfaces play an important role in modulating the microbiome of final products. Some species persisted with the highest relative abundance in raw materials, food processing environments and/or in the final product, including species from the genera Pseudomonas, Staphylococcus, Brochothrix, Acinetobacter and Psychrobacter. Processing environments showed a very diverse core microbiota, partially shared with the products. Pseudomonas fragi and Pseudomonas sp. Lz4W (in all sample and facility types) and Brochothrix thermosphacta, Psychrobacter sp. and Psychrobacter sp. P11F6 (in raw materials, FC surfaces and end products) were prominent members of the core microbiota for all facilities, while Latilactobacillus sakei was found as a dominant species exclusively in end products from the facilities producing fermented sausages. Processing environments showed a higher amount of antimicrobial resistance genes and virulence factors than raw materials and end products. One thousand four hundred twenty-one medium/high-quality metagenome-assembled genomes (MAGs) were reconstructed. Of these, 274 high-quality MAGs (completeness > 90%) corresponded to 210 putative new species, mostly found in processing environments. For two relevant taxa in meat curing and fermentation processes (S. equorum and L. sakei, respectively), phylogenetic variation was observed associated with the specific processing facility under study, which suggests that specific strains of these taxa may be selected in different meat processing plants, likely contributing to the peculiar sensorial traits of the end products produced in them.

CONCLUSIONS: Overall, our findings provide the most detailed metagenomics-based perspective up to now of the microbes that thrive in meat, meat products and associated environments and open avenues for future research activities to better understand the microbiome functionality and potential contribution to meat quality and safety. Video Abstract.}, } @article {pmid39407345, year = {2024}, author = {Salgado, JFM and Hervé, V and Vera, MAG and Tokuda, G and Brune, A}, title = {Unveiling lignocellulolytic potential: a genomic exploration of bacterial lineages within the termite gut.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {201}, pmid = {39407345}, issn = {2049-2618}, mesh = {Animals ; *Isoptera/microbiology ; *Lignin/metabolism ; *Gastrointestinal Microbiome ; Phylogeny ; Bacteria/genetics/classification/isolation & purification/enzymology ; Metagenome ; Polysaccharides/metabolism ; Genome, Bacterial ; Genomics ; Cellulose/metabolism ; }, abstract = {BACKGROUND: The microbial landscape within termite guts varies across termite families. The gut microbiota of lower termites (LT) is dominated by cellulolytic flagellates that sequester wood particles in their digestive vacuoles, whereas in the flagellate-free higher termites (HT), cellulolytic activity has been attributed to fiber-associated bacteria. However, little is known about the role of individual lineages in fiber digestion, particularly in LT.

RESULTS: We investigated the lignocellulolytic potential of 2223 metagenome-assembled genomes (MAGs) recovered from the gut metagenomes of 51 termite species. In the flagellate-dependent LT, cellulolytic enzymes are restricted to MAGs of Bacteroidota (Dysgonomonadaceae, Tannerellaceae, Bacteroidaceae, Azobacteroidaceae) and Spirochaetota (Breznakiellaceae) and reflect a specialization on cellodextrins, whereas their hemicellulolytic arsenal features activities on xylans and diverse heteropolymers. By contrast, the MAGs derived from flagellate-free HT possess a comprehensive arsenal of exo- and endoglucanases that resembles that of termite gut flagellates, underlining that Fibrobacterota and Spirochaetota occupy the cellulolytic niche that became vacant after the loss of the flagellates. Furthermore, we detected directly or indirectly oxygen-dependent enzymes that oxidize cellulose or modify lignin in MAGs of Pseudomonadota (Burkholderiales, Pseudomonadales) and Actinomycetota (Actinomycetales, Mycobacteriales), representing lineages located at the hindgut wall.

CONCLUSIONS: The results of this study refine our concept of symbiotic digestion of lignocellulose in termite guts, emphasizing the differential roles of specific bacterial lineages in both flagellate-dependent and flagellate-independent breakdown of cellulose and hemicelluloses, as well as a so far unappreciated role of oxygen in the depolymerization of plant fiber and lignin in the microoxic periphery during gut passage in HT. Video Abstract.}, } @article {pmid39407340, year = {2024}, author = {Chemel, M and Peru, E and Binsarhan, M and Logares, R and Lartaud, F and Galand, PE}, title = {Cold-water coral mortality under ocean warming is associated with pathogenic bacteria.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {76}, pmid = {39407340}, issn = {2524-6372}, support = {ANR-20-CE02-0006//Agence Nationale de la Recherche/ ; ANR-20-CE02-0006//Agence Nationale de la Recherche/ ; }, abstract = {Cold-water corals form vast reefs that are highly valuable habitats for diverse deep-sea communities. However, as the deep ocean is warming, it is essential to assess the resilience of cold-water corals to future conditions. The effects of elevated temperatures on the cold-water coral Lophelia pertusa (now named Desmophyllum pertusum) from the north-east Atlantic Ocean were experimentally investigated at the holobiont level, the coral host, and its microbiome. We show that at temperature increases of + 3 and + 5 °C, L. pertusa exhibits significant mortality concomitant with changes in its microbiome composition. In addition, a metagenomic approach revealed the presence of gene markers for bacterial virulence factors suggesting that coral death was due to infection by pathogenic bacteria. Interestingly, different coral colonies had different survival rates and, colony-specific microbiome signatures, indicating strong colony-specific variability in their response to warming waters. These results suggest that L. pertusa can only survive a long-term temperature increase of < 3 °C. Therefore, regional variations in deep-sea temperature increase should be considered in future estimates of the global distribution of cold-water corals.}, } @article {pmid39407289, year = {2024}, author = {Natasha, A and Pye, SE and Cho, SH and Pangestu, HS and Park, J and Park, K and Prayitno, SP and Kim, B and Lee, JS and Kim, J and Budhathoki, S and Oh, Y and Song, JW and López, CB and Suh, JG and Kim, WK}, title = {Molecular detection and genomic characterization of Samak Micromys paramyxovirus-1 and -2 in Micromys minutus, Republic of Korea.}, journal = {Virology journal}, volume = {21}, number = {1}, pages = {255}, pmid = {39407289}, issn = {1743-422X}, support = {20210466//Korea Institute of Marine Science and Technology promotion/ ; 20210466//Korea Institute of Marine Science and Technology promotion/ ; 20210466//Korea Institute of Marine Science and Technology promotion/ ; 20210466//Korea Institute of Marine Science and Technology promotion/ ; 20210466//Korea Institute of Marine Science and Technology promotion/ ; 20210466//Korea Institute of Marine Science and Technology promotion/ ; 20210466//Korea Institute of Marine Science and Technology promotion/ ; 20210466//Korea Institute of Marine Science and Technology promotion/ ; NF22SA0082041//Novo Nordisk Fonden/ ; NF22SA0082041//Novo Nordisk Fonden/ ; 2023R1A2C2006105//National Research Foundation of Korea/ ; 202300249142//National Research Foundation of Korea/ ; 2023R1A2C2006105//National Research Foundation of Korea/ ; 2023R1A2C2006105//National Research Foundation of Korea/ ; 202300249142//National Research Foundation of Korea/ ; IBS-R801-D9-A03//Institute for Basic Science/ ; IBS-R801-D9-A03//Institute for Basic Science/ ; IBS-R801-D9-A03//Institute for Basic Science/ ; HG23C1623//the Government-wide R&D to Advance Infectious Disease Prevention and Control, Republic of Korea/ ; }, mesh = {Animals ; *Phylogeny ; *Genome, Viral/genetics ; Republic of Korea ; *Paramyxoviridae/genetics/classification/isolation & purification ; Paramyxoviridae Infections/virology/veterinary/epidemiology ; Murinae/virology ; RNA, Viral/genetics ; Whole Genome Sequencing ; High-Throughput Nucleotide Sequencing ; Metagenomics ; }, abstract = {BACKGROUND: The discovery of viruses in small mammalian populations, particularly rodents, has expanded the family Paramyxoviridae. The overlap in habitats between rodents and humans increases the risk of zoonotic events, underscoring the importance of active surveillance. Rodent species, such as Apodemus agrarius, are natural hosts for Paramyxoviridae in the Republic of Korea (ROK). However, it is unknown whether Paramyxoviridae is present in Micromys minutus, another common rodent.

METHOD: Here, we screened M. minutus collected from the Gangwon Province in the ROK for paramyxoviruses using nested polymerase chain reaction and confirm positive samples by next-generation metagenomic sequencing. Complete paramyxovirus genomes were further characterized by phylogenetic analysis, amino acid similarity, secondary structure, and cophylogeny.

RESULT: Overall, 57 of 145 (39.3%) M. minutus kidney samples tested positive for paramyxoviruses. Among them, four whole genome sequences were identified and clustered within the genus Jeilongvirus. One sequence was determined as Samak Micromys paramyxovirus 1 (SMPV-1; 19,911 nucleotides long) and three sequences as Samak Micromys paramyxovirus 2 (SMPV-2; 18,199 nucleotides long). SMPV-1 has a smaller hydrophobic gene and a longer glycoprotein gene than SMPV-2. Cophylogenetic analysis suggests that SMPV-1 evolved through co-divergence, whereas SMPV-2 was inferred to have undergone transfer events.

CONCLUSION: These findings highlight the prevalence of paramyxoviruses in the wild and the potential of M. minutus as a natural viral reservoir. The discovery of SMPV-1 and SMPV - 2 also reveals the genetic diversity and evolutionary history of the genus Jeilongvirus in the Paramyxoviridae.}, } @article {pmid39406897, year = {2024}, author = {Westmeijer, G and van Dam, F and Kietäväinen, R and González-Rosales, C and Bertilsson, S and Drake, H and Dopson, M}, title = {Candidatus Desulforudis audaxviator dominates a 975 m deep groundwater community in central Sweden.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1332}, pmid = {39406897}, issn = {2399-3642}, support = {2018-04311//Vetenskapsrådet (Swedish Research Council)/ ; }, mesh = {*Groundwater/microbiology ; Sweden ; Microbiota/genetics ; Metagenome ; Phylogeny ; Deltaproteobacteria/genetics/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The continental bedrock contains groundwater-bearing fractures that are home to microbial populations that are vital in mediating the Earth's biogeochemical cycles. However, their diversity is poorly understood due to the difficulty of obtaining samples from this environment. Here, a groundwater-bearing fracture at 975 m depth was isolated by employing packers in order to characterize the microbial community via metagenomes combined with prokaryotic and eukaryotic marker genes (16S and 18S ribosomal RNA gene). Genome-resolved analyses revealed a community dominated by sulfate-reducing Bacillota, predominantly represented by Candidatus Desulforudis audaxviator and with Wood-Ljungdahl as the most prevalent pathway for inorganic carbon fixation. Moreover, the eukaryotic community had a considerable diversity and was comprised of mainly flatworms, chlorophytes, crustaceans, ochrophytes, and fungi. These findings support the important role of the Bacillota, with the sulfate reducer Candidatus Desulforudis audaxviator as its main representative, as primary producers in the often energy-limited groundwaters of the continental subsurface.}, } @article {pmid39406702, year = {2024}, author = {Wegner, H and Roitman, S and Kupczok, A and Braun, V and Woodhouse, JN and Grossart, HP and Zehner, S and Béjà, O and Frankenberg-Dinkel, N}, title = {Identification of Shemin pathway genes for tetrapyrrole biosynthesis in bacteriophage sequences from aquatic environments.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {8783}, pmid = {39406702}, issn = {2041-1723}, support = {FR1487/16-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 143/18//Israel Science Foundation (ISF)/ ; }, mesh = {*Tetrapyrroles/biosynthesis/metabolism ; *Bacteriophages/genetics/metabolism ; Escherichia coli/genetics/virology/metabolism ; 5-Aminolevulinate Synthetase/genetics/metabolism ; Amino Acid Sequence ; Heme/metabolism/biosynthesis ; Aminolevulinic Acid/metabolism ; Phylogeny ; Fresh Water/virology ; Biosynthetic Pathways/genetics ; }, abstract = {Tetrapyrroles such as heme, chlorophyll, and vitamin B12 are essential for various metabolic pathways. They derive from 5-aminolevulinic acid (5-ALA), which can be synthesized by a single enzyme (5-ALA synthase or AlaS, Shemin pathway) or by a two-enzyme pathway. The genomes of some bacteriophages from aquatic environments carry various tetrapyrrole biosynthesis genes. Here, we analyze available metagenomic datasets and identify alaS homologs (viral alaS, or valaS) in sequences corresponding to marine and freshwater phages. The genes are found individually or as part of complete or truncated three-gene loci encoding heme-catabolizing enzymes. Amino-acid sequence alignments and three-dimensional structure prediction support that the valaS sequences likely encode functional enzymes. Indeed, we demonstrate that is the case for a freshwater phage valaS sequence, as it can complement an Escherichia coli 5-ALA auxotroph, and an E. coli strain overexpressing the gene converts the typical AlaS substrates glycine and succinyl-CoA into 5-ALA. Thus, our work identifies valaS as an auxiliary metabolic gene in phage sequences from aquatic environments, further supporting the importance of tetrapyrrole metabolism in bacteriophage biology.}, } @article {pmid39406574, year = {2024}, author = {Steinberg, R and Moeller, A and Gisler, A and Mostacci, N and Hilty, M and Usemann, J}, title = {Longitudinal effects of elexacaftor/tezacaftor/ivacaftor on the oropharyngeal metagenome in adolescents with cystic fibrosis.}, journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jcf.2024.10.001}, pmid = {39406574}, issn = {1873-5010}, abstract = {BACKGROUND: Triple modulator therapy elexacaftor/tezacaftor/ivacaftor (ETI) improves lung function and impacts upon the respiratory microbiome in people with Cystic fibrosis (pwCF) with advanced lung disease. However, adolescents with cystic fibrosis (CF) are less colonized with bacterial pathogens than adult pwCF but their microbiota already differs from healthy individuals. The aim of this study was to longitudinally analyze the impact of ETI on the respiratory metagenome in adolescents with predominantly mild CF lung disease.

METHODS: In this prospective observational study, we included pwCF aged 12-20 years with at least one F508del mutation, who collected oropharyngeal swabs before and after initiation of ETI therapy twice per week to biweekly over three months. We performed whole metagenome shotgun sequencing, followed by host DNA filtering and taxonomic profiling. We used linear and additive mixed effects models adjusted for known confounders and corrected for multiple testing to study longitudinal development of the microbiome. We analyzed bacterial diversity, abundance, and strain-level phylogeny.

RESULTS: We analyzed the metagenomic data of 297 swabs of 20 pwCF. Microbiome composition changed after initiation of ETI therapy. We observed a slight diversification of the microbiome over time (Inv Simpson, Coef 0.085, 95 %CI 0.003, 0.17, p = 0.04). Strain-level analysis and clustering showed that strain retention of the most frequent bacterial species is predominant even during ETI therapy.

CONCLUSIONS: During three months of ETI therapy, commensal bacteria increased, which may help to prevent overgrowth of bacterial pathogens.}, } @article {pmid39406541, year = {2024}, author = {Liu, ZB and Zhang, F and Liang, CY and Chen, WH and Wang, YM and Cui, XJ and Zhao, L and Cao, B}, title = {[Clinical characteristics of 29 cases of pulmonary mucormycosis treated with and without surgery].}, journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases}, volume = {47}, number = {10}, pages = {946-954}, doi = {10.3760/cma.j.cn112147-20240426-00223}, pmid = {39406541}, issn = {1001-0939}, support = {ZRJY2023-GG13//China-Japan Friendship Hospital "Elite Plan" Talents Training Project/ ; }, mesh = {Humans ; Male ; *Mucormycosis/diagnosis/therapy ; Female ; Middle Aged ; Retrospective Studies ; Aged ; *Lung Diseases, Fungal/diagnosis/drug therapy/microbiology ; Antifungal Agents/therapeutic use ; }, abstract = {Objective: To analyze the clinical characteristics of patients with pulmonary mucormycosis treated with and without surgery. Methods: This was a single-center, retrospective study. We retrieved "pulmonary mucormycosis" from the electronic medical records of China-Japan Friendship Hospital between 2016 and 2022. A total of 29 patients with pulmonary mucormycosis were collected. There were 19 males and 10 females with a median age of 49 (47, 67) years. Mann-Whitney U test, χ[2] test, Kaplan-Meier curve and log-rank test were used to compare the differences between groups. Results: The most common underlying disease was diabetes (19, 65.5%). The most frequent imaging findings were consolidation (25, 86.2%) and nodule or mass (21, 72.4%). Bronchial stenosis (16, 55.2%), obstruction by fungal plugs (18, 62.1%), pseudomembranous necrotizing bronchitis (19, 65.5%) were common. Treatment strategies were developed by the multi-disciplinary team (MDT). Among 16 patients who did not undergo surgery, 10 had bilateral multifocal lesions and 6 had unifocal lesions. All patients received antifungal therapies, and surgeries were performed in 13 (44.8%) patients. Patients who underwent surgery had numerically lower in-hospital mortality (15.4% vs. 31.3%, P=0.410). Involvement of unilateral multiple lesions was more common in patients who underwent surgeries (6/13 vs. 1/16, P=0.019). Patients who underwent surgery were more likely to have lobar and segmental bronchial involvement (13/13 vs. 9/16, P=0.007). A total of 15 patients underwent mNGS, 14 (93.3%) had positive results. Performing metagenomic next generation sequencing for diagnosis shortened the time from disease onset to diagnosis (log-rank P=0.014). Conclusion: Metagenomic next-generation sequencing aided early diagnosis. The patients who underwent surgery included unilateral multiple lesions and visualisation of endobronchial abnormalities on lobar or segmental bronchus in unilateral lung.}, } @article {pmid39406503, year = {2024}, author = {Valentin-Alvarado, LE and Shi, LD and Appler, KE and Crits-Christoph, A and De Anda, V and Adler, BA and Cui, ML and Ly, L and Leão, P and Roberts, RJ and Sachdeva, R and Baker, BJ and Savage, DF and Banfield, JF}, title = {Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements.}, journal = {Genome research}, volume = {34}, number = {10}, pages = {1595-1609}, pmid = {39406503}, issn = {1549-5469}, mesh = {*Genome, Archaeal ; *Interspersed Repetitive Sequences ; *Archaea/genetics ; Plasmids/genetics ; Phylogeny ; Metagenomics/methods ; }, abstract = {Asgard archaea are of great interest as the progenitors of Eukaryotes, but little is known about the mobile genetic elements (MGEs) that may shape their ongoing evolution. Here, we describe MGEs that replicate in Atabeyarchaeia, a wetland Asgard archaea lineage represented by two complete genomes. We used soil depth-resolved population metagenomic data sets to track 18 MGEs for which genome structures were defined and precise chromosome integration sites could be identified for confident host linkage. Additionally, we identified a complete 20.67 kbp circular plasmid and two family-level groups of viruses linked to Atabeyarchaeia, via CRISPR spacer targeting. Closely related 40 kbp viruses possess a hypervariable genomic region encoding combinations of specific genes for small cysteine-rich proteins structurally similar to restriction-homing endonucleases. One 10.9 kbp integrative conjugative element (ICE) integrates genomically into the Atabeyarchaeum deiterrae-1 chromosome and has a 2.5 kbp circularizable element integrated within it. The 10.9 kbp ICE encodes an expressed Type IIG restriction-modification system with a sequence specificity matching an active methylation motif identified by Pacific Biosciences (PacBio) high-accuracy long-read (HiFi) metagenomic sequencing. Restriction-modification of Atabeyarchaeia differs from that of another coexisting Asgard archaea, Freyarchaeia, which has few identified MGEs but possesses diverse defense mechanisms, including DISARM and Hachiman, not found in Atabeyarchaeia. Overall, defense systems and methylation mechanisms of Asgard archaea likely modulate their interactions with MGEs, and integration/excision and copy number variation of MGEs in turn enable host genetic versatility.}, } @article {pmid39406043, year = {2024}, author = {Lv, J and Liu, C and Fan, L and Luo, P and Liu, S and Wu, C}, title = {Omadacycline for the treatment of severe Legionella pneumophila pneumonia complicated with multiple organ dysfunction: a case report.}, journal = {Diagnostic microbiology and infectious disease}, volume = {110}, number = {4}, pages = {116553}, doi = {10.1016/j.diagmicrobio.2024.116553}, pmid = {39406043}, issn = {1879-0070}, mesh = {Humans ; *Legionnaires' Disease/drug therapy/complications/microbiology ; *Tetracyclines/therapeutic use ; *Anti-Bacterial Agents/therapeutic use ; *Multiple Organ Failure/drug therapy/etiology ; *Legionella pneumophila/drug effects ; Male ; Treatment Outcome ; Aged ; Middle Aged ; }, abstract = {Omadacycline is a novel tetracycline antibiotic that has a strong in vitro antibacterial activity against atypical pathogen such as Legionella. It is approved for the treatment of adults with community-acquired bacterial pneumonia, including Legionella pneumonia. However, clinical data on the use of omadacycline in Legionella pneumonia is limited. In the present paper, we report a case of severe pneumonia induced by Legionella pneumophila (L.pneumophila) presenting with septic shock and multiple organ dysfunction including lung, liver and kidney. With omadacycline treaetment, inflammation indices of the patient markedly decreased, and the patient significantly improved with multiple organ dysfunction and was discharged from home. Due to its strong antibacterial activity against L.pneumophila, good safety profile and no dosage adjustment in patients with severe hepatic or renal impairment, omadacycline can be considered as an optimal treatment strategies for severe infections by such special pathogen. Whereas, more case reports are needed to support this conclusion.}, } @article {pmid39405960, year = {2024}, author = {Cheng, H and Zhang, ZY and Han, H and Wei, R and Zhao, W and Sun, YC and Xu, BB and Hou, XL and Wang, JL and He, YQ and Fu, Y and Wang, QS and Pan, YC and Zhang, Z and Wang, Z}, title = {Cross-ancestry meta-genome-wide association studies provide insights to the understanding of semen traits in pigs.}, journal = {Animal : an international journal of animal bioscience}, volume = {18}, number = {11}, pages = {101331}, doi = {10.1016/j.animal.2024.101331}, pmid = {39405960}, issn = {1751-732X}, mesh = {Animals ; Male ; *Genome-Wide Association Study/veterinary ; *Polymorphism, Single Nucleotide ; *Semen/physiology ; *Semen Analysis/veterinary ; Swine/genetics/physiology ; Sperm Motility/genetics ; Sus scrofa/genetics/physiology ; Sperm Count/veterinary ; }, abstract = {Semen traits play a crucial role in pig reproduction and fertility. However, limited data availability hinder a comprehensive understanding of the genetic mechanisms underlying these traits. In this study, we integrated 597 299 ejaculates and 3 596 sequence data to identify genetic variants and candidate genes related to four semen traits, including sperm progressive motility (MOT), semen volume, sperm concentration (CON), and effective sperm count (SUM). A cross-ancestry meta-genome-wide association study was conducted to detect 163 lead single nucleotide polymorphisms (SNPs) associated with MOT, CON, and SUM. Subsequently, transcriptome-wide association studies and colocalisation analyses were integrated to identify 176 candidate genes, many of which have documented roles in spermatogenesis or male mammal semen traits. Our analysis highlighted the potential involvement of CSM5, PDZD9, and LDAF1 in regulating semen traits through multiple methods. Finally, to validate the function of significant SNPs, we performed genomic feature best linear unbiased prediction in 348 independent pigs using identified trait-related SNP subsets as genomic features. We found that integrating the top 0.1, 1, and 5% significant SNPs as genomic features could enhance genomic prediction accuracy for CON and MOT compared to traditional genomic best linear unbiased prediction. This study contributes to a comprehensive understanding of the genetic mechanisms of boar semen traits and provides insight for developing genomic selection models.}, } @article {pmid39405850, year = {2024}, author = {Liu, Y and Wen, M and Hu, R and Zhao, F and Wang, J}, title = {Regulation of wheat yield by soil multifunctionality and metagenomic-based microbial degradation potentials under crop rotations.}, journal = {Journal of environmental management}, volume = {370}, number = {}, pages = {122897}, doi = {10.1016/j.jenvman.2024.122897}, pmid = {39405850}, issn = {1095-8630}, mesh = {*Triticum/growth & development ; *Soil/chemistry ; *Soil Microbiology ; Nitrogen/metabolism ; Metagenomics ; Agriculture ; Crops, Agricultural/growth & development ; Solanum tuberosum/growth & development/genetics ; }, abstract = {Crop rotation benefits soil fertility and crop yield by providing organic components including cellulose, lignin, chitin, and glucans that are mainly degraded by soil microbial carbohydrate-active enzymes (CAZymes). However, the impacts of crop rotation on soil microbial CAZyme genes are not well understood. Hence, CAZyme genes and families involved in the degradation of differentially originated organic components were investigated using metagenomics among distinct crop rotations. Crop rotation had a more significant effect on soil nitrogen than on carbon fractions with higher content in the complex rotation referring to alfalfa (Medicago sativa L.; 4 year)-potato (Solanum tuberosum L.; 1 year)-winter wheat (3 year; A4PoW3). The composition of soil microbial CAZyme genes related to the degradation of fungi-derived components was more affected by crop rotation compared with the degradation of plant- and bacteria-derived components. The total abundance of CAZyme genes and families was significantly higher in the complex rotation. Notably, CAZyme genes belonging to glycoside hydrolase and glycosyl transferase families had more connections in their network. Moreover, key genes including CE4, GH20, and GH23 assembled toward the middle of the network, and were significantly regulated by dominant soil nitrogen fractions including soil potential nitrogen mineralization and microbial biomass nitrogen. Soil multifunctionality was mostly explained by the composition and total abundance of CAZyme genes, but wheat grain yield was profoundly regulated by fungi-derived components degradation genes under effects of dominant nitrogen fractions. Overall, the findings provide deep insight into the degradation potentials of soil microbial CAZyme genes for developing sustainable crop rotational agroecosystems.}, } @article {pmid39405720, year = {2024}, author = {He, Y and Li, Y and Pan, Y and Shang, J and Sun, W and Wang, M and Fan, H and Sanford, RA and Wei, N and Peng, S and Xie, D and Zhang, W and Chen, S and Liu, Y and Jiang, Z and Jiang, Y and Hu, Y and Li, S and Hu, N and Dong, Y and Shi, L}, title = {Intimate microbe-water-mineral interactions mediate alkalization in the pyroxene-rich iron ore mines in Panxi area, Southwest China.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {136127}, doi = {10.1016/j.jhazmat.2024.136127}, pmid = {39405720}, issn = {1873-3336}, mesh = {*Mining ; China ; *Iron/chemistry/metabolism ; Hydrogen-Ion Concentration ; Thiobacillus/metabolism/genetics ; Minerals/chemistry ; Sulfur/chemistry/metabolism ; }, abstract = {In contrast to acid mine drainage, the microbial assembly and (bio)geochemical processes in alkaline mine conditions remain under-investigated. Here, microbe-water-mineral interactions were systematically investigated in two representative iron mines with alkaline conditions in the Panxi mining area, Southwest China. Compared to reference riverine samples less interfered by mining activities, the iron ore samples, composed of vanadium-titanium magnetite and pyroxene-rich bedrocks, exhibited elevated levels of Fe, HCl-extractable Fe(II), total sulfur, nitrate and sulfate, but lower total carbon (TC). Meanwhile, the mine drainage showed significantly higher sulfate, but lower TC concentrations than the riverine samples. Intriguingly, the Serpentinimonas spp., typically reported in serpentinites, prevailed in the microbial communities from the mine samples exhibiting higher pH. This suggests that the alkaline environments in Panxi mines result from serpentinization-like reactions. Enrichment of Thiobacillus spp. was observed in the mine-dwelling microbial communities, positively correlated with total sulfur, sulfate, nitrate, and Fe(II). Genome-resolved metagenomics suggested a chemoautotrophic lifestyle for the Thiobacillus species (e.g., carbon fixation, sulfur oxidation, and oxygen respiration), which may generate H[+] and mitigate alkalization. This study provides valuable insights into progressive development of alkaline mine ecosystems and offers guidance for developing appropriate engineering strategies to restore the abandoned alkaline mines.}, } @article {pmid39405686, year = {2024}, author = {Zhang, S and Hou, R and Wang, Y and Huang, Q and Lin, L and Li, H and Liu, S and Jiang, Z and Huang, X and Xu, X}, title = {Xenobiotic metabolism activity of gut microbiota from six marine species: Combined taxonomic, metagenomic, and in vitro transformation analysis.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {136152}, doi = {10.1016/j.jhazmat.2024.136152}, pmid = {39405686}, issn = {1873-3336}, mesh = {Animals ; *Xenobiotics/metabolism/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Bacteria/genetics/metabolism/classification ; Water Pollutants, Chemical/metabolism/toxicity ; RNA, Ribosomal, 16S/genetics ; Fishes/microbiology/metabolism ; Metagenomics ; Bivalvia/microbiology/metabolism ; Biotransformation ; }, abstract = {The xenobiotic metabolism driven by the gut microbiota significantly regulates the bioavailability and toxic effects of environmental pollutants such as plasticizers on aquatic organisms. However, it is still unknown whether the gut microbiota can exhibit variable metabolic ability across host species and which functional bacteria and genes are involved in xenobiotic transformation. This study investigated the enriched gut microbiota community composition and diversity of in vitro enrichment cultures from 6 marine species, namely, yellowfin seabream (Acanthopagrus latus), thorn fish (Terapon jarbua), shortnose ponyfish (Leiognathus brevirostris), mussel (Perna viridis), prawn (Parapenaeopsis hungerfordi) and crab (Charybdis riversandersoni). Pseudomonadota, Bacteroidota and Bacillota were the dominant phyla and Enterobacter, Raoultella, Klebsiella, Dysgonomanas and Lactococcus were the dominant genera in the enriched flora according to 16S rRNA sequencing. Furthermore, the metagenomic results revealed that all enriched gut microbiota presented metabolic genes for carbohydrates, amino acids, lipids, and xenobiotics. In particular, the gut microbiota of yellowfin seabream had the highest abundance of glycoside hydrolase family genes and CYP450 enzyme genes. Klebsiella was identified as a common potential degrader of xenobiotic metabolism. In addition, the Biolog plate test system confirmed that the gut microbiota can metabolize various carbon sources and drive the xenobiotic transformation. According to AWCD analysis of community level physiological profiling (CLPP), yellowfin seabream > mussel > prawn > shortnose ponyfish > crab > thorn fish. The gut microbiota of yellowfin seabream presented a stronger metabolic profile of phthalates and bisphenol analogs which reflected by their AWCD results and concentration variations. Overall, our results demonstrated the diverse metabolic abilities of the gut microbiota from six marine organisms and their potential for altering of the fate of xenobiotics in the ecosystem on the basis of combined taxonomic, metagenomic, and in vitro transformation analysis.}, } @article {pmid39405675, year = {2024}, author = {Xing, BS and Su, YM and Fu, YL and Wu, YF and Yan, CH and Wang, XC and Li, YY and Chen, R}, title = {Comparison of the short- and long-term effects of zinc ions on the anaerobic mesophilic co-digestion of food waste and waste activated sludge: Digester performance, antibiotic resistance gene reduction and the microbial community.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {136119}, doi = {10.1016/j.jhazmat.2024.136119}, pmid = {39405675}, issn = {1873-3336}, mesh = {*Zinc ; *Sewage/microbiology ; Anaerobiosis ; *Bioreactors ; *Methane/metabolism ; *Drug Resistance, Microbial/genetics ; *Microbiota/drug effects ; Food ; Waste Disposal, Fluid/methods ; Food Loss and Waste ; }, abstract = {Heavy metals contained in waste activated sludge (WAS), especially zinc ions, have an inhibitory effect on the anaerobic digestion. However, the effects of zinc ions on digester performance, antibiotic resistance genes (ARGs) reduction, and the microbial community involved in the anaerobic mesophilic co-digestion (AcoD) of WAS and food waste (FW) have not been fully characterized. Therefore, batch trials and continuous stirred tank reactors were used under different zinc-ion concentrations. Findings showed that the AcoD system can tolerate a maximum zinc ion of 540 mg/L in a short-term batch and 470 mg/L in a long-term AcoD system, promoting methane production of approximately 1.0-17.0 %. Metagenomic analysis revealed that syntrophic H2 transfer occurred between Syntrophomonas and Methanoculleus and the aceticlastic and hydrogenotrophic methanogenic pathways were both enhanced by 1.18- and 1.16 times, respectively. Moreover, the relative abundance of Methanosarcina increased from 58.4 % to 72.5 % at 470 mg/L to adapt to the high zinc ion concentration during long-term continuous operation. These results revealed that AcoD with a low zinc ion concentration can effectively increase the removal percentage of ARGs. The results provide guidance for biogas recovery and use of mesophilic AcoD with FW and WAS containing high zinc ion concentrations without pretreatment process.}, } @article {pmid39405634, year = {2024}, author = {Leijonhufvud, G and Soratto, TAT and Matos, GM and Bajalan, A and Eichler-Jonsson, C and Gustafsson, B and Bogdanovic, G and Allander, T and Ljungman, G and Andersson, B}, title = {Metagenomic characterization of viruses in the serum of children with newly diagnosed cancer.}, journal = {Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology}, volume = {175}, number = {}, pages = {105736}, doi = {10.1016/j.jcv.2024.105736}, pmid = {39405634}, issn = {1873-5967}, mesh = {Humans ; Child ; *Metagenomics ; *Neoplasms/virology/blood ; *Viruses/classification/genetics/isolation & purification ; Child, Preschool ; *Virus Diseases/virology/diagnosis/blood ; Male ; Female ; Infant ; Adolescent ; Genome, Viral ; }, abstract = {BACKGROUND AND OBJECTIVES: A large cohort of pediatric patients with various forms of childhood cancer was investigated for the presence of viruses using metagenomics. A total of 476 patient samples, collected between 1989 and 2018, were analyzed, representing various pediatric oncological diagnoses and a control group of non-malignant diagnoses.

STUDY DESIGN: The study was carried out using metagenomic sequencing of serum samples. Viruses were identified and analyzed using bioinformatics methods, followed by Polymerase chain reaction (PCR) confirmation RESULTS: The results indicate that a wide range of viruses can be detected in the bloodstream of children with newly diagnosed cancer. Nine viral genomes were identified: Human Pegivirus (HPgV), Hepatitis C virus, Parechovirus 1, Rhinovirus C, Human papillomavirus 116, Human polyomavirus 10, Parvovirus B19, and different variants of Torque Teno Virus (TTV). In this study, a previously unknown virus was found belonging to the Iflavirdae family in the order Picornavirales. HPGV was significantly more common in patients with leukemia compared to other conditions.

CONCLUSIONS: These results highlight the abundance of systemic virus infections in children, and the value of metagenomic sequencing for hypothesis forming regarding the associations between virus infections and cancer.}, } @article {pmid39405631, year = {2025}, author = {Guruge, SK and Han, Z and Dai, S and Islam, A and Ben, W and Tian, Z and Zhang, Y and Yang, M}, title = {Seasonal variation of antibiotic resistance genes in activated sludge of a full-scale municipal wastewater treatment plant: Contribution of activated sludge functional taxa and clinically relevant taxa.}, journal = {Water research}, volume = {268}, number = {Pt A}, pages = {122598}, doi = {10.1016/j.watres.2024.122598}, pmid = {39405631}, issn = {1879-2448}, mesh = {*Sewage/microbiology ; *Seasons ; *Wastewater/microbiology ; *Drug Resistance, Microbial/genetics ; Waste Disposal, Fluid ; Genes, Bacterial ; Bacteria/genetics ; }, abstract = {It has been demonstrated that antibiotic resistance genes (ARGs) exhibit seasonal variations in municipal wastewater treatment plants (MWTPs), but their relationship to bacterial phylogeny structure remains unclear. Using advanced metagenomic techniques and machine learning approach, the current study conducted a year-long investigation to explore the relationship between ARGs and the bacterial community of activated sludge in a full-scale MWTP in Beijing, where seasonal dynamics are remarkable. High abundance of ARGs, notably the clinically relevant high-risk ARGs, was observed in winter and spring, the cold season in Beijing. Seasonal patterns were also observed in the diversity of ARGs and the overall bacterial community. Machine learning-based random forest classification models were utilized to identify biomarkers for ARGs and bacterial genera as indicators of seasonal differences. Subsequent analysis of the relationship between ARGs and bacterial biomarkers was examined using random forest regression models. Results showed that the enrichment of potential pathogens such as Mycobacterium, Clostridium and Pseudomonas was high in winter and spring, strongly contributing to the abundance of high-risk ARGs (ermB, aac(6')-I, tetM, blaTEM, and mefA) during cold season. Conversely, functional taxa associated with activated sludge, such as Thauera, displayed seasonal fluctuations and a preference for ARGs with minor clinical implications. Metagenomic binning further illustrated the contribution of Mycobacterium to ARG enrichment in cold season. Our findings highlight the collective impact of human-derived clinically relevant taxa and functional bacterial taxa in activated sludge on the seasonal dynamics of ARGs in MWTPs. Additionally, this study offers valuable insights into the safe disposal of the excess sludge from MWTPs.}, } @article {pmid39405475, year = {2025}, author = {Rodríguez-Pérez, H and Ciuffreda, L and Hernández-Beeftink, T and Guillen-Guio, B and Domínguez, D and Corrales, A and Espinosa, E and Alcoba-Florez, J and Lorenzo-Salazar, JM and González-Montelongo, R and Villar, J and Flores, C}, title = {Tracheal Aspirate Metagenomics Reveals Association of Antibiotic Resistance with Nonpulmonary Sepsis Mortality.}, journal = {American journal of respiratory cell and molecular biology}, volume = {72}, number = {2}, pages = {219-222}, doi = {10.1165/rcmb.2024-0192LE}, pmid = {39405475}, issn = {1535-4989}, support = {OA23/074//Fundación DISA/United States ; PIFIISC21/37//Fundación Canaria Instituto de Investigación Sanitaria de Canarias/United States ; PIFUN48/18//Fundación Canaria Instituto de Investigación Sanitaria de Canarias/United States ; A0000014697//Cabildo Insular de Tenerife/United States ; CGIEU0000219140//Cabildo Insular de Tenerife/United States ; 221680/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; A way of making Europe//European Regional Development Funds/United States ; OA17/008//Instituto Tecnológico y de Energías Renovables/United States ; OA23/043//Instituto Tecnológico y de Energías Renovables/United States ; CB06/06/1088//Instituto de Salud Carlos III/United States ; CD22/00138//Instituto de Salud Carlos III/United States ; FI18/00230//Instituto de Salud Carlos III/United States ; IMP/00019//Instituto de Salud Carlos III/United States ; PI14/00844//Instituto de Salud Carlos III/United States ; PI17/00610//Instituto de Salud Carlos III/United States ; PI19/00141//Instituto de Salud Carlos III/United States ; AEI/FEDER//Ministerio de Ciencia e Innovación/United States ; RTC-2017-6471-1//Ministerio de Ciencia e Innovación/United States ; UE//Ministerio de Ciencia e Innovación/United States ; }, } @article {pmid39628520, year = {2023}, author = {Li, L}, title = {Next-generation synthetic biology approaches for the accelerated discovery of microbial natural products.}, journal = {Engineering microbiology}, volume = {3}, number = {1}, pages = {100060}, pmid = {39628520}, issn = {2667-3703}, abstract = {Microbial natural products (NPs) and their derivates have been widely used in health care and agriculture during the past few decades. Although large-scale bacterial or fungal (meta)genomic mining has revealed the tremendous biosynthetic potentials to produce novel small molecules, there remains a lack of universal approaches to link NP biosynthetic gene clusters (BGCs) to their associated products at a large scale and speed. In the last ten years, a series of emerging technologies have been established alongside the developments in synthetic biology to engineer cryptic metabolite BGCs and edit host genomes. Diverse computational tools, such as antiSMASH and PRISM, have also been simultaneously developed to rapidly identify BGCs and predict the chemical structures of their products. This review discusses the recent developments and trends pertaining to the accelerated discovery of microbial NPs driven by a wide variety of next-generation synthetic biology approaches, with an emphasis on the in situ activation of silent BGCs at scale, the direct cloning or refactoring of BGCs of interest for heterologous expression, and the synthetic-bioinformatic natural products (syn-BNP) approach for the guided rapid access of bioactive non-ribosomal peptides.}, } @article {pmid39575140, year = {2022}, author = {Lutz, KC and Jiang, S and Neugent, ML and De Nisco, NJ and Zhan, X and Li, Q}, title = {A Survey of Statistical Methods for Microbiome Data Analysis.}, journal = {Frontiers in applied mathematics and statistics}, volume = {8}, number = {}, pages = {}, pmid = {39575140}, issn = {2297-4687}, support = {R01 GM126479/GM/NIGMS NIH HHS/United States ; R01 GM140012/GM/NIGMS NIH HHS/United States ; R56 HG011035/HG/NHGRI NIH HHS/United States ; R01 GM141519/GM/NIGMS NIH HHS/United States ; P30 CA142543/CA/NCI NIH HHS/United States ; P50 CA070907/CA/NCI NIH HHS/United States ; R01 DK131267/DK/NIDDK NIH HHS/United States ; }, abstract = {In the last decade, numerous statistical methods have been developed for analyzing microbiome data generated from high-throughput next-generation sequencing technology. Microbiome data are typically characterized by zero inflation, overdispersion, high dimensionality, and sample heterogeneity. Three popular areas of interest in microbiome research requiring statistical methods that can account for the characterizations of microbiome data include detecting differentially abundant taxa across phenotype groups, identifying associations between the microbiome and covariates, and constructing microbiome networks to characterize ecological associations of microbes. These three areas are referred to as differential abundance analysis, integrative analysis, and network analysis, respectively. In this review, we highlight available statistical methods for differential abundance analysis, integrative analysis, and network analysis that have greatly advanced microbiome research. In addition, we discuss each method's motivation, modeling framework, and application.}, } @article {pmid39404832, year = {2024}, author = {Díaz-Martínez, C and Bolívar, A and Mercanoglu Taban, B and Kanca, N and Pérez-Rodríguez, F}, title = {Exploring the antibiotic resistance of Listeria monocytogenes in food environments - a review.}, journal = {Critical reviews in microbiology}, volume = {}, number = {}, pages = {1-24}, doi = {10.1080/1040841X.2024.2412007}, pmid = {39404832}, issn = {1549-7828}, abstract = {Listeria monocytogenes, a resilient bacterium in diverse food conditions, such as refrigeration, reduced water activity and low pH, poses a significant threat to the food industry and public health. In recent years, it has been documented an increase in the antibiotic resistance of zoonotic pathogens, including L. monocytogenes. This review provides new insight into the molecular mechanisms involved in both intrinsic and acquired antibiotic resistance of L. monocytogenes with an emphasis on the effect of different environmental and food-related factors. It also explores the relationship of these resistance mechanisms with virulence factors. An analysis of literature data (2009-2021) was conducted to investigate statistically and graphically potential associations between specific antibiotic resistance patterns in the pathogen and food categories using an unbiased variance analysis. The results evidenced that food type had an influence on the antibiotic resistance profiles of L. monocytogenes, with meat and vegetables being the food categories exhibiting the most prevalent profiles. The frequent detection of resistance to ampicillin, penicillin, and tetracycline (non-intrinsic resistances) indicates that specific processing conditions along the food chain may induce them. Many questions remain about the impact of food chain factors (e.g. thermal treatments, cold chain, preservatives, etc.) and food type (low pH, reduced water activity, etc.) on the antibiotic resistance patterns of the pathogen, particularly concerning food-related sources, the resistance mechanisms involved (e.g. cross-protection, horizontal gene transfer, etc.), and the evolutionary processes of antibiotic-resistant microbial populations. Metagenomics, in addition to other -omics technologies (metabolomics and transcriptomics), allows a better understanding of the processes involved in the acquisition of resistance.}, } @article {pmid39404267, year = {2024}, author = {Olie, SE and Andersen, CØ and van de Beek, D and Brouwer, MC}, title = {Molecular diagnostics in cerebrospinal fluid for the diagnosis of central nervous system infections.}, journal = {Clinical microbiology reviews}, volume = {37}, number = {4}, pages = {e0002124}, pmid = {39404267}, issn = {1098-6618}, support = {101001237//EC | European Research Council (ERC)/ ; }, mesh = {Humans ; Bacteria/isolation & purification/genetics/classification ; *Central Nervous System Infections/cerebrospinal fluid/diagnosis/microbiology/parasitology ; Cerebrospinal Fluid/microbiology/parasitology ; *Molecular Diagnostic Techniques/methods/standards ; Nucleic Acid Amplification Techniques/methods ; Viruses/isolation & purification/genetics/classification ; }, abstract = {SUMMARYCentral nervous system (CNS) infections can be caused by various pathogens, including bacteria, viruses, fungi, and parasites. Molecular diagnostic methods are pivotal for identifying the different causative pathogens of these infections in clinical settings. The efficacy and specificity of these methods can vary per pathogen involved, and in a substantial part of patients, no pathogen is identified in the cerebrospinal fluid (CSF). Over recent decades, various molecular methodologies have been developed and applied to patients with CNS infections. This review provides an overview of the accuracy of nucleic acid amplification methods in CSF for a diverse range of pathogens, examines the potential value of multiplex PCR panels, and explores the broad-range bacterial and fungal PCR/sequencing panels. In addition, it evaluates innovative molecular approaches to enhance the diagnosis of CNS infections.}, } @article {pmid39404262, year = {2024}, author = {Zhong, C and Yamanouchi, S and Li, Y and Chen, J and Wei, T and Wang, R and Zhou, K and Cheng, A and Hao, W and Liu, H and Konhauser, KO and Iwasaki, W and Qian, P-Y}, title = {Marine biofilms: cyanobacteria factories for the global oceans.}, journal = {mSystems}, volume = {9}, number = {11}, pages = {e0031724}, pmid = {39404262}, issn = {2379-5077}, support = {2021HJ01, SMSEGL20SC01//Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) ()/ ; JPMJCR19S2//MEXT | Japan Science and Technology Agency (JST)/ ; 19H05688, 18H04136//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; HKUST PDFS2223-6S03//Research Grants Council, University Grants Committee ()/ ; }, mesh = {*Biofilms/growth & development ; *Cyanobacteria/genetics/physiology/classification/isolation & purification ; *Seawater/microbiology ; *Oceans and Seas ; Metagenome ; Phylogeny ; Metagenomics ; }, abstract = {UNLABELLED: Marine biofilms were newly revealed as a giant microbial diversity pool for global oceans. However, the cyanobacterial diversity in marine biofilms within the upper seawater column and its ecological and evolutionary implications remains undetermined. Here, we reconstructed a full picture of modern marine cyanobacteria habitats by re-analyzing 9.3 terabyte metagenomic data sets and 2,648 metagenome-assembled genomes (MAGs). The abundances of cyanobacteria lineages exclusively detected in marine biofilms were up to ninefold higher than those in seawater at similar sample size. Analyses revealed that cyanobacteria in marine biofilms are specialists with strong geographical and environmental constraints on their genome and functional adaption, which is in stark contrast to the generalistic features of seawater-derived cyanobacteria. Molecular dating suggests that the important diversifications in biofilm-forming cyanobacteria appear to coincide with the Great Oxidation Event (GOE), "boring billion" middle Proterozoic, and the Neoproterozoic Oxidation Event (NOE). These new insights suggest that marine biofilms are large and important cyanobacterial factories for the global oceans.

IMPORTANCE: Cyanobacteria, highly diverse microbial organisms, play a crucial role in Earth's oxygenation and biogeochemical cycling. However, their connection to these processes remains unclear, partly due to incomplete surveys of oceanic niches. Our study uncovered significant cyanobacterial diversity in marine biofilms, showing distinct niche differentiation compared to seawater counterparts. These patterns reflect three key stages of marine cyanobacterial diversification, coinciding with major geological events in the Earth's history.}, } @article {pmid39402695, year = {2024}, author = {Nawaz, MA and Pamirsky, IE and Golokhvast, KS}, title = {Bioinformatics in Russia: history and present-day landscape.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {6}, pages = {}, pmid = {39402695}, issn = {1477-4054}, support = {075-15-2022-1152/7//Ministry of Science and Higher Education of the Russian Federation to Advanced Engineering School/ ; //National Research State University, Tomsk, Russia/ ; 20-53-56041//Russian Foundation for Basic Research/ ; }, mesh = {*Computational Biology/methods ; Russia ; Humans ; History, 21st Century ; History, 20th Century ; Genomics ; }, abstract = {Bioinformatics has become an interdisciplinary subject due to its universal role in molecular biology research. The current status of Russia's bioinformatics research in Russia is not known. Here, we review the history of bioinformatics in Russia, present the current landscape, and highlight future directions and challenges. Bioinformatics research in Russia is driven by four major industries: information technology, pharmaceuticals, biotechnology, and agriculture. Over the past three decades, despite a delayed start, the field has gained momentum, especially in protein and nucleic acid research. Dedicated and shared centers for genomics, proteomics, and bioinformatics are active in different regions of Russia. Present-day bioinformatics in Russia is characterized by research issues related to genetics, metagenomics, OMICs, medical informatics, computational biology, environmental informatics, and structural bioinformatics. Notable developments are in the fields of software (tools, algorithms, and pipelines), use of high computation power (e.g. by the Siberian Supercomputer Center), and large-scale sequencing projects (the sequencing of 100 000 human genomes). Government funding is increasing, policies are being changed, and a National Genomic Information Database is being established. An increased focus on eukaryotic genome sequencing, the development of a common place for developers and researchers to share tools and data, and the use of biological modeling, machine learning, and biostatistics are key areas for future focus. Universities and research institutes have started to implement bioinformatics modules. A critical mass of bioinformaticians is essential to catch up with the global pace in the discipline.}, } @article {pmid39402664, year = {2024}, author = {Ndiaye, M and Prieto-Baños, S and Fitzgerald, LM and Yazdizadeh Kharrazi, A and Oreshkov, S and Dessimoz, C and Sedlazeck, FJ and Glover, N and Majidian, S}, title = {When less is more: sketching with minimizers in genomics.}, journal = {Genome biology}, volume = {25}, number = {1}, pages = {270}, pmid = {39402664}, issn = {1474-760X}, mesh = {*Genomics/methods ; Metagenomics/methods ; Humans ; Software ; }, abstract = {The exponential increase in sequencing data calls for conceptual and computational advances to extract useful biological insights. One such advance, minimizers, allows for reducing the quantity of data handled while maintaining some of its key properties. We provide a basic introduction to minimizers, cover recent methodological developments, and review the diverse applications of minimizers to analyze genomic data, including de novo genome assembly, metagenomics, read alignment, read correction, and pangenomes. We also touch on alternative data sketching techniques including universal hitting sets, syncmers, or strobemers. Minimizers and their alternatives have rapidly become indispensable tools for handling vast amounts of data.}, } @article {pmid39402510, year = {2024}, author = {Abramova, A and Karkman, A and Bengtsson-Palme, J}, title = {Metagenomic assemblies tend to break around antibiotic resistance genes.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {959}, pmid = {39402510}, issn = {1471-2164}, mesh = {*Metagenomics/methods ; *Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; Metagenome ; Genes, Bacterial ; }, abstract = {BACKGROUND: Assembly of metagenomic samples can provide essential information about the mobility potential and taxonomic origin of antibiotic resistance genes (ARGs) and inform interventions to prevent further spread of resistant bacteria. However, similar to other conserved regions, such as ribosomal RNA genes and mobile genetic elements, almost identical ARGs typically occur in multiple genomic contexts across different species, representing a considerable challenge for the assembly process. Usually, this results in many fragmented contigs of unclear origin, complicating the risk assessment of ARG detections. To systematically investigate the impact of this issue on detection, quantification and contextualization of ARGs, we evaluated the performance of different assembly approaches, including genomic-, metagenomic- and transcriptomic-specialized assemblers. We quantified recovery and accuracy rates of each tool for ARGs both from in silico spiked metagenomic samples as well as real samples sequenced using both long- and short-read sequencing technologies.

RESULTS: The results revealed that none of the investigated tools can accurately capture genomic contexts present in samples of high complexity. The transcriptomic assembler Trinity showed a better performance in terms of reconstructing longer and fewer contigs matching unique genomic contexts, which can be beneficial for deciphering the taxonomic origin of ARGs. The currently commonly used metagenomic assembly tools metaSPAdes and MEGAHIT were able to identify the ARG repertoire but failed to fully recover the diversity of genomic contexts present in a sample. On top of that, in a complex scenario MEGAHIT produced very short contigs, which can lead to considerable underestimation of the resistome in a given sample.

CONCLUSIONS: Our study shows that metaSPAdes and Trinity would be the preferable tools in terms of accuracy to recover correct genomic contexts around ARGs in metagenomic samples characterized by uneven coverages. Overall, the inability of assemblers to reconstruct long ARG-containing contigs has impacts on ARG quantification, suggesting that directly mapping reads to an ARG database should be performed as a complementary strategy to get accurate ARG abundance and diversity measures.}, } @article {pmid39402441, year = {2024}, author = {Yang, M and Wang, Z and Yan, Z and Wang, W and Zhu, Q and Jin, C}, title = {DNASimCLR: a contrastive learning-based deep learning approach for gene sequence data classification.}, journal = {BMC bioinformatics}, volume = {25}, number = {1}, pages = {328}, pmid = {39402441}, issn = {1471-2105}, mesh = {*Deep Learning ; Neural Networks, Computer ; Metagenome/genetics ; }, abstract = {BACKGROUND: The rapid advancements in deep neural network models have significantly enhanced the ability to extract features from microbial sequence data, which is critical for addressing biological challenges. However, the scarcity and complexity of labeled microbial data pose substantial difficulties for supervised learning approaches. To address these issues, we propose DNASimCLR, an unsupervised framework designed for efficient gene sequence data feature extraction.

RESULTS: DNASimCLR leverages convolutional neural networks and the SimCLR framework, based on contrastive learning, to extract intricate features from diverse microbial gene sequences. Pre-training was conducted on two classic large scale unlabelled datasets encompassing metagenomes and viral gene sequences. Subsequent classification tasks were performed by fine-tuning the pretrained model using the previously acquired model. Our experiments demonstrate that DNASimCLR is at least comparable to state-of-the-art techniques for gene sequence classification. For convolutional neural network-based approaches, DNASimCLR surpasses the latest existing methods, clearly establishing its superiority over the state-of-the-art CNN-based feature extraction techniques. Furthermore, the model exhibits superior performance across diverse tasks in analyzing biological sequence data, showcasing its robust adaptability.

CONCLUSIONS: DNASimCLR represents a robust and database-agnostic solution for gene sequence classification. Its versatility allows it to perform well in scenarios involving novel or previously unseen gene sequences, making it a valuable tool for diverse applications in genomics.}, } @article {pmid39402236, year = {2024}, author = {Vera-Ponce de León, A and Hensen, T and Hoetzinger, M and Gupta, S and Weston, B and Johnsen, SM and Rasmussen, JA and Clausen, CG and Pless, L and Veríssimo, ARA and Rudi, K and Snipen, L and Karlsen, CR and Limborg, MT and Bertilsson, S and Thiele, I and Hvidsten, TR and Sandve, SR and Pope, PB and La Rosa, SL}, title = {Genomic and functional characterization of the Atlantic salmon gut microbiome in relation to nutrition and health.}, journal = {Nature microbiology}, volume = {9}, number = {11}, pages = {3059-3074}, pmid = {39402236}, issn = {2058-5276}, support = {300846//Norges Forskningsråd (Research Council of Norway)/ ; 757922//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 12/RC/2273-P2//Science Foundation Ireland (SFI)/ ; }, mesh = {Animals ; *Salmo salar/microbiology ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/classification/isolation & purification ; *Metagenomics ; *Aquaculture ; *Genome, Bacterial/genetics ; Seawater/microbiology ; Fresh Water/microbiology ; Phylogeny ; Genomics/methods ; }, abstract = {To ensure sustainable aquaculture, it is essential to understand the path 'from feed to fish', whereby the gut microbiome plays an important role in digestion and metabolism, ultimately influencing host health and growth. Previous work has reported the taxonomic composition of the Atlantic salmon (Salmo salar) gut microbiome; however, functional insights are lacking. Here we present the Salmon Microbial Genome Atlas consisting of 211 high-quality bacterial genomes, recovered by cultivation (n = 131) and gut metagenomics (n = 80) from wild and farmed fish both in freshwater and seawater. Bacterial genomes were taxonomically assigned to 14 different orders, including 35 distinctive genera and 29 previously undescribed species. Using metatranscriptomics, we functionally characterized key bacterial populations, across five phyla, in the salmon gut. This included the ability to degrade diet-derived fibres and release vitamins and other exometabolites with known beneficial effects, which was supported by genome-scale metabolic modelling and in vitro cultivation of selected bacterial species coupled with untargeted metabolomic studies. Together, the Salmon Microbial Genome Atlas provides a genomic and functional resource to enable future studies on salmon nutrition and health.}, } @article {pmid39401075, year = {2024}, author = {Oppermann, J and Rozenberg, A and Fabrin, T and González-Cabrera, C and Parker, R and Béjà, O and Prigge, M and Hegemann, P}, title = {Robust optogenetic inhibition with red-light-sensitive anion-conducting channelrhodopsins.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, pmid = {39401075}, issn = {2050-084X}, support = {SFB 1078 B2 221545957//Deutsche Forschungsgemeinschaft/ ; 3131/20//Israel Science Foundation/ ; 99999.001756/2014-01//Alexander von Humboldt-Stiftung/ ; JPco-FuND - NiPARK//EU Joint Programme - Neurodegenerative Disease Research/ ; Program 'BestMinds' MP J28/2017 SheLi//Leibniz-Gemeinschaft/ ; ASAP-020505//Aligning Science Across Parkinson's/ ; }, mesh = {*Optogenetics/methods ; Animals ; *Channelrhodopsins/genetics/metabolism ; Mice ; *Light ; *Neurons/metabolism/physiology/radiation effects ; Anions/metabolism ; Phylogeny ; Humans ; }, abstract = {Channelrhodopsins (ChRs) are light-gated ion channels widely used to optically activate or silence selected electrogenic cells, such as individual brain neurons. Here, we describe identifying and characterizing a set of anion-conducting ChRs (ACRs) from diverse taxa and representing various branches of the ChR phylogenetic tree. The Mantoniella squamata ACR (MsACR1) showed high sensitivity to yellow-green light (λmax at 555 nm) and was further engineered for optogenetic applications. A single amino-acid substitution that mimicked red-light-sensitive rhodopsins like Chrimson shifted the photosensitivity 20 nm toward red light and accelerated photocurrent kinetics. Hence, it was named red and accelerated ACR, raACR. Both wild-type and mutant are capable optical silencers at low light intensities in mouse neurons in vitro and in vivo, while raACR offers a higher temporal resolution.}, } @article {pmid39400741, year = {2024}, author = {Lemieux-Labonté, V and Pathmanathan, JS and Terrat, Y and Tromas, N and Simard, A and Haase, CG and Lausen, CL and Willis, CKR and Lapointe, FJ}, title = {Pseudogymnoascus destructans invasion stage impacts the skin microbial functions of highly vulnerable Myotis lucifugus.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {11}, pages = {}, pmid = {39400741}, issn = {1574-6941}, support = {RGPIN-2015-05219//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Animals ; *Chiroptera/microbiology ; *Skin/microbiology ; *Ascomycota/genetics/pathogenicity ; *Microbiota ; Hibernation ; Mycoses/microbiology/veterinary ; }, abstract = {The role of the skin microbiome in resistance and susceptibility of wildlife to fungal pathogens has been examined from a taxonomic perspective but skin microbial function, in the context of fungal infection, has yet to be studied. Our objective was to understand effects of a bat fungal pathogen site infection status and course of invasion on skin microbial function. We sampled seven hibernating colonies of Myotis lucifugus covering three-time points over the course of Pseudogymnoascus destructans (Pd) invasion and white nose syndrome (pre-invasion, epidemic, and established). Our results support three new hypotheses about Pd and skin functional microbiome: (1) there is an important effect of Pd invasion stage, especially at the epidemic stage; (2) disruption by the fungus at the epidemic stage could decrease anti-fungal functions with potential negative effects on the microbiome and bat health; (3) the collection site might have a larger influence on microbiomes at the pre-invasion stage rather than at epidemic and established stages. Future studies with larger sample sizes and using meta-omics approaches will help confirm these hypotheses, and determine the influence of the microbiome on wildlife survival to fungal disease.}, } @article {pmid39400446, year = {2024}, author = {Escuer, P and Guirao-Rico, S and Arnedo, MA and Sánchez-Gracia, A and Rozas, J}, title = {Population Genomics of Adaptive Radiations: Exceptionally High Levels of Genetic Diversity and Recombination in an Endemic Spider From the Canary Islands.}, journal = {Molecular ecology}, volume = {33}, number = {22}, pages = {e17547}, doi = {10.1111/mec.17547}, pmid = {39400446}, issn = {1365-294X}, support = {BES-2017-081740//Ministerio de Ciencia e Innovación/ ; MCIN/AEI/10.13039/501100011033//Ministerio de Ciencia e Innovación/ ; PID2019-103//Ministerio de Ciencia e Innovación/ ; PID2019-105794GB//Ministerio de Ciencia e Innovación/ ; PID2022-137758NB-I00//Ministerio de Ciencia e Innovación/ ; PID2022-138477NB-C22//Ministerio de Ciencia e Innovación/ ; 2021SGR00279//Comissió Interdepartamental de Recerca i Innovació Tecnològica/ ; }, mesh = {Animals ; *Spiders/genetics/classification ; *Genetics, Population ; *Genetic Variation ; Spain ; Recombination, Genetic/genetics ; Linkage Disequilibrium ; Selection, Genetic ; Genomics ; Metagenomics ; Polymorphism, Single Nucleotide/genetics ; }, abstract = {The spider genus Dysdera has undergone a remarkable diversification in the oceanic archipelago of the Canary Islands, with ~60 endemic species having originated during the 20 million years since the origin of the archipelago. This evolutionary radiation has been accompanied by substantial dietary shifts, often characterised by phenotypic modifications encompassing morphological, metabolic and behavioural changes. Hence, these endemic spiders represent an excellent model for understanding the evolutionary drivers and to pinpoint the genomic determinants underlying adaptive radiations. Recently, we achieved the first chromosome-level genome assembly of one of the endemic species, D. silvatica, providing a high-quality reference sequence for evolutionary genomics studies. Here, we conducted a low coverage-based resequencing study of a natural population of D. silvatica from La Gomera island. Taking advantage of the new high-quality genome, we characterised genome-wide levels of nucleotide polymorphism, divergence and linkage disequilibrium, and inferred the demographic history of this population. We also performed comprehensive genome-wide scans for recent positive selection. Our findings uncovered exceptionally high levels of nucleotide diversity and recombination in this geographically restricted endemic species, indicative of large historical effective population sizes. We also identified several candidate genomic regions that are potentially under positive selection, highlighting relevant biological processes, such as vision and nitrogen extraction as potential adaptation targets. These processes may ultimately drive species diversification in this genus. This pioneering study of spiders that are endemic to an oceanic archipelago lays the groundwork for broader population genomics analyses aimed at understanding the genetic mechanisms driving adaptive radiation in island ecosystems.}, } @article {pmid39400154, year = {2024}, author = {Takemae, N and Kuba, Y and Oba, K and Kageyama, T}, title = {Direct genome sequencing of respiratory viruses from low viral load clinical specimens using the target capture sequencing technology.}, journal = {Microbiology spectrum}, volume = {12}, number = {11}, pages = {e0098624}, pmid = {39400154}, issn = {2165-0497}, support = {JP22fk0108543//Japan Agency for Medical Research and Development (AMED)/ ; JP24fk0108692//Japan Agency for Medical Research and Development (AMED)/ ; JP22K10501//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; }, mesh = {Humans ; *Genome, Viral/genetics ; *SARS-CoV-2/genetics/isolation & purification/classification ; *High-Throughput Nucleotide Sequencing/methods ; *Viral Load/methods ; *COVID-19/diagnosis/virology ; *Influenza, Human/virology/diagnosis ; *Influenza A virus/genetics/isolation & purification/classification ; *Metagenomics/methods ; RNA, Viral/genetics/isolation & purification ; Whole Genome Sequencing/methods ; Respiratory Tract Infections/virology/diagnosis ; }, abstract = {The use of metagenomic next-generation sequencing technology to obtain complete viral genome sequences directly from clinical samples with low viral load remains challenging-especially in the case of respiratory viruses-due to the low copy number of viral versus host genomes. To overcome this limitation, target capture sequencing for the enrichment of specific genomes has been developed and applied for direct genome sequencing of viruses. However, as the efficiency of enrichment varies depending on the probes, the type of clinical sample, etc., validation is essential before target capture sequencing can be applied to clinical diagnostics. In this study, we evaluated the utility of target capture sequencing with a comprehensive viral probe panel for clinical respiratory specimens collected from patients diagnosed with SARS-CoV-2 or influenza type A. We focused on clinical specimens containing low copy numbers of viral genomes. Target capture sequencing yielded approximately 180- and 2,000-fold higher read counts of SARS-CoV-2 and influenza A virus, respectively, than metagenomic sequencing when the RNA extracted from specimens contained 59.3 copies/µL of SARS-CoV-2 or 625.1 copies/µL of influenza A virus. In addition, the target capture sequencing identified sequence reads in all SARS-CoV-2- or influenza type A-positive specimens with <26 RNA copies/µL, some of which also yielded >70% of the full-length genomes of SARS-CoV-2 or influenza A virus. Furthermore, the target capture sequencing using comprehensive probes identified co-infections with viruses other than SARS-CoV-2, suggesting that this approach will not only detect a wide range of viruses but also contribute to epidemiological studies.IMPORTANCETarget capture sequencing has been developed and applied for direct genome sequencing of viruses in clinical specimens to overcome the low detection sensitivity of metagenomic next-generation sequencing. In this study, we evaluated the utility of target capture sequencing with a comprehensive viral probe panel for clinical respiratory specimens collected from patients diagnosed with SARS-CoV-2 or influenza type A, focusing on clinical specimens containing low copy numbers of viral genomes. Our results showed that the target capture sequencing yielded dramatically higher read counts than metagenomic sequencing for both viruses. Furthermore, the target capture sequencing using comprehensive probes identified co-infections with other viruses, suggesting that this approach will not only detect a wide range of viruses but also contribute to epidemiological studies.}, } @article {pmid39400140, year = {2024}, author = {Laureano, G and Bermudez, AE and Rivera Vicéns, RE and Arun, A}, title = {Metagenome-assembled genome of Pseudomonas sp. from coenocytic alga Vaucheria bursata.}, journal = {Microbiology resource announcements}, volume = {13}, number = {11}, pages = {e0048524}, pmid = {39400140}, issn = {2576-098X}, support = {1928792//National Science Foundation (NSF)/ ; }, abstract = {Here, we report a draft metagenome-assembled genome and annotation of Pseudomonas sp. obtained from the sequenced genome of Vaucheria bursata. The genome completeness was 97.9% with a total of 5,322 open reading frames, of which 3,147 genes were annotated. The availability of the metagenome will elucidate the possible epiphytic interactions of bacteria with Vaucheria bursata.}, } @article {pmid39399973, year = {2024}, author = {Simpson, A and Wood-Charlson, EM and Smith, M and Koch, BJ and Beilsmith, K and Kimbrel, JA and Kellom, M and Hunter, CI and Walls, RL and Schriml, LM and Wilhelm, RC}, title = {MISIP: a data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence and experiment.}, journal = {GigaScience}, volume = {13}, number = {}, pages = {}, pmid = {39399973}, issn = {2047-217X}, support = {IND90024429//USDA/ ; //Purdue University/ ; //Lawrence Berkeley National Laboratory/ ; }, mesh = {*Isotope Labeling/methods ; Reproducibility of Results ; Microbiota/genetics ; Metadata ; Metagenomics/methods ; Sequence Analysis, DNA/methods ; Metagenome ; }, abstract = {DNA/RNA-stable isotope probing (SIP) is a powerful tool to link in situ microbial activity to sequencing data. Every SIP dataset captures distinct information about microbial community metabolism, process rates, and population dynamics, offering valuable insights for a wide range of research questions. Data reuse maximizes the information derived from the labor and resource-intensive SIP approaches. Yet, a review of publicly available SIP sequencing metadata showed that critical information necessary for reproducibility and reuse was often missing. Here, we outline the Minimum Information for any Stable Isotope Probing Sequence (MISIP) according to the Minimum Information for any (x) Sequence (MIxS) framework and include examples of MISIP reporting for common SIP experiments. Our objectives are to expand the capacity of MIxS to accommodate SIP-specific metadata and guide SIP users in metadata collection when planning and reporting an experiment. The MISIP standard requires 5 metadata fields-isotope, isotopolog, isotopolog label, labeling approach, and gradient position-and recommends several fields that represent best practices in acquiring and reporting SIP sequencing data (e.g., gradient density and nucleic acid amount). The standard is intended to be used in concert with other MIxS checklists to comprehensively describe the origin of sequence data, such as for marker genes (MISIP-MIMARKS) or metagenomes (MISIP-MIMS), in combination with metadata required by an environmental extension (e.g., soil). The adoption of the proposed data standard will improve the reuse of any sequence derived from a SIP experiment and, by extension, deepen understanding of in situ biogeochemical processes and microbial ecology.}, } @article {pmid39399683, year = {2024}, author = {Martin, C and Gitter, A and Anantharaman, K}, title = {Protein Set Transformer: A protein-based genome language model to power high diversity viromics.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {39399683}, issn = {2693-5015}, support = {R35 GM143024/GM/NIGMS NIH HHS/United States ; }, abstract = {Exponential increases in microbial and viral genomic data demand transformational advances in scalable, generalizable frameworks for their interpretation. Standard homology-based functional analyses are hindered by the rapid divergence of microbial and especially viral genomes and proteins that significantly decreases the volume of usable data. Here, we present Protein Set Transformer (PST), a protein-based genome language model that models genomes as sets of proteins without considering sparsely available functional labels. Trained on >100k viruses, PST outperformed other homology- and language model-based approaches for relating viral genomes based on shared protein content. Further, PST demonstrated protein structural and functional awareness by clustering capsid-fold-containing proteins with known capsid proteins and uniquely clustering late gene proteins within related viruses. Our data establish PST as a valuable method for diverse viral genomics, ecology, and evolutionary applications. We posit that the PST framework can be a foundation model for microbial genomics when trained on suitable data.}, } @article {pmid39399231, year = {2024}, author = {Scicchitano, D and Foresto, L and Laczny, CC and Cinti, N and Vitagliano, R and Halder, R and Morri, G and Turroni, S and D'Amico, F and Palladino, G and Fiori, J and Wilmes, P and Rampelli, S and Candela, M}, title = {A 15-day pilot biodiversity intervention with horses in a farm system leads to gut microbiome rewilding in 10 urban Italian children.}, journal = {One health (Amsterdam, Netherlands)}, volume = {19}, number = {}, pages = {100902}, pmid = {39399231}, issn = {2352-7714}, abstract = {To provide some glimpses on the possibility of shaping the human gut microbiome (GM) through probiotic exchange with natural ecosystems, here we explored the impact of 15 days of daily interaction with horses on the GM of 10 urban-living Italian children. Specifically, the children were in close contact with the horses in an "educational farm", where they spent almost 10 h/day interacting with the animals. The children's GM was assessed before and after the horse interaction using metabarcoding sequencing and shotgun metagenomics, along with the horses' skin, oral and fecal microbiomes. Targeted metabolomic analysis for GM-produced beneficial metabolites (i.e., short-chain fatty acids) in the children's feces was also performed. Interaction with horses facilitated the acquisition of health-related traits in the children's GM, such as increased diversity, enhanced butyrate production and an increase in several health-promoting species considered to be next-generation probiotics. Among these, the butyrate producers Facecalibacterium prausnitzii and F. duncaniae and a species belonging to the order Christensenellales. Interaction with horses was also associated with increased proportions of Eggerthella lenta, Gordonibacter pamelae and G. urolithinfaciens, GM components known to play a role in the bioconversion of dietary plant polyphenols into beneficial metabolites. Notably, no increase in potentially harmful traits, including toxin genes, was observed. Overall, our pilot study provides some insights on the existence of possible health-promoting exchanges between children and horses microbiomes. It lays the groundwork for an implemented and more systematic enrollment effort to explore the full complexity of human GM rewilding through exchange with natural ecosystems, aligning with the One Health approach.}, } @article {pmid39398609, year = {2024}, author = {Lin, S and Chen, Y and Li, H and Chen, T and Lin, Q}, title = {Diagnostic value and clinical use of metagenomic next-generation sequencing for invasive pulmonary aspergillosis.}, journal = {American journal of translational research}, volume = {16}, number = {9}, pages = {4885-4893}, pmid = {39398609}, issn = {1943-8141}, abstract = {OBJECTIVE: To compare the diagnostic efficacy of metagenomic next generation sequencing (mNGS) with traditional fungal culture, (1,3)-β-D glucan (G) test, and galactomannan (GM) test in diagnosing invasive pulmonary aspergillosis (IPA) and to explore the advantages and disadvantages of mNGS for IPA diagnosis.

METHODS: A retrospective analysis was conducted on 136 patients admitted to the Department of Respiratory and Critical Care Medicine of Affiliated Hospital of Putian University from March 2018 to March 2020. Among them, there were 66 patients with IPA (IPA group) and 70 without (non-IPA group). Baseline data, inflammatory factors, cytokines, and specimens such as bronchoalveolar lavage fluid (BALF) and blood of these patients were collected. Fungal culture test, G test, GM test and mNGS test were performed. Information included for analysis encompassed patients' host factors, clinical features, chest scanning images, laboratory test results, and treatment outcome.

RESULTS: There was no statistical difference in the baseline data or inflammatory factors in patients between the IPA group and the non-IPA group. Further analysis showed that the sensitivity of mNGS in diagnosing IPA was 53.03%, which was higher than that of traditional fungal culture test (27.27%), G test (31.82%), and GM test (34.85%). Notably, when combining fungal culture, G test, GM test, and mNGS, the sensitivity increased to 69.70%, with a specificity of 97.14%. The sensitivity of the combined test was higher than that any of the tests alone for diagnosing IPA.

CONCLUSION: mNGS test offers superior diagnostic performance for IPA in comparison to traditional tests, particularly for testing samples like bronchoalveolar lavage fluid and bronchial secretions. The test result remains valuable even after aspergillus treatment. In addition, the use of mNGS in conjunction with other traditional tests, such as fungal culture test, G test, and GM test, can enhance the diagnostic efficacy for IPA.}, } @article {pmid39398475, year = {2024}, author = {Kumar, G and Bhadury, P}, title = {Dataset of metagenomic profiles of human gut microbiome from frozen fecal samples sequenced using Illumina and ONT chemistries.}, journal = {Data in brief}, volume = {57}, number = {}, pages = {110961}, pmid = {39398475}, issn = {2352-3409}, abstract = {The data presented in this study are metagenomic profiles of human gut microbiome deduced from frozen fecal samples using two different sequencing chemistries namely, Illumina and Oxford Nanopore Technologies (ONT). The generated data is obtained from genomic DNA extracted from frozen fecal samples collected from a healthy individual on Day 3, Day 5, Day 9, Day 12, and Day 30, in addition to Day 1 (unfrozen). The metagenomic sequence data have been deposited at NCBI SRA as BioProject PRJNA827663. The taxonomic annotation undertaken using MG-RAST showed relative abundance of bacteria represented by different taxonomic levels varied significantly based on two sequencing chemistries. There was distinct temporal variation in the relative abundance of bacteria at different taxonomic levels based on the day of extraction of genomic DNA. This dataset can be used to study differences in functional profiles of human gut microbiome using different sequencing technologies. Moreover, generated data can aid in selection of most appropriate sequencing chemistry to study future human gut microbiome studies based on the appropriate preservation method of fecal samples.}, } @article {pmid39398427, year = {2024}, author = {Ji, J and Cai, F and Yuan, C and Huang, C and Zhang, H and Xu, C and Suo, W and Zhu, W and Shi, B and Tang, D and Wang, Y}, title = {Gut Microbiota in Primary Osteoporosis: a Systematic Review.}, journal = {Phenomics (Cham, Switzerland)}, volume = {4}, number = {3}, pages = {293-297}, pmid = {39398427}, issn = {2730-5848}, abstract = {UNLABELLED: The link between gut microbiota (GM) and primary osteoporosis has garnered substantial attention. In this study, we conducted a systematic review encompassing 10 studies that employed high-throughput sequencing methodologies. Notably, the taxonomic profiles exhibited pronounced heterogeneity across reviewed studies. A combined analysis of mechanistical studies screened out potential targets for osteoporosis prevention and treatment. We appraised the limitations in previous studies, and proposed suggestions for optimizing sequencing techniques and experimental designs. Larger-size longitudinal cohorts based on multi-omics and extended phenotypes are recommended to comprehensively characterize the involvement of GM in the pathogenesis of osteoporosis.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s43657-024-00164-y.}, } @article {pmid39398034, year = {2024}, author = {Ji, L and Wang, Y and Sun, Y and Ji, L and Wang, X and Liu, Y and Shen, Q and Yang, S and Zhang, W}, title = {Identification and characterization of multiple novel viruses in fecal samples of ruddy shelducks using viral metagenomics methods.}, journal = {Heliyon}, volume = {10}, number = {19}, pages = {e38338}, pmid = {39398034}, issn = {2405-8440}, abstract = {The viral metagenomics approach is an effective technique for investigating and analysing both existing and emerging viruses in humans and diverse animal samples. The ruddy shelduck, a nationally protected secondary key species of wild animals, has become the predominant species among overwintering waterbirds in Qinghai Lake. Viruses carried by ruddy shelducks can potentially infect humans or other animals; however, limited research on the faecal virome of ruddy shelducks is currently available. In the present study, faecal samples of ruddy shelducks collected from Saga County, Shigatse City, Tibet, China, were subjected to viral metagenomic analysis. The predominant viral families identified in ruddy shelduck samples were Picornaviridae, Parvoviridae, Microviridae, Vilyaviridae, Astroviridae, and Caliciviridae. Among these, two picornavirus genomes have been identified as new strains of the genus Megrivirus in the family Parvoviridae. In addition, viruses that infect parasites and bacteria have been identified and characterised. The present study enhances our comprehension of the composition of the viral community in ruddy shelducks faeces and highlights the dynamic nature of viral evolution and the significance of continuous monitoring to assess potential risks to wildlife and public health.}, } @article {pmid39397942, year = {2024}, author = {Chen, WY and Lee, CP and Pavlović, J and Pangallo, D and Wu, JH}, title = {Characterization of microbiome, resistome, mobilome, and virulome in anoxic and oxic wastewater treatment processes in Slovakia and Taiwan.}, journal = {Heliyon}, volume = {10}, number = {19}, pages = {e38723}, pmid = {39397942}, issn = {2405-8440}, abstract = {This study presents a comprehensive analysis of samples from urban wastewater treatment plants using anoxic/oxic processes in Slovakia and Taiwan, focusing on microbiome, resistome, mobilome, and virulome, which were analyzed using a shotgun metagenomic approach. Distinct characteristics were observed; in Taiwan, a higher abundance and diversity of antibiotic resistance genes were found in both influent and effluent samples, while there was a higher prevalence of mobile genetic elements and virulence factor genes in Slovakia. Variations were noted in microbial community structures; influent samples in Taiwan were reflected from fecal and hospital sources, and those in Slovakia were derived from environmental elements. At the genus level, the samples from Taiwan's sewage treatment plants were dominated by Cloacibacterium and Bacteroides, while Acinetobacter was predominant in samples from Slovakia. Despite similar antibiotic usage patterns, distinct wastewater characteristics and operational disparities influenced microbiome, resistome, mobilome, and virulome compositions, with limited reduction of most resistance genes by the studied anoxic/oxic processes. These findings underscore the importance of region-specific insights into microbial communities for understanding the dynamics of antimicrobial resistance and pathogenicity in urban wastewater treatment systems. Such insights may lay the groundwork for optimizing treatment processes and reducing the dissemination of antibiotic resistance and pathogenicity genes for safeguarding public health.}, } @article {pmid39397494, year = {2024}, author = {Fargeas, M and Faure, F and Douadi, C and Chevarin, C and Birer, A and Sivignon, A and Rodrigues, M and Denizot, J and Billard, E and Barnich, N and Buisson, A}, title = {ChiA: a major player in the virulence of Crohn's disease-associated adherent and invasive Escherichia coli (AIEC).}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2412667}, pmid = {39397494}, issn = {1949-0984}, mesh = {*Crohn Disease/microbiology/pathology ; Humans ; *Escherichia coli/genetics/pathogenicity/metabolism ; Animals ; *Bacterial Adhesion ; Mice ; *Intestinal Mucosa/microbiology/metabolism/pathology ; *Escherichia coli Infections/microbiology ; Virulence ; Disease Models, Animal ; Adhesins, Escherichia coli/metabolism/genetics ; Female ; Male ; Colitis/microbiology/pathology ; Virulence Factors/genetics/metabolism ; Mice, Inbred C57BL ; Mucins/metabolism ; }, abstract = {We investigated the role of ChiA and its associated polymorphisms in the interaction between Crohn's disease (CD)-associated adherent-invasive Escherichia coli (AIEC) and intestinal mucosa. We observed a higher abundance of chiA among the metagenome of CD patients compared to healthy subjects. In dextran sulfate sodium-induced colitis mice model, AIEC-LF82∆chiA colonization was reduced in ileal, colonic and fecal samples compared to wild-type LF82. The binding of ChiA to recombinant human CHI3L1 or mucus was higher with the pathogenic polymorphism. The strength of ChiA-mucin interaction was 300-fold stronger than ChiA-rhCHI3L1. ChiA was able to degrade mucin to promote its growth and enabled LF82 to get closer to epithelial cells. The pathogenic polymorphism of ChiA had a stronger impact on mucus degradation than on the binding capability of AIEC to adhere to the intestinal epithelium. We observed that ChiA could favor an efficient bacterial invasion of intestinal crypts, and that ChiA, especially its pathogenic polymorphism, gives LF82 an advantage to uptake within Peyer's patches, macrophages and mesenteric lymph nodes. All together, these data support the role of ChiA in the virulence of AIEC and show that it could be a promising target to reduce AIEC colonization in patients with CD.}, } @article {pmid39397304, year = {2024}, author = {Qing, Z and Jida, Y and Chengxiu, F and Yanli, Y and Xia, L and Sihe, D}, title = {Ralstonia solanacearum Infection Drives the Assembly and Functional Adaptation of Potato Rhizosphere Microbial Communities.}, journal = {The plant pathology journal}, volume = {40}, number = {5}, pages = {498-511}, pmid = {39397304}, issn = {1598-2254}, support = {202204BI090024//Yunnan Innovation Guidance and technology-based Enterprise Cultivation Program/ ; }, abstract = {Bacterial wilt caused by Ralstonia solanacearum is a destructive disease that affects potato production, leading to severe yield losses. Currently, little is known about the changes in the assembly and functional adaptation of potato rhizosphere microbial communities during different stages of R. solanacearum infection. In this study, using amplicon and metagenomic sequencing approaches, we analyzed the changes in the composition and functions of bacterial and fungal communities in the potato rhizosphere across four stages of R. solanacearum infection. The results showed that R. solanacearum infection led to significant changes in the composition and functions of bacterial and fungal communities in the potato rhizosphere, with various microbial properties (including α,β-diversity, species composition, and community ecological functions) all being driven by R. solanacearum infection. The relative abundance of some beneficial microorganisms in the potato rhizosphere, including Firmicutes, Bacillus, Pseudomonas, and Mortierella, decreased as the duration of infection increased. Moreover, the related microbial communities played a significant role in basic metabolism and signal transduction; however, the functions involved in soil C, N, and P transformation weakened. This study provides new insights into the dynamic changes in the composition and functions of potato rhizosphere microbial communities at different stages of R. solanacearum infection to adapt to the growth promotion or disease suppression strategies of host plants, which may provide guidance for formulating future strategies to regulate microbial communities for the integrated control of soil-borne plant diseases.}, } @article {pmid39396970, year = {2024}, author = {Zu, C and Li, W and Zhang, M and Dong, Y and Fu, S and Feng, J and Hong, R and Huang, H and Hu, Y and Su, J}, title = {Outcome of Pneumocystis Jirovecii pneumonia (PcP) in post-CAR-T patients with hematological malignancies.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {1147}, pmid = {39396970}, issn = {1471-2334}, support = {81800178//National Natural Science Foundation of China,China/ ; 81730008//National Natural Science Foundation of China/ ; 82270234//National Natural Science Foundation of China/ ; 2022YFC2304505//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Pneumonia, Pneumocystis/immunology ; Male ; Female ; Middle Aged ; Retrospective Studies ; *Hematologic Neoplasms/complications ; *Pneumocystis carinii ; Adult ; *Immunocompromised Host ; Immunotherapy, Adoptive/adverse effects ; Aged ; Treatment Outcome ; Opportunistic Infections/microbiology/immunology ; Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use ; Young Adult ; }, abstract = {BACKGROUND: Pneumocystis jirovecii pneumonia (PcP) is an opportunistic infection associated with immunocompromised patients. The development of novel immunotherapies has promoted the incidence of PcP. This study describes the clinical course and outcome of PcP in chimeric antigen receptor (CAR) T cell recipients with hematological malignancies.

METHODS: This is a retrospective case series of CAR-T recipients diagnosed with PcP in our center. The cases were all confirmed by metagenomic next-generation sequencing of clinical samples. The demographic, clinical, and outcome data were retrieved from the patients' medical charts and electronic medical record system.

RESULTS: In total, 8 cases of PcP were identified. The underlying malignancies included T-acute lymphoblastic leukemia (ALL) (n = 1), diffuse large B cell lymphoma (DLBCL) (n = 4), and B-ALL (n = 3). One patient received short-term sulfamethoxazole-trimethoprim (SMZ-TMP) while the others had no prophylaxis. Four patients had neutropenia/lymphopenia at the diagnosis of PcP, and two patients had immunosuppressants within one month before PcP manifestation. The median time from CAR-T infusion to PcP diagnosis was 98.5 days (range 52-251). Seven patients recovered from PcP after proper management while one died of septic shock.

CONCLUSION: PcP can occur after different CAR-T product, and the long-term depletion of immune cells seems to be related to PcP. SMZ-TMP is effective in this setting. More real-world experience of CAR-T therapy is required to assess the incidence and outcome of PcP in this population.}, } @article {pmid39396943, year = {2024}, author = {Li, H and Yu, J and Zeng, Z and Liu, C and Zhang, Y and Xia, H and Guo, S}, title = {Clinical and pathological features of cerebrospinal meningitis caused by Pantoea agglomerans : a case report.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {1150}, pmid = {39396943}, issn = {1471-2334}, mesh = {Humans ; Female ; *Pantoea/isolation & purification ; Middle Aged ; Meningitis, Bacterial/microbiology/diagnosis/pathology/drug therapy ; Enterobacteriaceae Infections/microbiology/pathology ; Magnetic Resonance Imaging ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {BACKGROUND: Pantoea agglomerans (P. agglomerans) is a gram-negative bacterium that is commonly isolated from plant surfaces, seeds, and the environment. As an opportunistic pathogen, it can cause blood, urinary and soft tissue infections in immunocompromised patients. In central nervous system, P. agglomerans infection has been report in children and immune-compromised patients, however, infection by such bacterium in nontraumatized immune competent adults has not been reported. Here, we report a case of P. agglomerans cerebrospinal meningitis accompanied by positive anti-myeloperoxidase (MPO) antibody in a 49-year-old female who has a history of black fungus planting.

CASE PRESENTATION: The patient manifested with repeated fever, headache, generalized muscle pain, and neurological defects. Cerebrospinal fluid (CSF) tests revealed a moderately elevated number of polymorphonuclear leukocytes (50-193 × 10[6]/L), low glucose levels (0.54-2.44 mmo1/L), and extremely high protein content (2.42-25.42 g/L). Blood tests showed positive anti-myeloperoxidase antibodies lasting for 1.5 year before turning negative. Spine MRI showed thickening and enhancement of the whole spinal meninges. CSF metagenomic next-generation sequencing (mNGS) revealed 75,189 specific DNA reads of P. agglomerans. The patient underwent spinal laminectomy due to meningeal adhesions. Pathological results revealed fibrous tissue proliferation, inflammatory infiltration with focal necrosis and calcification in the dura mater. The patient was successfully treated with sufficient antibiotics at 1-year follow-up.

CONCLUSIONS: People should be alert to CNS infections caused by P. agglomerans which presented with relatively mild clinical symptoms at onset, especially for those who contucts relevant agricultural and forestry work. The CSF characterization of P. agglomerans meningitis is elevated multiple nuclei white blood cells, significantly reduced glucose content, and markedly increased protein level which may be related to the secondary spinal membrane adhesions.}, } @article {pmid39396785, year = {2024}, author = {Su, XS and Zhang, YB and Jin, WJ and Zhang, ZJ and Xie, ZK and Wang, RY and Wang, YJ and Qiu, Y}, title = {Lily viruses regulate the viral community of the Lanzhou lily rhizosphere and indirectly affect rhizosphere carbon and nitrogen cycling.}, journal = {The Science of the total environment}, volume = {955}, number = {}, pages = {176808}, doi = {10.1016/j.scitotenv.2024.176808}, pmid = {39396785}, issn = {1879-1026}, mesh = {*Rhizosphere ; *Soil Microbiology ; *Lilium/virology/microbiology ; *Nitrogen/metabolism ; Nitrogen Cycle ; Carbon/metabolism ; Plant Viruses/physiology ; Virome ; China ; Plant Roots/virology/microbiology/metabolism ; Soil/chemistry ; Carbon Cycle ; Metagenomics ; Cucumovirus/physiology ; }, abstract = {The rhizosphere, where plant roots interact intensely with the soil, is a crucial but understudied area in terms of the impact of virus infection. In this study, we investigated the effects of lily symptomless virus (LSV) and cucumber mosaic virus (CMV) on the Lanzhou lily (Lilium davidii var. unicolor) rhizosphere using metagenomics and bioinformatics analysis. We found that virus infection significantly altered soil pH, inorganic carbon, nitrate nitrogen, and total sulfur. Co-infection with LSV and CMV had a greater influence than single infections on the α- and β-diversity of the rhizosphere viral community in which the absolute abundance of certain virus families (Siphoviridae, Podoviridae, and Myoviridae) increased significantly, whereas bacteria, fungi, and archaea remained relatively unaffected. These altered virus populations influenced the rhizosphere microbial carbon and nitrogen cycles by exerting top-down control on bacteria. Co-infection potentially weakened rhizosphere carbon fixation and promoted processes such as methane oxidation, nitrification, and denitrification. In addition, the co-occurrence network of bacteria and viruses in the rhizosphere revealed substantial changes in microbial community composition under co-infection. Our partial-least-squares path model confirmed that the diversity of the rhizosphere viral community indirectly regulated the carbon and nitrogen cycling functions of the microbial community, thus affecting the accumulation of carbon and nitrogen nutrients in the soil. Our results are the first report of the effects of virus infection on the lily rhizosphere, particularly for co-infection; they therefore complement research on the plant virus pathogenic mechanisms, and increase our understanding of the ecological role of rhizosphere soil viruses.}, } @article {pmid39396767, year = {2024}, author = {Zhao, F and Tie, N and Kwok, LY and Ma, T and Wang, J and Man, D and Yuan, X and Li, H and Pang, L and Shi, H and Ren, S and Yu, Z and Shen, X and Li, H and Zhang, H}, title = {Baseline gut microbiome as a predictive biomarker of response to probiotic adjuvant treatment in gout management.}, journal = {Pharmacological research}, volume = {209}, number = {}, pages = {107445}, doi = {10.1016/j.phrs.2024.107445}, pmid = {39396767}, issn = {1096-1186}, mesh = {Humans ; *Probiotics/therapeutic use/administration & dosage ; *Gout/drug therapy/blood ; *Gastrointestinal Microbiome/drug effects ; Male ; Double-Blind Method ; Middle Aged ; *Uric Acid/blood ; Female ; *Biomarkers/blood ; Aged ; Gout Suppressants/therapeutic use ; Febuxostat/therapeutic use ; Adult ; Treatment Outcome ; Feces/microbiology ; }, abstract = {Gout is characterized by dysregulation of uric acid (UA) metabolism, and the gut microbiota may serve as a regulatory target. This two-month randomized, double-blind, placebo-controlled trial aimed to investigate the additional benefits of coadministering Probio-X alongside febuxostat. A total of 160 patients with gout were randomly assigned to either the probiotic group (n = 120; Probio-X [3 × 10[10] CFU/day] with febuxostat) or the placebo group (n = 40; placebo material with febuxostat). Coadministration of Probio-X significantly decreased serum UA levels and the rate of acute gout attacks (P < 0.05). Based on achieving a target sUA level (360 μmol/L) after the intervention, the probiotic group was further subdivided into probiotic-responsive (ProA; n = 54) and probiotic-unresponsive (ProB; n = 66) subgroups. Post-intervention clinical indicators, metagenomic, and metabolomic changes in the ProB and placebo groups were similar, but differed from those in the ProA group, which exhibited significantly lower levels of acute gout attack, gout impact score, serum indicators (UA, XOD, hypoxanthine, and IL-1β), and fecal gene abundances of UA-producing pathways (KEGG orthologs of K13479 and K01487; gut metabolic modules for formate conversion and lactose and galactose degradation). Additionally, the ProA group showed significantly higher levels (P < 0.05) of gut SCFAs-producing bacteria and UA-related metabolites (xanthine, hypoxanthine, bile acids) after the intervention. Finally, we established a gout metagenomic classifier to predict probiotic responsiveness based on subjects' baseline gut microbiota composition. Our results indicate that probiotic-driven therapeutic responses are highly individual, with the probiotic-responsive cohort benefitting significantly from probiotic coadministration.}, } @article {pmid39395606, year = {2024}, author = {Wang, E and Sun, H and Xing, F and Zheng, Y and Chen, P and Lyu, T and Liu, R and Li, X and Dong, R and Guo, J}, title = {Metagenomic analysis reveals metabolic mechanism of enhancing lignocellulosic anaerobic digestion mediated by CO2/O2-nanobubble water.}, journal = {Bioresource technology}, volume = {414}, number = {}, pages = {131622}, doi = {10.1016/j.biortech.2024.131622}, pmid = {39395606}, issn = {1873-2976}, mesh = {Anaerobiosis ; *Lignin/metabolism ; *Carbon Dioxide/metabolism ; *Metagenomics/methods ; *Methane/metabolism ; *Water ; Oxygen/metabolism ; Oryza/metabolism ; }, abstract = {Nanobubble water (NW) has been reported to enhance anaerobic digestion (AD), but its influence on the metabolic pathways of microorganisms remains unclear. In this study, the specific methane yields of rice straw in the CO2NW and O2NW treatments increased by 6.9% and 18.3%, respectively. The electron transport system (ETS) and coenzyme F420 activities were enhanced by the addition of NW. Metagenomic analysis showed that the abundances of most enzymes in the acidification were significantly increased by both CO2NW and O2NW. Regarding methanogenesis, CO2NW promoted the expression of genes encoding enzymes of hydrogenotrophic methanogenesis, while O2NW stimulated both the acetoclastic and hydrogenotrophic methanogenesis. With the addition of O2NW, the expressions of modules related to the tricarboxylic acid (TCA) cycle and oxidative phosphorylation were enhanced, resulting in increased ATP production. This study provided fundamental evidence of the metabolic pathways of microorganisms mediated by NW at each stage of AD.}, } @article {pmid39395603, year = {2024}, author = {Wang, P and Lu, B and Chai, X}, title = {Novel insights into self-defense function of anammox sludge under magnesium ions (Mg[2+]) stress based on Mg[2+] transport system.}, journal = {Bioresource technology}, volume = {414}, number = {}, pages = {131615}, doi = {10.1016/j.biortech.2024.131615}, pmid = {39395603}, issn = {1873-2976}, mesh = {*Sewage/microbiology ; *Magnesium/metabolism ; *Oxidation-Reduction ; Anaerobiosis ; Ammonium Compounds/metabolism ; Stress, Physiological ; Nitrogen/metabolism ; Bacteria/metabolism ; }, abstract = {Magnesium ion (Mg[2+]) plays an important role in the accumulation and stability of anaerobic ammonium-oxidizing bacteria (AnAOB). In this study, the response of anammox sludge to Mg[2+] was comprehensively investigated by performance evaluation and metagenomics analysis. Appropriate Mg[2+] (0.8 mmol/L) could improve the nitrogen removal performance, AnAOB activity, and the synthesis potential of some hydrophobic substances, while high Mg[2+] (>1.6 mmol/L) has a negative effect. Meanwhile, Mg[2+] transmembrane transport theory was introduced to reveal the response principle of AnAOB to Mg[2+] from a novel insight. AnAOB may have a self-defense function based on the PhoQ/PhoP-MgtAB system. Low extracellular Mg[2+] will activate this function to enhance Mg[2+] influx, thereby improving the intracellular metabolism of AnAOB. Excessive Mg[2+], however, dormant this function and induces Mg[2+] efflux, which may decrease the intracellular Mg[2+] and thus affect AnAOB metabolism. These findings provide valuable references for the Mg[2+] regulation of anammox-based process.}, } @article {pmid39395415, year = {2024}, author = {de Flamingh, A and Gnoske, TP and Kerbis Peterhans, JC and Simeonovski, VA and Gitahi, N and Mwebi, O and Agwanda, BR and Catchen, JM and Roca, AL and Malhi, RS}, title = {Compacted hair in broken teeth reveals dietary prey of historic lions.}, journal = {Current biology : CB}, volume = {34}, number = {21}, pages = {5104-5111.e4}, doi = {10.1016/j.cub.2024.09.029}, pmid = {39395415}, issn = {1879-0445}, mesh = {Animals ; *Lions/genetics ; *Hair/chemistry ; Kenya ; Predatory Behavior ; Tooth/chemistry ; Diet/veterinary ; Phylogeny ; }, abstract = {With recent advances, nuclear genome data for phylogenomic analyses can now be sequenced from minuscule quantities of DNA[1] and from specimens that are more than a million years old.[2] DNA analysis from hair is a well-established approach[3] widely used in forensic science[4] and wildlife conservation.[5] Hair samples can be effectively decontaminated[6] and can be used to identify the mammalian species from which the hair was shed.[7][,][8] We aimed to use advances optimized for degraded DNA to systematically identify dietary prey species from hair compacted in the teeth of two Tsavo lions that lived during the 1890s in Kenya (see description of samples in the STAR Methods and Patterson[9] and Kerbis Peterhans and Gnoske[10] for background on the Tsavo "man-eaters"). Analysis of hair DNA identified giraffe, human, oryx, waterbuck, wildebeest, and zebra as prey and also identified hair that originated from lion. DNA preservation allowed for analyses of complete mitogenome profiles of zebra, giraffe, and lion. Giraffe mitogenomes are phylogeographically partitioned, and we found that the lions ate at least two individuals that belong to a subspecies of Masai giraffe (Giraffa tippelskirchi tippelskirchi) typically found in southeast Kenya. The lion mitogenome from a hair sample was identical to the Tsavo lion endogenous mitogenome and most closely matched other East African lions from Kenya and Tanzania. Our approach enables a better understanding of the hunting behaviors, diets, and ecology of historical individuals, populations, and species and holds promise for extinct populations and species.}, } @article {pmid39395412, year = {2024}, author = {Talwar, C and Davuluri, GVN and Kamal, AHM and Coarfa, C and Han, SJ and Veeraragavan, S and Parsawar, K and Putluri, N and Hoffman, K and Jimenez, P and Biest, S and Kommagani, R}, title = {Identification of distinct stool metabolites in women with endometriosis for non-invasive diagnosis and potential for microbiota-based therapies.}, journal = {Med (New York, N.Y.)}, volume = {}, number = {}, pages = {100517}, doi = {10.1016/j.medj.2024.09.006}, pmid = {39395412}, issn = {2666-6340}, abstract = {BACKGROUND: Endometriosis, a poorly studied gynecological condition, is characterized by the presence of ectopic endometrial lesions resulting in pelvic pain, inflammation, and infertility. These associated symptoms contribute to a significant burden, often exacerbated by delayed diagnosis. Current diagnostic methods involve invasive procedures, and existing treatments provide no cure.

METHODS: Microbiome-metabolome signatures in stool samples from individuals with and without endometriosis were determined using unbiased metabolomics and 16S bacteria sequencing. Functional studies for selected microbiota-derived metabolites were conducted in vitro using patient-derived cells and in vivo by employing murine and human xenograft pre-clinical disease models.

FINDINGS: We discovered a unique bacteria-derived metabolite signature intricately linked to endometriosis. The altered fecal metabolite profile exhibits a strong correlation with that observed in inflammatory bowel disease (IBD), revealing intriguing connections between these two conditions. Notably, we validated 4-hydroxyindole, a gut-bacteria-derived metabolite that is lower in stool samples of endometriosis. Extensive in vivo studies found that 4-hydroxyindole suppressed the initiation and progression of endometriosis-associated inflammation and hyperalgesia in heterologous mouse and in pre-clinical models of the disease.

CONCLUSIONS: Our findings are the first to provide a distinct stool metabolite signature in women with endometriosis, which could serve as stool-based non-invasive diagnostics. Further, the gut-microbiota-derived 4-hydroxyindole poses as a therapeutic candidate for ameliorating endometriosis.

FUNDING: This work was funded by the NIH/NICHD grants (R01HD102680, R01HD104813) and a Research Scholar Grant from the American Cancer Society to R.K.}, } @article {pmid39395391, year = {2024}, author = {Gong, K and Peng, C and Hu, S and Xie, W and Chen, A and Liu, T and Zhang, W}, title = {Aging of biodegradable microplastics and their effect on soil properties: Control from soil water.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {136053}, doi = {10.1016/j.jhazmat.2024.136053}, pmid = {39395391}, issn = {1873-3336}, abstract = {The ecological risks of biodegradable microplastics (BMPs) to soil ecosystems have received increasing attention. This study investigates the impacts of polylactic acid microplastics (PLA-MPs) and polybutylene adipate terephthalate microplastics (PBAT-MPs) on soil properties of black soil (BS) and fluvo-aquic soil (FS) under three water conditions including dry (Dry), flooded (FL), and alternate wetting and drying (AWD). The results show that BMPs exhibited more evident aging under Dry and AWD conditions compared to FL condition. However, BMPs aging under FL condition induced more substantial changes in soil properties, especially dissolved organic carbon (DOC) concentrations, than under Dry and AWD conditions. BMPs also increased the humification degree of soil dissolved organic matter (DOM), particularly in BS. Metagenomic analysis of PBAT-MPs treatments showed different changes in microbial community structure depending on soil moisture. Under Dry conditions, PBAT-MPs enhance the ammonium-producing process of soil microbial communities. Genes related to N nitrification and benzene degradation were enriched under AWD conditions. In contrast, PBAT-MPs do not change the abundance of genes related to the N cycle under FL conditions but significantly reduce genes related to benzene degradation. This reduction in benzene degradation genes under FL condition might potentially slow down the degradation of PBAT-MPs, and could lead to temporary accumulation of benzene-related intermediates. These findings highlight the complex interactions between BMPs, soil properties, and microbial communities, emphasizing the need for comprehensive evaluations of BMPs' environmental impacts under varying soil water conditions.}, } @article {pmid39388213, year = {2024}, author = {Lu, R and Dumonceaux, T and Anzar, M and Zovoilis, A and Antonation, K and Barker, D and Corbett, C and Nadon, C and Robertson, J and Eagle, SHC and Lung, O and Rudar, J and Surujballi, O and Laing, C}, title = {MNBC: a multithreaded Minimizer-based Naïve Bayes Classifier for improved metagenomic sequence classification.}, journal = {Bioinformatics (Oxford, England)}, volume = {40}, number = {10}, pages = {}, pmid = {39388213}, issn = {1367-4811}, support = {CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; }, mesh = {*Metagenomics/methods ; *Bayes Theorem ; *Software ; Metagenome ; Machine Learning ; Algorithms ; Sequence Analysis, DNA/methods ; }, abstract = {MOTIVATION: State-of-the-art tools for classifying metagenomic sequencing reads provide both rapid and accurate options, although the combination of both in a single tool is a constantly improving area of research. The machine learning-based Naïve Bayes Classifier (NBC) approach provides a theoretical basis for accurate classification of all reads in a sample.

RESULTS: We developed the multithreaded Minimizer-based Naïve Bayes Classifier (MNBC) tool to improve the NBC approach by applying minimizers, as well as plurality voting for closely related classification scores. A standard reference- and test-sequence framework using simulated variable-length reads benchmarked MNBC with six other state-of-the-art tools: MetaMaps, Ganon, Kraken2, KrakenUniq, CLARK, and Centrifuge. We also applied MNBC to the "marine" and "strain-madness" short-read metagenomic datasets in the Critical Assessment of Metagenome Interpretation (CAMI) II challenge using a corresponding database from the time. MNBC efficiently identified reads from unknown microorganisms, and exhibited the highest species- and genus-level precision and recall on short reads, as well as the highest species-level precision on long reads. It also achieved the highest accuracy on the "strain-madness" dataset.

MNBC is freely available at: https://github.com/ComputationalPathogens/MNBC.}, } @article {pmid39387577, year = {2024}, author = {Beck, KL and Haiminen, N and Agarwal, A and Carrieri, AP and Madgwick, M and Kelly, J and Pylro, V and Kawas, B and Wiedmann, M and Ganda, E}, title = {Development and evaluation of statistical and artificial intelligence approaches with microbial shotgun metagenomics data as an untargeted screening tool for use in food production.}, journal = {mSystems}, volume = {9}, number = {11}, pages = {e0084024}, pmid = {39387577}, issn = {2379-5077}, support = {#PEN04752, #PEN04731//U.S. Department of Agriculture (USDA)/ ; }, mesh = {*Metagenomics/methods ; *Artificial Intelligence ; *Milk/microbiology/chemistry ; Animals ; Food Microbiology/methods ; Microbiota/genetics ; Algorithms ; Principal Component Analysis ; Machine Learning ; }, abstract = {UNLABELLED: The increasing knowledge of microbial ecology in food products relating to quality and safety and the established usefulness of machine learning algorithms for anomaly detection in multiple scenarios suggests that the application of microbiome data in food production systems for anomaly detection could be a valuable approach to be used in food systems. These methods could be used to identify ingredients that deviate from their typical microbial composition, which could indicate food fraud or safety issues. The objective of this study was to assess the feasibility of using shotgun sequencing data as input into anomaly detection algorithms using fluid milk as a model system. Contrastive principal component analysis (PCA), cluster-based methods, and explainable artificial intelligence (AI) were evaluated for the detection of two anomalous sample classes using longitudinal metagenomic profiling of fluid milk compared to baseline (BL) samples collected under comparable circumstances. Traditional methods (alpha and beta diversity, clustering-based contrastive PCA, multidimensional scaling, and dendrograms) failed to differentiate anomalous sample classes; however, explainable AI was able to classify anomalous vs baseline samples and indicate microbial drivers in association with antibiotic use. We validated the potential for explainable AI to classify different milk sources using larger publicly available fluid milk 16S rDNA sequencing data sets and demonstrated that explainable AI is able to differentiate between milk storage methods, processing stages, and seasons. Our results indicate that the application of artificial intelligence continues to hold promise in the realm of microbiome data analysis and could present further opportunities for downstream analytic automation to aid in food safety and quality.

IMPORTANCE: We evaluated the feasibility of using untargeted metagenomic sequencing of raw milk for detecting anomalous food ingredient content with artificial intelligence methods in a study specifically designed to test this hypothesis. We also show through analysis of publicly available fluid milk microbial data that our artificial intelligence approach is able to successfully predict milk in different stages of processing. The approach could potentially be applied in the food industry for safety and quality control.}, } @article {pmid39387572, year = {2024}, author = {Ueno, K and Sawada, S and Ishibashi, M and Kanda, Y and Shimizu, H and Toya, Y}, title = {Identification of a novel NADPH generation reaction in the pentose phosphate pathway in Escherichia coli using mBFP.}, journal = {Journal of bacteriology}, volume = {206}, number = {11}, pages = {e0027624}, pmid = {39387572}, issn = {1098-5530}, support = {Grant-in-Aid for Scientific Research (S) No.19H05626//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; GteX Program Japan Grant Number JPMJGX23B4//MEXT | Japan Science and Technology Agency (JST)/ ; }, mesh = {*NADP/metabolism ; *Pentose Phosphate Pathway ; *Escherichia coli/genetics/metabolism ; *Xylose/metabolism ; Glucosephosphate Dehydrogenase/metabolism/genetics ; Escherichia coli Proteins/metabolism/genetics ; Luminescent Proteins/genetics/metabolism ; Glucose-6-Phosphate Isomerase/metabolism/genetics ; Gene Expression Regulation, Bacterial ; }, abstract = {NADPH is a redox cofactor that drives the anabolic reactions. Although major NADPH generation reactions have been identified in Escherichia coli, some minor reactions have not been identified. In the present study, we explored novel NADPH generation reactions by monitoring the fluorescence dynamics after the addition of carbon sources to starved cells, using a metagenome-derived blue fluorescent protein (mBFP) as an intracellular NADPH reporter. Perturbation analyses were performed on a glucose-6-phosphate isomerase (PGI) deletion strain and its parental strain. Interestingly, mBFP fluorescence increased not only in the parental strain but also in the ΔPGI strain after the addition of xylose. Because the ΔPGI strain cannot metabolize xylose through the oxidative pentose phosphate pathway, this suggests that an unexpected NADPH generation reaction contributes to an increase in fluorescence. To unravel this mystery, we deleted the NADPH generation enzymes including transhydrogenase, isocitrate dehydrogenase, NADP[+]-dependent malic enzyme, glucose-6-phosphate dehydrogenase (G6PDH), and 6-phosphogluconate dehydrogenase (6PGDH) in the ΔPGI strain, and revealed that G6PDH and 6PGDH contribute to an increase in fluorescence under xylose conditions. In vitro assays using purified enzymes showed that G6PDH can produce NADPH using erythrose-4-phosphate (E4P) as a substitute for glucose-6-phosphate. Because the Km (0.65 mM) for E4P was much higher than the reported intracellular E4P concentrations in E. coli, little E4P must be metabolized through this bypass in the parental strain. However, the flux would increase when E4P accumulates in the cells owing to genetic modifications. This finding provides a metabolic engineering strategy for generating NADPH to produce useful compounds using xylose as a carbon source.IMPORTANCEBecause NADPH is consumed during the synthesis of various useful compounds, enhancing NADPH regeneration is highly desirable in metabolic engineering. In this study, we explored novel NADPH generation reactions in Escherichia coli using a fluorescent NADPH reporter and found that glucose-6-phosphate dehydrogenase can produce NADPH using erythrose-4-phosphate as a substrate under xylose conditions. Xylose is an abundant sugar in nature and is an attractive carbon source for bioproduction. Therefore, this finding contributes to novel pathway engineering strategies using a xylose carbon source in E. coli to produce useful compounds that consume NADPH for their synthesis.}, } @article {pmid39395082, year = {2024}, author = {de Farias, BO and Saggioro, EM and Montenegro, KS and Magaldi, M and Santos, HSO and Gonçalves-Brito, AS and Pimenta, RL and Ferreira, RG and Spisso, BF and Pereira, MU and Bianco, K and Clementino, MM}, title = {Metagenomic insights into plasmid-mediated antimicrobial resistance in poultry slaughterhouse wastewater: antibiotics occurrence and genetic markers.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {51}, pages = {60880-60894}, pmid = {39395082}, issn = {1614-7499}, support = {E-21/201.271/2021//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; E-26/210.882/2021//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; 304571/2021-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, mesh = {*Wastewater ; Animals ; *Poultry ; *Abattoirs ; *Anti-Bacterial Agents/pharmacology ; *Plasmids ; Genetic Markers ; Drug Resistance, Microbial/genetics ; Metagenomics ; Escherichia coli/genetics/drug effects ; RNA, Ribosomal, 16S ; }, abstract = {Slaughterhouse wastewater represents important convergence and concentration points for antimicrobial residues, bacteria, and antibiotic resistance genes (ARG), which can promote antimicrobial resistance propagation in different environmental compartments. This study reports the assessment of the metaplasmidome-associated resistome in poultry slaughterhouse wastewater treated by biological processes, employing metagenomic sequencing. Antimicrobial residues from a wastewater treatment plant (WWTP) that treats poultry slaughterhouse influents and effluents were investigated through high-performance liquid chromatography coupled to tandem mass spectrometry (HPLC-MS/MS). Residues from the macrolide, sulfonamide, and fluoroquinolone classes were detected, the latter two persisting after the wastewater treatment. The genetic markers 16S rRNA rrs (bacterial community) and uidA (Escherichia coli) were investigated by RT-qPCR and the sul1 and int1 genes by qPCR. After treatment, the 16S rRNA rrs, uidA, sul1, and int1 markers exhibited reductions of 0.67, 1.07, 1.28, and 0.79 genes copies, respectively, with no statistical significance (p > 0.05). The plasmidome-focused metagenomics sequences (MiSeq platform (Illumina®)) revealed more than 100 ARG in the WWTP influent, which can potentially confer resistance to 14 pharmacological classes relevant in the human and veterinary clinical contexts, in which the qnr gene (resistance to fluoroquinolones) was the most prevalent. Only 7.8% of ARG were reduced after wastewater treatment, and the remaining 92.2% were associated with an increase in the prevalence of ARG linked to multidrug efflux pumps, substrate-specific for certain classes of antibiotics, or broad resistance to multiple medications. These data demonstrate that wastewater from poultry slaughterhouses plays a crucial role as an ARG reservoir and in the spread of AMR into the environment.}, } @article {pmid39394961, year = {2024}, author = {Branck, T and Hu, Z and Nickols, WA and Walsh, AM and Bhosle, A and Short, MI and Nearing, JT and Asnicar, F and McIver, LJ and Maharjan, S and Rahnavard, A and Louyakis, AS and Badri, DV and Brockel, C and Thompson, KN and Huttenhower, C}, title = {Comprehensive profile of the companion animal gut microbiome integrating reference-based and reference-free methods.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39394961}, issn = {1751-7370}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Dogs/microbiology ; Cats ; *Pets/microbiology ; *Feces/microbiology ; *Phylogeny ; *Metagenome ; Humans ; *Metagenomics ; Bacteria/genetics/classification/isolation & purification ; }, abstract = {The gut microbiome of companion animals is relatively underexplored, despite its relevance to animal health, pet owner health, and basic microbial community biology. Here, we provide the most comprehensive analysis of the canine and feline gut microbiomes to date, incorporating 2639 stool shotgun metagenomes (2272 dog and 367 cat) spanning 14 publicly available datasets (n = 730) and 8 new study populations (n = 1909). These are compared with 238 and 112 baseline human gut metagenomes from the Human Microbiome Project 1-II and a traditionally living Malagasy cohort, respectively, processed in a manner identical to the animal metagenomes. All microbiomes were characterized using reference-based taxonomic and functional profiling, as well as de novo assembly yielding metagenomic assembled genomes clustered into species-level genome bins. Companion animals shared 184 species-level genome bins not found in humans, whereas 198 were found in all three hosts. We applied novel methodology to distinguish strains of these shared organisms either transferred or unique to host species, with phylogenetic patterns suggesting host-specific adaptation of microbial lineages. This corresponded with functional divergence of these lineages by host (e.g. differences in metabolic and antibiotic resistance genes) likely important to companion animal health. This study provides the largest resource to date of companion animal gut metagenomes and greatly contributes to our understanding of the "One Health" concept of a shared microbial environment among humans and companion animals, affecting infectious diseases, immune response, and specific genetic elements.}, } @article {pmid39394504, year = {2024}, author = {Passarini, MRZ and Robayo, MIG and Ottoni, JR and Duarte, AWF and Rosa, LH}, title = {Biotechnological potential in agriculture of soil Antarctic microorganisms revealed by omics approach.}, journal = {World journal of microbiology & biotechnology}, volume = {40}, number = {11}, pages = {345}, pmid = {39394504}, issn = {1573-0972}, support = {Nº 205/2021//Program Institutional Triple Agenda EDITAL PRPPG/ ; }, mesh = {*Soil Microbiology ; Antarctic Regions ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Agriculture ; *Fungi/classification/genetics/isolation & purification/metabolism ; *Biotechnology ; *Metagenomics ; High-Throughput Nucleotide Sequencing ; Soil/chemistry ; Phylogeny ; Nitrogen/metabolism ; Microbiota ; }, abstract = {The biotechnological potential for agricultural applications in the soil in the thawing process on Whalers Bay, Deception Island, Antarctica was evaluated using a metagenomic approach through high-throughput sequencing. Approximately 22.70% of the sequences were affiliated to the phyla of the Bacteria dominion, followed by 0.26% to the Eukarya. Proteobacteria (Bacteria) and Ascomycota (Fungi) were the most abundant phyla. Thirty-two and thirty-six bacterial and fungal genera associated with agricultural biotechnological applications were observed. Streptomyces and Pythium were the most abundant genera related to the Bacteria and Oomycota, respectively. The main agricultural application associated with bacteria was nitrogen affixation; in contrast for fungi, was associated with phytopathogenic capabilities. The present study showed the need to use metagenomic technology to understand the dynamics and possible metabolic pathways associated with the microbial communities present in the soil sample in the process of thawing recovered from the Antarctic continent, which presented potential application in processes of agro-industrial interest.}, } @article {pmid39394213, year = {2024}, author = {Neshat, SA and Santillan, E and Seshan, H and Wuertz, S}, title = {Author Correction: Non-redundant metagenome-assembled genomes of activated sludge reactors at different disturbances and scales.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1120}, doi = {10.1038/s41597-024-03957-y}, pmid = {39394213}, issn = {2052-4463}, } @article {pmid39393653, year = {2024}, author = {Li, Y and Huang, F and Dong, S and Liu, L and Lin, L and Li, Z and Zheng, Y and Hu, Z}, title = {Microbiota succession, species interactions, and metabolic functions during autotrophic biofloc formation in zero-water-exchange shrimp farming without organic carbon supplements.}, journal = {Bioresource technology}, volume = {414}, number = {}, pages = {131584}, doi = {10.1016/j.biortech.2024.131584}, pmid = {39393653}, issn = {1873-2976}, mesh = {Animals ; *Aquaculture/methods ; *Microbiota ; *Carbon ; *Nitrogen ; *Bacteria/metabolism ; *Autotrophic Processes ; Penaeidae ; Microalgae/metabolism ; Ammonia/metabolism ; }, abstract = {Autotrophic bioflocs (ABF) exhibits lower energy consumption, more environment-friendly and cost-effective than heterotrophic bioflocs depending on organic carbon supplements. Whereas ABF has not been widely applied to aquaculture production. Here, ABF successfully performed to control ammonia and nitrite under harmless levels even when carbon-to-nitrogen ratio reduced to 2.0, during 12-week shrimp farming in commercial scale. ABF was mainly dominated by bacteria of Proteobacteria, Bacteroidota, Chloroflexi and eukaryotes of Bacillariophyta, Rotifera, Ciliophora. A notable shift occurred in ABF with the significant decreases of Proteobacteria and Rotifera replaced by Bacteroidota, Chloroflexi, and Bacillariophyta after four weeks. Nitrogen metabolism was synergistically executed by bacteria and microalgae, especially the positive interaction between Nitrospira and Halamphora for ABF nitrification establishment. Metagenomics confirmed the complete functional genes of key bacteria related to the cycling of carbon, nitrogen, and phosphorus by ABF. This study may promote the development application of ABF in low-carbon shrimp aquaculture.}, } @article {pmid39393455, year = {2024}, author = {Wang, R and Lu, P and Chen, F and Huang, Y and Ding, H and Cheng, T}, title = {Groundwater resistant gene accumulation in mining-agriculture complex zones: Insights from metagenomic analysis of subterranean mineral and terrestrial agricultural interactions.}, journal = {Environmental research}, volume = {263}, number = {Pt 2}, pages = {120138}, doi = {10.1016/j.envres.2024.120138}, pmid = {39393455}, issn = {1096-0953}, mesh = {*Groundwater/microbiology/chemistry ; *Mining ; *Agriculture ; Metagenomics ; Drug Resistance, Microbial/genetics ; Water Pollutants, Chemical/analysis/metabolism ; Minerals/metabolism ; }, abstract = {During the Mining-Agriculture Complex Areas, the mining and agriculture activities could lead to an excessive presence of sulfate content in the regional groundwater. Sulfate exhibits the potential to influence the positive accumulation of RGs, although its mechanisms remain inadequately explored. To address this gap, this study analyzed the RGs buildup mechanisms in the groundwater of the mining-agriculture complex area. Results showed a widespread presence of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs), especially in coal-seams crevice groundwater. And iron and sulfur are primary environmental factors conducive to RGs accumulation through a synergistic interaction. Microbial annotation of gene sets sourced from coal-seams crevice groundwater samples unveiled part of sulfur-metabolizing microorganisms that were hosts of both ARGs and MRGs. Mechanistic insights revealed that iron may stimulates reactive oxygen species (ROS) generation, facilitating RGs accumulation, while adjusting sulfur metabolism and the synthesis of iron-sulfur clusters, thereby augmenting microbial growth which as predominant hosts of RGs, thereby intensifying the buildup of RGs.}, } @article {pmid39393325, year = {2024}, author = {Yang, C and Huang, B and Lin, J and Yang, Q and Guo, Y and Liu, D and Sun, B}, title = {Isolation and screening of high biofilm producing lactic acid bacteria, and exploration of its effects on the microbial hazard in corn straw silage.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {136009}, doi = {10.1016/j.jhazmat.2024.136009}, pmid = {39393325}, issn = {1873-3336}, mesh = {*Biofilms ; *Zea mays/microbiology ; *Silage/microbiology ; Lactic Acid/metabolism ; Fermentation ; Lactobacillales/metabolism/genetics/isolation & purification ; Lactobacillus plantarum/metabolism/genetics ; }, abstract = {Silage is a well-established method for preserving feed. However, the preparation process still poses several potential microbial hazards. Lactic acid bacteria exhibiting a biofilm phenotype are considered the most advanced 'fourth-generation probiotics' due to their significant potential in enhancing fermentation quality. In this study, a strain of high-biofilm-producing lactic acid bacteria (HBP-LAB) was successfully isolated from silage samples using the crystal violet method and designated as Lactiplantibacillus plantarum S23Y. This strain was subsequently used as an inoculant in corn straw for experimental purposes. The results indicated that it effectively reduced dry matter loss caused by microorganisms, thereby enhancing the retention of dry matter in silage. Following aerobic exposure, this strain was able to maintain the population of Lactobacillus and the concentration of lactic acid, which significantly decreased the likelihood of yeast-induced aerobic spoilage and improved the aerobic stability of the silage. However, it is important to note that this HBP-LAB did not have a significant impact on antibiotic resistance genes (ARGs) or mobile genetic elements (MGEs) in the silage. In conclusion, using S23Y as a representative strain, we have demonstrated that HBP-LAB can enhance the fermentation quality of silage to a certain extent and mitigate the detrimental effects of microorganisms. The findings of this study provide valuable insights for the application of lactic acid bacteria with a biofilm phenotype in silage fermentation.}, } @article {pmid39393228, year = {2024}, author = {Dey, G and Maity, JP and Banerjee, P and Sharma, RK and Das, K and Gnanachandrasamy, G and Wang, CW and Lin, PY and Wang, SL and Chen, CY}, title = {Evaluation and mitigation of potentially toxic elements contamination in mangrove ecosystem: Insights into phytoremediation and microbial perspective.}, journal = {Marine pollution bulletin}, volume = {209}, number = {Pt A}, pages = {117035}, doi = {10.1016/j.marpolbul.2024.117035}, pmid = {39393228}, issn = {1879-3363}, mesh = {*Biodegradation, Environmental ; *Wetlands ; *Water Pollutants, Chemical/analysis ; Taiwan ; Avicennia ; Environmental Monitoring ; Geologic Sediments/chemistry/microbiology ; Microbiota ; Ecosystem ; }, abstract = {Mangroves, essential coastal ecosystems, are threatened by human-induced Potentially-toxic-elements (PTEs) pollution. This study analyzed PTEs distribution, phytoremediation potential, and rhizosphere microbial communities in Taiwan's Xinfeng mangrove forest. Significant variations in physicochemical and PTEs concentrations were observed across adjacent water bodies, with moderate contamination in the river, estuary, and overlying water of mangroves sediment. The partition-coefficient showed the mobility of Bi, Pb, Co, and Sr at the water-sediment interface. The geochemical-indices revealed high Bi and Pb contamination and moderate Zn, Sr, Cu, and Cd contamination in sediment. The overall pollution indices indicated the significant contamination, while moderate ecological risk was found for Cd (40 ≤ Er[i] < 80). Mangroves Kandelia obovata and Avicennia marina exhibited promising PTEs phytoremediation potential (Bi, Cd, Mn, Sr, and Co). Metagenomics indicated a diverse microbial community with N-fixation, P-solubilization, IAA synthesis, and PTEs-resistance genes. These findings underscore the need for targeted conservation to protect these critical habitats.}, } @article {pmid39392286, year = {2024}, author = {Rey Redondo, E and Leung, SKK and Yung, CCM}, title = {Genomic and biogeographic characterisation of the novel prasinovirus Mantoniella tinhauana virus 1.}, journal = {Environmental microbiology reports}, volume = {16}, number = {5}, pages = {e70020}, pmid = {39392286}, issn = {1758-2229}, support = {26100521//Research Grants Council, University Grants Committee, Hong Kong/ ; }, mesh = {*Genome, Viral/genetics ; *Phylogeny ; Host Specificity ; Seawater/virology ; China ; Genomics ; Phycodnaviridae/genetics/isolation & purification/classification ; Phylogeography ; Chlorophyta/virology/genetics ; }, abstract = {Mamiellophyceae are a ubiquitous class of unicellular green algae in the global ocean. Their ecological importance is highlighted in studies focused on the prominent genera Micromonas, Ostreococcus, and Bathycoccus. Mamiellophyceae are susceptible to prasinoviruses, double-stranded DNA viruses belonging to the nucleocytoplasmic large DNA virus group. Our study represents the first isolation of a prasinovirus in the South China Sea and the only one to infect the globally distributed genus Mantoniella. We conducted a comparative analysis with previously identified viral relatives, encompassing morphological characteristics, host specificity, marker-based phylogenetic placement, and whole-genome sequence comparisons. Although it shares morphological and genetic similarities with established prasinoviruses, this novel virus showed distinct genetic traits, confining its infection to the species Mantoniella tinhauana. We also explored the global biogeography of this prasinovirus and its host by mapping metagenomic data and analysing their relationship with various environmental parameters. Our results demonstrate a pronounced link between the virus and its host, both found predominantly in higher latitudes in the surface ocean. By gaining an increased understanding of the relationships between viruses, hosts, and environments, researchers can better make predictions and potentially implement measures to mitigate the consequences of climate change on oceanic processes.}, } @article {pmid39390720, year = {2024}, author = {Dzhuraeva, M and Bobodzhanova, K and Birkeland, NK}, title = {The metagenomic landscape of a high-altitude geothermal spring in Tajikistan reveals a novel Desulfurococcaceae member, Zestomicrobium tamdykulense gen. nov., sp. nov.}, journal = {MicrobiologyOpen}, volume = {13}, number = {5}, pages = {e70004}, pmid = {39390720}, issn = {2045-8827}, support = {CPEA-LT-2017/10061//Norwegian Directorate for Higher Education and Skills (HK-dir)/ ; }, mesh = {*Hot Springs/microbiology ; *Phylogeny ; Tajikistan ; *Altitude ; Metagenomics ; Archaea/genetics/classification ; Metagenome ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Bacteria/genetics/classification/isolation & purification ; }, abstract = {Metagenomic analysis was conducted to assess the microbial community in the high-altitude Tamdykul geothermal spring in Tajikistan. This analysis yielded six high-quality bins from the members of Thermaceae, Aquificaceae, and Halothiobacillaceae, with a 41.2%, 19.7%, and 18.1% share in the total metagenome, respectively. Minor components included Schleiferia thermophila (1.6%) and members of the archaeal taxa Pyrobaculum (1.2%) and Desulfurococcaceae (0.7%). Further analysis of the metagenome-assembled genome (MAG) from the Desulfurococcaceae family (MAG002) revealed novel taxonomy with only 80.95% closest placement average nucleotide identity value to its most closely related member of the Desulfurococcaceae family, which is part of the Thermoproteota phylum comprising hyperthermophilic members widespread in geothermal environments. MAG002 consisted of 1.3 Mbp, distributed into 48 contigs with 1504 predicted coding sequences, had an average GC content of 41.3%, a completeness and contamination rate of 98.7% and 2.6%, respectively, and branched phylogenetically between the Ignisphaera and Zestosphaera lineages. Digital DNA-DNA hybridization values compared with Ignisphaera aggregans and Zestosphaera tikiterensis were 33.7% and 19.4%, respectively, suggesting that this MAG represented a novel species and genus. Its 16S rRNA gene contained a large 421 bp intron. It encodes a complete gluconeogenesis pathway involving a bifunctional fructose-1,6-bisphosphate phosphatase/aldolase; however, the glycolysis pathway is incomplete. The ribulose monophosphate pathway enzymes could be used for pentose synthesis. MAG002 encodes several hydrogen-evolving hydrogenases, with possible roles as hydrogen sinks during fermentation. We propose the name Zestomicrobium tamdykulense gen. nov. sp. nov. for this organism; it is the first thermophilic genome reported from Tajikistan.}, } @article {pmid39390034, year = {2024}, author = {Delanghe, L and De Boeck, I and Van Malderen, J and Allonsius, CN and Van Rillaer, T and Bron, PA and Claes, I and Hagendorens, M and Lebeer, S and Leysen, J}, title = {Mild atopic dermatitis is characterized by increase in non-staphylococcus pathobionts and loss of specific species.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {23659}, pmid = {39390034}, issn = {2045-2322}, support = {HBC.2020.2873//Agentschap Innoveren en Ondernemen/ ; HBC.2020.2873//Agentschap Innoveren en Ondernemen/ ; 12S4222N//Fonds Wetenschappelijk Onderzoek/ ; 1S08523N//Fonds Wetenschappelijk Onderzoek/ ; 852600/ERC_/European Research Council/International ; }, mesh = {*Dermatitis, Atopic/microbiology ; Humans ; *Microbiota ; *Skin/microbiology/pathology ; Female ; Adult ; Male ; Staphylococcus aureus/genetics/isolation & purification/pathogenicity ; Bacteria/classification/genetics ; Middle Aged ; Metagenomics/methods ; }, abstract = {Atopic dermatitis is the most common inflammatory skin condition with a severe negative impact on patients' quality of life. The etiology of AD is complex and depends on age, genetics, the immune system, environmental factors, and the skin microbiome, with a key role for pathogenic Staphylococcus aureus in the development of severe AD. However, the composition of the skin microbiome in mild AD is understudied. Here, using metagenomic shallow shotgun sequencing, we showed that mild AD lesions did not show a significant difference in the diversity of the skin microbiome compared to samples from non-AD patients and that the relative abundance of S. aureus did not differ in these mild AD lesions. However, when we assessed other taxa, Mycobacterium ostraviense, Pedobacter panaciterrae_A and four Streptomyces species were identified with higher abundances in mild AD lesions and species of 15 genera were decreased in abundance. The highest fold decreases were observed for Paracoccus marcusii, Microbacterium lacticum, Micrococcus luteus, and Moraxella sp002478835. These microbiome compositional insights are a first step towards novel microbiome-based diagnostics and therapeutics for early intervention at the stage of mild AD and provide a path forward for the functional study of species involved in this often-overlooked patient population.}, } @article {pmid39390025, year = {2024}, author = {Larsson, A and Ericson, U and Jönsson, D and Miari, M and Athanasiadis, P and Baldanzi, G and Brunkwall, L and Hellstrand, S and Klinge, B and Melander, O and Nilsson, PM and Fall, T and Maziarz, M and Orho-Melander, M}, title = {New connections of medication use and polypharmacy with the gut microbiota composition and functional potential in a large population.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {23723}, pmid = {39390025}, issn = {2045-2322}, mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Polypharmacy ; Male ; Female ; Middle Aged ; Sweden ; Aged ; Adult ; }, abstract = {Medication can affect the gut microbiota composition and function. The aim of this study was to investigate connections between use of common non-antibiotic medicines and the gut microbiota composition and function in a large Swedish cohort (N = 2223). Use of 67 medications and polypharmacy (≥ 5 medications), based on self-reported and prescription registry data, were associated with the relative abundance of 881 gut metagenomic species (> 5% prevalence) and 103 gut metabolic modules (GMMs). Altogether, 97 associations of 26 medications with 40 species and of four medications with five GMMs were observed (false discovery rate < 5%). Several earlier findings were replicated like the positive associations of proton pump inhibitors (PPIs) with numerous oral species, and those of metformin with Escherichia species and with lactate consumption I and arginine degradation II. Several new associations were observed between, among others, use of antidepressants, beta-blockers, nonsteroidal anti-inflammatory drugs and calcium channel blockers, and specific species. Polypharmacy was positively associated with Enterococcus faecalis, Bacteroides uniformis, Rothia mucilaginosa, Escherichia coli and Limosilactobacillus vaginalis, and with 13 GMMs. We confirmed several previous findings and identified numerous new associations between use of medications/polypharmacy and the gut microbiota composition and functional potential. Further studies are needed to confirm the new findings.}, } @article {pmid39390011, year = {2024}, author = {Kim, HS and Oh, SJ and Kim, BK and Kim, JE and Kim, BH and Park, YK and Yang, BG and Lee, JY and Bae, JW and Lee, CK}, title = {Dysbiotic signatures and diagnostic potential of gut microbial markers for inflammatory bowel disease in Korean population.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {23701}, pmid = {39390011}, issn = {2045-2322}, support = {2017R1A5A2014768//National Research Foundation of Korea/ ; 2021R1C1C2008556//National Research Foundation of Korea/ ; HI23C0661//Korea Health Industry Development Institute/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Dysbiosis/diagnosis/microbiology ; Female ; Male ; Republic of Korea/epidemiology ; Adult ; Middle Aged ; *Biomarkers ; *RNA, Ribosomal, 16S/genetics ; *Feces/microbiology ; *Inflammatory Bowel Diseases/microbiology/diagnosis ; Colitis, Ulcerative/microbiology/diagnosis ; Metagenomics/methods ; Crohn Disease/microbiology/diagnosis ; Case-Control Studies ; Cross-Sectional Studies ; Young Adult ; Aged ; }, abstract = {Fecal samples were collected from 640 individuals in Korea, including 523 patients with IBD (223 with Crohn's disease [CD] and 300 with ulcerative colitis [UC]) and 117 healthy controls. The samples were subjected to cross-sectional gut metagenomic analysis using 16 S rRNA sequencing and bioinformatics analysis. Patients with IBD, particularly those with CD, exhibited significantly lower alpha diversities than the healthy subjects. Differential abundance analysis revealed dysbiotic signatures, characterized by an expansion of the genus Escherichia-Shigella in patients with CD. Functional annotations showed that functional pathways related to bacterial pathogenesis and production of hydrogen sulfide (H2S) were strongly upregulated in patients with CD. A dysbiosis score, calculated based on functional characteristics, highly correlated with disease severity. Markers distinguishing between healthy subjects and patients with IBD showed accurate classification based on a small number of microbial taxa, which may be used to diagnose ambiguous cases. These findings confirm the taxonomic and functional dysbiosis of the gut microbiota in patients with IBD, especially those with CD. Taxa indicative of dysbiosis may have significant implications for future clinical research on the management and diagnosis of IBD.}, } @article {pmid39389770, year = {2024}, author = {Xu, Y and Yan, Y and Zhou, T and Lu, Y and Yang, X and Tang, K and Liu, F}, title = {Synergy between Arbuscular Mycorrhizal Fungi and Rhizosphere Bacterial Communities Increases the Utilization of Insoluble Phosphorus and Potassium in the Soil by Maize.}, journal = {Journal of agricultural and food chemistry}, volume = {72}, number = {42}, pages = {23631-23642}, doi = {10.1021/acs.jafc.4c07428}, pmid = {39389770}, issn = {1520-5118}, mesh = {*Mycorrhizae/metabolism ; *Phosphorus/metabolism ; *Zea mays/microbiology/metabolism ; *Rhizosphere ; *Soil Microbiology ; *Potassium/metabolism ; *Bacteria/metabolism/genetics/classification/isolation & purification ; *Soil/chemistry ; Plant Roots/microbiology/metabolism ; }, abstract = {Arbuscular mycorrhizal (AM) fungi can enhance plant uptake of phosphorus (P) and potassium (K), but it is not yet clear whether rhizosphere bacteria can enhance the ability of AM fungi to acquire insoluble P and K from the soil. Here, pot experiments confirmed that AM fungus-promoted insoluble P and K uptake by plants requires rhizosphere bacteria. The changes of rhizosphere bacterial communities associated with AM fungi were explored by 16S rRNA amplicon sequencing and metagenomic sequencing. Five core bacteria genera identified were involved in P and K cycles. Synthetic community (SynCom) inoculation revealed that SynCom increased soil available P and K and its coinoculation with AM fungi increased P and K concentration in the plants. This study revealed that AM fungi interact with rhizosphere bacteria and promote insoluble P and K acquisition, which provided a foundation for the application of AM fungal-bacterial biofertilizers and was beneficial for the sustainable development of agriculture.}, } @article {pmid39389327, year = {2025}, author = {Narain Singh, D and Pandey, P and Shankar Singh, V and Kumar Tripathi, A}, title = {Evidence for high-risk pollutants and emerging microbial contaminants at two major bathing ghats of the river Ganga using high-resolution mass spectrometry and metagenomics.}, journal = {Gene}, volume = {933}, number = {}, pages = {148991}, doi = {10.1016/j.gene.2024.148991}, pmid = {39389327}, issn = {1879-0038}, mesh = {*Rivers/microbiology/chemistry ; *Metagenomics/methods ; *Wastewater/microbiology ; Bacteria/genetics/isolation & purification/classification ; Water Pollutants, Chemical/analysis ; India ; Mass Spectrometry/methods ; Environmental Monitoring/methods ; Water Microbiology ; }, abstract = {An efficient wastewater treatment plant is imperative to limit the entry of emerging pollutants (EPs) and emerging microbial contaminants (EMCs) in the river ecosystem. The detection of emerging EPs in aquatic environments is challenging due to complex sample preparation methods, and the need for sophisticated accurate analytical tools. In Varanasi (India), the river Ganga holds immense significance as a holy river but is consistently polluted with municipal (MWW) and hospital wastewater (HWW). We developed an efficient method for untargeted detection of EPs in the water samples using High-resolution mass spectrometry (HRMS), and identified 577 and 670 chemicals (or chemical components) in the water samples from two major bathing ghats, Assi Ghat (AG) and Dashashwamedh Ghat (DG), respectively. The presence of EPs of different categories viz chemicals from research labs, diagnostic labs, lifestyle and industrial chemicals, toxins, flavor and food additives indicated the unsafe disposal of MWW and HWW or inefficient wastewater treatment plants (WWTPs). Besides, shotgun metagenomic analysis depicted the presence of bacteria associated with MWW viz Cloacibacterium normanse, Sphaerotilus natans (sewage fungi), E. coli, and Prevotella. Also, the presence of human pathogens Arcobacter, Polynucleobacter, Pseudomonas, Klebsiella, Aeromonas, Acinetobacter, Vibrio, and Campylobacter suggests the discharge of HWW. EPs are linked to the development, and transmission of antimicrobial resistance (AMR). Occurrence of antibiotic resistance genes (ARGs), plasmid-borne β-lactamases, aminoglycoside transferases, and ARGs associated with integrons, transposons and plasmids viz mcr-3 gene that confer resistance to colistin, the last resort of antibiotics confirmed the presence of emerging microbial contaminants. Subsequent genome reconstruction studies showed the presence of uncultivable ARB and transmission of ARGs through horizontal gene transfer. This study can be used to monitor the health of aquatic bodies as well as the efficiency of WWTPs and raise an urgent need for efficient WWTPs to safeguard the river, Ganga.}, } @article {pmid39389287, year = {2024}, author = {Boycheva, S and Roberton, AM and Pisaniello, A and Pardesi, B and White, WL and Clements, KD}, title = {Oxygen exposure decreases the yield of high-molecular-weight DNA from some anaerobic bacteria and bacterial communities during DNA extraction.}, journal = {Anaerobe}, volume = {90}, number = {}, pages = {102915}, doi = {10.1016/j.anaerobe.2024.102915}, pmid = {39389287}, issn = {1095-8274}, mesh = {*DNA, Bacterial/genetics ; Animals ; *Oxygen/metabolism ; *Bacteria, Anaerobic/genetics/isolation & purification/classification ; Molecular Weight ; Metagenomics/methods ; Anaerobiosis ; Fishes/microbiology ; Aerobiosis ; }, abstract = {OBJECTIVES: The central challenge in third-generation sequencing lies in meeting the requirements for DNA quality (integrity and purity) and quantity. Therefore, novel improvements in DNA extraction methods are needed to satisfy these requirements. We reasoned that in anaerobic microbial communities, the presence of certain strict anaerobes containing oxygen-activated DNase activity might contribute substantially to the poor integrity of extracted metagenomic DNA (or genomic DNA from some pure cultures) if exposed to air.

METHODS: To test this hypothesis, we developed an enhanced genomic and metagenomic DNA isolation technique that we applied to a specifically chosen set of both strict and aerotolerant anaerobes, as well as to the hindgut microbiota of a herbivorous marine fish.

RESULTS: Considering the quality (or degradation) of extracted DNA obtained under anaerobic versus aerobic conditions, we found that DNA extracted aerobically from cells of some strict anaerobes showed more degradation of high molecular weight DNA than analogous preparations under anaerobic conditions. In contrast, with the selected aerotolerant anaerobes, no discernible difference was found between the molecular sizes of DNA extracted aerobically and anaerobically. Metagenomic DNA extracted from the fish hindgut microbiota showed higher yields and better quality under anaerobic conditions compared to aerobic conditions.

CONCLUSION: Our study effectively demonstrates the advantages of our improved extraction protocol in anaerobic conditions. This is evident through the improved quality of extracted DNA. Such findings may be valuable for studies, especially metagenomic studies, where the quality and quantity of DNA are crucial for downstream analysis.}, } @article {pmid39389249, year = {2024}, author = {Lu, CW and Kao, CM and Yao, CL and Chen, SC}, title = {Analyzing Dehalochip: A functional DNA microarray for reductive dichlorination in chloroethene-contaminated sites.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {363}, number = {Pt 1}, pages = {125096}, doi = {10.1016/j.envpol.2024.125096}, pmid = {39389249}, issn = {1873-6424}, mesh = {*Biodegradation, Environmental ; *Chloroflexi/genetics/metabolism ; *Oligonucleotide Array Sequence Analysis ; *Halogenation ; Water Pollutants, Chemical/metabolism ; RNA, Ribosomal, 16S/genetics ; Groundwater/chemistry ; }, abstract = {Interpreting high-throughput transcriptomic and metagenomic data from non-model microorganisms presents a challenge due to the significant number of genes with unknown functions and sequences. In this study, we applied an innovative microarray, Dehalochip, for detecting the expression of genes in various microorganisms, particularly focusing on genes involved in chloroethene degradation. Our results demonstrated that this approach can effectively identify dechlorination genes, such as 16S rRNA, tceA, bvcA, and vcrA, in Dehalococcoides mccartyi from samples of groundwater contaminated with chloroethene. Noticeably, the sensitivity and specificity of our Dehalochip are comparable to that of quantitative PCR. However, it stands out as a more viable option for in-situ applications due to its greater capacity to infer potential dechlorination genes. Consequently, we believe our dechlorination microarray offers valuable insights into the role of known microorganisms and their associated functional genes in chloroethene-contaminated environments. This contributes to a deeper understanding of the in-situ reductive dechlorination process.}, } @article {pmid39389057, year = {2024}, author = {Hou, X and He, Y and Fang, P and Mei, SQ and Xu, Z and Wu, WC and Tian, JH and Zhang, S and Zeng, ZY and Gou, QY and Xin, GY and Le, SJ and Xia, YY and Zhou, YL and Hui, FM and Pan, YF and Eden, JS and Yang, ZH and Han, C and Shu, YL and Guo, D and Li, J and Holmes, EC and Li, ZR and Shi, M}, title = {Using artificial intelligence to document the hidden RNA virosphere.}, journal = {Cell}, volume = {187}, number = {24}, pages = {6929-6942.e16}, doi = {10.1016/j.cell.2024.09.027}, pmid = {39389057}, issn = {1097-4172}, mesh = {*RNA Viruses/genetics/isolation & purification ; *RNA-Dependent RNA Polymerase/genetics ; *RNA, Viral/genetics ; Genome, Viral/genetics ; Artificial Intelligence ; Virome/genetics ; Phylogeny ; Metagenomics/methods ; Algorithms ; Deep Learning ; Hot Springs/virology ; Hydrothermal Vents/virology ; }, abstract = {Current metagenomic tools can fail to identify highly divergent RNA viruses. We developed a deep learning algorithm, termed LucaProt, to discover highly divergent RNA-dependent RNA polymerase (RdRP) sequences in 10,487 metatranscriptomes generated from diverse global ecosystems. LucaProt integrates both sequence and predicted structural information, enabling the accurate detection of RdRP sequences. Using this approach, we identified 161,979 potential RNA virus species and 180 RNA virus supergroups, including many previously poorly studied groups, as well as RNA virus genomes of exceptional length (up to 47,250 nucleotides) and genomic complexity. A subset of these novel RNA viruses was confirmed by RT-PCR and RNA/DNA sequencing. Newly discovered RNA viruses were present in diverse environments, including air, hot springs, and hydrothermal vents, with virus diversity and abundance varying substantially among ecosystems. This study advances virus discovery, highlights the scale of the virosphere, and provides computational tools to better document the global RNA virome.}, } @article {pmid39389029, year = {2024}, author = {Qian, J and Yeo, EN and Olm, MR}, title = {Hospitalization throws the preterm gut microbiome off-key.}, journal = {Cell host & microbe}, volume = {32}, number = {10}, pages = {1651-1653}, doi = {10.1016/j.chom.2024.09.009}, pmid = {39389029}, issn = {1934-6069}, mesh = {*Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; *Feces/microbiology ; *Intensive Care Units, Neonatal ; *Metagenomics ; *Infant, Premature ; Hospitalization ; Infant ; }, abstract = {Environmental exposures substantially influence the infant gut microbiome. In this issue of Cell Host & Microbe, Thänert et al.[1] characterize how medical interventions in the neonatal intensive care unit (NICU) shape gut microbiome dynamics in the first months of life by analyzing over 2,500 fecal samples with metagenomics and metatranscriptomics.}, } @article {pmid39387982, year = {2024}, author = {Xing, F and Deng, C and Zou, S and Tsang, CC and Lo, SKF and Lau, SKP and Woo, PCY}, title = {Emergence and Rapid Diagnosis of Talaromyces marneffei Infections in Renal Transplant Recipients by Next-Generation Sequencing.}, journal = {Mycopathologia}, volume = {189}, number = {6}, pages = {91}, pmid = {39387982}, issn = {1573-0832}, support = {SZSM201911014//Sanming Project of Medicine in Shenzen Municipality/ ; MOE-112-S-023-A//Ministry of Education/ ; }, mesh = {Humans ; *Talaromyces/genetics/isolation & purification ; *Kidney Transplantation/adverse effects ; *High-Throughput Nucleotide Sequencing ; Adult ; *Transplant Recipients ; *Mycoses/diagnosis/microbiology ; Male ; Metagenomics/methods ; China ; Bronchoalveolar Lavage Fluid/microbiology ; }, abstract = {In the last few years, next-generation sequencing (NGS) has emerged as a technology for laboratory diagnosis of many culture-negative infections and slow-growing microorganisms. In this study, we describe the use of metagenomic NGS (mNGS) for rapid diagnosis of T. marneffei infection in a 37-year-old renal transplant recipient who presented with chronic pneumonia syndrome. Bronchoalveolar lavage for mNGS was positive for T. marneffei sequence reads. Prolonged incubation of the bronchoalveolar lavage revealed T. marneffei colonies after 6 days of incubation. Analysis of 23 cases of T. marneffei infections in renal transplant recipients from the literature revealed that the number of cases ranged from 1 to 4 cases per five years from 1990 to 2020; but increased rapidly to 9 cases from 2021 to 2023, with 7 of them diagnosed by NGS. Twenty of the 23 cases were from T. marneffei-endemic areas [southern part of mainland China (n = 9); Hong Kong (n = 4); northeastern India (n = 2); Indonesia (n = 1) and Taiwan (n = 4)]. For the 3 patients from non-T. marneffei-endemic areas [United Kingdom (n = 2) and Australia (n = 1)], they had travel histories to China and Vietnam respectively. The time taken for diagnosis by mNGS [median 1 (range 1 to 2) day] was significantly shorter than that for fungal culture [median 6 (range 3 to 15) days] (P = 0.002). mNGS is useful for picking up more cases of T. marneffei infections in renal transplant recipients as well as providing a rapid diagnosis. Talaromycosis is an emerging fungal infection in renal transplant recipients.}, } @article {pmid39388238, year = {2024}, author = {Zhou, R and Hou, J and Fu, X and Wang, C and Liang, Y and Wang, D}, title = {A suprapubic refractory skin ulcer following keloid radiotherapy: from hyper-proliferation to hypo-proliferation.}, journal = {Journal of wound care}, volume = {33}, number = {Sup10}, pages = {S4-S8}, doi = {10.12968/jowc.2021.0314}, pmid = {39388238}, issn = {0969-0700}, mesh = {Humans ; Female ; Adult ; *Keloid/radiotherapy/etiology ; *Skin Ulcer/etiology ; Radiation Injuries/etiology ; Radiotherapy/adverse effects ; }, abstract = {Radiation-induced skin ulcer following cancer and/or tumour is well-documented in the literature. However, radiation-induced skin ulcer following the excision of keloid is yet to be reported. Here, we report the case of a 33-year-old female patient with a suprapubic skin ulcer of five months' duration following keloid treatment with electron beam therapy at recommended dosage. Various examinations, including a skin biopsy, metagenomic sequencing, magnetic resonance imaging and immunochemistry, indicated that the skin ulcer was induced by radiotherapy. While postoperative radiotherapy has been recommended immediately following keloid excision to reduce the risk of recurrence, the present case highlights the risk of skin refractory ulcer following keloid radiotherapy.}, } @article {pmid39386812, year = {2024}, author = {Cai, R and Yu, F and Cheng, J and Chen, C and Liu, Y and Lv, R and Ye, Z and Yuan, Y and Li, Z and Cheng, C and Wei, H}, title = {Diagnostic Value of Metagenomic next-generation sequencing and X-pert in Bronchoalveolar lavage fluid for pneumonia in HIV-infected and HIV-uninfected patients.}, journal = {Heliyon}, volume = {10}, number = {19}, pages = {e38208}, pmid = {39386812}, issn = {2405-8440}, abstract = {BACKGROUND: The pathogens causing unexplained pneumonia in both HIV-infected or HIV-unfected patients are likely to be complex. This retrospective study aimed to characterize the etiology of pneumonia in HIV-infected and HIV-uninfected patients using bronchoalveolar lavage fluid (BALF) analysis with metagenomic next-generation sequencing (mNGS) and X-pert MTB/RIF.

METHODS: Between January 2022 and May2024, 141 HIV-infected and 104 HIV-uninfected patients admitted to Nanjing Second Hospital with pneumonia were included. BALF samples were collected and analyzed using mNGS to detect bacteria, fungi, viruses, tuberculosis (TB) and non-tuberculous mycobacteria (NTM), and X-pert for TB detection. Clinical data including CD4 T-cell counts, comorbidities, and ART status were collected and analyzed.

RESULTS: HIV-uninfected patients were found to be older and exhibited a higher prevalence of comorbidities compared to HIV-infected patients. Despite higher median CD4 T-cell counts in HIV-uninfected individuals (412 cells/μL vs. 31 cells/μL in HIV-infected), TB detection rates using X-pert and mNGS were lower than anticipated, particularly in HIV-infected patients. Mixed-pathogen infections were significantly more prevalent in HIV-infected patients, especially those with lower CD4 T-cell counts. ART use showed variable impacts on pathogen diversity, with longer treatment durations associated with reduced infection complexity but persistent immunodeficiency in some cases.In patients with pneumonia, whether HIV-infected or HIV-uninfected, pathogens often exhibit complexity, underscoring the critical role of timely mNGS and X-pert analysis of BALF for early pathogen detection.}, } @article {pmid39386754, year = {2024}, author = {Wang, Q and Huang, Y and Ma, H and Fan, GK}, title = {A case report: Comorbidity of Rhinocerebral mucormycosis and pulmonary aspergillosis with challenging diagnosis.}, journal = {Frontiers in medicine}, volume = {11}, number = {}, pages = {1398714}, pmid = {39386754}, issn = {2296-858X}, abstract = {BACKGROUND: Mucormycosis is a rare opportunistic invasive fungal disease. Rhinocerebral mucormycosis (RCM) is clinically difficult to diagnose, and patients often die due to delayed diagnosis.

CASE DESCRIPTION: A patient with concurrent pulmonary aspergillosis was diagnosed with RCM caused by Rhizopus through metagenomic Next-Generation Sequencing (mNGS). Despite comprehensive treatment including surgery, amphotericin B, and posaconazole, the patient tragically passed away. The treatment was delayed due to repeated cultures of secretions were negative and pathological examination could not clarify which fungus is infected.

CONCLUSION: The clinical manifestations of RCM are not specific in the early stage, but the infection progresses rapidly. Therefore, early and accurate diagnosis is very important. mNGS is helpful for patients suspected of RCM, especially when conventional microbiology tests were negative.}, } @article {pmid39386737, year = {2024}, author = {Nunn, BL and Timmins-Schiffman, E and Mudge, MC and Plubell, D and Chebli, G and Kubanek, J and Riffle, M and Noble, WS and Harvey, E and Nunn, TA and Huntemann, M and Clum, A and Foster, B and Foster, B and Roux, S and Palaniappan, K and Mukherjee, S and Reddy, TBK and Daum, C and Copeland, A and Chen, IA and Ivanova, NN and Kyrpides, NC and Glavina Del Rio, T and Eloe-Fadrosh, EA}, title = {Microbial Metagenomes Across a Complete Phytoplankton Bloom Cycle: High-Resolution Sampling Every 4 Hours Over 22 Days.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39386737}, issn = {2692-8205}, support = {R21 ES034337/ES/NIEHS NIH HHS/United States ; }, abstract = {In May and June of 2021, marine microbial samples were collected for DNA sequencing in East Sound, WA, USA every 4 hours for 22 days. This high temporal resolution sampling effort captured the last 3 days of a Rhizosolenia sp. bloom, the initiation and complete bloom cycle of Chaetoceros socialis (8 days), and the following bacterial bloom (2 days). Metagenomes were completed on the time series, and the dataset includes 128 size-fractionated microbial samples (0.22-1.2 μm), providing gene abundances for the dominant members of bacteria, archaea, and viruses. This dataset also has time-matched nutrient analyses, flow cytometry data, and physical parameters of the environment at a single point of sampling within a coastal ecosystem that experiences regular bloom events, facilitating a range of modeling efforts that can be leveraged to understand microbial community structure and their influences on the growth, maintenance, and senescence of phytoplankton blooms.}, } @article {pmid39386697, year = {2024}, author = {Zelasko, S and Swaney, MH and Suh, WS and Sandstrom, S and Carlson, C and Cagnazzo, J and Golfinos, A and Fossen, J and Andes, D and Kalan, LR and Safdar, N and Currie, CR}, title = {Altered oral microbiota of drug-resistant organism carriers exhibit impaired gram-negative pathogen inhibition.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.09.24.614756}, pmid = {39386697}, issn = {2692-8205}, abstract = {The oral microbiome has been understudied as a reservoir for clinical pathogens, including drug-resistant strains. Understanding how alterations in microbiome functioning render this site vulnerable to colonization is essential, as multidrug-resistant organisms (MDRO) carriage is a major risk factor for developing serious infections. To advance our knowledge of oral MDRO carriage and protection against pathogen colonization conferred by native microbiota, we examined microbiomes from individuals colonized by MDROs (n=33) and non-colonized age-matched controls (n=30). Shotgun metagenomic analyses of oral swabs from study participants revealed significant differences in microbial communities with depletion of Streptococcus spp. among those colonized by multidrug-resistant gram-negative bacilli (RGNB), compared to non-carriers. We utilized metagenomic sequencing to characterize the oral resistome and find antimicrobial resistance genes are present in higher abundance among RNGB carriers versus non-carriers. High-throughput co-culture screening revealed oral bacteria isolated from MDRO non-carriers demonstrate greater inhibition of gram-negative pathogens, compared to isolates from carriers. Moreover, biosynthetic gene clusters from streptococci are found in higher abundance from non-carrier microbiomes, compared to RGNB carrier microbiomes. Bioactivity-guided fractionation of extracts from Streptococcus isolate SID2657 demonstrated evidence of strong E. coli and A. baumannii inhibition in a murine model of infection. Together, this provides evidence that oral microbiota shape this dynamic microbial community and may serve as an untapped source for much-needed antimicrobial small-molecules.}, } @article {pmid39386691, year = {2024}, author = {Gustafson, KL and Rodriguez, TR and McAdams, ZL and Coghill, LM and Ericsson, AC and Franklin, CL}, title = {Failure of colonization following gut microbiota transfer exacerbates DSS-induced colitis.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39386691}, issn = {2692-8205}, support = {T32 GM008396/GM/NIGMS NIH HHS/United States ; T32 OD011126/OD/NIH HHS/United States ; U42 OD010918/OD/NIH HHS/United States ; }, abstract = {To study the impact of differing specific pathogen-free gut microbiomes (GMs) on a murine model of inflammatory bowel disease, selected GMs were transferred using embryo transfer (ET), cross-fostering (CF), and co-housing (CH). Prior work showed that the GM transfer method and the microbial composition of donor and recipient GMs can influence microbial colonization and disease phenotypes in dextran sodium sulfate-induced colitis. When a low richness GM was transferred to a recipient with a high richness GM via CH, the donor GM failed to successfully colonize, and a more severe disease phenotype resulted when compared to ET or CF, where colonization was successful. By comparing CH and gastric gavage for fecal material transfer, we isolated the microbial component of this effect and determined that differences in disease severity and survival were associated with microbial factors rather than the transfer method itself. Mice receiving a low richness GM via CH and gastric gavage exhibited greater disease severity and higher expression of pro-inflammatory immune mediators compared to those receiving a high richness GM. This study provides valuable insights into the role of GM composition and colonization in disease modulation.}, } @article {pmid39386638, year = {2024}, author = {Liu, A and Tian, B and Qiu, C and Su, KJ and Jiang, L and Zhao, C and Song, M and Liu, Y and Qu, G and Zhou, Z and Zhang, X and Gnanesh, SSM and Thumbigere-Math, V and Luo, Z and Tian, Q and Zhang, LS and Wu, C and Ding, Z and Shen, H and Deng, HW}, title = {Multi-View Integrative Approach For Imputing Short-Chain Fatty Acids and Identifying Key factors predicting Blood SCFA.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39386638}, issn = {2692-8205}, support = {R01 AG061917/AG/NIA NIH HHS/United States ; R01 AG068232/AG/NIA NIH HHS/United States ; U19 AG055373/AG/NIA NIH HHS/United States ; P20 GM109036/GM/NIGMS NIH HHS/United States ; P20 GM103629/GM/NIGMS NIH HHS/United States ; }, abstract = {Short-chain fatty acids (SCFAs) are the main metabolites produced by bacterial fermentation of dietary fiber within gastrointestinal tract. SCFAs produced by gut microbiotas (GMs) are absorbed by host, reach bloodstream, and are distributed to different organs, thus influencing host physiology. However, due to the limited budget or the poor sensitivity of instruments, most studies on GMs have incomplete blood SCFA data, limiting our understanding of the metabolic processes within the host. To address this gap, we developed an innovative multi-task multi-view integrative approach (M[2]AE, Multi-task Multi-View Attentive Encoders), to impute blood SCFA levels using gut metagenomic sequencing (MGS) data, while taking into account the intricate interplay among the gut microbiome, dietary features, and host characteristics, as well as the nuanced nature of SCFA dynamics within the body. Here, each view represents a distinct type of data input (i.e., gut microbiome compositions, dietary features, or host characteristics). Our method jointly explores both view-specific representations and cross-view correlations for effective predictions of SCFAs. We applied M[2]AE to two in-house datasets, which both include MGS and blood SCFAs profiles, host characteristics, and dietary features from 964 subjects and 171 subjects, respectively. Results from both of two datasets demonstrated that M[2]AE outperforms traditional regression-based and neural-network based approaches in imputing blood SCFAs. Furthermore, a series of gut bacterial species (e.g., Bacteroides thetaiotaomicron and Clostridium asparagiforme), host characteristics (e.g., race, gender), as well as dietary features (e.g., intake of fruits, pickles) were shown to contribute greatly to imputation of blood SCFAs. These findings demonstrated that GMs, dietary features and host characteristics might contribute to the complex biological processes involved in blood SCFA productions. These might pave the way for a deeper and more nuanced comprehension of how these factors impact human health.}, } @article {pmid39386636, year = {2024}, author = {Boyd, AI and Kafer, LA and Escapa, IF and Kambal, A and Tariq, H and Hilsenbeck, SG and Nguyen-Phuc, H and Rajan, A and Lensmire, JM and Patras, KA and Piedra, PA and Blutt, SE and Lemon, KP}, title = {Nasal microbionts differentially colonize and elicit cytokines in human nasal epithelial organoids.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39386636}, issn = {2692-8205}, support = {U19 AI144297/AI/NIAID NIH HHS/United States ; U19 AI116497/AI/NIAID NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; U19 AI157981/AI/NIAID NIH HHS/United States ; P30 ES030285/ES/NIEHS NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; }, abstract = {Nasal colonization by Staphylococcus aureus or Streptococcus pneumoniae is associated with an increased risk of infection by these pathobionts, whereas nasal colonization by Dolosigranulum species is associated with health. Human nasal epithelial organoids (HNOs) physiologically recapitulate human nasal respiratory epithelium with a robust mucociliary blanket. We reproducibly monocolonized HNOs with these three bacteria for up to 48 hours with varying kinetics across species. HNOs tolerated bacterial monocolonization with localization of bacteria to the mucus layer and minimal cytotoxicity compared to uncolonized HNOs. Human nasal epithelium exhibited both species-specific and general cytokine responses, without induction of type I interferons, consistent with colonization rather than infection. Only live S. aureus colonization induced IL-1 family cytokines, suggestive of inflammasome signaling. D. pigrum and live S. aureus decreased CXCL10, whereas S. pneumoniae increased CXCL11, chemokines involved in antimicrobial responses. HNOs are a compelling model system to reveal host-microbe dynamics at the human nasal mucosa.}, } @article {pmid39386242, year = {2024}, author = {Zhang, R and Zhang, L and An, X and Li, J and Niu, C and Zhang, J and Geng, Z and Xu, T and Yang, B and Xu, Z and Yue, Y}, title = {Hybridization promotes growth performance by altering rumen microbiota and metabolites in sheep.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1455029}, pmid = {39386242}, issn = {2297-1769}, abstract = {Hybridization can substantially improve growth performance. This study used metagenomics and metabolome sequencing to examine whether the rumen microbiota and its metabolites contributed to this phenomenon. We selected 48 approximately 3 month-old male ♂Hu × ♀Hu (HH, n = 16), ♂Poll Dorset × ♀Hu (DH, n = 16), and ♂Southdown × ♀Hu (SH, n = 16) lambs having similar body weight. The sheep were fed individually under the same nutritional and management conditions for 95 days. After completion of the trial, seven sheep close to the average weight per group were slaughtered to collect rumen tissue and content samples to measure rumen epithelial parameters, fermentation patterns, microbiota, and metabolite profiles. The final body weight (FBW), average daily gain (ADG), and dry matter intake (DMI) values in the DH and SH groups were significantly higher and the feed-to-gain ratio (F/G) significantly lower than the value in the HH group; additionally, the papilla height in the DH group was higher than that in the HH group. Acetate, propionate, and total volatile fatty acid (VFA) concentrations in the DH group were higher than those in the HH group, whereas NH3-N concentration decreased in the DH and SH groups. Metagenomic analysis revealed that several Prevotella and Fibrobacter species were significantly more abundant in the DH group, contributing to an increased ability to degrade dietary cellulose and enrich their functions in enzymes involved in carbohydrate breakdown. Bacteroidaceae bacterium was higher in the SH group, indicating a greater ability to digest dietary fiber. Metabolomic analysis revealed that the concentrations of rumen metabolites (mainly lysophosphatidylethanolamines [LPEs]) were higher in the DH group, and microbiome-related metabolite analysis indicated that Treponema bryantii and Fibrobacter succinogenes were positively correlated with the LPEs. Moreover, we found methionine sulfoxide and N-methyl-4-aminobutyric acid were characteristic metabolites in the DH and SH groups, respectively, and are related to oxidative stress, indicating that the environmental adaptability of crossbred sheep needs to be further improved. These findings substantially deepen the general understanding of how hybridization promotes growth performance from the perspective of rumen microbiota, this is vital for the cultivation of new species and the formulation of precision nutrition strategies for sheep.}, } @article {pmid39385283, year = {2024}, author = {Li, Y and Chen, J and Lin, Y and Zhong, C and Jing, H and Liu, H}, title = {Thaumarchaeota from deep-sea methane seeps provide novel insights into their evolutionary history and ecological implications.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {197}, pmid = {39385283}, issn = {2049-2618}, mesh = {*Archaea/genetics/classification/metabolism ; *Methane/metabolism ; *Ammonia/metabolism ; *Phylogeny ; *Geologic Sediments/microbiology ; *Oxidation-Reduction ; *Seawater/microbiology ; Metagenomics ; Metagenome ; China ; Evolution, Molecular ; Nitrification ; }, abstract = {BACKGROUND: Ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota mediate the rate-limiting step of nitrification and remove the ammonia that inhibits the aerobic metabolism of methanotrophs. However, the AOA that inhabit deep-sea methane-seep surface sediments (DMS) are rarely studied. Here, we used global DMS metagenomics and metagenome-assembled genomes (MAGs) to investigate the metabolic activity, evolutionary history, and ecological contributions of AOA. Expression of AOA-specific ammonia-oxidizing gene (amoA) was examined in the sediments collected from the South China Sea (SCS) to identify their active ammonia metabolism in the DMS.

RESULTS: Our analysis indicated that AOA contribute > 75% to the composition of ammonia-utilization genes within the surface layers (above 30 cm) of global DMS. The AOA-specific ammonia-oxidizing gene was actively expressed in the DMS collected from the SCS. Phylogenomic analysis of medium-/high-quality MAGs from 18 DMS-AOA indicated that they evolved from ancestors in the barren deep-sea sediment and then expanded from the DMS to shallow water forming an amoA-NP-gamma clade-affiliated lineage. Molecular dating suggests that the DMS-AOA origination coincided with the Neoproterozoic oxidation event (NOE), which occurred ~ 800 million years ago (mya), and their expansion to shallow water coincided with the Sturtian glaciation (~ 713 mya). Comparative genomic analysis suggests that DMS-AOA exhibit higher requirement of carbon source for protein synthesis with enhanced genomic capability for osmotic regulation, motility, chemotaxis, and utilization of exogenous organic compounds, suggesting it could be more heterotrophic compared with other lineages.

CONCLUSION: Our findings provide new insights into the evolutionary history of AOA within the Thaumarchaeota, highlighting their critical roles in nitrogen cycling in the global DMS ecosystems. Video Abstract.}, } @article {pmid39385149, year = {2024}, author = {Asao, K and Hashida, N and Maruyama, K and Motooka, D and Nakamura, S and Nishida, K}, title = {Cases of endophthalmitis caused by Candida albicans and Candida dubliniensis identified via internal transcribed spacer deep sequencing.}, journal = {BMC ophthalmology}, volume = {24}, number = {1}, pages = {444}, pmid = {39385149}, issn = {1471-2415}, support = {23K159060//Japan Society for the Promotion of Science/ ; 21K08505//Japan Society for the Promotion of Science/ ; }, mesh = {Humans ; *Endophthalmitis/microbiology/diagnosis ; Middle Aged ; Female ; *Eye Infections, Fungal/microbiology/diagnosis ; Male ; *Candidiasis/microbiology/diagnosis/drug therapy ; *High-Throughput Nucleotide Sequencing ; *Candida albicans/isolation & purification/genetics ; *Candida/genetics/isolation & purification ; DNA, Fungal/genetics ; Vitrectomy ; Antifungal Agents/therapeutic use ; Vitreous Body/microbiology ; }, abstract = {BACKGROUND: We report two cases of fungal endophthalmitis induced by Candida species identified based on internal transcribed spacer 1 (ITS1) sequencing.

CASE PRESENTATION: In two cases, endophthalmitis was suspected, and the patients underwent pars plana vitrectomy. Case 1 was a 64-year-old woman with a history of cataract surgery 10 days prior. She had a history of anal primary melanoma, which metastasized throughout the body and subsequently relapsed. Vitreous culture and ITS-1 deep sequencing revealed the presence of the rare fungus, Candida dubliniensis. Case 2 was a 54-year-old man with a history of liver cancer and kidney failure. Culture methods and ITS1 deep sequencing both revealed the presence of Candida albicans. Both patients exhibited good visual prognoses after treatment with topical and systemic antibiotics.

CONCLUSIONS: We present two cases of fungal endophthalmitis caused by two Candida species identified by both the culture method and ITS1 deep sequencing. The fungal pathogen was identified by ITS deep sequencing three days after sample submission; the culture method yielded results after 1 week. These findings support the applicability of ITS1 sequencing for timely pathogen identification for cases of fungal endophthalmitis and provide detailed taxonomic information at the species level.}, } @article {pmid39385092, year = {2024}, author = {Haverkamp, THA and Spilsberg, B and Johannessen, GS and Torp, M and Sekse, C}, title = {Detection and characterization of Campylobacter in air samples from poultry houses using shot-gun metagenomics - a pilot study.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {399}, pmid = {39385092}, issn = {1471-2180}, mesh = {Animals ; Pilot Projects ; *Metagenomics/methods ; *Chickens/microbiology ; *Campylobacter/isolation & purification/genetics/classification ; *Air Microbiology ; Poultry/microbiology ; Feces/microbiology ; Housing, Animal ; Real-Time Polymerase Chain Reaction/methods ; Campylobacter Infections/veterinary/microbiology/diagnosis ; }, abstract = {BACKGROUND: Foodborne pathogens such as Campylobacter jejuni are responsible for a large proportion of the gastrointestinal infections worldwide associated with poultry meat. Campylobacter spp. can be found in the chicken fecal microbiome and can contaminate poultry meat during the slaughter process. Commonly used sampling methods to detect Campylobacter spp. at poultry farms use fecal droppings or boot swabs in combination with conventional culture techniques or PCR. In this pilot study, we have used air filtering and filters spiked with mock communities in combination with shotgun metagenomics to detect Campylobacter and test the applicability of this approach for the detection and characterization of foodborne pathogens. To the best of our knowledge is this the first study that combines air filtering with shotgun metagenomic sequencing for detection and characterization of Campylobacter.

RESULTS: Analysis of air filters spiked with different levels of Campylobacter, into a background of mock or poultry house communities, indicated that we could detect as little as 200 colony forming units (CFU) Campylobacter per sample using our protocols. The results indicate that even with limited sequencing effort we could detect Campylobacter in the samples analysed in this study. We observed significant amounts of Campylobacter in real-life samples from poultry houses using both real-time PCR as well as shotgun metagenomics, suggesting that the flocks in both houses were infected with Campylobacter spp. Interestingly, in both houses we find diverse microbial communities present in the indoor air which reflect the fecal microbiome of poultry. Some of the identified genera such as Staphylococcus, Escherichia and Pseudomonas are known to contain opportunistic pathogenic species.

CONCLUSIONS: These results show that air sampling of poultry houses in combination with shotgun metagenomics can detect and identify Campylobacter spp. present at low levels. This is important since early detection of Campylobacter enables measures to be put in place to ensure the safety of broiler products, animal health and public health. This approach has the potential to detect any pathogen present in poultry house air.}, } @article {pmid39384811, year = {2024}, author = {Devanga Ragupathi, NK and Muthuirulandi Sethuvel, DP and Ganesan, A and Murugan, D and Baskaran, A and Wannigama, DL and Monk, PN and Karunakaran, E and Veeraraghavan, B}, title = {Evaluation of mrkD, pgaC and wcaJ as biomarkers for rapid identification of K. pneumoniae biofilm infections from endotracheal aspirates and bronchoalveolar lavage.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {23572}, pmid = {39384811}, issn = {2045-2322}, support = {10065043//QR GCRF , UKRI/ ; GCRFNGR5\1293//Academy of Medical Sciences, UK/ ; }, mesh = {*Biofilms/growth & development ; *Klebsiella pneumoniae/genetics/isolation & purification ; Humans ; *Klebsiella Infections/microbiology/diagnosis ; *Biomarkers ; Bronchoalveolar Lavage Fluid/microbiology ; Bacterial Proteins/genetics ; }, abstract = {Klebsiella pneumoniae has been identified as one of the most important opportunistic pathogens responsible for nosocomial infections. Antibiotic resistance and the ability to form biofilms are the two main factors involved in the persistence of infections. Conventional detection methods involve culture isolation and identification followed by biofilm assay that takes 48-72 h. Timely detection of biofilm-forming resistant pathogens is essential to appropriately treat the infection with the right dose and combinations. The present study focuses on evaluating an RT-PCR panel using mrkD, pgaC, and wcaJ genes to screen for biofilm-forming K. pneumoniae from ETA/BAL specimens. The assay accurately identified K. pneumoniae harboring samples with a limit of detection of 1 ng/µl total RNA. Representative culture-negative-PCR-positive samples were subjected to metagenomics which identified K. pneumoniae reads in these samples confirming the specificity of RT-PCR. mrkD and pgaC act as K. pneumoniae specific identification whereas wcaJ acts as a negative marker for biofilm-forming K. pneumoniae. In addition, RT-PCR results correlated well with the phenotypic biofilm-forming assay. This RT-PCR assay is the first of its kind for rapid identification of biofilm-forming K. pneumoniae. The result of this study highlights that the rapid detection of K. pneumoniae biofilms based on the RT-PCR results coupled with clinical conditions would be appropriate to treat emerging infections or to prevent re-infections in clinical settings.}, } @article {pmid39384807, year = {2024}, author = {Minot, SS and Li, N and Srinivasan, H and Ayers, JL and Yu, M and Koester, ST and Stangis, MM and Dominitz, JA and Halberg, RB and Grady, WM and Dey, N}, title = {Colorectal cancer-associated bacteria are broadly distributed in global microbiomes and drivers of precancerous change.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {23646}, pmid = {39384807}, issn = {2045-2322}, support = {K08 DK111941/DK/NIDDK NIH HHS/United States ; R50 CA233042/CA/NCI NIH HHS/United States ; U54 CA274374/CA/NCI NIH HHS/United States ; R50CA233042//U.S. Department of Health and Human Services | NIH | National Cancer Institute (NCI)/ ; }, mesh = {*Colorectal Neoplasms/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; Animals ; Humans ; Mice ; *Bacteria/genetics/classification ; *Precancerous Conditions/microbiology ; Metagenomics/methods ; }, abstract = {The gut microbiome is implicated in the pathogenesis of colorectal cancer (CRC), but the full scope of this dialogue is unknown. Here we aimed to define the scale and membership of the body of CRC- and health-associated gut bacteria in global populations. We performed a microbiome-CRC correlation analysis of published ultra-deep shotgun metagenomic sequencing data from global microbiome surveys, utilizing a de novo (reference-agnostic) gene-level clustering approach to identify protein-coding co-abundant gene (CAGs) clusters. We link an unprecedented ~ 23-40% of gut bacteria to CRC or health, split nearly evenly as CRC- or health-associated. These microbes encode 2319 CAGs encompassing 427,261 bacterial genes significantly enriched or depleted in CRC. We identified many microbes that had not previously been linked to CRC, thus expanding the scope of "known unknowns" of CRC-associated microbes. We performed an agnostic CAG-based screen of bacterial isolates and validated predicted effects of previously unimplicated bacteria in preclinical models, in which we observed differential induction of precancerous adenomas and field effects. Single-cell RNA sequencing disclosed microbiome-induced senescence-associated gene expression signatures in discrete colonic populations including fibroblasts. In organoid co-cultures, primary colon fibroblasts from mice with microbiomes promoted significantly greater growth than fibroblasts from microbiome-depleted mice. These results offer proof-of-principle for gene-level metagenomic analysis enabling discovery of microbiome links to health and demonstrate that the microbiome can drive precancer states, thereby potentially revealing novel cancer prevention opportunities.}, } @article {pmid39384533, year = {2024}, author = {Vuillemin, A and Ruiz-Blas, F and Yang, S and Bartholomäus, A and Henny, C and Kallmeyer, J}, title = {Taxonomic and functional partitioning of Chloroflexota populations under ferruginous conditions at and below the sediment-water interface.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {12}, pages = {}, pmid = {39384533}, issn = {1574-6941}, support = {2293/8-1//German Research Foundation/ ; P2GEP2_148621/SNSF_/Swiss National Science Foundation/Switzerland ; //German Research Centre for Geosciences/ ; }, mesh = {*Geologic Sediments/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Phylogeny ; Chloroflexi/genetics/metabolism ; Ecosystem ; Lakes/microbiology ; Water Microbiology ; Metagenome ; Oxidation-Reduction ; }, abstract = {The adaptation of the phylum Chloroflexota to various geochemical conditions is thought to have originated in primitive microbial ecosystems, involving hydrogenotrophic energy conservation under ferruginous anoxia. Oligotrophic deep waters displaying anoxic ferruginous conditions, such as those of Lake Towuti, and their sediments may thus constitute a preferential ecological niche for investigating metabolic versatility in modern Chloroflexota. Combining pore water geochemistry, cell counts, sulfate reduction rates, and 16S rRNA genes with in-depth analysis of metagenome-assembled genomes, we show that Chloroflexota benefit from cross-feeding on metabolites derived from canonical respiration chains and fermentation. Detailing their genetic contents, we provide molecular evidence that Anaerolineae have metabolic potential to use unconventional electron acceptors, different cytochromes, and multiple redox metalloproteins to cope with oxygen fluctuations, and thereby effectively colonizing the ferruginous sediment-water interface. In sediments, Dehalococcoidia evolved to be acetogens, scavenging fatty acids, haloacids, and aromatic acids, apparently bypassing specific steps in carbon assimilation pathways to perform energy-conserving secondary fermentations combined with CO2 fixation via the Wood-Ljungdahl pathway. Our study highlights the partitioning of Chloroflexota populations according to alternative electron acceptors and donors available at the sediment-water interface and below. Chloroflexota would have developed analogous primeval features due to oxygen fluctuations in ancient ferruginous ecosystems.}, } @article {pmid39384050, year = {2024}, author = {Wu, H and Yu, Y and Su, Q and Zhang, TC and Du, D and Du, Y}, title = {Combined impact of antibiotics and Cr(VI) on antibiotic resistance, ARGs, and growth of Bacillussp. SH-1: A functionl analysis from gene to protease.}, journal = {Bioresource technology}, volume = {414}, number = {}, pages = {131579}, doi = {10.1016/j.biortech.2024.131579}, pmid = {39384050}, issn = {1873-2976}, mesh = {*Chromium/pharmacology ; *Anti-Bacterial Agents/pharmacology ; *Bacillus cereus/drug effects ; *Microbial Sensitivity Tests ; Drug Resistance, Microbial/genetics/drug effects ; Peptide Hydrolases/metabolism ; Genes, Bacterial ; Reactive Oxygen Species/metabolism ; Drug Resistance, Bacterial/genetics/drug effects ; Oxidative Stress/drug effects ; Bacterial Proteins/genetics/metabolism ; }, abstract = {The simultaneous selection of antibiotic resistance genes (ARGs) induced by heavy metals and antibiotics has emerged as a growing environmental problem. This study investigated the combined effects of chromium (Cr(VI)) and antibiotics on the ARGs of Bacillus cereus SH-1. As Cr(VI) concentration increased, it triggered reactive oxygen species oxidative stress in SH-1, increased antioxidant enzyme activity, enhanced plasmid conjugative transfer, and reduced the efficiency of Cr(VI) removal by SH-1. Antibiotic resistance varied with increasing tetracycline and amoxicillin minimum inhibitory concentrations (MICs), whereas azithromycin and chloramphenicol MICs decreased with Cr(VI) induction. The overexpression of eight genes of the HAE-1 family of efflux pumps was detected using metagenomics and proteomics. Co-contamination with Cr(VI) and antibiotics has led to the emergence and spread of antibiotic-resistant bacteria. Therefore, resistance gene contamination resulting from Cr(VI)-polluted environments cannot be overlooked.}, } @article {pmid39383807, year = {2025}, author = {Zhang, Q and Ji, XM and Wang, X and Wang, W and Xu, X and Zhang, Q and Xing, D and Ren, N and Lee, DJ and Chen, C}, title = {Differentiation of the Anammox core microbiome: Unraveling the evolutionary impetus of scalable gene flow.}, journal = {Water research}, volume = {268}, number = {Pt A}, pages = {122580}, doi = {10.1016/j.watres.2024.122580}, pmid = {39383807}, issn = {1879-2448}, mesh = {*Microbiota ; *Gene Flow ; Phylogeny ; Ammonium Compounds/metabolism ; Oxidation-Reduction ; Bacteria/metabolism/genetics ; Anaerobiosis ; }, abstract = {Anaerobic ammonium oxidation bacteria (AAOB), distinguished by their unique autotrophic nitrogen metabolism, hold pivotal positions in the global nitrogen cycle and environmental biotechnologies. However, the ecophysiology and evolution of AAOB remain poorly understood, attributed to the absence of monocultures. Hence, a comprehensive elucidation of the AAOB-dominated core microbiome, anammox core, is imperative to further completing the theory of engineered nitrogen removal and ecological roles of anammox. Performing taxonomic and phylogenetic analyses on collected genome repertoires, we show here that Candidatus Brocadia and Candidatus Kuenenia possesses a more compact core than Candidatus Jettenia, which partly explains why the latter has a less common ecological presence. Evidence of gene flow is particularly striking in functions related to biosynthesis and oxygen detoxification, underscoring the evolutionary forces driving lineage and core differentiation. Furthermore, CRISPR spacer traceback of the AAOB metagenome-assembled genomes (MAGs) reveals a series of genetic traces for the concealed phages. By reconceptualizing the functional divergence of AAOB with the historical role of phages, we ultimately propose a coevolutionary framework to understand the evolutionary trajectory of anammox microecology. The discoveries provided in this study offer new insights into understanding the evolution of AAOB and the ecology of anammox.}, } @article {pmid39383805, year = {2025}, author = {Trinh, HP and Lee, SH and Kim, NK and Nguyen, TV and Park, HD}, title = {Fimbriimonadales performed dissimilatory nitrate reduction to ammonium (DNRA) in an anammox reactor.}, journal = {Water research}, volume = {268}, number = {Pt A}, pages = {122575}, doi = {10.1016/j.watres.2024.122575}, pmid = {39383805}, issn = {1879-2448}, mesh = {*Bioreactors/microbiology ; *Nitrates/metabolism ; *Ammonium Compounds/metabolism ; RNA, Ribosomal, 16S/genetics ; Oxidation-Reduction ; Phylogeny ; Denitrification ; Wastewater/microbiology ; Bacteria/metabolism/genetics ; }, abstract = {Bacteria belonging to the order Fimbriimonadales are frequently detected in anammox reactors. However, the principal functions of these bacteria and their potential contribution to nitrogen removal remain unclear. In this study, we aimed to systematically validate the roles of Fimbriimonadales in an anammox reactor fed with synthetic wastewater. High-throughput 16S rRNA gene sequencing analysis revealed that heterotrophic denitrifying bacteria (HDB) were the most abundant bacterial group at the initial stage of reactor operation and the abundance of Fimbriimonadales members gradually increased to reach 38.8 % (day 196). At the end of reactor operation, Fimbriimonadales decreased to 0.9 % with an increase in anammox bacteria. Correlation analysis demonstrated nitrate competition between Fimbriimonadales and HDB during reactor operation. Based on the phylogenetic analysis, the Fimbriimonadales sequences acquired from the reactor were clustered into three distinct groups, which included the sequences obtained from other anammox reactors. Metagenome-assembled genome analysis of Fimbriimonadales allowed the identification of the genes narGHI and nrfAH, responsible for dissimilatory nitrate reduction to ammonium (DNRA), and nrt and nasA, responsible for nitrate and nitrite transport. In a simulation based on mass balance equations and quantified bacterial groups, the total nitrogen concentrations in the effluent were best predicted when Fimbriimonadales was assumed to perform DNRA (R[2] = 0.70 and RMSE = 18.9). Moreover, mass balance analysis demonstrated the potential contribution of DNRA in enriching anammox bacteria and promoting nitrogen removal. These results prove that Fimbriimonadales compete with HDB for nitrate utilization through DNRA in the anammox reactor under non-exogenous carbon supply conditions. Overall, our findings suggest that the DNRA pathway in Fimbriimonadales could enhance anammox enrichment and nitrogen removal by providing substrates (nitrite and/or ammonium) for anammox bacteria.}, } @article {pmid39383803, year = {2025}, author = {Xiang, Y and Song, X and Yang, Y and Deng, S and Fu, L and Yang, C and Chen, M and Pu, J and Zhang, H and Chai, H}, title = {Comammox rather than AOB dominated the efficient autotrophic nitrification-denitrification process in an extremely oxygen-limited environment.}, journal = {Water research}, volume = {268}, number = {Pt A}, pages = {122572}, doi = {10.1016/j.watres.2024.122572}, pmid = {39383803}, issn = {1879-2448}, mesh = {*Nitrification ; *Denitrification ; *Oxygen/metabolism ; *Autotrophic Processes ; *Ammonia/metabolism ; *Bacteria/metabolism/genetics ; *RNA, Ribosomal, 16S/genetics ; Nitrogen/metabolism ; Oxidation-Reduction ; Bioreactors/microbiology ; }, abstract = {The discovery of complete ammonia oxidizer (comammox) has challenged the traditional understanding of the two-step nitrification process. However, their functions in the oxygen-limited autotrophic nitrification-denitrification (OLAND) process remain unclear. In this study, OLAND was achieved using comammox-dominated nitrifying bacteria in an extremely oxygen-limited environment with a dissolved oxygen concentrations of 0.05 mg/L. The ammonia removal efficiency exceeded 97 %, and the total nitrogen removal efficiency reached 71 % when sodium bicarbonate was used as the carbon source. The pseudo-first- and second-order models were found to best fit the ammonia removal processes under low and high loads, respectively, suggesting distinct ammonia removal pathways. Full-length 16S rRNA gene sequencing and metagenomic results revealed that comammox-dominated under different oxygen levels, in conjunction with anammox and heterotrophic denitrifiers. The abundance of enzymes involved in energy metabolism indicates the coexistence of anammox and autotrophic nitrification-heterotrophic denitrification pathways. The binning results showed that comammox bacteria engaged in horizontal gene transfer with nitrifiers, anammox bacteria, and denitrifiers to adapt to an obligate environments. Therefore, this study demonstrated that comammox, anammox, and heterotrophic denitrifiers play important roles in the OLAND process and provide a reference for further reducing aeration energy in the autotrophic nitrogen removal process.}, } @article {pmid39383762, year = {2024}, author = {Serrano-Blanco, S and Zan, R and Harvey, AP and Velasquez-Orta, SB}, title = {Intensified microalgae production and development of microbial communities on suspended carriers and municipal wastewater.}, journal = {Journal of environmental management}, volume = {370}, number = {}, pages = {122717}, doi = {10.1016/j.jenvman.2024.122717}, pmid = {39383762}, issn = {1095-8630}, mesh = {*Microalgae/growth & development ; *Wastewater/microbiology ; Waste Disposal, Fluid/methods ; Bioreactors/microbiology ; }, abstract = {Wastewater represents an alternative source of nutrients in which to grow microalgae, whilst improving the quality of the wastewater, and reducing the downstream treatment required. However, commercialisation of microalgal cultures for such duties faces a number of challenges, predominantly high cost and low productivity. Suspended-solid reactors (ssPBR) can reduce the operational costs, while promoting attached and suspended microalgae growth. In the present study, a novel approach was developed by integrating microalgal wastewater treatment with carrier systems to favour the growth of both attached and suspended cells of T. obliquus. This study found that T. obliquus was able to uptake nutrients from municipal wastewater, achieving removals of 99.3-99.9 % NH3-N, 54.5-88.5 % PO4[3-] and 92.8-94.5 % DTC. The addition of a 12.5 % volumetric fill ratio of carriers in ssPBRs produced higher microalgal cell productivity (1.2·10[6] ± 2.5·10[5] cell ml[-1] d[-1]) than the control (4.3·10[5] ± 2.8·10[5] cell ml[-1] d[-1]). MinION nanopore sequencing was conducted to assess the impact of microalgal and carrier treatment on wastewater bacterial communities. It was found not only that bacterial communities had changed after the treatment but also the ones attached differed from the ones suspended. Untreated wastewater was characterised by the abundance of sewer bacteria genera such as Aliarcobacter and Arcobacter, whilst, after treatment, microbial communities were characterised by the presence of photosynthetic freshwater (Limnococcus, Stanieria) and bioremediation-like bacteria genera (Pseudomonas, Rheinheimera). In conclusion, the addition of 12.5 % fill carrier ratio increased microalgal productivity, while stimulating changes in the algal microbiome, and creating distinctly different populations in the free and attached environments.}, } @article {pmid39383754, year = {2024}, author = {Wu, Y and Sun, Q and Zhou, Z and Wang, Z and Fu, H}, title = {Efficient degradation of carbamazepine and metagenomic investigations of anodic biofilm in microbial fuel cells.}, journal = {Journal of environmental management}, volume = {370}, number = {}, pages = {122743}, doi = {10.1016/j.jenvman.2024.122743}, pmid = {39383754}, issn = {1095-8630}, mesh = {*Carbamazepine/metabolism ; *Bioelectric Energy Sources ; *Biofilms ; *Metagenomics ; Electrodes ; Biodegradation, Environmental ; }, abstract = {Environmental contamination with carbamazepine is a considerable global problem. In this study, two-compartment microbial fuel cells (MFCs) were constructed to investigate the degradation performance of carbamazepine, and the degradation mechanism was further explored by using metagenomic analysis. The results showed that MFCs exhibited excellent carbamazepine removal performance and also generated electricity. The removal rate of carbamazepine reached 73.56% over the 72-h operation period, which was 3.09 times higher than that of the traditional anaerobic method, and the peak voltage of the MFCs could reach 416 mV. Metagenomics revealed significant differences in microbial community composition between MFCs and the traditional anaerobic method (p < 0.05), and Proteobacteria (81.57%) was predominant bacterial phyla during the degradation of carbamazepine by MFCs. Among them, the microbial communities at the genus level were mainly composed of Pseudomonas, Pusillimonas, Burkholderia, Stenotrophomonas, Methyloversatilis and Nitrospirillum. Kyoto Encyclopedia of genes and genomes (KEGG) metabolic pathway analysis showed that the number of genes related to carbon and nitrogen metabolism increased by 85.12% and 142.25%, respectively. Importantly, a greater number of genes of microbial grown on the surface of anode were assigned to denitrification and the degradation of aromatic compounds. This research provides a cost-effective method for treating wastewater contaminated with carbamazepin.}, } @article {pmid39383151, year = {2024}, author = {Xing, F and Deng, C and Huang, J and Yuan, Y and Luo, Z and Lo, SKF and Lau, SKP and Woo, PCY}, title = {Usefulness of next-generation sequencing for laboratory diagnosis of rickettsiosis.}, journal = {PLoS neglected tropical diseases}, volume = {18}, number = {10}, pages = {e0012546}, pmid = {39383151}, issn = {1935-2735}, mesh = {Humans ; Female ; Male ; *Rickettsia Infections/diagnosis/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; Middle Aged ; *Rickettsia/genetics/isolation & purification ; Aged ; Metagenomics/methods ; Adult ; Orientia tsutsugamushi/genetics/isolation & purification ; Scrub Typhus/diagnosis/microbiology ; Molecular Diagnostic Techniques/methods ; }, abstract = {Rickettsiosis includes a diversity of culture-negative non-specific systemic infections. Laboratory diagnosis of rickettsiosis is often not easy. In this 12-month study, six patients with a variety of rickettsia infections of the spotted fever group, typhus group and scrub typhus were diagnosed directly or indirectly by metagenomic next-generation sequencing (mNGS). The patient with Japanese spotted fever was rapidly made when mNGS analysis of the patient's blood revealed Rickettsia japonica sequences. For the two patients with Rickettsia felis chest infections, the bacterium was detected in the bronchoalveolar lavage of one case and lung biopsy of the other. Both patients had underlying malignancies, carcinoma of the breast and carcinoma of the lung respectively, and were on chemotherapy with immunosuppressive effect. For the remaining three patients who presented over a period of 13 weeks, all had fever, headache and the typical eschar. They also had increased serum transaminases and responded promptly to doxycycline. However, the Weil-Felix test results of all three patients were negative. Since we considered the three cases typical of rickettsiosis, we submitted their serum samples for mNGS analysis. Results showed that Orientia tsutsugamushi sequences were present in the serum of one case. In view of the positive mNGS results, we repeated the Weil-Felix test for the residual sera of all three patients and it revealed that those of the other two cases showed OX-19 titers of 1:640 and 1:160 respectively, inferring that these two patients probably had rickettsiosis of the typhus group. As for the patient positive for O. tsutsugamushi sequences, we also detected IgM for O. tsutsugamushi in the serum, which double confirmed that it was a case of scrub typhus. mNGS is an important molecular tool and can complement serology for laboratory diagnosis of rickettsiosis.}, } @article {pmid39382920, year = {2024}, author = {Zhang, L and Sun, SY and Yao, XX and Fu, AS and Ge, YL}, title = {Non-Tuberculous Mycobacterial Pulmonary Disease with Detection of Mycobacterium Tuberculosis in Pleural Fluid.}, journal = {Clinical laboratory}, volume = {70}, number = {10}, pages = {}, doi = {10.7754/Clin.Lab.2024.240531}, pmid = {39382920}, issn = {1433-6510}, mesh = {Humans ; *Mycobacterium Infections, Nontuberculous/diagnosis/microbiology ; *Mycobacterium tuberculosis/isolation & purification/genetics ; *Pleural Effusion/microbiology/diagnosis ; Male ; High-Throughput Nucleotide Sequencing ; Antitubercular Agents/therapeutic use ; Middle Aged ; Female ; Tomography, X-Ray Computed/methods ; Tuberculosis, Pleural/diagnosis/microbiology/drug therapy ; }, abstract = {BACKGROUND: Tuberculous pleurisy (TP) is one of the most common types of extrapulmonary tuberculosis, often secondary to tuberculosis (TB). Clinical and imaging manifestations of non-tuberculous mycobacterial pulmonary diseases (NTM-PD) are usually similar to those of tuberculosis. Because of their similarity and the high incidence of tuberculosis, non-tuberculous mycobacterial infections are often overlooked for a long time. Especially in people without immunodeficiency.

METHODS: Mycobacterium tuberculosis (MTB) in pleural effusion was found by metagenomic next-generation sequencing (mNGS). During anti-tuberculosis treatment, mNGS of lung tissue by ultrasound-guided percutaneous lung puncture revealed that this patient had combined NTM-PD.

RESULTS: Mycobacterium chelonae (M. chelonae) was detected by mNGS, and after anti-NTM treatment, the patient's chest CT showed that the inflammation was absorbed more than before, and the patient's symptoms improved.

CONCLUSIONS: When TB is poorly treated with standardized anti-tuberculosis therapy, comorbid non-tuberculous mycobacterial infections may be considered, and mNGS may complement traditional pathogenetic testing.}, } @article {pmid39382160, year = {2024}, author = {Xue, S and Yi, X and Peng, J and Bak, F and Zhang, L and Duan, G and Liesack, W and Zhu, Y}, title = {Fulvic Acid Enhances Nitrogen Fixation and Retention in Paddy Soils through Microbial-Coupled Carbon and Nitrogen Cycling.}, journal = {Environmental science & technology}, volume = {58}, number = {42}, pages = {18777-18787}, doi = {10.1021/acs.est.4c07616}, pmid = {39382160}, issn = {1520-5851}, mesh = {*Soil/chemistry ; *Carbon/metabolism ; *Nitrogen Fixation ; *Soil Microbiology ; Nitrogen/metabolism ; Benzopyrans ; Nitrogen Cycle ; }, abstract = {Fulvic acid, the most soluble and active humic substance, is widely used as an agent to remediate contaminated soils and improve soil fertility. However, the influence of fulvic acid (FA), as a microbial carbon source, on carbon and nitrogen cycles in paddy soils remains elusive. Therefore, to investigate it, an incubation experiment was conducted. Gas analyses indicated that the carbon dioxide and methane emissions were enhanced in FA treatment, which increased up to 94.08-fold and 5.06-fold, respectively. [15]N-labeling experiments revealed that nitrogen fixation capability was promoted (1.2-fold) to reduce the carbon and nitrogen imbalance due to fulvic acid amendment. Metagenomic analysis further revealed that gene abundances of degradation of lignin-like compounds, gallate degradation, methanogenesis, nitrogen fixation, and urea hydrolysis increased, while the bacterial ammonia oxidation and anaerobic ammonium oxidation decreased, caused by FA application. Metabolic reconstruction of metagenome-assembled genomes revealed that Azospirillaceae, Methanosarcinaceae, and Bathyarchaeota, with higher abundance in FA treatment, were the key microorganisms to maintain the carbon and nitrogen balance. The metabolic pathways of fulvic acid degradation and coupled nitrogen fixation and retention were constructed. Collectively, our results provided novel insights into the theoretical basis of the use of humic substances for reducing nitrogen fertilization and climate change.}, } @article {pmid39382010, year = {2024}, author = {Wang, J and Fan, S and He, J and Jiang, X and Lin, R and Ji, Y and Ge, Y}, title = {A case report of fatal Rickettsia japonica bloodstream infection in Zhejiang, China.}, journal = {Future microbiology}, volume = {19}, number = {18}, pages = {1529-1534}, doi = {10.1080/17460913.2024.2406122}, pmid = {39382010}, issn = {1746-0921}, support = {20211214//New Project of Zhejiang Provincial People's Hospital entitled 'Construction of Rapid Nucleic Acid Detection Platform for Invasive Fungi'/ ; }, mesh = {Humans ; Female ; Middle Aged ; *Rickettsia/isolation & purification/pathogenicity/genetics ; China ; Fatal Outcome ; *Rickettsia Infections/diagnosis/drug therapy/microbiology ; *Anti-Bacterial Agents/therapeutic use ; Bacteremia/microbiology/diagnosis/drug therapy ; Doxycycline/therapeutic use ; Spotted Fever Group Rickettsiosis/diagnosis/microbiology/drug therapy ; Shock, Septic/microbiology ; Fever of Unknown Origin/etiology ; }, abstract = {Japanese spotted fever (JSF) is an emerging acute febrile natural infectious disease caused by the neglected zoonotic pathogen Rickettsia japonica. Here we reported a 64-year-old female patient who initially presented to the local hospital with an intermittent fever of unknown origin (FUO). A systemic, evident edema and eschar on the skin of the patient's upper limb was observed. The patient was diagnosed with critical Rickettsia japonica bloodstream infection by Q-mNGS and treated with doxycycline, as well as symptomatic treatments. Unfortunately, the patient passed away as a result of complications of septic shock and multiple organ and acute respiratory failure. Delayed treatment resulting from the nonspecific clinical symptoms in the early stages of infection can lead to fatal complications. Q-mNGS is an emerging pathogen detection method with the advantages of comprehensive detection, high accuracy and sensitivity and should be promoted and applied by clinicians.}, } @article {pmid39381854, year = {2025}, author = {Drahun, I and Morrison, K and Poole, EA and van Herk, WG and Cassone, BJ}, title = {Characterisation of the bacteriomes harboured by major wireworm pest species in the Canadian Prairies.}, journal = {Insect molecular biology}, volume = {34}, number = {1}, pages = {203-217}, pmid = {39381854}, issn = {1365-2583}, support = {RGPIN-2016-04335//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2023-04126//Natural Sciences and Engineering Research Council of Canada/ ; //Brandon University Research Committee/ ; }, mesh = {Animals ; *Coleoptera/microbiology/growth & development ; *Larva/microbiology/growth & development ; *RNA, Ribosomal, 16S/genetics ; Manitoba ; Microbiota ; Bacteria/classification/genetics ; Grassland ; Canada ; }, abstract = {Nearly all insects harbour bacterial communities that can have a profound effect on their life history, including regulating and shaping host metabolism, development, immunity and fitness. The bacteriomes of several coleopterans have been described; however, very little has been reported for wireworms. These long-lived larvae of click beetles (Coleoptera: Elateridae) are major agricultural pests of a variety of crops grown in the Canadian Prairies. Consequently, the goal of this study was to characterise the bacteriomes of five of the most significant pest species within the region: Limonius californicus, Hypnoidus abbreviatus, H. bicolor, Aeolus mellillus and Dalopius spp. To do this, we collected larvae from southern Manitoba fields (pre-seeding) and carried out 16S rRNA sequencing on individual specimens. Our results indicate wireworms have diverse and taxon-rich bacterial communities, with over 400 genera identified predominately from the phyla Proteobacteria, Actinobacteriota, Bacteroidota and Firmicutes. However, each species had nine or fewer genera comprising >80% of their bacteriome. Network analyses revealed some community structuring consistent among species, which may culminate in shaping/regulating host biology. Moreover, the microbial signatures were influenced by both ontogeny (early vs. late stage larvae) and reproductive strategy (sexual vs. parthenogenetic), with a myriad of other factors likely contributing to bacterial diversity that are impossible to resolve from our study. Overall, this metagenomics study represents the first to characterise the bacteriomes of wireworms in the Canadian Prairies and the findings could assist in the development of sustainable management strategies for these important agricultural pests.}, } @article {pmid39381756, year = {2024}, author = {Sun, Y and Zhang, C and Lu, B and Chen, J and Pan, X}, title = {Case report: Mycobacterium chimaera-induced lymph node infection in a patient with chronic myeloproliferative neoplasm misdiagnosed as tuberculous lymphadenitis.}, journal = {Frontiers in public health}, volume = {12}, number = {}, pages = {1387722}, pmid = {39381756}, issn = {2296-2565}, mesh = {Humans ; Female ; Middle Aged ; *Tuberculosis, Lymph Node/diagnosis/drug therapy ; *Diagnostic Errors ; *Mycobacterium/isolation & purification ; Lymphadenitis/microbiology/diagnosis ; Mycobacterium Infections, Nontuberculous/diagnosis/drug therapy ; Lymph Nodes/pathology/microbiology ; Myeloproliferative Disorders/diagnosis ; }, abstract = {Herein, we report a case of lymphadenitis caused by Mycobacterium chimaera. A 54-year-old woman with chronic myeloproliferative neoplasm was admitted to the hospital with cervical lymphadenopathy. After preliminary exclusion of various diseases such as lymphoma, Epstein-Barr virus infection, and autoimmune disease, a lymph node biopsy specimen showed epithelioid granulomatous lymphadenitis with caseous necrosis, epithelial-like cells, and multinucleated giant cells as seen in tuberculosis (TB). Although Mycobacterium tuberculosis was never isolated, diagnostic anti-TB treatment was commenced. Following over 9 months of treatment, there was no significant reduction in the size of her cervical lymph nodes, and she continued to experience recurrent low-grade fevers. One sample from the fourth lymph node biopsy tested negative for metagenomic next-generation sequencing (mNGS), and another sample tested positive in the BACTEC MGIT960 liquid culture system, identifying the strains as Mycobacterium chimaera. Anti-non-tuberculous mycobacteria (NTM) therapy was initiated, and the patient achieved symptom improvement. In conclusion, NTM lymphoid infection is easily misdiagnosed as long-term etiologic negativity.}, } @article {pmid39381141, year = {2024}, author = {Luo, Q and Lu, M and Butt, H and Lytal, N and Du, R and Jiang, H and An, L}, title = {TimeNorm: a novel normalization method for time course microbiome data.}, journal = {Frontiers in genetics}, volume = {15}, number = {}, pages = {1417533}, pmid = {39381141}, issn = {1664-8021}, abstract = {Metagenomic time-course studies provide valuable insights into the dynamics of microbial systems and have become increasingly popular alongside the reduction in costs of next-generation sequencing technologies. Normalization is a common but critical preprocessing step before proceeding with downstream analysis. To the best of our knowledge, currently there is no reported method to appropriately normalize microbial time-series data. We propose TimeNorm, a novel normalization method that considers the compositional property and time dependency in time-course microbiome data. It is the first method designed for normalizing time-series data within the same time point (intra-time normalization) and across time points (bridge normalization), separately. Intra-time normalization normalizes microbial samples under the same condition based on common dominant features. Bridge normalization detects and utilizes a group of most stable features across two adjacent time points for normalization. Through comprehensive simulation studies and application to a real study, we demonstrate that TimeNorm outperforms existing normalization methods and boosts the power of downstream differential abundance analysis.}, } @article {pmid39381012, year = {2024}, author = {Babalola, OO and Molefe, RR and Amoo, AE}, title = {Metagenome assembly and annotation of data from the rhizosphere soil of drought-stressed CRN-3505 maize cultivar.}, journal = {Data in brief}, volume = {57}, number = {}, pages = {110966}, pmid = {39381012}, issn = {2352-3409}, abstract = {This data article reports shotgun metagenomic data obtained from drought-stressed maize rhizosphere through the Illumina Novaseq platform, utilizing the KBase online platform. 428,339,852 high-quality post-sequences were obtained, showcasing an average GC content of 65.45 %. The investigation, conducted at Molelwane farm in Mafikeng, South Africa, identified 13 metagenome-assembled genomes (MAGs). Functional annotation of these MAGs revealed their involvement in essential plant growth and development functions, such as sulfur and nitrogen metabolism. The dataset was deposited into the NCBI database, and MAGs accessions are available at DDBJ/ENA/GenBank under the accession number PRJNA101755.}, } @article {pmid39381006, year = {2024}, author = {Lalbiakmawia, B and Pulapet, S and Kathir, S and Lalengkimi, R and Markkandan, K and Chhandama, MVL and Nachimuthu, SK and Zothanzama, J}, title = {Dataset on bacterial diversity using 16S metagenome analysis in fermented rice beer from two breweries and grape wine of Mizoram, Northeast India.}, journal = {Data in brief}, volume = {57}, number = {}, pages = {110932}, pmid = {39381006}, issn = {2352-3409}, abstract = {The microbial diversity of fermented rice beer and grape wine in Mizoram was explored using 16S metagenome analysis. The collected samples were marked as C1 and B1 for fermented rice beer and D1 for grape wine. Next-generation sequencing of the 16S rRNA (V3-V4 region) was performed using the Illumina NovoSeq 6000 platform. Operational taxonomic units (OTUs) were identified with QIIME2, and statistical analyses were performed using R packages. The metagenome of the three samples comprised 464,826 raw reads that represented 116,206,500 base pairs and were clustered into 336 OTUs. The phylum Firmicutes was predominant in C1 (55 %), B1 (53 %) and D1 (52 %), respectively and biosysnthesis, pyruvate fermentation to be abundant functions. By applying 16S metagenome analysis, this data provide insights in to the complex community of bacteria involved in the fermentation process and their potential roles and interactions.}, } @article {pmid39380680, year = {2024}, author = {Karavaeva, V and Sousa, FL}, title = {Navigating the archaeal frontier: insights and projections from bioinformatic pipelines.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1433224}, pmid = {39380680}, issn = {1664-302X}, abstract = {Archaea continues to be one of the least investigated domains of life, and in recent years, the advent of metagenomics has led to the discovery of many new lineages at the phylum level. For the majority, only automatic genomic annotations can provide information regarding their metabolic potential and role in the environment. Here, genomic data from 2,978 archaeal genomes was used to perform automatic annotations using bioinformatics tools, alongside synteny analysis. These automatic classifications were done to assess how good these different tools perform in relation to archaeal data. Our study revealed that even with lowered cutoffs, several functional models do not capture the recently discovered archaeal diversity. Moreover, our investigation revealed that a significant portion of archaeal genomes, approximately 42%, remain uncharacterized. In comparison, within 3,235 bacterial genomes, a diverse range of unclassified proteins is obtained, with well-studied organisms like Escherichia coli having a substantially lower proportion of uncharacterized regions, ranging from <5 to 25%, and less studied lineages being comparable to archaea with the range of 35-40% of unclassified regions. Leveraging this analysis, we were able to identify metabolic protein markers, thereby providing insights into the metabolism of the archaea in our dataset. Our findings underscore a substantial gap between automatic classification tools and the comprehensive mapping of archaeal metabolism. Despite advances in computational approaches, a significant portion of archaeal genomes remains unexplored, highlighting the need for extensive experimental validation in this domain, as well as more refined annotation methods. This study contributes to a better understanding of archaeal metabolism and underscores the importance of further research in elucidating the functional potential of archaeal genomes.}, } @article {pmid39380679, year = {2024}, author = {Narenkumar, J and Das, B and Abilaji, S and Sathishkumar, K and AlSalhi, MS and Devanesan, S and Rajasekar, A and Malik, T}, title = {Biosurfactant-assisted bio-electrokinetic enhanced remediation of heavy metal-contaminated soil.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1458369}, pmid = {39380679}, issn = {1664-302X}, abstract = {BACKGROUND: Environmental soil contamination is a serious problem for humans worldwide, as it causes many diseases.

METHODS: The present study focuses on utilizing biosurfactants produced by Pseudomonas stutzeri (P. stutzeri) NA3 and Bacillus cereus (B. cereus) EN6, as an electrolyte for removing chromium (Cr) from contaminated soil using the electrokinetic (EK) process.

RESULTS: As a result, biosurfactants produced by P. stutzeri NA3 and B. cereus EN6, being lipopeptides, increase heavy metal mobility in the EK process. The Cr removal efficiency of a novel electrolyte (biosurfactants) in the EK process was compared with that of NA3 and EN6 biosurfactants. The EK results revealed a maximum Cr removal of 75 and 70% by NA3 and EN6, respectively, at the end of 7 days.

DISCUSSION: The biosurfactant aids in the breaking down of the heavy metals that are present deeper into the soil matrix. From the metagenomics analysis, it was identified that biosurfactant changes the microbial community with an enhanced ability to remove heavy metals. The phytotoxicity assay confirms that NA3 biosurfactant solution showed 95% seed germination and can lower hazardous pollutants in the soil.

CONCLUSION: The application of biosurfactants as a potent electrolyte for the remediation of hazardous pollutants is an integrated process. Overall, the results of this study suggest that biosurfactants can serve as an economic and efficient electrolyte in the EK process to remove Cr from polluted soil.}, } @article {pmid39380672, year = {2024}, author = {Yumnam, H and Hazarika, P and Sharma, I}, title = {Metagenomic insights into traditional fermentation of rice-based beverages among ethnic tribes in southern Assam, Northeast India.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1410098}, pmid = {39380672}, issn = {1664-302X}, abstract = {INTRODUCTION: Traditional fermented foods have long been recognized for their numerous health benefits along with their potential to aid in the treatment of gastrointestinal disorders. These fermented foods have been shown to promote gut health and contribute to a longer, healthier life.

METHODS: The high-throughput sequencing using the Illumina MiSeq platform was employed to investigate the microbiome communities of rice-based fermented beverages consumed by ethnic tribes in Southern Assam, namely Zeme Naga, Dimasa Kachari, Hmar, Karbi and Tea tribes.

RESULTS: The fermented rice-based beverages were highly predominated by Firmicutes, Bacteroides, Proteobacteria, and Actinobacteria exhibiting the highest relative abundance across all tribes. At genus level, significant abundance of pediococcus, lactobacillus, bacillus, leuconostoc, acetobacter, staphylococcus, delftia, erwinia, klebsiella and chrysebacterium were found amongst these ethnic tribes.

DISCUSSION: Understanding the fermented food microbiome will help to know the relationships between microbial communities and their effect on health of humans amongst the tribes. Furthermore, the use of these fermented products could provide enhanced health benefits to southern Assam region of India.}, } @article {pmid39380403, year = {2024}, author = {Pang, R and Wang, X and Zhang, L and Lei, L and Han, Z and Xie, B and Su, Y}, title = {Genome-Centric Metagenomics Insights into the Plastisphere-Driven Natural Degradation Characteristics and Mechanism of Biodegradable Plastics in Aquatic Environments.}, journal = {Environmental science & technology}, volume = {58}, number = {42}, pages = {18915-18927}, doi = {10.1021/acs.est.4c04965}, pmid = {39380403}, issn = {1520-5851}, mesh = {*Biodegradable Plastics ; *Metagenomics ; *Biodegradation, Environmental ; Plastics ; }, abstract = {Biodegradable plastics (BPs) are pervasively available as alternatives to traditional plastics, but their natural degradation characteristics and microbial-driven degradation mechanisms are poorly understood, especially in aquatic environments, the primary sink of plastic debris. Herein, the three-month dynamic degradation process of BPs (the copolymer of poly(butylene adipate-co-terephthalate) and polylactic acid (PLA) (PBAT/PLA) and single PLA) in a natural aquatic environment was investigated, with nonbiodegradable plastics polyvinyl chloride, polypropylene, and polystyrene as controls. PBAT/PLA showed the weight loss of 47.4% at 50 days and severe fragmentation within two months, but no significant decay for other plastics. The significant increase in the specific surface area and roughness and the weakening of hydrophobicity within the first month promoted microbial attachment to the PBAT/PLA surface. Then, a complete microbial succession occurred, including biofilm formation, maturation, and dispersion. Metagenomic analysis indicated that plastispheres selectively enriched degraders. Based on the functional genes involved in BPs degradation, a total of 16 high-quality metagenome-assembled genomes of degraders (mainly Burkholderiaceae) were recovered from the PBAT/PLA plastisphere. These microbes showed the greatest degrading potential at the biofilm maturation stage and executed the functions by PLA_depolymerase, polyesterase, hydrolase, and esterase. These findings will enhance understanding of BPs' environmental behavior and microbial roles on plastic degradation.}, } @article {pmid39380016, year = {2024}, author = {Ju, Y and Zhang, Z and Liu, M and Lin, S and Sun, Q and Song, Z and Liang, W and Tong, X and Jie, Z and Lu, H and Cai, K and Chen, P and Jin, X and Zhang, W and Xu, X and Yang, H and Wang, J and Hou, Y and Xiao, L and Jia, H and Zhang, T and Guo, R}, title = {Integrated large-scale metagenome assembly and multi-kingdom network analyses identify sex differences in the human nasal microbiome.}, journal = {Genome biology}, volume = {25}, number = {1}, pages = {257}, pmid = {39380016}, issn = {1474-760X}, mesh = {Humans ; Male ; Female ; *Metagenome ; *Microbiota ; Adult ; Nose/microbiology ; Sex Characteristics ; Young Adult ; Bacteria/genetics/classification ; Sex Factors ; Metagenomics/methods ; }, abstract = {BACKGROUND: Respiratory diseases impose an immense health burden worldwide. Epidemiological studies have revealed extensive disparities in the incidence and severity of respiratory tract infections between men and women. It has been hypothesized that there might also be a nasal microbiome axis contributing to the observed sex disparities.

RESULTS: Here, we study the nasal microbiome of healthy young adults in the largest cohort to date with 1593 individuals, using shotgun metagenomic sequencing. We compile the most comprehensive reference catalog for the nasal bacterial community containing 4197 metagenome-assembled genomes and integrate the mycobiome, to provide a valuable resource and a more holistic perspective for the understudied human nasal microbiome. We systematically evaluate sex differences and reveal extensive sex-specific features in both taxonomic and functional levels in the nasal microbiome. Through network analyses, we capture markedly higher ecological stability and antagonistic potentials in the female nasal microbiome compared to the male's. The analysis of the keystone bacteria reveals that the sex-dependent evolutionary characteristics might have contributed to these differences.

CONCLUSIONS: In summary, we construct the most comprehensive catalog of metagenome-assembled-genomes for the nasal bacterial community to provide a valuable resource for the understudied human nasal microbiome. On top of that, comparative analysis in relative abundance and microbial co-occurrence networks identify extensive sex differences in the respiratory tract community, which may help to further our understanding of the observed sex disparities in the respiratory diseases.}, } @article {pmid39379947, year = {2024}, author = {Ariaeenejad, S and Zeinalabedini, M and Sadeghi, A and Gharaghani, S and Mardi, M}, title = {Enhancing nutritional and potential antimicrobial properties of poultry feed through encapsulation of metagenome-derived multi-enzymes.}, journal = {BMC biotechnology}, volume = {24}, number = {1}, pages = {76}, pmid = {39379947}, issn = {1472-6750}, mesh = {Animals ; *Animal Feed/analysis ; *Poultry ; Metagenome ; Escherichia coli/drug effects ; Anti-Infective Agents/pharmacology/chemistry ; Plant Gums/chemistry ; Galactans/chemistry ; Antioxidants/metabolism/chemistry/pharmacology ; Mannans/chemistry/metabolism/pharmacology ; }, abstract = {BACKGROUND: The encapsulation of metagenome-derived multi-enzymes presents a novel approach to improving poultry feed by enhancing nutrient availability and reducing anti-nutritional factors. By integrating and encapsulated enzymes such as carbohydrate-hydrolyzing enzymes, protease, lipase, and laccase into feed formulations, this method not only improves feed digestibility but also potentially contributes to animal health and productivity through antimicrobial properties.

RESULTS: This study investigates the encapsulation of metagenome-derived enzymes, including carbohydrate-hydrolyzing enzymes, protease, lipase, and laccase, using Arabic and Guar gums as encapsulating agents. The encapsulated multi-enzymes exhibited significant antimicrobial activity, achieving a 92.54% inhibition rate against Escherichia coli at a concentration of 6 U/mL. Fluorescence tracking with FITC-labeled enzymes confirmed efficient encapsulation and distribution, while physical characterization, including moisture content and solubility assessments, along with Atomic Force Microscopy (AFM) imaging, validated successful encapsulation. The encapsulated enzymes also effectively hydrolyzed poultry feed, leading to an increase in phenolic content and antioxidant activity, as confirmed by 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid (ABTS) and 2,2-diphenyl-1-picrylhydrazyl (DPPH) assays.

CONCLUSIONS: The encapsulated multi-enzymes improved the overall feed quality by increasing reducing sugars and enhancing physical properties such as solubility and water-holding capacity. The encapsulated multi-enzymes improved the overall feed quality by increasing reducing sugars, antioxidant activity and enhancing physical properties such as solubility and water-holding capacity. Scanning Electron Microscopy (SEM) and Fourier-Transform Infrared Spectroscopy (FTIR) analyses confirmed the enzymatic breakdown of the feed structure. These results suggest that supplementing poultry feed with encapsulated multi-enzymes can enhance its physical, nutritional, and functional properties, leading to improved digestibility and overall feed quality.}, } @article {pmid39379646, year = {2024}, author = {Shaw, J and Yu, YW}, title = {Rapid species-level metagenome profiling and containment estimation with sylph.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {39379646}, issn = {1546-1696}, support = {RGPIN-2022-03074//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada)/ ; DGDND-2022-03074//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada)/ ; CGS-D//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology)/ ; }, abstract = {Profiling metagenomes against databases allows for the detection and quantification of microorganisms, even at low abundances where assembly is not possible. We introduce sylph, a species-level metagenome profiler that estimates genome-to-metagenome containment average nucleotide identity (ANI) through zero-inflated Poisson k-mer statistics, enabling ANI-based taxa detection. On the Critical Assessment of Metagenome Interpretation II (CAMI2) Marine dataset, sylph was the most accurate profiling method of seven tested. For multisample profiling, sylph took >10-fold less central processing unit time compared to Kraken2 and used 30-fold less memory. Sylph's ANI estimates provided an orthogonal signal to abundance, allowing for an ANI-based metagenome-wide association study for Parkinson disease (PD) against 289,232 genomes while confirming known butyrate-PD associations at the strain level. Sylph took <1 min and 16 GB of random-access memory to profile metagenomes against 85,205 prokaryotic and 2,917,516 viral genomes, detecting 30-fold more viral sequences in the human gut compared to RefSeq. Sylph offers precise, efficient profiling with accurate containment ANI estimation even for low-coverage genomes.}, } @article {pmid39379175, year = {2024}, author = {Zheng, D and Wilén, BM and Öberg, O and Wik, T and Modin, O}, title = {"Metagenomics reveal the potential for geosmin and 2-methylisoborneol production across multiple bacterial phyla in recirculating aquaculture systems".}, journal = {Environmental microbiology}, volume = {26}, number = {10}, pages = {e16696}, doi = {10.1111/1462-2920.16696}, pmid = {39379175}, issn = {1462-2920}, support = {2020-02639//Svenska Forskningsrådet Formas/ ; }, mesh = {*Metagenomics ; *Bacteria/genetics/classification/metabolism ; *Aquaculture ; *Naphthols/metabolism ; *Camphanes/metabolism ; Phylogeny ; Archaea/genetics/metabolism/classification ; Microbiota ; Metagenome ; }, abstract = {Geosmin and 2-methylisoborneol (MIB) are known to cause taste-and-odour problems in recirculating aquaculture systems (RAS). Both geosmin and MIB are microbial metabolites belonging to terpenoids. Precursors for terpenoids are biosynthesized via the methylerythritol phosphate (MEP) and the mevalonate (MVA) pathways. We carried out a metagenomic analysis of 50 samples from five RAS to investigate terpenoid biosynthesis and metabolic potential for geosmin and MIB production in RAS microbiomes. A total of 1008 metagenome-assembled genomes (MAGs) representing 26 bacterial and three archaeal phyla were recovered. Although most archaea are thought to use the MVA pathway for terpenoid precursor biosynthesis, an Iainarchaeota archaeal MAG is shown to harbour a complete set of genes encoding the MEP pathway but lacking genes associated with the MVA pathway. In this study, a total of 16 MAGs affiliated with five bacterial phyla (Acidobacteriota, Actinobacteriota, Bacteroidota, Chloroflexota, and Myxococcota) were identified as possessing potential geosmin or MIB synthases. These putative taste and odour producers were diverse, many were taxonomically unidentified at the genus or species level, and their relative abundance differed between the investigated RAS farms. The metagenomic study of the RAS microbiomes revealed a previously unknown phylogenetic diversity of the potential to produce geosmin and MIB.}, } @article {pmid39378970, year = {2025}, author = {Zharikova, AA and Andrianova, NV and Silachev, DN and Nebogatikov, VO and Pevzner, IB and Makievskaya, CI and Zorova, LD and Maleev, GV and Baydakova, GV and Chistyakov, DV and Goriainov, SV and Sergeeva, MG and Burakova, IY and Gureev, AP and Popkov, VA and Ustyugov, AA and Plotnikov, EY}, title = {Analysis of the brain transcriptome, microbiome and metabolome in ketogenic diet and experimental stroke.}, journal = {Brain, behavior, and immunity}, volume = {123}, number = {}, pages = {571-585}, doi = {10.1016/j.bbi.2024.10.004}, pmid = {39378970}, issn = {1090-2139}, mesh = {Animals ; *Diet, Ketogenic/methods ; Rats ; *Brain/metabolism ; *Gastrointestinal Microbiome/physiology ; Male ; *Metabolome ; *Transcriptome ; *Stroke/metabolism ; *Infarction, Middle Cerebral Artery/metabolism ; Disease Models, Animal ; Rats, Sprague-Dawley ; }, abstract = {The ketogenic diet (KD) has been shown to be effective in treating various brain pathologies. In this study, we conducted detailed transcriptomic and metabolomic profiling of rat brains after KD and ischemic stroke in order to investigate the effects of KD and its underlying mechanisms. We evaluated the effect of a two-month KD on gene expression in intact brain tissue and after middle cerebral artery occlusion (MCAO). We analyzed the effects of KD on gut microbiome composition and blood metabolic profile as well as investigated the correlation between severity of neurological deficits and KD-induced changes. We found transcriptional reprogramming in the brain after stroke and KD treatment. The KD altered the expression of genes involved in the regulation of glucose and fatty acid metabolism, mitochondrial function, the immune response, Wnt-associated signaling, stem cell development, and neurotransmission, both in intact rats and after MCAO. The KD led to a significant change in the composition of gut microbiome and the levels of amino acids, acylcarnitines, polyunsaturated fatty acids, and oxylipins in the blood. However, the KD slightly worsened the neurological functions after MCAO, so that the therapeutic effect of the diet remained unproven.}, } @article {pmid39378879, year = {2024}, author = {Wu, G and Xu, T and Zhao, N and Lam, YY and Ding, X and Wei, D and Fan, J and Shi, Y and Li, X and Li, M and Ji, S and Wang, X and Fu, H and Zhang, F and Shi, Y and Zhang, C and Peng, Y and Zhao, L}, title = {A core microbiome signature as an indicator of health.}, journal = {Cell}, volume = {187}, number = {23}, pages = {6550-6565.e11}, doi = {10.1016/j.cell.2024.09.019}, pmid = {39378879}, issn = {1097-4172}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Diabetes Mellitus, Type 2/microbiology ; Case-Control Studies ; Dietary Fiber/metabolism ; Metagenome ; Metagenomics/methods ; Health ; Microbiota ; }, abstract = {The gut microbiota is crucial for human health, functioning as a complex adaptive system akin to a vital organ. To identify core health-relevant gut microbes, we followed the systems biology tenet that stable relationships signify core components. By analyzing metagenomic datasets from a high-fiber dietary intervention in type 2 diabetes and 26 case-control studies across 15 diseases, we identified a set of stably correlated genome pairs within co-abundance networks perturbed by dietary interventions and diseases. These genomes formed a "two competing guilds" (TCGs) model, with one guild specialized in fiber fermentation and butyrate production and the other characterized by virulence and antibiotic resistance. Our random forest models successfully distinguished cases from controls across multiple diseases and predicted immunotherapy outcomes through the use of these genomes. Our guild-based approach, which is genome specific, database independent, and interaction focused, identifies a core microbiome signature that serves as a holistic health indicator and a potential common target for health enhancement.}, } @article {pmid39378756, year = {2024}, author = {Wang, X and Chen, L and Yang, G and Cai, Y and Yu, G}, title = {Bacterial and fungal aerosols in poultry houses: PM2.5 metagenomics via single-molecule real-time sequencing.}, journal = {Poultry science}, volume = {103}, number = {12}, pages = {104348}, pmid = {39378756}, issn = {1525-3171}, mesh = {Animals ; *Housing, Animal ; *Fungi/isolation & purification/genetics/classification ; *Chickens/microbiology ; *Particulate Matter/analysis ; *Bacteria/isolation & purification/genetics/classification ; *Air Microbiology ; *Ducks ; *Aerosols/analysis ; China ; Metagenomics ; Air Pollutants/analysis ; }, abstract = {Microbial aerosol contamination is a common problem in poultry farms, posing potential health risks to poultry and their caretakers. Exploring the distribution and diversity of the microbial community in poultry farm aerosols is crucial for effective mitigation strategies. The composition of bacterial and fungal aerosols is poorly understood, particularly the prevalence of potential pathogenic microorganisms in fine particulate matter (PM2.5) in various types of poultry houses. In this study, 27 PM2.5 samples were collected from 5 chicken houses and 4 duck houses in Shandong Province, China. Species-level diversity of bacterial and fungal components in PM2.5 samples was determined using advanced single-molecule real-time sequencing (SMRT) technology, based on the 16S and internal transcribed spacer 1 (ITS) ribosomal genes. Microbial diversity and community composition varied significantly across the different poultry house. Notably, duck houses had higher concentrations (p < 0.01) of PM2.5 (92.8-143.1 μg/m[3]) than chicken houses (42.0-56.4 μg/m[3]). Furthermore, microbial variation in PM2.5 samples was associated with the type of poultry facility. The predominant pathogenic microorganisms included Aspergillus sydowii, Penicillium sp., Aspergillus insolitus, Cladosporium sp., Aspergillus sp., Aspergillus pseudoglaucus, Cladosporium sp. C4092-2-PD1, and Colletotrichum sp., all of which were classified as second category of pathogens. Aspergillus sydowii and Penicillium sp. were the dominant species in chicken houses, while Cladosporium sp., Aspergillus sp., and Aspergillus pseudoglaucus were the dominant species identified in duck houses. To our knowledge, this study is the first to investigate bacterial and fungal diversity in PM2.5 samples collected from various types of poultry houses. These findings advance our understanding of poultry environmental microbiology and have important implications for safeguarding the health of both poultry and their caretakers.}, } @article {pmid39378747, year = {2025}, author = {Yang, G and Luo, Y and Bian, Y and Chen, X and Chen, L and Huang, X}, title = {Electro-mediated cathodic oxygen drives respiration chain electron transfer of electroactive bacteria to enhance refractory organic biological oxidation.}, journal = {Water research}, volume = {268}, number = {Pt A}, pages = {122585}, doi = {10.1016/j.watres.2024.122585}, pmid = {39378747}, issn = {1879-2448}, mesh = {*Electrodes ; *Oxidation-Reduction ; Electron Transport ; *Oxygen/metabolism ; *Bioreactors ; Bacteria/metabolism ; Anaerobiosis ; Biofilms ; }, abstract = {In electro-mediated biological system (EMBS), biological anode and cathode components were incorporated into an anaerobic bioreactor, providing a small amount of oxygen to the cathode as an electron acceptor. Oxygen diffusion also impacts the anode's anaerobic ecological environment. This study unraveled how oxygen influences the metabolism and electron transport chain during the biological oxidation of refractory organics. Under the influence of electromotive force, the straight-chain model pollutant N,N-dimethylformamide (DMF) showed rapid degradation and better ammonification, with maximum rates reaching 0.53 h[-1] and 26.6 %, respectively. Elevated electromotive force promoted the enrichment of functional electroactive bacteria on the anode and enhanced the availability of electron storage sites, thereby facilitating electron transfer at the anode-biofilm interface. Conversely, the anodic micro-aerobic environment disrupted the anaerobic microbial community structure, and the competitive interactions among fermentative bacteria and electroactive bacteria inhibited DMF degradation. Metagenomic analysis confirmed that cathodic oxygen up-regulated the pyruvate metabolism and the tricarboxylic acid (TCA) cycle to generate NADH and synthesize ATP. The electromotive force induced by cathodic oxygen accelerated the electron transfer in respiratory chains of electroactive bacteria, driving the oxidation of NADH and enhancing the degradation of organics. This study improves our understanding of the regulatory mechanisms governing metabolic pathways under the influence of cathodic oxygen. It offers potential for developing more efficient EMBS in industrial wastewater pretreatment, ensuring that oxygen is prevented from diffusing to the anode during micro-aeration at the cathode.}, } @article {pmid39378744, year = {2025}, author = {Zhu, T and Li, S and Tao, C and Chen, W and Chen, M and Zong, Z and Wang, Y and Li, Y and Yan, B}, title = {Understanding the mechanism of microplastic-associated antibiotic resistance genes in aquatic ecosystems: Insights from metagenomic analyses and machine learning.}, journal = {Water research}, volume = {268}, number = {Pt A}, pages = {122570}, doi = {10.1016/j.watres.2024.122570}, pmid = {39378744}, issn = {1879-2448}, mesh = {*Machine Learning ; *Microplastics/toxicity ; *Drug Resistance, Microbial/genetics ; *Metagenomics ; *Ecosystem ; Water Pollutants, Chemical/toxicity ; }, abstract = {The pervasive presence of microplastics (MPs) in aquatic systems facilitates the transmission of antibiotic resistance genes (ARGs), thereby posing risks to ecosystems and human well-being. However, owing to variations in environmental backgrounds and the limited scope of research subjects, studies on ARGs in MPs lack unified conclusions, particularly regarding whether different types of MPs selectively promote ARG enrichment. Analysing large-scale datasets can better encompass broad spatiotemporal scales and diverse samples, facilitating a more extensive exploration of the complex ecological relationships between MPs and ARGs. The present study integrated existing metagenomic datasets to conduct a comprehensive risk assessment and comparative analysis of resistance groups across various MPs. In addition, we endeavoured to elucidate potential associations between ARGs and bacterial taxa, as well as MP structural features, using machine learning (ML) methods. The findings of our research highlight the pivotal role of MP type in shaping plastispheres, accounting for 9.56 % of the biotic variation (Adonis index) and explaining 18.59 % of the ARG variance. Compared to conventional MPs, biodegradable MPs, such as polyhydroxyalkanoates (PHA) and polylactic acid (PLA), exhibit lower species uniformity and diversity but pose a higher risk of ARG occurrence. These ML approaches effectively forecasted ARG abundance by using the bacterial taxa and molecular structure descriptors (MDs) of MPs (average R[2]tra = 0.882, R[2]test = 0.759). Feature analysis showed that MDs associated with lipophilicity, solubility, toxicity, and surface potential significantly influenced the relative abundance of ARGs in the plastispheres. The interpretable multiple linear regression (MLR) model, particularly notable, elucidated a linear relationship between bacterial genera and ARGs, offering promise for identifying potential ARG hosts. This study offers novel insights into ARG dynamics and ecological risks within aquatic plastispheres, highlighting the importance of comprehensive MP monitoring initiatives.}, } @article {pmid39378692, year = {2024}, author = {Lappan, R and Chown, SL and French, M and Perlaza-Jiménez, L and Macesic, N and Davis, M and Brown, R and Cheng, A and Clasen, T and Conlan, L and Goddard, F and Henry, R and Knight, DR and Li, F and Luby, S and Lyras, D and Ni, G and Rice, SA and Short, F and Song, J and Whittaker, A and Leder, K and Lithgow, T and Greening, C}, title = {Towards integrated cross-sectoral surveillance of pathogens and antimicrobial resistance: Needs, approaches, and considerations for linking surveillance to action.}, journal = {Environment international}, volume = {192}, number = {}, pages = {109046}, doi = {10.1016/j.envint.2024.109046}, pmid = {39378692}, issn = {1873-6750}, mesh = {Humans ; Animals ; *Drug Resistance, Bacterial ; Drug Resistance, Microbial ; Communicable Diseases/drug therapy/microbiology/transmission ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Pathogenic and antimicrobial-resistant (AMR) microorganisms are continually transmitted between human, animal, and environmental reservoirs, contributing to the high burden of infectious disease and driving the growing global AMR crisis. The sheer diversity of pathogens, AMR mechanisms, and transmission pathways connecting these reservoirs create the need for comprehensive cross-sectoral surveillance to effectively monitor risks. Current approaches are often siloed by discipline and sector, focusing independently on parts of the whole. Here we advocate that integrated surveillance approaches, developed through transdisciplinary cross-sector collaboration, are key to addressing the dual crises of infectious diseases and AMR. We first review the areas of need, challenges, and benefits of cross-sectoral surveillance, then summarise and evaluate the major detection methods already available to achieve this (culture, quantitative PCR, and metagenomic sequencing). Finally, we outline how cross-sectoral surveillance initiatives can be fostered at multiple scales of action, and present key considerations for implementation and the development of effective systems to manage and integrate this information for the benefit of multiple sectors. While methods and technologies are increasingly available and affordable for comprehensive pathogen and AMR surveillance across different reservoirs, it is imperative that systems are strengthened to effectively manage and integrate this information.}, } @article {pmid39378072, year = {2024}, author = {Koohi-Moghadam, M and Watt, RM and Leung, WK}, title = {Multi-site analysis of biosynthetic gene clusters from the periodontitis oral microbiome.}, journal = {Journal of medical microbiology}, volume = {73}, number = {10}, pages = {}, doi = {10.1099/jmm.0.001898}, pmid = {39378072}, issn = {1473-5644}, mesh = {Humans ; *Periodontitis/microbiology ; *Multigene Family ; *Mouth/microbiology ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification/metabolism ; Pilot Projects ; Metagenomics/methods ; Saliva/microbiology ; Adult ; Male ; Biosynthetic Pathways/genetics ; Female ; Middle Aged ; High-Throughput Nucleotide Sequencing ; Metagenome ; }, abstract = {Background. Bacteria significantly influence human health and disease, with bacterial biosynthetic gene clusters (BGCs) being crucial in the microbiome-host and microbe-microbe interactions.Gap statement. Despite extensive research into BGCs within the human gut microbiome, their roles in the oral microbiome are less understood.Aim. This pilot study utilizes high-throughput shotgun metagenomic sequencing to examine the oral microbiota in different niches, particularly focusing on the association of BGCs with periodontitis.Methodology. We analysed saliva, subgingival plaque and supragingival plaque samples from periodontitis patients (n=23) and controls (n=16). DNA was extracted from these samples using standardized protocols. The high-throughput shotgun metagenomic sequencing was then performed to obtain comprehensive genetic information from the microbial communities present in the samples.Results. Our study identified 10 742 BGCs, with certain clusters being niche-specific. Notably, aryl polyenes and bacteriocins were the most prevalent BGCs identified. We discovered several 'novel' BGCs that are widely represented across various bacterial phyla and identified BGCs that had different distributions between periodontitis and control subjects. Our systematic approach unveiled the previously unexplored biosynthetic pathways that may be key players in periodontitis.Conclusions. Our research expands the current metagenomic knowledge of the oral microbiota in both healthy and periodontally diseased states. These findings highlight the presence of novel biosynthetic pathways in the oral cavity and suggest a complex network of host-microbe and microbe-microbe interactions, potentially influencing periodontal disease. The BGCs identified in this study pave the way for future investigations into the role of small-molecule-mediated interactions within the human oral microbiota and their impact on periodontitis.}, } @article {pmid39377977, year = {2024}, author = {Tufail, MA and Schmitz, RA}, title = {Exploring the Probiotic Potential of Bacteroides spp. Within One Health Paradigm.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {39377977}, issn = {1867-1314}, support = {031B0846D//Bundesministerium für Bildung und Forschung/ ; 031B0846D//Bundesministerium für Bildung und Forschung/ ; }, abstract = {Probiotics are pivotal in maintaining or restoring the balance of human intestinal microbiota, a crucial factor in mitigating diseases and preserving the host's health. Exploration into Bacteroides spp. reveals substantial promise in their development as next-generation probiotics due to their profound interaction with host immune cells and capability to regulate the microbiome's metabolism by significantly impacting metabolite production. These beneficial bacteria exhibit potential in ameliorating various health issues such as intestinal disorders, cardiovascular diseases, behavioral disorders, and even cancer. Though it's important to note that a high percentage of them are as well opportunistic pathogens, posing risks under certain conditions. Studies highlight their role in modifying immune responses and improving health conditions by regulating lymphocytes, controlling metabolism, and preventing inflammation and cancer. The safety and efficacy of Bacteroides strains are currently under scrutiny by the European Commission for authorization in food processing, marking a significant step towards their commercialization. The recent advancements in bacterial isolation and sequencing methodologies, coupled with the integration of Metagenome-Assembled Genomes (MAGs) binning from metagenomics data, continue to unveil the potential of Bacteroides spp., aiding in the broader understanding and application of these novel probiotics in health and disease management.}, } @article {pmid39377603, year = {2024}, author = {Colberg, O and Hermes, GDA and Licht, TR and Wichmann, A and Baker, A and Laursen, MF and Wellejus, A}, title = {Development of an infant colon simulating in vitro model, I-TIM-2, to study the effects of modulation strategies on the infant gut microbiome composition and function.}, journal = {Microbiology spectrum}, volume = {12}, number = {11}, pages = {e0072424}, pmid = {39377603}, issn = {2165-0497}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology/drug effects ; Infant ; *Feces/microbiology ; *Colon/microbiology/metabolism ; *Fatty Acids, Volatile/metabolism/analysis ; *Milk, Human/microbiology ; *Bacteria/classification/genetics/metabolism/isolation & purification/growth & development ; Oligosaccharides/metabolism ; Female ; Breast Feeding ; Models, Biological ; Infant, Newborn ; Male ; }, abstract = {The early life stages are critical for the development of the gut microbiome. Variables such as antibiotics exposure, birth-mode via Cesarean section, and formula feeding are associated with disruptions in microbiome development and are related to adverse health effects later in life. Studying the effects of microbiome-modulating strategies in infants is challenged by appropriate ethical constraints. Therefore, we developed I-TIM-2, an infant in vitro colonic model based on the validated, computer-controlled, dynamic model of the colon, TIM-2. The system, consisting of four separate compartments, was inoculated with feces from four healthy, primarily breastfed infants, displaying distinctive microbiome profiles. For each infant's fecal sample, a 96-h experiment was performed, with two compartments receiving an infant diet adapted medium and two compartments additionally receiving five human milk oligosaccharides (HMOs) in physiological concentrations and proportions. Bacterial composition was determined by shotgun metagenomics and qPCR. Concentrations of short-chain fatty acids (SCFAs) and HMOs were determined by LC-MS. Microbial diversity and high amounts of inoculum-derived species were preserved in the model throughout each experiment. Microbiome composition and SCFA concentrations were consistent with published data from infants. HMOs strongly modulated the microbiome composition by stimulating relative proportions of Bifidobacterium. This affected the metabolic output and resulted in an increased production of acetic and formic acid, characteristic of bifidobacterial HMO metabolism. In conclusion, these data demonstrate the development of a valid model to study the dynamics and modulations of the infant gut microbiome and metabolome.IMPORTANCEThe infant gut microbiome is intricately linked to the health of its host. This is partly mediated through the bacterial production of metabolites that interact with the host cells. Human milk shapes the establishment of the infant gut microbiome as it contains human milk sugars that select for primarily bifidobacteria. The establishment can be disrupted by modern interventions such as formula feeding. This can alter the microbiome composition and metabolite production profile, which can affect the host. In this article, we set up an infant in vitro colonic model to study microbiome interactions and functions. In this model, we investigated the effects of human milk sugars and their promotion of bifidobacteria at the expense of other bacteria. The model is an ideal system to assess the effects of various modulating strategies on the infant gut microbiome and its interactions with its host.}, } @article {pmid39377587, year = {2024}, author = {McMillan, AS and Zhang, G and Dougherty, MK and McGill, SK and Gulati, AS and Baker, ES and Theriot, CM}, title = {Metagenomic, metabolomic, and lipidomic shifts associated with fecal microbiota transplantation for recurrent Clostridioides difficile infection.}, journal = {mSphere}, volume = {9}, number = {10}, pages = {e0070624}, pmid = {39377587}, issn = {2379-5042}, support = {RM1 GM145416/GM/NIGMS NIH HHS/United States ; R01 GM141277/GM/NIGMS NIH HHS/United States ; R01 GM141277, RM1 GM145416//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R35GM119438, R35GM149222//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; P42 ES027704/ES/NIEHS NIH HHS/United States ; R35 GM119438/GM/NIGMS NIH HHS/United States ; T32 DK007634/DK/NIDDK NIH HHS/United States ; STAR RD 84003201//Environmental Protection Agency (EPA)/ ; R35 GM149222/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Clostridium Infections/therapy/microbiology ; *Clostridioides difficile/genetics/metabolism ; *Metabolomics ; *Gastrointestinal Microbiome ; *Feces/microbiology ; *Metagenomics/methods ; *Metabolome ; Male ; Lipidomics ; Female ; Bile Acids and Salts/metabolism ; Recurrence ; Middle Aged ; Aged ; Adult ; Metagenome ; }, abstract = {Recurrent C. difficile infection (rCDI) is an urgent public health threat, for which the last resort and lifesaving treatment is a fecal microbiota transplant (FMT). However, the exact mechanisms that mediate a successful FMT are not well-understood. Here, we use longitudinal stool samples collected from patients undergoing FMT to evaluate intra-individual changes in the microbiome, metabolome, and lipidome after successful FMTs relative to their baselines pre-FMT. We show changes in the abundance of many lipids, specifically a decrease in acylcarnitines post-FMT, and a shift from conjugated bile acids pre-FMT to deconjugated secondary bile acids post-FMT. These changes correlate with a decrease in Enterobacteriaceae, which encode carnitine metabolism genes, and an increase in Lachnospiraceae, which encode bile acid altering genes such as bile salt hydrolases (BSHs) and the bile acid-inducible (bai) operon, post-FMT. We also show changes in gut microbe-encoded amino acid biosynthesis genes, of which Enterobacteriaceae was the primary contributor to amino acids C. difficile is auxotrophic for. Liquid chromatography, ion mobility spectrometry, and mass spectrometry (LC-IMS-MS) revealed a shift from microbial conjugation of primary bile acids pre-FMT to secondary bile acids post-FMT. Here, we define the structural and functional changes associated with a successful FMT and generate hypotheses that require further experimental validation. This information is meant to help guide the development of new microbiota-focused therapeutics to treat rCDI.IMPORTANCERecurrent C. difficile infection is an urgent public health threat, for which the last resort and lifesaving treatment is a fecal microbiota transplant. However, the exact mechanisms that mediate a successful FMT are not well-understood. Here, we show changes in the abundance of many lipids, specifically acylcarnitines and bile acids, in response to FMT. These changes correlate with Enterobacteriaceae pre-FMT, which encodes carnitine metabolism genes, and Lachnospiraceae post-FMT, which encodes bile salt hydrolases and baiA genes. There was also a shift from microbial conjugation of primary bile acids pre-FMT to secondary bile acids post-FMT. Here, we define the structural and functional changes associated with a successful FMT, which we hope will help aid in the development of new microbiota-focused therapeutics to treat rCDI.}, } @article {pmid39377582, year = {2024}, author = {Fukushima, K and Matsumoto, Y and Abe, Y and Hashimoto, K and Motooka, D and Kitada, S and Saito, H and Komukai, S and Fukui, E and Niitsu, T and Nabeshima, H and Nagahama, Y and Yamauchi, J and Nitta, T and Nii, T and Matsuki, T and Tsujino, K and Miki, K and Shintani, Y and Kumanogoh, A and Akira, S and Nakamura, S and Kida, H}, title = {Variability of macrolide-resistant profile in Mycobacterium avium complex pulmonary disease.}, journal = {Antimicrobial agents and chemotherapy}, volume = {68}, number = {11}, pages = {e0121324}, pmid = {39377582}, issn = {1098-6596}, support = {JP23fk0108673h0701//Japan Agency for Medical Research and Development (AMED)/ ; //Foundation of Kinoshita Memorial Enterprise (は)/ ; //Senri Life Science Foundation/ ; //Japan Intractable Diseases Research Foundation (JIDRF)/ ; //Shionogi (Shionogi & Co. Ltd.)/ ; JP21lm0203007//Japan Agency for Medical Research and Development (AMED)/ ; A-32//GlaxoSmithKline (GSK)/ ; JP21K16118//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP21K08194//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP24K11378//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; //Takeda Science Foundation (TSF)/ ; //MSD Life Science Foundation, Public Interest Incorporated Foundation (MSD Life Science Foundation)/ ; //Japanese Respiratory Society Boehringer Ingelheim Research Grant Program/ ; }, mesh = {*Mycobacterium avium Complex/drug effects ; Humans ; *Macrolides/pharmacology/therapeutic use ; *Mycobacterium avium-intracellulare Infection/drug therapy/microbiology ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Retrospective Studies ; *Drug Resistance, Bacterial ; Male ; Female ; Aged ; *Microbial Sensitivity Tests ; Middle Aged ; Lung Diseases/microbiology/drug therapy ; }, abstract = {This single-center retrospective study aimed to analyze the variability of macrolide resistance (MR) in 68 patients with Mycobacterium avium complex pulmonary disease. Among 25 patients treated without macrolides, 13 (52%) reverted to macrolide-susceptible (MS) profiles. Only one (2%) of 43 patients who continued macrolide treatment showed this change. We compared 30 MR isolates with recent specimens. Among them, seven shifted to MS (five attributed to clonally related strains; two resulting from reinfection or polyclonal infection).}, } @article {pmid39376708, year = {2024}, author = {Villacís, JF and López-Rosero, A and Bustillos, JJ and Cadena, M and Yumiseva, CA and Grijalva, MJ and Villacís, AG}, title = {Bacterial microbiota from the gut of Rhodnius ecuadoriensis, a vector of Chagas disease in Ecuador's Central Coast and Southern Andes.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1464720}, pmid = {39376708}, issn = {1664-302X}, abstract = {INTRODUCTION: Chagas disease is a neglected tropical disease caused by the parasite Trypanosoma cruzi that is transmitted mainly by the feces of infected Triatomines. In Ecuador the main vector is Rhodnius ecuadoriensis which is distributed in several provinces of the country. More than 40% of these insects in the wild have T. cruzi as part of their intestinal microbiota. For this reason, the objective of this research was to characterize the intestinal bacterial microbiota of R. ecuadoriensis.

METHODS: The methodology used was based on the DNA extraction of the intestinal contents from the wild collected insects (adults and nymphs V), as well as the insects maintained at the insectary of the CISeAL. Finally, the samples were analyzed by metagenomics extensions based on the different selected criteria.

RESULTS: The intestinal microbiota of R. ecuadoriensis presented a marked divergence between laboratory-raised and wild collected insects. This difference was observed in all stages and was similar between insects from Loja and Manabí. A large loss of microbial symbionts was observed in laboratory-raised insects.

DISCUSSION: This study is a crucial first step in investigating microbiota interactions and advancing new methodologies.}, } @article {pmid39376703, year = {2024}, author = {Karnachuk, OV and Lukina, AP and Avakyan, MR and Kadnikov, VV and Begmatov, S and Beletsky, AV and Vlasova, KG and Novikov, AA and Shcherbakova, VA and Mardanov, AV and Ravin, NV}, title = {Novel thermophilic genera Geochorda gen. nov. and Carboxydochorda gen. nov. from the deep terrestrial subsurface reveal the ecophysiological diversity in the class Limnochordia.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1441865}, pmid = {39376703}, issn = {1664-302X}, abstract = {The class Limnochordia harbors a single cultivated member, the mesophilic Limnochorda pilosa, which was isolated from a meromictic lake. Despite numerous molecular signatures reported in various ecosystems, the ecophysiological versatility of this deeply branched lineage of Firmicutes (Bacillota) remains poorly understood. The objective of this study was to use targeted cultivation, based on metagenome-assembled genomes from a deep terrestrial aquifer in Western Siberia, to isolate two new thermophilic members of the class. These isolates, described as Geochorda subterranea gen. nov. sp. nov. and Carboxydochorda subterranea gen. nov. sp. nov. within the Geochordaceae fam. nov., were capable of both anaerobic and aerobic respiration using fumarate and O2, respectively, with simple sugars as electron donors. The cultivated Geochordaceae have demonstrated fermentative growth and degradation of various polymers, including starch, maltose, maltodextrin, xylan, and chitin. The carboxydotrophic C. subterranea sp. nov. exhibited autotrophic growth via the Calvin-Benson-Bassham cycle, using CO, H2, and formate as electron donors and O2 as an electron acceptor, adding metabolic flexibility to the bacterium in the nutrient-depleted "deep biosphere" and supporting the possibility of aerobic metabolism in the deep subsurface. The broad physiological potential deciphered from physiological experiments and comparative genomic data explains the widespread distribution of uncultivated members of the class Limnochordia in various ecosystems, where they can oxidize complex organic substrates through both aerobic and anaerobic respiration, as well as pursue a chemolithotrophic lifestyle through the oxidation of H2 or CO.}, } @article {pmid39376702, year = {2024}, author = {Wang, S and Li, Q and Ye, C and Ma, W and Sun, Y and Zhao, B and Zeng, W and Yue, Z and Li, L and Li, D}, title = {Effects of mulch films with different thicknesses on the microbial community of tobacco rhizosphere soil in Yunnan laterite.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1458470}, pmid = {39376702}, issn = {1664-302X}, abstract = {The mulch film (MF) management model of the agricultural field affects the physical and chemical properties of soil (PCPS) and the structure of the microorganism community; however, studies on the relationship between the rhizosphere microorganism community structure and the thickness of MF are still limited. To understand the interactions among the MF thickness, PCPS, and rhizosphere microorganism, a study was conducted by using an integrated metagenomic strategy, where tobacco rhizosphere soil was treated with four commonly representative and used thicknesses of MFs (0.004, 0.006, 0.008, and 0.010 mm) in Yunnan laterite. The results showed that agronomic traits such as the tobacco plant height (TPH), leaf number (LN), fresh leaf weight (FLW), and dry leaf weight (DLW) were significantly (p < 0.01) improved in the field mulched with the thickest film (0.010 mm) compared with the exposed field (CK), and there was a 6.81 and 5.54% increase in the FLW and TPH, separately. The correlation analyses revealed a significant positive correlation of the MF thickness with the soil water content (SWC), soil organic matter (SOM), total nitrogen (TN), available nitrogen (AN), total phosphorus (TP), and available phosphorus (AP; all p < 0.01), while the MF thickness was negatively correlated with the soil temperature (ST; p < 0.01). In addition, the community structure of the rhizosphere soil bacteria was significantly changed overall by the MF thickness, which also interfered with the function of the rhizosphere soil bacteria. The correlation analyses also showed that the abundance of Bradyrhizobium and Nitrospira was positively correlated with the MF thickness, while the abundance of Sphinsinomonas and Massilia was negatively correlated with it. This indicated that with the increase of the MF thickness, the ability of the rhizosphere soil to utilize N and remove harmful molecules was strengthened, while the capacity of the rhizosphere soil to degrade pollutants was greatly reduced. These findings provide additional insights into the potential risks of the application of different thicknesses of MFs, particularly concerning the PCPS and soil microbial communities.}, } @article {pmid39376649, year = {2024}, author = {Kang, Y and Zhang, X and Qin, C and Zheng, Y and Gai, W and Jia, X and Shao, B and Zhang, S and Jiang, H and Huang, X and Jia, J}, title = {Rapid diagnosis of Aspergillus flavus infection in acute very severe aplastic anemia with metagenomic next-generation sequencing: a case report and literature review.}, journal = {Frontiers in medicine}, volume = {11}, number = {}, pages = {1413964}, pmid = {39376649}, issn = {2296-858X}, abstract = {Infection remains the leading cause of mortality in severe aplastic anemia (SAA) patients, with invasive fungal infections being the great threat. Aspergillus fumigatus accounts for most of the reported fungal infection cases. Here, we present a case of A. flavus infection in a patient with acute very severe aplastic anemia (VSAA) despite persistently negative clinical fungal tests. The patient was admitted to the hospital due to pancytopenia presisting for over a month and intermittent fever for 10 days. Elevated inflammatory indicators and abnormal lung imaging suggested infection, prompting consideration of fungal involvement. Despite negative results from multiple blood, sputum fungal cultures and the serum (1,3)-β-D-glucan/galactomannan tests. Metagenomic next-generation sequencing (mNGS) on multiple blood samples, alongside clinical symptoms, confirmed A. flavus infection. Targeted antifungal treatment with liposomal amphotericin B and voriconazole significantly ameliorated pulmonary symptoms. Additionally, this study reviewed and compared the symptoms, diagnostic approaches, and treatments from prior Aspergillus infections in AA patients. It emphasizes critical role of early mNGS utilization in diagnosing and managing infectious diseases, offering insights for diagnosing and treating fungal infections in VSAA.}, } @article {pmid39376581, year = {2024}, author = {Du, Y and Qian, C and Li, X and Zheng, X and Huang, S and Yin, Z and Chen, T and Pan, L}, title = {Unveiling intraspecific diversity and evolutionary dynamics of the foodborne pathogen Bacillus paranthracis through high-quality pan-genome analysis.}, journal = {Current research in food science}, volume = {9}, number = {}, pages = {100867}, pmid = {39376581}, issn = {2665-9271}, abstract = {Understanding the evolutionary dynamics of foodborne pathogens throughout host-associated habitats is of utmost importance. Bacterial pan-genomes, as dynamic entities, are strongly influenced by ecological lifestyles. As a phenotypically diverse species in the Bacillus cereus group, Bacillus paranthracis is recognized as an emerging foodborne pathogen and a probiotic simultaneously. This poorly understood species is a suitable study model for adaptive pan-genome evolution. In this study, we determined the biogeographic distribution, abundance, genetic diversity, and genotypic profiles of key genetic elements of B. paranthracis. Metagenomic read recruitment analyses demonstrated that B. paranthracis members are globally distributed and abundant in host-associated habitats. A high-quality pan-genome of B. paranthracis was subsequently constructed to analyze the evolutionary dynamics involved in ecological adaptation comprehensively. The open pan-genome indicated a flexible gene repertoire with extensive genetic diversity. Significant divergences in the phylogenetic relationships, functional enrichment, and degree of selective pressure between the different components demonstrated different evolutionary dynamics between the core and accessory genomes driven by ecological forces. Purifying selection and gene loss are the main signatures of evolutionary dynamics in B. paranthracis pan-genome. The plasticity of the accessory genome is characterized by horizontal gene transfer (HGT), massive gene losses, and weak purifying or positive selection, which might contribute to niche-specific adaptation. In contrast, although the core genome dominantly undergoes purifying selection, its association with HGT and positively selected mutations indicates its potential role in ecological diversification. Furthermore, host fitness-related dynamics are characterized by the loss of secondary metabolite biosynthesis gene clusters (BGCs) and CAZyme-encoding genes and the acquisition of antimicrobial resistance (AMR) and virulence genes via HGT. This study offers a case study of pan-genome evolution to investigate the ecological adaptations reflected by biogeographical characteristics, thereby advancing the understanding of intraspecific diversity and evolutionary dynamics of foodborne pathogens.}, } @article {pmid39376101, year = {2024}, author = {Trujillo-Gómez, J and Navarro, CE and Atehortúa-Muñoz, S and Florez, ID}, title = {Acute infections of the central nervous system in children and adults: diagnosis and management.}, journal = {Minerva medica}, volume = {115}, number = {4}, pages = {476-502}, doi = {10.23736/S0026-4806.24.09097-9}, pmid = {39376101}, issn = {1827-1669}, mesh = {Humans ; Child ; *Central Nervous System Infections/diagnosis/therapy/drug therapy/microbiology ; Adult ; Acute Disease ; Risk Factors ; }, abstract = {Central nervous system infections are due to different microorganisms such as viruses, bacteria, mycobacteria, fungi, amoebas, and other parasites. The etiology depends on multiple risk factors, and it defines the infection location because some microorganisms prefer meninges, brain tissue, cerebellum, brain stem or spinal cord. The microorganisms induce diseases in the nervous system through direct invasion, neurotoxin production, and the triggered immune response. To determine the infection etiology, there are several diagnostic tests which may be conducted with cerebrospinal fluid, blood, respiratory and stool samples. These tests include but are not limited to direct microscopic examination of the sample, stains, cultures, antigenic tests, nucleic acid amplification tests, metagenomic next-generation sequencing, immunologic biomarker and neuroimaging, especially contrast-enhanced magnetic resonance imaging. The treatment may consist of specific antimicrobial treatment and supportive standard care. Since viruses have no specific antiviral treatment, antimicrobial treatment is mainly targeted at non-viral infections. This article will focus on diagnosis and treatment of acute acquired infections of the central nervous system beyond the neonatal period. The discussion defines the disease, provides the clinical presentation, explains the etiology and risk factors, and briefly mentions potential complications. This updated review aims to provide the reader with all the elements needed to adequately approach a patient with a central nervous system infection. Mycobacterium tuberculosis infection, Cryptococcus spp. infection and vaccines are not within the scope of this article.}, } @article {pmid39375774, year = {2024}, author = {Kosmopoulos, JC and Klier, KM and Langwig, MV and Tran, PQ and Anantharaman, K}, title = {Viromes vs. mixed community metagenomes: choice of method dictates interpretation of viral community ecology.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {195}, pmid = {39375774}, issn = {2049-2618}, mesh = {*Virome/genetics ; *Viruses/genetics/classification/isolation & purification ; *Metagenomics/methods ; Humans ; *Metagenome ; *Genome, Viral/genetics ; Microbiota/genetics ; Soil Microbiology ; Fresh Water/virology/microbiology ; Gastrointestinal Microbiome/genetics ; }, abstract = {BACKGROUND: Viruses, the majority of which are uncultivated, are among the most abundant biological entities on Earth. From altering microbial physiology to driving community dynamics, viruses are fundamental members of microbiomes. While the number of studies leveraging viral metagenomics (viromics) for studying uncultivated viruses is growing, standards for viromics research are lacking. Viromics can utilize computational discovery of viruses from total metagenomes of all community members (hereafter metagenomes) or use physical separation of virus-specific fractions (hereafter viromes). However, differences in the recovery and interpretation of viruses from metagenomes and viromes obtained from the same samples remain understudied.

RESULTS: Here, we compare viral communities from paired viromes and metagenomes obtained from 60 diverse samples across human gut, soil, freshwater, and marine ecosystems. Overall, viral communities obtained from viromes had greater species richness and total viral genome abundances than those obtained from metagenomes, although there were some exceptions. Despite this, metagenomes still contained many viral genomes not detected in viromes. We also found notable differences in the predicted lytic state of viruses detected in viromes vs metagenomes at the time of sequencing. Other forms of variation observed include genome presence/absence, genome quality, and encoded protein content between viromes and metagenomes, but the magnitude of these differences varied by environment.

CONCLUSIONS: Overall, our results show that the choice of method can lead to differing interpretations of viral community ecology. We suggest that the choice of whether to target a metagenome or virome to study viral communities should be dependent on the environmental context and ecological questions being asked. However, our overall recommendation to researchers investigating viral ecology and evolution is to pair both approaches to maximize their respective benefits. Video Abstract.}, } @article {pmid39375368, year = {2024}, author = {Jeong, E and Abdellaoui, N and Lim, JY and Seo, JA}, title = {The presence of a significant endophytic fungus in mycobiome of rice seed compartments.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {23367}, pmid = {39375368}, issn = {2045-2322}, support = {320036-5//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry/ ; RS-2023-00230782//Rural Development Administration/ ; }, mesh = {*Seeds/anatomy & histology/microbiology ; *Mycobiome/genetics ; *Oryza/anatomy & histology/classification/microbiology ; *Fungi/classification/isolation & purification/pathogenicity ; Basidiomycota/physiology ; Metagenome/genetics ; Crops, Agricultural/anatomy & histology/microbiology ; Analysis of Variance ; Republic of Korea ; }, abstract = {Seed microbial communities have been known to have a crucial role in the life cycle of a plant. In this study, we examined the distribution of the fungal communities in three compartments (husk, brown rice, and milled rice) of the fourteen rice seed samples. Ten fungal genera distributed throughout the three compartments of the rice seeds were identified as the core mycobiome of the rice seeds, regardless of collecting regions or cultivars. Based on the diversity analysis, the distribution of the fungal community in milled rice was found to be more diversified, evenly distributed, and differently clustered from the other two compartments. Among the core mycobiome, Moesziomyces dominated almost 80% of the fungal communities in the outer compartments of rice seeds, whereas the abundances of other endophytic pathogenic fungi declined. Our results provide that antagonistic yeast Moesziomyces may be able to control the endogenous pathogenic fungal communities in rice seeds, hence maintaining the quality of rice seeds. In addition, the distribution of fungal communities differs depending on the rice seed's compartment, indicating that the compartment can affect the distribution of the seed microbial community.}, } @article {pmid39375348, year = {2024}, author = {Kang, X and Zhang, W and Li, Y and Luo, X and Schönhuth, A}, title = {HyLight: Strain aware assembly of low coverage metagenomes.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {8665}, pmid = {39375348}, issn = {2041-1723}, mesh = {*Metagenome/genetics ; *High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Microbiota/genetics ; Sequence Analysis, DNA/methods ; Bacteria/genetics/classification ; Genome, Bacterial ; Software ; }, abstract = {Different strains of identical species can vary substantially in terms of their spectrum of biomedically relevant phenotypes. Reconstructing the genomes of microbial communities at the level of their strains poses significant challenges, because sequencing errors can obscure strain-specific variants. Next-generation sequencing (NGS) reads are too short to resolve complex genomic regions. Third-generation sequencing (TGS) reads, although longer, are prone to higher error rates or substantially more expensive. Limiting TGS coverage to reduce costs compromises the accuracy of the assemblies. This explains why prior approaches agree on losses in strain awareness, accuracy, tendentially excessive costs, or combinations thereof. We introduce HyLight, a metagenome assembly approach that addresses these challenges by implementing the complementary strengths of TGS and NGS data. HyLight employs strain-resolved overlap graphs (OG) to accurately reconstruct individual strains within microbial communities. Our experiments demonstrate that HyLight produces strain-aware and contiguous assemblies at minimal error content, while significantly reducing costs because utilizing low-coverage TGS data. HyLight achieves an average improvement of 19.05% in preserving strain identity and demonstrates near-complete strain awareness across diverse datasets. In summary, HyLight offers considerable advances in metagenome assembly, insofar as it delivers significantly enhanced strain awareness, contiguity, and accuracy without the typical compromises observed in existing approaches.}, } @article {pmid39375020, year = {2024}, author = {Garritano, AN and Zhang, Z and Jia, Y and Allen, MA and Hill, LJ and Kuzhiumparambil, U and Hinkley, C and Raina, JB and Peixoto, RS and Thomas, T}, title = {Simple Porifera holobiont reveals complex interactions between the host, an archaeon, a bacterium, and a phage.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39375020}, issn = {1751-7370}, support = {BAS/1/1095-01-01//ANP R&D levy as "Compromisso de Investimentos com Pesquisa e Desenvolvimento"/ ; }, mesh = {*Symbiosis ; *Archaea/metabolism/genetics ; Animals ; *Bacteriophages/physiology/genetics ; *Porifera/microbiology ; *Bacteria/metabolism/genetics/classification ; Ammonia/metabolism ; Microbiota ; Phylogeny ; Vitamin B 12/metabolism ; }, abstract = {The basal metazoan phylum Porifera (sponges) is increasingly used as a model to investigate ecological and evolutionary features of microbe-animal symbioses. However, sponges often host complex microbiomes, which has hampered our understanding of their interactions with their microbial symbionts. Here, we describe the discovery and characterization of the simplest sponge holobiont reported to date, consisting of the deep-sea glass sponge Aphrocallistes beatrix and two newly-described microbial symbionts: an autotrophic ammonia-oxidizing archaeon and a bacterial heterotroph. Omics analyses and metabolic modeling revealed the dependency of the ammonia-oxidizing archaea on sponge-derived ammonia to drive primary production, which in turn supports the bacterium's growth by providing the dicarboxylate fumarate. Furthermore, virus-mediated archaeal lysis appears crucial to overcome the bacterium's vitamin B12 auxotrophy. These findings reveal that the exchanges of vitamin B12 and dicarboxylate may be evolutionarily conserved features of symbiosis as they can also be found in interactions between free-living marine bacteria, and between microbes and plants or diatoms.}, } @article {pmid39375018, year = {2024}, author = {Yang, Q and Zhong, Y and Feng, SW and Wen, P and Wang, H and Wu, J and Yang, S and Liang, JL and Li, D and Yang, Q and Tam, NFY and Peng, P}, title = {Temporal enrichment of comammox Nitrospira and Ca. Nitrosocosmicus in a coastal plastisphere.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39375018}, issn = {1751-7370}, support = {42 077 285//National Natural Science Foundation of China/ ; 2024A04J6534//Science and Technology Projects of Guangzhou/ ; ZDYF2023SHFZ171//Key Research and Development Program of Hainan Province/ ; 2023B1212060049//Guangdong Foundation for Program of Science and Technology Research/ ; 2023B0303000007//Guangdong Major Project of Basic and Applied Basic Research/ ; SKLOG2024-01//State Key Laboratory of Organic Geochemistry/ ; }, mesh = {*RNA, Ribosomal, 16S/genetics ; *Seawater/microbiology ; *Ammonia/metabolism ; *Nitrification ; Microbiota ; Bacteria/classification/genetics/metabolism/isolation & purification ; Oxidation-Reduction ; Phylogeny ; Archaea/metabolism/genetics/classification/isolation & purification ; Metagenome ; }, abstract = {Plastic marine debris is known to harbor a unique microbiome (termed the "plastisphere") that can be important in marine biogeochemical cycles. However, the temporal dynamics in the plastisphere and their implications for marine biogeochemistry remain poorly understood. Here, we characterized the temporal dynamics of nitrifying communities in the plastisphere of plastic ropes exposed to a mangrove intertidal zone. The 39-month colonization experiment revealed that the relative abundances of Nitrospira and Candidatus Nitrosocosmicus representatives increased over time according to 16S rRNA gene amplicon sequencing analysis. The relative abundances of amoA genes in metagenomes implied that comammox Nitrospira were the dominant ammonia oxidizers in the plastisphere, and their dominance increased over time. The relative abundances of two metagenome-assembled genomes of comammox Nitrospira also increased with time and positively correlated with extracellular polymeric substances content of the plastisphere but negatively correlated with NH4+ concentration in seawater, indicating the long-term succession of these two parameters significantly influenced the ammonia-oxidizing community in the coastal plastisphere. At the end of the colonization experiment, the plastisphere exhibited high nitrification activity, leading to the release of N2O (2.52 ng N2O N g-1) in a 3-day nitrification experiment. The predicted relative contribution of comammox Nitrospira to N2O production (17.9%) was higher than that of ammonia-oxidizing bacteria (4.8%) but lower than that of ammonia-oxidizing archaea (21.4%). These results provide evidence that from a long-term perspective, some coastal plastispheres will become dominated by comammox Nitrospira and thereby act as hotspots of ammonia oxidation and N2O production.}, } @article {pmid39374795, year = {2024}, author = {Behl, S and Kusuma, V and Cardoso, T and Hamed, A and Almheiri, G and Kazi, S and Shanmugam, B and Brudecki, G and Vaylombran, D and Quilez, J and Elamin, W}, title = {Whole genome sequencing approaches for taxonomic profiling and evaluation of wastewater quality.}, journal = {Journal of microbiological methods}, volume = {227}, number = {}, pages = {107051}, doi = {10.1016/j.mimet.2024.107051}, pmid = {39374795}, issn = {1872-8359}, mesh = {*Wastewater/microbiology ; *Bacteria/genetics/classification/isolation & purification ; United Arab Emirates ; *Metagenomics/methods ; *Whole Genome Sequencing/methods ; *Fungi/genetics/classification/isolation & purification ; High-Throughput Nucleotide Sequencing/methods ; Viruses/genetics/classification/isolation & purification ; Water Microbiology ; Water Quality ; Environmental Monitoring/methods ; }, abstract = {Tracking metagenomic abundance in wastewater is undoubtedly a powerful tool to detect emerging variants and improve community health. However, there are a few factors that limit environmental water-based genomic monitoring: sampling variability, incomplete coverage, genetic fragmentation, degradation, data analysis and interpretation. The decreasing costs of high-throughput sequencing and high-end supercomputers have increased the use and accuracy of genomic data for microbial detection and monitoring in wastewater samples within any given region. To better understand the microbial dynamics and to determine the target sequencing throughput required to establish taxa that may pose as bio-indicators of an epidemiological outbreak, wastewater samples were collected from distinct locations within the Emirate of Abu Dhabi, United Arab Emirates using appropriate sampling methods. A reference database of ∼27,000 known species was developed and used for further analysis. The results showed that 15 % of data in each sample matched any of ∼27,000 known bacterial, viral, fungal, or protozoan species. Despite the high fraction of unclassified data (85 %), more than 2000 species from >800 genera across >30 phyla were detected in each sample. Both 5 Gb and 10 Gb of sequenced data detected the top ∼2000 species with highest abundance. Doubling the target sequencing throughput (i.e., 10 Gb vs 5 Gb) detected ∼500 additional low-abundance species per sample however it did not affect the overall sample composition or translate into higher per-sample species diversity captured. There was a marginal increase in the number of species detected in each sample beyond 0.20 Gb of classified data. Overall, the results indicate that sequencing to a 3 Gb throughput detects nearly 95 % of all species in the samples.}, } @article {pmid39374754, year = {2024}, author = {Zhi, Q and Zheng, B and Teng, K and Xiao, Y and Zhou, X and Tang, Q and Li, J and Yin, H and Meng, D and Liu, T}, title = {Metagenomic approach reveals the role of bioagents in the environmental dissemination risk of rhizosphere soil antibiotic resistance genes pollution.}, journal = {Environmental research}, volume = {263}, number = {Pt 2}, pages = {120090}, doi = {10.1016/j.envres.2024.120090}, pmid = {39374754}, issn = {1096-0953}, mesh = {*Rhizosphere ; *Soil Microbiology ; *Metagenomics ; *Drug Resistance, Microbial/genetics ; Soil Pollutants/toxicity ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; }, abstract = {Antibiotic resistance genes (ARGs) have been identified as emerging contaminants, raising concerns around the world. As environmentally friendly bioagents (BA), plant growth-promoting rhizobacteria (PGPR) have been used in agricultural systems. The introduction of BA will lead to the turnover of the microbial communities structure. Nevertheless, it is still unclear how the colonization of the invaded microorganisms could affects the rhizosphere resistome. Consequently, 190 ARGs and 25 integrative and conjugative elements (ICEs) were annotated using the metagenomic approach in 18 samples from the Solanaceae crop rhizosphere soil under BA and conventional treatment (CK) groups. Our study found that, after 90 days of treatment, ARG abundance was lower in the CK group than in the BA group. The results showed that aminoglycoside antibiotic resistance (OprZ), phenicol antibiotic resistance (OprN), aminoglycoside antibiotic resistance (ceoA/B), aminocoumarin antibiotic resistance (mdtB) and phenicol antibiotic resistance (MexW) syntenic with ICEs. Moreover, in 11 sequences, OprN (phenicol antibiotic resistance) was observed to have synteny with ICEPaeLESB58-1, indicating that the ICEs could contribute to the spread of ARGs. Additionally, the binning result showed that the potential bacterial hosts of the ARGs were beneficial bacteria which could promote the nutrition cycle, such as Haliangium, Nitrospira, Sideroxydans, Burkholderia, etc, suggesting that bacterial hosts have a great influence on ARG profiles. According to the findings, considering the dissemination of ARGs, BA should be applied with caution, especially the use of beneficial bacteria in BA. In a nutshell, this study offers valuable insights into ARGs pollution control from the perspective of the development and application of BA, to make effective strategies for blocking pollution risk migration in the ecological environment.}, } @article {pmid39374753, year = {2024}, author = {Pushkareva, E and Hejduková, E and Elster, J and Becker, B}, title = {Microbial response to seasonal variation in arctic biocrusts with a focus on fungi and cyanobacteria.}, journal = {Environmental research}, volume = {263}, number = {Pt 2}, pages = {120110}, doi = {10.1016/j.envres.2024.120110}, pmid = {39374753}, issn = {1096-0953}, mesh = {Arctic Regions ; *Seasons ; *Cyanobacteria/genetics ; *Fungi/genetics/classification ; *Microbiota ; Ecosystem ; }, abstract = {Biocrusts are crucial components of Arctic ecosystems, playing significant roles in carbon and nitrogen cycling, especially in regions where plant growth is limited. However, the microbial communities within Arctic biocrusts and their strategies for surviving the harsh conditions remain poorly understood. In this study, the microbial profiles of Arctic biocrusts across different seasons (summer, autumn, and winter) were investigated in order to elucidate their survival strategies in extreme conditions. Metagenomic and metatranscriptomic analyses revealed significant differences in microbial community composition among the sites located in different elevations. The bacterial communities were dominated by Actinobacteria and Proteobacteria, while the fungal communities were mainly represented by Ascomycota and Basidiomycota, with lichenized and saprotrophic traits prevailing. Cyanobacteria were primarily composed of heterocystous cyanobacteria. Furthermore, the study identified molecular mechanisms underlying cold adaptation, including the expression of heat shock proteins and cold-inducible RNA helicases in cyanobacteria and fungi. Overall, the microbial communities appear to be permanently well adapted to the extreme environment.}, } @article {pmid39374327, year = {2024}, author = {Liu, Y and Rohwerder, T and Bonatelli, ML and von Postel, T and Kleinsteuber, S and Adrian, L and Ding, C}, title = {A Novel Sulfatase for Acesulfame Degradation in Wastewater Treatment Plants as Evidenced from Shinella Strains.}, journal = {Environmental science & technology}, volume = {58}, number = {42}, pages = {18892-18902}, pmid = {39374327}, issn = {1520-5851}, mesh = {*Wastewater ; *Sulfatases/metabolism ; Water Pollutants, Chemical/metabolism ; }, abstract = {The artificial sweetener acesulfame is a persistent pollutant in wastewater worldwide. So far, only a few bacterial isolates were recently found to degrade acesulfame efficiently. In Bosea and Chelatococcus strains, a Mn[2+]-dependent metallo-β-lactamase-type sulfatase and an amidase signature family enzyme catalyze acesulfame hydrolysis via acetoacetamide-N-sulfonate to acetoacetate. Here, we describe a new acesulfame sulfatase in Shinella strains isolated from wastewater treatment plants in Germany. Their genomes do not encode the Mn[2+]-dependent sulfatase. Instead, a formylglycine-dependent sulfatase gene was found, together with the acetoacetamide-N-sulfonate amidase gene on a plasmid shared by all known acesulfame-degrading Shinella strains. Heterologous expression, proteomics, and size exclusion chromatography corroborated the physiological function of the Shinella sulfatase in acesulfame hydrolysis. Since both acesulfame sulfatase types are absent in other bacterial genomes or metagenome-assembled genomes, we surveyed 73 tera base pairs of wastewater-associated metagenome raw data sets. Bosea/Chelatococcus sulfatase gene signatures were regularly found from 2013, particularly in North America, Europe, and East Asia, whereas Shinella sulfatase gene signatures were first detected in 2020. Moreover, signatures for the Shinella sulfatase and amidase genes co-occur only in six data sets from China, Finland, and Mexico, suggesting that the Shinella genes were enriched or introduced quite recently in wastewater treatment facilities.}, } @article {pmid39373542, year = {2025}, author = {Rolland, C and Wittmann, J and Reimer, LC and Sardà Carbasse, J and Schober, I and Dudek, CA and Ebeling, C and Koblitz, J and Bunk, B and Overmann, J}, title = {PhageDive: the comprehensive strain database of prokaryotic viral diversity.}, journal = {Nucleic acids research}, volume = {53}, number = {D1}, pages = {D819-D825}, pmid = {39373542}, issn = {1362-4962}, support = {SPP 2330//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Bacteriophages/genetics/classification ; *Databases, Genetic ; Genome, Viral ; Bacteria/virology/genetics/classification ; Host Specificity ; Prokaryotic Cells/virology ; Software ; }, abstract = {Prokaryotic viruses represent the most diverse and abundant biological entities on Earth. So far, data on bacteriophages are not standardized, not readily available for comparative analyses and cannot be linked to the rapidly growing (meta)genomic data. We developed PhageDive (https://phagedive.dsmz.de), a comprehensive database for prokaryotic viruses gathering all existing data dispersed across multiple sources, like scientific publications, specialized databases or internal files of culture collections. PhageDive allows to link own research data to the existing information through an easy and central access, providing fields for various experimental data (host range, genomic data, etc.) and available metadata (e.g. geographical origin, isolation source). An important feature is the link between experimental data, the culture collection number and the repository of the corresponding physical bioresource. To date, PhageDive covers 1167 phages from three different world-renowned public collections (DSMZ, Félix d'Hérelle Reference Center for Bacterial Viruses and NCTC) and features an advanced search function using all data fields from the sections like taxonomy or morphology by controlled vocabulary and ontologies. PhageDive is fully interoperable with other resources including NCBI, the Viral Host Range database (VHRdb) of Institute Pasteur or the BacDive and MediaDive databases of DSMZ.}, } @article {pmid39373498, year = {2024}, author = {Ojeda, A and Akinsuyi, O and McKinley, KL and Xhumari, J and Triplett, EW and Neu, J and Roesch, LFW}, title = {Increased antibiotic resistance in preterm neonates under early antibiotic use.}, journal = {mSphere}, volume = {9}, number = {10}, pages = {e0028624}, pmid = {39373498}, issn = {2379-5042}, support = {//Little Giraffe Foundation (LGF)/ ; }, mesh = {Female ; Humans ; Infant, Newborn ; Male ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; *Bacteria/drug effects/genetics/classification ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; *Feces/microbiology ; *Gastrointestinal Microbiome/drug effects/genetics ; *Infant, Premature ; *Metagenomics ; Retrospective Studies ; }, abstract = {UNLABELLED: The standard use of antibiotics in newborns to empirically treat early-onset sepsis can adversely affect the neonatal gut microbiome, with potential long-term health impacts. Research into the escalating issue of antimicrobial resistance in preterm infants and antibiotic practices in neonatal intensive care units is limited. A deeper understanding of the effects of early antibiotic intervention on antibiotic resistance in preterm infants is crucial. This retrospective study employed metagenomic sequencing to evaluate antibiotic resistance genes (ARGs) in the meconium and subsequent stool samples of preterm infants enrolled in the Routine Early Antibiotic Use in Symptomatic Preterm Neonates study. Microbial metagenomics was conducted using a subset of fecal samples from 30 preterm infants for taxonomic profiling and ARG identification. All preterm infants exhibited ARGs, with 175 unique ARGs identified, predominantly associated with beta-lactam, tetracycline, and aminoglycoside resistance. Notably, 23% of ARGs was found in preterm infants without direct or intrapartum antibiotic exposure. Post-natal antibiotic exposure increases beta-lactam/tetracycline resistance while altering mechanisms that aid bacteria in withstanding antibiotic pressure. Microbial profiling revealed 774 bacterial species, with antibiotic-naive infants showing higher alpha diversity (P = 0.005) in their microbiota and resistome compared with treated infants, suggesting a more complex ecosystem. High ARG prevalence in preterm infants was observed irrespective of direct antibiotic exposure and intensifies with age. Prolonged membrane ruptures and maternal antibiotic use during gestation and delivery are linked to alterations in the preterm infant resistome and microbiome, which are pivotal in shaping the ARG profiles in the neonatal gut.This study is registered with ClinicalTrials.gov as NCT02784821.

IMPORTANCE: A high burden of antibiotic resistance in preterm infants poses significant challenges to neonatal health. The presence of antibiotic resistance genes, along with alterations in signaling, energy production, and metabolic mechanisms, complicates treatment strategies for preterm infants, heightening the risk of ineffective therapy and exacerbating outcomes for these vulnerable neonates. Despite not receiving direct antibiotic treatment, preterm infants exhibit a concerning prevalence of antibiotic-resistant bacteria. This underscores the complex interplay of broader influences, including maternal antibiotic exposure during and beyond pregnancy and gestational complications like prolonged membrane ruptures. Urgent action, including cautious antibiotic practices and enhanced antenatal care, is imperative to protect neonatal health and counter the escalating threat of antimicrobial resistance in this vulnerable population.}, } @article {pmid39373481, year = {2024}, author = {Nesbø, CL and Yang, MI and Sharan, AA and Meyer, T and Edwards, EA}, title = {Metagenomes and metagenome assembled genomes from anaerobic digesters at three Canadian pulp and paper mills.}, journal = {Microbiology resource announcements}, volume = {13}, number = {11}, pages = {e0056124}, pmid = {39373481}, issn = {2576-098X}, support = {10405//Genome Canada (GC)/ ; }, abstract = {We present a dataset of six metagenomes and 323 metagenome assembled genomes (MAGs) describing the microbial community of anaerobic digesters at three Canadian pulp and paper mills. Our objective was to assess the coding potential of the microbial community and obtain draft genomes of key organisms in the digesters.}, } @article {pmid39372894, year = {2024}, author = {Liu, KL and Xu, SJ and Chen, SW and Zhang, MJ and Ye, N and Li, J}, title = {Correlation Analysis of Characteristics of Intestinal Microbiota and Cytokine Levels in Patients with Obstructive Sleep Apnea-Hypopnea Syndrome.}, journal = {Nature and science of sleep}, volume = {16}, number = {}, pages = {1533-1544}, pmid = {39372894}, issn = {1179-1608}, abstract = {OBJECTIVE: The aim of this study was to analyze the relationship between the characteristics of the intestinal microbiota and cytokine levels in individuals with different degrees of obstructive sleep apnea-hypopnea syndrome (OSAHS) as well as to investigate intestinal microbiota imbalances in patients with OSAHS and the associated mechanisms.

METHODS: Based on their sleep apnea hypopnea index (AHI), a total of 37 adults were assigned to a control group, a mild OSAHS group, or a moderate-to-severe OSAHS group. Fecal samples were collected to characterize the intestinal microbiota using metagenomic next-generation sequencing (mNGS), while blood samples were collected to detect levels of interleukin-17a (IL-17a), interleukin-10 (IL-10), tumor necrosis factor-alpha (TNF-α), and interleukin-6 (IL-6) in each group.

RESULTS: 1. There was no significant difference in the Shannon index among the three groups (P > 0.05). The three groups showed significant difference in the relative abundance of Faecalibacterium prausnitzii and Bifidobacterium adolescentis (with F values of 3.955 and 7.24, respectively, P < 0.05), while showed no significant difference in the relative abundance of B. pseudocatenulatum, Bifidobacterium longum, Klebsiella pneumoniae, and Haemophilus parainfluenzae (P > 0.05). 2. The three groups showed significant difference in the expression of serum IL-17A and TNF-α levels (with F values of 18.119 and 10.691, respectively, P < 0.05), while showed no significant difference in the expression of IL-10, IL-6, and CRP levels (P > 0.05). 3. Multiple linear regression analysis revealed that the relative abundance of F. prausnitzii was correlated with changes in BMI and AHI (with β values of 2.585 and -0.157, respectively, P < 0.05), while the relative abundance of B. adolescentis was correlated with changes in IL-17a (with β value of -0.161, P < 0.05).

CONCLUSION: The study revealed a significant correlation between intestinal microbiota abundance and cytokine levels, suggesting that gut microbiota disruption in OSAHS patients may be linked to systemic chronic inflammation.}, } @article {pmid39372735, year = {2024}, author = {Solazzo, G and Rovelli, S and Iodice, S and Chung, M and Frimpong, M and Bollati, V and Ferrari, L and Ghedin, E}, title = {The microbiome of Total Suspended Particles (TSP) and its influence on the respiratory microbiome of healthy office workers.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39372735}, issn = {2692-8205}, abstract = {Air particulate matter (PM) is widely recognized for its potential to negatively affect human health, including changes in the upper respiratory microbiome. However, research on PM-associated microbiota remains limited and mostly focused on PM (e.g., PM2.5 and PM10). This study aims to characterize for the first time the microbiome of Total Suspended Particles (TSP) and investigate the correlations of indoor TSP with the human upper respiratory microbiome. Biological and environmental samples were collected over three collection periods lasting three weeks each, between May and July 2022 at the University of Milan and the University of Insubria Como. TSP were sampled using a filter-based technique, while respiratory samples from both anterior nares (AN) and the nasopharynx (NP) were collected using swabs. Microbiome analysis of both human (N = 145) and TSP (N = 51) samples was conducted on metagenomic sequencing data. A comparison of indoor and outdoor TSP microbiomes revealed differences in microbial diversity and taxonomic composition. The indoor samples had higher relative abundance of environmental bacteria often associated with opportunistic infections like Paracoccus sp., as well as respiratory bacteria such as Staphylococcus aureus and Klebsiella pneumoniae. Additionally, both indoor and outdoor TSP samples contained broad spectrum antibiotic resistance genes. Indoor TSP exposure was negatively associated with commensal bacteria and positively associated with Staphylococcus aureus relative abundance. Finally, a correlation between the relative abundance of respiratory bacteria identified in the indoor TSP and the upper respiratory microbiome was found, suggesting a potential interaction between TSP and the upper airways.}, } @article {pmid39372409, year = {2024}, author = {Li, N and Zhao, J and Liu, Y and Zhang, Y}, title = {Dynamic findings of brain magnetic resonance imaging in a haploidentical hematopoietic stem cell transplantation recipient with cytomegalovirus ventriculoencephalitis: a case report and systematic review.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1450576}, pmid = {39372409}, issn = {1664-3224}, mesh = {Humans ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Male ; *Cytomegalovirus Infections/diagnostic imaging ; Middle Aged ; *Magnetic Resonance Imaging ; Brain/diagnostic imaging/pathology/virology ; Cytomegalovirus/genetics ; Encephalitis, Viral/etiology/diagnostic imaging ; Transplantation, Haploidentical ; Antiviral Agents/therapeutic use ; Graft vs Host Disease/etiology ; Cerebral Ventriculitis/diagnostic imaging/etiology ; Precursor Cell Lymphoblastic Leukemia-Lymphoma/therapy ; Fatal Outcome ; }, abstract = {Our case demonstrated unique cytomegalovirus (CMV) encephalitis post-haploidentical donor hematopoietic stem cell transplantation (HID-HSCT), with early findings on diffusion-weighted brain magnetic resonance imaging (MRI) in the absence of any neurologic symptoms. A 54-year-old Chinese man with acute lymphoblastic leukemia (Philadelphia chromosome-negative) underwent HID-HSCT. After HSCT, the patient developed CMV viremia and severe acute graft-versus-host disease. Recurrence of CMV viremia was observed. On day 129, brain MRI was performed to determine the cause for the intermittent fever. Diffusion-weighted imaging (DWI) revealed several bright spots in the cortex of the frontal lobes and anterior angle of the left lateral ventricle. Subsequently, he developed transplant-associated thrombotic microangiopathy, posterior reversible encephalopathy syndrome, and enlargement of lesions alongside the ventricular wall on a brain MRI series. Metagenomic next-generation sequencing (NGS) of the cerebrospinal fluid (CSF) led to the final diagnosis of CMV encephalitis. Although ganciclovir combined with foscarnet was administered, the patient's consciousness deteriorated, followed by respiratory failure. The patient died on day 198. Additionally, we performed a systematic review to comprehensively analyze this disease. Regarding treatment, immunological therapies, including virus-specific T cells from a third donor and CMV-cytotoxic T lymphocytes, may be more effective. This case report and systematic review underscores the complexities of managing CMV ventriculoencephalitis in HSCT recipients and emphasizes the importance of early diagnosis by brain MRI and CSF polymerase chain reaction or NGS and ongoing research in improving outcomes.}, } @article {pmid39372273, year = {2024}, author = {Chen, Q and Chen, X and Mo, P and Chen, L and Du, Q and Hu, W and Jiang, Q and Zhang, Z and Zhang, Y and Guo, Q and Xiong, Y and Deng, L}, title = {Diagnostic values of BALF metagenomic next-generation sequencing, BALF real-time PCR and serum BDG for Pneumocystis jirovecii pneumonia in HIV-infected patients.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1421660}, pmid = {39372273}, issn = {1664-302X}, abstract = {INTRODUCTION: This study aimed to assess the diagnostic values of bronchoalveolar lavage fluid (BALF) real-time polymerase chain reaction (PCR) and BALF metagenomic next-generation sequencing (mNGS) for Pneumocystis jirovecii pneumonia (PJP) in patients infected with human immunodeficiency virus (HIV).

METHODS: A total of 99 HIV-infected PJP patients and 61 HIV-infected patients diagnosed with non-PJP pneumonia between March 2019 and December 2022 were enrolled. P. jirovecii and multiple other co-pathogens detected in BALF by mNGS were analyzed. The clinical final diagnosis was employed as a benchmark. We compared the diagnostic performance of mNGS in PJP with serum BDG and BALF real-time PCR. The mixed infections detected by mNGS and modifications of antimicrobial treatment were also analyzed.

RESULTS: The sensitivity of mNGS test of BALF samples reached 85.86%, which was significantly higher than serum BDG (39.39%, P < 0.001). The sensitivity of BALF P. jirovecii PCR (84.85%) was similar with mNGS (P > 0.05). The specificity of mNGS (100%) was also same as PCR (100.0%), and superior to serum BDG (88.52%, P < 0.001). Besides, mNGS performs remarkably well in identifying co-pathogens of PJP patients infected with HIV. In addition to P. jirovecii, 82 cases (82.83%) of other co-pathogens were identified based on mNGS. Moreover, thirty-four patients (34.34%) increased therapeutic dose of trimethoprim-sulfamethoxazole (TMP-SMZ) based on BALF P. jirovecii PCR. Based on the mNGS results, initial antimicrobial treatment was modified in 86.87% (86/99) of PJP patients.

CONCLUSION: BALF mNGS and real-time PCR are two powerful techniques for rapid diagnosis of PJP with high specificity and sensitivity. Moreover, the benefit of mNGS is that it may identify other organisms besides PJP and it may benefit proper and prompt treatment.}, } @article {pmid39372272, year = {2024}, author = {Jiang, C and Peng, F and Zhang, L and Zhang, Y and Wang, J and Li, J and Cui, B and Cao, C and Wang, C and Qin, Y and Wang, R and Zhao, Z and Jiang, J and Yang, M and Sun, M and Yang, L and Zhang, Q}, title = {Isolation, identification, and mechanism analysis of plant growth-promoting rhizobacteria in tobacco.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1457624}, pmid = {39372272}, issn = {1664-302X}, abstract = {Plant growth, crop yield, and pest and disease control are enhanced by PGPR (Plant growth promoting rhizobacteria), which are beneficial microorganisms found in a close symbiosis with plant roots. Phytohormones are secreted, nutrient uptake is improved, and soil properties along with the microbiological environment are regulated by these microorganisms, making them a significant focus in agricultural research. In this study, the efficient PGPR strain T1 was isolated and screened from tobacco inter-root soil, and identified and confirmed by ITS sequencing technology. Tobacco growth indicators and soil property changes were observed and recorded through potting experiments. The activities of key enzymes (e.g., sucrase, catalase, urease) in soil were further determined. High-throughput sequencing technology was utilized to sequence the soil microbial community, and combined with macro-genomics analysis, the effects of T1 strain on soil microbial diversity and metabolic pathways were explored. Following the application of T1, significant improvements were observed in the height, leaf length, and width of tobacco plants. Furthermore, the physical and chemical properties of the soil were notably enhanced, including a 26.26% increase in phosphorus availability. Additionally, the activities of key soil enzymes such as sucrase, catalase, and urease were significantly increased, indicating improved soil health and fertility. Comprehensive joint microbiomics and macrogenomics analyses revealed a substantial rise in the populations of beneficial soil microorganisms and an enhancement in metabolic pathways, including amino acid metabolism, synthesis, and production of secondary metabolites. These increase in beneficial microorganisms and the enhancement of their metabolic functions are crucial for plant growth and soil fertility. This study provides valuable references for the development of innovative microbial fertilizers and offers programs for the sustainable development of modern agriculture.}, } @article {pmid39372270, year = {2024}, author = {Zheng, X and Chen, M and Zhuang, Y and Zhao, L and Qian, Y and Shi, C}, title = {Unveiling genetic links between gut microbiota and asthma: a Mendelian randomization.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1448629}, pmid = {39372270}, issn = {1664-302X}, abstract = {BACKGROUND: Multiple studies suggest a potential connection between the gut microbiome and asthma. Our objective is to use advanced genetic and metagenomic techniques to elucidate the causal relationships and underlying mechanisms between gut microbiota and asthma.

METHODS: The study utilized comprehensive Linkage Disequilibrium Score Regression (LDSC) and Mendelian randomization (MR) analyses to examine the relationship between 119 gut microbiota genera and asthma, using publicly accessible genome-wide association studies (GWAS). The meta-analysis synthesized summary effect estimates obtained from LDSC, forward MR, and reverse MR. The MiBioGen collaboration, involving 18,340 individuals, identified genetic variations associated with gut bacteria. Asthma data were collected from the UK Biobank, FinnGen, and GERA, encompassing a total of 82,060 cases and 641,049 controls.

RESULTS: LDSC analysis revealed significant negative genetic correlations between asthma and RuminococcaceaeUCG004 (Rg = -0.55, p = 7.66 × 10[-5]) and Subdoligranulum (Rg = -0.35, p = 3.61 × 10[-4]). Forward MR analysis suggested associations between Butyricicoccus (OR = 0.92, p = 0.01), Turicibacter (OR = 0.95, p = 0.025), Butyrivibrio (OR = 0.98, p = 0.047), and reduced asthma risk. Conversely, Coprococcus2 (OR = 1.10, p = 0.035) and Roseburia (OR = 1.07, p = 0.039) were associated with increased risk. Reverse MR analysis indicated significant associations between genetically predicted asthma and Eubacteriumxylanophilumgroup (Beta = -0.08, p = 9.25 × 10[-7]), LachnospiraceaeNK4A136group (Beta = -0.05, p = 1.26 × 10[-4]), and Eisenbergiella (Beta = 0.06, p = 0.015, Rg_P = 0.043).

CONCLUSION: The findings underscore significant genetic correlations and causal relationships between specific gut microbiota and asthma. These insights highlight the potential of gut microbiota as both markers and modulators of asthma risk, offering new avenues for targeted therapeutic strategies.}, } @article {pmid39372268, year = {2024}, author = {Wang, C and Hou, L and Jiang, N and Wang, Y and Mao, X and Zhou, P and Xia, Y and Wang, Y and Chen, C and Yang, X and Luo, Q and Pan, J}, title = {Microbial diversity in earthen site of exhibition Hall of pit no. 1 at the terracotta warriors Museum in Emperor Qinshihuang's mausoleum site museum and its correlation with environmental factors.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1378180}, pmid = {39372268}, issn = {1664-302X}, abstract = {INTRODUCTION: Earthen sites are essential cultural relic resources, and site museums are a fundamental component of China's cultural heritage protection. The mausoleum of the Qin Shi Huang Emperor is one of the largest, most peculiar, and richest imperial tombs in the world. The exhibition hall of the burial pit No. 1 of the Terra Cotta Warriors is the earliest exhibition hall built and opened to the public. However, after years of excavation and open exhibitions, the earthen site of the Emperor Qinshihuang's Mausoleum Site Museum has deteriorated to varying degrees due to changes in the modern environment. There is an urgent need to control microbial diseases and protect the earthen site.

METHODS: We analyzed the physical and chemical properties and bioindicators of the collected soil samples. We also established a metagenomic library and conducted a correlation analysis between microbial community composition and environmental factors. Cultivable fungi obtained from air and soil samples were identified, and allicin volatile gas fungistasis test was conducted.

RESULT: Research has found that four different areas of the exhibition hall have different types of microbial diseases owing to their different environments. The main pathogenic fungi in earthen site may lead to potential microbial diseases that affect important cultural relics such as the Terra Cotta Warriors. Penicillium, Aspergillus and Talaromyces showed relatively specific growth in relation to environmental factors and showed a better raw growth advantage.Allicin gas had a inhibitory effect on 12 types of fungi, therefore allicin gas had a potent inhibitory effect on the growth of the most culturable fungal hyphae.

DISCUSSION: This study provides basic data for the study of microbial diversity in the exhibition hall of Pit No. 1 at the Terracotta Warriors Museum in Emperor Qinshihuang's Mausoleum Site Museum. It provides a reference for future protection work, which is of great significance.}, } @article {pmid39372067, year = {2024}, author = {Liu, J and Shi, J and Zhang, T and Chen, M and Li, Z and Lu, C and Wang, F}, title = {Serum and Fecal Metabolite Profiles Linking With Gut Microbiome in Triple-Negative Breast Cancer Patients.}, journal = {Breast cancer : basic and clinical research}, volume = {18}, number = {}, pages = {11782234241285645}, pmid = {39372067}, issn = {1178-2234}, abstract = {BACKGROUND: Triple-negative breast cancer (TNBC) is a subtype of breast cancer characterized by poor prognosis due to the absence of effective targeted therapies. Emerging evidence indicates that the gut microbiota and its metabolites play a key role in the occurrence and development of TNBC. This study aimed to explore the metabolic changes and potential mechanisms associated with TNBC.

OBJECTIVES: This study aimed to explore the potential relationship between targeted metabolites and the gut microbiota in TNBC.

DESIGN: We recruited 8 participants, including 4 with TNBC and 4 with benign fibroadenomas as controls.

METHODS: The gut microbiota was analyzed using metagenomics on fecal samples. Liquid chromatography-mass spectrometry (LC-MS) was employed to identify differential metabolites in serum and fecal samples. The correlation between the gut microbiota and metabolites was analyzed using Spearman's correlation analysis.

RESULTS: Analysis of altered serum metabolites in the TNBC group revealed changes, particularly in carboxylic acids and derivatives, benzene, and substituted derivatives. Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analysis revealed significant enrichment in 18 pathways. Regarding fecal metabolites, differences between the 2 groups also included carboxylic acids and derivatives, benzene, and substituted derivatives, with 28 metabolic pathways enriched based on KEGG pathway analysis. Metagenomics analysis showed differences in the relative abundance of Anaerococcus, Fischerella, and Schizosaccharomyces at the genus level, which have been previously associated with breast cancer. Furthermore, 4 serum metabolites-L-glutamine, citrate, creatinine, and creatine-along with 9 fecal metabolites, were associated with the aforementioned microbiota.

CONCLUSION: Our findings highlight distinct metabolite profiles in the serum and feces of patients with TNBC. The identification of gut microbiota and their associated metabolites provides new insights into the pathophysiological mechanisms underlying TNBC.}, } @article {pmid39371578, year = {2024}, author = {Zhang, J and Wang, Z and Jiang, Y and Zhang, D and Den, W and Wang, D and Peng, J and Li, J and Huang, W}, title = {A Case of Necrotizing Fasciitis/Myositis and Streptococcal Toxic Shock Syndrome Caused by emm22/ST46 Strain of Streptococcus pyogenes.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {4251-4256}, pmid = {39371578}, issn = {1178-6973}, abstract = {Streptococcus pyogenes, also known as Group A Streptococcus (GAS), can cause severe invasive diseases with high fatality rates. We report a case of necrotizing fasciitis and myositis complicated by Streptococcal Toxic Shock-Like Syndrome (STSS) caused by the invasive emm22/ST46 strain of Streptococcus pyogenes in China. A previously healthy 57-year-old Chinese Canadian man presented with right calf pain and ulceration following a hike in the Gobi Desert, which progressed to unconsciousness and severe infection. Despite initial treatment, his condition deteriorated, leading to his transfer to our intensive care unit. Metagenomic Next-Generation Sequencing identified Streptococcus pyogenes, and antimicrobial susceptibility testing revealed resistance to erythromycin, tetracycline, and clindamycin. Despite broad-spectrum antimicrobial therapy, debridement, and supportive measures, the patient's condition necessitated amputation of the right lower limb. He recovered and was discharged from the hospital on Day 43. Whole-genome sequencing of the isolate identified 15 multiple virulence factors. Phylogenetic analysis revealed that the closest relative of the isolate was a strain identified in China. This case underscores the importance of early recognition and treatment of invasive GAS infections to prevent severe outcomes, and we should pay attention to invasive emm22/ST46 GAS infections in China.}, } @article {pmid39371337, year = {2024}, author = {Hu, X and Zhi, S and Wu, W and Tao, Y and Zhang, Y and Li, L and Li, X and Pan, L and Fan, H and Li, W}, title = {The application of metagenomics, radiomics and machine learning for diagnosis of sepsis.}, journal = {Frontiers in medicine}, volume = {11}, number = {}, pages = {1400166}, pmid = {39371337}, issn = {2296-858X}, abstract = {INTRODUCTION: Sepsis poses a serious threat to individual life and health. Early and accessible diagnosis and targeted treatment are crucial. This study aims to explore the relationship between microbes, metabolic pathways, and blood test indicators in sepsis patients and develop a machine learning model for clinical diagnosis.

METHODS: Blood samples from sepsis patients were sequenced. α-diversity and β-diversity analyses were performed to compare the microbial diversity between the sepsis group and the normal group. Correlation analysis was conducted on microbes, metabolic pathways, and blood test indicators. In addition, a model was developed based on medical records and radiomic features using machine learning algorithms.

RESULTS: The results of α-diversity and β-diversity analyses showed that the microbial diversity of sepsis group was significantly higher than that of normal group (p < 0.05). The top 10 microbial abundances in the sepsis and normal groups were Vitis vinifera, Mycobacterium canettii, Solanum pennellii, Ralstonia insidiosa, Ananas comosus, Moraxella osloensis, Escherichia coli, Staphylococcus hominis, Camelina sativa, and Cutibacterium acnes. The enriched metabolic pathways mainly included Protein families: genetic information processing, Translation, Protein families: signaling and cellular processes, and Unclassified: genetic information processing. The correlation analysis revealed a significant positive correlation (p < 0.05) between IL-6 and Membrane transport. Metabolism of other amino acids showed a significant positive correlation (p < 0.05) with Cutibacterium acnes, Ralstonia insidiosa, Moraxella osloensis, and Staphylococcus hominis. Ananas comosus showed a significant positive correlation (p < 0.05) with Poorly characterized and Unclassified: metabolism. Blood test-related indicators showed a significant negative correlation (p < 0.05) with microorganisms. Logistic regression (LR) was used as the optimal model in six machine learning models based on medical records and radiomic features. The nomogram, calibration curves, and AUC values demonstrated that LR performed best for prediction.

DISCUSSION: This study provides insights into the relationship between microbes, metabolic pathways, and blood test indicators in sepsis. The developed machine learning model shows potential for aiding in clinical diagnosis. However, further research is needed to validate and improve the model.}, } @article {pmid39371172, year = {2024}, author = {Akagbosu, CO and McCauley, KE and Namasivayam, S and Romero-Soto, HN and O'Brien, W and Bacorn, M and Bohrnsen, E and Schwarz, B and Mistry, S and Burns, AS and Perez-Chaparro, PJ and Chen, Q and LaPoint, P and Patel, A and Krausfeldt, LE and Subramanian, P and Sellers, BA and Cheung, F and Apps, R and Douagi, I and Levy, S and Nadler, EP and Hourigan, SK}, title = {Gut microbiome shifts in adolescents after sleeve gastrectomy with increased oral-associated taxa and pro-inflammatory potential.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {39371172}, support = {R25 DK096944/DK/NIDDK NIH HHS/United States ; }, abstract = {BACKGROUND: Bariatric surgery is highly effective in achieving weight loss in children and adolescents with severe obesity, however the underlying mechanisms are incompletely understood, and gut microbiome changes are unknown.

OBJECTIVES: 1) To comprehensively examine gut microbiome and metabolome changes after laparoscopic vertical sleeve gastrectomy (VSG) in adolescents and 2) to assess whether the microbiome/metabolome changes observed with VSG influence phenotype using germ-free murine models.

DESIGN: 1) A longitudinal observational study in adolescents undergoing VSG with serial stool samples undergoing shotgun metagenomic microbiome sequencing and metabolomics (polar metabolites, bile acids and short chain fatty acids) and 2) a human-to-mouse fecal transplant study.

RESULTS: We show adolescents exhibit significant gut microbiome and metabolome shifts several months after VSG, with increased alpha diversity and notably with enrichment of oral-associated taxa. To assess causality of the microbiome/metabolome changes in phenotype, pre-VSG and post-VSG stool was transplanted into germ-free mice. Post-VSG stool was not associated with any beneficial outcomes such as adiposity reduction compared pre-VSG stool. However, post-VSG stool exhibited an inflammatory phenotype with increased intestinal Th17 and decreased regulatory T cells. Concomitantly, we found elevated fecal calprotectin and an enrichment of proinflammatory pathways in a subset of adolescents post-VSG.

CONCLUSION: We show that in some adolescents, microbiome changes post-VSG may have inflammatory potential, which may be of importance considering the increased incidence of inflammatory bowel disease post-VSG.}, } @article {pmid39369676, year = {2024}, author = {Zhuang, Y and Liu, S and Xiao, J and Chen, T and Gao, D and Xu, Y and Jiang, W and Wang, J and Hou, G and Li, S and Zhao, X and Huang, Y and Li, S and Zhang, S and Li, M and Wang, W and Li, S and Cao, Z}, title = {Metagenomics reveals the characteristics and potential spread of microbiomes and virulence factor genes in the dairy cattle production system.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {136005}, doi = {10.1016/j.jhazmat.2024.136005}, pmid = {39369676}, issn = {1873-3336}, mesh = {Animals ; Cattle ; *Virulence Factors/genetics ; *Metagenomics ; *Feces/microbiology ; *Dairying ; Microbiota ; Female ; Colostrum/microbiology ; Soil Microbiology ; Wastewater/microbiology ; Rumen/microbiology ; }, abstract = {Virulence factor genes (VFGs) pose a potential threat to ecological security and animal health, and have attracted increasing attention in the livestock industry. As one of the primary livestock types, dairy cattle may be an important source of VFG transmission. However, the distribution, transmission, and evolution of VFGs in the gastrointestinal tract and surrounding environment of dairy cattle remain unclear. In the present study, a total of 263 samples were collected from cows, calves, colostrum, farm wastewater, and soil. Metagenomics was conducted to analyze changes in the microbiome and VFGs characteristics in these ecological niches. The VFGs of the cows showed distinct differences between the rumen and feces, and were influenced by the region. The dominant VFG hosts was regulated by their microbial structure. Colostrum administration of cows increased VFG abundance in their newborn calf feces sharply and Enterobacteriaceae became the primary host. While diet was the primary driving force for the temporal variation in calf VFGs. For samples of the surrounding environment, water and soil had higher VFG concentrations and were more structurally stable. Moreover, extensive interactions between the mobile genetic elements and VFGs and gene mobile analysis map based on metagenomic binning both displayed the potential horizontal transfer ability of VFGs in the cows and environment. Our study revealed the prevalence, diffusion, and regulatory factors of VFGs in dairy cattle production systems, providing novel insights into reducing livestock VFGs and limiting their spread.}, } @article {pmid39369510, year = {2024}, author = {Fang, R and Wang, X and Han, Z and Pang, R and Wu, D and Tai, J and Ouyang, C and Zhan, M and Kim, H and Xie, B and Su, Y}, title = {Dynamic responses of the inter-microbial synergism and thermodynamic conditions attribute to the inhibition-and-relief effects of chitosan towards anaerobic digestion.}, journal = {Water research}, volume = {267}, number = {}, pages = {122569}, doi = {10.1016/j.watres.2024.122569}, pmid = {39369510}, issn = {1879-2448}, mesh = {*Chitosan/pharmacology ; Anaerobiosis ; *Thermodynamics ; Methane/metabolism ; }, abstract = {Wide commercial applications of chitosan in food preservation and green packaging fields inevitably lead to the universal existence in food, as well as the food waste (FW) processing system. However, whether and how the chitosan, a class of biomacromolecule substances, lead to dysfunction of anaerobic digestion (AD) process of FW remains less understood. Herein, chitosan exhibited an inhibition-and-relief effect with the AD process proceeding, and 80 mg/g-FW of chitosan decreased the net methane yield of FW by 24.7 %. The dynamic effect was ascribed to the varied fates of chitosan and the coupling biotic/abiotic influencing on multi-steps. Chitosan enhanced substrate flocs agglomeration, restraining the release of organics to liquid phase and reducing the binding affinity to enzymes. Among the various microorganisms involved in different steps, chitosan severely inhibited aceticlastic and hydrogenotrophic methanogen at the levels of microbial abundance, activity and function. Genome-centric metagenomics analyses revealed that transient chitosan decreased the coenzyme-based synergism of various microbial taxa involved in acetic acid generation/consumption metabolisms, including syntrophic propionate-oxidizing bacteria, syntrophic butyrate-oxidizing bacteria and methanogen. With the elimination of chitosan, these inhibitions were relieved, and the accumulated acetic acid and the more favorable thermodynamic conditions finally attributed to the recovery of AD performance.}, } @article {pmid39369508, year = {2024}, author = {Jang, Y and Lee, SH and Kim, NK and Park, HD}, title = {Metagenomic analysis reveals abundance of mixotrophic, heterotrophic, and homoacetogenic bacteria in a hydrogen-based membrane biofilm reactor.}, journal = {Water research}, volume = {267}, number = {}, pages = {122564}, doi = {10.1016/j.watres.2024.122564}, pmid = {39369508}, issn = {1879-2448}, mesh = {*Biofilms ; *Bioreactors/microbiology ; *Hydrogen/metabolism ; *Bacteria/metabolism/genetics ; *Metagenomics ; *Heterotrophic Processes ; Denitrification ; Metagenome ; }, abstract = {Heterotrophic microorganisms are frequently observed in hydrogenotrophic denitrification systems and are presumed to contribute to their improved performance. However, their roles and metabolic pathways in the hydrogen-based membrane biofilm reactor (H2-MBfR) system remain unclear. The objective of this study was to elucidate the underlying mechanisms driving heterotrophic denitrification. For this purpose, metagenomic analysis was conducted on an H2-MBfR showing higher denitrification performance, focusing on the metabolic function of the microbial community. Functional genes related to H2 oxidation, organic carbon metabolism, and denitrification were the major targets of interest. This analysis revealed a substantial number of genes associated with the oxidation of organic carbon compounds in the biofilm, suggesting its potential for heterotrophic denitrification. Investigation of the genes of interest in metagenome-assembled genomes (MAGs) has demonstrated a predominance of mixotrophs or heterotrophs rather than obligate autotrophs. Notably, MAGs exhibiting the highest abundance of genes of interest were affiliated with Hydrogenophaga and Thauera, implying their significant role in denitrifying the H2-MBfR as mixotrophs utilizing both H2 and organic substrates. The identification of 11 MAGs, presumed to originate from homoacetogens suggested that acetate might contribute to the proliferation of heterotrophs. Based on these metagenomic findings, possible metabolic pathways were identified to explain heterotrophic denitrification within the H2-MBfR biofilms.}, } @article {pmid39369255, year = {2024}, author = {Figueroa-Gonzalez, PA and Bornemann, TLV and Hinzke, T and Maaß, S and Trautwein-Schult, A and Starke, J and Moore, CJ and Esser, SP and Plewka, J and Hesse, T and Schmidt, TC and Schreiber, U and Bor, B and Becher, D and Probst, AJ}, title = {Metaproteogenomics resolution of a high-CO2 aquifer community reveals a complex cellular adaptation of groundwater Gracilibacteria to a host-dependent lifestyle.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {194}, pmid = {39369255}, issn = {2049-2618}, support = {CRC 1439/1 426547801//German Research Foundation (DFG)/ ; }, mesh = {*Groundwater/microbiology ; Carbon Dioxide/metabolism ; Metagenomics ; Bacteria/genetics/classification/isolation & purification/metabolism ; Germany ; Genome, Bacterial ; Phylogeny ; Microbiota/genetics ; Proteogenomics ; Adaptation, Physiological ; Proteomics ; }, abstract = {BACKGROUND: Bacteria of the candidate phyla radiation (CPR), constituting about 25% of the bacterial biodiversity, are characterized by small cell size and patchy genomes without complete key metabolic pathways, suggesting a symbiotic lifestyle. Gracilibacteria (BD1-5), which are part of the CPR branch, possess alternate coded genomes and have not yet been cultivated. The lifestyle of Gracilibacteria, their temporal dynamics, and activity in natural ecosystems, particularly in groundwater, has remained largely unexplored. Here, we aimed to investigate Gracilibacteria activity in situ and to discern their lifestyle based on expressed genes, using the metaproteogenome of Gracilibacteria as a function of time in the cold-water geyser Wallender Born in the Volcanic Eifel region in Germany.

RESULTS: We coupled genome-resolved metagenomics and metaproteomics to investigate a cold-water geyser microbial community enriched in Gracilibacteria across a 12-day time-series. Groundwater was collected and sequentially filtered to fraction CPR and other bacteria. Based on 725 Gbps of metagenomic data, 1129 different ribosomal protein S3 marker genes, and 751 high-quality genomes (123 population genomes after dereplication), we identified dominant bacteria belonging to Gallionellales and Gracilibacteria along with keystone microbes, which were low in genomic abundance but substantially contributing to proteomic abundance. Seven high-quality Gracilibacteria genomes showed typical limitations, such as limited amino acid or nucleotide synthesis, in their central metabolism but no co-occurrence with potential hosts. The genomes of these Gracilibacteria were encoded for a high number of proteins involved in cell to cell interaction, supporting the previously surmised host-dependent lifestyle, e.g., type IV and type II secretion system subunits, transporters, and features related to cell motility, which were also detected on protein level.

CONCLUSIONS: We here identified microbial keystone taxa in a high-CO2 aquifer, and revealed microbial dynamics of Gracilibacteria. Although Gracilibacteria in this ecosystem did not appear to target specific organisms in this ecosystem due to lack of co-occurrence despite enrichment on 0.2-µm filter fraction, we provide proteomic evidence for the complex machinery behind the host-dependent lifestyle of groundwater Gracilibacteria. Video Abstract.}, } @article {pmid39369191, year = {2024}, author = {Zhao, J and Sun, Y and Tang, J and Guo, K and Wang, K and Zhuge, J and Fang, H}, title = {The clinical application of metagenomic next-generation sequencing in immunocompromised patients with severe respiratory infections in the ICU.}, journal = {Respiratory research}, volume = {25}, number = {1}, pages = {360}, pmid = {39369191}, issn = {1465-993X}, support = {No. 2023KY1296//Medical and Health Research Program of Zhejiang Province/ ; }, mesh = {Humans ; Male ; *Immunocompromised Host ; Female ; *Intensive Care Units ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; Aged ; *Metagenomics/methods ; *Respiratory Tract Infections/microbiology/diagnosis/drug therapy/immunology/mortality ; Bronchoalveolar Lavage Fluid/microbiology ; Adult ; Retrospective Studies ; Severity of Illness Index ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {BACKGROUND: Early targeted antibiotic therapy is crucial for improving the prognosis of immunocompromised patients with severe respiratory infections (SRIs) in the intensive care unit (ICU). Metagenomic next-generation sequencing (mNGS) has shown significant value in pathogen detection, but research on lower respiratory tract microorganisms remains limited.

METHODS: This study enrolled 234 patients with SRIs in the ICU, and individuals were categorized into immunocompromised and immunocompetent groups. We compared the diagnostic performance of mNGS using bronchoalveolar lavage fluid (BALF) with conventional microbiological tests (CMTs) and analyzed the value of mNGS in immunocompromised patients with SRIs in the ICU.

RESULTS: Among all patients, the pathogenic microorganism detection rate of mNGS was higher than that of CMTs (94.02% vs 66.67%, P < 0.05), both in the immunocompromised group (95.0% vs 58.75%, P < 0.05) and the immunocompetent group (93.51% vs 71.43%, P < 0.05). mNGS detected more pathogens than CMTs did (167 vs 51), identifying 116 organisms that were missed by CMTs. The proportion of antibiotic regimen adjustments based on mNGS results was significantly higher compared to CMTs in both the immunocompromised (70.00% vs 17.50%, P < 0.05) and immunocompetent groups (48.70% vs 15.58%, P < 0.05). In the immunocompromised group, patients who had their antibiotic treatment adjusted on mNGS results had improved prognosis, with significantly lower ICU mortality (8.93% vs 50%, P < 0.05) and 28-day mortality rates (30.36% vs 68.75%, P < 0.05) than CMTs. In the immunocompetent group, no statistically significant differences were observed in ICU mortality or 28-day mortality (20.00% vs 33.33%, P > 0.05; 42.67% vs 45.83%, P > 0.05).

CONCLUSION: mNGS shows significant value in detecting pathogens in immunocompromised patients with SRIs in ICU. For immunocompromised patients who respond poorly to empirical treatment, mNGS can provide an etiological basis, helping adjust antibiotic regimens more precisely and thereby improving patient prognosis.}, } @article {pmid39368785, year = {2025}, author = {Malan-Müller, S and Martín-Hernández, D and Caso, JR and Matthijnssens, J and Rodríguez-Urrutia, A and Lowry, CA and Leza, JC}, title = {Metagenomic symphony of the intestinal ecosystem: How the composition affects the mind.}, journal = {Brain, behavior, and immunity}, volume = {123}, number = {}, pages = {510-523}, doi = {10.1016/j.bbi.2024.09.033}, pmid = {39368785}, issn = {1090-2139}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Brain-Gut Axis/physiology ; Neurodegenerative Diseases/microbiology ; Metagenomics/methods ; Mental Disorders/microbiology/metabolism ; Animals ; Probiotics ; Mental Health ; Brain/metabolism/physiology ; Bacteria/metabolism ; Metagenome ; }, abstract = {Mental health disorders and neurodegenerative diseases place a heavy burden on patients and societies, and, although great strides have been made to understand the pathophysiology of these conditions, advancement in drug development is lagging. The importance of gastrointestinal health in maintaining overall health and preventing disease is not a new concept. Hundreds of years ago, healers from various cultures and civilizations recognized the crucial role of the gut in sustaining health. More than a century ago, scientists began exploring the restorative effects of probiotics, marking the early recognition of the importance of gut microbes. The omics era brought more enlightenment and enabled researchers to identify the complexity of the microbial ecosystems we harbour, encompassing bacteria, eukaryotes (including fungi), archaea, viruses, and other microorganisms. The extensive genetic capacity of the microbiota is dynamic and influenced by the environment. The microbiota therefore serves as a significant entity within us, with evolutionarily preserved functions in host metabolism, immunity, development, and behavior. The significant role of the bacterial gut microbiome in mental health and neurodegenerative disorders has been realized and described within the framework of the microbiota-gut-brain axis. However, the bacterial members do not function unaccompanied, but rather in concert, and there is a substantial knowledge gap regarding the involvement of non-bacterial microbiome members in these disorders. In this review, we will explore the current literature that implicates a role for the entire metagenomic ensemble, and how their complex interkingdom relationships could influence CNS functioning in mental health disorders and neurodegenerative diseases.}, } @article {pmid39368784, year = {2024}, author = {McCoubrey, LE and Shen, C and Mwasambu, S and Favaron, A and Sangfuang, N and Thomaidou, S and Orlu, M and Globisch, D and Basit, AW}, title = {Characterising and preventing the gut microbiota's inactivation of trifluridine, a colorectal cancer drug.}, journal = {European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences}, volume = {203}, number = {}, pages = {106922}, doi = {10.1016/j.ejps.2024.106922}, pmid = {39368784}, issn = {1879-0720}, mesh = {*Trifluridine/pharmacology ; Humans ; *Gastrointestinal Microbiome/drug effects ; *Colorectal Neoplasms/drug therapy/microbiology/prevention & control ; *Feces/microbiology ; *Uridine/pharmacology/analogs & derivatives/metabolism ; Antineoplastic Agents/pharmacology ; Male ; Female ; Clostridium perfringens/drug effects ; Adult ; Colon/microbiology/metabolism/drug effects ; Middle Aged ; }, abstract = {The gut microbiome can metabolise hundreds of drugs, potentially affecting their bioavailability and pharmacological effect. As most gut bacteria reside in the colon, drugs that reach the colon in significant proportions may be most impacted by microbiome metabolism. In this study the anti-colorectal cancer drug trifluridine was used as a model drug for characterising metabolism by the colonic microbiota, identifying correlations between bacterial species and individuals' rates of microbiome drug inactivation, and developing strategies to prevent drug inactivation following targeted colonic delivery. High performance liquid chromatography and ultra-high performance liquid chromatography coupled with high resolution tandem mass spectrometry demonstrated trifluridine's variable and multi-route metabolism by the faecal microbiota sourced from six healthy humans. Here, four drug metabolites were linked to the microbiome for the first time. Metagenomic sequencing of the human microbiota samples revealed their composition, which facilitated prediction of individual donors' microbial trifluridine inactivation. Notably, the abundance of Clostridium perfringens strongly correlated with the extent of trifluridine inactivation by microbiota samples after 2 hours (R[2] = 0.8966). Finally, several strategies were trialled for the prevention of microbial trifluridine metabolism. It was shown that uridine, a safe and well-tolerated molecule, significantly reduced the microbiota's metabolism of trifluridine by acting as a competitive enzyme inhibitor. Further, uridine was found to provide prebiotic effects. The findings in this study greatly expand knowledge on trifluridine's interactions with the gut microbiome and provide valuable insights for investigating the microbiome metabolism of other drugs. The results demonstrate how protection strategies could enhance the colonic stability of microbiome-sensitive drugs.}, } @article {pmid39368548, year = {2025}, author = {Navanandan, N and Jackson, ND and Hamlington, KL and Everman, JL and Pruesse, E and Secor, EA and Stewart, Z and Diener, K and Hardee, I and Edid, A and Sulbaran, H and Mistry, RD and Florin, TA and Yoder, AC and Moore, CM and Szefler, SJ and Liu, AH and Seibold, MA}, title = {Viral Determinants of Childhood Asthma Exacerbation Severity and Treatment Response.}, journal = {The journal of allergy and clinical immunology. In practice}, volume = {13}, number = {1}, pages = {95-104.e5}, pmid = {39368548}, issn = {2213-2201}, support = {U01 AI160033/AI/NIAID NIH HHS/United States ; R01 HL135156/HL/NHLBI NIH HHS/United States ; R01 HL128439/HL/NHLBI NIH HHS/United States ; UM1 TR004399/TR/NCATS NIH HHS/United States ; P01 HL132821/HL/NHLBI NIH HHS/United States ; UL1 TR002535/TR/NCATS NIH HHS/United States ; K23 HL161354/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; *Asthma/drug therapy/diagnosis ; Child ; Child, Preschool ; Female ; Adolescent ; Male ; *Severity of Illness Index ; Prospective Studies ; Rhinovirus ; Treatment Outcome ; Adrenal Cortex Hormones/therapeutic use ; Disease Progression ; Bronchodilator Agents/therapeutic use ; Picornaviridae Infections/diagnosis ; Emergency Service, Hospital ; Anti-Asthmatic Agents/therapeutic use ; }, abstract = {BACKGROUND: Although respiratory viruses are common triggers of asthma exacerbations, the influence of viral infection characteristics on exacerbation presentation and treatment response in the pediatric emergency department (ED) is unclear.

OBJECTIVE: To assess viral infection characteristics of children experiencing ED asthma exacerbations and to test their associations with severity and treatment response.

METHODS: This is a prospective study of children, aged 4 to 18 years, who received standard ED asthma exacerbation treatment with inhaled bronchodilators and systemic corticosteroids. Nasal swabs collected for viral metagenomic analyses determined virus presence, load, and species. Outcomes included exacerbation severity (Pediatric Asthma Severity [PAS] score, clinician impression, and vital signs) and treatment response (discharge home without needing additional asthma therapies).

RESULTS: Of 107 children, 47% had moderate/severe exacerbations by PAS and 64% demonstrated treatment response. Viral metagenomic analysis on nasal swabs from 73 children detected virus in 86%, with 10 different species identified, primarily rhinovirus A (RV-A), RV-C, and enterovirus D68. Exacerbations involving RV-A were milder (odds ratio [OR] = 0.25; 95% confidence interval [CI] = 0.07-0.83) and tended to be more responsive to treatment than non-RV-A infections, whereas exacerbations involving enterovirus D68 were more severe (OR = 8.3; 95% CI = 1.3-164.7) and had no treatment response association. Viral load was not associated with treatment response but exhibited a strong linear relationship with heart rate (rpartial = 0.48), respiratory rate (rpartial = 0.25), and oxygen saturation (rpartial = -0.25), indicative of severity.

CONCLUSIONS: The majority of ED asthma exacerbations are triggered by respiratory viruses. Viral species are associated with severity and treatment response, suggesting that early pathogen detection could inform ED treatment decisions. Additional studies are needed to identify differences in pathobiology underlying exacerbations triggered by different viral species, and how to effectively treat these heterogeneous exacerbations.}, } @article {pmid39368512, year = {2024}, author = {Niu, X and Lin, L and Zhang, T and An, X and Li, Y and Yu, Y and Hong, M and Shi, H and Ding, L}, title = {Research on antibiotic resistance genes in wild and artificially bred green turtles (Chelonia mydas).}, journal = {The Science of the total environment}, volume = {954}, number = {}, pages = {176716}, doi = {10.1016/j.scitotenv.2024.176716}, pmid = {39368512}, issn = {1879-1026}, mesh = {*Turtles/microbiology/genetics ; Animals ; *Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Anti-Bacterial Agents/pharmacology ; Gastrointestinal Microbiome/drug effects/genetics ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; }, abstract = {Sea turtles, vital to marine ecosystems, face population decline. Artificial breeding is a recovery strategy, yet it risks introducing antibiotic resistance genes (ARGs) to wild populations and ecosystems. This study employed metagenomic techniques to compare the distribution characteristics of ARGs in the guts of wild and artificially bred green turtles (Chelonia mydas). The findings revealed that the total abundance of ARGs in C. mydas that have been artificially bred was significantly higher than that in wild individuals. Additionally, the abundance of mobile genetic elements (MGEs) co-occurring with ARGs in artificially bred C. mydas was significantly higher than in wild C. mydas. In the analysis of bacteria carrying ARGs, wild C. mydas exhibited greater bacterial diversity. Furthermore, in artificially bred C. mydas, we discovered 23 potential human pathogenic bacteria (HPB) that contain antibiotic resistance genes. In contrast, in wild C. mydas, only one type of HPB carrying an antibiotic resistance gene was found. The findings of this study not only enhance our understanding of the distribution and dissemination of ARGs within the gut microbial communities of C. mydas, but also provide vital information for assessing the potential impact of releasing artificially bred C. mydas on the spread of antibiotic resistance.}, } @article {pmid39368509, year = {2024}, author = {Wen, M and Liu, Y and Yang, C and Dou, Y and Zhu, S and Tan, G and Wang, J}, title = {Effects of manure and nitrogen fertilization on soil microbial carbon fixation genes and associated communities in the Loess Plateau of China.}, journal = {The Science of the total environment}, volume = {954}, number = {}, pages = {176581}, doi = {10.1016/j.scitotenv.2024.176581}, pmid = {39368509}, issn = {1879-1026}, mesh = {*Soil Microbiology ; *Fertilizers ; China ; *Nitrogen/analysis ; *Soil/chemistry ; *Carbon Cycle ; *Manure ; *Carbon/analysis ; Bacteria/genetics ; Agriculture/methods ; Microbiota ; }, abstract = {The effects of long-term fertilization on soil carbon (C) cycling have been a key focus of agricultural sustainable development research. However, the influences of different fertilization treatments on soil microbial C fixation profiles are still unclear. Metagenomics technology and multivariate analysis were employed to inquire changes in soil properties, soil microbial C fixation genes and associated bacterial communities, and the influence of dominant soil properties on C fixation genes. The contents of soil C and nitrogen fractions were signicficantly higher in manure or combined with nitrogen fertilization (NM) than other treatments. The composition of soil microbial C fixation genes and associated bacterial communities varied among different fertilization treatments. Compared with other treatments, the total abundance of microbial C fixation genes and the abundance of Proteobacteria were significantly higher in NM than in other treatments, as well as the abundances of C fixation genes involved in dicarboxylate/4-hydroxybutyrate cycle and reductive citrate cycle. Key functional genes and main bacterial communities presented in the middle of the co-occurrence network. Soil organic carbon, total nitrogen, and microbial biomass nitrogen were the dominant soil properties influencing microbial C fixation genes and associated bacterial communitis. Fertilization increased the abundance of C fixation genes by affecting the changes in bacterial communities abundance mediated by soil properties. Overall, elucidating the responses of soil microbial C fixation genes and associated communities to different fertilization will enhance our understanding of the processes of soil C fixation in farmland.}, } @article {pmid39368386, year = {2024}, author = {Wang, W and Wang, X and Zhi, R and Zhang, L and Lei, S and Farooq, A and Yan, W and Song, Z and Zhang, C}, title = {Microbial mechanisms for CO2 and CH4 emissions in Robinia pseudoacacia forests along a North-South transect in the Loess Plateau.}, journal = {Journal of environmental management}, volume = {370}, number = {}, pages = {122802}, doi = {10.1016/j.jenvman.2024.122802}, pmid = {39368386}, issn = {1095-8630}, mesh = {*Methane/metabolism ; *Forests ; *Carbon Dioxide/metabolism ; *Robinia/metabolism ; *Soil/chemistry ; *Soil Microbiology ; Carbon Cycle ; }, abstract = {Forest soil microbes play a crucial role in regulating atmospheric-soil carbon fluxes. Environmental heterogeneity across forest types and regions may lead to differences in soil CO2 and CH4 emissions. However, the microbial mechanisms underlying these emission variations are currently unclear. In this study, we measured CO2 and CH4 emissions of Robinia pseudoacacia forests along a north-south transect in the Loess Plateau. Using metagenomic sequencing, we investigated the structural and functional profiles of soil carbon cycling microbial communities. Results indicated that the forest CO2 emissions of Robinia pseudoacacia was significantly higher in the north region than in the south region, while the CH4 emission was oppositely. This is mainly attributed to changes in gene abundance driven by soil pH and moisture in participating carbon degradation and methane oxidation processes across different forest regions. The gene differences in carbon fixation processes between regions primarily stem from the Calvin cycle, where the abundance of rbcL, rbcS, and prkB genes dominates microbial carbon fixation in forest soils. Random forest models revealed key genes involved in predicting forest soil CO2 emissions, including SGA1 and amyA for starch decomposition, TYR for lignin decomposition, chitinase for chitin decomposition, and pectinesterase for pectin decomposition. Microbial functional characterization revealed that interregional differences in CH4 emissions during methane metabolism may originate from methane oxidation processes, and the associated gene abundances (glyA, ppc, and pmoB) were key genes for predicting CH4 emissions from forest soils. Our results provide new insights into the microbial mechanisms of CO2 and CH4 emissions from forest soils, which will be crucial for accurate prediction of the forest soil carbon cycle in the future.}, } @article {pmid39368357, year = {2024}, author = {Zhao, Y and Zhao, Q and Liu, D and Xie, H and Zhang, J and Zheng, Y and Xu, X and Wu, H and Hu, Z}, title = {Antibiotic resistomes and ecological risk elimination in field-scale constructed wetland revealed by integrated metagenomics and metatranscriptomics.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {136045}, doi = {10.1016/j.jhazmat.2024.136045}, pmid = {39368357}, issn = {1873-3336}, mesh = {*Wetlands ; *Metagenomics ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Geologic Sediments/microbiology ; Transcriptome ; Bacteria/genetics/drug effects ; Wastewater/microbiology ; Water Pollutants, Chemical ; Gene Expression Profiling ; Plants/microbiology ; Genes, Bacterial ; Water Microbiology ; }, abstract = {Constructed wetlands (CWs) are identified as significant ecological systems for the potential control of antibiotic resistance genes (ARGs) in the environment. However, the precise mechanisms governing removal, persistence, expression, and associated risks of ARGs during wetland treatment remain poorly understood. In this study, the distribution, mobility, expression, and hosts of ARGs in water, sediments, and plants of a field-scale CW and its parallel natural river were systematically investigated through metagenomic and metatranscriptomic approaches. Results showed that both the abundance and diversity of ARGs in water gradually decreased along the way of CW, reaching a final abundance removal rate of 72.28 % in the effluent. Source tracking analysis indicted that the reduction of ARGs in water was mainly achieved by the dynamic accumulation of ARGs in sediments and plants of the CW. Proteobacteria were identified as primary hosts for ARGs, particularly in sediments and plants during CW treatment. Moreover, although ESKAPE pathogens carrying multiple ARGs persisted in all media throughout the CW treatment, ARG expression levels and risk of water were also significantly decreased after CW treatment. Collectively, our comprehensive multi-omics study would enhance the understanding of ARG removal by CWs, offering insights for controlling antimicrobial resistance in wastewater treatment system.}, } @article {pmid39367927, year = {2024}, author = {Wang, Q and Wang, M and Chen, Y and Miao, Q and Jin, W and Ma, Y and Pan, J and Hu, B}, title = {Deciphering microbiome and fungi-bacteria interactions in chronic wound infections using metagenomic sequencing.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {43}, number = {12}, pages = {2383-2396}, pmid = {39367927}, issn = {1435-4373}, support = {20YF1407700//Science and Technology Innovation Plan Of Shanghai Science and Technology Commission/ ; }, mesh = {Humans ; Male ; Female ; *Wound Infection/microbiology ; Middle Aged ; *Fungi/classification/genetics/isolation & purification ; Aged ; *Metagenomics/methods ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota/genetics ; *High-Throughput Nucleotide Sequencing ; Chronic Disease ; Adult ; Microbial Interactions ; Mycobiome/genetics ; Aged, 80 and over ; }, abstract = {PURPOSE: Chronic wounds caused by infections impose a considerable global healthcare burden. The microbial features of these infections and possible correlations between bacteria and fungi may influence wound healing. However, metagenomic next-generation sequencing (mNGS) analyses of these features remain sparse. Therefore, we performed mNGS on chronic wound infection samples to investigate features and correlations between the bacteriome and mycobiome in 66 patients (28: chronic wounds; 38: non-chronic wounds).

METHODS: Microbial community characteristics in patients with wound infections, microbiome-systemic inflammation associations, and bacteria-fungi correlations were analyzed.

RESULTS: Infections constituted the primary cause of wounds in this study. Nontuberculous mycobacteria (23%) and Mycobacterium tuberculosis (13%) were the most common pathogens associated with chronic wounds, whereas Staphylococcus aureus (15%) was the most prevalent in non-chronic wound infections. Patients with chronic wound infections had a higher abundance of Pseudomonas aeruginosa than those without chronic wounds. Microbes with a high relative abundance in chronic wound infections were less significantly associated with plasma inflammatory factors than those in non-chronic wound infections. Additionally, a positive correlation between Candida glabrata and P. aeruginosa and an association between Malassezia restricta and anaerobic species were detected in patients with chronic wound infections.

CONCLUSION: Our results further support the hypothesis that P. aeruginosa is a microbial biomarker of chronic wound infection regardless of the causative pathogens. Moreover, we propose a positive correlation between C. glabrata and P. aeruginosa in chronic wound infections, which advances the current understanding of fungi-bacteria correlations in patients with chronic wound infections.}, } @article {pmid39366491, year = {2024}, author = {Chen, G and Zhang, H and Shen, J and Yan, Q and Feng, G}, title = {Municipal-treated wastewater as a practical alternative to conventional rice irrigation: Effects on antibiotic resistance genes, virulence factors and human bacterial pathogens in soil, and responses of rice grain quality.}, journal = {Chemosphere}, volume = {366}, number = {}, pages = {143458}, doi = {10.1016/j.chemosphere.2024.143458}, pmid = {39366491}, issn = {1879-1298}, mesh = {*Wastewater/microbiology ; *Agricultural Irrigation/methods ; *Oryza/microbiology ; *Drug Resistance, Microbial/genetics ; *Virulence Factors/genetics ; *Soil Microbiology ; Humans ; *Bacteria/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; Soil/chemistry ; Genes, Bacterial ; Waste Disposal, Fluid/methods ; }, abstract = {Reuse of municipal-treated wastewater for agricultural irrigation is becoming increasingly prevalent due to growing demand and decline in freshwater supplies. However, the microbial contamination profile, including antibiotic resistance genes (ARGs), virulence factors (VFs), and human bacterial pathogens (HBPs) in agricultural soil irrigated with municipal-treated wastewater for paddy cultivation, was unknown. Here, metagenomic analysis was applied to provide a systematic insight into the resistome, VFs and HBPs in paddy soils irrigated with municipal-treated wastewater. The obtained results revealed that the residual antibiotics in municipal-treated wastewater has an impact on the antibiotic resistome by increasing both the total number and abundance of ARGs. Furthermore, it was found that sul1 could serve as a potential risk indicator for assessing ARG contamination. VFs, core HBP abundance, and dangerous pathogens remain unaffected by municipal-treated wastewater irrigation for paddy. The good coexistence patterns of ARGs-HBPs and ARGs-VFs demonstrated the presence of resistant pathogenic bacteria. The network analysis revealed that ARGs-bearing Legionella pneumophila, Mycobacterium marinum, Bordetella pertussis, Staphylococcus aureus, and Pseudomonas aeruginosa might be ranked as high-risk HBPs. Additionally, our investigation also demonstrated that reuse of municipal-treated wastewater for agricultural irrigation had no detrimental effects on rice plant growth and grain quality. This study was the first to investigate the response of VFs and HBPs in paddy soil under long-term municipal-treated wastewater irrigation. The obtained results provide a scientific basis for the safe application of municipal-treated wastewater.}, } @article {pmid39367538, year = {2024}, author = {Kong, Y and Zhang, R and Blain, S and Obernosterer, I}, title = {Seasonal dynamics in microbial trace metals transporters during phytoplankton blooms in the Southern Ocean.}, journal = {Environmental microbiology}, volume = {26}, number = {10}, pages = {e16695}, doi = {10.1111/1462-2920.16695}, pmid = {39367538}, issn = {1462-2920}, support = {202106230202//China Scholarship Council/ ; //Institut Polaire Français Paul Emile Victor/ ; //Centre National de la Recherche Scientifique/ ; //Climate Initiative of the BNP Paribas Foundation/ ; }, mesh = {*Phytoplankton/metabolism/genetics/classification/growth & development ; *Seasons ; *Bacteria/classification/metabolism/genetics ; *Trace Elements/metabolism ; Oceans and Seas ; Seawater/microbiology ; Metagenome ; Membrane Transport Proteins/genetics/metabolism ; Eutrophication ; Phylogeny ; }, abstract = {Trace metals are required as cofactors in metalloproteins that are essential in microbial metabolism and growth. The microbial requirements of diverse metals and the capabilities of prokaryotic taxa to acquire these metals remain poorly understood. We present here results from metagenomic observations over an entire productive season in the region off Kerguelen Island (Indian Sector of the Southern Ocean). We observed seasonal patterns in the abundance of prokaryotic transporters of seven trace elements (zinc [Zn], manganese [Mn], nickel [Ni], molybdenum [Mo], tungsten [W], copper [Cu] and cobalt [Co]) and the consecutive spring and summer phytoplankton blooms were strong drivers of these temporal trends. Taxonomic affiliation of the functional genes revealed that Rhodobacteraceae had a broad repertoire of trace metal transporters (Mn, Zn, Ni, W and Mo) and a more restricted set was observed for other prokaryotic groups, such as Flavobacteriaceae (Zn), Nitrincolaceae (Ni and W) and Thioglobaceae (Mo). The prevalence of trace metal transporters within a prokaryotic group, as determined on the family level, was overall confirmed in representative metagenome-assembled genomes. We discuss the potential involvement of prokaryotic groups in processes related to organic matter utilisation that require these metals and the consequences on carbon and trace metal cycling in surface waters of the Southern Ocean.}, } @article {pmid39367431, year = {2024}, author = {Gaber, M and Wilson, AS and Millen, AE and Hovey, KM and LaMonte, MJ and Wactawski-Wende, J and Ochs-Balcom, HM and Cook, KL}, title = {Visceral adiposity in postmenopausal women is associated with a pro-inflammatory gut microbiome and immunogenic metabolic endotoxemia.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {192}, pmid = {39367431}, issn = {2049-2618}, support = {W81XWH-20-1-0014//Congressionally Directed Medical Research Programs/ ; W81XWH-20-1-0014//Congressionally Directed Medical Research Programs/ ; W81XWH-20-1-0014//Congressionally Directed Medical Research Programs/ ; R01 DE013505, R01 DE024523/DE/NIDCR NIH HHS/United States ; R01 DE013505, R01 DE024523/DE/NIDCR NIH HHS/United States ; R01 DE013505, R01 DE024523/DE/NIDCR NIH HHS/United States ; R01 DE013505, R01 DE024523/DE/NIDCR NIH HHS/United States ; R01 DE013505, R01 DE024523/DE/NIDCR NIH HHS/United States ; HHSN268201600018C, HHSN268201600001C, HHSN268201600002C, HHSN268201600003C, and HHSN268201600004C/HL/NHLBI NIH HHS/United States ; HHSN268201600018C, HHSN268201600001C, HHSN268201600002C, HHSN268201600003C, and HHSN268201600004C/HL/NHLBI NIH HHS/United States ; }, mesh = {Female ; *Gastrointestinal Microbiome/drug effects ; *Endotoxemia/immunology/microbiology ; Humans ; *Postmenopause ; Animals ; Aged ; Mice ; *Lipopolysaccharides ; Intra-Abdominal Fat/metabolism/immunology ; Inflammation ; Aged, 80 and over ; Mice, Inbred C57BL ; Adiposity ; Bacteria/classification/isolation & purification/metabolism/genetics ; Acute-Phase Proteins/metabolism ; Feces/microbiology ; Obesity, Abdominal/microbiology/immunology ; Absorptiometry, Photon ; Carrier Proteins ; Membrane Glycoproteins ; }, abstract = {BACKGROUND: Obesity, and in particular abdominal obesity, is associated with an increased risk of developing a variety of chronic diseases. Obesity, aging, and menopause are each associated with differential shifts in the gut microbiome. Obesity causes chronic low-grade inflammation due to increased lipopolysaccharide (LPS) levels which is termed "metabolic endotoxemia." We examined the association of visceral adiposity tissue (VAT) area, circulating endotoxemia markers, and the gut bacterial microbiome in a cohort of aged postmenopausal women.

METHODS: Fifty postmenopausal women (mean age 78.8 ± 5.3 years) who had existing adipose measurements via dual x-ray absorptiometry (DXA) were selected from the extremes of VAT: n = 25 with low VAT area (45.6 ± 12.5 cm[2]) and n = 25 with high VAT area (177.5 ± 31.3 cm[2]). Dietary intake used to estimate the Healthy Eating Index (HEI) score was assessed with a food frequency questionnaire. Plasma LPS, LPS-binding protein (LBP), anti-LPS antibodies, anti-flagellin antibodies, and anti-lipoteichoic acid (LTA) antibodies were measured by ELISA. Metagenomic sequencing was performed on fecal DNA. Female C57BL/6 mice consuming a high-fat or low-fat diet were treated with 0.4 mg/kg diet-derived fecal isolated LPS modeling metabolic endotoxemia, and metabolic outcomes were measured after 6 weeks.

RESULTS: Women in the high VAT group showed increased Proteobacteria abundance and a lower Firmicutes/Bacteroidetes ratio. Plasma LBP concentration was positively associated with VAT area. Plasma anti-LPS, anti-LTA, and anti-flagellin IgA antibodies were significantly correlated with adiposity measurements. Women with high VAT showed significantly elevated LPS-expressing bacteria compared to low VAT women. Gut bacterial species that showed significant associations with both adiposity and inflammation (anti-LPS IgA and LBP) were Proteobacteria (Escherichia coli, Shigella spp., and Klebsiella spp.) and Veillonella atypica. Healthy eating index (HEI) scores negatively correlated with % body fat and anti-LPS IgA antibodies levels. Preclinical murine model showed that high-fat diet-fed mice administered a low-fat diet fecal-derived LPS displayed reduced body weight, decreased % body fat, and improved glucose tolerance test parameters when compared with saline-injected or high-fat diet fecal-derived LPS-treated groups consuming a high-fat diet.

CONCLUSIONS: Increased VAT in postmenopausal women is associated with elevated gut Proteobacteria abundance and immunogenic metabolic endotoxemia markers. Low-fat diet-derived fecal-isolated LPS improved metabolic parameters in high-fat diet-fed mice giving mechanistic insights into potential pro-health signaling mediated by under-acylated LPS isoforms. Video Abstract.}, } @article {pmid39367251, year = {2024}, author = {Zheng, J and Sun, Q and Zhang, M and Liu, C and Su, Q and Zhang, L and Xu, Z and Lu, W and Ching, J and Tang, W and Cheung, CP and Hamilton, AL and Wilson O'Brien, AL and Wei, SC and Bernstein, CN and Rubin, DT and Chang, EB and Morrison, M and Kamm, MA and Chan, FKL and Zhang, J and Ng, SC}, title = {Noninvasive, microbiome-based diagnosis of inflammatory bowel disease.}, journal = {Nature medicine}, volume = {30}, number = {12}, pages = {3555-3567}, pmid = {39367251}, issn = {1546-170X}, support = {R4030-22//Research Grants Council, University Grants Committee (RGC, UGC)/ ; 14121322//Research Grants Council, University Grants Committee (RGC, UGC)/ ; 2017PG-IBD003//Leona M. and Harry B. Helmsley Charitable Trust (Helmsley Charitable Trust)/ ; 10210816//Food and Health Bureau of the Government of the Hong Kong Special Administrative Region | Health and Medical Research Fund (HMRF)/ ; 82100573//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Humans ; *Feces/microbiology ; *Inflammatory Bowel Diseases/microbiology/diagnosis ; *Crohn Disease/microbiology/diagnosis ; *Gastrointestinal Microbiome/genetics ; *Biomarkers ; *Colitis, Ulcerative/microbiology/diagnosis ; Female ; Male ; Adult ; Leukocyte L1 Antigen Complex/analysis/metabolism ; Bacteria/genetics/isolation & purification ; Metagenomics/methods ; Middle Aged ; Case-Control Studies ; Microbiota/genetics ; }, abstract = {Despite recent progress in our understanding of the association between the gut microbiome and inflammatory bowel disease (IBD), the role of microbiome biomarkers in IBD diagnosis remains underexplored. Here we developed a microbiome-based diagnostic test for IBD. By utilization of metagenomic data from 5,979 fecal samples with and without IBD from different geographies and ethnicities, we identified microbiota alterations in IBD and selected ten and nine bacterial species for construction of diagnostic models for ulcerative colitis and Crohn's disease, respectively. These diagnostic models achieved areas under the curve >0.90 for distinguishing IBD from controls in the discovery cohort, and maintained satisfactory performance in transethnic validation cohorts from eight populations. We further developed a multiplex droplet digital polymerase chain reaction test targeting selected IBD-associated bacterial species, and models based on this test showed numerically higher performance than fecal calprotectin in discriminating ulcerative colitis and Crohn's disease from controls. Here we discovered universal IBD-associated bacteria and show the potential applicability of a multibacteria biomarker panel as a noninvasive tool for IBD diagnosis.}, } @article {pmid39367018, year = {2024}, author = {Baldi, A and Braat, S and Hasan, MI and Bennett, C and Barrios, M and Jones, N and Abdul Azeez, I and Wilcox, S and Roy, PK and Bhuiyan, MSA and Ataide, R and Clucas, D and Larson, LM and Hamadani, J and Zimmermann, M and Bowden, R and Jex, A and Biggs, BA and Pasricha, SR}, title = {Effects of iron supplements and iron-containing micronutrient powders on the gut microbiome in Bangladeshi infants: a randomized controlled trial.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {8640}, pmid = {39367018}, issn = {2041-1723}, support = {GNT1158696//Department of Health | National Health and Medical Research Council (NHMRC)/ ; GNT2009047//Department of Health | National Health and Medical Research Council (NHMRC)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; Infant ; Bangladesh ; *Dietary Supplements ; *Micronutrients/administration & dosage ; Female ; *Iron/metabolism/administration & dosage ; Male ; *RNA, Ribosomal, 16S/genetics ; *Powders ; Diarrhea/microbiology ; Feces/microbiology ; Anemia, Iron-Deficiency/microbiology ; }, abstract = {Anemia is highly prevalent globally, especially in young children in low-income countries, where it often overlaps with a high burden of diarrheal disease. Distribution of iron interventions (as supplements or iron-containing multiple micronutrient powders, MNPs) is a key anemia reduction strategy. Small studies in Africa indicate iron may reprofile the gut microbiome towards pathogenic species. We seek to evaluate the safety of iron and MNPs based on their effects on diversity, composition, and function of the gut microbiome in children in rural Bangladesh as part of a large placebo-controlled randomized controlled trial of iron or MNPs given for 3 months (ACTRN12617000660381). In 923 infants, we evaluate the microbiome before, immediately following, and nine months after interventions, using 16S rRNA gene sequencing and shotgun metagenomics in a subset. We identify no increase in diarrhea with either treatment. In our primary analysis, neither iron nor MNPs alter gut microbiome diversity or composition. However, when not adjusting for multiple comparisons, compared to placebo, children receiving iron and MNPs exhibit reductions in commensal species (e.g., Bifidobacterium, Lactobacillus) and increases in potential pathogens, including Clostridium. These increases are most evident in children with baseline iron repletion and are further supported by trend-based statistical analyses.}, } @article {pmid39365087, year = {2024}, author = {Hourdel, V and Balière, C and Vanhomwegen, J and Brisebarre, A and Grassin, Q and Manuguerra, J-C and Kallel, H and Demar, M and Dacheux, L and Caro, V}, title = {Complete genome sequence of a vampire bat-related rabies virus obtained by metagenomics from a patient with encephalitis of unknown etiology, French Guiana.}, journal = {Microbiology resource announcements}, volume = {13}, number = {11}, pages = {e0051424}, pmid = {39365087}, issn = {2576-098X}, abstract = {We report the complete genome sequence of a rabies virus obtained by direct metagenomics from the cerebellum of a gold panner who died of unknown encephalitis in French Guiana. Phylogenetic analysis exhibited a close genetic relationship with vampire bat-related isolates, confirming the second case of human rabies identified in this territory.}, } @article {pmid39365058, year = {2024}, author = {Corbett, GA and Moore, R and Feehily, C and Killeen, SL and O'Brien, E and Van Sinderen, D and Matthews, E and O'Flaherty, R and Rudd, PM and Saldova, R and Walsh, CJ and Lawton, EM and MacIntyre, DA and Corcoran, S and Cotter, PD and McAuliffe, FM}, title = {Dietary amino acids, macronutrients, vaginal birth, and breastfeeding are associated with the vaginal microbiome in early pregnancy.}, journal = {Microbiology spectrum}, volume = {12}, number = {11}, pages = {e0113024}, pmid = {39365058}, issn = {2165-0497}, support = {12/RC/2273//Science Foundation Ireland (SFI)/ ; 16/SP/3827//Science Foundation Ireland (SFI)/ ; }, mesh = {Humans ; Female ; *Vagina/microbiology ; Pregnancy ; Adult ; *Amino Acids/metabolism ; *Microbiota ; *Breast Feeding ; Nutrients ; Bacteria/classification/genetics/isolation & purification/metabolism ; Diet ; Young Adult ; Premature Birth/microbiology ; Delivery, Obstetric ; }, abstract = {UNLABELLED: The vaginal microbiome is a key player in the etiology of spontaneous preterm birth. This study aimed to illustrate maternal environmental factors associated with vaginal microbiota composition and function in pregnancy. Women in healthy pregnancy had vaginal microbial sampling from the posterior vaginal fornix performed at 16 weeks gestation. After shotgun metagenomic sequencing, heatmaps of relative abundance data were generated. Community state type (CST) was assigned, and alpha diversity was calculated. Demography, obstetric history, well-being, exercise, and diet using food frequency questionnaires were collected and compared against microbial parameters. A total of 119 pregnant participants had vaginal metagenomic sequencing performed. Factors with strongest association with beta diversity were dietary lysine (adj-R[2] 0.113, P = 0.002), valine (adj-R[2] 0.096, P = 0.004), leucine (adj-R[2] 0.086, P = 0.003), and phenylalanine (adj-R[2] 0.085, P = 0.005, Fig. 2D). Previous vaginal delivery and breastfeeding were associated with vaginal beta diversity (adj-R[2] 0.048, P = 0.003; adj-R[2] 0.045, P = 0.004), accounting for 8.5% of taxonomy variation on redundancy analysis. Dietary fat, starch, and maltose were positively correlated with alpha diversity (fat +0.002 SD/g, P = 0.025; starch +0.002 SD/g, P = 0.043; maltose +0.440 SD/g, P = 0.013), particularly in secretor-positive women. Functional signature was associated with CST, maternal smoking, and dietary phenylalanine, accounting for 8.9%-11% of the variation in vaginal microbiome functional signature. Dietary amino acids, previous vaginal delivery, and breastfeeding history were associated with vaginal beta diversity. Functional signature of the vaginal microbiome differed with community state type, smoking, dietary phenylalanine, and vitamin K. Increased alpha diversity correlated with dietary fat and starch. These data provide a novel snapshot into the associations between maternal environment, nutrition, and the vaginal microbiome.

IMPORTANCE: This secondary analysis of the MicrobeMom randomized controlled trial reveals that dietary amino acids, macronutrients, previous vaginal birth, and breastfeeding have the strongest associations with vaginal taxonomy in early pregnancy. Function of the vaginal niche is associated mainly by species composition, but smoking, vitamin K, and phenylalanine also play a role. These associations provide an intriguing and novel insight into the association between host factors and diet on the vaginal microbiome in pregnancy and highlight the need for further investigation into the complex interactions between the diet, human gut, and vaginal microbiome.}, } @article {pmid39365049, year = {2024}, author = {Won, S and Cho, S and Kim, H}, title = {rRNA operon improves species-level classification of bacteria and microbial community analysis compared to 16S rRNA.}, journal = {Microbiology spectrum}, volume = {12}, number = {11}, pages = {e0093124}, pmid = {39365049}, issn = {2165-0497}, mesh = {*RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; *Microbiota/genetics ; *rRNA Operon/genetics ; Phylogeny ; DNA, Bacterial/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {UNLABELLED: Precise identification of species is fundamental in microbial genomics and is crucial for understanding the microbial communities. While the 16S rRNA gene, particularly its V3-V4 regions, has been extensively employed for microbial identification, however has limitations in achieving species-level resolution. Advancements in long-read sequencing technologies have highlighted the rRNA operon as a more accurate marker for microbial classification and analysis than the 16S rRNA gene. This study aims to compare the accuracy of species classification and microbial community analysis using the rRNA operon versus the 16S rRNA gene. We evaluated the species classification accuracy of the rRNA operon,16S rRNA gene, and 16S rRNA V3-V4 regions using a BLAST-based method and a k-mer matching-based method with public data available from NCBI. We further performed simulations to model microbial community analysis. We accessed the performance using each marker in community composition estimation and differential abundance analysis. Our findings demonstrate that the rRNA operon offers an advantage over the 16S rRNA gene and its V3-V4 regions for species-level classification within the genus. When applied to microbial community analysis, the rRNA operon enables a more accurate determination of composition. Using the rRNA operon yielded more reliable results in differential abundance analysis as well.

IMPORTANCE: We quantitatively demonstrated that the rRNA operon outperformed the 16S rRNA and its V3-V4 regions in accuracy for both individual species identification and species-level microbial community analysis. Our findings can provide guidelines for selecting appropriate markers in the field of microbial research.}, } @article {pmid39364864, year = {2024}, author = {Dong, W and Hu, S and Yu, J and Liu, Y and Zeng, S and Duan, X and Deng, Y and Wang, Y and Yin, J and Xing, B and Shu, Z}, title = {Study on the Antidepressant Effect of Zhizichi Decoction by Regulating Metabolism and Intestinal Flora.}, journal = {Combinatorial chemistry & high throughput screening}, volume = {}, number = {}, pages = {}, doi = {10.2174/0113862073312654240918072945}, pmid = {39364864}, issn = {1875-5402}, abstract = {BACKGROUND: The incidence of depression is increasing year by year, and Zhizichi Decoction（ZZCD）has shown significant efficiency in the clinical treatment of mild depression, but its mechanism of action is still unclear. In this research, network pharmacology and metagenomics combined and metabolomics were used as research methods to explain the scientific connotation of the antidepressant effect of ZZCD from the aspects of the overall effect of organisms and microbial structure and function.

METHODS: The rat model of depression was established by chronic unpredictable mild stress (CUMS), and the improvement of depressive symptoms was evaluated by behavioral and histopathological methods. Network pharmacology predicted possible targets and important pathways of ZZCD. Metabolomics revealed its possible related biological pathways. Metagenomics showed the disturbance of ZZCD on intestinal microbial diversity structure and associated biological functions in depressed rats.

RESULTS: ZZCD can improve the behavioral performance of CUMS rats, and can significantly regulate the content of 5-HT, NE and other neurotransmitters in serum and brain tissue, and improve the damaged state of neurons in the hippocampus. Network pharmacology predicts that it mainly acts on biological processes such as inflammatory response and oxidative stress response. Metabolomics found that it affected metabolic pathways such as amino acid metabolism and lipid metabolism. The results of metagenomics showed that it significantly regulated the abundance of Firmicutes and Bacteroidetes. The above results predicted that it may affect signaling pathways such as the nervous system, inflammatory diseases and cell processing.

CONCLUSION: ZZCD may play an antidepressant role by regulating intestinal probiotics, energy metabolism, and inflammation reduction. This provides a scientific basis for the clinical application of ZZCD in traditional Chinese medicine and also makes it an optional alternative for the treatment of depression.}, } @article {pmid39364122, year = {2024}, author = {Zhang, S and Yang, S and Zhuang, Y and Yang, D and Gu, X and Wang, Y and Wang, Z and Chen, R and Yan, F}, title = {Lactobacillus acidophilus CICC 6075 attenuates high-fat diet-induced obesity by improving gut microbiota composition and histidine biosynthesis.}, journal = {Bioscience of microbiota, food and health}, volume = {43}, number = {4}, pages = {367-380}, pmid = {39364122}, issn = {2186-6953}, abstract = {This study aimed to investigate the potential anti-obesity efficacy of Lactobacillus acidophilus CICC 6075. The study analyzed fecal metagenomic data from 120 obese and 100 non-obese individuals. C57BL/6 mice on normal diet or high-fat diet (HFD) were treated with L. acidophilus CICC 6075 by daily oral gavage for 12 weeks, followed by evaluations of the obesity phenotype. Metagenomic analysis revealed depletion of L. acidophilus in obese individuals. Administration of L. acidophilus CICC 6075 attenuated excessive weight gain and fat accumulation and maintained the intestinal barrier in HFD-induced obese mice. Sequencing results showed that HFD hindered α- and β-diversity while reducing the relative abundance of Lactobacillus and norank_f_Muribaculaceae and significantly increasing the relative abundance of Ileibacterium. L. acidophilus CICC 6075 reversed these results and reduced the Firmicutes/Bacteroidetes ratio. Supplementation of L. acidophilus CICC 6075 enhanced histidine biosynthesis, inhibited the NF-κB pathway, and significantly reduced the expression levels of inflammatory factors in adipose tissue. These results indicate that L. acidophilus CICC 6075 alleviates HFD-induced obesity in mice by inhibiting the activation of the NF-κB pathway and enhancing gut microbiota functionality. This suggests that L. acidophilus CICC 6075 may be a good candidate probiotic for preventing obesity.}, } @article {pmid39364006, year = {2024}, author = {Rasal, KD and Kumar, PV and Risha, S and Asgolkar, P and Harshavarthini, M and Acharya, A and Shinde, S and Dhere, S and Rasal, A and Sonwane, A and Brahmane, M and Sundaray, JK and Nagpure, N}, title = {Genetic improvement and genomic resources of important cyprinid species: status and future perspectives for sustainable production.}, journal = {Frontiers in genetics}, volume = {15}, number = {}, pages = {1398084}, pmid = {39364006}, issn = {1664-8021}, abstract = {Cyprinid species are the most cultured aquatic species around the world in terms of quantity and total value. They account for 25% of global aquaculture production and significantly contribute to fulfilling the demand for fish food. The aquaculture of these species is facing severe concerns in terms of seed quality, rising feed costs, disease outbreaks, introgression of exotic species, environmental impacts, and anthropogenic activities. Numerous researchers have explored biological issues and potential methods to enhance cyprinid aquaculture. Selective breeding is extensively employed in cyprinid species to enhance specific traits like growth and disease resistance. In this context, we have discussed the efforts made to improve important cyprinid aquaculture practices through genetic and genomic approaches. The recent advances in DNA sequencing technologies and genomic tools have revolutionized the understanding of biological research. The generation of a complete genome and other genomic resources in cyprinid species has significantly strengthened molecular-level investigations into disease resistance, growth, reproduction, and adaptation to changing environments. We conducted a comprehensive review of genomic research in important cyprinid species, encompassing genome, transcriptome, proteome, metagenome, epigenome, etc. This review reveals that considerable data has been generated for cyprinid species. However, the seamless integration of this valuable data into genetic selection programs has yet to be achieved. In the upcoming years, genomic techniques, gene transfer, genome editing tools are expected to bring a paradigm shift in sustainable cyprinid aquaculture production. The comprehensive information presented here will offer insights for the cyprinid aquaculture research community.}, } @article {pmid39363816, year = {2024}, author = {Sarker, S and Klukowski, N and Talukder, S and Gupta, SD and Vaughan-Higgins, R}, title = {Evidence of a highly divergent novel parvovirus in Australia's critically endangered western ground parrot/kyloring (Pezoporus flaviventris).}, journal = {Australian veterinary journal}, volume = {102}, number = {11}, pages = {570-575}, doi = {10.1111/avj.13378}, pmid = {39363816}, issn = {1751-0813}, mesh = {Animals ; *Parrots/virology ; *Endangered Species ; *Phylogeny ; *Parvoviridae Infections/veterinary/virology/epidemiology ; Australia/epidemiology ; *Feces/virology ; Parvovirus/genetics/classification/isolation & purification ; Bird Diseases/virology/epidemiology ; Genome, Viral ; }, abstract = {Detecting pathogens in endangered animal populations is vital for understanding and mitigating threats to their survival. The critically endangered western ground parrot (Pezoporus flaviventris, WGP), with a population as low as 150 individuals in Australia, faces an imminent risk of extinction. Despite this urgency, research on viral pathogens in this species remains limited. This study aimed to identify and characterise viruses present in faecal samples from seven individual WGP using a viral metagenomic approach. Analysis of the sequenced datasets revealed the presence of a novel virus belonging to the Parvoviridae family, named psittaciform chaphamaparvovirus 7 (PsChPV-7). The genome of PsChPV-7 contains typical structural and functional gene sequences found in Parvoviridae but is highly divergent, indicating its classification as a distinct species. Phylogenetic analysis placed PsChPV-7 within a unique sub-clade of the Chaphamaparvovirus genus, suggesting its evolutionary significance as an ancient lineage within this group. These findings may contribute to the development of strategic management and biosecurity plans aimed at conserving this endangered WGP.}, } @article {pmid39363670, year = {2024}, author = {Wang, R and Tang, G and Lu, Y and Zhang, D and Cai, S and He, H and Zhang, H and Xiong, Q}, title = {Root physiological and soil microbial mechanisms underlying responses to nitrogen deficiency and compensation in Indica and Japonica rice.}, journal = {Physiologia plantarum}, volume = {176}, number = {5}, pages = {e14549}, doi = {10.1111/ppl.14549}, pmid = {39363670}, issn = {1399-3054}, support = {2021KY47//Jiangxi Province Postdoctoral Scientific Research Funding/ ; PAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; 32101816//National Natural Science Foundation of China/ ; SJCX23_1974//Postgraduate Research & Practice Innovation Program of Jiangsu Province/ ; 2021M702768//project funded by the China Postdoctoral Science Foundation/ ; 2021K292B//Jiangsu Province Postdoctoral Research Funding/ ; }, mesh = {*Oryza/microbiology/metabolism/genetics/physiology ; *Nitrogen/metabolism ; *Plant Roots/microbiology/metabolism ; *Soil Microbiology ; *Rhizosphere ; Fertilizers ; Bacteria/metabolism/genetics/classification ; }, abstract = {Compensatory effects are common biological phenomena in nature. In this study, we investigated the changes in root nitrogen uptake, root morphological and physiological responses, and changes in the rhizosphere soil microbial communities of indica and japonica rice during a nitrogen deficiency-sensitive period and an effective compensation period with double the nitrogen supply. We conducted a bucket experiment using Suxiu 867 (a japonica rice variety) and Yangxian You 918 (an indica rice variety). Treatments included CK (constant distribution of nitrogen fertilizer at each growth stage, represented by CK867 and CK918) and NDC (nitrogen deficiency in the tillering stage, double nitrogen application in the ear differentiation stage to compensate, represented by NDC867 and NDC918) variations. Both varieties presented the highest δ[15]N and [15]N abundances and Ndff (refers to the proportion of nitrogen in a plant's body that comes directly from the fertilizer applied.) in rice under the NDC treatment. Metagenomic sequencing of rhizospheric soil showed that the dominant bacterial groups at the phylum level among each treatment were Actinobacteria, Proteobacteria, Chloroflexi, Acidobacteria, Gemmatimonadetes, and Nitrospirae. The rhizosphere of indica rice was more enriched with the microbial communities involved in nitrogen metabolism, which contributed to higher nitrogen utilization efficiency. A correlation-based network was constructed and provides insights into the formation of nitrogen deficiency compensation effects and contributes to the enhancement of nitrogen uptake and utilization efficiency in rice production.}, } @article {pmid39363651, year = {2025}, author = {Vazquez Bucheli, JE and Lee, Y and Kim, B and Azevedo, NF and Azevedo, AS and Todorov, SD and Ji, Y and Kang, H and Holzapfel, WH}, title = {Use of FISH-FLOW as a Method for the Identification and Quantification of Bacterial Populations.}, journal = {Molecular nutrition & food research}, volume = {69}, number = {2}, pages = {e2400494}, doi = {10.1002/mnfr.202400494}, pmid = {39363651}, issn = {1613-4133}, support = {NRF-2018M3A9F3021964//NRF Korea/ ; RS-2023-00222687//NRF Korea/ ; 739489//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; 2023/05394-9//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; LA/P/0045/2020UIDP/00511/2020,POCI-01-0145-FEDER-030431//FCT Portugal/ ; }, mesh = {*In Situ Hybridization, Fluorescence/methods ; *RNA, Ribosomal, 16S/genetics ; *Feces/microbiology ; Humans ; *Gastrointestinal Microbiome ; *Flow Cytometry/methods ; *Bacteria/isolation & purification/genetics/classification ; Proteobacteria/isolation & purification/genetics ; Gastrointestinal Tract/microbiology ; Bacteroidetes/isolation & purification/genetics ; Actinobacteria/isolation & purification/genetics ; Firmicutes/isolation & purification/genetics ; Female ; Male ; }, abstract = {The gastrointestinal tract (GIT) harbors the largest group of microbiotas among the microbial communities of the human host. The resident organisms typical of a healthy gut are well adapted to the gastrointestinal environment while alteration of these populations can trigger disorders that may affect the health and well-being of the host. Various investigations have applied different tools to study bacterial communities in the gut and their correlation with gastrointestinal disorders such as inflammatory bowel disease (IBD), obesity, and diabetes. This study proposes fluorescent in situ hybridization, combined with flow cytometry (FISH-FLOW), as an alternative approach for phylum level identification of Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria and quantification of target bacteria from the GIT based on analysis of fecal samples, where results are validated by quantitative polymerase chain reaction (qPCR) and 16S ribosomal ribonucleic acid (16s rRNA) sequencing. The results obtained via FISH-FLOW experimental approach show high specificity for the developed probes for hybridization with the target bacteria. The study, therefore, suggests the FISH-FLOW as a reliable method for studying bacterial communities in the gut with results correlating well with those of metagenomic investigations of the same fecal samples.}, } @article {pmid39363203, year = {2024}, author = {Viana, PAB and Tschoeke, DA and de Moraes, L and Santos, LA and Barral-Netto, M and Khouri, R and Ramos, PIP and Meirelles, PM}, title = {Design and implementation of a metagenomic analytical pipeline for respiratory pathogen detection.}, journal = {BMC research notes}, volume = {17}, number = {1}, pages = {291}, pmid = {39363203}, issn = {1756-0500}, support = {2023-PPI-007//Rockefeller Foundation/ ; }, mesh = {*Metagenomics/methods ; Humans ; *Respiratory Tract Infections/microbiology/diagnosis ; Metagenome/genetics ; Computational Biology/methods ; Reproducibility of Results ; Nasopharynx/microbiology/virology ; }, abstract = {OBJECTIVE: We developed an in-house bioinformatics pipeline to improve the detection of respiratory pathogens in metagenomic sequencing data. This pipeline addresses the need for short-time analysis, high accuracy, scalability, and reproducibility in a high-performance computing environment.

RESULTS: We evaluated our pipeline using ninety synthetic metagenomes designed to simulate nasopharyngeal swab samples. The pipeline successfully identified 177 out of 204 respiratory pathogens present in the compositions, with an average processing time of approximately 4 min per sample (processing 1 million paired-end reads of 150 base pairs). For the estimation of all the 470 taxa included in the compositions, the pipeline demonstrated high accuracy, identifying 420 and achieving a correlation of 0.9 between their actual and predicted relative abundances. Among the identified taxa, 27 were significantly underestimated or overestimated, including only three clinically relevant pathogens. We also validated the pipeline by applying it to a clinical dataset from a study on metagenomic pathogen characterization in patients with acute respiratory infections and successfully identified all pathogens responsible for the diagnosed infections. These findings underscore the pipeline's effectiveness in pathogen detection and highlight its potential utility in respiratory pathogen surveillance.}, } @article {pmid39363100, year = {2025}, author = {Chu, VT and Glascock, A and Donnell, D and Grabow, C and Brown, CE and Ward, R and Love, C and Kalantar, KL and Cohen, SE and Cannon, C and Woodworth, MH and Kelley, CF and Celum, C and Luetkemeyer, AF and Langelier, CR}, title = {Impact of doxycycline post-exposure prophylaxis for sexually transmitted infections on the gut microbiome and antimicrobial resistome.}, journal = {Nature medicine}, volume = {31}, number = {1}, pages = {207-217}, pmid = {39363100}, issn = {1546-170X}, support = {K23 AI144036/AI/NIAID NIH HHS/United States ; R01 AI143439/AI/NIAID NIH HHS/United States ; R01 HL155418/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; *Doxycycline/pharmacology ; Male ; Female ; Adult ; *Anti-Bacterial Agents/pharmacology/administration & dosage ; Post-Exposure Prophylaxis ; Sexually Transmitted Diseases/microbiology/prevention & control ; Drug Resistance, Bacterial/genetics ; Homosexuality, Male ; Transgender Persons ; Middle Aged ; }, abstract = {Doxycycline post-exposure prophylaxis (doxy-PEP) reduces bacterial sexually transmitted infections among men who have sex with men and transgender women. Although poised for widespread clinical implementation, the impact of doxy-PEP on antimicrobial resistance remains a primary concern as its effects on the gut microbiome and resistome, or the antimicrobial resistance genes (ARGs) present in the gut microbiome, are unknown. To investigate these effects, we studied participants from the DoxyPEP trial, a randomized clinical trial comparing doxy-PEP use, a one-time doxycycline 200-mg dose taken after condomless sex (DP arm, n = 100), to standard of care (SOC arm, n = 50) among men who have sex with men and transgender women. From self-collected rectal swabs at enrollment (day-0) and after 6 months (month-6), we performed metagenomic DNA sequencing (DNA-seq) or metatranscriptomic RNA sequencing (RNA-seq). DNA-seq data were analyzable from 127 samples derived from 89 participants, and RNA-seq data were analyzable from 86 samples derived from 70 participants. We compared the bacterial microbiome and resistome between the two study arms and over time. The median number of doxycycline doses taken since enrollment by participants with DNA-seq data was zero (interquartile range (IQR): 0-7 doses) for the SOC arm and 42 (IQR: 27-64 doses) for the DP arm. Tetracycline ARGs were detected in all day-0 DNA-seq samples and in 85% of day-0 RNA-seq samples. The proportional mass of tetracycline ARGs in the resistome increased between day-0 and month-6 in DP participants from 46% to 51% in the metagenome (P = 2.3 × 10[-2]) and from 4% to 15% in the metatranscriptome (P = 4.5 × 10[-6]), but no statistically significant increases in other ARG classes were observed. Exposure to a higher number of doxycycline doses correlated with proportional enrichment of tetracycline ARGs in the metagenome (Spearman's ρ = 0.23, P = 9.0 × 10[-3]) and metatranscriptome (Spearman's ρ = 0.55, P = 3.7 × 10[-8]). Bacterial microbiome alpha diversity, beta diversity and total bacterial mass did not differ between day-0 and month-6 samples from DP participants when assessed by either DNA-seq or RNA-seq. In an abundance-based correlation analysis, we observed an increase over time in the strength of the correlation between tetracycline ARGs and specific bacterial taxa, including some common human pathogens. In sum, doxy-PEP use over a 6-month period was associated with an increase in the proportion of tetracycline ARGs comprising the gut resistome and an increase in the expression of tetracycline ARGs. At 6 months of doxy-PEP use, no residual differences were observed in alpha and beta diversity or taxonomic composition of the gut microbiome. As doxy-PEP is implemented as a public health strategy, further studies and population-level surveillance of doxycycline-resistant pathogens are needed to understand the implications of these findings. ClinicalTrials.gov registration number: NCT03980223 .}, } @article {pmid39362974, year = {2024}, author = {Khan, NA and Majumder, A and Singh, S and Ramamurthy, PC and Prakash, SK and Farooqi, IH and Mozaffari, N and Lawal, DU and Aljundi, IH}, title = {C/N ratio effect on oily wastewater treatment using column type SBR: machine learning prediction and metagenomics study.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {22950}, pmid = {39362974}, issn = {2045-2322}, mesh = {*Wastewater/chemistry ; *Nitrogen/metabolism ; *Carbon/metabolism ; *Machine Learning ; *Metagenomics/methods ; Bioreactors/microbiology ; Water Purification/methods ; Phosphorus/metabolism/analysis ; Waste Disposal, Fluid/methods ; }, abstract = {The sequencing batch reactor has emerged as a promising technology in treating wastewater; however, its application in the treatment of generated water still needs to be explored. This research gap led to the investigation of various carbon-to-nitrogen (C/N) ratios in a column-type sequencing batch reactor (cSBR). The resulting data and model demonstrated that augmenting the SND process with an external carbon source is effective until the C/N ratio reaches 15, ultimately eliminating nitrogen in the produced water. Conversely, a reduced C/N ratio can limit the ability of polyphosphate-accumulating organisms to incorporate carbon into polyphosphate synthesis, thereby decreasing phosphorus removal efficiency within the cSBR. When the C/N ratio ranged from 6 to 8, and the mixed liquor suspended solids concentration was high, the average phosphate removal was approximately 55%, compared to only around 25% when the C/N ratio was less than 6.}, } @article {pmid39362665, year = {2024}, author = {Tiew, PY and Leung, JM and Mac Aogáin, M and Johal, P and Jaggi, TK and Yuen, ACY and Ivan, FX and Yang, J and Afshar, T and Tee, A and Koh, MS and Lim, YH and Wong, A and Chandrasekaran, L and Dacanay, JG and Drautz-Moses, DI and Ong, TH and Abisheganaden, JA and Chew, FT and Schuster, SC and Carlsten, C and Chotirmall, SH}, title = {Residential exposure to Aspergillus spp. is associated with exacerbations in COPD.}, journal = {The European respiratory journal}, volume = {64}, number = {5}, pages = {}, pmid = {39362665}, issn = {1399-3003}, mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/immunology ; Male ; Female ; Singapore/epidemiology ; Aged ; Middle Aged ; *Aspergillus fumigatus/immunology ; *Environmental Exposure ; Prospective Studies ; Allergens/immunology ; Air Pollution, Indoor ; Disease Progression ; Housing ; Metagenomics ; British Columbia/epidemiology ; }, abstract = {BACKGROUND: Sensitisation to Aspergillus fumigatus is linked to worse outcomes in patients with COPD; however, its prevalence and clinical implications in domestic (residential) settings remains unknown.

METHODS: Individuals with COPD (n=43) recruited in Singapore had their residences prospectively sampled and assessed by shotgun metagenomic sequencing including indoor air, outdoor air and touch surfaces (a total of 126 specimens). The abundance of environmental A. fumigatus and the occurrence of A. fumigatus (Asp f) allergens in the environment were determined and immunological responses to A. fumigatus allergens determined in association with clinical outcomes including exacerbation frequency. Findings were validated in 12 individuals (31 specimens) with COPD in Vancouver, Canada, a climatically different region.

RESULTS: 157 metagenomes from 43 homes were assessed. 11 and nine separate Aspergillus spp. were identified in Singapore and Vancouver, respectively. Despite climatic, temperature and humidity variation, A. fumigatus was detectable in the environment from both locations. The relative abundance of environmental A. fumigatus was significantly associated with exacerbation frequency in both Singapore (r=0.27, p=0.003) and Vancouver (r=0.49, p=0.01) and individuals with higher Asp f 3 sensitisation responses lived in homes with a greater abundance of environmental Asp f 3 allergens (p=0.037). Patients exposed and sensitised to Asp f 3 allergens demonstrated a higher rate of COPD exacerbations at 1-year follow-up (p=0.021).

CONCLUSION: Environmental A. fumigatus exposure in the home environment including air and surfaces with resulting sensitisation carries pathogenic potential in individuals with COPD. Targeting domestic A. fumigatus abundance may reduce COPD exacerbations.}, } @article {pmid39362131, year = {2024}, author = {Yang, T and Wang, X and Ng, HY and Huang, S and Zheng, X and Bi, X}, title = {Airborne antibiotic resistome from sludge dewatering systems: Mobility, pathogen accessibility, cross-media migration propensity, impacting factors, and risks.}, journal = {Water research}, volume = {267}, number = {}, pages = {122552}, doi = {10.1016/j.watres.2024.122552}, pmid = {39362131}, issn = {1879-2448}, mesh = {*Sewage/microbiology ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Bacteria/drug effects/genetics ; Particulate Matter ; }, abstract = {Bioaerosol contamination was considered as a potential health threat in sludge dewatering systems (SDSs), while emission and risk of airborne antibiotic resistome remain largely unclear. Herein, seasonal investigations of fine particulate matter (PM2.5) were conducted using metagenomics-based methods within and around different SDSs, together with an analysis of sewage sludge. Featured with evident seasonality, antibiotic resistance genes (ARGs) in SDS-PM2.5 also possessed greater accumulation, transfer, and pathogen accessibility than those in ambient air PM2.5. Mobile ARGs in SDS-PM2.5 mainly encoded resistance to tetracycline, and most were flanked by integrase. Some pathogenic antibiotic resistant bacteria (PARB), including Enterobacter asburiae, Escherichia coli, Enterococcus faecium, and Staphylococcus aureus, also carried mobile genetic elements in SDS-PM2.5. Dewatering behavior actuated > 50.56% of ARG subtypes and > 42.86% of PARB in sewage sludge to aerosolize into air. Relative humidity, temperature, and PM2.5 concentration collectively drove the evolution of bacterial community and indirectly promoted the antibiotic resistance of SDS-PM2.5. SDS-PM2.5 posed more serious resistome risks than sewage sludge and ambient air PM2.5, and the highest levels were discovered in winter. These findings underline the role of dewatering behavior in facilitating resistome's aerosolization, and the need to mitigate this potential air pollution.}, } @article {pmid39362120, year = {2024}, author = {Gao, S and Li, S and Cao, S and Zhong, H and He, Z}, title = {Disclosing the key role of Fe/As/Cu in community co-occurrence and microbial recruitment in metallurgical ruins.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {135889}, doi = {10.1016/j.jhazmat.2024.135889}, pmid = {39362120}, issn = {1873-3336}, mesh = {*Iron/metabolism ; *Microbiota/drug effects ; Metallurgy ; Arsenic/metabolism ; Mining ; Copper ; Bacteria/metabolism/genetics ; Metals, Heavy/toxicity ; Soil Microbiology ; Soil Pollutants/metabolism/toxicity ; }, abstract = {Mining activities have led to the persistent presence of substantial heavy metals at metallurgical sites. However, the impact of long-term and complex heavy metal pollution in metallurgical ruins on the structure and spatial shift of microbiome remains unclear. In this study, we focused on various types of metallurgical sites to uncover the occurrence of heavy metals in abandoned mines and the response patterns of microbial communities. The results indicate that mining activities have caused severe exceedances of multiple heavy metals, with AsBio, CuBio, and FeBio being the primary factors affecting community structure and function. Co-occurrence network analyses suggest that several genera, including Ellin6515, Cupriavidus, Acidobacteria genus RB41, Vicinamibacteraceae, Blastococcus, and Sphingomonas, may play significant roles in the synergistic metabolism of communities responding to Fe-Cu-As stress. Although random dispersal contributed to community migration, null models emphasized that variable selection predominates in the spatial turnover of community composition. Additionally, metagenomic prediction (PICRUSt2) identified key genes involved in stress and detoxification strategies of heavy metals. The composite heavy metal stress strengthened the relationship between network structure and the potential function of the community, along with critical ecosystem functions. Our findings demonstrated that microbial interactions were crucial for ecosystem management and the ecological consequences of heavy metal pollution remediation.}, } @article {pmid39361891, year = {2024}, author = {Ramos-Barbero, MD and Gómez-Gómez, C and Vique, G and Sala-Comorera, L and Rodríguez-Rubio, L and Muniesa, M}, title = {Recruitment of complete crAss-like phage genomes reveals their presence in chicken viromes, few human-specific phages, and lack of universal detection.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39361891}, issn = {1751-7370}, mesh = {Humans ; *Bacteriophages/genetics/classification/isolation & purification ; Animals ; *Genome, Viral ; *Phylogeny ; *Virome/genetics ; *Chickens/virology ; Feces/virology ; Host Specificity ; }, abstract = {The order Crassvirales, which includes the prototypical crAssphage (p-crAssphage), is predominantly associated with humans, rendering it the most abundant and widely distributed group of DNA phages in the human gut. The reported human specificity and wide global distribution of p-crAssphage makes it a promising human fecal marker. However, the specificity for the human gut as well as the geographical distribution around the globe of other members of the order Crassvirales remains unknown. To determine this, a recruitment analysis using 91 complete, non-redundant genomes of crAss-like phages in human and animal viromes revealed that only 13 crAss-like phages among the 91 phages analyzed were highly specific to humans, and p-crAssphage was not in this group. Investigations to elucidate whether any characteristic of the phages was responsible for their prevalence in humans showed that the 13 human crAss-like phages do not share a core genome. Phylogenomic analysis placed them in three independent families, indicating that within the Crassvirales group, human specificity is likely not a feature of a common ancestor but rather was introduced on separate/independent occasions in their evolutionary history. The 13 human crAss-like phages showed variable geographical distribution across human metagenomes worldwide, with some being more prevalent in certain countries than in others, but none being universally identified. The varied geographical distribution and the absence of a phylogenetic relationship among the human crAss-like phages are attributed to the emergence and dissemination of their bacterial host, the symbiotic human strains of Bacteroides, across various human populations occupying diverse ecological niches worldwide.}, } @article {pmid39360992, year = {2024}, author = {Mayne, R and Secret, S and Geoghegan, C and Trebes, A and Kean, K and Reid, K and Lin, GL and Ansari, MA and de Cesare, M and Bonsall, D and Elliott, I and Piazza, P and Brown, A and Bray, J and Knight, JC and Harvala, H and Breuer, J and Simmonds, P and Bowden, RJ and Golubchik, T}, title = {Castanet: a pipeline for rapid analysis of targeted multi-pathogen genomic data.}, journal = {Bioinformatics (Oxford, England)}, volume = {40}, number = {10}, pages = {}, pmid = {39360992}, issn = {1367-4811}, support = {NIHR203338//UK National Institutes for Health Research/ ; }, mesh = {*Software ; Genomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Sequence Analysis, DNA/methods ; Metagenomics/methods ; }, abstract = {MOTIVATION: Target enrichment strategies generate genomic data from multiple pathogens in a single process, greatly improving sensitivity over metagenomic sequencing and enabling cost-effective, high-throughput surveillance and clinical applications. However, uptake by research and clinical laboratories is constrained by an absence of computational tools that are specifically designed for the analysis of multi-pathogen enrichment sequence data. Here we present an analysis pipeline, Castanet, for use with multi-pathogen enrichment sequencing data. Castanet is designed to work with short-read data produced by existing targeted enrichment strategies, but can be readily deployed on any BAM file generated by another methodology. Also included are an optional graphical interface and installer script.

RESULTS: In addition to genome reconstruction, Castanet reports method-specific metrics that enable quantification of capture efficiency, estimation of pathogen load, differentiation of low-level positives from contamination, and assessment of sequencing quality. Castanet can be used as a traditional end-to-end pipeline for consensus generation, but its strength lies in the ability to process a flexible, pre-defined set of pathogens of interest directly from multi-pathogen enrichment experiments. In our tests, Castanet consensus sequences were accurate reconstructions of reference sequences, including in instances where multiple strains of the same pathogen were present. Castanet performs effectively on standard computers and can process the entire output of a 96-sample enrichment sequencing run (50M reads) using a single batch process command, in $<$2 h.

Source code freely available under GPL-3 license at https://github.com/MultipathogenGenomics/castanet, implemented in Python 3.10 and supported in Ubuntu Linux 22.04. The data underlying this article are available in Europe Nucleotide Archives, at https://www.ebi.ac.uk/ena/browser/view/PRJEB77004.}, } @article {pmid39360442, year = {2024}, author = {Guo, N and Gui, YJ and Chen, Y}, title = {Vitrectomy Combined with Repeated Intravitreal Injection of Ceftazidime for the Treatment of Brucellosis Endophthalmitis: A Case Report and Literature Review.}, journal = {Seminars in ophthalmology}, volume = {}, number = {}, pages = {1-4}, doi = {10.1080/08820538.2024.2412050}, pmid = {39360442}, issn = {1744-5205}, abstract = {PURPOSE: To present a treatment regimen for Brucellosis endophthalmitis that resulted in a good visual outcome. Additionally, we conducted a literature review on the treatment and visual prognosis of related cases.

CASE PRESENTATION: A 49-year-old woman with the chief complaint of decreased vision and redness in the right eye was initially diagnosed with noninfectious uveitis and prescribed high-dose steroids which led to transient improvement followed by a decline in vision. An infectious cause was suspected. Metagenomic next-generation sequencing of vitreous fluid and serological testing confirmed Brucella melitensis infection. The patient underwent vitrectomy combined with six intravitreal injections of ceftazidime in the right eye in addition to systemic antibiotic treatment. The intraocular inflammation was completely resolved, and the visual acuity recovered to 20/25, which is the best-documented recovery in Brucella endophthalmitis cases, as revealed by the literature review.

CONCLUSION: Vitrectomy combined with repeated intravitreal injections of ceftazidime can enhance the treatment for brucellosis endophthalmitis and achieve a better visual prognosis.}, } @article {pmid39360247, year = {2024}, author = {Yepes-García, J and Falquet, L}, title = {Metagenome quality metrics and taxonomical annotation visualization through the integration of MAGFlow and BIgMAG.}, journal = {F1000Research}, volume = {13}, number = {}, pages = {640}, pmid = {39360247}, issn = {2046-1402}, mesh = {*Metagenome ; *Software ; Metagenomics/methods ; Molecular Sequence Annotation/methods ; }, abstract = {BACKGROUND: Building Metagenome-Assembled Genomes (MAGs) from highly complex metagenomics datasets encompasses a series of steps covering from cleaning the sequences, assembling them to finally group them into bins. Along the process, multiple tools aimed to assess the quality and integrity of each MAG are implemented. Nonetheless, even when incorporated within end-to-end pipelines, the outputs of these pieces of software must be visualized and analyzed manually lacking integration in a complete framework.

METHODS: We developed a Nextflow pipeline (MAGFlow) for estimating the quality of MAGs through a wide variety of approaches (BUSCO, CheckM2, GUNC and QUAST), as well as for annotating taxonomically the metagenomes using GTDB-Tk2. MAGFlow is coupled to a Python-Dash application (BIgMAG) that displays the concatenated outcomes from the tools included by MAGFlow, highlighting the most important metrics in a single interactive environment along with a comparison/clustering of the input data.

RESULTS: By using MAGFlow/BIgMAG, the user will be able to benchmark the MAGs obtained through different workflows or establish the quality of the MAGs belonging to different samples following the divide and rule methodology.

CONCLUSIONS: MAGFlow/BIgMAG represents a unique tool that integrates state-of-the-art tools to study different quality metrics and extract visually as much information as possible from a wide range of genome features.}, } @article {pmid39359923, year = {2024}, author = {Shi, Z and Zhu, X and Gao, W and Yu, S and Zhan, L}, title = {Extracorporeal membrane oxygenation in acute respiratory distress syndrome caused by elderly tuberculous meningitis: a case report and review of the literature.}, journal = {Frontiers in medicine}, volume = {11}, number = {}, pages = {1457413}, pmid = {39359923}, issn = {2296-858X}, abstract = {Diagnosing and clinical management of tuberculous meningitis (TBM) are still challenging for clinicians. Analysis of cerebrospinal fluid (CSF) is an important diagnostic tool for patients with suspected central nervous system (CNS) diseases. Acute respiratory distress syndrome (ARDS), an inflammatory lung injury, can be treated by mechanical ventilation, fluid management, and even extracorporeal membrane oxygenation (ECMO). In addition, metagenomic next-generation sequencing (mNGS) can facilitate the detection of atypical, rare pathogens in clinical specimens. We report a case of a 65-year-old man with ARDS caused by TBM. He was admitted with a fever and shaking. Despite aggressive initial treatment, the patient progressed rapidly and developed ARDS. Without positive results of mNGS and culture, anti-tuberculosis (TB) treatment was started. In order to improve oxygenation levels, he was placed on veno-venous ECMO for 8 days. On day 47, the tracheotomy catheter was pulled out and sealed. The patient was conscious and could communicate with family members as normal.}, } @article {pmid39359902, year = {2024}, author = {Haley, E and Luke, N}, title = {From Awareness to Action: Pioneering Solutions for Women's UTI Challenges in the Era of Precision Medicine.}, journal = {International journal of women's health}, volume = {16}, number = {}, pages = {1595-1605}, pmid = {39359902}, issn = {1179-1411}, abstract = {This article aims to bring clinicians' awareness to the widespread impact of urinary tract infection (UTI) on the lives of women and to the advances that offer hope for future improvements in the diagnosis and management of UTI. Thanks to physiological, anatomical, and lifestyle factor differences, women face heightened vulnerability to UTIs compared to men. In fact, women are four times more likely than men to develop a UTI and around half of these women encounter UTI recurrence, which is a significant source of both physical and psychosocial burdens. Despite the current shortcomings in diagnosis and management, emerging diagnostic technologies promise to identify UTIs more accurately and rapidly, offering women hope for a revolution in UTI management. Meanwhile, clinicians have the opportunity to reduce the psychosocial burden by recognizing the value of patients' lived experiences and ensuring their care plan is in alignment with their patients' goals and expectations for medical care.}, } @article {pmid39359838, year = {2024}, author = {Obeagu, EI and Okoroiwu, GIA and Ubosi, NI and Obeagu, GU and Onohuean, H and Muhammad, T and Adias, TC}, title = {Revolution in malaria detection: unveiling current breakthroughs and tomorrow's possibilities in biomarker innovation.}, journal = {Annals of medicine and surgery (2012)}, volume = {86}, number = {10}, pages = {5859-5876}, pmid = {39359838}, issn = {2049-0801}, abstract = {The ongoing battle against malaria has seen significant advancements in diagnostic methodologies, particularly through the discovery and application of novel biomarkers. Traditional diagnostic techniques, such as microscopy and rapid diagnostic tests, have their limitations in terms of sensitivity, specificity, and the ability to detect low-level infections. Recent breakthroughs in biomarker research promise to overcome these challenges, providing more accurate, rapid, and non-invasive detection methods. These advancements are critical in enhancing early detection, guiding effective treatment, and ultimately reducing the global malaria burden. Innovative approaches in biomarker detection are leveraging cutting-edge technologies like next-generation sequencing, proteomics, and metabolomics. These techniques have led to the identification of new biomarkers that can be detected in blood, saliva, or urine, offering less invasive and more scalable options for widespread screening. For instance, the discovery of specific volatile organic compounds in the breath of infected individuals presents a revolutionary non-invasive diagnostic tool. Additionally, the integration of machine learning algorithms with biomarker data is enhancing the precision and predictive power of malaria diagnostics, making it possible to distinguish between different stages of infection and identify drug-resistant strains. Looking ahead, the future of malaria detection lies in the continued exploration of multi-biomarker panels and the development of portable, point-of-care diagnostic devices. The incorporation of smartphone-based technologies and wearable biosensors promises to bring real-time monitoring and remote diagnostics to even the most resource-limited settings.}, } @article {pmid39359390, year = {2024}, author = {Karamendin, K and Goodman, SJ and Kasymbekov, Y and Kumar, M and Nuralibekov, S and Kydyrmanov, A}, title = {Viral metagenomic survey of Caspian seals.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1461135}, pmid = {39359390}, issn = {2297-1769}, abstract = {INTRODUCTION: Viral diseases of pinnipeds cause substantial mortality and morbidity and can influence population demography. Viral metagenomic studies can therefore play an important role in pinniped health assessments and disease surveillance relevant to both individual species and in a "One Health" context.

METHODS: This study used a metagenomic approach with high throughput sequencing to make the first assessment of viral diversity in Caspian seals (Pusa caspica), the only marine mammal species endemic to the Caspian Sea.

RESULTS: Sequencing libraries from 35 seals sampled 2009-2020 were analysed, finding sequences from the viral families Circoviridae, Parvoviridae, Herpesviridae, Papillomaviridae, Picornaviridae, Caliciviridae, Cruciviridae, Anelloviridae, Smacoviridae, and Orthomyxoviridae, with additional detection of Adenoviridae via PCR. The similarity of viral contigs from Caspian seal to sequences recovered from other pinnipeds ranged from 63.74% (San Miguel sea lion calicivirus) to 78.79% (Seal anellovirus 4).

DISCUSSION: Some findings represent novel viral species, but overall, the viral repertoire of Caspian seals is similar to available viromes from other pinnipeds. Among the sequences recovered were partial contigs for influenza B, representing only the second such molecular identification in marine mammals. This work provides a foundation for further studies of viral communities in Caspian seals, the diversity of viromes in pinnipeds more generally, and contributes data relevant for disease risk assessments in marine mammals.}, } @article {pmid39359379, year = {2024}, author = {Gao, X and Liu, J and Zhang, X and Zhao, T}, title = {Complete mitochondrial genome and phylogenetic analysis of Chloris chloris (Passeriformes: Fringillidae).}, journal = {Mitochondrial DNA. Part B, Resources}, volume = {9}, number = {10}, pages = {1327-1330}, pmid = {39359379}, issn = {2380-2359}, abstract = {In this study, we employed high-throughput metagenomic data to assemble the mitochondrial genome (mitogenome) of the European greenfinch (Chloris chloris; Linnaeus 1758). The circular mitogenome was 16,813 base pairs (bp) in length, containing 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and 1 control region. The base composition of the mitogenome is 30.6% A, 30.7% C, 14.2% G, and 24.5% T, resulting in a GC content of 44.9%. Phylogenetic analysis, utilizing the concatenation of the 13 mitochondrial PCGs from 32 related species of the order Passeriformes, indicated a closer relationship between C. chloris and C. sinica. Moreover, the genus Chloris was closely related to the genera of Serinus, Crithagra, Carduelis, and Acanthis. This mitogenomic data of C. chloris not only be helpful for species identification but also facilitates our understanding of the evolutionary relationship among different species in genus Chloris, which experienced rapid radiation evolution.}, } @article {pmid39358810, year = {2024}, author = {Meng, L and Jin, H and Yulug, B and Altay, O and Li, X and Hanoglu, L and Cankaya, S and Coskun, E and Idil, E and Nogaylar, R and Ozsimsek, A and Shoaie, S and Turkez, H and Nielsen, J and Zhang, C and Borén, J and Uhlén, M and Mardinoglu, A}, title = {Multi-omics analysis reveals the key factors involved in the severity of the Alzheimer's disease.}, journal = {Alzheimer's research & therapy}, volume = {16}, number = {1}, pages = {213}, pmid = {39358810}, issn = {1758-9193}, mesh = {Humans ; *Alzheimer Disease/genetics/microbiology/metabolism/blood ; *Proteomics ; Female ; Male ; Aged ; *Metabolomics/methods ; *Gastrointestinal Microbiome ; Severity of Illness Index ; Artificial Intelligence ; Aged, 80 and over ; Biomarkers/blood ; Metagenomics/methods ; Multiomics ; }, abstract = {Alzheimer's disease (AD) is a debilitating neurodegenerative disorder with a global impact, yet its pathogenesis remains poorly understood. While age, metabolic abnormalities, and accumulation of neurotoxic substances are potential risk factors for AD, their effects are confounded by other factors. To address this challenge, we first utilized multi-omics data from 87 well phenotyped AD patients and generated plasma proteomics and metabolomics data, as well as gut and saliva metagenomics data to investigate the molecular-level alterations accounting the host-microbiome interactions. Second, we analyzed individual omics data and identified the key parameters involved in the severity of the dementia in AD patients. Next, we employed Artificial Intelligence (AI) based models to predict AD severity based on the significantly altered features identified in each omics analysis. Based on our integrative analysis, we found the clinical relevance of plasma proteins, including SKAP1 and NEFL, plasma metabolites including homovanillate and glutamate, and Paraprevotella clara in gut microbiome in predicting the AD severity. Finally, we validated the predictive power of our AI based models by generating additional multi-omics data from the same group of AD patients by following up for 3 months. Hence, we observed that these results may have important implications for the development of potential diagnostic and therapeutic approaches for AD patients.}, } @article {pmid39358791, year = {2024}, author = {Wirajana, IN and Ariantari, NP and Shyu, DJH and Vaghamshi, N and Antaliya, K and Dudhagara, P}, title = {Prokaryotic communities profiling of Indonesian hot springs using long-read Oxford Nanopore sequencing.}, journal = {BMC research notes}, volume = {17}, number = {1}, pages = {286}, pmid = {39358791}, issn = {1756-0500}, support = {B/530-4/UN14.4A/PT.01.03/2023//Udayana University International Senior Fellowship (UNISERF) grant for year 2023 (Grant Number: B/530-4/UN14.4A/PT.01.03/2023), Udayana University, Bali, Indonesia/ ; }, mesh = {*Hot Springs/microbiology ; Indonesia ; *RNA, Ribosomal, 16S/genetics ; *Nanopore Sequencing/methods ; Microbiota/genetics ; Bacteria/genetics/isolation & purification/classification ; Metagenome/genetics ; Metagenomics/methods ; Water Microbiology ; Phylogeny ; DNA, Bacterial/genetics/analysis ; Sequence Analysis, DNA/methods ; }, abstract = {OBJECTIVES: Indonesia's location at the convergence of multiple tectonic plates results in a unique geomorphological feature with abundant hot springs. This study pioneers the metagenomic exploration of Indonesian hot springs, harbouring unique life forms despite high temperatures. The microbial community of hot springs is taxonomically versatile and biotechnologically valuable. 16s rRNA amplicon sequencing of the metagenome is a viable option for the microbiome investigation. This study utilized Oxford Nanopore's long-read 16 S rRNA sequencing for enhanced species identification, improved detection of rare members, and a more detailed community composition profile.

DATA DESCRIPTION: Water samples were taken from three hot springs of the Bali, Indonesia (i) Angseri, 8.362503 S, 115.133452 E; (ii) Banjar, 8.210270 S, 114.967063 E; and (iii) Batur, 8.228806 S, 115.404829 E. BioLit Genomic DNA Extraction Kit (SRL, Mumbai, India) was used to isolate DNA from water samples. The quantity and quality of the DNA were determined using a NanoDrop™ spectrophotometer and a Qubit fluorometer (Thermo Fisher Scientific, USA). The library was created using Oxford Nanopore Technology kits, and the sequencing was done using Oxford Nanopore's GridION platform. All sequencing data was obtained in FASTQ files and filtered using NanoFilt software. This dataset is valuable for searching novel bacteria diversity and their existence.}, } @article {pmid39358771, year = {2024}, author = {Kawano-Sugaya, T and Arikawa, K and Saeki, T and Endoh, T and Kamata, K and Matsuhashi, A and Hosokawa, M}, title = {A single amplified genome catalog reveals the dynamics of mobilome and resistome in the human microbiome.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {188}, pmid = {39358771}, issn = {2049-2618}, mesh = {Humans ; *Bacteria/genetics/classification ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; *Mouth/microbiology ; *Genome, Bacterial ; Interspersed Repetitive Sequences/genetics ; Microbiota/genetics ; Drug Resistance, Bacterial/genetics ; Metagenomics/methods ; Phylogeny ; }, abstract = {BACKGROUND: The increase in metagenome-assembled genomes (MAGs) has advanced our understanding of the functional characterization and taxonomic assignment within the human microbiome. However, MAGs, as population consensus genomes, often aggregate heterogeneity among species and strains, thereby obfuscating the precise relationships between microbial hosts and mobile genetic elements (MGEs). In contrast, single amplified genomes (SAGs) derived via single-cell genome sequencing can capture individual genomic content, including MGEs.

RESULTS: We introduce the first substantial SAG dataset (bbsag20) from the human oral and gut microbiome, comprising 17,202 SAGs above medium-quality without co-assembly. This collection unveils a diversity of bacterial lineages across 312 oral and 647 gut species, demonstrating different taxonomic compositions from MAGs. Moreover, the SAGs showed cellular-level evidence of the translocation of oral bacteria to the gut. We also identified broad-host-range MGEs harboring antibiotic resistance genes (ARGs), which were not detected in the MAGs.

CONCLUSIONS: The difference in taxonomic composition between SAGs and MAGs indicates that combining both methods would be effective in expanding the genome catalog. By connecting mobilomes and resistomes in individual samples, SAGs could meticulously chart a dynamic network of ARGs on MGEs, pinpointing potential ARG reservoirs and their spreading patterns in the microbial community. Video Abstract.}, } @article {pmid39358016, year = {2024}, author = {Liu, X and Ni, Y and Ye, L and Guo, Z and Tan, L and Li, J and Yang, M and Chen, S and Li, R}, title = {Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications.}, journal = {Genome research}, volume = {34}, number = {11}, pages = {2025-2038}, pmid = {39358016}, issn = {1549-5469}, mesh = {*DNA Methylation ; *DNA, Bacterial/genetics ; *Nanopore Sequencing/methods ; *Nanopores ; Genome, Bacterial ; Sequence Analysis, DNA/methods ; Bacteria/genetics ; }, abstract = {DNA modifications in bacteria present diverse types and distributions, playing crucial functional roles. Current methods for detecting bacterial DNA modifications via nanopore sequencing typically involve comparing raw current signals to a methylation-free control. In this study, we found that bacterial DNA modification induces errors in nanopore reads. And these errors are found only in one strand but not the other, showing a strand-specific bias. Leveraging this discovery, we developed Hammerhead, a pioneering pipeline designed for de novo methylation discovery that circumvents the necessity of raw signal inference and a methylation-free control. The majority (14 out of 16) of the identified motifs can be validated by raw signal comparison methods or by identifying corresponding methyltransferases in bacteria. Additionally, we included a novel polishing strategy employing duplex reads to correct modification-induced errors in bacterial genome assemblies, achieving a reduction of over 85% in such errors. In summary, Hammerhead enables users to effectively locate bacterial DNA methylation sites from nanopore FASTQ/FASTA reads, thus holds promise as a routine pipeline for a wide range of nanopore sequencing applications, such as genome assembly, metagenomic binning, decontaminating eukaryotic genome assemblies, and functional analysis for DNA modifications.}, } @article {pmid39357373, year = {2024}, author = {Liu, Y and Zhang, Q and Shi, Y and Hao, Z and Zhan, X}, title = {Anthropogenic activities significantly interfered distribution and co-occurrence patterns of antibiotic resistance genes in a small rural watershed in Southwest China.}, journal = {Ecotoxicology and environmental safety}, volume = {285}, number = {}, pages = {117118}, doi = {10.1016/j.ecoenv.2024.117118}, pmid = {39357373}, issn = {1090-2414}, mesh = {China ; *Drug Resistance, Microbial/genetics ; *Agriculture ; *Environmental Monitoring ; *Soil Microbiology ; *Anti-Bacterial Agents/analysis ; Genes, Bacterial ; Metagenomics ; Wastewater/microbiology ; Water Pollutants, Chemical/analysis ; Bacteria/genetics/drug effects ; Water Microbiology ; }, abstract = {The prevalence and spread of antibiotic resistance genes (ARGs) have been a significant concern for global public health in recent years. Small rural watersheds are the smallest units of factor mobility for agricultural production in China, and their ARG profiles are the best scale of the contamination status, but the mapping and the distribution and diffusion of ARGs in the water and soil of small rural watersheds are inadequate. In this study, based on microbial metagenomics, we invested prevalence maps of 209 ARGs corresponding to typical commonly used antibiotics (including multidrug, aminoglycoside, macrolide-lincosamide-streptogramin B (MLSB), and β-Lactamase) in water and soil in different agricultural types, as well as within water-soil interfaces in small rural watersheds in Southwest China. The results revealed that the most abundant ARGs in water and soil were consistent, but different in subtypes, and anthropogenic activities affect the transport of ARGs between water and soils. Livestock wastewater discharges influenced the diversity and abundance of ARGs in water, while in soil it is planting type and fertilizer management, and thus interfered with the co-occurrence patterns between bacteria and ARGs. Co-occurrence analysis revealed that Proteobacteria, Actinobacteria, and Bacteroidetes were the predominant ARG hosts in water and soil, but soil exhibited a more intricate ARG-bacterial association. Overall, this study provides integrated profiles of ARGs in water and soil influenced by anthropogenic activities at the small watershed scale in a typical rural area and provides a baseline for comparisons of ARGs.}, } @article {pmid39357281, year = {2024}, author = {Zhang, J and Gao, T and Chen, G and Liang, Y and Nie, X and Gu, W and Li, L and Tong, H and Huang, W and Lu, T and Bian, Z and Su, L}, title = {Vinegar-processed Schisandra Chinensis enhanced therapeutic effects on colitis-induced depression through tryptophan metabolism.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {135}, number = {}, pages = {156057}, doi = {10.1016/j.phymed.2024.156057}, pmid = {39357281}, issn = {1618-095X}, mesh = {Animals ; *Schisandra/chemistry ; *Depression/drug therapy ; Male ; Mice ; *Tryptophan/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Acetic Acid ; *Colitis, Ulcerative/drug therapy/chemically induced ; *Disease Models, Animal ; Mice, Inbred C57BL ; Blood-Brain Barrier/drug effects ; Dextran Sulfate ; Colon/drug effects/metabolism ; Cytokines/metabolism ; Hippocampus/drug effects/metabolism ; Plant Extracts/pharmacology ; Intestinal Mucosa/drug effects/metabolism ; }, abstract = {BACKGROUND: Ulcerative colitis (UC) is an inflammatory bowel disease characterized by its incurable nature and undefined etiology, which is often accompanied by a high prevalence of comorbid depression. The gut-brain axis has emerged as a promising treatment target in recent years.

PURPOSE: This study aimed to investigate how vinegar-processed Schisandra Chinensis (VSC) enhances therapeutic effects on depressive behavior in chronic UC mice.

METHODS: A chronic UC model was induced in mice using dextran sulfate sodium. The therapeutic effects of both raw and vinegar-processed Schisandra Chinensis on UC and associated depressive symptoms were assessed. Colonic mucosal damage was evaluated using hematoxylin and eosin (H&E) and Alcian blue staining. The integrity of the blood-brain barrier (BBB) and synaptic structures was visualized via transmission electron microscopy (TEM). Enzyme-linked immunosorbent assay (ELISA) was employed to quantify inflammatory cytokine levels in the colon, serum, and brain, while western blotting was performed for protein expression analysis. Additionally, metagenomic analysis was conducted to investigate gut microbiota composition. Nissl staining and immunofluorescence were used to assess hippocampal neuronal damage, and behavioral assessments including the morris water maze, open field test, forced swimming test and tail suspension test, were implemented to evaluate depressive states. Serum metabolites were analyzed using UPLC-MS/MS.

RESULTS: Both raw and vinegar-processed Schisandra Chinensis significantly upregulated aryl hydrocarbon receptor (AhR), inhibited NF-κB p-p65 activation, and reduced levels of pro-inflammatory cytokine. These treatments also enhanced the expression of tight junction proteins, restored colonic mucosal and BBB integrity, alleviated damage to hippocampal neurons, and improved synaptic structure. Behavioral assessments indicated that VSC was particularly effective in ameliorating depressive-like behaviors in chronic UC mice. In the gut, both treatments reshaped the gut microbial composition, restoring the relative abundance of Duncaniella, Candidatus_Amulumruptor, Alistipes, Parabacteroides, Lachnospiraceae_bacterium, uncultured_Bacteroides_sp., Candidatus_Amulumruptor_caecigallinarius, with VSC showing more pronounced effects. Serum metabolomics revealed an increase in tryptophan levels and a decrease in kynurenine and xanthurenic acid levels with VSC, indicating that tryptophan metabolism shifted from the kynurenine pathway to the 5-HT or indole pathway. However, this phenomenon did not occur with Schisandra Chinensis (SC).

CONCLUSION: This study demonstrated that the disruption of tryptophan metabolic balance served as a biological mechanism underlying the occurrence of depressive behaviors induced by UC. The application of SC following vinegar processing enhanced its regulatory effects on gut microbiota and tryptophan metabolism. This findings provided a new insight for the clinical management of gut-brain comorbidities.}, } @article {pmid39357183, year = {2024}, author = {Thapliyal, P and Sah, V and Rautela, I and Joshi, M and Tyagi, S and Verma, R and Sharma, MD}, title = {Next Generation Sequencing: Latent applications in clinical diagnostics with the advent of bioinformatic frameworks.}, journal = {Pathology, research and practice}, volume = {263}, number = {}, pages = {155606}, doi = {10.1016/j.prp.2024.155606}, pmid = {39357183}, issn = {1618-0631}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Computational Biology/methods ; *COVID-19/virology/diagnosis ; *SARS-CoV-2/genetics ; Precision Medicine/methods ; }, abstract = {For the past 3-4 decades, the discovery of Sanger's method of pyrosequencing was the only method unparalleled till 2005 being employed as a method of whole genome sequencing (WGS). Following this, a revolutionary extensive parallel sequencing method, Next Generation Sequencing (NGS), was engineered. NGS supported a substantial number of bases under a high throughput metagenomic interrogation. Bioinformatics contributed notably to this advancement. It provided alignment tools, assembly algorithms, and protocols such as Illumina and hybridization capture which have metamorphosed clinical and translational diagnostics. With the extension in precision medicine and targeted therapy under NGS sectors such as epigenetics, transcriptomics, mutation detection, prognosis, therapeutics, and patient management have been gaining progress. Using NGS in real-time clinical settings has been proven to produce positive outcomes. The most recent instrumental benefaction of NGS has been decoding the SARS-CoV-2 virus epidemiology with the assistance of multiplex PCR. So far, it had been employed to inspect different levels of viral loads from low to mid. This has been executed by amplification and phylogenetic examination of the load to raise a connective link with the evolutionary history leading up to the period of origin. The depletion in the consumed time and extensive genome size under analysis was further coupled by a cutback in the cost of sequencing while executing NGS. With the aid of this review paper, we aspire to manifest how the above-mentioned elements have boosted, tissue, microbial, and molecular data interrogation. Along with this, promoting, and stimulating an extensive evaluation and expansion in the paradigm of morphological and phenotypic study, via bioinformatics can facilitate further advancement in personalized and concise clinical research.}, } @article {pmid39357157, year = {2024}, author = {Zhao, Y and Fan, L and Gao, SH and Huang, F and Lei, Z and Wang, W and Gao, R and Dai, Z and Li, Q and Liang, B and Wang, A}, title = {Strain-level multidrug-resistant pathogenic bacteria in urban wastewater treatment plants: Transmission, source tracking and evolution.}, journal = {Water research}, volume = {267}, number = {}, pages = {122538}, doi = {10.1016/j.watres.2024.122538}, pmid = {39357157}, issn = {1879-2448}, mesh = {*Wastewater/microbiology ; Bacteria ; Waste Disposal, Fluid ; Drug Resistance, Multiple, Bacterial ; }, abstract = {Wastewater treatment plants (WWTPs) serve as reservoirs for various pathogens and play a pivotal role in safeguarding environmental safety and public health by mitigating pathogen release. Pathogenic bacteria, known for their potential to cause fatal infections, present a significant and emerging threat to global health and remain poorly understood regarding their origins and transmission in the environment. Using metagenomic approaches, we identified a total of 299 pathogens from three full-scale WWTPs. We comprehensively elucidated the occurrence, dissemination, and source tracking of the pathogens across the WWTPs, addressing deficiencies in traditional detection strategies. While indicator pathogens in current wastewater treatment systems such as Escherichia coli are effectively removed, specific drug-resistant pathogens, including Pseudomonas aeruginosa, Pseudomonas putida, and Aeromonas caviae, persist throughout the treatment process, challenging complete eradication efforts. The anoxic section plays a predominant role in controlling abundance but significantly contributes to downstream pathogen diversity. Additionally, evolution throughout the treatment process enhances pathogen diversity, except for upstream transmission, such as A. caviae str. WP8-S18-ESBL-04 and P. aeruginosa PAO1. Our findings highlight the necessity of expanding current biomonitoring indicators for wastewater treatment to optimize treatment strategies and mitigate the potential health risks posed by emerging pathogens. By addressing these research priorities, we can effectively mitigate risks and safeguard environmental safety and public health.}, } @article {pmid39353343, year = {2024}, author = {Zheng, X and Li, J and Ouyang, Y and Wu, G and He, X and Wang, D and Zhang, XX}, title = {Ecological linkages between top-down designed benzothiazole-degrading consortia and selection strength: From performance to community structure and functional genes.}, journal = {Water research}, volume = {267}, number = {}, pages = {122491}, doi = {10.1016/j.watres.2024.122491}, pmid = {39353343}, issn = {1879-2448}, mesh = {*Benzothiazoles ; *Biodegradation, Environmental ; Microbial Consortia ; Rhodococcus/genetics/metabolism ; }, abstract = {The inefficient biodegradation and incomplete mineralization of nitrogenous heterocyclic compounds (NHCs) have emerged as a pressing environmental concern. The top-down design offers potential solutions to this issue by targeting improvements in community function, but the ecological linkages between selection strength and the structure and function of desired microbiomes remain elusive. Herein, the integration of metagenomics, culture-based approach, non-targeted metabolite screening and enzymatic verification experiments revealed the effect of enrichment concentration on the top-down designed benzothiazole (BTH, a typical NHC)-degrading consortia. Significant differences were observed for the degradation efficiency and community structure under varying BTH selections. Notably, the enriched consortia at high concentrations of BTH were dominated by genus Rhodococcus, possessing higher degradation rates. Moreover, the isolate Rhodococcus pyridinivorans Rho48 displayed excellent efficiencies in BTH removal (98 %) and mineralization (∼ 60 %) through the hydroxylation and cleavage of thiazole and benzene rings, where cytochrome P450 enzyme was firstly reported to participate in BTH conversion. The functional annotation of 460 recovered genomes from the enriched consortia revealed diverse interspecific cooperation patterns that accounted for the BTH mineralization, particularly Nakamurella and Micropruina under low selection strength, and Rhodococcus and Marmoricola under high selection strength. This study highlights the significance of selection strength in top-down design of synthetic microbiomes for degrading refractory organic pollutants, providing valuable guidance for designing functionally optimized microbiomes used in environmental engineering.}, } @article {pmid39356745, year = {2024}, author = {Hartman, SJ and Hibberd, MC and Mostafa, I and Naila, NN and Islam, MM and Zaman, MU and Huq, S and Mahfuz, M and Islam, MT and Mukherji, K and Moghaddam, VA and Chen, RY and Province, MA and Webber, DM and Henrissat, S and Henrissat, B and Terrapon, N and Rodionov, DA and Osterman, AL and Barratt, MJ and Ahmed, T and Gordon, JI}, title = {A microbiome-directed therapeutic food for children recovering from severe acute malnutrition.}, journal = {Science translational medicine}, volume = {16}, number = {767}, pages = {eadn2366}, pmid = {39356745}, issn = {1946-6242}, support = {R01 DK030292/DK/NIDDK NIH HHS/United States ; R37 DK030292/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Severe Acute Malnutrition/diet therapy/therapy ; Infant ; Microbiota ; Male ; Female ; Bangladesh ; Gastrointestinal Microbiome ; }, abstract = {Globally, severe acute malnutrition (SAM), defined as a weight-for-length z-score more than three SDs below a reference mean (WLZ < -3), affects 14 million children under 5 years of age. Complete anthropometric recovery after standard, short-term interventions is rare, with children often left with moderate acute malnutrition (MAM; WLZ -2 to -3). We conducted a randomized controlled trial (RCT) involving 12- to 18-month-old Bangladeshi children from urban and rural sites, who, after initial hospital-based treatment for SAM, received a 3-month intervention with a microbiome-directed complementary food (MDCF-2) or a calorically more dense, standard ready-to-use supplementary food (RUSF). The rate of WLZ improvement was significantly greater in MDCF-2-treated children (P = 8.73 × 10[-3]), similar to our previous RCT of Bangladeshi children with MAM without antecedent SAM (P = 0.032). A correlated meta-analysis of plasma levels of 4520 proteins in both RCTs revealed 215 positively associated with WLZ (largely representing musculoskeletal and central nervous system development) and 44 negatively associated (primarily related to immune activation). Moreover, the positively associated proteins were significantly enriched by MDCF-2 (q = 1.1 × 10[-6]). Characterizing the abundances of 754 bacterial metagenome-assembled genomes in serially collected fecal samples disclosed the effects of acute rehabilitation for SAM on the microbiome and how, during treatment for MAM, specific strains of Prevotella copri function at the intersection between MDCF-2 glycan metabolism and anthropometric recovery. These results provide a rationale for further testing the generalizability of MDCF efficacy and for identifying biomarkers to define treatment responses.}, } @article {pmid39355420, year = {2024}, author = {Albin, D and Ramsahoye, M and Kochavi, E and Alistar, M}, title = {PhageScanner: a reconfigurable machine learning framework for bacteriophage genomic and metagenomic feature annotation.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1446097}, pmid = {39355420}, issn = {1664-302X}, abstract = {Bacteriophages are the most prolific organisms on Earth, yet many of their genomes and assemblies from metagenomic sources lack protein sequences with identified functions. While most bacteriophage proteins are structural proteins, categorized as Phage Virion Proteins (PVPs), a considerable number remain unclassified. Complicating matters further, traditional lab-based methods for PVP identification can be tedious. To expedite the process of identifying PVPs, machine-learning models are increasingly being employed. Existing tools have developed models for predicting PVPs from protein sequences as input. However, none of these efforts have built software allowing for both genomic and metagenomic data as input. In addition, there is currently no framework available for easily curating data and creating new types of machine learning models. In response, we introduce PhageScanner, an open-source platform that streamlines data collection for genomic and metagenomic datasets, model training and testing, and includes a prediction pipeline for annotating genomic and metagenomic data. PhageScanner also features a graphical user interface (GUI) for visualizing annotations on genomic and metagenomic data. We further introduce a BLAST-based classifier that outperforms ML-based models and an efficient Long Short-Term Memory (LSTM) classifier. We then showcase the capabilities of PhageScanner by predicting PVPs in six previously uncharacterized bacteriophage genomes. In addition, we create a new model that predicts phage-encoded toxins within bacteriophage genomes, thus displaying the utility of the framework.}, } @article {pmid39355269, year = {2024}, author = {Ding, Y and Liu, G and Li, Q and Zou, L and Dai, J and Chongsuvivatwong, V}, title = {Corrigendum: Distribution characteristics of human herpes viruses in the lower respiratory tract and their impact on 30-day mortality in community-acquired pneumonia patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1488546}, doi = {10.3389/fcimb.2024.1488546}, pmid = {39355269}, issn = {2235-2988}, abstract = {[This corrects the article DOI: 10.3389/fcimb.2024.1436509.].}, } @article {pmid39354675, year = {2024}, author = {Šardzíková, S and Gajewska, M and Gałka, N and Štefánek, M and Baláž, A and Garaiová, M and Holič, R and Świderek, W and Šoltys, K}, title = {Can longer lifespan be associated with gut microbiota involvement in lipid metabolism?.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {11}, pages = {}, pmid = {39354675}, issn = {1574-6941}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Lipid Metabolism ; Mice ; Male ; Female ; *Longevity ; *RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/metabolism/classification ; Mice, Inbred C57BL ; Feces/microbiology ; Cholesterol Esters/metabolism ; }, abstract = {Biological aging is linked to altered body composition and reduced neuroactive steroid hormones like dehydroepiandrosterone sulfate (DHEAS), which can stimulate the GABA signaling pathway via gut microbiota. Our study examined the association of gut microbiota with lifespan in mice through comprehensive analysis of its composition and functional involvement in cholesterol sulfate, a precursor of DHEAS, metabolism. We used 16S rRNA and metagenomic sequencing, followed by metabolic pathway prediction and thin layer chromatography and MALDI-TOF cholesterol sulfate identification. Significant increases in bacteria such as Bacteroides, typical for long-lived and Odoribacter and Colidextribacter, specific for short-lived mice were detected. Furthermore, for males (Rikenella and Alloprevotella) and females (Lactobacillus and Bacteroides), specific bacterial groups emerged as predictors (AUC = 1), highlighting sex-specific patterns. Long-lived mice showed a strong correlation of Bacteroides (0.918) with lipid and steroid hormone metabolism, while a negative correlation of GABAergic synapse with body weight (-0.589). We found that several Bacteroides species harboring the sulfotransferase gene and gene cluster for sulfonate donor synthesis are involved in converting cholesterol to cholesterol sulfate, significantly higher in the feces of long-lived individuals. Overall, we suggest that increased involvement of gut bacteria, mainly Bacteroides spp., in cholesterol sulfate synthesis could ameliorate aging through lipid metabolism.}, } @article {pmid39354646, year = {2024}, author = {Jochheim, A and Jochheim, FA and Kolodyazhnaya, A and Morice, É and Steinegger, M and Söding, J}, title = {Strain-resolved de-novo metagenomic assembly of viral genomes and microbial 16S rRNAs.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {187}, pmid = {39354646}, issn = {2049-2618}, support = {2019R1A6A1A10073437//National Research Foundation of Korea/ ; 031L0185//Bundesministerium für Bildung und Forschung/ ; 685778/ERC_/European Research Council/International ; }, mesh = {*RNA, Ribosomal, 16S/genetics ; *Genome, Viral/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification/virology ; Software ; Humans ; Bayes Theorem ; Viruses/genetics/classification ; Metagenome ; }, abstract = {BACKGROUND: Metagenomics is a powerful approach to study environmental and human-associated microbial communities and, in particular, the role of viruses in shaping them. Viral genomes are challenging to assemble from metagenomic samples due to their genomic diversity caused by high mutation rates. In the standard de Bruijn graph assemblers, this genomic diversity leads to complex k-mer assembly graphs with a plethora of loops and bulges that are challenging to resolve into strains or haplotypes because variants more than the k-mer size apart cannot be phased. In contrast, overlap assemblers can phase variants as long as they are covered by a single read.

RESULTS: Here, we present PenguiN, a software for strain resolved assembly of viral DNA and RNA genomes and bacterial 16S rRNA from shotgun metagenomics. Its exhaustive detection of all read overlaps in linear time combined with a Bayesian model to select strain-resolved extensions allow it to assemble longer viral contigs, less fragmented genomes, and more strains than existing assembly tools, on both real and simulated datasets. We show a 3-40-fold increase in complete viral genomes and a 6-fold increase in bacterial 16S rRNA genes.

CONCLUSION: PenguiN is the first overlap-based assembler for viral genome and 16S rRNA assembly from large and complex metagenomic datasets, which we hope will facilitate studying the key roles of viruses in microbial communities. Video Abstract.}, } @article {pmid39354152, year = {2024}, author = {Freire-Zapata, V and Holland-Moritz, H and Cronin, DR and Aroney, S and Smith, DA and Wilson, RM and Ernakovich, JG and Woodcroft, BJ and Bagby, SC and , and , and Rich, VI and Sullivan, MB and Stegen, JC and Tfaily, MM}, title = {Microbiome-metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient.}, journal = {Nature microbiology}, volume = {9}, number = {11}, pages = {2892-2908}, pmid = {39354152}, issn = {2058-5276}, support = {DE-SC0021349//DOE | SC | Biological and Environmental Research (BER)/ ; 2022070//NSF | Directorate for Biological Sciences (BIO)/ ; }, mesh = {*Permafrost/microbiology ; *Greenhouse Gases/metabolism/analysis ; *Microbiota ; *Methane/metabolism ; *Metagenomics ; *Carbon Dioxide/metabolism ; *Bacteria/metabolism/genetics/classification ; Sweden ; Ecosystem ; Soil Microbiology ; }, abstract = {Interactions between microbiomes and metabolites play crucial roles in the environment, yet how these interactions drive greenhouse gas emissions during ecosystem changes remains unclear. Here we analysed microbial and metabolite composition across a permafrost thaw gradient in Stordalen Mire, Sweden, using paired genome-resolved metagenomics and high-resolution Fourier transform ion cyclotron resonance mass spectrometry guided by principles from community assembly theory to test whether microorganisms and metabolites show concordant responses to changing drivers. Our analysis revealed divergence between the inferred microbial versus metabolite assembly processes, suggesting distinct responses to the same selective pressures. This contradicts common assumptions in trait-based microbial models and highlights the limitations of measuring microbial community-level data alone. Furthermore, feature-scale analysis revealed connections between microbial taxa, metabolites and observed CO2 and CH4 porewater variations. Our study showcases insights gained by using feature-level data and microorganism-metabolite interactions to better understand metabolic processes that drive greenhouse gas emissions during ecosystem changes.}, } @article {pmid39354019, year = {2024}, author = {Oaikhena, AO and Coker, ME and Cyril-Okoh, D and Wicaksono, WA and Olimi, E and Berg, G and Okeke, IN}, title = {The phyllosphere of Nigerian medicinal plants, Euphorbia lateriflora and Ficus thonningii is inhabited by a specific microbiota.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {22806}, pmid = {39354019}, issn = {2045-2322}, mesh = {*Euphorbia ; *Ficus/microbiology ; *Microbiota/genetics ; *Plants, Medicinal/microbiology ; *Bacteria/genetics/classification/isolation & purification ; *RNA, Ribosomal, 16S/genetics ; *Plant Leaves/microbiology ; *Fungi/genetics/classification/isolation & purification ; Nigeria ; Phylogeny ; }, abstract = {The microbiota of medicinal plants is known to be highly specific and can contribute to medicinal activity. However, the majority of plant species have not yet been studied. Here, we investigated the phyllosphere composition of two common Nigerian medicinal plants, Euphorbia lateriflora and Ficus thonningii, by a polyphasic approach combining analyses of metagenomic DNA and isolates. Microbial abundance estimated via qPCR using specific marker gene primers showed that all leaf samples were densely colonized, with up to 10[8] per gram of leaf, with higher bacterial and fungal abundance than Archaea. While no statistically significant differences between both plant species were found for abundance, amplicon sequencing of 16S rRNA and ITS genes revealed distinct microbiota compositions. Only seven of the 27 genera isolated were represented on both plants, e.g. dominant Sphingomonas spp., and numerous members of Xanthomonadaceae and Enterobacteriaceae. The most dominant fungal families on both plants were Cladosporiaceae, Mycosphaerellaceae and Trichosphaeriaceae. In addition, 225 plant-specific isolates were identified, with Pseudomonadota and Enterobacteriaceae being dominant. Interestingly, 29 isolates are likely species previously unknown, and 14 of these belong to Burkholderiales. However, a high proportion, 56% and 40% of the isolates from E. lateriflora and F. thonningii, respectively, were characterized as various Escherichia coli. The growth of most of the bacterial isolates was not influenced by extractable secondary metabolites of plants. Our results suggest that a specific and diverse microbial community inhabits the leaves of both E. lateriflora and F. thonningii, including potentially new species and producers of antimicrobials.}, } @article {pmid39354003, year = {2024}, author = {Li, Y and Liu, H and Xiao, Y and Jing, H}, title = {Metagenome sequencing and 982 microbial genomes from Kermadec and Diamantina Trenches sediments.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1067}, pmid = {39354003}, issn = {2052-4463}, mesh = {*Geologic Sediments/microbiology ; *Metagenome ; *Archaea/genetics ; *Phylogeny ; *Bacteria/genetics/classification ; Genome, Microbial ; Microbiota ; Genome, Archaeal ; }, abstract = {Deep-sea trenches representing an intriguing ecosystem for exploring the survival and evolutionary strategies of microbial communities in the highly specialized deep-sea environments. Here, 29 metagenomes were obtained from sediment samples collected from Kermadec and Diamantina trenches. Notably, those samples covered a varying sampling depths (from 5321 m to 9415 m) and distinct layers within the sediment itself (from 0~40 cm in Kermadec trench and 0~24 cm in Diamantina trench). Through metagenomic binning process, we reconstructed 982 metagenome assembled genomes (MAGs) with completeness >60% and contamination <5%. Within them, completeness of 351 MAGs were >90%, while an additional 331 were >80%. Phylogenomic analysis for the MAGs revealed nearly all of them were distantly related to known cultivated isolates. The abundant bacterial MAGs affiliated to phyla of Proteobacteria, Planctomycetota, Nitrospirota, Acidobacteriota, Actinobacteriota, and Chlorofexota, while the abundant archaeal phyla affiliated with Nanoarchaeota and Thermoproteota. These results provide a dataset available for further interrogation of diversity, distribution and ecological function of deep-sea microbes existed in the trenches.}, } @article {pmid39352141, year = {2024}, author = {Coclet, C and Camargo, AP and Roux, S}, title = {MVP: a modular viromics pipeline to identify, filter, cluster, annotate, and bin viruses from metagenomes.}, journal = {mSystems}, volume = {9}, number = {10}, pages = {e0088824}, pmid = {39352141}, issn = {2379-5077}, mesh = {*Metagenome/genetics ; *Genome, Viral/genetics ; *Metagenomics/methods ; *Viruses/genetics/classification/isolation & purification ; Software ; Virome/genetics ; Computational Biology/methods ; Molecular Sequence Annotation ; }, abstract = {While numerous computational frameworks and workflows are available for recovering prokaryote and eukaryote genomes from metagenome data, only a limited number of pipelines are designed specifically for viromics analysis. With many viromics tools developed in the last few years alone, it can be challenging for scientists with limited bioinformatics experience to easily recover, evaluate quality, annotate genes, dereplicate, assign taxonomy, and calculate relative abundance and coverage of viral genomes using state-of-the-art methods and standards. Here, we describe Modular Viromics Pipeline (MVP) v.1.0, a user-friendly pipeline written in Python and providing a simple framework to perform standard viromics analyses. MVP combines multiple tools to enable viral genome identification, characterization of genome quality, filtering, clustering, taxonomic and functional annotation, genome binning, and comprehensive summaries of results that can be used for downstream ecological analyses. Overall, MVP provides a standardized and reproducible pipeline for both extensive and robust characterization of viruses from large-scale sequencing data including metagenomes, metatranscriptomes, viromes, and isolate genomes. As a typical use case, we show how the entire MVP pipeline can be applied to a set of 20 metagenomes from wetland sediments using only 10 modules executed via command lines, leading to the identification of 11,656 viral contigs and 8,145 viral operational taxonomic units (vOTUs) displaying a clear beta-diversity pattern. Further, acting as a dynamic wrapper, MVP is designed to continuously incorporate updates and integrate new tools, ensuring its ongoing relevance in the rapidly evolving field of viromics. MVP is available at https://gitlab.com/ccoclet/mvp and as versioned packages in PyPi and Conda.IMPORTANCEThe significance of our work lies in the development of Modular Viromics Pipeline (MVP), an integrated and user-friendly pipeline tailored exclusively for viromics analyses. MVP stands out due to its modular design, which ensures easy installation, execution, and integration of new tools and databases. By combining state-of-the-art tools such as geNomad and CheckV, MVP provides high-quality viral genome recovery and taxonomy and host assignment, and functional annotation, addressing the limitations of existing pipelines. MVP's ability to handle diverse sample types, including environmental, human microbiome, and plant-associated samples, makes it a versatile tool for the broader microbiome research community. By standardizing the analysis process and providing easily interpretable results, MVP enables researchers to perform comprehensive studies of viral communities, significantly advancing our understanding of viral ecology and its impact on various ecosystems.}, } @article {pmid39351905, year = {2024}, author = {Feng, M and Robinson, S and Qi, W and Edwards, A and Stierli, B and van der Heijden, M and Frey, B and Varliero, G}, title = {Microbial genetic potential differs among cryospheric habitats of the Damma glacier.}, journal = {Microbial genomics}, volume = {10}, number = {10}, pages = {}, pmid = {39351905}, issn = {2057-5858}, mesh = {*Ice Cover/microbiology ; *Ecosystem ; Soil Microbiology ; Nitrogen Fixation/genetics ; Microbiota/genetics ; Metagenomics ; Geologic Sediments/microbiology ; Bacteria/genetics/classification/isolation & purification ; Metagenome ; Nitrogen Cycle/genetics ; }, abstract = {Climate warming has led to glacier retreat worldwide. Studies on the taxonomy and functions of glacier microbiomes help us better predict their response to glacier melting. Here, we used shotgun metagenomic sequencing to study the microbial functional potential in different cryospheric habitats, i.e. surface snow, supraglacial and subglacial sediments, subglacial ice, proglacial stream water and recently deglaciated soils. The functional gene structure varied greatly among habitats, especially for snow, which differed significantly from all other habitats. Differential abundance analysis revealed that genes related to stress responses (e.g. chaperones) were enriched in ice habitat, supporting the fact that glaciers are a harsh environment for microbes. The microbial metabolic capabilities related to carbon and nitrogen cycling vary among cryospheric habitats. Genes related to auxiliary activities were overrepresented in the subglacial sediment, suggesting a higher genetic potential for the degradation of recalcitrant carbon (e.g., lignin). As for nitrogen cycling, genes related to nitrogen fixation were more abundant in barren proglacial soils, possibly due to the presence of Cyanobacteriota in this habitat. Our results deepen our understanding of microbial processes in glacial ecosystems, which are vulnerable to ongoing global warming, and they have implications for downstream ecosystems.}, } @article {pmid39351368, year = {2024}, author = {Tolstoganov, I and Chen, Z and Pevzner, P and Korobeynikov, A}, title = {SpLitteR: diploid genome assembly using TELL-Seq linked-reads and assembly graphs.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e18050}, pmid = {39351368}, issn = {2167-8359}, mesh = {*Diploidy ; Animals ; Humans ; Genome, Human/genetics ; Sheep/genetics ; Software ; Sequence Analysis, DNA/methods ; Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing/methods ; Genome/genetics ; }, abstract = {BACKGROUND: Recent advances in long-read sequencing technologies enabled accurate and contiguous de novo assemblies of large genomes and metagenomes. However, even long and accurate high-fidelity (HiFi) reads do not resolve repeats that are longer than the read lengths. This limitation negatively affects the contiguity of diploid genome assemblies since two haplomes share many long identical regions. To generate the telomere-to-telomere assemblies of diploid genomes, biologists now construct their HiFi-based phased assemblies and use additional experimental technologies to transform them into more contiguous diploid assemblies. The barcoded linked-reads, generated using an inexpensive TELL-Seq technology, provide an attractive way to bridge unresolved repeats in phased assemblies of diploid genomes.

RESULTS: We developed the SpLitteR tool for diploid genome assembly using linked-reads and assembly graphs and benchmarked it against state-of-the-art linked-read scaffolders ARKS and SLR-superscaffolder using human HG002 genome and sheep gut microbiome datasets. The benchmark showed that SpLitteR scaffolding results in 1.5-fold increase in NGA50 compared to the baseline LJA assembly and other scaffolders while introducing no additional misassemblies on the human dataset.

CONCLUSION: We developed the SpLitteR tool for assembly graph phasing and scaffolding using barcoded linked-reads. We benchmarked SpLitteR on assembly graphs produced by various long-read assemblers and have demonstrated that TELL-Seq reads facilitate phasing and scaffolding in these graphs. This benchmarking demonstrates that SpLitteR improves upon the state-of-the-art linked-read scaffolders in the accuracy and contiguity metrics. SpLitteR is implemented in C++ as a part of the freely available SPAdes package and is available at https://github.com/ablab/spades/releases/tag/splitter-preprint.}, } @article {pmid39351299, year = {2024}, author = {Meng, Q and Tang, Z and Yang, F and Shi, J and Liu, T and Cheng, S}, title = {Functional analysis of microorganisms and metabolites in the cecum of different sheep populations and their effects on production traits.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1437250}, pmid = {39351299}, issn = {1664-302X}, abstract = {The purpose of this study was to investigate the effects of intestinal microbiota on the growth and production performance of different groups of sheep, focusing on the role of cecal microbiota in regulating intestinal function, enhancing digestion and absorption, and improving feed utilization. The production performance of MG × STH (Mongolia × Small Tailed Han) F1 hybrids and purebred STH (Small Tailed Han) sheep by measuring various factors, including enzyme activities and VFAs (volatile fatty acids), to analyze changes in cecal fermentation parameters across different sheep groups. Metagenomic and metabolomic sequencing combined with bioinformatics to analyze the cecal contents of the two sheep populations. The study findings indicated that the MG × STH F1 hybrids outperformed the purebred STH in terms of body weight, height, oblique body length, and VFAs (p < 0.05). Additionally, the MG × STH F1 higher levels of protease and cellulase in the cecum compared to the purebred sheep (p < 0.05). Metagenomic analysis identified 4,034 different microorganisms at the species level. Five differential organisms (Akkermansiaceae bacterium, Escherichia coli, unclassified p Firmicutes, Streptococcus equinus, Methanobrevibacter millerae) positively regulated sheep performance. Metabolomics identified 822 differential metabolites indoleacetaldehyde, 2-aminobenzoic acid, phenyl-Alanine, enol-phenylpyruvate and n-acetylserotonin were associated with improved performance of sheep. The combined results from the metagenomic and metabolomic studies suggest a positive correlation between specific microbes and metabolites and the performance of the sheep. In conclusion, the MG × STH F1 hybrids demonstrated superior growth performance compared to the purebred STH sheep. The identified microorganisms and metabolites have promising roles in positively regulating sheep growth and can be considered key targets for enhancing sheep performance.}, } @article {pmid39351096, year = {2024}, author = {Yue, Y and Ke, Y and Zheng, J and Wang, Z and Liu, H and Liu, S}, title = {Microbiota-derived tryptophan metabolism and AMPK/mTOR pathway mediate antidepressant-like effect of Shugan Hewei Decoction.}, journal = {Frontiers in pharmacology}, volume = {15}, number = {}, pages = {1466336}, pmid = {39351096}, issn = {1663-9812}, abstract = {INTRODUCTION: Depression is a common psychological disorder, accompanied by a disturbance of the gut microbiota and its metabolites. Recently, microbiota-derived tryptophan metabolism and AMPK/mTOR pathway were found to be strongly linked to the development of depression. Shugan Hewei Decoction (SHD) is a classical anti-depression traditional Chinese medicine formula. Although, we have shown that SHD exerted antidepressant effects via cecal microbiota and cecum NLRP3 inflammasome, the specific mechanism of SHD on metabolism driven by gut microbiota is unknown. In this study, we focus on the tryptophan metabolism and AMPK/mTOR pathway to elucidate the multifaceted mechanisms of SHD.

METHODS: Male rats were established to the chronic unpredictable stress (CUS)/social isolation for 6 weeks, and SHD-L (7.34 g/kg/d), SHD-H (14.68 g/kg/d), Fructooligosaccharide (FOS) (3.15 g/kg/d) were given by intragastric administration once daily during the last 2 weeks. Behavioral experiments were carried out to evaluate the model. The colonic content was taken out for shotgun metagenomic sequencing combined with the untargeted metabolomics, the targeted tryptophan metabolomics. ELISA was used to detect the levels of zonula occludens 1 (ZO-1), Occludin in colon, as well as lipopolysaccharide (LPS), diamine oxidase (DAO), D-lactate (DLA) in serum. The expressions of mRNA and proteins of adenosine monophosphate-activated protein kinase (AMPK)/mammalian target of rapamycin (mTOR) pathway of autophagy were examined using RT-qPCR and Western blot in colon.

RESULTS: SHD modulated gut microbiota function and biological pathways, which were related to tryptophan metabolism. In addition, SHD could regulate microbiota-derived tryptophan production (such as reduction of 3-HK, 3-HAA etc., increment of ILA, IAA etc.), which metabolites belong to kynurenine (KYN) and indole derivatives. Further, SHD reduced intestinal permeability and enhanced the intestinal barrier function. Moreover, SHD could upregulate the levels of AMPK, microtubule associated protein light chain 3 (LC3), autophagy related protein 5 (ATG5) and Beclin1, downregulate the levels of mTOR, p62, promoted autophagy in colon. Spearman's analysis illustrated the close correlation between tryptophan metabolites and intestinal barrier, AMPK/mTOR pathway.

CONCLUSION: SHD may exert antidepressant-like effects by regulating microbiota-derived tryptophan metabolism, and triggering the AMPK/mTOR pathway of autophagy, enhancing the intestinal barrier function.}, } @article {pmid39350160, year = {2024}, author = {Wei, M and Mao, S and Li, S and Gu, K and Gu, D and Bai, S and Lu, X and Li, M}, title = {Comparing the diagnostic value of targeted with metagenomic next-generation sequencing in immunocompromised patients with lower respiratory tract infection.}, journal = {Annals of clinical microbiology and antimicrobials}, volume = {23}, number = {1}, pages = {88}, pmid = {39350160}, issn = {1476-0711}, support = {23YF1431300//Yangfan Project of Science and Technology Commission of Shanghai Municipality/ ; 2022YFC2603800//National Key Research and Development Program/ ; GWVI-11.1-1//3-Year Action Plan for Strengthening Public Health System in Shanghai/ ; }, mesh = {Humans ; *Immunocompromised Host ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Female ; *Metagenomics/methods ; *Respiratory Tract Infections/diagnosis/microbiology ; Middle Aged ; *Bronchoalveolar Lavage Fluid/microbiology ; Aged ; Adult ; Sensitivity and Specificity ; Bacteria/genetics/isolation & purification/classification ; Young Adult ; }, abstract = {BACKGROUND: Accurate identification of the etiology of lower respiratory tract infections (LRTI) is crucial, particularly for immunocompromised patients with more complex etiologies. The advent of next-generation sequencing (NGS) has enhanced the effectiveness of pathogen detection. However, assessments of the clinical diagnostic value of targeted NGS (tNGS) in immunocompromised patients with LRTI are limited.

METHODS: To evaluate the diagnostic value of tNGS in immunocompromised patients with LRTI, a total of 88 patients, of whom 54 were immunocompromised, were enrolled. These patients underwent tNGS testing of bronchoalveolar lavage fluid (BALF). Results from both metagenomic next-generation sequencing (mNGS) and conventional microbiological tests (CMT) were also available for all participants. The performance of tNGS was assessed by comparing its findings against mNGS, CMT, and the clinical composite diagnosis.

RESULTS: In the cohort of 88 patients, tNGS showed comparable diagnostic value to mNGS and was significantly superior to CMT. Compared to CMT and composite reference standard, tNGS showed sensitivity of 94.55% and 90.48%, respectively. In immunocompromised patients, despite a more diverse pathogen variety, tNGS maintained similar sensitivity to mNGS and outperformed CMT. tNGS positively influenced etiologic diagnosis and antibiotic decision-making in 72.72% of cases, leading to a change in antibiotic regimen in 17.05% of cases. We also compared the detection of microbial nucleic acids by tNGS with mNGS and found that tNGS could identify 87.99% of the microbial nucleic acids identified by mNGS.

CONCLUSION: In summary, our study demonstrated that tNGS offers promising clinical diagnostic accuracy in immunocompromised patients, as evidenced by its favorable comparison with CMT, the composite reference standard, and mNGS.}, } @article {pmid39350124, year = {2024}, author = {Wang, Y and He, X and Liu, S and Li, X}, title = {Pneumocystis jirovecii and Nocardia pneumonia in a middle-aged male with Nephrotic syndrome: a case report and literature review.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {1071}, pmid = {39350124}, issn = {1471-2334}, mesh = {Humans ; Male ; Middle Aged ; *Pneumocystis carinii/isolation & purification/genetics ; *Nephrotic Syndrome/complications ; *Pneumonia, Pneumocystis/drug therapy/diagnosis/microbiology/complications ; *Nocardia/isolation & purification/genetics ; *Nocardia Infections/drug therapy/microbiology/diagnosis/complications ; Pneumonia, Bacterial/microbiology/complications/drug therapy/diagnosis ; }, abstract = {INTRODUCTION: Nephrotic syndrome (NS) is a common chronic kidney disease that is often accompanied by a state of immunodeficiency. Immunosuppression increases the risk of infections, with Pneumocystis jirovecii and Nocardia brasiliensis being two opportunistic pathogens that can cause severe infections in patients with compromised immune function. This study presents a case of a middle-aged male patient with NS concurrently infected with Pneumocystis jirovecii and Nocardia brasiliensis. It aims to synthesize the pertinent diagnostic approaches and treatment experiences. Notably, there have been no reported cases of NS occurring simultaneously with both Pneumocystis jirovecii pneumonia and Nocardia pneumonia.

CASE PRESENTATION: A 58-year-old male farmer presented to the hospital with a one-week history of persistent fever, cough, and sputum production. His maximum body temperature was recorded at 39 °C, and he produced yellow viscous sputum. This patient had a one-year history of NS, managed with long-term oral corticosteroid and cyclophosphamide therapy. Admission chest computed tomography displayed interstitial changes in both lungs. After failing to detect any pathogens through routine etiological tests, we successfully identified Nocardia brasiliensis, Pneumocystis jirovecii, and Lodderomyces elongisporus using bronchoscopy-guided sputum samples through metagenomic next-generation sequencing (mNGS) technology. Subsequently, we initiated a combined treatment regimen for the patient using trimethoprim-sulfamethoxazole, meropenem, and moxifloxacin, which yielded remarkable therapeutic outcomes.

CONCLUSION: The adoption and promotion of mNGS technologies have significantly resolved the difficulty in early pathogen detection, guiding clinicians from empirical to genomic diagnosis, achieving prevention before treatment, and thereby enhancing patient survival rates.}, } @article {pmid39349736, year = {2024}, author = {Karačić, S and Suarez, C and Hagelia, P and Persson, F and Modin, O and Martins, PD and Wilén, BM}, title = {Microbial acidification by N, S, Fe and Mn oxidation as a key mechanism for deterioration of subsea tunnel sprayed concrete.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {22742}, pmid = {39349736}, issn = {2045-2322}, mesh = {*Oxidation-Reduction ; *Manganese/metabolism ; *Iron/metabolism ; *Construction Materials/microbiology ; Corrosion ; *Biofilms/growth & development ; Nitrogen/metabolism ; Sulfur/metabolism ; Steel/chemistry ; Bacteria/metabolism/genetics ; Hydrogen-Ion Concentration ; }, abstract = {The deterioration of fibre-reinforced sprayed concrete was studied in the Oslofjord subsea tunnel (Norway). At sites with intrusion of saline groundwater resulting in biofilm growth, the concrete exhibited significant concrete deterioration and steel fibre corrosion. Using amplicon sequencing and shotgun metagenomics, the microbial taxa and surveyed potential microbial mechanisms of concrete degradation at two sites over five years were identified. The concrete beneath the biofilm was investigated with polarised light microscopy, scanning electron microscopy and X-ray diffraction. The oxic environment in the tunnel favoured aerobic oxidation processes in nitrogen, sulfur and metal biogeochemical cycling as evidenced by large abundances of metagenome-assembled genomes (MAGs) with potential for oxidation of nitrogen, sulfur, manganese and iron, observed mild acidification of the concrete, and the presence of manganese- and iron oxides. These results suggest that autotrophic microbial populations involved in the cycling of several elements contributed to the corrosion of steel fibres and acidification causing concrete deterioration.}, } @article {pmid39349606, year = {2024}, author = {Guo, X and Lin, S and Zhang, X and Li, M and Wang, Z and Peng, Y and He, X and Liu, J}, title = {Integrated metabolomic and microbiome analysis identifies Cupriavidus metallidurans as a potential therapeutic target for β-thalassemia.}, journal = {Annals of hematology}, volume = {103}, number = {12}, pages = {5169-5179}, pmid = {39349606}, issn = {1432-0584}, support = {21B0827//The Hunan Provincial Department of Education/ ; 202201065317//The Hunan Provincial Health Commission/ ; kq2004076//The Changsha Science and Technology Bureau/ ; 81920108004//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *beta-Thalassemia/metabolism/microbiology/therapy ; Mice ; *Gastrointestinal Microbiome ; *Metabolomics/methods ; *Cupriavidus/metabolism ; Disease Models, Animal ; Bilirubin/metabolism/blood ; Mice, Inbred C57BL ; Metabolome ; Feces/microbiology ; }, abstract = {β-thalassemia(β-TH) is an inherited hemoglobin disorder marked by ineffective erythropoiesis, anemia, splenomegaly, and systemic iron overload, predominantly affecting developing countries in tropical and subtropical regions. Despite extensive research on its pathogenesis, the interactions between gut microbiota and metabolites in β-TH remain poorly understood. This study compares fecal metabolomics and metagenomics between wildtype (Wt) and heterozygous Th3/+ mice, a model for non-transfusion-dependent β-thalassemia intermedia. Our results show increased intestinal bilirubin metabolism, with significant elevations in metabolites such as biliverdin, bilirubin, and stercobilin. Metagenomic analysis revealed notable differences in bacterial composition between Th3/+ and Wt mice. Specifically, Cupriavidus metallidurans was identified as a key bacterium that mitigates anemia by reducing liver and spleen iron deposition. This is the first study to ameliorate anemia in mice by altering gut microbiota, presenting new strategies for β-TH management.}, } @article {pmid39349486, year = {2024}, author = {Sun, W and Zhang, Y and Guo, R and Sha, S and Chen, C and Ullah, H and Zhang, Y and Ma, J and You, W and Meng, J and Lv, Q and Cheng, L and Fan, S and Li, R and Mu, X and Li, S and Yan, Q}, title = {A population-scale analysis of 36 gut microbiome studies reveals universal species signatures for common diseases.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {96}, pmid = {39349486}, issn = {2055-5008}, support = {5050071720001//Beijing University of Chinese Medicine (BUCM)/ ; 2180072120049//Beijing University of Chinese Medicine (BUCM)/ ; 81503455//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Feces/microbiology ; Case-Control Studies ; *Bacteria/classification/genetics/isolation & purification ; Metagenome ; Metagenomics/methods ; China ; Biodiversity ; }, abstract = {The gut microbiome has been implicated in various human diseases, though findings across studies have shown considerable variability. In this study, we reanalyzed 6314 publicly available fecal metagenomes from 36 case-control studies on different diseases to investigate microbial diversity and disease-shared signatures. Using a unified analysis pipeline, we observed reduced microbial diversity in many diseases, while some exhibited increased diversity. Significant alterations in microbial communities were detected across most diseases. A meta-analysis identified 277 disease-associated gut species, including numerous opportunistic pathogens enriched in patients and a depletion of beneficial microbes. A random forest classifier based on these signatures achieved high accuracy in distinguishing diseased individuals from controls (AUC = 0.776) and high-risk patients from controls (AUC = 0.825), and it also performed well in external cohorts. These results offer insights into the gut microbiome's role in common diseases in the Chinese population and will guide personalized disease management strategies.}, } @article {pmid39347544, year = {2024}, author = {Yergaliyev, T and Künzel, S and Hanauska, A and Rees, A and Wild, KJ and Pétursdóttir, ÁH and Gunnlaugsdóttir, H and Reynolds, CK and Humphries, DJ and Rodehutscord, M and Camarinha-Silva, A}, title = {The effect of Asparagopsis taxiformis, Ascophyllum nodosum, and Fucus vesiculosus on ruminal methanogenesis and metagenomic functional profiles in vitro.}, journal = {Microbiology spectrum}, volume = {12}, number = {11}, pages = {e0394223}, pmid = {39347544}, issn = {2165-0497}, support = {19084,19084-20//EC | H2020 | H2020 European Institute of Innovation and Technology (EIT)/ ; }, mesh = {*Methane/metabolism ; Animals ; *Seaweed/microbiology ; *Rumen/microbiology ; *Ascophyllum/metabolism ; *Fucus/microbiology/metabolism ; *Bacteria/classification/genetics/metabolism/drug effects/isolation & purification ; Metagenomics ; Scotland ; Archaea/classification/metabolism/genetics/drug effects/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Portugal ; Ruminants/microbiology ; Microbiota/drug effects ; Animal Feed/analysis ; Gastrointestinal Microbiome/drug effects ; Rhodophyta ; }, abstract = {UNLABELLED: The ruminant-microorganism symbiosis is unique by providing high-quality food from fibrous materials but also contributes to the production of one of the most potent greenhouse gases-methane. Mitigating methanogenesis in ruminants has been a focus of interest in the past decades. One of the promising strategies to combat methane production is the use of feed supplements, such as seaweeds, that might mitigate methanogenesis via microbiome modulation and direct chemical inhibition. We conducted in vitro investigations of the effect of three seaweeds (Ascophyllum nodosum, Asparagopsis taxiformis, and Fucus vesiculosus) harvested at different locations (Iceland, Scotland, and Portugal) on methane production. We applied metataxonomics (16S rRNA gene amplicons) and metagenomics (shotgun) methods to uncover the interplay between the microbiome's taxonomical and functional states, methanogenesis rates, and seaweed supplementations. Methane concentration was reduced by A. nodosum and F. vesiculosus, both harvested in Scotland and A. taxiformis, with the greatest effect of the latter. A. taxiformis acted through the reduction of archaea-to-bacteria ratios but not eukaryotes-to-bacteria. Moreover, A. taxiformis application was accompanied by shifts in both taxonomic and functional profiles of the microbial communities, decreasing not only archaeal ratios but also abundances of methanogenesis-associated functions. Methanobrevibacter "SGMT" (M. smithii, M. gottschalkii, M. millerae or M. thaueri; high methane yield) to "RO" (M. ruminantium and M. olleyae; low methane yield) clades ratios were also decreased, indicating that A. taxiformis application favored Methanobrevibacter species that produce less methane. Most of the functions directly involved in methanogenesis were less abundant, while the abundances of the small subset of functions that participate in methane assimilation were increased.

IMPORTANCE: The application of A. taxiformis significantly reduced methane production in vitro. We showed that this reduction was linked to changes in microbial function profiles, the decline in the overall archaeal community counts, and shifts in ratios of Methanobrevibacter "SGMT" and "RO" clades. A. nodosum and F. vesiculosus, obtained from Scotland, also decreased methane concentration in the total gas, while the same seaweed species from Iceland did not.}, } @article {pmid39347539, year = {2024}, author = {Yuan, Y and Hu, H and Sun, Z and Wang, W and Wang, Z and Zheng, M and Xing, Y and Zhang, W and Wang, M and Lu, X and Li, Y and Liang, C and Lin, Z and Xie, C and Li, J and Mao, T}, title = {Combining Metagenomics, Network Pharmacology and RNA-Seq Strategies to Reveal the Therapeutic Effects and Mechanisms of Qingchang Wenzhong Decoction on Inflammatory Bowel Disease in Mice.}, journal = {Drug design, development and therapy}, volume = {18}, number = {}, pages = {4273-4289}, pmid = {39347539}, issn = {1177-8881}, mesh = {Animals ; Mice ; *Drugs, Chinese Herbal/pharmacology/chemistry ; *Inflammatory Bowel Diseases/drug therapy ; *Metagenomics ; *Gastrointestinal Microbiome/drug effects ; *Network Pharmacology ; *Dextran Sulfate ; *Mice, Inbred C57BL ; Disease Models, Animal ; Male ; RNA-Seq ; }, abstract = {BACKGROUND: Inflammatory bowel disease (IBD) is a chronic and recurrent inflammatory disease that lacks effective treatments. Qingchang Wenzhong Decoction (QCWZD) is a clinically effective herbal prescription that has been proven to attenuate intestinal inflammation in IBD. However, its molecular mechanism of action has not been clearly elucidated.

PURPOSE: We aimed to probe the mechanism of QCWZD for the treatment of IBD.

METHODS: The dextran sulfate sodium (DSS)-induced mouse model of IBD was used to identify the molecular targets involved in the mechanism of action of QCWZD. Metagenomics sequencing was utilized to analyze the differences in gut microbiota and the functional consequences of these changes. Network pharmacology combined with RNA sequencing (RNA-seq) were employed to predict the molecular targets and mechanism of action of QCWZD, and were validated through in vivo experiments.

RESULTS: Our results demonstrated that QCWZD treatment alleviated intestinal inflammation and accelerated intestinal mucosal healing that involved restoration of microbial homeostasis. This hypothesis was supported by the results of bacterial metagenomics sequencing that showed attenuation of gut dysbiosis by QCWZD treatment, especially the depletion of the pathogenic bacterial genus Bacteroides, while increasing the beneficial microorganism Akkermansia muciniphila that led to altered bacterial gene functions, such as metabolic regulation. Network pharmacology and RNA-seq analyses showed that Th17 cell differentiation plays an important role in QCWZD-based treatment of IBD. This was confirmed by in vivo experiments showing a marked decrease in the percentage of CD3[+]CD4[+]IL-17[+] (Th17) cells. Furthermore, our results also showed that the key factors associated with Th17 cell differentiation (IL-17, NF-κB, TNF-α and IL-6) in the colon were significantly reduced in QCWZD-treated colitis mice.

CONCLUSION: QCWZD exerted beneficial effects in the treatment of IBD by modulating microbial homeostasis while inhibiting Th17 cell differentiation and its associated pathways, providing a novel and promising therapeutic strategy for the treatment of IBD.}, } @article {pmid39346682, year = {2024}, author = {Child, HT and Wierzbicki, L and Joslin, GR and Tennant, RK}, title = {Comparative evaluation of soil DNA extraction kits for long read metagenomic sequencing.}, journal = {Access microbiology}, volume = {6}, number = {9}, pages = {}, pmid = {39346682}, issn = {2516-8290}, abstract = {Metagenomics has been transformative in our understanding of the diversity and function of soil microbial communities. Applying long read sequencing to whole genome shotgun metagenomics has the potential to revolutionise soil microbial ecology through improved taxonomic classification, functional characterisation and metagenome assembly. However, optimisation of robust methods for long read metagenomics of environmental samples remains undeveloped. In this study, Oxford Nanopore sequencing using samples from five commercially available soil DNA extraction kits was compared across four soil types, in order to optimise read length and reproducibility for comparative long read soil metagenomics. Average extracted DNA lengths varied considerably between kits, but longer DNA fragments did not translate consistently into read lengths. Highly variable decreases in the length of resulting reads from some kits were associated with poor classification rate and low reproducibility in microbial communities identified between technical repeats. Replicate samples from other kits showed more consistent conversion of extracted DNA fragment size into read length and resulted in more congruous microbial community representation. Furthermore, extraction kits showed significant differences in the community representation and structure they identified across all soil types. Overall, the QIAGEN DNeasy PowerSoil Pro Kit displayed the best suitability for reproducible long-read WGS metagenomic sequencing, although further optimisation of DNA purification and library preparation may enable translation of higher molecular weight DNA from other kits into longer read lengths. These findings provide a novel insight into the importance of optimising DNA extraction for achieving replicable results from long read metagenomic sequencing of environmental samples.}, } @article {pmid39346055, year = {2024}, author = {Knobloch, S and Salimi, F and Buaya, A and Ploch, S and Thines, M}, title = {RAPiD: a rapid and accurate plant pathogen identification pipeline for on-site nanopore sequencing.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e17893}, pmid = {39346055}, issn = {2167-8359}, mesh = {*Nanopore Sequencing/methods ; Metagenomics/methods ; Plant Diseases/microbiology ; Bacteria/genetics/isolation & purification/classification ; Sequence Analysis, DNA/methods ; Fungi/genetics/isolation & purification/classification ; Plants/microbiology ; Computational Biology/methods ; }, abstract = {Nanopore sequencing technology has enabled the rapid, on-site taxonomic identification of samples from anything and anywhere. However, sequencing errors, inadequate databases, as well as the need for bioinformatic expertise and powerful computing resources, have hampered the widespread use of the technology for pathogen identification in the agricultural sector. Here we present RAPiD, a lightweight and accurate real-time taxonomic profiling pipeline. Compared to other metagenomic profilers, RAPiD had a higher classification precision achieved through the use of a curated, non-redundant database of common agricultural pathogens and extensive quality filtering of alignments. On a fungal, bacterial and mixed mock community RAPiD was the only pipeline to detect all members of the communities. We also present a protocol for in-field sample processing enabling pathogen identification from plant sample to sequence within 3 h using low-cost equipment. With sequencing costs continuing to decrease and more high-quality reference genomes becoming available, nanopore sequencing provides a viable method for rapid and accurate pathogen identification in the field. A web implementation of the RAPiD pipeline for real-time analysis is available at https://agrifuture.senckenberg.de.}, } @article {pmid39346007, year = {2024}, author = {Eisenhofer, R and Alberdi, A and Woodcroft, BJ}, title = {Quantifying microbial DNA in metagenomes improves microbial trait estimation.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae111}, pmid = {39346007}, issn = {2730-6151}, abstract = {Shotgun metagenomics is a powerful tool for studying the genomic traits of microbial community members, such as genome size, gene content, etc. While such traits can be used to better understand the ecology and evolution of microbial communities, the accuracy of their estimations can be critically influenced by both known and unknown factors. One factor that can bias trait estimations is the proportion of eukaryotic and viral DNA in a metagenome, as some bioinformatic tools assume that all DNA reads in a metagenome are bacterial or archaeal. Here, we add to a recent debate about the influence of eukaryotic DNA in the estimation of average genome size from a global soil sample dataset using a new bioinformatic tool. Contrary to what was assumed, our reanalysis of this dataset revealed that soil samples can contain a substantial proportion of non-microbial DNA, which severely inflated the original estimates of average genome size. Correcting for this bias significantly improves the statistical support for the negative relationship between average bacterial genome size and soil pH. These results highlight that metagenomes can contain large quantities of non-microbial DNA and that new methods that correct for this can improve microbial trait estimation.}, } @article {pmid39345755, year = {2024}, author = {Deng, Y and Mao, J and Choi, J and Lê Cao, KA}, title = {StableMate: a statistical method to select stable predictors in omics data.}, journal = {NAR genomics and bioinformatics}, volume = {6}, number = {4}, pages = {lqae130}, pmid = {39345755}, issn = {2631-9268}, abstract = {Identifying statistical associations between biological variables is crucial to understanding molecular mechanisms. Most association studies are based on correlation or linear regression analyses, but the identified associations often lack reproducibility and interpretability due to the complexity and variability of omics datasets, making it difficult to translate associations into meaningful biological hypotheses. We developed StableMate, a regression framework, to address these challenges through a process of variable selection across heterogeneous datasets. Given datasets from different environments, such as experimental batches, StableMate selects environment-agnostic (stable) and environment-specific predictors in predicting the response of interest. Stable predictors represent robust functional dependencies with the response, and can be used to build regression models that make generalizable predictions in unseen environments. We applied StableMate to (i) RNA sequencing data of breast cancer to discover genes that consistently predict estrogen receptor expression across disease status; (ii) metagenomics data to identify microbial signatures that show persistent association with colon cancer across study cohorts; and (iii) single-cell RNA sequencing data of glioblastoma to discern signature genes associated with the development of pro-tumour microglia regardless of cell location. Our case studies demonstrate that StableMate is adaptable to regression and classification analyses and achieves comprehensive characterization of biological systems for different omics data types.}, } @article {pmid39345650, year = {2024}, author = {Bhamidipati, SV and Surathu, A and Chao, H and Agustinho, DP and Xiang, Q and Kottapalli, K and Santhanam, A and Momin, Z and Walker, K and Menon, VK and Weissenberger, G and Emerick, N and Mahjabeen, F and Meng, Q and Hu, J and Sucgang, R and Henke, D and Sedlazeck, FJ and Khan, Z and Metcalf, GA and Avadhanula, V and Piedra, PA and Ramani, S and Atmar, RL and Estes, MK and Petrosino, JF and Gibbs, RA and Muzny, DM and Cregeen, SJ and Doddapaneni, H}, title = {Complete Genomic Characterization of Global Pathogens, Respiratory Syncytial Virus (RSV), and Human Norovirus (HuNoV) Using Probe-based Capture Enrichment.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39345650}, issn = {2692-8205}, support = {U19 AI144297/AI/NIAID NIH HHS/United States ; }, abstract = {Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infections in children worldwide, while human noroviruses (HuNoV) are a leading cause of epidemic and sporadic acute gastroenteritis. Generating full-length genome sequences for these viruses is crucial for understanding viral diversity and tracking emerging variants. However, obtaining high-quality sequencing data is often challenging due to viral strain variability, quality, and low titers. Here, we present a set of comprehensive oligonucleotide probe sets designed from 1,570 RSV and 1,376 HuNoV isolate sequences in GenBank. Using these probe sets and a capture enrichment sequencing workflow, 85 RSV positive nasal swab samples and 55 (49 stool and six human intestinal enteroids) HuNoV positive samples encompassing major subtypes and genotypes were characterized. The Ct values of these samples ranged from 17.0-29.9 for RSV, and from 20.2-34.8 for HuNoV, with some HuNoV having below the detection limit. The mean percentage of post-processing reads mapped to viral genomes was 85.1% for RSV and 40.8% for HuNoV post-capture, compared to 0.08% and 1.15% in pre-capture libraries, respectively. Full-length genomes were>99% complete in all RSV positive samples and >96% complete in 47/55 HuNoV positive samples-a significant improvement over genome recovery from pre-capture libraries. RSV transcriptome (subgenomic mRNAs) sequences were also characterized from this data. Probe-based capture enrichment offers a comprehensive approach for RSV and HuNoV genome sequencing and monitoring emerging variants.}, } @article {pmid39345370, year = {2024}, author = {Leon, F and Espinoza-Esparza, JM and Deng, V and Coyle, MC and Espinoza, S and Booth, DS}, title = {Cell differentiation controls iron assimilation in a choanoflagellate.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39345370}, issn = {2692-8205}, support = {R35 GM147404/GM/NIGMS NIH HHS/United States ; S10 OD018174/OD/NIH HHS/United States ; T32 GM139786/GM/NIGMS NIH HHS/United States ; }, abstract = {Marine microeukaryotes have evolved diverse cellular features that link their life histories to surrounding environments. How those dynamic life histories intersect with the ecological functions of microeukaryotes remains a frontier to understand their roles in essential biogeochemical cycles[1,2]. Choanoflagellates, phagotrophs that cycle nutrients through filter feeding, provide models to explore this intersection, for many choanoflagellate species transition between life history stages by differentiating into distinct cell types[3-6]. Here we report that cell differentiation in the marine choanoflagellate Salpingoeca rosetta endows one of its cell types with the ability to utilize insoluble ferric colloids for improved growth through the expression of a cytochrome b561 iron reductase (cytb561a). This gene is an ortholog of the mammalian duodenal cytochrome b561 (DCYTB) that reduces ferric cations prior to their uptake in gut epithelia[7] and is part of an iron utilization toolkit that choanoflagellates and their closest living relatives, the animals, inherited from a last common eukaryotic ancestor. In a database of oceanic metagenomes[8,9], the abundance of cytb561a transcripts from choanoflagellates positively correlates with upwellings, which are a major source of ferric colloids in marine environments[10]. As this predominant form of iron[11,12] is largely inaccessible to cell-walled microbes[13,14], choanoflagellates and other phagotrophic eukaryotes may serve critical ecological roles by first acquiring ferric colloids through phagocytosis and then cycling this essential nutrient through iron utilization pathways[13-15]. These findings provide insight into the ecological roles choanoflagellates perform and inform reconstructions of early animal evolution where functionally distinct cell types became an integrated whole at the origin of animal multicellularity[16-22].}, } @article {pmid39345270, year = {2023}, author = {Hanssen, F and Gabernet, G and Bäuerle, F and Stöcker, B and Wiegand, F and Smith, NH and Mertes, C and Neogi, AG and Brandhoff, L and Ossowski, A and Altmueller, J and Becker, K and Petzold, A and Sturm, M and Stöcker, T and Sivalingam, S and Brand, F and Schmidt, A and Buness, A and Probst, AJ and Motameny, S and Köster, J}, title = {NCBench: providing an open, reproducible, transparent, adaptable, and continuous benchmark approach for DNA-sequencing-based variant calling.}, journal = {F1000Research}, volume = {12}, number = {}, pages = {1125}, pmid = {39345270}, issn = {2046-1402}, mesh = {Humans ; *Benchmarking/methods ; *High-Throughput Nucleotide Sequencing/methods ; *Sequence Analysis, DNA/methods/standards ; Software ; Genome, Human ; Genetic Variation ; Reproducibility of Results ; Genomics/methods ; }, abstract = {We present the results of the human genomic small variant calling benchmarking initiative of the German Research Foundation (DFG) funded Next Generation Sequencing Competence Network (NGS-CN) and the German Human Genome-Phenome Archive (GHGA). In this effort, we developed NCBench, a continuous benchmarking platform for the evaluation of small genomic variant callsets in terms of recall, precision, and false positive/negative error patterns. NCBench is implemented as a continuously re-evaluated open-source repository. We show that it is possible to entirely rely on public free infrastructure (Github, Github Actions, Zenodo) in combination with established open-source tools. NCBench is agnostic of the used dataset and can evaluate an arbitrary number of given callsets, while reporting the results in a visual and interactive way. We used NCBench to evaluate over 40 callsets generated by various variant calling pipelines available in the participating groups that were run on three exome datasets from different enrichment kits and at different coverages. While all pipelines achieve high overall quality, subtle systematic differences between callers and datasets exist and are made apparent by NCBench.These insights are useful to improve existing pipelines and develop new workflows. NCBench is meant to be open for the contribution of any given callset. Most importantly, for authors, it will enable the omission of repeated re-implementation of paper-specific variant calling benchmarks for the publication of new tools or pipelines, while readers will benefit from being able to (continuously) observe the performance of tools and pipelines at the time of reading instead of at the time of writing.}, } @article {pmid39345197, year = {2024}, author = {Wei, Y and Zhang, Y and Zhuang, Y and Tang, Y and Nie, H and Haung, Y and Liu, T and Yang, W and Yan, F and Zhu, Y}, title = {Veillonella parvula acts as a pathobiont promoting the biofilm virulence and cariogenicity of Streptococcus mutans in adult severe caries.}, journal = {Microbiology spectrum}, volume = {12}, number = {11}, pages = {e0431823}, pmid = {39345197}, issn = {2165-0497}, support = {82201055//MOST | National Natural Science Foundation of China (NSFC)/ ; 0223A205//2015 cultivation program for reserve talents for academic leaders of Nanjing Stomatological Hospital/ ; 2022-R-203 0222C116//3456 cultivation program for junior talents of Nanjing Stomatological Hospital/ ; ZKX23053//Nanjing Medical Science and Technique Development Foundation/ ; }, mesh = {*Biofilms/growth & development ; *Streptococcus mutans/genetics/pathogenicity/physiology ; *Dental Caries/microbiology ; *Dental Plaque/microbiology ; Humans ; Virulence ; Animals ; Adult ; *Veillonella/genetics/physiology/pathogenicity ; Rats ; Male ; Mice ; Female ; Microbiota ; }, abstract = {Adult severe caries (ASC) brings severe oral dysfunction and treatment difficulties to patients, and yet no clear pathogenic mechanism for it has been found. This study is focused on the composition of dental plaque microbiome profiles in order to identify disease-relevant species and to investigate into their interactions with the S. mutans. Samples of dental plaque were collected for metagenomic analysis. The acidification, aciduricity, oxidative stress tolerance, and gtf (glucosyltransferase) gene expression of S. mutans cocultured with V. parvula which was identified as ASC-related dominant bacterium. The biofilm formation and extracellular exopolysaccharide (EPS) synthesis of dual-strain were analyzed with scanning electron microscopy (SEM), crystal violet (CV) staining, live/dead bacterial staining, and confocal laser scanning microscopy (CLSM). Furthermore, rodent model experiments were performed to validate the in vivo cariogenicity of the dual-species biofilm. The most significantly abundant taxon found associated with ASC was V. parvula. In vitro experiments found that V. parvula can effectively promote S. mutans mature biofilm formation with enhanced acid resistance, hydrogen peroxide detoxicity, and biofilm virulence. Rodent model experiments revealed that V. parvula was incapable of causing disease on its own, but it significantly heightened the biofilm virulence of S. mutans when being co-infected and augmented the progression, quantity, and severity of dental caries. Our findings demonstrated that V. parvula may act as a synergistic pathobiont to modulate the metabolic activity, spatial structure, and pathogenicity of biofilms of S. mutans in the context of ASC.IMPORTANCEAdult severe caries (ASC), as a special type of acute caries, is rarely reported and its worthiness of further study is still in dispute. Yet studies on the etiology of severe caries in adults have not found a clear pathogenic mechanism for it. Knowledge of the oral microbiota is important for the treatment of dental caries. We discovered that the interaction between V. parvula and S. mutans augments the severity of dental caries in vivo, suggesting V. parvula may act as a synergistic pathobiont exacerbating biofilm virulence of S. mutans in ASC. Our findings may improve the understanding of ASC pathogenesis and are likely to provide a basis for planning appropriate therapeutic strategies.}, } @article {pmid39345178, year = {2024}, author = {Hernandez-Velazquez, D and Vasquez, MK and Petre, R and Kyndt, JA}, title = {Genome sequences of Mycobacterium sp. Elmwood and accompanying phage, isolated from a public swimming pool in Nebraska.}, journal = {Microbiology resource announcements}, volume = {13}, number = {11}, pages = {e0089624}, pmid = {39345178}, issn = {2576-098X}, abstract = {Genome sequencing of a non-tuberculosis Mycobacterium species, isolated from a public pool, shows that the genome contains several genes for antibiotic resistance and anti-phage defense, which are absent from other related Mycobacteria. Metagenomic binning also provided the genome of the accompanying phage, which is distinct from other mycobacterial phages.}, } @article {pmid39344648, year = {2024}, author = {Taylor, KD and Wood, AC and Rotter, JI and Guo, X and Herrington, DM and Johnson, WC and Post, WS and Tracy, RP and Rich, SS and Malik, S}, title = {Metagenomic Study of the MESA: Detection of Gemella Morbillorum and Association With Coronary Heart Disease.}, journal = {Journal of the American Heart Association}, volume = {13}, number = {19}, pages = {e035693}, pmid = {39344648}, issn = {2047-9980}, support = {75N92020D00005/HL/NHLBI NIH HHS/United States ; U54 HG003067/HG/NHGRI NIH HHS/United States ; R01 HL071259/HL/NHLBI NIH HHS/United States ; OT3 HL142481/HL/NHLBI NIH HHS/United States ; R01 HL105756/HL/NHLBI NIH HHS/United States ; HHSN268201800001C/HL/NHLBI NIH HHS/United States ; 75N92020D00004/HL/NHLBI NIH HHS/United States ; OT3 HL142479/HL/NHLBI NIH HHS/United States ; 75N92020D00006/HL/NHLBI NIH HHS/United States ; UL1 TR001881/TR/NCATS NIH HHS/United States ; OT3 HL142478/HL/NHLBI NIH HHS/United States ; UL1 RR033176/RR/NCRR NIH HHS/United States ; 75N92020D00002/HL/NHLBI NIH HHS/United States ; HHSN268201500003C/HL/NHLBI NIH HHS/United States ; OT3 HL147154/HL/NHLBI NIH HHS/United States ; 75N92020D00003/HL/NHLBI NIH HHS/United States ; P30 DK063491/DK/NIDDK NIH HHS/United States ; R01 HL146860/HL/NHLBI NIH HHS/United States ; OT3 HL142480/HL/NHLBI NIH HHS/United States ; 75N92020D00007/HL/NHLBI NIH HHS/United States ; HHSN268201500014C/HL/NHLBI NIH HHS/United States ; HHSN268201500003I/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; Male ; Female ; Aged ; *Metagenomics/methods ; Middle Aged ; *Coronary Disease/microbiology/genetics/diagnosis ; United States/epidemiology ; Aged, 80 and over ; Risk Factors ; Gram-Positive Bacterial Infections/microbiology/diagnosis/epidemiology ; Incidence ; }, abstract = {BACKGROUND: Inflammation is a feature of coronary heart disease (CHD), but the role of proinflammatory microbial infection in CHD remains understudied.

METHODS AND RESULTS: CHD was defined in the MESA (Multi-Ethnic Study of Atherosclerosis) as myocardial infarction (251 participants), resuscitated arrest (2 participants), and CHD death (80 participants). We analyzed sequencing reads from 4421 MESA participants in the National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine program using the PathSeq workflow of the Genome Analysis Tool Kit and a 65-gigabase microbial reference. Paired reads aligning to 840 microbes were detected in >1% of participants. The association of the presence of microbe reads with incident CHD (follow-up, ~18 years) was examined. First, important variables were ascertained using a single regularized Cox proportional hazard model, examining change of risk as a function of presence of microbe with age, sex, education level, Life's Simple 7, and inflammation. For variables of importance, the hazard ratio (HR) was estimated in separate (unregularized) Cox proportional hazard models including the same covariates (significance threshold Bonferroni corrected P<6×10[-5], 0.05/840). Reads from 2 microbes were significantly associated with CHD: Gemella morbillorum (HR, 3.14 [95% CI, 1.92-5.12]; P=4.86×10[-6]) and Pseudomonas species NFACC19-2 (HR, 3.22 [95% CI, 2.03-5.41]; P=1.58×10[-6]).

CONCLUSIONS: Metagenomics of whole-genome sequence reads opens a possible frontier for detection of pathogens for chronic diseases. The association of G morbillorum and Pseudomonas species reads with CHD raises the possibilities that microbes may drive atherosclerotic inflammation and that treatments for specific pathogens may provide clinical utility for CHD reduction.}, } @article {pmid39343535, year = {2024}, author = {Masuda, N and Kato, S and Ohkuma, M and Endo, K}, title = {Metagenomic Insights into Ecophysiology of Zetaproteobacteria and Gammaproteobacteria in Shallow Zones within Deep-sea Massive Sulfide Deposits.}, journal = {Microbes and environments}, volume = {39}, number = {3}, pages = {}, pmid = {39343535}, issn = {1347-4405}, mesh = {*Sulfides/metabolism ; *Gammaproteobacteria/genetics/classification/isolation & purification ; *Metagenomics ; *Seawater/microbiology ; *Metagenome ; Geologic Sediments/microbiology/chemistry ; Phylogeny ; Ecosystem ; Pacific Ocean ; Oxidation-Reduction ; Microbiota/genetics ; Carbon Cycle ; }, abstract = {Deep-sea massive sulfide deposits serve as energy sources for chemosynthetic ecosystems in dark, cold environments even after hydrothermal activity ceases. However, the vertical distribution of microbial communities within sulfide deposits along their depth from the seafloor as well as their ecological roles remain unclear. We herein conducted a culture-independent metagenomic ana-lysis of a core sample of massive sulfide deposits collected in a hydrothermally inactive field of the Southern Mariana Trough, Western Pacific, by drilling (sample depth: 0.52‍ ‍m below the seafloor). Based on the gene context of the metagenome-assembled genomes (MAGs) obtained, we showed the metabolic potential of as-yet-uncultivated microorganisms, particularly those unique to the shallow zone rich in iron hydroxides. Some members of Gammaproteobacteria have potential for the oxidation of reduced sulfur species (such as sulfide and thiosulfate) to sulfate coupled to nitrate reduction to ammonia and carbon fixation via the Calvin-Benson-Bassham (CBB) cycle, as the primary producers. The Zetaproteobacteria member has potential for iron oxidation coupled with microaerobic respiration. A comparative ana-lysis with previously reported metagenomes from deeper zones (~2‍ ‍m below the seafloor) of massive sulfide deposits revealed a difference in the relative abundance of each putative primary producer between the shallow and deep zones. Our results expand knowledge on the ecological potential of uncultivated microorganisms in deep-sea massive sulfide deposits and provide insights into the vertical distribution patterns of chemosynthetic ecosystems.}, } @article {pmid39342853, year = {2024}, author = {Li, Z and He, Y and Zhang, H and Qian, H and Wang, Y}, title = {Biotransformations of arsenic in marine sediments across marginal slope to hadal zone.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {135955}, doi = {10.1016/j.jhazmat.2024.135955}, pmid = {39342853}, issn = {1873-3336}, mesh = {*Geologic Sediments/microbiology ; *Biotransformation ; *Arsenic/metabolism ; *Water Pollutants, Chemical/metabolism ; Phylogeny ; Methyltransferases/genetics/metabolism ; Bacteria/metabolism/genetics ; Metagenome ; China ; }, abstract = {Arsenic compounds are accumulating in deep ocean, but their ecological impacts on deep-sea ecosystem remain elusive. We studied 32 sediment cores (101 layers for metagenomes, along with 41 global reference sediment metagenomes) collected from the South China Sea and the Mariana Trench (MT), characterized with high arsenic accumulation in MT. In these metagenomes we revealed a significantly positive correlation between relative abundance of arsenite methyltransferase gene (arsM) and sampling depth, which suggests that arsenic methylation is the most prevalent arsenic biotransformation process in the deep sea. Lower relative abundance of arsenic efflux gene, compared with arsM, indicates that microbes in deep-sea sediments were prone to methylate arsenite and retain it rather than efflux it. Phylogenetic analysis identified seven clades of ArsM proteins, including two new clades derived primarily from deep-sea microorganisms. Five metagenome-assembled genomes containing aioA for arsenite oxidation also harbor carbon fixation genes in the deep-sea sediment layers, suggesting previously unnoticed contribution of arsenite-oxidizing autotrophic bacteria to the carbon cycle. Therefore, deep-sea microorganisms adopt different detoxification and transformation strategies in response to arsenic compounds, which renews our understanding of arsenic in their ecological impacts and potential contribution in deep ocean.}, } @article {pmid39342753, year = {2024}, author = {Zou, S and Hu, R and Liang, S and Lu, T and Kang, D and Li, D}, title = {Assessment of health risk of antibiotics resistance genes from human disturbed habitat to wild animals: Metagenomic insights into availability and functional changes of gut microbiome.}, journal = {Ecotoxicology and environmental safety}, volume = {285}, number = {}, pages = {117117}, doi = {10.1016/j.ecoenv.2024.117117}, pmid = {39342753}, issn = {1090-2414}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Ecosystem ; *Drug Resistance, Microbial/genetics ; Humans ; *Animals, Wild/microbiology ; Risk Assessment ; Colobinae/microbiology/genetics ; Metagenomics ; Metagenome ; Environmental Monitoring ; Anti-Bacterial Agents/pharmacology/toxicity ; }, abstract = {Not all antibiotic resistance genes (ARGs) pose an ecological risk to their host animals. A standard should be developed to study which types of ARGs posed an ecological risk to wild animals under human disturbances (HDs). In this study, the golden snub-nosed monkeys (Rhinopithecus roxellana) were used as sentinel species. According to the animals-associated enrichment, mobility, and pathogenicity, the ARGs in habitat of sentinel species were divided into four levels. If the mobile and pathogenic ARGs that could be collinear with the metagenome-assembled genome (MAGs) in the gut of the sentinel species, the ARGs were defined as Rank I ARGs and they were considered to have ecological risk to sentinel species. Functional genes in the MAGs that collinear with the Rank I ARGs were used to predict the health risks of sentinel species. The ecological risk to sentinel species was present in 0.158 % of the ARGs-contigs in the habitat. Cultivation and villages, but not grazing, agriculture and ecotourism, increased the ecological risk of the ARGs to wild animals, The ability of gut microbiome to acquire mobile and pathogenic ARGs increased, as did the collinear functional genes, and the health risks of the wild animals also enhanced by the disturbances of cultivation and villages. Cultivation and villages increased the nutrient content of the soil, and they had a positive effect on the ecological risk of Rank I ARGs by affecting the mobile genetic elements (MGEs), microbiome and the resistant group in the habitat, which was why the cultivation and villages increased the health risks of wild animals. We proposed that cultivation and living should be controlled, while grazing, agriculture and ecotourism could be developed in nature reserves of wild animals, but the nutrients in the wild animals' habitat should be monitored.}, } @article {pmid39342656, year = {2024}, author = {Silva-Solar, S and Viver, T and Wang, Y and Orellana, LH and Knittel, K and Amann, R}, title = {Acidimicrobiia, the actinomycetota of coastal marine sediments: Abundance, taxonomy and genomic potential.}, journal = {Systematic and applied microbiology}, volume = {47}, number = {6}, pages = {126555}, doi = {10.1016/j.syapm.2024.126555}, pmid = {39342656}, issn = {1618-0984}, mesh = {*Geologic Sediments/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Phylogeny ; *Genome, Bacterial/genetics ; *DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Actinobacteria/genetics/classification/isolation & purification ; Arctic Regions ; Metagenome ; Genomics ; Seawater/microbiology ; }, abstract = {Microbial communities in marine sediments represent some of the densest and most diverse biological communities known, with up to a billion cells and thousands of species per milliliter. Among this taxonomic diversity, the class Acidimicrobiia, within the phylum Actinomycetota, stands out for its consistent presence, yet its limited taxonomic understanding obscures its ecological role. We used metagenome-assembled genomes from a 5-year Arctic fjord sampling campaign and compared them to publicly available Acidimicrobiia genomes using 16S rRNA gene and whole-genome phylogenies, alongside gene prediction and annotation to study their taxonomy and genomic potential. Overall, we provide a taxonomic overview of the class Acidimicrobiia and show its significant prevalence in Isfjorden and Helgoland coastal sediments, representing over 90% of Actinomycetota 16S rRNA gene sequences, and 3-7% of Bacteria. We propose Benthobacter isfjordensis gen. nov., sp. nov., Hadalibacter litoralis gen. nov., sp. nov., and two new species from Ilumatobacter, following SeqCode guidelines. In addition, we report the first in situ quantification of the family Ilumatobacteraceae, revealing its substantial presence (1-6%) in coastal sediments. This work highlights the need of refining the taxonomy of Acidimicrobiia to better understand their ecological contributions.}, } @article {pmid39342284, year = {2024}, author = {Seitz, VA and McGivern, BB and Borton, MA and Chaparro, JM and Schipanski, ME and Prenni, JE and Wrighton, KC}, title = {Cover crop root exudates impact soil microbiome functional trajectories in agricultural soils.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {183}, pmid = {39342284}, issn = {2049-2618}, support = {P30 CA046934/CA/NCI NIH HHS/United States ; 507580//Facilities Integrating Collaborations for User Science/ ; 2021-67019-34814//U.S. Department of Agriculture/ ; P30CA046934//Cancer Center Support Grant/ ; }, mesh = {*Soil Microbiology ; *Plant Roots/microbiology ; *Crops, Agricultural/microbiology ; *Microbiota ; *Rhizosphere ; *Soil/chemistry ; Bacteria/classification/metabolism/isolation & purification ; Agriculture ; Plant Growth Regulators/metabolism ; Plant Exudates/metabolism ; Sorghum/metabolism/microbiology ; }, abstract = {BACKGROUND: Cover cropping is an agricultural practice that uses secondary crops to support the growth of primary crops through various mechanisms including erosion control, weed suppression, nutrient management, and enhanced biodiversity. Cover crops may elicit some of these ecosystem services through chemical interactions with the soil microbiome via root exudation, or the release of plant metabolites from roots. Phytohormones are one metabolite type exuded by plants that activate the rhizosphere microbiome, yet managing this chemical interaction remains an untapped mechanism for optimizing plant-soil-microbiome interactions. Currently, there is limited understanding on the diversity of cover crop phytohormone root exudation patterns and our aim was to understand how phytochemical signals selectively enrich specific microbial taxa and functionalities in agricultural soils.

RESULTS: Here, we link variability in cover crop root exudate composition to changes in soil microbiome functionality. Exudate chemical profiles from 4 cover crop species (Sorghum bicolor, Vicia villosa, Brassica napus, and Secale cereal) were used as the chemical inputs to decipher microbial responses. These distinct exudate profiles, along with a no exudate control, were amended to agricultural soil microcosms with microbial responses tracked over time using metabolomes and genome-resolved metatranscriptomes. Our findings illustrated microbial metabolic patterns were unique in response to cover crop exudate inputs over time, particularly by sorghum and cereal rye amended microcosms. In these microcosms, we identify novel microbial members (at the genera and family level) who produced IAA and GA4 over time. Additionally, we identified cover crop exudates exclusively enriched for bacterial nitrite oxidizers, while control microcosms were discriminated for nitrogen transport, mineralization, and assimilation, highlighting distinct changes in microbial nitrogen cycling in response to chemical inputs.

CONCLUSIONS: We highlight that root exudate amendments alter microbial community function (i.e., N cycling) and microbial phytohormone metabolisms, particularly in response to root exudates isolated from cereal rye and sorghum plants. Additionally, we constructed a soil microbial genomic catalog of microorganisms responding to commonly used cover crops, a public resource for agriculturally relevant microbes. Many of our exudate-stimulated microorganisms are representatives from poorly characterized or novel taxa, revealing the yet to be discovered metabolic reservoir harbored in agricultural soils. Our findings emphasize the tractability of high-resolution multi-omics approaches to investigate processes relevant for agricultural soils, opening the possibility of targeting specific soil biogeochemical outcomes through biological precision agricultural practices that use cover crops and the microbiome as levers for enhanced crop production. Video Abstract.}, } @article {pmid39342129, year = {2024}, author = {García-Estrada, DA and Selem-Mojica, N and Martínez-Hernández, A and Lara-Reyna, J and Dávila-Ramos, S and Verdel-Aranda, K}, title = {Diversity of bacterial communities in wetlands of Calakmul Biosphere Reserve: a comparative analysis between conserved and semi-urbanized zones in pre-Mayan Train era.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {376}, pmid = {39342129}, issn = {1471-2180}, support = {No. 320237//Consejo Nacional de Humanidades, Ciencias y Tecnologías, México/ ; }, mesh = {*Wetlands ; *Bacteria/classification/genetics/isolation & purification ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Biodiversity ; Metagenomics ; Phylogeny ; DNA, Bacterial/genetics ; Soil Microbiology ; }, abstract = {BACKGROUND: The Calakmul Biosphere Reserve (CBR) is known for its rich animal and plant biodiversity, yet its microbial communities remain largely unknown. The reserve does not possess permanent bodies of water; nevertheless, seasonal depressions associated with fractures create wetlands, known locally as aguadas. Given the recent construction of the Maya train that crosses the CRB, it is essential to assess the biodiversity of its microorganisms and recognize their potential as a valuable source of goods. This evaluation is pivotal in mitigating potential mismanagement of the forest ecosystem. To enhance comprehension of microbial communities, we characterized the microbiota in three different wetlands. Ag-UD1 and Ag-UD2 wetlands are located in a zone without human disturbances, while the third, Ag-SU3, is in a semi-urbanized zone. Sampling was carried out over three years (2017, 2018, and 2019), enabling the monitoring of spatiotemporal variations in bacterial community diversity. The characterization of microbiome composition was conducted using 16S rRNA metabarcoding. Concurrently, the genomic potential of select samples was examined through shotgun metagenomics.

RESULTS: Statistical analysis of alpha and beta diversity indices showed significant differences among the bacterial communities found in undisturbed sites Ag-UD1 and Ag-UD2 compared to Ag-SU3. However, no significant differences were observed among sites belonging to the undisturbed area. Furthermore, a comparative analysis at the zone level reveals substantial divergence among the communities, indicating that the geographic location of the samples significantly influences these patterns. The bacterial communities in the CBR wetlands predominantly consist of genera from phyla Actinobacteria, Acidobacteria, and Proteobacteria.

CONCLUSION: This characterization has identified the composition of microbial communities and provided the initial overview of the metabolic capacities of the microbiomes inhabiting the aguadas across diverse conservation zones. The three sites exhibit distinct microbial compositions, suggesting that variables such as chemical composition, natural and anthropogenic disturbances, vegetation, and fauna may play a pivotal role in determining the microbial structure of the aguadas. This study establishes a foundational baseline for evaluating the impact of climatic factors and human interventions on critical environments such as wetlands.}, } @article {pmid39342083, year = {2024}, author = {Wang, X and Yao, S and Yang, X and Li, Y and Yu, Z and Huang, J and Wang, J}, title = {Peritoneal dialysis promotes microbial-driven biosynthesis pathways of sesquiterpenes and triterpenes compounds in end-stage renal disease patients.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {377}, pmid = {39342083}, issn = {1471-2180}, support = {32170071//National Natural Science Foundation of China/ ; 32300051//National Natural Science Foundation of China/ ; 2022JJ40663//Natural Science Foundation of Hunan Province/ ; C2023045//Hunan Province Traditional Chinese Medicine Research Program Project/ ; }, mesh = {Humans ; *Kidney Failure, Chronic/therapy/metabolism/microbiology ; *Gastrointestinal Microbiome ; *Peritoneal Dialysis ; *Sesquiterpenes/metabolism ; Male ; Female ; *Feces/microbiology ; Middle Aged ; *Triterpenes/metabolism ; Bacteria/metabolism/classification/genetics/isolation & purification ; Biosynthetic Pathways ; Adult ; Metagenomics ; Aged ; }, abstract = {The concept of the gut-kidney axis is gaining significant attention due to the close relationship between gut microbiota and kidney disease. Peritoneal dialysis is recognized as a crucial renal replacement therapy for end-stage renal disease (ESRD). The alterations in gut microbiota and related mechanisms after receiving this dialysis method are not fully understood. This study conducted shotgun metagenomic sequencing on fecal samples from 11 end-stage renal disease patients who did not receive dialysis (ESRD_N) and 7 patients who received peritoneal dialysis (ESRD_P). After quality control and correlation analysis of the data, our study is aimed at exploring the impact of peritoneal dialysis on the gut microbiota and health of ESRD patients. Our research findings indicate that the complexity and aggregation characteristics of gut microbiota interactions increase in ESRD_P. In addition, the gut microbiota drives the biosynthesis pathways of sesquiterpenes and triterpenes in ESRD_P patients, which may contribute to blood purification and improve circulation. Therefore, our research will lay the foundation for the prevention and treatment of ESRD.}, } @article {pmid39342060, year = {2024}, author = {Amin, A and Khan, IU and Amin, M and Fatima, M and Sajjad, W and Shah, TA and Dawoud, TM and Wondmie, GF}, title = {Resurrected microorganisms: a plethora of resting bacteria underway for human interaction.}, journal = {AMB Express}, volume = {14}, number = {1}, pages = {106}, pmid = {39342060}, issn = {2191-0855}, abstract = {Glaciers, which form due to the accumulation of snow, play a crucial role in providing freshwater resources, supporting river systems, and maintaining ecosystem stability. Pakistan is habitat to over 5000 glaciers, primarily located in the Hindukash, Himalaya, and Karakoram mountain ranges. Understanding the microbial communities thriving in these extreme environments becomes of utmost importance. These glaciers offer a unique perspective on extremophile adaptation, as they harbor microorganisms that are capable of surviving and thriving under harsh conditions. Glacial melting poses a significant threat to ancient microbiomes, potentially leading to the resurgence of epidemics and exposure of life to paleomicrobiota. Mostly glacial microbiome is evenly distributed and shows similar diversity. With the threat of resurrection of ages old microbiome and its incorporation into the waters have raised a major concern for revival of epidemics and exposure of life with paleanmicrobiota again. This has led the scientist to deeply observe the bacterial flora embedded in the cryonite holes of glaciers. This study aims to investigate the bacterial diversity within various glaciers of Pakistan using metagenomic techniques. Kamri, Burzil, Siachin, Baltoro, Shigar Basin, Biafo and Panama Glaciers designated from G1 to G7 respectively were chosen from Pakistan. Through rigorous physicochemical analyses, distinct characteristics among glaciers are revealed, including variations in temperature, depth, electrical conductivity, pH levels, and nutrient concentrations. The exploration of alpha diversity, employing metrics such as Chao1, Shannon, Simpson, and Inverse Simpson indices, offers valuable insights into the richness, evenness, and dominance of species within different samples. Beta diversity was calculated by using R software. The vegan package was used for NMSD, cluster and PCoA analysis based on Bray-Curtis distance. PCA analysis was done by using prcomp package from R software. Based on OTU abundance and environmental factor data, DCA analysis was done to determine the linear model from the gradient value (RDA) and the unimodal model (CCA). results were compiled by drawing cluster dendrogram which predicts the patterns of similarity and dissimilarity between different samples. Notably, phyla Proteobacteria emerge as the dominant phylum, accompanied by Actinobacteria, Firmicutes, and Bacteroidetes. The dendrogram shows five clusters, with close similarity between G1 and G4, glacier samples G3 and G8, and G2 and G7. Seasonal variations in glacier physicochemical properties were also observed, with summer samples having shallower depths, lower temperatures, and slightly acidic pH. In contrast, winter samples have higher electrical conductivity and sulfur content. Ultimately, this research provides a foundational framework for comprehending glacier ecosystems, their resident microbial communities, and their broader ecological significance. The study highlights the potential public health risks linked to the release of ancient microorganisms due to climate change, emphasizing the need for comprehensive monitoring and research to mitigate potential public health threats.}, } @article {pmid39341984, year = {2024}, author = {Pandolfo, E and Durán-Wendt, D and Martínez-Cuesta, R and Montoya, M and Carrera-Ruiz, L and Vazquez-Arias, D and Blanco-Romero, E and Garrido-Sanz, D and Redondo-Nieto, M and Martin, M and Rivilla, R}, title = {Metagenomic analyses of a consortium for the bioremediation of hydrocarbons polluted soils.}, journal = {AMB Express}, volume = {14}, number = {1}, pages = {105}, pmid = {39341984}, issn = {2191-0855}, support = {TED2021-130996B-I00//Ministerio de Ciencia e Innovación/ ; GREENER Grant agreement 826312//Horizon 2020 Framework Programme/ ; }, abstract = {A bacterial consortium was isolated from a soil in Noblejas (Toledo, Spain) with a long history of mixed hydrocarbons pollution, by enrichment cultivation. Serial cultures of hydrocarbons polluted soil samples were grown in a minimal medium using diesel (1 mL/L) as the sole carbon and energy source. The bacterial composition of the Noblejas Consortium (NC) was determined by sequencing 16S rRNA gene amplicon libraries. The consortium contained around 50 amplicon sequence variants (ASVs) and the major populations belonged to the genera Pseudomonas, Enterobacter, Delftia, Stenotrophomonas, Achromobacter, Acinetobacter, Novosphingobium, Allorhizobium-Neorhizobium-Rhizobium, Ochrobactrum and Luteibacter. All other genera were below 1%. Metagenomic analysis of NC has shown a high abundance of genes encoding enzymes implicated in aliphatic and (poly) aromatic hydrocarbons degradation, and almost all pathways for hydrocarbon degradation are represented. Metagenomic analysis has also allowed the construction of metagenome assembled genomes (MAGs) for the major players of NC. Metatranscriptomic analysis has shown that several of the ASVs are implicated in hydrocarbon degradation, being Pseudomonas, Acinetobacter and Delftia the most active populations.}, } @article {pmid39341578, year = {2024}, author = {Gawande, PS and Manigandan, V and Ganesh R, S and Kannan, VR and Ramu, K and Murthy, MVR}, title = {Metagenomic analysis of pathogenic bacteria and virulence factor genes in coastal sediments from highly urbanized cities of India.}, journal = {Microbial pathogenesis}, volume = {196}, number = {}, pages = {106984}, doi = {10.1016/j.micpath.2024.106984}, pmid = {39341578}, issn = {1096-1208}, mesh = {*Virulence Factors/genetics ; India ; *Geologic Sediments/microbiology ; *Metagenomics ; *Cities ; *Bacteria/genetics/classification/pathogenicity/isolation & purification ; Phylogeny ; Bacterial Proteins/genetics ; Vibrio/genetics/pathogenicity/classification/isolation & purification ; Pseudomonas aeruginosa/genetics/pathogenicity/isolation & purification/classification ; }, abstract = {A metagenomic approach was employed to investigate the diversity and distribution of Virulence Factors Genes (VFGs) and Pathogenic Bacteria (PB) in sediment samples collected from highly urbanized cities along the Indian coastline. Among the study locations, Mumbai, Veraval and Paradeep showed a higher abundance of PB, with Vibrio and Pseudomonas as dominant at the genus level, and Escherichia coli and Pseudomonas aeruginosa at the species level. In total, 295 VFGs were detected across all sediment samples, of which 40 VFGs showed a similarity of ≥90 % with the Virulence Database (VFDB) and were focused in this study. Among the virulent proteins, twitching motility protein and flagellar P-ring were found to be prevalent and significantly associated with Vibrio spp., and Pseudomonas spp., indicating potential bacterial pathogenicity. This investigation serves as the basis for future studies and provides insights into the comprehensive taxonomic profiles of PB, VFGs and their associated PB in the coastal sediments of India.}, } @article {pmid39341403, year = {2024}, author = {Chen, X and Balliew, J and Bauer, CX and Deegan, J and Gitter, A and Hanson, BM and Maresso, AW and Tisza, MJ and Troisi, CL and Rios, J and Mena, KD and Boerwinkle, E and Wu, F}, title = {Revealing patterns of SARS-CoV-2 variant emergence and evolution using RBD amplicon sequencing of wastewater.}, journal = {The Journal of infection}, volume = {89}, number = {5}, pages = {106284}, doi = {10.1016/j.jinf.2024.106284}, pmid = {39341403}, issn = {1532-2742}, mesh = {*Wastewater/virology ; *SARS-CoV-2/genetics/isolation & purification ; Humans ; *COVID-19/epidemiology/virology ; Texas/epidemiology ; Genome, Viral ; Evolution, Molecular ; Spike Glycoprotein, Coronavirus/genetics ; }, abstract = {OBJECTIVES: Rapid evolution of SARS-CoV-2 has resulted in the emergence of numerous variants, posing significant challenges to public health surveillance. Clinical genome sequencing, while valuable, has limitations in capturing the full epidemiological dynamics of circulating variants in the general population. This study aimed to monitor the SARS-CoV-2 variant community dynamics and evolution using receptor-binding domain (RBD) amplicon sequencing of wastewater samples.

METHODS: We sequenced wastewater from El Paso, Texas, over 17 months, compared the sequencing data with clinical genome data, and performed biodiversity analysis to reveal SARS-CoV-2 variant dynamics and evolution.

RESULTS: We identified 91 variants and observed waves of dominant variants transitioning from BA.2 to BA.2.12.1, BA.4&5, BQ.1, and XBB.1.5. Comparison with clinical genome sequencing data revealed earlier detection of variants and identification of unreported outbreaks. Our results also showed strong consistency with clinical data for dominant variants at the local, state, and national levels. Alpha diversity analyses revealed significant seasonal variations, with the highest diversity observed in winter. By segmenting the outbreak into lag, growth, stationary, and decline phases, we found higher variant diversity during the lag phase, likely due to lower inter-variant competition preceding outbreak growth.

CONCLUSIONS: Our findings underscore the importance of low transmission periods in facilitating rapid mutation and variant evolution. Our approach, integrating RBD amplicon sequencing with wastewater surveillance, demonstrates effectiveness in tracking viral evolution and understanding variant emergence, thus enhancing public health preparedness.}, } @article {pmid39341204, year = {2024}, author = {Takewaki, D and Kiguchi, Y and Masuoka, H and Manu, MS and Raveney, BJE and Narushima, S and Kurokawa, R and Ogata, Y and Kimura, Y and Sato, N and Ozawa, Y and Yagishita, S and Araki, T and Miyake, S and Sato, W and Suda, W and Yamamura, T}, title = {Tyzzerella nexilis strains enriched in mobile genetic elements are involved in progressive multiple sclerosis.}, journal = {Cell reports}, volume = {43}, number = {10}, pages = {114785}, doi = {10.1016/j.celrep.2024.114785}, pmid = {39341204}, issn = {2211-1247}, mesh = {Animals ; Humans ; *Encephalomyelitis, Autoimmune, Experimental/genetics/pathology ; Mice ; *Multiple Sclerosis/genetics/pathology/microbiology ; Female ; Interspersed Repetitive Sequences/genetics ; Male ; Gastrointestinal Microbiome/genetics ; Mice, Inbred C57BL ; Clostridiales/genetics ; Middle Aged ; Adult ; }, abstract = {Multiple sclerosis (MS) is an autoimmune-demyelinating disease with an inflammatory pathology formed by self-reactive lymphocytes with activated glial cells. Progressive MS, characterized by resistance to medications, significantly differs from the non-progressive form in gut microbiome profiles. After confirming an increased abundance of "Tyzzerella nexilis" in various cohorts of progressive MS, we identified a distinct cluster of T. nexilis strains enriched in progressive MS based on long-read metagenomics. The distinct T. nexilis cluster is characterized by a large number of mobile genetic elements (MGEs) and a lack of defense systems against MGEs. Microbial genes for sulfate reduction and flagella formation with pathogenic implications are specific to this cluster. Moreover, these flagellar genes are encoded on MGEs. Mono-colonization with MGE-enriched T. nexilis made germ-free mice more susceptible to experimental autoimmune encephalomyelitis. These results indicate that the progression of MS may be promoted by MGE-enriched T. nexilis with potentially pathogenic properties.}, } @article {pmid39341154, year = {2024}, author = {Gough, EK and Edens, TJ and Carr, L and Robertson, RC and Mutasa, K and Ntozini, R and Chasekwa, B and Geum, HM and Baharmand, I and Gill, SK and Mutasa, B and Mbuya, MNN and Majo, FD and Tavengwa, N and Francis, F and Tome, J and Evans, C and Kosek, M and Prendergast, AJ and Manges, AR and , }, title = {Bifidobacterium longum and microbiome maturation modify a nutrient intervention for stunting in Zimbabwean infants.}, journal = {EBioMedicine}, volume = {108}, number = {}, pages = {105362}, pmid = {39341154}, issn = {2352-3964}, mesh = {Humans ; Infant ; *Gastrointestinal Microbiome ; *Growth Disorders/prevention & control/microbiology ; Female ; Male ; Zimbabwe ; Fucosyltransferases/genetics ; Feces/microbiology ; Bifidobacterium ; Dietary Supplements ; Nutrients ; }, abstract = {BACKGROUND: Small-quantity lipid-based nutrient supplements (SQ-LNS), which has been widely tested to reduce child stunting, has largely modest effects to date, but the mechanisms underlying these modest effects are unclear. Child stunting is a longstanding indicator of chronic undernutrition and it remains a prevalent public health problem. The infant gut microbiome may be a key contributor to stunting; and mother and infant fucosyltransferase (FUT) phenotypes are important determinants of infant microbiome composition.

METHODS: We investigated whether mother-infant FUT status (n = 792) and infant gut microbiome composition (n = 354 fecal specimens from 172 infants) modified the impact of an infant and young child feeding (IYCF) intervention, that included SQ-LNS, on stunting at age 18 months in secondary analysis of a randomized trial in rural Zimbabwe.

FINDINGS: We found that the impact of the IYCF intervention on stunting was modified by: (i) mother-infant FUT2+/FUT3- phenotype (difference-in-differences -32.6% [95% CI: -55.3%, -9.9%]); (ii) changes in species composition that reflected microbiome maturation (difference-in-differences -68.1% [95% CI: -99.0%, -28.5%); and (iii) greater relative abundance of B. longum (differences-in-differences 49.1% [95% CI: 26.6%, 73.6%]). The dominant strains of B. longum when the intervention started were most similar to the proficient milk oligosaccharide utilizer subspecies infantis, which decreased with infant age and differed by mother-infant FUT2+/FUT3- phenotypes.

INTERPRETATION: These findings indicate that a persistently "younger" microbiome at initiation of the intervention reduced its benefits on stunting in areas with a high prevalence of growth restriction.

FUNDING: Bill and Melinda Gates Foundation, UK DFID/Aid, Wellcome Trust, Swiss Agency for Development and Cooperation, US National Institutes of Health, UNICEF, and Nutricia Research Foundation.}, } @article {pmid39340864, year = {2024}, author = {Wang, XW and Tan, X and Dang, CC and Liu, LY and Wang, X and Zhao, ZC and Ren, HY and Liu, BF and Xie, GJ}, title = {Enrichment and characterization of thermophilic anaerobic ammonium oxidizing bacteria from hot spring.}, journal = {Water research}, volume = {267}, number = {}, pages = {122497}, doi = {10.1016/j.watres.2024.122497}, pmid = {39340864}, issn = {1879-2448}, mesh = {*Hot Springs/microbiology ; *Ammonium Compounds/metabolism ; *Oxidation-Reduction ; Anaerobiosis ; Bacteria/metabolism/genetics ; Phylogeny ; Bacteria, Anaerobic/genetics/metabolism ; }, abstract = {Anaerobic ammonium oxidization (Anammox) process plays a crucial role in the global nitrogen cycle and sustainable biological nitrogen removal from wastewater. Although Anammox bacteria have been detected across mesophilic and thermophilic conditions, the direct cultivation of Anammox bacteria from thermal environments has remained elusive. This impedes limiting our understanding of their physiology and ecology in high-temperature habitats. Here, we successfully enriched Anammox bacteria from hot spring sediments at 45 °C, achieving an ammonium oxidation rate of 158.0 mg NH4[+]-N l[-1]d[-1], with the genus 'Candidatus Brocadia' presenting 22.9 % of the total microbial community after about 500 days of operation. Metagenomic analysis recovered two high-quality genomes of novel Anammox bacteria, which we designed as 'Candidatus Brocadia thermophilus' and 'Candidatus Brocadia thermoanammoxidans'. Both of them encoded and actively expressed key metabolic genes involved in Anammox process and several genes associated with thermotolerance, demonstrating their remarkable ability to perform Anammox reaction in thermophilic environments. Notably, phylotypes related to 'Candidatus Brocadia thermoanammoxidans' have frequently been retrieved from geographically distinct natural habitats. These findings expand our understanding of thermophilic Anammox bacteria and underscore their potential in the nitrogen cycle of thermal natural and engineering ecosystems.}, } @article {pmid39340684, year = {2024}, author = {Vinothini, K and Nakkeeran, S and Saranya, N and Jothi, P and Richard, JI and Perveen, K and Bukhari, NA and Glick, BR and Sayyed, RZ and Mastinu, A}, title = {Rhizosphere Engineering of Biocontrol Agents Enriches Soil Microbial Diversity and Effectively Controls Root-Knot Nematodes.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {120}, pmid = {39340684}, issn = {1432-184X}, mesh = {Animals ; *Solanum lycopersicum/microbiology/parasitology ; *Soil Microbiology ; *Rhizosphere ; *Bacillus/genetics/physiology ; *Plant Roots/microbiology/parasitology ; *Pest Control, Biological ; Plant Diseases/parasitology/prevention & control/microbiology ; Trichoderma/physiology/genetics ; Tylenchoidea/physiology ; Microbiota ; Antinematodal Agents/pharmacology ; Biological Control Agents/pharmacology ; Bacteria/genetics/classification ; }, abstract = {The root-knot nematode (RKN) causes significant yield loss in tomatoes. Understanding the interaction of biocontrol agents (BCAs)-nematicides-soil microbiomes and RKNs is essential for enhancing the efficacy of biocontrol agents and nematicides to curb RKN damage to crops. The present study aimed to evaluate the in vitro effectiveness of BACa and nematicide against RKN and to apply the amplicon sequencing to assess the interaction of Bacillus velezensis (VB7) and Trichoderma koningiopsis (TK) against RKNs. Metagenomic analysis revealed the relative abundance of three phyla such as Proteobacteria (42.16%), Firmicutes (19.57%), and Actinobacteria (17.69%) in tomato rhizospheres. Those tomato rhizospheres treated with the combined application of B. velezensis VB7 + T. koningiopsis TK and RKN had a greater frequency of diversity and richness than the control. RKN-infested tomato rhizosphere drenched with bacterial and fungal antagonists had the maximum diversity index of bacterial communities. A strong correlation with a maximum number of interconnection edges in the phyla Proteobacteria, Firmicutes, and Actinobacteria was evident in soils treated with both B. velezensis VB7 and T. koningiopsis TK challenged against RKN in infected soil. The present study determined a much greater diversity of bacterial taxa observed in tomato rhizosphere soils treated with B. velezensis VB7 and T. koningiopsis TK than in untreated soil. It is suggested that the increased diversity and abundance of bacterial communities might be responsible for increased nematicidal properties in tomato plants. Hence, the combined applications of B. velezensis VB7 and T. koningiopsis TK can enhance the nematicidal action to curb RKN infecting tomatoes.}, } @article {pmid39340212, year = {2024}, author = {Avellaneda-Franco, L and Xie, L and Nakai, M and Barr, JJ and Marques, FZ}, title = {Dietary fiber intake impacts gut bacterial and viral populations in a hypertensive mouse model.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2407047}, pmid = {39340212}, issn = {1949-0984}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Dietary Fiber/administration & dosage ; Mice ; Male ; *Hypertension/virology ; *Mice, Inbred C57BL ; *Bacteria/classification/genetics/isolation & purification ; *Bacteriophages/physiology/genetics ; *Disease Models, Animal ; Angiotensin II/metabolism ; Genome, Viral ; }, abstract = {The gut microbiome is an emerging factor in preventing hypertension, yet the influence of gut bacteriophages, viruses infecting bacteria, on this condition remains unclear. Bacteriophage-bacteria interactions, which impact the gut microbiome, are influenced differentially by temperate and virulent bacteriophages. However, the standard technique for studying viral populations, viral-like particles (VLPs)-metagenomes, often overlook prophages, the intracellular stage of temperate bacteriophages, creating a knowledge gap. To address this, we investigated alterations in extracellular and intracellular bacteriophages, alongside bacterial populations, in the angiotensin II-hypertension model. We sequenced VLPs and bulk DNA from cecal-colonic samples collected from male C57BL/6J mice implanted with minipumps containing saline or angiotensin II. We assembled 106 bacterial and 816 viral genomes and found that gut viral and bacterial populations remained stable between hypertensive and normotensive mice. A higher number of temperate viruses were observed across all treatments. Although temperate viruses outnumbered virulent viruses, sequencing of both VLPs and bulk revealed that virions from virulent viruses were more abundant in the murine gut. We then evaluated the impact of low- and high-fiber intake on gut microbiome composition in the angiotensin II model. Fiber intake significantly influenced the gut microbiome composition and hypertension development. Mice receiving high-fiber had lower blood pressure, a higher bacterial-encoded carbohydrate-associated enzyme, and a higher total relative abundance of temperate viruses than those receiving low-fiber. Our findings suggest that phages are not associated with hypertension development in the angiotensin II model. However, they support a complex diet-bacteria/phage interaction that may be involved in blood pressure regulation.}, } @article {pmid39339905, year = {2024}, author = {Chaves, M and Hashish, A and Osemeke, O and Sato, Y and Suarez, DL and El-Gazzar, M}, title = {Evaluation of Commercial RNA Extraction Protocols for Avian Influenza Virus Using Nanopore Metagenomic Sequencing.}, journal = {Viruses}, volume = {16}, number = {9}, pages = {}, pmid = {39339905}, issn = {1999-4915}, support = {AP22VSD&B000C010//United States Department of Agriculture/ ; }, mesh = {Animals ; *Influenza in Birds/virology/diagnosis ; *RNA, Viral/genetics/isolation & purification ; *Nanopore Sequencing/methods ; *Influenza A virus/genetics/isolation & purification/classification ; *Metagenomics/methods ; Birds/virology ; High-Throughput Nucleotide Sequencing/methods ; Poultry/virology ; Chickens/virology ; Nanopores ; }, abstract = {Avian influenza virus (AIV) is a significant threat to the poultry industry, necessitating rapid and accurate diagnosis. The current AIV diagnostic process relies on virus identification via real-time reverse transcription-polymerase chain reaction (rRT-PCR). Subsequently, the virus is further characterized using genome sequencing. This two-step diagnostic process takes days to weeks, but it can be expedited by using novel sequencing technologies. We aim to optimize and validate nucleic acid extraction as the first step to establishing Oxford Nanopore Technologies (ONT) as a rapid diagnostic tool for identifying and characterizing AIV from clinical samples. This study compared four commercially available RNA extraction protocols using AIV-known-positive clinical samples. The extracted RNA was evaluated using total RNA concentration, viral copies as measured by rRT-PCR, and purity as measured by a 260/280 absorbance ratio. After NGS testing, the number of total and influenza-specific reads and quality scores of the generated sequences were assessed. The results showed that no protocol outperformed the others on all parameters measured; however, the magnetic particle-based method was the most consistent regarding CT value, purity, total yield, and AIV reads, and it was less error-prone. This study highlights how different RNA extraction protocols influence ONT sequencing performance.}, } @article {pmid39339865, year = {2024}, author = {Chacón, RD and Sánchez-Llatas, CJ and da Costa, AC and Valdeiglesias Ichillumpa, S and Cea-Callejo, P and Marín-Sánchez, O and Astolfi-Ferreira, CS and Santander-Parra, S and Nuñez, LFN and Piantino Ferreira, AJ}, title = {Molecular and Evolutionary Characteristics of Chicken Parvovirus (ChPV) Genomes Detected in Chickens with Runting-Stunting Syndrome.}, journal = {Viruses}, volume = {16}, number = {9}, pages = {}, pmid = {39339865}, issn = {1999-4915}, support = {Article Processing Charge//Universidad de Las Américas/ ; 301084/2019-0//Conselho Nacional de Pesquisa e Desenvolvimento Tecnológico (CNPq)/ ; }, mesh = {Animals ; *Genome, Viral ; *Chickens/virology ; *Phylogeny ; *Poultry Diseases/virology ; *Parvoviridae Infections/veterinary/virology ; *Evolution, Molecular ; Metagenomics ; Parvovirinae/genetics/classification ; Parvovirus/genetics/classification ; }, abstract = {Chicken Parvovirus (ChPV) belongs to the genus Aveparvovirus and is implicated in enteric diseases like runting-stunting syndrome (RSS) in poultry. In RSS, chicken health is affected by diarrhea, depression, and increased mortality, causing significant economic losses in the poultry industry. This study aimed to characterize the ChPV genomes detected in chickens with RSS through a metagenomic approach and compare the molecular and evolutionary characteristics within the Aveparvovirus galliform1 species. The intestinal content of broiler flocks affected with RSS was submitted to viral metagenomics. The assembled prevalent genomes were identified as ChPV after sequence and phylogenetic analysis, which consistently clustered separately from Turkey Parvovirus (TuPV). The strain USP-574-A presented signs of genomic recombination. The selective pressure analysis indicated that most of the coding genes in A. galliform1 are evolving under diversifying (negative) selection. Protein modeling of ChPV and TuPV viral capsids identified high conservancy over the VP2 region. The prediction of epitopes identified several co-localized antigenic peptides from ChPV and TuPV, especially for T-cell epitopes, highlighting the immunological significance of these sites. However, most of these peptides presented host-specific variability, obeying an adaptive scenario. The results of this study show the evolutionary path of ChPV and TuPV, which are influenced by diversifying events such as genomic recombination and selective pressure, as well as by adaptation processes, and their subsequent immunological impact.}, } @article {pmid39339826, year = {2024}, author = {Laubscher, F and Kaiser, L and Cordey, S}, title = {SCANellome V2: Update of the Primate Anellovirus Reference Sequences Database.}, journal = {Viruses}, volume = {16}, number = {9}, pages = {}, pmid = {39339826}, issn = {1999-4915}, mesh = {Animals ; *Primates/virology ; *Phylogeny ; *Anelloviridae/genetics/classification ; Humans ; *Genome, Viral ; *Metagenomics/methods ; Databases, Genetic ; Genotype ; Open Reading Frames ; }, abstract = {Anelloviruses are ubiquitous in humans and represent a major component of the human virome. Its best-known representative is Torque teno virus (i.e., the Alphatorquevirus genus), which is considered a potential immunity biomarker. Recent metagenomic investigations revealed not only the extraordinary genomic diversity of anellovirus sequences, but also that co-detection of genera, genotypes, or species seems to be the rule in humans. SCANellome was developed to represent a user-friendly tool to analyze the primate (both human and non-human) anellovirus composition at the genus, species, and genotype level from metagenomics data based on an up-to-date database. This SCANellome update includes >900 additional reference sequences from GenBank. Using a clustering at 90% identity, the FASTA database was updated and generated 134 new representative sequences. Based on ORF1, the analysis of these new sequences indicates the presence of 206 potential new species, including four nonhuman primates, and adds four new non-human primate species which will be the subject of a proposal to the International Committee on Taxonomy of Viruses (ICTV). In addition, SCANellome V2 provides now the user with an interactive up-to-date phylogenetic analysis (of ORF1) to show the distribution among the 12 human and nonhuman primate genera of these new potential species. Finally, the Anelloviridae taxonomy was updated to rename species names in binomial format as required by the ICTV.}, } @article {pmid39339638, year = {2024}, author = {Galbács, ZN and Agyemang, ED and Pásztor, G and Takács, AP and Várallyay, É}, title = {Viromes of Monocotyledonous Weeds Growing in Crop Fields Reveal Infection by Several Viruses Suggesting Their Virus Reservoir Role.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {18}, pages = {}, pmid = {39339638}, issn = {2223-7747}, support = {K146087//NKFIH/ ; Flagship Research Group Programme//Hungarian University of Agriculture and Life Sciences/ ; }, abstract = {In 2019, random samples of Panicum miliaceum growing as a weed were surveyed to uncover their virus infections at two locations in Hungary. This pilot study revealed infection with three viruses, two appearing for the first time in the country. As follow-up research, in the summer of 2021, we collected symptomatic leaves of several monocotyledonous plants in the same locations and determined their viromes using small RNA high-throughput sequencing (HTS). As a result, we have identified the presence of wheat streak mosaic virus (WSMV), barley yellow striate mosaic virus (BYSMV), barley virus G (BVG), and two additional viruses, namely Aphis glycines virus 1 (ApGlV1) and Ljubljana dicistrovirus 1 (LDV1), which are described for the first time in Hungary. New hosts of the viruses were identified: Cynodon dactylon is a new host of BYSMV and LDV1, Echinocloa crus-galli is a new host of BVG, ApGlV1 and LDV1, Sorghum halepense is a new host of ApGlV1, and Panicum miliaceum is a new host of LDV1. At the same time, Zea mays is a new host of ApGlV1 and LDV1. Small RNA HTS diagnosed acute infections but failed to detect persistent ones, which could be revealed using RT-PCR. The infection rates at the different locations and plant species were different. The phylogenetic analyses of the sequenced virus variants suggest that the tested monocotyledonous weeds can host different viruses and play a virus reservoir role. Viral spread from the reservoir species relies on the activity of insect vectors, which is why their management requires an active role in plant protection strategies, which need careful planning in the changing environment.}, } @article {pmid39339601, year = {2024}, author = {Cheng, X and Li, X and Cai, Z and Wang, Z and Zhou, J}, title = {The Structural and Functional Responses of Rhizosphere Bacteria to Biodegradable Microplastics in the Presence of Biofertilizers.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {18}, pages = {}, pmid = {39339601}, issn = {2223-7747}, support = {41976126//NSFC/ ; 2023KCXTD052//the Innovation Team Project for Guangdong's Universities/ ; RCJC20200714114433069, KCXFZ20201221173211033, and ZDSYS20230626091459009//the Shenzhen Science and Technology Program/ ; }, abstract = {Biodegradable microplastics (Bio-MPs) are a hot topic in soil research due to their potential to replace conventional microplastics. Biofertilizers are viewed as an alternative to inorganic fertilizers in agriculture due to their potential to enhance crop yields and food safety. The use of both can have direct and indirect effects on rhizosphere microorganisms. However, the influence of the coexistence of "Bio-MPs and biofertilizers" on rhizosphere microbial characteristics remains unclear. We investigated the effects of coexisting biofertilizers and Bio-MPs on the structure, function, and especially the carbon metabolic properties of crop rhizosphere bacteria, using a pot experiment in which polyethylene microplastics (PE-MPs) were used as a reference. The results showed that the existence of both microplastics (MPs) changed the physicochemical properties of the rhizosphere soil. Exposure to MPs also remarkably changed the composition and diversity of rhizosphere bacteria. The network was more complex in the Bio-MPs group. Additionally, metagenomic analyses showed that PE-MPs mainly affected microbial vitamin metabolism. Bio-MPs primarily changed the pathways related to carbon metabolism, such as causing declined carbon fixation/degradation and inhibition of methanogenesis. After partial least squares path model (PLS-PM) analysis, we observed that both materials influenced the rhizosphere environment through the bacterial communities and functions. Despite the degradability of Bio-MPs, our findings confirmed that the coexistence of biofertilizers and Bio-MPs affected the fertility of the rhizosphere. Regardless of the type of plastic, its use in soil requires an objective and scientifically grounded approach.}, } @article {pmid39338979, year = {2024}, author = {Opitz-Ríos, C and Burgos-Pacheco, A and Paredes-Cárcamo, F and Campanini-Salinas, J and Medina, DA}, title = {Metagenomics Insight into Veterinary and Zoonotic Pathogens Identified in Urban Wetlands of Los Lagos, Chile.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {9}, pages = {}, pmid = {39338979}, issn = {2076-0817}, support = {11230295//Agencia Nacional de Investigación y Desarrollo/ ; VRID_FAPPE21-07//Universidad San Sebastián/ ; VRID_INTER23/02//Universidad San Sebastián/ ; VRID_DocI22/06//Universidad San Sebastián/ ; }, abstract = {Wetlands are ecosystems that are essential to ecological balance and biodiversity; nevertheless, human activity is a constant threat to them. Excess nutrients are caused by intensive livestock and agricultural operations, pollution, and population growth, which in turn leads to uncontrolled microbiological development. This impairment in water quality can constitute a risk to animal, human, and environmental health. To thoroughly characterize the microbial communities, shotgun metagenomics was used to characterize the taxonomic and functional pattern of microorganisms that inhabit urban wetlands in the Los Lagos Region of Chile. The main objective was to identify microorganisms of veterinary relevance, assess their potential antibiotic resistance, and characterize the main virulence mechanism. As expected, a high diversity of microorganisms was identified, including bacteria described as animal or human pathogens, such as Pasteurella multocida, Pseudomonas aeruginosa, Staphylococcus aureus, and Escherichia coli. Also, a diverse repertory of antimicrobial-resistant genes (ARGs) was detected in metagenomic assembled sequences and inside the sequence of mobile genetic elements, genes that confer mainly resistance to beta-lactams, consistent with the families of antibiotics most used in Chile. In addition, a diverse collection of virulence mechanisms was also identified. Given the significance of the relationship between environmental, animal, and human health-a concept known as One Health-there is a need to establish molecular surveillance programs that monitor the environmental biohazard elements using molecular tools. This work is the first report of the presence of these harmful biological elements in urban wetlands subjected to anthropogenic pressure, located in the south of Chile.}, } @article {pmid39338934, year = {2024}, author = {Rimoldi, SG and Tamoni, A and Rizzo, A and Longobardi, C and Pagani, C and Salari, F and Matinato, C and Vismara, C and Gagliardi, G and Cutrera, M and Gismondo, MR}, title = {Evaluation of 16S-Based Metagenomic NGS as Diagnostic Tool in Different Types of Culture-Negative Infections.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {9}, pages = {}, pmid = {39338934}, issn = {2076-0817}, abstract = {Bacterial infections pose significant global health challenges, often underestimated due to difficulties in accurate diagnosis, especially when culture-based diagnostics fail. This study assesses the effectiveness of 16S-based metagenomic next generation sequencing (NGS) for identifying pathogens in culture-negative clinical samples across various medical settings. Overall, 48% of samples were collected from orthopedics, 15% from neurosurgery, and 12% in cardiac surgery, among others. The detection rate of monomicrobial infections was 68.6%, and 5.7% for polymicrobial infections. In addition, NGS detected bacteria in all samples from the lungs, head and neck, and eye specimens. Cutibacterium acnes (11%, 12/105) was the most frequent microorganism, followed by Staphylococcus epidermidis (10.4%, 11/105), and Staphylococcus aureus (9.5%, 10/105). In conclusion, 16S-targeted metagenomic sequencing enhances pathogen detection capabilities, particularly in instances where traditional cultures fail. By the combination of NGS and bacterial cultures, microbiologists might provide a more accurate diagnosis, guiding more effective treatments and potentially reducing healthcare costs associated with empirical treatments.}, } @article {pmid39338575, year = {2024}, author = {Yin, X and Chen, H and Jiang, K and Zhang, B and Li, R and Zhu, X and Sun, L and Ng, ZL and Su, M}, title = {Distribution Characteristics of Nitrogen-Cycling Microorganisms in Deep-Sea Surface Sediments of Western South China Sea.}, journal = {Microorganisms}, volume = {12}, number = {9}, pages = {}, pmid = {39338575}, issn = {2076-2607}, support = {2023B1111050014//Guangdong Key Areas R & D Project/ ; SML2021SP307//Project supported by Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; 23qnpy96//Fundamental Research Funds for the Central Universities, Sun Yat-sen University/ ; 24xkjc010//Fundamental Research Funds for the Central Universities, Sun Yat-sen University/ ; }, abstract = {Nitrogen-cycling processes in the deep sea remain understudied. This study investigates the distribution of nitrogen-cycling microbial communities in the deep-sea surface sediments of the western South China Sea, using metagenomic sequencing and real-time fluorescent quantitative PCR techniques to analyze their composition and abundance, and the effects of 11 environmental parameters, including NH4[+]-N, NO3[-]-N, NO2[-]-N, PO4[3-]-P, total nitrogen (TN), total organic carbon (TOC), C/N ratio, pH, electrical conductivity (EC), SO4[2-], and Cl[-]. The phylum- and species-level microbial community compositions show that five sites can be grouped as a major cluster, with sites S1 and S9 forming a sub-cluster, and sites S13, S19, and S26 forming the other; whereas sites S3 and S5 constitute a separate cluster. This is also evident for nitrogen-cycling functional genes, where their abundance is influenced by distinct environmental conditions, including water depths (shallower at sites S1 and S9 against deeper at sites S13, S19, and S26) and unique geological features (sites S3 and S5), whereas the vertical distribution of nitrogen-cycling gene abundance generally shows a decreasing trend against sediment depth. Redundancy analysis (RDA) exploring the correlation between the 11 environmental parameters and microbial communities revealed that the NO2[-]-N, C/N ratio, and TN significantly affect microbial community composition (p < 0.05). This study assesses the survival strategies of microorganisms within deep-sea surface sediments and their role in the marine nitrogen cycle.}, } @article {pmid39338573, year = {2024}, author = {Chen, S and Fang, Y and Fujita, R and Khater, EIM and Li, Y and Wang, W and Qian, P and Huang, L and Guo, Z and Zhang, Y and Li, S}, title = {An Exploration of the Viral Coverage of Mosquito Viromes Using Meta-Viromic Sequencing: A Systematic Review and Meta-Analysis.}, journal = {Microorganisms}, volume = {12}, number = {9}, pages = {}, pmid = {39338573}, issn = {2076-2607}, support = {No.32161143036, No.32311540013//National Natural Science Foundation of China/ ; No. 2022FY100900, 2022FY100904//the Science & Technology Fundamental Resources Investigation Program/ ; No. GWVI-11.1-12//Three-Year Initiative Plan for Strengthening Public Health System Construction in Shanghai (2023-2025) Key Discipline Project/ ; }, abstract = {The aim of this review was to delve into the extent of mosquito virome coverage (proportion of viral reads) via meta-viromic sequencing and uncover potential factors of heterogeneity that could impact this coverage. Data sources were PubMed, Web of Science, Embase, Scopus, Science-Direct, Google Scholar, and the China National Knowledge Infrastructure. Pooled coverage was estimated using random-effects modeling, and subgroup analyses further reveal potential heterogeneous factors. Within the three mosquito genera studied, Culex exhibited the highest pooled viral coverage of mosquito viromes at 7.09% (95% CI: 3.44-11.91%), followed by Anopheles at 5.28% (95% CI: 0.45-14.93%), and Aedes at 2.11% (95% CI: 0.58-7.66%). Subgroup analyses showed that multiple processing methods significantly affected the viral coverage of mosquito viromes, especially pre-treatment of mosquito samples with saline buffer/medium and antibiotics prior to DNase/RNase treatment and removal of the host genome prior to RNA library construction. In conclusion, the results of this study demonstrate that the viral coverage of mosquito viromes varies between mosquito genera and that pre-treatment of mosquito samples with saline buffer/medium and antibiotics before DNase/RNase treatment and removing host genomes prior to RNA library construction are critical for the detection of RNA viruses in mosquito vectors using meta-viromic sequencing.}, } @article {pmid39338498, year = {2024}, author = {Liborio, MP and Harris, PNA and Ravi, C and Irwin, AD}, title = {Getting Up to Speed: Rapid Pathogen and Antimicrobial Resistance Diagnostics in Sepsis.}, journal = {Microorganisms}, volume = {12}, number = {9}, pages = {}, pmid = {39338498}, issn = {2076-2607}, abstract = {Sepsis is a life-threatening organ dysfunction caused by a dysregulated host response to infection. Time to receive effective therapy is a primary determinant of mortality in patients with sepsis. Blood culture is the reference standard for the microbiological diagnosis of bloodstream infections, despite its low sensitivity and prolonged time to receive a pathogen detection. In recent years, rapid tests for pathogen identification, antimicrobial susceptibility, and sepsis identification have emerged, both culture-based and culture-independent methods. This rapid narrative review presents currently commercially available approved diagnostic molecular technologies in bloodstream infections, including their clinical performance and impact on patient outcome, when available. Peer-reviewed publications relevant to the topic were searched through PubMed, and manufacturer websites of commercially available assays identified were also consulted as further sources of information. We have reviewed data about the following technologies for pathogen identification: fluorescence in situ hybridization with peptide nucleic acid probes (Accelerate Pheno[TM]), microarray-based assay (Verigene[®]), multiplex polymerase chain reaction (cobas[®] eplex, BioFire[®] FilmArray[®], Molecular Mouse, Unyvero BCU System[TM]), matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (Rapid MBT Sepsityper[®]), T2 magnetic resonance (T2Bacteria Panel), and metagenomics-based assays (Karius[©], DISQVER[®], Day Zero Diagnostics). Technologies for antimicrobial susceptibility testing included the following: Alfed 60 AST[TM], VITEK[®] REVEAL[TM], dRAST[TM], ASTar[®], Fastinov[®], QuickMIC[®], Resistell[TM], and LifeScale. Characteristics, microbiological performance, and issues of each method are described, as well as their clinical performance, when available.}, } @article {pmid39338467, year = {2024}, author = {Wang, Z and Sun, J and Yang, P and Zhang, W and Jiang, Y and Liu, Q and Yang, Y and Hao, R and Guo, G and Huo, W and Zhang, Q and Li, Q}, title = {Molecular Analysis of Indole and Skatole Decomposition Metabolism in Acinetobacter piscicola p38 Utilizing Biochemical and Omics Approaches.}, journal = {Microorganisms}, volume = {12}, number = {9}, pages = {}, pmid = {39338467}, issn = {2076-2607}, support = {20211331-15//the Shanxi Province "1331 Project" funded project (20211331-15)/ ; }, abstract = {Indole and skatole (3-methylindole, C9H9N) are common nitrogen-containing heterocyclic pollutants found in waste, wastewater treatment plants, and public restrooms and are the most notorious compounds in animal feces. Biodegradation was considered a feasible method for the removal of indole and skatole, but a comprehensive understanding of the metabolic pathways under both aerobic and anaerobic conditions was lacking, and the functional genes responsible for skatole biodegradation remained a mystery. Through metagenomic and gene cluster functional analysis, Acinetobacter piscicola p38 (NCBI: CP167896), genes 1650 (styrene monooxygenase: ACDW34_08180), and 1687 (styrene monooxygenase: ACDW34_08350) were identified as having the potential to degrade indole and skatole. The heterologous expression results demonstrate that the genes 1650 and 1651 (flavin reductase: ACDW34_08185), when combined, are capable of degrading indole, while the genes 1687 and 1688 (flavin reductase: ACDW34_08355), in combination, can degrade indole as well as skatole. These reactions necessitate the involvement of flavin reductase and NAD(P)H to catalyze the oxygenation process. This work aimed to provide new experimental evidence for the biodegradation of indole and skatole. This study offered new insights into our understanding of skatole degradation. The Acinetobacter_piscicola p38 strain provided an effective bacterial resource for the bioremediation of fecal indole and skatole.}, } @article {pmid39338426, year = {2024}, author = {Guimarães, LO and Bahia, SL and Ribeiro, GO and Ramos, EDSF and Villanova, F and Dos Santos Morais, V and Telles-de-Deus, J and Helfstein, VC and Santos, JMD and Pandey, RP and Deng, X and Delwart, E and Camargo-Neves, VLF and da Costa, AC and Kirchgatter, K and Leal, É}, title = {New Iflavirus Species Characterized from Mosquitoes Captured in the Sao Paulo Zoological Facilities.}, journal = {Microorganisms}, volume = {12}, number = {9}, pages = {}, pmid = {39338426}, issn = {2076-2607}, support = {2017/50345-5//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2018/16232-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 309396/2021-2//National Council for Scientific and Technological Development/ ; }, abstract = {Metagenomic studies of mosquito viromes demonstrated a more diverse composition than just an exclusive composition of pathogenic arboviruses transmitted to humans. In our study, the virome of 866 female mosquitoes collected throughout 2020 at the São Paulo Zoo, located in the city of São Paulo/SP-Brazil, was obtained. Specifically, in this paper, we describe a new virus found by viral RNA extraction and next-generation MiSeq sequencing of a group of 23 specimens of Anopheles (Nys.) strodei. The complete genome with a length of 9709 nucleotides was characterized by a positive orientation and a single strand, with a single large ORF, which encodes a polyprotein of 2987 amino acids. The phylogenetic analysis showed an association with the viral family Iflaviridae and the Riboviria realm. We carried out comparisons with translated sequences of the capsid regions of other iflavirus, and the identities in relation to our sequence were below the minimum limit of 90%, indicating that possibly it is a new species of iflavirus. Our findings contribute to expanding knowledge of virome composition among mosquito species in Brazil and globally. Moreover, we provide a viral genome reference specific to this geographic region and Culicidae family of mosquitoes. This resource facilitates future in silico recognition and assembly of viral genomes within metagenomic datasets.}, } @article {pmid39338129, year = {2024}, author = {Mayer, MH and Woldemariam, S and Gisinger, C and Dorner, TE}, title = {Association of Gut Microbiome with Muscle Mass, Muscle Strength, and Muscle Performance in Older Adults: A Systematic Review.}, journal = {International journal of environmental research and public health}, volume = {21}, number = {9}, pages = {}, pmid = {39338129}, issn = {1660-4601}, mesh = {Aged ; Aged, 80 and over ; Humans ; *Gastrointestinal Microbiome/physiology ; *Muscle Strength/physiology ; *Muscle, Skeletal/physiology ; *Sarcopenia/microbiology/physiopathology ; }, abstract = {Sarcopenia, characterized by reduced muscle mass, strength, or performance, is a common condition in older adults. The association between the gut microbiome and sarcopenia remains poorly understood. This systematic review aims to evaluate the relationship between muscle parameters and the intestinal microbiome. A systematic search was conducted in PubMed, EMBASE, Cochrane Library, and Google Scholar for studies published between 2002 and 2022 involving participants aged 50+. Studies were included if they assessed sarcopenia using at least one measure of muscle mass (skeletal muscle mass, bioelectrical impedance analysis, MRI), muscle strength, or muscle performance (SARC-F questionnaire, Timed-Up-and-Go Test, Chair Stand Test, grip strength, gait speed, Short Physical Performance Battery, 400 m Walk Test). The microbiome was measured using at least RNA/DNA sequencing or shotgun metagenomic sequencing. Twelve studies were analyzed. Findings revealed that a higher abundance of bacterial species such as Desulfovibrio piger, and Clostridium symbiosum and reduced diversity of butyrate-producing bacteria was associated with sarcopenia severity, as indicated by decreased grip strength, muscle mass, or physical performance. The gut microbiome plays a significant role in age-related muscle loss. Probiotics, prebiotics, and bacterial products could be potential interventions to improve muscle health in older adults.}, } @article {pmid39336713, year = {2024}, author = {Dyall-Smith, M and Pfeiffer, F}, title = {Global Distribution and Diversity of Haloarchaeal pL6-Family Plasmids.}, journal = {Genes}, volume = {15}, number = {9}, pages = {}, pmid = {39336713}, issn = {2073-4425}, mesh = {*Plasmids/genetics ; Phylogeny ; Halobacteriaceae/genetics ; Australia ; Metagenome ; Argentina ; Spain ; Base Composition/genetics ; Puerto Rico ; Genetic Variation ; }, abstract = {Australian isolates of Haloquadratum walsbyi, a square-shaped haloarchaeon, often harbor small cryptic plasmids of the pL6-family, approximately 6 kb in size, and five examples have been previously described. These plasmids exhibit a highly conserved gene arrangement and encode replicases similar to those of betapleolipoviruses. To assess their global distribution and recover more examples for analysis, fifteen additional plasmids were reconstructed from the metagenomes of seven hypersaline sites across four countries: Argentina, Australia, Puerto Rico, and Spain. Including the five previously described plasmids, the average plasmid size is 6002 bp, with an average G+C content of 52.5%. The tetramers GGCC and CTAG are either absent or significantly under-represented, except in the two plasmids with the highest %G+C. All plasmids share a similar arrangement of genes organized as outwardly facing replication and ATPase modules, but variations were observed in some core genes, such as F2, and some plasmids had acquired accessory genes. Two plasmids, pCOLO-c1 and pISLA-c6, shared 92.7% nt identity despite originating from Argentina and Spain, respectively. Numerous metagenomic CRISPR spacers matched sequences in the fifteen reconstructed plasmids, indicating frequent invasion of haloarchaea. Spacers could be assigned to haloarchaeal genera by mapping their associated direct repeats (DR), with half of these matching Haloquadratum. Finally, strand-specific metatranscriptome (RNA-seq) data could be used to demonstrate the active transcription of two pL6-family plasmids, including antisense transcripts.}, } @article {pmid39335716, year = {2024}, author = {Thomas-White, K and Hilt, EE and Olmschenk, G and Gong, M and Phillips, CD and Jarvis, C and Sanford, N and White, J and Navarro, P}, title = {A Metagenomics Pipeline to Characterize Self-Collected Vaginal Microbiome Samples.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {14}, number = {18}, pages = {}, pmid = {39335716}, issn = {2075-4418}, abstract = {Vaginitis is a widespread issue for women worldwide, yet current diagnostic tools are lacking. Bacterial vaginosis (BV) is the most prevalent type of vaginitis, found in 10-50% of reproductive-aged women. Current diagnostic methods for BV rely on clinical criteria, microscopy, or the detection of a few microbes by qPCR. However, many vaginal infections lack a single etiological agent and are characterized by changes in the vaginal microbiome community structure (e.g., BV is defined as a loss of protective lactobacilli resulting in an overgrowth of anaerobic bacteria). Shotgun metagenomic sequencing provides a comprehensive view of all the organisms present in the vaginal microbiome (VMB), allowing for a better understanding of all potential etiologies. Here, we describe a robust VMB metagenomics sequencing test with a sensitivity of 93.1%, a specificity of 90%, a negative predictive value of 93.4%, and a positive predictive value of 89.6% certified by Clinical Laboratory Improvement Amendments (CLIA), the College of American Pathologist (CAP), and the Clinical Laboratory Evaluation Program (CLEP). We sequenced over 7000 human vaginal samples with this pipeline and described general findings and comparisons to US census data.}, } @article {pmid39335298, year = {2024}, author = {Tang, J and Wang, Q and Yu, H and Dong, L and Tang, M and Arif, A and Zhang, G and Zhang, T and Xie, K and Su, S and Zhao, Z and Dai, G}, title = {A Comparison of the Cecal Microbiota between the Infection and Recovery Periods in Chickens with Different Susceptibilities to Eimeria tenella.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {18}, pages = {}, pmid = {39335298}, issn = {2076-2615}, support = {JATS [2023]447//the Jiangsu Agricultural Industry Technology System/ ; }, abstract = {To investigate the effect of Eimeria tenella (E. tenella) infection on the cecal microbiota, resistant and susceptible families were screened out based on the coccidiosis resistance evaluation indexes after E. tenella infection. Subsequently, a comparative analysis of cecal microorganisms among control, resistant, and susceptible groups as well as between different periods following the E. tenella challenge was conducted using metagenomic sequencing technology. The results showed that the abundance of opportunistic pathogens, such as Pantoea, Sporomusa, and Pasteurella in the susceptible group and Helicobacter and Sutterella in the resistant group, was significantly higher on day 27 post-inoculation (PI) (the recovery period) than on day 5 PI (the infection period). Additionally, the abundance of Alistipes, Butyricicoccus, and Eubacterium in the susceptible group and Coprococcus, Roseburia, Butyricicoccus, and Lactobacillus in the resistant group showed a significant upward trend during the infection period compared with that in the recovery period. On day 5 PI, the abundance of Faecalibacterium and Lactobacillus was decreased in both the resistant and susceptible groups when compared with that in the control group and was greater in the resistant group than in the susceptible group, while Alistipes in the susceptible group had a relatively higher abundance than that in other groups. A total of 49 biomarker taxa were identified using the linear discriminant analysis (LDA) effect size (LEfSe) method. Of these, the relative abundance of Lactobacillus aviarius, Lactobacillus salivarius, Roseburia, and Ruminococcus gauvreauii was increased in the resistant group, while Bacteroides_sp__AGMB03916, Fusobacterium_mortiferum, Alistipes_sp__An31A, and Alistipes_sp__Marseille_P5061 were enriched in the susceptible group. On day 27 PI, LDA scores identified 43 biomarkers, among which the relative abundance of Elusimicrobium_sp__An273 and Desulfovibrio_sp__An276 was increased in the resistant group, while that of Bacteroides_sp__43_108, Chlamydiia, Chlamydiales, and Sutterella_sp__AM11 39 was augmented in the susceptible group. Our results indicated that E. tenella infection affects the structure of the cecal microbiota during both the challenge and recovery periods. These findings will enhance the understanding of the effects of changes in the cecal microbiota on chickens after coccidia infection and provide a reference for further research on the mechanisms underlying how the intestinal microbiota influence the growth and health of chickens.}, } @article {pmid39335279, year = {2024}, author = {Cheng, Z and Huang, H and Qiao, G and Wang, Y and Wang, X and Yue, Y and Gao, Q and Peng, S}, title = {Metagenomic and Metabolomic Analyses Reveal the Role of Gut Microbiome-Associated Metabolites in the Muscle Elasticity of the Large Yellow Croaker (Larimichthys crocea).}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {18}, pages = {}, pmid = {39335279}, issn = {2076-2615}, support = {2021Z01//the Central Nonprofit Basic Scientific Research Project for the Scientific Research Institutes of China/ ; 2022YFD2401004//This work was supported by a grant from the National Key Research and Development Program of China/ ; }, abstract = {The large yellow croaker (LYC, Larimichthys crocea) is highly regarded for its delicious taste and unique flavor. The gut microbiota has the ability to affect the host muscle performance and elasticity by regulating nutrient metabolism. The purpose of this study is to establish the relationship between muscle quality and intestinal flora in order to provide reference for the improvement of the muscle elasticity of LYC. In this study, the intestinal contents of high muscle elasticity males (IEHM), females (IEHF), and low muscle elasticity males (IELM) and females (IELF) were collected and subjected to metagenomic and metabolomic analyses. Metagenomic sequencing results showed that the intestinal flora structures of LYCs with different muscle elasticities were significantly different. The abundance of Streptophyta in the IELM (24.63%) and IELF (29.68%) groups was significantly higher than that in the IEHM and IEHF groups. The abundance of Vibrio scophthalmi (66.66%) in the IEHF group was the highest. Based on metabolomic analysis by liquid chromatograph-mass spectrometry, 107 differentially abundant metabolites were identified between the IEHM and IELM groups, and 100 differentially abundant metabolites were identified between the IEHF and IELF groups. Based on these metabolites, a large number of enriched metabolic pathways related to muscle elasticity were identified. Significant differences in the intestinal metabolism between groups with different muscle elasticities were identified. Moreover, the model of the relationship between the intestinal flora and metabolites was constructed, and the molecular mechanism of intestinal flora regulation of the nutrient metabolism was further revealed. The results help to understand the molecular mechanism of different muscle elasticities of LYC and provide an important reference for the study of the mechanism of the effects of LYC intestinal symbiotic bacteria on muscle development, and the development and application of probiotics in LYC.}, } @article {pmid39334245, year = {2024}, author = {Van Herzele, C and Coppens, S and Vereecke, N and Theuns, S and de Graaf, DC and Nauwynck, H}, title = {New insights into honey bee viral and bacterial seasonal infection patterns using third-generation nanopore sequencing on honey bee haemolymph.}, journal = {Veterinary research}, volume = {55}, number = {1}, pages = {118}, pmid = {39334245}, issn = {1297-9716}, support = {1SB3123N//Fonds Wetenschappelijk Onderzoek/ ; Baekeland mandate HBC.2020.2889//Agentschap Innoveren en Ondernemen/ ; }, mesh = {Animals ; Bees/virology/microbiology ; *Seasons ; *Hemolymph/virology/microbiology ; Nanopore Sequencing/methods/veterinary ; Bacteria/genetics/isolation & purification/classification ; Virome ; }, abstract = {Honey bees are rapidly declining, which poses a significant threat to our environment and agriculture industry. These vital insects face a disease complex believed to be caused by a combination of parasites, viruses, pesticides, and nutritional deficiencies. However, the real aetiology is still enigmatic. Due to the conventional analysis methods, we still lack complete insights into the honey bee virome and the presence of pathogenic bacteria. To fill this knowledge gap, we employed third-generation nanopore metagenomic sequencing on honey bee haemolymph to monitor the presence of pathogens over almost a year. This study provides valuable insights into the changes in bacterial and viral loads within honey bee colonies. We identified different pathogens in the honey bee haemolymph, which are not included in honey bee screenings. These pathogens comprise the Apis mellifera filamentous virus, Apis rhabdoviruses, and various bacteria such as Frischella sp. and Arsenophonus sp. Furthermore, a sharp contrast was observed between young and old bees. Our research proposes that transgenerational immune priming may play a role in shaping infection patterns in honey bees. We observed a significant increase in pathogen loads in the spring, followed by a notable decrease in pathogen presence during the summer and autumn months. However, certain pathogens seem to be able to evade this priming effect, making them particularly intriguing as potential factors contributing to mortality. In the future, we aim to expand our research on honey bee transgenerational immune priming and investigate its potential in natural settings. This knowledge will ultimately enhance honey bee health and decrease colony mortality.}, } @article {pmid39334144, year = {2024}, author = {Foro Ramos, EDS and da Silva Couto, R and Tozetto-Mendoza, TR and Bortoletto, P and Barbosa, EMG and Ferreira, NE and Linhares, IM and Spandorfer, SD and da Costa, AC and Leal, E and Mendes-Correa, MC and Witkin, SS}, title = {Characterization of multiple human papillomavirus types in the human vagina following ovarian hormonal stimulation.}, journal = {Virology journal}, volume = {21}, number = {1}, pages = {229}, pmid = {39334144}, issn = {1743-422X}, support = {CAPES//scholarship provided by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior-Brasil/ ; CAPES//scholarship provided by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior-Brasil/ ; HCFMUSP//scholarship from HCFMUSP with funds donated by NUBANK under the #HCCOMVIDA scheme/ ; }, mesh = {Humans ; Female ; *Vagina/virology ; *Papillomavirus Infections/virology ; Adult ; *Phylogeny ; *Papillomaviridae/genetics/classification/isolation & purification ; *Ovulation Induction ; DNA, Viral/genetics ; Sequence Analysis, DNA ; Young Adult ; Metagenomics ; Genotype ; Human Papillomavirus Viruses ; }, abstract = {The objective of study was to characterize HPV in vaginal samples from women being seen at the Center for Reproductive Medicine and Infertility at Weill Cornell Medicine before and following ovarian stimulation. A total of 29 women made samples available for analysis by viral metagenomics. Eighteen women were HPV-positive, six (33.3%) at their initial visit and 15 (83.3%) following hormone stimulation (p = 0.0059). Pairwise comparison of nucleotide sequences and phylogenetic analysis showed the classification sequences into two genera: Alphapapillomavirus and Gammapapillomavirus. Sequences were from 8 HPV types: HPV 51 (n = 2), HPV 68 (n = 1), HPV 83 (n = 9), HPV 84 (n = 2), HPV 121 (n = 6), HPV 175 (n = 1) and HPV 190 (n = 1). Additionally, C16b and C30 likely represent new types. In summary, multiple HPV types are present in the vagina of reproductive age women and are induced by hormone used to stimulate ovulation.}, } @article {pmid39334057, year = {2024}, author = {Wang, C and Hu, ZW and Li, ZY and Zhao, MH and Little, MA and Chen, M}, title = {Advantages of metagenomic next-generation sequencing in the management of ANCA-associated vasculitis patients with suspected pulmonary infection as a rule-out tool.}, journal = {BMC pulmonary medicine}, volume = {24}, number = {1}, pages = {478}, pmid = {39334057}, issn = {1471-2466}, support = {BJPSTP-2024-15//Beijing Physician Scientist Training Project/ ; BMU2024PYJH009//Peking University Clinical Scientist Training Program, supported by "the Fundamental Research Funds for the Central Universities"/ ; 2022YFC2502500/2022YFC2502502//National Key Research and Development Program of China/ ; 2022YFC2502500/2022YFC2502502//National Key Research and Development Program of China/ ; 82090020/82090021 and 82270754//National Natural Science Fund/ ; 82090020/82090021 and 82270754//National Natural Science Fund/ ; 2019RU023//Chinese Academy of Medical Sciences Research Unit/ ; 2019RU023//Chinese Academy of Medical Sciences Research Unit/ ; 2022CR52//National High Level Hospital Clinical Research Funding (Multi-center Clinical Research Project of Peking University First Hospital)/ ; 2022CR52//National High Level Hospital Clinical Research Funding (Multi-center Clinical Research Project of Peking University First Hospital)/ ; 2024HQ01//National High Level Hospital Clinical Research Funding (High Quality Clinical Research Project of Peking University First Hospital)/ ; 2024HQ01//National High Level Hospital Clinical Research Funding (High Quality Clinical Research Project of Peking University First Hospital)/ ; }, mesh = {Humans ; *Anti-Neutrophil Cytoplasmic Antibody-Associated Vasculitis/diagnosis/drug therapy ; Male ; Female ; Middle Aged ; *Bronchoalveolar Lavage Fluid/microbiology ; Retrospective Studies ; Aged ; *High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; Bronchoscopy ; Hospital Mortality ; Respiratory Tract Infections/microbiology/diagnosis/drug therapy ; Adult ; }, abstract = {OBJECTIVE: Pulmonary infection is one of the leading causes of death in patients with ANCA-associated vasculitis (AAV). It is sometimes difficult to differentiate pulmonary infection from pulmonary involvement of vasculitis in AAV patients. Fiberoptic bronchoscopy and bronchoalveolar lavage fluid (BALF) assays are useful diagnostic methods. In addition to conventional microbiological tests (CMTs), metagenomic next-generation sequencing (mNGS) facilitates rapid and sensitive detection of various pathogens. The current study aimed to evaluate the advantages of additional BALF mNGS in the management of pulmonary infection in AAV patients.

METHODS: 27 patients with active AAV and suspected pulmonary infection whose BALF samples were tested by mNGS and CMTs and 17 active AAV patients whose BALF were tested by CMTs alone were retrospectively recruited. The results of microbiological tests, and adjustments of treatment following BALF mNGS, were described. The durations of antimicrobial treatment and in-hospital mortality in patients were compared.

RESULTS: Among the 27 patients whose BALF samples were tested by mNGS, 25.9% of patients did not have evidence of pathogenic microorganism in their BALF samples, 55.6% had polymicrobial infections, including bacteria, fungi and viruses. Of these 27 patients, 40.7% did not have evidence of pathogenic microorganism in their BALF or serum samples according to CMTs. Patients in the BALF mNGS/CMT group received a significantly shorter duration of antibacterial and total antimicrobial treatment than patients in the CMT alone group (17.3 ± 14.7 vs. 27.9 ± 19.0 days, P = 0.044; 18.9 ± 15.0 vs. 29.5 ± 17.7 days, P = 0.040, respectively). Fewer patients in the BALF mNGS/CMT group died than in the CMT alone group (4/27 vs. 7/17, P = 0.049).

CONCLUSION: Compared with CMT alone, additional mNGS tests may shorten the duration of antimicrobial treatment and possibly decrease death from severe infection by providing precise and quick diagnosis of infection.}, } @article {pmid39333982, year = {2024}, author = {Kanagiri, T and Meena, DS and Kumar, D and Midha, NK and Kombade, S and Yadav, T}, title = {Recurrent pulmonary nocardiosis due to Nocardia Otitidiscaviarum in a patient with isolated CD4 lymphocytopenia: a case report.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {1033}, pmid = {39333982}, issn = {1471-2334}, mesh = {Humans ; Female ; *Nocardia Infections/drug therapy/microbiology/diagnosis ; Middle Aged ; *Nocardia/isolation & purification/genetics ; Recurrence ; T-Lymphocytopenia, Idiopathic CD4-Positive/complications ; Anti-Bacterial Agents/therapeutic use ; Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use ; CD4 Lymphocyte Count ; Lymphopenia/complications ; }, abstract = {BACKGROUND: Idiopathic CD4 lymphocytopenia (ICL) is an underdiagnosed immunodeficiency syndrome characterised by persistent low CD4 counts in the absence of HIV and other causes of lymphocytopenia. ICL patients are susceptible to opportunistic infections, with human papillomavirus, cryptococcal, and tuberculosis being the most common infections reported. Nocardiosis is rarely reported in patient with ICL.

CASE PRESENTATION: We herein discuss a 46-year-old female presented with complaints of weight loss, low grade fever and cough with expectoration from last four months. The patient was diagnosed with pulmonary nocardiosis and aspergillosis co-infection four years back; in addition she also had ICL. Subsequently, the patient was lost in follow-up and readmitted four years later. Bronchoalveolar lavage sample shows the presence of acid-fast bacilli in modified gram stain, which later identified as Nocardia otitidiscaviarum by metagenomic next-generation sequencing. Her CD4 counts were still found low (298 cells/mm[3]). After an initial improvement with trimethoprim-sulfamethoxazole (TMP-SMX), she was commenced on indefinite secondary prophylaxis.

CONCLUSIONS: Nocardiosis without usual risk factors should be evaluated for ICL. This case emphasize the importance of periodic follow-up with CD4 count monitoring and secondary prophylaxis therapy to prevent recurrence or the emergence of new infections in ICL.

CLINICAL TRIAL NUMBER: Not applicable.}, } @article {pmid39333956, year = {2024}, author = {Ai, L and Qi, Y and Hu, Y and Zhu, C and Liu, K and Li, F and Ye, F and Dai, H and Wu, Y and Kuai, Q and Nie, D and Shan, L and Zhang, Y and Wang, C and Tan, W}, title = {The epidemiological and infectious characteristics of novel types of Coxiella burnetii co-infected with Coxiella-like microorganisms from Xuyi County, Jiangsu province, China.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {1041}, pmid = {39333956}, issn = {1471-2334}, support = {2024YQZL02//Incubation Project of Huadong Research Institute for Medicine and Biotechniques/ ; H2019015, M2020087//Project of Medical Research Topics of Jiangsu Provincial Health Planning Commission/ ; H2019015, M2020087//Project of Medical Research Topics of Jiangsu Provincial Health Planning Commission/ ; BK20221196, BE2022682//Jiangsu Science and Technology Plan/ ; BK20221196, BE2022682//Jiangsu Science and Technology Plan/ ; U1602223//National Natural Science Foundation of China/ ; }, mesh = {*Q Fever/epidemiology/microbiology ; *Coxiella burnetii/genetics/isolation & purification ; Animals ; China/epidemiology ; Humans ; *Ticks/microbiology ; *Hedgehogs/microbiology ; Mice ; Coinfection/microbiology/epidemiology ; Female ; Male ; Seroepidemiologic Studies ; Genotype ; Antibodies, Bacterial/blood ; High-Throughput Nucleotide Sequencing ; Zoonoses/microbiology/epidemiology ; Coxiella/genetics/isolation & purification ; Molecular Epidemiology ; Phylogeny ; }, abstract = {Coxiella burnetii (C. burnetii) is the causative agent of Q fever, a type of zoonoses withwidespread distribution. In 2019, a case of Q fever was diagnosed by metagenomic next-generation sequencing (mNGS) method in Xuyi County (Jiangsu province, China). The seroprevalence of previous fever patients and the molecular epidemiology of Coxiella in wild hedgehogs and harbouring ticks around the confirmed patient were detected to reveal the genetic characteristics and pathogenicity of the Coxiella strains. Four of the 90 serum samples (4.44%) were positive for specific C. burnetii IgM antibody, suggesting that local humans are at risk of Q fever. The positive rates of C. burnetii in hedgehogs and ticks were 21.9% (7/32) and 70.5% (122/173), respectively. At least 3 strains of Coxiella were found prevalent in the investigated area, including one new genotype of pathogenic C. burnetii (XYHT29) and two non-pathogenic Coxiella-like organisms (XYHT19 and XYHT3). XYHT29 carried by ticks and wild hedgehogs successfully infected mice, imposing a potential threat to local humans. XYHT19, a novel Coxiella-like microorganism, was first discovered in the world to co-infect with C. burnetii in Haemaphysalis flava. The study provided significant epidemic information that could be used for prevention and control strategies against Q fever for local public health departments and medical institutions.}, } @article {pmid39333778, year = {2024}, author = {Msango, K and Gouda, MNR and Ramakrishnan, B and Kumar, A and Subramanian, S}, title = {Variation and functional profile of gut bacteria in the scarab beetle, Anomala dimidiata, under a cellulose-enriched microenvironment.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {22400}, pmid = {39333778}, issn = {2045-2322}, mesh = {Animals ; *Coleoptera/microbiology ; *Cellulose/metabolism ; *Gastrointestinal Microbiome ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Larva/microbiology ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Symbiosis ; }, abstract = {This study utilized cultivable methods and 16 S amplicon sequencing to compare taxonomic profiles and functional potential of gut bacteria in the scarab beetle, Anomola dimidiata, under cellulose-enriched conditions. Eight culturable cellulolytic gut bacteria were isolated from the midgut and hindgut of the scarab larvae, respectively. 16 S amplicon sequencing evinced that the most represented taxonomic profiles at phylum level in the fermentation chamber and midgut were Bacillota (71.62 and 56.76%), Pseudomonadota (22.66 and 36.89%) and Bacteroidota (2.7 and 2.81%). Bacillota (56.74 and 91.39%) were significantly enriched in the midgut with the addition of cellulose. In contrast, Bacillota and Psedomonadota were significantly enriched in the fermentation chamber. Carbohydrate metabolism was up-regulated in the midgut, while nitrogen and phosphorus metabolism were up-regulated in the fermentation chamber, suggesting these symbionts' possible metabolic roles to the host. An analysis of total cellulases as well as amplicon sequence variants indicated that the gut bacteria belonging to Acinetobacter, Bacillus, Brucella, Brevibacillus, Enterobacter, Lysinibacillus and Paenibacillus are involved in nutrition provisioning. These results have provided additional insights into the gut bacteria associated with cellulose digestion in A. dimidiata and created a platform for bioprospecting novel isolates to produce biomolecules for biotechnological use, besides identifying eco-friendly targets for its management.}, } @article {pmid39333734, year = {2024}, author = {Ishak, S and Rondeau-Leclaire, J and Faticov, M and Roy, S and Laforest-Lapointe, I}, title = {Boreal moss-microbe interactions are revealed through metagenome assembly of novel bacterial species.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {22168}, pmid = {39333734}, issn = {2045-2322}, mesh = {*Bryophyta/microbiology ; *Bacteria/genetics/metabolism/classification ; *Metagenome ; Taiga ; Metagenomics/methods ; Microbiota ; Quebec ; Nitrogen Fixation ; Photosynthesis ; }, abstract = {Moss-microbe interactions contribute to ecosystem processes in boreal forests. Yet, how host-specific characteristics and the environment drive the composition and metabolic potential of moss microbiomes is still poorly understood. In this study, we use shotgun metagenomics to identify the taxonomy and metabolic potential of the bacteria of four moss species of the boreal forests of Northern Québec, Canada. To characterize moss bacterial community composition and diversity, we assembled the genomes of 110 potentially novel bacterial species. Our results highlight that moss genus, species, gametophyte section, and to a lesser extent soil pH and soil temperature, drive moss-associated bacterial community composition and diversity. In the brown gametophyte section, two Stigonema spp. showed partial pathway completeness for photosynthesis and nitrogen fixation, while all brown-associated Hyphomicrobiales had complete assimilatory nitrate reduction pathways and many nearly complete carbon fixation pathways. Several brown-associated species showed partial to complete pathways for coenzyme M and F420 biosynthesis, important for methane metabolism. In addition, green-associated Hyphomicrobiales (Methylobacteria spp.) displayed potential for the anoxygenic photosystem II pathway. Overall, our findings demonstrate how host-specific characteristics and environmental factors shape the composition and metabolic potential of moss bacteria, highlighting their roles in carbon fixation, nitrogen cycling, and methane metabolism in boreal forests.}, } @article {pmid39333577, year = {2024}, author = {Zhao, B and Zi, M and Zhang, X and Wang, Y}, title = {Microbial communities and metagenomes in methane-rich deep coastal sediments.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1043}, pmid = {39333577}, issn = {2052-4463}, support = {U22B2012//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Methane/metabolism ; *Geologic Sediments/microbiology ; *Microbiota ; *Metagenome ; *Archaea/genetics ; *RNA, Ribosomal, 16S/genetics ; Phylogeny ; }, abstract = {Coastal sediments are rich in embedded recalcitrant organic carbons that are biotransformed into methane. In this study, gas composition (carbon dioxide, methane and nitrogen) and chemical indicators (total nitrogen, total carbon, and total sulfate) were examined in five deep sediment cores (up to 130 m in length) obtained from the Hangzhou Bay. The V3-V4 region of the 16S rRNA gene amplicons was amplified and sequenced for the prokaryotic community analysis. The species composition, along with the physicochemical factors of the sediments, revealed a strong correlation with methane content in one of the sediment cores. We then obtained metagenomes of the two sediment samples selected for their high methane content and enrichment of methanogenic Bathyarchaeota with phylogenetic evidence. A total of 27 draft genomes were retrieved through metagenomic binning methodologies and were classified into Bathyarchaeota, Asgard archaea, Planctomycetes, and other microbial groups. The data provided are valuable for understanding the relationship between methane generation and microbial community composition in deep sediment core samples from coastal to marine environments.}, } @article {pmid39333527, year = {2024}, author = {Cheng, M and Xu, Y and Cui, X and Wei, X and Chang, Y and Xu, J and Lei, C and Xue, L and Zheng, Y and Wang, Z and Huang, L and Zheng, M and Luo, H and Leng, Y and Jiang, C}, title = {Deep longitudinal lower respiratory tract microbiome profiling reveals genome-resolved functional and evolutionary dynamics in critical illness.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {8361}, pmid = {39333527}, issn = {2041-1723}, mesh = {Humans ; *Critical Illness ; *Microbiota/genetics ; *Intensive Care Units ; *Metagenome/genetics ; Metagenomics/methods ; Longitudinal Studies ; Male ; Female ; Plasmids/genetics ; Genome, Bacterial/genetics ; Respiratory System/microbiology ; Aged ; Middle Aged ; Bacteria/genetics/classification/isolation & purification ; Pneumonia/microbiology ; Evolution, Molecular ; }, abstract = {The lower respiratory tract (LRT) microbiome impacts human health, especially among critically ill patients. However, comprehensive characterizations of the LRT microbiome remain challenging due to low microbial mass and host contamination. We develop a chelex100-based low-biomass microbial-enrichment method (CMEM) that enables deep metagenomic profiling of LRT samples to recover near-complete microbial genomes. We apply the method to 453 longitudinal LRT samples from 157 intensive care unit (ICU) patients in three geographically distant hospitals. We recover 120 high-quality metagenome-assembled genomes (MAGs) and associated plasmids without culturing. We detect divergent longitudinal microbiome dynamics and hospital-specific dominant opportunistic pathogens and resistomes in pneumonia patients. Diagnosed pneumonia and the ICU stay duration were associated with the abundance of specific antibiotic-resistance genes (ARGs). Moreover, CMEM can serve as a robust tool for genome-resolved analyses. MAG-based analyses reveal strain-specific resistome and virulome among opportunistic pathogen strains. Evolutionary analyses discover increased mobilome in prevailing opportunistic pathogens, highly conserved plasmids, and new recombination hotspots associated with conjugative elements and prophages. Integrative analysis with epidemiological data reveals frequent putative inter-patient strain transmissions in ICUs. In summary, we present a genome-resolved functional, transmission, and evolutionary landscape of the LRT microbiota in critically ill patients.}, } @article {pmid39333501, year = {2024}, author = {Kutuzova, S and Nielsen, M and Piera, P and Nissen, JN and Rasmussen, S}, title = {Taxometer: Improving taxonomic classification of metagenomics contigs.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {8357}, pmid = {39333501}, issn = {2041-1723}, support = {NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF21SA0072102//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; }, mesh = {*Metagenomics/methods ; *Software ; Neural Networks, Computer ; Classification/methods ; Metagenome/genetics ; Algorithms ; Contig Mapping/methods ; Rhizosphere ; }, abstract = {For taxonomy based classification of metagenomics assembled contigs, current methods use sequence similarity to identify their most likely taxonomy. However, in the related field of metagenomic binning, contigs are routinely clustered using information from both the contig sequences and their abundance. We introduce Taxometer, a neural network based method that improves the annotations and estimates the quality of any taxonomic classifier using contig abundance profiles and tetra-nucleotide frequencies. We apply Taxometer to five short-read CAMI2 datasets and find that it increases the average share of correct species-level contig annotations of the MMSeqs2 tool from 66.6% to 86.2%. Additionally, it reduce the share of wrong species-level annotations in the CAMI2 Rhizosphere dataset by an average of two-fold for Metabuli, Centrifuge, and Kraken2. Futhermore, we use Taxometer for benchmarking taxonomic classifiers on two complex long-read metagenomics data sets where ground truth is not known. Taxometer is available as open-source software and can enhance any taxonomic annotation of metagenomic contigs.}, } @article {pmid39333274, year = {2024}, author = {Licheri, M and Licheri, MF and Probst, L and Sägesser, C and Bittel, P and Suter-Riniker, F and Dijkman, R}, title = {A novel isothermal whole genome sequencing approach for Monkeypox Virus.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {22333}, pmid = {39333274}, issn = {2045-2322}, mesh = {Humans ; Disease Outbreaks ; DNA, Viral/genetics ; *Genome, Viral ; *Monkeypox virus/genetics ; Mpox, Monkeypox/virology/epidemiology ; Nucleic Acid Amplification Techniques/methods ; *Whole Genome Sequencing/methods ; }, abstract = {Monkeypox virus (MPXV) is the zoonotic agent responsible for mpox, an often-self-limiting pox-like disease. Since May 2022, an outbreak characterized by increased human-to-human transmission was detected outside the endemic regions. Whole genome sequencing (WGS) has been successfully used to keep track of viral evolution during outbreaks or for surveillance of multiple pathogens of public health significance. Current WGS protocols for MPXV are either based on metagenomic sequencing or tiled-PCR amplification. The latter allows multiplexing due to the efficient enrichment of the viral DNA, however, mutations or the presence of different clades can negatively influence genome coverage yield. Here, we present the establishment of a novel isothermal WGS method for MPXV based on Phi29 DNA polymerase-based multiple displacement amplification (MDA) properties making use of only 6 primers. This approach yielded from 88% up to 100% genome coverage using either alkaline denatured extracted DNA or clinical material as starting material, with the highest coverage generated by clinical material. We demonstrate that this novel isothermal WGS protocol is suitable for monitoring viral evolution during MPXV outbreaks and surveillance in any conventional laboratory setting.}, } @article {pmid39333204, year = {2024}, author = {Martin Říhová, J and Gupta, S and Nováková, E and Hypša, V}, title = {Fur microbiome as a putative source of symbiotic bacteria in sucking lice.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {22326}, pmid = {39333204}, issn = {2045-2322}, support = {GA20-07674S//Grantová Agentura České Republiky/ ; }, mesh = {Animals ; *Symbiosis ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Phthiraptera/microbiology ; Bacteria/genetics/classification/isolation & purification ; }, abstract = {Symbiosis between insects and bacteria has been established countless times. While it is well known that the symbionts originated from a variety of different bacterial taxa, it is usually difficult to determine their environmental source and a route of their acquisition by the host. In this study, we address this question using a model of Neisseriaceae symbionts in rodent lice. These bacteria established their symbiosis independently with different louse taxa (Polyplax, Hoplopleura, Neohaematopinus), most likely from the same environmental source. We first applied amplicon analysis to screen for candidate source bacterium in the louse environment. Since lice are permanent ectoparasites, often specific to the particular host, we screened various microbiomes associated with three rodent species (Microtus arvalis, Clethrionomys glareolus, and Apodemus flavicollis). The analyzed samples included fur, skin, spleen, and other ectoparasites sampled from these rodents. The fur microbiome data revealed a Neisseriaceae bacterium, closely related to the known louse symbionts. The draft genomes of the environmental Neisseriaceae, assembled from all three rodent hosts, converged to a remarkably small size of approximately 1.4 Mbp, being even smaller than the genomes of the related symbionts. Our results suggest that the rodent fur microbiome can serve as a source for independent establishment of bacterial symbiosis in associated louse species. We further propose a hypothetical scenario of the genome evolution during the transition of a free-living bacterium to the member of the rodent fur-associated microbiome and subsequently to the facultative and obligate louse symbionts.}, } @article {pmid39333145, year = {2024}, author = {Boie, W and Schemmel, M and Ye, W and Hasler, M and Goll, M and Verreet, JA and Cai, D}, title = {An assessment of the species diversity and disease potential of Pythium communities in Europe.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {8369}, pmid = {39333145}, issn = {2041-1723}, support = {031B0910-A//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; 221NR-058B//Fachagentur Nachwachsende Rohstoffe (Agency for Renewable Resources)/ ; }, mesh = {*Pythium/genetics/isolation & purification ; Europe ; *Plant Diseases/microbiology ; *Zea mays/microbiology ; Soil Microbiology ; Biodiversity ; Metagenomics/methods ; }, abstract = {Pythium sensu lato (s.l.) is a genus of parasitic oomycetes that poses a serious threat to agricultural production worldwide, but their severity is often neglected because little knowledge about them is available. Using an internal transcribed spacer (ITS) amplicon-based-metagenomics approach, we investigate the occurrence, abundance, and diversity of Pythium spp. s.l. in 127 corn fields of 11 European countries from the years 2019 to 2021. We also identify 73 species, with up to 20 species in a single soil sample, and the prevalent species, which show high species diversity, varying disease potential, and are widespread in most countries. Further, we show species-species co-occurrence patterns considering all detected species and link species abundance to soil parameter using the LUCAS topsoil dataset. Infection experiments with recovered isolates show that Pythium s.l. differ in disease potential, and that effective interference with plant hormone networks suppressing JA (jasmonate)-mediated defenses is an essential component of the virulence mechanism of Pythium s.l. species. This study provides a valuable dataset that enables deep insights into the structure and species diversity of Pythium s.l. communities in European corn fields and knowledge for better understanding plant-Pythium interactions, facilitating the development of an effective strategy to cope with this pathogen.}, } @article {pmid39333115, year = {2024}, author = {Liao, H and Liu, C and Zhou, S and Liu, C and Eldridge, DJ and Ai, C and Wilhelm, SW and Singh, BK and Liang, X and Radosevich, M and Yang, QE and Tang, X and Wei, Z and Friman, VP and Gillings, M and Delgado-Baquerizo, M and Zhu, YG}, title = {Prophage-encoded antibiotic resistance genes are enriched in human-impacted environments.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {8315}, pmid = {39333115}, issn = {2041-1723}, mesh = {*Prophages/genetics ; Humans ; *Drug Resistance, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/virology/drug effects ; Genome, Bacterial/genetics ; Metagenome/genetics ; Ecosystem ; Escherichia coli/genetics/virology/drug effects ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; }, abstract = {The spread of antibiotic resistance genes (ARGs) poses a substantial threat to human health. Phage-mediated transduction could exacerbate ARG transmission. While several case studies exist, it is yet unclear to what extent phages encode and mobilize ARGs at the global scale and whether human impacts play a role in this across different habitats. Here, we combine 38,605 bacterial genomes, 1432 metagenomes, and 1186 metatranscriptomes across 12 contrasting habitats to explore the distribution of prophages and their cargo ARGs in natural and human-impacted environments. Worldwide, we observe a significant increase in the abundance, diversity, and activity of prophage-encoded ARGs in human-impacted habitats linked with relatively higher risk of past antibiotic exposure. This effect was driven by phage-encoded cargo ARGs that could be mobilized to provide increased resistance in heterologous E. coli host for a subset of analyzed strains. Our findings suggest that human activities have altered bacteria-phage interactions, enriching ARGs in prophages and making ARGs more mobile across habitats globally.}, } @article {pmid39333059, year = {2024}, author = {Lin, W and Li, R and Cao, S and Li, H and Yang, K and Yang, Z and Su, J and Zhu, YG and Cui, L}, title = {High-Throughput Single-Cell Metabolic Labeling, Sorting, and Sequencing of Active Antibiotic-Resistant Bacteria in the Environment.}, journal = {Environmental science & technology}, volume = {58}, number = {40}, pages = {17838-17849}, doi = {10.1021/acs.est.4c02906}, pmid = {39333059}, issn = {1520-5851}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics ; Single-Cell Analysis ; Drug Resistance, Microbial/genetics ; Wastewater/microbiology ; }, abstract = {Active antibiotic-resistant bacteria (ARB) play a major role in spreading antimicrobial resistance (AMR) in the environment; however, they have remained largely unexplored. Herein, we coupled bio-orthogonal noncanonical amino acid tagging with high-throughput fluorescence-activated single-cell sorting (FACS) and sequencing to characterize the phenome and genome of active ARB in complex environmental matrices. Active ARB, conferring resistance to six antibiotics throughout wastewater treatment, were distinguished and quantified. The percentage and concentration of active ARB ranged from 0.28% to 45.3% and from 1.1 × 10[4] to 2.09 × 10[7] cells/mL, respectively. Notably, the final effluents retained up to 4.79 × 10[4] cells/mL of active ARB. Targeted FACS and genomic sequencing revealed a distinct taxonomic composition of active ARB compared with that of the overall population. The coexistence of antibiotic resistome and mobilome in active ARB was also identified, including three high-quality metagenomic assembly genomes assigned to pathogenic bacteria, highlighting the substantial health risks due to their activity, phenotypic resistance, mobility, and pathogenicity. This study advances our understanding of previously overlooked active ARB in the environment by linking their resistance phenotype to their genotype. This high-throughput method will enable efficient quantitative surveillance of active AMR, providing valuable insights into risk control and management.}, } @article {pmid39332981, year = {2024}, author = {Olsen, M and Goldsworthy, A and Morgan, M and Leggett, J and Demaneuf, T and Van Der Bruggen, N and Singh, G and Ghemrawi, R and Senok, A and Almheiri, R and McKirdy, S and Alghafri, R and Tajouri, L}, title = {Microbial laden mobile phones from international conference attendees pose potential risks to public health and biosecurity.}, journal = {Infection, disease & health}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.idh.2024.08.004}, pmid = {39332981}, issn = {2468-0869}, abstract = {INTRODUCTION: Mobile phones, contaminated with pathogenic microorganisms, have the potential to act as "trojan horses". The microbial signatures present on their surfaces most probably vary across different geographical regions. As a result, mobile phones belonging to international conference attendees may serve as a model for global microbial dissemination, posing potential risks to public health and biosecurity.

AIM: This study aimed to profile the microbes present on mobile phones belonging to delegates attending an international scientific conference through use of metagenomic shotgun DNA sequencing.

METHODS: Twenty mobile phones, representing ten different geographical zones from around the world, were swabbed and pooled together into ten geographical-specific samples for high definition next-generation DNA sequencing. WONCA council members were invited to participate and provided verbal consent. Following DNA extraction, next generation sequencing, to a depth of approximately 10Gbp per sample, was undertaken on a v1.5 Illumina NovaSeq6000 system. Bioinformatic analysis was performed via the CosmosID platform.

RESULTS: A total of 2204 microbial hits were accumulated across 20 mobile phones inclusive of 882 bacteria, 1229 viruses, 88 fungi and 5 protozoa. Of particular concern was the identification of 65 distinct antibiotic resistance genes and 86 virulence genes. Plant, animal and human pathogens, including ESKAPE and HACEK bacteria were found on mobile phones.

DISCUSSION/CONCLUSION: Mobile phones of international attendees are contaminated with many & varied microorganisms. Further research is required to characterize the risks these devices pose for biosecurity and public health. Development of new policies which appropriately address and prevent such risks maybe warranted.}, } @article {pmid39332349, year = {2024}, author = {Sun, Q and Zhang, Z and Ping, Q and Wang, L and Li, Y}, title = {Insight into using multi-omics analysis to elucidate nitrogen removal mechanisms in a novel improved constructed rapid infiltration system: Functional gene and metabolite signatures.}, journal = {Water research}, volume = {267}, number = {}, pages = {122502}, doi = {10.1016/j.watres.2024.122502}, pmid = {39332349}, issn = {1879-2448}, mesh = {*Nitrogen/metabolism ; *Wastewater/chemistry ; Waste Disposal, Fluid/methods ; Denitrification ; Nitrification ; Metabolomics ; Metagenomics ; Ammonium Compounds/metabolism ; Multiomics ; }, abstract = {In this study, a laboratory-scale improved constructed rapid infiltration (imCRI) system with non-saturated and saturated layers was constructed, and corn cobs as solid carbon source were added to the saturated layer to enhance the removal of nitrogen. Combined analyses of metagenomics and metabolomics were conducted to elucidate the nitrogen removal mechanism in the imCRI system. The results showed that the hydraulic load significantly influenced the treatment performance of the imCRI system, and a hydraulic load of 1.25 m[3]/(m[2]⋅d) was recommended. Under optimal conditions, the imCRI system using simulated wastewater achieved average removal efficiencies of 97.8 % for chemical oxygen demand, 85.7 % for total nitrogen (TN), and 97.6 % for ammonia nitrogen. Metagenomic and metabolomic analyses revealed that besides nitrification and denitrification, dissimilatory nitrate reduction to ammonium (DNRA), anammox, etc., are also involved in nitrogen metabolism in the imCRI system. Although nitrification was the predominant pathway in the non-saturated layer, aerobic denitrification also occurred, accounting for 22.59 % of the TN removal. In the saturated layer, nitrogen removal was attributed to synergistic effects of denitrification, DNRA and anammox. Moreover, correlation analysis among nitrogen removal, functional genes and metabolites suggested that metabolites related to the tricarboxylic acid cycle generated from the glycolysis of corn cobs provided sufficient energy for denitrification. Our results can offer a promising technology for decentralized wastewater treatment with stringent nitrogen removal requirements, and provide a foundation for understanding the underlying nitrogen transformation and removal mechanism.}, } @article {pmid39332305, year = {2024}, author = {Zhang, J and Chen, J and Wang, C and Wang, P and Gao, H and Feng, B and Fu, J}, title = {Vertical variation of antibiotic resistance genes and their interaction with environmental nutrients in sediments of Taihu lake.}, journal = {Journal of environmental management}, volume = {370}, number = {}, pages = {122661}, doi = {10.1016/j.jenvman.2024.122661}, pmid = {39332305}, issn = {1095-8630}, mesh = {*Lakes/microbiology ; *Drug Resistance, Microbial/genetics ; Geologic Sediments/microbiology ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Bacteria/genetics ; China ; }, abstract = {Antibiotic resistance is a growing environmental issue. As a sink for antibiotic resistance genes (ARGs), lake surface sediments are well known for the spread of ARGs. However, the distribution pattern of ARGs and their relationship with environmental factors in vertical sediment layers are unclear. In this study, we investigated the resistome distribution in sediment cores from Taihu Lake using metagenomic analysis. The results showed that the abundance of total ARGs increased by 153% as the sediment depth rose from 0 to 50 cm, and the ARG Shannon index significantly increased. Among all the ARG types, efflux pump genes (e.g., mexT and mexW) were dominant, especially in 40-50 cm sediment. The variation in ARG with depth described above was related to the changes in bacterial adaptation to environmental gradients. Specifically, sulfate and nitrate concentrations decreased with depth, and random forest analysis showed that they were the main factors affecting the changes in ARG abundance. Environmental factors were also found to indirectly impact the distribution of ARGs by affecting the bacterial community. Potential sulfate-reducing gene/nitrate-reducing gene-ARG co-hosts were annotated through metagenomic assembly. The dominant co-hosts, Curvibacter, and Comamonas, which were enriched in deeper sediments, may have contributed to the enrichment of ARGs in deep sediments. Overall, our findings demonstrated that bacterial-mediated sulfate and nitrate reduction was closely related to sediment resistance, which provided new insights into the control of antibiotic resistance.}, } @article {pmid39332086, year = {2024}, author = {Sung, YH and Jeong, WK and Lee, HJ and Suh, JW and Kim, JY and Yoon, YK}, title = {Innovative approach of nanopore-based metagenomic sequencing for rapid identification of bacterial pathogens in joint fluid: A pilot study.}, journal = {Diagnostic microbiology and infectious disease}, volume = {110}, number = {4}, pages = {116545}, doi = {10.1016/j.diagmicrobio.2024.116545}, pmid = {39332086}, issn = {1879-0070}, mesh = {Pilot Projects ; Humans ; *Metagenomics/methods ; *Arthritis, Infectious/diagnosis/microbiology ; *Bacteria/genetics/isolation & purification/classification ; *Nanopore Sequencing/methods ; Sensitivity and Specificity ; Synovial Fluid/microbiology ; Nanopores ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Analysis of 11 clinical samples of joint fluid in this pilot study demonstrated proof-of-concept for nanopore-based metagenomic sequencing to serve as a complementary real-time diagnostic technique for septic arthritis, with a sensitivity of 75.0 % and specificity of 57.1 %, compared to the gold standard method of bacterial culture.}, } @article {pmid39331873, year = {2024}, author = {Wang, L and Zhang, L and Ying, C and Jin, X and Ying, M and Chen, H and Zhu, D}, title = {Cryptogenic organizing pneumonia caused by solanine: A case report.}, journal = {Medicine}, volume = {103}, number = {39}, pages = {e39807}, pmid = {39331873}, issn = {1536-5964}, mesh = {Humans ; Male ; Adult ; *Cryptogenic Organizing Pneumonia/diagnosis/drug therapy/chemically induced ; Glucocorticoids/therapeutic use ; Tomography, X-Ray Computed ; Oxygen Inhalation Therapy ; }, abstract = {RATIONALE: Cryptogenic organizing pneumonia (COP) is a type of pneumonia with unknown cause, presenting with symptoms like dyspnea, fever, and cough. Solanine poisoning can cause symptoms like increased heart rate, rapid breathing, sore throat, diarrhea, vomiting, and fever, but there are no known cases of it causing COP.

PATIENT CONCERNS: A 43-year-old man had a dry cough, worse at night, with phlegm and chest tightness after eating sprouted potatoes. No history of surgeries or family medical issues.

DIAGNOSIS: Laboratory tests and metagenomic next-generation sequencing of bronchoalveolar lavage fluid from the bilateral lower lobes did not yield a definitive pathogen. Further evaluation included testing for vasculitis-associated antibodies and rheumatologic immune markers for myositis spectra to rule out connective tissue disease-associated interstitial lung disease as the etiology of organizing pneumonia. As a result, the final diagnosis was determined to be COP.

INTERVENTIONS: The patient received glucocorticoid therapy and oxygen therapy, and responded well to the treatment.

OUTCOMES: On the 10th day of hospitalization, the patient was discharged with success. A follow-up chest CT conducted over a month later revealed that the lesions in both lungs had essentially resolved, with only minor residual fibrotic changes present.

LESSONS: Regularly monitoring disease progression is crucial for patients with solanine poisoning who have pulmonary symptoms. Promptly conducting chest CT scans and bronchoscopy is advised to check for any infections. It is also important to rule out pneumonia related to connective tissue disease-associated interstitial lung disease and provide appropriate treatment promptly.}, } @article {pmid39331712, year = {2024}, author = {Fellows, RC and Chun, SK and Larson, N and Fortin, BM and Mahieu, AL and Song, WA and Seldin, MM and Pannunzio, NR and Masri, S}, title = {Disruption of the intestinal clock drives dysbiosis and impaired barrier function in colorectal cancer.}, journal = {Science advances}, volume = {10}, number = {39}, pages = {eado1458}, pmid = {39331712}, issn = {2375-2548}, support = {R01 CA244519/CA/NCI NIH HHS/United States ; R01 CA259370/CA/NCI NIH HHS/United States ; R01 CA276470/CA/NCI NIH HHS/United States ; R37 CA266042/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; *Colorectal Neoplasms/microbiology/metabolism/pathology ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology ; Mice ; *Circadian Clocks/genetics ; Intestinal Mucosa/metabolism/microbiology ; Disease Models, Animal ; Humans ; Permeability ; }, abstract = {Diet is a robust entrainment cue that regulates diurnal rhythms of the gut microbiome. We and others have shown that disruption of the circadian clock drives the progression of colorectal cancer (CRC). While certain bacterial species have been suggested to play driver roles in CRC, it is unknown whether the intestinal clock impinges on the microbiome to accelerate CRC pathogenesis. To address this, genetic disruption of the circadian clock, in an Apc-driven mouse model of CRC, was used to define the impact on the gut microbiome. When clock disruption is combined with CRC, metagenomic sequencing identified dysregulation of many bacterial genera including Bacteroides, Helicobacter, and Megasphaera. We identify functional changes to microbial pathways including dysregulated nucleic acid, amino acid, and carbohydrate metabolism, as well as disruption of intestinal barrier function. Our findings suggest that clock disruption impinges on microbiota composition and intestinal permeability that may contribute to CRC pathogenesis.}, } @article {pmid39331699, year = {2024}, author = {Yang, Z and Shan, Y and Liu, X and Chen, G and Pan, Y and Gou, Q and Zou, J and Chang, Z and Zeng, Q and Yang, C and Kong, J and Sun, Y and Li, S and Zhang, X and Wu, WC and Li, C and Peng, H and Holmes, EC and Guo, D and Shi, M}, title = {VirID: Beyond Virus Discovery-An Integrated Platform for Comprehensive RNA Virus Characterization.}, journal = {Molecular biology and evolution}, volume = {41}, number = {10}, pages = {}, pmid = {39331699}, issn = {1537-1719}, support = {82341118//National Natural Science Foundation of China/ ; 2022A1515011854//Natural Science Foundation of Guangdong Province of China/ ; JCYJ20210324124414040//Shenzhen Science and Technology Program/ ; //Hong Kong Innovation and Technology Fund (ITF/ ; GZNL2023A01001//Major Project of Guangzhou National Laboratory/ ; 2019ZT08Y464//Guangdong Province "Pearl River Talent Plan" Innovation, Entrepreneurship Team Project/ ; ZDSYS20220606100803007//Fund of Shenzhen Key Laboratory/ ; GNT2017197//NHMRC (Australia) Investigator Award/ ; //Innovation and Technology Commission, Hong Kong Special Administrative Region, China/ ; }, mesh = {*RNA Viruses/genetics ; *Software ; *Metagenomics/methods ; *Phylogeny ; Humans ; RNA-Dependent RNA Polymerase/genetics ; Computational Biology/methods ; }, abstract = {RNA viruses exhibit vast phylogenetic diversity and can significantly impact public health and agriculture. However, current bioinformatics tools for viral discovery from metagenomic data frequently generate false positive virus results, overestimate viral diversity, and misclassify virus sequences. Additionally, current tools often fail to determine virus-host associations, which hampers investigation of the potential threat posed by a newly detected virus. To address these issues we developed VirID, a software tool specifically designed for the discovery and characterization of RNA viruses from metagenomic data. The basis of VirID is a comprehensive RNA-dependent RNA polymerase database to enhance a workflow that includes RNA virus discovery, phylogenetic analysis, and phylogeny-based virus characterization. Benchmark tests on a simulated data set demonstrated that VirID had high accuracy in profiling viruses and estimating viral richness. In evaluations with real-world samples, VirID was able to identify RNA viruses of all types, but also provided accurate estimations of viral genetic diversity and virus classification, as well as comprehensive insights into virus associations with humans, animals, and plants. VirID therefore offers a robust tool for virus discovery and serves as a valuable resource in basic virological studies, pathogen surveillance, and early warning systems for infectious disease outbreaks.}, } @article {pmid39331310, year = {2024}, author = {Deézsi-Magyar, N and Novák, N and Lukács, A and Tarcsai, KR and Hajdu, Á and Takács, L and Farkas, FB and Rigó, Z and Barcsay, E and Kis, Z and Szomor, K}, title = {First whole genome sequencing and analysis of human parechovirus type 3 causing a healthcare-associated outbreak among neonates in Hungary.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {43}, number = {12}, pages = {2341-2350}, pmid = {39331310}, issn = {1435-4373}, mesh = {Humans ; *Parechovirus/genetics/isolation & purification/classification ; Hungary/epidemiology ; *Picornaviridae Infections/epidemiology/virology ; Infant, Newborn ; *Whole Genome Sequencing ; *Phylogeny ; *Disease Outbreaks ; *Genotype ; *Genome, Viral ; Male ; Cross Infection/epidemiology/virology ; Feces/virology ; Female ; }, abstract = {PURPOSE: In November 2023, the National Reference Laboratory for Enteroviruses (Budapest, Hungary) received stool, pharyngeal swab and cerebrospinal fluid samples from five newborns suspected of having human parechovirus (PEV-A) infection. The neonates were born in the same hospital and presented with fever and sepsis-like symptoms at 8-9 days of age, and three of them showed symptoms consistent with central nervous system involvement. PEV-A positivity was confirmed by quantitative reverse transcription polymerase chain reaction.

METHODS: To determine the PEV-A genotype responsible for the infections, fecal samples of four neonates were subjected to metagenomic sequencing. For further analyses, amplicon-based whole genome sequencing was performed directly from the clinical samples.

RESULTS: On the basis of whole genome analysis, sequences were allocated to PEV-A genotype 3 (PEV-A3) and consensus sequences were identical. Two ambiguities were identified in the viral protein 1 (VP1) region of all sequences at a frequency of 17.7-53.7%, indicating the simultaneous presence of at least two quasispecies in the clinical samples. The phylogenetic analysis and similarity plotting showed that all sequences clustered without any topological inconsistencies between the P1 capsid and P2, P3 non-capsid regions, suggesting that recombination events during evolution were unlikely.

CONCLUSION: Our findings suggest that the apparent cluster of cases were microbiologically related, and the results may also inform future investigations on the evolution and pathogenicity of PEV-A3 infections.}, } @article {pmid39330355, year = {2024}, author = {Abbà, S and Valentini, B and Stefanini, I}, title = {Fungal Identifier (FId): An Updated Polymerase Chain Reaction-Restriction Fragment Length Polymorphism Approach to Ease Ascomycetous Yeast Isolates' Identification in Ecological Studies.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {10}, number = {9}, pages = {}, pmid = {39330355}, issn = {2309-608X}, support = {RGP0060/2021//HFSP/ ; 20225SXSHY//PRIN 2022/ ; }, abstract = {Culturomics has been temporarily exceeded by the advent of omics approaches such as metabarcoding and metagenomics. However, despite improving our knowledge of microbial population composition, both metabarcoding and metagenomics are not suitable for investigating and experimental testing inferences about microbial ecological roles and evolution. This leads to a recent revival of culturomics approaches, which should be supported by improvements in the available tools for high-throughput microbial identification. This study aimed to update the classical PCR-RFLP approach in light of the currently available knowledge on yeast genomics. We generated and analyzed a database including more than 1400 ascomycetous yeast species, each characterized by PCR-RFLP profiles obtained with 143 different endonucleases. The results allowed for the in silico evaluation of the performance of the tested endonucleases in the yeast species' identification and the generation of FId (Fungal Identifier), an online freely accessible tool for the identification of yeast species according to experimentally obtained PCR-RFLP profiles.}, } @article {pmid39329490, year = {2024}, author = {Maday, SDM and Kingsbury, JM and Weaver, L and Pantos, O and Wallbank, JA and Doake, F and Masterton, H and Hopkins, M and Dunlop, R and Gaw, S and Theobald, B and Risani, R and Abbel, R and Smith, D and Handley, KM and Lear, G}, title = {Taxonomic variation, plastic degradation, and antibiotic resistance traits of plastisphere communities in the maturation pond of a wastewater treatment plant.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {10}, pages = {e0071524}, pmid = {39329490}, issn = {1098-5336}, support = {C03X1802//Ministry of Business, Innovation and Employment (MBIE)/ ; }, mesh = {*Plastics ; *Wastewater/microbiology ; *Ponds/microbiology ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Biodegradation, Environmental ; *RNA, Ribosomal, 16S/genetics ; Biofilms/drug effects/growth & development ; Microbiota/drug effects ; Drug Resistance, Microbial/genetics ; Waste Disposal, Fluid ; Water Pollutants, Chemical/analysis ; Water Purification ; }, abstract = {Wastewater treatment facilities can filter out some plastics before they reach the open environment, yet microplastics often persist throughout these systems. As they age, microplastics in wastewater may both leach and sorb pollutants and fragment to provide an increased surface area for bacterial attachment and conjugation, possibly impacting antimicrobial resistance (AMR) traits. Despite this, little is known about the effects of persistent plastic pollution on microbial functioning. To address this knowledge gap, we deployed five different artificially weathered plastic types and a glass control into the final maturation pond of a municipal wastewater treatment plant in Ōtautahi-Christchurch, Aotearoa/New Zealand. We sampled the plastic-associated biofilms (plastisphere) at 2, 6, 26, and 52 weeks, along with the ambient pond water, at three different depths (20, 40, and 60 cm from the pond water surface). We investigated the changes in plastisphere microbial diversity and functional potential through metagenomic sequencing. Bacterial 16S ribosomal RNA genes composition did not vary among plastic types and glass controls (P = 0.997) but varied among sampling times [permutational multivariate analysis of variance (PERMANOVA), P = 0.001] and depths (PERMANOVA, P = 0.011). Overall, there was no polymer-substrate specificity evident in the total composition of genes (PERMANOVA, P = 0.67), but sampling time (PERMANOVA, P = 0.002) and depth were significant factors (PERMANOVA, P = 0.001). The plastisphere housed diverse AMR gene families, potentially influenced by biofilm-meditated conjugation. The plastisphere also harbored an increased abundance of genes associated with the biodegradation of nylon, or nylon-associated substances, including nylon oligomer-degrading enzymes and hydrolases.IMPORTANCEPlastic pollution is pervasive and ubiquitous. Occurrences of plastics causing entanglement or ingestion, the leaching of toxic additives and persistent organic pollutants from environmental plastics, and their consequences for marine macrofauna are widely reported. However, little is known about the effects of persistent plastic pollution on microbial functioning. Shotgun metagenomics sequencing provides us with the necessary tools to examine broad-scale community functioning to further investigate how plastics influence microbial communities. This study provides insight into the functional consequence of continued exposure to waste plastic by comparing the prokaryotic functional potential of biofilms on five types of plastic [linear low-density polyethylene (LLDPE), nylon-6, polyethylene terephthalate, polylactic acid, and oxygen-degradable LLDPE], glass, and ambient pond water over 12 months and at different depths (20, 40, and 60 cm) within a tertiary maturation pond of a municipal wastewater treatment plant.}, } @article {pmid39329142, year = {2024}, author = {Khomutovska, N and Jasser, I and Sarapultseva, P and Spirina, V and Zaitsev, A and Masłowiecka, J and Isidorov, VA}, title = {Seasonal dynamics in leaf litter decomposing microbial communities in temperate forests: a whole-genome- sequencing-based study.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e17769}, pmid = {39329142}, issn = {2167-8359}, mesh = {*Plant Leaves/microbiology/metabolism ; *Forests ; *Seasons ; *Microbiota/genetics/physiology ; Bacteria/genetics/classification/metabolism ; Fungi/genetics/classification/metabolism/isolation & purification ; Whole Genome Sequencing ; Metagenome/genetics ; Trees/microbiology ; }, abstract = {Leaf litter decomposition, a crucial component of the global carbon cycle, relies on the pivotal role played by microorganisms. However, despite their ecological importance, leaf-litter-decomposing microorganism taxonomic and functional diversity needs additional study. This study explores the taxonomic composition, dynamics, and functional role of microbial communities that decompose leaf litter of forest-forming tree species in two ecologically unique regions of Europe. Twenty-nine microbial metagenomes isolated from the leaf litter of eight forest-forming species of woody plants were investigated by Illumina technology using read- and assembly-based approaches of sequences analysis. The taxonomic structure of the microbial community varies depending on the stage of litter decomposition; however, the community's core is formed by Pseudomonas, Sphingomonas, Stenotrophomonas, and Pedobacter genera of Bacteria and by Aureobasidium, Penicillium, Venturia genera of Fungi. A comparative analysis of the taxonomic structure and composition of the microbial communities revealed that in both regions, seasonal changes in structure take place; however, there is no clear pattern in its dynamics. Functional gene analysis of MAGs revealed numerous metabolic profiles associated with leaf litter degradation. This highlights the diverse metabolic capabilities of microbial communities and their implications for ecosystem processes, including the production of volatile organic compounds (VOCs) during organic matter decomposition. This study provides important advances in understanding of ecosystem processes and the carbon cycle, underscoring the need to unravel the intricacies of microbial communities within these contexts.}, } @article {pmid39328911, year = {2024}, author = {Lemos Junior, WJF and Marques Costa, L and Alberto Guerra, C and Sales de Oliveira, V and Gava Barreto, A and Alves de Oliveira, F and de Paula, BP and Esmerino, EA and Corich, V and Giacomini, A and Guerra, AF}, title = {Microbial landscape of cooked meat products: evaluating quality and safety in vacuum-packaged sausages using culture-dependent and culture-independent methods over 1 year in a sustainable food chain.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1457819}, pmid = {39328911}, issn = {1664-302X}, abstract = {Over the last few decades, advancements in process safety and quality methods have been significantly improved, yet new challenges continue to emerge in the sustainable food supply chain. This study aimed to investigate some physicochemical and microbiological parameters impacting meat products, particularly cooked sausages, within a sustainable supply chain, focusing on quality, spoilage populations, and syneresis formation under vacuum conditions. A comprehensive analysis was conducted on 355 samples collected over four seasons using high-throughput sequencing (16S/ITS) and microbiological and physicochemical [pH and water activity (aw)] assessments. The microbial growth predictor MicroLab_ShelfLife was employed, and multiple factor analysis (MFA) and agglomerative hierarchical clustering (AHC) were utilized to understand how these variables influence the microbiome resilience of these products. Lactic and acetic acids were correlated with the microbiome of the sausages and the liquid coating covering them using metagenomic analyses. The study highlighted that 52% of the evaluated meat industries in southeastern Brazil are implementing effective protocols for sustainable chain production. The results indicated that the durability of vacuum-packaged cooked sausages was primarily influenced by storage temperature (RV coefficient of 0.906), initial microbial load (0.755), and aw (0.624). Average microbial counts were 4.30 log cfu/g (initial), 4.61 (7°C/4 days), 4.90 (7°C/8 days), 6.06 (36°C/4 days), and 6.79 (36°C/8 days). Seasonal durability analysis revealed that winter had the highest average durability of 45.58 days, while summer had the lowest at 26.33 days. Yeast populations, including Trichosporon sp. and Candida sp., were identified as key genera influencing spoilage dynamics. In addition, Bacillus species emerged as dominant spoilage microorganisms, highlighting the need for new critical controls. This study demonstrates the impact of metagenomic approaches, including ITS and 16S amplicon sequencing, in revealing microbial community dynamics, storage temperature, and aw, which are essential for developing targeted interventions to enhance food safety and quality sustainably.}, } @article {pmid39328895, year = {2024}, author = {McAdams, ZL and Yates, J and Turner, G and Dorfmeyer, RA and Wight-Carter, M and Amos-Landgraf, J and Franklin, CL and Ericsson, AC}, title = {Effect of shipping on the microbiome of donor mice used to reconstitute germ-free recipients.}, journal = {Gut microbes reports}, volume = {1}, number = {1}, pages = {1-8}, pmid = {39328895}, issn = {2993-3935}, support = {U42 OD010918/OD/NIH HHS/United States ; }, abstract = {The gut microbiota (GM) influences multiple processes during host development and maintenance. To study these events, fecal microbiota transfer (FMT) to germ-free (GF) recipients is often performed. Mouse models of disease are also susceptible to GM-dependent effects, and cryo-repositories often store feces from donated mouse strains. Shipping live mice may affect the GM and result in an inaccurate representation of the baseline GM. We hypothesize that the use of such fecal samples for FMT would transfer shipping-induced changes in the donor GM to GF recipients. To test this, donor mice originating from two suppliers were shipped to the University of Missouri. Fecal samples collected pre- and post-shipping were used to inoculate GF mice. Pre- and post-shipping fecal samples from donors, and fecal and/or cecal contents were collected from recipients at one and two weeks post-FMT. 16S rRNA sequencing revealed supplier-dependent effects of shipping on the donor microbiome. FMT efficiency was independent of shipping timepoint or supplier, resulting in transmission of shipping-induced changes to recipient mice, however the effect of supplier-origin microbiome remained evident. While shipping may cause subtle changes in fecal samples collected for FMT, such effects are inconsistent among supplier-origin GMs and minor in comparison to other biological variables.}, } @article {pmid39328586, year = {2024}, author = {Huang, M and Jiang, N and Ren, Y and Peng, Y and Wu, X}, title = {Very severe aplastic anemia in a child with pulmonary mucormycosis: a case report.}, journal = {Frontiers in pediatrics}, volume = {12}, number = {}, pages = {1453059}, pmid = {39328586}, issn = {2296-2360}, abstract = {Aplastic anemia (AA), is a rare but potentially life-threatening disease characterized by pancytopenia and a hypocellular bone marrow. Pulmonary mucormycosis (PM) is a rare but life-threatening fungal infection observed in immunocompromised patients, particularly those with neutropenia and those using corticosteroids, with a high mortality rate from 40 to 80%. However, PM diagnosis and treatment remain challenging. This study reports a case of very severe aplastic anemia (VSAA) in a male child with PM. The innovation of this article lies in the following aspects: the patient exhibited typical clinical manifestations, the reverse halo sign (RHS) on chest computed tomography (CT), and a positive metagenomic next-generation sequencing (mNGS) analysis; despite aggressive anti-infective treatment and left lower lobectomy, he experienced a poor clinical outcome. Reflecting on cases with poor prognosis can indeed offer valuable insights and opportunities for learning. This study underlines the diagnostic challenges in mucormycosis, which should be considered in persistent fever that is unresponsive to standard antibiotic and antifungal therapies, and conduct a comprehensive examination to achieve early detection, diagnosis and treatment. It was concluded that, in addition to antifungal treatment, early surgery is essential for treating mucormycosis.}, } @article {pmid39328446, year = {2024}, author = {Sizova, EA and Yausheva, EV and Nechitailo, KS and Kamirova, AM and Ryazanceva, KV and Shoshin, DE and Skalny, AV and Tinkov, AA}, title = {Influence of the Saccharomyces cerevisiae-based probiotic complex on gut microbiota, serum biochemistry, and circulating trace element and mineral levels in lactating dairy cows.}, journal = {Veterinary world}, volume = {17}, number = {8}, pages = {1864-1871}, pmid = {39328446}, issn = {0972-8988}, abstract = {BACKGROUND AND AIM: The existing data demonstrate that gut microbiota is involved in regulating mineral metabolism in cattle, although the data are quite contradictory. The study aimed to evaluate Saccharomyces cerevisiae-based probiotic's effects on gut microbiota, systemic metabolism, and dairy cows' essential trace element and mineral body burden.

MATERIALS AND METHODS: Fifteen cows received a daily supplement of a 50 g S. cerevisiae-based probiotic, fortified with methionine, choline, eugenol, cinnamaldehyde, and Capsicum oleoresin, for a month. 16S metagenomic sequencing was used to evaluate the taxonomic features of fecal microbiota. Serum trace elements and minerals levels were determined through inductively coupled plasma mass spectrometry.

RESULTS: Supplementation with S. cerevisiae-based probiotic complex significantly increased alpha and beta diversity, as well as the abundance of Mediterranea and Clostridium IV within the Bacillota phylum, whereas that of Bacteroidota and specifically unclassified Bacteroidales and unclassified Oscillospiraceae decreased. Following probiotic supplementation with the S. cerevisiae-based complex, gut microbiota modulation led to a significant boost in circulating levels of calcium, copper, selenium, and zinc. Creatinine levels decreased while total cholesterol levels increased within normal limits in the serum analysis.

CONCLUSION: The observed improvement in trace elements and minerals in dairy cows might be due to changes in intestinal microflora caused by supplementation. Therefore, probiotic supplementation in cattle may be considered a potential tool for improvement of mineral nutrition in cattle. However, the influence of probiotic treatment and modulation of mineral metabolism on milk productivity and overall performance in cattle is yet to be estimated.}, } @article {pmid39328398, year = {2024}, author = {Abuljadayel, D and Alotibi, A and Algothmi, K and Basingab, F and Alhazmi, S and Almuhammadi, A and Alharthi, A and Alyoubi, R and Bahieldin, A}, title = {Gut microbiota of children with autism spectrum disorder and healthy siblings: A comparative study.}, journal = {Experimental and therapeutic medicine}, volume = {28}, number = {5}, pages = {430}, pmid = {39328398}, issn = {1792-1015}, abstract = {Autism spectrum disorder (ASD) is a neurodevelopmental abnormality that impairs social communication. The human gut microbiome (GM) influences a variety of local processes, including dysbiosis and the defense against pathogenic microorganisms. The aim of the present study was to categorize and identify molecular biomarkers for ASD. In the present study, metagenomics whole genome shotgun sequencing was used to identify the gut microbiota in autistic individuals. Fecal samples from four children with ASD and four healthy control siblings, aged 3-10 years old, were examined using bioinformatics analysis. A total of 673,091 genes were cataloged, encompassing 25 phyla and 2 kingdoms based on the taxonomy analysis. The results revealed 257 families, 34 classes, 84 orders, and 1,314 genera among 4,339 species. The top 10 most abundant genes and corresponding functional genes for each group were determined after the abundance profile was screened. The results showed that children with ASD had a higher abundance of certain gut microbiomes than their normal siblings and vice versa. The phyla Firmicutes and Proteobacteria were the most abundant in ASD. The Thermoanaerobacteria class was also restricted to younger healthy individuals. Moreover, the Lactobacillaceae family was more abundant in children with ASD. Additionally, it was discovered that children with ASD had a higher abundance of the Bacteroides genus and a lower abundance of the Bifidobacterium and Prevotella genera. In conclusion, there were more pathogenic genera and species and higher levels of biomass, diversity and richness in the GM of children with ASD.}, } @article {pmid39328319, year = {2024}, author = {Chen, Y and Lan, P and Liu, L and Zhou, K}, title = {Prone positioning ventilation treatment rescuing a patient with chlamydia abortus-induced ARDS diagnosed by next generation sequencing: a case report.}, journal = {Frontiers in medicine}, volume = {11}, number = {}, pages = {1428300}, pmid = {39328319}, issn = {2296-858X}, abstract = {BACKGROUND: Chlamydia abortus is a pathogen capable of infecting both humans and animals. In most known cases, this pathogen primarily infects pregnant women, leading to miscarriage and preterm birth. However, it is exceedingly rare for this pathogen to cause pneumonia that progresses to severe Acute Respiratory Distress Syndrome (ARDS).

CASE INTRODUCTION: We present a case of a 76-year-old male patient who was clinically diagnosed with Acute Respiratory Distress Syndrome (ARDS) caused by Chlamydia abortus and successfully treated. The patient's condition rapidly deteriorated over six days, evolving from a lung infection to severe pneumonia, ultimately leading to ARDS and sepsis. Initially, he was admitted to a local hospital for a lung infection where routine etiological examinations failed to identify any significant pathogens, and he received only empirical antimicrobial therapy. However, the lung infection was not controlled, and the patient's condition rapidly worsened, resulting in severe respiratory distress. This necessitated tracheal intubation and assisted ventilation, after which he was transferred to our hospital for treatment. Due to the patient's family's inability to afford the cost of ECMO treatment, we adopted a prone positioning ventilation strategy to improve the patient's ventilation-perfusion matching. Additionally, we performed metagenomic next-generation sequencing on the patient's bronchoalveolar lavage fluid, which confirmed the infection with Chlamydia abortus. These measures ultimately led to the successful treatment of the patient.

CONCLUSION: Chlamydia abortus infection can lead to severe ARDS, necessitating timely diagnosis and active intervention by clinicians. This case highlights the crucial role of metagenomic next-generation sequencing in diagnosing rare pathogens. Timely adoption of prone positioning ventilation can significantly improve ventilation-perfusion matching, effectively treating ARDS caused by Chlamydia abortus. Additionally, the combination of moxifloxacin and piperacillin-tazobactam can treat ARDS caused by Chlamydia abortus.}, } @article {pmid39327897, year = {2024}, author = {Dai, Z and Wang, H and Xu, J and Lu, X and Ni, P and Yang, S and Shen, Q and Wang, X and Li, W and Wang, X and Zhou, C and Zhang, W and Shan, T}, title = {Unveiling the Virome of Wild Birds: Exploring CRESS-DNA Viral Dark Matter.}, journal = {Genome biology and evolution}, volume = {16}, number = {10}, pages = {}, pmid = {39327897}, issn = {1759-6653}, support = {2023YFD1801301//National Key Research and Development Programs of China/ ; 82341106//National Natural Science Foundation of China/ ; 20229152//The Special Funds for Science Development of the Clinical Teaching Hospitals of Jiangsu Vocational College of Medicine/ ; }, mesh = {Animals ; *Birds/virology ; *Virome/genetics ; *DNA Viruses/genetics/classification ; Phylogeny ; Animals, Wild/virology ; Metagenomics ; DNA, Viral/genetics ; }, abstract = {Amid global health concerns and the constant threat of zoonotic diseases, this study delves into the diversity of circular replicase-encoding single-stranded DNA (CRESS-DNA) viruses within Chinese wild bird populations. Employing viral metagenomics to tackle the challenge of "viral dark matter," the research collected and analyzed 3,404 cloacal swab specimens across 26 bird families. Metagenomic analysis uncovered a rich viral landscape, with 67.48% of reads classified as viral dark matter, spanning multiple taxonomic levels. Notably, certain viral families exhibited host-specific abundance patterns, with Galliformes displaying the highest diversity. Diversity analysis categorized samples into distinct groups, revealing significant differences in viral community structure, particularly noting higher diversity in terrestrial birds compared to songbirds and unique diversity in migratory birds versus perching birds. The identification of ten novel Circoviridae viruses, seven Smacoviridae viruses, and 167 Genomoviridae viruses, along with 100 unclassified CRESS-DNA viruses, underscores the expansion of knowledge on avian-associated circular DNA viruses. Phylogenetic and structural analyses of Rep proteins offered insights into evolutionary relationships and potential functional variations among CRESS-DNA viruses. In conclusion, this study significantly enhances our understanding of the avian virome, shedding light on the intricate relationships between viral communities and host characteristics in Chinese wild bird populations. The diverse array of CRESS-DNA viruses discovered opens avenues for future research into viral evolution, spread factors, and potential ecosystem impacts.}, } @article {pmid39327796, year = {2024}, author = {McLeish, M and Peláez, A and Pagán, I and Gavilán, RG and Fraile, A and García-Arenal, F}, title = {Plant virus community structuring is shaped by habitat heterogeneity and traits for host plant resource utilisation.}, journal = {The New phytologist}, volume = {244}, number = {4}, pages = {1585-1596}, doi = {10.1111/nph.20054}, pmid = {39327796}, issn = {1469-8137}, support = {BES-2016-077810//Formación de Personal Investigador/ ; PID2021-124671OB-I00//Agencia Nacional de Investigación e Innovación/ ; RTI2018-094302-B-I00//Ministerio de Ciencia e Innovación/ ; }, mesh = {*Ecosystem ; *Plant Viruses/physiology ; *Plants/virology ; Host Specificity ; Plant Diseases/virology ; }, abstract = {Host plants provide resources critical to viruses and the spatial structuring of plant communities affects the niches available for colonisation and disease emergence. However, large gaps remain in the understanding of mechanisms that govern plant-virus disease ecology across heterogeneous plant assemblages. We combine high-throughput sequencing, network, and metacommunity approaches to test whether habitat heterogeneity in plant community composition corresponded with virus resource utilisation traits of transmission mode and host range. A majority of viruses exhibited habitat specificity, with communities connected by key generalist viruses and potential host reservoirs. There was an association between habitat heterogeneity and virus community structuring, and between virus community structuring and resource utilisation traits of host range and transmission. The relationship between virus species distributions and virus trait responses to habitat heterogeneity was scale-dependent, being stronger at finer (site) than larger (habitat) spatial scales. Results indicate that habitat heterogeneity has a part in plant virus community assembly, and virus community structuring corresponds to virus trait responses that vary with the scale of observation. Distinctions in virus communities caused by plant resource compartmentalisation can be used to track trait responses of viruses to hosts important in forecasting disease emergence.}, } @article {pmid39327508, year = {2024}, author = {Akhtar, A and Lata, M and Sunsunwal, S and Yadav, A and Lnu, K and Subramanian, S and Ramya, TNC}, title = {Author Correction: New carbohydrate binding domains identified by phage display based functional metagenomic screens of human gut microbiota.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1190}, doi = {10.1038/s42003-024-06920-0}, pmid = {39327508}, issn = {2399-3642}, } @article {pmid39327484, year = {2024}, author = {Kazantseva, E and Donmez, A and Frolova, M and Pop, M and Kolmogorov, M}, title = {Strainy: phasing and assembly of strain haplotypes from long-read metagenome sequencing.}, journal = {Nature methods}, volume = {21}, number = {11}, pages = {2034-2043}, pmid = {39327484}, issn = {1548-7105}, support = {R01 AI100947/AI/NIAID NIH HHS/United States ; Intramural Research Program of the Center for Cancer Research//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; }, mesh = {*Haplotypes ; *Algorithms ; *Metagenome/genetics ; *Metagenomics/methods ; Genome, Bacterial ; Bacteria/genetics/classification ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Bacterial species in microbial communities are often represented by mixtures of strains, distinguished by small variations in their genomes. Short-read approaches can be used to detect small-scale variation between strains but fail to phase these variants into contiguous haplotypes. Long-read metagenome assemblers can generate contiguous bacterial chromosomes but often suppress strain-level variation in favor of species-level consensus. Here we present Strainy, an algorithm for strain-level metagenome assembly and phasing from Nanopore and PacBio reads. Strainy takes a de novo metagenomic assembly as input and identifies strain variants, which are then phased and assembled into contiguous haplotypes. Using simulated and mock Nanopore and PacBio metagenome data, we show that Strainy assembles accurate and complete strain haplotypes, outperforming current Nanopore-based methods and comparable with PacBio-based algorithms in completeness and accuracy. We then use Strainy to assemble strain haplotypes of a complex environmental metagenome, revealing distinct strain distribution and mutational patterns in bacterial species.}, } @article {pmid39327438, year = {2024}, author = {Schmartz, GP and Rehner, J and Gund, MP and Keller, V and Molano, LG and Rupf, S and Hannig, M and Berger, T and Flockerzi, E and Seitz, B and Fleser, S and Schmitt-Grohé, S and Kalefack, S and Zemlin, M and Kunz, M and Götzinger, F and Gevaerd, C and Vogt, T and Reichrath, J and Diehl, L and Hecksteden, A and Meyer, T and Herr, C and Gurevich, A and Krug, D and Hegemann, J and Bozhueyuek, K and Gulder, TAM and Fu, C and Beemelmanns, C and Schattenberg, JM and Kalinina, OV and Becker, A and Unger, M and Ludwig, N and Seibert, M and Stein, ML and Hanna, NL and Martin, MC and Mahfoud, F and Krawczyk, M and Becker, SL and Müller, R and Bals, R and Keller, A}, title = {Decoding the diagnostic and therapeutic potential of microbiota using pan-body pan-disease microbiomics.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {8261}, pmid = {39327438}, issn = {2041-1723}, mesh = {Humans ; *Microbiota/genetics ; *Metagenome/genetics ; *Metagenomics/methods ; Bacteria/genetics/isolation & purification/classification ; Feces/microbiology ; Male ; Female ; Multigene Family ; Saliva/microbiology ; Adult ; }, abstract = {The human microbiome emerges as a promising reservoir for diagnostic markers and therapeutics. Since host-associated microbiomes at various body sites differ and diseases do not occur in isolation, a comprehensive analysis strategy highlighting the full potential of microbiomes should include diverse specimen types and various diseases. To ensure robust data quality and comparability across specimen types and diseases, we employ standardized protocols to generate sequencing data from 1931 prospectively collected specimens, including from saliva, plaque, skin, throat, eye, and stool, with an average sequencing depth of 5.3 gigabases. Collected from 515 patients, these samples yield an average of 3.7 metagenomes per patient. Our results suggest significant microbial variations across diseases and specimen types, including unexpected anatomical sites. We identify 583 unexplored species-level genome bins (SGBs) of which 189 are significantly disease-associated. Of note, the existence of microbial resistance genes in one specimen was indicative of the same resistance genes in other specimens of the same patient. Annotated and previously undescribed SGBs collectively harbor 28,315 potential biosynthetic gene clusters (BGCs), with 1050 significant correlations to diseases. Our combinatorial approach identifies distinct SGBs and BGCs, emphasizing the value of pan-body pan-disease microbiomics as a source for diagnostic and therapeutic strategies.}, } @article {pmid39327429, year = {2024}, author = {Schmartz, GP and Rehner, J and Schuff, MJ and Molano, LG and Becker, SL and Krawczyk, M and Tagirdzhanov, A and Gurevich, A and Francke, R and Müller, R and Keller, V and Keller, A}, title = {Exploring microbial diversity and biosynthetic potential in zoo and wildlife animal microbiomes.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {8263}, pmid = {39327429}, issn = {2041-1723}, support = {469073465//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {Animals ; *Animals, Wild/microbiology ; *Animals, Zoo/microbiology ; *Gastrointestinal Microbiome/genetics ; *Anti-Bacterial Agents/pharmacology ; *Microbiota/genetics/drug effects ; Bacteria/genetics/metabolism/classification/drug effects ; Multigene Family ; Humans ; Biodiversity ; Drug Resistance, Bacterial/genetics ; Vancomycin/pharmacology ; Biosynthetic Pathways/genetics ; }, abstract = {Understanding human, animal, and environmental microbiota is essential for advancing global health and combating antimicrobial resistance (AMR). We investigate the oral and gut microbiota of 48 animal species in captivity, comparing them to those of wildlife animals. Specifically, we characterize the microbiota composition, metabolic pathways, AMR genes, and biosynthetic gene clusters (BGCs) encoding the production of specialized metabolites. Our results reveal a high diversity of microbiota, with 585 novel species-level genome bins (SGBs) and 484 complete BGCs identified. Functional gene analysis of microbiomes shows diet-dependent variations. Furthermore, by comparing our findings to wildlife-derived microbiomes, we observe the impact of captivity on the animal microbiome, including examples of converging microbiome compositions. Importantly, our study identifies AMR genes against commonly used veterinary antibiotics, as well as resistance to vancomycin, a critical antibiotic in human medicine. These findings underscore the importance of the 'One Health' approach and the potential for zoonotic transmission of pathogenic bacteria and AMR. Overall, our study contributes to a better understanding of the complexity of the animal microbiome and highlights its BGC diversity relevant to the discovery of novel antimicrobial compounds.}, } @article {pmid39327011, year = {2024}, author = {Ruff, SE and Schwab, L and Vidal, E and Hemingway, JD and Kraft, B and Murali, R}, title = {Widespread occurrence of dissolved oxygen anomalies, aerobic microbes, and oxygen-producing metabolic pathways in apparently anoxic environments.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {11}, pages = {}, pmid = {39327011}, issn = {1574-6941}, support = {RGEC34/2023//Human Frontier Science Program/ ; 824763//Simons Foundation/ ; 946150/ERC_/European Research Council/International ; }, mesh = {*Oxygen/metabolism ; *Metabolic Networks and Pathways ; Groundwater/microbiology ; Phylogeny ; Bacteria/metabolism/genetics/classification ; Ecosystem ; Anaerobiosis ; }, abstract = {Nearly all molecular oxygen (O2) on Earth is produced via oxygenic photosynthesis by plants or photosynthetically active microorganisms. Light-independent O2 production, which occurs both abiotically, e.g. through water radiolysis, or biotically, e.g. through the dismutation of nitric oxide or chlorite, has been thought to be negligible to the Earth system. However, recent work indicates that O2 is produced and consumed in dark and apparently anoxic environments at a much larger scale than assumed. Studies have shown that isotopically light O2 can accumulate in old groundwaters, that strictly aerobic microorganisms are present in many apparently anoxic habitats, and that microbes and metabolisms that can produce O2 without light are widespread and abundant in diverse ecosystems. Analysis of published metagenomic data reveals that the enzyme putatively capable of nitric oxide dismutation forms four major phylogenetic clusters and occurs in at least 16 bacterial phyla, most notably the Bacteroidota. Similarly, a re-analysis of published isotopic signatures of dissolved O2 in groundwater suggests in situ production in up to half of the studied environments. Geochemical and microbiological data support the conclusion that "dark oxygen production" is an important and widespread yet overlooked process in apparently anoxic environments with far-reaching implications for subsurface biogeochemistry and ecology.}, } @article {pmid39326916, year = {2024}, author = {Zhu, Z and Shibata, R and Hoffman, KL and Cormier, J and Mansbach, JM and Liang, L and Camargo, CA and Hasegawa, K}, title = {Integrated nasopharyngeal airway metagenome and asthma genetic risk endotyping of severe bronchiolitis in infancy and risk of childhood asthma.}, journal = {The European respiratory journal}, volume = {64}, number = {6}, pages = {}, pmid = {39326916}, issn = {1399-3003}, support = {R01 AI127507/AI/NIAID NIH HHS/United States ; R01 AI148338/AI/NIAID NIH HHS/United States ; R01 AI134940/AI/NIAID NIH HHS/United States ; U01 AI087881/AI/NIAID NIH HHS/United States ; R01 AI137091/AI/NIAID NIH HHS/United States ; K01 AI153558/AI/NIAID NIH HHS/United States ; UG3 OD023253/OD/NIH HHS/United States ; R01 AI114552/AI/NIAID NIH HHS/United States ; UH3 OD023253/OD/NIH HHS/United States ; }, mesh = {Humans ; *Asthma/genetics ; Female ; Male ; Infant ; *Bronchiolitis/virology/genetics ; Prospective Studies ; *Metagenome ; *Nasopharynx/microbiology/virology ; Child, Preschool ; Risk Factors ; Genetic Predisposition to Disease ; Hospitalization ; Child ; Infant, Newborn ; Rhinovirus/genetics ; }, abstract = {BACKGROUND: Infants with bronchiolitis are at increased risk of developing asthma. Growing evidence suggests bronchiolitis is a heterogeneous condition. However, little is known about its biologically distinct subgroups based on the integrated metagenome and asthma genetic risk signature and their longitudinal relationships with asthma development.

METHODS: In a multicentre prospective cohort study of infants with severe bronchiolitis (i.e. bronchiolitis requiring hospitalisation), we profiled nasopharyngeal airway metagenome and virus at hospitalisation, and calculated the polygenic risk score of asthma. Using similarity network fusion clustering approach, we identified integrated metagenome-asthma genetic risk endotypes. In addition, we examined their longitudinal association with the risk of developing asthma by the age of 6 years.

RESULTS: Out of 450 infants with bronchiolitis (median age 3 months), we identified five distinct endotypes, characterised by their nasopharyngeal metagenome, virus and asthma genetic risk profiles. Compared with endotype A infants (who clinically resembled "classic" bronchiolitis), endotype E infants (characterised by a high abundance of Haemophilus influenzae, high proportion of rhinovirus (RV)-A and RV-C infections and high asthma genetic risk) had a significantly higher risk of developing asthma (16.7% versus 35.9%; adjusted OR 2.24, 95% CI 1.02-4.97; p=0.046). The pathway analysis showed that endotype E had enriched microbial pathways (e.g. glycolysis, l-lysine, arginine metabolism) and host pathways (e.g. interferons, interleukin-6/Janus kinase/signal transducers and activators of transcription-3, fatty acids, major histocompatibility complex and immunoglobin-related) (false discovery rate (FDR)<0.05). Additionally, endotype E had a significantly higher proportion of neutrophils (FDR<0.05).

CONCLUSION: In this multicentre prospective cohort study of infant bronchiolitis, the clustering analysis of integrated-omics data identified biologically distinct endotypes with differential risks of developing asthma.}, } @article {pmid39326354, year = {2024}, author = {Li, J and Li, X and Zuo, R and Yang, L and Xu, Y and Yu, S and Wang, J and Yang, J}, title = {Exploring the microbe-mediated biological processes of BTEX and toxic metal(loid)s in aging petrochemical landfills.}, journal = {Ecotoxicology and environmental safety}, volume = {285}, number = {}, pages = {117103}, doi = {10.1016/j.ecoenv.2024.117103}, pmid = {39326354}, issn = {1090-2414}, mesh = {*Soil Pollutants/toxicity/analysis ; *Benzene Derivatives/toxicity ; *Benzene/toxicity ; *Toluene/toxicity ; *Soil Microbiology ; *Xylenes/toxicity ; *Waste Disposal Facilities ; Biodegradation, Environmental ; Environmental Monitoring ; Metals, Heavy/toxicity/analysis ; Water Pollutants, Chemical/analysis/toxicity ; Metals/toxicity/analysis ; Groundwater/chemistry/microbiology ; }, abstract = {Aging petrochemical landfills serve as reservoirs of inorganic and organic contaminants, posing potential risks of contamination to the surrounding environment. Identifying the pollution characteristics and elucidating the translocation/ transformation processes of typical contaminants in aging petrochemical landfills are crucial yet challenging endeavors. In this study, we employed a combination of chemical analysis and microbial metagenomic technologies to investigate the pollution characteristics of benzene, toluene, ethylbenzene, and xylene (BTEX) as well as metal(loid)s in a representative aging landfill, surrounding soils, and underlying groundwater. Furthermore, we aimed to explore their transformations driven by microbial activity. Our findings revealed widespread distribution of metal(loid)s, including Cd, Ni, Cu, As, Mn, Pb, and Zn, in these environmental media, surpassing soil background values and posing potential ecological risks. Additionally, microbial processes were observed to contribute significantly to the degradation of BTEX compounds and the transformation of metal(loid)s in landfills and surrounding soils, with identified microbial communities and functions playing key roles. Notably, co-occurrence network analysis unveiled the coexistence of functional genes associated with BTEX degradation and metal(loid) transformation, driven primarily by As, Ni, and Cd. These results shed light on the co-selection of resistance traits against BTEX and metal(loid) contaminants in soil microbial consortia under co-contamination scenarios, supporting microbial adaptive evolution in aging petrochemical landfills. The insights gained from this study enhance our understanding of characteristic pollutants and microbial transformation processes in aging landfills, thereby facilitating improved landfill management and contamination remediation strategies.}, } @article {pmid39326312, year = {2025}, author = {Wang, X and Cui, J and Gu, Z and Guo, L and Liu, R and Guo, Y and Qin, N and Yang, Y}, title = {Aged garlic oligosaccharides modulate host metabolism and gut microbiota to alleviate high-fat and high-cholesterol diet-induced atherosclerosis in ApoE[-/-] mice.}, journal = {Food chemistry}, volume = {463}, number = {Pt 3}, pages = {141409}, doi = {10.1016/j.foodchem.2024.141409}, pmid = {39326312}, issn = {1873-7072}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Atherosclerosis/metabolism/microbiology/drug therapy ; Mice ; *Oligosaccharides/pharmacology/administration & dosage/metabolism ; *Diet, High-Fat/adverse effects ; Male ; *Apolipoproteins E/genetics/metabolism ; *Garlic/chemistry ; Mice, Inbred C57BL ; Bacteria/isolation & purification/classification/genetics/metabolism/drug effects ; Humans ; Mice, Knockout ; Fatty Acids, Volatile/metabolism ; Feces/microbiology/chemistry ; }, abstract = {Atherosclerosis (AS) is a cardiovascular disease caused by excessive accumulation of lipids in arterial walls. In this study, we developed an AS model in ApoE[-/-] mice using a high-fat, high-cholesterol diet and investigated the anti-AS mechanism of aged garlic oligosaccharides (AGOs) by focusing on the gut microbiota. Results revealed that AGOs exhibited significant anti-AS effects, reduced trimethylamine N-oxide levels from 349.9 to 189.2 ng/mL, and reduced aortic lipid deposition from 31.7 % to 9.5 %. AGOs significantly increased the levels of short-chain fatty acids in feces, in which acetic, propionic, and butyric acids were increased from 1.580, 0.364, and 0.469 mg/g to 2.233, 0.774, and 0.881 mg/g, respectively. An analysis of the gut microbiota indicated that AGOs restored alpha and beta diversity, decreased the Firmicutes/Bacteroidetes ratio, and promoted the dominance of the genus Akkermansia. A metagenomic analysis revealed that AGOs alleviated AS through the ABC transporter pathway and the lipopolysaccharide biosynthesis pathway.}, } @article {pmid39326073, year = {2024}, author = {Dong, S and Feng, H and Du, Y and Zhou, J and Xu, J and Lin, D and Ding, D and Xia, Y and Wang, M and Ding, Y}, title = {Source elimination of antibiotic resistance risk in aquaculture water by VUV/sulfite pretreatment.}, journal = {Journal of environmental management}, volume = {370}, number = {}, pages = {122644}, doi = {10.1016/j.jenvman.2024.122644}, pmid = {39326073}, issn = {1095-8630}, mesh = {*Aquaculture ; *Drug Resistance, Microbial/genetics ; *Anti-Bacterial Agents/pharmacology ; Sulfites ; Wastewater ; }, abstract = {Antibiotic resistance risk in the aquaculture industry is increasing with the excessive consumption of antibiotics. Although various efficient technologies for the degradation of antibiotics are available, the potential risk from antibiotic resistance in treated waters is often overlooked. This study compared the risks of antibiotic resistance in anaerobic sludge fed with pretreated florfenicol (FLO) containing wastewater after four UV or vacuum UV (VUV)-driven ((V)UV-driven) pretreatments, and established the VUV/sulfite recirculating water system to validate the effect of controlling the antibiotic resistance risk in the actual aquaculture water. Metagenomics sequencing revealed that a remarkable decrease in the abundance of antibiotic resistance genes (ARGs) was observed in four different pretreated groups, and results among the four pretreated groups were sorted in descending order based on ARG abundance: UV > VUV > UV/sulfite > VUV/sulfite. The low abundance of ARGs from VUV/sulfite group was close to that in the CK group (wastewater without FLO and without any pretreatments), which was 0.41 copies/cell. From the perspective of the temporal changes in the relative abundance of floR, the abundance in VUV/sulfite group remained lower than 11.67 ± 0.73 during the cultivation time. Additionally, microbial diversity analysis found that Proteobacteria and Firmicutes were major carriers of ARGs. Two species from Burkholderiaceae and Rhodocyclales were identified as potential co-hosts to spread by the correlation analysis of the abundances between floR or intI1 and the top 50 genera. Finally, the abundances of ARGs and MGEs in the VUV/sulfite recirculating water system with actual aquaculture water were reduced by 39.15% and 46.04%, respectively, compared to that in the blank group without any pretreatment. This study verified that VUV/sulfite pretreatment system could effectively control the antibiotic resistance risk of ARGs proliferation and transfer in aquaculture water. Furthermore, the study demonstrated that the reduction of antibiotic antibacterial activity plays an important role in the source control of resistance risk.}, } @article {pmid39325867, year = {2024}, author = {Fan, K and Cheng, Y and Hao, S}, title = {Lymph node histology and metagenomic sequencing in a child with cat scratch disease.}, journal = {QJM : monthly journal of the Association of Physicians}, volume = {117}, number = {12}, pages = {889-891}, doi = {10.1093/qjmed/hcae188}, pmid = {39325867}, issn = {1460-2393}, } @article {pmid39325235, year = {2024}, author = {Xing, S and Zhang, Z and Liu, C and Zhang, W and Zhang, Z and Tang, X and Chen, Y and He, W and Zhao, X and An, Y}, title = {Characteristics of Endemic Mycoses Talaromyces marneffei Infection Associated with Inborn Errors of Immunity.}, journal = {Journal of clinical immunology}, volume = {45}, number = {1}, pages = {17}, pmid = {39325235}, issn = {1573-2592}, support = {82070135//National Natural Science Foundation of China/ ; 2021YFC2700804//National Key R&D Program of China/ ; W0100//CQMU Program for Youth Innovation in Future Medicine/ ; }, mesh = {Humans ; *Talaromyces ; *Mycoses/diagnosis/immunology ; Endemic Diseases ; Antifungal Agents/therapeutic use ; Genotype ; Immunologic Deficiency Syndromes/complications/diagnosis ; Opportunistic Infections/immunology/diagnosis ; }, abstract = {BACKGROUND: Talaromyces marneffei (T. marneffei) is an opportunistic pathogen that causes endemic mycoses, which could lead to multiple organ damage. Talaromycosis is frequently disregarded as an early cautionary sign of immune system disorders in non-HIV-infected children.

OBJECTIVE: We conduct a comprehensive review of the genotypes and clinical features of talaromycosis in patients with IEI to enhance clinical awareness regarding T. marneffei as a potential opportunistic pathogen in individuals with immune deficiencies.

METHODS: A systematic literature review was performed by searching PubMed, Cochrane Central Register of Controlled Trials, Web of Science, EMBASE, and Scopus. Data on IEI patients with talaromycosis, including genotypes and their immunological and clinical features, were collected.

RESULTS: Fifty patients with talaromycosis and IEI were included: XHIM (30.0%), STAT3-LOF deficiency (20.0%), STAT1-GOF (20.0%), IL2RG (6.00%), IFNGR1 (6.0%), IL12RB1 (4.0%), CARD9 (4.0%), COPA (4.0%), ADA (2.0%), RELB deficiency (2.0%), and NFKB2 (2.0%). Common symptoms of respiratory (43/50, 86.0%), skin (17/50, 34.0%), lymph node (31/50, 62.0%), digestive (34/50, 68.0%), and hematologic (22/50, 44.0%) systems were involved. The CT findings of the lungs may include lymph node calcification (9/30), interstitial lesions (8/30), pulmonary cavities (8/30), or specific pathogens (4/30), which could be easily misdiagnosed as tuberculosis infection. Amphotericin B (26/43), Voriconazole (24/43) and Itraconazole (22/43) were used for induction therapy. Ten patients were treated with Itraconazole sequentially and prophylaxis. 68.0% (34/50) of patients were still alive, and 4.0% (2/50) of were lost to follow-up. The disseminated T. marneffei infection resulted in the deaths of 14 individuals.

CONCLUSIONS: The XHIM, STAT1-GOF, and STAT3-LOF demonstrated the highest susceptibility to talaromycosis, indicating the potential involvement of cellular immunity, IL-17 signaling, and the IL-12/IFN-γ axis in T. marneffei defense. T. marneffei infection may serve as an early warning indicator of IEI. For IEI patients suspected of T. marneffei, metagenomic next-generation sequencing (mNGS) could rapidly and effectively identify the causative pathogen. Prompt initiation of antifungal therapy is crucial for optimizing patient outcomes.}, } @article {pmid39324818, year = {2024}, author = {Li, F and Jia, M and Chen, H and Chen, M and Su, R and Usman, S and Ding, Z and Hao, L and Franco, M and Guo, X}, title = {Responses of microbial community composition and CAZymes encoding gene enrichment in ensiled Elymus nutans to altitudinal gradients in alpine region.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {10}, pages = {e0098624}, pmid = {39324818}, issn = {1098-5336}, support = {U20A2002//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {*Altitude ; *Silage/microbiology/analysis ; *Microbiota ; *Bacteria/genetics/classification/isolation & purification ; *Elymus/microbiology/genetics ; Fermentation ; Tibet ; Acetic Acid/metabolism ; }, abstract = {UNLABELLED: High-throughput metagenomic sequence technology was employed to evaluate changes in microbial community composition and carbohydrate-active enzymes encoding gene enrichment status in Elymus nutans silages to altitudinal gradients in the world's highest alpine region of Qinghai-Tibetan Plateau (QTP). E. nutans were collected from three different altitudes in QTP: 2,600 m (low altitude), 3600 m (moderate altitude), and 4,600 m [high (H) altitude], and ensiled for 7, 14, 30, and 60 d. Results indicated an improvement in silage quality with the increasing altitude, although the acetic acid concentration and dry matter loss were greater in H altitude silages after 30 d of ensiling. Harmful bacteria or potential pathogens predominated in the microbial community on d 7 and 14 of fermentation, while genera belonging to lactic acid bacteria gradually became the main microorganisms with the increasing altitude on d 30 and 60 of ensiling. The abundance of carbohydrate-active enzymes genes responsible for macromolecular carbohydrate degradation in silage increased with increasing altitude, and those genes were mainly carried by Lactiplantibacillus and Pediococcus at 30 and 60 d of ensiling. The abundance of key enzymatic genes associated with glycolysis and organic acid production in carbohydrate metabolism pathway was higher in H altitude silages, and Lactiplantibacillus and Pediococcus were also the main hosts after 30 d of silage fermentation, except for the fact that acetic acid production was also related to genera Leuconostoc, Latilactobacillus, and Levilactobacillus.

IMPORTANCE: The fermentation quality of Elymus nutans silage was getting better with the increase of altitude in the Qinghai-Tibetan Plateau. The abundance of hosts carrying carbohydrate-active enzymes genes and key enzyme genes related to organic acid production increased with increasing altitude during the later stages of fermentation. Lactiplantibacillus and Pediococcus were the core microorganisms responsible for both polysaccharide hydrolysis and silage fermentation in the late stage of ensiling. This study provided insights on the influence of different altitudes on the composition and function of silage microbiome in the Qinghai-Tibetan Plateau, and provided a reference approach for improving the quality and controllability of silage production in high altitude areas of the Qinghai-Tibetan Plateau.}, } @article {pmid39324627, year = {2024}, author = {Bigatton, ED and Verdenelli, RA and Haro, RJ and Ayoub, I and Barbero, FM and Martín, MP and Dubini, LE and Jorrín Novo, JV and Lucini, EI and Castillejo, MÁ}, title = {Metagenomic Analysis to Assess the Impact of Plant Growth-Promoting Rhizobacteria on Peanut (Arachis hypogaea L.) Crop Production and Soil Enzymes and Microbial Diversity.}, journal = {Journal of agricultural and food chemistry}, volume = {72}, number = {40}, pages = {22385-22397}, pmid = {39324627}, issn = {1520-5118}, mesh = {*Arachis/microbiology/growth & development/metabolism/genetics ; *Soil Microbiology ; *Bacillus/genetics/metabolism ; *Bradyrhizobium/genetics/metabolism/growth & development/physiology ; *Pseudomonas/genetics/physiology/growth & development ; *Metagenomics ; *Rhizosphere ; *Soil/chemistry ; Crop Production/methods ; Bacteria/genetics/classification/metabolism/enzymology/isolation & purification ; Biodiversity ; Nitrogen Fixation ; Plant Roots/microbiology/growth & development/metabolism ; }, abstract = {Peanut production could be increased through plant growth-promoting rhizobacteria (PGPR). In this regard, the present field research aimed at elucidating the impact of PGPR on peanut yield, soil enzyme activity, microbial diversity, and structure. Three PGPR strains (Bacillus velezensis, RI3; Bacillus velezensis, SC6; Pseudomonas psychrophila, P10) were evaluated, along with Bradyrhizobium japonicum (BJ), taken as a control. PGPR increased seed yield by 8%, improving the radiation use efficiency (4-14%). PGPR modified soil enzymes (fluorescein diacetate activity by 17% and dehydrogenase activity by 28%) and microbial abundance (12%). However, PGPR did not significantly alter microbial diversity; nonetheless, it modified the relative abundance of key phyla (Actinobacteria > Proteobacteria > Firmicutes) and genera (Bacillus > Arthrobacter > Pseudomonas). PGPRs modified the relative abundance of genes associated with N-fixation and nitrification while increasing genes related to N-assimilation and N-availability. PGPR improved agronomic traits without altering rhizosphere diversity.}, } @article {pmid39324179, year = {2024}, author = {Wu, X and Qi, T and Zhang, M and Bi, J}, title = {A rare case report of Prevotella lung abscess diagnosed using third-generation metagenomic sequencing.}, journal = {The Journal of international medical research}, volume = {52}, number = {9}, pages = {3000605241271757}, pmid = {39324179}, issn = {1473-2300}, mesh = {Humans ; *Prevotella/isolation & purification/genetics ; *Lung Abscess/microbiology/diagnosis ; *Metagenomics/methods ; Bacteroidaceae Infections/diagnosis/microbiology ; High-Throughput Nucleotide Sequencing/methods ; Female ; Male ; Tomography, X-Ray Computed ; }, abstract = {The Prevotella genus consists of obligate anaerobic Gram-negative bacteria that are symbiotic with the oral, intestinal, and vaginal mucosa. While several species of Prevotella have been implicated in pulmonary infections, identification of Prevotella as the causative agent of lung abscess is uncommon because of the requirement for stringent anaerobic culture conditions. In this report, we highlight a case of lung abscess caused by Prevotella salivae and Prevotella veroralis, underscoring the importance of third-generation metagenomic sequencing using devices from Oxford Nanopore Technologies for the precise diagnosis of specific pathogens.}, } @article {pmid39323466, year = {2024}, author = {Chen, L and Pei, M and Wang, X and Zhang, Y and Ma, Y and Chen, Y and Ahmad, I}, title = {Analysis of a case report of meningitis caused by Listeria monocytogenes.}, journal = {Frontiers in medicine}, volume = {11}, number = {}, pages = {1440225}, pmid = {39323466}, issn = {2296-858X}, abstract = {BACKGROUND: Listeria monocytogenes is a Gram-positive bacterium transmitted to humans through contaminated food, water, and animal faeces, posing a public health risk. Listeria monocytogenes is difficult to isolate and is not sensitive to first-line treatment with broad-spectrum cephalosporins for bacterial meningitis. Listeria meningitis is rare but can progress rapidly and may be accompanied by serious complications (hydrocephalus, ventricular inflammation, cerebral palsy, and brain abscess) and a high mortality rate.

CASE PRESENTATION: It is a retrospective analysis of the clinical characteristics and treatment of a rare case of Listeria monocytogenes infection. Using laboratory indicators such as white blood cells (WBC), C-reactive protein (CRP), and procalcitonin (PCT), three detection methods (cerebrospinal fluid/blood culture), Targeted gene sequencing technology (tNGS), and Metagenomic next-generation sequencing technology (mNGS) combined with clinical manifestations of patients, analyze the use plan and prognosis of antibiotics in patients. The patient in this case initially had neurological symptoms such as fever, headache, unclear consciousness, and vomiting; laboratory indicators include elevated WBC, CRP, and PCT. Listeria monocytogenes was cultured in both the patient's cerebrospinal fluid and blood samples. After treatment with penicillin and meropenem, the patient recovered and was discharged without any sequelae.

CONCLUSION: Due to the rarity of Listeria monocytogenes, there may be deficiencies and difficulties in clinical differential diagnosis, making it difficult to achieve targeted antibiotic treatment. Therefore, accurate identification of Listeria monocytogenes and relevant laboratory inflammation indicator testing, combined with traditional culture methods and NGS testing, through empirical coverage of Listeria monocytogenes, targeted antibiotic treatment ultimately impacts clinical outcomes significantly.}, } @article {pmid39323103, year = {2024}, author = {Abdisa, E and Esmaeily, M and Kwon, J and Jin, G and Kim, Y}, title = {A Nematode Isolate, Oscheius Tipulae, Exhibiting a Wide Entomopathogenic Spectrum and its Application to Control Dipteran Insect Pests.}, journal = {Archives of insect biochemistry and physiology}, volume = {117}, number = {1}, pages = {e22152}, doi = {10.1002/arch.22152}, pmid = {39323103}, issn = {1520-6327}, support = {//This work was supported by a grant (No. 2022R1A2B5B03001792) from the National Research Foundation (NRF) funded by the Minifistry of Science, ICT and Future Planning, Republic of Korea. This study was also funded by a research grant from Andong National University./ ; }, mesh = {Animals ; *Diptera/microbiology ; Pest Control, Biological ; Rhabditida/pathogenicity/physiology ; Virulence ; Symbiosis ; Nematoda ; Xenorhabdus/genetics/pathogenicity/physiology ; }, abstract = {An entomopathogenic nematode, Oscheius tipulae, was isolated from a soil sample. The identification of this species was supported by morphological and molecular markers. The nematode isolate exhibited pathogenicity against different target insects including lepidopteran, coleopteran, and dipteran insects. The virulence of this nematode was similar to that of a well-known entomopathogenic nematode, Steinernema carpocapsae, against the same insect targets. A comparative metagenomics analysis of these two nematode species predicted the existence of a combined total of 272 bacterial species in their intestines, of which 51 bacterial species were shared between the two nematode species. In particular, the common gut bacteria included several entomopathogenic bacteria including Xenorhabdus nematophila, which is known as a symbiotic bacterium to S. carpocapsae. The nematode virulence of O. tipulae to insects was enhanced by an addition of dexamethasone but suppressed by an addition of arachidonic acid, suggesting that the immune defenses of the target insects against the nematode infection is mediated by eicosanoids, which would be manipulated by the symbiotic bacteria of the nematode. Unlike S. carpocapsae, O. tipulae showed high virulence against dipteran insects including fruit flies, onion flies, and mosquitoes. O. tipulae showed particularly high control efficacies against the onion maggot, Delia platura, infesting the Welsh onion in the rhizosphere in both pot and field assays.}, } @article {pmid39322959, year = {2024}, author = {Wirbel, J and Essex, M and Forslund, SK and Zeller, G}, title = {A realistic benchmark for differential abundance testing and confounder adjustment in human microbiome studies.}, journal = {Genome biology}, volume = {25}, number = {1}, pages = {247}, pmid = {39322959}, issn = {1474-760X}, mesh = {Humans ; *Microbiota ; *Benchmarking ; RNA, Ribosomal, 16S/genetics ; Computer Simulation ; }, abstract = {BACKGROUND: In microbiome disease association studies, it is a fundamental task to test which microbes differ in their abundance between groups. Yet, consensus on suitable or optimal statistical methods for differential abundance testing is lacking, and it remains unexplored how these cope with confounding. Previous differential abundance benchmarks relying on simulated datasets did not quantitatively evaluate the similarity to real data, which undermines their recommendations.

RESULTS: Our simulation framework implants calibrated signals into real taxonomic profiles, including signals mimicking confounders. Using several whole meta-genome and 16S rRNA gene amplicon datasets, we validate that our simulated data resembles real data from disease association studies much more than in previous benchmarks. With extensively parametrized simulations, we benchmark the performance of nineteen differential abundance methods and further evaluate the best ones on confounded simulations. Only classic statistical methods (linear models, the Wilcoxon test, t-test), limma, and fastANCOM properly control false discoveries at relatively high sensitivity. When additionally considering confounders, these issues are exacerbated, but we find that adjusted differential abundance testing can effectively mitigate them. In a large cardiometabolic disease dataset, we showcase that failure to account for covariates such as medication causes spurious association in real-world applications.

CONCLUSIONS: Tight error control is critical for microbiome association studies. The unsatisfactory performance of many differential abundance methods and the persistent danger of unchecked confounding suggest these contribute to a lack of reproducibility among such studies. We have open-sourced our simulation and benchmarking software to foster a much-needed consolidation of statistical methodology for microbiome research.}, } @article {pmid39322164, year = {2024}, author = {Gao, YY and Zhou, YH and Liu, XP and Di, B and He, JY and Wang, YT and Guo, PT and Zhang, J and Wang, CK and Jin, L}, title = {Ganoderma lucidum polysaccharide promotes broiler health by regulating lipid metabolism, antioxidants, and intestinal microflora.}, journal = {International journal of biological macromolecules}, volume = {280}, number = {Pt 3}, pages = {135918}, doi = {10.1016/j.ijbiomac.2024.135918}, pmid = {39322164}, issn = {1879-0003}, abstract = {Ganoderma lucidum polysaccharides (GLP) are the primary bioactive macromolecular compounds of Ganoderma lucidum, possessing antioxidant and immunomodulatory effects. Hot water extract of Juncao-substrate Ganoderma Lucidum residue (HWE-JGLR) is abundant in GLP. There are few research reports on the application of HWE-JGLR in animal husbandry. Therefore, this study aims to investigate the effects of HWE-JGLR supplementation on growth performance, serum biochemistry, the antioxidant function of serum and liver, and the intestinal microbiota of yellow-feathered broilers. The control group was fed a corn-soybean meal basal diet, while the HJ I, II, and III groups received diets supplemented with 0.25 %, 0.5 %, and 1 % of HWE-JGLR, respectively. Results showed that HWE-JGLR increased the serum HDL-C content and decreased the TG content in broilers. Moreover, HWE-JGLR enhanced the antioxidant function by the Keap1-Nrf2/ARE signaling pathway and the antioxidative enzyme in broilers. In addition, the cecum of the metagenomic analysis of 16S rRNA showed that the relative abundance of no-rank Ruminococcacea was increased in the HJ I group. Our findings indicate that HWE-JGLR has strong potential for development as a green feed additive based on its functions of lipid-lowering, antioxidation, and the modulation of gut microbiota composition.}, } @article {pmid39322110, year = {2024}, author = {Liu, K and Li, Y and Ge, Z and Huang, D and Zhang, J}, title = {Microbial communities and mobile genetic elements determine the variations of antibiotic resistance genes for a continuous year in the urban river deciphered by metagenome assembly.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {362}, number = {}, pages = {125018}, doi = {10.1016/j.envpol.2024.125018}, pmid = {39322110}, issn = {1873-6424}, mesh = {*Rivers/microbiology/chemistry ; *Drug Resistance, Microbial/genetics ; *Microbiota/genetics ; Metagenome ; Bacteria/genetics ; Interspersed Repetitive Sequences ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Environmental Monitoring/methods ; }, abstract = {Antibiotic resistance genes (ARGs) have become emerging environmental contaminants influenced by intricate regulatory factors. However, there is a lack of comprehensive studies on the evolution and distribution of ARGs over a full year in urban rivers, which serve as significant reservoirs of ARGs due to dynamic human activities. In this study, we conducted a 12-month metagenomic assembly to explore the microbial communities, ARGs, mobile genetic elements (MGEs) coexisting with ARGs, ARGs hosts, and the impact of environmental factors. Bacitracin (32%-47%) and multidrug (13%-24%) were detected throughout the year, constituting over 60% of the total abundance, making them the primary ARGs types. The assembly mechanisms of microbial communities and ARGs were primarily driven by stochastic processes. Integrase, IntI1, recombinase, and transposase were identified as the main MGEs coexisting with ARGs. Procrustes analysis revealed a significant structural association, indicating that the composition of host communities likely plays crucial roles in the seasonal composition and distribution of ARGs. Human pathogenic bacteria (HPBs) were identified in the summer, autumn, and winter, with Escherichia coli, Klebsiella pneumoniae, Acinetobacter lwoffii, and Burkholderiales bacterium being the primary HPBs. Mantle tests and PLS-PM equation analysis indicated that microbial communities and MGEs are the most critical factors determining the distribution and composition of ARGs in the river. Environmental factors (including water properties and nutrients) and ARGs hosts influence the evolution and abundance of ARGs by directly regulating microbial communities and MGEs. This study provides critical insights into risk assessment and management of ARGs in urban rivers.}, } @article {pmid39322056, year = {2024}, author = {Chen, J and Lin, Y and Zhu, Y and Zhang, Y and Qian, Q and Chen, C and Xie, S}, title = {Spatiotemporal profiles and underlying mechanisms of the antibiotic resistome in two water-diversion lakes.}, journal = {Environmental research}, volume = {263}, number = {Pt 1}, pages = {120051}, doi = {10.1016/j.envres.2024.120051}, pmid = {39322056}, issn = {1096-0953}, mesh = {*Lakes/microbiology ; China ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Seasons ; Drug Resistance, Microbial/genetics ; Spatio-Temporal Analysis ; Environmental Monitoring ; Bacteria/drug effects/genetics ; Drug Resistance, Bacterial/genetics ; }, abstract = {Human-induced interventions have altered the local characteristics of the lake ecosystems through changes in hydraulic exchange, which in turn impacts the ecological processes of antibiotic resistance genes (ARGs) in the lakes. However, the current understanding of the spatiotemporal patterns and driving factors of ARGs in water-diversion lakes is still seriously insufficient. In the present study, we investigated antibiotic resistome in the main regulation and storage hubs, namely Nansi Lake and Dongping Lake, of the eastern part of the South-to-North Water Diversion project in Shandong Province (China) using a metagenomic-based approach. A total of 653 ARG subtypes belonging to 25 ARG types were detected with a total abundance of 0.125-0.390 copies/cell, with the dominance of bacitracin, multidrug, and macrolide-lincosamide streptogramin resistance genes. The ARG compositions were sensitive to seasonal variation and also interfered by artificial regulation structures along the way. Human pathogenic bacteria such as Acinetobacter calcoaceticus, Acinetobacter lwoffii, Klebsiella pneumoniae, along with the multidrug resistance genes they carried, were the focus of risk control in the two studied lakes, especially in summer. Plasmids were the key mobile genetic elements (MGEs) driving the horizontal gene transfer of ARGs, especially multidrug and sulfonamide resistance genes. The null model revealed that stochastic process was the main driver of ecological drift for ARGs in the lakes. The partial least squares structural equation model further determined that seasonal changes of pH and temperature drove a shift in the bacterial community, which in turn shaped the profile of ARGs by altering the composition of MGEs, antibacterial biocide- and metal-resistance genes (BMGs), and virulence factor genes (VFGs). Our results highlighted the importance of seasonal factors in determining the water transfer period. These findings can aid in a deeper understanding of the spatiotemporal variations of ARGs in lakes and their driving factors, offering a scientific basis for antibiotic resistance management.}, } @article {pmid39321940, year = {2024}, author = {Wang, P and Li, L and Zhang, Y and Ren, D and Feng, Y and Li, X and Wu, D and Xie, B and Ma, J}, title = {Triclosan facilitates the dissemination of antibiotic resistance genes during anaerobic digestion: Focusing on horizontal transfer and microbial response.}, journal = {Bioresource technology}, volume = {413}, number = {}, pages = {131522}, doi = {10.1016/j.biortech.2024.131522}, pmid = {39321940}, issn = {1873-2976}, mesh = {*Triclosan/pharmacology ; Anaerobiosis ; *Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Bioreactors ; }, abstract = {The present study aims to investigate the mechanism by which triclosan influences the dissemination of antibiotic resistance genes (ARGs) during the whole anaerobic digestion process. qPCR and metagenomic analyses revealed that triclosan facilitated ARGs dissemination in a dose- and time-dependent manner. Furthermore, integrons exhibited a significant correlation with the majority of quantified ARGs, and various ARGs were frequently linked on integron gene cassettes. Microbial community and redundancy analyses indicated that triclosan altered the components of dominant ARGs hosts Firmicutes, Synergistetes and Bacteroidetes. Path modeling analysis confirmed integrons were the main driving force for facilitating ARGs dissemination. The promoted ARGs dissemination may be associated with the increased reactive oxygen species generation, cell membrane permeability, close-connected the ARGs transfer related regulatory proteins induced by triclosan. This study broadens the understanding of triclosan facilitates ARGs dissemination through anaerobic treatment, the strategies for preventing potential risks should be proposed in practice.}, } @article {pmid39321483, year = {2024}, author = {Vinyes-Nadal, M and Kümmel, S and Espín, Y and Gómez-Alday, JJ and Gehre, M and Otero, N and Torrentó, C}, title = {Dual C and Cl compound-specific isotope analysis and metagenomic insights into the degradation of the pesticide methoxychlor.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {135929}, doi = {10.1016/j.jhazmat.2024.135929}, pmid = {39321483}, issn = {1873-3336}, mesh = {*Methoxychlor/metabolism/chemistry ; *Biodegradation, Environmental ; *Chlorine/chemistry ; Carbon Isotopes ; Insecticides/chemistry/metabolism ; Oxidation-Reduction ; Metagenomics ; Kinetics ; Bacteria/metabolism ; Pesticides/chemistry/metabolism ; Water Pollutants, Chemical/chemistry/metabolism ; }, abstract = {This study investigates the use of multi-element compound-specific isotope analysis (ME-CSIA) to monitor degradation processes of methoxychlor, a persistent organochlorine insecticide. Laboratory experiments examined the kinetics, release of transformation products, and carbon and chlorine isotope effects during methoxychlor degradation through alkaline hydrolysis, oxidation with alkaline-activated persulfate, and biotic reductive dechlorination. Results showed that hydrolysis and oxidation did not cause significant carbon and chlorine isotope fractionation, indicating that C-H rather than C-Cl bond cleavage was the rate-determining step. Conversely, biotic reductive dechlorination by a field-derived microcosm under strictly anoxic conditions displayed significant carbon (εC = -0.9 ± 0.3 ‰) and chlorine (εCl = -1.9 ± 1.0 ‰) isotope fractionation. Its corresponding calculated dual isotope slope (ΛC/Cl = 0.4 ± 0.1) and apparent kinetic isotope effects (AKIEC = 1.014 ± 0.005 and AKIECl = 1.006 ± 0.003) indicate a C-Cl bond cleavage as the rate-determining step, highlighting the difference with respect to the other studied degradation mechanisms. Changes in the microbial community diversity revealed that families such as Dojkabacteria, Anaerolineaceae, Dysgonomonadaceae, Bacteroidetes vadinHA17, Pseudomonadaceae, and Spirochaetaceae, may be potential agents of methoxychlor reductive dechlorination under anoxic conditions. This study advances the understanding of degradation mechanisms of methoxychlor and improves the ability to track its transformation in contaminated environments, including for the first time an isotopic perspective.}, } @article {pmid39320990, year = {2024}, author = {Mian, E and Petrucci, E and Pizzi, C and Comin, M}, title = {MISSH: Fast Hashing of Multiple Spaced Seeds.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {PP}, number = {}, pages = {}, doi = {10.1109/TCBB.2024.3467368}, pmid = {39320990}, issn = {1557-9964}, abstract = {Alignment-free analysis of sequences has revolutionized the high-throughput processing of sequencing data within numerous bioinformatics pipelines. Hashing k-mers represents a common function across various alignment-free applications, serving as a crucial tool for indexing, querying, and rapid similarity searching. More recently, spaced seeds, a specialized pattern that accommodates errors or mutations, have become a standard choice over traditional k-mers. Spaced seeds offer enhanced sensitivity in many applications when compared to k-mers. However, it's important to note that hashing spaced seeds significantly increases computational time. Furthermore, if multiple spaced seeds are employed, accuracy can be further improved, albeit at the expense of longer processing times. This paper addresses the challenge of efficiently hashing multiple spaced seeds. The proposed algorithms leverage the similarity of adjacent spaced seed hash values within an input sequence, allowing for the swift computation of subsequent hashes. Our experimental results, conducted across various tests, demonstrate a remarkable performance improvement over previously suggested algorithms, with potential speedups of up to 20 times. Additionally, we apply these efficient spaced seed hashing algorithms to a metagenomic application, specifically the classification of reads using Clark-S [Ounit and Lonardi, 2016]. Our findings reveal a substantial speedup, effectively mitigating the slowdown caused by the utilization of multiple spaced seeds.}, } @article {pmid39320471, year = {2024}, author = {Zou, W and Zhang, J and Li, Y and Zhang, Z and Yang, R and Yan, Y and Zhu, W and Ma, F and Jiang, P and Wang, Y and Zhang, X and Chen, J}, title = {Interstitial lung disease presents with varying characteristics in patients with non-Hodgkin lymphoma undergoing rituximab-containing therapies.}, journal = {Annals of hematology}, volume = {}, number = {}, pages = {}, pmid = {39320471}, issn = {1432-0584}, abstract = {Although the incidence and outcomes of rituximab-induced interstitial lung disease (RILD) have been partially reported, there are no systematic studies on the characteristics and types of RILD. This study aimed to investigate the clinical characteristics, bronchoalveolar lavage (BAL) findings, and treatment course of RILD in patients with non-Hodgkin lymphoma. We retrospectively analyzed the data from 321 patients with non-Hodgkin lymphoma who developed RILD between 2020 and 2022. The extent, distribution, and radiologic patterns of interstitial lung disease were determined using high-resolution computed tomography of the chest. BAL was performed in 299 (93.1%) patients to determine cellular distribution patterns and identify pathogenic microorganisms using metagenomic next-generation sequencing. All patients received combination therapy, with cyclophosphamide, doxorubicin, vincristine, and prednisone being the most commonly administered regimens. The median time from treatment to RILD development was 1.7 months. In the 217 patients who underwent metagenomic next-generation sequencing, 179 pathogenic microorganisms were detected, including 77 (43.0%) bacteria, 45 (25.1%) viruses, 28 (15.6%) Pneumocystis jirovecii strains, 17 (9.5%) fungi, 6 (3.5%) Mycobacterium tuberculosis, and 6 (3.5%) atypical pathogens. All RILD diagnoses were based on multidisciplinary team discussions and compliance with international standards. In conclusion, RILD exhibits a range of radiological and BAL patterns, reflecting different interstitial lung disease types. The most common patterns of RILD are infectious lung disease, organizing pneumonia, and nonspecific interstitial pneumonia. These findings enhance the understanding of RILD in patients with non-Hodgkin lymphoma and serve as a reference for best management guidelines in these patients.}, } @article {pmid39320367, year = {2024}, author = {Kayser, E and He, F and Nixon, S and Howard-Varona, A and Lamelas, A and Martinez-Blanch, J and Chenoll, E and Davenport, GM and de Godoy, MRC}, title = {Effects of supplementation of live and heat-treated Bifidobacterium animalis subspecies lactis CECT 8145 on glycemic and insulinemic response, fecal microbiota, systemic biomarkers of inflammation, and white blood cell gene expression of adult dogs.}, journal = {Journal of animal science}, volume = {102}, number = {}, pages = {}, pmid = {39320367}, issn = {1525-3163}, mesh = {Animals ; Dogs ; *Bifidobacterium animalis ; *Feces/microbiology/chemistry ; *Probiotics/pharmacology/administration & dosage ; Male ; Female ; *Diet/veterinary ; Dietary Supplements/analysis ; Animal Feed/analysis ; Biomarkers/blood ; Inflammation/veterinary ; Gastrointestinal Microbiome ; Blood Glucose ; Leukocytes/metabolism ; Hot Temperature ; Insulin/blood/metabolism ; Gene Expression ; }, abstract = {The popularity of functional ingredients such as probiotics and postbiotics has increased as pet owners seek ways to improve the health quality and longevity of their pets. Limited research has been conducted regarding the use of probiotics and postbiotics and their effects on canine health. The objective of this study was to evaluate the effects of daily supplementation of Bifidobacterium animalis subsp. lactis CECT 8145, in both live probiotic (PRO) and heat-treated postbiotic (POST) forms, on fecal fermentative end-products and microbiome, insulin sensitivity, serum gut hormones, oxidative stress, inflammatory biomarkers, and white blood cell gene expression of adult dogs. Eighteen adult beagles and 18 adult English pointers were used in a double-blinded placebo-controlled parallel group design, with 12 animals per group (6 English pointers and 6 beagles). The study began with a 60 d adaptation period followed by a 90 d period of daily supplementation with either PRO, POST, or placebo (maltodextrin; CON). Longitudinal assessment of body weight, body condition score, and pelvic circumference did not differ among dietary supplements (P > 0.05). Throughout the experimental period, fecal scores did not differ (P > 0.05); however, fecal pH was lower (P = 0.0049) in the dogs fed POST compared with CON. A higher fecal concentration of propionate (P = 0.043) was observed in dogs fed PRO and POST when compared with CON. While PRO and POST supplementation were associated with changes in bacterial composition at the family and genus level, the overall richness and diversity of the microbiome were not significantly affected. Functional analysis of the metagenome also suggests that PRO and POST supplementation induced potentially beneficial changes in the abundance of pathways involved in pathogenicity, amino acid biosynthesis, and DNA repair. No differences in glycemic or insulinemic responses were observed among the groups (P > 0.05). Dogs supplemented with PRO had a higher (P < 0.05) mean white blood cell leptin relative fold gene expression compared with groups POST and CON. Serum metabolites and complete blood cell counts were within normal ranges and all dogs remained healthy throughout the study. Together, these data suggest that the PRO and POST can safely be supplemented for dogs. Moreover, the results of this study support further investigation of the role of PRO and POST in supporting parameters related to gut health and hormonal regulation.}, } @article {pmid39320101, year = {2024}, author = {Xue, H and Wang, Y and Mei, C and Han, L and Lu, M and Li, X and Chen, T and Wang, F and Tang, X}, title = {Gut microbiome and serum metabolome alterations associated with lactose intolerance (LI): a case‒control study and paired-sample study based on the American Gut Project (AGP).}, journal = {mSystems}, volume = {9}, number = {10}, pages = {e0083924}, pmid = {39320101}, issn = {2379-5077}, mesh = {*Gastrointestinal Microbiome/physiology ; Animals ; Male ; Case-Control Studies ; *Metabolome ; Humans ; *Lactose Intolerance/microbiology ; Rats ; Female ; Adult ; Fecal Microbiota Transplantation ; Rats, Sprague-Dawley ; Middle Aged ; }, abstract = {UNLABELLED: Lactose intolerance (LI) is a prevalent condition characterized by gastrointestinal symptoms that arise following lactose consumption. Recent evidence suggests that the gut microbiome may influence lactose levels in the gut. However, there is limited understanding regarding the alterations in microbiota and metabolism between individuals with LI and non-LI. This study conducted a paired-sample investigation utilizing data from the American Gut Project (AGP) and performed metagenomic and untargeted metabolomic analyses in a Chinese cohort to explore the interaction between the gut microbiome and serum metabolites. In addition, fecal microbiota transplantation (FMT) experiments were conducted to further examine the impact of the LI-associated gut microbiome on inflammatory outcomes. We identified 14 microbial genera that significantly differed between LI and controls from AGP data. Using a machine learning approach, group separation was predicted based on seven species and nine metabolites in the Chinese cohort. Notably, increased levels of Escherichia coli in the LI group were negatively correlated with several metabolites, including PC (22:6/0:0), indole, and Lyso PC, while reduced levels of Faecalibacterium prausnitzii and Eubacterium rectale were positively correlated with indole and furazolidone. FMT-LI rats displayed visceral hypersensitivity and an altered gut microbiota composition compared to FMT-HC rats. Metagenomic and metabolomic analyses revealed an enrichment of MAPK signaling in LI, which was confirmed by FMT-LI rats showing higher expression of ERK and RAS, along with increased concentrations of proinflammatory cytokines. This study provides valuable insights into the disrupted microbial and metabolic traits associated with LI, emphasizing potential microbiome-based approaches for its prevention and treatment.

IMPORTANCE: Lactose intolerance (LI) is a prevalent condition characterized by gastrointestinal symptoms after lactose consumption due to a deficiency of lactase. There is limited understanding regarding the microbiota and metabolic alterations between individuals with LI and non-LI. This study represents the first exploration to investigate metagenomic and metabolomic signatures among subjects with lactose intolerance as far as our knowledge. We identified 14 microbial genera in the Western cohort and 7 microbial species, along with 9 circulating metabolites in the Chinese cohort, which significantly differed in LI patients. Metagenomic and metabolomic analyses revealed an enrichment of MAPK signaling in LI patients. This finding was confirmed by FMT-LI rats, exhibiting increased expression of ERK and RAS, along with higher concentrations of pro-inflammatory cytokines. Our study provides insights into the disrupted functional and metabolic traits of the gut microbiome in LI, highlighting potential microbiome-based approaches for preventing and treating LI.}, } @article {pmid39319930, year = {2024}, author = {Schuelter, AR and Pedron, LEC and Silva, GJD and Bonett, LP and Souza, IRP and Grignet, RS and Stathacos, JVG and Alves Netto, AF and Coelho, SRM}, title = {Metagenomics and vegetative growth of Salvia hispanica inoculated with Trichoderma harzianum.}, journal = {Brazilian journal of biology = Revista brasleira de biologia}, volume = {84}, number = {}, pages = {e284877}, doi = {10.1590/1519-6984.284877}, pmid = {39319930}, issn = {1678-4375}, mesh = {*Salvia/microbiology ; *Soil Microbiology ; *Metagenomics ; Rhizosphere ; Biomass ; Hypocreales/physiology ; Plant Roots/microbiology ; }, abstract = {The soil is a dynamic environment, influenced by abiotic and biotic factors, which can result in changes in plant development. This study aimed to assess the impact on vegetative growth of chia (Salvia hispanica L) inoculated with Trichoderma harzianum and on the rhizosphere microbiome. The experimentation was conducted in a greenhouse under controlled conditions growing chia plants in pots containing soil with a clayey texture. Different concentrations of T. harzianum (0; 2.5; 5.0; 10.0; 20.0 µL. g-1 of seed) were applied to the chia seeds before planting. Morphological parameters, including plant height (cm), number of branches, stem diameter (mm), number of days to flowering and shoot and root dry masses (g) were quantitatively assessed. After the cultivation period, soil samples from the rhizosphere region were collected for subsequent chemical and metagenomic analyses. These samples were also compared with the control soil, collected before installing the experiment. The results showed that increasing doses of T. harzianum promoted a significant increase in the diameter of the stem, number of branches, dry biomass of the root system and the number of days to flowering, without modifying the overall height of the plants. Soil metagenomics indicated that T. harzianum inoculation modified the microbial diversity of the rhizosphere environment, with more pronounced effects observed in samples treated with higher concentrations of the inoculant. Furthermore, there were changes in the chemical composition and enzymes related to soil quality in correlation with the concentrations of the applied inoculant. This study demonstrated that inoculating chia seeds with T. harzianum not only promotes specific morphogenetic characteristics of the plant, but it also has a significant impact on the microbial diversity and biochemical functionality of the soil, including an observed increase in the populations of T. harzianum and T. asperellum.}, } @article {pmid39319624, year = {2025}, author = {Shi, Q and Fu, Q and Zhang, J and Hao, G and Liang, C and Duan, F and Ma, J and Zhao, H and Song, W}, title = {Paenibacillus polymyxa J2-4 induces cucumber to enrich rhizospheric Pseudomonas and contributes to Meloidogyne incognita management under field conditions.}, journal = {Pest management science}, volume = {81}, number = {1}, pages = {266-276}, doi = {10.1002/ps.8429}, pmid = {39319624}, issn = {1526-4998}, support = {2023YFD1400400//National Key R&D Program of China/ ; 2022CXGC020710-6//Subproject of Shandong Province Key R&D Plan Project/ ; QNYCX23027//Qingdao Agricultural University Graduate Student Innovation Program/ ; QNYCX24076//Qingdao Agricultural University Graduate Student Innovation Program/ ; }, mesh = {*Tylenchoidea/physiology ; Animals ; *Paenibacillus polymyxa/genetics/physiology ; *Pseudomonas/physiology ; *Rhizosphere ; *Cucumis sativus/microbiology/parasitology ; *Plant Diseases/prevention & control/parasitology/microbiology ; Soil Microbiology ; Pest Control, Biological ; Microbiota ; }, abstract = {BACKGROUND: Root knot nematodes (RKNs) pose a great threat to agricultural production worldwide. The bacterial nematocides have received increasing attention due to their safe and efficient control against RKNs. Here, we investigated the biocontrol efficacy of Paenibacillus polymyxa J2-4 against Meloidogyne incognita in the field and analyzed the rhizosphere microbiome of cucumber under nematode infection after application of the J2-4 strain. Furthermore, a biomarker strain of Pseudomonas spp. was isolated from the J2-4-inoculated rhizosphere soil, and its nematocidal activity and growth-promoting effect on host plants were determined. In addition, chemotaxis assay of P. fluroescens ZJ5 toward root exudates was carried out.

RESULTS: The field experiment demonstrated that P. polymyxa J2-4 could effectively suppressed gall formation in cucumber plants, with the galling index reduced by 67.63% in 2022 and 65.50% in 2023, respectively, compared with controls. Meanwhile, plant height and yield were significantly increased in J2-4 treated plants compared with controls. Metagenomic analysis indicated that J2-4 altered the rhizosphere microbial communities. The relative abundance of Pseudomonas spp. was notably enhanced in the J2-4 group, which was consistent with Linear discriminant analysis Effect Size results that Pseudomonas was determined as one of the biomarkers in the J2-4 group. Furthermore, the ZJ5 strain, one of the biomarker Pseudomonas strains, was isolated from the J2-4-inoculated rhizosphere soil and was identified as Pseudomonas fluorescens. In addition, P. fluorescens ZJ5 exhibited high nematicidal activity in vitro and in vivo, with 99.20% of the mortality rate of M. incognita at 24 h and 69.75% of gall index reduction. The biocontrol efficiency of the synthetic community of ZJ5 plus J2-4 was superior to that of any other single bacteria against M. incognita. Additionally, ZJ5 exhibited great chemotaxis ability toward root exudates inoculated with J2-4.

CONCLUSION: Paenibacillus polymyxa J2-4 has good potential in the biological control against M. incognita under field conditions. Enrichment of the beneficial bacteria Pseudomonas fluorescens ZJ5 in the J2-4-inoculated rhizosphere soil contributes to M. incognita management. © 2024 Society of Chemical Industry.}, } @article {pmid39318437, year = {2024}, author = {Sharma, P and Pandey, R and Chauhan, NS}, title = {Unveiling wheat growth promotion potential of phosphate solubilizing Pantoea agglomerans PS1 and PS2 through genomic, physiological, and metagenomic characterizations.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1467082}, pmid = {39318437}, issn = {1664-302X}, abstract = {INTRODUCTION: Phosphorus is an abundant element in the earth's crust and is generally found as complex insoluble conjugates. Plants cannot assimilate insoluble phosphorus and require external supplementation as chemical fertilizers to achieve a good yield. Continuous use of fertilizers has impacted soil ecology, and a sustainable solution is needed to meet plant elemental requirements. Phosphate solubilizing microbes could enhance phosphorus bioavailability for better crop production and can be employed to attain sustainable agriculture practices.

METHODS: The current study unveils the biofertilizer potential of wheat rhizospheric bacteria through physiological, taxonomic, genomic, and microbiomics experimentations.

RESULTS AND DISCUSSION: Culture-dependent exploration identified phosphate-solubilizing PS1 and PS2 strains from the wheat rhizosphere. These isolates were rod-shaped, gram-negative, facultative anaerobic bacteria, having optimum growth at 37°C and pH 7. Phylogenetic and phylogenomic characterization revealed their taxonomic affiliation as Pantoea agglomerans subspecies PS1 & PS2. Both isolates exhibited good tolerance against saline (>10% NaCl (w/v), >11.0% KCl (w/v), and >6.0% LiCl (w/v)), oxidizing (>5.9% H2O2 (v/v)) conditions. PS1 and PS2 genomes harbor gene clusters for biofertilization features, root colonization, and stress tolerance. PS1 and PS2 showed nitrate reduction, phosphate solubilization, auxin production, and carbohydrate utilization properties. Treatment of seeds with PS1 and PS2 significantly enhanced seed germination percentage (p = 0.028 and p = 0.008, respectively), number of tillers (p = 0.0018), number of leaves (p = 0.0001), number of spikes (p = 0.0001) and grain production (p = 0.0001). Wheat rhizosphere microbiota characterizations indicated stable colonization of PS1 and PS2 strains in treated seeds at different feek stages. Pretreatment of seeds with both strains engineered the wheat rhizosphere microbiota by recruiting plant growth-promoting microbial groups. In vitro, In vivo, and microbiota characterization studies indicated the biofertilizer potential of Pantoea sp. PS1 & PS2 to enhance wheat crop production. The employment of these strains could fulfill plant nutrient requirements and be a substitute for chemical fertilizers for sustainable agriculture.}, } @article {pmid39318431, year = {2024}, author = {Robinson, D and Morgan-Kiss, RM and Wang, Z and Takacs-Vesbach, C}, title = {Antarctic lake viromes reveal potential virus associated influences on nutrient cycling in ice-covered lakes.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1422941}, pmid = {39318431}, issn = {1664-302X}, abstract = {The McMurdo Dry Valleys (MDVs) of Antarctica are a mosaic of extreme habitats which are dominated by microbial life. The MDVs include glacial melt holes, streams, lakes, and soils, which are interconnected through the transfer of energy and flux of inorganic and organic material via wind and hydrology. For the first time, we provide new data on the viral community structure and function in the MDVs through metagenomics of the planktonic and benthic mat communities of Lakes Bonney and Fryxell. Viral taxonomic diversity was compared across lakes and ecological function was investigated by characterizing auxiliary metabolic genes (AMGs) and predicting viral hosts. Our data suggest that viral communities differed between the lakes and among sites: these differences were connected to microbial host communities. AMGs were associated with the potential augmentation of multiple biogeochemical processes in host, most notably with phosphorus acquisition, organic nitrogen acquisition, sulfur oxidation, and photosynthesis. Viral genome abundances containing AMGs differed between the lakes and microbial mats, indicating site specialization. Using procrustes analysis, we also identified significant coupling between viral and bacterial communities (p = 0.001). Finally, host predictions indicate viral host preference among the assembled viromes. Collectively, our data show that: (i) viruses are uniquely distributed through the McMurdo Dry Valley lakes, (ii) their AMGs can contribute to overcoming host nutrient limitation and, (iii) viral and bacterial MDV communities are tightly coupled.}, } @article {pmid39318384, year = {2024}, author = {Yin, C and Liu, L and Xu, D and Li, M and Li, M and Qin, Y and Zhang, B and Sun, Y and Liu, Y and Xiao, Y}, title = {Integrative metagenomic and lipidomic analyses reveal alterations in children with obesity and after lifestyle intervention.}, journal = {Frontiers in nutrition}, volume = {11}, number = {}, pages = {1423724}, pmid = {39318384}, issn = {2296-861X}, abstract = {BACKGROUND: Despite emerging evidence linking alterations in gut microbiota to childhood obesity, the metabolic mechanisms linking gut microbiota to the lipid profile during childhood obesity and weight loss remain poorly understood.

METHODOLOGY: In this study, children with obesity were treated with lifestyle weight loss therapy. Metagenomics association studies and serum untargeted lipidomics analyses were performed in children with obesity and healthy controls before and after weight loss.

MAIN FINDINGS: We identified alterations in gut microbiota associated with childhood obesity, as well as variations in circulating metabolite concentrations. Children with obesity showed significant decreases in the levels of s-Rothia_kristinae and s-Enterobacter_roggenkampii, alongsige elevated levels of s-Clostridiales_bacterium_Marseille-P5551. Following weight loss, the levels of s-Streptococcus_infantarius and s-Leuconostoc_citreum increased by factors of 3.354 and 1.505, respectively, in comparison to their pre-weight loss levels. Correlation analyses indicated a significant positive relationship between ChE(2:0) levels and both with s-Lachnospiraceae_bacterium_TF09-5 and fasting glucose levels. CoQ8 levels were significantly negatively correlated with s-Rothia_kristinae and HOMA-IR.

CONCLUSION: We linked altered gut microbiota and serum lipid levels in children with obesity to clinical indicators, indicating a potential impact on glucose metabolism via lipids. This study contributes to understanding the mechanistic relationship between altered gut microbiota and childhood obesity and weight loss, suggesting gut microbiome as a promising target for intervention.

CLINICAL TRIAL REGISTRATION: https://www.chictr.org.cn/showproj.html?proj=178971, ChiCTR2300072179.}, } @article {pmid39317249, year = {2024}, author = {Liu, YH and Huang, JN and Wen, B and Gao, JZ and Chen, ZZ}, title = {Comprehensive assessment of three crayfish culture modes: From production performance to environmental sustainability.}, journal = {The Science of the total environment}, volume = {954}, number = {}, pages = {176470}, doi = {10.1016/j.scitotenv.2024.176470}, pmid = {39317249}, issn = {1879-1026}, mesh = {*Astacoidea ; Animals ; *Aquaculture ; }, abstract = {Integrated agriculture-aquaculture has emerged as a promising ecological development model. Crayfish, a popular aquaculture species, are traditionally reared either in monoculture ponds (mono-C) or in rice-crayfish polyculture system (poly-RC). In this study, we introduced a novel polyculture system by combining fruit tree with crayfish (poly-FC), aiming to compare these three crayfish culture modes in terms of production performance and ecological sustainability. The results indicated that crayfish reared in the two polyculture modes exhibited significantly higher specific growth rate and condition factor compared to those in mono-C. Crayfish cultured in poly-FC also showed better muscle quality and higher levels of crude fat and flavor or essential amino acids. Isotope mixing model showed that feed and benthic animals were the primary food sources of crayfish in mono-C, whereas aquatic plants, fruit litter or rice contributed more to those in polyculture modes. For greenhouse gas emissions, poly-FC mode emitted almost no CO2 and N2O even favored negative CH4 emission, while poly-RC and mono-C modes showed positive emissions of CH4 and CO2, respectively. Supported by metagenomics, the sink of CH4 in poly-FC was probably due to the lower mcr abundance but the higher pmo abundance in water. The low production and emission of N2O in poly-FC might result from the low-abundant Nitrospirae_bacterium and its coding gene norC in sediment, consistent with the lower denitrification rate but the higher NO3[-] concentration than mono-C. Overall, our findings reveal the superiority of polyculture of fruit tree with crayfish in terms of production performance and greenhouse gas emissions in the system.}, } @article {pmid39316987, year = {2024}, author = {Yang, H and Liu, Y and Cao, G and Liu, J and Xiao, S and Xiao, P and Tao, Y and Gao, H}, title = {Effects of lycopene on the growth performance, meat quality, cecal metagenome, and hepatic untargeted metabolome in heat stressed broilers.}, journal = {Poultry science}, volume = {103}, number = {12}, pages = {104299}, pmid = {39316987}, issn = {1525-3171}, mesh = {Animals ; *Chickens/physiology/growth & development ; *Animal Feed/analysis ; *Diet/veterinary ; *Meat/analysis ; *Liver/drug effects/metabolism ; *Lycopene/pharmacology/administration & dosage ; *Cecum/microbiology/drug effects/metabolism ; *Dietary Supplements/analysis ; *Metabolome/drug effects ; Male ; Metagenome ; Random Allocation ; Gastrointestinal Microbiome/drug effects ; Heat-Shock Response/drug effects ; }, abstract = {The occurrence of heat stress in poultry houses is inevitable and leads to oxidative stress in the birds. Lycopene, a natural hydrocarbon carotenoid, possesses potent antioxidant properties. This study aimed to investigate the impact of lycopene on growth performance, meat quality, cecal microflora, and liver metabolome in broilers subjected to heat stress. A total of 480 yellow feather broilers were randomly allocated into 4 treatment groups: birds fed standard diet (Con), birds fed standard diet and supplemented with lycopene (Lyc), birds fed standard diet and subjected to heat stress (Hs), and birds fed with lycopene and subjected to heat stress (Hs-Lyc). As compared with the normal temperature groups, Hs decreased the average daily gain (ADG) of birds during d 1 to 28, lowered the pH value either in breast meat or thigh meat, increased the L* value of breast meat, and decreased the a* value of thigh meat. In comparison with non-Lyc feeding birds, Lyc supplement elevated the ADG during d 1 to 56, increased the pH of breast meat, decrease the L* and b* values of thigh meat, simultaneously increase the a* value of thigh meat. The L* of breast meat and pH of thigh meat exhibited significant differences under Hs-Lyc treatment. Lyc-treated birds exhibited higher elasticity, gumminess, and resilience in breast meat than those in non-Lyc feeding birds. The cecal metagenome analysis indicated that Hs-Lyc treatment increased the abundance of Phocaeicola salanitronis and Prevotella sp.CAG:1058, Bacteroides sp.An269, and Bacteroides sp.An19 at the species level compared with other treatments. The hepatic untargeted metabolome analysis showed that administration of Lyc upregulated 20 metabolites and downregulated 60 metabolites compared to the Con birds. Futhermore, the Hs-Lyc treatment upregulated 34 metabolites and downregulated 45 metabolites compared to the Hs birds. The correlation between the metagenome and metabolome showed that Lyc supplementation induced significant alterations in the citrate cycle, metabolism of butanoate, glycolysis/gluconeogenesis, glyoxylate and dicarboxylate, alanine, aspartate, and glutamate compared with standard supplement. In contrast, Hs-Lyc treatment induced alterations in the citrate cycle, metabolism of pyruvate, glyoxylate, and dicarboxylate, glycolysis/gluconeogenesis, arginine, proline, alanine, aspartate, and glutamate compared with the standard supplement of heat-challenged broilers. In summary, dietary Lyc supplementation promoted the growth performance, changed the meat quality, modulated the cecal metagenome and hepatic metabolome in heat-stressed broilers.}, } @article {pmid39316964, year = {2024}, author = {Pi, K and Xie, X and Sun, S and Van Cappellen, P and Xiao, Z and Zhang, D and Wang, Y}, title = {Arsenic redox disequilibrium in geogenic contaminated groundwater: Bioenergetic insights from organic molecular characterization and gene-informed modeling.}, journal = {Water research}, volume = {267}, number = {}, pages = {122459}, doi = {10.1016/j.watres.2024.122459}, pmid = {39316964}, issn = {1879-2448}, mesh = {*Groundwater/chemistry ; *Arsenic ; *Oxidation-Reduction ; *Water Pollutants, Chemical ; }, abstract = {Biotransformation of arsenic (As) influences its speciation and mobility, obscuring mechanistic comprehension on spatiotemporal variation of As concentration in geogenic contaminated groundwater. In particular, unresolved processes underlying As redox disequilibrium in comparison to major redox couples discourage practical efforts to rehabilitate the As-contaminated groundwater. Here, quantitative metagenomic sequencing and ultrahigh-resolution mass spectrometry (FT-ICR-MS) were jointly applied to reveal the links between vertical distribution of As metabolic gene assemblages and that of free energy density of dissolved organic matter (DOM) in As-contaminated groundwater of Datong Basin. Observed small excess of Gibbs free energy available by DOM relative to that required for As(V)-to-As(III) reduction exerts thermodynamic constraint on metabolism-mediated redox transformation of As. Accordingly, the vertical distribution of dissolved As(V)/As(III) ratio correlated significantly with that of ars+acr3 and arr encoding As(V) reduction and aio encoding As(III) oxidation in the moderately/strongly reducing groundwater. Further gene-informed biogeochemical modeling suggests that a net effect of these kinetics-restricted bidirectional metabolic pathways leads to co-preservation of As(V) and As(III) even at relatively high rates of ars+acr3 encoded As(V) reduction. This study therefore provides new insights into bioenergetic constraints on As hydrobiogeochemical behavior, with implications for other redox-sensitive contaminants in the groundwater systems.}, } @article {pmid39316963, year = {2024}, author = {Ping, J and Dong, Y and Xie, L and Zhou, Y and Zhang, L and Huang, Y and Liao, L and Cheng, W and Peng, F and Song, H}, title = {Effect of reactive oxygen species (ROS) produced by pyridine and quinoline on NH4[+]-N removal under phenol stress: The shift of nitrification pathway and its potential mechanisms.}, journal = {Water research}, volume = {267}, number = {}, pages = {122478}, doi = {10.1016/j.watres.2024.122478}, pmid = {39316963}, issn = {1879-2448}, mesh = {*Nitrification ; *Pyridines/metabolism ; *Quinolines/metabolism ; *Reactive Oxygen Species/metabolism ; Wastewater/chemistry ; Ammonium Compounds ; Nitrogen ; Oxidative Stress ; Water Pollutants, Chemical ; Waste Disposal, Fluid ; Phenol ; Bioreactors ; }, abstract = {Pyridine and quinoline are typical nitrogenous heterocyclic compounds with different structures that are found in coking wastewater. However, neither the corresponding mechanism nor its effect on the degradation of NH4[+]-N under phenol stress is known. In this study, the effects of pyridine and quinoline degradation on NH4[+]-N removal under phenol stress were evaluated using three lab-scale sequencing batch reactors. The average NH4[+]-N removal efficiencies of the reactors were 99.46 %, 88.86 %, and 98.64 %. With the increased concentration of pyridine and quinoline, NH4[+]-N and NO3[-]-N accumulated to 58.37 mg/L and 141.37 mg/L, respectively, due to the lack of an electron donor and anaerobic environment. The addition of pyridine and quinoline significantly improved antioxidant response and altered the nitrification pathway. The nitrification process shifted from the mediation of amo and hao to the mediation of Ncd2 due to oxidative stress induced by pyridine and quinoline. Furthermore, oxidative stress interferes with the metabolism of carbon sources, resulting in decreased biomass. These results provide a new perspective for coking wastewater treatment processes.}, } @article {pmid39316685, year = {2024}, author = {Ke, S and Gálvez, JAV and Sun, Z and Cao, Y and Pollock, NR and Chen, X and Kelly, CP and Liu, YY}, title = {Rational Design of Live Biotherapeutic Products for the Prevention of Clostridioides difficile Infection.}, journal = {The Journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/infdis/jiae470}, pmid = {39316685}, issn = {1537-6613}, abstract = {Clostridioides difficile infection (CDI) is a major cause of healthcare- and antibiotic-associated diarrhea. While fecal microbiota transplantation (FMT) shows promise for recurrent CDI, its mechanisms and long-term safety are not fully understood. Live biotherapeutic products (LBPs) using pre-defined bacterial consortia offer an alternative option, but the rational designing LBPs remains challenging. Here, we employ a computational pipeline and three metagenomic datasets to identify microbial strains for LBPs targeting CDI. We constructed the CDI-related microbial genome catalog, comprising 3,741 non-redundant metagenome-assembled genomes (nrMAGs) and identified multiple potential protective nrMAGs, including strains from Dorea formicigenerans, Oscillibacter welbionis, and Faecalibacterium prausnitzii. Importantly, some of these protective nrMAGs were found to play an important role in FMT success, and most top protective nrMAGs can be validated by various previous findings. Our results demonstrate a framework for selecting microbial strains targeting CDI, paving the way for the computational design of LBPs against other enteric infections.}, } @article {pmid39316448, year = {2024}, author = {Wang, Y and Shi, YN and Xiang, H and Shi, YM}, title = {Exploring nature's battlefield: organismic interactions in the discovery of bioactive natural products.}, journal = {Natural product reports}, volume = {41}, number = {11}, pages = {1630-1651}, doi = {10.1039/d4np00018h}, pmid = {39316448}, issn = {1460-4752}, mesh = {*Biological Products/pharmacology/chemistry/metabolism ; *Drug Discovery ; Animals ; Humans ; Fungi/metabolism ; Plants/metabolism/chemistry ; }, abstract = {Covering: up to March 2024.Microbial natural products have historically been a cornerstone for the discovery of therapeutic agents. Advanced (meta)genome sequencing technologies have revealed that microbes harbor far greater biosynthetic capabilities than previously anticipated. However, despite the application of CRISPR/Cas-based gene editing and high-throughput technologies to activate silent biosynthetic gene clusters, the rapid identification of new natural products has not led to a proportional increase in the discovery rate of lead compounds or drugs. A crucial issue in this gap may be insufficient knowledge about the inherent biological and physiological functions of microbial natural products. Addressing this gap necessitates recognizing that the generation of functional natural products is deeply rooted in the interactions between the producing microbes and other (micro)organisms within their ecological contexts, an understanding that is essential for harnessing their potential therapeutic benefits. In this review, we highlight the discovery of functional microbial natural products from diverse niches, including those associated with humans, nematodes, insects, fungi, protozoa, plants, and marine animals. Many of these findings result from an organismic-interaction-guided strategy using multi-omic approaches. The current importance of this topic lies in its potential to advance drug discovery in an era marked by increasing antimicrobial resistance.}, } @article {pmid39315852, year = {2024}, author = {Tian, W and Tang, Y and Ducey, TF and Khan, E and Tsang, DCW}, title = {Facilitating Intracellular Electron Bifurcation by Mediating Flavin-Based Extracellular and Transmembrane Electron Transfer: A Novel Role of Pyrogenic Carbon in Dark Fermentation for Hydrogen Production.}, journal = {Environmental science & technology}, volume = {58}, number = {40}, pages = {17766-17776}, doi = {10.1021/acs.est.4c05994}, pmid = {39315852}, issn = {1520-5851}, mesh = {Electron Transport ; *Hydrogen/metabolism ; *Fermentation ; Carbon/metabolism ; Flavins/metabolism ; Electrons ; }, abstract = {Pyrogenic carbon is considered an enhancer to H2-yielding dark fermentation (DF), but little is known about how it regulates extracellular electron transfer (EET) and influences transmembrane respiratory chains and intracellular metabolisms. This study addressed these knowledge gaps and demonstrated that wood waste pyrogenic carbon (biochar) could significantly improve the DF performance; e.g., addition of pyrogenic carbon produced by pyrolysis at 800 °C (PC800) increased H2 yield by 369.7%. Biochemical quantification, electrochemical analysis, and electron respiratory chain inhibition tests revealed that PC800 promoted the extracellular flavin-based electron transfer process and further activated the acceleration of the transmembrane electron transfer. Comparative metagenome/metatranscriptome analyses indicated that the flavin-containing Rnf complex was the potential transmembrane respiratory enzyme associated with PC800-mediated EET. Based on NADH/NAD[+] circulation, the promoted Rnf complex could stimulate the functions of the electron bifurcating Etf/Bcd complex and startup of glycolysis. The promoted Etf/Bcd could further contribute to balance the NADH/NAD[+] level for glycolytic reactions and meanwhile provide reduced ferredoxin for group A1 [FeFe]-hydrogenases. This proton-energy-linked mechanism could achieve coupling production of ATP and H2. This study verified the important roles of pyrogenic carbon in mediating EET and transmembrane/intracellular pathways and revealed the crucial roles of electron bifurcation in DF for hydrogen production.}, } @article {pmid39315850, year = {2024}, author = {Yao, G and Zhang, X and Zhang, T and Jin, J and Qin, Z and Ren, X and Wang, X and Zhang, S and Yin, X and Tian, Z and Zhang, Y and Zhang, J and Wang, Z and Zhang, Q}, title = {The role of dysbiotic gut mycobiota in modulating risk for abdominal aortic aneurysm.}, journal = {Microbiology spectrum}, volume = {12}, number = {11}, pages = {e0177624}, pmid = {39315850}, issn = {2165-0497}, support = {2021YFA1301102//MOST | National Key Research and Development Program of China (NKPs)/ ; 82170495, 82070820, 82370481//MOST | National Natural Science Foundation of China (NSFC)/ ; ZR2023ZD58//SDMOST|Natural Science Foundation of Shandong Province（SDNSF）/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology ; Animals ; *Aortic Aneurysm, Abdominal/microbiology/pathology ; Mice ; Male ; *Feces/microbiology ; Female ; Aged ; Fungi/isolation & purification/classification/genetics/physiology ; Saccharomyces cerevisiae/genetics ; Mycobiome ; Mice, Inbred C57BL ; Candida/isolation & purification/genetics/physiology/pathogenicity ; Metagenomics ; }, abstract = {UNLABELLED: Abdominal aortic aneurysm (AAA) is a large-vessel disease with high mortality, characterized by complex pathogenic mechanisms. Current therapeutic approaches remain insufficient to halt its progression. Fungi are important members of the gut microbiota. However, their characteristic alterations and roles in AAA remain unclear. This study investigated the role of gut fungal communities in the development of AAA through metagenomic sequencing of fecal samples from 31 healthy individuals and 33 AAA patients. We observed significant dysbiosis in the gut mycobiomes of AAA patients compared to healthy individuals, characterized by an increase in pathogenic fungi like Candida species and a decrease in beneficial yeasts such as Saccharomyces cerevisiae. The changes in fungal populations correlated strongly with clinical indicators of AAA, highlighting their potential for diagnosing and predicting AAA progression. Furthermore, our animal experiments demonstrated that Saccharomyces cerevisiae significantly ameliorated pathological alterations in AAA mice, suggesting a protective role for specific yeast strains against AAA development. These findings underscore the significant impact of gut mycobiomes on AAA and suggest that modulating these fungal communities could offer a novel therapeutic approach. Our research advances the understanding of the influence of gut microbiome on vascular diseases and suggests potential non-surgical approaches for managing AAA. By elucidating the diagnostic and therapeutic potential of gut fungi in AAA, this study provided important clues for future clinical strategies and therapeutic developments in the field of vascular medicine.

IMPORTANCE: Our research highlights the crucial role of gut fungi in abdominal aortic aneurysm (AAA) development. By analyzing fecal samples from AAA patients and healthy controls, we discovered significant dysbiosis in gut fungal communities, characterized by an increase in harmful Candida species and a decrease in beneficial yeasts like Saccharomyces cerevisiae. This dysbiosis was correlated with the severity of AAA. Importantly, in animal experiments, supplementing with Saccharomyces cerevisiae significantly slowed AAA progression. These findings suggest that modulating gut fungi may offer a novel, non-surgical approach to the diagnosis and treatment of AAA, potentially reducing the need for invasive procedures.}, } @article {pmid39315838, year = {2024}, author = {Bulka, O and Edwards, EA}, title = {Two distinct Dehalobacter metagenome-assembled genomes from anaerobic chloroform and dichloromethane degrading consortia.}, journal = {Microbiology resource announcements}, volume = {13}, number = {11}, pages = {e0080324}, pmid = {39315838}, issn = {2576-098X}, support = {PGS-D//Canadian Government | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; Discovery//Canadian Government | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; BCB project 285MPR//Genome Canada (GC)/ ; }, abstract = {Here we present two metagenomes and two Dehalobacter metagenome-assembled genomes from subcultures of an anaerobic chloroform and dichloromethane degrading microbial community used for bioremediation. Our objective was to assemble and curate the genome(s) of Dehalobacter, key biodegraders in the culture, through repeated sequencing and joint assembly with previous datasets.}, } @article {pmid39315801, year = {2024}, author = {Tenorio-Carnalla, K and Aguilar-Vera, A and Hernández-Alvarez, AJ and López-Leal, G and Mateo-Estrada, V and Santamaria, RI and Castillo-Ramírez, S}, title = {Host population structure and species resolution reveal prophage transmission dynamics.}, journal = {mBio}, volume = {15}, number = {10}, pages = {e0237724}, pmid = {39315801}, issn = {2150-7511}, support = {CVU 1204437//CONAHCYT postdoctoral fellowship/ ; }, mesh = {*Prophages/genetics/physiology/classification ; *Host Specificity ; Acinetobacter baumannii/virology/genetics/classification ; Metagenomics ; Phylogeny ; Genome, Viral ; Bacteriophages/genetics/physiology/classification/isolation & purification ; }, abstract = {UNLABELLED: Much knowledge about bacteriophages has been obtained via genomics and metagenomics over the last decades. However, most studies dealing with prophage diversity have rarely conducted phage species delimitation (aspect 1) and have hardly integrated the population structure of the host (aspect 2). Yet, these two aspects are essential in assessing phage diversity. Here, we implemented an operational definition of phage species (clustering at 95% identity, 90% coverage) and integrated the host's population structure to understand prophage diversity better. Gathering the most extensive data set of Acinetobacter baumannii phages (4,152 prophages + 122 virulent phages, distributed in 46 countries in the world), we show that 91% (875 out of 963) of the prophage species have four or fewer prophages per species, and just five prophage species have more than 100 prophages. Most prophage species have a narrow host range and are geographically restricted; yet, very few have a broad host range being well spread in distant lineages of A. baumannii. These few broad host range prophage species are not only cosmopolitan but also the most abundant species. We also noted that polylysogens had very divergent prophages, belonging to different prophage species, and prophages can easily be gained and lost within the bacterial lineages. Finally, even with this extensive data set, the prophage diversity has not been fully grasped. Our study highlights how integrating the host population structure and a solid operational definition of phage species allows us to better appreciate phage diversity and its transmission dynamics.

IMPORTANCE: Much knowledge about bacteriophages has been obtained via genomics and metagenomics over the last decades. However, most studies dealing with prophage diversity have rarely conducted phage species delimitation (aspect 1) and have hardly integrated the population structure of the host (aspect 2). Yet, these two aspects are essential in assessing phage diversity. Here, we implemented an operational definition of phage species (clustering at 95% identity, 90% coverage) and integrated the host's population structure to understand prophage diversity better. Gathering the most extensive data set of Acinetobacter baumannii phages, we show that most prophage species have four or fewer prophages per species, and just five prophage species have more than 100 prophages. Most prophage species have a narrow host range and are geographically restricted; yet, very few have a broad host range being well spread in distant lineages of A. baumannii. These few broad host range prophage species are cosmopolitan and the most abundant species. Prophages in the same bacterial genome are very divergent, and prophages can easily be gained and lost within the bacterial lineages. Finally, even with this extensive data set, the prophage diversity has not been fully grasped. This study shows how integrating the host population structure and clustering at the species level allows us to better appreciate phage diversity and its transmission dynamics.}, } @article {pmid39315792, year = {2024}, author = {Gu Liu, C and Thompson, BE and Chang, JD and Min, L and Maresso, AW}, title = {Construction and characterization of DNA libraries from cultured phages and environmental viromes.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {10}, pages = {e0117124}, pmid = {39315792}, issn = {1098-5336}, support = {VA I01-RX002595//U.S. Department of Veterans Affairs (VA)/ ; //The Mike Hogg Foundation/ ; I01 RX002595/RX/RRD VA/United States ; Roderick D. MacDonald Research Fund//Baylor St. Luke's Medical Center/ ; Levy-Longenbaugh fund//Baylor College of Medicine/ ; Seed Funds to TAILΦR//Baylor College of Medicine (BCM)/ ; }, mesh = {*Gene Library ; *Bacteriophages/genetics/isolation & purification/classification ; *Metagenomics ; Virome/genetics ; Wastewater/virology/microbiology ; Seawater/virology/microbiology ; DNA, Viral/genetics ; High-Throughput Nucleotide Sequencing ; Genome, Viral ; Fresh Water/virology/microbiology ; Escherichia coli/genetics/virology ; }, abstract = {Despite many efforts to understand and leverage the functional potential of environmental viromes, most bacteriophage genes are largely uncharacterized. To explore novel biology from uncultivated microbes like phages, metagenomics has emerged as a powerful tool to directly mine new genes without the need to culture the diverse microbiota and the viruses within. When a pure computational approach cannot infer gene function, it may be necessary to create a DNA library from environmental genomic DNA, followed by the screening of that library for a particular function. However, these screens are often initiated without a metagenomic analysis of the completed DNA library being reported. Here, we describe the construction and characterization of DNA libraries from a single cultured phage (ΦT4), five cultured Escherichia coli phages, and three metagenomic viral sets built from freshwater, seawater, and wastewater samples. Through next-generation sequencing of five independent samplings of the libraries, we found a consistent number of recovered genes per replicate for each library, with many genes classifiable via the KEGG and Pharokka databases. By characterizing the size of the genes and inserts, we found that our libraries contain a median of one to two genes per contig with a median gene length of 303-381 bp for all libraries, reflective of the small genomes of viruses. The environmental libraries were genetically diverse compared to the single phage and multi-phage libraries. Additionally, we found reduced coverage of individual genomes when five phages were used as opposed to one. Taken together, this work provides a comprehensive analysis of the DNA libraries from phage genomes that can be used for metagenomic exploration and functional screens to infer and identify new biology.IMPORTANCEFunctional metagenomics is an approach that aims to characterize the putative biological function of genes in the microbial world. This includes an examination of the sequencing data collected from a pooled source of diverse microbes and inference of gene function by comparison to annotated and studied genes from public databases. At times, DNA libraries are made from these genes, and the library is screened for a specific function. Hits are validated using a combination of biological, computational, and structural analysis. Left unresolved is a detailed characterization of the library, both its diversity and content, for the purposes of imputing function entirely by computational means, a process that may yield findings that aid in designing useful screens to identify novel gene functions. In this study, we constructed libraries from cultured phages and uncultured viromes from the environment and characterized some important parameters, such as gene number, genes per contig, ratio of hypothetical to known proteins, total genomic coverage and recovery, and the effect of pooling genetic information from multiple sources, to provide a better understanding of the nature of these libraries. This work will aid the design and implementation of future screens of pooled DNA libraries to discover and isolate viral genes with novel biology across various biomes.}, } @article {pmid39315779, year = {2024}, author = {Rajeev, M and Jung, I and Kang, I and Cho, J-C}, title = {Genome-centric metagenomics provides insights into the core microbial community and functional profiles of biofloc aquaculture.}, journal = {mSystems}, volume = {9}, number = {10}, pages = {e0078224}, pmid = {39315779}, issn = {2379-5077}, support = {KIMST-20210646//Korea Institute of Marine Science and Technology promotion (KIMST)/ ; NRF-2022R1A2C3008502,NRF-2018R1A5A1025077//National Research Foundation of Korea (NRF)/ ; }, mesh = {*Aquaculture ; *Metagenomics/methods ; Animals ; *Microbiota/genetics ; Bacteria/genetics/metabolism/classification ; Archaea/genetics/metabolism/classification ; Metagenome ; Phylogeny ; Penaeidae/microbiology/genetics ; }, abstract = {UNLABELLED: Bioflocs are microbial aggregates that play a pivotal role in shaping animal health, gut microbiota, and water quality in biofloc technology (BFT)-based aquaculture systems. Despite the worldwide application of BFT in aquaculture industries, our comprehension of the community composition and functional potential of the floc-associated microbiota (FAB community; ≥3 µm size fractions) remains rudimentary. Here, we utilized genome-centric metagenomic approach to investigate the FAB community in shrimp aquaculture systems, resulting in the reconstruction of 520 metagenome-assembled genomes (MAGs) spanning both bacterial and archaeal domains. Taxonomic analysis identified Pseudomonadota and Bacteroidota as core community members, with approximately 93% of recovered MAGs unclassified at the species level, indicating a large uncharacterized phylogenetic diversity hidden in the FAB community. Functional annotation of these MAGs unveiled their complex carbohydrate-degrading potential and involvement in carbon, nitrogen, and sulfur metabolisms. Specifically, genomic evidence supported ammonium assimilation, autotrophic nitrification, denitrification, dissimilatory nitrate reduction to ammonia, thiosulfate oxidation, and sulfide oxidation pathways, suggesting the FAB community's versatility for both aerobic and anaerobic metabolisms. Conversely, genes associated with heterotrophic nitrification, anaerobic ammonium oxidation, assimilatory nitrate reduction, and sulfate reduction were undetected. Members of Rhodobacteraceae emerged as the most abundant and metabolically versatile taxa in this intriguing community. Our MAGs compendium is expected to expand the available genome collection from such underexplored aquaculture environments. By elucidating the microbial community structure and metabolic capabilities, this study provides valuable insights into the key biogeochemical processes occurring in biofloc aquacultures and the major microbial contributors driving these processes.

IMPORTANCE: Biofloc technology has emerged as a sustainable aquaculture approach, utilizing microbial aggregates (bioflocs) to improve water quality and animal health. However, the specific microbial taxa within this intriguing community responsible for these benefits are largely unknown. Compounding this challenge, many bacterial taxa resist laboratory cultivation, hindering taxonomic and genomic analyses. To address these gaps, we employed metagenomic binning approach to recover over 500 microbial genomes from floc-associated microbiota of biofloc aquaculture systems operating in South Korea and China. Through taxonomic and genomic analyses, we deciphered the functional gene content of diverse microbial taxa, shedding light on their potential roles in key biogeochemical processes like nitrogen and sulfur metabolisms. Notably, our findings underscore the taxa-specific contributions of microbes in aquaculture environments, particularly in complex carbon degradation and the removal of toxic substances like ammonia, nitrate, and sulfide.}, } @article {pmid39315152, year = {2024}, author = {Zheng, B and Xu, J and Zhang, Y and Qin, J and Yuan, D and Fan, T and Wu, W and Chen, Y and Jiang, Y}, title = {MBCN: A novel reference database for Effcient Metagenomic analysis of human gut microbiome.}, journal = {Heliyon}, volume = {10}, number = {18}, pages = {e37422}, pmid = {39315152}, issn = {2405-8440}, abstract = {Metagenomic shotgun sequencing data can identify microbes and their proportions. But metagenomic shotgun data profiling results obtained from multiple projects using different reference databases are difficult to compare and apply meta-analysis. Our work aims to create a novel collection of human gut prokaryotic genomes, named Microbiome Collection Navigator (MBCN). 2379 human gut metagenomic samples are screened, and 16,785 metagenome-assembled genomes (MAGs) are assembled using a standardized pipeline. In addition, MAGs are combined with the representative genomes from public prokaryotic genomes collections to cluster, and pan-genomes for each cluster's genomes are constructed to build Kraken2 and Bracken databases. The databases built by MBCN are more comprehensive and accurate for profiling metagenomic reads comparing with other collections on simulated reads and virtual bio-projects. We profile 1082 human gut metagenomic samples with MBCN database and organize profiles and metadata on the web program. Meanwhile, using MBCN as a reference database, we also develop a unified, standardized, and systematic metagenomic analysis pipeline and platform, named MicrobiotaCN (http://www.microbiota.cn) and common statistical and visualization tools for microbiome research are integrated into the web program. Taken together, MBCN and MicrobiotaCN can be a valuable resource and a powerful tool that allows researchers to perform metagenomic analysis by a unified pipeline efficiently.}, } @article {pmid39315098, year = {2024}, author = {Li, K and Zhang, Y and Zhang, D and Chen, Q and Fang, X}, title = {Case report: Systemic multi-organ involvement in an adult-onset immunodeficiency patient infected with Talaromyces marneffei.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1430179}, pmid = {39315098}, issn = {1664-3224}, mesh = {Humans ; *Talaromyces ; Female ; Middle Aged ; *Mycoses/immunology/diagnosis/microbiology/drug therapy ; Antifungal Agents/therapeutic use ; Autoantibodies/immunology/blood ; High-Throughput Nucleotide Sequencing ; }, abstract = {Adult-onset immunodeficiency (AOID) mediated by anti-interferon-γ autoantibodies (AIGA) is a rare condition, particularly prevalent in Southeast Asia and southern China. We present a case study of a 62-year-old female with AOID who developed a severe pulmonary infection caused by Talaromyces marneffei (TM), leading to acute respiratory failure, generalized rash, multiple lymphadenopathies, bone destruction, and a mediastinal mass. Treatment included mechanical ventilation, antifungal medication, and corticosteroids, resulting in complete recovery and discharge. This case underscores the challenges of managing complex infections in AOID patients and highlights the importance of early diagnosis through metagenomic next-generation sequencing (mNGS) and appropriate intervention to improve clinical outcomes.}, } @article {pmid39314983, year = {2024}, author = {Golob, J and Rao, K and Berinstein, JA and Singh, P and Chey, WD and Owyang, C and Kamada, N and Higgins, PDR and Young, V and Bishu, S and Lee, AA}, title = {Why Symptoms Linger in Quiescent Crohn's Disease: Investigating the Impact of Sulfidogenic Microbes and Sulfur Metabolic Pathways.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.09.08.24313266}, pmid = {39314983}, abstract = {INTRODUCTION: Even in the absence of inflammation, persistent symptoms in patients with Crohn's disease (CD) are prevalent and worsen quality of life. We previously demonstrated enrichment in sulfidogenic microbes in quiescent Crohn's disease patients with (qCD+S) vs. without persistent GI symptoms (qCD-S). Thus, we hypothesized that sulfur metabolic pathways would be enriched in stool while differentially abundant microbes would be associated with important sulfur-metabolic pathways in qCD+S.

METHODS: We performed a multi-center observational study nested within SPARC IBD. Quiescent inflammation was defined by fecal calprotectin level <150 mcg/g. Persistent symptoms were defined by CD-PRO2. Active CD (aCD) and non-IBD diarrhea-predominant irritable bowel syndrome (IBS-D) were included as controls.

RESULTS: Thirty-nine patients with qCD+S, 274 qCD-S, 21 aCD, and 40 IBS-D underwent paired shotgun metagenomic sequencing and untargeted metabolomic profiling. The fecal metabolome in qCD+S was significantly different relative to qCD-S and IBS-D but not aCD. Patients with qCD+S were enriched in sulfur-containing amino acid pathways, including cysteine and methionine, as well as serine, glycine, and threonine. Glutathione and nicotinate/nicotinamide pathways were also enriched in qCD+S relative to qCD-S, suggestive of mitochondrial dysfunction, a downstream target of H 2 S signaling. Multi-omic integration demonstrated that enriched microbes in qCD+S were associated with important sulfur-metabolic pathways. Bacterial sulfur-metabolic genes, including CTH , isfD , sarD , and asrC , were dysregulated in qCD+S. Finally, sulfur metabolites with and without sulfidogenic microbes showed good accuracy in predicting presence of qCD+S.

DISCUSSION: Microbial-derived sulfur pathways and downstream mitochondrial function are perturbed in qCD+S, which implicate H 2 S signaling in the pathogenesis of this condition. Future studies will determine whether targeting H 2 S pathways results in improved quality of life in qCD+S.

KEY MESSAGES: What is Already Known Even in the absence of inflammation, persistent gastrointestinal symptoms are common in Crohn's disease.The microbiome is altered in quiescent Crohn's disease patients with persistent symptoms, but the functional significance of these changes is unknown. What is New Here Sulfur metabolites and sulfur metabolic pathways were enriched in stool in quiescent Crohn's disease patients with persistent symptoms.Multi-omic integration showed enriched microbes were associated with important sulfur metabolic pathways in quiescent Crohn's disease patients with persistent symptoms. How Can This Study Help Patient Care Strategies to decrease sulfidogenic microbes and associated sulfur metabolic pathways could represent a novel strategy to improve quality of life in quiescent Crohn's disease with persistent GI symptoms.}, } @article {pmid39314969, year = {2024}, author = {Laiho, JE and Oikarinen, S and Morfopoulou, S and Oikarinen, M and Renner, A and Depledge, D and Ross, MC and Gerling, IC and Breuer, J and Petrosino, JF and Plagnol, V and Pugliese, A and Toniolo, A and Lloyd, RE and Hyöty, H and , }, title = {Detection of enterovirus RNA in pancreas and lymphoid tissues of organ donors with type 1 diabetes.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {39314969}, support = {R01 AI050237/AI/NIAID NIH HHS/United States ; }, abstract = {AIMS/HYPOTHESIS: The nPOD-Virus group collaboratively applied innovative technologies to detect and sequence viral RNA in pancreas and other tissues from organ donors with type 1 diabetes. These analyses involved the largest number of pancreas samples collected to date.

METHODS: We analysed pancreas, spleen, pancreatic lymph nodes, and duodenum samples from the following donor groups: a) donors with type 1 diabetes (n=71), with (n=35) or without (n=36) insulin-containing islets, (b) donors with single or double islet autoantibody positivity without diabetes (n=22) and c) autoantibody-negative donors without diabetes (control donors) (n=74). Five research laboratories participated in this collaborative effort using approaches for unbiased discovery of RNA viruses (two RNA-Seq platforms), targeted detection of Enterovirus A-D species using RT-PCR, and tests for virus growth in cell-culture.

RESULTS: Direct RNA-Seq did not detect virus signal in pancreas samples, whereas RT-PCR detected enterovirus RNA confirmed by sequencing in low amounts in pancreas samples in three of the five donor groups, namely donors with type 1 diabetes with insulin-containing islets, 16% (5/32) donors being positive, donors with single islet autoantibody positivity with 53% (8/15) donors being positive, and non-diabetic donors with 8% (4/49) being enterovirus RNA positive. Detection of enterovirus RNA was significantly more frequent in single islet autoantibody-positive donors compared to donors with type 1 diabetes with insulin-deficient islets (p-value <0.001) and control donors (p-value 0.004). In some donors, pancreatic lymph nodes were also positive. RT-PCR detected enterovirus RNA also in spleen of a small number of donors and virus enrichment in susceptible cell lines before RT-PCR resulted in much higher rate in spleen positivity, particularly in donors with type 1 diabetes. Interestingly, the enterovirus strains detected did not cause a typical lytic infection, possibly reflecting their persistence-prone nature.

CONCLUSIONS/INTERPRETATION: This was the largest coordinated effort to examine the presence of enterovirus RNA in pancreas of organ donors with type 1 diabetes, using a multitude of assays. These findings are consistent with the notion that both the subjects with type 1 diabetes and those with islet autoantibodies may carry a low-grade enterovirus infection in the pancreas and lymphoid tissues.}, } @article {pmid39314554, year = {2024}, author = {Bulata-Pop, I and Stirbu, I and Simionescu, B and Grama, A and Junie, LM}, title = {Clinical, Biological, and Radiological Findings and Management of Lower Respiratory Tract Infections in a Tertiary Hospital in Romania.}, journal = {Cureus}, volume = {16}, number = {8}, pages = {e67685}, pmid = {39314554}, issn = {2168-8184}, abstract = {Background Lower respiratory tract infections (LRTIs) remain a significant concern in pediatrics due to their substantial burden among childhood diseases. Romania has recently attained the status of a high-income country. Even though the mortality rate from respiratory diseases has significantly declined from 24.1 per 100,000 individuals in 2000 to 5.3 per 100,000 in 2022, the rate remains notably higher than the European average. Diagnosing LRTI is challenging due to its clinical similarity to noninfectious respiratory illness and frequent false-positive results or incidental findings on microbiologic tests. This often leads to antimicrobial overuse and adverse outcomes. Additionally, antibiotic resistance poses a significant global public health threat. Patients and method We conducted a retrospective analysis of pediatric LRTI cases at a tertiary pediatric center in Romania to evaluate diagnostic testing, imaging use, etiology identification, and treatment approaches. Children under 18, admitted to the Emergency Clinical Hospital for Children in Cluj-Napoca during an eight-month peak respiratory season, were included. Data from electronic medical records were analyzed for demographics, symptoms, physical exams, laboratory data, presence of fever, etiology, treatment, and outcomes. Results In total, 222 children were included in this study, with a median age of 29 months. Among the participants, 58% were male. The average hospital stay was 11 days. The total number of cases was almost equally split between bronchiolitis and pneumonia, with lobar pneumonia accounting for 12% of the included patients. We found two statistically significant correlations between the presence of fever, intercostal retracting, and the subtype of LRTI. An inflammatory response defined as an elevated leucocyte count and elevated C-reactive protein (CRP) was more likely to appear in pneumonia cases than bronchiolitis. From a therapeutic point of view, the prescription of hydrocortisone was statistically linked to bronchiolitis, but its use did not shorten hospitalization time. Conclusion Policy interventions and targeted treatments can reduce LRTI incidence and improve outcomes. Based on our correlations between specific clinical traits and subtypes of LRTIs, the use of assessment scores in children helps predict severe illness and the need for hospitalization. Promoting hygiene, social distancing, and addressing socioeconomic factors are crucial. Larger sample sizes and advanced diagnostics are needed to refine treatment strategies further. Early antibiotic use in children has long-term health implications, including a higher risk of respiratory-caused premature death in adulthood. This emphasizes the need for improved diagnostic processes and specific etiological identification, with metagenomics showing promise in this area.}, } @article {pmid39314343, year = {2024}, author = {Fuhrmeister, ER and Kim, S and Mairal, SA and McCormack, C and Chieng, B and Swarthout, JM and Harvey Paulos, A and Njenga, SM and Pickering, AJ}, title = {Context-Seq: CRISPR-Cas9 Targeted Nanopore Sequencing for Transmission Dynamics of Antimicrobial Resistance.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39314343}, issn = {2692-8205}, support = {R01 AI108695/AI/NIAID NIH HHS/United States ; UL1 TR002544/TR/NCATS NIH HHS/United States ; }, abstract = {Antimicrobial resistance (AMR) aligns with a One Health framework in that resistant bacteria and antibiotic resistance genes (ARGs) can be transmitted between humans, animals, and the environment. However, there is a critical need to more precisely understand how and to what extent AMR is exchanged between animals and humans. Metagenomic sequencing has low detection for rare targets such as ARGs, while whole genome sequencing of isolates is burdensome and misses exchange between uncultured bacterial species. We developed a novel, targeted sequencing assay using CRISPR-Cas9 to selectively sequence ARGs and their genomic context with long-read sequencing. Using this method, termed Context-Seq, we investigated overlapping AMR elements containing the ARGs bla CTX-M and bla TEM between adults, children, poultry, and dogs in animal-owning households in Nairobi, Kenya. We identified 22 genetically distinct clusters (> 80%ID over ≥ 3000 bp) containing bla TEM and one cluster containing bla CTX-M that were shared within and between households. Half of the clusters were shared between humans and animals, while the other half were shared only between animals (poultry-poultry, dog-dog, and dog-poultry). We identified potentially pathogenic hosts of ARGs including Escherichia coli, Klebsiella pneumonia, and Haemophilus influenzae across sample types. Context-Seq complements conventional methods to obtain an additional view of bacterial and mammalian hosts in the proliferation of AMR.}, } @article {pmid39314094, year = {2024}, author = {Jiang, OY and Zhang, SY and Zhao, XD and Liu, ZT and Kappler, A and Xu, JM and Tang, XJ}, title = {Arsenic Reduces Methane Emissions from Paddy Soils: Insights from Continental Investigation and Laboratory Incubations.}, journal = {Environmental science & technology}, volume = {58}, number = {40}, pages = {17685-17694}, doi = {10.1021/acs.est.4c06809}, pmid = {39314094}, issn = {1520-5851}, mesh = {*Methane/metabolism ; *Arsenic/metabolism ; *Soil/chemistry ; Soil Microbiology ; China ; Soil Pollutants/metabolism ; Oxidation-Reduction ; }, abstract = {Arsenic (As) contamination and methane (CH4) emissions co-occur in rice paddies. However, how As impacts CH4 production, oxidation, and emission dynamics is unknown. Here, we investigated the abundances and activities of CH4-cycling microbes from 132 paddy soils with different As concentrations across continental China using metagenomics and the reverse transcription polymerase chain reaction. Our results revealed that As was a crucial factor affecting the abundance and distribution patterns of the mcrA gene, which is responsible for CH4 production and anaerobic CH4 oxidation. Laboratory incubation experiments showed that adding 30 mg kg[-1] arsenate increased [13]CO2 production by 10-fold, ultimately decreasing CH4 emissions by 68.5%. The inhibition of CH4 emissions by As was induced through three aspects: (1) the toxicity of As decreased the abundance and activity of the methanogens; (2) the adaptability and response of methanotrophs to As is beneficial for CH4 oxidation under As stress; and (3) the more robust arsenate reduction would anaerobically consume more CH4 in paddies. Additionally, significant positive correlations were observed between arsC and pmoA gene abundance in both the observational study and incubation experiment. These findings enhance our understanding of the mechanisms underlying the interactions between As and CH4 cycling in soils.}, } @article {pmid39313845, year = {2024}, author = {Maaskant, A and Voermans, B and Levin, E and de Goffau, MC and Plomp, N and Schuren, F and Remarque, EJ and Smits, A and Langermans, JAM and Bakker, J and Montijn, R}, title = {Microbiome signature suggestive of lactose-intolerance in rhesus macaques (Macaca mulatta) with intermittent chronic diarrhea.}, journal = {Animal microbiome}, volume = {6}, number = {1}, pages = {53}, pmid = {39313845}, issn = {2524-4671}, abstract = {BACKGROUND: Chronic diarrhea is a common cause of mortality and morbidity in captive rhesus macaques (Macaca mulatta). The exact etiology of chronic diarrhea in macaques remains unidentified. The occurrence of diarrhea is frequently linked to dysbiosis within the gut microbiome. Research into microbiome signatures correlated with diarrhea in macaques have predominantly been conducted with single sample collections. Our analysis was based on the metagenomic composition of longitudinally acquired fecal samples from rhesus macaques with chronic diarrhea and clinically healthy rhesus macaques that were obtained over the course of two years. We aimed to investigate potential relationships between the macaque gut microbiome, the presence of diarrhea and diet interventions with a selection of commercially available monkey diets.

RESULTS: The microbiome signature of macaques with intermittent chronic diarrhea showed a significant increase in lactate producing bacteria e.g. lactobacilli, and an increase in fermenters of lactate and succinate. Strikingly, two lactose free diets were associated with a lower incidence of diarrhea.

CONCLUSION: A lactose intolerance mechanism is suggested in these animals by the bloom of Lactobacillus in the presence of lactose resulting in an overproduction of intermediate fermentation products likely led to osmotically induced diarrhea. This study provides new insights into suspected microbiome-lactose intolerance relationship in rhesus macaques with intermittent chronic diarrhea. The integration of machine learning with metagenomic data analysis holds potential for developing targeted dietary interventions and therapeutic strategies and therefore ensuring a healthier and more resilient primate population.}, } @article {pmid39313703, year = {2024}, author = {Talib, N and Mohamad, NE and Ho, CL and Masarudin, MJ and Alitheen, NB}, title = {Modulatory Effects of Isolated Lactobacillus paracasei from Malaysian Water Kefir Grains on the Intestinal Barrier and Gut Microbiota in Diabetic Mice.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {39313703}, issn = {1867-1314}, support = {FRGS/1/2017/SKK10/UPM/02/4 and FRGS-MRSA/1/2018/SKK10/UPM/02/1//Ministry of Education, Government of Malaysia./ ; }, abstract = {Type 2 diabetes (T2DM) is one of the four major types of non-communicable diseases that have become a global health concern. Water kefir is a product of a brown sugar solution fermented with kefir grains which comprises around 30 microbial species in its grains. Water kefir possesses a wide range of health benefits, including anti-hyperlipidemic effects, and reduces hypertension and blood glucose levels in animal models. Reportedly, consuming water kefir containing probiotics may enhance the intestinal barrier and positively influence the composition of the intestinal microflora. The present study aimed to evaluate the regulatory effects of Lactobacillus paracasei isolated from Malaysian water kefir grains (MWKG) on the alterations of intestinal barrier and gut microbiota in diabetic mice via histopathological analysis of the distal colon and 16S rRNA gene sequencing on fecal microbiome. Results indicated that the administration of isolated Lactobacillus paracasei from MWKG to diabetic mice ameliorated the dominant probiotic phyla in the gut microbiota. Results showed that lower dose (LD) and high dose (HD) treatments of the isolated Lactobacillus paracasei could significantly reduce inflammatory cell infiltration in the distal colon of diabetic mice. The treatments revealed a significant decrease in the relative abundance of Firmicutes in the gut, 0.27 ± 0.06% for LD and 0.34 ± 0.04% for HD, compared to untreated (UN) diabetic mice, 0.40 ± 0.02%. These results suggest that L. paracasei isolated from MWKG could serve as a potential dietary supplement against intestinal inflammation and modify gut microbiota composition in patients with T2DM.}, } @article {pmid39313592, year = {2024}, author = {Hemapriya, M and Nataraja, KN and Suryanarayanan, TS and Uma Shaanker, R}, title = {Comparative Metagenomic Analysis of Seed Endobiome of Domesticated and Wild Finger Millet Species (Eleusine spp.): Unveiling Microbial Diversity and Composition.}, journal = {Current microbiology}, volume = {81}, number = {11}, pages = {373}, pmid = {39313592}, issn = {1432-0991}, mesh = {*Seeds/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Metagenomics ; *Eleusine/microbiology/genetics ; *Domestication ; *Microbiota ; Biodiversity ; Fungi/classification/genetics/isolation & purification ; }, abstract = {Domestication, which involves selective breeding, modern agricultural practices, and specific growing conditions, can influence the microbial and endophytic communities in crop plants. In this study, we examined the microbial diversity and community composition in the seeds of wild and domesticated finger millet species. We employed a metagenomic approach to investigate the seed microbial diversity and community composition of wild (Eleusine africana) and domesticated finger millet species (Eleusine coracana (L.) Gaertn) grown in the same habitat. While our findings indicated no significant change in seed endobiome diversity due to domestication, there were differences in microbial community composition between wild and domesticated species. Seeds of domesticated species had higher relative abundance of certain bacterial genera including Helicobacter, Akkermansia, Streptococcus, Bacteroides, and Pseudomonas, whereas seeds of wild species had higher relative abundance of unclassified Streptophyta. The seed-associated microbiota also varied among domesticated finger millet accessions. Co-occurrence network analysis revealed a strong relationship between bacteria and fungi in domesticated compared to wild species. We discuss the results obtained in the larger context of the importance of seed endobiome and how domestication processes in crop plants may have impacted the seed endobiome diversity, composition, and function compared to their wild counterparts.}, } @article {pmid39313228, year = {2024}, author = {Kirtipal, N and Seo, Y and Son, J and Lee, S}, title = {Systems Biology of Human Microbiome for the Prediction of Personal Glycaemic Response.}, journal = {Diabetes & metabolism journal}, volume = {48}, number = {5}, pages = {821-836}, pmid = {39313228}, issn = {2233-6087}, support = {//Ministry of Science ICT/ ; 2021R1C1C1006336//National Research Foundation of Korea/ ; 2021M3A9G8022959//National Research Foundation of Korea/ ; RS-2024-00419699//National Research Foundation of Korea/ ; //Korea Health Industry Development Institute/ ; HR22C141105//Ministry of Health and Welfare/ ; 2024-ER2108-00//Korea National Institute of Health/ ; 2024-ER0608-00//Korea National Institute of Health/ ; //GIST Research Institute/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Precision Medicine/methods ; *Systems Biology/methods ; Machine Learning ; Dysbiosis ; Blood Glucose/analysis ; Diabetes Mellitus/microbiology ; Diabetes Mellitus, Type 2/microbiology ; Hypoglycemic Agents/therapeutic use ; }, abstract = {The human gut microbiota is increasingly recognized as a pivotal factor in diabetes management, playing a significant role in the body's response to treatment. However, it is important to understand that long-term usage of medicines like metformin and other diabetic treatments can result in problems, gastrointestinal discomfort, and dysbiosis of the gut flora. Advanced sequencing technologies have improved our understanding of the gut microbiome's role in diabetes, uncovering complex interactions between microbial composition and metabolic health. We explore how the gut microbiota affects glucose metabolism and insulin sensitivity by examining a variety of -omics data, including genomics, transcriptomics, epigenomics, proteomics, metabolomics, and metagenomics. Machine learning algorithms and genome-scale modeling are now being applied to find microbiological biomarkers associated with diabetes risk, predicted disease progression, and guide customized therapy. This study holds promise for specialized diabetic therapy. Despite significant advances, some concerns remain unanswered, including understanding the complex relationship between diabetes etiology and gut microbiota, as well as developing user-friendly technological innovations. This mini-review explores the relationship between multiomics, precision medicine, and machine learning to improve our understanding of the gut microbiome's function in diabetes. In the era of precision medicine, the ultimate goal is to improve patient outcomes through personalized treatments.}, } @article {pmid39313124, year = {2024}, author = {Wu, C and Hang, S and Li, F and Wu, Y and Yi, S and Liu, X and Chen, M and Ge, F and Tian, J and Zhang, M and Zhang, D}, title = {DNA-stable isotope probing and metagenomics reveal Fe(II) oxidation by core microflora in microoxic rhizospheric habitats to mitigate the accumulation of cadmium and phenanthrene in rice.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {362}, number = {}, pages = {125012}, doi = {10.1016/j.envpol.2024.125012}, pmid = {39313124}, issn = {1873-6424}, mesh = {*Rhizosphere ; *Cadmium/metabolism ; *Oryza/microbiology/metabolism ; *Phenanthrenes/metabolism ; *Soil Pollutants/metabolism ; *Soil Microbiology ; *Oxidation-Reduction ; *Metagenomics ; Iron/metabolism ; Ferrous Compounds/metabolism ; Ecosystem ; Biodegradation, Environmental ; Bacteria/metabolism/genetics ; }, abstract = {Rice rhizosphere soil-porewater microdomains exist within an iron (Fe)-rich microoxic habitat during paddy soil flooding. However, the response mechanisms of core microflora in this habitat to Fe(II)-oxidation-mediated cadmium (Cd) and phenanthrene (Phen) remain unclear. Using gel-stabilized gradient systems to replicate the microoxic conditions in the rice rhizosphere porewater, we found that microaerophilic rhizobacteria drove Fe(II) oxidation to yield iron oxides, thereby reducing the Cd and Phen contents in the rhizosphere porewater and rice (Cd and Phen decreased by 15.9%-78.0% and 10.1%-37.4%, respectively). However, co-exposure to Cd and Phen resulted in a greater reduction in the Cd uptake and a greater increase in the Phen uptake in rice as compared to those in the Cd or Phen treatments, possibly attributing to the cation-π interactions between Cd and Phen, as well as competition between the adsorption sites on the roots. The elevation of Cd-tolerant genes and Phen-degradation genes in biogenic cell-mineral aggregates unveiled the survival strategies of rhizobacteria with respect to Cd and Phen in the microoxic habitat. Potential Cd-tolerant rhizobacteria (e.g., Pandoraea and Comamonas) and Phen-degradation rhizobacteria (e.g., Pseudoxanthobacter) were identified through the DNA-SIP and 16S rRNA gene amplicon sequencing. Metagenomic analysis further confirmed that these core microbes harbor Cd-tolerant, Phen-degradation, and Fe(II) oxidation genes, supporting their metabolic potential for Cd and/or Phen in the microoxic habitat of the rice rhizosphere. These findings suggest the potential mechanism and ecological significance of core rhizospheric microbial-driven Fe(II) oxidation in mitigating the bioavailability of Cd and Phen in paddy soil during flooding.}, } @article {pmid39312587, year = {2024}, author = {de Campos, GM and Santos, HO and Lima, ARJ and Leite, AB and Ribeiro, G and Todão Bernardino, JS and do Nascimento, JPM and Souza, JVC and de Lima, LPO and Lima, MBZ and de Araújo, MA and Giovanetti, M and Kallas, EG and Sampaio, SC and Elias, MC and Slavov, SN}, title = {Unveiling viral pathogens in acute respiratory disease: Insights from viral metagenomics in patients from the State of Alagoas, Brazil.}, journal = {PLoS neglected tropical diseases}, volume = {18}, number = {9}, pages = {e0012536}, pmid = {39312587}, issn = {1935-2735}, mesh = {Humans ; Brazil/epidemiology ; *Metagenomics/methods ; Female ; Adult ; Adolescent ; Male ; Child ; Child, Preschool ; Young Adult ; Middle Aged ; *Respiratory Tract Infections/virology/epidemiology ; *Nasopharynx/virology ; Virus Diseases/virology/epidemiology ; Viruses/genetics/classification/isolation & purification ; Infant ; Aged ; Acute Disease ; }, abstract = {BACKGROUND: Respiratory illness affects individuals across all age demographics on a global scale, often precipitated by viral infections. The symptomatic manifestations of these diseases bear clinical resemblance, complicating the accurate determination of their etiological origins. Furthermore, the diagnostic panels for respiratory pathogens used within local medical practices, may not encompass the full spectrum of viral agents responsible for such ailments. Consequently, a significant number of clinically important viral pathogens may remain undetected.

METHODS AND FINDINGS: In the light of this, we conducted a metagenomic examination of 66 nasopharyngeal swab specimens, obtained from patients presenting with acute respiratory conditions yet tested negative by the standard diagnostic panels available locally. These specimens were obtained from the Public Health Laboratory, Maceio, State of Alagoas. Our findings indicate a predominant diagnostic escape of rhinoviruses and notably enterovirus D68. Moreover, our study identified a substantial quantity of sequence reads attributed to human respirovirus 3 (human parainfluenza 3) along with various herpresviruses including human herpesvirus-1, Epstein-Barr virus (Human herpesvirus-4), Human herpesviruses 6 and 7 and human parvovirus B19 (B19V). Notably, the metagenomic analysis uncovered a widespread presence of the emerging human vientovirus FB in most of sample pools, though its clinical importance remains to be elucidated.

CONCLUSIONS: The obtained results in this study underscore the invaluable role of viral metagenomics in the identification of underrecognized viruses bearing clinical relevance. Furthermore, it offers insights into the dissemination of these pathogens within the studied area, thereby informing public health strategies aimed at enhancing diagnostic accuracy and improving patient care.}, } @article {pmid39312489, year = {2024}, author = {Zhang, L and Meng, L and Fang, Y and Ogata, H and Okazaki, Y}, title = {Spatiotemporal dynamics of giant viruses within a deep freshwater lake reveal a distinct dark-water community.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39312489}, issn = {1751-7370}, support = {//Kyoto University Foundation/ ; JPMJFR2273//JST FOREST Program/ ; 22H00384//Japan Society for the Promotion of Science/ ; }, mesh = {*Lakes/virology ; *Metagenomics ; *Giant Viruses/genetics/classification/isolation & purification ; *Genome, Viral ; *Metagenome ; *Phylogeny ; Ecosystem ; Spatio-Temporal Analysis ; Fresh Water/virology ; Genetic Variation ; }, abstract = {Giant viruses (GVs) significantly regulate the ecological dynamics of diverse ecosystems. Although metagenomics has expanded our understanding of their diversity and ecological roles played in marine environments, little is known about GVs of freshwater ecosystems. Most previous studies have employed short-read sequencing and therefore resulted in fragmented genomes, hampering accurate assessment of genetic diversity. We sought to bridge this knowledge gap and overcome previous technical limitations. We subjected spatiotemporal (2 depths × 12 months) samples from Lake Biwa to metagenome-assembled genome reconstruction enhanced by long-read metagenomics. This yielded 293 GV metagenome-assembled genomes. Of these, 285 included previously unknown species in five orders of nucleocytoviruses and the first representatives of freshwater mirusviruses, which exhibited marked divergence from marine-derived lineages. The good performance of our long-read metagenomic assembly was demonstrated by the detection of 42 (14.3%) genomes composed of single contigs with completeness values >90%. GVs were partitioned across water depths, with most species specific to either the sunlit epilimnion or the dark hypolimnion. Epilimnion-specific members tended to be transient and exhibit short and intense abundance peaks, in line with the fact that they regulate the surface algal blooms. During the spring bloom, mirusviruses and members of three nucleocytovirus families were among the most abundant viruses. In contrast, hypolimnion-specific ones, including a mirusvirus genome, were typically more persistent in the hypolimnion throughout the water-stratified period, suggesting that they infect hosts specific to the hypolimnion and play previously unexplored ecological roles in dark water microbial ecosystems.}, } @article {pmid39311770, year = {2024}, author = {Zhou, B and Wang, C and Putzel, G and Hu, J and Liu, M and Wu, F and Chen, Y and Pironti, A and Li, H}, title = {An integrated strain-level analytic pipeline utilizing longitudinal metagenomic data.}, journal = {Microbiology spectrum}, volume = {12}, number = {11}, pages = {e0143124}, pmid = {39311770}, issn = {2165-0497}, support = {R01 CA159036/CA/NCI NIH HHS/United States ; R01CA204113//HHS | National Institutes of Health (NIH)/ ; P20 CA252728/CA/NCI NIH HHS/United States ; R01 LM014085/LM/NLM NIH HHS/United States ; P20CA252728,R01LM014085//HHS | National Institutes of Health (NIH)/ ; R01 CA204113/CA/NCI NIH HHS/United States ; R01 CA164964/CA/NCI NIH HHS/United States ; }, mesh = {*Metagenomics/methods ; Humans ; Longitudinal Studies ; Software ; Microbiota/genetics ; Polymorphism, Single Nucleotide ; High-Throughput Nucleotide Sequencing ; Metagenome ; Gastrointestinal Microbiome/genetics ; Bacteria/genetics/classification/isolation & purification ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; }, abstract = {UNLABELLED: With the development of sequencing technology and analytic tools, studying within-species variations enhances the understanding of microbial biological processes. Nevertheless, most existing methods designed for strain-level analysis lack the capability to concurrently assess both strain proportions and genome-wide single nucleotide variants (SNVs) across longitudinal metagenomic samples. In this study, we introduce LongStrain, an integrated pipeline for the analysis of large-scale metagenomic data from individuals with longitudinal or repeated samples. In LongStrain, we first utilize two efficient tools, Kraken2 and Bowtie2, for the taxonomic classification and alignment of sequencing reads, respectively. Subsequently, we propose to jointly model strain proportions and shared haplotypes across samples within individuals. This approach specifically targets tracking a primary strain and a secondary strain for each subject, providing their respective proportions and SNVs as output. With extensive simulation studies of a microbial community and single species, our results demonstrate that LongStrain is superior to two genotyping methods and two deconvolution methods across a majority of scenarios. Furthermore, we illustrate the potential applications of LongStrain in the real data analysis of The Environmental Determinants of Diabetes in the Young study and a gastric intestinal metaplasia microbiome study. In summary, the proposed analytic pipeline demonstrates marked statistical efficiency over the same type of methods and has great potential in understanding the genomic variants and dynamic changes at strain level. LongStrain and its tutorial are freely available online at https://github.com/BoyanZhou/LongStrain.

IMPORTANCE: The advancement in DNA-sequencing technology has enabled the high-resolution identification of microorganisms in microbial communities. Since different microbial strains within species may contain extreme phenotypic variability (e.g., nutrition metabolism, antibiotic resistance, and pathogen virulence), investigating within-species variations holds great scientific promise in understanding the underlying mechanism of microbial biological processes. To fully utilize the shared genomic variants across longitudinal metagenomics samples collected in microbiome studies, we develop an integrated analytic pipeline (LongStrain) for longitudinal metagenomics data. It concurrently leverages the information on proportions of mapped reads for individual strains and genome-wide SNVs to enhance the efficiency and accuracy of strain identification. Our method helps to understand strains' dynamic changes and their association with genome-wide variants. Given the fast-growing longitudinal studies of microbial communities, LongStrain which streamlines analyses of large-scale raw sequencing data should be of great value in microbiome research communities.}, } @article {pmid39311668, year = {2024}, author = {Rigkos, K and Filis, G and Antonopoulou, I and de Oliveira Maciel, A and Saridis, P and Zarafeta, D and Skretas, G}, title = {Biomimetic CO2 Capture Unlocked through Enzyme Mining: Discovery of a Highly Thermo- and Alkali-Stable Carbonic Anhydrase.}, journal = {Environmental science & technology}, volume = {58}, number = {40}, pages = {17732-17742}, pmid = {39311668}, issn = {1520-5851}, mesh = {*Carbon Dioxide/metabolism ; *Carbonic Anhydrases/metabolism ; Biomimetics ; Alkalies/chemistry ; }, abstract = {Taking immediate action to combat the urgent threat of CO2-driven global warming is crucial for ensuring a habitable planet. Decarbonizing the industrial sector requires implementing sustainable carbon-capture technologies, such as biomimetic hot potassium carbonate capture (BioHPC). BioHPC is superior to traditional amine-based strategies due to its eco-friendly nature. This innovative technology relies on robust carbonic anhydrases (CAs), enzymes that accelerate CO2 hydration and endure harsh industrial conditions like high temperature and alkalinity. Thus, the discovery of highly stable CAs is crucial for the BioHPC technology advancement. Through high-throughput bioinformatics analysis, we identified a highly thermo- and alkali-stable CA, termed CA-KR1, originating from a metagenomic sample collected at a hot spring in Kirishima, Japan. CA-KR1 demonstrates remarkable stability at high temperatures and pH, with a half-life of 24 h at 80 °C and retains activity and solubility even after 30 d in a 20% (w/v) K2CO3/pH 11.5 solution─a standard medium for HPC. In pressurized batch reactions, CA-KR1 enhanced CO2 absorption by >90% at 90 °C, 20% K2CO3, and 7 bar. To our knowledge, CA-KR1 constitutes the most resilient CA biocatalyst for efficient CO2 capture under HPC-relevant conditions, reported to date. CA-KR1 integration into industrial settings holds great promise in promoting efficient BioHPC, a potentially game-changing development for enhancing carbon-capture capacity toward industrial decarbonization.}, } @article {pmid39310785, year = {2024}, author = {Li, Z and Tan, L and Zhang, J and Long, Q and Chen, Z and Xiang, Z and Wu, W and Guo, Z and Liu, H and Hu, B and Yang, B and Hu, M}, title = {Diagnostic performance of metagenomic sequencing in patients with suspected infection: a large-scale retrospective study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1463081}, pmid = {39310785}, issn = {2235-2988}, mesh = {Humans ; Retrospective Studies ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Female ; Male ; Middle Aged ; Adult ; *Sensitivity and Specificity ; Communicable Diseases/diagnosis/microbiology ; Aged ; Young Adult ; Adolescent ; Child ; Molecular Diagnostic Techniques/methods ; Respiratory Tract Infections/diagnosis/microbiology ; Child, Preschool ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) has been widely reported to identify pathogens in infectious diseases (IDs). In this work, we intended to investigate the diagnostic value and clinical acceptance of paired-samples mNGS as compared to the culture method.

METHODS: A total of 361 patients with suspected infection were retrospectively included. With reference to the clinical diagnosis, we compared the diagnostic performance and clinical acceptance in pathogen detection between mNGS and culture tests. Moreover, the pathogen concordance of paired blood and respiratory tract (RT) samples in mNGS assay was investigated.

RESULTS: Among 511 samples, 62.04% were shown to be pathogen positive by mNGS, and that for clinical diagnosis was 51.86% (265/511). When compared to culture assay (n = 428), mNGS had a significantly higher positivity rate (51.87% vs. 33.18%). With reference to the clinical diagnosis, the sensitivity of mNGS outperformed that of culture (89.08% vs. 56.72%). Importantly, mNGS exhibited a clinically accepted rate significantly superior to that of culture. In addition, the mNGS result from 53 paired blood and RT samples showed that most pairs were pathogen positive by both blood and RT, with pathogens largely being partially matched.

CONCLUSION: Through this large-scale study, we further illustrated that mNGS had a clinically accepted rate and sensitivity superior to those of the traditional culture method in diagnosing infections. Moreover, blood and paired RT samples mostly shared partial-matched positive pathogens, especially for pathogens with abundant read numbers in RT, indicating that both blood and RT mNGS can aid the identification of pathogens for respiratory system infection.}, } @article {pmid39309265, year = {2024}, author = {Zeng, T and Lin, C and Deng, Y and Zhu, W}, title = {Effect of BF839 + earthworm protein supplement on motor and some non-motor symptoms of Parkinson's disease: a randomized clinical trial.}, journal = {Frontiers in neurology}, volume = {15}, number = {}, pages = {1371791}, pmid = {39309265}, issn = {1664-2295}, abstract = {INTRODUCTION: Some studies have found that probiotics have the potential to treat PD, and earthworm protein is a traditional Chinese medicine used for the treatment of PD. The purpose of this study was to evaluate the safety and efficacy of Bacteroides fragilis 839 (BF839) + earthworm protein supplement as an adjunctive therapy for PD and to observe changes in the gut microbiota.

METHODS: Forty-six patients with PD were recruited for a 12-week 1:1 randomized, double-blind, placebo-controlled clinical trial to evaluate changes in motor and some non-motor symptom scores and detect metagenomic changes in the gut microbiota.

RESULTS: From baseline to 12 weeks, compared with placebo, the trial group showed significant reductions in the United Parkinson's Disease Rate Scale (UPDRS) total score (-7.74 ± 5.92 vs. -1.83 ± 4.14, p < 0.001), UPDRS part I (-0.72 ± 0.81 vs. -0.20 ± 0.72, p = 0.026), UPDRS part II (-2.50 ± 2.24 vs. -0.22 ± 1.98, p = 0.001), UPDRS part III (-3.43 ± 3.42 vs. -1.33 ± 2.65, p = 0.024), and UPDRS part IV (-1.13 ± 1.19 vs. -0.15 ± 0.57, p = 0.001). Significant reductions in the Hamilton Depression Scale-24 score (-3.91 ± 3.99 vs. +1.15 ± 3.42, p < 0.001), Self-Rating Anxiety Scale scores (-7.04 ± 5.71 vs. -1.23 ± 2.34, p < 0.001), and Constipation scoring system scores (-8.59 ± 4.75 vs. 0.27 ± 1.24, p < 0.001), were also noted. In the trial group, one patient experienced mild eczema and one suffered low blood pressure, which could not be conclusively attributed to supplementation. Compared to the placebo group, the trial group showed a marked increase in Enterococcus faecium and a decrease in Klebsiella.

CONCLUSION: This study is the first to report that probiotics plus earthworm protein can remarkably improve the motor and some non-motor symptoms of PD without serious adverse effects. However, further clinical trials and exploration of the underlying mechanisms are required.

CLINICAL TRIAL REGISTRATION: Clinical trial registry http://www.chictr.org.cn/, Identification No: ChiCTR2000035122.}, } @article {pmid39308956, year = {2024}, author = {Junier, P and Cailleau, G and Fatton, M and Udriet, P and Hashmi, I and Bregnard, D and Corona-Ramirez, A and Francesco, ED and Kuhn, T and Mangia, N and Zhioua, S and Hunkeler, D and Bindschedler, S and Sieber, S and Gonzalez, D}, title = {A cohesive Microcoleus strain cluster causes benthic cyanotoxic blooms in rivers worldwide.}, journal = {Water research X}, volume = {24}, number = {}, pages = {100252}, pmid = {39308956}, issn = {2589-9147}, abstract = {Over the last two decades, proliferations of benthic cyanobacteria producing derivatives of anatoxin-a have been reported in rivers worldwide. Here, we follow up on such a toxigenic event happening in the Areuse river in Switzerland and investigate the diversity and genomics of major bloom-forming riverine benthic cyanobacteria. We show, using 16S rRNA-based community profiling, that benthic communities are dominated by Oscillatoriales. We correlate the detection of one Microcoleus sequence variant matching the Microcoleus anatoxicus species with the presence of anatoxin-a derivatives and use long-read metagenomics to assemble complete circular genomes of the strain. The main dihydro-anatoxin-a-producing strain in the Areuse is distinct from strains isolated in New Zealand, the USA, and Canada, but forms a monophyletic strain cluster with them with average nucleotide identity values close to the species threshold. Compared to the rest of the Microcoleus genus, the toxin-producing strains encode a 15 % smaller genome, lacking genes for the synthesis of some essential vitamins. Toxigenic mats harbor a distinct microbiome dominated by proteobacteria and bacteroidetes, which may support cyanobacterial growth by providing them with essential nutrients. We recommend that strains closely related to M. anatoxicus be monitored internationally in order to help predict and mitigate similar cyanotoxic events.}, } @article {pmid39308639, year = {2024}, author = {Prosperi, M and Marini, S and Boucher, C}, title = {An average-case efficient two-stage algorithm for enumerating all longest common substrings of minimum length k between genome pairs.}, journal = {Proceedings. IEEE International Conference on Healthcare Informatics}, volume = {2024}, number = {}, pages = {93-102}, pmid = {39308639}, issn = {2575-2626}, support = {R01 AI141810/AI/NIAID NIH HHS/United States ; R01 AI145552/AI/NIAID NIH HHS/United States ; }, abstract = {A problem extension of the longest common substring (LCS) between two texts is the enumeration of all LCSs given a minimum length k (ALCS- k), along with their positions in each text. In bioinformatics, an efficient solution to the ALCS- k for very long texts -genomes or metagenomes- can provide useful insights to discover genetic signatures responsible for biological mechanisms. The ALCS- k problem has two additional requirements compared to the LCS problem: one is the minimum length k , and the other is that all common strings longer than k must be reported. We present an efficient, two-stage ALCS- k algorithm exploiting the spectrum of text substrings of length k (k -mers). Our approach yields a worst-case time complexity loglinear in the number of k -mers for the first stage, and an average-case loglinear in the number of common k -mers for the second stage (several orders of magnitudes smaller than the total k -mer spectrum). The space complexity is linear in the first phase (disk-based), and on average linear in the second phase (disk- and memory-based). Tests performed on genomes for different organisms (including viruses, bacteria and animal chromosomes) show that run times are consistent with our theoretical estimates; further, comparisons with MUMmer4 show an asymptotic advantage with divergent genomes.}, } @article {pmid39308020, year = {2024}, author = {Kong, X and Dong, Z and Hu, W and Mi, J and Xiao, J and Wang, Y and Chen, W and Pei, Z and Hao, Z and Liang, C and Wang, Q and Wang, Z}, title = {The role of gut microbiota involved in prostate microenvironment and symptoms improvement in chronic prostatitis/chronic pelvic pain syndrome patients treated with low-intensity extracorporeal shock wave.}, journal = {The Prostate}, volume = {84}, number = {16}, pages = {1525-1536}, doi = {10.1002/pros.24794}, pmid = {39308020}, issn = {1097-0045}, support = {2020QN-15//"Cuiying Science and Technology Innovation" Program/ ; CYXZ2022-40, CYXZ2022-23//Of the Second Hospital of Lanzhou University, The "Cuiying Scholars" Program of the Second Hospital of Lanzhou University/ ; 2021B-042//The Innovation Fund Project of the Gansu Provincial Education Department/ ; PRO133011//National Natural Science Foundation of China/ ; lzujbky-2021-kb29//The Fundamental Research Funds for the Central Universities of Lanzhou University/ ; //and Natural Science Foundation of G/ ; }, mesh = {Humans ; Male ; *Prostatitis/microbiology/therapy ; *Gastrointestinal Microbiome/physiology ; Middle Aged ; Adult ; *Extracorporeal Shockwave Therapy/methods ; *Pelvic Pain/therapy/microbiology ; *Prostate/microbiology ; Treatment Outcome ; Chronic Pain/therapy/microbiology ; Semen/microbiology ; }, abstract = {BACKGROUND: Low-intensity extracorporeal shockwave therapy (Li-ESWT) is emerging as a promising and safe treatment for Chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS). In this study, we aimed to investigate the role of the gut microbiota involved in the prostate microenvironment and symptom improvement during the Li-ESWT for CP/CPPS patients.

METHODS: CP/CPPS patients not taking antibiotics or other treatments were included. NIH-Chronic Prostatitis Symptom Index (NIH-CPSI), International Prostate Symptom Score (IPSS), and International Index of Erectile Function (IIEF-5) were used to evaluate the effectiveness of Li-ESWT at the end of treatment. Visual analogue scale/score was used to evaluate the pain during procedure. Stool and semen samples were collected before and after Li-ESWT. Shotgun metagenomics analyzed gut microbiota, while ELISA and other diagnostic kits detected biochemical changes in seminal plasma.

RESULT: Of the 60 enrolled patients, 52 completed treatment. Li-ESWT response rate was 78.8% (41/52) at end of treatment. Among responders, the subitems of the NIH-CPSI; IPSS; and IIEF-5 scores improved significantly, and the seminal plasma analysis showed decreased TNF-a and MDA levels and increased SOD and Zn[2+] levels posttreatment. Gut microbiome analysis indicated that posttreatment, both α and β diversity increased, and the abundance of certain specific species significantly increased. Fifty-eight pathways significantly enriched posttreatment, notably in branched-chain amino acid synthesis and butyrate synthesis. The abundance of several specific species was found to be significantly higher in non-responders than responders. Among responders, at the species level, some bacteria associated with NIH-CPSI and its subscales, IPSS, IIEF-5, and prostate microenvironment markers (TNF-a, MDA, Zn[2+], and SOD) were identified.

CONCLUSIONS: Our study demonstrates for the first time that Li-ESWT improves the prostate microenvironment and gut microbiota in CP/CPPS patients. Treatment nonresponse may be associated with a high abundance of specific pathogens before treatment. The gut microbiota could have a significant impact on Li-ESWT response and the prostate microenvironment.}, } @article {pmid39307865, year = {2024}, author = {Gundogdu, A and Nalbantoglu, OU and Karis, G and Sarikaya, I and Erdogan, MN and Hora, M and Aslan, H}, title = {Comparing microbial communities in mucilage and seawater samples: Metagenomic insights into mucilage formation in the Marmara Sea.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {48}, pages = {58363-58374}, pmid = {39307865}, issn = {1614-7499}, support = {121G128//The Scientific and Technological Research Council of Turkey (TUBITAK)/ ; }, mesh = {*Seawater/microbiology ; *Microbiota ; Metagenomics ; Bacteria/genetics ; }, abstract = {Marine environments are subject to various naturally occurring phenomena, including marine snow and mucilage. In 2021, the rapid emergence of mucilage in the Marmara Sea raised concerns about its environmental impact. This study investigates the microbial communities in mucilage and seawater samples from the Marmara Sea using metagenomic-scale comparative analyses. The results indicate significant differences in microbial composition and diversity, with mucilage samples showing higher levels of polysaccharide biosynthesis-related enzymes. Over 50% of reads in mucilage samples remained unclassified (dark matter), highlighting unknown microbial taxa. Clean seawater was characterized by a higher presence of Euryarchaeota, Proteobacteria, and Rhodothermaeota, while Chlamydiae and Fusobacteria were dominant in mucilage. The study underscores the necessity for comprehensive metagenomic analyses to understand microbial roles in mucilage formation and persistence. Early detection of microbial shifts could serve as a warning system for mucilage outbreaks, aiding in the development of management strategies.}, } @article {pmid39307589, year = {2025}, author = {Koike, Y and Kuwatsuka, S and Motooka, D and Murota, H}, title = {Dysbiosis of the human skin mycobiome in patients receiving systemic IL-23 inhibitors.}, journal = {Allergology international : official journal of the Japanese Society of Allergology}, volume = {74}, number = {1}, pages = {72-77}, doi = {10.1016/j.alit.2024.06.003}, pmid = {39307589}, issn = {1440-1592}, mesh = {Humans ; *Mycobiome ; *Skin/microbiology ; *Dysbiosis/microbiology ; Female ; Male ; Middle Aged ; Adult ; Interleukin-23/antagonists & inhibitors/immunology ; Psoriasis/drug therapy/microbiology ; Aged ; }, abstract = {BACKGROUND: Systemic inhibition of pro-inflammatory cytokines affects the skin microbiome; however, the impact of systemic anti-inflammatory therapy on the skin fungal microbiome is poorly understood. To examine the effects of cytokine inhibition on the fungal community on human skin and oral mucosa, we analyzed the composition of the skin mycobiome before and after IL-23 inhibition.

METHODS: The study enrolled 15 psoriasis patients. Swab samples were collected from the psoriasis-free skin of antecubital fossa, post-auricular, and the tongue surface before and after 16 weeks of treatment with anti-IL-23 antibodies. Fungal DNA was sequenced by ITS1 metagenomic analysis, and taxonomic classification was performed.

RESULTS: Data from samples collected from the antecubital fossa revealed that the α diversity of the skin mycobiome decreased significantly after treatment with anti-IL-23 antibodies (p = 0.0120). Fungal DNAs were not amplified in 6/15 swab samples after 16 weeks of IL-23 inhibition; by contrast, sufficiently detected in all 15 samples before treatment (p = 0.0554). A comparison of 9/15 paired samples containing well-detected reads revealed that the percentage of genus Malassezia in the mycobiome fell significantly after treatment with IL-23 inhibitors (before, 29.3% ± 9.9%; after; 8.5% ± 3.4%, p = 0.0137). The mycobiome on post-auricular skin and on the tongue surface showed no marked changes after IL-23 inhibition.

CONCLUSIONS: Taken together, the data suggest that inhibition of systemic IL-23 provokes dysbiosis of the mycobiome at the antecubital fossa skin, a finding characterized by reduced fungal diversity and a reduction in the percentage of the genus Malassezia.}, } @article {pmid39306935, year = {2024}, author = {Liu, Y and Chen, H and Zhang, Y and Liu, C and Song, L}, title = {Metagenomics-resolved genomics provide novel ecological insights into resistome community coalescence of wastewater in river environment.}, journal = {Water research}, volume = {267}, number = {}, pages = {122473}, doi = {10.1016/j.watres.2024.122473}, pmid = {39306935}, issn = {1879-2448}, mesh = {*Wastewater/microbiology ; *Rivers/microbiology ; *Metagenomics ; Drug Resistance, Microbial/genetics ; Genomics ; }, abstract = {The discharge of wastewater into rivers can lead to resistome coalescence, thereby enhancing the spread risk of antibiotic resistance genes (ARGs) through mixing of exogenous wastewater resistome communities with indigenous riverine communities. At present, the understanding on the role of resistome community coalescence in the dissemination of ARGs is still very limited, and little is known about the process and its ecological implications. To bridge the gap, this study has conducted field-based surveys and microcosm experiments to deeply dissect the coalescence of resistome community in wastewater within river environment, utilizing genome-centric metagenomic analysis approach. The field investigation suggests resistome coalescence enhances the abundance and diversity of ARGs in the receiving river. Furthermore, the microcosm experiments reveal the effect of mixing ratio on resistome coalescence in the water-sediment system and decipher the temporal attenuation dynamics of the coalesced resistome in the environment. The results show the higher proportion of wastewater has a greater impact on ARGs in the water, whereas the effect of mixing ratio is lesser in the sediments. Temporally, the source-specific ARGs originating from wastewater exhibit decreasing trends over the experimental duration, and relatively, the attenuation in the water is more pronounced than that in the sediments. Interestingly, natural light not only facilitates the attenuation of ARGs in the water but may also induce their deposition at the water-sediment interface. Variance partitioning analyses suggest the microbiome, mobilome, and abiotic factors collectively shape the coalescence of the resistome communities in the environment. The study provides empirical evidence on resistome coalescence in river systems, which is instrumental in gaining a better understanding of the spread mechanism of ARGs in the environment.}, } @article {pmid39306821, year = {2024}, author = {Yang, D and Zhang, C and Ge, S and Xie, Y and Yuan, L}, title = {Performance of single PN/A reactor under wide fluctuation of nitrogen load.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {47}, pages = {58083-58092}, pmid = {39306821}, issn = {1614-7499}, support = {No.2019XKQYMS79//Fundamental Research Funds for the Central Universities/ ; No. 52270171//National Natural Science Foundation of China/ ; }, mesh = {*Nitrogen ; *Bioreactors ; *Waste Disposal, Fluid/methods ; *Wastewater/chemistry ; *Ammonia/metabolism ; Denitrification ; }, abstract = {Partial nitritation-anammox (PN/A) is a cost-effective technology in high ammonia-nitrogen wastewater treatment. However, PN/A is prone to instability as the ammonia-nitrogen sharply fluctuates. In this study, a packed bed reactor is employed to construct a single-stage PN/A system to investigate the operational characteristics and explore the denitrification mechanism. The effluent NH4[+]-N concentration, ammonia nitrogen removal rate (ARE), and total nitrogen removal rate (TNR) could be sustained at about 60 mg/L, 80%, and over 70%, respectively, when the influent nitrogen load rate (NLR) is changed from 0.733 to 0.879 kg-N/m[3]/day. Both ARE and TNR are decreased when NLR continues increasing to 1.026 kg-N/m[3]/day. The influent NLR decreases from 0.879 to 0.147 kg-N/m[3]/day, and ARE and TNR reached 98% and 85.4%, respectively. Therefore, the denitrification effect of the reactor could be recovered, and the excellent nitrogen removal capacity could be obtained within a wide range of influent NLR. Moreover, the high-throughput sequencing and metagenomic testing indicate that the Proteobacteria and Planctomycetes that the PN/A functional strains (i.e., ammonia-oxidizing bacteria (AOB) and anammox bacteria (AnAOB)) account for 38.8% in the sludge. The relative abundance of Nitrospira containing the nitrite-oxidizing bacteria (NOB) has dropped to 0.01%, and the functional gene nxr of the nitrite oxidation process is also inhibited. The relative expression of the functional gene is dominated by the short-range nitritation and anammox oxidation, which demonstrates that the nitrogen removal is mainly dominated by nitritation-anammox.}, } @article {pmid39306820, year = {2024}, author = {Li, J and Huang, W and Li, Q}, title = {New insights into pathogenic performances during peroxydisulfate composting: sources, pathways, and influencing factors.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {47}, pages = {58093-58108}, pmid = {39306820}, issn = {1614-7499}, support = {21878057//National Natural Science Foundation of China/ ; }, mesh = {*Composting ; Soil Microbiology ; Virulence Factors ; Soil/chemistry ; Quorum Sensing ; }, abstract = {Livestock manure treatment technology and composting and its products have been widely used in agricultural soil. However, little was known about the variations in the fate of pathogens and the factors affecting their pathogenic ability during this process, which posed threats to ecological safety and public health globally. This study used a metagenomic approach to profile the behaviors of pathogens during peroxydisulfate composting. Results showed that Pseudomonas aeruginosa, Klebsiella pneumoniae, Escherichia coli, Burkholderia pseudomallei, and Mycobacterium tuberculosis were the main secretors of virulence factors (VFs) in composting system; their abundance and the virulence factor-related genes they carried were better downregulated under the role of peroxydisulfate. In addition, peroxydisulfate composting ensured the lower moisture, weakening the swimming mobility behavior of pathogens through suppressing the abundance of genes associated with flagellar formation, and impaired the communication between pathogens by regulating quorum sensing (QS)- and quorum quenching (QQ)-related genes. Moreover, reduced abundance of resistomes restricted pathogens disseminating infection. In summary, this study provided useful strategies in managing pathogen pathogenic ability during composting based on pathogenic source (pathogens), pathway (VFs), influencing factors (QS/QQ, physicochemical habitats), and resistomes.}, } @article {pmid39306400, year = {2025}, author = {Guo, F and Yan, G and Wang, H and Shi, L and Zhang, Y and Ling, Y and Wei, Y and Wang, H and Dong, W and Chang, Y and Tian, Z}, title = {Denitrification enhanced by composite carbon sources in AAO-biofilter: Efficiency and metagenomics research.}, journal = {Journal of environmental sciences (China)}, volume = {150}, number = {}, pages = {25-35}, doi = {10.1016/j.jes.2024.03.013}, pmid = {39306400}, issn = {1001-0742}, mesh = {*Denitrification ; *Carbon/metabolism ; *Metagenomics ; *Waste Disposal, Fluid/methods ; Nitrogen/metabolism ; Bioreactors ; Anaerobiosis ; Sewage ; Filtration/methods ; }, abstract = {Nitrogen removal from domestic sewage is usually limited by insufficient carbon source and electron donor. An economical solid carbon source was developed by composition of polyvinyl alcohol, sodium alginate, and corncob, which was utilized as external carbon source in the anaerobic anoxic oxic (AAO)-biofilter for the treatment of low carbon-to-nitrogen ratio domestic sewage, and the nitrogen removal was remarkably improved from 63.2% to 96.5%. Furthermore, the effluent chemical oxygen demand maintained at 35 mg/L or even lower, and the total nitrogen was reduced to less than 2 mg/L. Metagenomic analysis demonstrated that the microbial communities responsible for potential denitrification and organic matter degradation in both AAO and the biofilter reactors were mainly composed of Proteobacteria and Bacteroides, respectively. The solid carbon source addition resulted in relatively high abundance of functional enzymes responsible for NO3[-]-N to NO2[-]-N conversion in both AAO and the biofilter reactors, thus enabled stable reaction. The carbon source addition during glycolysis primarily led to the increase of genes associated with the metabolic conversion of fructose 1.6P2 to glycerol-3P The reactor maintained high abundance of genes related to the tricarboxylic acid cycle, and then guaranteed efficient carbon metabolism. The results indicate that the composite carbon source is feasible for denitrification enhancement of AAO-biofilter, which contribute to the theoretical foundation for practical nitrogen removal application.}, } @article {pmid39306146, year = {2024}, author = {Martínez-Aranzales, JR and Córdoba-Agudelo, M and Pérez-Jaramillo, JE}, title = {Fecal microbiome and functional prediction profiles of horses with and without crib-biting behavior: A comparative study.}, journal = {Journal of equine veterinary science}, volume = {142}, number = {}, pages = {105198}, doi = {10.1016/j.jevs.2024.105198}, pmid = {39306146}, issn = {0737-0806}, mesh = {Animals ; Horses/microbiology ; *Feces/microbiology ; Male ; Female ; Bacteria/genetics/classification/isolation & purification ; Behavior, Animal/physiology ; Gastrointestinal Microbiome/physiology/genetics ; RNA, Bacterial/genetics/analysis ; }, abstract = {Crib-biting is a stereotyped oral behavior with poorly understood etiology and pathophysiology. The relationship between the gut microbiome and brain function has been described in behavioral disorders such as schizophrenia, depression and anxiety in humans. In horses, studies of behavioral problems and the microbiome are very limited. This study aimed to characterize the fecal microbiome and the predicted functional profile of horses with and without aerophagia. Fecal samples were collected from 12 Colombian Creole Horses of both sexes, divided into two groups: group 1, composed of six horses with crib-biting (3 females and 3 males), average body weight of 330 ± 10 kg, age of 7.0 ± 1.2 years and body condition score (BCS) of 5/9 ± 1 and group 2, consisting of six horses without crib-biting (3 females and 3 males), average body weight of 335 ± 5 kg, age 6.5 ± 1 years and BCS of 6/9 ± 1. From each horse in both groups fecal total DNA was obtained and 16S ribosomal RNA gene amplicons were sequenced to characterize the bacterial community structure. Community structure and differential abundance analyses revealed significant differences between the two conditions (p < 0.05). Specifically, the fecal microbiota at the family level in crib-biting horses, showing a decrease in Bacteroidales and an increase in Bacillota and Clostridia, differed from that of healthy horses without crib-biting, consistent with findings from previous studies. Furthermore, metagenome prediction suggests metabolic profile changes in bacterial communities between both conditions in horses. Further studies are required to validate the role of the microbiota-gut-brain axis in the etiology of crib-biting and other abnormal and stereotyped behaviors.}, } @article {pmid39305955, year = {2024}, author = {Masuda, R and Phyu Thant, KP and Kawahara, K and Oki, H and Kadonosono, T and Kobayashi, Y and Koide, T}, title = {A yeast two-hybrid system to obtain triple-helical ligands from combinatorial random peptide libraries.}, journal = {The Journal of biological chemistry}, volume = {300}, number = {11}, pages = {107794}, pmid = {39305955}, issn = {1083-351X}, mesh = {*Peptide Library ; *Nerve Growth Factors/metabolism/chemistry/genetics ; *Two-Hybrid System Techniques ; Ligands ; *Eye Proteins/metabolism/chemistry/genetics ; *Serpins/metabolism/chemistry/genetics ; Protein Binding ; Collagen/chemistry/metabolism ; Peptides/chemistry/metabolism ; Humans ; Saccharomyces cerevisiae/metabolism/genetics ; Amino Acid Sequence ; Combinatorial Chemistry Techniques ; }, abstract = {Many bioactive proteins interact with collagen, recognizing amino acid sequences displayed on the triple helix. We report here a selection strategy to obtain triple-helical peptides that interact with the proteins from a combinatorial random library constructed in yeast cells. This system enables us to select them using the standard two-hybrid protocol, detecting interactions between triple-helical peptides and target proteins fused to the GAL4-activating and binding domains, respectively. The library was constructed having triple-helical peptides with a "host-guest" design in which host helix-stabilizing regions flanked guest random sequences. Using this system, we selected peptides that bind to pigment epithelium-derived factor (PEDF), a collagen-binding protein that shows anti-angiogenic and neurotrophic activities, from the libraries. Two-step selections from the total random library and subsequently from the second focused library yielded new PEDF-binding sequences that exhibited a comparable affinity to or more potent than that of the native PEDF-binding sequence in collagen. The obtained sequences also contained a variant of the PEDF-binding motif that did not match the known motif identified from the native collagen sequences. This combinatorial library system allows the chemical space of triple-helical peptides to be screened more widely than that found in native collagen, thus increasing the expectation of obtaining more specific and high-affinity peptides.}, } @article {pmid39305900, year = {2025}, author = {Liu, Q and Huang, B and Zhou, Y and Wei, Y and Li, Y and Li, B and Li, Y and Zhang, J and Qian, Q and Chen, R and Lyu, Z and Wang, R and Cao, Q and Xu, Q and Wang, Q and Miao, Q and You, Z and Lian, M and Gershwin, ME and Jin, Q and Xiao, X and Ma, X and Tang, R}, title = {Gut microbiome pattern impacts treatment response in primary biliary cholangitis.}, journal = {Med (New York, N.Y.)}, volume = {6}, number = {1}, pages = {100504}, doi = {10.1016/j.medj.2024.08.003}, pmid = {39305900}, issn = {2666-6340}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Liver Cirrhosis, Biliary/drug therapy/microbiology ; *Ursodeoxycholic Acid/therapeutic use ; Female ; Male ; Middle Aged ; Prospective Studies ; Dysbiosis/microbiology ; Feces/microbiology ; Aged ; Cholagogues and Choleretics/therapeutic use ; Clostridium/isolation & purification/drug effects/genetics ; Adult ; Metagenomics/methods ; Metagenome/drug effects ; Metabolomics ; }, abstract = {BACKGROUND: Primary biliary cholangitis (PBC) is a progressive autoimmune liver disease. An inadequate response to ursodeoxycholic acid (UDCA) poses a high risk of progression toward end-stage liver disease. Gut dysbiosis has been implicated in PBC. Here, we aimed to investigate microbial signatures that permit risk stratification and provide mechanistic insights into novel therapies for PBC.

METHODS: We prospectively recruited UDCA treatment-naive patients with PBC and performed metagenomic sequencing and metabolomic profiling using stool and serum samples obtained before (n = 132) and after (n = 59) treatment. PBC microbiome subtypes were identified using unsupervised machine learning methods and validated in two independent cohorts.

FINDINGS: PBC baseline metagenomes clustered into two community subtypes characterized by varying abundances of Clostridia taxa. Compared with Clostridia[low] microbiomes, Clostridia[high] microbiomes were more similar to healthy controls. Notably, patients in the Clostridia[low] subtype exhibited a 2-fold higher UDCA non-response rate compared to those in the Clostridia[high] subtype (41% vs. 20%, p = 0.015). Integrative analysis of metagenomic and metabolomic data revealed divergent functional modules and metabolic activities between the two metacommunities. In particular, anaerobic fermentation and the production of bioactive metabolites, including tryptophan derivatives and secondary bile acids, crucial for immune regulation and gut barrier maintenance, were markedly diminished in the Clostridia[low] subtype. Moreover, UDCA administration reconfigured the fecal microbial and metabolic profiles only in the Clostridia[high] group. Importantly, the microbiome subtypes and their associations with UDCA response were reproducible in two independent treatment-naive PBC cohorts.

CONCLUSIONS: Characterizing baseline microbiota patterns may enable the prediction of treatment outcomes in PBC and facilitate personalized treatment strategies.

FUNDING: This research was mainly supported by the National Natural Science Foundation of China.}, } @article {pmid39305897, year = {2024}, author = {Zampirolo, G and Holman, LE and Sawafuji, R and Ptáková, M and Kovačiková, L and Šída, P and Pokorný, P and Pedersen, MW and Walls, M}, title = {Tracing early pastoralism in Central Europe using sedimentary ancient DNA.}, journal = {Current biology : CB}, volume = {34}, number = {20}, pages = {4650-4661.e4}, doi = {10.1016/j.cub.2024.08.047}, pmid = {39305897}, issn = {1879-0445}, mesh = {*DNA, Ancient/analysis ; Animals ; *Archaeology ; Forests ; Sheep/genetics ; Microbiota/genetics ; Agriculture/history ; Geologic Sediments/analysis ; Europe ; }, abstract = {Central European forests have been shaped by complex human interactions throughout the Holocene, with significant changes following the introduction of domesticated animals in the Neolithic (∼7.5-6.0 ka before present [BP]). However, understanding early pastoral practices and their impact on forests is limited by methods for detecting animal movement across past landscapes. Here, we examine ancient sedimentary DNA (sedaDNA) preserved at the Velký Mamuťák rock shelter in northern Bohemia (Czech Republic), which has been a forested enclave since the early Holocene. We find that domesticated animals, their associated microbiomes, and plants potentially gathered for fodder have clear representation by the Late Neolithic, around 6.0 ka BP, and persist throughout the Bronze Age into recent times. We identify a change in dominant grazing species from sheep to pigs in the Bronze Age (∼4.1-3.0 ka BP) and interpret the impact this had in the mid-Holocene retrogressions that still define the structure of Central European forests today. This study highlights the ability of ancient metagenomics to bridge archaeological and paleoecological methods and provide an enhanced perspective on the roots of the "Anthropocene."}, } @article {pmid39305601, year = {2024}, author = {Wang, F and Hu, Z and Wang, W and Wang, J and Xiao, Y and Shi, J and Wang, C and Mai, W and Li, G and An, T}, title = {Selective enrichment of high-risk antibiotic resistance genes and priority pathogens in freshwater plastisphere: Unique role of biodegradable microplastics.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {135901}, doi = {10.1016/j.jhazmat.2024.135901}, pmid = {39305601}, issn = {1873-3336}, mesh = {*Microplastics/toxicity ; *Drug Resistance, Microbial/genetics ; *Fresh Water/microbiology ; Water Pollutants, Chemical/toxicity ; Biofilms/drug effects ; Bacteria/genetics/drug effects ; Genes, Bacterial ; Virulence Factors/genetics ; Polyhydroxyalkanoates ; Polyesters/metabolism ; Microbiota/drug effects/genetics ; Biodegradation, Environmental ; Biodegradable Plastics ; }, abstract = {Microplastics (MPs) has been concerned as emerging vectors for spreading antibiotic resistance and pathogenicity in aquatic environments, but the role of biodegradable MPs remains largely unknown. Herein, field in-situ incubation method combined with metagenomic sequencing were employed to reveal the dispersal characteristics of microbial community, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and virulence factors (VFs) enriched by MPs biofilms. Results showed that planktonic microbes were more prone to enrich on biodegradable MPs (i.e., polyhydroxyalkanoate and polylactic acid) than non-biodegradable MPs (i.e., polystyrene, polypropylene and polyethylene). Distinctive microbial communities were assembled on biodegradable MPs, and the abundances of ARGs, MGEs, and VFs on biofilms of biodegradable MPs were much higher than that of non-biodegradable MPs. Notably, network analysis showed that the biodegradable MPs selectively enriched pathogens carrying ARGs, VFs and MGEs concurrently, suggesting a strong potential risks of co-spreading antibiotic resistance and pathogenicity through horizontal gene transfer. According to WHO priority list of Antibiotic Resistant Pathogens (ARPs) and ARGs health risk assessment framework, the highest abundances of Priority 1 ARPs and Rank I risk ARGs were found on polylactic acid and polyhydroxyalkanoate, respectively. These findings elucidate the unique and critical role of biodegradable MPs for selective enrichment of high-risk ARGs and priority pathogens in freshwater environments.}, } @article {pmid39305563, year = {2024}, author = {Albuquerque, L and Viver, T and Barroso, C and Claudino, R and Galvan, M and Simões, G and Lobo-da-Cunha, A and Egas, C}, title = {Halorubrum miltondacostae sp. nov., a potential polyhydroxyalkanoate producer isolated from an inland solar saltern in Rio Maior, Portugal.}, journal = {Systematic and applied microbiology}, volume = {47}, number = {6}, pages = {126553}, doi = {10.1016/j.syapm.2024.126553}, pmid = {39305563}, issn = {1618-0984}, mesh = {*Phylogeny ; *RNA, Ribosomal, 16S/genetics ; *Sequence Analysis, DNA ; *Polyhydroxyalkanoates ; *Halorubrum/genetics/classification/isolation & purification ; Portugal ; *DNA, Archaeal/genetics/chemistry ; Random Amplified Polymorphic DNA Technique ; Base Composition ; Fatty Acids/analysis/chemistry ; Genes, Essential/genetics ; Phospholipids/analysis/chemistry ; }, abstract = {One hundred and sixty-three extreme halophiles were recovered from a single sample collected from an inland solar saltern in Rio Maior. Based on random amplified polymorphic DNA (RAPD) profiles and partial 16S rRNA gene sequencing 125 isolates were identified as members of the Archaea domain within the genus Halorubrum. Two strains, RMP-11[T] and RMP-47, showed 99.1 % sequence similarity with the species Halorubrum californiense based on phylogenetic analysis of the 16S rRNA gene sequence. However, phylogenetic analysis based on five housekeeping genes, atpB, EF-2, glnA, ppsA and rpoB', showed Halorubrum coriense as the closest related species with 96.7 % similarity. The average nucleotide identity (ANI) of strains RMP-11[T], RMP-47 and species Hrr. coriense were within the range of 90.0-90.5 %, supporting that strains RMP-11[T] and RMP-47 represent a novel species of the genus Halorubrum. These strains formed red-pigmented colonies that were able to grow in a temperature range of 25-50 °C. Polyhydroxyalkanoate (PHA) granules were detected in both strains. The polar lipid profile was identical to the neutrophilic species of the genus Halorubrum. The Rio Maior sample from which both strains were isolated was metagenome sequenced. We identified five metagenome-assembled genomes representing novel Halorubrum species but distinct from the species represented by strains RMP-11[T] and RMP-47. Based on phylogenetic, phylogenomic, comparative genomics, physiological and chemotaxonomic parameters, we describe a new species of the genus Halorubrum represented by strains RMP-11[T] (=CECT 30760[T] = DSM 115521[T]) and RMP-47 (=CECT 30761 = DSM 115541) for which we propose the name Halorubrum miltondacostae sp. nov.}, } @article {pmid39297677, year = {2024}, author = {Bulka, O and Edwards, E}, title = {Metagenome from ACT-3/CF: an anaerobic chloroform-degrading microbial community.}, journal = {Microbiology resource announcements}, volume = {13}, number = {10}, pages = {e0067424}, pmid = {39297677}, issn = {2576-098X}, support = {PGS-D//Canadian Government | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; Discovery//Canadian Government | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; BCB project 285MPR//Genome Canada (GC)/ ; }, abstract = {Here, we present the metagenome of an anaerobic chloroform respiring mixed microbial community used for bioremediation. Our objective was to obtain draft genomes of key microorganisms in the culture.}, } @article {pmid39305530, year = {2024}, author = {Jiang, H and Jiang, M and Zhang, Q}, title = {Coupled sulfur and nitrogen cycling at a catchment scale: insights from isotopic and molecular techniques.}, journal = {Water research}, volume = {267}, number = {}, pages = {122438}, doi = {10.1016/j.watres.2024.122438}, pmid = {39305530}, issn = {1879-2448}, mesh = {*Nitrogen ; *Nitrogen Cycle ; *Sulfur ; Oxidation-Reduction ; Rivers/chemistry ; Denitrification ; Nitrogen Isotopes ; Seasons ; }, abstract = {The biogeochemical cycles of nitrogen (N) and sulfur (S) play important roles in sustaining the Earth's ecosystem. However, their potential coupling process and underlying mechanisms in the nature remain unclear. Through joint applications of river water's isotopic compositions, isotope-pairing experiments, and molecular techniques, this study revealed the coupled N-S cycling processes at a catchment scale from both geochemical and biological perspectives. The river water's natural abundance isotopic compositions indicated that sulfide oxidation was an important source (67.0 ± 5.5 % in summer and 72.0 ± 5.5 % in winter) of riverine sulfate (SO4[2-]). In addition, sulfide oxidation and NOx reduction (especially denitrification) were tightly coupled in summer but less significantly so in winter. However, the coupling of sulfide oxidation and dissimilatory nitrate reduction to ammonium (DNRA) could not be overlooked in winter. The [15]N pairing experiments quantitatively showed that the high sulfide oxidation rates in summer (4.7 ± 2.3 mol/km[2]/h) were significantly associated with the denitrification. Metagenomics and qPCR analyses of the soils supported the isotopic interpretations, substantiating the metabolic potential and coexistence of bacterial denitrification, DNRA, and sulfide oxidation, which was more prevalent in summer. This study reveals comprehensive evidence that sulfide oxidation and NOx reduction are tightly coupled at the catchment scale, which provides a new perspective towards a better understanding of N-S cycling.}, } @article {pmid39304820, year = {2024}, author = {Silva, MH and Batista, LL and Malta, SM and Santos, ACC and Mendes-Silva, AP and Bonetti, AM and Ueira-Vieira, C and Dos Santos, AR}, title = {Unveiling the Brazilian kefir microbiome: discovery of a novel Lactobacillus kefiranofaciens (LkefirU) genome and in silico prospection of bioactive peptides with potential anti-Alzheimer properties.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {884}, pmid = {39304820}, issn = {1471-2164}, mesh = {*Kefir/microbiology ; *Alzheimer Disease ; *Lactobacillus/genetics ; *Genome, Bacterial ; *Microbiota ; Brazil ; *Peptides/chemistry/pharmacology ; Humans ; Molecular Docking Simulation ; Amyloid beta-Peptides/metabolism/genetics ; Amyloid Precursor Protein Secretases/metabolism ; Aspartic Acid Endopeptidases/genetics/metabolism ; Metagenomics/methods ; }, abstract = {BACKGROUND: Kefir is a complex microbial community that plays a critical role in the fermentation and production of bioactive peptides, and has health-improving properties. The composition of kefir can vary by geographic localization and weather, and this paper focuses on a Brazilian sample and continues previous work that has successful anti-Alzheimer properties. In this study, we employed shotgun metagenomics and peptidomics approaches to characterize Brazilian kefir further.

RESULTS: We successfully assembled the novel genome of Lactobacillus kefiranofaciens (LkefirU) and conducted a comprehensive pangenome analysis to compare it with other strains. Furthermore, we performed a peptidome analysis, revealing the presence of bioactive peptides encrypted by L. kefiranofaciens in the Brazilian kefir sample, and utilized in silico prospecting and molecular docking techniques to identify potential anti-Alzheimer peptides, targeting β-amyloid (fibril and plaque), BACE, and acetylcholinesterase. Through this analysis, we identified two peptides that show promise as compounds with anti-Alzheimer properties.

CONCLUSIONS: These findings not only provide insights into the genome of L. kefiranofaciens but also serve as a promising prototype for the development of novel anti-Alzheimer compounds derived from Brazilian kefir.}, } @article {pmid39304351, year = {2025}, author = {Jiménez, DJ and Chaparro, D and Sierra, F and Custer, GF and Feuerriegel, G and Chuvochina, M and Diaz-Garcia, L and Mendes, LW and Ortega Santiago, YP and Rubiano-Labrador, C and Salcedo Galan, F and Streit, WR and Dini-Andreote, F and Reyes, A and Rosado, AS}, title = {Engineering the mangrove soil microbiome for selection of polyethylene terephthalate-transforming bacterial consortia.}, journal = {Trends in biotechnology}, volume = {43}, number = {1}, pages = {162-183}, doi = {10.1016/j.tibtech.2024.08.013}, pmid = {39304351}, issn = {1879-3096}, mesh = {*Polyethylene Terephthalates/metabolism ; *Soil Microbiology ; *Microbiota/genetics ; Microbial Consortia/genetics ; Biodegradation, Environmental ; Wetlands ; Bacteria/genetics/metabolism/classification ; Seawater/microbiology ; Metagenome/genetics ; }, abstract = {Mangroves are impacted by multiple environmental stressors, including sea level rise, erosion, and plastic pollution. Thus, mangrove soil may be an excellent source of as yet unknown plastic-transforming microorganisms. Here, we assess the impact of polyethylene terephthalate (PET) particles and seawater intrusion on the mangrove soil microbiome and report an enrichment culture experiment to artificially select PET-transforming microbial consortia. The analysis of metagenome-assembled genomes of two bacterial consortia revealed that PET catabolism can be performed by multiple taxa, of which particular species harbored putative novel PET-active hydrolases. A key member of these consortia (Mangrovimarina plasticivorans gen. nov., sp. nov.) was found to contain two genes encoding monohydroxyethyl terephthalate hydrolases. This study provides insights into the development of strategies for harnessing soil microbiomes, thereby advancing our understanding of the ecology and enzymology involved in microbial-mediated PET transformations in marine-associated systems.}, } @article {pmid39304154, year = {2024}, author = {Wang, Q and Liu, M and Huang, J and Han, C and Jiang, Y and Deng, H and Liu, K and Zhong, W}, title = {Organic manure rather than chemical fertilization improved dark CO2 fixation by regulating associated microbial functional traits in upland red soils.}, journal = {The Science of the total environment}, volume = {954}, number = {}, pages = {176337}, doi = {10.1016/j.scitotenv.2024.176337}, pmid = {39304154}, issn = {1879-1026}, mesh = {*Soil Microbiology ; *Manure ; *Carbon Dioxide/analysis ; *Fertilizers ; *Soil/chemistry ; Carbon Cycle ; Carbon Sequestration ; }, abstract = {Dark microbial fixation of CO2 is an indispensable process for soil carbon sequestration. However, the whole genetic information involved in dark CO2 fixation and its influence on dark CO2 fixation rates under diversified fertilization regimes were largely unclear. Here, revealed by [13]C-CO2 labeling, dark CO2 fixation rates in upland red soils ranged from 0.029 mg kg[-1] d[-1] to 0.092 mg kg[-1] d[-1], and it was 75.49 % higher (P < 0.05) in organic manure (OM) soil but 44.2 % decline (P < 0.05) in chemical nitrogen fertilizer (N) soil compared to unfertilized (CK) soil. In addition, the normalized abundance and Chao1 index of dark CO2 fixation genes (KO level) were significantly different between OM and N soils, showing the highest and lowest, respectively. And they were positively (P < 0.05) correlated with dark CO2 fixation rate. Besides, among the identified CO2 fixation pathways in this study, the DC/4-HB cycle (M00374) was enriched in OM soil, yet the 3-HP cycle (M00376) was enriched in N soil, and their relative abundances were positively and negatively correlated (P < 0.05) with dark CO2 fixation rate, respectively. The PLS-SEM analysis revealed that dark CO2 fixation-related functional traits (i.e. normalized abundance, Chao1 index and gene composition) were directly and positively associated with dark CO2 fixation rate, and organic manure could exert a positive effect on soil dark CO2 fixation rate through enhancing soil properties (e.g., pH and soil organic carbon) and further altering associated microbial functional traits. These results have implications for explaining and predicting the soil CO2 fixation process from the perspective of microbial functional potential.}, } @article {pmid39303948, year = {2024}, author = {Xu, M and Chen, HQ and Gao, P and Shen, XX}, title = {Fulvic acid impact on constructed wetland-microbial electrolysis cell system performance: Metagenomic insights.}, journal = {Bioresource technology}, volume = {413}, number = {}, pages = {131504}, doi = {10.1016/j.biortech.2024.131504}, pmid = {39303948}, issn = {1873-2976}, mesh = {*Wetlands ; *Benzopyrans/pharmacology ; *Electrolysis ; Bacteria/metabolism/genetics ; Nitrogen ; Biological Oxygen Demand Analysis ; Metagenomics/methods ; Phosphorus/pharmacology ; Biodegradation, Environmental ; Bioelectric Energy Sources ; }, abstract = {This study explores the roles of fulvic acid (FA) in both a conventionally constructed wetland (CCW) and a newly constructed wetland-microbial electrolysis cell (ECW). The results showed that FA increased the average removal efficiency of chemical oxygen demand, total phosphorus, total nitrogen, and ammonia nitrogen in ECW by 8.6, 46.2, 33.0, and 27.9 %, respectively, compared to CCW, and reduced the global warming potential by > 60 %. FA promoted the proliferation of electroactive bacteria (e.g., Chlorobaculum and Candidatus Tenderia) and FA-degrading bacteria (e.g., Anaerolineaceae and Gammaproteobacteria) and reduced methanogens (e.g., Methanothrix) via type-changing. The study's findings suggest that FA influences pollutant removal and microbiome dynamics by altering dissolved oxygen levels and redox potential. In summary, FA and ECW enhanced the efficiency of constructed wetlands by facilitating electron transfer and consumption, and supporting microbial growth and metabolism.}, } @article {pmid39303692, year = {2024}, author = {Crits-Christoph, A and Levy, JI and Pekar, JE and Goldstein, SA and Singh, R and Hensel, Z and Gangavarapu, K and Rogers, MB and Moshiri, N and Garry, RF and Holmes, EC and Koopmans, MPG and Lemey, P and Peacock, TP and Popescu, S and Rambaut, A and Robertson, DL and Suchard, MA and Wertheim, JO and Rasmussen, AL and Andersen, KG and Worobey, M and Débarre, F}, title = {Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic.}, journal = {Cell}, volume = {187}, number = {19}, pages = {5468-5482.e11}, pmid = {39303692}, issn = {1097-4172}, support = {U19 AI135995/AI/NIAID NIH HHS/United States ; R01 AI153044/AI/NIAID NIH HHS/United States ; T15 LM011271/LM/NLM NIH HHS/United States ; T32 AI007244/AI/NIAID NIH HHS/United States ; 75N93021C00015/AI/NIAID NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; U01 AI151812/AI/NIAID NIH HHS/United States ; R01 AI135992/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *COVID-19/epidemiology/virology ; *SARS-CoV-2/genetics/isolation & purification ; *Animals, Wild/virology ; *Phylogeny ; Humans ; Pandemics ; }, abstract = {Zoonotic spillovers of viruses have occurred through the animal trade worldwide. The start of the COVID-19 pandemic was traced epidemiologically to the Huanan Seafood Wholesale Market. Here, we analyze environmental qPCR and sequencing data collected in the Huanan market in early 2020. We demonstrate that market-linked severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic diversity is consistent with market emergence and find increased SARS-CoV-2 positivity near and within a wildlife stall. We identify wildlife DNA in all SARS-CoV-2-positive samples from this stall, including species such as civets, bamboo rats, and raccoon dogs, previously identified as possible intermediate hosts. We also detect animal viruses that infect raccoon dogs, civets, and bamboo rats. Combining metagenomic and phylogenetic approaches, we recover genotypes of market animals and compare them with those from farms and other markets. This analysis provides the genetic basis for a shortlist of potential intermediate hosts of SARS-CoV-2 to prioritize for serological and viral sampling.}, } @article {pmid39303598, year = {2024}, author = {Wu, T and Ding, J and Sun, HJ and Pang, JW and Zhong, L and Zhao, L and Zhang, LY and Ren, NQ and Yang, SS}, title = {Deciphering the roles of attached and suspended sludges in simultaneous nitrogen and phosphorus removal in an IFAS system based on metagenomic analysis.}, journal = {Journal of environmental management}, volume = {370}, number = {}, pages = {122567}, doi = {10.1016/j.jenvman.2024.122567}, pmid = {39303598}, issn = {1095-8630}, mesh = {*Phosphorus/metabolism ; *Nitrogen/metabolism ; *Sewage ; *Metagenomics ; Waste Disposal, Fluid/methods ; }, abstract = {Integrated fixed-film activated sludge (IFAS) system, an improvement of the activated sludge process, combines the advantages of both attached sludge (AS) and suspended sludge (SS). This study aimed to fully decipher the roles of AS and SS in simultaneous N and P removal in an IFAS system through metagenomic analysis. It was found that AS contributed about 84.04%, 97%, and 95.12% to exogenous NO3[-]-N reduction, endogenous NO3[-]-N reduction, and endogenous NO2[-]-N reduction, respectively. Compared with AS, SS exhibited a greater contribution to anaerobic P release (69.06%) and aerobic P uptake (73.48%). Nitrate and nitrite reductase enzymes showed higher activities in AS, while the activities of exopolyphosphatase and alkaline phosphatase D were more active in SS. P content further indicated that in AS, only a small amount of P was stored in EPS, with most presented intracellularly. In SS, the amount of P stored in EPS was found to be higher. Metagenomic analysis revealed genes related to the synthesis and degradation of endogenous carbon were higher in AS, whereas the TCA cycle exhibited higher activity in SS. P removal-related genes (such as ppk2, ppx, and adk) was significantly higher in SS than in AS. The alteration of genes associated with nitrogen metabolism suggested that the microbes in AS had a higher capacity for nitrification and denitrification. In summary, the discrepancy in the roles of AS and SS in N and P removal in IFAS can be attributed to variations in enzyme activity, P storage in EPS, microbial community composition, and functional gene abundance.}, } @article {pmid39303414, year = {2024}, author = {Sipes, K and Buongiorno, J and Steen, AD and Abramov, AA and Abuah, C and Peters, SL and Gianonne, RJ and Hettich, RL and Boike, J and Garcia, SL and Vishnivetskaya, TA and Lloyd, KG}, title = {Depth-specific distribution of bacterial MAGs in permafrost active layer in Ny Ålesund, Svalbard (79°N).}, journal = {Systematic and applied microbiology}, volume = {47}, number = {6}, pages = {126544}, doi = {10.1016/j.syapm.2024.126544}, pmid = {39303414}, issn = {1618-0984}, mesh = {*Permafrost/microbiology ; *Soil Microbiology ; Svalbard ; *Bacteria/classification/genetics ; Arctic Regions ; Metagenome ; Genome, Bacterial/genetics ; Phylogeny ; Temperature ; Climate Change ; }, abstract = {Arctic soil microbial communities may shift with increasing temperatures and water availability from climate change. We examined temperature and volumetric liquid water content (VWC) in the upper 80 cm of permafrost-affected soil over 2 years (2018-2019) at the Bayelva monitoring station, Ny Ålesund, Svalbard. We show VWC increases with depth, whereas in situ temperature is more stable vertically, ranging from -5°C to 5 °C seasonally. Prokaryotic metagenome-assembled genomes (MAGs) were obtained at 2-4 cm vertical resolution collected while frozen in April 2018 and at 10 cm vertical resolution collected while thawed in September 2019. The most abundant MAGs were Acidobacteriota, Actinomycetota, and Chloroflexota. Actinomycetota and Chloroflexota increase with depth, while Acidobacteriota classes Thermoanaerobaculia Gp7-AA8, Blastocatellia UBA7656, and Vicinamibacteria Vicinamibacterales are found above 6 cm, below 6 cm, and below 20 cm, respectively. All MAGs have diverse carbon-degrading genes, and Actinomycetota and Chloroflexota have autotrophic genes. Genes encoding β -glucosidase, N-acetyl-β-D-glucosaminidase, and xylosidase increase with depth, indicating a greater potential for organic matter degradation with higher VWC. Acidobacteriota dominate the top 6 cm with their classes segregating by depth, whereas Actinomycetota and Chloroflexota dominate below ∼6 cm. This suggests that Acidobacteriota classes adapt to lower VWC at the surface, while Actinomycetota and Chloroflexota persist below 6 cm with higher VWC. This indicates that VWC may be as important as temperature in microbial climate change responses in Arctic mineral soils. Here we describe MAG-based Seqcode type species in the Acidobacteriota, Onstottus arcticum, Onstottus frigus, and Gilichinskyi gelida and in the Actinobacteriota, Mayfieldus profundus.}, } @article {pmid39301264, year = {2024}, author = {Zhao, Y and Ma, S and Liang, L and Cao, S and Fan, Z and He, D and Shi, X and Zhang, Y and Liu, B and Zhai, M and Wu, S and Kuang, F and Zhang, H}, title = {Gut Microbiota-Metabolite-Brain Axis Reconstitution Reverses Sevoflurane-Induced Social and Synaptic Deficits in Neonatal Mice.}, journal = {Research (Washington, D.C.)}, volume = {7}, number = {}, pages = {0482}, pmid = {39301264}, issn = {2639-5274}, abstract = {Background: The mechanisms underlying social dysfunction caused by repeated sevoflurane in early life remain unclear. Whether the gut microbiota-metabolite-brain axis is involved in the mechanism of sevoflurane developmental neurotoxicity still lacks report. Methods: Mice received 3% sevoflurane at postnatal day (PND) 6, 7, and 8 for 2 h per day. Metagenomic sequencing and untargeted metabolomic analysis were applied to investigate the effects of sevoflurane on gut microbiota and metabolism. The animal social behavior and the synaptic development were analyzed during PND 35. Subsequently, fecal microbiota transplantation (FMT) from the control group and bile acid administration were performed to see the expected rescuing effect on socially related behaviors that were impaired by repeated sevoflurane exposure in the mice. Results: In the 3-chamber test, sevoflurane-exposed mice spent less time with stranger mice compared with the control group. The density of both the apical and basal spine decreased in mice exposed to sevoflurane. In addition, repeated sevoflurane exposure led to a notable alteration in the gut microbiota and metabolite synthesis, particularly bile acid. FMT reduced the production of intestinal bile acid and attenuated the effect of sevoflurane exposure on social function and synaptic development. Cholestyramine treatment mimics the protective effects of FMT. Conclusions: The gut microbiota-metabolite-brain axis underlies social dysfunction caused by sevoflurane exposure in early age, and bile acid regulation may be a promising intervention to this impairment.}, } @article {pmid39301212, year = {2024}, author = {Nong, Y and Walsh, DM and Maloh, J and Dadlani, M and Sivamani, R}, title = {Whole-Genome Shotgun Metagenomic Sequencing Reveals Shifts in the Skin Microbiome and Bacteriophages of Psoriasis: An Extended Analysis of Published Data.}, journal = {Journal of psoriasis and psoriatic arthritis}, volume = {9}, number = {3}, pages = {98-107}, pmid = {39301212}, issn = {2475-5311}, abstract = {BACKGROUND: Psoriasis is an immune-mediated cutaneous disease that may have shifts in the skin microbiome. Prior research on the skin microbiome in psoriasis has been limited to rRNA based approaches that lack resolution of taxonomic and functional level assessment.

OBJECTIVE: To further illuminate strain and sub-strain level analysis of psoriatic lesions using the CosmosID-HUB Microbiome pipeline.

METHODS: A previous study completed by Tett et al recruited patients with psoriasis who had skin microbiome samples taken from psoriatic plaques on the ear and the elbow as well as sites on the skin unaffected by psoriasis. They performed whole genome shotgun sequencing and made their dataset publicly available. We analyzed the dataset using the CosmosID-HUB Microbiome pipeline to evaluate the strain and sub-strain taxonomic analysis as well as functional gene profiling.

RESULTS: When analyzed with the CosmosID pipeline, both ear and elbow sites in affected areas had decreased alpha diversity compared to unaffected areas. There was an increased relative abundance of Staphylococcus and Corynebacteria at affected sites. We identified distinguishing species and strains of the yeast Malassezia, including M. restricta. that were significantly enriched in healthy elbow samples. Vitamin B12 production genes were not present in psoriatic skin whereas it was present in healthy samples, supporting the notion of relative vitamin B12 deficiency in psoriatic plaques. Phage analysis revealed a greater diversity of Staphylococcus-related phages in unaffected elbow samples.

CONCLUSION: A greater diversity of microbial strains and their functional roles identified in this study may help to tailor treatment for psoriasis.}, } @article {pmid39303138, year = {2024}, author = {Boukheloua, R and Mukherjee, I and Park, H and Šimek, K and Kasalický, V and Ngochera, M and Grossart, HP and Picazo-Mozo, A and Camacho, A and Cabello-Yeves, PJ and Rodriguez-Valera, F and Callieri, C and Andrei, AS and Pernthaler, J and Posch, T and Alfreider, A and Sommaruga, R and Hahn, MW and Sonntag, B and López-García, P and Moreira, D and Jardillier, L and Lepère, C and Biderre-Petit, C and Bednarska, A and Ślusarczyk, M and Tóth, VR and Banciu, HL and Kormas, K and Orlić, S and Šantić, D and Muyzer, G and Herlemann, DPR and Tammert, H and Bertilsson, S and Langenheder, S and Zechmeister, T and Salmaso, N and Storelli, N and Capelli, C and Lepori, F and Lanta, V and Vieira, HH and Kostanjšek, F and Kabeláčová, K and Chiriac, MC and Haber, M and Shabarova, T and Fernandes, C and Rychtecký, P and Znachor, P and Szőke-Nagy, T and Layoun, P and Wong, HL and Kavagutti, VS and Bulzu, PA and Salcher, MM and Piwosz, K and Ghai, R}, title = {Global freshwater distribution of Telonemia protists.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39303138}, issn = {1751-7370}, support = {20-12496X//Grant Agency of the Czech Republic/ ; 017/2022/P//GAJU/ ; 2021/03/Y/NZ8/00076//National Science Centre/ ; }, mesh = {*Fresh Water/microbiology/parasitology ; *Phylogeny ; *RNA, Ribosomal, 18S/genetics ; *In Situ Hybridization, Fluorescence ; Metagenome ; Lakes/microbiology/parasitology ; Biodiversity ; Metagenomics ; }, abstract = {Telonemia are one of the oldest identified marine protists that for most part of their history have been recognized as a distinct incertae sedis lineage. Today, their evolutionary proximity to the SAR supergroup (Stramenopiles, Alveolates, and Rhizaria) is firmly established. However, their ecological distribution and importance as a natural predatory flagellate, especially in freshwater food webs, still remain unclear. To unravel the distribution and diversity of the phylum Telonemia in freshwater habitats, we examined over a thousand freshwater metagenomes from all over the world. In addition, to directly quantify absolute abundances, we analyzed 407 samples from 97 lakes and reservoirs using Catalyzed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH). We recovered Telonemia 18S rRNA gene sequences from hundreds of metagenomic samples from a wide variety of habitats, indicating a global distribution of this phylum. However, even after this extensive sampling, our phylogenetic analysis did not reveal any new major clades, suggesting current molecular surveys are near to capturing the full diversity within this group. We observed excellent concordance between CARD-FISH analyses and estimates of abundances from metagenomes. Both approaches suggest that Telonemia are largely absent from shallow lakes and prefer to inhabit the colder hypolimnion of lakes and reservoirs in the Northern Hemisphere, where they frequently bloom, reaching 10%-20% of the total heterotrophic flagellate population, making them important predatory flagellates in the freshwater food web.}, } @article {pmid39303118, year = {2024}, author = {Doré, J and Sansonetti, PJ}, title = {[The human microbiome: 340 years of history, 140 years of interrogations, technological innovations and emergence of "microbial medicine"].}, journal = {Medecine sciences : M/S}, volume = {40}, number = {8-9}, pages = {654-660}, doi = {10.1051/medsci/2024101}, pmid = {39303118}, issn = {1958-5381}, mesh = {Humans ; Gastrointestinal Microbiome/physiology ; History, 18th Century ; History, 19th Century ; History, 20th Century ; History, 21st Century ; Inventions/history/trends ; *Microbiota/physiology ; Symbiosis ; History, 17th Century ; }, abstract = {For 350 years, we have known that the human body hosts microbes, then called "animalcules". For over a century, following the demonstration of the role of some of these microbes in diseases, questions have arisen about the role of the largely predominant ones colonizing human skin and mucous surfaces, particularly the rich microbial ecosystem of the intestine, the gut microbiota. From the invention of germ-free life - axenism - which experimentally validated the human-microbe symbiosis, resulting from a long coevolution, to the development of anaerobic culture methods, then to the invention of molecular diagnosis, deep sequencing opening up metagenomic and omics approaches in general, a remarkable race has taken place between technological innovations and conceptual advances. This race, beyond the exhaustive description of the microbiota in its intra- and inter-human diversity, and the essential symbiotic functions of the microbiome, has paved the way for a new field of medicine: microbial medicine.}, } @article {pmid39302083, year = {2024}, author = {Cui, Y and Pan, D and Feng, J and Zhao, D and Liu, M and Dong, Z and Liu, S and Wang, S}, title = {Untargeted Metabolomics and Soil Community Metagenomics Analyses Combined with Machine Learning Evaluation Uncover Geographic Differences in Ginseng from Different Locations.}, journal = {Journal of agricultural and food chemistry}, volume = {72}, number = {39}, pages = {21922-21934}, doi = {10.1021/acs.jafc.4c04708}, pmid = {39302083}, issn = {1520-5118}, mesh = {*Panax/chemistry/metabolism/microbiology/growth & development/genetics ; *Metabolomics ; *Soil Microbiology ; *Soil/chemistry ; China ; *Metagenomics ; *Machine Learning ; Chromatography, High Pressure Liquid ; Bacteria/genetics/classification/metabolism/isolation & purification ; Ginsenosides/metabolism/analysis ; Mass Spectrometry ; }, abstract = {Panax ginseng C.A. Meyer, known as the "King of Herbs," has been used as a nutritional supplement for both food and medicine with the functions of relieving fatigue and improving immunity for thousands of years in China. In agricultural planting, soil environments of different geographical origins lead to obvious differences in the quality of ginseng, but the potential mechanism of the differences remains unclear. In this study, 20 key differential metabolites, including ginsenoside Rb1, glucose 6-phosphate, etc., were found in ginseng from 10 locations in China using an ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UHPLC-QTOF-MS)-untargeted metabolomics approach. The soil properties were analyzed and combined with metagenomics technology to explore the possible relationships among microbial elements in planting soil. Through Spearman correlation analysis, it was found that the top 10 microbial colonies with the highest abundance in the soil were significantly correlated with key metabolites. In addition, the relationship model established by the random forest algorithm and the quantitative relationship between soil microbial abundance and ginseng metabolites were successfully predicted. The XGboost model was used to determine 20(R)-ginseng Rg2 and 2'(R)-ginseng Rg3 as feature labeled metabolites, and the optimal ginseng production area was discovered. These results prove that the accumulation of metabolites in ginseng was influenced by microorganisms in the planting soil, which led to geographical differences in ginseng quality.}, } @article {pmid39300577, year = {2024}, author = {Lezcano, MÁ and Bornemann, TLV and Sánchez-García, L and Carrizo, D and Adam, PS and Esser, SP and Cabrol, NA and Probst, AJ and Parro, V}, title = {Hyperexpansion of genetic diversity and metabolic capacity of extremophilic bacteria and archaea in ancient Andean lake sediments.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {176}, pmid = {39300577}, issn = {2049-2618}, support = {FJC2018-037246-I//Spanish Ministry of Science and Innovation/State Agency of Research/ ; RYC2018-023943-I//Spanish Ministry of Science and Innovation/State Agency of Research/ ; RYC-2014-19446//Spanish Ministry of Science and Innovation/State Agency of Research/ ; RTI2018-094368-B-I0//Spanish Ministry of Science and Innovation/State Agency of Research/ ; PEJD-2017- POST/TIC-4119//Spanish Ministry of Science and Innovation/State Agency of Research (EU Youth Employment Initiative)/ ; NAI-CAN7, 13NAI7_2-0018//NASA Astrobiology Institute/ ; DFG PR1603/2-1//German Research Foundation/ ; 161L0285E//German Federal Ministry of Education and Research/ ; }, mesh = {*Lakes/microbiology ; *Archaea/genetics/metabolism/classification ; *Geologic Sediments/microbiology ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Genetic Variation ; Chile ; Phylogeny ; Microbiota ; Extremophiles/metabolism/genetics/classification ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: The Andean Altiplano hosts a repertoire of high-altitude lakes with harsh conditions for life. These lakes are undergoing a process of desiccation caused by the current climate, leaving terraces exposed to extreme atmospheric conditions and serving as analogs to Martian paleolake basins. Microbiomes in Altiplano lake terraces have been poorly studied, enclosing uncultured lineages and a great opportunity to understand environmental adaptation and the limits of life on Earth. Here we examine the microbial diversity and function in ancient sediments (10.3-11 kyr BP (before present)) from a terrace profile of Laguna Lejía, a sulfur- and metal/metalloid-rich saline lake in the Chilean Altiplano. We also evaluate the physical and chemical changes of the lake over time by studying the mineralogy and geochemistry of the terrace profile.

RESULTS: The mineralogy and geochemistry of the terrace profile revealed large water level fluctuations in the lake, scarcity of organic carbon, and high concentration of SO4[2-]-S, Na, Cl and Mg. Lipid biomarker analysis indicated the presence of aquatic/terrestrial plant remnants preserved in the ancient sediments, and genome-resolved metagenomics unveiled a diverse prokaryotic community with still active microorganisms based on in silico growth predictions. We reconstructed 591 bacterial and archaeal metagenome-assembled genomes (MAGs), of which 98.8% belonged to previously unreported species. The most abundant and widespread metabolisms among MAGs were the reduction and oxidation of S, N, As, and halogenated compounds, as well as aerobic CO oxidation, possibly as a key metabolic trait in the organic carbon-depleted sediments. The broad redox and CO2 fixation pathways among phylogenetically distant bacteria and archaea extended the knowledge of metabolic capacities to previously unknown taxa. For instance, we identified genomic potential for dissimilatory sulfate reduction in Bacteroidota and α- and γ-Proteobacteria, predicted an enzyme for ammonia oxidation in a novel Actinobacteriota, and predicted enzymes of the Calvin-Benson-Bassham cycle in Planctomycetota, Gemmatimonadota, and Nanoarchaeota.

CONCLUSIONS: The high number of novel bacterial and archaeal MAGs in the Laguna Lejía indicates the wide prokaryotic diversity discovered. In addition, the detection of genes in unexpected taxonomic groups has significant implications for the expansion of microorganisms involved in the biogeochemical cycles of carbon, nitrogen, and sulfur. Video Abstract.}, } @article {pmid39300575, year = {2024}, author = {Li, Q and Ruscheweyh, HJ and Østergaard, LH and Libertella, M and Simonsen, KS and Sunagawa, S and Scoma, A and Schwab, C}, title = {Trait-based study predicts glycerol/diol dehydratases as a key function of the gut microbiota of hindgut-fermenting carnivores.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {178}, pmid = {39300575}, issn = {2049-2618}, support = {9152//EMBO/ ; AUFF-F-2020-7//Aarhus Universitet Forsknings Fonden/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Feces/microbiology ; *Fermentation ; *Glycerol/metabolism ; *Metagenomics/methods ; Hydro-Lyases/genetics/metabolism ; Propylene Glycols/metabolism ; Vitamin B 12/metabolism ; Bacteria/classification/genetics/isolation & purification/enzymology ; Phylogeny ; Animals, Wild/microbiology ; }, abstract = {BACKGROUND: Microbial pdu and cob-cbi-hem gene clusters encode the key enzyme glycerol/diol dehydratase (PduCDE), which mediates the transformation of dietary nutrients glycerol and 1,2-propanediol (1,2-PD) to a variety of metabolites, and enzymes for cobalamin synthesis, a co-factor and shared good of microbial communities. It was the aim of this study to relate pdu as a multipurpose functional trait to environmental conditions and microbial community composition. We collected fecal samples from wild animal species living in captivity with different gut physiology and diet (n = 55, in total 104 samples), determined occurrence and diversity of pdu and cob-cbi-hem using a novel approach combining metagenomics with quantification of metabolic and genetic biomarkers, and conducted in vitro fermentations to test for trait-based activity.

RESULTS: Fecal levels of the glycerol transformation product 1,3-propanediol (1,3-PD) were higher in hindgut than foregut fermenters. Gene-based analyses indicated that pduC harboring taxa are common feature of captive wild animal fecal microbiota that occur more frequently and at higher abundance in hindgut fermenters. Phylogenetic analysis of genomes reconstructed from metagenomic sequences identified captive wild animal fecal microbiota as taxonomically rich with a total of 4150 species and > 1800 novel species but pointed at only 56 species that at least partially harbored pdu and cbi-cob-hem. While taxonomic diversity was highest in fecal samples of foregut-fermenting herbivores, higher pduC abundance and higher diversity of pdu/cbi-cob-hem related to higher potential for glycerol and 1,2-PD utilization of the less diverse microbiota of hindgut-fermenting carnivores in vitro.

CONCLUSION: Our approach combining metabolite and gene biomarker analysis with metagenomics and phenotypic characterization identified Pdu as a common function of fecal microbiota of captive wild animals shared by few taxa and stratified the potential of fecal microbiota for glycerol/1,2-PD utilization and cobalamin synthesis depending on diet and physiology of the host. This trait-based study suggests that the ability to utilize glycerol/1,2-PD is a key function of hindgut-fermenting carnivores, which does not relate to overall community diversity but links to the potential for cobalamin formation. Video Abstract.}, } @article {pmid39300163, year = {2024}, author = {Myeong, NR and Choe, YH and Shin, SC and Kim, J and Sul, WJ and Kim, M}, title = {Genomic profiling of Antarctic geothermal microbiomes using long-read, Hi-C, and single-cell techniques.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1023}, pmid = {39300163}, issn = {2052-4463}, support = {PE24460//Korea Polar Research Institute (KOPRI)/ ; PE24070//Korea Polar Research Institute (KOPRI)/ ; PE24460//Korea Polar Research Institute (KOPRI)/ ; PE24460//Korea Polar Research Institute (KOPRI)/ ; Graduate Research Scholarship in 2017//Chung-Ang University (CAU)/ ; }, mesh = {Antarctic Regions ; *Microbiota ; *Single-Cell Analysis ; Hot Springs/microbiology ; Metagenomics ; Metagenome ; }, abstract = {Geothermal features in Antarctica provide favorable conditions for diverse microorganisms, yet their genomic diversity remains poorly understood. Here, we present an integrated dataset comprising PacBio HiFi and Hi-C metagenomic sequencing, along with single-cell amplified genomes (SAGs) from two high-altitude geothermal sites, Mount Melbourne and Mount Rittmann, in Antarctica. The long-read HiFi sequencing, coupled with Hi-C, enhances the understanding of microbiome diversity and functionality in this unique ecosystem by providing more complete and accurate genomic information. SAGs complement this by recovering rare microbial taxa and offering a strain-resolved perspective. This dataset aims to deepen our understanding of microbial evolution and ecology in Antarctic geothermal environments, and facilitate cross-comparison with other geothermal environments globally.}, } @article {pmid39299940, year = {2024}, author = {Obayori, OS and Salam, LB and Ashade, AO and Oseni, TD and Kalu, MD and Mustapha, FM}, title = {An animal charcoal contaminated cottage industry soil highlighted by halophilic archaea dominance and decimation of bacteria.}, journal = {World journal of microbiology & biotechnology}, volume = {40}, number = {10}, pages = {327}, pmid = {39299940}, issn = {1573-0972}, mesh = {*Metals, Heavy/analysis ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Archaea/classification/genetics/isolation & purification/metabolism ; *Charcoal ; *Soil Pollutants/analysis ; *Soil/chemistry ; Nigeria ; High-Throughput Nucleotide Sequencing ; Animals ; Hydrocarbons/metabolism/analysis ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; }, abstract = {An animal charcoal contaminated cottage industry soil in Lagos, Nigeria (ACGT) was compared in an ex post facto study with a nearby unimpacted soil (ACGC). Hydrocarbon content was higher than regulatory limits in ACGT (180.2 mg/kg) but lower in ACGC (19.28 mg/kg). Heavy metals like nickel, cadmium, chromium and lead were below detection limit in ACGC. However, all these metals, except cadmium, were detected in ACGT, but at concentrations below regulatory limits. Furthermore, copper (253.205 mg/kg) and zinc (422.630 mg/kg) were above regulatory limits in ACGT. Next generation sequencing revealed that the procaryotic community was dominated by bacteria in ACGC (62%) while in ACGT archaea dominated (76%). Dominant phyla in ACGC were Euryarchaeota (37%), Pseudomonadota (16%) and Actinomycetota (12%). In ACGT it was Euryarchaeota (76%), Bacillota (9%), Pseudomonadota (7%) and Candidatus Nanohaloarchaeota (5%). Dominant Halobacteria genera in ACGT were Halobacterium (16%), Halorientalis (16%), unranked halophilic archaeon (13%) Salarchaeum (6%) and Candidatus Nanohalobium (5%), whereas ACGC showed greater diversity dominated by bacterial genera Salimicrobium (7%) and Halomonas (3%). Heavy metals homeostasis genes, especially for copper, were fairly represented in both soils but with bacterial taxonomic affiliations. Sites like ACGT, hitherto poorly studied and understood, could be sources of novel bioresources.}, } @article {pmid39299726, year = {2024}, author = {Zhou, H and Balint, D and Shi, Q and Vartanian, T and Kriegel, MA and Brito, I}, title = {Lupus and inflammatory bowel disease share a common set of microbiome features distinct from other autoimmune disorders.}, journal = {Annals of the rheumatic diseases}, volume = {}, number = {}, pages = {}, doi = {10.1136/ard-2024-225829}, pmid = {39299726}, issn = {1468-2060}, abstract = {OBJECTIVES: This study aims to elucidate the microbial signatures associated with autoimmune diseases, particularly systemic lupus erythematosus (SLE) and inflammatory bowel disease (IBD), compared with colorectal cancer (CRC), to identify unique biomarkers and shared microbial mechanisms that could inform specific treatment protocols.

METHODS: We analysed metagenomic datasets from patient cohorts with six autoimmune conditions-SLE, IBD, multiple sclerosis, myasthenia gravis, Graves' disease and ankylosing spondylitis-contrasting these with CRC metagenomes to delineate disease-specific microbial profiles. The study focused on identifying predictive biomarkers from species profiles and functional genes, integrating protein-protein interaction analyses to explore effector-like proteins and their targets in key signalling pathways.

RESULTS: Distinct microbial signatures were identified across autoimmune disorders, with notable overlaps between SLE and IBD, suggesting shared microbial underpinnings. Significant predictive biomarkers highlighted the diverse microbial influences across these conditions. Protein-protein interaction analyses revealed interactions targeting glucocorticoid signalling, antigen presentation and interleukin-12 signalling pathways, offering insights into possible common disease mechanisms. Experimental validation confirmed interactions between the host protein glucocorticoid receptor (NR3C1) and specific gut bacteria-derived proteins, which may have therapeutic implications for inflammatory disorders like SLE and IBD.

CONCLUSIONS: Our findings underscore the gut microbiome's critical role in autoimmune diseases, offering insights into shared and distinct microbial signatures. The study highlights the potential importance of microbial biomarkers in understanding disease mechanisms and guiding treatment strategies, paving the way for novel therapeutic approaches based on microbial profiles.

TRIAL REGISTRATION NUMBER: NCT02394964.}, } @article {pmid39299446, year = {2024}, author = {Wei, ZY and Feng, M and Zhang, DX and Jiang, CY and Deng, Y and Wang, ZJ and Feng, K and Song, Y and Zhou, N and Wang, YL and Liu, SJ}, title = {Deep insights into the assembly mechanisms, co-occurrence patterns, and functional roles of microbial community in wastewater treatment plants.}, journal = {Environmental research}, volume = {263}, number = {Pt 1}, pages = {120029}, doi = {10.1016/j.envres.2024.120029}, pmid = {39299446}, issn = {1096-0953}, mesh = {*Microbiota ; *Wastewater/microbiology ; Waste Disposal, Fluid/methods ; Seasons ; RNA, Ribosomal, 16S/genetics ; Sewage/microbiology ; Bacteria/genetics/classification ; Phosphorus/analysis ; }, abstract = {The understanding of activated sludge microbial status and roles is imperative for improving and enhancing the performance of wastewater treatment plants (WWTPs). In this study, we conducted a deep analysis of activated sludge microbial communities across five compartments (inflow, effluent, and aerobic, anoxic, anaerobic tanks) over temporal scales, employing high-throughput sequencing of 16S rRNA amplicons and metagenome data. Clearly discernible seasonal patterns, exhibiting cyclic variations, were observed in microbial diversity, assembly, co-occurrence network, and metabolic functions. Notably, summer samples exhibited higher α-diversity and were distinctly separated from winter samples. Our analysis revealed that microbial community assembly is influenced by both stochastic processes (66%) and deterministic processes (34%), with winter samples demonstrating more random assembly compared to summer. Co-occurrence patterns were predominantly mutualistic, with over 96% positive correlations, and summer networks were more organized than those in winter. These variations were significantly correlated with temperature, total phosphorus and sludge volume index. However, no significant differences were found among microbial community across five compartments in terms of β diversity. A core community of keystone taxa was identified, playing key roles in eight nitrogen and eleven phosphorus cycling pathways. Understanding the assembly mechanisms, co-occurrence patterns, and functional roles of microbial communities is essential for the design and optimization of biotechnological treatment processes in WWTPs.}, } @article {pmid39299138, year = {2024}, author = {Ren, WT and He, ZL and Lv, Y and Wang, HZ and Deng, L and Ye, SS and Du, JS and Wu, QL and Guo, WQ}, title = {Carbon chain elongation characterizations of electrode-biofilm microbes in electro-fermentation.}, journal = {Water research}, volume = {267}, number = {}, pages = {122417}, doi = {10.1016/j.watres.2024.122417}, pmid = {39299138}, issn = {1879-2448}, mesh = {*Biofilms ; *Electrodes ; *Bioreactors/microbiology ; Fermentation ; Fatty Acids/metabolism ; Bacteria/metabolism ; Carbon ; Sewage/microbiology ; }, abstract = {The higher efficiency of electro-fermentation in synthesizing medium-chain fatty acids (MCFAs) compared to traditional fermentation has been acknowledged. However, the functional mechanisms of electrode-biofilm enhancing MCFAs synthesis remain research gaps. To address this, this study proposed a continuous flow electrode-biofilm reactor for chain elongation (CE). After 225 days of operation, stable electrode-biofilms formed and notably improved caproate yield by more than 38 %. The electrode-biofilm was enriched with more CE microorganisms and electroactive bacteria compared to the suspended sludge microorganisms, including Caproicibacterium, Oscillibacter and Pseudoramibacter. Besides, the upregulated CE pathways were evaluated by metagenomic analysis, and the results indicated that the pathways such as acetyl-CoA and malonyl-[acp] formation, reverse beta-oxidation, and fatty acid biosynthesis pathway were all markedly enhanced in cathodic biofilm, more than anodic biofilm and suspended microorganisms. Moreover, microbial community regulated processes like bacterial chemotaxis, flagellar assembly and quorum sensing, crucial for electrode-biofilm formation. Electron transfer, energy metabolism, and microbial interactions were found to be prominently upregulated in the cathodic biofilm, surpassing levels observed in anodic biofilm and suspended sludge microorganisms, which further enhanced CE efficiency. In addition, the statistical analyses further highlighted key microbial functions and interactions within the cathodic biofilm. Oscillospiraceae_bacterium was identified to be the most active microbe, alongside pivotal roles played by Caproiciproducens_sp._NJN-50, Clostridiales_bacterium, Prevotella_sp. and Pseudoclavibacter_caeni. Eventually, the proposed microbial collaboration mechanisms of cathodic biofilm were ascertained. Overall, this study uncovered the biological effects of the electrode-biofilm on MCFAs electrosynthesis, thereby advancing biochemicals production and filling the knowledge gaps in CE electroactive biofilm reactors.}, } @article {pmid39298952, year = {2024}, author = {Liu, J and Shi, J and Hu, Y and Su, Y and Zhang, Y and Wu, X}, title = {Flumethrin exposure perturbs gut microbiota structure and intestinal metabolism in honeybees (Apis mellifera).}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {135886}, doi = {10.1016/j.jhazmat.2024.135886}, pmid = {39298952}, issn = {1873-3336}, mesh = {Animals ; Bees/drug effects/metabolism ; *Pyrethrins/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Insecticides/toxicity ; Catalase/metabolism ; Superoxide Dismutase/metabolism ; Glutathione Transferase/metabolism ; Intestines/drug effects/microbiology ; }, abstract = {Flumethrin mitigates Varroa's harm to honeybee colonies; however, its residues in colonies threaten the fitness of honeybee hosts and gut microbiota. Our previous research has shown that flumethrin induces significant physiological effects on honeybee larvae; but the effects of flumethrin on the gut microbiota and metabolism of adult honeybees are still unknown. In this study, 1-day-old honeybees were exposed to 0, 0.01, 0.1, and 1 mg/L flumethrin for 14 days and the impacts of flumethrin on the intestinal system were evaluated. The results showed that exposure to 1 mg/L flumethrin significantly reduced honeybee survival and the activities of antioxidative enzymes (superoxide dismutase and catalase) and detoxification enzymes (glutathione S-transferase) in honeybee heads. Moreover, exposure to 0.01, 0.1, and 1 mg/L flumethrin significantly decreased the diversity of the honeybee gut microbiota. Results from untargeted metabolomics showed that long-term exposure to 0.01, 0.1, and 1 mg/L flumethrin caused changes in the metabolic pathways of honeybee gut microbes. Furthermore, increased metabolism of phenylalanine, tyrosine, and tryptophan derivatives was observed in honeybee gut microbes. These findings underscore the importance of careful consideration in using pesticides in apiculture and provide a basis for safeguarding honeybees from pollutants, considering the effects on gut microbes.}, } @article {pmid39298898, year = {2024}, author = {Seller-Brison, C and Brison, A and Yu, Y and Robinson, SL and Fenner, K}, title = {Adaptation towards catabolic biodegradation of trace organic contaminants in activated sludge.}, journal = {Water research}, volume = {266}, number = {}, pages = {122431}, doi = {10.1016/j.watres.2024.122431}, pmid = {39298898}, issn = {1879-2448}, mesh = {*Sewage/microbiology ; *Biodegradation, Environmental ; *Water Pollutants, Chemical/metabolism ; Bioreactors ; Waste Disposal, Fluid ; RNA, Ribosomal, 16S/genetics ; Wastewater ; }, abstract = {Trace organic contaminants (TrOCs) are omnipresent in wastewater treatment plants (WWTPs), yet, their removal during wastewater treatment is oftentimes incomplete and underlying biotransformation mechanisms are not fully understood. In this study, we elucidate how different factors, including pre-exposure levels and duration, influence microbial adaptation towards catabolic TrOC biodegradation and its potential role in biological wastewater treatment. Four sequencing batch reactors (SBRs) were operated in parallel in three succeeding phases, adding and removing a selection of 26 TrOCs at different concentration levels. After each phase of SBR operation, a series of batch experiments was conducted to monitor biotransformation kinetics of those same TrOCs across various spike concentrations. For half of our test TrOCs, we detected increased biotransformation in sludge pre-exposed to TrOC concentrations ≥5 µg L[-1] over a 30-day period, with most significant differences observed for the insect repellent DEET and the artificial sweetener saccharin. Accordingly, 16S rRNA amplicon sequencing revealed enrichment of taxa that have previously been linked to catabolic biodegradation of several test TrOCs, e.g., Bosea sp. and Shinella sp. for acesulfame degradation, and Pseudomonas sp. for caffeine, cyclamate, DEET, metformin, paracetamol, and isoproturon degradation. We further conducted shotgun metagenomics to query for gene products previously reported to be involved in the TrOCs' biodegradation pathways. In the future, directed microbial adaptation may be a solution to improve bioremediation of TrOCs in contaminated environments or in WWTPs.}, } @article {pmid39298897, year = {2024}, author = {Wang, N and Li, S and Shi, M and Ni, N and Zhang, X and Guo, X and Lin, H and Luo, Y}, title = {Trajectory of antibiotic resistome response to antibiotics gradients: A comparative study from pharmaceutical and associated wastewater treatment plants to receiving river.}, journal = {Water research}, volume = {266}, number = {}, pages = {122444}, doi = {10.1016/j.watres.2024.122444}, pmid = {39298897}, issn = {1879-2448}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Wastewater/microbiology ; *Rivers/microbiology/chemistry ; *Drug Resistance, Microbial/genetics ; Waste Disposal, Fluid ; Water Pollutants, Chemical ; Microbiota/drug effects ; }, abstract = {Pharmaceutical wastewater often contains significant levels of antibiotic residues, which continuously induce and promote antibiotic resistance during the sewage treatment process. However, the specific impact of antibiotics on the emergence of antibiotic resistance genes (ARGs), microbiomes, and mobile genetic elements (MGEs), as well as the dose-response relationship remain unclear. Herein, through metagenomic sequencing and analysis, we investigated the fate, transmission, and associated risk of ARGs over a ten-year period of exposure to a gradient of sulfonamide antibiotics at a pharmaceutical wastewater treatment plant (PWWTP), an associated wastewater treatment plant (WWTP), and the receiving river. Through abundance comparison and principal co-ordinates analysis (PCoA), our results revealed distinct ARG, microbiome, and MGE profiles across different antibiotic concentrations. Notably, there was a decreasing trend in the abundance of ARGs and MGEs as the antibiotic concentrations were attenuated (p < 0.05). Further partial least squares path modeling analysis, Procrustes analysis and network analysis indicated that variation in MGEs and microbiomes were the driving forces behind the distribution of ARGs. Based on these findings, we proposed an antibiotic-microbiome-MGE-ARG dissemination paradigm, in which integrons as key drivers were closely associated with prevalent ARGs such as sul1, sul2, and aadA. With a focus on human pathogenic bacteria and the associated health risks of ARGs, we conducted pathogen source analysis and calculated the antibiotic resistome risk index (ARRI). Our findings highlighted potential risks associated with the transition from PWWTP to WWTP, raising concerns regarding risk amplification due to the mixed treatment of antibiotic-laden industrial wastewater and domestic sewage. Overall, the results of our study provide valuable information for optimizing wastewater treatment practices to better manage antibiotic resistance.}, } @article {pmid39298862, year = {2024}, author = {Karadayı, S and Yılmaz, İ and Özbek, T and Karadayı, B}, title = {Transfer and persistence of microbiota markers from the human hand to the knife: A preliminary study.}, journal = {Journal of forensic and legal medicine}, volume = {107}, number = {}, pages = {102757}, doi = {10.1016/j.jflm.2024.102757}, pmid = {39298862}, issn = {1878-7487}, mesh = {Humans ; *Microbiota ; *Hand/microbiology ; *Touch ; RNA, Ribosomal, 16S ; Male ; High-Throughput Nucleotide Sequencing ; Bacteria/isolation & purification/genetics ; Female ; Adult ; }, abstract = {New scientific techniques and methods are always needed to link the perpetrators to the incident or the crime scene. Recent microbiota studies based on NGS (Next-generation sequencing) show that various biological samples from crime scenes have the potential to be used in forensic investigations. Especially when DNA traces belonging to more than one person are insufficient to fully determine the genetic profile, a secret sample, such as a microbiota sample created by the suspect's touch, can be used. In this preliminary study, a fictionalized experimental model was designed to investigate the transfer and persistence of the hand microbiome on the knife handle, which has a high potential to be used in criminal incidents, by metagenomic analysis methods. In addition, it was aimed to determine the transfer of specific bacterial species identified only to the person among the five participants onto the knife handle and their persistence over time. In the first stage of the research, samples were collected from the hands of 5 volunteer participants using the swap method, including their palms. Then, after each participant held a different knife, samples were collected from the knife handles via swabs from different angles of the knives at 4 and 24 h and analyzed by metagenomic methods. The findings of this preliminary study showed that the heatmap graphs generated after UniFrac distance analysis were not successful in establishing any similarity between the hand samples and the post-transfer knife handle samples. Nonetheless, it was observed that the transfer of bacterial species detected in the hand samples to knives differed according to the individuals and some bacterial species were transferred to the knife samples held by the participants. The number of bacterial species detected that are specific to each participant's hand sample was 302 in total, and it was determined that a total of 8.28 % of these bacterial species were transferred to the knife handle samples of the 4th hour and 6.95 % to the knife samples of the 24th hour. In the presented study, considering the transfer of some bacterial species in the hand microbiome, which are effective in the variation between individuals, onto the knife; It has been evaluated that some rare bacterial species can be important potential markers to associate the object with the perpetrator.}, } @article {pmid39298515, year = {2024}, author = {Kandathil, AJ and Blair, PW and Lu, J and Anantharam, R and Kobba, K and Robinson, ML and Alharthi, S and Ndawula, EC and Dumler, JS and Kakooza, F and Lamorde, M and Thomas, DL and Salzberg, SL and Manabe, YC}, title = {Metagenomic next generation sequencing of plasma RNA for diagnosis of unexplained, acute febrile illness in Uganda.}, journal = {PLoS neglected tropical diseases}, volume = {18}, number = {9}, pages = {e0012451}, pmid = {39298515}, issn = {1935-2735}, support = {R01 HG006677/HG/NHGRI NIH HHS/United States ; R35 GM130151/GM/NIGMS NIH HHS/United States ; D43 TW009771/TW/FIC NIH HHS/United States ; R21 DA053145/DA/NIDA NIH HHS/United States ; R01 DA048063/DA/NIDA NIH HHS/United States ; U54 EB007958/EB/NIBIB NIH HHS/United States ; }, mesh = {Humans ; Uganda/epidemiology ; Adult ; *Metagenomics/methods ; Female ; Male ; *High-Throughput Nucleotide Sequencing/methods ; Young Adult ; Bacteria/genetics/isolation & purification/classification ; Viruses/genetics/isolation & purification/classification ; Virus Diseases/diagnosis/blood/virology ; Fever of Unknown Origin/diagnosis ; Fever/diagnosis ; }, abstract = {Metagenomic next generation metagenomic sequencing (mNGS) has proven to be a useful tool in the diagnosis and identification of novel human pathogens and pathogens not identified on routine clinical microbiologic tests. In this study, we applied mNGS to characterize plasma RNA isolated from 42 study participants with unexplained acute febrile illness (AFI) admitted to tertiary referral hospitals in Mubende and Arua, Uganda. Study participants were selected based on clinical criteria suggestive of viral infection (i.e., thrombocytopenia, leukopenia). The study population had a median age of 28 years (IQR:24 to 38.5) and median platelet count of 114 x103 cells/mm3 (IQR:66,500 to 189,800). An average of 25 million 100 bp reads were generated per sample. We identified strong signals from diverse virus, bacteria, fungi, or parasites in 10 (23.8%) of the study participants. These included well recognized pathogens like Helicobacter pylori, human herpes virus-8, Plasmodium falciparum, Neisseria gonorrhoeae, and Rickettsia conorii. We further confirmed Rickettsia conorii infection, the cause of Mediterranean Spotted Fever (MSF), using PCR assays and Sanger sequencing. mNGS was a useful addition for detection of otherwise undetected pathogens and well-recognized non-pathogens. This is the first report to describe the molecular confirmation of a hospitalized case of MSF in sub-Saharan Africa (SSA). Further studies are needed to determine the utility of mNGS for disease surveillance in similar settings.}, } @article {pmid39298488, year = {2024}, author = {Worthan, SB and McCarthy, RDP and Delaleau, M and Stikeleather, R and Bratton, BP and Boudvillain, M and Behringer, MG}, title = {Evolution of pH-sensitive transcription termination in Escherichia coli during adaptation to repeated long-term starvation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {39}, pages = {e2405546121}, pmid = {39298488}, issn = {1091-6490}, support = {ANR-19-CE44-0009-01//Agence Nationale de la Recherche (ANR)/ ; R35 GM150625/GM/NIGMS NIH HHS/United States ; P30 DK058404/DK/NIDDK NIH HHS/United States ; W911NF-21-1-0161//DOD | USA | AFC | CCDC | ARO | Life Sciences Division, Army Research Office (Life Sciences Division ARO)/ ; R35GM150625//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; P30 EY008126/EY/NEI NIH HHS/United States ; P30 DK020593/DK/NIDDK NIH HHS/United States ; P30 CA068485/CA/NCI NIH HHS/United States ; S10 OD018075/OD/NIH HHS/United States ; U24 DK059637/DK/NIDDK NIH HHS/United States ; }, mesh = {*Escherichia coli/genetics/metabolism ; Hydrogen-Ion Concentration ; *Escherichia coli Proteins/genetics/metabolism ; Adaptation, Physiological/genetics ; Mutation ; Transcription Termination, Genetic ; Gene Expression Regulation, Bacterial ; Rho Factor/metabolism/genetics ; Evolution, Molecular ; }, abstract = {Fluctuating environments that consist of regular cycles of co-occurring stress are a common challenge faced by cellular populations. For a population to thrive in constantly changing conditions, an ability to coordinate a rapid cellular response is essential. Here, we identify a mutation conferring an arginine-to-histidine (Arg to His) substitution in the transcription terminator Rho. The rho R109H mutation frequently arose in Escherichia coli populations experimentally evolved under repeated long-term starvation conditions, during which the accumulation of metabolic waste followed by transfer into fresh media results in drastic environmental pH fluctuations associated with feast and famine. Metagenomic sequencing revealed that populations containing the rho mutation also possess putative loss-of-function mutations in ydcI, which encodes a recently characterized transcription factor associated with pH homeostasis. Genetic reconstructions of these mutations show that the rho allele confers plasticity via an alkaline-induced reduction of Rho function that, when found in tandem with a ΔydcI allele, leads to intracellular alkalization and genetic assimilation of Rho mutant function. We further identify Arg to His substitutions at analogous sites in rho alleles from species that regularly experience neutral to alkaline pH fluctuations in their environments. Our results suggest that Arg to His substitutions in Rho may serve to rapidly coordinate complex physiological responses through pH sensing and shed light on how cellular populations use environmental cues to coordinate rapid responses to complex, fluctuating environments.}, } @article {pmid39298196, year = {2024}, author = {Barber, DG and Davies, CA and Hartley, IP and Tennant, RK}, title = {Evaluation of commercial RNA extraction kits for long-read metatranscriptomics in soil.}, journal = {Microbial genomics}, volume = {10}, number = {9}, pages = {}, pmid = {39298196}, issn = {2057-5858}, mesh = {*Soil Microbiology ; Microbiota/genetics ; Soil/chemistry ; Transcriptome ; Gene Expression Profiling/methods ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, RNA/methods ; RNA/genetics/isolation & purification ; RNA, Bacterial/genetics/isolation & purification ; }, abstract = {Metatranscriptomic analysis of the soil microbiome has the potential to reveal molecular mechanisms that drive soil processes regulated by the microbial community. Therefore, RNA samples must be of sufficient yield and quality to robustly quantify differential gene expression. While short-read sequencing technology is often favoured for metatranscriptomics, long-read sequencing has the potential to provide several benefits over short-read technologies. The ability to resolve complete transcripts on a portable sequencing platform for a relatively low capital expenditure makes Oxford Nanopore Technology an attractive prospect for addressing many of the challenges of soil metatranscriptomics. To fully enable long-read metatranscriptomic analysis of the functional molecular pathways expressed in these diverse habitats, RNA purification methods from soil must be optimised for long-read sequencing. Here we compare RNA samples purified using five commercially available extraction kits designed for use with soil. We found that the Qiagen RNeasy PowerSoil Total RNA Kit performed the best across RNA yield, quality and purity and was robust across different soil types. We found that sufficient sequencing depth can be achieved to characterise the active community for total RNA samples using Oxford Nanopore Technology, and discuss its current limitations for differential gene expression analysis in soil studies.}, } @article {pmid39298479, year = {2024}, author = {Hellewell, J and Horsfield, ST and von Wachsmann, J and Gurbich, TA and Finn, RD and Iqbal, Z and Roberts, LW and Lees, JA}, title = {CELEBRIMBOR: core and accessory genes from metagenomes.}, journal = {Bioinformatics (Oxford, England)}, volume = {40}, number = {9}, pages = {}, pmid = {39298479}, issn = {1367-4811}, support = {//European Molecular Biology Laboratory, European Bioinformatics Institute/ ; }, mesh = {*Software ; *Metagenome ; Metagenomics/methods ; }, abstract = {MOTIVATION: Metagenome-Assembled Genomes (MAGs) or Single-cell Amplified Genomes (SAGs) are often incomplete, with sequences missing due to errors in assembly or low coverage. This presents a particular challenge for the identification of true gene frequencies within a microbial population, as core genes missing in only a few assemblies will be mischaracterized by current pangenome approaches.

RESULTS: Here, we present CELEBRIMBOR, a Snakemake pangenome analysis pipeline which uses a measure of genome completeness to automatically adjust the frequency threshold at which core genes are identified, enabling accurate core gene identification in MAGs and SAGs.

CELEBRIMBOR is published under open source Apache 2.0 licence at https://github.com/bacpop/CELEBRIMBOR and is available as a Docker container from this repository. Supplementary material is available in the online version of the article.}, } @article {pmid39296299, year = {2024}, author = {Wang, X and Li, H and Yang, Y and Wu, Z and Wang, Z and Li, D and Xia, W and Zou, S and Liu, Y and Wang, F}, title = {Geographic and environmental impacts on gut microbiome in Himalayan langurs (Semnopithecus schistaceus) and Xizang macaques (Macaca mulatta vestita).}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1452101}, pmid = {39296299}, issn = {1664-302X}, abstract = {INTRODUCTION: Gut microbiome plays a crucial role in the health of wild animals. Their structural and functional properties not only reflect the host's dietary habits and habitat conditions but also provide essential support for ecological adaptation in various environments.

METHODS: This study investigated the gut microbiome of Himalayan langurs (Semnopithecus schistaceus) and Xizang macaques (Macaca mulatta vestita) across different geographic regions using 16S rRNA gene and metagenomic sequencing.

RESULTS: Results showed distinct clustering patterns in gut microbiota based on geographic location. Soil had an insignificant impact on host gut microbiome. Himalayan langurs from mid-altitude regions exhibited higher levels of antibiotic resistance genes associated with multidrug resistance, while Xizang macaques from high-altitude regions showed a broader range of resistance genes. Variations in carbohydrate-active enzymes and KEGG pathways indicated unique metabolic adaptations to different environments.

DISCUSSION: These findings provide valuable insights into the health and conservation of these primates and the broader implications of microbial ecology and functional adaptations in extreme conditions.}, } @article {pmid39295709, year = {2024}, author = {Mariam, S and Kshirsagar, R and Hasan, S and Khadtare, Y and Rajpurohit, KS and Rai, H and Newaskar, D and Deo, P}, title = {Implant Mechanics, Biological Milieu, and Peri-Implantitis: A Narrative Review.}, journal = {Cureus}, volume = {16}, number = {8}, pages = {e67173}, pmid = {39295709}, issn = {2168-8184}, abstract = {Dental implants constitute an important treatment modality for rehabilitating edentulous and partially edentulous arches. With more implant systems in the market, understanding the mechanical aspects of implants is crucial in understanding this indispensable therapy. However, microflora-related factors i.e. biological factors are also crucial. Despite the tremendous success rate of dental implants, it is not averse to failure. Both mechanical and microbial aspects in seclusion or together predispose to implant failure. Newer technological advances have paved the way for advanced techniques to identify the not-so-common flora causing implant failure. This review focuses on detailed mechanical and biological aspects and the sealing agent used to seal the implant-abutment interface. It also focuses on advanced molecular techniques like metagenomics and transcriptomics. A thorough literature search was performed with selected articles from electronic databases. A combination of in-vivo and in-vitro studies were considered to provide comprehensive information on the subject. Both the biomechanical aspects like micro gap, and microleakage, as well as microbial movements play confluent roles in implant failure. The focus should be on the different aspects through which microflora can penetrate the inner parts of the implant. Also, newer culture-independent techniques of detecting previously undetected oral flora should be included in future studies.}, } @article {pmid39294762, year = {2024}, author = {Cruz-Cano, R and Kolb, M and Saldaña-Vázquez, RA and Bretón-Deval, L and Cruz-Cano, N and Aldama-Cervantes, A}, title = {Existing evidence on the use of environmental DNA as an operational method for studying rivers: a systematic map and thematic synthesis.}, journal = {Environmental evidence}, volume = {13}, number = {1}, pages = {2}, pmid = {39294762}, issn = {2047-2382}, support = {IN211921//UNAM-PAPIIT/ ; CVU: 516486//CONACYT/ ; }, abstract = {BACKGROUND: Environmental DNA (eDNA) is the DNA that can be extracted from an environmental sample, enabling the monitoring of whole biological communities across a large number of samples, at a potentially lower cost, which can significantly benefit river conservation. A systematic mapping protocol was designed to investigate the use of eDNA in rivers, specifically in terms of research topics, geographic and taxonomic biases, as well as information gaps. Furthermore, the potential research opportunities of eDNA in rivers and possible paths to find this kind of information on available platforms are identified.

METHODS: A published systematic map protocol was applied, consisting of a search for published articles and gray literature in two bibliographic databases and one search engine. All search results were submitted to a 2-stage screening for relevance and pertinence in accordance with pre-defined eligibility criteria. Data extraction and codification regarding country of study, year, taxonomic group, sequencing platform, and type of technique employed resulted in a publicly available database.

RESULTS: From 7372 studies initially obtained by the search, 545 met the inclusion criteria spanning a period from 2003 to 2022. The five countries with most studies are: USA (134), Japan (61), China (54), Brazil (29) and the UK (25). The most used fragments to analyze DNA are 16S and COI, whilst 26S and 23S are the least used. Only 84 (15%) of the studies reported hypervariable regions, among which the most used are V4 and V5. Regarding taxonomic groups, fishes are most often studied (176), followed by bacteria (138) and virus (52), while fungi is the least studied group (3). Concerning data availability, 229 (42%) studies provided access to sequencing data.

CONCLUSIONS: This study presents a comprehensive analysis of the available evidence regarding the implementation of the eDNA methods in rivers. The findings indicate that since the year 2003, this approach has been applied to aquatic lotic systems, and their recent increase can be attributed to the development of Next-Generation-Sequencing technologies and their reduced costs. However, there is a bias towards high-income countries, particularly USA and Europe. Widespread use and applications of this approach at a global level would allow for the generation of a large amount of information that can be compared between countries to understand if responses of aquatic systems follow similar patterns worldwide.}, } @article {pmid39294752, year = {2024}, author = {Góngora, E and Lirette, AO and Freyria, NJ and Greer, CW and Whyte, LG}, title = {Metagenomic survey reveals hydrocarbon biodegradation potential of Canadian high Arctic beaches.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {72}, pmid = {39294752}, issn = {2524-6372}, support = {Multi-Partner Research Initiative//Fisheries and Oceans Canada/ ; 273122//Fonds de recherche du Québec - Nature et technologies/ ; Polar Continental Shelf Project//Natural Resources Canada/ ; Northern Scientific Training Program//Polar Knowledge Canada/ ; }, abstract = {BACKGROUND: Decreasing sea ice coverage across the Arctic Ocean due to climate change is expected to increase shipping activity through previously inaccessible shipping routes, including the Northwest Passage (NWP). Changing weather conditions typically encountered in the Arctic will still pose a risk for ships which could lead to an accident and the uncontrolled release of hydrocarbons onto NWP shorelines. We performed a metagenomic survey to characterize the microbial communities of various NWP shorelines and to determine whether there is a metabolic potential for hydrocarbon degradation in these microbiomes.

RESULTS: We observed taxonomic and functional gene evidence supporting the potential of NWP beach microbes to degrade various types of hydrocarbons. The metagenomic and metagenome-assembled genome (MAG) taxonomy showed that known hydrocarbon-degrading taxa are present in these beaches. Additionally, we detected the presence of biomarker genes of aerobic and anaerobic degradation pathways of alkane and aromatic hydrocarbons along with complete degradation pathways for aerobic alkane degradation. Alkane degradation genes were present in all samples and were also more abundant (33.8 ± 34.5 hits per million genes, HPM) than their aromatic hydrocarbon counterparts (11.7 ± 12.3 HPM). Due to the ubiquity of MAGs from the genus Rhodococcus (23.8% of the MAGs), we compared our MAGs with Rhodococcus genomes from NWP isolates obtained using hydrocarbons as the carbon source to corroborate our results and to develop a pangenome of Arctic Rhodococcus. Our analysis revealed that the biodegradation of alkanes is part of the core pangenome of this genus. We also detected nitrogen and sulfur pathways as additional energy sources and electron donors as well as carbon pathways providing alternative carbon sources. These pathways occur in the absence of hydrocarbons allowing microbes to survive in these nutrient-poor beaches.

CONCLUSIONS: Our metagenomic analyses detected the genetic potential for hydrocarbon biodegradation in these NWP shoreline microbiomes. Alkane metabolism was the most prevalent type of hydrocarbon degradation observed in these tidal beach ecosystems. Our results indicate that bioremediation could be used as a cleanup strategy, but the addition of adequate amounts of N and P fertilizers, should be considered to help bacteria overcome the oligotrophic nature of NWP shorelines.}, } @article {pmid39294577, year = {2024}, author = {He, S and Liu, H and Hu, X and Zhao, J and Liang, J and Zhang, X and Chen, J and Zeng, H and Sun, G}, title = {Exploring the clinical and diagnostic value of metagenomic next-generation sequencing for urinary tract infection: a systematic review and meta-analysis.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {1000}, pmid = {39294577}, issn = {1471-2334}, mesh = {*Urinary Tract Infections/diagnosis/microbiology ; Humans ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Sensitivity and Specificity ; ROC Curve ; }, abstract = {BACKGROUND: A new pathogen detection tool, metagenomic next-generation sequencing (mNGS), has been widely used for infection diagnosis, but the clinical and diagnostic value of mNGS in urinary tract infection (UTI) remains inconclusive. This systematic review with meta-analysis aimed to investigate the efficacy of mNGS in treating UTIs.

METHODS: A comprehensive literature search was performed in PubMed, Web of Science, Embase, and the Cochrane Library, and eligible studies were selected based on the predetermined criteria. The quality of the included studies was assessed via the Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) tool, and the certainty of evidence (CoE) was measured by the Grading of Recommendations, Assessment, Development, and Evaluations (GRADE) score. Then, the positive detection rate (PDR), pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR), and area under the curve of the summary receiver operating characteristic curve (AUROC) was estimated in Review Manager, Stata, and MetaDisc. Subgroup analysis, meta-regression, and sensitivity analysis were performed to reveal the potential factors that influence internal heterogeneity.

RESULTS: A total of 17 studies were selected for further analysis. The PDR of mNGS was markedly greater than that of culture (odds ratio (OR) = 2.87, 95% confidence interval [CI]: 1.72-4.81, p < 0.001, I[2] = 90%). The GRADE score presented a very low CoE. Then, the pooled sensitivity was 0.89 (95% CI: 0.86-0.91, I[2] = 39.65%, p = 0.06), and the pooled specificity was 0.75 (95% CI: 0.51-0.90, I[2] = 88.64%, p < 0.001). The AUROC of the studies analyzed was 0.89 (95% CI: 0.86-0.92). The GRADE score indicated a low CoE.

CONCLUSION: The current evidence shows that mNGS has favorable diagnostic performance for UTIs. More high-quality prospective randomized controlled trials (RCTs) are expected to verify these findings and provide more information about mNGS in UTI treatment and prognosis.}, } @article {pmid39294312, year = {2024}, author = {Li, D and Wang, Y and Li, X and Zhang, Z and Wang, G and Zhang, Y and Chen, L}, title = {Exploring microbial diversity and function in companion planting systems of white clover and orchard grass.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {21609}, pmid = {39294312}, issn = {2045-2322}, support = {32172769//National Natural Science Foundation of China/ ; }, mesh = {*Trifolium/microbiology/genetics/growth & development ; *Soil Microbiology ; *Rhizosphere ; *Microbiota/genetics ; Dactylis/genetics/microbiology ; Metagenomics/methods ; Bacteria/genetics/classification ; Biodiversity ; }, abstract = {Companion planting of white clover (Trifolium repens L.) with orchard grass (Dactylis glomerata L.), a famous hay grass, improves the forage quality of orchard grass. Microbiome profiling techniques can reveal the specific role of white clover companion planting with orchard grass. This study aimed to explore the microbiome distribution and gene functions of rhizosphere and non-rhizosphere soil via companion planting systems of white clover and orchard grass. From metagenomics sequencing analysis, we confirmed the significant role of white clover on soil environment modeling during companion planting with orchard grass. Twenty-eight biomarkers of rhizosphere soil organisms were identified during companion planting, including Proteobacteria, Betaproteobacteria, Flavobacteriia, and Caulobacterales. The number of gene functions of nitrogen and carbon fixation in companion planting was higher than that in single plants, indicating new functional flora for companion planting. We characterized specific rhizosphere effects, typical biomarker flora, and potential regulatory mechanisms for white clover-related companion planting by metagenomics analyses.}, } @article {pmid39294129, year = {2024}, author = {Bozzi, D and Neuenschwander, S and Cruz Dávalos, DI and Sousa da Mota, B and Schroeder, H and Moreno-Mayar, JV and Allentoft, ME and Malaspinas, AS}, title = {Towards predicting the geographical origin of ancient samples with metagenomic data.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {21794}, pmid = {39294129}, issn = {2045-2322}, mesh = {Humans ; *DNA, Ancient/analysis ; *Metagenomics/methods ; *Metagenome ; Geography ; Microbiota/genetics ; }, abstract = {Reconstructing the history-such as the place of birth and death-of an individual sample is a fundamental goal in ancient DNA (aDNA) studies. However, knowing the place of death can be particularly challenging when samples come from museum collections with incomplete or erroneous archives. While analyses of human DNA and isotope data can inform us about the ancestry of an individual and provide clues about where the person lived, they cannot specifically trace the place of death. Moreover, while ancient human DNA can be retrieved, a large fraction of the sequenced molecules in ancient DNA studies derive from exogenous DNA. This DNA-which is usually discarded in aDNA analyses-is constituted mostly by microbial DNA from soil-dwelling microorganisms that have colonized the buried remains post-mortem. In this study, we hypothesize that remains of individuals buried in the same or close geographic areas, exposed to similar microbial communities, could harbor more similar metagenomes. We propose to use metagenomic data from ancient samples' shotgun sequencing to locate the place of death of a given individual which can also help to solve cases of sample mislabeling. We used a k-mer-based approach to compute similarity scores between metagenomic samples from different locations and propose a method based on dimensionality reduction and logistic regression to assign a geographical origin to target samples. We apply our method to several public datasets and observe that individual samples from closer geographic locations tend to show higher similarities in their metagenomes compared to those of different origin, allowing good geographical predictions of test samples. Moreover, we observe that the genus Streptomyces commonly infiltrates ancient remains and represents a valuable biomarker to trace the samples' geographic origin. Our results provide a proof of concept and show how metagenomic data can also be used to shed light on the place of origin of ancient samples.}, } @article {pmid39293811, year = {2024}, author = {Liu, Y and Ong, SL and Gedye, K and Truglio, M and Prabakar, S}, title = {Behind the scenes: metagenomic analysis of bacterial communities in sustainable depilation of sheepskin.}, journal = {Journal of applied microbiology}, volume = {135}, number = {11}, pages = {}, doi = {10.1093/jambio/lxae244}, pmid = {39293811}, issn = {1365-2672}, support = {LSRX-1801//the New Zealand Ministry of Business, Innovation and Employment (MBIE)/ ; }, mesh = {*Bacteria/genetics/isolation & purification/classification ; *Metagenomics ; *Microbiota ; Animals ; Acetic Acid/metabolism ; Hair Removal ; }, abstract = {AIM: The leather industry is embracing eco-friendly technologies for both regulatory compliance and sustainable growth. While enzymatic depilation provides a greener alternative to traditional beamhouse methods, its complexity often leads to higher costs. To address this, we examined the performance of sheepskins' native bacterial flora in acetic acid conditions with low-environmental impact.

METHODS AND RESULTS: Utilizing metagenomic techniques, we analyzed the bacterial community dynamics during the depilation process. This investigation revealed a notable increase in microbial diversity and richness in acetic acid treatments compared to water treatments. At the class level, a post-processing decrease in Gammaproteobacteria dominance was observed, while Actinomycetia numbers surged in the acetic acid group. In contrast, the water group showed an increase in Bacteroidia. Order-level analysis indicated reductions in Pseudomonadales and increases in Actinomycetales with acetic acid treatment, whereas Flavobacteriales was more prevalent in water-treated liquors. At the family level, Moraxellaceae decreased and Micrococcaceae increased in the acetic acid group, in contrast to the marked rise of Weeksellaceae in the water group. Temporal analyses further highlighted the evolving bacterial landscapes under different treatments. Moreover, acetic acid treatment fostered a stable microbial community, beneficial for sustainable leather processing. Functional pathways were predicted using PICRUSt2. It showed that significantly enriched degradation pathways in the water group were less abundant in the acetic acid group, potentially preventing substrate matrix damage during depilation.

CONCLUSION: The study underscores the transformative potential of acetic acid for the leather industry, offering a pathway to reduce pollution while maintaining economic viability. By enhancing our understanding of microbial interactions during depilation, this study opens avenues for refining these eco-friendly techniques. Our findings advocate for a shift towards greener depilation methods and contribute to the broader dialogue on sustainable manufacturing practices, emphasizing the importance of leveraging indigenous microbial communities for environmental and economic gains.}, } @article {pmid39293760, year = {2024}, author = {Chen, L and Zhang, P and Li, Y and Liang, J and Zhang, G}, title = {Genome-centric metagenomic analysis reveals mechanisms of quorum sensing promoting anaerobic digestion under sulfide stress: Syntrophic metabolism and microbial self-adaptation.}, journal = {The Science of the total environment}, volume = {954}, number = {}, pages = {176240}, doi = {10.1016/j.scitotenv.2024.176240}, pmid = {39293760}, issn = {1879-1026}, mesh = {*Quorum Sensing ; *Sulfides/metabolism ; Anaerobiosis ; Metagenomics ; Methane/metabolism ; Bacteria/metabolism ; Acyl-Butyrolactones/metabolism ; }, abstract = {Sulfide stress is a common inhibition factor in anaerobic digestion systems with sulfur-rich feedstocks. Quorum sensing (QS) signaling molecule N-acyl-homoserine lactones (AHLs) possess positive effect on promoting anaerobic digestion. However, the micro-biological mechanisms of AHLs affecting syntrophic metabolism and microbial self-adaptation have not yet been deciphered in anaerobic digestion under sulfide stress. In this study, the CH4 production increased by 21.34 % at 20 μM AHLs addition in anaerobic digestion under sulfide stress. AHLs contributed to establishing potential syntrophic relationship between acidifying bacteria (unclassified_o__Bacteroidales, Lentimicrobium, Acetoanaerobium, Longilinea, and Sphaerochaetaa) and Methanothrix. AHLs promoted syntrophic metabolism by boosting microbial metabolic activity and interspecies electron transfer (IET) process under sulfide stress. For microbial metabolic activity, AHLs promoted the key enzyme synthesis in acidogenesis and methanogenesis. For IET process, AHLs promoted the assembly and synthesis of conductive pili, and synthesis and secretion of riboflavin. Furthermore, AHLs promoted microbial self-adaptation including two component system, lipopolysaccharide biosynthesis, and DNA repair, which were important evidences that microbial resistance to sulfide stress was enhanced by AHLs. Microbial self-adaptation provided favorable foundation and safeguard for syntrophic metabolisms under sulfide stress. These findings deciphered the micro-biological mechanisms of AHLs enhancing anaerobic digestion under sulfide stress.}, } @article {pmid39293510, year = {2024}, author = {Zhang, T and Li, H and Jiang, M and Hou, H and Gao, Y and Li, Y and Wang, F and Wang, J and Peng, K and Liu, YX}, title = {Nanopore sequencing: flourishing in its teenage years.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {51}, number = {12}, pages = {1361-1374}, doi = {10.1016/j.jgg.2024.09.007}, pmid = {39293510}, issn = {1673-8527}, mesh = {Humans ; Genomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; *Nanopore Sequencing/methods ; Sequence Analysis, DNA/methods ; }, abstract = {Over the past decade, nanopore sequencing has experienced significant advancements and changes, transitioning from an initially emerging technology to a significant instrument in the field of genomic sequencing. However, as advancements in next-generation sequencing technology persist, nanopore sequencing also improves. This paper reviews the developments, applications, and outlook on nanopore sequencing technology. Currently, nanopore sequencing supports both DNA and RNA sequencing, making it widely applicable in areas such as telomere-to-telomere (T2T) genome assembly, direct RNA sequencing (DRS), and metagenomics. The openness and versatility of nanopore sequencing have established it as a preferred option for an increasing number of research teams, signaling a transformative influence on life science research. As the nanopore sequencing technology advances, it provides a faster, more cost-effective approach with extended read lengths, demonstrating the significant potential for complex genome assembly, pathogen detection, environmental monitoring, and human disease research, offering a fresh perspective in sequencing technologies.}, } @article {pmid39293343, year = {2024}, author = {Mao, TQ and Zhang, Y and Ou, YF and Li, XF and Zheng, YL and Liang, X and Liu, M and Hou, LJ and Dong, HP}, title = {Temperature differentially regulates estuarine microbial N2O production along a salinity gradient.}, journal = {Water research}, volume = {267}, number = {}, pages = {122454}, doi = {10.1016/j.watres.2024.122454}, pmid = {39293343}, issn = {1879-2448}, mesh = {*Nitrous Oxide/metabolism ; *Salinity ; *Temperature ; *Estuaries ; Denitrification ; Bacteria/metabolism ; }, abstract = {Nitrous oxide (N2O) is atmospheric trace gas that contributes to climate change and affects stratospheric and ground-level ozone concentrations. Ammonia oxidizers and denitrifiers contribute to N2O emissions in estuarine waters. However, as an important climate factor, how temperature regulates microbial N2O production in estuarine water remains unclear. Here, we have employed stable isotope labeling techniques to demonstrate that the N2O production in estuarine waters exhibited differential thermal response patterns between nearshore and offshore regions. The optimal temperatures (Topt) for N2O production rates (N2OR) were higher at nearshore than offshore sites. [15]N-labeled nitrite ([15]NO2[-]) experiments revealed that at the nearshore sites dominated by ammonia-oxidizing bacteria (AOB), the thermal tolerance of [15]N-N2OR increases with increasing salinity, suggesting that N2O production by AOB-driven nitrifier denitrification may be co-regulated by temperature and salinity. Metatranscriptomic and metagenomic analyses of enriched water samples revealed that the denitrification pathway of AOB is the primary source of N2O, while clade II N2O-reducers dominated N2O consumption. Temperature regulated the expression patterns of nitrite reductase (nirK) and nitrous oxide reductase (nosZ) genes from different sources, thereby influencing N2O emissions in the system. Our findings contribute to understanding the sources of N2O in estuarine waters and their response to global warming.}, } @article {pmid39293338, year = {2024}, author = {Bakir-Gungor, B and Temiz, M and Inal, Y and Cicekyurt, E and Yousef, M}, title = {CCPred: Global and population-specific colorectal cancer prediction and metagenomic biomarker identification at different molecular levels using machine learning techniques.}, journal = {Computers in biology and medicine}, volume = {182}, number = {}, pages = {109098}, doi = {10.1016/j.compbiomed.2024.109098}, pmid = {39293338}, issn = {1879-0534}, mesh = {*Colorectal Neoplasms/microbiology/genetics/metabolism ; Humans ; *Machine Learning ; *Biomarkers, Tumor/genetics ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Metagenome/genetics ; Software ; }, abstract = {Colorectal cancer (CRC) ranks as the third most common cancer globally and the second leading cause of cancer-related deaths. Recent research highlights the pivotal role of the gut microbiota in CRC development and progression. Understanding the complex interplay between disease development and metagenomic data is essential for CRC diagnosis and treatment. Current computational models employ machine learning to identify metagenomic biomarkers associated with CRC, yet there is a need to improve their accuracy through a holistic biological knowledge perspective. This study aims to evaluate CRC-associated metagenomic data at species, enzymes, and pathway levels via conducting global and population-specific analyses. These analyses utilize relative abundance values from human gut microbiome sequencing data and robust classification models are built for disease prediction and biomarker identification. For global CRC prediction and biomarker identification, the features that are identified by SelectKBest (SKB), Information Gain (IG), and Extreme Gradient Boosting (XGBoost) methods are combined. Population-based analysis includes within-population, leave-one-dataset-out (LODO) and cross-population approaches. Four classification algorithms are employed for CRC classification. Random Forest achieved an AUC of 0.83 for species data, 0.78 for enzyme data and 0.76 for pathway data globally. On the global scale, potential taxonomic biomarkers include ruthenibacterium lactatiformanas; enzyme biomarkers include RNA 2' 3' cyclic 3' phosphodiesterase; and pathway biomarkers include pyruvate fermentation to acetone pathway. This study underscores the potential of machine learning models trained on metagenomic data for improved disease prediction and biomarker discovery. The proposed model and associated files are available at https://github.com/TemizMus/CCPRED.}, } @article {pmid39288738, year = {2024}, author = {Cai, P and Korem, T}, title = {Microsynteny is a powerful front for microbial strain tracking.}, journal = {Cell reports methods}, volume = {4}, number = {9}, pages = {100862}, pmid = {39288738}, issn = {2667-2375}, mesh = {*Metagenomics/methods ; Bacteria/genetics/classification ; Software ; }, abstract = {Genomic diversity within species can be driven by both point mutations and larger structural variations, but so far, strain-tracking approaches have focused mostly on the former. In a recent issue of Nature Biotechnology, Ley and colleagues[1] introduce SynTracker, a tool designed for scalable strain tracking with microsynteny in low-coverage metagenomic settings.}, } @article {pmid39293053, year = {2024}, author = {Quarton, S and Livesey, A and Jeff, C and Hatton, C and Scott, A and Parekh, D and Thickett, D and McNally, A and Sapey, E}, title = {Metagenomics in the Diagnosis of Pneumonia: Protocol for a Systematic Review.}, journal = {JMIR research protocols}, volume = {13}, number = {}, pages = {e57334}, pmid = {39293053}, issn = {1929-0748}, mesh = {Humans ; *Metagenomics/methods ; *Pneumonia/diagnosis/microbiology ; Systematic Reviews as Topic ; High-Throughput Nucleotide Sequencing/methods ; Pneumonia, Ventilator-Associated/diagnosis/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; }, abstract = {BACKGROUND: Causative pathogens are currently identified in only a minority of pneumonia cases, which affects antimicrobial stewardship. Metagenomic next-generation sequencing (mNGS) has potential to enhance pathogen detection due to its sensitivity and broad applicability. However, while studies have shown improved sensitivity compared with conventional microbiological methods for pneumonia diagnosis, it remains unclear whether this can translate into clinical benefit. Most existing studies focus on patients who are ventilated, readily allowing for analysis of bronchoalveolar lavage fluid (BALF). The impact of sample type on the use of metagenomic analysis remains poorly defined. Similarly, previous studies rarely differentiate between the types of pneumonia involved-community-acquired pneumonia (CAP), hospital-acquired pneumonia (HAP), or ventilator-associated pneumonia (VAP)-which have different clinical profiles.

OBJECTIVE: This study aims to determine the clinical use of mNGS in CAP, HAP, and VAP, compared with traditional microbiological methods.

METHODS: We aim to review all studies (excluding case reports of a series of fewer than 10 people) of adult patients with suspected or confirmed pneumonia that compare metagenomic analysis with traditional microbiology techniques, including culture, antigen-based testing, and polymerase chain reaction-based assays. Relevant studies will be identified through systematic searches of the Embase, MEDLINE, Scopus, and Cochrane CENTRAL databases. Screening of titles, abstracts, and subsequent review of eligible full texts will be done by 2 separate reviewers (SQ and 1 of AL, CJ, or CH), with a third clinician (ES) providing adjudication in case of disagreement. Our focus is on the clinical use of metagenomics for patients with CAP, HAP, and VAP. Data extracted will focus on clinically important outcomes-pathogen positivity rate, laboratory turnaround time, impact on clinical decision-making, length of stay, and 30-day mortality. Subgroup analyses will be performed based on the type of pneumonia (CAP, HAP, or VAP) and sample type used. The risk of bias will be assessed using the QUADAS-2 tool for diagnostic accuracy studies. Outcome data will be combined in a random-effects meta-analysis, and where this is not possible, a narrative synthesis will be undertaken.

RESULTS: The searches were completed with the assistance of a medical librarian on January 13, 2024, returning 5750 records. Screening and data extraction are anticipated to be completed by September 2024.

CONCLUSIONS: Despite significant promise, the impact of metagenomic analysis on clinical pathways remains unclear. Furthermore, it is unclear whether the use of this technique will alter depending on whether the pneumonia is a CAP, HAP, or VAP or the sample type that is collected. This systematic review will assess the current evidence base to support the benefit of clinical outcomes for metagenomic analysis, depending on the setting of pneumonia diagnosis or specimen type used. It will identify areas where further research is needed to advance this methodology into routine care.

TRIAL REGISTRATION: PROSPERO CRD42023488096; https://tinyurl.com/3suy7cma.

DERR1-10.2196/57334.}, } @article {pmid39292721, year = {2024}, author = {Bastien, GE and Cable, RN and Batterbee, C and Wing, AJ and Zaman, L and Duhaime, MB}, title = {Virus-host interactions predictor (VHIP): Machine learning approach to resolve microbial virus-host interaction networks.}, journal = {PLoS computational biology}, volume = {20}, number = {9}, pages = {e1011649}, pmid = {39292721}, issn = {1553-7358}, mesh = {*Machine Learning ; Humans ; *Viruses/genetics ; *Computational Biology/methods ; *Host-Pathogen Interactions/genetics/physiology ; Host Microbial Interactions/genetics/physiology ; }, abstract = {Viruses of microbes are ubiquitous biological entities that reprogram their hosts' metabolisms during infection in order to produce viral progeny, impacting the ecology and evolution of microbiomes with broad implications for human and environmental health. Advances in genome sequencing have led to the discovery of millions of novel viruses and an appreciation for the great diversity of viruses on Earth. Yet, with knowledge of only "who is there?" we fall short in our ability to infer the impacts of viruses on microbes at population, community, and ecosystem-scales. To do this, we need a more explicit understanding "who do they infect?" Here, we developed a novel machine learning model (ML), Virus-Host Interaction Predictor (VHIP), to predict virus-host interactions (infection/non-infection) from input virus and host genomes. This ML model was trained and tested on a high-value manually curated set of 8849 virus-host pairs and their corresponding sequence data. The resulting dataset, 'Virus Host Range network' (VHRnet), is core to VHIP functionality. Each data point that underlies the VHIP training and testing represents a lab-tested virus-host pair in VHRnet, from which meaningful signals of viral adaptation to host were computed from genomic sequences. VHIP departs from existing virus-host prediction models in its ability to predict multiple interactions rather than predicting a single most likely host or host clade. As a result, VHIP is able to infer the complexity of virus-host networks in natural systems. VHIP has an 87.8% accuracy rate at predicting interactions between virus-host pairs at the species level and can be applied to novel viral and host population genomes reconstructed from metagenomic datasets.}, } @article {pmid39292303, year = {2024}, author = {Singh, K and Malla, MA and Kumar, A and Yadav, S}, title = {Biological monitoring of soil pollution caused by two different zinc species using earthworms.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {47}, pages = {57789-57803}, pmid = {39292303}, issn = {1614-7499}, mesh = {*Oligochaeta/drug effects ; Animals ; *Soil Pollutants/toxicity ; *Zinc Oxide/toxicity ; *Soil/chemistry ; *Zinc/toxicity ; *Environmental Monitoring ; Metal Nanoparticles/toxicity ; }, abstract = {Zinc oxide nanoparticles (ZnO-NPs) are commonly used in both commercial and agricultural sectors. As a result, ZnO-NPs are extensively discharged into soil ecosystems, creating a significant environmental issue. Therefore, it is crucial to assess their influence on the soil ecology to ensure its secure and enduring utilization in the future. The exact degree of toxicity associated with ZnO-NPs and their ionic form is still uncertain. To address the challenges, the study used the soil bioindicator earthworm species Eudrilus eugeniae as an experimental model to evaluate the effects of two zinc species (ZnO-NPs and ZnCl2) at 100, 250, 500, and 750 mg kg[-1] and control (0 mg kg[-1]) in garden soil over 28 days. The investigation also examined the impact of exposure on survival, reproduction, neuro-biomarker, avoidance behavior, and accumulation. The highest avoidance rates were 27.5% for ZnO-NP and 37.5% for ZnCl2 at 750 mg kg[-1]. ZnCl2 treatment reduced juvenile production by 3.73 ± 1.73, while ZnO-NPs showed 4.67 ± 1.15. At 750 mg kg[-1], soils with ZnCl2 (63.3%) demonstrated lower survival rates than those with ZnO-NPs (53.3%), likely because of higher Zn ion levels. After 28 days of exposure, ZnCl2 (536.32 ± 11 mol min[-1]) activated AChE enzymes more than ZnO-NPs (497.7 ± 59 mol min[-1]) at the same dose, compared to control (145.88 ± 28 to 149.41 ± 23 mol min[-1]). Nanoparticles and zinc ions bioaccumulated and reacted negatively with the neurotoxic marker AChE, affecting earthworm reproduction and behavior. However, earthworms exposed to ZnCl2 exhibited less intestinal Zn than those exposed to NPs. The present work contradicts the finding that ZnO-NPs have hazardous effects on soil organisms. The results indicate that earthworm E. eugeniae may significantly affect soil metal uptake from metallic nanoparticles (NPs). This may help design NP soil pollution mitigation strategies. The study offers valuable information for establishing a relationship between the environmental toxicity of ZnO-NPs and soil ecosystems.}, } @article {pmid39290858, year = {2024}, author = {Zhou, G and Li, J and Liang, X and Yang, B and He, X and Tang, H and Guo, H and Liu, G and Cui, W and Chen, Y and Yang, Y}, title = {Multi-omics revealed the mechanism of feed efficiency in sheep by the combined action of the host and rumen microbiota.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {18}, number = {}, pages = {367-379}, pmid = {39290858}, issn = {2405-6383}, abstract = {This study was conducted to investigate potential regulatory mechanisms of feed efficiency (FE) in sheep by linking rumen microbiota with its host by the multi-omics analysis. One hundred and ninety-eight hybrid female sheep (initial body weight = 30.88 ± 4.57 kg; 4-month-old) were selected as candidate sheep. Each test sheep was fed in an individual pen for 60 days, and the residual feed intake (RFI) was calculated. The ten candidate sheep with the highest RFI were divided into the Low-FE group, and the ten with the lowest RFI were divided into the High-FE group, all selected for sample collection. The RFI, average daily gain and average daily feed intake were highly significantly different between the two experimental groups (P < 0.05). Compared with Low-FE group, the insulin-like growth factor-1 and very low-density lipoprotein in serum and the propionate in rumen significantly increased in High-FE group (P < 0.01), but the acetate:propionate ratio in rumen significantly decreased in High-FE group (P = 0.034). Metagenomics revealed Selenomonas ruminantium, Selenomonas sp. and Faecalibacterium prausnitzi i were key bacteria, and increased abundance of the genes encoding the enzymes for cellulose degradation and production of propionate in High-FE group. The results of proteomics and section showed the rumen papilla length (P < 0.001) and expression of carbonic anhydrase and Na[+]/K[+]-ATPase were significantly higher in High-FE group (P < 0.05). On the other hand, the acetyl-CoA content significantly increased in the liver of High-FE group (P = 0.002). The relative expression levels of insulin-like growth factor-1 and apolipoprotein A4 genes were significantly up-regulated in the liver of High-FE group (P < 0.01), but relative expression level of monoacylglycerol O-acyltransferase 3 gene was significantly down-regulated (P = 0.037). These findings provide the mechanism by which the collaborative interaction between rumen microbiota fermentation and host uptake and metabolism of fermentation products impacts feed efficiency traits in sheep.}, } @article {pmid39290728, year = {2024}, author = {Scholpp, AC and Schilbert, HM and Viehöver, P and Weisshaar, B and Beckstette, M and Neumann, JM and Bednarz, H and Niehaus, K}, title = {Differential gene expression in leaves and roots of Hydrangea serrata treated with aluminium chloride.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1412189}, pmid = {39290728}, issn = {1664-462X}, abstract = {Hydrangea serrata, also knowen as the Japanese tea hortensia, is known for its sweet taste and health properties of bevarages produced from this plant. The H. serrata 3,4-dihydroisocoumarins, hydrangenol and phyllodulcin harbour a variety of biological activities and pharmacological properties. Therefore, a detailed understanding of dihydroisocoumarin biosynthesis in H. serrata is of major interest. Their biosynthesis is assumed to be enhanced by elicitors and mediated by polyketide synthases like in cases of phenylpropanoid derived phytoalexins. A de-novo transcriptome assembly of leaves and roots from the aluminium chloride treatment group versus the control group alongside with annotation was generated. Secondary plant metabolites were analysed by LC-MS. It revealed that a terpene synthase and a triterpenoid synthase gene as well as lignin biosynthesis encoding genes were upregulated in roots. Many genes for transporters, glycosyl, and other transferases as well as glycosylases were found to be differentially expressed in both organs. As no differentially expressed polyketide synthase gene homolog was found, the relative leaf and root 3,4-dihydroisocoumarin content was analysed by LC-MS measurement. Although Hydrangea species are known for their aluminium detoxification using phenylpropanoid-derived compounds, the levels of 3,4- dihydroisocoumarins were not enhanced. In this metabolite analysis, an organ- specific accumulation profile of hydrangenol, phyllodulcin, hydrangeic acid and their mono- and di-glycosides was figured out.}, } @article {pmid39290662, year = {2024}, author = {Thormar, EA and Hansen, SB and Jørgensen, LVG and Limborg, MT}, title = {Sampling fish gut microbiota - A genome-resolved metagenomic approach.}, journal = {Ecology and evolution}, volume = {14}, number = {9}, pages = {e70302}, pmid = {39290662}, issn = {2045-7758}, abstract = {Despite a surge in microbiota-focused studies in teleosts, few have reported functional data on whole metagenomes as it has proven difficult to extract high biomass microbial DNA from fish intestinal samples. The zebrafish is a promising model organism in functional microbiota research, yet studies on the functional landscape of the zebrafish gut microbiota through shotgun based metagenomics remain scarce. Thus, a consensus on an appropriate sampling method accurately representing the zebrafish gut microbiota, or any fish species is lacking. Addressing this, we systematically tested four methods of sampling the zebrafish gut microbiota: collection of faeces from the tank, the whole gut, intestinal content, and the application of ventral pressure to facilitate extrusion of gut material. Additionally, we included water samples as an environmental control to address the potential influence of the environmental microbiota on each sample type. To compare these sampling methods, we employed a combination of genome-resolved metagenomics and 16S metabarcoding techniques. We observed differences among sample types on all levels including sampling, bioinformatic processing, metagenome co-assemblies, generation of metagenome-assembled genomes (MAGs), functional potential, MAG coverage, and population level microdiversity. Comparison to the environmental control highlighted the potential impact of the environmental contamination on data interpretation. While all sample types tested are informative about the zebrafish gut microbiota, the results show that optimal sample type for studying fish microbiomes depends on the specific objectives of the study, and here we provide a guide on what factors to consider for designing functional metagenome-based studies on teleost microbiomes.}, } @article {pmid39289490, year = {2024}, author = {Bai, B and Tuerxun, G and Tuerdi, A and Maimaiti, R and Sun, Y and Abudukerimu, A}, title = {Analysis of vaginal flora diversity and study on the role of Porphyromonas asaccharolytica in promoting IL-1β in regulating cervical cancer.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {21731}, pmid = {39289490}, issn = {2045-2322}, support = {2022D01C185//Natural Science Foundation of the Xinjiang Uygur Autonomous Region/ ; }, mesh = {Female ; Humans ; *Uterine Cervical Neoplasms/microbiology/virology/pathology/genetics ; *Vagina/microbiology ; *Porphyromonas/genetics/isolation & purification ; *Interleukin-1beta/genetics/metabolism ; *Microbiota/genetics ; Adult ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Papillomavirus Infections/virology/microbiology/complications ; }, abstract = {Cervical cancer, a prevalent malignancy in the female reproductive tract, exhibits a high incidence. Existing evidence indicates a robust correlation between alterations in vaginal flora composition and the progression of cervical cancer. Nevertheless, there is a lack of clarity concerning the specific microorganisms within the vaginal microbiota that are linked to the onset and development of cervical cancer, as well as the mechanisms through which they exert carcinogenic effects. The 16 S ribosomal (rRNA) and metagenomic sequencing technology were used to analyze vaginal microorganisms, and screening for human papillomavirus (HPV) positive cervical cancer-associated microbial markers using fold change in mean bacterial abundance. Moreover, vaginal microenvironmental factors were detected, and the local vaginal inflammatory state in patients with cervical cancer was subjected to assay via qRT-PCR and ELISA. The hub inflammatory genes were screened by transcriptome sequencing after co-culture of bacteria and normal cervical epithelial cells, and an in vitro model was utilized to assess the impacts of inflammatory factors on cervical cancer. Both cervical cancer patients and HPV-positive patients showed significant changes in the composition of the vaginal flora, characterised by a decrease in the abundance of Lactobacillus and an increase in the abundance of a variety of anaerobic bacteria; The microbial sequencing identified Porphyromonas, Porphyromonas_asaccharolytica, and Porphyromonas_uenonis as microbial markers for HPV-associated cervical cancer. Vaginal inflammatory factors in patients with cervical cancer were overexpressed. After Porphyromonas_asaccharolytica intervention on cervical epithelial H8 cells, interleukin (IL)-1β, a hub differential gene, markedly promoted tumor-associated biological behaviors at the in vitro cytological level in cervical cancer. This study for the first demonstrated that Porphyromonas, Porphyromonas_asaccharolytica, and Porphyromonas_uenonis could serve as novel microbial markers for cervical cancer. Moreover, Porphyromonas_asaccharolytica was identified as having the ability to induce the overexpression of inflammatory genes in cervical epithelial cells to create a favorable microenvironment for the onset and development of cervical cancer. The effects of dysbacteriosis on cervical cancer were microbiologically elucidated.}, } @article {pmid39289365, year = {2024}, author = {Peng, X and Wang, S and Wang, M and Feng, K and He, Q and Yang, X and Hou, W and Li, F and Zhao, Y and Hu, B and Zou, X and Deng, Y}, title = {Metabolic interdependencies in thermophilic communities are revealed using co-occurrence and complementarity networks.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {8166}, pmid = {39289365}, issn = {2041-1723}, mesh = {*Metabolic Networks and Pathways/genetics ; *Archaea/genetics/metabolism ; *Bacteria/metabolism/genetics/classification ; *Metagenome/genetics ; *Microbiota ; Hot Springs/microbiology ; Phylogeny ; Microbial Interactions ; Hot Temperature ; }, abstract = {Microbial communities exhibit intricate interactions underpinned by metabolic dependencies. To elucidate these dependencies, we present a workflow utilizing random matrix theory on metagenome-assembled genomes to construct co-occurrence and metabolic complementarity networks. We apply this approach to a temperature gradient hot spring, unraveling the interplay between thermal stress and metabolic cooperation. Our analysis reveals an increase in the frequency of metabolic interactions with rising temperatures. Amino acids, coenzyme A derivatives, and carbohydrates emerge as key exchange metabolites, forming the foundation for syntrophic dependencies, in which commensalistic interactions take a greater proportion than mutualistic ones. These metabolic exchanges are most prevalent between phylogenetically distant species, especially archaea-bacteria collaborations, as a crucial adaptation to harsh environments. Furthermore, we identify a significant positive correlation between basal metabolite exchange and genome size disparity, potentially signifying a means for streamlined genomes to leverage cooperation with metabolically richer partners. This phenomenon is also confirmed by another composting system which has a similar wide range of temperature fluctuations. Our workflow provides a feasible way to decipher the metabolic complementarity mechanisms underlying microbial interactions, and our findings suggested environmental stress regulates the cooperative strategies of thermophiles, while these dependencies have been potentially hardwired into their genomes during co-evolutions.}, } @article {pmid39288877, year = {2024}, author = {Wang, X and Zhang, Y and Zhou, H and Wu, M and Shan, J and Yan, X}, title = {Investigating drivers of N2 loss and N2O reducers in paddy soils across China.}, journal = {The Science of the total environment}, volume = {954}, number = {}, pages = {176287}, doi = {10.1016/j.scitotenv.2024.176287}, pmid = {39288877}, issn = {1879-1026}, mesh = {China ; *Soil/chemistry ; *Oryza ; *Soil Microbiology ; *Nitrogen/analysis ; *Agriculture/methods ; Nitrous Oxide/analysis ; Denitrification ; Environmental Monitoring ; }, abstract = {Denitrification plays a pivotal role in nitrogen (N) cycling in rice paddies, significantly impacting N loss and greenhouse gas emissions. Accurate quantification of net N2 emissions from paddy fields is therefore essential for improving fertilizer N use efficiency. However, challenges in directly measuring gaseous N2 hinder our understanding of microbially-mediated N loss in paddy soils at large scales. In this study, we investigated net N2 loss and its influencing factors in 45 paddy soils across China using membrane inlet mass spectrometry and N2/Ar technique, complemented by microbial community analysis via metagenomics. Potential N2 loss rates varied from 0.41 to 3.58 nmol N g[-1] h[-1], with no significant regional differences. However, soils from rice-upland rotation (1.72 ± 0.64 nmol N g[-1] h[-1]) and mono-rice cropping systems (1.41 ± 0.53 nmol N g[-1] h[-1]) exhibited higher N2 loss rates compared to double-rice cropping soils (1.13 ± 0.62 nmol N g[-1] h[-1]). Our results revealed a unimodal relationship between soil N2 loss rates and soil pH, with N2O reducers and soil properties primarily regulating regional variations in N2 loss. Significant ecological differentiation was observed within both nosZ Clade I and Clade II, with soil pH emerging as the key factor shaping their community composition. Specifically, in rice-upland rotations, soil moisture and pH significantly influenced nosZ Clade I, while in double-rice cropping systems, soil texture and pH were the main factors affecting nosZ Clade II, thereby driving N2 loss. These findings enhance our understanding of N2 loss dynamics in paddy soil ecosystems, underscoring the critical role of N2O reducers on microbial-derived N2 loss and highlighting the importance of developing strategies to mitigate N2O emissions by balancing N2 loss through the manipulation of N2O-reducing and N2O-producing microbes.}, } @article {pmid39288380, year = {2024}, author = {Ye, LY and Zhao, XL and Qin, JJ and Lin, J}, title = {Metagenomic next-generation sequencing assisted in the successful treatment of pneumonia caused by Talaromyces marneffei in an immunocompetent patient.}, journal = {Journal of infection in developing countries}, volume = {18}, number = {8}, pages = {1296-1300}, doi = {10.3855/jidc.19061}, pmid = {39288380}, issn = {1972-2680}, mesh = {Humans ; *Talaromyces/genetics/isolation & purification ; Male ; *High-Throughput Nucleotide Sequencing ; Middle Aged ; *Metagenomics/methods ; *Voriconazole/therapeutic use ; *Antifungal Agents/therapeutic use ; Pneumonia/microbiology/drug therapy ; Mycoses/microbiology/drug therapy/diagnosis ; Treatment Outcome ; Immunocompetence ; }, abstract = {INTRODUCTION: Talaromyces marneffei (T. marneffei), a kind of endemic opportunistic pathogen, was previously thought to occur in HIV-positive individuals and non-HIV hosts with impaired immune function. However, the infection of T. marneffei in patient with normal immune function was rarely reported.

CASE PRESENTATION: We report a case of severe pneumonia caused by T. marneffei in an immunocompetent and HIV-negative patient, which was rapidly confirmed by metagenomics next-generation sequencing (mNGS) and treated successfully. The patient was a previously healthy 63-year-old male, who was admitted to hospital with fever for 11 days, cough and sputum for 1 week, and chest distress for 4 days. The infection of T. marneffei was quickly determined by alveolar lavage under bedside bronchoscope and mNGS test.

RESULTS: Patient's condition improved rapidly after voriconazole treatment, and he was evaluated as a HIV-negative case of T. marneffei infection with normal immune function. This is a sporadic case of T. marneffei in non-endemic areas, and mNGS played a very important role in the treatment of the disease. The patient's immune function was relatively normal which was rare in clinical practice.}, } @article {pmid39287428, year = {2024}, author = {Andreani-Gerard, CM and Cambiazo, V and González, M}, title = {Biosynthetic gene clusters from uncultivated soil bacteria of the Atacama Desert.}, journal = {mSphere}, volume = {9}, number = {10}, pages = {e0019224}, pmid = {39287428}, issn = {2379-5042}, support = {CN2021-044//Agencia Nacional de Investigación y Desarrollo (ANID)/ ; 1201278//ANID | Fondo Nacional de Desarrollo Científico y Tecnológico (FONDECYT)/ ; 1241424//ANID | Fondo Nacional de Desarrollo Científico y Tecnológico (FONDECYT)/ ; 1211893//ANID | Fondo Nacional de Desarrollo Científico y Tecnológico (FONDECYT)/ ; }, mesh = {*Soil Microbiology ; *Multigene Family ; *Desert Climate ; *Bacteria/genetics/classification/metabolism ; *Metagenome ; *Metagenomics ; Phylogeny ; Biosynthetic Pathways/genetics ; Chile ; Genome, Bacterial ; }, abstract = {Soil microorganisms mediate several biological processes through the secretion of natural products synthesized in specialized metabolic pathways, yet functional characterization in ecological contexts remains challenging. Using culture-independent metagenomic analyses of microbial DNA derived directly from soil samples, we examined the potential of biosynthetic gene clusters (BGCs) from six bacterial communities distributed along an altitudinal gradient of the Andes Mountains in the Atacama Desert. We mined 38 metagenome-assembled genomes (MAGs) and identified 168 BGCs. Results indicated that most predicted BGCs were classified as non-ribosomal-peptides (NRP), post-translational modified peptides (RiPP), and terpenes, which were mainly identified in genomes of species from Acidobacteriota and Proteobacteria phyla. Based on BGC composition according to types of core biosynthetic genes, six clusters of MAGs were observed, three of them with predominance for a single phylum, of which two also showed specificity to a single sampling site. Comparative analyses of accessory genes in BGCs showed associations between membrane transporters and other protein domains involved in specialized metabolism with classes of biosynthetic cores, such as resistance-nodulation-cell division (RND) multidrug efflux pumps with RiPPs and the iron-dependent transporter TonB with terpenes. Our findings increase knowledge regarding the biosynthetic potential of uncultured bacteria inhabiting pristine locations from one of the oldest and driest nonpolar deserts on Earth.IMPORTANCEMuch of what we know about specialized metabolites in the Atacama Desert, including Andean ecosystems, comes from isolated microorganisms intended for drug development and natural product discovery. To complement research on the metabolic potential of microbes in extreme environments, comparative analyses on functional annotations of biosynthetic gene clusters (BGCs) from uncultivated bacterial genomes were carried out. Results indicated that in general, BGCs encode for structurally unique metabolites and that metagenome-assembled genomes did not show an obvious relationship between the composition of their core biosynthetic potential and taxonomy or geographic distribution. Nevertheless, some members of Acidobacteriota showed a phylogenetic relationship with specific metabolic traits and a few members of Proteobacteria and Desulfobacterota exhibited niche adaptations. Our results emphasize that studying specialized metabolism in environmental samples may significantly contribute to the elucidation of structures, activities, and ecological roles of microbial molecules.}, } @article {pmid39287376, year = {2024}, author = {Bucher-Johannessen, C and Senthakumaran, T and Avershina, E and Birkeland, E and Hoff, G and Bemanian, V and Tunsjø, H and Rounge, TB}, title = {Species-level verification of Phascolarctobacterium association with colorectal cancer.}, journal = {mSystems}, volume = {9}, number = {10}, pages = {e0073424}, pmid = {39287376}, issn = {2379-5077}, support = {2020056//Ministry of Health and Care Services | Helse Sør-Øst RHF (sorost)/ ; 2022067//Ministry of Health and Care Services | Helse Sør-Øst RHF (sorost)/ ; 190179//Kreftforeningen (NCS)/ ; 198048//Kreftforeningen (NCS)/ ; 202401/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; *Colorectal Neoplasms/microbiology/pathology ; Male ; Female ; *RNA, Ribosomal, 16S/genetics ; Gastrointestinal Microbiome/genetics ; Norway/epidemiology ; Metagenome ; Middle Aged ; Adenoma/microbiology/genetics ; Aged ; }, abstract = {We have previously demonstrated an association between increased abundance of Phascolarctobacterium and colorectal cancer (CRC) and adenomas in two independent Norwegian cohorts. Here we seek to verify our previous findings using new cohorts and methods. In addition, we characterize lifestyle and sex specificity, the functional potential of the Phascolarctobacterium species, and their interaction with other microbial species. We analyze Phascolarctobacterium with 16S rRNA sequencing, shotgun metagenome sequencing, and species-specific qPCR, using 2350 samples from three Norwegian cohorts-CRCAhus, NORCCAP, and CRCbiome-and a large publicly available data set, curatedMetagenomicData. Using metagenome-assembled genomes from the CRCbiome study, we explore the genomic characteristics and functional potential of the Phascolarctobacterium pangenome. Three species of Phascolarctobacterium associated with adenoma/CRC were consistently detected by qPCR and sequencing. Positive associations with adenomas/CRC were verified for Phascolarctobacterium succinatutens and negative associations were shown for Phascolarctobacterium faecium and adenoma in curatedMetagenomicData. Men show a higher prevalence of P. succinatutens across cohorts. Co-occurrence among Phascolarctobacterium species was low (<6%). Each of the three species shows distinct microbial composition and forms distinct correlation networks with other bacterial taxa, although Dialister invisus was negatively correlated to all investigated Phascolarctobacterium species. Pangenome analyses showed P. succinatutens to be enriched for genes related to porphyrin metabolism and degradation of complex carbohydrates, whereas glycoside hydrolase enzyme 3 was specific to P. faecium.IMPORTANCEUntil now Phascolarctobacterium has been going under the radar as a CRC-associated genus despite having been noted, but overseen, as such for over a decade. We found not just one, but two species of Phascolarctobacterium to be associated with CRC-Phascolarctobacterium succinatutens was more abundant in adenoma/CRC, while Phascolarctobacterium faecium was less abundant in adenoma. Each of them represents distinct communities, constituted by specific microbial partners and metabolic capacities-and they rarely occur together in the same patients. We have verified that P. succinatutens is increased in adenoma and CRC and this species should be recognized among the most important CRC-associated bacteria.}, } @article {pmid39287374, year = {2024}, author = {Vinogradova, E and Mukhanbetzhanov, N and Nurgaziyev, M and Jarmukhanov, Z and Aipova, R and Sailybayeva, A and Bekbossynova, M and Kozhakhmetov, S and Kushugulova, A}, title = {Impact of urbanization on gut microbiome mosaics across geographic and dietary contexts.}, journal = {mSystems}, volume = {9}, number = {10}, pages = {e0058524}, pmid = {39287374}, issn = {2379-5077}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Urbanization ; Male ; Female ; Kazakhstan/epidemiology ; *Diet ; Adult ; Rural Population/statistics & numerical data ; Middle Aged ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Urban Population/statistics & numerical data ; Bacteria/genetics/classification/isolation & purification ; Feces/microbiology ; Young Adult ; }, abstract = {UNLABELLED: This study provides a comprehensive assessment of how urban-rural divides influence gut microbial diversity and composition across the distinct geographical landscapes of Kazakhstan, elucidating the intricate interplay between lifestyle, environment, and gut microbiome. In this prospective cohort study, we enrolled 651 participants from urban centers and rural settlements across Kazakhstan, following ethical approval and informed consent. Comprehensive demographic, dietary, and stool sample data were collected. 16S rRNA gene sequencing and shotgun metagenomics techniques were employed to delineate the intricate patterns of the gut microbiome. A rigorous statistical framework dissected the interplay between urbanization gradients, geography, dietary lifestyles, and microbial dynamics. Our findings demonstrate a stark microbial divide between urban and rural gut ecosystems. The study found significant differences in gut microbiome diversity and composition between urban and rural populations in Kazakhstan. Urban microbiomes exhibited reduced diversity, higher Firmicutes/Bacteroidetes ratios, and increased prevalence of genera Coprococcus and Parasutterella. In contrast, rural populations had greater microbial diversity and abundance of Ligilactobacillus, Sutterella, and Paraprevotella. Urbanization also influenced dietary patterns, with urban areas consuming more salt, cholesterol, and protein, while rural areas had diets richer in carbohydrates and fiber. The study also identified distinct patterns in the prevalence of antibiotic resistance genes and virulence factors between urban and rural gut microbiomes. This study sheds light on how urbanization may be deeply involved in shaping the intricate mosaic of the gut microbiome across Kazakhstan's diverse geographical and dietary landscapes, underscoring the complex interplay between environmental exposures, dietary lifestyles, and the microbial residents inhabiting our intestines.

IMPORTANCE: The study examined gut microbiome composition across diverse geographical locations in Kazakhstan, spanning urban centers and rural settlements. This allows for thoroughly investigating how urbanization gradients and geographic factors shape the gut microbiome. The study's examination of the gut resistome and prevalence of virulence-associated genes provide essential insights into the public health implications of urbanization-driven microbiome alterations. Collecting comprehensive demographic, dietary, and stool sample data enables the researchers to better understand the relationships between urbanization, nutritional patterns, and gut microbiome composition. The findings have important implications for understanding how urbanization-driven microbiome changes may impact human health and well-being, paving the way for tailored interventions to restore a balanced gut microbial ecology.}, } @article {pmid39287279, year = {2024}, author = {Xing, W and Yu, J and Cui, S and Liu, L and Zhi, Y and Zhang, T and Zhou, J}, title = {Analysis of the correlation between gut microbiome imbalance and the development of endometrial cancer based on metagenomics.}, journal = {Medicine}, volume = {103}, number = {37}, pages = {e39596}, pmid = {39287279}, issn = {1536-5964}, mesh = {Humans ; Female ; *Endometrial Neoplasms/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; Case-Control Studies ; Middle Aged ; Prospective Studies ; *Metagenomics/methods ; Aged ; Adult ; }, abstract = {Endometrial cancer (EC) is the most prevalent gynecologic malignancy, with a higher risk in obese women, suggesting the potential involvement of gut microbiota in the progression of EC. However, there is no direct evidence of a connection between EC and the human gut microbiota. Using metagenomic sequencing, we investigated the relationship between gut microbiome imbalance and cancer development in patients with EC. In this prospective case-control study, we included 15 patients with EC based on endometrial biopsy in the case group and 15 women admitted to the hospital for female pelvic floor issues during the same time who did not have endometrial lesions from January 2023 to June 2023 in control group. The microbiota structure of EC cases and controls without benign or malignant endometrial lesions during the same time period was analyzed using metagenomic sequencing technology. We employed Alpha diversity analysis to reflect the richness and diversity of microbial communities. Statistical algorithm Bray-Curtis was utilized to calculate pairwise distances between samples, obtaining a beta diversity distance matrix. Subsequently, hierarchical clustering analysis was conducted based on the distance matrix. The results showed that the composition of bacterial colonies in both groups was dominated by Firmicutes, which had a higher proportion in the control group, followed by Bacteroidetes in the control group and Proteobacteria and Bacteroidetes in the case group. The abundance of Klebsiella (P = .02) was significantly higher, and the abundance of Alistipes (P = .04), Anearobutyricum (P = .01), and bacteria in Firmicutes such as Oscillospira and Catenibacterium was markedly lower in the case group than in the control group. These results demonstrated conclusively that a gut microbiome imbalance was associated with the development of EC.}, } @article {pmid39287139, year = {2024}, author = {Pu, L and Shamir, R}, title = {4CAC: 4-class classifier of metagenome contigs using machine learning and assembly graphs.}, journal = {Nucleic acids research}, volume = {52}, number = {19}, pages = {e94}, pmid = {39287139}, issn = {1362-4962}, support = {1339/18//Israel Science Foundation/ ; //Edmond J. Safra Center for Bioinformatics at Tel-Aviv University/ ; //Planning & Budgeting Committee/ ; //Council for Higher Education/ ; }, mesh = {*Machine Learning ; *Metagenome/genetics ; Bacteria/genetics/classification ; Plasmids/genetics ; Archaea/genetics/classification ; Software ; Metagenomics/methods ; Viruses/genetics/classification ; Contig Mapping/methods ; Algorithms ; }, abstract = {Microbial communities usually harbor a mix of bacteria, archaea, plasmids, viruses and microeukaryotes. Within these communities, viruses, plasmids, and microeukaryotes coexist in relatively low abundance, yet they engage in intricate interactions with bacteria. Moreover, viruses and plasmids, as mobile genetic elements, play important roles in horizontal gene transfer and the development of antibiotic resistance within microbial populations. However, due to the difficulty of identifying viruses, plasmids, and microeukaryotes in microbial communities, our understanding of these minor classes lags behind that of bacteria and archaea. Recently, several classifiers have been developed to separate one or more minor classes from bacteria and archaea in metagenome assemblies. However, these classifiers often overlook the issue of class imbalance, leading to low precision in identifying the minor classes. Here, we developed a classifier called 4CAC that is able to identify viruses, plasmids, microeukaryotes, and prokaryotes simultaneously from metagenome assemblies. 4CAC generates an initial four-way classification using several sequence length-adjusted XGBoost models and further improves the classification using the assembly graph. Evaluation on simulated and real metagenome datasets demonstrates that 4CAC substantially outperforms existing classifiers and combinations thereof on short reads. On long reads, it also shows an advantage unless the abundance of the minor classes is very low. 4CAC runs 1-2 orders of magnitude faster than the other classifiers. The 4CAC software is available at https://github.com/Shamir-Lab/4CAC.}, } @article {pmid39287136, year = {2024}, author = {Pérot, P and Tondeur, L and Moutailler, S and Chrétien, D and Corre-Catelin, N and Vayssier-Taussat, M and Eloit, M and Chirouze, C and Cazorla, C and , }, title = {Broad range molecular detection methods identify only Borrelia spp. in erythema migrans biopsies and blood of tick-bitten patients.}, journal = {One health (Amsterdam, Netherlands)}, volume = {19}, number = {}, pages = {100886}, pmid = {39287136}, issn = {2352-7714}, abstract = {In this multicenter study conducted in France, we challenged the hypothesis of the transmission of pathogens other than Borrelia spp. in 22 patients developing erythema migrans following a tick bite. Using a combination of high-throughput microfluidic PCRs and agnostic metagenomics on skin biopsies and blood samples, no microorganisms other than Borrelia spp. was found.}, } @article {pmid39287058, year = {2024}, author = {Irankhah, L and Khorsand, B and Naghibzadeh, M and Savadi, A}, title = {Analyzing the performance of short-read classification tools on metagenomic samples toward proper diagnosis of diseases.}, journal = {Journal of bioinformatics and computational biology}, volume = {22}, number = {5}, pages = {2450012}, doi = {10.1142/S0219720024500124}, pmid = {39287058}, issn = {1757-6334}, mesh = {*Metagenomics/methods ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; Bacteria/genetics/classification/isolation & purification ; Inflammatory Bowel Diseases/microbiology/diagnosis ; Computational Biology/methods ; Software ; Metagenome ; }, abstract = {Accurate knowledge of the genome, virus and bacteria that have invaded our bodies is crucial for diagnosing many human diseases. The field of bioinformatics encompasses the complex computational methods required for this purpose. Metagenomics employs next-generation sequencing (NGS) technology to study and identify microbial communities in environmental samples. This technique allows for the measurement of the relative abundance of different microbes. Various tools are available for detecting bacterial species in sequenced metagenomic samples. In this study, we focus on well-known taxonomic classification tools such as MetaPhlAn4, Centrifuge, Kraken2, and Bracken, and evaluate their performance at the species level using synthetic and real datasets. The results indicate that MetaPhlAn4 exhibited high precision in identifying species in the simulated dataset, while Kraken2 had the best area under the precision-recall curve (AUPR) performance. Centrifuge, Kraken2, and Bracken showed accurate estimation of species abundances, unlike MetaPhlAn4, which had a higher L2 distance. In the real dataset analysis with samples from an inflammatory bowel disease (IBD) research, MetaPhlAn4, and Kraken2 had faster execution times, with differences in performance at family and species levels among the tools. Enterobacteriaceae and Pasteurellaceae were highlighted as the most abundant families by Centrifuge, Kraken2, and MetaPhlAn4, with variations in abundance among ulcerative colitis (UC), Crohn's disease (CD), and control non-IBD (CN) groups. Escherichia coli (E. coli) has the highest abundance among Enterobacteriaceae species in the CD and UC groups in comparison with the CN group. Bracken overestimated E. coli abundance, emphasizing result interpretation caution. The findings of this research can assist in selecting the appropriate short-read classifier, thereby aiding in the diagnosis of target diseases.}, } @article {pmid39286813, year = {2024}, author = {Luo, J and An, N and Liu, Y and Li, Y}, title = {Disseminated emergomyces orientalis infection in a patient with systemic lupus erythematosus.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1401463}, pmid = {39286813}, issn = {2235-2988}, mesh = {Middle Aged ; Male ; Humans ; *Lupus Erythematosus, Systemic/complications ; Bone Marrow/pathology/microbiology ; Mycoses/microbiology/diagnosis ; Spores, Fungal ; }, abstract = {A case of Eimonosis orientalis was reported in a 52-year-old male farmer who presented with cough, phlegm, fever, headache, and nausea for more than 4 days. Haemophilic cells and fungal spores were identified in the bone marrow smear and confirmed as Aemon orientalis by culture. The same bacteria were also isolated from blood cultures.}, } @article {pmid39286492, year = {2024}, author = {Kouraki, A and Zheng, AS and Miller, S and Kelly, A and Ashraf, W and Bazzani, D and Bonadiman, A and Tonidandel, G and Bolzan, M and Vijay, A and Nightingale, J and Menni, C and Ollivere, BJ and Valdes, AM}, title = {Metagenomic changes in response to antibiotic treatment in severe orthopedic trauma patients.}, journal = {iScience}, volume = {27}, number = {9}, pages = {110783}, pmid = {39286492}, issn = {2589-0042}, abstract = {We investigated changes in microbiome composition and abundance of antimicrobial resistance (AMR) genes post-antibiotic treatment in severe trauma patients. Shotgun sequencing revealed beta diversity (Bray-Curtis) differences between 16 hospitalized multiple rib fractures patients and 10 age- and sex-matched controls (p = 0.043), and between antibiotic-treated and untreated patients (p = 0.015). Antibiotic-treated patients had lower alpha diversity (Shannon) at discharge (p = 0.003) and 12-week post-discharge (p = 0.007). At 12 weeks, they also exhibited a 5.50-fold (95% confidence interval [CI]: 2.86-8.15) increase in Escherichia coli (p = 0.0004) compared to controls. Differential analysis identified nine AMRs that increased in antibiotic-treated compared to untreated patients between hospital discharge and 6 and 12 weeks follow-up (false discovery rate [FDR] < 0.20). Two aminoglycoside genes and a beta-lactamase gene were directly related to antibiotics administered, while five were unrelated. In trauma patients, lower alpha diversity, higher abundance of pathobionts, and increases in AMRs persisted for 12 weeks post-discharge, suggesting prolonged microbiome disruption. Probiotic or symbiotic therapies may offer future treatment avenues.}, } @article {pmid39284445, year = {2024}, author = {Huo, C and Zhang, J and Yang, X and Li, X and Su, Y and Chen, Z}, title = {Dry season irrigation promotes nutrient cycling by reorganizing Eucalyptus rhizosphere microbiome.}, journal = {The Science of the total environment}, volume = {954}, number = {}, pages = {176307}, doi = {10.1016/j.scitotenv.2024.176307}, pmid = {39284445}, issn = {1879-1026}, mesh = {*Eucalyptus ; *Rhizosphere ; *Microbiota ; *Soil Microbiology ; *Agricultural Irrigation/methods ; China ; *Fertilizers ; Phosphorus ; Soil/chemistry ; Nitrogen/metabolism ; Seasons ; Bacteria/metabolism ; }, abstract = {In southern China, seasonal droughts and low soil phosphorus content constrain the productivity of Eucalyptus trees. To understand the rhizosphere microbiome response to the dry season, metagenomic sequencing analysis was used to investigate the 6-year-old Eucalyptus rhizosphere microbiome under four different irrigation and fertilization treatments. The results showed that irrigation and fertilization during the dry season significantly altered the composition of microbiome in the rhizosphere soil of Eucalyptus plantations. The soil physicochemical properties and enzyme activity explained 30.73 % and 29.75 % of the changes in bacterial and fungal community structure in Eucalyptus rhizosphere soil, respectively. Irrigation and fertilization during the dry season significantly altered the physicochemical properties of rhizosphere soil. Compared with the seasonal drought without fertilizer treatment (CK), the dry season irrigation with fertilizer treatment (WF) significantly increased the content of total nitrogen (46.34 %), available nitrogen (37.72 %), available phosphorus (440.9 %), and organic matter (35.34 %). Soil organic matter (OM), pH, and available phosphorus (AP) were key environmental factors influencing the microbial community composition. Moreover, irrigation and fertilization promoted carbon fixation and nitrogen and phosphorus mineralization, increasing soil OM content and the availability of inorganic nitrogen and phosphorus. Meanwhile, compared to the CK, the increase of acid phosphatase (16.81 %), invertase (146.89 %)and urease (59.45 %) in rhizosphere soil under irrigation (W) treatment further proves that dry season irrigation promote the soil carbon, nitrogen and phosphorus cycles. Irrigation and fertilization treatment alleviated the constraints of low phosphorus in southern China's soil, which promoted Eucalyptus productivity. In conclusion, we suggest implementing reasonable irrigation and fertilization strategies in the production practice of Eucalyptus and utilizing microbial resources to improve soil fertility and Eucalyptus productivity.}, } @article {pmid39284373, year = {2024}, author = {Wu, Q and Deng, L and Lan, T and Wang, H and Wang, K and Zhu, H and Zhou, Y and Guo, W}, title = {Outstanding enhancement of caproate production with microwave pyrolyzed highly reductive biochar addition.}, journal = {Bioresource technology}, volume = {413}, number = {}, pages = {131457}, doi = {10.1016/j.biortech.2024.131457}, pmid = {39284373}, issn = {1873-2976}, mesh = {*Charcoal/chemistry ; *Microwaves ; *Oxidation-Reduction ; Pyrolysis ; }, abstract = {The integration of biochar into microbial Chain Elongation (CE) proves to be an effective tool of producing high-value bio-based products. This study innovatively applied biochar fabricated under microwave irradiation with carbon fiber cloth assistance into CE system. Results highlighted that microwave biochar achieved maximal CE efficiency yielding 8 g COD/L, with 3-fold increase to the blank group devoid of any biochar. Microwave biochar also obtained the highest substrate utilization rate of 94 %, while conventional biochar group recorded 90 % and the blank group was of 74 %. Mechanistic insights revealed that the reductive surface properties facilitated CE performance, which is relevant to fostering dominant genera of Parabacteroides, Bacteroides, and Macellibacteroides. By metagenomics, microwave biochar up-regulated functional genes and enzymes involved in CE process including ethanol oxidation, the reverse β-oxidation pathway, and the fatty acid biosynthesis pathway. This study effectively facilitated caproate production by utilizing a new microwave biochar preparation strategy.}, } @article {pmid39283495, year = {2024}, author = {Bellankimath, AB and Chapagain, C and Branders, S and Ali, J and Wilson, RC and Johansen, TEB and Ahmad, R}, title = {Culture and amplification-free nanopore sequencing for rapid detection of pathogens and antimicrobial resistance genes from urine.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {43}, number = {11}, pages = {2177-2190}, pmid = {39283495}, issn = {1435-4373}, mesh = {Humans ; *Urinary Tract Infections/microbiology/diagnosis ; *Nanopore Sequencing/methods ; Bacteria/genetics/isolation & purification/drug effects ; Drug Resistance, Bacterial/genetics ; DNA, Bacterial/genetics ; Urine/microbiology ; }, abstract = {PURPOSE: Urinary Tract Infections (UTIs) are among the most prevalent infections globally. Every year, approximately 150 million people are diagnosed with UTIs worldwide. The current state-of-the-art diagnostic methods are culture-based and have a turnaround time of 2-4 days for pathogen identification and susceptibility testing.

METHODS: This study first establishes an optical density culture-based method for spiking healthy urine samples with the six most prevalent uropathogens. Urine samples were spiked at clinically significant concentrations of 10[3]-10[5] CFU/ml. Three DNA extraction kits (BioStic, PowerFood, and Blood and Tissue) were investigated based on the DNA yield, average processing time, elution volume, and the average cost incurred per extraction. After DNA extraction, the samples were sequenced using MinION and Flongle flow cells.

RESULTS: The Blood and Tissue kit outperformed the other kits based on the investigated parameters. Using nanopore sequencing, all the pathogens and corresponding genes were only identified at a spike concentration of 10[5] CFU/ml, achieved after 10 min and 3 hours of sequencing, respectively. However, some pathogens and antibiotic-resistance genes (ARG) could be identified from spikes at 10[3] colony formation units (CFU/mL). The overall turnaround time was five hours, from sample preparation to sequencing-based identification of pathogen ID and antimicrobial resistance genes.

CONCLUSION: This study demonstrates excellent promise in reducing the time required for informed antibiotic administration from 48 to 72 h to five hours, thereby reducing the number of empirical doses and increasing the chance of saving lives.}, } @article {pmid39283138, year = {2024}, author = {Tarasov, K and Kravchenko, E and Zarubin, M and Yakhnenko, A}, title = {Deep underground metagenome-assembled genomes from hydrothermal spring.}, journal = {Microbiology resource announcements}, volume = {13}, number = {10}, pages = {e0057424}, pmid = {39283138}, issn = {2576-098X}, support = {24-24-00003//Russian Science Foundation (RSF)/ ; 24-24-00003//Russian Science Foundation (RSF)/ ; }, abstract = {We report 19 metagenome-assembled genomes from a deep underground microbial community found in mineralized hydrothermal spring in the Baksan Neutrino Observatory tunnel. The community is predominantly occupied by members of Pseudomonadota (Gamma-, Beta-, and Alphaproteobacteria), Planctomycetota, Myxococcota, Nitrospirota, Cyanobacteria, Gemmatimonadota, and Armatimonadota.}, } @article {pmid39283121, year = {2024}, author = {Machado, DT and Dias, BdC and Cayô, R and Gales, AC and Marques de Carvalho, F and Vasconcelos, ATR}, title = {Uncovering new Firmicutes species in vertebrate hosts through metagenome-assembled genomes with potential for sporulation.}, journal = {Microbiology spectrum}, volume = {12}, number = {11}, pages = {e0211324}, pmid = {39283121}, issn = {2165-0497}, support = {E-26/210.012/2020//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ)/ ; 88887.677436/2022-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)/ ; 402659/2018-0,443805/2018-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; OPP1193112//Bill and Melinda Gates Foundation (GF)/ ; 88887.508687/2020-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)/ ; 302023/2024-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; 307915/2022-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; 312066/2019-8//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; 307145/2021-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; E-26/201.046/2022//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ)/ ; }, mesh = {Animals ; *Spores, Bacterial/genetics/growth & development ; *Phylogeny ; *Metagenome ; *Genome, Bacterial/genetics ; *Firmicutes/genetics/classification ; Humans ; Cattle ; Swine ; Gastrointestinal Microbiome/genetics ; Vertebrates/microbiology ; Poultry/microbiology ; }, abstract = {Metagenome-assembled genomes (MAGs) have contributed to identifying non-culturable microorganisms and understanding their ecological functions. MAGs offer an advantage in investigating sporulation-associated genes, especially given the difficulty of isolating many species residing in the gut microbiota of multiple hosts. Bacterial sporulation is a key survival mechanism with implications for pathogenicity and biotechnology. Here, we investigate MAGs from vertebrate hosts, emphasizing taxonomic identification and identifying sporulation-associated genes in potential novel species within the Firmicutes phylum. We identified potential new species in the classes Clostridia (Borkfalkiaceae, Lachnospiraceae, Monoglobaceae, and Oscillospiraceae families) and Bacilli (Bacillaceae and Erysipelotrichaceae families) through phylogenetic and functional pathway analyses, highlighting their sporulation potential. Our study covers 146 MAGs, 124 of them without refined taxonomic assignments at the family level. We found that Clostridia and Bacilli have unique sporulation gene profiles in the refined family MAGs for cattle, swine, poultry, and human hosts. The presence of genes related to Spo0A regulon, engulfment, and spore cortex in MAGs underscores fundamental mechanisms in sporulation processes in currently uncharacterized species with sporulation potential from metagenomic dark matter. Furthermore, genomic analyses predict sporulation potential based on gene presence, genome size, and metabolic pathways involved in spore formation. We emphasize MAGs covering families not yet characterized through the phylogenetic analysis, and with extensive potential for spore-forming bacteria within Clostridia, Bacilli, UBA4882, and UBA994 classes. These findings contribute to exploring spore-forming bacteria, which provides evidence for novel species diversity in multiple hosts, their adaptive strategies, and potential applications in biotechnology and host health.IMPORTANCESpores are essential for bacterial survival in harsh environments, facilitating their persistence and adaptation. Exploring sporulation-associated genes in metagenome-assembled genomes (MAGs) from different hosts contributes to clinical and biotechnological domains. Our study investigated the extent of genes associated with bacterial sporulation in MAGs from poultry, swine, cattle, and humans, revealing these genes in uncultivated bacteria. We identified potential novel Firmicutes species with sporulation capabilities through phylogenetic and functional analyses. Notably, MAGs belonging to Clostridia, Bacilli, and unknown classes, namely UBA4882 and UBA994, remained uncharacterized at the family level, which raises the hypothesis that sporulation would also be present in these genomes. These findings contribute to our understanding of microbial adaptation and have implications for microbial ecology, underlining the importance of sporulation in Firmicutes across different hosts. Further studies into novel species and their sporulation capability can contribute to bacterial maintenance mechanisms in various organisms and their applications in biotechnology studies.}, } @article {pmid39283083, year = {2024}, author = {Brennan, C and Belda-Ferre, P and Zuffa, S and Charron-Lamoureux, V and Mohanty, I and Ackermann, G and Allaband, C and Ambre, M and Boyer, T and Bryant, M and Cantrell, K and Gonzalez, A and McDonald, D and Salido, RA and Song, SJ and Wright, G and Dorrestein, PC and Knight, R}, title = {Clearing the plate: a strategic approach to mitigate well-to-well contamination in large-scale microbiome studies.}, journal = {mSystems}, volume = {9}, number = {10}, pages = {e0098524}, pmid = {39283083}, issn = {2379-5077}, support = {U19 AG063744/AG/NIA NIH HHS/United States ; U19AG063744//HHS | National Institutes of Health (NIH)/ ; }, mesh = {*Microbiota/genetics ; Humans ; *RNA, Ribosomal, 16S/genetics ; Specimen Handling/methods ; }, abstract = {UNLABELLED: Large-scale studies are essential to answer questions about complex microbial communities that can be extremely dynamic across hosts, environments, and time points. However, managing acquisition, processing, and analysis of large numbers of samples poses many challenges, with cross-contamination being the biggest obstacle. Contamination complicates analysis and results in sample loss, leading to higher costs and constraints on mixed sample type study designs. While many researchers opt for 96-well plates for their workflows, these plates present a significant issue: the shared seal and weak separation between wells leads to well-to-well contamination. To address this concern, we propose an innovative high-throughput approach, termed as the Matrix method, which employs barcoded Matrix Tubes for sample acquisition. This method is complemented by a paired nucleic acid and metabolite extraction, utilizing 95% (vol/vol) ethanol to stabilize microbial communities and as a solvent for extracting metabolites. Comparative analysis between conventional 96-well plate extractions and the Matrix method, measuring 16S rRNA gene levels via quantitative polymerase chain reaction, demonstrates a notable decrease in well-to-well contamination with the Matrix method. Metagenomics, 16S rRNA gene amplicon sequencing (16S), and untargeted metabolomics analysis via liquid chromatography-tandem mass spectrometry (LC-MS/MS) confirmed that the Matrix method recovers reproducible microbial and metabolite compositions that can distinguish between subjects. This advancement is critical for large-scale study design as it minimizes well-to-well contamination and technical variation, shortens processing times, and integrates with automated infrastructure for enhancing sample randomization and metadata generation.

IMPORTANCE: Understanding dynamic microbial communities typically requires large-scale studies. However, handling large numbers of samples introduces many challenges, with cross-contamination being a major issue. It not only complicates analysis but also leads to sample loss and increased costs and restricts diverse study designs. The prevalent use of 96-well plates for nucleic acid and metabolite extractions exacerbates this problem due to their wells having little separation and being connected by a single plate seal. To address this, we propose a new strategy using barcoded Matrix Tubes, showing a significant reduction in cross-contamination compared to conventional plate-based approaches. Additionally, this method facilitates the extraction of both nucleic acids and metabolites from a single tubed sample, eliminating the need to collect separate aliquots for each extraction. This innovation improves large-scale study design by shortening processing times, simplifying analysis, facilitating metadata curation, and producing more reliable results.}, } @article {pmid39283018, year = {2024}, author = {Yu, H and Liu, S and Weng, W and Peng, Y and Cai, X and Zhu, Y and Chen, P and Zhang, D and Liu, H and Zeng, J and Liu, S and He, Z and Yan, Q}, title = {Generational Specific Recruitment of Arsenic- and Antimony-Reducing Microorganisms in Plant Root-Associated Niches for Adapting to Metalloid-Metal Pollution.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c05291}, pmid = {39283018}, issn = {1520-5851}, abstract = {The recruitment of microorganisms by plants can enhance their adaptability to environmental stressors, but how root-associated niches recruit specific microorganisms for adapting to metalloid-metal contamination is not well-understood. This study investigated the generational recruitment of microorganisms in different root niches of Vetiveria zizanioides (V. zizanioides) under arsenic (As) and antimony (Sb) stress. The V. zizanioides was cultivated in As- and Sb-cocontaminated mine soils (MS) and artificial pollution soils (PS) over two generations in controlled conditions. The root-associated microbial communities were analyzed through 16S rRNA, arsC, and aioA gene amplicon and metagenomics sequencing. V. zizanioides accumulated higher As(III) and Sb(III) in its endosphere in MS in the second generation, while its physiological indices in MS were better than those observed in PS. SourceTracker analysis revealed that V. zizanioides in MS recruited As(V)- and Sb(V)-reducing microorganisms (e.g., Sphingomonales and Rhodospirillaceae) into the rhizoplane and endosphere. Metagenomics analysis further confirmed that these recruited microorganisms carrying genes encoding arsenate reductases with diverse carbohydrate degradation abilities were enriched in the rhizoplane and endosphere, suggesting their potential to reduce As(V) and Sb(V) and to decompose root exudates (e.g., xylan and starch). These findings reveal that V. zizanioides selectively recruits As- and Sb-reducing microorganisms to mitigate As-Sb cocontamination during the generational growth, providing insights into novel strategies for enhancing phytoremediation of metalloid-metal contaminants.}, } @article {pmid39282562, year = {2024}, author = {Chang, Y and Zhang, Z and Cai, J and Wang, C and Liu, D and Liu, Z and Xu, C}, title = {Coevolution of specific gut microbiota of Min pig with host cold adaptation through enhanced vitamin B1 synthesis.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1448090}, pmid = {39282562}, issn = {1664-302X}, abstract = {Min pigs exhibit remarkable cold tolerance, where vitamin B1 synthesis by gut microbiota is crucial for the host's energy metabolism. However, the role of this synthesis in cold adaptation of Min pigs are not yet fully understood. This study utilized 16S rRNA amplicon and metagenomic sequencing to examine seasonal variations in the gut microbiota of Min pigs. Results indicated a significant rise in microbial diversity in winter, with the Bacteroidetes group being the most notably increased. The vitamin B1 biosynthetic pathway was significantly enriched during winter, with six significantly upregulated genes (ThiC, ThiD, ThiE, ThiG, ThiH, and ThiL) showing strong evidence of purifying selection. Among the six vitamin B1 synthesis genes significantly upregulated during winter, the increase was mainly due to a marked elevation in several sequences from specific microbial species. Binding energy analysis revealed that, except for ThiL, the average substrate binding energy of the top 10 sequences with the largest seasonal differences was significantly lower than those of the 10 sequences with the smallest differences. Furthermore, most of these sequences were uniquely prevalent in Min pigs and were not found in the homologous sequences of Duroc pigs. Bacteroidetes and Bacteroidales were identified as the primary contributors to these gene sequences. This research provides valuable insights for developing innovative cold-resistant feed and probiotics.}, } @article {pmid39282340, year = {2024}, author = {Singh, H and Wiscovitch-Russo, R and Kuelbs, C and Espinoza, J and Appel, AE and Lyons, RJ and Vashee, S and Förtsch, HEA and Foster, JE and Ramdath, D and Hayes, VM and Nelson, KE and Gonzalez-Juarbe, N}, title = {Multiomic Insights into Human Health: Gut Microbiomes of Hunter-Gatherer, Agropastoral, and Western Urban Populations.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39282340}, issn = {2692-8205}, support = {R01 DK112381/DK/NIDDK NIH HHS/United States ; }, abstract = {Societies with exposure to preindustrial diets exhibit improved markers of health. Our study used a comprehensive multi-omic approach to reveal that the gut microbiome of the Ju/'hoansi hunter-gatherers, one of the most remote KhoeSan groups, exhibit a higher diversity and richness, with an abundance of microbial species lost in the western population. The Ju/'hoansi microbiome showed enhanced global transcription and enrichment of complex carbohydrate metabolic and energy generation pathways. The Ju/'hoansi also show high abundance of short-chain fatty acids that are associated with health and optimal immune function. In contrast, these pathways and their respective species were found in low abundance or completely absent in Western populations. Amino acid and fatty acid metabolism pathways were observed prevalent in the Western population, associated with biomarkers of chronic inflammation. Our study provides the first in-depth multi-omic characterization of the Ju/'hoansi microbiome, revealing uncharacterized species and functional pathways that are associated with health.}, } @article {pmid39282334, year = {2024}, author = {Olivos-Caicedo, KY and Fernandez, F and Daniel, SL and Anantharaman, K and Ridlon, JM and Alves, JMP}, title = {Pangenome analysis of Clostridium scindens : a collection of diverse bile acid and steroid metabolizing commensal gut bacterial strains.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.09.06.610859}, pmid = {39282334}, issn = {2692-8205}, abstract = {Clostridium scindens is a commensal gut bacterium capable of forming the secondary bile acids deoxycholic acid and lithocholic acid from the primary bile acids cholic acid and chenodeoxycholic acid, respectively, as well as converting glucocorticoids to androgens. Historically, only two strains, C. scindens ATCC 35704 and C. scindens VPI 12708, have been characterized in vitro and in vivo to any significant extent. The formation of secondary bile acids is important in maintaining normal gastrointestinal function, in regulating the structure of the gut microbiome, in the etiology of such diseases such as cancers of the GI tract, and in the prevention of Clostridium difficile infection. We therefore wanted to determine the pangenome of 34 cultured strains of C. scindens and a set of 200 metagenome-assembled genomes (MAGs) to understand the variability among strains. The results indicate that the 34 strains of C. scindens have an open pangenome with 12,720 orthologous gene groups, and a core genome with 1,630 gene families, in addition to 7,051 and 4,039 gene families in the accessory and unique (i.e., strain-exclusive) genomes, respectively. The core genome contains 39% of the proteins with predicted metabolic function, and, in the unique genome, the function of storage and processing of information prevails, with 34% of the proteins being in that category. The pangenome profile including the MAGs also proved to be open. The presence of bile acid inducible (bai) and steroid-17,20-desmolase (des) genes was identified among groups of strains. The analysis reveals that C. scindens strains are distributed into two clades, indicating the possible onset of C. scindens separation into two species, confirmed by gene content, phylogenomic, and average nucleotide identity (ANI) analyses. This study provides insight into the structure and function of the C. scindens pangenome, offering a genetic foundation of significance for many aspects of research on the intestinal microbiota and bile acid metabolism.}, } @article {pmid39282326, year = {2024}, author = {Ramani, S and Javornik Cregeen, SJ and Surathu, A and Neill, FH and Muzny, DM and Doddapaneni, H and Menon, VK and Hoffman, KL and Ross, MC and Metcalf, G and Opekun, AR and Graham, DY and Gibbs, RA and Petrosino, JF and Estes, MK and Atmar, RL}, title = {INTRA- AND INTER-HOST EVOLUTION OF HUMAN NOROVIRUS IN HEALTHY ADULTS.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39282326}, issn = {2692-8205}, support = {P01 AI057788/AI/NIAID NIH HHS/United States ; U19 AI144297/AI/NIAID NIH HHS/United States ; }, abstract = {BACKGROUND: Human noroviruses are a leading cause of acute and sporadic gastroenteritis worldwide. The evolution of human noroviruses in immunocompromised persons has been evaluated in many studies. Much less is known about the evolutionary dynamics of human norovirus in healthy adults.

METHODS: We used sequential samples collected from a controlled human infection study with GI.1/Norwalk/US/68 virus to evaluate intra- and inter-host evolution of a human norovirus in healthy adults. Up to 12 samples from day 1 to day 56 post-challenge were sequenced using a norovirus-specific capture probe method.

RESULTS: Complete genomes were assembled, even in samples that were below the limit of detection of standard RT-qPCR assays, up to 28 days post-challenge. Analysis of 123 complete genomes showed changes in the GI.1 genome in all persons, but there were no conserved changes across all persons. Single nucleotide variants resulting in non-synonymous amino acid changes were observed in all proteins, with the capsid VP1 and nonstructural protein NS3 having the largest numbers of changes.

CONCLUSIONS: These data highlight the potential of a new capture-based sequencing approach to assemble human norovirus genomes with high sensitivity and demonstrate limited conserved immune pressure-driven evolution of GI.1 virus in healthy adults.}, } @article {pmid39282201, year = {2024}, author = {Lata, P and Bhargava, V and Gupta, S and Singh, A and Bala, K and Lal, R}, title = {SeqCode: A Nomenclatural Code for Prokaryotes.}, journal = {Indian journal of microbiology}, volume = {64}, number = {3}, pages = {859-866}, pmid = {39282201}, issn = {0046-8991}, abstract = {SeqCode is a nomenclatural code for naming prokaryotes based on genetic information. With the majority of prokaryotes being inaccessible as pure cultures, they are not eligible for naming under the International Code of Nomenclature of Prokaryotes. To address this challenge, a new concept that is SeqCode, which assign names to prokaryotes on the basis of genome sequence, has been announced in 2022. The valid publication of names for prokaryotes based on isolated genome, metagenome-assembled genomes, or single-amplified genome sequences. It operates through a registration portal, SeqCode Registry, where metadata is linked to names and nomenclatural types. This code provides a framework for reproducible nomenclature for all prokaryotes, either culturable or not and facilitates communication across all microbiological disciplines. Additionally, the SeqCode includes provisions for updating and revising names as new data becomes available. By providing a standardized system for naming and classifying these microorganisms based on their genetic information, the SeqCode will facilitate the discovery, understanding and comparison of these microorganisms, helping us to understand their role in the environment and how they contribute to the functioning of the Earth.}, } @article {pmid39282167, year = {2024}, author = {Rangra, S and Sharma, N and Lata, P and Sharma, KB and Kumari, R and Singh, SP and Savitri, }, title = {NGS-Based Metagenomics Depicting Taxonomic and Functional Insights into North-Western Himalayan Hot Springs.}, journal = {Indian journal of microbiology}, volume = {64}, number = {3}, pages = {1099-1109}, pmid = {39282167}, issn = {0046-8991}, abstract = {UNLABELLED: Hot springs have tremendous significance due to their divulging physiochemical features. In the recent past, metagenomics has emerged as a unique methodology to explore microbiota as well as new biocatalysts possessing advantageous biochemical properties from hot springs. In the present study, metagenomics has been employed for microbial diversity exploration and identification of genes involved in various metabolic pathways among two hot springs, Manikaran and Tatapani, located in Himachal Pradesh, India. Taxonomic analysis of both metagenomes revealed the dominance of the Proteobacteria phylum. Genomic signatures of other bacterial phyla such as Chloroflexi, Actinobacteria, Bacteroidetes, Cyanobacteria, Planctomycetes, and Firmicutes were also found in significant abundance in both the metagenomes. The abundance of microorganisms belonging to genera, especially Nitrospira, Thauera, Meiothermus, Thiobacillus, Massilia, and Anaerolinea, was reported to be prevalent in the hot springs. A significant amount of metagenomic data remained taxonomically unclassified, which indeed emphasizes the scientific importance of these thermoaquatic niches. The functional potential analysis of both metagenomes revealed pathways related to carbohydrate metabolism, followed by amino acid metabolism, energy metabolism, genetic information processing, metabolism of cofactors and vitamins, membrane transporter, and signal transduction. Exploration of biomass-modifying biocatalysts enumerated the presence of glycoside hydrolases, glycosyl transferases, polysaccharide lyases, and carbohydrate esterases in the metagenomic data. Together, these findings offer an in-depth understanding of the microbial inhabitants in North-Western Himalayan hot springs and their underlying potential for various biotechnological and industrial applications.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-024-01248-z.}, } @article {pmid39281749, year = {2024}, author = {Kang, JW and Khatib, LA and Heston, MB and Dilmore, AH and Labus, JS and Deming, Y and Schimmel, L and Blach, C and McDonald, D and Gonzalez, A and Bryant, M and Sanders, K and Schwartz, A and Ulland, TK and Johnson, SC and Asthana, S and Carlsson, CM and Chin, NA and Blennow, K and Zetterberg, H and Rey, FE and , and Kaddurah-Daouk, R and Knight, R and Bendlin, BB}, title = {Gut Microbiome Compositional and Functional Features Associate with Alzheimer's Disease Pathology.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {39281749}, support = {R21 AG089348/AG/NIA NIH HHS/United States ; R01 AG092220/AG/NIA NIH HHS/United States ; U19 AG063744/AG/NIA NIH HHS/United States ; S10 OD026929/OD/NIH HHS/United States ; U01 AG061359/AG/NIA NIH HHS/United States ; P30 AG062715/AG/NIA NIH HHS/United States ; R01 AG083883/AG/NIA NIH HHS/United States ; R01 AG070973/AG/NIA NIH HHS/United States ; }, abstract = {BACKGROUND: The gut microbiome is a potentially modifiable factor in Alzheimer's disease (AD); however, understanding of its composition and function regarding AD pathology is limited.

METHODS: Shallow-shotgun metagenomic data was used to analyze fecal microbiome from participants enrolled in the Wisconsin Microbiome in Alzheimer's Risk Study, leveraging clinical data and cerebrospinal fluid (CSF) biomarkers. Differential abundance and ordinary least squares regression analyses were performed to find differentially abundant gut microbiome features and their associations with CSF biomarkers of AD and related pathologies.

RESULTS: Gut microbiome composition and function differed between people with AD and cognitively unimpaired individuals. The compositional difference was replicated in an independent cohort. Differentially abundant gut microbiome features were associated with CSF biomarkers of AD and related pathologies.

DISCUSSION: These findings enhance our understanding of alterations in gut microbial composition and function in AD, and suggest that gut microbes and their pathways are linked to AD pathology.}, } @article {pmid39281597, year = {2024}, author = {Yuan, X and Zhang, D and Li, D and Ji, Q and Gao, J and Hou, F and Chen, Y}, title = {Metagenomic and metabolite analysis reveals microbial community and metabolite dynamics in fermented Indigo naturalis.}, journal = {Heliyon}, volume = {10}, number = {17}, pages = {e36733}, pmid = {39281597}, issn = {2405-8440}, abstract = {The soaking and fermentation of the stems and leaves is an important intermediate step in the processing of Indigo Naturalis. However, the relationship between microbiota and Indigo Naturalis yields is still poorly understood. This study aimed to compare microbial communities and metabolite profiles at various stages of soaking fermentation, followed by validation of the results using HPLC. A total of 731 compounds were identified through metabolite analysis, with the levels of indigo and indirubin peaking after 36 h of fermentation. Metagenomes revealed Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria were identified as the most abundant microbial phyla in soaking fermentation. Correlation analysis indicated that the yields of indigo and indirubin may be affected by Lactococcus, Clostridium, and Enterobacter through the regulation of related synthetic enzymes. The findings offered novel perspectives on the relationship of microorganisms and Indigo Naturalis yields.}, } @article {pmid39281050, year = {2024}, author = {Yang, Z and Zheng, Y and Liu, S and Xie, T and Wang, Q and Wang, Z and Li, S and Wang, W}, title = {Rumen metagenome reveals the mechanism of mitigation methane emissions by unsaturated fatty acid while maintaining the performance of dairy cows.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {18}, number = {}, pages = {296-308}, pmid = {39281050}, issn = {2405-6383}, abstract = {Dietary fat content can reduce the methane production of dairy cows; however, the relevance fatty acid (FA) composition has towards this inhibitory effect is debatable. Furthermore, in-depth studies elucidating the effects of unsaturated fatty acids (UFA) on rumen function and the mechanism of reducing methane (CH4) production are lacking. This study exposed 10 Holstein cows with the same parity, similar milk yield to two total mixed rations: low unsaturated FA (LUFA) and high unsaturated FA (HUFA) with similar fat content. The LUFA group mainly added fat powder (C16:0 > 90%), and the HUFA group mainly replaced fat powder with extruded flaxseed. The experiment lasted 26 d, the last 5 d of which, gas exchange in respiratory chambers was conducted to measure gas emissions. We found that an increase in the UFA in diet did not affect milk production (P > 0.05) and could align the profile of milk FAs more closely with modern human nutritional requirements. Furthermore, we found that increasing the UFA content in the diet lead to a decrease in the abundance of Methanobrevibacter in the rumen (|linear discriminant analysis [LDA] score| > 2 and P < 0.05), which resulted in a decrease in the relative abundance of multiple enzymes (EC:1.2.7.12, EC:2.3.1.101, EC:3.5.4.27, EC:1.5.98.1, EC:1.5.98.2, EC:6.2.1.1, EC:2.1.1.86 and EC:2.8.4.1) during methanogenesis (P < 0.05). Compared with the LUFA group, the pathway of CH4 metabolism was inhibited in the HUFA group (|LDA| > 2 and P < 0.05), which ultimately decreased CH4 production (P < 0.05). Our results illustrated the mechanism involving decreased CH4 production when fed a UFA diet in dairy cows. We believe that our study provides new evidence to explore CH4 emission reduction measures for dairy cows.}, } @article {pmid39280079, year = {2024}, author = {Lindner, BG and Choudhury, RA and Pinamang, P and Bingham, L and D'Amico, I and Hatt, JK and Konstantinidis, KT and Graham, KE}, title = {Advancing Source Tracking: Systematic Review and Source-Specific Genome Database Curation of Fecally Shed Prokaryotes.}, journal = {Environmental science & technology letters}, volume = {11}, number = {9}, pages = {931-939}, pmid = {39280079}, issn = {2328-8930}, abstract = {Advancements within fecal source tracking (FST) studies are complicated by a lack of knowledge regarding the genetic content and distribution of fecally shed microbial populations. To address this gap, we performed a systematic literature review and curated a large collection of genomes (n = 26,018) representing fecally shed prokaryotic species across broad and narrow source categories commonly implicated in FST studies of recreational waters (i.e., cats, dogs, cows, seagulls, chickens, pigs, birds, ruminants, human feces, and wastewater). We find that across these sources the total number of prokaryotic genomes recovered from materials meeting our initial inclusion criteria varied substantially across fecal sources: from none in seagulls to 9,085 in pigs. We examined genome sequences recovered from these metagenomic and isolation-based studies extensively via comparative genomic approaches to characterize trends across source categories and produce a finalized genome database for each source category which is available online (n = 12,730). On average, 81% of the genomes representing species-level populations occur only within a single source. Using fecal slurries to test the performance of each source database, we report read capture rates that vary with fecal source alpha diversity and database size. We expect this resource to be useful to FST-related objectives, One Health research, and sanitation efforts globally.}, } @article {pmid39277915, year = {2024}, author = {Zeng, X and Tang, S and Dong, X and Dong, M and Shao, R and Liu, R and Li, T and Zhang, X and Wong, YH and Xie, Q}, title = {Corrigendum to "Analysis of metagenome and metabolome disclosed the mechanisms of Dendrobium officinale polysaccharide on DSS-induced ulcerative colitis-affected mice" [Int. J. Biol. Macromol. 277 (2024) 134229].}, journal = {International journal of biological macromolecules}, volume = {279}, number = {Pt 4}, pages = {135575}, doi = {10.1016/j.ijbiomac.2024.135575}, pmid = {39277915}, issn = {1879-0003}, } @article {pmid39277616, year = {2024}, author = {Jia, Y and Shi, Y and Wang, J and Liu, H and Huang, Y and Wang, H and Liu, Y and Peng, J}, title = {Integrating metagenomics with metabolomics for gut microbiota and metabolites profiling in acute pancreatitis.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {21491}, pmid = {39277616}, issn = {2045-2322}, support = {GZC20242045//Postdoctoral Fellowship Program of CPSF/ ; 2023zzts896//Fundamental Research Funds for Central Universities of the Central South University/ ; 82170661//National Natural Science Foundation of China/ ; 2023DK2002//Key Project of Research and Development Plan of Hunan Province/ ; }, mesh = {*Gastrointestinal Microbiome ; *Pancreatitis/microbiology/metabolism ; Animals ; *Metabolomics/methods ; *Metagenomics/methods ; Mice ; Metabolome ; Disease Models, Animal ; Dysbiosis/microbiology/metabolism ; Mice, Inbred C57BL ; Male ; Acute Disease ; }, abstract = {Acute pancreatitis (AP) is an inflammatory disease of the pancreas. Despite of a steadily increasing in morbidity and mortality, there is still no effective therapy. Gut microbial dysbiosis and its derived-metabolites disorder have been shown to play an important role in the development of AP, however, little is known regarding the crosstalk between gut microbiota and metabolites. In this study, we assessed the alterations in gut microbiota and metabolites by constructing three AP mouse models by means of metagenomic and metabolomic sequencing, and further clarified their relationship by correlation analysis. The results revealed that each model exhibited unique flora and metabolite profiles. KEGG analysis showed that the differential flora and metabolite-enriched pathway functions were correlated with lipid metabolism and amino acid metabolism. Moreover, two core differential bacterial species on Burkholderiales bacterium YL45 and Bifidobacterium pseudolongum along with eleven differential metabolites appeared to exert certain effects during the course of AP. In conclusion, further exploration of the crosstalk between microbiota and derived metabolites may provide novel insights and strategies into the diagnosis and treatment of AP.}, } @article {pmid39277613, year = {2024}, author = {da Silva, S and Vuong, P and Amaral, JRV and da Silva, VAS and de Oliveira, SS and Vermelho, AB and Beale, DJ and Bissett, A and Whiteley, AS and Kaur, P and Macrae, A}, title = {The piranha gut microbiome provides a selective lens into river water biodiversity.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {21518}, pmid = {39277613}, issn = {2045-2322}, support = {Bolsa de Doutorado//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; Bolsa de Iniciacao Cientifica//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; Bolsa de doutordo//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; PRINT 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; }, mesh = {*Rivers/microbiology ; *Gastrointestinal Microbiome/genetics ; Animals ; *Biodiversity ; Metagenome ; Metagenomics/methods ; Water Microbiology ; Bacteria/genetics/classification/isolation & purification ; }, abstract = {Advances in omics technologies have enabled the in-depth study of microbial communities and their metabolic profiles from all environments. Here metagenomes were sampled from piranha (Serrasalmus rhombeus) and from river water from the Rio São Benedito (Amazon Basin). Shotgun metagenome sequencing was used to explore diversity and to test whether fish microbiomes are a good proxy for river microbiome studies. The results showed that the fish microbiomes were not significantly different from the river water microbiomes at higher taxonomic ranks. However, at the genus level, fish microbiome alpha diversity decreased, and beta diversity increased. This result repeated for functional gene abundances associated with specific metabolic categories (SEED level 3). A clear delineation between water and fish was seen for beta diversity. The piranha microbiome provides a good and representative subset of its river water microbiome. Variations seen in beta biodiversity were expected and can be explained by temporal variations in the fish microbiome in response to stronger selective forces on its biodiversity. Metagenome assembled genomes construction was better from the fish samples. This study has revealed that the microbiome of a piranha tells us a lot about its river water microbiome and function.}, } @article {pmid39277504, year = {2024}, author = {Fida, M and Tande, AJ}, title = {State-of-the-Art Metagenomic Sequencing and Its Role in the Diagnosis of Periprosthetic Joint Infections.}, journal = {Infectious disease clinics of North America}, volume = {38}, number = {4}, pages = {813-825}, doi = {10.1016/j.idc.2024.07.011}, pmid = {39277504}, issn = {1557-9824}, mesh = {Humans ; *Prosthesis-Related Infections/diagnosis/microbiology ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing ; }, abstract = {Metagenomic next-generation sequencing (mNGS) is increasingly being recognized as a valuable diagnostic tool for periprosthetic joint infections (PJIs). This study reviews the diagnostic utility of mNGS, highlighting its improved sensitivity in detecting pathogens, particularly in culture-negative and polymicrobial infections. However, the clinical application of this method is hindered by challenges such as the prevalence of host DNA, the necessity for extensive bioinformatic analysis, and the potential for contamination, which can lead to misinterpretation of results. As mNGS continues to evolve, it holds significant potential to improve the management of PJI and enhance the application of precision medicine in orthopedic infections.}, } @article {pmid39276831, year = {2024}, author = {Li, C and Zhang, Y and Shi, W and Peng, Y and Han, Y and Jiang, S and Dong, X and Zhang, R}, title = {Viral diversity within marine biofilms and interactions with corrosive microbes.}, journal = {Environmental research}, volume = {263}, number = {Pt 1}, pages = {119991}, doi = {10.1016/j.envres.2024.119991}, pmid = {39276831}, issn = {1096-0953}, mesh = {*Biofilms/growth & development ; Corrosion ; Bacteria/genetics ; Viruses/genetics/classification ; Phylogeny ; Metagenome ; Archaea/virology/genetics ; }, abstract = {In marine environments, a wide variety of microbes like bacteria, and archaea influence on the corrosion of materials. Viruses are widely distributed in biofilms among these microbes and may affect the corrosion process through interactions with key corrosive prokaryotes. However, understanding of the viral communities within biofilms and their interactions with corrosive microbes remains is limited. To improve this knowledge gap, 53 metagenomes were utilized to investigate the diversity of viruses within biofilms on 8 different materials and their interactions with corrosive microbes. Notably, the viruses within biofilms predominantly belonged to Caudoviricetes, and phylogenetic analysis of Caudoviricetes and protein-sharing networks with other environments revealed the presence of numerous novel viral clades in biofilms. The virus‒host linkages revealed a close association between viruses and corrosive microbes in biofilms. This means that viruses may modulate host corrosion-related metabolism through auxiliary metabolic genes. It was observed that the virus could enhance host resistance to metals and antibiotics via horizontal gene transfer. Interestingly, viruses could protect themselves from host antiviral systems through anti-defense systems. This study illustrates the diversity of viruses within biofilms formed on materials and the intricate interactions between viruses and corrosive microbes, showing the potential roles of viruses in corrosive biofilms.}, } @article {pmid39276741, year = {2024}, author = {Kumar, A and Lakhawat, SS and Singh, K and Kumar, V and Verma, KS and Dwivedi, UK and Kothari, SL and Malik, N and Sharma, PK}, title = {Metagenomic analysis of soil from landfill site reveals a diverse microbial community involved in plastic degradation.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {135804}, doi = {10.1016/j.jhazmat.2024.135804}, pmid = {39276741}, issn = {1873-3336}, mesh = {*Soil Microbiology ; *Waste Disposal Facilities ; *Biodegradation, Environmental ; *Plastics ; *Bacteria/genetics/classification/metabolism ; *Fungi/genetics ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Microbiota ; Soil Pollutants/metabolism ; }, abstract = {In this study, we have investigated microbial communities structure and function using high throughput amplicon sequencing and whole metagenomic sequencing of DNA extracted from different depths of a plastic-laden landfill site. With diverse taxonomic groups inhabiting the plastic-rich soil, our study demonstrates the remarkable adaptability of microbes to use this new substrate as a carbon source. FTIR spectroscopic analysis of soil indicated degradation of plastic as perceived from the carbonyl index of 0.16, 0.72, and 0.44 at 0.6, 0.9 and 1.2 m depth, respectively. Similarly, water contact angles of 108.7 degree, 99.7 degree, 62.7 degree, and 77.8 degree of plastic pieces collected at 0.3, 0.6, 0.9, and 1.2 m depths respectively showed increased wettability and hydrophilicity of the plastic. Amplicon analysis of 16S and 18 S rRNA revealed a high abundance of several plastic-degrading bacterial groups, including Pseudomonas, Rhizobiales, Micrococcaceae, Chaetomium, Methylocaldum, Micromonosporaceae, Rhodothermaceae and fungi, including Trichoderma, Aspergillus, Candida at 0.9 m. The co-existence of specific microbial groups at different depths of landfill site indicates importance of bacterial and fungal interactions for plastic. Whole metagenome analysis of soil sample at 0.9 m depth revealed a high abundance of genes encoding enzymes that participate in the biodegradation of PVC, polyethylene, PET, and polyurethane. Curation of the pathways related to the degradation of these materials provided a blueprint for plastic biodegradation in this ecosystem. Altogether, our study has highlighted the importance of microbial cooperation for the biodegradation of pollutants. Our metagenome-based investigation supports the current perception that consortia of fungi-bacteria are preferable to axenic cultures for effective bioremediation of the environment.}, } @article {pmid39276731, year = {2024}, author = {Shan, M and Zheng, C and Song, J and Qiu, M and Huang, C and Cui, M and Wang, J and Chen, W and Zhang, L and Yu, Y and Fang, H}, title = {Biochar and theaflavins mitigate the antibiotic resistome and antibiotic-resistant pathogens in a soil-lettuce continuum.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {135821}, doi = {10.1016/j.jhazmat.2024.135821}, pmid = {39276731}, issn = {1873-3336}, mesh = {*Lactuca/microbiology ; *Biflavonoids/pharmacology ; *Soil Microbiology ; *Catechin/pharmacology/chemistry ; *Charcoal/pharmacology/chemistry ; *Anti-Bacterial Agents/pharmacology ; Plant Leaves/microbiology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial/drug effects ; Bacteria/drug effects/genetics ; Drug Resistance, Bacterial/genetics/drug effects ; }, abstract = {Antibiotic resistance can be transferred into the food chain, leading to increased risks to human health from ready-to-eat vegetables. Mitigating the transmission of antibiotic resistance from soil to vegetables by green materials is of great significance. Here, we deciphered the roles of biochar and theaflavins in mitigating antibiotic resistance genes (ARGs) and antibiotic-resistant pathogens (ARPs) in a soil-lettuce continuum. Metagenomic results showed that biochar led to a significant decrease in the abundance of ARGs in lettuce leaves, while theaflavins contributed to a significant reduction in the diversity and abundance of ARGs in soil, particularly targeting dominant ARG types such as sulfonamide and aminoglycoside resistance genes. Meanwhile, biochar and theaflavins alleviated the potential mobility of ARGs, in lettuce leaves and soil, respectively, including the spread of ARGs to human pathogens. In addition, the diversity of ARG hosts was reduced in the soil-lettuce continuum and ARPs were not detected in lettuce leaves after the application of biochar or theaflavins. Overall, this study provides a novel perspective on green materials for mitigating the antibiotic resistome and ARPs in the soil-lettuce continuum, contributing to food security and human health.}, } @article {pmid39267516, year = {2024}, author = {Liu, YZ and Zhang, R and Xie, JJ and Guo, Q and Zhan, CX and Chen, MY and Li, JS and Peng, XM}, title = {[Two cases of neonatal Legionella pneumonia].}, journal = {Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics}, volume = {26}, number = {9}, pages = {986-988}, pmid = {39267516}, issn = {1008-8830}, mesh = {Humans ; Female ; Infant, Newborn ; *Legionnaires' Disease/diagnosis/drug therapy ; }, abstract = {Patient 1, a 12-day-old female infant, presented with fever, cough, dyspnea, and elevated infection markers, requiring respiratory support. Metagenomic next-generation sequencing (mNGS) of blood and bronchoalveolar lavage fluid revealed Legionella pneumophila (LP), leading to diagnoses of LP pneumonia and LP sepsis. The patient was treated with erythromycin for 15 days and azithromycin for 5 days, resulting in recovery and discharge. Patient 2, an 11-day-old female infant, presented with dyspnea, fever, elevated infection markers, and multiple organ dysfunction, requiring mechanical ventilation. mNGS of blood and cerebrospinal fluid indicated LP, leading to diagnoses of LP pneumonia, LP sepsis, and LP intracranial infection. The patient was treated with erythromycin for 19 days and was discharged after recovery. Neonatal LP pneumonia lacks specific clinical symptoms, and azithromycin is the preferred antimicrobial agent. The use of mNGS can provide early and definitive diagnosis for severe neonatal pneumonia of unknown origin.}, } @article {pmid39267333, year = {2024}, author = {Fujii, N and Kuroda, K and Narihiro, T and Aoi, Y and Ozaki, N and Ohashi, A and Kindaichi, T}, title = {Unique episymbiotic relationship between Candidatus Patescibacteria and Zoogloea in activated sludge flocs at a municipal wastewater treatment plant.}, journal = {Environmental microbiology reports}, volume = {16}, number = {5}, pages = {e70007}, pmid = {39267333}, issn = {1758-2229}, support = {23KJ16420A//JSPS KAKENHI/ ; JP16H04833//JSPS KAKENHI/ ; JP20H02287//JSPS KAKENHI/ ; }, mesh = {*Sewage/microbiology ; *Symbiosis ; *Zoogloea/genetics/metabolism ; *Wastewater/microbiology ; In Situ Hybridization, Fluorescence ; Metagenome ; Phylogeny ; }, abstract = {Candidatus Patescibacteria, also known as candidate phyla radiation (CPR), including the class-level uncultured clade JAEDAM01 (formerly a subclass of Gracilibacteria/GN02/BD1-5), are ubiquitous in activated sludge. However, their characteristics and relationships with other organisms are largely unknown. They are believed to be episymbiotic, endosymbiotic or predatory. Despite our understanding of their limited metabolic capacity, their precise roles remain elusive due to the difficulty in cultivating and identifying them. In previous research, we successfully recovered high-quality metagenome-assembled genomes (MAGs), including a member of JAEDAM01 from activated sludge flocs. In this study, we designed new probes to visualize the targeted JAEDAM01-associated MAG HHAS10 and identified its host using fluorescence in situ hybridization (FISH). The FISH observations revealed that JAEDAM01 HHAS10-like cells were located within dense clusters of Zoogloea, and the fluorescence brightness of zoogloeal cells decreased in the vicinity of the CPR cells. The Zoogloea MAGs possessed genes related to extracellular polymeric substance biosynthesis, floc formation and nutrient removal, including a polyhydroxyalkanoate (PHA) accumulation pathway. The JAEDAM01 MAG HHAS10 possessed genes associated with type IV pili, competence protein EC and PHA degradation, suggesting a Zoogloea-dependent lifestyle in activated sludge flocs. These findings indicate a new symbiotic relationship between JAEDAM01 and Zoogloea.}, } @article {pmid39267241, year = {2024}, author = {Doni, L and Azzola, A and Oliveri, C and Bosi, E and Auguste, M and Morri, C and Bianchi, CN and Montefalcone, M and Vezzulli, L}, title = {Genome-resolved metagenomics revealed novel microbial taxa with ancient metabolism from macroscopic microbial mat structures inhabiting anoxic deep reefs of a Maldivian Blue Hole.}, journal = {Environmental microbiology reports}, volume = {16}, number = {5}, pages = {e13315}, pmid = {39267241}, issn = {1758-2229}, support = {CN_00000033//Centro Nazionale di Ricerca - Biodiversità (Italy) project (PNRR CN00000033 - Centro Nazionale Biodiversità/ ; CUP D33C22000960007//Italian Ministry of University and Research/ ; }, mesh = {*Metagenomics ; *Phylogeny ; *Metagenome ; Bacteria/classification/genetics/isolation & purification/metabolism ; Geologic Sediments/microbiology ; Genome, Bacterial/genetics ; Anaerobiosis ; Deltaproteobacteria/genetics/classification/isolation & purification/metabolism ; Chloroflexi/genetics/classification/isolation & purification/metabolism ; Proteobacteria/genetics/classification/isolation & purification ; Microbiota ; }, abstract = {Blue holes are vertical water-filled openings in carbonate rock that exhibit complex morphology, ecology, and water chemistry. In this study, macroscopic microbial mat structures found in complete anoxic conditions in the Faanu Mudugau Blue Hole (Maldives) were studied by metagenomic methods. Such communities have likely been evolutionary isolated from the surrounding marine environment for more than 10,000 years since the Blue Hole formation during the last Ice Age. A total of 48 high-quality metagenome-assembled genomes (MAGs) were recovered, predominantly composed of the phyla Chloroflexota, Proteobacteria and Desulfobacterota. None of these MAGs have been classified to species level (<95% ANI), suggesting the discovery of several new microbial taxa. In particular, MAGs belonging to novel bacterial genera within the order Dehalococcoidales accounted for 20% of the macroscopic mat community. Genome-resolved metabolic analysis of this dominant microbial fraction revealed a mixotrophic lifestyle based on energy conservation via fermentation, hydrogen metabolism and anaerobic CO2 fixation through the Wood-Ljungdahl pathway. Interestingly, these bacteria showed a high proportion of ancestral genes in their genomes providing intriguing perspectives on mechanisms driving microbial evolution in this peculiar environment. Overall, our results provide new knowledge for understanding microbial life under extreme conditions in blue hole environments.}, } @article {pmid39275913, year = {2024}, author = {Takada, K and Nakagawa, S and Kryukov, K and Ozawa, M and Watanabe, T}, title = {Metagenomic analysis of the gut microbiota of hooded cranes (Grus monacha) on the Izumi plain in Japan.}, journal = {FEBS open bio}, volume = {14}, number = {12}, pages = {1972-1984}, pmid = {39275913}, issn = {2211-5463}, support = {//Crane Conservation by the City of Izumi/ ; //Tokyo Biochemical Research Foundation/ ; JPMJCR20H6//Core Research for Evolutional Science and Technology/ ; //2020 Tokai University School of Medicine Research Aid/ ; 22gm1610010h0001//Japan Agency for Medical Research and Development/ ; JP223fa627002h//Japan Agency for Medical Research and Development/ ; //Takeda Science Foundation/ ; 16H06429//Japan Society for the Promotion of Science/ ; 16H06434//Japan Society for the Promotion of Science/ ; 16K21723//Japan Society for the Promotion of Science/ ; 19H04843//Japan Society for the Promotion of Science/ ; 19fk0108171//Japan Society for the Promotion of Science/ ; 21J01036//Japan Society for the Promotion of Science/ ; 22K15469//Japan Society for the Promotion of Science/ ; JP19fk0108113//Japan Society for the Promotion of Science/ ; JP22H02521//Japan Society for the Promotion of Science/ ; }, mesh = {Animals ; Japan ; *Gastrointestinal Microbiome/genetics ; *Birds/microbiology/virology ; *Metagenomics/methods ; Feces/microbiology ; Bacteria/genetics/classification/isolation & purification ; High-Throughput Nucleotide Sequencing ; Metagenome/genetics ; }, abstract = {Recent advances in DNA sequencing technology have dramatically improved our understanding of the gut microbiota of various animal species. However, research on the gut microbiota of birds lags behind that of many other vertebrates, and information about the gut microbiota of wild birds such as migratory waterfowl is particularly lacking. Because the ecology of migratory waterfowl (e.g., lifestyle, diet, physiological characteristics) differs from that of other birds, the gut microbiota of migratory waterfowl likely also differs, but much is still unknown. The hooded crane (Grus monacha) is an important representative migratory waterbird species and is listed as endangered on the International Union for Conservation of Nature and Natural Resources Red List of Threatened Species. In this study, we analyzed the bacterial and viral microbiota in the gut of hooded cranes by using deep sequencing data from fecal samples of hooded cranes that winter on the Izumi plain in Japan, and found that Cetobacterium, Clupeiformes, and Pbunavirus were clearly present in the fecal samples of hooded cranes. These findings advance our understanding of the ecology of hooded cranes.}, } @article {pmid39275258, year = {2024}, author = {Wang, M and Chen, Y and Song, AX and Weng, X and Meng, Y and Lin, J and Mao, YH}, title = {The Combination of Exercise and Konjac Glucomannan More Effectively Prevents Antibiotics-Induced Dysbiosis in Mice Compared with Singular Intervention.}, journal = {Nutrients}, volume = {16}, number = {17}, pages = {}, pmid = {39275258}, issn = {2072-6643}, support = {2023A1515010004//Guangdong Basic and Applied Basic Research Foundation/ ; 2023ZDZX2035//Special Funds in Key Areas of Guangdong Provincial Department of Education/ ; S202410585045//The College Students Innovation and Entrepreneurship Training Program/ ; 202410585015//The College Students Innovation and Entrepreneurship Training Program/ ; 82003434//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Mannans/pharmacology ; *Dysbiosis/prevention & control/chemically induced ; *Mice, Inbred C57BL ; *Anti-Bacterial Agents/pharmacology/adverse effects ; *Gastrointestinal Microbiome/drug effects ; *Physical Conditioning, Animal ; Mice ; Male ; Combined Modality Therapy ; }, abstract = {Our previous studies have demonstrated that konjac glucomannan (KGM) can prevent dysbiosis induced by antibiotics. While exercise may also impact the gut microbiome, there are limited studies reporting its protective effect on antibiotic-induced dysbiosis. Therefore, this study investigated the preventive and regulatory effects of a combination of 6-week exercise and KGM intervention on antibiotic-induced dysbiosis in C57BL/6J mice compared with a single intervention. The results showed that combined exercise and KGM intervention could restore the changes in the relative abundance of Bacteroides (3.73% with CTL versus 14.23% with ATBX versus 4.46% with EK) and Prevotellaceae_Prevotella (0.33% with CTL versus 0.00% with ATBX versus 0.30% with EK) induced by antibiotics (p < 0.05), and minimized the Bray-Curtis distance induced by antibiotics (0.55 with CTL versus 0.81 with ATBX versus 0.80 with EXC versus 0.83 with KGM versus 0.75 with EK). Compared with the combined intervention, exercise intervention also produced a certain level of recovery effects; the relative abundance of Rikenellaceae (1.96% with CTL versus 0.09% with ATBX versus 0.49% with EXC) was restored, while KGM supplementation showed the best preventive effect. In addition, the combination of exercise and KGM significantly enriched microbial purine metabolic pathways (p < 0.05). These findings indicate that combining exercise with KGM could be a promising approach to reducing the side effects of antibiotics on the gut microbiome.}, } @article {pmid39274545, year = {2024}, author = {Dera, N and Żeber-Lubecka, N and Ciebiera, M and Kosińska-Kaczyńska, K and Szymusik, I and Massalska, D and Dera, K and Bubień, K}, title = {Intrauterine Shaping of Fetal Microbiota.}, journal = {Journal of clinical medicine}, volume = {13}, number = {17}, pages = {}, pmid = {39274545}, issn = {2077-0383}, abstract = {Mechanisms resulting from the physiological immaturity of the digestive system in children delivered before 32 weeks of gestation and, in particular, different interactions between the microbiome and the body have not been fully elucidated yet. Next-generation sequencing methods demonstrated the presence of bacterial DNA in the placenta and amniotic fluid, which may reflect bacterial populations that initiate intestinal colonization in utero. Numerous studies confirmed the hypothesis stating that intestinal bacteria played an important role in the pathogenesis of necrotizing enterocolitis (NEC) early- and late-onset neonatal sepsis (EONS and LONS). The model and scale of disorders within the intestinal microbiome are the subject of active research in premature infants. Neonatal meconium was primarily used as an indicator defining the environment in utero, as it is formed before birth. Metagenomic results and previous data from microbiological bacterial cultures showed a correlation between the time from birth to sample collection and the detection of bacteria in the neonatal meconium. Therefore, it may be determined that the colonization of the newborn's intestines is influenced by numerous factors, which may be divided into prenatal, perinatal, and postnatal, with particular emphasis put on the mode of delivery and contact with the parent immediately after birth. Background: The aim of this review was to collect available data on the intrauterine shaping of the fetal microbiota. Methods: On 13 March 2024, the available literature in the PubMed National Library of Medicine search engine was reviewed using the following selected keywords: "placental microbiome", "intestinal bacteria in newborns and premature infants", and "intrauterine microbiota". Results: After reviewing the available articles and abstracts and an in-depth analysis of their content, over 100 articles were selected for detailed elaboration. We focused on the origin of microorganisms shaping the microbiota of newborns. We also described the types of bacteria that made up the intrauterine microbiota and the intestinal microbiota of newborns. Conclusions: The data presented in the review on the microbiome of both term newborns and those with a body weight below 1200 g indicate a possible intrauterine colonization of the fetus depending on the duration of pregnancy. The colonization occurs both via the vaginal and intestinal route (hematogenous route). However, there are differences in the demonstrated representatives of various types of bacteria, phyla Firmicutes and Actinobacteria in particular, taking account of the distribution in their abundance in the individual groups of pregnancy duration. Simultaneously, the distribution of the phyla Actinobacteria and Proteobacteria is consistent. Considering the duration of pregnancy, it may also be concluded that the bacterial flora of vaginal origin dominates in preterm newborns, while the flora of intestinal origin dominates in term newborns. This might explain the role of bacterial and infectious factors in inducing premature birth with the rupture of fetal membranes.}, } @article {pmid39273435, year = {2024}, author = {Di Chiano, M and Sallustio, F and Fiocco, D and Rocchetti, MT and Spano, G and Pontrelli, P and Moschetta, A and Gesualdo, L and Gadaleta, RM and Gallone, A}, title = {Psychobiotic Properties of Lactiplantibacillus plantarum in Neurodegenerative Diseases.}, journal = {International journal of molecular sciences}, volume = {25}, number = {17}, pages = {}, pmid = {39273435}, issn = {1422-0067}, support = {1062//PON "RICERCA E INNOVAZIONE" 2014-2020-Innovazione/ ; Call for tender No. 341 of 15 March 2022 of Italian Ministry of University and Research funded by the European Union - Next Generation EU//National Recovery and Resilience Plan (NRRP)/ ; Concession Decree No. 1550 of 11 October 2022 adopted by the Italian Ministry of University and Research, CUP D93C22000890001//Italian Ministry of University and Research, CUP D93C22000890001/ ; Codice progetto n. 2022H9MPZ5//MIUR- PRIN Progetti di Ricerca di Rilevante Interesse Nazionale 2022/ ; Id. 23239//AIRC IG 2019/ ; Call for tender No. 3138 of 16/12/2021 of Italian Ministry of University and Research funded by the European Union//National Recovery and Resilience Plan (NRRP)/ ; Project code: CN00000041, CUP H93C22000430007//NextGenerationEU/ ; PNRR-MR1-2022-12376395//European Union - Next Generation EU - PNRR M6C2/ ; "POFACS" - ARS01_00640 -", D.D. 1211/2020 and 1104/2021//Italian Ministry of University and Research (MIUR)/ ; PRA-HE 2021//University of Foggia/ ; }, mesh = {Humans ; *Neurodegenerative Diseases/microbiology/metabolism ; *Gastrointestinal Microbiome ; *Probiotics/therapeutic use ; Dysbiosis/microbiology ; Brain-Gut Axis ; Animals ; }, abstract = {Neurodegenerative disorders are the main cause of cognitive and physical disabilities, affect millions of people worldwide, and their incidence is on the rise. Emerging evidence pinpoints a disturbance of the communication of the gut-brain axis, and in particular to gut microbial dysbiosis, as one of the contributors to the pathogenesis of these diseases. In fact, dysbiosis has been associated with neuro-inflammatory processes, hyperactivation of the neuronal immune system, impaired cognitive functions, aging, depression, sleeping disorders, and anxiety. With the rapid advance in metagenomics, metabolomics, and big data analysis, together with a multidisciplinary approach, a new horizon has just emerged in the fields of translational neurodegenerative disease. In fact, recent studies focusing on taxonomic profiling and leaky gut in the pathogenesis of neurodegenerative disorders are not only shedding light on an overlooked field but are also creating opportunities for biomarker discovery and development of new therapeutic and adjuvant strategies to treat these disorders. Lactiplantibacillus plantarum (LBP) strains are emerging as promising psychobiotics for the treatment of these diseases. In fact, LBP strains are able to promote eubiosis, increase the enrichment of bacteria producing beneficial metabolites such as short-chain fatty acids, boost the production of neurotransmitters, and support the homeostasis of the gut-brain axis. In this review, we summarize the current knowledge on the role of the gut microbiota in the pathogenesis of neurodegenerative disorders with a particular focus on the benefits of LBP strains in Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, autism, anxiety, and depression.}, } @article {pmid39273328, year = {2024}, author = {Zhu, N and Qian, Y and Song, L and Yu, Q and Sheng, H and Li, Y and Zhu, X}, title = {Regulating Leaf Photosynthesis and Soil Microorganisms through Controlled-Release Nitrogen Fertilizer Can Effectively Alleviate the Stress of Elevated Ambient Ozone on Winter Wheat.}, journal = {International journal of molecular sciences}, volume = {25}, number = {17}, pages = {}, pmid = {39273328}, issn = {1422-0067}, support = {BE2022312//Special Technology Innovation Fund of Carbon Neutrality in Jiangsu Province/ ; }, mesh = {*Fertilizers ; *Triticum/growth & development/metabolism/microbiology/drug effects ; *Photosynthesis/drug effects ; *Soil Microbiology ; *Plant Leaves/drug effects/metabolism ; *Nitrogen/metabolism ; *Ozone/pharmacology ; Stress, Physiological ; Soil/chemistry ; Bacteria/drug effects/metabolism/genetics ; }, abstract = {The mitigation mechanisms of a kind of controlled-release nitrogen fertilizer (sulfur-coated controlled-release nitrogen fertilizer, SCNF) in response to O3 stress on a winter wheat (Triticum aestivum L.) variety (Nongmai-88) were studied in crop physiology and soil biology through the ozone-free-air controlled enrichment (O3-FACE) simulation platform and soil microbial metagenomics. The results showed that SCNF could not delay the O3-induced leaf senescence of winter wheat but could enhance the leaf size and photosynthetic function of flag leaves, increase the accumulation of nutrient elements, and lay the foundation for yield by regulating the release rate of nitrogen (N). By regulating the soil environment, SCNF could maintain the diversity and stability of soil bacterial and archaeal communities, but there was no obvious interaction with the soil fungal community. By alleviating the inhibition effects of O3 on N-cycling-related genes (ko00910) of soil microorganisms, SCNF improved the activities of related enzymes and might have great potential in improving soil N retention. The results demonstrated the ability of SCNF to improve leaf photosynthetic function and increase crop yield under O3-polluted conditions in the farmland ecosystem, which may become an effective nitrogen fertilizer management measure to cope with the elevated ambient O3 and achieve sustainable production.}, } @article {pmid39273112, year = {2024}, author = {Druker, S and Sicsic, R and Ravid, S and Scheinin, S and Raz, T}, title = {Reproductive Tract Microbial Transitions from Late Gestation to Early Postpartum Using 16S rRNA Metagenetic Profiling in First-Pregnancy Heifers.}, journal = {International journal of molecular sciences}, volume = {25}, number = {17}, pages = {}, pmid = {39273112}, issn = {1422-0067}, mesh = {Female ; Animals ; Pregnancy ; *RNA, Ribosomal, 16S/genetics ; Cattle ; *Postpartum Period ; *Vagina/microbiology ; *Microbiota/genetics ; *Uterus/microbiology ; Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; Metagenome ; }, abstract = {Studies in recent years indicate that reproductive tract microbial communities are crucial for shaping mammals' health and reproductive outcomes. Following parturition, uterine bacterial contamination often occurs due to the open cervix, which may lead to postpartum uterine inflammatory diseases, especially in primiparous individuals. However, investigations into spatio-temporal microbial transitions in the reproductive tract of primigravid females remain limited. Our objective was to describe and compare the microbial community compositions in the vagina at late gestation and in the vagina and uterus at early postpartum in first-pregnancy heifers. Three swab samples were collected from 33 first-pregnancy Holstein Friesian heifers: one vaginal sample at gestation day 258 ± 4, and vaginal and uterine samples at postpartum day 7 ± 2. Each sample underwent 16S rRNA V4 region metagenetic analysis via Illumina MiSeq, with bioinformatics following Mothur MiSeq SOP. The reproductive tract bacterial communities were assigned to 1255 genus-level OTUs across 30 phyla. Dominant phyla, accounting for approximately 90% of the communities, included Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Fusobacteria. However, the results revealed distinct shifts in microbial composition between the prepartum vagina (Vag-pre), postpartum vagina (Vag-post), and postpartum uterus (Utr-post). The Vag-pre and Utr-post microbial profiles were the most distinct. The Utr-post group had lower relative abundances of Proteobacteria but higher abundances of Bacteroidetes, Fusobacteria, and Tenericutes compared to Vag-pre, while Vag-post displayed intermediate values for these phyla, suggesting a transitional profile. Additionally, the Utr-post group exhibited lower bacterial richness and diversity compared to both Vag-pre and Vag-post. The unsupervised probabilistic Dirichlet Multinomial Mixtures model identified two distinct community types: most Vag-pre samples clustered into one type and Utr-post samples into another, while Vag-post samples were distributed evenly between the two. LEfSe analysis revealed distinct microbial profiles at the genus level. Overall, specific microbial markers were associated with anatomical and temporal transitions, revealing a dynamic microbial landscape during the first pregnancy and parturition. These differences highlight the complexity of these ecosystems and open new avenues for research in reproductive biology and microbial ecology.}, } @article {pmid39271469, year = {2024}, author = {Ciuchcinski, K and Stokke, R and Steen, IH and Dziewit, L}, title = {Landscape of the metaplasmidome of deep-sea hydrothermal vents located at Arctic Mid-Ocean Ridges in the Norwegian-Greenland Sea: ecological insights from comparative analysis of plasmid identification tools.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {10}, pages = {}, pmid = {39271469}, issn = {1574-6941}, support = {UMO-2019/34/H/NZ2/00584//National Science Centre/ ; }, mesh = {*Plasmids/genetics ; *Hydrothermal Vents/microbiology ; Arctic Regions ; *Metagenomics ; Seawater/microbiology ; Bacteria/genetics/classification/isolation & purification ; Microbiota/genetics ; Norway ; Oceans and Seas ; Metagenome ; }, abstract = {Plasmids are one of the key drivers of microbial adaptation and evolution. However, their diversity and role in adaptation, especially in extreme environments, remains largely unexplored. In this study, we aimed to identify, characterize, and compare plasmid sequences originating from samples collected from deep-sea hydrothermal vents located in Arctic Mid-Ocean Ridges. To achieve this, we employed, and benchmarked three recently developed plasmid identification tools-PlasX, GeNomad, and PLASMe-on metagenomic data from this unique ecosystem. To date, this is the first direct comparison of these computational methods in the context of data from extreme environments. Upon recovery of plasmid contigs, we performed a multiapproach analysis, focusing on identifying taxonomic and functional biases within datasets originating from each tool. Next, we implemented a majority voting system to identify high-confidence plasmid contigs, enhancing the reliability of our findings. By analysing the consensus plasmid sequences, we gained insights into their diversity, ecological roles, and adaptive significance. Within the high-confidence sequences, we identified a high abundance of Pseudomonadota and Campylobacterota, as well as multiple toxin-antitoxin systems. Our findings ensure a deeper understanding of how plasmids contribute to shaping microbial communities living under extreme conditions of hydrothermal vents, potentially uncovering novel adaptive mechanisms.}, } @article {pmid39271424, year = {2024}, author = {Bokulich, NA and Robeson, MS}, title = {Bioinformatics challenges for profiling the microbiome in cancer: pitfalls and opportunities.}, journal = {Trends in microbiology}, volume = {32}, number = {12}, pages = {1163-1166}, doi = {10.1016/j.tim.2024.08.011}, pmid = {39271424}, issn = {1878-4380}, mesh = {Humans ; *Neoplasms/microbiology ; *Microbiota ; *Computational Biology/methods ; *Metagenomics/methods ; *Machine Learning ; Sequence Analysis, DNA/methods ; }, abstract = {Increasing evidence suggests that the human microbiome plays an important role in cancer risk and treatment. Untargeted 'omics' techniques have accelerated research into microbiome-cancer interactions, supporting the discovery of novel associations and mechanisms. However, these techniques require careful selection and use to avoid biases and other pitfalls. In this essay, we discuss selected challenges involved in the analysis of microbiome data in the context of cancer, including the application of machine learning (ML). We focus on DNA sequencing-based (e.g., metagenomics) methods, but many of the pitfalls and opportunities generalize to other omics technologies as well. We advocate for extended training opportunities, community standards, and best practices for sharing data and code to advance transparency and reproducibility in cancer microbiome research.}, } @article {pmid39271095, year = {2024}, author = {do Socorro Foro Ramos, E and Barbosa, MRF and Villanova, F and Silva, RLO and Garcia, SC and Mendes-Correa, MC and Pandey, RP and Luchs, A and Sato, MIZ and da Costa, AC and Leal, E}, title = {Novel members of the order Picornavirales identified in freshwater from Guarapiranga reservoir in São Paulo.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {124}, number = {}, pages = {105668}, doi = {10.1016/j.meegid.2024.105668}, pmid = {39271095}, issn = {1567-7257}, mesh = {Brazil ; *Fresh Water/virology ; *Phylogeny ; Metagenomics/methods ; Genome, Viral ; Picornaviridae/genetics/classification/isolation & purification ; }, abstract = {The global challenge of water resource availability is exacerbated by anthropogenic influences that promote the emergence of pollutants. Among these pollutants are microbiological agents, including viruses, which are ubiquitous in the biosphere and play a pivotal role in both ecological balance and the occurrence of diseases in animals and plants. Consequently, monitoring viruses in water sources becomes indispensable for the establishment of effective prevention, promotion, and control strategies. Within this context, the study focuses on the identification of novel viruses belonging to the Picornavirales order in freshwater from the Guarapiranga Reservoir in the state of São Paulo, Brazil. The samples were subjected to viral metagenomics. Our analysis led to the characterization of four distinct sequences (GinkV-05, AquaV_10, MarV_14, and MarV_64), which exhibited significant divergence compared to other members of the Picornavirales order. This remarkable diversity prompted the identification of a potential new genus within the Marnaviridae family, tentatively named Ginkgonavirus. Additionally, we characterized four sequences in a very distinct clade and propose the recognition of a novel family (named Aquaviridae) within the Picornavirales order. Our findings contribute valuable insights into the previously uncharted diversity of Picornavirales present in water sources, shedding light on an important facet of viral ecology and evolution in aquatic environments.}, } @article {pmid39271075, year = {2024}, author = {Xu, X and Chen, H and Du, L and Deng, C and Ma, R and Li, B and Li, J and Liu, S and Karthikeyan, R and Chen, Q and Sun, W}, title = {Distribution and drivers of co-hosts of antibiotic and metal(loid) resistance genes in the fresh-brackish-saline groundwater.}, journal = {Chemosphere}, volume = {365}, number = {}, pages = {143332}, doi = {10.1016/j.chemosphere.2024.143332}, pmid = {39271075}, issn = {1879-1298}, mesh = {*Groundwater/chemistry ; *Anti-Bacterial Agents/pharmacology ; China ; *Water Pollutants, Chemical/analysis ; *Drug Resistance, Microbial/genetics ; *Metals, Heavy/analysis ; Environmental Monitoring ; Salinity ; Metagenome ; Genes, Bacterial ; }, abstract = {Groundwater is an essential source of drinking water and agricultural irrigation water, and its protection has become a global goal for public health. However, knowledge about heavy metal(loid) resistance genes (MRGs) in groundwater and the potential co-selection of antibiotic resistance genes (ARGs) have seldom been developed. Here, during the wet and dry seasons, we collected 66 groundwater samples (total dissolved solids = 93.9-9530 mg/L) adjacent to Baiyangdian Lake in Northern China, which presented the few metal(loid) and antibiotic contamination. We identified 160 MRGs whose composition exhibited significant seasonal variation, and dissolved metal(loid)s (particularly Ba) played a determinative role in promoting the MRGs proliferation though with relatively low concentrations, suggesting the relatively vulnerable groundwater ecosystems. Moreover, 27.4% of MRG-carrying metagenome-assembled genomes (MAGs) simultaneously carried ARGs, with the most frequently detected MRG types of Cu, Hg, and As, and ARG types of multidrug and bacitracin. Physicochemical variables, variables related to total dissolved solids, metal(loid)s, and antibiotics synthetically shaped the variation of MRG-ARG hosts in groundwater. We found that the increase of MRG-ARG hosts was critically responsible for the spread of MRGs and ARGs in groundwater. Our findings revealed the widespread co-occurrence of MRGs and ARGs in few-contaminated groundwater and highlighted the crucial roles of salinity in their propagation and transmission.}, } @article {pmid39270978, year = {2024}, author = {Fang, Z and Zang, Q and Chen, J and Li, Z and Yang, D and Wu, C and Yang, H and Guo, N}, title = {Whole-body mass spectrometry imaging reveals the systemic metabolic disorder and catecholamines biosynthesis alteration on heart-gut axis in heart failure rat.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2024.09.001}, pmid = {39270978}, issn = {2090-1224}, abstract = {INTRODUCTION: Heart failure (HF) is a systemic metabolic disorder disease, across multiorgan investigations advancing knowledge of progression and treatment of HF. Whole-body MSI provides spatiotemporal information of metabolites in multiorgan and is expected to be a potent tool to dig out the complex mechanism of HF.

OBJECTIVES: This study aimed at exploring the systemic metabolic disorder in multiorgan and catecholamines biosynthesis alteration on heart-gut axis after HF.

METHODS: Whole-body MSI was used to characterize metabolic disorder of the whole rat body after HF. An integrated method by MSI, LC-MS/MS and ELISA was utilized to analyze key metabolites and enzymes on heart, small intestine, cecum and colon tissues of rat. Gut microbiota dysbiosis was investigated by 16S rDNA sequencing and metagenomic sequencing. Validation experiments and in vitro experiments were performed to verify the effect of catecholamines biosynthesis alteration on heart-gut axis after HF.

RESULTS: Whole-body MSI exhibited varieties of metabolites alteration in multiple organs. Remarkably, catecholamine biosynthesis was significantly altered in the serum, heart and intestines of rats. Furthermore, catecholamines and tyrosine hydroxylase were obviously upregulated in heart and colon tissue. Turicibacter_sanguinis was relevant to catecholamines of heart and colon. Validation experiments demonstrated excessive norepinephrine induced cardio-intestinal injury, including significantly elevating the levels of BNP, pro-BNP, LPS, DAO, and increased the abundance of Turicibacter_sanguinis. These alterations could be reversed by metoprolol treatment blocking the effect of norepinephrine. Additionally, in vitro studies demonstrated that norepinephrine promoted the growth of Turicibacter_sanguinis and Turicibacter_sanguinis could import and metabolize norepinephrine. Collectively, excessive norepinephrine exerted bidirectional effects on cardio-intestinal function to participate in the progression of HF.

CONCLUSION: Our study provides a new approach to elucidate multiorgan metabolic disorder and proposes new insights into heart-gut axis in HF development.}, } @article {pmid39270881, year = {2025}, author = {Bai, M and Zhou, Z and Yin, M and Wang, M and Gao, X and Zhao, J}, title = {The use of metagenomic and untargeted metabolomics in the analysis of the effects of the Lycium barbarum glycopeptide on allergic airway inflammation induced by Artemesia annua pollen.}, journal = {Journal of ethnopharmacology}, volume = {337}, number = {Pt 1}, pages = {118816}, doi = {10.1016/j.jep.2024.118816}, pmid = {39270881}, issn = {1872-7573}, mesh = {Animals ; *Pollen ; *Metabolomics ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Artemisia annua/chemistry ; Mice, Inbred BALB C ; Lycium/chemistry ; Anti-Inflammatory Agents/pharmacology ; Metagenomics/methods ; Disease Models, Animal ; Female ; Drugs, Chinese Herbal/pharmacology ; Respiratory Hypersensitivity/drug therapy ; Male ; Plant Extracts/pharmacology ; }, abstract = {The prevalence of allergic airway inflammation (AAI) worldwide is high. Artemisia annua L. pollen is spread worldwide, and allergic diseases caused by its plant polysaccharides, which are closely related to the intestinal microbiota, have anti-inflammatory effects. Further isolation and purification of Lycium barbarum L. yielded its most effective component Lycium barbarum L. glycopeptide (LbGP), which can inhibit inflammation in animal models. However, its therapeutic effect on AAI and its mechanism of regulating the intestinal flora have not been fully investigated.

AIM OF THE STUDY: To explore LbGP in APE-induced immunological mechanisms of AAI and the interaction mechanism of the intestinal flora and metabolites.

METHODS: A mouse model of AAI generated from Artemisia annua pollen was constructed, and immunological indices related to the disease were examined. A combination of macrogenomic and metabolomic analyses was used to investigate the effects of LbGP on the gut microbial and metabolite profiles of mice with airway inflammation.

RESULTS: LbGP effectively alleviated Artemisia. annua pollen extract (APE)-induced AAI, corrected Th1/Th2 immune dysregulation, decreased Th17 cells, increased Treg cells, and altered the composition and function of the intestinal microbiota. LbGP treatment increased the number of OdoribacterandDuncaniella in the intestines of the mice, but the numble of Alistipes and Ruminococcus decreased. Metabolite pathway enrichment analysis were used to determine the effects of taurine and hypotaurine metabolism, bile acid secretion, and pyrimidine metabolism pathways on disease.

CONCLUSION: Our results revealed significant changes in the macrogenome and metabolome following APE and LbGP intervention, revealed potential correlations between gut microbial species and metabolites, and highlighted the beneficial effects of LbGP on AAI through the modulation of the gut microbiome and host metabolism.}, } @article {pmid39270504, year = {2024}, author = {Deng, J and Kang, D and Zhang, Y and Chen, B and Xia, C and Yu, C and Peng, Y}, title = {Genome-resolved metagenomics reveals the nitrifiers enrichment and species succession in activated sludge under extremely low dissolved oxygen.}, journal = {Water research}, volume = {266}, number = {}, pages = {122420}, doi = {10.1016/j.watres.2024.122420}, pmid = {39270504}, issn = {1879-2448}, mesh = {*Sewage/microbiology ; *Nitrification ; *Metagenomics ; *Bioreactors/microbiology ; *Oxygen/metabolism ; Wastewater/microbiology ; Waste Disposal, Fluid ; Nitrites/metabolism ; }, abstract = {Nitrification, a process carried out by aerobic microorganisms that oxidizes ammonia to nitrate via nitrite, is an indispensable step in wastewater nitrogen removal. To facilitate energy and carbon savings, applying low dissolved oxygen (DO) is suggested to shortcut the conventional biological nitrogen removal pathway, however, the impact of low DO on nitrifying communities within activated sludge is not fully understood. This study used genome-resolved metagenomics to compare nitrifying communities under extremely low- and high-DO. Two bioreactors were parallelly operated to perform nitrification and DO was respectively provided by limited gas-liquid mass transfer from the atmosphere (AN reactor, DO < 0.1 mg/L) and by sufficient aeration (AE reactor, DO > 5.0 mg/L). Low DO was thought to limit nitrifiers growth; however, we demonstrated that complete nitrification could still be achieved under the extremely low-DO conditions, but with no nitrite accumulation observed. Kinetic analysis showed that after long-term exposure to low DO, nitrifiers had a higher oxygen affinity constant and could maintain a relatively high nitrification rate, particularly at low levels of DO (<0.2 mg/L). Community-level gene analysis indicated that low DO promoted enrichment of nitrifiers (the genera Nitrosomonas and Nitrospira, increased by 2.3- to 4.3-fold), and also harbored with 2.3 to 5.3 times higher of nitrification functional genes. Moreover, 46 high-quality (>90 % completeness and <5 % contamination) with 3 most abundant medium-quality metagenome-assembled genomes (MAGs) were retrieved using binning methods. Genome-level phylogenetic analysis revealed the species succession within nitrifying populations. Surprisingly, compared to DO-rich conditions, low-DO conditions were found to efficiently suppressed the ordinary heterotrophic microorganisms (e.g., the families Anaerolineales, Phycisphaerales, and Chitinophagales), but selected for the specific candidate denitrifiers (within phylum Bacteroidota). This study provides new microbial insights to demonstrate that low-DO favors the enrichment of autotrophic nitrifiers over heterotrophs with species-level successions, which would facilitate the optimization of energy and carbon management in wastewater treatment.}, } @article {pmid39270468, year = {2024}, author = {Erdemir, F and Karabulut, A and Aydin, U and Guler, S and Cicek, A and Gokduman, SN and Eser, E and Birdogan, S and Kocagoz, T}, title = {Metagenomic analysis of atheroma plaques for identification of microorganisms indicates presence of Toxoplasma gondii as a possible etiological agent.}, journal = {Journal of infection and public health}, volume = {17}, number = {10}, pages = {102539}, doi = {10.1016/j.jiph.2024.102539}, pmid = {39270468}, issn = {1876-035X}, mesh = {Humans ; *Toxoplasma/genetics/isolation & purification ; *Plaque, Atherosclerotic/microbiology ; *Metagenomics/methods ; Female ; Male ; Aged ; Middle Aged ; Carotid Stenosis/microbiology ; Polymerase Chain Reaction/methods ; Toxoplasmosis/parasitology/microbiology/diagnosis ; DNA, Protozoan/genetics ; Aged, 80 and over ; Whole Genome Sequencing ; Carotid Arteries ; Bacteria/isolation & purification/classification/genetics ; }, abstract = {BACKGROUND: Cardiovascular diseases (CVDs) are the leading cause of death worldwide. Vital organs like the heart are affected by the occlusion of blood vessels due to atherosclerotic plaque formation. However, the role of infectious agents has always been an essential subject of investigation. This study investigated the presence of microorganisms, including nanobacteria, in atherosclerotic plaques removed from human carotid arteries by microbiological and metagenomic examination.

METHODS: Atheroma plaque samples were obtained from 20 patients with carotid artery stenosis who had atherectomy by surgery or percutaneous intervention. Nanobacteria were grown by culturing homogenates of the atheroma plaques. Whole genome sequencing was done for samples. Because of the high percentage of Toxoplasma gondii (T. gondii) DNA, PCR investigation was applied to detect T. gondii DNA in the samples.

RESULTS: A molecular analysis of nanobacteria revealed them to be made of human proteins, supporting the theory that they are not living organisms. According to sequencing results, samples showed that more than 50 % of the metagenomic sequences belonged to Toxoplasma gondii. PCR investigation indicated that T. gondii DNA was positive in 8 (40 %) of 20 plaques.

CONCLUSIONS: Further evidence regarding the role of T. gondii in the etiology of plaque formation may help determine the strategy for prevention and treatment of infections in preventing atheroma plaque formation in the future.}, } @article {pmid39269772, year = {2024}, author = {Rahal, Z and Liu, Y and Peng, F and Yang, S and Jamal, MA and Sharma, M and Moreno, H and Damania, AV and Wong, MC and Ross, MC and Sinjab, A and Zhou, T and Chen, M and Tarifa Reischle, I and Feng, J and Chukwuocha, C and Tang, E and Abaya, C and Lim, JK and Leung, CH and Lin, HY and Deboever, N and Lee, JJ and Sepesi, B and Gibbons, DL and Wargo, JA and Fujimoto, J and Wang, L and Petrosino, JF and Ajami, NJ and Jenq, RR and Moghaddam, SJ and Cascone, T and Hoffman, K and Kadara, H}, title = {Inflammation Mediated by Gut Microbiome Alterations Promotes Lung Cancer Development and an Immunosuppressed Tumor Microenvironment.}, journal = {Cancer immunology research}, volume = {12}, number = {12}, pages = {1736-1752}, pmid = {39269772}, issn = {2326-6074}, support = {P30 CA016672/CA/NCI NIH HHS/United States ; R01 CA205608/CA/NCI NIH HHS/United States ; S10 OD024977/OD/NIH HHS/United States ; R01CA248731//National Cancer Institute (NCI)/ ; R01 CA248731/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome/immunology ; *Tumor Microenvironment/immunology ; *Lung Neoplasms/immunology/microbiology/pathology ; Mice ; Humans ; *Inflammation/immunology ; Adenocarcinoma of Lung/immunology/microbiology/pathology ; Lipocalin-2/metabolism ; Mice, Inbred C57BL ; Disease Models, Animal ; Fecal Microbiota Transplantation ; Mice, Knockout ; }, abstract = {Accumulating evidence indicates that the gut microbiome influences cancer progression and therapy. We recently showed that progressive changes in gut microbial diversity and composition are closely coupled with tobacco-associated lung adenocarcinoma in a human-relevant mouse model. Furthermore, we demonstrated that the loss of the antimicrobial protein Lcn2 in these mice exacerbates protumor inflammatory phenotypes while further reducing microbial diversity. Yet, how gut microbiome alterations impinge on lung adenocarcinoma development remains poorly understood. In this study, we investigated the role of gut microbiome changes in lung adenocarcinoma development using fecal microbiota transfer and delineated a pathway by which gut microbiome alterations incurred by loss of Lcn2 fostered the proliferation of proinflammatory bacteria of the genus Alistipes, triggering gut inflammation. This inflammation propagated systemically, exerting immunosuppression within the tumor microenvironment, augmenting tumor growth through an IL6-dependent mechanism and dampening response to immunotherapy. Corroborating our preclinical findings, we found that patients with lung adenocarcinoma with a higher relative abundance of Alistipes species in the gut showed diminished response to neoadjuvant immunotherapy. These insights reveal the role of microbiome-induced inflammation in lung adenocarcinoma and present new potential targets for interception and therapy.}, } @article {pmid39269181, year = {2024}, author = {Quan, Q and Liu, J and Li, C and Ke, Z and Tan, Y}, title = {Insights into prokaryotic communities and their potential functions in biogeochemical cycles in cold seep.}, journal = {mSphere}, volume = {9}, number = {10}, pages = {e0054924}, pmid = {39269181}, issn = {2379-5042}, mesh = {*Bacteria/classification/genetics/metabolism ; *Microbiota ; *Nitrogen/metabolism ; *Geologic Sediments/microbiology ; *Seawater/microbiology/chemistry ; *Sulfur/metabolism ; Phosphorus/metabolism/analysis ; Cold Temperature ; Metagenomics ; }, abstract = {UNLABELLED: Microorganisms are significant drivers of organic matter mineralization and are essential in marine biogeochemical cycles. However, the variations and influencing factors in prokaryotic communities from cold-seep sediments to the water column and the specific role of these microorganisms in biogeochemical cycles in the water column above cold seep remain unclear. Here, we investigated prokaryotic communities and their roles in nitrogen/sulfur cycling processes and conducted in situ dissolved organic matter (DOM) enrichment experiments to explore the effects of diverse sources of DOM on prokaryotic communities. Field investigations showed that the prokaryotic communities in the near-bottom water were more similar to those in the deep layer of the euphotic zone (44.60%) and at a depth of 400 m (50.89%) than those in the sediment (18.00%). DOM enrichment experiments revealed that adding dissolved organic nitrogen (DON) and phosphorus DOP caused a notable increase in the relative abundances of Rhodobacterales and Vibrionales, respectively. A remarkable increase was observed in the relative abundance of Alteromonadales and Pseudomonadales after the addition of dissolved organic sulfur (DOS). The metagenomic results revealed that Proteobacteria served as the keystone taxa in mediating the biogeochemical cycles of nitrogen, phosphorus, and sulfur in the Haima cold seep. This study highlights the responses of prokaryotes to DOM with different components and the microbially driven elemental cycles in cold seeps, providing a foundational reference for further studies on material energy metabolism and the coupled cycling of essential elements mediated by deep-sea microorganisms.

IMPORTANCE: Deep-sea cold seeps are among the most productive ecosystems, sustaining unique fauna and microbial communities through the release of methane and other hydrocarbons. Our study revealed that the influence of seepage fluid on the prokaryotic community in the water column is surprisingly limited, which challenges conventional views regarding the impact of seepage fluids. In addition, we identified that different DOM compositions play a crucial role in shaping the prokaryotic community composition, providing new insights into the factors driving microbial diversity in cold seeps. Furthermore, the study highlighted Proteobacteria as key and multifaceted drivers of biogeochemical cycles in cold seeps, emphasizing their significant contribution to complex interactions and processes. These findings offer a fresh perspective on the dynamics of cold-seep environments and their microbial communities, advancing our understanding of the biogeochemical functions in deep-sea environments.}, } @article {pmid39268953, year = {2024}, author = {Dai, Z and Lu, Q and Sun, M and Chen, H and Zhu, R and Wang, H}, title = {Identification of a Novel Parvovirus in the Arctic Wolf (Canis lupus arctos).}, journal = {Polish journal of microbiology}, volume = {73}, number = {3}, pages = {395-401}, pmid = {39268953}, issn = {2544-4646}, mesh = {Animals ; *Phylogeny ; *Genome, Viral ; *Wolves/virology ; *Open Reading Frames ; *Parvovirus/genetics/classification/isolation & purification ; Capsid Proteins/genetics ; Parvoviridae Infections/virology/veterinary ; Base Composition ; China ; DNA, Viral/genetics ; }, abstract = {A novel virus, temporarily named "Arctic wolf parvovirus" (AWPV), was discovered in a pharyngeal metagenomic library derived from an Arctic wolf (Canis lupus arctos) in China. The genome sequence was assigned GenBase accession number C_AA071902.1. AWPV has a genome comprised of 4,920 base pairs with a nucleotide composition of 36.4% A, 23.4% T, 18.2% G, and 22.0% C, with a GC content of 40.2%. Its structure resembles parvoviruses, containing two open reading frames: the nonstructural (NS) region encoding replication enzymes and the structural (VP) region encoding capsid protein. Pairwise sequence comparison and phylogenetic analysis suggest AWPV may represent a novel species within the genus Protoparvovirus. This discovery enhances our understanding of mammalian virus ecology and potential future infectious diseases.}, } @article {pmid39268488, year = {2024}, author = {Hu, L and Huang, X and Yee, NH and Meng, H and Jiang, L and Liang, L and Chen, X}, title = {Pythium insidiosum: an emerging pathogen that is easily misdiagnosed and given treatment as a fungus.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1430032}, pmid = {39268488}, issn = {2235-2988}, mesh = {*Pythium/isolation & purification/drug effects/genetics ; Humans ; *Pythiosis/diagnosis/microbiology/drug therapy ; *Antifungal Agents/pharmacology/therapeutic use ; *Microbial Sensitivity Tests ; Male ; Diagnostic Errors ; Communicable Diseases, Emerging/microbiology/diagnosis/drug therapy ; Keratitis/microbiology/diagnosis/drug therapy ; Middle Aged ; High-Throughput Nucleotide Sequencing ; Female ; Aged ; }, abstract = {BACKGROUND: Pythium insidiosum (P. insidiosum) is the causative agent of pythiosis, an infectious disease with a high morbidity and fatality rate. Pythiosis cases have increased dramatically during the past ten years, particularly in tropical and subtropical areas. Sadly, microbiologists and medical professionals know very little about pythiosis, and the disease is frequently challenging to identify. It is frequently misdiagnosed as a fungal infection.

METHODS: We report two cases of pythiosis, one was Pythium keratitis, the other was cutaneous pythiosis. The patient with corneal infection had no underlying disease, while the patient with cutaneous pythiosis had a history of liver cirrhosis, diabetes, and psoriasis. The corneal sample and subcutaneous pus were sent for metagenomic Next-Generation Sequencing (mNGS). To further diagnose the isolated strain, P. insidiosum zoospores were induced to produce by co-incubation with sterile grass leaves in sterile pond water. Their zoospores were used as an inoculum for drug susceptibility testing by disk diffusion and broth microdilution method.

RESULTS: The mNGS of two cases were reported as P. insidiosum. Zoospores were produced after incubation 48h. The zoospores were collected for drug susceptibility assay. All antifungal drugs, antibacterial drugs of β-Lactams, vancomycin, levofloxacin, ciprofloxacin, gentamicin, trimethoprim-sulfamethoxazole, clindamycin have no inhibitory activity against P. insidiosum in vitro. Minocycline, tigecycline, linezolid, erythromycin and azithromycin have significant in vitro activity against P. insidiosum. Based on the susceptibility results, the drug was changed from itraconazole to linezolid and minocycline, along with multiple debridements and drainage for cutaneous pythiosis. The patient was discharged after 24 days of treatment.

CONCLUSIONS: Early and accurate identification, combined with aggressive surgical debridement and appropriate drug therapy, can greatly improve patient managements. Conventional culture and zoospore induction remain gold standard for diagnosis; however, DNA-based method should be performed simultaneously. The drug susceptibility testing provides profound effects on proper drug selection against P. insidiosum.}, } @article {pmid39268238, year = {2024}, author = {Wang, J and Su, C and Qian, M and Wang, X and Chen, C and Liu, Y and Liu, W and Xiang, Z and Xu, B}, title = {Subchronic toxic effects of bisphenol A on the gut-liver-hormone axis in rats via intestinal flora and metabolism.}, journal = {Frontiers in endocrinology}, volume = {15}, number = {}, pages = {1415216}, pmid = {39268238}, issn = {1664-2392}, mesh = {Animals ; *Phenols/toxicity ; Male ; Female ; Rats ; *Gastrointestinal Microbiome/drug effects ; *Benzhydryl Compounds/toxicity ; *Liver/drug effects/metabolism/pathology ; *Endocrine Disruptors/toxicity ; Rats, Sprague-Dawley ; Hormones/blood ; }, abstract = {BACKGROUND: Bisphenol A (BPA), a characteristic endocrine disruptor, is a substance that seriously interferes with the human endocrine system and causes reproductive disorders and developmental abnormalities. However, its toxic effects on the gut-liver-hormone axis are still unclear.

METHOD: Male and female rats were exposed to BPA (300 mg/kg) by oral gavage for 60 consecutive days. H&E staining was used for histopathological evaluation, and the serum biochemical indexes were determined using an automatic analyzer. The 16S rRNA gene sequencing was used to detect the intestinal microbial diversity, and the GC-MS was used to analyze the contents of short-chain fatty acids (SCFAs) in colon contents. UPLC-QTOF MS was used to analyze the related metabolites. The ELISA method was used to assess the levels of serum inflammatory factors.

RESULTS: Histopathological analysis indicated that the liver, heart, and testis were affected by BPA. There was a significant effect on alanine aminotransferase (ALT), triglyceride (TG), total cholesterol (TC), and low-density lipoprotein (LDL) in the male-BPA group (P < 0.05), and globulin (GLB), indirect bilirubin (IBIL), alkaline phosphatase (ALP), ALT, TG, TC, high-density lipoprotein (HDL), and creatinine (Cr) in the female-BPA group (P < 0.05). Metagenomics (16S rRNA gene sequencing) analysis indicated that BPA reduced the diversity and changed the composition of gut microbiota in rats significantly. Compared with the control and blank groups, the contents of caproic acid, isobutyric acid, isovaleric acid, and propanoic acid in the colon contents decreased in the male-BPA group (P < 0.05), and caproic acid, isobutyric acid, isovaleric acid, and valeric acid in the colon contents decreased in the female-BPA group (P < 0.05). Metabolomic analysis of the serum indicated that BPA could regulate bile acid levels, especially ursodeoxycholic acid (UDCA) and its conjugated forms. The contents of amino acids, hormones, and lipids were also significantly affected after exposure to BPA. The increase in interleukin-6 (IL-6), interleukin-23 (IL-23), and transforming growth factor-β (TGF-β) in the serum of the male-BPA group suggests that BPA exposure affects the immune system.

CONCLUSION: BPA exposure will cause toxicity to rats via disrupting the gut-liver-hormone axis.}, } @article {pmid39268134, year = {2024}, author = {Liu, X and Zhao, Q and He, X and Min, J and Yao, RSY and Chen, Z and Ma, J and Hu, W and Huang, J and Wan, H and Guo, Y and Zhou, M}, title = {Clinical characteristics and microbial signatures in the lower airways of diabetic and nondiabetic patients with pneumonia.}, journal = {Journal of thoracic disease}, volume = {16}, number = {8}, pages = {5262-5273}, pmid = {39268134}, issn = {2072-1439}, abstract = {BACKGROUND: The microbial signatures in diabetes with pneumonia and the risk factors of severe pneumonia (SP) in diabetic patients are not clear. Our study explored microbial signatures and the association between clinical characteristics and SP then constructed a risk model to find effective biomarkers for predicting pneumonia severity.

METHODS: Our study was conducted among 273 patients with pneumonia diagnosed and treated in our hospital from January 2018 to May 2021. Bronchoalveolar lavage fluid (BALF) samples and clinical data were collected. Metagenomic sequencing was applied after extracting the DNA from samples. Appropriate statistical methods were used to compare the microbial signatures and clinical characteristics in patients with or without diabetes mellitus (DM).

RESULTS: In total, sixty-one pneumonia patients with diabetes and 212 pneumonia patients without diabetes were included. Sixty-six differential microorganisms were found to be associated with SP in diabetic patients. Some microbes correlated with clinical indicators of SP. The prediction model for SP was established and the receiver operating characteristic (ROC) curve demonstrated its accuracy, with the sensitivity and specificity of 0.82 and 0.91, respectively.

CONCLUSIONS: Some microorganisms affect the severity of pneumonia. We identified the microbial signatures in the lower airways and the association between clinical characteristics and SP. The predictive model was more accurate in predicting SP by combining microbiological indicators and clinical characteristics, which might be beneficial to the early identification and management of patients with SP.}, } @article {pmid39267171, year = {2024}, author = {Gandasegui, J and Fleitas, PE and Petrone, P and Grau-Pujol, B and Novela, V and Rubio, E and Muchisse, O and Cossa, A and Jamine, JC and Sacoor, C and Brienen, EAT and van Lieshout, L and Muñoz, J and Casals-Pascual, C}, title = {Baseline gut microbiota diversity and composition and albendazole efficacy in hookworm-infected individuals.}, journal = {Parasites & vectors}, volume = {17}, number = {1}, pages = {387}, pmid = {39267171}, issn = {1756-3305}, mesh = {*Albendazole/therapeutic use/pharmacology/administration & dosage ; Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; *Anthelmintics/therapeutic use/administration & dosage ; *Hookworm Infections/drug therapy ; *Feces/parasitology/microbiology ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; Adult ; Treatment Outcome ; Animals ; Young Adult ; Middle Aged ; Ancylostomatoidea/drug effects/genetics ; Adolescent ; Child ; }, abstract = {Soil-transmitted helminth (STH) infections account for a significant global health burden, necessitating mass drug administration with benzimidazole-class anthelmintics, such as albendazole (ALB), for morbidity control. However, ALB efficacy shows substantial variability, presenting challenges for achieving consistent treatment outcomes. We have explored the potential impact of the baseline gut microbiota on ALB efficacy in hookworm-infected individuals through microbiota profiling and machine learning (ML) techniques. Our investigation included 89 stool samples collected from hookworm-infected individuals that were analyzed by microscopy and quantitative PCR (qPCR). Of these, 44 were negative by microscopy for STH infection using the Kato-Katz method and qPCR 21 days after treatment, which entails a cure rate of 49.4%. Microbiota characterization was based on amplicon sequencing of the V3-V4 16S ribosomal RNA gene region. Alpha and beta diversity analyses revealed no significant differences between participants who were cured and those who were not cured, suggesting that baseline microbiota diversity does not influence ALB treatment outcomes. Furthermore, differential abundance analysis at the phylum, family and genus levels yielded no statistically significant associations between bacterial communities and ALB efficacy. Utilizing supervised ML models failed to predict treatment response accurately. Our investigation did not provide conclusive insights into the relationship between gut microbiota and ALB efficacy. However, the results highlight the need for future research to incorporate longitudinal studies that monitor changes in the gut microbiota related to the infection and the cure with ALB, as well as functional metagenomics to better understand the interaction of the microbiome with the drug, and its role, if there is any, in modulating anthelmintic treatment outcomes in STH infections. Interdisciplinary approaches integrating microbiology, pharmacology, genetics and data science will be pivotal in advancing our understanding of STH infections and optimizing treatment strategies globally.}, } @article {pmid39267108, year = {2024}, author = {Zheng, YR and Chen, XH and Chen, Q and Cao, H}, title = {Comparison of targeted next-generation sequencing and metagenomic next-generation sequencing in the identification of pathogens in pneumonia after congenital heart surgery: a comparative diagnostic accuracy study.}, journal = {Italian journal of pediatrics}, volume = {50}, number = {1}, pages = {174}, pmid = {39267108}, issn = {1824-7288}, mesh = {Humans ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing ; Male ; Female ; *Heart Defects, Congenital/surgery ; Infant ; *Metagenomics/methods ; *Cardiac Surgical Procedures/adverse effects ; Postoperative Complications/diagnosis ; Infant, Newborn ; Pneumonia/diagnosis/microbiology ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: This study aimed to compare targeted next-generation sequencing (tNGS) with metagenomic next-generation sequencing (mNGS) for pathogen detection in infants with severe postoperative pneumonia after congenital heart surgery.

METHODS: We conducted a retrospective observational study using data from the electronic medical record system of infants who developed severe pneumonia after surgery for congenital heart disease from August 2021 to August 2022. Infants were divided into tNGS and mNGS groups based on the pathogen detection methods. The primary outcome was the efficiency of pathogen detection, and the secondary outcomes were the timeliness and cost of each method.

RESULTS: In the study, 91 infants were included, with tNGS detecting pathogens in 84.6% (77/91) and mNGS in 81.3% (74/91) of cases (P = 0.55). No significant differences were found in sensitivity, specificity, PPA, and NPA between the two methods (P > 0.05). tNGS identified five strains with resistance genes, while mNGS detected one strain. Furthermore, tNGS had a faster detection time (12 vs. 24 h) and lower cost ($150 vs. $500) compared to mNGS.

CONCLUSION: tNGS offers similar sensitivity to mNGS but with greater efficiency and cost-effectiveness, making it a promising approach for respiratory pathogen detection.}, } @article {pmid39267031, year = {2024}, author = {Liu, H and Ran, Q and Ma, J and Zhang, J and Tan, N and Xi, L and Li, X and Zhang, J and Lu, S}, title = {Retrospective clinical and microbiologic analysis of metagenomic next-generation sequencing in the microbiological diagnosis of cutaneous infectious granulomas.}, journal = {Annals of clinical microbiology and antimicrobials}, volume = {23}, number = {1}, pages = {84}, pmid = {39267031}, issn = {1476-0711}, support = {82172289//National Natural Science Foundation of China/ ; 202201020345//Guangzhou Municipal Science and Technology Project/ ; }, mesh = {Humans ; Retrospective Studies ; Male ; Female ; Middle Aged ; Adult ; *Granuloma/microbiology/diagnosis ; *High-Throughput Nucleotide Sequencing/methods ; Bacteria/isolation & purification/genetics/classification ; Aged ; Sensitivity and Specificity ; Fungi/isolation & purification/genetics/classification ; Young Adult ; Metagenomics/methods ; Skin Diseases, Infectious/diagnosis/microbiology ; Adolescent ; Skin/microbiology/pathology ; Child ; }, abstract = {BACKGROUND: Cutaneous infectious granulomas (CIG) are localized and chronic skin infection caused by a variety of pathogens such as protozoans, bacteria, worms, viruses and fungi. The diagnosis of CIG is difficult because microbiological examination shows low sensitivity and the histomorphological findings of CIG caused by different pathogens are commonly difficult to be distinguished.

OBJECTIVE: The objective of this study is to explore the application of mNGS in tissue sample testing for CIG cases, and to compare mNGS with traditional microbiological methods by evaluating sensitivity and specificity.

METHODS: We conducted a retrospective study at the Department of Dermatology of Sun Yat-sen Memorial Hospital, Sun Yat-sen University from January 1st, 2020, to May 31st, 2024. Specimens from CIG patients with a clinical presentation of cutaneous infection that was supported by histological examination were retrospectively enrolled. Specimens were delivered to be tested for microbiological examinations and mNGS.

RESULTS: Our data show that mNGS detected Non-tuberculosis mycobacteria, Mycobacterium tuberculosis, fungi and bacteria in CIG. Compared to culture, mNGS showed a higher positive rate (80.77% vs. 57.7%) with high sensitivity rate (100%) and negative predictive value (100%). In addition, mNGS can detect more pathogens in one sample and can be used to detect variable samples including the samples of paraffin-embedded tissue with shorter detective time. Of the 21 patients who showed clinical improvement within a 30-day follow-up, eighteen had their treatments adjusted, including fifteen who continued treatment based on the results of mNGS.

CONCLUSIONS: mNGS could provide a potentially rapid and effective alternative detection method for diagnosis of cutaneous infectious granulomas and mNGS results may affect the clinical prognosis resulting from enabling the patients to initiate timely treatment.}, } @article {pmid39266944, year = {2024}, author = {Meirelles, PM and Viana, PAB and Tschoeke, DA and de Moraes, L and Santos, LA and Barral-Netto, M and Khouri, R and Ramos, PIP}, title = {Optimizing next-generation sequencing efficiency in clinical settings: analysis of read length impact on cost and performance.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {856}, pmid = {39266944}, issn = {1471-2164}, support = {2023-PPI-007//Rockefeller Foundation/ ; }, mesh = {*High-Throughput Nucleotide Sequencing/methods ; *COVID-19/virology ; Humans ; *SARS-CoV-2/genetics ; *Metagenomics/methods ; Bacteria/genetics ; }, abstract = {BACKGROUND: The expansion of sequencing technologies as a result of the response to the COVID-19 pandemic enabled pathogen (meta)genomics to be deployed as a routine component of surveillance in many countries. Scaling genomic surveillance, however, comes with associated costs in both equipment and sequencing reagents, which should be optimized. Here, we evaluate the cost efficiency and performance of different read lengths in identifying pathogens in metagenomic samples. We carefully evaluated performance metrics, costs, and time requirements relative to choices of 75, 150 and 300 base pairs (bp) read lengths in pathogen identification.

RESULTS: Our findings revealed that moving from 75 bp to 150 bp read length approximately doubles both the cost and sequencing time. Opting for 300 bp reads leads to approximately two- and three-fold increases, respectively, in cost and sequencing time compared to 75 bp reads. For viral pathogen detection, the sensitivity median ranged from 99% with 75 bp reads to 100% with 150-300 bp reads. However, bacterial pathogens detection was less effective with shorter reads: 87% with 75 bp, 95% with 150 bp, and 97% with 300 bp reads. These findings were consistent across different levels of taxa abundance. The precision of pathogen detection using shorter reads was comparable to that of longer reads across most viral and bacterial taxa.

CONCLUSIONS: During disease outbreak situations, when swift responses are required for pathogen identification, we suggest prioritizing 75 bp read lengths, especially if detection of viral pathogens is aimed. This practical approach allows better use of resources, enabling the sequencing of more samples using streamlined workflows, while maintaining a reliable response capability.}, } @article {pmid39266528, year = {2024}, author = {Liu, S and Chen, Q and Hou, C and Dong, C and Qiu, X and Tang, K}, title = {Recovery of 1559 metagenome-assembled genomes from the East China Sea's low-oxygen region.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {994}, pmid = {39266528}, issn = {2052-4463}, mesh = {China ; *Metagenome ; *Archaea/genetics ; Bacteria/genetics/classification ; Oxygen ; Seawater/microbiology ; Phylogeny ; Metagenomics ; Oceans and Seas ; Microbiota ; }, abstract = {The Changjiang Estuary and adjacent East China Sea are well-known hypoxic aquatic environments. Eutrophication-driven hypoxia frequently occurs in coastal areas, posing a major threat to the ecological environment, including altering community structure and metabolic processes of marine organisms, and enhancing diversion of energy shunt into microbial communities. However, the responses of microbial communities and their metabolic pathways to coastal hypoxia remain poorly understood. Here, we studied the microbial communities collected from spatiotemporal samplings using metagenomic sequencing in the Changjiang Estuary and adjacent East China Sea. This generated 1.31 Tbp of metagenomics data, distributed across 103 samples corresponding to 8 vertical profiles. We further reported 1,559 metagenome-assembled genomes (MAGs), of which 508 were high-quality MAGs (Completeness > 90% and Contamination < 10%). Phylogenomic analysis classified them into 181 archaeal and 1,378 bacterial MAGs. These results provided a valuable metagenomic dataset available for further investigation of the effects of hypoxia on marine microorganisms.}, } @article {pmid39266450, year = {2024}, author = {Gnimpieba, EZ and Hartman, TW and Do, T and Zylla, J and Aryal, S and Haas, SJ and Agany, DDM and Gurung, BDS and Doe, V and Yosufzai, Z and Pan, D and Campbell, R and Huber, VC and Sani, R and Gadhamshetty, V and Lushbough, C}, title = {Biofilm marker discovery with cloud-based dockerized metagenomics analysis of microbial communities.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {Supplement_1}, pages = {}, pmid = {39266450}, issn = {1477-4054}, support = {#1849206//National Science Foundation/ ; //Institutional Development Award/ ; /GM/NIGMS NIH HHS/United States ; P20GM103443/NH/NIH HHS/United States ; }, mesh = {*Biofilms/growth & development ; *Metagenomics/methods ; Microbiota/genetics ; Cloud Computing ; Humans ; Computational Biology/methods ; }, abstract = {In an environment, microbes often work in communities to achieve most of their essential functions, including the production of essential nutrients. Microbial biofilms are communities of microbes that attach to a nonliving or living surface by embedding themselves into a self-secreted matrix of extracellular polymeric substances. These communities work together to enhance their colonization of surfaces, produce essential nutrients, and achieve their essential functions for growth and survival. They often consist of diverse microbes including bacteria, viruses, and fungi. Biofilms play a critical role in influencing plant phenotypes and human microbial infections. Understanding how these biofilms impact plant health, human health, and the environment is important for analyzing genotype-phenotype-driven rule-of-life functions. Such fundamental knowledge can be used to precisely control the growth of biofilms on a given surface. Metagenomics is a powerful tool for analyzing biofilm genomes through function-based gene and protein sequence identification (functional metagenomics) and sequence-based function identification (sequence metagenomics). Metagenomic sequencing enables a comprehensive sampling of all genes in all organisms present within a biofilm sample. However, the complexity of biofilm metagenomic study warrants the increasing need to follow the Findability, Accessibility, Interoperability, and Reusable (FAIR) Guiding Principles for scientific data management. This will ensure that scientific findings can be more easily validated by the research community. This study proposes a dockerized, self-learning bioinformatics workflow to increase the community adoption of metagenomics toolkits in a metagenomics and meta-transcriptomics investigation. Our biofilm metagenomics workflow self-learning module includes integrated learning resources with an interactive dockerized workflow. This module will allow learners to analyze resources that are beneficial for aggregating knowledge about biofilm marker genes, proteins, and metabolic pathways as they define the composition of specific microbial communities. Cloud and dockerized technology can allow novice learners-even those with minimal knowledge in computer science-to use complicated bioinformatics tools. Our cloud-based, dockerized workflow splits biofilm microbiome metagenomics analyses into four easy-to-follow submodules. A variety of tools are built into each submodule. As students navigate these submodules, they learn about each tool used to accomplish the task. The downstream analysis is conducted using processed data obtained from online resources or raw data processed via Nextflow pipelines. This analysis takes place within Vertex AI's Jupyter notebook instance with R and Python kernels. Subsequently, results are stored and visualized in Google Cloud storage buckets, alleviating the computational burden on local resources. The result is a comprehensive tutorial that guides bioinformaticians of any skill level through the entire workflow. It enables them to comprehend and implement the necessary processes involved in this integrated workflow from start to finish. This manuscript describes the development of a resource module that is part of a learning platform named "NIGMS Sandbox for Cloud-based Learning" https://github.com/NIGMS/NIGMS-Sandbox. The overall genesis of the Sandbox is described in the editorial NIGMS Sandbox [1] at the beginning of this Supplement. This module delivers learning materials on the analysis of bulk and single-cell ATAC-seq data in an interactive format that uses appropriate cloud resources for data access and analyses.}, } @article {pmid39265854, year = {2024}, author = {Viglioli, M and Rizzo, SM and Alessandri, G and Fontana, F and Milani, C and Turroni, F and Mancabelli, L and Croci, N and Rivara, S and Vacondio, F and Ventura, M and Mor, M}, title = {Investigating drug-gut microbiota interactions: reductive and hydrolytic metabolism of oral glucocorticoids by in vitro artificial gut microbiota.}, journal = {International journal of pharmaceutics}, volume = {665}, number = {}, pages = {124663}, doi = {10.1016/j.ijpharm.2024.124663}, pmid = {39265854}, issn = {1873-3476}, mesh = {*Gastrointestinal Microbiome/drug effects ; *Glucocorticoids/metabolism/administration & dosage ; Humans ; *Feces/microbiology ; Hydrolysis ; Administration, Oral ; Prodrugs/metabolism ; Fermentation ; }, abstract = {Elucidation of the role of gut microbiota in the metabolism of orally administered drugs may improve therapeutic effectiveness and contribute to the development of personalized medicine. In this study, ten different artificial gut microbiota (AGM), obtained by culturing fecal samples in a continuous fermentation system, were challenged for their metabolizing capacity on a panel of six glucocorticoids selected from either prodrugs or drugs. Data from metabolic stability assays highlighted that, while the hydrolysis-mediated conversion of prodrugs to drugs represented only a minor metabolic pathway, significant differences in the stability of parent compounds and in their conversion rates to multiple reductive metabolites were obtained for the selected drugs. In the latter case, a taxonomic composition-dependent ability to convert parent drugs to metabolites was observed. Indeed, the artificial microbial communities dominated by the genus Bacteroides showed the maximal conversion of parent glucocorticoids to several metabolites. Furthermore, the effect of drugs on AGM was also evaluated through shallow shotgun sequencing and flow cytometry-based total bacterial cell count highlighting that these drugs can affect both the taxonomic composition and growth performances of the human gut microbiota.}, } @article {pmid39265811, year = {2024}, author = {Nataraj, BH and Ranveer, SA and K, J and Nagpal, R and Behare, PV}, title = {Immune and microbiome modulatory effects of Limosilactobacillus fermentum NCDC 400 in an immunocompromised mouse model.}, journal = {Microbial pathogenesis}, volume = {196}, number = {}, pages = {106927}, doi = {10.1016/j.micpath.2024.106927}, pmid = {39265811}, issn = {1096-1208}, mesh = {Animals ; Mice ; *Probiotics/administration & dosage ; *Limosilactobacillus fermentum ; *Immunocompromised Host ; *Disease Models, Animal ; *Cyclophosphamide ; *Gastrointestinal Microbiome/drug effects ; *Spleen/immunology ; Oxidative Stress ; Male ; Cell Differentiation ; }, abstract = {The present study was aimed to assess and validate the safety and functional efficacy of an indigenous probiotic strain Limosilactobacillus fermentum NCDC 400 (hereafter, LFN400) in an immunocompromised murine model. The study included four groups; a normal control (NC) group without immune suppression; an experimental model control (MC) with immune suppression induced via intraperitoneal cyclophosphamide (Cy) administration; and two MC groups orally administered with either low dose (LD) or high dose (HD) of LFN400 at dose 10[8] and 10[10] CFU/mouse/day, respectively, for 15-days. Both control groups received normal saline as placebo control. LFN400 improved specific experimental characteristics including hematological and serum biochemical markers. Compared to MC group, LFN400-fed groups showed markedly (P < 0.05) decreased arrays of detrimental caecal enzymes. We did not observe instances of bacterial translocation of LFN400 from gut to bloodstream or extra-intestinal organs. LFN400 intake significantly (P < 0.05) enhanced spleen cell differentiation, immune and oxidative stress markers, and restored Cy-induced histopathological changes in multiple tissues, including the spleen. There was no genotoxic effect of LFN400 on bone marrow cells. Although not statistically significant, LFN400 feeding moderately increased gut microbiome diversity, supporting the growth of beneficial saccharolytic microorganisms and reducing the presence of pathobionts. The findings demonstrate that the probiotic strain LFN400 possesses in vivo safety and immunomodulatory potency and thus should be considered a potential candidate for future human clinical studies.}, } @article {pmid39265779, year = {2024}, author = {Xiao, X and Wu, Y and Jie, Z and Lin, L and Li, Y and Hu, W and Li, Y and Zhong, S}, title = {Akkermansia Muciniphila supplementation improves hyperlipidemia, cardiac function, and gut microbiota in high fat fed apolipoprotein E-deficient mice.}, journal = {Prostaglandins & other lipid mediators}, volume = {175}, number = {}, pages = {106906}, doi = {10.1016/j.prostaglandins.2024.106906}, pmid = {39265779}, issn = {1098-8823}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Akkermansia ; Mice ; *Hyperlipidemias ; *Diet, High-Fat/adverse effects ; *Apolipoproteins E/deficiency/genetics ; Male ; Atherosclerosis ; Humans ; Mice, Inbred C57BL ; Dietary Supplements ; Mice, Knockout, ApoE ; Verrucomicrobia ; }, abstract = {Hyperlipidemia, obesity and gut dysbiosis are pivotal risk factors for atherosclerotic cardiovascular disease (ACVD). Supplementation of Akkermansia muciniphila (AKK) has also been proven to be effective in the prevention and treatment of obesity and other metabolic disorders. Here we found that AKK was more abundant in healthy control than ACVD patients via metagenomic sequencing on fecal samples. Subsequently, we investigated the role and underlying mechanism of AKK on obesity-associated atherosclerosis. AKK intervention partially reversed the exacerbation of atherosclerotic lesion formation in ApoE[-/-] mice by improving dyslipidemia. Interestingly, replenishment with AKK significantly enhanced cardiac function and reduced the body weight. It also reduced pro-inflammatory cytokine IL-6 and increased anti-inflammatory IL-10 in the circulation. Additionally, AKK colonization dramatically regulated gut microbiota and increased the abundance of Lactobacillaceae. Our findings have provided novel insights into the therapeutic potential of AKK as a beneficial microbe for treating atherosclerotic-associated cardiovascular diseases.}, } @article {pmid39264803, year = {2024}, author = {Tang, D and Hu, W and Fu, B and Zhao, X and You, G and Xie, C and Wang, HY and Guo, X and Zhang, Q and Liu, Z and Ye, L}, title = {Gut microbiota-mediated C-sulfonate metabolism impairs the bioavailability and anti-cholestatic efficacy of andrographolide.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2387402}, pmid = {39264803}, issn = {1949-0984}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Diterpenes/metabolism/pharmacology ; *Biological Availability ; Mice ; Cholestasis/metabolism/drug therapy/microbiology ; Male ; RNA, Ribosomal, 16S/genetics ; Bile Acids and Salts/metabolism ; Bacteria/metabolism/classification/genetics/drug effects/isolation & purification ; Humans ; Mice, Inbred C57BL ; Liver/metabolism/drug effects ; Receptors, Cytoplasmic and Nuclear/metabolism/genetics ; Disease Models, Animal ; }, abstract = {Cholestatic liver injury results from the accumulation of toxic bile acids in the liver, presenting a therapeutic challenge with no effective treatment available to date. Andrographolide (AP) has exhibited potential as a treatment for cholestatic liver disease. However, its limited oral bioavailability poses a significant obstacle to harnessing its potent therapeutic properties and restricts its clinical utility. This limitation is potentially attributed to the involvement of gut microbiota in AP metabolism. In our study, employing pseudo-germ-free, germ-free and strain colonization animal models, along with 16S rRNA and shotgun metagenomic sequencing analysis, we elucidate the pivotal role played by gut microbiota in the C-sulfonate metabolism of AP, a process profoundly affecting its bioavailability and anti-cholestatic efficacy. Subsequent investigations pinpoint a specific enzyme, adenosine-5'-phosphosulfate (APS) reductase, predominantly produced by Desulfovibrio piger, which catalyzes the reduction of SO4[2-] to HSO3[-]. HSO3[-] subsequently interacts with AP, targeting its C=C unsaturated double bond, resulting in the formation of the C-sulfonate metabolite, 14-deoxy-12(R)-sulfo andrographolide (APM). Inhibition of APS reductase leads to a notable enhancement in AP bioavailability and anti-cholestatic efficacy. Furthermore, employing RNA sequencing analysis and farnesoid X receptor (FXR) knockout mice, our findings suggest that AP may exert its anti-cholestatic effects by activating the FXR pathway to promote bile acid efflux. In summary, our study unveils the significant involvement of gut microbiota in the C-sulfonate metabolism of AP and highlights the potential benefits of inhibiting APS reductase to enhance its therapeutic effects. These discoveries provide valuable insights into enhancing the clinical applicability of AP as a promising treatment for cholestatic liver injury.}, } @article {pmid39264585, year = {2025}, author = {Lou, H and Wang, X and Jiang, Q and Li, X and Yao, Y and Chen, Q and Chen, L and Zhang, S and Yu, Y and Liu, C and Zhou, H}, title = {Clinical evaluation of a highly multiplexed CRISPR-based diagnostic assay for diagnosing lower respiratory tract infection: a prospective cohort study.}, journal = {Infectious diseases (London, England)}, volume = {57}, number = {2}, pages = {167-177}, doi = {10.1080/23744235.2024.2402921}, pmid = {39264585}, issn = {2374-4243}, mesh = {Humans ; Prospective Studies ; Male ; Female ; Middle Aged ; *Respiratory Tract Infections/diagnosis/microbiology ; Aged ; *Sensitivity and Specificity ; Adult ; *Multiplex Polymerase Chain Reaction/methods ; High-Throughput Nucleotide Sequencing/methods ; Molecular Diagnostic Techniques/methods ; Bacteria/genetics/isolation & purification/classification ; Young Adult ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Aged, 80 and over ; CRISPR-Cas Systems ; Bacterial Infections/diagnosis/microbiology ; Adolescent ; }, abstract = {OBJECTIVE: Accurate and rapid identification of causative pathogens is essential to guide the clinical management of lower respiratory tract infections (LRTIs). Here we conducted a single-centre prospective study in 284 patients suspected of lower respiratory tract infections to evaluate the utility of a nucleic acid test based on highly multiplexed polymerase chain reaction (PCR) and CRISPR-Cas12a.

METHODS: We determined the analytical and diagnostic performance of the CRISPR assay using a combination of reference standards, including conventional microbiological tests (CMTs), metagenomic Next-Generation Sequencing (mNGS), and clinical adjudication by a panel of experts on infectious diseases and microbiology.

RESULTS: The CRISPR assay showed a higher detection rate (63.0%) than conventional microbiological tests (38.4%) and was lower than metagenomic Next-Generation Sequencing (72.9%). In detecting polymicrobial infections, the positivity rate of the CRISPR assay (19.4%) was higher than conventional microbiological tests (3.5%) and lower than metagenomic Next-Generation Sequencing (28.9%). The overall diagnostic sensitivity of the CRISPR assay (67.8%) was higher than conventional microbiological tests (41.8%), and lower than metagenomic Next-Generation Sequencing (93.2%).

CONCLUSIONS: Considering the low cost, ease of operation, short turnaround time, and broad range of pathogens detected in a single test, the CRISPR assay has the potential to be implemented as a screening tool for the aetiological diagnosis of lower respiratory tract infections patients, especially in cases where atypical bacteria or coinfections are suspected.}, } @article {pmid39264513, year = {2024}, author = {Angebault, C and Botterel, F}, title = {Metagenomics Applied to the Respiratory Mycobiome in Cystic Fibrosis.}, journal = {Mycopathologia}, volume = {189}, number = {5}, pages = {82}, pmid = {39264513}, issn = {1573-0832}, mesh = {*Cystic Fibrosis/microbiology/complications ; Humans ; *Mycobiome ; *Metagenomics/methods ; Fungi/genetics/classification/isolation & purification ; Respiratory System/microbiology ; Bacteria/genetics/classification/isolation & purification ; Lung/microbiology ; Microbiota ; }, abstract = {Cystic fibrosis (CF) is a genetic disorder characterized by chronic microbial colonization and inflammation of the respiratory tract (RT), leading to pulmonary exacerbation (PEx) and lung damage. Although the lung bacterial microbiota has been extensively studied, the mycobiome remains understudied. However, its importance as a contributor to CF pathophysiology has been highlighted. The objective of this review is to provide an overview of the current state of knowledge regarding the mycobiome, as described through NGS-based studies, in patients with CF (pwCF).Several studies have demonstrated that the mycobiome in CF lungs is a dynamic entity, exhibiting a lower diversity and abundance than the bacterial microbiome. Nevertheless, the progression of lung damage is associated with a decrease in fungal and bacterial diversity. The core mycobiome of the RT in pwCFs is mainly composed of yeasts (Candida spp., Malassezia spp.) and molds with lower abundance. Some fungi (Aspergillus, Scedosporium/Pseudallescheria) have been demonstrated to play a role in PEx, while the involvement of others (Candida, Pneumocystis) remains uncertain. The "climax attack" ecological model has been proposed to explain the complexity and interplay of microbial populations in the RT, leading to PEx and lung damage. NGS-based studies also enable the detection of intra- and interkingdom correlations between fungi and bacteria. Further studies are required to ascertain the biological and pathophysiological relevance of these correlations. Finally, with the recent advent of CFTR modulators, our understanding of the pulmonary microbiome and mycobiome in pwCFs is about to change.}, } @article {pmid39264158, year = {2024}, author = {Wang, X and Guo, X and Liu, H and Wang, B and Wu, J and Chen, S and Zhang, W and Zhang, X and Wang, X}, title = {Augmented pathogen detection in brain abscess using metagenomic next-generation sequencing: a retrospective cohort study.}, journal = {Microbiology spectrum}, volume = {12}, number = {10}, pages = {e0032524}, pmid = {39264158}, issn = {2165-0497}, support = {No. 82001685//MOST | National Natural Science Foundation of China (NSFC)/ ; No. 82300010//MOST | National Natural Science Foundation of China (NSFC)/ ; GWVI-11.2-YQ05//Shanghai Three-year Action Plan to Strengthen Public System Construction (2023-2025) Outstanding Youth Project/ ; HS2021SHZX001//Science and Technology Commission of Shanghai Municipality (STCSM)/ ; 2023YFC2306501//MOST | National Key Research and Development Program of China (NKPs)/ ; }, mesh = {Humans ; *Brain Abscess/microbiology/diagnosis ; Retrospective Studies ; Male ; Middle Aged ; *High-Throughput Nucleotide Sequencing ; Female ; *Metagenomics/methods ; Adult ; Aged ; Bacteria/isolation & purification/genetics/classification ; Young Adult ; Adolescent ; Gram-Positive Bacteria/isolation & purification/genetics/classification ; Gram-Negative Bacteria/isolation & purification/genetics/classification ; }, abstract = {Brain abscess is a severe infection characterized by the accumulation of pus within the brain parenchyma. Accurate identification of the causative pathogens is crucial for effective treatment and improved patient outcomes. This 10-year retrospective, single-center study aimed to compare the detection performance of conventional culture methods and metagenomic next-generation sequencing (mNGS) in brain abscess. We reviewed 612 patients diagnosed with brain abscess and identified 174 cases with confirmed etiology. The median age was 52 years, with 69.5% males. Culture tests predominately identified gram-positive bacteria, particularly Streptococcus spp. Gram-negative bacteria, including Klebsiella spp., were also detected. However, mNGS revealed a more diverse pathogen spectrum, focusing on anaerobes (e.g., Fusobacterium spp., Parvimonas spp., Porphyromonas spp., Prevotella spp., and Tannerella spp.). mNGS exhibited significantly higher overall pathogen-positive rates in pus samples (85.0% vs 50.0%, P = 0.0181) and CSF samples (84.2% vs 7.9%, P < 0.0001) compared to culture. Furthermore, the detection rates for anaerobes displayed a notable disparity, with mNGS yielding significantly higher positive detections in both pus samples (50.0% vs 10%, P = 0.0058) and CSF samples (18.4% vs 0%, P = 0.0115) when compared to culture methods. The assistance of mNGS in pathogen detection, particularly anaerobes in brain abscess, was evident in our findings. mNGS demonstrated the ability to identify rare and fastidious pathogens, even in culture-negative cases. These results emphasize the clinical value of mNGS as a supplement for brain abscess, enabling more comprehensive and accurate pathogen identification.IMPORTANCEThe accurate identification of pathogens causing brain abscess is crucial for effective treatment and improved patient outcomes. In this 10-year retrospective study, the detection performance of conventional culture methods and metagenomic next-generation sequencing (mNGS) was compared. The study analyzed 612 patients with brain abscess and confirmed etiology in 174 cases. The results showed that culture tests predominantly identified gram-positive bacteria, while mNGS unveiled a broader diverse pathogen spectrum, particularly anaerobes. The mNGS method exhibited significantly higher overall rates of pathogen positivity both in pus and cerebrospinal fluid (CSF) samples, surpassing the culture methods. Notably, mNGS detected a significantly higher number of anaerobes in both pus and CSF samples compared to culture methods. These findings underscore the clinical value of mNGS as a supplement for brain abscess diagnosis, enabling more comprehensive and accurate pathogen identification, particularly for rare and fastidious pathogens that evade detection by conventional culture methods.}, } @article {pmid39264053, year = {2024}, author = {Ho, L and Lai, C and Daim, LDJ and Noh, NM and Yap, Y and Ibrahim, J and Teh, C}, title = {Deciphering root-associated microbial communities in asymptomatic oil palm seedlings exposed to Ganoderma boninense: new insight into disease tolerance of oil palms.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {10}, pages = {}, pmid = {39264053}, issn = {1574-6941}, support = {//SD Guthrie Research Sdn Bhd/ ; }, mesh = {*Ganoderma/genetics ; *Seedlings/microbiology ; *Arecaceae/microbiology ; *Soil Microbiology ; *Plant Diseases/microbiology ; *Microbiota ; *Rhizosphere ; *Plant Roots/microbiology ; Ascomycota/genetics ; Disease Resistance ; Metagenomics ; }, abstract = {Understanding the microbial communities in asymptomatic oil palm seedlings is crucial for developing disease-suppressive microbiota against basal stem rot (BSR) in oil palm. In this study, we compared the microbial communities in bulk soil, rhizosphere, and endosphere of control, asymptomatic, and symptomatic seedlings following inoculation with Ganoderma boninense. Our findings revealed significant shifts in microbial structure and interactions, particularly in asymptomatic seedlings. Both Actinobacteriota and Ascomycota were notably enriched in these samples, with Actinobacteriota identified as keystone taxa. Long-read shotgun metagenomics demonstrated that 67.4% of enriched Actinobacteriota taxa were unique to asymptomatic seedlings. Similarly, Ascomycota members showed significant enrichment, suggesting their potential role in BSR suppression. The consistent identification of these phyla across various analyses underscores their importance in disease resistance. This is the first report detailing the shifts in prokaryotic and fungal communities in asymptomatic and symptomatic seedlings, offering insights into potential disease-suppressive taxa across three compartments: bulk soil, rhizosphere, and endosphere of oil palm seedlings.}, } @article {pmid39263696, year = {2024}, author = {Nag, M and Pallavi, J and Chakraborty, S and Roychoudhury, T and Mondal, S and Ghosh, A and Saha, C and Banerjee, M and Seal, A}, title = {Bacterial endosymbionts of a nitrogen-fixing yeast Rhodotorula mucilaginosa JGTA-S1 - insights into a yet unknown micro-ecosystem.}, journal = {Molecular omics}, volume = {20}, number = {10}, pages = {630-641}, doi = {10.1039/d3mo00273j}, pmid = {39263696}, issn = {2515-4184}, mesh = {*Rhodotorula/genetics/metabolism ; *Symbiosis ; *Nitrogen Fixation/genetics ; *Nitrogen/metabolism ; Ecosystem ; Metagenomics/methods ; Bacteria/metabolism/genetics ; Phylogeny ; Bacillus/genetics/metabolism ; }, abstract = {Rhodotorula mucilaginosa JGTA-S1 is a yeast strain capable of fixing nitrogen and improving nitrogen nutrition in rice plants because of its nitrogen-fixing endobacteria, namely Stutzerimonas (Pseudomonas) stutzeri and Bradyrhizobium sp. To gain a deeper understanding of yeast endosymbionts, we conducted a whole-genome shotgun metagenomic analysis of JGTA-S1 cells grown under conditions of nitrogen sufficiency and deficiency. Our results showed that the endosymbiont population varied depending on the nitrogen regime. Upon mechanical disruption of yeast cells, we obtained endosymbionts in culturable form viz. Bacillus velezensis and Staphylococcus sp. under nitrogen-replete conditions and Lysinibacillus telephonicus., Brevibacillus sp., and Niallia circulans under nitrogen-depleted conditions. S. stutzeri and Bradyrhizobium sp. the previously reported endosymbionts remained unculturable. The culturable endosymbionts Staphylococcus sp. and Bacillus velezensis appear to possess genes for dissimilatory nitrate reduction (DNRA), an alternative pathway for ammonia synthesis. However, our findings suggest that these endosymbionts are facultative as they survive outside the host. The fitness of the yeast was not affected by curing of these microbes. Curing the yeast diazotrophic endosymbionts took a toll on its fitness. Our results also showed that the populations of S. stutzeri and B. velezensis increased significantly under nitrogen-depleted conditions compared to nitrogen-sufficient conditions. The importance of DNRA and nitrogen fixation is also reflected in the metagenomic reads of JGTA-S1.}, } @article {pmid39263550, year = {2024}, author = {Bell, E and Chen, J and Richardson, WDL and Fustic, M and Hubert, CRJ}, title = {Denitrification genotypes of endospore-forming Bacillota.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae107}, pmid = {39263550}, issn = {2730-6151}, abstract = {Denitrification is a key metabolic process in the global nitrogen cycle and is performed by taxonomically diverse microorganisms. Despite the widespread importance of this metabolism, challenges remain in identifying denitrifying populations and predicting their metabolic end-products based on their genotype. Here, genome-resolved metagenomics was used to explore the denitrification genotype of Bacillota enriched in nitrate-amended high temperature incubations with confirmed N2O and N2 production. A set of 12 hidden Markov models (HMMs) was created to target the diversity of denitrification genes in members of the phylum Bacillota. Genomic potential for complete denitrification was found in five metagenome-assembled genomes from nitrate-amended enrichments, including two novel members of the Brevibacillaceae family. Genomes of complete denitrifiers encode N2O reductase gene clusters with clade II-type nosZ and often include multiple variants of the nitric oxide reductase gene. The HMM set applied to all genomes of Bacillota from the Genome Taxonomy Database identified 17 genera inferred to contain complete denitrifiers based on their gene content. Among complete denitrifiers it was common for three distinct nitric oxide reductases to be present (qNOR, bNOR, and sNOR) that may reflect the metabolic adaptability of Bacillota in environments with variable redox conditions.}, } @article {pmid39263297, year = {2024}, author = {Wang, A and Cui, X and Shi, C}, title = {Metagenomic analysis of rats with diarrhea treated with mixed probiotics: response to consecutive and alternate-hour supplementation.}, journal = {Translational pediatrics}, volume = {13}, number = {8}, pages = {1336-1358}, pmid = {39263297}, issn = {2224-4344}, abstract = {BACKGROUND: Diarrhea is the leading contributory factor of sickness and mortality among children under five and an economic burden for families. This study aimed to investigate the effects of mixed probiotics supplementation at different times (consecutive and alternate-hour) on intestinal microecology in Sprague-Dawley (SD) rats with acute diarrhea.

METHODS: A total of 40 SD rats were randomly assigned to four groups, including the control group, model group, probiotic group A, and probiotic group B. An acute diarrhea model was induced by administration of 5% dextran sulfate sodium. Rats in probiotic group A and probiotic group B were fed with Clostridium butyricum (C. butyricum), Bifidobacterium infantis (B. infantis), and Saccharomyces boulardii (S. boulardii) for a total of 7 days. Probiotic group A was fed with all probiotics simultaneously. Probiotic group B was fed with C. butyricum and B. infantis simultaneously, and then after a 2-hour interval, with S. boulardii. Metagenomic next-generation sequencing was used to analyze the fecal samples from every rat. The metagenomic sequencing used in this experiment was used to evaluate the effect of probiotics on the composition as well as function of the gut microbiota in order to gain a deeper comprehension of probiotic-host interactions on health and disease.

RESULTS: The structure of the gut microbiota in probiotic group A showed significant changes. Compared to the model group, the abundance of some beneficial bacteria had increased, including Actinobacteria (P=0.048), Lactobacillus (P=0.050), and Lactobacillus johnsonii (P=0.042), and many opportunistic pathogenic bacteria has decreased, such as Ruminococcus (P=0.001). Compared to the control group, the abundance of some beneficial bacteria had increased, including Fusobacteria (P=0.02) and Phascolarium (P=0.002), and there was a reduction in the abundance of many opportunistic pathogenic bacteria such as Roseburia (P=0.03), Lachnoclosterium (P=0.009), and Oscillibacter_sp_1-3 (P=0.002). In addition, metagenomic analysis showed that as well as an up-regulation of glycoside hydrolase expression, amino acid and inorganic ion transport, and metabolism-related pathways, there was a down-regulation of cell motility.

CONCLUSIONS: Simultaneous administration of probiotics may have more positive implications in improving the gut microbiota of acute diarrhea rats.}, } @article {pmid39262445, year = {2023}, author = {Borry, M and Forsythe, A and Andrades Valtueña, A and Hübner, A and Ibrahim, A and Quagliariello, A and White, AE and Kocher, A and Vågene, ÅJ and Bartholdy, BP and Spurīte, D and Ponce-Soto, GY and Neumann, G and Huang, IT and Light, I and Velsko, IM and Jackson, I and Frangenberg, J and Serrano, JG and Fumey, J and Özdoğan, KT and Blevins, KE and Daly, KG and Lopopolo, M and Moraitou, M and Michel, M and van Os, M and Bravo-Lopez, MJ and Sarhan, MS and Dagtas, ND and Oskolkov, N and Smith, OS and Lebrasseur, O and Rozwalak, P and Eisenhofer, R and Wasef, S and Ramachandran, SL and Vanghi, V and Warinner, C and Fellows Yates, JA}, title = {Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT.}, journal = {F1000Research}, volume = {12}, number = {}, pages = {926}, pmid = {39262445}, issn = {2046-1402}, support = {T32 GM139782/GM/NIGMS NIH HHS/United States ; }, mesh = {*Metagenomics/methods ; Humans ; *Metadata ; High-Throughput Nucleotide Sequencing/methods ; Software ; Metagenome ; Computational Biology/methods ; DNA, Ancient/analysis ; }, abstract = {BACKGROUND: Access to sample-level metadata is important when selecting public metagenomic sequencing datasets for reuse in new biological analyses. The Standards, Precautions, and Advances in Ancient Metagenomics community (SPAAM, https://spaam-community.org) has previously published AncientMetagenomeDir, a collection of curated and standardised sample metadata tables for metagenomic and microbial genome datasets generated from ancient samples. However, while sample-level information is useful for identifying relevant samples for inclusion in new projects, Next Generation Sequencing (NGS) library construction and sequencing metadata are also essential for appropriately reprocessing ancient metagenomic data. Currently, recovering information for downloading and preparing such data is difficult when laboratory and bioinformatic metadata is heterogeneously recorded in prose-based publications.

METHODS: Through a series of community-based hackathon events, AncientMetagenomeDir was updated to provide standardised library-level metadata of existing and new ancient metagenomic samples. In tandem, the companion tool 'AMDirT' was developed to facilitate rapid data filtering and downloading of ancient metagenomic data, as well as improving automated metadata curation and validation for AncientMetagenomeDir.

RESULTS: AncientMetagenomeDir was extended to include standardised metadata of over 6000 ancient metagenomic libraries. The companion tool 'AMDirT' provides both graphical- and command-line interface based access to such metadata for users from a wide range of computational backgrounds. We also report on errors with metadata reporting that appear to commonly occur during data upload and provide suggestions on how to improve the quality of data sharing by the community.

CONCLUSIONS: Together, both standardised metadata reporting and tooling will help towards easier incorporation and reuse of public ancient metagenomic datasets into future analyses.}, } @article {pmid39262440, year = {2024}, author = {Hallgren, MB and Clausen, PTLC and Aarestrup, FM}, title = {NanoMGT: Marker gene typing of low complexity mono-species metagenomic samples using noisy long reads.}, journal = {Biology methods & protocols}, volume = {9}, number = {1}, pages = {bpae057}, pmid = {39262440}, issn = {2396-8923}, abstract = {Rapid advancements in sequencing technologies have led to significant progress in microbial genomics, yet challenges persist in accurately identifying microbial strain diversity in metagenomic samples, especially when working with noisy long-read data from platforms like Oxford Nanopore Technologies (ONT). In this article, we introduce NanoMGT, a tool designed to enhance marker gene typing in low-complexity mono-species samples, leveraging the unique properties of long reads. NanoMGT excels in its ability to accurately identify mutations amidst high error rates, ensuring the reliable detection of multiple strain-specific marker genes. Our tool implements a novel scoring system that rewards mutations co-occurring across different reads and penalizes densely grouped, likely erroneous variants, thereby achieving a good balance between sensitivity and precision. A comparative evaluation of NanoMGT, using a simulated multi-strain sample of seven bacterial species, demonstrated superior performance relative to existing tools and the advantages of using a threshold-based filtering approach to calling minority variants in ONT's sequencing data. NanoMGT's potential as a post-binning tool in metagenomic pipelines is particularly notable, enabling researchers to more accurately determine specific alleles and understand strain diversity in microbial communities. Our findings have significant implications for clinical diagnostics, environmental microbiology, and the broader field of genomics. The findings offer a reliable and efficient approach to marker gene typing in complex metagenomic samples.}, } @article {pmid39261970, year = {2024}, author = {Wan, X and Shahrear, S and Chew, SW and Vilaplana, F and Mäkelä, MR}, title = {Discovery of alkaline laccases from basidiomycete fungi through machine learning-based approach.}, journal = {Biotechnology for biofuels and bioproducts}, volume = {17}, number = {1}, pages = {120}, pmid = {39261970}, issn = {2731-3654}, support = {NNF21OC0071410//Novo Nordisk Fonden/ ; HiLIFE Fellows grant 2023-2025//Helsinki Institute of Life Science, Helsingin Yliopisto/ ; }, abstract = {BACKGROUND: Laccases can oxidize a broad spectrum of substrates, offering promising applications in various sectors, such as bioremediation, biomass fractionation in future biorefineries, and synthesis of biochemicals and biopolymers. However, laccase discovery and optimization with a desirable pH optimum remains a challenge due to the labor-intensive and time-consuming nature of the traditional laboratory methods.

RESULTS: This study presents a machine learning (ML)-integrated approach for predicting pH optima of basidiomycete fungal laccases, utilizing a small, curated dataset against a vast metagenomic data. Comparative computational analyses unveiled the structural and pH-dependent solubility differences between acidic and neutral-alkaline laccases, helping us understand the molecular bases of enzyme pH optimum. The pH profiling of the two ML-predicted alkaline laccase candidates from the basidiomycete fungus Lepista nuda further validated our computational approach, showing the accuracy of this comprehensive method.

CONCLUSIONS: This study uncovers the efficacy of ML in the prediction of enzyme pH optimum from minimal datasets, marking a significant step towards harnessing computational tools for systematic screening of enzymes for biotechnology applications.}, } @article {pmid39261503, year = {2024}, author = {Schwab, S and Hu, Y and van Erp, B and Cajili, MKM and Hartmann, MD and Hernandez Alvarez, B and Alva, V and Boyle, AL and Dame, RT}, title = {Histones and histone variant families in prokaryotes.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {7950}, pmid = {39261503}, issn = {2041-1723}, support = {OCENW.GROOT.2019.012//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; }, mesh = {*Histones/metabolism/chemistry/genetics ; *Archaea/metabolism/genetics ; *Bacteria/metabolism/genetics ; Prokaryotic Cells/metabolism ; Phylogeny ; Nucleosomes/metabolism ; Models, Molecular ; Archaeal Proteins/metabolism/chemistry/genetics ; Amino Acid Sequence ; }, abstract = {Histones are important chromatin-organizing proteins in eukaryotes and archaea. They form superhelical structures around which DNA is wrapped. Recent studies have shown that some archaea and bacteria contain alternative histones that exhibit different DNA binding properties, in addition to highly divergent sequences. However, the vast majority of these histones are identified in metagenomes and thus are difficult to study in vivo. The recent revolutionary breakthroughs in computational protein structure prediction by AlphaFold2 and RoseTTAfold allow for unprecedented insights into the potential function and structure of previously uncharacterized proteins. Here, we categorize the prokaryotic histone space into 17 distinct groups based on AlphaFold2 predictions. We identify a superfamily of histones, termed α3 histones, which are common in archaea and present in several bacteria. Importantly, we establish the existence of a large family of histones throughout archaea and in some bacteriophages that, instead of wrapping DNA, bridge DNA, thereby diverging from conventional nucleosomal histones.}, } @article {pmid39260724, year = {2024}, author = {Ke, Y and Sun, W and Xue, Y and Yuan, Z and Zhu, Y and Chen, X and Yan, S and Li, Y and Xie, S}, title = {Pipe material and natural organic matter impact drinking water biofilm microbial community, pathogen profiles and antibiotic resistome deciphered by metagenomics assembly.}, journal = {Environmental research}, volume = {262}, number = {Pt 2}, pages = {119964}, doi = {10.1016/j.envres.2024.119964}, pmid = {39260724}, issn = {1096-0953}, mesh = {*Biofilms/drug effects ; *Drinking Water/microbiology ; *Metagenomics ; Microbiota/drug effects ; Drug Resistance, Microbial/genetics ; Water Supply ; Anti-Bacterial Agents/pharmacology ; Polyethylene ; Water Microbiology ; }, abstract = {Biofilms in drinking water distribution systems (DWDSs) are a determinant to drinking water biosafety. Yet, how and why pipe material and natural organic matter (NOM) affect biofilm microbial community, pathogen composition and antibiotic resistome remain unclear. We characterized the biofilms' activity, microbial community, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs) and pathogenic ARG hosts in Centers for Disease Control and Prevention (CDC) reactors with different NOM dosages and pipe materials based on metagenomics assembly. Biofilms in cast iron (CI) pipes exhibited higher activity than those in polyethylene (PE) pipes. NOM addition significantly decreased biofilm activity in CI pipes but increased it in PE pipes. Pipe material exerted more profound effects on microbial community structure than NOM. Azospira was significantly enriched in CI pipes and Sphingopyxis was selected in PE pipes, while pathogen (Ralstonia pickettii) increased considerably in NOM-added reactors. Microbial community network in CI pipes showed more edges (CI 13520, PE 7841) and positive correlation proportions (CI 72.35%, PE 61.69%) than those in PE pipes. Stochastic processes drove assembly of both microbial community and antibiotic resistome in DWDS biofilms based on neutral community model. Bacitracin, fosmidomycin and multidrug ARGs were predominant in both PE and CI pipes. Both pipe materials and NOM regulated the biofilm antibiotic resistome. Plasmid was the major MGE co-existing with ARGs, facilitating ARG horizontal transfer. Pathogens (Achromobacter xylosoxidans and Ralstonia pickettii) carried multiple ARGs (qacEdelta1, OXA-22 and aadA) and MGEs (integrase, plasmid and transposase), which deserved more attention. Microbial community contributed more to ARG change than MGEs. Structure equation model (SEM) demonstrated that turbidity and ammonia affected ARGs by directly mediating Shannon diversity and MGEs. These findings might provide a technical guidance for controlling pathogens and ARGs from the point of pipe material and NOM in drinking water.}, } @article {pmid39260513, year = {2024}, author = {Tan, J and Wang, Y and Niu, H and Li, L and Zhao, H and Fang, L and Jiang, L and Zhao, Y}, title = {Metagenomic insights into the mechanistic differences of plant polyphenols and nitrocompounds in reducing methane emissions using the rumen simulation technique.}, journal = {The Science of the total environment}, volume = {953}, number = {}, pages = {176135}, doi = {10.1016/j.scitotenv.2024.176135}, pmid = {39260513}, issn = {1879-1026}, mesh = {*Methane/metabolism ; Animals ; *Rumen/metabolism/microbiology ; *Polyphenols/metabolism/analysis ; Animal Feed/analysis ; Fermentation ; Metagenomics ; }, abstract = {Methane (CH4) emissions from ruminants contribute significantly to greenhouse gas levels and also result in considerable feed energy losses. Plant polyphenols and nitrocompounds are two typical types of methane inhibitors. The study investigates the mechanistic differences between 2-nitroethanol (NE) and proanthocyanidins (PAC) in reducing methane emissions from ruminant livestock using the rumen simulation technique (RUSITEC) combined with metagenomic analyses. The experiment was performed as a complete randomized block design with 3 runs. Run was used as a blocking factor. The treatments included a control (CON) with no additive, NE at 0.5 g/kg dry matter (DM), and PAC at 20 g/kg DM, all incubated in vitro for 24 h (h) with eight replicates per treatment. The results showed that NE significantly reduced CH4 production by 94.9 % (P < 0.01) and total volatile fatty acid (TVFA) concentration by 11.1 % (P < 0.05) compared to the control. NE also decreased the acetate-to-propionate ratio (A/P) from 1.93 to 1.60 (P < 0.01), indicating a shift towards more efficient fermentation. In contrast, PAC reduced methane production by 11.7 % (P < 0.05) and decreased the A/P (P < 0.05) while maintaining microbial diversity and fermentation stability, with no significant impact on TVFA concentration (P > 0.05). Metagenomic analysis revealed that NE markedly suppressed the abundance of key genera involved in carbohydrate metabolism, including Prevotella and Bacteroides, leading to reduced acetate and butyrate pathways. NE also selectively inhibited methanogenic archaea, particularly Methanobrevibacter spp., which are integral to the hydrogenotrophic pathway (P < 0.01). On the other hand, PAC showed selective inhibition of Methanosphaera spp., targeting the methylotrophic pathway (P < 0.01). These findings provide valuable insights into the distinct microbial and metabolic pathways modulated by NE and PAC, offering potential strategies for developing effective dietary interventions to mitigate methane emissions in ruminant livestock.}, } @article {pmid39260494, year = {2024}, author = {Ejaz, MR and Badr, K and Hassan, ZU and Al-Thani, R and Jaoua, S}, title = {Metagenomic approaches and opportunities in arid soil research.}, journal = {The Science of the total environment}, volume = {953}, number = {}, pages = {176173}, doi = {10.1016/j.scitotenv.2024.176173}, pmid = {39260494}, issn = {1879-1026}, mesh = {*Soil Microbiology ; *Metagenomics ; *Soil/chemistry ; Desert Climate ; Microbiota ; }, abstract = {Arid soils present unique challenges and opportunities for studying microbial diversity and bioactive potential due to the extreme environmental conditions they bear. This review article investigates soil metagenomics as an emerging tool to explore complex microbial dynamics and unexplored bioactive potential in harsh environments. Utilizing advanced metagenomic techniques, diverse microbial populations that grow under extreme conditions such as high temperatures, salinity, high pH levels, and exposure to metals and radiation can be studied. The use of extremophiles to discover novel natural products and biocatalysts emphasizes the role of functional metagenomics in identifying enzymes and secondary metabolites for industrial and pharmaceutical purposes. Metagenomic sequencing uncovers a complex network of microbial diversity, offering significant potential for discovering new bioactive compounds. Functional metagenomics, connecting taxonomic diversity to genetic capabilities, provides a pathway to identify microbes' mechanisms to synthesize valuable secondary metabolites and other bioactive substances. Contrary to the common perception of desert soil as barren land, the metagenomic analysis reveals a rich diversity of life forms adept at extreme survival. It provides valuable findings into their resilience and potential applications in biotechnology. Moreover, the challenges associated with metagenomics in arid soils, such as low microbial biomass, high DNA degradation rates, and DNA extraction inhibitors and strategies to overcome these issues, outline the latest advancements in extraction methods, high-throughput sequencing, and bioinformatics. The importance of metagenomics for investigating diverse environments opens the way for future research to develop sustainable solutions in agriculture, industry, and medicine. Extensive studies are necessary to utilize the full potential of these powerful microbial communities. This research will significantly improve our understanding of microbial ecology and biotechnology in arid environments.}, } @article {pmid39260483, year = {2024}, author = {Li, W and Wang, H and Lv, G and Wang, J and Li, J}, title = {Regulation of drought stress on nutrient cycle and metabolism of rhizosphere microorganisms in desert riparian forest.}, journal = {The Science of the total environment}, volume = {954}, number = {}, pages = {176148}, doi = {10.1016/j.scitotenv.2024.176148}, pmid = {39260483}, issn = {1879-1026}, mesh = {*Rhizosphere ; *Droughts ; *Soil Microbiology ; *Forests ; Desert Climate ; China ; Stress, Physiological ; Nitrogen/metabolism ; Phosphorus/metabolism ; Soil/chemistry ; }, abstract = {Microbial communities in desert riparian forest ecosystems have developed unique adaptive strategies to thrive in harsh habitats shaped by prolonged exposure to abiotic stressors. However, the influence of drought stress on the functional and metabolic characteristics of soil rhizosphere microorganisms remains unknown. Therefore, this study aimed to investigate the effects of drought stress on soil biogeochemistry and metabolism and analyze the relationship between the biogeochemical cycle processes and network of differentially-expressed metabolites. Using metagenomics and metabolomics, this study explored the microbial functional cycle and differential metabolic pathways within desert riparian forests. The predominant biogeochemical cycles in the study area were the Carbon and Nitrogen cycles, comprising 78.90 % of C, N, Phosphorus, Sulfur and Iron cycles. Drought led to increased soil C fixation, reduced C degradation and methane metabolism, weakened denitrification, and decreased N fixation. Furthermore, drought can disrupt iron homeostasis and reduce its absorption. The differential metabolic pathways of drought stress include flavonoid biosynthesis, arachidonic acid metabolism, steroid hormone biosynthesis, and starch and sucrose degradation. Network analysis of functional genes and metabolism revealed a pronounced competitive relationship between the C cycle and metabolic network, whereas the Fe cycle and metabolic network promoted each other, optimizing resource utilization. Partial least squares analysis revealed that drought hindered the expression and metabolic processes and functional genes, whereas the rhizosphere environment facilitated metabolic expression and the functional genes. The rhizosphere effect primarily promoted metabolic processes indirectly through soil enzyme activities. The integrated multi-omics analysis further revealed that the effects of drought and the rhizosphere play a predominant role in shaping soil functional potential and the accumulation of metabolites. These insights deepen our comprehension of desert riparian forest ecosystems and offer strong support for the functionality of nutrient cycling and metabolite dynamics.}, } @article {pmid39260018, year = {2024}, author = {Chen, M and Chen, Y and He, X and Hao, R and Jiang, X and Ji, Y and Zhuo, B and Xu, W and Lin, R and Ge, Y}, title = {A case of Bartonella vinsonii endocarditis.}, journal = {Diagnostic microbiology and infectious disease}, volume = {110}, number = {4}, pages = {116535}, doi = {10.1016/j.diagmicrobio.2024.116535}, pmid = {39260018}, issn = {1879-0070}, mesh = {Humans ; Female ; Middle Aged ; *Bartonella/genetics/isolation & purification ; *Bartonella Infections/diagnosis/microbiology/drug therapy ; *Endocarditis, Bacterial/microbiology/diagnosis/drug therapy ; *Anti-Bacterial Agents/therapeutic use ; Doxycycline/therapeutic use ; High-Throughput Nucleotide Sequencing ; Ceftriaxone/therapeutic use ; Treatment Outcome ; Metagenomics ; }, abstract = {The diagnosis of Bartonella is challenging due to its rarity and negative culture results. Once the diagnosis is delayed and proper treatment is not given, it can develop into infective endocarditis, which can be fatal. We reported a 60-year-old female patient who had recurrent fever for 5 months. After receiving ineffective treatment at the local hospital, she sought medical attention at our hospital. Laboratory blood indicators testing and imaging indicated infective endocarditis, and metagenomic Next Generation Sequencing (m-NGS) testing confirmed the diagnosis of Bartonella vinsonii infection. After surgical treatment and the combination of doxycycline and ceftriaxone sodium for anti-infective therapy, the patient recovered. Valuing the combination of multiple auxiliary diagnostic methods and improving the application of m-NGS in the detection of unknown pathogens can compensate for the current limitations in the diagnosis of Bartonella. Early diagnosis and treatment are extremely important for Bartonella endocarditis.}, } @article {pmid39259188, year = {2024}, author = {Liu, C and Wang, Y and Zhou, Z and Wang, S and Wei, Z and Ravanbakhsh, M and Shen, Q and Xiong, W and Kowalchuk, GA and Jousset, A}, title = {Protist predation promotes antimicrobial resistance spread through antagonistic microbiome interactions.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39259188}, issn = {1751-7370}, support = {42090064//National Natural Science Foundation of China/ ; 2023YFD1901402//National Key Research and Development Program of China/ ; YDZX2023023//Fundamental Research Funds for the Central Universities/ ; }, mesh = {*Microbiota/drug effects ; *Soil Microbiology ; *Bacteria/drug effects/genetics/classification ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial ; Microbial Interactions ; Drug Resistance, Bacterial ; Eukaryota/drug effects ; }, abstract = {Antibiotic resistance has grown into a major public health threat. In this study, we reveal predation by protists as an overlooked driver of antibiotic resistance dissemination in the soil microbiome. While previous studies have primarily focused on the distribution of antibiotic resistance genes, our work sheds light on the pivotal role of soil protists in shaping antibiotic resistance dynamics. Using a combination of metagenomics and controlled experiments in this study, we demonstrate that protists cause an increase in antibiotic resistance. We mechanistically link this increase to a fostering of antimicrobial activity in the microbiome. Protist predation gives a competitive edge to bacteria capable of producing antagonistic secondary metabolites, which secondary metabolites promote in turn antibiotic-resistant bacteria. This study provides insights into the complex interplay between protists and soil microbiomes in regulating antibiotic resistance dynamics. This study highlights the importance of top-down control on the spread of antibiotic resistance and directly connects it to cross-kingdom interactions within the microbiome. Managing protist communities may become an important tool to control outbreaks of antibiotic resistance in the environment.}, } @article {pmid39258944, year = {2024}, author = {Zhu, W and Zeng, Z and Xia, J and Li, L}, title = {Achieving rapid start-up and efficient nitrogen removal of partial-denitrification/anammox process using organic matter in brewery wastewater as carbon source.}, journal = {Environmental technology}, volume = {}, number = {}, pages = {1-13}, doi = {10.1080/09593330.2024.2401157}, pmid = {39258944}, issn = {1479-487X}, abstract = {To find a cost-efficient carbon source for the partial denitrification/anaerobic ammonium oxidation (anammox) (PD/A) process, the practicability of using the organic matter contained in brewery wastewater as carbon source was investigated. Quick self-enrichment of denitrifying bacteria was achieved by supplying brewery wastewater as organic carbon source and using the mature anammox sludge as the seeding sludge. The PD/A process was successfully established after 33-day operation and then the average total nitrogen removal efficiency reached 92.29% when the influent CODCr: NO3[-]-N: NH4[+]-N ratio was around 2.5: 1.0: 0.67. The relative abundance of Thauera increased from 0.03% in the seeding sludge to 54.29% on day 110, whereas Candidatus brocadia decreased from 30.66% to 2.08%. The metagenomic analysis indicated that the sludge on day 110 contained more nar and napA (total of 41.24%) than nirK and nirS (total of 11.93%). Thus NO2[-]-N was accumulated efficiently in the process of denitrification and sufficient NO2[-]-N was supplied for anammox bacteria in the PD/A process. Using brewery wastewater as carbon source not only saved the cost of nitrogen removal but also converted waste into resource and reduced the treatment expense of brewery wastewater.}, } @article {pmid39258715, year = {2024}, author = {Vats, R and Yadav, P and Bano, A and Wadhwa, S and Bhardwaj, R}, title = {Salivary biomarkers in non-invasive oral cancer diagnostics: a comprehensive review.}, journal = {Journal of applied oral science : revista FOB}, volume = {32}, number = {}, pages = {e20240151}, pmid = {39258715}, issn = {1678-7765}, mesh = {Humans ; *Mouth Neoplasms/diagnosis ; *Saliva/chemistry/virology ; *Biomarkers, Tumor/analysis ; Early Detection of Cancer/methods ; }, abstract = {OBJECTIVE: This review aims to provide a comprehensive analysis of the effectiveness of saliva as a non-invasive diagnostic marker for oral cancer. Despite progress in oral cancer diagnosis and prognosis, the 5-year survival rate remains low due to the resistance to treatment and delayed diagnosis, which can be attributed to various factors including tobacco and alcohol consumption, genetic damage, and human papillomavirus (HPV). The potential use of saliva as an easily accessible non-invasive screening and diagnostic method arises from its direct contact with the lesion site.

METHODOLOGY: Data for this study were gathered via a comprehensive literature evaluation using search engines such as the PubMed, Web of Science, Google Scholar, and SciFinder.

RESULTS: Identifying salivary biomarkers shows potential to transform oral cancer diagnostics by offering a reliable alternative to the traditional invasive methods. Saliva is an abundant reservoir for both cell-bound and cell-free organic and inorganic constituents. Thus, saliva is an appropriate field for research in proteomics, genomics, metagenomics, and metabolomics.

CONCLUSION: This review provides a comprehensive elucidation of salivary biomarkers and their function in non-invasive oral cancer diagnosis, demonstrating their potential to enhance patient outcomes and reduce the impact of this devastating disease.}, } @article {pmid39258254, year = {2024}, author = {Sun, W and Zheng, L and Kang, L and Chen, C and Wang, L and Lu, L and Wang, F}, title = {Comparative analysis of metagenomic and targeted next-generation sequencing for pathogens diagnosis in bronchoalveolar lavage fluid specimens.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1451440}, pmid = {39258254}, issn = {2235-2988}, mesh = {*Bronchoalveolar Lavage Fluid/microbiology/virology ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Female ; Male ; Middle Aged ; Adult ; Multiplex Polymerase Chain Reaction/methods ; Aged ; Bacteria/isolation & purification/genetics/classification ; Respiratory Tract Infections/diagnosis/virology/microbiology ; Viruses/isolation & purification/genetics/classification ; Molecular Diagnostic Techniques/methods ; Young Adult ; }, abstract = {BACKGROUND: Although the emerging NGS-based assays, metagenomic next-generation sequencing (mNGS) and targeted next-generation sequencing (tNGS), have been extensively utilized for the identification of pathogens in pulmonary infections, there have been limited studies systematically evaluating differences in the efficacy of mNGS and multiplex PCR-based tNGS in bronchoalveolar lavage fluid (BALF) specimens.

METHODS: In this study, 85 suspected infectious BALF specimens were collected. Parallel mNGS and tNGS workflows to each sample were performed; then, we comparatively compared their consistency in detecting pathogens. The differential results for clinically key pathogens were confirmed using PCR.

RESULTS: The microbial detection rates of BALF specimens by the mNGS and tNGS workflows were 95.18% (79/83) and 92.77% (77/83), respectively, with no significant difference. mNGS identified 55 different microorganisms, whereas tNGS detected 49 pathogens. The comparative analysis of mNGS and tNGS revealed that 86.75% (72/83) of the specimens were complete or partial concordance. Particularly, mNGS and tNGS differed significantly in detection rates for some of the human herpesviruses only, including Human gammaherpesvirus 4 (P<0.001), Human betaherpesvirus 7 (P<0.001), Human betaherpesvirus 5 (P<0.05) and Human betaherpesvirus 6 (P<0.01), in which tNGS always had higher detection rates. Orthogonal testing of clinically critical pathogens showed a total coincidence rate of 50% for mNGS and PCR, as well as for tNGS and PCR.

CONCLUSIONS: Overall, the performance of mNGS and multiplex PCR-based tNGS assays was similar for bacteria and fungi, and tNGS may be superior to mNGS for the detection of DNA viruses. No significant differences were seen between the two NGS assays compared to PCR.}, } @article {pmid39257939, year = {2024}, author = {Markam, SS and Raj, A and Kumar, A and Khan, ML}, title = {Microbial biosurfactants: Green alternatives and sustainable solution for augmenting pesticide remediation and management of organic waste.}, journal = {Current research in microbial sciences}, volume = {7}, number = {}, pages = {100266}, pmid = {39257939}, issn = {2666-5174}, abstract = {Pesticide pollution remains a significant environmental challenge, necessitating the exploration of sustainable alternatives. Biosurfactants are a class of unconventional surface-active chemicals that are produced by microorganisms. Biosurfactants have many applications in treating oil spills, emulsifiers, pharmaceuticals, and agriculture. Compared to chemical surfactants, they have benefits such as biodegradability, less toxicity, and a greener option because they are derived from microbes. Biosurfactants have recently been shown to have the potential to speed up pesticide cleanup. Biosurfactants are used in pesticide remediation because of their exceptional foaming ability, high selectivity, and wide range of pH, salinity, and temperature operating windows. Microbial biosurfactants emerged as potential agents for the treatment of organic waste and agricultural residue. This review unfolds the promising realm of microbial biosurfactants as green solutions for environmental sustainability, particularly in agricultural practices, with special reference to pesticide remediation. This article highlights the escalating need for eco-friendly alternatives, paving the way for discussing biosurfactants. Moreover, the articles discuss in detail various advancements in the field of rapid screening of biosurfactants, either using a conventional approach or via advanced instruments such as GC-MS, HPLC, NMR, FTIR, etc. Furthermore, the article unveils the molecular mechanisms and the microbial genes driving biosurfactant synthesis, offering insights into enhancing production efficiency. Moreover, the article explores diverse applications of microbial biosurfactants in sustainable agriculture, ranging from soil remediation to crop protection. The article also highlights the various functions of microbial biosurfactants for enhancing the decomposition and recycling of organic waste and agricultural residues, emphasizing their potential for sustainable waste management strategies. Overall, the review underscores the pivotal role of microbial biosurfactants as green alternatives for addressing pesticide pollution and advancing environmental sustainability.}, } @article {pmid39257733, year = {2024}, author = {Rienzi, SCD and Danhof, HA and Forshee, MD and Roberts, A and Britton, RA}, title = {Limosilactobacillus reuteri promotes the expression and secretion of enteroendocrine- and enterocyte-derived hormones.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39257733}, issn = {2692-8205}, support = {F32 AI136404/AI/NIAID NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; T15 LM007093/LM/NLM NIH HHS/United States ; }, abstract = {Observations that intestinal microbes can beneficially impact host physiology have prompted investigations into the therapeutic usage of such microbes in a range of diseases. For example, the human intestinal microbe Limosilactobacillus reuteri strains ATCC PTA 6475 and DSM 17938 are being considered for use for intestinal ailments including colic, infection, and inflammation as well as non-intestinal ailments including osteoporosis, wound healing, and autism spectrum disorder. While many of their beneficial properties are attributed to suppressing inflammatory responses in the gut, we postulated that L. reuteri may also regulate hormones of the gastrointestinal tract to affect physiology within and outside of the gut. To determine if L. reuteri secreted factors impact the secretion of enteric hormones, we treated an engineered jejunal organoid line, NGN3-HIO, which can be induced to be enriched in enteroendocrine cells, with L. reuteri 6475 or 17938 conditioned medium and performed transcriptomics. Our data suggest that these L. reuteri strains affect the transcription of many gut hormones, including vasopressin and luteinizing hormone subunit beta, which have not been previously recognized as being produced in the gut epithelium. Moreover, we find that these hormones appear to be produced in enterocytes, in contrast to canonical gut hormones which are produced in enteroendocrine cells. Finally, we show that L. reuteri conditioned media promotes the secretion of several enteric hormones including serotonin, GIP, PYY, vasopressin, and luteinizing hormone subunit beta. These results support L. reuteri affecting host physiology through intestinal hormone secretion, thereby expanding our understanding of the mechanistic actions of this microbe.}, } @article {pmid39257028, year = {2024}, author = {Jotta, VFM and García, GJY and Fonseca, PLC and de Mello Ferreira, A and Azevedo, V and Brenig, B and Góes-Neto, A and Badotti, F}, title = {Taxonomic and functional characterization of biofilms from a photovoltaic panel reveals high genetic and metabolic complexity of the communities.}, journal = {Journal of applied microbiology}, volume = {135}, number = {9}, pages = {}, doi = {10.1093/jambio/lxae231}, pmid = {39257028}, issn = {1365-2672}, support = {//Omics Sciences NETWORK/ ; //CEFET-MG/ ; }, mesh = {*Biofilms/growth & development ; Brazil ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Metagenomics ; Ferric Compounds/metabolism ; Microbiota ; Minerals/metabolism ; Bioelectric Energy Sources/microbiology ; Iron Compounds ; }, abstract = {AIMS: Biofilms are complex microbial cell aggregates that attach to different surfaces in nature, industrial environments, or hospital settings. In photovoltaic panels (PVs), biofilms are related to significant energy conversion losses. In this study, our aim was to characterize the communities of microorganisms and the genes involved in biofilm formation.

METHODS AND RESULTS: In this study, biofilm samples collected from a PV system installed in southeastern Brazil were analyzed through shotgun metagenomics, and the microbial communities and genes involved in biofilm formation were investigated. A total of 2030 different genera were identified in the samples, many of which were classified as extremophiles or producers of exopolysaccharides. Bacteria prevailed in the samples (89%), mainly the genera Mucilaginibacter, Microbacterium, Pedobacter, Massilia, and Hymenobacter. The functional annotation revealed >12 000 genes related to biofilm formation and stress response. Genes involved in the iron transport and synthesis of c-di-GMP and c-AMP second messengers were abundant in the samples. The pathways related to these components play a crucial role in biofilm formation and could be promising targets for preventing biofilm formation in the PV. In addition, Raman spectroscopy analysis indicated the presence of hematite, goethite, and ferrite, consistent with the mineralogical composition of the regional soil and metal-resistant bacteria.

CONCLUSIONS: Taken together, our findings reveal that PV biofilms are a promising source of microorganisms of industrial interest and genes of central importance in regulating biofilm formation and persistence.}, } @article {pmid39256724, year = {2024}, author = {Gamage, BD and Ranasinghe, D and Sahankumari, A and Malavige, GN}, title = {Metagenomic analysis of colonic tissue and stool microbiome in patients with colorectal cancer in a South Asian population.}, journal = {BMC cancer}, volume = {24}, number = {1}, pages = {1124}, pmid = {39256724}, issn = {1471-2407}, support = {ASP/01/RE/MED/2018/52//University of Sri Jayewardenepura/ ; ASP/01/RE/MED/2018/52//University of Sri Jayewardenepura/ ; }, mesh = {Adult ; Aged ; Female ; Humans ; Male ; Middle Aged ; Bacteria/classification/isolation & purification ; Colon/microbiology ; *Colorectal Neoplasms/microbiology ; *Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; South Asian People ; }, abstract = {BACKGROUND: The gut microbiome is thought to play an important role in the development of colorectal cancer (CRC). However, as the gut microbiome varies widely based on diet, we sought to investigate the gut microbiome changes in patients with CRC in a South Asian population.

METHODS: The gut microbiome was assessed by 16s metagenomic sequencing targeting the V4 hypervariable region of the bacterial 16S rRNA in stool samples (n = 112) and colonic tissue (n = 36) in 112 individuals. The cohort comprised of individuals with CRC (n = 24), premalignant lesions (n = 10), healthy individuals (n = 50) and in those with diabetes (n = 28).

RESULTS: Overall, the relative abundances of genus Fusobacterium (p < 0.001), Acinetobacter (p < 0.001), Escherichia-Shigella (p < 0.05) were significantly higher in gut tissue, while Romboutsia (p < 0.01) and Prevotella (p < 0.05) were significantly higher in stool samples. Bacteroides and Fusobacterium were the most abundant genera found in stool samples in patients with CRC. Patients with pre-malignant lesions had significantly high abundances of Christensenellaceae, Enterobacteriaceae, Mollicutes and Ruminococcaceae (p < 0.001) compared to patients with CRC, and healthy individuals. Romboutsia was significantly more abundant (p < 0.01) in stool samples in healthy individuals compared to those with CRC and diabetes.

CONCLUSION: Despite marked differences in the Sri Lankan diet compared to the typical Western diet, Bacteroides and Fusobacterium species were the most abundant in those with CRC, with Prevotella species, being most abundant in many individuals. We believe these results pave the way for possible dietary interventions for prevention of CRC in the South Asian population.}, } @article {pmid39256682, year = {2024}, author = {Wu, LH and Hu, CX and Liu, TX}, title = {Metagenomic profiling of gut microbiota in Fall Armyworm (Spodoptera frugiperda) larvae fed on different host plants.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {337}, pmid = {39256682}, issn = {1471-2180}, mesh = {Animals ; *Spodoptera/microbiology/genetics ; *Larva/microbiology ; *Gastrointestinal Microbiome/genetics ; *Metagenomics ; *Zea mays/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Sorghum/microbiology ; Solanum lycopersicum/microbiology ; Capsicum/microbiology ; Metagenome ; }, abstract = {BACKGROUND: The fall armyworm (FAW, Spodoptera frugiperda) is a polyphagous pest known for causing significant crop damage. The gut microbiota plays a pivotal role in influencing the biology, physiology and adaptation of the host. However, understanding of the taxonomic composition and functional characteristics of the gut microbiota in FAW larvae fed on different host plants remains limited.

METHODS: This study utilized metagenomic sequencing to explore the structure, function and antibiotic resistance genes (ARGs) of the gut microbiota in FAW larvae transferred from an artificial diet to four distinct host plants: maize, sorghum, tomato and pepper.

RESULTS: The results demonstrated significant variations in gut microbiota structure among FAW larvae fed on different host plants. Firmicutes emerged as the dominant phylum, with Enterococcaceae as the dominant family and Enterococcus as the prominent genus. Notably, Enterococcus casseliflavus was frequently observed in the gut microbiota of FAW larvae across host plants. Metabolism pathways, particularly those related to carbohydrate and amino acid metabolism, played a crucial role in the adaptation of the FAW gut microbiota to different host plants. KEGG orthologs associated with the regulation of the peptide/nickel transport system permease protein in sorghum-fed larvae and the 6-phospho-β-glucosidase gene linked to glycolysis/gluconeogenesis as well as starch and sucrose metabolism in pepper-fed larvae were identified. Moreover, the study identified the top 20 ARGs in the gut microbiota of FAW larvae fed on different host plants, with the maize-fed group exhibiting the highest abundance of vanRC.

CONCLUSIONS: Our metagenomic sequencing study reveals significant variations in the gut microbiota composition and function of FAW larvae across diverse host plants. These findings underscore the intricate co-evolutionary relationship between hosts and their gut microbiota, suggesting that host transfer profoundly influences the gut microbiota and, consequently, the adaptability and pest management strategies for FAW.}, } @article {pmid39256599, year = {2024}, author = {Chen, Y and Zhang, KX and Liu, H and Zhu, Y and Bu, QY and Song, SX and Li, YC and Zou, H and You, XY and Zhao, GP}, title = {Impact of ginsenoside Rb1 on gut microbiome and associated changes in pharmacokinetics in rats.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {21168}, pmid = {39256599}, issn = {2045-2322}, support = {TSBICIP-CXRC-042//Tianjin Synthetic Biotechnology Innovation Capacity Improvement Projects/ ; TSBICIP-CXRC-008//Tianjin Synthetic Biotechnology Innovation Capacity Improvement Projects/ ; E2M9560201//Major Project of Haihe Laboratory of Synthetic Biology/ ; 31200035//National Natural Science Foundation of China/ ; XDC 0110300//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; }, mesh = {*Ginsenosides/pharmacokinetics/pharmacology ; Animals ; *Gastrointestinal Microbiome/drug effects ; Rats ; Male ; *Bacteroides/drug effects ; Rats, Sprague-Dawley ; Glycoside Hydrolases/metabolism ; }, abstract = {Ginsenoside Rb1 exhibits a wide range of biological activities, and gut microbiota is considered the main metabolic site for Rb1. However, the impact of gut microbiota on the pharmacokinetics of Rb1 are still uncertain. In this study, we investigated the gut microbiome changes and the pharmacokinetics after a 30 d Rb1 intervention. Results reveal that the systemic exposure and metabolic clearance rate of Rb1 and Rd were substantially affected after orally supplementing Rb1 (60 mg/kg) to rats. Significant increase in the relative abundance of Bacteroides cellulosilyticus in gut microbiota and specific glycoside hydrolase (GH) families, such as GH2, GH92, and GH20 were observed based on microbiome and metagenomic analysis. Moreover, a robust association was identified between the pharmacokinetic parameters of Rb1 and the relative abundance of specific Bacteroides species, and glycoside hydrolase families. Our study demonstrates that Rb1 administration significantly affects the gut microbiome, revealing a complex relationship between B. cellulosilyticus, key GH families, and Rb1 pharmacokinetics.}, } @article {pmid39256479, year = {2024}, author = {Campese, L and Russo, L and Abagnale, M and Alberti, A and Bachi, G and Balestra, C and Bellardini, D and Buondonno, A and Cardini, U and Carotenuto, Y and Checcucci, G and Chiusano, ML and D'Ambra, I and d'Ippolito, G and Di Capua, I and Donnarumma, V and Fontana, A and Furia, M and Galarza-Verkovitch, D and Gallia, R and Labadie, K and Leone, S and Licandro, P and Longo, A and Maselli, M and Merquiol, L and Murano, C and Oliveira, PH and Passarelli, A and Percopo, I and Perdereau, A and Piredda, R and Raffini, F and Roncalli, V and Ruscheweyh, HJ and Russo, E and Saggiomo, M and Santinelli, C and Sarno, D and Sunagawa, S and Tramontano, F and Trano, AC and Uttieri, M and Wincker, P and Zampicinini, G and Casotti, R and Conversano, F and D'Alelio, D and Iudicone, D and Margiotta, F and Montresor, M}, title = {The NEREA Augmented Observatory: an integrative approach to marine coastal ecology.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {989}, pmid = {39256479}, issn = {2052-4463}, mesh = {*Ecosystem ; Plankton ; Metagenome ; Biodiversity ; Metagenomics ; }, abstract = {The NEREA (Naples Ecological REsearch for Augmented observatories) initiative aims to establish an augmented observatory in the Gulf of Naples (GoN), designed to advance the understanding of marine ecosystems through a holistic approach. Inspired by the Tara Oceans expedition and building on the scientific legacy of the MareChiara Long-Term Ecological Research (LTER-MC) site, NEREA integrates traditional physical, chemical, and biological measurements with state-of-the-art methodologies such as metabarcoding and metagenomics. Here we present the first 10 months of NEREA data, collected from April 2019 to January 2020, encompassing physico-chemical parameters, plankton biodiversity (e.g., microscopy and flow cytometry), prokaryotic and eukaryotic metabarcoding, a prokaryotic gene catalogue, and a collection of 3818 prokaryotic Metagenome-Assembled Genomes (MAGs). NEREA's efforts produce a significant volume of multifaceted data, which enhances our understanding of marine ecosystems and promotes the development of scientific hypotheses and ideas.}, } @article {pmid39256206, year = {2024}, author = {Ashade, AO and Obayori, OS and Salam, LB and Fashola, MO and Nwaokorie, FO}, title = {Effects of anthropogenic activities on the microbial community diversity of Ologe Lagoon sediment in Lagos State, Nigeria.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {10}, pages = {918}, pmid = {39256206}, issn = {1573-2959}, mesh = {Nigeria ; *Geologic Sediments/microbiology/chemistry ; *Environmental Monitoring ; *Microbiota ; *Water Pollutants, Chemical/analysis ; Metals, Heavy/analysis ; Anthropogenic Effects ; Bacteria/classification/genetics ; Hydrocarbons/analysis ; }, abstract = {The impact of pollution on the Ologe Lagoon was assessed by comparing physicochemical properties, hydrocarbon concentrations and microbial community structures of the sediments obtained from distinct sites of the lagoon. The locations were the human activity site (OLHAS), industrial-contaminated sites (OLICS) and relatively undisturbed site (OLPS). The physicochemical properties, heavy metal concentrations and hydrocarbon profiles were determined using standard methods. The microbial community structures of the sediments were determined using shotgun next-generation sequencing (NGS), taxonomic profiling was performed using centrifuge and statistical analysis was done using statistical analysis for metagenomics profile (STAMP) and Microsoft Excel. The result showed acidic pH across all sampling points, while the nitrogen content at OLPS was low (7.44 ± 0.085 mg/L) as compared with OLHAS (44.380 ± 0.962 mg/L) and OLICS (59.485 ± 0.827 mg/L). The levels of the cadmium, lead and nickel in the three sites were above the regulatory limits. The gas chromatography flame ionization detector (GC-FID) profile revealed hydrocarbon contaminations with nC14 tetradecane > alpha xylene > nC9 nonane > acenaphthylene more enriched at OLPS. Structurally, the sediments metagenomes consisted of 43 phyla,75 classes each, 165, 161, 166 orders, 986, 927 and 866 bacterial genera and 1476, 1129, 1327 species from OLHAS, OLICS and OLPS, respectively. The dominant phyla in the sediments were Proteobacteria, Firmicutes, Actinobacteria, and Chloroflexi. The principal component ordination (PCO) showed that OLPS microbial community had a total variance of 87.7% PCO1, setting it apart from OLHAS and OLICS. OLICS and OLHAS were separated by PCO2 accounting for 12.3% variation, and the most polluted site is the OLPS.}, } @article {pmid39255933, year = {2024}, author = {Kim, Y and Choe, S and Cho, Y and Moon, H and Shin, H and Seo, J and Myung, J}, title = {Biodegradation of poly(butylene adipate terephthalate) and poly(vinyl alcohol) within aquatic pathway.}, journal = {The Science of the total environment}, volume = {953}, number = {}, pages = {176129}, doi = {10.1016/j.scitotenv.2024.176129}, pmid = {39255933}, issn = {1879-1026}, mesh = {*Biodegradation, Environmental ; *Water Pollutants, Chemical/analysis/metabolism ; *Polyesters/metabolism ; *Polyvinyl Alcohol ; *Wastewater/chemistry ; Seawater/chemistry ; Biodegradable Plastics/metabolism ; }, abstract = {Understanding the environmental fate of biodegradable plastics in aquatic systems is crucial, given the alarming amount of plastic waste and microplastic particles transported through aquatic pathways. In particular, there is a need to analyze the biodegradation of commercialized biodegradable plastics upon release from wastewater treatment plants into natural aquatic systems. This study investigates the biodegradation behaviors of poly(butylene adipate terephthalate) (PBAT) and poly(vinyl alcohol) (PVA) in wastewater, freshwater, and seawater. Biodegradation of PBAT and PVA assessed through biochemical oxygen demand (BOD) experiments and microcosm tests revealed that the type of aquatic system governs the biodegradation behaviors of each plastic, with the highest biodegradation rate achieved in wastewater for both PBAT and PVA (25.6 and 32.2 % in 30 d, respectively). Plastic release pathway from wastewater into other aquatic systems simulated by sequential incubation in different microcosms suggested that PBAT exposed to wastewater and freshwater before reaching seawater was more prone to degradation than when directly exposed to seawater. On the other hand, PVA displayed comparable biodegradation rate regardless of whether it was directly exposed to seawater or had passed through other environments beforehand. Metagenome amplicon sequencing of 16S rRNA genes revealed distinct community shifts dependent on the type of plastics in changing environments along the simulated aquatic pathway. Several bacterial species putatively implicated in the biodegradation of PBAT and PVA are discussed. Our findings underscore the significant influence of pollution routes on the biodegradation of PBAT and PVA, highlighting the potential for wastewater treatment to facilitate rapid degradation compared to direct exposure to pristine aquatic environments.}, } @article {pmid39255566, year = {2024}, author = {Quan, H and Jia, Y and Zhang, H and Ji, F and Shi, Y and Deng, Q and Hao, T and Khanal, SK and Sun, L and Lu, H}, title = {Insights into the role of electrochemical stimulation on sulfur-driven biodegradation of antibiotics in wastewater treatment.}, journal = {Water research}, volume = {266}, number = {}, pages = {122385}, doi = {10.1016/j.watres.2024.122385}, pmid = {39255566}, issn = {1879-2448}, mesh = {*Wastewater/chemistry ; *Anti-Bacterial Agents ; *Sulfur/metabolism ; *Biodegradation, Environmental ; Water Pollutants, Chemical/metabolism ; Waste Disposal, Fluid/methods ; Electrochemical Techniques ; }, abstract = {The presence of antibiotics in wastewater poses significant threat to our ecosystems and health. Traditional biological wastewater treatment technologies have several limitations in treating antibiotic-contaminated wastewaters, such as low removal efficiency and poor process resilience. Here, a novel electrochemical-coupled sulfur-mediated biological system was developed for treating wastewater co-contaminated with several antibiotics (e.g., ciprofloxacin (CIP), sulfamethoxazole (SMX), chloramphenicol (CAP)). Superior removal of CIP, SMX, and CAP with efficiencies ranging from 40.6 ± 2.6 % to 98.4 ± 1.6 % was achieved at high concentrations of 1000 μg/L in the electrochemical-coupled sulfur-mediated biological system, whereas the efficiencies ranged from 30.4 ± 2.3 % to 98.2 ± 1.4 % in the control system (without electrochemical stimulation). The biodegradation rates of CIP, SMX, and CAP increased by 1.5∼1.9-folds under electrochemical stimulation compared to the control. The insights into the role of electrochemical stimulation for multiple antibiotics biodegradation enhancement was elucidated through a combination of metagenomic and electrochemical analyses. Results showed that sustained electrochemical stimulation significantly enriched the sulfate-reducing and electroactive bacteria (e.g., Desulfobulbus, Longilinea, and Lentimicrobiumin on biocathode and Geobactor on bioanode), and boosted the secretion of electron transport mediators (e.g., cytochrome c and extracellular polymeric substances), which facilitated the microbial extracellular electron transfer processes and subsequent antibiotics removal in the sulfur-mediated biological system. Furthermore, under electrochemical stimulation, functional genes associated with sulfur and carbon metabolism and electron transfer were more abundant, and the microbial metabolic processes were enhanced, contributing to antibiotics biodegradation. Our study for the first time demonstrated that the synergistic effects of electrochemical-coupled sulfur-mediated biological system was capable of overcoming the limitations of conventional biological treatment processes. This study shed light on the mechanism of enhanced antibiotics biodegradation via electrochemical stimulation, which could be employed in sulfur-mediated bioprocess for treating antibiotic-contaminated wastewaters.}, } @article {pmid39255397, year = {2024}, author = {Park, G and Kadyan, S and Hochuli, N and Salazar, G and Laitano, O and Chakrabarty, P and Efron, PA and Zafar, MA and Wilber, A and Nagpal, R}, title = {An Enteric Bacterial Infection Triggers Neuroinflammation and Neurobehavioral Impairment in 3xTg-AD Transgenic Mice.}, journal = {The Journal of infectious diseases}, volume = {230}, number = {Supplement_2}, pages = {S95-S108}, pmid = {39255397}, issn = {1537-6613}, support = {23A02//Florida Department of Health/ ; R01 AG070094/NH/NIH HHS/United States ; R01 AG070094/AG/NIA NIH HHS/United States ; //Foundation/ ; R21 AI166642/AI/NIAID NIH HHS/United States ; 440658//US Department of Agriculture/ ; R01 AI173244/AI/NIAID NIH HHS/United States ; //Infectious Diseases Society of America/ ; //Florida State University/ ; R01AI173244//US Public Health Service/ ; }, mesh = {Animals ; Mice ; *Mice, Transgenic ; *Klebsiella pneumoniae ; *Disease Models, Animal ; *Dysbiosis/microbiology/chemically induced ; *Alzheimer Disease/microbiology ; *Neuroinflammatory Diseases/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Klebsiella Infections/microbiology ; *Blood-Brain Barrier/microbiology ; Brain/pathology/microbiology ; Anti-Bacterial Agents/pharmacology ; Brain-Gut Axis ; Male ; Humans ; }, abstract = {BACKGROUND: Klebsiella pneumoniae is infamous for hospital-acquired infections and sepsis, which have also been linked to Alzheimer disease (AD)-related neuroinflammatory and neurodegenerative impairment. However, its causative and mechanistic role in AD pathology remains unstudied.

METHODS: A preclinical model of K. pneumoniae enteric infection and colonization is developed in an AD model (3xTg-AD mice) to investigate whether and how K. pneumoniae pathogenesis exacerbates neuropathogenesis via the gut-blood-brain axis.

RESULTS: K. pneumoniae, particularly under antibiotic-induced dysbiosis, was able to translocate from the gut to the bloodstream by penetrating the gut epithelial barrier. Subsequently, K. pneumoniae infiltrated the brain by breaching the blood-brain barrier. Significant neuroinflammatory phenotype was observed in mice with K. pneumoniae brain infection. K. pneumoniae-infected mice also exhibited impaired neurobehavioral function and elevated total tau levels in the brain. Metagenomic analyses revealed an inverse correlation of K. pneumoniae with gut biome diversity and commensal bacteria, highlighting how antibiotic-induced dysbiosis triggers an enteroseptic "pathobiome" signature implicated in gut-brain perturbations.

CONCLUSIONS: The findings demonstrate how infectious agents following hospital-acquired infections and consequent antibiotic regimen may induce gut dysbiosis and pathobiome and increase the risk of sepsis, thereby increasing the predisposition to neuroinflammatory and neurobehavioral impairments via breaching the gut-blood-brain barrier.}, } @article {pmid39254351, year = {2024}, author = {Wasmund, K and Singleton, C and Dahl Dueholm, MK and Wagner, M and Nielsen, PH}, title = {The predicted secreted proteome of activated sludge microorganisms indicates distinct nutrient niches.}, journal = {mSystems}, volume = {9}, number = {10}, pages = {e0030124}, pmid = {39254351}, issn = {2379-5077}, mesh = {*Sewage/microbiology ; *Proteome/metabolism/analysis ; Bacterial Proteins/genetics/metabolism ; Nutrients/metabolism/analysis ; Bacteria/metabolism/genetics/classification ; Metagenome ; Microbiota/genetics ; }, abstract = {In wastewater treatment plants (WWTPs), complex microbial communities process diverse chemical compounds from sewage. Secreted proteins are critical because many are the first to interact with or degrade external (macro)molecules. To better understand microbial functions in WWTPs, we predicted secreted proteomes of WWTP microbiota from more than 1,000 high-quality metagenome-assembled genomes (MAGs) from 23 Danish WWTPs with biological nutrient removal. Focus was placed on examining secreted catabolic exoenzymes that target major classes of macromolecules. We demonstrate that Bacteroidota has a high potential to digest complex polysaccharides, but also proteins and nucleic acids. Poorly understood activated sludge members of Acidobacteriota and Gemmatimonadota also have high capacities for extracellular polysaccharide digestion. Secreted nucleases are encoded by 61% of MAGs indicating an importance for extracellular DNA and/or RNA digestion in WWTPs. Secreted lipases were the least common macromolecule-targeting enzymes predicted, encoded mainly by Gammaproteobacteria and Myxococcota. In contrast, diverse taxa encode extracellular peptidases, indicating that proteins are widely used nutrients. Diverse secreted multi-heme cytochromes suggest capabilities for extracellular electron transfer by various taxa, including some Bacteroidota that encode undescribed cytochromes with >100 heme-binding motifs. Myxococcota have exceptionally large secreted protein complements, probably related to predatory lifestyles and/or complex cell cycles. Many Gammaproteobacteria MAGs (mostly former Betaproteobacteria) encode few or no secreted hydrolases, but many periplasmic substrate-binding proteins and ABC- and TRAP-transporters, suggesting they are mostly sustained by small molecules. Together, this study provides a comprehensive overview of how WWTPs microorganisms interact with the environment, providing new insights into their functioning and niche partitioning.IMPORTANCEWastewater treatment plants (WWTPs) are critical biotechnological systems that clean wastewater, allowing the water to reenter the environment and limit eutrophication and pollution. They are also increasingly important for the recovery of resources. They function primarily by the activity of microorganisms, which act as a "living sponge," taking up and transforming nutrients, organic material, and pollutants. Despite much research, many microorganisms in WWTPs are uncultivated and poorly characterized, limiting our understanding of their functioning. Here, we analyzed a large collection of high-quality metagenome-assembled genomes from WWTPs for encoded secreted enzymes and proteins, with special emphasis on those used to degrade organic material. This analysis showed highly distinct secreted proteome profiles among different major phylogenetic groups of microorganisms, thereby providing new insights into how different groups function and co-exist in activated sludge. This knowledge will contribute to a better understanding of how to efficiently manage and exploit WWTP microbiomes.}, } @article {pmid39254336, year = {2024}, author = {Jung, D and Park, S and Kurban, D and Dufour, S and Ronholm, J}, title = {The occurrence of Aerococcus urinaeequi and non-aureus staphylococci in raw milk negatively correlates with Escherichia coli clinical mastitis.}, journal = {mSystems}, volume = {9}, number = {10}, pages = {e0036224}, pmid = {39254336}, issn = {2379-5077}, support = {Dairy Research Cluster 3//Dairy Farmers of Canada (DFC)/ ; }, mesh = {Animals ; Female ; *Milk/microbiology ; Cattle ; *Mastitis, Bovine/microbiology ; *Escherichia coli/isolation & purification/genetics ; *Aerococcus/isolation & purification/genetics ; *Escherichia coli Infections/microbiology/veterinary ; *Staphylococcus/isolation & purification/genetics ; Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Escherichia coli is a common environmental pathogen associated with clinical mastitis (CM) in dairy cattle. There is an interest in optimizing the udder microbiome to increase the resistance of dairy cattle to E. coli CM; however, the details of which members of the healthy udder microbiome may play a role in antagonizing E. coli are unknown. In this study, we characterized the bacterial community composition in raw milk collected from quarters of lactating Holstein dairy cows that developed E. coli CM during lactation, including milk from both healthy and diseased quarters (n = 1,172). The milk microbiome from infected quarters was compared before, during, and after CM. A combination of 16S rRNA gene amplicon and metagenomic sequencing was used generate data sets with a high level of both depth and breadth. The microbial diversity present in raw milk significantly decreased in quarters experiencing E. coli CM, indicating that E. coli displaces other members of the microbiome. However, the diversity recovered very rapidly after infection. Two genera, Staphylococcus and Aerococcus, and the family Oscillospiraceae were significantly more abundant in healthy quarters with low inflammation. Species of these genera, Staphylococcus auricularis, Staphylococcus haemolyticus, and Aerocussus urinaeequi, were identified by metagenomics. Thus, these species are of interest for optimizing the microbiome to discourage E. coli colonization without triggering inflammation.IMPORTANCEIn this study, we show that E. coli outcompetes and displaces several members of the udder microbiome during CM, but that microbial diversity recovers post-infection. In milk from quarters which remained healthy, the community composition was often highly dominated by S. auricularis, S. haemolyticus, A. urinaeequi, and S. marcescens without increases in somatic cell count (SCC). Community dominance by these organisms, without inflammation, could indicate that these species might have potential as prophylactic probiotics which could contribute to colonization resistance and prevent future instances of E. coli CM.}, } @article {pmid39254265, year = {2024}, author = {Anandakumar, H and Rauch, A and Wimmer, MI and Yarritu, A and Koch, G and McParland, V and Bartolomaeus, H and Wilck, N}, title = {Segmental patterning of microbiota and immune cells in the murine intestinal tract.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2398126}, pmid = {39254265}, issn = {1949-0984}, mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; *Mice, Inbred C57BL ; *Bacteria/classification/genetics/isolation & purification/immunology ; Intestines/microbiology/immunology/cytology ; Metagenomics ; Germ-Free Life ; Female ; T-Lymphocyte Subsets/immunology ; Male ; Intestinal Mucosa/microbiology/immunology/cytology ; }, abstract = {The intestine exhibits distinct characteristics along its length, with a substantial immune cell reservoir and diverse microbiota crucial for maintaining health. This study investigates how anatomical location and regional microbiota influence intestinal immune cell abundance. Using conventionally colonized and germ-free mice, segment-specific immune cell composition and microbial communities were assessed. Metagenomic sequencing analyzed microbiome variations, while flow cytometry and immunofluorescence examined immune cell composition. Microbiome composition varied significantly along the intestine, with diversity and abundance increasing from upper to lower segments. Immune cells showed distinct segment-specific patterning influenced by microbial colonization and localization. T cell subsets displayed varied dependence on microbiome presence and anatomical location. This study highlights locoregional differences in intestinal immune cell and microbiome composition, identifying immune subsets susceptible to microbiota presence. The findings provide context for understanding immune cell alterations in disease models.}, } @article {pmid39254230, year = {2024}, author = {Qi, Q and Ning, S and Guo, X and Zhao, J and Tian, R and Gui, H and He, JS and Wang, H and Zhang, Z and Konstantinidis, KT and Gao, Q and Wang, Y and Li, S and Zhao, W and Yang, Y and Zhou, J}, title = {More sensitive microbial responses to the interactive effects of warming and altered precipitation in subsoil than topsoil of an alpine grassland ecosystem.}, journal = {Global change biology}, volume = {30}, number = {9}, pages = {e17487}, doi = {10.1111/gcb.17487}, pmid = {39254230}, issn = {1365-2486}, support = {//the CAS Youth Interdisciplinary Team/ ; 32161123002//National Natural Science Foundation of China/ ; 42277213//National Natural Science Foundation of China/ ; 41907209//National Natural Science Foundation of China/ ; 41877048//National Natural Science Foundation of China/ ; 32130065//National Natural Science Foundation of China/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; }, mesh = {*Soil Microbiology ; *Grassland ; *Climate Change ; *Rain ; *Carbon Cycle ; *Soil/chemistry ; Tibet ; Carbon/analysis/metabolism ; Global Warming ; Bacteria/genetics/classification ; }, abstract = {Subsoil is a large organic carbon reservoir, storing more than half of the total soil organic carbon (SOC) globally. Conventionally, subsoil is assumed to not be susceptible to climate change, but recent studies document that climate change could significantly alter subsoil carbon cycling. However, little is known about subsoil microbial responses to the interactive effects of climate warming and altered precipitation. Here, we investigated carbon cycling and associated microbial responses in both subsoil (30-40 cm) and topsoil (0-10 cm) in a Tibetan alpine grassland over 4 years of warming and altered precipitation. Compared to the unchanged topsoil carbon (β = .55, p = .587), subsoil carbon exhibited a stronger response to the interactive effect of warming and altered precipitation (β = 2.04, p = .021), that is, warming decreased subsoil carbon content by 28.20% under decreased precipitation while warming increased subsoil carbon content by 18.02% under increased precipitation.Furthermore, 512 metagenome-assembled genomes (MAGs) were recovered, including representatives of phyla with poor genomic representation. Compared to only one changed topsoil MAG, 16 subsoil MAGs were significantly affected by altered precipitation, and 5 subsoil MAGs were significantly affected by the interactive effect of warming and precipitation. More than twice as many populations whose MAG abundances correlated significantly with the variations of carbon content, components and fluxes were observed in the subsoil than topsoil, suggesting their potential contribution in mediating subsoil carbon cycling. Collectively, our findings highlight the more sensitive responses of specific microbial lineages to the interactive effects of warming and altered precipitation in the subsoil than topsoil, and provide key information for predicting subsoil carbon cycling under future climate change scenarios.}, } @article {pmid39254049, year = {2024}, author = {Harris, RM and Pace, F and Kuntz, TM and Morgan, XC and Hyland, P and Summers, K and McDermott, E and Blumen, K and Watnick, PI}, title = {Testosterone treatment impacts the intestinal microbiome of transgender individuals.}, journal = {mSphere}, volume = {9}, number = {10}, pages = {e0055724}, pmid = {39254049}, issn = {2379-5042}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Testosterone ; Male ; *Transgender Persons ; Female ; Pilot Projects ; *Feces/microbiology ; Adult ; Metagenomics ; Middle Aged ; Glutamic Acid/metabolism ; Bacteria/classification/genetics/drug effects/metabolism/isolation & purification ; }, abstract = {Medical modulation of sex hormone levels is a cornerstone of treatment for many conditions that impact well-being, including cancer, fertility/infertility, gender dysphoria, and chronic metabolic diseases such as diabetes and obesity. The microbial residents of the intestine, known as the microbiota, interact with sex hormones in the intestine, and there is correlative evidence that this interaction is bidirectional. Based on these published findings, we hypothesized that transgender individuals receiving exogenous testosterone as part of their gender-affirming medical treatment might undergo changes in their intestinal microbiome. To test this, we collected 26 stool samples from nine individuals before and up to 8 months after initiation of treatment with exogenous testosterone and subjected these samples to metagenomic analysis. While no species were significantly associated with the duration of testosterone therapy, pathways that generate glutamate increased in abundance, while those that consume glutamate decreased. Glutamate is a precursor of arginine, and testosterone is known to increase levels of arginine and its metabolites in the plasma. We hypothesize that testosterone increases the uptake of glutamate by enterocytes, thus decreasing access of the microbiota to this amino acid. While this pilot study establishes the impact of testosterone therapy on the intestinal microbiome, a more comprehensive study is necessary to establish the impact of testosterone-driven metagenomic shifts on the stool metatranscriptome, the stool metabolome, and the plasma metabolome.IMPORTANCEThe human intestine is inhabited by a large community of microbes known as the microbiome. Members of the microbiome consume the diet along with their human host. Thus, the metabolomes of the host and microbe are intricately linked. Testosterone alters the plasma metabolome. In particular, plasma levels of arginine and its metabolites and testosterone are positively correlated. To investigate the impact of exogenous testosterone on the microbiome, we analyzed the stool metagenomes of transgender individuals before and after the initiation of testosterone treatment. In this pilot project, we found a modest impact on the microbiome community structure but an increase in the abundance of metabolic pathways that generate glutamate and spare glutamate consumption. We propose that the host uses glutamate to generate arginine, decreasing the amount available for the microbiome.}, } @article {pmid39253815, year = {2024}, author = {Wimmer, MI and Bartolomaeus, H and Anandakumar, H and Chen, CY and Vecera, V and Kedziora, S and Kamboj, S and Schumacher, F and Pals, S and Rauch, A and Meisel, J and Potapenko, O and Yarritu, A and Bartolomaeus, TUP and Samaan, M and Thiele, A and Stürzbecher, L and Geisberger, SY and Kleuser, B and Oefner, PJ and Haase, N and Löber, U and Gronwald, W and Forslund-Startceva, SK and Müller, DN and Wilck, N}, title = {Metformin modulates microbiota and improves blood pressure and cardiac remodeling in a rat model of hypertension.}, journal = {Acta physiologica (Oxford, England)}, volume = {240}, number = {11}, pages = {e14226}, doi = {10.1111/apha.14226}, pmid = {39253815}, issn = {1748-1716}, support = {//Deutsche Forschungsgemeinschaft/ ; //Deutsches Zentrum für Herz-Kreislaufforschung/ ; }, mesh = {Animals ; *Metformin/pharmacology ; *Hypertension/drug therapy/metabolism ; Male ; *Gastrointestinal Microbiome/drug effects ; *Blood Pressure/drug effects ; *Ventricular Remodeling/drug effects ; Rats ; *Rats, Transgenic ; Disease Models, Animal ; Hypoglycemic Agents/pharmacology ; Fatty Acids, Volatile/metabolism ; }, abstract = {AIMS: Metformin has been attributed to cardiovascular protection even in the absence of diabetes. Recent observations suggest that metformin influences the gut microbiome. We aimed to investigate the influence of metformin on the gut microbiota and hypertensive target organ damage in hypertensive rats.

METHODS: Male double transgenic rats overexpressing the human renin and angiotensinogen genes (dTGR), a model of angiotensin II-dependent hypertension, were treated with metformin (300 mg/kg/day) or vehicle from 4 to 7 weeks of age. We assessed gut microbiome composition and function using shotgun metagenomic sequencing and measured blood pressure via radiotelemetry. Cardiac and renal organ damage and inflammation were evaluated by echocardiography, histology, and flow cytometry.

RESULTS: Metformin treatment increased the production of short-chain fatty acids (SCFA) acetate and propionate in feces without altering microbial composition and diversity. It significantly reduced systolic and diastolic blood pressure and improved cardiac function, as measured by end-diastolic volume, E/A, and stroke volume despite increased cardiac hypertrophy. Metformin reduced cardiac inflammation by lowering macrophage infiltration and shifting macrophage subpopulations towards a less inflammatory phenotype. The observed improvements in blood pressure, cardiac function, and inflammation correlated with fecal SCFA levels in dTGR. In vitro, acetate and propionate altered M1-like gene expression in macrophages, reinforcing anti-inflammatory effects. Metformin did not affect hypertensive renal damage or microvascular structure.

CONCLUSION: Metformin modulated the gut microbiome, increased SCFA production, and ameliorated blood pressure and cardiac remodeling in dTGR. Our findings confirm the protective effects of metformin in the absence of diabetes, highlighting SCFA as a potential mediators.}, } @article {pmid39253787, year = {2024}, author = {Cheng, S and Gong, X and Xue, W and Kardol, P and Delgado-Baquerizo, M and Ling, N and Chen, X and Liu, M}, title = {Evolutionarily conserved core microbiota as an extended trait in nitrogen acquisition strategy of herbaceous species.}, journal = {The New phytologist}, volume = {244}, number = {4}, pages = {1570-1584}, doi = {10.1111/nph.20118}, pmid = {39253787}, issn = {1469-8137}, support = {42077047//National Foundation of Sciences in China/ ; lzujbky-2022-ct04//Fundamental Research Funds for the Central University of China/ ; 2021YFD1700202//National Key R&D program/ ; }, mesh = {*Nitrogen/metabolism ; *Rhizosphere ; *Microbiota ; *Phylogeny ; Biological Evolution ; Plants/microbiology/metabolism ; Soil Microbiology ; Species Specificity ; Quantitative Trait, Heritable ; }, abstract = {Microbiota have co-evolved with plants over millions of years and are intimately linked to plants, ranging from symbiosis to pathogenesis. However, our understanding of the existence of a shared core microbiota across phylogenetically diverse plants remains limited. A common garden field experiment was conducted to investigate the rhizosphere microbial communities of phylogenetically contrasting herbaceous families. Through a combination of metagenomic sequencing, analysis of plant economic traits, and soil biochemical properties, we aimed to elucidate the eco-evolutionary role of the core rhizosphere microbiota in light of plant economic strategies. We identified a conserved core microbiota consisting of 278 taxa that was closely associated with the phylogeny of the plants studied. This core microbiota actively participated in multiple nitrogen metabolic processes and showed a strong correlation with the functional potential of rhizosphere nitrogen cycling, thereby serving as an extended trait in the plant nitrogen acquisition. Furthermore, our examination of simulated species loss revealed the crucial role of the core microbiota in maintaining the rhizosphere community's network stability. Our study highlighted that the core microbiota, which exhibited a phylogenetically conserved association with plants, potentially represented an extension of the plant phenotype and played an important role in nitrogen acquisition. These findings held implications for the utilization of microbiota-mediated plant functions.}, } @article {pmid39253606, year = {2024}, author = {Qin, Y and Zou, X and Jin, Y and Li, J and Cai, Q}, title = {Cryptococcus Neoformans Osteomyelitis of the Right Ankle Diagnosed by Metagenomic Next-Generation Sequencing in a HIV-Negative Patient with Tuberculous Lymphadenitis and Pulmonary Tuberculosis: A Case Report and Recent Literature Review.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {3805-3812}, pmid = {39253606}, issn = {1178-6973}, abstract = {AIM: Cryptococcus neoformans osteomyelitis coupled with tuberculosis and tuberculous lymphadenitis, is a rare occurrence in clinical. Diagnostic challenges arise due to the clinical radiological similarity of this condition to other lung infections and the limited and sensitive nature of traditional approaches. Here, we present a case of co-infection diagnosed using Metagenomic Next-Generation Sequencing, highlighting the effectiveness of advanced genomic techniques in such complex scenarios.

CASE PRESENTATION: We present a case of a 67-year-old female infected with cryptococcal osteomyelitis and presented with swelling and pain in the right ankle. Following a biopsy of the right ankle joint, Metagenomic Next-Generation Sequencing (mNGS) of the biopsy tissue revealed Cryptococcus neoformans infection. Positive results for Cryptococcus capsular antigen and pathological findings confirmed the presence of Cryptococcus neoformans. The patient underwent surgical debridement, coupled with oral fluconazole treatment (300mg/day), leading to the resolution of symptoms.

CONCLUSION: Cryptococcus neoformans is an uncommon cause of ankle infection. Metagenomic Next-Generation Sequencing (mNGS) serves as a valuable diagnostic tool, aiding clinicians in differentiating cryptococcal osteomyelitis from other atypical infections.}, } @article {pmid39253579, year = {2024}, author = {Wang, X and Yang, J and Ren, B and Yang, G and Liu, X and Xiao, R and Ren, J and Zhou, F and You, L and Zhao, Y}, title = {Comprehensive multi-omics profiling identifies novel molecular subtypes of pancreatic ductal adenocarcinoma.}, journal = {Genes & diseases}, volume = {11}, number = {6}, pages = {101143}, pmid = {39253579}, issn = {2352-3042}, abstract = {Pancreatic cancer, a highly fatal malignancy, is predicted to rank as the second leading cause of cancer-related death in the next decade. This highlights the urgent need for new insights into personalized diagnosis and treatment. Although molecular subtypes of pancreatic cancer were well established in genomics and transcriptomics, few known molecular classifications are translated to guide clinical strategies and require a paradigm shift. Notably, chronically developing and continuously improving high-throughput technologies and systems serve as an important driving force to further portray the molecular landscape of pancreatic cancer in terms of epigenomics, proteomics, metabonomics, and metagenomics. Therefore, a more comprehensive understanding of molecular classifications at multiple levels using an integrated multi-omics approach holds great promise to exploit more potential therapeutic options. In this review, we recapitulated the molecular spectrum from different omics levels, discussed various subtypes on multi-omics means to move one step forward towards bench-to-beside translation of pancreatic cancer with clinical impact, and proposed some methodological and scientific challenges in store.}, } @article {pmid39253328, year = {2024}, author = {Gao, Z and Zheng, W and Zhang, M and Gao, Y and Huang, J and Chen, X and Dai, Z and Song, Z and Feng, J and Cao, Q and Jin, Y}, title = {Metagenomic next-generation sequencing promotes pathogen detection over culture in joint infections with previous antibiotic exposure.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1388765}, pmid = {39253328}, issn = {2235-2988}, mesh = {Humans ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Male ; Female ; Middle Aged ; Aged ; *Synovial Fluid/microbiology ; *Bacteria/genetics/isolation & purification/classification/drug effects ; Sensitivity and Specificity ; Adult ; Arthritis, Infectious/microbiology/diagnosis/drug therapy ; }, abstract = {OBJECTIVE: To investigate the diagnostic value of metagenomic next-generation sequencing (mNGS) in detecting pathogens from joint infection (JI) synovial fluid (SF) samples with previous antibiotic exposure.

METHODS: From January 2019 to January 2022, 59 cases with suspected JI were enrolled. All cases had antibiotic exposure within 2 weeks before sample collection. mNGS and conventional culture were performed on SF samples. JI was diagnosed based on history and clinical symptoms in conjunction with MSIS criteria. The diagnostic values, including sensitivity, specificity, positive/negative predictive values (PPV/NPV), and accuracy, were in comparison with mNGS and culture.

RESULTS: There were 47 of the 59 cases diagnosed with JI, while the remaining 12 were diagnosed with non-infectious diseases. The sensitivity of mNGS was 68.1%, which was significantly higher than that of culture (25.5%, p<0.01). The accuracy of mNGS was significantly higher at 71.2% compared to the culture at 39.0% (p <0.01). Eleven pathogenic strains were detected by mNGS but not by microbiological culture, which included Staphylococcus lugdunensis, Staphylococcus cohnii, Finegoldia magna, Enterococcus faecalis, Staphylococcus saprophytics, Escherichia coli, Salmonella enterica, Pseudomonas aeruginosa, Acinetobacter pittii, Brucella ovis, andCoxiella burnetii. Antibiotic therapy was adjusted based on the mNGS results in 32 (68.1%) patients, including 12 (25.5%) and 20 (42.6%) patients, in whom treatment was upgraded and changed, respectively. All JI patients underwent surgery and received subsequent antibiotic therapy. They were followed up for an average of 23 months (20-27 months), and the success rate of treatment was 89.4%. Out of the 33 patients who had positive results for pathogens, reoperation was performed in 1 case (3.03%), while out of the 14 cases with negative results for both mNGS and cultures, reoperation was performed in 4 cases (28.6%).

CONCLUSIONS: mNGS has advantages over conventional culture in detecting pathogens in SF samples from JI patients previously treated with antibiotics, potentially improving clinical outcomes.}, } @article {pmid39253237, year = {2024}, author = {Zhuang, L and Zhu, C and Ma, J and Zhu, D and Zhu, H and Zhong, S and Liu, X and Wang, Z and Yang, Z and Zhang, W and Ding, R and Chen, D and Zheng, S}, title = {Predictive performance of Metagenomic Next Generation Sequencing in early detection of post-liver transplantation infections.}, journal = {Heliyon}, volume = {10}, number = {16}, pages = {e36405}, pmid = {39253237}, issn = {2405-8440}, abstract = {OBJECTIVE: To evaluate the predictive performance of metagenomic next-generation sequencing (mNGS) in identifying and predicting pulmonary infections following liver transplantation and to investigate its association with patient outcomes within the initial four-week post-transplantation period.

METHODS: We retrospectively analyzed 41 liver transplant patients with suspected pulmonary infections from August 2022 to May 2023. Bronchoalveolar lavage fluid (BALF) samples were collected on the first postoperative day for metagenomic next generation sequencing (mNGS) and culture. The predictive capability of mNGS for subsequent infections was assessed by monitoring inflammatory biomarkers and comparing the detection rates with culture methods. Real-time Polymerase Chain Reaction (Rt-PCR) was used to monitor Human betaherpesvirus 5 (CMV) and Human parvovirus B19 (B19) weekly during a four-week postoperative period. Inflammatory biomarkers and blood coagulation function were evaluated on specific days throughout the first, third, fifth, and during four weeks following surgery. The study was conducted until August 2023 to evaluate the patients' prognostic survival outcome, classifying them into groups based on the mortality and survival.

RESULTS: The analysis included a total of 41 patients, comprising 32 males and 9 females, with an average age of 52 (47, 63) years. Within one week after liver transplantation, there were 7 cases of bacterial infections, 5 cases of fungal infections, 19 cases of mixed infections, 8 cases without any infection, and 2 cases with unidentified pathogen-associated infections. mNGS successfully predicted 39 (72 %) strains of pathogens, while culture-based methods only detected 28 (52 %) strains. Among the 8 patients diagnosed as non-infected, culture methods identified positive results in 4 cases (50 %), whereas mNGS yielded positive results in 7 cases (87.5 %). The detection rates of CMV and B19 by Rt-PCR within 4 weeks after liver transplantation were 61 % and 17 %, respectively (25/41, 7/41) among the patients. During the study period, a total of 9 patients succumbed while 32 patients survived. The death group and the survival group exhibited significant differences in CRP, HGB, and INR levels at specific monitoring time points. The proportion of CMV detection in blood was significantly higher in the death group compared to the surviving group. Elevated CRP level was identified as a prognostic risk factor.

CONCLUSIONS: Despite the presence of false positives, mNGS still presents a potential advantage in predicting pulmonary infection pathogens following liver transplantation. Furthermore, the levels of CRP and CMV carrier status within four weeks post-surgery exhibit significant associations with patient survival and prognosis.}, } @article {pmid39253087, year = {2024}, author = {Huang, Z and Hu, B and Li, J and Feng, M and Wang, Z and Huang, F and Xu, H and Liu, L and Shang, W}, title = {Metagenomic versus targeted next-generation sequencing for detection of microorganisms in bronchoalveolar lavage fluid among renal transplantation recipients.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1443057}, pmid = {39253087}, issn = {1664-3224}, mesh = {Humans ; *Kidney Transplantation/adverse effects ; *Bronchoalveolar Lavage Fluid/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Middle Aged ; Male ; Female ; Adult ; Bacteria/isolation & purification/genetics ; Transplant Recipients ; Aged ; Fungi/isolation & purification/genetics ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS), which provides untargeted and unbiased pathogens detection, has been extensively applied to improve diagnosis of pulmonary infection. This study aimed to compare the clinical performance between mNGS and targeted NGS (tNGS) for microbial detection and identification in bronchoalveolar lavage fluid (BALF) from kidney transplantation recipients (KTRs).

METHODS: BALF samples with microbiological results from mNGS and conventional microbiological test (CMT) were included. For tNGS, samples were extracted, amplified by polymerase chain reaction with pathogen-specific primers, and sequenced on an Illumina Nextseq.

RESULTS: A total of 99 BALF from 99 KTRs, among which 93 were diagnosed as pulmonary infection, were analyzed. Compared with CMT, both mNGS and tNGS showed higher positive rate and sensitivity (p<0.001) for overall, bacterial and fungal detection. Although the positive rate for mNGS and tNGS was comparable, mNGS significantly outperformed tNGS in sensitivity (100% vs. 93.55%, p<0.05), particularly for bacteria and virus (p<0.001). Moreover, the true positive rate for detected microbes of mNGS was superior over that of tNGS (73.97% vs. 63.15%, p<0.05), and the difference was also significant when specific for bacteria (94.59% vs. 64.81%, p<0.001) and fungi (93.85% vs. 72.58%, p<0.01). Additionally, we found that, unlike most microbes such as SARS-CoV-2, Aspergillus, and EBV, which were predominantly detected from recipients who underwent surgery over 3 years, Torque teno virus (TTV) were principally detected from recipients within 1-year post-transplant, and as post-transplantation time increased, the percentage of TTV positivity declined.

CONCLUSION: Although tNGS was inferior to mNGS owing to lower sensitivity and true positive rate in identifying respiratory pathogens among KTRs, both considerably outperformed CMT.}, } @article {pmid39252839, year = {2024}, author = {Murovec, B and Deutsch, L and Stres, B}, title = {Predictive modeling of colorectal cancer using exhaustive analysis of microbiome information layers available from public metagenomic data.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1426407}, pmid = {39252839}, issn = {1664-302X}, abstract = {This study aimed to compare the microbiome profiles of patients with colorectal cancer (CRC, n = 380) and colorectal adenomas (CRA, n = 110) against generally healthy participants (n = 2,461) from various studies. The overarching objective was to conduct a real-life experiment and develop a robust machine learning model applicable to the general population. A total of 2,951 stool samples underwent a comprehensive analysis using the in-house MetaBakery pipeline. This included various data matrices such as microbial taxonomy, functional genes, enzymatic reactions, metabolic pathways, and predicted metabolites. The study found no statistically significant difference in microbial diversity among individuals. However, distinct clusters were identified for healthy, CRC, and CRA groups through linear discriminant analysis (LDA). Machine learning analysis demonstrated consistent model performance, indicating the potential of microbiome layers (microbial taxa, functional genes, enzymatic reactions, and metabolic pathways) as prediagnostic indicators for CRC and CRA. Notable biomarkers on the taxonomy level and microbial functionality (gene families, enzymatic reactions, and metabolic pathways) associated with CRC were identified. The research presents promising avenues for practical clinical applications, with potential validation on external clinical datasets in future studies.}, } @article {pmid39252828, year = {2024}, author = {Ng, CWW and Yan, WH and Xia, YT and Tsim, KWK and To, JCT}, title = {Plant growth-promoting rhizobacteria enhance active ingredient accumulation in medicinal plants at elevated CO2 and are associated with indigenous microbiome.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1426893}, pmid = {39252828}, issn = {1664-302X}, abstract = {INTRODUCTION: Plant growth-promoting rhizobacteria (PGPR) and elevated CO2 (eCO2) have demonstrated their individual potential to enhance plant yield and quality through close interaction with rhizosphere microorganisms and plant growth. However, the efficacy of PGPR under eCO2 on rhizosphere microbiome and, ultimately, plant yield and active ingredient accumulation are not yet fully understood.

METHODS: This study investigated how the medicinal plant Pseudostellaria heterophylla (P. heterophylla) and its rhizosphere microbes respond to PGPR (Bacillus subtilis and Pseudomonas fluorescens) at eCO2 (1,000 ppm).

RESULTS AND DISCUSSION: It was found that the yield and active ingredient polysaccharides accumulation in the tuber of P. heterophylla were significantly increased by 38 and 253%, respectively. This promotion has been associated with increased root development and changes in the indigenous microbial community. Metagenomics analysis revealed a significant reduction in pathogenic Fusarium abundance in the rhizosphere. Potential biocontrol bacteria Actinobacteria and Proteobacteria were enriched, especially the genera Bradyrhizobium and Rhodanobacter. The reshaping of the rhizosphere microbiome was accompanied by the upregulation of biological pathways related to metabolite biosynthesis in the rhizosphere. These modifications were related to the promotion of the growth and productivity of P. heterophylla. Our findings highlighted the significant role played by PGPR in medicinal plant yield and active ingredient accumulation when exposed to eCO2.}, } @article {pmid39252782, year = {2024}, author = {Tan, JH and Liew, KJ and Goh, KM}, title = {Dataset of 313 metagenome-assemble genomes from streamer hot spring water.}, journal = {Data in brief}, volume = {56}, number = {}, pages = {110829}, pmid = {39252782}, issn = {2352-3409}, abstract = {This data report presents prokaryotic metagenome-assembled genomes (MAGs) from a hot spring stream with temperatures between 64 and 100°C. The stream water was filtered and the extracted total DNA was sequenced using the Illumina HiSeq 2500 platform. Approximately 80 Gb of raw data were generated, which were subsequently assembled using MEGAHIT v1.2.9. The MAGs were generated using MetaWRAP with binning approaches of MetaBAT2, CONCOCT and MaxBin2. We constructed 25 medium-quality and 24 high-quality archaeal MAGs, and 152 medium-quality and 112 high-quality bacterial MAGs. The fasta files of these MAGs are available in the NCBI database as well as Mendeley Data. Major phyla identified include Bacteroidota, Chloroflexota, Desulfobacterota, Firmicutes, Patescibacteria, Proteobacteria, Spirochaetota, Verrucomicrobiota, Armatimonadota, Nitrospirota, Acidobacteriota, Elusimicrobiota, Planctomycetota, Candidate division WOR-3, Aquificota, Thermoproteota, and Micrarchaeota. This dataset is valuable for studies on thermophilic genomes, reconstruction of biochemical pathways and gene discovery.}, } @article {pmid39252128, year = {2024}, author = {Wu, H and Li, A and Zhang, H and Li, S and Yang, C and Lv, H and Yao, Y}, title = {Microbial mechanisms for higher hydrogen production in anaerobic digestion at constant temperature versus gradient heating.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {170}, pmid = {39252128}, issn = {2049-2618}, mesh = {*Hydrogen/metabolism ; *Lignin/metabolism ; Anaerobiosis ; Hot Temperature ; Cellulose/metabolism ; Polysaccharides/metabolism ; Metagenomics/methods ; Temperature ; Bacteria/metabolism/classification/genetics ; }, abstract = {BACKGROUND: Clean energy hydrogen (H2) produced from abundant lignocellulose is an alternative to fossil energy. As an essential influencing factor, there is a lack of comparison between constant temperatures (35, 55 and 65 °C) and gradient heating temperature (35 to 65 °C) on the H2 production regulation potential from lignocellulose-rich straw via high-solid anaerobic digestion (HS-AD). More importantly, the microbial mechanism of temperature regulating H2 accumulation needs to be investigated.

RESULTS: Constant 65 °C led to the lowest lignin residue (1.93%) and the maximum release of cellulose and hemicellulose, and the highest H2 production (26.01 mL/g VS). H2 production at 35 and 55 °C was only 14.56 and 24.13 mL/g VS, respectively. In order to further explore the potential of ultra-high temperature (65 °C), HS-AD was performed by gradient heating conditions (35 to 65 °C). However, compared to constant 65 °C, gradient heating conditions led to higher lignin residue (2.49%) and lower H2 production (13.53 mL/g VS) than gradient heating conditions (47.98%). In addition, metagenomic analysis showed the cellulose/hemicellulose hydrolyzing bacteria and genes (mainly Thermoclostridium, and xynA, xynB, abfA, bglB and xynD), H2-producing bacteria and related genes (mainly Thermoclostridium, and nifD, nifH and nifK), and microbial movement and metabolic functions were enriched at 65 °C. However, the enrichment of two-component systems under gradient heating conditions resulted in a lack of highly-enriched ultra-high-temperature cellulose/hemicellulose hydrolyzing genera and related genes but rather enriched H2 consumption genera and genes (mainly Acetivibrio, and hyaB and hyaA) resulting in a weaker H2 production.

CONCLUSIONS: The lignin degradation process does not directly determine H2 accumulation, which was actually regulated by bacteria/genes contributing to H2 production/consumption. In addition, it is temperature that enhances the hydrolysis process of lignin rather than lignin-degrading enzymes, bacteria and genes by promoting microbial material transfer and metabolism. In terms of temperature, one of the key parameters of HS-AD for H2 production, we developed an important regulatory strategy, enriched the theoretical basis of temperature regulation for H2 production to further expanded the research horizon in this field. Video Abstract.}, } @article {pmid39252078, year = {2024}, author = {Vojvoda Zeljko, T and Kajan, K and Jalžić, B and Hu, A and Cukrov, N and Marguš, M and Cukrov, N and Marković, T and Sabatino, R and Di Cesare, A and Orlić, S}, title = {Genome-centric metagenomes unveiling the hidden resistome in an anchialine cave.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {67}, pmid = {39252078}, issn = {2524-6372}, support = {KK.01.2.1.02.0335//European Union through the European Regional Development Fund/ ; KK.01.1.1.01.0003//European Union through the European Regional Development Fund/ ; KK.01.2.1.02.0335//European Union through the European Regional Development Fund/ ; CN_00000033//European Union - NextGenerationEU/ ; CN_00000033//European Union - NextGenerationEU/ ; }, abstract = {BACKGROUND: Antibiotic resistance is a critical global concern, posing significant challenges to human health and medical treatments. Studying antibiotic resistance genes (ARGs) is essential not only in clinical settings but also in diverse environmental contexts. However, ARGs in unique environments such as anchialine caves, which connect both fresh and marine water, remain largely unexplored despite their intriguing ecological characteristics.

RESULTS: We present the first study that comprehensively explores the occurrence and distribution of ARGs and mobile genetic elements (MGEs) within an anchialine cave. Utilizing metagenomic sequencing we uncovered a wide array of ARGs with the bacitracin resistance gene, bacA and multidrug resistance genes, being the most dominant. The cave's microbial community and associated resistome were significantly influenced by the salinity gradient. The discovery of novel β-lactamase variants revealed the cave's potential as a reservoir for previously undetected resistance genes. ARGs in the cave demonstrated horizontal transfer potential via plasmids, unveiling ecological implications.

CONCLUSIONS: These findings highlight the need for further exploration of the resistome in unique environments like anchialine caves. The interconnected dynamics of ARGs and MGEs within anchialine caves offer valuable insights into potential reservoirs and mechanisms of antibiotic resistance in natural ecosystems. This study not only advances our fundamental understanding but also highlights the need for a comprehensive approach to address antibiotic resistance in diverse ecological settings.}, } @article {pmid39252069, year = {2024}, author = {Buddle, S and Forrest, L and Akinsuyi, N and Martin Bernal, LM and Brooks, T and Venturini, C and Miller, C and Brown, JR and Storey, N and Atkinson, L and Best, T and Roy, S and Goldsworthy, S and Castellano, S and Simmonds, P and Harvala, H and Golubchik, T and Williams, R and Breuer, J and Morfopoulou, S and Torres Montaguth, OE}, title = {Evaluating metagenomics and targeted approaches for diagnosis and surveillance of viruses.}, journal = {Genome medicine}, volume = {16}, number = {1}, pages = {111}, pmid = {39252069}, issn = {1756-994X}, mesh = {*Metagenomics/methods ; Humans ; *Viruses/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing/methods ; Virus Diseases/diagnosis/virology ; Metagenome ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Metagenomics is a powerful approach for the detection of unknown and novel pathogens. Workflows based on Illumina short-read sequencing are becoming established in diagnostic laboratories. However, high sequencing depth requirements, long turnaround times, and limited sensitivity hinder broader adoption. We investigated whether we could overcome these limitations using protocols based on untargeted sequencing with Oxford Nanopore Technologies (ONT), which offers real-time data acquisition and analysis, or a targeted panel approach, which allows the selective sequencing of known pathogens and could improve sensitivity.

METHODS: We evaluated detection of viruses with readily available untargeted metagenomic workflows using Illumina and ONT, and an Illumina-based enrichment approach using the Twist Bioscience Comprehensive Viral Research Panel (CVRP), which targets 3153 viruses. We tested samples consisting of a dilution series of a six-virus mock community in a human DNA/RNA background, designed to resemble clinical specimens with low microbial abundance and high host content. Protocols were designed to retain the host transcriptome, since this could help confirm the absence of infectious agents. We further compared the performance of commonly used taxonomic classifiers.

RESULTS: Capture with the Twist CVRP increased sensitivity by at least 10-100-fold over untargeted sequencing, making it suitable for the detection of low viral loads (60 genome copies per ml (gc/ml)), but additional methods may be needed in a diagnostic setting to detect untargeted organisms. While untargeted ONT had good sensitivity at high viral loads (60,000 gc/ml), at lower viral loads (600-6000 gc/ml), longer and more costly sequencing runs would be required to achieve sensitivities comparable to the untargeted Illumina protocol. Untargeted ONT provided better specificity than untargeted Illumina sequencing. However, the application of robust thresholds standardized results between taxonomic classifiers. Host gene expression analysis is optimal with untargeted Illumina sequencing but possible with both the CVRP and ONT.

CONCLUSIONS: Metagenomics has the potential to become standard-of-care in diagnostics and is a powerful tool for the discovery of emerging pathogens. Untargeted Illumina and ONT metagenomics and capture with the Twist CVRP have different advantages with respect to sensitivity, specificity, turnaround time and cost, and the optimal method will depend on the clinical context.}, } @article {pmid39251745, year = {2024}, author = {Serwecińska, L and Font-Nájera, A and Strapagiel, D and Lach, J and Tołoczko, W and Bołdak, M and Urbaniak, M}, title = {Sewage sludge fertilization affects microbial community structure and its resistome in agricultural soils.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {21034}, pmid = {39251745}, issn = {2045-2322}, support = {No. 2020/39/B/NZ9/01772//Narodowe Centrum Nauki/ ; No. 2020/39/B/NZ9/01772//Narodowe Centrum Nauki/ ; }, mesh = {*Sewage/microbiology ; *Soil Microbiology ; *Agriculture/methods ; *Fertilizers ; *Soil/chemistry ; *Microbiota/genetics/drug effects ; Bacteria/genetics/drug effects/classification ; Metagenomics/methods ; Drug Resistance, Microbial/genetics ; Poland ; }, abstract = {Global sewage sludge production is rapidly increasing, and its safe disposal is becoming an increasingly serious issue. One of the main methods of municipal sewage sludge management is based on its agricultural use. The wastewater and sewage sludge contain numerous antibiotic resistance genes (ARGs), and its microbiome differs significantly from the soil microbial community. The aim of the study was to assess the changes occurring in the soil microbial community and resistome after the addition of sewage sludge from municipal wastewater treatment plant (WWTP) in central Poland, from which the sludge is used for fertilizing agricultural soils on a regular basis. This study used a high-throughput shotgun metagenomics approach to compare the microbial communities and ARGs present in two soils fertilized with sewage sludge. The two soils represented different land uses and different physicochemical and granulometric properties. Both soils were characterized by a similar taxonomic composition of the bacterial community, despite dissimilarities between soils properties. Five phyla predominated, viz. Planctomycetes, Actinobacteria, Proteobacteria, Chloroflexi and Firmicutes, and they were present in comparable proportions in both soils. Network analysis revealed that the application of sewage sludge resulted in substantial qualitative and quantitative changes in bacterial taxonomic profile, with most abundant phyla being considerably depleted and replaced by Proteobacteria and Spirochaetes. In addition, the ratio of oligotrophic to copiotrophic bacteria substantially decreased in both amended soils. Furthermore, fertilized soils demonstrated greater diversity and richness of ARGs compared to control soils. The increased abundance concerned mainly genes of resistance to antibiotics most commonly used in human and animal medicine. The level of heavy metals in sewage sludge was low and did not exceed the standards permitted in Poland for sludge used in agriculture, and their level in fertilized soils was still inconsiderable.}, } @article {pmid39251728, year = {2024}, author = {Cai, X and Dai, J and Xie, Y and Xu, S and Liu, M}, title = {Multi-omics study unravels gut microbiota and metabolites alteration in patients with Wilson's disease.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {21025}, pmid = {39251728}, issn = {2045-2322}, support = {JCYJ20220530165400002//Shenzhen Science and Technology Innovation Program/ ; 2021R01132//Shenzhen Guangming District Economic Development Special Fund/ ; }, mesh = {Humans ; *Hepatolenticular Degeneration/metabolism/microbiology/genetics ; *Gastrointestinal Microbiome ; Female ; Male ; Adult ; RNA, Ribosomal, 16S/genetics ; Metabolomics/methods ; Feces/microbiology ; Metabolome ; Young Adult ; Bacteria/classification/metabolism/genetics/isolation & purification ; Metagenomics/methods ; Adolescent ; Multiomics ; }, abstract = {Hepatolenticular degeneration (HLD), also known as Wilson's disease (WD), is a rare autosomal recessive disorder regarding copper metabolism. Whether gut microbiota imbalance is involved in developing HLD remains unknown. A comprehensive 16S rRNA amplicon sequencing, metagenomic sequencing, and metabonomic analysis were undertaken in patients with WD to analyze the composition and function profiles of gut microbiota in patients with WD. The data demonstrated differences in gut microbiota and metabolic pathways between WD patients and normal individuals, significantly decreasing bacterial richness and diversity. The levels of Selenomonaceae and Megamonas in WD patients are significantly higher than those in healthy individuals. The relative abundances of Roseburia inulinivorans in patients with WD are lower than in healthy individuals. Compared with healthy people, the level of metabolites in patients with WD is abnormal. Leucylproline, 5-Phenylvaleric Acid and N-Desmethylclobazam, which have nutritional and protective effects, are significantly reduced fecal metabolites in patients with WD. D-Gluconic acid, which can chelate metal ions, may be a potential treatment for WD. The positive correlation it demonstrates with Alistipes indistinctus and Prevotella stercora indicates potential bacteria able to treat WD. These metabolites are mainly related to the biosynthesis of antibiotics, alpha-linolenic acid metabolism, one carbon pool by folate, nicotinate and nicotinamide metabolism. In conclusion, the data from this study elucidate novel mechanisms describing how abnormal gut miccrobiota contribute to the pathogenesis of WD and outlines new molecules for the treatment of WD.}, } @article {pmid39250478, year = {2024}, author = {Pusa, T and Rousu, J}, title = {Stable biomarker discovery in multi-omics data via canonical correlation analysis.}, journal = {PloS one}, volume = {19}, number = {9}, pages = {e0309921}, pmid = {39250478}, issn = {1932-6203}, mesh = {Humans ; *Biomarkers/metabolism ; *Inflammatory Bowel Diseases/metabolism ; *Metabolomics/methods ; Metagenomics/methods ; Machine Learning ; Gastrointestinal Microbiome ; Multiomics ; }, abstract = {Multi-omics analysis offers a promising avenue to a better understanding of complex biological phenomena. In particular, untangling the pathophysiology of multifactorial health conditions such as the inflammatory bowel disease (IBD) could benefit from simultaneous consideration of several omics levels. However, taking full advantage of multi-omics data requires the adoption of suitable new tools. Multi-view learning, a machine learning technique that natively joins together heterogeneous data, is a natural source for such methods. Here we present a new approach to variable selection in unsupervised multi-view learning by applying stability selection to canonical correlation analysis (CCA). We apply our method, StabilityCCA, to simulated and real multi-omics data, and demonstrate its ability to find relevant variables and improve the stability of variable selection. In a case study on an IBD microbiome data set, we link together metagenomics and metabolomics, revealing a connection between their joint structure and the disease, and identifying potential biomarkers. Our results showcase the usefulness of multi-view learning in multi-omics analysis and demonstrate StabilityCCA as a powerful tool for biomarker discovery.}, } @article {pmid39250184, year = {2024}, author = {Pallen, MJ}, title = {The dynamic history of prokaryotic phyla: discovery, diversity and division.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {74}, number = {9}, pages = {}, pmid = {39250184}, issn = {1466-5034}, mesh = {Archaea/genetics/classification ; *Bacteria/genetics/classification ; Classification/methods ; History, 20th Century ; History, 21st Century ; *Phylogeny ; Prokaryotic Cells/classification ; History, 19th Century ; }, abstract = {Here, I review the dynamic history of prokaryotic phyla. Following leads set by Darwin, Haeckel and Woese, the concept of phylum has evolved from a group sharing common phenotypes to a set of organisms sharing a common ancestry, with modern taxonomy based on phylogenetic classifications drawn from macromolecular sequences. Phyla came as surprising latecomers to the formalities of prokaryotic nomenclature in 2021. Since then names have been validly published for 46 prokaryotic phyla, replacing some established names with neologisms, prompting criticism and debate within the scientific community. Molecular barcoding enabled phylogenetic analysis of microbial ecosystems without cultivation, leading to the identification of candidate divisions (or phyla) from diverse environments. The introduction of metagenome-assembled genomes marked a significant advance in identifying and classifying uncultured microbial phyla. The lumper-splitter dichotomy has led to disagreements, with experts cautioning against the pressure to create a profusion of new phyla and prominent databases adopting a conservative stance. The Candidatus designation has been widely used to provide provisional status to uncultured prokaryotic taxa, with phyla named under this convention now clearly surpassing those with validly published names. The Genome Taxonomy Database (GTDB) has offered a stable, standardized prokaryotic taxonomy with normalized taxonomic ranks, which has led to both lumping and splitting of pre-existing phyla. The GTDB framework introduced unwieldy alphanumeric placeholder labels, prompting recent publication of over 100 user-friendly Latinate names for unnamed prokaryotic phyla. Most candidate phyla remain 'known unknowns', with limited knowledge of their genomic diversity, ecological roles, or environments. Whether phyla still reflect significant evolutionary and ecological partitions across prokaryotic life remains an area of active debate. However, phyla remain of practical importance for microbiome analyses, particularly in clinical research. Despite potential diminishing returns in discovery of biodiversity, prokaryotic phyla offer extensive research opportunities for microbiologists for the foreseeable future.}, } @article {pmid39248562, year = {2024}, author = {Xiao, JZ and Nesbø, CL and Molenda, O and Toth, CRA and Edwards, EA}, title = {Metagenomic and genomic sequences from a nitrate-reducing benzene-degrading enrichment culture.}, journal = {Microbiology resource announcements}, volume = {13}, number = {10}, pages = {e0029424}, pmid = {39248562}, issn = {2576-098X}, support = {OGI-102 and OGI-107//Genome Canada (GC)/ ; }, abstract = {Metagenome-assembled genomes (MAGs) were recovered from metagenomic assemblies from a nitrate-reducing benzene-degrading enrichment culture. Ten MAGs of high quality or functional interest to benzene degradation are reported, seven of which are single contig genomes.}, } @article {pmid39248477, year = {2024}, author = {Hu, N-n and Wang, Z-q and Zhang, S-j and Wang, Z-z and Chen, X-x}, title = {Characterization of larval gut microbiota of two endoparasitoid wasps associated with their common host, Plutella xylostella (Linnaeus) (Lepidoptera: Plutellidae).}, journal = {Microbiology spectrum}, volume = {12}, number = {10}, pages = {e0120824}, pmid = {39248477}, issn = {2165-0497}, support = {2023YFD1400800//National Key R&D Program of China/ ; U22A20485//MOST | National Natural Science Foundation of China (NSFC)/ ; 32272607//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Wasps/microbiology/physiology ; *Larva/microbiology/growth & development ; *Moths/parasitology/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics ; Host-Parasite Interactions ; Phylogeny ; }, abstract = {Insect gut microbes play important roles in digestion, metabolism, development, and environmental adaptation. Parasitoid wasps are one of the most important biological control agents in pest control, while the gut microbial species compositions and the associated functions have been poorly investigated. Two endoparasitoid wasps, Cotesia vestalis and Diadromus collaris, parasitize the larval stage and pupal stage of the diamondback moth, Plutella xylostella, respectively. Using whole-genome shotgun metagenomic sequencing, we characterized the gut microbial composition, diversity, and potential functional roles associated with the two parasitoid wasp larvae. The results reveal that Proteobacteria and Firmicutes are the dominant phyla in the gut of C. vestalis and D. collaris larvae, with Rhizobium and Enterococcus being the dominant genera. The putative microbial functions associated with the two parasitoid wasps might play a virtual role in assisting in consuming the host's nutritional composition. The enriched CAZymes family genes are primarily involved in the degradation and synthesis of chitin. Despite the richness of microbial species and communities, the microbes species and the microbial community structure exhibit significant similarity between the two parasitoid wasps and between the parasitoid wasp and the host P. xylostella. Notably, the prevalence of the genus Enterococcus shared among them suggests a possible link of gut microbes between the host and their associated parasitoids. Our study offers insights into the gut microbe-based interactions between the host and parasitoid wasps for the first time, potentially paving the way for the development of an ecologically friendly biocontrol strategy against the pest P. xylostella.IMPORTANCEEndoparasitoid wasps spend the majority of their lifespan within their host and heavily rely on the host's nutrition for survival. There is limited understanding regarding the composition and physiological impacts of gut microbial communities in parasitoid wasps, particularly during the larval stage, which is directly linked to the host. Based on a thorough characterization of the gut microbe and comprehensive comparative analysis, we found the microbial species of the larval parasitoid wasp Cotesia vestalis and the pupal parasitoid wasp Diadromus collaris were similar, sharing 159 genera and 277 species, as were the microbial community structure. Certain of the dominant microbial strains of the two parasitoid wasps were similar to that of their host Plutella xylostella larvae, revealing host insect may affect the microbial community of the parasitoid wasps. The putative microbial functions associated with the parasitoid wasp larvae play an important role in dietary consumption.}, } @article {pmid39248463, year = {2024}, author = {Zhang, X and Wu, N and Geng, K and Yuan, C and Wang, B and Shi, J and Qiu, J and He, J}, title = {Identification of a chlorosalicylic acid decarboxylase (CsaD) involved in decarboxylation of 3,6-DCSA from an anaerobic dicamba-degrading sludge.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {10}, pages = {e0131924}, pmid = {39248463}, issn = {1098-5336}, support = {32170128, U23A20200//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {*Sewage/microbiology ; *Carboxy-Lyases/metabolism/genetics ; Decarboxylation ; *Dicamba/metabolism ; Anaerobiosis ; Biodegradation, Environmental ; Bacterial Proteins/metabolism/genetics ; Salicylates/metabolism ; Herbicides/metabolism ; }, abstract = {3,6-Dichlorosalicylic acid (3,6-DCSA) is the demethylation metabolite of herbicide 3,6-dichloro-2-methoxy benzoic acid (dicamba). Previous studies have shown that anaerobic sludge further transformed 3,6-DCSA through decarboxylation and dechlorination. However, the anaerobe, enzyme, and gene involved in the anaerobic degradation of 3,6-DCSA are still unknown. In this study, an anaerobic sludge that efficiently degraded dicamba was enriched, and a 3,6-DCSA decarboxylase, designated chlorosalicylic acid decarboxylase (CsaD), was partially purified and identified from the anaerobic sludge. Metagenomic analysis showed that the csaD gene was located in a gene cluster of metagenome-assembled genome 8 (MAG8). MAG8 belonged to an uncultured order, OPB41, in the class Coriobacteriia of the phylum Actinobacteria, and its abundance increased approximately once during the enrichment process. CsaD was a non-oxidative decarboxylase in the amidohydrolase 2 family catalyzing the decarboxylation of 3,6-DCSA and 6-chlorosalicylic acid (6-CSA). Its affinity and catalytic efficiency for 3,6-DCSA were significantly higher than those for 6-CSA. This study provides new insights into the anaerobic catabolism of herbicide dicamba.IMPORTANCEDicamba, an important hormone herbicide, easily migrates to anoxic habitats such as sediment, ground water, and deep soil. Thus, the anaerobic catabolism of dicamba is of importance. Anaerobic bacteria or sludge demethylated dicamba to 3,6-DCSA, and in a previous study, based on metabolite identification, it was proposed that 3,6-DCSA be further degraded via two pathways: decarboxylation to 2,5-dichlorophenol, then dechlorination to 3-chlorophenol (3-CP); or dechlorination to 6-CSA, then decarboxylation to 3-CP. However, there was no physiological and genetic validation for the pathway. In this study, CsaD catalyzed the decarboxylation of both 3,6-DCSA and 6-CSA, providing enzyme-level evidence for the anaerobic catabolism of 3,6-DCSA through the two pathways. CsaD was located in MAG8, which belonged to an uncultured anaerobic actinomycetes order, OPB41, indicating that anaerobic actinomycetes in OPB41 was involved in the decarboxylation of 3,6-DCSA. This study provides a basis for understanding the anaerobic catabolism of dicamba and the demethylation product, 3,6-DCSA.}, } @article {pmid39248279, year = {2024}, author = {Ohuchi, H and Asano, R and Mori, A and Ishibashi, T and Motooka, D and Nakai, M and Nakaoka, Y}, title = {Gut Dysbiosis in Patients With Fontan Circulation.}, journal = {Journal of the American Heart Association}, volume = {13}, number = {18}, pages = {e034538}, doi = {10.1161/JAHA.124.034538}, pmid = {39248279}, issn = {2047-9980}, mesh = {Humans ; Male ; *Dysbiosis ; *Fontan Procedure/adverse effects ; Female ; *Gastrointestinal Microbiome/physiology ; Adolescent ; Child ; Heart Defects, Congenital/surgery ; Case-Control Studies ; Young Adult ; Feces/microbiology ; Hemodynamics ; Biomarkers/blood/metabolism ; Adult ; }, abstract = {BACKGROUND: The process underlying Fontan pathophysiology is multifactorial and may include gut dysbiosis (GD). We investigated the presence of GD and elucidated its correlation with Fontan pathophysiology.

METHODS AND RESULTS: Gut microbiomes of 155 consecutive patients with Fontan pathophysiology and 44 healthy individuals were analyzed using 16S rRNA sequencing of bacterial DNA extracted from fecal samples. GD was evaluated on the basis of α and ß diversities of the gut microbiome and was compared with natural log-transformed C-reactive protein, hemodynamics, von Willebrand factor antigen (a bacterial translocation marker), Mac-2 binding protein glycosylation isomer (a liver fibrosis indicator), peak oxygen uptake, and heart failure hospitalization. Patients with Fontan exhibited GD in terms of α and ß diversities as compared with controls (P<0.01). Reduced α diversity was associated with a failed hemodynamic phenotype, hypoxia, high natural log-transformed C-reactive protein levels, and elevated von Willebrand factor antigen and Mac-2 binding protein glycosylation isomer levels (P<0.05-0.01). In addition to elevated von Willebrand factor antigen and hypoxia, decreased α diversity was independently correlated with a high natural log-transformed C-reactive protein level (P<0.05), which was associated with liver imaging abnormalities and a heightened risk of heart failure hospitalization (P<0.01 for both).

CONCLUSIONS: Patients with Fontan pathophysiology exhibited GD compared with healthy individuals, and GD was linked to failed hemodynamics and systemic inflammation with a poor prognosis. Therefore, GD may play a pivotal role in a failing Fontan status, including Fontan-associated liver disease, through GD-associated systemic inflammation.}, } @article {pmid39248272, year = {2024}, author = {Chen, X and He, Y and Zhou, L and Li, X and Jiang, M and Wu, M and Li, J and Chen, L and Xu, H and Gui, L and Zhou, Z}, title = {Microbial Heterogeneity Identification of Cerebral Thrombi Via Metagenomic Next-Generation Sequencing-Based Strategy.}, journal = {Journal of the American Heart Association}, volume = {13}, number = {18}, pages = {e033221}, doi = {10.1161/JAHA.123.033221}, pmid = {39248272}, issn = {2047-9980}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; Female ; Male ; Middle Aged ; *Intracranial Thrombosis/microbiology/genetics ; Aged ; Ischemic Stroke/microbiology/genetics ; Bacteria/genetics/isolation & purification ; Microbiota/genetics ; }, abstract = {BACKGROUND: Diagnosis of the cause of cerebral thrombi is vital for recurrence prevention but also challenging. The presence of the microbiome has recently been confirmed in thrombus, suggesting a novel approach to distinguish cerebral thrombi of different origins. However, little is known about whether there is heterogeneity in microbiological colonization of cerebral thrombi of different sources.

METHODS AND RESULTS: Forty patients experiencing acute ischemic stroke were included and clinical data were collected. Metagenomic next-generation sequencing was adopted to detect bacterial and genomic signatures of human cerebral thrombi samples. We found similar species diversity between the large-artery atherosclerosis thrombi and cardioembolic thrombi but different species composition and distribution of cerebral thrombus microbiota. Compared with the group with cardioembolism, the group with large-artery atherosclerosis showed a significantly higher relative abundance of Ralstonia insidiosa among the top 10 bacterial species in cerebral thrombi. Twenty operational taxonomy units were correlated with 11 clinical indicators of ischemic stroke. The Gene Ontology enrichment analysis revealed 9 different enriched biological processes (translation and carbohydrate metabolic process, etc). The enriched Kyoto Encyclopedia of Genes and Genomes pathways included ribosome, butanoate metabolism, and sulfur metabolism.

CONCLUSIONS: This study, based on the approach of metagenomic next-generation sequencing, provides a diagnostic microbiological method to discriminate individuals with cardioembolic thrombi from those with large-artery atherosclerosis thrombi with human cerebral thrombi samples. Our findings provide a fresh perspective on microbial heterogeneity of cerebral thrombi and demonstrate biological processes and pathway features of cerebral thrombi.}, } @article {pmid39247916, year = {2024}, author = {Lyu, X and Xu, X and Shen, S and Qin, F}, title = {Genetics causal analysis of oral microbiome on type 2 diabetes in East Asian populations: a bidirectional two-sample Mendelian randomized study.}, journal = {Frontiers in endocrinology}, volume = {15}, number = {}, pages = {1452999}, pmid = {39247916}, issn = {1664-2392}, mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/genetics ; East Asian People/genetics ; Genetic Predisposition to Disease ; *Genome-Wide Association Study ; *Mendelian Randomization Analysis ; *Microbiota/genetics ; Mouth/microbiology ; *Saliva/microbiology ; Tongue/microbiology ; }, abstract = {INTRODUCTION: The dysbiosis of the oral microbiome is associated with the progression of various systemic diseases, including diabetes. However, the precise causal relationships remain elusive. This study aims to investigate the potential causal associations between oral microbiome and type 2 diabetes (T2D) using Mendelian randomization (MR) analyses.

METHODS: We conducted bidirectional two-sample MR analyses to investigate the impact of oral microbiome from saliva and the tongue T2D. This analysis was based on metagenome-genome-wide association studies (mgGWAS) summary statistics of the oral microbiome and a large meta-analysis of GWAS of T2D in East Asian populations. Additionally, we utilized the T2D GWAS summary statistics from the Biobank Japan (BBJ) project for replication. The MR methods employed included Wald ratio, inverse variance weighting (IVW), weighted median, MR-Egger, contamination mixture (ConMix), and robust adjusted profile score (RAPS).

RESULTS: Our MR analyses revealed genetic associations between specific bacterial species in the oral microbiome of saliva and tongue with T2D in East Asian populations. The MR results indicated that nine genera were shared by both saliva and tongue. Among these, the genera Aggregatibacter, Pauljensenia, and Prevotella were identified as risk factors for T2D. Conversely, the genera Granulicatella and Haemophilus D were found to be protective elements against T2D. However, different species within the genera Catonella, Lachnoanaerobaculum, Streptococcus, and Saccharimonadaceae TM7x exhibited multifaceted influences; some species were positively correlated with the risk of developing T2D, while others were negatively correlated.

DISCUSSION: This study utilized genetic variation tools to confirm the causal effect of specific oral microbiomes on T2D in East Asian populations. These findings provide valuable insights for the treatment and early screening of T2D, potentially informing more targeted and effective therapeutic strategies.}, } @article {pmid39247756, year = {2024}, author = {Lu, Y and Zhang, D and Han, D and Yu, F and Ye, X and Zheng, S}, title = {Case Report: Diagnosis of Hemolytic Anemia from Babesia and Secondary Multi-Pathogen Pneumonia Using a Metagenomic Next-Generation Sequencing Approach.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {3785-3791}, pmid = {39247756}, issn = {1178-6973}, abstract = {Babesiosis, as a vector-borne infectious disease, remains relatively rare and is prone to being overlooked and misdiagnosed. Therefore, understanding the epidemiological characteristics and clinical manifestations of babesiosis is crucial for the prompt detection and treatment of the disease. We reported a 63-year-old male patient presenting with spontaneous fever and chills. Laboratory investigations revealed erythrocytopenia, reduced hemoglobin levels, and increased reticulocytes and total bilirubin. Bone marrow examination indicated vigorous cell proliferation, a decreased granulocyte to red cell ratio, and predominant erythroid cell proliferation, with a higher prevalence of intermediate and late-stage juvenile granulocyte and erythroid cells. Initial treatment focused on hemophagocytic syndrome triggered by Epstein-Barr virus infection yielded unsatisfactory results, leading to secondary multiple pulmonary infections. Metagenomic next-generation sequencing (mNGS) of sputum samples pointed to hemolytic anemia induced by Babesia infection, which was subsequently confirmed through peripheral blood smear analysis. The patient responded well to prompt administration of atovaquone and azithromycin, with symptoms resolving and laboratory parameters normalizing. Hemolytic anemia resulting from babesiosis should be distinguished from hemophagocytic syndrome caused by Epstein-Barr virus and other hematologic conditions. mNGS represents an efficient technique for Babesia detection.}, } @article {pmid39247454, year = {2024}, author = {Rajguru, B and Shri, M and Bhatt, VD}, title = {Exploring microbial diversity in the rhizosphere: a comprehensive review of metagenomic approaches and their applications.}, journal = {3 Biotech}, volume = {14}, number = {10}, pages = {224}, pmid = {39247454}, issn = {2190-572X}, abstract = {The rhizosphere, the soil region influenced by plant roots, represents a dynamic microenvironment where intricate interactions between plants and microorganisms shape soil health, nutrient cycling, and plant growth. Soil microorganisms are integral players in the transformation of materials, the dynamics of energy flows, and the intricate cycles of biogeochemistry. Considerable research has been dedicated to investigating the abundance, diversity, and intricacies of interactions among different microbes, as well as the relationships between plants and microbes present in the rhizosphere. Metagenomics, a powerful suite of techniques, has emerged as a transformative tool for dissecting the genetic repertoire of complex microbial communities inhabiting the rhizosphere. The review systematically navigates through various metagenomic approaches, ranging from shotgun metagenomics, enabling unbiased analysis of entire microbial genomes, to targeted sequencing of the 16S rRNA gene for taxonomic profiling. Each approach's strengths and limitations are critically evaluated, providing researchers with a nuanced understanding of their applicability in different research contexts. A central focus of the review lies in the practical applications of rhizosphere metagenomics in various fields including agriculture. By decoding the genomic content of rhizospheric microbes, researchers gain insights into their functional roles in nutrient acquisition, disease suppression, and overall plant health. The review also addresses the broader implications of metagenomic studies in advancing our understanding of microbial diversity and community dynamics in the rhizosphere. It serves as a comprehensive guide for researchers, agronomists, and policymakers, offering a roadmap for harnessing metagenomic approaches to unlock the full potential of the rhizosphere microbiome in promoting sustainable agriculture.}, } @article {pmid39246231, year = {2024}, author = {Du, Y and Zuo, W and Sun, F}, title = {Imputing Metagenomic Hi-C Contacts Facilitates the Integrative Contig Binning Through Constrained Random Walk with Restart.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {31}, number = {10}, pages = {1008-1021}, doi = {10.1089/cmb.2024.0663}, pmid = {39246231}, issn = {1557-8666}, mesh = {*Metagenomics/methods ; *Algorithms ; Animals ; *Metagenome ; *Gastrointestinal Microbiome/genetics ; Sheep ; Contig Mapping/methods ; Software ; }, abstract = {Metagenomic Hi-C (metaHi-C) has shown remarkable potential for retrieving high-quality metagenome-assembled genomes from complex microbial communities. Nevertheless, existing metaHi-C-based contig binning methods solely rely on Hi-C interactions between contigs, disregarding crucial biological information such as the presence of single-copy marker genes. To overcome this limitation, we introduce ImputeCC, an integrative contig binning tool optimized for metaHi-C datasets. ImputeCC integrates both Hi-C interactions and the discriminative power of single-copy marker genes to group marker-gene-containing contigs into preliminary bins. It also introduces a novel constrained random walk with restart algorithm to enhance Hi-C connectivity among contigs. Comprehensive assessments using both mock and real metaHi-C datasets from diverse environments demonstrate that ImputeCC consistently outperforms other Hi-C-based contig binning tools. A genus-level analysis of the sheep gut microbiota reconstructed by ImputeCC underlines its capability to recover key species from dominant genera and identify previously unknown genera.}, } @article {pmid39245657, year = {2024}, author = {Lee, S and Meslier, V and Bidkhori, G and Garcia-Guevara, F and Etienne-Mesmin, L and Clasen, F and Park, J and Plaza Oñate, F and Cai, H and Le Chatelier, E and Pons, N and Pereira, M and Seifert, M and Boulund, F and Engstrand, L and Lee, D and Proctor, G and Mardinoglu, A and Blanquet-Diot, S and Moyes, D and Almeida, M and Ehrlich, SD and Uhlen, M and Shoaie, S}, title = {Transient colonizing microbes promote gut dysbiosis and functional impairment.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {80}, pmid = {39245657}, issn = {2055-5008}, support = {EP/S001301/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; BB/S016899/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; N/A//Science for Life Laboratory (SciLifeLab)/ ; }, mesh = {*Dysbiosis/microbiology ; *Gastrointestinal Microbiome ; Humans ; *Metagenomics/methods ; Sweden ; *Bacteria/classification/genetics/isolation & purification ; *Feces/microbiology ; Longitudinal Studies ; Metagenome ; Adult ; Bioreactors/microbiology ; Fermentation ; }, abstract = {Species composition of the healthy adult gut microbiota tends to be stable over time. Destabilization of the gut microbiome under the influence of different factors is the main driver of the microbial dysbiosis and subsequent impacts on host physiology. Here, we used metagenomics data from a Swedish longitudinal cohort, to determine the stability of the gut microbiome and uncovered two distinct microbial species groups; persistent colonizing species (PCS) and transient colonizing species (TCS). We validated the continuation of this grouping, generating gut metagenomics data for additional time points from the same Swedish cohort. We evaluated the existence of PCS/TCS across different geographical regions and observed they are globally conserved features. To characterize PCS/TCS phenotypes, we performed bioreactor fermentation with faecal samples and metabolic modeling. Finally, using chronic disease gut metagenome and other multi-omics data, we identified roles of TCS in microbial dysbiosis and link with abnormal changes to host physiology.}, } @article {pmid39245322, year = {2024}, author = {Jiménez, JD and Godoy, MS and Del Cerro, C and Prieto, MA}, title = {Hints from nature for a PHA circular economy: Carbon synthesis and sharing by Pseudomonas solani GK13.}, journal = {New biotechnology}, volume = {84}, number = {}, pages = {9-23}, doi = {10.1016/j.nbt.2024.09.002}, pmid = {39245322}, issn = {1876-4347}, mesh = {*Polyhydroxyalkanoates/biosynthesis/metabolism ; *Carbon/metabolism ; *Pseudomonas/metabolism/genetics ; }, abstract = {Polyhydroxyalkanoates (PHAs) are a well-known group of biodegradable and biocompatible bioplastics that are synthesised and stored by microorganisms as carbon and energy reservoirs. Extracellular PHA depolymerases (ePhaZs), secreted by a limited range of microorganisms, are the main hydrolytic enzymes responsible for their environmental degradation. Pseudomonas sp. GK13, initially identified as P. fluorescens GK13, produces PHA and a prototypic ePhaZ that specifically degrades mcl-PHA. In this study, a comprehensive characterization of strain GK13 was performed. The whole genomic sequence of GK13 was consolidated into one complete chromosome, leading to its reclassification as P. solani GK13. We conducted a detailed in silico examination of the bacteria genomic sequence, specifically targeting PHA metabolic functions. From the different growth conditions explored, PHA accumulation occurred only under carbon/nitrogen (C/N) imbalance, whereas ePhaZ production was induced even at balanced C/N ratios in mineral media. We extend our study to other bacteria belonging to the Pseudomonas genus revealing that the ePhaZ production capacity is closely associated with mcl-PHA synthesis capacity, as also suggested by metagenomic samples. This finding suggests that these types of microorganisms could contribute to the carbon economy of the microbial community, by storing PHA in carbon-rich times, and sharing it with the rest of the population during times of carbon scarcity through PHA hydrolysis. The conclusion pointed that carbon cycle metabolism performed by P. solani GK13 may contribute to the environmental circular economy at a microscopic scale.}, } @article {pmid39245190, year = {2024}, author = {Huang, J and Liu, S and Li, P and Wei, L and Lin, G and Lin, J and Luo, Y and Liu, Y and Mao, Y and Ruan, H and Qin, B and Fan, P and Lu, T and Cai, W and Yi, H and Mou, X and Lu, Z and Zhao, W and Wu, A}, title = {Multi-omics analysis of gut-brain axis reveals novel microbial and neurotransmitter signatures in patients with arteriosclerotic cerebral small vessel disease.}, journal = {Pharmacological research}, volume = {208}, number = {}, pages = {107385}, doi = {10.1016/j.phrs.2024.107385}, pmid = {39245190}, issn = {1096-1186}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Cerebral Small Vessel Diseases/metabolism/microbiology ; Male ; *Brain-Gut Axis ; Female ; Aged ; Middle Aged ; *Neurotransmitter Agents/metabolism ; *Dysbiosis/microbiology ; Metabolomics ; Bacteria/metabolism/genetics ; Metabolome ; Multiomics ; }, abstract = {Arteriosclerotic cerebral small vessel disease (aCSVD) is a major cause of stroke and dementia. Although its underlying pathogenesis remains poorly understood, both inflammaging and gut microbiota dysbiosis have been hypothesized to play significant roles. This study investigated the role of gut microbiota in the pathogenesis of aCSVD through a comparative analysis of the gut microbiome and metabolome between CSVD patients and healthy controls. The results showed that patients with aCSVD exhibited a marked reduction in potentially beneficial bacterial species, such as Faecalibacterium prausnitzli and Roseburia intestinalis, alongside an increase in taxa from Bacteroides and Proteobacteria. Integrated metagenomic and metabolomic analyses revealed that alterations in microbial metabolic pathways, including LPS biosynthesis and phenylalanine-tyrosine metabolism, were associated with the status of aCSVD. Our findings indicated that microbial LPS biosynthesis and phenylalanine-tyrosine metabolism potentially influenced the symptoms and progression of aCSVD via pro-inflammatory effect and modulation of systemic neurotransmitters, respectively. These results imply that gut microbiota characteristics may serve as indicators for early detection of aCSVD and as potential gut-directed therapeutic intervention target.}, } @article {pmid39245157, year = {2024}, author = {Zhang, L and Xu, W and Zhao, Y and Sui, L and Song, M and Liu, Q}, title = {Identification and characterization of Jingmen tick virus from Rhipicephalus microplus in Hunan, China.}, journal = {Acta tropica}, volume = {260}, number = {}, pages = {107378}, doi = {10.1016/j.actatropica.2024.107378}, pmid = {39245157}, issn = {1873-6254}, mesh = {Animals ; *Rhipicephalus/virology ; China ; *Phylogeny ; Cattle ; *Genome, Viral ; Flaviviridae/genetics/classification/isolation & purification ; Cell Line ; Metagenomics ; Cattle Diseases/virology/epidemiology ; Virus Replication ; }, abstract = {Jingmen tick virus (JMTV) is a tick-borne pathogen known to affect human beings, characterized by a segmented genome structure that defies the conventional understanding of the Flaviviridae family. In the present study, we employed metagenomic analysis to screen for tick-borne viruses in Hunan Province, China, and identified five JMTV variants with complete genomes from Rhipicephalus microplus ticks sampled from cattle. These viral strains exhibited the highest sequence similarity to JMTV isolates previously reported in Hubei Province, China. However, evidence of genomic reassortment was detected, particularly with the S2 segment showing greater similarity to the strains from Japan. Phylogenetic analysis demonstrated that JMTV strains cluster predominantly based on their geographic origin. In agreement with the homology data, the S1, S3, and S4 segments of the strains identified in this study grouped with those from Hubei Province, while the S2 segment displayed a distinct topological structure. Moreover, JMTV displayed limited replication in mammal-derived cells, but thrived in tick-derived cell lines. In addition to the commonly used R. microplus-derived BME/CTVM23 cells, we found that JMTV also proliferated robustly in both Ixodes scapularis-derived ISE6 and Ixodes ricinus-derived IRE/CTVM19 cells, offering new avenues for in vitro production of the virus. In summary, this study expands the known geographic distribution and genetic diversity of JMTV, providing valuable insights into its epidemiology and potential for in vitro cultivation.}, } @article {pmid39244980, year = {2024}, author = {Zhao, S and Zhang, Q and Huang, Q and Zhang, C and Li, H and Siddique, KHM}, title = {Polyvinyl chloride microplastics disseminate antibiotic resistance genes in Chinese soil: A metagenomic analysis.}, journal = {Journal of hazardous materials}, volume = {479}, number = {}, pages = {135727}, doi = {10.1016/j.jhazmat.2024.135727}, pmid = {39244980}, issn = {1873-3336}, mesh = {*Polyvinyl Chloride ; *Microplastics/toxicity ; *Soil Microbiology ; China ; *Soil Pollutants/toxicity ; *Drug Resistance, Microbial/genetics ; *Bacteria/genetics/drug effects ; *Genes, Bacterial ; Metagenomics ; Drug Resistance, Bacterial/genetics ; }, abstract = {The widespread prevalence of microplastics (MPs) in the environment poses concerns as they are vectors of antibiotic resistance genes (ARGs). The relationships between antibiotic resistomes and MPs remain unexplored in soil which was considered as the reservoirs of MPs and ARGs. This study investigated the effects of polyvinyl chloride (PVC) MPs on soil bacterial communities and ARG abundance which soil samples sourced from 20 provinces across China. We found that PVC significantly influences soil bacterial community structure and ARG abundance. Structural equation modeling revealed that PVC alters soil characteristics, ultimately affecting soil bacterial communities, including ARG-containing bacterial hosts, and the relative abundance of ARGs. This study enhances our understanding of how MPs influence the proliferation and hosts of ARGs within diverse soil environments, offering crucial insights for future strategies in plastic management and disposal.}, } @article {pmid39244926, year = {2024}, author = {Zhang, C and Hu, J and Wang, H and Cheng, H and Cao, X and Sakamaki, T and Li, X}, title = {Sulfamethoxazole degradation in tri-electrode microbial electrochemical systems: Metabolomic and Metagenomic insights into organic pollution effects.}, journal = {Journal of environmental management}, volume = {370}, number = {}, pages = {122410}, doi = {10.1016/j.jenvman.2024.122410}, pmid = {39244926}, issn = {1095-8630}, mesh = {*Sulfamethoxazole/metabolism ; *Electrodes ; Metabolomics ; Metagenomics ; Biodegradation, Environmental ; Water Pollutants, Chemical/metabolism ; Bacteria/metabolism/genetics ; }, abstract = {Organic pollutants can alter the physicochemical properties and microbial communities of water bodies. In water contaminated with organic pollutants, the unique extracellular electron transfer mechanisms that promote sulfamethoxazole (SMX) degradation in tri-electrode microbial electrochemical systems (TE-MES) may be impacted. To simulate biodegradable organic matter contamination, glucose (GLU) was added. Metagenomics and metabolomics were used to analyze changes in microbial community structure, metabolism, and function on the electrodes. GLU addition accelerated water quality deterioration, and enhanced SMX degradation. Microbial taxa on the electrodes experienced selective enrichment. Notably, methanogens and SMX-degrading bacteria were enriched, while denitrifying bacteria and antibiotic-resistant bacteria were suppressed. Enriched metabolites were linked to 15 metabolic pathways and other functions like microbial signaling and genetics. Non-redundant genes also clustered in metabolic pathways, aligning with metabolite enrichment results. Additional pathways involved life cycle processes and protein interactions. Enzymes related to carbon metabolism, particularly glycoside hydrolases, increased significantly, indicating a shift in carbon metabolism on microbial electrodes after GLU addition. The abundance of intracellular electron transfer enzymes rose, while outer membrane proteins decreased. This contrasts with the typical TE-MES mechanism where outer membrane proteins facilitate SMX degradation. The presence of organic pollution may shift SMX degradation from an extracellular electrochemical process to an intracellular metabolic process, possibly involving co-metabolism with simple organic compounds. This study provides mechanistic insights and theoretical guidance for using TE-MES with embedded microbial electrodes to treat antibiotic-contaminated water affected by organic pollution.}, } @article {pmid39244633, year = {2024}, author = {Li, F and Liu, J and Maldonado-Gómez, MX and Frese, SA and Gänzle, MG and Walter, J}, title = {Highly accurate and sensitive absolute quantification of bacterial strains in human fecal samples.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {168}, pmid = {39244633}, issn = {2049-2618}, mesh = {Humans ; *Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; *Limosilactobacillus reuteri/genetics/classification ; Reproducibility of Results ; DNA, Bacterial/genetics ; Real-Time Polymerase Chain Reaction/methods ; High-Throughput Nucleotide Sequencing/methods ; Limit of Detection ; Sensitivity and Specificity ; Bacteria/genetics/classification/isolation & purification ; }, abstract = {BACKGROUND: Next-generation sequencing (NGS) approaches have revolutionized gut microbiome research and can provide strain-level resolution, but these techniques have limitations in that they are only semi-quantitative, suffer from high detection limits, and generate data that is compositional. The present study aimed to systematically compare quantitative PCR (qPCR) and droplet digital PCR (ddPCR) for the absolute quantification of Limosilactobacillus reuteri strains in human fecal samples and to develop an optimized protocol for the absolute quantification of bacterial strains in fecal samples.

RESULTS: Using strain-specific PCR primers for L. reuteri 17938, ddPCR showed slightly better reproducibility, but qPCR was almost as reproducible and showed comparable sensitivity (limit of detection [LOD] around 10[4] cells/g feces) and linearity (R[2] > 0.98) when kit-based DNA isolation methods were used. qPCR further had a wider dynamic range and is cheaper and faster. Based on these findings, we conclude that qPCR has advantages over ddPCR for the absolute quantification of bacterial strains in fecal samples. We provide an optimized and easy-to-follow step-by-step protocol for the design of strain-specific qPCR assays, starting from primer design from genome sequences to the calibration of the PCR system. Validation of this protocol to design PCR assays for two L. reuteri strains, PB-W1 and DSM 20016[ T], resulted in a highly accurate qPCR with a detection limit in spiked fecal samples of around 10[3] cells/g feces. Applying our strain-specific qPCR assays to fecal samples collected from human subjects who received live L. reuteri PB-W1 or DSM 20016[ T] during a human trial demonstrated a highly accurate quantification and sensitive detection of these two strains, with a much lower LOD and a broader dynamic range compared to NGS approaches (16S rRNA gene sequencing and whole metagenome sequencing).

CONCLUSIONS: Based on our analyses, we consider qPCR with kit-based DNA extraction approaches the best approach to accurately quantify gut bacteria at the strain level in fecal samples. The provided step-by-step protocol will allow scientists to design highly sensitive strain-specific PCR systems for the accurate quantification of bacterial strains of not only L. reuteri but also other bacterial taxa in a broad range of applications and sample types. Video Abstract.}, } @article {pmid39244624, year = {2024}, author = {Yang, X and Feng, K and Wang, S and Yuan, MM and Peng, X and He, Q and Wang, D and Shen, W and Zhao, B and Du, X and Wang, Y and Wang, L and Cao, D and Liu, W and Wang, J and Deng, Y}, title = {Unveiling the deterministic dynamics of microbial meta-metabolism: a multi-omics investigation of anaerobic biodegradation.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {166}, pmid = {39244624}, issn = {2049-2618}, support = {No. 2019YFC1905001//National Key Research and Development Program of China/ ; }, mesh = {Anaerobiosis ; *Biodegradation, Environmental ; *Bioreactors/microbiology ; *Metabolomics ; *Microbiota ; Bacteria/metabolism/genetics/classification ; Metagenomics ; Methane/metabolism ; Thermodynamics ; Multiomics ; }, abstract = {BACKGROUND: Microbial anaerobic metabolism is a key driver of biogeochemical cycles, influencing ecosystem function and health of both natural and engineered environments. However, the temporal dynamics of the intricate interactions between microorganisms and the organic metabolites are still poorly understood. Leveraging metagenomic and metabolomic approaches, we unveiled the principles governing microbial metabolism during a 96-day anaerobic bioreactor experiment.

RESULTS: During the turnover and assembly of metabolites, homogeneous selection was predominant, peaking at 84.05% on day 12. Consistent dynamic coordination between microbes and metabolites was observed regarding their composition and assembly processes. Our findings suggested that microbes drove deterministic metabolite turnover, leading to consistent molecular conversions across parallel reactors. Moreover, due to the more favorable thermodynamics of N-containing organic biotransformations, microbes preferentially carried out sequential degradations from N-containing to S-containing compounds. Similarly, the metabolic strategy of C18 lipid-like molecules could switch from synthesis to degradation due to nutrient exhaustion and thermodynamical disadvantage. This indicated that community biotransformation thermodynamics emerged as a key regulator of both catabolic and synthetic metabolisms, shaping metabolic strategy shifts at the community level. Furthermore, the co-occurrence network of microbes-metabolites was structured around microbial metabolic functions centered on methanogenesis, with CH4 as a network hub, connecting with 62.15% of total nodes as 1st and 2nd neighbors. Microbes aggregate molecules with different molecular traits and are modularized depending on their metabolic abilities. They established increasingly positive relationships with high-molecular-weight molecules, facilitating resource acquisition and energy utilization. This metabolic complementarity and substance exchange further underscored the cooperative nature of microbial interactions.

CONCLUSIONS: All results revealed three key rules governing microbial anaerobic degradation. These rules indicate that microbes adapt to environmental conditions according to their community-level metabolic trade-offs and synergistic metabolic functions, further driving the deterministic dynamics of molecular composition. This research offers valuable insights for enhancing the prediction and regulation of microbial activities and carbon flow in anaerobic environments. Video Abstract.}, } @article {pmid39244357, year = {2024}, author = {Abo-Ismail, M and Sadek, MAA and Humagain, K and Banjara, N and Pokharel, S}, title = {Spatiotemporal distribution of environmental microbiota around animal farms adjacent to produce fields in central coast California.}, journal = {Food microbiology}, volume = {124}, number = {}, pages = {104598}, doi = {10.1016/j.fm.2024.104598}, pmid = {39244357}, issn = {1095-9998}, mesh = {Animals ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota ; *Seasons ; *Soil Microbiology ; *Farms ; California ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Water Microbiology ; Spatio-Temporal Analysis ; Metagenomics ; }, abstract = {This study aimed to identify different environmental microbiota in animal farms adjacent to produce fields and to understand their potential flow pattern. Soil and water samples were collected from 16 locations during the winter, spring, summer, and fall seasons. In addition, a high-resolution digital elevation model helped to create a stream network to understand the potential flow of the microbiome. Metagenomic analysis of the 16 S rRNA gene revealed that soil and water samples from the four seasons harbor diverse microbiome profiles. The phylogenetic relationship of operational taxonomic units (OTUs) is separated by a maximum of 0.6 Bray-Curtis distance. Similarly, the Principal Component Analysis (P = 0.001) demonstrated the soil and water microbiome clustering across different locations and seasons. The relative abundance of Proteobacteria, Bacteroidetes, and Firmicutes was higher in the water samples than in the soil samples. In contrast, the relative abundance of Actinobacteria and Chloroflexi was higher in the soil compared to the water samples. Soil samples in summer and water samples in spring had the highest abundance of Bacteroidetes and Firmicutes, respectively. A unique microbial community structure was found in water samples, with an increased abundance of Hydrogenophaga and Solirubrobacter. Genera that were significantly abundant at a 1% false discovery rate (FDR) among seasons and soil or water samples, include Nocardioides, Gemmatimonas, JG30-KF-CM45, Massilia, Gaiellales, Sphingomonas, KD4-96, Bacillus, Streptomyces, Gaiella, and Gemmatimonadaceae. The relative abundance of pathogenic genera, including Mycobacterium, Bacteroides, Nocardia, Clostridium, and Corynebacterium, were significantly (at 1% FDR) affected by seasons and environmental type. The elevation-based stream network model suggests the potential flow of microbiomes from the animal farm to the produce fields.}, } @article {pmid39244165, year = {2024}, author = {Choi, MH and Kim, D and Lee, KH and Kim, HJ and Sul, WJ and Jeong, SH}, title = {Dysbiosis of the gut microbiota is associated with in-hospital mortality in patients with antibiotic-associated diarrhoea: A metagenomic analysis.}, journal = {International journal of antimicrobial agents}, volume = {64}, number = {5}, pages = {107330}, doi = {10.1016/j.ijantimicag.2024.107330}, pmid = {39244165}, issn = {1872-7913}, mesh = {Humans ; *Diarrhea/microbiology/mortality ; Male ; *Gastrointestinal Microbiome/drug effects/genetics ; Female ; *Anti-Bacterial Agents/adverse effects/therapeutic use ; *Dysbiosis/microbiology ; Aged ; Middle Aged ; *Metagenomics ; *Hospital Mortality ; *Feces/microbiology ; *Clostridium Infections/mortality/microbiology ; Clostridioides difficile/genetics/isolation & purification/drug effects ; Aged, 80 and over ; Adult ; Machine Learning ; }, abstract = {BACKGROUND: The increasing incidence of antibiotic-associated diarrhoea (AAD) is a serious health care problem. Dysbiosis of the gut microbiota is suspected to play a role in the pathogenesis of AAD, but its impact on the clinical outcomes of patients remains unclear.

METHODS: Between May and October 2022, 210 patients with AAD admitted to a university hospital and 100 healthy controls were recruited. DNA extraction from stool specimens and shotgun sequencing were performed. Machine learning was conducted to assess profiling at different taxonomic levels and to select variables for multivariable analyses.

RESULTS: Patients were classified into two groups: Clostridioides difficile infection (CDI, n = 39) and non-CDI AAD (n = 171). The in-hospital mortality rate for the patients was 20.0%, but the presence of C. difficile in the gut microbiota was not associated with mortality. Machine learning showed that taxonomic profiling at the genus level best reflected patient prognosis. The in-hospital mortality of patients was associated with the relative abundance of specific gut microbial genera rather than alpha-diversity: each of the five genera correlated either positively (Enterococcus, Klebsiella, Corynebacterium, Pseudomonas, and Anaerofustis) or negatively (Bifidobacterium, Bacteroides, Streptococcus, Faecalibacterium, and Dorea). Genes for vancomycin resistance were significantly associated with in-hospital mortality in patients with AAD (adjusted hazard ratios, 2.45; 95% CI, 1.20-4.99).

CONCLUSION: This study demonstrates the potential utility of metagenomic studies of the gut microbial community as a biomarker for prognosis prediction in AAD patients.}, } @article {pmid39244052, year = {2024}, author = {Wang, Q and Chen, J and Qi, W and Bai, Y and Mao, J and Qu, J}, title = {Dam construction alters the traits of health-related microbes along the Yangtze River.}, journal = {The Science of the total environment}, volume = {953}, number = {}, pages = {176077}, doi = {10.1016/j.scitotenv.2024.176077}, pmid = {39244052}, issn = {1879-1026}, mesh = {*Rivers/microbiology ; China ; Water Microbiology ; Drug Resistance, Microbial/genetics ; Microbiota ; Environmental Monitoring ; Ecosystem ; Virulence Factors/genetics ; }, abstract = {Dams, constructed globally for energy production and water conservation, fragment rivers, and modify flow regimes, thereby altering the composition of biological communities and ecosystem functions. Despite the extensive use of dams, few studies have explored their potential health impacts, particularly concerning changes in health-related genes, such as antibiotic resistance genes (ARGs) and virulence factor genes (VFGs), and their hosts (i.e., ARB and potential pathogens). Understanding these health-related effects is crucial because they can impact human health through water quality and pathogen prevalence. In this study, we investigated the planktonic microbial community in the Three Gorges Reservoir (TGR) and adjacent upstream and downstream areas of the Yangtze River during both the dry and wet season. Our metagenomic analysis showed that dam construction significantly decreased the abundance of ARGs, but it had an insignificant effect on VFGs. The observed reduction in ARGs abundance could be mainly attributed to the decrease abundance of the major ARGs carrier - Limnohabitansin the TGR and downstream areas due to high grazing pressure and fitness cost. Conversely, the abundance of microbes carrying VFGs (potential pathogens) remained stable from upstream to the dam reservoir, which may explain the negligible impact on VFG abundance. Overall, our results provide a detailed understanding of the ecological health implications of dam construction in large river ecosystems.}, } @article {pmid39244041, year = {2024}, author = {Su, Y and Rahaman, MH and Liu, W and Wen, Y and Zhai, J}, title = {Methane oxidation driven by multiple electron acceptors in the water level fluctuation zone of the Three Gorges Reservoir area, China.}, journal = {The Science of the total environment}, volume = {953}, number = {}, pages = {176041}, doi = {10.1016/j.scitotenv.2024.176041}, pmid = {39244041}, issn = {1879-1026}, abstract = {Water level fluctuations in China's Three Gorges Reservoir (TGR) area are typical of many reservoirs and significantly impact water level fluctuation zones (WLFZ), including upstream rivers. Understanding methane oxidation in the TGR-WLFZ is crucial for evaluating the impact of large-scale reservoir construction on global climate change. In this study, we investigated methane oxidation rates in the TGR-WLFZ, focusing on periods of drying and flooding. The highest methane oxidation rates were observed during the drying period, ranging from 35.69 to 56.32 nmol/(g soil)/d, while the lowest rates were recorded during the flooding period, at 11.58 to 11.98 nmol/(g soil)/d, in lab-scale simulated columns. Using [13]CH4 labeling experiments, we measured CH4 oxidation potentials for aerobic methane oxidation (AMO) using oxygen and anaerobic oxidation of methane (AOM) using nitrite, nitrate, sulfate, ferric iron, and manganese oxide as electron acceptors at varying concentrations. AMO was the dominant process across all experiments, with potentials ranging from 145.71 to 180.77 nmol [13]CO2/(g soil)/d. For AOM, metal-dependent oxidation, particularly with Fe (III) and Mn(IV), was predominant (12.64-17.59 and 3.91-12.69 nmol [13]CO2/(g soil)/d, respectively), followed by nitrite and nitrate-dependent pathways (1.49-9.10 nmol [13]CO2/(g soil)/d). Sulfate-dependent AOM was limited (1.33-3.27 nmol [13]CO2/(g soil)/d). Metagenomic analysis identified key microorganisms responsible for AMO, such as unclassified_f_Methylobacteriaeae and Methylobacterium sp., and for AOM are Ca. Methylomirabilis oxyfera, Ca. Methanoperedens nitroreducens and Ca. Methylomirabilis sp. Complete functional genes and enzymes for the methane oxidation and reverse methanogenesis pathways were obtained in each hydrological period, with the highest content during the drying period and the lowest during flooding. Our study shows that reservoirs, traditionally considered significant sources of methane, may also act as methane sinks. This finding raises new questions: How do different methane oxidation pathways respond to water level fluctuations in reservoirs, and are some pathways more resilient to changes in hydrological conditions?}, } @article {pmid39243646, year = {2024}, author = {Liu, P and Guo, Z and Wang, Y and He, M and Kang, Y and Wu, H and Hu, Z and Zhang, J}, title = {Occurrence of polycyclic aromatic hydrocarbons in the Yellow River delta: Sources, ecological risks, and microbial response.}, journal = {Journal of environmental management}, volume = {370}, number = {}, pages = {122432}, doi = {10.1016/j.jenvman.2024.122432}, pmid = {39243646}, issn = {1095-8630}, mesh = {*Polycyclic Aromatic Hydrocarbons/analysis/toxicity ; *Rivers/chemistry/microbiology ; China ; Water Pollutants, Chemical/toxicity/analysis ; Environmental Monitoring ; Bacteria/metabolism/genetics ; Soil Microbiology ; }, abstract = {This research investigated the distribution, sources, and ecological risks of polycyclic aromatic hydrocarbons (PAHs) in the Yellow River Delta (YRD), China, emphasizing the response of soil microorganisms. The study involved quantitative analyses of 16 PAHs specified by the U.S. Environmental Protection Agency (USEPA) in both water and soil, utilizing metagenomic technique to determine the response of microbial communities and metabolism within the soil. Results noted that PAHs in the water mainly originate from pyrogenic source and in the soil originate from mixture source, with higher concentrations found in wetland areas compared to river regions. The ecological risk assessment revealed low-to-moderate risk. Microbial analysis demonstrated increased diversity and abundance of bacteria associated with PAHs in areas with higher PAHs pollution. Metagenomic insights revealed significant effects of organic carbon on PAHs degradation genes (ko00624 and ko00626), as well as significant differences in specific metabolic pathways including phenanthrene degradation, with key enzymes showing significant differences between the two environments. The study underscores the importance of understanding PAHs distribution and microbial responses to effectively manage and mitigate pollution in estuarine environments.}, } @article {pmid39243610, year = {2025}, author = {Jiang, L and Shen, S and Zuo, A and Chi, Y and Lu, Y and He, Q}, title = {Characterizing flavor development in low-salt Chinese horse bean-chili paste through integrated metabolomics and metagenomics.}, journal = {Food chemistry}, volume = {463}, number = {Pt 1}, pages = {141076}, doi = {10.1016/j.foodchem.2024.141076}, pmid = {39243610}, issn = {1873-7072}, mesh = {*Bacteria/classification/isolation & purification ; Capsicum/chemistry/microbiology ; Fermentation ; *Fermented Foods/analysis/microbiology ; *Metabolomics ; *Metagenomics ; Microbiota ; Sodium Chloride/analysis ; *Taste ; }, abstract = {This study utilized metabolomics and metagenomics to investigate the microbial composition and functions in low- and high-salt Chinese horse bean-chili pastes (CHCPs). The results showed that 25 key metabolites were identified to distinguish the flavor attributes between the two samples. Leuconostoc was identified as the dominant microbiota in low-salt CHCP, while Pantoea prevailed in the high-salt CHCP. Compared to traditional high-salt fermentation, low-salt and inoculated fermentation promoted the increase in the relative abundances of Companionlactobacillus, Levilactobacillus, Tetragenococcus, Zygosaccharomyces and Wickerhamiella as well as the enrichment of carbohydrate and amino acid metabolic pathways, which contributed to the enhancement of characteristic flavor compounds. Further metabolic pathway reconstruction elucidated 21 potential microbial genera associated with the formation of key metabolites, such as Leuconostoc, Levilactobacillus, Pantoea, and Pectobacterium. This study may provide insights for optimizing the fermentation process and improving the flavor quality of low-salt CHCP and similar fermentation products. KEYWORDS: Low-salt fermentation Hight-salt fermentation Chinese horse-bean chili paste Flavor formation Metabolomics Metagenomics.}, } @article {pmid39243538, year = {2024}, author = {Lin, L and Li, L and Yang, X and Hou, L and Wu, D and Wang, B and Ma, B and Liao, X and Yan, X and Gad, M and Su, J and Liu, Y and Liu, K and Hu, A}, title = {Unnoticed antimicrobial resistance risk in Tibetan cities unveiled by sewage metagenomic surveillance: Compared to the eastern Chinese cities.}, journal = {Journal of hazardous materials}, volume = {479}, number = {}, pages = {135730}, doi = {10.1016/j.jhazmat.2024.135730}, pmid = {39243538}, issn = {1873-3336}, mesh = {*Sewage/microbiology ; Tibet ; China ; *Cities ; *Metagenomics ; Drug Resistance, Microbial/genetics ; Bacteria/genetics/drug effects ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; }, abstract = {Sewage surveillance is a cost-effective tool for assessing antimicrobial resistance (AMR) in urban populations. However, research on sewage AMR in remote areas is still limited. Here, we used shotgun metagenomic sequencing to profile antibiotic resistance genes (ARGs) and ARG-carrying pathogens (APs) across 15 cities in Tibetan Plateau (TP) and the major cities in eastern China. Notable regional disparities in sewage ARG composition were found, with a significantly higher ARG abundance in TP (2.97 copies/cell). A total of 542 and 545 APs were identified in sewage from TP and the East, respectively, while more than 40 % carried mobile genetic elements (MGEs). Moreover, 65 MGEs-carrying APs were identified as World Health Organization (WHO) priority-like bacterial and fungal pathogens. Notably, a fungal zoonotic pathogen, Enterocytozoon bieneusi, was found for the first time to carry a nitroimidazole resistance gene (nimJ). Although distinct in AP compositions, the relative abundances of APs were comparable in these two regions. Furthermore, sewage in TP was found to be comparable to the cities in eastern China in terms of ARG mobility and AMR risks. These findings provide insights into ARGs and APs distribution in Chinese sewage and stress the importance of AMR surveillance and management strategies in remote regions.}, } @article {pmid39243471, year = {2024}, author = {Cai, M and Zhang, H and Zheng, L and Tang, X}, title = {A global microbiome analysis reveals the ecological feature of Tistrella and its production of the bioactive didemnins in the marine ecosystem.}, journal = {Marine pollution bulletin}, volume = {207}, number = {}, pages = {116939}, doi = {10.1016/j.marpolbul.2024.116939}, pmid = {39243471}, issn = {1879-3363}, mesh = {*Microbiota ; *Ecosystem ; Aquatic Organisms ; Metagenomics ; Seawater/microbiology/chemistry ; }, abstract = {Marine microorganisms like Tistrella are essential for producing bioactive compounds, including didemnins with antitumor and antiviral properties. However, our understanding of Tistrella's ecological features and didemnin production in natural environments is limited. In this study, we used genomics and metagenomics to show that Tistrella is widely distributed across natural habitats, especially in marine environments from the surface to 5000 m deep, with distinct non-random distribution patterns revealed by co-occurrence analysis. Importantly, transcriptional profiling of didemnin biosynthetic gene clusters indicates active in situ production of this compound within marine ecosystems. These findings enhance our understanding of Tistrella's ecology and secondary metabolite production in natural environments. Further research is needed to explore the ecological dynamics and functional impacts of Tistrella in these ecosystems.}, } @article {pmid39243463, year = {2024}, author = {Ren, M and Hu, A and Zhang, L and Yao, X and Zhao, Z and Kimirei, IA and Wang, J}, title = {Acidic proteomes are linked to microbial alkaline preference in African lakes.}, journal = {Water research}, volume = {266}, number = {}, pages = {122393}, doi = {10.1016/j.watres.2024.122393}, pmid = {39243463}, issn = {1879-2448}, mesh = {*Lakes/microbiology ; *Proteome ; Hydrogen-Ion Concentration ; Bacteria/metabolism/genetics ; Amino Acids/metabolism ; Microbiota ; }, abstract = {Microbial amino acid composition (AA) reflects adaptive strategies of cellular and molecular regulations such as a high proportion of acidic AAs, including glutamic and aspartic acids in alkaliphiles. It remains understudied how microbial AA content is linked to their pH adaptation especially in natural environments. Here we examined prokaryotic communities and their AA composition of genes with metagenomics for 39 water and sediments of East African lakes along a gradient of pH spanning from 7.2 to 10.1. We found that Shannon diversity declined with the increasing pH and that species abundance were either positively or negatively associated with pH, indicating their distinct habitat preference in lakes. Microbial communities showed higher acidic proteomes in alkaline than neutral lakes. Species acidic proteomes were also positively correlated with their pH preference, which was consistent across major bacterial lineages. These results suggest selective pressure associated with high pH likely shape microbial amino acid composition both at the species and community levels. Comparative genome analyses further revealed that alkaliphilic microbes contained more functional genes with higher acidic AAs when compared to those in neutral conditions. These traits included genes encoding diverse classes of cation transmembrane transporters, antiporters, and compatible solute transporters, which are involved in cytoplasmic pH homeostasis and osmotic stress defense under high pH conditions. Our results provide the field evidence for the strong relationship between prokaryotic AA composition and their habitat preference and highlight amino acid optimization as strategies for environmental adaptation.}, } @article {pmid39243461, year = {2024}, author = {Wu, B and Lin, R and Gu, J and Yuan, H and Murphy, JD}, title = {Biochar confers significant microbial resistance to ammonia toxicity in n-caproic acid production.}, journal = {Water research}, volume = {266}, number = {}, pages = {122367}, doi = {10.1016/j.watres.2024.122367}, pmid = {39243461}, issn = {1879-2448}, mesh = {*Ammonia/metabolism ; *Charcoal ; Fermentation ; Bacteria/metabolism/drug effects ; }, abstract = {Microbial chain elongation integrating innovative bioconversion technologies with organic waste utilization can transition current energy-intensive n-caproic acid production to sustainable circular bioeconomy systems. However, ammonia-rich waste streams, despite their suitability, pose inhibitory challenges to these bioconversion processes. Herein, biochar was employed as an additive to enhance the activity of chain elongating microbes under ammonia inhibition conditions, with an objective to detail underlying mechanisms of improvements. Biochar addition significantly improved chain elongation performance even under severe ammonia stress (exceeding 8 g N/L), increasing n-caproic acid yields by 40 % to 158 % and reducing lag times by 51 % to 90 %, compared with the best-performing group without biochar addition. The material contribution to n-caproic production reached up to 94.3 % (at 4 g N/L). These enhancements were mainly attributed to the new electron syntrophy induced by biochar, which improved electron transfer system activity and electrical conductivity of the fermentation system. This is further substantiated by increased relative abundances of the genus Sporanaerobacter, electroactive bacteria, and up-regulated direct electron transfer-related genes including conductive pili and c-type cytochrome. This study demonstrates that biochar can confer robust resilience to ammonia toxicity in functional microbes, paving a way for efficient and sustainable n-caproic acid production.}, } @article {pmid39243135, year = {2024}, author = {Shi, K and Liu, X and Duan, Y and Ding, J and Jia, Y and Jiang, Z and Feng, C}, title = {Multi-omics analysis reveals associations between host gene expression, gut microbiota, and metabolites in chickens.}, journal = {Journal of animal science}, volume = {102}, number = {}, pages = {}, pmid = {39243135}, issn = {1525-3163}, mesh = {Animals ; *Chickens/microbiology/metabolism ; *Gastrointestinal Microbiome ; Female ; *Metabolome ; Transcriptome ; Liver/metabolism ; Gene Expression Profiling ; Gene Expression ; Multiomics ; }, abstract = {Egg-laying is an important trait in chickens, and it is affected by many factors, such as hormones regulated by the hypothalamic-pituitary axis and precursors synthesized by the liver. Recent studies showed that gut microbiota was associated with egg-laying, however, its underlying mechanism remains unclear. We comprehensively analyzed the host transcriptome, gut microbiota, and metabolome in broiler breeder hens during the pre-laying, peak-laying, and late-laying periods. The transcriptome analysis of the tissues related to the hypothalamic-pituitary-liver (HPL) axis revealed dynamic gene expression during egg-laying periods. Differentially expressed genes (DEGs) (i.e., PENK, NPY, AVP, PRL, RLN3, and FST) from the hypothalamus and pituitary gland were involved in female gonadal development, hormone secretion, response to endogenous stimulus, liver development, and amide metabolism. In liver, DEGs (i.e., FABP3, VTG1, LPL, APOA5, APOV1, and RBP5) were enriched in efferocytosis, sphingolipid metabolism, amide, and peptide biosynthesis. Alpha and beta diversity changed significantly in cecum microbiota during different laying periods. The abundance of Firmicutes was decreased and the abundance of Bacteroidota was increased during the peak-laying period. Functional analysis showed that the biosynthesis of secondary metabolites, amino acids, purine, and steroid hormones was altered during laying. The metabolome analysis from cecal contents showed that amino acid metabolism and steroid hormone biosynthesis changed during laying. Integrated analysis of the cecal microbiota and metabolites showed the genus Megasphaera was involved in amino acid metabolism, which included 3-phenyllatic acid, quinic acid, caffeic acid, and folic acid, and the genus Hungatella participated in steroid hormone biosynthesis through its strong correlation with estradiol. These results explored the dynamic changes in tissues related to the HPL axis and cecal microbiota and provided new insights into the interaction between the host and microbiota during egg-laying in chickens.}, } @article {pmid39242818, year = {2024}, author = {Porras, MÁG and Assié, A and Tietjen, M and Violette, M and Kleiner, M and Gruber-Vodicka, H and Dubilier, N and Leisch, N}, title = {An intranuclear bacterial parasite of deep-sea mussels expresses apoptosis inhibitors acquired from its host.}, journal = {Nature microbiology}, volume = {9}, number = {11}, pages = {2877-2891}, pmid = {39242818}, issn = {2058-5276}, support = {340535//EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; Gottfried Wilhelm Leibniz Prize//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Heisenberggrant GR 5028/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; OIA 1934844//National Science Foundation (NSF)/ ; IOS 2003107//National Science Foundation (NSF)/ ; }, mesh = {Animals ; *Phylogeny ; *Apoptosis ; *Gene Transfer, Horizontal ; Bivalvia/microbiology/parasitology ; Cell Nucleus/metabolism ; Transcriptome ; Bacteroidetes/genetics/metabolism ; Apoptosis Regulatory Proteins/genetics/metabolism ; }, abstract = {A limited number of bacteria are able to colonize the nuclei of eukaryotes. 'Candidatus Endonucleobacter' infects the nuclei of deep-sea mussels, where it replicates to ≥80,000 bacteria per nucleus and causes nuclei to swell to 50 times their original size. How these parasites are able to replicate and avoid apoptosis is not known. Dual RNA-sequencing transcriptomes of infected nuclei isolated using laser-capture microdissection revealed that 'Candidatus Endonucleobacter' does not obtain most of its nutrition from nuclear DNA or RNA. Instead, 'Candidatus Endonucleobacter' upregulates genes for importing and digesting sugars, lipids, amino acids and possibly mucin from its host. It likely prevents apoptosis of host cells by upregulating 7-13 inhibitors of apoptosis, proteins not previously seen in bacteria. Comparative phylogenetic analyses revealed that 'Ca. Endonucleobacter' acquired inhibitors of apoptosis through horizontal gene transfer from their hosts. Horizontal gene transfer from eukaryotes to bacteria is assumed to be rare, but may be more common than currently recognized.}, } @article {pmid39242817, year = {2024}, author = {Shao, Y and Garcia-Mauriño, C and Clare, S and Dawson, NJR and Mu, A and Adoum, A and Harcourt, K and Liu, J and Browne, HP and Stares, MD and Rodger, A and Brocklehurst, P and Field, N and Lawley, TD}, title = {Primary succession of Bifidobacteria drives pathogen resistance in neonatal microbiota assembly.}, journal = {Nature microbiology}, volume = {9}, number = {10}, pages = {2570-2582}, pmid = {39242817}, issn = {2058-5276}, support = {/WT_/Wellcome Trust/United Kingdom ; WT101169MA, 206194 and 108413/A/15/D//Wellcome Trust (Wellcome)/ ; }, mesh = {Humans ; *Feces/microbiology ; Animals ; Infant, Newborn ; *Gastrointestinal Microbiome ; *Bifidobacterium/genetics/isolation & purification ; Mice ; Female ; United Kingdom ; Metagenomics ; Enterococcus faecalis/genetics/isolation & purification ; Milk, Human/microbiology ; Male ; }, abstract = {Human microbiota assembly commences at birth, seeded by both maternal and environmental microorganisms. Ecological theory postulates that primary colonizers dictate microbial community assembly outcomes, yet such microbial priority effects in the human gut remain underexplored. Here using longitudinal faecal metagenomics, we characterized neonatal microbiota assembly for a cohort of 1,288 neonates from the UK. We show that the pioneering neonatal gut microbiota can be stratified into one of three distinct community states, each dominated by a single microbial species and influenced by clinical and host factors, such as maternal age, ethnicity and parity. A community state dominated by Enterococcus faecalis displayed stochastic microbiota assembly with persistent high pathogen loads into infancy. In contrast, community states dominated by Bifidobacterium, specifically B. longum and particularly B. breve, exhibited a stable assembly trajectory and long-term pathogen colonization resistance, probably due to strain-specific functional adaptions to a breast milk-rich neonatal diet. Consistent with our human cohort observation, B. breve demonstrated priority effects and conferred pathogen colonization resistance in a germ-free mouse model. Our findings solidify the crucial role of Bifidobacteria as primary colonizers in shaping the microbiota assembly and functions in early life.}, } @article {pmid39242698, year = {2024}, author = {Lu, X and Gong, G and Zhang, Q and Yang, S and Wu, H and Zhao, M and Wang, X and Shen, Q and Ji, L and Liu, Y and Wang, Y and Liu, J and Suolang, S and Ma, X and Shan, T and Zhang, W}, title = {Metagenomic analysis reveals high diversity of gut viromes in yaks (Bos grunniens) from the Qinghai-Tibet Plateau.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1097}, pmid = {39242698}, issn = {2399-3642}, mesh = {Animals ; Cattle ; *Metagenomics ; *Gastrointestinal Microbiome/genetics ; *Virome/genetics ; Tibet ; Metagenome ; }, abstract = {The Qinghai-Tibet Plateau (QTP), renowned for its exceptional biological diversity, is home to numerous endemic species. However, research on the virology of vulnerable vertebrates like yaks remains limited. In this study, our objective was to use metagenomics to provide a comprehensive understanding of the diversity and evolution of the gut virome in yak populations across different regions of the QTP. Our findings revealed a remarkably diverse array of viruses in the gut of yaks, including those associated with vertebrates and bacteriophages. Notably, some vertebrate-associated viruses, such as astrovirus and picornavirus, showed significant sequence identity across diverse yak populations. Additionally, we observed differences in the functional profiles of genes carried by the yak gut virome across different regions. Moreover, the virus-bacterium symbiotic network that we discovered holds potential significance in maintaining the health of yaks. Overall, this research expands our understanding of the viral communities in the gut of yaks and highlights the importance of further investigating the interactions between viruses and their hosts. These data will be beneficial for revealing the crucial role that viruses play in the yak gut ecology in future studies.}, } @article {pmid39242694, year = {2024}, author = {Oren, A}, title = {Novel insights into the diversity of halophilic microorganisms and their functioning in hypersaline ecosystems.}, journal = {npj biodiversity}, volume = {3}, number = {1}, pages = {18}, pmid = {39242694}, issn = {2731-4243}, abstract = {Our understanding of the microbial diversity inhabiting hypersaline environments, here defined as containing >100-150 g/L salts, has greatly increased in the past five years. Halophiles are found in each of the three domains of life. Many novel types have been cultivated, and metagenomics and other cultivation-independent approaches have revealed the existence of many previously unrecognized lineages. Syntrophic interactions between different phylogenetic lineages have been discovered, such as the symbiosis between members of the archaeal class Halobacteria and the 'Candidatus Nanohalarchaeota'. Metagenomics techniques also have shed light on the biogeography of halophiles, especially of the genera Salinibacter (Bacteria) and Haloquadratum and Halorubrum (Archaea). Exploration of the microbiome of hypersaline lakes led to the discovery of novel types of metabolism previously unknown to occur at high salt concentrations. Studies of environments with high concentrations of chaotropic ions such as magnesium, calcium, and lithium have refined our understanding of the limits of life.}, } @article {pmid39242568, year = {2024}, author = {Zhou, T and Wu, J and Khan, A and Hu, T and Wang, Y and Salama, ES and Su, S and Han, H and Jin, W and Li, X}, title = {A probiotic Limosilactobacillus fermentum GR-3 mitigates colitis-associated tumorigenesis in mice via modulating gut microbiome.}, journal = {NPJ science of food}, volume = {8}, number = {1}, pages = {61}, pmid = {39242568}, issn = {2396-8370}, support = {32200080//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Bacterial therapy for colorectal cancer (CRC) represents a burgeoning frontier. The probiotic Limosilactobacillus fermentum GR-3, derived from traditional food "Jiangshui", exhibited superior antioxidant capacity by producing indole derivatives ICA and IPA. In an AOM/DSS-induced CRC mouse model, GR-3 treatment alleviated weight loss, colon shortening, rectal bleeding and intestinal barrier disruption by reducing oxidative stress and inflammation. GR-3 colonization in distant colon induced apoptosis and reduced tumor incidence by 51.2%, outperforming the control strain and vitamin C. The beneficial effect of GR-3 on CRC was associated with gut microbiome modulation, increasing SCFA producer Lachnospiraceae NK4A136 group and suppressing pro-inflammatory strain Bacteroides. Metagenomic and metabolic analyses revealed that GR-3 intervention upregulated antioxidant genes (xseA, ALDH) and butyrate synthesis gene (bcd), while increasing beneficial metabolites (SCFAs, ICA, IPA, VB12 and VD3) and reducing harmful secondary bile acids. Overall, GR-3 emerges as a promising candidate in CRC therapy, offering effective gut microbiome remediation.}, } @article {pmid39242535, year = {2024}, author = {Attrah, M and Schärer, MR and Esposito, M and Gionchetta, G and Bürgmann, H and Lens, PNL and Fenner, K and van de Vossenberg, J and Robinson, SL}, title = {Disentangling abiotic and biotic effects of treated wastewater on stream biofilm resistomes enables the discovery of a new planctomycete beta-lactamase.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {164}, pmid = {39242535}, issn = {2049-2618}, support = {109070/WT_/Wellcome Trust/United Kingdom ; Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, 186531 (ANTIVERSA as part of biodeversa+, European Biodiversity Partnership)//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, 186531 (ANTIVERSA as part of biodeversa+, European Biodiversity Partnership)//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 200021L_201006//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; PZPGP2_209124//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; }, mesh = {*Biofilms/drug effects ; *Wastewater/microbiology ; *beta-Lactamases/genetics ; *Rivers/microbiology ; *Metagenomics ; Microbiota/drug effects ; Bacteria/genetics/classification/drug effects/isolation & purification ; Anti-Bacterial Agents/pharmacology ; Planctomycetales/genetics/drug effects ; Metagenome ; Bacterial Proteins/genetics/metabolism ; }, abstract = {BACKGROUND: Environmental reservoirs of antibiotic resistance pose a threat to human and animal health. Aquatic biofilms impacted by wastewater effluent (WW) are known environmental reservoirs for antibiotic resistance; however, the relative importance of biotic factors and abiotic factors from WW on the abundance of antibiotic resistance genes (ARGs) within aquatic biofilms remains unclear. Additionally, experimental evidence is limited within complex aquatic microbial communities as to whether genes bearing low sequence similarity to validated reference ARGs are functional as ARGs.

RESULTS: To disentangle the effects of abiotic and biotic factors on ARG abundances, natural biofilms were previously grown in flume systems with different proportions of stream water and either ultrafiltered or non-ultrafiltered WW. In this study, we conducted deep shotgun metagenomic sequencing of 75 biofilm, stream, and WW samples from these flume systems and compared the taxonomic and functional microbiome and resistome composition. Statistical analysis revealed an alignment of the resistome and microbiome composition and a significant association with experimental treatment. Several ARG classes exhibited an increase in normalized metagenomic abundances in biofilms grown with increasing percentages of non-ultrafiltered WW. In contrast, sulfonamide and extended-spectrum beta-lactamase ARGs showed greater abundances in biofilms grown in ultrafiltered WW compared to non-ultrafiltered WW. Overall, our results pointed toward the dominance of biotic factors over abiotic factors in determining ARG abundances in WW-impacted stream biofilms and suggested gene family-specific mechanisms for ARGs that exhibited divergent abundance patterns. To investigate one of these specific ARG families experimentally, we biochemically characterized a new beta-lactamase from the Planctomycetota (Phycisphaeraceae). This beta-lactamase displayed activity in the cleavage of cephalosporin analog despite sharing a low sequence identity with known ARGs.

CONCLUSIONS: This discovery of a functional planctomycete beta-lactamase ARG is noteworthy, not only because it was the first beta-lactamase to be biochemically characterized from this phylum, but also because it was not detected by standard homology-based ARG tools. In summary, this study conducted a metagenomic analysis of the relative importance of biotic and abiotic factors in the context of WW discharge and their impact on both known and new ARGs in aquatic biofilms. Video Abstract.}, } @article {pmid39241602, year = {2024}, author = {Zheng, Y and Xu, F and Gan, J and Jin, H and Lou, J}, title = {Impact of operating conditions on N2O accumulation in Nitrate-DAMO system: Kinetics and microbiological analysis.}, journal = {Journal of environmental management}, volume = {369}, number = {}, pages = {122389}, doi = {10.1016/j.jenvman.2024.122389}, pmid = {39241602}, issn = {1095-8630}, mesh = {*Nitrous Oxide/metabolism ; *Nitrates/metabolism ; Kinetics ; *Methane/metabolism ; Oxidation-Reduction ; Anaerobiosis ; Nitrogen/metabolism ; Denitrification ; Bacteria/metabolism ; }, abstract = {Nitrate-dependent anaerobic methane oxidation (Nitrate-DAMO) is a novel and sustainable process that removes both nitrogen and methane. Previously, the metabolic pathway of Nitrate-DAMO has been intensively studied with some results. However, the production and consumption of nitrous oxide (N2O) in the Nitrate-DAMO system were widely disregarded. In this study, a Nitrate-DAMO system was used to investigate the effect of operational parameters (C/N ratio, pH, and temperature) on N2O accumulation, and the optimal operating conditions were determined (C/N = 3, pH = 6.5, and temperature = 20 °C). In this study, an enzyme kinetic model was used to fit the nitrate nitrogen degradation and the nitrous oxide production and elimination under different operating conditions. The thermodynamic model of N2O production and elimination in the system also has been constructed. Multiple linear regression analysis found that pH was the most important factor influencing N2O accumulation. The Metagenomics sequencing results showed that alkaline pH promoted the abundance of Nor genes and denitrifying bacteria, which were significantly and positively correlated with N2O emissions. And alkaline pH also promoted the production of Mdo genes related to the N2O-driven AOM reaction, indicating that part of the N2O was consumed by denitrifying bacteria and the other part was consumed by the N2O-driven AOM reaction. These findings reveal the mechanism of N2O production and consumption in DAMO systems and provide a theoretical basis for reducing N2O production and greenhouse gas emissions in actual operation.}, } @article {pmid39241588, year = {2024}, author = {Wang, S and Jiang, T and Hao, X and Dai, Y and Yang, J and Wang, B}, title = {Enhanced and robust nitrogen removal using an integrated zeolite and partial denitrification anammox process.}, journal = {Journal of environmental management}, volume = {369}, number = {}, pages = {122381}, doi = {10.1016/j.jenvman.2024.122381}, pmid = {39241588}, issn = {1095-8630}, mesh = {*Zeolites ; *Denitrification ; *Nitrogen/metabolism ; Bioreactors ; Sewage ; RNA, Ribosomal, 16S/genetics ; Ammonium Compounds/metabolism ; Anaerobiosis ; Waste Disposal, Fluid/methods ; }, abstract = {Anammox has received increased attention due to its enhanced and cost-efficient approach to nitrogen removal. However, its practical application is complicated by strict influent NO2[-]-N to NH4[+]-N ratio demands and an 11% nitrate production from the anammox process. This study was the first known research to propose and verify a system of zeolite integrated with partial denitrification and anammox (Z-PDA) in an up-flow anaerobic sludge bed (UASB) reactor. The enhanced and robust nitrogen removal resulted in an ultra-high nitrogen removal efficiency (NRE, 93.0 ± 2.0%). Zeolite adsorption and biological desorption of ammonium contributed to robust nitrogen removal with fluctuating influent NO2[-]-N to NH4[+]-N ratios. Applying 16S rRNA gene sequencing found that Candidatus Brocadia and Thauera were the key bacteria responsible for anammox and partial denitrification (PD), respectively. Zeolite also acted as a biological carrier. This significantly enriched anammox bacteria with a higher relative abundance of Candidatus Brocadia, reaching 49.2%. Metagenomic analysis demonstrated that the multiple functional genes related to nitrogen removal (nrfA/H, narG/H/I) and the metabolic pathways (Biosynthesis of cofactors, the Two-component system, the Biosynthesis of nucleotide sugars, and Purine metabolism) ensured the resilience of the Z-PDA system despite influent fluctuations. Overall, this study provided novel insights into the impacts of zeolite in the PDA system. It described the fundamental mechanism of zeolite based on adsorption and biological desorption, and demonstrated a meaningful application of the anammox process in sewage treatment.}, } @article {pmid39241382, year = {2024}, author = {Hao, S and Zhang, L and Gao, J and Dong, T and Peng, Y and Miyazawa, A}, title = {Genomic synergistic efficient carbon fixation and nitrogen removal induced by excessive inorganic carbon in the anammox-centered coupling system.}, journal = {Water research}, volume = {266}, number = {}, pages = {122366}, doi = {10.1016/j.watres.2024.122366}, pmid = {39241382}, issn = {1879-2448}, mesh = {*Nitrogen ; *Carbon ; Carbon Cycle ; Bioreactors ; Denitrification ; Bacteria/metabolism ; Oxidation-Reduction ; Autotrophic Processes ; Anaerobiosis ; }, abstract = {Given the significance of HCO3[-] for autotrophic anammox bacteria (AnAOB), excessive HCO3[-] was always provided in anammox-related systems and engineering applications. However, its impact mechanism on anammox process at genome-level remains unknown. This study firstly established an anammox-centered coupling system that entails heterotrophic partial denitrification (PD) and hydrolytic acidification (A-PDHA) fed mainly with inorganic carbon (high HCO3[-] concentration and low C/N ratio). Metagenomic binning and metatranscriptomics analyses indicated that high HCO3[-] concentration enhanced expression of natural most efficient phosphoenolpyruvate (PEP) carboxylase within AnAOB, by up to 30.59 folds. This further induced AnAOB to achieve high-speed carbon-fixing reaction through cross-feeding of phosphate and PEP precursors with heterotrophs. Additionally, the enhanced activity of transporters and catalytic enzymes (up to 4949-fold) induced by low C/N ratio enabled heterotrophs to eliminate extracellular accumulated energy precursors mainly derived from carbon fixation products of AnAOB. This maintained high-speed carbon-fixing reaction within AnAOB and supplemented heterotrophs with organics. Moreover, assimilated energy precursors stimulated nitrogen metabolism enzymes, especially NO2[-] reductase (968.14 times), in heterotrophs. This established an energy-saving PD-A process mediated by interspecies NO shuttle. These variation resulted in efficient nitrogen removal (>95 %) and reduced external organic carbon demand (67 %) in A-PDHA system. This study unveils the great potential of an anammox-centered autotrophic-heterotrophic coupling system for achieving cost-effective nitrogen removal and enhancing carbon fixation under excessive HCO3[-] doses.}, } @article {pmid39241365, year = {2024}, author = {Zhang, X and Xu, D and Usman, S and Li, Y and Liang, Y and Bai, J and Guo, X}, title = {Heterofermentative Lentilactobacillus buchneri and low dry matter reduce high-risk antibiotic resistance genes in corn silage by regulating pathogens and mobile genetic element.}, journal = {Journal of hazardous materials}, volume = {479}, number = {}, pages = {135700}, doi = {10.1016/j.jhazmat.2024.135700}, pmid = {39241365}, issn = {1873-3336}, mesh = {*Zea mays/microbiology ; *Silage/microbiology ; Genes, Bacterial ; Interspersed Repetitive Sequences ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Lactobacillus/genetics/drug effects ; Fermentation ; }, abstract = {The study of antibiotic resistance in the silage microbiome has attracted initial attention. However, the influences of lactic acid bacteria inoculants and dry matter (DM) content on antibiotic resistance genes (ARGs) reduction in whole-plant corn silage remain poorly studied. This study accessed the ARGs' risk and transmission mechanism in whole-plant corn silage with different DM levels and treated with Lactiplantibacillus plantarum or Lentilactobacillus buchneri. The macrolide and tetracycline were the main ARGs in corn silage. The dominant species (Lent. buchneri and Lactobacillus acetotolerans) were the main ARGs carriers in whole-plant corn silage. The application of Lent. buchneri increased total ARGs abundance regardless of corn DM. Whole-plant corn silage with 30 % DM reduced the abundances of integrase and plasmid compared with 40 % DM. The correlation and structural equation model analysis demonstrated that bacterial community succession, resulting from changes in DM content, was the primary driving factor influencing the ARGs distribution in whole-plant corn silage. Interestingly, whole-plant corn silage inoculated with Lent. buchneri reduced abundances of high-risk ARGs (mdtG, mepA, tetM, mecA, vatE and tetW) by regulating pathogens (Escherichia coli), mobile genetic elements (MGEs) genes (IS3 and IS1182), and this effect was more pronounced at 30 % DM level. In summary, although whole-plant corn silage inoculated with Lent. buchneri increased the total ARGs abundance at both DM levels, it decreased the abundance of high-risk ARGs by reducing the abundances of the pathogens and MGEs, and this effect was more noticeable at 30 % DM level.}, } @article {pmid39241334, year = {2024}, author = {Ouyang, B and Yang, C and Lv, Z and Chen, B and Tong, L and Shi, J}, title = {Recent advances in environmental antibiotic resistance genes detection and research focus: From genes to ecosystems.}, journal = {Environment international}, volume = {191}, number = {}, pages = {108989}, doi = {10.1016/j.envint.2024.108989}, pmid = {39241334}, issn = {1873-6750}, mesh = {*Drug Resistance, Microbial/genetics ; *Ecosystem ; Metagenomics/methods ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Environmental Microbiology ; Environmental Monitoring/methods ; }, abstract = {Antibiotic resistance genes (ARGs) persistence and potential harm have become more widely recognized in the environment due to its fast-paced research. However, the bibliometric review on the detection, research hotspot, and development trend of environmental ARGs has not been widely conducted. It is essential to provide a comprehensive overview of the last 30 years of research on environmental ARGs to clarify the changes in the research landscape and ascertain future prospects. This study presents a visualized analysis of data from the Web of Science to enhance our understanding of ARGs. The findings indicate that solid-phase extraction provides a reliable method for extracting ARG. Technological advancements in commercial kits and microfluidics have facilitated the efficacy of ARGs extraction with significantly reducing processing times. PCR and its derivatives, DNA sequencing, and multi-omics technology are the prevalent methodologies for ARGs detection, enabling the expansion of ARG research from individual strains to more intricate microbial communities in the environment. Furthermore, due to the development of combination, hybridization and mass spectrometer technologies, considerable advancements have been achieved in terms of sensitivity and accuracy as well as lowering the cost of ARGs detection. Currently, high-frequency terms such as "Antibiotic Resistance, Antibiotics, and Metagenomics" are the center of attention for study in this area. Prominent topics include the investigation of anthropogenic impacts on environmental resistance, as well as the dynamics of migration, dissemination, and adaptation of environmental ARGs, etc. The research on environmental ARGs has made significant advancements in the fields of "Microbiology" and "Biotechnology Applied Microbiology". Over the past decade, there has been a notable increase in the fields of "Environmental Sciences Ecology" and "Engineering" with a similar growth trend observed in "Water Resources". These three domains are expected to continue driving extensive study within the realm of environmental ARGs.}, } @article {pmid39240096, year = {2024}, author = {Ruiz-Perez, D and Gimon, I and Sazal, M and Mathee, K and Narasimhan, G}, title = {Unfolding and de-confounding: biologically meaningful causal inference from longitudinal multi-omic networks using METALICA.}, journal = {mSystems}, volume = {9}, number = {10}, pages = {e0130323}, pmid = {39240096}, issn = {2379-5077}, support = {R15 AI128714/AI/NIAID NIH HHS/United States ; Dissertation Year Fellowship//University Graduate School, Florida International University (UGS)/ ; 1R15AI128714-01//HHS | NIH | OSC | Common Fund (NIH Common Fund)/ ; }, mesh = {Humans ; *Algorithms ; Microbiota/genetics ; Longitudinal Studies ; Gastrointestinal Microbiome/genetics ; Metabolomics ; Computational Biology/methods ; Multiomics ; }, abstract = {UNLABELLED: A key challenge in the analysis of microbiome data is the integration of multi-omic datasets and the discovery of interactions between microbial taxa, their expressed genes, and the metabolites they consume and/or produce. In an effort to improve the state of the art in inferring biologically meaningful multi-omic interactions, we sought to address some of the most fundamental issues in causal inference from longitudinal multi-omics microbiome data sets. We developed METALICA, a suite of tools and techniques that can infer interactions between microbiome entities. METALICA introduces novel unrolling and de-confounding techniques used to uncover multi-omic entities that are believed to act as confounders for some of the relationships that may be inferred using standard causal inferencing tools. The results lend support to predictions about biological models and processes by which microbial taxa interact with each other in a microbiome. The unrolling process helps identify putative intermediaries (genes and/or metabolites) to explain the interactions between microbes; the de-confounding process identifies putative common causes that may lead to spurious relationships to be inferred. METALICA was applied to the networks inferred by existing causal discovery, and network inference algorithms were applied to a multi-omics data set resulting from a longitudinal study of IBD microbiomes. The most significant unrollings and de-confoundings were manually validated using the existing literature and databases.

IMPORTANCE: We have developed a suite of tools and techniques capable of inferring interactions between microbiome entities. METALICA introduces novel techniques called unrolling and de-confounding that are employed to uncover multi-omic entities considered to be confounders for some of the relationships that may be inferred using standard causal inferencing tools. To evaluate our method, we conducted tests on the inflammatory bowel disease (IBD) dataset from the iHMP longitudinal study, which we pre-processed in accordance with our previous work. From this dataset, we generated various subsets, encompassing different combinations of metagenomics, metabolomics, and metatranscriptomics datasets. Using these multi-omics datasets, we demonstrate how the unrolling process aids in the identification of putative intermediaries (genes and/or metabolites) to explain the interactions between microbes. Additionally, the de-confounding process identifies potential common causes that may give rise to spurious relationships to be inferred. The most significant unrollings and de-confoundings were manually validated using the existing literature and databases.}, } @article {pmid39240085, year = {2024}, author = {Cheng, L-l and Li, Z-t and Wu, H-k and Li, F and Qiu, Y and Wang, T and Peng, H and Liu, Z-h and Huang, P-r and Zhou, L and Gao, L-f and Huang, H-j and Zhang, B and Deng, X-l and Chen, X and Ye, F and Liu, X-q and Guan, W-j and Li, Y-p and Li, Y-m and Li, S-y and Zhong, N-s}, title = {Clinical and pathogen features of COVID-19-associated infections during an Omicron strain outbreak in Guangzhou, China.}, journal = {Microbiology spectrum}, volume = {12}, number = {10}, pages = {e0340623}, pmid = {39240085}, issn = {2165-0497}, support = {No. 2023YFC3041700//MOST | National Key Research and Development Program of China (NKPs)/ ; No. SRPG23-001//R&D Program of Guangzhou Laboratory/ ; No. 82170003//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Humans ; *COVID-19/epidemiology/virology ; China/epidemiology ; Male ; Female ; Middle Aged ; *Coinfection/epidemiology/virology/microbiology ; *SARS-CoV-2/genetics/isolation & purification ; Adult ; Retrospective Studies ; Aged ; *Disease Outbreaks ; }, abstract = {UNLABELLED: Although the Omicron variant has been associated with greater transmissibility and tropism of the upper respiratory tract, the clinical and pathogenic features of patients infected with the Omicron variant during an outbreak in China have been unclear. Adults with COVID-19 were retrospectively enrolled from seven medical centers in Guangzhou, China, and clinical information and specimens (BALF, sputum, and throat swabs) from participants were collected. Conventional detection methods, metagenomics next-generation sequencing (mNGS), and other methods were used to detect pathogens in lower respiratory tract samples. From December 2022 to January 2023, we enrolled 836 patients with COVID-19, among which 56.7% patients had severe/critical illness. About 91.4% of patients were infected with the Omicron strain (BA.5.2). The detection rate of possible co-infection pathogens was 53.4% by mNGS, including Klebsiella pneumoniae (16.3%), Aspergillus fumigatus (12.2%), and Pseudomonas aeruginosa (11.8%). The co-infection rate was 19.5%, with common pathogens being Streptococcus pneumoniae (11.5%), Haemophilus influenzae (9.2%), and Adenovirus (6.9%). The superinfection rate was 75.4%, with common pathogens such as Klebsiella pneumoniae (26.1%) and Pseudomonas aeruginosa (19.4%). Klebsiella pneumoniae (27.1%% vs 6.1%, P < 0.001), Aspergillus fumigatus (19.6% vs 5.3%, P = 0.001), Acinetobacter baumannii (18.7% vs 4.4%, P = 0.001), Pseudomonas aeruginosa (16.8% vs 7.0%, P = 0.024), Staphylococcus aureus (14.0% vs 5.3%, P = 0.027), and Streptococcus pneumoniae (0.9% vs 10.5%, P = 0.002) were more common in severe cases. Co-infection and superinfection of bacteria and fungi are common in patients with severe pneumonia associated with Omicron variant infection. Sequencing methods may aid in the diagnosis and differential diagnosis of pathogens.

IMPORTANCE: Our study has analyzed the clinical characteristics and pathogen spectrum of the lower respiratory tract associated with co-infection or superinfection in Guangzhou during the outbreak of the Omicron strain, particularly after the relaxation of the epidemic prevention and control strategy in China. This study will likely prompt further research into the specific issue, which will benefit clinical practice.}, } @article {pmid39240026, year = {2024}, author = {Sheldon, RA}, title = {Waste Valorization in a Sustainable Bio-Based Economy: The Road to Carbon Neutrality.}, journal = {Chemistry (Weinheim an der Bergstrasse, Germany)}, volume = {30}, number = {54}, pages = {e202402207}, doi = {10.1002/chem.202402207}, pmid = {39240026}, issn = {1521-3765}, abstract = {The development of sustainable chemistry underlying the quest to minimize and/or valorize waste in the carbon-neutral manufacture of chemicals is followed over the last four to five decades. Both chemo- and biocatalysis have played an indispensable role in this odyssey. in particular developments in protein engineering, metagenomics and bioinformatics over the preceding three decades have played a crucial supporting role in facilitating the widespread application of both whole cell and cell-free biocatalysis. The pressing need, driven by climate change mitigation, for a drastic reduction in greenhouse gas (GHG) emissions, has precipitated an energy transition based on decarbonization of energy and defossilization of organic chemicals production. The latter involves waste biomass and/or waste CO2 as the feedstock and green electricity generated using solar, wind, hydroelectric or nuclear energy. The use of waste polysaccharides as feedstocks will underpin a renaissance in carbohydrate chemistry with pentoses and hexoses as base chemicals and bio-based solvents and polymers as environmentally friendly downstream products. The widespread availability of inexpensive electricity and solar energy has led to increasing attention for electro(bio)catalysis and photo(bio)catalysis which in turn is leading to myriad innovations in these fields.}, } @article {pmid39239875, year = {2024}, author = {Kwan, SY and Gonzales, KA and Jamal, MA and Stevenson, HL and Tan, L and Lorenzi, PL and Futreal, PA and Hawk, ET and McCormick, JB and Fisher-Hoch, SP and Jenq, RR and Beretta, L}, title = {Protection against fibrosis by a bacterial consortium in metabolic dysfunction-associated steatohepatitis and the role of amino acid metabolism.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2399260}, pmid = {39239875}, issn = {1949-0984}, support = {P30 CA016672/CA/NCI NIH HHS/United States ; P50 CA217674/CA/NCI NIH HHS/United States ; UL1 TR000371/TR/NCATS NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Humans ; *Liver Cirrhosis/microbiology/metabolism ; Mice ; *Amino Acids/metabolism ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Male ; *Liver/metabolism/pathology/microbiology ; Female ; Feces/microbiology ; Mice, Inbred C57BL ; Middle Aged ; Fatty Liver/metabolism/microbiology ; Disease Models, Animal ; Metagenome ; Adult ; }, abstract = {The gut microbiota drives progression to liver fibrosis, the main determinant of mortality in metabolic dysfunction-associated steatohepatitis (MASH). In this study, we aimed to identify bacterial species associated with protection against liver fibrosis in a high-risk population, and test their potential to protect against liver fibrosis in vivo. Based on stool shotgun metagenomic sequencing of 340 subjects from a population cohort disproportionally affected by MASH, we identified bacterial species from the Bacteroidales and Clostridiales orders associated with reduced risk of liver fibrosis. A bacterial consortium was subsequently tested in a mouse model of MASH, which demonstrated protective effects against liver fibrosis. Six of the eight inoculated bacteria were detected in mouse stool and liver. Intrahepatic presence of bacteria was further confirmed by bacterial culture of mouse liver tissue. Changes in liver histological parameters, gut functional profiles, and amino acid profiles were additionally assessed. Comparison between fibrosis-associated human metagenome and bacteria-induced metagenome changes in mice identified microbial functions likely to mediate the protective effect against liver fibrosis. Amino acid profiling confirmed an increase in cysteine synthase activity, associated with reduced fibrosis. Other microbiota-induced changes in amino acids associated with reduced fibrosis included increased gut asparaginase activity and decreased hepatic tryptophan-to-kynurenine conversion. This human-to-mouse study identified bacterial species and their effects on amino acid metabolism as innovative strategies to protect against liver fibrosis in MASH.}, } @article {pmid39239243, year = {2024}, author = {Ma, R and Wang, YM and Guan, H and Zhang, L and Zhang, W and Chen, LC}, title = {Pulmonary abscess caused by Streptococcus pseudopneumoniae in a child: A case report and review of literature.}, journal = {World journal of radiology}, volume = {16}, number = {8}, pages = {362-370}, pmid = {39239243}, issn = {1949-8470}, abstract = {BACKGROUND: Lung abscess found on chest X-ray and computed tomography examinations is rare in infants and young children. Several pathogens can cause lung abscesses, with the most common pathogens being anaerobes, Streptococci and Staphylococcus aureus. Streptococcus pseudopneumoniae (S. pseudopneumoniae) is a member of the Streptococcaceae family, and is mainly isolated from respiratory tract specimens. There are currently no cases of lung abscess caused by S. pseudopneumoniae in the literature.

CASE SUMMARY: A 2-year-old boy was admitted to hospital due to persistent cough and fever. Lung computed tomography examination suggested the formation of a lung abscess. His diagnosis was not confirmed by testing for serum respiratory pathogens (6 items), respiratory pathogen nucleic acid (27 items), and laboratory culture. Finally, metagenomic next-generation sequencing of bronchoalveolar lavage fluid revealed the presence of S. pseudopneumoniae, confirming its role in causing the lung abscess. After receiving antibiotic treatment, reexamination with lung computed tomography showed that the abscess was resorbed and the patient's outcome was good.

CONCLUSION: This is the first report of a lung abscess in a child caused by S. pseudopneumoniae infection. Metagenomic next-generation sequencing of bronchoalveolar lavage fluid is helpful in achieving rapid and accurate pathogen identification.}, } @article {pmid39239090, year = {2024}, author = {Haidar, G and Kline, EG and Kitsios, GD and Wang, X and Kwak, EJ and Newbrough, A and Friday, K and Hughes Kramer, K and Shields, RK}, title = {Emergence of high-level aztreonam-avibactam and cefiderocol resistance following treatment of an NDM-producing Escherichia coli bloodstream isolate exhibiting reduced susceptibility to both agents at baseline.}, journal = {JAC-antimicrobial resistance}, volume = {6}, number = {5}, pages = {dlae141}, pmid = {39239090}, issn = {2632-1823}, support = {K23 AI154546/AI/NIAID NIH HHS/United States ; }, abstract = {BACKGROUND: Cefiderocol (FDC) or ceftazidime-avibactam with aztreonam (CZA-ATM) are frontline agents for New Delhi metallo-β-lactamase (NDM)-producing Enterobacterales; however, clinical data are scarce, and mechanisms of treatment-emergent resistance are ill-defined. Our objectives were to characterize serial isolates and stool microbiota from a liver transplant recipient with NDM-producing Escherichia coli bacteraemia.

METHODS: Isolates collected pre- and post-CZA-ATM treatment underwent broth microdilution susceptibility testing and whole-genome sequencing. Longitudinal stool collected during CZA-ATM therapy underwent metagenomic sequencing (Nanopore MinION).

RESULTS: The baseline isolate exhibited elevated MICs for ATM-AVI (16/4 µg/mL) and FDC (8 µg/mL). Posttreatment, a rectal surveillance isolate exhibited high-level resistance to ATM-AVI (> 128/4 µg/mL) and FDC (32 µg/mL). Both isolates belonged to ST361 and harboured WT bla NDM-5. The baseline isolate contained wild type (WT) bla CMY-145 and mutations in ftsI (which encodes PBP3), including a YRIN insertion at residue 338 and the non-synonymous substitutions Q227H, E353K and I536L. The posttreatment isolate harboured new mutations in ftsI (A417 V) and bla CMY-145 (L139R and N366Y). Analysis of four stool samples collected during CZA-ATM treatment revealed high E. coli abundance. E. coli relative abundance increased from 34.5% (first sample) to 61.9% (last sample).

CONCLUSIONS: Baseline mutations in ftsI were associated with reduced susceptibility to ATM-AVI and FDC in an ST361 NDM-5-producing E. coli bloodstream isolate. High-level resistance was selected after CZA-ATM treatment, resulting in new ftsl and bla CMY-145 mutations. These findings underscore the need for ATM-AVI susceptibility testing for NDM producers, and the potential for PBP3 mutations to confer cross-resistance to ATM-AVI and FDC, which can emerge after CZA-ATM treatment.}, } @article {pmid39238444, year = {2024}, author = {Zhang, W and Liu, F and Liang, E and Zhang, L}, title = {Evolution of Treatment Modalities for Disseminated HAdV Infection in Neonates.}, journal = {Pediatrics}, volume = {154}, number = {4}, pages = {}, doi = {10.1542/peds.2024-066677}, pmid = {39238444}, issn = {1098-4275}, mesh = {Humans ; Infant, Newborn ; *Adenovirus Infections, Human/drug therapy/diagnosis ; Adenoviruses, Human/genetics ; Anticoagulants/therapeutic use ; Glucocorticoids/therapeutic use ; *Immunoglobulins, Intravenous/therapeutic use/administration & dosage ; Methylprednisolone/therapeutic use/administration & dosage ; }, abstract = {Human adenovirus (HAdV) infection in newborns is a rare condition that typically affects multiple organ systems and has a high mortality rate. We report a case of neonatal HAdV-D37 infection that presented with fever and respiratory distress that was confirmed by metagenomic next-generation sequencing using blood and bronchoalveolar lavage fluid. We treated the patient with intravenous immunoglobulin, methylprednisolone, and anticoagulants, and the patient recovered. Our review of 41 cases of HAdV found that treatment with intravenous immunoglobin might have improved the outcome of HAdV-D infection. We further suggest that glucocorticoid therapy may have additional therapeutic validity in the setting of severe or disseminated disease and that monitoring coagulation function and timely anticoagulation treatment should be considered to prevent complications associated with disseminated intravascular coagulation.}, } @article {pmid39238368, year = {2024}, author = {Hansen, AK and Argondona, JA and Miao, S and Percy, DM and Degnan, PH}, title = {Rapid Loss of Nutritional Symbionts in an Endemic Hawaiian Herbivore Radiation Is Associated with Plant Galling Habit.}, journal = {Molecular biology and evolution}, volume = {41}, number = {9}, pages = {}, pmid = {39238368}, issn = {1537-1719}, mesh = {Animals ; *Symbiosis ; *Herbivory ; *Hemiptera/microbiology ; RNA, Ribosomal, 16S/genetics ; Hawaii ; Phylogeny ; Biological Evolution ; Microbiota ; }, abstract = {Insect herbivores frequently cospeciate with symbionts that enable them to survive on nutritionally unbalanced diets. While ancient symbiont gain and loss events have been pivotal for insect diversification and feeding niche specialization, evidence of recent events is scarce. We examine the recent loss of nutritional symbionts (in as little as 1 MY) in sap-feeding Pariaconus, an endemic Hawaiian insect genus that has undergone adaptive radiation, evolving various galling and free-living ecologies on a single host-plant species, Metrosideros polymorpha within the last ∼5 MY. Using 16S rRNA sequencing, we investigated the bacterial microbiomes of 19 Pariaconus species and identified distinct symbiont profiles associated with specific host-plant ecologies. Phylogenetic analyses and metagenomic reconstructions revealed significant differences in microbial diversity and functions among psyllids with different host-plant ecologies. Within a few millions of years, Pariaconus species convergently evolved the closed-gall habit twice. This shift to enclosed galls coincided with the loss of the Morganella-like symbiont that provides the essential amino acid arginine to free-living and open-gall sister species. After the Pariaconus lineage left Kauai and colonized younger islands, both open- and closed-gall species lost the Dickeya-like symbiont. This symbiont is crucial for synthesizing essential amino acids (phenylalanine, tyrosine, and lysine) as well as B vitamins in free-living species. The recurrent loss of these symbionts in galling species reinforces evidence that galls are nutrient sinks and, combined with the rapidity of the evolutionary timeline, highlights the dynamic role of insect-symbiont relationships during the diversification of feeding ecologies. We propose new Candidatus names for the novel Morganella-like and Dickeya-like symbionts.}, } @article {pmid39237540, year = {2024}, author = {Ravikrishnan, A and Wijaya, I and Png, E and Chng, KR and Ho, EXP and Ng, AHQ and Mohamed Naim, AN and Gounot, JS and Guan, SP and Hanqing, JL and Guan, L and Li, C and Koh, JY and de Sessions, PF and Koh, WP and Feng, L and Ng, TP and Larbi, A and Maier, AB and Kennedy, BK and Nagarajan, N}, title = {Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {7751}, pmid = {39237540}, issn = {2041-1723}, mesh = {Aged, 80 and over ; Female ; Humans ; Male ; *Aging ; Asian People/genetics ; Bacteria/genetics/classification/metabolism/isolation & purification ; Bacteroides/genetics/metabolism ; Cohort Studies ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; Metagenomics/methods ; Phenotype ; Singapore ; Octogenarians ; }, abstract = {While rapid demographic changes in Asia are driving the incidence of chronic aging-related diseases, the limited availability of high-quality in vivo data hampers our ability to understand complex multi-factorial contributions, including gut microbial, to healthy aging. Leveraging a well-phenotyped cohort of community-living octogenarians in Singapore, we used deep shotgun-metagenomic sequencing for high-resolution taxonomic and functional characterization of their gut microbiomes (n = 234). Joint species-level analysis with other Asian cohorts identified distinct age-associated shifts characterized by reduction in microbial richness, and specific Alistipes and Bacteroides species enrichment (e.g., Alistipes shahii and Bacteroides xylanisolvens). Functional analysis confirmed these changes correspond to metabolic potential expansion in aging towards alternate pathways synthesizing and utilizing amino-acid precursors, vis-à-vis dominant microbial guilds producing butyrate in gut from pyruvate (e.g., Faecalibacterium prausnitzii, Roseburia inulinivorans). Extending these observations to key clinical markers helped identify >10 robust microbial associations to inflammation, cardiometabolic and liver health, including potential probiotic species (e.g., Parabacteroides goldsteinii) and pathobionts (e.g., Klebsiella pneumoniae), highlighting the microbiome's role as biomarkers and potential targets for promoting healthy aging.}, } @article {pmid39237364, year = {2024}, author = {Chae, JB and Shin, SU and Kim, S and Chae, H and Kim, WG and Chae, JS and Song, H and Kang, JW}, title = {Identification of a new bovine picornavirus (Boosepivirus) in the Republic of Korea.}, journal = {Journal of veterinary science}, volume = {25}, number = {5}, pages = {e59}, pmid = {39237364}, issn = {1976-555X}, support = {122061-2/iPET/Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry/Korea ; }, mesh = {Animals ; Cattle ; Republic of Korea/epidemiology ; *Cattle Diseases/virology/epidemiology ; *Picornaviridae Infections/veterinary/epidemiology/virology ; *Picornaviridae/isolation & purification/genetics/classification ; *Diarrhea/veterinary/virology/epidemiology ; *Phylogeny ; Prevalence ; Feces/virology ; Genome, Viral ; Animals, Newborn ; }, abstract = {IMPORTANCE: Despite advancements in herd management, feeding, and pharmaceutical interventions, neonatal calf diarrhea (NCD) remains a major global health concern. Bacteria, viruses, and parasites are the major contributors to NCD. Although several pathogens have been identified in the Republic of Korea (ROK), the etiological agents of numerous NCD cases have not been identified.

OBJECTIVE: To identify, for the first time, the prevalence and impact of Boosepivirus (BooV) on calf diarrhea in the ROK.

METHODS: Here, the unknown cause of calf diarrhea was determined using metagenomics We then explored the prevalence of certain pathogens, including BooV, that cause NCD. Seventy diarrheal fecal samples from Hanwoo (Bos taurus coreanae) calves were analyzed using reverse transcriptase and quantitative real-time polymerase chain reaction for pathogen detection and BooV isolate sequencing.

RESULTS: The complete genome of BooV was detected from unknown causes of calf diarrhea. And also, BooV was the most frequently detected pathogen (35.7%) among 8 pathogens in 70 diarrheic feces from Hanwoo calves. Co-infection analyses indicated that most BooV-positive samples were solely infected with BooV, indicating its significance in NCD in the ROK. All isolates were classified as BooV B in phylogenetic analysis.

CONCLUSIONS AND RELEVANCE: This is the first study to determine the prevalence and molecular characteristics of BooV in calf diarrhea in the ROK, highlighting the potential importance of BooV as a causative agent of calf diarrhea and highlighting the need for further research on its epidemiology and pathogenicity.}, } @article {pmid39236909, year = {2024}, author = {Chen, H and Tang, M and He, L and Xiao, X and Yang, F and He, Q and Sun, S and Gao, Y and Zhou, L and Li, Y and Sun, J and Zhang, W}, title = {Exploring the impact of fulvic acid on electrochemical hydrogen-driven autotrophic denitrification system: Performance, microbial characteristics and mechanism.}, journal = {Bioresource technology}, volume = {412}, number = {}, pages = {131432}, doi = {10.1016/j.biortech.2024.131432}, pmid = {39236909}, issn = {1873-2976}, mesh = {*Denitrification ; *Autotrophic Processes ; *Benzopyrans ; *Hydrogen/metabolism ; Nitrates/metabolism ; Nitrogen ; Bacteria/metabolism ; Electrochemical Techniques/methods ; }, abstract = {In this study, the effect of modulating fulvic acid (FA) concentrations (0, 25 and 50 mg/L) on nitrogen removal in a bioelectrochemical hydrogen autotrophic denitrification system (BHDS) was investigated. Results showed that FA increased the nitrate (NO3[-]-N) removal rate of the BHDSs from 37.8 to 46.2 and 45.2 mg N/(L·d) with a current intensity of 40 mA. The metagenomic analysis revealed that R2 (25 mg/L) was predominantly populated by autotrophic denitrifying microorganisms, which enhanced denitrification performance by facilitating electron transfer. Conversely, R3 (50 mg/L) exhibited an increase in genes related to the heterotrophic process, which improved the denitrification performance through the collaborative action of both autotrophic and heterotrophic denitrification pathways. Besides, the study also identified a potential for nitrogen removal in Serpentinimonas, which have been rarely studied. The interesting set of findings provide valuable reference for optimizing BHDS for nitrogen removal and promoting specific denitrifying genera within the system.}, } @article {pmid39236908, year = {2024}, author = {Cui, P and Wan, N and Li, C and Zou, L and Ma, M and Du, J and Jiang, Y}, title = {Comparative analysis of sulfur-driven autotrophic denitrification for pilot-scale application: Pollutant removal performance and metagenomic function.}, journal = {Bioresource technology}, volume = {413}, number = {}, pages = {131433}, doi = {10.1016/j.biortech.2024.131433}, pmid = {39236908}, issn = {1873-2976}, mesh = {*Denitrification ; *Sulfur/metabolism ; *Autotrophic Processes ; *Bioreactors ; *Nitrogen/metabolism ; Water Pollutants, Chemical/metabolism ; Pilot Projects ; Thiosulfates/metabolism ; Wastewater/chemistry ; Water Purification/methods ; Bacteria/metabolism ; Metagenomics/methods ; }, abstract = {Two parallel pilot-scale reactors were operated to investigate pollutant removal performance and metabolic pathways in elemental sulfur-driven autotrophic denitrification (SDAD) process under low temperature and after addition of external electron donors. The results showed that low temperature slightly inhibited SDAD (average total nitrogen removal of ∼4.7 mg L[-1]) while supplement of sodium thiosulfate (stage 2) and sodium acetate (stage 3) enhanced denitrification and secretion of extracellular polymeric substances (EPS), leading to the average removal rate of 0.75 and 1.01 kg N m[-3] d[-1], respectively with over twice higher total EPS. Correspondingly, nitrogen and sulfur related microbial metabolisms especially nitrite reductase and nitric oxide reductase encoding were promoted by genera including Thermomonas and Thiobacillus. The variations revealed that extra sodium acetate improved denitrification and enriched more SDAD-related microorganisms compared with sodium thiosulfate, which potentially catalyzed the refinement of practical strategies for optimizing denitrification in low carbon to nitrogen ratio wastewater treatment.}, } @article {pmid39236827, year = {2024}, author = {Xu, W and Xu, Y and Sun, R and Rey Redondo, E and Leung, KK and Wan, SH and Li, J and Yung, CCM}, title = {Revealing the intricate temporal dynamics and adaptive responses of prokaryotic and eukaryotic microbes in the coastal South China Sea.}, journal = {The Science of the total environment}, volume = {952}, number = {}, pages = {176019}, doi = {10.1016/j.scitotenv.2024.176019}, pmid = {39236827}, issn = {1879-1026}, mesh = {China ; *Phytoplankton/physiology/genetics ; *Seawater/microbiology ; Microbiota ; Cyanobacteria/genetics/physiology ; Photosynthesis ; Seasons ; Metagenome ; }, abstract = {This comprehensive two-year investigation in the coastal South China Sea has advanced our understanding of marine microbes at both community and genomic levels. By combining metagenomics and metatranscriptomics, we have revealed the intricate temporal dynamics and remarkable adaptability of microbial communities and phytoplankton metagenome-assembled genomes (MAGs) in response to environmental fluctuations. We observed distinct seasonal shifts in microbial community composition and function: cyanobacteria were predominant during warmer months, whereas photosynthetic protists were more abundant during colder seasons. Notably, metabolic marker KOs of photosynthesis were consistently active throughout the year, underscoring the persistent role of these processes irrespective of seasonal changes. Our analysis reveals that environmental parameters such as temperature, salinity, and nitrate concentrations profoundly influence microbial community composition, while temperature and silicate have emerged as crucial factors shaping their functional traits. Through the recovery and analysis of 37 phytoplankton MAGs, encompassing nine prokaryotic cyanobacteria and 28 eukaryotic protists from diverse phyla, we have gained insights into their genetic diversity and metabolic capabilities. Distinct profiles of photosynthesis-related pathways including carbon fixation, carotenoid biosynthesis, photosynthesis-antenna proteins, and photosynthesis among the MAGs indicated their genetic adaptations to changing environmental conditions. This study not only enhances our understanding of microbial dynamics in coastal marine ecosystems but also sheds light on the ecological roles and adaptive responses of different microbial groups to environmental changes.}, } @article {pmid39236545, year = {2024}, author = {Wang, R and Wang, Z and Yuan, H and Li, C and Zhu, N}, title = {Mechanistic exploration of COVlD-19 antiviral drug ritonavir on anaerobic digestion through experimental validation coupled with metagenomics analysis.}, journal = {Journal of hazardous materials}, volume = {479}, number = {}, pages = {135603}, doi = {10.1016/j.jhazmat.2024.135603}, pmid = {39236545}, issn = {1873-3336}, mesh = {Anaerobiosis ; *Antiviral Agents/pharmacology ; *Metagenomics ; *Ritonavir ; *Sewage/microbiology ; *Methane/metabolism ; COVID-19 Drug Treatment ; Bioreactors ; }, abstract = {Aggregation of antiviral drugs (ATVs) in waste activated sludge (WAS) poses considerable environmental risk, so it is crucial to understand the behavior of these agents during WAS treatment. This study investigated the effects of ritonavir (RIT), an ATV used to treat human immunodeficiency virus infection and coronavirus disease 2019, on anaerobic digestion (AD) of WAS to reveal the mechanisms by which it interferes with anaerobic flora. The dosage influence results showed that methane production in AD of WAS decreased by 46.56 % when RIT concentration was increased to 1000 μg/kg total suspended solids (TSS). The AD staging test revealed that RIT mainly stimulated microbial synthesis of the extracellular polymeric substance (EPS), limiting organic matter solubilization. At 500 μg/kg TSS, RIT decreased CHO and CHON levels in dissolved organic matter by 23.12 % and 56.68 %, respectively, significantly reducing substrate availability to microorganisms. Metagenomic analysis of microbial functional gene sets revealed that RIT had greater inhibitory effects on protein and amino acid metabolism than on carbohydrate metabolism. Under RIT stress, methanogens switched from hydrogenotrophic and acetotrophic methanogenesis to methylotrophic and acetotrophic methanogenesis.}, } @article {pmid39236503, year = {2024}, author = {Wang, D and Meng, Y and Huang, LN and Zhang, XX and Luo, X and Meng, F}, title = {A comprehensive catalog encompassing 1376 species-level genomes reveals the core community and functional diversity of anammox microbiota.}, journal = {Water research}, volume = {266}, number = {}, pages = {122356}, doi = {10.1016/j.watres.2024.122356}, pmid = {39236503}, issn = {1879-2448}, mesh = {*Microbiota ; Bacteria/genetics/classification/metabolism ; Metagenome ; Wastewater/microbiology ; }, abstract = {Research on the microbial community and function of the anammox process for environmentally friendly wastewater treatment has achieved certain success, which may mean more universal insights are needed. However, the comprehensive understanding of the anammox process is constrained by the limited taxonomic assignment and functional characterization of anammox microbiota, primarily due to the scarcity of high-quality genomes for most organisms. This study reported a global genome catalog of anammox microbiotas based on numerous metagenomes obtained from both lab- and full-scale systems. A total of 1376 candidate species from 7474 metagenome-assembled genomes were used to construct the genome catalog, providing extensive microbial coverage (averaged of 92.40 %) of anammox microbiota. Moreover, a total of 64 core genera and 44 core species were identified, accounting for approximately 64.25 % and 43.97 %, respectively, of anammox microbiota. The strict core genera encompassed not only functional bacteria (e.g., Brocadia, Desulfobacillus, Zeimonas, and Nitrosomonas) but also two candidate genera (UBA12294 and OLB14) affiliated with the order Anaerolineales. In particular, core denitrifying bacteria with observably taxonomic diversity exhibited diverse functional profiles; for instance, the potential of carbohydrate metabolism in Desulfobacillus and Zeimonas likely improves the mixotrophic lifestyle of anammox microbiota. Besides, a noteworthy association was detected between anammox microbiota and system type. Microbiota in coupling system exhibited complex diversity and interspecies interactions by limiting numerous core denitrifying bacteria. In summary, the constructed catalog substantially expands our understanding of the core community and their functions of anammox microbiota, providing a valuable resource for future studies on anammox systems.}, } @article {pmid39235833, year = {2024}, author = {Hsouna, J and Gritli, T and Ilahi, H and Han, JC and Ellouze, W and Zhang, XX and Mansouri, M and Rahi, P and El Idrissi, MM and Lamrabet, M and Courty, PE and Wipf, D and Bekki, A and Tambong, JT and Mnasri, B}, title = {Rhizobium aouanii sp. nov., efficient nodulating rhizobia isolated from Acacia saligna roots in Tunisia.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {74}, number = {9}, pages = {}, pmid = {39235833}, issn = {1466-5034}, mesh = {*Phylogeny ; *Rhizobium/genetics/classification/isolation & purification ; *DNA, Bacterial/genetics ; *Acacia/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Sequence Analysis, DNA ; *Bacterial Typing Techniques ; *Fatty Acids/analysis ; Tunisia ; *Nucleic Acid Hybridization ; *Root Nodules, Plant/microbiology ; Genes, Essential/genetics ; Genes, Bacterial ; Base Composition ; Symbiosis ; }, abstract = {Three bacterial strains, 1AS14I[T], 1AS12I and 6AS6, isolated from root nodules of Acacia saligna, were characterized using a polyphasic approach. Phylogenetic analysis based on rrs sequences placed all three strains within the Rhizobium leguminosarum complex. Further phylogeny, based on 1 756 bp sequences of four concatenated housekeeping genes (recA, atpD, glnII and gyrB), revealed their distinction from known rhizobia species of the R. leguminosarum complex (Rlc), forming a distinct clade. The closest related species, identified as Rhizobium laguerreae, with a sequence identity of 96.4% based on concatenated recA-atpD-glnII-gyrB sequences. The type strain, 1AS14I[T], showed average nucleotide identity (ANI) values of 94.9, 94.3 and 94.1% and DNA-DNA hybridization values of 56.1, 57.4 and 60.0% with the type strains of closest known species: R. laguerreae, Rhizobium acaciae and 'Rhizobium indicum', respectively. Phylogenomic analyses using 81 up-to-date bacteria core genes and the Type (Strain) Genome Server pipeline further supported the uniqueness of strains 1AS14I[T], 1AS12I and 6AS6. The relatedness of the novel strains to NCBI unclassified Rhizobium sp. (396 genomes) and metagenome-derived genomes showed ANI values from 76.7 to 94.8% with a species-level cut-off of 96%, suggesting that strains 1AS14I, 1AS12I and 6AS6 are a distinct lineage. Additionally, differentiation of strains 1AS14I[T], 1AS12I and 6AS6 from their closest phylogenetic neighbours was achieved using phenotypic, physiological and fatty acid content analyses. Based on the genomic, phenotypic and biochemical data, we propose the establishment of a novel rhizobial species, Rhizobium aouanii sp. nov., with strain 1AS14I[T] designated as the type strain (=DSM 113914[T]=LMG 33206[T]). This study contributes to the understanding of microbial diversity in nitrogen-fixing symbioses, specifically within Acacia saligna ecosystems in Tunisia.}, } @article {pmid39235751, year = {2025}, author = {Lemée, P and Bridier, A}, title = {Bioinformatic Pipeline for Profiling Foodborne Bacterial Ecology and Resistome from Short-Read Metagenomics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2852}, number = {}, pages = {289-309}, pmid = {39235751}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; *Computational Biology/methods ; *Food Microbiology/methods ; *Bacteria/genetics ; *High-Throughput Nucleotide Sequencing/methods ; Metagenome ; Microbiota/genetics ; }, abstract = {Next-generation sequencing revolutionized food safety management these last years providing access to a huge quantity of valuable data to identify, characterize, and monitor bacterial pathogens on the food chain. Shotgun metagenomics emerged as a particularly promising approach as it enables in-depth taxonomic profiling and functional investigation of food microbial communities. In this chapter, we provide a comprehensive step-by-step bioinformatical workflow to characterize bacterial ecology and resistome composition from metagenomic short-reads obtained by shotgun sequencing.}, } @article {pmid39235268, year = {2024}, author = {Sudarshan, AS and Dai, Z and Gabrielli, M and Oosthuizen-Vosloo, S and Konstantinidis, KT and Pinto, AJ}, title = {New Drinking Water Genome Catalog Identifies a Globally Distributed Bacterial Genus Adapted to Disinfected Drinking Water Systems.}, journal = {Environmental science & technology}, volume = {58}, number = {37}, pages = {16475-16487}, pmid = {39235268}, issn = {1520-5851}, mesh = {*Drinking Water/microbiology ; Disinfection ; Bacteria/genetics ; Microbiota ; Genome, Bacterial ; Metagenome ; }, abstract = {Genome-resolved insights into the structure and function of the drinking water microbiome can advance the effective management of drinking water quality. To enable this, we constructed and curated thousands of metagenome-assembled and isolate genomes from drinking water distribution systems globally to develop a Drinking Water Genome Catalog (DWGC). The current DWGC disproportionately represents disinfected drinking water systems due to a paucity of metagenomes from nondisinfected systems. Using the DWGC, we identify core genera of the drinking water microbiome including a genus (UBA4765) within the order Rhizobiales that is frequently detected and highly abundant in disinfected drinking water systems. We demonstrate that this genus has been widely detected but incorrectly classified in previous amplicon sequencing-based investigations of the drinking water microbiome. Further, we show that a single genome variant (genomovar) within this genus is detected in 75% of drinking water systems included in this study. We propose a name for this uncultured bacterium as "Raskinella chloraquaticus" and describe the genus as "Raskinella" (endorsed by SeqCode). Metabolic annotation and modeling-based predictions indicate that this bacterium is capable of necrotrophic growth, is able to metabolize halogenated compounds, proliferates in a biofilm-based environment, and shows clear indications of disinfection-mediated selection.}, } @article {pmid39235252, year = {2024}, author = {Sweet, P and Burroughs, M and Jang, S and Contreras, L}, title = {TolRad, a model for predicting radiation tolerance using Pfam annotations, identifies novel radiosensitive bacterial species from reference genomes and MAGs.}, journal = {Microbiology spectrum}, volume = {12}, number = {10}, pages = {e0383823}, pmid = {39235252}, issn = {2165-0497}, support = {HDTRA1-17-1-0025//DOD | Defense Threat Reduction Agency (DTRA)/ ; FA9550-20-1-0131//DOD | USAF | AMC | Air Force Office of Scientific Research (AFOSR)/ ; W911NF22S0002//DNI | Intelligence Advanced Research Projects Activity (IARPA)/ ; }, mesh = {*Radiation Tolerance/genetics ; *Bacteria/genetics/radiation effects/classification ; *Genome, Bacterial ; Humans ; Radiation, Ionizing ; Bacterial Proteins/genetics/metabolism ; Microbiota/genetics/radiation effects ; Proteome ; Metagenome ; Molecular Sequence Annotation ; }, abstract = {UNLABELLED: The trait of ionizing radiation (IR) tolerance is variable between bacterium, with species succumbing to acute doses as low as 60 Gy and extremophiles able to survive doses exceeding 10,000 Gy. While survival screens have identified multiple highly radioresistant bacteria, such systemic searches have not been conducted for IR-sensitive bacteria. The taxonomy-level diversity of IR sensitivity is poorly understood, as are genetic elements that influence IR sensitivity. Using the protein domain (Pfam) frequencies from 61 bacterial species with experimentally determined D10 values (the dose at which only 10% of the population survives), we trained TolRad, a random forest binary classifier, to distinguish between radiosensitive (D10 < 200 Gy) and radiation-tolerant (D10 > 200 Gy) bacteria. On untrained species, TolRad had an accuracy of 0.900. We applied TolRad to 152 UniProt-hosted bacterial proteomes associated with the human microbiome, including 37 strains from the ATCC Human Microbiome Collection, and classified 34 species as radiosensitive. Whereas IR-sensitive species (D10 < 200 Gy) in the training data set had been confined to the phylum Proteobacterium, this initial TolRad screen identified radiosensitive bacteria in two additional phyla. We experimentally validated the predicted radiosensitivity of a Bacteroidota species from the human microbiome. To demonstrate that TolRad can be applied to metagenome-assembled genomes (MAGs), we tested the accuracy of TolRad on Egg-NOG assembled proteomes (0.965) and partial proteomes. Finally, three collections of MAGs were screened using TolRad, identifying further phyla with radiosensitive species and suggesting that environmental conditions influence the abundance of radiosensitive bacteria.

IMPORTANCE: Bacterial species have vast genetic diversity, allowing for life in extreme environments and the conduction of complex chemistry. The ability to harness the full potential of bacterial diversity is hampered by the lack of high-throughput experimental or bioinformatic methods for characterizing bacterial traits. Here, we present a computational model that uses de novo-generated genome annotations to classify a bacterium as tolerant of ionizing radiation (IR) or as radiosensitive. This model allows for rapid screening of bacterial communities for low-tolerance species that are of interest for both mechanistic studies into bacterial sensitivity to IR and biomarkers of IR exposure.}, } @article {pmid39235142, year = {2024}, author = {Zhao, HX and He, H and Zeng, C and Zhang, TY and Hu, CY and Pan, R and Xu, MY and Tang, YL and Xu, B}, title = {Overlooked Role of Fungi in Drinking Water Taste and Odor Issues.}, journal = {Environmental science & technology}, volume = {58}, number = {40}, pages = {17817-17827}, doi = {10.1021/acs.est.4c02575}, pmid = {39235142}, issn = {1520-5851}, mesh = {*Drinking Water/microbiology ; *Odorants ; *Fungi ; *Taste ; Water Purification ; }, abstract = {Taste and odor (T&O) are among the most frequently encountered aesthetic issues in drinking water. While fungi have been reported to produce offensive odors, their contribution to T&O in drinking water remains understudied and often overlooked. In this study, the profiles of fungal community and odorants produced by 10 native fungal isolates were investigated in 36 samples collected from two drinking water treatment plants and a premise plumbing system. A total of 17 odorants were identified with Penicillium, Aspergillus, Paecilomyces, and Alternaria genera exhibiting the highest odorant yields. Significant concentrations of musty/earthy compounds were produced by these fungal isolates, such as 2-methylisoborneol (2-MIB) (26-256 ng/L), geosmin (10-13 ng/L), and 2-isobutyl-3-methoxy-pyrazine (IBMP) (3-13 ng/L). The high odor activity value of the odorants primarily occurred within 4 d, while toxicity continued to increase during the 8 d incubation. UV treatment in premise plumbing significantly (p < 0.05) reduced the gene read counts of Ascomycota phylum, Aspergillus spp., Fusarium spp., Rhizopus spp., and Trichoderma spp., by 2.3-4.0 times. These findings underscore the previously underestimated role of fungi in contributing to T&O issues in drinking water and corresponding risks to consumers and indicate UV as a promising strategy for fungal control in drinking water.}, } @article {pmid39235032, year = {2024}, author = {Zhou, Y and Cheng, SL and Fang, HJ and Yang, Y and Guo, YF and Li, YN and Shi, FY and Wang, H and Chen, L}, title = {[Research advances in the response of soil nitrogen emissions from peatlands to climate warming and drying].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {35}, number = {6}, pages = {1725-1734}, doi = {10.13287/j.1001-9332.202406.030}, pmid = {39235032}, issn = {1001-9332}, mesh = {*Soil/chemistry ; *Nitrogen/analysis/metabolism ; *Climate Change ; *Global Warming ; *Soil Microbiology ; Ecosystem ; Droughts ; Nitrous Oxide/analysis/metabolism ; }, abstract = {Climate warming and drying has led to a sharp increase in nitrogen (N) emissions from the boreal peatland soils, but the underlying microbial-mediated mechanism is still unclear. We reviewed the responses of soil N transformation and emission in alpine peatland to temperature increases and water table changes, the interaction between soil anaerobic ammonia oxidation (Anammox) and NO3[-] dissimilatory reduction processes, and soil N2O production pathways and their contributions. There are several knowledge gaps. First, the amount of N loss in peatlands in alpine areas is seriously underestimated because most studies focused only on soil N2O emissions and ignored the release of N2. Second, the contribution of Anammox process to N2 emissions from peatlands is not quantified. Third, there is a lack of quantification of the relative contributions of Anammox, bacterial denitrification, and fungal co-denitrification processes to N2 loss. Finally, the decoupling mechanism of Anammox and NO3[-] reduction processes under a warming and drying climate scenario is not clear. Considering aforementioned shortages in previous studies, we proposed the directions and contents for future research. Through building an experimental platform with field warming and water level controlling, combining stable isotope, molecular biology, and metagenomics technology, the magnitude, composition ratio and main controlling factors of N emissions (N2O, NO, and N2) in boreal peatlands should be systematically investigated. The interaction among the main N loss processes in soils as well as the relative contributions of nitrification, anaerobic ammonia oxidation, and denitrification to N2O and N2 productions should be investigated and quantified. Furthermore, the sensitive microbial groups and the coupling between soil N transformations and microbial community succession should be clarified to reveal the microbiological mechanism underlying the responses of soil N turnover process to climate warming and drying.}, } @article {pmid39234039, year = {2024}, author = {Wang, L and Zhang, W and Dai, S and Gao, Y and Zhu, C and Yu, Y}, title = {Correlation between the gut microbiota characteristics of hosts with severe acute pancreatitis and secondary intra-abdominal infection.}, journal = {Frontiers in medicine}, volume = {11}, number = {}, pages = {1409409}, pmid = {39234039}, issn = {2296-858X}, abstract = {OBJECTIVE: The objective of the study is to investigate the changes in the composition of intestinal microecology in severe acute pancreatitis (SAP) patients with or without intra-abdominal infection and also to analyze the expression of antibiotic resistance genes to provide evidence for early warning of infectious diseases and the rational use of antibiotics.

METHODS: Twenty patients with SAP were enrolled in the study. According to whether the enrolled patients had a secondary intra-abdominal infection, they were divided into two groups, each consisting of 10 patients. Stool specimens were collected when the patients were admitted to the emergency intensive care unit (EICU), and nucleic acid extraction was performed. Next-generation gene sequencing was used to compare the differences in intestinal microflora diversity and drug resistance gene expression between the two groups.

RESULTS: The gut microbiota of patients in the infection group exhibited distribution on multiple clustered branches with some intra-group heterogeneity, and their flora diversity was compromised. The infected group showed an enrichment of various opportunistic bacteria in the gut microbiota, along with a high number of metabolic functions, stress functions to external signals, and genes associated with pathogenesis. Drug resistance genes were expressed in the gut microbiota of both groups, but their abundance was significantly lower in the non-infected group.

CONCLUSION: The intestinal microbiota of patients in the infection group exhibited distribution on multiple clustered branches with some intra-group heterogeneity, and their flora diversity was compromised. Additionally, drug resistance genes were expressed in the gut microbiota of both groups, although their abundance was significantly lower in the non-infected group.}, } @article {pmid39233907, year = {2024}, author = {Yuan, J and Wang, L and Zhang, W and Deng, C and Li, Q and Meng, Y and Chen, Y}, title = {Performance of metagenomic Next-Generation Sequencing and metagenomic Nanopore Sequencing for the diagnosis of tuberculosis in HIV-positive patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1423541}, pmid = {39233907}, issn = {2235-2988}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Male ; *Tuberculosis/diagnosis/microbiology ; Female ; *HIV Infections/complications ; *Mycobacterium tuberculosis/genetics/isolation & purification ; Retrospective Studies ; Adult ; *Sensitivity and Specificity ; Middle Aged ; *Coinfection/diagnosis/microbiology/virology ; *Nanopore Sequencing/methods ; *Metagenomics/methods ; }, abstract = {BACKGROUND: Patients who were infected by the Human Immunodeficiency Virus (HIV) could have weakened immunity that is complicated by opportunistic infections, especially for Mycobacterium tuberculosis (MTB). Notably, the HIV-MTB co-infection will accelerate the course of disease progress and greatly increase the mortality of patients. Since the traditional diagnostic methods are time-consuming and have low sensitivity, we aim to investigate the performance of mNGS (metagenomic Next-Generation Sequencing) and mNPS (metagenomic NanoPore Sequencing) for the rapid diagnosis of tuberculosis in HIV-infected patients.

METHODS: The 122 HIV-infected patients were enrolled for the retrospective analysis. All of the patients underwent traditional microbiological tests, mNGS, and (or) mNPS tests. The clinical comprehensive diagnosis was used as the reference standard to compare the diagnostic performance of culture, mNGS, and mNPS on tuberculosis. We also investigate the diagnostic value of mNGS and mNPS on mixed-infection. Furthermore, the treatment adjustment directed by mNGS and mNPS was analyzed.

RESULTS: Compared with the composite reference standard, the culture showed 42.6% clinical sensitivity and 100% specificity, and the OMT(other microbiological testing) had 38.9% sensitivity and 100% specificity. The mNGS had 58.6% clinical sensitivity and 96.8% specificity, and the mNPS had 68.0% clinical sensitivity and 100% specificity. The proportion of mixed-infection cases (88.9%) in the TB group was higher than those in the non-TB group (54.8%) and the mNGS and mNPS are more competitive on mixed-infection diagnosis compared with the traditional methods. Furthermore, there are 63 patients (69.2%) and 36 patients (63.2%) achieved effective treatment after receiving the detection of mNPS and mNGS, respectively.

CONCLUSION: Our study indicated that mNPS and mNGS have high sensitivity and specificity for TB diagnosis compared with the traditional methods, and mNPS seems to have better diagnostic performance than mNGS. Moreover, mNGS and mNPS showed apparent advantages in detecting mixed infection. The mNPS and mNGS-directed medication adjustment have effective treatment outcomes for HIV-infected patients who have lower immunity.}, } @article {pmid39233549, year = {2025}, author = {Yin, C and Cong, Y and Wang, H and Wang, D and Yang, X and Wang, X and Wang, T}, title = {Pathogenic Detection by Metagenomic Next-generation Sequencing in Spinal Infections.}, journal = {Spine}, volume = {50}, number = {4}, pages = {E70-E75}, pmid = {39233549}, issn = {1528-1159}, mesh = {Humans ; Retrospective Studies ; Male ; *High-Throughput Nucleotide Sequencing/methods ; Female ; Middle Aged ; *Metagenomics/methods ; Adult ; Aged ; Spinal Diseases/microbiology/diagnosis ; Young Adult ; Adolescent ; }, abstract = {STUDY DESIGN: A retrospective, observational study.

OBJECTIVE: To evaluate the ability and value of metagenomic next-generation sequencing (mNGS) in detecting pathogens from spinal infections.

BACKGROUND: The pathogenic diagnosis of primary spinal infection is challenging. The widespread application of mNGs in clinical practice makes it particularly useful in detecting rare, emerging, and atypical complex infectious diseases.

METHODS: From January 2019 to December 2023, 120 samples were retrospectively collected from patients suspected of spinal infections and undergoing treatment. Pairwise comparisons between traditional laboratory tests and mNGS were conducted for all cases.

RESULTS: Among the 120 cases, 95 were diagnosed as spinal infections, while 25 were classified as noninfectious. Microbiological evidence was found in 59 cases, while 36 cases were clinically diagnosed as spinal infections without definitive microbiological evidence. Rare microorganisms such as Aspergillus fumigatus , Taifanglania major , and Coxiella burnetii were detected by mNGS. The positive rate of mNGS was significantly higher at 88.42% compared with microbiological culture (43.16%), P <0.001. At the genus level, mNGS exhibited a consistency rate of 86.44% (51/59) with confirmed microorganisms. MNGS demonstrated very good agreement with clinically confirmed microorganisms at the genus level (κ=0.833). The sensitivity, specificity, positive predictive value, and negative predictive value of mNGS were 86.44%, 92.00%, 96.23%, and 74.19%, respectively.

CONCLUSIONS: The mNGS test exhibits rapidity, efficiency, and accuracy, rendering it of immense diagnostic and therapeutic value in the realm of spinal infection diseases.}, } @article {pmid39233185, year = {2024}, author = {Huang, J and Wang, C and Huang, X and Zhang, Q and Feng, R and Wang, X and Zhang, S and Wang, J}, title = {Long-term effect of phenol, quinoline, and pyridine on nitrite accumulation in the nitrification process: performance, microbial community, metagenomics and molecular docking analysis.}, journal = {Bioresource technology}, volume = {412}, number = {}, pages = {131407}, doi = {10.1016/j.biortech.2024.131407}, pmid = {39233185}, issn = {1873-2976}, mesh = {*Molecular Docking Simulation ; *Nitrification ; *Nitrites/metabolism ; *Quinolines/pharmacology ; *Metagenomics/methods ; *Pyridines/pharmacology/metabolism ; Phenol ; Bacteria/metabolism/drug effects ; Microbiota/drug effects ; Wastewater ; Oxidoreductases/metabolism ; Ammonia/metabolism ; }, abstract = {Phenol, quinoline, and pyridine, commonly found in industrial wastewater, disrupt the nitrification process, leading to nitrite accumulation. This study explores the potential mechanisms through which these biotoxic organic compounds affect nitrite accumulation, using metagenomic and molecular docking analyses. Despite increasing concentrations of these compounds from 40 to 160 mg/L, ammonia nitrogen removal was not hindered, and stable nitrite accumulation rates exceeding 90 % were maintained. Additionally, these compounds inhibited nitrite-oxidizing bacteria (NOB) and enriched ammonia-oxidizing bacteria (AOB) in situ. As the concentration of these compounds rose, protein (PN) and polysaccharide (PS) concentrations also increased, along with a higher PN/PS ratio. Metagenomic analysis further revealed an increase in hao relative abundance, while microbial community analysis showed increased Nitrosomonas abundance, which contributed to nitrite accumulation stability. Molecular docking indicated that these compounds have lower binding energy with hydroxylamine oxidoreductase (HAO) and nitrate reductase (NAR), theoretically supporting the observed sustained nitrite accumulation.}, } @article {pmid39233139, year = {2024}, author = {Chawla, K and Shaji, R and Siddalingaiah, N and P K, SM and M D, S and Lewis, LES and Nagaraja, SB}, title = {Next generation sequencing to detect pathogens causing paediatric community-acquired pneumonia - A systematic review and meta-analysis.}, journal = {Indian journal of medical microbiology}, volume = {52}, number = {}, pages = {100730}, doi = {10.1016/j.ijmmb.2024.100730}, pmid = {39233139}, issn = {1998-3646}, mesh = {Humans ; *Community-Acquired Infections/microbiology/diagnosis ; *High-Throughput Nucleotide Sequencing/methods ; Child ; Anti-Bacterial Agents/therapeutic use ; Pneumonia/diagnosis/microbiology ; Child, Preschool ; Infant ; Bacteria/genetics/isolation & purification/classification ; Adolescent ; }, abstract = {BACKGROUND: Paediatric community-acquired pneumonia (CAP) is a major public health challenge in children, requiring accurate and timely diagnosis of causative pathogens for effective antibiotic treatment. We aimed to explore the utility of next-generation sequencing (NGS) in precise diagnosis of pediatric CAP and its effect on treatment outcome of these children.

METHODS: A systematic review and meta-analysis was conducted to compare NGS-guided antibiotic therapy with conventional methods in pediatric CAP. The study followed PRISMA guidelines and searched for electronic databases including PubMed/MEDLINE, Embase, Scopus, and Web of Sciences from 2012 to 2023. Studies on pediatric CAP (<18 years) using NGS alongside conventional diagnostics, were included.

RESULTS: Database search identified 721 studies and 6 were finally included for review, published between 2019 and 2023. Meta-analysis revealed an overall odds ratio of 2.39 (95 % CI 1.22, 3.56) for NGS vs conventional methods. Detection rates using NGS ranged from 86% to 100 %, surpassing conventional methods (26%-78.51 %). Five out of selected 6 studies (83.33 %) have documented that change in treatment based on NGS finding resulted in clinical improvement of patients. There was no significant heterogeneity and potential bias among the studies. Nearly 80 % of the studies were of good quality.

CONCLUSION: The NGS (particularly metagenomic sequencing) is a promising tool for diagnosing paediatric CAP with high accuracy. It can improve antibiotic usage practices and patient outcomes, potentially reducing antibiotic resistance. Based on meta-analysis, training of healthcare professionals in NGS methodologies and result interpretation is highly recommended.}, } @article {pmid39232827, year = {2024}, author = {Sun, C and Hu, G and Yi, L and Ge, W and Yang, Q and Yang, X and He, Y and Liu, Z and Chen, WH}, title = {Integrated analysis of facial microbiome and skin physio-optical properties unveils cutotype-dependent aging effects.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {163}, pmid = {39232827}, issn = {2049-2618}, support = {2019YFA0905600//National Key Research and Development Program of China/ ; }, mesh = {Adult ; Aged ; Female ; Humans ; Male ; Middle Aged ; Young Adult ; Aging ; *Bacteria/classification/genetics/isolation & purification ; *Face/microbiology ; High-Throughput Nucleotide Sequencing ; Metagenome ; *Microbiota ; Sebum/metabolism ; *Skin/microbiology ; *Skin Aging/physiology ; }, abstract = {BACKGROUND: Our facial skin hosts millions of microorganisms, primarily bacteria, crucial for skin health by maintaining the physical barrier, modulating immune response, and metabolizing bioactive materials. Aging significantly influences the composition and function of the facial microbiome, impacting skin immunity, hydration, and inflammation, highlighting potential avenues for interventions targeting aging-related facial microbes amidst changes in skin physiological properties.

RESULTS: We conducted a multi-center and deep sequencing survey to investigate the intricate interplay of aging, skin physio-optical conditions, and facial microbiome. Leveraging a newly-generated dataset of 2737 species-level metagenome-assembled genomes (MAGs), our integrative analysis highlighted aging as the primary driver, influencing both facial microbiome composition and key skin characteristics, including moisture, sebum production, gloss, pH, elasticity, and sensitivity. Further mediation analysis revealed that skin characteristics significantly impacted the microbiome, mostly as a mediator of aging. Utilizing this dataset, we uncovered two consistent cutotypes across sampling cities and identified aging-related microbial MAGs. Additionally, a Facial Aging Index (FAI) was formulated based on the microbiome, uncovering the cutotype-dependent effects of unhealthy lifestyles on skin aging. Finally, we distinguished aging related microbial pathways influenced by lifestyles with cutotype-dependent effect.

CONCLUSIONS: Together, our findings emphasize aging's central role in facial microbiome dynamics, and support personalized skin microbiome interventions by targeting lifestyle, skin properties, and aging-related microbial factors. Video Abstract.}, } @article {pmid39232674, year = {2024}, author = {Pan, TJ and Luo, WW and Zhang, SS and Xie, JY and Xu, Z and Zhong, YY and Zou, XF and Gong, HJ and Ye, ML}, title = {The clinical application value of multi-site mNGS detection of patients with sepsis in intensive care units.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {920}, pmid = {39232674}, issn = {1471-2334}, mesh = {Humans ; *Sepsis/diagnosis/microbiology ; *Intensive Care Units ; Male ; Female ; Middle Aged ; Retrospective Studies ; Aged ; *High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; Adult ; Bacteria/isolation & purification/genetics/classification ; Aged, 80 and over ; }, abstract = {BACKGROUND: Sepsis remains a leading cause of mortality in intensive care units, and rapid and accurate pathogen detection is crucial for effective treatment. This study evaluated the clinical application of multi-site metagenomic next-generation sequencing (mNGS) for the diagnosis of sepsis, comparing its performance against conventional methods.

METHODS: A retrospective analysis was conducted on 69 patients with sepsis consecutively admitted to the Department of Intensive Care Medicine, Meizhou People's Hospital. Samples of peripheral blood and infection sites were collected for mNGS and conventional method tests to compare the positive rate of mNGS and traditional pathogen detection methods and the distribution of pathogens. The methods used in this study included a comprehensive analysis of pathogen consistency between peripheral blood and infection site samples. Additionally, the correlation between the pathogens detected and clinical outcomes was investigated.

RESULTS: Of the patients with sepsis, 57.97% experienced dyspnea, and 65.2% had underlying diseases, with hypertension being the most common. mNGS demonstrated a significantly higher pathogen detection rate (88%) compared to the conventional method tests (26%). The pathogen consistency rate was 60% between plasma and bronchoalveolar lavage fluid samples, and that of plasma and local body fluid samples was 63%. The most frequently detected pathogens were gram-negative bacteria, and Klebsiella pneumonia. There were no significant differences in the clinical features between the pathogens.

CONCLUSION: mNGS is significantly superior to conventional methods in pathogen detection. There was a notable high pathogen consistency detection between blood and local body fluid samples, supporting the clinical relevance of mNGS. This study highlights the superiority of mNGS in detecting a broad spectrum of pathogens quickly and accurately.

TRIAL REGISTRATION: Not applicable.}, } @article {pmid39232327, year = {2024}, author = {Wang, D and Zhang, J and Han, W and Wu, P and Deng, L and Wang, W}, title = {Ammonia oxidizing bacteria (AOB) denitrification and bacterial denitrification as the main culprit of high N2O emission in SBR with low C/N ratio wastewater.}, journal = {Journal of environmental management}, volume = {369}, number = {}, pages = {122357}, doi = {10.1016/j.jenvman.2024.122357}, pmid = {39232327}, issn = {1095-8630}, mesh = {*Denitrification ; *Wastewater/chemistry ; *Ammonia/metabolism ; *Bacteria/metabolism ; *Nitrous Oxide/metabolism ; *Nitrogen/metabolism ; Carbon/metabolism ; Bioreactors ; Waste Disposal, Fluid/methods ; Oxidation-Reduction ; }, abstract = {A large amount of greenhouse gas nitrous oxide (N2O) will be produced during the biological nitrogen removal process for organic wastewater of low C/N ratio. One of the effective methods to solve this problem is to incorporate inexpensive carbon source. In this study, raw wastewater (RW) from pig farm, that was not anaerobically digested, was utilized as exogenous carbon in both A/O and SBR aerobic reactor to treat liquid digestate with high ammonia nitrogen and low C/N ratio. The results showed that N2O emission in SBR was higher than that of A/O process under the same nitrogen load. The N2O conversion in the biological nitrogen removal process was investigated by the strategy of integrating stable isotope method and metagenomics. The δO[18]-N2O, δN[15]-N2O, and SP values of the SBR were closer to the denitrification values of Ammonia-Oxidizing Bacteria (AOB) than those of A/O. The abundance of AOB in the SBR reactor was higher than that in the A/O reactor, while the abundance of denitrifying bacteria was lower. The amoA/B/C gene abundance in the SBR was greater than that in the A/O, and the NOS gene abundance was the opposite. The results indicated that both AOB denitrification and bacterial denitrification led to the increase of N2O emissions of the SBR.}, } @article {pmid39232318, year = {2024}, author = {Yadav, P and Kumari, SP and Hooda, S and Gupta, RK and Diwan, P}, title = {Comparative assessment of microbiome and resistome of influent and effluent of sewage treatment plant and common effluent treatment plant located in Delhi, India using shotgun approach.}, journal = {Journal of environmental management}, volume = {369}, number = {}, pages = {122342}, doi = {10.1016/j.jenvman.2024.122342}, pmid = {39232318}, issn = {1095-8630}, mesh = {India ; *Microbiota ; *Sewage/microbiology ; *Wastewater/microbiology ; Drug Resistance, Microbial/genetics ; Bacteria/genetics/drug effects ; Waste Disposal, Fluid ; }, abstract = {Antimicrobial resistance (AMR) is a significant threat that demands surveillance to identify and analyze trends of the emerging antibiotic resistance genes (ARGs) and potential microbial carriers. The influent of the wastewater treatment plants (WWTPs) reflects the microbes derived from the population and effluent being the source of dissemination of potential pathogenic microbes and AMR. The present study aimed to monitor microbial communities and antibiotic resistance genes in WWTPs employing a whole metagenome shotgun sequencing approach. The samples were collected from a sewage treatment plant (STP) and a common effluent treatment plant (CETP) in Delhi, India. The results showed the influent of STP to be rich in Bifidobacterium, Bacteroides, Escherichia, Arcobacter, and Pseudomonas residents of gut microbiota and known to cause diseases in humans and animals; whereas the CETP sample was abundant in Aeromonas, Escherichia, and Shewanella known to be involved in the degradation of different compounds. Interestingly, the effluent samples from both STPs and CETP were rich in microbial diversity, comprising organic and xenobiotic compound degrading and disease-causing bacteria, indicating the effluent being the source of dissemination of concerning bacteria to the environment. The functional profile at both sites displayed similarity with an abundance of housekeeping function genes as analyzed by Clusters of Orthologous Genes (COG), KEGG Orthology (KO), and subsystem databases. Resistome profiling by MEGARes showed the dominance of ARGs corresponding to beta-lactams having relative abundance ranging from 16% to 34% in all the metagenome datasets, followed by tetracycline (8%-16%), aminoglycosides (7%-9%), multi-drug (5%-9%), and rifampin (3%-9%). Also, AMR genes oxa, ant3-DPRIME, and rpoB, which are of clinical importance were predominantly and most prevalently present in all the samples. The presence of AMR in effluents from both types of treatment plants indicates that wastewater from both sources contributes to the spread of pathogenic bacteria and resistance genes, increasing the environmental AMR burden and therefore requires tertiary treatment before discharge. This work will facilitate further research towards the identification of suitable biomarkers for monitoring antibiotic resistance.}, } @article {pmid39232205, year = {2024}, author = {Quek, S and Hadermann, A and Wu, Y and De Coninck, L and Hegde, S and Boucher, JR and Cresswell, J and Foreman, E and Steven, A and LaCourse, EJ and Ward, SA and Wanji, S and Hughes, GL and Patterson, EI and Wagstaff, SC and Turner, JD and Parry, RH and Kohl, A and Heinz, E and Otabil, KB and Matthijnssens, J and Colebunders, R and Taylor, MJ}, title = {Diverse RNA viruses of parasitic nematodes can elicit antibody responses in vertebrate hosts.}, journal = {Nature microbiology}, volume = {9}, number = {10}, pages = {2488-2505}, pmid = {39232205}, issn = {2058-5276}, support = {V474923N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; 11L1323N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; G0A0522N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; BB/V011278/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, mesh = {Animals ; *RNA Viruses/immunology/genetics ; Humans ; *Brugia malayi/immunology/genetics ; Onchocerca volvulus/immunology/genetics ; Vertebrates/virology/immunology/parasitology ; Nematoda/immunology/genetics/virology ; Transcriptome ; Antibody Formation/immunology ; Phylogeny ; RNA Interference ; }, abstract = {Parasitic nematodes have an intimate, chronic and lifelong exposure to vertebrate tissues. Here we mined 41 published parasitic nematode transcriptomes from vertebrate hosts and identified 91 RNA viruses across 13 virus orders from 24 families in ~70% (28 out of 41) of parasitic nematode species, which include only 5 previously reported viruses. We observe widespread distribution of virus-nematode associations across multiple continents, suggesting an ancestral acquisition event and host-virus co-evolution. Characterization of viruses of Brugia malayi (BMRV1) and Onchocerca volvulus (OVRV1) shows that these viruses are abundant in reproductive tissues of adult parasites. Importantly, the presence of BMRV1 RNA in B. malayi parasites mounts an RNA interference response against BMRV1 suggesting active viral replication. Finally, BMRV1 and OVRV1 were found to elicit antibody responses in serum samples from infected jirds and infected or exposed humans, indicating direct exposure to the immune system.}, } @article {pmid39232160, year = {2024}, author = {Chen, J and Jia, Y and Sun, Y and Liu, K and Zhou, C and Liu, C and Li, D and Liu, G and Zhang, C and Yang, T and Huang, L and Zhuang, Y and Wang, D and Xu, D and Zhong, Q and Guo, Y and Li, A and Seim, I and Jiang, L and Wang, L and Lee, SMY and Liu, Y and Wang, D and Zhang, G and Liu, S and Wei, X and Yue, Z and Zheng, S and Shen, X and Wang, S and Qi, C and Chen, J and Ye, C and Zhao, F and Wang, J and Fan, J and Li, B and Sun, J and Jia, X and Xia, Z and Zhang, H and Liu, J and Zheng, Y and Liu, X and Wang, J and Yang, H and Kristiansen, K and Xu, X and Mock, T and Li, S and Zhang, W and Fan, G}, title = {Global marine microbial diversity and its potential in bioprospecting.}, journal = {Nature}, volume = {633}, number = {8029}, pages = {371-379}, pmid = {39232160}, issn = {1476-4687}, mesh = {Antimicrobial Cationic Peptides/genetics/isolation & purification ; *Aquatic Organisms/classification/genetics/isolation & purification ; Archaea/genetics/classification ; Bacteria/genetics/classification ; *Biodiversity ; Biomedical Technology ; *Bioprospecting/trends ; Biotechnology ; CRISPR-Associated Protein 9/genetics/isolation & purification ; CRISPR-Cas Systems/genetics ; Drug Resistance, Bacterial/genetics ; Genome, Archaeal/genetics ; Genome, Bacterial/genetics ; *Geographic Mapping ; *Metagenome/genetics ; Oceans and Seas ; Phylogeny ; Seawater/microbiology ; Water Microbiology ; }, abstract = {The past two decades has witnessed a remarkable increase in the number of microbial genomes retrieved from marine systems[1,2]. However, it has remained challenging to translate this marine genomic diversity into biotechnological and biomedical applications[3,4]. Here we recovered 43,191 bacterial and archaeal genomes from publicly available marine metagenomes, encompassing a wide range of diversity with 138 distinct phyla, redefining the upper limit of marine bacterial genome size and revealing complex trade-offs between the occurrence of CRISPR-Cas systems and antibiotic resistance genes. In silico bioprospecting of these marine genomes led to the discovery of a novel CRISPR-Cas9 system, ten antimicrobial peptides, and three enzymes that degrade polyethylene terephthalate. In vitro experiments confirmed their effectiveness and efficacy. This work provides evidence that global-scale sequencing initiatives advance our understanding of how microbial diversity has evolved in the oceans and is maintained, and demonstrates how such initiatives can be sustainably exploited to advance biotechnology and biomedicine.}, } @article {pmid39232089, year = {2024}, author = {Melo, T and Sousa, CA and Delacour-Estrella, S and Bravo-Barriga, D and Seixas, G}, title = {Characterization of the microbiome of Aedes albopictus populations in different habitats from Spain and São Tomé.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {20545}, pmid = {39232089}, issn = {2045-2322}, mesh = {Animals ; *Aedes/microbiology ; Spain ; *Microbiota ; *Wolbachia/genetics/isolation & purification/physiology ; Female ; *RNA, Ribosomal, 16S/genetics ; Mosquito Vectors/microbiology ; Ecosystem ; Male ; }, abstract = {The mosquito microbiome significantly influences vector competence, including in Aedes albopictus, a globally invasive vector. Describing the microbiome and Wolbachia strains of Ae. albopictus from different regions can guide area-specific control strategies. Mosquito samples from Spain and São Tomé were analyzed using 16S rRNA gene sequencing and metagenomic sequencing. Wolbachia infection patterns were observed by sex and population. Female mosquitoes were blood-fed, a factor considered in analyzing their microbiota. Results revealed a dominance of dual Wolbachia infections, strains A and B, in the microbiome of both populations of Ae. albopictus, especially among females. Both populations shared a core microbiome, although 5 and 9 other genera were only present in Spain and São Tomé populations, respectively. Genera like Pelomonas and Nevskia were identified for the first time in Aedes mosquitoes. This study is the first to describe the Ae. albopictus bacteriome in Spain and São Tomé, offering insights for the development of targeted mosquito control strategies. Understanding the specific microbiome composition can help in designing more effective interventions, such as microbiome manipulation and Wolbachia-based approaches, to reduce vector competence and transmission potential of these mosquitoes.}, } @article {pmid39231974, year = {2024}, author = {Oliver, T and Varghese, N and Roux, S and Schulz, F and Huntemann, M and Clum, A and Foster, B and Foster, B and Riley, R and LaButti, K and Egan, R and Hajek, P and Mukherjee, S and Ovchinnikova, G and Reddy, TBK and Calhoun, S and Hayes, RD and Rohwer, RR and Zhou, Z and Daum, C and Copeland, A and Chen, IA and Ivanova, NN and Kyrpides, NC and Mouncey, NJ and Del Rio, TG and Grigoriev, IV and Hofmeyr, S and Oliker, L and Yelick, K and Anantharaman, K and McMahon, KD and Woyke, T and Eloe-Fadrosh, EA}, title = {Coassembly and binning of a twenty-year metagenomic time-series from Lake Mendota.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {966}, pmid = {39231974}, issn = {2052-4463}, support = {DEB-2025982//NSF | BIO | Division of Environmental Biology (DEB)/ ; DEB-1344254//NSF | BIO | Division of Environmental Biology (DEB)/ ; MCB-0702395//NSF | BIO | Division of Molecular and Cellular Biosciences (MCB)/ ; WIS01516, WIS01789, WIS03004//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; DBI-2011002//NSF | BIO | Division of Biological Infrastructure (DBI)/ ; 89233218CNA000001//U.S. Department of Energy (DOE)/ ; DE-AC05-76RL01830//U.S. Department of Energy (DOE)/ ; DE-AC05-00OR22725//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; 17-SC-20-SC//U.S. Department of Energy (DOE)/ ; }, mesh = {Bacteria/genetics/classification ; *Lakes/microbiology ; *Metagenome ; Metagenomics ; Phylogeny ; }, abstract = {The North Temperate Lakes Long-Term Ecological Research (NTL-LTER) program has been extensively used to improve understanding of how aquatic ecosystems respond to environmental stressors, climate fluctuations, and human activities. Here, we report on the metagenomes of samples collected between 2000 and 2019 from Lake Mendota, a freshwater eutrophic lake within the NTL-LTER site. We utilized the distributed metagenome assembler MetaHipMer to coassemble over 10 terabases (Tbp) of data from 471 individual Illumina-sequenced metagenomes. A total of 95,523,664 contigs were assembled and binned to generate 1,894 non-redundant metagenome-assembled genomes (MAGs) with ≥50% completeness and ≤10% contamination. Phylogenomic analysis revealed that the MAGs were nearly exclusively bacterial, dominated by Pseudomonadota (Proteobacteria, N = 623) and Bacteroidota (N = 321). Nine eukaryotic MAGs were identified by eukCC with six assigned to the phylum Chlorophyta. Additionally, 6,350 high-quality viral sequences were identified by geNomad with the majority classified in the phylum Uroviricota. This expansive coassembled metagenomic dataset provides an unprecedented foundation to advance understanding of microbial communities in freshwater ecosystems and explore temporal ecosystem dynamics.}, } @article {pmid39231841, year = {2024}, author = {Yi, P and Li, Q and Zhou, X and Liang, R and Ding, X and Wu, M and Wang, K and Li, J and Wang, W and Lu, G and Zhu, T}, title = {Inoculation of Saccharomyces cerevisiae for facilitating aerobic composting of acidified food waste.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {43}, pages = {55507-55521}, pmid = {39231841}, issn = {1614-7499}, support = {2022-SF-147//Key Research and Development and Transformation Program of Qinghai Province of China/ ; 32272538//National Natural Science Foundation of China/ ; }, mesh = {*Saccharomyces cerevisiae ; *Composting ; Hydrogen-Ion Concentration ; Food ; Fermentation ; Aerobiosis ; Food Loss and Waste ; }, abstract = {In aerobic composting of food waste, acidification of the material (acidified food waste, AFW) often occurs and consequently leads to failure of fermentation initiation. In this study, we solved this problem by adding Saccharomyces cerevisiae inoculants. The results showed that the inoculation with S. cerevisiae effectively promoted the composting process. In 2 kg composting, inoculation with S. cerevisiae significantly elevated the pile temperatures by 4 ~ 14 °C, accompanied by a rapid increase in pH from 4.5 to 6.0. In 15 kg composting, total acid decreased faster and the thermophilic stage above 50 °C was prolonged by 3 days longer than in the control. The residual oxygen content in the reactor indicated that S. cerevisiae, which proliferated during composting, increased microbial activity and reduced ammonia emission during the thermophilic phase. Cell density analysis showed that compost inoculated with S. cerevisiae promoted thermophilic bacterial propagation. Metagenomic analysis showed that the dominant bacteria in the AFW compost were Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria, and the relative abundance of Bacillus, Thermobacillus, and Thermobifida increased when inoculated with S. cerevisiae. These results indicate that the inoculation of S. cerevisiae is an effective strategy to improve the aerobic composting process of AFW by accelerating the initial phase and altering microbial community structure in the thermophilic phase. Our findings suggest that S. cerevisiae can be applied to aerobic composting of organic wastes to effectively address the problem of acidification.}, } @article {pmid39230701, year = {2024}, author = {Hera, MR and Liu, S and Wei, W and Rodriguez, JS and Ma, C and Koslicki, D}, title = {Metagenomic functional profiling: to sketch or not to sketch?.}, journal = {Bioinformatics (Oxford, England)}, volume = {40}, number = {Suppl 2}, pages = {ii165-ii173}, pmid = {39230701}, issn = {1367-4811}, support = {R01 GM146462/GM/NIGMS NIH HHS/United States ; R01GM146462/GF/NIH HHS/United States ; }, mesh = {*Metagenomics/methods ; *Software ; *Algorithms ; *Metagenome/genetics ; Humans ; Microbiota/genetics ; Databases, Genetic ; }, abstract = {MOTIVATION: Functional profiling of metagenomic samples is essential to decipher the functional capabilities of microbial communities. Traditional and more widely used functional profilers in the context of metagenomics rely on aligning reads against a known reference database. However, aligning sequencing reads against a large and fast-growing database is computationally expensive. In general, k-mer-based sketching techniques have been successfully used in metagenomics to address this bottleneck, notably in taxonomic profiling. In this work, we describe leveraging FracMinHash (implemented in sourmash, a publicly available software), a k-mer-sketching algorithm, to obtain functional profiles of metagenome samples.

RESULTS: We show how pieces of the sourmash software (and the resulting FracMinHash sketches) can be put together in a pipeline to functionally profile a metagenomic sample. We named our pipeline fmh-funprofiler. We report that the functional profiles obtained using this pipeline demonstrate comparable completeness and better purity compared to the profiles obtained using other alignment-based methods when applied to simulated metagenomic data. We also report that fmh-funprofiler is 39-99× faster in wall-clock time, and consumes up to 40-55× less memory. Coupled with the KEGG database, this method not only replicates fundamental biological insights but also highlights novel signals from the Human Microbiome Project datasets.

This fast and lightweight metagenomic functional profiler is freely available and can be accessed here: https://github.com/KoslickiLab/fmh-funprofiler. All scripts of the analyses we present in this manuscript can be found on GitHub.}, } @article {pmid39230289, year = {2024}, author = {Flamholz, ZN and Li, C and Kelly, L}, title = {Improving viral annotation with artificial intelligence.}, journal = {mBio}, volume = {15}, number = {10}, pages = {e0320623}, pmid = {39230289}, issn = {2150-7511}, support = {R01 HL069438/HL/NHLBI NIH HHS/United States ; T32 GM007288/GM/NIGMS NIH HHS/United States ; 2T32GM007288//HHS | National Institutes of Health (NIH)/ ; R01HL069438//HHS | National Institutes of Health (NIH)/ ; }, mesh = {*Metagenomics/methods ; *Artificial Intelligence ; *Genome, Viral/genetics ; *Bacteriophages/genetics/classification ; *Molecular Sequence Annotation/methods ; Metagenome ; High-Throughput Nucleotide Sequencing ; Humans ; }, abstract = {Viruses of bacteria, "phages," are fundamental, poorly understood components of microbial community structure and function. Additionally, their dependence on hosts for replication positions phages as unique sensors of ecosystem features and environmental pressures. High-throughput sequencing approaches have begun to give us access to the diversity and range of phage populations in complex microbial community samples, and metagenomics is currently the primary tool with which we study phage populations. The study of phages by metagenomic sequencing, however, is fundamentally limited by viral diversity, which results in the vast majority of viral genomes and metagenome-annotated genomes lacking annotation. To harness bacteriophages for applications in human and environmental health and disease, we need new methods to organize and annotate viral sequence diversity. We recently demonstrated that methods that leverage self-supervised representation learning can supplement statistical sequence representations for remote viral protein homology detection in the ocean virome and propose that consideration of the functional content of viral sequences allows for the identification of similarity in otherwise sequence-diverse viruses and viral-like elements for biological discovery. In this review, we describe the potential and pitfalls of large language models for viral annotation. We describe the need for new approaches to annotate viral sequences in metagenomes, the fundamentals of what protein language models are and how one can use them for sequence annotation, the strengths and weaknesses of these models, and future directions toward developing better models for viral annotation more broadly.}, } @article {pmid39230261, year = {2024}, author = {Tu, V and Ren, Y and Tanes, C and Mukhopadhyay, S and Daniel, SG and Li, H and Bittinger, K}, title = {A quantitative approach to measure and predict microbiome response to antibiotics.}, journal = {mSphere}, volume = {9}, number = {9}, pages = {e0048824}, pmid = {39230261}, issn = {2379-5042}, support = {SAP # 4100068710//Pennsylvania Department of Health (PA DOH)/ ; //Children's Hospital of Philadelphia (CHOP)/ ; }, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Microbiota/drug effects/genetics ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/drug effects/genetics/classification ; Gastrointestinal Microbiome/drug effects/genetics ; Metagenomics/methods ; Microbial Sensitivity Tests/methods ; Skin/microbiology ; Mouth/microbiology ; Software ; }, abstract = {UNLABELLED: Although antibiotics induce sizable perturbations in the human microbiome, we lack a systematic and quantitative method to measure and predict the microbiome's response to specific antibiotics. Here, we introduce such a method, which takes the form of a microbiome response index (MiRIx) for each antibiotic. Antibiotic-specific MiRIx values quantify the overall susceptibility of the microbiota to an antibiotic, based on databases of bacterial phenotypes and published data on intrinsic antibiotic susceptibility. We applied our approach to five published microbiome studies that carried out antibiotic interventions with vancomycin, metronidazole, ciprofloxacin, amoxicillin, and doxycycline. We show how MiRIx can be used in conjunction with existing microbiome analytical approaches to gain a deeper understanding of the microbiome response to antibiotics. Finally, we generate antibiotic response predictions for the oral, skin, and gut microbiome in healthy humans. Our approach is implemented as open-source software and is readily applied to microbiome data sets generated by 16S rRNA marker gene sequencing or shotgun metagenomics.

IMPORTANCE: Antibiotics are potent influencers of the human microbiome and can be a source for enduring dysbiosis and antibiotic resistance in healthcare. Existing microbiome data analysis methods can quantify perturbations of bacterial communities but cannot evaluate whether the differences are aligned with the expected activity of a specific antibiotic. Here, we present a novel method to quantify and predict antibiotic-specific microbiome changes, implemented in a ready-to-use software package. This has the potential to be a critical tool to broaden our understanding of the relationship between the microbiome and antibiotics.}, } @article {pmid39230075, year = {2024}, author = {Kim, N and Kim, CY and Ma, J and Yang, S and Park, DJ and Ha, SJ and Belenky, P and Lee, I}, title = {MRGM: an enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2393791}, pmid = {39230075}, issn = {1949-0984}, support = {R01 DK125382/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Mice ; *Bacteria/classification/genetics/isolation & purification ; *Genome, Bacterial ; Humans ; Phylogeny ; Diet ; }, abstract = {Mouse gut microbiome research is pivotal for understanding the human gut microbiome, providing insights into disease modeling, host-microbe interactions, and the dietary influence on the gut microbiome. To enhance the translational value of mouse gut microbiome studies, we need detailed and high-quality catalogs of mouse gut microbial genomes. We introduce the Mouse Reference Gut Microbiome (MRGM), a comprehensive catalog with 42,245 non-redundant mouse gut bacterial genomes across 1,524 species. MRGM marks a 40% increase in the known taxonomic diversity of mouse gut microbes, capturing previously underrepresented lineages through refined genome quality assessment techniques. MRGM not only broadens the taxonomic landscape but also enriches the functional landscape of the mouse gut microbiome. Using deep learning, we have elevated the Gene Ontology annotation rate for mouse gut microbial proteins from 3.2% with orthology to 60%, marking an over 18-fold increase. MRGM supports both DNA- and marker-based taxonomic profiling by providing custom databases, surpassing previous catalogs in performance. Finally, taxonomic and functional comparisons between human and mouse gut microbiota reveal diet-driven divergences in their taxonomic composition and functional enrichment. Overall, our study highlights the value of high-quality microbial genome catalogs in advancing our understanding of the co-evolution between gut microbes and their host.}, } @article {pmid39229966, year = {2024}, author = {Garner, E and Maile-Moskowitz, A and Angeles, LF and Flach, CF and Aga, DS and Nambi, I and Larsson, DGJ and Bürgmann, H and Zhang, T and Vikesland, PJ and Pruden, A}, title = {Metagenomic Profiling of Internationally Sourced Sewage Influents and Effluents Yields Insight into Selecting Targets for Antibiotic Resistance Monitoring.}, journal = {Environmental science & technology}, volume = {58}, number = {37}, pages = {16547-16559}, pmid = {39229966}, issn = {1520-5851}, mesh = {*Sewage/microbiology ; *Drug Resistance, Microbial/genetics ; *Metagenomics ; *Wastewater/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/drug effects ; }, abstract = {It has been debated whether wastewater treatment plants (WWTPs) primarily act to attenuate or amplify antibiotic resistance genes (ARGs). However, ARGs are highly diverse with respect to their resistance mechanisms, mobilities, and taxonomic hosts and therefore their behavior in WWTPs should not be expected to be universally conserved. We applied metagenomic sequencing to wastewater influent and effluent samples from 12 international WWTPs to classify the behavior of specific ARGs entering and exiting WWTPs. In total, 1079 different ARGs originating from a variety of bacteria were detected. This included ARGs that could be mapped to assembled scaffolds corresponding to nine human pathogens. While the relative abundance (per 16S rRNA gene) of ARGs decreased during treatment at 11 of the 12 WWTPs sampled and absolute abundance (per mL) decreased at all 12 WWTPs, increases in relative abundance were observed for 40% of the ARGs detected at the 12th WWTP. Also, the relative abundance of mobile genetic elements (MGE) increased during treatment, but the fraction of ARGs known to be transmissible between species decreased, thus demonstrating that increased MGE prevalence may not be generally indicative of an increase in ARGs. A distinct conserved resistome was documented in both influent and effluent across samples, suggesting that well-functioning WWTPs generally attenuate influent antibiotic resistance loads. This work helps inform strategies for wastewater surveillance of antibiotic resistance, highlighting the utility of tracking ARGs as indicators of treatment performance and relative risk reduction.}, } @article {pmid39229615, year = {2024}, author = {Zhang, L and Zhang, Z and Huang, J and Zhou, R and Wu, C}, title = {Revealing salt concentration for microbial balance and metabolite enrichment in secondary fortified fermented soy sauce: A multi-omics perspective.}, journal = {Food chemistry: X}, volume = {23}, number = {}, pages = {101722}, pmid = {39229615}, issn = {2590-1575}, abstract = {This study examined the impact of varying salt concentrations on microbiota, physicochemical properties, and metabolites in a secondary fortified fermentation process using multi-omics techniques. It aimed to determine the influence of salt stress on microbiota shifts and metabolic activities. The findings demonstrated that moderate salt reduction (MS) was found to enhance moromi's flavor and quality, while mitigating the negative effects of excessive low salt (LS). MS samples had 1.22, 1.13, and 2.92 times more amino acid nitrogen (AAN), non-volatiles, and volatiles, respectively, than high salt (HS) samples. In contrast, lactic acid and biogenic amines in LS samples were 1.56 g/100 g and 4115.11 mg/kg, respectively, decreasing to 0.15 g/100 g and 176.76 mg/kg in MS samples. Additionally, the contents of ethanol and small peptides increased in MS due to the growth of specific functional microorganisms such as Staphylococcus gallinarum, Weissella confusa, and Zygosaccharomyces rouxii, while food-borne pathogens were inhibited. Network analysis revealed that the core microbial interactions were enhanced in MS samples, promoting a balanced fermentation environment. Redundancy analysis (RDA) and correlation analyses underscored that the physicochemical properties significantly impacted bacterial community structure and the correlations between key microbes and flavor compounds. These findings provided a theoretical foundation for developing innovative reduced-salt fermentation techniques, contributing to the sustainable production of high-quality soy sauce.}, } @article {pmid39229329, year = {2024}, author = {Li, J and Liu, L and Gao, Z and Chuai, X and Liu, X and Zhang, X and Zhang, X and Su, X and Xu, Q and Deng, Z}, title = {Bronchoalveolar Lavage Fluid Metagenomic Second-Generation Sequencing Assists in Guiding the Treatment of Visceral Leishmaniasis: A Case Report.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {3769-3775}, pmid = {39229329}, issn = {1178-6973}, abstract = {PURPOSE: The incidence of visceral leishmaniasis (VL), a global infectious disease, has been on the rise in China's Hebei province. When patients achieve clinical cure, they often do not reach an etiological cure, which may lead to recurrence of the disease. Here, we report a case of visceral leishmaniasis with a negative blood smear and bone marrow cytology.

PATIENTS AND METHODS: A 65-year-old man and bronchoalveolar lavage fluid mNGS.

RESULTS: A 65-year-old man developed a chronic fever, anorexia, splenomegaly, and pancytopenia. The blood metagenomic second-generation sequencing (mNGS) revealed Leishmania sequence readings, which led to the diagnosis of VL. After sodium antimony gluconate treatment, the blood smear and bone marrow cytology revealed no Leishmania bodies. However, pancytopenia and respiratory failure did not fully subside, and cardiotoxic damage emerged. The bronchoalveolar lavage fluid (BALF) mNGS was performed to detect the pathogen. Through BALF mNGS, Leishmania sequence was still detectable. Therefore, after the ECG returned to normal, antimony sodium gluconate was administered as a next course of treatment.

CONCLUSION: BALF mNGS may assist in evaluating the therapeutic efficacy of VL with respiratory failure, especially in patients with negative blood and bone marrow cytology.}, } @article {pmid39229115, year = {2024}, author = {Fan, P and Ni, M and Fan, Y and Ksiezarek, M and Fan, P}, title = {Predictive power of different Akkermansia phylogroups in clinical response to PD-1 blockade against non-small cell lung cancer.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.08.21.608814}, pmid = {39229115}, issn = {2692-8205}, abstract = {Immune checkpoint blockade has emerged as a promising form of cancer therapy. However, only some patients respond to checkpoint inhibitors, while a significant proportion of patients do not, calling for the discovery of reliable biomarkers. Recent studies reported the importance of the gut microbiome in the clinical response to PD-1 blockade against advanced non-small cell lung cancer (NSCLC), highlighting Akkermansia muciniphila as a candidate biomarker. Motivated by the genomic and phenotypic differences across Akkermansia muciniphila strains and Akkermansia (Akk) phylogroups (AmIa, AmIb, AmII, AmIII and AmIV), we analyzed fecal metagenomic sequencing data from three publicly available NSCLC cohorts (n=425). Encouragingly, we found that patients' responses to PD-1 blockade are significantly different across different Akk phylogroups, highlighting the relatively stronger association between AmIa and positive response than the other phylogroups. We built a machine learning model based on Akk gene profiles, which improved the predictive power and shed light on a group of Akk genes that may be associated with the response to PD-1 blockade. In summary, our study underlines the benefits of high-resolution analysis of Akk genomes in the search for biomarkers that may improve the prediction of patients' responses to cancer immunotherapy.}, } @article {pmid39229008, year = {2024}, author = {Clark, CM and Kwan, JC}, title = {Creating and leveraging bespoke large-scale knowledge graphs for comparative genomics and multi-omics drug discovery with SocialGene.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39229008}, issn = {2692-8205}, support = {R35 GM133776/GM/NIGMS NIH HHS/United States ; T15 LM007359/LM/NLM NIH HHS/United States ; }, abstract = {The rapid expansion of multi-omics data has transformed biological research, offering unprecedented opportunities to explore complex genomic relationships across diverse organisms. However, the vast volume and heterogeneity of these datasets presents significant challenges for analyses. Here we introduce SocialGene, a comprehensive software suite designed to collect, analyze, and organize multi-omics data into structured knowledge graphs, with the ability to handle small projects to repository-scale analyses. Originally developed to enhance genome mining for natural product drug discovery, SocialGene has been effective across various applications, including functional genomics, evolutionary studies, and systems biology. SocialGene's concerted Python and Nextflow libraries streamline data ingestion, manipulation, aggregation, and analysis, culminating in a custom Neo4j database. The software not only facilitates the exploration of genomic synteny but also provides a foundational knowledge graph supporting the integration of additional diverse datasets and the development of advanced search engines and analyses. This manuscript introduces some of SocialGene's capabilities through brief case studies including targeted genome mining for drug discovery, accelerated searches for similar and distantly related biosynthetic gene clusters in biobank-available organisms, integration of chemical and analytical data, and more. SocialGene is free, open-source, MIT-licensed, designed for adaptability and extension, and available from github.com/socialgene.}, } @article {pmid39228743, year = {2024}, author = {Jules, E and Decker, C and Bixler, BJ and Ahmed, A and Zhou, ZC and Arora, I and Tafesse, H and Dakanay, H and Bombin, A and Wang, E and Ingersoll, J and Bifulco, K and Frediani, JK and Parsons, R and Sullivan, J and Greenleaf, M and Waggoner, JJ and Martin, GS and Lam, WA and Piantadosi, A}, title = {Respiratory virus detection and sequencing from negative SARS-CoV-2 rapid antigen tests.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {39228743}, support = {U54 EB027690/EB/NIBIB NIH HHS/United States ; UL1 TR002378/TR/NCATS NIH HHS/United States ; }, abstract = {Genomic epidemiology offers important insight into the transmission and evolution of respiratory viruses. We used metagenomic sequencing from negative SARS-CoV-2 antigen tests to identify a wide range of respiratory viruses and generate full genome sequences, offering a streamlined mechanism for broad respiratory virus genomic surveillance.}, } @article {pmid39228385, year = {2024}, author = {Xu, ZX and Zeng, B and Chen, S and Xiao, S and Jiang, LG and Li, X and Wu, YF and You, LX}, title = {Soil microbial community composition and nitrogen enrichment responses to the operation of electric power substation.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1453162}, pmid = {39228385}, issn = {1664-302X}, abstract = {The surge in global energy demand mandates a significant expansion of electric power substations. Nevertheless, the ecological consequences of electric power substation operation, particularly concerning the electromagnetic field, on soil microbial communities and nitrogen enrichment remain unexplored. In this study, we collected soil samples from six distinct sites at varying distances from an electric power substation in Xintang village, southeastern China, and investigated the impacts of electromagnetic field on the microbial diversity and community structures employing metagenomic sequencing technique. Our results showed discernible dissimilarities in the fungal community across the six distinct sites, each characterized by unique magnetic and electric intensities, whereas comparable variations were not evident within bacterial communities. Correlation analysis revealed a diminished nitrogen fixation capacity at the site nearest to the substation, characterized by low moisture content, elevated pH, and robust magnetic induction intensity and electric field intensity. Conversely, heightened nitrification processes were observed at this location compared to others. These findings were substantiated by the relative abundance of key genes associated with ammonium nitrogen and nitrate nitrogen production. This study provides insights into the relationships between soil microbial communities and the enduring operation of electric power substations, thereby contributing fundamental information essential for the rigorous environmental impact assessments of these facilities.}, } @article {pmid39227168, year = {2024}, author = {Salmaso, N and Cerasino, L and Pindo, M and Boscaini, A}, title = {Taxonomic and functional metagenomic assessment of a Dolichospermum bloom in a large and deep lake south of the Alps.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {10}, pages = {}, pmid = {39227168}, issn = {1574-6941}, support = {CN00000033//European Union/ ; }, mesh = {*Lakes/microbiology ; *Metagenomics ; *Metagenome ; *Phylogeny ; Eutrophication ; Cyanobacteria/genetics/classification/growth & development/metabolism ; Aphanizomenon/genetics/growth & development/metabolism ; }, abstract = {Untargeted genetic approaches can be used to explore the high metabolic versatility of cyanobacteria. In this context, a comprehensive metagenomic shotgun analysis was performed on a population of Dolichospermum lemmermannii collected during a surface bloom in Lake Garda in the summer of 2020. Using a phylogenomic approach, the almost complete metagenome-assembled genome obtained from the analysis allowed to clarify the taxonomic position of the species within the genus Dolichospermum and contributed to frame the taxonomy of this genus within the ADA group (Anabaena/Dolichospermum/Aphanizomenon). In addition to common functional traits represented in the central metabolism of photosynthetic cyanobacteria, the genome annotation uncovered some distinctive and adaptive traits that helped define the factors that promote and maintain bloom-forming heterocytous nitrogen-fixing Nostocales in oligotrophic lakes. In addition, genetic clusters were identified that potentially encode several secondary metabolites that were previously unknown in the populations evolving in the southern Alpine Lake district. These included geosmin, anabaenopetins, and other bioactive compounds. The results expanded the knowledge of the distinctive competitive traits that drive algal blooms and provided guidance for more targeted analyses of cyanobacterial metabolites with implications for human health and water resource use.}, } @article {pmid39226954, year = {2024}, author = {Zhang, Z and Yang, H and Linghu, M and Li, J and Chen, C and Wang, B}, title = {Cattle manure composting driven by a microbial agent: A coupled mechanism involving microbial community succession and organic matter conversion.}, journal = {The Science of the total environment}, volume = {952}, number = {}, pages = {175953}, doi = {10.1016/j.scitotenv.2024.175953}, pmid = {39226954}, issn = {1879-1026}, mesh = {*Composting ; *Manure/microbiology ; Animals ; Cattle ; Microbiota ; Soil Microbiology ; Bacillus/physiology ; }, abstract = {Aerobic composting has been used as a mainstream treatment technology for agricultural solid waste resourcing. In the present study, we investigated the effects and potential mechanisms of the addition of a microbial agent (LD) prepared by combining Bacillus subtilis, Bacillus paralicheniformis and Irpex lacteus in improving the efficiency of cattle manure composting. Our results showed that addition of 1.5 % LD significantly accelerated compost humification, i.e., the germination index and lignocellulose degradation rate of the final compost product reached values of 92.20 and 42.29 %, respectively. Metagenomic sequencing results showed that inoculation of cattle manure with LD increased the abundance of functional microorganisms. LD effectively promoted the production of humus precursors, which then underwent reactions through synergistic abiotic and biotic pathways to achieve compost humification. This research provides a theoretical basis for the study of microbial enhancement strategies and humus formation mechanisms in the composting of livestock manure.}, } @article {pmid39226940, year = {2024}, author = {Wang, M and Li, Y and Peng, H and Liu, K and Wang, X and Xiang, W}, title = {A cyclic shift-temperature operation method to train microbial communities of mesophilic anaerobic digestion.}, journal = {Bioresource technology}, volume = {412}, number = {}, pages = {131410}, doi = {10.1016/j.biortech.2024.131410}, pmid = {39226940}, issn = {1873-2976}, mesh = {Anaerobiosis ; *Temperature ; *Biofuels/microbiology ; Bioreactors/microbiology ; Methane/metabolism ; Methanosarcina/metabolism ; Microbiota/physiology ; }, abstract = {Temperature is the critical factor affecting the efficiency and cost of anaerobic digestion (AD). The current work develops a shift-temperature AD (STAD) between 35 °C and 55 °C, intending to optimise microbial community and promote substrate conversion. The experimental results showed that severe inhibition of biogas production occurred when the temperature was firstly increased stepwise from 35 °C to 50 °C, whereas no inhibition was observed at the second warming cycle. When the organic load rate was increased to 6.37 g VS/L/d, the biogas yield of the STAD reached about 400 mL/g VS, nearly double that of the constant-temperature AD (CTAD). STAD promoted the proliferation of Methanosarcina (up to 57.32 %), while severely suppressed hydrogenophilic methanogens. However, when the temperature was shifted to 35 °C, most suppressed species recovered quickly and the excess propionic acid was quickly consumed. Metagenomic analysis showed that STAD also promoted gene enrichment related to pathways metabolism, membrane functions, and methyl-based methanogenesis.}, } @article {pmid39226813, year = {2024}, author = {Guan, X and Xu, Y and Zhang, D and Li, H and Li, R and Shi, R}, title = {Microbial nitrogen transformation regulates pathogenic virulence in soil environment.}, journal = {Journal of environmental management}, volume = {369}, number = {}, pages = {122280}, doi = {10.1016/j.jenvman.2024.122280}, pmid = {39226813}, issn = {1095-8630}, mesh = {*Nitrogen/metabolism ; *Soil Microbiology ; Virulence ; *Soil/chemistry ; }, abstract = {Soil nitrogen addition induces the generation and proliferation of some bacterial virulence, yet the interactive mechanisms between the two remain unclear. Here we investigated the variation of virulence genes (VGs) abundance during soil nitrogen transformation, and explored the biological mechanism and key pathways involved in the regulation of VGs by nitrogen transformation. The results showed that the diversity and abundance of virulence genes in soil under high nitrogen input (100 mg/kg) were markedly higher than those under low nitrogen input (50 mg/kg), suggesting a trade-off between the prevalence of virulence genes and nitrogen metabolism. Nutritional/metabolic factor, regulation, immune modulation and motility were the dominant virulence types. Linear regression analysis showed that soil nitrogen mineralization and nitrification rate were closely correlated with the abundance of virulence genes, mainly involving adherence, nutritional/metabolic factors and immune modulation (p < 0.05). Structural equations indicated that microbial community succession associated with nitrogen transformation largely contributed to the changes in VGs abundance. Metagenomic analysis revealed that major virulence genes pilE, pchB, and galE were regulated by nitrogen-functional genes gdh, ureC, and amoC, implying that microbial nitrogen transformation influences immune modulation, nutritional/metabolic factors, and adherence-like virulence. The meta-transcriptome reiterated their co-regulation, and the key pathway may be glutamate/urea> α-ketoglutarate/ammonia > pyruvate/amino acid. The outcome provides strong evidence on the linkage between microbial nitrogen transformation and pathogenic virulence factors development in the soil environment, which will aid in the effective suppression of the prevalence of soil pathogenic virulence.}, } @article {pmid39226681, year = {2024}, author = {Yin, Y and Zhu, P and Guo, Y and Li, Y and Chen, H and Liu, J and Sun, L and Ma, S and Hu, C and Wang, H}, title = {Enhancing lower respiratory tract infection diagnosis: implementation and clinical assessment of multiplex PCR-based and hybrid capture-based targeted next-generation sequencing.}, journal = {EBioMedicine}, volume = {107}, number = {}, pages = {105307}, pmid = {39226681}, issn = {2352-3964}, mesh = {Humans ; *Multiplex Polymerase Chain Reaction/methods/economics ; *High-Throughput Nucleotide Sequencing/methods ; *Respiratory Tract Infections/diagnosis/microbiology ; Male ; Female ; Middle Aged ; *Bronchoalveolar Lavage Fluid/microbiology ; Aged ; Adult ; Metagenomics/methods ; Sensitivity and Specificity ; Young Adult ; Computational Biology/methods ; Aged, 80 and over ; Retrospective Studies ; Adolescent ; }, abstract = {BACKGROUND: Shotgun metagenomic next-generation sequencing (mNGS) is widely used to detect pathogens in bronchoalveolar lavage fluid (BALF). However, mNGS is complex and expensive. This study explored the feasibility of targeted next-generation sequencing (tNGS) in distinguishing lower respiratory tract infections in clinical practice.

METHODS: We used 229 retrospective BALF samples to establish thresholds and diagnostic values in a prospective cohort of 251 patients. After target pathogen selection, primer and probe design, optimization experiments, and bioinformatics analysis, multiplex PCR-based tNGS (mp-tNGS) and hybrid capture-based tNGS (hc-tNGS), targeting 198 and 3060 pathogens (DNA and RNA co-detection workflow) were established and performed.

FINDINGS: mp-tNGS and hc-tNGS took 10.3 and 16 h, respectively, with low sequencing data sizes of 0.1 M and 1 M reads, and test costs reduced to a quarter and half of mNGS. The LoDs of mp-tNGS and hc-tNGS were 50-450 CFU/mL. mp-tNGS and hc-tNGS were highly accurate, with 86.5% and 87.3% (vs. 85.5% for mNGS) sensitivities and 90.0% and 88.0% (vs. 92.1% for mNGS) specificities. tNGS detection rates for casual pathogens were 84.3% and 89.5% (vs. 88.5% for mNGS), significantly higher than conventional microbiological tests (P < 0.001). In seven samples, tNGS detected Pneumocystis jirovecii, a fungus not detected by mNGS. Whereas mNGS detected six samples with filamentous fungi (Rhizopus oryzae, Aureobasidium pullulans, Aspergillus niger complex, etc.) which missed by tNGS. The anaerobic bacteria as pathogen in eight samples was failed to detect by mp-tNGS.

INTERPRETATION: tNGS may offer a new, broad-spectrum, rapid, accurate and cost-effective approach to diagnosing respiratory infections.

FUNDING: National Natural Science Foundation of China (81625014 and 82202535).}, } @article {pmid39226177, year = {2024}, author = {Boulton, W and Fidan, FR and Denise, H and De Maio, N and Goldman, N}, title = {SWAMPy: simulating SARS-CoV-2 wastewater amplicon metagenomes.}, journal = {Bioinformatics (Oxford, England)}, volume = {40}, number = {9}, pages = {}, pmid = {39226177}, issn = {1367-4811}, mesh = {*Wastewater/virology ; *SARS-CoV-2/genetics/isolation & purification ; *Metagenome ; *COVID-19/virology/diagnosis ; Metagenomics/methods ; Software ; Humans ; Genome, Viral ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {MOTIVATION: Tracking SARS-CoV-2 variants through genomic sequencing has been an important part of the global response to the pandemic and remains a useful tool for surveillance of the virus. As well as whole-genome sequencing of clinical samples, this surveillance effort has been aided by amplicon sequencing of wastewater samples, which proved effective in real case studies. Because of its relevance to public healthcare decisions, testing and benchmarking wastewater sequencing analysis methods is also crucial, which necessitates a simulator. Although metagenomic simulators exist, none is fit for the purpose of simulating the metagenomes produced through amplicon sequencing of wastewater.

RESULTS: Our new simulation tool, SWAMPy (Simulating SARS-CoV-2 Wastewater Amplicon Metagenomes with Python), is intended to provide realistic simulated SARS-CoV-2 wastewater sequencing datasets with which other programs that rely on this type of data can be evaluated and improved. Our tool is suitable for simulating Illumina short-read RT-PCR amplified metagenomes.

The code for this project is available at https://github.com/goldman-gp-ebi/SWAMPy. It can be installed on any Unix-based operating system and is available under the GPL-v3 license.}, } @article {pmid39225809, year = {2024}, author = {Sangodkar, N and Gonsalves, MJ}, title = {Role of Nitrifiers Associated with Mangrove clam Polymesoda Erosa in Bioremediation.}, journal = {Bulletin of environmental contamination and toxicology}, volume = {113}, number = {3}, pages = {38}, pmid = {39225809}, issn = {1432-0800}, mesh = {Animals ; *Biodegradation, Environmental ; *Bivalvia/metabolism/microbiology ; *Nitrification ; *Ammonia/metabolism ; *Wastewater/microbiology ; Water Pollutants, Chemical/metabolism ; Nitrites/metabolism ; Nitrates/metabolism ; Waste Disposal, Fluid/methods ; }, abstract = {Polymesoda erosa is a mangrove clam known for its water filtration ability. This clam was investigated for its bioremediation potential and growth in synthetic wastewater during 40 days of incubation. Variation in the nutrient composition of water, biochemical composition of the clams, and metagenomic analysis of the microorganisms associated with clam tissue were carried out. Significant differences in the concentration of ammonia (p ≤ 0.01), nitrite (p ≤ 0.001), and nitrate (p ≤ 0.05) in the wastewater were observed between day 0 and day 40. A reduction of approximately 89% in ammonia concentration at the end of the experiment was recorded indicating nitrification activity. However, biochemical parameters showed negligible differences before and after the incubation experiment. Thus suggesting that the chemosynthetic-based nutrition aids in the survival of the clam as no organic matter was added to the medium. The substantial decline in levels of ammonia in the presence of clams as compared to its absence suggests the significant role of clams in improving the water quality. Furthermore, the metagenomic analysis of the gill tissue of P. erosa revealed ~ 50% of the microbial population to consist of nitrifiers. The study highlights the contribution by the nitrifers associated with the clams not only to its growth and resilience but also to bioremediation.}, } @article {pmid39225513, year = {2024}, author = {Han, K and Kuo, B and Khalili, H and Staller, K}, title = {Metagenomics Analysis Reveals Unique Gut Microbiota Signature of Slow-Transit Constipation.}, journal = {Clinical and translational gastroenterology}, volume = {15}, number = {10}, pages = {e1}, pmid = {39225513}, issn = {2155-384X}, support = {K23 DK120945/DK/NIDDK NIH HHS/United States ; KSN2022210 and KSN2211010//Korea Institute of Oriental Medicine/ ; K23 DK120945/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Constipation/microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Middle Aged ; *Metagenomics/methods ; Male ; Case-Control Studies ; Adult ; Feces/microbiology ; Aged ; Gastrointestinal Transit ; Bile Acids and Salts/metabolism ; Bacteria/genetics/isolation & purification/classification ; }, abstract = {INTRODUCTION: Altered gut microbiota may play a role in slow-transit constipation (STC). We conducted a study of gut microbiota composition and functionality in STC using metagenomic analyses.

METHODS: We assembled a clinical cohort of 24 patients with STC physiology age- and sex-matched to 24 controls. We performed shotgun metagenomic sequencing followed by prediction of metabolite composition from functional profiles.

RESULTS: In a middle-aged (mean 55.3 years), predominantly female cohort, there were no significant differences in α-diversity indices, but permutational multivariate analysis of variance analysis showed significant between-group differences (R 2 = 0.050, P < 0.001) between STC patients and controls. Gordonibacter pamelaeae , Bifidobacterium longum , Firmicutes bacterium co-abundance gene group 94, and Anaerotruncus colihominis were more abundant in STC, whereas Coprococcus comes and Roseburia intestinalis were more abundant in controls. Gut-derived metabolites varying in STC relative to controls were related to bile acid and cholesterol metabolism.

DISCUSSION: We found a unique metagenomic and metabolomic signature of STC.}, } @article {pmid39224904, year = {2024}, author = {Li, Q and Li, M and Wang, S and Geater, AF and Dai, J}, title = {Clinical Diagnostic Challenge in a Case of Disseminated Talaromyces marneffei Infection Misdiagnosed Initially as Pulmonary Tuberculosis: A Case Report and Literature Review.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {3751-3757}, pmid = {39224904}, issn = {1178-6973}, abstract = {This case reports a middle-aged male patient who was HIV-negative and initially misdiagnosed as pulmonary tuberculosis but was eventually diagnosed with disseminated Talaromyces marneffei (T. marneffei) infection by next-generation sequencing. The patient presented with respiratory symptoms, recurrent bone pain, and subcutaneous masses as the main symptoms. After one year of antifungal treatment, the symptoms improved obviously, but the symptoms recurred after two weeks of drug withdrawal, and the symptoms were relieved after re-administration of antifungal drugs again. This report highlights the need for the rapid evaluation of fungal infections with metagenomic next-generation sequencing (mNGS) in patients with an inadequate diagnostic basis for tuberculosis infection or a poor response to antituberculosis drugs. In addition, long-term follow-up is needed to observe disease recurrence in patients with disseminated T. marneffei infection.}, } @article {pmid39224706, year = {2024}, author = {Sun, L and Zhang, K and Liu, Y and Che, L and Zhang, P and Wang, B and Du, N}, title = {Metagenomic next-generation sequencing targeted and metagenomic next-generation sequencing for pulmonary infection in HIV-infected and non-HIV-infected individuals.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1438982}, pmid = {39224706}, issn = {2235-2988}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *HIV Infections/complications/virology ; Male ; Female ; *Metagenomics/methods ; *Bronchoalveolar Lavage Fluid/microbiology/virology ; Middle Aged ; Adult ; Bacteria/genetics/isolation & purification/classification ; Aged ; Sensitivity and Specificity ; Viruses/genetics/isolation & purification/classification ; Metagenome ; Respiratory Tract Infections/virology/microbiology/diagnosis ; }, abstract = {BACKGROUND: When individuals infected with human immunodeficiency virus (HIV) experience pulmonary infections, they often exhibit severe symptoms and face a grim prognosis. Consequently, early, rapid, and accurate pathogen diagnosis is vital for informing effective treatment strategies. This study aimed to use metagenomic next-generation sequencing (mNGS) and targeted mNGS (tNGS) to elucidate the characteristics of pulmonary infections in HIV and non-HIV individuals.

METHODS: This study enrolled 90 patients with pulmonary infection at the Department of Infectious Diseases of The First Hospital of Jilin University from June 2022 to May 2023, and they were divided into HIV (n=46) and non-HIV (n=44) infection groups. Their bronchoalveolar lavage fluid (BALF) was collected for mNGS analysis to evaluate the differences in pulmonary infection pathogens, and tNGS detection was performed on BALF samples from 15 HIV-infected patients.

RESULTS: A total of 37 pathogens were identified in this study, including 21 bacteria, 5 fungi, 5 viruses, 5 mycobacteria, and 1 mycoplasma. The sensitivity of mNGS was 78.9% (71/90), which is significantly higher than that of conventional methods (CTM) (39/90, P=1.5E-8). The combination of mNGS with CTM can greatly enhance the sensitivity of pathogen detection. The prevalence of Pneumocystis jirovecii (82.6% vs. 9.1%), cytomegalovirus (CMV) (58.7% vs. 0%), and Epstein-Barr virus (EBV) (17.4% vs. 2.3%) was significantly higher in the HIV infection group than in the non-HIV infection group (P<0.05). Although no statistically significant difference was observed, the detection rate of Mycobacteria was higher in HIV-infected patients (17.4%) than in the non-HIV group (6.8%). Furthermore, the tNGS results of BALF from 15 HIV-infected patients were not entirely consistent with the mNGS results., and the concordance rate of tNGS for the detection of main pathogens reached 86.7% (13/15).

CONCLUSION: Next-generation sequencing (NGS) can accurately detect pathogens in the BALF of patients with pulmonary infection. The sensitivity of tNGS is comparable to that of mNGS. Therefore, this technique should be promoted in the clinic for better patient outcomes.}, } @article {pmid39224703, year = {2024}, author = {Shi, Y and Zhang, W and Li, L and Wu, W and Li, M and Xiao, K and Wang, K and Sheng, Z and Xie, F and Wang, X and Shi, X and Tong, Y and Xie, L}, title = {Evaluation of phage-based decontamination in respiratory intensive care unit environments using ddPCR and 16S rRNA targeted sequencing techniques.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1442062}, pmid = {39224703}, issn = {2235-2988}, mesh = {*RNA, Ribosomal, 16S/genetics ; *Klebsiella pneumoniae/virology/genetics ; *Intensive Care Units ; *Decontamination/methods ; *Bacteriophages/genetics ; Humans ; Polymerase Chain Reaction/methods ; Cross Infection/prevention & control/microbiology ; Disinfectants/pharmacology ; Klebsiella Infections/prevention & control/microbiology ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Klebsiella pneumoniae is a major cause of hospital-acquired infections (HAIs), primarily spread through environmental contamination in hospitals. The effectiveness of current chemical disinfectants is waning due to emerging resistance, which poses environmental hazards and fosters new resistance in pathogens. Developing environmentally friendly and effective disinfectants against multidrug-resistant organisms is increasingly important.

METHODS: This study developed a bacteriophage cocktail targeting two common carbapenem-resistant Klebsiella pneumoniae (CRKP) strains, ST11 KL47 and ST11 KL64. The cocktail was used as an adjunctive disinfectant in a hospital's respiratory intensive care unit (RICU) via ultrasonic nebulization. Digital PCR was used to quantify CRKP levels post-intervention. The microbial community composition was analyzed via 16S rRNA sequencing to assess the intervention's impact on overall diversity.

RESULTS: The phage cocktail significantly reduced CRKP levels within the first 24 hours post-treatment. While a slight increase in pathogen levels was observed after 24 hours, they remained significantly lower than those treated with conventional disinfectants. 16S rRNA sequencing showed a decrease in the target pathogens' relative abundance, while overall species diversity remained stable, confirming that phages selectively target CRKP without disrupting ecological balance.

DISCUSSION: The findings highlight the efficacy and safety of phage-based biocleaners as a sustainable alternative to conventional disinfectants. Phages selectively reduce multidrug-resistant pathogens while preserving microbial diversity, making them a promising tool for infection control.}, } @article {pmid39224188, year = {2024}, author = {Looijesteijn, E and Schoemaker, MH and van den Belt, M and Hester, ER and Kortman, GAM and Viskaal-van Dongen, M and Nauta, A}, title = {A double-blind intervention trial in healthy women demonstrates the beneficial impact on Bifidobacterium with low dosages of prebiotic galacto-oligosaccharides.}, journal = {Frontiers in nutrition}, volume = {11}, number = {}, pages = {1440319}, pmid = {39224188}, issn = {2296-861X}, abstract = {INTRODUCTION: Galacto-oligosaccharides (GOS) are well-substantiated prebiotic substrates. Multiple studies have demonstrated a positive impact of GOS on gut microbiota composition and activity, so-far mainly related to Bifidobacterium. However, data on the beneficial impact at lower dosages in a healthy female population are limited. The primary aim of the current study was to reveal the effect of low dosages (1.3 and 2.0 g) of GOS on fecal Bifidobacterium abundance in healthy women. Other outcomes included the effect of low dosage of GOS on overall fecal microbiota composition and on self-perceived GI comfort, sleep quality and mental wellbeing.

METHOD: Eighty-eight healthy women (42-70 years, BMI 18.7-30 kg/m[2]) were included in this randomized, parallel, double-blind study of 6 weeks. The participants were stratified for fiber intake, BMI and age and randomized to consume either 1.3 or 2.0 g of GOS per day for 3 weeks after a control period of 3 weeks without any intervention. Fecal samples were collected for shotgun metagenomics sequencing at the start (t = -3) and end (t = 0) of the control period and at the end of the intervention period (t = 3). Self-perceived gut comfort, sleep quality, and mental wellbeing were assessed weekly. Hierarchical clustering of principal components was applied to data collected from study participants.

RESULTS: The relative abundance of Bifidobacterium in feces increased significantly after 3 weeks of daily consumption of both 1.3 g (p < 0.01) and 2.0 g GOS (p < 0.01). This was accompanied by a significant shift in the overall microbiota composition for the dosage of 2.0 g GOS (p < 0.01). Participants that showed a larger increase in Bifidobacterium in the intervention period compared to the change in Bifidobacterium in the control period, defined as responders, showed a significant overall difference in initial fecal microbiota composition as compared to non-responders (p = 0.04) and a trend towards lower baseline levels of Bifidobacterium in responders (p = 0.10).

CONCLUSION: Daily consumption of a low dose of GOS can lead to an increase in the relative abundance of Bifidobacterium in feces of healthy women. Additionally, with 2.0 g GOS, the enrichment of Bifidobacterium is accompanied with a shift in the overall microbiota composition.Clinical trial registration: clinicaltrials.gov, identifier NCT05762965.}, } @article {pmid39222819, year = {2024}, author = {Yang, X and Wen, D and Liu, Z and Zhang, Y and Danzengjicha, and Yixiduoji, and Huang, X and Li, B}, title = {Biofermentation of aquatic plants: Potential novel feed ingredients for dairy cattle production.}, journal = {The Science of the total environment}, volume = {952}, number = {}, pages = {175955}, doi = {10.1016/j.scitotenv.2024.175955}, pmid = {39222819}, issn = {1879-1026}, mesh = {Animals ; Cattle ; *Silage ; *Animal Feed/analysis ; Dairying ; Diet/veterinary ; Female ; Zea mays ; Bacillus subtilis ; Fermentation ; Rumen/metabolism ; }, abstract = {The study assessed the impacts of aquatic plant silages on feeding efficiency and dairy cattle health as an alternative to conventional corn silage under high altitude conditions. Mid-lactation Holstein cows were assigned to treatment groups according to a randomized complete block design of parity, previous 105-d milk yield, and body weight. Cows (n = 8 per group) were fed with aquatic plant silage inoculated with Bacillus subtilis (BS), Yeast (YS), or conventional corn silage without inoculants (control) in addition to [standard grain feed] for 75 consecutive days. BS and YS had higher protein contents than control silage (111.20 ± 7.68, 112.10 ± 6.83 vs 76.94 ± 3.48 g/kg DM), while feeding efficiency was comparable between treatments (1.07, 0.99, and 0.90, respectively). In addition, the addition of aquatic plant silage in ruminant diets enhanced immunity and antioxidant capacity when compared with control group. Metagenomic analysis showed similar composition in rumen microbiota between YS and control groups, with higher enrichment for energy and nitrogen utilization pathways in YS-treated cows. This study highlights the use of aquatic plant silage as an alternative feed for dairy cattle with higher protein than corn silage. Our results suggest YS or BS could potentially boost immune and antioxidant functions, improving adaptation to high-altitudes and reducing demand for high input corn production on the Qinghai-Tibetan Plateau.}, } @article {pmid39222807, year = {2024}, author = {Shi, X and Zhang, J and Wang, Q and Wang, K and Han, J and Hui, Y and Jin, X and Jin, P}, title = {The sewer advances: How to select eco-friendly pipe materials for environmental protection.}, journal = {The Science of the total environment}, volume = {952}, number = {}, pages = {175853}, doi = {10.1016/j.scitotenv.2024.175853}, pmid = {39222807}, issn = {1879-1026}, mesh = {*Biofilms ; Sewage/microbiology ; Waste Disposal, Fluid/methods ; Wastewater ; }, abstract = {Sewer pipe materials exhibit diverse inner-surface features, which can affect the attachment of biofilm and influence microbial metabolic processes. To investigate the role of the type of pipe material on the composition and metabolic capabilities of the adhering microorganisms, three sets of urban sewers (High-Density Polyethylene Pipe (HDPE), Ductile Iron Pipe (DIP), and Concrete Pipe (CP)) were constructed. Measurements of biofilm thickness and environmental factors revealed that the thickest biofilm in CP pipes reached 2000 μm, with ORP values as low as -325 mV, indicating a more suitable anaerobic microbial habitat. High-throughput sequencing showed similar relative abundances of genera related to carbon and sulfur metabolism in the DIP and CP pipes, whereas HDPE exhibited only half the relative abundance compared to that found in the other pipes. To explore the impact of pipe materials on the mechanisms of microbial response, a metagenomic approach was used to investigate the biological transformation of carbon and sulfur in wastewater. The annotations of the crucial enzyme-encoding genes related to methyl coenzyme M and sulfite reductase in DIP and CP were 50 and 110, respectively, whereas HDPE exhibited lower counts (25 and 70, respectively). This resulted in significantly lower carbon and sulfur metabolism capabilities in the HDPE biofilm than in the other two pipes. The stability of wastewater quality during the transmission process in HDPE pipes reduces the metabolic generation of toxic and harmful gases within the pipes, favoring the preservation of carbon sources for sewer systems. This study reveals the variations in carbon and sulfur metabolism in wastewater pipe systems influenced by pipe materials and provides insights for designing future sewers.}, } @article {pmid39222589, year = {2024}, author = {Qiu, Y and Fu, Q and Yang, Y and Zhao, J and Li, J and Yi, F and Fu, X and Huang, Y and Tian, Z and Heitman, JL and Yao, Z and Dai, Z and Qiu, Y and Chen, H}, title = {Soil and stone terraces offset the negative impacts of sloping cultivation on soil microbial diversity and functioning by protecting soil carbon.}, journal = {Journal of environmental management}, volume = {369}, number = {}, pages = {122339}, doi = {10.1016/j.jenvman.2024.122339}, pmid = {39222589}, issn = {1095-8630}, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Carbon/metabolism ; Fungi/metabolism ; Bacteria/metabolism ; Nitrogen/metabolism ; }, abstract = {Cultivation of sloping land is a main cause for soil erosion. Conservation practices, such as soil and stone terraces, may reduce the impacts of erosion but their impacts on soil microbial diversity and functioning related to carbon (C) and nutrient metabolisms remain unclear. This study was conducted to evaluate the effects of slope gradients (5°, 8°, 15°, 25°) and conservation practices (cultivated, uncultivated, soil terrace, and stone terrace) on bacterial and fungal diversities, metagenomic and metabolomic functioning associated with basic soil properties. Our results showed that steep slopes at 25° significantly decreased soil pH, silt percentage, and bacterial and fungal abundances, but that soil and stone terraces increased soil organic C (SOC), silt and clay contents, and fungal abundance compared to sloping cultivated lands. In addition, soil and stone terraces increased both bacterial and fungal alpha diversities, and relative abundances of Crenarchaeota, Nitrospirota, and Latescibacterota, but reduced the proportions of Actinobacteriota and Patescibacteria, thus shifting microbial beta diversities, which were significantly associated with increased SOC and silt content. For metagenomics, soil and stone terraces greatly increased the relative abundance of functional genes related to Respiration, Virulence, disease and defense, Stress response, and nitrogen and potassium metabolisms, such as Denitrification and Potassium homeostasis. For soil metabolomics, a total of 22 soil metabolites was enriched by soil and stone terraces, such as Lipids and lipid-like molecules (Arachidonic acid, Gamma-Linolenic acid, and Pentadecanoic acid), and Organoheterocyclic compounds (Adenine, Laudanosine, Methylpyrazine, and Nicotinic acid). To sum up, soil and stone terraces could reduce some of the negative impacts of steep slope cultivation on soil microbial diversity as well as their metagenomic and metabolomic functioning related to C and nutrient metabolism useful for soil health improvement, potentially bolstering the impact of sustainable practices in erosion hotspots around the world.}, } @article {pmid39222347, year = {2024}, author = {Glendinning, L and Wu, Z and Vervelde, L and Watson, M and Balic, A}, title = {Infectious bronchitis virus vaccination, but not the presence of XCR1, is correlated with large differences in chicken caecal microbiota.}, journal = {Microbial genomics}, volume = {10}, number = {9}, pages = {}, pmid = {39222347}, issn = {2057-5858}, mesh = {Animals ; *Chickens/microbiology ; *Infectious bronchitis virus/immunology/genetics ; *Cecum/microbiology ; *Gastrointestinal Microbiome ; Vaccination ; Poultry Diseases/microbiology/virology/immunology ; Coronavirus Infections/veterinary/prevention & control/immunology ; Viral Vaccines/immunology/genetics ; Receptors, G-Protein-Coupled/genetics ; Metagenome ; Dendritic Cells/immunology ; Bacteria/classification/genetics ; Metagenomics ; }, abstract = {The chicken immune system and microbiota play vital roles in maintaining gut homeostasis and protecting against pathogens. In mammals, XCR1+ conventional dendritic cells (cDCs) are located in the gut-draining lymph nodes and play a major role in gut homeostasis. These cDCs sample antigens in the gut luminal contents and limit the inflammatory response to gut commensal microbes by generating appropriate regulatory and effector T-cell responses. We hypothesized that these cells play similar roles in sustaining gut homeostasis in chickens, and that chickens lacking XCR1 were likely to contain a dysbiotic caecal microbiota. Here we compare the caecal microbiota of chickens that were either heterozygous or homozygous XCR1 knockouts, that had or had not been vaccinated for infectious bronchitis virus (IBV). We used short-read (Illumina) and long-read (PacBio HiFi) metagenomic sequencing to reconstruct 670 high-quality, strain-level metagenome assembled genomes. We found no significant differences between alpha diversity or the abundance of specific microbial taxa between genotypes. However, IBV vaccination was found to correlate with significant differences in the richness and beta diversity of the microbiota, and to the abundance of 40 bacterial genera. In conclusion, we found that a lack of XCR1 was not correlated with significant changes in the chicken microbiota, but IBV vaccination was.}, } @article {pmid39222062, year = {2024}, author = {Acheampong, DA and Jenjaroenpun, P and Wongsurawat, T and Kurilung, A and Pomyen, Y and Kandel, S and Kunadirek, P and Chuaypen, N and Kusonmano, K and Nookaew, I}, title = {CAIM: coverage-based analysis for identification of microbiome.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {5}, pages = {}, pmid = {39222062}, issn = {1477-4054}, support = {P20 GM125503/GM/NIGMS NIH HHS/United States ; R01 CA143130/CA/NCI NIH HHS/United States ; P20GM125503//National Institute of General Medical Sciences of the National Institutes of Health/ ; R01CA143130/NH/NIH HHS/United States ; }, mesh = {Humans ; *Microbiota/genetics ; *Metagenomics/methods ; Computational Biology/methods ; Metagenome ; High-Throughput Nucleotide Sequencing/methods ; Software ; Algorithms ; Sequence Analysis, DNA/methods ; }, abstract = {Accurate taxonomic profiling of microbial taxa in a metagenomic sample is vital to gain insights into microbial ecology. Recent advancements in sequencing technologies have contributed tremendously toward understanding these microbes at species resolution through a whole shotgun metagenomic approach. In this study, we developed a new bioinformatics tool, coverage-based analysis for identification of microbiome (CAIM), for accurate taxonomic classification and quantification within both long- and short-read metagenomic samples using an alignment-based method. CAIM depends on two different containment techniques to identify species in metagenomic samples using their genome coverage information to filter out false positives rather than the traditional approach of relative abundance. In addition, we propose a nucleotide-count-based abundance estimation, which yield lesser root mean square error than the traditional read-count approach. We evaluated the performance of CAIM on 28 metagenomic mock communities and 2 synthetic datasets by comparing it with other top-performing tools. CAIM maintained a consistently good performance across datasets in identifying microbial taxa and in estimating relative abundances than other tools. CAIM was then applied to a real dataset sequenced on both Nanopore (with and without amplification) and Illumina sequencing platforms and found high similarity of taxonomic profiles between the sequencing platforms. Lastly, CAIM was applied to fecal shotgun metagenomic datasets of 232 colorectal cancer patients and 229 controls obtained from 4 different countries and 44 primary liver cancer patients and 76 controls. The predictive performance of models using the genome-coverage cutoff was better than those using the relative-abundance cutoffs in discriminating colorectal cancer and primary liver cancer patients from healthy controls with a highly confident species markers.}, } @article {pmid39221872, year = {2025}, author = {Wang, Z and Xu, M and Li, Q and Lu, S and Liu, Z}, title = {Subchronic Chloroform Exposure Causes Intestinal Damage and Induces Gut Microbiota Disruption and Metabolic Dysregulation in Mice.}, journal = {Environmental toxicology}, volume = {40}, number = {1}, pages = {5-18}, doi = {10.1002/tox.24417}, pmid = {39221872}, issn = {1522-7278}, support = {LH2021C095//Natural Science Foundation of Heilongjiang Province of China/ ; 1452TD008//Heilongjiang Provincial Department of Education filing project/ ; 1451TD002//Heilongjiang Provincial Department of Education filing project/ ; }, mesh = {Animals ; *Chloroform/toxicity ; *Gastrointestinal Microbiome/drug effects ; Female ; Mice ; Cecum/microbiology/drug effects ; Intestines/drug effects/microbiology/pathology ; Environmental Pollutants/toxicity ; }, abstract = {Chloroform is a prevalent toxic environmental pollutant in urban settings, posing risks to human health through exposure via various mediums such as air and tap water. The gut microbiota plays a pivotal role in maintaining host health. However, there is a paucity of research elucidating the impact of chloroform exposure on the gut microbiota. In this investigation, 18 SPF Kunming female mice were stratified into three groups (n = 6) and subjected to oral gavage with chloroform doses equivalent to 0, 50, and 150 mg/kg of body weight over 30 days. Our findings demonstrate that subchronic chloroform exposure significantly perturbs hematological parameters in mice and induces histopathological alterations in cecal tissues, consequently engendering marked disparities in the functional composition of cecal microbiota and metabolic equilibrium of cecal contents. Ultimately, our investigation revealed a statistically robust correlation, exhibiting a high degree of significance, between the intestinal microbiome composition and the metabolites that were differentially expressed consequent to chloroform exposure.}, } @article {pmid39221224, year = {2024}, author = {Song, CY and Yang, J and Jiang, S and Du, GL}, title = {HNF1β, LHX1, and GGNBP2 deletion contributed to kidney and reproductive dysfunction in 17q12 deletion syndrome: evidence from a case report.}, journal = {Frontiers in genetics}, volume = {15}, number = {}, pages = {1391804}, pmid = {39221224}, issn = {1664-8021}, abstract = {17q12 deletion syndrome is a chromosomal abnormality, where there is a small missing piece (deletion) of genetic material on the long arm (q) of chromosome 17. Sign and symptoms can vary widely among different patients. Recently, a patient was diagnosed with 17q12 deletion syndrome in our hospital, and the clinical characteristics presented as absence of the right kidney, compensatory hypertrophy of the left kidney, multiple small cysts in the left kidney, pancreatic atrophy, hypomagnesemia, bowed uterus, multiple follicular cysts in both lobes of the thyroid gland, and maturity-onset diabetes of the young type 5 (MODY-5). A 1.5-Mb deletion with haploinsufficiency for 20 genes within the 17q12 region was found through copy number variation (CNV) analysis based on metagenomic next-generation sequencing (mNGS) technology. In addition to HNF1B absence, the LIM-class homeobox 1 transcription factor (LHX1) and GGNBP2 absence was also involved in regulation of kidney development and the reproductive system through bioinformatics analysis. The inheriting risk of 17q12 deletion syndrome is about 50%, and it is recommended to provide genetic counseling to all patients who are suspected or diagnosed with the syndrome.}, } @article {pmid39221074, year = {2024}, author = {Qiu, Z and Zhu, Y and Zhang, Q and Qiao, X and Mu, R and Xu, Z and Yan, Y and Wang, F and Zhang, T and Zhuang, WQ and Yu, K}, title = {Unravelling biosynthesis and biodegradation potentials of microbial dark matters in hypersaline lakes.}, journal = {Environmental science and ecotechnology}, volume = {20}, number = {}, pages = {100359}, pmid = {39221074}, issn = {2666-4984}, abstract = {Biosynthesis and biodegradation of microorganisms critically underpin the development of biotechnology, new drugs and therapies, and environmental remediation. However, most uncultured microbial species along with their metabolic capacities in extreme environments, remain obscured. Here we unravel the metabolic potential of microbial dark matters (MDMs) in four deep-inland hypersaline lakes in Xinjiang, China. Utilizing metagenomic binning, we uncovered a rich diversity of 3030 metagenome-assembled genomes (MAGs) across 82 phyla, revealing a substantial portion, 2363 MAGs, as previously unclassified at the genus level. These unknown MAGs displayed unique distribution patterns across different lakes, indicating a strong correlation with varied physicochemical conditions. Our analysis revealed an extensive array of 9635 biosynthesis gene clusters (BGCs), with a remarkable 9403 being novel, suggesting untapped biotechnological potential. Notably, some MAGs from potentially new phyla exhibited a high density of these BGCs. Beyond biosynthesis, our study also identified novel biodegradation pathways, including dehalogenation, anaerobic ammonium oxidation (Anammox), and degradation of polycyclic aromatic hydrocarbons (PAHs) and plastics, in previously unknown microbial clades. These findings significantly enrich our understanding of biosynthesis and biodegradation processes and open new avenues for biotechnological innovation, emphasizing the untapped potential of microbial diversity in hypersaline environments.}, } @article {pmid39220937, year = {2024}, author = {Wei, L and Luo, J and Wu, W and Yin, J and Sun, Z and Xu, X and Gong, W and Xu, J}, title = {Clinical diagnostic value of metagenomic next-generation sequencing in patients with acute infection in emergency department.}, journal = {Heliyon}, volume = {10}, number = {16}, pages = {e35802}, pmid = {39220937}, issn = {2405-8440}, abstract = {OBJECTIVE: To explore the value of metagenomic next-generation sequencing (mNGS) and culture in microbial diagnosis of patients with acute infection.

METHODS: We retrospectively analyzed 206 specimens from 163 patients who were admitted to the emergency department of The First Affiliated Hospital of Sun Yat-sen University between July 2020, and July 2021. We evaluated the diagnostic efficacy of mNGS and in-hospital traditional culture.

RESULTS: The total positive rate of mNGS was significantly higher than that culture methods (71.4 % vs 40.8 %, p < 0.001), while the sensitivity and accuracy of mNGS were found to be 92.9 % and 88.2 % respectively. However, culture exhibited superior specificity with a value of 92.6 % compared to 75.9 % for mNGS. The detection efficiency of mNGS and culture for fungi was comparable, but mNGS showed superior performance for bacterial detection. In the analysis of sepsis samples, mNGS outperformed traditional culture methods in diagnosing various types of samples, especially for sputum and bronchoalveolar lavage fluid. Among the identified infections, bacterial infections were the most common single infection (37.5 %). Additionally, bacterial-fungal infections represented the most prevalent form of mixed infection (77.3 %). Candida albicans and Staphylococcus aureus were identified as the predominant pathogens in the survival and death groups, respectively. No significant differences in microbial diversity were observed.

CONCLUSION: Compared to culture methods, mNGS demonstrates superior positive rates, sensitivity, and accuracy in the rapid detection of acute infections, particularly in critically ill patients such as those with sepsis. This capability establishes a foundation for the swift and precise identification of pathogens, allowing for the analysis of clinical indicators and patient prognosis based on the extensive data generated from mNGS.}, } @article {pmid39220283, year = {2024}, author = {Ding, Y and Liu, G and Li, Q and Zou, L and Dai, J and Chongsuvivatwong, V}, title = {Distribution characteristics of human herpes viruses in the lower respiratory tract and their impact on 30-day mortality in community-acquired pneumonia patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1436509}, pmid = {39220283}, issn = {2235-2988}, mesh = {Humans ; Roseolovirus Infections/diagnosis ; *Bronchoalveolar Lavage Fluid/virology ; Male ; Female ; Adult ; Middle Aged ; Aged ; *Pneumonia/microbiology/mortality/therapy/virology ; Severity of Illness Index ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; *Herpesviridae/genetics/isolation & purification ; }, abstract = {Human herpes viruses (HHVs) are commonly detected in community-acquired pneumonia (CAP) patients, particularly those with complex complications, attracting increased attention from clinical practitioners. However, the significance of detecting HHVs in bronchoalveolar lavage fluid (BALF) with CAP patients is still unclear. This study retrospectively analyzed BALF samples from 64 CAP patients at the Kunming Third People's Hospital between August 2021 and December 2023. Metagenomic next generation sequencing (mNGS) was conducted on BALF samples during CAP onset. Multivariate Cox regression models were used to identify independent risk factors for 30-day all-cause mortality in CAP. HHVs were found in 84.4% of CAP patients, which were the most common pathogens (45.1%), followed by bacteria (30.2%) and fungi (11.5%). Bacterial-viral co-infections were most common, occurring in 39 patients. Notably, there was no significant difference in HHV presence between severe and non-severe CAP patients (EBV: P = 0.431, CMV: P = 0.825), except for HHV-7 (P = 0.025). In addition, there was no significant difference in the 30-day mortality between HHV positive and HHV negative groups (P = 0.470), as well as between the HHV-7 positive and HHV-7 negative groups (P = 0.910). However, neither HHVs nor HHV-7 was independent risk factors for 30-day mortality in CAP patients (HHVs: HR 1.171, P = 0.888; HHV-7: HR 1.947, P = 0.382). In summary, among the prevalent presence of multiple HHVs, EBV and CMV were the most prevalent in CAP patients. Patients with sCAP were more susceptible to HHV-7 than those with non-sCAP. These results provide valuable insights for clinicians in guiding appropriate interventions for CAP treatment.}, } @article {pmid39219687, year = {2024}, author = {Peng, Z and Wang, P and Luo, X and Deng, Q and Yang, Z and Wu, J and Xian, W and Yan, W and Mou, X and Yuan, Y and Li, W and Li, J}, title = {Community structure and carbon metabolism functions of bacterioplankton in the Guangdong coastal zone.}, journal = {Marine life science & technology}, volume = {6}, number = {3}, pages = {547-561}, pmid = {39219687}, issn = {2662-1746}, abstract = {UNLABELLED: Coastal ecosystems are an important region for biogeochemical cycling, are a hotspot of anthropogenic disturbance and play a crucial role in global carbon cycling through the metabolic activities of bacterioplankton. Bacterioplankton can be broadly classified into two lifestyles: free-living (FL) and particle-attached (PA). However, how coastal bacterioplankton the community structure, co-occurrence networks and carbon metabolic functions with different lifestyles are differentiated is still largely unknown. Understanding these processes is necessary to better determine the contributions of coastal bacterioplankton to carbon cycling. Here, the characteristics of community structure and carbon metabolism function of bacterioplankton with two lifestyles in the coastal areas of Guangdong Province were investigated using amplicon sequencing, metagenomic, and metatranscriptomic techniques. The results show that the main bacterioplankton responsible for carbon metabolism were the Pseudomonadota, Bacteroidota, and Actinomycetota. The microbial community structure, carbon metabolic function, and environmental preferences differ between different lifestyles. FL and PA bacteria exhibited higher carbon fixation and degradation potentials, respectively. A range of environmental factors, such as dissolved oxygen, pH, and temperature, were associated with the community structure and carbon metabolic functions of the bacterioplankton. Human activities, such as nutrient discharge, may affect the distribution of functional genes and enhance the carbon degradation functions of bacterioplankton. In conclusion, this study increased the understanding of the role of microorganisms in regulating carbon export in coastal ecosystems with intense human activity.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-024-00245-x.}, } @article {pmid39218875, year = {2024}, author = {Liwinski, T and Auer, MK and Schröder, J and Pieknik, I and Casar, C and Schwinge, D and Henze, L and Stalla, GK and Lang, UE and von Klitzing, A and Briken, P and Hildebrandt, T and Desbuleux, JC and Biedermann, SV and Holterhus, PM and Bang, C and Schramm, C and Fuss, J}, title = {Gender-affirming hormonal therapy induces a gender-concordant fecal metagenome transition in transgender individuals.}, journal = {BMC medicine}, volume = {22}, number = {1}, pages = {346}, pmid = {39218875}, issn = {1741-7015}, mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; Young Adult ; *Feces/microbiology ; *Gastrointestinal Microbiome/drug effects/genetics ; Metagenome ; Prospective Studies ; *Transgender Persons ; Gender-Affirming Procedures/methods ; Gonadal Steroid Hormones/administration & dosage ; }, abstract = {BACKGROUND: Limited data exists regarding gender-specific microbial alterations during gender-affirming hormonal therapy (GAHT) in transgender individuals. This study aimed to investigate the nuanced impact of sex steroids on gut microbiota taxonomy and function, addressing this gap. We prospectively analyzed gut metagenome changes associated with 12 weeks of GAHT in trans women and trans men, examining both taxonomic and functional shifts.

METHODS: Thirty-six transgender individuals (17 trans women, 19 trans men) provided pre- and post-GAHT stool samples. Shotgun metagenomic sequencing was used to assess the changes in gut microbiota structure and potential function following GAHT.

RESULTS: While alpha and beta diversity remained unchanged during transition, specific species, including Parabacteroides goldsteinii and Escherichia coli, exhibited significant abundance shifts aligned with affirmed gender. Overall functional metagenome analysis showed a statistically significant effect of gender and transition (R[2] = 4.1%, P = 0.0115), emphasizing transitions aligned with affirmed gender, particularly in fatty acid-related metabolism.

CONCLUSIONS: This study provides compelling evidence of distinct taxonomic and functional profiles in the gut microbiota between trans men and women. GAHT induces androgenization in trans men and feminization in trans women, potentially impacting physiological and health-related outcomes.

TRIAL REGISTRATION: Clinicaltrials.gov NCT02185274.}, } @article {pmid39218360, year = {2024}, author = {Park, DG and Kang, W and Shin, IJ and Chalita, M and Oh, HS and Hyun, DW and Kim, H and Chun, J and An, YS and Lee, EJ and Yoon, JH}, title = {Difference in gut microbial dysbiotic patterns between body-first and brain-first Parkinson's disease.}, journal = {Neurobiology of disease}, volume = {201}, number = {}, pages = {106655}, doi = {10.1016/j.nbd.2024.106655}, pmid = {39218360}, issn = {1095-953X}, mesh = {Humans ; *Parkinson Disease/microbiology/metabolism ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Cross-Sectional Studies ; Aged ; Middle Aged ; *Dysbiosis/microbiology ; REM Sleep Behavior Disorder/microbiology ; Brain/metabolism/microbiology ; }, abstract = {BACKGROUND: This study aims to identify distinct microbial and functional biomarkers characteristic of body-first or brain-first subtypes of Parkinson's disease (PD). This could illuminate the unique pathogenic mechanisms within these subtypes.

METHODS: In this cross-sectional study, we classified 36 well-characterized PD patients into body-first, brain-first, or undetermined subtypes based on the presence of premotor REM sleep behavior disorder (RBD) and cardiac meta-iodobenzylguanidine (MIBG) uptake. We then conducted an in-depth shotgun metagenomic analysis of the gut microbiome for each subtype and compared the results with those from age- and sex-matched healthy controls.

RESULTS: Significant differences were found in the gut microbiome of body-first PD patients (n = 15) compared to both brain-first PD patients (n = 9) and healthy controls. The gut microbiome in body-first PD showed a distinct profile, characterized by an increased presence of Escherichia coli and Akkermansia muciniphila, and a decreased abundance of short-chain fatty acid-producing commensal bacteria. These shifts were accompanied by a higher abundance of microbial genes associated with curli protein biosynthesis and a lower abundance of genes involved in putrescine and spermidine biosynthesis. Furthermore, the combined use of premotor RBD and MIBG criteria was more strongly correlated with these microbiome differences than the use of each criterion independently.

CONCLUSIONS: Our findings highlight the significant role of dysbiotic and pathogenic gut microbial alterations in body-first PD, supporting the body-first versus brain-first hypothesis. These insights not only reinforce the gut microbiome's potential as a therapeutic target in PD but also suggest the possibility of developing subtype-specific treatment strategies.}, } @article {pmid39218260, year = {2024}, author = {Tang, M and Du, R and Han, X and Peng, Y}, title = {Enhancing collaboration of anammox with heterotrophic microbes mediated selectively by iron of different valences: Activities balance, metabolic mechanism, and functional genes regulation.}, journal = {Chemosphere}, volume = {364}, number = {}, pages = {143226}, doi = {10.1016/j.chemosphere.2024.143226}, pmid = {39218260}, issn = {1879-1298}, mesh = {*Iron/metabolism ; *Oxidation-Reduction ; *Nitrogen/metabolism ; *Denitrification ; *Ammonia/metabolism ; Heterotrophic Processes ; Bacteria/metabolism/genetics ; Nitrates/metabolism ; Waste Disposal, Fluid/methods ; }, abstract = {The partial denitrification/anammox (PD/A) process is receiving increasing attention due to its cost-effectiveness advantages. However, effective strategies to alleviate organic matter inhibition and promote anammox activity have been proven to be a big challenge. This study investigated the effects of three types of iron (nano zero-valent iron (nZVI), Fe(II), and Fe(III)) on the PD/A process. It is worth noting that nZVI of 5-50 mg/L and Fe(III) of 5-120 mg/L promoted both PD and anammox activity. Long-term intermittent addition of nZVI (50 mg/L) resulted in a nitrogen removal efficiency of 98.2% in the mixotrophic PD/A system driven by iron and organic matter. The contribution of anammox for nitrogen removal reached as high as 93.8%. The organic carbon demand decreased due to the external electron donor provided by nZVI for PD. Multiple Fe-N metabolic pathways, primarily involving ammonia oxidation by Fe(III) and nitrate reduction by nZVI, play a crucial role in facilitating nitrogen transformation. Conversely, the direct addition of 30-120 mg/L Fe (II) resulted in a significant decrease in pH to below 5.0 and severe inhibition of PD and anammox activity. Following prolonged operation in the presence of nZVI, it was demonstrated that there is an enhancing effect on robust nitrite production for anammox. This was accompanied by a remarkable up-regulation of genes encoding nitrate reductase and iron-transporting proteins dominated by Thauera. Overall, this study has provided an efficient approach for advanced nitrogen removal through organic- and iron-driven anammox processes.}, } @article {pmid39217893, year = {2024}, author = {Wang, J and Ou, Y and Li, R and Tao, C and Liu, H and Li, R and Shen, Z and Shen, Q}, title = {The occurrence of banana Fusarium wilt aggravates antibiotic resistance genes dissemination in soil.}, journal = {Ecotoxicology and environmental safety}, volume = {283}, number = {}, pages = {116982}, doi = {10.1016/j.ecoenv.2024.116982}, pmid = {39217893}, issn = {1090-2414}, mesh = {*Musa/microbiology ; *Soil Microbiology ; *Fusarium/genetics ; *Drug Resistance, Microbial/genetics ; Plant Diseases/microbiology ; Soil/chemistry ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The spread of antibiotic resistance genes (ARGs) and subsequent soil-borne disease outbreaks are major threats to soil health and sustainable crop production. However, the relationship between occurrences of soil-borne diseases and the transmission of soil ARGs remains unclear. Here, soil ARGs, mobile genetic elements and microbial communities from co-located disease suppressive and conducive banana orchards were deciphered using metagenomics and metatranscriptomics approaches. In total, 23 ARG types, with 399 subtypes, were detected using a metagenomics approach, whereas 23 ARG types, with 452 subtypes, were discovered using a metatranscriptomics method. Furthermore, the metagenomics analysis revealed that the ARG total abundance levels were greater in rhizospheres (0.45 ARGs/16S rRNA on average) compared with bulk (0.32 ARGs/16S rRNA on average) soils. Interestingly, metatranscriptomics revealed that the total ARG abundances were greater in disease-conducive (8.85 ARGs/16S rRNA on average) soils than disease suppressive (1.45 ARGs/16S rRNA on average) soils. Mobile genetic elements showed the same trends as ARGs. Network and binning analyses indicated that Mycobacterium, Streptomyces, and Blastomonas are the main potential hosts of ARGs. Furthermore, Bacillus was significantly and negatively correlated with Fusarium (P < 0.05, r = -0.84) and hosts of ARGs (i.e., Mycobacterium, Streptomyces, and Blastomonas). By comparing metagenomic and metatranscriptomic analyses，this study demonstrated that metatranscriptomics may be more sensitive in indicating ARGs activities in soil. Our findings enable the more accurate assessment of the transmission risk of ARGs. The data provide a new perspective for recognizing soil health, in which soil-borne disease outbreaks appear to be associated with ARG spread, whereas beneficial microbe enrichment may mitigate wilt disease and ARG transmission.}, } @article {pmid39217664, year = {2024}, author = {Yu, Y and Wei, R and Yi, S and Teng, Y and Ning, R and Wei, S and Bai, L and Liu, H and Li, L and Xu, H and Han, C}, title = {Research Note: Integrative analysis of transcriptome and gut microbiome reveals foie gras capacity difference between cage and floor rearing systems.}, journal = {Poultry science}, volume = {103}, number = {11}, pages = {104248}, pmid = {39217664}, issn = {1525-3171}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Geese ; *Transcriptome ; *Animal Husbandry/methods ; Housing, Animal ; Liver/metabolism ; Lipid Metabolism ; Male ; Gene Expression Profiling/veterinary ; }, abstract = {To explore the differences in foie gras performance between geese raised in cages and on the ground, we conducted an integrative analysis of liver transcriptome and gut microbial metagenomes. The results showed extremely significant differences in the liver weight (P < 0.01) and liver lipid accumulation of FRS and CRS groups. The levels of triglyceride (TG), high-density lipoprotein cholesterol (HDL-C) and low-density lipoprotein cholesterol (LDL-C) of CRS were significantly higher than those of FRS (P < 0.05). Transcriptome analysis showed that 3,917 upregulated and 1,395 downregulated genes were identified, and lipid metabolism pathway and fatty acid metabolism were significantly enriched. Analysis of cecum microbiota revealed that several inflammation-related bacteria (including Gallibacterium, Escherichia-Shigella, Desulfovibrio, Alistipes, and Fournierella) were enriched in CRS, while beneficial bacteria (including Lactobacillus, Limosilactobacillus, and Ligilactobacillus) were significantly enriched in FRS. In conclusion, CRS was better than FRS in foie gras production, which was more conducive to lipid deposition in the goose liver.}, } @article {pmid39217640, year = {2024}, author = {Shi, Y and Ji, B and Li, A and Zhang, X and Liu, Y}, title = {Enhancing the performance of microalgal-bacterial systems with sodium bicarbonate: A step forward to carbon neutrality of municipal wastewater treatment.}, journal = {Water research}, volume = {266}, number = {}, pages = {122345}, doi = {10.1016/j.watres.2024.122345}, pmid = {39217640}, issn = {1879-2448}, mesh = {*Sodium Bicarbonate/pharmacology ; *Wastewater/chemistry ; *Carbon ; *Microalgae ; *Waste Disposal, Fluid/methods ; Sewage/microbiology ; Bacteria ; Bioreactors ; Nitrogen ; Water Purification/methods ; }, abstract = {The microalgal-bacterial granular sludge (MBGS) process, enhanced with sodium bicarbonate (NaHCO3), offers a sustainable alternative for wastewater treatment aiming for carbon neutrality. This study demonstrates that NaHCO3, which can be derived from the flue gases and alkaline textile wastewater, significantly enhances pollutant removal and biomass production. Optimal addition of NaHCO3 was found to achieve an inorganic-to-organic carbon ratio of 1.0 and a total carbon-to-nitrogen ratio of 5.0. Metagenomic analysis and structural equation modeling showed that NaHCO3 addition increased dissolved oxygen concentrations and pH levels, creating a more favorable environment for key microbial communities, including Proteobacteria, Chloroflexi, and Cyanobacteria. Confocal laser scanning microscopy further confirmed enhanced interactions between Cyanobacteria and Proteobacteria/Chloroflexi, facilitating the MBGS process. These microbes harbored functional genes (gap2, GLU, and ppk) critical for removing organics, nitrogen, and phosphorus. Carbon footprint analysis revealed significant reductions in CO2 emissions by the NaHCO3-added MBGS process in representative countries (China, Australia, Canada, Germany, and Morocco), compared to the conventional activated sludge process. These findings highlight the effectiveness of NaHCO3 in optimizing MBGS process, establishing it as a key strategy in achieving carbon-neutral wastewater treatment globally.}, } @article {pmid39217389, year = {2024}, author = {Zhang, Y and Cheng, TY and Liu, GH and Liu, L and Duan, DY}, title = {Metagenome reveals the midgut microbial community of Haemaphysalis qinghaiensis ticks collected from yaks and Tibetan sheep.}, journal = {Parasites & vectors}, volume = {17}, number = {1}, pages = {370}, pmid = {39217389}, issn = {1756-3305}, support = {No. 31902294//the National Natural Science Foundation of China/ ; }, mesh = {Animals ; Sheep ; Cattle ; Female ; *Metagenome ; *Ixodidae/microbiology ; Gastrointestinal Microbiome ; Bacteria/classification/isolation & purification/genetics ; Tick Infestations/veterinary/parasitology ; Sheep Diseases/microbiology/parasitology ; China ; Metagenomics ; Tibet ; Cattle Diseases/microbiology/parasitology ; }, abstract = {BACKGROUND: Haemaphysalis qinghaiensis is a tick species distributed only in China. Due to its ability to transmit a variety of pathogens, including species of the genera Anaplasma, Rickettsia, Babesia, and Theileria, it seriously endangers livestock husbandry. However, the microbial community of the midgut of H. qinghaiensis females collected from yaks and Tibetan sheep has not yet been characterized using metagenomic sequencing technology.

METHODS: Haemaphysalis qinghaiensis were collected from the skins of yaks and Tibetan sheep in Gansu Province, China. Genomic DNA was extracted from the midguts and midgut contents of fully engorged H. qinghaiensis females collected from the two hosts. Metagenomic sequencing technology was used to analyze the microbial community of the two groups.

RESULTS: Fifty-seven phyla, 483 genera, and 755 species were identified in the two groups of samples. The ticks from the two hosts harbored common and unique microorganisms. At the phylum level, the dominant common phyla were Proteobacteria, Firmicutes, and Mucoromycota. At the genus level, the dominant common genera were Anaplasma, Ehrlichia, and Pseudomonas. At the species level, bacteria including Anaplasma phagocytophilum, Ehrlichia minasensis, and Pseudomonas aeruginosa along with eukaryotes such as Synchytrium endobioticum and Rhizophagus irregularis, and viruses such as the orf virus, Alphadintovirus mayetiola, and Parasteatoda house spider adintovirus were detected in both groups. In addition, the midgut of H. qinghaiensis collected from yaks had unique microbial taxa including two phyla, eight genera, and 23 species. Unique microorganisms in the midgut of H. qinghaiensis collected from Tibetan sheep included two phyla, 14 genera, and 32 species. Kyoto Encyclopedia of Genes and Genomes enrichment analysis revealed that the functional genes of the microbiome of H. qinghaiensis were annotated to six pathways, and the metabolic pathways included 11 metabolic processes, in which the genes involved in carbohydrate metabolism were the most abundant, followed by the genes involved in lipid metabolism.

CONCLUSIONS: These findings indicate that most of the microbial species in the collected H. qinghaiensis ticks were the same in both hosts, but there were also slight differences. The analytical data from this study have enhanced our understanding of the midgut microbial composition of H. qinghaiensis collected from different hosts. The database of H. qinghaiensis microbe constructed from this study will lay the foundation for predicting tick-borne diseases. Furthermore, a comprehensive understanding of tick microbiomes will be useful for understanding vector competency and interactions with ticks and midgut microorganisms.}, } @article {pmid39217229, year = {2024}, author = {Gyaltshen, Y and Ishii, Y and Charvet, S and Goetz, E and Maruyama, S and Kim, E}, title = {Molecular diversity of green-colored microbial mats from hot springs of northern Japan.}, journal = {Extremophiles : life under extreme conditions}, volume = {28}, number = {3}, pages = {43}, pmid = {39217229}, issn = {1433-4909}, support = {KAKENHI 17H05713//Japan Society for the Promotion of Science/ ; 19H04713//Japan Society for the Promotion of Science/ ; CAREER 1453639//Division of Integrative Organismal Systems/ ; }, mesh = {*Hot Springs/microbiology ; Japan ; RNA, Ribosomal, 16S/genetics ; Metagenome ; Microbiota ; Bacteria/genetics/classification/isolation & purification ; Phylogeny ; }, abstract = {We acquired and analyzed metagenome and 16S/18S rRNA gene amplicon data of green-colored microbial mats from two hot springs within the Onikobe geothermal region (Miyagi Prefecture, Japan). The two collection sites-Tamago and Warabi-were in proximity and had the same temperature (40 °C), but the Tamago site was connected to a nearby stream, whereas the Warabi site was isolated. Both the amplicon and metagenome data suggest the bacterial, especially cyanobacterial, dominance of the mats; other abundant groups include Chloroflexota, Pseudomonadota, Bacteroidota/Chlorobiota, and Deinococcota. At finer resolution, however, the taxonomic composition entirely differed between the mats. A total of 5 and 21 abundant bacterial 16S rRNA gene OTUs were identified for Tamago and Warabi, respectively; of these, 12 are putative chlorophyll- or rhodopsin-based phototrophs. The presence of phylogenetically diverse microbial eukaryotes was noted, with ciliates and amoebozoans being the most abundant eukaryote groups for Tamago and Warabi, respectively. Fifteen metagenome-assembled genomes (MAGs) were obtained, represented by 13 bacteria, one ciliate (mitochondrion), and one giant virus. A total of 15 novel taxa, including a new deeply branching Chlorobiota species, is noted from the amplicon and MAG data, highlighting the importance of environmental sequencing in uncovering hidden microorganisms.}, } @article {pmid39216995, year = {2024}, author = {Gekenidis, MT and Vollenweider, V and Joyce, A and Murphy, S and Walser, JC and Ju, F and Bürgmann, H and Hummerjohann, J and Walsh, F and Drissner, D}, title = {Unde venis? Bacterial resistance from environmental reservoirs to lettuce: tracking microbiome and resistome over a growth period.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {10}, pages = {}, pmid = {39216995}, issn = {1574-6941}, support = {407240_167068//National Research Program "Antimicrobial Resistance"/ ; /SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {*Lactuca/microbiology ; *Manure/microbiology ; Animals ; *Soil Microbiology ; *Microbiota/genetics ; *Bacteria/genetics/growth & development/drug effects/classification/isolation & purification ; *RNA, Ribosomal, 16S/genetics ; Drug Resistance, Bacterial/genetics ; Swine ; Plant Leaves/microbiology ; Wastewater/microbiology ; Water Microbiology ; Anti-Bacterial Agents/pharmacology ; Metagenomics ; Agricultural Irrigation ; Soil/chemistry ; Water Quality ; }, abstract = {Fresh produce is suggested to contribute highly to shaping the gut resistome. We investigated the impact of pig manure and irrigation water quality on microbiome and resistome of field-grown lettuce over an entire growth period. Lettuce was grown under four regimes, combining soil amendment with manure (with/without) with sprinkler irrigation using river water with an upstream wastewater input, disinfected by UV (with/without). Lettuce leaves, soil, and water samples were collected weekly and analysed by bacterial cultivation, 16S rRNA gene amplicon sequencing, and shotgun metagenomics from total community DNA. Cultivation yielded only few clinically relevant antibiotic-resistant bacteria (ARB), but numbers of ARB on lettuce increased over time, while no treatment-dependent changes were observed. Microbiome analysis confirmed a temporal trend. Antibiotic resistance genes (ARGs) unique to lettuce and water included multidrug and β-lactam ARGs, whereas lettuce and soil uniquely shared mainly glycopeptide and tetracycline ARGs. Surface water carried clinically relevant ARB (e.g. ESBL-producing Escherichia coli or Serratia fonticola) without affecting the overall lettuce resistome significantly. Resistance markers including biocide and metal resistance were increased in lettuce grown with manure, especially young lettuce (increased soil contact). Overall, while all investigated environments had their share as sources of the lettuce resistome, manure was the main source especially on young plants. We therefore suggest minimizing soil-vegetable contact to minimize resistance markers on fresh produce.}, } @article {pmid39216705, year = {2024}, author = {Li, Y and Chen, Y and Kang, L and Cao, Z and Lv, J and Wang, S and Guo, C and Wang, J}, title = {Metagenomic analysis reveals enhanced sludge dewaterability through acidified sludge inoculation: Regulation of Fe (II) oxidation electron transport pathway.}, journal = {Bioresource technology}, volume = {412}, number = {}, pages = {131367}, doi = {10.1016/j.biortech.2024.131367}, pmid = {39216705}, issn = {1873-2976}, mesh = {*Sewage/microbiology ; *Oxidation-Reduction ; *Metagenomics/methods ; Electron Transport ; Ferrous Compounds/metabolism ; Iron/metabolism ; Water/chemistry ; }, abstract = {The bioleaching utilizing indigenous microbial inoculation can continuously improve the dewaterability of sludge. In this study, metagenomic analysis was innovative employed to identify the key microorganisms and functional genes that affect the dewatering performance of sludge in the bioleaching conditioning process. The results demonstrated that long-term repeated inoculation of acidified sludge resulted in increased abundance of many functional genes associated with the transport of carbohydrate and amino acid. Additionally, genes encoding key iron transport proteins (such as afuA, fhuC, and fhuD) and genes related to electron transfer carriers in ferrous iron oxidation process (such as rus and cyc2) were significantly enriched, thereby promoting the improvement of sludge dewatering performance through enhanced iron oxidation. Notably, Acidithiobacillus, Betaproteobacteria, and Hyphomicrobium were the major sources of functional genes. This study reveals the microscopic mechanisms underlying the improvement of sludge dewaterability through bioleaching based on mixed culture from a novel perspective of gene metabolism.}, } @article {pmid39216617, year = {2024}, author = {Borrego, A and Koury Cabrera, WH and Souza, AT and Eto, SF and de Oliveira, SL and Rodrigues, J and Jensen, JR}, title = {Microbiota transfer early after birth modulates genetic susceptibility to chronic arthritis in mice.}, journal = {Microbes and infection}, volume = {}, number = {}, pages = {105411}, doi = {10.1016/j.micinf.2024.105411}, pmid = {39216617}, issn = {1769-714X}, abstract = {Genetics is central to the susceptibility or resistance to autoimmunity, and mounting evidence indicates that the intestinal microbiota also plays an essential role. In murine arthritis models, short-chain fat acid supplementation reduces disease severity by modulating tryptophan-metabolizing bacteria. Common microbiota transfer methods modulate arthritis severity, however, they are not practical for chronic models such as pristane-induced arthritis (PIA). PIA-resistant (HIII) and PIA-susceptible (LIII) mice harbor diverse intestinal microbiomes, which might be implicated in their divergent susceptibility. To investigate this hypothesis, we used cross-fostering to stably transfer the microbiota. In this study, we show that extreme susceptibility to arthritis can be modulated by early microbiota transfer, with long-lasting effects. HIII and LIII pups were cross-fostered and injected with pristane after weaning. PIA severity in cross-fostered LIII mice was significantly reduced in the chronic phase. Metagenomic analyses showed that HIII and LIII microbiomes were partly shifted by cross-fostering. Microbial groups whose abundance was associated with either HIII or LIII mice presented similar composition in cross-fostered mice of the opposite strains, suggesting a role in PIA susceptibility. Identification of bacterial groups that modulate chronic arthritis will contribute novel insights on the pathogenesis of human rheumatoid arthritis and targets for replication and functional studies.}, } @article {pmid39216430, year = {2024}, author = {Gupta, A and Shivachandran, A and Saleena, LM}, title = {Oral microbiome insights: Tracing acidic culprits in dental caries with functional metagenomics.}, journal = {Archives of oral biology}, volume = {168}, number = {}, pages = {106064}, doi = {10.1016/j.archoralbio.2024.106064}, pmid = {39216430}, issn = {1879-1506}, mesh = {*Dental Caries/microbiology ; Humans ; *Metagenomics/methods ; *Microbiota ; Mouth/microbiology ; Acids/metabolism ; Bacteria/classification/genetics ; DNA, Bacterial ; Sequence Analysis, DNA ; Male ; Female ; }, abstract = {OBJECTIVE: This study aimed to investigate the presence and abundance of acid-producing bacteria in dental caries samples using functional gene prediction techniques.

DESIGN: A total of 24 dental caries samples were collected for analysis. DNA isolation was performed followed by shotgun metagenomic sequencing. Functional gene prediction techniques were used to identify enzymes responsible for acid production from primary metabolites. Enzymes responsible for converting primary metabolites into acids were identified from the KEGG database. Subsequently, 840 contigs were examined, and their genus and species were characterized.

RESULTS: Analysis of the obtained data revealed 31 KEGG IDs corresponding to enzymes involved in the conversion of primary metabolites into acids. All 117 identified genera from the contig analysis were found to be part of the oral microbiome. In addition, A higher prevalence of acid-producing bacteria was noted in dental caries samples compared to earlier reports.

CONCLUSION: The study indicates the significant role of acid-producing bacteria in the initiation and progression of dental caries. The findings highlight the importance of microbial activity in the demineralization process of tooth enamel. Methods for preventing dental decay may be promising if specific measures are implemented to reduce the amount of acid produced by oral bacteria.}, } @article {pmid39216362, year = {2024}, author = {Zhuang, J and Hou, Y and Wang, Y and Gao, Y and Chen, Y and Qi, J and Li, P and Bian, Y and Ju, N}, title = {Relationship between microorganisms and milk metabolites during quality changes in refrigerated raw milk: A metagenomic and metabolomic exploration.}, journal = {International journal of food microbiology}, volume = {425}, number = {}, pages = {110891}, doi = {10.1016/j.ijfoodmicro.2024.110891}, pmid = {39216362}, issn = {1879-3460}, mesh = {*Milk/microbiology ; Animals ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Refrigeration ; Metagenomics ; Food Storage ; Metabolomics ; Food Microbiology ; Cattle ; }, abstract = {Although cold storage at 4 °C can effectively prolong the shelf life of raw milk, it cannot prevent its eventual spoilage. In this study, we analyzed the main physicochemical and microbial indexes of raw milk stored at 4 °C for 6 days. The changes in microbial profiles and milk metabolites and their relationship during refrigeration were also explored. Metagenomic analysis performed using the Illumina Hiseq Xten sequencing platform revealed that the dominant genera in raw milk evolved from Acinetobacter, Streptococcus, Staphylococcus, and Anaplasma to Flavobacterium, Pseudomonas, and Lactococcus during cold storage. Using the UHPLC-Q-TOF MS method, 77 significantly different metabolites (p < 0.05) were identified, among which lipids were the most abundant (37). The most significant metabolic changes largely occurred at 3-4 days of refrigeration, coinciding with the rapid increase in dominant psychrotrophic bacteria. Subsequently, correlation analysis demonstrated that these lipid-related metabolites were significantly associated with Acinetobacter, Flavobacterium, and Pseudomonas. Both macro indicators and microanalysis indicated that the key stage of quality changes in raw milk was 3-4 days. Thus, this stage can be targeted for the quality control of raw milk.}, } @article {pmid39216241, year = {2024}, author = {Liao, X and Hou, L and Zhang, L and Grossart, HP and Liu, K and Liu, J and Chen, Y and Liu, Y and Hu, A}, title = {Distinct influences of altitude on microbiome and antibiotic resistome assembly in a glacial river ecosystem of Mount Everest.}, journal = {Journal of hazardous materials}, volume = {479}, number = {}, pages = {135675}, doi = {10.1016/j.jhazmat.2024.135675}, pmid = {39216241}, issn = {1873-3336}, mesh = {*Rivers/microbiology ; *Altitude ; *Microbiota/drug effects ; *Drug Resistance, Microbial/genetics ; Ecosystem ; Bacteria/genetics/drug effects/classification ; Geologic Sediments/microbiology ; Viruses/drug effects/genetics ; Anti-Bacterial Agents/pharmacology ; Ice Cover/microbiology ; China ; }, abstract = {The profound influences of altitude on aquatic microbiome were well documented. However, differences in the responses of different life domains (bacteria, microeukaryotes, viruses) and antibiotics resistance genes (ARGs) in glacier river ecosystems to altitude remain unknown. Here, we employed shotgun metagenomic and amplicon sequencing to characterize the altitudinal variations of microbiome and ARGs in the Rongbu River, Mount Everest. Our results indicated the relative influences of stochastic processes on microbiome and ARGs assembly in water and sediment were in the following order: microeukaryotes < ARGs < viruses < bacteria. Moreover, distinct assembly patterns of the microbiome and ARGs were found in response to differences in altitude, the latter of which shift from deterministic to stochastic processes with increasing differences in altitude. Partial least squares path modeling revealed that mobile genetic elements (MGEs) and viral β-diversity were the major factors influencing the ARG abundances. Taken together, our work revealed that altitude-caused environmental changes led to significant changes in the composition and assembly processes of the microbiome and ARGs, while ARGs had a unique response pattern to altitude. Our findings provide novel insights into the impacts of altitude on the biogeographic distribution of microbiome and ARGs, and the associated driving forces in glacier river ecosystems.}, } @article {pmid39216231, year = {2024}, author = {Xu, J and Li, P and Li, Z and Liu, S and Guo, H and Lesser, CF and Ke, J and Zhao, W and Mou, X}, title = {Gut bacterial type III secretion systems aggravate colitis in mice and serve as biomarkers of Crohn's disease.}, journal = {EBioMedicine}, volume = {107}, number = {}, pages = {105296}, pmid = {39216231}, issn = {2352-3964}, mesh = {Animals ; Mice ; *Crohn Disease/microbiology/metabolism/pathology ; Humans ; *Biomarkers ; *Disease Models, Animal ; *Gastrointestinal Microbiome ; *Type III Secretion Systems/metabolism/genetics ; Colitis/microbiology/metabolism ; Metagenomics/methods ; Feces/microbiology ; Female ; Male ; }, abstract = {BACKGROUND: Mesenteric adipose tissue (mAT) hyperplasia, known as creeping fat, is a pathologic characteristic of Crohn's disease (CD). In our previously reported cohort, we observed that Achromobacter pulmonis was the most abundant and prevalent bacteria cultivated from creeping fat.

METHODS: A whole genomic sequencing and identification of T3SS orthologs of mAT-derived A. pulmonis were used. A functional type III secretion system (T3SS) mediated the pathogenic potential of A. pulmonis in vitro and in mouse colitis model. Furthermore, a T3SS Finder pipeline was introduced to evaluate gut bacterial T3SS orthologs in the feces of CD patients, ulcerative colitis and colorectal cancer patients.

FINDINGS: Here, we reveal that mAT-derived A. pulmonis possesses a functional T3SS, aggravates colitis in mice via T3SS, and exhibits T3SS-dependent cytotoxicity via a caspase-independent mechanism in macrophages and epithelial cells, which demonstrated the pathogenic potential of the T3SS-harboring A. pulmonis. Metagenomic analyses demonstrate an increased abundance of Achromobacter in the fecal of Crohn's disease patients compared to healthy controls. A comprehensive comparison of total microbial vT3SS abundance in various intestine diseases demonstrated that the specific enrichment of vT3SS genes was shown in fecal samples of CD, neither ulcerative colitis nor colorectal cancer patients, and ten T3SS gene-based biomarkers for CD were discovered and validated in a newly recruited CD cohort. Furthermore, treatment with exclusive enteral nutrition (EEN), an intervention that improves CD patient symptomatology, was found associated with a significant reduction in the prevalence of T3SS genes in fecal samples.

INTERPRETATION: These findings highlight the pathogenic significance of T3SSs in the context of CD and identify specific T3SS genes that could potentially function as biomarkers for diagnosing and monitoring the clinical status of CD patients.

FUNDING: This work is supported by the National Key Research and Development Program of China (2020YFA0907800), the China Postdoctoral Science Foundation (2023M744089), the National Natural Science Foundation of China (32000096), the Shenzhen Science and Technology Programs (KQTD20200820145822023, RCIC20231211085944057, and ZDSYS20220606100803007), National Key Clinical Discipline, Guangdong Provincial Clinical Research Center for Digestive Diseases (2020B1111170004), Qingfeng Scientific Research Fund of the China Crohn's & Colitis Foundation (CCCF) (CCCF-QF-2022B71-1), and the Sixth Affiliated Hospital, Sun Yat-sen University Clinical Research 1010 Program 1010CG(2023)-08. These funding provided well support for this research work, which involved data collection, analysis, interpretation, patient recruitment and so on.}, } @article {pmid39216125, year = {2024}, author = {Kim, DW and Woo, DU and Kim, UI and Kang, YJ and Koo, OK}, title = {Development of a novel crAss-like phage detection method with a broad spectrum for microbial source tracking.}, journal = {Water research}, volume = {266}, number = {}, pages = {122330}, doi = {10.1016/j.watres.2024.122330}, pmid = {39216125}, issn = {1879-2448}, mesh = {*Bacteriophages/isolation & purification/genetics ; *Feces/virology/microbiology ; Humans ; Republic of Korea ; Animals ; Environmental Monitoring/methods ; }, abstract = {CrAssphage has been recognized as the most abundant and human-specific bacteriophage in the human gut. Consequently, crAssphage has been used as a microbial source tracking (MST) marker to monitor human fecal contamination. Many crAss-like phages (CLPs) have been recently discovered, expanding the classification into the new order Crassvirales. This study aims to assess CLP prevalence in South Korea and develop a detection system for MST applications. Thirteen CLPs were identified in six human fecal samples and categorized into seven genera via metagenomic analysis. The major head protein (MHP) displayed increased sequence similarity within each genus. Eight PCR primer candidates, designed from MHP sequences, were evaluated in animal and human feces. CLPs were absent in animal feces except for those from raccoons, which hosted genera VI, VIIa, and VIIb. CLPs were detected in 91.52% (54/59) of humans, with genus VI (38 out of 59) showing the highest prevalence, nearly double that of p-crAssphage in genus I (22 out of 59). This study highlights genus VI as a potent MST marker, broadening the detection range for CLPs. Human-specific and selectively targeted MST markers can significantly impact hygiene regulations, lowering public health costs through their application in screening liver, sewage, wastewater, and various environmental samples.}, } @article {pmid39215755, year = {2024}, author = {Cannarozzi, AL and Latiano, A and Massimino, L and Bossa, F and Giuliani, F and Riva, M and Ungaro, F and Guerra, M and Brina, ALD and Biscaglia, G and Tavano, F and Carparelli, S and Fiorino, G and Danese, S and Perri, F and Palmieri, O}, title = {Inflammatory bowel disease genomics, transcriptomics, proteomics and metagenomics meet artificial intelligence.}, journal = {United European gastroenterology journal}, volume = {12}, number = {10}, pages = {1461-1480}, pmid = {39215755}, issn = {2050-6414}, support = {PNRR-MAD-2022-12375729//Italian Next Generation Eu Program/ ; }, mesh = {Humans ; *Artificial Intelligence ; Colitis, Ulcerative/genetics/immunology/microbiology/pathology ; Crohn Disease/genetics/immunology/microbiology/pathology ; Gastrointestinal Microbiome/immunology ; *Inflammatory Bowel Diseases/genetics/immunology/microbiology/pathology ; *Metagenomics/methods ; Precision Medicine/methods ; *Proteomics/methods ; Transcriptome ; Multiomics/methods ; }, abstract = {Various extrinsic and intrinsic factors such as drug exposures, antibiotic treatments, smoking, lifestyle, genetics, immune responses, and the gut microbiome characterize ulcerative colitis and Crohn's disease, collectively called inflammatory bowel disease (IBD). All these factors contribute to the complexity and heterogeneity of the disease etiology and pathogenesis leading to major challenges for the scientific community in improving management, medical treatments, genetic risk, and exposome impact. Understanding the interaction(s) among these factors and their effects on the immune system in IBD patients has prompted advances in multi-omics research, the development of new tools as part of system biology, and more recently, artificial intelligence (AI) approaches. These innovative approaches, supported by the availability of big data and large volumes of digital medical datasets, hold promise in better understanding the natural histories, predictors of disease development, severity, complications and treatment outcomes in complex diseases, providing decision support to doctors, and promising to bring us closer to the realization of the "precision medicine" paradigm. This review aims to provide an overview of current IBD omics based on both individual (genomics, transcriptomics, proteomics, metagenomics) and multi-omics levels, highlighting how AI can facilitate the integration of heterogeneous data to summarize our current understanding of the disease and to identify current gaps in knowledge to inform upcoming research in this field.}, } @article {pmid39211485, year = {2024}, author = {Tran, DM and Nguyen, DS and Nguyen, TH and Tran, TPH and Nguyen, AD}, title = {Shotgun metagenomic dataset of root endophytic microbiome of citrus (Citrus nobilis L.).}, journal = {Data in brief}, volume = {56}, number = {}, pages = {110777}, pmid = {39211485}, issn = {2352-3409}, abstract = {Citrus (Citrus nobilis L.) is one of the main fruit crops in Dak Lak Province of Vietnam; however, a dataset on the endophytic microbiome of this plant has yet to be discovered. This article presented the endophytic microbial dataset from roots of healthy Citrus nobilis L. collected in Dak Lak for the first time. We found that 4 kingdoms, 30 phyla, 58 classes, 125 orders, 242 families, 722 genera, and 1637 species of endophytic microorganisms were identified from the sample. Actinomycetota was shown to be the main phylum (64.36 %) and biosynthesis to be the most abundant function (55.64 %) of the endophytic microbial community. Data provided insights into the composition and functional diversity of the Citrus nobilis L. endophytic microbiome, especially novel microbial resources. They could be used for the next works towards applying the endophytic microbiome for sustainable citrus production.}, } @article {pmid39209868, year = {2024}, author = {Gonzalez, E and Lee, MD and Tierney, BT and Lipieta, N and Flores, P and Mishra, M and Beckett, L and Finkelstein, A and Mo, A and Walton, P and Karouia, F and Barker, R and Jansen, RJ and Green, SJ and Weging, S and Kelliher, J and Singh, NK and Bezdan, D and Galazska, J and Brereton, NJB}, title = {Spaceflight alters host-gut microbiota interactions.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {71}, pmid = {39209868}, issn = {2055-5008}, mesh = {*Gastrointestinal Microbiome ; Animals ; *Space Flight ; Mice ; *Bacteria/classification/genetics ; Liver/microbiology ; Host Microbial Interactions ; Metagenomics/methods ; Colon/microbiology ; Bile Acids and Salts/metabolism ; Energy Metabolism ; Male ; Humans ; Mice, Inbred C57BL ; }, abstract = {The ISS rodent habitat has provided crucial insights into the impact of spaceflight on mammals, inducing symptoms characteristic of liver disease, insulin resistance, osteopenia, and myopathy. Although these physiological responses can involve the microbiome on Earth, host-microbiota interactions during spaceflight are still being elucidated. We explore murine gut microbiota and host gene expression in the colon and liver after 29 and 56 days of spaceflight using multiomics. Metagenomics revealed significant changes in 44 microbiome species, including relative reductions in bile acid and butyrate metabolising bacteria like Extibacter muris and Dysosmobacter welbionis. Functional prediction indicate over-representation of fatty acid and bile acid metabolism, extracellular matrix interactions, and antibiotic resistance genes. Host gene expression described corresponding changes to bile acid and energy metabolism, and immune suppression. These changes imply that interactions at the host-gut microbiome interface contribute to spaceflight pathology and that these interactions might critically influence human health and long-duration spaceflight feasibility.}, } @article {pmid39209853, year = {2024}, author = {Mi, J and Jing, X and Ma, C and Yang, Y and Li, Y and Zhang, Y and Long, R and Zheng, H}, title = {Massive expansion of the pig gut virome based on global metagenomic mining.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {76}, pmid = {39209853}, issn = {2055-5008}, mesh = {Animals ; Swine ; *Virome/genetics ; *Metagenomics/methods ; *Gastrointestinal Microbiome ; *Viruses/genetics/classification/isolation & purification ; *Genome, Viral ; Data Mining ; Metagenome ; Phylogeny ; }, abstract = {The pig gut virome plays a vital role in the gut microbial ecosystem of pigs. However, a comprehensive understanding of their diversity and a reference database for the virome are currently lacking. To address this gap, we established a Pig Virome Database (PVD) that comprised of 5,566,804 viral contig sequences from 4650 publicly available gut metagenomic samples using a pipeline designated "metav". By clustering sequences, we identified 48,299 viral operational taxonomic units (vOTUs) genomes of at least medium quality, of which 92.83% of which were not found in existing major databases. The majority of vOTUs were identified as Caudoviricetes (72.21%). The PVD database contained a total of 2,362,631 protein-coding genes across the above medium-quality vOTUs genomes that can be used to explore the functional potential of the pig gut virome. These findings highlight the extensive diversity of viruses in the pig gut and provide a pivotal reference dataset for forthcoming research concerning the pig gut virome.}, } @article {pmid39209850, year = {2024}, author = {Colman, DR and Keller, LM and Arteaga-Pozo, E and Andrade-Barahona, E and St Clair, B and Shoemaker, A and Cox, A and Boyd, ES}, title = {Covariation of hot spring geochemistry with microbial genomic diversity, function, and evolution.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {7506}, pmid = {39209850}, issn = {2041-1723}, support = {80NSSC19M0150//National Aeronautics and Space Administration (NASA)/ ; 80NSSC19M0150//National Aeronautics and Space Administration (NASA)/ ; 80NSSC19M0150//National Aeronautics and Space Administration (NASA)/ ; 4069947046//National Aeronautics and Space Administration (NASA)/ ; 4069947046//National Aeronautics and Space Administration (NASA)/ ; 4069947046//National Aeronautics and Space Administration (NASA)/ ; 4069947046//National Aeronautics and Space Administration (NASA)/ ; }, mesh = {*Hot Springs/microbiology/chemistry ; *Metagenome ; *Phylogeny ; Bacteria/genetics/classification/metabolism ; Hydrogen-Ion Concentration ; Archaea/genetics/classification/metabolism ; Genome, Microbial ; Ecosystem ; Microbiota/genetics ; }, abstract = {The geosphere and the microbial biosphere have co-evolved for ~3.8 Ga, with many lines of evidence suggesting a hydrothermal habitat for life's origin. However, the extent that contemporary thermophiles and their hydrothermal habitats reflect those that likely existed on early Earth remains unknown. To address this knowledge gap, 64 geochemical analytes were measured and 1022 metagenome-assembled-genomes (MAGs) were generated from 34 chemosynthetic high-temperature springs in Yellowstone National Park and analysed alongside 444 MAGs from 35 published metagenomes. We used these data to evaluate co-variation in MAG taxonomy, metabolism, and phylogeny as a function of hot spring geochemistry. We found that cohorts of MAGs and their functions are discretely distributed across pH gradients that reflect different geochemical provinces. Acidic or circumneutral/alkaline springs harbor MAGs that branched later and are enriched in sulfur- and arsenic-based O2-dependent metabolic pathways that are inconsistent with early Earth conditions. In contrast, moderately acidic springs sourced by volcanic gas harbor earlier-branching MAGs that are enriched in anaerobic, gas-dependent metabolisms (e.g. H2, CO2, CH4 metabolism) that have been hypothesized to support early microbial life. Our results provide insight into the influence of redox state in the eco-evolutionary feedbacks between thermophiles and their habitats and suggest moderately acidic springs as early Earth analogs.}, } @article {pmid39215001, year = {2024}, author = {Becsei, Á and Fuschi, A and Otani, S and Kant, R and Weinstein, I and Alba, P and Stéger, J and Visontai, D and Brinch, C and de Graaf, M and Schapendonk, CME and Battisti, A and De Cesare, A and Oliveri, C and Troja, F and Sironen, T and Vapalahti, O and Pasquali, F and Bányai, K and Makó, M and Pollner, P and Merlotti, A and Koopmans, M and Csabai, I and Remondini, D and Aarestrup, FM and Munk, P}, title = {Time-series sewage metagenomics distinguishes seasonal, human-derived and environmental microbial communities potentially allowing source-attributed surveillance.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {7551}, pmid = {39215001}, issn = {2041-1723}, support = {NNF16OC0021856//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF16OC0021856//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 874735//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 874735//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; }, mesh = {*Sewage/microbiology ; *Metagenomics/methods ; *Seasons ; Humans ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification ; *Metagenome/genetics ; Europe ; }, abstract = {Sewage metagenomics has risen to prominence in urban population surveillance of pathogens and antimicrobial resistance (AMR). Unknown species with similarity to known genomes cause database bias in reference-based metagenomics. To improve surveillance, we seek to recover sewage genomes and develop a quantification and correlation workflow for these genomes and AMR over time. We use longitudinal sewage sampling in seven treatment plants from five major European cities to explore the utility of catch-all sequencing of these population-level samples. Using metagenomic assembly methods, we recover 2332 metagenome-assembled genomes (MAGs) from prokaryotic species, 1334 of which were previously undescribed. These genomes account for ~69% of sequenced DNA and provide insight into sewage microbial dynamics. Rotterdam (Netherlands) and Copenhagen (Denmark) show strong seasonal microbial community shifts, while Bologna, Rome, (Italy) and Budapest (Hungary) have occasional blooms of Pseudomonas-dominated communities, accounting for up to ~95% of sample DNA. Seasonal shifts and blooms present challenges for effective sewage surveillance. We find that bacteria of known shared origin, like human gut microbiota, form communities, suggesting the potential for source-attributing novel species and their ARGs through network community analysis. This could significantly improve AMR tracking in urban environments.}, } @article {pmid39214983, year = {2024}, author = {Duan, Y and Santos-Júnior, CD and Schmidt, TS and Fullam, A and de Almeida, BLS and Zhu, C and Kuhn, M and Zhao, XM and Bork, P and Coelho, LP}, title = {A catalog of small proteins from the global microbiome.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {7563}, pmid = {39214983}, issn = {2041-1723}, support = {61932008//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Microbiota/genetics ; *Open Reading Frames/genetics ; *Bacteria/genetics/classification/metabolism ; *Metagenome/genetics ; *Archaea/genetics/metabolism/classification ; Molecular Sequence Annotation ; Bacterial Proteins/genetics/metabolism ; }, abstract = {Small open reading frames (smORFs) shorter than 100 codons are widespread and perform essential roles in microorganisms, where they encode proteins active in several cell functions, including signal pathways, stress response, and antibacterial activities. However, the ecology, distribution and role of small proteins in the global microbiome remain unknown. Here, we construct a global microbial smORFs catalog (GMSC) derived from 63,410 publicly available metagenomes across 75 distinct habitats and 87,920 high-quality isolate genomes. GMSC contains 965 million non-redundant smORFs with comprehensive annotations. We find that archaea harbor more smORFs proportionally than bacteria. We moreover provide a tool called GMSC-mapper to identify and annotate small proteins from microbial (meta)genomes. Overall, this publicly-available resource demonstrates the immense and underexplored diversity of small proteins.}, } @article {pmid39214976, year = {2024}, author = {Yi, X and Liang, JL and Wen, P and Jia, P and Feng, SW and Liu, SY and Zhuang, YY and Guo, YQ and Lu, JL and Zhong, SJ and Liao, B and Wang, Z and Shu, WS and Li, JT}, title = {Giant viruses as reservoirs of antibiotic resistance genes.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {7536}, pmid = {39214976}, issn = {2041-1723}, mesh = {*Phylogeny ; *Giant Viruses/genetics ; *Genome, Viral/genetics ; Drug Resistance, Microbial/genetics ; Bacteriophages/genetics/isolation & purification ; Anti-Bacterial Agents/pharmacology ; Metagenome/genetics ; Gene Transfer, Horizontal ; Trimethoprim/pharmacology ; Drug Resistance, Bacterial/genetics ; }, abstract = {Nucleocytoplasmic large DNA viruses (NCLDVs; also called giant viruses), constituting the phylum Nucleocytoviricota, can infect a wide range of eukaryotes and exchange genetic material with not only their hosts but also prokaryotes and phages. A few NCLDVs were reported to encode genes conferring resistance to beta‑lactam, trimethoprim, or pyrimethamine, suggesting that they are potential vehicles for the transmission of antibiotic resistance genes (ARGs) in the biome. However, the incidence of ARGs across the phylum Nucleocytoviricota, their evolutionary characteristics, their dissemination potential, and their association with virulence factors remain unexplored. Here, we systematically investigated ARGs of 1416 NCLDV genomes including those of almost all currently available cultured isolates and high-quality metagenome-assembled genomes from diverse habitats across the globe. We reveal that 39.5% of them carry ARGs, which is approximately 37 times higher than that for phage genomes. A total of 12 ARG types are encoded by NCLDVs. Phylogenies of the three most abundant NCLDV-encoded ARGs hint that NCLDVs acquire ARGs from not only eukaryotes but also prokaryotes and phages. Two NCLDV-encoded trimethoprim resistance genes are demonstrated to confer trimethoprim resistance in Escherichia coli. The presence of ARGs in NCLDV genomes is significantly correlated with mobile genetic elements and virulence factors.}, } @article {pmid39214237, year = {2025}, author = {Macowan, M and Pattaroni, C and Bonner, K and Chatzis, R and Daunt, C and Gore, M and Custovic, A and Shields, MD and Power, UF and Grigg, J and Roberts, G and Ghazal, P and Schwarze, J and Turner, S and Bush, A and Saglani, S and Lloyd, CM and Marsland, BJ}, title = {Deep multiomic profiling reveals molecular signatures that underpin preschool wheeze and asthma.}, journal = {The Journal of allergy and clinical immunology}, volume = {155}, number = {1}, pages = {94-106}, doi = {10.1016/j.jaci.2024.08.017}, pmid = {39214237}, issn = {1097-6825}, mesh = {Humans ; *Respiratory Sounds/genetics/immunology ; *Asthma/genetics/immunology ; Child, Preschool ; Child ; Female ; Male ; Adolescent ; Infant ; Microbiota ; Gene Expression Profiling ; Transcriptome ; }, abstract = {BACKGROUND: Wheezing in childhood is prevalent, with over one-half of all children experiencing at least 1 episode by age 6. The pathophysiology of wheeze, especially why some children develop asthma while others do not, remains unclear.

OBJECTIVES: This study addresses the knowledge gap by investigating the transition from preschool wheeze to asthma using multiomic profiling.

METHODS: Unsupervised, group-agnostic integrative multiomic factor analysis was performed using host/bacterial (meta)transcriptomic and bacterial shotgun metagenomic datasets from bronchial brush samples paired with metabolomic/lipidomic data from bronchoalveolar lavage samples acquired from children 1-17 years old.

RESULTS: Two multiomic factors were identified: one characterizing preschool-aged recurrent wheeze and another capturing an inferred trajectory from health to wheeze and school-aged asthma. Recurrent wheeze was driven by type 1-immune signatures, coupled with upregulation of immune-related and neutrophil-associated lipids and metabolites. Comparatively, progression toward asthma from ages 1 to 18 was dominated by changes related to airway epithelial cell gene expression, type 2-immune responses, and constituents of the airway microbiome, such as increased Haemophilus influenzae.

CONCLUSIONS: These factors highlighted distinctions between an inflammation-related phenotype in preschool wheeze, and the predominance of airway epithelial-related changes linked with the inferred trajectory toward asthma. These findings provide insights into the differential mechanisms driving the progression from wheeze to asthma and may inform targeted therapeutic strategies.}, } @article {pmid39214173, year = {2024}, author = {Pan, K and Qian, Z and Guo, T and Chen, Y and Li, F and Ding, M and Ma, X and Li, J}, title = {Effects of iron-carbon on nitrogen metabolism of floc and aerobic granular sludge.}, journal = {Bioresource technology}, volume = {413}, number = {}, pages = {131376}, doi = {10.1016/j.biortech.2024.131376}, pmid = {39214173}, issn = {1873-2976}, mesh = {*Sewage/microbiology ; *Nitrogen/metabolism ; *Iron/metabolism ; *Carbon/metabolism ; Aerobiosis ; Denitrification ; Bioreactors ; Ammonia/metabolism ; Nitrites/metabolism ; }, abstract = {The aerobic granular sludge (AGS) process had been extensively studied for its simultaneous nitrification and denitrification (SND) capabilities. Iron-carbon (IC) had enhanced AGS nitrogen removal efficiency, but the mechanism remained unclear. In this study, four reactors had been added with 50, 30, 10, and 0 g/L of IC. Total nitrogen removal efficiency increased with IC dosage under the same operation mode. IC enhanced sludge ammonia oxidation rate, denitrification rate, and specific oxygen uptake rate, allowing SND to complete 60 min earlier, potentially reducing wastewater treatment costs. Notably, IC eliminated nitrite accumulation in conventional AGS effluent. IC decreased the abundance of genes and enzyme activities related to NOR expression, while increasing those related to NOS, which may mitigate the potential for nitrous oxide formation by microorganisms. In this study, IC acted as an enzymatic reaction activator, affecting granules more than flocs, with the activity gap gradually decreasing with the IC dosage.}, } @article {pmid39214080, year = {2024}, author = {Carlino, N and Blanco-Míguez, A and Punčochář, M and Mengoni, C and Pinto, F and Tatti, A and Manghi, P and Armanini, F and Avagliano, M and Barcenilla, C and Breselge, S and Cabrera-Rubio, R and Calvete-Torre, I and Coakley, M and Cobo-Díaz, JF and De Filippis, F and Dey, H and Leech, J and Klaassens, ES and Knobloch, S and O'Neil, D and Quijada, NM and Sabater, C and Skírnisdóttir, S and Valentino, V and Walsh, L and , and Alvarez-Ordóñez, A and Asnicar, F and Fackelmann, G and Heidrich, V and Margolles, A and Marteinsson, VT and Rota Stabelli, O and Wagner, M and Ercolini, D and Cotter, PD and Segata, N and Pasolli, E}, title = {Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome.}, journal = {Cell}, volume = {187}, number = {20}, pages = {5775-5795.e15}, doi = {10.1016/j.cell.2024.07.039}, pmid = {39214080}, issn = {1097-4172}, mesh = {Humans ; *Metagenome/genetics ; *Gastrointestinal Microbiome/genetics ; Microbiota/genetics ; Food Microbiology ; Metagenomics/methods ; Bacteria/genetics/classification ; }, abstract = {Complex microbiomes are part of the food we eat and influence our own microbiome, but their diversity remains largely unexplored. Here, we generated the open access curatedFoodMetagenomicData (cFMD) resource by integrating 1,950 newly sequenced and 583 public food metagenomes. We produced 10,899 metagenome-assembled genomes spanning 1,036 prokaryotic and 108 eukaryotic species-level genome bins (SGBs), including 320 previously undescribed taxa. Food SGBs displayed significant microbial diversity within and between food categories. Extension to >20,000 human metagenomes revealed that food SGBs accounted on average for 3% of the adult gut microbiome. Strain-level analysis highlighted potential instances of food-to-gut transmission and intestinal colonization (e.g., Lacticaseibacillus paracasei) as well as SGBs with divergent genomic structures in food and humans (e.g., Streptococcus gallolyticus and Limosilactobabillus mucosae). The cFMD expands our knowledge on food microbiomes, their role in shaping the human microbiome, and supports future uses of metagenomics for food quality, safety, and authentication.}, } @article {pmid39213166, year = {2024}, author = {Djeghout, B and Le-Viet, T and Martins, LO and Savva, GM and Evans, R and Baker, D and Page, A and Elumogo, N and Wain, J and Janecko, N}, title = {Capturing clinically relevant Campylobacter attributes through direct whole genome sequencing of stool.}, journal = {Microbial genomics}, volume = {10}, number = {8}, pages = {}, pmid = {39213166}, issn = {2057-5858}, mesh = {*Feces/microbiology ; Humans ; *Campylobacter/genetics/isolation & purification/classification ; *Whole Genome Sequencing/methods ; *Campylobacter Infections/microbiology ; Genome, Bacterial ; Metagenome ; Metagenomics/methods ; Diarrhea/microbiology ; Phylogeny ; }, abstract = {Campylobacter is the leading bacterial cause of infectious intestinal disease, but the pathogen typically accounts for a very small proportion of the overall stool microbiome in each patient. Diagnosis is even more difficult due to the fastidious nature of Campylobacter in the laboratory setting. This has, in part, driven a change in recent years, from culture-based to rapid PCR-based diagnostic assays which have improved diagnostic detection, whilst creating a knowledge gap in our clinical and epidemiological understanding of Campylobacter genotypes - no isolates to sequence. In this study, direct metagenomic sequencing approaches were used to assess the possibility of replacing genome sequences with metagenome sequences; metagenomic sequencing outputs were used to describe clinically relevant attributes of Campylobacter genotypes. A total of 37 diarrhoeal stool samples with Campylobacter and five samples with an unknown pathogen result were collected and processed with and without filtration, DNA was extracted, and metagenomes were sequenced by short-read sequencing. Culture-based methods were used to validate Campylobacter metagenome-derived genome (MDG) results. Sequence output metrics were assessed for Campylobacter genome quality and accuracy of characterization. Of the 42 samples passing quality checks for analysis, identification of Campylobacter to the genus and species level was dependent on Campylobacter genome read count, coverage and genome completeness. A total of 65% (24/37) of samples were reliably identified to the genus level through Campylobacter MDG, 73% (27/37) by culture and 97% (36/37) by qPCR. The Campylobacter genomes with a genome completeness of over 60% (n=21) were all accurately identified at the species level (100%). Of those, 72% (15/21) were identified to sequence types (STs), and 95% (20/21) accurately identified antimicrobial resistance (AMR) gene determinants. Filtration of stool samples enhanced Campylobacter MDG recovery and genome quality metrics compared to the corresponding unfiltered samples, which improved the identification of STs and AMR profiles. The phylogenetic analysis in this study demonstrated the clustering of the metagenome-derived with culture-derived genomes and revealed the reliability of genomes from direct stool sequencing. Furthermore, Campylobacter genome spiking percentages ranging from 0 to 2% total metagenome abundance in the ONT MinION sequencer, configured to adaptive sequencing, exhibited better assembly quality and accurate identification of STs, particularly in the analysis of metagenomes containing 2 and 1% of Campylobacter jejuni genomes. Direct sequencing of Campylobacter from stool samples provides clinically relevant and epidemiologically important genomic information without the reliance on cultured genomes.}, } @article {pmid39212408, year = {2024}, author = {Child, HT and Airey, G and Maloney, DM and Parker, A and Wild, J and McGinley, S and Evens, N and Porter, J and Templeton, K and Paterson, S and van Aerle, R and Wade, MJ and Jeffries, AR and Bassano, I}, title = {Erratum for Child et al., "Comparison of metagenomic and targeted methods for sequencing human pathogenic viruses from wastewater".}, journal = {mBio}, volume = {15}, number = {10}, pages = {e0255824}, doi = {10.1128/mbio.02558-24}, pmid = {39212408}, issn = {2150-7511}, } @article {pmid39212280, year = {2024}, author = {Taylor, W and Devane, ML and Russell, K and Lin, S and Roxburgh, C and Williamson, J and Gilpin, BJ}, title = {Metagenomic evaluation of bacteria in drinking water using full-length 16S rRNA amplicons.}, journal = {Journal of water and health}, volume = {22}, number = {8}, pages = {1429-1443}, pmid = {39212280}, issn = {1477-8920}, support = {Strategic Science Internal Funding (SSIF)//Ministry of Business, Innovation and Employment/ ; }, mesh = {*Drinking Water/microbiology ; *RNA, Ribosomal, 16S/analysis/genetics ; *Metagenomics/methods ; *Water Microbiology ; *Bacteria/genetics/classification/isolation & purification ; Water Purification ; Escherichia coli/isolation & purification/genetics ; Feces/microbiology ; Environmental Monitoring/methods ; }, abstract = {Escherichia coli and total coliforms are important tools for identifying potential faecal contamination in drinking water. However, metagenomics offers a powerful approach for delving deeper into a bacterial community when E. coli or total coliforms are detected. Metagenomics can identify microbes native to water systems, track community changes and potential pathogens introduced by contamination events, and evaluate the effectiveness of treatment processes. Here, we demonstrate how the dual application of traditional monitoring practices and metagenomics can improve monitoring and surveillance for water resource management. The robustness of long-read metagenomics across replicates is demonstrated by the effect and interaction between manganese filters and bacterial communities, as well as the impact of chlorination after coliform detection. These examples reveal how metagenomics can identify the complex bacterial communities in the distribution system and the source waters used to supply drinking water treatment plants (DWTPs). The knowledge gained increases confidence in identified causes and mitigations of potential contamination events. By exploring bacterial communities, we can gain additional insights into the impact of faecal contamination events and treatment processes. This insight enables more precise remediation actions and enhances confidence in communicating health risks to drinking water operators and the public.}, } @article {pmid39211470, year = {2024}, author = {Graboski, AL and Simpson, JB and Pellock, SJ and Mehta, N and Creekmore, BC and Ariyarathna, Y and Bhatt, AP and Jariwala, PB and Sekela, JJ and Kowalewski, ME and Barker, NK and Mordant, AL and Borlandelli, VB and Overkleeft, H and Herring, LE and Jin, J and I James, L and Redinbo, MR}, title = {Advanced piperazine-containing inhibitors target microbial β-glucuronidases linked to gut toxicity.}, journal = {RSC chemical biology}, volume = {5}, number = {9}, pages = {853-865}, pmid = {39211470}, issn = {2633-0679}, support = {R01 GM135218/GM/NIGMS NIH HHS/United States ; R01 GM137286/GM/NIGMS NIH HHS/United States ; R35 GM152079/GM/NIGMS NIH HHS/United States ; }, abstract = {The gut microbiome plays critical roles in human homeostasis, disease progression, and pharmacological efficacy through diverse metabolic pathways. Gut bacterial β-glucuronidase (GUS) enzymes reverse host phase 2 metabolism, in turn releasing active hormones and drugs that can be reabsorbed into systemic circulation to affect homeostasis and promote toxic side effects. The FMN-binding and loop 1 gut microbial GUS proteins have been shown to drive drug and toxin reactivation. Here we report the structure-activity relationships of two selective piperazine-containing bacterial GUS inhibitors. We explore the potency and mechanism of action of novel compounds using purified GUS enzymes and co-crystal structures. Our results establish the importance of the piperazine nitrogen placement and nucleophilicity as well as the presence of a cyclohexyl moiety appended to the aromatic core. Using these insights, we synthesized an improved microbial GUS inhibitor, UNC10206581, that potently inhibits both the FMN-binding and loop 1 GUS enzymes in the human gut microbiome, does not inhibit bovine GUS, and is non-toxic within a relevant dosing range. Kinetic analyses demonstrate that UNC10206581 undergoes a slow-binding and substrate-dependent mechanism of inhibition similar to that of the parent scaffolds. Finally, we show that UNC10206581 displays potent activity within the physiologically relevant systems of microbial cultures and human fecal protein lysates examined by metagenomic and metaproteomic methods. Together, these results highlight the discovery of more effective bacterial GUS inhibitors for the alleviation of microbe-mediated homeostatic dysregulation and drug toxicities and potential therapeutic development.}, } @article {pmid39211202, year = {2024}, author = {Grodner, B and Wu, DT and Hahm, S and Takayasu, L and Wen, N and Kim, DM and Chen, CY and De Vlaminck, I}, title = {Microscale Spatial Dysbiosis in Oral biofilms Associated with Disease.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.07.24.604873}, pmid = {39211202}, issn = {2692-8205}, abstract = {Microbiome dysbiosis has largely been defined using compositional analysis of metagenomic sequencing data; however, differences in the spatial arrangement of bacteria between healthy and diseased microbiomes remain largely unexplored. In this study, we measured the spatial arrangement of bacteria in dental implant biofilms from patients with healthy implants, peri-implant mucositis, or peri-implantitis, an oral microbiome-associated inflammatory disease. We discovered that peri-implant biofilms from patients with mild forms of the disease were characterized by large single-genus patches of bacteria, while biofilms from healthy sites were more complex, mixed structures. Based on these findings, we propose a model of peri-implant dysbiosis where changes in biofilm spatial architecture allow the colonization of new community members. This model indicates that spatial structure could be used as a potential biomarker for community stability and has implications in diagnosis and treatment of peri-implant diseases. These results enhance our understanding of peri-implant disease pathogenesis and may be broadly relevant for spatially structured microbiomes.}, } @article {pmid39210977, year = {2024}, author = {Ekpruke, CD and Alford, R and Rousselle, D and Babayev, M and Sharma, S and Parker, E and Davis, K and Hemmerich, C and Rusch, DB and Silveyra, P}, title = {Sex-specific alterations in the gut and lung microbiome of allergen-induced mice.}, journal = {Frontiers in allergy}, volume = {5}, number = {}, pages = {1451846}, pmid = {39210977}, issn = {2673-6101}, support = {T32 HD049336/HD/NICHD NIH HHS/United States ; }, abstract = {INTRODUCTION: Recent evidence has demonstrated that the microbiome is a driver of the underlying pathophysiological mechanisms of respiratory disease. Studies have indicated that bacterial metabolites produced in the gut and lung can impact lung inflammation and immune cell activity, affecting disease pathology. Despite asthma being a disease with marked sex differences, experimental work linking microbiomes and asthma has not considered the sex variable.

METHODS: To test the hypothesis that the lung and gut microbial composition impacts allergic lung inflammation in a sex-specific manner, we evaluated lung and gut microbiome alterations in a mouse model of allergic inflammation and assessed their association with lung function and inflammation phenotypes. For this, we exposed male and female adult C57BL/6J mice intranasally to 25 µg of a house dust mite extract mix (HDM) daily, or phosphate-buffered saline (PBS) as control, for 5 weeks (n = 4-6/group). DNA from fecal pellets collected before and after the 5-week treatment, and from lung tissue collected at endpoint, was extracted using the ZymoBIOMICS®-96 MagBead DNA Kit and analyzed to determine the 16S microbiome via Targeted Metagenomic Sequencing.

RESULTS: The HDM treatment induced a sex-specific allergic inflammation phenotype with significantly higher neutrophilia, lymphocytosis, inflammatory gene expression, and histopathological changes in females than males following exposure to HDM, but higher airway hyperresponsiveness (AHR) in males than females. In addition, sex-specific lung gene expression and associated pathways were identified HDM mix after challenge. These changes corresponded to sex-specific alterations in the gut microbiome, where the Firmicutes to Bacteroidetes ratio (F:B) was significantly reduced in fecal samples from only male mice after HDM challenge, and alpha diversity was increased in males, but decreased in females, after 5-weeks of HDM treatment.

DISCUSSION: Overall, our findings indicate that intranasal allergen challenge triggers sex-specific changes in both gut and lung microbiomes, and induces sex-specific lung inflammation, AHR, and lung inflammatory gene expression pathways, suggesting a contribution of the lung-gut axis in allergic airway disease.}, } @article {pmid39210818, year = {2025}, author = {Souza, KL and Dias, CP and Callegari, MA and Friderichs, A and Paes, AOS and de Carvalho, RH and da Silva, CA}, title = {Performance and intestinal health of piglets in the nursery phase subjected to diets with condensed black wattle (Acacia mearnsii) tannin.}, journal = {Animal bioscience}, volume = {38}, number = {1}, pages = {117-130}, pmid = {39210818}, issn = {2765-0189}, abstract = {OBJECTIVE: The objective of this study was to evaluate the use of condensed tannin from black acacia (Acacia mearnsii) as a substitute additive for zinc oxide and growth-promoting antibiotics on the performance, digestibility, and intestinal health of piglets in the nursery phase.

METHODS: A total of 200 PIC piglets that were 22 days old and weighed 6.0±0.9 kg were subjected to four treatments in the nursery phase (22 to 64 days of age): CONTR (control diet); ENR+ZnO (control diet + 10 mg/kg of enramycin + 2,500 mg/kg of zinc oxide during the first 21 days); BUT (control diet + 900 mg/kg of sodium butyrate) and TAN (control diet + 2,000 mg/kg of condensed tannin). The experimental design was a randomized block with 4 treatments and 10 replicates, with a pen of five animals each as the experimental unit. The zootechnical performance, diarrhea index score, dietary digestibility and metagenomics of the deep rectum microbiota were evaluated.

RESULTS: The TAN had greater weight gain in the nursery phase and final weight (p<0.05) than the CONTR (394 vs 360 g/d, and 22.6 vs 21.1 kg, respectively), with these values being intermediate for the ENR+ZnO and BUT (365 and 382 g/d, and 21.3 and 22.1 kg, respectively). There was no difference between treatments for semi-liquid diarrhea (score 2), but CONTR had more cases of severe diarrhea (score 3; p<0.05) than ENR+ZnO, BUT and TAN, with 42, 18, 29, and 21 cases, respectively. The treatments had no impact on rare taxa or the relative abundances of taxonomic groups (uniformity), but the use of TAN promoted an increase in the abundances of Brevibacillus spp. and Enterococcus spp. compared to the other treatments (p<0.05).

CONCLUSION: The use of condensed tannin from black wattle as a performance-enhancing additive was effective, with effects on performance and intestinal health, demonstrating its potential as a substitute for zinc oxide and enramycin in the diets of piglets in nursery phase.}, } @article {pmid39210613, year = {2024}, author = {Xu, Y and Wu, X and Li, Y and Liu, X and Fang, L and Jiang, Z}, title = {Probiotics and the Role of Dietary Substrates in Maintaining the Gut Health: Use of Live Microbes and Their Products for Anticancer Effects against Colorectal Cancer.}, journal = {Journal of microbiology and biotechnology}, volume = {34}, number = {10}, pages = {1933-1946}, pmid = {39210613}, issn = {1738-8872}, mesh = {*Probiotics/therapeutic use ; *Colorectal Neoplasms/microbiology ; Humans ; *Gastrointestinal Microbiome ; Fecal Microbiota Transplantation ; Animals ; Diet ; Bacteria/classification/genetics/metabolism ; Gastrointestinal Tract/microbiology ; Bifidobacterium ; Antineoplastic Agents ; }, abstract = {The gut microbiome is an important and the largest endocrine organ linked to the microbes of the GI tract. The bacterial, viral and fungal communities are key regulators of the health and disease status in a host at hormonal, neurological, immunological, and metabolic levels. The useful microbes can compete with microbes exhibiting pathogenic behavior by maintaining resistance against their colonization, thereby maintaining eubiosis. As diagnostic tools, metagenomic, proteomic and genomic approaches can determine various microbial markers in clinic for early diagnosis of colorectal cancer (CRC). Probiotics are live non-pathogenic microorganisms such as lactic acid bacteria, Bifidobacteria, Firmicutes and Saccharomyces that can help maintain eubiosis when administered in appropriate amounts. In addition, the type of dietary intake contributes substantially to the composition of gut microbiome. The use of probiotics has been found to exert antitumor effects at preclinical levels and promote the antitumor effects of immunotherapeutic drugs at clinical levels. Also, modifying the composition of gut microbiota by Fecal Microbiota Transplantation (FMT), and using live lactic acid producing bacteria such as Lactobacillus, Bifidobacteria and their metabolites (termed postbiotics) can contribute to immunomodulation of the tumor microenvironment. This can lead to tumor-preventive effects at early stages and antitumor effects after diagnosis of CRC. To conclude, probiotics are presumably found to be safe to use in humans and are to be studied further to promote their appliance at clinical levels for management of CRC.}, } @article {pmid39210307, year = {2024}, author = {Zheng, Y and Liu, W and Xiao, T and Chen, H and Liu, Y}, title = {Clinical utility of metagenomic next-generation sequencing on bronchoalveolar lavage fluid in diagnosis of lower respiratory tract infections.}, journal = {BMC pulmonary medicine}, volume = {24}, number = {1}, pages = {422}, pmid = {39210307}, issn = {1471-2466}, support = {2019A1515110566//Basic and Applied Basic Research Foundation of Guangdong Province/ ; }, mesh = {Humans ; *Bronchoalveolar Lavage Fluid/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Retrospective Studies ; Female ; Middle Aged ; *Respiratory Tract Infections/diagnosis/microbiology ; *Metagenomics/methods ; Adult ; Aged ; Sensitivity and Specificity ; Young Adult ; }, abstract = {BACKGROUND: In this study, we aimed to evaluate the clinical utility of Metagenomic Next-Generation sequencing (mNGS) on bronchoalveolar lavage fluid (BALF) in diagnosis of Lower Respiratory Tract Infections (LRTIs).

METHODS: In this study, we retrospectively analyzed 186 hospitalized patients who were suspected with LRTIs and performed mNGS (DNA) test of BALF simultaneously at The Fifth Affiliated Hospital of Sun Yat-Sen University from March 2023 to August 2023. Suspected LRTI was based on LRTI related clinical manifestations or imaging examination. Among them, 155 patients had undergone conventional culture and mNGS (DNA) testing simultaneously. Finally, 138 cases (89.03%,138/155) were diagnosed as LRTI and 17 cases (10.97%,17/155) were diagnosed as non-LRTI. Both detecting rate and diagnostic efficacy of mNGS and conventional culture were compared.

RESULTS: The positive detection rates of pathogens between mNGS and conventional culture were significant different (81.29% VS 39.35%, P < 0.05). Compared with paired conventional culture result, the sensitivity of mNGS in diagnosis of LRTIs was more superior (88.41% VS 43.48%; P < 0.05), the specificity was opposite (76.47% VS 94.12%; P > 0.05). Furthermore, 77.54% and 35.51% of LRTI cases were being etiologically diagnosed by mNGS and culture respectively. Importantly, mNGS directly led to a change of treatment regimen in 58 (37.42%) cases, including antibiotic adjustment (29.68%) and ruling out active infection (7.74%). Moreover, treatment regimen remained unchanged in 97 (62.58%) cases, considering the current antibiotic therapy already covered the detected pathogens (36.13%) or empirical treatment was effective (11.61%).

CONCLUSIONS: mNGS can identify a wide range of pathogens in LRTIs, with improved sensitivity and being more superior at diagnosing LRTIs etiologically. mNGS has the potential to enhance clinical outcomes by optimizing the treatment regimens.}, } @article {pmid39210095, year = {2024}, author = {Lu, J and Rincon, N and Wood, DE and Breitwieser, FP and Pockrandt, C and Langmead, B and Salzberg, SL and Steinegger, M}, title = {Author Correction: Metagenome analysis using the Kraken software suite.}, journal = {Nature protocols}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41596-024-01064-1}, pmid = {39210095}, issn = {1750-2799}, } @article {pmid39209985, year = {2024}, author = {Maini Rekdal, V and Villalobos-Escobedo, JM and Rodriguez-Valeron, N and Olaizola Garcia, M and Prado Vásquez, D and Rosales, A and Sörensen, PM and Baidoo, EEK and Calheiros de Carvalho, A and Riley, R and Lipzen, A and He, G and Yan, M and Haridas, S and Daum, C and Yoshinaga, Y and Ng, V and Grigoriev, IV and Munk, R and Wijaya, CH and Nuraida, L and Damayanti, I and Cruz-Morales, P and Keasling, JD}, title = {Neurospora intermedia from a traditional fermented food enables waste-to-food conversion.}, journal = {Nature microbiology}, volume = {9}, number = {10}, pages = {2666-2683}, pmid = {39209985}, issn = {2058-5276}, mesh = {*Fermentation ; *Fermented Foods/microbiology ; *Neurospora/genetics/metabolism/classification ; *Phylogeny ; Indonesia ; Food Microbiology ; Metagenomics ; Humans ; Metabolomics/methods ; }, abstract = {Fungal fermentation of food and agricultural by-products holds promise for improving food sustainability and security. However, the molecular basis of fungal waste-to-food upcycling remains poorly understood. Here we use a multi-omics approach to characterize oncom, a fermented food traditionally produced from soymilk by-products in Java, Indonesia. Metagenomic sequencing of samples from small-scale producers in Western Java indicated that the fungus Neurospora intermedia dominates oncom. Further transcriptomic, metabolomic and phylogenomic analysis revealed that oncom-derived N. intermedia utilizes pectin and cellulose degradation during fermentation and belongs to a genetically distinct subpopulation associated with human-generated by-products. Finally, we found that N. intermedia grew on diverse by-products such as fruit and vegetable pomace and plant-based milk waste, did not encode mycotoxins, and could create foods that were positively perceived by consumers outside Indonesia. These results showcase the traditional significance and future potential of fungal fermentation for creating delicious and nutritious foods from readily available by-products.}, } @article {pmid39209935, year = {2024}, author = {Starkova, D and Gladyshev, N and Polev, D and Saitova, A and Egorova, S and Svarval, A}, title = {First insight into the whole genome sequence variations in clarithromycin resistant Helicobacter pylori clinical isolates in Russia.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {20108}, pmid = {39209935}, issn = {2045-2322}, mesh = {*Clarithromycin/pharmacology ; *Helicobacter pylori/genetics/drug effects ; Russia/epidemiology ; Humans ; *Drug Resistance, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; *Microbial Sensitivity Tests ; *Whole Genome Sequencing/methods ; *Helicobacter Infections/microbiology/drug therapy ; Mutation ; RNA, Ribosomal, 23S/genetics ; Genome, Bacterial ; Male ; Genetic Variation ; Female ; Adult ; Middle Aged ; Aged ; }, abstract = {Clarithromycin (CLR) is currently a key antibiotic for Helicobacter pylori infection treatment, however, the data on CLR resistance patterns in Russia are missing. Here, we applied WGS-based approach to H. pylori clinical isolates from Russia to comprehensively investigate sequence variation, identify putative markers of CLR resistance and correlate them with phenotypic susceptibility testing. The phenotypic susceptibility of 44 H. pylori isolates (2014-2022) to CLR was determined by disc diffusion method: 23 isolates were CLR-resistant and 21-CLR-susceptible. All isolates were subjected to WGS and submitted to GenBank. Based on complete sequence analysis, we showed that among all sequence variants, the combination of mutations A2146G/A2147G in the 23S rRNA gene is the most reliable for prediction of phenotypic susceptibility. For the first time, the average number of mutations in 106 virulence-associated genes between resistant and susceptible groups were compared. Moreover, this study presents the first WGS insight into genetic diversity of H. pylori in Russia with a particular focus on the molecular basis of drug resistance: the novel mutations were described as potential markers for the resistance development. Of these, the most prominent was a frameshift deletion (252:CGGGT) in HP0820 coding region, which is a good candidate for further investigation.}, } @article {pmid39209855, year = {2024}, author = {Whittle, MJ and Castillo-Fernandez, J and Amos, GCA and Watson, P}, title = {Metagenomic characterisation of canine skin reveals a core healthy skin microbiome.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {20104}, pmid = {39209855}, issn = {2045-2322}, mesh = {Dogs ; Animals ; *Skin/microbiology ; *Microbiota ; *Metagenomics/methods ; Metagenome ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; }, abstract = {Furthering our knowledge of the skin microbiome is essential to understand health and disease in canines. To date, studies into the canine skin microbiome have focused on 16S rRNA high throughput sequencing however, these lack the granularity of species and strain level taxonomic characterisation and their associated functions. The aim of this study was to provide a comprehensive assessment of the skin microbiome by analysing the skin microbiome of 72 healthy adult colony dogs, across four distinct skin sites and four breeds, using metagenomic sequencing. Our analysis revealed that breed and skin site are drivers of variation, and a core group of taxa and genes are present within the skin microbiome of healthy dogs, comprising 230 taxa and 1219 gene families. We identified 15 species within the core microbiome that are represented by more than one strain. The biosynthesis of secondary metabolites pathway was enriched in the core microbiome suggesting the skin microbiome may play a role in colonisation resistance and protection from invading pathogens. Additionally, we uncovered the novelty of the canine skin microbiome and show that further investigation is required to increase the suitability of current databases for metagenomic sequencing of canine skin samples.}, } @article {pmid39209553, year = {2024}, author = {Şapcı, AOB and Mirarab, S}, title = {Memory-bound k-mer selection for large and evolutionarily diverse reference libraries.}, journal = {Genome research}, volume = {34}, number = {9}, pages = {1455-1467}, pmid = {39209553}, issn = {1549-5469}, support = {R35 GM142725/GM/NIGMS NIH HHS/United States ; }, mesh = {*Algorithms ; Metagenomics/methods ; Humans ; Gene Library ; Software ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; Databases, Genetic ; Metagenome ; }, abstract = {Using k-mers to find sequence matches is increasingly used in many bioinformatic applications, including metagenomic sequence classification. The accuracy of these downstream applications relies on the density of the reference databases, which are rapidly growing. Although the increased density provides hope for improvements in accuracy, scalability is a concern. Reference k-mers are kept in the memory during the query time, and saving all k-mers of these ever-expanding databases is fast becoming impractical. Several strategies for subsampling have been proposed, including minimizers and finding taxon-specific k-mers. However, we contend that these strategies are inadequate, especially when reference sets are taxonomically imbalanced, as are most microbial libraries. In this paper, we explore approaches for selecting a fixed-size subset of k-mers present in an ultra-large data set to include in a library such that the classification of reads suffers the least. Our experiments demonstrate the limitations of existing approaches, especially for novel and poorly sampled groups. We propose a library construction algorithm called k-mer RANKer (KRANK) that combines several components, including a hierarchical selection strategy with adaptive size restrictions and an equitable coverage strategy. We implement KRANK in highly optimized code and combine it with the locality-sensitive hashing classifier CONSULT-II to build a taxonomic classification and profiling method. On several benchmarks, KRANK k-mer selection significantly reduces memory consumption with minimal loss in classification accuracy. We show in extensive analyses based on CAMI benchmarks that KRANK outperforms k-mer-based alternatives in terms of taxonomic profiling and comes close to the best marker-based methods in terms of accuracy.}, } @article {pmid39209175, year = {2024}, author = {Dong, Q and Sun, B and Liu, Y and Huang, X}, title = {Sewerage surveillance tracking characteristics of human antibiotic resistance genes in sewer system.}, journal = {The Science of the total environment}, volume = {952}, number = {}, pages = {175850}, doi = {10.1016/j.scitotenv.2024.175850}, pmid = {39209175}, issn = {1879-1026}, mesh = {*Sewage/microbiology ; Humans ; *Drug Resistance, Microbial/genetics ; *Environmental Monitoring/methods ; Anti-Bacterial Agents/analysis ; COVID-19 ; Wastewater/microbiology ; Drug Resistance, Bacterial/genetics ; Waste Disposal, Fluid ; Genes, Bacterial ; }, abstract = {Sewage surveillance is widely applied to track valid human excretion information and identify public health conditions during corona virus disease 2019 (COVID-19) pandemic. This approach can be applied to monitor the antibiotic resistance level in sewers and to assess the risk of spreading antibiotic resistance in municipal wastewater systems. However, there is still little information about human antibiotic resistance occurrence characteristics in sewer system. This study conducted a field trial for whole year to advance understanding on spatial and temporal occurrence of antibiotic resistance genes (ARGs) in gravity sewerage. The spatial distribution of ARGs along the drainage pipe line (from human settlements to wastewater treatement pant (WWTP)) was insignificant, which may be affected by irregular human emission alongside the pipeline. The correlation between ARGs and antibiotics in sewage was insignificant. The temporal distribution showed that the effect of temperature on ARGs abundance was evident, the ARGs abundance in sewage was generally higher during the cold season. Metagenomic analysis revealed that the detected ARGs were mainly distributed in Proteobacteria (47.51 %) and Antinobacteria (20.11 %). Potential hosts of ARGs in sewage were mainly identified as human gut microorganisms, including human pathogenic bacteria, such as Prevotella, Kocuria, and Propionibacterium, etc. This study provides a new insight into the sewerage surveillance tracking characteristics of human ARGs in sewer system, and suggesting that the sewage-carried ARGs surveillance is a promising method for assessment and management of antibiotic resistance level on population size.}, } @article {pmid39208976, year = {2024}, author = {Su, Z and Cui, S and Wen, D and Chen, L}, title = {Metagenomic insights into resistome, mobilome and virulome in different fecal waste.}, journal = {Environmental research}, volume = {262}, number = {Pt 1}, pages = {119861}, doi = {10.1016/j.envres.2024.119861}, pmid = {39208976}, issn = {1096-0953}, mesh = {*Feces/microbiology ; Animals ; Cattle ; Humans ; Swine ; Metagenome ; Chickens/microbiology ; Metagenomics ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Virulence Factors/genetics ; }, abstract = {Fecal waste is a significant source of antimicrobial resistance (AMR) pollution and provides valuable insights into the AMR development in animal and human populations within the "One health" framework. Various genetic elements, including antibiotic resistance genes (ARGs), biocide and metal resistance genes (BMGs), mobile genetic elements (MGEs), and virulence factor genes (VFGs), are crucial AMR risk determinants (ARDs). However, few studies focused on compositional characteristics of ARDs in different feces. Here, we analyzed 753 public metagenomes from human, pig, chicken, and cattle feces, revealing significant differences in ARD richness and abundance across fecal types, notably lowest in cattle samples. Tetracycline, multi-metal, and -biocide resistance genes were dominant resistome. A few core genes contributed to 25.6%-91.1% of gene abundance, and their correlations were stronger in cattle samples. Procrustes analysis showed that microbial composition had higher correlations with ARGs (M[2] = 0.579) and BMGs (M[2] = 0.519). Gammaproteobacteria was identified as major ARD-hosts especially in human and pig feces, and they mainly carried multi-resistance genes. MGEs exhibited direct positive effects on ARGs and BMGs, indirectly impacting VFGs. Utilizing random forest methods, we identified 42 indicator genes for tracking AMR pollution originating from fecal sources in the environments. This study offers new insights into understanding and controlling the AMR pollution of fecal waste from human and food animals.}, } @article {pmid39208627, year = {2024}, author = {Chen, T and Deng, C and Li, S and Li, B and Liang, Y and Zhang, Y and Li, J and Xu, N and Yu, K}, title = {Multi-omics illuminates the functional significance of previously unknown species in a full-scale landfill leachate treatment plant.}, journal = {Journal of hazardous materials}, volume = {479}, number = {}, pages = {135669}, doi = {10.1016/j.jhazmat.2024.135669}, pmid = {39208627}, issn = {1873-3336}, mesh = {*Water Pollutants, Chemical/metabolism/analysis ; *Bacteria/genetics/metabolism ; *Biodegradation, Environmental ; Archaea/genetics/metabolism ; Waste Disposal Facilities ; Metagenomics ; Multiomics ; }, abstract = {Landfill leachate treatment plants (LLTPs) harbor a vast reservoir of uncultured microbes, yet limited studies have systematically unraveled their functional potentials within LLTPs. Combining 36 metagenomic and 18 metatranscriptomic datasets from a full-scale LLTP, we unveiled a double-edged sword role of unknown species in leachate biotreatment and environmental implication. We identified 655 species-level genome bins (SGBs) spanning 47 bacterial and 3 archaeal phyla, with 75.9 % unassigned to any known species. Over 90 % of up-regulated functional genes in biotreatment units, compared to the leachate influent, were carried by unknown species and actively participated in carbon, nitrogen, and sulfur cycles. Approximately 79 % of the 37,366 carbohydrate active enzymes (CAZymes), with ∼90 % novelty and high expression, were encoded by unknown species, exhibiting great potential in biodegrading carbohydrate compounds linked to human meat-rich diets. Unknown species offered a valuable genetic resource of thousands of versatile, abundant, and actively expressed metabolic gene clusters (MGCs) and biosynthetic gene clusters (BGCs) for enhancing leachate treatment. However, unknown species may contribute to the emission of hazardous N2O/H2S and represented significant reservoirs for antibiotic-resistant pathogens that posed environmental safety risks. This study highlighted the significance of considering both positive and adverse effects of LLTP microbes to optimize LLTP performance.}, } @article {pmid39207726, year = {2024}, author = {Lu, C and Wang, X and Ye, P and Lu, Z and Ma, J and Luo, W and Wang, S and Chen, X}, title = {Antimicrobial Peptides From the Gut Microbiome of the Centenarians: Diversification of Biosynthesis and Youthful Development of Resistance Genes.}, journal = {The journals of gerontology. Series A, Biological sciences and medical sciences}, volume = {79}, number = {11}, pages = {}, doi = {10.1093/gerona/glae218}, pmid = {39207726}, issn = {1758-535X}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics/physiology ; Aged, 80 and over ; *Antimicrobial Peptides/genetics ; Male ; Female ; Aged ; Adult ; Drug Resistance, Bacterial/genetics ; Middle Aged ; Probiotics ; }, abstract = {Antimicrobial peptides (AMPs) offer a potential solution to the antibiotic crisis owing to their antimicrobial properties, and the human gut biome may be a source of these peptides. However, the potential AMPs and AMP resistance genes (AMPRGs) of gut microbes in different age groups have not been thoroughly assessed. Here, we investigated the potential development of AMPs and the distribution pattern of AMPRGs in the gut microbiome at different ages by analyzing the intestinal metagenomic data of healthy individuals at different life stages (CG: centenarians group n = 20; OAG: older adults group: n = 15; YG: young group: n = 15). Age-related increases were observed in the potential AMPs within the gut microbiome, with centenarians showing a greater diversity of these peptides. However, the gut microbiome of the CG group had a lower level of AMPRGs compared to that of the OAG group, and it was similar to the level found in the YG group. Additionally, conventional probiotic strains showed a significant positive correlation with certain potential AMPs and were associated with a lower detection of resistance genes. Furthermore, comparing potential AMPs with existing libraries revealed limited similarity, indicating that current machine learning models can identify novel peptides in the gut microbiota. These results indicate that longevity may benefit from the diversity of AMPs and lower resistance genes. Our findings help explain the age advantage of the centenarians and identify the potential for antimicrobial peptide biosynthesis in the human gut microbiome, offering insights into the development of antimicrobial peptide resistance and the screening of probiotic strains.}, } @article {pmid39207532, year = {2024}, author = {Laczi, K and Bodor, A and Kovács, T and Magyar, B and Perei, K and Rákhely, G}, title = {Methanogenesis coupled hydrocarbon biodegradation enhanced by ferric and sulphate ions.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {449}, pmid = {39207532}, issn = {1432-0614}, support = {EFOP-3.6.2-16-2017-00010//The European Union and the State of Hungary/ ; NTP-NFTÖ-20-B-0027//Hungarian Prime Minister's Office/ ; 7036//University of Szeged Open Access Found/ ; }, mesh = {*Biodegradation, Environmental ; *Sulfates/metabolism ; *Methane/metabolism ; *Hydrocarbons/metabolism ; *Soil Microbiology ; Bacteria/metabolism/genetics/classification ; Ferric Compounds/metabolism ; Metagenome ; Soil Pollutants/metabolism ; }, abstract = {Bioremediation provides an environmentally sound solution for hydrocarbon removal. Although bioremediation under anoxic conditions is slow, it can be coupled with methanogenesis and is suitable for energy recovery. By altering conditions and supplementing alternative terminal electron acceptors to the system to induce syntrophic partners of the methanogens, this process can be enhanced. In this study, we investigated a hydrocarbon-degrading microbial community derived from chronically contaminated soil. Various hydrocarbon mixtures were used during our experiments in the presence of different electron acceptors. In addition, we performed whole metagenome sequencing to identify the main actors of hydrocarbon biodegradation in the samples. Our results showed that the addition of ferric ions or sulphate increased the methane yield. Furthermore, the addition of CO2, ferric ion or sulphate enhanced the biodegradation of alkanes. A significant increase in biodegradation was observed in the presence of ferric ions or sulphate in the case of all aromatic components, while naphthalene and phenanthrene degradation was also enhanced by CO2. Metagenome analysis revealed that Cellulomonas sp. is the most abundant in the presence of alkanes, while Ruminococcus and Faecalibacterium spp. are prevalent in aromatics-supplemented samples. From the recovery of 25 genomes, it was concluded that the main pathway of hydrocarbon activation was fumarate addition in both Cellulomonas, Ruminococcus and Faecalibacterium. Chloroflexota bacteria can utilise the central metabolites of aromatics biodegradation via ATP-independent benzoyl-CoA reduction. KEY POINTS: • Methanogenesis and hydrocarbon biodegradation were enhanced by Fe[3+] or SO4[2-] • Cellulomonas, Ruminococcus and Faecalibacterium can be candidates for the main hydrocarbon degraders • Chloroflexota bacteria can utilise the central metabolites of aromatics degradation.}, } @article {pmid39207169, year = {2024}, author = {Baker, BJ and Sarno, N}, title = {Small archaea may form intimate partnerships to maximize their metabolic potential.}, journal = {mBio}, volume = {15}, number = {10}, pages = {e0034724}, pmid = {39207169}, issn = {2150-7511}, support = {687165, LI-SIAME-00002001//Simons Foundation (SF)/ ; }, mesh = {*Archaea/metabolism/genetics/classification ; *Genome, Archaeal ; *Symbiosis ; Metabolic Networks and Pathways/genetics ; Nitrous Oxide/metabolism ; }, abstract = {DPANN archaea have characteristically small cells and unique genomes that were long overlooked in diversity surveys. Their reduced genomes often lack essential metabolic pathways, requiring symbiotic relationships with other archaeal and bacterial hosts for survival. Yet a long-standing question remains, what is the advantage of maintaining ultrasmall cells. A recent study by Zhang et al. examined genomes of DPANN archaea from marine oxygen deficient zones (ODZs) (I. H. Zhang, B. Borer, R. Zhao, S. Wilbert, et al., mBio 15:e02918-23, 2024, https://doi.org/10.1128/mbio.02918-23). Surprisingly, these genomes contain a broad array of metabolic pathways including genes predicted to be involved in nitrous oxide (N2O) reduction. However, N2O levels are likely too low in ODZs to make this metabolically feasible. Modeling co-localization of DPANN archaea (N2O consumers) with other larger cells (N2O producers) demonstrates that N2O uptake rates can be optimized by maximizing the producer-to-consumer size ratio and proximity of consumer cells to producers. This may explain why such a diversity of archaea maintain extremely small cell sizes.}, } @article {pmid39207108, year = {2024}, author = {Crouch, AL and Monsey, L and Rambeau, M and Ramos, C and Yracheta, JM and Anderson, MZ}, title = {Metagenomic discovery of microbial eukaryotes in stool microbiomes.}, journal = {mBio}, volume = {15}, number = {10}, pages = {e0206324}, pmid = {39207108}, issn = {2150-7511}, support = {//Ohio State University (OSU)/ ; 2046863//National Science Foundation (NSF)/ ; //Chan Zuckerberg Initiative (CZI)/ ; }, mesh = {Humans ; *Metagenomics/methods ; *Feces/microbiology ; *Eukaryota/genetics/classification/isolation & purification ; Gastrointestinal Microbiome/genetics ; Metagenome ; Fungi/genetics/classification/isolation & purification ; Sequence Analysis, DNA/methods ; Microbiota/genetics ; }, abstract = {Host-associated microbiota form complex microbial communities that are increasingly associated with host behavior and disease. While these microbes include bacterial, archaeal, viral, and eukaryotic constituents, most studies have focused on bacteria due to their dominance in the human host and available tools for investigation. Accumulating evidence suggests microbial eukaryotes in the microbiome play pivotal roles in host health, but our understandings of these interactions are limited to a few readily identifiable taxa because of technical limitations in unbiased eukaryote exploration. Here, we combined cell sorting, optimized eukaryotic cell lysis, and shotgun sequencing to accelerate metagenomic discovery and analysis of host-associated microbial eukaryotes. Using synthetic communities with a 1% microbial eukaryote representation, the eukaryote-optimized cell lysis and DNA recovery method alone yielded a 38-fold increase in eukaryotic DNA. Automated sorting of eukaryotic cells from stool samples of healthy adults increased the number of microbial eukaryote reads in metagenomic pools by up to 28-fold compared to commercial kits. Read frequencies for identified fungi increased by 10,000× on average compared to the Human Microbiome Project and allowed for the identification of novel taxa, de novo assembly of contigs from previously unknown microbial eukaryotes, and gene prediction from recovered genomic segments. These advances pave the way for the unbiased inclusion of microbial eukaryotes in deciphering determinants of health and disease in the host-associated microbiome.IMPORTANCEMicrobial eukaryotes are common constituents of the human gut where they can contribute to local ecology and host health, but they are often overlooked in microbiome studies. The lack of attention is due to current technical limitations that are heavily biased or poorly recovered DNA from microbial eukaryotes. We developed a method to increase the representation of these eukaryotes in metagenomic sequencing of microbiome samples that allows to improve their detection compared to prior methods and allows for the identification of new species. Application of the technique to gut microbiome samples improved detection of fungi, protists, and helminths. New eukaryotic taxa and their encoded genes could be identified by sequencing a small number of samples. This approach can improve the inclusion of eukaryotes into microbiome research.}, } @article {pmid39206688, year = {2024}, author = {Klier, KM and Martin, C and Langwig, MV and Anantharaman, K}, title = {Evolutionary history and origins of Dsr-mediated sulfur oxidation.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39206688}, issn = {1751-7370}, support = {//UW-Madison Science and Medicine Graduate Research Fellowship (SciMed GRS)/ ; OCE2049478//National Science Foundation Graduate Research Fellowship/ ; //National Science Foundation/ ; }, mesh = {*Oxidation-Reduction ; *Sulfur/metabolism ; *Archaea/genetics/metabolism ; *Phylogeny ; *Bacteria/genetics/metabolism/classification ; Evolution, Molecular ; Hydrogensulfite Reductase/genetics/metabolism ; }, abstract = {Microorganisms play vital roles in sulfur cycling through the oxidation of elemental sulfur and reduction of sulfite. These metabolisms are catalyzed by dissimilatory sulfite reductases (Dsr) functioning in either the reductive or reverse, oxidative direction. Dsr-mediated sulfite reduction is an ancient metabolism proposed to have fueled energy metabolism in some of Earth's earliest microorganisms, whereas sulfur oxidation is believed to have evolved later in association with the widespread availability of oxygen on Earth. Organisms are generally believed to carry out either the reductive or oxidative pathway, yet organisms from diverse phyla have been discovered with gene combinations that implicate them in both pathways. A comprehensive investigation into the metabolisms of these phyla regarding Dsr is currently lacking. Here, we selected one of these phyla, the metabolically versatile candidate phylum SAR324, to study the ecology and evolution of Dsr-mediated metabolism. We confirmed that diverse SAR324 encode genes associated with reductive Dsr, oxidative Dsr, or both. Comparative analyses with other Dsr-encoding bacterial and archaeal phyla revealed that organisms encoding both reductive and oxidative Dsr proteins are constrained to a few phyla. Further, DsrAB sequences from genomes belonging to these phyla are phylogenetically positioned at the interface between well-defined oxidative and reductive bacterial clades. The phylogenetic context and dsr gene content in these organisms points to an evolutionary transition event that ultimately gave way to oxidative Dsr-mediated metabolism. Together, this research suggests that SAR324 and other phyla with mixed dsr gene content are associated with the evolution and origins of Dsr-mediated sulfur oxidation.}, } @article {pmid39206173, year = {2024}, author = {Yu, F and Zhang, X and Li, Y and Gai, W and Zheng, Y and Cai, X}, title = {Severe pneumonia with empyema due to multiple anaerobic infections: case report and literature review.}, journal = {Frontiers in medicine}, volume = {11}, number = {}, pages = {1435823}, pmid = {39206173}, issn = {2296-858X}, abstract = {BACKGROUND: Cases of severe pneumonia complicated by empyema due to normal anaerobic flora from the oral cavity are infrequent. Diagnosing anaerobic infections through conventional microbiological test (CMT) is often challenging.

CASE PRESENTATION: This study describes the case of a 67-year-old man, bedridden long-term, who developed severe pneumonia with empyema caused by multiple anaerobic bacterial infections. The patient was hospitalized with a 5-day history of cough, sputum and fever, accompanied by a 2-day history of dyspnea. Despite CMT, the specific etiology remained elusive. However, metagenomic next-generation sequencing (mNGS) identified various anaerobic bacteria in bronchoalveolar lavage fluid (BALF), blood and pleural effusion. The patient was diagnosed with a polymicrobial infection involving multiple anaerobic bacteria. Following treatment with metronidazole and moxifloxacin, the patient's pulmonary symptoms improved.

CONCLUSION: mNGS serves as a valuable adjunctive tool for diagnosting and managing patients whose etiology remains unidentified following CMT.}, } @article {pmid39206169, year = {2024}, author = {Zhou, Y and Zhai, Y and Wang, Y and Zhang, D and Feng, G}, title = {Case report: The use of metagenomic next-generation sequencing to diagnose Lemierre's syndrome caused by lost root canal fillings in a 33-year-old patient with metabolic syndrome.}, journal = {Frontiers in medicine}, volume = {11}, number = {}, pages = {1402444}, pmid = {39206169}, issn = {2296-858X}, abstract = {BACKGROUND: Lemierre's syndrome is a rare and serious complication of pharyngitis with an estimated annual incidence of 1 in 100,000 people worldwide. It is characterized by septic thrombophlebitis of the internal jugular vein with metastatic infection, usually after oropharyngeal infection. Rare cases of Lemierre's syndrome have been reported to be caused by odontogenic infection.

CASE REPORT: A 33-year-old male visited our hospital with symptoms of fever and sore throat for 16 days. The other symptoms included pain in his left neck and shoulder. In addition, metabolic syndrome was diagnosed based on waist circumference, diabetes, and hyperlipidemia. Fusobacterium necrophorum bacteria was detected using the metagenomic next-generation sequencing (mNGS) technique. The enhanced computerized tomography (CT) scan showed thrombosis of the left proximal jugular vein and brachiocephalic vein. Based on these observations, Lemierre's syndrome was diagnosed. The etiology was that the fillings in the root canal tooth were lost with no blood or pain about 2 weeks before the onset. The patient recovered after treatment with antibiotics and blood purification.

CONCLUSION: Lemierre's syndrome should be evaluated for patients with fever, sore throat, and neck pain. If the loss of fillings from root canal therapy occurs, especially for those with metabolic syndrome, we should be aware of the possibility of this disease. Furthermore, the mNGS test can be used as a crucial supplementary diagnostic tool for patients with undetermined fever.}, } @article {pmid39206042, year = {2024}, author = {Zhen, J and Zhang, Y and Li, Y and Zhou, Y and Cai, Y and Huang, G and Xu, A}, title = {The gut microbiota intervenes in glucose tolerance and inflammation by regulating the biosynthesis of taurodeoxycholic acid and carnosine.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1423662}, pmid = {39206042}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology ; *Carnosine/metabolism ; Male ; *Feces/microbiology ; Glucose Intolerance/metabolism ; Inflammation/metabolism ; Hep G2 Cells ; Metagenomics ; Female ; Middle Aged ; Taurochenodeoxycholic Acid/metabolism/pharmacology ; Hyperglycemia/metabolism ; Neutrophils/metabolism ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/metabolism/genetics ; }, abstract = {OBJECTIVE: This study aims to investigate the pathogenesis of hyperglycemia and its associated vasculopathy using multiomics analyses in diabetes and impaired glucose tolerance, and validate the mechanism using the cell experiments.

METHODS: In this study, we conducted a comprehensive analysis of the metagenomic sequencing data of diabetes to explore the key genera related to its occurrence. Subsequently, participants diagnosed with impaired glucose tolerance (IGT), and healthy subjects, were recruited for fecal and blood sample collection. The dysbiosis of the gut microbiota (GM) and its associated metabolites were analyzed using 16S rDNA sequencing and liquid chromatograph mass spectrometry, respectively. The regulation of gene and protein expression was evaluated through mRNA sequencing and data-independent acquisition technology, respectively. The specific mechanism by which GM dysbiosis affects hyperglycemia and its related vasculopathy was investigated using real-time qPCR, Western blotting, and enzyme-linked immunosorbent assay techniques in HepG2 cells and neutrophils.

RESULTS: Based on the published data, the key alterable genera in the GM associated with diabetes were identified as Blautia, Lactobacillus, Bacteroides, Prevotella, Faecalibacterium, Bifidobacterium, Ruminococcus, Clostridium, and Lachnoclostridium. The related metabolic pathways were identified as cholate degradation and L-histidine biosynthesis. Noteworthy, Blautia and Faecalibacterium displayed similar alterations in patients with IGT compared to those observed in patients with diabetes, and the GM metabolites, tauroursodeoxycholic acid (TUDCA) and carnosine (CARN, a downstream metabolite of histidine and alanine) were both found to be decreased, which in turn regulated the expression of proteins in plasma and mRNAs in neutrophils. Subsequent experiments focused on insulin-like growth factor-binding protein 3 and interleukin-6 due to their impact on blood glucose regulation and associated vascular inflammation. Both proteins were found to be suppressed by TUDCA and CARN in HepG2 cells and neutrophils.

CONCLUSION: Dysbiosis of the GM occurred throughout the entire progression from IGT to diabetes, characterized by an increase in Blautia and a decrease in Faecalibacterium, leading to reduced levels of TUDCA and CARN, which alleviated their inhibition on the expression of insulin-like growth factor-binding protein 3 and interleukin-6, contributing to the development of hyperglycemia and associated vasculopathy.}, } @article {pmid39205800, year = {2024}, author = {Zhang, X and Ye, J and Wang, L and Zhang, L and Wang, L and Jin, H}, title = {Nanopore Sequencing Technology: A Reliable Method for Pathogen Diagnosis in Elderly Patients with Community-Acquired Pneumonia.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {3659-3667}, pmid = {39205800}, issn = {1178-6973}, abstract = {PURPOSE: Next-generation sequencing of the metagenome (mNGS) is gaining traction as a valuable tool for diagnosing infectious diseases. Compared to mNGS, pathogen detection based on Oxford Nanopore Technology further shortens the detection time. This study seeks to assess the efficacy of Nanopore sequencing in identifying pathogens associated with community-acquired pneumonia (CAP) among elderly individuals in China.

PATIENTS AND METHODS: From January 2023 to June 2023, elderly patients with CAP were prospectively recruited from Hangzhou First People's Hospital. A comprehensive set of clinical data was gathered, and bronchoalveolar lavage (BAL) fluid samples were collected. Concurrently, pathogen identification was performed using conventional microbiological diagnostic methods, Illumina sequencing, and Nanopore sequencing, and the diagnostic efficacy of pathogen detection was compared.

RESULTS: The study included a total of 29 patients. The diagnostic positivity rates of traditional microbiological detection, Illumina sequencing, and Nanopore sequencing were 24.1%, 51.7%, and 48.3%, respectively. Their diagnostic specificities were 91.7%, 50%, and 75%, respectively. Compared to traditional microbiological detection, both Nanopore and Illumina sequencing showed significantly increased sensitivity. However, Nanopore sequencing exhibited relatively better consistency with the final clinical comprehensive diagnosis, with a Kappa value of 0.574. This outperformed traditional microbiological detection and Illumina sequencing, which had a Kappa value of 0.296 and 0.402, respectively. In addition, Nanopore sequencing required the shortest turnaround time.

CONCLUSION: Nanopore sequencing technology demonstrates as a reliable and rapid method for detecting pathogens in elderly patients with CAP.}, } @article {pmid39205247, year = {2024}, author = {Jansen van Vuren, P and Parry, RH and Pawęska, JT}, title = {Detection of Dengue Virus 1 and Mammalian Orthoreovirus 3, with Novel Reassortments, in a South African Family Returning from Thailand, 2017.}, journal = {Viruses}, volume = {16}, number = {8}, pages = {}, pmid = {39205247}, issn = {1999-4915}, support = {Annual strategic funding for disease surveillance//National Institute for Communicable Diseases/ ; }, mesh = {Animals ; Child ; Female ; Humans ; Male ; Mice ; Middle Aged ; *Dengue/virology/epidemiology ; *Dengue Virus/genetics/isolation & purification/classification ; Genome, Viral ; Genotype ; Orthoreovirus, Mammalian/genetics/isolation & purification/classification ; *Phylogeny ; *Reassortant Viruses/genetics/isolation & purification/classification ; Reoviridae Infections/virology/veterinary ; South Africa ; Thailand ; Travel ; Vero Cells ; }, abstract = {In July 2017, a family of three members, a 46-year-old male, a 45-year-old female and their 8-year-old daughter, returned to South Africa from Thailand. They presented symptoms consistent with mosquito-borne diseases, including fever, headache, severe body aches and nausea. Mosquito bites in all family members suggested recent exposure to arthropod-borne viruses. Dengue virus 1 (Genus Orthoflavivirus) was isolated (isolate no. SA397) from the serum of the 45-year-old female via intracerebral injection in neonatal mice and subsequent passage in VeroE6 cells. Phylogenetic analysis of this strain indicated close genetic identity with cosmopolitan genotype 1 DENV1 strains from Southeast Asia, assigned to major lineage K, minor lineage 1 (DENV1I_K.1), such as GZ8H (99.92%) collected in November 2018 from China, and DV1I-TM19-74 isolate (99.72%) identified in Bangkok, Thailand, in 2019. Serum samples from the 46-year-old male yielded a virus isolate that could not be confirmed as DENV1, prompting unbiased metagenomic sequencing for virus identification and characterization. Illumina sequencing identified multiple segments of a mammalian orthoreovirus (MRV), designated as Human/SA395/SA/2017. Genomic and phylogenetic analyses classified Human/SA395/SA/2017 as MRV-3 and assigned a tentative genotype, MRV-3d, based on the S1 segment. Genomic analyses suggested that Human/SA395/SA/2017 may have originated from reassortments of segments among swine, bat, and human MRVs. The closest identity of the viral attachment protein σ1 (S1) was related to a human isolate identified from Tahiti, French Polynesia, in 1960. This indicates ongoing circulation and co-circulation of Southeast Asian and Polynesian strains, but detailed knowledge is hampered by the limited availability of genomic surveillance. This case represents the rare concurrent detection of two distinct viruses with different transmission routes in the same family with similar clinical presentations. It highlights the complexity of diagnosing diseases with similar sequelae in travelers returning from tropical areas.}, } @article {pmid39205216, year = {2024}, author = {Patiño, L and Benítez, AD and Carrazco-Montalvo, A and Regato-Arrata, M}, title = {Genomics for Arbovirus Surveillance: Considerations for Routine Use in Public Health Laboratories.}, journal = {Viruses}, volume = {16}, number = {8}, pages = {}, pmid = {39205216}, issn = {1999-4915}, support = {Proyecto INÉDITA-PIC-21-INE-INSPI-001//Secretaría de Educación Superior, Ciencia, Tecnología e Innovación/ ; }, mesh = {*Arboviruses/genetics/isolation & purification ; *Arbovirus Infections/epidemiology/diagnosis/virology ; Humans ; *Genomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; *Public Health ; Animals ; Laboratories ; Computational Biology/methods ; Genome, Viral ; Epidemiological Monitoring ; }, abstract = {The emergence and re-emergence of arthropod-borne viruses is a public health threat. For routine surveillance in public health laboratories, cost-effective and reproducible methods are essential. In this review, we address the technical considerations of high-throughput sequencing methods (HTS) for arbovirus surveillance in national health laboratories, focusing on pre-sequencing, sequencing, and post-sequencing approaches, underlining the importance of robust wet and dry laboratory workflows for reproducible analysis. We aim to provide insights for researchers and clinicians interested in arbovirus, diagnosis, and surveillance by discussing current advances in sequencing methods and bioinformatics pipelines applied to arboviruses.}, } @article {pmid39205200, year = {2024}, author = {Santos, JPN and Rodrigues, GVP and Ferreira, LYM and Monteiro, GP and Fonseca, PLC and Lopes, ÍS and Florêncio, BS and da Silva Junior, AB and Ambrósio, PE and Pirovani, CP and Aguiar, ERGR}, title = {The Virome of Cocoa Fermentation-Associated Microorganisms.}, journal = {Viruses}, volume = {16}, number = {8}, pages = {}, pmid = {39205200}, issn = {1999-4915}, support = {Financial code 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior-Brazil (CAPES)/ ; Researcher fellowship//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; }, mesh = {*Cacao/virology/microbiology ; *Fermentation ; *Virome ; Viruses/genetics/classification/isolation & purification ; Fungi/virology/genetics/classification ; Phylogeny ; Bacteriophages/genetics/classification/isolation & purification ; Costa Rica ; Bacteria/genetics/classification/virology ; Metagenomics ; Genome, Viral ; }, abstract = {Theobroma cacao plantations are of significant economic importance worldwide, primarily for chocolate production. During the harvest and processing of cocoa beans, they are subjected to fermentation either by microorganisms present in the environment (spontaneous fermentation) or the addition of starter cultures, with different strains directly contributing distinct flavor and color characteristics to the beans. In addition to fungi and bacteria, viruses are ubiquitous and can affect the quality of the fermentation process by infecting fermenting organisms, destabilizing microbial diversity, and consequently affecting fermentation quality. Therefore, in this study, we explored publicly available metatranscriptomic libraries of cocoa bean fermentation in Limon Province, Costa Rica, looking for viruses associated with fermenting microorganisms. Libraries were derived from the same sample at different time points: 7, 20, and 68 h of fermentation, corresponding to yeast- and lactic acid bacteria-driven phases. Using a comprehensive pipeline, we identified 68 viral sequences that could be assigned to 62 new viral species and 6 known viruses distributed among at least nine families, with particular abundance of elements from the Lenarviricota phylum. Interestingly, 44 of these sequences were specifically associated with ssRNA phages (Fiersviridae) and mostly fungi-infecting viral families (Botourmiaviridae, Narnaviridae, and Mitoviridae). Of note, viruses from those families show a complex evolutionary relationship, transitioning from infecting bacteria to infecting fungi. We also identified 10 and 3 viruses classified within the Totiviridae and Nodaviridae families, respectively. The quantification of the virus-derived RNAs shows a general pattern of decline, similar to the dynamic profile of some microorganism genera during the fermentation process. Unexpectedly, we identified narnavirus-related elements that showed similarity to segmented viral species. By exploring the molecular characteristics of these viral sequences and applying Hidden Markov Models, we were capable of associating these additional segments with a specific taxon. In summary, our study elucidates the complex virome associated with the microbial consortia engaged in cocoa bean fermentation that could contribute to organism/strain selection, altering metabolite production and, consequently, affecting the sensory characteristics of cocoa beans.}, } @article {pmid39204265, year = {2024}, author = {Ariyadasa, S and van Hamelsveld, S and Taylor, W and Lin, S and Sitthirit, P and Pang, L and Billington, C and Weaver, L}, title = {Diversity of Free-Living Amoebae in New Zealand Groundwater and Their Ability to Feed on Legionella pneumophila.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {8}, pages = {}, pmid = {39204265}, issn = {2076-0817}, support = {ESR2023SA1//Ministry of Business, Innovation, and Employment New Zealand/ ; }, abstract = {Free-living amoebae (FLA) are common in both natural and engineered freshwater ecosystems. They play important roles in biofilm control and contaminant removal through the predation of bacteria and other taxa. Bacterial predation by FLA is also thought to contribute to pathogen dispersal and infectious disease transmission in freshwater environments via the egestion of viable bacteria. Despite their importance in shaping freshwater microbial communities, the diversity and function of FLA in many freshwater ecosystems are poorly understood. In this study, we isolated and characterized FLA from two groundwater sites in Canterbury, New Zealand using microbiological, microscopic, and molecular techniques. Different methods for groundwater FLA isolation and enrichment were trialed and optimized. The ability of these isolated FLA to predate on human pathogen Legionella pneumophila was assessed. FLA were identified by 18S metagenomic amplicon sequencing. Our study showed that Acanthamoeba spp. (including A. polyphaga) and Vermamoeba veriformis were the main FLA species present in both groundwater sites examined. While most of the isolated FLA co-existed with L. pneumophila, the FLA populations in the L. pneumophila co-culture experiments predominantly consisted of A. polyphaga, Acanthamoeba spp., Naegleria spp., V. vermiformis, Paravahlkampfia spp., and Echinamoeba spp. These observations suggest that FLA may have the potential to act as reservoirs for L. pneumophila in Canterbury, New Zealand groundwater systems and could be introduced into the local drinking water infrastructure, where they may promote the survival, multiplication, and dissemination of Legionella. This research addresses an important gap in our understanding of FLA-mediated pathogen dispersal in freshwater ecosystems.}, } @article {pmid39204226, year = {2024}, author = {Kibenge, F and Kibenge, M and Montes de Oca, M and Godoy, M}, title = {Parvoviruses of Aquatic Animals.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {8}, pages = {}, pmid = {39204226}, issn = {2076-0817}, abstract = {Family Parvoviridae consists of small, non-enveloped viruses with linear, single-stranded DNA genomes of approximately 4-6 kilobases, subdivided into three subfamilies, Parvovirinae, Densovirinae, and Hamaparvovirinae, and unassigned genus Metalloincertoparvovirus. Parvoviruses of aquatic animals infect crustaceans, mollusks, and finfish. This review describes these parvoviruses, which are highly host-specific and associated with mass morbidity and mortality in both farmed and wild aquatic animals. They include Cherax quadricarinatus densovirus (CqDV) in freshwater crayfish in Queensland, Australia; sea star-associated densovirus (SSaDV) in sunflower sea star on the Northeastern Pacific Coast; Clinch densovirus 1 in freshwater mussels in the Clinch River, Virginia, and Tennessee, USA, in subfamily Densovirinae; hepatopancreatic parvovirus (HPV) and infectious hypodermal and hematopoietic necrosis virus (IHHNV) in farmed shrimp worldwide; Syngnathid ichthamaparvovirus 1 in gulf pipefish in the Gulf of Mexico and parts of South America; tilapia parvovirus (TiPV) in farmed tilapia in China, Thailand, and India, in the subfamily Hamaparvovirinae; and Penaeus monodon metallodensovirus (PmMDV) in Vietnamese P. monodon, in unassigned genus Metalloincertoparvovirus. Also included in the family Parvoviridae are novel parvoviruses detected in both diseased and healthy animals using metagenomic sequencing, such as zander parvovirus from zander in Hungary and salmon parvovirus from sockeye salmon smolts in British Columbia, Canada.}, } @article {pmid39204040, year = {2024}, author = {Zhang, LN and Tan, JT and Ng, HY and Liao, YS and Zhang, RQ and Chan, KH and Hung, IF and Lam, TT and Cheung, KS}, title = {Baseline Gut Microbiota Was Associated with Long-Term Immune Response at One Year Following Three Doses of BNT162b2.}, journal = {Vaccines}, volume = {12}, number = {8}, pages = {}, pmid = {39204040}, issn = {2076-393X}, support = {COVID1903010//Food and Health Bureau, The Government of HKSAR/ ; }, abstract = {BACKGROUND: This study explored neutralizing IgG antibody levels against COVID-19 decline over time post-vaccination. We conducted this prospective cohort study to investigate the function of gut microbiota in the host immune response following three doses of BNT162b2.

METHODS: Subjects who received three doses of BNT162b2 were recruited from three centers in Hong Kong. Blood samples were obtained before the first dose and at the one-year timepoint for IgG ELISA to determine the level of neutralizing antibody (NAb). The primary outcome was a high immune response (NAb > 600 AU/mL). We performed shotgun DNA metagenomic sequencing on baseline fecal samples to identify bacterial species and metabolic pathways associated with high immune response using linear discriminant analysis effect size analysis.

RESULTS: A total of 125 subjects were recruited (median age: 52 years [IQR: 46.2-59.0]; male: 43 [34.4%]), and 20 were regarded as low responders at the one-year timepoint. Streptococcus parasanguinis (log10LDA score = 2.38, p = 0.003; relative abundance of 2.97 × 10[-5] vs. 0.03%, p = 0.001), Bacteroides stercoris (log10LDA score = 4.29, p = 0.024; relative abundance of 0.14% vs. 2.40%, p = 0.014) and Haemophilus parainfluenzae (log10LDA score = 2.15, p = 0.022; relative abundance of 0.01% vs. 0, p = 0.010) were enriched in low responders. Bifidobacterium pseudocatenulatum (log10LDA score = 2.99, p = 0.048; relative abundance of 0.09% vs. 0.36%, p = 0.049) and Clostridium leptum (log10LDA score = 2.38, p = 0.014; relative abundance of 1.2 × 10[-5]% vs. 0, p = 0.044) were enriched in high responders. S. parasanguinis was negatively correlated with the superpathway of pyrimidine ribonucleotides de novo biosynthesis (log10LDA score = 2.63), which contributes to inflammation and antibody production. H. parainfluenzae was positively correlated with pathways related to anti-inflammatory processes, including the superpathway of histidine, purine, and pyrimidine biosynthesis (log10LDA score = 2.14).

CONCLUSION: Among three-dose BNT162b2 recipients, S. parasanguinis, B. stercoris and H. parainfluenzae were associated with poorer immunogenicity at one year, while B. pseudocatenulatum and C. leptum was associated with a better response.}, } @article {pmid39203557, year = {2024}, author = {Gaenssle, ALO and Bertran-Llorens, S and Deuss, PJ and Jurak, E}, title = {Enrichment of Aquatic Xylan-Degrading Microbial Communities.}, journal = {Microorganisms}, volume = {12}, number = {8}, pages = {}, pmid = {39203557}, issn = {2076-2607}, support = {ENTEG//University of Groningen (ENTEG)/ ; }, abstract = {The transition towards a sustainable society involves the utilization of lignocellulosic biomass as a renewable feedstock for materials, fuel, and base chemicals. Lignocellulose consists of cellulose, hemicellulose, and lignin, forming a complex, recalcitrant matrix where efficient enzymatic saccharification is pivotal for accessing its valuable components. This study investigated microbial communities from brackish Lauwersmeer Lake, in The Netherlands, as a potential source of xylan-degrading enzymes. Environmental sediment samples were enriched with wheat arabinoxylan (WAX) and beechwood glucuronoxylan (BEX), with enrichment on WAX showing higher bacterial growth and complete xylan degradation compared to BEX. Metagenomic sequencing revealed communities consisting almost entirely of bacteria (>99%) and substantial shifts in composition during the enrichment. The first generation of seven-day enrichments on both xylans led to a high accumulation of Gammaproteobacteria (49% WAX, 84% BEX), which were largely replaced by Alphaproteobacteria (42% WAX, 69% BEX) in the fourth generation. Analysis of the protein function within the sequenced genomes showed elevated levels of genes associated with the carbohydrate catabolic process, specifically targeting arabinose, xylose, and xylan, indicating an adaptation to the primary monosaccharides present in the carbon source. The data open up the possibility of discovering novel xylan-degrading proteins from other sources aside from the thoroughly studied Bacteroidota.}, } @article {pmid39203545, year = {2024}, author = {Gheorghe-Barbu, I and Dragomir, RI and Gradisteanu Pircalabioru, G and Surleac, M and Dinu, IA and Gaboreanu, MD and Czobor Barbu, I}, title = {Tracing Acinetobacter baumannii's Journey from Hospitals to Aquatic Ecosystems.}, journal = {Microorganisms}, volume = {12}, number = {8}, pages = {}, pmid = {39203545}, issn = {2076-2607}, support = {ERANET 243/2021//ERANET/ ; PN-III-P4-PCE-2021-1797 (PCE 96/2022)//Unitatea Executiva Pentru Finantarea Invatamantului Superior a Cercetarii Dezvoltarii si Inovarii/ ; PN-III-P1-1.1-TE-2021-1515 (TE112/2022)//Unitatea Executiva Pentru Finantarea Invatamantului Superior a Cercetarii Dezvoltarii si Inovarii/ ; PN-III-P1-1.1-PD-2021-0540 (PD102/2022)//Unitatea Executiva Pentru Finantarea Invatamantului Superior a Cercetarii Dezvoltarii si Inovarii/ ; }, abstract = {BACKGROUND: This study provides a comprehensive analysis of Acinetobacter baumannii in aquatic environments and fish microbiota by integrating culture-dependent methods, 16S metagenomics, and antibiotic resistance profiling.

METHODS: A total of 83 A. baumannii isolates were recovered using culture-dependent methods from intra-hospital infections (IHI) and wastewater (WW) and surface water (SW) samples from two southern Romanian cities in August 2022. The antibiotic susceptibility was screened using disc diffusion, microdilution, PCR, and Whole Genome Sequencing assays.

RESULTS: The highest microbial load in the analyzed samples was found in Glina, Bucharest, for both WW and SW samples across all investigated phenotypes. For Bucharest isolates, the resistance levels corresponded to fluoroquinolones > aminoglycosides > β-lactam antibiotics. In contrast, A. baumannii from upstream SW samples in Târgoviște showed the highest resistance to aminoglycosides. The blaOXA-23 gene was frequently detected in IHI, WW, and SW isolates in Bucharest, but was absent in Târgoviște. Molecular phylogeny revealed the presence of ST10 in Târgoviște isolates and ST2 in Bucharest isolates, while other minor STs were not specifically correlated with a sampling point. Using 16S rRNA sequencing, significant differences in microbial populations between the two locations was identified. The low abundance of Alphaproteobacteria and Actinobacteria in both locations suggests environmental pressures or contamination events.

CONCLUSIONS: These findings indicate significant fecal contamination and potential public health risks, emphasizing the need for improved water quality monitoring and management.}, } @article {pmid39203533, year = {2024}, author = {Chiba, T and Hattori, Y and Motooka, D and Tanaka, T and Ihara, M}, title = {Paraclostridium tenue Causing an Anaerobic Brain Abscess Identified by Whole-Metagenome Sequencing: A Case Report.}, journal = {Microorganisms}, volume = {12}, number = {8}, pages = {}, pmid = {39203533}, issn = {2076-2607}, support = {N/A//Nature Holdings/ ; }, abstract = {When treating anaerobic brain abscesses, healthcare professionals often face the difficulty of identifying the causal pathogens, necessitating empiric therapies with uncertain efficacy. We present the case of a 57-year-old woman who was admitted to our hospital with a fever and headache. Brain magnetic resonance imaging revealed a hemorrhagic lesion with wall enhancement at the left hemisphere on contrast-enhanced T1-weighted imaging. Cerebrospinal fluid examination showed pleocytosis (23 cells/μL), an elevated protein level (125 mg/dL), and decreased glucose level (51 mg/dL; blood glucose was 128 mg/dL). Intracerebral hemorrhage accompanied by a brain abscess was clinically suspected. The patient received empirical treatment with intravenous meropenem and vancomycin for 2 weeks. However, conventional bacterial culture tests failed to identify the pathogen. We then performed shotgun sequencing and ribosomal multilocus sequence typing, which identified Paraclostridium tenue. Based on this finding, we de-escalated to benzylpenicillin potassium for 4 weeks, leading to a 2.5-year remission of the anaerobic brain abscess. Therefore, Paraclostridium can be a causative pathogen for brain abscesses. Furthermore, whole-metagenome sequencing is a promising method for detecting rare pathogens that are not identifiable by conventional bacterial culture tests. This approach enables more targeted treatment and contributes to achieving long-term remission in clinical settings.}, } @article {pmid39203491, year = {2024}, author = {Zhang, R and Wang, S and Zhong, H and Fu, X and Li, L and Wang, L and Liu, Y}, title = {Microbial C and N Metabolism Alterations Based on Soil Metagenome and Different Shrub Invasion Stages in Sanjiang Plain Wetlands.}, journal = {Microorganisms}, volume = {12}, number = {8}, pages = {}, pmid = {39203491}, issn = {2076-2607}, support = {HC202332//Open Project of State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology/ ; }, abstract = {Shrub invasion affects plant growth and soil physicochemical properties, resulting in soil microbiota metabolic pathway changes. However, little is known about the shrub expansion intensity of microbial metabolic pathway processes. In this study, we used metagenome sequencing technology to investigate changes in soil microbial C and N metabolic pathways and community structures, along with different shrub invasion intensities, in the Sanjiang Plain wetlands. Different shrub invasion intensities significantly affected the soil microbial composition (β diversity), with no significant effect on the α diversity compared to CK. AN, pH, and TP were the major factors influencing the microbial community's structures. Compared to CK, the shrub expansion intensity did not significantly affect C fixation and central metabolism but significantly reduced methanogenesis, which involves the CO2-to-methane transition that occurs in methane metabolism, and denitrification, the nitrite to nitric oxide (nirK or nirS) transition that occurs in N metabolism. This study provides an in-depth understanding of the biogeochemical cycles of wetland ecosystems in cold northern regions undergoing shrub invasion.}, } @article {pmid39203451, year = {2024}, author = {Onyeaghala, GC and Sharma, S and Oyenuga, M and Staley, CM and Milne, GL and Demmer, RT and Shaukat, A and Thyagarajan, B and Straka, RJ and Church, TR and Prizment, AE}, title = {The Effects of Aspirin Intervention on Inflammation-Associated Lingual Bacteria: A Pilot Study from a Randomized Clinical Trial.}, journal = {Microorganisms}, volume = {12}, number = {8}, pages = {}, pmid = {39203451}, issn = {2076-2607}, support = {UL1 TR002494/TR/NCATS NIH HHS/United States ; UL1TR002494//National Institutes of Health's National Center for Advancing Translational Sciences/ ; }, abstract = {Several bacterial taxa enriched in inflammatory bowel diseases and colorectal cancer (CRC) are found in the oral cavity. We conducted a pilot study nested within a six-week aspirin intervention in a randomized placebo-controlled trial to test their response to aspirin intervention. Fifty healthy subjects, 50-75 years old, were randomized to receive 325 mg aspirin (n = 30) or placebo (n = 20) orally once daily for six weeks. Oral tongue swabs were collected at baseline and week six. We estimated the association between aspirin use and the temporal changes in the relative abundance of pre-specified genus level taxa from pre- to post-treatment. The temporal change in relative abundance differed for eight genus level taxa between the aspirin and placebo groups. In the aspirin group, there were significant increases in the relative abundances of Neisseria, Streptococcus, Actinomyces, and Rothia and significant decreases in Prevotella, Veillonella, Fusobacterium, and Porphyromonas relative to placebo. The log ratio of Neisseria to Fusobacterium declined more in the aspirin group than placebo, signaling a potential marker associated with aspirin intervention. These preliminary findings should be validated using metagenomic sequencing and may guide future studies on the role of aspirin on taxa in various oral ecological niches.}, } @article {pmid39203445, year = {2024}, author = {Pomari, E and Orza, P and Bernardi, M and Fracchetti, F and Campedelli, I and De Marta, P and Recchia, A and Paradies, P and Buonfrate, D}, title = {A Pilot Study for the Characterization of Bacillus spp. and Analysis of Possible B. thuringiensis/Strongyloides stercoralis Correlation.}, journal = {Microorganisms}, volume = {12}, number = {8}, pages = {}, pmid = {39203445}, issn = {2076-2607}, support = {"5×1000 -2020", project: "Bacillus thuringiensis (gruppo Bacillus cereus) come possibile antagonista di Strongyloides stercoralis e di altri elminti correlati con malattie tropicali neglette (NTD), alla base di una strategia di prevenzione"//Italian Ministry of Health/ ; "Ricerca Corrente", project L2P11//Italian Ministry of Health/ ; }, abstract = {Differentiating between Bacillus species is relevant in human medicine. Bacillus thuringiensis toxins might be effective against Strongyloides stercoralis, a nematode causing relevant human morbidity. Our first objective was to evaluate genomic and MALDI-TOF identification methods for B. thuringiensis. Our secondary objective was to evaluate a possible negative selection pressure of B. thuringiensis against S. stercoralis. PCR and Sanger were compared to MALDI-TOF on a collection of 44 B. cereus group strains. B. thuringiensis toxin genes were searched on 17 stool samples from S. stercoralis-infected and uninfected dogs. Metagenomic 16S rRNA was used for microbiome composition. The inter-rate agreement between PCR, Sanger, and MALDI-TOF was 0.631 k (p-value = 6.4 × 10[-10]). B. thuringiensis toxins were not found in dogs' stool. Bacteroidota and Bacillota were the major phyla in the dogs' microbiome (both represented >20% of the total bacterial community). Prevotella was underrepresented in all Strongyloides-positive dogs. However, the general composition of bacterial communities was not significantly linked with S. stercoralis infection. The genomic methods allowed accurate differentiation between B. thuringiensis and B. cereus. There was no association between B. thuringiensis and S. stercoralis infection, but further studies are needed to confirm this finding. We provide the first descriptive results about bacterial fecal composition in dogs with S. stercoralis infection.}, } @article {pmid39203436, year = {2024}, author = {Majeed, A and Liu, J and Knight, AJ and Pajerowska-Mukhtar, KM and Mukhtar, MS}, title = {Bacterial Communities Associated with the Leaves and the Roots of Salt Marsh Plants of Bayfront Beach, Mobile, Alabama, USA.}, journal = {Microorganisms}, volume = {12}, number = {8}, pages = {}, pmid = {39203436}, issn = {2076-2607}, support = {IOS-2038872//National Science Foundation/ ; }, abstract = {Salt marshes are highly dynamic and biologically diverse ecosystems that serve as natural habitats for numerous salt-tolerant plants (halophytes). We investigated the bacterial communities associated with the roots and leaves of plants growing in the coastal salt marshes of the Bayfront Beach, located in Mobile, Alabama, United States. We compared external (epiphytic) and internal (endophytic) communities of both leaf and root plant organs. Using 16S rDNA amplicon sequencing methods, we identified 10 bacterial phyla and 59 different amplicon sequence variants (ASVs) at the genus level. Bacterial strains belonging to the phyla Proteobacteria, Bacteroidetes, and Firmicutes were highly abundant in both leaf and root samples. At the genus level, sequences of the genus Pseudomonas were common across all four sample types, with the highest abundance found in the leaf endophytic community. Additionally, Pantoea was found to be dominant in leaf tissue compared to roots. Our study revealed that plant habitat (internal vs. external for leaves and roots) was a determinant of the bacterial community structure. Co-occurrence network analyses enabled us to discern the intricate characteristics of bacterial taxa. Our network analysis revealed varied levels of ASV complexity in the epiphytic networks of roots and leaves compared to the endophytic networks. Overall, this study advances our understanding of the intricate composition of the bacterial microbiota in habitats (epiphytic and endophytic) and organs (leaf and root) of coastal salt marsh plants and suggests that plants might recruit habitat- and organ-specific bacteria to enhance their tolerance to salt stress.}, } @article {pmid39203404, year = {2024}, author = {Corrigan, A and McCooey, P and Taylor-Pickard, J and Stockdale, S and Murphy, R}, title = {Breaking the Cycle: A Yeast Mannan-Rich Fraction Beneficially Modulates Egg Quality and the Antimicrobial Resistome Associated with Layer Hen Caecal Microbiomes under Commercial Conditions.}, journal = {Microorganisms}, volume = {12}, number = {8}, pages = {}, pmid = {39203404}, issn = {2076-2607}, abstract = {Antibiotics and antibiotic growth promoters have been extensively employed in poultry farming to enhance growth performance, maintain bird health, improve nutrient uptake efficiency, and mitigate enteric diseases at both sub-therapeutic and therapeutic doses. However, the extensive use of antimicrobials in poultry farming has led to the emergence of antimicrobial resistance (AMR) in microbial reservoirs, representing a significant global public health concern. In response, non-antibiotic dietary interventions, such as yeast mannan-rich fraction (MRF), have emerged as a promising alternative to modulate the gut microbiota and combat the AMR crisis. This study investigated whether a yeast mannan-rich fraction containing feed supplement impacted the performance of laying hens, their microbiomes, and the associated carriage of antimicrobial resistance genes under commercial conditions. High-throughput DNA sequencing was utilised to profile the bacterial community and assess changes in the antibiotic resistance genomes detected in the metagenome, the "resistome", in response to MRF supplementation. It was found that supplementation favourably influenced laying hen performance and microbial composition. Notably, there was a compositional shift in the MRF supplemented group associated with a lower relative abundance of pathobionts, e.g., Escherichia, Brachyspira and Trueperella, and their AMR-encoded genes, relative to beneficial microbes. Overall, the findings further demonstrate the ability of prebiotics to improve laying hen performance through changes associated with their microbiome and resistome.}, } @article {pmid39203393, year = {2024}, author = {Wang, Y and Weng, MY and Zhong, JW and He, L and Guo, DJ and Luo, D and Xue, JY}, title = {Microbial Metagenomics Revealed the Diversity and Distribution Characteristics of Groundwater Microorganisms in the Middle and Lower Reaches of the Yangtze River Basin.}, journal = {Microorganisms}, volume = {12}, number = {8}, pages = {}, pmid = {39203393}, issn = {2076-2607}, support = {SWJ-CJX23Z11//the 2023 Science and Technology Innovation Fund Project of Hydrology Bureau of Yangtze River Water Resources Commission/ ; }, abstract = {Groundwater is one of the important freshwater resources on Earth and is closely related to human activities. As a good biological vector, a more diverse repertory of antibiotic resistance genes in the water environment would have a profound impact on human medical health. Therefore, this study conducted a metagenomic sequencing analysis of water samples from groundwater monitoring points in the middle and lower reaches of the Yangtze River to characterize microbial community composition and antibiotic resistance in the groundwater environment. Our results show that different microbial communities and community composition were the driving factors in the groundwater environment, and a diversity of antibiotic resistance genes in the groundwater environment was detected. The main source of antibiotic resistance gene host was determined by correlation tests and analyses. In this study, metagenomics was used for the first time to comprehensively analyze microbial communities in groundwater systems in the middle and lower reaches of the Yangtze River basin. The data obtained from this study serve as an invaluable resource and represent the basic metagenomic characteristics of groundwater microbial communities in the middle and lower reaches of the Yangtze River basin. These findings will be useful tools and provide a basis for future research on water microbial community and quality, greatly expanding the depth and breadth of our understanding of groundwater.}, } @article {pmid39203351, year = {2024}, author = {Liang, J and Zheng, X and Ning, T and Wang, J and Wei, X and Tan, L and Shen, F}, title = {Revealing the Viable Microbial Community of Biofilm in a Sewage Treatment System Using Propidium Monoazide Combined with Real-Time PCR and Metagenomics.}, journal = {Microorganisms}, volume = {12}, number = {8}, pages = {}, pmid = {39203351}, issn = {2076-2607}, support = {42307051//National Natural Science Foundation of China/ ; 2022M713416//China Postdoctoral Science Foundation/ ; CAAS-ZDRW202306//Special Fund for Basic Scientific Research of Central Public Welfare Institutes/ ; }, abstract = {Microbial community composition, function, and viability are important for biofilm-based sewage treatment technologies. Most studies of microbial communities mainly rely on the total deoxyribonucleic acid (DNA) extracted from the biofilm. However, nucleotide materials released from dead microorganisms may interfere with the analysis of viable microorganisms and their metabolic potential. In this study, we developed a protocol to assess viability as well as viable community composition and function in biofilm in a sewage treatment system using propidium monoazide (PMA) coupled with real-time quantitative polymerase chain reaction (qPCR) and metagenomic technology. The optimal removal of PMA from non-viable cells was achieved by a PMA concentration of 4 μM, incubation in darkness for 5 min, and exposure for 5 min. Simultaneously, the detection limit can reach a viable bacteria proportion of 1%, within the detection concentration range of 10[2]-10[8] CFU/mL (colony forming unit/mL), showing its effectiveness in removing interference from dead cells. Under the optimal conditions, the result of PMA-metagenomic sequencing revealed that 6.72% to 8.18% of non-viable microorganisms were influenced and the composition and relative abundance of the dominant genera were changed. Overall, this study established a fast, sensitive, and highly specific biofilm viability detection method, which could provide technical support for accurately deciphering the structural composition and function of viable microbial communities in sewage treatment biofilms.}, } @article {pmid39202671, year = {2024}, author = {Jalal, RS and Sonbol, HS}, title = {Resistome Signature and Antibiotic Resistance Mechanisms in Rhizospheric Soil Bacteriomes of Mecca Region, Saudi Arabia: Insights into Impact on Human Health.}, journal = {Life (Basel, Switzerland)}, volume = {14}, number = {8}, pages = {}, pmid = {39202671}, issn = {2075-1729}, support = {PNURSP2024R83//Princess Nourah bint Abdulrahman University/ ; }, abstract = {The objective of this investigation is to ascertain the distinctive profile of the rhizospheric soil resistome within the Mecca region, while also evaluating the potential risks associated with the horizontal transfer of resistome determinants to the open environment and human clinical isolates. We have made metagenomic whole-genome shotgun sequencing for rhizospheric microbiomes of two endemic plants, namely Moringa oleifera and Abutilon fruticosum. The rhizospheric resistomes of the two plants and the abundance of antibiotic resistance genes (ARGs) were identified by cross-referencing encoded proteins with the comprehensive antibiotic resistance database (CARD). The identified ARGs were then analyzed for their antimicrobial resistance (AMR) mechanisms. Predominantly within this soil are the two bacterial species Pseudomonas aeruginosa and Mycobacterium tuberculosis. These opportunistic human pathogens are implicated in respiratory infections and are correlated with heightened mortality rates. The most prevalent array of ARGs existing in this soil comprises mexA, mexC, mexE, and cpxR, associated with mechanisms of antibiotic active efflux, along with ACC(2), ACC(3), AAC(6), and APH(6), in addition to arr1, arr3, arr4, iri, rphA, and rphB, implicated in antibiotic inactivation. Furthermore, vanS, vanR, and vanJ are identified for antibiotic target alteration, while rpoB2 and RbpA are noted for antibiotic target replacement and protection, respectively. These mechanisms confer resistance against a diverse spectrum of drug classes encompassing fluoroquinolones, aminoglycosides, glycopeptides, and rifampicins. This study underscores the potential hazards posed to human health by the presence of these pathogenic bacteria within the rhizospheric soil of the Mecca region, particularly in scenarios where novel ARGs prevalent in human populations are harbored and subsequently transmitted through the food chain to human clinical isolates. Consequently, stringent adherence to good agricultural and food transportation practices is imperative, particularly with regard to edible plant parts and those utilized in folkloric medicine.}, } @article {pmid39202448, year = {2024}, author = {Minelli, M and Anaclerio, F and Calisi, D and Onofrj, M and Antonucci, I and Gatta, V and Stuppia, L}, title = {Application of Metagenomics Sequencing in a Patient with Dementia: A New Case Report.}, journal = {Genes}, volume = {15}, number = {8}, pages = {}, pmid = {39202448}, issn = {2073-4425}, mesh = {Humans ; *Dementia/genetics/microbiology ; *Metagenomics/methods ; *RNA, Ribosomal, 16S/genetics ; Male ; Aged ; High-Throughput Nucleotide Sequencing/methods ; Female ; DNA, Bacterial/genetics ; }, abstract = {(1) Background: The study of the microbiome is crucial for its role in major systemic diseases, in particular the oral and gut microbiota. In recent years, the study of microorganisms correlated, for example, with neurodegenerative disease has increased the prospect of a possible link between gut microbiota and the brain. Here, we report a new case concerning a patient who was initially evaluated genetically for dementia and late-onset dyskinesia, and later tested with 16S metagenomics sequencing. (2) Methods: Starting from a buccal swab, we extracted bacterial DNA and then we performed NGS metagenomics sequencing based on the amplification of the hypervariable regions of the 16S rRNA gene in bacteria. (3) Results: The sequencing revealed the presence of the Spirochaetes phylum, a pathogenic bacterium generally known to be capable of migrating to the Central Nervous System. (4) Conclusions: Oral infections, as our results suggest, could be possible contributing factors to various neurodegenerative conditions.}, } @article {pmid39202441, year = {2024}, author = {Li, L and Miao, W and Li, Z and Huang, L and Hau, E and Khan, MF and Liu, Q and Zeng, Q and Cui, K}, title = {Meta-Genomic Analysis of Different Bacteria and Their Genomes Found in Raw Buffalo Milk Obtained in Various Farms Using Different Milking Methods.}, journal = {Genes}, volume = {15}, number = {8}, pages = {}, pmid = {39202441}, issn = {2073-4425}, support = {No. AA22068099//Guangxi Science and Technology Department/ ; No. nycytxgxcxtd-2021-21-02//Guangxi Innovation Team Construction of National Modern Agricultural Industrial Tech-nology System/ ; }, mesh = {Animals ; *Milk/microbiology ; *Buffaloes/microbiology ; Bacteria/genetics/classification/isolation & purification ; Female ; Dairying/methods ; Genome, Bacterial ; Farms ; China ; Metagenomics/methods ; Staphylococcus/genetics/isolation & purification ; }, abstract = {Milking methods have significant impacts on the microbiological composition, which could affect the quality of raw buffalo milk. Hence, the current study was conducted on the impact of milking methods on microorganisms in buffalo tank raw milk from 15 farms in Guangxi, China. The farms were divided into two groups based on the milking method: mechanical milking (MM, n = 6) and hand milking (HM, n = 9). Somatic cell counts, bacterial cell counts and nutrients of the raw buffalo milk samples were analyzed. The comparison of raw buffalo milk samples was analyzed using metagenomic sequencing to detect any differences between the two groups. There was no significant difference in the basic nutritional compositions and somatic cell count of raw buffalo milk between the two milking methods. However, the HM samples had significantly higher bacterial counts and diversity compared to the MM samples. The results showed that Staphylococcus spp., Klebsiella spp., Streptococcus spp., and Pseudomonas spp. were the major microbes present in canned raw buffalo milk. However, the differences between the two milking methods were the relative abundance of core microorganisms and their potential mastitis-causing genera, including the content of antibiotic-resistance genes and virulence genes. Our study revealed that Staphylococcus spp. and Streptococcus spp. were significantly more abundant in the MM group, while Klebsiella spp. was more abundant in the HM group. Regardless of the milking method used, Pseudomonas spp. was identified as the primary genus contributing to antibiotic resistance and virulence genes in canned raw buffalo milk. These findings affirm that there are differences in the microbial and genomic levels in canned raw milk. To prove the functional roles of the discovered genes and how these genes affect milk quality, further research and experimental validation are necessary.}, } @article {pmid39202331, year = {2024}, author = {Zheng, X and Xu, L and Tang, Q and Shi, K and Wang, Z and Shi, L and Ding, Y and Yin, Z and Zhang, X}, title = {Integrated Metagenomic and Metabolomics Profiling Reveals Key Gut Microbiota and Metabolites Associated with Weaning Stress in Piglets.}, journal = {Genes}, volume = {15}, number = {8}, pages = {}, pmid = {39202331}, issn = {2073-4425}, support = {202103a06020013//Major special science and technology project of Anhui Province/ ; GXXT-2023-059//the Cooperative Innovation Project of Anhui Provincial Universities/ ; 340000211260001000431//the Joint Research Project on Local Pig Breeding in Anhui Province/ ; 2021YFD1301200//National Key research and development Program of China/ ; }, mesh = {Animals ; *Weaning ; *Gastrointestinal Microbiome ; Swine ; *Metabolomics/methods ; *Metagenomics/methods ; Stress, Physiological ; Metabolome ; Animals, Newborn ; Cecum/microbiology/metabolism ; }, abstract = {(1) Background: Weaning is a challenging and stressful event in the pig's life, which disrupts physiological balance and induces oxidative stress. Microbiota play a significant role during the weaning process in piglets. Therefore, this study aimed to investigate key gut microbiota and metabolites associated with weaning stress in piglets. (2) Methods: A total of ten newborn piglet littermates were randomly assigned to two groups: S (suckling normally) and W (weaned at 21 d; all euthanized at 23 d). Specimens of the cecum were dehydrated with ethanol, cleared with xylene, embedded in paraffin, and cut into 4 mm thick serial sections. After deparaffinization, the sections were stained with hematoxylin and eosin (H&E) for morphometric analysis. Cecal metagenomic and liver LC-MS-based metabolomics were employed in this study. Statistical comparisons were performed by a two-tailed Student's t-test, and p < 0.05 indicated statistical significance. (3) Results: The results showed that weaning led to intestinal morphological damage in piglets. The intestinal villi of suckling piglets were intact, closely arranged in an orderly manner, and finger-shaped, with clear contours of columnar epithelial cells. In contrast, the intestines of weaned piglets showed villous atrophy and shedding, as well as mucosal bleeding. Metagenomics and metabolomics analyses showed significant differences in composition and function between suckling and weaned piglets. The W piglets showed a decrease and increase in the relative abundance of Bacteroidetes and Proteobacteria (p < 0.05), respectively. The core cecal flora in W piglets were Campylobacter and Clostridium, while those in S piglets were Prevotella and Lactobacillus. At the phylum level, the relative abundance of Bacteroidetes significantly decreased (p < 0.05) in weaned piglets, while Proteobacteria significantly increased (p < 0.05). Significant inter-group differences were observed in pathways and glycoside hydrolases in databases, such as the KEGG and CAZymes, including fructose and mannose metabolism, salmonella infection, antifolate resistance, GH135, GH16, GH32, and GH84. We identified 757 differential metabolites between the groups through metabolomic analyses-350 upregulated and 407 downregulated (screened in positive ion mode). In negative ion mode, 541 differential metabolites were identified, with 270 upregulated and 271 downregulated. Major differential metabolites included glycerophospholipids, histidine, nitrogen metabolism, glycine, serine, threonine, β-alanine, and primary bile acid biosynthesis. The significant differences in glycine, serine, and threonine metabolites may be potentially related to dysbiosis caused by weaning stress. Taken together, the identification of microbiome and metabolome signatures of suckling and weaned piglets has paved the way for developing health-promoting nutritional strategies, focusing on enhancing bacterial metabolite production in early life stages.}, } @article {pmid39201814, year = {2024}, author = {Gillani, SW and Teng, L and Khan, A and Xu, Y and Powell, CA and Zhang, M}, title = {Fungal Diversity and Gibberellin Hormones Associated with Long Whips of Smut-Infected Sugarcanes.}, journal = {International journal of molecular sciences}, volume = {25}, number = {16}, pages = {}, pmid = {39201814}, issn = {1422-0067}, support = {CARS 170109//China Agricultural Research System/ ; Guike AA22117001//Guangxi Scientific and Technological Department/ ; }, mesh = {*Gibberellins/metabolism ; *Saccharum/microbiology/metabolism ; *Plant Diseases/microbiology ; Fusarium/metabolism/genetics/pathogenicity ; Plant Growth Regulators/metabolism ; Metagenomics/methods ; }, abstract = {Sugarcane smut, caused by the fungus Sporisorium scitamineum (Sydow), significantly affects sugarcane crops worldwide. Infected plants develop whip-like structures known as sori. Significant variations in these whip lengths are commonly observed, but the physiological and molecular differences causing these morphological differences remain poorly documented. To address this, we employed conventional microbe isolation, metagenomic, and metabolomic techniques to investigate smut-infected sugarcane stems and whips of varying lengths. Metagenomics analysis revealed a diverse fungal community in the sugarcane whips, with Sporisorium and Fusarium genera notably present (>1%) in long whips. Isolation techniques confirmed these findings. Ultra-performance liquid chromatography analysis (UHPLC-MS/MS) showed high levels of gibberellin hormones (GA3, GA1, GA4, GA8, and GA7) in long whips, with GA4 and GA7 found exclusively in long whips and stems. Among the prominent genera present within long whips, Fusarium was solely positively correlated with these gibberellin (GA) hormones, with the exception of GA8, which was positively correlated with Sporisorium. KEGG enrichment analysis linked these hormones to pathways like diterpenoid biosynthesis and plant hormone signal transduction. These findings suggest that Fusarium may influence GA production leading to whip elongation. Our study reveals fungal dynamics and gibberellin responses in sugarcane smut whips. Future research will explore the related molecular gibberellin synthesis mechanisms.}, } @article {pmid39201270, year = {2024}, author = {Su, H and Yang, S and Chen, S and Chen, X and Guo, M and Zhu, L and Xu, W and Liu, H}, title = {What Happens in the Gut during the Formation of Neonatal Jaundice-Underhand Manipulation of Gut Microbiota?.}, journal = {International journal of molecular sciences}, volume = {25}, number = {16}, pages = {}, pmid = {39201270}, issn = {1422-0067}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Jaundice, Neonatal/therapy/microbiology/etiology ; Infant, Newborn ; *Probiotics ; *Bilirubin/metabolism/blood ; Breast Feeding ; Milk, Human/microbiology/metabolism ; }, abstract = {Jaundice is a symptom of high blood bilirubin levels affecting about 80% of neonates. In neonates fed with breast milk, jaundice is particularly prevalent and severe, which is likely multifactorial. With the development of genomics and metagenomics, a deeper understanding of the neonatal gut microbiota has been achieved. We find there are accumulating evidence to indicate the importance of the gut microbiota in the mechanism of jaundice. In this paper, we present new comprehensive insight into the relationship between the microbiota and jaundice. In the new perspective, the gut is a crucial crossroad of bilirubin excretion, and bacteria colonizing the gut could play different roles in the excretion of bilirubin, including Escherichia coli as the main traffic jam causers, some Clostridium and Bacteroides strains as the traffic police, and most probiotic Bifidobacterium and Lactobacillus strains as bystanders with no effect or only a secondary indirect effect on the metabolism of bilirubin. This insight could explain why breast milk jaundice causes a longer duration of blood bilirubin and why most probiotics have limited effects on neonatal jaundice. With the encouragement of breastmilk feeding, our perspective could guide the development of new therapy methods to prevent this side effect of breastfeeding.}, } @article {pmid39201260, year = {2024}, author = {Ryu, HM and Islam, SMS and Riaz, B and Sayeed, HM and Choi, B and Sohn, S}, title = {Immunomodulatory Effects of a Probiotic Mixture: Alleviating Colitis in a Mouse Model through Modulation of Cell Activation Markers and the Gut Microbiota.}, journal = {International journal of molecular sciences}, volume = {25}, number = {16}, pages = {}, pmid = {39201260}, issn = {1422-0067}, mesh = {Animals ; *Probiotics/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Disease Models, Animal ; *Colitis/microbiology/therapy/diet therapy/chemically induced ; *Dextran Sulfate/toxicity ; RNA, Ribosomal, 16S/genetics ; Colitis, Ulcerative/microbiology/therapy/immunology/diet therapy ; Biomarkers ; Mice, Inbred C57BL ; Colon/microbiology/pathology/metabolism ; }, abstract = {Ulcerative colitis (UC) is a persistent inflammatory intestinal disease that consistently affects the colon and rectum. Its exact cause remains unknown. UC causes a considerable challenge in healthcare, prompting research for novel therapeutic strategies. Although probiotics have gained popularity as possible candidates for managing UC, studies are still ongoing to identify the best probiotics or probiotic mixtures for clinical applications. This study aimed to determine the efficacy of a multi-strain probiotic mixture in mitigating intestinal inflammation in a colitis mouse model induced by dextran sulfate sodium. Specifically, a multi-strain probiotic mixture consisting of Tetragenococcus halophilus and Eubacterium rectale was used to study its impact on colitis symptoms. Anti-inflammatory effects were evaluated using ELISA and flow cytometry. The configuration of gut microbial communities was determined using 16S rRNA metagenomic analysis. According to this study, colitis mice treated with the probiotic mixture experienced reduced weight loss and significantly less colonic shortening compared to untreated mice. Additionally, the treated mice exhibited increased levels of forkhead box P3 (Foxp3) and interleukin 10, along with decreased expression of dendritic cell activation markers, such as CD40+, CD80+, and CD83+, in peripheral blood leukocytes and intraepithelial lymphocytes. Furthermore, there was a significant decrease in the frequencies of CD8+N.K1.1+ cells and CD11b+Ly6G+ cells. In terms of the gut microbiota, probiotic-mixture treatment of colitis mice significantly increased the abundance of the phyla Actinobacteria and Verrucomicrobia (p < 0.05). These results provide valuable insights into the therapeutic promise of multi-strain probiotics, shedding light on their potential to alleviate colitis symptoms. This research contributes to the ongoing exploration of effective probiotic interventions for managing inflammatory bowel disease.}, } @article {pmid39201258, year = {2024}, author = {Al-Sarraj, F and Albiheyri, R and Qari, M and Alotaibi, M and Al-Zahrani, M and Anwar, Y and Alghamdi, MA and Nass, NM and Bouback, T and Alotibi, I and Radhwi, O and Sajer, BH and Redhwan, A and Al-Matary, MA and Almanzalawi, EA and Elshafie, HS}, title = {Genetic Patterns of Oral Cavity Microbiome in Patients with Sickle Cell Disease.}, journal = {International journal of molecular sciences}, volume = {25}, number = {16}, pages = {}, pmid = {39201258}, issn = {1422-0067}, support = {grant no. J: 007-130-1443.//Deanship of Scientific Research (DSR) at King Abdulaziz University (KAU), Jeddah/ ; }, mesh = {Humans ; *Anemia, Sickle Cell/microbiology/genetics ; *Mouth/microbiology ; *Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; Female ; Male ; Adult ; *Saliva/microbiology ; Bacteria/genetics/classification/isolation & purification ; Young Adult ; Case-Control Studies ; Adolescent ; High-Throughput Nucleotide Sequencing ; Middle Aged ; }, abstract = {The Middle Eastern prevalence of sickle cell anemia, a genetic disorder that affects red blood cells, necessitates additional research. On a molecular level, we sought to identify and sort the oral microbiota of healthy individuals and those with sickle cell anemia. Furthermore, it is crucial to comprehend how changes in the genetic makeup of the oral microbiota impact the state of sickle cell anemia. Using next-generation sequencing, the 16S rRNA amplicon was examined using saliva samples from 36 individuals with sickle cell anemia and healthy individuals. These samples were obtained from sickle cell anemia patients (18 samples) and healthy control participants (controls, 18 samples). Various analyses are conducted using bioinformatic techniques to identify distinct species and their relative abundance. Streptococcus, followed by Fusobacterium nucleatum, Prevotella, and Veillonella were the most prevalent genera of bacteria in the saliva of the SCA and non-SCA individuals according to our findings. Rothia mucilaginosa, Prevotella scoposa, and Veillonella dispar species were the dominant species in both sickle cell anemia and non-sickle cell anemia subjects. Streptococcus salivarius, Actinomyces graevenitzii, Actinomyces odontolyticus, and Actinomyces georgiae spp. were the most prevalent bacterial spp. in the studied SCA cases. The sequencing of the 16S rRNA gene yielded relative abundance values that were visualized through a heatmap analysis. Alterations in the oral microflora's constitution can significantly affect the susceptibility of sickle cell anemia patients to develop more severe health complications. Salivary diagnosis is a potential tool for predicting and preventing oral microbiome-related diseases in the future.}, } @article {pmid39200000, year = {2024}, author = {Lowe, M and Strasheim, W and Chan, WY and Perovic, O}, title = {Bacterial and Genetic Features of Raw Retail Pork Meat: Integrative Analysis of Antibiotic Susceptibility, Whole-Genome Sequencing, and Metagenomics.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {8}, pages = {}, pmid = {39200000}, issn = {2079-6382}, support = {D43 TW011255/TW/FIC NIH HHS/United States ; GRANT AE89 (ANTIMICROBIAL RESISTANCE PREVALENCE AND TRANSMISSION BETWEEN ANIMAL FEED AND HUMANS)//South African Medical Research Council/ ; }, abstract = {The global antibiotic resistance crisis, driven by overuse and misuse of antibiotics, is multifaceted. This study aimed to assess the microbiological and genetic characteristics of raw retail pork meat through various methods, including the isolation, antibiotic susceptibility testing (AST), whole-genome sequencing (WGS) of selected indicator bacteria, antibiotic residue testing, and metagenomic sequencing. Samples were purchased from 10 pre-selected retail stores in Gauteng, South Africa. The samples were aseptically separated, with portions sent to an external laboratory for isolating indicator bacteria and testing for antibiotic residues. Identification of the isolated bacteria was reconfirmed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). AST was performed using the Microscan Walkaway system (Beckman Coulter, Brea, CA, USA). WGS and metagenomic sequencing were performed using the Illumina NextSeq 550 instrument (San Diego, CA, USA). The isolated E. coli and E. faecalis exhibited minimal phenotypic resistance, with WGS revealing the presence of tetracycline resistance genes. Both the isolated bacteria and meat samples harboured tetracycline resistance genes and the antibiotic residue concentrations were within acceptable limits for human consumption. In the metagenomic context, most identified bacteria were of food/meat spoilage and environmental origin. The resistome analysis primarily indicated beta-lactam, tetracycline and multidrug resistance genes. Further research is needed to understand the broader implications of these findings on environmental health and antibiotic resistance.}, } @article {pmid39199499, year = {2024}, author = {Mabrok, HB and Ramadan, AA and Hamed, IM and Mohamed, DA}, title = {Obesity as Inducer of Cognitive Function Decline via Dysbiosis of Gut Microbiota in Rats.}, journal = {Brain sciences}, volume = {14}, number = {8}, pages = {}, pmid = {39199499}, issn = {2076-3425}, support = {a626035bfd925943, 4c6c6a0dc9645904, 175e6bf937114ef5, 18dca4e8f29e587c, aaf09103eb8bd6ee, 3740a1d4a23d772f, 1b07773fd3c8c954, 4f8fa1a570a3a4b7, 490e7e4e51713e71, 1e87a07edec11a96, 7642f29d62c1068b, c06bc3bf279a8491, c78b30a55528e880, e160d996ffb69ed4, 133//Discount Vouchers/ ; }, abstract = {Diet-induced obesity is a global phenomenon that affects the population worldwide with manifestations at both the phenotypic and genotypic levels. Cognitive function decline is a major global health challenge. The relation between obesity and cognitive function is a debatable issue. The main goal of the current research was to study the implications of obesity on cognitive function and gut microbiota diversity and its impact on plasma and brain metabolic parameters in rats. Obesity was induced in rats by feeding on a high-fat (HF) or a high-fat/high-sucrose (HFHS) diet. The results reveal that both the HF (0.683) and HFHS (0.688) diets were effective as obesity inducers, which was confirmed by a significant increase in the body mass index (BMI). Both diet groups showed dyslipidemia and elevation of oxidative stress, insulin resistance (IR), and inflammatory markers with alterations in liver and kidney functions. Obesity led to a reduction in cognitive function through a reduction in short-term memory by 23.8% and 30.7% in the rats fed HF and HFHS diets, respectively, and learning capacity and visuo-spatial memory reduced by 8.9 and 9.7 s in the rats fed an HF or HFHS diet, respectively. Bacteroidetes, Firmicutes, Proteobacteria, Fusobacteria, and Spirochaetes phyla were detected. The Firmicutes/Bacteroidetes ratio (F/B) significantly decreased in the HF group, while it increased in the HFHS group compared to the normal control. The two species, Bacteroides acidifaciens and Bacteroides ovatus, which are associated with IR, were drastically compromised by the high-fat/high-sucrose diet. Some species that have been linked to reduced inflammation showed a sharp decrease in the HFHS group, while Prevotella copri, which is linked to carbohydrate metabolism, was highly enriched. In conclusion: Obesity led to cognitive impairment through changes in short-term and visuo-spatial memory. A metagenomic analysis revealed alterations in the abundance of some microbial taxa associated with obesity, inflammation, and insulin resistance in the HF and HFHS groups.}, } @article {pmid39198891, year = {2024}, author = {Tian, F and Wainaina, JM and Howard-Varona, C and Domínguez-Huerta, G and Bolduc, B and Gazitúa, MC and Smith, G and Gittrich, MR and Zablocki, O and Cronin, DR and Eveillard, D and Hallam, SJ and Sullivan, MB}, title = {Prokaryotic-virus-encoded auxiliary metabolic genes throughout the global oceans.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {159}, pmid = {39198891}, issn = {2049-2618}, support = {T32 GM141955/GM/NIGMS NIH HHS/United States ; ABI#1759874, ABI#2149505, OCE#1536989, OCE#1829831, and OCE#2019589//National Science Foundation/ ; #3790//Gordon and Betty Moore Foundation Investigator Award/ ; }, mesh = {*Oceans and Seas ; *Seawater/virology/microbiology ; Metagenomics ; Bacteria/genetics/classification/metabolism ; Viruses/genetics/classification/isolation & purification ; Prokaryotic Cells/metabolism/virology ; Metagenome ; Metabolic Networks and Pathways/genetics ; Gene Transfer, Horizontal ; Phosphatidylethanolamines/metabolism ; }, abstract = {BACKGROUND: Prokaryotic microbes have impacted marine biogeochemical cycles for billions of years. Viruses also impact these cycles, through lysis, horizontal gene transfer, and encoding and expressing genes that contribute to metabolic reprogramming of prokaryotic cells. While this impact is difficult to quantify in nature, we hypothesized that it can be examined by surveying virus-encoded auxiliary metabolic genes (AMGs) and assessing their ecological context.

RESULTS: We systematically developed a global ocean AMG catalog by integrating previously described and newly identified AMGs and then placed this catalog into ecological and metabolic contexts relevant to ocean biogeochemistry. From 7.6 terabases of Tara Oceans paired prokaryote- and virus-enriched metagenomic sequence data, we increased known ocean virus populations to 579,904 (up 16%). From these virus populations, we then conservatively identified 86,913 AMGs that grouped into 22,779 sequence-based gene clusters, 7248 (~ 32%) of which were not previously reported. Using our catalog and modeled data from mock communities, we estimate that ~ 19% of ocean virus populations carry at least one AMG. To understand AMGs in their metabolic context, we identified 340 metabolic pathways encoded by ocean microbes and showed that AMGs map to 128 of them. Furthermore, we identified metabolic "hot spots" targeted by virus AMGs, including nine pathways where most steps (≥ 0.75) were AMG-targeted (involved in carbohydrate, amino acid, fatty acid, and nucleotide metabolism), as well as other pathways where virus-encoded AMGs outnumbered cellular homologs (involved in lipid A phosphates, phosphatidylethanolamine, creatine biosynthesis, phosphoribosylamine-glycine ligase, and carbamoyl-phosphate synthase pathways).

CONCLUSIONS: Together, this systematically curated, global ocean AMG catalog and analyses provide a valuable resource and foundational observations to understand the role of viruses in modulating global ocean metabolisms and their biogeochemical implications. Video Abstract.}, } @article {pmid39198832, year = {2024}, author = {Su, W and Gong, C and Zhong, H and Yang, H and Chen, Y and Wu, X and Jin, J and Xi, H and Zhao, J}, title = {Vaginal and endometrial microbiome dysbiosis associated with adverse embryo transfer outcomes.}, journal = {Reproductive biology and endocrinology : RB&E}, volume = {22}, number = {1}, pages = {111}, pmid = {39198832}, issn = {1477-7827}, support = {437606312//Wenzhou Medical University advantageous and distinctive Discipline Construction Project/ ; }, mesh = {Humans ; Female ; *Embryo Transfer/methods ; *Dysbiosis/microbiology ; Adult ; *Vagina/microbiology ; *Microbiota/genetics/physiology ; *Endometrium/microbiology/metabolism ; *Embryo Implantation/physiology ; Pregnancy ; *Infertility, Female/microbiology/therapy ; Fertilization in Vitro/methods ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Assisted reproductive technology (ART) is the most effective method to treat infertility and the pathogenesis of implantation failure after in vitro fertilization-embryo transfer (IVF-ET) is a challenging filed in infertility. Microbes in the female reproductive tract are considered to be associated with gynecological and obstetric diseases. However, its effects on embryo implantation failure are unsured.

PURPOSE: This study aimed to investigate reproductive tract dysbiosis, identify different bacteria in reproductive tract as potential biomarkers of embryo implantation failure and demonstrate the pathogenesis through metabolites analysis.

METHODS: We compared the data from 16S rRNA gene and metagenome in reproductive tracts through QIIME2 and HUMAnN2 by the times of embryo implantation failure on 239 infertile patients and 17 healthy women.

RESULTS: Our study revealed a strong positive correlation between Lactobacillus abundance and embryo implantation success (IS) after IVF-ET. The microbial community composition and structure in reproductive tract showed substantially difference between the embryo implantation failure (IF) and healthy control. Moreover, we established a diagnostic model through receiver operating characteristic (ROC) with 0.913 area under curve (AUC) in IS and multiple implantation failures (MIF), verified its effectiveness with an AUC = 0.784 demonstrating microbial community alterations could efficiently discriminate MIF patients. Metagenome functional analyses of vaginal samples from another independent infertile patients after IVF-ET revealed the L-lysine synthesis pathway enriched in IF patients, along with ascended vaginal pH and decreased Lactobacillus abundance.

CONCLUSIONS: This study clarifies several independent relationships of bacteria in vagina and endometrial fluid on embryo implantation failure and undoubtedly broadens the understanding about female reproductive health.}, } @article {pmid39198826, year = {2024}, author = {Su, Q and Zhuang, DH and Li, YC and Chen, Y and Wang, XY and Ge, MX and Xue, TY and Zhang, QY and Liu, XY and Yin, FQ and Han, YM and Gao, ZL and Zhao, L and Li, YX and Lv, MJ and Yang, LQ and Xia, TR and Luo, YJ and Zhang, Z and Kong, QP}, title = {Gut microbiota contributes to high-altitude hypoxia acclimatization of human populations.}, journal = {Genome biology}, volume = {25}, number = {1}, pages = {232}, pmid = {39198826}, issn = {1474-760X}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Acclimatization ; *Altitude ; Animals ; Adult ; Male ; *Hypoxia/genetics ; Mice ; Female ; Longitudinal Studies ; Altitude Sickness/microbiology/genetics ; Middle Aged ; }, abstract = {BACKGROUND: The relationship between human gut microbiota and high-altitude hypoxia acclimatization remains highly controversial. This stems primarily from uncertainties regarding both the potential temporal changes in the microbiota under such conditions and the existence of any dominant or core bacteria that may assist in host acclimatization.

RESULTS: To address these issues, and to control for variables commonly present in previous studies which significantly impact the results obtained, namely genetic background, ethnicity, lifestyle, and diet, we conducted a 108-day longitudinal study on the same cohort comprising 45 healthy Han adults who traveled from lowland Chongqing, 243 masl, to high-altitude plateau Lhasa, Xizang, 3658 masl, and back. Using shotgun metagenomic profiling, we study temporal changes in gut microbiota composition at different timepoints. The results show a significant reduction in the species and functional diversity of the gut microbiota, along with a marked increase in functional redundancy. These changes are primarily driven by the overgrowth of Blautia A, a genus that is also abundant in six independent Han cohorts with long-term duration in lower hypoxia environment in Shigatse, Xizang, at 4700 masl. Further animal experiments indicate that Blautia A-fed mice exhibit enhanced intestinal health and a better acclimatization phenotype to sustained hypoxic stress.

CONCLUSIONS: Our study underscores the importance of Blautia A species in the gut microbiota's rapid response to high-altitude hypoxia and its potential role in maintaining intestinal health and aiding host adaptation to extreme environments, likely via anti-inflammation and intestinal barrier protection.}, } @article {pmid39198450, year = {2024}, author = {Licht, P and Dominelli, N and Kleemann, J and Pastore, S and Müller, ES and Haist, M and Hartmann, KS and Stege, H and Bros, M and Meissner, M and Grabbe, S and Heermann, R and Mailänder, V}, title = {The skin microbiome stratifies patients with cutaneous T cell lymphoma and determines event-free survival.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {74}, pmid = {39198450}, issn = {2055-5008}, mesh = {Humans ; *Microbiota ; *Skin/microbiology ; Female ; Middle Aged ; Male ; *Staphylococcus aureus/genetics/pathogenicity/isolation & purification ; *Lymphoma, T-Cell, Cutaneous/microbiology ; Aged ; *Mycosis Fungoides/microbiology ; Dysbiosis/microbiology ; Skin Neoplasms/microbiology/pathology ; Adult ; Aged, 80 and over ; Metagenomics/methods ; Virulence Factors/genetics ; Bacteria/classification/genetics/isolation & purification ; }, abstract = {Mycosis fungoides (MF) is the most common entity of Cutaneous T cell lymphomas (CTCL) and is characterized by the presence of clonal malignant T cells in the skin. The role of the skin microbiome for MF development and progression are currently poorly understood. Using shotgun metagenomic profiling, real-time qPCR, and T cell receptor sequencing, we compared lesional and nonlesional skin of 20 MF patients with early and advanced MF. Additionally, we isolated Staphylococcus aureus and other bacteria from MF skin for functional profiling and to study the S. aureus virulence factor spa. We identified a subgroup of MF patients with substantial dysbiosis on MF lesions and concomitant outgrowth of S. aureus on plaque-staged lesions, while the other MF patients had a balanced microbiome on lesional skin. Dysbiosis and S. aureus outgrowth were accompanied by ectopic levels of cutaneous antimicrobial peptides (AMPs), including adaptation of the plaque-derived S. aureus strain. Furthermore, the plaque-derived S. aureus strain showed a reduced susceptibility towards antibiotics and an upregulation of the virulence factor spa, which may activate the NF-κB pathway. Remarkably, patients with dysbiosis on MF lesions had a restricted T cell receptor repertoire and significantly lower event-free survival. Our study highlights the potential for microbiome-modulating treatments targeting S. aureus to prevent MF progression.}, } @article {pmid39198444, year = {2024}, author = {Chang, D and Gupta, VK and Hur, B and Cobo-López, S and Cunningham, KY and Han, NS and Lee, I and Kronzer, VL and Teigen, LM and Karnatovskaia, LV and Longbrake, EE and Davis, JM and Nelson, H and Sung, J}, title = {Gut Microbiome Wellness Index 2 enhances health status prediction from gut microbiome taxonomic profiles.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {7447}, pmid = {39198444}, issn = {2041-1723}, support = {UL1 TR002377/TR/NCATS NIH HHS/United States ; UL1 TR002494/TR/NCATS NIH HHS/United States ; UL1TR002377//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; }, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Feces/microbiology ; *Health Status ; Metagenome ; Bacteria/classification/genetics/isolation & purification ; Female ; }, abstract = {Recent advancements in translational gut microbiome research have revealed its crucial role in shaping predictive healthcare applications. Herein, we introduce the Gut Microbiome Wellness Index 2 (GMWI2), an enhanced version of our original GMWI prototype, designed as a standardized disease-agnostic health status indicator based on gut microbiome taxonomic profiles. Our analysis involves pooling existing 8069 stool shotgun metagenomes from 54 published studies across a global demographic landscape (spanning 26 countries and six continents) to identify gut taxonomic signals linked to disease presence or absence. GMWI2 achieves a cross-validation balanced accuracy of 80% in distinguishing healthy (no disease) from non-healthy (diseased) individuals and surpasses 90% accuracy for samples with higher confidence (i.e., outside the "reject option"). This performance exceeds that of the original GMWI model and traditional species-level α-diversity indices, indicating a more robust gut microbiome signature for differentiating between healthy and non-healthy phenotypes across multiple diseases. When assessed through inter-study validation and external validation cohorts, GMWI2 maintains an average accuracy of nearly 75%. Furthermore, by reevaluating previously published datasets, GMWI2 offers new insights into the effects of diet, antibiotic exposure, and fecal microbiota transplantation on gut health. Available as an open-source command-line tool, GMWI2 represents a timely, pivotal resource for evaluating health using an individual's unique gut microbial composition.}, } @article {pmid39198442, year = {2024}, author = {Campos-Madueno, EI and Aldeia, C and Endimiani, A}, title = {Nanopore R10.4 metagenomic detection of blaCTX-M/blaDHA antimicrobial resistance genes and their genetic environments in stool.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {7450}, pmid = {39198442}, issn = {2041-1723}, support = {192514//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; }, mesh = {*Feces/microbiology ; *Escherichia coli/genetics/isolation & purification ; Humans ; *beta-Lactamases/genetics/metabolism ; *Metagenomics/methods ; *Nanopores ; Escherichia coli Proteins/genetics ; Plasmids/genetics ; Nanopore Sequencing/methods ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Gastrointestinal Microbiome/genetics ; }, abstract = {The increasing prevalence of gut colonization with CTX-M extended-spectrum β-lactamase- and/or DHA plasmid-mediated AmpC-producing Escherichia coli is a concern. Here, we evaluate Nanopore-shotgun metagenomic sequencing (Nanopore-SMS) latest V14 chemistry to detect blaCTX-M and blaDHA genes from healthy stools. We test 25 paired samples characterized with culture-based methods (native and pre-enriched). Antimicrobial resistant genes (ARGs) are detected from reads and meta-assembled genomes (MAGs) to determine their associated genetic environments (AGEs). Sensitivity and specificity of native Nanopore-SMS are 61.1% and 100%, compared to 81.5% and 75% for pre-enriched Nanopore-SMS, respectively. Native Nanopore-SMS identifies only one sample with an AGE, whereas pre-enriched Nanopore-SMS recognizes 9/18 plasmids and 5/9 E. coli chromosomes. Pre-enriched Nanopore-SMS identifies more ARGs than native Nanopore-SMS (p < 0.001). Notably, blaCTX-Ms and blaDHAs AGEs (plasmid and chromosomes) are identified within 1 hour of sequencing. Furthermore, microbiota analyses show that pre-enriched Nanopore-SMS results in more E. coli classified reads (47% vs. 3.1%), higher differential abundance (5.69 log2 fold) and lower Shannon diversity index (p < 0.0001). Nanopore-SMS has the potential to be used for intestinal colonization screening. However, sample pre-enrichment is necessary to increase sensitivity. Further computational improvements are needed to reduce the turnaround time for clinical applications.}, } @article {pmid39198293, year = {2024}, author = {Joseph, B and Babu, S}, title = {Effect of Organic and Chemical Fertilizer on the Diversity of Rhizosphere and Leaf Microbial Composition in Sunflower Plant.}, journal = {Current microbiology}, volume = {81}, number = {10}, pages = {331}, pmid = {39198293}, issn = {1432-0991}, mesh = {*Fertilizers/analysis ; *Rhizosphere ; *Helianthus/microbiology ; *Bacteria/classification/genetics/isolation & purification/drug effects ; *Plant Leaves/microbiology ; *Soil Microbiology ; *Fungi/classification/genetics/isolation & purification ; *Manure/microbiology ; Microbiota ; Biodiversity ; Metagenomics ; }, abstract = {Applying organic manure to crops positively impacts the soil microbial community which is negatively impacted when chemical fertilizers are used. Organic manures also add new microbes to the soil in addition to influencing the growth of native ones. Metagenomic analysis of different organic manures, soil, and pot culture experiments conducted under various fertilizer conditions constitute the primary methodologies employed in this study. We compared the effect of two organic manure combinations and an inorganic fertilizer combination on microbial community of rhizosphere soil and leaves of sunflower plants. Metagenomic sequencing data analysis revealed that the diversity of bacteria and fungi is higher in organic manure than in chemical fertilizers. Each organic manure combination selectively increased population of some specific microbes and supported new microbes. Application of chemical fertilizer hurts many plant beneficial fungi and bacteria. In summary, our study points out the superiority of organic manure combinations in enhancing microbial diversity and supporting beneficial microbes. These findings enhance the profound influence of fertilizer types on sunflower microbial communities, shedding light on the intricate dynamics within the rhizosphere and leaf microbiome. Bacterial genera such as Bacillus, Serratia, Sphingomonas, Pseudomonas, Methylobacterium, Acinetobacter, Stenotrophomonas, and fungal genera such as Wallemia, Aspergillus, Cladosporium, and Penicillium constitute the key microbes of sunflower plants.}, } @article {pmid39197657, year = {2024}, author = {Khan, AS and Afrin, S and Ahmed, F and Rahman, SR}, title = {Shotgun metagenomic analysis reveals the emergence of plasmid-encoded mcr-5.1 gene in hospital wastewater in Bangladesh.}, journal = {Journal of global antimicrobial resistance}, volume = {39}, number = {}, pages = {22-26}, doi = {10.1016/j.jgar.2024.08.007}, pmid = {39197657}, issn = {2213-7173}, mesh = {Bangladesh ; *Plasmids/genetics ; *Wastewater/microbiology ; *Metagenomics ; *Hospitals ; *Anti-Bacterial Agents/pharmacology ; Humans ; *Colistin/pharmacology ; *Phylogeny ; Enterobacteriaceae/genetics/drug effects/isolation & purification ; Microbial Sensitivity Tests ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; DNA Transposable Elements ; }, abstract = {Colistin is considered the last line therapy for treating multidrug-resistant (MDR) bacterial infections in humans. Therefore, the spread of colistin resistance poses a serious threat to human, and environmental health. Though Bangladesh is known as a hotspot of AMR, limited studies have been carried out regarding the status of colistin resistance. Information on the emerging bacterial resistance is inevitable for protecting public health. Nowadays, wastewater analysis has been prioritized for metagenomics-enabled AMR surveillance. Our study on the metagenomic analysis of untreated hospital effluents first detected the colistin resistance-conferring mcr-5.1 gene in the hospital environment of Bangladesh. Phylogenetic tree and in silico AMR analysis confirmed the detection of this mcr-5 variant, which is located in a plasmid contig. The plasmid was untypeable and belonged to the bacteria from the Enterobacteriaceae family. The mcr-5.1 operon was embedded in a Tn3 transposon, suggesting the mobility of the gene. Tnshfr1 transposon, chromate resistance protein ChrB, DNA invertase hin, and two MFS-type proteins were present in the genetic environment of mcr-5.1. Our findings provide evidence of the occurrence of mcr-5.1 in a hospital environment in Bangladesh, which calls for immediate attention and effective measures to contain the dissemination of colistin resistance in the environment.}, } @article {pmid39197649, year = {2024}, author = {Pinel-Cabello, M and Wasmund, K and Soder-Walz, JM and Vega, M and Rosell, M and Marco-Urrea, E}, title = {Divergent dual C-H isotopic fractionation pattern during anaerobic biodegradation of toluene within Aromatoleum species under nitrate-reducing conditions.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {361}, number = {}, pages = {124823}, doi = {10.1016/j.envpol.2024.124823}, pmid = {39197649}, issn = {1873-6424}, mesh = {*Toluene/metabolism ; *Biodegradation, Environmental ; *Nitrates/metabolism ; Anaerobiosis ; *Oxidation-Reduction ; Groundwater/chemistry/microbiology ; Water Pollutants, Chemical/metabolism ; Carbon Isotopes/metabolism ; RNA, Ribosomal, 16S/genetics ; Carbon-Carbon Lyases/metabolism/genetics ; }, abstract = {Toluene is a pollutant frequently detected in contaminated groundwater, mostly due to leakage from underground gasoline storage tanks and pipeline ruptures. Multi-element compound-specific isotope analysis provides a framework to understand transformation processes and design efficient remediation strategies. In this study, we enriched an anaerobic bacterial culture derived from a BTEX-contaminated aquifer that couples toluene and phenol oxidation with nitrate reduction and the concomitant production of carbon dioxide and biomass. The 16S rRNA gene amplicon data indicated that the toluene-degrading consortium was dominated by an Aromatoleum population (87 ± 2 % relative abundance), and metagenome sequencing confirmed that the genome of this Aromatoleum sp. encoded glycyl-radical enzyme benzylsuccinate synthase (BssABC) and phenylphospate synthase (PpsA1BC) homologous genes involved in the first step of toluene and phenol transformation, respectively. Carbon and hydrogen isotopic fractionation were εbulk, C = - 3.5 ± 0.6 ‰ and εrp, H = - 85 ± 11 ‰, respectively, leading to a dual C-H isotope slope of Λ[H/C] = 26 ± 2. This value fits with a previously reported value for a consortium dominated by an Azoarcus species (Λ[H/C] = 19 ± 5) but differs from that reported for Aromatoleum aromaticum (Λ[H/C] = 14 ± 1), both of which grow with toluene under nitrate-reducing conditions. Overall, this suggests the existence of different BssABC enzymes with different mechanistic motifs even within the same Aromatoleum genus.}, } @article {pmid39197646, year = {2024}, author = {Yang, T and Zhou, X and Wu, Y and Liang, Y and Zeng, X and Yu, Z}, title = {Metagenomic analyses of aerobic bacterial enrichment cultures that degraded Tris(2-chloroethyl) phosphate (TCEP) and its transformation products.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {361}, number = {}, pages = {124825}, doi = {10.1016/j.envpol.2024.124825}, pmid = {39197646}, issn = {1873-6424}, mesh = {*Biodegradation, Environmental ; Metagenomics ; Organophosphates/metabolism ; Bacteria, Aerobic/genetics/metabolism ; }, abstract = {Tris(2-chloroethyl) phosphate (TCEP) is of growing public concern worldwide because of its ubiquitous contamination, toxicity, and persistence. In this study, we investigated bacterial communities in aerobic enrichment cultures with TCEP and its two major transformation products bis(2-chloroethyl) phosphate (BCEP) and 2-chloroethanol (2-CE) as the sole carbon source. Burkholderiales and Rhizobiales were likely two main bacterial guilds involved in the hydrolysis of TCEP, while Rhizobiales and Sphingomonadales may play an important role in the hydrolysis of BCEP, given the increase of Rhizobiales and Sphingomonadales-related phosphoesterase genes when the carbon source was switched from TCEP to BCEP. All Burkholderiales, Rhizobiales, Sphingomonadales were probably efficient in 2-CE metabolism, because their dehydrogenase genes and dehalogenase genes increased after 2-CE enrichment. The different substrate preference of different bacterial guilds highlighted the importance to understand the diversity and collaboration among functional bacteria. Meanwhile, two TCEP-degrading strains affiliated with Xanthobacter and Ancylobacter were isolated. Xanthobacter sp. strain T2-1 was able to degrade both TCEP and BCEP following the pseudo-first-order kinetics with reaction rates of 1.66 h[-1] for TCEP and 1.02 h[-1] for BCEP, respectively. Ancylobacter sp. strain T3-4 could degrade TCEP following the pseudo-first-order kinetics with a reaction rate of 2.54 h[-1], but is unable to degrade BCEP. Additionally, strains that were phylogenetically closely related were found to have different degradation capabilities toward TCEP and/or BCEP, indicating the importance to investigate functional genes such as phosphoesterase genes.}, } @article {pmid39197642, year = {2024}, author = {Ning, Z and Sheng, Y and Gan, S and Guo, C and Wang, S and Cai, P and Zhang, M}, title = {Metagenomic and isotopic insights into carbon fixation by autotrophic microorganisms in a petroleum hydrocarbon impacted red clay aquifer.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {361}, number = {}, pages = {124824}, doi = {10.1016/j.envpol.2024.124824}, pmid = {39197642}, issn = {1873-6424}, mesh = {*Groundwater/chemistry/microbiology ; *Petroleum/metabolism ; *Hydrocarbons/metabolism ; *Carbon Cycle ; *Autotrophic Processes ; *Water Pollutants, Chemical/metabolism/analysis ; *Clay/chemistry ; *Carbon Isotopes ; China ; Metagenomics ; Bacteria/metabolism/genetics ; }, abstract = {Autotrophic microorganisms, the pivotal carbon fixers, exhibit a broad distribution across diverse environments, playing critical roles in the process of carbon sequestration. However, insights into their distribution characteristics in aquifers, particularly in those petroleum-hydrocarbon-contaminated (PHC) aquifers that were known for rich in heterotrophs, have been limited. In the study, groundwater samples were collected from red clay aquifers in the storage tank leakage area of a PHC site, a prevalent aquifer type in southern China and other regions. Metagenomics combined with hydrochemical and inorganic carbon isotope analyses were employed to elucidate the presence of microbial carbon fixation and its driving forces. Results showed that there were hundreds of autotrophic microorganisms participating in distinct carbon fixation processes in the red clay PHC aquifers. Reductive tricarboxylic acid (rTCA) and dicarboxylate/4-hydroxybutyrate (DC/4HB), as well as 3-hydroxypropionate (3HP or/and 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB)) were the predominant carbon fixation pathways. The abundances of carbon fixation genes and autotrophic microorganisms were significantly and positively correlated with hydrocarbon concentrations and δ[13]C of dissolved inorganic carbon (δ[13]C-DIC) values. This finding indicated that the petroleum hydrocarbon significantly promoted the proliferation of carbon fixation microorganisms, leading to a substantial uptake of inorganic carbon. Therefore, we deduce that this process holds considerable potential for carbon sequestration in PHC-contaminated aquifers.}, } @article {pmid39197546, year = {2024}, author = {Kim, H and Lee, E and Park, M and Min, K and Diep, YN and Kim, J and Ahn, H and Lee, E and Kim, S and Kim, Y and Kang, YJ and Jung, JH and Byun, MS and Joo, Y and Jeong, C and Lee, DY and Cho, H and Park, H and Kim, T}, title = {Microbiome-derived indole-3-lactic acid reduces amyloidopathy through aryl-hydrocarbon receptor activation.}, journal = {Brain, behavior, and immunity}, volume = {122}, number = {}, pages = {568-582}, doi = {10.1016/j.bbi.2024.08.051}, pmid = {39197546}, issn = {1090-2139}, mesh = {Animals ; Female ; Humans ; Male ; Mice ; *Alzheimer Disease/metabolism ; *Amyloid beta-Peptides/metabolism ; Amyloidosis/metabolism ; Astrocytes/metabolism ; Brain/metabolism ; Cognitive Dysfunction/metabolism ; *Disease Models, Animal ; *Gastrointestinal Microbiome/drug effects ; *Indoles/pharmacology ; Mice, Transgenic ; Microbiota/drug effects ; Microglia/metabolism ; *Receptors, Aryl Hydrocarbon/metabolism ; Signal Transduction/drug effects ; Tryptophan/metabolism/pharmacology ; }, abstract = {Alzheimer's disease (AD) pathogenesis has been associated with the gut microbiome and its metabolites, though the specific mechanisms have remained unclear. In our study, we used a multi-omics approach to identify specific microbial strains and metabolites that could potentially mitigate amyloidopathy in 5xFAD mice, a widely used model for AD research. Among the microbial strains tested, three showed promising results in reducing soluble amyloid-beta (Aβ) levels. Plasma metabolomics analysis revealed an enrichment of tryptophan (Trp) and indole-3-lactic acid (ILA) in mice with reduced soluble Aβ levels, suggesting a potential preventative role. The administration of a combined treatment of Trp and ILA prevented both Aβ accumulation and cognitive impairment in the 5xFAD mice. Our investigation into the mechanism revealed that ILA's effect on reducing Aβ levels was mediated through the activation of microglia and astrocytes, facilitated by the aryl hydrocarbon receptor (AhR) signaling pathway. These mechanisms were verified through experiments in 5xFAD mice that included an additional group with the administration of ILA alone, as well as in vitro experiments using an AhR inhibitor. Clinical data analysis revealed a greater abundance of Lactobacillus reuteri in the gut of healthy individuals compared to those at early stages of Aβ accumulation or with mild cognitive impairment. Additionally, human post-mortem brain analyses showed an increased expression of genes associated with the AhR signaling pathway in individuals without AD, suggesting a protective effect against AD progression. Our results indicate that ILA from gut microbes could inhibit the progression of amyloidopathy in 5xFAD mice through activation of AhR signaling in the brain.}, } @article {pmid39197493, year = {2024}, author = {Fu, R and Xu, J and Fan, Z and Qu, H and Jiang, Y and Xiong, W and Huang, F and Xuan, L and Xu, N and Liu, H and Wang, Z and Sun, J and Liu, Q and Lin, R}, title = {Metagenomic Next-Generation Sequencing in the Diagnosis of Pulmonary Infections after Allogeneic Hematopoietic Stem Cell Transplantation.}, journal = {Transplantation and cellular therapy}, volume = {30}, number = {11}, pages = {1110.e1-1110.e10}, doi = {10.1016/j.jtct.2024.08.014}, pmid = {39197493}, issn = {2666-6367}, mesh = {Humans ; *Hematopoietic Stem Cell Transplantation/adverse effects ; *High-Throughput Nucleotide Sequencing ; Male ; Female ; Middle Aged ; Adult ; *Metagenomics/methods ; Retrospective Studies ; Transplantation, Homologous/adverse effects ; Bronchoalveolar Lavage Fluid/microbiology/virology ; Adolescent ; Aged ; Young Adult ; Respiratory Tract Infections/diagnosis/microbiology/virology ; }, abstract = {Early and accurate identification of pathogens in pulmonary infections after allogeneic hematopoietic stem cell transplantation (allo-HSCT) is critically important. The clinical usefulness of metagenomic next-generation sequencing (mNGS) in the diagnosis of pulmonary infections after allo-HSCT remains under discussion. This multicenter retrospective study was conducted to compare mNGS and conventional microbiological tests (CMTs) in identifying the pathogens of pulmonary infections in allo-HSCT recipients. One hundred forty allo-HSCT recipients with suspected pulmonary infections who underwent bronchoscopy were included. mNGS and CMTs performed on bronchoalveolar lavage fluid specimens showed 71.4% positivity on mNGS compared to 55.0% positivity on CMTs. mNGS identified 182 pathogens, including bacteria (n = 88), fungi (n = 35) and viruses (n = 59), compared to 106 pathogens detected by CMTs (bacteria, n = 31; fungi, n = 24; viruses, n = 51). Pulmonary infection was finally diagnosed in 98 patients, including 22 bacterial, 7 fungal, 18 viral, and 48 mixed infections and 3 infections with an unknown pathogen. Mixed infections were identified in 50.5% of the patients with pulmonary infection. The sensitivity of mNGS and CMTs for diagnosing pulmonary infections was 88.8% and 69.4%, respectively (P = .001), and the specificity were 81.0% and 85.7%, respectively (P = .688). Our findings suggest that mNGS may be a promising technology for diagnosing pulmonary infections in allo-HSCT recipients.}, } @article {pmid39197484, year = {2024}, author = {Lu, W and Zheng, Y and Wang, Y and Song, J and Weng, Y and Ma, W and Arslan, M and Gamal El-Din, M and Wang, D and Wang, Q and Chen, C}, title = {Survival strategies and assembly mechanisms of microbial communities in petroleum-contaminated soils.}, journal = {Environmental research}, volume = {262}, number = {Pt 1}, pages = {119857}, doi = {10.1016/j.envres.2024.119857}, pmid = {39197484}, issn = {1096-0953}, mesh = {*Soil Microbiology ; *Soil Pollutants/analysis ; *Petroleum ; China ; Bacteria/genetics/classification/metabolism ; Archaea/genetics ; Microbiota ; Fungi/genetics/metabolism ; Soil/chemistry ; }, abstract = {This study analyzed petroleum-contaminated soils from south and north locations in China to explore the structure, diversity, functional genes and assembly processes of microbial communities' . Compared with soils from south locations, soils from northern regions exhibited elevated pH, total nitrogen (TN), and total petroleum hydrocarbon (TPH) levels. Among these, TN and TPH were the most influential on the microbial community. The dominant phyla for bacteria, archaea, and fungi were Proteobacteria, Thaumarchaeota, and Ascomycota, respectively. Among them, Proteobacteria was strongly correlated with various functional genes including alkB and many aromatics degradation and denitrification genes (r > 0.9, p < 0.01), suggesting that Proteobacteria play an important role in petroleum-contaminated soils. Metabolism in northern regions was more active than that in southern regions. The northern regions showed a pronounced tendency for denitrification, while the southern regions were characterized by acetoclastic methanogenesis. The assembly of microbial communities exhibited regional patterns, the deterministic assembly was more prominent in the northern soils, while the stochastic assembly was evident in the southern soils. Overall, these findings provide a new conceptual framework to understand the biosphere in petroleum-contaminated soil, potentially guiding improved management practices in the environmental remediation.}, } @article {pmid39197454, year = {2024}, author = {Thänert, R and Schwartz, DJ and Keen, EC and Hall-Moore, C and Wang, B and Shaikh, N and Ning, J and Rouggly-Nickless, LC and Thänert, A and Ferreiro, A and Fishbein, SRS and Sullivan, JE and Radmacher, P and Escobedo, M and Warner, BB and Tarr, PI and Dantas, G}, title = {Clinical sequelae of gut microbiome development and disruption in hospitalized preterm infants.}, journal = {Cell host & microbe}, volume = {32}, number = {10}, pages = {1822-1837.e5}, pmid = {39197454}, issn = {1934-6069}, support = {K99 AI175674/AI/NIAID NIH HHS/United States ; P30 ES030283/ES/NIEHS NIH HHS/United States ; R01 AI184858/AI/NIAID NIH HHS/United States ; T32 DK077653/DK/NIDDK NIH HHS/United States ; R01 AI155893/AI/NIAID NIH HHS/United States ; UH3 AI083265/AI/NIAID NIH HHS/United States ; 2021081/DDCF/Doris Duke Charitable Foundation/United States ; R01 HD092414/HD/NICHD NIH HHS/United States ; P30 DK052574/DK/NIDDK NIH HHS/United States ; K08 AI159384/AI/NIAID NIH HHS/United States ; T32 HD007409/HD/NICHD NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Infant, Premature ; Infant, Newborn ; *Feces/microbiology ; *Enterocolitis, Necrotizing/microbiology ; Female ; *Metagenomics ; *Anti-Bacterial Agents/pharmacology ; Male ; Clostridioides difficile/genetics ; Intensive Care Units, Neonatal ; Infant ; Hospitalization ; Enterobacteriaceae/genetics ; Enterococcus/genetics ; Staphylococcus epidermidis ; Bacteria/classification/genetics/isolation & purification ; }, abstract = {Aberrant preterm infant gut microbiota assembly predisposes to early-life disorders and persistent health problems. Here, we characterize gut microbiome dynamics over the first 3 months of life in 236 preterm infants hospitalized in three neonatal intensive care units using shotgun metagenomics of 2,512 stools and metatranscriptomics of 1,381 stools. Strain tracking, taxonomic and functional profiling, and comprehensive clinical metadata identify Enterobacteriaceae, enterococci, and staphylococci as primarily exploiting available niches to populate the gut microbiome. Clostridioides difficile lineages persist between individuals in single centers, and Staphylococcus epidermidis lineages persist within and, unexpectedly, between centers. Collectively, antibiotic and non-antibiotic medications influence gut microbiome composition to greater extents than maternal or baseline variables. Finally, we identify a persistent low-diversity gut microbiome in neonates who develop necrotizing enterocolitis after day of life 40. Overall, we comprehensively describe gut microbiome dynamics in response to medical interventions in preterm, hospitalized neonates.}, } @article {pmid39197279, year = {2024}, author = {Guo, Y and Cheng, S and Fang, H and Geng, J and Li, Y and Shi, F and Wang, H and Chen, L and Zhou, Y}, title = {Copper and cadmium co-contamination increases the risk of nitrogen loss in red paddy soils.}, journal = {Journal of hazardous materials}, volume = {479}, number = {}, pages = {135626}, doi = {10.1016/j.jhazmat.2024.135626}, pmid = {39197279}, issn = {1873-3336}, mesh = {*Cadmium/toxicity/metabolism ; *Soil Pollutants/metabolism ; *Copper/toxicity ; *Soil Microbiology ; *Nitrogen/metabolism ; China ; Bacteria/metabolism/genetics/classification ; Soil/chemistry ; Oryza/metabolism/growth & development ; Nitrogen Cycle ; Denitrification ; Microbiota/drug effects ; }, abstract = {The microbiome plays a crucial role in soil nitrogen (N) cycling and in regulating its bioavailability. However, the functional and genomic information of microorganisms encoding N cycling in response to copper (Cu) and cadmium (Cd) contamination is largely unknown. Here, metagenomics and genome binning were used to examine microbial N cycling in Cu and Cd co-contaminated red paddy soils collected from a polluted watershed in southern China. The results showed that soil Cu and Cd concentrations induced more drastic changes in microbial N functional and taxonomic traits than soil general properties. Soil Cu and Cd co-contamination stimulated microbial nitrification, denitrification, and dissimilatory nitrate reduction processes mainly by increasing the abundance of Nitrospira (phylum Nitrospirota), while inhibiting N fixation by decreasing the abundance of Desulfobacca. These contrasting changes in microbial N cycling processes suggested a potential risk of N loss in paddy soils. A high-quality genome was identified as belonging to Nitrospirota with the highest abundance in heavily contaminated soils. This novel Nitrospirota strain possessed metabolic capacities for N transformation and metal resistance. These findings elucidate the genetic mechanisms underlying soil N bioavailability under long-term Cu and Cd contamination, which is essential for maintaining agricultural productivity and controlling heavy metal pollution.}, } @article {pmid39197244, year = {2025}, author = {Zhang, C and Gu, C and Wang, M and Chen, J and Chang, H and Chang, Z and Zhou, J and Yue, M and Zhang, W and Zhang, Q and Feng, Z}, title = {Effect of temperature regulation on microbial community, volatile flavours, amino acid profiles, and iridoid glycosides during noni (Morinda citrifolia L.) fruit fermentation.}, journal = {Food chemistry}, volume = {462}, number = {}, pages = {140966}, doi = {10.1016/j.foodchem.2024.140966}, pmid = {39197244}, issn = {1873-7072}, mesh = {*Fermentation ; *Fruit/chemistry/metabolism/microbiology ; *Amino Acids/metabolism/analysis ; *Bacteria/metabolism/classification/genetics/isolation & purification ; *Microbiota ; *Morinda/chemistry/metabolism ; *Iridoid Glycosides/metabolism/analysis/chemistry ; *Temperature ; Volatile Organic Compounds/metabolism/chemistry ; Flavoring Agents/metabolism/chemistry ; }, abstract = {Noni fruit has an unpleasant flavour but is highly bioactive. Therefore, it is necessary to clarify the effect of temperature regulation on quality of fermented noni fruit. In the present study, the formation of flavours, amino acid profiles, and iridoid glycosides during noni fruit fermentation at different temperatures were investigated. We initially found that different temperatures affected core microbial communities. The general evolutionary trends of Acetobacter and Gluconobacter were influenced by different temperatures. Furthermore, high temperature helped maintain low octanoic and hexanoic acids. Subsequently, we found that high temperature improved total amino acids and iridoid glycosides. The correlation network analysis revealed that bacterial communities impacted the quality (volatile flavours, amino acid profiles, and iridoid glycosides) of fermented noni fruit. Overall, altering the temperature induced variations in microbial communities and quality during the noni fruit fermentation process. These results are instrumental in the pursuit of quality control in natural fermentation processes.}, } @article {pmid39197040, year = {2024}, author = {Chen, S and Zhang, Z and Liu, S and Chen, T and Lu, Z and Zhao, W and Mou, X and Liu, S}, title = {Consistent signatures in the human gut microbiome of longevous populations.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2393756}, pmid = {39197040}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Longevity ; Aged, 80 and over ; *Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Female ; Adult ; Male ; Aged ; Young Adult ; Metagenomics ; Middle Aged ; Desulfovibrio/genetics/metabolism ; }, abstract = {Gut microbiota of centenarians has garnered significant attention in recent years, with most studies concentrating on the analysis of microbial composition. However, there is still limited knowledge regarding the consistent signatures of specific species and their biological functions, as well as the potential causal relationship between gut microbiota and longevity. To address this, we performed the fecal metagenomic analysis of eight longevous populations at the species and functional level, and employed the Mendelian randomization (MR) analysis to infer the causal associations between microbial taxa and longevity-related traits. We observed that several species including Eisenbergiella tayi, Methanobrevibacter smithii, Hungatella hathewayi, and Desulfovibrio fairfieldensis were consistently enriched in the gut microbiota of long-lived individuals compared to younger elderly and young adults across multiple cohorts. Analysis of microbial pathways and enzymes indicated that E. tayi plays a role in the protein N-glycosylation, while M. smithii is involved in the 3-dehydroquinate and chorismate biosynthesis. Furthermore, H. hathewayi makes a distinct contribution to the purine nucleobase degradation I pathway, potentially assisting the elderly in maintaining purine homeostasis. D. fairfieldensis contributes to the menaquinone (vitamin K2) biosynthesis, which may help prevent age-related diseases such as osteoporosis-induced fractures. According to MR results, Hungatella was significantly positively correlated with parental longevity, and Desulfovibrio also exhibited positive associations with lifespan and multiple traits related to parental longevity. Additionally, Alistipes and Akkermansia muciniphila were consistently enriched in the gut microbiota of the three largest cohorts of long-lived individuals, and MR analysis also suggests their potential causal relationships with longevity. Our findings reveal longevity-associated gut microbial signatures, which are informative for understanding the role of microbiota in regulating longevity and aging.}, } @article {pmid39196943, year = {2024}, author = {Rodríguez-Varela, R and Yaka, R and Pochon, Z and Sanchez-Pinto, I and Solaun, JL and Naidoo, T and Guinet, B and Pérez-Ramallo, P and Lagerholm, VK and de Anca Prado, V and Valdiosera, C and Krzewińska, M and Herrasti, L and Azkarate, A and Götherström, A}, title = {Five centuries of consanguinity, isolation, health, and conflict in Las Gobas: A Northern Medieval Iberian necropolis.}, journal = {Science advances}, volume = {10}, number = {35}, pages = {eadp8625}, pmid = {39196943}, issn = {2375-2548}, mesh = {Humans ; Spain ; History, Medieval ; *Consanguinity ; Phylogeny ; Archaeology ; Female ; Male ; Animals ; }, abstract = {Between the 8th and 11th centuries CE, the Iberian Peninsula underwent profound upheaval due to the Umayyad invasion against the Visigoths, resulting in population shifts and lasting demographic impacts. Our understanding of this period is hindered by limited written sources and few archaeogenetic studies. We analyzed 33 individuals from Las Gobas, a necropolis in northern Spain, spanning the 7th to 11th centuries. By combining archaeological and osteological data with kinship, metagenomics, and ancestry analyses, we investigate conflicts, health, and demography of these individuals. We reveal intricate family relationships and genetic continuity within a consanguineous population while also identifying several zoonoses indicative of close interactions with animals. Notably, one individual was infected with a variola virus phylogenetically clustering with the northern European variola complex between ~885 and 1000 CE. Last, we did not detect a significant increase of North African or Middle East ancestries over time since the Islamic conquest of Iberia, possibly because this community remained relatively isolated.}, } @article {pmid39196507, year = {2024}, author = {Qian, Y and Sorgen, AA and Steffen, KJ and Heinberg, LJ and Reed, K and Carroll, IM}, title = {Intestinal Energy Harvest Mediates Gut Microbiota-Associated Weight Loss Following Bariatric Surgery.}, journal = {Obesity surgery}, volume = {34}, number = {10}, pages = {3771-3780}, pmid = {39196507}, issn = {1708-0428}, support = {1R01DK112585-01//National Institute of Health/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Weight Loss/physiology ; Female ; Male ; *Bariatric Surgery ; *Obesity, Morbid/surgery/microbiology ; Adult ; Middle Aged ; Energy Metabolism ; Feces/microbiology ; }, abstract = {PURPOSE: Metabolic and bariatric surgery (MBS) is the most effective treatment for class III obesity. The capacity to efficiently extract intestinal energy is potentially a determinant of varying weight loss outcomes post-MBS. Prior research indicated that intestinal energy harvest is correlated with post-MBS weight loss. Studies have also demonstrated that the gut microbiota is associated with weight loss post-MBS. We aim to investigate whether gut microbiota-associated weight loss is mediated by intestinal energy harvest in patients post-MBS.

MATERIALS AND METHODS: We examined the relationship between specific gut microbiota, intestinal energy harvest, diet, and weight loss using fecal metagenomic sequence data, bomb calorimetry (fecal energy content as a proxy for calorie absorption), and a validated dietary questionnaire on 67 individuals before and after MBS. Mediation analysis and a machine learning algorithm were conducted.

RESULTS: Intestinal energy harvest was a mediator in the relationship between the intestinal microbiota (Bacteroides caccae) and weight loss outcomes in patients post-MBS at 18 months (M). The association between the abundance of B. caccae and post-MBS weight loss rate at 18 M was partly mediated by 1 M intestinal energy harvest (β = 0.001 ± 0.001, P = 0.020). This mediation represents 2.83% of the total effect (β = 0.050 ± 0.047; P = 0.028). Intestinal microbiota and energy harvest improved random forest model's accuracy in predicting weight loss results.

CONCLUSION: Energy harvest partly mediates the relationship between the intestinal microbiota and weight loss outcomes among patients post-MBS. This study elucidates a potential mechanism regarding how intestinal energy absorption facilitates the effect of intestinal microbiota on energy metabolism and weight loss outcomes.}, } @article {pmid39195462, year = {2024}, author = {Pan, D and Xiao, P and Li, F and Liu, J and Zhang, T and Zhou, X and Zhang, Y}, title = {High Degree of Polymerization of Chitin Oligosaccharides Produced from Shrimp Shell Waste by Enrichment Microbiota Using Two-Stage Temperature-Controlled Technique of Inducing Enzyme Production and Metagenomic Analysis of Microbiota Succession.}, journal = {Marine drugs}, volume = {22}, number = {8}, pages = {}, pmid = {39195462}, issn = {1660-3397}, support = {32100065//National Natural Science Foundation of China/ ; 32300031//National Natural Science Foundation of China/ ; 2023KJ207//Shandong Province Youth Entrepreneurship Technology Support Program for Higher Education Institutions/ ; ZR2023MB095//Natural Science Foundation of Shandong Province of China/ ; }, mesh = {*Chitin/chemistry ; Animals ; *Oligosaccharides/chemistry ; *Microbiota ; *Chitinases/metabolism ; *Animal Shells/chemistry ; Metagenomics/methods ; Temperature ; Polymerization ; Bacteria ; }, abstract = {The direct enzymatic conversion of untreated waste shrimp and crab shells has been a key problem that plagues the large-scale utilization of chitin biological resources. The microorganisms in soil samples were enriched in two stages with powdered chitin (CP) and shrimp shell powder (SSP) as substrates. The enrichment microbiota XHQ10 with SSP degradation ability was obtained. The activities of chitinase and lytic polysaccharide monooxygenase of XHQ10 were 1.46 and 54.62 U/mL. Metagenomic analysis showed that Chitinolyticbacter meiyuanensis, Chitiniphilus shinanonensis, and Chitinimonas koreensis, with excellent chitin degradation performance, were highly enriched in XHQ10. Chitin oligosaccharides (CHOSs) are produced by XHQ10 through enzyme induction and two-stage temperature control technology, which contains CHOSs with a degree of polymerization (DP) more significant than ten and has excellent antioxidant activity. This work is the first study on the direct enzymatic preparation of CHOSs from SSP using enrichment microbiota, which provides a new path for the large-scale utilization of chitin bioresources.}, } @article {pmid39194557, year = {2024}, author = {Wang, L and Lu, X and Xing, Z and Teng, X and Wang, S and Liu, T and Zheng, L and Wang, X and Qu, J}, title = {Macrogenomics Reveals Effects on Marine Microbial Communities during Oplegnathus punctatus Enclosure Farming.}, journal = {Biology}, volume = {13}, number = {8}, pages = {}, pmid = {39194557}, issn = {2079-7737}, support = {MEEST-2021-05//The Key Funded with the MNR Key Laboratory of Eco-Environmental Science and Technology, China/ ; 2021CXGC011306//Research and Development Program of Shandong Province, China (Major Science and Technology Innovation Project)/ ; ZR2020MD002//the Natural Science Foundation Shandong Province/ ; 20230304002YY//Science and Technology Major Projects of Jilin Province/ ; Grant SM15B01, SM19B70, and SM19B28//The Doctoral Science Research Foundation of Yantai University/ ; 2320004-SM20RC02//"double-hundred action" of Yantai/ ; }, abstract = {(1) Background: Laizhou Bay is an important aquaculture area in the north of China. Oplegnathus punctatus is one of the species with high economic benefits. In recent years, the water environment of Laizhou Bay has reached a mild eutrophication level, while microorganisms are an important group between the environment and species. In this study, we evaluated alterations in environmental elements, microbial populations, and antibiotic resistance genes (ARGs) along with their interconnections during Oplegnathus punctatus net culture. (2) Methods: A total of 142 samples from various water layers were gathered for metagenome assembly analysis. Mariculture increases the abundance of microorganisms in this culture area and makes the microbial community structure more complex. The change had more significant effects on sediment than on seawater. (3) Results: Certain populations of cyanobacteria and Candidatus Micrarchaecta in seawater, and Actinobacteria and Thaumarchaeota in sediments showed high abundance in the mariculture area. Antibiotic resistance genes in sediments were more sensitive to various environmental factors, especially oxygen solubility and salinity. (4) Conclusions: These findings highlight the complex and dynamic nature of microorganism-environment-ARG interactions, characterized by regional specificity and providing insights for a more rational use of marine resources.}, } @article {pmid39194508, year = {2024}, author = {Zhong, Z and An, R and Ma, S and Zhang, N and Zhang, X and Chen, L and Wu, X and Lin, H and Xiang, T and Tan, H and Chen, M}, title = {Association between the Maternal Gut Microbiome and Macrosomia.}, journal = {Biology}, volume = {13}, number = {8}, pages = {}, pmid = {39194508}, issn = {2079-7737}, support = {81773535//National Natural Science Foundation of China/ ; 81973137//National Natural Science Foundation of China/ ; 82173608//National Natural Science Foundation of China/ ; 82360665//National Natural Science Foundation of China/ ; 2018SK2061//Key Research and Development Program of Hunan Province/ ; 2022JJ40343//the Natural Science Foundation of Hunan Province/ ; 21B0513//the Scientific Research Project of Education Department of Hunan Province/ ; 202212053368//the Scientific Research Project of Hunan Provincial Health Commission/ ; }, abstract = {Fetal macrosomia is defined as a birthweight ≥4000 g and causes harm to pregnant women and fetuses. Studies reported that the maternal intestinal microbiome plays a key role in the establishment, growth, and development of the fetal intestinal microbiome. However, whether there is a relationship between maternal gut microbiota and macrosomia remains unclear. Our study aimed to identify gut microbiota that may be related to the occurrence of macrosomia, explore the possible mechanisms by which it causes macrosomia, and establish a prediction model to determine the feasibility of predicting macrosomia by early maternal gut microbiota. We conducted a nested case-control study based on an early pregnancy cohort (ChiCTR1900020652) in the Maternity and Child Health Hospital of Hunan Province on fecal samples of 93 women (31 delivered macrosomia as the case group and 62 delivered normal birth weight newborns as the control group) collected and included in this study. We performed metagenomic analysis to compare the composition and function of the gut microbiome between cases and controls. Correlation analysis was used to explore the association of differential species and differential functional pathways. A random forest model was used to construct an early pregnancy prediction model for macrosomia. At the species level, there were more Bacteroides salyersiae, Bacteroides plebeius, Ruminococcus lactaris, and Bacteroides ovatus in the intestinal microbiome of macrosomias' mothers compared with mothers bearing fetuses that had normal birth weight. Functional pathways of the gut microbiome including gondoate biosynthesis, L-histidine degradation III, cis-vaccenate biosynthesis, L-arginine biosynthesis III, tRNA processing, and mannitol cycle, which were more abundant in the macrosomia group. Significant correlations were found between species and functional pathways. Bacteroides plebeius was significantly associated with the pathway of cis-vaccenate biosynthesis (r = 0.28, p = 0.005) and gondoate biosynthesis (r = 0.28, p < 0.001) and Bacteroides ovatus was positively associated with the pathway of cis-vaccenate biosynthesis (r = 0.29, p = 0.005) and gondoate biosynthesis (r = 0.32, p = 0.002). Bacteroides salyersiae was significantly associated with the pathway of cis-vaccenate biosynthesis (r = 0.24, p = 0.018), gondoate biosynthesis (r = 0.31, p = 0.003), and L-histidine degradation III (r = 0.22, p = 0.291). Finally, four differential species and four clinical indicators were included in the random forest model for predicting macrosomia. The areas under the working characteristic curves of the training and validation sets were 0.935 (95% CI: 0.851~0.979) and 0.909 (95% CI: 0.679~0.992), respectively. Maternal gut microbiota in early pregnancy may play an important role in the development of macrosomia and can be used as potential predictors to prevent macrosomia.}, } @article {pmid39194269, year = {2024}, author = {Christians, FC and Akhund-Zade, J and Jarman, K and Venkatasubrahmanyam, S and Noll, N and Blauwkamp, TA and Bercovici, S and Zielinska, A and Carr, AL and Craney, A and Pike, M and Farrell, JJ and Dadwal, S and Wood, JB and Matkovich, E and McAdams, S and Nolte, FS}, title = {Analytical and clinical validation of direct detection of antimicrobial resistance markers by plasma microbial cell-free DNA sequencing.}, journal = {Journal of clinical microbiology}, volume = {62}, number = {10}, pages = {e0042524}, pmid = {39194269}, issn = {1098-660X}, support = {AMORTISE//Karius/ ; }, mesh = {Humans ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/drug effects/classification/isolation & purification ; Reproducibility of Results ; Cell-Free Nucleic Acids/blood ; Bacterial Infections/diagnosis/microbiology/blood ; Microbial Sensitivity Tests ; Sequence Analysis, DNA ; Genetic Markers ; DNA, Bacterial/genetics/blood ; Molecular Diagnostic Techniques/methods/standards ; Anti-Bacterial Agents/pharmacology ; Female ; Male ; }, abstract = {UNLABELLED: Sequencing of plasma microbial cell-free DNA (mcfDNA) has gained increased acceptance as a valuable adjunct to standard-of-care testing for diagnosis of infections throughout the body. Here, we report the analytical and clinical validation of a novel application of mcfDNA sequencing, the non-invasive detection of seven common antimicrobial resistance (AMR) genetic markers in 18 important pathogens. The AMR markers include SCCmec, mecA, mecC, vanA, vanB, blaCTX-M, and blaKPC. The AMR markers were computationally linked to the pathogens detected. Analytical validation showed high reproducibility (100%), inclusivity (54 to 100%), and exclusivity (100%). Clinical accuracy was assessed with 114 unique plasma samples from patients at seven study sites with concordant culture results for target bacteria from a variety of specimen types and correlated with available phenotypic antimicrobial susceptibility test results and genotypic results. The positive percent agreement (PPA), negative percent agreement (NPA), and diagnostic yield (DY) were estimated for each AMR marker. DY was defined as the percentage of tests that yielded an actionable result of either detected or not detected. The results for the combination of SCCmec and mecA for staphylococci were PPA 19/20 (95.0%), NPA 21/22 (95.4%), DY 42/60 (70.0%); vanA for enterococci were PPA 3/3 (100%), NPA 2/2 (100%), DY 5/6 (83.3%); blaCTX-M for gram-negative bacilli were PPA 5/6 (83.3%), NPA 29/29 (100%), DY 35/49 (71.4%); and blaKPC for gram-negative bacilli were PPA 0/2 (0%), NPA: 23/23 (100%), DY 25/44 (56.8%). The addition of AMR capability to plasma mcfDNA sequencing should provide clinicians with an effective new culture-independent tool for optimization of therapy.

IMPORTANCE: This manuscript is ideally suited for the Innovative Diagnostic Methods sections as it reports the analytical and clinical validation of a novel application of plasma microbial cell-free DNA sequencing for direct detection of seven selected antimicrobial resistance markers in 18 target pathogens. Clearly, it has potential clinical utility in optimizing therapy and was incorporated into the Karius test workflow in September 2023. In addition, the workflow could readily be adapted to expand the number of target bacteria and antimicrobial resistance markers as needed.}, } @article {pmid39194141, year = {2024}, author = {Cruvinel, VRN and Carvalho, E and Alves, DCC and Marques, CP and Bezerra, RDS and Giovanetti, M and Sampaio, SC and Elias, MC and Araújo, WN and Haddad, R and Slavov, SN}, title = {Unveiling microbial worlds: exploring viral metagenomics among waste pickers at Latin America's largest dumpsite.}, journal = {Revista do Instituto de Medicina Tropical de Sao Paulo}, volume = {66}, number = {}, pages = {e49}, pmid = {39194141}, issn = {1678-9946}, mesh = {Humans ; *Metagenomics ; Brazil ; Male ; Adult ; Female ; Viruses/genetics/classification/isolation & purification ; Occupational Exposure ; Case-Control Studies ; Middle Aged ; Refuse Disposal ; }, abstract = {Waste pickers constitute a marginalized demographic engaged in the collection of refuse, facing considerable occupational hazards that heighten their susceptibility to contract infectious diseases. Moreover, waste pickers contend with societal stigmatization and encounter barriers to accessing healthcare services. To explore the viral profile of waste pickers potentially linked to their occupational environment, we conducted a metagenomic analysis on 120 plasma specimens sampled from individuals employed at the Cidade Estrutural dumpsite in Brasilia city, Brazil. In total, 60 blood donors served as a comparative control group. Specimens were pooled and subjected to Illumina NextSeq 2000 sequencing. Viral abundance among waste pickers revealed the presence of significant pathogens, including HIV, HCV, and Chikungunya, which were not detected in the control group. Additionally, elevated levels of anelloviruses and Human pegivirus-1 were noted, with a comparable incidence in the control group. These findings underscore the utility of metagenomics in identifying clinically relevant viral agents within underserved populations. The implications of this study extend to informing public health policies aimed at surveilling infectious diseases among individuals facing socioeconomic disparities and limited access to healthcare resources.}, } @article {pmid39193958, year = {2024}, author = {Zhong, Y and Xing, Y}, title = {Diagnosis of Mycobacterium marinum Infection by Metagenomic next-generation sequencing.}, journal = {Clinical laboratory}, volume = {70}, number = {8}, pages = {}, doi = {10.7754/Clin.Lab.2024.240327}, pmid = {39193958}, issn = {1433-6510}, mesh = {Humans ; Female ; *Mycobacterium marinum/isolation & purification/genetics ; *Mycobacterium Infections, Nontuberculous/diagnosis/drug therapy/microbiology ; *High-Throughput Nucleotide Sequencing ; Metagenomics/methods ; Anti-Bacterial Agents/therapeutic use/administration & dosage ; Fingers/microbiology ; Middle Aged ; }, abstract = {BACKGROUND: In December 2023, our hospital confirmed a case of finger infection with Mycobacterium marinum. The patient sought medical attention at our hospital due to a hard scratch on her left middle finger, which was red, swollen, and ulcerated for one month.

PHYSICAL EXAMINATION: A lesion of approximately 1.5 cm x 2 cm in the patient's left middle finger, surrounded by redness and swelling, unclear boundaries, surface rupture, partial scabbing, and no tenderness during compression. She was treated at the previous clinic, common infectious diseases were considered, and was given intravenous infusion treatment: cefotaxime and clarithromycin, and erythromycin ointment was applied externally. She came to our hospital after poor treatment results. The patient has had hypertension for 3 years, no other systemic diseases, no similar medical history among family members, no history of drug or food allergies.

METHODS: Clean the wound and remove the scab from the affected area, and use a surgical blade to scrape off necrotic tissue. Send the scraped tissue for pathogen testing: tissue bacterial culture+identification (matrix assisted laser desorption/ionization time-of-flight mass spectrometry, MALDI-TOF), tissue acid fast staining, and tissue metagenomic next-generation sequencing (mNGS). Other auxiliary examinations: blood routine, urine routine, blood fat, liver function, and kidney function.

RESULTS: Tissue bacterial culture+identification: growth of Mycobacterium marinum; Acid fast staining of tissue: positive; Tissue mNGS: Mycobacterium marinum. Clinical treatment plan: clarithromycin 0.5 g bid po+rifampicin 0.45 g qd po+5-aminolevulinic acid photodynamic therapy (ALA-PDT) qw+boric acid wash wet compress tid. After 14 days of treatment, the area of redness and swelling significantly decreased, and the degree of redness and swelling was significantly reduced compared to admission. The degree of ulcer edge protrusion was also reduced compared to admission. There was a small amount of exudation from the wound, and no necrotic tissue was observed. The patient improved and was discharged.

CONCLUSIONS: This article reports a case of finger infection with Mycobacterium marinum. Mycobacterium marinum was quickly and accurately identified by mNGS, and reasonable treatment measures were adopted clinically. The patient improved and was discharged. This study has important reference significance for the clinical diagnosis and treatment of Mycobacterium infection. In addition, mNGS as a novel detection method has considerable prospects for rapid diagnosis of pathogens.}, } @article {pmid39193957, year = {2024}, author = {Yuan, XH and Chen, QC and Wang, Y and Hao, JH and Guo, AJ and Zhang, JB and Fu, AS and Ge, YL}, title = {Allergic Bronchopulmonary Mycosis with Eosinophilia Caused by Schizophyllum Infection.}, journal = {Clinical laboratory}, volume = {70}, number = {8}, pages = {}, doi = {10.7754/Clin.Lab.2024.240235}, pmid = {39193957}, issn = {1433-6510}, mesh = {Humans ; *Schizophyllum/isolation & purification/genetics ; *Antifungal Agents/therapeutic use ; Eosinophilia/diagnosis/microbiology ; Male ; Bronchoscopy ; High-Throughput Nucleotide Sequencing ; Tomography, X-Ray Computed ; Lung Diseases, Fungal/diagnosis/microbiology/drug therapy ; Middle Aged ; Mycoses/diagnosis/microbiology/drug therapy/complications ; }, abstract = {BACKGROUND: As an opportunistic pathogenic fungus, Schizophyllum has been rarely reported to infect humans. By reporting a case of definite diagnosis of Schizophyllum infection, we aim to improve clinicians' understanding of this bacterium.

METHODS: By reporting a case with cough and sputum as the main manifestations, after empirical antiinfective chest CT suggesting a more progressive inflammatory lesion and a mass-like lesion in the paratracheal area of the main airways, a diagnosis of Schizophyllum infection was finally made by bronchoscopy with the delivery of metagenomic next-generation sequencing (mNGS).

RESULTS: The patient was finally diagnosed with rare Schizophyllum infection. After antifungal treatment, the symptoms improved, and the patient was discharged.

CONCLUSIONS: Although Schizophyllum is a rare fungal infection, it should be taken seriously in patients with diabetes or who are immunocompromised. At the same time, mNGS plays a key role in the detection of rare and emerging pathogens, which is worthy of clinical interest.}, } @article {pmid39193769, year = {2024}, author = {Smith, TA and Srikanth, K and Huson, HJ}, title = {Comparative Population Genomics of Arctic Sled Dogs Reveals a Deep and Complex History.}, journal = {Genome biology and evolution}, volume = {16}, number = {9}, pages = {}, pmid = {39193769}, issn = {1759-6653}, support = {2021-22//University of Maryland, Baltimore County/ ; //Neogen Genomics/ ; //Siberian Husky Club of America/ ; }, mesh = {*Dogs/classification/genetics ; *Metagenomics ; Arctic Regions ; Phylogeny ; }, abstract = {Recent evidence demonstrates genomic and morphological continuity in the Arctic ancestral lineage of dogs. Here, we use the Siberian Husky to investigate the genomic legacy of the northeast Eurasian Arctic lineage and model the deep population history using genome-wide single nucleotide polymorphisms. Utilizing ancient dog-calibrated molecular clocks, we found that at least two distinct lineages of Arctic dogs existed in ancient Eurasia at the end of the Pleistocene. This pushes back the origin of sled dogs in the northeast Siberian Arctic with humans likely intentionally selecting dogs to perform different functions and keeping breeding populations that overlap in time and space relatively reproductively isolated. In modern Siberian Huskies, we found significant population structure based on how they are used by humans, recent European breed introgression in about half of the dogs that participate in races, moderate levels of inbreeding, and fewer potentially harmful variants in populations under strong selection for form and function (show, sled show, and racing populations of Siberian Huskies). As the struggle to preserve unique evolutionary lineages while maintaining genetic health intensifies across pedigreed dogs, understanding the genomic history to guide policies and best practices for breed management is crucial to sustain these ancient lineages and their unique evolutionary identity.}, } @article {pmid39192744, year = {2024}, author = {Metcalfe-Roach, A and Cirstea, MS and Yu, AC and Ramay, HR and Coker, O and Boroomand, S and Kharazyan, F and Martino, D and Sycuro, LK and Appel-Cresswell, S and Finlay, BB}, title = {Metagenomic Analysis Reveals Large-Scale Disruptions of the Gut Microbiome in Parkinson's Disease.}, journal = {Movement disorders : official journal of the Movement Disorder Society}, volume = {39}, number = {10}, pages = {1740-1751}, doi = {10.1002/mds.29959}, pmid = {39192744}, issn = {1531-8257}, support = {GR008160//Pacific Parkinson's Research Institute/ ; FDN-159935/CAPMC/CIHR/Canada ; PPG-2020-0000000052//Parkinson Canada/ ; FDN-159935/CAPMC/CIHR/Canada ; }, mesh = {Humans ; *Parkinson Disease/microbiology ; *Gastrointestinal Microbiome/genetics/physiology ; Male ; Female ; Aged ; Middle Aged ; *Metagenomics/methods ; *Feces/microbiology ; Disease Progression ; }, abstract = {BACKGROUND: Parkinson's disease (PD) has been consistently linked to alterations within the gut microbiome.

OBJECTIVE: Our goal was to identify microbial features associated with PD incidence and progression.

METHODS: Metagenomic sequencing was used to characterize taxonomic and functional changes to the PD microbiome and to explore their relation to bacterial metabolites and disease progression. Motor and non-motor symptoms were tracked using Movement Disorder Society Unified Parkinson's Disease Rating Scale (MDS-UPDRS) and levodopa equivalent dose across ≤5 yearly study visits. Stool samples were collected at baseline for metagenomic sequencing (176 PD, 100 controls).

RESULTS: PD-derived stool samples had reduced intermicrobial connectivity and seven differentially abundant species compared to controls. A suite of bacterial functions differed between PD and controls, including depletion of carbohydrate degradation pathways and enrichment of ribosomal genes. Faecalibacterium prausnitzii-specific reads contributed significantly to more than half of all differentially abundant functional terms. A subset of disease-associated functional terms correlated with faster progression of MDS-UPDRS part IV and separated those with slow and fast progression with moderate accuracy within a random forest model (area under curve = 0.70). Most PD-associated microbial trends were stronger in those with symmetric motor symptoms.

CONCLUSION: We provide further evidence that the PD microbiome is characterized by reduced intermicrobial communication and a shift to proteolytic metabolism in lieu of short-chain fatty acid production, and suggest that these microbial alterations may be relevant to disease progression. We also describe how our results support the existence of gut-first versus brain-first PD subtypes. © 2024 The Author(s). Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.}, } @article {pmid39192682, year = {2024}, author = {Flynn, PJ and Moreau, CS}, title = {Viral diversity and co-evolutionary dynamics across the ant phylogeny.}, journal = {Molecular ecology}, volume = {33}, number = {19}, pages = {e17519}, doi = {10.1111/mec.17519}, pmid = {39192682}, issn = {1365-294X}, support = {2210800//Division of Biological Infrastructure/ ; 1900357//Division of Environmental Biology/ ; //National Science Foundation Graduate Research Fellowship Program/ ; }, mesh = {*Ants/virology/microbiology/genetics ; Animals ; *Phylogeny ; *Biodiversity ; Genome, Viral/genetics ; Metagenome/genetics ; DNA Viruses/genetics/classification ; Bacteria/genetics/virology/classification ; RNA Viruses/genetics/classification ; Ecosystem ; Bacteriophages/genetics/classification ; Virome/genetics ; }, abstract = {Knowledge of viral biodiversity within insects, particularly within ants, is extremely limited with only a few environmental viruses from invasive ant species identified to date. This study documents and explores the viral communities in ants. We comprehensively profile the metagenomes of a phylogenetically broad group of 35 ant species with varied ecological traits and report the discovery of 3710 novel and unique ant-associated viral genomes. These previously unknown viruses discovered within this study constitute over 95% of all currently described ant viruses, significantly increasing our knowledge of the ant virosphere. The identified RNA and DNA viruses fill gaps in insect-associated viral phylogenies and uncover evolutionary histories characterized by both frequent host switching and co-divergence. Many ants also host diverse bacterial communities, and we discovered that approximately one-third of these new ant-associated viruses are bacteriophages. Two ecological categories, bacterial abundance in the host and habitat degradation are both correlated with ant viral diversity and help to structure viral communities within ants. These data demonstrate that the ant virosphere is remarkably diverse phylogenetically and genomically and provide a substantial foundation for studies in virus ecology and evolution within eukaryotes. We highlight the importance of studying insect-associated viruses in natural ecosystems in order to more thoroughly and effectively understand host-microbe evolutionary dynamics.}, } @article {pmid39192352, year = {2024}, author = {Zeng, G and Zeng, L and Wang, Y and Cao, Z and Zeng, X and Xue, Z and Liu, S and Li, Y and He, L}, title = {Correlation between gut microbiota characteristics and non-small cell lung cancer based on macrogenomics sequencing.}, journal = {Hereditas}, volume = {161}, number = {1}, pages = {26}, pmid = {39192352}, issn = {1601-5223}, support = {No. 2023349//Chengdu Municipal Health Commission/ ; }, mesh = {*Carcinoma, Non-Small-Cell Lung/genetics ; Humans ; *Gastrointestinal Microbiome ; *Lung Neoplasms/genetics/microbiology ; Male ; Middle Aged ; Female ; Feces/microbiology ; Aged ; Metagenome ; Metagenomics/methods ; Bacteria/genetics/classification ; }, abstract = {OBJECTIVE: Non-small cell lung cancer (NSCLC) patients undergoing chemotherapy and immunotherapy experience disturbances in the gut microbiota. This study intends to find out the correlation between gut microbiota and clinical indices before and after radiotherapy for NSCLC.

METHODS: Ten patients with primary NSCLC were screened, and plasma and fecal samples were collected before and after radiotherapy, respectively. Inflammatory indices in plasma were detected. Genomic DNA was extracted from fecal specimens and sequenced on on Illumina HiSeq2000 sequencing platform. Thee sequenced data were subjected to Metagenome assembly, gene prediction, species annotation, and gene function analysis to study and analyze gut microbiota and metabolic functions. The correlation between the diversity of gut microbiota and the clinical indicators of NSCLC patients was evaluated, and the changes of gut microbiota before and after radiotherapy were observed.

RESULTS: The diversity of gut microbiota in NSCLC patients did not correlate with smoking, pathology, and inflammatory markers. The abundance of phylum (p)_Bacteroidetes increased; p_Firmicutes and p_Bacteroidetes accounted for the highest proportion in NSCLC patients, and the abundance of both was dominantly exchanged after radiotherapy. There was a decrease in genus (g)_Bifidobacterium after radiotherapy in NSCLC patients. There was no significant correlation between the diversity of gut microbiota after radiotherapy and radiotherapy sensitivity, and the structural composition and abundance of gut microbiota remained stable.

CONCLUSION: The diversity of gut microbiota is altered after radiotherapy in NSCLC patients, showing an increase in harmful bacteria and a decrease in beneficial bacteria.}, } @article {pmid39192225, year = {2024}, author = {He, X and Tia, AB and Yin, Q and Gao, L and Wang, L and Tian, T and Xiao, K and Zhang, Y and Tian, F and Ma, X and Harding, D and Dong, X}, title = {A retrospective study revealing complex viral diversity and a substantial burden of HPV infection in SARS-CoV-2 positive individuals, Sierra Leone.}, journal = {Virology journal}, volume = {21}, number = {1}, pages = {201}, pmid = {39192225}, issn = {1743-422X}, support = {2020YFE0205700//National Key Research and Development Program of China/ ; 2022-1G-1131//Capital's Funds for Health Improvement and Research/ ; }, mesh = {Humans ; Sierra Leone/epidemiology ; Retrospective Studies ; *COVID-19/virology/epidemiology ; *Papillomavirus Infections/virology/epidemiology ; *SARS-CoV-2/genetics/isolation & purification/classification ; *Coinfection/virology/epidemiology ; Female ; Adult ; Male ; Middle Aged ; Young Adult ; Nasopharynx/virology ; Adolescent ; Metagenomics ; Phylogeny ; Papillomaviridae/genetics/classification/isolation & purification ; Aged ; Child ; }, abstract = {BACKGROUND: The COVID-19 pandemic has underscored the critical role of sequencing technology in disease control and outbreak response. However, resource limitations and challenging environments often impede such efforts in low and middle-income countries. This study aimed to investigate the spectrum of viral co-infections, particularly with human viral pathogens, in SARS-CoV-2 positive individuals in Sierra Leone using metagenomic sequencing, evaluating the feasibility of utilizing this technology for epidemiological and evolutionary surveillance of pathogens related to public health in low-income environments.

METHODS: We retrospectively collected and analyzed 98 nasopharyngeal swab specimens from SARS-CoV-2 positive individuals in Sierra Leone. Samples were pre-processed locally and transferred to China via FTA cards for metagenomic sequencing, which was performed using the Novaseq platform. The study focused on the identification of nasopharyngeal viruses co-infecting with SARS-CoV-2, with a deeper analysis of significant human viral pathogens such as HPV.

RESULTS: The study identified 22 viral taxa from 20 families, including 4 human viruses. Notably, 19.4% of samples showed HPV co-infection with 34 distinct types, predominantly beta and gamma HPVs. Multiple HPV types were found in individual samples, indicating a high complexity of viral co-infections.

CONCLUSIONS: The identification of a wide range of co-infecting viruses, particularly multiple HPV genotypes, highlights the complexity of viral interactions and their potential implications for public health. These findings enhance our understanding of viral co-infections and provide valuable insights for public health interventions in Sierra Leone. Further research is needed to explore the clinical significance of these findings and their impact on disease outcomes.}, } @article {pmid39192220, year = {2024}, author = {Samak, ME and Solyman, SM and Hanora, A and Zakeer, S}, title = {Metagenomic mining of two Egyptian Red Sea sponges associated microbial community.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {315}, pmid = {39192220}, issn = {1471-2180}, support = {59/2020//Academy of Scientific Research and Technology/ ; 6420/2009//SIDA/ ; }, mesh = {*Porifera/microbiology ; Animals ; Indian Ocean ; *Metagenomics ; *Microbiota/genetics ; Egypt ; Bacteria/genetics/classification ; Phylogeny ; Biodiversity ; Multigene Family ; Biological Products/metabolism ; Metagenome ; Proteobacteria/genetics/classification/isolation & purification ; }, abstract = {The Red Sea is a promising habitat for the discovery of new bioactive marine natural products. Sponges associated microorganisms represent a wealthy source of compounds with unique chemical structures and diverse biological activities. Metagenomics is an important omics-based culture-independent technique that is used as an effective tool to get genomic and functional information on sponge symbionts. In this study, we used metagenomic analysis of two Egyptian Red Sea sponges Hyrtios erectus and Phorbas topsenti microbiomes to study the biodiversity and the biosynthetic potential of the Red Sea sponges to produce bioactive compounds. Our data revealed high biodiversity of the two sponges' microbiota with phylum Proteobacteria as the most dominant phylum in the associated microbial community with an average of 31% and 70% respectively. The analysis also revealed high biosynthetic potential of sponge Hyrtios erectus microbiome through detecting diverse types of biosynthetic gene clusters (BGCs) with predicted cytotoxic, antibacterial and inhibitory action. Most of these BGCs were predicted to be novel as they did not show any similarity with any MIBiG database known cluster. This study highlights the importance of the microbiome of the collected Red Sea sponge Hyrtios erectus as a valuable source of new bioactive natural products.}, } @article {pmid39191812, year = {2024}, author = {Feng, Y and Wei, R and Chen, Q and Shang, T and Zhou, N and Wang, Z and Chen, Y and Chen, G and Zhang, G and Dong, K and Zhong, Y and Zhao, H and Hu, F and Zheng, H}, title = {Host specificity and cophylogeny in the "animal-gut bacteria-phage" tripartite system.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {72}, pmid = {39191812}, issn = {2055-5008}, mesh = {Animals ; *Host Specificity ; *Bacteriophages/genetics/physiology ; *Gastrointestinal Microbiome ; Bees/virology/microbiology ; *Bacteria/virology/genetics/classification ; *Phylogeny ; Metagenomics/methods ; Metagenome ; }, abstract = {Cophylogeny has been identified between gut bacteria and their animal host and is highly relevant to host health, but little research has extended to gut bacteriophages. Here we use bee model to investigate host specificity and cophylogeny in the "animal-gut bacteria-phage" tripartite system. Through metagenomic sequencing upon different bee species, the gut phageome revealed a more variable composition than the gut bacteriome. Nevertheless, the bacteriome and the phageome showed a significant association of their dissimilarity matrices, indicating a reciprocal interaction between the two kinds of communities. Most of the gut phages were host generalist at the viral cluster level but host specialist at the viral OTU level. While the dominant gut bacteria Gilliamella and Snodgrassella exhibited matched phylogeny with bee hosts, most of their phages showed a diminished level of cophylogeny. The evolutionary rates of the bee, the gut bacteria and the gut phages showed a remarkably increasing trend, including synonymous and non-synonymous substitution and gene content variation. For all of the three codiversified tripartite members, however, their genes under positive selection and genes involving gain/loss during evolution simultaneously enriched the functions into metabolism of nutrients, therefore highlighting the tripartite coevolution that results in an enhanced ecological fitness for the whole holobiont.}, } @article {pmid39191760, year = {2024}, author = {Hartikainen, AK and Jalanka, J and Lahtinen, P and Ponsero, AJ and Mertsalmi, T and Finnegan, L and Crispie, F and Cotter, PD and Arkkila, P and Satokari, R}, title = {Fecal microbiota transplantation influences microbiota without connection to symptom relief in irritable bowel syndrome patients.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {73}, pmid = {39191760}, issn = {2055-5008}, support = {316338//Academy of Finland (Suomen Akatemia)/ ; 323156//Academy of Finland (Suomen Akatemia)/ ; }, mesh = {*Irritable Bowel Syndrome/therapy/microbiology ; Humans ; *Fecal Microbiota Transplantation/methods ; *RNA, Ribosomal, 16S/genetics ; Female ; Male ; Adult ; Treatment Outcome ; *Gastrointestinal Microbiome ; Middle Aged ; Feces/microbiology ; Metagenomics/methods ; Bacteria/classification/genetics/isolation & purification ; }, abstract = {Imbalanced microbiota may contribute to the pathophysiology of irritable bowel syndrome (IBS), thus fecal microbiota transplantation (FMT) has been suggested as a potential treatment. Previous studies on the relationship between clinical improvement and microbiota after FMT have been inconclusive. In this study, we used 16S rRNA gene amplicon and shotgun metagenomics data from a randomized, placebo controlled FMT trial on 49 IBS patients to analyze changes after FMT in microbiota composition and its functional potential, and to identify connections between microbiota and patients' clinical outcome. As a result, we found that the successful modulation of microbiota composition and functional profiles by FMT from a healthy donor was not associated with the resolution of symptoms in IBS patients. Notably, a donor derived strain of Prevotella copri dominated the microbiota in those patients in the FMT group who had a low relative abundance of P. copri pre-FMT. The results highlight the multifactorial nature of IBS and the role of recipient's microbiota in the colonization of donor's strains.}, } @article {pmid39191378, year = {2024}, author = {da Silva, VG and Smith, NW and Mullaney, JA and Wall, C and Roy, NC and McNabb, WC}, title = {Food-breastmilk combinations alter the colonic microbiome of weaning infants: an in silico study.}, journal = {mSystems}, volume = {9}, number = {9}, pages = {e0057724}, pmid = {39191378}, issn = {2379-5077}, support = {//High-Value Nutrition National Science Challenge/ ; }, mesh = {Humans ; *Milk, Human/chemistry/microbiology/metabolism ; *Gastrointestinal Microbiome/physiology ; Infant ; *Weaning ; *Colon/microbiology/metabolism ; *Computer Simulation ; Fatty Acids, Volatile/metabolism/analysis ; }, abstract = {The introduction of solid foods to infants, also known as weaning, is a critical point for the development of the complex microbial community inhabiting the human colon, impacting host physiology in infancy and later in life. This research investigated in silico the impact of food-breastmilk combinations on growth and metabolite production by colonic microbes of New Zealand weaning infants using the metagenome-scale metabolic model named Microbial Community. Eighty-nine foods were individually combined with breastmilk, and the 12 combinations with the strongest influence on the microbial production of short-chain fatty acids (SCFAs) and branched-chain fatty acids (BCFAs) were identified. Fiber-rich and polyphenol-rich foods, like pumpkin and blackcurrant, resulted in the greatest increase in predicted fluxes of total SCFAs and individual fluxes of propionate and acetate when combined, respectively, with breastmilk. Identified foods were further combined with other foods and breastmilk, resulting in 66 multiple food-breastmilk combinations. These combinations altered in silico the impact of individual foods on the microbial production of SCFAs and BCFAs, suggesting that the interaction between the dietary compounds composing a meal is the key factor influencing colonic microbes. Blackcurrant combined with other foods and breastmilk promoted the greatest increase in the production of acetate and total SCFAs, while pork combined with other foods and breastmilk decreased the production of total BCFAs.IMPORTANCELittle is known about the influence of complementary foods on the colonic microbiome of weaning infants. Traditional in vitro and in vivo microbiome methods are limited by their resource-consuming concerns. Modeling approaches represent a promising complementary tool to provide insights into the behavior of microbial communities. This study evaluated how foods combined with other foods and human milk affect the production of short-chain fatty acids and branched-chain fatty acids by colonic microbes of weaning infants using a rapid and inexpensive in silico approach. Foods and food combinations identified here are candidates for future experimental investigations, helping to fill a crucial knowledge gap in infant nutrition.}, } @article {pmid39191330, year = {2024}, author = {Wang, H and Ma, X and Ran, X and Wang, T and Zhou, M and Liu, C and Li, X and Wu, M and Wang, Y}, title = {Analyzing performance and microbial mechanisms in an incineration leachate treatment after waste separation: Integrated metagenomic and metaproteomic analyses.}, journal = {The Science of the total environment}, volume = {951}, number = {}, pages = {175821}, doi = {10.1016/j.scitotenv.2024.175821}, pmid = {39191330}, issn = {1879-1026}, mesh = {*Water Pollutants, Chemical/analysis ; *Biodegradation, Environmental ; *Metagenomics ; Incineration ; Waste Disposal, Fluid/methods ; Nitrification ; Nitrogen ; Proteomics ; }, abstract = {The absence of food waste after separation poses a significant challenge to incineration leachate treatment, as it decreases the C/N ratio and COD of leachate, greatly impacting the biological treatment process. A one-year in-situ study was systematically conducted in an incineration leachate treatment plant that experienced waste separation, focusing on the variations in carbon and nitrogen removal performance as well as the involved microbial mechanism of the "anaerobic digestion (AD) + two-stage A/O" process. Results indicated that the biodegradability of leachate significantly decreased over time, with COD concentration decreasing by 10 times and the average C/N ratio decreasing from 12.3 to 1.4. The AD process was maintained stable, achieving a COD removal efficiency exceeding 92 %. The nitrification process also remained stable; while the denitrification process was significantly affected, and a nine-fold increase in external glucose addition was required to achieve a nitrogen removal efficiency of 85 %. Metagenomic analysis indicated that comammox Nitrospira (contributing 90 % to ammonia monooxygenase) occupied the dominant position over Nitrosomonas for nitrification due to the low NH4[+]-N concentration in A/O tanks (<35 mg/L), and Methanothrix was substituted by Methanosarcina for methanogenesis in AD unit. Metaproteomic results further elucidated that the expression of enzymes responsible for denitrification process, i.e., Nir, Nor, Nos (convert NO2[-] to N2), was decreased significantly, although the expression of enzymes related to glycolysis and TCA cycle were stimulated by glucose addition. The expression of Nar (convert NO3[-]-N to NO2[-]-N) remained stable, while the imbalance expression within denitrifying enzymes might have facilitated occurrence of partial denitrification, attributed to the low C/N ratio. The results prove that the function robustness and metabolic versatility were achieved in leachate treatment plant after waste separation but at the cost of the high external carbon resource addition, highlighting the urgent requirement for low-carbon nitrogen removal technologies.}, } @article {pmid39191326, year = {2024}, author = {Chen, Y and Wang, F and Gao, J and He, X and Liu, Q and Liu, L}, title = {Enhancing bioremediation of petroleum-contaminated soil by sophorolipids-modified biochar: Combined metagenomic and metabolomic analyses.}, journal = {The Science of the total environment}, volume = {951}, number = {}, pages = {175772}, doi = {10.1016/j.scitotenv.2024.175772}, pmid = {39191326}, issn = {1879-1026}, mesh = {*Biodegradation, Environmental ; *Charcoal/chemistry ; *Petroleum/metabolism ; *Soil Pollutants/metabolism ; *Soil Microbiology ; *Metabolomics ; Metagenomics ; }, abstract = {In this study, sophorolipids (SLs)-modified biochar (BC-SLs) was used to enhance the bioremediation of petroleum hydrocarbons (PHs) contaminated soil. The biodegradation rate of petroleum hydrocarbons (PHs) by BC-SLs and BC treatments were 62.86 % and 52.64 % after 60 days of remediation experiments, respectively, higher than non-biochar treatment group (24.09 %). The metagenomic analysis showed that the abundance of petroleum-degrading bacteria Actinobacteria and Proteobacteria were increased by 3.8 % and 5.3 %, respectively in BC-SLs treatment, and the abundance of functional genes for PHs degradation, such as alkB, nidA and pcaG, were significantly increased by 12.85 %, 30.08 % and 21.01 %, respectively. The metabolomic analysis showed that BC-SLs facilitated the metabolic process of PHs, the microbial metabolism of petroleum hydrocarbons (PHs) became more active. Fatty acid degradation and polycyclic aromatic hydrocarbons (PAHs) degradation were up-regulated, indicating the promoting effect of the BC-SLs for PHs metabolism. The combined metagenomic and metabolomic analysis demonstrated the strong positive correlations between PHs metabolites and PHs-degrading bacteria, such as lauric acid vs. Actinobacteria, benzoic vs. Proteobacteria. The strong positive correlations between PHs metabolites and PHs-degrading genes were also observed, such as o-ehyltoluene vs. nahD, 4-isopropylbenzoic acid vs. etbAa. The modification of biochar with SLs increased the oxygen-containing functional groups on the surface of biochar. Meanwhile, the emulsification and solubilization of SLs promoted the bioavailability of PHs. The effects of BC-SLs on the nitrogen cycle during PHs remediation showed that it facilitated the accumulation of nitrogen-fixing genes, promoted nitrification but inhibited denitrification process. This study confirms that the application of BC-SLs is an effective remediation of PHs contamination and a sustainable method for controlling agricultural waste resources.}, } @article {pmid39190031, year = {2024}, author = {Li, X and Zheng, T and Xiao, Y and Zhao, Y and Wu, P}, title = {Field-Deployable Colorimetric Array for On-Site Diagnosis of Urinary Tract Infection and Identification of Causative Pathogens.}, journal = {Analytical chemistry}, volume = {96}, number = {36}, pages = {14679-14687}, doi = {10.1021/acs.analchem.4c03617}, pmid = {39190031}, issn = {1520-6882}, mesh = {*Urinary Tract Infections/diagnosis/microbiology ; *Colorimetry ; Humans ; *Polymerase Chain Reaction ; DNA, Bacterial/analysis ; }, abstract = {Urinary tract infection (UTI) is a common and prevalent disease caused by a spectrum of pathogens. Lack of access to rapid, portable, and high-quality diagnostics in resource-limited settings aggravates the improper treatment of UTIs, which is also a major driver of antibiotic misuse worldwide. Here, we describe a custom-made portable colorimetric array (PoCA) for reading out polymerase chain reaction (PCR) amplicons, the rationale of which is to transfer the previously developed dsDNA-based photosensitization colorimetric assay (solution) onto paper discs for detection. By integrating mini-LED irradiation and paper discs, the PoCA can read out 96 PCR tests in one pot, thus allowing diagnosis and identification of 12 prevailing UTI pathogens in less than 2 h, coupled with a portable thermal cycler for PCR. After analyzing 200 clinical urine samples, the pathogen profiling accuracy of the PoCA was demonstrated to be higher than the standard urine culture (confirmed with metagenomic next-generation sequencing). The PoCA platform could be used in primary care for rapid UTI diagnosis and pathogen identification.}, } @article {pmid39189780, year = {2024}, author = {Liu, L and He, X and Wang, J and Li, M and Wei, X and Yang, J and Cheng, G and Du, W and Liu, Z and Xiao, X}, title = {Exploring the associations between gut microbiota composition and SARS-CoV-2 inactivated vaccine response in mice with type 2 diabetes mellitus.}, journal = {mSphere}, volume = {9}, number = {9}, pages = {e0038024}, pmid = {39189780}, issn = {2379-5042}, support = {82002149//MOST | National Natural Science Foundation of China (NSFC)/ ; 2022CFB451//| Natural Science Foundation of Hubei Province ()/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; *Diabetes Mellitus, Type 2/immunology ; *Mice, Inbred C57BL ; *Vaccines, Inactivated/immunology ; *COVID-19/prevention & control/immunology ; *SARS-CoV-2/immunology ; *Feces/microbiology ; *COVID-19 Vaccines/immunology ; Immunoglobulin G/blood ; RNA, Ribosomal, 16S/genetics ; Lung/microbiology/immunology ; Female ; Male ; Probiotics/administration & dosage ; Antibodies, Viral/blood ; Vaccine Efficacy ; }, abstract = {UNLABELLED: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination is crucial for protecting vulnerable individuals, yet individuals with type 2 diabetes mellitus (T2DM) often exhibit impaired vaccine responses. Emerging evidence suggests that the composition of the host microbiota, crucial in immune regulation and development, influences vaccine efficacy. This study aimed to characterize the relationships between the SARS-CoV-2 inactivated vaccine and the host microbiota (specifically, gut and lung microbiota) of C57BL/6 mice with T2DM. Employing 16S rRNA metagenomic sequencing and ultra-high-performance liquid chromatography-mass spectrometry, we observed lower alpha diversity and distinct beta diversity in fecal microbiota before vaccination and in gut microbiota 28 days post-vaccination between T2DM mice and healthy mice. Compared with healthy mice, T2DM mice showed a higher Firmicutes/Bacteroidetes ratio 28 days post-vaccination. Significant alterations in gut microbiota composition were detected following vaccination, while lung microbiota remained unchanged. T2DM was associated with a diminished initial IgG antibody response against the spike protein, which subsequently normalized after 28 days. Notably, the initial IgG response positively correlated with fecal microbiota alpha diversity pre-vaccination. Furthermore, after 28 days, increased relative abundance of gut probiotics (Bifidobacterium and Lactobacillus) and higher levels of the gut bacterial tryptophan metabolite, indole acrylic acid, were positively associated with IgG levels. These findings suggest a potential link between vaccine efficacy and gut microbiota composition. Nonetheless, further research is warranted to elucidate the precise mechanisms underlying the impact of the gut microbiome on vaccine response. Overall, this study enhances our understanding of the intricate relationships among host microbiota, SARS-CoV-2 vaccination, and T2DM, with potential implications for improving vaccine efficacy.

IMPORTANCE: Over 7 million deaths attributed to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by 6 May 2024 underscore the urgent need for effective vaccination strategies. However, individuals with type 2 diabetes mellitus (T2DM) have been identified as particularly vulnerable and display compromised immune responses to vaccines. Concurrently, increasing evidence suggests that the composition and diversity of gut microbiota, crucial regulators of immune function, may influence the efficacy of vaccines. Against this backdrop, our study explores the complex interplay among SARS-CoV-2 inactivated vaccination, T2DM, and host microbiota. We discover that T2DM compromises the initial immune response to the SARS-CoV-2 inactivated vaccine, and this response is positively correlated with specific features of the gut microbiota, such as alpha diversity. We also demonstrate that the vaccination itself induces alterations in the composition and structure of the gut microbiota. These findings illuminate potential links between the gut microbiota and vaccine efficacy in individuals with T2DM, offering valuable insights that could enhance vaccine responses in this high-risk population.}, } @article {pmid39189742, year = {2024}, author = {Wurzbacher, CE and Hammer, J and Haufschild, T and Wiegand, S and Kallscheuer, N and Jogler, C}, title = {"Candidatus Uabimicrobium helgolandensis"-a planctomycetal bacterium with phagocytosis-like prey cell engulfment, surface-dependent motility, and cell division.}, journal = {mBio}, volume = {15}, number = {10}, pages = {e0204424}, pmid = {39189742}, issn = {2150-7511}, support = {AWI_BAH_o4//Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research (AWI)/ ; EXC 2051 - Project-ID 390713860//German Research foundation/ ; SFB 1076 - Project Number 218627073//German Research foundation/ ; Project-ID 239748522 - CRC 1127 ChemBioSys//German Research foundation/ ; //Studienstiftung des Deutschen Volkes (Studienstiftung)/ ; //Landesgraduiertenstipendium/ ; //Jena School for Microbial Communications/ ; }, mesh = {*Phagocytosis ; *Cell Division ; Phylogeny ; Planctomycetales/genetics/classification/physiology/isolation & purification ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The unique cell biology presented by members of the phylum Planctomycetota has puzzled researchers ever since their discovery. Initially thought to have eukaryotic-like features, their traits are now recognized as exceptional but distinctly bacterial. However, recently discovered strains again added novel and stunning aspects to the planctomycetal cell biology-shapeshifting by members of the "Saltatorellus" clade to an extent that is unprecedented in any other bacterial phylum, and phagocytosis-like cell engulfment in the bacterium "Candidatus Uabimicrobium amorphum." These recent additions to the phylum Planctomycetota indicate hitherto unexplored members with unique cell biology, which we aimed to make accessible for further investigations. Targeting bacteria with features like "Ca. U. amorphum", we first studied both the morphology and behavior of this microorganism in more detail. While similar to eukaryotic amoeboid organisms at first sight, we found "Ca. U. amorphum" to be rather distinct in many regards. Presenting a detailed description of "Ca. U. amorphum," we furthermore found this organism to divide in a fashion that has never been described in any other organism. Employing the obtained knowledge, we isolated a second "bacterium of prey" from the harbor of Heligoland Island (North Sea, Germany). Our isolate shares key features with "Ca. U. amorphum": phagocytosis-like cell engulfment, surface-dependent motility, and the same novel mode of cell division. Being related to "Ca. U. amorphum" within genus thresholds, we propose the name "Ca. Uabimicrobium helgolandensis" for this strain.IMPORTANCE"Candidatus Uabimicrobium helgolandensis" HlEnr_7 adds to the explored bacterial biodiversity with its phagocytosis-like uptake of prey bacteria. Enrichment of this strain indicates that there might be "impossible" microbes out there, missed by metagenomic analyses. Such organisms have the potential to challenge our understanding of nature. For example, the origin of eukaryotes remains enigmatic, with a contentious debate surrounding both the mitochondrial host entity and the moment of uptake. Currently, favored models involve a proteobacterium as the mitochondrial progenitor and an Asgard archaeon as the fusion partner. Models in which a eukaryotic ancestor engulfed the mitochondrial ancestor via phagocytosis had been largely rejected due to bioenergetic constraints. Thus, the phagocytosis-like abilities of planctomycetal bacteria might influence the debate, demonstrating that prey engulfment is possible in a prokaryotic cellular framework.}, } @article {pmid39189724, year = {2024}, author = {Xiao, JZ and Nesbø, CL and Molenda, O and Toth, CRA and Edwards, EA}, title = {Draft genome of an anaerobic nitrate-reducing, benzene-degrading member of the order Thermincolales.}, journal = {Microbiology resource announcements}, volume = {13}, number = {10}, pages = {e0029524}, pmid = {39189724}, issn = {2576-098X}, support = {OGI-102 and OGI-107//Genome Canada (GC)/ ; }, abstract = {We present a metagenome assembled genome (MAG) of an anaerobic bacterium from a nitrate-reducing, benzene-degrading enrichment culture (NRBC). The draft Thermincolales genome consists of 20 contigs with a total length of 4.09 Mbp and includes putative carboxylase genes likely involved in benzene activation.}, } @article {pmid39189169, year = {2024}, author = {Hejazirad, SP and de Abreu, CM and Carneiro, GHF and Gomes, CR and Spinola Filho, PRC and da Costa, MR and Santos, JBD}, title = {The Impact of Metolachlor Applications and Phytoremediation Processes on Soil Microorganisms: Insights from Functional Metagenomics Analysis.}, journal = {Journal of xenobiotics}, volume = {14}, number = {3}, pages = {970-988}, pmid = {39189169}, issn = {2039-4713}, support = {PQD//National Council for Scientific and Technological Development/ ; 00097-22//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; 001//Coordenação de Aperfeicoamento de Pessoal de Nível Superior/ ; }, abstract = {This study assessed the impact of phytoremediation on reducing the residual concentration of metolachlor in soil treated with doses of 530.7 and 1061.4 g/ha and its effect on microbial biodiversity in contaminated areas. For the plant species Avena sativa and Medicago sativa, a significant efficacy of 54.5 and 36.4% was observed in the dissipation of the herbicide, especially at higher doses. Although metolachlor application reduced soil microbial biodiversity, phytoremediating plants, especially M. sativa, promoted greater richness and distribution of microbial species, mitigating the negative effects of the herbicide. Principal component analysis revealed the influence of these plants and metolachlor on the composition of the microbial community. These results highlight the importance of phytoremediation in promoting soil biodiversity and reducing herbicide contamination, providing crucial insights for remediation strategies in contaminated areas.}, } @article {pmid39189041, year = {2024}, author = {Haussmann, AJ and McMahan, ZH and Volkmann, ER}, title = {Understanding the gastrointestinal microbiome in systemic sclerosis: methodological advancements and emerging research.}, journal = {Current opinion in rheumatology}, volume = {36}, number = {6}, pages = {401-409}, pmid = {39189041}, issn = {1531-6963}, support = {K23 HL150237/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; *Scleroderma, Systemic/microbiology ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/microbiology ; Fecal Microbiota Transplantation/methods ; }, abstract = {PURPOSE OF REVIEW: This review highlights the role of the gastrointestinal (GI) microbiome in systemic sclerosis (SSc). We describe techniques for evaluating the GI microbiome in humans, and emerging research linking GI microbiome alterations (i.e., dysbiosis) and distinct SSc clinical manifestations. We also address the evolving treatment landscape targeting dysbiosis in SSc.

RECENT FINDINGS: Recent literature brings into focus the complex relationship between the GI microbiome and SSc pathogenesis. Advanced techniques (e.g., shotgun metagenomics, meta-transcriptomics) provide deeper insights into microbial taxonomy and active gene expression, exposing dysbiosis as a potential driver of SSc. New studies demonstrate that SSc patients who possess specific SSc clinical features, (e.g., interstitial lung disease), have unique GI microbiome profiles.

SUMMARY: Dysbiosis is associated with specific clinical features in patients with SSc. New tools for studying the GI microbiome have furthered our understanding of the relationship between dysbiosis and SSc complications. Therapeutic avenues such as dietary adjustments, probiotics, antibiotics, mindfulness practices, and fecal transplants offer potential for managing SSc and preventing its progression through GI microbiome modulation. By clarifying what is known about the relationship between the GI dysbiosis, GI dysfunction, and SSc, this review enhances our understanding of SSc pathogenesis and proposes targeted interventions.}, } @article {pmid39187935, year = {2024}, author = {Versi, A and Azim, A and Ivan, FX and Abdel-Aziz, MI and Bates, S and Riley, J and Uddin, M and Zounemat Kermani, N and Maitland-Van Der Zee, AH and Dahlen, SE and Djukanovic, R and Chotirmall, SH and Howarth, P and Adcock, IM and Chung, KF and , }, title = {A severe asthma phenotype of excessive airway Haemophilus influenzae relative abundance associated with sputum neutrophilia.}, journal = {Clinical and translational medicine}, volume = {14}, number = {9}, pages = {e70007}, pmid = {39187935}, issn = {2001-1326}, support = {115010//Innovative Medicines Initiative/ ; FP7/2007-2013//European Union Seventh Framework Programme/ ; //European Federation of Pharmaceutical Industries and Associations/ ; //UK Research and Innovation/ ; //BBSRC/ ; }, mesh = {Humans ; *Asthma/microbiology ; *Haemophilus influenzae/pathogenicity/genetics ; *Sputum/microbiology ; Male ; Female ; Adult ; *Neutrophils/metabolism ; Middle Aged ; Phenotype ; Haemophilus Infections/microbiology ; }, abstract = {BACKGROUND: Severe asthma (SA) encompasses several clinical phenotypes with a heterogeneous airway microbiome. We determined the phenotypes associated with a low α-diversity microbiome.

METHODS: Metagenomic sequencing was performed on sputum samples from SA participants. A threshold of 2 standard deviations below the mean of α-diversity of mild-moderate asthma and healthy control subjects was used to define those with an abnormal abundance threshold as relative dominant species (RDS).

FINDINGS: Fifty-one out of 97 SA samples were classified as RDSs with Haemophilus influenzae RDS being most common (n = 16), followed by Actinobacillus unclassified (n = 10), Veillonella unclassified (n = 9), Haemophilus aegyptius (n = 9), Streptococcus pseudopneumoniae (n = 7), Propionibacterium acnes (n = 5), Moraxella catarrhalis (n = 5) and Tropheryma whipplei (n = 5). Haemophilus influenzae RDS had the highest duration of disease, more exacerbations in previous year and greatest number on daily oral corticosteroids. Hierarchical clustering of RDSs revealed a C2 cluster (n = 9) of highest relative abundance of exclusively Haemophilus influenzae RDSs with longer duration of disease and higher sputum neutrophil counts associated with enrichment pathways of MAPK, NF-κB, TNF, mTOR and necroptosis, compared to the only other cluster, C1, which consisted of 7 Haemophilus influenzae RDSs out of 42. Sputum transcriptomics of C2 cluster compared to C1 RDSs revealed higher expression of neutrophil extracellular trap pathway (NETosis), IL6-transignalling signature and neutrophil activation.

CONCLUSION: We describe a Haemophilus influenzae cluster of the highest relative abundance associated with neutrophilic inflammation and NETosis indicating a host response to the bacteria. This phenotype of severe asthma may respond to specific antibiotics.}, } @article {pmid39187802, year = {2024}, author = {Anitua, E and Murias-Freijo, A and Tierno, R and Tejero, R and Alkhraisat, MH}, title = {Assessing peri-implant bacterial community structure: the effect of microbiome sample collection method.}, journal = {BMC oral health}, volume = {24}, number = {1}, pages = {1001}, pmid = {39187802}, issn = {1472-6831}, mesh = {Humans ; *Microbiota ; *Biofilms ; *Gingival Crevicular Fluid/microbiology ; *Dental Implants/microbiology ; Middle Aged ; Specimen Handling/methods ; Female ; Male ; High-Throughput Nucleotide Sequencing ; Bacteria/classification/isolation & purification ; Aged ; }, abstract = {BACKGROUND: Oral microbiota comprises polymicrobial communities shaped by mutualistic coevolution with the host, contributing to homeostasis and regulating immune function. Nevertheless, dysbiosis of oral bacterial communities is associated with a number of clinical symptoms that ranges from infections to oral cancer. Peri-implant diseases are biofilm-associated inflammatory conditions affecting the soft and hard tissues around dental implants. Characterization and identification of the biofilm community are essential for the understanding of the pathophysiology of such diseases. For that sampling methods should be representative of the biofilm communities Therefore, there is a need to know the effect of different sampling strategies on the biofilm characterization by next generation sequencing.

METHODS: With the aim of selecting an appropriate microbiome sampling procedure for periimplant biofilms, next generation sequencing was used for characterizing the bacterial communities obtained by three different sampling strategies two months after transepithelial abutment placement: adjacent periodontal crevicular fluid (ToCF), crevicular fluid from transepithelial abutment (TACF) and transepithelial abutment (TA).

RESULTS: Significant differences in multiple alpha diversity indices were detected at both the OTU and the genus level between different sampling procedures. Differentially abundant taxa were detected between sample collection strategies, including peri-implant health and disease related taxa. At the community level significant differences were also detected between TACF and TA and also between TA and ToCF. Moreover, differential network properties and association patterns were identified.

CONCLUSIONS: The selection of sample collection strategy can significantly affect the community composition and structure.

TRIAL REGISTRATION: This research is part of a randomized clinical trial that was designed to assess the effect of transepithelial abutment surface on the biofilm formation. The trial was registered at Trial Registration ClinicalTrials.gov under the number NCT03554876.}, } @article {pmid39187328, year = {2024}, author = {Yeh, TK and Huang, YT and Liu, PY and Mao, YC and Lai, CS and Lai, KL and Tseng, CH and Liu, CW and Huang, WH and Huang, HP and Lin, KP}, title = {Pathogenic Detection by Metagenomic Next-generation Sequencing in Skin and Soft Tissue Infection.}, journal = {In vivo (Athens, Greece)}, volume = {38}, number = {5}, pages = {2364-2373}, pmid = {39187328}, issn = {1791-7549}, mesh = {Humans ; *Soft Tissue Infections/microbiology/diagnosis ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Male ; Female ; Middle Aged ; Aged ; Adult ; Bacteria/genetics/isolation & purification/classification ; Metagenome ; Aged, 80 and over ; }, abstract = {BACKGROUND/AIM: Skin and soft tissue infections (SSTIs) can be life-threatening, but the conventional bacterial cultures have low sensitivity and are time-consuming. Metagenomic next-generation sequencing (mNGS) is widely used as a diagnostic tool for detecting pathogens from infection sites. However, the use of mNGS for pathogen detection in SSTIs and related research is still relatively limited.

PATIENTS AND METHODS: From January 2020 to October 2021, 19 SSTI samples from 16 patients were collected in a single center (Taichung Veterans General Hospital, Taichung, Taiwan). The clinical samples were simultaneously subjected to mNGS and conventional bacterial culture methods to detect pathogens. Clinical characteristics were prospectively collected through electronic chart review. The microbiological findings from conventional bacterial culture and mNGS were analyzed and compared.

RESULTS: The mNGS method detected a higher proportion of multiple pathogens in SSTIs compared to conventional bacterial culture methods. Pseudomonas spp. was among the most commonly identified Gram-negative bacilli using mNGS. Additionally, the mNGS method identified several rare pathogens in patients with SSTIs, including Granulicatella adiacens, Bacillus thuringiensis, and Bacteroides fragilis. Antimicrobial resistance genes were detected in 10 samples (52.6%) using the mNGS method, including genes for extended-spectrum beta-lactamase, Ambler class C β-lactamases, and carbapenemase.

CONCLUSION: mNGS not only plays an important role in the detection of pathogens in soft tissue infections, but also informs clinical professionals about the presence of additional microbes that may be important for treatment decisions. Further studies comparing conventional pathogen culture with the mNGS method in SSTIs are required.}, } @article {pmid39186902, year = {2024}, author = {Pan, Y and Zeng, J and Zhang, L and Hu, J and Hao, H and Zeng, Z and Li, Y}, title = {The fate of antibiotics and antibiotic resistance genes in Large-Scale chicken farm Environments: Preliminary view of the performance of National veterinary Antimicrobial use reduction Action in Guangdong, China.}, journal = {Environment international}, volume = {191}, number = {}, pages = {108974}, doi = {10.1016/j.envint.2024.108974}, pmid = {39186902}, issn = {1873-6750}, mesh = {*Chickens ; Animals ; China ; *Anti-Bacterial Agents/pharmacology ; *Farms ; *Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; Animal Husbandry ; Genes, Bacterial ; Escherichia coli/drug effects/genetics ; }, abstract = {In 2018, China implemented the Veterinary Antimicrobial Use Reduction Action to curb the rapid development of antibiotic resistance (AR). However, the AR-related pollutions in animal farms after the reduction policy has been poorly investigated. Here, we performed a comprehensive investigation combining UPLC-MS/MS, metagenomic, and bacterial genomic analyses in eight representative large-scale chicken farms in Guangdong, China. Our results showed that antibiotics and ARGs contaminations were more severe in broiler farms than in layer farms. Notably, diverse tet(X) variants were prevalent in the chicken farms. These tet(X)s was carried by diverse E. coli lineages and obviously correlated with ISCR2 and IS1B transposases. The resistomes in chicken farms was significantly correlated with microbial community, and multiple factor analyses indicated that the joint effect of antibiotics-microbial community-MGEs was the most dominant driver of ARGs. Host tracking identified a variety of ARG bacterial hosts and the co-occurrence of ARGs-MRGs-MGEs. Source tracking indicated that the inherent component represented the main feature of resistomes in different hosts, while ARG transfer between the chicken gut and farm environments were frequent. A multiperspective evaluation of AR risk revealed that the early effect of antibiotic reduction was exhibited by the mitigation of maximum level of risky ARGs, prevalence of environmental AR pathogens, and HGT potential of ARGs mediated by phage structures. Overall, our findings provide insights into the antibiotic and ARG profiles in large-scale chicken farms with different rearing strategies and demonstrate a preliminary view of the performance of antibiotic reduction actions in China.}, } @article {pmid39186711, year = {2024}, author = {Smith, AM and Ramudzulu, M and Munk, P and Avot, BJP and Esterhuyse, KCM and van Blerk, N and Kwenda, S and Sekwadi, P}, title = {Metagenomics analysis of sewage for surveillance of antimicrobial resistance in South Africa.}, journal = {PloS one}, volume = {19}, number = {8}, pages = {e0309409}, pmid = {39186711}, issn = {1932-6203}, mesh = {South Africa ; *Sewage/microbiology ; *Metagenomics/methods ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Humans ; Wastewater/microbiology ; }, abstract = {Our 24-month study used metagenomics to investigate antimicrobial resistance (AMR) abundance in raw sewage from wastewater treatment works (WWTWs) in two municipalities in Gauteng Province, South Africa. At the AMR class level, data showed similar trends at all WWTWs, showing that aminoglycoside, beta-lactam, sulfonamide and tetracycline resistance was most abundant. AMR abundance differences were shown between municipalities, where Tshwane Metropolitan Municipality (TMM) WWTWs showed overall higher abundance of AMR compared to Ekurhuleni Metropolitan Municipality (EMM) WWTWs. Also, within each municipality, there were differing trends in AMR abundance. Notably, within TMM, certain AMR classes (macrolides and macrolides_streptogramin B) were in higher abundance at a WWTW serving an urban high-income area, while other AMR classes (aminoglycosides) were in higher abundance at a WWTW serving a semi-urban low income area. At the AMR gene level, all WWTWs samples showed the most abundance for the sul1 gene (encoding sulfonamide resistance). Following this, the next 14 most abundant genes encoded resistance to sulfonamides, aminoglycosides, macrolides, tetracyclines and beta-lactams. Notably, within TMM, some macrolide-encoding resistance genes (mefC, msrE, mphG and mphE) were in highest abundance at a WWTW serving an urban high-income area; while sul1, sul2 and tetC genes were in highest abundance at a WWTW serving a semi-urban low income area. Differential abundance analysis of AMR genes at WWTWs, following stratification of data by season, showed some notable variance in six AMR genes, of which blaKPC-2 and blaKPC-34 genes showed the highest prevalence of seasonal abundance differences when comparing data within a WWTW. The general trend was to see higher abundances of AMR genes in colder seasons, when comparing seasonal data within a WWTW. Our study investigated wastewater samples in only one province of South Africa, from WWTWs located within close proximity to one another. We would require a more widespread investigation at WWTWs distributed across all regions/provinces of South Africa, in order to describe a more comprehensive profile of AMR abundance across the country.}, } @article {pmid39186442, year = {2024}, author = {Chen, Y and Ma, W and Zhao, J and Stanton, C and Ross, RP and Zhang, H and Chen, W and Yang, B}, title = {Lactobacillus plantarum Ameliorates Colorectal Cancer by Ameliorating the Intestinal Barrier through the CLA-PPAR-γ Axis.}, journal = {Journal of agricultural and food chemistry}, volume = {72}, number = {36}, pages = {19766-19785}, doi = {10.1021/acs.jafc.4c02824}, pmid = {39186442}, issn = {1520-5118}, mesh = {*Lactobacillus plantarum/metabolism ; *PPAR gamma/metabolism/genetics ; Animals ; Mice ; *Colorectal Neoplasms/metabolism ; Humans ; *Probiotics/administration & dosage/pharmacology ; Male ; *Linoleic Acids, Conjugated/pharmacology/metabolism ; *Mice, Inbred C57BL ; *Gastrointestinal Microbiome ; *Intestinal Mucosa/metabolism/microbiology ; Female ; NF-kappa B/metabolism/genetics ; Apoptosis/drug effects ; Claudin-1/metabolism/genetics ; Zonula Occludens-1 Protein/metabolism/genetics ; }, abstract = {Colorectal cancer (CRC) is the third-largest cancer worldwide. Lactobacillus can regulate the intestinal barrier and gut microbiota. However, the mechanisms of Lactobacillus that alleviate CRC remained unknown. This study aimed to explore the regulatory effect of Lactobacillus plantarum on CRC and its potential mechanism. CCFM8661 treatment significantly ameliorated CRC compared with phosphate-buffered solution (PBS) treatment in Apc[Min/+] mice. In addition, conjugated linoleic acid (CLA) was proved to be the key metabolite for CCFM8661 in ameliorating CRC by molecular biology techniques. Peroxisome proliferator-activated receptor γ (PPAR-γ) was proved to be the key receptor in ameliorating CRC by inhibitor intervention experiments. Moreover, supplementation with CCFM8661 ameliorated CRC by producing CLA to inhibit NF-κB pathway and pro-inflammatory cytokines, up-regulate ZO-1, Claudin-1, and MUC2, and promote tumor cell apoptosis in a PPAR-γ-dependent manner. Metagenomic analysis showed that CCFM8661 treatment significantly increased Odoribacter splanchnicus, which could ameliorate CRC by repairing the intestinal barrier. Clinical results showed that intestinal CLA, butyric acid, PPAR-γ, and Lactobacillus were significantly decreased in CRC patients, and these indicators were significantly negatively correlated with CRC. CCFM8661 alleviated CRC by ameliorating the intestinal barrier through the CLA-PPAR-γ axis. These results will promote the development of dietary probiotic supplements for CRC.}, } @article {pmid39185682, year = {2024}, author = {Maqsood, R and Holland, LA and Wu, LI and Begnel, ER and Adhiambo, J and Owiti, P and Chohan, BH and Gantt, S and Kinuthia, J and Wamalwa, D and Ojee, E and Richardson, BA and Slyker, J and Lehman, DA and Lim, ES}, title = {Gut virome and microbiome dynamics before and after SARS-CoV-2 infection in women living with HIV and their infants.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2394248}, pmid = {39185682}, issn = {1949-0984}, support = {R01 HD092311/HD/NICHD NIH HHS/United States ; }, mesh = {Humans ; Female ; *COVID-19/microbiology/virology ; *HIV Infections/microbiology/virology ; *Virome ; *Gastrointestinal Microbiome ; *SARS-CoV-2/genetics/isolation & purification ; Adult ; Infant, Newborn ; *Feces/microbiology/virology ; Infant ; Bacteria/classification/isolation & purification/genetics ; Longitudinal Studies ; }, abstract = {Microbiome perturbations can have long-term effects on health. The dynamics of the gut microbiome and virome in women living with HIV (WLHIV) and their newborn infants is poorly understood. Here, we performed metagenomic sequencing analyses on longitudinal stool samples including 23 mothers (13 WLHIV, 10 HIV-negative) and 12 infants that experienced SARS-CoV-2 infection with mild disease, as well as 40 mothers (18 WLHIV, 22 HIV-negative) and 60 infants that remained SARS-CoV-2 seronegative throughout the study follow-up. Regardless of HIV or SARS-CoV-2 status, maternal bacterial and viral profiles were distinct from infants. Using linear mixed effects models, we showed that the microbiome alpha diversity trajectory was not significantly different between SARS-CoV-2 seropositive and seronegative women. However, seropositive women's positive trajectory while uninfected was abruptly reversed after SARS-CoV-2 infection (p = 0.015). Gut virome signatures of women were not associated with SARS-CoV-2. Alterations in infant microbiome and virome diversities were generally not impacted by SARS-CoV-2 but were rather driven by development. We did not find statistically significant interactions between HIV and SARS-CoV-2 on the gut microbiome and virome. Overall, our study provides insights into the complex interplay between maternal and infant bacterial microbiome, virome, and the influence of SARS-CoV-2 and HIV status.}, } @article {pmid39185240, year = {2024}, author = {Laperriere, SM and Minch, B and Weissman, JL and Hou, S and Yeh, YC and Ignacio-Espinoza, JC and Ahlgren, NA and Moniruzzaman, M and Fuhrman, JA}, title = {Phylogenetic proximity drives temporal succession of marine giant viruses in a five-year metagenomic time-series.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39185240}, issn = {2692-8205}, support = {R01 GM120624/GM/NIGMS NIH HHS/United States ; }, abstract = {Nucleocytoplasmic Large DNA Viruses (NCLDVs, also called giant viruses) are widespread in marine systems and infect a broad range of microbial eukaryotes (protists). Recent biogeographic work has provided global snapshots of NCLDV diversity and community composition across the world's oceans, yet little information exists about the guiding 'rules' underpinning their community dynamics over time. We leveraged a five-year monthly metagenomic time-series to quantify the community composition of NCLDVs off the coast of Southern California and characterize these populations' temporal dynamics. NCLDVs were dominated by Algavirales (Phycodnaviruses, 59%) and Imitervirales (Mimiviruses, 36%). We identified clusters of NCLDVs with distinct classes of seasonal and non-seasonal temporal dynamics. Overall, NCLDV population abundances were often highly dynamic with a strong seasonal signal. The Imitervirales group had highest relative abundance in the more oligotrophic late summer and fall, while Algavirales did so in winter. Generally, closely related strains had similar temporal dynamics, suggesting that evolutionary history is a key driver of the temporal niche of marine NCLDVs. However, a few closely-related strains had drastically different seasonal dynamics, suggesting that while phylogenetic proximity often indicates ecological similarity, occasionally phenology can shift rapidly, possibly due to host-switching. Finally, we identified distinct functional content and possible host interactions of two major NCLDV orders-including connections of Imitervirales with primary producers like the diatom Chaetoceros and widespread marine grazers like Paraphysomonas and Spirotrichea ciliates. Together, our results reveal key insights on season-specific effect of phylogenetically distinct giant virus communities on marine protist metabolism, biogeochemical fluxes and carbon cycling.}, } @article {pmid39185189, year = {2024}, author = {Midani, FS and Danhof, HA and Mathew, N and Ardis, CK and Garey, KW and Spinler, JK and Britton, RA}, title = {Emerging Clostridioides difficile ribotypes have divergent metabolic phenotypes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39185189}, issn = {2692-8205}, support = {U01 AI124290/AI/NIAID NIH HHS/United States ; F32 AI136404/AI/NIAID NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; R01 AI123278/AI/NIAID NIH HHS/United States ; U19 AI157981/AI/NIAID NIH HHS/United States ; T32 DK007664/DK/NIDDK NIH HHS/United States ; }, abstract = {UNLABELLED: Clostridioides difficile is a gram-positive spore-forming pathogen that commonly causes diarrheal infections in the developed world. Although C. difficile is a genetically diverse species, certain ribotypes are overrepresented in human infections. It is unknown if metabolic adaptations are essential for the emergence of these epidemic ribotypes. Here, we tested carbon substrate utilization by 88 C. difficile isolates and looked for differences in growth between 22 ribotypes. By profiling clinical isolates, we assert that C. difficile is a generalist species capable of growing on a variety of carbon substrates. Further, C. difficile strains clustered by phylogenetic relationship and displayed ribotype-specific and clade-specific metabolic capabilities. Surprisingly, we observed that two emerging lineages, ribotypes 023 and 255, have divergent metabolic phenotypes. In addition, although C. difficile Clade 5 is the most evolutionary distant clade and often detected in animals, it displayed more robust growth on simple dietary sugars than Clades 1-4. Altogether, our results corroborate the generalist metabolic strategy of C. difficile and demonstrate lineage-specific metabolic capabilities. In addition, our approach can be adapted to the study of additional pathogens to ascertain their metabolic niches in the gut.

IMPORTANCE: The gut pathogen Clostridioides difficile utilizes a wide range of carbon sources. Microbial communities can be rationally designed to combat C. difficile by depleting its preferred nutrients in the gut. However, C. difficile is genetically diverse with hundreds of identified ribotypes and most of its metabolic studies were performed with lab-adapted strains. Here, we profiled carbon metabolism by a myriad of C. difficile clinical isolates. While the metabolic capabilities of these isolates clustered by their genetic lineage, we observed surprising metabolic divergence between two emerging lineages. We also found that the most genetically distant clade grew robustly on simple dietary sugars, posing intriguing questions about the adaptation of C. difficile to the human gut. Altogether, our results underscore the importance of considering the metabolic diversity of pathogens in the study of their evolution and the rational design of therapeutic interventions.}, } @article {pmid39185088, year = {2024}, author = {Hu, L and Xu, Y and Li, J and Zhang, M and Sun, Z and Ban, Y and Tian, X and Liu, D and Hu, L}, title = {Gut microbiome characteristics of women with hypothyroidism during early pregnancy detected by 16S rRNA amplicon sequencing and shotgun metagenomic.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1369192}, pmid = {39185088}, issn = {2235-2988}, mesh = {Humans ; Female ; Pregnancy ; *Hypothyroidism/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Adult ; *Dysbiosis/microbiology ; Bacteria/classification/genetics/isolation & purification ; Pregnancy Complications/microbiology ; Metagenome ; Feces/microbiology ; }, abstract = {OBJECTIVE: This study aimed to explore the correlation between microbiota dysbiosis and hypothyroidism in early pregnancy by 16S rRNA amplicon sequencing combined with metagenomic sequencing.

METHODS: Sixty pregnant women (30 with hypothyroidism and 30 normal controls) were recruited for 16S rRNA amplicon sequencing, and 6 patients from each group were randomly selected for metagenomic sequencing to assess the gut microbiome profile.

RESULTS: The 16S rRNA results showed that beta-diversity in the hypothyroidism group was decreased. The relative abundances of the Prevotella and Paraprevotella genera increased in the hypothyroidism group, and Blautia predominated in the controls. The metagenomics results revealed that Prevotella_stercorea_CAG_629, Prevotella_hominis, Prevotella_sp_AM34_19LB, etc. were enriched in the hypothyroidism group at the species level. Functional analysis revealed that the pyridoxal 5'-phosphate synthase pdxT subunit module was decreased, and the short-chain fatty acid (SCFA) transporter and phospholipase/carboxylesterase modules were strongly enriched in the hypothyroidism group. Hypothyroidism patients had increased C-reactive protein (CRP), interleukin-2 (IL-2), IL-4, IL-10, and tumor necrosis factor (TNF)-α levels. The pyridoxal 5'-phosphate synthase pdxT subunit, the SCFA transporter, and the phospholipase/carboxylesterase module were associated with different Prevotella species.

CONCLUSION: In early pregnancy, women with hypothyroidism exhibit microbiota dysbiosis, and Prevotella may affect the metabolism of glutamate, SCFA, and phospholipases, which could be involved in the development of hypothyroidism during pregnancy.}, } @article {pmid39185086, year = {2024}, author = {Wang, X and Xiao, T and Lu, M and Wu, Z and Chen, L and Zhang, Z and Lu, W}, title = {Lower respiratory tract microbiome and lung cancer risk prediction in patients with diffuse lung parenchymal lesions.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1410681}, pmid = {39185086}, issn = {2235-2988}, mesh = {Humans ; *Lung Neoplasms/microbiology/pathology ; Male ; Female ; *Microbiota ; Middle Aged ; *Bronchoalveolar Lavage Fluid/microbiology ; Retrospective Studies ; Aged ; Lung/microbiology/pathology/diagnostic imaging ; High-Throughput Nucleotide Sequencing ; Adult ; Respiratory System/microbiology ; Metagenomics/methods ; Risk Factors ; }, abstract = {OBJECTIVE: In clinical practice, imaging manifestations of diffuse lung parenchymal lesions are common and indicative of various diseases, making differential diagnosis difficult. Some of these lesions are eventually diagnosed as lung cancer.

METHODS: Because respiratory microorganisms play an important role in lung cancer development, we searched for microbial markers that could predict the risk of lung cancer by retrospectively analyzing the lower respiratory tract (LRT) microbiome of 158 patients who were hospitalized in the First Affiliated Hospital of Guangzhou Medical University (March 2021-March 2023) with diffuse lung parenchymal lesions. The final diagnosis was lung cancer in 21 cases, lung infection in 93 cases, and other conditions (other than malignancy and infections) in 44 cases. The patient's clinical characteristics and the results of metagenomic next-generation sequencing of bronchoalveolar lavage fluid (BALF) were analyzed.

RESULTS: Body mass index (BMI) and LRT microbial diversity (Shannon, Simpson, species richness, and Choa1 index) were significantly lower (P< 0.001, respectively) and Lactobacillus acidophilus relative abundance in the LRT was significantly higher (P< 0.001) in patients with lung cancer. The relative abundance of L. acidophilus in BALF combined with BMI was a good predictor of lung cancer risk (area under the curve = 0.985, accuracy = 98.46%, sensitivity = 95.24%, and specificity = 100.00%; P< 0.001).

CONCLUSION: Our study showed that an imbalance in the component ratio of the microbial community, diminished microbial diversity, and the presence of specific microbial markers in the LRT predicted lung cancer risk in patients with imaging manifestations of diffuse lung parenchymal lesions.}, } @article {pmid39184378, year = {2024}, author = {Chung, HC and Friedberg, I and Bromberg, Y}, title = {Assembling bacterial puzzles: piecing together functions into microbial pathways.}, journal = {NAR genomics and bioinformatics}, volume = {6}, number = {3}, pages = {lqae109}, pmid = {39184378}, issn = {2631-9268}, abstract = {Functional metagenomics enables the study of unexplored bacterial diversity, gene families, and pathways essential to microbial communities. However, discovering biological insights with these data is impeded by the scarcity of quality annotations. Here, we use a co-occurrence-based analysis of predicted microbial protein functions to uncover pathways in genomic and metagenomic biological systems. Our approach, based on phylogenetic profiles, improves the identification of functional relationships, or participation in the same biochemical pathway, between enzymes over a comparable homology-based approach. We optimized the design of our profiles to identify potential pathways using minimal data, clustered functionally related enzyme pairs into multi-enzymatic pathways, and evaluated our predictions against reference pathways in the KEGG database. We then demonstrated a novel extension of this approach to predict inter-bacterial protein interactions amongst members of a marine microbiome. Most significantly, we show our method predicts emergent biochemical pathways between known and unknown functions. Thus, our work establishes a basis for identifying the potential functional capacities of the entire metagenome, capturing previously unknown and abstract functions into discrete putative pathways.}, } @article {pmid39184367, year = {2024}, author = {Frolov, AV and Vishnevskaya, MS and Viljanen, H and Montreuil, O and Akhmetova, LA}, title = {New data on trophic associations of dung beetles (Coleoptera, Scarabaeidae, Scarabaeinae) and lemurs (Primates, Lemuroidea) in Madagascar revealed by metabarcoding.}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e130400}, pmid = {39184367}, issn = {1314-2828}, abstract = {Resource use and diet specialisation of Madagascan dung beetles have been little studied especially concerning the possible associations between specific dung beetle and lemur species. Pilot studies have demonstrated that amplicon sequencing is a promising tool for the lemur inventories. In the present contribution, we report the results of the gut content analysis of three endemic Madagascan dung beetles species: Helictopleurusclouei (Harold), Epilissusapotolamproides (Lebis) and Nanosdubitatus (Lebis). Amplicon metagenomics revealed trophic associations of these species with Eulemursanfordi (Archbold), Eu.fulvus (É.Geoffroy Saint-Hilaire) and Cheirogaleuscrossleyi (Grandidier), respectively. The reads of other mammal species, revealed by the analysis, including putative contaminations, are discussed.}, } @article {pmid39184200, year = {2024}, author = {Reynolds, G and Mumey, B and Strnadova-Neeley, V and Lachowiec, J}, title = {Hijacking a rapid and scalable metagenomic method reveals subgenome dynamics and evolution in polyploid plants.}, journal = {Applications in plant sciences}, volume = {12}, number = {4}, pages = {e11581}, pmid = {39184200}, issn = {2168-0450}, support = {P20 GM103474/GM/NIGMS NIH HHS/United States ; }, abstract = {PREMISE: The genomes of polyploid plants archive the evolutionary events leading to their present forms. However, plant polyploid genomes present numerous hurdles to the genome comparison algorithms for classification of polyploid types and exploring genome dynamics.

METHODS: Here, the problem of intra- and inter-genome comparison for examining polyploid genomes is reframed as a metagenomic problem, enabling the use of the rapid and scalable MinHashing approach. To determine how types of polyploidy are described by this metagenomic approach, plant genomes were examined from across the polyploid spectrum for both k-mer composition and frequency with a range of k-mer sizes. In this approach, no subgenome-specific k-mers are identified; rather, whole-chromosome k-mer subspaces were utilized.

RESULTS: Given chromosome-scale genome assemblies with sufficient subgenome-specific repetitive element content, literature-verified subgenomic and genomic evolutionary relationships were revealed, including distinguishing auto- from allopolyploidy and putative progenitor genome assignment. The sequences responsible were the rapidly evolving landscape of transposable elements. An investigation into the MinHashing parameters revealed that the downsampled k-mer space (genomic signatures) produced excellent approximations of sequence similarity. Furthermore, the clustering approach used for comparison of the genomic signatures is scrutinized to ensure applicability of the metagenomics-based method.

DISCUSSION: The easily implementable and highly computationally efficient MinHashing-based sequence comparison strategy enables comparative subgenomics and genomics for large and complex polyploid plant genomes. Such comparisons provide evidence for polyploidy-type subgenomic assignments. In cases where subgenome-specific repeat signal may not be adequate given a chromosomes' global k-mer profile, alternative methods that are more specific but more computationally complex outperform this approach.}, } @article {pmid39184027, year = {2024}, author = {Liu, Z and Qi, CJ and Shi, Y and Li, T and Fang, Y and Zhang, Q}, title = {Active herpesviruses are associated with intensive care unit (ICU) admission in patients pulmonary infection and alter the respiratory microbiome.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1441476}, pmid = {39184027}, issn = {1664-302X}, abstract = {BACKGROUND: The Herpesviridae family contains several human-related viruses, which are able to establish colonizing and latency in the human body, posing a significant threat to the prognosis of patients. Pulmonary infections represent one of the predominant infectious diseases globally, characterized by diverse and multifaceted clinical manifestations that have consistently attracted clinician's concern. However, the relationship of herpesviruses on the prognosis of pulmonary infections and the respiratory microbiota remains poorly understood.

METHODS: Here, we retrospectively analyzed respiratory samples from 100 patients with pulmonary infection detected by metagenomic next-generation sequencing (mNGS).

RESULTS: Employing mNGS, five herpesvirus species were detected: Human alphaherpesvirus 1 (HSV-1), Human gammaherpesvirus 4 (EBV), Human betaherpesvirus 5 (CMV), Human betaherpesvirus 7 (HHV-7), and Human betaherpesvirus 6B (HHV-6B). Regression analysis showed that the age and positivity of herpesviruses in patients were independently correlated with ICU admission rates. In addition, positivity of herpesvirus was related with increased ICU days and total hospital stay. The herpesvirus-positive group demonstrated markedly higher incidences of co-infections and fungi-positive, predominantly involving Pneumocystis jirovecii and Aspergillus fumigatus. Analysis of respiratory microbiota revealed a substantially altered community composition within the herpesvirus-positive group, and herpesviruses were significantly positively correlated with the diverse respiratory opportunistic pathogens.

CONCLUSION: Overall results substantiate that the active herpesviruses in patients with pulmonary infections were significantly associated with high ICU admission rate. Moreover, the herpesviruses promotes the dysbiosis of the respiratory microbiota and an increased proportion of co-infections. These insights could contribute to unraveling the underlying mechanisms connecting active herpesviruses to the progression of severe illnesses.}, } @article {pmid39183848, year = {2024}, author = {Bhuvaneshwar, K and Madhavan, S and Gusev, Y}, title = {Integrative genomic analysis of the lung tissue microenvironment in SARS-CoV-2 and NL63 patients.}, journal = {Heliyon}, volume = {10}, number = {12}, pages = {e32772}, pmid = {39183848}, issn = {2405-8440}, abstract = {The coronavirus disease 2019 (COVID-19) pandemic caused by the SARS-CoV-2 virus has affected over 700 million people, and caused over 7 million deaths throughout the world as of April 2024, and continues to affect people through seasonal waves. While over 675 million people have recovered from this disease globally, the lingering effects of the disease are still under study. Long term effects of SARS-CoV-2 infection, known as 'long COVID,' include a wide range of symptoms including fatigue, chest pain, cellular damage, along with a strong innate immune response characterized by inflammatory cytokine production. Three years after the pandemic, data about long covid studies are finally emerging. More clinical studies and clinical trials are needed to understand and determine the factors that predispose individuals to these long-term side effects. In this methodology paper, our goal was to apply data driven approaches in order to explore the multidimensional landscape of infected lung tissue microenvironment to better understand complex interactions between viral infection, immune response and the lung microbiome of patients with (a) SARS-CoV-2 virus and (b) NL63 coronavirus. The samples were analyzed with several machine learning tools allowing simultaneous detection and quantification of viral RNA amount at genome and gene level; human gene expression and fractions of major types of immune cells, as well as metagenomic analysis of bacterial and viral abundance. To contrast and compare specific viral response to SARS-COV-2, we analyzed deep sequencing data from additional cohort of patients infected with NL63 strain of corona virus. Our correlation analysis of three types of RNA-seq based measurements in patients i.e. fraction of viral RNA (at genome and gene level), Human RNA (transcripts and gene level) and bacterial RNA (metagenomic analysis), showed significant correlation between viral load as well as level of specific viral gene expression with the fractions of immune cells present in lung lavage as well as with abundance of major fractions of lung microbiome in COVID-19 patients. Our methodology-based proof-of-concept study has provided novel insights into complex regulatory signaling interactions and correlative patterns between the viral infection, inhibition of innate and adaptive immune response as well as microbiome landscape of the lung tissue. These initial findings could provide better understanding of the diverse dynamics of immune response and the side effects of the SARS-CoV-2 infection and demonstrates the possibilities of the various types of analyses that could be performed from this type of data.}, } @article {pmid39183814, year = {2024}, author = {Li, GX and Gopchandani, K and Brazer, N and Tippett, A and Choi, C and Hsiao, HM and Oseguera, M and Foresythe, A and Bhattacharya, S and Servellita, V and Sotomayor Gonzalez, A and Spinler, JK and Gonzalez, MD and Gulick, D and Kraft, C and Kasinathan, V and Wang, YFW and Dien Bard, J and Chen, PY and Flores-Vazquez, J and Odom John, AR and Planet, PJ and Devaraj, S and Annapragada, AV and Luna, RA and Chiu, CY and Rostad, CA}, title = {Clinical Features and Outcomes of Pediatric and Adult Patients Hospitalized for Coronavirus Disease 2019: A Comparison Across Age Strata.}, journal = {Open forum infectious diseases}, volume = {11}, number = {8}, pages = {ofae443}, pmid = {39183814}, issn = {2328-8957}, support = {R61 HD105618/HD/NICHD NIH HHS/United States ; }, abstract = {BACKGROUND: Coronavirus disease 2019 (COVID-19) continues to cause hospitalizations and severe disease in children and adults.

METHODS: This study compared the risk factors, symptoms, and outcomes of children and adults hospitalized for COVID-19 from March 2020 to May 2023 across age strata at 5 US sites participating in the Predicting Viral-Associated Inflammatory Disease Severity in Children with Laboratory Diagnostics and Artificial Intelligence consortium. Eligible patients had an upper respiratory swab that tested positive for severe acute respiratory syndrome coronavirus 2 by nucleic acid amplification. Adjusted odds ratios (aOR) of clinical outcomes were determined for children versus adults, for pediatric age strata compared to adolescents (12-17 years), and for adult age strata compared to young adults (22-49 years).

RESULTS: Of 9101 patients in the Predicting Viral-Associated Inflammatory Disease Severity in Children with Laboratory Diagnostics and Artificial Intelligence cohort, 1560 were hospitalized for COVID-19 as the primary reason. Compared to adults (22-105 years, n = 675), children (0-21 years, n = 885) were less commonly vaccinated (14.3% vs 34.5%), more commonly infected with the Omicron variant (49.5% vs 26.1%) and had fewer comorbidities (P < .001 for most comparisons), except for lung disease (P = .24). After adjusting for confounding variables, children had significantly lower odds of receiving supplemental oxygen (aOR, 0.57; 95% confidence interval, .35-.92) and death (aOR, 0.011; 95% confidence interval, <.01-.58) compa--red to adults. Among pediatric age strata, adolescents 12-17 years had the highest odds of receiving supplemental oxygen, high-flow oxygen, and ICU admission. Among adults, those 50-64 years had the highest odds of mechanical ventilation and ICU admission.

CONCLUSIONS: Clinical outcomes of COVID-19 differed across pediatric and adult age strata. Adolescents experienced the most severe disease among children, whereas adults 50-64 years experienced the most severe disease among adults.}, } @article {pmid39182818, year = {2024}, author = {Fang, C and Liu, KD and Tian, FJ and Li, JY and Li, SJ and Zhang, RM and Sun, J and Fang, LX and Ren, H and Wang, MG and Liao, XP}, title = {Metagenomic analysis unveiled the response of microbial community and antimicrobial resistome in natural water body to duck farm sewage.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {361}, number = {}, pages = {124784}, doi = {10.1016/j.envpol.2024.124784}, pmid = {39182818}, issn = {1873-6424}, mesh = {*Ducks ; Animals ; *Sewage/microbiology ; *Microbiota/drug effects ; Farms ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Environmental Monitoring ; Bacteria/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Sewages from duck farms are often recognized as a major source of antimicrobial resistance and pathogenic bacteria discharged to natural water bodies, but few studies depicted the dynamic changes in resistome and microbial communities in the rivers under immense exposure of sewage discharge. In this study, we investigated the ecological and environmental risks of duck sewages to the rivers that geographically near to the duck farms with short-distance (<1 km) using 16S rRNA amplicon and metagenomic sequencing. The results showed that a total of 20 ARG types were identified with abundances ranged from 0.61 to 1.33 cpc. Of note, the genes modulate resistances against aminoglycoside, bacitracin and beta-lactam were the most abundant ARGs. Limnohabitans, Fluviibacter and Cyanobium were the top 3 predominant genera in the microbial community. The alpha diversity of overall microbial community decrease while the abundance of pathogen increase during the input of sewage within 200 m. Sul1 and bacA were the dominant ARGs brought from duck farm sewage. The community variations of ARGs and microbiome were primarily driven by pH and temperature. Total phosphorus was significantly correlated to alpha diversity and top 30 ARGs subtype. Stochastic processes was the dominated microbial assembly pattern and did not be altered by sewage. We also highlighted the ecological risk caused by blaGES which possibly could be mitigated by Cyanobacteria, and the natural water body can purify partial ARGs as well as microbiome from duck farms sewage. These findings expanded our knowledge regarding the ecological risks by wastes from the livestock farm, and underscoring the necessity to monitor ARGs in farm-surrounding water bodies.}, } @article {pmid39182795, year = {2024}, author = {Wang, SP and Sun, ZY and Wang, ST and Tang, YQ}, title = {Microbial mechanisms of biochar addition on carbon and nitrogen synergistic retention during distilled grain waste composting: Insights from metagenomic analysis.}, journal = {Bioresource technology}, volume = {411}, number = {}, pages = {131346}, doi = {10.1016/j.biortech.2024.131346}, pmid = {39182795}, issn = {1873-2976}, mesh = {*Nitrogen ; *Carbon/pharmacology ; *Charcoal/chemistry/pharmacology ; *Composting/methods ; Metagenomics/methods ; Edible Grain/metabolism ; Soil Microbiology ; Soil/chemistry ; }, abstract = {To elucidate the mechanism of biochar addition on carbon and nitrogen retention during distilled grain (DGW) composting, this study investigated the losses of carbon and nitrogen and functional genes related to carbon and nitrogen metabolisms between biochar-treated and control composts. The addition of biochar significantly increased carbon and nitrogen retention by 13.5% and 33.8%, respectively. The difference in core carbon metabolism genes indicated that biochar addition inhibited CO2 release and promoted carbon fixation during the later composting phase, leading to improved carbon retention. Nitrogen metabolism analysis indicated that biochar addition suppressed early-phase ammoniation and late-phase denitrification and promoted nitrification and ammonia assimilation during the later stages of composting, thereby preserving nitrogen. During the later composting phase, biochar addition enhanced carbon-nitrogen coupling metabolism activity, leading to the synchronous retention of carbon and nitrogen. These findings elucidate the mechanism of biochar addition on carbon and nitrogen retention during DGW composting.}, } @article {pmid39182764, year = {2024}, author = {Zhao, Y and Tan, J and Fang, L and Jiang, L}, title = {Harnessing meta-omics to unveil and mitigate methane emissions in ruminants: Integrative approaches and future directions.}, journal = {The Science of the total environment}, volume = {951}, number = {}, pages = {175732}, doi = {10.1016/j.scitotenv.2024.175732}, pmid = {39182764}, issn = {1879-1026}, mesh = {*Methane/metabolism ; Animals ; *Ruminants ; Metabolomics ; Metagenomics ; Air Pollutants/analysis ; Greenhouse Gases ; Rumen/metabolism ; Gastrointestinal Microbiome ; Genomics ; }, abstract = {Methane emissions from enteric fermentation present a dual challenge globally: they not only contribute significantly to atmospheric greenhouse gases but also represent a considerable energy loss for ruminant animals. Utilizing high-throughput omics technologies to analyze rumen microbiome samples (meta-omics, i.e., metagenomics, metatranscriptomics, metaproteomics, metabolomics) holds vast potential for uncovering the intricate interplay between diet, microbiota, and methane emissions in these animals. The primary obstacle is the effective integration of diverse meta-omic approaches and their broader application across different ruminant species. Genetic variability significantly impacts methane production in ruminants, suggesting that genomic selection could be a viable strategy to reduce emissions. While substantial research has been conducted on the microbiological aspects of methane production, there remains a critical need to delineate the specific genetic interactions between the host and its microbiome. Advancements in meta-omics technologies are poised to shed light on these interactions, enhancing our understanding of the genetic factors that govern methane output. This review explores the potential of meta-omics to accelerate genetic advancements that could lead to reduced methane emissions in ruminants. By employing a systems biology approach, the integration of various omics technologies allows for the identification of key genomic regions and genetic markers linked to methane production. These markers can then be leveraged in selective breeding programs to cultivate traits associated with lower emissions. Moreover, the review addresses current challenges in applying genomic selection for this purpose and discusses how omics technologies can overcome these obstacles. The systematic integration and analysis of diverse biological data provide deeper insights into the genetic underpinnings and overall biology of methane production traits in ruminants. Ultimately, this comprehensive approach not only aids in reducing the environmental impact of agriculture but also contributes to the sustainability and efficiency of livestock management.}, } @article {pmid39182301, year = {2024}, author = {Peruzzo, A and Petrin, S and Boscolo Anzoletti, A and Mancin, M and Di Cesare, A and Sabatino, R and Lavagnolo, MC and Beggio, G and Baggio, G and Danesi, P and Barco, L and Losasso, C}, title = {The integration of omics and cultivation-dependent methods could effectively determine the biological risks associated with the utilization of soil conditioners in agriculture.}, journal = {Journal of hazardous materials}, volume = {478}, number = {}, pages = {135567}, doi = {10.1016/j.jhazmat.2024.135567}, pmid = {39182301}, issn = {1873-3336}, mesh = {*Agriculture ; *Soil Microbiology ; *Sewage/microbiology ; *Bacteria/genetics ; Soil/chemistry ; Composting ; Metagenomics ; Fertilizers ; }, abstract = {In the circular economy, reusing agricultural residues, treated biowaste, and sewage sludges-commonly referred to as soil conditioners-in agriculture is essential for converting waste into valuable resources. However, these materials can also contribute to the spread of antimicrobial-resistant pathogens in treated soils. In this study, we analyzed different soil conditioners categorized into five groups: compost from source-separated biowaste and green waste, agro-industrial digestate, digestate from anaerobic digestion of source-separated biowaste, compost from biowaste digestate, and sludges from wastewater treatment plants. Under Italian law, only the first two categories are approved for agricultural use, despite Regulation 1009/2019/EU allowing the use of digestate from anaerobic digestion of source-separated biowaste in CE-marked fertilizers. We examined the bacterial community and associated resistome of each sample using metagenomic approaches. Additionally, we detected and isolated various pathogens to provide a comprehensive understanding of the potential risks associated with sludge application in agriculture. The compost samples exhibited higher bacterial diversity and a greater abundance of potentially pathogenic bacteria compared to other samples, except for wastewater treatment plant sludges, which had the highest frequency of Salmonella isolation and resistome diversity. Our findings suggest integrating omics and cultivation-dependent methods to accurately assess the biological risks of using sludge in agriculture.}, } @article {pmid39182227, year = {2024}, author = {Chilton, PM and Ghare, SS and Charpentier, BT and Myers, SA and Rao, AV and Petrosino, JF and Hoffman, KL and Greenwell, JC and Tyagi, N and Behera, J and Wang, Y and Sloan, LJ and Zhang, J and Shields, CB and Cooper, GE and Gobejishvili, L and Whittemore, SR and McClain, CJ and Barve, SS}, title = {Age-associated temporal decline in butyrate-producing bacteria plays a key pathogenic role in the onset and progression of neuropathology and memory deficits in 3×Tg-AD mice.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2389319}, pmid = {39182227}, issn = {1949-0984}, support = {P20 GM113226/GM/NIGMS NIH HHS/United States ; R01 AG061065/AG/NIA NIH HHS/United States ; U01 AA022618/AA/NIAAA NIH HHS/United States ; P50 AA024337/AA/NIAAA NIH HHS/United States ; U01 AA026936/AA/NIAAA NIH HHS/United States ; I01 CX002219/CX/CSRD VA/United States ; }, mesh = {Animals ; *Butyrates/metabolism ; *Gastrointestinal Microbiome ; Mice ; *Alzheimer Disease/microbiology/pathology/metabolism ; *Memory Disorders/microbiology/metabolism/pathology ; *Bacteria/classification/metabolism/genetics/isolation & purification ; *Disease Models, Animal ; *Dysbiosis/microbiology ; Hippocampus/metabolism/pathology ; Mice, Transgenic ; Male ; Disease Progression ; Brain-Gut Axis/physiology ; Brain/metabolism/pathology ; }, abstract = {Alterations in the gut-microbiome-brain axis are increasingly being recognized to be involved in Alzheimer's disease (AD) pathogenesis. However, the functional consequences of enteric dysbiosis linking gut microbiota and brain pathology in AD progression remain largely undetermined. The present work investigated the causal role of age-associated temporal decline in butyrate-producing bacteria and butyrate in the etiopathogenesis of AD. Longitudinal metagenomics, neuropathological, and memory analyses were performed in the 3×Tg-AD mouse model. Metataxonomic analyses showed a significant temporal decline in the alpha diversity marked by a decrease in butyrate-producing bacterial communities and a concurrent reduction in cecal butyrate production. Inferred metagenomics analysis identified the bacterial acetyl-CoA pathway as the main butyrate synthesis pathway impacted. Concomitantly, there was an age-associated decline in the transcriptionally permissive acetylation of histone 3 at lysines 9 and 14 (H3K9/K14-Ac) in hippocampal neurons. Importantly, these microbiome-gut-brain changes preceded AD-related neuropathology, including oxidative stress, tau hyperphosphorylation, memory deficits, and neuromuscular dysfunction, which manifest by 17-18 months. Initiation of oral administration of tributyrin, a butyrate prodrug, at 6 months of age mitigated the age-related decline in butyrate-producing bacteria, protected the H3K9/K14-Ac status, and attenuated the development of neuropathological and cognitive changes associated with AD pathogenesis. These data causally implicate age-associated decline in butyrate-producing bacteria as a key pathogenic feature of the microbiome-gut-brain axis affecting the onset and progression of AD. Importantly, the regulation of butyrate-producing bacteria and consequent butyrate synthesis could be a significant therapeutic strategy in the prevention and treatment of AD.}, } @article {pmid39182147, year = {2024}, author = {Ji, R and Wan, J and Liu, J and Zheng, J and Xiao, T and Pan, Y and Lin, W}, title = {Linking morphology, genome, and metabolic activity of uncultured magnetotactic Nitrospirota at the single-cell level.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {158}, pmid = {39182147}, issn = {2049-2618}, support = {42388101//National Natural Science Foundation of China/ ; T2225011//National Natural Science Foundation of China/ ; YSBR-097//CAS Project for Young Scientists in Basic Research/ ; }, mesh = {*Genome, Bacterial ; *Phylogeny ; *Single-Cell Analysis ; Bacteria/metabolism/classification/genetics ; Magnetosomes/metabolism/genetics ; Lakes/microbiology ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Magnetotactic bacteria (MTB) are a unique group of microorganisms that sense and navigate through the geomagnetic field by biomineralizing magnetic nanoparticles. MTB from the phylum Nitrospirota (previously known as Nitrospirae) thrive in diverse aquatic ecosystems. They are of great interest due to their production of hundreds of magnetite (Fe3O4) magnetosome nanoparticles per cell, which far exceeds that of other MTB. The morphological, phylogenetic, and genomic diversity of Nitrospirota MTB have been extensively studied. However, the metabolism and ecophysiology of Nitrospirota MTB are largely unknown due to the lack of cultivation techniques.

METHODS: Here, we established a method to link the morphological, genomic, and metabolic investigations of an uncultured Nitrospirota MTB population (named LHC-1) at the single-cell level using nanoscale secondary-ion mass spectrometry (NanoSIMS) in combination with rRNA-based in situ hybridization and target-specific mini-metagenomics.

RESULTS: We magnetically separated LHC-1 from a freshwater lake and reconstructed the draft genome of LHC-1 using genome-resolved mini-metagenomics. We found that 10 LHC-1 cells were sufficient as a template to obtain a high-quality draft genome. Genomic analysis revealed that LHC-1 has the potential for CO2 fixation and NO3[-] reduction, which was further characterized at the single-cell level by combining stable-isotope incubations and NanoSIMS analyses over time. Additionally, the NanoSIMS results revealed specific element distributions in LHC-1, and that the heterogeneity of CO2 and NO3[-] metabolisms among different LHC-1 cells increased with incubation time.

CONCLUSIONS: To our knowledge, this study provides the first metabolic measurements of individual Nitrospirota MTB cells to decipher their ecophysiological traits. The procedure constructed in this study provides a promising strategy to simultaneously investigate the morphology, genome, and ecophysiology of uncultured microbes in natural environments. Video Abstract.}, } @article {pmid39182035, year = {2024}, author = {Velázquez-Fernández, JB and Aceves Suriano, CE and Thalasso, F and Montoya-Ciriaco, N and Dendooven, L}, title = {Structural and functional bacterial biodiversity in a copper, zinc and nickel amended bioreactor: shotgun metagenomic study.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {313}, pmid = {39182035}, issn = {1471-2180}, mesh = {*Bioreactors/microbiology ; *Zinc/metabolism ; *Nickel/metabolism ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Metagenomics ; *Copper/metabolism ; *Biodiversity ; Wastewater/microbiology/chemistry ; }, abstract = {BACKGROUND: At lower concentrations copper (Cu), zinc (Zn) and nickel (Ni) are trace metals essential for some bacterial enzymes. At higher concentrations they might alter and inhibit microbial functioning in a bioreactor treating wastewater. We investigated the effect of incremental concentrations of Cu, Zn and Ni on the bacterial community structure and their metabolic functions by shotgun metagenomics. Metal concentrations reported in previous studies to inhibit bacterial metabolism were investigated.

RESULTS: At 31.5 μM Cu, 112.4 μM Ni and 122.3 μM Zn, the most abundant bacteria were Achromobacter and Agrobacterium. When the metal concentration increased 2 or fivefold their abundance decreased and members of Delftia, Stenotrophomonas and Sphingomonas dominated. Although the heterotrophic metabolic functions based on the gene profile was not affected when the metal concentration increased, changes in the sulfur biogeochemical cycle were detected. Despite the large variations in the bacterial community structure when concentrations of Cu, Zn and Ni increased in the bioreactor, functional changes in carbon metabolism were small.

CONCLUSIONS: Community richness and diversity replacement indexes decreased significantly with increased metal concentration. Delftia antagonized Pseudomonas and members of Xanthomonadaceae. The relative abundance of most bacterial genes remained unchanged despite a five-fold increase in the metal concentration, but that of some EPS genes required for exopolysaccharide synthesis, and those related to the reduction of nitrite to nitrous oxide decreased which may alter the bioreactor functioning.}, } @article {pmid39181512, year = {2024}, author = {Li, Y and Barati, B and Li, J and Verhoestraete, E and Rousseau, DPL and Van Hulle, SWH}, title = {Lab-scale evaluation of Microalgal-Bacterial granular sludge as a sustainable alternative for brewery wastewater treatment.}, journal = {Bioresource technology}, volume = {411}, number = {}, pages = {131331}, doi = {10.1016/j.biortech.2024.131331}, pmid = {39181512}, issn = {1873-2976}, mesh = {*Microalgae/metabolism ; *Sewage/microbiology ; *Wastewater/chemistry ; *Nitrogen ; *Bacteria/metabolism ; Biological Oxygen Demand Analysis ; Water Purification/methods ; Phosphorus ; Carbon/pharmacology ; Waste Disposal, Fluid/methods ; Beer ; Phosphates ; Bioreactors ; }, abstract = {Microalgal-bacterial granular sludge (MBGS) could offer a sustainable alternative to traditional aerobic methods in brewery wastewater (BWW) treatment. This study compared MBGS with conventional activated sludge (AS) in treating real BWW and highlighted its advantages and challenges. MBGS achieved comparable chemical oxygen demand removal efficiency (93%) compared to AS (89%). Additionally, MBGS exhibited higher phosphate removal capabilities than AS. Extra nitrogen was added to influent to balance C/N ratio of BWW. MBGS was robust in handling C/N ratio fluctuations with an 82% total nitrogen removal efficiency. Metagenomic analysis further indicated that most of the genes involved in carbon, nitrogen and phosphorus metabolism were up-regulated in MBGS compared to AS. Despite changes in the microbial community and settling ability due to high starch and sugar content in BWW, MBGS demonstrated high efficiency and sustainability. Further research should optimize MBGS operation strategies to fully realize its potential for sustainable BWW treatment.}, } @article {pmid39181304, year = {2024}, author = {Yu, Y and Ai, T and Huang, J and Jin, L and Yu, X and Zhu, X and Sun, J and Zhu, L}, title = {Metabolism of isodecyl diphenyl phosphate in rice and microbiome system: Differential metabolic pathways and underlying mechanisms.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {361}, number = {}, pages = {124803}, doi = {10.1016/j.envpol.2024.124803}, pmid = {39181304}, issn = {1873-6424}, mesh = {*Oryza/metabolism/microbiology ; *Microbiota ; *Rhizosphere ; Metabolic Networks and Pathways ; Soil Pollutants/metabolism ; Organophosphorus Compounds/metabolism ; Soil Microbiology ; Organophosphates/metabolism ; }, abstract = {Isodecyl diphenyl phosphate (IDDP) is among the emerging aromatic organophosphate esters (aryl-OPEs) that pose risks to both human beings and other organisms. This study aims to investigate the translocation and biotransformation behavior of IDDP in rice and the rhizosphere microbiome through hydroponic exposure (the duration of hydroponic exposure was 10 days). The rhizosphere microbiome 9-FY was found to efficiently eliminate IDDP, thereby reducing its uptake in rice tissues and mitigating the negative impact of IDDP on rice growth. Furthermore, this study proposed the first-ever transformation pathways of IDDP, identifying hydrolysis, hydroxylation, methylation, methoxylation, carboxylation, and glucuronidation products. Notably, the methylation and glycosylation pathways were exclusively observed in rice, indicating that the transformation of IDDP in rice may be more complex than in microbiome 9-FY. Additionally, the presence of the product COOH-IDDP in rice suggested that there might be an exchange of degradation products between rice and rhizobacteria, implying their potential interaction. This finding highlights the significance of rhizobacteria's role which cannot be overlooked in the accumulation and transformation of organic pollutants in grain crops. The study revealed active members in 9-FY during IDDP degradation, and metagenomic analysis indicated that most of the active populations contained IDDP-degrading genes. Moreover, transcriptome sequencing showed that cytochrome P450, acid phosphatase, glucosyltransferase, and methyltransferases genes in rice were up-regulated, which was further confirmed by RT-qPCR. This provides insight into the intermediate products identified in rice, such as hydrolysis, hydroxylated, glycosylated, and methylated products. These results significantly contribute to our understanding of the translocation and transformation of organophosphate esters (OPEs) in plants and the rhizosphere microbiome, and reveal the fate of OPEs in rice and microbiome system to ensure the paddy yield and rice safety.}, } @article {pmid39181265, year = {2024}, author = {Dong, W and Zhou, J and Zhang, CJ and Yang, Q and Li, M}, title = {Methylotrophic substrates stimulated higher methane production than competitive substrates in mangrove sediments.}, journal = {The Science of the total environment}, volume = {951}, number = {}, pages = {175677}, doi = {10.1016/j.scitotenv.2024.175677}, pmid = {39181265}, issn = {1879-1026}, mesh = {*Methane/metabolism ; *Geologic Sediments/microbiology ; *Wetlands ; China ; Microbiota ; Bacteria/metabolism/classification ; }, abstract = {Although mangrove forests can uptake atmospheric CO2 and store carbon as organic matter called "blue carbon", it is also an important natural source of greenhouse gas methane. Methanogens are major contributors to methane and play important roles in the global carbon cycle. However, our understanding of the key microbes and metabolic pathways responsible for methanogenesis under specific substrates in mangrove sediments is still very limited. Here, we set an anaerobic incubation to evaluate the responses of methanogens in mangrove sediments from South China to the addition of diverse methanogenic substrates (H2/CO2, acetate, trimethylamine (TMA), and methanethiol (MT)) and further investigated the dynamics of the whole microbial community. Our results showed that diverse substrates stimulated methanogenic activities at different times. The stimulation of methanogenesis was more pronounced at early and late periods by the addition of methylotrophic substrates TMA and MT, respectively. The amplicon sequencing analysis showed that genus Methanococcoides was mainly responsible for TMA-utilized methanogenesis in mangrove sediment, while the multitrophic Methanococcus was most abundant in H2/CO2 and MT treatments. Apart from that, the bacteria enrichments of Syntrophotalea, Clostridium_sensu_stricto_12, Fusibacter in MT treatments might also be associated with the stimulation of methane production. In addition, the metagenomic analysis suggested that Methanosarcinaceae was also one of the key methanogens in MT treatments with different genomic information compared to that in TMA treatments. Finally, the total relative abundances of methanogenesis-related genes were also highest in TMA and MT treatments. These results will help advance our understanding of the contributions of different methanogenesis pathways and methanogens to methane emissions in mangrove sediments.}, } @article {pmid39181210, year = {2025}, author = {Zhang, YH and Xie, R and Dai, CS and Gao, HW and Zhou, G and Qi, TT and Wang, WY and Wang, H and Cui, YM}, title = {Thyroid hormone receptor-beta agonist HSK31679 alleviates MASLD by modulating gut microbial sphingolipids.}, journal = {Journal of hepatology}, volume = {82}, number = {2}, pages = {189-202}, doi = {10.1016/j.jhep.2024.08.008}, pmid = {39181210}, issn = {1600-0641}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Sphingolipids/metabolism ; *Thyroid Hormone Receptors beta/agonists/metabolism ; Male ; Humans ; Spiro Compounds/pharmacology/administration & dosage/therapeutic use ; Double-Blind Method ; Disease Models, Animal ; Liver/metabolism/drug effects ; Mice, Inbred C57BL ; Pyridazines ; Uracil/analogs & derivatives ; }, abstract = {BACKGROUND & AIMS: As the first approved medication for metabolic dysfunction-associated steatohepatitis (MASH), the thyroid hormone receptor-β (THR-β) agonist MGL-3196 (resmetirom) has garnered much attention as a liver-directed, bioactive oral drug. However, studies on MGL-3196 have also identified remarkable heterogeneity of individual clinical efficacy and its interference with gut microbiota in host hepatoenteral circulation remains to be elucidated.

METHODS: We compared MASH attenuation by MGL-3196 and its derivative drug HSK31679 between germ-free (GF) and specific-pathogen free (SPF) mice to evaluate the role of gut microbiota. Then cross-omics analyses of microbial metagenome, metabolome and single-cell RNA-sequencing were applied to a randomized, double-blind, placebo-controlled multiple ascending dose cohort receiving HSK31679 treatment (n = 32) or placebo (n = 8), to comprehensively investigate the altered gut microbiota metabolism and circulating immune signatures.

RESULTS: HSK31679 outperformed MGL-3196 in ameliorating MASH diet-induced steatohepatitis of SPF mice but not GF mice. In the multiple ascending dose cohort of HSK31679, the relative abundance of B. thetaiotaomicron was significantly enriched, impairing glucosylceramide synthase (GCS)-catalyzed monoglucosylation of microbial Cer(d18:1/16:0) and Cer(d18:1/24:1). In contrast to the non-inferior effect of MGL-3196 and HSK31679 on MASH resolution in GF[BTΔGCS] mice, HSK31679 led to superior benefit on steatohepatitis in GF[BTWT] mice, due to its steric hindrance of R123 and Y401 of gut microbial GCS. For participants with high fecal GCS activity, the administration of 160 mg HSK31679 induced a shift in peripheral compartments towards an immunosuppressive niche, characterized by decreased CD8α[+] dendritic cells and MINCLE[+] macrophages.

CONCLUSIONS: This study provided novel insights into the gut microbiota that are key to the efficacy of HSK31679 treatment, revealing microbial GCS as a potential predictive biomarker in MASH, as well as a new target for further microbiota-based treatment strategies for MASH.

IMPACT AND IMPLICATIONS: Remarkable heterogeneity in individual clinical efficacy of thyroid hormone receptor-β agonists and their interferences with the microbiome in host hepatoenteral circulation are poorly understood. In our current germ-free mouse models and a randomized, double-blind, multiple-dose cohort study, we identified microbial glucosylceramide synthase as a key mechanistic node in the resolution of metabolic dysfunction-associated steatohepatitis. Microbial glucosylceramide synthase activity could be a predictive biomarker of response to HSK31679 treatment or a new target for microbiota-based therapeutics in metabolic dysfunction-associated steatohepatitis.}, } @article {pmid39181078, year = {2024}, author = {Wei, Q and Yin, Y and Tong, Q and Gong, Z and Shi, Y}, title = {Multi-omics analysis of excessive nitrogen fertilizer application: Assessing environmental damage and solutions in potato farming.}, journal = {Ecotoxicology and environmental safety}, volume = {284}, number = {}, pages = {116916}, doi = {10.1016/j.ecoenv.2024.116916}, pmid = {39181078}, issn = {1090-2414}, mesh = {*Solanum tuberosum/microbiology ; *Fertilizers ; *Nitrogen/analysis ; *Soil Microbiology ; Transcriptome ; Metabolome/drug effects ; Agriculture/methods ; Metagenomics ; Soil/chemistry ; Multiomics ; }, abstract = {Potatoes (Solanum tuberosum L.) are the third largest food crop globally and are pivotal for global food security. Widespread N fertilizer waste in potato cultivation has caused diverse environmental issues. This study employed microbial metagenomic sequencing to analyze the causes behind the declining N use efficiency (NUE) and escalating greenhouse gas emissions resulting from excessive N fertilizer application. Addressing N fertilizer inefficiency through breeding has emerged as a viable solution for mitigating overuse in potato cultivation. In this study, transcriptome and metabolome analyses were applied to identify N fertilizer-responsive genes. Metagenomic sequencing revealed that excessive N fertilizer application triggered alterations in the population dynamics of 11 major bacterial phyla, consequently affecting soil microbial functions, particularly N metabolism pathways and bacterial secretion systems. Notably, the enzyme levels associated with NO3[-] increased, and those associated with NO and N2O increased. Furthermore, excessive N fertilizer application enhanced soil virulence factors and increased potato susceptibility to diseases. Transcriptome and metabolome sequencing revealed significant impacts of excessive N fertilizer use on lipid and amino acid metabolism pathways. Weighted gene co‑expression network analysis (WGCNA) was adopted to identify two genes associated with N fertilizer response: PGSC0003DMG400021157 and PGSC0003DMG400009544.}, } @article {pmid39180955, year = {2024}, author = {Li, Y and Yang, B and Kong, Y and Tao, Y and Zhao, Z and Li, Y and Zhang, Y}, title = {Correlation between intracellular electron transfer and gene expression for electrically conductive pili in electroactive bacteria during anaerobic digestion with ethanol.}, journal = {Water research}, volume = {265}, number = {}, pages = {122307}, doi = {10.1016/j.watres.2024.122307}, pmid = {39180955}, issn = {1879-2448}, mesh = {Electron Transport ; *Ethanol/metabolism ; Anaerobiosis ; Electric Conductivity ; Fimbriae, Bacterial/metabolism ; Bacteria/metabolism ; Gene Expression ; }, abstract = {Ethanol feeding has been widely documented as an economical and effective strategy for establishing direct interspecies electron transfer (DIET) during anaerobic digestion. However, the mechanisms involved are still unclear, especially on correlation between intracellular electron transfer in electroactive bacteria and their gene expression for electrically conductive pili (e-pili), the most essential electrical connection component for DIET. Upon cooling from room temperature, the conductivity of digester aggregates with ethanol exponentially increased by an order of magnitude (from 45.5 to 125.4 μS/cm), whereas which with its metabolites (acetaldehyde [from 40.5 to 54.4 μS/cm] or acetate [from 32.1 to 50.4 μS/cm]) did not increase significantly. In addition, the digester aggregates only with ethanol were observed with a strong dependence of conductivity on pH. Metagenomic and metatranscriptomic analysis showed that Desulfovibrio desulfuricans was the most dominant and metabolically active bacterium that contained and highly expressed the genes for e-pili. Abundance of genes encoding the total type IV pilus assembly proteins (6.72E-04 vs 1.24E-03, P < 0.05), PilA that determined the conductive properties (2.22E-04 vs 2.44E-04, P > 0.05), and PilB that proceeded the polymerization of pilin (1.56E-04 vs 3.52E-03, P < 0.05) with ethanol was lower than that with acetaldehyde. However, transcript abundance of these genes with ethanol was generally higher than that with acetaldehyde. In comparison to acetaldehyde, ethanol increased the transcript abundance of genes encoding the key enzymes involved in NADH/NAD[+] transformation on complex I and ATP synthesis on complex V in intracellular electron transport chain. The improvement of intracellular electron transfer in D. desulfuricans suggested that electrons were intracellularly energized with high energy to activate e-pili during DIET.}, } @article {pmid39180787, year = {2024}, author = {Seara-Morais, GJ and Miraglia, FFO and Hidal, JT and Camargo, LFA and Mangueira, CLP and Doi, AM and Amgarten, DE and Dorlass, EG and Santana, RAF and Pinho, JRR}, title = {Identification of a Orthohantavirus strain by clinical metagenomics in Brazil.}, journal = {Diagnostic microbiology and infectious disease}, volume = {110}, number = {4}, pages = {116501}, doi = {10.1016/j.diagmicrobio.2024.116501}, pmid = {39180787}, issn = {1879-0070}, mesh = {Humans ; Male ; Adult ; Brazil ; *Metagenomics/methods ; Orthohantavirus/genetics/classification/isolation & purification ; Genome, Viral/genetics ; Hantavirus Infections/diagnosis/virology ; Phylogeny ; RNA, Viral/genetics ; }, abstract = {We describe a case of a 33-year-old male presented with fever, myalgia, nausea, and asthenia for six days. The patient lived in a rural area. Initial hypotheses included arbovirus infection, viral hepatitis, and Lyme disease. Reverse transcriptase polymerase chain reaction (RT-PCR) tests for Dengue, Zika, and Chikungunya resulted negative. We were able to recover complete S, L, and M segments of virus in the Orthohantavirus genome.}, } @article {pmid39180723, year = {2024}, author = {Jiang, L and Hao, Y and Han, D and Dong, W and Yang, A and Sun, Z and Ge, Y and Duan, S and Zhang, X and Dai, Z}, title = {Gut microbiota dysbiosis deteriorates immunoregulatory effects of tryptophan via colonic indole and LBP/HTR2B-mediated macrophage function.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39180723}, issn = {1751-7370}, support = {2022YFA1304204//National Key Research and Development Program of China/ ; 32072689//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Dysbiosis/microbiology ; Mice ; *Colitis/chemically induced/immunology/microbiology ; *Tryptophan/metabolism ; *Indoles/pharmacology ; *Macrophages/immunology/drug effects ; *Mice, Inbred C57BL ; *Colon/microbiology/immunology ; *Disease Models, Animal ; *Carrier Proteins/genetics/metabolism ; *Dextran Sulfate ; Acute-Phase Proteins/metabolism ; Male ; Fecal Microbiota Transplantation ; Anti-Bacterial Agents/pharmacology ; Signal Transduction ; Membrane Glycoproteins ; }, abstract = {Tryptophan (Trp) has been shown to regulate immune function by modulating gut serotonin (5-HT) metabolism and signaling. However, the mechanisms underlying the microbial modulation of gut 5-HT signaling in gut inflammation with gut microbiota dysbiosis require further investigation. Here, we investigated the effects of Trp supplementation on the composition and metabolism of the gut microbiome and 5-HT signaling-related gut immune function using a dextran sodium sulfate (DSS)-induced colitis mouse model coupled with antibiotic exposure. The results showed that antibiotic treatment before but not during DSS treatment decreased the immunoregulatory effects of Trp and aggravated gut inflammation and body weight loss in mice. Metagenomic analysis revealed that the fecal microbiota transplantation of Trp-enriched gut microbiota to recipient mice subject to antibiotic pre-exposure and DSS treatment alleviated inflammation by increasing the relative abundances of Lactobacillus and Parabacteroides and the microbial production of indole coupled with the activation of the 5-HT receptor 2B (HTR2B) in the colon. Transcriptomic analysis showed that HTR2B agonist administration strengthened the beneficial effects of Trp in DSS-induced colitis mice with antibiotic exposure by reducing gut lipopolysaccharide-binding protein (LBP) production, IκB-α/nuclear factor-κB signaling, and M1 macrophage polarization. Indole treatment reduced LBP production and M1 macrophage polarization both in mice with DSS-induced colitis and in lipopolysaccharide-treated mouse macrophages; however, the HTR2B antagonist reversed the effects of indole. Our findings provide the basis for developing new dietary and therapeutic interventions to improve gut microbiota dysbiosis-associated inflammatory gut disorders and diseases.}, } @article {pmid39180208, year = {2024}, author = {Wang, YC and Jiang, TM and Mo, L and Lu, HZ and Quan, LH and Zhong, P and Guan, Y}, title = {Distribution of Antibiotic-Resistant Genes in Intestines of Infants and Influencing Factors.}, journal = {Critical reviews in eukaryotic gene expression}, volume = {34}, number = {8}, pages = {59-73}, pmid = {39180208}, issn = {1045-4403}, mesh = {Humans ; Female ; *Feces/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Milk, Human/microbiology ; Infant ; Infant, Newborn ; Intestines/microbiology ; Male ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Gastrointestinal Microbiome/genetics/drug effects ; Bacteria/genetics/drug effects ; Drug Resistance, Microbial/genetics ; }, abstract = {The objective of this study is to assess the prevalence of antibiotic-resistant genes (ARGs) in the intestines of infants and the factors affecting their distribution. Breast milk and infant stool samples were collected from nine full-term, healthy mother-infant pairs. The bacterial distribution and various types of ARGs present in the samples were analyzed using metagenomic next-generation sequencing. Over a period spanning from 2 to 240 d after birth, a total of 273 types of ARGs were identified in both infant feces and breast milk, exhibiting a trend of increasing prevalence over time. High concentrations of representative ARG populations were identified in the intestines of infants, especially at 12-15 d after birth. These populations included APH3-Ib, tetW/N/W, mphA, and Haemophilus influenzae PBP3, and multiple ARG Escherichia coli soxS that were resistant to common clinically used aminoglycoside, tetracycline, macrolide, and beta-lactam antibiotics. Gammaproteobacteria and Bacilli, especially Enterococcus, Staphylococcus, Acinetobacter, Streptococcus, and Escherichia were among the identified ARG carriers. Maternal age and body mass index (present and before pregnancy), infant sex, maternal consumption of probiotic yogurt during pregnancy, and lactation might be substantial factors influencing the occurrence of ARG-carrying bacteria and ARG distribution in the infant feces. These results indicate that environmental factors may influence the distribution of ARG-carrying bacteria and ARGs themselves in infants during early life. Providing appropriate recommendations regarding maternal age, body mass index during pregnancy, and use of probiotic products could potentially mitigate the transmission of antibiotic-resistant microbiota and ARGs, thereby diminishing the risk of antibiotic-resistant infections and safeguarding children's health.}, } @article {pmid39180123, year = {2024}, author = {Horigan, S and Kettenburg, G and Kistler, A and Ranaivoson, HC and Andrianiaina, A and Andry, S and Raharinosy, V and Randriambolamanantsoa, TH and Tato, CM and Lacoste, V and Heraud, JM and Dussart, P and Brook, CE}, title = {Detection, characterization, and phylogenetic analysis of novel astroviruses from endemic Malagasy fruit bats.}, journal = {Virology journal}, volume = {21}, number = {1}, pages = {195}, pmid = {39180123}, issn = {1743-422X}, support = {001/WHO_/World Health Organization/International ; GCE/ID OPP1211841//Bill and Melinda Gates Foundation/ ; 1R01A|129822-01/NH/NIH HHS/United States ; PREEMPT Program Cooperative Agreement no D18AC00031//Defense Sciences Office, DARPA/ ; }, mesh = {Animals ; *Chiroptera/virology ; *Phylogeny ; *Astroviridae/genetics/isolation & purification/classification ; *Astroviridae Infections/veterinary/virology/epidemiology ; *Metagenomics ; High-Throughput Nucleotide Sequencing ; Madagascar ; Genome, Viral/genetics ; Sequence Analysis, DNA ; }, abstract = {Bats (order: Chiroptera) are known to host a diverse range of viruses, some of which present a human public health risk. Thorough viral surveillance is therefore essential to predict and potentially mitigate zoonotic spillover. Astroviruses (family: Astroviridae) are an understudied group of viruses with a growing amount of indirect evidence for zoonotic transfer. Astroviruses have been detected in bats with significant prevalence and diversity, suggesting that bats may act as important astrovirus hosts. Most astrovirus surveillance in wild bat hosts has, to date, been restricted to single-gene PCR detection and concomitant Sanger sequencing; additionally, many bat species and many geographic regions have not yet been surveyed for astroviruses at all. Here, we use metagenomic Next Generation Sequencing (mNGS) to detect astroviruses in three species of Madagascar fruit bats, Eidolon dupreanum, Pteropus rufus, and Rousettus madagascariensis. We detect numerous partial sequences from all three species and one near-full length astrovirus sequence from Rousettus madagascariensis, which we use to characterize the evolutionary history of astroviruses both within bats and the broader mammalian clade, Mamastrovirus. Taken together, applications of mNGS implicate bats as important astrovirus hosts and demonstrate novel patterns of bat astrovirus evolutionary history, particularly in the Southwest Indian Ocean region.}, } @article {pmid39180058, year = {2024}, author = {Hua, X and McGoldrick, J and Nakrour, N and Staller, K and Chung, DC and Xavier, RJ and Khalili, H}, title = {Gut microbiome structure and function in asymptomatic diverticulosis.}, journal = {Genome medicine}, volume = {16}, number = {1}, pages = {105}, pmid = {39180058}, issn = {1756-994X}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 AG068390/AG/NIA NIH HHS/United States ; DK043351//Center for the study of inflammatory bowel disease/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; Aged ; Metagenomics/methods ; Colonoscopy ; Metagenome ; Bacteria/classification/genetics ; }, abstract = {BACKGROUND: Colonic diverticulosis, the most common lesion found in routine colonoscopy, affects more than 50% of individuals aged ≥ 60 years. Emerging evidence suggest that dysbiosis of gut microbiota may play an important role in the pathophysiology of diverticular disease. However, specific changes in microbial species and metabolic functions in asymptomatic diverticulosis remain unknown.

METHODS: In a cohort of US adults undergoing screening colonoscopy, we analyzed the gut microbiota using shotgun metagenomic sequencing. Demographic factors, lifestyle, and medication use were assessed using a baseline questionnaire administered prior to colonoscopy. Taxonomic structures and metabolic pathway abundances were determined using MetaPhlAn3 and HUMAnN3. We used multivariate association with linear models to identify microbial species and metabolic pathways that were significantly different between asymptomatic diverticulosis and controls, while adjusting for confounders selected a priori including age at colonoscopy, sex, body mass index (BMI), and dietary pattern.

RESULTS: Among 684 individuals undergoing a screening colonoscopy, 284 (42%) had diverticulosis. Gut microbiome composition explained 1.9% variation in the disease status of asymptomatic diverticulosis. We observed no significant differences in the overall diversity of gut microbiome between asymptomatic diverticulosis and controls. However, microbial species Bifidobacterium pseudocatenulatum and Prevotella copri were significantly enriched in controls (q value = 0.19 and 0.14, respectively), whereas Roseburia intestinalis, Dorea sp. CAG:317, and Clostridium sp. CAG: 299 were more abundant in those with diverticulosis (q values = 0.17, 0.24, and 0.10, respectively). We observed that the relationship between BMI and diverticulosis appeared to be limited to carriers of Bifidobacterium pseudocatenulatum and Roseburia intestinalis (Pinteraction = 0.09).

CONCLUSIONS: Our study provides the first large-scale evidence supporting taxonomic and functional shifts of the gut microbiome in individuals with asymptomatic diverticulosis. The suggestive interaction between gut microbiota and BMI on prevalent diverticulosis deserves future investigations.}, } @article {pmid39179660, year = {2024}, author = {Wang, S and Sun, S and Wang, Q and Chen, H and Guo, Y and Cai, M and Yin, Y and Ma, S and Wang, H}, title = {PathoTracker: an online analytical metagenomic platform for Klebsiella pneumoniae feature identification and outbreak alerting.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1038}, pmid = {39179660}, issn = {2399-3642}, support = {32141001//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81991533//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Klebsiella pneumoniae/genetics/isolation & purification ; *Metagenomics/methods ; Humans ; *Disease Outbreaks ; *Klebsiella Infections/microbiology/epidemiology/diagnosis ; *Phylogeny ; China/epidemiology ; Nanopore Sequencing/methods ; Databases, Genetic ; Genome, Bacterial ; }, abstract = {Clinical metagenomics (CMg) Nanopore sequencing can facilitate infectious disease diagnosis. In China, sub-lineages ST11-KL64 and ST11-KL47 Carbapenem-resistant Klebsiella pneumoniae (CRKP) are widely prevalent. We propose PathoTracker, a specially compiled database and arranged method for strain feature identification in CMg samples and CRKP traceability. A database targeting high-prevalence horizontal gene transfer in CRKP strains and a ST11-only database for distinguishing two sub-lineages in China were created. To make the database user-friendly, facilitate immediate downstream strain feature identification from raw Nanopore metagenomic data, and avoid the need for phylogenetic analysis from scratch, we developed data analysis methods. The methods included pre-performed phylogenetic analysis, gene-isolate-cluster index and multilevel pan-genome database and reduced storage space by 10-fold and random-access memory by 52-fold compared with normal methods. PathoTracker can provide accurate and fast strain-level analysis for CMg data after 1 h Nanopore sequencing, allowing early warning of outbreaks. A user-friendly page (http://PathoTracker.pku.edu.cn/) was developed to facilitate online analysis, including strain-level feature, species identifications and phylogenetic analyses. PathoTracker proposed in this study will aid in the downstream analysis of CMg.}, } @article {pmid39179206, year = {2024}, author = {Barone Lumaga, R and Tagliamonte, S and De Rosa, T and Valentino, V and Ercolini, D and Vitaglione, P}, title = {Consumption of a Sourdough-Leavened Croissant Enriched with a Blend of Fibers Influences Fasting Blood Glucose in a Randomized Controlled Trial in Healthy Subjects.}, journal = {The Journal of nutrition}, volume = {154}, number = {10}, pages = {2976-2987}, doi = {10.1016/j.tjnut.2024.08.015}, pmid = {39179206}, issn = {1541-6100}, mesh = {Humans ; *Dietary Fiber/administration & dosage/pharmacology ; Male ; Female ; *Blood Glucose/analysis ; Adult ; *Bread/analysis ; Gastrointestinal Microbiome ; Middle Aged ; Fasting ; Young Adult ; Healthy Volunteers ; Diet ; }, abstract = {BACKGROUND: An incorrect lifestyle, including diet, is responsible for the worldwide dramatic increase in obesity and type 2 diabetes. Increasing dietary fiber consumption may lead to health benefits, and reformulation of bakery products may be a strategy to globally improve the diet.

OBJECTIVES: This study aimed to assess the impact of a 2-wk breakfast consumption with a sourdough-leavened croissant containing a blend of dietary fiber from 10 sources (4.8 g/100 g, croissant enriched with dietary fibers [FIBCRO]), compared with a control croissant (dietary fibers 1.3 g/100 g, CONCRO) on daily energy intake, appetite, metabolic variables, and the gut microbiome.

METHODS: Thirty-two healthy participants were randomly allocated to 2 groups consuming FIBCRO or CONCRO. Participants self-recorded their diet and appetite through 7-d weighted food diaries and visual analog scales every day over the 2 wk. At baseline and after the intervention, fasting blood and urine samples, and fecal samples were collected beside blood pressure, anthropometry, and body composition. Serum glucose, lipids, C-reactive protein, and insulin according to the official methods and serum dipeptidyl peptidase-4 (DPPIV) activity by photometric method were measured. Polyphenols and urolithins in urines were analyzed by Liquid chromatography-tandem mass spectrometry (LC/MS/MS), whereas gut microbiome in feces by shotgun metagenomics.

RESULTS: FIBCRO consumption improved fasting blood glucose compared with CONCRO (mean changes from baseline -2.0 mg/dL in FIBCRO compared with +3.1 mg/dL in CONCRO, P = 0.022), also reducing serum DPPIV activity by 1.7 IU/L (P = 0.01) and increasing urinary excretion of urolithin A-sulfate by 6.9 ng/mg creatinine (P = 0.04) compared with baseline. No further changes in any of the monitored variables or in the gut microbiome were detected.

CONCLUSIONS: Results suggested that a 2-wk consumption of a sourdough croissant claimed as "source of dietary fiber" improved fasting glycemia compared with a conventional sourdough croissant in healthy subjects. The reduced serum DPPIV activity and increased bioavailability of urolithin likely contributed to determine that effect independently from gut microbiome changes. This trial was registered at clinicaltrials.gov as NCT04999280.}, } @article {pmid39179139, year = {2024}, author = {Gao, N and Zhuang, Y and Zheng, Y and Li, Y and Wang, Y and Zhu, S and Fan, M and Tian, W and Jiang, Y and Wang, Y and Cui, M and Suo, C and Zhang, T and Jin, L and Chen, X and Xu, K}, title = {Investigating the link between gut microbiome and bone mineral density: The role of genetic factors.}, journal = {Bone}, volume = {188}, number = {}, pages = {117239}, doi = {10.1016/j.bone.2024.117239}, pmid = {39179139}, issn = {1873-2763}, mesh = {Humans ; *Bone Density/genetics ; Female ; *Gastrointestinal Microbiome/genetics ; Male ; Middle Aged ; Aged ; *Osteoporosis/genetics/microbiology ; Feces/microbiology ; }, abstract = {Osteoporosis is a complex metabolic bone disease that severely undermines the quality of life and overall health of the elderly. While previous studies have established a close relationship between gut microbiome and host bone metabolism, the role of genetic factors has received less scrutiny. This research aims to identify potential taxa associated with various bone mineral density states, incorporating assessments of genetic factors. Fecal microbiome profiles from 605 individuals (334 females and 271 males) aged 55-65 from the Taizhou Imaging Study with osteopenia (n = 270, 170 women) or osteoporosis (n = 94, 85 women) or normal (n = 241, 79 women) were determined using shotgun metagenomic sequencing. The linear discriminant analysis was employed to identify differentially enriched taxa. Utilizing the Kyoto Encyclopedia of Genes and Genomes for annotation, functional pathway analysis was conducted to identify differentially metabolic pathways. Polygenic risk score for osteoporosis was estimated to represent genetic susceptibility to osteoporosis, followed by stratification and interaction analyses. Gut flora diversity did not show significant differences among various bone mineral groups. After multivariable adjustment, certain species, such as Clostridium leptum, Fusicatenibacter saccharivorans and Roseburia hominis, were enriched in osteoporosis patients. Statistically significant interactions between the polygenic risk score and taxa Roseburia faecis, Megasphaera elsdenii were observed (P for interaction = 0.005, 0.018, respectively). Stratified analyses revealed a significantly negative association between Roseburia faecis and bone mineral density in the low-genetic-risk group (β = -0.045, P < 0.05), while Turicimonas muris was positively associated with bone mineral density in the high-genetic-risk group (β = 4.177, P < 0.05) after multivariable adjustments. Functional predictions of the gut microbiome indicated an increase in pathways related to structural proteins in high-genetic-risk patients, while low-genetic-risk patients exhibited enrichment in enzyme-related pathways. This study emphasizes the association between gut microbes and bone mass, offering new insights into the interaction between genetic background and gut microbiome.}, } @article {pmid39179065, year = {2024}, author = {Abedanzadeh, S and Ariaeenejad, S and Karimi, B and Moosavi-Movahedi, AA}, title = {Revolutionizing protein hydrolysis in wastewater: Innovative immobilization of metagenome-derived protease in periodic mesoporous organosilica with imidazolium framework.}, journal = {International journal of biological macromolecules}, volume = {278}, number = {Pt 4}, pages = {134966}, doi = {10.1016/j.ijbiomac.2024.134966}, pmid = {39179065}, issn = {1879-0003}, mesh = {*Enzymes, Immobilized/chemistry/metabolism ; *Wastewater/chemistry ; *Metagenome ; Porosity ; Hydrolysis ; Peptide Hydrolases/chemistry/metabolism ; Enzyme Stability ; Imidazoles/chemistry ; Adsorption ; Organosilicon Compounds/chemistry ; Metal-Organic Frameworks/chemistry ; }, abstract = {This research focused on utilizing periodic mesoporous organosilica with imidazolium framework (PMO-IL), to immobilize a metagenome-sourced protease (PersiProtease1), thereby enhancing its functional efficiency and catalytic effectiveness in processing primary proteins found in tannery wastewater. The successful immobilization of enzyme was confirmed through the use of N2 adsorption-desorption experiment, XRD, FTIR, TEM, FESEM, EDS and elemental analytical techniques. The immobilized enzyme exhibited greater stability in the presence of various metal ions and inhibitors compared to its free form. Furthermore, enzyme binding to PMO-IL nanoparticles (NPs) reduced leaching, evidenced by only 11.41 % of enzyme leakage following a 120-min incubation at 80 °C and 6.99 % after 240 min at 25 °C. Additionally, PersiPro@PMO-IL maintained impressive operational consistency, preserving 62.24 % of its activity over 20 cycles. It also demonstrated notable stability under saline conditions, with an increase of 1.5 times compared to the free enzyme in the presence of 5 M NaCl. The rate of collagen hydrolysis by the immobilized protease was 46.82 % after a 15-minute incubation at 60 °C and marginally decreased to 39.02 % after 20 cycles indicative of sustained efficacy without significant leaching throughout the cycles. These findings underscore the effectiveness of PMO-IL NPs as a viable candidate for treating wastewater containing protein.}, } @article {pmid39178987, year = {2024}, author = {Shukla, V and Singh, S and Verma, S and Verma, S and Rizvi, AA and Abbas, M}, title = {Targeting the microbiome to improve human health with the approach of personalized medicine: Latest aspects and current updates.}, journal = {Clinical nutrition ESPEN}, volume = {63}, number = {}, pages = {813-820}, doi = {10.1016/j.clnesp.2024.08.005}, pmid = {39178987}, issn = {2405-4577}, mesh = {Humans ; *Precision Medicine ; *Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; *Probiotics/therapeutic use ; *Prebiotics ; *Dysbiosis/therapy ; Microbiota ; Synbiotics ; }, abstract = {The intricate ecosystem of microorganisms residing within and on the human body, collectively known as the microbiome, significantly influences human health. Imbalances in this microbiome, referred to as dysbiosis, have been associated with various diseases, prompting the exploration of novel therapeutic approaches. Personalized medicine, Tailors treatments to individual patient characteristics, offers a promising avenue for addressing microbiome-related health issues. This review highlights recent developments in utilizing personalized medicine to target the microbiome, aiming to enhance health outcomes. Noteworthy strategies include fecal microbiota transplantation (FMT), where healthy donor microbes are transferred to patients, showing promise in treating conditions such as recurrent Clostridium difficile infection. Additionally, probiotics, which are live microorganisms similar to beneficial gut inhabitants, and prebiotics, non-digestible compounds promoting microbial growth, are emerging as tools to restore microbiome balance. The integration of these approaches, known as synbiotics, enhances microbial colonization and therapeutic effects. Advances in metagenomics and sequencing technologies provide the means to understand individual microbiome profiles, enabling tailored interventions. This paper aims to present the latest insights in leveraging personalized medicine to address microbiome-related health concerns, envisioning a future where microbiome-based therapies reshape disease management and promote human health.}, } @article {pmid39178591, year = {2024}, author = {Gao, FZ and Hu, LX and Liu, YS and Qiao, LK and Chen, ZY and Su, JQ and He, LY and Bai, H and Zhu, YG and Ying, GG}, title = {Unveiling the overlooked small-sized microbiome in river ecosystems.}, journal = {Water research}, volume = {265}, number = {}, pages = {122302}, doi = {10.1016/j.watres.2024.122302}, pmid = {39178591}, issn = {1879-2448}, mesh = {*Rivers/microbiology ; *Microbiota ; *Ecosystem ; Metagenomics ; Bacteria/genetics ; }, abstract = {Enriching microorganisms using a 0.22-μm pore size is a general pretreatment procedure in river microbiome research. However, it remains unclear the extent to which this method loses microbiome information. Here, we conducted a comparative metagenomics-based study on microbiomes with sizes over 0.22 μm (large-sized) and between 0.22 μm and 0.1 μm (small-sized) in a subtropical river. Although the absolute concentration of small-sized microbiome was about two orders of magnitude lower than that of large-sized microbiome, sequencing only large-sized microbiome resulted in a significant loss of microbiome diversity. Specifically, the microbial community was different between two sizes, and 347 genera were only detected in small-sized microbiome. Small-sized microbiome had much more diverse viral community than large-sized fraction. The viruses had abundant ecological functions and were hosted by 825 species of 169 families, including pathogen-related families. Small-sized microbiome had distinct antimicrobial resistance risks from large-sized microbiome, showing an enrichment of eight antibiotic resistance gene (ARG) types as well as the detection of 140 unique ARG subtypes and five enriched risk rank I ARGs. Draft genomes of five major resistant pathogens having diverse ecological and pollutant-degrading functions were only assembled in small-sized microbiome. These findings provide novel insights into river ecosystems, and highlight the overlooked small-sized microbiome in the environment.}, } @article {pmid39178299, year = {2024}, author = {Han, X and Zhang, L and Zhang, M and Xin, Q and Zhao, Y and Wen, Y and Deng, H and Zhu, J and Dai, Q and Han, M and Yang, T and Lahu, S and Jiang, F and Chen, Z}, title = {Amugulang virus, a novel hantavirus harboured by small rodents in Hulunbuir, China.}, journal = {Emerging microbes & infections}, volume = {13}, number = {1}, pages = {2396893}, pmid = {39178299}, issn = {2222-1751}, mesh = {Animals ; China ; *Orthohantavirus/genetics/classification/isolation & purification ; *Phylogeny ; *Rodentia/virology ; Humans ; Hantavirus Infections/virology/veterinary/epidemiology ; Genome, Viral ; Metagenomics ; Hemorrhagic Fever with Renal Syndrome/virology/veterinary/epidemiology ; }, abstract = {The Hulunbuir region, known for its diverse terrain and rich wildlife, is a hotspot for various natural epidemic diseases. Between 2021 and 2023, we collected 885 wild rodent samples from this area, representing three families, seven genera, and eleven species. Metagenomic analysis identified three complete nucleic acid sequences from the S, M, and L segments of the Hantaviridae family, which were closely related to the Khabarovsk virus. The nucleotide coding sequences for S, M, and L (1392 nt, 3465 nt, and 6491 nt, respectively) exhibited similarities of 82.34%, 81.68%, and 81.94% to known sequences, respectively, while protein-level analysis indicated higher similarities of 94.92%, 94.41%, and 95.87%, respectively. Phylogenetic analysis placed these sequences within the same clade as the Khabarovsk, Puumala, Muju, Hokkaido, Topografov, and Tatenalense viruses, all of which are known to cause febrile diseases in humans. Immunofluorescence detection of nucleic acid-positive rodent kidney samples using sera from patients with hemorrhagic fever and renal syndrome confirmed the presence of viral particles. Based on these findings, we propose that this virus represents a new member of the Hantaviridae family, tentatively named the Amugulang virus, after its primary distribution area.}, } @article {pmid39178288, year = {2024}, author = {Buscaglia, M and Iriarte, JL and Schulz, F and Díez, B}, title = {Adaptation strategies of giant viruses to low-temperature marine ecosystems.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39178288}, issn = {1751-7370}, support = {21190726//ANID/ ; DG_06-20//INACH/ ; RT_04-19//INACH/ ; RT_05-18//INACH/ ; //CONA-SHOA CIMAR 25F/ ; AUB1900003//ANID/ ; ANID-FONDAP 1523A0002//Center for Climate and Resilience Research/ ; ANID-MILENIO-ICN2021_044//Millennium Institute Center for Genome Regulation/ ; ANID/FONDAP/151500003//Center for Dynamic Research on High Latitude Marine Ecosystems/ ; }, mesh = {*Cold Temperature ; *Seawater/virology ; *Ecosystem ; Antarctic Regions ; Arctic Regions ; *Genome, Viral ; *Metagenome ; Giant Viruses/genetics/classification/isolation & purification ; Phylogeny ; Adaptation, Physiological ; }, abstract = {Microbes in marine ecosystems have evolved their gene content to thrive successfully in the cold. Although this process has been reasonably well studied in bacteria and selected eukaryotes, less is known about the impact of cold environments on the genomes of viruses that infect eukaryotes. Here, we analyzed cold adaptations in giant viruses (Nucleocytoviricota and Mirusviricota) from austral marine environments and compared them with their Arctic and temperate counterparts. We recovered giant virus metagenome-assembled genomes (98 Nucleocytoviricota and 12 Mirusviricota MAGs) from 61 newly sequenced metagenomes and metaviromes from sub-Antarctic Patagonian fjords and Antarctic seawater samples. When analyzing our data set alongside Antarctic and Arctic giant viruses MAGs already deposited in the Global Ocean Eukaryotic Viral database, we found that Antarctic and Arctic giant viruses predominantly inhabit sub-10°C environments, featuring a high proportion of unique phylotypes in each ecosystem. In contrast, giant viruses in Patagonian fjords were subject to broader temperature ranges and showed a lower degree of endemicity. However, despite differences in their distribution, giant viruses inhabiting low-temperature marine ecosystems evolved genomic cold-adaptation strategies that led to changes in genetic functions and amino acid frequencies that ultimately affect both gene content and protein structure. Such changes seem to be absent in their mesophilic counterparts. The uniqueness of these cold-adapted marine giant viruses may now be threatened by climate change, leading to a potential reduction in their biodiversity.}, } @article {pmid39178040, year = {2024}, author = {Liu, L and Feng, T and Liu, Q and Liao, M and Liu, B and Li, M}, title = {Characterization of the vaginal microbiota in infertile women with repeated implantation failure.}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {71}, number = {3}, pages = {263-271}, doi = {10.1556/030.2024.02323}, pmid = {39178040}, issn = {1588-2640}, mesh = {Humans ; Female ; *Vagina/microbiology ; Adult ; *Infertility, Female/microbiology ; *Microbiota ; *Bacteria/classification/isolation & purification/genetics ; Embryo Implantation ; Pregnancy ; Fertilization in Vitro ; }, abstract = {Although the relationship between vaginal microorganisms and fertility has been well established, only few studies have investigated vaginal microorganisms in women undergoing in vitro fertilization (IVF). Our aim was to study the differences in vaginal microbiota between infertile women with repeated implantation failure (RIF) and those who achieved clinical pregnancy in their first frozen embryo transfer cycle. We compared the vaginal microbiota of patients with a history of RIF (n = 37) with that of the control group (n = 43). Following DNA extraction, metagenomic sequencing was employed for the analysis of alpha and beta diversities, distinctions in bacterial species, and the functional annotation of microbial genes. Furthermore, disparities between the two groups were revealed. Alpha diversity analysis revealed that the Shannon index was higher in the RIF group (P < 0.05). There were differences in the beta diversity between groups (P = 0.16). At the bacterial family level, the relative abundance of Actinomycetaceae (P = 0.013) and Ruminococcaceae (P = 0.013) were significantly higher in the RIF group. At the genus level, the abundances of Actinomyces (P = 0.028) and Subdoligranulum (P = 0.013) were significantly higher in the RIF group. At the species level, the abundances of Prevotella timonensis (P = 0.028), Lactobacillus jensenii (P = 0.049), and Subdoligranulum (P = 0.013) were significantly higher in the RIF group. Significant differences in family, genus, species, alpha and beta diversity were observed in the vaginal microbiota between groups. Notably, among these findings, the Subdoligranulum genus emerged as the most prominent correlating factor.}, } @article {pmid39177328, year = {2024}, author = {Howe, KL and Zaugg, J and Mason, OU}, title = {Novel, active, and uncultured hydrocarbon-degrading microbes in the ocean.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {9}, pages = {e0122424}, pmid = {39177328}, issn = {1098-5336}, support = {DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; RFP-VI: Research Grants [Consortium for Simulation of Oil-Microbial Interactions in the Ocean (CSOMIO)]//Gulf of Mexico Research Initiative (GoMRI)/ ; }, mesh = {*Hydrocarbons/metabolism ; *Seawater/microbiology ; *Biodegradation, Environmental ; *Bacteria/metabolism/classification/genetics/isolation & purification ; Oceans and Seas ; Metagenome ; Metagenomics ; Petroleum Pollution ; Phylogeny ; }, abstract = {Given the vast quantity of oil and gas input to the marine environment annually, hydrocarbon degradation by marine microorganisms is an essential ecosystem service. Linkages between taxonomy and hydrocarbon degradation capabilities are largely based on cultivation studies, leaving a knowledge gap regarding the intrinsic ability of uncultured marine microbes to degrade hydrocarbons. To address this knowledge gap, metagenomic sequence data from the Deepwater Horizon (DWH) oil spill deep-sea plume was assembled to which metagenomic and metatranscriptomic reads were mapped. Assembly and binning produced new DWH metagenome-assembled genomes that were evaluated along with their close relatives, all of which are from the marine environment (38 total). These analyses revealed globally distributed hydrocarbon-degrading microbes with clade-specific substrate degradation potentials that have not been reported previously. For example, methane oxidation capabilities were identified in all Cycloclasticus. Furthermore, all Bermanella encoded and expressed genes for non-gaseous n-alkane degradation; however, DWH Bermanella encoded alkane hydroxylase, not alkane 1-monooxygenase. All but one previously unrecognized DWH plume member in the SAR324 and UBA11654 have the capacity for aromatic hydrocarbon degradation. In contrast, Colwellia were diverse in the hydrocarbon substrates they could degrade. All clades encoded nutrient acquisition strategies and response to cold temperatures, while sensory and acquisition capabilities were clade specific. These novel insights regarding hydrocarbon degradation by uncultured planktonic microbes provides missing data, allowing for better prediction of the fate of oil and gas when hydrocarbons are input to the ocean, leading to a greater understanding of the ecological consequences to the marine environment.IMPORTANCEMicrobial degradation of hydrocarbons is a critically important process promoting ecosystem health, yet much of what is known about this process is based on physiological experiments with a few hydrocarbon substrates and cultured microbes. Thus, the ability to degrade the diversity of hydrocarbons that comprise oil and gas by microbes in the environment, particularly in the ocean, is not well characterized. Therefore, this study aimed to utilize non-cultivation-based 'omics data to explore novel genomes of uncultured marine microbes involved in degradation of oil and gas. Analyses of newly assembled metagenomic data and previously existing genomes from other marine data sets, with metagenomic and metatranscriptomic read recruitment, revealed globally distributed hydrocarbon-degrading marine microbes with clade-specific substrate degradation potentials that have not been previously reported. This new understanding of oil and gas degradation by uncultured marine microbes suggested that the global ocean harbors a diversity of hydrocarbon-degrading bacteria, which can act as primary agents regulating ecosystem health.}, } @article {pmid39177227, year = {2024}, author = {Deng, Y and Nong, Z and Wei, M and Xu, Y and Luo, Y and Li, X and Zhao, R and Yang, Z and Pan, L}, title = {Characteristics and function of the gut microbiota in patients with IgA nephropathy via metagenomic sequencing technology.}, journal = {Renal failure}, volume = {46}, number = {2}, pages = {2393754}, pmid = {39177227}, issn = {1525-6049}, mesh = {Humans ; *Glomerulonephritis, IGA/microbiology ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Adult ; *Feces/microbiology ; *Metagenomics/methods ; Case-Control Studies ; Middle Aged ; Moraxella/isolation & purification/genetics ; Escherichia coli/isolation & purification/genetics ; Acinetobacter/isolation & purification/genetics ; Metagenome ; Young Adult ; }, abstract = {OBJECTIVE: The aim of this study was to investigate the characteristics and related functional pathways of the gut microbiota in patients with IgA nephropathy (IgAN) through metagenomic sequencing technology.

METHODS: We enrolled individuals with primary IgAN, including patients with normal and abnormal renal function. Additionally, we recruited healthy volunteers as the healthy control group. Stool samples were collected, and species and functional annotation were performed through fecal metagenome sequencing. We employed linear discriminant analysis effect size (LEfSe) analysis to identify significantly different bacterial microbiota and functional pathways. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis was used to annotate microbiota functions, and redundancy analysis (RDA) was performed to analyze the factors affecting the composition and distribution of the gut microbiota.

RESULTS: LEfSe analysis revealed differences in the gut microbiota between IgAN patients and healthy controls. The characteristic microorganisms in the IgAN group were classified as Escherichia coli, with a significantly greater abundance than that in the healthy control group (p < 0.05). The characteristic microorganisms in the IgAN group with abnormal renal function were identified as Enterococcaceae, Moraxella, Moraxella, and Acinetobacter. KEGG functional analysis demonstrated that the functional pathways of the microbiota that differed between IgAN patients and healthy controls were related primarily to bile acid metabolism.

CONCLUSIONS: The status of the gut microbiota is closely associated not only with the onset of IgAN but also with the renal function of IgAN patients. The characteristic gut microbiota may serve as a promising diagnostic biomarker and therapeutic target for IgAN.}, } @article {pmid39176710, year = {2024}, author = {Sy, MA and Prosperi, M and Serajian, M and Boucher, C and Benos, PT and Marini, S}, title = {Prediction of A. Baumannii Amikacin Resistance in Clinical Metagenomics.}, journal = {Studies in health technology and informatics}, volume = {316}, number = {}, pages = {212-213}, doi = {10.3233/SHTI240381}, pmid = {39176710}, issn = {1879-8365}, mesh = {*Amikacin/pharmacology/therapeutic use ; *Metagenomics ; *Acinetobacter baumannii/drug effects/genetics ; Humans ; *Drug Resistance, Bacterial/genetics ; Respiratory Tract Infections/drug therapy/microbiology ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Acinetobacter Infections/drug therapy/microbiology ; }, abstract = {Respiratory tract infections are a serious threat to health, especially in the presence of antimicrobial resistance (AMR). Existing AMR detection methods are limited by slow turnaround times and low accuracy due to the presence of false positives and negatives. In this study, we simulate 1,116 clinical metagenomics samples on both Illumina and Nanopore sequencing from curated, real-world sequencing of A. baumannii respiratory infections and build AI models to predict resistance to amikacin. The best performance is achieved by XGBoost on Illumina sequencing (area under the ROC curve = 0.7993 on 5-fold cross-validation).}, } @article {pmid39176455, year = {2024}, author = {Li, Y and Wang, GQ and Ma, XL and Li, YB}, title = {A rare case of acute meningitis caused by Moraxella osloensis.}, journal = {CNS neuroscience & therapeutics}, volume = {30}, number = {8}, pages = {e70011}, pmid = {39176455}, issn = {1755-5949}, support = {2019QL013//Academic promotion programme of Shandong First Medical University/ ; ZR2023MH127//Nature Science Foundation of Shandong/ ; }, mesh = {Humans ; *Moraxella/isolation & purification/genetics ; *Moraxellaceae Infections/diagnosis/drug therapy/microbiology/complications ; *Meningitis, Bacterial/diagnosis/microbiology/drug therapy ; Male ; Female ; }, abstract = {Meningitis caused by Moraxella osloensis is rare and easily misdiagnosed clinically. Here, we report the first case of meningitis caused by M. osloensis in China by taking advantage of the metagenomic next-generation sequencing technology in cerebrospinal fluid for pathogen screening. In addition, we extend the neurological signs, clinical symptoms, diagnostic methods, and treatment of this rare disease.}, } @article {pmid39176082, year = {2024}, author = {Jiang, C and He, Y and Chen, X and Xia, F and Shi, F and Xu, X and Sun, T and You, K}, title = {X-linked severe combined immunodeficiency complicated by disseminated bacillus Calmette-Guérin disease caused by a novel pathogenic mutation in exon 3 of the IL2RG gene: a case report and literature review.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1453046}, pmid = {39176082}, issn = {1664-3224}, mesh = {Humans ; Infant ; Male ; BCG Vaccine/administration & dosage/adverse effects/immunology ; Exons ; *Interleukin Receptor Common gamma Subunit/genetics ; Mutation ; Mycobacterium bovis/immunology/pathogenicity ; *Tuberculosis/immunology/prevention & control ; *X-Linked Combined Immunodeficiency Diseases/complications/diagnosis/genetics/immunology ; }, abstract = {X-linked severe combined immunodeficiency (X-SCID), caused by mutations in the gamma-chain gene of the interleukin-2 receptor (IL2RG), is a prevalent form of SCID characterized by recurrent and fatal opportunistic infections that occur early in life. The incidence of disseminated bacillus Calmette-Guérin (BCG) disease among children with SCID is much higher than in the general population. Here, we report the case of a 4-month-old male infant who presented with subcutaneous induration, fever, an unhealed BCG vaccination site, and hepatosplenomegaly. Metagenomic next-generation sequencing in blood, and the detection of gastric juice and skin nodule pus all confirmed the infection of Mycobacterium tuberculosis. Lymphocyte subset analysis confirmed the presence of T-B+NK immunodeficiency. Whole-exome and Sanger sequencing revealed a novel microdeletion insertion mutation (c.316_318delinsGTGAT p.Leu106ValfsTer42) in the IL2RG gene, resulting in a rare shift in the amino acid sequence of the coding protein. Consequently, the child was diagnosed with X-SCID caused by a novel mutation in IL2RG, complicated by systemic disseminated BCG disease. Despite receiving systemic anti-infection treatment and four days of hospitalization, the patient died three days after discharge. To the best of our knowledge, this specific IL2RG mutation has not been previously reported. In our systemic review, we outline the efficacy of systemic anti-tuberculosis therapy, hematopoietic stem cell transplantation, and gene therapy in children with SCID and BCG diseases caused by IL2RG gene mutation.}, } @article {pmid39175669, year = {2024}, author = {Zhan, L and Lv, Z and Zhang, Y and Chen, J and Wang, L and Huang, R and Sun, Y and Wu, W}, title = {Use of Metagenomic Next-Generation Sequencing to Identify Pathogens Involved in Central Nervous System Infections.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {3605-3615}, pmid = {39175669}, issn = {1178-6973}, abstract = {PURPOSE: Application of metagenomic next-generation sequencing (mNGS) in identifying nosocomial central nervous system (CNS) infections in critical care units remains understudied.

METHODS: We conducted a retrospective analysis of microbiological results through both mNGS and routine examination of cerebrospinal fluid (CSF) samples from patients with nosocomial CNS infections. The aim of this study was to assess the clinical diagnostic effect of nosocomial mNGS in this population.

RESULTS: The study included 26 cases of nosocomial CNS infections in total. A total of 69.2% (18/26) of the samples tested positive for mNGS, which is substantially greater than the 7.7% (2/26; p<0.05) detected through conventional techniques. Administration of antibiotics before culture is most likely the cause of the low CSF culture rate. Twenty-five pathogenic strains that were missed by standard testing. Three pathogens that were consistent with the mNGS results were positive by routine tests. Eight cases were negative by mNGS due to low pathogen CSF titres. Compared to traditional testing, mNGS demonstrated 100% sensitivity and 33.3% specificity in diagnosing CNS infections. The thirty-day mortality rate was 26.9% (7/26).

CONCLUSION: Routine microbiologic testing frequently falls short of detecting all neuroinvasive pathogens. Our research suggests that mNGS offers an alternative means of detecting nosocomial CNS infections. By applying mNGS to CSF samples from patients with meningitis or encephalitis, we were able to improve the ability to diagnose nosocomial neurologic infections.}, } @article {pmid39175323, year = {2024}, author = {Zhu, J and Sun, J and Ma, B and Zhang, C and Cao, X and Zheng, S and Chen, Z and Zhang, C and Shen, J and Xia, T}, title = {[Study on effectiveness of antibiotics guided by metagenomic next-generation sequencing to control infection after total knee arthroplasty].}, journal = {Zhongguo xiu fu chong jian wai ke za zhi = Zhongguo xiufu chongjian waike zazhi = Chinese journal of reparative and reconstructive surgery}, volume = {38}, number = {8}, pages = {995-1000}, pmid = {39175323}, issn = {1002-1892}, mesh = {Humans ; *Arthroplasty, Replacement, Knee/adverse effects ; Male ; Aged ; Female ; Middle Aged ; *Prosthesis-Related Infections/microbiology/diagnosis ; *Anti-Bacterial Agents/therapeutic use ; Aged, 80 and over ; Adult ; *High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; C-Reactive Protein/analysis ; Knee Prosthesis/adverse effects ; }, abstract = {OBJECTIVE: To explore the clinical value of metagenomic next-generation sequencing (mNGS) in diagnosis and treatment of periprosthetic joint infection (PJI) after total knee arthroplasty (TKA).

METHODS: Between April 2020 and March 2023, 10 patients with PJI after TKA were admitted. There were 3 males and 7 females with an average age of 69.9 years (range, 44-83 years). Infection occurred after 8-35 months of TKA (mean, 19.5 months). The duration of infection ranged from 16 to 128 days (mean, 37 days). The preoperative erythrocyte sedimentation rate (ESR) was 15-85 mm/1 h (mean, 50.2 mm/1 h). The C reactive protein (CRP) was 4.4-410.0 mg/L (mean, 192.8 mg/L). The white blood cell counting was (3.4-23.8)×10 [9]/L (mean, 12.3×10 [9]/L). The absolute value of neutrophils was (1.1-22.5)×10 [9]/L (mean, 9.2×10 [9]/L). After admission, the joint fluid was extracted for bacterial culture method and mNGS test, and sensitive antibiotics were chosen according to the results of the test, and the infection was controlled in combination with surgery.

RESULTS: Seven cases (70%) were detected as positive by bacterial culture method, and 7 types of pathogenic bacteria were detected; the most common pathogenic bacterium was Streptococcus lactis arrestans. Ten cases (100%) were detected as positive by mNGS test, and 11 types of pathogenic bacteria were detected; the most common pathogenic bacterium was Propionibacterium acnes. The difference in the positive rate between the two methods was significant (P=0.211). Three of the 7 patients who were positive for both the bacterial culture method and the mNGS test had the same results for the type of pathogenic bacteria, with a compliance rate of 42.86% (3/7). The testing time (from sample delivery to results) was (4.95±2.14) days for bacterial culture method and (1.60±0.52) days for mNGS test, and the difference was significant (t=4.810, P<0.001). The corresponding sensitive antibiotic treatment was chosen according to the results of bacterial culture method and mNGS test. At 3 days after the one-stage operation, the CRP was 6.8-48.2 mg/L (mean, 23.6 mg/L); the ESR was 17-53 mm/1 h (mean, 35.5 mm/1 h); the white blood cell counting was (4.5-8.1)×10 [9]/L (mean, 6.1×10 [9]/L); the absolute value of neutrophils was (2.3-5.7)×10 [9]/L (mean, 4.1×10 [9]/L). All patients were followed up 12-39 months (mean, 23.5 months). One case had recurrence of infection at 6 months after operation, and the remaining 9 cases showed no signs of infection, with an infection control rate of 90%.

CONCLUSION: Compared with bacterial culture method, mNGS test can more rapidly and accurately detect pathogenic bacteria for PJI after TKA, which is important for guiding antibiotics combined with surgical treatment of PJI.}, } @article {pmid39175129, year = {2025}, author = {Hotchkiss, MZ and Forrest, JRK and Poulain, AJ}, title = {Changes in bumblebee queen gut microbiotas during and after overwintering diapause.}, journal = {Insect molecular biology}, volume = {34}, number = {1}, pages = {136-150}, pmid = {39175129}, issn = {1365-2583}, support = {//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Animals ; Bees/microbiology/physiology ; *Gastrointestinal Microbiome ; *Diapause, Insect ; Female ; Seasons ; }, abstract = {Bumblebees are key pollinators with gut microbiotas that support host health. After bumblebee queens undergo winter diapause, which occurs before spring colony establishment, their gut microbiotas are disturbed, but little is known about community dynamics during diapause itself. Queen gut microbiotas also help seed worker microbiotas, so it is important that they recover post-diapause to a typical community structure, a process that may be impeded by pesticide exposure. We examined how bumblebee queen gut microbiota community structure and metabolic potential shift during and after winter diapause, and whether post-diapause recovery is affected by pesticide exposure. To do so, we placed commercial Bombus impatiens queens into diapause, euthanizing them at 0, 2 and 4 months of diapause. Additionally, we allowed some queens to recover from diapause for 1 week before euthanasia, exposing half to the common herbicide glyphosate. Using whole-community, shotgun metagenomic sequencing, we found that core bee gut phylotypes dominated queen gut microbiotas before, during and after diapause, but that two phylotypes, Schmidhempelia and Snodgrassella, ceased to be detected during late diapause and recovery. Despite fluctuations in taxonomic community structure, metabolic potential remained constant through diapause and recovery. Also, glyphosate exposure did not affect post-diapause microbiota recovery. However, metagenomic assembly quality and our ability to detect microbial taxa and metabolic pathways declined alongside microbial abundance, which was substantially reduced during diapause. Our study offers new insights into how bumblebee queen gut microbiotas change taxonomically and functionally during a key life stage and provides guidance for future microbiota studies in diapausing bumblebees.}, } @article {pmid39175061, year = {2024}, author = {Carrascosa-Sàez, M and Buigues, J and Viñals, A and Andreu-Moreno, I and Martínez-Recio, R and Soriano-Tordera, C and Monrós, JS and Cuevas, JM and Sanjuán, R}, title = {Genetic diversity and cross-species transmissibility of bat-associated picornaviruses from Spain.}, journal = {Virology journal}, volume = {21}, number = {1}, pages = {193}, pmid = {39175061}, issn = {1743-422X}, support = {PRE2021-099824//Ministerio de Ciencia e Innovación/ ; PID2020-118602RB-I00//Ministerio de Ciencia e Innovación/ ; CIAICO/2022/110//Conselleria de Educación, Universidades y Empleo, Generalitat Valenciana, Spain/ ; }, mesh = {*Chiroptera/virology ; Animals ; Spain ; *Picornaviridae/genetics/classification/isolation & purification ; *Genetic Variation ; *Genome, Viral ; *Phylogeny ; *Feces/virology ; *Picornaviridae Infections/transmission/virology/veterinary ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Humans ; Zoonoses/virology/transmission ; }, abstract = {BACKGROUND: Emerging zoonotic diseases arise from cross-species transmission events between wild or domesticated animals and humans, with bats being one of the major reservoirs of zoonotic viruses. Viral metagenomics has led to the discovery of many viruses, but efforts have mainly been focused on some areas of the world and on certain viral families.

METHODS: We set out to describe full-length genomes of new picorna-like viruses by collecting feces from hundreds of bats captured in different regions of Spain. Viral sequences were obtained by high-throughput Illumina sequencing and analyzed phylogenetically to classify them in the context of known viruses. Linear discriminant analysis (LDA) was performed to infer likely hosts based on genome composition.

RESULTS: We found five complete or nearly complete genomes belonging to the family Picornaviridae, including a new species of the subfamily Ensavirinae. LDA suggested that these were true vertebrate viruses, rather than viruses from the bat diet. Some of these viruses were related to picornaviruses previously found in other bat species from distant geographical regions. We also found a calhevirus genome that most likely belongs to a proposed new family within the order Picornavirales, and for which genome composition analysis suggested a plant host.

CONCLUSIONS: Our findings describe new picorna-like viral species and variants circulating in the Iberian Peninsula, illustrate the wide geographical distribution and interspecies transmissibility of picornaviruses, and suggest new hosts for calheviruses.}, } @article {pmid39175056, year = {2024}, author = {Sbardellati, DL and Vannette, RL}, title = {Targeted viromes and total metagenomes capture distinct components of bee gut phage communities.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {155}, pmid = {39175056}, issn = {2049-2618}, support = {2023-67011-40501//U.S. Department of Agriculture/ ; 1929516//National Science Foundation/ ; }, mesh = {Bees/virology/microbiology ; Animals ; *Bacteriophages/genetics/isolation & purification/classification ; *Virome ; *Metagenome ; Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; Gastrointestinal Tract/microbiology/virology ; }, abstract = {BACKGROUND: Despite being among the most abundant biological entities on earth, bacteriophage (phage) remain an understudied component of host-associated systems. One limitation to studying host-associated phage is the lack of consensus on methods for sampling phage communities. Here, we compare paired total metagenomes and viral size fraction metagenomes (viromes) as methods for investigating the dsDNA viral communities associated with the GI tract of two bee species: the European honey bee Apis mellifera and the eastern bumble bee Bombus impatiens.

RESULTS: We find that viromes successfully enriched for phage, thereby increasing phage recovery, but only in honey bees. In contrast, for bumble bees, total metagenomes recovered greater phage diversity. Across both bee species, viromes better sampled low occupancy phage, while total metagenomes were biased towards sampling temperate phage. Additionally, many of the phage captured by total metagenomes were absent altogether from viromes. Comparing between bees, we show that phage communities in commercially reared bumble bees are significantly reduced in diversity compared to honey bees, likely reflecting differences in bacterial titer and diversity. In a broader context, these results highlight the complementary nature of total metagenomes and targeted viromes, especially when applied to host-associated environments.

CONCLUSIONS: Overall, we suggest that studies interested in assessing total communities of host-associated phage should consider using both approaches. However, given the constraints of virome sampling, total metagenomes may serve to sample phage communities with the understanding that they will preferentially sample dominant and temperate phage. Video Abstract.}, } @article {pmid39174918, year = {2024}, author = {Wang, D and Xue, D and Chen, X and Wu, X and Gao, W and Liang, X and Yuan, W and Wang, H and Wang, Q}, title = {Mycobacterium marseillense bloodstream infection combined with skin fungal infection: a case report and literature review.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {853}, pmid = {39174918}, issn = {1471-2334}, mesh = {Humans ; Male ; Middle Aged ; *Mycobacterium Infections, Nontuberculous/microbiology/drug therapy ; Dermatomycoses/microbiology/drug therapy ; Kidney Transplantation/adverse effects ; Immunocompromised Host ; Anti-Bacterial Agents/therapeutic use ; Nontuberculous Mycobacteria/isolation & purification/drug effects ; Bacteremia/microbiology/drug therapy ; Mycobacterium/isolation & purification/drug effects ; Skin/microbiology/pathology ; }, abstract = {BACKGROUND: Non-tuberculous mycobacteria (NTM) are present widely in the natural environment and can invade the human body through the respiratory tract, gastrointestinal tract, and skin. Immunocompromised patients are particularly prone to infection, which primarily affects multiple organs, including the lungs, lymph nodes, and skin. However, cases of NTM bloodstream infections are rare. Here, we report a rare case of Mycobacterium marseillense bloodstream infection with concurrent skin fungal infection in a patient after kidney transplantation. Related literature was reviewed to enhance the understanding of this rare condition.

CASE PRESENTATION: A 58-year-old male with a history of long-term steroid and immunosuppressant use after kidney transplantation presented with limb swelling that worsened over the past two months. Physical examination revealed redness and swelling of the skin in all four limbs, with a non-healing wound on the lower left limb. Skin tissue analysis by metagenomic next-generation sequencing (mNGS) and fungal culture indicated infection with Trichophyton rubrum. Blood culture results suggested infection with Mycobacterium marseillense. After receiving anti-NTM treatment, the patient's symptoms significantly improved, and he is currently undergoing treatment.

CONCLUSION: Mycobacterium marseillense is a NTM. Gram staining suffered from misdetection, and the acid-fast staining result was positive. This bacterium was identified by mass spectrometry and mNGS analyses. Antimicrobial susceptibility tests for NTM were performed using the broth microdilution method. The results of the susceptibility test showed that Mycobacterium marseillense was sensitive to clarithromycin, an intermediary between moxifloxacin and linezolid. Bacterial clearance requires a combination of drugs and an adequate course of treatment. NTM bloodstream infections are relatively rare, and early identification and proactive intervention are key to their successful management.}, } @article {pmid39174663, year = {2024}, author = {Jafari, M and Moghimi, H and Tirandaz, H and Ebrahim-Habibi, MB}, title = {Corrosion behavior of predominant Halodesulfovibrio in a marine SRB consortium and its mitigation using ZnO nanoparticles.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {19545}, pmid = {39174663}, issn = {2045-2322}, mesh = {Corrosion ; *Zinc Oxide/chemistry/pharmacology ; *Biofilms/drug effects ; *Bioreactors/microbiology ; Steel/chemistry ; Nanoparticles/chemistry ; Microbial Consortia/drug effects ; }, abstract = {Formation of Sulfate Reducing Bacteria (SRB) biofilm accelerates microbiologically influenced corrosion (MIC). The aim of this study was to investigate both the corrosivity of a marine SRB consortium on carbon steel coupons and its mitigation in the presence of ZnO. Metagenomics analysis revealed that Halodesulfovibrio (78.9%) was predominant and could be related to MIC. The analysis also showed a remarkable shift from a highly corrosive SRB consortium in the control bioreactors to a far less corrosive consortium when ZnO was added to the bioreactors. Further results indicated that the corrosion rate of the SRB consortium was 8.17 mpy on the carbon steel coupons. In the ZnO-treated bioreactors, the count of SRB and MIC in the carbon steel coupons simultaneously reduced. Moreover, Confocal Laser Scanning Microscopy and profilometry analysis determined that ZnO could significantly decrease the amount of biofilm and the corrosion rate. Electrochemical experiments revealed higher corrosion current density (icorr) and lower charge transfer resistance (Rct) in the control bioreactors relative to the ZnO-treated bioreactors. We introduce Halodesulfovibrio as a potentially important corrosive genus in a marine SRB consortium. Additionally, ZnO could be considered a proper candidate to control the corrosion induced by Halodesulfovibrio.}, } @article {pmid39173973, year = {2024}, author = {Oliver, A and Alkan, Z and Stephensen, CB and Newman, JW and Kable, ME and Lemay, DG}, title = {Diet, Microbiome, and Inflammation Predictors of Fecal and Plasma Short-Chain Fatty Acids in Humans.}, journal = {The Journal of nutrition}, volume = {154}, number = {11}, pages = {3298-3311}, pmid = {39173973}, issn = {1541-6100}, mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; Young Adult ; Biomarkers/blood ; Cohort Studies ; *Diet ; *Fatty Acids, Volatile/metabolism/blood ; *Feces/microbiology/chemistry ; *Gastrointestinal Microbiome ; *Inflammation/blood ; }, abstract = {BACKGROUND: Gut microbes produce short-chain fatty acids (SCFAs), which are associated with broad health benefits. However, it is not fully known how diet and/or the gut microbiome could be modulated to improve SCFA production.

OBJECTIVES: The objective of this study was to identify dietary, inflammatory, and/or microbiome predictors of SCFAs in a cohort of healthy adults.

METHODS: SCFAs were measured in fecal and plasma samples from 359 healthy adults in the United States Department of Agriculture Nutritional Phenotyping Study. Habitual and recent diet was assessed using a Food Frequency Questionnaire and Automated Self-Administered 24-h Dietary Assesment Tool dietary recalls. Markers of systemic and gut inflammation were measured in fecal and plasma samples. The gut microbiome was assessed using shotgun metagenomics. Using statistics and machine learning, we determined how the abundance and composition of SCFAs varied with measures of diet, inflammation, and the gut microbiome.

RESULTS: We show that fecal pH may be a good proxy for fecal SCFA abundance. A higher Healthy Eating Index for a habitual diet was associated with a compositional increase in fecal butyrate relative to acetate and propionate. SCFAs were associated with markers of subclinical gastrointestinal (GI) inflammation. Fecal SCFA abundance was inversely related to plasma lipopolysaccharide-binding protein. When we analyzed hierarchically organized diet and microbiome data with taxonomy-aware algorithms, we observed that diet and microbiome features were far more predictive of fecal SCFA abundances compared to plasma SCFA abundances. The top diet and microbiome predictors of fecal butyrate included potatoes and the thiamine biosynthesis pathway, respectively.

CONCLUSIONS: These results suggest that resistant starch in the form of potatoes and microbially produced thiamine provide a substrate and essential cofactor, respectively, for butyrate synthesis. Thiamine may be a rate-limiting nutrient for butyrate production in adults. Overall, these findings illustrate the complex biology underpinning SCFA production in the gut. This trial was registered at clinicaltrials.gov as NCT02367287.}, } @article {pmid39173422, year = {2024}, author = {Silva, JM and Almeida, JR}, title = {Enhancing metagenomic classification with compression-based features.}, journal = {Artificial intelligence in medicine}, volume = {156}, number = {}, pages = {102948}, doi = {10.1016/j.artmed.2024.102948}, pmid = {39173422}, issn = {1873-2860}, mesh = {*Metagenomics/methods ; *Data Compression/methods ; *Algorithms ; High-Throughput Nucleotide Sequencing/methods ; Humans ; }, abstract = {Metagenomics is a rapidly expanding field that uses next-generation sequencing technology to analyze the genetic makeup of environmental samples. However, accurately identifying the organisms in a metagenomic sample can be complex, and traditional reference-based methods may need to be more effective in some instances. In this study, we present a novel approach for metagenomic identification, using data compressors as a feature for taxonomic classification. By evaluating a comprehensive set of compressors, including both general-purpose and genomic-specific, we demonstrate the effectiveness of this method in accurately identifying organisms in metagenomic samples. The results indicate that using features from multiple compressors can help identify taxonomy. An overall accuracy of 95% was achieved using this method using an imbalanced dataset with classes with limited samples. The study also showed that the correlation between compression and classification is insignificant, highlighting the need for a multi-faceted approach to metagenomic identification. This approach offers a significant advancement in the field of metagenomics, providing a reference-less method for taxonomic identification that is both effective and efficient while revealing insights into the statistical and algorithmic nature of genomic data. The code to validate this study is publicly available at https://github.com/ieeta-pt/xgTaxonomy.}, } @article {pmid39173390, year = {2024}, author = {Pan, P and Gu, Y and Li, T and Zhou, NY and Xu, Y}, title = {Deciphering the triclosan degradation mechanism in Sphingomonas sp. strain YL-JM2C: Implications for wastewater treatment and marine resources.}, journal = {Journal of hazardous materials}, volume = {478}, number = {}, pages = {135511}, doi = {10.1016/j.jhazmat.2024.135511}, pmid = {39173390}, issn = {1873-3336}, mesh = {*Triclosan/metabolism ; *Sphingomonas/metabolism/genetics ; *Biodegradation, Environmental ; *Wastewater ; Water Pollutants, Chemical/metabolism ; Molecular Docking Simulation ; Dioxygenases/metabolism/genetics ; Bacterial Proteins/metabolism/genetics ; Anti-Infective Agents, Local/metabolism ; Waste Disposal, Fluid/methods ; }, abstract = {Triclosan (TCS), an antimicrobial agent extensively incorporated into pharmaceuticals and personal care products, poses significant environmental risks because of its persistence and ecotoxicity. So far, a few microorganisms were suggested to degrade TCS, but the microbial degradation mechanism remains elusive. Here, a two-component angular dioxygenase (TcsAaAb) responsible for the initial TCS degradation was characterized in Sphingomonas sp. strain YL-JM2C. Whole-cell biotransformation and crude enzyme assays demonstrated that TcsAaAb catalyzed the conversion of TCS to 4-chlorocatechol and 3,5-dichlorocatechol rather than the commonly suggested product 2,4-dichlorophenol. Then two intermediates were catabolized by tcsCDEF cluster via an ortho-cleavage pathway. Critical residues (N262, F279, and F391) for substrate binding were identified via molecular docking and mutagenesis. Further, TcsAaAb showed activity toward methyl triclosan and nitrofen, suggesting its versatile potential for bioremediation. In addition, TCS-degrading genes were also present in diverse bacterial genomes in wastewater, ocean and soil, and a relatively high gene abundance was observed in marine metagenomes, revealing the transformation fate of TCS in environments and the microbial potential in pollutant removal. These findings extend the understanding of the microbe-mediated TCS degradation and contribute to the mining of TCS-degrading strains and enzymes, as well as their application in the bioremediation of contaminated environments.}, } @article {pmid39173381, year = {2024}, author = {Hu, S and Xu, C and Lu, P and Wu, M and Chen, A and Zhang, M and Xie, Y and Han, G}, title = {Widespread distribution of the DyP-carrying bacteria involved in the aflatoxin B1 biotransformation in Proteobacteria and Actinobacteria.}, journal = {Journal of hazardous materials}, volume = {478}, number = {}, pages = {135493}, doi = {10.1016/j.jhazmat.2024.135493}, pmid = {39173381}, issn = {1873-3336}, mesh = {*Aflatoxin B1/metabolism ; *Actinobacteria/metabolism/genetics ; *Proteobacteria/metabolism/genetics ; *Biotransformation ; Paracoccus/metabolism/genetics ; Biodegradation, Environmental ; }, abstract = {Aflatoxin is one of the most notorious mycotoxins, of which aflatoxin B1 (AFB1) is the most harmful and prevalent. Microbes play a crucial role in the environment for the biotransformation of AFB1. In this study, a bacterial consortium, HS-1, capable of degrading and detoxifying AFB1 was obtained. Here, we combined multi-omics and cultivation-based techniques to elucidate AFB1 biotransformation by consortium HS-1. Co-occurrence network analysis revealed that the key taxa responsible for AFB1 biotransformation in consortium HS-1 mainly belonged to the phyla Proteobacteria and Actinobacteria. Moreover, metagenomic analysis showed that diverse microorganisms, mainly belonging to the phyla Proteobacteria and Actinobacteria, carry key functional enzymes involved in the initial step of AFB1 biotransformation. Metatranscriptomic analysis indicated that Paracoccus-related bacteria were the most active in consortium HS-1. A novel bacterium, Paracoccus sp. strain XF-30, isolated from consortium HS-1, contains a novel dye-decolorization peroxidase (DyP) enzyme capable of effectively degrading AFB1. Taxonomic profiling by bioinformatics revealed that DyP, which is involved in the initial biotransformation of AFB1, is widely distributed in metagenomes from various environments, primarily taxonomically affiliated with Proteobacteria and Actinobacteria. The in-depth examination of AFB1 biotransformation in consortium HS-1 will help us to explore these crucial bioresources more sensibly and efficiently.}, } @article {pmid39173358, year = {2024}, author = {Chen, X and Duan, F and Yu, X and Xie, Y and Wang, Z and El-Baz, A and Ni, BJ and Ni, SQ}, title = {One-stage anammox and thiocyanate-driven autotrophic denitrification for simultaneous removal of thiocyanate and nitrogen: Pathway and mechanism.}, journal = {Water research}, volume = {265}, number = {}, pages = {122268}, doi = {10.1016/j.watres.2024.122268}, pmid = {39173358}, issn = {1879-2448}, mesh = {*Denitrification ; *Thiocyanates/metabolism ; *Nitrogen/metabolism ; *Autotrophic Processes ; Bioreactors ; Wastewater/chemistry ; Waste Disposal, Fluid/methods ; Sewage ; Oxidation-Reduction ; Anaerobiosis ; }, abstract = {The coupled process of anammox and reduced-sulfur driven autotrophic denitrification can simultaneously remove nitrogen and sulfur from wastewater, while minimizing energy consumption and sludge production. However, the research on the coupled process for removing naturally toxic thiocyanate (SCN[-]) is limited. This work successfully established and operated a one-stage coupled system by co-cultivating mature anammox and SCN[-]-driven autotrophic denitrification sludge in a single reactor. In this one-stage coupled system, the average total nitrogen removal efficiency was 89.68±3.33 %, surpassing that of solo anammox (81.80±2.10 %) and SCN[-]-driven autotrophic denitrification (85.20±1.54 %). Moreover, the average removal efficiency of SCN[-] reached 99.50±3.64 %, exceeding that of solo SCN[-]-driven autotrophic denitrification (98.80±0.65 %). The results of the [15]N stable isotope tracer labeling experiment revealed the respective reaction rates of anammox and denitrification as 106.38±10.37 μmol/L/h and 69.07±8.07 μmol/L/h. By analyzing metagenomic sequencing data, Thiobacillus_denitrificans was identified as the primary contributor to SCN[-] degradation in this coupled system. Furthermore, based on the comprehensive analysis of nitrogen and sulfur metabolic pathways, as well as the genes associated with SCN[-] degradation, it can be inferred that the cyanate (CNO) pathway was responsible for SCN[-] degradation. This work provided a deeper insight into coupling anammox with SCN[-]-driven autotrophic denitrification in a one-stage coupled system, thereby contributing to the development of an effective approach for wastewater treatment involving both SCN[-] and nitrogen.}, } @article {pmid39173234, year = {2024}, author = {Jia, P and Liang, JL and Lu, JL and Zhong, SJ and Xiong, T and Feng, SW and Wang, Y and Wu, ZH and Yi, XZ and Gao, SM and Zheng, J and Wen, P and Li, F and Li, Y and Liao, B and Shu, WS and Li, JT}, title = {Soil keystone viruses are regulators of ecosystem multifunctionality.}, journal = {Environment international}, volume = {191}, number = {}, pages = {108964}, doi = {10.1016/j.envint.2024.108964}, pmid = {39173234}, issn = {1873-6750}, mesh = {*Soil Microbiology ; China ; *Ecosystem ; *Viruses/genetics ; Soil/chemistry ; Microbiota ; Fungi/genetics ; Forests ; Metagenomics ; Biodiversity ; }, abstract = {Ecosystem multifunctionality reflects the capacity of ecosystems to simultaneously maintain multiple functions which are essential bases for human sustainable development. Whereas viruses are a major component of the soil microbiome that drive ecosystem functions across biomes, the relationships between soil viral diversity and ecosystem multifunctionality remain under-studied. To address this critical knowledge gap, we employed a combination of amplicon and metagenomic sequencing to assess prokaryotic, fungal and viral diversity, and to link viruses to putative hosts. We described the features of viruses and their potential hosts in 154 soil samples from 29 farmlands and 25 forests distributed across China. Although 4,460 and 5,207 viral populations (vOTUs) were found in the farmlands and forests respectively, the diversity of specific vOTUs rather than overall soil viral diversity was positively correlated with ecosystem multifunctionality in both ecosystem types. Furthermore, the diversity of these keystone vOTUs, despite being 10-100 times lower than prokaryotic or fungal diversity, was a better predictor of ecosystem multifunctionality and more strongly associated with the relative abundances of prokaryotic genes related to soil nutrient cycling. Gemmatimonadota and Actinobacteria dominated the host community of soil keystone viruses in the farmlands and forests respectively, but were either absent or showed a significantly lower relative abundance in that of soil non-keystone viruses. These findings provide novel insights into the regulators of ecosystem multifunctionality and have important implications for the management of ecosystem functioning.}, } @article {pmid39172545, year = {2024}, author = {Chen, G and Jiang, J and Sun, Y}, title = {RNAVirHost: a machine learning-based method for predicting hosts of RNA viruses through viral genomes.}, journal = {GigaScience}, volume = {13}, number = {}, pages = {}, pmid = {39172545}, issn = {2047-217X}, support = {//Research Grants Council, University Grants Committee/ ; }, mesh = {*Machine Learning ; *Genome, Viral ; *RNA Viruses/genetics/classification ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; Software ; }, abstract = {BACKGROUND: The high-throughput sequencing technologies have revolutionized the identification of novel RNA viruses. Given that viruses are infectious agents, identifying hosts of these new viruses carries significant implications for public health and provides valuable insights into the dynamics of the microbiome. However, determining the hosts of these newly discovered viruses is not always straightforward, especially in the case of viruses detected in environmental samples. Even for host-associated samples, it is not always correct to assign the sample origin as the host of the identified viruses. The process of assigning hosts to RNA viruses remains challenging due to their high mutation rates and vast diversity.

RESULTS: In this study, we introduce RNAVirHost, a machine learning-based tool that predicts the hosts of RNA viruses solely based on viral genomes. RNAVirHost is a hierarchical classification framework that predicts hosts at different taxonomic levels. We demonstrate the superior accuracy of RNAVirHost in predicting hosts of RNA viruses through comprehensive comparisons with various state-of-the-art techniques. When applying to viruses from novel genera, RNAVirHost achieved the highest accuracy of 84.3%, outperforming the alignment-based strategy by 12.1%.

CONCLUSIONS: The application of machine learning models has proven beneficial in predicting hosts of RNA viruses. By integrating genomic traits and sequence homologies, RNAVirHost provides a cost-effective and efficient strategy for host prediction. We believe that RNAVirHost can greatly assist in RNA virus analyses and contribute to pandemic surveillance.}, } @article {pmid39171911, year = {2024}, author = {Quan, Q and Liu, J and Xia, X and Zhang, S and Ke, Z and Wang, M and Tan, Y}, title = {Cold seep nitrogen fixation and its potential relationship with sulfur cycling.}, journal = {Microbiology spectrum}, volume = {12}, number = {10}, pages = {e0053624}, pmid = {39171911}, issn = {2165-0497}, support = {SCSIO202205//Development Fund of the South China Sea Institute of Oceanology of the Chinese Academy of Sciences/ ; GML2019ZD0401//the Key Special Project for Introduced Talents Team of Southern Marine Science and Engineering Guangdong Laboratory(Guangzhou)/ ; //Guangdong Science and Technology Plan Project (Observation of Tropical Marine Environment in Yuexi)/ ; 42090042//National Natural Science Foundation of China/ ; }, mesh = {*Nitrogen Fixation ; *Sulfur/metabolism ; *Nitrogen/metabolism ; *Seawater/microbiology/chemistry ; Oxidation-Reduction ; Geologic Sediments/microbiology ; Bacteria/metabolism/genetics/classification ; Phosphorus/metabolism ; Carbon/metabolism ; }, abstract = {UNLABELLED: Dinitrogen (N2) fixation is a crucial source of bioavailable nitrogen in carbon-dominated cold seep systems. Previous studies have shown that diazotrophy is not necessarily dependent on sulfate-dependent anaerobic oxidation of methane for energy, and diverse catabolism can fuel the high-energy-demanding process in sediments. However, it remains unclear whether diazotroph can obtain energy by sulfur oxidation in sulfur-rich cold seep water column. Here, field investigations and in situ experiments were conducted in Haima cold seep to examine the effects of diverse sources of dissolved organic matter (DOM) on N2 fixation, specifically containing sulfur, carbon, nitrogen, and phosphorus. We found that active N2 fixation occurred in the water column above the Haima cold seep, with the Dechloromonas genus dominating the diazotroph community as revealed by nifH gene using high-throughput sequencing. In situ experiments showed an increased rate of N2 fixation (1.15- to 12.70-fold compared to that in control group) and a greater relative abundance of the Dechloromonas genus following enrichment with sulfur-containing organic matter. Furthermore, metagenomic assembly and binning revealed that Dechloromonas sp. carried genes related to N2 fixation (nifDHK) and sulfur compound oxidation (fccAB and soxABCXYZ), implying that the genus potentially serves as a multifunctional mediator for N2 fixation and sulfur cycling. Our results provide new insights regarding potential coupling mechanism associated with sulfur-driven N2 fixation in methane- and sulfide-rich environments.

IMPORTANCE: N2 fixation is an important source of biologically available in carbon-dominated cold seep systems as little nitrogen is released by hydrocarbon seepage, thereby promoting biological productivity and the degradation of non-nitrogenous organic matter. Cold seeps are rich in diverse sources of dissolved organic matter (DOM) derived from the sinking of photosynthetic products in euphotic layer and the release of chemosynthesis products on the seafloor. However, it remains unclear whether N2 fixation is coupled to the metabolic processes of DOM, as determined by e.g., carbon, nitrogen, phosphorus, and sulfur content, for energy acquisition in sulfur-rich cold seeps. In this study, diazotroph community structure and its response to DOM compositions were revealed. Moreover, the metagenomics analysis suggested that Dechloromonas genus plays a dominant role in potential coupling N2 fixation and sulfur oxidation. Our study highlighted that sulfur oxidation in deep-sea cold seeps may serve as an energy source to drive N2 fixation.}, } @article {pmid39171900, year = {2024}, author = {, }, title = {Expression of Concern for Huang et al., "Long-Read Metagenomics of Marine Microbes Reveals Diversely Expressed Secondary Metabolites".}, journal = {Microbiology spectrum}, volume = {12}, number = {10}, pages = {e0185124}, doi = {10.1128/spectrum.01851-24}, pmid = {39171900}, issn = {2165-0497}, mesh = {*Metagenomics/methods ; *Secondary Metabolism/genetics ; Aquatic Organisms/genetics ; Bacteria/genetics/metabolism/classification ; Seawater/microbiology ; }, } @article {pmid39170984, year = {2024}, author = {Rajendhran, J and Muthuirulan, P and Lakshmanan, AP and Sundararaju, S}, title = {Editorial: Clinical metagenomics-based diagnostics for infectious diseases.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1459621}, pmid = {39170984}, issn = {2235-2988}, mesh = {*Metagenomics/methods ; Humans ; *Communicable Diseases/diagnosis ; }, } @article {pmid39170962, year = {2024}, author = {Yue, M and Tao, S and Gaietto, K and Chen, W}, title = {Omics approaches in asthma research: Challenges and opportunities.}, journal = {Chinese medical journal pulmonary and critical care medicine}, volume = {2}, number = {1}, pages = {1-9}, pmid = {39170962}, issn = {2772-5588}, support = {K12 HD052892/HD/NICHD NIH HHS/United States ; }, abstract = {Asthma, a chronic respiratory disease with a global prevalence of approximately 300 million individuals, presents a significant societal and economic burden. This multifaceted syndrome exhibits diverse clinical phenotypes and pathogenic endotypes influenced by various factors. The advent of omics technologies has revolutionized asthma research by delving into the molecular foundation of the disease to unravel its underlying mechanisms. Omics technologies are employed to systematically screen for potential biomarkers, encompassing genes, transcripts, methylation sites, proteins, and even the microbiome components. This review provides an insightful overview of omics applications in asthma research, with a special emphasis on genetics, transcriptomics, epigenomics, and the microbiome. We explore the cutting-edge methods, discoveries, challenges, and potential future directions in the realm of asthma omics research. By integrating multi-omics and non-omics data through advanced statistical techniques, we aspire to advance precision medicine in asthma, guiding diagnosis, risk assessment, and personalized treatment strategies for this heterogeneous condition.}, } @article {pmid39170784, year = {2024}, author = {Li, K and Lin, H and Han, M and Yang, L}, title = {Soil metagenomics reveals the effect of nitrogen on soil microbial communities and nitrogen-cycle functional genes in the rhizosphere of Panax ginseng.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1411073}, pmid = {39170784}, issn = {1664-462X}, abstract = {Nitrogen (N) is the primary essential nutrient for ginseng growth, and a reasonable nitrogen application strategy is vital for maintaining the stability of soil microbial functional communities. However, how microbial-mediated functional genes involved in nitrogen cycling in the ginseng rhizosphere respond to nitrogen addition is largely unknown. In this study, metagenomic technology was used to study the effects of different nitrogen additions (N0: 0, N1: 20, N2: 40 N g/m[2]) on the microbial community and functional nitrogen cycling genes in the rhizosphere soil of ginseng, and soil properties related to the observed changes were evaluated. The results showed that N1 significantly increased the soil nutrient content compared to N0, and the N1 ginseng yield was the highest (29.90% and 38.05% higher than of N0 and N2, respectively). N2 significantly decreased the soil NO3 [-]N content (17.18 mg/kg lower than N0) and pH. This resulted in a decrease in the diversity of soil microorganisms, a decrease in beneficial bacteria, an increase in the number of pathogenic microorganisms, and an significant increase in the total abundance of denitrification, assimilatory nitrogen reduction, and dissimilatory nitrogen reduction genes, as well as the abundance of nxrA and napA genes (17.70% and 65.25% higher than N0, respectively), which are functional genes involved in nitrification that promote the soil nitrogen cycling process, and reduce the yield of ginseng. The results of the correlation analysis showed that pH was correlated with changes in the soil microbial community, and the contents of soil total nitrogen (TN), ammonium nitrogen (NH4 [+]-N), and alkaline-hydrolyzed nitrogen (AHN) were the main driving factors affecting the changes in nitrogen cycling functional genes in the rhizosphere soil of ginseng. In summary, nitrogen addition affects ginseng yield through changes in soil chemistry, nitrogen cycling processes, and functional microorganisms.}, } @article {pmid39170756, year = {2024}, author = {Bumrungthai, S and Duangjit, S and Passorn, S and Pongpakdeesakul, S and Butsri, S and Janyakhantikul, S}, title = {Comprehensive breast cancer risk analysis with whole exome sequencing and the prevalence of BRCA1 and ABCG2 mutations and oncogenic HPV.}, journal = {Biomedical reports}, volume = {21}, number = {4}, pages = {144}, pmid = {39170756}, issn = {2049-9442}, abstract = {Breast cancer is the most prevalent cancer and also the leading cause of cancer death in women worldwide. A comprehensive understanding of breast cancer risk factors and their incidences is useful information for breast cancer prevention and control planning. The present study aimed to provide information on single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) in breast cancer, the allele frequency of two SNPs in breast cancer-related genes BRCA1 DNA repair associated (BRCA1; rs799917) and ATP binding cassette subfamily G member 2 (ABCG2; rs2231142), and the prevalence of human papillomavirus (HPV) infections in a normal population living in Phayao Province, Northern Thailand. One breast cancer and 10 healthy samples were investigated by whole exome sequencing (WES) and compared for genetic variation. The WES data contained SNPs in genes previously implicated in breast cancer and provided data on CNVs. The allele frequencies for SNPs rs799917 and rs2231142 were also examined. The SNP genotype frequencies were 35.88% CC, 46.54% CT, and 17.58% TT for rs799917 and 33.20% CC, 46.88% CA, and 19.92% AA for rs2231142. A total of 825 human whole blood samples were examined for HPV infection by PCR, and the pooled DNA was tested for HPV infection using metagenomic sequencing. No HPV infections were detected among all 825 samples or the pooled blood samples. The incidence of breast cancer among the tested samples was estimated based on acceptable breast cancer risk factors and demographic data and was 1.47%. The present study provided data on SNPs and CNVs in breast cancer-related genes. The associations between SNPs rs2231142 and rs799917 and breast cancer should be further investigated in a case-control study since heterozygous and homozygous variants are more common. Based on the detection of HPV infection in the blood samples, HPV may not be associated with breast cancer, at least in the Northern Thai population.}, } @article {pmid39170755, year = {2024}, author = {Li, S and Zhang, Y and Han, D}, title = {Severe community‑acquired pneumonia caused by Legionella gormanii in combination with influenza A subtype (H1N1) virus in an immunocompetent patient detected by metagenomic next‑generation sequencing: A case report.}, journal = {Biomedical reports}, volume = {21}, number = {4}, pages = {145}, pmid = {39170755}, issn = {2049-9442}, abstract = {Legionella pneumonia is an atypical form of pneumonia caused by Legionella gormanii that can also lead to multiple organ diseases, including acute respiratory distress syndrome and multiple organ dysfunction syndrome. Legionella gormanii requires a long incubation period for culture in clinical practice using BCYE medium. The specificity of serum for serological detection is low, resulting in a relatively high rate of missed Legionella diagnoses. Contracting the H1N1 virus can lead to the misdiagnosis of Legionella gormanii. Metagenomic next-generation sequencing (mNGS) is a novel tool that can rapidly and accurately identify potential Legionella gormanii strains. A severe case of community-acquired pneumonia in a 79-year-old patient was reported. The patient was diagnosed with Legionella gormanii and influenza A subtype (H1N1) virus using mNGS at The First Affiliated Hospital, Zhejiang University School of Medicine. After anti-Legionella and antiviral therapy, the number of reads identifying Legionella gormanii in bronchoalveolar lavage fluid using mNGS decreased from 665 to 112 as the patient's condition gradually improved. A search of PubMed revealed few reports of Legionella gormanii in association with the influenza A subtype (H1N1) virus. Patients with severe pneumonia caused by Legionella and influenza A subtype H1N1 virus infections should be screened early for infections using methods such as mNGS. This approach enables early and precise treatment, simplifying the administration of antibiotics and enhancing patient outcomes.}, } @article {pmid39170692, year = {2024}, author = {Iwan, E and Grenda, A and Bomba, A and Bielińska, K and Wasyl, D and Kieszko, R and Rolska-Kopińska, A and Chmielewska, I and Krawczyk, P and Rybczyńska-Tkaczyk, K and Olejnik, M and Milanowski, J}, title = {Gut resistome of NSCLC patients treated with immunotherapy.}, journal = {Frontiers in genetics}, volume = {15}, number = {}, pages = {1378900}, pmid = {39170692}, issn = {1664-8021}, abstract = {BACKGROUND: The newest method of treatment for patients with NSCLC (non-small cell lung cancer) is immunotherapy directed at the immune checkpoints PD-1 (Programmed Cell Death 1) and PD-L1 (Programmed Cell Death Ligand 1). PD-L1 is the only validated predictor factor for immunotherapy efficacy, but it is imperfect. Some patients do not benefit from immunotherapy and may develop primary or secondary resistance. This study aimed to assess the intestinal resistome composition of non-small cell lung cancer (NSCLC) patients treated with immune checkpoint inhibitors in the context of clinical features and potentially new prediction factors for assessing immunotherapy efficacy.

METHODS: The study included 30 advanced NSCLC patients, 19 (57%) men and 11 (33%) women treated with first- or second-line immunotherapy (nivolumab, pembrolizumab or atezolizumab). We evaluated the patient's gut resistome composition using the high sensitivity of targeted metagenomics.

RESULTS: Studies have shown that resistome richness is associated with clinical and demographic factors of NSCLC patients treated with immunotherapy. Smoking seems to be associated with an increased abundance of macrolides, lincosamides, streptogramins and vancomycin core resistome. The resistome of patients with progression disease appears to be more abundant and diverse, with significantly higher levels of genomic markers of resistance to lincosamides (lnuC). The resistance genes lnuC, msrD, ermG, aph(6), fosA were correlated with progression-free survival or/and overall survival, thus may be considered as factors potentially impacting the disease.

CONCLUSION: The results indicate that the intestinal resistome of NSCLC patients with immune checkpoint inhibitors treatment differs depending on the response to immunotherapy, with several distinguished markers. Since it might impact treatment efficacy, it must be examined more deeply.}, } @article {pmid39170628, year = {2024}, author = {Bi, B and Fu, X and Jian, X and Zhang, Y and Jiang, Y and Zhou, W and Zhao, H}, title = {Assessment of the potential risks in SD rats gavaged with genetically modified yeast containing the cp4-epsps gene.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1411520}, pmid = {39170628}, issn = {2297-1769}, abstract = {INTRODUCTION: Despite the absence of definitive evidence indicating that the cp4-epsps gene and its resultant recombinant proteins have significant harmful effects on either human or animal health, the safety assessment of genetically modified (GM) crops expressing the CP4-EPSPS proteins has been controversial. This study endeavor was aimed at evaluating the potential risks posed by the CP4-EPSPS protein in transgenic crops, thereby contributing to the advancement of risk assessment methodologies in the context of genetically engineered crops.

METHODS: To ascertain the appropriate daily dosages for oral gavage administration, the expression levels of the CP4-EPSPS protein in a recombinant yeast were quantified. Subsequently, physiological and biochemical analysis, metabolomics, and metagenomic analysis were conducted based on a 90-day Sprague-Dawley (SD) rats feeding experiment, respectively, thereby enhancing the depth and precision of our risk assessment framework.

RESULTS: The results from the physiological and biochemical analysis, organ pathological, blood metabolism, gut microbiota, and correlation analysis of metabolites and gut microbiota revealed several biomarkers for further risk assessment. These biomarkers include clinical biochemical indexes such as total bilirubin (TBIL), direct bilirubin (DBIL), creatine kinase (CK), and lactate dehydrogenase (LDH); metabolites like Methionine, 2-Oxovaleric acid, and LysoPC (16:0); and gut microbiota including Blautia wexlerae, Holdemanella biformis, Dorea sp. CAG 317, Coriobacteriaceae and Erysipelotrichaceae.

CONCLUSION: In conclusion, the risk can be significantly reduced by directly consuming inactivated recombinant CP4-EPSPS. Therefore, in everyday life, the risk associated with consuming GM foods containing recombinant CP4-EPSPS is substantially reduced after heat treatment.}, } @article {pmid39170256, year = {2024}, author = {Yuan, M and Dong, G and Han, N and Yan, L and Tang, H}, title = {Disseminated Mycobacterium tilburgii infection in a person with AIDS: A case report.}, journal = {Heliyon}, volume = {10}, number = {15}, pages = {e35616}, pmid = {39170256}, issn = {2405-8440}, abstract = {BACKGROUND: Mycobacterium tilburgii is a nonculturable, nontuberculous mycobacterium that occasionally causes serious infections in individuals with immune deficiencies. Owing to its nonculturable nature, its antimicrobial susceptibility has not been assessed, and the optimal treatment regimen is unclear. Herein, we report a case of disseminated M. tilburgii infection in a person with AIDS, identified using metagenomics next-generation sequencing (mNGS) and polymerase chain reaction (PCR).

CASE PRESENTATION: A 33-year-old man presented with a 3-month history of abdominal pain, lymphadenopathy, intermittent night hot flashes, night sweats, and weight loss. No pathogen was detected during initial routine investigations. M. tilburgii was subsequently identified in a left cervical lymph node sample using mNGS. Furthermore, M. tilburgii infection was detected in a bone marrow sample based on PCR of 16S rRNA and hsp65 gene sequencing. The person was treated with a combination of moxifloxacin, clarithromycin, ethambutol, rifabutin, and amikacin. The laboratory results improved, and the patient's symptoms resolved.

CONCLUSION: M. tilburgii may be missed in diagnostic tests because it cannot be grown using routine culture techniques. Early diagnosis and timely and effective treatment are critical in patients with M. tilburgii infection; therefore, molecular techniques are recommended for patients with suspected M. tilburgii infection.}, } @article {pmid39170217, year = {2024}, author = {Lu, L and Zhao, Z and Liu, C and Zhang, B and Fu, M and Wang, D and Shen, J and Cai, H and Shang, W}, title = {Multiple lymph nodes enlargement and fever as main manifestations of nocardiosis in immunocompetent individuals: Two case reports.}, journal = {Heliyon}, volume = {10}, number = {15}, pages = {e35681}, pmid = {39170217}, issn = {2405-8440}, abstract = {Nocardia farcinica is an aerobic gram-positive bacterium that is pathogenic to humans. It usually causes local and adjacent tissues' diseases at the entry of infection (most commonly occur in the lungs, skin, or central nervous system), which can also spread to other organs through the bloodstream such as joints, kidneys, and liver. However, these infections are often seen as opportunistic that occur in immunocompromised patients. Here, we report for the first time two immunocompetent patients lacking evidence of local infections, with multiple lymph node enlargements and fever as main clinical manifestations, finally diagnosed as nocardiosis by Metagenomic Next-Generation Sequencing testing (mNGS) from formalin-fixed and paraffin-embedded (FFPE) lymph node tissue, after all the other standard tests were negative. Both patients recovered after receiving anti-nocardia therapies. These two cases indicates that in healthy population, there may be more potential nocardia infections than we expected. Multiple lymph node enlargements and fever suggest a possibility of nocardiosis, especially in patients with fever of unknown origin (FUO). mNGS detection from FFPE lymph node tissue is an accurate, reliable and traceable method for diagnosis of nocardiosis.}, } @article {pmid39170112, year = {2024}, author = {Zhang, H and Lu, M and Guo, C and Wang, L and Ye, K and Zhao, Q and Yang, J and Yang, L and Li, T}, title = {Clinical impact of metagenomic next-generation sequencing of bronchoalveolar lavage fluids for the diagnosis of pulmonary infections in respiratory intensive care unit.}, journal = {Heliyon}, volume = {10}, number = {15}, pages = {e35287}, pmid = {39170112}, issn = {2405-8440}, abstract = {BACKGROUND: The real-world clinical impact of mNGS on BALF in the respiratory intensive care unit (RICU) is not yet fully understood.

METHODS: We investigated the clinical impact of mNGS on BALF samples obtained from 92 patients admitted to the RICU over a 2-year period. We utilized both mNGS and culture methods to evaluate the effectiveness of mNGS in diagnosing pulmonary infections. The clinical impact of mNGS were evaluated by the clinician committees.

RESULTS: Among the 92 diagnosed patients, 78 cases (84.7 %) were determined to have infectious diseases caused by pathogenic microorganisms, and the bacterial infections constituted the most prevalent diagnostic category. For mixed infection, the most common type was the Pneumocystis jironecii and cytomegalovirus co-infection. The mNGS results had a positive impact on the clinical management of 43 cases (46.7 %). Moreover, 19 cases (44.2 %) of positive clinical impacts were solely based on new diagnoses made possible by mNGS results. These new diagnoses were particularly helpful for identifying rare pathogens, which could not be detected by conventional diagnostic methods.

CONCLUSIONS: The BALF mNGS has a positive real-world impact in RICU. Clinician committee play a critical role in ensuring the appropriate use of mNGS.}, } @article {pmid39169078, year = {2024}, author = {Lin, J and Yang, Z and Hong, Y and Cai, W and Pan, H and Lin, J and Ye, L}, title = {A novel infrared spectroscopy marker for assessing the postoperative infection risk in patients with upper urinary tract calculus.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {19398}, pmid = {39169078}, issn = {2045-2322}, support = {Grant number 2021J01398//Natural Science Foundation of Fujian Province/ ; }, mesh = {Humans ; Male ; Female ; Middle Aged ; *Spectrophotometry, Infrared ; *Postoperative Complications/etiology/diagnosis ; *Urinary Calculi/surgery ; Adult ; Urinary Tract Infections/diagnosis ; Aged ; Biomarkers/urine ; Risk Factors ; Risk Assessment/methods ; }, abstract = {The aim of this study is to evaluate the ability of infrared wavenumber of calculus to predict postoperative infection in patients with upper urinary tract calculus (UUTC), and to establish a predictive model based on this. From March 2018 to March 2023, 480 UUTC patients from Fujian Provincial Hospital were included in this study. The infrared-wavenumbers related infection score (IR-infection score) was constructed by univariate analysis, multicollinearity screening, and Lasso analysis to predict postoperative infection. Continually, the Delong test was used to compare the predictive power between the IR-infection score and traditional indicators. Afterward, we performed urine metagene sequencing and stone culture to prove the correlation between calculus toxicity and IR-infection score. Finally, logistic regression was used to build a nomogram. IR-infection score composed of four independent wavenumbers could precisely predict postoperative infection (AUCvalidation cohort = 0.707) and sepsis (AUCvalidation cohort = 0.824). IR-infection score had better predictive ability than commonly used clinical indicators. Moreover, metagenomics sequencing and calculus culture confirmed the correlation between IR-infection score and calculus toxicity (all P < 0.05). The nomogram based on the IR-infection score had high predictive power (all AUCs > 0.803). Our study first developed a novel infrared spectroscopy marker and nomogram, which can help urologists better predict postoperative infection in UUTC patients.}, } @article {pmid39168909, year = {2024}, author = {Wang, X and Li, Y and Kang, L and Zhang, Z and Zhang, D and Li, P and Zhang, Q and Ma, X and Wang, J and Hou, Y and Li, Q and Fu, J and Hong, M}, title = {Diversity, functions, and antibiotic resistance genes of bacteria and fungi are examined in the bamboo plant phyllosphere that serve as food for the giant pandas.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {39168909}, issn = {1618-1905}, support = {2019QZKK05010502//by the Second Qinghai-Tibet Plateau Comprehensive Scientific Survey/ ; KCXTD2022-7//the Innovation Team Funds of China West Normal University/ ; }, abstract = {The phyllosphere of bamboo is rich in microorganisms that can disrupt the intestinal microbiota of the giant pandas that consume them, potentially leading to their death. In the present study, the abundance, diversity, biological functions (e.g., KEGG and CAZyme), and antibiotic resistance genes (ARGs) of bacteria and fungi in two bamboo species phyllosphere (Chimonobambusa szechuanensis, CS; Bashania fangiana, BF) in Daxiangling Nature Reserve (an important part of the Giant Panda National Park) were investigated respectively by amplicon sequencing of the whole 16S rRNA and ITS1-ITS2 genes on PacBio Sequel and whole-metagenome shotgun sequencing on Illumina NovaSeq 6000 platform. The results suggested that there were respectively 18 bacterial and 34 fungi biomarkers between the phyllosphere of the two species of bamboo. Beta diversity of bacteria and fungi communities exited between the two bamboos according to the (un)weighted UniFrac distance matrix. Moreover, the functional analysis showed that the largest relative abundance was found in the genes related to metabolism and global and overview maps. Glycoside hydrolases (GHs) and glycosyl transferases (GTs) have a higher abundance in two bamboo phyllospheres. Co-occurrence network modeling suggested that bacteria and fungi communities in CS phyllosphere employed a much more complex metabolic network than that in BF, and the abundance of multidrug, tetracycline, and glycopeptide resistance genes was higher and closely correlated with other ARGs. This study references the basis for protecting bamboo resources foraged by wild giant pandas and predicts the risk of antibiotic resistance in bamboo phyllosphere bacterial and fungal microbiota in the Giant Panda National Park, China.}, } @article {pmid39168671, year = {2024}, author = {Yang, T and Wang, XY and Sui, X and Hui, XL and Wang, ZX and Jiang, B and Zhang, ZP and Li, XL}, title = {[Analysis of Antibiotic Resistance of Bioaerosols from Wastewater Treatment Process].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {45}, number = {8}, pages = {4512-4519}, doi = {10.13227/j.hjkx.202309002}, pmid = {39168671}, issn = {0250-3301}, mesh = {*Wastewater/microbiology ; *Aerosols/analysis ; *Air Microbiology ; *Waste Disposal, Fluid/methods ; Pseudomonas aeruginosa/genetics/drug effects/isolation & purification ; Genes, Bacterial ; Escherichia coli/isolation & purification/genetics/drug effects ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents ; Drug Resistance, Bacterial/genetics ; Bacteria/classification/genetics/isolation & purification/drug effects ; Drug Resistance, Multiple, Bacterial/genetics ; }, abstract = {To explore the prevalence and source of antibiotic resistant genes （ARGs） and pathogenic antibiotic resistant bacteria （PARB） associated with bioaerosols in wastewater treatment plants （WWTPs）, metagenomic sequencing and assembly were applied to elucidate the antibiotic resistome of bioaerosols and wastewater in WWTPs. The results showed that more subtypes of ARGs and a higher abundance of PARB were found in bioaerosols from WWTPs and downwind than those from upwind. Multidrug and macB were respectively the most dominant type and subtype of ARGs in bioaerosols from WWTPs. In total, 37 types of PARB carried at least two or more ARG types and were characterized by multiple drug resistance. At the fine grid, aerated tank, and sludge dewatering room, wastewater was the main source of bioaerosol ARGs and PARB. A total of 32 PARB were easily aerosolized in at least one wastewater treatment unit, such as Pseudomonas aeruginosa and Escherichia coli. This study will provide theoretical support for the risk assessment and health protection of antibiotic resistant pollution associated with bioaerosols from WWTPs.}, } @article {pmid39168387, year = {2024}, author = {K Benny, C and Chakraborty, S}, title = {Mechanistic investigation of azo dye removal from carbon-deficient dyeing wastewater using horizontal-vertical constructed wetlands.}, journal = {Chemosphere}, volume = {364}, number = {}, pages = {143148}, doi = {10.1016/j.chemosphere.2024.143148}, pmid = {39168387}, issn = {1879-1298}, mesh = {*Wetlands ; *Azo Compounds ; *Wastewater/chemistry ; *Coloring Agents/metabolism/chemistry ; *Water Pollutants, Chemical/metabolism/analysis ; *Waste Disposal, Fluid/methods ; *Biodegradation, Environmental ; *Carbon/metabolism ; *Nitrogen/metabolism/analysis ; Biological Oxygen Demand Analysis ; Typhaceae/metabolism ; }, abstract = {Azo dye degradation can be achieved by simulating a series of anaerobic and aerobic conditions within the constructed wetland (CW) system. The current investigation evaluated the effectiveness of a baffled horizontal-vertical CW system, planted with Typha angustifolia, simulating anaerobic-aerobic conditions to treat carbon-deficient synthetic dyeing wastewater containing 100 mg/L Reactive Yellow 145 (RY145) azo dye. In the absence of an available carbon source in dyeing wastewater, an optimum quantity of sodium acetate was supplemented as the substrate for microbial degradation of RY145. Influent dyeing wastewater characteristics were 5555 ADMI colour, 461 mg/L chemical oxygen demand (COD) and 39 mg/L total nitrogen (TN). During the operation period, the CW system achieved 97% colour, 87% COD, 95% ammonium nitrogen (NH4[+]-N) and 71% TN removals at 4 d hydraulic retention time (HRT). Favourable environmental conditions, such as low redox conditions and substrate availability in horizontal CW, contributed to a significant reduction in colour (96%). Most TN reduction (67%) happened in horizontal CW by denitrification and plant assimilation. The metagenomic study revealed that Proteobacteria, Bacteroidetes, Chloroflexi and Firmicutes were responsible for pollutant degradation within horizontal CW. The UV-visible spectra and high-resolution liquid chromatograph mass spectrometer (HR-LCMS) analysis confirmed that dye degradation intermediates generated from the breakage of azo bonds were eliminated in vertical CW with high redox conditions. The results of the phytotoxicity and fish toxicity experiments demonstrated a substantial toxicity reduction in the CW system-treated effluent.}, } @article {pmid39168346, year = {2024}, author = {Li, J and Li, C and Han, Y and Yang, J and Hu, Y and Xu, H and Zhou, Y and Zuo, J and Tang, Y and Lei, C and Li, C and Wang, H}, title = {Bacterial membrane vesicles from swine farm microbial communities harboring and safeguarding diverse functional genes promoting horizontal gene transfer.}, journal = {The Science of the total environment}, volume = {951}, number = {}, pages = {175639}, doi = {10.1016/j.scitotenv.2024.175639}, pmid = {39168346}, issn = {1879-1026}, mesh = {*Gene Transfer, Horizontal ; Animals ; Swine ; Farms ; Microbiota ; Bacteria/genetics ; Feces/microbiology ; Drug Resistance, Microbial/genetics ; Wastewater/microbiology ; Drug Resistance, Bacterial/genetics ; Soil Microbiology ; Genes, Bacterial ; }, abstract = {Antibiotic resistance (AMR) poses a significant global health challenge, with swine farms recognized as major reservoirs of antibiotic resistance genes (ARGs). Recently, bacterial membrane vesicles (BMVs) have emerged as novel carriers mediating horizontal gene transfer. However, little is known about the ARGs carried by BMVs in swine farm environments and their transfer potential. This study investigated the distribution, sources, and microbiological origins of BMVs in three key microbial habitats of swine farms (feces, soil, and fecal wastewater), along with the ARGs and mobile genetic elements (MGEs) they harbor. Characterization of BMVs revealed particle sizes ranging from 20 to 500 nm and concentrations from 10[8] to 10[12] particles/g, containing DNA and proteins. Metagenomic sequencing identified BMVs predominantly composed of members of the Proteobacteria phyla, including Pseudomonadaceae, Moraxellaceae, and Enterobacteriaceae, carrying diverse functional genes encompassing resistance to 14 common antibiotics and 74,340 virulence genes. Notably, multidrug resistance, tetracycline, and chloramphenicol resistance genes were particularly abundant. Furthermore, BMVs harbored various MGEs, primarily plasmids, and demonstrated the ability to protect their DNA cargo from degradation and facilitate horizontal gene transfer, including the transmission of resistance genes. In conclusion, this study reveals widespread presence of BMVs carrying ARGs and potential virulence genes in swine farm feces, soil, and fecal wastewater. These findings not only provide new insights into the role of extracellular DNA in the environment but also highlight concerns regarding the gene transfer potential mediated by BMVs and associated health risks.}, } @article {pmid39167968, year = {2024}, author = {Tang, A and Zhang, J and Huang, J and Deng, Y and Wang, D and Yu, P and Zhao, R and Wang, Y and Chen, Z and Zhang, T and Li, B}, title = {Decrypting the viral community in aerobic activated sludge reactors treating antibiotic production wastewater.}, journal = {Water research}, volume = {265}, number = {}, pages = {122253}, doi = {10.1016/j.watres.2024.122253}, pmid = {39167968}, issn = {1879-2448}, mesh = {*Sewage/virology ; *Bioreactors ; *Wastewater ; *Anti-Bacterial Agents ; Waste Disposal, Fluid ; Drug Resistance, Microbial/genetics ; Viruses/genetics ; }, abstract = {Viruses are the most abundant yet understudied members that may influence microbial metabolism in activated sludge treating antibiotic production wastewater. This study comprehensively investigated virome community characteristics under the selection pressure of nine types and different concentrations of antibiotics using a metagenomics approach. Of the 15,514 total viral operational taxonomic units (tOTUs) recovered, only 37.5 % were annotated. Antibiotics altered the original viral community structure in activated sludge. The proportion of some pathogenic viral families, including Herpesviridae_like, increased significantly in reactors treating erythromycin production wastewater. In total, 16.5 % of the tOTUs were associated with two or more hosts. tOTUs rarely carried antibiotic resistance genes (ARGs), and the ARG types in the tOTUs did not match the ARGs carried by the bacterial hosts. This suggests that transduction contributes little to the horizontal ARG transfer. Auxiliary metabolic genes (AMGs) were prevalent in tOTUs, and those involved in folate biosynthesis were particularly abundant, indicating their potential to mitigate antibiotic-induced host damage. This study provides comprehensive insights into the virome community in activated sludge treating antibiotic production wastewater and sheds light on the potential role of viral AMGs in mitigating antibiotic-induced stress.}, } @article {pmid39167702, year = {2024}, author = {Prins, FM and Hidding, IJ and Klaassen, MAY and Collij, V and Schultheiss, JPD and Uniken Venema, WTC and Bangma, A and Aardema, JB and Jansen, BH and Mares, WGN and Witteman, BJM and Festen, EAM and Dijkstra, G and Visschedijk, MC and Fidder, HH and Vich Vila, A and Oldenburg, B and Gacesa, R and Weersma, RK}, title = {Limited predictive value of the gut microbiome and metabolome for response to biological therapy in inflammatory bowel disease.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2391505}, pmid = {39167702}, issn = {1949-0984}, mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Inflammatory Bowel Diseases/drug therapy/microbiology/metabolism ; *Metabolome/drug effects ; *Ustekinumab/therapeutic use ; Prospective Studies ; *Antibodies, Monoclonal, Humanized/therapeutic use/pharmacology ; *Feces/microbiology ; Female ; Male ; Adult ; Biological Therapy/methods ; Treatment Outcome ; Middle Aged ; Bacteria/genetics/classification/metabolism/drug effects/isolation & purification ; Biomarkers/analysis/metabolism ; }, abstract = {Emerging evidence suggests the gut microbiome's potential in predicting response to biologic treatments in patients with inflammatory bowel disease (IBD). In this prospective study, we aimed to predict treatment response to vedolizumab and ustekinumab, integrating clinical data, gut microbiome profiles based on metagenomic sequencing, and untargeted fecal metabolomics. We aimed to identify predictive biomarkers and attempted to replicate microbiome-based signals from previous studies. We found that the predictive utility of the gut microbiome and fecal metabolites for treatment response was marginal compared to clinical features alone. Testing our identified microbial ratios in an external cohort reinforced the lack of predictive power of the microbiome. Additionally, we could not confirm previously published predictive signals observed in similar sized cohorts. Overall, these findings highlight the importance of external validation and larger sample sizes, to better understand the microbiome's impact on therapy outcomes in the setting of biologicals in IBD before potential clinical implementation.}, } @article {pmid39167161, year = {2024}, author = {Çakar, MM and Milčić, N and Andreadaki, T and Charnock, S and Fessner, WD and Blažević, ZF}, title = {Kinetic characterization of two neuraminic acid synthases and evaluation of their application potential.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {446}, pmid = {39167161}, issn = {1432-0614}, support = {956631//Horizon 2020 Framework Programme/ ; }, mesh = {Kinetics ; Hydrogen-Ion Concentration ; *Enzyme Stability ; *Neisseria meningitidis/enzymology/genetics ; Oxo-Acid-Lyases/metabolism/genetics/chemistry ; Coenzymes/metabolism ; }, abstract = {Neuraminic acid synthases are an important yet underexplored group of enzymes. Thus, in this research, we performed a detailed kinetic and stability analysis and a comparison of previously known neuraminic acid synthase from Neisseria meningitidis, and a novel enzyme, PNH5, obtained from a metagenomic library. A systematic analysis revealed a high level of similarity of PNH5 to other known neuraminic acid synthases, except for its pH optimum, which was found to be at 5.5 for the novel enzyme. This is the first reported enzyme from this family that prefers an acidic pH value. The effect of different metal cofactors on enzyme activity, i.e. Co[2+], Mn[2+] and Mg[2+], was studied systematically. The kinetics of neuraminic acid synthesis was completely elucidated, and an appropriate kinetic model was proposed. Enzyme stability study revealed that the purified enzyme exhibits changes in its structure during time as observed by differential light scattering, which cause a drop in its activity and protein concentration. The operational enzyme stability for the neuraminic acid synthase from N. meningitidis is excellent, where no activity drop was observed during the batch reactor experiments. In the case of PNH5, some activity drop was observed at higher concentration of substrates. The obtained results present a solid platform for the future application of these enzymes in the synthesis of sialic acids. KEY POINTS: • A novel neuraminic acid synthase was characterized. • The effect of cofactors on NeuS activity was elucidated. • Kinetic and stability characterization of two neuraminic acid synthases was performed.}, } @article {pmid39166878, year = {2024}, author = {Lu, Q and Zhu, R and Zhou, L and Zhang, R and Li, Z and Xu, P and Wang, Z and Wu, G and Ren, J and Jiao, D and Song, Y and Li, J and Wang, W and Liang, R and Ma, X and Sun, Y}, title = {Gut dysbiosis contributes to the development of Budd-Chiari syndrome through immune imbalance.}, journal = {mSystems}, volume = {9}, number = {9}, pages = {e0079424}, pmid = {39166878}, issn = {2379-5077}, support = {81870457//MOST | National Natural Science Foundation of China (NSFC)/ ; 82172944//MOST | National Natural Science Foundation of China (NSFC)/ ; 81900558//MOST | National Natural Science Foundation of China (NSFC)/ ; 232102311048//Key science and technology project s of Henan Province/ ; }, mesh = {*Dysbiosis/microbiology/immunology ; *Gastrointestinal Microbiome/physiology ; *Budd-Chiari Syndrome/immunology/microbiology/pathology ; Humans ; Animals ; Mice ; Male ; Case-Control Studies ; Female ; *Cytokines/metabolism/immunology/genetics ; Adult ; Fecal Microbiota Transplantation ; Middle Aged ; }, abstract = {UNLABELLED: Budd-Chiari syndrome (B-CS) is a rare and lethal condition characterized by hepatic venous outflow tract blockage. Gut microbiota has been linked to numerous hepatic disorders, but its significance in B-CS pathogenesis is uncertain. First, we performed a case-control study (Ncase = 140, Ncontrol = 63) to compare the fecal microbiota of B-CS and healthy individuals by metagenomics sequencing. B-CS patients' gut microbial composition and activity changed significantly, with a different metagenomic makeup, increased potentially pathogenic bacteria, including Prevotella, and disease-linked microbial function. Imbalanced cytokines in patients were demonstrated to be associated with gut dysbiosis, which led us to suspect that B-CS is associated with gut microbiota and immune dysregulation. Next, 16S ribosomal DNA sequencing on fecal microbiota transplantation (FMT) mice models examined the link between gut dysbiosis and B-CS. FMT models showed damaged liver tissues, posterior inferior vena cava, and increased Prevotella in the disturbed gut microbiota of FMT mice. Notably, B-CS-FMT impaired the morphological structure of colonic tissues and increased intestinal permeability. Furthermore, a significant increase of the same cytokines (IL-5, IL-6, IL-9, IL-10, IL-17A, IL-17F, and IL-13) and endotoxin levels in B-CS-FMT mice were observed. Our study suggested that gut microbial dysbiosis may cause B-CS through immunological dysregulation.

IMPORTANCE: This study revealed that gut microbial dysbiosis may cause Budd-Chiari syndrome (B-CS). Gut dysbiosis enhanced intestinal permeability, and toxic metabolites and imbalanced cytokines activated the immune system. Consequently, the escalation of causative factors led to their concentration in the portal vein, thereby compromising both the liver parenchyma and outflow tract. Therefore, we proposed that gut microbial dysbiosis induced immune imbalance by chronic systemic inflammation, which contributed to the B-CS development. Furthermore, Prevotella may mediate inflammation development and immune imbalance, showing potential in B-CS pathogenesis.}, } @article {pmid39166873, year = {2024}, author = {Kwan, S-Y and Sabotta, CM and Cruz, LR and Wong, MC and Ajami, NJ and McCormick, JB and Fisher-Hoch, SP and Beretta, L}, title = {Gut phageome in Mexican Americans: a population at high risk for metabolic dysfunction-associated steatotic liver disease and diabetes.}, journal = {mSystems}, volume = {9}, number = {9}, pages = {e0043424}, pmid = {39166873}, issn = {2379-5077}, support = {P50 CA217674/CA/NCI NIH HHS/United States ; UL1 TR000371/TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; Male ; Female ; *Gastrointestinal Microbiome/genetics ; *Bacteriophages/genetics ; Middle Aged ; *Virome/genetics ; *Mexican Americans ; *Fatty Liver/genetics ; Cross-Sectional Studies ; Adult ; Diabetes Mellitus ; Feces/microbiology/virology ; Aged ; }, abstract = {Mexican Americans are disproportionally affected by metabolic dysfunction-associated steatotic liver disease (MASLD), which often co-occurs with diabetes. Despite extensive evidence on the causative role of the gut microbiome in MASLD, studies determining the involvement of the gut phageome are scarce. In this cross-sectional study, we characterized the gut phageome in Mexican Americans of South Texas by stool shotgun metagenomic sequencing of 340 subjects, concurrently screened for liver steatosis by transient elastography. Inter-individual variations in the phageome were associated with gender, country of birth, diabetes, and liver steatosis. The phage signatures for diabetes and liver steatosis were subsequently determined. Enrichment of Inoviridae was associated with both diabetes and liver steatosis. Diabetes was further associated with the enrichment of predominantly temperate Escherichia phages, some of which possessed virulence factors. Liver steatosis was associated with the depletion of Lactococcus phages r1t and BK5-T, and enrichment of the globally prevalent Crassvirales phages, including members of genus cluster IX (Burzaovirus coli, Burzaovirus faecalis) and VI (Kahnovirus oralis). The Lactococcus phages showed strong correlations and co-occurrence with Lactococcus lactis, while the Crassvirales phages, B. coli, B. faecalis, and UAG-readthrough crAss clade correlated and co-occurred with Prevotella copri. In conclusion, we identified the gut phageome signatures for two closely linked metabolic diseases with significant global burden. These phage signatures may have utility in risk modeling and disease prevention in this high-risk population, and identification of potential bacterial targets for phage therapy.IMPORTANCEPhages influence human health and disease by shaping the gut bacterial community. Using stool samples from a high-risk Mexican American population, we provide insights into the gut phageome changes associated with diabetes and liver steatosis, two closely linked metabolic diseases with significant global burden. Common to both diseases was an enrichment of Inoviridae, a group of phages that infect bacterial hosts chronically without lysis, allowing them to significantly influence bacterial growth, virulence, motility, biofilm formation, and horizontal gene transfer. Diabetes was additionally associated with the enrichment of Escherichia coli-infecting phages, some of which contained virulence factors. Liver steatosis was additionally associated with the depletion of Lactococcus lactis-infecting phages, and enrichment of Crassvirales phages, a group of virulent phages with high global prevalence and persistence across generations. These phageome signatures may have utility in risk modeling, as well as identify potential bacterial targets for phage therapy.}, } @article {pmid39166863, year = {2024}, author = {Cheney, C and Johnson, JD and Ste Marie, JP and Gacosta, KYM and Denlinger Drumm, NB and Jones, GD and Waite-Cusic, J and Navab-Daneshmand, T}, title = {Resolved genomes of wastewater ESBL-producing Escherichia coli and metagenomic analysis of source wastewater samples.}, journal = {Microbiology spectrum}, volume = {12}, number = {10}, pages = {e0071724}, pmid = {39166863}, issn = {2165-0497}, support = {2018-67017-27631//U.S. Department of Agriculture (USDA)/ ; 2018-67017-27631//U.S. Department of Agriculture (USDA)/ ; in-kind supplement from the Oregon State University's Center for Quantitative Life Sciences//Oregon State University (OSU)/ ; Agricultural Research Foundation//Oregon State University (OSU)/ ; Agricultural Research Foundation//Oregon State University (OSU)/ ; }, mesh = {*Wastewater/microbiology ; *Escherichia coli/genetics/isolation & purification/drug effects/enzymology ; *beta-Lactamases/genetics ; *Metagenomics ; *Plasmids/genetics ; *Genome, Bacterial ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Microbial Sensitivity Tests ; Humans ; Oregon ; beta-Lactam Resistance/genetics ; }, abstract = {Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli pose a serious threat to human health because of their resistance to the most commonly prescribed antibiotics: penicillins and cephalosporins. In this study, we provide a genomic and metagenomic context for the determinant beta-lactam resistance genes of ESBL-positive E. coli isolated from various wastewater treatment utilities in Oregon, USA. Class A beta-lactamase genes on chromosomes (blaCTX-M, blaTEM) were clustered with antibiotic resistance genes associated with other classes of antibiotics (sulfonamides and aminoglycosides) along with insertional elements. ESBL genes such as blaCTX-M, blaTEM, and blaSHV were also detected on conjugable plasmids of IncF and IncI incompatibility types. One novel IncF plasmid (pSHV2A_ESBLF) was identified, which carried a multidrug resistance genotype (blaSHV-2A, aadA22, aac3, aph6, tetA, and sul1) in addition to a mer (mercury resistance) operon, colicin, and aerobactin genes. Shotgun metagenomic analysis of the ESBL-producing E. coli-originating wastewater samples showed the presence of class A beta-lactamases; however, the ESBL genes identified in the E. coli genomes were below the detection limits. Other ESBL-associated genes (i.e., blaOXA.11, blaFOX.7, and blaGES.17) were identified in the wastewater samples, and their occurrences were correlated with the core microbial genera (e.g., Paraprevotella). In the E. coli genomes and wastewater samples, tetracycline, aminoglycoside, and beta-lactam resistance determinants frequently co-occurred. The combination of whole-genome and metagenomic analysis provides a holistic description of ESBL-producing organisms and genes in wastewater systems.IMPORTANCEUsing a hybrid sequencing and assembly strategy (short- and long-read sequencing), we identified the distribution of ARGs and virulence factors harbored on plasmids and chromosomes. We further characterized plasmids' incompatibility types and the co-occurrences of ARGs and virulence factors on plasmids and chromosomes. We investigated the transferability of plasmid-mediated beta-lactams via conjugation. Finally, using shotgun metagenomic analysis of the ESBL-producing Escherichia coli-originated wastewater samples, we described the microbial community, the resistome composition, and the potential associations with plasmid-mediated beta-lactam genes and other ARGs.}, } @article {pmid39166855, year = {2024}, author = {Lian, J and Ma, X and Li, X and Xia, L}, title = {The environmental microbial retrieving assessment of cell-processing facilities for cell therapy in a hospital laboratory.}, journal = {Microbiology spectrum}, volume = {12}, number = {10}, pages = {e0125724}, pmid = {39166855}, issn = {2165-0497}, support = {3502Z20214001, 3502Z20234008, 3502Z20244ZD1009, and 3502Z20244ZD2004//Xiamen Municipal Bureau of Science and Technology ()/ ; 2021J011364//Fujian Provincial Department of Science and Technology ()/ ; XMFHIIT-2023SL063//First Affiliated Hospital of Xiamen University/ ; }, mesh = {Humans ; *Environmental Microbiology ; *Cell- and Tissue-Based Therapy/methods ; *Bacteria/genetics/classification/isolation & purification ; Hospitals ; Disinfection/methods ; Environment, Controlled ; Laboratories ; }, abstract = {Cell therapy represents a promising treatment modality. A critical component in the production of cell therapy products is maintaining the sterility of cell therapy clean rooms (CTCRs). This study aimed to evaluate the environmental microbial load within CTCRs. We systematically monitored microbial load in CTCRs, following established guidelines. Cultured microbial samples underwent metagenomic sequencing, and alpha and beta diversity analyses, functional annotation, and resistance gene profiling were performed using various bioinformatics tools to assess microbial diversity and function. From November 2023 to January 2024, we collected 42 environmental microbial colony samples from various sources within the CTCR and performed metagenomic sequencing on 39 samples. Alpha diversity analysis revealed no significant differences among surface, settle_plate, and airborne categories, but significant disparities within surface subgroups were revealed. Beta diversity analysis showed notable differences between surface and airborne categories and among surface subgroups. Species distribution analysis identified Bacillus as the predominant genus on surfaces. Functional annotation and resistance gene analysis indicated distinct resistance patterns, with significant variations between subgroups, such as microscopes and transfer windows, and hands and other Grade_B environments. Resistance to hydrogen peroxide was notably higher in the transfer window group. These findings highlight the importance of stringent disinfection protocols and enhanced hand hygiene to maintain sterility in CTCRs. These findings provide valuable insights for implementing effective measures to maintain cleanliness throughout CTCRs. The annotation and study of resistance genes can help rapidly identify methods to control cellular contamination under circumstances of environmental microbial pollution.IMPORTANCEMaintaining the sterility of cell therapy clean rooms (CTCRs) is crucial for the production of safe and effective cell therapy products. Our study systematically evaluated the environmental microbial load within CTCRs, revealing significant microbial diversity and distinct resistance patterns to disinfection methods. These findings underscore the need for stringent disinfection protocols and enhanced hand hygiene practices to ensure CTCR sterility. By identifying key microbial species and their resistance genes, our research provides essential insights into controlling contamination and safeguarding the production environment, ultimately contributing to the reliability and success of cell therapy treatments.}, } @article {pmid39165919, year = {2024}, author = {Liu, Y and Wu, W and Xiao, Y and Zou, H and Hao, S and Jiang, Y}, title = {Application of metagenomic next-generation sequencing and targeted metagenomic next-generation sequencing in diagnosing pulmonary infections in immunocompetent and immunocompromised patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1439472}, pmid = {39165919}, issn = {2235-2988}, mesh = {Humans ; *Immunocompromised Host ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Male ; *Bronchoalveolar Lavage Fluid/microbiology/virology ; Female ; Middle Aged ; China ; Adult ; Aged ; Young Adult ; Bacteria/genetics/isolation & purification/classification ; Sputum/microbiology/virology ; Community-Acquired Infections/diagnosis/microbiology/virology ; Adolescent ; Immunocompetence ; Pneumonia/diagnosis/microbiology/virology ; Aged, 80 and over ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) technology has been widely used to diagnose various infections. Based on the most common pathogen profiles, targeted mNGS (tNGS) using multiplex PCR has been developed to detect pathogens with predesigned primers in the panel, significantly improving sensitivity and reducing economic burden on patients. However, there are few studies on summarizing pathogen profiles of pulmonary infections in immunocompetent and immunocompromised patients in Jilin Province of China on large scale.

METHODS: From January 2021 to December 2023, bronchoalveolar lavage fluid (BALF) or sputum samples from 546 immunocompetent and immunocompromised patients with suspected community-acquired pneumonia were collected. Pathogen profiles in those patients on whom mNGS was performed were summarized. Additionally, we also evaluated the performance of tNGS in diagnosing pulmonary infections.

RESULTS: Combined with results of mNGS and culture, we found that the most common bacterial pathogens were Pseudomonas aeruginosa, Klebsiella pneumoniae, and Acinetobacter baumannii in both immunocompromised and immunocompetent patients with high detection rates of Staphylococcus aureus and Enterococcus faecium, respectively. For fungal pathogens, Pneumocystis jirovecii was commonly detected in patients, while fungal infections in immunocompetent patients were mainly caused by Candida albicans. Most of viral infections in patients were caused by Human betaherpesvirus 5 and Human gammaherpesvirus 4. It is worth noting that, compared with immunocompetent patients (34.9%, 76/218), more mixed infections were found in immunocompromised patients (37.8%, 14/37). Additionally, taking final comprehensive clinical diagnoses as reference standard, total coincidence rate of BALF tNGS (81.4%, 48/59) was much higher than that of BALF mNGS (40.0%, 112/280).

CONCLUSIONS: Our findings supplemented and classified the pathogen profiles of pulmonary infections in immunocompetent and immunocompromised patients in Jilin Province of China. Most importantly, our findings can accelerate the development and design of tNGS specifically used for regional pulmonary infections.}, } @article {pmid39165848, year = {2024}, author = {Xu, X and Zheng, Y and Zhang, X and Zhang, C and Gai, W and Yang, Z}, title = {Utility of Metagenomic Next-Generation Sequencing for Diagnosis of Infectious Diseases in Critically Ill Immunocompromised Pediatric Patients.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {3579-3591}, pmid = {39165848}, issn = {1178-6973}, abstract = {PURPOSE: Infections cause high rates of illness and death in children worldwide. However, studies on the clinical value of metagenomic next-generation sequencing (mNGS) for immunocompromised children are still limited.

PATIENTS AND METHODS: From June 2021 to December 2023, 119 samples were collected at Pediatric Intensive Care Unit (PICU) of a single-center pediatric hospital and classified into two groups based on their immune states. We compared the diagnostic performance of mNGS and conventional microbiological test (CMT) for pathogen identification, and assessed the clinical impacts of mNGS.

RESULTS: Among the 119 samples, 48 (40.34%) belonged to the immunocompromised children. mNGS had a higher positivity rate than CMT (76.47% vs 55.46%, P = 0.0006). The positive percent agreement (PPA) of mNGS for immunocompromised children was higher compared to immunocompetent children (95.24% vs 77.78%). The most common pathogens for immunocompromised patients were gram-negative bacteria and herpesvirus. However, immunocompetent children showed a higher detection rate for gram-positive bacteria and respiratory viruses. Furthermore, the proportions of the positive impact of mNGS results were significantly higher in immunocompromised patients compared to immunocompetent patients for both diagnosis (91.67% vs 57.75%) and treatment (95.83% vs 64.79%) (P < 0.0001). Immunocompromised state, length of hospital stays, times stay in ICU, Pediatric Risk of Mortality (PRISM) score, neutrophil percentage (NEUT%) and the ratio of arterial oxygen partial pressure to fractional inspired oxygen (PaO2/FiO2) were considered independent factors for poor prognosis in critically ill pediatric patients.

CONCLUSION: In patients from PICU, mNGS had a greater clinical significance in immunocompromised children compared to immunocompetent children. mNGS technology is an important auxiliary method for achieving accurate diagnosis and treatment of critically ill pediatric patients.}, } @article {pmid39165786, year = {2024}, author = {Po, TL and Huang, CH and Lin, CH and Hung, HF}, title = {Diagnosis of a Rare Rickettsia felis Infection Complicated with Unusual Pericardial Effusion and Cardiac Tamponade Using an mNGS Test.}, journal = {Case reports in infectious diseases}, volume = {2024}, number = {}, pages = {8877876}, pmid = {39165786}, issn = {2090-6625}, abstract = {The occurrence of sporadic rickettsial infections has been consistently undervalued and overlooked, primarily owing to a limited emphasis on routine examinations for rickettsioses in clinical practice. At present, the immunofluorescence assay is the prevailing diagnostic method for suspected rickettsioses that enables the detection of specific antibodies against rickettsia in human serum. Herein, we present an exceptional instance of rickettsial infection that was characterized by a rare manifestation of extensive pericardial effusion leading to dyspnea and cardiac tamponade. A diagnosis of chronic fibrosing pericarditis was established based on pericardium tissue obtained through pericardiotomy, and a conclusive metagenomic next-generation sequencing test confirmed the presence of Rickettsia felis infection. The cat flea, scientifically known as Ctenocephalides felis, is the predominant carrier of R. felis. An escalating incidence of human R. felis infections has raised concerns, particularly in light of the burgeoning population of domesticated animals in many contemporary societies.}, } @article {pmid39165569, year = {2024}, author = {Murray, L and Fullerton, H and Moyer, CL}, title = {Microbial metabolic potential of hydrothermal vent chimneys along the submarine ring of fire.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1399422}, pmid = {39165569}, issn = {1664-302X}, abstract = {Hydrothermal vents host a diverse community of microorganisms that utilize chemical gradients from the venting fluid for their metabolisms. The venting fluid can solidify to form chimney structures that these microbes adhere to and colonize. These chimney structures are found throughout many different locations in the world's oceans. In this study, comparative metagenomic analyses of microbial communities on five chimney structures from around the Pacific Ocean were elucidated focusing on the core taxa and genes that are characteristic of each of these hydrothermal vent chimneys. The differences among the taxa and genes found at each chimney due to parameters such as physical characteristics, chemistry, and activity of the vents were highlighted. DNA from the chimneys was sequenced, assembled into contigs, and annotated for gene function. Genes used for carbon, oxygen, sulfur, nitrogen, iron, and arsenic metabolisms were found at varying abundances at each of the chimneys, largely from either Gammaproteobacteria or Campylobacteria. Many taxa shared an overlap of these functional metabolic genes, indicating that functional redundancy is critical for life at these hydrothermal vents. A high relative abundance of oxygen metabolism genes coupled with a low abundance of carbon fixation genes could be used as a unique identifier for inactive chimneys. Genes used for DNA repair, chemotaxis, and transposases were found at high abundances at each of these hydrothermal chimneys allowing for enhanced adaptations to the ever-changing chemical and physical conditions encountered.}, } @article {pmid39165395, year = {2024}, author = {Armbrecht, L and Bolch, CJS and Paine, B and Cooper, A and McMinn, A and Woodward, C and Hallegraeff, G}, title = {Recovering sedimentary ancient DNA of harmful dinoflagellates accumulated over the last 9000 years off Eastern Tasmania, Australia.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae098}, pmid = {39165395}, issn = {2730-6151}, abstract = {Harmful algal blooms (HABs) have had significant adverse impacts on the seafood industry along the Tasmanian east coast over the past 4 decades. To investigate the history of regional HABs, we performed analyses of sedimentary ancient DNA (sedaDNA) in coastal sediments up to ~9000 years old collected inshore and offshore of Maria Island, Tasmania. We used metagenomic shotgun sequencing and a hybridisation capture array ("HABbaits1") to target three harmful dinoflagellate genera, Alexandrium, Gymnodinium, and Noctiluca. Bioinformatic and DNA damage analyses verified the authenticity of the sedaDNA sequences. Our results show that dinoflagellates of Alexandrium genera have been present off eastern Tasmania during the last ~8300 years, and we sporadically detected and unambiguously verified sequences of Gymnodinium catenatum that were present offshore up to ~7600 years ago. We also recovered sedaDNA of the fragile, soft-bodied Noctiluca scintillans with increased relative abundance since 2010, consistent with plankton surveys. This study enabled us to identify challenges of sedaDNA sequence validation (in particular for G. catenatum, a microreticulate gymnodinoid species) and provided guidance for the development of tools to monitor past and present HAB species and improvement of future HAB event predictions.}, } @article {pmid39165393, year = {2024}, author = {Facimoto, CT and Clements, KD and White, WL and Handley, KM}, title = {Bacteroidia and Clostridia are equipped to degrade a cascade of polysaccharides along the hindgut of the herbivorous fish Kyphosus sydneyanus.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae102}, pmid = {39165393}, issn = {2730-6151}, abstract = {The gut microbiota of the marine herbivorous fish Kyphosus sydneyanus are thought to play an important role in host nutrition by supplying short-chain fatty acids (SCFAs) through fermentation of dietary red and brown macroalgae. Here, using 645 metagenome-assembled genomes (MAGs) from wild fish, we determined the capacity of different bacterial taxa to degrade seaweed carbohydrates along the gut. Most bacteria (99%) were unclassified at the species level. Gut communities and CAZyme-related transcriptional activity were dominated by Bacteroidia and Clostridia. Both classes possess genes CAZymes acting on internal polysaccharide bonds, suggesting their role initiating glycan depolymerization, followed by rarer Gammaproteobacteria and Verrucomicrobiae. Results indicate that Bacteroidia utilize substrates in both brown and red algae, whereas other taxa, namely, Clostridia, Bacilli, and Verrucomicrobiae, utilize mainly brown algae. Bacteroidia had the highest CAZyme gene densities overall, and Alistipes were especially enriched in CAZyme gene clusters (n = 73 versus just 62 distributed across all other taxa), pointing to an enhanced capacity for macroalgal polysaccharide utilization (e.g., alginate, laminarin, and sulfated polysaccharides). Pairwise correlations of MAG relative abundances and encoded CAZyme compositions provide evidence of potential inter-species collaborations. Co-abundant MAGs exhibited complementary degradative capacities for specific substrates, and flexibility in their capacity to source carbon (e.g., glucose- or galactose-rich glycans), possibly facilitating coexistence via niche partitioning. Results indicate the potential for collaborative microbial carbohydrate metabolism in the K. sydneyanus gut, that a greater variety of taxa contribute to the breakdown of brown versus red dietary algae, and that Bacteroidia encompass specialized macroalgae degraders.}, } @article {pmid39165128, year = {2024}, author = {Trost, K and Knopp, MR and Wimmer, JLE and Tria, FDK and Martin, WF}, title = {A universal and constant rate of gene content change traces pangenome flux to LUCA.}, journal = {FEMS microbiology letters}, volume = {371}, number = {}, pages = {}, pmid = {39165128}, issn = {1574-6968}, support = {101018894/ERC_/European Research Council/International ; 101018894/ERC_/European Research Council/International ; }, mesh = {*Bacteria/genetics/classification ; *Genome, Bacterial ; *Archaea/genetics/classification ; *Evolution, Molecular ; *Genome, Archaeal ; Gene Transfer, Horizontal ; Phylogeny ; }, abstract = {Prokaryotic genomes constantly undergo gene flux via lateral gene transfer, generating a pangenome structure consisting of a conserved core genome surrounded by a more variable accessory genome shell. Over time, flux generates change in genome content. Here, we measure and compare the rate of genome flux for 5655 prokaryotic genomes as a function of amino acid sequence divergence in 36 universally distributed proteins of the informational core (IC). We find a clock of gene content change. The long-term average rate of gene content flux is remarkably constant across all higher prokaryotic taxa sampled, whereby the size of the accessory genome-the proportion of the genome harboring gene content difference for genome pairs-varies across taxa. The proportion of species-level accessory genes per genome, varies from 0% (Chlamydia) to 30%-33% (Alphaproteobacteria, Gammaproteobacteria, and Clostridia). A clock-like rate of gene content change across all prokaryotic taxa sampled suggest that pangenome structure is a general feature of prokaryotic genomes and that it has been in existence since the divergence of bacteria and archaea.}, } @article {pmid39164677, year = {2024}, author = {Zhan, S and Li, S and Cao, Y and Liu, D and Feng, J}, title = {Value of bronchoalveolar lavage fluid metagenomic next-generation sequencing in acute exacerbation of fibrosing interstitial lung disease: an individualized treatment protocol based on microbiological evidence.}, journal = {BMC pulmonary medicine}, volume = {24}, number = {1}, pages = {400}, pmid = {39164677}, issn = {1471-2466}, support = {82300120//National Natural Science Foundation of China/ ; 82170097//National Natural Science Foundation of China/ ; }, mesh = {Aged ; Female ; Humans ; Male ; Middle Aged ; *Bronchoalveolar Lavage Fluid/microbiology ; Cross-Sectional Studies ; *Disease Progression ; *High-Throughput Nucleotide Sequencing ; Immunosuppressive Agents/administration & dosage ; *Lung Diseases, Interstitial/drug therapy/genetics/microbiology ; *Metagenomics/methods ; Methylprednisolone/administration & dosage ; Retrospective Studies ; *Precision Medicine ; *Pulmonary Fibrosis/genetics/microbiology ; }, abstract = {BACKGROUND: Acute exacerbation of fibrosing interstitial lung diseases (AE-ILD) is a serious life-threatening event per year. Methylprednisolone and/or immunosuppressive agents (ISA) are a mainstay in any regimen, under the premise that pulmonary infection has been promptly identified and controlled. We investigated the value of bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) on the treatment adjustment of AE-ILD.

METHODS: We conducted a cross-sectional observational study. All data were collected prospectively and retrospectively analyzed. We included fifty-six patients with AE-ILD and nineteen stable ILD who underwent BALF mNGS at the beginning of admission.

RESULTS: Patients with a variety of ILD classification were included. Connective-tissue disease related ILD (CTD-ILD) occupy the most common underlying non-idiopathic pulmonary fibrosis (non-IPF). The infection-triggered AE accounted for 39.29%, with the majority of cases being mixed infections. The microorganisms load in the AE-ILD group was significantly higher. After adjusted by mNGS, the therapy coverage number of pathogens was significantly higher compared to the initial treatment (p < 0.001). After treatment, the GGO score and the consolidation score were significantly lower during follow up in survivors (1.57 ± 0.53 vs. 2.38 ± 0.83 with p < 0.001, 1.11 ± 0.24 vs. 1.49 ± 0.47 with p < 0.001, respectively). Some detected microorganisms, such as Tropheryma whipplei, Mycobacterium, Aspergillus, and mixed infections were difficult to be fully covered by empirical medication. BALF mNGS was also very helpful for excluding infections and early administration of methylprednisolone and/or ISA.

CONCLUSIONS: mNGS has been shown to be a useful tool to determine pathogens in patients with AE-ILD, the results should be fully analyzed. The comprehensive treatment protocol based on mNGS has been shown crucial in AE-ILD patients.}, } @article {pmid39164622, year = {2024}, author = {Dielentheis-Frenken, MRE and Wibberg, D and Blank, LM and Tiso, T}, title = {Draft genome sequence and annotation of the polyextremotolerant polyol lipid-producing fungus aureobasidium pullulans NRRL 62042.}, journal = {BMC genomic data}, volume = {25}, number = {1}, pages = {75}, pmid = {39164622}, issn = {2730-6844}, mesh = {*Genome, Fungal ; *Aureobasidium/genetics/metabolism ; *Polymers/metabolism/chemistry ; Molecular Sequence Annotation ; Lipids ; Base Composition ; }, abstract = {OBJECTIVES: The ascomycotic yeast-like fungus Aureobasidium exhibits the natural ability to synthesize several secondary metabolites, like polymalic acid, pullulan, or polyol lipids, with potential biotechnological applications. Combined with its polyextremotolerance, these properties make Aureobasidium a promising production host candidate. Hence, plenty of genomes of Aureobasidia have been sequenced recently. Here, we provide the annotated draft genome sequence of the polyol lipid-producing strain A. pullulans NRRL 62042.

DATA DESCRIPTION: The genome of A. pullulans NRRL 62042 was sequenced using Illumina NovaSeq 6000. Genome assembly revealed a genome size of 24.2 Mb divided into 39 scaffolds with a GC content of 50.1%. Genome annotation using Genemark v4.68 and GenDBE yielded 9,596 genes.}, } @article {pmid39164259, year = {2024}, author = {Seong, HJ and Kim, JJ and Kim, T and Ahn, SJ and Rho, M and Lee, KJ and Sul, WJ}, title = {Recovery of 240 metagenome-assembled genomes from coastal mariculture environments in South Korea.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {902}, pmid = {39164259}, issn = {2052-4463}, mesh = {Republic of Korea ; *Metagenome ; *Aquaculture ; Animals ; Bacteria/genetics/classification ; Microbiota ; Ostreidae/microbiology ; Archaea/genetics ; Pectinidae/microbiology/genetics ; Penaeidae/microbiology/genetics ; }, abstract = {The mariculture industry has seen a rapid expansion in recent years due to the increasing global demand for seafood. However, the industry faces challenges from climate change and increased pathogen pressure. Additionally, the chemicals used to enhance mariculture productivity are changing ocean ecosystems. This study analyzed 36 surface-water metagenomes from South Korean mussel, oyster, scallop, and shrimp farms to expand our understanding of aquaculture microbial genetic resources and the potential impacts of these anthropogenic inputs. We recovered 240 non-redundant species-level metagenome-assembled genomes (MAGs), comprising 224 bacteria, 13 archaea, and three eukaryotes. Most MAGs were assigned to Proteobacteria, Bacteroidota, and Actinobacteriota, with 40.7% remaining unclassified at the species level. Among the three eukaryotic MAGs, one was identified as a novel lineage of green algae, highlighting the uncharacterized genetic diversity in mariculture environments. Additionally, 22 prokaryotic MAGs harbored 26 antibiotic and metal resistance genes, with MAGs carrying beta-lactamases being particularly prevalent in most farms. The obtained microbiome data from mariculture environments can be utilized in future studies to foster healthy, sustainable mariculture practices.}, } @article {pmid39163860, year = {2024}, author = {Torres, MDT and Brooks, EF and Cesaro, A and Sberro, H and Gill, MO and Nicolaou, C and Bhatt, AS and de la Fuente-Nunez, C}, title = {Mining human microbiomes reveals an untapped source of peptide antibiotics.}, journal = {Cell}, volume = {187}, number = {19}, pages = {5453-5467.e15}, doi = {10.1016/j.cell.2024.07.027}, pmid = {39163860}, issn = {1097-4172}, mesh = {Humans ; Animals ; Mice ; *Anti-Bacterial Agents/pharmacology ; *Microbiota/drug effects ; *Antimicrobial Peptides/pharmacology/chemistry ; Metagenome ; Female ; Open Reading Frames ; Bacteria/drug effects/genetics/classification ; Prevotella/drug effects ; }, abstract = {Drug-resistant bacteria are outpacing traditional antibiotic discovery efforts. Here, we computationally screened 444,054 previously reported putative small protein families from 1,773 human metagenomes for antimicrobial properties, identifying 323 candidates encoded in small open reading frames (smORFs). To test our computational predictions, 78 peptides were synthesized and screened for antimicrobial activity in vitro, with 70.5% displaying antimicrobial activity. As these compounds were different compared with previously reported antimicrobial peptides, we termed them smORF-encoded peptides (SEPs). SEPs killed bacteria by targeting their membrane, synergizing with each other, and modulating gut commensals, indicating a potential role in reconfiguring microbiome communities in addition to counteracting pathogens. The lead candidates were anti-infective in both murine skin abscess and deep thigh infection models. Notably, prevotellin-2 from Prevotella copri presented activity comparable to the commonly used antibiotic polymyxin B. Our report supports the existence of hundreds of antimicrobials in the human microbiome amenable to clinical translation.}, } @article {pmid39163656, year = {2024}, author = {Sun, F and Yang, H and Zhang, X and Tan, F and Wang, G and Shi, Q}, title = {Significant response of coral-associated bacteria and their carbohydrate-active enzymes diversity to coral bleaching.}, journal = {Marine environmental research}, volume = {201}, number = {}, pages = {106694}, doi = {10.1016/j.marenvres.2024.106694}, pmid = {39163656}, issn = {1879-0291}, mesh = {Animals ; *Anthozoa/microbiology ; *Bacteria/genetics/enzymology ; Symbiosis ; Microbiota ; }, abstract = {Analysis of bacterial carbohydrate-active enzymes (CAZymes) contributes significantly to comprehending the response exhibited by coral symbionts to the external environment. This study explored the impact of bleaching on the bacteria and their CAZymes in coral Favites sp. through metagenomic sequencing. Notably, principal coordinates analysis (PCoA) unveiles substantial difference in bacterial communities between bleached and unbleached corals. Proteobacteria, Actinobacteria, Acidobacteria, Bacteroidota, and Chloroflexi, exhibit noteworthy alterations during coral bleaching. CAZymes profiles in bleached coral disclosed a significant increase in Glycosyltransferases (GTs) abundance, suggesting an intensified biosynthesis of polysaccharides. Conversely, there is a marked reduction in other CAZymes abundance in bleached coral. Proteobacteria, Bacteroidota, Chlorobi, and Planctomycetota exhibit greater contributions to CAZymes in bleached corals, with Rhodobacterales, Cytophagales, Burkholderiales, Caulobacterales, and Hyphomicrobiales being the main contributors. While Acidobacteria, Actinobacteria, and Chloroflexi demonstrate higher contributions to CAZymes in unbleached corals. The changes in bacteria and their CAZymes reflect the ecological adaptability of coral holobionts when facing environmental stress. The alterations in CAZymes composition caused by bleaching events may have profound impacts on coral nutrient absorption and ecosystem stability. Therefore, understanding the dynamic changes in CAZymes is crucial for assessing the health and recovery potential of coral ecosystems.}, } @article {pmid39163484, year = {2024}, author = {Dede, B and Reeves, EP and Walter, M and Bach, W and Amann, R and Meyerdierks, A}, title = {Bacterial chemolithoautotrophy in ultramafic plumes along the Mid-Atlantic Ridge.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39163484}, issn = {1751-7370}, support = {EXC-309-49926684//Deutsche Forschungsgemeinschaft/ ; //Norwegian Research Council/ ; 179560//University of Bergen Centre for Geobiology/ ; //Max Planck Society/ ; }, mesh = {*Hydrothermal Vents/microbiology ; Atlantic Ocean ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; *Chemoautotrophic Growth ; *Seawater/microbiology ; Microbiota ; Hydrogen/metabolism ; Phylogeny ; Sulfur/metabolism ; Oxidation-Reduction ; In Situ Hybridization, Fluorescence ; Carbon Dioxide/metabolism ; }, abstract = {Hydrothermal vent systems release reduced chemical compounds that act as an important energy source in the deep sea. Chemolithoautotrophic microbes inhabiting hydrothermal plumes oxidize these compounds, in particular, hydrogen and reduced sulfur, to obtain the energy required for CO2 fixation. Here, we analysed the planktonic communities of four hydrothermal systems located along the Mid-Atlantic Ridge: Irinovskoe, Semenov-2, Logatchev-1, and Ashadze-2, by combining long-read 16S rRNA gene analysis, fluorescence in situ hybridization, meta-omics, and thermodynamic calculations. Sulfurimonas and SUP05 dominated the microbial communities in these hydrothermal plumes. Investigation of Sulfurimonas and SUP05 MAGs, and their gene transcription in plumes indicated a niche partitioning driven by hydrogen and sulfur. In addition to sulfur and hydrogen oxidation, a novel SAR202 clade inhabiting the plume, here referred to as genus Carboxydicoccus, harbours the capability for CO oxidation and CO2 fixation via reverse TCA cycle. Both pathways were also highly transcribed in other hydrogen-rich plumes, including the Von Damm vent field. Carboxydicoccus profundi reached up to 4% relative abundance (1.0 x 103 cell ml- 1) in Irinovskoe non-buoyant plume and was also abundant in non-hydrothermally influenced deep-sea metagenomes (up to 5 RPKM). Therefore, CO, which is probably not sourced from the hydrothermal fluids (1.9-5.8 μM), but rather from biological activities within the rising fluid, may serve as a significant energy source in hydrothermal plumes. Taken together, this study sheds light on the chemolithoautotrophic potential of the bacterial community in Mid-Atlantic Ridge plumes.}, } @article {pmid39162848, year = {2024}, author = {Cupples, AM}, title = {Propane Monooxygenases in Soil Associated Metagenomes Align Most Closely to those in the Genera Kribbella, Amycolatopsis, Bradyrhizobium, Paraburkholderia and Burkholderia.}, journal = {Current microbiology}, volume = {81}, number = {10}, pages = {314}, pmid = {39162848}, issn = {1432-0991}, support = {2129228//National Science Foundation/ ; }, mesh = {*Soil Microbiology ; *Phylogeny ; *Metagenome ; Multigene Family ; Cytochrome P-450 CYP4A/genetics/metabolism ; Burkholderia/genetics/classification/enzymology ; Bradyrhizobium/genetics/classification/enzymology ; Bacterial Proteins/genetics/metabolism ; Genome, Bacterial ; }, abstract = {Propanotrophs are a focus of interest because of their ability to degrade numerous environmental contaminants. To explore the phylogeny of microorganisms containing the propane monooxygenase gene cluster (prmABCD), NCBI bacterial genomes and publicly available soil associated metagenomes (from soils, rhizospheres, tree roots) were both examined. Nucleic acid sequences were collected only if all four subunits were located together, were of the expected length and were annotated as propane monooxygenase subunits. In the bacterial genomes, this resulted in data collection only from the phyla Actinomycetota and Pseudomonadota. For the soil associated metagenomes, reads from four studies were subject to quality control, assembly and annotation. Following this, the propane monooxygenase subunit nucleic acid sequences were collected and aligned to the collected bacterial sequences. In total, forty-two propane monooxygenase gene clusters were annotated from the soil associated metagenomes. The majority aligned closely to those from the Actinomycetota, followed by the Alphaproteobacteria, then the Betaproteobacteria. Actinomycetota aligning propane monooxygenase sequences were obtained from all four datasets and most closely aligned to the genera Kribbella and Amycolatopsis. Alphaproteobacteria aligning sequences largely originated from metagenomes associated with miscanthus and switchgrass rhizospheres and primarily aligned with the genera Bradyrhizobium, Acidiphilium and unclassified Rhizobiales. Betaproteobacteria aligning sequences were obtained from only the Red Oak root metagenomes and primarily aligned with the genera Paraburkholderia, Burkholderia and Caballeronia. Interestingly, sequences from the environmental metagenomes were not closely aligned to those from well-studied propanotrophs, such as Mycobacterium and Rhodococcus. Overall, the study highlights the previously unreported diversity of putative propanotrophs in environmental samples. The common occurrence of propane monooxygenase gene clusters has implications for their potential use for contaminant biodegradation.}, } @article {pmid39162547, year = {2024}, author = {Jin, M and Yu, M and Feng, X and Li, Y and Zhang, M}, title = {Characterization and comparative genomic analysis of a marine Bacillus phage reveal a novel viral genus.}, journal = {Microbiology spectrum}, volume = {12}, number = {10}, pages = {e0003724}, pmid = {39162547}, issn = {2165-0497}, support = {2019013, 2024025//Scientific Research Foundation of the Third Institute of Oceanography, MNR/ ; 41976084//National Natural Science Foundation of China/ ; DY-XZ-04//Deep Sea Habitats Discovery Project/ ; }, mesh = {*Bacillus Phages/genetics/classification/isolation & purification/physiology ; *Genome, Viral ; *Phylogeny ; *Genomics ; *Bacillus pumilus/virology/genetics ; Lysogeny ; Geologic Sediments/microbiology/virology ; Bacillus/virology/genetics/classification ; Viral Proteins/genetics/metabolism ; }, abstract = {UNLABELLED: Bacillus pumilus exhibits substantial economic significance, with its metabolism, adaptability, and ecological functions regulated by its bacteriophages. Here, we isolated and characterized a novel temperate phage vB_BpuM-ZY1 from B. pumilus derived from mangrove sediments by mitomycin C induction. Phage vB_BpuM-ZY1 is a typical myophage, which has an icosahedral head with a diameter of 43.34 ± 2.14 nm and a long contractible tail with a length of 238.58 ± 5.18 nm. Genomic analysis indicated that vB_BpuM-ZY1 encodes genes for lysogeny control, and its life cycle may be intricately regulated by multiple mechanisms. vB_BpuM-ZY1 was predicted to employ P2-like 5'-extended-cos packaging strategy. In addition, genome-wide phylogenetic tree and proteome tree analyses indicated that vB_BpuM-ZY1 belongs to the Peduoviridae family but forms a separate branch at a deeper taxonomic level. Particularly, the comparative genomic analysis showed that vB_BpuM-ZY1 has less than 70% intergenomic similarities with its most similar phages. Thus, we propose that vB_BpuM-ZY1 is a novel Bacillus phage belonging to a new genus under the Peduoviridae family. The protein-sharing network analysis identified 44 vB_BpuM-ZY1-related phages. Interestingly, these evolutionarily related myophages infect a broad range of hosts across different phyla, which may be explained by the high structural variations of the host recognition domain in their central spike proteins. Collectively, our study will contribute to our understanding of Bacillus phage diversity and Bacillus-phage interactions, as well as provide essential knowledge for the industrial application of B. pumilus.

IMPORTANCE: Although recent metagenomics research has obtained a wealth of phage genetic information, much of it is considered "dark matter" because of the lack of similarity with known sequences in the database. Therefore, the isolation and characterization of novel phages will help to interpret the vast unknown viral metagenome data and improve our understanding of phage diversity and phage-host interactions. Bacillus pumilus shows high economic relevance due to its wide applications in biotechnology, industry, biopharma, and environmental sectors. Since phages influence the abundance, metabolism, evolution, fitness, and ecological functions of bacteria through complex interactions, the significance of isolation and characterization of novel phages infecting B. pumilus is apparent. In this study, we isolated and characterized a B. pumilus phage belonging to a novel viral genus, which provides essential knowledge for phage biology as well as the industrial application of B. pumilus.}, } @article {pmid39162524, year = {2024}, author = {Hu, F and Cheng, Y and Fan, B and Li, W and Ye, B and Wu, Z and Tan, Z and He, Z}, title = {Ruminal microbial metagenomes and host transcriptomes shed light on individual variability in the growth rate of lambs before weaning: the regulated mechanism and potential long-term effect on the host.}, journal = {mSystems}, volume = {9}, number = {9}, pages = {e0087324}, pmid = {39162524}, issn = {2379-5077}, support = {XDA26040304, XDA26050102//strategic priority research program/ ; 32072760//MOST | National Natural Science Foundation of China (NSFC)/ ; 2022JJ10054//HSTD | Natural Science Foundation of Hunan Province/ ; 2022JBGS0023//the Inner Mongolia major technology project/ ; 2019RS3021//Innovation province project/ ; }, mesh = {Animals ; *Weaning ; Sheep/growth & development/microbiology ; *Rumen/microbiology/metabolism ; *Transcriptome ; *Metagenome ; Female ; Gastrointestinal Microbiome/physiology ; Amino Acids/metabolism/blood ; Liver/metabolism ; Fermentation ; }, abstract = {UNLABELLED: Weaning weight is a reflection of management during the breastfeeding phase and will influence animal performance in subsequent phases, considered important indicators within production systems. The aims of this study were as follows: (i) to investigate variability in the growth rate among individual lambs from ewes rearing single or twin lambs fed with two different diets and (ii) to explore the molecular mechanisms regulating the growth rate and the potential long-term effects on the host. No significant change in lamb average daily gain (ADG) was observed in litter size and diet treatment, and there were large variations among individual lambs (ranging from 0.13 to 0.41 kg/day). Further analysis was conducted on serum amino acids, rumen fermentation characteristics, rumen metagenomics and transcriptome, and hepatic transcriptome of lambs with extremely high (HA; n = 6) and low (LA; n = 6) ADG. We observed significant increases in serum lysine, leucine, alanine, and phenylalanine in the HA group. The metagenome revealed that the HA group presented a higher rumen propionate molar proportion via increasing gene abundance in the succinate pathway for propionate synthesis. For the rumen transcriptome, higher expressed gene sets in the HA group were mainly related to rumen epithelial growth, including cytokine-cytokine receptor interaction, Jak-STAT signaling pathway, and adherens junction. For the liver transcriptome, the upregulated KEGG pathways in the HA group were primarily associated with fatty acid degradation, glyoxylate and dicarboxylate metabolism, cholesterol metabolism, and the immune system. This research suggests that preweaning lambs with high ADG may benefit from rumen development and enhanced liver metabolic and immune function.

IMPORTANCE: There is accumulating evidence indicating that the early-life rumen microbiome plays vital roles in rumen development and microbial fermentation, which subsequently affects the growth of young ruminants. The liver is also vital to regulate the metabolism and distribution of nutrients. Our results demonstrate that lambs with high average daily gain (ADG) enhanced microbial volatile fatty acid (VFA) metabolism toward rumen propionate and serum amino acid (AA) production to support host growth. The study highlights that high ADG in the preweaning period is beneficial for the rumen development and liver energy metabolism, leading to better growth later in life. Overall, this study explores the molecular mechanisms regulating the growth rate and the potential long-term effects of increased growth rate on the host metabolism, providing fundamental knowledge about nutrient manipulation in pre-weaning.}, } @article {pmid39162518, year = {2024}, author = {Hu, D and Zhang, T and He, S and Pu, T and Yin, Y and Hu, Y}, title = {Mining metagenomic data to gain a new insight into the gut microbial biosynthetic potential in placental mammals.}, journal = {Microbiology spectrum}, volume = {12}, number = {10}, pages = {e0086424}, pmid = {39162518}, issn = {2165-0497}, support = {32370552//MOST | National Natural Science Foundation of China (NSFC)/ ; 32070414,32325010//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Metagenomics ; *Mammals/microbiology ; *Metagenome ; *Multigene Family ; Bacteria/genetics/classification/metabolism ; Polyketides/metabolism ; Data Mining ; Biological Products/metabolism ; Female ; Biosynthetic Pathways/genetics ; }, abstract = {Mammals host a remarkable diversity and abundance of gut microbes. Biosynthetic gene clusters (BGCs) in microbial genomes encode biologically active chemical products and play an important role in microbe-host interactions. Traditionally, the exploration of gut microbial metabolic functions has relied on the pure culture method. However, given the limited amounts of microbes being cultivated, insights into the metabolism of gut microbes in mammals continued to be very limited. In this study, we adopted a computational pipeline for mining the metagenomic data (named taxonomy-guided identification of biosynthetic gene clusters, TaxiBGC) to identify experimentally verified BGCs in 373 metagenomes across 53 mammalian species in an unbiased manner. We demonstrated that polyketides (PKs) and nonribosomal peptides (NRPs) are representative of mammals, and the products derived from them were associated with cell-cell communication and resistance to inflammation. Large carnivores had the highest number of BGCs, followed by large herbivores and small mammals. We also observed that the large mammals had more common BGCs that aid in the biosynthesis of a variety of natural products. However, small mammals not only had fewer BGCs but were also unique to each species. Our results provide novel insights into the mining of metagenomic data sets to identify active BGCs and their products across mammals.IMPORTANCEThe gut microbes host numerous biosynthetic gene clusters (BGCs) that biosynthesize natural products and impact the host's physiology. Historically, our understanding of BGCs in mammalian gut microbes was largely based on studies on cultured isolates; however, only a small fraction of mammal-associated microbes have been investigated. The biochemical diversity of the mammalian gut microbiota is poorly understood. Metagenomic sequencing contains data from a vast number of organisms and provides information on the total gene content of communities. Unfortunately, the existing BGC prediction tools are designed for individual microbial genomes. Recently, a BGC prediction tool called the taxonomy-guided identification of biosynthetic gene clusters (TaxiBGC) that directly mine the metagenome was developed. To gain new insights into the microbial metabolism, we used TaxiBGC to predict BGCs from 373 metagenomes across 53 mammalian species representing seven orders. Our findings elucidate the functional activities of complex microbial communities in the gut.}, } @article {pmid39162509, year = {2024}, author = {Liu, L and Hakhverdyan, M and Wallgren, P and Vanneste, K and Fu, Q and Lucas, P and Blanchard, Y and de Graaf, M and Oude Munnink, BB and van Boheemen, S and Bossers, A and Hulst, M and Van Borm, S}, title = {An interlaboratory proficiency test using metagenomic sequencing as a diagnostic tool for the detection of RNA viruses in swine fecal material.}, journal = {Microbiology spectrum}, volume = {12}, number = {10}, pages = {e0420823}, pmid = {39162509}, issn = {2165-0497}, mesh = {Animals ; *Feces/virology ; Swine ; *Metagenomics/methods ; *Swine Diseases/virology/diagnosis ; *RNA Viruses/genetics/isolation & purification/classification ; Computational Biology/methods ; Genome, Viral/genetics ; Laboratory Proficiency Testing ; RNA, Viral/genetics ; Astroviridae Infections/veterinary/diagnosis/virology ; Metagenome ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {UNLABELLED: Metagenomic shotgun sequencing (mNGS) can serve as a generic molecular diagnostic tool. An mNGS proficiency test (PT) was performed in six European veterinary and public health laboratories to detect porcine astroviruses in fecal material and the extracted RNA. While different mNGS workflows for the generation of mNGS data were used in the different laboratories, the bioinformatic analysis was standardized using a metagenomic read classifier as well as read mapping to selected astroviral reference genomes to assess the semiquantitative representation of astrovirus species mixtures. All participants successfully identified and classified most of the viral reads to the two dominant species. The normalized read counts obtained by aligning reads to astrovirus reference genomes by Bowtie2 were in line with Kraken read classification counts. Moreover, participants performed well in terms of repeatability when the fecal sample was tested in duplicate. However, the normalized read counts per detected astrovirus species differed substantially between participants, which was related to the different laboratory methods used for data generation. Further modeling of the mNGS data indicated the importance of selecting appropriate reference data for mNGS read classification. As virus- or sample-specific biases may apply, caution is needed when extrapolating this swine feces-based PT for the detection of other RNA viruses or using different sample types. The suitability of experimental design to a given pathogen/sample matrix combination, quality assurance, interpretation, and follow-up investigation remain critical factors for the diagnostic interpretation of mNGS results.

IMPORTANCE: Metagenomic shotgun sequencing (mNGS) is a generic molecular diagnostic method, involving laboratory preparation of samples, sequencing, bioinformatic analysis of millions of short sequences, and interpretation of the results. In this paper, we investigated the performance of mNGS on the detection of porcine astroviruses, a model for RNA viruses in a pig fecal material, among six European veterinary and public health laboratories. We showed that different methods for data generation affect mNGS performance among participants and that the selection of reference genomes is crucial for read classification. Follow-up investigation remains a critical factor for the diagnostic interpretation of mNGS results. The paper contributes to potential improvements of mNGS as a diagnostic tool in clinical settings.}, } @article {pmid39162465, year = {2024}, author = {Chen, Z and Grim, CJ and Ramachandran, P and Meng, J}, title = {Oxford Nanopore long read-based shotgun metagenomic data sets of simulated bacterial communities originating from fresh spinach and surface water.}, journal = {Microbiology resource announcements}, volume = {13}, number = {9}, pages = {e0058624}, pmid = {39162465}, issn = {2576-098X}, abstract = {Oxford Nanopore long reads of simulated bacterial communities from fresh spinach and surface water were generated (R9.4.1+SQK-LSK109 and R10.4+SQK-LSK112; 0.5, one, and two million reads). Salmonella enterica serotype Heidelberg, Montevideo, or Typhimurium was included alone or in combination in the spinach community, while the water community harbored Pseudomonas aeruginosa.}, } @article {pmid39162437, year = {2024}, author = {Shean, RC and Garrett, E and Malleis, J and Lieberman, JA and Bradley, BT}, title = {A retrospective observational study of mNGS test utilization to examine the role of diagnostic stewardship at two academic medical centers.}, journal = {Journal of clinical microbiology}, volume = {62}, number = {9}, pages = {e0060524}, pmid = {39162437}, issn = {1098-660X}, mesh = {Humans ; Retrospective Studies ; *Academic Medical Centers ; *High-Throughput Nucleotide Sequencing ; Metagenomics/methods ; Antimicrobial Stewardship ; Utah ; Anti-Bacterial Agents/therapeutic use/pharmacology ; }, abstract = {UNLABELLED: Given the cost and unclear clinical impact of metagenomic next-generation sequencing (mNGS), laboratory stewardship may improve utilization. This retrospective observational study examines mNGS results from two academic medical centers employing different stewardship approaches. Eighty mNGS orders [54 cerebrospinal fluid (CSF) and 26 plasma] were identified from 2019 to 2021 at the University of Washington (UW), which requires director-level approval for mNGS orders, and the University of Utah (Utah), which does not restrict ordering. The impact of mNGS results and the relationship to traditional microbiology orders were evaluated. Nineteen percent (10/54) of CSF and 65% (17/26) of plasma studies detected at least one organism. Compared to CSF results, plasma results more frequently identified clinically significant organisms (31% vs 7%) and pathogens not detected by traditional methods (12% vs 0%). Antibiotic management was more frequently impacted by plasma versus CSF results (31% vs 4%). These outcome measures were not statistically different between study sites. The number and cumulative cost of traditional microbiology tests at UW were greater than Utah for CSF mNGS testing (UW: 46 tests, $6,237; Utah: 26 tests, $2,812; P < 0.05) but similar for plasma mNGS (UW: 31 tests, $3,975; Utah: 21 tests, $2,715; P = 0.14). mNGS testing accounted for 30%-50% of the total microbiology costs. Improving the diagnostic performance of mNGS by stewardship remains challenging due to low positivity rates and difficulties assessing clinical impact. From a fiscal perspective, stewardship efforts should focus on reducing testing in low-yield populations given the high costs of mNGS relative to overall microbiology testing expenditures.

IMPORTANCE: Metagenomic next-generation sequencing (mNGS) stewardship practices remain poorly standardized. This study aims to provide actionable insights for institutions that seek to reduce the unnecessary usage of mNGS. Importantly, we highlight that clinical impact remains challenging to measure without standardized guidelines, and we provide an actual cost estimate of microbiology expenditures on individuals undergoing mNGS.}, } @article {pmid39161470, year = {2024}, author = {Ye, D and Li, Y and Yan, K and Peng, W}, title = {A Case Study of Severe Pneumonia Caused by mixed Infection of Chlamydia Abortus and Influenza a in a Female Patient.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {3561-3567}, pmid = {39161470}, issn = {1178-6973}, abstract = {BACKGROUND: Chlamydia abortus is a zoonotic pathogen that causes miscarriage, stillbirth, and sepsis of pregnancy in pregnant women when it infects humans. However, it rarely causes pneumonia in humans.

CASE PRESENTATION: This case reports a case of severe pneumonia characterized by high fever and cough, and the disease rapidly progressed to dyspnea. The patient was treated with moxifloxacin and doxycycline. Chlamydia abortus was detected in bronchoscopy examination and bronchoalveolar lavage fluid (BALF) through metagenomic next-generation sequencing (mNGS)-DNA. A weak positive for influenza A (H1N1) antigen was also found in the throat swab tested. Subsequently, we added mabaloxavir and replaced doxycycline with an intravenous infusion of omadacycline. After effective treatment, the patient developed a urinary tract infection, and the treatment plan was adjusted to meropenem combined with omadacycline. The patient's condition improved, and she was discharged on the 14th day of admission.

CONCLUSION: This is the first report of cases of non-pregnant female patients with Chlamydia abortus infection pneumonia. Consequently, infections with Chlamydia abortus can result in severe respiratory distress, disturbance of water and electrolyte balance, and abnormal liver function, which requires timely diagnosis and correct use of antibiotics by clinicians. Consequently, the mixed infection of H1N1 and Chlamydia abortus aggravated the complexity of the condition and treatment. Combining tetracycline and quinolone is effective for treating severe pneumonia with Chlamydia abortus infection.}, } @article {pmid39161223, year = {2024}, author = {Stokholm, J and Thorsen, J and Schoos, AM and Rasmussen, MA and Brandt, S and Sørensen, SJ and Vahman, N and Chawes, B and Bønnelykke, K}, title = {Infantile colic is associated with development of later constipation and atopic disorders.}, journal = {Allergy}, volume = {79}, number = {12}, pages = {3360-3372}, pmid = {39161223}, issn = {1398-9995}, support = {//Region Hovedstaden/ ; //Strategiske Forskningsråd/ ; //Lundbeck Foundation/ ; //Sundhed og Sygdom, Det Frie Forskningsråd/ ; }, mesh = {Humans ; *Constipation/epidemiology/etiology ; *Colic/epidemiology/etiology ; *Gastrointestinal Microbiome ; Male ; Female ; Infant ; Child, Preschool ; Dermatitis, Atopic/epidemiology/complications ; Child ; Prospective Studies ; Asthma/epidemiology/diagnosis/microbiology/etiology ; Hypersensitivity, Immediate/epidemiology/complications ; Risk Factors ; }, abstract = {BACKGROUND: Infantile colic is a common condition with limited knowledge about later clinical manifestations. We evaluated the role of the early life gut microbiome in infantile colic and later development of atopic and gastrointestinal disorders.

METHODS: Copenhagen Prospective Studies on Asthma in Childhood2010 cohort was followed with 6 years of extensive clinical phenotyping. The 1-month gut microbiome was analyzed by 16S rRNA sequencing. Infantile colic was evaluated at age 3 months by interviews. Clinical endpoints included constipation to age 3 years and prospectively diagnosed asthma and atopic dermatitis in the first 6 years of life, and allergic sensitization from skin prick tests, specific Immunoglobulin E, and component analyses.

RESULTS: Of 695 children, 55 children (7.9%) had infantile colic. Several factors were associated with colic including race, breastfeeding, and pets. The 1-month gut microbiome composition and taxa abundances were not associated with colic, however a sparse Partial Least Squares model including combined abundances of nine species was moderately predictive of colic: median, cross-validated AUC = 0.627, p = .003. Children with infantile colic had an increased risk of developing constipation (aOR, 2.88 [1.51-5.35], p = .001) later in life, but also asthma (aHR, 1.69 [1.02-2.79], p = .040), atopic dermatitis (aHR, 1.84 [1.20-2.81], p = .005) and had a higher number of positive allergic components (adjusted difference, 116% [14%-280%], p = .012) in the first 6 years. These associations were not mediated by gut microbiome differences.

CONCLUSIONS: We link infantile colic with risk of developing constipation and atopic disorders in the first 6 years of life, which was not mediated through an altered gut microbiome at age 1-month. These results suggest infantile colic to involve gastrointestinal and/or atopic mechanisms.}, } @article {pmid39160620, year = {2024}, author = {Yu, T and Luo, Y and Tan, X and Zhao, D and Bi, X and Li, C and Zheng, Y and Xiang, H and Hu, S}, title = {Global Marine Cold Seep Metagenomes Reveal Diversity of Taxonomy, Metabolic Function, and Natural Products.}, journal = {Genomics, proteomics & bioinformatics}, volume = {22}, number = {2}, pages = {}, doi = {10.1093/gpbjnl/qzad006}, pmid = {39160620}, issn = {2210-3244}, support = {//Center for Ocean Mega-Science, Chinese Academy of Sciences/ ; 2021QZKK0100//Second Tibetan Plateau Scientific Expedition and Research Program/ ; }, mesh = {*Metagenome/genetics ; *Archaea/genetics/metabolism/classification ; *Microbiota/genetics ; Bacteria/genetics/classification/metabolism ; Biological Products/metabolism ; Cold Temperature ; Phylogeny ; Seawater/microbiology ; Metagenomics/methods ; Biodiversity ; }, abstract = {Cold seeps in the deep sea are closely linked to energy exploration as well as global climate change. The alkane-dominated chemical energy-driven model makes cold seeps an oasis of deep-sea life, showcasing an unparalleled reservoir of microbial genetic diversity. Here, by analyzing 113 metagenomes collected from 14 global sites across 5 cold seep types, we present a comprehensive Cold Seep Microbiomic Database (CSMD) to archive the genomic and functional diversity of cold seep microbiomes. The CSMD includes over 49 million non-redundant genes and 3175 metagenome-assembled genomes, which represent 1895 species spanning 105 phyla. In addition, beta diversity analysis indicates that both the sampling site and cold seep type have a substantial impact on the prokaryotic microbiome community composition. Heterotrophic and anaerobic metabolisms are prevalent in microbial communities, accompanied by considerable mixotrophs and facultative anaerobes, highlighting the versatile metabolic potential in cold seeps. Furthermore, secondary metabolic gene cluster analysis indicates that at least 98.81% of the sequences potentially encode novel natural products, with ribosomally synthesized and post-translationally modified peptides being the predominant type widely distributed in archaea and bacteria. Overall, the CSMD represents a valuable resource that would enhance the understanding and utilization of global cold seep microbiomes.}, } @article {pmid39160615, year = {2024}, author = {Hugerth, LW and Krog, MC and Vomstein, K and Du, J and Bashir, Z and Kaldhusdal, V and Fransson, E and Engstrand, L and Nielsen, HS and Schuppe-Koistinen, I}, title = {Defining Vaginal Community Dynamics: daily microbiome transitions, the role of menstruation, bacteriophages, and bacterial genes.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {153}, pmid = {39160615}, issn = {2049-2618}, support = {KAW 2020.0239//Science for Life Laboratory/ ; E-22614-01, E-22614-02//Rigshospitalet/ ; 2021-01683//Vetenskapsrådet/ ; }, mesh = {Humans ; Female ; *Vagina/microbiology ; *Bacteriophages/genetics/physiology ; *Microbiota/genetics ; *Menstruation ; *Bacteria/classification/genetics ; Adult ; *Dysbiosis/microbiology ; *Menstrual Cycle ; Young Adult ; Genes, Bacterial/genetics ; Metagenomics/methods ; }, abstract = {BACKGROUND: The composition of the vaginal microbiota during the menstrual cycle is dynamic, with some women remaining eu- or dysbiotic and others transitioning between these states. What defines these dynamics, and whether these differences are microbiome-intrinsic or mostly driven by the host is unknown. To address this, we characterized 49 healthy, young women by metagenomic sequencing of daily vaginal swabs during a menstrual cycle. We classified the dynamics of the vaginal microbiome and assessed the impact of host behavior as well as microbiome differences at the species, strain, gene, and phage levels.

RESULTS: Based on the daily shifts in community state types (CSTs) during a menstrual cycle, the vaginal microbiome was classified into four Vaginal Community Dynamics (VCDs) and reported in a classification tool, named VALODY: constant eubiotic, constant dysbiotic, menses-related, and unstable dysbiotic. The abundance of bacteria, phages, and bacterial gene content was compared between the four VCDs. Women with different VCDs showed significant differences in relative phage abundance and bacterial composition even when assigned to the same CST. Women with unstable VCDs had higher phage counts and were more likely dominated by L. iners. Their Gardnerella spp. strains were also more likely to harbor bacteriocin-coding genes.

CONCLUSIONS: The VCDs present a novel time series classification that highlights the complexity of varying degrees of vaginal dysbiosis. Knowing the differences in phage gene abundances and the genomic strains present allows a deeper understanding of the initiation and maintenance of permanent dysbiosis. Applying the VCDs to further characterize the different types of microbiome dynamics qualifies the investigation of disease and enables comparisons at individual and population levels. Based on our data, to be able to classify a dysbiotic sample into the accurate VCD, clinicians would need two to three mid-cycle samples and two samples during menses. In the future, it will be important to address whether transient VCDs pose a similar risk profile to persistent dysbiosis with similar clinical outcomes. This framework may aid interdisciplinary translational teams in deciphering the role of the vaginal microbiome in women's health and reproduction. Video Abstract.}, } @article {pmid39160591, year = {2024}, author = {Lee, H and Hwang, K and Cho, A and Kim, S and Kim, M and Morgan-Kiss, R and Priscu, JC and Kim, KM and Kim, OS}, title = {Microbial assemblages and associated biogeochemical processes in Lake Bonney, a permanently ice-covered lake in the McMurdo Dry Valleys, Antarctica.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {60}, pmid = {39160591}, issn = {2524-6372}, support = {PE23130//Korea Polar Research Institute/ ; PE23130//Korea Polar Research Institute/ ; PE23130//Korea Polar Research Institute/ ; PE23130//Korea Polar Research Institute/ ; PE23130//Korea Polar Research Institute/ ; PE23130//Korea Polar Research Institute/ ; PE23130//Korea Polar Research Institute/ ; OPP 1637708//National Science Foundation/ ; OPP 1637708//National Science Foundation/ ; }, abstract = {BACKGROUND: Lake Bonney, which is divided into a west lobe (WLB) and an east lobe (ELB), is a perennially ice-covered lake located in the McMurdo Dry Valleys of Antarctica. Despite previous reports on the microbial community dynamics of ice-covered lakes in this region, there is a paucity of information on the relationship between microbial genomic diversity and associated nutrient cycling. Here, we applied gene- and genome-centric approaches to investigate the microbial ecology and reconstruct microbial metabolic potential along the depth gradient in Lake Bonney.

RESULTS: Lake Bonney is strongly chemically stratified with three distinct redox zones, yielding different microbial niches. Our genome enabled approach revealed that in the sunlit and relatively freshwater epilimnion, oxygenic photosynthetic production by the cyanobacterium Pseudanabaena and a diversity of protists and microalgae may provide new organic carbon to the environment. CO-oxidizing bacteria, such as Acidimicrobiales, Nanopelagicales, and Burkholderiaceae were also prominent in the epilimnion and their ability to oxidize carbon monoxide to carbon dioxide may serve as a supplementary energy conservation strategy. In the more saline metalimnion of ELB, an accumulation of inorganic nitrogen and phosphorus supports photosynthesis despite relatively low light levels. Conversely, in WLB the release of organic rich subglacial discharge from Taylor Glacier into WLB would be implicated in the possible high abundance of heterotrophs supported by increased potential for glycolysis, beta-oxidation, and glycoside hydrolase and may contribute to the growth of iron reducers in the dark and extremely saline hypolimnion of WLB. The suboxic and subzero temperature zones beneath the metalimnia in both lobes supported microorganisms capable of utilizing reduced nitrogens and sulfurs as electron donors. Heterotrophs, including nitrate reducing sulfur oxidizing bacteria, such as Acidimicrobiales (MAG72) and Salinisphaeraceae (MAG109), and denitrifying bacteria, such as Gracilimonas (MAG7), Acidimicrobiales (MAG72) and Salinisphaeraceae (MAG109), dominated the hypolimnion of WLB, whereas the environmental harshness of the hypolimnion of ELB was supported by the relatively low in metabolic potential, as well as the abundance of halophile Halomonas and endospore-forming Virgibacillus.

CONCLUSIONS: The vertical distribution of microbially driven C, N and S cycling genes/pathways in Lake Bonney reveals the importance of geochemical gradients to microbial diversity and biogeochemical cycles with the vertical water column.}, } @article {pmid39160564, year = {2024}, author = {Chen, X and Yin, X and Shi, X and Yan, W and Yang, Y and Liu, L and Zhang, T}, title = {Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes.}, journal = {Genome biology}, volume = {25}, number = {1}, pages = {226}, pmid = {39160564}, issn = {1474-760X}, support = {T21-705/20-N//University Grants Committee/ ; }, mesh = {*Metagenomics/methods ; Metagenome ; Genetic Markers ; Wastewater/microbiology ; Software ; }, abstract = {Long-read sequencing holds great potential for characterizing complex microbial communities, yet taxonomic profiling tools designed specifically for long reads remain lacking. We introduce Melon, a novel marker-based taxonomic profiler that capitalizes on the unique attributes of long reads. Melon employs a two-stage classification scheme to reduce computational time and is equipped with an expectation-maximization-based post-correction module to handle ambiguous reads. Melon achieves superior performance compared to existing tools in both mock and simulated samples. Using wastewater metagenomic samples, we demonstrate the applicability of Melon by showing it provides reliable estimates of overall genome copies, and species-level taxonomic profiles.}, } @article {pmid39160043, year = {2024}, author = {Merino, N and Pagán, E and Berdejo, D and Worby, CJ and Young, M and Manson, AL and Pagán, R and Earl, AM and García-Gonzalo, D}, title = {Dynamics of microbiome and resistome in a poultry burger processing line.}, journal = {Food research international (Ottawa, Ont.)}, volume = {193}, number = {}, pages = {114842}, doi = {10.1016/j.foodres.2024.114842}, pmid = {39160043}, issn = {1873-7145}, mesh = {Animals ; *Microbiota/genetics ; *Food Microbiology ; *Bacteria/genetics/classification/isolation & purification/drug effects ; *Food Handling/methods ; Poultry/microbiology ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; Drug Resistance, Bacterial/genetics ; Meat/microbiology ; Poultry Products/microbiology ; }, abstract = {Traditionally, surveillance programs for food products and food processing environments have focused on targeted pathogens and resistance genes. Recent advances in high throughput sequencing allow for more comprehensive and untargeted monitoring. This study assessed the microbiome and resistome in a poultry burger processing line using culturing techniques and whole metagenomic sequencing (WMS). Samples included meat, burgers, and expired burgers, and different work surfaces. Microbiome analysis revealed spoilage microorganisms as the main microbiota, with substantial shifts observed during the shelf-life period. Core microbiota of meat and burgers included Pseudomonas spp., Psychrobacter spp., Shewanella spp. and Brochothrix spp., while expired burgers were dominated by Latilactobacillus spp. and Leuconostoc spp. Cleaning and disinfection (C&D) procedures altered the microbial composition of work surfaces, which still harbored Hafnia spp. and Acinetobacter spp. after C&D. Resistome analysis showed a low overall abundance of resistance genes, suggesting that effective interventions during processing may mitigate their transmission. However, biocide resistance genes were frequently found, indicating potential biofilm formation or inefficient C&D protocols. This study demonstrates the utility of combining culturing techniques and WMS for comprehensive of the microbiome and resistome characterization in food processing lines.}, } @article {pmid39160038, year = {2024}, author = {Coria-Hinojosa, LM and Velásquez-Reyes, D and Alcázar-Valle, M and Kirchmayr, MR and Calva-Estrada, S and Gschaedler, A and Mojica, L and Lugo, E}, title = {Exploring volatile compounds and microbial dynamics: Kluyveromyces marxianus and Hanseniaspora opuntiae reduce Forastero cocoa fermentation time.}, journal = {Food research international (Ottawa, Ont.)}, volume = {193}, number = {}, pages = {114821}, doi = {10.1016/j.foodres.2024.114821}, pmid = {39160038}, issn = {1873-7145}, mesh = {*Fermentation ; *Volatile Organic Compounds/analysis/metabolism ; *Kluyveromyces/metabolism ; *Hanseniaspora/metabolism ; *Cacao/microbiology/metabolism/chemistry ; Food Microbiology ; Gas Chromatography-Mass Spectrometry ; Acetic Acid/metabolism ; Time Factors ; }, abstract = {Traditional cocoa bean fermentation is a spontaneous process and can result in heterogeneous sensory quality. For this reason, yeast-integrated starter cultures may be an option for creating consistent organoleptic profiles. This study proposes the mixture of Hanseniaspora opuntiae and Kluyveromyces marxianus (from non-cocoa fermentation) as starter culture candidates. The microorganisms and volatile compounds were analyzed during the cocoa fermentation process, and the most abundant were correlated with predominant microorganisms. Results showed that Kluyveromyces marxianus, isolated from mezcal fermentation, was identified as the dominant yeast by high-throughput DNA sequencing. A total of 63 volatile compounds identified by HS-SPME-GC-MS were correlated with the more abundant bacteria and yeast using Principal Component Analysis and Agglomerative Hierarchical Clustering. This study demonstrates that yeasts from other fermentative processes can be used as starter cultures in cocoa fermentation and lead to the formation of more aromatic esters, decrease the acetic acid content.}, } @article {pmid39159777, year = {2024}, author = {Fang, XM and Li, J and Wang, NF and Zhang, T and Yu, LY}, title = {Metagenomics uncovers microbiome and resistome in soil and reindeer faeces from Ny-Ålesund (Svalbard, High Arctic).}, journal = {Environmental research}, volume = {262}, number = {Pt 1}, pages = {119788}, doi = {10.1016/j.envres.2024.119788}, pmid = {39159777}, issn = {1096-0953}, mesh = {Animals ; *Feces/microbiology ; *Reindeer/microbiology ; *Microbiota/drug effects/genetics ; *Soil Microbiology ; Svalbard ; *Metagenomics ; Drug Resistance, Microbial/genetics ; Bacteria/genetics/drug effects/classification ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Arctic Regions ; Soil/chemistry ; Genes, Bacterial ; }, abstract = {Research on the microbiome and resistome in polar environments, such as the Arctic, is crucial for understanding the emergence and spread of antibiotic resistance genes (ARGs) in the environment. In this study, soil and reindeer faeces samples collected from Ny-Ålesund (Svalbard, High Arctic) were examined to analyze the microbiome, ARGs, and biocide/metal resistance genes (BMRGs). The dominant phyla in both soil and faeces were Pseudomonadota, Actinomycetota, and Bacteroidota. A total of 2618 predicted Open Reading Frames (ORFs) containing antibiotic resistance genes (ARGs) were detected. These ARGs belong to 162 different genes across 17 antibiotic classes, with rifamycin and multidrug resistance genes being the most prevalent. We focused on investigating antibiotic resistance mechanisms in the Ny-Ålesund environment by analyzing the resistance genes and their biological pathways. Procrustes analysis demonstrated a significant correlation between bacterial communities and ARG/BMRG profiles in soil and faeces samples. Correlation analysis revealed that Pseudomonadota contributed most to multidrug and triclosan resistance, while Actinomycetota were predominant contributors to rifamycin and aminoglycoside resistance. The geochemical factors, SiO4[2-] and NH4[+], were found to significantly influence the microbial composition and ARG distribution in the soil samples. Analysis of ARGs, BMRGs, virulence factors (VFs), and pathogens identified potential health risks associated with certain bacteria, such as Cryobacterium and Pseudomonas, due to the presence of different genetic elements. This study provided valuable insights into the molecular mechanisms and geochemical factors contributing to antibiotic resistance and enhanced our understanding of the evolution of antibiotic resistance genes in the environment.}, } @article {pmid39159729, year = {2024}, author = {Ma, J and Li, M and Bao, Y and Huang, W and He, X and Hong, Y and Wei, W and Liu, Z and Gao, X and Yang, Y and Cui, Z and Wang, W and Wang, J and Zhu, W and Zheng, N and Pan, L and Wang, D and Ke, Z and Zhou, B and Sheng, L and Li, H}, title = {Gut microbiota-brain bile acid axis orchestrates aging-related neuroinflammation and behavior impairment in mice.}, journal = {Pharmacological research}, volume = {208}, number = {}, pages = {107361}, doi = {10.1016/j.phrs.2024.107361}, pmid = {39159729}, issn = {1096-1186}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Aging/metabolism ; Male ; *Bile Acids and Salts/metabolism ; *Neuroinflammatory Diseases/metabolism ; Female ; *Brain-Gut Axis/physiology ; *Mice, Inbred C57BL ; Mice ; *Brain/metabolism ; *Behavior, Animal ; Caenorhabditis elegans/microbiology ; Microglia/metabolism ; }, abstract = {Emerging evidence shows that disrupted gut microbiota-bile acid (BA) axis is critically involved in the development of neurodegenerative diseases. However, the alterations in spatial distribution of BAs among different brain regions that command important functions during aging and their exact roles in aging-related neurodegenerative diseases are poorly understood. Here, we analyzed the BA profiles in cerebral cortex, hippocampus, and hypothalamus of young and natural aging mice of both sexes. The results showed that aging altered brain BA profiles sex- and region- dependently, in which TβMCA was consistently elevated in aging mice of both sexes, particularly in the hippocampus and hypothalamus. Furthermore, we found that aging accumulated-TβMCA stimulated microglia inflammation in vitro and shortened the lifespan of C. elegans, as well as behavioral impairment and neuroinflammation in mice. In addition, metagenomic analysis suggested that the accumulation of brain TβMCA during aging was partially attributed to reduction in BSH-carrying bacteria. Finally, rejuvenation of gut microbiota by co-housing aged mice with young mice restored brain BA homeostasis and improved neurological dysfunctions in natural aging mice. In conclusion, our current study highlighted the potential of improving aging-related neuro-impairment by targeting gut microbiota-brain BA axis.}, } @article {pmid39159726, year = {2024}, author = {Zhang, Y and Wang, N and Wan, J and Jousset, A and Jiang, G and Wang, X and Wei, Z and Xu, Y and Shen, Q}, title = {Exploring the antibiotic resistance genes removal dynamics in chicken manure by composting.}, journal = {Bioresource technology}, volume = {410}, number = {}, pages = {131309}, doi = {10.1016/j.biortech.2024.131309}, pmid = {39159726}, issn = {1873-2976}, mesh = {Animals ; *Manure/microbiology ; *Chickens ; *Composting ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Bacteria/genetics/drug effects ; Microbiota/drug effects ; Gene Transfer, Horizontal ; }, abstract = {Prolonged antibiotic usage in livestock farming leads to the accumulation of antibiotic resistance genes in animal manure. Composting has been shown as an effective way of removing antibiotic resistance from manures, but the specific mechanisms remain unclear. This study used time-series sampling and metagenomics to analyse the resistome types and their bacterial hosts in chicken manures. Composting significantly altered the physicochemical properties and microbiome composition, reduced antibiotic resistance genes by 65.71 %, mobile genetic elements by 68.15 % and horizontal gene transfer frequency. Source tracking revealed that Firmicutes, Actinobacteria, and Proteobacteria are the major bacterial hosts involved in the resistome and gene transfer events. Composting reduces the resistome risk by targeting pathogens such as Staphylococcus aureus. Structural equation modelling confirmed that composting reduces resistome risk by changing pH and pathogen abundance. This study demonstrates that composting is an effective strategy for mitigating resistome risk in chicken manure, thereby supporting the One Health initiative.}, } @article {pmid39159437, year = {2024}, author = {Pozarycki, C and Seaton, KM and C Vincent, E and Novak Sanders, C and Nuñez, N and Castillo, M and Ingall, E and Klempay, B and Pontefract, A and Fisher, LA and Paris, ER and Buessecker, S and Alansson, NB and Carr, CE and Doran, PT and Bowman, JS and Schmidt, BE and Stockton, AM}, title = {Biosignature Molecules Accumulate and Persist in Evaporitic Brines: Implications for Planetary Exploration.}, journal = {Astrobiology}, volume = {24}, number = {8}, pages = {795-812}, doi = {10.1089/ast.2023.0122}, pmid = {39159437}, issn = {1557-8070}, mesh = {*Exobiology/methods ; *Extraterrestrial Environment/chemistry ; *Salts/analysis/chemistry ; Adenosine Triphosphate/analysis/metabolism ; Amino Acids/analysis ; Salinity ; Organic Chemicals/analysis ; Space Flight ; Seawater/chemistry/microbiology/analysis ; }, abstract = {The abundance of potentially habitable hypersaline environments in our solar system compels us to understand the impacts of high-salt matrices and brine dynamics on biosignature detection efforts. We identified and quantified organic compounds in brines from South Bay Salt Works (SBSW), where evapoconcentration of ocean water enables exploration of the impact of NaCl- and MgCl2-dominated brines on the detection of potential biosignature molecules. In SBSW, organic biosignature abundance and distribution are likely influenced by evapoconcentration, osmolyte accumulation, and preservation effects. Bioluminescence assays show that adenosine triphosphate (ATP) concentrations are higher in NaCl-rich, low water activity (aw) samples (<0.85) from SBSW. This is consistent with the accumulation and preservation of ATP at low aw as described in past laboratory studies. The water-soluble small organic molecule inventory was determined by using microchip capillary electrophoresis paired with high-resolution mass spectrometry (µCE-HRMS). We analyzed the relative distribution of proteinogenic amino acids with a recently developed quantitative method using CE-separation and laser-induced fluorescence (LIF) detection of amino acids in hypersaline brines. Salinity trends for dissolved free amino acids were consistent with amino acid residue abundance determined from the proteome of the microbial community predicted from metagenomic data. This highlights a tangible connection up and down the "-omics" ladder across changing geochemical conditions. The detection of water-soluble organic compounds, specifically proteinogenic amino acids at high abundance (>7 mM) in concentrated brines, demonstrates that potential organic biomarkers accumulate at hypersaline sites and suggests the possibility of long-term preservation. The detection of such molecules in high abundance when using diverse analytical tools appropriate for spacecraft suggests that life detection within hypersaline environments, such as evaporates on Mars and the surface or subsurface brines of ocean world Europa, is plausible and argues such environments should be a high priority for future exploration. Key Words: Salts-Analytical chemistry-Amino acids-Biosignatures-Capillary electrophoresis-Preservation. Astrobiology 24, 795-812.}, } @article {pmid39159427, year = {2024}, author = {Yagi, K and Ethridge, AD and Falkowski, NR and Huang, YJ and Elesela, S and Huffnagle, GB and Lukacs, NW and Fonseca, W and Asai, N}, title = {Microbiome modifications by steroids during viral exacerbation of asthma and in healthy mice.}, journal = {American journal of physiology. Lung cellular and molecular physiology}, volume = {327}, number = {5}, pages = {L646-L660}, pmid = {39159427}, issn = {1522-1504}, support = {R01 AI138348/AI/NIAID NIH HHS/United States ; AI089473//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; HL150682//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; AI138348//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; }, mesh = {Animals ; *Asthma/virology/microbiology/drug therapy ; *Respiratory Syncytial Virus Infections/virology/drug therapy/microbiology/immunology ; *Fluticasone/pharmacology ; Mice ; *Gastrointestinal Microbiome/drug effects ; Lung/virology/microbiology/metabolism/drug effects ; Female ; Mice, Inbred BALB C ; Microbiota/drug effects ; Respiratory Syncytial Viruses/drug effects ; }, abstract = {In the present studies, the assessment of how viral exacerbation of asthmatic responses with and without pulmonary steroid treatment alters the microbiome in conjunction with immune responses presents striking data. The overall findings identify that although steroid treatment of allergic animals diminished the severity of the respiratory syncytial virus (RSV)-induced exacerbation of airway function and mucus hypersecretion, there were local increases in IL-17 expression. Analysis of the lung and gut microbiome suggested that there are differences in RSV exacerbation that are further altered by fluticasone (FLUT) treatment. Using metagenomic inference software, PICRUSt2, we were able to predict that the metabolite profile produced by the changed gut microbiome was significantly different with multiple metabolic pathways and associated with specific treatments with or without FLUT. Importantly, measuring plasma metabolites in an unbiased manner, our data indicate that there are significant changes associated with chronic allergen exposure, RSV exacerbation, and FLUT treatment that are reflective of responses to the disease and treatment. In addition, the changes in metabolites appeared to have contributions from both host and microbial pathways. To understand if airway steroids on their own altered lung and gut microbiome along with host responses to RSV infection, naïve animals were treated with lung FLUT before RSV infection. The naïve animals treated with FLUT before RSV infection demonstrated enhanced disease that corresponded to an altered microbiome and the related PICRUSt2 metagenomic inference analysis. Altogether, these findings set the foundation for identifying important correlations of severe viral exacerbated allergic disease with microbiome changes and the relationship of host metabolome with a potential for early life pulmonary steroid influence on subsequent viral-induced disease.NEW & NOTEWORTHY These studies outline a novel finding that airway treatment with fluticasone, a commonly used inhaled steroid, has significant effects on not only the local lung environment but also on the mucosal microbiome, which may have significant disease implications. The findings further provide data to support that pulmonary viral exacerbations of asthma with or without steroid treatment alter the lung and gut microbiome, which have an impact on the circulating metabolome that likely alters the trajectory of disease progression.}, } @article {pmid39159233, year = {2024}, author = {Katsumi, T and Sato, H and Murakami, R and Hanatani, T and Uchiyama, F and Suzuki, F and Maki, K and Hoshikawa, K and Haga, H and Saito, T and Ueno, Y}, title = {Identification of microbial antigens in liver tissues involved in the pathogenesis of primary biliary cholangitis using 16S rRNA metagenome analysis.}, journal = {PloS one}, volume = {19}, number = {8}, pages = {e0308912}, pmid = {39159233}, issn = {1932-6203}, mesh = {*RNA, Ribosomal, 16S/genetics ; Humans ; *Liver/microbiology/pathology ; *Liver Cirrhosis, Biliary/microbiology/genetics ; Metagenome ; Antigens, Bacterial/genetics ; Female ; Male ; Middle Aged ; Metagenomics/methods ; Bacteria/genetics/classification/isolation & purification ; Aged ; }, abstract = {BACKGROUND: Multiple factors are involved in the pathogenesis of primary biliary cholangitis (PBC), a chronic cholestatic liver disease, characterized by intrahepatic cholangiopathy. In particular, studies have suggested that environmental factors such as the presence of granulomas in the portal vein region are important for the development of PBC. This study aimed to comprehensively analyze and identify foreign-derived antigens in PBC liver tissue to confirm their involvement in PBC pathogenesis.

METHODS: Portal areas and hepatocyte regions were selectively dissected from formalin-fixed paraffin-embedded PBC liver tissue samples using the microlaser method, followed by total DNA extraction. We then validated whether the bacterial strains identified through 16S rRNA metagenomic analysis were detected in PBC liver tissues.

RESULTS: The most frequently detected bacterial genera in the PBC liver tissue samples were Sphingomonas panacis, Providencia, and Cutibacterium. These bacterial genera were also detected in the other PBC samples. Validation for the detection of S. panacis, the most abundant genus, revealed polymerase chain reaction bands extracted from the portal areas of all samples. They were also more highly expressed than bands detected in the hepatocyte region.

CONCLUSION: S. panacis antigen was specifically detected in the portal areas of PBC liver tissues. The introduction of foreign-derived antigens into the liver as an environmental factor could be a possible mechanism for the development of PBC.}, } @article {pmid39158759, year = {2024}, author = {Li, EC and Lai, QL and Zhang, TY and Du, BQ and Zhao, J and Cai, MT and Zhang, YX and Fang, GL}, title = {Type 2 herpes simplex virus-induced anti-N-methyl-D-aspartate receptor encephalitis responsive to immunoglobulin monotherapy.}, journal = {Journal of neurovirology}, volume = {30}, number = {4}, pages = {445-449}, pmid = {39158759}, issn = {1538-2443}, mesh = {Humans ; *Anti-N-Methyl-D-Aspartate Receptor Encephalitis/drug therapy/virology/immunology ; *Immunoglobulins, Intravenous/therapeutic use ; *Herpesvirus 2, Human/drug effects/immunology/genetics ; *Encephalitis, Herpes Simplex/drug therapy/immunology/virology ; Male ; Treatment Outcome ; Female ; Adult ; }, abstract = {Herpes simplex virus-2 encephalitis (HSV2E) in immunocompetent adults is exceptionally rare, and the subsequent onset of autoimmune encephalitis after HSV2E is even less common. This report presents the inaugural Chinese case of anti-N-methyl-D-aspartate receptor encephalitis (NMDARE) induced by HSV2E, confirmed via metagenomic next-generation sequencing (mNGS). The patient demonstrated a favorable response to intravenous immunoglobulin (IVIG) monotherapy. This case emphasizes the importance of considering autoimmune encephalitis in patients exhibiting new or recurrent neurological symptoms after HSV2E recovery. Comprehensive mNGS and neuronal antibody testing are essential for timely diagnosis. Moreover, IVIG monotherapy can serve as an effective treatment for NMDARE induced by HSV2, providing a viable alternative, particularly when steroid therapy is contraindicated.}, } @article {pmid39158623, year = {2024}, author = {Sankaranarayanan, G and Kodiveri Muthukaliannan, G}, title = {Deeper Exploration of Gut Microbiome: Profile of Resistome, Virome and Viral Auxiliary Metabolic Genes of Three Ethnic Indian Groups.}, journal = {Molecular biotechnology}, volume = {}, number = {}, pages = {}, pmid = {39158623}, issn = {1559-0305}, support = {AMR/Fellowship/20/2022-ECD-lI//Indian Council of Medical Research/ ; }, abstract = {The current study explored the resistomes and viromes of three Indian ethnic populations: Jaisalmer, Khargone, and Ladakh. These three groups had different dietary habits and antibiotic consumption rates. A resistome analysis indicated that compared to the Jaisalmer (n = 10) group, the burden of antibiotic resistance genes in the gut microbiome was higher in the Khargone (n = 12) and Ladakh (n = 9) groups. However, correlational analysis factoring in food habits, healthcare, and economic status was not statistically significant due to the limited number of samples. A considerable number of antibiotic resistance genes (ARGs) were present in well-known gut commensals such as Bifidobacteriaceae, Acidomonococcaceae, etc., as retrieved directly by mapping to the Resfinder database using the Groot tool. Further, the raw reads were assembled using MEGAHIT, and putative bacteriophages were retrieved using the VIBRANT tool. Many of the classified bacteriophages of the virome revealed that bacteria belonging to the families Bifidobacteriaceae and Enterocococcaceae were their hosts. The prophages identified in these groups primarily contained auxiliary metabolic genes (AMGs) for primary amino acid metabolism. However, there were significantly fewer AMGs in the Ladakh group than in the Jaisalmer group (p < 0.05). None of the classified bacteriophages or prophages contained ARGs. This indicates that phages do not normally carry antibiotic resistance genes.}, } @article {pmid39158621, year = {2024}, author = {Borah, K and Das, HS and Seth, S and Mallick, K and Rahaman, Z and Mallik, S}, title = {A review on advancements in feature selection and feature extraction for high-dimensional NGS data analysis.}, journal = {Functional & integrative genomics}, volume = {24}, number = {5}, pages = {139}, pmid = {39158621}, issn = {1438-7948}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Machine Learning ; Deep Learning ; }, abstract = {Recent advancements in biomedical technologies and the proliferation of high-dimensional Next Generation Sequencing (NGS) datasets have led to significant growth in the bulk and density of data. The NGS high-dimensional data, characterized by a large number of genomics, transcriptomics, proteomics, and metagenomics features relative to the number of biological samples, presents significant challenges for reducing feature dimensionality. The high dimensionality of NGS data poses significant challenges for data analysis, including increased computational burden, potential overfitting, and difficulty in interpreting results. Feature selection and feature extraction are two pivotal techniques employed to address these challenges by reducing the dimensionality of the data, thereby enhancing model performance, interpretability, and computational efficiency. Feature selection and feature extraction can be categorized into statistical and machine learning methods. The present study conducts a comprehensive and comparative review of various statistical, machine learning, and deep learning-based feature selection and extraction techniques specifically tailored for NGS and microarray data interpretation of humankind. A thorough literature search was performed to gather information on these techniques, focusing on array-based and NGS data analysis. Various techniques, including deep learning architectures, machine learning algorithms, and statistical methods, have been explored for microarray, bulk RNA-Seq, and single-cell, single-cell RNA-Seq (scRNA-Seq) technology-based datasets surveyed here. The study provides an overview of these techniques, highlighting their applications, advantages, and limitations in the context of high-dimensional NGS data. This review provides better insights for readers to apply feature selection and feature extraction techniques to enhance the performance of predictive models, uncover underlying biological patterns, and gain deeper insights into massive and complex NGS and microarray data.}, } @article {pmid39158294, year = {2024}, author = {Baker, BJ and Hyde, E and Leão, P}, title = {Nature should be the model for microbial sciences.}, journal = {Journal of bacteriology}, volume = {206}, number = {9}, pages = {e0022824}, pmid = {39158294}, issn = {1098-5530}, support = {LI-SIAME-00002001//Simons Foundation (SF)/ ; }, mesh = {*Bacteria/genetics/classification ; *Archaea/genetics/classification ; }, abstract = {Until recently, microbiologists have relied on cultures to understand the microbial world. As a result, model organisms have been the focus of research into understanding Bacteria and Archaea at a molecular level. Diversity surveys and metagenomic sequencing have revealed that these model species are often present in low abundance in the environment; instead, there are microbial taxa that are cosmopolitan in nature. Due to the numerical dominance of these microorganisms and the size of their habitats, these lineages comprise mind-boggling population sizes upward of 10[28] cells on the planet. Many of these dominant groups have cultured representatives and have been shown to be involved in mediating key processes in nature. Given their importance and the increasing need to understand changes due to climate change, we propose that members of Nitrosophaerota (Nitrosopumilus maritimus), SAR11 (Pelagibacter ubique), Hadesarchaeia, Bathyarchaeia, and others become models in the future. Abundance should not be the only measure of a good model system; there are other organisms that are well suited to advance our understanding of ecology and evolution. For example, the most well-studied symbiotic bacteria, like Buchnera, Aliivibrio, and Rhizobium, should be models for understanding host-associations. Also, there are organisms that hold new insights into major transitions in the evolution of life on the planet like the Asgard Archaea (Heimdallarchaeia). Innovations in a variety of in situ techniques have enabled us to circumvent culturing when studying everything from genetics to physiology. Our deepest understanding of microbiology and its impact on the planet will come from studying these microbes in nature. Laboratory-based studies must be grounded in nature, not the other way around.}, } @article {pmid39158287, year = {2024}, author = {Lui, LM and Nielsen, TN}, title = {Decomposing a San Francisco estuary microbiome using long-read metagenomics reveals species- and strain-level dominance from picoeukaryotes to viruses.}, journal = {mSystems}, volume = {9}, number = {9}, pages = {e0024224}, pmid = {39158287}, issn = {2379-5077}, support = {DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; }, mesh = {*Microbiota/genetics ; *Metagenomics/methods ; *Estuaries ; San Francisco ; *Viruses/genetics/classification/isolation & purification ; Metagenome/genetics ; Bacteria/genetics/classification ; Archaea/genetics/virology ; Eukaryota/genetics ; Genome, Viral/genetics ; }, abstract = {UNLABELLED: Although long-read sequencing has enabled obtaining high-quality and complete genomes from metagenomes, many challenges still remain to completely decompose a metagenome into its constituent prokaryotic and viral genomes. This study focuses on decomposing an estuarine metagenome to obtain a more accurate estimate of microbial diversity. To achieve this, we developed a new bead-based DNA extraction method, a novel bin refinement method, and obtained 150 Gbp of Nanopore sequencing. We estimate that there are ~500 bacterial and archaeal species in our sample and obtained 68 high-quality bins (>90% complete, <5% contamination, ≤5 contigs, contig length of >100 kbp, and all ribosomal and tRNA genes). We also obtained many contigs of picoeukaryotes, environmental DNA of larger eukaryotes such as mammals, and complete mitochondrial and chloroplast genomes and detected ~40,000 viral populations. Our analysis indicates that there are only a few strains that comprise most of the species abundances.

IMPORTANCE: Ocean and estuarine microbiomes play critical roles in global element cycling and ecosystem function. Despite the importance of these microbial communities, many species still have not been cultured in the lab. Environmental sequencing is the primary way the function and population dynamics of these communities can be studied. Long-read sequencing provides an avenue to overcome limitations of short-read technologies to obtain complete microbial genomes but comes with its own technical challenges, such as needed sequencing depth and obtaining high-quality DNA. We present here new sampling and bioinformatics methods to attempt decomposing an estuarine microbiome into its constituent genomes. Our results suggest there are only a few strains that comprise most of the species abundances from viruses to picoeukaryotes, and to fully decompose a metagenome of this diversity requires 1 Tbp of long-read sequencing. We anticipate that as long-read sequencing technologies continue to improve, less sequencing will be needed.}, } @article {pmid39158216, year = {2024}, author = {Wang, C and Yang, S and Liu, Q and Liu, H and Jin, S and Zheng, J and Xiao, X and Hou, X and Li, J and Ma, S and Cui, L}, title = {Application of Second-Generation Sequencing Technology in Lower Respiratory Tract Infection.}, journal = {Journal of clinical laboratory analysis}, volume = {38}, number = {15-16}, pages = {e25090}, pmid = {39158216}, issn = {1098-2825}, support = {//Hospital-Enterprise Joint Funding Project/ ; //Key Clinical Specialty Funding Project of Beijing/ ; }, mesh = {Humans ; *Respiratory Tract Infections/diagnosis/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Polymerase Chain Reaction/methods ; }, abstract = {BACKGROUND: Lower respiratory tract infection (LRTI) has long been an important threat to people's life and health, so the rapid diagnosis of LRTI is of great significance in clinical treatment. In recent years, the development of the sequencing technology provides a new direction for the rapid diagnosis of LRTI. In this review, the advantages and disadvantages of second-generation sequencing techniques represented by metagenomics next-generation sequencing (mNGS) and droplet digital polymerase chain reaction (ddPCR) in LRTI were reviewed. Furthermore, it offers insights into the future trajectory of this technology, highlighting its potential to revolutionise the field of respiratory infection diagnostics.

OBJECTIVE: This review summarises developments in mechanistic research of second-generation sequencing technology their relationship with clinical practice, providing insights for future research.

METHODS: Authors conducted a search on PubMed and Web of Science using the professional terms 'Lower respiratory tract infection' and 'droplet digital polymerase chain reaction' and 'metagenomics next generation sequencing'. The obtained literature was then roughly categorised based on their research content. Similar studies were grouped into the same sections, and further searches were conducted based on the keywords of each section.

RESULTS: Different studies discussed the application of second-generation sequencing technology in LRTI from different angles, including the detection of pathogens of LRTI by mNGS and ddPCR, the prediction ability of drug-resistant bacteria, and comparison with traditional methods. We try to analyse the advantages and disadvantages of the second-generation sequencing technology by combing the research results of mNGS and ddPCR. In addition, the development direction of the second-generation sequencing technology is prospected.}, } @article {pmid39158107, year = {2024}, author = {Ming, Y and Abdullah Al, M and Zhang, D and Zhu, W and Liu, H and Cai, L and Yu, X and Wu, K and Niu, M and Zeng, Q and He, Z and Yan, Q}, title = {Insights into the evolutionary and ecological adaption strategies of nirS- and nirK-type denitrifying communities.}, journal = {Molecular ecology}, volume = {33}, number = {18}, pages = {e17507}, doi = {10.1111/mec.17507}, pmid = {39158107}, issn = {1365-294X}, support = {SML2020SP004//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2023SP237//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2021SP203//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2023SP205//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; 42377111//National Natural Science Foundation of China/ ; //Ocean Negative Carbon Emissions (ONCE) Program/ ; }, mesh = {*Denitrification/genetics ; *Nitrite Reductases/genetics ; China ; *Phylogeny ; *Metagenome/genetics ; Lakes/microbiology ; Bioreactors/microbiology ; Gene Transfer, Horizontal ; Microbiota/genetics ; Metagenomics ; Geologic Sediments/microbiology ; Bacteria/genetics/classification/metabolism ; Nitrogen/metabolism ; Adaptation, Physiological/genetics ; }, abstract = {Denitrification is a crucial process in the global nitrogen cycle, in which two functionally equivalent genes, nirS and nirK, catalyse the critical reaction and are usually used as marker genes. The nirK gene can function independently, whereas nirS requires additional genes to encode nitrite reductase and is more sensitive to environmental factors than nirK. However, the ecological differentiation mechanisms of those denitrifying microbial communities and their adaptation strategies to environmental stresses remain unclear. Here, we conducted metagenomic analysis for sediments and bioreactor samples from Lake Donghu, China. We found that nirS-type denitrifying communities had a significantly lower horizontal gene transfer frequency than that of nirK-type denitrifying communities, and nirS gene phylogeny was more congruent with taxonomy than that of nirK gene. Metabolic reconstruction of metagenome-assembled genomes further revealed that nirS-type denitrifying communities have robust metabolic systems for energy conservation, enabling them to survive under environmental stresses. Nevertheless, nirK-type denitrifying communities seemed to adapt to oxygen-limited environments with the ability to utilize various carbon and nitrogen compounds. Thus, this study provides novel insights into the ecological differentiation mechanism of nirS and nirK-type denitrifying communities, as well as the regulation of the global nitrogen cycle and greenhouse gas emissions.}, } @article {pmid39158097, year = {2024}, author = {Coyle, MC and Elya, CN and Bronski, MJ and Eisen, MB}, title = {Entomophthovirus: an insect-derived iflavirus that infects a behavior-manipulating fungal pathogen of dipterans.}, journal = {G3 (Bethesda, Md.)}, volume = {14}, number = {10}, pages = {}, pmid = {39158097}, issn = {2160-1836}, support = {//Howard Hughes Medical Institute Investigator/ ; }, mesh = {Animals ; *Entomophthora/genetics ; Genome, Viral ; Phylogeny ; Drosophila melanogaster/virology/microbiology ; Positive-Strand RNA Viruses/genetics ; Insect Viruses/genetics/classification ; Fungal Viruses/genetics/classification ; RNA, Viral/genetics ; }, abstract = {We report a virus infecting Entomophthora muscae, a behavior-manipulating fungal pathogen of dipterans. The virus, which we name Berkeley Entomophthovirus, is a positive-strand RNA virus in the iflaviridae family of capsid-forming viruses, which are mostly known to infect insects. The viral RNA is expressed at high levels in fungal cells in vitro and during in vivo infections of Drosophila melanogaster, and virus particles can be seen intracellularly in E. muscae. This virus, of which we find two closely related variants in our culture of E. muscae, is also closely related to three different viruses reported from metagenomic surveys, two of which were isolated from wild dipterans, and a third isolated from wild ticks. By analyzing sequencing data from these earlier reports, we find abundant reads aligning to E. muscae specifically in the samples from which viral reads were sequenced. These data establish a wide and perhaps obligate association with E. muscae in the wild, consistent with our laboratory data that E. muscae is the host for these closely related viruses. Because of this, we propose the name Entomophthovirus (EV) for this group of highly related virus variants. As other members of the iflaviridae have been reported to cause behavioral changes in insects, we speculate on the possibility that EV plays a role in the behavioral manipulation of flies infected with E. muscae.}, } @article {pmid39157704, year = {2024}, author = {Jevnikar, BE and Khan, ST and Huffman, N and Pasqualini, I and Surace, PA and Deren, ME and Piuzzi, NS}, title = {Advancements in treatment strategies for periprosthetic joint infections: A comprehensive review.}, journal = {Journal of clinical orthopaedics and trauma}, volume = {55}, number = {}, pages = {102496}, pmid = {39157704}, issn = {0976-5662}, abstract = {Periprosthetic joint infection (PJI) presents a critical challenge in orthopedic care, contributing to significant patient morbidity and healthcare costs. This burden is expected to increase secondary to growing demand for total joint arthroplasty (TJA). Despite the profound significance of PJI, there is currently no universally accepted "gold standard" diagnostic criteria using serum biomarker thresholds; latest criteria fail to differentiate acute infections from chronic or consider time since initial surgery. Furthermore, contemporary PJI treatment, which conventionally requires 2-stage revision surgery in conjunction with rigorous antibiotic treatment, can be particularly taxing on patients. Fortunately, recent years have seen marked evolution in both PJI diagnosis and treatment methods. Contemporary research supports time-dependent serum biomarker thresholds with greater sensitivity and specificity than previously reported, as well as alternative surgical options which may be more suitable for certain patients. The following narrative review aims to describe the significance and pathogenesis of PJI before characterizing current challenges, novel innovations, and the future landscape of PJI diagnosis and management. Here, we spotlight the emerging utility of novel biomarkers and metagenomic next-generation sequencing for diagnosis, advancements in patient-centered surgical outcome prediction tools for PJI risk assessment and prevention, and evolving surgical techniques including 1-stage and a "hybrid" 1.5-stage revision surgeries. Additionally, we explore cutting-edge therapeutic modalities including peptide and bacteriophage-based treatments, intraoperative anti-biofilm gel, the VT-X7 antibiotic pump, and promising immune-based interventions. Ultimately, these advancements hold the potential to revolutionize PJI management, offering hope for improved outcomes and reduced burdens on healthcare systems.}, } @article {pmid39157462, year = {2024}, author = {Salgado, JFM and Premkrishnan, BNV and Oliveira, EL and Vettath, VK and Goh, FG and Hou, X and Drautz-Moses, DI and Cai, Y and Schuster, SC and Junqueira, ACM}, title = {The dynamics of the midgut microbiome in Aedes aegypti during digestion reveal putative symbionts.}, journal = {PNAS nexus}, volume = {3}, number = {8}, pages = {pgae317}, pmid = {39157462}, issn = {2752-6542}, abstract = {Blood-feeding is crucial for the reproductive cycle of the mosquito Aedes aegypti, as well as for the transmission of arboviruses to hosts. It is postulated that blood meals may influence the mosquito microbiome but shifts in microbial diversity and function during digestion remain elusive. We used whole-genome shotgun metagenomics to monitor the midgut microbiome in 60 individual females of A. aegypti throughout digestion, after 12, 24, and 48 h following blood or sugar meals. Additionally, ten individual larvae were sequenced, showing microbiomes dominated by Microbacterium sp. The high metagenomic coverage allowed for microbial assignments at the species taxonomic level, also providing functional profiling. Females in the post-digestive period and larvae displayed low microbiome diversities. A striking proliferation of Enterobacterales was observed during digestion in blood-fed mosquitoes. The compositional shift was concomitant with enrichment in genes associated with carbohydrate and protein metabolism, as well as virulence factors for antimicrobial resistance and scavenging. The bacterium Elizabethkingia anophelis (Flavobacteriales), a known human pathogen, was the dominant species at the end of blood digestion. Phylogenomics suggests that its association with hematophagous mosquitoes occurred several times. We consider evidence of mutually beneficial host-microbe interactions raised from this association, potentially pivotal for the mosquito's resistance to arbovirus infection. After digestion, the observed shifts in blood-fed females' midguts shifted to a sugar-fed-like microbial profile. This study provides insights into how the microbiome of A. aegypti is modulated to fulfil digestive roles following blood meals, emphasizing proliferation of potential symbionts in response to the dynamic midgut environment.}, } @article {pmid39157177, year = {2024}, author = {Huang, SS and Qiu, JY and Li, SP and Ma, YQ and He, J and Han, LN and Jiao, LL and Xu, C and Mao, YM and Zhang, YM}, title = {Microbial signatures predictive of short-term prognosis in severe pneumonia.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1397717}, pmid = {39157177}, issn = {2235-2988}, mesh = {Humans ; Male ; Female ; Prognosis ; Retrospective Studies ; Middle Aged ; Aged ; *Bronchoalveolar Lavage Fluid/microbiology ; *Microbiota ; Pneumonia/microbiology/mortality ; Bacteria/classification/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; Lung/microbiology/pathology ; Metagenomics ; Machine Learning ; }, abstract = {OBJECTIVE: This retrospective cohort study aimed to investigate the composition and diversity of lung microbiota in patients with severe pneumonia and explore its association with short-term prognosis.

METHODS: A total of 301 patients diagnosed with severe pneumonia underwent bronchoalveolar lavage fluid metagenomic next-generation sequencing (mNGS) testing from February 2022 to January 2024. After applying exclusion criteria, 236 patients were included in the study. Baseline demographic and clinical characteristics were compared between survival and non-survival groups. Microbial composition and diversity were analyzed using alpha and beta diversity metrics. Additionally, LEfSe analysis and machine learning methods were employed to identify key pathogenic microorganism associated with short-term mortality. Microbial interaction modes were assessed through network co-occurrence analysis.

RESULTS: The overall 28-day mortality rate was 37.7% in severe pneumonia. Non-survival patients had a higher prevalence of hypertension and exhibited higher APACHE II and SOFA scores, higher procalcitonin (PCT), and shorter hospitalization duration. Microbial α and β diversity analysis showed no significant differences between the two groups. However, distinct species diversity patterns were observed, with the non-survival group showing a higher abundance of Acinetobacter baumannii, Klebsiella pneumoniae, and Enterococcus faecium, while the survival group had a higher prevalence of Corynebacterium striatum and Enterobacter. LEfSe analysis identified 29 distinct terms, with 10 potential markers in the non-survival group, including Pseudomonas sp. and Enterococcus durans. Machine learning models selected 16 key pathogenic bacteria, such as Klebsiella pneumoniae, significantly contributing to predicting short-term mortality. Network co-occurrence analysis revealed greater complexity in the non-survival group compared to the survival group, with differences in central genera.

CONCLUSION: Our study highlights the potential significance of lung microbiota composition in predicting short-term prognosis in severe pneumonia patients. Differences in microbial diversity and composition, along with distinct microbial interaction modes, may contribute to variations in short-term outcomes. Further research is warranted to elucidate the clinical implications and underlying mechanisms of these findings.}, } @article {pmid39155949, year = {2024}, author = {Hu, P and Qian, Y and Xu, Y and Radian, A and Yang, Y and Gu, JD}, title = {A positive contribution to nitrogen removal by a novel NOB in a full-scale duck wastewater treatment system.}, journal = {Water research X}, volume = {24}, number = {}, pages = {100237}, pmid = {39155949}, issn = {2589-9147}, abstract = {Nitrite-oxidizing bacteria (NOB) are undesirable in the anaerobic ammonium oxidation (anammox)-driven nitrogen removal technologies in the modern wastewater treatment plants (WWTPs). Diverse strategies have been developed to suppress NOB based on their physiological properties that we have understood. But our knowledge of the diversity and mechanisms employed by NOB for survival in the modern WWTPs remains limited. Here, Three NOB species (NOB01-03) were recovered from the metagenomic datasets of a full-scale WWTP treating duck breeding wastewater. Among them, NOB01 and NOB02 were classified as newly identified lineage VII, tentatively named Candidatus (Ca.) Nitrospira NOB01 and Ca. Nitrospira NOB02. Analyses of genomes and in situ transcriptomes revealed that these two novel NOB were active and showed a high metabolic versatility. The transcriptional activity of Ca. Nitrospira could be detected in all tanks with quite different dissolved oxygen (DO) (0.01-5.01 mg/L), illustrating Ca. Nitrospira can survive in fluctuating DO conditions. The much lower Ca. Nitrospira abundance on the anammox bacteria-enriched sponge carrier likely originated from the intensification substrate (NO2 [-]) competition from anammox and denitrifying bacteria. In particular, a highlight is that Ca. Nitrospira encoded and treanscribed cyanate hydratase (CynS), amine oxidase, urease (UreC), and copper-containing nitrite reductase (NirK) related to ammonium and NO production, driving NOB to interact with the co-existed AOB and anammox bacteria. Ca. Nitrospira strains NOB01 and NOB02 showed quite different niche preference in the same aerobic tank, which dominanted the NOB communities in activated sludge and biofilm, respectively. In addition to the common rTCA cycle for CO2 fixation, a reductive glycine pathway (RGP) was encoded and transcribed by NOB02 likely for CO2 fixation purpose. Additionally, a 3b group hydrogenase and respiratory nitrate reductase were uniquely encoded and transcribed by NOB02, which likely confer a survival advantage to this strain in the fluctuant activated sludge niche. The discovery of this new genus significantly broadens our understanding of the ecophysiology of NOB. Furthermore, the impressive metabolic versatility of the novel NOB revealed in this study advances our understanding of the survival strategy of NOB and provides valuable insight for suppressing NOB in the anammox-based WWTP.}, } @article {pmid39155347, year = {2024}, author = {Dos-Santos, CM and Nascimento, WBA and Cesar, MJSC and Baldani, JI and Schwab, S}, title = {Diversity of bacteria of the genus Sphingomonas associated with sugarcane (Saccharum spp.) culm apoplast fluid and their agrotechnological potential.}, journal = {World journal of microbiology & biotechnology}, volume = {40}, number = {10}, pages = {304}, pmid = {39155347}, issn = {1573-0972}, support = {015/2014//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 12.16.05.017.00.00//Empresa Brasileira de Pesquisa Agropecuária/ ; }, mesh = {*Saccharum/microbiology ; *Sphingomonas/isolation & purification/classification/genetics ; *Phylogeny ; *RNA, Ribosomal, 16S/genetics ; *In Situ Hybridization, Fluorescence ; DNA, Bacterial/genetics ; Plant Roots/microbiology ; Plant Leaves/microbiology ; Sequence Analysis, DNA ; }, abstract = {In sugarcane, sequences related to the genus Sphingomonas have been widely detected by microbiome studies. In this work, the presence of bacteria of this genus was confirmed using culture-dependent and independent techniques. A collection of thirty isolates was obtained using semispecific cultivation conditions, and a specific PCR assay was applied to help confirm the isolates as belonging to the genus. A series of laboratory evaluations were carried out to identify potential properties among the isolates in the collection, which consequently allowed the identification of some most promising isolates for the development of new agricultural bioinputs. In a separate analysis, the culture-independent fluorescence in situ hybridization (FISH) methodology was applied to demonstrate the natural occurrence of Sphingomonas in different organs and tissues of sugarcane. The results showed the presence of bacteria of the genus in the spaces between cells (apoplast) of the culm parenchyma, in vessels in the region of the leaf vein, on the adaxial surface of the leaf blade, and on the root surface, sometimes close to the base of root hairs, which suggests extensive colonization on the host plant. In summary, the present study corroborates previous metagenomic amplicon sequencing results that indicated a high occurrence of Sphingomonas associated with sugarcane. This is the first study that uses approaches other than amplicon sequencing to confirm the occurrence of the genus in sugarcane and, at the same time, demonstrates potentially beneficial activities to be explored by sugarcane cultivation.}, } @article {pmid39155203, year = {2025}, author = {Zhang, P and Lu, Z and Cao, L and Fu, L and Chen, H and Sun, Y}, title = {Diagnostic performance of pancreatic fluid aspiration through metagenomic next-generation sequencing for suspected infected pancreatic necrosis.}, journal = {Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver}, volume = {57}, number = {2}, pages = {401-407}, doi = {10.1016/j.dld.2024.07.036}, pmid = {39155203}, issn = {1878-3562}, mesh = {Humans ; Retrospective Studies ; Male ; Female ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; *Pancreatitis, Acute Necrotizing/diagnosis/microbiology ; *Metagenomics/methods ; Aged ; Adult ; Sensitivity and Specificity ; Pancreas/microbiology/pathology ; }, abstract = {AIMS: This study aimed to evaluate the diagnostic performance of metagenomic next-generation sequencing (mNGS) with pancreatic fluid aspiration for the detection of infected pancreatic necrosis (IPN).

METHODS: This retrospective observational study included 66 patients with suspected IPN. The participants simultaneously underwent pancreatic fluid aspiration mNGS, and microbial and blood culture. We compared the diagnostic performance of mNGS with that of culture in the detection of pathogens associated with IPN.

RESULTS: Of the 66 patients, 45 (68.2 %) were confirmed to have IPN. Pancreatic fluid aspiration mNGS yielded positive results in 32 of these patients (71.1 %), significantly outperforming microbial culture results (25 patients, 55.6 %; P = 0.039); however, both methods exhibited similar specificity (95.2% vs. 100 %). The results of pancreatic fluid aspiration mNGS and microbial culture matched in 73.3 % (33/45) of patients with IPN. The turnaround time for the mNGS results was significantly shorter than that for the microbial culture method (P < 0.001). In addition, survival analysis demonstrated that a positive mNGS result was not associated with increased mortality (hazard ratio, 0.652; 95 % confidence interval 0.157-2.699, P = 0.555).

CONCLUSIONS: Our study highlights the potential of mNGS for diagnosing IPN, with implications for improving patient care by facilitating early and accurate diagnosis, guiding appropriate interventions, and possibly improving patient outcomes.}, } @article {pmid39155040, year = {2024}, author = {Zhang, J and Wang, L and Li, H and Yu, J and Wang, H}, title = {Effect of elemental sulfur on anaerobic ammonia oxidation: Performance and mechanism.}, journal = {Environmental research}, volume = {262}, number = {Pt 1}, pages = {119778}, doi = {10.1016/j.envres.2024.119778}, pmid = {39155040}, issn = {1096-0953}, mesh = {*Sulfur/metabolism ; *Ammonia/metabolism ; *Oxidation-Reduction ; Anaerobiosis ; *Bioreactors ; *Denitrification ; Waste Disposal, Fluid/methods ; Nitrogen/metabolism ; Wastewater/chemistry ; }, abstract = {Biological nitrogen removal processes provide effective means to mitigate nitrogen-related issues in wastewater treatment. Previous studies have highlighted the collaborative efficiency between sulfur autotrophic denitrification and Anammox processes. However, the trigger point induced the combination of nitrogen and sulfur metabolism is unclear. In this study, elemental sulfur (S[0]) was introduced to Anammox system to figure out the performance and mechanism of S[0]-mediated autotrophic denitrification and Anammox (S[0]SAD-A) systems. The results showed that the nitrogen removal performance of the Anammox reactor decreased with the increasing concentrations of NH4[+]-N and NO2[-]-N in influent, denitrification occurred when NH4[+]-N concentration reached 100 mg/L. At stage ⅳ (150 mg/L NH4[+]-N), the total nitrogen removal efficiency in S[0]SAD-A system (95.99%) was significantly higher than that in the Anammox system (77.22%). Throughout a hydraulic retention time, the consumption rate of NH4[+]-N in S[0]SAD-A was faster than that in Anammox reactor. And there existed a nitrate-concentration peak in S[0]SAD-A system. Metagenomic sequencing was performed to reveal functional microbes as well as key genes involved in sulfur and nitrogen metabolism. The results showed that the introduction of S[0] elevated the abundance of Ca. Brocadia. Moreover, the relative abundance of Anammox genes, such as hao, hzsA and hzsC were also stimulated by sulfur. Notably, unclassified members in Rhodocyclaceae acted as the primary contributor to key genes involved in the sulfur metabolism. Overall, the interactions between Anammox and denitrification were stimulated by sulfur metabolism. Our study shed light on the potential significance of Rhodocyclaceae members in the S[0]SAD-A process and disclosed the relationship between anammox and denitrification.}, } @article {pmid39155018, year = {2024}, author = {Jin, Z and Liang, L and Zhao, Z and Zhang, Y}, title = {Enhancing assimilatory sulfate reduction with ferrihydrite-humic acid coprecipitate in anaerobic sulfate-containing wastewater treatment.}, journal = {Bioresource technology}, volume = {411}, number = {}, pages = {131308}, doi = {10.1016/j.biortech.2024.131308}, pmid = {39155018}, issn = {1873-2976}, mesh = {*Sulfates/metabolism/chemistry ; *Ferric Compounds/chemistry ; *Wastewater/chemistry ; Anaerobiosis ; *Humic Substances ; *Oxidation-Reduction ; *Water Purification/methods ; }, abstract = {Sulfide produced from dissimilatory sulfate reduction can combine with hydrogen to form hydrogen sulfide, causing odor issues and environmental pollution. To address this problem, ferrihydrite-humic acid coprecipitate was added to improve assimilatory sulfate reduction (ASR), resulting in a decrease in sulfide production (190.2 ± 14.6 mg/L in the Fh-HA group vs. 246.3 ± 8.1 mg/L in the Fh group) with high sulfate removal. Humic acid, adsorbed on the surface of ferrihydrite, delayed secondary mineralization of ferrihydrite under sulfate reduction condition. Therefore, more iron-reducing species (e.g. Trichococcus, Geobacter) were enriched with ferrihydrite-humic acid coprecipitate to transfer more electrons to other species, which led to more COD reduction, an increase in electron transfer capacity, and a decrease in the NADH/NAD[+] ratio. Metagenomic analysis also indicated that functional genes related to ASR was enhanced with ferrihydrite-humic acid coprecipitate. Thus, the addition of ferrihydrite-humic acid coprecipitate can be considered as a promising candidate for anaerobic sulfate wastewater treatment.}, } @article {pmid39154684, year = {2024}, author = {Li, C and Zhou, X and Wang, J and Ye, H and Sun, C and Alhomrani, M and Alamri, AS and Guo, N}, title = {Preparation of sanguinarine/glabridin loaded antifungal double-layer nanoemulsion edible coating using arabic gum/WPI for forest frog's oviduct oil preservation.}, journal = {International journal of biological macromolecules}, volume = {278}, number = {Pt 2}, pages = {134826}, doi = {10.1016/j.ijbiomac.2024.134826}, pmid = {39154684}, issn = {1879-0003}, mesh = {*Emulsions ; Animals ; *Antifungal Agents/pharmacology/chemistry ; Female ; *Gum Arabic/chemistry ; Benzophenanthridines/chemistry/pharmacology ; Whey Proteins/chemistry/pharmacology ; Microbial Sensitivity Tests ; Isoquinolines ; }, abstract = {Forest frog's oviduct oil (FFOO) is highly susceptible to microbial spoilage during storage, which causes serious safety concerns and economic losses. However, little information is available regarding the preservation of it up to now. The aim of this research is to understand the dominant microbial community of FFOO spoilage, and based on this, develop a kind of edible nanoemulsion coating for preserving FFOO. Microbial metagenomic analysis indicated that the Aspergillus genus increased significantly during storage. In the present study, gum arabic and whey protein isolate were chosen as the coating matrix, the natural compounds sanguinarine and glabridin were selected as antimicrobial agents to prepare double-layer nanoemulsion edible coating. When the ratio of sanguinarine and glabridin in the nanoemulsion was 1:3, it exhibited strongest storage stability and antifungal activity. The mycelial inhibition rate of 1:3 nanoemulsion against dominant microbial community (Aspergillus niger and Aspergillus glaucus) reached 88.89 ± 1.37 % and 89.68 ± 1.37 %, respectively. The experimental results indicated that the edible nanoemulsion coating not only had outstanding antifungal activity, but also had excellent fresh-keeping effect on FFOO. This nanoemulsion coating could be a promising and potential candidate for food preservation.}, } @article {pmid39154675, year = {2024}, author = {Ariaeenejad, S and Barani, M and Roostaee, M and Lohrasbi-Nejad, A and Mohammadi-Nejad, G and Hosseini Salekdeh, G}, title = {Enhanced pollutant degradation via green-synthesized core-shell mesoporous Si@Fe magnetic nanoparticles immobilized with metagenomic laccase.}, journal = {International journal of biological macromolecules}, volume = {278}, number = {Pt 2}, pages = {134813}, doi = {10.1016/j.ijbiomac.2024.134813}, pmid = {39154675}, issn = {1879-0003}, mesh = {*Laccase/chemistry/metabolism ; *Enzymes, Immobilized/chemistry/metabolism ; *Magnetite Nanoparticles/chemistry ; *Water Pollutants, Chemical/chemistry ; *Green Chemistry Technology/methods ; Hydrogen-Ion Concentration ; Wastewater/chemistry ; Temperature ; Porosity ; Rosaniline Dyes/chemistry ; Enzyme Stability ; Iron/chemistry ; Water Purification/methods ; Metagenome ; }, abstract = {With rapid industrial expansion, environmental pollution from emerging contaminants has increased, posing severe ecosystem threats. Laccases offer an eco-friendly solution for degrading hazardous substances, but their use as free-form biocatalysts face challenges. This study immobilized laccase (PersiLac1) on green-synthesized Si@Fe nanoparticles (MSFM NPs) to remove pollutants like Malachite Green-containing wastewater and degrade plastic films. Characterization techniques (FTIR, VSM, XRD, SEM, EDS, BET) confirmed the properties and structure of MSFM NPs, revealing a surface area of 31.297 m[2].g[-1] and a pore diameter of 12.267 nm. The immobilized PersiLac1 showed enhanced activity across various temperatures and pH levels, retaining over 82 % activity after 15 cycles at 80°C with minimal leaching. It demonstrated higher stability, half-life, and decimal reduction time than free laccase. Under 1 M NaCl, its activity was 1.8 times higher than the non-immobilized enzyme. The immobilized laccase removed 98.11 % of Malachite Green-containing wastewater and retained 82.92 % activity over twenty cycles of dye removal. Additionally, FTIR and SEM confirmed superior plastic degradation under saline conditions. These findings suggest that immobilizing PersiLac1 on magnetic nanoparticles enhances its function and potential for contaminant removal. Future research should focus on scalable, cost-effective laccase immobilization methods for large-scale environmental applications.}, } @article {pmid39154625, year = {2024}, author = {Juli, MSB and Boe-Hansen, GB and Raza, A and Forutan, M and Ong, CT and Siddle, HV and Tabor, AE}, title = {A systematic review of predictive, diagnostic, and prognostic biomarkers for detecting reproductive diseases in cattle using traditional and omics approaches.}, journal = {Journal of reproductive immunology}, volume = {165}, number = {}, pages = {104315}, doi = {10.1016/j.jri.2024.104315}, pmid = {39154625}, issn = {1872-7603}, mesh = {Animals ; Cattle ; Female ; Male ; *Biomarkers/analysis/metabolism ; *Cattle Diseases/diagnosis/immunology ; Cytokines/analysis/metabolism ; Metabolomics/methods ; Prognosis ; Proteomics/methods ; Reproduction/immunology ; }, abstract = {Reproductive diseases and illnesses pose significant challenges in cattle farming, affecting fertility, milk production, and overall herd health. In recent years, the integration of various omics approaches, including transcriptomics, proteomics, metagenomics, miRNAomics, and metabolomics, has revolutionized the study of these conditions. This systematic review summarised the findings from studies that investigated reproductive disease biomarkers in both male and female cattle. After extracting 6137 studies according to exclusion and inclusion criteria, a total of 60 studies were included in this review. All studies identified were associated with female cattle and none were related to reproductive diseases in bulls. The analysis highlights specific biomarkers, metabolic pathways, and microbial compositions associated with bovine reproductive disease conditions, providing valuable insights into the underlying molecular mechanisms of disease. Pro-inflammatory cytokines such as IL-1β, IL-8, IL-4, IL-6, TNFα and acute-phase response proteins such as SAA and HP have been identified as promising biomarkers for bovine reproductive diseases. However, further research is needed to validate these markers clinically and to explore potential strategies for improving cow reproductive health. The role of bulls as carriers of venereal diseases has been underestimated in the current literature and therefore needs more attention to understand their impact on infectious reproductive diseases of female cattle.}, } @article {pmid39154602, year = {2024}, author = {García-Roldán, A and de la Haba, RR and Sánchez-Porro, C and Ventosa, A}, title = {'Altruistic' cooperation among the prokaryotic community of Atlantic salterns assessed by metagenomics.}, journal = {Microbiological research}, volume = {288}, number = {}, pages = {127869}, doi = {10.1016/j.micres.2024.127869}, pmid = {39154602}, issn = {1618-0623}, mesh = {*Metagenomics ; *Bacteria/genetics/classification ; *Salinity ; *Archaea/genetics/classification ; Spain ; Seawater/microbiology ; Phylogeny ; Atlantic Ocean ; Biodiversity ; Salts ; Microbiota/genetics ; Ecosystem ; Metagenome ; }, abstract = {Hypersaline environments are extreme habitats with a limited prokaryotic diversity, mainly restricted to halophilic or halotolerant archaeal and bacterial taxa adapted to highly saline conditions. This study attempts to analyze the taxonomic and functional diversity of the prokaryotes that inhabit a solar saltern located at the Atlantic Coast, in Isla Cristina (Huelva, Southwest Spain), and the influence of salinity on the diversity and metabolic potential of these prokaryotic communities, as well as the interactions and cooperation among the individuals within that community. Brine samples were obtained from different saltern ponds, with a salinity range between 19.5 % and 39 % (w/v). Total prokaryotic DNA was sequenced using the Illumina shotgun metagenomic strategy and the raw sequence data were analyzed using supercomputing services following the MetaWRAP and SqueezeMeta protocols. The most abundant phyla at moderate salinities (19.5-22 % [w/v]) were Methanobacteriota (formerly "Euryarchaeota"), Pseudomonadota and Bacteroidota, followed by Balneolota and Actinomycetota and Uroviricota in smaller proportions, while at high salinities (36-39 % [w/v]) the most abundant phylum was Methanobacteriota, followed by Bacteroidota. The most abundant genera at intermediate salinities were Halorubrum and the bacterial genus Spiribacter, while the haloarchaeal genera Halorubrum, Halonotius, and Haloquadratum were the main representatives at high salinities. A total of 65 MAGs were reconstructed from the metagenomic datasets and different functions and pathways were identified in them, allowing to find key taxa in the prokaryotic community able to synthesize and supply essential compounds, such as biotin, and precursors of other bioactive molecules, like β-carotene, and bacterioruberin, to other dwellers in this habitat, lacking the required enzymatic machinery to produce them. This work shed light on the ecology of aquatic hypersaline environments, such as the Atlantic Coast salterns, and on the dynamics and factors affecting the microbial populations under such extreme conditions.}, } @article {pmid39154578, year = {2024}, author = {Liang, T and Liu, Y and Guo, N and Li, Y and Niu, L and Liu, J and Ma, Q and Zhang, J and Shan, M}, title = {Jinhong decoction ameliorates injury in septic mice without disrupting the equilibrium of gut microbiota.}, journal = {Journal of pharmaceutical and biomedical analysis}, volume = {251}, number = {}, pages = {116404}, doi = {10.1016/j.jpba.2024.116404}, pmid = {39154578}, issn = {1873-264X}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Sepsis/drug therapy/microbiology ; *Drugs, Chinese Herbal/pharmacology ; Mice ; Male ; *Disease Models, Animal ; Anti-Bacterial Agents/pharmacology ; Chromatography, High Pressure Liquid/methods ; Cecum/microbiology ; Mice, Inbred C57BL ; }, abstract = {Sepsis is a life-threatening condition and usually be treated with antibiotics, which however often has severe side effects. This work proposed a novel Chinese traditional medicine JINHONG (JH) decoction for therapy of sepsis. We first identified the chemical constituents of JH decoction by using high-performance liquid chromatography and mass spectrometry (HPLC-MS). Then, we constructed a model mouse for sepsis by using cecal ligation and puncture (CLP). Metagenomic sequencing method was used to compare the diversity and abundance of the gut microbiota between normal, disease model, JH decoction-treatment and antibiotic-treatment mice. Many indices including the number of platelets, CD62p and CD63 content, AQP2 and AQP8 level, as well as the expression level of protein C confirmed that the sepsis resulted in serious pathological damage, while all of these indices could be reversed by JH decoction and antibiotics. The diversity and abundance of intestinal flora decreased in CLP mice, and the decrements aggravated after antibiotic treatment while can be recovered by JH decoction treatment. The abundance of anti-inflammatory Ruminococcaceae increased after JH decoction treatment, indicating that JH decoction could ameliorate pathology associated with sepsis in CLP model via modulating the intestinal flora. This study demonstrates that JH decoction could treat sepsis clinically without obvious adverse effects on gut microbiota.}, } @article {pmid39154395, year = {2024}, author = {Deng, D and Yang, Z and Yang, Y and Wan, W and Liu, W and Xiong, X}, title = {Metagenomic insights into nitrogen-cycling microbial communities and their relationships with nitrogen removal potential in the Yangtze River.}, journal = {Water research}, volume = {265}, number = {}, pages = {122229}, doi = {10.1016/j.watres.2024.122229}, pmid = {39154395}, issn = {1879-2448}, mesh = {*Rivers/microbiology ; *Nitrogen/metabolism ; Metagenomics ; Nitrogen Cycle ; China ; Denitrification ; Metagenome ; Bacteria/metabolism/genetics ; }, abstract = {Nitrogen (N) pollution is a major threat to river ecosystems worldwide. Elucidating the community structure of N-cycling microorganisms in rivers is essential to understanding how ecosystem processes and functions will respond to increasing N inputs. However, previous studies generally focus on limited functional genes through amplicon sequencing or quantitative PCR techniques and cannot cover all N-cycling microorganisms. Here, metagenomic sequencing and genome binning were used to determine N-cycling genes in water, channel sediments, and riparian soils of the Yangtze River, which has been heavily polluted by N. Additionally, the denitrification and anaerobic ammonium oxidation (anammox) rates that reflect N removal potential were measured using [15]N isotope pairing technique. Results showed that functional genes involved in organic N metabolism (i.e., organic degradation and synthesis) and nitrate reduction pathways (i.e., dissimilatory and assimilatory nitrate reduction to ammonium and denitrification) were more abundant and diverse than other N-cycling genes. A total of 121 metagenome-assembled genomes (MAGs) were identified to be involved in N-cycling processes, and the key MAGs were mainly taxonomically classified as Alphaproteobacteria and Gammaproteobacteria. The abundance and diversity of most N-cycling genes were higher in soils and sediments than in water, as well as higher in downstream and midstream than in upstream sites. These spatial variations were explained not only by local environment and vegetation but also by geographical and climatic factors. N removal process (i.e., denitrification and anammox) rates were significantly related to the abundance or diversity of several N-cycling genes, and climate and edaphic factors could regulate denitrification and anammox rates directly and indirectly through their effects on functional genes. Overall, these results provide a new avenue for further understanding the biogeographic patterns and environmental drivers of N-cycling microorganisms in rivers from the metagenomic perspective.}, } @article {pmid39154041, year = {2024}, author = {Ma, T and Zhuang, Y and Lu, W and Tu, Y and Diao, Q and Fan, X and Zhang, N}, title = {Seven hundred and ninety-seven metagenome-assembled genomes from the goat rumen during early life.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {897}, pmid = {39154041}, issn = {2052-4463}, mesh = {Animals ; Gastrointestinal Microbiome ; *Goats/microbiology ; *Metagenome ; *Rumen/microbiology ; }, abstract = {The rumen microbiome plays an important role in providing energy and protein to the host. Manipulation of rumen microbiome during early life may have a long-term beneficial effect on the health, growth performance, and feed efficiency of ruminants. To better understand the profiles and functional potentials of rumen microbiome in young ruminants, metagenomic binning was performed to investigate the rumen microbiome of goat kids from one to 84 days of age. A total of 797 metagenome-assembled genomes (MAGs) were recovered from the rumen of 42 Laiwu black goat kids. Our findings provide fundamental knowledge of the rumen microbiome during early life based on metagenomic binning, which may provide insights into effective strategies to achieve long-term beneficial effects on animal health and production.}, } @article {pmid39153763, year = {2024}, author = {Cleminson, JS and Thomas, J and Stewart, CJ and Campbell, D and Gennery, A and Embleton, ND and Köglmeier, J and Wong, T and Spruce, M and Berrington, JE}, title = {Gut microbiota and intestinal rehabilitation: a prospective childhood cohort longitudinal study of short bowel syndrome (the MIRACLS study): study protocol.}, journal = {BMJ open gastroenterology}, volume = {11}, number = {1}, pages = {}, pmid = {39153763}, issn = {2054-4774}, mesh = {Adolescent ; Child ; Child, Preschool ; Female ; Humans ; Infant ; Infant, Newborn ; Male ; *Feces/microbiology ; *Gastrointestinal Microbiome/physiology ; Intestines/microbiology ; Longitudinal Studies ; *Parenteral Nutrition/methods/statistics & numerical data ; Prospective Studies ; *Quality of Life/psychology ; RNA, Ribosomal, 16S ; *Short Bowel Syndrome/microbiology/epidemiology ; Observational Studies as Topic ; }, abstract = {INTRODUCTION: Short bowel syndrome (SBS) is the predominant cause of paediatric intestinal failure. Although life-saving, parenteral nutrition (PN) is linked to complications and may impact quality of life (QoL). Most children will experience intestinal rehabilitation (IR), but the mechanisms underpinning this remain to be understood. SBS is characterised by abnormal microbiome patterns, which might serve as predictive indicators for IR. We aim to characterise the microbiome profiles of children with SBS during IR, concurrently exploring how parental perspectives of QoL relate to IR.

METHODS AND ANALYSIS: This study will enrol a minimum of 20 paediatric patients with SBS (0-18 years). Clinical data and biological samples will be collected over a 2-year study period. We will apply 16S rRNA gene sequencing to analyse the microbiome from faecal and gut tissue samples, with additional shotgun metagenomic sequencing specifically on samples obtained around the time of IR. Gas chromatography with flame ionisation detection will profile faecal short-chain fatty acids. Plasma citrulline and urinary intestinal fatty acid binding proteins will be measured annually. We will explore microbiome-clinical covariate interactions. Furthermore, we plan to assess parental perspectives on QoL during PN and post-IR by inviting parents to complete the Paediatric Quality of Life questionnaire at recruitment and after the completion of IR.

ETHICS AND DISSEMINATION: Ethical approval was obtained from the East Midlands-Nottingham 2 Research Ethics Committee (22/EM/0233; 28 November 2022). Recruitment began in February 2023. Outcomes of the study will be published in peer-reviewed scientific journals and presented at scientific meetings. A lay summary of the results will be made available to participants and the public.

TRIAL REGISTRATION NUMBER: ISRCTN90620576.}, } @article {pmid39153640, year = {2024}, author = {Du, L and Zhong, H and Guo, X and Li, H and Xia, J and Chen, Q}, title = {Nitrogen fertilization and soil nitrogen cycling: Unraveling the links among multiple environmental factors, functional genes, and transformation rates.}, journal = {The Science of the total environment}, volume = {951}, number = {}, pages = {175561}, doi = {10.1016/j.scitotenv.2024.175561}, pmid = {39153640}, issn = {1879-1026}, mesh = {*Fertilizers ; *Nitrogen Cycle ; *Nitrogen/metabolism ; *Soil Microbiology ; *Soil/chemistry ; *Agriculture/methods ; Fungi ; Bacteria ; Phosphorus/analysis ; Ecosystem ; }, abstract = {Anthropogenic nitrogen (N) inputs substantially influence the N cycle in agricultural ecosystems. However, the potential links among various environmental factors, nitrogen functional genes, and transformation rates under N fertilization remain poorly understood. Here, we conducted a five-year field experiment and collected 54 soil samples from three 0-4 m boreholes across different treatments: control, N-addition (nitrogen fertilizer) and NPK-addition (combined application of nitrogen, phosphorus and potassium fertilizers) treatments. Our results revealed pronounced variations in soil physiochemical parameters, metal concentrations and antibiotic levels under both N and NPK treatments. These alternations induced significant shifts in bacterial and fungal communities, altered NFG abundance and composition, and greatly enhanced rates of nitrate reduction processes. Notably, nutrients, antibiotics and bacteria exerted a more pronounced influence on NFGs and nitrate reduction under N treatment, whereas nutrients, metals, bacteria and fungi had a significant impact under NPK treatment. Furthermore, we established multidimensional correlations between nitrate reduction gene profiles and the activity rates under N and NPK treatments, contrasting with the absence of significant relationships in the control treatment. These findings shed light on the intricate relationships between microbial genetics and ecosystem functions in agricultural ecosystem, which is of significance for predicting and managing metabolic processes effectively.}, } @article {pmid39153624, year = {2024}, author = {Barquero, MB and García-Díaz, C and Dobbler, PT and Jehmlich, N and Moreno, JL and López-Mondéjar, R and Bastida, F}, title = {Contrasting fertilization and phenological stages shape microbial-mediated phosphorus cycling in a maize agroecosystem.}, journal = {The Science of the total environment}, volume = {951}, number = {}, pages = {175571}, doi = {10.1016/j.scitotenv.2024.175571}, pmid = {39153624}, issn = {1879-1026}, mesh = {*Zea mays ; *Phosphorus/metabolism ; *Fertilizers ; *Soil Microbiology ; Microbiota ; Bacteria/metabolism ; Agriculture/methods ; Archaea/physiology/metabolism ; Soil/chemistry ; }, abstract = {Phosphorus (P) is essential for plants but often limited in soils, with microbes playing a key role in its cycling. P deficiency in crops can be mitigated by applying by-products like sludge and struvite to enhance yield and sustainability. Here, we evaluated the contribution of four different types of fertilizers: i) conventional NPK; ii) sludge; iii) struvite; and iv) struvite+sludge in a semiarid maize plantation to the availability of P and the responses of the soil microbiome. We investigated the effects of these treatments on the relative abundance of bacterial and archaeal genes and proteins related to organic P mineralization, inorganic P solubilization, and the P starvation response regulation through a multi-omic approach. Moreover, we explored the impact of maize phenology by collecting samples at germination and flowering stages. Our findings suggest that the phenological stage has a notable impact on the abundance of P cycle genes within bacterial and archaeal communities, particularly regarding the solubilization of inorganic P. Furthermore, significant variations were observed in the relative abundance of genes associated with different P cycles in response to various fertilizer treatments. Sludge and struvite application improved P availability, which was related to an increase in the relative abundance of Sphingomonas (Proteobacteria) and Luteitalea (Acidobacteria) respectively, and genes related to inorganic P solubilization. Furthermore, we observed a substantial taxonomic clustering of functional processes associated with the P cycle. Among the dominant bacterial populations containing P-related genes, those microbes possessing genes linked to the solubilization of inorganic P typically did not harbor genes associated with the mineralization of organic P. This phenomenon was particularly evident among members of Actinobacteria. Overall, we reveal important shifts in bacterial and archaeal communities and associated molecular processes, stressing the intricate interplay between fertilization, phenology, and P cycling in agroecosystems.}, } @article {pmid39153612, year = {2024}, author = {Chen, T and Wang, Z and Ruan, X}, title = {Antibiotic resistome dynamics in agricultural river systems: Elucidating transmission mechanisms and associated risk to water security.}, journal = {The Science of the total environment}, volume = {951}, number = {}, pages = {175580}, doi = {10.1016/j.scitotenv.2024.175580}, pmid = {39153612}, issn = {1879-1026}, mesh = {*Rivers/microbiology ; China ; *Agriculture ; *Drug Resistance, Microbial/genetics ; *Environmental Monitoring ; Anti-Bacterial Agents ; Water Pollutants, Chemical/analysis ; }, abstract = {Usage of antibiotics in agriculture has increased dramatically recently, significantly raising the influx of antibiotic resistance genes (ARGs) into river systems through organic manure runoff, seriously threatening water security. However, the dynamics, transmission mechanisms, and potential water security risk of ARGs, as well as their response to land use spatial scale and seasonal variations in agricultural river systems remain unclear. To address these challenges, this work employed metagenomic technique to systematically evaluate the pollution and dissemination of ARGs in overlying water and sediment within a typical agricultural catchment in China. The results demonstrated significant differences between overlying water and sediment ARGs. Overlying water dominated by multidrug ARGs exhibited higher diversity, whereas sediment predominantly containing sulfonamide ARGs had higher abundance. The dynamics of ARGs in overlying water were more responsive to seasonal variations compared to sediment due to greater changes in hydrodynamics and nutrient conditions. The profiles of ARGs in overlying water were largely regulated by microbiota, whereas mobile genetic elements (MGEs) were the main forces driving the dissemination of ARGs in sediment. The variation in dissemination mechanisms led to different resistance risks, with sediment presenting a higher resistance risk than overlying water. Furthermore, Mantel test was applied to discover the impact of land use spatial scale and composition on the transmission of ARGs in river systems. The findings showed that cultivated land within 5 km of the riverbank was the key influencing factor. Cultivated land exacerbated ARGs spread by increasing MGEs abundance and nutrient concentrations, resulting in the abundance of ARGs in high-cultivated sites being twice that in low-cultivated sites, and raising the regional water security risk, with a more pronounced effect in sediment. These findings contribute to a better understanding of ARGs dissemination in agricultural watersheds, providing a basis for implementing effective resistance control measures and ensuring water security.}, } @article {pmid39153565, year = {2024}, author = {Yang, C and Yan, S and Zhang, B and Yao, X and Mo, J and Rehman, F and Guo, J}, title = {Spatiotemporal distribution of the planktonic microbiome and antibiotic resistance genes in a typical urban river contaminated by macrolide antibiotics.}, journal = {Environmental research}, volume = {262}, number = {Pt 1}, pages = {119808}, doi = {10.1016/j.envres.2024.119808}, pmid = {39153565}, issn = {1096-0953}, mesh = {*Rivers/microbiology/chemistry ; *Microbiota/drug effects ; *Macrolides/analysis ; *Anti-Bacterial Agents/pharmacology/analysis ; *Plankton/drug effects/genetics ; *Drug Resistance, Microbial/genetics ; *Water Pollutants, Chemical/analysis ; Environmental Monitoring ; Genes, Bacterial ; Bacteria/genetics/drug effects/classification ; }, abstract = {The widespread application of macrolide antibiotics has caused antibiotic resistance pollution, threatening the river ecological health. In this study, five macrolide antibiotics (azithromycin, clarithromycin, roxithromycin, erythromycin, and anhydro erythromycin A) were monitored in the Zao River across three hydrological periods (April, July, and December). Simultaneously, the changes in antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and planktonic bacterial communities were determined using metagenomic sequencing. A clear pollution gradient was observed for azithromycin and roxithromycin, with the concentrations in the dry season surpassing those in other seasons. The highest concentration was observed for azithromycin (1.36 μg/L). The abundance of MLS resistance genes increased along the Zao River during the dry season, whereas the opposite trend was obtained during the wet season. A significant correlation between the levels of MLS resistance genes and macrolide antibiotics was identified during the dry season. Notably, compared with the reference site, the abundance of transposase in the effluent from wastewater treatment plants (WWTPs) was significantly elevated in both dry and wet seasons, whereas the abundance of insertion sequences (IS) and plasmids declined during the dry season. The exposure to wastewater containing macrolide antibiotics altered the diversity of planktonic bacterial communities. The bacterial host for ARGs appeared to be Pseudomonas, primarily associated with multidrug subtypes. Moreover, the ARG subtypes were highly correlated with MGEs (transposase and istA). The partial least-squares path model (PLS-PM) demonstrated a positive correlation between the abundance of MGEs and ARGs, indicating the significance of horizontal gene transfer (HGT) in the dissemination of ARGs within the Zao River. Environmental variables, such as TN and NO3[-]-N, were significantly correlated with the abundance of MGEs, ARGs, and bacteria. Collectively, our findings could provide insights into the shift patterns of the microbiome and ARGs across the contamination gradient of AZI and ROX in the river.}, } @article {pmid39153385, year = {2024}, author = {Shen, J and Yu, D and Liu, Z and Di, H and He, JZ}, title = {Land use conversion to uplands significantly increased the risk of antibiotic resistance genes in estuary area.}, journal = {Environment international}, volume = {191}, number = {}, pages = {108953}, doi = {10.1016/j.envint.2024.108953}, pmid = {39153385}, issn = {1873-6750}, mesh = {*Estuaries ; *Wetlands ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Metagenomics ; Agriculture ; Anti-Bacterial Agents ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Land use conversion in estuary wetlands may affect the transmission of antibiotic resistance genes (ARGs), while the risk rank of the ARGs and the change of clinically relevant ARGs under various land-use types are not well understood. This study used metagenomics to reveal the diversity and abundance of ARGs across five distinct land uses: reed wetland, tidal flat, grassland, agricultural land and fallow land, as well as their distribution and potential health risks. Results showed that high numbers of ARG subtypes and classes were detected irrespective of land-use types, notably higher in agricultural land (144 ARG subtypes). The most shared ARG subtypes were multidrug resistance genes across all the land uses (29 subtypes, 4.7 × 10[-2]-1.5 × 10[-1] copies per 16S rRNA gene copy). Proteobacteria and Actinobacteria were primary ARG hosts, with 18 and 15 ARGs were found in both of them, respectively. The ARG subtype mdtB was the most dominant clinical ARG detected with 90 % amino acid identity. The change of ARGs exhibited a consistent trend across land uses in terms of health risk ranks, with the highest observed in fallow land and the lowest in reed wetland. This study reveals the distribution pattern of ARGs across various land-use types, and enhances our understanding of the potential health risks associated with ARGs in the context of coastal wetland conversion in estuary areas.}, } @article {pmid39152661, year = {2024}, author = {Leugger, F and Schmidlin, M and Lüthi, M and Kontarakis, Z and Pellissier, L}, title = {Scanning amplicons with CRISPR-Dx detects endangered amphibians in environmental DNA.}, journal = {Molecular ecology resources}, volume = {24}, number = {8}, pages = {e14009}, doi = {10.1111/1755-0998.14009}, pmid = {39152661}, issn = {1755-0998}, support = {//Swiss Federal Institute for Forest, Snow and Landscape Research/ ; 40B2-0_203550//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; }, mesh = {Animals ; *Amphibians/genetics/classification ; *DNA, Environmental/genetics ; *Endangered Species ; Switzerland ; *Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; DNA Barcoding, Taxonomic/methods ; Ponds ; Biodiversity ; Metagenomics/methods ; }, abstract = {More efficient methods for extensive biodiversity monitoring are required to support rapid measures to address the biodiversity crisis. While environmental DNA (eDNA) metabarcoding and quantitative PCR (qPCR) methods offer advantages over traditional monitoring approaches, their large-scale application is limited by the time and labour required for developing assays and/or for analysis. CRISPR (clustered regularly interspaced short palindromic repeats) diagnostic technologies (Dx) may overcome some of these limitations, but they have been used solely with species-specific primers, restricting their versatility for biodiversity monitoring. Here, we demonstrate the feasibility of designing species-specific CRISPR-Dx assays in silico within a short metabarcoding fragment using a general primer set, a methodology we term 'ampliscanning', for 18 of the 22 amphibian species in Switzerland. We sub-selected nine species, including three classified as regionally endangered, to test the methodology using eDNA sampled from ponds at nine sites. We compared the ampliscanning detections to data from traditional monitoring at these sites. Ampliscanning was successful at detecting target species with different prevalences across the landscape. With only one visit, we detected more species per site than three traditional monitoring visits (visual and acoustic detections by trained experts), in particular more elusive species and previously undocumented but expected populations. Ampliscanning detected 25 species/site combinations compared to 12 with traditional monitoring. Sensitivity analyses showed that larger numbers of field visits and PCR replicates are more important for reliable detection than many technical replicates at the CRISPR-Dx assay level. Given the reduced sampling and analysis effort, our results highlight the benefits of eDNA and CRISPR-Dx combined with universal primers for large-scale monitoring of multiple endangered species across landscapes to inform conservation measures.}, } @article {pmid39152482, year = {2024}, author = {Luo, W and Zhao, M and Dwidar, M and Gao, Y and Xiang, L and Wu, X and Medema, MH and Xu, S and Li, X and Schäfer, H and Chen, M and Feng, R and Zhu, Y}, title = {Microbial assimilatory sulfate reduction-mediated H2S: an overlooked role in Crohn's disease development.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {152}, pmid = {39152482}, issn = {2049-2618}, support = {82370551//National Natural Science Foundation of China/ ; 82270579//National Natural Science Foundation of China/ ; 82100577//National Natural Science Foundation of China/ ; 2024GXNSFFA010009//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; }, mesh = {*Crohn Disease/microbiology ; Humans ; *Gastrointestinal Microbiome ; *Hydrogen Sulfide/metabolism ; Animals ; Mice ; *Sulfates/metabolism ; Escherichia coli/genetics/metabolism ; Feces/microbiology ; Dysbiosis/microbiology ; Colon/microbiology ; Metagenomics ; Oxidation-Reduction ; Disease Models, Animal ; Female ; }, abstract = {BACKGROUND: H2S imbalances in the intestinal tract trigger Crohn's disease (CD), a chronic inflammatory gastrointestinal disorder characterized by microbiota dysbiosis and barrier dysfunction. However, a comprehensive understanding of H2S generation in the gut, and the contributions of both microbiota and host to systemic H2S levels in CD, remain to be elucidated. This investigation aimed to enhance comprehension regarding the sulfidogenic potential of both the human host and the gut microbiota.

RESULTS: Our analysis of a treatment-naive CD cohorts' fecal metagenomic and biopsy metatranscriptomic data revealed reduced expression of host endogenous H2S generation genes alongside increased abundance of microbial exogenous H2S production genes in correlation with CD. While prior studies focused on microbial H2S production via dissimilatory sulfite reductases, our metagenomic analysis suggests the assimilatory sulfate reduction (ASR) pathway is a more significant contributor in the human gut, given its high prevalence and abundance. Subsequently, we validated our hypothesis experimentally by generating ASR-deficient E. coli mutants ∆cysJ and ∆cysM through the deletion of sulfite reductase and L-cysteine synthase genes. This alteration significantly affected bacterial sulfidogenic capacity, colon epithelial cell viability, and colonic mucin sulfation, ultimately leading to colitis in murine model. Further study revealed that gut microbiota degrade sulfopolysaccharides and assimilate sulfate to produce H2S via the ASR pathway, highlighting the role of sulfopolysaccharides in colitis and cautioning against their use as food additives.

CONCLUSIONS: Our study significantly advances understanding of microbial sulfur metabolism in the human gut, elucidating the complex interplay between diet, gut microbiota, and host sulfur metabolism. We highlight the microbial ASR pathway as an overlooked endogenous H2S producer and a potential therapeutic target for managing CD. Video Abstract.}, } @article {pmid39152290, year = {2024}, author = {Chen, J and Qin, Z and Jia, Z}, title = {The application status of sequencing technology in global respiratory infectious disease diagnosis.}, journal = {Infection}, volume = {52}, number = {6}, pages = {2169-2181}, pmid = {39152290}, issn = {1439-0973}, support = {INV-045088//Bill and Melinda Gates Foundation/ ; }, mesh = {Humans ; *Respiratory Tract Infections/diagnosis/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Molecular Diagnostic Techniques/methods ; }, abstract = {Next-generation sequencing (NGS) has revolutionized clinical microbiology, particularly in diagnosing respiratory infectious diseases and conducting epidemiological investigations. This narrative review summarizes conventional methods for routine respiratory infection diagnosis, including culture, smear microscopy, immunological assays, image techniques as well as polymerase chain reaction(PCR). In contrast to conventional methods, there is a new detection technology, sequencing technology, and here we mainly focus on the next-generation sequencing NGS, especially metagenomic NGS(mNGS). NGS offers significant advantages over traditional methods. Firstly, mNGS eliminates assumptions about pathogens, leading to faster and more accurate results, thus reducing diagnostic time. Secondly, it allows unbiased identification of known and novel pathogens, offering broad-spectrum coverage. Thirdly, mNGS not only identifies pathogens but also characterizes microbiomes, analyzes human host responses, and detects resistance genes and virulence factors. It can complement targeted sequencing for bacterial and fungal classification. Unlike traditional methods affected by antibiotics, mNGS is less influenced due to the extended survival of pathogen DNA in plasma, broadening its applicability. However, barriers to full integration into clinical practice persist, primarily due to cost constraints and limitations in sensitivity and turnaround time. Despite these challenges, ongoing advancements aim to improve cost-effectiveness and efficiency, making NGS a cornerstone technology for global respiratory infection diagnosis.}, } @article {pmid39152146, year = {2024}, author = {Mizsei, E and Radovics, D and Rák, G and Budai, M and Bancsik, B and Szabolcs, M and Sos, T and Lengyel, S}, title = {Alpine viper in changing climate: thermal ecology and prospects of a cold-adapted reptile in the warming Mediterranean.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {18988}, pmid = {39152146}, issn = {2045-2322}, support = {150510498//Mohamed bin Zayed Species Conservation Fund/ ; 15478-1//Rufford Foundation/ ; PD146621//Nemzeti Kutatási Fejlesztési és Innovációs Hivatal/ ; K106133//Nemzeti Kutatási Fejlesztési és Innovációs Hivatal/ ; K134391//Nemzeti Kutatási Fejlesztési és Innovációs Hivatal,Hungary/ ; }, mesh = {Animals ; *Viperidae/physiology ; *Climate Change ; Male ; Female ; Ecosystem ; Body Temperature Regulation/physiology ; Greece ; Cold Temperature ; Adaptation, Physiological ; Mediterranean Region ; Acclimatization/physiology ; Phylogeny ; Body Temperature/physiology ; }, abstract = {In a rapidly changing thermal environment, reptiles are primarily dependent on in situ adaptation because of their limited ability to disperse and the restricted opportunity to shift their ranges. However, the rapid pace of climate change may surpass these adaptation capabilities or elevate energy expenditures. Therefore, understanding the variability in thermal traits at both individual and population scales is crucial, offering insights into reptiles' vulnerability to climate change. We studied the thermal ecology of the endangered Greek meadow viper (Vipera graeca), an endemic venomous snake of fragmented alpine-subalpine meadows above 1600 m of the Pindos mountain range in Greece and Albania, to assess its susceptibility to anticipated changes in the alpine thermal environment. We measured preferred body temperature in artificial thermal gradient, field body temperatures of 74 individuals in five populations encompassing the entire geographic range of the species, and collected data on the available of temperatures for thermoregulation. We found that the preferred body temperature (Tp) differed only between the northernmost and the southernmost populations and increased with female body size but did not depend on sex or the gravidity status of females. Tp increased with latitude but was unaffected by the phylogenetic position of the populations. We also found high accuracy of thermoregulation in V. graeca populations and variation in the thermal quality of habitats throughout the range. The overall effectiveness of thermoregulation was high, indicating that V. graeca successfully achieves its target temperatures and exploits the thermal landscape. Current climatic conditions limit the activity period by an estimated 1278 h per year, which is expected to increase considerably under future climate scenarios. Restricted time available for thermoregulation, foraging and reproduction will represent a serious threat to the fitness of individuals and the persistence of populations in addition to habitat loss due to mining, tourism or skiing and habitat degradation due to overgrazing in the shrinking mountaintop habitats of V. graeca.}, } @article {pmid39151634, year = {2024}, author = {Xu, WJ and Meng, L and Zhao, YK and Wu, J and Liu, HM and Wang, JQ and Zheng, N}, title = {Characteristics of psychrophilic bacterial communities and associated metabolism pathways in different environments by a metagenomic analysis.}, journal = {The Science of the total environment}, volume = {953}, number = {}, pages = {175496}, doi = {10.1016/j.scitotenv.2024.175496}, pmid = {39151634}, issn = {1879-1026}, mesh = {China ; *Bacteria/classification/metabolism/genetics ; *Metagenomics ; *Milk/microbiology ; Animals ; Microbiota ; }, abstract = {Psychrophilic bacteria, the dominant spoilage organisms in raw milk, secrete heat-stable extracellular proteases and lipases that lead to the decomposition of milk and dairy products. In this study, we investigated psychrophilic bacteria in 165 raw milk samples collected across four seasons and six regions in China using shotgun metagenomic sequencing and traditional culture methods. The isolated psychrophilic bacteria were classified into 40 genera and 185 species. Pseudomonas was the most prevalent, accounting for 51.13 % of the genera, while Lactococcus and Chryseobacterium were also notably abundant (> 6.0 %). Metagenomic sequencing revealed that Pseudomonas (47.9 %), Stenotrophomonas (9.75 %), Sphingomonas (6.73 %), Latilactobacillus (6.38 %) and Lactococcus (5.16 %) were the dominant genera in the raw milk samples. The diversity of psychrophilic bacteria in raw milk was strongly influenced by seasonal variations, with the sampling region being a less significant factor. KEGG annotation indicated that carbohydrate and amino acid metabolism were the primary metabolic pathways in these bacteria. Metagenomic sequencing not only accurately identifies species but also provides functional insights into psychrophilic bacteria in raw milk, aiding in understanding their activities, promoting their control on farms, and ultimately improving raw milk quality.}, } @article {pmid39151620, year = {2024}, author = {Zheng, Y and Wu, Z and Wang, P and Wei, Y and Jia, K and Zhang, M and Shi, X and Zhang, L and Li, J}, title = {Long-chain fatty acids facilitate acidogenic fermentation of food waste: Attention to the microbial response and the change of core metabolic pathway under saturated and unsaturated fatty acids loading.}, journal = {The Science of the total environment}, volume = {951}, number = {}, pages = {175565}, doi = {10.1016/j.scitotenv.2024.175565}, pmid = {39151620}, issn = {1879-1026}, mesh = {*Fermentation ; *Fatty Acids/metabolism ; Metabolic Networks and Pathways ; Fatty Acids, Volatile/metabolism ; Fatty Acids, Unsaturated/metabolism ; Food Loss and Waste ; }, abstract = {Long-chain fatty acids (LCFAs) are recognized as a significant inhibitory factor in anaerobic digestion of food waste (FW), yet they are inevitably present in FW due to lipid hydrolysis. Given their distinct synthesis mechanism from traditional anaerobic digestion, little is known about the effect of LCFAs on FW acidogenic fermentation. This study reveals that total volatile fatty acids (VFAs) production increased by 9.98 % and 4.03 % under stearic acid and oleic acid loading, respectively. Acetic acid production increased by 20.66 % under stearic acid loading compared to the control group (CK). However, the LCFA stress restricted the degradation of solid organic matter, particularly under oleic acid stress. Analysis of microbial community structure and quorum sensing (QS) indicates that LCFA stress enhanced the relative abundance of Lactobacillus and Klebsiella. In QS system, the relative abundance of luxS declined from 0.157 % to 0.116 % and 0.125 % under oleic acid and stearic acid stress, respectively. LCFA stress limited the Autoinducer-2 (AI-2) biosynthesis, suggesting that microorganisms cannot use QS to resist the LCFA stress. Metagenomic sequencing showed that LCFA stress promoted acetic acid production via the conversion of pyruvate and acetyl-CoA to acetate. Direct conversion of pyruvate to acetic acid increased by 47.23 % compared to the CK group, accounting for the enhanced acetic acid production under stearic acid loading. The abundance of β-oxidation pathway under stearic acid loading was lower than under oleic acid loading. Overall, the stimulating direct conversion of pyruvate plays a pivotal role in enhancing acetic acid biosynthesis under stearic acid loading, providing insights into the effect of LCFA on mechanism of FW acidogenic fermentation.}, } @article {pmid39151617, year = {2024}, author = {Galisteo, C and Puente-Sánchez, F and de la Haba, RR and Bertilsson, S and Sánchez-Porro, C and Ventosa, A}, title = {Metagenomic insights into the prokaryotic communities of heavy metal-contaminated hypersaline soils.}, journal = {The Science of the total environment}, volume = {951}, number = {}, pages = {175497}, doi = {10.1016/j.scitotenv.2024.175497}, pmid = {39151617}, issn = {1879-1026}, mesh = {*Soil Microbiology ; *Metals, Heavy/analysis ; *Soil Pollutants/analysis ; *Bacteria/metabolism/classification ; *Microbiota ; *Archaea/genetics ; Soil/chemistry ; Spain ; Salinity ; Metagenome ; Metagenomics ; }, abstract = {Saline soils and their microbial communities have recently been studied in response to ongoing desertification of agricultural soils caused by anthropogenic impacts and climate change. Here we describe the prokaryotic microbiota of hypersaline soils in the Odiel Saltmarshes Natural Area of Southwest Spain. This region has been strongly affected by mining and industrial activity and feature high levels of certain heavy metals. We sequenced 18 shotgun metagenomes through Illumina NovaSeq from samples obtained from three different areas in 2020 and 2021. Taxogenomic analyses demonstrate that these soils harbored equal proportions of archaea and bacteria, with Methanobacteriota, Pseudomonadota, Bacteroidota, Gemmatimonadota, and Balneolota as most abundant phyla. Functions related to the transport of heavy metal outside the cytoplasm are among the most relevant features of the community (i.e., ZntA and CopA enzymes). They seem to be indispensable to avoid the increase of zinc and copper concentration inside the cell. Besides, the archaeal phylum Methanobacteriota is the main arsenic detoxifier within the microbiota although arsenic related genes are widely distributed in the community. Regarding the osmoregulation strategies, "salt-out" mechanism was identified in part of the bacterial population, whereas "salt-in" mechanism was present in both domains, Bacteria and Archaea. De novo biosynthesis of two of the most universal compatible solutes was detected, with predominance of glycine betaine biosynthesis (betAB genes) over ectoine (ectABC genes). Furthermore, doeABCD gene cluster related to the use of ectoine as carbon and energy source was solely identified in Pseudomonadota and Methanobacteriota.}, } @article {pmid39151562, year = {2024}, author = {Rahimian, M and Panahi, B}, title = {Metagenome sequence data mining for viral interaction studies: Review on progress and prospects.}, journal = {Virus research}, volume = {349}, number = {}, pages = {199450}, pmid = {39151562}, issn = {1872-7492}, mesh = {*Metagenomics/methods ; *Metagenome ; *Viruses/genetics/classification ; *Computational Biology/methods ; *Data Mining ; *High-Throughput Nucleotide Sequencing ; Humans ; Animals ; }, abstract = {Metagenomics has been greatly accelerated by the development of next-generation sequencing (NGS) technologies, which allow scientists to discover and describe novel microorganisms without the need for conventional culture techniques. Examining integrative bioinformatics methods used in viral interaction research, this study highlights metagenomic data from various contexts. Accurate viral identification depends on high-purity genetic material extraction, appropriate NGS platform selection, and sophisticated bioinformatics tools like VirPipe and VirFinder. The efficiency and precision of metagenomic analysis are further improved with the advent of AI-based techniques. The diversity and dynamics of viral communities are demonstrated by case studies from a variety of environments, emphasizing the seasonal and geographical variations that influence viral populations. In addition to speeding up the discovery of new viruses, metagenomics offers thorough understanding of virus-host interactions and their ecological effects. This review provides a promising framework for comprehending the complexity of viral communities and their interactions with hosts, highlighting the transformational potential of metagenomics and bioinformatics in viral research.}, } @article {pmid39151360, year = {2024}, author = {Ou, Y and Wu, M and Yu, Y and Liu, Z and Zhang, Y and Yi, N}, title = {Nitrogen utilization efficiency assessment during bioremediation of petroleum-contaminated loess soils: insights from metagenomic analysis.}, journal = {Journal of hazardous materials}, volume = {478}, number = {}, pages = {135506}, doi = {10.1016/j.jhazmat.2024.135506}, pmid = {39151360}, issn = {1873-3336}, mesh = {*Biodegradation, Environmental ; *Soil Pollutants/metabolism ; *Petroleum/metabolism ; *Nitrogen/metabolism ; *Soil Microbiology ; Hydrocarbons/metabolism ; Metagenomics ; }, abstract = {Nitrogen addition is commonly used to remediate total petroleum hydrocarbons (TPH) in petroleum-contaminated soils. However, acceptable exogenous nitrogen dosages and their utilization efficiency for the degradation of hydrocarbons in oil-polluted soils are not well understood. This study compared the hydrocarbon bioremediation capacity by applying different doses of NH4Cl as a stimulant in soils contaminated with TPH at 8553 and 17090 mg/kg. The results showed acceptable exogenous nitrogen levels ranging from 60 to 360 mg N/kg soil, and the optimal nitrogen dosage for TPH remediation was 136 mg N/kg in soils with different TPH concentrations. The nitrogen availability efficiency (NAE) and nitrogen polarization factor availability (NPFA) in the 136 mg N/kg addition treatments were 6.69 and 20.47 mg/mg in 8533 mg/kg TPH-polluted soil, and 6.03 and 31.11 mg/mg in 17090 mg/kg TPH-polluted soil, respectively. Metagenomic analysis revealed that the application of 136 mg/kg nitrogen facilitated ammonia oxidation and nitrite reduction to nitric oxide, and induced soil microorganisms to undergo regulatory or adaptive changes in energy supply and metabolic state, which could aid in restoring the ecological functions of petroleum-contaminated soils. These findings underscore that 136 mg/kg of nitrogen dosage application is optimal for remediation of petroleum-contaminated soils irrespective of the TPH concentrations. This exogenous nitrogen application dosage for TPH remediation aligns with the nitrogen requirements for crop growth in agriculture.}, } @article {pmid39151267, year = {2024}, author = {Yan, W and Bai, R and Zhang, Q and Jiang, Y and Chen, G and Zhang, Y and Wu, Y and Guo, X and Xiao, Y and Zhao, F}, title = {Metagenomic insights into ecological risk of antibiotic resistome and mobilome in riverine plastisphere under impact of urbanization.}, journal = {Environment international}, volume = {190}, number = {}, pages = {108946}, doi = {10.1016/j.envint.2024.108946}, pmid = {39151267}, issn = {1873-6750}, mesh = {*Urbanization ; *Rivers/microbiology/chemistry ; Humans ; Drug Resistance, Microbial/genetics ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; Microplastics ; }, abstract = {Microplastics (MPs) are of increasing concern due to their role as reservoirs for antibiotic resistance genes (ARGs) and pathogens. To date, few studies have explored the influence of anthropogenic activities on ARGs and mobile genetic elements (MGEs) within various riverine MPs, in comparison to their natural counterparts. Here an in-situ incubation was conducted along heavily anthropogenically-impacted Houxi River to characterize the geographical pattern of antibiotic resistome, mobilome and pathogens inhabiting MPs- and leaf-biofilms. The metagenomics result showed a clear urbanization-driven profile in the distribution of ARGs, MGEs and pathogens, with their abundances sharply increasing 4.77 to 19.90 times from sparsely to densely populated regions. The significant correlation between human fecal marker crAssphage and ARG (R[2] = 0.67, P=0.003) indicated the influence of anthropogenic activity on ARG proliferation in plastisphere and natural leaf surfaces. And mantel tests and random forest analysis revealed the impact of 17 socio-environmental factors, e.g., population density, antibiotic concentrations, and pore volume of materials, on the dissemination of ARGs. Partial least squares-path modeling further unveiled that intensifying human activities not only directly boosted ARGs abundance but also exerted a comparable indirect impact on ARGs propagation. Furthermore, the polyvinylchloride plastisphere created a pathogen-friendly habitat, harboring higher abundances of ARGs and MGEs, while polylactic acid are not likely to serve as vectors for pathogens in river, with a lower resistome risk score than that in leaf-biofilms. This study highlights the diverse ecological risks associated with the dissemination of ARGs and pathogens in varied MPs, offering insights for the policymaking of usage and control of plastics within urbanization.}, } @article {pmid39151014, year = {2024}, author = {Schickele, A and Debeljak, P and Ayata, SD and Bittner, L and Pelletier, E and Guidi, L and Irisson, JO}, title = {The genomic potential of photosynthesis in piconanoplankton is functionally redundant but taxonomically structured at a global scale.}, journal = {Science advances}, volume = {10}, number = {33}, pages = {eadl0534}, pmid = {39151014}, issn = {2375-2548}, mesh = {*Photosynthesis/genetics ; *Ribulose-Bisphosphate Carboxylase/genetics/metabolism ; Plankton/genetics/metabolism ; Genomics/methods ; Phylogeny ; Carbon Cycle ; Metagenomics/methods ; Metagenome ; Seawater ; }, abstract = {Carbon fixation is a key metabolic function shaping marine life, but the underlying taxonomic and functional diversity involved is only partially understood. Using metagenomic resources targeted at marine piconanoplankton, we provide a reproducible machine learning framework to derive the potential biogeography of genomic functions through the multi-output regression of gene read counts on environmental climatologies. Leveraging the Marine Atlas of Tara Oceans Unigenes, we investigate the genomic potential of primary production in the global ocean. The latter is performed by ribulose-1,5-bisphosphate carboxylase/oxygenase (RUBISCO) and is often associated with carbon concentration mechanisms in piconanoplankton, major marine unicellular photosynthetic organisms. We show that the genomic potential supporting C4 enzymes and RUBISCO exhibits strong functional redundancy and important affinity toward tropical oligotrophic waters. This redundancy is taxonomically structured by the dominance of Mamiellophyceae and Prymnesiophyceae in mid and high latitudes. These findings enhance our understanding of the relationship between functional and taxonomic diversity of microorganisms and environmental drivers of key biogeochemical cycles.}, } @article {pmid39150994, year = {2025}, author = {Malham, M and Vestergaard, MV and Bataillon, T and Villesen, P and Dempfle, A and Bang, C and Engsbro, AL and Jakobsen, C and Franke, A and Wewer, V and Thingholm, LB and Petersen, AM}, title = {The Composition of the Fecal and Mucosa-adherent Microbiota Varies Based on Age and Disease Activity in Ulcerative Colitis.}, journal = {Inflammatory bowel diseases}, volume = {31}, number = {2}, pages = {501-513}, doi = {10.1093/ibd/izae179}, pmid = {39150994}, issn = {1536-4844}, support = {//Aage and Johann Louis-Hansens Foundation/ ; //Aase and Ejnar Danielsens Foundation/ ; //German Research Foundation/ ; }, mesh = {Humans ; *Colitis, Ulcerative/microbiology ; *Feces/microbiology ; Prospective Studies ; Female ; Male ; Adult ; Longitudinal Studies ; *Gastrointestinal Microbiome ; Child ; Adolescent ; *Intestinal Mucosa/microbiology/pathology ; *RNA, Ribosomal, 16S/analysis/genetics ; Young Adult ; Middle Aged ; Age Factors ; }, abstract = {BACKGROUND: Pediatric-onset ulcerative colitis (pUC) represents a more aggressive disease phenotype compared with adult-onset UC. We hypothesized that this difference can, in part, be explained by the composition of the microbiota.

METHODS: In a prospective, longitudinal study, we included pediatric (N = 30) and adult (N = 30) patients with newly or previously (>1 year) diagnosed UC. We analyzed the microbiota composition in the mucosa-adherent microbiota at baseline, using 16S rRNA gene sequencing, and the fecal microbiota at baseline and at 3-month intervals, using shotgun metagenomics.

RESULTS: For fecal samples, the bacterial composition differed between pUC and aUC in newly diagnosed patients (β-diversity, Bray Curtis: R2 = 0.08, P = .02). In colon biopsies, microbial diversity was higher in aUC compared with pUC (α-diversity, Shannon: estimated difference 0.54, P = .006). In the mucosa-adherent microbiota, Alistipes finegoldii was negatively associated with disease activity in pUC while being positively associated in aUC (estimate: -0.255 and 0.098, P = .003 and P = .02 in pUC and aUC, respectively). Finally, we showed reduced stability of the fecal microbiota in pediatric patients, evidenced by a different composition of the fecal microbiota in newly and previously diagnosed pUC, a pattern not found in adults.

CONCLUSIONS: Our results indicate that pediatric UC patients have a more unstable fecal microbiota and a lower α diversity than adult patients and that the microbiota composition differs between aUC and pUC patients. These findings offer some explanation for the observed differences between pUC and aUC and indicate that individualized approaches are needed if microbiota modifications are to be used in the future treatment of UC.}, } @article {pmid39150770, year = {2024}, author = {}, title = {Correction to: A novel bioinformatic method for the identification of antimicrobial peptides in metagenomes.}, journal = {Journal of applied microbiology}, volume = {135}, number = {8}, pages = {}, doi = {10.1093/jambio/lxae207}, pmid = {39150770}, issn = {1365-2672}, } @article {pmid39150504, year = {2024}, author = {Sessa, R and Filardo, S and Viscardi, MF and Brandolino, G and Muzii, L and Di Pietro, M and Porpora, MG}, title = {Characterization of the vaginal microbiota in Italian women with endometriosis: preliminary study.}, journal = {Archives of gynecology and obstetrics}, volume = {310}, number = {4}, pages = {2141-2151}, pmid = {39150504}, issn = {1432-0711}, mesh = {Humans ; Female ; *Endometriosis/microbiology ; Adult ; *Vagina/microbiology ; Cross-Sectional Studies ; Italy ; *Microbiota ; Young Adult ; Dysbiosis/microbiology ; Bacteria/isolation & purification/classification/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {PURPOSE: This cross-sectional study aims to assess the interplay between the vaginal microbiota and endometriosis.

METHODS: 123 consecutive Italian fertile women, aged between 20 and 40 years old, were enrolled during a routine gynecological consultation; 24 were diagnosed with endometriosis and 99 did not complain of any gynecological disease. All women underwent a vaginal swab for the evaluation of the composition and diversity of vaginal microbiota by means of 16 s rDNA metagenomic sequencing.

RESULTS: Compared to women with no gynecological disease, the vaginal microbiota in women with endometriosis showed a similar abundance of Lactobacillus spp.; however, a statistically significant lower abundance in the genera Pseudomonas (p < 0.01), Bifidobacterium (p < 0.05), Novispirillum (p < 0.0000001) and Sphingomonas (p < 0.0000001), and a statistically significant increase in the abundance of the genera Escherichia (p < 0.00001), Megasphaera (p < 0.00001), and Sneathia (p < 0.0001) were observed.

CONCLUSIONS: There is a complex interplay between vaginal microbiota composition and endometriosis, showing a distinct microbial signature in the bacterial genera usually found in dysbiosis.}, } @article {pmid39150251, year = {2024}, author = {Lv, Y and Zhen, C and Liu, A and Hu, Y and Yang, G and Xu, C and Lou, Y and Cheng, Q and Luo, Y and Yu, J and Fang, Y and Zhao, H and Peng, K and Yu, Y and Lou, J and Chen, J and Ni, Y}, title = {Profiles and interactions of gut microbiome and intestinal microRNAs in pediatric Crohn's disease.}, journal = {mSystems}, volume = {9}, number = {9}, pages = {e0078324}, pmid = {39150251}, issn = {2379-5077}, mesh = {Humans ; *MicroRNAs/genetics/metabolism ; *Crohn Disease/microbiology/genetics/metabolism ; *Gastrointestinal Microbiome ; Child ; Male ; Female ; Adolescent ; Feces/microbiology ; Dysbiosis/genetics/microbiology ; Intestines/microbiology ; Bacteria/genetics/isolation & purification ; Intestinal Mucosa/microbiology/metabolism ; }, abstract = {UNLABELLED: Gut dysbiosis is closely related to dysregulated microRNAs (miRNAs) in the intestinal epithelial cells, which plays an important role in the pathogenesis of Crohn's disease (CD). We investigated the relationship between fecal gut microbiome (GM) and intestinal tissue miRNAs in different stages of pediatric CD. Metagenomic analysis and miRNA sequencing were conducted to examine the GM and intestinal miRNA profiles of CD patients before and after clinical induction therapy and the controls. Twenty-seven newly diagnosed, therapy-naïve pediatric patients with active CD and 11 non-inflammatory bowel disease (IBD) controls were recruited in this study. Among CD patients, 11 patients completed induction treatment and reached clinical remission. Both GM and miRNA profiles were significantly changed between CD patients and controls. Seven key bacteria were identified at species level including Defluviitalea raffinosedens, Thermotalea metallivorans, Roseburia intestinalis, Dorea sp. AGR2135, Escherichia coli, Shigella sonnei, and Salmonella enterica, the exact proportions of which were further validated by real-time quantitative PCR analysis. Eight key miRNAs were also identified including hsa-miR-215-5p, hsa-miR-194-5p, hsa-miR-12135, hsa-miR-509-3-5p, hsa-miR-212-5p, hsa-miR-4448, hsa-miR-501-3p, and hsa-miR-503-5p. The functional enrichment analysis of differential miRNAs indicated the significantly altered cyclin protein, cyclin-dependent protein, and cell cycle pathway. The close interactions between seven key bacteria and eight key miRNAs were further investigated by miRNA target prediction. The association between specific miRNA expressions and key gut bacteria at different stages of CD supported their important roles as potential molecular biomarkers. Understanding the relationship between them will help us to explore the molecular mechanisms of CD.

IMPORTANCE: Since previous studies have focused on the change of the fecal gut microbiome and intestinal tissue miRNA in pediatric Crohn's disease (CD), the relationship between them in different stages is still not clear. This is the first study to explore the gut microbiota and miRNA and their correlations with the Pediatric Crohn's Disease Activity Index (PCDAI). Crohn's Disease Endoscopic Index of Severity (CDEIS), and calprotectin, by applying two omics approach in three different groups (active CD, CD in remission with exclusive enteral nutrition or infliximab induction therapy, and the healthy controls). Both gut microbiome structure and the miRNA profiles were significantly changed in the different stage of CD. Seven key gut microbiome at species and eight key miRNAs were found, and their close interactions were further fully investigated by miRNA target prediction.}, } @article {pmid39149810, year = {2024}, author = {Liu, J and Wang, WJ and Xu, GF and Wang, YX and Lin, Y and Zheng, X and Yao, SH and Zheng, KH}, title = {Does Microbiome Contribute to Longevity? Compositional and Functional Differences in Gut Microbiota in Chinese Long-Living (>90 Years) and Elderly (65-74 Years) Adults.}, journal = {Omics : a journal of integrative biology}, volume = {28}, number = {9}, pages = {461-469}, doi = {10.1089/omi.2024.0120}, pmid = {39149810}, issn = {1557-8100}, mesh = {Humans ; Aged ; *Longevity ; *Gastrointestinal Microbiome/physiology ; Aged, 80 and over ; Male ; Female ; China ; Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; East Asian People ; }, abstract = {The study of longevity and its determinants has been revitalized with the rise of microbiome scholarship. The gut microbiota have been established to play essential protective, metabolic, and physiological roles in human health and disease. The gut dysbiosis has been identified as an important factor contributing to the development of multiple diseases. Accordingly, it is reasonable to hypothesize that the gut microbiota of long-living individuals have healthy antiaging-associated gut microbes, which, by extension, might provide specific molecular targets for antiaging treatments and interventions. In the present study, we compared the gut microbiota of Chinese individuals in two different age groups, long-living adults (aged over 90 years) and elderly adults (aged 65-74 years) who were free of major diseases. We found significantly lower relative abundances of bacteria in the genera Sutterella and Megamonas in the long-living individuals. Furthermore, we established that while biological processes such as autophagy (GO:0006914) and telomere maintenance through semiconservative replication (GO:0032201) were enhanced in the long-living group, response to lipopolysaccharide (GO:0032496), nicotinamide adenine dinucleotide oxidation (GO:0006116), and S-adenosyl methionine metabolism (GO:0046500) were weakened. Moreover, the two groups were found to differ with respect to amino acid metabolism. We suggest that these compositional and functional differences in the gut microbiota may potentially be associated with mechanisms that contribute to determining longevity or aging.}, } @article {pmid39149494, year = {2024}, author = {Lewis, ZJ and Scott, A and Madden, C and Vik, D and Zayed, AA and Smith, GJ and Justice, SS and Rudinsky, A and Hokamp, J and Hale, VL}, title = {Evaluating urine volume and host depletion methods to enable genome-resolved metagenomics of the urobiome.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {39149494}, issn = {2693-5015}, support = {K08 ES034821/ES/NIEHS NIH HHS/United States ; }, abstract = {BACKGROUND: The gut microbiome has emerged as a clear player in health and disease, in part by mediating host response to environment and lifestyle. The urobiome (microbiota of the urinary tract) likely functions similarly. However, efforts to characterize the urobiome and assess its functional potential have been limited due to technical challenges including low microbial biomass and high host cell shedding in urine. Here, to begin addressing these challenges, we evaluate urine sample volume (100 ml - 5 mL), and host DNA depletion methods and their effects on urobiome profiles in healthy dogs, which are a robust large animal model for the human urobiome. We collected urine from seven dogs and fractionated samples into aliquots. One set of samples was spiked with host (canine) cells to model a biologically relevant host cell burden in urine. Samples then underwent DNA extraction followed by 16S rRNA gene and shotgun metagenomic sequencing. We then assembled metagenome assembled genomes (MAGs) and compared microbial composition and diversity across groups. We tested six methods of DNA extraction: QIAamp BiOstic Bacteremia (no host depletion), QIAamp DNA Microbiome, Molzym MolYsis, NEBNext Microbiome DNA Enrichment, Zymo HostZERO, and Propidium Monoazide.

RESULTS: In relation to urine sample volume, [3] 3.0 mL resulted in the most consistent urobiome profiling. In relation to host depletion, individual (dog) but not extraction method drove overall differences in microbial composition. DNA Microbiome yielded the greatest microbial diversity in 16S rRNA sequencing data and shotgun metagenomic sequencing data, and maximized MAG recovery while effectively depleting host DNA in host-spiked urine samples. As proof-of-principle, we then mined MAGs for core metabolic functions and environmental chemical metabolism. We identified long chain alkane utilization in two of the urine MAGs. Long chain alkanes are common pollutants that result from industrial combustion processes and end up in urine.

CONCLUSIONS: This is the first study, to our knowledge, to demonstrate environmental chemical degradation potential in urine microbes through genome-resolved metagenomics. These findings provide guidelines for studying the urobiome in relation to sample volume and host depletion, and lay the foundation for future evaluation of urobiome function in relation to health and disease.}, } @article {pmid39149418, year = {2024}, author = {Zhang, J and Gao, L and Zhu, C and Jin, J and Song, C and Dong, H and Li, Z and Wang, Z and Chen, Y and Yang, Z and Tan, Y and Wang, L}, title = {Corrigendum: Clinical value of metagenomic next-generation sequencing by Illumina and Nanopore for the detection of pathogens in bronchoalveolar lavage fluid in suspected community-acquired pneumonia patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1468511}, doi = {10.3389/fcimb.2024.1468511}, pmid = {39149418}, issn = {2235-2988}, abstract = {[This corrects the article DOI: 10.3389/fcimb.2022.1021320.].}, } @article {pmid39149354, year = {2024}, author = {Heber, K and Tian, S and Betancurt-Anzola, D and Koo, H and Bisanz, JE}, title = {StrainR2 accurately deconvolutes strain-level abundances in synthetic microbial communities.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39149354}, issn = {2692-8205}, support = {R00 AI147165/AI/NIAID NIH HHS/United States ; R35 GM151045/GM/NIGMS NIH HHS/United States ; }, abstract = {BACKGROUND: Synthetic microbial communities offer an opportunity to conduct reductionist research in tractable model systems. However, deriving abundances of highly related strains within these communities is currently unreliable. 16S rRNA gene sequencing does not resolve abundance at the strain level, standard methods for analysis of shotgun metagenomic sequencing do not account for ambiguous mapping between closely related strains, and other methods such as quantitative PCR (qPCR) scale poorly and are resource prohibitive for complex communities. We present StrainR2, which utilizes shotgun metagenomic sequencing paired with a k-mer-based normalization strategy to provide high accuracy strain-level abundances for all members of a synthetic community, provided their genomes.

RESULTS: Both in silico, and using sequencing data derived from gnotobiotic mice colonized with a synthetic fecal microbiota, StrainR2 resolves strain abundances with greater accuracy than other tools utilizing shotgun metagenomic sequencing reads and can resolve complex mixtures of highly related strains. Through experimental validation and benchmarking, we demonstrate that StrainR2's accuracy is comparable to that of qPCR on a subset of strains resolved using absolute quantification. Further, it is capable of scaling to communities of hundreds of strains and efficiently utilizes memory being capable of running both on personal computers and high-performance computing nodes.

CONCLUSIONS: Using shotgun metagenomic sequencing reads is a viable method for determining accurate strain-level abundances in synthetic communities using StrainR2.}, } @article {pmid39148859, year = {2024}, author = {Sumner, JT and Pickens, CI and Huttelmaier, S and Moghadam, AA and Abdala-Valencia, H and , and Hauser, AR and Seed, PC and Wunderink, RG and Hartmann, EM}, title = {Transitions in lung microbiota landscape associate with distinct patterns of pneumonia progression.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {39148859}, support = {R01 HL153122/HL/NHLBI NIH HHS/United States ; U19 AI181102/AI/NIAID NIH HHS/United States ; U19 AI135964/AI/NIAID NIH HHS/United States ; P01 HL154998/HL/NHLBI NIH HHS/United States ; R01 HL149883/HL/NHLBI NIH HHS/United States ; }, abstract = {The precise microbial determinants driving clinical outcomes in severe pneumonia are unknown. Competing ecological forces produce dynamic microbiota states in health; infection and treatment effects on microbiota state must be defined to improve pneumonia therapy. Here, we leverage our unique clinical setting, which includes systematic and serial bronchoscopic sampling in patients with suspected pneumonia, to determine lung microbial ecosystem dynamics throughout pneumonia therapy. We combine 16S rRNA gene amplicon, metagenomic, and transcriptomic sequencing with bacterial load quantification to reveal clinically-relevant pneumonia progression drivers. Microbiota states are predictive of pneumonia category and exhibit differential stability and pneumonia therapy response. Disruptive forces, like aspiration, associate with cohesive changes in gene expression and microbial community structure. In summary, we show that host and microbiota landscapes change in unison with clinical phenotypes and that microbiota state dynamics reflect pneumonia progression. We suggest that distinct pathways of lung microbial community succession mediate pneumonia progression.}, } @article {pmid39148686, year = {2024}, author = {Oki, H and Niwa, R and Pranee, S and Motooka, D and Onda, Y and Nakata, J and Nakajima, H and Oka, Y and Sugiyama, H and Yoshii, Y and Anzai, N and Nakamura, S and Iida, T}, title = {Identification of causative fungus from sterile abscess using metagenomics followed by in situ hybridization.}, journal = {Access microbiology}, volume = {6}, number = {8}, pages = {}, pmid = {39148686}, issn = {2516-8290}, abstract = {Introduction. Invasive fungal infections require early diagnosis for treatment. Microscopic observation of biopsy and blood culture is the gold standard for the identification of the causative fungus, but it is difficult to identify the causative pathogen by a sterile abscess biopsy. Case Presentation. We present a case report of breakthrough invasive trichosporonosis in a 65-year-old Japanese male with acute myeloid leukaemia receiving antifungal prophylaxis. Blood cultures showed no fungal growth, and a liver biopsy and a removed spleen with abscess showed fragmented fungi, but no fungal identification was possible. This report demonstrates that retrospective analyses were able to identify the causative fungus. Conclusion. We narrowed down the candidate fungi by deep sequencing of the ITS1 region of fungal genome and confirmed that the fungus observed in the specimen was Trichosporon asahii by in situ hybridization using a DNA probe targeting 26S rRNA.}, } @article {pmid39147851, year = {2024}, author = {Földvári, G and Tauber, Z and Tóth, GE and Cadar, D and Bialonski, A and Horváth, B and Szabó, É and Lanszki, Z and Zana, B and Varga, Z and Földes, F and Kemenesi, G}, title = {Genomic characterization of Volzhskoe tick virus (Bunyaviricetes) from a Hyalomma marginatum tick, Hungary.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {18945}, pmid = {39147851}, issn = {2045-2322}, support = {CA21170//COST/ ; CA21170//COST/ ; CA21170//COST/ ; RRF-2.3.1-21-2022-00006//National Research, Development and Innovation Office/ ; RRF-2.3.1-21-2022-00006//National Research, Development and Innovation Office/ ; RRF-2.3.1-21-2022-00006//National Research, Development and Innovation Office/ ; RRF-2.3.1-21-2022-00006//National Research, Development and Innovation Office/ ; RRF-2.3.1-21-2022-00006//National Research, Development and Innovation Office/ ; RRF-2.3.1-21-2022-00006//National Research, Development and Innovation Office/ ; RRF-2.3.1-21-2022-00006//National Research, Development and Innovation Office/ ; RRF-2.3.1-21-2022-00006//National Research, Development and Innovation Office/ ; RRF-2.3.1-21-2022-00006//National Research, Development and Innovation Office/ ; RRF-2.3.1-21-2022-00006//National Research, Development and Innovation Office/ ; 13N15449//German Federal Ministry of Education and Research/ ; 13N15449//German Federal Ministry of Education and Research/ ; }, mesh = {Animals ; Hungary ; *Phylogeny ; *Genome, Viral ; Ixodidae/virology ; Ticks/virology ; Genomics/methods ; Metagenomics/methods ; }, abstract = {Hyalomma marginatum, a vector for the high-consequence pathogen, the Crimean-Congo hemorrhagic fever virus (CCHFV), needs particular attention due to its impact on public health. Although it is a known vector for CCHFV, its general virome is largely unexplored. Here, we report findings from a citizen science monitoring program aimed to understand the prevalence and diversity of tick-borne pathogens, particularly focusing on Hyalomma ticks in Hungary. In 2021, we identified one adult specimen of Hyalomma marginatum and subjected it to Illumina-based viral metagenomic sequencing. Our analysis revealed sequences of the uncharacterized Volzhskoe tick virus, an unclassified member of the class Bunyaviricetes. The in silico analysis uncovered key genetic regions, including the glycoprotein and the RNA-dependent RNA polymerase (RdRp) coding regions. Phylogenetic analysis indicated a close relationship between our Volzhskoe tick virus sequences and other unclassified Bunyaviricetes species. These related species of unclassified Bunyaviricetes were detected in vastly different geolocations. These findings highlight the remarkable diversity of tick specific viruses and emphasize the need for further research to understand the transmissibility, seroreactivity or the potential pathogenicity of Volzhskoe tick virus and related species.}, } @article {pmid39147792, year = {2024}, author = {Zhang, Y and Jing, H}, title = {Metagenome sequencing and 107 microbial genomes from seamount sediments along the Yap and Mariana trenches.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {887}, pmid = {39147792}, issn = {2052-4463}, mesh = {*Archaea/genetics ; *Bacteria/genetics/classification ; Genome, Archaeal ; Genome, Bacterial ; Genome, Microbial ; *Geologic Sediments/microbiology ; *Metagenome ; *Phylogeny ; }, abstract = {Microbes in the sediments across a series of seamounts along the island arc of the Yap and Mariana trenches were investigated by metagenome. In this study, we reconstructed 107 metagenome-assembled genomes (MAGs), including 100 bacteria and 7 archaea. All the MAGs exhibited >75% completeness and <10% contamination, with 26 MAGs being classified as 'nearly complete' (completeness >90%), while 50 falling within 80-90% range and 31 between 75-80% complete. Phylogenomic analysis revealed that 86% (n = 92) of these MAGs represented new taxa at different taxonomical levels. The species composition of these MAGs was most consistent with the previous reports, with the most abundant phyla being Proteobacteria (n = 39), Methylomirabilota (n = 27), and Nitrospirota (n = 7). These draft genomes provided novel data on species diversity and function in the seamount microbial community, which will provide reference data for extensive comparative genomic studies across crucial phylogenetic groups worldwide.}, } @article {pmid39147529, year = {2024}, author = {Xiang, L and Zhuo, S and Luo, W and Tian, C and Xu, S and Li, X and Zhu, Y and Feng, R and Chen, M}, title = {Decoding polyphenol metabolism in patients with Crohn's disease: Insights from diet, gut microbiota, and metabolites.}, journal = {Food research international (Ottawa, Ont.)}, volume = {192}, number = {}, pages = {114852}, doi = {10.1016/j.foodres.2024.114852}, pmid = {39147529}, issn = {1873-7145}, mesh = {Humans ; *Crohn Disease/microbiology/metabolism/drug therapy ; *Gastrointestinal Microbiome/physiology ; *Polyphenols/metabolism ; Female ; Male ; Adult ; *Diet ; Hippurates/metabolism ; Middle Aged ; Young Adult ; Bacteria/classification/metabolism/genetics ; Feces/microbiology ; }, abstract = {Crohn's disease (CD) is a chronic and progressive inflammatory disease that can involve any part of the gastrointestinal tract. The protective role of dietary polyphenols has been documented in preclinical models of CD. Gut microbiota mediates the metabolism of polyphenols and affects their bioactivity and physiological functions. However, it remains elusive the capacity of microbial polyphenol metabolism in CD patients and healthy controls (HCs) along with its correlation with polyphenols intake and polyphenol-derived metabolites. Thus, we aimed to decode polyphenol metabolism in CD patients through aspects of diet, gut microbiota, and metabolites. Dietary intake analysis revealed that CD patients exhibited decreased intake of polyphenols. Using metagenomic data from two independent clinical cohorts (FAH-SYSU and PRISM), we quantified abundance of polyphenol degradation associated bacteria and functional genes in CD and HCs and observed a lower capacity of flavonoids degradation in gut microbiota residing in CD patients. Furthermore, through analysis of serum metabolites and enterotypes in participants of FAH-SYSU cohort, we observed that CD patients exhibited reduced levels of serum hippuric acid (HA), one of polyphenol-derived metabolites. HA level was higher in healthier enterotypes (characterized by dominance of Ruminococcaceae and Prevotellaceae, dominant by HCs) and positively correlated with multiple polyphenols intake and abundance of bacteria engaged in flavonoids degradation as well as short-chain fatty acid production, which could serve as a biomarker for effective polyphenol metabolism by the gut microbiota and a healthier gut microbial community structure. Overall, our findings provide a foundation for future work exploring the polyphenol-based or microbiota-targeted therapeutic strategies in CD.}, } @article {pmid39147499, year = {2024}, author = {Magliulo, R and Valentino, V and Balivo, A and Esposito, A and Genovese, A and Ercolini, D and De Filippis, F}, title = {Microbiome signatures associated with flavor development differentiate Protected Designation of origin water Buffalo Mozzarella cheese from different production areas.}, journal = {Food research international (Ottawa, Ont.)}, volume = {192}, number = {}, pages = {114798}, doi = {10.1016/j.foodres.2024.114798}, pmid = {39147499}, issn = {1873-7145}, mesh = {*Cheese/microbiology/analysis ; Animals ; *Volatile Organic Compounds/analysis ; *Microbiota ; *Buffaloes ; Italy ; *Gas Chromatography-Mass Spectrometry ; *Taste ; Food Microbiology ; Lactobacillus helveticus ; Streptococcus thermophilus/classification ; }, abstract = {Water Buffalo Mozzarella (BM) is a typical cheese from Southern Italy with unique flavor profile and texture. It is produced following a traditional back-slopping procedure and received the Protected Designation of Origin (PDO) label. To better understand the link between the production area, the microbiome composition and the flavor profile of the products, we performed a multiomic characterization of PDO BM collected from 57 different dairies located in the two main PDO production area, i.e. Caserta (n = 35) and Salerno (n = 22). Thus, we assessed the microbiome by high-throughput shotgun metagenomic sequencing and the Volatile Organic Compounds (VOCs) by gas chromatography/mass spectrometry (GC/MS). Streptococcus thermophilus, Lactobacillus helveticus, and Lactobacillus delbrueckii subsp. delbrueckii were identified as the core microbiome present in all samples. However, the microbiome taxonomic profiles resulted in a clustering of the samples based on their geographical origin, also showing that BM from Caserta had a greater microbial diversity. Consistently, Caserta and Salerno samples also showed different VOC profiles. These results suggest that the microbiome and its specific metabolic activity are part of the terroir that shape BM specific features, linking this traditional product with the area of production, thus opening new clues for improving traceability and fraud protection of traditional products.}, } @article {pmid39147372, year = {2024}, author = {Jara-Servin, A and Mejia, G and Romero, MF and Peimbert, M and Alcaraz, LD}, title = {Unravelling the genomic and environmental diversity of the ubiquitous Solirubrobacter.}, journal = {Environmental microbiology}, volume = {26}, number = {8}, pages = {e16685}, doi = {10.1111/1462-2920.16685}, pmid = {39147372}, issn = {1462-2920}, support = {CVU 725278//Consejo Nacional de Ciencia y Tecnología/ ; IN206824//Universidad Nacional Autónoma de México, DGAPA-PAPIIT-UNAM/ ; }, mesh = {*Soil Microbiology ; *Phylogeny ; *Genome, Bacterial ; *RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Genomics ; Metagenomics ; Genetic Variation ; }, abstract = {Solirubrobacter, though widespread in soils and rhizospheres, has been relatively unexplored despite its ubiquity. Previously acknowledged as a common soil bacterium, our research explores its phylogenomics, pangenomics, environmental diversity, and interactions within bacterial communities. By analysing seven genomic sequences, we have identified a pangenome consisting of 19,645 protein families, of which 2644 are shared across all studied genomes, forming the core genome. Interestingly, despite the non-motility of reported isolates, we discovered genes for flagellin and a partial flagellum assembly pathway. Examining the 16S ribosomal RNA genes of Solirubrobacter revealed substantial diversity, with 3166 operational taxonomic units identified in Mexican soils. Co-occurrence network analysis further demonstrated its significant integration within bacterial communities. Through phylogenomic scrutiny, we conclusively excluded the NCBI's GCA_009993245.1 genome from being classified as a Solirubrobacter. Our research into the metagenomic diversity of Solirubrobacter across various environments confirmed its presence in rhizospheres and certain soils, underscoring its adaptability. The geographical ubiquity of Solirubrobacter in rhizospheres raises intriguing questions regarding its potential interactions with plant hosts and the biotic and abiotic factors influencing its presence in soil. Given its ecological significance and genetic diversity, Solirubrobacter warrants further investigation as a potentially crucial yet underappreciated keystone species.}, } @article {pmid39147334, year = {2024}, author = {Hu, Z and Yao, Y and Chen, F and Feng, L and Yuan, Z and Deng, J and Huang, L and Yin, Y and Tang, X}, title = {Integrated analyses of the intestinal microbiome and transcriptome in Ningxiang piglets.}, journal = {Genomics}, volume = {116}, number = {5}, pages = {110919}, doi = {10.1016/j.ygeno.2024.110919}, pmid = {39147334}, issn = {1089-8646}, mesh = {Animals ; *Gastrointestinal Microbiome ; Swine ; *Transcriptome ; }, abstract = {Ningxiang (NX) pig has been recognized as one of the most famous Chinese indigenous breeds due to its characteristics in stress resistance. However, intestinal microbial feature and gene profiling in NX piglets have not been studied. Here, we compared the intestinal microbiome and transcriptome between NX and Duroc × Landrace × Large white (DLY) piglets and found the high enrichment of several colonic Bacteroides, Prevotella and Clostridium species in NX piglets. Further functional analyses revealed their predominant function in methane, glycolysis and gluconeogenesis metabolism. Our mRNA-sequencing data unraveled the distinct colonic gene expression between these two breeds. In particular, we showed that the improved intestinal function in NX piglets may be determined by enhanced intestinal barrier gene expression and varied immune gene expression through modulating the composition of the gut microbes. Together, our study revealed the intestinal characteristics of NX piglets, providing their potential application in improving breeding strategies and developing dietary interventions.}, } @article {pmid39147284, year = {2024}, author = {Zhang, D and Yang, A and Sheng, K and Fang, S and Zhou, L}, title = {Application of the second-generation sequencing technology of metagenomics in the detection of pathogens in respiratory patients.}, journal = {Journal of microbiological methods}, volume = {225}, number = {}, pages = {107021}, doi = {10.1016/j.mimet.2024.107021}, pmid = {39147284}, issn = {1872-8359}, mesh = {Humans ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; *Bacteria/isolation & purification/genetics/classification ; Male ; Middle Aged ; Female ; *Respiratory Tract Infections/microbiology/diagnosis/virology ; *Fungi/isolation & purification/genetics/classification ; Aged ; Adult ; Viruses/isolation & purification/genetics/classification ; China ; Sensitivity and Specificity ; Aged, 80 and over ; }, abstract = {OBJECTIVE: To explore the application value of the second-generation metagenomic next-generation sequencing (mNGS) in the detection of pathogens in patients with pulmonary infection.

METHODS: We conducted a retrospective analysis of 65 pulmonary infection cases treated at our institution and the Fifth People's Hospital of Shanghai between January 2021 and May 2023. All subjects were subjected to mNGS, targeted next-generation sequencing (tNGS), and conventional microbiological culture. A comparative analysis was performed to evaluate the diversity and quantity of pathogens identified by these methodologies and to appraise their respective diagnostic capabilities in pulmonary infection diagnostics.

RESULTS: The mNGS successfully identified etiological agents in 60 of the 65 cases, compared to tNGS, which yielded positive results in 42 cases, and conventional laboratory cultures, which detected pathogens in 24 cases. At the bacterial genus level, mNGS discerned 9 genera, 11 species, and 92 isolates of pathogenic bacteria, whereas tNGS identified 8 genera, 8 species, and 71 isolates. Conventional methods were less sensitive, detecting only 6 genera, 7 species, and 33 isolates. In terms of fungal detection, mNGS identified 4 fungal species, tNGS detected 4 isolates of the Candida genus, and conventional methods identified 2 isolates of the same genus. Viral detection at the species level revealed 10 species and 46 isolates by mNGS, whereas tNGS detected only 3 species and 7 isolates. The area under the receiver operating characteristic curve (AUC) with 95% confidence intervals for diagnosing pulmonary infections was 0.818 (0.671 to 0.966) for mNGS, 0.668 (0.475 to 0.860) for tNGS, and 0.721 (0.545 to 0.897) for conventional culture.The mNGS demonstrates superior diagnostic efficacy and pathogen detection breadth in critically ill patients with respiratory infections, offering a significant advantage by reducing the time to diagnosis. The enhanced sensitivity and comprehensive pathogen profiling of mNGS underscore its potential as a leading diagnostic tool in clinical microbiology.}, } @article {pmid39147198, year = {2024}, author = {Zeng, Y and Guo, M and Wu, Q and Tan, X and Jiang, C and Teng, F and Chen, J and Zhang, F and Ma, X and Li, X and Gu, J and Huang, W and Zhang, C and Yuen-Kwan Law, B and Long, Y and Xu, Y}, title = {Gut microbiota-derived indole-3-propionic acid alleviates diabetic kidney disease through its mitochondrial protective effect via reducing ubiquitination mediated-degradation of SIRT1.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2024.08.018}, pmid = {39147198}, issn = {2090-1224}, abstract = {INTRODUCTION: Gut microbes and their metabolites play crucial roles in the pathogenesis of diabetic kidney disease (DKD). However, which one and how specific gut-derived metabolites affect the progression of DKD remain largely unknown.

OBJECTIVES: This study aimed to investigate the potential roles of indole-3-propionic acid (IPA), a microbial metabolite of tryptophan, in DKD.

METHODS: Metagenomic sequencing was performed to analyze the microbiome structure in DKD. Metabolomics screening and validation were conducted to identify characteristic metabolites associated with DKD. The protective effect of IPA on DKD glomerular endothelial cells (GECs) was assessed through in vivo and in vitro experiments. Further validation via western blot, immunoprecipitation, gene knockout, and site-directed mutation elucidated the mechanism of IPA on mitochondrial injury.

RESULTS: Alterations in gut microbial community structure and dysregulated tryptophan metabolism were evident in DKD mice. Serum IPA levels were significantly reduced in DKD patients and correlated with fasting blood glucose, HbA1c, urine albumin-to-creatinine ratio (UACR), and estimated glomerular filtration rate (eGFR). IPA supplementation ameliorated albuminuria, bolstered the integrity of the glomerular filtration barrier, and mitigated mitochondrial impairments in GECs. Mechanistically, IPA hindered SIRT1 phosphorylation-mediated ubiquitin-proteasome degradation, restoring SIRT1's role in promoting PGC-1α deacetylation and nuclear translocation, thereby upregulating genes associated with mitochondrial biosynthesis and antioxidant defense.

CONCLUSION: Our findings underscore the potential of the microbial metabolite IPA to attenuate DKD progression, offering novel insights and potential therapeutic strategies for its management.}, } @article {pmid39147055, year = {2024}, author = {Lu, J and Qing, C and Huang, X and Zeng, J and Zheng, Y and Xia, P}, title = {Seasonal dynamics and driving mechanisms of microbial biogenic elements cycling function, assembly process, and co-occurrence network in plateau lake sediments.}, journal = {The Science of the total environment}, volume = {951}, number = {}, pages = {175510}, doi = {10.1016/j.scitotenv.2024.175510}, pmid = {39147055}, issn = {1879-1026}, mesh = {*Lakes/microbiology/chemistry ; *Geologic Sediments/microbiology ; *Seasons ; *Phosphorus/analysis ; *Microbiota ; *Nitrogen/analysis ; China ; Environmental Monitoring ; Bacteria/classification/genetics ; Carbon/analysis/metabolism ; }, abstract = {Microbial community diversity significantly varies with seasonality. However, little is known about seasonal variation of microbial community functions in lake sediments and their associated environmental influences. In this study, metagenomic sequencing of sediments collected from winter, summer, and autumn from Caohai Lake, Guizhou Plateau, were used to evaluate the composition and function of sediment microbial communities, the potential interactions of functional genes, key genes associated with seasons, and community assembly mechanisms. The average concentrations of nitrogen (TN) and phosphorus (TP) in lake sediments were higher, which were 6.136 and 0.501 g/kg, respectively. TN and organic matter (OM) were the primary factors associated with sediment community composition and functional profiles. The diversity and structure of the microbial communities varied with seasons, and Proteobacteria relative abundances were significantly lower in summer than in other seasons (58.43-44.12 %). Seasons were also associated with the relative abundances of functional genes, and in particular korA, metF, narC, nrfA, pstC/S, and soxB genes. Network complexity was highest in the summer and key genes in the network also varied across seasons. Neutral community model analysis revealed that the assembly mechanisms related to carbon (C), nitrogen (N), phosphorus (P), and sulfur (S) cycle-related genes were primarily associated with random processes. In summary, diverse functional genes were identified in lake sediments and exhibited evidence for synergistic interactions (Positive proportion: 74.91-99.82 %), while seasonal factors influenced their distribution. The results of this study provide new insights into seasonal impacts on microbial-driven biogeochemical cycling in shallow lakes.}, } @article {pmid39146922, year = {2024}, author = {Yuan, Y and Mo, C and Huang, F and Liao, X and Yang, Y}, title = {Microbial metabolism affects the antibiotic resistome in the intestine of laying hens.}, journal = {Poultry science}, volume = {103}, number = {10}, pages = {104138}, pmid = {39146922}, issn = {1525-3171}, mesh = {Animals ; *Chickens/microbiology ; *Gastrointestinal Microbiome/drug effects ; Female ; Anti-Bacterial Agents/pharmacology ; Escherichia coli/drug effects/genetics ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial ; Bacteria/drug effects/genetics/classification ; Intestines/microbiology/drug effects ; Cecum/microbiology ; }, abstract = {Intestinal microbial metabolism has an important impact on the health of laying hens, and microbes are also important hosts for ARGs. However, the relationship between intestinal microbes and antibiotic resistance in laying hens is unclear. In this study, a slaughtering experiment, an in vitro fermentation experiment and a single-bacteria culture experiment were carried out, and metagenomic and metabolomic analyses were used to investigate the relationships between microbial metabolism and the antibiotic resistome in the cecum of laying hens. The results showed that there were different types of ARGs in the intestines of laying hens, and the risk scores of the ARGs tended to decrease with growth stage. A total of 1142 metagenome-assembled genomes (MAGs) were obtained, and Escherichia coli was found to be the dominant ARG host, carrying 62 ARGs. Metabolomics revealed that indole and its derivatives, such as indole-3-lactic acid, were negatively correlated with a variety of ARGs. Moreover, in vitro fermentation experiment and single-bacteria culture experiment demonstrated that indole-3-lactic acid reduced the abundance and risk of multiple ARGs in the intestine and inhibited the growth of the ARG host Escherichia coli. In the context of high concern about intestinal microbial metabolism and antibiotic resistance, this is the first study to focus on the relationship between intestinal microbial metabolism and antibiotic resistance in laying hens. These findings have important implications for healthy farming and antibiotic resistance control.}, } @article {pmid39146704, year = {2024}, author = {Li, G and Wu, M and Xiao, Y and Tong, Y and Li, S and Qian, H and Zhao, T}, title = {Multi-omics reveals the ecological and biological functions of Enterococcus mundtii in the intestine of lepidopteran insects.}, journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics}, volume = {52}, number = {}, pages = {101309}, doi = {10.1016/j.cbd.2024.101309}, pmid = {39146704}, issn = {1878-0407}, mesh = {Animals ; *Bombyx/microbiology/genetics ; *Enterococcus/genetics ; *Gastrointestinal Microbiome ; *Intestines/microbiology ; Proteomics ; Symbiosis ; Multiomics ; }, abstract = {Insect guts offer unique habitats for microbial colonization, with gut bacteria potentially offering numerous benefits to their hosts. Although Enterococcus has emerged as one of the predominant gut commensal bacteria in insects, its establishment in various niches within the gut has not been characterized well. In this study, Enterococcus mundtii was inoculated into the silkworm (Bombyx mori L.) to investigate its biological functions. Genome-based analysis revealed that its successful colonization is related to adherence genes (ebpA, ebpC, efaA, srtC, and scm). This bacterium did not alter the activities of related metabolic enzymes or the intestinal barrier function. However, significant changes in the gene expressions levels of Att2, CecA, and Lys suggest potential adaptive mechanisms of host immunity to symbiotic E. mundtii. Moreover, 16S metagenomics analysis revealed a significant increase in the relative abundance of E. mundtii in the intestines of silkworms following inoculation. The intestinal microbiome displayed marked heterogeneity, an elevated gut microbiome health index, a reduced microbial dysbiosis index, and low potential pathogenicity in the treatment group. Additionally, E. mundtii enhanced the breakdown of carbohydrates in host intestines. Overall, E. mundtii serves as a beneficial microbe for insects, promoting intestinal homeostasis by providing competitive advantage. This characteristic helps E. mundtii dominate complex microbial environments and remain prevalent across Lepidoptera, likely fostering long-term symbiosis between the both parties. The present study contributes to clarifying the niche of E. mundtii in the intestine of lepidopteran insects and further reveals its potential roles in their insect hosts.}, } @article {pmid39146635, year = {2024}, author = {Jang, TL and Scherger, SJ and Kalil, AC and Gomez, CA}, title = {Ehrlichiosis and anaplasmosis in solid organ transplantation: A case series and review of the literature.}, journal = {Diagnostic microbiology and infectious disease}, volume = {110}, number = {3}, pages = {116484}, doi = {10.1016/j.diagmicrobio.2024.116484}, pmid = {39146635}, issn = {1879-0070}, mesh = {Humans ; *Anaplasmosis/diagnosis/microbiology ; *Ehrlichiosis/diagnosis/drug therapy/microbiology ; Male ; Middle Aged ; Female ; *Organ Transplantation/adverse effects ; Adult ; Aged ; DNA, Bacterial/genetics ; Transplant Recipients ; }, abstract = {Ehrlichiosis and anaplasmosis are rising tickborne infections posing significant risks to solid-organ transplant (SOT) patients. We present three cases highlighting clinical presentations, diagnostic challenges, and the benefits of microbial cell-free DNA (mcfDNA) sequencing. Emphasizing early diagnosis and preventive measures, we advocate for advanced diagnostic modalities to improve outcomes in this vulnerable population.}, } @article {pmid39145585, year = {2024}, author = {Liu, B and Wang, G and Wang, L and Yan, J and Zhu, K and Liu, Q and Zhao, J and Jia, B and Fang, M and Rudich, Y and Morawska, L and Chen, J}, title = {Unraveling Cross-Organ Impacts of Airborne Pollutants: A Multiomics Study on Respiratory Exposure and Gastrointestinal Health.}, journal = {Environmental science & technology}, volume = {58}, number = {35}, pages = {15511-15521}, doi = {10.1021/acs.est.4c06035}, pmid = {39145585}, issn = {1520-5851}, mesh = {Mice ; Animals ; *Air Pollutants/toxicity ; Inhalation Exposure ; Gastrointestinal Microbiome/drug effects ; Gastrointestinal Tract/drug effects ; Multiomics ; }, abstract = {Poor air quality is increasingly linked to gastrointestinal diseases, suggesting a potential correlation with human intestine health. However, this relationship remains largely unexplored due to limited research. This study used a controlled mouse model exposed to cooking oil fumes (COFs) and metagenomics, transcriptomics, and metabolomics to elucidate interactions between intestine microbiota and host metabolism under environmental stress. Our findings reveal that short-term COF inhalation induces pulmonary inflammation within 3 days and leads to gastrointestinal disturbances, elucidating a pathway connecting respiratory exposure to intestinal dysfunction. The exposure intensity significantly correlates with changes in intestinal tissue integrity, microbial composition, and metabolic function. Extended exposure of 7 days disrupts intestine microbiota and alters tryptophan metabolism, with further changes observed after 14 days, highlighting an adaptive response. These results highlight the vulnerability of intestinal health to airborne pollutants and suggest a pathway through which inhaled pollutants may affect distant organ systems.}, } @article {pmid39145536, year = {2024}, author = {Pipes, L and Nielsen, R}, title = {A rapid phylogeny-based method for accurate community profiling of large-scale metabarcoding datasets.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, pmid = {39145536}, issn = {2050-084X}, support = {BIO180028//Pittsburgh Supercomputing Center/ ; 1R01GM138634-01/GM/NIGMS NIH HHS/United States ; 1K99GM144747-01/GM/NIGMS NIH HHS/United States ; BIO180028//Advanced Cyberinfrastructure Coordination Ecosystem: Services & Support/ ; R01 GM138634/GM/NIGMS NIH HHS/United States ; K99 GM144747/GM/NIGMS NIH HHS/United States ; }, mesh = {*Phylogeny ; *DNA Barcoding, Taxonomic/methods ; Computational Biology/methods ; DNA, Environmental/genetics ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Environmental DNA (eDNA) is becoming an increasingly important tool in diverse scientific fields from ecological biomonitoring to wastewater surveillance of viruses. The fundamental challenge in eDNA analyses has been the bioinformatical assignment of reads to taxonomic groups. It has long been known that full probabilistic methods for phylogenetic assignment are preferable, but unfortunately, such methods are computationally intensive and are typically inapplicable to modern next-generation sequencing data. We present a fast approximate likelihood method for phylogenetic assignment of DNA sequences. Applying the new method to several mock communities and simulated datasets, we show that it identifies more reads at both high and low taxonomic levels more accurately than other leading methods. The advantage of the method is particularly apparent in the presence of polymorphisms and/or sequencing errors and when the true species is not represented in the reference database.}, } @article {pmid39144681, year = {2024}, author = {Páez-Watson, T and Tomás-Martínez, S and de Wit, R and Keisham, S and Tateno, H and van Loosdrecht, MCM and Lin, Y}, title = {Sweet Secrets: Exploring Novel Glycans and Glycoconjugates in the Extracellular Polymeric Substances of "Candidatus Accumulibacter".}, journal = {ACS ES&T water}, volume = {4}, number = {8}, pages = {3391-3399}, pmid = {39144681}, issn = {2690-0637}, abstract = {Biological wastewater treatment relies on microorganisms that grow as flocs, biofilms, or granules for efficient separation of biomass from cleaned water. This biofilm structure emerges from the interactions between microbes that produce, and are embedded in, extracellular polymeric substances (EPS). The true composition and structure of the EPS responsible for dense biofilm formation are still obscure. We conducted a bottom-up approach utilizing advanced glycomic techniques to explore the glycan diversity in the EPS from a highly enriched "Candidatus Accumulibacter" granular sludge. Rare novel sugar monomers such as N-Acetylquinovosamine (QuiNAc) and 2-O-Methylrhamnose (2-OMe-Rha) were identified to be present in the EPS of both enrichments. Further, a high diversity in the glycoprotein structures of said EPS was identified by means of lectin based microarrays. We explored the genetic potential of "Ca. Accumulibacter" high quality metagenome assembled genomes (MAGs) to showcase the shortcoming of top-down bioinformatics based approaches at predicting EPS composition and structure, especially when dealing with glycans and glycoconjugates. This work suggests that more bottom-up research is necessary to understand the composition and complex structure of EPS in biofilms since genome based inference cannot directly predict glycan structures and glycoconjugate diversity.}, } @article {pmid39144493, year = {2024}, author = {Geraldi, NR and Acinas, SG and Alam, I and Gasol, JM and Fernández-de-Puelles, ML and Giner, CR and Hernández León, S and Logares, R and Massana, R and Sánchez, P and Bajic, V and Gojobori, T and Duarte, CM}, title = {Assessing patterns of metazoans in the global ocean using environmental DNA.}, journal = {Royal Society open science}, volume = {11}, number = {8}, pages = {240724}, pmid = {39144493}, issn = {2054-5703}, abstract = {Documenting large-scale patterns of animals in the ocean and determining the drivers of these patterns is needed for conservation efforts given the unprecedented rates of change occurring within marine ecosystems. We used existing datasets from two global expeditions, Tara Oceans and Malaspina, that circumnavigated the oceans and sampled down to 4000 m to assess metazoans from environmental DNA (eDNA) extracted from seawater. We describe patterns of taxonomic richness within metazoan phyla and orders based on metabarcoding and infer the relative abundance of phyla using metagenome datasets, and relate these data to environmental variables. Arthropods had the greatest taxonomic richness of metazoan phyla at the surface, while cnidarians had the greatest richness in pelagic zones. Half of the marine metazoan eDNA from metagenome datasets was from arthropods, followed by cnidarians and nematodes. We found that mean surface temperature and primary productivity were positively related to metazoan taxonomic richness. Our findings concur with existing knowledge that temperature and primary productivity are important drivers of taxonomic richness for specific taxa at the ocean's surface, but these correlations are less evident in the deep ocean. Massive sequencing of eDNA can improve understanding of animal distributions, particularly for the deep ocean where sampling is challenging.}, } @article {pmid39144222, year = {2024}, author = {Li, Y and Liu, M and Kong, B and Zhang, G and Zhang, Q}, title = {The role of selenium intervention in gut microbiota homeostasis and gene function in mice with breast cancer on a high-fat diet.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1439652}, pmid = {39144222}, issn = {1664-302X}, abstract = {OBJECTIVE: This study aimed to investigate the effect of selenium on gut microbiota in mice with breast cancer under a high-fat diet.

METHODS: A total of 12 female BALB/c mice were randomly divided into two groups: 4 T1 + selenium+ high-fat diet group and 4 T1 + high-fat diet group. Mice were injected with 4 T1 cells on the right 4th mammary fat pad and kept on a high-fat diet. Fecal samples were collected, and DNA was extracted for metagenomic sequencing and bioinformatics analysis. Relevant target genes and pathways were annotated and metabolically analyzed to explore the intervention effect of selenium on breast cancer in the high-fat diet state.

RESULTS: Selenium supplementation in the high-fat diet altered the composition and diversity of gut microbiota in mice with breast cancer. The gut microbial composition was significantly different in the selenium intervention group, with an increased abundance of Proteobacteria, Actinobacteria, and Verrucomicrobia phyla and species such as Helicobacter ganmani, Helicobacter japonicus, and Akkermansia muciniphila, while phyla, such as Bacteroidetes, Firmicutes, Deferribacteres, and Spirochaetes, and species, such as Prevotella sp. MGM2, Muribaculum intestinale, Lactobacillus murinus, and Prevotella sp. MGM1, were decreased. Functional analysis revealed differential expression of genes related to carbohydrate-active enzymes, pathogen-host interactions, cell communication, cell auto-induction, membrane transporters, and virulence factors. Furthermore, 37 COGs and 48 metabolites with rising metabolic potential in the selenium intervention group were predicted.

CONCLUSION: Selenium alters the homeostasis of gut microbiota in mice with breast cancer on a high-fat diet, affecting their composition, abundance, and associated metabolism. These findings suggest that the mechanism involves interfering with gut microbiota homeostasis, leading to altered synthesis of tumor-associated proteins and fatty acids and inducing tumor cell apoptosis and pyroptosis.}, } @article {pmid39144212, year = {2024}, author = {Gtari, M and Maaoui, R and Ghodhbane-Gtari, F and Ben Slama, K and Sbissi, I}, title = {MAGs-centric crack: how long will, spore-positive Frankia and most Protofrankia, microsymbionts remain recalcitrant to axenic growth?.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1367490}, pmid = {39144212}, issn = {1664-302X}, abstract = {Nearly 50 years after the ground-breaking isolation of the primary Comptonia peregrina microsymbiont under axenic conditions, efforts to isolate a substantial number of Protofrankia and Frankia strains continue with enduring challenges and complexities. This study aimed to streamline genomic insights through comparative and predictive tools to extract traits crucial for isolating specific Frankia in axenic conditions. Pangenome analysis unveiled significant genetic diversity, suggesting untapped potential for cultivation strategies. Shared metabolic strategies in cellular components, central metabolic pathways, and resource acquisition traits offered promising avenues for cultivation. Ecological trait extraction indicated that most uncultured strains exhibit no apparent barriers to axenic growth. Despite ongoing challenges, potential caveats, and errors that could bias predictive analyses, this study provides a nuanced perspective. It highlights potential breakthroughs and guides refined cultivation strategies for these yet-uncultured strains. We advocate for tailored media formulations enriched with simple carbon sources in aerobic environments, with atmospheric nitrogen optionally sufficient to minimize contamination risks. Temperature adjustments should align with strain preferences-28-29°C for Frankia and 32-35°C for Protofrankia-while maintaining an alkaline pH. Given potential extended incubation periods (predicted doubling times ranging from 3.26 to 9.60 days, possibly up to 21.98 days), patience and rigorous contamination monitoring are crucial for optimizing cultivation conditions.}, } @article {pmid39143609, year = {2024}, author = {Shaw, J and Yu, YW}, title = {Fairy: fast approximate coverage for multi-sample metagenomic binning.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {151}, pmid = {39143609}, issn = {2049-2618}, support = {CGS-D//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2022-309 03074//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {*Metagenomics/methods ; *Metagenome ; Software ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Archaea/genetics/classification ; Algorithms ; }, abstract = {BACKGROUND: Metagenomic binning, the clustering of assembled contigs that belong to the same genome, is a crucial step for recovering metagenome-assembled genomes (MAGs). Contigs are linked by exploiting consistent signatures along a genome, such as read coverage patterns. Using coverage from multiple samples leads to higher-quality MAGs; however, standard pipelines require all-to-all read alignments for multiple samples to compute coverage, becoming a key computational bottleneck.

RESULTS: We present fairy (https://github.com/bluenote-1577/fairy), an approximate coverage calculation method for metagenomic binning. Fairy is a fast k-mer-based alignment-free method. For multi-sample binning, fairy can be > 250 × faster than read alignment and accurate enough for binning. Fairy is compatible with several existing binners on host and non-host-associated datasets. Using MetaBAT2, fairy recovers 98.5 % of MAGs with > 50 % completeness and < 5 % contamination relative to alignment with BWA. Notably, multi-sample binning with fairy is always better than single-sample binning using BWA (> 1.5 × more > 50 % complete MAGs on average) while still being faster. For a public sediment metagenome project, we demonstrate that multi-sample binning recovers higher quality Asgard archaea MAGs than single-sample binning and that fairy's results are indistinguishable from read alignment.

CONCLUSIONS: Fairy is a new tool for approximately and quickly calculating multi-sample coverage for binning, resolving a computational bottleneck for metagenomics. Video Abstract.}, } @article {pmid39143554, year = {2024}, author = {Francis, D and Sun, F}, title = {A comparative analysis of mutual information methods for pairwise relationship detection in metagenomic data.}, journal = {BMC bioinformatics}, volume = {25}, number = {1}, pages = {266}, pmid = {39143554}, issn = {1471-2105}, support = {EF-2125142//National Science Foundation/ ; EF-2125142//National Science Foundation/ ; }, mesh = {*Metagenomics/methods ; Algorithms ; Metagenome/genetics ; }, abstract = {BACKGROUND: Construction of co-occurrence networks in metagenomic data often employs correlation to infer pairwise relationships between microbes. However, biological systems are complex and often display qualities non-linear in nature. Therefore, the reliance on correlation alone may overlook important relationships and fail to capture the full breadth of intricacies presented in underlying interaction networks. It is of interest to incorporate metrics that are not only robust in detecting linear relationships, but non-linear ones as well.

RESULTS: In this paper, we explore the use of various mutual information (MI) estimation approaches for quantifying pairwise relationships in biological data and compare their performances against two traditional measures-Pearson's correlation coefficient, r, and Spearman's rank correlation coefficient, ρ. Metrics are tested on both simulated data designed to mimic pairwise relationships that may be found in ecological systems and real data from a previous study on C. diff infection. The results demonstrate that, in the case of asymmetric relationships, mutual information estimators can provide better detection ability than Pearson's or Spearman's correlation coefficients. Specifically, we find that these estimators have elevated performances in the detection of exploitative relationships, demonstrating the potential benefit of including them in future metagenomic studies.

CONCLUSIONS: Mutual information (MI) can uncover complex pairwise relationships in biological data that may be missed by traditional measures of association. The inclusion of such relationships when constructing co-occurrence networks can result in a more comprehensive analysis than the use of correlation alone.}, } @article {pmid39143383, year = {2024}, author = {Vijayan, J and Ezhuthanikkunnel, AP and Punnorkodu, SAK and Poikayil, SS and Mohan, M and Ammanamveetil, MHA}, title = {Sediment microbial diversity, functional potentials, and antibiotic resistance pattern: a case study of Cochin Estuary core sediment.}, journal = {Environmental science and pollution research international}, volume = {31}, number = {39}, pages = {52132-52146}, pmid = {39143383}, issn = {1614-7499}, mesh = {*Geologic Sediments/microbiology ; *Estuaries ; India ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Phylogeny ; Biodiversity ; }, abstract = {Marine sediments are an important part of the marine environment and the world's greatest organic carbon source. Sediment microorganisms are important regulators of major geochemical and eco-environmental processes in marine environments, especially nutrient dynamics and biogeochemical cycles. Despite their importance, core marine microorganisms are virtually unknown due to a lack of consensus on how to identify them. Most core microbiotas have been characterized thus far based on species abundance and occurrence. The combined effects of habitat and depth on benthic bacterial communities and ecological functions were studied using "Next-Generation sequencing (NGS) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) predictive functional profiling" at the surface (0.2 cm) and bottom depth (250 cm) in a sediment core sample from Cochin Estuary, Kerala, India. The results showed that bacterial diversity and richness were significantly higher in the surface sediment sample with the most abundant phyla being Proteobacteria, Acidobacteria, Chloroflexi, and Bacteroidetes. The major metabolic functions were metabolism, followed by environmental information processing and genetic information processing. Antibiotic resistance genes between the surface and bottom samples help to understand the resistance pattern among multidrug resistance is the most prominent one. Among viruses, Siphoviridae is the dominant family, followed by Myoviridae. In the case of Archea, Crenarchaeota is dominant, whereas among eukaryotes phyla Streptophyta and Chordata were dominant in the surface and the bottom samples respectively.}, } @article {pmid39143364, year = {2024}, author = {Akhlaghi, E and Salari, E and Mansouri, M and Shafiei, M and Kalantar-Neyestanaki, D and Aghassi, H and Fasihi Harandi, M}, title = {Identification and comparison of intestinal microbial diversity in patients at different stages of hepatic cystic echinococcosis.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {18912}, pmid = {39143364}, issn = {2045-2322}, support = {400000473//Kerman University of Medical Sciences/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Echinococcosis, Hepatic/microbiology/parasitology ; Male ; Female ; *RNA, Ribosomal, 16S/genetics ; Adult ; Middle Aged ; Feces/microbiology/parasitology ; Bacteria/classification/genetics/isolation & purification ; Biodiversity ; High-Throughput Nucleotide Sequencing ; }, abstract = {There is a significant focus on the role of the host microbiome in different outcomes of human parasitic diseases, including cystic echinococcosis (CE). This study was conducted to identify the intestinal microbiome of patients with CE at different stages of hydatid cyst compared to healthy individuals. Stool samples from CE patients as well as healthy individuals were collected. The samples were divided into three groups representing various stages of hepatic hydatid cyst: active (CE1 and CE2), transitional (CE3), and inactive (CE4 and CE5). One family member from each group was selected to serve as a control. The gut microbiome of patients with different stages of hydatid cysts was investigated using metagenomic next-generation amplicon sequencing of the V3-V4 region of the 16S rRNA gene. In this study, we identified 4862 Operational Taxonomic Units from three stages of hydatid cysts in CE patients and healthy individuals with a combined frequency of 2,955,291. The most abundant genera observed in all the subjects were Blautia, Agathobacter, Faecalibacterium, Bacteroides, Bifidobacterium, and Prevotella. The highest microbial frequency was related to inactive forms of CE, and the lowest frequency was observed in the group with active forms. However, the lowest OTU diversity was found in patients with inactive cysts compared with those with active and transitional cyst stages. The genus Agatobacter had the highest OTU frequency. Pseudomonas, Gemella, and Ligilactobacillus showed significant differences among the patients with different stages of hydatid cysts. Additionally, Anaerostipes and Candidatus showed significantly different reads in CE patients compared to healthy individuals. Our findings indicate that several bacterial genera can play a role in the fate of hydatid cysts in patients at different stages of the disease.}, } @article {pmid39143178, year = {2024}, author = {Duru, IC and Lecomte, A and Shishido, TK and Laine, P and Suppula, J and Paulin, L and Scheperjans, F and Pereira, PAB and Auvinen, P}, title = {Metagenome-assembled microbial genomes from Parkinson's disease fecal samples.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {18906}, pmid = {39143178}, issn = {2045-2322}, support = {NNF22OC0080109//Novo Nordisk Foundation/ ; }, mesh = {*Parkinson Disease/genetics/microbiology ; Humans ; *Feces/microbiology ; *Metagenome ; *Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; Genome, Bacterial ; Male ; Aged ; Female ; Genome, Microbial ; Middle Aged ; High-Throughput Nucleotide Sequencing ; }, abstract = {The human gut microbiome composition has been linked to Parkinson's disease (PD). However, knowledge of the gut microbiota on the genome level is still limited. Here we performed deep metagenomic sequencing and binning to build metagenome-assembled genomes (MAGs) from 136 human fecal microbiomes (68 PD samples and 68 control samples). We constructed 952 non-redundant high-quality MAGs and compared them between PD and control groups. Among these MAGs, there were 22 different genomes of Collinsella and Prevotella, indicating high variability of those genera in the human gut environment. Microdiversity analysis indicated that Ruminococcus bromii was statistically significantly (p < 0.002) more diverse on the strain level in the control samples compared to the PD samples. In addition, by clustering all genes and performing presence-absence analysis between groups, we identified several control-specific (p < 0.05) related genes, such as speF and Fe-S oxidoreductase. We also report detailed annotation of MAGs, including Clusters of Orthologous Genes (COG), Cas operon type, antiviral gene, prophage, and secondary metabolites biosynthetic gene clusters, which can be useful for providing a reference for future studies.}, } @article {pmid39143108, year = {2024}, author = {Grahnemo, L and Kambur, O and Lahti, L and Jousilahti, P and Niiranen, T and Knight, R and Salomaa, V and Havulinna, AS and Ohlsson, C}, title = {Associations between gut microbiota and incident fractures in the FINRISK cohort.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {69}, pmid = {39143108}, issn = {2055-5008}, support = {NNF 190C0055250 and 22OC0078421//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 101096347/ERC_/European Research Council/International ; KAW 2015.0317//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; LU2021-0096//IngaBritt och Arne Lundbergs Forskningsstiftelse (Ingabritt and Arne Lundberg Research Foundation)/ ; 2020-01392//Vetenskapsrådet (Swedish Research Council)/ ; }, mesh = {*Gastrointestinal Microbiome ; Humans ; Male ; Female ; *Fractures, Bone/microbiology/epidemiology/etiology ; Middle Aged ; Finland/epidemiology ; Aged ; Bacteria/classification/genetics/isolation & purification ; Metagenome ; Cohort Studies ; Incidence ; Metagenomics/methods ; Proteobacteria/genetics/isolation & purification ; Risk Factors ; Adult ; }, abstract = {The gut microbiota (GM) can regulate bone mass, but its association with incident fractures is unknown. We used Cox regression models to determine whether the GM composition is associated with incident fractures in the large FINRISK 2002 cohort (n = 7043, 1092 incident fracture cases, median follow-up time 18 years) with information on GM composition and functionality from shotgun metagenome sequencing. Higher alpha diversity was associated with decreased fracture risk (hazard ratio [HR] 0.92 per standard deviation increase in Shannon index, 95% confidence interval 0.87-0.96). For beta diversity, the first principal component was associated with fracture risk (Aitchison distance, HR 0.90, 0.85-0.96). In predefined phyla analyses, we observed that the relative abundance of Proteobacteria was associated with increased fracture risk (HR 1.14, 1.07-1.20), while the relative abundance of Tenericutes was associated with decreased fracture risk (HR 0.90, 0.85-0.96). Explorative sub-analyses within the Proteobacteria phylum showed that higher relative abundance of Gammaproteobacteria was associated with increased fracture risk. Functionality analyses showed that pathways related to amino acid metabolism and lipopolysaccharide biosynthesis associated with fracture risk. The relative abundance of Proteobacteria correlated with pathways for amino acid metabolism, while the relative abundance of Tenericutes correlated with pathways for butyrate synthesis. In conclusion, the overall GM composition was associated with incident fractures. The relative abundance of Proteobacteria, especially Gammaproteobacteria, was associated with increased fracture risk, while the relative abundance of Tenericutes was associated with decreased fracture risk. Functionality analyses demonstrated that pathways known to regulate bone health may underlie these associations.}, } @article {pmid39143045, year = {2024}, author = {Baldi, A and Braat, S and Imrul Hasan, M and Bennett, C and Barrios, M and Jones, N and Moir-Meyer, G and Abdul Azeez, I and Wilcox, S and Saiful Alam Bhuiyan, M and Ataide, R and Clucas, D and Harrison, LC and Arifeen, SE and Bowden, R and Biggs, BA and Jex, A and Pasricha, SR}, title = {Community use of oral antibiotics transiently reprofiles the intestinal microbiome in young Bangladeshi children.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {6980}, pmid = {39143045}, issn = {2041-1723}, support = {GNT1103262//Department of Health | National Health and Medical Research Council (NHMRC)/ ; GNT1158696//Department of Health | National Health and Medical Research Council (NHMRC)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; Bangladesh/epidemiology ; Infant ; *Anti-Bacterial Agents/administration & dosage/pharmacology ; *RNA, Ribosomal, 16S/genetics ; Male ; Female ; Administration, Oral ; Drug Resistance, Bacterial/genetics ; Feces/microbiology ; Metagenomics/methods ; Bacteria/genetics/drug effects/classification/isolation & purification ; Cephalosporins/administration & dosage/pharmacology/therapeutic use ; Enterococcus/drug effects/genetics/isolation & purification ; Antimicrobial Stewardship ; }, abstract = {Antibiotics may alter the gut microbiome, and this is one of the mechanisms by which antimicrobial resistance may be promoted. Suboptimal antimicrobial stewardship in Asia has been linked to antimicrobial resistance. We aim to examine the relationship between oral antibiotic use and composition and antimicrobial resistance in the gut microbiome in 1093 Bangladeshi infants. We leverage a trial of 8-month-old infants in rural Bangladesh: 61% of children were cumulatively exposed to antibiotics (most commonly cephalosporins and macrolides) over the 12-month study period, including 47% in the first 3 months of the study, usually for fever or respiratory infection. 16S rRNA amplicon sequencing in 11-month-old infants reveals that alpha diversity of the intestinal microbiome is reduced in children who received antibiotics within the previous 7 days; these samples also exhibit enrichment for Enterococcus and Escherichia/Shigella genera. No effect is seen in children who received antibiotics earlier. Using shotgun metagenomics, overall abundance of antimicrobial resistance genes declines over time. Enrichment for an Enterococcus-related antimicrobial resistance gene is observed in children receiving antibiotics within the previous 7 days, but not earlier. Presence of antimicrobial resistance genes is correlated to microbiome composition. In Bangladeshi children, community use of antibiotics transiently reprofiles the gut microbiome.}, } @article {pmid39142773, year = {2024}, author = {Zaytsev, V and Tutukina, MN and Chetyrkina, MR and Shelyakin, PV and Ovchinnikov, G and Satybaldina, D and Kondrashov, VA and Bandurist, MS and Seilov, S and Gorin, DA and Fedorov, FS and Gelfand, MS and Nasibulin, AG}, title = {Monitoring of meat quality and change-point detection by a sensor array and profiling of bacterial communities.}, journal = {Analytica chimica acta}, volume = {1320}, number = {}, pages = {343022}, doi = {10.1016/j.aca.2024.343022}, pmid = {39142773}, issn = {1873-4324}, mesh = {*Electronic Nose ; *Bacteria/isolation & purification ; Meat/microbiology/analysis ; Microbiota ; Animals ; Food Quality ; Food Microbiology ; }, abstract = {BACKGROUND: Real-time monitoring of food consumer quality remains challenging due to diverse bio-chemical processes taking place in the food matrices, and hence it requires accurate analytical methods. Thresholds to determine spoiled food are often difficult to set. The existing analytical methods are too complicated for rapid in situ screening of foodstuff.

RESULTS: We have studied the dynamics of meat spoilage by electronic nose (e-nose) for digitizing the smell associated with volatile spoilage markers of meat, comparing the results with changes in the microbiome composition of the spoiling meat samples. We apply the time series analysis to follow dynamic changes in the gas profile extracted from the e-nose responses and to identify the change-point window of the meat state. The obtained e-nose features correlate with changes in the microbiome composition such as increase in the proportion of Brochothrix and Pseudomonas spp. and disappearance of Mycoplasma spp., and with representative gas sensors towards hydrogen, ammonia, and alcohol vapors with R[2] values of 0.98, 0.93, and 0.91, respectively. Integration of e-nose and computer vision into a single analytical panel improved the meat state identification accuracy up to 0.85, allowing for more reliable meat state assessment.

SIGNIFICANCE: Accurate identification of the change-point in the meat state achieved by digitalizing volatile spoilage markers from the e-nose unit holds promises for application of smart miniaturized devices in food industry.}, } @article {pmid39142657, year = {2024}, author = {Hu, H and Ding, H and Lyu, J and Chen, Y and Huang, C and Zhang, C and Li, W and Fang, X and Zhang, W}, title = {Detection of rare microorganisms in bone and joint infections by metagenomic next-generation sequencing.}, journal = {Bone & joint research}, volume = {13}, number = {8}, pages = {401-410}, pmid = {39142657}, issn = {2046-3758}, support = {//Natural Science Foundation of Fujian Province/ ; //Joint Funds for the Innovation of Science and Technology, Fujian province/ ; //Fujian Orthopaedic Bone and Joint Disease and Sports Rehabilitation Clinical Medical Research Center/ ; //Foreign Cooperation Project of Science and Technology, Fujian province/ ; }, abstract = {AIMS: This aim of this study was to analyze the detection rate of rare pathogens in bone and joint infections (BJIs) using metagenomic next-generation sequencing (mNGS), and the impact of mNGS on clinical diagnosis and treatment.

METHODS: A retrospective analysis was conducted on 235 patients with BJIs who were treated at our hospital between January 2015 and December 2021. Patients were divided into the no-mNGS group (microbial culture only) and the mNGS group (mNGS testing and microbial culture) based on whether mNGS testing was used or not.

RESULTS: A total of 147 patients were included in the no-mNGS group and 88 in the mNGS group. The mNGS group had a higher detection rate of rare pathogens than the no-mNGS group (21.6% vs 10.2%, p = 0.016). However, the mNGS group had lower rates of antibiotic-related complications, shorter hospital stays, and higher infection control rates compared with the no-mNGS group (p = 0.017, p = 0.003, and p = 0.028, respectively), while there was no significant difference in the duration of antibiotic use (p = 0.957). In culture-negative cases, the mNGS group had lower rates of antibiotic-related complications, shorter hospital stays, and a higher infection control rate than the no-mNGS group (p = 0.036, p = 0.033, p = 0.022, respectively), while there was no significant difference in the duration of antibiotic use (p = 0.748).

CONCLUSION: mNGS improves detection of rare pathogens in BJIs. mNGS testing reduces antibiotic-related complications, shortens hospital stay and antibiotic use duration, and improves treatment success rate, benefits which are particularly evident in culture-negative cases.}, } @article {pmid39142630, year = {2024}, author = {Li, Y and Qu, P and Ye, Y and Chen, L}, title = {Strongyloides stercoralis hyperinfection syndrome in immunocompetent patients.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {30}, number = {11}, pages = {1408-1409}, doi = {10.1016/j.cmi.2024.08.008}, pmid = {39142630}, issn = {1469-0691}, } @article {pmid39142392, year = {2024}, author = {Carpenter, L and Miller, S and Flynn, E and Choo, JM and Collins, J and Shoubridge, AP and Gordon, D and Lynn, DJ and Whitehead, C and Leong, LEX and Ivey, KL and Wesselingh, SL and Inacio, MC and Crotty, M and Papanicolas, LE and Taylor, SL and Rogers, GB}, title = {Exposure to doxycycline increases risk of carrying a broad range of enteric antimicrobial resistance determinants in an elderly cohort.}, journal = {The Journal of infection}, volume = {89}, number = {4}, pages = {106243}, doi = {10.1016/j.jinf.2024.106243}, pmid = {39142392}, issn = {1532-2742}, mesh = {Humans ; Female ; Male ; Aged, 80 and over ; *Doxycycline/therapeutic use/pharmacology ; *Anti-Bacterial Agents/pharmacology ; Cross-Sectional Studies ; *Feces/microbiology ; Drug Resistance, Bacterial/genetics ; Cohort Studies ; South Australia/epidemiology ; Aged ; Metagenomics ; Carrier State/microbiology/epidemiology ; }, abstract = {OBJECTIVES: High rates of antibiotic prescription in residential aged care are likely to promote enteric carriage of antibiotic-resistant pathogens and increase the risk of antibiotic treatment failure. Despite their importance, relationships between antibiotic exposures and patterns of enteric resistance carriage in this population remain poorly understood.

METHODS: We conducted a cross-sectional metagenomic cohort analysis of stool samples from residents of five long-term aged-care facilities in South Australia. Taxonomic composition was determined, and enteric carriage of antibiotic resistance genes (ARGs) was identified and quantified against the Comprehensive Antibiotic Resistance Database. Both the detection and abundance of stool taxa and ARGs were related to antibiotic exposures up to 12 months prior. Factors associated with the abundance of ARGs of high clinical concern were identified.

RESULTS: Stool samples were provided by 164 participants (median age: 88 years, IQR 81-93; 72% female). Sixty-one percent (n = 100) of participants were prescribed antibiotics at least once in the prior 12 months (median prescriptions: 4, range: 1-52), most commonly a penicillin (n = 55, 33.5%), cephalosporin (n = 53, 32.3%), diaminopyrimidine (trimethoprim) (n = 36, 22%), or tetracycline (doxycycline) (n = 21, 12.8%). More than 1100 unique ARGs, conferring resistance to 38 antibiotic classes, were identified, including 20 ARGs of high clinical concern. Multivariate logistic regression showed doxycycline exposure to be the greatest risk factor for high ARG abundance (adjusted odds ratio [aOR]=14.8, q<0.001) and a significant contributor to inter-class selection, particularly for ARGs relating to penicillins (aOR=3.1, q=0.0004) and cephalosporins (aOR=3.4, q=0.003). High enteric ARG abundance was associated with the number of separate antibiotic exposures (aOR: 6.4, q<0.001), exposures within the prior 30 days (aOR: 4.6, q=0.008) and prior 30-100 days (aOR: 2.6, q=0.008), high duration of antibiotic exposure (aOR: 7.9, q<0.001), and exposure to 3 or more antibiotic classes (aOR: 7.4, q<0.001). Carriage of one or more ARGs of high clinical concern was identified in 99% of participants (n = 162, median: 3, IQR: 2-4), involving 11 ARGs conferring resistance to aminoglycosides, four to beta-lactams, one to glycopeptides, three to fluoroquinolones, and one to oxazolidinones. Carriage of ARGs of high clinical concern was positively associated with exposure to doxycycline (aminoglycoside, fluoroquinolone, and oxazolidinone ARGs) and trimethoprim (fluoroquinolone and beta-lactam ARGs). Analysis of doxycycline impact on microbiota composition suggested that observed resistome changes arose principally through direct ARG selection, rather than through the antibiotic depletion of sensitive bacterial populations.

CONCLUSIONS: The gut microbiome of aged care residents is a major reservoir of antibiotic resistance. As a critical antibiotic in medical practice, a comprehensive understanding of the impact of doxycycline exposure on the gut resistome is paramount for informed antibiotic use, particularly in an evolving landscape of prophylactic applications. Near-universal asymptomatic carriage of clinically critical resistance determinants is highly concerning and reinforces the urgent need for improved management of antibiotic use in long-term aged care.}, } @article {pmid39142045, year = {2024}, author = {Xu, D and Pan, C and Liu, S and Guo, J and Zheng, P and Zhang, M}, title = {Efficient alleviation granular sludge floatation in a high-rate anammox reactor by dosing folate.}, journal = {Water research}, volume = {264}, number = {}, pages = {122249}, doi = {10.1016/j.watres.2024.122249}, pmid = {39142045}, issn = {1879-2448}, mesh = {*Sewage/microbiology ; *Bioreactors ; *Folic Acid/metabolism ; Waste Disposal, Fluid/methods ; Nitrogen/metabolism ; Bacteria/metabolism ; Anaerobiosis ; }, abstract = {Although granular floatation has been recognized as a significant issue hindering the application of high-rate anammox biotechnology, limited knowledge is available about its causes and control strategies. This study proposed a novel control strategy by adding folate, and demonstrated its role in the granular floatation alleviation through long-term operation and granular characterizations. It was found that the floatation of anammox granular sludge was obviously relieved with the decreased sludge floatation potential by 67.1% after dosing with folate (8 mg/L) at a high nitrogen loading rate of 12.3 kg-N/(m[3]·d). Physiochemical analyses showed that the decrease of extracellular polymeric substances (EPS) content (mainly protein), the alleviation of granular surface pore plugging in conjunction with the smooth discharge of generated nitrogen gas were collectively responsible for efficient floatation control. Moreover, metagenomic analysis suggested that the synergistic interactions between anammox bacteria and their symbionts were attenuated after dosing exogenous folate. Anammox bacteria would reduce their synergistic dependence on the symbionts, and decline the supply of metabolites (e.g., amino acids and carbohydrates in EPS) to symbiotic bacteria. The declined EPS excretion contributed to the alleviation of granular floatation by dredging pores blockage, thus leading to a stable system performance. The findings not only offer insights into the role of microbial interaction in granular sludge floatation, but also provide a feasible approach for controlling the floatation issue in anammox granular-based processes.}, } @article {pmid39141834, year = {2024}, author = {Xu, Y and Leung, SKK and Li, TMW and Yung, CCM}, title = {Hidden genomic diversity drives niche partitioning in a cosmopolitan eukaryotic picophytoplankton.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39141834}, issn = {1751-7370}, support = {26100521//Research Grants Council of Hong Kong/ ; }, mesh = {*Phytoplankton/genetics/classification ; *Phylogeny ; *Genetic Variation ; Metagenomics ; Genomics ; Temperature ; Ecosystem ; }, abstract = {Marine eukaryotic phytoplankton are fundamental to the marine food web, yet the lack of reference genomes or just a single genome representing a taxon has led to an underestimation of their taxonomic, adaptive, and functional diversity. Here, we integrated strain isolation with metagenomic binning to recover genomes from the cosmopolitan picophytoplankton genus Bathycoccus, traditionally considered monospecific. Our recovery and analysis of 37 Bathycoccus genomes delineated their global genomic diversity and established four evolutionary clades (BI, BII, BIII, BIV). Our metagenomic abundance survey revealed well-differentiated ecological niches and distinct biogeographic distributions for each clade, predominantly shaped by temperature, salinity, and nutrient availability. Comparative genomics analyses further revealed clade-specific genomic traits that underpin niche adaptation and contribute to the global prevalence of Bathycoccus. Our findings underscore temperature as a major driver of genome diversification in this genus, with clade divergences coinciding with major paleoclimatic events that influenced their contemporary thermal niches. Moreover, the unique enrichment of C2H2 zinc finger and ankyrin repeat gene families in polar-adapted clades suggests previously unrecognized cold-adaptation mechanisms in marine eukaryotic phytoplankton. Our study offers a comprehensive genomic landscape of this crucial eukaryotic picophytoplankton, providing insights into their microdiversity and adaptive evolution in response to changing environments.}, } @article {pmid39141752, year = {2024}, author = {Gu, J and Lei, B and Wang, Z and Zhang, T and Jiang, T and Zhang, P and Chen, W and Zhang, Y and Jiang, R and Xu, G and Chang, Q and Zhou, M}, title = {DYNAMIC VIRAL LOAD MONITORING AND METAGENOMIC SEQUENCING IN ACUTE RETINAL NECROSIS CAUSED BY VARICELLA-ZOSTER VIRUS.}, journal = {Retina (Philadelphia, Pa.)}, volume = {44}, number = {11}, pages = {1966-1975}, doi = {10.1097/IAE.0000000000004214}, pmid = {39141752}, issn = {1539-2864}, mesh = {Humans ; *Retinal Necrosis Syndrome, Acute/diagnosis/virology/drug therapy ; *Herpesvirus 3, Human/genetics/isolation & purification ; *Viral Load ; Female ; Male ; *Eye Infections, Viral/virology/diagnosis/drug therapy ; *Aqueous Humor/virology ; Middle Aged ; *Antiviral Agents/therapeutic use ; *Herpes Zoster Ophthalmicus/diagnosis/virology/drug therapy ; *DNA, Viral/genetics/analysis ; Adult ; Metagenomics/methods ; Aged ; Polymerase Chain Reaction ; Retrospective Studies ; Varicella Zoster Virus Infection/diagnosis/virology/drug therapy ; }, abstract = {PURPOSE: To analyze the trend of intraocular viral load after antiviral treatment in patients with varicella-zoster virus-induced acute retinal necrosis and to explore the effect of viral genotypes on clinical manifestations.

METHODS: In this case series, viral load was detected using polymerase chain reaction from aqueous humor during treatment; viral load curves were fitted, and the time required to reach the inflection point between plateau phase and logarithmic reduction phase was estimated. Variations in viral genomes were detected by metagenomic sequencing.

RESULTS: Twenty eyes of 20 patients were included. The median (interquartile range) initial viral load was 5.9 × 10 7 (1.1 × 10 7 -1.1 × 10 8) copies/mL. The average duration of retinitis was 5 ± 3 weeks. The average time required to reach the inflection point was 4.2 ± 1.6 days. Time required to reach the inflection point was correlated with the duration of retinitis (P = 0.025). Patients with varicella-zoster virus carrying the p.S715* variation in ribonucleotide reductase (RNR) subunit 1 gene had lower initial viral loads (median 1.3 × 10 7 copies/mL) than those without (median 1.1 × 10 8 copies/mL; adjusted P = 0.030).

CONCLUSIONS: The inflection of viral load curve is helpful to estimate the length of plateau phase and the duration of retinitis during antiviral treatment in patients with acute retinal necrosis. Loss-of-function variation in RNR gene might be correlated with lower virulence of varicella-zoster virus.}, } @article {pmid39141729, year = {2024}, author = {Lai, S and Wang, H and Bork, P and Chen, WH and Zhao, XM}, title = {Long-read sequencing reveals extensive gut phageome structural variations driven by genetic exchange with bacterial hosts.}, journal = {Science advances}, volume = {10}, number = {33}, pages = {eadn3316}, pmid = {39141729}, issn = {2375-2548}, mesh = {*Bacteriophages/genetics ; Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteria/virology/genetics ; *Gene Transfer, Horizontal ; Metagenomics/methods ; Genetic Variation ; Virome/genetics ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; }, abstract = {Genetic variations are instrumental for unraveling phage evolution and deciphering their functional implications. Here, we explore the underlying fine-scale genetic variations in the gut phageome, especially structural variations (SVs). By using virome-enriched long-read metagenomic sequencing across 91 individuals, we identified a total of 14,438 nonredundant phage SVs and revealed their prevalence within the human gut phageome. These SVs are mainly enriched in genes involved in recombination, DNA methylation, and antibiotic resistance. Notably, a substantial fraction of phage SV sequences share close homology with bacterial fragments, with most SVs enriched for horizontal gene transfer (HGT) mechanism. Further investigations showed that these SV sequences were genetic exchanged between specific phage-bacteria pairs, particularly between phages and their respective bacterial hosts. Temperate phages exhibit a higher frequency of genetic exchange with bacterial chromosomes and then virulent phages. Collectively, our findings provide insights into the genetic landscape of the human gut phageome.}, } @article {pmid39141562, year = {2024}, author = {Karan, J and Mandal, S and Khan, G and Arya, H and Samhita, L}, title = {Enhanced Extraction of Low-Molecular Weight DNA from Wastewater for Comprehensive Assessment of Antimicrobial Resistance.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {209}, pages = {}, doi = {10.3791/66899}, pmid = {39141562}, issn = {1940-087X}, mesh = {*Wastewater/microbiology/chemistry ; Polyethylene Glycols/chemistry ; Molecular Weight ; DNA, Bacterial/genetics/isolation & purification ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; }, abstract = {Environmental surveillance is recognized as an important tool for assessing public health in the post-pandemic era. Water, in particular wastewater, has emerged as the source of choice to sample pathogen burdens in the environment. Wastewater from open drains and community water treatment plants is a reservoir of both pathogens and antimicrobial resistance (AMR) genes, and frequently comes in contact with humans. While there are many methods of tracking AMR from water, isolating good-quality DNA at high yields from heterogeneous samples remains a challenge. To compensate, sample volumes often need to be high, creating practical constraints. Additionally, environmental DNA is frequently fragmented, and the sources of AMR (plasmids, phages, linear DNA) consist of low-molecular-weight DNA. Yet, few extraction processes have focused on methods for high-yield extraction of linear and low-molecular-weight DNA. Here, a simple method for high-yield linear DNA extraction from small volumes of wastewater using the precipitation properties of polyethylene glycol (PEG) is reported. This study makes a case for increasing overall DNA yields from water samples collected for metagenomic analyses by enriching the proportion of linear DNA. In addition, enhancing low-molecular-weight DNA overcomes the current problem of under-sampling environmental AMR due to a focus on high-molecular-weight and intracellular DNA. This method is expected to be particularly useful when extracellular DNA exists but at low concentrations, such as with effluents from treatment plants. It should also enhance the environmental sampling of AMR gene fragments that spread through horizontal gene transfer.}, } @article {pmid39140734, year = {2024}, author = {Tian, Y and Rimal, B and Bisanz, JE and Gui, W and Wolfe, TM and Koo, I and Murray, IA and Nettleford, SK and Yokoyama, S and Dong, F and Koshkin, S and Prabhu, KS and Turnbaugh, PJ and Walk, ST and Perdew, GH and Patterson, AD}, title = {Effects of Early Life Exposures to the Aryl Hydrocarbon Receptor Ligand TCDF on Gut Microbiota and Host Metabolic Homeostasis in C57BL/6J Mice.}, journal = {Environmental health perspectives}, volume = {132}, number = {8}, pages = {87005}, pmid = {39140734}, issn = {1552-9924}, support = {R01 DK114034/DK/NIDDK NIH HHS/United States ; R35 ES028244/ES/NIEHS NIH HHS/United States ; R15 AI047165/AI/NIAID NIH HHS/United States ; R01 HL122593/HL/NHLBI NIH HHS/United States ; R01 ES028288/ES/NIEHS NIH HHS/United States ; S10 OD021750/OD/NIH HHS/United States ; R35 GM151045/GM/NIGMS NIH HHS/United States ; R35 ES035027/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/physiology ; *Receptors, Aryl Hydrocarbon/metabolism ; Mice ; *Mice, Inbred C57BL ; *Homeostasis/drug effects ; *Benzofurans ; Persistent Organic Pollutants ; Male ; Ligands ; }, abstract = {BACKGROUND: Exposure to persistent organic pollutants (POPs) and disruptions in the gastrointestinal microbiota have been positively correlated with a predisposition to factors such as obesity, metabolic syndrome, and type 2 diabetes; however, it is unclear how the microbiome contributes to this relationship.

OBJECTIVE: This study aimed to explore the association between early life exposure to a potent aryl hydrocarbon receptor (AHR) agonist and persistent disruptions in the microbiota, leading to impaired metabolic homeostasis later in life.

METHODS: This study used metagenomics, nuclear magnetic resonance (NMR)- and mass spectrometry (MS)-based metabolomics, and biochemical assays to analyze the gut microbiome composition and function, as well as the physiological and metabolic effects of early life exposure to 2,3,7,8-tetrachlorodibenzofuran (TCDF) in conventional, germ-free (GF), and Ahr-null mice. The impact of TCDF on Akkermansia muciniphila (A. muciniphila) in vitro was assessed using optical density (OD 600), flow cytometry, transcriptomics, and MS-based metabolomics.

RESULTS: TCDF-exposed mice exhibited lower abundances of A. muciniphila, lower levels of cecal short-chain fatty acids (SCFAs) and indole-3-lactic acid (ILA), as well as lower levels of the gut hormones glucagon-like peptide 1 (GLP-1) and peptide YY (PYY), findings suggestive of disruption in the gut microbiome community structure and function. Importantly, microbial and metabolic phenotypes associated with early life POP exposure were transferable to GF recipients in the absence of POP carry-over. In addition, AHR-independent interactions between POPs and the microbiota were observed, and they were significantly associated with growth, physiology, gene expression, and metabolic activity outcomes of A. muciniphila, supporting suppressed activity along the ILA pathway.

CONCLUSIONS: These data obtained in a mouse model point to the complex effects of POPs on the host and microbiota, providing strong evidence that early life, short-term, and self-limiting POP exposure can adversely impact the microbiome, with effects persisting into later life with associated health implications. https://doi.org/10.1289/EHP13356.}, } @article {pmid39140417, year = {2024}, author = {Hummel, G and Aagaard, K}, title = {Arthropods to Eutherians: A Historical and Contemporary Comparison of Sparse Prenatal Microbial Communities Among Animalia Species.}, journal = {American journal of reproductive immunology (New York, N.Y. : 1989)}, volume = {92}, number = {2}, pages = {e13897}, doi = {10.1111/aji.13897}, pmid = {39140417}, issn = {1600-0897}, mesh = {Animals ; Humans ; *Microbiota ; Pregnancy ; Female ; }, abstract = {Since the advent of next-generation sequencing, investigators worldwide have sought to discern whether a functional and biologically or clinically relevant prenatal microbiome exists. One line of research has led to the hypothesis that microbial DNA detected in utero/in ovo or prior to birth/hatching is a result of contamination and does not belong to viable and functional microbes. Many of these preliminary evaluations have been conducted in humans, mice, and nonhuman primates due to sample and specimen availability. However, a comprehensive review of the literature across animal species suggests organisms that maintain an obligate relationship with microbes may act as better models for interrogating the selective pressures placed on vertical microbial transfer over traditional laboratory species. To date, studies in humans and viviparous laboratory species have failed to illustrate the clear presence and transfer of functional microbes in utero. Until a ground truth regarding the status and relevance of prenatal microbes can be ascertained, it is salient to conduct parallel investigations into the prevalence of a functional prenatal microbiome across the developmental lifespan of multiple organisms in the kingdom Animalia. This comprehensive understanding is necessary not only to determine the role of vertically transmitted microbes and their products in early human health but also to understand their full One Health impact. This review is among the first to compile such comprehensive primary conclusions from the original investigator's conclusions, and hence collectively illustrates that prenatal microbial transfer is supported by experimental evidence arising from over a long and rigorous scientific history encompassing a breadth of species from kingdom Animalia.}, } @article {pmid39139486, year = {2024}, author = {Han, DM and Baek, JH and Choi, DG and Jeon, CO}, title = {Fermentative metabolic features of doenjang-meju as revealed by genome-centered metatranscriptomics.}, journal = {Food chemistry: X}, volume = {23}, number = {}, pages = {101658}, pmid = {39139486}, issn = {2590-1575}, abstract = {Fermentative features of doenjang-meju, a traditional Korean soybean brick, were investigated over 45 days via genome-centered metatranscriptomics. The pH value rapidly decreased within 10 days and successively increased after 20 days, along with an initial bacterial growth, including lactic acid bacteria, and subsequent fungal growth, suggesting their association. Polysaccharides and lipids underwent degradation, and amino acids, free sugars, and organic acids increased during the early stage. Metagenome analysis identified Aspergillus, Bacillus, Enterococcus, Staphylococcus, and Leuconostoc as major microbes, which were isolated and genome-sequenced. Metatranscriptomic analysis revealed the major roles of Bacillus and Enterococcus during the early period, shifting to Aspergillus dominance after 10 days. Metabolic pathway reconstruction and transcriptional analysis reveal that Aspergillus primarily decomposed polysaccharides to free sugars; Aspergillus and Bacillus metabolized lipids, free sugars, and organic acids generated by Enterococcus; and Aspergillus and Bacillus were instrumental in amino acid metabolism: their contributions varied by compounds and pathways.}, } @article {pmid39139380, year = {2024}, author = {Han, D and Bao, X and Wang, Y and Liao, X and Wang, K and Chen, J and Li, X and Yang, Z and Wang, Y}, title = {The impact of lactic acid bacteria inoculation on the fermentation and metabolomic dynamics of indigenous Beijing douzhi microbial communities.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1435834}, pmid = {39139380}, issn = {1664-302X}, abstract = {BACKGROUND: Douzhi, a traditional Chinese fermented beverage, features microbial communities primarily composed of lactic acid bacteria (LAB). As fermented foods continue to gain recognition and popularity, douzhi is attracting growing interest. However, investigation of the critical aspects of douzhi's fermentation processes, including fermentation characteristics and microbial community dynamics, remains vital for enhancing food safety and quality for douzhi, as well as for similar fermented food products.

METHOD: In this study, we collected douzhi microbial communities from four chain stores, using them as fermentation starter cultures. The microbial dynamics of the fermentation were analyzed, focusing on the inoculation of LAB strains and the transition from a mung bean-based matrix to skimmed milk. The metabolomic profiles of the fermented mung bean matrices were also studied.

RESULTS: Douzhi samples obtained from representative chain stores were found to be overwhelmingly dominated by LAB. When inoculated along with the douzhi community, both LAB strains exhibited notable and substantial reductions in the pH value of the designated mung bean matrices compared to those inoculated indigenous microbiota. Specifically, Lactiplantibacillus plantarum CGMCC 1.1856 retained its population, whereas Pediococcus pentosaceus CGMCC 1.2695 exhibited a decrease in relative abundance. Using skimmed milk as a fermentation substrate instead of the mung bean matrix resulted in significant shifts in microbial communities, particularly leading to an increase in Escherichia sp. The metagenomic analyses and functional predictions illustrated that various metabolic functions were enhanced during the fermentation process due to LAB inoculation. The liquid chromatography-mass spectrometry based metabolomic analysis revealed that the inoculation of Lactiplantibacillus plantarum and Pediococcus pentosaceus in mung bean matrix did not introduce new metabolites but significantly altered the concentration and profile of existing metabolites, especially increased low molecular carbohydrates, which may enhance the nutritional potential of the fermented product.

DISCUSSION: This study examines the microbial dynamics of douzhi microbiota fermentation, emphasizing the role of lactic acid bacteria in enhancing fermentation activity and metabolite profiles. These insights contribute to improving manufacturing processes and ensuring the safety and quality of douzhi and similar fermented foods.}, } @article {pmid39139377, year = {2024}, author = {Murovec, B and Deutsch, L and Osredkar, D and Stres, B}, title = {MetaBakery: a Singularity implementation of bioBakery tools as a skeleton application for efficient HPC deconvolution of microbiome metagenomic sequencing data to machine learning ready information.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1426465}, pmid = {39139377}, issn = {1664-302X}, abstract = {In this study, we present MetaBakery (http://metabakery.fe.uni-lj.si), an integrated application designed as a framework for synergistically executing the bioBakery workflow and associated utilities. MetaBakery streamlines the processing of any number of paired or unpaired fastq files, or a mixture of both, with optional compression (gzip, zip, bzip2, xz, or mixed) within a single run. MetaBakery uses programs such as KneadData (https://github.com/bioBakery/kneaddata), MetaPhlAn, HUMAnN and StrainPhlAn as well as integrated utilities and extends the original functionality of bioBakery. In particular, it includes MelonnPan for the prediction of metabolites and Mothur for calculation of microbial alpha diversity. Written in Python 3 and C++ the whole pipeline was encapsulated as Singularity container for efficient execution on various computing infrastructures, including large High-Performance Computing clusters. MetaBakery facilitates crash recovery, efficient re-execution upon parameter changes, and processing of large data sets through subset handling and is offered in three editions with bioBakery ingredients versions 4, 3 and 2 as versatile, transparent and well documented within the MetaBakery Users' Manual (http://metabakery.fe.uni-lj.si/metabakery_manual.pdf). It provides automatic handling of command line parameters, file formats and comprehensive hierarchical storage of output to simplify navigation and debugging. MetaBakery filters out potential human contamination and excludes samples with low read counts. It calculates estimates of alpha diversity and represents a comprehensive and augmented re-implementation of the bioBakery workflow. The robustness and flexibility of the system enables efficient exploration of changing parameters and input datasets, increasing its utility for microbiome analysis. Furthermore, we have shown that the MetaBakery tool can be used in modern biostatistical and machine learning approaches including large-scale microbiome studies.}, } @article {pmid39139260, year = {2024}, author = {Zawadzki, R and Rogalska, W and Pałdyna, M and Głuszczuk, D and Zajkowska, J and Kubas, B}, title = {Imaging modalities in neurolisteriosis: a literature review.}, journal = {Polish journal of radiology}, volume = {89}, number = {}, pages = {e345-e357}, pmid = {39139260}, issn = {1733-134X}, abstract = {Listeriosis caused by Listeria monocytogenes due to its ability to withstand harsh conditions and form biofilms on post-processed food poses a serious public health issue. It typically manifests itself with fever and gastrointestinal symptoms, but it can escalate with life-threatening conditions, especially in immunocompromised patients, the elderly, oncologically sick, and even pregnant women. The diagnosis is based on blood and cerebrospinal fluid culture growth, but it presents significant challenges due to deceptive findings and low positivity rates, the golden standard includes molecular diagnostic tests such as real-time PCR and metagenomic next-generation sequencing, which offer higher sensitivity and rapid detection. Radiological imaging, particularly magnetic resonance imaging, can play a crucial role in diagnosis of central nervous system (CNS) invasion by L. monocytogenes, enabling the detection of characteristic CNS lesions. The aim of the paper was to sum up the imaging features of L. monocytogenes CNS invasions in conventional imaging techniques, which can potentially speed up the diagnostic workflow for patients presenting with neurological symptoms associated with L. monocytogenes infection, particularly when conventional tests yield inconclusive results.}, } @article {pmid39139158, year = {2024}, author = {Zeng, W and Liang, Y and He, X and Chen, F and Xiong, J and Wen, Z and Tang, L and Chen, X and Zhang, J}, title = {Exploring the pathogen diagnosis and prognostic factors of severe COVID-19 using metagenomic next-generation sequencing: A retrospective study.}, journal = {Journal of medical biochemistry}, volume = {43}, number = {4}, pages = {528-536}, pmid = {39139158}, issn = {1452-8258}, abstract = {BACKGROUND: This study aimed to identify pathogens and factors that predict the outcome of severe COVID-19 by utilizing metagenomic next-generation sequencing (mNGS) technology.

METHODS: We retrospectively analyzed data from 56 severe COVID-19 patients admitted to our hospital between December 2022 and March 2023. We analyzed the pathogen types and strains detected through mNGS and conventional microbiological testing and collected general patient information.

RESULTS: In this study, 42 pathogens were detected using mNGS and conventional microbiological testing. mNGS had a significantly higher detection rate of 90.48% compared to 71.43% for conventional testing (P=0.026). A total of 196 strains were detected using both methods, with a significantly higher detection rate of 70.92% for mNGS compared to 49.49% for conventional testing (P=0.000). The 56 patients were divided into a survival group (33 cases) and a death group (23 cases) based on clinical outcomes. The survival group had significantly lower age, number of pathogens detected by mNGS, number of pathogens detected by conventional testing, APACHE-II score, SOFA score, high-sensitivity troponin, creatine kinase-MB subtype, and lactate dehydrogenase compared to the death group (P<0.05). Multivariate logistic regression analysis showed that these factors were risk factors for mortality in severe COVID-19 patients (P<0.05). In contrast, ROC curve analysis revealed that these factors had diagnostic values for mortality, with AUC values ranging from 0.657 to 0.963. The combined diagnosis of these indicators had an AUC of 0.924.

CONCLUSIONS: The use of mNGS technology can significantly enhance the detection of pathogens in severe cases of COVID-19 and also has a solid ability to predict clinical outcomes.}, } @article {pmid39138687, year = {2024}, author = {Singh, A and T V, A and Singh, S and Saxena, AK and Nain, L}, title = {Application of fungal inoculants enhances colonization of secondary bacterial degraders during in situ paddy straw degradation: a genomic insights into cross-domain synergism.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {39138687}, issn = {1618-1905}, support = {2017-20//ICAR-AMAAS/ ; }, abstract = {Rice cultivation generates huge amounts of on farm residues especially under mechanical harvesting. Paddy straw being recalcitrant hinders sowing of upcoming rabi crops like wheat and mustard. Non-environmental sustainable practice of on-farm burning of the paddy residues is being popularly followed for quick disposal of the agro-residues and land preparation. However, conservation agriculture involving in situ residue incorporation can be a sustainable option to utilize the residues for improvement of soil biological health. However, low temperature coupled with poor nitrogen status of soil reduces the decomposition rate of residues that may lead to nitrogen immobilization and hindrance in land preparation. In this direction, ecological impact of two approaches viz priming with urea and copiotrophic fungus-based bioformulation (CFB) consisting of Coprinopsis cinerea LA2 and Cyathus stercoreus ITCC3745 was studied for in situ degradation of residues. Succession of bacterial diversity was deciphered through high throughput whole metagenomic sequencing along with studies on dynamics of soil microbial enzymes. Treatments receiving CFB (T1) and urea (T2) when compared with bulk soil (absolute control) showed an increase in richness of the microbial diversity as compared to control straw retained treatment control (T3). The β diversity indices also indicated sufficient group variations among the treatments receiving CFB and urea as compared to only straw retained treatment and bulk soil. Priming of paddy straw with CFB and urea also induced significant rewiring of the bacterial co-occurrence networks. Quantification of soil ligno-cellulolytic activity as well as abundance of carbohydrate active enzymes (CAZy) genes indicated high activities of hydrolytic enzymes in CFB primed straw retention treatment as compared to urea primed straw retention treatment. The genomic insights on effectiveness of copiotrophic fungus bioformulation for in situ degradation of paddy straw will further help in developing strategies for management of crop residues in eco-friendly manner.}, } @article {pmid39138568, year = {2024}, author = {Belda, E and Capeau, J and Zucker, JD and Chatelier, EL and Pons, N and Oñate, FP and Quinquis, B and Alili, R and Fellahi, S and Katlama, C and Clément, K and Fève, B and Jaureguiberry, S and Goujard, C and Lambotte, O and Doré, J and Prifti, E and Bastard, JP}, title = {Major depletion of insulin sensitivity-associated taxa in the gut microbiome of persons living with HIV controlled by antiretroviral drugs.}, journal = {BMC medical genomics}, volume = {17}, number = {1}, pages = {209}, pmid = {39138568}, issn = {1755-8794}, support = {ANRS 157 study trial//Agence Nationale de Recherches sur le Sida et les Hépatites Virales/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *HIV Infections/drug therapy/microbiology ; Male ; Female ; Middle Aged ; *Insulin Resistance ; Adult ; Feces/microbiology ; Anti-Retroviral Agents/therapeutic use ; Metagenome ; }, abstract = {BACKGROUND: Persons living with HIV (PWH) harbor an altered gut microbiome (higher abundance of Prevotella and lower abundance of Bacillota and Ruminococcus lineages) compared to non-infected individuals. Some of these alterations are linked to sexual preference and others to the HIV infection. The relationship between these lineages and metabolic alterations, often present in aging PWH, has been poorly investigated.

METHODS: In this study, we compared fecal metagenomes of 25 antiretroviral-treatment (ART)-controlled PWH to three independent control groups of 25 non-infected matched individuals by means of univariate analyses and machine learning methods. Moreover, we used two external datasets to validate predictive models of PWH classification. Next, we searched for associations between clinical and biological metabolic parameters with taxonomic and functional microbiome profiles. Finally, we compare the gut microbiome in 7 PWH after a 17-week ART switch to raltegravir/maraviroc.

RESULTS: Three major enterotypes (Prevotella, Bacteroides and Ruminococcaceae) were present in all groups. The first Prevotella enterotype was enriched in PWH, with several of characteristic lineages associated with poor metabolic profiles (low HDL and adiponectin, high insulin resistance (HOMA-IR)). Conversely butyrate-producing lineages were markedly depleted in PWH independently of sexual preference and were associated with a better metabolic profile (higher HDL and adiponectin and lower HOMA-IR). Accordingly with the worst metabolic status of PWH, butyrate production and amino-acid degradation modules were associated with high HDL and adiponectin and low HOMA-IR. Random Forest models trained to classify PWH vs. control on taxonomic abundances displayed high generalization performance on two external holdout datasets (ROC AUC of 80-82%). Finally, no significant alterations in microbiome composition were observed after switching to raltegravir/maraviroc.

CONCLUSION: High resolution metagenomic analyses revealed major differences in the gut microbiome of ART-controlled PWH when compared with three independent matched cohorts of controls. The observed marked insulin resistance could result both from enrichment in Prevotella lineages, and from the depletion in species producing butyrate and involved into amino-acid degradation, which depletion is linked with the HIV infection.}, } @article {pmid39138557, year = {2024}, author = {Lu, Y and Li, Q and Li, T}, title = {A novel hierarchical network-based approach to unveil the complexity of functional microbial genome.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {786}, pmid = {39138557}, issn = {1471-2164}, support = {2020YFA0907402//National Key Research and Development Program of China/ ; 92251304//National Natural Science Foundation of China/ ; }, mesh = {*Microcystis/genetics ; *Genome, Bacterial ; Lakes/microbiology ; Gene Regulatory Networks ; Metagenomics/methods ; Metagenome ; Genome, Microbial ; Genomics/methods ; Deep Learning ; }, abstract = {Biological networks serve a crucial role in elucidating intricate biological processes. While interspecies environmental interactions have been extensively studied, the exploration of gene interactions within species, particularly among individual microorganisms, is less developed. The increasing amount of microbiome genomic data necessitates a more nuanced analysis of microbial genome structures and functions. In this context, we introduce a complex structure using higher-order network theory, "Solid Motif Structures (SMS)", via a hierarchical biological network analysis of genomes within the same genus, effectively linking microbial genome structure with its function. Leveraging 162 high-quality genomes of Microcystis, a key freshwater cyanobacterium within microbial ecosystems, we established a genome structure network. Employing deep learning techniques, such as adaptive graph encoder, we uncovered 27 critical functional subnetworks and their associated SMSs. Incorporating metagenomic data from seven geographically distinct lakes, we conducted an investigation into Microcystis' functional stability under varying environmental conditions, unveiling unique functional interaction models for each lake. Our work compiles these insights into an extensive resource repository, providing novel perspectives on the functional dynamics within Microcystis. This research offers a hierarchical network analysis framework for understanding interactions between microbial genome structures and functions within the same genus.}, } @article {pmid39137850, year = {2024}, author = {Kou, L and Huang, T and Zhang, H and Wen, G and Li, K}, title = {Aerobic denitrifying bacterial community with low C/N ratio remove nitrate from micro-polluted water: Metagenomics unravels denitrification pathways.}, journal = {The Science of the total environment}, volume = {951}, number = {}, pages = {175457}, doi = {10.1016/j.scitotenv.2024.175457}, pmid = {39137850}, issn = {1879-1026}, mesh = {*Denitrification ; *Nitrates/metabolism ; *Water Pollutants, Chemical/metabolism/analysis ; *Nitrogen/metabolism ; *Metagenomics ; *Carbon/metabolism ; Bacteria/metabolism ; Aerobiosis ; Biodegradation, Environmental ; }, abstract = {The efficient nitrogen removal from micro-polluted source water is an international challenge to be solved urgently. However, the inner denitrification mechanism of native aerobic denitrifying bacterial communities in response to carbon scarcity remains relatively unclear. Here, the bacterial community XT6, screened from an oligotrophic reservoir, exhibited aerobic denitrifying capacity under low-carbon environments. Up to 76.79-81.64 % of total organic carbon (TOC) and 51.48-67.60 % of NO3[-]-N were removed by XT6 within 48 h at C/N ratios of 2.0-3.0. Additionally, the nitrogen balance experiments further manifested that 26.27-38.13 % of NO3[-]-N was lost in gaseous form. As the C/N ratio decreased, XT6 tended to generate more extracellular polymeric substances (EPS), with the tightly bound EPS showing the largest increase. Pseudomonas and Variovorax were quite abundant in XT6, constituting 59.69 % and 28.65 % of the total sequences, respectively. Furthermore, metagenomics analysis evidenced that XT6 removed TOC and nitrate mainly through the tricarboxylic acid cycle and aerobic denitrification. Overall, the abovementioned results provide a deeper understanding of the nitrogen metabolic pathways of indigenous aerobic denitrifying bacterial communities with low C/N ratios and offer useful guidance for controlling nitrogen pollution in oligotrophic ecosystems.}, } @article {pmid39137667, year = {2024}, author = {Ma, ZS}, title = {Metagenome comparison (MC): A new framework for detecting unique/enriched OMUs (operational metagenomic units) derived from whole-genome sequencing reads.}, journal = {Computers in biology and medicine}, volume = {180}, number = {}, pages = {108852}, doi = {10.1016/j.compbiomed.2024.108852}, pmid = {39137667}, issn = {1879-0534}, mesh = {Humans ; *Metagenomics/methods ; *Metagenome/genetics ; Whole Genome Sequencing/methods ; Algorithms ; }, abstract = {BACKGROUND: Current methods for comparing metagenomes, derived from whole-genome sequencing reads, include top-down metrics or parametric models such as metagenome-diversity, and bottom-up, non-parametric, model-free machine learning approaches like Naïve Bayes for k-mer-profiling. However, both types are limited in their ability to effectively and comprehensively identify and catalogue unique or enriched metagenomic genes, a critical task in comparative metagenomics. This challenge is significant and complex due to its NP-hard nature, which means computational time grows exponentially, or even faster, with the problem size, rendering it impractical for even the fastest supercomputers without heuristic approximation algorithms.

METHOD: In this study, we introduce a new framework, MC (Metagenome-Comparison), designed to exhaustively detect and catalogue unique or enriched metagenomic genes (MGs) and their derivatives, including metagenome functional gene clusters (MFGC), or more generally, the operational metagenomic unit (OMU) that can be considered the counterpart of the OTU (operational taxonomic unit) from amplicon sequencing reads. The MC is essentially a heuristic search algorithm guided by pairs of new metrics (termed MG-specificity or OMU-specificity, MG-specificity diversity or OMU-specificity diversity). It is further constrained by statistical significance (P-value) implemented as a pair of statistical tests.

RESULTS: We evaluated the MC using large metagenomic datasets related to obesity, diabetes, and IBD, and found that the proportions of unique and enriched metagenomic genes ranged from 0.001% to 0.08 % and 0.08%-0.82 % respectively, and less than 10 % for the MFGC.

CONCLUSION: The MC provides a robust method for comparing metagenomes at various scales, from baseline MGs to various function/pathway clusters of metagenomes, collectively termed OMUs.}, } @article {pmid39137550, year = {2024}, author = {Gao, SM and Wang, P and Li, Q and Shu, WS and Tang, LY and Lin, ZL and Li, JT and Huang, LN}, title = {Deciphering microbial metabolic interactions and their implications for community dynamics in acid mine drainage sediments.}, journal = {Journal of hazardous materials}, volume = {478}, number = {}, pages = {135478}, doi = {10.1016/j.jhazmat.2024.135478}, pmid = {39137550}, issn = {1873-3336}, mesh = {*Geologic Sediments/microbiology ; *Mining ; *Microbiota ; *Biodegradation, Environmental ; Bacteria/metabolism/genetics ; China ; Metagenomics ; Acids/metabolism ; Microbial Interactions ; }, abstract = {The microbially-mediated reduction processes have potential for the bioremediation of acid mine drainage (AMD), which represents a worldwide environment problem. However, we know little about the microbial interactions in anaerobic AMD sediments. Here we utilized genome-resolved metagenomics to uncover the nature of cooperative and competitive metabolic interactions in 90 AMD sediments across Southern China. Our analyses recovered well-represented prokaryotic communities through the reconstruction of 2625 population genomes. Functional analyses of these genomes revealed extensive metabolic handoffs which occurred more frequently in nitrogen metabolism than in sulfur metabolism, as well as stable functional redundancy across sediments resulting from populations with low genomic relatedness. Genome-scale metabolic modeling showed that metabolic competition promoted microbial co-occurrence relationships, suggesting that community assembly was dominated by habitat filtering in sediments. Notably, communities colonizing more extreme conditions tended to be highly competitive, which was typically accompanied with increased network complexity but decreased stability of the microbiome. Finally, our results demonstrated that heterotrophic Thermoplasmatota associated with ferric iron and sulfate reduction contributed most to the elevated levels of competition. Our study shed light on the cooperative and competitive metabolisms of microbiome in the hazardous AMD sediments, which may provide preliminary clues for the AMD bioremediation in the future.}, } @article {pmid39137456, year = {2024}, author = {Li, J and Yang, W and Hao, X and Lin, Y and van Loosdrecht, MCM}, title = {Little alginates synthesized in EPS: Evidences from high-throughput community and metagenes.}, journal = {Water research}, volume = {265}, number = {}, pages = {122211}, doi = {10.1016/j.watres.2024.122211}, pmid = {39137456}, issn = {1879-2448}, mesh = {*Alginates ; *Extracellular Polymeric Substance Matrix/metabolism ; Sewage/microbiology ; Bacteria/metabolism/genetics ; Bioreactors ; }, abstract = {As a significant structure in activated sludge, extracellular polymeric substances (EPS) hold considerable value regarding resource recovery and applications. The present study aimed to elucidate the relationship between the microbial community and the composition and properties of EPS. A biological nutrient removal (BNR) reactor was set up in the laboratory and controlled under different solid retention times (SRT), altering microbial species within the system. Then EPS was extracted from activated and analyzed by chemical and spectroscopic methods. High-throughput sequencing and metagenomic approaches were employed to investigate bacterial community and metabolic pathways. The results showed that lower SRT with a higher abundance of the family-level Proteobacteria (27.7%-53.5%) favored EPS synthesis, while another dominant group Bacteroidetes (20.0%-32.6%) may not significantly affect EPS synthesis. Furthermore, the abundance of alginates-producing bacteria including Pseudomonas spp. and Azotobacter vinelandii was only 2.53%-6.76% and 1.98%-6.34%, respectively. The alginate synthesis pathway genes Alg8 and Alg44 were also present at very low levels (0.05‱-0.11‱, 0.01‱-0.02‱, respectively). Another important gene related to alginates operons, AlgK, was absent across all the SRT-operated reactors. These findings suggest an impossible and incomplete alginate synthesis pathway within sludge. In light of these results, it can be concluded that EPS does not necessarily contain alginate components.}, } @article {pmid39137184, year = {2024}, author = {Tang, X and Shang, J and Chen, G and Chan, KHK and Shi, M and Sun, Y}, title = {SegVir: Reconstruction of Complete Segmented RNA Viral Genomes from Metatranscriptomes.}, journal = {Molecular biology and evolution}, volume = {41}, number = {8}, pages = {}, pmid = {39137184}, issn = {1537-1719}, mesh = {*Genome, Viral ; *RNA Viruses/genetics ; Transcriptome ; RNA, Viral/genetics ; Software ; Metagenome ; Metagenomics/methods ; }, abstract = {Segmented RNA viruses are a complex group of RNA viruses with multisegment genomes. Reconstructing complete segmented viruses is crucial for advancing our understanding of viral diversity, evolution, and public health impact. Using metatranscriptomic data to identify known and novel segmented viruses has sped up the survey of segmented viruses in various ecosystems. However, the high genetic diversity and the difficulty in binning complete segmented genomes present significant challenges in segmented virus reconstruction. Current virus detection tools are primarily used to identify nonsegmented viral genomes. This study presents SegVir, a novel tool designed to identify segmented RNA viruses and reconstruct their complete genomes from complex metatranscriptomes. SegVir leverages both close and remote homology searches to accurately detect conserved and divergent viral segments. Additionally, we introduce a new method that can evaluate the genome completeness and conservation based on gene content. Our evaluations on simulated datasets demonstrate SegVir's superior sensitivity and precision compared to existing tools. Moreover, in experiments using real data, we identified some virus segments missing in the NCBI database, underscoring SegVir's potential to enhance viral metagenome analysis. The source code and supporting data of SegVir are available via https://github.com/HubertTang/SegVir.}, } @article {pmid39136809, year = {2024}, author = {Kulshreshtha, NM and Chauhan, K and Singh, A and Soti, A and Kumari, M and Gupta, AB}, title = {Intertwining of the C-N-S cycle in passive and aerated constructed wetlands.}, journal = {World journal of microbiology & biotechnology}, volume = {40}, number = {10}, pages = {301}, pmid = {39136809}, issn = {1573-0972}, support = {DST/TM/WTI/WIC/2K17/83//Department of Science and Technology, Ministry of Science and Technology, India/ ; }, mesh = {*Wetlands ; *Bacteria/metabolism/classification/genetics/isolation & purification ; *Nitrogen/metabolism ; *Denitrification ; *Sulfur/metabolism ; Carbon/metabolism ; Autotrophic Processes ; Carbon Cycle ; Wastewater/microbiology/chemistry ; Metagenomics ; }, abstract = {The microbial processes occurring in constructed wetlands (CWs) are difficult to understand owing to the complex interactions occurring between a variety of substrates, microorganisms, and plants under the given physicochemical conditions. This frequently leads to very large unexplained nitrogen losses in these systems. In continuation of our findings on Anammox contributions, our research on full-scale field CWs has suggested the significant involvement of the sulfur cycle in the conventional C-N cycle occurring in wetlands, which might closely explain the nitrogen losses in these systems. This paper explored the possibility of the sulfur-driven autotrophic denitrification (SDAD) pathway in different types of CWs, shallow and deep and passive and aerated systems, by analyzing the metagenomic bacterial communities present within these CWs. The results indicate a higher abundance of SDAD bacteria (Paracoccus and Arcobacter) in deep passive systems compared to shallow systems and presence of a large number of SDAD genera (Paracoccus, Thiobacillus, Beggiatoa, Sulfurimonas, Arcobacter, and Sulfuricurvum) in aerated CWs. The bacteria belonging to the functional category of dark oxidation of sulfur compounds were found to be enriched in deep and aerated CWs hinting at the possible role of the SDAD pathway in total nitrogen removal in these systems. As a case study, the percentage nitrogen removal through SDAD pathway was calculated to be 15-20% in aerated wetlands. The presence of autotrophic pathways for nitrogen removal can prove highly beneficial in terms of reducing sludge generation and hence reducing clogging, making aerated CWs a sustainable wastewater treatment solution.}, } @article {pmid39136491, year = {2024}, author = {Schacksen, PS and Nielsen, JL}, title = {Unraveling the genetic potential of nitrous oxide reduction in wastewater treatment: insights from metagenome-assembled genomes.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {9}, pages = {e0217723}, pmid = {39136491}, issn = {1098-5336}, support = {9041-00367B//Teknologi og Produktion, Det Frie Forskningsråd (FTP, DFF)/ ; }, mesh = {*Nitrous Oxide/metabolism ; *Wastewater/microbiology ; *Metagenome ; Bacteria/genetics/metabolism/classification/isolation & purification ; Oxidation-Reduction ; Oxidoreductases/genetics/metabolism ; Genome, Bacterial ; Waste Disposal, Fluid ; Denmark ; Phylogeny ; }, abstract = {UNLABELLED: This study explores the genetic landscape of nitrous oxide (N2O) reduction in wastewater treatment plants (WWTPs) by profiling 1,083 high-quality metagenome-assembled genomes (HQ MAGs) from 23 Danish full-scale WWTPs. The focus is on the distribution and diversity of nitrous oxide reductase (nosZ) genes and their association with other nitrogen metabolism pathways. A custom pipeline for clade-specific nosZ gene identification with higher sensitivity revealed 503 nosZ sequences in 489 of these HQ MAGs, outperforming existing Kyoto Encyclopedia of Genes and Genomes (KEGG) module-based methods. Notably, 48.7% of the total 1,083 HQ MAGs harbored nosZ genes, with clade II being predominant, accounting for 93.7% of these genes. Taxonomic profiling highlighted the prevalence of nosZ-containing taxa within Bacteroidota and Pseudomonadota. Chloroflexota exhibited unexpected affiliations with both the sec and tat secretory pathways, and all were found to contain the accessory nosB gene, underscoring the importance of investigating the secretory pathway. The majority of non-denitrifying N2O reducers were found within Bacteroidota and Chloroflexota. Additionally, HQ MAGs with genes for dissimilatory nitrate reduction to ammonium and assimilatory nitrate reduction frequently co-occurred with the nosZ gene. Traditional primers targeting nosZ often focus on short-length amplicons. Therefore, we introduced custom-designed primer sets targeting near-full-length nosZ sequences. These new primers demonstrate efficacy in capturing diverse and well-characterized sequences, providing a valuable tool with higher resolution for future research. In conclusion, this comprehensive analysis enhances our understanding of N2O-reducing organisms in WWTPs, highlighting their potential as N2O sinks with the potential for optimizing wastewater treatment processes and mitigating greenhouse gas emissions.

IMPORTANCE: This study provides critical insights into the genetic diversity of nitrous oxide reductase (nosZ) genes and the microorganisms harboring them in wastewater treatment plants (WWTPs) by exploring 1,083 high-quality metagenome-assembled genomes (MAGs) from 23 Danish full-scale WWTPs. Despite the pivotal role of nosZ-containing organisms, their diversity remains largely unexplored in WWTPs. Our custom pipeline for detecting nosZ provides near-full-length genes with detailed information on secretory pathways and accessory nos genes. Using these genes as templates, we developed taxonomically diverse clade-specific primers that generate nosZ amplicons for phylogenetic annotation and gene-to-MAG linkage. This approach improves detection and expands the discovery of novel sequences, highlighting the prevalence of non-denitrifying N2O reducers and their potential as N2O sinks. These findings have the potential to optimize nitrogen removal processes and mitigate greenhouse gas emissions from WWTPs by fully harnessing the capabilities of the microbial communities.}, } @article {pmid39136455, year = {2024}, author = {Majzoub, ME and Luu, LDW and Haifer, C and Paramsothy, S and Borody, TJ and Leong, RW and Thomas, T and Kaakoush, NO}, title = {Refining microbial community metabolic models derived from metagenomics using reference-based taxonomic profiling.}, journal = {mSystems}, volume = {9}, number = {9}, pages = {e0074624}, pmid = {39136455}, issn = {2379-5077}, support = {988415//Crohn's and Colitis Foundation (CCF)/ ; 2011047//DHAC | National Health and Medical Research Council (NHMRC)/ ; //Bioplatforms Australia (Bioplatforms)/ ; //Integrated Marine Observing System (IMOS)/ ; Emerging leader grant//DHAC | National Health and Medical Research Council (NHMRC)/ ; Scientia fellowship//University of New South Wales (UNSW)/ ; }, mesh = {Humans ; *Metagenomics/methods ; *Metabolomics/methods ; *Microbiota/genetics ; Metagenome/genetics ; }, abstract = {Characterization of microbial community metabolic output is crucial to understanding their functions. Construction of genome-scale metabolic models from metagenome-assembled genomes (MAG) has enabled prediction of metabolite production by microbial communities, yet little is known about their accuracy. Here, we examined the performance of two approaches for metabolite prediction from metagenomes, one that is MAG-guided and another that is taxonomic reference-guided. We applied both on shotgun metagenomics data from human and environmental samples, and validated findings in the human samples using untargeted metabolomics. We found that in human samples, where taxonomic profiling is optimized and reference genomes are readily available, when number of input taxa was normalized, the reference-guided approach predicted more metabolites than the MAG-guided approach. The two approaches showed significant overlap but each identified metabolites not predicted in the other. Pathway enrichment analyses identified significant differences in inferences derived from data based on the approach, highlighting the need for caution in interpretation. In environmental samples, when the number of input taxa was normalized, the reference-guided approach predicted more metabolites than the MAG-guided approach for total metabolites in both sample types and non-redundant metabolites in seawater samples. Nonetheless, as was observed for the human samples, the approaches overlapped substantially but also predicted metabolites not observed in the other. Our findings report on utility of a complementary input to genome-scale metabolic model construction that is less computationally intensive forgoing MAG assembly and refinement, and that can be applied on shallow shotgun sequencing where MAGs cannot be generated.IMPORTANCELittle is known about the accuracy of genome-scale metabolic models (GEMs) of microbial communities despite their influence on inferring community metabolic outputs and culture conditions. The performance of GEMs for metabolite prediction from metagenomes was assessed by applying two approaches on shotgun metagenomics data from human and environmental samples, and validating findings in the human samples using untargeted metabolomics. The performance of the approach was found to be dependent on sample type, but collectively, the reference-guided approach predicted more metabolites than the MAG-guided approach. Despite the differences, the predictions from the approaches overlapped substantially but each identified metabolites not predicted in the other. We found significant differences in biological inferences based on the approach, with some examples of uniquely enriched pathways in one group being invalidated when using the alternative approach, highlighting the need for caution in interpretation of GEMs.}, } @article {pmid39136189, year = {2024}, author = {Wang, J and Zhu, YG and Ge, Y}, title = {Global distribution pattern of soil phosphorus-cycling microbes under the influence of human activities.}, journal = {Global change biology}, volume = {30}, number = {8}, pages = {e17477}, doi = {10.1111/gcb.17477}, pmid = {39136189}, issn = {1365-2486}, support = {2023YFD1700803//National Key Research and Development Program of China/ ; 42177274//National Natural Science Foundation of China/ ; 42307162//National Natural Science Foundation of China/ ; 2019QZKK0306//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2019QZKK0308//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; }, mesh = {*Phosphorus/metabolism/analysis ; *Soil Microbiology ; Human Activities ; Humans ; Bacteria/genetics/metabolism ; Microbiota ; Soil/chemistry ; }, abstract = {Human activities have profoundly altered the Earth's phosphorus (P) cycling process and its associated microbial communities, yet their global distribution pattern and response to human influences remain unclear. Here, we estimated the abundances of P-cycling genes from 3321 global soil metagenomic samples and mapped the global distribution of five key P-cycling processes, that is, organic phosphoester hydrolysis, inorganic phosphorus solubilization, two-component system, phosphotransferase system, and transporters. Structural equation modeling and random forest analysis were employed to assess the impact of anthropogenic and environmental factors on the abundance of P-cycling genes. Our findings suggest that although less significant than the climate and soil profile, human-related factors, such as economic activities and population, are important drivers for the variations in P-cycling gene abundance. Notably, the gene abundances were increased parallel to the extent of human intervention, but generally at low and moderate levels of human activities. Furthermore, we identified critical genera, such as Pseudomonas and Lysobacter, which were sensitive to the changes in human activities. This study provides insights into the responses of P-cycling microbes to human activities at a global scale, enhancing our understanding of soil microbial P cycling and underscoring the importance of sustainable human activities in the Earth's biogeochemical cycle.}, } @article {pmid39135873, year = {2024}, author = {Zhang, H and Wei, T and Li, Q and Fu, L and Li, M and He, L and Wang, Y}, title = {Metagenomic 18S rDNA reads revealed zonation of eukaryotic communities in the Yongle blue hole.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1420899}, pmid = {39135873}, issn = {1664-302X}, abstract = {The Yongle blue hole (YBH), situated in the South China Sea, represents a compelling subject of study in marine microbiology due to its unique redox-layered microbial ecosystems. However, the diversity and ecology of microbial eukaryotes within the YBH remains underexplored. This study endeavors to bridge this gap through the application of the in situ microbial filtration and fixation (ISMIFF) device to collect 0.22-30 μm microbial samples from 21 water layers of YBH. Subsequent extraction of 18S rRNA metagenomic reads of 21 metagenomes and 10 metatranscriptomes facilitated a comprehensive analysis of community structures. Findings revealed a pronounced superiority in the diversity and richness of eukaryotic microorganisms in the oxic zone compared to its suboxic and anoxic counterparts. Notably, Dinophyceae and Maxillopoda emerged as the predominant taxa based on the analysis of the 18S rRNA reads for the V4 and V9 regions, which showed stratification In their relative abundance and suggested their potential role in the thermo-halocline boundaries and oxic-anoxic interface. Specifically, In these eukaryotic microbial communities, Dinophyceae exhibited significant abundance at 20 m (20.01%) and 105 m (26.13%) water depths, while Maxillopoda was prevalent at 40 m (22.84%), 80 m (23.19%), and 100 m (15.42%) depths. A part of these organisms, identified as larvae and protists, were likely attracted by swarming chemosynthetic bacterial prey prevailing at the thermo-halocline boundaries and oxic-anoxic interface. Furthermore, the phylogenetic relationships of the major 18S operational taxonomic units (OTUs) showed a close adjacency to known species, except for three Dinophyceae OTUs. In conclusion, this study provides critical insights into the vertical distribution and transcriptional activity of <30-μm eukaryotic microbes, shedding light on the taxonomic novelty of eukaryotic microorganisms within the semi-enclosed blue holes.}, } @article {pmid39135694, year = {2024}, author = {Yu, J and Li, W and Xu, R and Liu, X and Gao, G and Kwok, LY and Chen, Y and Sun, Z and Liu, W and Zhang, H}, title = {Probio-M9, a breast milk-originated probiotic, alleviates mastitis and enhances antibiotic efficacy: Insights into the gut-mammary axis.}, journal = {iMeta}, volume = {3}, number = {4}, pages = {e224}, pmid = {39135694}, issn = {2770-596X}, abstract = {Breast milk naturally contains lactic acid bacteria, but their precise origin remains a subject of debate. In this study, we utilized a rat mastitis animal model to investigate the potential of a breast milk-derived probiotic strain, Lacticaseibacillus rhamnosus Probio-M9, in alleviating mastitis and enhancing the efficacy of antibiotic treatment. Through histopathological analysis of mammary tissue, we observed that Probio-M9 effectively relieved mastitis, mitigated inflammation, and improved the response to antibiotic treatment. Metagenomic analysis further revealed that Probio-M9 enhanced interactions among gut microbes, accompanied by an increase in the relative abundance of Ruminococcaceae and the regulation of specific genes and carbohydrate-active enzymes, subsequently impacting host immunity. Additionally, an intriguing finding was the translocation of live Probio-M9 from the gut to the mammary tissue only during bacterial mastitis and lactation, likely facilitated through lymphatic circulation. These findings advance our understanding of the intricate gut-mammary axis and provide valuable insights into the potential health benefits of probiotic interventions.}, } @article {pmid39135692, year = {2024}, author = {Wei, X and Guo, L and Cai, H and Gu, S and Tang, L and Leng, Y and Cheng, M and He, G and Han, Y and Ren, X and Lin, B and Lv, L and Shao, H and Wang, M and Wang, H and Dang, D and Wang, S and Wang, N and Shen, P and Wang, Q and Xu, Y and Jiang, Y and Zhang, N and He, X and Deng, X and Dai, M and Zhong, L and Xiong, Y and Pan, Y and Tang, K and Liu, F and Yang, B and Ren, L and Wang, J and Jiang, C and Huang, L}, title = {MASS cohort: Multicenter, longitudinal, and prospective study of the role of microbiome in severe pneumonia and host susceptibility.}, journal = {iMeta}, volume = {3}, number = {4}, pages = {e218}, pmid = {39135692}, issn = {2770-596X}, abstract = {The MASS cohort comprises 2000 ICU patients with severe pneumonia, covering community-acquired pneumonia, hospital-acquired pneumonia, and ventilator-associated pneumonia, sourced from 19 hospitals across 10 cities in three provinces. A wide array of samples including bronchoalveolar lavage fluid, sputum, feces, and whole blood are longitudinally collected throughout patients' ICU stays. The cohort study seeks to uncover the dynamics of lung and gut microbiomes and their associations with severe pneumonia and host susceptibility, integrating deep metagenomics and transcriptomics with detailed clinical data.}, } @article {pmid39135686, year = {2024}, author = {Geng, M and Li, M and Li, Y and Zhu, J and Sun, C and Wang, Y and Chen, WH}, title = {A universal oral microbiome-based signature for periodontitis.}, journal = {iMeta}, volume = {3}, number = {4}, pages = {e212}, pmid = {39135686}, issn = {2770-596X}, abstract = {We analyzed eight oral microbiota shotgun metagenomic sequencing cohorts from five countries and three continents, identifying 54 species biomarkers and 26 metabolic biomarkers consistently altered in health and disease states across three or more cohorts. Additionally, machine learning models based on taxonomic profiles achieved high accuracy in distinguishing periodontitis patients from controls (internal and external areas under the receiver operating characteristic curves of 0.86 and 0.85, respectively). These results support metagenome-based diagnosis of periodontitis and provide a foundation for further research and effective treatment strategies.}, } @article {pmid39135685, year = {2024}, author = {Ma, L and Lyu, W and Zeng, T and Wang, W and Chen, Q and Zhao, J and Zhang, G and Lu, L and Yang, H and Xiao, Y}, title = {Duck gut metagenome reveals the microbiome signatures linked to intestinal regional, temporal development, and rearing condition.}, journal = {iMeta}, volume = {3}, number = {4}, pages = {e198}, pmid = {39135685}, issn = {2770-596X}, abstract = {The duck gastrointestinal tract (GIT) harbors an abundance of microorganisms that play an important role in duck health and production. Here, we constructed the first relatively comprehensive duck gut microbial gene catalog (24 million genes) and 4437 metagenome-assembled genomes using 375 GIT metagenomic samples from four different duck breeds across five intestinal segments under two distinct rearing conditions. We further characterized the intestinal region-specific microbial taxonomy and their assigned functions, as well as the temporal development and maturation of the duck gut microbiome. Our metagenomic analysis revealed the similarity within the microbiota of the foregut and hindgut compartments, but distinctive taxonomic and functional differences between distinct intestinal segments. In addition, we found a significant shift in the microbiota composition of newly hatched ducks (3 days), followed by increased diversity and enhanced stability across growth stages (14, 42, and 70 days), indicating that the intestinal microbiota develops into a relatively mature and stable community as the host duck matures. Comparing the impact of different rearing conditions (with and without water) on duck cecal microbiota communities and functions, we found that the bacterial capacity for lipopolysaccharide biosynthesis was significantly increased in ducks that had free access to water, leading to the accumulation of pathogenic bacteria and antibiotic-resistance genes. Taken together, our findings expand the understanding of the microbiome signatures linked to intestinal regional, temporal development, and rearing conditions in ducks, which highlight the significant impact of microbiota on poultry health and production.}, } @article {pmid39135636, year = {2024}, author = {Cai, X and Sun, C and Zhong, H and Cai, Y and Cao, M and Wang, L and Sun, W and Tao, Y and Ma, G and Huang, B and Yan, S and Zhong, J and Wang, J and Lu, Y and Guan, Y and Song, M and Wang, Y and Li, Y and Su, X}, title = {The value of metagenomic next-generation sequencing with different nucleic acid extracting methods of cell-free DNA or whole-cell DNA in the diagnosis of non-neutropenic pulmonary aspergillosis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1398190}, pmid = {39135636}, issn = {2235-2988}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Bronchoalveolar Lavage Fluid/microbiology ; *Pulmonary Aspergillosis/diagnosis ; *Metagenomics/methods ; *Cell-Free Nucleic Acids ; Male ; Female ; *DNA, Fungal/genetics/isolation & purification ; Middle Aged ; *ROC Curve ; Molecular Diagnostic Techniques/methods ; Aged ; Sensitivity and Specificity ; Adult ; }, abstract = {PURPOSE: Metagenomic next-generation sequencing(mNGS) is a novel molecular diagnostic technique. For nucleic acid extraction methods, both whole-cell DNA (wcDNA) and cell-free DNA (cfDNA) are widely applied with the sample of bronchoalveolar lavage fluid (BALF). We aim to evaluate the clinical value of mNGS with cfDNA and mNGS with wcDNA for the detection of BALF pathogens in non-neutropenic pulmonary aspergillosis.

METHODS: mNGS with BALF-cfDNA, BALF-wcDNA and conventional microbiological tests (CMTs) were performed in suspected non-neutropenic pulmonary aspergillosis. The diagnostic value of different assays for pulmonary aspergillosis was compared.

RESULTS: BALF-mNGS (cfDNA, wcDNA) outperformed CMTs in terms of microorganisms detection. Receiver operating characteristic (ROC) analysis indicated BALF-mNGS (cfDNA, wcDNA) was superior to culture and BALF-GM. Combination diagnosis of either positive for BALF-mNGS (cfDNA, wcDNA) or CMTs is more sensitive than CMTs alone in the diagnosis of pulmonary aspergillosis (BALF-cfDNA+CMTs/BALF-wcDNA+CMTs vs. CMTs: ROC analysis: 0.813 vs.0.66, P=0.0142/0.796 vs.0.66, P=0.0244; Sensitivity: 89.47% vs. 47.37%, P=0.008/84.21% vs. 47.37%, P=0.016). BALF-cfDNA showed a significantly greater reads per million (RPM) than BALF-wcDNA. The area under the ROC curve (AUC) for RPM of Aspergillus detected by BALF-cfDNA, used to predict "True positive" pulmonary aspergillosis patients, was 0.779, with a cut-off value greater than 4.5.

CONCLUSION: We propose that the incorporation of BALF-mNGS (cfDNA, wcDNA) with CMTs improves diagnostic precision in the identification of non-neutropenic pulmonary aspergillosis when compared to CMTs alone. BALF-cfDNA outperforms BALF-wcDNA in clinical value.}, } @article {pmid39135559, year = {2024}, author = {Song, Q and Li, Y and Zhou, T and Xiao, M and Xiao, B and Wang, M and Zhu, Y}, title = {Maternal vitamin D status during pregnancy and infant's gut microbiota: a prospective cohort study.}, journal = {Frontiers in nutrition}, volume = {11}, number = {}, pages = {1428356}, pmid = {39135559}, issn = {2296-861X}, abstract = {OBJECTIVES: To prospectively explore the association of maternal serum 25(OH)D levels with the infant's gut microbiota in Chinese populations, and to evaluate its potential influence on the dynamic change patterns of offspring's gut microbiota from 1 to 6 months old.

METHODS: Eighty-seven mother-infant dyads (vitamin D insufficient group vs. normal group = 59 vs. 28) were included in this longitudinal study. Two fecal samples were collected for the included infant at home by the parents at 1 month of age ("M1 phase") and 6 months of age ("M6 phase"). Gut microbiota were profiled by 16S rRNA gene sequencing. We performed mixed effects models on alpha diversity metrics, PERMANOVA tests on beta diversity distances, and linear discriminant analysis (LDA) to identify differently abundant taxa.

RESULTS: We observed significantly lower Pielou's evenness and Shannon diversity in the vitamin D insufficient group in the M6 phase (p = 0.049 and 0.015, respectively), but not in the M1 phase (p > 0.05), and the dynamic changes in alpha diversity from 1 to 6 months old were significantly different according to maternal vitamin D status (p < 0.05). There were also significant differences in gut microbiota composition between the vitamin D insufficient group and normal group, both in the M1 and M6 phases (LDA score > 2.0, p < 0.05). Moreover, among the predicted metagenome functions, pathways related to amino acid biosynthesis, starch degradation, and purine nucleotides biosynthesis were enriched in the vitamin D insufficient group.

CONCLUSION: Our findings highlight that maternal vitamin D status plays a pivotal role in shaping the early-life gut microbiota of the next generation.}, } @article {pmid39134956, year = {2024}, author = {Liu, D and Li, N and Zhu, Y and Chen, Q and Fan, X and Feng, J}, title = {Diagnosis of human angiostrongyliasis in a case of hydrocephalus using next-generation sequencing: a case report and literature review.}, journal = {BMC neurology}, volume = {24}, number = {1}, pages = {281}, pmid = {39134956}, issn = {1471-2377}, mesh = {Humans ; *Strongylida Infections/diagnosis/drug therapy/complications ; Male ; *Angiostrongylus cantonensis/genetics/isolation & purification ; *High-Throughput Nucleotide Sequencing/methods ; Adolescent ; Animals ; *Hydrocephalus/diagnosis/parasitology ; }, abstract = {BACKGROUND: Angiostrongyliasis cantonensis is a severe yet rare parasitic infection caused by the larvae of Angiostrongylus cantonensis. The primary characteristic feature of this foodborne illness in humans is eosinophilic meningitis. Recently, there has been a gradual increase in reported cases globally. Due to the lack of typical clinical symptoms, signs, and specific laboratory tests, early diagnosis of this disease poses significant challenges. Failure to diagnose and treat this condition promptly can result in fatalities.

METHODS: We present the case of a 13-year-old male patient who initially presented with fever and headache. The patient was preliminarily diagnosed with bacterial meningitis and received treatment with antibacterial drugs. However, the patient's condition worsened, and he developed progressive consciousness disturbances. Eventually, metagenomic next-generation sequencing (mNGS) testing of cerebrospinal fluid samples indicated Angiostrongylus cantonensis infection. Following treatment with albendazole and prednisone, the patient made a full recovery. We include this case report as part of a literature review to emphasize the potential applications of mNGS in the early diagnosis of Angiostrongyliasis cantonensis.

CONCLUSION: mNGS technology plays a crucial role in the diagnosis of angiostrongyliasis cantonensis. As this technology continues to evolve and be applied, we believe it will play an increasingly important role in diagnosing, treating, and monitoring angiostrongyliasis cantonensis.}, } @article {pmid39134651, year = {2024}, author = {Gutiérrez-Preciado, A and Dede, B and Baker, BA and Eme, L and Moreira, D and López-García, P}, title = {Extremely acidic proteomes and metabolic flexibility in bacteria and highly diversified archaea thriving in geothermal chaotropic brines.}, journal = {Nature ecology & evolution}, volume = {8}, number = {10}, pages = {1856-1869}, pmid = {39134651}, issn = {2397-334X}, support = {doi.org/10.37807/GBMF9739//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 787904//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, mesh = {*Proteome ; *Archaea/genetics/metabolism ; *Bacteria/metabolism/genetics/classification ; Lakes/microbiology ; Metagenome ; Salinity ; Archaeal Proteins/genetics/metabolism ; Genome, Archaeal ; Hot Springs/microbiology ; }, abstract = {Few described archaeal, and fewer bacterial, lineages thrive under salt-saturating conditions, such as solar saltern crystallizers (salinity above 30% w/v). They accumulate molar K[+] cytoplasmic concentrations to maintain osmotic balance ('salt-in' strategy) and have proteins adaptively enriched in negatively charged acidic amino acids. Here we analysed metagenomes and metagenome-assembled genomes from geothermally influenced hypersaline ecosystems with increasing chaotropicity in the Danakil Depression. Normalized abundances of universal single-copy genes confirmed that haloarchaea and Nanohaloarchaeota encompass 99% of microbial communities in the near-life-limiting conditions of the Western-Canyon Lakes. Danakil metagenome- and metagenome-assembled-genome-inferred proteomes, compared with those of freshwater, seawater and solar saltern ponds up to saturation (6-14-32% salinity), showed that Western-Canyon Lake archaea encode the most acidic proteomes ever observed (median protein isoelectric points ≤4.4). We identified previously undescribed haloarchaeal families as well as an Aenigmatarchaeota family and a bacterial phylum independently adapted to extreme halophily. Despite phylum-level diversity decreasing with increasing salinity-chaotropicity, and unlike in solar salterns, adapted archaea exceedingly diversified in Danakil ecosystems, challenging the notion of decreasing diversity under extreme conditions. Metabolic flexibility to utilize multiple energy and carbon resources generated by local hydrothermalism along feast-and-famine strategies seemingly shapes microbial diversity in these ecosystems near life limits.}, } @article {pmid39134606, year = {2024}, author = {Austin, RM and Honap, TP and Mann, AE and Hübner, A and DeGaglia, CMS and Warinner, C and Zuckerman, MK and Hofman, CA}, title = {Publisher Correction: Metagenomic and paleopathological analyses of a historic documented collection explore ancient dental calculus as a diagnostic tool.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {18723}, doi = {10.1038/s41598-024-69609-8}, pmid = {39134606}, issn = {2045-2322}, } @article {pmid39134593, year = {2024}, author = {Trosvik, P and Noordzij, HT and de Muinck, EJ}, title = {Antibiotic resistance gene dynamics in the commensal infant gut microbiome over the first year of life.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {18701}, pmid = {39134593}, issn = {2045-2322}, support = {300948//Norges Forskningsråd/ ; }, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; Infant ; *Feces/microbiology ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Metagenomics/methods ; Metagenome ; Genes, Bacterial ; Bacteria/genetics/classification ; Infant, Newborn ; Female ; }, abstract = {Colonization of the infant gut is an important developmental process characterized by high carriage of antimicrobial resistance genes (ARGs) and high abundances of pathobionts. The horizontal transfer of ARGs to pathogenic bacteria represents a major public health concern. However, there is still a paucity of longitudinal studies surveilling ARGs in healthy infant guts at high temporal resolution. Furthermore, we do not yet have a clear view of how temporal variation in ARG carriage relates to the dynamics of specific bacterial populations, as well as community virulence potential. Here, we performed deep shotgun metagenomic sequencing of monthly fecal samples from a cohort of 12 infants, covering the first year of life to interrogate the infant gut microbiome for ARG content. We further relate ARG dynamics to the dynamics of taxa, virulence potential, as well as the potential for ARG mobilization. We identify a core resistome dominated by efflux systems typically associated with Enterobacteriaceae. Overall ARG carriage declined over the first year of life and showed strong contemporaneous correlation with the population dynamics of Proteobacteria. Furthermore, the majority of ARGs could be further mapped to metagenome-assembled genomes (MAGs) classified to this phylum. We were able to assign a large number of ARGs to E. coli by correlating the temporal dynamics of individual genes with species dynamics, and we show that the temporal dynamics of ARGs and virulence factors are highly correlated, suggesting close taxonomic associations between these two gene classes. Finally, we identify ARGs linked with various categories of mobile genetic elements, demonstrating preferential linkage among mobility categories and resistance to different drug classes. While individual variation in ARG carriage is substantial during infancy there is a clear reduction over the first year of life. With few exceptions, ARG abundances closely track the dynamics of pathobionts and community virulence potential. These findings emphasize the potential for development of resistant pathogens in the developing infant gut, and the importance of effective surveillance in order to detect such events.}, } @article {pmid39133581, year = {2024}, author = {Attaway, C and Mathison, BA and Misra, A}, title = {No longer stuck in the past: new advances in artificial intelligence and molecular assays for parasitology screening and diagnosis.}, journal = {Current opinion in infectious diseases}, volume = {37}, number = {5}, pages = {357-366}, pmid = {39133581}, issn = {1473-6527}, mesh = {*Artificial Intelligence ; Humans ; *Parasitic Diseases/diagnosis ; Molecular Diagnostic Techniques/methods ; Parasitology/methods ; Sensitivity and Specificity ; }, abstract = {PURPOSE OF REVIEW: Emerging technologies are revolutionizing parasitology diagnostics and challenging traditional methods reliant on microscopic analysis or serological confirmation, which are known for their limitations in sensitivity and specificity. This article sheds light on the transformative potential of artificial intelligence and molecular assays in the field, promising more accurate and efficient detection methods.

RECENT FINDINGS: Artificial intelligence has emerged as a promising tool for blood and stool parasite review, when paired with comprehensive databases and expert oversight result in heightened specificity and sensitivity of diagnoses while also increasing efficiency. Significant strides have been made in nucleic acid testing for multiplex panels for enteric pathogen. Both multiplex and single target panels for Plasmodium , Babesia , filaria, and kinetoplastids have been developed and garnered regulatory approval, notably for blood donor screening in the United States. Additional technologies such as MALDI-TOF, metagenomics, flow cytometry, and CRISPR-Cas are under investigation for their diagnostic utility and are currently in the preliminary stages of research and feasibility assessment.

SUMMARY: Recent implementation of artificial intelligence and digital microscopy has enabled swift smear screening and diagnosis, although widespread implementation remains limited. Simultaneously, molecular assays - both targeted and multiplex panels are promising and have demonstrated promise in numerous studies with some assays securing regulatory approval recently. Additional technologies are under investigation for their diagnostic utility and are compelling avenues for future proof-of-concept diagnostics.}, } @article {pmid39295898, year = {2023}, author = {Houtkamp, IM and van Zijll Langhout, M and Bessem, M and Pirovano, W and Kort, R}, title = {Multiomics characterisation of the zoo-housed gorilla gut microbiome reveals bacterial community compositions shifts, fungal cellulose-degrading, and archaeal methanogenic activity.}, journal = {Gut microbiome (Cambridge, England)}, volume = {4}, number = {}, pages = {e12}, pmid = {39295898}, issn = {2632-2897}, abstract = {We carried out a comparative analysis between the bacterial microbiota composition of zoo-housed western lowland gorillas and their wild counterparts through 16S rRNA gene amplicon sequencing. In addition, we characterised the carbohydrate-active and methanogenic potential of the zoo-housed gorilla (ZHG) microbiome through shotgun metagenomics and RNA sequencing. The ZHG microbiota showed increased alpha diversity in terms of bacterial species richness and a distinct composition from that of the wild gorilla microbiota, including a loss of abundant fibre-degrading and hydrogenic Chloroflexi. Metagenomic analysis of the CAZyome indicated predominant oligosaccharide-degrading activity, while RNA sequencing revealed diverse cellulase and hemi-cellulase activities in the ZHG gut, contributing to a total of 268 identified carbohydrate-active enzymes. Metatranscriptome analysis revealed a substantial contribution of 38% of the transcripts from anaerobic fungi and archaea to the gorilla microbiome. This activity originates from cellulose-degrading and hydrogenic fungal species belonging to the class Neocallimastigomycetes, as well as from methylotrophic and hydrogenotrophic methanogenic archaea belonging to the classes Thermoplasmata and Methanobacteria, respectively. Our study shows the added value of RNA sequencing in a multiomics approach and highlights the contribution of eukaryotic and archaeal activities to the gut microbiome of gorillas.}, } @article {pmid39242808, year = {2023}, author = {Voolstra, CR and Hume, BCC and Armstrong, EJ and Mitushasi, G and Porro, B and Oury, N and Agostini, S and Boissin, E and Poulain, J and Carradec, Q and Paz-García, DA and Zoccola, D and Magalon, H and Moulin, C and Bourdin, G and Iwankow, G and Romac, S and Banaigs, B and Boss, E and Bowler, C and de Vargas, C and Douville, E and Flores, M and Furla, P and Galand, PE and Gilson, E and Lombard, F and Pesant, S and Reynaud, S and Sullivan, MB and Sunagawa, S and Thomas, OP and Troublé, R and Thurber, RV and Wincker, P and Planes, S and Allemand, D and Forcioli, D}, title = {Disparate genetic divergence patterns in three corals across a pan-Pacific environmental gradient highlight species-specific adaptation.}, journal = {npj biodiversity}, volume = {2}, number = {1}, pages = {15}, pmid = {39242808}, issn = {2731-4243}, support = {AFF funding//University of Konstanz/ ; "France Génomique" ANR-10-INBS-09//Agence Nationale de la Recherche/ ; "Coralgene"ANR-17-CE02-0020//Agence Nationale de la Recherche/ ; "Coralgene"ANR-17-CE02-0020//Agence Nationale de la Recherche/ ; "Coralgene"ANR-17-CE02-0020//Agence Nationale de la Recherche/ ; JPMJSP2124//JST Spring/ ; ANR-11-LABX-0028//Labex Signalife/ ; ANR-11-LABX-0028//Labex Signalife/ ; ANR-11-LABX-0028//Labex Signalife/ ; ANR-15-IDEX-0001//IDEX UCAJedi/ ; ANR-15-IDEX-0001//IDEX UCAJedi/ ; ANR-15-IDEX-0001//IDEX UCAJedi/ ; MC-CIG-618480//H2020 Marie Skłodowska-Curie Actions/ ; }, abstract = {Tropical coral reefs are among the most affected ecosystems by climate change and face increasing loss in the coming decades. Effective conservation strategies that maximize ecosystem resilience must be informed by the accurate characterization of extant genetic diversity and population structure together with an understanding of the adaptive potential of keystone species. Here we analyzed samples from the Tara Pacific Expedition (2016-2018) that completed an 18,000 km longitudinal transect of the Pacific Ocean sampling three widespread corals-Pocillopora meandrina, Porites lobata, and Millepora cf. platyphylla-across 33 sites from 11 islands. Using deep metagenomic sequencing of 269 colonies in conjunction with morphological analyses and climate variability data, we can show that despite a targeted sampling the transect encompasses multiple cryptic species. These species exhibit disparate biogeographic patterns and, most importantly, distinct evolutionary patterns in identical environmental regimes. Our findings demonstrate on a basin scale that evolutionary trajectories are species-specific and can only in part be predicted from the environment. This highlights that conservation strategies must integrate multi-species investigations to discern the distinct genomic footprints shaped by selection as well as the genetic potential for adaptive change.}, } @article {pmid39295907, year = {2023}, author = {Ibarra-Mendoza, B and Gomez-Gil, B and Betancourt-Lozano, M and Raggi, L and Yáñez-Rivera, B}, title = {Microbial gut dysbiosis induced by xenobiotics in model organisms and the relevance of experimental criteria: a minireview.}, journal = {Gut microbiome (Cambridge, England)}, volume = {4}, number = {}, pages = {e7}, pmid = {39295907}, issn = {2632-2897}, abstract = {The gut microbiota is a dynamic ecosystem involved in multiple physiological processes that affect host health. Several factors affect intestinal microbial communities including dietary exposure to xenobiotics, which is highly concerning due to their widespread distribution. Current knowledge of this topic comes from culture-dependent methods, 16S rRNA amplicon fingerprinting, and metagenomics, but a standardised procedures framework remains lacking. This minireview integrates 45 studies from a systematic search using terms related to gut microbiota and its disruption. Only publications encompassing dietary-oral exposure and experimental gut microbiota assessments were included. The results were divided and described according to the biological model used and the disruption observed in the gut microbiota. An overall dysbiotic effect was unclear due to the variety of contaminants and hosts evaluated and the experimental gaps between publications. More standardised experimental designs, including WGS and physiological tests, are needed to establish how a particular xenobiotic can alter the gut microbiota and how the results can be extrapolated.}, } @article {pmid39295912, year = {2023}, author = {Sulit, AK and Kolisnik, T and Frizelle, FA and Purcell, R and Schmeier, S}, title = {MetaFunc: taxonomic and functional analyses of high throughput sequencing for microbiomes.}, journal = {Gut microbiome (Cambridge, England)}, volume = {4}, number = {}, pages = {e4}, pmid = {39295912}, issn = {2632-2897}, abstract = {The identification of functional processes taking place in microbiome communities augment traditional microbiome taxonomic studies, giving a more complete picture of interactions taking place within the community. While there are applications that perform functional annotation on metagenomes or metatranscriptomes, very few of these are able to link taxonomic identity to function or are limited by their input types or databases used. Here we present MetaFunc, a workflow which takes RNA sequences as input reads, and from these (1) identifies species present in the microbiome sample and (2) provides gene ontology annotations associated with the species identified. In addition, MetaFunc allows for host gene analysis, mapping the reads to a host genome, and separating these reads, prior to microbiome analyses. Differential abundance analysis for microbe taxonomies, and differential gene expression analysis and gene set enrichment analysis may then be carried out through the pipeline. A final correlation analysis between microbial species and host genes can also be performed. Finally, MetaFunc builds an R shiny application that allows users to view and interact with the microbiome results. In this paper, we showed how MetaFunc can be applied to metatranscriptomic datasets of colorectal cancer.}, } @article {pmid39296724, year = {2020}, author = {Hill, C}, title = {You have the microbiome you deserve.}, journal = {Gut microbiome (Cambridge, England)}, volume = {1}, number = {}, pages = {e3}, pmid = {39296724}, issn = {2632-2897}, abstract = {The human microbiome is one of the most exciting areas of microbiology. From a starting point of tens of papers annually a couple of decades ago, there are now thousands of papers published every year on the microbiome. Huge strides have been made in terms of defining the individual members of complex human microbiomes from different body sites. The individuality and diversity of the human microbiome almost surpasses our ability to comprehend it. Advances in metagenomics and computational sciences have increased the complexity of the field, while at the same time we have moved from regarding the human microbiome as a benign passenger to a situation where it has been linked to almost every chronic disease, including obesity, cancer and infectious disease. The microbiome tantalizes us with the promise of novel therapeutic molecules and modalities for a range of intractable diseases. And yet, very few microbiome-based therapies have made it to the clinic or the pharmacy and we still cannot really define a healthy microbiome. We are entering the most exciting phase of microbiome research, as we develop effective, evidence-based interventions to preserve and restore human health. But we need rigour and numeracy if we are to realize this vision.}, } @article {pmid39133323, year = {2024}, author = {Nehra, C and Harshini, V and Shukla, N and Chavda, P and Savaliya, K and Patil, S and Shah, T and Pandit, R and Patil, NV and Patel, AK and Kachhawaha, S and Kumawat, RN and Joshi, M and Joshi, CG}, title = {Moringa leaf meal exerts growth benefits in small ruminants through modulating the gastrointestinal microbiome.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {438}, pmid = {39133323}, issn = {1432-0614}, support = {Project Reference No: BT/AQ/1/SP41105/2020//Department of Biotechnology, Ministry of Science and Technology, India/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Animal Feed/analysis ; *Plant Leaves ; *Moringa/chemistry ; Sheep ; *Feces/microbiology ; *Goats ; Dietary Supplements ; Fatty Acids, Volatile/metabolism ; Rumen/microbiology ; Bacteria/classification/genetics/isolation & purification/metabolism ; Weight Gain/drug effects ; Diet/veterinary ; Metagenomics ; }, abstract = {This study investigated the impact of feeding 17% moringa leaf meal (MLM) on the ruminal and fecal microbial composition and body weight gain (BWG) performance of lambs (Ovis aries) and kids (Capra hircus). A total of n = 28 lambs (n = 14, no-moringa, n = 14, 17% moringa) and 24 kids (n = 12, no-moringa, n = 12, 17% moringa) were involved in the experiment and body weight was recorded fortnightly. Metagenomic shotgun sequencing was performed on 28, 22, and 26 ruminal solid, liquid fraction, and fecal samples from lambs, and 23, 22, and 23 samples from kids. Moringa supplementation significantly increased BWG in lambs (21.09 ± 0.78 to 26.12 ± 0.81 kg) and kids (14.60 ± 1.29 to 18.28 ± 1.09 kg) (p-value ≤ 0.01). Microbiome analysis revealed an elevated Firmicutes:Bacteroidetes ratio in the moringa diet group. Moringa-fed animals exhibited increased microbial genera associated with volatile fatty acids (VFAs) production (Prevotella, Anaerovibrio, Lachnospiraceae, Butyrivibrio, Christensenella) and starch and fiber digesters (Proteobacteria, Ruminococcus). The increase in the bacterial genus Sharpea suggested possible methane reduction and decreased proportion of pathogens, Aliarcobacter_ID28198, Campylobacter_ID194 and Campylobacter_ID1660076 suggest health benefits. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated significant alterations in microbial gene pool and metabolic pathways related to carbohydrate, protein, lipid and energy metabolism, indicating potential improvements in animal health. Overall, moringa feeding showed higher energy recovery, improved growth, and potential benefits in methane reduction and reduced pathogenic bacteria.}, } @article {pmid39133000, year = {2024}, author = {Tothero, GK and Hoover, RL and Farag, IF and Kaplan, DI and Weisenhorn, P and Emerson, D and Chan, CS}, title = {Leptothrix ochracea genomes reveal potential for mixotrophic growth on Fe(II) and organic carbon.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {9}, pages = {e0059924}, pmid = {39133000}, issn = {1098-5336}, support = {P20GM103446//HHS | National Institutes of Health (NIH)/ ; EAR-2243577//National Science Foundation (NSF)/ ; DE-AC02-06CH11357//U.S. Department of Energy (DOE)/ ; OIA-1826734//National Science Foundation (NSF)/ ; P20 GM103446/GM/NIGMS NIH HHS/United States ; DE-SC0021010//U.S. Department of Energy (DOE)/ ; DE-EM0005228//U.S. Department of Energy (DOE)/ ; EAR-1833525//National Science Foundation/ ; }, mesh = {*Carbon/metabolism ; *Genome, Bacterial ; *Leptothrix/metabolism/genetics/growth & development ; Wetlands ; Ferrous Compounds/metabolism ; Oxidation-Reduction ; Iron/metabolism ; Carbon Cycle ; Autotrophic Processes ; Metagenome ; }, abstract = {UNLABELLED: Leptothrix ochracea creates distinctive iron-mineralized mats that carpet streams and wetlands. Easily recognized by its iron-mineralized sheaths, L. ochracea was one of the first microorganisms described in the 1800s. Yet it has never been isolated and does not have a complete genome sequence available, so key questions about its physiology remain unresolved. It is debated whether iron oxidation can be used for energy or growth and if L. ochracea is an autotroph, heterotroph, or mixotroph. To address these issues, we sampled L. ochracea-rich mats from three of its typical environments (a stream, wetlands, and a drainage channel) and reconstructed nine high-quality genomes of L. ochracea from metagenomes. These genomes contain iron oxidase genes cyc2 and mtoA, showing that L. ochracea has the potential to conserve energy from iron oxidation. Sox genes confer potential to oxidize sulfur for energy. There are genes for both carbon fixation (RuBisCO) and utilization of sugars and organic acids (acetate, lactate, and formate). In silico stoichiometric metabolic models further demonstrated the potential for growth using sugars and organic acids. Metatranscriptomes showed a high expression of genes for iron oxidation; aerobic respiration; and utilization of lactate, acetate, and sugars, as well as RuBisCO, supporting mixotrophic growth in the environment. In summary, our results suggest that L. ochracea has substantial metabolic flexibility. It is adapted to iron-rich, organic carbon-containing wetland niches, where it can thrive as a mixotrophic iron oxidizer by utilizing both iron oxidation and organics for energy generation and both inorganic and organic carbon for cell and sheath production.

IMPORTANCE: Winogradsky's observations of L. ochracea led him to propose autotrophic iron oxidation as a new microbial metabolism, following his work on autotrophic sulfur-oxidizers. While much culture-based research has ensued, isolation proved elusive, so most work on L. ochracea has been based in the environment and in microcosms. Meanwhile, the autotrophic Gallionella became the model for freshwater microbial iron oxidation, while heterotrophic and mixotrophic iron oxidation is not well-studied. Ecological studies have shown that Leptothrix overtakes Gallionella when dissolved organic carbon content increases, demonstrating distinct niches. This study presents the first near-complete genomes of L. ochracea, which share some features with autotrophic iron oxidizers, while also incorporating heterotrophic metabolisms. These genome, metabolic modeling, and transcriptome results give us a detailed metabolic picture of how the organism may combine lithoautotrophy with organoheterotrophy to promote Fe oxidation and C cycling and drive many biogeochemical processes resulting from microbial growth and iron oxyhydroxide formation in wetlands.}, } @article {pmid39132143, year = {2024}, author = {Zhao, Z and Zhao, Y and Marotta, F and Xamxidin, M and Li, H and Xu, J and Hu, B and Wu, M}, title = {The microbial community structure and nitrogen cycle of high-altitude pristine saline lakes on the Qinghai-Tibetan plateau.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1424368}, pmid = {39132143}, issn = {1664-302X}, abstract = {The nitrogen (N) cycle is the foundation of the biogeochemistry on Earth and plays a crucial role in global climate stability. It is one of the most important nutrient cycles in high-altitude lakes. The biogeochemistry of nitrogen is almost entirely dependent on redox reactions mediated by microorganisms. However, the nitrogen cycling of microbial communities in the high-altitude saline lakes of the Qinghai-Tibet Plateau (QTP), the world's "third pole" has not been investigated extensively. In this study, we used a metagenomic approach to investigate the microbial communities in four high-altitude pristine saline lakes in the Altun mountain on the QTP. We observed that Proteobacteria, Bacteroidota, and Actinobacteriota were dominant in these lakes. We reconstructed 1,593 bacterial MAGs and 8 archaeal MAGs, 1,060 of which were found to contain nitrogen cycle related genes. Our analysis revealed that nitrite reduction, nitrogen fixation, and assimilatory nitrate reduction processes might be active in the lakes. Denitrification might be a major mechanism driving the potential nitrogen loss, while nitrification might be inactive. A wide variety of microorganisms in the lake, dominated by Proteobacteria, participate together in the nitrogen cycle. The prevalence of the dominant taxon Yoonia in these lakes may be attributed to its well-established nitrogen functions and the coupled proton dynamics. This study is the first to systematically investigate the structure and nitrogen function of the microbial community in the high-altitude pristine saline lakes in the Altun mountain on the QTP. As such, it contributes to a better comprehension of biogeochemistry of high-altitude saline lakes.}, } @article {pmid39132136, year = {2024}, author = {Sun, Y and Wang, Y and Ji, L and Zhao, Q and Shen, Q and Wang, X and Liu, Y and Ji, L and Yang, S and Zhang, W}, title = {Identification and characterization of multiple novel picornaviruses in fecal samples of bar-headed goose.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1440801}, pmid = {39132136}, issn = {1664-302X}, abstract = {INTRODUCTION: The bar-headed goose (Anser indicus), one of the most well-known high-altitude birds, is renowned for its adaptation to high-altitude environments. Previous studies have shown that they can be infected with highly pathogenic avian influenza; however, there is currently limited research on other viruses in bar-headed geese.

METHODS: In this study, 10 fecal samples of healthy bar-headed geese were collected, and viral metagenomics method was conducted to identify novel picornaviruses.

RESULTS: Seven novel picornaviruses were identified in the fecal samples of bar-headed geese. Most of these picornaviruses were genetically different from other currently known viruses in the NCBI dataset. Among them, PICV4 was determined to be a new species belonging to the Anativirus genus, PICV5 and PICV13 were classified as novel species belonging to the Hepatovirus genus, and the remaining four picornaviruses (PICV1, PICV19, PICV21, and PICV22) were identified as part of the Megrivirus A species of the Megrivirus genus. Recombinant analysis indicates that PICV21 was a potential recombinant, and the major and minor parents were PICV1 and PICV22, respectively.

CONCLUSION: The findings of this study increase our understanding of the diversity of picornaviruses in bar-headed geese and provide practical viral genome information for the prevention and treatment of potential viral diseases affecting this species.}, } @article {pmid39132133, year = {2024}, author = {Ayaz, M and Zhao, JT and Zhao, W and Chi, YK and Ali, Q and Ali, F and Khan, AR and Yu, Q and Yu, JW and Wu, WC and Qi, RD and Huang, WK}, title = {Biocontrol of plant parasitic nematodes by bacteria and fungi: a multi-omics approach for the exploration of novel nematicides in sustainable agriculture.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1433716}, pmid = {39132133}, issn = {1664-302X}, abstract = {Plant parasitic nematodes (PPNs) pose a significant threat to global crop productivity, causing an estimated annual loss of US $157 billion in the agriculture industry. While synthetic chemical nematicides can effectively control PPNs, their overuse has detrimental effects on human health and the environment. Biocontrol agents (BCAs), such as bacteria and fungi in the rhizosphere, are safe and promising alternatives for PPNs control. These BCAs interact with plant roots and produce extracellular enzymes, secondary metabolites, toxins, and volatile organic compounds (VOCs) to suppress nematodes. Plant root exudates also play a crucial role in attracting beneficial microbes toward infested roots. The complex interaction between plants and microbes in the rhizosphere against PPNs is mostly untapped which opens new avenues for discovering novel nematicides through multi-omics techniques. Advanced omics approaches, including metagenomics, transcriptomics, proteomics, and metabolomics, have led to the discovery of nematicidal compounds. This review summarizes the status of bacterial and fungal biocontrol strategies and their mechanisms for PPNs control. The importance of omics-based approaches for the exploration of novel nematicides and future directions in the biocontrol of PPNs are also addressed. The review highlighted the potential significance of multi-omics techniques in biocontrol of PPNs to ensure sustainable agriculture.}, } @article {pmid39131798, year = {2024}, author = {Liu, W and Li, C and Xie, W and Fan, Y and Zhang, X and Wang, Y and Li, L and Zhang, Z}, title = {The signature of the gut microbiota associated with psoriatic arthritis revealed by metagenomics.}, journal = {Therapeutic advances in musculoskeletal disease}, volume = {16}, number = {}, pages = {1759720X241266720}, pmid = {39131798}, issn = {1759-720X}, abstract = {BACKGROUND: Gut microbiota is involved in the development of psoriatic arthritis (PsA), but until now, there has been a lack of understanding of the PsA host-bacteria interaction.

OBJECTIVES: To reveal the labels of gut microbiota in PsA patients and the species and functions related to disease activity.

DESIGN: Observational research (cross-sectional) with an exploratory nature.

METHODS: Metagenomics sequencing was used to analyze stool samples from 20 treatment-naïve PsA patients and 10 age-matched healthy individuals. All samples were qualified for subsequent analysis.

RESULTS: Compared with the healthy group, α-diversity was reduced in the PsA group, and β-diversity could distinguish the two groups. Two bacteria with high abundance and correlation with PsA disease activity were identified, Bacteroides sp. 3_1_19 and Blautia AF 14-40. In different functions, K07114 (calcium-activated chloride channel (CaCC) homolog) showed a positive correlation with PsA disease activity (disease activity in psoriatic arthritis, DAPSA) and Tet32 (an antibiotic-resistant gene), and carbohydrate-binding module family 50 was negatively correlated with erythrocyte sedimentation rate. A bacterial co-expression network associated with DAPSA was constructed. The network was centered on the bacteria in the Bacteroides genus, which formed a closely related network and were positively correlated with DAPSA. As another core of the network, K07114 was closely related to multiple bacteria in the Bacteroides genus and is also positively correlated with disease activity.

CONCLUSION: The network composed of Bacteroides is associated with PsA disease activity, and its therapeutic value needs to be further explored. CaCCs may be a key channel for the interaction between Bacteroides and PsA-host.}, } @article {pmid39131619, year = {2024}, author = {Kahsen, J and Sherwani, SK and Naqib, A and Jeon, T and Wu, LYA and Green, SJ}, title = {Quantitating primer-template interactions using deconstructed PCR.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e17787}, pmid = {39131619}, issn = {2167-8359}, mesh = {*Polymerase Chain Reaction/methods ; *DNA Primers/genetics ; Templates, Genetic ; Metagenomics/methods ; DNA/genetics ; }, abstract = {When the polymerase chain reaction (PCR) is used to amplify complex templates such as metagenomic DNA using single or degenerate primers, preferential amplification of templates (PCR bias) leads to a distorted representation of the original templates in the final amplicon pool. This bias can be influenced by mismatches between primers and templates, the locations of mismatches, and the nucleotide pairing of mismatches. Many studies have examined primer-template interactions through interrogation of the final products of PCR amplification with controlled input templates. Direct measurement of primer-template interactions, however, has not been possible, leading to uncertainty when optimizing PCR reactions and degenerate primer pools. In this study, we employed a method developed to reduce PCR bias (i.e., Deconstructed PCR, or DePCR) that also provides empirical data regarding primer-template interactions during the first two cycles of PCR amplification. We systematically examined interactions between primers and templates using synthetic DNA templates and varying primer pools, amplified using standard PCR and DePCR protocols. We observed that in simple primer-template systems, perfect match primer-template interactions are favored, particularly when mismatches are close to the 3' end of the primer. In more complex primer-template systems that better represent natural samples, mismatch amplifications can dominate, and heavily degenerate primer pools can improve representation of input templates. When employing the DePCR methodology, mismatched primer-template annealing led to amplification of source templates with significantly lower distortion relative to standard PCR. We establish here a quantitative experimental system for interrogating primer-template interactions and demonstrate the efficacy of DePCR for amplification of complex template mixtures with complex primer pools.}, } @article {pmid39131363, year = {2024}, author = {Martin, C and Gitter, A and Anantharaman, K}, title = {Protein Set Transformer: A protein-based genome language model to power high diversity viromics.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39131363}, issn = {2692-8205}, support = {R35 GM143024/GM/NIGMS NIH HHS/United States ; }, abstract = {Exponential increases in microbial and viral genomic data demand transformational advances in scalable, generalizable frameworks for their interpretation. Standard homology-based functional analyses are hindered by the rapid divergence of microbial and especially viral genomes and proteins that significantly decreases the volume of usable data. Here, we present Protein Set Transformer (PST), a protein-based genome language model that models genomes as sets of proteins without considering sparsely available functional labels. Trained on >100k viruses, PST outperformed other homology- and language model-based approaches for relating viral genomes based on shared protein content. Further, PST demonstrated protein structural and functional awareness by clustering capsid-fold-containing proteins with known capsid proteins and uniquely clustering late gene proteins within related viruses. Our data establish PST as a valuable method for diverse viral genomics, ecology, and evolutionary applications. We posit that the PST framework can be a foundation model for microbial genomics when trained on suitable data.}, } @article {pmid39131354, year = {2024}, author = {Özcan, E and Yu, KB and Dinh, L and Lum, GR and Lau, K and Hsu, J and Arino, M and Paramo, J and Lopez-Romero, A and Hsiao, EY}, title = {Dietary fiber content in clinical ketogenic diets modifies the gut microbiome and seizure resistance in mice.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39131354}, issn = {2692-8205}, support = {R01 NS115537/NS/NINDS NIH HHS/United States ; }, abstract = {The gut microbiome is emerging as an important modulator of the anti-seizure effects of the classic ketogenic diet. However, many variations of the ketogenic diet are used clinically to treat refractory epilepsy, and how different dietary formulations differentially modify the gut microbiome in ways that impact seizure outcome is poorly understood. We find that clinically prescribed ketogenic infant formulas vary in macronutrient ratio, fat source, and fiber content and also in their ability to promote resistance to 6-Hz psychomotor seizures in mice. By screening specific dietary variables for their effects on a model human infant microbial community, we observe that dietary fiber, rather than fat ratio or source, drives substantial metagenomic shifts. Addition of dietary fiber to a fiber-deficient ketogenic formula restores seizure resistance, and supplementing protective ketogenic formulas with excess dietary fiber further potentiates seizure resistance. By screening 13 fiber sources and types, we identify distinct subsets of metagenomic responses in the model human infant microbial community that correspond with increased seizure resistance in mice. In particular, supplementation with seizure-protective fibers enriches microbial representation of genes related to queuosine biosynthesis and preQ0 biosynthesis and decreases representation of microbial genes related to sucrose degradation, which is also seen in seizure-protected mice that are fed fiber-containing ketogenic infant formulas. Overall, this study reveals that different formulations of clinical ketogenic diets, and dietary fiber content in particular, differentially impact seizure outcome in mice, likely through modification of the gut microbiome. Understanding interactions between dietary components of the ketogenic diet, the gut microbiome, and host susceptibility to seizures could inform novel microbiome-guided approaches to treat refractory epilepsy.}, } @article {pmid39130737, year = {2024}, author = {Hinds, J and Apaa, T and Parry, RH and Withers, AJ and MacKenzie, L and Staley, C and Morrison, J and Bennett, M and Bremner-Harrison, S and Chadwick, EA and Hailer, F and Harrison, SWR and Lambin, X and Loose, M and Mathews, F and Tarlinton, R and Blanchard, A}, title = {Multiple novel caliciviruses identified from stoats (Mustela erminea) in the United Kingdom.}, journal = {Access microbiology}, volume = {6}, number = {7}, pages = {}, pmid = {39130737}, issn = {2516-8290}, abstract = {The Caliciviridae family, comprising positive-sense RNA viruses, is characterised by its non-enveloped, small virions, broad host range, and notable tendency for host switching. These viruses are primarily associated with gastroenteric disease, though they can lead to haemorrhagic or respiratory infections. Our study employed a metagenomics analysis of faecal samples from stoats (Mustela erminea), identifying two novel calicivirus species, named stoat vesivirus and stoat valovirus. Stoat vesivirus was identified in three samples (ST008, ST006, ST004), exhibiting a genome wide nucleotide identity of approximately 92 %. The complete coding sequences of these samples were 8471 (ST004) and 8322 (ST006) nucleotides in length, respectively. Each comprised three open reading frames (ORF), closely resembling the Vesivirus mink calicivirus (China/2/2016), with 70-72 % similarity in ORF1, 61-62 % in ORF2 and 71 % in ORF3. Phylogenetic analysis robustly supported stoat vesivirus as belonging within the Vesivirus genus. The second calivicirus (stoat valovirus), detected solely in sample ST008, was 6527 nucleotides in length and with complete coding sequences present. It shared highest similarity with St-Valérien swine virus and marmot norovirus HT16, showing 39.5 and 38.8 % protein identity with ORF1 and 43.3 and 42.9 % for VP1. Stoat valovirus is borderline for meeting the ICTV criteria for a new genus, demonstrating 60 % divergence in ORF1 compared to the other valovirus', however it clusters basally within the Valovirus genus, supporting leaving it included in this genus.}, } @article {pmid39130570, year = {2024}, author = {Gao, Y and Wang, W and Jiang, S and Jin, Z and Guo, M and Wang, M and Li, H and Cui, K}, title = {Response Characteristics of the Community Structure and Metabolic Genes of Oil-Recovery Bacteria after Targeted Activation of Petroleum Hydrocarbon-Degrading Bacteria in Low-Permeability Oil Reservoirs.}, journal = {ACS omega}, volume = {9}, number = {31}, pages = {33448-33458}, pmid = {39130570}, issn = {2470-1343}, abstract = {The microbial enhanced oil recovery (MEOR) process has been identified as a promising alternative to conventional enhanced oil recovery methods because it is eco-friendly and economically advantageous. However, the knowledge about the composition and diversity of microbial communities in artificially regulated reservoirs, especially after activating petroleum hydrocarbon-degrading bacteria (PHDB) by injecting exogenous nutrients, is still insufficient. This study utilized a combination of high-throughput sequencing and metagenomics technology to reveal the structural evolution characteristics of the indigenous microbial community in the reservoir during the PHDB activated for enhanced oil recovery, as well as the response relationship between the expression of its oil production functional genes and crude oil biodegradation. Results showed that Pseudomonas (>75%) gradually evolves into a stable dominant microbial community in the reservoir during the activation of PHDB. Besides, the gene expression and KEGG pathways after crude oil undergoes biodegradation by PHDB show that the number of genes related to petroleum hydrocarbon metabolism dominates the metabolism (21.98%). Meanwhile, a preliminary schematic diagram was drawn to illustrate the evolution mechanism of the EOR metabolic pathway after the targeted activation of PHDB. Additionally, it was found that the abundance of hydrocarbon-degrading enzymes increased significantly, and the activity of alcohol dehydrogenase was higher than that of aldehyde dehydrogenase and monooxygenase after PHDB activation. These research results not only filled in and expanded the theoretical knowledge of MEOR based on artificial interference or regulation of reservoir oil-recovery functional microbial community structure but also provided guidance for the future application of MEOR technology in oil field operations.}, } @article {pmid39130256, year = {2024}, author = {Kanodia, A and Monga, R and Ilyas, M and Verma, Y and Mohapatra, S and Rao, NS and Vyas, M and Sikka, K and Atmakuri, K}, title = {Metagenome Analysis of Cholesteatoma-associated Bacteria: A Pilot Study.}, journal = {Indian journal of otolaryngology and head and neck surgery : official publication of the Association of Otolaryngologists of India}, volume = {76}, number = {4}, pages = {3307-3318}, pmid = {39130256}, issn = {2231-3796}, abstract = {INTRODUCTION: Cholesteatoma usually harbors a poly-microbial infection. As the diversity of bacterial pathogens in the Indian COM is unknown, we set out to identify the bacteria associated with cholesteatoma disease in different patients of North India using targeted metagenomic analysis of the 16 S rRNA gene.

METHODS: We recruited 15 patients of cholesteatomatous chronic otitis media (COM), who underwent surgical disease clearance. We divided these patients into four groups based on the four clinic-radiological stages categorized as per the EAONO/JOS joint consensus statement classification. Representative samples were extracted during the surgery and sent for bacterial culture and sensitivity and 16 S rRNA gene metagenomic analysis.

RESULTS: While 12 (80%) of the patients belonged to clinical Stage I/II; one patient had an extracranial complication (stage III) and two patients had an intracranial complication (stage IV). Our detailed bacterial metagenomics analyses showed that while phylum Proteobacteria was most abundant (reads up to ∼ 95%) in specimens from nine patients, phylum Firmicutes was most abundant (up to ∼ 80%) in specimens from four patients. Gamma (γ) Proteobacteria and Epsilon (ε) Proteobacteria were the most abundant class amongst Proteobacteria. Class Tissierellia stood out as the most abundant Firmicutes (40-60%), followed by Clostridia (20%) and Bacilli (10%). There was negligible difference in the bacterial profiles across all four clinical stages.

CONCLUSION: Cholesteatoma is primarily associated with Proteobacteria and Firmicutes phyla, even in complicated disease. Further studies with a larger sample size are required to validate our findings.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12070-024-04678-9.}, } @article {pmid39129952, year = {2024}, author = {Golob, J and Rao, K and Berinstein, JA and Chey, WD and Owyang, C and Kamada, N and Higgins, PDR and Young, V and Bishu, S and Lee, AA}, title = {The Microbiome in Quiescent Crohn's Disease With Persistent Symptoms Show Disruptions in Microbial Sulfur and Tryptophan Pathways.}, journal = {Gastro hep advances}, volume = {3}, number = {2}, pages = {167-177}, pmid = {39129952}, issn = {2772-5723}, support = {K23 DK124567/DK/NIDDK NIH HHS/United States ; R01 DK119219/DK/NIDDK NIH HHS/United States ; R01 HS027431/HS/AHRQ HHS/United States ; R01 DK108901/DK/NIDDK NIH HHS/United States ; K08 DK123403/DK/NIDDK NIH HHS/United States ; }, abstract = {BACKGROUND AND AIMS: Even in the absence of inflammation, persistent symptoms in Crohn's disease (CD) are prevalent and worsen quality of life. Amongst patients without inflammation (quiescent CD), we hypothesized that microbial community structure and function, including tryptophan metabolism, would differ between patients with persistent symptoms (qCD + S) and without persistent symptoms (qCD-S).

METHODS: We performed a multicenter observational study nested within the Study of a Prospective Adult Research Cohort with Inflammatory Bowel Disease. Quiescent inflammation was defined by fecal calprotectin level <150 mcg/g. Persistent symptoms were defined by Crohn's Disease Patient-Reported Outcome-2. Active CD, diarrhea-predominant irritable bowel syndrome, and healthy controls were included as controls. Stool samples underwent whole-genome shotgun metagenomic sequencing.

RESULTS: Thirty-nine patients with qCD + S, 274 qCD-S, 21 active CD, 40 diarrhea-predominant irritable bowel syndrome, and 50 healthy controls were included for analysis. Patients with qCD + S had a less-diverse microbiome. Furthermore, patients with qCD + S showed significant enrichment of bacterial species that are normal inhabitants of the oral microbiome (eg Rothia dentocariosa, Fusobacterium nucleatum) and sulfidogenic microbes (eg Prevotella copri, Bilophila spp.). Depletion of important butyrate and indole producers (eg Eubacterium rectale, Faecalibacterium prausnitzii) was also noted in qCD + S. Potential metagenome-related functional changes in cysteine and methionine metabolism, ATP transport, and redox reactions were disturbed in qCD + S, also suggestive of altered sulfur metabolism. Finally, qCD + S showed significant reductions in bacterial tnaA genes, which mediate tryptophan metabolism to indole, and significant tnaA allelic variation compared with qCD-S.

CONCLUSION: The microbiome in qCD + S showed significant differences in sulfidogenesis, butyrate producers, and typically oral microbes compared to qCD-S and active CD. These results suggest that inflammation may lead to durable microbiome alterations which may mediate persistent symptoms through testable mechanisms.}, } @article {pmid39129834, year = {2024}, author = {Sabsay, KR and Te Velthuis, AJW}, title = {Using structure prediction of negative sense RNA virus nucleoproteins to assess evolutionary relationships.}, journal = {Virus evolution}, volume = {10}, number = {1}, pages = {veae058}, pmid = {39129834}, issn = {2057-1577}, support = {/WT_/Wellcome Trust/United Kingdom ; R01 AI170520/AI/NIAID NIH HHS/United States ; }, abstract = {Negative sense RNA viruses (NSV) include some of the most detrimental human pathogens, including the influenza, Ebola, and measles viruses. NSV genomes consist of one or multiple single-stranded RNA molecules that are encapsidated into one or more ribonucleoprotein (RNP) complexes. These RNPs consist of viral RNA, a viral RNA polymerase, and many copies of the viral nucleoprotein (NP). Current evolutionary relationships within the NSV phylum are based on the alignment of conserved RNA-dependent RNA polymerase (RdRp) domain amino acid sequences. However, the RdRp domain-based phylogeny does not address whether NP, the other core protein in the NSV genome, evolved along the same trajectory or whether several RdRp-NP pairs evolved through convergent evolution in the segmented and non-segmented NSV genome architectures. Addressing how NP and the RdRp domain evolved may help us better understand NSV diversity. Since NP sequences are too short to infer robust phylogenetic relationships, we here used experimentally obtained and AlphaFold 2.0-predicted NP structures to probe whether evolutionary relationships can be estimated using NSV NP sequences. Following flexible structure alignments of modeled structures, we find that the structural homology of the NSV NPs reveals phylogenetic clusters that are consistent with RdRp-based clustering. In addition, we were able to assign viruses for which RdRp sequences are currently missing to phylogenetic clusters based on the available NP sequence. Both our RdRp-based and NP-based relationships deviate from the current NSV classification of the segmented Naedrevirales, which cluster with the other segmented NSVs in our analysis. Overall, our results suggest that the NSV RdRp and NP genes largely evolved along similar trajectories and even short pieces of genetic, protein-coding information can be used to infer evolutionary relationships, potentially making metagenomic analyses more valuable.}, } @article {pmid39129757, year = {2023}, author = {Bloom, JD}, title = {Association between SARS-CoV-2 and metagenomic content of samples from the Huanan Seafood Market.}, journal = {Virus evolution}, volume = {9}, number = {2}, pages = {vead050}, pmid = {39129757}, issn = {2057-1577}, support = {S10 OD020069/OD/NIH HHS/United States ; S10 OD028685/OD/NIH HHS/United States ; }, abstract = {The role of the Huanan Seafood Market in the early severe acute respiratory syndrome virus 2 (SARS-CoV-2) outbreak remains unclear. Recently, the Chinese Centers for Disease Control (CDC) released data from deep sequencing of environmental samples collected from the market after it was closed on 1 January 2020. Prior to this release, Crits-Christoph et al. analyzed data from a subset of the samples. Both that study and the Chinese CDC study concurred that the samples contained genetic material from a variety of species, including some like raccoon dogs that are susceptible to SARS-CoV-2. However, neither study systematically analyzed the relationship between the amount of genetic material from SARS-CoV-2 and different animal species. Here I implement a fully reproducible computational pipeline that jointly analyzes the number of reads mapping to SARS-CoV-2 and the mitochondrial genomes of chordate species across the full set of samples. I validate the presence of genetic material from numerous species and calculate mammalian mitochondrial compositions similar to those reported by Crits-Christoph et al. However, the SARS-CoV-2 content of the environmental samples is generally very low: only 21 of 176 samples contain more than ten SARS-CoV-2 reads, despite most samples being sequenced to depths exceeding 10[8] total reads. None of the samples with double-digit numbers of SARS-CoV-2 reads have a substantial fraction of their mitochondrial material from any non-human susceptible species. Only one of the fourteen samples with at least a fifth of the chordate mitochondrial material from raccoon dogs contains any SARS-CoV-2 reads, and that sample only has 1 of ~200,000,000 reads mapping to SARS-CoV-2. Instead, SARS-CoV-2 reads are most correlated with reads mapping to various fish, such as catfish and largemouth bass. These results suggest that while metagenomic analysis of the environmental samples is useful for identifying animals or animal products sold at the market, co-mingling of animal and viral genetic material is unlikely to reliably indicate whether any animals were infected by SARS-CoV-2.}, } @article {pmid39128916, year = {2024}, author = {Osburn, ED and McBride, SG and Bahram, M and Strickland, MS}, title = {Global patterns in the growth potential of soil bacterial communities.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {6881}, pmid = {39128916}, issn = {2041-1723}, support = {2020-67034-41310//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; 2021-03724//Vetenskapsrådet (Swedish Research Council)/ ; 1845417//National Science Foundation (NSF)/ ; }, mesh = {*Soil Microbiology ; *Bacteria/classification/genetics/growth & development/metabolism ; *Soil/chemistry ; *Ecosystem ; *Carbon/metabolism ; Nitrogen/metabolism ; Metagenome ; Forests ; Carbon Cycle ; Microbiota ; Codon Usage ; }, abstract = {Despite the growing catalogue of studies detailing the taxonomic and functional composition of soil bacterial communities, the life history traits of those communities remain largely unknown. This study analyzes a global dataset of soil metagenomes to explore environmental drivers of growth potential, a fundamental aspect of bacterial life history. We find that growth potential, estimated from codon usage statistics, was highest in forested biomes and lowest in arid latitudes. This indicates that bacterial productivity generally reflects ecosystem productivity globally. Accordingly, the strongest environmental predictors of growth potential were productivity indicators, such as distance to the equator, and soil properties that vary along productivity gradients, such as pH and carbon to nitrogen ratios. We also observe that growth potential was negatively correlated with the relative abundances of genes involved in carbohydrate metabolism, demonstrating tradeoffs between growth and resource acquisition in soil bacteria. Overall, we identify macroecological patterns in bacterial growth potential and link growth rates to soil carbon cycling.}, } @article {pmid39128772, year = {2024}, author = {Mo, Y and Lim, LS and Ng, SK}, title = {A systematic review on current approaches in bat virus discovered between 2018 and 2022.}, journal = {Journal of virological methods}, volume = {329}, number = {}, pages = {115005}, doi = {10.1016/j.jviromet.2024.115005}, pmid = {39128772}, issn = {1879-0984}, mesh = {*Chiroptera/virology ; Animals ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; Viruses/classification/genetics/isolation & purification ; Genome, Viral ; RNA Viruses/genetics/classification/isolation & purification ; Phylogeny ; DNA Viruses/genetics/classification/isolation & purification ; Virus Diseases/virology/veterinary ; Viral Zoonoses/virology ; }, abstract = {Zoonotic viruses are widely seen as the primary threat for future pandemics. Bats are the most diverse group of mammals, with more than 1400 species distributed across most habitats on Earth. So far, 31 known virus families were associated with bats, although the understanding of most viruses were insufficient. Continuous efforts to discover, understand and monitor these bats viruses, is thereby an area of public health interest. This systematic review was designed to catalogue publications reporting novel bat virus discoveries within PubMed, SCOPUS, and Web of Science databases, within a 5-year period from 2018 to 2022. Various experimental parameters, including sampling locations, methodology, bat species diversity, similarity to known viruses, species demarcation of new viruses, and genomic sequencing strategies, were extracted from 41 publications and analyzed. In total, 72 novel viruses from 19 virus families were identified between 2018 and 2022, particularly from Genomoviridae (DNA viruses) and Coronaviridae (RNA viruses). That said, only a limited number of bat families featured extensively despite noticeable shift towards next generation sequencing methods and metagenomics pipeline for virus identification across different sampling methods. This review aims to provide a comprehensive analysis of the global efforts made over the past five years to identify and characterize emerging viruses in bat species, and to provide a detailed overview of the current technologies and methodologies used in these studies.}, } @article {pmid39128520, year = {2024}, author = {Wang, C and Zhu, J and Wang, H and Zhang, L and Li, Y and Zhang, Y and Wu, Z and Zhou, Q}, title = {Sedimentary organic matter load influences the ecological effects of submerged macrophyte restoration through rhizosphere metabolites and microbial communities.}, journal = {The Science of the total environment}, volume = {951}, number = {}, pages = {175419}, doi = {10.1016/j.scitotenv.2024.175419}, pmid = {39128520}, issn = {1879-1026}, mesh = {*Rhizosphere ; *Microbiota ; *Geologic Sediments/microbiology/chemistry ; Lakes ; Phosphorus/metabolism ; Nitrogen/metabolism ; Environmental Restoration and Remediation/methods ; }, abstract = {Organic matter (OM) accumulation in lake sediments has doubled owing to human activities over the past 100 years, which has negatively affected the restoration of submerged vegetation and ecological security. Changes in the pollution structure of sediments caused by plant recovery and rhizosphere chemical processes under different sediment OM levels are the theoretical basis for the rational application of plant rehabilitation technology in lake management. This study explored how Vallisneria natans mediates changes in sediment N and P through rhizospheric metabolites and microbial community and function under low (4.94 %) and high (17.35 %) sediment OM levels. V. natans promoted the accumulation of NH4-N in the high-OM sediment and the transformation of Fe/Al-P to Ca-P in the low-OM sediment. By analyzing 63 rhizospheric metabolites and the sediment microbial metagenome, the metabolites lactic acid and 3-hydroxybutyric acid and the genus Anammoximicrobium were found to mediate NH4-N accumulation in the high-OM sediment. Additionally, 3-hydroxy-decanoic acid, adipic acid, and the genus Bdellovibrionaceae mediated the transformation of Fe/Al-P to Ca-P in the low-OM sediment. The growth of V. natans enriched the abundance of functional genes mediating each step from nitrate to ammonia and the genes encoding urease in the high-OM sediment, and it up-regulated three genes related to microbial phosphorus uptake in the low-OM sediment. This study revealed the necessity of controlling endogenous pollution by recovering submerged macrophytes under high- and low-OM conditions from the perspective of the transformation of inorganic nitrogen and phosphorus.}, } @article {pmid39128495, year = {2024}, author = {De Pessemier, B and López, CD and Taelman, S and Verdonck, M and Chen, Y and Stockman, A and Lambert, J and Van de Wiele, T and Callewaert, C}, title = {Comparative Whole Metagenome Analysis in Lesional and Nonlesional Scalp Areas of Patients with Psoriasis Capitis and Healthy Individuals.}, journal = {The Journal of investigative dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jid.2024.07.020}, pmid = {39128495}, issn = {1523-1747}, abstract = {Psoriasis is an immune-mediated inflammatory disorder, where the majority of the patients suffer from psoriasis capitis or scalp psoriasis. Current therapeutics remain ineffective to treat scalp lesions. In this study, we present a whole-metagenome characterization of the scalp microbiome in psoriasis capitis. We investigated how changes in the homeostatic cutaneous microbiome correlate with the condition and identified metagenomic biomarkers (taxonomic, functional, virulence factors, antimicrobial resistance genes) that could partly explain its emergence. Within this study, 83 top and back scalp samples from healthy individuals and 64 lesional and nonlesional scalp samples from subjects with untreated psoriasis capitis were analyzed. Using qPCR targeting the 16S and 18S ribosomal RNA genes, we found a significant decrease in microbial load within scalp regions affected by psoriasis compared with that in their nonlesional counterparts. Metagenomic analysis revealed that psoriatic lesions displayed significant lower Cutibacterium species (including C. modestum, C. namnetense, C. granulosum, C. porci), along with an elevation in Staphylococcus aureus. A heightened relative presence of efflux pump protein-encoding genes was detected, suggesting potential antimicrobial resistance mechanisms. These mechanisms are known to specifically target human antimicrobial peptides (including cathelicidin LL-37), which are frequently encountered within psoriasis lesions. These shifts in microbial community dynamics may contribute to psoriasis disease pathogenesis.}, } @article {pmid39127908, year = {2024}, author = {Jabeen, MF and Sanderson, ND and Tinè, M and Donachie, G and Barber, C and Azim, A and Lau, LCK and Brown, T and Pavord, ID and Chauhan, A and Klenerman, P and Street, TL and Marchi, E and Howarth, PH and Hinks, TSC}, title = {Species-level, metagenomic and proteomic analysis of microbe-immune interactions in severe asthma.}, journal = {Allergy}, volume = {79}, number = {11}, pages = {2966-2980}, doi = {10.1111/all.16269}, pmid = {39127908}, issn = {1398-9995}, support = {//NIHR Primary Care Research Network/ ; //National Institute for Health Research Southampton Biomedical Research Centre/ ; //NIHR Oxford Biomedical Research Centre/ ; /WT_/Wellcome Trust/United Kingdom ; /MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; *Asthma/immunology/microbiology ; *Metagenomics/methods ; Female ; *Proteomics/methods ; *Microbiota/immunology ; Male ; Adult ; Middle Aged ; Sputum/microbiology/immunology ; Metagenome ; Cross-Sectional Studies ; Severity of Illness Index ; Cytokines/metabolism ; }, abstract = {BACKGROUND: The airway microbiome in severe asthma has not been characterised at species-level by metagenomic sequencing, nor have the relationships between specific species and mucosal immune responses in 'type-2 low', neutrophilic asthma been defined. We performed an integrated species-level metagenomic data with inflammatory mediators to characterise prevalence of dominant potentially pathogenic organisms and host immune responses.

METHODS: Sputum and nasal lavage samples were analysed using long-read metagenomic sequencing with Nanopore and qPCR in two cross-sectional adult severe asthma cohorts, Wessex (n = 66) and Oxford (n = 30). We integrated species-level data with clinical parameters and 39 selected airway proteins measured by immunoassay and O-link.

RESULTS: The sputum microbiome in health and mild asthma displayed comparable microbial diversity. By contrast, 23% (19/81) of severe asthma microbiomes were dominated by a single respiratory pathogen, namely H. influenzae (n = 10), M. catarrhalis (n = 4), S. pneumoniae (n = 4) and P. aeruginosa (n = 1). Neutrophilic asthma was associated with H. influenzae, M. catarrhalis, S. pneumoniae and T. whipplei with elevated type-1 cytokines and proteases; eosinophilic asthma with higher M. catarrhalis, but lower H. influenzae, and S. pneumoniae abundance. H. influenzae load correlated with Eosinophil Cationic Protein, elastase and IL-10. R. mucilaginosa associated positively with IL-6 and negatively with FGF. Bayesian network analysis also revealed close and distinct relationships of H. influenzae and M. catarrhalis with type-1 airway inflammation. The microbiomes and cytokine milieu were distinct between upper and lower airways.

CONCLUSIONS: This species-level integrated analysis reveals central, but distinct associations between potentially pathogenic bacteria and airways inflammation in severe asthma.}, } @article {pmid39127849, year = {2024}, author = {Vigil, BE and Ascue, F and Ayala, RY and Murúa, P and Calderon, MS and Bustamante, DE}, title = {Functional prediction based on 16S rRNA metagenome data from bacterial microbiota associated with macroalgae from the Peruvian coast.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {18577}, pmid = {39127849}, issn = {2045-2322}, support = {Project FitoAlga N° PE501079919-2022-PROCIENCIA//Consejo Nacional de Ciencia, Tecnología e Innovación Tecnológica/ ; }, mesh = {*Seaweed/microbiology ; *RNA, Ribosomal, 16S/genetics ; Peru ; *Metagenome ; *Bacteria/genetics/classification ; *Microbiota/genetics ; Phylogeny ; Biodiversity ; }, abstract = {Macroalgae are vital reservoirs for essential epibiotic microorganisms. Among these are growth-promoting bacteria that support the growth and healthy development of their host macroalgae, and these macroalgae can be utilized in agriculture as biostimulants, offering an alternative to traditional agrochemicals. However, to date, no comparative studies have been conducted on the functional profile and bacterial diversity associated with coastal macroalgae of Peru. In this study, we employed amplicon sequencing of the V3-V4 region of 16S rRNA gene in twelve host macroalgae collected from two rocky shores in central Peru to compare their bacterial communities. The results revealed high bacterial diversity across both sites, but differences in microbial composition were noted. The phyla Bacteroidota and Pseudomonadota were predominant. The functional prediction highlighted 44 significant metabolic pathways associated with the bacterial microbiota when comparing host macroalgae. These active pathways are related to metabolism and genetic and cellular information processing. No direct association was detected between the macroalgal genera and the associated microbiota, suggesting that the bacterial community is largely influenced by their genetic functions than the taxonomic composition of their hosts. Furthermore, some species of Chlorophyta and Rhodophyta were observed to host growth-promoting bacteria, such as Maribacter sp. and Sulfitobacter sp.}, } @article {pmid39127718, year = {2024}, author = {Van Uffelen, A and Posadas, A and Roosens, NHC and Marchal, K and De Keersmaecker, SCJ and Vanneste, K}, title = {Benchmarking bacterial taxonomic classification using nanopore metagenomics data of several mock communities.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {864}, pmid = {39127718}, issn = {2052-4463}, mesh = {*Bacteria/genetics/classification ; Datasets as Topic ; *Metagenomics/methods ; Microbiota ; Nanopore Sequencing ; Nanopores ; }, abstract = {Taxonomic classification is crucial in identifying organisms within diverse microbial communities when using metagenomics shotgun sequencing. While second-generation Illumina sequencing still dominates, third-generation nanopore sequencing promises improved classification through longer reads. However, extensive benchmarking studies on nanopore data are lacking. We systematically evaluated performance of bacterial taxonomic classification for metagenomics nanopore sequencing data for several commonly used classifiers, using standardized reference sequence databases, on the largest collection of publicly available data for defined mock communities thus far (nine samples), representing different research domains and application scopes. Our results categorize classifiers into three categories: low precision/high recall; medium precision/medium recall, and high precision/medium recall. Most fall into the first group, although precision can be improved without excessively penalizing recall with suitable abundance filtering. No definitive 'best' classifier emerges, and classifier selection depends on application scope and practical requirements. Although few classifiers designed for long reads exist, they generally exhibit better performance. Our comprehensive benchmarking provides concrete recommendations, supported by publicly available code for reassessment and fine-tuning by other scientists.}, } @article {pmid39127363, year = {2024}, author = {Yun, Y and Lv, T and Gui, Z and Su, T and Cao, W and Tian, X and Chen, Y and Wang, S and Jia, Z and Li, G and Ma, T}, title = {Composition and metabolic flexibility of hydrocarbon-degrading consortia in oil reservoirs.}, journal = {Bioresource technology}, volume = {409}, number = {}, pages = {131244}, doi = {10.1016/j.biortech.2024.131244}, pmid = {39127363}, issn = {1873-2976}, mesh = {*Hydrocarbons/metabolism ; *Biodegradation, Environmental ; *Oil and Gas Fields/microbiology ; Microbial Consortia/physiology ; Bacteria/metabolism ; Petroleum/metabolism ; Phylogeny ; }, abstract = {Hydrocarbon-degrading consortia (HDC) play an important role in petroleum exploitation. However, the real composition and metabolic mechanism of HDC in the microbial enhanced oil recovery (MEOR) process remain unclear. By combining [13]C-DNA stable isotope probing microcosms with metagenomics, some newly reported phyla, including Chloroflexi, Synergistetes, Thermotogae, and Planctomycetes, dominated the HDC in the oil reservoirs. In the field trials, the HDC in the aerobic-facultative-anaerobic stage of oilfields jointly promoted the MEOR process, with monthly oil increments of up to 189 tons. Pseudomonas can improve oil recovery by producing rhamnolipid in the facultative condition. Roseovarius was the novel taxa potentially oxidizing alkane and producing acetate to improve oil porosity and permeability in the aerobic condition. Ca. Bacteroidia were the new members potentially degrading hydrocarbons by fumarate addition in the anaerobic environment. Comprehensive identification of the active HDC in oil reservoirs provides a novel theoretical basis for oilfield regulatory scheme.}, } @article {pmid39127355, year = {2024}, author = {Wang, P and Tan, J and Xiao, Z and Xu, F and Jin, Q and He, D}, title = {New insights and enhancement mechanisms of activated carbon in autotrophic denitrification system utilizing zero-valent iron as indirect electron donors.}, journal = {Bioresource technology}, volume = {410}, number = {}, pages = {131237}, doi = {10.1016/j.biortech.2024.131237}, pmid = {39127355}, issn = {1873-2976}, mesh = {*Denitrification ; *Iron/metabolism ; *Autotrophic Processes ; *Electrons ; *Nitrogen/metabolism ; Charcoal/chemistry ; Oxidation-Reduction ; Sewage/microbiology ; Bacteria/metabolism ; Bioreactors ; Nitrates/metabolism ; }, abstract = {Zero-valent iron acts as an indirect electron donor, supplying ferrous iron for the nitrate-dependent ferrous oxidation (NDFO) process. The addition of activated carbon (AC) increased the specific NDFO activity in situ and ex situ by 0.4 mg-N/(d·g VSS) and 2.2 mg-N/(d·g VSS), respectively, due to the enrichment of NDFO bacteria. Furthermore, AC reduced the nitrous oxide emission potential of the sludge, a mechanism that metagenomic analysis suggests may act as a cellular energy storage strategy. During a 196-day experiment, a total nitrogen removal efficiency of 53.7 % was achieved, which may be attributed to the upregulation of key genes involved in iron oxidation and denitrification. Based on these findings, a model involving pilin, 'nanowires,' and a cyc2/?→/(FoxE→FoxY)/?→cymA/Complex III/?-mediated pathway for extracellular electron uptake was proposed. Overall, this work provides a feasible strategy for enhancing the nitrogen removal performance of the ZVI-NDFO process.}, } @article {pmid39127317, year = {2024}, author = {Tang, W and Wang, Q and Sun, M and Liu, C and Huang, Y and Zhou, M and Zhang, X and Meng, Z and Zhang, J}, title = {The gut microbiota-oligodendrocyte axis: A promising pathway for modulating oligodendrocyte homeostasis and demyelination-associated disorders.}, journal = {Life sciences}, volume = {354}, number = {}, pages = {122952}, doi = {10.1016/j.lfs.2024.122952}, pmid = {39127317}, issn = {1879-0631}, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Animals ; *Oligodendroglia/metabolism ; *Homeostasis/physiology ; *Demyelinating Diseases/metabolism/microbiology ; *Brain-Gut Axis/physiology ; Dysbiosis/microbiology ; Myelin Sheath/metabolism ; }, abstract = {The bidirectional regulation between the gut microbiota and brain, known as gut-brain axis, has received significant attention. The myelin sheath, produced by oligodendrocytes or Schwann cells, is essential for efficient nervous signal transmission and the maintenance of brain function. Growing evidence shows that both oligodendrogenesis and myelination are modulated by gut microbiota and its metabolites, and when dysbiosis occurs, changes in the microbiota composition and/or associated metabolites may impact developmental myelination and the occurrence of neurodevelopmental disabilities. Although the link between the microbiota and demyelinating disease such as multiple sclerosis has been extensively studied, our knowledge about the role of the microbiota in other myelin-related disorders, such as neurodegenerative diseases, is limited. Mechanistically, the microbiota-oligodendrocyte axis is primarily mediated by factors such as inflammation, the vagus nerve, endocrine hormones, and microbiota metabolites as evidenced by metagenomics, metabolomics, vagotomy, and morphological and molecular approaches. Treatments targeting this axis include probiotics, prebiotics, microbial metabolites, herbal bioactive compounds, and specific dietary management. In addition to the commonly used approaches, viral vector-mediated tracing and gene manipulation, integrated multiomics and multicenter clinical trials will greatly promote the mechanistic and interventional studies and ultimately, the development of new preventive and therapeutic strategies against gut-oligodendrocyte axis-mediated brain impairments. Interestingly, recent findings showed that microbiota dysbiosis can be induced by hippocampal myelin damage and is reversible by myelin-targeted drugs, which provides new insights into understanding how hippocampus-based functional impairment (such as in neurodegenerative Alzheimer's disease) regulates the peripheral homeostasis of microbiota and associated systemic disorders.}, } @article {pmid39127210, year = {2024}, author = {Liu, R and Chang, D and Zhou, G and Liang, H and Zhang, J and Chai, Q and Cao, W}, title = {Green manuring combined with zeolite reduced nitrous oxide emissions in maize field by targeting microbial nitrogen transformations.}, journal = {The Science of the total environment}, volume = {950}, number = {}, pages = {175382}, doi = {10.1016/j.scitotenv.2024.175382}, pmid = {39127210}, issn = {1879-1026}, mesh = {*Zeolites ; *Nitrous Oxide/analysis ; *Zea mays ; *Manure ; *Nitrogen/analysis ; Air Pollutants/analysis ; Agriculture/methods ; Fertilizers/analysis ; Soil Microbiology ; }, abstract = {Green manure is a crucial strategy for increasing cereal yield and mitigating environmental burden while reducing chemical N fertilizer. To effectively tackle climate change, finding ways to reduce nitrous oxide (N2O) emissions from green manuring systems is vital. Herein, field and [15]N labeled microcosm experiments were arranged to investigate the effect and mechanisms of green manuring and zeolite application on N2O emission. Both experiments comprised four treatments: conventional chemical N (N100), 70 % chemical N (N70), N70 with green manure (N70 + CV), and N70 + CV combined with zeolite (N70 + CV + Z). Compared with N100, both N70 + CV and N70 + CV + Z maintained maize yield, cumulative N2O emissions decreased by 37.7 % and 34.9 % in N70 + CV + Z in 2022-yr and 2023-yr, and by 12.8 % in N70 + CV in 2022-yr. Moreover, the reduction of N2O emission primarily occurred after incorporating green manure. The N100 and N70 + CV demonstrated a similar transformed proportion of chemical N to N2O (i.e., 4.9 % and 4.7 %) while reducing it to 2.7 % in N70 + CV + Z. Additionally, a mere 0.7 % of green manure N was transformed to N2O in both N70 + CV and N70 + CV + Z treatments. Compared with N100, both N70 + CV and N70 + CV + Z decreased the relative abundances of ammonia oxidation microbes, increased denitrifier and the ratios of (nirK + nirS)/nosZ and norBC/nosZ. Furthermore, compared with N70 + CV, N70 + CV + Z decreased the relative abundances of N2O-producer and the ratios of (nirK + nirS)/nosZ and norBC/nosZ in denitrification. These findings revealed that the reduction of N2O emissions resulting from green manure replaced chemical N was mainly due to weakened nitrification, while zeolite reduced N2O emissions attributed to enhanced conversion of N2O to N2. Moreover, certain key N-cycling functional bacteria, such as Phycisphaerae, Rubrobacteria, and Thermoflexia, were positively correlated with N2O emission. In contrast, Dehalococcoidia, Gammaproteobacteria, and Betaproteobacteria were negatively correlated with N2O emission. This investigation uncovered the underlying mechanisms for effectively reducing N2O emissions through green manuring combined with zeolite.}, } @article {pmid39126385, year = {2025}, author = {Jangi, S and Zhao, N and Hsia, K and Park, YS and Michaud, DS and Yoon, H}, title = {Specific Bacterial Co-abundance Groups Are Associated With Inflammatory Status in Patients With Ulcerative Colitis.}, journal = {Journal of Crohn's & colitis}, volume = {19}, number = {1}, pages = {}, pmid = {39126385}, issn = {1876-4479}, support = {/TR/NCATS NIH HHS/United States ; /NH/NIH HHS/United States ; //National Research Foundation/ ; }, mesh = {Humans ; *Colitis, Ulcerative/microbiology ; *Gastrointestinal Microbiome ; Male ; Adult ; Female ; Prospective Studies ; Middle Aged ; Clostridiales/isolation & purification ; Candida/isolation & purification ; Republic of Korea ; Feces/microbiology ; }, abstract = {BACKGROUND AND AIMS: While there is increasing interest in microbiome-directed therapies for patients with ulcerative colitis (UC), the identification of microbial targets remains elusive, underlining the need for novel approaches.

METHODS: Utilizing metagenomic data from the Study of a Prospective Adult Research Cohort with Inflammatory Bowel Disease (SPARC IBD), available via the IBD Plexus Program of the Crohn's & Colitis Foundation, we used a tree-based dichotomous approach to assemble distinct clusters of species-level bacterial co-abundance groups (CAGs). We evaluated the abundance of bacterial CAGs and fungal taxa during remission (n = 166) and activity (n = 46). We examined if the bacterial CAGs identified in our cohorts were conserved in 2 healthy cohorts and a Korean UC cohort.

RESULTS: CAG3 and CAG8, dominated by bacteria from the family Lachnospiraceae, were associated with remission. Low abundance of CAG8 and elevated abundance of Candida genus were predictive of active UC. Constituents from CAG8 were influential hub species of the remission-associated microbial UC network, including Ruminococcus gnavus, Erysipelatoclostridium ramosum, Blautia, and Dorea species. These hub species interactions were preserved in 2 healthy cohorts and were partially recapitulated in a Korean UC cohort. CAG8 abundance correlated with the secondary bile acid production pathway. Bacterial CAGs did not correlate with Candida; however, Bifidobacterium adolescentis and Alistipes putredinis were negatively associated with Candida.

CONCLUSIONS: Lachnospiraceae-dominated bacterial CAGs were associated with remission in UC, with key bacterial interactions within the CAG also observed in 2 healthy cohorts and a Korean UC cohort. Bacterial CAG-based analyses may aid in designing candidate consortia for microbiome-based therapeutics.}, } @article {pmid39125688, year = {2024}, author = {Ercolano, C and Iacono, R and Cafaro, V and Pizzo, E and Giovannelli, D and Feuerriegel, G and Streit, WR and Strazzulli, A and Moracci, M}, title = {Biochemical Characterisation of Sis: A Distinct Thermophilic PETase with Enhanced NanoPET Substrate Hydrolysis and Thermal Stability.}, journal = {International journal of molecular sciences}, volume = {25}, number = {15}, pages = {}, pmid = {39125688}, issn = {1422-0067}, support = {2020SBNHLH_003//Ministero dell'Università e della Ricerca (MUR)/ ; }, mesh = {*Polyethylene Terephthalates/chemistry/metabolism ; Hydrolysis ; *Enzyme Stability ; Phylogeny ; Temperature ; Substrate Specificity ; Kinetics ; Hydrolases/chemistry/metabolism ; Bacterial Proteins/chemistry/metabolism/genetics ; }, abstract = {Polyethylene terephthalate (PET) degradation by enzymatic hydrolysis is significant for addressing plastic pollution and fostering sustainable waste management practices. Identifying thermophilic and thermostable PET hydrolases is particularly crucial for industrial bioprocesses, where elevated temperatures may enhance enzymatic efficiency and process kinetics. In this study, we present the discovery of a novel thermophilic and thermostable PETase enzyme named Sis, obtained through metagenomic sequence-based analysis. Sis exhibits robust activity on nanoPET substrates, demonstrating effectiveness at temperatures up to 70 °C and displaying exceptional thermal stability with a melting temperature (Tm) of 82 °C. Phylogenetically distinct from previously characterised PET hydrolases, Sis represents a valuable addition to the repertoire of enzymes suitable for PET degradation.}, } @article {pmid39125621, year = {2024}, author = {Jelin-Uhlig, S and Weigel, M and Ott, B and Imirzalioglu, C and Howaldt, HP and Böttger, S and Hain, T}, title = {Bisphosphonate-Related Osteonecrosis of the Jaw and Oral Microbiome: Clinical Risk Factors, Pathophysiology and Treatment Options.}, journal = {International journal of molecular sciences}, volume = {25}, number = {15}, pages = {}, pmid = {39125621}, issn = {1422-0067}, support = {DZIF-MD / 80325MD058//German Center for Infection Research/ ; }, mesh = {Humans ; *Bisphosphonate-Associated Osteonecrosis of the Jaw/etiology/microbiology ; *Microbiota/drug effects ; Risk Factors ; *Diphosphonates/adverse effects/therapeutic use ; Mouth/microbiology ; }, abstract = {Bisphosphonate-related osteonecrosis of the jaw (BRONJ) represents a serious health condition, impacting the lives of many patients worldwide. The condition challenges clinical care due to its complex etiology and limited therapeutic options. A thorough understanding of the pathophysiological and patient-related factors that promote disease development is essential. Recently, the oral microbiome has been implicated as a potential driver and modulating factor of BRONJ by several studies. Modern genomic sequencing methods have provided a wealth of data on the microbial composition of BRONJ lesions; however, the role of individual species in the process of disease development remains elusive. A comprehensive PubMed search was conducted to identify relevant studies on the microbiome of BRONJ patients using the terms "microbiome", "osteonecrosis of the jaws", and "bisphosphonates". Studies focusing on symptoms, epidemiology, pathophysiology, risk factors, and treatment options were included. The principal risk factors for BRONJ are tooth extraction, surgical procedures, and the administration of high doses of bisphosphonates. Importantly, the oral microbiome plays a significant role in the progression of the disease. Several studies have identified alterations of microbial composition in BRONJ lesions. However, there is no consensus regarding bacterial species that are associated with BRONJ across studies. The bacterial genera typically found include Actinomyces, Fusobacterium, and Streptococcus. It is postulated that these microbes contribute to the pathogenesis of BRONJ by promoting inflammation and disrupting normal bone remodeling processes. Current therapeutic approaches are disease-stage-specific and the necessity for more effective treatment strategies remains. This review examines the potential causes of and therapeutic approaches to BRONJ, highlighting the link between microbial colonization and BRONJ development. Future research should seek to more thoroughly investigate the interactions between bisphosphonates, the oral microbiome, and the immune system in order to develop targeted therapies.}, } @article {pmid39125593, year = {2024}, author = {Kulecka, M and Czarnowski, P and Bałabas, A and Turkot, M and Kruczkowska-Tarantowicz, K and Żeber-Lubecka, N and Dąbrowska, M and Paszkiewicz-Kozik, E and Walewski, J and Ługowska, I and Koseła-Paterczyk, H and Rutkowski, P and Kluska, A and Piątkowska, M and Jagiełło-Gruszfeld, A and Tenderenda, M and Gawiński, C and Wyrwicz, L and Borucka, M and Krzakowski, M and Zając, L and Kamiński, M and Mikula, M and Ostrowski, J}, title = {Microbial and Metabolic Gut Profiling across Seven Malignancies Identifies Fecal Faecalibacillus intestinalis and Formic Acid as Commonly Altered in Cancer Patients.}, journal = {International journal of molecular sciences}, volume = {25}, number = {15}, pages = {}, pmid = {39125593}, issn = {1422-0067}, support = {2017/27/B/NZ5/01504//National Science Center/ ; 2018/31/B/NZ7/02675//National Science Center/ ; 2020/ABM/01/00004//The Medical Research Agency/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; *Feces/microbiology ; Male ; *Formates/metabolism ; Middle Aged ; Aged ; Neoplasms/metabolism/microbiology ; Adult ; Dysbiosis/microbiology ; Metabolomics/methods ; Metabolome ; Gas Chromatography-Mass Spectrometry ; Metagenomics/methods ; }, abstract = {The key association between gut dysbiosis and cancer is already known. Here, we used whole-genome shotgun sequencing (WGS) and gas chromatography/mass spectrometry (GC/MS) to conduct metagenomic and metabolomic analyses to identify common and distinct taxonomic configurations among 40, 45, 71, 34, 50, 60, and 40 patients with colorectal cancer, stomach cancer, breast cancer, lung cancer, melanoma, lymphoid neoplasms and acute myeloid leukemia (AML), respectively, and compared the data with those from sex- and age-matched healthy controls (HC). α-diversity differed only between the lymphoid neoplasm and AML groups and their respective HC, while β-diversity differed between all groups and their HC. Of 203 unique species, 179 and 24 were under- and over-represented, respectively, in the case groups compared with HC. Of these, Faecalibacillus intestinalis was under-represented in each of the seven groups studied, Anaerostipes hadrus was under-represented in all but the stomach cancer group, and 22 species were under-represented in the remaining five case groups. There was a marked reduction in the gut microbiome cancer index in all case groups except the AML group. Of the short-chain fatty acids and amino acids tested, the relative concentration of formic acid was significantly higher in each of the case groups than in HC, and the abundance of seven species of Faecalibacterium correlated negatively with most amino acids and formic acid, and positively with the levels of acetic, propanoic, and butanoic acid. We found more differences than similarities between the studied malignancy groups, with large variations in diversity, taxonomic/metabolomic profiles, and functional assignments. While the results obtained may demonstrate trends rather than objective differences that correlate with different types of malignancy, the newly developed gut microbiota cancer index did distinguish most of the cancer cases from HC. We believe that these data are a promising step forward in the search for new diagnostic and predictive tests to assess intestinal dysbiosis among cancer patients.}, } @article {pmid39125549, year = {2024}, author = {Brożek-Mądry, E and Burska, Z and Życińska, K and Sierdziński, J}, title = {Nasal Microbiome in Granulomatosis with Polyangiitis Compared to Chronic Rhinosinusitis.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {14}, number = {15}, pages = {}, pmid = {39125549}, issn = {2075-4418}, abstract = {Rhinosinusitis in granulomatosis with polyangiitis (GPA) is categorised as a secondary, diffuse and inflammatory chronic rhinosinusitis (CRS). It is one of the conditions that impacts the nasal microbiota. This study aimed to compare the nasal microbiomes of patients with GPA, CRS and NSP. A total of 31 patients were included in the study (18 GPA, 6 CRS and 7 nasal septum perforation (NSP)). In all patients, SNOT 22, a nasal endoscopy (Lund-Kennedy scale) and a brush swab were performed. The metagenomic analysis was carried out based on the hypervariable V3-V4 region of the 16S rRNA gene. At the genus level, statistically significant differences were observed in two comparisons: the GPA/NSP and the GPA/CRS groups. In the GPA/NSP group, the differences were related to four genera (Actinomyces, Streptococcus, Methylobacterium-Methylorubrum, Paracoccus), while in the GPA/CRS group, they were related to six (Kocuria, Rothia, Cutibacterium, Streptococcus, Methylobacterium-Methylorubrum, Tepidimonas). Patients with GPA had lower diversity compared to CRS and NSP patients. There were no statistically significant differences found for the Staphylococcus family and Staphylococcus aureus between the three groups.}, } @article {pmid39125474, year = {2024}, author = {Mirabile, A and Sangiorgio, G and Bonacci, PG and Bivona, D and Nicitra, E and Bonomo, C and Bongiorno, D and Stefani, S and Musso, N}, title = {Advancing Pathogen Identification: The Role of Digital PCR in Enhancing Diagnostic Power in Different Settings.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {14}, number = {15}, pages = {}, pmid = {39125474}, issn = {2075-4418}, support = {PE 00000007 INF-ACT//Ministry of Education, Universities and Research/ ; SAMOTHRACE ECS00000022//Ministry of Education, Universities and Research/ ; }, abstract = {Digital polymerase chain reaction (dPCR) has emerged as a groundbreaking technology in molecular biology and diagnostics, offering exceptional precision and sensitivity in nucleic acid detection and quantification. This review highlights the core principles and transformative potential of dPCR, particularly in infectious disease diagnostics and environmental surveillance. Emphasizing its evolution from traditional PCR, dPCR provides accurate absolute quantification of target nucleic acids through advanced partitioning techniques. The review addresses the significant impact of dPCR in sepsis diagnosis and management, showcasing its superior sensitivity and specificity in early pathogen detection and identification of drug-resistant genes. Despite its advantages, challenges such as optimization of experimental conditions, standardization of data analysis workflows, and high costs are discussed. Furthermore, we compare various commercially available dPCR platforms, detailing their features and applications in clinical and research settings. Additionally, the review explores dPCR's role in water microbiology, particularly in wastewater surveillance and monitoring of waterborne pathogens, underscoring its importance in public health protection. In conclusion, future prospects of dPCR, including methodological optimization, integration with innovative technologies, and expansion into new sectors like metagenomics, are explored.}, } @article {pmid39123781, year = {2024}, author = {Wang, H and Zhan, J and Jiang, H and Jia, H and Pan, Y and Zhong, X and Huo, J and Zhao, S}, title = {Metagenomics-Metabolomics Exploration of Three-Way-Crossbreeding Effects on Rumen to Provide Basis for Crossbreeding Improvement of Sheep Microbiome and Metabolome of Sheep.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {15}, pages = {}, pmid = {39123781}, issn = {2076-2615}, support = {JXSNKYJCRC202407, JXSNKYJCRC202445//Basic Research and Talent Training, Jiangxi Academy of Agricultural Sciences/ ; JXARS-13//Earmarked Fund for Jiangxi Agriculture Research System/ ; }, abstract = {The objective of this experiment was to explore the effects of three-way hybridization on rumen microbes and metabolites in sheep using rumen metagenomics and metabolomics. Healthy Hu and CAH (Charolais × Australian White × Hu) male lambs of similar birth weight and age were selected for short-term fattening after intensive weaning to collect rumen fluid for sequencing. Rumen metagenomics diversity showed that Hu and CAH sheep were significantly segregated at the species, KEGG-enzyme, and CAZy-family levels. Moreover, the CAH significantly increased the ACE and Chao1 indices. Further, correlation analysis of the abundance of the top 80 revealed that the microorganisms were interrelated at the species, KEGG-enzyme, and CAZy-family levels. Overall, the microbiome significantly affected metabolites of the top five pathways, with the strongest correlation found with succinic acid. Meanwhile, species-level microbial markers significantly affected rumen differential metabolites. In addition, rumen microbial markers in Hu sheep were overall positively correlated with down-regulated metabolites and negatively correlated with up-regulated metabolites. In contrast, rumen microbial markers in CAH lambs were overall negatively correlated with down-regulated metabolites and positively correlated with up-regulated metabolites. These results suggest that three-way crossbreeding significantly affects rumen microbial community and metabolite composition, and that significant interactions exist between rumen microbes and metabolites.}, } @article {pmid39123724, year = {2024}, author = {Wei, P and Sun, W and Hao, S and Deng, L and Zou, W and Wu, H and Lu, W and He, Y}, title = {Dietary Supplementation of Crossbred Pigs with Glycerol, Vitamin C, and Niacinamide Alters the Composition of Gut Flora and Gut Flora-Derived Metabolites.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {15}, pages = {}, pmid = {39123724}, issn = {2076-2615}, support = {JXXTCX2016003-02//Jiangxi Modern Agricultural Research Collaborative Innovation Project/ ; }, abstract = {The addition of glycerin, vitamin C, and niacinamide to pig diets increased the redness of longissimus dorsi; however, it remains unclear how these supplements affect gut microbiota and metabolites. A total of 84 piglets (20.35 ± 2.14 kg) were randomly allotted to groups A (control), B (glycerin-supplemented), C (vitamin C and niacinamide-supplemented), and D (glycerin, vitamin C and niacinamide-supplemented) during a feeding experiment. Metagenomic and metabolomic technologies were used to analyze the fecal compositions of bile acids, metabolites, and microbiota. The results showed that compared to pigs in group A, pigs in group D had lower virulence factor expressions of lipopolysaccharide (p < 0.05), fatty acid resistance system (p < 0.05), and capsule (p < 0.01); higher fecal levels of ferric ion (p < 0.05), allolithocholic acid (p < 0.01), deoxycholic acid (p < 0.05), tauroursodeoxycholic acid dihydrate (p < 0.01), glycodeoxycholic acid (p < 0.05), L-proline (p < 0.01) and calcitriol (p < 0.01); and higher (p < 0.05) abundances of iron-acquiring microbiota (Methanobrevibacter, Clostridium, Clostridiaceae, Clostridium_sp_CAG_1000, Faecalibacterium_sp_CAG_74_58_120, Eubacteriales_Family_XIII_Incertae_Sedis, Alistipes_sp_CAG_435, Alistipes_sp_CAG_514 and Methanobrevibacter_sp_YE315). Supplementation with glycerin, vitamin C, and niacinamide to pigs significantly promoted the growth of iron-acquiring microbiota in feces, reduced the expression of some virulence factor genes of fecal pathogens, and increased the fecal levels of ferric ion, L-proline, and some secondary bile acids. The administration of glycerol, vitamin C, and niacinamide to pigs may serve as an effective measure for muscle redness improvement by altering the compositions of fecal microbiota and metabolites.}, } @article {pmid39123642, year = {2024}, author = {Yan, Y and Liang, Z and Huo, Y and Wu, Q and Ni, L and Lv, X}, title = {A Comparative Study of Microbial Communities, Biogenic Amines, and Volatile Profiles in the Brewing Process of Rice Wines with Hongqu and Xiaoqu as Fermentation Starters.}, journal = {Foods (Basel, Switzerland)}, volume = {13}, number = {15}, pages = {}, pmid = {39123642}, issn = {2304-8158}, support = {No. 2022J01101//Natural Science Foundation of Fujian Province of China/ ; No. 32072204//National Natural Science Foundation of China/ ; No. 2022L3075//Central Leading Local Science and Technology Development Fund Project of China/ ; }, abstract = {Rice wine is primarily crafted from grains through saccharification and liquification with the help of Qu. Qu plays an important role in the formation of the flavor quality of rice wine. Hongqu and Xiaoqu represent two prevalent varieties of Qu that are typically utilized in the brewing process of rice wine and play a crucial role in its production. In this study, GC, GC-MS, HPLC, and metagenomic sequencing techniques were used to contrast the microbial flora, biogenic amines, and aroma characteristics developed during the fermentation of rice wines, with Hongqu and Xiaoqu being used as initiating agents for the brewing process. The results show that the content of higher alcohols (including n-propanol, isobutanol, 3-methyl-1-butanol, and phenethyl alcohol) in rice wine brewed with Xiaoqu (XQW) was significantly higher than that in rice wine brewed with Hongqu (HQW). Contrarily, the concentration of biogenic amines in HQW surpassed that of XQW by a notable margin, but tyramine was significantly enriched in XQW and not detected in HQW. In addition, a multivariate statistical analysis revealed distinct disparities in the constitution of volatile components between HQW and XQW. Hexanoic acid, ethyl acetate, isoamyl acetate, ethyl caproate, ethyl decanoate, 2-methoxy-4-vinylphenol, etc., were identified as the characteristic aroma-active compounds in HQW and XQW. A microbiome analysis based on metagenomic sequencing showed that HQW and XQW had different dominant microorganisms in the brewing process. Burkholderia, Klebsiella, Leuconostoc, Monascus, and Aspergillus were identified as the primary microbial genera in the HQW fermentation period, while Pediococcus, Enterobacter, Rhizopus, Ascoidea, and Wickerhamomyces were the main microbial genera in the XQW brewing process. A bioinformatics analysis revealed that the concentrations of microbial genes involved in biogenic amines and esters biosynthesis were significantly higher in HQW than those in XQW, while the content of genes relevant to glycolysis, higher alcohol biosynthesis, and fatty acid metabolism was significantly higher in XQW than in HQW, which are the possible reasons for the difference in flavor quality between the two kinds of rice wine from the perspective of microbial functional genes.}, } @article {pmid39123524, year = {2024}, author = {Todhanakasem, T and Van Tai, N and Pornpukdeewattana, S and Charoenrat, T and Young, BM and Wattanachaisaereekul, S}, title = {The Relationship between Microbial Communities in Coffee Fermentation and Aroma with Metabolite Attributes of Finished Products.}, journal = {Foods (Basel, Switzerland)}, volume = {13}, number = {15}, pages = {}, pmid = {39123524}, issn = {2304-8158}, support = {RE-KRIS/FF66/66//Fundamental fund/ ; }, abstract = {Coffee is a critical agricultural commodity and is used to produce premium beverages enjoyed by people worldwide. The microbiome of coffee beans has proven to be an essential tool that improves the flavor profile of coffee by creating aromatic flavor compounds through natural fermentation. This study investigated the natural microbial consortium during the wet process fermentation of coffee onsite in Thailand in order to identify the correlation between microbial diversity and biochemical characteristics including flavor, aroma, and metabolic attributes. Our study found 64 genera of bacteria and 59 genera of yeast/fungi present during the fermentation process. Group of microbes, mainly yeast and lactic acid bacteria, that predominated in the process were significantly correlated with preferable flavor and aroma compounds, including linalyl formate, linalool, cis-isoeugenol, trans-geraniol, and (-)-isopulegol. Some of the detected metabolites were found to be active compounds which could play a role in health.}, } @article {pmid39123456, year = {2024}, author = {Kafida, M and Karela, M and Giakountis, A}, title = {RNA-Independent Regulatory Functions of lncRNA in Complex Disease.}, journal = {Cancers}, volume = {16}, number = {15}, pages = {}, pmid = {39123456}, issn = {2072-6694}, abstract = {During the metagenomics era, high-throughput sequencing efforts both in mice and humans indicate that non-coding RNAs (ncRNAs) constitute a significant fraction of the transcribed genome. During the past decades, the regulatory role of these non-coding transcripts along with their interactions with other molecules have been extensively characterized. However, the study of long non-coding RNAs (lncRNAs), an ncRNA regulatory class with transcript lengths that exceed 200 nucleotides, revealed that certain non-coding transcripts are transcriptional "by-products", while their loci exert their downstream regulatory functions through RNA-independent mechanisms. Such mechanisms include, but are not limited to, chromatin interactions and complex promoter-enhancer competition schemes that involve the underlying ncRNA locus with or without its nascent transcription, mediating significant or even exclusive roles in the regulation of downstream target genes in mammals. Interestingly, such RNA-independent mechanisms often drive pathological manifestations, including oncogenesis. In this review, we summarize selective examples of lncRNAs that regulate target genes independently of their produced transcripts.}, } @article {pmid39123272, year = {2024}, author = {Gong, X and Xu, L and Langwig, MV and Chen, Z and Huang, S and Zhao, D and Su, L and Zhang, Y and Francis, CA and Liu, J and Li, J and Baker, BJ}, title = {Globally distributed marine Gemmatimonadota have unique genomic potentials.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {149}, pmid = {39123272}, issn = {2049-2618}, support = {2020YFA0608301//National Key Research and Development Program of China/ ; 92351302//National Natural Science Foundation of China/ ; 42072333//National Natural Science Foundation of China/ ; MGK202009//State Key Laboratory of Marine Geology, Tongji University/ ; 2021HJ01//PI Project of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; LI-SIAME-00002001//Simons Foundation/ ; }, mesh = {*Phylogeny ; *Metagenome ; Genome, Bacterial ; Geologic Sediments/microbiology ; Genomics ; Seawater/microbiology ; Aquatic Organisms/genetics ; Secondary Metabolism ; Metagenomics ; }, abstract = {BACKGROUND: Gemmatimonadota bacteria are widely distributed in nature, but their metabolic potential and ecological roles in marine environments are poorly understood.

RESULTS: Here, we obtained 495 metagenome-assembled genomes (MAGs), and associated viruses, from coastal to deep-sea sediments around the world. We used this expanded genomic catalog to compare the protein composition and update the phylogeny of these bacteria. The marine Gemmatimonadota are phylogenetically different from those previously reported from terrestrial environments. Functional analyses of these genomes revealed these marine genotypes are capable of degradation of complex organic carbon, denitrification, sulfate reduction, and oxidizing sulfide and sulfite. Interestingly, there is widespread genetic potential for secondary metabolite biosynthesis across Gemmatimonadota, which may represent an unexplored source of novel natural products. Furthermore, viruses associated with Gemmatimonadota have the potential to "hijack" and manipulate host metabolism, including the assembly of the lipopolysaccharide in their hosts.

CONCLUSIONS: This expanded genomic diversity advances our understanding of these globally distributed bacteria across a variety of ecosystems and reveals genetic distinctions between those in terrestrial and marine communities. Video Abstract.}, } An unhandled exception occurred at $0000000000402653 : EAccessViolation : Access violation $0000000000402653 $0000000000404849